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Publications in peer reviewed journals

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

    Miguel Angel Marazuela, Martin Stockhausen, Thilo Hofmann
    2023 - MethodsX, 10: 101965


    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


  • Benchmarking biochar with activated carbon for immobilizing leachable PAH and heterocyclic PAH in contaminated soils

    Carlotta Carlini, Sampriti Chaudhuri, Oliver Mann, Daniel Tomsik, Thorsten Hüffer, Nicolas Greggio, Diego Marazza, Thilo Hofmann, Gabriel Sigmund
    2023 - Environmental Pollution, 325: 121417


    Remediation of residually contaminated soils remains a widespread problem. Biochar can immobilize polycyclic aromatic hydrocarbons (PAH). However, studies on its ability to immobilize PAH and N, S, and O substituted PAH (hetero-PAH) in real soils, and benchmarking with commercial activated carbon are missing. Here, we compared the ability of pristine biochar (BC), steam-activated biochar (SABC), and commercial activated carbon (AC) to immobilize PAH and hetero-PAH. The three carbons were tested on soils from four different contaminated sites in Austria. Different amendment rates (w/w) of the carbons were investigated (BC: 1.0, 2.5, and 5%; SABC: 0.5, 1.0, and 2.0%; AC: 1%) in batch experiments to cover meaningful ranges in relation to their performance. SABC performed better than AC, removing at least 80% PAH with the lowest application rate of 0.5%, and achieving a complete removal at an application rate of 1.0%. BC performed slightly worse but still acceptable in residually contaminated soils (40 and 100% removal at 1 and 5% amendment, respectively). The ability of BC and SABC to immobilize PAH decreased as the PAH-molar volume increased. PAH with three or more rings were preferentially removed by AC compared to SABC or BC. This can be explained by the difference in pore size distribution of the carbons which could limit the accessibility of PAH and hetero-PAH to reach sorption sites for π- π electron donor-acceptor interactions, which drive PAH and hetero-PAH sorption to carbons. Column percolation tests confirmed the results obtained in batch tests, indicating, that decisions for soil remediation can be derived from simpler batch experiments. In soil samples with 1% BC, a reduction of over 90% in the total concentration of PAH in the leached water was observed. Overall, BC and SABC were demonstrated to be valid substitutes for AC for stabilizing residually contaminated soils.

  • A versatile test system to determine nanomaterial heteroagglomeration attachment efficiency

    Helene Walch, Nada Bašić, Antonia Praetorius, Frank von der Kammer, Thilo Hofmann
    2023 - Environmental Science: Nano, in press


    Engineered and incidental nanomaterials are emerging contaminants of environmental concern. In aquatic systems, their transport, fate, and bioavailability strongly depend on heteroagglomeration with natural suspended particulate matter (SPM). Since particulate contaminants underlie different mechanisms than dissolved contaminants, harmonized, particle-specific test systems and protocols are needed for environmental risk assessment and for the comparability of environmental fate studies. The heteroagglomeration attachment efficiency (α_het) can parametrize heteroagglomeration in fate models which inform exposure assessment. It describes the attachment probability upon nanomaterial-SPM collision and reflects the physicochemical affinity between their surfaces. This work introduces a new versatile test system to determine α_het under environmentally relevant conditions. The test matrix combines model SPM analogs and an adjustable model hydrochemistry, both designed to represent the process-relevant characteristics of natural freshwater systems, while being standardizable and reproducible. We developed a stirred-batch method that addresses shortcomings of existing strategies for α_het determination and conducted heteroagglomeration experiments with CeO2 (<25 nm) as a model nanomaterial. Single-particle ICP-MS allowed working at environmentally relevant concentrations and determination of α_het values by following the decrease of non-reacted nanomaterial over time. The α_het values received for the model freshwater test matrix were evaluated against a natural river-water sample. Almost identical α_het values show that the model test system adequately reflects the natural system, and the experimental setup proved to be robust and in line with the theoretical concept for α_het determination. Combinations of natural SPM in model water and model SPM in natural water allowed further insight into their respective impacts. The α_het values determined for nano-CeO2 in the natural river water sample (0.0044-0.0051) translate to a travel distance of 143-373 km downstream until 50% is heteroagglomerated, assuming an average flow velocity of 5 km h-1 and an SPM concentration of 20-45 mg L-1. These half-lives illustrate the importance of heteroagglomeration kinetics.

  • Tree stem and soil methane and nitrous oxide fluxes, but not carbon dioxide fluxes, switch sign along a topographic gradient in a tropical forest

    Daniel W, Stahl C, Burban B, Goret J-Y, Cazal J, Richter A, Janssens IA, Bréchet LM
    2023 - Plant and Soil, 488: 533-549



    Tropical forests exchange large amounts of greenhouse gases (GHGs: carbon dioxide, CO2; methane, CH4; and nitrous oxide, N2O) with the atmosphere. Forest soils and stems can be either sources or sinks for CH4 and N2O, but little is known about what determines the sign and magnitude of these fluxes. Here, we aimed to study how stem and soil GHG fluxes vary along a topographic gradient in a tropical forest.


    Fluxes of GHG from 56 individual tree stems and adjacent soils were measured with manual static chambers. The topographic gradient was characterized by a soil moisture gradient, with one end in a wetland area (“seasonally flooded”; SF), the other end in an upland area (“terra firme”; TF) and in between a transitional area on the slope (SL).


    Tree stems and soils were always sources of CO2 with higher fluxes in SF compared to TF and SL. Fluxes of CH4 and N2O were more variable, even within one habitat. Results showed that, in TF, soils acted as sinks for N2O whereas, in SF and SL, they acted as sources. In contrast, tree stems which were predominantly sources of N2O in SF and TF, were sinks in SL. In the soil, N2O fluxes were significantly influenced by both temperature and soil water content, whereas CH4 fluxes were only significantly correlated with soil water content.


    SF areas were major sources of the three gases, whereas SL and TF soils and tree stems acted as either sources or sinks for CH4 and N2O. Our results indicate that tree stems represent overlooked sources of CH4 and N2O in tropical forests that need to be further studied to refine GHG budgets.

  • 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
    2023 - Water Research, 229: 119385


    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.

  • 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: 119670


    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.

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

    Daebler A, Güell-Bujons Q, Mooshammer M, Zechmeister T, Herbold CW, Richter A, Wagner M, Daims H
    2023 - Environmental microbiology, 25: 1055-1067


    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.

  • One-time freeze-thawing or carbon input events have long-term legacies in soil microbial communities

    Gorka S, Ranits C, zhang S, Imai B, Guseva K, Kaiser C
    2023 - Geoderma, 432: Article 116399


    Soil microbial communities are regularly exposed to sudden changes in environmental conditions, such as root exudation pulses or freeze-thaw events. As microbial communities have a high potential to adapt to changing conditions, they are expected to be resilient towards this kind of short-term perturbations and return to their pre-perturbed state quickly. Here, we conducted a lab incubation experiment to evaluate the resilience of soil microbial communities to single-pulse perturbations.

    We incubated temperate forest soil at constant temperature (20 °C) and water content, and exposed it to strong single-pulse perturbations, which nonetheless mimic common pulse-events in temperate soils (glucose addition at 4 mg g−1 soil, or freeze-thawing overnight at −20 °C). We subsequently measured microbial community composition and microbial storage compounds via phospho- and neutral lipid fatty acid (PLFA and NLFA) profiling, as well as C/N stoichiometry of microbial biomass and dissolved organic carbon and nitrogen in the soil solution shortly after (0.4, 1, 4, and 6 days) and after longer time periods (84 and 160 days) following the perturbations.

    Transferring the soils from their natural environment to the laboratory and incubating them under controlled conditions led to a continuous change of microbial community structure over time, along with an increase in microbial biomass and dissolved N in both perturbed and control soils over the time of the experiment. Against the background of this ‘press-disturbance’, caused by the permanently changed conditions, we see immediate and long-lasting effects of the single pulse events on microbial community composition, C storage and C/N stoichiometry. Both perturbations significantly influenced the microbial community structure (based on PLFA profiles), microbial biomass N and dissolved N up to 160 days, as well as fungal and bacterial biomass and storage (based on absolute PLFA and NLFA concentrations) up to 84 days. Both perturbations increased microbial N (+59.6 µg g−1 dw) and decreased dissolved N (−40.3 µg g−1 dw) after 160 days, and significantly altered C/N ratios in microbial and dissolved pools (particularly in the first 6 days of the experiment).

    Our results demonstrate that single-pulse perturbations can have long-term legacies in soil microbial ecosystems. In our experiment they led to alternative system states which differed from the unperturbed control in multiple parameters even after 160 days. This indicates that soil microbial communities exhibit a low resistance and resilience towards single-pulse perturbations, and may easily be pushed on alternative trajectories by short but strong environmental pulses.

  • Chemical characteristics of wildfire ash across the globe and their environmental and socio-economic implications

    Carmen Sanchez-García, Cristina Santín, Jonay Neris, Gabriel Sigmund, Xosé Lois Otero, J. Manley, Gil Gonzalez-Rodríguez, Claire M. Belcher, Artemi Cerda, Abbey L. Marcotte, Sheila F. Murphy, Charles C. Rhoades, Gary Sheridan, Tercia Strydom, Peter R. Robichaud, Stefan H. Doerr
    2023 - Environment International, 178: 108065


    The mobilisation of potentially harmful chemical constituents in wildfire ash can be a major consequence of wildfires, posing widespread societal risks. Knowledge of wildfire ash chemical composition is crucial to anticipate and mitigate these risks.

    Here we present a comprehensive dataset on the chemical characteristics of a wide range of wildfire ashes (42 types and a total of 148 samples) from wildfires across the globe and examine their potential societal and environmental implications. An extensive review of studies analysing chemical composition in ash was also performed to complement and compare our ash dataset.

    Most ashes in our dataset had an alkaline reaction (mean pH 8.8, ranging between 6 and 11.2). Important constituents of wildfire ash were organic carbon (mean: 204 g kg−1), calcium, aluminium, and iron (mean: 47.9, 17.9 and 17.1 g kg−1). Mean nitrogen and phosphorus ranged between 1 and 25 g kg−1, and between 0.2 and 9.9 g kg−1, respectively. The largest concentrations of metals of concern for human and ecosystem health were observed for manganese (mean: 1488 mg kg−1; three ecosystems > 1000 mg kg−1), zinc (mean: 181 mg kg−1; two ecosystems > 500 mg kg−1) and lead (mean: 66.9 mg kg−1; two ecosystems > 200 mg kg−1). Burn severity and sampling timing were key factors influencing ash chemical characteristics like pH, carbon and nitrogen concentrations. The highest readily dissolvable fractions (as a % of ash dry weight) in water were observed for sodium (18 %) and magnesium (11.4 %). Although concentrations of elements of concern were very close to, or exceeded international contamination standards in some ashes, the actual effect of ash will depend on factors like ash loads and the dilution into environmental matrices such as water, soil and sediment. Our approach can serve as an initial methodological standardisation of wildfire ash sampling and chemical analysis protocols.

  • Taurine as a key intermediate for host-symbiont interaction in the tropical sponge Ianthella basta

    Moeller FU, Herbold CW, Schintlmeister A, Mooshammer M, Motti C, Glasl B, Kitzinger K, Behnam F, Watzka M, Schweder T, Albertsen M, Richter A, Webster NS, Wagner M
    2023 - The ISME journal, 17: 1208-1223


    Marine sponges are critical components of marine benthic fauna assemblages, where their filter-feeding and reef-building capabilities provide bentho-pelagic coupling and crucial habitat. As potentially the oldest representation of a metazoan-microbe symbiosis, they also harbor dense, diverse, and species-specific communities of microbes, which are increasingly recognized for their contributions to dissolved organic matter (DOM) processing. Recent omics-based studies of marine sponge microbiomes have proposed numerous pathways of dissolved metabolite exchange between the host and symbionts within the context of the surrounding environment, but few studies have sought to experimentally interrogate these pathways. By using a combination of metaproteogenomics and laboratory incubations coupled with isotope-based functional assays, we showed that the dominant gammaproteobacterial symbiont, ‘Candidatus Taurinisymbion ianthellae’, residing in the marine sponge, Ianthella basta, expresses a pathway for the import and dissimilation of taurine, a ubiquitously occurring sulfonate metabolite in marine sponges. ‘Candidatus Taurinisymbion ianthellae’ incorporates taurine-derived carbon and nitrogen while, at the same time, oxidizing the dissimilated sulfite into sulfate for export. Furthermore, we found that taurine-derived ammonia is exported by the symbiont for immediate oxidation by the dominant ammonia-oxidizing thaumarchaeal symbiont, ‘Candidatus Nitrosospongia ianthellae’. Metaproteogenomic analyses also suggest that ‘Candidatus Taurinisymbion ianthellae’ imports DMSP and possesses both pathways for DMSP demethylation and cleavage, enabling it to use this compound as a carbon and sulfur source for biomass, as well as for energy conservation. These results highlight the important role of biogenic sulfur compounds in the interplay between Ianthella basta and its microbial symbionts.

  • Engineered yeasts and lignocellulosic biomaterials: shaping a new dimension for biorefinery and global bioeconomy

    Asemoloye MD, Bello TS, Oladoye PO, Gbadamosi MR, Babarinde SO, Adebami GE, Olowe OM, Temporiti MEE, Wanek W, Marchisio MA
    2023 - Bioengineered, 14: Article 2269328


    The next milestone of synthetic biology research relies on the development of customized microbes for specific industrial purposes. Metabolic pathways of an organism, for example, depict its chemical repertoire and its genetic makeup. If genes controlling such pathways can be identified, scientists can decide to enhance or rewrite them for different purposes depending on the organism and the desired metabolites. The lignocellulosic biorefinery has achieved good progress over the past few years with potential impact on global bioeconomy. This principle aims to produce different bio-based products like biochemical(s) or biofuel(s) from plant biomass under microbial actions. Meanwhile, yeasts have proven very useful for different biotechnological applications. Hence, their potentials in genetic/metabolic engineering can be fully explored for lignocellulosic biorefineries. For instance, the secretion of enzymes above the natural limit (aided by genetic engineering) would speed-up the down-line processes in lignocellulosic biorefineries and the cost. Thus, the next milestone would greatly require the develop-ment of synthetic yeasts with much more efficient metabolic capacities to achieve basic requirements for particular biorefinery. This review gave comprehensive overview of lignocellulosic biomaterials and their importance in bioeconomy. Many researchers have demonstrated the engineering of several ligninolytic enzymes in heterologous yeast hosts. However, there are still many factors needing to be well under-stood like the secretion time, titter value, thermal stability, pH tolerance, and reactivity of the recombi-nant enzymes. Here, we give a detailed account of the potentials of engineered yeasts being discussed, as well as the constraints associated with their development and applications.

  • Soil CH4 and N2O response diminishes during decadal soil warming in a temperate mountain forest

    Heinzle J, Kitzler B, Zechmeister-Boltenstern S, Tian Y, Kengdo SW, Wanek W, Borken W, Schindlbacher A
    2023 - Agricultural and Forest Meteorology, 329: Article 109287


    Global warming is considered to impact the fluxes of methane (CH4) and nitrous oxide (N2O) between forest soils and the atmosphere, but it is unclear whether the responses change over time. In this study the response of soil CH4 and N2O fluxes to field soil warming (+4 °C) were determined during years 2–5 and 14–16 in a soil warming experiment in a temperate forest. In the second and sixteenth year of soil warming, temperature sensitivities of CH4 and N2O fluxes were assessed in-situ by gradually rising field soil temperatures to ∼10 °C above ambient within a short period of three to four days. Production of dinitrogen (N2) was measured ex-situ in the sixteenth year of warming. Soil warming significantly reduced CH4 uptake (-19.5%) and increased N2O emissions (+41.6%) during the first years of warming, whereas no warming effects on soil CH4 and N2O fluxes were observed during the later years. Dinitrogen production was up to ten times higher than N2O production, though the high spatiotemporal variability masked any significant effects of soil warming on soil N2 fluxes. Temperature sensitivities (Q10) for CH4 uptake and N2O emissions were 2.07 and 4.06, respectively, in the second year of warming and 1.52 and 1.79, respectively, in the sixteenth year of soil warming. The diminishing warming response of the soil N2O fluxes likely were caused by longer-term changes in soil N availability and/or simultaneous acclimation of the soil microbial community to soil warming. Soil moisture was largely unaffected by soil warming, and soil temperature alone was only a weak predictor of soil CH4 fluxes. Methane fluxes therefore can be expected to be generally less affected than N2O fluxes. Overall, our results suggest that soil warming has only limited and transient effects on soil CH4 and N2O fluxes in this type of temperate forest.

  • Modeling the carbon costs of plant phosphorus acquisition in Amazonian forests

    Reichert T, Rammig A, Papastefanou P, Lugli LF, Filho JPD, Gregor K, Fuchslueger L, Quesada CA, Fleischer K
    2023 - Ecological Modelling, 485: Article 110491


    Plants growing in low phosphorus (P) soils, such as in the predominant soils of Amazonia, are believed to devote more energy to acquiring P through absorptive root production, symbionts, and root exudates than plants in more fertile soils. Accounting for these energy costs in vegetation models is essential, as underestimating carbon (C) allocation to nutrient acquisition may lead to overestimating plant biomass growth. We developed a quantitative model to test a theoretical framework of C costs of P acquisition across soil P gradients. The model considers four strategies: P foraging via absorptive roots and arbuscular mycorrhizal fungi and P mining via root exudation of phosphatases and organic acids. We used field observations (i.e., soil data, plant biomass production, and stoichiometry of different organs) from ten sites across Amazonia to calibrate the model and explore different scenarios of (i) experimental soil P addition and (ii) elevated atmospheric 

    CO2 concentrations (

    eCO2). Our model reproduced expected trends in P-acquisition strategies, with plants increasingly investing in foraging strategies as soil soluble inorganic P (Pi) increases and increasingly investing in mining strategies as total P and less available P forms decrease. Relative investment in P acquisition was within observed ranges. Plants, on average and across all sites, invested the equivalent of 20.5% of their estimated total net primary production (NPP) in P acquisition. On average, plants allocated 15.3% of their NPP to P acquisition in the three most fertile sites, compared to 29.0% in the least fertile sites. C allocation to arbuscular mycorrhizas, phosphatases, and organic acids, which are not commonly measured components of total NPP, was up to 25.8% (16.9% on average) of the total NPP. We highlight the need for quantitative data on plant C allocation to P acquisition from the soil to strengthen further model development and future model projections.

  • The phageome in normal and inflamed human skin

    Wielscher M, Pfisterer K, Samardzic D, Balsini P, Bangert C, Jäger K, Buchberger M, Selitsch B, Pjevac P, Willinger B, Weninger W
    2023 - Science Advances, in press


    Dysbiosis of skin microbiota drives the progression of atopic dermatitis (AD). The contribution of bacteriophages to bacterial community compositions in normal and inflamed skin is unknown. Using shotgun metagenomics from skin swabs of healthy individuals and patients with AD, we found 13,586 potential viral contiguous DNA sequences, which could be combined into 164 putative viral genomes including 133 putative phages. The Shannon diversity index for the viral metagenome-assembled genomes (vMAGs) did not correlate with AD. In total, we identified 28 vMAGs that differed significantly between normal and AD skin. Quantitative polymerase chain reaction validation of three complete vMAGs revealed their independence from host bacterium abundance. Our data indicate that normal and inflamed skin harbor distinct phageomes and suggest a causative relationship between changing viral and bacterial communities as a driver of skin pathology.

  • Towards Harmonisation of Testing of Nanomaterials for EU Regulatory Requirements on Chemical Safety – A Proposal for Further Actions

    Eric A. J. Bleeker, Elmer Swart, Hedwig Braakhuis, Maria Luisa Fernandez Cruz, Steffi Friedrichs, Ilse Gosens, Frank Herzberg, Keld Alstrup Jensen, Frank von der Kammer, Jolinde A.B. Kettelarij, José María Navas, Kirsten Rasmussen, Kathrin Schwirn, Maaike Visser
    2023 - Regulatory Toxicology and Pharmacology, 139: 105360


    Over the recent years, EU chemicals legislation, guidance and test guidelines have been developed or adapted for nanomaterials to facilitate safe use of nanomaterials. This paper provides an overview of the information requirements across different EU regulatory areas. For each information requirement, a group of 22 experts identified potential needs for further action to accommodate guidance and test guidelines to nanomaterials. Eleven different needs for action were identified, capturing twenty-two information requirements that are specific to nanomaterials and relevant to multiple regulatory areas. These were further reduced to three overarching issues: 1) resolve issues around nanomaterial dispersion stability and dosing in toxicity testing, in particular for human health endpoints, 2) further develop tests or guidance on degradation and transformation of organic nanomaterials or nanomaterials with organic components, and 3) further develop tests and guidance to measure (a)cellular reactivity of nanomaterials. Efforts towards addressing these issues will result in better fit-for-purpose test methods for (EU) regulatory compliance. Moreover, it secures validity of hazard and risk assessments of nanomaterials. The results of the study accentuate the need for a structural process of identification of information needs and knowledge generation, preferably as part of risk governance and closely connected to technological innovation policy.

  • Jellyfish detritus supports niche partitioning and metabolic interactions among pelagic marine bacteria

    Tinta T, Zhao Z, Bayer B, Herndl GJ
    2023 - Microbiome, in press



    Jellyfish blooms represent a significant but largely overlooked source of labile organic matter (jelly-OM) in the ocean, characterized by a high protein content. Decaying jellyfish are important carriers for carbon export to the ocean’s interior. To accurately incorporate them into biogeochemical models, the interactions between microbes and jelly-OM have yet to be fully characterized. We conducted jelly-OM enrichment experiments in microcosms to simulate the scenario experienced by the coastal pelagic microbiome after the decay of a jellyfish bloom. We combined metagenomics, endo- and exo-metaproteomic approaches to obtain a mechanistic understanding on the metabolic network operated by the jelly-OM degrading bacterial consortium.


    Our analysis revealed that OM released during the decay of jellyfish blooms triggers a rapid shuffling of the taxonomic and functional profile of the pelagic bacterial community, resulting in a significant enrichment of protein/amino acid catabolism-related enzymes in the jelly-OM degrading community dominated by PseudoalteromonadaceaeAlteromonadaceae and Vibrionaceae, compared to unamended control treatments. In accordance with the proteinaceous character of jelly-OM, Pseudoalteromonadaceae synthesized and excreted enzymes associated with proteolysis, while Alteromonadaceae contributed to extracellular hydrolysis of complex carbohydrates and organophosphorus compounds. In contrast, Vibrionaceae synthesized transporter proteins for peptides, amino acids and carbohydrates, exhibiting a cheater-type lifestyle, i.e. benefiting from public goods released by others. In the late stage of jelly-OM degradation, Rhodobacteraceae and Alteromonadaceae became dominant, growing on jelly-OM left-overs or bacterial debris, potentially contributing to the accumulation of dissolved organic nitrogen compounds and inorganic nutrients, following the decay of jellyfish blooms.


    Our findings indicate that specific chemical and metabolic fingerprints associated with decaying jellyfish blooms are substantially different to those previously associated with decaying phytoplankton blooms, potentially altering the functioning and biogeochemistry of marine systems. We show that decaying jellyfish blooms are associated with the enrichment in extracellular collagenolytic bacterial proteases, which could act as virulence factors in human and marine organisms’ disease, with possible implications for marine ecosystem services. Our study also provides novel insights into niche partitioning and metabolic interactions among key jelly-OM degraders operating a complex metabolic network in a temporal cascade of biochemical reactions to degrade pulses of jellyfish-bloom-specific compounds in the water column.

  • The change in metabolic activity of a large benthic foraminifera as a function of light supply

    Lintner M, Lintner B, Schagerl M, Wanek W, Heinz P
    2023 - Scientific Reports, 13: Article 8240


    We studied metabolic activity of the symbiont-bearing large benthic foraminifer Heterostegina depressa under different light conditions. Besides the overall photosynthetic performance of the photosymbionts estimated by means of variable fluorescence, the isotope uptake (13C and 15N) of the specimens (= holobionts) was measured. Heterostegina depressa was either incubated in darkness over a period of 15 days or exposed to an 16:8 h light:dark cycle mimicking natural light conditions. We found photosynthetic performance to be highly related to light supply. The photosymbionts, however, survived prolonged darkness and could be reactivated after 15 days of darkness. The same pattern was found in the isotope uptake of the holobionts. Based on these results, we propose that 13C-carbonate and 15N-nitrate assimilation is mainly controlled by the photosymbionts, whereas 15N-ammonium and 13C-glucose utilization is regulated by both, the symbiont and the host cells.

  • 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: 116326


    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.

  • Water availability is a stronger driver of soil microbial processing of organic nitrogen than tree species composition

    Maxwell TL, Augusto L, Tian Y, Wanek W, Fanin N
    2023 - European Journal of Soil Science, 74: Article e13350


    Soil organic nitrogen (N) cycling processes constitute a bottleneck of soil N cycling, yet little is known about how tree species composition may influence these rates, and even less under changes in soil water availability such as those that are being induced by climate change. In this study, we used a 12-year-old tree biodiversity experiment in southwestern France to assess the interactive effects of soil water availability (half of the blocks seasonally irrigated to double precipitation) and tree species composition (monocultural vs. mixed plots of coniferous Pinus pinaster, and of broadleaf Betula pendula). We measured gross protein depolymerisation rates using a novel high-throughput isotope pool dilution method, along with soil microbial biomass carbon and N to calculate microbial biomass-specific activities of soil organic N processes. Overall, high soil water availability led to a 42% increase in soil protein depolymerisation rates compared to the unirrigated plots, but we found no effect of species composition on these soil organic N cycling processes. When investigating the interactive effect of tree species mixing and soil water availability, the results suggest that mixing tree species had a negative effect on soil organic N cycling processes in the non-irrigated blocks subject to dry summers, but that this effect tended to become positive at higher soil water availability in irrigated plots. These results put forth that soil water availability could influence potential tree species mixing effects on soil organic N cycling processes in dry conditions.

  • Hydrochemical and seasonally conditioned changes of microbial communities in the tufa-forming freshwater network ecosystem

    Čačković A, Kajan K, Selak L, Marković T, Brozičević A, Pjevac P, Orlić S
    2023 - mSphere, in press


    Freshwater network ecosystems consist of interconnected lotic and lentic environments within the same catchment area. Using Plitvice Lakes as an example, we studied the changes in environmental conditions and microbial communities (bacteria and fungi) that occur with downstream flow. Water samples from tributaries, interlake streams, connections of the cascading lakes, and the Korana River, the main outflow of the system, were characterized using amplicon sequencing of bacterial 16S rRNA and fungal ITS2 genes. Our results show that different environmental conditions and bacterial and fungal communities prevail among the three stream types within the freshwater network ecosystem during multiple sampling seasons. Microbial community differences were also confirmed along the longitudinal gradient between the most distant sampling sites. The higher impact of “mass effect” was evident during spring and winter, while “species sorting” and “environmental selection” was more pronounced during summer. Prokaryotic community assembly was majorly influenced by deterministic processes, while fungal community assembly was highly dominated by stochastic processes, more precisely by the undominated fraction, which is not dominated by any process. Despite the differences between stream types, the microbial community of Plitvice Lakes is shown to be very stable by the core microbiome that makes up the majority of stream communities. Our results suggest microbial community succession along the river-lake continuum of microbial communities in small freshwater network ecosystems with developed tufa barriers.
    IMPORTANCE Plitvice Lakes represent a rare freshwater ecosystem consisting of a complex network of lakes and waterfalls connecting them, as well as rivers and streams supplying water to the lake basin. The unique geomorphological, hydrological, biogeochemical, and biological phenomenon of Plitvice Lakes lies in the biodynamic process of forming tufa barriers. In addition to microbial communities, abiotic water factors also have a major influence on the formation of tufa. Therefore, it is important to understand how changes in environmental conditions and microbial community assembly affect the functioning of the ecosystem of a freshwater network with developed tufa barriers.

  • Machine learning and phylogenetic analysis allow for predicting antibiotic resistance in M. tuberculosis

    Yurtseven A, Buyanova S, Agrawal AA, Bochkareva OO, Kalinina OV
    2023 - in press
  • Exogenous nitrogen input skews estimates of microbial nitrogen use efficiency by ecoenzymatic stoichiometry

    Sun L, Moorhead DL, Cui Y, Wanek W, Li S, Wang C
    2023 - Ecological Processes, 12: 46



    Ecoenzymatic stoichiometry models (EEST) are often used to evaluate microbial nutrient use efficiency, but the validity of these models under exogenous nitrogen (N) input has never been clarified. Here, we investigated the effects of long-term N addition (as urea) on microbial N use efficiency (NUE), compared EEST and 18O-labeling methods for determining NUE, and evaluated EEST’s theoretical assumption that the ratios of standard ecoenzymatic activities balance resource availability with microbial demand.


    We found that NUE estimated by EEST ranged from 0.94 to 0.98. In contrast, estimates of NUE by the 18O-labeling method ranged from 0.07 to 0.30. The large differences in NUE values estimated by the two methods may be because the sum of β-N-acetylglucosaminidase and leucine aminopeptidase activities in the EEST model was not limited to microbial N acquisition under exogenous N inputs, resulting in an overestimation of microbial NUE by EEST. In addition, the acquisition of carbon by N-acquiring enzymes also likely interferes with the evaluation of NUE by EEST.


    Our results demonstrate that caution must be exercised when using EEST to evaluate NUE under exogenous N inputs that may skew standard enzyme assays.

  • Uptake, Metabolism, and Accumulation of Tire Wear Particle- Derived Compounds in Lettuce

    Stephanie Castan, Anya Sherman, Ruoting Peng, Michael Zumstein, Wolfgang Wanek, Thorsten Hüffer, Thilo Hofmann
    2023 - Environ. Sci. Technol., 57: 168-178


    Tire wear particle (TWP)-derived compounds may be of high concern to consumers when released in the root zone of edible plants. We exposed lettuce plants to the TWP-derived compounds diphenylguanidine (DPG), hexamethoxymethylmelamine (HMMM), benzothiazole (BTZ), N-phenyl-N′-(1,3-dimethylbutyl)-p-phenylenediamine (6PPD), and its quinone transformation product (6PPD-q) at concentrations of 1 mg L–1 in hydroponic solutions over 14 days to analyze if they are taken up and metabolized by the plants. Assuming that TWP may be a long-term source of TWP-derived compounds to plants, we further investigated the effect of leaching from TWP on the concentration of leachate compounds in lettuce leaves by adding constantly leaching TWP to the hydroponic solutions. Concentrations in leaves, roots, and nutrient solution were quantified by triple quadrupole mass spectrometry, and metabolites in the leaves were identified by Orbitrap high resolution mass spectrometry. This study demonstrates that TWP-derived compounds are readily taken up by lettuce with measured maximum leaf concentrations between ∼0.75 (6PPD) and 20 μg g–1 (HMMM). Although these compounds were metabolized in the plant, we identified several transformation products, most of which proved to be more stable in the lettuce leaves than the parent compounds. Furthermore, continuous leaching from TWP led to a resupply and replenishment of the metabolized compounds in the lettuce leaves. The stability of metabolized TWP-derived compounds with largely unknown toxicities is particularly concerning and is an important new aspect for the impact assessment of TWP in the environment.

  • A rapid and sensitive assay to quantify amino sugars, neutral sugars and uronic acid necromass biomarkers using pre-column derivatization, ultra-high-performance liquid chromatography and high-resolution mass spectrometry

    Salas E, Gorfer M, Bandian D, Wang B, Kaiser C, Wanek W
    2023 - Soil Biology and Biochemistry, 177: Article 108927


    Microbial necromass comprises a large fraction of soil organic matter (SOM) due to the accumulation and stabilization of microbial residues from dead archaea, bacteria and fungi. Amino sugars, neutral sugars and uronic acids have been used as microbial necromass biomarkers to trace the origin and composition of microbial residues in the SOM pool. Due to the structural complexity of sugars, derivatization reactions and high-throughput analytical methods are required to separate and quantify these sugar-related compounds. Our aim was to develop a rapid and sensitive assay to measure amino sugar, neutral sugar and uronic acid compounds using pre-column 1-phenyl-3-methyl-5-pyrazolone (PMP) derivatization. PMP-derivatives were separated and quantified via reversed phase (RP) ultra-high-performance liquid chromatography (UPLC) coupled to high-resolution Orbitrap mass spectrometry (MS). The method was validated and applied on hydrolyzed peptidoglycans and the biomass of archaeal, bacterial, fungal and plant species, as well as with soils. This developed PMP method allowed the separation and quantification of 18 sugar-related compounds, including four amino sugars, three N-acetyl amino sugars, eight neutral sugars, and three uronic acids within 20 min. This PMP method showed a precision for isotope enrichment detection of 0.03–0.05 atom % 13C for D-glucose and D-glucosamine. This is the first time talosaminuronic acid (deriving from archaeal pseudopeptidoglycan) was identified and quantified using PMP derivatization. The application of this novel PMP method on pure hydrolyzed biomass and soils, showed the successful chromatographic and mass spectrometric separation and quantification of amino sugar, neutral sugar and uronic acid compounds. A multivariate analysis using these sugar-related PMP derivatives showed a clustering of the species according to their respective taxonomic group (archaea, gram-positive bacteria, gram-negative bacteria, fungi and plants). The modified PMP method can be applied to identify and quantify soil microbial necromass biomarkers, as well as their contribution to SOM. The sensitive isotope tracer detection allows tracing isotopically labeled materials into necromass biomarkers in SOM pools.

  • Addressing Chemical Pollution in Biodiversity Research

    Gabriel Sigmund, Marlene Ågerstrand, Alexandre Antonelli, Thomas Backhaus, Tomas Brodin, Miriam L. Diamond, Walter R. Erdelen, David C. Evers, Thilo Hofmann, Thorsten Hueffer, Adelene Lai, Joao P. M. Torres, Leonie Mueller, Allison L. Perrigo, Matthias C. Rillig, Andreas Schaeffer, Martin Scheringer, Kristin Schirmer, Ahmed Tlili, Anna Soehl, Rita Triebskorn, Penny Vlahos, Colette vom Berg, Zhanyun Wang, Ksenia J. Groh
    2023 - Global Change Biology, 12: 3240-3255


    Climate change, biodiversity loss, and chemical pollution are planetary-scale emergencies requiring urgent mitigation actions. As these “triple crises” are deeply interlinked, they need to be tackled in an integrative manner. However, while climate change and biodiversity are often studied together, chemical pollution as a global change factor contributing to worldwide biodiversity loss has received much less attention in biodiversity research so far. Here, we review evidence showing that the multifaceted effects of anthropogenic chemicals in the environment are posing a growing threat to biodiversity and ecosystems. Therefore, failure to account for pollution effects may significantly undermine the success of biodiversity protection efforts. We argue that progress in understanding and counteracting the negative impact of chemical pollution on biodiversity requires collective efforts of scientists from different disciplines, including but not limited to ecology, ecotoxicology, and environmental chemistry. Importantly, recent developments in these fields have now enabled comprehensive studies that could efficiently address the manifold interactions between chemicals and ecosystems. Based on their experience with intricate studies of biodiversity, ecologists are well equipped to embrace the additional challenge of chemical complexity through interdisciplinary collaborations. This offers a unique opportunity to jointly advance a seminal frontier in pollution ecology and facilitate the development of innovative solutions for environmental protection.

  • Soil organic carbon accumulation and microbial carbon use efficiency in subalpine coniferous forest as influenced by forest floor vegetative communities

    Xiong J, Wang G, Richter A, DeLuca TH, Zhang W, Sun H, Hu Z, Sun X, Sun S
    2023 - Geoderma, 438: Article 11664



    The importance of forest floor plants (herbs and mosses) and understory communities on soil C dynamics has been grossly understudied in forest ecosystems; however, there is currently very little knowledge on the impact of forest floor vegetation composition on soil organic C (SOC) accumulation and the microbial metabolic processes. To bridge this gap of knowledge, a forest floor vegetation-removal experiment involving nonvascular mosses (Pleurozium schreberi (PS); Rhizomnium tuomikoskii (RT); and Hylocomiastrum pyrenaicum (HP)) and vascular sedges (Carex sp., CS) was conducted in a subalpine coniferous forest on the eastern edge of Tibetan Plateau, to investigate the associations of different forest floor vegetation communities with mineral soil C accumulation and microbial physiology (C use efficiency (CUE) and microbial biomass turnover). Soils beneath the forest floor vegetative communities differed in soil C and nitrogen (N) concentrations and had distinctively different microbial community structure and physiology. Compared to bare soils, sedge soils had significantly greater SOC and dissolved organic C (DOC) accumulation, greater microbial DNA, biomass C and phospholipid fatty acids (PLFAs) concentrations, and higher microbial CUE and shorter microbial biomass turnover time. While effects of mosses differed among species, P. schreberi had similar effects as sedges, but the effects of H. pyrenaicum and R. tuomikoskii were minimal. Relative to bare soil, P. schreberi and Carex sp. soils were 61.5% and 51.6% higher in microbial CUE and had an obviously shorter microbial biomass turnover time. Variations in the level of DOC and PLFAs (rather than their portion relative to SOC) were the most important regulators of microbial CUE and biomass turnover rate in soils with different forest floor vegetation covers. These results highlight how differences in soil organic matter quality that are directly related to the forest floor vegetation community influence the microbial CUE and biomass turnover and the long-term soil C dynamics.

  • Beyond PLFA: Concurrent extraction of neutral and glycolipid fatty acids provides new insights into soil microbial communities

    Gorka S, Darcy S, Horak J, Imai B, Mohrlok M, Salas E, Richter A, Schmidt H, Wanke W, Kaiser C, Canarini A
    2023 - Soil Biology and Biochemistry, 187: Article 109205


    The analysis of phospholipid fatty acids (PLFAs) is one of the most common methods used to quantify the abundance, and analyse the community structure, of soil microbes. The PLFA extraction method can yield two additional lipid fractions—neutral lipids and glycolipids—which potentially hold additional, valuable information on soil microbial communities. Yet its quantitative sensitivity on complete neutral lipid (NLFA) and glycolipid fatty acid (GLFA) profiles has never been validated. In this study we tested (i) if the high-throughput PLFA method can be expanded to concurrently extract complete NLFA and GLFA profiles, as well as sterols, (ii) whether taxonomic specificities of signature fatty acids are retained across the three lipid fractions in pure culture strains, and (iii) whether NLFAs and GLFAs allow soil-specific fingerprinting to the same extent as PLFA analysis. By adjusting the polarity of chloroform with 2% ethanol for solid phase extraction, pure lipid standards were fully fractionated into neutral lipidsglycolipids, and phospholipids. Sterols eluted in the neutral lipid fraction, and a betaine lipid co-eluted with phospholipids. We found consistent taxonomic specificities of fatty acid markers across the three lipid fractions by analysing pure culture extracts representative of soil microbes. Fatty acid profiles from soil extracts, however, showed stronger differences between PLFAs, NLFAs, and GLFAs than between soil types. This indicates that PLFAs and NLFAs signify different community properties (biomass vs. carbon storage, putatively), and that GLFAs are sensitive markers for community traits which behave differently than PLFAs. Although we consistently found high abundances of characteristic sterols in fungal extracts, the PLFA extraction method only yielded miniscule amounts of ergosterol from soil extracts. We argue that concomitant measurement of fatty acid profiles from all three lipid fractions is a low-effort and potentially information-rich addition to the PLFA method, and discuss its applicability for soil microbial community analyses.

  • 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, 2: 151-161


    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 fluctuations of extracellular enzyme activities are related to the biogeochemical cycling of C, N and P in a tropical terra-firme forest

    Schaap KJ, Fuchslueger L, Quesada CA, Hofhansl F, Valverde-Barrantes O, Camargo PB, Hoosbeek MR
    2023 - Biogeochemistry, 163: 1-15


    Extracellular enzymes (EE) play a vital role in soil nutrient cycling and thus affect terrestrial ecosystem functioning. Yet the drivers that regulate microbial activity, and therefore EE activity, remain under debate. In this study we investigate the temporal variation of soil EE in a tropical terra-firme forest. We found that EE activity peaked during the drier season in association with increased leaf litterfall, which was also reflected in negative relationships between EE activities and precipitation. Soil nutrients were weakly related to EE activities, although extractable N was related to EE activities in the top 5 cm of the soil. These results suggest that soil EE activity is synchronized with precipitation-driven substrate inputs and depends on the availability of N. Our results further indicate high investments in P acquisition, with a higher microbial N demand in the month before the onset of the drier season, shifting to higher P demand towards the end of the drier season. These seasonal fluctuations in the potential acquisition of essential resources imply dynamic shifts in microbial activity in coordination with climate seasonality and resource limitation of central-eastern Amazon forests.

  • Environmental factors strongly influence the leaching of di(2-ethylhexyl) phthalate from polyvinyl chloride microplastics

    Charlotte Henkel, Jonas Lamprecht, Thorsten Hüffer, Thilo Hofmann
    2023 - Water Research, 242: 120235


    Phthalic acid esters (phthalates) are an important group of additives (plasticizers) to ensure the flexibility and stability especially of polyvinyl chloride (PVC) and to enable its processing. However, phthalates like di(2-ethylhexyl) phthalate (DEHP) are harmful for aquatic organisms due to their endocrine disrupting effects and toxicity. For the assessment of exposure concentrations, thorough understanding of leaching kinetics of phthalates from PVC (micro-) plastics into aqueous environments is necessary. This study investigates how environmental factors influence the leaching of phthalates from PVC microplastics into aquatic systems. The leaching of phthalates from PVC microplastics into aqueous media is limited by aqueous boundary layer diffusion (ABLD) and thus, process-specific parameters can be affected by environmental factors such as salinity and the flow conditions. We conducted batch leaching experiments to assess the influence of salinity and flow conditions (turbulence) on the leaching of DEHP from PVC microplastics into aqueous media. DEHP is salted out with increasing salinity of the solution and a salting-out coefficient for DEHP of 0.46 was determined. The partitioning coefficient of DEHP between PVC and water KPVC/W increased with increasing salinity from 108.52 L kg−1 in a 1 mM KCl solution to 108.75 L kg−1 in artificial seawater thereby slowing down leaching. Increasing flow velocities led to higher leaching rates because the ABL thickness decreased from 1315 µm at 0 rpm shaking speed (no-flow conditions) to 38.4 µm at 125 rpm (turbulent conditions). Compared to salinity, turbulence had a more pronounced effect on leaching. Increasing the flow velocity led to a 35-fold decrease in the leaching rate, while increasing salinity led to a 2-fold increase. By calculating specific leaching times, that is, leaching half-lives (t1/2), time frames for leaching in different aquatic systems such as rivers and the ocean were determined. Given ABLD-limited leaching, DEHP is leached faster from PVC microplastics in rivers (t1/2 > 49 years) than in the ocean (t1/2 > 398 years). In both systems, PVC microplastics are a long-term source of phthalates.

  • Cultivation and genomic characterization of novel and ubiquitous marine nitrite-oxidizing bacteria from the Nitrospirales

    Mueller AJ, Daebeler A, Herbold CW, Kirkegaard RH, Daims H
    2023 - ISME J., in press


    Nitrospirales, including the genus Nitrospira, are environmentally widespread chemolithoautotrophic nitrite-oxidizing bacteria. These mostly uncultured microorganisms gain energy through nitrite oxidation, fix CO2, and thus play vital roles in nitrogen and carbon cycling. Over the last decade, our understanding of their physiology has advanced through several new discoveries, such as alternative energy metabolisms and complete ammonia oxidizers (comammox Nitrospira). These findings mainly resulted from studies of terrestrial species, whereas less attention has been given to marine Nitrospirales. In this study, we cultured three new marine Nitrospirales enrichments and one isolate. Three of these four NOB represent new Nitrospira species while the fourth represents a novel genus. This fourth organism, tentatively named “Ca. Nitronereus thalassa”, represents the first cultured member of a Nitrospirales lineage that encompasses both free-living and sponge-associated nitrite oxidizers, is highly abundant in the environment, and shows distinct habitat distribution patterns compared to the marine Nitrospira species. Partially explaining this, “Ca. Nitronereus thalassa” harbors a unique combination of genes involved in carbon fixation and respiration, suggesting differential adaptations to fluctuating oxygen concentrations. Furthermore, “Ca. Nitronereus thalassa” appears to have a more narrow substrate range compared to many other marine nitrite oxidizers, as it lacks the genomic potential to utilize formate, cyanate, and urea. Lastly, we show that the presumed marine Nitrospirales lineages are not restricted to oceanic and saline environments, as previously assumed.

  • Genome rearrangements drive evolution of ANK genes in Wolbachia

    Vostokova EV, Dranenko NO, Gelfand MS, Bochkareva OO
    2023 - in press


    Genus Wolbachia comprises endosymbionts infecting many arthropods and nematodes; it is a model for studying symbiosis as its members feature numerous, diverse mutualistic and parasitic adaptations to different hosts. In contrast to nematode-infecting Wolbachia, genomes of arthropod-infecting strains contain a high fraction of repetitive elements creating possibilities for multiple recombination events and causing genome rearrangements. The mechanisms and role of these features are still not fully understood. Transposons cover up to 18% of an arthropod-infecting Wolbachia genome and drive numerous genome rearrangements including inversions and segmental amplifications. ANK (ankyrin-repeat domain family) genes are also often found at the breakpoints of rearrangements, while less than 7% of them were found within locally collinear blocks (LCBs). We observed a strong correlation between the number of ANK genes and the genome size as well as significant overrepresentation of transposons adjacent to these genes. We also revealed numerous cases of integration of transposases to the ANK genes affecting the sequences and putative products of the latter. Our results uncover the role of mobile elements in the amplification and diversification of ANK genes. Evolution of arthropod-infecting Wolbachia was accompanied by diverse genome rearrangements driving the evolution of ANK genes important for bacteria-host interactions. This study demonstrates the effectiveness of our LCB-based approach to the Wolbachia genomics and provides a framework for understanding the impact of genome rearrangements on their rapid host adaptation.

  • Responses of soil hexapod communities to warming are mediated by microbial carbon and nitrogen in a subarctic grassland

    Ferrín M. Peñuelas J, Gargallo-Garriga A, Iribar A, Janssens IA, Marañon-Jimenez S, Murienne J, Richter A, Sigurdsson BD, Peguero G
    2023 - European Journal of Soil Biology, 117: Article 103513


    Warming in subarctic ecosystems will be two-fold higher compared to lower latitudes under current climate change projections. While the effects of warming in northern ecosystems on plants and microorganisms have been extensively studied, the responses of soil fauna have received much less attention, despite their important role in regulating key soil processes. We analyzed the response of soil hexapod communities in a subarctic grassland exposed to a natural geothermal gradient in Iceland with increases of +3 and + 6 °C above ambient temperature. We characterized hexapod communities using environmental DNA (eDNA) metabarcoding. We analyzed the amounts of microbial carbon (Cmic), microbial N (Nmic), dissolved organic C (DOC) and dissolved organic N (DON) and then assessed whether these variables could help to account for the compositional dissimilarity of ground hexapod communities across temperatures. The increases in soil temperature did lead to changes in the composition of hexapod communities. The compositional differences caused by +6 °C plots were correlated with a decrease in Cmic and Nmic, soil DOC and DON. Our results highlight the response of soil hexapods to warming, and their interaction with microbial biomass ultimately correlated with changes in the availabilities of soil C and N.

  • Microbial growth under drought is confined to distinct taxa and modified by potential future climate conditions

    Metze M, Schnecker J, Canarini A, Fuchslueger L, Koch BJ, Stone BW, Hungate BA, Hausmann B, Schmidt H, Schaumberger A, Bahn M, Kaiser C, Richter A
    2023 - Nature Communication, 14: Article 5895


    Climate change increases the frequency and intensity of drought events, affecting soil functions including carbon sequestration and nutrient cycling, which are driven by growing microorganisms. Yet we know little about microbial responses to drought due to methodological limitations. Here, we estimate microbial growth rates in montane grassland soils exposed to ambient conditions, drought, and potential future climate conditions (i.e., soils exposed to 6 years of elevated temperatures and elevated CO2 levels). For this purpose, we combined 18O-water vapor equilibration with quantitative stable isotope probing (termed ‘vapor-qSIP’) to measure taxon-specific microbial growth in dry soils. In our experiments, drought caused >90% of bacterial and archaeal taxa to stop dividing and reduced the growth rates of persisting ones. Under drought, growing taxa accounted for only 4% of the total community as compared to 35% in the controls. Drought-tolerant communities were dominated by specialized members of the Actinobacteriota, particularly the genus Streptomyces. Six years of pre-exposure to future climate conditions (3 °C warming and + 300 ppm atmospheric CO2) alleviated drought effects on microbial growth, through more drought-tolerant taxa across major phyla, accounting for 9% of the total community. Our results provide insights into the response of active microbes to drought today and in a future climate, and highlight the importance of studying drought in combination with future climate conditions to capture interactive effects and improve predictions of future soil-climate feedbacks.

  • Isolation of Carbon Black from Soils by Dispersion for Analysis: Quantitation and Characterization by Field Flow Fractionation Techniques

    Lorenzo Sanjuan-Navarro, Aaron Boughbina-Portolés, Yolanda Moliner-Martinéz, Frank von der Kammer, Pilar Campíns-Falcó
    2023 - ACS Omega, 8: 34795−34804


    In the present work, a procedure based on a dispersive medium for carbon black (CB) isolation from soil samples for analysis was proposed for the first time. Polymeric and biological dispersants and a sequential use of both dispersants were assayed. Asymmetrical flow field flow fractionation with dynamic light scattering detector (AF4-DLS) and sedimentation field flow fractionation with multi-angle light scattering detector (SdF3-MALS) were used for CB quantitation and characterization in the achieved dispersions. Soil samples contaminated with CB were processed, and CB isolation depended on the solid size distribution and composition and dispersant nature. More quantitative isolations were achieved for the four soils treated by the biological dispersant. As the organic matter percentage is higher in soil, the CB isolation was better, varying between 75 and 99% with standard deviation (s) ⩽ 2% for all soils. A soil contaminated with a CB-based pigment paste was analyzed, achieving (99 ± 2)% expressed as expanded uncertainty (K = 2) of dispersive isolation by the biological dispersant, and the sampling was scaled to 250 g of soil with positive results. The procedure was completed by CB recovery to obtain a solid residue able to be reused if necessary. For the filter-aided recovery step, different membranes (fiberglass, nylon, and Teflon) with a pore size between 0.1 and 5 μm were tested. The quantitation of the CB retained in the filter was measured by diffuse reflectance spectroscopy. Teflon (0.10 μm) provided better results for CB recovery, and its re-dispersion was also studied with suitable results. Determination of CB from the filters by diffuse reflectance spectrometry provided the same results than AF4 for CB dispersions.

  • Revisiting process-based simulations of soil nitrite dynamics: Tighter cycling between nitrite and nitrate than considered previously

    Zheng J, Fujii K, Koba K, Wanek W, Muller C, Jansen-Willems AB, Nakajima Y, Wagai R, Canarini A
    2023 - Soil Biology and Biochemistry, 178: Article 108958


    Nitrite is an important precursor of many environmentally hazardous compounds (e.g., nitrate, nitrous oxide, and nitrous acid). However, its dynamics in the soil environment are not yet fully understood. The NtraceNitrite tool has been successful in analyzing 15N tracing data. Here, based on a 15N tracing experiment (under aerobic condition) where either the nitrite, the nitrate, or the ammonium pool was labelled, we developed an extended model (NO2Trace), which was featured by the addition of coupled nitrate reduction and nitrite re-oxidation and the separation of the nitrate pool in two sub-pools. With 5 additional parameters optimized, NO2Trace was able to achieve a superior fit to the data, as compared to the NtraceNitrite tool. The additional features might offer a suitable explanation for the isotopic composition of nitrate produced via nitrification in terrestrial ecosystems. Our results carry two important implications: (i) a key assumption of the classical isotope pool dilution technique (i.e., no reflux of tracer) for estimating gross nitrate fluxes is violated, leading to considerable underestimations (22–99% in the datasets tested); (ii) re-oxidation can dominate the consumption (∼75%) of nitrite derived from nitrate reduction, indicating the potential of this process as a target for nitrogen retention mechanism against gaseous nitrogen losses (through nitrite reduction). The additional features of the extended model show a tighter cycle between soil nitrite and nitrate than considered previously and provide a more comprehensive description of soil nitrite transformations. This study also highlights that more work is needed to develop methods capable of separating process- and pathways-specific nitrate and nitrite pools.

  • Eco-Corona Dictates Mobility of Nanoplastics in Saturated Porous Media: The Critical Role of Preferential Binding of Macromolecules

    Meiling Zhu, Zhanhua Zhang, Tong Zhang, Thilo Hofmann, Wei Chen
    2023 - Environ. Sci. Technol., 57: 331-339


    Nanoplastics are an increasing environmental concern. In aquatic environments, nanoplastics will acquire an eco-corona by interacting with macromolecules (e.g., humic substances and extracellular polymeric substances (EPS)). Here, we show that the properties of the eco-corona and, consequently, its ability to enhance the transport of nanoplastics vary significantly with the surface functionality of nanoplastics and sources of macromolecules. The eco-corona derived from the EPS of Gram-negative Escherichia coli MG1655 enhances the transport of polystyrene (PS) nanospheres in saturated porous media to a much greater extent than the eco-corona derived from soil humic acid and fulvic acid. In comparison, the eco-corona from all three sources significantly enhance the transport of carboxylated PS (HOOC-PS). We show that the eco-corona inhibits the deposition of the two types of nanoplastics to the porous media mainly via steric repulsion. Accordingly, an eco-corona consisting of a higher mass of larger-sized macromolecules is generally more effective in enhancing transport. Notably, HOOC-PS tends to acquire macromolecules of lower hydrophobicity than PS. The more disordered and flexible structures of such macromolecules may result in greater elastic repulsion between the nanoplastics and sand grains and, consequently, greater transport enhancement. The findings of this study highlight the critical role of eco-corona formation in regulating the mobility of nanoplastics, as well as the complexity of this process.

  • 24-norursodeoxycholic acid ameliorates experimental alcohol-related liver disease and activates hepatic PPARγ

    Grander C, Meyer M, Steinacher D, Claudel T, Hausmann B, Pjevac P, Grabherr F, Oberhuber G, Grander M, Brigo N, Jukic A, Schwärzler J, Weiss G, Adolph TE, Trauner M, Tilg H
    2023 - JHEP reports, in press



    Alcohol-related liver disease (ALD) is a global health care challenge with limited treatment options. 24-norursodeoxycholic acid (norUDCA) is a synthetic bile acid with anti-inflammatory properties in experimental and human cholestatic liver diseases. In the present study we explored the efficacy of norUDCA in experimental ALD.


    NorUDCA was tested in a preventive and a therapeutic setting in an experimental ALD model (Lieber-DeCarli diet enriched with ethanol). Liver disease was phenotypically evaluated by histology and biochemical methods, and anti-inflammatory properties and peroxisome proliferator-activated receptor gamma (PPARg) activation by norUDCA were evaluated in cellular model systems.


    NorUDCA administration ameliorated ethanol-induced liver injury, hepatocyte death and reduced the expression of hepatic pro-inflammatory cytokines including tumor necrosis factor (Tnf), interleukin (Il)-1β, Il-6 and Il-10. NorUDCA shifted hepatic macrophages towards an anti-inflammatory M2 phenotype. Further norUDCA administration altered the composition of the intestinal microbiota, specifically increasing the abundance of RoseburiaEnterobacteriaceae and Clostridum spp.. In a therapeutic model norUDCA also ameliorated ethanol-induced liver injury. Moreover, norUDCA suppressed lipopolysaccharide (LPS)-induced IL-6 expression in human peripheral blood mononuclear cells and evoked PPARg activation.


    NorUDCA ameliorated experimental ALD, protected against hepatic inflammation and affected gut microbial commensalism. NorUDCA could serve as a novel therapeutic agent in the future management of patients with ALD.
  • Increase in fine root biomass enhances root exudation by long-term soil warming in a temperate forest

    Heinzle J, Liu X, Tian Y, Kengdo SK, Heinze B, Nirschi A, Borken W, Inselsbacher E, Wanek W, Schindlbacher A
    2023 - Frontiers in Forests and Global Change, 6: Article 1152142


    Trees can invest up to one-third of the carbon (C) fixed by photosynthesis into belowground allocation, including fine root exudation into the rhizosphere. It is still unclear how climate and soil warming affect tree root C exudation, in particular quantifying longer-term warming effects remains a challenge. In this study, using a C-free cuvette incubation method, in situ C exudation rates from tree fine roots of a mature spruce dominated temperate forest were measured in regular intervals during the 14th and 15th year of experimental soil warming (+ 4°C). In addition, a short-term temperature sensitivity experiment (up to + 10°C warming within 4 days) was conducted to determine the inherent temperature sensitivity of root exudation. Root exudation rates in the long-term warmed soil (17.9 μg C g–1 root biomass h–1) did not differ from those in untreated soil (16.2 μg C g–1 root biomass h–1). However, a clear increase (Q10 ∼5.0) during the short-term temperature sensitivity experiment suggested that fine root exudation can be affected by short-term changes in soil temperature. The absence of response in long-term warmed soils suggests a downregulation of C exudation from the individual fine roots in the warmed soils. The lack of any relationship between exudation rates and the seasonal temperature course, further suggests that plant phenology and plant C allocation dynamics have more influence on seasonal changes in fine root C exudation. Although exudation rates per g dry mass of fine roots were only marginally higher in the warmed soil, total fine root C exudation per m2 soil surface area increased by ∼30% from 0.33 to 0.43 Mg C ha–1 yr–1 because long-term soil warming has led to an increase in total fine root biomass. Mineralization of additional fine root exudates could have added to the sustained increase in soil CO2 efflux from the warmed forest soil at the experimental site.

  • 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: 121301


    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.

  • The nasal microbiome in patients suffering from non-steroidal anti-inflammatory drugs-exacerbated respiratory disease (N-ERD) in absence of corticosteroids

    Bartosik TJ, Campion NJ, Freisl K, Liu DT, Gangl K, Stanek V, Tu A, Pjevac P, Hausmann B, Eckl-Dorna J, Schneider S
    2023 - Front. Immunol., in press


    Chronic rhinosinusitis (CRS) is an inflammatory disease phenotypically classified by the absence (CRSsNP) or presence of nasal polyps (CRSwNP). The latter may also be associated with asthma and hypersensitivity towards non-steroidal anti-inflammatory drugs (NSAID) as a triad termed NSAID-exacerbated respiratory disease (N-ERD). The role of the microbiome in these disease entities with regard to the underlying inflammatory process and disease burden is yet not fully understood. To address this question, we measured clinical parameters and collected nasal samples (nasal mucosal fluids and microbiome swabs) of patients suffering from CRSsNP (n=20), CRSwNP (n=20) or N-ERD (n=20) as well as from patients without CRS (=disease controls, n=20). Importantly, all subjects refrained from taking local or systemic corticosteroids or immunosuppressants for at least two weeks prior to sampling. The nasal microbiome was analyzed using 16S rRNA gene amplicon sequencing, and levels of 33 inflammatory cytokines were determined in nasal mucosal fluids using the MSD platform.

    Patients suffering from N-ERD and CRSwNP showed significantly worse smell perception and significantly higher levels of type 2 associated cytokines IL-5, IL-9, Eotaxin and CCL17. Across all 4 patient groups, Corynebacteria and Staphylococci showed the highest relative abundances. Although no significant difference in alpha and beta diversity was observed between the control and the CRS groups, pairwise testing revealed a higher relative abundance of Staphylococci in the middle meatus in N-ERD patients as compared to CRSwNP (p<0.001), CRSsNP (p<0.01) and disease controls (p<0.05) and of Lawsonella in patients suffering from CRSwNP in middle meatus and anterior naris in comparison to CRSsNP (p<0.0001 for both locations) and disease controls (p<0.01 and p<0.0001). Furthermore, we observed a positive correlation of Staphylococci with IL-5 (Pearson r=0.548) and a negative correlation for Corynebacteria and Eotaxin-3 (r=-0.540). Thus, in patients refraining from oral and nasal corticosteroid therapy for at least two weeks known to alter microbiome composition, we did not observe differences in microbiome alpha or beta diversity between various CRS entities and disease controls. However, our data suggest a close association between increased bacterial colonization with Staphylococci and decreased colonization by Corynebacteria as well as increased type 2 inflammation and disease burden.

  • Is sorption technology fit for the removal of persistent and mobile organic contaminants from water?

    Benedikt M. Aumeier, Anett Georgi, Navid Saeidi, Gabriel Sigmund
    2023 - Science of The Total Environment, 880: 163343


    Persistent, Mobile, and Toxic (PMT) and very persistent and very mobile (vPvM) substances are a growing threat to water security and safety. Many of these substances are distinctively different from other more traditional contaminants in terms of their charge, polarity, and aromaticity. This results in distinctively different sorption affinities towards traditional sorbents such as activated carbon. Additionally, an increasing awareness on the environmental impact and carbon footprint of sorption technologies puts some of the more energy-intensive practices in water treatment into question. Commonly used approaches may thus need to be readjusted to become fit for purpose to remove some of the more challenging PMT and vPvM substances, including for example short chained per- and polyfluoroalkyl substances (PFAS). We here critically review the interactions that drive sorption of organic compounds to activated carbon and related sorbent materials and identify opportunities and limitations of tailoring activated carbon for PMT and vPvM removal. Other less traditional sorbent materials, including ion exchange resins, modified cyclodextrins, zeolites and metal-organic frameworks are then discussed for potential alternative or complementary use in water treatment scenarios. Sorbent regeneration approaches are evaluated in terms of their potential, considering reusability, potential for on-site regeneration, and potential for local production. In this context, we also discuss the benefits of coupling sorption to destructive technologies or to other separation technologies. Finally, we sketch out possible future trends in the evolution of sorption technologies for PMT and vPvM removal from water.

  • Defects in microvillus crosslinking sensitize to colitis and inflammatory bowel disease

    Mödl B, Awad M, Zwolanek D, Scharf I, Schwertner K, Milovanovic D, Moser D, Schmidt K, Pjevac P, Hausmann B, Krauß D, Mohr T, Svinka J, Kenner L, Casanova E, Timelthaler G, Sibilia M, Krieger S, Eferl R
    2023 - EMBO Reports, in press


    Intestinal epithelial cells are covered by the brush border, which consists of densely packed microvilli. The Intermicrovillar Adhesion Complex (IMAC) links the microvilli and is required for proper brush border organization. Whether microvillus crosslinking is involved in the intestinal barrier function or colitis is currently unknown. We investigate the role of microvillus crosslinking in colitis in mice with deletion of the IMAC component CDHR5. Electron microscopy shows pronounced brush border defects in CDHR5-deficient mice. The defects result in severe mucosal damage after exposure to the colitis-inducing agent DSS. DSS increases the permeability of the mucus layer and brings bacteria in direct contact with the disorganized brush border of CDHR5-deficient mice. This correlates with bacterial invasion into the epithelial cell layer which precedes epithelial apoptosis and inflammation. Single-cell RNA sequencing data of patients with ulcerative colitis reveals downregulation of CDHR5 in enterocytes of diseased areas. Our results provide experimental evidence that a combination of microvillus crosslinking defects with increased permeability of the mucus layer sensitizes to inflammatory bowel disease.

  • Functional redundant soil fauna and microbial groups and processes were fairly resistant to drought in an agroecosystem

    Watzinger A, Prommer J, Spiridon A, Kisielinska W, Hood-Nowotny R, Leitner S, Wanek W, Resch C, Heiling M, Murer E, Formayer H, Wawra A, Miloczki J
    2023 - Ecological Processes, 59: 629-641


    Climate change scenarios predict more frequent and intense drought periods for 2071 to 2100 for many regions of the world including Austria. Current and predicted lower precipitation scenarios were simulated at a lysimeter station containing a fertile and less fertile agricultural soil for 9 years. 13C and 15N-labeled green manure was added in year 8 with the aim to analyze how the predicted precipitation regime affects soil fauna and microbial groups and consequently nitrogen (N) and carbon (C) cycling. Among the investigated mesofauna (collembola and oribatida), the abundance and biodiversity of oribatida was significantly reduced by drought, possibly because they mainly represent K-strategist species with low mobility and consequently the need to adapt to long-term adverse environmental conditions. Microbial community composition and microbial biomass, investigated by phospholipid fatty acid (PLFA) analysis, was indistinguishable between the current and the predicted precipitation scenarios. Nonetheless, soil 13C-CO2 emissions and soil water 15N-NO3 data revealed decelerated mineralization of green manure under reduced precipitation in the first 2 weeks, but no effects were observed on soil C sequestration or on 13C incorporation into microbial PLFAs in the following 1.2 years. We found that over a 1-year time period, decomposition was rather driven by plant residue availability than water limitation of microorganisms in the investigated agroecosystem. In contrast, N2O emissions were significantly reduced under drought, and green manure derived 15N accumulated in the soil under drought, which might necessitate the adjustment of future fertilization regimes. The impacts of reduced precipitation and drought were less pronounced in the more fertile agricultural soil, due to its greater buffering capacity in terms of water storage and organic matter and nutrient availability.

  • Results of an interlaboratory comparison for characterization of Pt nanoparticles using singleparticle ICP-TOFMS

    Lyndsey Hendriks, Robert Brünjes, Sara Taskula, Jovana Kocic, Bodo Hattendorf, Garret Bland, Gregory Lowry, Eduardo Bolea-Fernandez, Frank Vanhaecke, Jingjing Wang, Mohammed Baalousha, Marcus von der Au, Björn Meermann, Timothy Ronald Holbrook, Stephan Wagner, Stasia Harycki, Alexander Gundlach-Graham, Frank von der Kammer
    2023 - Nanoscale, 15: 11268-11279


    This study describes an interlaboratory comparison (ILC) among nine (9) laboratories to evaluate and validate
    the standard operation procedure (SOP) for single-particle (sp) ICP-TOFMS developed within the
    context of the Horizon 2020 project ACEnano. The ILC was based on the characterization of two different Pt
    nanoparticle (NP) suspensions in terms of particle mass, particle number concentration, and isotopic composition.
    The two Pt NP suspensions were measured using icpTOF instruments (TOFWERK AG, Switzerland). Two Pt NP samples were characterized and mass equivalent spherical sizes (MESSs) of 40.4 ± 7 nm and 58.8 ± 8 nm were obtained, respectively. MESSs showed <16% relative standard deviation (RSD) among all participating labs and <4% RSD after exclusion of the two outliers. A good agreement was achieved between the different participating laboratories regarding particle mass, but the particle number concentration results were more scattered, with <53% RSD among all laboratories, which is consistent with results from previous ILC studies conducted using ICP-MS instrumentation equipped with a sequential mass spectrometer. Additionally, the capabilities of sp-ICP-TOFMS to determine masses on a particle basis are discussed with respect to the potential for particle density determination. Finally, because quasi-simultaneous multi-isotope and multielement determinations are a strength of ICP-TOFMS instrumentation, the precision and trueness of isotope ratio determinations were assessed. The average of 1000 measured particles yielded a precision of below ±1% for intensity ratios of the most abundant Pt isotopes, i.e. 194Pt and 195Pt, while the accuracy of isotope ratios with the lower abundant isotopes was limited by counting statistics.

  • Climate change impacts on soil biology

    Canarini A, Fuchslueger L, Joly FX, Richter A
    2023 - Encyclopedia of Soils in the Environment, 1: 578-586



    Human activities have caused a rapid climate change affecting all parts of the biosphere, including soils. Soil organisms from all three domains of life, their interactions, and all soil processes for which they are responsible are influenced by and in turn respond to climate change. The understanding of how soil organisms and their processes react to climate changes, is thus central to our ability to manage ecosystems and develop strategies to mitigate climate change. This chapter examines the current state of soil biology (from organisms and communities to the processes they control) in the context of climate change and identifies current gaps in knowledge and promising ways forward.

  • High resolution mapping shows differences in soil carbon and nitrogen stocks in areas of varying landscape history in Canadian lowland tundra

    Wagner J, Martin V, Speetjens NJ, A'campo W, Durstewitz L, Lodi R, Fritz M, Tanski G, Vonk JE, Richter A, Bartsch A, Lantuit H, Hugelius G
    2023 - Geoderma, 438: Article 116652


    Soil organic carbon (SOC) in Arctic coastal polygonal tundra is vulnerable to climate change, especially in soils with occurrence of large amounts of ground ice. Pan-arctic studies of mapping SOC exist, yet they fail to describe the high spatial variability of SOC storage in permafrost landscapes. An important factor is the landscape history which determines landform development and consequently the spatial variability of SOC. Our aim was to map SOC stocks, and which environmental variables that determine SOC, in two adjacent coastal areas along Canadian Beaufort Sea coast with different glacial history. We used the machine learning technique random forest and environmental variables to map the spatial distribution of SOC stocks down to 1 m depth at a spatial resolution of 2 m for depth increments of 0–5, 5–15, 15–30, 30–60 and 60–100 cm.

    The results show that the two study areas had large differences in SOC stocks in the depth 60–100 cm due to high amounts of ground ice in one of the study areas. There are also differences in variable importance of the explanatory variables between the two areas. The area low in ground ice content had with 66.6 kg C/m−2 more stored SOC than the area rich in ground ice content with 40.0 kg C/m−2. However, this SOC stock could be potentially more vulnerable to climate change if ground ice melts and the ground subsides. The average N stock of the area low in ground ice is 3.77 kg m−2 and of the area rich in ground ice is 3.83 kg m−2.

    These findings support that there is a strong correlation between ground ice and SOC, with less SOC in ice-rich layers on a small scale. In addition to small scale studies of SOC mapping, detailed maps of ground ice content and distribution are needed for a validation of large-scale quantifications of SOC stocks and transferability of models.

  • Acesulfame allows the tracing of multiple sources of wastewater and riverbank filtration

    Miguel Angel Marazuela, Giovanni Formentin, Klaus Erlmeier, Thilo Hofmann
    2023 - Environmental Pollution, 323: 121223


    Aquifers providing drinking water are increasingly threatened by emerging contaminants due to wastewater inputs from multiple sources. These inputs have to be identified, differentiated, and characterized to allow an accurate risk assessment and thus ensure the safety of drinking water through appropriate management. We hypothesize, that in climates with seasonal temperature variations, the sweetener acesulfame potassium (ACE) provides new pathways to study wastewater inputs to aquifers. Specifically, this study investigates the temperature-driven seasonal oscillation of ACE to assess multiple sources of wastewater inputs at a riverbank filtration site. ACE concentrations in the river water varied from 0.2 to 1 μg L−1 in the cold season (T < 10 °C) to 0–0.1 μg L−1 in the warm season (T > 10 °C), due to temperature-dependent biodegradation during wastewater treatment. This oscillating signal could be traced throughout the aquifer over distances up to 3250 m from two different infiltration sources. A transient numerical model of groundwater flow and ACE transport was calibrated over hydraulic heads and ACE concentrations, allowing the accurate calculation of mixing ratios, travel times, and flow-path directions for each of the two infiltration sources. The calculated travel time from the distant infiltration source was of 67 days, while that from the near source was of 20 days. The difference in travel times leads to different potential degradation of contaminants flowing into the aquifer from the river, thus demonstrating the importance of individually assessing the locations of riverbank infiltration. The calibrated ACE transport model allowed calculating transient mixing ratios, which confirmed the impact of river stage and groundwater levels on the mixing ratio of the original groundwater and the bank filtrate. Therefore, continuous monitoring of ACE concentrations can help to optimize the management of the water works with the aim to avoid collection of water with very short travel times, which has important regulative aspects. Our findings demonstrate the suitability of ACE as a transient tracer for identifying multiple sources of wastewater, including riverbank filtration sites affected by wastewater treatment plant effluents. ACE seasonal oscillation tracking thus provides a new tool to be used in climates with pronounced seasonal temperature variations to assess the origins of contamination in aquifers, with time and cost advantages over multi-tracer approaches.

  • Phosphorus limitation reduces microbial nitrogen use efficiency by increasing extracellular enzyme investments

    Sun L, Li J, Qu L, Wang X, Sang C, Wang J, Sun M, Wanek W, Moorhead DL, Bai E, Wang C
    2023 - Geoderma, 432: Article 116416


    Microbial nitrogen use efficiency (NUE), which reflects the proportion of nitrogen (N) taken up to be allocated to microbial biomass and growth, is central to our understanding of soil N cycling. However, the factors influencing microbial NUE remain unclear. Here, we explored the effects of climate factors, soil properties, and microbial variables on microbial NUE based on a survey of soils from 11 locations along a forest transect in eastern China. We found microbial NUE decreased with the ratio of acid phosphatase (AP) activity versus microbial growth rate. This suggested that increased microbial phosphorus acquisition decreased microbial NUE due to increasing investment in AP. However, microbial NUE increased with soil organic carbon content, because soil organic carbon is the source of material and energy for microbial growth and metabolism. Soil pH and mean annual temperature indirectly affected microbial NUE through their effects on the ratio of AP activity relative to microbial growth rate and soil organic carbon content, respectively. Our results improve our understanding and prediction of microbial NUE on a large spatial scale and emphasize the importance of phosphorus in affecting microbial metabolic efficiency.

  • Plastics can be used more sustainably in agriculture

    Thilo Hofmann, Subhasis Ghoshal, Nathalie Tufenkji, Jan Franklin Adamowski, Stéphane Bayen, Qiqing Chen, Philip Demokritou, Markus Flury, Thorsten Hüffer, Natalia P. Ivleva, Rong Ji, Richard L. Leask, Milan Maric, Denise M. Mitrano, Michael Sander, Sabine Pahl, Matthias C. Rillig, Tony R. Walker, Jason C. White, Kevin J. Wilkinson
    2023 - Nature Communications Earth & Environment, 4: 332


    Plastics have become an integral component in agricultural production as mulch films, nets, storage bins and in many other applications, but their widespread use has led to the accumulation of large quantities in soils. Rational use and reduction, collection, reuse, and innovative recycling are key measures to curb plastic pollution from agriculture. Plastics that cannot be collected after use must be biodegradable in an environmentally benign manner. Harmful plastic additives must be replaced with safer alternatives to reduce toxicity burdens and included in the ongoing negotiations surrounding the United Nations Plastics Treaty. Although full substitution of plastics is currently not possible without increasing the overall environmental footprint and jeopardizing food security, alternatives with smaller environmental impacts should be used and endorsed within a clear socio-economic framework. Better monitoring and reporting, technical innovation, education and training, and social and economic incentives are imperative to promote more sustainable use of plastics in agriculture.

  • 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., 6: 2205–2208


    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.


  • Conservation of energetic pathways for electroautotrophy in the uncultivated candidate order Tenderiales

    Eddie BJ, Bird LJ, Pelikan C, Greuter L, Martinez-Perez C, Pinamang P, Malanoski AP, Glaven SM
    2023 - mSphere, in press


    Electromicrobiology can be used to understand extracellular electron uptake in previously undescribed chemolithotrophs. Enrichment and characterization of the uncultivated electroautotroph "Candidatus Tenderia electrophaga" using electromicrobiology led to the designation of the order Tenderiales. Representative Tenderiales metagenome-assembled genomes (MAGs) have been identified in a number of environmental surveys, yet a comprehensive characterization of conserved genes for extracellular electron uptake has thus far not been conducted. Using comparative genomics, we identified conserved orthologous genes within the Tenderiales and nearest-neighbor orders important for extracellular electron uptake based on a previously proposed pathway from "Ca. Tenderia electrophaga." The Tenderiales contained a conserved cluster we designated uetABCDEFGHIJ, which encodes proteins containing features that would enable transport of extracellular electrons to cytoplasmic membrane-bound energy-transducing complexes such as two conserved cytochrome cbb3 oxidases. For example, UetJ is predicted to be an extracellular undecaheme c-type cytochrome that forms a heme wire. We also identified clusters of genes predicted to facilitate assembly and maturation of electron transport proteins, as well as cellular attachment to surfaces. Autotrophy among the Tenderiales is supported by the presence of carbon fixation and stress response pathways that could allow cellular growth by extracellular electron uptake. Key differences between the Tenderiales and other known neutrophilic iron oxidizers were revealed, including very few Cyc2 genes in the Tenderiales. Our results reveal a possible conserved pathway for extracellular electron uptake and suggest that the Tenderiales have an ecological role in coupling metal or mineral redox chemistry and the carbon cycle in marine and brackish sediments. IMPORTANCE Chemolithotrophic bacteria capable of extracellular electron uptake to drive energy metabolism and CO2 fixation are known as electroautotrophs. The recently described order Tenderiales contains the uncultivated electroautotroph "Ca. Tenderia electrophaga." The "Ca. Tenderia electrophaga" genome contains genes proposed to make up a previously undescribed extracellular electron uptake pathway. Here, we use comparative genomics to show that this pathway is well conserved among Tenderiales spp. recovered by metagenome-assembled genomes. This conservation extends to near neighbors of the Tenderiales but not to other well-studied chemolithotrophs, including iron and sulfur oxidizers, indicating that these genes may be useful markers of growth using insoluble extracellular electron donors. Our findings suggest that extracellular electron uptake and electroautotrophy may be pervasive among the Tenderiales, and the geographic locations from which metagenome-assembled genomes were recovered offer clues to their natural ecological niche.

  • Microbial diversity and activity of biofilms from geothermal springs in Croatia

    Kostešić E, Mitrović M, Kajan K, Marković T, Hausmann B, Orlić S, Pjevac P
    2023 - Microbial ecology, in press


    Hot spring biofilms are stable, highly complex microbial structures. They form at dynamic redox and light gradients and are composed of microorganisms adapted to the extreme temperatures and fluctuating geochemical conditions of geothermal environments. In Croatia, a large number of poorly investigated geothermal springs host biofilm communities. Here, we investigated the microbial community composition of biofilms collected over several seasons at 12 geothermal springs and wells. We found biofilm microbial communities to be temporally stable and highly dominated by Cyanobacteria in all but one high-temperature sampling site (Bizovac well). Of the physiochemical parameters recorded, temperature had the strongest influence on biofilm microbial community composition. Besides Cyanobacteria, the biofilms were mainly inhabited by Chloroflexota, Gammaproteobacteria, and Bacteroidota. In a series of incubations with Cyanobacteria-dominated biofilms from Tuhelj spring and Chloroflexota- and Pseudomonadota-dominated biofilms from Bizovac well, we stimulated either chemoorganotrophic or chemolithotrophic community members, to determine the fraction of microorganisms dependent on organic carbon (in situ predominantly produced via photosynthesis) versus energy derived from geochemical redox gradients (here simulated by addition of thiosulfate). We found surprisingly similar levels of activity in response to all substrates in these two distinct biofilm communities, and observed microbial community composition and hot spring geochemistry to be poor predictors of microbial activity in the study systems.

  • Integrated Data-Driven Cross-Disciplinary Framework to Prevent Chemical Water Pollution

    Mohamed Ateia, Gabriel Sigmund, Michael J. Bentel, John W. Washington, Adelene Lai, Nathaniel H. Merrill, Zhanyun Wang
    2023 - One Earth, 8: 952-963


    Access to a clean and healthy environment is a human right and a prerequisite for maintaining a sustainable ecosystem. Experts across domains along the chemical life cycle have traditionally operated in isolation, leading to limited connectivity between upstream chemical innovation to downstream development of water-treatment technologies. This fragmented and historically reactive approach to managing emerging contaminants has resulted in significant externalized societal costs. Herein, we propose an integrated data-driven framework to foster proactive action across domains to effectively address chemical water pollution. By implementing this integrated framework, it will not only enhance the capabilities of experts in their respective fields but also create opportunities for novel approaches that yield co-benefits across multiple domains. To successfully operationalize the integrated framework, several concerted efforts are warranted, including adopting open and FAIR (findable, accessible, interoperable, and reusable) data practices, developing common knowledge bases/platforms, and staying vigilant against new substance “properties” of concern.

  • Decadal soil warming decreased vascular plant above and belowground production in a subarctic grassland by inducing nitrogen limitation

    Fang C, Verbrigghe N, Sigurdsson BD, Ostonen I, Leblans NIW, Marañon-Jimenez S, Fuchslueger L, Sigurðsson P, Meeran K, Portillo-Estrada M, Verbruggen E, Richter A, Sardans J, Schiestl RH, Bahn M, Vicca S, Janssens IA
    2023 - New Phytologist, 240: 565-576


    • Below and aboveground vegetation dynamics are crucial in understanding how climate warming may affect terrestrial ecosystem carbon cycling. In contrast to aboveground biomass, the response of belowground biomass to long-term warming has been poorly studied.
    • Here, we characterized the impacts of decadal geothermal warming at two levels (on average +3.3°C and +7.9°C) on below and aboveground plant biomass stocks and production in a subarctic grassland.
    • Soil warming did not change standing root biomass and even decreased fine root production and reduced aboveground biomass and production. Decadal soil warming also did not significantly alter the root–shoot ratio. The linear stepwise regression model suggested that following 10 yr of soil warming, temperature was no longer the direct driver of these responses, but losses of soil N were. Soil N losses, due to warming-induced decreases in organic matter and water retention capacity, were identified as key driver of the decreased above and belowground production. The reduction in fine root production was accompanied by thinner roots with increased specific root area.
    • These results indicate that after a decade of soil warming, plant productivity in the studied subarctic grassland was affected by soil warming mainly by the reduction in soil N.
    • Below and aboveground vegetation dynamics are crucial in understanding how climate warming may affect terrestrial ecosystem carbon cycling. In contrast to aboveground biomass, the response of belowground biomass to long-term warming has been poorly studied.
    • Here, we characterized the impacts of decadal geothermal warming at two levels (on average +3.3°C and +7.9°C) on below and aboveground plant biomass stocks and production in a subarctic grassland.
    • Soil warming did not change standing root biomass and even decreased fine root production and reduced aboveground biomass and production. Decadal soil warming also did not significantly alter the root–shoot ratio. The linear stepwise regression model suggested that following 10 yr of soil warming, temperature was no longer the direct driver of these responses, but losses of soil N were. Soil N losses, due to warming-induced decreases in organic matter and water retention capacity, were identified as key driver of the decreased above and belowground production. The reduction in fine root production was accompanied by thinner roots with increased specific root area.
    • These results indicate that after a decade of soil warming, plant productivity in the studied subarctic grassland was affected by soil warming mainly by the reduction in soil N.
  • Long-term warming-induced trophic downgrading in the soil microbial food web

    Borg Dahl M, Söllinger A, Sigurðsson P, Janssens I, Schiestl RH, Sigurdsson BD, Richter A, Tveit AT, Urich T
    2023 - Soil Biology and Biochemistry, 181: Article 109044


    Climatic warming has been hypothesized to accelerate organic matter decomposition by soil microorganisms and thereby enhance carbon (C) release to the atmosphere. However, the long-term consequences of soil warming on belowground biota interactions are poorly understood. Here we investigate how geothermal warming by 6 °C for more than 50 years affects soil microbiota. Using metatranscriptomics we obtained comprehensive profiles of the prokaryotic, eukaryotic and viral players of the soil microbial food web. When compared to ambient soil temperature conditions, we found pronounced differences in taxa abundances within and between trophic modules of the soil food web. Specifically, we observed a ‘trophic downgrading’ at elevated temperature, with soil fauna decreasing in abundance, while predatory bacteria and viruses became relatively more abundant. We propose that the drivers for this shift are previously observed decreases in microbial biomass and soil organic carbon, and the increase in soil bulk density (decrease in soil porosity) at elevated temperature. We conclude that a trophic downgrading may have important implications for soil carbon sequestration and nutrient dynamics in a warming world.

  • Fiber consumption stimulates the activity of microbial bile salt hydrolases

    Gregor A, Auernigg-Haselmaier S, Malleier M, Bruckberger S, Séneca J, Pjevac P, Pignitter M, Duszka K
    2023 - Journal of Functional Foods, in press


    Previously we reported a microbiota-dependent caloric restriction (CR)-triggered increase in the levels of taurine and taurine-conjugated bile acids (BA) in the gut. Now, we show that restrictive diets, including intermittent fasting and fasting-mimicking diet, had a similar impact to CR. The type of cage bedding that CR mice were housed with affected the levels of BAs and taurine in the ileum. Removal of cage bedding neutralized CR phenotype in terms of taurine levels, BAs deconjugation, and fecal microbiota composition. Microbiota transplant from CR mice housed with bedding increased BAs deconjugation. Inhibition of bile salt hydrolase (BSH) prevented the increase in free taurine concentration while increasing taurine-conjugated BA levels. Ad libitum consumption of diets high in fiber increased the levels of taurine conjugates but did not elevate the levels of BAs. Dietary restriction is required to stimulate BAs secretion, while ingestion of fiber stimulates the capacity of microbiota to deconjugate BAs.

  • The Challenge of Interdisciplinarity at the Intersection of Groundwater Management and Visualization Research

    Laura Lotteraner, Thilo Hofmann, Torsten Möller
    2023 - IEEE Computer Graphics and Applications, 6: 50-63


    This design study presents an analysis and abstraction of temporal and spatial data, and workflows in the domain of hydrogeology and the design and development of an interactive visualization prototype. Developed in close collaboration with a group of hydrogeological researchers, the interface supports them in data exploration, selection of data for their numerical model calibration, and communication of findings to their industry partners. We highlight both pitfalls and learnings of the iterative design and validation process and explore the role of rapid prototyping. Some of the main lessons were that the ability to see their own data changed the engagement of skeptical users dramatically and that interactive rapid prototyping tools are thus powerful to unlock the advantage of visual analysis for novice users. Further, we observed that the process itself helped the domain scientists understand the potential and challenges of their data more than the final interface prototype.

  • Single-cell mass distributions reveal simple rules for achieving steady-state growth

    Roller BRK, Hellerschmied C, Wu Y, Miettinen TP, Gomez AL, Manalis SR, Polz MF
    2023 - mBio, in press


    ABSTRACT Optical density is a proxy of total biomass concentration and is commonly used for measuring the growth of bacterial cultures. However, there is a misconception that exponential optical density growth is equivalent to steady-state population growth. Many cells comprise a culture and individuals can differ from one another. Hallmarks of steady-state population growth are stable frequency distributions of cellular properties over time, something total biomass growth alone cannot quantify. Using single-cell mass sensors paired with optical density measurements, we explore when steady-state population growth prevails in typical batch cultures. We find the average cell mass of Escherichia coli and Vibrio cyclitrophicus growing in several media increases by 0.5–1 orders of magnitude within a few hours of inoculation, and that time-invariant mass distributions are only achieved for short periods when cultures are inoculated with low initial biomass concentrations from overnight cultures. These species achieve an effective steady-state after approximately 2.5–4 total biomass doublings in rich media, which can be decomposed to 1 doubling of cell number and 1.5–3 doublings of average cell mass. We also show that typical batch cultures in rich media depart steady-state early in their growth curves at low cell and biomass concentrations. Achieving steady-state population growth in batch culture is a delicate balancing act, so we provide general guidance for commonly used rich media. Quantifying single-cell mass outside of steady-state population growth is an important first step toward understanding how microbes grow in their natural context, where fluctuations pervade at the scale of individuals.

  • Loss of nitrogen fixing capacity in a montane lichen is linked to increased nitrogen deposition

    Crittenden PD, Ellis CJ, Smith RI, Wanek W, Thornton B
    2023 - Journal of Ecology, 111: 288-299


    1. The circumboreal/circumpolar N2-fixing lichen Stereocaulon vesuvianum is among the most widespread and abundant fruticose species in montane Britain but has lost the capacity to fix N2 over large areas of the country.
    2. To investigate whether loss of N2-fixation in S. vesuvianum is linked to increased N deposition, we examined thallus morphology, physiology and chemistry at twelve locations representing an N deposition gradient of 3–40 kg ha−1 year−1. Measurements were made in parallel on a non-N2-fixing reference species (Parmelia saxatilis). The presence or absence of cephalodia (N2-fixing nodules containing the cyanobacterium Stigonema sp) was recorded in over 500 herbarium specimens of S. vesuvianum dating back to 1820.
    3. Cephalodium abundance in S. vesuvianum, and 15N concentration in S. vesuvianum and P. saxatilis, were strongly negatively correlated with N deposition and particularly with dry deposited N; cephalodia do not form at total N deposition rates ≥8–9 kg ha−1 year−1. Other morphological oddities in S. vesuvianum at N-polluted sites include increased apothecium (fungal reproductive structure) production and green algal biofilm development. Biofilm covered thalli without cephalodia lacked nitrogenase activity and cephalodia at sites where they rarely develop had nitrogenase activities typical for this species. The presence or absence of cephalodia in herbarium specimens of S. vesuvianum suggest that the present-day N-deposition linked gradient in N2-fixing capacity did not exist in the 19th century and largely developed between 1900–1940.
    4. Synthesis. We provide clear evidence that N2-fixing capacity in S. vesuvianum has been lost in regions subjected to many decades of enhanced atmospheric N deposition. This loss is consistent with established models of diazotrophy, which identify supply of combined N as an inhibitor of N2-fixation. Progressive depletion of thallus 15N with increasing N deposition is in line with available data indicating that much atmospheric N pollution is 15N-depleted. Rates of nitrogenase activity in S. vesuvianum are low compared to other symbiotic systems and perhaps more likely supplanted by elevated N deposition. We suggest that other ecosystem compartments with low rates of fixation (e.g. soils) might also be susceptible to N pollution and merit investigation.
    • The circumboreal/circumpolar N2-fixing lichen Stereocaulon vesuvianum is among the most widespread and abundant fruticose species in montane Britain but has lost the capacity to fix N2 over large areas of the country.
    • To investigate whether loss of N2-fixation in S. vesuvianum is linked to increased N deposition, we examined thallus morphology, physiology and chemistry at twelve locations representing an N deposition gradient of 3–40 kg ha−1 year−1. Measurements were made in parallel on a non-N2-fixing reference species (Parmelia saxatilis). The presence or absence of cephalodia (N2-fixing nodules containing the cyanobacterium Stigonema sp) was recorded in over 500 herbarium specimens of S. vesuvianum dating back to 1820.
    • Cephalodium abundance in S. vesuvianum, and 15N concentration in S. vesuvianum and P. saxatilis, were strongly negatively correlated with N deposition and particularly with dry deposited N; cephalodia do not form at total N deposition rates ≥8–9 kg ha−1 year−1. Other morphological oddities in S. vesuvianum at N-polluted sites include increased apothecium (fungal reproductive structure) production and green algal biofilm development. Biofilm covered thalli without cephalodia lacked nitrogenase activity and cephalodia at sites where they rarely develop had nitrogenase activities typical for this species. The presence or absence of cephalodia in herbarium specimens of S. vesuvianum suggest that the present-day N-deposition linked gradient in N2-fixing capacity did not exist in the 19th century and largely developed between 1900–1940.
    • Synthesis. We provide clear evidence that N2-fixing capacity in S. vesuvianum has been lost in regions subjected to many decades of enhanced atmospheric N deposition. This loss is consistent with established models of diazotrophy, which identify supply of combined N as an inhibitor of N2-fixation. Progressive depletion of thallus 15N with increasing N deposition is in line with available data indicating that much atmospheric N pollution is 15N-depleted. Rates of nitrogenase activity in S. vesuvianum are low compared to other symbiotic systems and perhaps more likely supplanted by elevated N deposition. We suggest that other ecosystem compartments with low rates of fixation (e.g. soils) might also be susceptible to N pollution and merit investigation.
  • Iron Nitride Nanoparticles for Rapid Dechlorination of Mixed Chlorinated Ethene Contamination

    Miroslav Brumovský, Malfatti SE, Jana Oborná, Jan Filip, Thilo Hofmann, Daniel Tunega
    2023 - Journal of Hazardous Materials, 442: 129988


    Sulfidation and, more recently, nitriding have been recognized as promising modifications to enhance the selectivity of nanoscale zero-valent iron (nZVI) particles for trichloroethene (TCE). Herein, we investigated the performance of iron nitride (FexN) nanoparticles in the removal of a broader range of chlorinated ethenes (CEs), including tetrachloroethene (PCE), cis-1,2-dichloroethene (cis-DCE), and their mixture with TCE, and compared it to the performance of sulfidated nZVI (S-nZVI) prepared from the same precursor nZVI. Two distinct types of iron nitride (FexN) nanoparticles, containing γ′-Fe4N and ε-Fe2–3N phases, exhibited substantially higher PCE and cis-DCE dechlorination rates compared to S-nZVI. A similar effect was observed with a CE mixture, which was completely dechlorinated by both types of FexN nanoparticles within 10 days, whereas S-nZVI was able to remove only about half of the amount, most of which being TCE. Density functional theory calculations further revealed that the cleavage of the first C–Cl bond was the rate-limiting step for all CEs dechlorinated on the γ′-Fe4N(001) surface, with the reaction barriers of PCE and cis-DCE being 29.9, and 40.8 kJ mol–1, respectively. FexN nanoparticles proved to be highly effective in the remediation of PCE, cis-DCE, and mixed CE contamination.

  • Seasonal patterns in microbial carbon and iron transporter expression in the Southern Ocean

    Debeljak P, Bayer B, Sun Y, Herndl GJ, Obernosterer I
    2023 - Microbiome, in press



    Heterotrophic microbes in the Southern Ocean are challenged by the double constraint of low concentrations of organic carbon (C) and iron (Fe). These essential elements are tightly coupled in cellular processes; however, the prokaryotic requirements of C and Fe under varying environmental settings remain poorly studied. Here, we used a combination of metatranscriptomics and metaproteomics to identify prokaryotic membrane transporters for organic substrates and Fe in naturally iron-fertilized and high-nutrient, low-chlorophyll waters of the Southern Ocean during spring and late summer.


    Pronounced differences in membrane transporter profiles between seasons were observed at both sites, both at the transcript and protein level. When specific compound classes were considered, the two approaches revealed different patterns. At the transcript level, seasonal patterns were only observed for subsets of genes belonging to each transporter category. At the protein level, membrane transporters of organic compounds were relatively more abundant in spring as compared to summer, while the opposite pattern was observed for Fe transporters. These observations suggest an enhanced requirement for organic C in early spring and for Fe in late summer. Mapping transcripts and proteins to 50 metagenomic-assembled genomes revealed distinct taxon-specific seasonal differences pointing to potentially opportunistic clades, such as Pseudomonadales and Nitrincolaceae, and groups with a more restricted repertoire of expressed transporters, such as Alphaproteobacteria and Flavobacteriaceae.


    The combined investigations of C and Fe membrane transporters suggest seasonal changes in the microbial requirements of these elements under different productivity regimes. The taxon-specific acquisition strategies of different forms of C and Fe illustrate how diverse microbes could shape transcript and protein expression profiles at the community level at different seasons. Our results on the C- and Fe-related metabolic capabilities of microbial taxa provide new insights into their potential role in the cycling of C and Fe under varying nutrient regimes in the Southern Ocean.

  • Long-term warming of a forest soil reduces microbial biomass and its carbon and nitrogen use efficiencies

    Tian Y, Schindlbacher A, Urbina-Malo C, Shi C, Heinzle J, Kengdo SK, Inselsbacher E, Borken W, Wanek W
    2023 - Soil Biology and Biochemistry, 184: Article 109109


    Global warming impacts biogeochemical cycles in terrestrial ecosystems, but it is still unclear how the simultaneous cycling of carbon (C) and nitrogen (N) in soils could be affected in the longer-term. Here, we evaluated how 14 years of soil warming (+4 °C) affected the soil C and N cycle across different soil depths and seasons in a temperate mountain forest. We used H218O incorporation into DNA and 15N isotope pool dilution techniques to determine gross rates of C and N transformation processes. Our data showed different warming effects on soil C and N cycling, and these were consistent across soil depths and seasons. Warming decreased microbial biomass C (−22%), but at the same time increased microbial biomass-specific growth (+25%) and respiration (+39%), the potential activity of β-glucosidase (+31%), and microbial turnover (+14%). Warming reduced gross rates of protein depolymerization (−19%), but stimulated gross N mineralization (+63%) and the potential activities of N-acetylglucosaminidase (+106%) and leucine-aminopeptidase (+46%), and had no impact on gross nitrification (+1%). Microbial C and N use efficiencies were both lower in the warming treatment (−15% and −17%, respectively). Overall, our results suggest that long-term warming drives soil microbes to incorporate less C and N into their biomass (and necromass), and to release more inorganic C and N to the environment, causing lower soil C and N storage in this forest, as indicated by lower soil C and total N contents. The decreases in microbial CUE and NUE were likely triggered by increasing microbial P constraints in warmed soils, limiting anabolic processes and microbial growth and promoting pervasive losses of C and N from the soil.

    Global warming impacts biogeochemical cycles in terrestrial ecosystems, but it is still unclear how the simultaneous cycling of carbon (C) and nitrogen (N) in soils could be affected in the longer-term. Here, we evaluated how 14 years of soil warming (+4 °C) affected the soil C and N cycle across different soil depths and seasons in a temperate mountain forest. We used H218O incorporation into DNA and 15N isotope pool dilution techniques to determine gross rates of C and N transformation processes. Our data showed different warming effects on soil C and N cycling, and these were consistent across soil depths and seasons. Warming decreased microbial biomass C (−22%), but at the same time increased microbial biomass-specific growth (+25%) and respiration (+39%), the potential activity of β-glucosidase (+31%), and microbial turnover (+14%). Warming reduced gross rates of protein depolymerization (−19%), but stimulated gross N mineralization (+63%) and the potential activities of N-acetylglucosaminidase (+106%) and leucine-aminopeptidase (+46%), and had no impact on gross nitrification (+1%). Microbial C and N use efficiencies were both lower in the warming treatment (−15% and −17%, respectively). Overall, our results suggest that long-term warming drives soil microbes to incorporate less C and N into their biomass (and necromass), and to release more inorganic C and N to the environment, causing lower soil C and N storage in this forest, as indicated by lower soil C and total N contents. The decreases in microbial CUE and NUE were likely triggered by increasing microbial P constraints in warmed soils, limiting anabolic processes and microbial growth and promoting pervasive losses of C and N from the soil.


  • 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.

  • Tracing 33P-labelled organic phosphorus compounds in two soils: New insights into decomposition dynamics and direct use by microbes

    Wasner D, Prommer J, Zezula D, Mooshammer M, Hu Y, Wanek W
    2023 - Frontiers in Soil Science, 3: Article 1097965


    Introduction: Organic phosphorus (Po) compounds constitute an important pool in soil P cycling, but their decomposition dynamics are poorly understood. Further, it has never been directly tested whether low molecular weight Po compounds are taken up by soil microbes in an intact form, which reduces the dependence of their P acquisition on extracellular phosphatases.

    Methods: We investigated the short-term fate (24 h) of five 33P-labelled Po compounds (teichoic acids, phospholipids, DNA, RNA and soluble organophosphates) and 33P-labelled inorganic P (Pi) in two soils.

    Results: We found indications that soil microbial breakdown of phosphodiesters was limited by the depolymerization step, and that direct microbial uptake of Po occurred to a substantial extent.

    Discussion: We postulate a trade-off between direct Po uptake and complete extracellular Po mineralization. These findings have profound consequences for our understanding of microbial P cycling in soils.

  • Simultaneous sulfate and nitrate reduction in coastal sediments

    Bourceau OM, Ferdelman T, Lavik G, Greuter L, Kuypers MMM, Marchant HK
    2023 - ISME Communications, in press


    The oscillating redox conditions that characterize coastal sandy sediments foster microbial communities capable of respiring oxygen and nitrate simultaneously, thereby increasing the potential for organic matter remineralization, nitrogen (N)-loss and emissions of the greenhouse gas nitrous oxide. It is unknown to what extent these conditions also lead to overlaps between dissimilatory nitrate and sulfate respiration. Here, we show that sulfate and nitrate respiration co-occur in the surface sediments of an intertidal sand flat. Furthermore, we found strong correlations between dissimilatory nitrite reduction to ammonium (DNRA) and sulfate reduction rates. Until now, the nitrogen and sulfur cycles were assumed to be mainly linked in marine sediments by the activity of nitrate-reducing sulfide oxidisers. However, transcriptomic analyses revealed that the functional marker gene for DNRA (nrfA) was more associated with microorganisms known to reduce sulfate rather than oxidise sulfide. Our results suggest that when nitrate is supplied to the sediment community upon tidal inundation, part of the sulfate reducing community may switch respiratory strategy to DNRA. Therefore increases in sulfate reduction rate in-situ may result in enhanced DNRA and reduced denitrification rates. Intriguingly, the shift from denitrification to DNRA did not influence the amount of N2O produced by the denitrifying community. Our results imply that microorganisms classically considered as sulfate reducers control the potential for DNRA within coastal sediments when redox conditions oscillate and therefore retain ammonium that would otherwise be removed by denitrification, exacerbating eutrophication.

  • Fragmentation and Mineralization of a Compostable Aromatic–Aliphatic Polyester during Industrial Composting

    Wendel Wohlleben, Markus Rückel, Lars Meyer, Patricia Pfohl, Glauco Battagliarin, Thorsten Hüffer, Michael Zumstein, Thilo Hofmann
    2023 - Environ. Sci. Technol., 8: 698-704


    Compostable plastics support the separate collection of organic waste. However, there are concerns that the fragments generated during disintegration might not fully biodegrade and leave persistent microplastic in compost. We spiked particles of an aromatic–aliphatic polyester containing polylactide into compost and then tracked disintegration under industrial composting conditions. We compared the yields against polyethylene. The validity of the extraction protocol and complementary microscopic methods (μ-Raman and fluorescence) was assessed by blank controls, spike controls, and prelabeled plastics. Fragments of 25–75 μm size represented the most pronounced peak of interim fragmentation, which was reached already after 1 week of industrial composting. Larger sizes peaked earlier, while smaller sizes peaked later and remained less frequent. For particles of all sizes, count and mass decreased to blank level when 90% of the polymer carbon were transformed into CO2. Gel permeation chromatography (GPC) analysis suggested depolymerization as the main driving force for disintegration. A transient shift of the particle composition to a lower percentage of polylactide was observed. Plastic fragmentation during biodegradation is the expected route for decomposing, but no accumulation of particulate fragments of any size was observed.

  • How temperature and aridity drive lignin decomposition along a latitudinal transect in western Siberia

    Dao TT, Mikutta R, Wild B, Sauheitl L, Gentsch N, Shibistova O, Schnecker J, Lashchinskiy N, Richter A, Guggenberger G
    2023 - European Journal of Soil Science, 74: e13408


    Climate change drives a northward shift of biomes in high-latitude regions. This might have consequences on the decomposition of plant litter entering the soil, including its lignin component, which is one of the most abundant components of vascular plants. In order to elucidate the combined effect of climate and soil characteristics on the decomposition pattern of lignin, we investigated lignin contents and its degree of oxidative decomposition within soil profiles along a climosequence in western Siberia. Soil samples were collected from organic topsoil to mineral subsoil at six sites along a 1500-km latitudinal transect, stretching from tundra, through taiga and forest steppe to typical steppe. The stage of lignin degradation, as mirrored by decreasing organic carbon-normalized lignin contents and increasing oxidative alteration of the remnant lignin (acid-to-aldehyde ratios of vanillyl- and syringyl-units [(Ac/Al)V and (Ac/Al)S]) within soil horizons, increased from tundra to forest steppe and then decreased to the steppe. Principal component analysis, involving also climatic conditions such as mean annual temperature and aridity index, showed that the different states of lignin degradation between horizons related well to the activity of phenoloxidases and peroxidases, enzymes involved in lignin depolymerization that are produced primarily by fungi and less importantly by bacteria. The low microbial lignin decomposition in the tundra was likely due to low temperature and high soil moisture, which do not favour the fungi. Increasing temperature and decreasing soil moisture, facilitating a higher abundance of fungi, led to increased fungal lignin decomposition towards the forest-steppe biome, while drought and high pH might be responsible for the reduced lignin decomposition in the steppe. We infer that a shift of biomes to the north, driven by climate change, might promote lignin decomposition in the northern parts, whereas in the south a further retardation might be likely.



    • Lack of lignin contribution to soil organic matter and its degradation in different Siberian biomes.
    • The dependency of lignin decomposition predicts the fate of lignin under climate warming.
    • Climate warming accelerates lignin degradation at high latitude, while in the south it is likely retarded.
    • Lignin alteration with climate change has impacted on long-term development of soil carbon stock.

  • Microclimate shapes the phylosymbiosis of rodent gut microbiota in Jordan's Great Rift Valley.

    Al-Khlifeh E, Khadem S, Hausmann B, Berry D
    2023 - Front Microbiol, 1258775


    Host phylogeny and the environment play vital roles in shaping animal microbiomes. However, the effects of these variables on the diversity and richness of the gut microbiome in different bioclimatic zones remain underexplored. In this study, we investigated the effects of host phylogeny and bioclimatic zone on the diversity and composition of the gut microbiota of two heterospecific rodent species, the spiny mouse and the house mouse , in three bioclimatic zones of the African Great Rift Valley (GRV). We confirmed host phylogeny using the sequencing method and analyzed the influence of host phylogeny and bioclimatic zone parameters on the rodent gut microbiome using high-throughput amplicon sequencing of 16S rRNA gene fragments. Phylogenetic analysis supported the morphological identification of the rodents and revealed a marked genetic difference between the two heterospecific species. We found that bioclimatic zone had a significant effect on the gut microbiota composition while host phylogeny did not. Microbial alpha diversity of heterospecific hosts was highest in the Mediterranean forest bioclimatic zone, followed by the Irano-Turanian shrubland, and was lowest in the Sudanian savanna tropical zone. The beta diversity of the two rodent species showed significant differences across the Mediterranean, Irano-Turanian, and Sudanian regions. The phyla and were highly abundant, and and were also prominent. Amplicon sequence variants (ASVs) were identified that were unique to the Sudanian bioclimatic zone. The core microbiota families recovered in this study were consistent among heterospecific hosts. However, diversity decreased in conspecific host populations found at lower altitudes in Sudanian bioclimatic zone. The composition of the gut microbiota is linked to the adaptation of the host to its environment, and this study underscores the importance of incorporating climatic factors such as elevation and ambient temperature, in empirical microbiome research and is the first to describe the rodent gut microbiome from the GRV.

  • Global diversity and inferred ecophysiology of microorganisms with the potential for dissimilatory sulfate/sulfite reduction.

    Diao M, Dyksma S, Koeksoy E, Ngugi DK, Anantharaman K, Loy A, Pester M
    2023 - FEMS Microbiol Rev, fuad058


    Sulfate/sulfite-reducing microorganisms (SRM) are ubiquitous in nature, driving the global sulfur cycle. A hallmark of SRM is the dissimilatory sulfite reductase encoded by the genes dsrAB. Based on analysis of 950 mainly metagenome-derived dsrAB-carrying genomes, we redefine the global diversity of microorganisms with the potential for dissimilatory sulfate/sulfite reduction and uncover genetic repertoires that challenge earlier generalizations regarding their mode of energy metabolism. We show: (i) 19 out of 23 bacterial and 2 out of 4 archaeal phyla harbor uncharacterized SRM, (ii) four phyla including the Desulfobacterota harbor microorganisms with the genetic potential to switch between sulfate/sulfite reduction and sulfur oxidation, and (iii) the combination as well as presence/absence of different dsrAB-types, dsrL-types and dsrD provides guidance on the inferred direction of dissimilatory sulfur metabolism. We further provide an updated dsrAB database including >60% taxonomically resolved, uncultured family-level lineages and recommendations on existing dsrAB-targeted primers for environmental surveys. Our work summarizes insights into the inferred ecophysiology of newly discovered SRM, puts SRM diversity into context of the major recent changes in bacterial and archaeal taxonomy, and provides an up-to-date framework to study SRM in a global context.

  • Ecophysiology and interactions of a taurine-respiring bacterium in the mouse gut.

    Ye H, Borusak S, Eberl C, Krasenbrink J, Weiss AS, Chen SC, Hanson BT, Hausmann B, Herbold CW, Pristner M, Zwirzitz B, Warth B, Pjevac P, Schleheck D, Stecher B, Loy A
    2023 - Nat Commun, 1: 5533


    Taurine-respiring gut bacteria produce HS with ambivalent impact on host health. We report the isolation and ecophysiological characterization of a taurine-respiring mouse gut bacterium. Taurinivorans muris strain LT0009 represents a new widespread species that differs from the human gut sulfidogen Bilophila wadsworthia in its sulfur metabolism pathways and host distribution. T. muris specializes in taurine respiration in vivo, seemingly unaffected by mouse diet and genotype, but is dependent on other bacteria for release of taurine from bile acids. Colonization of T. muris in gnotobiotic mice increased deconjugation of taurine-conjugated bile acids and transcriptional activity of a sulfur metabolism gene-encoding prophage in other commensals, and slightly decreased the abundance of Salmonella enterica, which showed reduced expression of galactonate catabolism genes. Re-analysis of metagenome data from a previous study further suggested that T. muris can contribute to protection against pathogens by the commensal mouse gut microbiota. Together, we show the realized physiological niche of a key murine gut sulfidogen and its interactions with selected gut microbiota members.

  • The Fish Pathogen "Candidatus Clavichlamydia salmonicola"-A Missing Link in the Evolution of Chlamydial Pathogens of Humans.

    Collingro A, Köstlbacher S, Siegl A, Toenshoff ER, Schulz F, Mitchell SO, Weinmaier T, Rattei T, Colquhoun DJ, Horn M
    2023 - Genome Biol Evol, 8: evad147


    Chlamydiae like Chlamydia trachomatis and Chlamydia psittaci are well-known human and animal pathogens. Yet, the chlamydiae are a much larger group of evolutionary ancient obligate intracellular bacteria that includes predominantly symbionts of protists and diverse animals. This makes them ideal model organisms to study evolutionary transitions from symbionts in microbial eukaryotes to pathogens of humans. To this end, comparative genome analysis has served as an important tool. Genome sequence data for many chlamydial lineages are, however, still lacking, hampering our understanding of their evolutionary history. Here, we determined the first high-quality draft genome sequence of the fish pathogen "Candidatus Clavichlamydia salmonicola", representing a separate genus within the human and animal pathogenic Chlamydiaceae. The "Ca. Clavichlamydia salmonicola" genome harbors genes that so far have been exclusively found in Chlamydia species suggesting that basic mechanisms important for the interaction with chordate hosts have evolved stepwise in the history of chlamydiae. Thus, the genome sequence of "Ca. Clavichlamydia salmonicola" allows to constrain candidate genes to further understand the evolution of chlamydial virulence mechanisms required to infect mammals.

  • Close coupling of plant functional types with soil microbial community composition drives soil carbon and nutrient cycling in tundra heath

    Koranda M, Rinnan R, Michelsen A
    2023 - Plant and Soil, 488: 551-572



    This study aimed at elucidating divergent effects of two dominant plant functional types (PFTs) in tundra heath, dwarf shrubs and mosses, on soil microbial processes and soil carbon (C) and nutrient availability, and thereby to enhance our understanding of the complex interactions between PFTs, soil microbes and soil functioning.


    Samples of organic soil were collected under three dwarf shrub species (of distinct mycorrhizal association and life form) and three moss species in early and late growing season. We analysed soil C and nutrient pools, extracellular enzyme activities and phospholipid fatty acid profiles, together with a range of plant traits, soil and abiotic site characteristics.


    Shrub soils were characterised by high microbial biomass C and phosphorus and phosphatase activity, which was linked with a fungal-dominated microbial community, while moss soils were characterised by high soil nitrogen availability, peptidase and peroxidase activity associated with a bacterial-dominated microbial community. The variation in soil microbial community structure was explained by mycorrhizal association, root morphology, litter and soil organic matter quality and soil pH-value. Furthermore, we found that the seasonal variation in microbial biomass and enzyme activities over the growing season, likely driven by plant belowground C allocation, was most pronounced under the tallest shrub Betula nana.


    Our study demonstrates a close coupling of PFTs with soil microbial communities, microbial decomposition processes and soil nutrient availability in tundra heath, which suggests potential strong impacts of global change-induced shifts in plant community composition on carbon and nutrient cycling in high-latitude ecosystems.

  • Genome dynamics and temperature adaptation during experimental evolution of obligate intracellular bacteria

    Herrera P, Schuster L, Zojer M, Na H, Schwarz J, Wascher F, Kempinger T, Regner A, Rattei T, Horn M
    2023 - Genome Biol Evol, 8: evad139


    Evolution experiments with free-living microbes have radically improved our understanding of genome evolution and how microorganisms adapt. Yet there is a paucity of such research focusing on strictly host-associated bacteria, even though they are widespread in nature. Here, we used the Acanthamoeba symbiont Protochlamydia amoebophila, a distant relative of the human pathogen Chlamydia trachomatis and representative of a large group of protist-associated environmental chlamydiae, as a model to study how obligate intracellular symbionts evolve and adapt to elevated temperature, a prerequisite for the pivotal evolutionary leap from protist to endothermic animal hosts. We established 12 replicate populations under two temperatures (20 °C, 30 °C) for 510 bacterial generations (38 months). We then used infectivity assays and pooled whole-genome resequencing to identify any evolved phenotypes and the molecular basis of adaptation in these bacteria. We observed an overall reduction in infectivity of the symbionts evolved at 30 °C, and we identified numerous nonsynonymous mutations and small indels in these symbiont populations, with several variants persisting throughout multiple time points and reaching high frequencies. This suggests that many mutations may have been beneficial and played an adaptive role. Mutated genes within the same temperature regime were more similar than those between temperature regimes. Our results provide insights into the molecular evolution of intracellular bacteria under the constraints of strict host dependance and highly structured populations and suggest that for chlamydial symbionts of protists, temperature adaptation was facilitated through attenuation of symbiont infectivity as a tradeoff to reduce host cell burden.

  • A predicted CRISPR-mediated symbiosis between uncultivated archaea.

    Esser SP, Rahlff J, Zhao W, Predl M, Plewka J, Sures K, Wimmer F, Lee J, Adam PS, McGonigle J, Turzynski V, Banas I, Schwank K, Krupovic M, Bornemann TLV, Figueroa-Gonzalez PA, Jarett J, Rattei T, Amano Y, Blaby IK, Cheng JF, Brazelton WJ, Beisel CL, Woyke T, Zhang Y, Probst AJ
    2023 - Nat Microbiol, 9: 1619-1633


    CRISPR-Cas systems defend prokaryotic cells from invasive DNA of viruses, plasmids and other mobile genetic elements. Here, we show using metagenomics, metatranscriptomics and single-cell genomics that CRISPR systems of widespread, uncultivated archaea can also target chromosomal DNA of archaeal episymbionts of the DPANN superphylum. Using meta-omics datasets from Crystal Geyser and Horonobe Underground Research Laboratory, we find that CRISPR spacers of the hosts Candidatus Altiarchaeum crystalense and Ca. A. horonobense, respectively, match putative essential genes in their episymbionts' genomes of the genus Ca. Huberiarchaeum and that some of these spacers are expressed in situ. Metabolic interaction modelling also reveals complementation between host-episymbiont systems, on the basis of which we propose that episymbionts are either parasitic or mutualistic depending on the genotype of the host. By expanding our analysis to 7,012 archaeal genomes, we suggest that CRISPR-Cas targeting of genomes associated with symbiotic archaea evolved independently in various archaeal lineages.

  • Microbial responses to soil cooling might explain increases in microbial biomass in winter

    SchneckerJ, Spiegel F, Li Y, Richter A, Sandén T, Spiegel H, Zechmeister-Boltenstern S, Fuchslueger L
    2023 - Biogeochemistry, 164: 521-535


    In temperate, boreal and arctic soil systems, microbial biomass often increases during winter and decreases again in spring. This build-up and release of microbial carbon could potentially lead to a stabilization of soil carbon during winter times. Whether this increase is caused by changes in microbial physiology, in community composition, or by changed substrate allocation within microbes or communities is unclear. In a laboratory incubation study, we looked into microbial respiration and growth, as well as microbial glucose uptake and carbon resource partitioning in response to cooling. Soils taken from a temperate beech forest and temperate cropland system in October 2020, were cooled down from field temperature of 11 °C to 1 °C. We determined microbial growth using 18O-incorporation into DNA after the first two days of cooling and after an acclimation phase of 9 days; in addition, we traced 13C-labelled glucose into microbial biomass, CO2 respired from the soil, and into microbial phospholipid fatty acids (PLFAs). Our results show that the studied soil microbial communities responded strongly to soil cooling. The 18O data showed that growth and cell division were reduced when soils were cooled from 11 to 1 °C. Total respiration was also reduced but glucose uptake and glucose-derived respiration were unchanged. We found that microbes increased the investment of glucose-derived carbon in unsaturated phospholipid fatty acids at colder temperatures. Since unsaturated fatty acids retain fluidity at lower temperatures compared to saturated fatty acids, this could be interpreted as a precaution to reduced temperatures. Together with the maintained glucose uptake and reduced cell division, our findings show an immediate response of soil microorganisms to soil cooling, potentially to prepare for freezing events. The discrepancy between C uptake and cell division could explain previously observed high microbial biomass carbon in temperate soils in winter.

  • Nitrification in acidic and alkaline environments

    Ni G, Leung PM, Daebeler A, Guo J, Hu S, Cook P, Nicol GW, Daims H, Greening C
    2023 - Essays Biochem, in press


    Aerobic nitrification is a key process in the global nitrogen cycle mediated by microorganisms. While nitrification has primarily been studied in near-neutral environments, this process occurs at a wide range of pH values, spanning ecosystems from acidic soils to soda lakes. Aerobic nitrification primarily occurs through the activities of ammonia-oxidising bacteria and archaea, nitrite-oxidising bacteria, and complete ammonia-oxidising (comammox) bacteria adapted to these environments. Here, we review the literature and identify knowledge gaps on the metabolic diversity, ecological distribution, and physiological adaptations of nitrifying microorganisms in acidic and alkaline environments. We emphasise that nitrifying microorganisms depend on a suite of physiological adaptations to maintain pH homeostasis, acquire energy and carbon sources, detoxify reactive nitrogen species, and generate a membrane potential at pH extremes. We also recognize the broader implications of their activities primarily in acidic environments, with a focus on agricultural productivity and nitrous oxide emissions, as well as promising applications in treating municipal wastewater.

  • Individual and interactive effects of warming and nitrogen supply on CO2 fluxes and carbon allocation in subarctic grassland

    Meeran K, Verbrigge N, Ingrisch J, Fuchslueger L, Müller L, Sigurðsson P, Sigurdsson BD, Wachter H, Watzka M, Soong JL, Vicca S, Janssens IA, Bahn M
    2023 - Global Change Biology, 29: 5276-5291


    Climate warming has been suggested to impact high latitude grasslands severely, potentially causing considerable carbon (C) losses from soil. Warming can also stimulate nitrogen (N) turnover, but it is largely unclear whether and how altered N availability impacts belowground C dynamics. Even less is known about the individual and interactive effects of warming and N availability on the fate of recently photosynthesized C in soil. On a 10-year geothermal warming gradient in Iceland, we studied the effects of soil warming and N addition on CO2 fluxes and the fate of recently photosynthesized C through CO2 flux measurements and a 13CO2 pulse-labeling experiment. Under warming, ecosystem respiration exceeded maximum gross primary productivity, causing increased net CO2 emissions. N addition treatments revealed that, surprisingly, the plants in the warmed soil were N limited, which constrained primary productivity and decreased recently assimilated C in shoots and roots. In soil, microbes were increasingly C limited under warming and increased microbial uptake of recent C. Soil respiration was increased by warming and was fueled by increased belowground inputs and turnover of recently photosynthesized C. Our findings suggest that a decade of warming seemed to have induced a N limitation in plants and a C limitation by soil microbes. This caused a decrease in net ecosystem CO2 uptake and accelerated the respiratory release of photosynthesized C, which decreased the C sequestration potential of the grassland. Our study highlights the importance of belowground C allocation and C-N interactions in the C dynamics of subarctic ecosystems in a warmer world.

  • Use of gene sequences as type for naming prokaryotes: Recommendations of the international committee on the taxonomy of chlamydiae.

    Greub G, Pillonel T, Bavoil PM, Borel N, Campbell LA, Dean D, Hefty S, Horn M, Morré SA, Ouellette SP, Pannekoek Y, Puolakkainen M, Timms P, Valdivia R, Vanrompay D
    2023 - New Microbes New Infect, 101158


    The International Committee on Systematics of Prokaryotes (ICSP) discussed and rejected in 2020 a proposal to modify the International Code of Nomenclature of Prokaryotes to allow the use of gene sequences as type for naming prokaryotes. An alternative nomenclatural code, the (SeqCode), which considers genome sequences as type material for naming species, was published in 2022. Members of the ICSP subcommittee for the taxonomy of the phylum () consider that the use of gene sequences as type would benefit the taxonomy of microorganisms that are difficult to culture such as the chlamydiae and other strictly intracellular bacteria. We recommend the registration of new names of uncultured prokaryotes in the SeqCode registry.

  • RGS4 impacts carbohydrate and siderophore metabolism in Trichoderma reesei

    Schalamun M, Molin EM, Schmoll M
    2023 - BMC genomics, 24: Article 372



    Adaptation to complex, rapidly changing environments is crucial for evolutionary success of fungi. The heterotrimeric G-protein pathway belongs to the most important signaling cascades applied for this task. In Trichoderma reesei, enzyme production, growth and secondary metabolism are among the physiological traits influenced by the G-protein pathway in a light dependent manner.


    Here, we investigated the function of the SNX/H-type regulator of G-protein signaling (RGS) protein RGS4 of T. reesei. We show that RGS4 is involved in regulation of cellulase production, growth, asexual development and oxidative stress response in darkness as well as in osmotic stress response in the presence of sodium chloride, particularly in light. Transcriptome analysis revealed regulation of several ribosomal genes, six genes mutated in RutC30 as well as several genes encoding transcription factors and transporters. Importantly, RGS4 positively regulates the siderophore cluster responsible for fusarinine C biosynthesis in light. The respective deletion mutant shows altered growth on nutrient sources related to siderophore production such as ornithine or proline in a BIOLOG phenotype microarray assay. Additionally, growth on storage carbohydrates as well as several intermediates of the D-galactose and D-arabinose catabolic pathway is decreased, predominantly in light.


    We conclude that RGS4 mainly operates in light and targets plant cell wall degradation, siderophore production and storage compound metabolism in T. reesei.

  • Gold-FISH enables targeted NanoSIMS analysis of plant-associated bacteria

    Schmidt H, Gorka S, Seki D, Schintlmeister A, Woebken D
    2023 - New Phytologist, in press


    Bacteria colonize plant roots and engage in reciprocal interactions with their hosts. However, the contribution of individual taxa or groups of bacteria to plant nutrition and fitness is not well characterized due to a lack of in situ evidence of bacterial activity. To address this knowledge gap, we developed an analytical approach that combines the identification and localization of individual bacteria on root surfaces via gold-based in situ hybridization with correlative NanoSIMS imaging of incorporated stable isotopes, indicative of metabolic activity. We incubated Kosakonia strain DS-1-associated, gnotobiotically grown rice plants with 15 N-N2 gas to detect in situ N2 fixation activity. Bacterial cells along the rhizoplane showed heterogeneous patterns of 15 N enrichment, ranging from the natural isotope abundance levels up to 12.07 at% 15 N (average and median of 3.36 and 2.85 at% 15 N, respectively, n = 697 cells). The presented correlative optical and chemical imaging analysis is applicable to a broad range of studies investigating plant-microbe interactions. For example, it enables verification of the in situ metabolic activity of host-associated commercialized strains or plant growth-promoting bacteria, thereby disentangling their role in plant nutrition. Such data facilitate the design of plant-microbe combinations for improvement of crop management.

  • Food systems microbiome-related educational needs.

    Olmo R, Wetzels SU, Berg G, Cocolin L, Hartmann M, Hugas M, Kostic T, Rattei T, Ruthsatz M, Rybakova D, Sessitsch A, Shortt C, Timmis K, Selberherr E, Wagner M
    2023 - Microb Biotechnol, 7: 1412-1422


    Within the European-funded Coordination and Support Action MicrobiomeSupport (, the Workshop 'Education in Food Systems Microbiome Related Sciences: Needs for Universities, Industry and Public Health Systems' brought together over 70 researchers, public health and industry partners from all over the world to work on elaborating microbiome-related educational needs in food systems. This publication provides a summary of discussions held during and after the workshop and the resulting recommendations.

  • Colocalization and potential interactions of and chlamydiae in microbial aggregates of the coral Pocillopora acuta

    Maire J, Tandon K, Collingro A, van de Meene A, Damjanovic K, Gotze CR, Stephenson S, Philip GK, Horn M, Cantin NE, Blackall LL, van Oppen MJH
    2023 - Sci Adv, 20: eadg0773


    Corals are associated with a variety of bacteria, which occur in the surface mucus layer, gastrovascular cavity, skeleton, and tissues. Some tissue-associated bacteria form clusters, termed cell-associated microbial aggregates (CAMAs), which are poorly studied. Here, we provide a comprehensive characterization of CAMAs in the coral . Combining imaging techniques, laser capture microdissection, and amplicon and metagenome sequencing, we show that (i) CAMAs are located in the tentacle tips and may be intracellular; (ii) CAMAs contain (Gammaproteobacteria) and (Chlamydiota) bacteria; (iii) may provide vitamins to its host and use secretion systems and/or pili for colonization and aggregation; (iv) and occur in distinct, but adjacent, CAMAs; and (v) may receive acetate and heme from neighboring . Our study provides detailed insight into coral endosymbionts, thereby improving our understanding of coral physiology and health and providing important knowledge for coral reef conservation in the climate change era.

  • Taurine as a key intermediate for host-symbiont interaction in the tropical sponge Ianthella basta.

    Moeller FU, Herbold CW, Schintlmeister A, Mooshammer M, Motti C, Glasl B, Kitzinger K, Behnam F, Watzka M, Schweder T, Albertsen M, Richter A, Webster NS, Wagner M
    2023 - ISME J, in press
    sponge Ianthella basta microbiome


    Marine sponges are critical components of marine benthic fauna assemblages, where their filter-feeding and reef-building capabilities provide bentho-pelagic coupling and crucial habitat. As potentially the oldest representation of a metazoan-microbe symbiosis, they also harbor dense, diverse, and species-specific communities of microbes, which are increasingly recognized for their contributions to dissolved organic matter (DOM) processing. Recent omics-based studies of marine sponge microbiomes have proposed numerous pathways of dissolved metabolite exchange between the host and symbionts within the context of the surrounding environment, but few studies have sought to experimentally interrogate these pathways. By using a combination of metaproteogenomics and laboratory incubations coupled with isotope-based functional assays, we showed that the dominant gammaproteobacterial symbiont, 'Candidatus Taurinisymbion ianthellae', residing in the marine sponge, Ianthella basta, expresses a pathway for the import and dissimilation of taurine, a ubiquitously occurring sulfonate metabolite in marine sponges. 'Candidatus Taurinisymbion ianthellae' incorporates taurine-derived carbon and nitrogen while, at the same time, oxidizing the dissimilated sulfite into sulfate for export. Furthermore, we found that taurine-derived ammonia is exported by the symbiont for immediate oxidation by the dominant ammonia-oxidizing thaumarchaeal symbiont, 'Candidatus Nitrosospongia ianthellae'. Metaproteogenomic analyses also suggest that 'Candidatus Taurinisymbion ianthellae' imports DMSP and possesses both pathways for DMSP demethylation and cleavage, enabling it to use this compound as a carbon and sulfur source for biomass, as well as for energy conservation. These results highlight the important role of biogenic sulfur compounds in the interplay between Ianthella basta and its microbial symbionts.

  • Hot spring distribution and survival mechanisms of thermophilic comammox Nitrospira

    Zhang Y, Liu T, Li MM, Hua Z-S, Evans P, Qu Y, Tan S, Zheng M, Lu H, Jiao J-Y, Lücker S, Daims H, Li W-J, Guo J
    2023 - ISME J., 17: 993-1003


    The recent discovery of Nitrospira species capable of complete ammonia oxidation (comammox) in non-marine natural and engineered ecosystems under mesothermal conditions has changed our understanding of microbial nitrification. However, little is known about the occurrence of comammox bacteria or their ability to survive in moderately thermal and/or hyperthermal habitats. Here, we report the wide distribution of comammox Nitrospira in five terrestrial hot springs at temperatures ranging from 36 to 80°C and provide metagenome-assembled genomes of 11 new comammox strains. Interestingly, the identification of dissimilatory nitrate reduction to ammonium (DNRA) in thermophilic comammox Nitrospira lineages suggests that they have versatile ecological functions as both sinks and sources of ammonia, in contrast to the described mesophilic comammox lineages, which lack the DNRA pathway. Furthermore, the in situ expression of key genes associated with nitrogen metabolism, thermal adaptation, and oxidative stress confirmed their ability to survive in the studied hot springs and their contribution to nitrification in these environments. Additionally, the smaller genome size and higher GC content, less polar and more charged amino acids in usage profiles, and the expression of a large number of heat shock proteins compared to mesophilic comammox strains presumably confer tolerance to thermal stress. These novel insights into the occurrence, metabolic activity, and adaptation of comammox Nitrospira in thermal habitats further expand our understanding of the global distribution of comammox Nitrospira and have significant implications for how these unique microorganisms have evolved thermal tolerance strategies.

  • Phosphorus scarcity contributes to nitrogen limitation in lowland tropical rainforests

    Vallicrosa H, Lugli LF, Fuchslueger L, Sardans J, Ramírez-Rojas I, Verbruggen E, Grau O, Bréchet L, Peguero G, Van Langenhove L, Verryckt LT, Terrer C, Llusià J, Ogaya R, Márquez L, Roc-Fernández P, Janssens I, Schiestl RH
    2023 - Ecology, Article e4049


    There is increasing evidence to suggest that soil nutrient availability can limit the carbon sink capacity of forests, a particularly relevant issue considering today's changing climate. This question is especially important in the tropics, where most part of the Earth's plant biomass is stored. To assess whether tropical forest growth is limited by soil nutrients and to explore N and P limitations, we analyzed stem growth and foliar elemental composition of the 5 stem widest trees per plot at two sites in French Guiana after three years of nitrogen (N), phosphorus (P), and N+P addition. We also compared the results between potential N-fixer and non-N-fixer species. We found a positive effect of N fertilization on stem growth and foliar N, as well as a positive effect of P fertilization on stem growth, foliar N, and foliar P. Potential N-fixing species had greater stem growth, greater foliar N and greater foliar P concentrations than non-N-fixers. In terms of growth, there was a negative interaction between N-fixer status, N+P, and P fertilization, but no interaction with N fertilization. Since N-fixing plants does not show to be completely N saturated, we do not anticipate N providing from N-fixing plants would supply non-N-fixers. Although the soil age hypothesis only anticipates P limitation in highly weathered systems, our results for stem growth and foliar elemental composition indicate the existence of considerable N and P co-limitation, which is alleviated in N-fixing plants. The evidence suggests that certain mechanisms invest in N to obtain the scarce P through soil phosphatases, which potentially contributes to the N limitation detected by this study.

  • Antiviral immune response reveals host-specific virus infections in natural ant populations.

    Viljakainen L, Fürst MA, Grasse AV, Jurvansuu J, Oh J, Tolonen L, Eder T, Rattei T, Cremer S
    2023 - Front Microbiol, 1119002


    Hosts can carry many viruses in their bodies, but not all of them cause disease. We studied ants as a social host to determine both their overall viral repertoire and the subset of actively infecting viruses across natural populations of three subfamilies: the Argentine ant (, Dolichoderinae), the invasive garden ant (, Formicinae) and the red ant (, Myrmicinae). We used a dual sequencing strategy to reconstruct complete virus genomes by RNA-seq and to simultaneously determine the small interfering RNAs (siRNAs) by small RNA sequencing (sRNA-seq), which constitute the host antiviral RNAi immune response. This approach led to the discovery of 41 novel viruses in ants and revealed a host ant-specific RNAi response (21 vs. 22 nt siRNAs) in the different ant species. The efficiency of the RNAi response (sRNA/RNA read count ratio) depended on the virus and the respective ant species, but not its population. Overall, we found the highest virus abundance and diversity per population in , followed by and . Argentine ants also shared a high proportion of viruses between populations, whilst overlap was nearly absent in . Only one of the 59 viruses was found to infect two of the ant species as hosts, revealing high host-specificity in active infections. In contrast, six viruses actively infected one ant species, but were found as contaminants only in the others. Disentangling spillover of disease-causing infection from non-infecting contamination across species is providing relevant information for disease ecology and ecosystem management.

  • Cable bacteria with electric connection to oxygen attract flocks of diverse bacteria.

    Bjerg JJ, Lustermans JJM, Marshall IPG, Mueller AJ, Brokjær S, Thorup CA, Tataru P, Schmid M, Wagner M, Nielsen LP, Schramm A
    2023 - Nat Commun, 1: 1614
    Cable bacteria


    Cable bacteria are centimeter-long filamentous bacteria that conduct electrons via internal wires, thus coupling sulfide oxidation in deeper, anoxic sediment with oxygen reduction in surface sediment. This activity induces geochemical changes in the sediment, and other bacterial groups appear to benefit from the electrical connection to oxygen. Here, we report that diverse bacteria swim in a tight flock around the anoxic part of oxygen-respiring cable bacteria and disperse immediately when the connection to oxygen is disrupted (by cutting the cable bacteria with a laser). Raman microscopy shows that flocking bacteria are more oxidized when closer to the cable bacteria, but physical contact seems to be rare and brief, which suggests potential transfer of electrons via unidentified soluble intermediates. Metagenomic analysis indicates that most of the flocking bacteria appear to be aerobes, including organotrophs, sulfide oxidizers, and possibly iron oxidizers, which might transfer electrons to cable bacteria for respiration. The association and close interaction with such diverse partners might explain how oxygen via cable bacteria can affect microbial communities and processes far into anoxic environments.

  • Complete genome sequence of Nitrospina watsonii 347, isolated from the Black Sea

    Kop LFM, Koch H, Spieck E, van Alen T, Cremers G, Daims H, Lücker L
    2023 - Microbiol Resour Announc, 12: e0007823


    Here, we present the complete genome sequence of Nitrospina watsonii 347, a nitrite-oxidizing bacterium isolated from the Black Sea at a depth of 100 m. The genome has a length of 3,011,914 bp with 2,895 predicted coding sequences. Its predicted metabolism is similar to that of Nitrospina gracilis with differences in defense against reactive oxygen species.

  • Gut microbiome signatures of Yorkshire Terrier enteropathy during disease and remission.

    Doulidis PG, Galler AI, Hausmann B, Berry D, Rodríguez-Rojas A, Burgener IA
    2023 - Sci Rep, 1: 4337


    The role of the gut microbiome in developing Inflammatory Bowel Disease (IBD) in humans and dogs has received attention in recent years. Evidence suggests that IBD is associated with alterations in gut microbial composition, but further research is needed in veterinary medicine. The impact of IBD treatment on the gut microbiome needs to be better understood, especially in a breed-specific form of IBD in Yorkshire Terriers known as Yorkshire Terrier Enteropathy (YTE). This study aimed to investigate the difference in gut microbiome composition between YTE dogs during disease and remission and healthy Yorkshire Terriers. Our results showed a significant increase in specific taxa such as Clostridium sensu stricto 1, Escherichia-Shigella, and Streptococcus, and a decrease in Bacteroides, Prevotella, Alloprevotella, and Phascolarctobacterium in YTE dogs compared to healthy controls. No significant difference was found between the microbiome of dogs in remission and those with active disease, suggesting that the gut microbiome is affected beyond clinical recovery.

  • Neutral and Pectic Heteropolysaccharides Isolated from Mucilage: Composition, Molecular Dimensions and Prebiotic Potential.

    Cruz-Rubio JM, Riva A, Cybulska J, Zdunek A, Berry D, Loeppert R, Viernstein H, Praznik W, Maghuly F
    2023 - Int J Mol Sci, 4: in press


    is a semi-wild cactus cultivated for its fruit. However, the cladodes are often discarded, wasting the potentially useful mucilage in them. The mucilage is composed primarily of heteropolysaccharides, characterized by their molar mass distribution, monosaccharide composition, structural features (by vibrational spectroscopy, FT IR, and atomic force microscopy, AFM), and fermentability by known saccharolytic commensal members of the gut microbiota. After fractionation with ion exchange chromatography, four polysaccharides were found: one neutral (composed mainly of galactose, arabinose, and xylose) and three acidic, with a galacturonic acid content from 10 to 35%. Their average molar masses ranged from 1.8 × 10 to 2.8 × 10 g·mol. Distinct structural features such as galactan, arabinan, xylan, and galacturonan motifs were present in the FT IR spectra. The intra- and intermolecular interactions of the polysaccharides, and their effect on the aggregation behavior, were shown by AFM. The composition and structural features of these polysaccharides were reflected in their prebiotic potential. and were not able to utilize them, whereas members of showed utilization capacity. The obtained data suggest a high economic potential for this species, with potential uses such as animal feed in arid areas, precise prebiotic, and symbiotic formulations, or as the carbon skeleton source in a green refinery. Our methodology can be used to evaluate the saccharides as the phenotype of interest, helping to guide the breeding strategy.

  • Metagenomic Antimicrobial Susceptibility Testing from Simulated Native Patient Samples.

    Lüftinger L, Májek P, Rattei T, Beisken S
    2023 - Antibiotics (Basel), 2: in press


    Genomic antimicrobial susceptibility testing (AST) has been shown to be accurate for many pathogens and antimicrobials. However, these methods have not been systematically evaluated for clinical metagenomic data. We investigate the performance of in-silico AST from clinical metagenomes (MG-AST). Using isolate sequencing data from a multi-center study on antimicrobial resistance (AMR) as well as shotgun-sequenced septic urine samples, we simulate over 2000 complicated urinary tract infection (cUTI) metagenomes with known resistance phenotype to 5 antimicrobials. Applying rule-based and machine learning-based genomic AST classifiers, we explore the impact of sequencing depth and technology, metagenome complexity, and bioinformatics processing approaches on AST accuracy. By using an optimized metagenomics assembly and binning workflow, MG-AST achieved balanced accuracy within 5.1% of isolate-derived genomic AST. For poly-microbial infections, taxonomic sample complexity and relatedness of taxa in the sample is a key factor influencing metagenomic binning and downstream MG-AST accuracy. We show that the reassignment of putative plasmid contigs by their predicted host range and investigation of whole resistome capabilities improved MG-AST performance on poly-microbial samples. We further demonstrate that machine learning-based methods enable MG-AST with superior accuracy compared to rule-based approaches on simulated native patient samples.

  • Extending and improving metagenomic taxonomic profiling with uncharacterized species using MetaPhlAn 4.

    Blanco-Míguez A, Beghini F, Cumbo F, McIver LJ, Thompson KN, Zolfo M, Manghi P, Dubois L, Huang KD, Thomas AM, Nickols WA, Piccinno G, Piperni E, Punčochář M, Valles-Colomer M, Tett A, Giordano F, Davies R, Wolf J, Berry SE, Spector TD, Franzosa EA, Pasolli E, Asnicar F, Huttenhower C, Segata N
    2023 - Nat Biotechnol, in press


    Metagenomic assembly enables new organism discovery from microbial communities, but it can only capture few abundant organisms from most metagenomes. Here we present MetaPhlAn 4, which integrates information from metagenome assemblies and microbial isolate genomes for more comprehensive metagenomic taxonomic profiling. From a curated collection of 1.01 M prokaryotic reference and metagenome-assembled genomes, we define unique marker genes for 26,970 species-level genome bins, 4,992 of them taxonomically unidentified at the species level. MetaPhlAn 4 explains ~20% more reads in most international human gut microbiomes and >40% in less-characterized environments such as the rumen microbiome and proves more accurate than available alternatives on synthetic evaluations while also reliably quantifying organisms with no cultured isolates. Application of the method to >24,500 metagenomes highlights previously undetected species to be strong biomarkers for host conditions and lifestyles in human and mouse microbiomes and shows that even previously uncharacterized species can be genetically profiled at the resolution of single microbial strains.

  • Long-term soil warming decreases microbial phosphorus utilization by increasing abiotic phosphorus sorption and phosphorus losses

    Tian Y, Shi C, Malo CU, Kendo SK, Heinzle J, Inselsbacher E, Ottner F, Borken W, Michel K, Schindlbacher A, Wanek W
    2023 - Nature communications, 14: Article 864


    Phosphorus (P) is an essential and often limiting element that could play a crucial role in terrestrial ecosystem responses to climate warming. However, it has yet remained unclear how different P cycling processes are affected by warming. Here we investigate the response of soil P pools and P cycling processes in a mountain forest after 14 years of soil warming (+4 °C). Long-term warming decreased soil total P pools, likely due to higher outputs of P from soils by increasing net plant P uptake and downward transportation of colloidal and particulate P. Warming increased the sorption strength to more recalcitrant soil P fractions (absorbed to iron oxyhydroxides and clays), thereby further reducing bioavailable P in soil solution. As a response, soil microbes enhanced the production of acid phosphatase, though this was not sufficient to avoid decreases of soil bioavailable P and microbial biomass P (and biotic phosphate immobilization). This study therefore highlights how long-term soil warming triggers changes in biotic and abiotic soil P pools and processes, which can potentially aggravate the P constraints of the trees and soil microbes and thereby negatively affect the C sequestration potential of these forests.

  • One to host them all: genomics of the diverse bacterial endosymbionts of the spider Oedothorax gibbosus

    Halter T, Köstlbacher S, Rattei T, Hendrickx F, Küsel K, Horn M
    2023 - Microb. Genomics, 9: 10.1099/mgen.0.00094


    Bacterial endosymbionts of the groups Wolbachia, Cardinium and Rickettsiaceae are well known for their diverse effects on their arthropod hosts, ranging from mutualistic relationships to reproductive phenotypes. Here, we analysed a unique system in which the dwarf spider Oedothorax gibbosus is co-infected with up to five different endosymbionts affiliated with Wolbachia, ‘Candidatus Tisiphia’ (formerly Torix group Rickettsia), Cardinium and Rhabdochlamydia. Using short-read genome sequencing data, we show that the endosymbionts are heterogeneously distributed among O. gibbosus populations and are frequently found co-infecting spider individuals. To study this intricate host–endosymbiont system on a genome-resolved level, we used long-read sequencing to reconstruct closed genomes of the Wolbachia, ‘Ca. Tisiphia’ and Cardinium endosymbionts. We provide insights into the ecology and evolution of the endosymbionts and shed light on the interactions with their spider host. We detected high quantities of transposable elements in all endosymbiont genomes and provide evidence that ancestors of the Cardinium, ‘Ca. Tisiphia’ and Wolbachia endosymbionts have co-infected the same hosts in the past. Our findings contribute to broadening our knowledge about endosymbionts infecting one of the largest animal phyla on Earth and show the usefulness of transposable elements as an evolutionary ‘contact-tracing’ tool.

  • MAPkinases regulate secondary metabolism, sexual development and light dependent cellulase regulation in Trichoderma reesei

    Schalamun M, Beier S, Hinterdobler W, Wanko N, Schinnerl J, Brecher L, Engl DE, Schmoll M
    2023 - Scientific Reports, 13: Article 1912


    The filamentous fungus Trichoderma reesei is a prolific producer of plant cell wall degrading enzymes, which are regulated in response to diverse environmental signals for optimal adaptation, but also produces a wide array of secondary metabolites. Available carbon source and light are the strongest cues currently known to impact secreted enzyme levels and an interplay with regulation of secondary metabolism became increasingly obvious in recent years. While cellulase regulation is already known to be modulated by different mitogen activated protein kinase (MAPK) pathways, the relevance of the light signal, which is transmitted by this pathway in other fungi as well, is still unknown in T. reesei as are interconnections to secondary metabolism and chemical communication under mating conditions. Here we show that MAPkinases differentially influence cellulase regulation in light and darkness and that the Hog1 homologue TMK3, but not TMK1 or TMK2 are required for the chemotropic response to glucose in T. reesei. Additionally, MAPkinases regulate production of specific secondary metabolites including trichodimerol and bisorbibutenolid, a bioactive compound with cytostatic effect on cancer cells and deterrent effect on larvae, under conditions facilitating mating, which reflects a defect in chemical communication. Strains lacking either of the MAPkinases become female sterile, indicating the conservation of the role of MAPkinases in sexual fertility also in T. reesei. In summary, our findings substantiate the previously detected interconnection of cellulase regulation with regulation of secondary metabolism as well as the involvement of MAPkinases in light dependent gene regulation of cellulase and secondary metabolite genes in fungi.

  • 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.

  • Questioning the fetal microbiome illustrates pitfalls of low-biomass microbial studies.

    Kennedy KM, de Goffau MC, Perez-Muñoz ME, Arrieta MC, Bäckhed F, Bork P, Braun T, Bushman FD, Dore J, de Vos WM, Earl AM, Eisen JA, Elovitz MA, Ganal-Vonarburg SC, Gänzle MG, Garrett WS, Hall LJ, Hornef MW, Huttenhower C, Konnikova L, Lebeer S, Macpherson AJ, Massey RC, McHardy AC, Koren O, Lawley TD, Ley RE, O'Mahony L, O'Toole PW, Pamer EG, Parkhill J, Raes J, Rattei T, Salonen A, Segal E, Segata N, Shanahan F, Sloboda DM, Smith GCS, Sokol H, Spector TD, Surette MG, Tannock GW, Walker AW, Yassour M, Walter J
    2023 - Nature, 7945: 639-649


    Whether the human fetus and the prenatal intrauterine environment (amniotic fluid and placenta) are stably colonized by microbial communities in a healthy pregnancy remains a subject of debate. Here we evaluate recent studies that characterized microbial populations in human fetuses from the perspectives of reproductive biology, microbial ecology, bioinformatics, immunology, clinical microbiology and gnotobiology, and assess possible mechanisms by which the fetus might interact with microorganisms. Our analysis indicates that the detected microbial signals are likely the result of contamination during the clinical procedures to obtain fetal samples or during DNA extraction and DNA sequencing. Furthermore, the existence of live and replicating microbial populations in healthy fetal tissues is not compatible with fundamental concepts of immunology, clinical microbiology and the derivation of germ-free mammals. These conclusions are important to our understanding of human immune development and illustrate common pitfalls in the microbial analyses of many other low-biomass environments. The pursuit of a fetal microbiome serves as a cautionary example of the challenges of sequence-based microbiome studies when biomass is low or absent, and emphasizes the need for a trans-disciplinary approach that goes beyond contamination controls by also incorporating biological, ecological and mechanistic concepts.

  • Exo- and endophytic fungi enable rapid transfer of nutrients from ant waste to orchid tissue

    Gegenbauer C, Bellaire A, Schintlmeister A, Schmid MC, Kubicek M, Voglmayr H, Zotz G, Richter A, Mayer VE
    2023 - New Phytologist, 238: 2210-2223




    • The epiphytic orchid Caularthron bilamellatum sacrifices its water storage tissue for nutrients from the waste of ants lodging inside its hollow pseudobulb. Here, we investigate whether fungi are involved in the rapid translocation of nutrients.
    • Uptake was analysed with a 15N labelling experiment, subsequent isotope-ratio mass spectrometry (IRMS) and secondary ion mass spectrometry (ToF-SIMS and NanoSIMS).
    • We encountered two hyphae types: a thick melanized type assigned to “black fungi” (Chaetothyriales, Cladosporiales, Mycosphaerellales) in ant waste, and a thin endophytic type belonging to Hypocreales. In few cell layers both hyphae types co-occurred. 15N accumulation in both hyphae types was conspicuous, while for translocation to the vessels only Hypocreales were involved. There is evidence that the occurrence of the two hyphae types result in a synergism in terms of nutrient uptake.
    • Our study provides the first evidence that a pseudobulb (=stem)-born endophytic network of Hypocreales is involved in the rapid translocation of nitrogen from insect derived waste to the vegetative and reproductive tissue of the host orchid. For C. bilamellatum that has no contact with the soil, ant waste in the hollow pseudobulbs serves as equivalent to soil in terms of nutrient sources.
  • 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.

  • The person-to-person transmission landscape of the gut and oral microbiomes.

    Valles-Colomer M, Blanco-Míguez A, Manghi P, Asnicar F, Dubois L, Golzato D, Armanini F, Cumbo F, Huang KD, Manara S, Masetti G, Pinto F, Piperni E, Punčochář M, Ricci L, Zolfo M, Farrant O, Goncalves A, Selma-Royo M, Binetti AG, Becerra JE, Han B, Lusingu J, Amuasi J, Amoroso L, Visconti A, Steves CM, Falchi M, Filosi M, Tett A, Last A, Xu Q, Qin N, Qin H, May J, Eibach D, Corrias MV, Ponzoni M, Pasolli E, Spector TD, Domenici E, Collado MC, Segata N
    2023 - Nature, 7946: 125-135


    The human microbiome is an integral component of the human body and a co-determinant of several health conditions. However, the extent to which interpersonal relations shape the individual genetic makeup of the microbiome and its transmission within and across populations remains largely unknown. Here, capitalizing on more than 9,700 human metagenomes and computational strain-level profiling, we detected extensive bacterial strain sharing across individuals (more than 10 million instances) with distinct mother-to-infant, intra-household and intra-population transmission patterns. Mother-to-infant gut microbiome transmission was considerable and stable during infancy (around 50% of the same strains among shared species (strain-sharing rate)) and remained detectable at older ages. By contrast, the transmission of the oral microbiome occurred largely horizontally and was enhanced by the duration of cohabitation. There was substantial strain sharing among cohabiting individuals, with 12% and 32% median strain-sharing rates for the gut and oral microbiomes, and time since cohabitation affected strain sharing more than age or genetics did. Bacterial strain sharing additionally recapitulated host population structures better than species-level profiles did. Finally, distinct taxa appeared as efficient spreaders across transmission modes and were associated with different predicted bacterial phenotypes linked with out-of-host survival capabilities. The extent of microorganism transmission that we describe underscores its relevance in human microbiome studies, especially those on non-infectious, microbiome-associated diseases.

  • 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, 4: 2398-2405
    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, 25: 1055-1067


    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.

  • Thermal acclimation of methanotrophs from the genus Methylobacter.

    Tveit AT, Söllinger A, Rainer EM, Didriksen A, Hestnes AG, Motleleng L, Hellinger HJ, Rattei T, Svenning MM
    2023 - ISME J, 4: 502-513


    Methanotrophs oxidize most of the methane (CH) produced in natural and anthropogenic ecosystems. Often living close to soil surfaces, these microorganisms must frequently adjust to temperature change. While many environmental studies have addressed temperature effects on CH oxidation and methanotrophic communities, there is little knowledge about the physiological adjustments that underlie these effects. We have studied thermal acclimation in Methylobacter, a widespread, abundant, and environmentally important methanotrophic genus. Comparisons of growth and CH oxidation kinetics at different temperatures in three members of the genus demonstrate that temperature has a strong influence on how much CH is consumed to support growth at different CH concentrations. However, the temperature effect varies considerably between species, suggesting that how a methanotrophic community is composed influences the temperature effect on CH uptake. To understand thermal acclimation mechanisms widely we carried out a transcriptomics experiment with Methylobacter tundripaludum SV96. We observed, at different temperatures, how varying abundances of transcripts for glycogen and protein biosynthesis relate to cellular glycogen and ribosome concentrations. Our data also demonstrated transcriptional adjustment of CH oxidation, oxidative phosphorylation, membrane fatty acid saturation, cell wall composition, and exopolysaccharides between temperatures. In addition, we observed differences in M. tundripaludum SV96 cell sizes at different temperatures. We conclude that thermal acclimation in Methylobacter results from transcriptional adjustment of central metabolism, protein biosynthesis, cell walls and storage. Acclimation leads to large shifts in CH consumption and growth efficiency, but with major differences between species. Thus, our study demonstrates that physiological adjustments to temperature change can substantially influence environmental CH uptake rates and that consideration of methanotroph physiology might be vital for accurate predictions of warming effects on CH emissions.

  • 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.

  • Does long-term soil warming affect microbial element limitation? A test by short-term assays of microbial growth responses to labile C, N and P additions

    Shi C, Urbina-Malo C, Tian Y, Heinzle J, Kendo SK, Inselsbacher E, Borken W, Schindlbacher A, Wanek W
    2023 - Global Change Biology, 29: 2188-2202


    Increasing global temperatures have been reported to accelerate soil carbon (C) cycling, but also to promote nitrogen (N) and phosphorus (P) dynamics in terrestrial ecosystems. However, warming can differentially affect ecosystem C, N and P dynamics, potentially intensifying elemental imbalances between soil resources, plants and soil microorganisms. Here, we investigated the effect of long-term soil warming on microbial resource limitation, based on measurements of microbial growth (18O incorporation into DNA) and respiration after C, N and P amendments. Soil samples were taken from two soil depths (0–10, 10–20 cm) in control and warmed (>14 years warming, +4°C) plots in the Achenkirch soil warming experiment. Soils were amended with combinations of glucose-C, inorganic/organic N and inorganic/organic P in a full factorial design, followed by incubation at their respective mean field temperatures for 24 h. Soil microbes were generally C-limited, exhibiting 1.8-fold to 8.8-fold increases in microbial growth upon C addition. Warming consistently caused soil microorganisms to shift from being predominately C limited to become C-P co-limited. This P limitation possibly was due to increased abiotic P immobilization in warmed soils. Microbes further showed stronger growth stimulation under combined glucose and inorganic nutrient amendments compared to organic nutrient additions. This may be related to a prolonged lag phase in organic N (glucosamine) mineralization and utilization compared to glucose. Soil respiration strongly positively responded to all kinds of glucose-C amendments, while responses of microbial growth were less pronounced in many of these treatments. This highlights that respiration–though easy and cheap to measure—is not a good substitute of growth when assessing microbial element limitation. Overall, we demonstrate a significant shift in microbial element limitation in warmed soils, from C to C-P co-limitation, with strong repercussions on the linkage between soil C, N and P cycles under long-term warming.

  • 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.

  • Uptake, Metabolism, and Accumulation of Tire Wear Particle-Derived Compounds in Lettuce

    Castan S, Sherman A, Peng R, Zumstein MT, Wanek W, Hüffer T, Hofmann T
    2023 - Environmental Science & Technology, 57: 168-178


    Tire wear particle (TWP)-derived compounds may be of high concern to consumers when released in the root zone of edible plants. We exposed lettuce plants to the TWP-derived compounds diphenylguanidine (DPG), hexamethoxymethylmelamine (HMMM), benzothiazole (BTZ), N-phenyl-N′-(1,3-dimethylbutyl)-p-phenylenediamine (6PPD), and its quinone transformation product (6PPD-q) at concentrations of 1 mg L–1 in hydroponic solutions over 14 days to analyze if they are taken up and metabolized by the plants. Assuming that TWP may be a long-term source of TWP-derived compounds to plants, we further investigated the effect of leaching from TWP on the concentration of leachate compounds in lettuce leaves by adding constantly leaching TWP to the hydroponic solutions. Concentrations in leaves, roots, and nutrient solution were quantified by triple quadrupole mass spectrometry, and metabolites in the leaves were identified by Orbitrap high resolution mass spectrometry. This study demonstrates that TWP-derived compounds are readily taken up by lettuce with measured maximum leaf concentrations between ∼0.75 (6PPD) and 20 μg g–1 (HMMM). Although these compounds were metabolized in the plant, we identified several transformation products, most of which proved to be more stable in the lettuce leaves than the parent compounds. Furthermore, continuous leaching from TWP led to a resupply and replenishment of the metabolized compounds in the lettuce leaves. The stability of metabolized TWP-derived compounds with largely unknown toxicities is particularly concerning and is an important new aspect for the impact assessment of TWP in the environment.

  • Spectroscopic analysis of sequestered chloroplasts in Elphidium williamsoni (Foraminifera)

    Lintner M, Wildner M, Lintner B, Wanek W, Heinz P
    2023 - Journal of Photochemistry and Photobiology B: Biology, 238: Article 112623


    Foraminifera are unicellular, marine organisms that occur worldwide. A very common species in the German Wadden Sea is Elphidium williamsoni. Some foraminifera (such as elphidia) are able to use kleptoplastidy, which allows them to incorporate chloroplasts from their algal food source into their own cell body. The experiments reported here are based on the fact that chlorophyll (a and c) can be detected in the intact cells with spectroscopic methods in the visible spectral range, which allows an indirect investigation of the presence of sequestered chloroplasts. Starving experiments of E. williamsoni in the light (24 h continuous) showed that the greatest decrease in chlorophyll content was recorded within the first 20–30 days. From day 60 on, chlorophyll was hardly detectable. Through subsequent feeding on a renewed algal food source a significant increase in the chlorophyll content in foraminifera was noticed. The degradation of chlorophyll in the dark (24 h continuous darkness) during the starving period was much more complex. Chlorophyll was still detected in the cells after 113 days of starving time. Therefore, we hypotheses that the effect of photoinhibition applies to chloroplasts in foraminifera under continuous illumination.

  • Cytoscape stringApp 2.0: Analysis and Visualization of Heterogeneous Biological Networks.

    Doncheva NT, Morris JH, Holze H, Kirsch R, Nastou KC, Cuesta-Astroz Y, Rattei T, Szklarczyk D, von Mering C, Jensen LJ
    2023 - J Proteome Res, 2: 637-646


    Biological networks are often used to represent complex biological systems, which can contain several types of entities. Analysis and visualization of such networks is supported by the Cytoscape software tool and its many apps. While earlier versions of stringApp focused on providing intraspecies protein-protein interactions from the STRING database, the new stringApp 2.0 greatly improves the support for heterogeneous networks. Here, we highlight new functionality that makes it possible to create networks that contain proteins and interactions from STRING as well as other biological entities and associations from other sources. We exemplify this by complementing a published SARS-CoV-2 interactome with interactions from STRING. We have also extended stringApp with new data and query functionality for protein-protein interactions between eukaryotic parasites and their hosts. We show how this can be used to retrieve and visualize a cross-species network for a malaria parasite, its host, and its vector. Finally, the latest stringApp version has an improved user interface, allows retrieval of both functional associations and physical interactions, and supports group-wise enrichment analysis of different parts of a network to aid biological interpretation. stringApp is freely available at

  • Metabolic reconstruction of the near complete microbiome of the model sponge Ianthella basta.

    Engelberts JP, Robbins SJ, Herbold CW, Moeller FU, Jehmlich N, Laffy PW, Wagner M, Webster NS
    2023 - Environ Microbiol, 3: 646-660
    Ianthella basta microbiome


    Many marine sponges host highly diverse microbiomes that contribute to various aspects of host health. Although the putative function of individual groups of sponge symbionts has been increasingly described, the extreme diversity has generally precluded in-depth characterization of entire microbiomes, including identification of syntrophic partnerships. The Indo-Pacific sponge Ianthella basta is emerging as a model organism for symbiosis research, hosting only three dominant symbionts: a Thaumarchaeotum, a Gammaproteobacterium, and an Alphaproteobacterium and a range of other low abundance or transitory taxa. Here, we retrieved metagenome assembled genomes (MAGs) representing >90% of I. basta's microbial community, facilitating the metabolic reconstruction of the sponge's near complete microbiome. Through this analysis, we identified metabolic complementarity between microbes, including vitamin sharing, described the importance of low abundance symbionts, and characterized a novel microbe-host attachment mechanism in the Alphaproteobacterium. We further identified putative viral sequences, highlighting the role viruses can play in maintaining symbioses in I. basta through the horizontal transfer of eukaryotic-like proteins, and complemented this data with metaproteomics to identify active metabolic pathways in bacteria, archaea, and viruses. This data provide the framework to adopt I. basta as a model organism for studying host-microbe interactions and provide a basis for in-depth physiological experiments.

  • eggNOG 6.0: enabling comparative genomics across 12 535 organisms.

    Hernández-Plaza A, Szklarczyk D, Botas J, Cantalapiedra CP, Giner-Lamia J, Mende DR, Kirsch R, Rattei T, Letunic I, Jensen LJ, Bork P, von Mering C, Huerta-Cepas J
    2023 - Nucleic Acids Res, 1: D389-D394


    The eggNOG (evolutionary gene genealogy Non-supervised Orthologous Groups) database is a bioinformatics resource providing orthology data and comprehensive functional information for organisms from all domains of life. Here, we present a major update of the database and website (version 6.0), which increases the number of covered organisms to 12 535 reference species, expands functional annotations, and implements new functionality. In total, eggNOG 6.0 provides a hierarchy of over 17M orthologous groups (OGs) computed at 1601 taxonomic levels, spanning 10 756 bacterial, 457 archaeal and 1322 eukaryotic organisms. OGs have been thoroughly annotated using recent knowledge from functional databases, including KEGG, Gene Ontology, UniProtKB, BiGG, CAZy, CARD, PFAM and SMART. eggNOG also offers phylogenetic trees for all OGs, maximising utility and versatility for end users while allowing researchers to investigate the evolutionary history of speciation and duplication events as well as the phylogenetic distribution of functional terms within each OG. Furthermore, the eggNOG 6.0 website contains new functionality to mine orthology and functional data with ease, including the possibility of generating phylogenetic profiles for multiple OGs across species or identifying single-copy OGs at custom taxonomic levels. eggNOG 6.0 is available at

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

    Kengdo SK, Ahrens B, Tian Y, Heinzle J, Wanek W, Schindlbacher A, Borken W
    2023 - Science of The Total Environment, 855: Article 15800


    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.

Book chapters and other publications

1 Publication found
  • Pitfalls in sampling and analyzing low-biomass human nasal microbiome samples

    Pjevac P, Bartosik T, Schneider S, Eckl-Dorna J
    2023 - Allergy and Clinical Immunology, in press
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