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Publications

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Publications in peer reviewed journals

119 Publications found
  • Identifying Functional Groups that Determine Rates of Micropollutant Biotransformations Performed by Wastewater Microbial Communities

    Stephanie L. Rich, Michael Zumstein, Damian E. Helbling
    2022 - Environmental Science & Technology, 56: 984–994

    Abstract: 

    The goal of this research was to identify functional groups that determine rates of micropollutant (MP) biotransformations performed by wastewater microbial communities. To meet this goal, we performed a series of incubation experiments seeded with four independent wastewater microbial communities and spiked them with a mixture of 40 structurally diverse MPs. We collected samples over time and used high-resolution mass spectrometry to estimate biotransformation rate constants for each MP in each experiment and to propose structures of 46 biotransformation products. We then developed random forest models to classify the biotransformation rate constants based on the presence of specific functional groups or observed biotransformations. We extracted classification importance metrics from each random forest model and compared them across wastewater microbial communities. Our analysis revealed 30 functional groups that we define as either biotransformation promoters, biotransformation inhibitors, structural features that can be biotransformed based on uncharacterized features of the wastewater microbial community, or structural features that are not rate-determining. Our experimental data and analysis provide novel insights into MP biotransformations that can be used to more accurately predict MP biotransformations or to inform the design of new chemical products that may be more readily biodegradable during wastewater treatment.

  • Crop rotational complexity affects plant-soil nitrogen cycling during water deficit

    Bowles TM, Jilling A, Morán-Rivera K, Schnecker J, Grandy AS
    2022 - Soil Biology and Biochemistry, 166: Article 108552

    Abstract: 

    One of the biggest environmental challenges facing agriculture is how to both supply and retain nitrogen (N), especially as precipitation becomes more variable with climate change. We used a greenhouse experiment to assess how contrasting histories of crop rotational complexity affect plant-soil-microbe interactions that govern N processes, including during water stress. With higher levels of carbon and N cycling hydrolytic enzymes, higher mineral-associated organic matter N concentrations, and an altered microbial community, soils from the most complex rotation enabled 80% more corn N uptake under two moisture regimes, compared to soil from monoculture corn. Higher levels of plant N likely drove the changes in corn leaf gas exchange, particularly increasing intrinsic water use efficiency by 9% in the most complex rotation. The water deficit increased the standing pool of nitrate 44-fold in soils with a history of complex crop rotations, compared to an 11-fold increase in soils from the corn monoculture. The implications of this difference must be considered in a whole cropping systems and field context. Cycling of 15N-labeled fresh clover residue into soil N pools did not depend on the water regime or rotation history, with 2-fold higher recovery in the mineral vs. particulate organic N pool. In contrast, the water deficit reduced recovery of clover 15N in corn shoots by 37%, showing greater impacts of water deficit on plant N uptake compared to organic N cycling in soil. This study provides direct experimental evidence that long-term crop rotational complexity influences microbial N cycling and availability with feedbacks to plant physiology. Collectively, these results could help explain general observations of higher yields in more complex crop rotations, including specifically during dry conditions.

  • Sulfur in lucinid bivalves inhibits intake rates of a molluscivore shorebird

    Tim Oortwijn, Jimmy de Fouw, Jillian Petersen, Jan A. van Gils
    2022 - Oecologia, in press

    Abstract: 

    A forager’s energy intake rate is usually constrained by a combination of handling time, encounter rate and digestion rate. On top of that, food intake may be constrained when a forager can only process a maximum amount of certain toxic compounds. The latter constraint is well described for herbivores with a limited tolerance to plant secondary metabolites. In sulfidic marine ecosystems, many animals host chemoautotrophic endosymbionts, which store sulfur compounds as an energy resource, potentially making their hosts toxic to predators. The red knot Calidris canutus canutus is a molluscivore shorebird that winters on the mudflats of Banc d’Arguin, where the most abundant bivalve prey Loripes orbiculatus hosts sulfide-oxidizing bacteria. In this system, we studied the potential effect of sulfur on the red knots’ intake rates, by offering Loripes with various sulfur content to captive birds. To manipulate toxicity, we starved Loripes for 10 days by removing them from their symbiont’s energy source sulfide. As predicted, we found lower sulfur concentrations in starved Loripes. We also included natural variation in sulfur concentrations by offering Loripes collected at two different locations. In both cases lower sulfur levels in Loripes resulted in higher consumption rates in red knots. Over time the red knots increased their intake rates on Loripes, showing their ability to adjust to a higher intake of sulfur.

  • Broad- and small-scale environmental gradients drive variation in chemical, but not morphological, leaf traits of vascular epiphytes

    Guzmán-Jacob V, Guerrero-Ramírez NR, Craven D, Brant PAterno G, Taylor A, Kromer T, Wanek W, Zotz G, Kreft H
    2022 - Functional Ecology, in press

    Abstract: 

    1. Variation in leaf functional traits along environmental gradients can reveal how vascular epiphytes respond to broad- and small-scale environmental gradients. Along elevational gradients, both temperature and precipitation likely play an important role as drivers of leaf trait variation, but these traits may also respond to small-scale changes in light, temperature and humidity along the vertical environmental gradient within forest canopies. However, the relative importance of broad- and small-scale environmental gradients as drivers of variation in leaf functional traits of vascular epiphytes is poorly understood.
    2. Here, we examined variation in morphological and chemical leaf traits of 102 vascular epiphyte species spanning two environmental gradients along Cofre de Perote mountain in Mexico: (i) a broad-scale environmental gradient approximated by elevation as well as by species' lower and upper elevational limits, and (ii) small-scale environmental gradients using the relative height of attachment of an epiphyte on a host tree as a proxy for variation in environmental conditions within the forest canopy. We also assessed whether variation in morphological and chemical leaf traits along these gradients was consistent across photosynthetic pathways (CAM and C3).
    3. Broad- and small-scale environmental gradients explained more variation in chemical traits (marginal R2: 11%–89%) than in morphological traits (marginal R2: 2%–31%). For example, leaf carbon isotope signatures (δ13C), which reflects water-use efficiency, varied systematically across both environmental gradients, suggesting a decrease in water-use efficiency with increasing lower and upper elevational limits and an increase in water-use efficiency with relative height of attachment. The influence of lower and upper elevational limits on trait variation differed between photosynthetic pathways, except for leaf dry matter content and leaf nitrogen-to-phosphorus ratio. Contrary to our expectations, broad- and small-scale environmental gradients explained minimal variation in morphological leaf traits, suggesting that environmental conditions do not constrain morphological leaf trait values of vascular epiphytes.
    4. Our findings suggest that assessing multiple drivers of leaf trait variation among photosynthetic pathways is key for disentangling the mechanisms underlying responses of vascular epiphytes to environmental conditions.

     

    Read the free Plain Language Summary for this article on the Journal blog.

     

    1. Variation in leaf functional traits along environmental gradients can reveal how vascular epiphytes respond to broad- and small-scale environmental gradients. Along elevational gradients, both temperature and precipitation likely play an important role as drivers of leaf trait variation, but these traits may also respond to small-scale changes in light, temperature and humidity along the vertical environmental gradient within forest canopies. However, the relative importance of broad- and small-scale environmental gradients as drivers of variation in leaf functional traits of vascular epiphytes is poorly understood.
    2. Here, we examined variation in morphological and chemical leaf traits of 102 vascular epiphyte species spanning two environmental gradients along Cofre de Perote mountain in Mexico: (i) a broad-scale environmental gradient approximated by elevation as well as by species' lower and upper elevational limits, and (ii) small-scale environmental gradients using the relative height of attachment of an epiphyte on a host tree as a proxy for variation in environmental conditions within the forest canopy. We also assessed whether variation in morphological and chemical leaf traits along these gradients was consistent across photosynthetic pathways (CAM and C3).
    3. Broad- and small-scale environmental gradients explained more variation in chemical traits (marginal R2: 11%–89%) than in morphological traits (marginal R2: 2%–31%). For example, leaf carbon isotope signatures (δ13C), which reflects water-use efficiency, varied systematically across both environmental gradients, suggesting a decrease in water-use efficiency with increasing lower and upper elevational limits and an increase in water-use efficiency with relative height of attachment. The influence of lower and upper elevational limits on trait variation differed between photosynthetic pathways, except for leaf dry matter content and leaf nitrogen-to-phosphorus ratio. Contrary to our expectations, broad- and small-scale environmental gradients explained minimal variation in morphological leaf traits, suggesting that environmental conditions do not constrain morphological leaf trait values of vascular epiphytes.
    4. Our findings suggest that assessing multiple drivers of leaf trait variation among photosynthetic pathways is key for disentangling the mechanisms underlying responses of vascular epiphytes to environmental conditions.

     

    Read the free Plain Language Summary for this article on the Journal blog.

  • Soil carbon loss in warmed subarctic grasslands is rapid and restricted to topsoil

    Verbrigghe N, Leblans NIW, Sigurdsson BD, Vicca S, Fang C, Fuchslueger L, Soong JL, Weedon JT, Poeplau C, Ariza-Carricondo C, Bahn M, Guenet B, Gundersen P, Gunnarsdóttir GE, Kätterer T, Liu Z, Maljanen M, Marañon-Jimenez S, Meeran K, Oddsdóttir ES, Ostonen I, Schiestl RH, Richter A, Sardans J, Sigurðsson P, Torn MS, Van Bodegom PM, Verbruggen E, Walker TWN, Wallander H, Janssens IA
    2022 - Biogeosciences, 19: 3381-3393

    Abstract: 

    Global warming may lead to carbon transfers from soils to the atmosphere, yet this positive feedback to the climate system remains highly uncertain, especially in subsoils (Ilyina and Friedlingstein2016Shi et al.2018). Using natural geothermal soil warming gradients of up to +6.4C in subarctic grasslands (Sigurdsson et al.2016), we show that soil organic carbon (SOC) stocks decline strongly and linearly with warming (−2.8 t ha−1C−1). Comparison of SOC stock changes following medium-term (5 and 10 years) and long-term (>50 years) warming revealed that all SOC stock reduction occurred within the first 5 years of warming, after which continued warming no longer reduced SOC stocks. This rapid equilibration of SOC observed in Andosol suggests a critical role for ecosystem adaptations to warming and could imply short-lived soil carbon–climate feedbacks. Our data further revealed that the soil C loss occurred in all aggregate size fractions and that SOC stock reduction was only visible in topsoil (0–10 cm). SOC stocks in subsoil (10–30 cm), where plant roots were absent, showed apparent conservation after >50 years of warming. The observed depth-dependent warming responses indicate that explicit vertical resolution is a prerequisite for global models to accurately project future SOC stocks for this soil type and should be investigated for soils with other mineralogies.

  • Soil warming delays leaf litter decomposition but exerts no effect on litter nutrient release in a subtropical natural forest over 450 days

    Liu X, Chen S, Li X, Yang Z, Xiong D, Xu C, Wanek W, Yang Y
    2022 - Geoderma, 427: Article 116139

    Abstract: 

    Litter decomposition is a fundamental ecosystem process, influencing soil carbon storage, nutrient availability, and forest productivity. Climate change may affect litter decomposition and thus nutrient dynamics via altering plant phenology, litter quality, and the composition of soil microbial communities. However, the effects of climate change on litter decomposition are not well understood, especially in tropical and subtropical forest ecosystems, which are less temperature limited. We conducted a manipulative study to assess how soil warming affects litter decomposition rates and its relation to litter chemistry, extracellular enzyme activities, and microbial biomass in an evergreen broad-leaved forest in subtropical China. The temperature at 0–10 cm soil depth was experimentally increased by 4 °C, starting from June 2016 to October 2017. Soil warming did not affect litter mass loss during the initial stage (0–270 day), but reduced litter mass loss by 12.9 % at the later stages (days 350 to 450). Structural equation modeling showed that litter moisture content was reduced by warming, but this was not the main effector leading to the reduction in late-stage litter decomposition in the warming treatment. The model suggested that warming reduced litter decomposition rates likely indirectly, through its negative effects on extractable organic carbon and microbial biomass (e.g., microbial carbon and nitrogen), and on litter enzyme activities (a composite variable of β-glucosidase, cellobiohydrolase, acid phosphatase, and phenoloxidase). These results show that warming may slow down litter carbon cycling, but this subtropical forest ecosystem did not affect litter N and P cycling and soil nutrient availability.

  • Generation of Reproducible Model Freshwater Particulate Matter Analogues to Study the Interaction with Particulate Contaminants.

    Helene Walch, Antonia Praetorius, Frank von der Kammer, Thilo Hofmann
    2022 - Water Research, in press

    Abstract: 

    Aquatic fate models and risk assessment require experimental information on the potential of contaminants to interact with riverine suspended particulate matter (SPM). While for dissolved contaminants partition or sorption coefficients are used, the underlying assumption of chemical equilibrium is invalid for particulate contaminants, such as engineered nanomaterials, incidental nanoparticles, micro- or nanoplastics. Their interactions with SPM are governed by physicochemical forces between contaminant-particle and SPM surfaces. The availability of a standard SPM material is thus highly relevant for the development of reproducible test systems to evaluate the fate of particulate contaminants in aquatic systems. Finding suitable SPM analogues, however, is challenging considering the complex composition of natural SPM, which features floc-like structures comprising minerals and organic components from the molecular to the microorganism level. Complex composition comes with a heterogeneity in physicochemical surface properties, that cannot be neglected. We developed a procedure to generate SPM analogue flocs from components selected to represent the most abundant and crucial constituents of natural riverine SPM, and the process-relevant SPM surface characteristics regarding interactions with particulate contaminants. Four components, i.e., illite, hematite, quartz and tryptophan, combined at environmentally realistic mass-ratios, were associated to complex flocs. Flocculation was reproducible regarding floc size and fractal dimension, and multiple tests on floc resilience towards physical impacts (agitation, sedimentation-storage-resuspension, dilution) and hydrochemical changes (pH, electrolytes, dissolved organic matter concentration) confirmed their robustness. These reproducible, ready-to-use SPM analogue flocs will strongly support future research on emerging particulate contaminants.

  • Nitrogen fixation by diverse diazotrophic communities can support population growth of arboreal ants

    Nepel M, Pfeifer J, Oberhauser FB, Richter A, Woebken D, Mayer VE
    2022 - BMC Biology, 20: 135

    Abstract: 

    Background: Symbiotic ant-plant associations, in which ants live on plants, feed on plant-provided food, and protect host trees against threats, are ubiquitous across the tropics, with the Azteca-Cecropia associations being amongst the most widespread interactions in the Neotropics. Upon colonization of Cecropia’s hollow internodes, Azteca queens form small patches with plant parenchyma, which are then used as waste piles when the colony grows. Patches—found in many ant-plant mutualisms—are present throughout the colony life cycle and may supplement larval food. Despite their initial nitrogen (N)-poor substrate, patches in Cecropia accommodate fungi, nematodes, and bacteria. In this study, we investigated the atmospheric N2 fixation as an N source in patches of early and established ant colonies. Results: Via 15N2 tracer assays, N2 fixation was frequently detected in all investigated patch types formed by three Azteca ant species. Quantified fixation rates were similar in early and established ant colonies and higher than in various tropical habitats. Based on amplicon sequencing, the identified microbial functional guild—the diazotrophs—harboring and transcribing the dinitrogenase reductase (nifH) gene was highly diverse and heterogeneous across Azteca colonies. The community composition differed between early and established ant colonies and partly between the ant species. Conclusions: Our data show that N2 fixation can result in reasonable amounts of N in ant colonies, which might not only enable bacterial, fungal, and nematode growth in the patch ecosystems but according to our calculations can even support the growth of ant populations. The diverse and heterogeneous diazotrophic community implies a functional redundancy, which could provide the ant-plant-patch system with a higher resilience towards changing environmental conditions. Hence, we propose that N2 fixation represents a previously unknown potential to overcome N limitations in arboreal ant colonies.

  • Geometry of the modelled freshwater/salt-water interface under variable-density-driven flow (Pétrola Lake, SE Spain)

    Sanz D, Valiente N, Dountcheva I, Muñoz-Martín A, Cassiraga E, Gómez-Alday JJ
    2022 - Hydrogeology Journal, 30: 975-988

    Abstract: 

    Pétrola Lake in southeast Spain is one of the most representative examples of hypersaline wetlands in southern Europe. The rich ecosystem and environmental importance of this lake are closely associated with the hydrogeological behaviour of the system. The wetland is fed by the underlying aquifer with relatively fresh groundwater—1 g L−1 of total dissolved solids (TDS)—with a centripetal direction towards the wetland. In addition, the high evaporation rates of the region promote an increase in the concentration of salts in the lake water, occasionally higher than 80 g L−1 TDS. The density difference between the superficial lake water and the regional groundwater can reach up to 0.25 g cm−3, causing gravitational instability and density-driven flow (DDF) under the lake bottom. The objective of this study was to gain an understanding of the geometry of the freshwater–saltwater interface by means of two-dimensional mathematical modelling and geophysical-resistivity-profile surveys. The magnitude and direction of mixed convective flows, generated by DDF, support the hypothesis that the autochthonous reactive organic matter produced in the lake by biomass can be transported effectively towards the freshwater–saltwater interface areas (e.g. springs in the lake edge), where previous research described biogeochemical processes of natural attenuation of nitrate pollution.

  • Enhanced nitrogen and carbon removal in natural seawater by electrochemical enrichment in a bioelectrochemical reactor

    De La Fuente MJ, de la Iglesia R, Farías L, Glasner B, Torres-Rojas F, Muñoz D, Daims H, Lukumbuzya M, Vargas I
    2022 - J Environ Manage, 323: 116294

    Abstract: 

    Municipal and industrial wastewater discharges in coastal and marine environments are of major concern due to their high carbon and nitrogen loads and the resulted phenomenon of eutrophication. Bioelectrochemical reactors (BERs) for simultaneous nitrogen and carbon removal have gained attention owing to their cost efficiency and versatility, as well as the possibility of electrochemical enrich specific groups. This study presented a scalable two-chamber BERs using graphite granules as electrode material. BERs were inoculated and operated for 37 days using natural seawater with high concentrations of ammonium and acetate. The BERs demonstrated a maximum current density of 0.9 A m−3 and removal rates of 7.5 mg NH4+-N L−1 d−1 and 99.5 mg L−1 d−1 for total organic carbon (TOC). Removals observed for NH4+-N and TOC were 96.2% and 68.7%, respectively. The results of nutrient removal (i.e., ammonium, nitrate, nitrite and TOC) and microbial characterization (i.e., next-generation sequencing of the 16S rRNA gene and fluorescence in situ hybridization) showed that BERs operated with a poised cathode at −260 mV (vs. Ag/AgCl) significantly enriched nitrifying microorganisms in the anode and denitrifying microorganisms and planctomycetes in the cathode. Interestingly, the electrochemical enrichment did not increase the total number of microorganisms in the formed biofilms but controlled their composition. Thus, this work shows the first successful attempt to electrochemically enrich marine nitrifying and denitrifying microorganisms and presents a technique to accelerate the start-up process of BERs to remove dissolved inorganic nitrogen and total organic carbon from seawater.

  • Catchment properties as predictors of greenhouse gas concentrations across a gradient of boreal lakes

    Valiente N, Eiler A, Allesson L, Andersen T, Clayer F, Crapart C, Dörsch P, Fontaine L, Heuschele J, Vogt RD, Wei J, de Wit HA, Hessen DO
    2022 - Front. Environ. Sci., 10: Article 880619

    Abstract: 

    Boreal lakes are the most abundant lakes on Earth. Changes in acid rain deposition, climate, and catchment land use have increased lateral fluxes of terrestrial dissolved organic matter (DOM), resulting in a widespread browning of boreal freshwaters. This browning affects the aqueous communities and ecosystem processes, and boost emissions of the greenhouse gases (GHG) CH4, CO2, and N2O. In this study, we predicted biotic saturation of GHGs in boreal lakes by using a set of chemical, hydrological, climate, and land use parameters. For this purpose, concentrations of GHGs and nutrients (organic C, -P, and -N) were determined in surface water samples from 73 lakes in south-eastern Norway covering wide ranges in DOM and nutrient concentrations, as well as catchment properties and land use. The spatial variation in saturation of each GHG is related to explanatory variables. Catchment characteristics (hydrological and climate parameters) such as lake size and summer precipitation, as well as NDVI, were key determinants when fitting GAM models for CH4 and CO2 saturation (explaining 71 and 54%, respectively), while summer precipitation and land use data were the best predictors for the N2O saturation, explaining almost 50% of deviance. Our results suggest that lake size, precipitation, and terrestrial primary production in the watershed control the saturation of GHG in boreal lakes. These predictions based on the 73-lake dataset was validated against an independent dataset from 46 lakes in the same region. Together, this provides an improved understanding of drivers and spatial variation in GHG saturation in boreal lakes across wide gradients of lake and catchment properties. The assessment highlights the need to incorporate multiple explanatory parameters in prediction models of GHGs for extrapolation across the boreal biome.

  • Plant-microbial linkages underpin carbon sequestration in contrasting mountain tundra vegetation types

    Gavazov K, Canarini A, Jassey VEJ, Mills R, Richter A, Sundqvist MK, Väisänen M, Walker TWN, Wardle DA, Dorrepaal E
    2022 - Soil Biology and Biochemistry, Article 108530

    Abstract: 

    Tundra ecosystems hold large stocks of soil organic matter (SOM), likely due to low temperatures limiting rates of microbial SOM decomposition more than those of SOM accumulation from plant primary productivity and microbial necromass inputs. Here we test the hypotheses that distinct tundra vegetation types and their carbon supply to characteristic rhizosphere microbes determine SOM cycling independent of temperature. In the subarctic Scandes, we used a three-way factorial design with paired heath and meadow vegetation at each of two elevations, and with each combination of vegetation type and elevation subjected during one growing season to either ambient light (i.e., ambient plant productivity), or 95% shading (i.e., reduced plant productivity). We assessed potential above- and belowground ecosystem linkages by uni- and multivariate analyses of variance, and structural equation modelling. We observed direct coupling between tundra vegetation type and microbial community composition and function, which underpinned the ecosystem's potential for SOM storage. Greater primary productivity at low elevation and ambient light supported higher microbial biomass and nitrogen immobilisation, with lower microbial mass-specific enzymatic activity and SOM humification. Congruently, larger SOM at lower elevation and in heath sustained fungal-dominated microbial communities, which were less substrate-limited, and invested less into enzymatic SOM mineralisation, owing to a greater carbon-use efficiency (CUE). Our results highlight the importance of tundra plant community characteristics (i.e., productivity and vegetation type), via their effects on soil microbial community size, structure and physiology, as essential drivers of SOM turnover. The here documented concerted patterns in above- and belowground ecosystem functioning is strongly supportive of using plant community characteristics as surrogates for assessing tundra carbon storage potential and its evolution under climate and vegetation changes.

  • Exploring Nanogeochemical Environments: New Insights from Single Particle ICP-TOFMS and AF4-ICPMS

    Manuel D. Montaño, Chad W. Cuss, Haley M. Holliday, Muhammad B. Javed, William Shotyk, Kathryn L. Sobocinski, Thilo Hofmann, Frank von der Kammer, James F. Ranville
    2022 - ACS Earth & Space Chemistry, 6: 943–952

    Abstract: 

    Nanogeochemistry is an emerging focus area recognizing the role of nanoparticles in Earth systems. Engineered nanotechnology has cultivated advanced analytical techniques that are also applicable to nanogeochemistry. Single particle inductively coupled plasma ICP-time-of-flight-mass spectrometry (ICP-TOF-MS) promises a significant step forward, as time-of-flight mass analyzers enable simultaneous quantification of the entire atomic mass spectrum (∼7–250 m/z+). To demonstrate the utility of this approach, samples were collected and analyzed from a large, boreal river, and its surrounding tributaries. These samples provided us with a diversity of particle compositions and morphologies, while their interconnected nature allowed for an examination of the various nanogeochemical processes present in this system. To further expand on this effort, we combined this high-throughput technique with AF4-ICPMS, focusing on major carriers of trace elements. Using spICP-TOF-MS, Al, Si, and Fe were grouped into classes having all combinations of one or more of these elements. Particle-by-particle ICP-TOF-MS analysis found chemically heterogeneous populations, indicating the predominance of diverse mineralogy or heteroaggregates. The importance of suspended Fe and Mn for the speciation of Pb was observed by single particle ICP-TOF-MS and complemented by AF4-ICPMS analysis of dissolved organic matter and nanoparticulate Fe/Mn. Our study exploits the combination of spICP-TOF-MS and AF4-ICP-MS for studying isotopic and elemental ratios (mineralogy) of individual nanoparticles, which opens the door to further explore the mechanisms of colloid facilitated transport of trace elements.

  • The breakthrough paradox - how focusing on one form of innovation jeopardizes the advancement of science

    Falkenberg F, Fochler M, Sigl L, Bürstmayr, Eichorst SA, Michel S, Oburger E, Staudinger C, Steiner B, Woebken D
    2022 - EMBO Reports, e54772

    Abstract: 

    Science is about venturing into the unknown to find unexpected insights and establish new knowledge. Increasingly, academic institutions and funding agencies such as the European Research Council (ERC) explicitly encourage and support scientists to foster risky and hopefully ground-breaking research. Such incentives are important and have been greatly appreciated by the scientific community. However, the success of the ERC has had its downsides, as other actors in the funding ecosystem have adopted the ERC’s focus on “breakthrough science” and respective notions of scientific excellence. We argue that these tendencies are concerning since disruptive breakthrough innovation is not the only form of innovation in research. While continuous, gradual innovation is often taken for granted, it could become endangered in a research and funding ecosystem that places ever higher value on breakthrough science. This is problematic since, paradoxically, breakthrough potential in science builds on gradual innovation. If the value of gradual innovation is not better recognized, the potential for breakthrough innovation may well be stifled.

  • Screening for genes involved in cellulase regulation by expression under the control of a novel constitutive promoter in Trichoderma reesei

    Beier S, Stiegler M, Hitzenhammer E, Schmoll M
    2022 - Current Research in Biotechnology, 4: 238-246

    Abstract: 

    The filamentous ascomycete Trichoderma reesei is a biotechnological workhorse used in the production of homologous and heterologous proteins for diverse applications including biofuel production, textile finishing and food additives. This fungus uses a complex adaptation machinery to regulate its cellulases in response to environmental conditions. Detailed understanding of this regulation allows for improvement of enzyme production using the strong enzyme gene promotors. Here, we selected six genes with characteristic transcript levels associated with cellulase production to be tested for their enzyme regulatory function. Machine learning for inference of a gene regulatory network (GRN) was applied to support the association of these genes with cellulase induction. Additionally, we screened available transcriptomic data for genes with strong constitutive transcript levels and selected the promoter of the gene cfe1, whose transcript levels were above those of tef1 and cDNA1 and near those of cbh1, for gene overexpression testing. Using this promoter, we explored the relevance to cellulose degradation efficiency of three transporters, two ferric reductases and one gene of unknown function, which were overexpressed in T. reesei grown on cellulose. This promoter enabled up to 400 fold overexpression and yielded transcript levels above those of tef1 or cDNA1. We provide evidence of effects of a ferric reductase, an ammonium permease and a gene of unknown function on the regulatory machinery of cellulase expression in T. reesei. In summary we identified the cfe1 promoter, a novel constitutive promoter with promising efficiency, as well as three genes relevant to cellulase regulation in T. reesei.

  • Broaden chemicals scope in biodiversity targets

    Gabriel Sigmund, Marlene Ågerstrand, Tomas Brodin, Miriam L. Diamond, Walter R. Erdelen, David C. Evers, Adelene Lai, Matthias C. Rillig, Andreas Schäffer, Anna Soehl, João Paulo M. Torres, Zhanyun Wang, Ksenia J. Groh
    2022 - Science, 376: 1280

    Abstract: 

    On 21 June, the next round of negotiations on the post-2020 global biodiversity framework will be held in Nairobi. In the draft document listing 21 targets, target 7 addresses chemical pollution by explicitly mentioning nutrients, pesticides, and plastic waste. Limiting this target’s scope to these three groups does not do justice to the immense variety of anthropogenic chemicals polluting the environment, which also include, for example, toxic metals, industrial chemicals, chemicals from consumer products, and pharmaceuticals, as well as the (often unknown) transformation products of substances from each group. We urge the negotiators to broaden the scope of target 7 to reflect the complexity of chemical pollution.

  • Fatty acid 16:1ω5 as a proxy for arbuscular mycorrhizal fungal biomass: current challenges and ways forward

    Lekberg Y, Bååth E, Frostegård Å, Hammer E, Hedlund K, Jansa J, Kaiser C, Ramsey PW, Řezanka T, Rousk J, Wallander H, Welc M, Olsson PA
    2022 - Biology and Fertility of Soils, 58: 835-842

    Abstract: 

    Fatty acid biomarkers have emerged as a useful tool to quantify biomass of various microbial groups. Here we focus on the frequent use of the fatty acid 16:1ω5 as a biomarker for arbuscular mycorrhizal (AM) fungi in soils. We highlight some issues with current applications of this method and use several examples from the literature to show that the phospholipid fatty acid (PLFA) 16:1ω5 can occur in high concentrations in soils where actively growing AM fungi are absent. Unless the study includes a control where the contribution of other microbes can be estimated, we advocate for the use of the neutral lipid fatty acid (NLFA) 16:1ω5. This biomarker has higher specificity, is more responsive to shifts in AM fungal biomass, and quantification can be conducted along with PLFA analysis without doubling analytical efforts. We conclude by contrasting various methods used to measure AM fungal biomass in soil and highlight future research needs to optimize fatty acid analyses.

  • Vertical profiles of leaf photosynthesis and leaf traits and soil nutrients in two tropical rainforests in French Guiana before and after a 3-year nitrogen and phosphorus addition experiment

    Verryckt LT, Vicca S, Van Langenhove L, Stahl C, Asensio D, Urbina I, Ogaya R, Llusià J, Grau O, Peguero G, Gargallo-Garriga A, Courtois EA, Margalef O, Portillo-Estrada M, Ciais P, Obersteiner M, Fuchslueger L, Lugli LF, Fernandez-Garberi PR, Vallicrosa H, Verlinden M, Ranits C, Vermeir P, Coste S, Verbruggen E, Bréchet L, Sardans J, Chave J, Schiestl RH, Janssens IA
    2022 - Earth Syst. Sci. Data, 14: 5-8

    Abstract: 

    Terrestrial biosphere models typically use the biochemical model of Farquhar, von Caemmerer, and Berry (1980) to simulate photosynthesis, which requires accurate values of photosynthetic capacity of different biomes. However, data on tropical forests are sparse and highly variable due to the high species diversity, and it is still highly uncertain how these tropical forests respond to nutrient limitation in terms of C uptake. Tropical forests often grow on soils low in phosphorus (P) and are, in general, assumed to be P rather than nitrogen (N) limited. However, the relevance of P as a control of photosynthetic capacity is still debated. Here, we provide a comprehensive dataset of vertical profiles of photosynthetic capacity and important leaf traits, including leaf N and P concentrations, from two 3-year, large-scale nutrient addition experiments conducted in two tropical rainforests in French Guiana. These data present a unique source of information to further improve model representations of the roles of NP, and other leaf nutrients in photosynthesis in tropical forests. To further facilitate the use of our data in syntheses and model studies, we provide an elaborate list of ancillary data, including important soil properties and nutrients, along with the leaf data. As environmental drivers are key to improve our understanding of carbon (C) and nutrient cycle interactions, this comprehensive dataset will aid to further enhance our understanding of how nutrient availability interacts with C uptake in tropical forests. The data are available at https://doi.org/10.5281/zenodo.5638236 (Verryckt, 2021).

  • Global grassland diazotrophic communities are structured by combined abiotic, biotic, and spatial distance factors but resilient to fertilization

    Nepel M, Angel R, Borer ET, Frey B, MacDougall AS, McCulley RL, Risch AC, Schütz M, Seasbloom EW, Woebken D
    2022 - Front Microbiol, 13: 821030

    Abstract: 

    Grassland ecosystems cover around 37% of the ice-free land surface on Earth and have critical socioeconomic importance globally. As in many terrestrial ecosystems, biological dinitrogen (N2) fixation represents an essential natural source of nitrogen (N). The ability to fix atmospheric N2 is limited to diazotrophs, a diverse guild of bacteria and archaea. To elucidate the abiotic (climatic, edaphic), biotic (vegetation), and spatial factors that govern diazotrophic community composition in global grassland soils, amplicon sequencing of the dinitrogenase reductase gene—nifH—was performed on samples from a replicated standardized nutrient [N, phosphorus (P)] addition experiment in 23 grassland sites spanning four continents. Sites harbored distinct and diverse diazotrophic communities, with most of reads assigned to diazotrophic taxa within the Alphaproteobacteria (e.g., Rhizobiales), Cyanobacteria (e.g., Nostocales), and Deltaproteobacteria (e.g., Desulforomonadales) groups. Likely because of the wide range of climatic and edaphic conditions and spatial distance among sampling sites, only a few of the taxa were present at all sites. The best model describing the variation among soil diazotrophic communities at the OTU level combined climate seasonality (temperature in the wettest quarter and precipitation in the warmest quarter) with edaphic (C:N ratio, soil texture) and vegetation factors (various perennial plant covers). Additionally, spatial variables (geographic distance) correlated with diazotrophic community variation, suggesting an interplay of environmental variables and spatial distance. The diazotrophic communities appeared to be resilient to elevated nutrient levels, as 2–4 years of chronic N and P additions had little effect on the community composition. However, it remains to be seen, whether changes in the community composition occur after exposure to long-term, chronic fertilization regimes.

  • Targeting Gut Bacteria using Inulin-Conjugated Mesoporous Silica Nanoparticles

    von Baeckmann C, Riva A, Guggenberger P, Kählig H, Han SW, Inan D, Del Favero G, Berry D, Kleitz F
    2022 - Advanced Materials Interfaces, in press

    Abstract: 

    To facilitate the creation of novel nanocarrier systems targeting the intestinal microbiome, inulin-conjugated mesoporous silica nanoparticles (MSNs) are described herein for the first time. Surface functionalization is achieved on either hydrophilic or hydrophobic mesoporous nanoparticles using different conjugation methods. The targeting performance of the resulting materials is assessed and compared upon incubation with human stool. It appears that amide formation is the most favorable coupling method on hydrophilic MSNs to achieve the desired bioconjugate. Remarkably, high affinity of gut bacteria to the conjugated particles can be obtained, paving the way to novel targeted drug delivery systems.

  • Microbes From Mum: Symbiont transmission in the tropical reef sponge Ianthella basta

    Engelberts JP, Wahab MAA, Maldonado M, Rix L, Marangon E, Robbins SJ, Wagner M, Webster NS
    2022 - ISME Commun, in press

    Abstract: 

    Most marine sponge species harbour distinct communities of microorganisms which contribute to various aspects of their host’s health and physiology. In addition to their key roles in nutrient transformations and chemical defence, these symbiotic microbes may shape sponge phenotype by mediating important developmental stages and influencing the environmental tolerance of the host. However, the characterisation of each microbial taxa throughout a sponge’s life cycle remains challenging, with several sponge species hosting up to 3 000 distinct microbial species. Ianthella basta, an abundant broadcast spawning species in the Indo-Pacific is an emerging model for sponge symbiosis research as it harbours only three dominant symbionts: a Thaumarchaeotum, a Gammaproteobacterium, and an Alphaproteobacterium. Here, we successfully spawned Ianthella basta, characterised its mode of reproduction, and used 16S rRNA gene amplicon sequencing, fluorescence in situ hybridisation, and transmission electron microscopy to characterise the microbial community throughout its life cycle. We confirmed I. basta as being gonochoric and showed that the three dominant symbionts, which together make up >90% of the microbiome according to 16S rRNA gene abundance, are vertically transmitted from mother to offspring by a unique method involving encapsulation in the peri-oocytic space, suggesting an obligate relationship between these microbes and their host.

  • Getting in control of persistent, mobile and toxic (PMT) and very persistent and very mobile (vPvM) substances to protect water resources: strategies from diverse perspectives

    Sarah E. Hale, Michael Neumann, Ivo Schliebner, Jona Schulze, Frauke S. Averbeck, Claudia Castell-Exner, Marie Collard, Dunja Drmač, Julia Hartmann, Roberta Hofman-Caris, Juliane Hollender, Martin de Jonge, Thomas Kullick, Anna Lennquist, Thomas Letzel, Karsten Nödler, Sascha Pawlowski, Ninja Reineke, Emiel Rorije, Marco Scheurer, Gabriel Sigmund, Harrie Timmer, Xenia Trier, Eric Verbruggen, Hans Peter H. Arp
    2022 - Environmental Sciences Europe, 34: in press

    Abstract: 

    Background

    Safe and clean drinking water is essential for human life. Persistent, mobile and toxic (PMT) substances and/or very persistent and very mobile (vPvM) substances are an important group of substances for which additional measures to protect water resources may be needed to avoid negative environmental and human health effects. PMT/vPvM substances do not sufficiently biodegrade in the environment, they can travel long distances with water and are toxic (those that are PMT substances) to the environment and/or human health. PMT/vPvM substance research and regulation is arguably in its infancy and in order to get in control of these substances the following (non-exhaustive list of) knowledge gaps should to be addressed: environmental occurrence; the suitability of currently available analytical methods; the effectiveness and availability of treatment technologies; the ability of regional governance and industrial stewardship to contribute to safe drinking water while supporting innovation; the ways in which policies and regulations can be used most effectively to govern these substances; and, the identification of safe and sustainable alternatives.

    Methods

    The work is the outcome of the third PMT workshop, held in March 2021, that brought together diverse scientists, regulators, NGOs, and representatives from the water sector and the chemical sector, all concerned with protecting the quality of our water resources. The online workshop was attended by over 700 people. The knowledge gaps above were discussed in the presentations given and the attendees were invited to provide their opinions about knowledge gaps related to PMT/vPvM substance research and regulation.

    Results

    Strategies to closing the knowledge, technical and practical gaps to get in control of PMT/vPvM substances can be rooted in the Chemicals Strategy for Sustainability Towards a Toxic Free Environment from the European Commission, as well as recent advances in the research and industrial stewardship. Key to closing these gaps are: (i) advancing remediation and removal strategies for PMT/vPvM substances that are already in the environment, however this is not an effective long-term strategy; (ii) clear and harmonized definitions of PMT/vPvM substances across diverse European and international legislations; (iii) ensuring wider availability of analytical methods and reference standards; (iv) addressing data gaps related to persistence, mobility and toxicity of chemical substances, particularly transformation products and those within complex substance mixtures; and (v) advancing monitoring and risk assessment tools for stewardship and regulatory compliance. The two most effective ways to get in control were identified to be source control through risk governance efforts, and enhancing market incentives for alternatives to PMT/vPvM substances by using safe and sustainable by design strategies.

  • Applying the 15N labelling technique to material derived from a landfill simulation experiment to understand nitrogen cycle processes under aerobic and anaerobic conditions

    Fricko N, Wanek W, Fellner J
    2022 - Biodegradation, 33: 557-573

    Abstract: 

    Reactive nitrogen (N) species, such as ammonium (NH4+), nitrate (NO3) and gaseous nitrous oxide (N2O), are released into the environment during the degradation of municipal solid waste (MSW), causing persistent environmental problems. Landfill remediation measures, such as in-situ aeration, may accelerate the degradation of organic compounds and reduce the discharge of ammonium via leachate. Nonetheless, the actual amount of N in the waste material remains relatively constant and a coherent explanation for the decline in leachate ammonium concentrations is still lacking. Hence, the present study aimed to elucidate the dynamics of N and its transformation processes during waste degradation. To this end, the gross rates of organic N mineralization and nitrification were measured using 15N pool dilution in waste material derived from a landfill simulation reactor (LSR) experiment. The results revealed a high potential for N mineralization and nitrification, the latter of which declined with the diminishing amount of extractable ammonium (after aeration). The analysis of the concentration and isotopic composition of N2O formed confirmed incomplete denitrification as the main source for N2O. Moreover, the natural abundance of 15N was investigated in various waste N pools to verify the conclusions drawn from the 15N tracing experiment. δ15N values of total waste N increased during aeration, indicating that nitrification is the major driver for N losses from aerated waste. The application of stable isotopes thereby allowed unprecedented insights into the complex N dynamics in decomposing landfill waste, of their response to aeration and their effect on hydrological versus gaseous loss pathways.

  • How low can they go? Aerobic respiration by microorganisms under apparent anoxia

    Berg J, Ahmerkamp S, Pjevac P, Hausmann B, Milucka J, Kuypers MMM
    2022 - FEMS Microbiology Reviews, in press

    Abstract: 

    Oxygen (O2) is the ultimate oxidant on Earth and its respiration confers such an energetic advantage that microorganisms have evolved the capacity to scavenge O2 down to nanomolar concentrations. The respiration of O2 at extremely low levels is proving to be common to diverse microbial taxa, including organisms formerly considered strict anaerobes. Motivated by recent advances in O2 sensing and DNA/RNA sequencing technologies, we performed a systematic review of environmental metatranscriptomes revealing that microbial respiration of O2 at nanomolar concentrations is ubiquitous and drives microbial activity in seemingly anoxic aquatic habitats. These habitats were key to the early evolution of life and are projected to become more prevalent in the near future due to anthropogenic-driven environmental change. Here we summarize our current understanding of aerobic microbial respiration under apparent anoxia, including novel processes, their underlying biochemical pathways, the involved microorganisms, and their environmental importance and evolutionary origin.

  • Ecology and evolution of chlamydial symbionts of arthropods

    Halter T, Koestlbacher S, Collingro A, Sixt BS, Toenshoff ER, Hendrickx F, Kostanjšek R, Horn M
    2022 - ISME Commun., 2: 45

    Abstract: 

    The phylum Chlamydiae consists of obligate intracellular bacteria including major human pathogens and diverse environmental representatives. Here we investigated the Rhabdochlamydiaceae, which is predicted to be the largest and most diverse chlamydial family, with the few described members known to infect arthropod hosts. Using published 16S rRNA gene sequence data we identified at least 388 genus-level lineages containing about 14 051 putative species within this family. We show that rhabdochlamydiae are mainly found in freshwater and soil environments, suggesting the existence of diverse, yet unknown hosts. Next, we used a comprehensive genome dataset including metagenome assembled genomes classified as members of the family Rhabdochlamydiaceae, and we added novel complete genome sequences of Rhabdochlamydia porcellionis infecting the woodlouse Porcellio scaber, and of 'Candidatus R. oedothoracis' associated with the linyphiid dwarf spider Oedothorax gibbosus. Comparative analysis of basic genome features and gene content with reference genomes of well-studied chlamydial families with known host ranges, namely Parachlamydiaceae (protist hosts) and Chlamydiaceae (human and other vertebrate hosts) suggested distinct niches for members of the Rhabdochlamydiaceae. We propose that members of the family represent intermediate stages of adaptation of chlamydiae from protists to vertebrate hosts. Within the genus Rhabdochlamydia, pronounced genome size reduction could be observed (1.49-1.93 Mb). The abundance and genomic distribution of transposases suggests transposable element expansion and subsequent gene inactivation as a mechanism of genome streamlining during adaptation to new hosts. This type of genome reduction has never been described before for any member of the phylum Chlamydiae. This study provides new insights into the molecular ecology, genomic diversity, and evolution of representatives of one of the most divergent chlamydial families.

  • CT295 Is Chlamydia trachomatis’ phosphoglucomutase and a type 3 secretion substrate

    Triboulet A, N’Gadjaga MD, Niragire B, Köstlbacher S, Horn M, Aimanianda V, Subtil A
    2022 - Front Cell Infect Microbiol, 12: 866729

    Abstract: 

    The obligate intracellular bacteria Chlamydia trachomatis store glycogen in the lumen of the vacuoles in which they grow. Glycogen catabolism generates glucose-1-phosphate (Glc1P), while the bacteria can take up only glucose-6-phosphate (Glc6P). We tested whether the conversion of Glc1P into Glc6P could be catalyzed by a phosphoglucomutase (PGM) of host or bacterial origin. We found no evidence for the presence of the host PGM in the vacuole. Two C. trachomatis proteins, CT295 and CT815, are potential PGMs. By reconstituting the reaction using purified proteins, and by complementing PGM deficient fibroblasts, we demonstrated that only CT295 displayed robust PGM activity. Intriguingly, we showed that glycogen accumulation in the lumen of the vacuole of a subset of Chlamydia species (C. trachomatis, C. muridarum, C. suis) correlated with the presence, in CT295 orthologs, of a secretion signal recognized by the type three secretion (T3S) machinery of Shigella. C. caviae and C. pneumoniae do not accumulate glycogen, and their CT295 orthologs lack T3S signals. In conclusion, we established that the conversion of Glc1P into Glc6P was accomplished by a bacterial PGM, through the acquisition of a T3S signal in a “housekeeping” protein. Acquisition of this signal likely contributed to shaping glycogen metabolism within Chlamydiaceae.

  • Mercury Removal from Contaminated Water by Wood-Based Biochar Depends on Natural Organic Matter and Ionic Composition

    Sampriti Chaudhuri, Gabriel Sigmund, Sharon E. Bone, Naresh Kumar, Thilo Hofmann
    2022 - Environ. Sci. Technol., 56: 11354–11362

    Abstract: 

    Biochars can remove potentially toxic elements, such as inorganic mercury [Hg(II)] from contaminated waters. However, their performance in complex water matrices is rarely investigated, and the combined roles of natural organic matter (NOM) and ionic composition in the removal of Hg(II) by biochar remain unclear. Here, we investigate the influence of NOM and major ions such as chloride (Cl-), nitrate (NO3-), calcium (Ca2+), and sodium (Na+) on Hg(II) removal by a wood-based biochar (SWP700). Multiple sorption sites containing sulfur (S) were located within the porous SWP700. In the absence of NOM, Hg(II) removal was driven by these sites. Ca2+ bridging was important in enhancing removal of negatively charged Hg(II)-chloro complexes. In the presence of NOM, formation of soluble Hg-NOM complexes (as seen from speciation calculations), which have limited access to biochar pores, suppressed Hg(II) removal, but Cl- and Ca2+ could still facilitate it. The ability of Ca2+ to aggregate NOM, including Hg-NOM complexes, promoted Hg(II) removal from the dissolved fraction (<0.45 μm). Hg(II) removal in the presence of Cl- followed a stepwise mechanism. Weakly bound oxygen functional groups in NOM were outcompeted by Cl-, forming smaller-sized Hg(II)-chloro complexes, which could access additional intraparticle sorption sites. Therein, Cl- was outcompeted by S, which finally immobilized Hg(II) in SWP700 as confirmed by extended X-ray absorption fine structure spectroscopy. We conclude that in NOM containing oxic waters, with relatively high molar ratios of Cl-: NOM and Ca2+: NOM, Hg(II) removal can still be effective with SWP700.

  • A high-spatial resolution soil carbon and nitrogen dataset for the northern permafrost region, based on circumpolar land cover upscaling

    Palmtag J, Obu J, Kuhry P, Richter A, Siewert MB, Weiss N, Westermann S, Hugelius G
    2022 - Earth Systems Science Data, 14: 4095–4110

    Abstract: 

    Soils in the northern high latitudes are a key component in the global carbon cycle; the northern permafrost region covers 22 % of the Northern Hemisphere land surface area and holds almost twice as much carbon as the atmosphere. Permafrost soil organic matter stocks represent an enormous long-term carbon sink which is in risk of switching to a net source in the future. Detailed knowledge about the quantity and the mechanisms controlling organic carbon storage is of utmost importance for our understanding of potential impacts of and feedbacks on climate change. Here we present a geospatial dataset of physical and chemical soil properties calculated from 651 soil pedons encompassing more than 6500 samples from 16 different study areas across the northern permafrost region. The aim of our dataset is to provide a basis to describe spatial patterns in soil properties, including quantifying carbon and nitrogen stocks. There is a particular need for spatially distributed datasets of soil properties, including vertical and horizontal distribution patterns, for modeling at local, regional, or global scales. This paper presents this dataset, describes in detail soil sampling; laboratory analysis, and derived soil geochemical parameters; calculations; and data clustering. Moreover, we use this dataset to estimate soil organic carbon and total nitrogen storage estimates in soils in the northern circumpolar permafrost region (17.9×106 km2) using the European Space Agency's (ESA's) Climate Change Initiative (CCI) global land cover dataset at 300 m pixel resolution. We estimate organic carbon and total nitrogen stocks on a circumpolar scale (excluding Tibet) for the 0–100 and 0–300 cm soil depth to be 380 and 813 Pg for carbon, and 21 and 55 Pg for nitrogen, respectively. Our organic carbon estimates agree with previous studies, with most recent estimates of 1000 Pg (−170 to +186 Pg) to 300 cm depth. Two separate datasets are freely available on the Bolin Centre Database repository (https://doi.org/10.17043/palmtag-2022-pedon-1, Palmtag et al., 2022a; and https://doi.org/10.17043/palmtag-2022-spatial-1, Palmtag et al., 2002b).

  • The Impacts of Post-Fire Straw Mulching and Salvage Logging on Soil Properties and Plant Diversity in a Mediterranean Burned Pine Forest

    ortega R, Zema DA, Valiente N, Soria R, Miralles I, Lucas-Borja ME
    2022 - Forests, 13: Article 1580

    Abstract: 

    In the Mediterranean forests, wildfires and post-fire management actions may degrade soil properties and negatively impact vegetation characteristics. These effects may reduce soil functionality and result in loss of plant diversity. Although straw mulching and salvage logging are commonly carried out in burned forests, their impacts on respiration of forest soils as well as on species richness and evenness of forest plants have been little explored. To fill these gaps, this study has evaluated the soil respiration, different soil physico-chemical properties, as well as plant diversity in a forest of Castilla La Mancha (Central Eastern Spain), burned by a wildfire and then subjected alternatively to salvage logging or straw mulching or to both techniques. Compared to the unburned soils, immediately after the fire mulching and salvage logging alone increased (+146%) and reduced the soil respiration (−9%), respectively, the latter especially in combination with mulching. However, these differences decreased over time, and the mulched and non-logged areas always showed the maximum soil respiration. The post-fire treatments also significantly influenced the main physico-chemical properties of the experimental soils. No evident changes were found for the pH of the logged and mulched soils compared to the control. Mulching coupled with logging did not modify the OM increase due to fire, while the lowest increase was measured in the logged but non-mulched areas. Mulched and non-logged soils maintained high OM and TN one year after fire, but also in areas that were treated with logging (with or without mulching) these parameters were significantly higher compared to the unburned areas. Mulching increased the species richness and evenness, especially when itis carried out without logging, in comparison to the unburned areas. Logging without mulching did not exert negative impacts on plant biodiversity, whose species richness increased and evenness was unvaried compared to the burned and unburned areas. The results of this study can provide land managers easy to measure tools such as soil respiration and plant diversity, which can serve to assess and evaluate the effectiveness of management measures that are taken post-forest fire in order to conserve the delicate ecosystems of the Mediterranean forests.

  • Rapid analysis of gunshot residues with single-particle inductively coupled plasma time-of-flight mass spectrometry

    Robert Brünjes, Jan Schüürman, Frank von der Kammer, Thilo Hofmann
    2022 - Forensic Science International, 332: in press

    Abstract: 

    Gunshot residues (GSRs) from different types of ammunition have been characterized using a new method based on single-particle inductively coupled plasma time-of-flight mass spectrometry (sp-ICP-TOF-MS). This method can analyze thousands of particles per minute enabling rapid sample screening for GSR detection with minimal sample preparation. GSR particles are multi-elemental nanoparticles that are mainly defined by the elements lead, barium, and antimony. Sp-ICP-TOF-MS was also used to identify other elements contained in GSR particles while standard particle classification protocols do not consider the complexities of GSR compositions and can therefore miss out on valuable information. The proposed method can be used to support existing GSR detection methods, especially when lead-free, antimony-free, or tagged ammunition has been used; it also provides a possibility for multi-elemental fingerprinting of GSR particles.

  • Long-term warming reduced microbial biomass but increased recent plant-derived C in microbes of a subarctic grassland

    Verbrigghe N, Meeran K, Bahn M, Canarini A, Fransen E, Fuchslueger L, Ingrisch J, Janssens IA, Richter A, Sigurdsson BD, Soong JL, Vicca S
    2022 - Soil Biology and Biochemistry, 167: Article 108590

    Abstract: 

    Long-term soil warming and nitrogen (N) availability have been shown to affect microbial biomass and community composition. Altered assimilation patterns of recent plant-derived C and changes in soil C stocks following warming as well as increased N availability are critical in mediating the direction and magnitude of these community shifts. A 13C pulse labelling experiment was done on a warming gradient in an Icelandic grassland (Sigurdsson et al., 2016), to investigate the role of recent plant-derived C and warming on the microbial community structure and size. We observed an overall increase of microbial 13C (e.g., root-exudate) uptake, while warming led to significant microbial biomass loss in all microbial groups. The increase of microbial 13C uptake with warming differed between microbial groups: an increase was only observed in the general and Gram-positive bacterial phospholipid fatty acid (PLFA) markers and in the PLFA and neutral lipid fatty acid (NLFA) markers of arbuscular mycorrhizal fungi (AMF). Nitrogen addition of 50 kg ha−1 y−1 for two years had no effect on the microbial uptake, microbial biomass or community composition, indicating that microbes were not N limited, and no plant-mediated N addition effects occurred. Additionally, we show that both warming and soil C depletion were responsible for the microbial biomass loss. Soil warming caused stronger loss in microbial groups with higher 13C uptake. In our experiment, warming caused a general reduction of microbial biomass, despite a relative increase in microbial 13C uptake, and altered microbial community composition. The warming effects on microbial biomass and community composition were partly mediated through soil C depletion with warming and changes in recent plant-derived C uptake patterns of the microbial community.

  • Ligand-Induced U Mobilization from Chemogenic Uraninite and Biogenic Noncrystalline U(IV) under Anoxic Conditions

    Kyle J. Chardi, Anshuman Satpathy, Walter D. C. Schenkeveld*, Naresh Kumar, Vincent Noël, Stephan M. Kraemer, and Daniel E. Giammar
    2022 - Environmental Science and Technology, 56: 6369–6379

    Abstract: 

    Microbial reduction of soluble hexavalent uranium (U(VI)) to sparingly soluble tetravalent uranium (U(IV)) has been explored as an in situ strategy to immobilize U. Organic ligands might pose a potential hindrance to the success of such remediation efforts. In the current study, a set of structurally diverse organic ligands were shown to enhance the dissolution of crystalline uraninite (UO2) for a wide range of ligand concentrations under anoxic conditions at pH 7.0. Comparisons were made to ligand-induced U mobilization from noncrystalline U(IV). For both U phases, aqueous U concentrations remained low in the absence of organic ligands (<25 nM for UO2; 300 nM for noncrystalline U(IV)). The tested organic ligands (2,6-pyridinedicarboxylic acid (DPA), desferrioxamine B (DFOB), N,N′-di(2-hydroxybenzyl)ethylene-diamine-N,N′-diacetic acid (HBED), and citrate) enhanced U mobilization to varying extents. Over 45 days, the ligands mobilized only up to 0.3% of the 370 μM UO2, while a much larger extent of the 300 μM of biomass-bound noncrystalline U(IV) was mobilized (up to 57%) within only 2 days (>500 times more U mobilization). This work shows the potential of numerous organic ligands present in the environment to mobilize both recalcitrant and labile U forms under anoxic conditions to hazardous levels and, in doing so, undermine the stability of immobilized U(IV) sources.

  • Soil greenhouse gas fluxes in floodplain forests of the Danube National Park – Effects of flooding and soil microclimate

    Schindlbacher A, Heinzle J, Gollobich G, Wanek W, Michel K, Kitzler K
    2022 - Biogeochemistry, 159: 193-213

    Abstract: 

    The relevance of soil greenhouse gas (GHG) fluxes from temperate floodplain forests has yet remained elusive. We studied the soil methane (CH4), nitrous oxide (N2O) and carbon dioxide (CO2) dynamics at three forest sites along a flooding gradient in the Danube National Park (Austria) to estimate annual GHG budgets and to assess if and how seasonal flooding affects individual GHG fluxes. Soil surface GHG fluxes were determined along with GHG concentrations in soil air and pore-water at a non-flooded (NF), an infrequently-flooded (IF), and a frequently-flooded (FF) site. Both study years were characterized by dry summers, and only the FF site was flooded during the study period. Soils at all sites were annual CH4 sinks (NF: − 4.50 ± 0.85, IF: − 2.54 ± 0.57, FF: − 0.67 ± 1.06 kg CH4-C ha−1 year−1) and the sink strength correlated positively with soil moisture. Pulse-like CH4 emissions were not observed during or after flooding. Soil N2O fluxes showed large temporal and spatial variations, without any significant differences between sites (average NF: 6.5 ± 7.1, IF: 10.4 ± 14.3, FF: 9.4 ± 10.5 µg N2O-N m−2 h−1). Pulse N2O emissions (up to ~ 80 µg N2O-N m−2 h−1) occurred during freeze/thaw events, but not during or after flooding. Mean annual soil CO2 effluxes at NF and IF were 9.4 ± 1.1 and 9.4 ± 2.1 t C ha−1 year−1, respectively. Soil CO2 efflux was significantly higher at the FF site (18.54 ± 6.21 t C ha−1 year−1). High soil air CO2 concentrations (> 10%) in aerated deeper soil layers indicated a substantial contribution of the usually waterlogged sub-soils to the summertime soil CO2 efflux at the FF site. Overall, our results suggest that the studied temperate floodplain forest soils do not absorb/emit substantially more CH4 and N2O than soils of comparable upland forests, whereas low groundwater level can lead to periodically enhanced CO2 emissions from normally waterlogged soil layers.

  • Broad- and small-scale environmental gradients drive variation in chemical, but not morphological, leaf traits of vascular epiphytes

    Guzmán-Jacob V, Guerrero-Ramírez NR, Craven D, Paterno GB, Taylor A, Kromer T, Wanek W, Zotz G, Kreft H
    2022 - Functional Ecology, 36: 1858-1872

    Abstract: 

    1. Variation in leaf functional traits along environmental gradients can reveal how vascular epiphytes respond to broad- and small-scale environmental gradients. Along elevational gradients, both temperature and precipitation likely play an important role as drivers of leaf trait variation, but these traits may also respond to small-scale changes in light, temperature and humidity along the vertical environmental gradient within forest canopies. However, the relative importance of broad- and small-scale environmental gradients as drivers of variation in leaf functional traits of vascular epiphytes is poorly understood.
    2. Here, we examined variation in morphological and chemical leaf traits of 102 vascular epiphyte species spanning two environmental gradients along Cofre de Perote mountain in Mexico: (i) a broad-scale environmental gradient approximated by elevation as well as by species' lower and upper elevational limits, and (ii) small-scale environmental gradients using the relative height of attachment of an epiphyte on a host tree as a proxy for variation in environmental conditions within the forest canopy. We also assessed whether variation in morphological and chemical leaf traits along these gradients was consistent across photosynthetic pathways (CAM and C3).
    3. Broad- and small-scale environmental gradients explained more variation in chemical traits (marginal R2: 11%–89%) than in morphological traits (marginal R2: 2%–31%). For example, leaf carbon isotope signatures (δ13C), which reflects water-use efficiency, varied systematically across both environmental gradients, suggesting a decrease in water-use efficiency with increasing lower and upper elevational limits and an increase in water-use efficiency with relative height of attachment. The influence of lower and upper elevational limits on trait variation differed between photosynthetic pathways, except for leaf dry matter content and leaf nitrogen-to-phosphorus ratio. Contrary to our expectations, broad- and small-scale environmental gradients explained minimal variation in morphological leaf traits, suggesting that environmental conditions do not constrain morphological leaf trait values of vascular epiphytes.
    4. Our findings suggest that assessing multiple drivers of leaf trait variation among photosynthetic pathways is key for disentangling the mechanisms underlying responses of vascular epiphytes to environmental conditions.
  • Challenges in measuring nitrogen isotope signatures in inorganic nitrogen forms: an inter-laboratory comparison of three common measurement approaches

    Biasi C, Jokinen S, Prommer J, Ambus P, Dörsch P, Yu L, Granger S, Boeckx P, Van Nieuland K, Brüggemann N, Wissel H, Voropaev A, Zilberman T, Jäntti H, Trubnikova T, Welti N, Voigt C, Gebus-Czupyt B, Czupyt Z,  Wanek W
    2022 - Rapid Communications in Mass Spectrometry, 36: Article e9370

    Abstract: 

    Rationale

    Stable isotope approaches are increasingly applied to better understand the cycling of inorganic nitrogen (Ni) forms, key limiting nutrients in terrestrial and aquatic ecosystems. A systematic comparison of the accuracy and precision of the most commonly used methods to analyze δ15N in NO3 and NH4+ and interlaboratory comparison tests to evaluate the comparability of isotope results between laboratories are, however, still lacking.

    Methods

    Here, we conducted an interlaboratory comparison involving 10 European laboratories to compare different methods and laboratory performance to measure δ15N in NO3 and NH4+. The approaches tested were (a) microdiffusion (MD), (b) chemical conversion (CM), which transforms Ni to either N2O (CM-N2O) or N2 (CM-N2), and (c) the denitrifier (DN) methods.

    Results

    The study showed that standards in their single forms were reasonably replicated by the different methods and laboratories, with laboratories applying CM-N2O performing superior for both NO3 and NH4+, followed by DN. Laboratories using MD significantly underestimated the “true” values due to incomplete recovery and also those using CM-N2 showed issues with isotope fractionation. Most methods and laboratories underestimated the at%15N of Ni of labeled standards in their single forms, but relative errors were within maximal 6% deviation from the real value and therefore acceptable. The results showed further that MD is strongly biased by nonspecificity. The results of the environmental samples were generally highly variable, with standard deviations (SD) of up to ± 8.4‰ for NO3 and ± 32.9‰ for NH4+; SDs within laboratories were found to be considerably lower (on average 3.1‰). The variability could not be connected to any single factor but next to errors due to blank contamination, isotope normalization, and fractionation, and also matrix effects and analytical errors have to be considered.

    Conclusions

    The inconsistency among all methods and laboratories raises concern about reported δ15N values particularly from environmental samples.

  • Disturbances in microbial skin recolonization and cutaneous immune response following allogeneic stem cell transfer

    Bayer N, Hausman B, Pandey RV, Deckert F, Gail LM, Strobl J, Pjevac P, Krall C, Unterluggauer L, Redl A, Bachmayr V, Kleissl L, Nehr M, Kirkegaard R, Makrisathis A, Watzenboeck ML, Nica R, Staud C, Hammerl L, Wohlfarth P, Ecker RC, Knapp S, Rabitsch W, Berry D, Stary G
    2022 - Leukemia, in press

    Abstract: 

    The composition of the gut microbiome influences the clinical course after allogeneic hematopoietic stem cell transplantation (HSCT), but little is known about the relevance of skin microorganisms. In a single-center, observational study, we recruited a cohort of 50 patients before undergoing conditioning treatment and took both stool and skin samples up to one year after HSCT. We could confirm intestinal dysbiosis following HSCT and report that the skin microbiome is likewise perturbed in HSCT-recipients. Overall bacterial colonization of the skin was decreased after conditioning. Particularly patients that developed acute skin graft-versus-host disease (aGVHD) presented with an overabundance of Staphylococcus spp. In addition, a loss in alpha diversity was indicative of aGVHD development already before disease onset and correlated with disease severity. Further, co-localization of CD45+ leukocytes and staphylococci was observed in the skin of aGVHD patients even before disease development and paralleled with upregulated genes required for antigen-presentation in mononuclear phagocytes. Overall, our data reveal disturbances of the skin microbiome as well as cutaneous immune response in HSCT recipients with changes associated with cutaneous aGVHD.

  • Lignin Preservation and Microbial Carbohydrate Metabolism in Permafrost Soils

    Dao TT, Mikutta R, Sauheitl L, Gentsch N, Shibistova O, Wild B, Schnecker J, Barta J, Capek P, Gittel A, Lashchinskiy N, Urich T, Santruckova H, Richter A, Guggenberger G
    2022 - JGR Biogeosciences, 127: Article e2020JG00618

    Abstract: 

    Permafrost-affected soils in the northern circumpolar region store more than 1,000 Pg soil organic carbon (OC), and are strongly vulnerable to climatic warming. However, the extent to which changing soil environmental conditions with permafrost thaw affects different compounds of soil organic matter (OM) is poorly understood. Here, we assessed the fate of lignin and non-cellulosic carbohydrates in density fractionated soils (light fraction, LF vs. heavy fraction, HF) from three permafrost regions with decreasing continentality, expanding from east to west of northern Siberia (Cherskiy, Logata, Tazovskiy, respectively). In soils at the Tazovskiy site with thicker active layers, the LF showed smaller OC-normalized contents of lignin-derived phenols and plant-derived sugars and a decrease of these compounds with soil depth, while a constant or even increasing trend was observed in soils with shallower active layers (Cherskiy and Logata). Also in the HF, soils at the Tazovskiy site had smaller contents of OC-normalized lignin-derived phenols and plant-derived sugars along with more pronounced indicators of oxidative lignin decomposition and production of microbial-derived sugars. Active layer deepening, thus, likely favors the decomposition of lignin and plant-derived sugars, that is, lignocelluloses, by increasing water drainage and aeration. Our study suggests that climate-induced degradation of permafrost soils may promote carbon losses from lignin and associated polysaccharides by abolishing context-specific preservation mechanisms. However, relations of OC-based lignin-derived phenols and sugars in the HF with mineralogical properties suggest that future OM transformation and carbon losses will be modulated in addition by reactive soil minerals.

  • From diversity to complexity: Microbial networks in soils

    Guseva K, Darcy S, Simon E, Alteio LV, Montesinos-Navarro A, Kaiser C
    2022 - Soil Biology and Biochemistry, 169: Article 108604

    Abstract: 

    Network analysis has been used for many years in ecological research to analyze organismal associations, for example in food webs, plant-plant or plant-animal interactions. Although network analysis is widely applied in microbial ecology, only recently has it entered the realms of soil microbial ecology, shown by a rapid rise in studies applying co-occurrence analysis to soil microbial communities. While this application offers great potential for deeper insights into the ecological structure of soil microbial ecosystems, it also brings new challenges related to the specific characteristics of soil datasets and the type of ecological questions that can be addressed. In this Perspectives Paper we assess the challenges of applying network analysis to soil microbial ecology due to the small-scale heterogeneity of the soil environment and the nature of soil microbial datasets. We review the different approaches of network construction that are commonly applied to soil microbial datasets and discuss their features and limitations. Using a test dataset of microbial communities from two depths of a forest soil, we demonstrate how different experimental designs and network constructing algorithms affect the structure of the resulting networks, and how this in turn may influence ecological conclusions. We will also reveal how assumptions of the construction method, methods of preparing the dataset, and definitions of thresholds affect the network structure. Finally, we discuss the particular questions in soil microbial ecology that can be approached by analyzing and interpreting specific network properties. Targeting these network properties in a meaningful way will allow applying this technique not in merely descriptive, but in hypothesis-driven research. Analysing microbial networks in soils opens a window to a better understanding of the complexity of microbial communities. However, this approach is unfortunately often used to draw conclusions which are far beyond the scientific evidence it can provide, which has damaged its reputation for soil microbial analysis. In this Perspectives Paper, we would like to sharpen the view for the real potential of microbial co-occurrence analysis in soils, and at the same time raise awareness regarding its limitations and the many ways how it can be misused or misinterpreted.

  • Lowland plant arrival in alpine ecosystems facilitates a decrease in soil carbon content under experimental climate warming

    Walker TWN, Gavazov K, Guillaume T, Lambert T, Mariotte P, Routh D, Signarbieux C, Block S, Münkemüller T, Nomoto H, Crowther TW, Richter A, Buttler A, Alexander JM
    2022 - Elife, 11: Article e78555

    Abstract: 

    Climate warming is releasing carbon from soils around the world, constituting a positive climate feedback. Warming is also causing species to expand their ranges into new ecosystems. Yet, in most ecosystems, whether range expanding species will amplify or buffer expected soil carbon loss is unknown. Here, we used two whole-community transplant experiments and a follow-up glasshouse experiment to determine whether the establishment of herbaceous lowland plants in alpine ecosystems influences soil carbon content under warming. We found that warming (transplantation to low elevation) led to a negligible decrease in alpine soil carbon content, but its effects became significant and 52% ± 31% (mean ± 95% confidence intervals) larger after lowland plants were introduced at low density into the ecosystem. We present evidence that decreases in soil carbon content likely occurred via lowland plants increasing rates of root exudation, soil microbial respiration, and CO2 release under warming. Our findings suggest that warming-induced range expansions of herbaceous plants have the potential to alter climate feedbacks from this system, and that plant range expansions among herbaceous communities may be an overlooked mediator of warming effects on carbon dynamics.

  • Effect of light on the metabolism of the foraminifera Cribroelphidium selseyense lacking photosymbionts and kleptoplasts

    Lintner M, Schagerl M, Lintner B, Wanek W, Keul N, Heinz P
    2022 - Journal of Photochemistry and Photobiology, 11: Article 100133

    Abstract: 

    Foraminifera are essential contributors to the marine carbon and nitrogen cycle. A small group of foraminifera hosts symbiotic microalgae and kleptoplasts and irradiance is a key variable influencing their metabolism. However, the majority of foraminifera is fully heterotrophic, and whether irradiance influences food ingestion patterns has remained an open question. We studied the food uptake of fully heterotrophic Cribroelphidium selseyense specimens exposed to varying light-dark cycles. Specimens obtained from the Baltic Sea were fed with lyophilised, isotopically labelled diatoms from the species of Phaeodactylum triconutum, to estimate the rate of food ingestion. We exposed the specimens to different light-dark cycles (0:24, 8:16, 16:8, 24:0 = light: dark) and irradiance intensities (0, 50, 100 and 200 µmol photons m−2 s−1) in this experiment. Differences in light-dark regime did not affect the food uptake rates of C. selseyense. Irradiance intensity, however, strongly affected food uptake, increasing with incubation time from day 1 to day 15. In parallel, the food uptake decreased with higher irradiance intensity. Therefore, we can conclude irradiance intensity and not the light-dark cycle affected food uptake of fully heterotrophic C. selseyense, leaving the mechanisms of how light intensity regulates food intake being unresolved yet.

  • Harnessing belowground processes for sustainable intensification of agricultural systems

    Oburger E, Schmidt H, Staudinger C
    2022 - Plant and Soil, 478: 177-209

    Abstract: 

    Increasing food demand coupled with climate change pose a great challenge to agricultural systems. In this review we summarize recent advances in our knowledge of how plants, together with their associated microbiota, shape rhizosphere processes. We address (molecular) mechanisms operating at the plant–microbe-soil interface and aim to link this knowledge with actual and potential avenues for intensifying agricultural systems, while at the same time reducing irrigation water, fertilizer inputs and pesticide use. Combining in-depth knowledge about above and belowground plant traits will not only significantly advance our mechanistic understanding of involved processes but also allow for more informed decisions regarding agricultural practices and plant breeding. Including belowground plant-soil-microbe interactions in our breeding efforts will help to select crops resilient to abiotic and biotic environmental stresses and ultimately enable us to produce sufficient food in a more sustainable agriculture in the upcoming decades.

  • Both abundant and rare fungi colonizing Fagus sylvatica ectomycorrhizal root-tips shape associated bacterial communities

    Dietrich M, Montesinos-Navarro A, Gabriel R, Strasser F, Meier DV, Mayerhofer W, Gorka S, Wiesenbauer J, Martin V, Weidinger M, Richter A, Kaiser C, Woebken D
    2022 - Commun Biol, 5: 1261

    Abstract: 

    Ectomycorrhizal fungi live in close association with their host plants and form complex interactions with bacterial/archaeal communities in soil. We investigated whether abundant or rare ectomycorrhizal fungi on root-tips of young beech trees (Fagus sylvatica) shape bacterial/archaeal communities. We sequenced 16S rRNA genes and fungal internal transcribed spacer regions of individual root-tips and used ecological networks to detect the tendency of certain assemblies of fungal and bacterial/archaeal taxa to inhabit the same root-tip (i.e. modularity). Individual ectomycorrhizal root-tips hosted distinct fungal communities associated with unique bacterial/archaeal communities. The structure of the fungal-bacterial/archaeal association was determined by both, dominant and rare fungi. Integrating our data in a conceptual framework suggests that the effect of rare fungi on the bacterial/archaeal communities of ectomycorrhizal root-tips contributes to assemblages of bacteria/archaea on root-tips. This highlights the potential impact of complex fine-scale interactions between root-tip associated fungi and other soil microorganisms for the ectomycorrhizal symbiosis.

  • Decay of similarity across tropical forest communities: integrating spatial distance with soil nutrients

    Peguero G, Ferrín M, Sardans J, Verbruggen E, Ramírez-Rojas I, Van Langenhove L, Verryckt LT, Murienne J, Iribar A, Zinger L, Grau O, Orivel J, Stahl C, Courtois EA, Asensio D, Gargallo-Garriga A, Llusià J, Margalef O, Ogaya R, Richter A, Janssens IA, Schiestl RH
    2022 - Ecology, 103: Article e03599

    Abstract: 

    Understanding the mechanisms that drive the change of biotic assemblages over space and time is the main quest of community ecology. Assessing the relative importance of dispersal and environmental species selection in a range of organismic sizes and motilities has been a fruitful strategy. A consensus for whether spatial and environmental distances operate similarly across spatial scales and taxa, however, has yet to emerge. We used censuses of four major groups of organisms (soil bacteria, fungi, ground insects, and trees) at two observation scales (1-m2 sampling point vs. 2,500-m2 plots) in a topographically standardized sampling design replicated in two tropical rainforests with contrasting relationships between spatial distance and nutrient availability. We modeled the decay of assemblage similarity for each taxon set and site to assess the relative contributions of spatial distance and nutrient availability distance. Then, we evaluated the potentially structuring effect of tree composition over all other taxa. The similarity of nutrient content in the litter and topsoil had a stronger and more consistent selective effect than did dispersal limitation, particularly for bacteria, fungi, and trees at the plot level. Ground insects, the only group assessed with the capacity of active dispersal, had the highest species turnover and the flattest nonsignificant distance−decay relationship, suggesting that neither dispersal limitation nor nutrient availability were fundamental drivers of their community assembly at this scale of analysis. Only the fungal communities at one of our study sites were clearly coordinated with tree composition. The spatial distance at the smallest scale was more important than nutrient selection for the bacteria, fungi, and insects. The lower initial similarity and the moderate variation in composition identified by these distance-decay models, however, suggested that the effects of stochastic sampling were important at this smaller spatial scale. Our results highlight the importance of nutrients as one of the main environmental drivers of rainforest communities irrespective of organismic or propagule size and how the overriding effect of the analytical scale influences the interpretation, leading to the perception of greater importance of dispersal limitation and ecological drift over selection associated with environmental niches at decreasing observation scales.

  • Growth of soil microbes is not limited by the availability of nitrogen and phosphorus in a Mediterranean oak-savanna

    Morris KA, Richter A, Migliavacca M, Schrumpf M
    2022 - Soil Biology and Biochemistry, 169: Article 108680

    Abstract: 

    The environmental conditions under which the availability of inorganic nutrients such as nitrogen (N) and phosphorus (P) influence soil microbial growth are poorly understood, especially with regards to how fertilization changes specific aspects of microbial growth such as carbon-use efficiency (CUE). Microbial CUE is the fraction of C converted into biomass out of all C taken in and plays a critical role in global C budgets. Using the 18O labeled water method we tested short vs. long-term effects of N and/or P fertilization on microbial growth, CUE, and C, N, and P-acquiring enzyme activities in two soils from an oak-savanna, which differ in their soil organic matter (SOM) content. We hypothesized that soils with more SOM (from under tree canopies) would have higher microbial growth rates than soils with less SOM (from open grassland), and that microbial growth and CUE would increase with fertilization. We further hypothesized that these increases would be associated with a decrease in enzyme activity and a shift towards older SOM substrates in the short-term, in contrast to substrates from recently fixed C resulting from increased plant productivity in the long-term. We found that nutrient additions did not affect microbial growth or CUE in the relatively high SOM habitat on either time scale. In contrast, the low SOM habitat had lower growth and CUE when single nutrients were added, with significantly reduced growth when P alone was added, but was unchanged when N and P were added together. Our results show that short-term, stoichiometric imbalances can reduce microbial growth and that microbial growth at this site is limited not by nutrients but by the amount of C available to soil microbes.

  • Dissolved organic matter characterization in soils and streams in a small coastal low-Arctic catchment

    Speetjens NJ, Tanski G, Martin V, Wagner J, Richter A, Hugelius G, Boucher C, Lodi R, Knoblauch C, Koch BP, Wünsch U, Lantuit H, Vonk JE
    2022 - Biogeosciences, 19: 3073-3097

    Abstract: 

    Ongoing climate warming in the western Canadian Arctic is leading to thawing of permafrost soils and subsequent mobilization of its organic matter pool. Part of this mobilized terrestrial organic matter enters the aquatic system as dissolved organic matter (DOM) and is laterally transported from land to sea. Mobilized organic matter is an important source of nutrients for ecosystems, as it is available for microbial breakdown, and thus a source of greenhouse gases. We are beginning to understand spatial controls on the release of DOM as well as the quantities and fate of this material in large Arctic rivers. Yet, these processes remain systematically understudied in small, high-Arctic watersheds, despite the fact that these watersheds experience the strongest warming rates in comparison. Here, we sampled soil (active layer and permafrost) and water (porewater and stream water) from a small ice wedge polygon (IWP) catchment along the Yukon coast, Canada, during the summer of 2018. We assessed the organic carbon (OC) quantity (using dissolved (DOC) and particulate OC (POC) concentrations and soil OC content), quality (δ13C DOC, optical properties and source apportionment) and bioavailability (incubations; optical indices such as slope ratio, Sr; and humification index, HIX) along with stream water properties (temperature, T; pH; electrical conductivity, EC; and water isotopes). We classify and compare different landscape units and their soil horizons that differ in microtopography and hydrological connectivity, giving rise to differences in drainage capacity. Our results show that porewater DOC concentrations and yield reflect drainage patterns and waterlogged conditions in the watershed. DOC yield (in mg DOC g−1 soil OC) generally increases with depth but shows a large variability near the transition zone (around the permafrost table). Active-layer porewater DOC generally is more labile than permafrost DOC, due to various reasons (heterogeneity, presence of a paleo-active-layer and sampling strategies). Despite these differences, the very long transport times of porewater DOC indicate that substantial processing occurs in soils prior to release into streams. Within the stream, DOC strongly dominates over POC, illustrated by  ratios around 50, yet storm events decrease that ratio to around 5. Source apportionment of stream DOC suggests a contribution of around 50 % from permafrost/deep-active-layer OC, which contrasts with patterns observed in large Arctic rivers (12 ± 8 %; Wild et al., 2019). Our 10 d monitoring period demonstrated temporal DOC patterns on multiple scales (i.e., diurnal patterns, storm events and longer-term trends), underlining the need for high-resolution long-term monitoring. First estimates of Black Creek annual DOC (8.2 ± 6.4 t DOC yr−1) and POC (0.21 ± 0.20 t yr−1) export allowed us to make a rough upscaling towards the entire Yukon Coastal Plain (34.51 ± 2.7 kt DOC yr−1 and 8.93 ± 8.5 kt POC yr−1). Rising Arctic temperatures, increases in runoff, soil organic matter (OM) leaching, permafrost thawing and primary production are likely to increase the net lateral OC flux. Consequently, altered lateral fluxes may have strong impacts on Arctic aquatic ecosystems and Arctic carbon cycling.

  • Single-cell stable isotope probing in microbial ecology

    Alcolombri U, Pioli R, Stocker R, Berry D
    2022 - ISME Commun, 2: 55

    Abstract: 

    Environmental and host-associated microbiomes are typically diverse assemblages of organisms performing myriad activities and engaging in a network of interactions that play out in spatially structured contexts. As the sum of these activities and interactions give rise to overall microbiome function, with important consequences for environmental processes and human health, elucidating specific microbial activities within complex communities is a pressing challenge. Single-cell stable isotope probing (SC-SIP) encompasses multiple techniques that typically utilize Raman microspectroscopy or nanoscale secondary ion mass spectrometry (NanoSIMS) to enable spatially resolved tracking of isotope tracers in cells, cellular components, and metabolites. SC-SIP techniques are uniquely suited for illuminating single-cell activities in microbial communities and for testing hypotheses about cellular functions generated for example from meta-omics datasets. Here, we illustrate the insights enabled by SC-SIP techniques by reviewing selected applications in microbiology and offer a perspective on their potential for future research.

  • Sorption and Mobility of Charged Organic Compounds: How to Confront and Overcome Limitations in Their Assessment

    Gabriel Sigmund, Hans Peter H. Arp, Benedikt M. Aumeier, Thomas D. Bucheli, Benny Chefetz, Wei Chen, Steven T. J. Droge, Satoshi Endo, Beate I. Escher, Sarah E. Hale, Thilo Hofmann, Joseph Pignatello, Thorsten Reemtsma, Torsten C. Schmidt, Carina D. Schönsee, Martin Scheringer
    2022 - Environ. Sci. Technol., 56: 4702-2710

    Abstract: 

    Permanently charged and ionizable organic compounds (IOC) are a large and diverse group of compounds belonging to many contaminant classes, including pharmaceuticals, pesticides, industrial chemicals, and natural toxins. Sorption and mobility of IOCs are distinctively different from those of neutral compounds. Due to electrostatic interactions with natural sorbents, existing concepts for describing neutral organic contaminant sorption, and by extension mobility, are inadequate for IOC. Predictive models developed for neutral compounds are based on octanol–water partitioning of compounds (Kow) and organic-carbon content of soil/sediment, which is used to normalize sorption measurements (KOC). We revisit those concepts and their translation to IOC (Dow and DOC) and discuss compound and soil properties determining sorption of IOC under water saturated conditions. Highlighting possible complementary and/or alternative approaches to better assess IOC mobility, we discuss implications on their regulation and risk assessment. The development of better models for IOC mobility needs consistent and reliable sorption measurements at well-defined chemical conditions in natural porewater, better IOC-, as well as sorbent characterization. Such models should be complemented by monitoring data from the natural environment. The state of knowledge presented here may guide urgently needed future investigations in this field for researchers, engineers, and regulators.

  • Tools for adapting to a complex habitat: G-protein coupled receptors in Trichoderma

    Schmoll M, Hinterdobler W
    2022 - Progress in Molecular Biology and Translational Science, 1: 65-97

    Abstract: 

    Sensing the environment and interpretation of the received signals are crucial competences of living organisms in order to properly adapt to their habitat, succeed in competition and to reproduce. G-protein coupled receptors (GPCRs) are members of a large family of sensors for extracellular signals and represent the starting point of complex signaling cascades regulating a plethora of intracellular physiological processes and output pathways in fungi. In Trichoderma spp. current research involves a wide range of topics from enzyme production, light response and secondary metabolism to sexual and asexual development as well as biocontrol, all of which require delicate balancing of resources in response to the environmental challenges or biotechnological needs at hand, which are crucially impacted by the surroundings of the fungi and their intercellular signaling cascades triggering a precisely tailored response. In this review we summarize recent findings on sensing by GPCRs in Trichoderma, including the function of pheromone receptors, glucose sensing by CSG1 and CSG2, regulation of secondary metabolism by GPR8 and impacts on mycoparasitism by GPR1. Additionally, we provide an overview on structural determinants, posttranslational modifications and interactions for regulation, activation and signal termination of GPCRs in order to inspire future in depth analyses of their function and to understand previous regulatory outcomes of natural and biotechnological processes modulated or enabled by GPCRs.

  • Stormwater management in urban areas using dry gallery infiltration systems

    Miguel Angel Marazuela, Alejandro García-Gil, Juan C. Santamarta, Samanta Gasco-Cavero, Noelia Cruz-Pérez, Thilo Hofmann
    2022 - Science of The Total Environment, 823: 153705

    Abstract: 

    The increase in the frequency of extreme precipitation events due to climate change, together with the continuous development of cities and surface sealing that hinder water infiltration into the subsoil, is accelerating the search for new facilities to manage stormwater. The Canary Islands (Spain) are taking advantage of the knowledge acquired in the construction of water mines to exploit a novel stormwater management facility, which we have defined as a dry gallery. Dry galleries are constituted by a vertical well connected to a horizontal gallery dug into highly permeable volcanic layers of the vadose zone, from where infiltration takes place. However, the lack of scientific knowledge about these facilities prevents them from being properly dimensioned and managed. In this work, we simulate for the first time the infiltration process and the wetting front propagation from dry galleries based on a 3D unsaturated flow model and provide some recommendations for the installation and sizing of these facilities. The fastest advance of the wetting front takes place during the earliest times of infiltration (<2 h), with plausible propagation velocities and infiltration rates higher than 1000 m∙d−1 and 2 m3∙s−1. As time progresses, the propagation velocity and infiltration rate decrease as a consequence of the hydraulic gradient attenuation between the gallery and the aquifer. Therefore, stormwater infiltration is a highly transient process in which a sizing underestimation of 100% may be committed if unsaturated conditions or geological configuration are neglected.

  • Interleukin-11 drives human and mouse alcohol-related liver disease

    Effenberger M, Widjaja AA, Grabherr F, Schaefer B, Grander C, Mayr L, Schwaerzler J, Enrich B, Moser P, Fink J, Pedrini A, Jaschke N, Kirchmair A, Pfister A, Hausmann B, Bale R, Putzer D, Zoller H, Schafer S, Pjevac P, Trajanoski Z, Oberhuber G, Adolph T Cook S, Tilg H
    2022 - BMJ, in press

    Abstract: 

    Objective Alcoholic hepatitis (AH) reflects acute exacerbation of alcoholic liver disease (ALD) and is a growing healthcare burden worldwide. Interleukin-11 (IL-11) is a profibrotic, proinflammatory cytokine with increasingly recognised toxicities in parenchymal and epithelial cells. We explored IL-11 serum levels and their prognostic value in patients suffering from AH and cirrhosis of various aetiology and experimental ALD.
    Design IL-11 serum concentration and tissue expression was determined in a cohort comprising 50 patients with AH, 110 patients with cirrhosis and 19 healthy volunteers. Findings were replicated in an independent patient cohort (n=186). Primary human hepatocytes exposed to ethanol were studied in vitro. Ethanol-fed wildtype mice were treated with a neutralising murine IL-11 receptor-antibody (anti-IL11RA) and examined for severity signs and markers of ALD.
    Results IL-11 serum concentration and hepatic expression increased with severity of liver disease, mostly pronounced in AH. In a multivariate Cox-regression, a serum level above 6.4 pg/mL was a model of end-stage liver disease independent risk factor for transplant-free survival in patients with compensated and decompensated cirrhosis. In mice, severity of alcohol-induced liver inflammation correlated with enhanced hepatic IL-11 and IL11RA expression. In vitro and in vivo, anti-IL11RA reduced pathogenic signalling pathways (extracellular signal-regulated kinases, c-Jun N-terminal kinase, NADPH oxidase 4) and protected hepatocytes and murine livers from ethanol-induced inflammation and injury.
    Conclusion Pathogenic IL-11 signalling in hepatocytes plays a crucial role in the pathogenesis of ALD and could serve as an independent prognostic factor for transplant-free survival. Blocking IL-11 signalling might be a therapeutic option in human ALD, particularly AH.
  • Elucidating the role of the gut microbiota in the physiological effects of dietary fiber

    Deehan EC, Zhang Z, Riva A, Armet AM, Perez-Muñoz ME, Nguyen NK, Krysa JA, Seethaler, B Zhao Y-Y, Cole J, Li F, Hausmann B, Spittler A, Nazare J-A, Delzenne NM, Curtis JM, Wismer WV, Proctor SD, Bakal JA, Bischoff SC, Knights D, Field CJ, Berry D, Prado CM, Walter J
    2022 - Microbiome, in press

    Abstract: 

    Dietary fiber is an integral part of a healthy diet, but questions remain about the mechanisms that underlie effects and the causal contributions of the gut microbiota. Here, we performed a 6-week exploratory trial in adults with excess weight (BMI: 25–35 kg/m2) to compare the effects of a high-dose (females: 25 g/day; males: 35 g/day) supplement of fermentable corn bran arabinoxylan (AX; n = 15) with that of microbiota-non-accessible microcrystalline cellulose (MCC; n = 16). Obesity-related surrogate endpoints and biomarkers of host-microbiome interactions implicated in the pathophysiology of obesity (trimethylamine N-oxide, gut hormones, cytokines, and measures of intestinal barrier integrity) were assessed. We then determined whether clinical outcomes could be predicted by fecal microbiota features or mechanistic biomarkers.

  • Specific localization and quantification of the Oligo-Mouse-Microbiota (OMM12) by fluorescence in situ hybridization (FISH)

    Brugiroux S, Berry D, Ring D, Barnich N, Daims H, Stecher B
    2022 - Current Protocols, 2: e548

    Abstract: 

    The oligo-mouse-microbiota (OMM12) is a widely used syncom that colonizes gnotobiotic mice in a stable manner. It provides several fundamental functions to its murine host, including colonization resistance against enteric pathogens. Here, we designed and validated specific fluorescence in situ hybridization (FISH) probes to detect and quantify OMM12 strains on intestinal tissue cross sections. 16S rRNA‒specific probes were designed, and specificity was validated on fixed pure cultures. A hybridization protocol was optimized for sensitive detection of the individual bacterial cells in cryosections. Using this method, we showed that the intestinal mucosal niche of Akkermansia muciniphila can be influenced by global gut microbial community context.

  • About “Controls” in Pollution-Ecology Experiments in the Anthropocene

    Matthias C. Rillig, Shin Woong Kim, Andreas Schäffer, Gabriel Sigmund, Ksenia J. Groh, Zhanyun Wang
    2022 - Environ. Sci. Technol., 56: 11928-11930

    Abstract: 

    Controls are an essential component of experimental design, serving the purpose of accounting for all aspects of an experimental treatment except for the factor(s) under investigation in any given study. Especially in pollution ecology, proper controls are essential for attributing effects, describing dose–response relationships, and assessing risks. We here highlight that the interpretation of and communication about controls have become more complex, given the ubiquitous presence in the environment of a large number of anthropogenic factors, in part simultaneously affecting ecosystems. We therefore recommend a more conscious use of language when discussing effects in environmental matrices such as soil, water, or air.

  • Towards Standardization for Determining Dissolution Kinetics of Nanomaterials in Natural Aquatic Environments: Continuous Flow Dissolution of Ag Nanoparticles

    Lucie Stetten, Aiga Mackevica, Nathalie Tepe, Thilo Hofmann, Frank von der Kammer
    2022 - Nanomaterials, 12: 519

    Abstract: 

    The dissolution of metal-based engineered nanomaterials (ENMs) in aquatic environments is an important mechanism governing the release of toxic dissolved metals. For the registration of ENMs at regulatory bodies such as REACH, their dissolution behavior must therefore be assessed using standardized experimental approaches. To date, there are no standardized procedures for dissolution testing of ENMs in environmentally relevant aquatic media, and the Organisation for Economic Co-operation and Development (OECD) strongly encourages their development into test guidelines. According to a survey of surface water hydrochemistry, we propose to use media with low concentrations of Ca2+ and Mg2+ for a better simulation of the ionic background of surface waters, at pH values representing acidic (5 < pH < 6) and near-neutral/alkaline (7 < pH < 8) waters. We evaluated a continuous flow setup adapted to expose small amounts of ENMs to aqueous media, to mimic ENMs in surface waters. For this purpose, silver nanoparticles (Ag NPs) were used as model for soluble metal-bearing ENMs. Ag NPs were deposited onto a 10 kg.mol−1 membrane through the injection of 500 µL of a 5 mg.L−1 or 20 mg.L−1 Ag NP dispersion, in order to expose only a few micrograms of Ag NPs to the aqueous media. The dissolution rate of Ag NPs in 10 mM NaNO3 was more than two times higher for ~2 µg compared with ~8 µg of Ag NPs deposited onto the membrane, emphasizing the importance of evaluating the dissolution of ENMs at low concentrations in order to keep a realistic scenario. Dissolution rates of Ag NPs in artificial waters (2 mM Ca(NO3)2, 0.5 mM MgSO4, 0–5 mM NaHCO3) were also determined, proving the feasibility of the test using environmentally relevant media. In view of the current lack of harmonized methods, this work encourages the standardization of continuous flow dissolution methods toward OECD guidelines focused on natural aquatic environments, for systematic comparisons of nanomaterials and adapted risk assessments.

  • Iron Nitride Nanoparticles for Enhanced Reductive Dechlorination of Trichloroethylene

    Miroslav Brumovský, Jana Oborná, Malfatti SE, Ondřej Malina, Josef Kašlík, Daniel Tunega, Miroslav Kolos, Thilo Hofmann, František Karlický, Jan Filip
    2022 - Environmental Science & Technology, 56: 4425-4436

    Abstract: 

    Nitriding has been used for decades to improve the corrosion resistance of iron and steel materials. Moreover, iron nitrides (FexN) have been shown to give an outstanding catalytic performance in a wide range of applications. We demonstrate that nitriding also substantially enhances the reactivity of zerovalent iron nanoparticles (nZVI) used for groundwater remediation, alongside reducing particle corrosion. Two different types of FexN nanoparticles were synthesized by passing gaseous NH3/N2 mixtures over pristine nZVI at elevated temperatures. The resulting particles were composed mostly of face-centered cubic (γ′-Fe4N) and hexagonal close-packed (ε-Fe2–3N) arrangements. Nitriding was found to increase the particles’ water contact angle and surface availability of iron in reduced forms. The two types of FexN nanoparticles showed a 20- and 5-fold increase in the trichloroethylene (TCE) dechlorination rate, compared to pristine nZVI, and about a 3-fold reduction in the hydrogen evolution rate. This was related to a low energy barrier of 27.0 kJ mol–1 for the first dechlorination step of TCE on the γ′-Fe4N(001) surface, as revealed by density functional theory calculations with an implicit solvation model. TCE dechlorination experiments with aged particles showed that the γ′-Fe4N nanoparticles retained high reactivity even after three months of aging. This combined theoretical-experimental study shows that FexN nanoparticles represent a new and potentially important tool for TCE dechlorination.

  • Environmental Biodegradation of Water-Soluble Polymers: Key Considerations and Ways Forward

    Michael Zumstein, Glauco Battagliarin, Andreas Kuenkel, Michael Sander
    2022 - Accounts of Chemical Research, 55: 2163–2167

    Abstract: 

    Water-soluble polymers (WSPs) have unique properties that are valuable in diverse applications ranging from home and personal care products to agricultural formulations. For applications that result in the release of WSPs into natural environments or engineered systems, such as agricultural soils and wastewater streams, biodegradable as opposed to nonbiodegradable WSPs have the advantage of breaking down and, thereby, eliminating the risk of persistence and accumulation. In this Commentary, we emphasize central steps in WSP biodegradation, discuss how these steps depend on both WSP properties and characteristics of the receiving environment, and highlight critical requirements for testing WSP biodegradability.

  • Impaired mucosal homeostasis in short-term fiber deprivation is due to reduced mucus production rather than overgrowth of mucus-degrading bacteria

    Overbeeke A, Lang M, Hausmann B, Watzka M, Nikolov G, Schwarz J, Kohl G, De Paepe K, Eislmayr K, Decker T, Richter A, Berry D
    2022 - Nutrients, 14: Article 3802

    Abstract: 

    The gut mucosal environment is key in host health; protecting against pathogens and providing a niche for beneficial bacteria, thereby facilitating a mutualistic balance between host and microbiome. Lack of dietary fiber results in erosion of the mucosal layer, suggested to be a result of increased mucus-degrading gut bacteria. This study aimed to use quantitative analyses to investigate the diet-induced imbalance of mucosal homeostasis. Seven days of fiber-deficiency affected intestinal anatomy and physiology, seen by reduced intestinal length and loss of the colonic crypt-structure. Moreover, the mucus layer was diminished, muc2 expression decreased, and impaired mucus secretion was detected by stable isotope probing. Quantitative microbiome profiling of the gut microbiota showed a diet-induced reduction in bacterial load and decreased diversity across the intestinal tract, including taxa with fiber-degrading and butyrate-producing capabilities. Most importantly, there was little change in the absolute abundance of known mucus-degrading bacteria, although, due to the general loss of taxa, relative abundance would erroneously indicate an increase in mucus degraders. These findings underscore the importance of using quantitative methods in microbiome research, suggesting erosion of the mucus layer during fiber deprivation is due to diminished mucus production rather than overgrowth of mucus degraders. View Full-Text

  • Secondary succession and parent material drive soil bacterial community composition in terraced abandoned olive groves from a Mediterranean hyper-humid mountainous area

    Company J, Valiente N, Forstesa J, García-Comendador J, Lucas-Borja ME, ortega R, Miralles I, Estrany J
    2022 - Agriculture Ecosystems & Environment, 332: Article 107932

    Abstract: 

    Mediterranean humid mountains are ecological hotspots with high water availability that may accelerate their recovery after farmland abandonment, a widespread phenomenon in marginal areas of the European Mediterranean Region. This land use change led to secondary succession processes triggering changes in soil properties and soil microorganisms. This is the first study in assessing the environmental influence of both ecological succession and parent material over soil properties and soil bacterial communities in these habitats. To examine the effects of secondary succession and elucidate the role of parent material in soil bacterial communities, six soil plots were sampled from the combination of abandoned and rainfed olive groves, terraced or non-terraced, and over four parent materials in Lluc Valley, a Mediterranean hyper-humid mountainous area on the island of Mallorca, Spain. Soil bacterial diversity and taxonomic composition at phylum and family level in each field were analyzed by rRNA 16 S amplicon sequencing. In addition, a series of soil physicochemical and microbiological properties, together with enzyme activities were assessed. Results showed that secondary succession and parent material significantly affected soil physicochemical and microbiological properties, soil enzyme activities and soil bacterial communities’ diversity and taxonomic composition. Secondary succession following farmland abandonment triggered higher total organic carbon (TOC), microbial biomass carbon (Cmic), basal soil respiration (REB), alkaline phosphatase activity (Php) and dehydrogenase activity (DHA), thus enhancing soil quality. In contrast, parent material significantly shaped pH, specific surface area (SSA), TOC, CmicREB and soil enzyme activities, playing a key role in land use effects modulation. According to the distance-based redundancy analysis (db-RDA), SSA, TOC, REB, Cmicurease activity (Ur) and Php were the soil properties that contributed to significant changes in bacterial communities’ composition at the family level. This study evidenced that farmland abandonment led to improve soil quality in Mediterranean humid mountains, with positive feedbacks provided by parent material.

  • Demystifying mercury geochemistry in contaminated soil–groundwater systems with complementary mercury stable isotope, concentration, and speciation analyses

    David S. McLagan, Lorenz Schwab, Jan G. Wiederhold, Lu Chen, Jan Pietrucha, Stephan M. Kraemer, Harald Biester
    2022 - Environmental Science: Processes & Impacts, 9: 1406-1429

    Abstract: 

    Interpretation of mercury (Hg) geochemistry in environmental systems remains a challenge. This is largely associated with the inability to identify specific Hg transformation processes and species using established analytical methods in Hg geochemistry (total Hg and Hg speciation). In this study, we demonstrate the improved Hg geochemical interpretation, particularly related to process tracing, that can be achieved when Hg stable isotope analyses are complemented by a suite of more established methods and applied to both solid- (soil) and liquid-phases (groundwater) across two Hg2+-chloride (HgCl2) contaminated sites with distinct geological and physicochemical properties. This novel approach allowed us to identify processes such as Hg2+ (i.e., HgCl2) sorption to the solid-phase, Hg2+ speciation changes associated with changes in groundwater level and redox conditions (particularly in the upper aquifer and capillary fringe), Hg2+ reduction to Hg0, and dark abiotic redox equilibration between Hg0 and Hg(II). Hg stable isotope analyses play a critical role in our ability to distinguish, or trace, these in situ processes. While we caution against the non-critical use of Hg isotope data for source tracing in environmental systems, due to potentially variable source signatures and overprinting by transformation processes, our study demonstrates the benefits of combining multiple analytical approaches, including Hg isotope ratios as a process tracer, to obtain an improved picture of the enigmatic geochemical behavior and fate of Hg at contaminated legacy sites.

  • Isotopically characterised N2O reference materials for use as community standards

    Mohn J, Biasi C, Bodé S, Boeckx P, Brewer PJ, Eggleston S, Geilmann H, Guillevic M, Kaiser J, Kantnerová K, Moossen H, Muller J, Nakagawa M, Pearce R, von Rein I, Steger D, Toyoda S, Wanek W, Wexler SK, Yoshida N, Yu L
    2022 - Rapid Communications in Mass Spectrometry, 36: Article e9296

    Abstract: 

    Rationale

    Information on the isotopic composition of nitrous oxide (N2O) at natural abundance supports the identification of its source and sink processes. In recent years, a number of mass spectrometric and laser spectroscopic techniques have been developed and are increasingly used by the research community. Advances in this active research area, however, critically depend on the availability of suitable N2O isotope Reference Materials (RMs).

    Methods

    Within the project Metrology for Stable Isotope Reference Standards (SIRS), seven pure N2O isotope RMs have been developed and their 15N/14N, 18O/16O, 17O/16O ratios and 15N site preference (SP) have been analysed by specialised laboratories against isotope reference materials. A particular focus was on the 15N site-specific isotopic composition, as this measurand is both highly diagnostic for source appointment and challenging to analyse and link to existing scales.

    Results

    The established N2O isotope RMs offer a wide spread in delta (δ) values: δ15N: 0 to +104‰, δ18O: +39 to +155‰, and δ15NSP: −4 to +20‰. Conversion and uncertainty propagation of δ15N and δ18O to the Air-N2 and VSMOW scales, respectively, provides robust estimates for δ15N(N2O) and δ18O(N2O), with overall uncertainties of about 0.05‰ and 0.15‰, respectively. For δ15NSP, an offset of >1.5‰ compared with earlier calibration approaches was detected, which should be revisited in the future.

    Conclusions

    A set of seven N2O isotope RMs anchored to the international isotope-ratio scales was developed that will promote the implementation of the recommended two-point calibration approach. Particularly, the availability of δ17O data for N2O RMs is expected to improve data quality/correction algorithms with respect to δ15NSP and δ15N analysis by mass spectrometry. We anticipate that the N2O isotope RMs will enhance compatibility between laboratories and accelerate research progress in this emerging field.

  • Microbial community composition and hydrochemistry of underexplored geothermal waters in Croatia

    Mitrović M, Kostešić E, Marković T, Selak L, Hausmann B, Pjevac P, Orlić S
    2022 - Systematic and Applied Microbiology, in press

    Abstract: 

    In Croatia, a variety of geothermal springs with a wide temperature range and varied hydrochemical conditions exist, and they may harbor different niches for the distribution of microbial communities. In this study, 19 different sites, mainly located in central and eastern Croatia, were selected for primary characterization of spring hydrochemistry and microbial community composition. Using 16S rRNA gene amplicon sequencing, it was found that the bacterial communities that dominated most geothermal waters were related to Proteobacteria and Campylobacteria, while most archaeal sequences were related to Crenarchaeota. At the genus level, the prokaryotic community was highly site-specific and was often dominated by a single genus, including sites dominated by HydrogenophilusSulfuricurvumSulfurovumThiofaba and Nitrospira, while the most abundant archaeal genera were affiliated to the ammonia-oxidizing archaea, Candidatus Nitrosotenuis and Candidatus Nitrososphaera. Whereas the microbial communities were overall highly location-specific, temperature, pH, ammonia, nitrate, total nitrogen, sulfate and hydrogen sulfide, as well as dissolved organic and inorganic carbon, were the abiotic factors that significantly affected microbial community composition. Furthermore, an aquifer-type effect was observed in the community composition, but there was no pronounced seasonal variability for geothermal spring communities (i.e. the community structure was mainly stable during the three seasons sampled). These results surprisingly pointed to stable and geographically unique microbial communities that were adapted to different geothermal water environments throughout Croatia. Knowing which microbial communities are present in these extreme habitats is essential for future research. They will allow us to explore further the microbial metabolisms prevailing at these geothermal sites that have high potential for biotechnological uses, as well as the establishment of the links between microbial community structure and the physicochemical environment of geothermal waters.

  • How to Verify Non-Presence—The Challenge of Axenic Algae Cultivation

    Pokorny L, Hausmann B, Pjevac P, Schagerl M
    2022 - Cells, in press

    Abstract: 

    Many phycological applications require the growth and maintenance of pure algae cultures. In some research areas, such as biochemistry and physiology, axenic growth is essential to avoid misinterpretations caused by contaminants. Nonetheless, axenicity—defined as the state of only a single strain being present, free of any other organism—needs to be verified. We compare the available methods to assess axenicity. We first purified unialgal Limnospira fusiformis cultures with an established series of axenicity treatments, and by including two additional treatment steps. The presumable axenic cultures were then tested for their axenic state by applying conventional tests on LB (lysogeny broth) agar-plates, 16S rRNA gene amplicon sequencing, flow-cytometry and epifluorescence microscopy. Only the plate tests indicated axenic conditions. We found a linear relationship between total cell counts of contaminants achieved by flow cytometry and epifluorescence microscopy, with flow cytometry counts being consistently higher. In addition, 16S rRNA gene amplicon sequencing demonstrated its superiority by not only being an efficient tool for axenicity testing, but also for identification of persistent contaminants. Although classic plate tests are still commonly used to verify axenicity, we found the LB-agar-plate technique to be inappropriate. Cultivation-independent methods are highly recommended to test for axenic conditions. A combination of flow-cytometry and 16S rRNA gene amplicon sequencing complement each other and will yield the most reliable result.

  • Contrasting drivers of belowground nitrogen cycling in a montane grassland exposed to a multifactorial global change experiment with elevated CO, warming, and drought

    Maxwell TL, Canarini A, Bogdanovic I, Böckle T, Martin V, Noll L, Prommer J, Séneca J, Simon E, Piepho HP, Herndl M, Pötsch EM, Kaiser C, Richter A, Bahn M, Wanek W
    2022 - Global Change Biology, 28: 2425-2441

    Abstract: 

    Depolymerization of high-molecular weight organic nitrogen (N) represents the major bottleneck of soil N cycling and yet is poorly understood compared to the subsequent inorganic N processes. Given the importance of organic N cycling and the rise of global change, we investigated the responses of soil protein depolymerization and microbial amino acid consumption to increased temperature, elevated atmospheric CO2, and drought. The study was conducted in a global change facility in a managed montane grassland in Austria, where elevated CO2 (eCO2) and elevated temperature (eT) were stimulated for 4 years, and were combined with a drought event. Gross protein depolymerization and microbial amino acid consumption rates (alongside with gross organic N mineralization and nitrification) were measured using 15N isotope pool dilution techniques. Whereas eCO2 showed no individual effect, eT had distinct effects which were modulated by season, with a negative effect of eT on soil organic N process rates in spring, neutral effects in summer, and positive effects in fall. We attribute this to a combination of changes in substrate availability and seasonal temperature changes. Drought led to a doubling of organic N process rates, which returned to rates found under ambient conditions within 3 months after rewetting. Notably, we observed a shift in the control of soil protein depolymerization, from plant substrate controls under continuous environmental change drivers (eT and eCO2) to controls via microbial turnover and soil organic N availability under the pulse disturbance (drought). To the best of our knowledge, this is the first study which analyzed the individual versus combined effects of multiple global change factors and of seasonality on soil organic N processes and thereby strongly contributes to our understanding of terrestrial N cycling in a future world.

  • Stoichiometric regulation of priming effects and soil carbon balance by microbial life strategies

    Zhu Z, Fang Y, Liang Y, Li Y, Liu S, Li B, Gao W, Yuan H, Kuzyakov Y, Wu J, Richter A, Ge T
    2022 - Soil Biology and Biochemistry, 169: Article 108669

    Abstract: 

    Carbon and nutrient inputs are required to stimulate the formation and mineralization of soil organic carbon (SOC) through processes related to microbial growth and priming effects (PEs). PEs are thought to affect microbial life strategies, however, the mechanisms underlying their role in SOC formation and microbial dynamics remain largely unknown, particularly in paddy soils. Here, we examined the underlying strategies and response mechanisms of microorganisms in regulating PEs and C accumulation in flooded paddy soil. Levels and stoichiometric ratios of resources were evaluated over a 60-day incubation period. Low (equivalent to 50% soil microbial biomass C [MBC]) and high (500% MBC) doses of 13C-labeled glucose were added to the soil, along with mineral N, P, and S (NPS) fertilizers at five concentrations. Glucose mineralization increased linearly with NPS concentration under both low and high glucose inputs. However, glucose addition without nutrients induced the preferential microbial utilization of the readily available C, leading to negative PEs. Under high-glucose input, the intensity of negative PEs increased with increasing NPS addition (PE: from −460 to −710 mg C kg−1 soil). In contrast, under low-glucose inputs, the intensity of positive PEs increased with increasing NPS addition (PE: 60–100 mg C kg−1 soil). High-glucose input with NPS fertilization favored high-yield microbial strategists (Y-strategists), increasing glucose-derived SOC accumulation. This phenomenon was evidenced by the large quantities of 13C detected in microbial biomass and phospholipid fatty acids (PLFAs), increasing the soil net C balance (from 0.76 to 1.2 g C kg−1). In contrast, low levels of glucose and NPS fertilization shifted the microbial community composition toward dominance of resource-acquisition strategists (A-strategists), increasing SOC mineralization. This was evidenced by 13C incorporation into the PLFAs of gram-positive bacteria, increased activity of N- and P-hydrolases, and positive PEs for acquiring C and nutrients from soil organic matter. Consequently, the soil net C balance decreased from 0.31 to 0.01 g C kg−1 soil. In conclusion, high C input (i.e., 500% MBC), particularly alongside hig NPS addition, increases SOC content via negative priming and microbial-derived C accumulation due to the shift toward Y-strategist communities which efficiently utilize resources. This study highlights the importance of mineral fertilization management when incorporating organic supplements in paddy soils to stimulate microbial turnover and C sequestration.

  • Long-term soil warming alters fine root dynamics and morphology, and their ectomycorrhizal fungal community in a temperate forest soil

    Kwatcho Kengdo S, Peršoh D, Schindlbacher A, Heinzle J, Tian Y, Wanek W, Borken W
    2022 - Global Change Biology, in press

    Abstract: 

    Climate warming is predicted to affect temperate forests severely, but the response of fine roots, key to plant nutrition, water uptake, soil carbon, and nutrient cycling is unclear. Understanding how fine roots will respond to increasing temperature is a prerequisite for predicting the functioning of forests in a warmer climate. We studied the response of fine roots and their ectomycorrhizal (EcM) fungal and root-associated bacterial communities to soil warming by 4°C in a mixed spruce-beech forest in the Austrian Limestone Alps after 8 and 14 years of soil warming, respectively. Fine root biomass (FRB) and fine root production were 17% and 128% higher in the warmed plots, respectively, after 14 years. The increase in FRB (13%) was not significant after 8 years of treatment, whereas specific root length, specific root area, and root tip density were significantly higher in warmed plots at both sampling occasions. Soil warming did not affect EcM exploration types and diversity, but changed their community composition, with an increase in the relative abundance of Cenoccocum at 0–10 cm soil depth, a drought-stress-tolerant genus, and an increase in short- and long-distance exploration types like Sebacina and Boletus at 10–20 cm soil depth. Warming increased the root-associated bacterial diversity but did not affect their community composition. Soil warming did not affect nutrient concentrations of fine roots, though we found indications of limited soil phosphorus (P) and potassium (K) availability. Our findings suggest that, in the studied ecosystem, global warming could persistently increase soil carbon inputs due to accelerated fine root growth and turnover, and could simultaneously alter fine root morphology and EcM fungal community composition toward improved nutrient foraging.

  • Limnospira fusiformis harbors dinitrogenase reductase (nifH)-like genes, but does not show N2 fixation activity

    Schagerl M, Angel R, Donabaum U, Gschwandner AM, Woebken D
    2022 - Algal Research, 66: 102771

    Abstract: 

    East African soda lakes (EASLs), some of them world-renowned for their large flocks of flamingos, range amongst the most productive aquatic ecosystems worldwide. The non-heterocytous filamentous cyanobacterium Limnospira fusiformis (formerly Arthrospira fusiformis or Spirulina platensis), forming almost unialgal blooms, is supposed to be a key driver in those ecosystems and is gaining increasing attention because of its nutritional value. Compared to phosphorus and carbon availability, these lakes show reduced nitrogen supply. We studied the possibility of molecular nitrogen (N2) fixation in Limnospira, as contradictory statements have been published, and some closely related taxa were confirmed as N2 fixers (diazotrophs). We cultivated nine isolates originating from various EASLs under nitrate-rich and nitrate-depleted conditions. We detected dinitrogenase reductase (nifH)-like genes in all strains; however, the genes grouped within nifH cluster IV that mostly contains nitrogenases not functioning in N2 fixation. Accordingly, incubations with 15N2 gas did not support N2 fixation activity of the investigated strains. Under laboratory conditions, all strains faded during nitrate-depleted growth after approximately three weeks. Both phycocyanin and chlorophyll-a dropped to a threshold, and chlorophyll fluorescence indicated a severe problem with nitrogen supply. In summary, our data indicate that the investigated Limnospira fusiformis strains are not capable of N2 fixation.

     

  • Extracellular enzyme stoichiometry reflects the metabolic C-and P-limitations along a grassland succession on the Loess Plateau in China

    Xue Z, Liu C, Zhou Z, Wanek W
    2022 - Applied Soil Ecology, 179: Article 104594

    Abstract: 

    Soil extracellular enzyme stoichiometry (EES) reflects the biogeochemical balance between microbial metabolic requirements and environmental nutrient availability. Recent research suggests that EES well effect on soil microbial metabolic limitations (SMMLs), however, few field studies have explicitly tested this based on a herbaceous successional chronosequence. We used the EES models to identify the response of SMMLs, and investigated the potential implications of microbial nutritional limitations across the time series (herbaceous succession) and space (transformation interface soil [TIS] and underlying topsoil [UTS] layer) in the grassland restoration series. We show that soil microorganisms were generally limited by C, both in the TIS and UTS. Microbial C-limitation exhibited a unimodal direction, peaking in intermediate successional stages, however, P-limitation presented the opposite trend. During herbaceous succession, microbial P-limitation was more substantial than that in N-limitation. SMMLs gradually transferred from P- to N- and back to P-limitation at later successional stages in the TIS layer. Furthermore, we demonstrate that biotic factors, soil basic index, and soil nutrients explained 92.2 % of the variations in microbial C-limitation and 84.4 % of the variations in microbial P-limitation. Multi–interaction factors exhibited the most significant relative influences of 65.11 % (TIS) and 43 % (UTS) on the SMMLs. Microbial C-limitation was induced by the imbalance between C supply and microbial C demand, whereas the changes in microbial P-limitation were due to the changes in the competition for P between plants and microorganisms. Overall, our findings provide support for microbial C- and P-limitation in the process of herbaceous succession during the restoration. We also highlight the possibility of additive effects on soil SMMLs via interactions of vegetation composition, soil properties, and microbial nutritional demands, which might constrain soil microbial metabolism requirements despite greater living root and litter resource inputs.

  • Development of micro-zymography: Visualization of enzymatic activity at the microscopic scale for aggregates collected from the rhizosphere

    Ghaderi N, Schmidt H, Schlüter S, Banfield C, Blagodatskaya E
    2022 - Plant and Soil, 478: 253-271

    Abstract: 

    Aims

    Visualization of enzymatic activity links microbial functioning to localization in heterogeneous soil habitats. To assess enzymatic reactions in soil thin layer at the microscopic level, we developed a micro-zymography approach and tested it by visualization of the potential activity of phosphomonoesterase for aggregates collected from the rhizosphere of Zea mays L.

    Methods

    We evaluated micro-zymography by applying fluorogenically-labeled substrate i) on individual soil aggregates freshly sampled from the rhizosphere, ii) on thin layers of aggregates (≈ 500 µm) saturated with substrate to assess the dynamics of phosphomonoesterase activity, and iii) on maize roots under laser scanning microscope upon the identified hotspots by membrane-based zymography.

    Results

    We found super transparent silicon as the most appropriate fixative to prevent sample drying. We optimized microscope settings to eliminate the soil auto-fluorescence. The fluorescent signal shifted from the free liquid phase towards the aggregate boundaries within 30 min after substrate addition and was finally detectable at the surface of a few aggregates. This was probably due to higher microbial abundance and enzymatic activity on the soil aggregates compared to the liquid phase. The enzymatic activity appeared patchy at the aggregate and root surfaces indicating heterogeneous distribution of hotspots.

    Conclusions

    The methodology including calibration, sample preparation, fixation, and monitoring was developed. The novel membrane-free micro-zymography approach is a promising tool to identify functional specificity and niche differentiation on roots and soil aggregates. This approach revealed unexplained complexity of competing processes (biochemical, hydrolytic, and physical) due to differently charged reaction products and enzyme-clay complexes.

  • Effect of Polymer Properties on the Biodegradation of Polyurethane Microplastics

    Patrizia Pfohl, Daniel Bahl, Markus Rückel, Marion Wagner, Lars Meyer, Patrick Bolduan, Glauco Battagliarin, Thorsten Hüffer, Michael Zumstein, Thilo Hofmann, Wendel Wohlleben
    2022 - Environ. Sci. Technol., in press

    Abstract: 

    The release of fragments from plastic products, that is, secondary microplastics, is a major concern in the context of the global plastic pollution. Currently available (thermoplastic) polyurethanes [(T)PU] are not biodegradable and therefore should be recycled. However, the ester bond in (T)PUs might be sufficiently hydrolysable to enable at least partial biodegradation of polyurethane particles. Here, we investigated biodegradation in compost of different types of (T)PU to gain insights into their fragmentation and biodegradation mechanisms. The studied (T)PUs varied regarding the chemistry of their polymer backbone (aromatic/aliphatic), hard phase content, cross-linking degree, and presence of a hydrolysis-stabilizing additive. We developed and validated an efficient and non-destructive polymer particle extraction process for partially biodegraded (T)PUs based on ultrasonication and density separation. Our results showed that biodegradation rates and extents decreased with increasing cross-linking density and hard-segment content. We found that the presence of a hydrolysis stabilizer reduced (T)PU fragmentation while not affecting the conversion of (T)PU carbon into CO2. We propose a biodegradation mechanism for (T)PUs that includes both mother particle shrinkage by surface erosion and fragmentation. The presented results help to understand structure–degradation relationships of (T)PUs and support recycling strategies.

  • Putting vascular epiphytes on the traits map

    Hietz P, Wagner K, Nunes Ramos F, Cabral J, Agudelo C, Benavides AM, Cach-Pérez MJ, Cardelús C, Chilpa Galván N, Costa L, de Paula Oliveira R, Einzmann H, Farias R, Guzmán JV, Kattge J, Kessler M, Kirby C, Kreft H, Kromer T, Males J, Monsalve Correa S, Moreno-Chacón M, Petter G, Reyes-Garcia C, Saldana A, Schellenberger Costa D, Taylor A, Velázquez Rosas N, Wanek W, Woods C, Zotz G
    2022 - Journal of Ecology, 110: 340-358

    Abstract: 

    1. Plant functional traits impact the fitness and environmental niche of plants. Major plant functional types have been characterized by their trait spectrum, and the environmental and phylogenetic imprints on traits have advanced several ecological fields. Yet, very few trait data on epiphytes, which represent almost 10% of vascular plants, are available.
    2. We collated 76,561 trait observations for 2,882 species of vascular epiphytes and compared these to non-epiphytic herbs and trees to test hypotheses related to how the epiphytic habit affects traits, and if epiphytes occupy a distinct region in the global trait space. We also compared variation in traits among major groups of epiphytes, and investigated the coordination of traits in epiphytes, ground-rooted herbs and trees.
    3. Epiphytes differ from ground-rooted plants mainly in traits related to water relations. Unexpectedly, we did not find lower leaf nutrient concentrations, except for nitrogen. Mean photosynthetic rates are much lower than in ground-rooted plants and lower than expected from the nitrogen concentrations. Trait syndromes clearly distinguish epiphytes from trees and from most non-epiphytic herbs.
    4. Among the three largest epiphytic taxa, orchids differ from bromeliads and ferns mainly by having smaller and more numerous stomata, while ferns differ from bromeliads by having thinner leaves, higher nutrient concentrations, and lower water content and water use efficiency.
    5. Trait networks differ among epiphytes, herbs and trees. While all have central nodes represented by SLA and mass-based photosynthesis, in epiphytes, traits related to plant water relations have stronger connections, and nutrients other than potassium have weaker connections to the remainder of the trait network. Whereas stem-specific density reflects mechanical support related to plant size in herbs and trees, in epiphytes it mostly reflects water storage and scales with leaf water content.
    6. Synthesis. Our findings advance our understanding of epiphyte ecology, but we note that currently mainly leaf traits are available. Important gaps are root, shoot and whole plant, demographic and gas exchange traits. We suggest how future research might use available data and fill data gaps.
    • We collated 76,561 trait observations for 2,882 species of vascular epiphytes and compared these to non-epiphytic herbs and trees to test hypotheses related to how the epiphytic habit affects traits, and if epiphytes occupy a distinct region in the global trait space. We also compared variation in traits among major groups of epiphytes, and investigated the coordination of traits in epiphytes, ground-rooted herbs and trees.
    • Epiphytes differ from ground-rooted plants mainly in traits related to water relations. Unexpectedly, we did not find lower leaf nutrient concentrations, except for nitrogen. Mean photosynthetic rates are much lower than in ground-rooted plants and lower than expected from the nitrogen concentrations. Trait syndromes clearly distinguish epiphytes from trees and from most non-epiphytic herbs.
    • Among the three largest epiphytic taxa, orchids differ from bromeliads and ferns mainly by having smaller and more numerous stomata, while ferns differ from bromeliads by having thinner leaves, higher nutrient concentrations, and lower water content and water use efficiency.
    • Trait networks differ among epiphytes, herbs and trees. While all have central nodes represented by SLA and mass-based photosynthesis, in epiphytes, traits related to plant water relations have stronger connections, and nutrients other than potassium have weaker connections to the remainder of the trait network. Whereas stem-specific density reflects mechanical support related to plant size in herbs and trees, in epiphytes it mostly reflects water storage and scales with leaf water content.
    • Synthesis. Our findings advance our understanding of epiphyte ecology, but we note that currently mainly leaf traits are available. Important gaps are root, shoot and whole plant, demographic and gas exchange traits. We suggest how future research might use available data and fill data gaps.
  • Litter diversity accelerates labile carbon but slows recalcitrant carbon decomposition

    Wang L, Zhou Y, Chen Y, Xu Z, Zhang J, Liu Y, Joly FX
    2022 - Soil Biology and Biochemistry, 168: Article 108632

    Abstract: 

    In biodiverse ecosystems, leaf litter of different plant species decomposes in mixtures, for which decomposition rates notoriously deviate from that expected from monospecific treatments. Despite important research efforts in past decades, these litter diversity effects remain difficult to predict. We hypothesized that this is due to a focus on bulk litter decomposition, while different carbon fractions constituting the litter may respond differently to litter diversity, thereby blurring the overall response. To test this hypothesis, we determined how the decomposition of (i) soluble compounds, (ii) cellulose, and (iii) lignin responded to litter mixing in a 3.5-year field experiment in an alpine forest. We found that the decomposition of soluble compounds and cellulose in mixtures was faster than expected from monospecific treatments, while that of lignin was slower. These deviations from expected decomposition rates of each litter carbon fraction were driven by different aspects of the litter functional diversity. This suggests that different mechanisms operating on distinct litter fractions lead to synergistic and antagonistic interactions that simultaneously affect bulk litter decomposition. Furthermore, the magnitude of these fraction-specific deviations from expected decomposition rates consistently decreased throughout decomposition. Considering the response of litter fractions and their temporality, rather than focusing on bulk litter thus seems critical to evaluate the response of decomposition to plant diversity and identify underlying mechanisms.

  • Freshwater suspended particulate matter—Key components and processes in floc formation and dynamics

    Helene Walch, Frank von der Kammer, Thilo Hofmann
    2022 - Water Research, 220: in press

    Abstract: 

    Freshwater suspended particulate matter (SPM) plays an important role in many biogeochemical cycles and serves multiple ecosystem functions. Most SPM is present as complex floc-like aggregate structures composed of various minerals and organic matter from the molecular to the organism level. Flocs provide habitat for microbes and feed for larger organisms. They constitute microbial bioreactors, with prominent roles in carbon and inorganic nutrient cycles, and transport nutrients as well as pollutants, affecting sediments, inundation zones, and the ocean. Composition, structure, size, and concentration of SPM flocs are subject to high spatiotemporal variability. Floc formation processes and compositional or morphological dynamics can be established around three functional components: phyllosilicates, iron oxides/(oxy)hydroxides (FeOx), and microbial extracellular polymeric substances (EPS). These components and their interactions increase heterogeneity in surface properties, enhancing flocculation. Phyllosilicates exhibit intrinsic heterogeneities in surface charge and hydrophobicity. They are preferential substrates for precipitation or attachment of reactive FeOx. FeOx form patchy coatings on minerals, especially on phyllosilicates, which increase surface charge heterogeneities. Both, phyllosilicates and FeOx strongly adsorb natural organic matter (NOM), preferentially certain EPS. EPS comprise various substances with heterogeneous properties that make them a sticky mixture, enhancing flocculation. Microbial metabolism, and thus EPS release, is supported by the high adsorption capacity and favorable nutrient composition of phyllosilicates, and FeOx supply essential Fe.

  • Trichoderma reesei

    Schmoll M
    2022 - Trends in microbiology, 30: 403-404

    Abstract: 

    The filamentous fungus Trichoderma reesei (teleomorph: Hypocrea jecorina) grows on rotting plant material in its natural habitat. It is among the most prolific producers of plant cell-wall-degrading enzymes and is frequently used in industry for production of those and other performance proteins. A complete telomere-to-telomere genome sequence is now available (34 Mb, 10 877 genes, 7 chromosomes). Sexual reproduction of the haploid T. reesei in the laboratory was achieved only about a decade ago and requires pheromones, but also other chemical signals. T. reesei is readily transformable, and a plethora of tools, including CRISPR/Cas, have been developed which facilitate functional genomics, genome-wide investigations, and live-cell imaging, and tools to investigate chemical communication. Studies focused on a detailed understanding of enzyme expression and its improvement revealed the interplay of numerous transcription factors, connections to signaling pathways, and a significant impact of light. Detailed understanding of the physiology of T. reesei will enable optimized enzyme expression and thereby support development of more sustainable, yet commercially viable, solutions for biofuel production, textile production and recycling, chemical conversions using enzymes, food processing, production of pharmaceuticals including antibodies, bioremediation, and agriculture.

  • Arbuscular Mycorrhiza and Nitrification: Disentangling Processes and Players by Using Synthetic Nitrification Inhibitors

    Dudáš M, Pjevac P, kotianová M, Gančarčíková K, Rozmoš M, Hršelová H, Bukovská P, Jansa J
    2022 - Applied and environmental microbiology, in press

    Abstract: 

    Both plants and their associated arbuscular mycorrhizal (AM) fungi require nitrogen (N) for their metabolism and growth. This can result in both positive and negative effects of AM symbiosis on plant N nutrition. Either way, the demand for and efficiency of uptake of mineral N from the soil by mycorrhizal plants are often higher than those of nonmycorrhizal plants. In consequence, the symbiosis of plants with AM fungi exerts important feedbacks on soil processes in general and N cycling in particular. Here, we investigated the role of the AM symbiosis in N uptake by Andropogon gerardii from an organic source (15N-labeled plant litter) that was provided beyond the direct reach of roots. In addition, we tested if pathways of 15N uptake from litter by mycorrhizal hyphae were affected by amendment with different synthetic nitrification inhibitors (dicyandiamide [DCD], nitrapyrin, or 3,4-dimethylpyrazole phosphate [DMPP]). We observed efficient acquisition of 15N by mycorrhizal plants through the mycorrhizal pathway, independent of nitrification inhibitors. These results were in stark contrast to 15N uptake by nonmycorrhizal plants, which generally took up much less 15N, and the uptake was further suppressed by nitrapyrin or DMPP amendments. Quantitative real-time PCR analyses showed that bacteria involved in the rate-limiting step of nitrification, ammonia oxidation, were suppressed similarly by the presence of AM fungi and by nitrapyrin or DMPP (but not DCD) amendments. On the other hand, abundances of ammonia-oxidizing archaea were not strongly affected by either the AM fungi or the nitrification inhibitors.
    IMPORTANCE Nitrogen is one of the most important elements for all life on Earth. In soil, N is present in various chemical forms and is fiercely competed for by various microorganisms as well as plants. Here, we address competition for reduced N (ammonia) between ammonia-oxidizing prokaryotes and arbuscular mycorrhizal fungi. These two functionally important groups of soil microorganisms, participating in nitrification and plant mineral nutrient acquisition, respectively, have often been studied in separation in the past. Here, we showed, using various biochemical and molecular approaches, that the fungi systematically suppress ammonia-oxidizing bacteria to an extent similar to that of some widely used synthetic nitrification inhibitors, whereas they have only a limited impact on abundance of ammonia-oxidizing archaea. Competition for free ammonium is a plausible explanation here, but it is also possible that the fungi produce some compounds acting as so-called biological nitrification inhibitors.
  • richoderma – genomes and genomics as treasure troves for research towards biology, biotechnology and agriculture

    Schalamun M, Schmoll M
    2022 - Front. Fungal Biol., 3: Article 1002161

    Abstract: 

    The genus Trichoderma is among the best studied groups of filamentous fungi, largely because of its high relevance in applications from agriculture to enzyme biosynthesis to biofuel production. However, the physiological competences of these fungi, that led to these beneficial applications are intriguing also from a scientific and ecological point of view. This review therefore summarizes recent developments in studies of fungal genomes, updates on previously started genome annotation efforts and novel discoveries as well as efforts towards bioprospecting for enzymes and bioactive compounds such as cellulases, enzymes degrading xenobiotics and metabolites with potential pharmaceutical value. Thereby insights are provided into genomes, mitochondrial genomes and genomes of mycoviruses of Trichoderma strains relevant for enzyme production, biocontrol and mycoremediation. In several cases, production of bioactive compounds could be associated with responsible genes or clusters and bioremediation capabilities could be supported or predicted using genome information. Insights into evolution of the genus Trichoderma revealed large scale horizontal gene transfer, predominantly of CAZyme genes, but also secondary metabolite clusters. Investigation of sexual development showed that Trichoderma species are competent of repeat induced point mutation (RIP) and in some cases, segmental aneuploidy was observed. Some random mutants finally gave away their crucial mutations like T. reesei QM9978 and QM9136 and the fertility defect of QM6a was traced back to its gene defect. The Trichoderma core genome was narrowed down to 7000 genes and gene clustering was investigated in the genomes of multiple species. Finally, recent developments in application of CRISPR/Cas9 in Trichoderma, cloning and expression strategies for the workhorse T. reesei as well as the use genome mining tools for bioprospecting Trichoderma are highlighted. The intriguing new findings on evolution, genomics and physiology highlight emerging trends and illustrate worthwhile perspectives in diverse fields of research with Trichoderma.

  • Pharmaceutical pollution of the world’s rivers

    John L. Wilkinson, Alistair B. A. Boxall, Dana W. Kolpin, Kenneth M. Y. Leung, Racliffe W. S. Lai, Cristobal Galban-Malagon, Aiko D. Adell, Julie Mondon, Marc Metian, Robert A. Marchant, Alejandra Bouzas-Monroy, Aida Cuni-Sanchez, Anja Coors, Pedro Carriquiriborde, Macarena Rojo, Chris Gordon, Magdalena Cara, Monique Moermond, Thais Luarte, Vahagn Petrosyan, Yekaterina Perikhanyan, Clare S. Mahon, Christopher J. McGurk, Thilo Hofmann, Tapos Kormoker, Volga Iniguez, Jessica Guzman-Otazo, Jean L. Tavares, Francisco Gildasio De Figueiredo, Maria T. P. Razzolini, Victorien Dougnon, Gildas Gbaguidi, Oumar Traore, Jules M. Blais, Linda E. Kimpe, Michelle Wong, Donald Wong, Romaric Ntchantcho, Jaime Pizarro, Guang-Guo Ying, Chang-Er Chen, Martha Paez, Jina Martinez-Lara, Jean-Paul Otamonga, John Pote, Suspense A. Ifo, Penelope Wilson, Silvia Echeverria-Saenz, Nikolina Udikovic-Kolic, Milena Milakovic, Despo Fatta-Kassinos, Lida Ioannou-Ttofa, Vladimira Belusova, Jan Vymazal, Maria Cardenas-Bustamante, Bayable A. Kas
    2022 - PNAS, 119: e2113947119

    Abstract: 

    Environmental exposure to active pharmaceutical ingredients (APIs) can have negative effects on the health of ecosystems and humans. While numerous studies have monitored APIs in rivers, these employ different analytial methods, measure different APIs, and have ignored many of the countries of the world. This makes it difficult to quantify the scale of the problem from a global perspective. Furthermore, comparison of the existing data, generated for different studies/regions/continents, is challenging due to the vast differences between the analytical methodologies employed. Here, we present a global-scale study of API pollution in 258 of the world’s rivers, representing the environmental influence of 471.4 million people across 137 geographic regions. Samples were obtained from 1,052 locations in 104 countries (representing all continents and 36 countries not previously studied for API contamination) and analyzed for 61 APIs. Highest cumulative API concentrations were observed in sub-Saharan Africa, south Asia, and South America. The most contaminated sites were in low- to middle-income countries and were associated with areas with poor wastewater and waste management infrastructure and pharmaceutical manufacturing. The most frequently detected APIs were carbamazepine, metformin, and caffeine (a compound also arising from lifestyle use), which were detected at over half of the sites monitored. Concentrations of at least one API at 25.7% of the sampling sites were greater than concentrations considered safe for aquatic organisms, or which are of concern in terms of selection for antimicrobial resistance. Therefore, pharmaceutical pollution poses a global threat to environmental and human health, as well as to delivery of the United Nations Sustainable Development Goals.

  • Targeting Gut Bacteria Using Inulin-Conjugated Mesoporous Silica Nanoparticles

    von Baeckmann C, Riva A, Guggenberger P, Kählig H, Han SW, Inan D, Del Favero G, Berry D, Kleitz F
    2022 - Adv Mater Interfaces, 9: 202102558

    Abstract: 

    To facilitate the creation of novel nanocarrier systems targeting the intestinal microbiome, inulin-conjugated mesoporous silica nanoparticles (MSNs) are described herein for the first time. Surface functionalization is achieved on either hydrophilic or hydrophobic mesoporous nanoparticles using different conjugation methods. The targeting performance of the resulting materials is assessed and compared upon incubation with human stool. It appears that amide formation is the most favorable coupling method on hydrophilic MSNs to achieve the desired bioconjugate. Remarkably, high affinity of gut bacteria to the conjugated particles can be obtained, paving the way to novel targeted drug delivery systems.

  • Microbiome assembly in thawing permafrost and its feedbacks to climate

    Ernakovich JG, Barbato RA, Rich VI, Schädel C, Hewitt RE, Doherty SJ, Whalen ED, Abbott BW, Barta J, Biasi C, Chabot CL, Hultman J, Knoblauch C, Lau Vetter MCY, Leewis M-C, Liebner S, Mackelprang R, Onstott TC, Richter A, Schütte UME, Siljanen HMP, Taş N, Timling I, Vishnivetskaya TA, Waldrop MP, Winkel M
    2022 - Global Change Biology, in press

    Abstract: 

    The physical and chemical changes that accompany permafrost thaw directly influence the microbial communities that mediate the decomposition of formerly frozen organic matter, leading to uncertainty in permafrost–climate feedbacks. Although changes to microbial metabolism and community structure are documented following thaw, the generality of post-thaw assembly patterns across permafrost soils of the world remains uncertain, limiting our ability to predict biogeochemistry and microbial community responses to climate change. Based on our review of the Arctic microbiome, permafrost microbiology, and community ecology, we propose that Assembly Theory provides a framework to better understand thaw-mediated microbiome changes and the implications for community function and climate feedbacks. This framework posits that the prevalence of deterministic or stochastic processes indicates whether the community is well-suited to thrive in changing environmental conditions. We predict that on a short timescale and following high-disturbance thaw (e.g., thermokarst), stochasticity dominates post-thaw microbiome assembly, suggesting that functional predictions will be aided by detailed information about the microbiome. At a longer timescale and lower-intensity disturbance (e.g., active layer deepening), deterministic processes likely dominate, making environmental parameters sufficient for predicting function. We propose that the contribution of stochastic and deterministic processes to post-thaw microbiome assembly depends on the characteristics of the thaw disturbance, as well as characteristics of the microbial community, such as the ecological and phylogenetic breadth of functional guilds, their functional redundancy, and biotic interactions. These propagate across space and time, potentially providing a means for predicting the microbial forcing of greenhouse gas feedbacks to global climate change.

  • Comparing biochar and hydrochar for reducing the risk of organic contaminants in polluted river sediments used for growing energy crops

    Snežana Maletić, Marijana Kragulj Isakovski, Gabriel Sigmund, Thilo Hofmann, Thorsten Hüffer, Jelena Beljin, Srđan Rončević
    2022 - Science of The Total Environment, 843: in press

    Abstract: 

    In Europe alone, >200 million m3 of river sediments are dredged each year, part of which are contaminated to such an extent that they have to be landfilled. This study compares the use of biochar and hydrochar for the remediation of sediment contaminated with pentachlorobenzene, hexachlorobenzene, lindane, trifluralin, alachlor, simazine, and atrazine with the motivation to make sediments contaminated by such priority substances usable as arable land for growing energy crops. Biochar and hydrochar originating from Miscanthus giganteus and Beta vulgaris shreds were compared for their potential to reduce contaminant associated risk in sediments. Specifically, by investigating the effects of sorbent amendment rate (1, 5, and 10 %) and incubation time (14, 30, and 180 d) on contaminant bioaccessibility, toxicity to the bacteria Vibrio fischeri, as well as toxicity and plant uptake in Zea mays. Biochar reduced contaminant bioaccessibility up to five times more than hydrochar. The bioaccessibility of contaminants decreased up to sevenfold with increasing incubation time, indicating that the performance of carbonaceous sorbents may be underestimated in short-term lab experiments. Biochar reduced contaminants toxicity to Vibrio fischeri, whereas hydrochar was itself toxic to the bacteria. Toxicity to Zea mays was determined by contaminant bioaccessibility but also sorbent feedstock with cellulose rich Beta vulgaris based sorbents exhibiting toxic effects. The plant uptake of all contaminants decreased after sorbent amendment.

  • Agricultural management affects active carbon and nitrogen mineralisation potential in soils

    Hendricks S, Zechmeister­‐Boltenstern S, Kandeler E, Sandén T, Díaz-Pinés E, Schnecker J, Alber O, Miloczki J, Spiegel H
    2022 - Journal of Plant Nutrition and Soil Science, 185: 513-528

    Abstract: 

    Background

    Soil organic matter (SOM) is important for soil fertility and climate change mitigation. Agricultural management can improve soil fertility and contribute to climate change mitigation by stabilising carbon in soils. This calls for cost-effective parameters to assess the influence of management practices on SOM contents.

    Aims

    The current study aimed at understanding how sensitively the parameters active carbon (AC) and nitrogen mineralisation potential (NMP) react to different agricultural management practices compared to total organic carbon (TOC) and total nitrogen (Nt). We aimed to gain a better understanding of SOM processes, mainly regarding depth distribution and seasonality of SOM dynamics using AC and NMP.

    Methods

    We looked mainly at four parameters, namely permanganate oxidisable carbon (AC), nitrogen minerlaisation potential (NMP), total organic carbon (TOC) and total nitrogen (Nt). Data were obtained in five long-term field experiments (LTEs) testing four management practices: (1) tillage, (2) compost application, (3) crop residue management, and (4) mineral fertilization.

    Results

    AC was specifically sensitive in detecting the effect of tillage treatment at different soil depths. NMP differentiated between all different tillage treatments in the upper soil layer, it showed the temporal dynamics between the years in the compost LTE, and it was identified as an early detection property in the crop residue LTE. Both AC and NMP detected short-term fluctuations better than TOC and Nt over the course of two years in the crop residue LTE.

    Conclusion

    We suggest that AC and NMP are two valuable soil biochemical parameters providing more detailed information on C and N dynamics regarding depth distribution and seasonal dynamics and react more sensitively to different agricultural management practices compared to TOC and Nt. They should be integrated in monitoring agricultural long-term experiments (LTEs) and in field analyses conducted by farmers. However, when evaluating results towards long-term carbon storage, their sensitivity toward annual fluctuations should be taken into account.

  • Negative priming of soil organic matter following long-term in situ warming of sub-arctic soils

    Verbrigghe N, Meeran K, Bahn M, Fuchslueger L, Janssens IA, Richter A, Sigurdsson BD, Soong JL, Vicca A
    2022 - Geoderma, 410: Article 115652

    Abstract: 

    Priming is the change of microbial soil organic matter (SOM) decomposition induced by a labile carbon (C) source. It is recognised as an important mechanism influencing soil C dynamics and C storage in terrestrial ecosystems. Microbial nitrogen (N) mining in SOM and preferential substrate utilisation, i.e., a shift in microbial carbon use from SOM to more labile energy sources, are possible, counteracting, mechanisms driving the priming effect. Climate warming and increased N availability might affect these mechanisms, and thus determine the direction and magnitude of the priming effect. Hence, these abiotic factors can indirectly affect soil C stocks, which makes their understanding crucial for predicting the soil C feedback in a warming world. We conducted a short-term incubation experiment (6 days) with soils from a subarctic grassland that had been subjected to long-term geothermal warming (>55 years) by 2-4°C above unwarmed soil. Soil samples were amended with 13C-labelled glucose and 15N-labelled NH4NO3. We found a significantly negative relationship between in situ warming and cumulative primed C, with negative priming in the warmed soils. The negative priming suggests that preferential substrate utilisation was a key mechanism in our experiment. Our results indicate that changes in SOM characteristics associated with the in situ warming gradient can play a major role in determining the rate and direction of the priming effect. Additionally, we found that neither microbial N limitation nor N addition affected the priming effect, providing evidence that in our experiment, N mining did not lead to positive priming.

  • Human follicular mites: Ectoparasites becoming symbionts

    Smith G, Manzano-Marín A, Reyes-Prieto M, Ribeiro Antunes CS, Ashworth V, Goselle ON, Jan AAA, Moya A, Latorre A, Perotti MA, Braig HR
    2022 - Mol Biol Evol, 39: msac125

    Abstract: 

    Most humans carry mites in the hair follicles of their skin for their entire lives. Follicular mites are the only metazoans that continuously live on humans. We propose that Demodex folliculorum (Acari) represents a transitional stage from a host-injuring obligate parasite to an obligate symbiont. Here, we describe the profound impact of this transition on the genome and physiology of the mite. Genome sequencing revealed that the permanent host association of D. folliculorum led to an extensive genome reduction through relaxed selection and genetic drift, resulting in the smallest number of protein-coding genes yet identified among panarthropods. Confocal microscopy revealed that this gene loss coincided with an extreme reduction in the number of cells. Single uninucleate muscle cells are sufficient to operate each of the three segments that form each walking leg. While it has been assumed that the reduction of the cell number in parasites starts early in development, we identified a greater total number of cells in the last developmental stage (nymph) than in the terminal adult stage, suggesting that reduction starts at the adult or ultimate stage of development. This is the first evolutionary step in an arthropod species adopting a reductive, parasitic, or endosymbiotic lifestyle. Somatic nuclei show under-replication at the diploid stage. Novel eye structures or photoreceptors as well as a unique human host melatonin-guided day/night rhythm are proposed for the first time. The loss of DNA repair genes coupled with extreme endogamy might have set this mite species on an evolutionary dead-end trajectory.

  • Defensive symbiosis against giant viruses in amoebae

    Arthofer P, Delafont V, Willemsen A, Panhölzl F, Horn M
    2022 - PNAS, 119: e2205856119

    Abstract: 

    Protists are important regulators of microbial communities and key components in food webs with impact on nutrient cycling and ecosystem functioning. In turn, their activity is shaped by diverse intracellular parasites, including bacterial symbionts and viruses. Yet, bacteria–virus interactions within protists are poorly understood. Here, we studied the role of bacterial symbionts of free-living amoebae in the establishment of infections with nucleocytoplasmic large DNA viruses (Nucleocytoviricota). To investigate these interactions in a system that would also be relevant in nature, we first isolated and characterized a giant virus (Viennavirus, family Marseilleviridae) and a sympatric potential Acanthamoeba host infected with bacterial symbionts. Subsequently, coinfection experiments were carried out, using the fresh environmental isolates as well as additional amoeba laboratory strains. Employing fluorescence in situ hybridization and qPCR, we show that the bacterial symbiont, identified as Parachlamydia acanthamoebae, represses the replication of the sympatric Viennavirus in both recent environmental isolates as well as Acanthamoeba laboratory strains. In the presence of the symbiont, virions are still taken up, but viral factory maturation is inhibited, leading to survival of the amoeba host. The symbiont also suppressed the replication of the more complex Acanthamoeba polyphaga mimivirus and Tupanvirus deep ocean (Mimiviridae). Our work provides an example of an intracellular bacterial symbiont protecting a protist host against virus infections. The impact of virus–symbiont interactions on microbial population dynamics and eventually ecosystem processes requires further attention.

  • Polyvinyl Chloride Microplastics Leach Phthalates into the Aquatic Environment over Decades

    Charlotte Henkel, Thorsten Hüffer, Thilo Hofmann
    2022 - Environ. Sci. Technol., in press

    Abstract: 

    Phthalic acid esters (phthalates) have been detected everywhere in the environment, but data on leaching kinetics and the governing mass transfer process into aqueous systems remain largely unknown. In this study, we experimentally determined time-dependent leaching curves for three phthalates di(2-ethylhexyl) phthalate, di(2-ethylhexyl) terephthalate, and diisononyl phthalate from polyvinyl chloride (PVC) microplastics and thereby enabled a better understanding of their leaching kinetics. This is essential for exposure assessment and to predict microplastic-bound environmental concentrations of phthalates. Leaching curves were analyzed using models for intraparticle diffusion (IPD) and aqueous boundary layer diffusion (ABLD). We show that ABLD is the governing diffusion process for the continuous leaching of phthalates because phthalates are very hydrophobic (partitioning coefficients between PVC and water log KPVC/W were higher than 8.6), slowing down the diffusion through the ABL. Also, the diffusion coefficient in the polymer DPVC is relatively high (∼8 × 10–14 m2 s–1) and thus enhances IPD. Desorption half-lives of the studied PVC microplastics are greater than 500 years but can be strongly influenced by environmental factors. By combining leaching experiments and modeling, our results reveal that PVC microplastics are a long-term source of phthalates in the environment.

  • Reverse microdialysis: A window into root exudation hotspots

    König A, Wiesenbauer J, Gorka S, Marchand L, Kitzler B, Inselsbacher E, Kaiser C
    2022 - Soil Biology and Biochemistry, 174: Article 108829

    Abstract: 

    Plant roots release a variety of low-molecular weight compounds, such as sugars, amino acids or organic acids into the soil, impacting microbial activities and physico-chemical soil processes in their surroundings. These compounds are a source of easily available Carbon (C) and energy for soil microbes, potentially accelerating microbial decomposition of soil organic matter in the immediate vicinity of roots. However, knowledge about processes in root exudation hotspots remains limited due to experimental difficulties in investigating such hotspots in soil.

    Microdialysis, a passive sampling technique based on diffusion, has been successfully used to collect soil solutes at small spatial scales. Reverse microdialysis, also termed retrodialysis, can be used to introduce solutes into the soil, mimicking passive root exudation. However, little is known about the dynamics of substances released by passive diffusion into intact soil, a crucial prerequisite for applying reverse microdialysis to study root exudation hotspots in undisturbed soils.

    Here, we used reverse microdialysis to investigate the spatial and temporal dynamics of thirteen different organic compounds passively introduced into two different intact soils. Diffusion of compounds into soils was substantially lower than into water, and was not – as in water – determined by molecular size. Interestingly, butyrate, oxalate and propionate showed the highest diffusive fluxes into soil combined with the lowest rate of back retrieval after input, indicating that they were quickly removed from the soil solution by biotic or abiotic processes. In contrast, glucose and fructose unexpectedly accumulated around the membrane after input without removal. Furthermore, diffusive fluxes of compounds into soils showed a fluctuating temporal pattern, which may be explained by an observed 2-h delay of microbial respiration of added 13C-labelled compounds. During the course of 12 days, approximately one third of 13C-labelled compounds introduced into soil was respired while 8% ended up in microbial biomass.

    Our results demonstrate that introducing compounds into intact soil triggers complex biotic and abiotic responses at the time scale of hours. Reverse microdialysis proved to be an excellent tool to investigate such responses as well as the dynamics and metabolic consequences of passively released compounds into intact soil, and – in combination with 13C labelled substrate and respiration measurements - to shed light on potential priming effects that may be triggered by them.

  • Omics research on abalone (Haliotis spp.): Current state and perspectives

    Nguyen TV, Alfaro AC, Mundy C, Petersen JM, Ragg NLC
    2022 - Aquaculture, 547: 737438

    Abstract: 

    The steady increase in abalone aquaculture production throughout the world has attracted growing interest in the application of new technologies, such as omics approaches for abalone research. Many omics techniques, such as genomics, transcriptomics, proteomics, and metabolomics are becoming established in abalone research and are beginning to reveal key molecules and pathways underlying many biological processes, and to identify associated candidate biomarkers of biological or environmental processes. In this contribution, we synthesize the published omics studies on abalone to highlight the current state of knowledge, open questions, and future directions. In addition, we outline the challenges and limitations of each omics field, some of which could be overcome by integrating multiple omics approaches – a future strategy with great potential for contributing to improve abalone production. Full text

  • Multi-strain probiotics show increased protection of intestinal epithelial cells against pathogens in rainbow trout (Oncorhynchus mykiss)

    Pillinger M, Weber B, Standen B, Schmid MC, Kesselring JC
    2022 - Aquaculture, 560: 738487

    Abstract: 

    The use of antibiotics to treat bacterial infections in aquaculture facilities adversely affects fish and environmental health, motivating the search for alternative products such as probiotics. The present study investigated the immune modulatory effects of inoculating the intestinal epithelial cells of rainbow trout (Oncorhynchus mykiss) with the probiotic bacteria Enterococcus faeciumPediococcus acidilacticiLactobacillus reuteri, and Bacillus subtilis alone (single-strains) or as mixtures, which either include or exclude B. subtilis (PWBsubtilis or PWOBsubtilis, respectively). To this end, isolated intestinal epithelial cells were either incubated without probiotics or with the single- or multi-strain probiotics and then challenged with common pathogens in aquaculture. The adhesion of probiotic and pathogenic bacteria to the intestinal cells was examined by flow cytometry and confocal microscopy and the relative expression of pro- and anti-inflammatory cytokine genes was assessed through quantitative real-time PCR. Although the highest inhibition of pathogen adhesion was observed for L. reuteri alone (88%), PWOBsubtilis and PWBsubtilis inhibited 77% and 71% of pathogen attachment, respectively. Single- and multi-strain probiotics were able to elicit an immune response by activation of both pro-inflammatory and anti-inflammatory cytokines production in rainbow trout intestinal epithelial cells. This expression was generally highest for multi-strain probiotics, particularly for PWBsubtilis. The tested probiotics present different modes of action, considering their inhibition capability and immunomodulatory effects. Hence the use of multi-strain products may promote a wider range of synergies on pathogens invasion and inhibition, and immunomodulatory effects that can represent an advantage to disease outbreaks prevention in rainbow trout production.

  • Microbial marker for seawater intrusion in a coastal Mediterranean shallow Lake, Lake Vrana, Croatia

    Selak L, Marković T, Pjevac P, Orlić S
    2022 - Science of The Total Environment, in press

    Abstract: 

    Climate change-induced rising sea levels and prolonged dry periods impose a global threat to the freshwater scarcity on the coastline: salinization. Lake Vrana is the largest surface freshwater resource in mid-Dalmatia, while the local springs are heavily used in agriculture. The karstified carbonate ridge that separates this shallow lake from the Adriatic Sea enables seawater intrusion if the lakes' precipitation-evaporation balance is disturbed. In this study, the impact of anthropogenic activities and drought exuberated salinization on microbial communities was tracked in Lake Vrana and its inlets, using 16S rRNA gene sequencing. The lack of precipitation and high water temperatures in summer months introduced an imbalance in the water regime of the lake, allowing for seawater intrusion, mainly via the karst conduit Jugovir. The determined microbial community spatial differences in the lake itself and the main drainage canals were driven by salinity, drought, and nutrient loading. Particle-associated and free-living microorganisms both strongly responded to the ecosystem perturbations, and their co-occurrence was driven by the salinization event. Notably, a bloom of halotolerant taxa, predominant the sulfur-oxidizing genus Sulfurovum, emerged with increased salinity and sulfate concentrations, having the potential to be used as an indicator for salinization of shallow coastal lakes. Following summer salinization, lake water column homogenization took from a couple of weeks up to a few months, while the entire system displayed increased salinity despite increased precipitation. This study represents a valuable contribution to understanding the impact of the Freshwater Salinization Syndrome on Mediterranean lakes' microbial communities and the ecosystem resilience.

  • Negative erosion and negative emissions: Combining multiple land-based carbon dioxide removal techniques to rebuild fertile topsoils and enhance food production

    Janssens IA, Roobroeck D, Sardans J, Obersteiner M, Schiestl RH, Richter A, Smith P, Verbruggen E, Vicca S
    2022 - Frontiers in Climate, 4: Article 928403

    Abstract: 

    Carbon dioxide removal (CDR) that increases the area of forest cover or bio-energy crops inherently competes for land with crop and livestock systems, compromising food security, or will encroach natural lands, compromising biodiversity. Mass deployment of these terrestrial CDR technologies to reverse climate change therefore cannot be achieved without a substantial intensification of agricultural output, i.e., producing more food on less land. This poses a major challenge, particularly in regions where arable land is little available or severely degraded and where agriculture is crucial to sustain people's livelihoods, such as the Global South. Enhanced silicate weathering, biochar amendment, and soil carbon sequestration are CDR techniques that avoid this competition for land and may even bring about multiple co-benefits for food production. This paper elaborates on the idea to take these latter CDR technologies a step further and use them not only to drawdown CO2 from the atmosphere, but also to rebuild fertile soils (negative erosion) in areas that suffer from pervasive land degradation and have enough water available for agriculture. This way of engineering topsoil could contribute to the fight against malnutrition in areas where crop and livestock production currently is hampered by surface erosion and nutrient depletion, and thereby alleviate pressure on intact ecosystems. The thrust of this perspective is that synergistically applying multiple soil-related CDR strategies could restore previously degraded soil, allowing it to come back into food production (or become more productive), potentially alleviating pressure on intact ecosystems. In addition to removing CO2 from the atmosphere, this practice could thus contribute to reducing poverty and hunger and to protection of biodiversity.

  • Using Stable Isotopes to Assess Groundwater Recharge and Solute Transport in a Density-Driven Flow-Dominated Lake–Aquifer System

    Valiente N, Dountcheva I, Sanz D, Gómez-Alday JJ
    2022 - Water, 14: Article 1628

    Abstract: 

    Saline lakes are mostly located in endorheic basins in arid and semi-arid regions, where the excess of evaporation over precipitation promotes the accumulation of salts on the surface. As the salinity of these lakes increases, their mass balance changes, and biogeochemical processes may be intensified. In that sense, Pétrola Lake (SE Spain) is a terminal lake located in an endorheic basin with elevated anthropic pressure, mainly derived from agricultural inputs and wastewater discharge. The goal of this study was to evaluate the interaction between groundwater and saline water from Pétrola Lake to improve our knowledge of groundwater recharge processes by density-driven flow (DDF) in terminal lakes. A combination of hydrochemical (chloride concentration) and stable isotope (δ18OH2O and δ2HH2O) data were used. In order to test the conceptual model, a simple numerical experiment was performed using a one-dimensional column that represents the relationship between the lake and the aquifer incorporating the variable density coupling control in solute migration. The isotopic composition of 190 groundwater and surface water samples collected between September 2008 and July 2015 provides a regression line (δ2HH2O = 5.0·δ18OH2O − 14.3‰, R2 = 0.95) consistent with dominant evaporation processes in the lake. The DDF towards the underlying aquifer showed a strong influence on the mixing processes between the groundwater and surface water. Nevertheless, groundwater chemistry at different depths beneath the lake remains almost constant over time, suggesting an equilibrium between DDF and regional groundwater flow (RGF). Modelling isotope changes allowed inferring the temporal pattern of saline water recharge, coinciding with the summer season when water loss through evaporation is most significant. Consequently, the transport of solutes suitable for chemical reactions is then feasible to deeper zones of the aquifer.

  • Atypical enteropathogenic are associated with disease activity in ulcerative colitis.

    Baumgartner M, Zirnbauer R, Schlager S, Mertens D, Gasche N, Sladek B, Herbold C, Bochkareva O, Emelianenko V, Vogelsang H, Lang M, Klotz A, Moik B, Makristathis A, Berry D, Dabsch S, Khare V, Gasche C
    2022 - Gut Microbes, 1: 2143218

    Abstract: 

    With increasing urbanization and industrialization, the prevalence of inflammatory bowel diseases (IBDs) has steadily been rising over the past two decades. IBD involves flares of gastrointestinal (GI) inflammation accompanied by microbiota perturbations. However, microbial mechanisms that trigger such flares remain elusive. Here, we analyzed the association of the emerging pathogen atypical enteropathogenic (aEPEC) with IBD disease activity. The presence of diarrheagenic was assessed in stool samples from 630 IBD patients and 234 age- and sex-matched controls without GI symptoms. Microbiota was analyzed with 16S ribosomal RNA gene amplicon sequencing, and 57 clinical aEPEC isolates were subjected to whole-genome sequencing and in vitro pathogenicity experiments including biofilm formation, epithelial barrier function and the ability to induce pro-inflammatory signaling. The presence of aEPEC correlated with laboratory, clinical and endoscopic disease activity in ulcerative colitis (UC), as well as microbiota dysbiosis. In vitro, aEPEC strains induce epithelial p21-activated kinases, disrupt the epithelial barrier and display potent biofilm formation. The effector proteins and distinguish aEPEC cultured from UC and Crohn's disease patients, respectively. EspV-positive aEPEC harbor more virulence factors and have a higher pro-inflammatory potential, which is counteracted by 5-ASA. aEPEC may tip a fragile immune-microbiota homeostasis and thereby contribute to flares in UC. aEPEC isolates from UC patients display properties to disrupt the epithelial barrier and to induce pro-inflammatory signaling in vitro.

  • A novel widespread MITE wlement in the repeat-rich genome of the endosymbiont of the spider Oedothorax gibbosus

    Halter T, Hendrickx F, Horn M, Manzano-Marín A
    2022 - Microbiol Spectr, e0262722

    Abstract: 

    Free-living bacteria have evolved multiple times to become host-restricted endosymbionts. The transition from a free-living to a host-restricted lifestyle comes with a number of different genomic changes, including a massive loss of genes. In host-restricted endosymbionts, gene inactivation and genome reduction are facilitated by mobile genetic elements, mainly insertion sequences (ISs). ISs are small autonomous mobile elements, and one of, if not the most, abundant transposable elements in bacteria. Proliferation of ISs is common in some facultative endosymbionts, and is likely driven by the transmission bottlenecks, which increase the level of genetic drift. In this study, we present a manually curated genome annotation for a Cardinium endosymbiont of the dwarf spider Oedothorax gibbosus. Cardinium species are host-restricted endosymbionts that, similarly to Colbachia spp., include strains capable of manipulating host reproduction. Through the focus on mobile elements, the annotation revealed a rampant spread of ISs, extending earlier observations in other Cardinium genomes. We found that a large proportion of IS elements are pseudogenized, with many displaying evidence of recent inactivation. Most notably, we describe the lineage-specific emergence and spread of a novel IS-derived Miniature Inverted repeat Transposable Element (MITE), likely being actively maintained by intact copies of its parental IS982-family element. This study highlights the relevance of manual curation of these repeat-rich endosymbiont genomes for the discovery of novel MITEs, as well as the possible role these understudied elements might play in genome streamlining.

    IMPORTANCE: Cardinium bacteria, a widespread symbiont lineage found across insects and nematodes, have been linked to reproductive manipulation of their hosts. However, the study of Cardinium has been hampered by the lack of comprehensive genomic resources. The high content of mobile genetic elements, namely, insertion sequences (ISs), has long complicated the analyses and proper annotations of these genomes. In this study, we present a manually curated annotation of the Cardinium symbiont of the spider Oedothorax gibbosus. Most notably, we describe a novel IS-like element found exclusively in this strain. We show that this mobile element likely evolved from a defective copy of its parental IS and then spread throughout the genome, contributing to the pseudogenization of several other mobile elements. We propose this element is likely being maintained by the intact copies of its parental IS element and that other similar elements in the genome could potentially follow this route.

  • Impaired Mucosal Homeostasis in Short-Term Fiber Deprivation Is Due to Reduced Mucus Production Rather Than Overgrowth of Mucus-Degrading Bacteria.

    Overbeeke A, Lang M, Hausmann B, Watzka M, Nikolov G, Schwarz J, Kohl G, De Paepe K, Eislmayr K, Decker T, Richter A, Berry D
    2022 - Nutrients, 18: in press

    Abstract: 

    The gut mucosal environment is key in host health; protecting against pathogens and providing a niche for beneficial bacteria, thereby facilitating a mutualistic balance between host and microbiome. Lack of dietary fiber results in erosion of the mucosal layer, suggested to be a result of increased mucus-degrading gut bacteria. This study aimed to use quantitative analyses to investigate the diet-induced imbalance of mucosal homeostasis. Seven days of fiber-deficiency affected intestinal anatomy and physiology, seen by reduced intestinal length and loss of the colonic crypt-structure. Moreover, the mucus layer was diminished, expression decreased, and impaired mucus secretion was detected by stable isotope probing. Quantitative microbiome profiling of the gut microbiota showed a diet-induced reduction in bacterial load and decreased diversity across the intestinal tract, including taxa with fiber-degrading and butyrate-producing capabilities. Most importantly, there was little change in the absolute abundance of known mucus-degrading bacteria, although, due to the general loss of taxa, relative abundance would erroneously indicate an increase in mucus degraders. These findings underscore the importance of using quantitative methods in microbiome research, suggesting erosion of the mucus layer during fiber deprivation is due to diminished mucus production rather than overgrowth of mucus degraders.

  • Increase in carbon input by enhanced fine root turnover in a long-term warmed forest soil

    Kwatcho Kengdo S, Ahrens B, Tian Y, Heinzle J, Wanek W, Schindlbacher A, Borken W
    2022 - Sci Total Environ, 855: Article 158800

    Abstract: 

    Fine root litter represents an important carbon input to soils, but the effect of global warming on fine root turnover (FRT) is hardly explored in forest ecosystems. Understanding tree fine roots' response to warming is crucial for predicting soil carbon dynamics and the functioning of forests as a sink for atmospheric carbon dioxide (CO2). We studied fine root production (FRP) with ingrowth cores and used radiocarbon signatures of first-order, second- to third-order, and bulk fine roots to estimate fine root turnover times after 8 and 14 years of soil warming (+4 °C) in a temperate forest. Fine root turnover times of the individual root fractions were estimated with a one-pool model. Soil warming strongly increased fine root production by up to 128 % within one year, but after two years, the production was less pronounced (+35 %). The first-year production was likely very high due to the rapid exploitation of the root-free ingrowth cores. The radiocarbon signatures of fine roots were overall variable among treatments and plots. Soil warming tended to decrease fine root turnover times of all the measured root fractions after 8 and 14 years of warming, and there was a tendency for trees to use older carbon reserves for fine root production in warmed plots. Furthermore, soil warming increased fine root turnover from 50 to 106 g C m-2 yr-1 (based on two different approaches). Our findings suggest that future climate warming may increase carbon input into soils by enhancing fine root turnover. If this increase may partly offset carbon losses by increased mineralization of soil organic matter in temperate forest soils is still unclear and should guide future research.

  • A look beyond dietary (poly)phenols: The low molecular weight phenolic metabolites and their concentrations in human circulation.

    Carregosa D, Pinto C, Ávila-Gálvez MÁ, Bastos P, Berry D, Santos CN
    2022 - Compr Rev Food Sci Food Saf, 5: 3931-3962

    Abstract: 

    A large number of epidemiological studies have shown that consumption of fruits, vegetables, and beverages rich in (poly)phenols promote numerous health benefits from cardiovascular to neurological diseases. Evidence on (poly)phenols has been applied mainly to flavonoids, yet the role of phenolic acids has been largely overlooked. Such phenolics present in food combine with those resulting from gut microbiota catabolism of flavonoids and chlorogenic acids and those produced by endogenous pathways, resulting in large concentrations of low molecular weight phenolic metabolites in human circulation. Independently of the origin, in human intervention studies using diets rich in (poly)phenols, a total of 137 low molecular weight phenolic metabolites have been detected and quantified in human circulation with largely unknown biological function. In this review, we will pinpoint two main aspects of the low molecular weight phenolic metabolites: (i) the microbiota responsible for their generation, and (ii) the analysis (quali- and quantitative) in human circulation and their respective pharmacokinetics. In doing so, we aim to drive scientific advances regarding the ubiquitous roles of low molecular weight phenolic metabolites using physiologically relevant concentrations and under (patho)physiologically relevant conditions in humans.

  • Sulfur and methane oxidation by a single microorganism.

    Gwak JH, Awala SI, Nguyen NL, Yu WJ, Yang HY, von Bergen M, Jehmlich N, Kits KD, Loy A, Dunfield PF, Dahl C, Hyun JH, Rhee SK
    2022 - Proc Natl Acad Sci U S A, 32: e2114799119

    Abstract: 

    Natural and anthropogenic wetlands are major sources of the atmospheric greenhouse gas methane. Methane emissions from wetlands are mitigated by methanotrophic bacteria at the oxic-anoxic interface, a zone of intense redox cycling of carbon, sulfur, and nitrogen compounds. Here, we report on the isolation of an aerobic methanotrophic bacterium, '' strain HY1, which possesses metabolic capabilities never before found in any methanotroph. Most notably, strain HY1 is the first bacterium shown to aerobically oxidize both methane and reduced sulfur compounds for growth. Genomic and proteomic analyses showed that soluble methane monooxygenase and XoxF-type alcohol dehydrogenases are responsible for methane and methanol oxidation, respectively. Various pathways for respiratory sulfur oxidation were present, including the Sox-rDsr pathway and the SI system. Strain HY1 employed the Calvin-Benson-Bassham cycle for CO fixation during chemolithoautotrophic growth on reduced sulfur compounds. Proteomic and microrespirometry analyses showed that the metabolic pathways for methane and thiosulfate oxidation were induced in the presence of the respective substrates. Methane and thiosulfate could therefore be independently or simultaneously oxidized. The discovery of this versatile bacterium demonstrates that methanotrophy and thiotrophy are compatible in a single microorganism and underpins the intimate interactions of methane and sulfur cycles in oxic-anoxic interface environments.

  • A time-resolved multi-omics atlas of Acanthamoeba castellanii encystment.

    Bernard C, Locard-Paulet M, Noël C, Duchateau M, Giai Gianetto Q, Moumen B, Rattei T, Hechard Y, Jensen LJ, Matondo M, Samba-Louaka A
    2022 - Nat Commun, 1: 4104

    Abstract: 

    Encystment is a common stress response of most protists, including free-living amoebae. Cyst formation protects the amoebae from eradication and can increase virulence of the bacteria they harbor. Here, we mapped the global molecular changes that occur in the facultatively pathogenic amoeba Acanthamoeba castellanii during the early steps of the poorly understood process of encystment. By performing transcriptomic, proteomic, and phosphoproteomic experiments during encystment, we identified more than 150,000 previously undescribed transcripts and thousands of protein sequences absent from the reference genome. These results provide molecular details to the regulation of expected biological processes, such as cell proliferation shutdown, and reveal new insights such as a rapid phospho-regulation of sites involved in cytoskeleton remodeling and translation regulation. This work constitutes the first time-resolved molecular atlas of an encysting organism and a useful resource for further investigation of amoebae encystment to allow for a better control of pathogenic amoebae.

  • Bacterial growth in multicellular aggregates leads to the emergence of complex life cycles.

    Schwartzman JA, Ebrahimi A, Chadwick G, Sato Y, Roller BRK, Orphan VJ, Cordero OX
    2022 - Curr Biol, In press
    Picture credit to Julia Schwartzman, MIT

    Abstract: 

    Facultative multicellular behaviors expand the metabolic capacity and physiological resilience of bacteria. Despite their ubiquity in nature, we lack an understanding of how these behaviors emerge from cellular-scale phenomena. Here, we show how the coupling between growth and resource gradient formation leads to the emergence of multicellular lifecycles in a marine bacterium. Under otherwise carbon-limited growth conditions, Vibrio splendidus 12B01 forms clonal multicellular groups to collectively harvest carbon from soluble polymers of the brown-algal polysaccharide alginate. As they grow, groups phenotypically differentiate into two spatially distinct sub-populations: a static "shell" surrounding a motile, carbon-storing "core." Differentiation of these two sub-populations coincides with the formation of a gradient in nitrogen-source availability within clusters. Additionally, we find that populations of cells containing a high proportion of carbon-storing individuals propagate and form new clusters more readily on alginate than do populations with few carbon-storing cells. Together, these results suggest that local metabolic activity and differential partitioning of resources leads to the emergence of reproductive cycles in a facultatively multicellular bacterium.

  • Phage-host coevolution in natural populations.

    Piel D, Bruto M, Labreuche Y, Blanquart F, Goudenège D, Barcia-Cruz R, Chenivesse S, Le Panse S, James A, Dubert J, Petton B, Lieberman E, Wegner KM, Hussain FA, Kauffman KM, Polz MF, Bikard D, Gandon S, Rocha EPC, Le Roux F
    2022 - Nat Microbiol, 7: 1075-1086

    Abstract: 

    Coevolution between bacteriophages (phages) and their bacterial hosts occurs through changes in resistance and counter-resistance mechanisms. To assess phage-host evolution in wild populations, we isolated 195 Vibrio crassostreae strains and 243 vibriophages during a 5-month time series from an oyster farm and combined these isolates with existing V. crassostreae and phage isolates. Cross-infection studies of 81,926 host-phage pairs delineated a modular network where phages are best at infecting co-occurring hosts, indicating local adaptation. Successful propagation of phage is restricted by the ability to adsorb to closely related bacteria and further constrained by strain-specific defence systems. These defences are highly diverse and predominantly located on mobile genetic elements, and multiple defences are active within a single genome. We further show that epigenetic and genomic modifications enable phage to adapt to bacterial defences and alter host range. Our findings reveal that the evolution of bacterial defences and phage counter-defences is underpinned by frequent genetic exchanges with, and between, mobile genetic elements.

  • A nitrite-oxidising bacterium constitutively consumes atmospheric hydrogen

    Leung PM, Daebeler A, Chiri E, Hanchapola I, Gillett DL, Schittenhelm RB, Daims H, Greening C
    2022 - ISME J, 16: 2213-2219

    Abstract: 

    Chemolithoautotrophic nitrite-oxidising bacteria (NOB) of the genus Nitrospira contribute to nitrification in diverse natural environments and engineered systems. Nitrospira are thought to be well-adapted to substrate limitation owing to their high affinity for nitrite and capacity to use alternative energy sources. Here, we demonstrate that the canonical nitrite oxidiser Nitrospira moscoviensis oxidises hydrogen (H2) below atmospheric levels using a high-affinity group 2a nickel-iron hydrogenase [Km(app) = 32 nM]. Atmospheric H2 oxidation occurred under both nitrite-replete and nitrite-deplete conditions, suggesting low-potential electrons derived from H2 oxidation promote nitrite-dependent growth and enable survival during nitrite limitation. Proteomic analyses confirmed the hydrogenase was abundant under both conditions and indicated extensive metabolic changes occur to reduce energy expenditure and growth under nitrite-deplete conditions. Thermodynamic modelling revealed that H2 oxidation theoretically generates higher power yield than nitrite oxidation at low substrate concentrations and significantly contributes to growth at elevated nitrite concentrations. Collectively, this study suggests atmospheric H2 oxidation enhances the growth and survival of NOB amid variability of nitrite supply, extends the phenomenon of atmospheric H2 oxidation to an eighth phylum (Nitrospirota), and reveals unexpected new links between the global hydrogen and nitrogen cycles. Long classified as obligate nitrite oxidisers, our findings suggest H2 may primarily support growth and survival of certain NOB in natural environments.

  • SRS-FISH: A high-throughput platform linking microbiome metabolism to identity at the single-cell level

    Gea X, Pereira FC, Mitteregger M, Berry D, Zhanga M, Hausmann B, Zhange J, Schintlmeister A, Wagner M, Cheng J-X
    2022 - Proc Natl Acad Sci U S A, 119: e2203519119
    Stimulated Raman Spectroscopy

    Abstract: 

    One of the biggest challenges in microbiome research in environmental and medicalsamples is to better understand functional properties of microbial community membersat a single-cell level. Single-cell isotope probing has become a key tool for this purpose,but the current detection methods for determination of isotope incorporation into singlecells do not allow high-throughput analyses. Here, we report on the development of animaging-based approach termed stimulated Raman scattering–two-photon fluorescencein situ hybridization (SRS-FISH) for high-throughput metabolism and identity analysesof microbial communities with single-cell resolution. SRS-FISH offers an imaging speedof 10 to 100 ms per cell, which is two to three orders of magnitude faster than achievableby state-of-the-art methods. Using this technique, we delineated metabolic responses of 30,000 individual cells to various mucosal sugars in the human gut microbiome viaincorporation of deuterium from heavy water as an activity marker. Application of SRS-FISH to investigate the utilization of host-derived nutrients by two major human gutmicrobiome taxa revealed that response to mucosal sugars tends to be dominated byBacteroidales, with an unexpected finding that Clostridia can outperform Bacteroidalesat foraging fucose. With high sensitivity and speed, SRS-FISH will enable researchers toprobe the fine-scale temporal, spatial, and individual activity patterns of microbial cellsin complex communities with unprecedented detail.

  • Early-life chemical exposome and gut microbiome development: African research perspectives within a global environmental health context.

    Ayeni KI, Berry D, Wisgrill L, Warth B, Ezekiel CN
    2022 - Trends Microbiol, 11: 1084-1100

    Abstract: 

    The gut microbiome of neonates, infants, and toddlers (NITs) is very dynamic, and only begins to stabilize towards the third year of life. Within this period, exposure to xenobiotics may perturb the gut environment, thereby driving or contributing to microbial dysbiosis, which may negatively impact health into adulthood. Despite exposure of NITs globally, but especially in Africa, to copious amounts and types of xenobiotics - such as mycotoxins, pesticide residues, and heavy metals - little is known about their influence on the early-life microbiome or their effects on acute or long-term health. Within the African context, the influence of fermented foods, herbal mixtures, and the delivery environment on the early-life microbiome are often neglected, despite being potentially important factors that influence the microbiome. Consequently, data on in-depth understanding of the microbiome-exposome interactions is lacking in African cohorts. Collecting and evaluating such data is important because exposome-induced gut dysbiosis could potentially favor disease progression.

  • Individual Sweet Taste Perception Influences Salivary Characteristics After Orosensory Stimulation With Sucrose and Noncaloric Sweeteners.

    Karl CM, Vidakovic A, Pjevac P, Hausmann B, Schleining G, Ley JP, Berry D, Hans J, Wendelin M, König J, Somoza V, Lieder B
    2022 - Front Nutr, 831726

    Abstract: 

    Emerging evidence points to a major role of salivary flow and viscoelastic properties in taste perception and mouthfeel. It has been proposed that sweet-tasting compounds influence salivary characteristics. However, whether perceived differences in the sensory properties of structurally diverse sweet-tasting compounds contribute to salivary flow and saliva viscoelasticity as part of mouthfeel and overall sweet taste perception remains to be clarified. In this study, we hypothesized that the sensory diversity of sweeteners would differentially change salivary characteristics in response to oral sweet taste stimulation. Therefore, we investigated salivary flow and saliva viscoelasticity from 21 healthy test subjects after orosensory stimulation with sucrose, rebaudioside M (RebM), sucralose, and neohesperidin dihydrochalcone (NHDC) in a crossover design and considered the basal level of selected influencing factors, including the basal oral microbiome. All test compounds enhanced the salivary flow rate by up to 1.51 ± 0.12 g/min for RebM compared to 1.10 ± 0.09 g/min for water within the 1st min after stimulation. The increase in flow rate was moderately correlated with the individually perceived sweet taste ( = 0.3, < 0.01) but did not differ between the test compounds. The complex viscosity of saliva was not affected by the test compounds, but the analysis of covariance showed that it was associated ( < 0.05) with mucin 5B (Muc5B) concentration. The oral microbiome was of typical composition and diversity but was strongly individual-dependent (permutational analysis of variance (PERMANOVA): = 0.76, < 0.001) and was not associated with changes in salivary characteristics. In conclusion, this study indicates an impact of individual sweet taste impressions on the flow rate without measurable changes in the complex viscosity of saliva, which may contribute to the overall taste perception and mouthfeel of sweet-tasting compounds.

  • Elucidating the role of the gut microbiota in the physiological effects of dietary fiber.

    Deehan EC, Zhang Z, Riva A, Armet AM, Perez-Muñoz ME, Nguyen NK, Krysa JA, Seethaler B, Zhao YY, Cole J, Li F, Hausmann B, Spittler A, Nazare JA, Delzenne NM, Curtis JM, Wismer WV, Proctor SD, Bakal JA, Bischoff SC, Knights D, Field CJ, Berry D, Prado CM, Walter J
    2022 - Microbiome, 1: 77

    Abstract: 

    Dietary fiber is an integral part of a healthy diet, but questions remain about the mechanisms that underlie effects and the causal contributions of the gut microbiota. Here, we performed a 6-week exploratory trial in adults with excess weight (BMI: 25-35 kg/m) to compare the effects of a high-dose (females: 25 g/day; males: 35 g/day) supplement of fermentable corn bran arabinoxylan (AX; n = 15) with that of microbiota-non-accessible microcrystalline cellulose (MCC; n = 16). Obesity-related surrogate endpoints and biomarkers of host-microbiome interactions implicated in the pathophysiology of obesity (trimethylamine N-oxide, gut hormones, cytokines, and measures of intestinal barrier integrity) were assessed. We then determined whether clinical outcomes could be predicted by fecal microbiota features or mechanistic biomarkers.
    AX enhanced satiety after a meal and decreased homeostatic model assessment of insulin resistance (HOMA-IR), while MCC reduced tumor necrosis factor-α and fecal calprotectin. Machine learning models determined that effects on satiety could be predicted by fecal bacterial taxa that utilized AX, as identified by bioorthogonal non-canonical amino acid tagging. Reductions in HOMA-IR and calprotectin were associated with shifts in fecal bile acids, but correlations were negative, suggesting that the benefits of fiber may not be mediated by their effects on bile acid pools. Biomarkers of host-microbiome interactions often linked to bacterial metabolites derived from fiber fermentation (short-chain fatty acids) were not affected by AX supplementation when compared to non-accessible MCC.
    This study demonstrates the efficacy of purified dietary fibers when used as supplements and suggests that satietogenic effects of AX may be linked to bacterial taxa that ferment the fiber or utilize breakdown products. Other effects are likely microbiome independent. The findings provide a basis for fiber-type specific therapeutic applications and their personalization.
    Clinicaltrials.gov, NCT02322112 , registered on July 3, 2015. Video Abstract.

  • Next-generation biomonitoring of the early-life chemical exposome in neonatal and infant development.

    Jamnik T, Flasch M, Braun D, Fareed Y, Wasinger D, Seki D, Berry D, Berger A, Wisgrill L, Warth B
    2022 - Nat Commun, 1: 2653

    Abstract: 

    Exposure to synthetic and natural chemicals is a major environmental risk factor in the etiology of many chronic diseases. Investigating complex co-exposures is necessary for a holistic assessment in exposome-wide association studies. In this work, a sensitive liquid chromatography-tandem mass spectrometry approach was developed and validated. The assay enables the analysis of more than 80 highly-diverse xenobiotics in urine, serum/plasma, and breast milk; with detection limits generally in the pg-ng mL range. In plasma of extremely-premature infants, 27 xenobiotics are identified; including contamination with plasticizers, perfluorinated alkylated substances and parabens. In breast milk samples collected longitudinally over the first 211 days post-partum, 29 analytes are detected, including pyrrolizidine- and tropane alkaloids which have not been identified in this matrix before. A preliminary estimation of daily toxicant intake via breast milk is conducted. In conclusion, we observe significant early-life co-exposure to multiple toxicants, and demonstrate the method's applicability for large-scale exposomics-type cohort studies.

  • Differential Modulation of the European Sea Bass Gut Microbiota by Distinct Insect Meals.

    Rangel F, Enes P, Gasco L, Gai F, Hausmann B, Berry D, Oliva-Teles A, Serra CR, Pereira FC
    2022 - Front Microbiol, 831034

    Abstract: 

    The aquaculture industry is one of the fastest-growing sectors in animal food production. However, farming of carnivorous fish strongly relies on the use of wild fish-based meals, a practice that is environmentally and economically unsustainable. Insect-based diets constitute a strong candidate for fishmeal substitution, due to their high nutritional value and low environmental footprint. Nevertheless, data on the impact of insect meal (IM) on the gut microbiome of farmed fish are so far inconclusive, and very scarce in what concerns modulation of microbial-mediated functions. Here we use high-throughput 16S rRNA gene amplicon sequencing and quantitative PCR to evaluate the impact of different IMs on the composition and chitinolytic potential of the European sea bass gut digesta- and mucosa-associated communities. Our results show that insect-based diets of distinct origins differently impact the gut microbiota of the European sea bass (). We detected clear modulatory effects of IM on the gut microbiota, which were more pronounced in the digesta, where communities differed considerably among the diets tested. Major community shifts were associated with the use of black soldier fly larvae (, HM) and pupal exuviae (HEM) feeds and were characterized by an increase in the relative abundance of the Firmicutes families , , and and the Actinobacteria family , which all include taxa considered beneficial for fish health. Modulation of the digesta community by HEM was characterized by a sharp increase in and a decrease of several Gammaproteobacteria and Bacteroidota members. In turn, a mealworm larvae-based diet (, TM) had only a modest impact on microbiota composition. Further, using quantitative PCR, we demonstrate that shifts induced by HEM were accompanied by an increase in copy number of chitinase ChiA-encoding genes, predominantly originating from species with effective chitinolytic activity. Our study reveals an HEM-driven increase in chitin-degrading taxa and associated chitinolytic activity, uncovering potential benefits of adopting exuviae-supplemented diets, a waste product of insect rearing, as a functional ingredient.

  • Individuality of the Extremely Premature Infant Gut Microbiota Is Driven by Ecological Drift.

    Seki D, Schauberger C, Hausmann B, Berger A, Wisgrill L, Berry D
    2022 - mSystems, e0016322

    Abstract: 

    The initial contact between humans and their colonizing gut microbiota after birth is thought to have expansive and long-lasting consequences for physiology and health. Premature infants are at high risk of suffering from lifelong impairments, due in part to aberrant development of gut microbiota that can contribute to early-life infections and inflammation. Despite their importance to health, the ecological assembly and succession processes governing gut microbiome composition in premature infants remained incompletely understood. Here, we quantified these ecological processes in a spatiotemporally resolved 16S rRNA gene amplicon sequencing data set of 60 extremely premature neonates using an established mathematical framework. We found that gut colonization during the first months of life is predominantly stochastic, whereby interindividual diversification of microbiota is driven by ecological drift. Dispersal limitations are initially small but have increasing influence at later stages of succession. Furthermore, we find similar trends in a cohort of 32 healthy term-born infants. These results suggest that the uniqueness of individual gut microbiota of extremely premature infants is largely due to stochastic assembly. Our knowledge concerning the initial gut microbiome assembly in human neonates is limited, and scientific progression in this interdisciplinary field is hindered due to the individuality in composition of gut microbiota. Our study addresses the ecological processes that result in the observed individuality of microbes in the gastrointestinal tract between extremely premature and term-born infants. We find that initial assembly is mainly driven by neutral ecological processes. Interestingly, while this progression is predominantly random, limitations to the dispersal of microbiota between infants become increasingly important with age and are concomitant features of gut microbiome stability. This indicates that while we cannot predict gut microbiota assembly due to its random nature, we can expect the establishment of certain ecological features that are highly relevant for neonatal health.

  • Down-regulation of the bacterial protein biosynthesis machinery in response to weeks, years, and decades of soil warming

    Söllinger A, Séneca J, Dahl MB, Motleleng LL, Prommer J, Verbruggen E, Sigurdsson BD, Janssens I, Schiestl RH, Urich T, Richter A, Tveit AT
    2022 - Science Advances, 12: eabm3230

    Abstract: 

    How soil microorganisms respond to global warming is key to infer future soil-climate feedbacks, yet poorly understood. Here, we applied metatranscriptomics to investigate microbial physiological responses to medium-term (8 years) and long-term (>50 years) subarctic grassland soil warming of +6°C. Besides indications for a community-wide up-regulation of centralmetabolic pathways and cell replication, we observed a down-regulation of the bacterial protein biosynthesis machinery in the warmed soils, coinciding with a lower microbial biomass, RNA, and soil substrate content. We conclude that permanently accelerated reaction rates at higher temperatures and reduced substrate concentrations result in cellular reduction of ribosomes, the macromolecular complexes carrying out protein biosynthesis. Later efforts to test this, including a short-term warming experiment (6 weeks, +6°C), further supported our conclusion. Down-regulating the protein biosynthesis machinery liberates energy and matter, allowing soil bacteria to maintain high metabolic activities and cell division rates even after decades of warming.

  • Ecological Processes Shaping Microbiomes of Extremely Low Birthweight Infants.

    Zioutis C, Seki D, Bauchinger F, Herbold C, Berger A, Wisgrill L, Berry D
    2022 - Front Microbiol, 812136

    Abstract: 

    The human microbiome has been implicated in affecting health outcomes in premature infants, but the ecological processes governing early life microbiome assembly remain poorly understood. Here, we investigated microbial community assembly and dynamics in extremely low birth weight infants (ELBWI) over the first 2 weeks of life. We profiled the gut, oral cavity and skin microbiomes over time using 16S rRNA gene amplicon sequencing and evaluated the ecological forces shaping these microbiomes. Though microbiomes at all three body sites were characterized by compositional instability over time and had low body-site specificity (PERMANOVA, = 0.09, = 0.001), they could nonetheless be clustered into four discrete community states. Despite the volatility of these communities, deterministic assembly processes were detectable in this period of initial microbial colonization. To further explore these deterministic dynamics, we developed a probabilistic approach in which we modeled microbiome state transitions in each ELBWI as a Markov process, or a "memoryless" shift, from one community state to another. This analysis revealed that microbiomes from different body sites had distinctive dynamics as well as characteristic equilibrium frequencies. Time-resolved microbiome sampling of premature infants may help to refine and inform clinical practices. Additionally, this work provides an analysis framework for microbial community dynamics based on Markov modeling that can facilitate new insights, not only into neonatal microbiomes but also other human-associated or environmental microbiomes.

  • The novel genus, 'Candidatus Phosphoribacter', previously identified as Tetrasphaera, is the dominant polyphosphate accumulating lineage in EBPR wastewater treatment plants worldwide.

    Singleton CM, Petriglieri F, Wasmund K, Nierychlo M, Kondrotaite Z, Petersen JF, Peces M, Dueholm MS, Wagner M, Nielsen PH
    2022 - ISME J, 6: 1605-1616
    Phosphoribacter

    Abstract: 

    The bacterial genus Tetrasphaera encompasses abundant polyphosphate accumulating organisms (PAOs) that are responsible for enhanced biological phosphorus removal (EBPR) in wastewater treatment plants. Recent analyses of genomes from pure cultures revealed that 16S rRNA genes cannot resolve the lineage, and that Tetrasphaera spp. are from several different genera within the Dermatophilaceae. Here, we examine 14 recently recovered high-quality metagenome-assembled genomes from wastewater treatment plants containing full-length 16S rRNA genes identified as Tetrasphaera, 11 of which belong to the uncultured Tetrasphaera clade 3. We find that this clade represents two distinct genera, named here Ca. Phosphoribacter and Ca. Lutibacillus, and reveal that the widely used model organism Tetrasphaera elongata is less relevant for physiological predictions of this uncultured group. Ca. Phosphoribacter incorporates species diversity unresolved at the 16S rRNA gene level, with the two most abundant and often co-occurring species encoding identical V1-V3 16S rRNA gene amplicon sequence variants but different metabolic capabilities, and possibly, niches. Both Ca. P. hodrii and Ca. P. baldrii were visualised using fluorescence in situ hybridisation (FISH), and PAO capabilities were confirmed with FISH-Raman microspectroscopy and phosphate cycling experiments. Ca. Phosphoribacter represents the most abundant former Tetrasphaera lineage and PAO in EPBR systems in Denmark and globally.

  • Persistence of the antagonistic effects of a natural mixture of Alternaria mycotoxins on the estrogen-like activity of human feces after anaerobic incubation.

    Crudo F, Aichinger G, Dellafiora L, Kiss E, Mihajlovic J, Del Favero G, Berry D, Dall'Asta C, Marko D
    2022 - Toxicol Lett, 88-99

    Abstract: 

    Several Alternaria mycotoxins are believed to act as endocrine disruptive chemicals (EDCs), since they are reported to bind estrogen receptors in several experimental models. After ingestion of contaminated food commodities, the mycotoxins reach the intestine, where they come into direct contact with food constituents as well as the gut microbiota. Thus, the aim of the present work was to evaluate the modulatory potential of a complex extract of cultured Alternaria fungi (CE; containing eleven chemically characterized compounds) on the estrogenic signaling cascade of mammalian cells before and after anaerobic incubation with fecal slurries, in order to simulate an in vivo-like condition in the gut. Assessing alkaline phosphatase expression in Ishikawa cells as a measure for estrogenicity, we found the CE to partially quench the intrinsic estrogenic properties of fecal slurries and fecal waters, even after 3 h of fecal incubation. Investigation of the mechanisms underlying the effects observed carried out through an in vitro/in silico approach revealed the ability of the extract to decrease the ERα/ERβ nuclear ratio, while a possible action of the mycotoxins as ER-antagonists was excluded. Our results suggest that Alternaria mycotoxins might act as EDCs in vivo, and warrant further investigation in animal models.

  • Plant phosphorus-use and -acquisition strategies in Amazonia

    Reichert T, Rammig A, Fuchslueger L, Lugli LF, Quesada CA, Fleischer K
    2022 - New Phytologist, 234: 1126-1143

    Abstract: 

    In the tropical rainforest of Amazonia, phosphorus (P) is one of the main nutrients controlling forest dynamics, but its effects on the future of the forest biomass carbon (C) storage under elevated atmospheric CO2 concentrations remain uncertain. Soils in vast areas of Amazonia are P-impoverished, and little is known about the variation or plasticity in plant P-use and -acquisition strategies across space and time, hampering the accuracy of projections in vegetation models. Here, we synthesize current knowledge of leaf P resorption, fine-root P foraging, arbuscular mycorrhizal symbioses, and root acid phosphatase and organic acid exudation and discuss how these strategies vary with soil P concentrations and in response to elevated atmospheric CO2. We identify knowledge gaps and suggest ways forward to fill those gaps. Additionally, we propose a conceptual framework for the variations in plant P-use and -acquisition strategies along soil P gradients of Amazonia. We suggest that in soils with intermediate to high P concentrations, at the plant community level, investments are primarily directed to P foraging strategies via roots and arbuscular mycorrhizas, whereas in soils with intermediate to low P concentrations, investments shift to prioritize leaf P resorption and mining strategies via phosphatases and organic acids.

  • Resolving the structure of phage-bacteria interactions in the context of natural diversity.

    Kauffman KM, Chang WK, Brown JM, Hussain FA, Yang J, Polz MF, Kelly L
    2022 - Nat Commun, 1: 372

    Abstract: 

    Microbial communities are shaped by viral predators. Yet, resolving which viruses (phages) and bacteria are interacting is a major challenge in the context of natural levels of microbial diversity. Thus, fundamental features of how phage-bacteria interactions are structured and evolve in the wild remain poorly resolved. Here we use large-scale isolation of environmental marine Vibrio bacteria and their phages to obtain estimates of strain-level phage predator loads, and use all-by-all host range assays to discover how phage and host genomic diversity shape interactions. We show that lytic interactions in environmental interaction networks (as observed in agar overlay) are sparse-with phage predator loads being low for most bacterial strains, and phages being host-strain-specific. Paradoxically, we also find that although overlap in killing is generally rare between tailed phages, recombination is common. Together, these results suggest that recombination during cryptic co-infections is an important mode of phage evolution in microbial communities. In the development of phages for bioengineering and therapeutics it is important to consider that nucleic acids of introduced phages may spread into local phage populations through recombination, and that the likelihood of transfer is not predictable based on lytic host range.

  • The life cycle-dependent transcriptional profile of the obligate intracellular amoeba symbiont Amoebophilus asiaticus.

    Selberherr E, Penz T, König L, Conrady B, Siegl A, Horn M, Schmitz-Esser S
    2022 - FEMS Microbiol Ecol, in press

    Abstract: 

    Free-living amoebae often harbor obligate intracellular bacterial symbionts. Amoebophilus (A.) asiaticus is a representative of a lineage of amoeba symbionts in the phylum Bacteroidota. Here, we analyze the transcriptome of A. asiaticus strain 5a2 at four time points during its infection cycle and replication within the Acanthamoeba host using RNA sequencing. Our results reveal a dynamic transcriptional landscape throughout different A. asiaticus life cycle stages. Many intracellular bacteria and pathogens utilize eukaryotic-like proteins (ELPs) for host cell interaction and the A. asiaticus 5a2 genome shows a particularly high abundance of ELPs. We show the expression of all genes encoding ELPs and found many ELPs to be differentially expressed. At the replicative stage of A. asiaticus, ankyrin repeat proteins and tetratricopeptide/Sel1-like repeat proteins were upregulated. At the later time points, high expression levels of a type 6 secretion system that likely prepares for a new infection cycle after lysing its host, were found. This study reveals comprehensive insights into the intracellular lifestyle of A. asiaticus and highlights candidate genes for host cell interaction. The results from this study have implications for other intracellular bacteria such as other amoeba-associated bacteria and the arthropod symbionts forming the sister lineage of A. asiaticus.

  • Genus-specific carbon fixation activity measurements reveal distinct responses to oxygen among hydrothermal vent Campylobacteria

    McNichol J, Dyksma S, Greuter L, Seewald JS, Sylva SP, Sievert SM
    2022 - Appl Environ Microbiol, 2: e0208321

    Abstract: 

    Molecular surveys of low temperature deep-sea hydrothermal vent fluids have shown that Campylobacteria (previously Epsilonproteobacteria) often dominate the microbial community and that three genera, ArcobacterSulfurimonas, and Sulfurovum, frequently coexist. In this study, we used replicated radiocarbon incubations of deep-sea hydrothermal fluids to investigate activity of each genus under three experimental conditions. To quantify genus-specific radiocarbon incorporation, we used newly designed oligonucleotide probes for ArcobacterSulfurimonas, and Sulfurovum to quantify their activity using catalyzed-reporter deposition fluorescence in situhybridization (CARD-FISH) combined with fluorescence-activated cell sorting. All three genera actively fixed CO2 in short-term (∼ 20 h) incubations, but responded differently to the additions of nitrate and oxygen. Oxygen additions had the largest effect on community composition, and caused a pronounced shift in community composition at the amplicon sequence variant (ASV) level after only 20 h of incubation. The effect of oxygen on carbon fixation rates appeared to depend on the initial starting community. The presented results support the hypothesis that these chemoautotrophic genera possess functionally redundant core metabolic capabilities, but also reveal finer-scale differences in growth likely reflecting adaptation of physiologically-distinct phylotypes to varying oxygen concentrations in situ. Overall, our study provides new insights into how oxygen controls community composition and total chemoautotrophic activity, and underscores how quickly deep-sea vent microbial communities respond to disturbances. IMPORTANCE Sulfidic environments worldwide are often dominated by sulfur-oxidizing, carbon-fixing Campylobacteria. Environmental factors associated with this group's dominance are now understood, but far less is known about the ecology and physiology of members of subgroups of chemoautotrophic Campylobacteria. In this study, we used a novel method to differentiate the genus-specific chemoautotrophic activity of three subtypes of Campylobacteria. In combination with evidence from microscopic counts, chemical consumption/production during incubations, and DNA-based measurements, our data show that oxygen concentration affects both community composition and chemoautotrophic function in situ. These results help us better understand factors controlling microbial diversity at deep-sea hydrothermal vents, and provide first-order insights into the ecophysiological differences between these distinct microbial taxa.

  • Lipid synthesis at the trophic base as the source for energy management to build complex structures.

    Schnorr SL, Berry D
    2022 - Curr Opin Biotechnol, 364-373

    Abstract: 

    The review explores the ecological basis for bacterial lipid metabolism in marine and terrestrial ecosystems. We discuss ecosystem stressors that provoked early organisms to modify their lipid membrane structures, and where these stressors are found across a variety of environments. A major role of lipid membranes is to manage cellular energy utility, including how energy is used for signal propagation. As different environments are imbued with properties that necessitate variation in energy regulation, bacterial lipid synthesis has undergone incalculable permutations of functional trial and error. This may hold clues for how biotechnology can improvise a short-hand version of the evolutionary gauntlet to stimulate latent functional competences for the synthesis of rare lipids. Reducing human reliance on marine resources and deriving solutions for production of essential nutrients is a pressing problem in sustainable agriculture and aquaculture, as well as timely considering the increasing fragility of human health in an aging population.

  • The role of coupled DNRA-Anammox during nitrate removal in a highly saline lake

    Valiente N, Jirsa F, Hein T, Wanek W, Prommer J, Bonin P, Gómez-Alday JJ
    2022 - Science of The Total Environment, 806: Article 150726

    Abstract: 

    Nitrate (NO3) removal from aquatic ecosystems involves several microbially mediated processes, including denitrification, dissimilatory nitrate reduction to ammonium (DNRA), and anaerobic ammonium oxidation (anammox), controlled by slight changes in environmental gradients. In addition, some of these processes (i.e. denitrification) may involve the production of undesirable compounds such as nitrous oxide (N2O), an important greenhouse gas. Saline lakes are prone to the accumulation of anthropogenic contaminants, making them highly vulnerable environments to NO3 pollution. The aim of this paper was to investigate the effect of light and oxygen on the different NO3 removal pathways under highly saline conditions. For this purpose, mesocosm experiments were performed using lacustrine, undisturbed, organic-rich sediments from the Pétrola Lake (Spain), a highly saline waterbody subject to anthropogenic NO3 pollution. The revised 15N-isotope pairing technique (15N-IPT) was used to determine NO3 sink processes. Our results demonstrate for the first time the coexistence of denitrification, DNRA, and anammox processes in a highly saline lake, and how their contribution was determined by environmental conditions (oxygen and light). DNRA, and especially denitrification to N2O, were the dominant nitrogen (N) removal pathways when oxygen and/or light were present (up to 82%). In contrast, anoxia and darkness promoted NO3 reduction by DNRA (52%), combined with N loss by anammox (28%). Our results highlight the role of coupled DNRA-anammox, which has not yet been investigated in lacustrine sediments. We conclude that anoxia and darkness favored DNRA and anammox processes over denitrification and therefore to restrict N2O emissions to the atmosphere.

  • Ammonia-oxidizing archaea possess a wide range of cellular ammonia affinities.

    Jung MY, Sedlacek CJ, Kits KD, Mueller AJ, Rhee SK, Hink L, Nicol GW, Bayer B, Lehtovirta-Morley L, Wright C, De La Torre JR, Herbold CW, Pjevac P, Daims H, Wagner M
    2022 - ISME J, 16: 272-283
    Kinetics of nitrifiers

    Abstract: 

    Nitrification, the oxidation of ammonia to nitrate, is an essential process in the biogeochemical nitrogen cycle. The first step of nitrification, ammonia oxidation, is performed by three, often co-occurring guilds of chemolithoautotrophs: ammonia-oxidizing bacteria (AOB), archaea (AOA), and complete ammonia oxidizers (comammox). Substrate kinetics are considered to be a major niche-differentiating factor between these guilds, but few AOA strains have been kinetically characterized. Here, the ammonia oxidation kinetic properties of 12 AOA representing all major cultivated phylogenetic lineages were determined using microrespirometry. Members of the genus Nitrosocosmicus have the lowest affinity for both ammonia and total ammonium of any characterized AOA, and these values are similar to previously determined ammonia and total ammonium affinities of AOB. This contrasts previous assumptions that all AOA possess much higher substrate affinities than their comammox or AOB counterparts. The substrate affinity of ammonia oxidizers correlated with their cell surface area to volume ratios. In addition, kinetic measurements across a range of pH values supports the hypothesis that-like for AOB-ammonia and not ammonium is the substrate for the ammonia monooxygenase enzyme of AOA and comammox. Together, these data will facilitate predictions and interpretation of ammonia oxidizer community structures and provide a robust basis for establishing testable hypotheses on competition between AOB, AOA, and comammox.

  • Evolutionarily recent dual obligatory symbiosis among adelgids indicates a transition between fungus- and insect-associated lifestyles.

    Szabó G, Schulz F, Manzano-Marín A, Toenshoff ER, Horn M
    2022 - ISME J, 1: 247-256

    Abstract: 

    Adelgids (Insecta: Hemiptera: Adelgidae) form a small group of insects but harbor a surprisingly diverse set of bacteriocyte-associated endosymbionts, which suggest multiple replacement and acquisition of symbionts over evolutionary time. Specific pairs of symbionts have been associated with adelgid lineages specialized on different secondary host conifers. Using a metagenomic approach, we investigated the symbiosis of the Adelges laricis/Adelges tardus species complex containing betaproteobacterial ("Candidatus Vallotia tarda") and gammaproteobacterial ("Candidatus Profftia tarda") symbionts. Genomic characteristics and metabolic pathway reconstructions revealed that Vallotia and Profftia are evolutionary young endosymbionts, which complement each other's role in essential amino acid production. Phylogenomic analyses and a high level of genomic synteny indicate an origin of the betaproteobacterial symbiont from endosymbionts of Rhizopus fungi. This evolutionary transition was accompanied with substantial loss of functions related to transcription regulation, secondary metabolite production, bacterial defense mechanisms, host infection, and manipulation. The transition from fungus to insect endosymbionts extends our current framework about evolutionary trajectories of host-associated microbes.

Book chapters and other publications

1 Publication found
  • Editorial: Acidobacteriota-Towards unraveling the secrets of a widespread though enigmatic phylum

    Huber KJ, Pester M, Eichorst SA, Navarrete AA, Fösel BU
    2022 - Front Microbiol., 13: 960602
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