Metamenu

Publications

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Publications in peer reviewed journals

33 Publications found
  • Lability classification of soil organic matter in the northern permafrost region

    Kuhry P, Barta J, Blok D, Elberling B, Faucherre S, Hugelius G, Jørgensen C J, Richter A, Santruckova H, Weiss N
    2020 - Biogeosciences, 17: 361-379

    Abstract: 

    The large stocks of soil organic carbon (SOC) in soils and deposits of the northern permafrost region are sensitive to global warming and permafrost thawing. The potential release of this carbon (C) as greenhouse gases to the atmosphere does not only depend on the total quantity of soil organic matter (SOM) affected by warming and thawing, but it also depends on its lability (i.e., the rate at which it will decay). In this study we develop a simple and robust classification scheme of SOM lability for the main types of soils and deposits in the northern permafrost region. The classification is based on widely available soil geochemical parameters and landscape unit classes, which makes it useful for upscaling to the entire northern permafrost region. We have analyzed the relationship between C content and C-CO2 production rates of soil samples in two different types of laboratory incubation experiments. In one experiment, ca. 240 soil samples from four study areas were incubated using the same protocol (at 5 C, aerobically) over a period of 1 year. Here we present C release rates measured on day 343 of incubation. These long-term results are compared to those obtained from short-term incubations of ca. 1000 samples (at 12 C, aerobically) from an additional three study areas. In these experiments, C-CO2 production rates were measured over the first 4 d of incubation. We have focused our analyses on the relationship between C-CO2 production per gram dry weight per day (µgC-CO2 gdw−1 d−1) and C content (%C of dry weight) in the samples, but we show that relationships are consistent when using C ∕ N ratios or different production units such as µgC per gram soil C per day (µgC-CO2 gC−1 d−1) or per cm3 of soil per day (µgC-CO2 cm−3 d−1). C content of the samples is positively correlated to C-CO2 production rates but explains less than 50 % of the observed variability when the full datasets are considered. A partitioning of the data into landscape units greatly reduces variance and provides consistent results between incubation experiments. These results indicate that relative SOM lability decreases in the order of Late Holocene eolian deposits to alluvial deposits and mineral soils (including peaty wetlands) to Pleistocene yedoma deposits to C-enriched pockets in cryoturbated soils to peat deposits. Thus, three of the most important SOC storage classes in the northern permafrost region (yedoma, cryoturbated soils and peatlands) show low relative SOM lability. Previous research has suggested that SOM in these pools is relatively undecomposed, and the reasons for the observed low rates of decomposition in our experiments need urgent attention if we want to better constrain the magnitude of the thawing permafrost carbon feedback on global warming.

  • Deep Learning Neural Network Approach for Predicting the Sorption of Ionizable and Polar Organic Pollutants to a Wide Range of Carbonaceous Materials

    Gabriel Sigmund, Mehdi Gharasoo, Thorsten Hüffer, Thilo Hofmann
    2020 - Environmental Science & Technology, 54: 4583-4591

    Abstract: 

    Most contaminants of emerging concern are polar and/or ionizable organic compounds, whose removal from engineered and environmental systems is difficult. Carbonaceous sorbents include activated carbon, biochar, fullerenes, and carbon nanotubes, with applications such as drinking water filtration, wastewater treatment, and contaminant remediation. Tools for predicting sorption of many emerging contaminants to these sorbents are lacking because existing models were developed for neutral compounds. A method to select the appropriate sorbent for a given contaminant based on the ability to predict sorption is required by researchers and practitioners alike. Here, we present a widely applicable deep learning neural network approach that excellently predicted the conventionally used Freundlich isotherm fitting parameters log KF and n (R2 > 0.98 for log KF, and R2 > 0.91 for n). The neural network models are based on parameters generally available for carbonaceous sorbents and/or parameters freely available from online databases. A freely accessible graphical user interface is provided.

  • A systemic overreaction to years versus decades of warming in a subarctic grassland ecosystem

    Walker TWN, Janssens IA, Weedon JT, Sigurdsson BD, Richter A, Peñuelas J, Leblans NI Bahn M, Bartrons M, De Jonge C, Fuchslueger L, Gargallo-Garriga A, Gunnarsdóttir GE, Marañon-Jimenez S, Oddsdóttir ES, Ostonen I, Poeplau C, Prommer J, Radujković D, Sardans J, Sigurðsson P, Soong JL, Vicca S, Wallander H, Ilieva-Makulec K, Verbruggen E
    2020 - Nature Ecology & Evolution, 4: 101-108

    Abstract: 

    Temperature governs most biotic processes, yet we know little about how warming affects whole ecosystems. Here we examined the responses of 128 components of a subarctic grassland to either 5–8 or >50 years of soil warming. Warming of >50 years drove the ecosystem to a new steady state possessing a distinct biotic composition and reduced species richness, biomass and soil organic matter. However, the warmed state was preceded by an overreaction to warming, which was related to organism physiology and was evident after 5–8 years. Ignoring this overreaction yielded errors of >100% for 83 variables when predicting their responses to a realistic warming scenario of 1 °C over 50 years, although some, including soil carbon content, remained stable after 5–8 years. This study challenges long-term ecosystem predictions made from short-term observations, and provides a framework for characterization of ecosystem responses to sustained climate change.

  • Redox Heterogeneities Promote Thioarsenate Formation and Release into Groundwater from Low Arsenic Sediments

    Naresh Kumar, Vincent Noël, Britta Planer-Friedrich, Johannes BesoldJ, uan Lezama-Pacheco, John R. Bargar, Gordon E. Brown Jr., Scott Fendorf, Kristin Boye
    2020 - Environmental Science & Technology, in press

    Abstract: 

    Groundwater contamination by As from natural and anthropogenic sources is a worldwide concern. Redox heterogeneities over space and time are common and can influence the molecular-level speciation of As, and thus, As release/retention but are largely unexplored. Here, we present results from a dual-domain column experiment, with natural organic-rich, fine-grained, and sulfidic sediments embedded as lenses (referred to as “reducing lenses”) within natural aquifer sand. We show that redox interfaces in sulfur-rich, alkaline aquifers may release concerning levels of As, even when sediment As concentration is low (<2 mg/kg), due to the formation of mobile thioarsenates at aqueous sulfide/Fe molar ratios <1. In our experiments, this behavior occurred in the aquifer sand between reducing lenses and was attributed to the spreading of sulfidic conditions and subsequent Fe reductive dissolution. In contrast, inside reducing lenses (and some locations in the aquifer) the aqueous sulfide/Fe molar ratios exceeded 1 and aqueous sulfide/As molar ratios exceeded 100, which partitioned As(III)–S to the solid phase (associated with organics or as realgar (As4S4)). These results highlight the importance of thioarsenates in natural sediments and indicate that redox interfaces and sediment heterogeneities could locally degrade groundwater quality, even in aquifers with unconcerning solid-phase As concentrations.

  • Copper limiting threshold in the terrestrial ammonia oxidizing archaeon Nitrososphaera viennensis

    Carolina Reyes, Logan H.Hodgskiss, Oliver Baars, Melina Kerou, Barbara Bayer, Christa Schleper, Stephan M Kraemer
    2020 - Research in microbiology, in press

    Abstract: 

    Ammonia oxidizing archaea (AOA) inhabiting soils have a central role in the global nitrogen cycle. Copper (Cu) is central to many enzymes in AOA including ammonia monooxygenase (AMO), the enzyme involved in the first step of ammonia oxidation. This study explored the physiological response of the AOA soil isolate, Nitrososphaera viennensis (EN76T) to Cu-limiting conditions in order to approach its limiting threshold under laboratory conditions. The chelator TETA (1,4,8,11-tetraazacyclotetradecane N, N′, N″, N‴-tetraacetic acid hydrochloride hydrate) with selective affinity for Cu2+ was used to lower bioavailable Cu2+ in culture experiments as predicted by thermodynamic speciation calculations. Results show that N. viennensis is Cu-limited at concentrations ≤10−15 mol L−1 free Cu2+ compared to standard conditions (10−12 mol L−1). This Cu2+ limiting threshold is similar to pure cultures of denitrifying bacteria and other AOA and AOB inhabiting soils, freshwaters and sewage (<10−16 mol L−1), and lower than pure cultures of the marine AOA Nitrosopumilus maritimus (<10−12.7 mol L−1), which also possesses a high amount of Cu-dependent enzymes.

  • Intra-laboratory assessment of a method for the detection of TiO2 nanoparticles present in sunscreens based on multi-detector asymmetrical flow field-flow fractionation

    Milica Velimirovic, Stephan Wagner, Robert Koeber, Thilo Hofmann, Frank von der Kammer
    2020 - NanoImpact, 19: 100233

    Abstract: 

    In this study, an intra-laboratory assessment was carried out to establish the effectiveness of a method for the detection of TiO2 engineered nanoparticles (ENPs) present in sunscreen containing nano-scale TiO2 and a higher nanometer-range (approx. 200–500 nm) TiO2, as well as iron oxide particles. Three replicate measurements were performed on five separate days to generate the measurement uncertainties associated with the quantitative asymmetrical flow field-flow fractionation (AF4) measurement of the hydrodynamic radius rh,mode1 (MALS), rh,mode1 (ICP-MS), rh,mode2 (ICP-MS), and calculated mass-based particle size distribution (d10, d50, d90). The validation study demonstrates that the analysis of TiO2 ENPs present in sunscreen by AF4 separation-multi detection produces quantitative data (mass-based particle size distribution) after applying the sample preparation method developed within the NanoDefine project with uncertainties based on the precision (uIP) of 3.9–8.8%. This method can, therefore, be considered as the method with a good precision. Finally, the bias data shows that the trueness of the method (ut = 5.5–52%) can only be taken as a proxy due to the lack of a sunscreen standard containing certified TiO2 ENPs.

  • Harmonizing across environmental nanomaterial testing media for increased comparability of nanomaterial datasets

    Nicholas K. Geitner, Christine Ogilvie Hendren, Geert Cornelis, Ralf Kaegi, Jamie R. Lead, Gregory V. Lowry, Iseult Lynch, Bernd Nowack, Elijah Petersen, Emily Bernhardt, Scott Brown, Wei Chen, Camille de Garidel-Thoron, Jaydee Hanson, Stacey Harper, Kim Jones, Frank von der Kammer, Alan Kennedy, Justin Kidd, Cole Matson, Chris D. Metcalfe, Joel Pedersen, Willie J. G. M. Peijnenburg, Joris T. K. Quik, Sónia M. Rodrigues, Jerome Rose, Phil Sayre, Marie Simonin, Claus Svendsen, Robert Tanguay, Nathalie Tefenkji, Tom van Teunenbroek, Gregory Thies, Yuan Tian, Jacelyn Rice, Amalia Turner, Jie Liu, Jason Unrine, Marina Vance, Jason C. White, Mark R. Wiesner
    2020 - Environmental Science: Nano, 7: 13-36

    Abstract: 

    The chemical composition and properties of environmental media determine nanomaterial (NM) transport, fate, biouptake, and organism response. To compare and interpret experimental data, it is essential that sufficient context be provided for describing the physical and chemical characteristics of the setting in which a nanomaterial may be present. While the nanomaterial environmental, health and safety (NanoEHS) field has begun harmonization to allow data comparison and re-use (e.g. using standardized materials, defining a minimum set of required material characterizations), there is limited guidance for standardizing test media. Since most of the NM properties driving environmental behaviour and toxicity are medium-dependent, harmonization of media is critical. A workshop in March 2016 at Duke University identified five categories of test media: aquatic testing media, soil and sediment testing media, biological testing media, engineered systems testing media and product matrix testing media. For each category of test media, a minimum set of medium characteristics to report in all NM tests is recommended. Definitions and detail level of the recommendations for specific standardized media vary across these media categories. This reflects the variation in the maturity of their use as a test medium and associated measurement techniques, variation in utility and relevance of standardizing medium properties, ability to simplify standardizing reporting requirements, and in the availability of established standard reference media. Adoption of these media harmonization recommendations will facilitate the generation of integrated comparable datasets on NM fate and effects. This will in turn allow testing of the predictive utility of functional assay measurements on NMs in relevant media, support investigation of first principles approaches to understand behavioral mechanisms, and support categorization strategies to guide research, commercial development, and policy.

  • Remediation of fluoride contaminated water using encapsulated active growing blue-green algae, Phormidium sp.

    Yamini Mittal, Pratiksha Srivastav, Naresh Kumar, Asheesh KumarYadav
    2020 - Environmental Technology and Innovation, in press

    Abstract: 

    Elevated fluoride concentration in drinking water is a global concern that impacts health of millions. Developing low cost remediation methods empower communities with fewer resources available to protect their health.

    Together with colleagues from CSIR India, and University of Tasmania in Australia, we have demonstrated that fluoride can be removed by using common blue-green algae, Phormidium sp. Using Response Surface Methodology (RSM) we were able to optimize parameters for the highest fluoride removal in our system. Further work is currently ongoing on process optimization to develop a household level pilot scale experimental reactor in a small village in eastern India.

  • Direct measurement of the in situ decomposition of microbial-derived soil organic matter

    Hu Y, Zheng Q, Noll L, zhang S, Wanek W
    2020 - Soil Biology and Biochemistry, 141: Article 107660

    Abstract: 

    Soil organic matter (SOM) is the dominant reservoir of terrestrial organic carbon and nitrogen, and microbial necromass represents a primary input to it. However, knowledge of stabilization mechanisms and direct measurements of the decomposition of microbial-derived SOM are lacking. Here we report a novel 15N isotope pool dilution approach using labeled amino sugars and muropeptides as tracers to quantify the decomposition of proteins and microbial cell walls, which allows to estimate in situ decomposition rates of microbial-derived SOM. Our results demonstrate that microbial cell walls are as recalcitrant as soil protein, exhibiting comparable turnover times across various ecosystems. The bacterial peptidoglycan in soils was primarily decomposed to muropeptides which can be directly utilized by microbes without being further depolymerized to free amino compounds. Moreover, bacterial peptidoglycan decomposition was correlated with soil microbial biomass while fungal chitin and soil protein decomposition were correlated with high soil pH and fine soil texture. This approach thereby provides new insights into the decomposition pathways and stabilization mechanisms of microbial-derived SOM constituents pertaining to SOM persistence.

  • Wood-based activated biochar to eliminate organic micropollutants from biologically treated wastewater

    Nikolas Hagemann, Hans-Peter Schmidt, Ralf Kaegi, Mark Boehler, Gabriel Sigmund, Andreas Maccagnan, Christa S. McArdell, Thomas D. Bucheli
    2020 - Science of The Total Environment, in press

    Abstract: 

    Implementing advanced wastewater treatment (WWT) to eliminate organic micropollutants (OMPs) is a necessary step to protect vulnerable freshwater ecosystems and water resources. To this end, sorption of OMP by activated carbon (AC) is one viable technology among others. However, conventional AC production based on fossil precursor materials causes environmental pollution, including considerable emissions of greenhouse gases. In this study, we produced activated biochar (AB) from wood and woody residues by physical activation and evaluated their capability to eliminate OMPs in treated wastewater. Activated biochar produced under optimized conditions sorbed 15 model OMPs, of which most were dissociated at circumneutral pH, to the same or higher extent than commercial AC used as a reference. While wood quality played a minor role, the dosage of the activation agent was the main parameter controlling the capacity of ABs to eliminate OMP. Our results highlight the possibility for local production of AB from local wood or woody residues as a strategy to improve WWT avoiding negative side effects of conventional AC production.

  • Identifying the reactive sites of hydrogen peroxide decomposition and hydroxyl radical formation on chrysotile asbestos surfaces

    Martin Walter, Walter D. C. Schenkeveld, Gerald Geroldinger, Lars Gille, Michael Reissner & Stephan M. Kraemer
    2020 - Particle and Fibre Toxicology, 17: 3

    Abstract: 

    Chrysotile asbestos is a carcinogenic mineral that has been abundantly used in different industrial and consumer applications. The fibers’ toxicity is partly goverend by the formation of highly reative radicals by active surface sites.

    Stephan Kraemer from EDGE together with the former PhD student Martin Walter and university assistant Walter Schenkeveld investigated these reactive sites on chrysotile asbestos surfaces, in cooperation with the collegues Lars Gille and Gerald Geroldinger from VetMed Vienna and Michael Reissner from TU Vienna.

    The authors identified tetrahedrally coordinated Fe on the surface of chrysotile asbestos as the only relevant site in the formation of the highly reactive and toxic hydroxyl radicals, which readily damage DNA, proteins and lipids and hence contribute to the pathogenicity of the fibers. Fe added to chrysotile fibers increased the formation of hydroxyl radicals only when it became incorporated and coordinated into tetrahedral vacancy sites on asbestos surfaces.

  • Quantification and Characterization of Nanoparticulate Zinc in an Urban Watershed

    Shaun Bevers, Manuel David Montano, Laya Rybicki, Thilo Hofmann, Frank von der Kammer, James F. Ranville
    2020 - Frontiers in Environmental Science, 8: 84

    Abstract: 

    The recent expansion in the use of nanomaterials in consumer and industrial applications has led to a growing concern over their behavior, fate, and impacts in environmental systems. However, engineered nanoparticles comprise only a small fraction of the total nanoparticle mass in aquatic systems. Human activities, particularly in urban watersheds, are increasing the population of incidental nanoparticles and are likely  altering the cycling of more abundant natural nanoparticles. Accurate detection, quantification, characterization, and tracking of these different populations is important for assessing both the ecological risks of anthropogenic particles, and their impact on environmental health. The urban portion of the South Platte watershed in Denver, Colorado (United States) was sampled for zinc to identify and quantify different nanomaterial sources. Single particle ICP-QMS was employed, to provide single elemental (Zn) signals arising from particle detection events. Coupling spICP-QMS to sample pre-fractionation (sedimentation, filtration) provided some insights into Zn association with nanoparticulate, colloidal, and suspended sediment phases. Single particle ICP-TOFMS (spICP-TOFMS) provided quantification across a large atomic mass range, yielding an even more detailed characterization (elemental ratios) on a particle-by-particle basis, providing some delineation of multiple sources of particles. Across the watershed, on average, 21% of zinc mass was present as zinc-only particles with a rather uniform mean size of 40.2 nm. Zinc that was detected with one or more other elements, primarily Al, Fe, and Si, is likely to be present as heteroagglomerates or within mineral colloids. Although spICP-TOFMS provides a substantial amount of information, it is still in its early stages as an analytical technique and currently lacks the requisite sensitivity to study the smallest of nanoparticles. As this technique continues to develop, it is anticipated that this methodology can be broadly applied to study sources, behavior and effects of a disparate variety of nanoparticles from both geogenic and anthropogenic origins.

  • Groundwater Chemistry Has a Greater Influence on the Mobility of Nanoparticles Used for Remediation than the Chemical Heterogeneity of Aquifer Media

    Malfatti SE, Nathan Bossa, Doris Schmid, Mark R. Wiesner, Thilo Hofmann
    2020 - Environmental Science & Technology, 54: 1250-1257

    Abstract: 

    The application of nanoscale zerovalent iron (nano-ZVI) particles for groundwater remediation has spurred research into the influence of the collector heterogeneity on the  nano-ZVI mobility. The chemical heterogeneity of surfaces within aquifer media affects their surface charge distribution and their affinity for nano-ZVI. The groundwater chemistry affects the properties of both aquifer surfaces and the nano-ZVI particles. Commercial poly(acrylic acid)-coated nano-ZVI (PAA−nano-ZVI) particles were tested in column experiments using two solution chemistries and silica collectors with different degrees of chemical heterogeneity, achieved by ferrihydrite coating. A porous media filtration model was used to determine the attachment efficiency of PAA−nano-ZVI particles, and the Derjaguin−Landau−Verwey−Overbeek (DLVO) theory was used to describe the interactions between PAA−nano-ZVI particles and the aquifer “collectors”. The mobility of PAA−nano-ZVI particles suspended in ultrapure water depended on the extent of ferrihydrite coating on the collector surfaces. The mobility of PAA−nano-ZVI particles under environmentally relevant conditions was independent of the collector chemical heterogeneity. The size of PAA−nano-ZVI aggregates doubled, inducing gravitational sedimentation and possibly straining as mechanisms of particle deposition. There was no repulsive energy barrier between particles and collectors, and the DLVO theory was unable to explain the observed particle attachment. Our results suggest that the groundwater chemistry has a greater influence on the mobility of PAA−nano-ZVI particles than the collector chemical heterogeneity. A better understanding of polymer adsorption to nanoparticles and its conformation under natural groundwater conditions is needed to further elucidate nanoparticle−collector interactions.

  • scikit-hubness: Hubness Reduction and Approximate Neighbor Search

    Feldbauer R, Rattei T, Flexer A
    2020 - The Journal of Open Source Software, 5: 1957

    Abstract: 

    scikit-hubness is a Python package for efficient nearest neighbor search in high-dimensional spaces. Hubness is an aspect of the curse of dimensionality in nearest neighbor graphs. Specifically, it describes the increasing occurrence of hubs and antihubs with growing data dimensionality: Hubs are objects, that appear unexpectedly often among the nearest neighbors of others objects, while antihubs are never retrieved as neighbors. As a consequence, hubs may propagate their information (for example, class labels) too widely within the neighbor graph, while information from antihubs is depleted. These semantically distorted graphs can reduce learning performance in various tasks, such as classification, clustering, or visualization. Hubness is known to affect a variety of applied learning systems, or improper transport mode detection.

    Currently, there is a lack of fully-featured, up-to-date, user-friendly software dealing with hubness. Available packages miss critical features and have not been updated in years, or are not particularly user-friendly. In this paper we describe scikit-hubness, which provides powerful, readily available, and easy-to-use hubness-related methods.

  • The removal of lead, copper, zinc and cadmium from aqueous solution by biochar and amended biochars

    Stuart Cairns, Ian Robertson, Gabriel Sigmund, Alayne Street-Perrott
    2020 - Environmental Science and Pollution Research, in press

    Abstract: 

    The exponential growth in the use of motor vehicles is a key contributor to freshwater degradation. Current remediation techniques require prohibitively expensive contaminant treatment and extraction. Biochar represents an inexpensive option to ameliorate contaminants from motorway runoff. Biochar from Norway spruce (Picea abies (L.) Karst.) was produced under fast pyrolysis-gasification (450–500 °C for 90 s) and amended with wood ash and basaltic rock dust to evaluate sorption of Pb, Cu, Zn and Cd. The column study, designed to mimic field conditions, confirmed that unamended biochar can bind contaminants for short periods, but that the addition of amendments, particularly wood ash, significantly improves contaminant removal. Wood ash-amended biochar removed 98–100% of all contaminants during the study, driven by pH (r = 0.73–0.74; p < 0.01 dependent on metal species) and phosphorus levels causing precipitation (r = 0.47–0.59; p < 0.01, dependent on metal species). The contaminants’ progression through the biochar subsections in the column indicated that increasing the thickness of the biochar layer increased contaminant residence time and removal.

  • Accurate quantification of TiO2 nanoparticles in commercial sunscreens using standard materials and orthogonal particle sizing methods for verification

    Milica Velimirovic, Stephan Wagner, Fazel Abdolahpur Monikh, Toni Uusimäki, Ralf Kaegi, Thilo Hofmann, Frank von der Kammer
    2020 - Talanta, 215: in press

    Abstract: 

    The implementation and enforcement of product labeling obligation as required, for example, by the cosmetic product regulation, needs simple and precise validated analytical methods. This also applies to the analysis of nanoparticles in products such as cosmetics. However, the provision of such methods is often hampered by inaccurate sizing due to unwanted nanoparticle changes, interference of matrix components with sizing and interactions between nanoparticles and analytical instrumentation. It is, therefore, necessary to develop appropriate sample preparation methods that preserve NP properties and reduce or remove matrix compounds that interfere with sizing. Further, accurate particle size analysis of samples containing unknown and possibly multiple nanoparticulate constituents is needed. In this study, we evaluated three sample preparation methods to identify and quantify TiO2 nanoparticles in sunscreens. Specifically, we used a combination of ultracentrifugation and hexane washing, thermal destruction of the matrix, and surfactant assisted particle extraction. The method accuracy was assessed by two internal reference samples: pristine TiO2 nanoparticles (NM104) and similar TiO2 nanoparticles dispersed in a sunscreen matrix. The PSDs were determined using an asymmetrical flow field-flow fractionation hyphenated with multi-angle light scattering and inductively coupled plasma-mass spectroscopy. Particle sizing was based on size calibration of the particle retention time in the AF4. Computation of radius of gyration from MALS data was used as an orthogonal particle sizing approach to verify ideal elution and particle size data from the AF4 calibration. Among the three tested sample preparation methods surfactant assisted particle extraction revealed TiO2 nanoparticle recoveries of above 90% and no increase in particle size due to sample preparation was observed. Finally, the sample preparation methods were applied to two commercial sunscreen samples revealing the existence of TiO2-NP < 100 nm. Conclusively, the surfactant assisted particle extraction method can provide valid data for TiO2-NPs in sunscreen and possibly for cosmetic samples of similar matrix.

  • Anthropogenic gadolinium in freshwater and drinking water systems

    Robert Brünjes and Thilo Hofmann
    2020 - Water Research, 182: 115966

    Abstract: 

    The increasing use of gadolinium-based contrast agents (GBCAs) for magnetic resonance imaging is leading to widespread contamination of freshwater and drinking water systems. Contrary to previous assumptions that GBCAs are stable throughout the water cycle, they can degrade. The stability of GBCAs depends largely on their organic ligands, but also on the physicochemical conditions. There is specific concern regarding UV end-of-pipe water treatments, which may degrade GBCAs. Degradation products in drinking water supplies can increase the risk of adverse health effects. This is of particular relevance where the raw water for drinking water production has a higher proportion of recycled wastewater. GBCAs concentrations in aquatic systems, often referred to as anthropogenic gadolinium, are determined using a variety of calculation methods. Where anthropogenic gadolinium concentrations are low, the inconsistent use of these methods results in high discrepancies and high levels of uncertainty. The current COVID-19 crisis will, in the short-term, drastically decrease the input of GBCAs to freshwater systems. Temporal variations in anthropogenic gadolinium concentrations in river water can be used to better understand river-aquifer interactions and groundwater flow velocities. Collecting urine from all patients following MRI examinations could be a way forward to halt the generally increasing concentrations of Gd in drinking water systems and recover this technologically critical element.

  • Enhanced chromium(VI) treatment in electroactive constructed wetlands: Influence of conductive material

    Pratiksha Srivastava, Rouzbeh Abbassi, Asheesh Kumar Yadav, Vikram Garaniya, Naresh Kumar, Stuart J.Khan, Trevor Lewis
    2020 - Journal of Hazardous Materials, 387: 121722

    Abstract: 

    A constructed wetland (CW) microcosm based on conductive graphite gravel was investigated for hexavalent chromium (Cr(VI)) treatment from synthetic wastewater. Its performance was evaluated and compared with a traditional gravel-based CW microcosm. The microcosms were operated at varying initial Cr(VI) concentrations (5−20 mg/L) and hydraulic retention times (HRT) (3–7.5 h). Near complete treatment (99.9 ± 0.06 %) was achieved in the graphite-based microcosm throughout the experiment. The performance was consistently high throughout with 42.9 % improvement in Cr (VI) treatment compared to a traditional gravel microcosm. Scanning electron microscopy with energy dispersive X-ray spectroscopy (SEM-EDX) analysis indicated that chromium was adsorbed to microbial biofilms. Moreover, microbial diversity profiling suggested that the microbial population in both microcosms differed in diversity and communities. The results suggest that the use of conductive materials in CW significantly enhances the treatment of Cr(VI) and more importantly, allows microbial activity even at high levels of Cr(VI) in the CW.

  • Microbiome definition re-visited: old concepts and new challenges.

    Berg G, Rybakova D, Fischer D, Cernava T, Vergès MC, Charles T, Chen X, Cocolin L, Eversole K, Corral GH, Kazou M, Kinkel L, Lange L, Lima N, Loy A, Macklin JA, Maguin E, Mauchline T, McClure R, Mitter B, Ryan M, Sarand I, Smidt H, Schelkle B, Roume H, Kiran GS, Selvin J, Souza RSC, van Overbeek L, Singh BK, Wagner M, Walsh A, Sessitsch A, Schloter M
    2020 - Microbiome, 1: 103

    Abstract: 

    The field of microbiome research has evolved rapidly over the past few decades and has become a topic of great scientific and public interest. As a result of this rapid growth in interest covering different fields, we are lacking a clear commonly agreed definition of the term "microbiome." Moreover, a consensus on best practices in microbiome research is missing. Recently, a panel of international experts discussed the current gaps in the frame of the European-funded MicrobiomeSupport project. The meeting brought together about 40 leaders from diverse microbiome areas, while more than a hundred experts from all over the world took part in an online survey accompanying the workshop. This article excerpts the outcomes of the workshop and the corresponding online survey embedded in a short historical introduction and future outlook. We propose a definition of microbiome based on the compact, clear, and comprehensive description of the term provided by Whipps et al. in 1988, amended with a set of novel recommendations considering the latest technological developments and research findings. We clearly separate the terms microbiome and microbiota and provide a comprehensive discussion considering the composition of microbiota, the heterogeneity and dynamics of microbiomes in time and space, the stability and resilience of microbial networks, the definition of core microbiomes, and functionally relevant keystone species as well as co-evolutionary principles of microbe-host and inter-species interactions within the microbiome. These broad definitions together with the suggested unifying concepts will help to improve standardization of microbiome studies in the future, and could be the starting point for an integrated assessment of data resulting in a more rapid transfer of knowledge from basic science into practice. Furthermore, microbiome standards are important for solving new challenges associated with anthropogenic-driven changes in the field of planetary health, for which the understanding of microbiomes might play a key role. Video Abstract.

  • Chlamydiae in the Environment.

    Collingro A, Köstlbacher S, Horn M
    2020 - Trends Microbiol., in press

    Abstract: 

    Chlamydiae have been known for more than a century as major pathogens of humans. Yet they are also found ubiquitously in the environment where they thrive within protists and in an unmatched wide range of animals. This review summarizes recent advances in understanding chlamydial diversity and distribution in nature. Studying these environmental chlamydiae provides a novel perspective on basic chlamydial biology and evolution. A picture is beginning to emerge with chlamydiae representing one of the evolutionarily most ancient and successful groups of obligate intracellular bacteria.

  • Roadmap for naming uncultivated Archaea and Bacteria.

    Murray AE, Freudenstein J, Gribaldo S, Hatzenpichler R, Hugenholtz P, Kämpfer P, Konstantinidis KT, Lane CE, Papke RT, Parks DH, Rosselló-Móra R, Stott MB, Sutcliffe IC, Thrash JC, Venter SN, Whitman WB, Acinas SG, Amann RI, Anantharaman K, Armengaud J, Baker BJ, Barco RA, Bode HB, Boyd ES, Brady CL, Carini P, Chain PSG, Colman DR, DeAngelis KM, de Los Rios MA, Estrada-de los Santos P, Dunlap CA, Eisen JA, Emerson D, Ettema TJG, Eveillard D, Girguis PR, Hentschel U, Hollibaugh JT, Hug LA, Inskeep WP, Ivanova EP, Klenk HP, Li WJ, Lloyd KG, Löffler FE, Makhalanyane TP, Moser DP, Nunoura T, Palmer M, Parro V, Pedrós-Alió C, Probst AJ, Smits THM, Steen AD, Steenkamp ET, Spang A, Stewart FJ, Tiedje JM, Vandamme P, Wagner M, Wang FP, Hedlund BP, Reysenbach AL
    2020 - Nat Microbiol, in press
    Roadmap for naming uncultured microbes

    Abstract: 

    The assembly of single-amplified genomes (SAGs) and metagenome-assembled genomes (MAGs) has led to a surge in genome-based discoveries of members affiliated with Archaea and Bacteria, bringing with it a need to develop guidelines for nomenclature of uncultivated microorganisms. The International Code of Nomenclature of Prokaryotes (ICNP) only recognizes cultures as 'type material', thereby preventing the naming of uncultivated organisms. In this Consensus Statement, we propose two potential paths to solve this nomenclatural conundrum. One option is the adoption of previously proposed modifications to the ICNP to recognize DNA sequences as acceptable type material; the other option creates a nomenclatural code for uncultivated Archaea and Bacteria that could eventually be merged with the ICNP in the future. Regardless of the path taken, we believe that action is needed now within the scientific community to develop consistent rules for nomenclature of uncultivated taxa in order to provide clarity and stability, and to effectively communicate microbial diversity.

  • Crypt residing bacteria and proximal colonic carcinogenesis in a mouse model of Lynch syndrome.

    Lang M, Baumgartner M, Rożalska A, Frick A, Riva A, Jarek M, Berry D, Gasche C
    2020 - Int. J. Cancer, in press

    Abstract: 

    Colorectal cancer is a multifactorial disease involving inherited DNA mutations, environmental factors, gut inflammation, and intestinal microbiota. Certain germline mutations within the DNA mismatch repair system are associated with Lynch syndrome tumors including right-sided colorectal cancer with mucinous phenotype and presence of an inflammatory infiltrate. Such tumors are more often associated with bacterial biofilms, which may contribute to disease onset and progression. Inflammatory bowel diseases are also associated with colorectal cancer and intestinal dysbiosis. Herein we addressed the question, whether inflammation can aggravate colorectal cancer development under mismatch repair deficiency. MSH2 mice were crossed into the IL-10 background to study the importance of inflammation and mucosal bacteria as a driver of tumorigenesis in a Lynch syndrome mouse model. An increase in large bowel tumorigenesis was found in double knockout mice both under conventional housing and under specific pathogen-free conditions. This increase was mostly due to the development of proximal tumors, a hotspot for tumorigenesis in Lynch syndrome, and was associated with a higher degree of inflammation. Additionally, bacterial invasion into the mucus of tumor crypts was observed in the proximal tumors. Inflammation shifted fecal and mucosal microbiota composition and was associated with enrichment in Escherichia-Shigella as well as Akkermansia, Bacteroides, and Parabacteroides genera in fecal samples. Tumor-bearing double knockout mice showed a similar enrichment for Escherichia-Shigella and Parabacteroides. Lactobacilli, Lachnospiraceae and Muribaculaceae family members were depleted upon inflammation. In summary, chronic inflammation aggravates colonic tumorigenesis under mismatch repair deficiency and is associated with a shift in microbiota composition. This article is protected by copyright. All rights reserved.

  • Energetic Basis of Microbial Growth and Persistence in Desert Ecosystems.

    Leung PM, Bay SK, Meier DV, Chiri E, Cowan DA, Gillor O, Woebken D, Greening C
    2020 - mSystems, 2: in press

    Abstract: 

    Microbial life is surprisingly abundant and diverse in global desert ecosystems. In these environments, microorganisms endure a multitude of physicochemical stresses, including low water potential, carbon and nitrogen starvation, and extreme temperatures. In this review, we summarize our current understanding of the energetic mechanisms and trophic dynamics that underpin microbial function in desert ecosystems. Accumulating evidence suggests that dormancy is a common strategy that facilitates microbial survival in response to water and carbon limitation. Whereas photoautotrophs are restricted to specific niches in extreme deserts, metabolically versatile heterotrophs persist even in the hyper-arid topsoils of the Atacama Desert and Antarctica. At least three distinct strategies appear to allow such microorganisms to conserve energy in these oligotrophic environments: degradation of organic energy reserves, rhodopsin- and bacteriochlorophyll-dependent light harvesting, and oxidation of the atmospheric trace gases hydrogen and carbon monoxide. In turn, these principles are relevant for understanding the composition, functionality, and resilience of desert ecosystems, as well as predicting responses to the growing problem of desertification.

  • The ecology of heterogeneity: soil bacterial communities and C dynamics

    Nunan N, Schmidt H, Raynaud X
    2020 - Phil. Trans. R. Soc. B, 1798: 11

    Abstract: 

    Heterogeneity is a fundamental property of soil that is often overlooked in microbial ecology. Although it is generally accepted that the heterogeneity of soil underpins the emergence and maintenance of microbial diversity, the profound and far-reaching consequences that heterogeneity can have on many aspects of microbial ecology and activity have yet to be fully apprehended and have not been fully integrated into our understanding of microbial functioning. In this contribution we first discuss how the heterogeneity of the soil microbial environment, and the consequent uncertainty associated with acquiring resources, may have affected how microbial metabolism, motility and interactions evolved and, ultimately, the overall microbial activity that is represented in ecosystem models, such as heterotrophic decomposition or respiration. We then present an analysis of predicted metabolic pathways for soil bacteria, obtained from the MetaCyc pathway/genome database collection (https://metacyc.org/). The analysis suggests that while there is a relationship between phylogenic affiliation and the catabolic range of soil bacterial taxa, there does not appear to be a trade-off between the 16S rRNA gene copy number, taken as a proxy of potential growth rate, of bacterial strains and the range of substrates that can be used. Finally, we present a simple, spatially explicit model that can be used to understand how the interactions between decomposers and environmental heterogeneity affect the bacterial decomposition of organic matter, suggesting that environmental heterogeneity might have important consequences on the variability of this process.

  • Activity and metabolic versatility of complete ammonia oxidizers in full-scale wastewater treatment systems.

    Yang Y, Daims H, Liu Y, Herbold CW, Pjevac P, Lin JG, Li M, Gu JD
    2020 - mBio, 11: e03175-19

    Abstract: 

    The recent discovery of complete ammonia oxidizers (comammox) contradicts the paradigm that chemolithoautotrophic nitrification is always catalyzed by two different microorganisms. However, our knowledge of the survival strategies of comammox in complex ecosystems, such as full-scale wastewater treatment plants (WWTPs), remains limited. Analyses of genomes and transcriptomes of four comammox organisms from two full-scale WWTPs revealed that comammox were active and showed a surprisingly high metabolic versatility. A gene cluster for the utilization of urea and a gene encoding cyanase suggest that comammox may use diverse organic nitrogen compounds in addition to free ammonia as the substrates. The comammox organisms also encoded the genomic potential for multiple alternative energy metabolisms, including respiration with hydrogen, formate, and sulfite as electron donors. Pathways for the biosynthesis and degradation of polyphosphate, glycogen, and polyhydroxyalkanoates as intracellular storage compounds likely help comammox survive unfavorable conditions and facilitate switches between lifestyles in fluctuating environments. One of the comammox strains acquired from the anaerobic tank encoded and transcribed genes involved in homoacetate fermentation or in the utilization of exogenous acetate, both pathways being unexpected in a nitrifying bacterium. Surprisingly, this strain also encoded a respiratory nitrate reductase which has not yet been found in any other genome and might confer a selective advantage to this strain over other strains in anoxic conditions. The discovery of comammox in the genus changes our perception of nitrification. However, genomes of comammox organisms have not been acquired from full-scale WWTPs, and very little is known about their survival strategies and potential metabolisms in complex wastewater treatment systems. Here, four comammox metagenome-assembled genomes and metatranscriptomic data sets were retrieved from two full-scale WWTPs. Their impressive and-among nitrifiers-unsurpassed ecophysiological versatility could make comammox an interesting target for optimizing nitrification in current and future bioreactor configurations.

  • Raman-based sorting of microbial cells to link functions to their genes.

    Lee KS, Wagner M, Stocker R
    2020 - Microb Cell, 3: 62-65

    Abstract: 

    In our recent work, we developed an optofluidic platform that allows a direct link to be made between the phenotypes (functions) and the genotypes (genes) of microbial cells within natural communities. By combining stable isotope probing, optical tweezers, Raman microspectroscopy, and microfluidics, the platform performs automated Raman-based sorting of taxa from within a complex community in terms of their functional properties. In comparison with manual sorting approaches, our method provides high throughput (up to 500 cells per hour) and very high sorting accuracy (98.3 ± 1.7%), and significantly reduces the human labour required. The system provides an efficient manner to untangle the contributions of individual members within environmental and host-associated microbiomes. In this News and Thoughts, we provide an overview of our platform, describe potential applications, suggest ways in which the system could be improved, and discuss future directions in which Raman-based analysis of microbial populations might be developed.

  • Complementary Metagenomic Approaches Improve Reconstruction of Microbial Diversity in a Forest Soil.

    Alteio LV, Schulz F, Seshadri R, Varghese N, Rodriguez-Reillo W, Ryan E, Goudeau D, Eichorst SA, Malmstrom RR, Bowers RM, Katz LA, Blanchard JL, Woyke T
    2020 - mSystems, 2: in press

    Abstract: 

    Soil ecosystems harbor diverse microorganisms and yet remain only partially characterized as neither single-cell sequencing nor whole-community sequencing offers a complete picture of these complex communities. Thus, the genetic and metabolic potential of this "uncultivated majority" remains underexplored. To address these challenges, we applied a pooled-cell-sorting-based mini-metagenomics approach and compared the results to bulk metagenomics. Informatic binning of these data produced 200 mini-metagenome assembled genomes (sorted-MAGs) and 29 bulk metagenome assembled genomes (MAGs). The sorted and bulk MAGs increased the known phylogenetic diversity of soil taxa by 7.2% with respect to the Joint Genome Institute IMG/M database and showed clade-specific sequence recruitment patterns across diverse terrestrial soil metagenomes. Additionally, sorted-MAGs expanded the rare biosphere not captured through MAGs from bulk sequences, exemplified through phylogenetic and functional analyses of members of the phylum Analysis of 67 sorted-MAGs showed conserved patterns of carbon metabolism across four clades. These results indicate that mini-metagenomics enables genome-resolved investigation of predicted metabolism and demonstrates the utility of combining metagenomics methods to tap into the diversity of heterogeneous microbial assemblages. Microbial ecologists have historically used cultivation-based approaches as well as amplicon sequencing and shotgun metagenomics to characterize microbial diversity in soil. However, challenges persist in the study of microbial diversity, including the recalcitrance of the majority of microorganisms to laboratory cultivation and limited sequence assembly from highly complex samples. The uncultivated majority thus remains a reservoir of untapped genetic diversity. To address some of the challenges associated with bulk metagenomics as well as low throughput of single-cell genomics, we applied flow cytometry-enabled mini-metagenomics to capture expanded microbial diversity from forest soil and compare it to soil bulk metagenomics. Our resulting data from this pooled-cell sorting approach combined with bulk metagenomics revealed increased phylogenetic diversity through novel soil taxa and rare biosphere members. In-depth analysis of genomes within the highly represented phylum provided insights into conserved and clade-specific patterns of carbon metabolism.

  • The Signal and the Noise: Characteristics of Antisense RNA in Complex Microbial Communities.

    Michaelsen TY, Brandt J, Singleton CM, Kirkegaard RH, Wiesinger J, Segata N, Albertsen M
    2020 - mSystems, 1: in press

    Abstract: 

    High-throughput sequencing has allowed unprecedented insight into the composition and function of complex microbial communities. With metatranscriptomics, it is possible to interrogate the transcriptomes of multiple organisms simultaneously to get an overview of the gene expression of the entire community. Studies have successfully used metatranscriptomics to identify and describe relationships between gene expression levels and community characteristics. However, metatranscriptomic data sets contain a rich suite of additional information that is just beginning to be explored. Here, we focus on antisense expression in metatranscriptomics, discuss the different computational strategies for handling it, and highlight the strengths but also potentially detrimental effects on downstream analysis and interpretation. We also analyzed the antisense transcriptomes of multiple genomes and metagenome-assembled genomes (MAGs) from five different data sets and found high variability in the levels of antisense transcription for individual species, which were consistent across samples. Importantly, we challenged the conceptual framework that antisense transcription is primarily the product of transcriptional noise and found mixed support, suggesting that the total observed antisense RNA in complex communities arises from the combined effect of unknown biological and technical factors. Antisense transcription can be highly informative, including technical details about data quality and novel insight into the biology of complex microbial communities. This study systematically evaluated the global patterns of microbial antisense expression across various environments and provides a bird's-eye view of general patterns observed across data sets, which can provide guidelines in our understanding of antisense expression as well as interpretation of metatranscriptomic data in general. This analysis highlights that in some environments, antisense expression from microbial communities can dominate over regular gene expression. We explored some potential drivers of antisense transcription, but more importantly, this study serves as a starting point, highlighting topics for future research and providing guidelines to include antisense expression in generic bioinformatic pipelines for metatranscriptomic data.

  • Single cell analyses reveal contrasting life strategies of the two main nitrifiers in the ocean.

    Kitzinger K, Marchant HK, Bristow LA, Herbold CW, Padilla CC, Kidane AT, Littmann S, Daims H, Pjevac P, Stewart FJ, Wagner M, Kuypers MMM
    2020 - Nat Commun, 1: 767
    Nitrospina AOA in situ growth rates

    Abstract: 

    Nitrification, the oxidation of ammonia via nitrite to nitrate, is a key process in marine nitrogen (N) cycling. Although oceanic ammonia and nitrite oxidation are balanced, ammonia-oxidizing archaea (AOA) vastly outnumber the main nitrite oxidizers, the bacterial Nitrospinae. The ecophysiological reasons for this discrepancy in abundance are unclear. Here, we compare substrate utilization and growth of Nitrospinae to AOA in the Gulf of Mexico. Based on our results, more than half of the Nitrospinae cellular N-demand is met by the organic-N compounds urea and cyanate, while AOA mainly assimilate ammonium. Nitrospinae have, under in situ conditions, around four-times higher biomass yield and five-times higher growth rates than AOA, despite their ten-fold lower abundance. Our combined results indicate that differences in mortality between Nitrospinae and AOA, rather than thermodynamics, biomass yield and cell size, determine the abundances of these main marine nitrifiers. Furthermore, there is no need to invoke yet undiscovered, abundant nitrite oxidizers to explain nitrification rates in the ocean.

  • SciPy 1.0: fundamental algorithms for scientific computing in Python.

    Virtanen P, Gommers R, Oliphant TE, Haberland M, Reddy T, Cournapeau D, Burovski E, Peterson P, Weckesser W, Bright J, van der Walt SJ, Brett M, Wilson J, Millman KJ, Mayorov N, Nelson ARJ, Jones E, Kern R, Larson E, Carey CJ, Polat İ, Feng Y, Moore EW, VanderPlas J, Laxalde D, Perktold J, Cimrman R, Henriksen I, Quintero EA, Harris CR, Archibald AM, Ribeiro AH, Pedregosa F, van Mulbregt P
    2020 - Nat. Methods, in press

    Abstract: 

    SciPy is an open-source scientific computing library for the Python programming language. Since its initial release in 2001, SciPy has become a de facto standard for leveraging scientific algorithms in Python, with over 600 unique code contributors, thousands of dependent packages, over 100,000 dependent repositories and millions of downloads per year. In this work, we provide an overview of the capabilities and development practices of SciPy 1.0 and highlight some recent technical developments.

  • Transcriptomic Response of Nitrosomonas europaea Transitioned from Ammonia- to Oxygen-Limited Steady-State Growth.

    Sedlacek CJ, Giguere AT, Dobie MD, Mellbye BL, Ferrell RV, Woebken D, Sayavedra-Soto LA, Bottomley PJ, Daims H, Wagner M, Pjevac P
    2020 - mSystems, 1: e00562-19
    N. europaea electron flow

    Abstract: 

    Ammonia-oxidizing microorganisms perform the first step of nitrification, the oxidation of ammonia to nitrite. The bacterium is the best-characterized ammonia oxidizer to date. Exposure to hypoxic conditions has a profound effect on the physiology of , e.g., by inducing nitrifier denitrification, resulting in increased nitric and nitrous oxide production. This metabolic shift is of major significance in agricultural soils, as it contributes to fertilizer loss and global climate change. Previous studies investigating the effect of oxygen limitation on have focused on the transcriptional regulation of genes involved in nitrification and nitrifier denitrification. Here, we combine steady-state cultivation with whole-genome transcriptomics to investigate the overall effect of oxygen limitation on Under oxygen-limited conditions, growth yield was reduced and ammonia-to-nitrite conversion was not stoichiometric, suggesting the production of nitrogenous gases. However, the transcription of the principal nitric oxide reductase (cNOR) did not change significantly during oxygen-limited growth, while the transcription of the nitrite reductase-encoding gene () was significantly lower. In contrast, both heme-copper-containing cytochrome oxidases encoded by were upregulated during oxygen-limited growth. Particularly striking was the significant increase in transcription of the B-type heme-copper oxidase, proposed to function as a nitric oxide reductase (sNOR) in ammonia-oxidizing bacteria. In the context of previous physiological studies, as well as the evolutionary placement of sNOR with regard to other heme-copper oxidases, these results suggest sNOR may function as a high-affinity terminal oxidase in and other ammonia-oxidizing bacteria. Nitrification is a ubiquitous microbially mediated process in the environment and an essential process in engineered systems such as wastewater and drinking water treatment plants. However, nitrification also contributes to fertilizer loss from agricultural environments, increasing the eutrophication of downstream aquatic ecosystems, and produces the greenhouse gas nitrous oxide. As ammonia-oxidizing bacteria are the most dominant ammonia-oxidizing microbes in fertilized agricultural soils, understanding their responses to a variety of environmental conditions is essential for curbing the negative environmental effects of nitrification. Notably, oxygen limitation has been reported to significantly increase nitric oxide and nitrous oxide production during nitrification. Here, we investigate the physiology of the best-characterized ammonia-oxidizing bacterium, , growing under oxygen-limited conditions.

  • Archaeal nitrification is constrained by copper complexation with organic matter in municipal wastewater treatment plants.

    Gwak JH, Jung MY, Hong H, Kim JG, Quan ZX, Reinfelder JR, Spasov E, Neufeld JD, Wagner M, Rhee SK
    2020 - ISME J, 2: 335-346

    Abstract: 

    Consistent with the observation that ammonia-oxidizing bacteria (AOB) outnumber ammonia-oxidizing archaea (AOA) in many eutrophic ecosystems globally, AOB typically dominate activated sludge aeration basins from municipal wastewater treatment plants (WWTPs). In this study, we demonstrate that the growth of AOA strains inoculated into sterile-filtered wastewater was inhibited significantly, in contrast to uninhibited growth of a reference AOB strain. In order to identify possible mechanisms underlying AOA-specific inhibition, we show that complex mixtures of organic compounds, such as yeast extract, were highly inhibitory to all AOA strains but not to the AOB strain. By testing individual organic compounds, we reveal strong inhibitory effects of organic compounds with high metal complexation potentials implying that the inhibitory mechanism for AOA can be explained by the reduced bioavailability of an essential metal. Our results further demonstrate that the inhibitory effect on AOA can be alleviated by copper supplementation, which we observed for pure AOA cultures in a defined medium and for AOA inoculated into nitrifying sludge. Our study offers a novel mechanistic explanation for the relatively low abundance of AOA in most WWTPs and provides a basis for modulating the composition of nitrifying communities in both engineered systems and naturally occurring environments.

  • Horizontal acquisition of a patchwork Calvin cycle by symbiotic and free-living Campylobacterota (formerly Epsilonproteobacteria).

    Assié A, Leisch N, Meier DV, Gruber-Vodicka H, Tegetmeyer HE, Meyerdierks A, Kleiner M, Hinzke T, Joye S, Saxton M, Dubilier N, Petersen JM
    2020 - ISME J, 1: 104-122

    Abstract: 

    Most autotrophs use the Calvin-Benson-Bassham (CBB) cycle for carbon fixation. In contrast, all currently described autotrophs from the Campylobacterota (previously Epsilonproteobacteria) use the reductive tricarboxylic acid cycle (rTCA) instead. We discovered campylobacterotal epibionts ("Candidatus Thiobarba") of deep-sea mussels that have acquired a complete CBB cycle and may have lost most key genes of the rTCA cycle. Intriguingly, the phylogenies of campylobacterotal CBB cycle genes suggest they were acquired in multiple transfers from Gammaproteobacteria closely related to sulfur-oxidizing endosymbionts associated with the mussels, as well as from Betaproteobacteria. We hypothesize that "Ca. Thiobarba" switched from the rTCA cycle to a fully functional CBB cycle during its evolution, by acquiring genes from multiple sources, including co-occurring symbionts. We also found key CBB cycle genes in free-living Campylobacterota, suggesting that the CBB cycle may be more widespread in this phylum than previously known. Metatranscriptomics and metaproteomics confirmed high expression of CBB cycle genes in mussel-associated "Ca. Thiobarba". Direct stable isotope fingerprinting showed that "Ca. Thiobarba" has typical CBB signatures, suggesting that it uses this cycle for carbon fixation. Our discovery calls into question current assumptions about the distribution of carbon fixation pathways in microbial lineages, and the interpretation of stable isotope measurements in the environment.

Book chapters and other publications

4 Publications found
  • Is too much fertilizer a problem?

    Sedlacek CJ, Giguere AT, Pjevac P
    2020 - Frontiers for Young Minds, 8: 63

    Abstract: 

    Fertilizers are added to crops in order to produce enough food to feed the human population. Fertilizers provide crops with nutrients like potassium, phosphorus, and nitrogen, which allow crops to grow bigger, faster, and to produce more food. Nitrogen in particular is an essential nutrient for the growth of every organismon Earth.Nitrogen is all around us and makes up about 78% of the air you breathe. However, plants and animals cannot use the nitrogen gas in the air. To grow, plants require nitrogen compounds fromthe soil,which can be produced naturally or be provided by fertilizers. However, applying excessive amounts of fertilizer leads to the release of harmful greenhouse gases into the atmosphere and the eutrophication of our waterways. Scientists are currently trying to find solutions to reduce the environmentally harmful effects of fertilizers, without reducing the amount of food we can produce when using them.

  • Thinking outside the Chlamydia box

    A Taylor-Brown, T Halter, A Polkinghorne, M Horn
    2020 - 429-458. in Chlamydia Biology. (M Tan, JH Hegemann, C Sütterlin). Caister Academic Press

    Abstract: 

    Chlamydiae have long been studied exclusively in the context of disease. Yet, accumulating evidence over nearly three decades shows that chlamydiae are ubiquitous in the environment, thriving as symbionts of unicellular eukaryotes such as amoeba and infecting a broad range of animal hosts. These chlamydiae share the characteristic chlamydial developmental cycle and other chlamydial hallmarks. Their discovery fundamentally changed our perspective on chlamydial diversity. Instead of a single genus, Chlamydia, including closely related pathogens, the chlamydiae comprise hundreds of families and genera. Investigating isolates and non-cultured representatives provided insights into features that are in common with or divergent from known Chlamydia species, and suggested that some of these chlamydiae may also be considered pathogens. Importantly, these studies have contributed to a better understanding of the biology of all chlamydiae, and they provide a framework for investigating the evolution of the chlamydial intracellular lifestyle and pathogenicity.

  • One complete and seven draft genome sequences of subdivision 1 and 3 Acidobacteria from soil

    Eichorst SA, Trojan D, Huntemann M, Clum A, Pillay M, Palaniappan K, Varghese N, Mikhailova N, Stamatis D, Reddy TBK, Daum C, Goodwin LA, Shapiro N, Ivanova N, Kyrpides N, Woyke T, Woebken D
    2020 - Microbiology Resource Announcements, 9: 1-4

    Abstract: 

    We report eight genomes from representatives of the phylum Acidobacteriasubdivisions 1 and 3, isolated from soils. The genome sizes range from 4.9 to 6.7 Mb. Genomic analysis reveals putative genes for low- and high-affinity respiratory oxygen reductases, high-affinity hydrogenases, and the capacity to use a diverse collection of carbohydrates.

  • Draft genome sequences of Chlamydiales bacterium STE3 and Neochlamydia sp. AcF84, endosymbionts of Acanthamoeba spp.

    Köstlbacher S, Michels S, Siegl A, Schulz F, Domman D, Jongwutiwes S, Putaporntip C, Horn M, Collingro A
    2020 - Microbiol Resour Announc, 9: e00220-20

    Abstract: 

    Chlamydiales bacterium STE3 and Neochlamydia sp. strain AcF84 are obligate intracellular symbionts of Acanthamoeba spp. isolated from the biofilm of a littoral cave wall and gills from striped tiger leaf fish, respectively. We report the draft genome sequences of these two environmental chlamydiae affiliated with the family Parachlamydiaceae.

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