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Publications in peer reviewed journals

14 Publications found
  • Stromatolitic carbonates from the Middle Miocene of the western Pannonian Basin reflect trace metal availability in microbial habitats during the Badenian Salinity Crisis

    Sebastian Viehmann, Robert Kujawa, Simon V. Hohl, Nathalie Tepe, Alexandra S. Rodler, Thilo Hofmann, Erich Draganits
    2023 - Chemical Geology, 618: in press


    Stromatolitic carbonates of the Middle Miocene Oberpullendorf Basin (Austria) provide a great opportunity to study the evolution of microbial habitats under extreme environmental changes during the Badenian (Langhian and early Serravallian) Salinity Crisis. We here present the first geochemical data for Badenian stromatolites and show in a combined approach using major, trace element, and C – O isotope compositions obtained in individual stromatolitic carbonate laminae that short-term variations of palaeo-environmental conditions within the Oberpullendorf Basin coincide with individual microbialite morphologies.

    The studied carbonates were affected by both detrital contamination and post-depositional alteration processes to different degrees. While fluid-mobile elements show clear evidence for post-depositional alteration processes, the rare earth element and yttrium (REY) as well as bio-essential element (Fe, Mn, Co, Zn, Mo, W) compositions of the carbonates remained unaffected. Stromatolitic carbonates that are devoid of detrital contamination (< 300 ppm Al) show typical shale-normalized seawater-like rare earth element and yttrium (REYSN) patterns with positive LaSN, GdSN anomalies, super-chondritic Y/Ho ratios, and heavy over light REYSN enrichments in the lower stromatolite units. These features suggest an open ocean seawater influenced depositional setting at the north-western margin of the Paratethys Sea. Stratigraphically upwards, pure stromatolitic carbonates show suppressed seawater-like REYSN signatures that argue for the development of a (semi)closed lagoon with restricted access to the open sea. Seawater-like REYSN patterns in the uppermost part resemble a reappearance of open marine environmental conditions. Interestingly, geochemical data of the upper part of the section contradict the ambient fossil record, showing the urge for future interdisciplinary approaches targeting the understanding and interplay of geochemistry, palaeontology, and geomicrobiology in modern and ancient microbial habitats. Enrichment factors of bio-essential trace elements that are either used as co-factors in metalloenzymes or metal-activated enzymes in biochemical reactions can be directly linked to the reconstructed environmental conditions: Sufficient element availability is ensured during marine conditions in the lower and uppermost stratigraphic sections; in contrast, continuous decreasing element availability of these elements is directly related to the temporary development of a (semi)closed lagoon.

  • Key Principles for the Intergovernmental Science–Policy Panel on Chemicals and Waste

    Marlene Ågerstrand, Kenneth Arinaitwe, Thomas Backhaus, Ricardo O. Barra, Miriam L. Diamond, Joan O. Grimalt, Ksenia Groh, Faith Kandie, Perihan Binnur Kurt-Karakus, Robert J. Letcher, Rainer Lohmann, Rodrigo O. Meire, Temilola Oluseyi, Andreas Schäffer, Mochamad Septiono, Gabriel Sigmund, Anna Soehl, Temitope O. Sogbanmu, Noriyuki Suzuki, Marta Venier, Penny Vlahos, Martin Scheringer
    2023 - Environ. Sci. Technol., 57: in press


    In 2021, the United Nations Environment Programme (UNEP) recognized chemical pollution as a planetary crisis tantamount to climate change and biodiversity decline. In an important next step, the international community agreed in March 2022 on establishing an independent, intergovernmental science–policy panel on chemicals, waste, and pollution prevention (hereafter termed “the Panel”). This Panel will take its place among two other intergovernmental bodies, the Intergovernmental Panel on Climate Change (IPCC) and the Intergovernmental Science-Policy Platform on Biodiversity and Ecosystem Services (IPBES). Now is a crucial time for establishing the Panel, following a process facilitated by UNEP to negotiate the Panel’s scope, functions, and institutional design, with the ambition to formally establish the Panel in 2024.
    As a group of international scientists working on chemical pollution, we applaud this milestone of progress to initiate the establishment of a panel for chemicals, waste, and pollution prevention. At the beginning of the negotiating process, we would like to highlight the following 10 critical aspects for consideration in determining the settings of the Panel.


  • Nutrient controls on carbohydrate and lignin decomposition in beech litter

    Kohl L, Wanek W, Keiblinger K, Hämmerle I, Fuchslueger L, Schneider T, Riedel K, Eberl L, Zechmeister-Boltenstern S, Richter A
    2023 - Geoderma, 429: Article 116276


    Nutrient pollution has increased plant litter nutrient concentrations in many ecosystems, which may profoundly impact litter decomposition and change the chemical composition of litter inputs to soils. Here, we report on a mesocosm experiment to study how variations in the nitrogen (N) and phosphorus (P) concentrations in Fagus sylvatica (European beech) litter from four sites differing in bedrock, atmospheric deposition, and climate affect lignin and carbohydrate loss rates and residual litter chemistry. We show with pyrolysis GC/MS and elemental analysis that nutrient concentrations had a strong influence on changes in litter chemistry during early decomposition (0–181 days), when greater lignin loss rates were associated with low P concentrations, whereas carbohydrate and bulk C loss were associated with high N concentrations. Nutrient concentrations, in contrast, did not influence changes in litter chemistry in the later decomposition stage (181–475 days), where the decomposition rates of lignin, carbohydrates, and bulk C all increased with litter N concentration and no differences in decomposition rates between major compound classes were detected. Our data indicate that these differences were related to the transition from increasing to constant or declining microbial biomass, and an associated decrease in microbial dependence on the mobilization of nutrients from the insoluble litter fraction.

  • Policy options to account for multiple chemical pollutants threatening biodiversity

    Leonie Katharina Mueller, Marlene Ågerstrand, Thomas Backhaus, Miriam Diamond, Walter Erdelen, David Evers, Ksenia Groh, Martin Scheringer, Gabriel Sigmund, Zhanyun Wang, Andreas Schäffer
    2023 - Environmental Science: Advances, in press


    Chemical pollution poses a threat to biodiversity on a global scale. This has been acknowledged in the Post-2020 Biological Diversity Framework which proposes to regulate the release of chemicals to the environment and names specific indicators focusing on pesticides, nutrients and plastic waste. We fully endorse the inclusion of these substances but argue that in order to protect biodiversity from hazardous chemicals, the scope of Target 7 should feature other groups of pollutants with potential to contribute to biodiversity loss. We propose the inclusion of non-agricultural biocides, per- and polyfluoroalkyl substances (PFASs), toxic metal(loid)s, and endocrine disrupting chemcials (EDCs). Furthermore, data on emerging pollutants (e.g., rare earth elements, industrial chemicals, liquid crystal monomers, pharmaceuticals, personal care products) need to be regularly scanned and these pollutants added to Target 7 in case of biodiversity risk. We suggest to amend Target 7 to postulate the aim for the overall reduction of chemical production and emissions, as well as the addition of the described substance groups of high concern to biodiversity for discussion and implementation in the Post-2020 Biodiversity Framework. We further elaborate on different strategies for the reduction of emissions of hazardous chemicals through chemical simplification and grouping, reduction of chemicals with non-essential use, and innovative synthesis strategies (“benign by design”). In this context the full life cycle of chemicals, i.e., production, use, end of life needs to be considered. Lastly, we propose to set up data inventories that transparently inform about production, transport and emissions of chemicals in cooperation with industry, that can serve as basis for indicators related to monitoring the effectiveness of the goals set under Target 7.

  • Seasonal biodegradation of the artificial sweetener acesulfame enhances its use as a transient wastewater tracer

    Miguel Angel Marazuela, Giovanni Formentin, Klaus Erlmeier, Thilo Hofmann
    2023 - Water Research, 232: in press


    The persistence of the artificial sweetener acesulfame potassium (ACE) during wastewater treatment and subsequently in the aquatic environment has made it a widely used tracer of wastewater inputs to both surface water and groundwater. However, the recently observed biodegradation of ACE during wastewater treatment has questioned the validity of this application. In this study, we assessed the use of ACE not only as a marker of wastewater, but also as a transient wastewater tracer that allows both the calculation of mixing ratios and travel times through the aquifer as well as the calibration of transient groundwater flow and mass transport models. Our analysis was based on data obtained in a nearly 8-year river water and groundwater sampling campaign along a confirmed wastewater-receiving riverbank filtration site located close to a drinking water supply system. We provide evidence that temperature controls ACE concentration and thus its seasonal oscillation. River water data showed that ACE loads decreased from 1.5–4 mg·s−1 in the cold season (December to June; T<10 °C) to 0–0.5 mg·s−1 in the warm season (July to November; T>10 °C). This seasonal variability of >600% was detectable in the aquifer and preserved >3 km, with ACE concentrations oscillating between <LOQ in the warm season up to 1 μg·L−1 in the cold season. The large seasonal variation in ACE concentrations during wastewater treatment, compared to the other sweeteners (sucralose, cyclamate, and saccharin) and chloride enables its use as a transient tracer of wastewater inflows and riverbank filtration. In addition, the arrival time of the ACE concentration peak can be used to estimate groundwater flow velocity and mixing ratios, thereby demonstrating its potential in the calibration of groundwater numerical models.

  • Small biochar particles hardly disintegrate under cryo-stress

    Gabriel Sigmund, Andrea Schmid, Hans-Peter Schmidt, Nikolas Hagemann, Thomas D. Bucheli, Thilo Hofmann
    2023 - Geoderma, 430: in press


    Physical disintegration of biochar has been postulated to determine the persistence and mobility in soil of this recalcitrant carbon pool. Therein, freeze–thaw cycling can induce substantial physical stress to biochars. We here investigated the physical disintegration and subsequent mobilisation of five different biochars under “realistic worst-case scenarios” in a laboratory soil column setup as well as in shaking and sonication batch experiments. The mobilization of carbon from biochar particles (0.25–1 mm) was investigated in the absence of clay at a pH of 6.3 with and without 80 freeze–thaw cycles. The small biochar particles used in this study did not strongly disintegrate after freeze–thaw cycling, possibly because of freezing point depression in biochar micropores. Our results in comparison with findings in literature suggest that freeze–thaw-induced physical disintegration of biochar is a process more pronounced for large biochar particles containing substantial meso- and macropores. Biochars with larger ash fractions disintegrated more, presumably because of the ash-associated formation of unstable cavities within the biochar. Physical stability of biochars produced from the same feedstock at different pyrolysis temperatures decreased with increasing aromaticity, which may be linked to a higher rigidity of more aromatic structures. Moisture content in the soil increased carbon mobilization from biochar more than physical stress such as freeze–thaw cycling. The physical disintegration of biochar and subsequent mobilization of micro-and nanosized carbon should thus be considered of minor relevance and is often not a driving factor for biochar stability in soil.

  • Analytical strategies to measure gadolinium as a wastewater marker in surface and groundwater systems

    Miguel Angel Marazuela, Martin Stockhausen, Thilo Hofmann
    2023 - MethodsX, 10: in press


    The increasing use of gadolinium (Gd)-based contrast agents in magnetic resonance imaging and the recalcitrant behavior of Gd during municipal wastewater treatment have led to increased concentrations of the tracer in aquatic environments. These anthropogenic Gd emissions to wastewater and, subsequently, to surface and groundwater systems can be exploited to calculate groundwater travel times and mixing ratios, identify wastewater inputs, and calibrate groundwater models. However, analytical complexity, costs, and the time needed to directly measure anthropogenic inputs hinder the practical use of Gd. While direct measurements with inductively coupled plasma-mass spectrometry (ICP-MS) are highly efficient and feasible, only total Gd can be detected with this approach. In unknown hydrogeological systems, the differentiation between total, anthropogenic, and geogenic Gd by interpolating rare earth element patterns requires complex sample pre-treatment and pre-concentration. Direct measurements of Gd can be obtained using anion-exchange chromatography coupled to ICP-MS but the limit of quantification will be higher. Here we provide guidelines for selecting the optimal method for the analysis of Gd as a wastewater tracer in surface-groundwater systems.

    • The cost-effectiveness of existing analytical strategies to measure Gd when used as a wastewater tracer in surface-groundwater systems is addressed
    • A novel analytical strategy for direct determination of total Gd is presented


  • Secondary Metabolite Production Potential in a Microbiome of the Freshwater Sponge Spongilla lacustris

    Graffius S, Garzón JFG, Zehl M, Pjevac P, Kirkegaard R, Flieder M, Loy A, Rattei T, Ostrovsky A, Zotchev SB
    2023 - Microbiol Spectr, e0435322


    Marine and freshwater sponges harbor diverse communities of bacteria with vast potential to produce secondary metabolites that may play an important role in protecting the host from predators and infections. In this work, we initially used cultivation and metagenomics to investigate the microbial community of the freshwater sponge Spongilla lacustris collected in an Austrian lake. Representatives of 41 bacterial genera were isolated from the sponge sample and classified according to their 16S rRNA gene sequences. The genomes of 33 representative isolates and the 20 recovered metagenome-assembled genomes (MAGs) contained in total 306 secondary metabolite biosynthesis gene clusters (BGCs). Comparative 16S rRNA gene and genome analyses showed very little taxon overlap between the recovered isolates and the sponge community as revealed by cultivation-independent methods. Both culture-independent and -dependent analyses suggested high biosynthetic potential of the S. lacustris microbiome, which was confirmed experimentally even at the subspecies level for two isolates. To our knowledge, this is the most thorough description of the secondary metabolite production potential of a freshwater sponge microbiome to date. A large body of research is dedicated to marine sponges, filter-feeding animals harboring rich bacterial microbiomes believed to play an important role in protecting the host from predators and infections. Freshwater sponges have received so far much less attention with respect to their microbiomes, members of which may produce bioactive secondary metabolites with potential to be developed into drugs to treat a variety of diseases. In this work, we investigated the potential of bacteria associated with the freshwater sponge to biosynthesize diverse secondary metabolites. Using culture-dependent and -independent methods, we discovered over 300 biosynthetic gene clusters in sponge-associated bacteria and proved production of several compounds by selected isolates using genome mining. Our results illustrate the importance of a complex approach when dealing with microbiomes of multicellular organisms that may contain producers of medically important secondary metabolites.

  • Pathometagenomics reveals susceptibility to intestinal infection by Morganella to be mediated by the blood group-related B4galnt2 gene in wild mice.

    Vallier M, Suwandi A, Ehrhardt K, Belheouane M, Berry D, Čepić A, Galeev A, Johnsen JM, Grassl GA, Baines JF
    2023 - Gut Microbes, 1: 2164448


    Infectious disease is widely considered to be a major driver of evolution. A preponderance of signatures of balancing selection at blood group-related genes is thought to be driven by inherent trade-offs in susceptibility to disease. B4galnt2 is subject to long-term balancing selection in house mice, where two divergent allele classes direct alternative tissue-specific expression of a glycosyltransferase in the intestine versus blood vessels. The blood vessel allele class leads to prolonged bleeding times similar to von Willebrand disease in humans, yet has been maintained for millions of years. Based on in vivo functional studies in inbred lab strains, it is hypothesized that the cost of prolonged bleeding times may be offset by an evolutionary trade-off involving susceptibility to a yet unknown pathogen(s). To identify candidate pathogens for which resistance could be mediated by B4galnt2 genotype, we here employed a novel "pathometagenomic" approach in a wild mouse population, which combines bacterial 16S rRNA gene-based community profiling with histopathology of gut tissue. Through subsequent isolation, genome sequencing and controlled experiments in lab mice, we show that the presence of the blood vessel allele is associated with resistance to a newly identified subspecies of Morganella morganii, a clinically important opportunistic pathogen. Given the increasing importance of zoonotic events, the approach outlined here may find useful application in the detection of emerging diseases in wild animal populations.

  • Mid-Infrared Photothermal-Fluorescence In Situ Hybridization for Functional Analysis and Genetic Identification of Single Cells

    Bai Y, Guo Z, Pereira FC, Wagner M, Cheng JX
    2023 - Anal Chem, in press
    Mid-Infrared Photothermal-Fluorescence In Situ Hybridization


    Simultaneous identification and metabolic analysis of microbes with single-cell resolution and high throughput are necessary to answer the question of "who eats what, when, and where" in complex microbial communities. Here, we present a mid-infrared photothermal-fluorescence in situ hybridization (MIP-FISH) platform that enables direct bridging of genotype and phenotype. Through multiple improvements of MIP imaging, the sensitive detection of isotopically labeled compounds incorporated into proteins of individual bacterial cells became possible, while simultaneous detection of FISH labeling with rRNA-targeted probes enabled the identification of the analyzed cells. In proof-of-concept experiments, we showed that the clear spectral red shift in the protein amide I region due to incorporation of C atoms originating from C-labeled glucose can be exploited by MIP-FISH to discriminate and identify C-labeled bacterial cells within a complex human gut microbiome sample. The presented methods open new opportunities for single-cell structure-function analyses for microbiology.

  • Rapid nitrification involving comammox and canonical Nitrospira at extreme pH in saline-alkaline lakes

    Daebeler A, Güell-Bujons Q, Mooshammer M, Zechmeister T, Herbold CW, Richter A, Wagner M, Daims H
    2023 - Environ Microbiol, in press


    Nitrite-oxidizing bacteria (NOB) catalyse the second nitrification step and are the main biological source of nitrate. The most diverse and widespread NOB genus is Nitrospira, which also contains complete ammonia oxidizers (comammox) that oxidize ammonia to nitrate. To date, little is known about the occurrence and biology of comammox and canonical nitrite oxidizing Nitrospira in extremely alkaline environments. Here, we studied the seasonal distribution and diversity, and the effect of short-term pH changes on comammox and canonical Nitrospira in sediments of two saline, highly alkaline lakes. We identified diverse canonical and comammox Nitrospira clade A-like phylotypes as the only detectable NOB during more than a year, suggesting their major importance for nitrification in these habitats. Gross nitrification rates measured in microcosm incubations were highest at pH 10 and considerably faster than reported for other natural, aquatic environments. Nitrification could be attributed to canonical and comammox Nitrospira and to Nitrososphaerales ammonia-oxidizing archaea. Furthermore, our data suggested that comammox Nitrospira contributed to ammonia oxidation at an extremely alkaline pH of 11. These results identify saline, highly alkaline lake sediments as environments of uniquely strong nitrification with novel comammox Nitrospira as key microbial players.

  • Differential carbon utilization enables co-existence of recently speciated Campylobacteraceae in the cow rumen epithelial microbiome.

    Strachan CR, Yu XA, Neubauer V, Mueller AJ, Wagner Ma, Zebeli Q, Selberherr E, Polz MF
    2023 - Nat Microbiol, in press


    The activities of different microbes in the cow rumen have been shown to modulate the host's ability to utilize plant biomass, while the host-rumen interface has received little attention. As datasets collected worldwide have pointed to Campylobacteraceae as particularly abundant members of the rumen epithelial microbiome, we targeted this group in a subset of seven cows with meta- and isolate genome analysis. We show that the dominant Campylobacteraceae lineage has recently speciated into two populations that were structured by genome-wide selective sweeps followed by population-specific gene import and recombination. These processes led to differences in gene expression and enzyme domain composition that correspond to the ability to utilize acetate, the main carbon source for the host, at the cost of inhibition by propionate. This trade-off in competitive ability further manifests itself in differential dynamics of the two populations in vivo. By exploring population-level adaptations that otherwise remain cryptic in culture-independent analyses, our results highlight how recent evolutionary dynamics can shape key functional roles in the rumen microbiome.

  • Gene gain facilitated endosymbiotic evolution of Chlamydiae.

    Dharamshi JE, Köstlbacher S, Schön ME, Collingro A, Ettema TJG, Horn M
    2023 - Nat Microbiol, 1: 40-54


    Chlamydiae is a bacterial phylum composed of obligate animal and protist endosymbionts. However, other members of the Planctomycetes-Verrucomicrobia-Chlamydiae superphylum are primarily free living. How Chlamydiae transitioned to an endosymbiotic lifestyle is still largely unresolved. Here we reconstructed Planctomycetes-Verrucomicrobia-Chlamydiae species relationships and modelled superphylum genome evolution. Gene content reconstruction from 11,996 gene families suggests a motile and facultatively anaerobic last common Chlamydiae ancestor that had already gained characteristic endosymbiont genes. Counter to expectations for genome streamlining in strict endosymbionts, we detected substantial gene gain within Chlamydiae. We found that divergence in energy metabolism and aerobiosis observed in extant lineages emerged later during chlamydial evolution. In particular, metabolic and aerobic genes characteristic of the more metabolically versatile protist-infecting chlamydiae were gained, such as respiratory chain complexes. Our results show that metabolic complexity can increase during endosymbiont evolution, adding an additional perspective for understanding symbiont evolutionary trajectories across the tree of life.

  • The microbiome of kidney stones and urine of patients with nephrolithiasis.

    Lemberger U, Pjevac P, Hausmann B, Berry D, Moser D, Jahrreis V, Özsoy M, Shariat SF, Veser J
    2023 - Urolithiasis, 1: 27


    The incidence of nephrolithiasis is rising worldwide. Although it is a multifactorial disease, lifestyle plays a major role in its etiology. Another considerable factor could be an aberrant microbiome. In our observational single-center study, we aimed to investigate the composition of bacteria in kidney stones and urine focusing on patients with features of metabolic syndrome. Catheterized urine and kidney stones were collected prospectively from 100 consecutive patients undergoing endoscopic nephrolithotomy between 2020 and 2021 at our clinic. Microbiome composition was analyzed via 16S rRNA gene amplicon sequencing. Detection of bacteria was successful in 24% of the analyzed kidney stones. These patients had a prolonged length of stay compared to patients without verifiable bacteria in their stones (2.9 vs 1.5 days). Patients with features of metabolic syndrome were characterized by kidney stones colonized with classical gastrointestinal bacteria and displayed a significant enrichment of Enterococcaceae and Enterobacteriaceae. Stones of patients without features of metabolic syndrome characterized by Ureaplasma and Staphylococcaceae. Patients with bacteria in their kidney stones exhibit a longer length of stay, possibly due to more complex care. Patients presenting with features of metabolic syndrome displayed a distinct stone microbiome compared to metabolically fit patients. Understanding the role of bacteria in stone formation could enable targeted therapy, prevention of post-operative complications and new therapeutic strategies.

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