Metamenu

Publications

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Publications in peer reviewed journals

80 Publications found
  • Increased microbial growth, biomass, and turnover drive soil organic carbon accumulation at higher plant diversity

    Prommer J, Walker TWN, Wanek W, Braun J, Zezula D, Hu Y, Hofhansl F, Richter A
    2020 - Global Change Biology, 2: 669-681

    Abstract: 

    Species‐rich plant communities have been shown to be more productive and to exhibit increased long‐term soil organic carbon (SOC) storage. Soil microorganisms are central to the conversion of plant organic matter into SOC, yet the relationship between plant diversity, soil microbial growth, turnover as well as carbon use efficiency (CUE) and SOC accumulation is unknown. As heterotrophic soil microbes are primarily carbon limited, it is important to understand how they respond to increased plant‐derived carbon inputs at higher plant species richness (PSR). We used the long‐term grassland biodiversity experiment in Jena, Germany, to examine how microbial physiology responds to changes in plant diversity and how this affects SOC content. The Jena Experiment considers different numbers of species (1–60), functional groups (1–4) as well as functional identity (small herbs, tall herbs, grasses, and legumes). We found that PSR accelerated microbial growth and turnover and increased microbial biomass and necromass. PSR also accelerated microbial respiration, but this effect was less strong than for microbial growth. In contrast, PSR did not affect microbial CUE or biomass‐specific respiration. Structural equation models revealed that PSR had direct positive effects on root biomass, and thereby on microbial growth and microbial biomass carbon. Finally, PSR increased SOC content via its positive influence on microbial biomass carbon. We suggest that PSR favors faster rates of microbial growth and turnover, likely due to greater plant productivity, resulting in higher amounts of microbial biomass and necromass that translate into the observed increase in SOC. We thus identify the microbial mechanism linking species‐rich plant communities to a carbon cycle process of importance to Earth's climate system.

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

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

    Abstract: 

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

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

    Naresh Kumar, Vincent Noël, Britta Planer-Friedrich, Johannes BesoldJ, uan Lezama-Pacheco, John R. Bargar, Gordon E. Brown Jr., Scott Fendorf, Kristin Boye
    2020 - Environmental Science & Technology, 54, 6, 3237–3244

    Abstract: 

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

  • Technology readiness and overcoming barriers to sustainably implement nanotechnology-enabled plant agriculture

    Thilo Hofmann, Gregory Victor Lowry, Subhasis Ghoshal, Nathalie Tufenkji, Davide Brambilla, John Robert Dutcher, Leanne M. Gilbertson, Juan Pablo Giraldo, Joseph Matthew Kinsella, Markita Patricia Landry, Wess Lovell, Rafik Naccache, Mathews Paret, Joel Alexander Pedersen, Jason Michael Unrine, Jason Christopher White, Kevin James Wilkinson
    2020 - Nature food, 1: 416–425

    Abstract: 

    Nanotechnology offers potential solutions for sustainable agriculture, including increasing nutrient utilization efficiency, improving the efficacy of pest management, mitigating the impacts of climate change, and reducing adverse environmental impacts of agricultural food production. Many promising nanotechnologies have been proposed and evaluated at different scales, but several barriers to implementation must be addressed for technology to be adopted, including efficient delivery at field scale, regulatory and safety concerns, and consumer acceptance. Here we explore these barriers, and rank technology readiness and potential impacts of a wide range of agricultural applications of nanotechnology. We propose pathways to overcome these barriers and develop effective, safe and acceptable nanotechnologies for agriculture.

  • Acidobacteria are active and abundant members of diverse atmospheric H2-oxidizing communities detected in temperate soils

    Giguere AT, Eichorst SA, Meier D, Herbold CW, Richter A, Greening C, Woebken D
    2020 - ISME J, in press

    Abstract: 

    Significant rates of atmospheric H2 consumption have been observed in temperate soils due to the activity of high-affinity enzymes, such as the group 1h [NiFe]-hydrogenase. We designed broadly inclusive primers targeting the large subunit gene (hhyL) of group 1h [NiFe]-hydrogenases for long-read sequencing to explore its taxonomic distribution across soils. This approach revealed a diverse collection of microorganisms harboring hhyL, including previously unknown groups and taxonomically not assignable sequences. Acidobacterial group 1h [NiFe]-hydrogenases genes were abundant and expressed in temperate soils. To support the participation of acidobacteria in H2 consumption, we studied two representative mesophilic soil acidobacteria, which expressed group 1h [NiFe]-hydrogenases and consumed atmospheric H2 during carbon starvation. This is the first time mesophilic acidobacteria, which are abundant in ubiquitous temperate soils, have been shown to oxidize H2 down to below atmospheric concentrations. As this physiology allows bacteria to survive periods of carbon starvation, it could explain the success of soil acidobacteria. With our long-read sequencing approach of group 1h [NiFe]-hydrogenases genes, we show that the ability to oxidize atmospheric levels of His more widely distributed among soil bacteria than previously recognized and could represent a common mechanism enabling bacteria to persist during periods of carbon deprivation.

  • Cutting out the middle clam: lucinid endosymbiotic bacteria are also associated with seagrass roots worldwide

    Martin BC, Middleton JA, Fraser MW, Marshall IPG, Scholz VV, Hausl B, Schmidt H
    2020 - The ISME journal, in press

    Abstract: 

    Seagrasses and lucinid bivalves inhabit highly reduced sediments with elevated sulphide concentrations. Lucinids house symbiotic bacteria (Ca. Thiodiazotropha) capable of oxidising sediment sulphide, and their presence in sediments has been proposed to promote seagrass growth by decreasing otherwise phytotoxic sulphide levels. However, vast and productive seagrass meadows are present in ecosystems where lucinids do not occur. Hence, we hypothesised that seagrasses themselves host these sulphur-oxidising Ca. Thiodiazotropha that could aid their survival when lucinids are absent. We analysed newly generated and publicly available 16S rRNA gene sequences from seagrass roots and sediments across 14 seagrass species and 10 countries and found that persistent and colonising seagrasses across the world harbour sulphur-oxidising Ca. Thiodiazotropha, regardless of the presence of lucinids. We used fluorescence in situ hybridisation to visually confirm the presence of Ca. Thiodiazotropha on roots of Halophila ovalis, a colonising seagrass species with wide geographical, water depth range, and sedimentary sulphide concentrations. We provide the first evidence that Ca. Thiodiazotropha are commonly present on seagrass roots, providing another mechanism for seagrasses to alleviate sulphide stress globally.

  • Carbonates and cherts as archives of seawater chemistry and habitability on a carbonate platform 3.35 Ga ago: Insights from Sm/Nd dating and trace element analysis from the Strelley Pool Formation, Western Australia

    Sebastian Viehmann. Joachim Reitner, NathalieTepe, Simon V. Hohl, Martin Van Kranendonk, Thilo Hofmann, Christian Koeberl, Patrick Meister
    2020 - Precambrian Research, 344: 105742

    Abstract: 

    Carbonates and cherts in the 3.35 billion-year-old Strelley Pool Formation (Fm.; Australia) host stromatolites that are among the oldest remnants of life on Earth. However, it is still not entirely clear whether these mineral phases are authigenic precipitates, and whether they represent reliable geochemical archives of early Earth environments. Here we present major/trace-element and Nd-isotope data of stromatolitic carbonates, associated crystal-fan carbonates, and cherts in the Strelley Pool Fm. (i) to assess the reliability of these chemical sediments as geochemical archives of the fluids from which they precipitated, (ii) to date the time of formation of carbonate and silica phases, and (iii) to trace the sources of elements prevailing in microbial habitats 3.35 Ga ago.

    Stromatolitic carbonates plot together with the stratigraphically underlying Marble Bar cherts on a Sm-Nd regression line yielding 3253 ± 320 Ma. In contrast, associated crystal-fan carbonates together with altered Marble Bar cherts yield 2718 ± 220 Ma, suggesting that their Sm-Nd isotope system was reset after deposition. Both types of carbonates, as well as white cherts, show shale-normalized rare earth element and yttrium patterns (REYSN; with the exception of redox-sensitive Ce and Eu and heavy REYSN to middle REYSN depletion) that are parallel to those of modern seawater, indicating a predominantly seawater-derived origin. Positive EuSN anomalies (2.1–2.4), combined with heterogeneous ɛNd3.35Ga values between −3.2 and +5.8 within individual alternating stromatolite laminae, further support that the dissolved fraction of seawater on the ancient carbonate platform was variably affected by both continental weathering and high-temperature hydrothermal fluids contributing elements of both young mafic or older felsic rocks. In conclusion, trace element and Nd isotope data presented here match well with the depositional environment, as characterized based on lithological, geochemical, and stratigraphic relationships, on an early continent, showing at least episodic emergence above the sea level, supporting microbial life on a shallow marine platform.

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

      Carolina Reyes, Logan H.Hodgskiss, Oliver Baars, Melina Kerou, Barbara Bayer, Christa Schleper, Stephan M Kraemer
      2020 - Research in microbiology, 171: 134-142

      Abstract: 

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

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

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

      Abstract: 

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

    • Persistence of soil organic carbon caused by functional complexity

      Lehmann J, Hansel CM, Kaiser C, Kleber M, Maher K, Manzoni S, Nunan N, Reichstein M, Schimel J, Torn MS, Wieder WR, Kögl-Knabner I
      2020 - Nature Geoscience, 13: 529-534

      Abstract: 

      Soil organic carbon management has the potential to aid climate change mitigation through drawdown of atmospheric carbon dioxide. To be effective, such management must account for processes influencing carbon storage and re-emission at different space and time scales. Achieving this requires a conceptual advance in our understanding to link carbon dynamics from the scales at which processes occur to the scales at which decisions are made. Here, we propose that soil carbon persistence can be understood through the lens of decomposers as a result of functional complexity derived from the interplay between spatial and temporal variation of molecular diversity and composition. For example, co-location alone can determine whether a molecule is decomposed, with rapid changes in moisture leading to transport of organic matter and constraining the fitness of the microbial community, while greater molecular diversity may increase the metabolic demand of, and thus potentially limit, decomposition. This conceptual shift accounts for emergent behaviour of the microbial community and would enable soil carbon changes to be predicted without invoking recalcitrant carbon forms that have not been observed experimentally. Functional complexity as a driver of soil carbon persistence suggests soil management should be based on constant care rather than one-time action to lock away carbon in soils.

    • The molecular interactions of organic compounds with tire crumb materials differ substantially from those with other microplastics

      Thorsten Hüffer, Maren Wehrhahn, Thilo Hofmann
      2020 - Environmental Science: Processes & Impacts, 22: 121-130

      Abstract: 

      Tire materials are the most commonly found elastomers in the environment and they account for a significant fraction of microplastic pollution. In the discussions on the environmental impact of microplastics tire materials and their sorption properties have been largely overlooked. In this study we used experimental sorption data from six organic probe sorbates sorbing to two tire materials and their major components, styrene butadiene rubber and carbon black, to gain a better understanding of the underlying sorption processes of tire materials. Commonly applied models used to describe non-linear sorption processes were unable to fully explain sorption to tire materials but showed that absorption into the rubber fraction dominated the sorption process. Hydrophobicity was approximated using the hexadecane–water partitioning constant, which correlated very well with the distribution data obtained for styrene rubber, whereas the correlations between hydrophobicity of sorbates and the sorption data to the tire materials were poor. Although hydrophobicity plays an important role in sorption to tire materials, additional interactions must be taken into account. Overall, the processes involved in sorption to tire materials differed significantly from those governing sorption to other microplastics.

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

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

      Abstract: 

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

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

      Yamini Mittal, Pratiksha Srivastav, Naresh Kumar, Asheesh KumarYadav
      2020 - Environmental Technology and Innovation, 19: 100855

      Abstract: 

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

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

    • Regulation of nitrogen fixation from free-living organisms in soil and leaf litter of two tropical forests of the Guiana shield

      Van Langenhove L, Depaepe T, Vicca S, Van den Berge J, Stahl C, Courtois E, Weedon J, Urbina I, Grau O, Asensio D, Peñuelas J, Boeckx P, Richter A, Van Der Straeten D, Janssens IA
      2020 - Plant and Soil, 450: 93-110

      Abstract: 

      Background and aims

      Biological fixation of atmospheric nitrogen (N2) is the main pathway for introducing N into unmanaged ecosystems. While recent estimates suggest that free-living N fixation (FLNF) accounts for the majority of N fixed in mature tropical forests, the controls governing this process are not completely understood. The aim of this study was to quantify FLNF rates and determine its drivers in two tropical pristine forests of French Guiana.

      Methods

      We used the acetylene reduction assay to measure FLNF rates at two sites, in two seasons and along three topographical positions, and used regression analyses to identify which edaphic explanatory variables, including carbon (C), nitrogen (N), phosphorus (P) and molybdenum (Mo) content, pH, water and available N and P, explained most of the variation in FLNF rates.

      Results

      Overall, FLNF rates were lower than measured in tropical systems elsewhere. In soils seasonal variability was small and FLNF rates differed among topographies at only one site. Water, P and pH explained 24% of the variation. In leaf litter, FLNF rates differed seasonally, without site or topographical differences. Water, C, N and P explained 46% of the observed variation. We found no regulatory role of Mo at our sites.

      Conclusions

      Rates of FLNF were low in primary rainforest on poor soils on the Guiana shield. Water was the most important rate-regulating factor and FLNF increased with increasing P, but decreased with increasing N. Our results support the general assumption that N fixation in tropical lowland forests is limited by P availability.

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

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

      Abstract: 

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

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

      Nikolas Hagemann, Hans-Peter Schmidt, Ralf Kaegi, Mark Boehler, Gabriel Sigmund, Andreas Maccagnan, Christa S. McArdell, Thomas D. Bucheli
      2020 - Science of The Total Environment, 730: 138417

      Abstract: 

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

    • Microbial carbon limitation: The need for integrating microorganisms into our understanding of ecosystem carbon cycling

      Soong JL, Fuchslueger L, Marañon‐Jimenez S, Torn MS, Janssens IA, Peñuelas J, Richter A
      2020 - Global Change Biology, 4: 1953-1961

      Abstract: 

      Numerous studies have demonstrated that fertilization with nutrients such as nitrogen, phosphorus, and potassium increases plant productivity in both natural and managed ecosystems, demonstrating that primary productivity is nutrient limited in most terrestrial ecosystems. In contrast, it has been demonstrated that heterotrophic microbial communities in soil are primarily limited by organic carbon or energy. While this concept of contrasting limitations, that is, microbial carbon and plant nutrient limitation, is based on strong evidence that we review in this paper, it is often ignored in discussions of ecosystem response to global environment changes. The plant‐centric perspective has equated plant nutrient limitations with those of whole ecosystems, thereby ignoring the important role of the heterotrophs responsible for soil decomposition in driving ecosystem carbon storage. To truly integrate carbon and nutrient cycles in ecosystem science, we must account for the fact that while plant productivity may be nutrient limited, the secondary productivity by heterotrophic communities is inherently carbon limited. Ecosystem carbon cycling integrates the independent physiological responses of its individual components, as well as tightly coupled exchanges between autotrophs and heterotrophs. To the extent that the interacting autotrophic and heterotrophic processes are controlled by organisms that are limited by nutrient versus carbon accessibility, respectively, we propose that ecosystems by definition cannot be ‘limited’ by nutrients or carbon alone. Here, we outline how models aimed at predicting non‐steady state ecosystem responses over time can benefit from dissecting ecosystems into the organismal components and their inherent limitations to better represent plant–microbe interactions in coupled carbon and nutrient models.

    • Co-infection of chicken layers with Histomonas meleagridis and avian pathogenic Escherichia coli is associated with dysbiosis, cecal colonization and translocation of the bacteria from the gut lumen

      Abdelhamid MK, Quijada NM, Dzieciol M, Hatfaludi T, Bilic I, Selberherr E, Liebhart D, Hess C, Hess M, Paudel S
      2020 - Front Microbiol, 11: 586437

      Abstract: 

      Histomonosis in chickens often appears together with colibacillosis in the field. Thus, we have experimentally investigated consequences of the co-infection of birds with Histomonas meleagridisand avian pathogenic Escherichia coli (APEC) on the pathology, host microbiota and bacterial translocation from the gut. Commercial chicken layers were infected via oral and cloacal routes with lux-tagged APEC with or without H. meleagridis whereas negative controls were left uninfected. Except one bird, which died due to colibacillosis, no clinical signs were recorded in birds infected with bioluminescence lux gene tagged E. coli. In co-infected birds, depression and ruffled feathers were observed in 4 birds and average body weight gain significantly decreased. Typhlitis caused by H. meleagridis was present only in co-infected birds, which also had pronounced microscopic lesions in systemic organs such as liver, heart and spleen. The 16S rRNA gene amplicon sequencing showed that in co-infected birds, corresponding to the severity of cecal lesions, microbial species richness and diversity in caeca greatly decreased and the abundance of the Escherichia group, Helicobacter and Bacteroides was relatively higher with a reduction of commensals. Most of the shared Amplicon Sequencing Variants between cecum and blood in co-infected birds belonged to Pseudomonas, Staphylococcus, and members of Enterobacteriaceae while those assigned as Lactobacillus and members of Ruminococcaceae and Lachnospiraceae were found mainly in negative controls. In infected birds, E. coli in the cecal lumen penetrated into deeper layers, a phenomenon noticed with higher incidence in the dead and co-infected birds. Furthermore, numbers of lux-tagged E. coli in caeca were significantly higher at every sampling date in co-infected birds. Altogether, infection of layers with H. meleagridis and E. coli resulted in more severe pathological changes, dramatic shift in the cecal mucosa-associated microbiota, higher tissue colonization of pathogenic bacteria such as avian pathogenic E. coli in the gut and increased penetration of E. coli from the cecal lumen toward peritoneum. This study provides novel insights into the parasite-bacteria interaction in vivohighlighting the role of H. meleagridis to support E. coli in the pathogenesis of colibacillosis in chickens.

    • Genomic and kinetic analysis of novel Nitrospinae enriched by cell sorting

      Mueller AJ, Jung MY, Strachan CR, Herbold CW, Kirkegaard RH, Wagner M, Daims H
      2020 - ISME J., in press

      Abstract: 

      Chemolithoautotrophic nitrite-oxidizing bacteria (NOB) are key players in global nitrogen and carbon cycling. Members of the phylum Nitrospinae are the most abundant, known NOB in the oceans. To date, only two closely affiliated Nitrospinae species have been isolated, which are only distantly related to the environmentally abundant uncultured Nitrospinae clades. Here, we applied live cell sorting, activity screening, and subcultivation on marine nitrite-oxidizing enrichments to obtain novel marine Nitrospinae. Two binary cultures were obtained, each containing one Nitrospinae strain and one alphaproteobacterial heterotroph. The Nitrospinae strains represent two new genera, and one strain is more closely related to environmentally abundant Nitrospinae than previously cultured NOB. With an apparent half-saturation constant of 8.7±2.5 µM, this strain has the highest affinity for nitrite among characterized marine NOB, while the other strain (16.2±1.6 µM) and Nitrospina gracilis (20.1±2.1 µM) displayed slightly lower nitrite affinities. The new strains and N. gracilis share core metabolic pathways for nitrite oxidation and CO2 fixation but differ remarkably in their genomic repertoires of terminal oxidases, use of organic N sources, alternative energy metabolisms, osmotic stress and phage defense. The new strains, tentatively named “Candidatus Nitrohelix vancouverensis” and “Candidatus Nitronauta litoralis”, shed light on the niche differentiation and potential ecological roles of Nitrospinae.

    • Recovery of aboveground biomass, species richness and composition in tropical secondary forests in SW Costa Rica

      Oberleitner F, Egger C, Oberdorfer S, Dullinger S, Wanek W, Hietz P
      2020 - Forest Ecology and Management, 479: Article 118580

      Abstract: 

      Tropical secondary forests comprise about half of the world’s tropical forests and are important as carbon sinks and to conserve biodiversity. Their rate of recovery varies widely; however, particularly older secondary forests are difficult to date so that the recovery rate is uncertain. As a consequence, factors affecting recovery are difficult to analyse. We used aerial surveys going back to 1968 to date 12 secondary forests in the wet tropics of SW Costa Rica and evaluated the recovery of aboveground biomass, tree species richness and tree species composition in relation to nearby old-growth forests and previous land use. To confirm the validity of the space-for-time substitution, the plots were re-censused after four years. We found fast rates of aboveground biomass accumulation, especially in the first years of succession. After 20 years AGB had reached c. 164 Mg/ha equivalent to 52% of the biomass in old-growth forests in the region. Species richness increased at a slower pace and had reached c. 31% of old-growth forests after 20 years. Recovery rates differed substantially among forests, with biomass at least initially recovering faster in forests after clearcuts whereas species numbers increased faster in forests recovering from pastures. Biomass recovery was positively related to the forest cover in the vicinity and negatively to species richness, whereas species richness was related to soil parameters. The change during the four years between the censuses is broadly in line with the initial chronosequence. While the recovery of tropical secondary forests has been studied in many places, our study shows that various environmental parameters affect the speed of recovery, which is important to include in efforts to manage and restore tropical landscapes.

    • A Large-Scale 3D Study on Transport of Humic Acid-Coated Goethite Nanoparticles for Aquifer Remediation

      Milica Velimirovic, Carlo Bianco, Natalia Ferrantello, Tiziana Tosco, Alessandro Casasso, Rajandrea Sethi, Doris Schmid, Stephan Wagner, Kumiko Miyajima, Norbert Klaas, Rainer U. Meckenstock, Frank von der Kammer, Bert Engelen, Thilo Hofmann
      2020 - Water, 12: 1207

      Abstract: 

      Humic acid-coated goethite nanoparticles (HA-GoeNPs) have been recently proposed as an effective reagent for the in situ nanoremediation of contaminated aquifers. However, the effective dosage of these particles has been studied only at laboratory scale to date. This study investigates the possibility of using HA-GoeNPs in remediation of real field sites by mimicking the injection and transport of HA-GoeNPs under realistic conditions. To this purpose, a three-dimensional (3D) transport experiment was conducted in a large-scale container representing a heterogeneous unconfined aquifer. Monitoring data, including particle size distribution, total iron (Fetot) content and turbidity measurements, revealed a good subsurface mobility of the HA-GoeNP suspension, especially within the higher permeability zones. A radius of influence of 2 m was achieved, proving that HA-GoeNPs delivery is feasible for aquifer restoration. A flow and transport model of the container was built using the numerical code Micro and Nanoparticle transport Model in 3D geometries (MNM3D) to predict the particle behavior during the experiment. The agreement between modeling and experimental results validated the capability of the model to reproduce the HA-GoeNP transport in a 3D heterogeneous aquifer. Such result confirms MNM3D as a valuable tool to support the design of field-scale applications of goethite-based nanoremediation.

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

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

      Abstract: 

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

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

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

    • Quantification and Characterization of Nanoparticulate Zinc in an Urban Watershed

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

      Abstract: 

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

    • Strategies for determining heteroaggregation attachment efficiencies of engineered nanoparticles in aquatic environments

      Antonia Praetorius, Elena Badetti, Andrea Brunelli, Arnaud Clavier, Julián Alberto Gallego-Urrea, Andreas Gondikas, Gaul T, Thilo Hofmann, Aiga Mackevica, Antonio Marcomini, Willie Peijnenburg, Joris T. K. Quik, Marianne Seijo, Serge Stoll, Nathalie Tepe, Helene Walch, Frank von der Kammer
      2020 - Environmental Science: Nano, 7: 351–367

      Abstract: 

      Heteroaggregation of engineered nanoparticles (ENPs) with suspended particulate matter (SPM) ubiquitous in natural waters often dominates the transport behaviour and overall fate of ENPs in aquatic environments. In order to provide meaningful exposure predictions and support risk assessment for ENPs, environmental fate and transport models require quantitative information about this process, typically in the form of the so-called attachment efficiency for heteroaggregation αhetero. The inherent complexity of heteroaggregation—encompassing at least two different particle populations, various aggregation pathways and several possible attachment efficiencies (α values)—makes its theoretical and experimental determination challenging. In this frontier review we assess the current state of knowledge on heteroaggregation of ENPs with a focus on natural surface waters. A theoretical analysis presents relevant equations, outlines the possible aggregation pathways and highlights different types of α. In a second part, experimental approaches to study heteroaggregation and derive α values are reviewed and three possible strategies are identified: i) monitoring changes in size, ii) monitoring number or mass distribution and iii) studying indirect effects, such as sedimentation. It becomes apparent that the complexity of heteroaggregation creates various challenges and no single best method for its assessment has been developed yet. Nevertheless, many promising strategies have been identified and meaningful data can be derived from carefully designed experiments when accounting for the different concurrent aggregation pathways and clearly stating the type of α reported. For future method development a closer connection between experiments and models is encouraged.

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

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

      Abstract: 

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

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

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

      Abstract: 

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

    • Quantifying microbial growth and carbon use efficiency in dry soil environments via 18O water vapor equilibration

      Canarini A, Wanek W, Watzka M, Sandén T, Spiegel H, Šantrůček J, Schnecker J
      2020 - Global Change Biology, 9: 5333-5341

      Abstract: 

      Soil microbial physiology controls large fluxes of C to the atmosphere, thus, improving our ability to accurately quantify microbial physiology in soil is essential. However, current methods to determine microbial C metabolism require liquid water addition, which makes it practically impossible to measure microbial physiology in dry soil samples without stimulating microbial growth and respiration (namely, the “Birch effect”). We developed a new method based on in vivo 18O‐water vapor equilibration to minimize soil rewetting effects. This method allows the isotopic labeling of soil water without direct liquid water addition. This was compared to the main current method (direct 18O‐liquid water addition) in moist and air‐dry soils. We determined the time kinetics and calculated the average 18O enrichment of soil water over incubation time, which is necessary to calculate microbial growth from 18O incorporation in genomic DNA. We tested isotopic equilibration patterns in three natural and six artificially constructed soils covering a wide range of soil texture and soil organic matter content. We then measured microbial growth, respiration and carbon use efficiency (CUE) in three natural soils (either air‐dry or moist). The proposed 18O‐vapor equilibration method provided similar results as the current method of liquid 18O‐water addition when used for moist soils. However, when applied to air‐dry soils the liquid 18O‐water addition method overestimated growth by up to 250%, respiration by up to 500%, and underestimated CUE by up to 40%. We finally describe the new insights into biogeochemical cycling of C that the new method can help uncover, and we consider a range of questions regarding microbial physiology and its response to global change that can now be addressed.

    • Transparent soil microcosms for live-cell imaging and non-destructive stable isotope probing of soil microorganisms

      Sharma K, Palatinszky M, Nikolov G, Berry D, Shank EA
      2020 - Elife, 9: e56275

      Abstract: 

      Microscale processes are critically important to soil ecology and biogeochemistry yet are difficult to study due to soil’s opacity and complexity. To advance the study of soil processes, we constructed transparent soil microcosms that enable the visualization of microbes via fluorescence microscopy and the non-destructive measurement of microbial activity and carbon uptake in situ via Raman microspectroscopy. We assessed the polymer Nafion and the crystal cryolite as optically transparent soil substrates. We demonstrated that both substrates enable the growth, maintenance, and visualization of microbial cells in three dimensions over time, and are compatible with stable isotope probing using Raman. We applied this system to ascertain that after a dry-down/rewetting cycle, bacteria on and near dead fungal hyphae were more metabolically active than those far from hyphae. These data underscore the impact fungi have facilitating bacterial survival in fluctuating conditions and how these microcosms can yield insights into microscale microbial activities.

    • scikit-hubness: Hubness Reduction and Approximate Neighbor Search

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

      Abstract: 

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

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

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

      Stuart Cairns, Ian Robertson, Gabriel Sigmund, Alayne Street-Perrott
      2020 - Environmental Science and Pollution Research, 27: 21702-21715

      Abstract: 

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

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

      Milica Velimirovic, Stephan Wagner, Fazel Abdolahpur Monikh, Toni Uusimäki, Ralf Kaegi, Thilo Hofmann, Frank von der Kammer
      2020 - Talanta, 215: 120921

      Abstract: 

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

    • Key principles and operational practices for improved nanotechnology environmental exposure assessment

      Claus Svendsen, Lee A. Walker, Marianne Matzke, Elma Lahive, Samuel Harrison, Alison Crossley, Barry Park, Stephen Lofts, Iseult Lynch, Socorro Vázquez-Campos, Ralf Kaegi, Alexander Gogos, Christof Asbach, Geert Cornelis, Frank von der Kammer, Nico W. van den Brink, Claire Mays, David J. Spurgeon
      2020 - Nature Nanotechnology, 15: 731–742

      Abstract: 

      Nanotechnology is identified as a key enabling technology due to its potential to contribute to economic growth and societal well-being across industrial sectors. Sustainable nanotechnology requires a scientifically based and proportionate risk governance structure to support innovation, including a robust framework for environmental risk assessment (ERA) that ideally builds on methods established for conventional chemicals to ensure alignment and avoid duplication. Exposure assessment developed as a tiered approach is equally beneficial to nano-specific ERA as for other classes of chemicals. Here we present the developing knowledge, practical considerations and key principles need to support exposure assessment for engineered nanomaterials for regulatory and research applications.

    • Anthropogenic gadolinium in freshwater and drinking water systems

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

      Abstract: 

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

    • Environmental and intestinal phylum Firmicutes bacteria metabolize the plant sugar sulfoquinovose via a 6-deoxy-6-sulfofructose transaldolase pathway

      Frommeyer B, Fiedler AW, Oehler SR, Hanson BT, Loy A, Franchini P, Spiteller D, Schleheck D
      2020 - iScience, In press

      Abstract: 

      Bacterial degradation of the sugar sulfoquinovose (SQ, 6-deoxy-6-sulfoglucose) produced by plants, algae and cyanobacteria, is an important component of the biogeochemical carbon and sulfur cycles. Here, we reveal a third biochemical pathway for primary SQ degradation in an aerobic Bacillus aryabhattaistrain. An isomerase converts SQ to 6-deoxy-6-sulfofructose (SF). A novel transaldolase enzyme cleaves the SF to 3-sulfolactaldehyde (SLA), while the non-sulfonated C3-(glycerone)-moiety is transferred to an acceptor molecule, glyceraldehyde phosphate (GAP), yielding fructose-6-phosphate (F6P). Intestinal anaerobic bacteria such as Enterococcus gilvus, Clostridium symbiosum and Eubacterium rectale strains also express transaldolase-pathway gene clusters during fermentative growth with SQ. The now three known biochemical strategies for SQ catabolism reflect adaptations to the aerobic or anaerobic life-style of the different bacteria. The occurrence of these pathways in intestinal (family) Enterobacteriaceae and (phylum) Firmicutes strains further highlights a potential importance of metabolism of green-diet SQ by gut microbial communities to, ultimately, hydrogen sulfide.

    • Climatic and edaphic controls over tropical forest diversity and vegetation carbon storage

      Hofhansl F, Chacón-Madrigal E, Fuchslueger L, Jenking D, Morera-Beita A, Plutzar C, Silla F, Andersen KM, Buchs DM, Dullinger S, Fiedler K, Franklin O, Hietz P, Huber W, Quesada CA, Rammig A, Schrodt F, Vincent AG, Weissenhofer A, Wanek W
      2020 - Scientific Reports, 10: Article 5066

      Abstract: 

      Tropical rainforests harbor exceptionally high biodiversity and store large amounts of carbon in vegetation biomass. However, regional variation in plant species richness and vegetation carbon stock can be substantial, and may be related to the heterogeneity of topoedaphic properties. Therefore, aboveground vegetation carbon storage typically differs between geographic forest regions in association with the locally dominant plant functional group. A better understanding of the underlying factors controlling tropical forest diversity and vegetation carbon storage could be critical for predicting tropical carbon sink strength in response to projected climate change. Based on regionally replicated 1-ha forest inventory plots established in a region of high geomorphological heterogeneity we investigated how climatic and edaphic factors affect tropical forest diversity and vegetation carbon storage. Plant species richness (of all living stems >10 cm in diameter) ranged from 69 to 127 ha−1 and vegetation carbon storage ranged from 114 to 200 t ha−1. While plant species richness was controlled by climate and soil water availability, vegetation carbon storage was strongly related to wood density and soil phosphorus availability. Results suggest that local heterogeneity in resource availability and plant functional composition should be considered to improve projections of tropical forest ecosystem functioning under future scenarios.

    • Core–Shell Fe/FeS Nanoparticles with Controlled Shell Thickness for Enhanced Trichloroethylene Removal

      Miroslav Brumovský, Jan Filip, Ondřej Malina, Jana Oborná, Ondra Sracek, Thomas G. Reichenauer, Pavlína Andrýsková, Radek Zbořil
      2020 - ACS Applied Materials & Interfaces, 12: 35424–35434

      Abstract: 

      Zero-valent iron nanoparticles (nZVI) treated by reduced sulfur compounds (i.e., sulfidated nZVI, S-nZVI) have attracted increased attention as promising materials for environmental remediation. While the preparation of S-nZVI and its reactions with various groundwater contaminants such as trichloroethylene (TCE) were already a subject of several studies, nanoparticle synthesis procedures investigated so far were suited mainly for laboratory-scale preparation with only a limited possibility of easy and cost-effective large-scale production and FeS shell property control. This study presents a novel approach for synthesizing S-nZVI using commercially available nZVI particles that are treated with sodium sulfide in a concentrated slurry. This leads to S-nZVI particles that do not contain hazardous boron residues and can be easily prepared off-site. The resulting S-nZVI exhibits a core–shell structure where zero-valent iron is the dominant phase in the core, while the shell contains mostly amorphous iron sulfides. The average FeS shell thickness can be controlled by the applied sulfide concentration. Up to a 12-fold increase in the TCE removal and a 7-fold increase in the electron efficiency were observed upon amending nZVI with sulfide. Although the FeS shell thickness correlated with surface-area-normalized TCE removal rates, sulfidation negatively impacted the particle surface area, resulting in an optimal FeS shell thickness of approximately 7.3 nm. This corresponded to a particle S/Fe mass ratio of 0.0195. At all sulfide doses, the TCE degradation products were only fully dechlorinated hydrocarbons. Moreover, a nearly 100% chlorine balance was found at the end of the experiments, further confirming complete TCE degradation and the absence of chlorinated transformation products. The newly synthesized S-nZVI particles thus represent a promising remedial agent applicable at sites contaminated with TCE.

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

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

      Abstract: 

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

    • The importance of aromaticity to describe the interactions of organic matter with carbonaceous materials depends on molecular weight and sorbent geometry

      Stephanie Castan, Gabriel Sigmund, Thorsten Hüffer, Nathalie Tepe, Frank von der Kammer, Benny Chefetz, Thilo Hofmann
      2020 - Environmental Science.: Processes & Impacts, 22: 1888-1897

      Abstract: 

      Dissolved organic matter (DOM) is ubiquitous in aquatic environments where it interacts with a variety of particles including carbonaceous materials (CMs). The complexity of both DOM and the CMs makes DOM–CM interactions difficult to predict. In this study we have identified the preferential sorption of specific DOM fractions as being dependent on their aromaticity and molecular weight, as well as on the surface properties of the CMs. This was achieved by conducting sorption batch experiments with three types of DOM (humic acid, Suwannee River natural organic matter, and a compost extract) and three types of CMs (graphite, carbon nanotubes, and biochar) with different geometries and surface complexities. The non-adsorbed DOM fraction was analyzed by size exclusion chromatography and preferentially sorbed molecular weight fractions were analyzed by UV/vis and fluorescence spectroscopy. All three sorbent types were found to preferentially sorb aromatic DOM fractions, but DOM fractionation depended on the particular combination of sorbent and sorbate characteristics. Single-walled carbon nanotubes only sorbed the smaller molecular weight fractions (<1 kDa). The sorption of smaller DOM fractions was not accompanied by a preference for less aromatic compounds, contrary to what was suggested in previous studies. While graphite preferentially sorbed the most aromatic DOM fraction (1–3 kDa), the structural heterogeneity of biochar resulted in reduced selectivity, sorbing all DOM > 1 kDa. The results explain the lack of correlation found in previous studies between the amount of aromatic carbon in a bulk DOM and its sorption coefficient. DOM sorption by CMs was generally controlled by DOM aromaticity but complex sorbent surfaces with high porosity, curvatures and functional groups strongly reduced the importance of aromaticity.

    • Carbon loss from northern circumpolar permafrost soils amplified by rhizosphere priming

      Keuper F, Wild B, Kummu M, Beer C, Blume-Werry G, Fontaine S, Gavazov K, Gentsch N, Guggenberger G, Hugelius G, Jalava M, Koven C, Krab EJ, Kuhry P, Monteux S, Richter A, Shahzad T, Weedon J, Dorrepaal E
      2020 - Nature Geoscience, 13: 560-565

      Abstract: 

      As global temperatures continue to rise, a key uncertainty of climate projections is the microbial decomposition of vast organic carbon stocks in thawing permafrost soils. Decomposition rates can accelerate up to fourfold in the presence of plant roots, and this mechanism—termed the rhizosphere priming effect—may be especially relevant to thawing permafrost soils as rising temperatures also stimulate plant productivity in the Arctic. However, priming is currently not explicitly included in any model projections of future carbon losses from the permafrost area. Here, we combine high-resolution spatial and depth-resolved datasets of key plant and permafrost properties with empirical relationships of priming effects from living plants on microbial respiration. We show that rhizosphere priming amplifies overall soil respiration in permafrost-affected ecosystems by ~12%, which translates to a priming-induced absolute loss of ~40 Pg soil carbon from the northern permafrost area by 2100. Our findings highlight the need to include fine-scale ecological interactions in order to accurately predict large-scale greenhouse gas emissions, and suggest even tighter restrictions on the estimated 200 Pg anthropogenic carbon emission budget to keep global warming below 1.5 °C.

    • Abiotic factors influence patterns of bacterial diversity and community composition in the Dry Valleys of Antarctica

      Bottos EM, Laughlin DC, Herbold CW, Lee CK, McDonald IR, Cary SC
      2020 - FEMS microbiology ecology, 96: in press

      Abstract: 

      The Dry Valleys of Antarctica are a unique ecosystem of simple trophic structure, where the abiotic factors that influence soil bacterial communities can be resolved in the absence of extensive biotic interactions. This study evaluated the degree to which aspects of topographic, physicochemical and spatial variation explain patterns of bacterial richness and community composition in 471 soil samples collected across a 220 square kilometer landscape in Southern Victoria Land. Richness was most strongly influenced by physicochemical soil properties, particularly soil conductivity, though significant trends with several topographic and spatial variables were also observed. Structural equation modeling (SEM) supported a final model in which variation in community composition was best explained by physicochemical variables, particularly soil water content, and where the effects of topographic variation were largely mediated through their influence on physicochemical variables. Community dissimilarity increased with distance between samples, and though most of this variation was explained by topographic and physicochemical variation, a small but significant relationship remained after controlling for this environmental variation. As the largest survey of terrestrial bacterial communities of Antarctica completed to date, this work provides fundamental knowledge of the Dry Valleys ecosystem, and has implications globally for understanding environmental factors that influence bacterial distributions.

    • C:N:P stoichiometry regulates soil organic carbon mineralization and concomitant shifts in microbial community composition in paddy soil

      Wei X, Zhu Z, Liu Y, Luo Y, Deng Y, Xu X, Liu S, Richter A, Shibistova O, Guggenberger G, Wu J, Ge T
      2020 - Biology and Fertility of Soils, in press

      Abstract: 

      Stoichiometric control of input substrate (glucose) and native soil organic C (SOC) mineralization was assessed by performing a manipulation experiment based on N or P fertilization in paddy soil. Glucose mineralization increased with nutrient addition up to 11.6% with combined N and P application compared with that without nutrient addition. During 100 days of incubation, approximately 4.5% of SOC was mineralized and was stimulated by glucose addition. Glucose and SOC mineralization increased exponentially with dissolved organic C (DOC):NH4+-N, DOC:Olsen P, and microbial biomass (MB)C:MBN ratios. The relative abundances of Clostridia and β-Proteobacteria (r-strategists) were increased with combined C and NP application at the beginning of the experiment, while the relative abundances of Acidobacteria (K-strategists) were enhanced with the exhaustion of available resource at the end of incubation. The bacteria abundance and diversity were negatively related to the DOC:NH4+-N and DOC:Olsen P, which had direct positive effects (+ 0.63) on SOC mineralization. Combined glucose and NP application decreased the network density of the bacterial community. Moreover, P addition significantly decreased the negative associations among bacterial taxa, which suggested that microbial competition for nutrients was alleviated. The relative abundances of keystone species showed significant positive correlations with SOC mineralization in the soils without P application, revealing that microbes increased their activity for mining of limited nutrients from soil organic matter. Hence, bacteria shifted their community composition and their interactions to acquire necessary elements by increasing SOC mineralization to maintain the microbial biomass C:N:P stoichiometric balance in response to changes in resource stoichiometry.

    • Coevolving plasmids drive gene flow and genome plasticity in host-associated intracellular bacteria

      Köstlbacher S, Collingro A, Halter T, Domman D, Horn M
      2020 - Curr. Biol., in press

      Abstract: 

      Plasmids are important in microbial evolution and adaptation to new environments. Yet, carrying a plasmid can be costly, and long-term association of plasmids with their hosts is poorly understood. Here, we provide evidence that the Chlamydiae, a phylum of strictly host-associated intracellular bacteria, have coevolved with their plasmids since their last common ancestor. Current chlamydial plasmids are amalgamations of at least one ancestral plasmid and a bacteriophage. We show that the majority of plasmid genes are also found on chromosomes of extant chlamydiae. The most conserved plasmid gene families are predominantly vertically inherited, while accessory plasmid gene families show significantly increased mobility. We reconstructed the evolutionary history of plasmid gene content of an entire bacterial phylum over a period of around one billion years. Frequent horizontal gene transfer and chromosomal integration events illustrate the pronounced impact of coevolution with these extrachromosomal elements on bacterial genome dynamics in host-dependent microbes.

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

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

      Abstract: 

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

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

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

      Abstract: 

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

    • Anaerobic bacterial degradation of protein and lipid macromolecules in subarctic marine sediment

      Pelikan C, Wasmund K, Glombitza C, Hausmann H, Herbold CW, Flieder M, Loy A
      2020 - ISME J, In press

      Abstract: 

      Microorganisms in marine sediments play major roles in marine biogeochemical cycles by mineralizing substantial quantities of organic matter from decaying cells. Proteins and lipids are abundant components of necromass, yet the taxonomic identities of microorganisms that actively degrade them remain poorly resolved. Here, we revealed identities, trophic interactions and genomic features of bacteria that degraded 13C-labelled proteins and lipids in cold anoxic microcosms containing sulfidic subarctic marine sediment. Supplemented proteins and lipids were rapidly fermented to various volatile fatty acids within five days. DNA-stable isotope probing (SIP) suggested Psychrilyobacter atlanticus was an important primary degrader of proteins, and Psychromonas members were important primary degraders of both proteins and lipids. Closely related Psychromonas populations, as represented by distinct 16S rRNA gene variants, differentially utilized either proteins or lipids. DNA-SIP also showed 13C-labeling of various Deltaproteobacteria within ten days, indicating trophic transfer of carbon to putative sulfate-reducers. Metagenome-assembled genomes revealed the primary hydrolyzers encoded secreted peptidases or lipases, and enzymes for catabolism of protein or lipid degradation products. Psychromonas species are prevalent in diverse marine sediments, suggesting they are important players in organic carbon processing in situ. Together, this study provides new insights into the identities, functions and genomes of bacteria that actively degrade abundant necromass macromolecules in the seafloor.

    • Redox-informed models of global biogeochemical cycles.

      Zakem EJ, Polz MF, Follows MJ
      2020 - Nat Commun, 1: 5680

      Abstract: 

      Microbial activity mediates the fluxes of greenhouse gases. However, in the global models of the marine and terrestrial biospheres used for climate change projections, typically only photosynthetic microbial activity is resolved mechanistically. To move forward, we argue that global biogeochemical models need a theoretically grounded framework with which to constrain parameterizations of diverse microbial metabolisms. Here, we explain how the key redox chemistry underlying metabolisms provides a path towards this goal. Using this first-principles approach, the presence or absence of metabolic functional types emerges dynamically from ecological interactions, expanding model applicability to unobserved environments."Nothing is less real than realism. It is only by selection, by elimination, by emphasis, that we get at the real meaning of things." -Georgia O'Keefe.

    • The genetic law of the minimum.

      Polz MF, Cordero OX
      2020 - Science, 6517: 655-656
    • Proposal to reclassify the proteobacterial classes Deltaproteobacteria and Oligoflexia, and the phylum Thermodesulfobacteria into four phyla reflecting major functional capabilities

      Waite DW, Chuvochina M, Pelikan C, Parks DH, Yilmaz P, Wagner M, Loy A, Naganuma T, Nakai R, Whitman WB, Hahn MW, Kuever J, Hugenholtz P
      2020 - Int J Syst Evol Microbiol, in press

      Abstract: 

      The class Deltaproteobacteria comprises an ecologically and metabolically diverse group of bacteria best known for dissimilatory sulphate reduction and predatory behaviour. Although this lineage is the fourth described class of the phylum Proteobacteria, it rarely affiliates with other proteobacterial classes and is frequently not recovered as a monophyletic unit in phylogenetic analyses. Indeed, one branch of the class Deltaproteobacteria encompassing Bdellovibrio-like predators was recently reclas- sified into a separate proteobacterial class, the Oligoflexia. Here we systematically explore the phylogeny of taxa currently assigned to these classes using 120 conserved single-copy marker genes as well as rRNA genes. The overwhelming majority of markers reject the inclusion of the classes Deltaproteobacteria and Oligoflexia in the phylum Proteobacteria. Instead, the great majority of currently recognized members of the class Deltaproteobacteria are better classified into four novel phylum-level lineages. We propose the names Desulfobacterota phyl. nov. and Myxococcota phyl. nov. for two of these phyla, based on the oldest validly published names in each lineage, and retain the placeholder name SAR324 for the third phylum pending formal description of type material. Members of the class Oligoflexia represent a separate phylum for which we propose the name Bdellovibrionota phyl. nov. based on priority in the literature and general recognition of the genus Bdellovibrio. Desulfobacterota phyl. nov. includes the taxa previously classified in the phylum Thermodesulfobacteria, and these reclassifications imply that the ability of sulphate reduction was vertically inherited in the phylum Thermodesulfobacteria rather than laterally acquired as previously inferred. Our analysis also indicates the independent acquisition of predatory behaviour in the phyla Myxococcota and Bdellovibrionota, which is consistent with their distinct modes of action. This work represents a stable reclassification of one of the most taxonomically challenging areas of the bacterial tree and provides a robust framework for future ecological and systematic studies.

    • Rational design of a microbial consortium of mucosal sugar utilizers reduces Clostridiodes difficile colonization.

      Pereira FC, Wasmund K, Cobankovic I, Jehmlich N, Herbold CW, Lee KS, Sziranyi B, Vesely C, Decker T, Stocker R, Warth B, von Bergen M, Wagner M, Berry D
      2020 - Nat Commun, 1: 5104

      Abstract: 

      Many intestinal pathogens, including Clostridioides difficile, use mucus-derived sugars as crucial nutrients in the gut. Commensals that compete with pathogens for such nutrients are therefore ecological gatekeepers in healthy guts, and are attractive candidates for therapeutic interventions. Nevertheless, there is a poor understanding of which commensals use mucin-derived sugars in situ as well as their potential to impede pathogen colonization. Here, we identify mouse gut commensals that utilize mucus-derived monosaccharides within complex communities using single-cell stable isotope probing, Raman-activated cell sorting and mini-metagenomics. Sequencing of cell-sorted fractions reveals members of the underexplored family Muribaculaceae as major mucin monosaccharide foragers, followed by members of Lachnospiraceae, Rikenellaceae, and Bacteroidaceae families. Using this information, we assembled a five-member consortium of sialic acid and N-acetylglucosamine utilizers that impedes C. difficile's access to these mucosal sugars and impairs pathogen colonization in antibiotic-treated mice. Our findings underscore the value of targeted approaches to identify organisms utilizing key nutrients and to rationally design effective probiotic mixtures.

    • A refined set of rRNA-targeted oligonucleotide probes for in situ detection and quantification of ammonia-oxidizing bacteria

      Lukumbuzya M, Kristensen JM, Kitzinger K, Pommerening-Roser A, Nielsen PH, Wagner M, Daims H, Pjevac P
      2020 - Water Res., 186: 116372
      ammonia oxidizing bacteria FISH picture

      Abstract: 

      Ammonia-oxidizing bacteria (AOB) of the betaproteobacterial genera Nitrosomonas and Nitrosospira are key nitrifying microorganisms in many natural and engineered ecosystems. Since many AOB remain uncultured, fluorescence in situ hybridization (FISH) with rRNA-targeted oligonucleotide probes has been one of the most widely used approaches to study the community composition, abundance, and other features of AOB directly in environmental samples. However, the established and widely used AOB-specific 16S rRNA-targeted FISH probes were designed up to two decades ago, based on much smaller rRNA gene sequence datasets than available today. Several of these probes cover their target AOB lineages incompletely and suffer from a weak target specificity, which causes cross-hybridization of probes that should detect different AOB lineages. Here, a set of new highly specific 16S rRNA-targeted oligonucleotide probes was developed and experimentally evaluated that complements the existing probes and enables the specific detection and differentiation of the known, major phylogenetic clusters of betaproteobacterial AOB. The new probes were successfully applied to visualize and quantify AOB in activated sludge and biofilm samples from seven pilot- and full-scale wastewater treatment systems. Based on its improved target group coverage and specificity, the refined probe set will facilitate future in situ analyses of AOB.

    • Flow-through stable isotope probing (Flow-SIP) minimizes cross-feeding in complex microbial communities.

      Mooshammer M, Kitzinger K, Schintlmeister A, Ahmerkamp S, Nielsen JL, Nielsen PH, Wagner M
      2020 - ISME J, in press

      Abstract: 

      Stable isotope probing (SIP) is a key tool for identifying the microorganisms catalyzing the turnover of specific substrates in the environment and to quantify their relative contributions to biogeochemical processes. However, SIP-based studies are subject to the uncertainties posed by cross-feeding, where microorganisms release isotopically labeled products, which are then used by other microorganisms, instead of incorporating the added tracer directly. Here, we introduce a SIP approach that has the potential to strongly reduce cross-feeding in complex microbial communities. In this approach, the microbial cells are exposed on a membrane filter to a continuous flow of medium containing isotopically labeled substrate. Thereby, metabolites and degradation products are constantly removed, preventing consumption of these secondary substrates. A nanoSIMS-based proof-of-concept experiment using nitrifiers in activated sludge and C-bicarbonate as an activity tracer showed that Flow-SIP significantly reduces cross-feeding and thus allows distinguishing primary consumers from other members of microbial food webs.

    • Woeseiales transcriptional response to shallow burial in Arctic fjord surface sediment

      Buongiorno J, Sipes K, Wasmund K, Loy A, Lloyd K
      2020 - PloS one, 15: e0234839

      Abstract: 

      Distinct lineages of Gammaproteobacteria clade Woeseiales are globally distributed in marine sediments, based on metagenomic and 16S rRNA gene analysis. Yet little is known about why they are dominant or their ecological role in Arctic fjord sediments, where glacial retreat is rapidly imposing change. This study combined 16S rRNA gene analysis, metagenome-assembled genomes (MAGs), and genome-resolved metatranscriptomics uncovered the in situ abundance and transcriptional activity of Woeseiales with burial in four shallow sediment sites of Kongsfjorden and Van Keulenfjorden of Svalbard (79°N). We present five novel Woeseiales MAGs and show transcriptional evidence for metabolic plasticity during burial, including sulfur oxidation with reverse dissimilatory sulfite reductase (dsrAB) down to 4 cm depth and nitrite reduction down to 6 cm depth. A single stress protein, spore protein SP21 (hspA), had a tenfold higher mRNA abundance than any other transcript, and was a hundredfold higher on average than other transcripts. At three out of the four sites, SP21 transcript abundance increased with depth, while total mRNA abundance and richness decreased, indicating a shift in investment from metabolism and other cellular processes to build-up of spore protein SP21. The SP21 gene in MAGs was often flanked by genes involved in membrane-associated stress response. The ability of Woeseiales to shift from sulfur oxidation to nitrite reduction with burial into marine sediments with decreasing access to overlying oxic bottom waters, as well as enter into a dormant state dominated by SP21, may account for its ubiquity and high abundance in marine sediments worldwide, including those of the rapidly shifting Arctic.

    • It Takes a Village: Discovering and Isolating the Nitrifiers.

      Sedlacek CJ
      2020 - Front Microbiol, 1900

      Abstract: 

      It has been almost 150 years since Jean-Jacques Schloesing and Achille Müntz discovered that the process of nitrification, the oxidation of ammonium to nitrate, is a biological process carried out by microorganisms. In the following 15 years, numerous researchers independently contributed paradigm shifting discoveries that formed the foundation of nitrification and nitrification-related research. One of them was Sergei Winogradsky, whose major accomplishments include the discovery of both lithotrophy (in sulfur-oxidizing bacteria) and chemoautotrophy (in nitrifying bacteria). However, Winogradsky often receives most of the credit for many other foundational nitrification discoveries made by his contemporaries. This accumulation of credit over time is at least in part due to the increased attention, Winogradsky receives in the scientific literature and textbooks as a "founder of microbiology" and "the founder of microbial ecology." Here, some light is shed on several other researchers who are often overlooked, but whose work was instrumental to the emerging field of nitrification and to the work of Winogradsky himself. Specifically, the discovery of the biological process of nitrification by Schloesing and Müntz, the isolation of the first nitrifier by Grace and Percy Frankland, and the observation that nitrification is carried out by two distinct groups of microorganisms by Robert Warington are highlighted. Finally, the more recent discoveries of the chemolithoautotrophic ammonia-oxidizing archaea and complete ammonia oxidizers are put into this historical context.

    • Nitrogen Isotope Fractionation During Archaeal Ammonia Oxidation: Coupled Estimates From Measurements of Residual Ammonium and Accumulated Nitrite

      Mooshammer M, Alves RJE, Bayer B, Melcher M, Stieglmeier M, Jochum L, Rittmann SK-MR, Watzka M, Schleper C, Herndl G, Wanek W
      2020 - Frontiers in microbiology, 11: Article 1710

      Abstract: 

      The naturally occurring nitrogen (N) isotopes, 15N and 14N, exhibit different reaction rates during many microbial N transformation processes, which results in N isotope fractionation. Such isotope effects are critical parameters for interpreting natural stable isotope abundances as proxies for biological process rates in the environment across scales. The kinetic isotope effect of ammonia oxidation (AO) to nitrite (NO2), performed by ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB), is generally ascribed to the enzyme ammonia monooxygenase (AMO), which catalyzes the first step in this process. However, the kinetic isotope effect of AMO, or εAMO, has been typically determined based on isotope kinetics during product formation (cumulative product, NO2) alone, which may have overestimated εAMO due to possible accumulation of chemical intermediates and alternative sinks of ammonia/ammonium (NH3/NH4+). Here, we analyzed 15N isotope fractionation during archaeal ammonia oxidation based on both isotopic changes in residual substrate (RS, NH4+) and cumulative product (CP, NO2) pools in pure cultures of the soil strain Nitrososphaera viennensis EN76 and in highly enriched cultures of the marine strain Nitrosopumilus adriaticus NF5, under non-limiting substrate conditions. We obtained εAMO values of 31.9–33.1‰ for both strains based on RS (δ15NH4+) and showed that estimates based on CP (δ15NO2) give larger isotope fractionation factors by 6–8‰. Complementary analyses showed that, at the end of the growth period, microbial biomass was 15N-enriched (10.1‰), whereas nitrous oxide (N2O) was highly 15N depleted (−38.1‰) relative to the initial substrate. Although we did not determine the isotope effect of NH4+ assimilation (biomass formation) and N2O production by AOA, our results nevertheless show that the discrepancy between εAMO estimates based on RS and CP might have derived from the incorporation of 15N-enriched residual NH4+ after AMO reaction into microbial biomass and that N2O production did not affect isotope fractionation estimates significantly.

    • Dietary Supplementation with Sugar Beet Fructooligosaccharides and Garlic Residues Promotes Growth of Beneficial Bacteria and Increases Weight Gain in Neonatal Lambs.

      Quijada NM, Bodas R, Lorenzo JM, Schmitz-Esser S, Rodríguez-Lázaro D, Hernández M
      2020 - Biomolecules, 8: in press

      Abstract: 

      The proper development of the early gastrointestinal tract (GIT) microbiota is critical for newborn ruminants. This microbiota is susceptible to modification by diverse external factors (such as diet) that can lead to long-lasting results when occurring in young ruminants. Dietary supplementation with prebiotics, ingredients nondigestible and nonabsorbable by the host that stimulate the growth of beneficial GIT bacteria, has been applied worldwide as a potential approach in order to improve ruminant health and production yields. However, how prebiotics affect the GIT microbiota during ruminants' early life is still poorly understood. We investigated the effect of milk supplementation with a combination of two well-known prebiotics, fructooligosaccharides (FOS) from sugar beet and garlic residues (all together named as "additive"), exerted on preweaned lamb growth and the composition of their fecal microbiota, by using 16S rRNA gene amplicon high-throughput sequencing. The results showed a significant increase in the mean daily weight gain of lambs fed with the additive. Lamb fecal microbiota was also influenced by the additive intake, as additive-diet lambs showed lower bacterial diversity and were significantly more abundant in , , and . These bacteria have been previously reported to confer beneficial properties to the ruminant, including promotion of growth and health status, and our results showed that they were strongly linked to the additive intake and the increased weight gain of lambs. This study points out the combination of FOS from sugar beet and garlic residues as a potential prebiotic to be used in young ruminants' nutrition in order to improve production yields.

    • Molecular causes of an evolutionary shift along the parasitism-mutualism continuum in a bacterial symbiont.

      Herrera P, Schuster L, Wentrup C, König L, Kempinger T, Na H, Schwarz J, Köstlbacher S, Wascher F, Zojer M, Rattei T, Horn M
      2020 - Proc. Natl. Acad. Sci. U.S.A., in press

      Abstract: 

      Symbiosis with microbes is a ubiquitous phenomenon with a massive impact on all living organisms, shaping the world around us today. Theoretical and experimental studies show that vertical transmission of symbionts leads to the evolution of mutualistic traits, whereas horizontal transmission facilitates the emergence of parasitic features. However, these studies focused on phenotypic data, and we know little about underlying molecular changes at the genomic level. Here, we combined an experimental evolution approach with infection assays, genome resequencing, and global gene expression analysis to study the effect of transmission mode on an obligate intracellular bacterial symbiont. We show that a dramatic shift in the frequency of genetic variants, coupled with major changes in gene expression, allow the symbiont to alter its position in the parasitism-mutualism continuum depending on the mode of between-host transmission. We found that increased parasitism in horizontally transmitted chlamydiae residing in amoebae was a result of processes occurring at the infectious stage of the symbiont's developmental cycle. Specifically, genes involved in energy production required for extracellular survival and the type III secretion system-the symbiont's primary virulence mechanism-were significantly up-regulated. Our results identify the genomic and transcriptional dynamics sufficient to favor parasitic or mutualistic strategies.

    • Composition and activity of nitrifier communities in soil are unresponsive to elevated temperature and CO, but strongly affected by drought.

      Séneca J, Pjevac P, Canarini A, Herbold CW, Zioutis C, Dietrich M, Simon E, Prommer J, Bahn M, Pötsch EM, Wagner M, Wanek W, Richter A
      2020 - ISME J, in press
      soil nitrifier response to climate change

      Abstract: 

      Nitrification is a fundamental process in terrestrial nitrogen cycling. However, detailed information on how climate change affects the structure of nitrifier communities is lacking, specifically from experiments in which multiple climate change factors are manipulated simultaneously. Consequently, our ability to predict how soil nitrogen (N) cycling will change in a future climate is limited. We conducted a field experiment in a managed grassland and simultaneously tested the effects of elevated atmospheric CO, temperature, and drought on the abundance of active ammonia-oxidizing bacteria (AOB) and archaea (AOA), comammox (CMX) Nitrospira, and nitrite-oxidizing bacteria (NOB), and on gross mineralization and nitrification rates. We found that N transformation processes, as well as gene and transcript abundances, and nitrifier community composition were remarkably resistant to individual and interactive effects of elevated CO and temperature. During drought however, process rates were increased or at least maintained. At the same time, the abundance of active AOB increased probably due to higher NH availability. Both, AOA and comammox Nitrospira decreased in response to drought and the active community composition of AOA and NOB was also significantly affected. In summary, our findings suggest that warming and elevated CO have only minor effects on nitrifier communities and soil biogeochemical variables in managed grasslands, whereas drought favors AOB and increases nitrification rates. This highlights the overriding importance of drought as a global change driver impacting on soil microbial community structure and its consequences for N cycling.

    • Exploring the upper pH limits of nitrite oxidation: diversity, ecophysiology, and adaptive traits of haloalkalitolerant Nitrospira

      Daebeler A, Kitzinger K, Koch H, Herbold CW, Steinberger M, Schwarz J, Zechmeister T, Karst S, Albertsen M, Nielsen PH, Wagner M, Daims H
      2020 - ISME J, in press
      Ca. N. alkalitolerans

      Abstract: 

      Nitrite-oxidizing bacteria of the genus Nitrospira are key players of the biogeochemical nitrogen cycle. However, little is known about their occurrence and survival strategies in extreme pH environments. Here, we report on the discovery of physiologically versatile, haloalkalitolerant Nitrospira that drive nitrite oxidation at exceptionally high pH. Nitrospiradistribution, diversity, and ecophysiology were studied in hypo- and subsaline (1.3-12.8 g salt/l), highly alkaline (pH 8.9-10.3) lakes by amplicon sequencing, metagenomics, and cultivation-based approaches. Surprisingly, not only were Nitrospira populations detected, but they were also considerably diverse with presence of members of Nitrospira lineages I, II and IV. Furthermore, the ability of Nitrospira enrichment cultures to oxidize nitrite at neutral to highly alkaline pH of 10.5 was demonstrated. Metagenomic analysis of a newly enriched Nitrospira lineage IV species, “Candidatus Nitrospira alkalitolerans”, revealed numerous adaptive features of this organism to its extreme environment. Among them were a sodium-dependent N-type ATPase and NADH:quinone oxidoreductase next to the proton-driven forms usually found in Nitrospira. Other functions aid in pH and cation homeostasis and osmotic stress defense. “Ca. Nitrospira alkalitolerans” also possesses group 2a and 3b [NiFe] hydrogenases, suggesting it can use hydrogen as alternative energy source. These results reveal how Nitrospira cope with strongly fluctuating pH and salinity conditions and expand our knowledge of nitrogen cycling in extreme habitats.

    • Gut microbiota and undigested food constituents modify toxin composition and suppress the genotoxicity of a naturally occurring mixture of Alternaria toxins in vitro.

      Crudo F, Aichinger G, Mihajlovic J, Dellafiora L, Varga E, Puntscher H, Warth B, Dall'Asta C, Berry D, Marko D
      2020 - Arch. Toxicol., in press

      Abstract: 

      Molds of the genus Alternaria produce several mycotoxins, some of which may pose a threat for health due to their genotoxicity. Due to the lack of adequate toxicological and occurrence data, they are currently not regulated. Interactions between mycotoxins, gut microbiota and food constituents might occur after food ingestion, modifying the bioavailability and, therefore, overall toxicity of mycotoxins. The present work aimed to investigate the impact of in vitro short-term fecal incubation on the in vitro DNA-damaging effects exerted by 5 µg/mL of an Alternaria alternata extract, containing, among others, 15 nM alternariol, 12 nM alternariol monomethyl ether, 241 nM altertoxin II and 301 nM stemphyltoxin III, all of which are known as genotoxic. The involvement of microorganisms, undigested food constituents and soluble substances of human fecal samples in modifying the composition and the genotoxicity of the extract was investigated through the application of LC-MS/MS analysis and comet assays in HT-29 cells. Results showed that the potential of the mycotoxins to induce DNA strand breaks was almost completely quenched, even before anaerobic incubation, by contact with the different fractions of the fecal samples, while the potency to induce formamidopyrimidine DNA glycosylase (FPG)-sensitive sites was only slightly reduced. These effects were in line with a reduction of mycotoxin concentrations found in samples analyzed by LC-MS/MS. Although a direct correlation between the metabolic activity of the gut microbiota and modifications in mycotoxin contents was not clearly observed, adsorptive phenomena to bacterial cells and to undigested food constituents might explain the observed modifications.

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

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

      Abstract: 

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

    • Chlamydiae in the Environment.

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

      Abstract: 

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

    • Roadmap for naming uncultivated Archaea and Bacteria.

      Murray AE, Freudenstein J, Gribaldo S, Hatzenpichler R, Hugenholtz P, Kämpfer P, Konstantinidis KT, Lane CE, Papke RT, Parks DH, Rosselló-Móra R, Stott MB, Sutcliffe IC, Thrash JC, Venter SN, Whitman WB, Acinas SG, Amann RI, Anantharaman K, Armengaud J, Baker BJ, Barco RA, Bode HB, Boyd ES, Brady CL, Carini P, Chain PSG, Colman DR, DeAngelis KM, de Los Rios MA, Estrada-de los Santos P, Dunlap CA, Eisen JA, Emerson D, Ettema TJG, Eveillard D, Girguis PR, Hentschel U, Hollibaugh JT, Hug LA, Inskeep WP, Ivanova EP, Klenk HP, Li WJ, Lloyd KG, Löffler FE, Makhalanyane TP, Moser DP, Nunoura T, Palmer M, Parro V, Pedrós-Alió C, Probst AJ, Smits THM, Steen AD, Steenkamp ET, Spang A, Stewart FJ, Tiedje JM, Vandamme P, Wagner M, Wang FP, Hedlund BP, Reysenbach AL
      2020 - Nat Microbiol, 8: 987-994
      Roadmap for naming uncultured microbes

      Abstract: 

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

    • The role of metal contamination in shaping microbial communities in heavily polluted marine sediments

      Di Cesare A, Pjevac P, Eckert E, Curkov N, Miko Šparica M, Corno G, Orlić S
      2020 - Environ. Pollut., 265: 114823

      Abstract: 

      Microorganisms in coastal sediments are fundamental for ecosystem functioning, and regulate processes relevant in global biogeochemical cycles. Still, our understanding of the effects anthropogenic perturbation and pollution can have on microbial communities in marine sediments is limited. We surveyed the microbial diversity, and the occurrence and abundance of metal and antibiotic resistance genes is sediments collected from the Pula Bay (Croatia), one of the most significantly polluted sites along the Croatian coast. With a collection of 14 samples from the bay area, we were able to generate a detailed status quo picture of a site that only recently started a cleaning and remediation process (closing of sewage pipes and reduction of industrial activity). The concentrations of heavy metals in Pula Bay sediments are significantly higher than in pristine sediments from the Adriatic Sea, and in some cases, manifold exceed international sediment quality guidelines. While the sedimentary concentrations of heavy metals did significantly influence the abundance of the tested metal resistance genes, no strong effect of heavy metal pollution on the overall microbial community composition was observed. Like in many other marine sediments, Gammaproteobacteria, Bacteroidota and Desulfobacterota dominated the microbial community composition in most samples, and community assembly was primarily driven by water column depth and nutrient (carbon and nitrogen) availability, regardless of the degree of heavy metal pollution.

    • Verrucomicrobia use hundreds of enzymes to digest the algal polysaccharide fucoidan.

      Sichert A, Corzett CH, Schechter MS, Unfried F, Markert S, Becher D, Fernandez-Guerra A, Liebeke M, Schweder T, Polz MF, Hehemann JH
      2020 - Nat Microbiol, 8: 1026-1039

      Abstract: 

      Brown algae are important players in the global carbon cycle by fixing carbon dioxide into 1 Gt of biomass annually, yet the fate of fucoidan-their major cell wall polysaccharide-remains poorly understood. Microbial degradation of fucoidans is slower than that of other polysaccharides, suggesting that fucoidans are more recalcitrant and may sequester carbon in the ocean. This may be due to the complex, branched and highly sulfated structure of fucoidans, which also varies among species of brown algae. Here, we show that 'Lentimonas' sp. CC4, belonging to the Verrucomicrobia, acquired a remarkably complex machinery for the degradation of six different fucoidans. The strain accumulated 284 putative fucoidanases, including glycoside hydrolases, sulfatases and carbohydrate esterases, which are primarily located on a 0.89-megabase pair plasmid. Proteomics reveals that these enzymes assemble into substrate-specific pathways requiring about 100 enzymes per fucoidan from different species of brown algae. These enzymes depolymerize fucoidan into fucose, which is metabolized in a proteome-costly bacterial microcompartment that spatially constrains the metabolism of the toxic intermediate lactaldehyde. Marine metagenomes and microbial genomes show that Verrucomicrobia including 'Lentimonas' are abundant and highly specialized degraders of fucoidans and other complex polysaccharides. Overall, the complexity of the pathways underscores why fucoidans are probably recalcitrant and more slowly degraded, since only highly specialized organisms can effectively degrade them in the ocean.

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

      Lang M, Baumgartner M, Rożalska A, Frick A, Riva A, Jarek M, Berry D, Gasche C
      2020 - Int. J. Cancer, 8: 2316-2326

      Abstract: 

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

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

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

      Abstract: 

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

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

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

      Abstract: 

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

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

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

      Abstract: 

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

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

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

      Abstract: 

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

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

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

      Abstract: 

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

    • Using Colonization Assays and Comparative Genomics To Discover Symbiosis Behaviors and Factors in Vibrio fischeri.

      Bongrand C, Moriano-Gutierrez S, Arevalo P, McFall-Ngai M, Visick KL, Polz M, Ruby EG
      2020 - mBio, 2: in press

      Abstract: 

      The luminous marine Gram-negative bacterium () is the natural light organ symbiont of several squid species, including the Hawaiian bobtail squid, , and the Japanese bobtail squid, Work with has shown how the bacteria establish their niche in the light organ of the newly hatched host. Two types of strains have been distinguished based upon their behavior in cocolonization competition assays in juvenile , i.e., (i) niche-sharing or (ii) niche-dominant behavior. This study aimed to determine whether these behaviors are observed with other strains or whether they are specific to those isolated from light organs. Cocolonization competition assays between strains isolated from the congeneric squid or from other marine animals revealed the same sharing or dominant behaviors. In addition, whole-genome sequencing of these strains showed that the dominant behavior is polyphyletic and not associated with the presence or absence of a single gene or genes. Comparative genomics of 44 squid light organ isolates from around the globe led to the identification of symbiosis-specific candidates in the genomes of these strains. Colonization assays using genetic derivatives with deletions of these candidates established the importance of two such genes in colonization. This study has allowed us to expand the concept of distinct colonization behaviors to strains isolated from a number of squid and fish hosts. There is an increasing recognition of the importance of strain differences in the ecology of a symbiotic bacterial species and, in particular, how these differences underlie crucial interactions with their host. Nevertheless, little is known about the genetic bases for these differences, how they manifest themselves in specific behaviors, and their distribution among symbionts of different host species. In this study, we sequenced the genomes of isolated from the tissues of squids and fishes and applied comparative genomics approaches to look for patterns between symbiont lineages and host colonization behavior. In addition, we identified the only two genes that were exclusively present in all strains isolated from the light organs of sepiolid squid species. Mutational studies of these genes indicated that they both played a role in colonization of the squid light organ, emphasizing the value of applying a comparative genomics approach in the study of symbioses.

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

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

      Abstract: 

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

    • Diarrhoeal events can trigger long-term Clostridium difficile colonization with recurrent blooms.

      VanInsberghe D, Elsherbini JA, Varian B, Poutahidis T, Erdman S, Polz MF
      2020 - Nat Microbiol, 4: 642-650

      Abstract: 

      Although Clostridium difficile is widely considered an antibiotic- and hospital-associated pathogen, recent evidence indicates that this is an insufficient depiction of the risks and reservoirs. A common thread that links all major risk factors of infection is their association with gastrointestinal disturbances, but this relationship to C. difficile colonization has never been tested directly. Here, we show that disturbances caused by diarrhoeal events trigger susceptibility to C. difficile colonization. Using survey data of the human gut microbiome, we detected C. difficile colonization and blooms in people recovering from food poisoning and Vibrio cholerae infections. Carriers remained colonized for year-long time scales and experienced highly variable patterns of C. difficile abundance, where increased shedding over short periods of 1-2 d interrupted week-long periods in which C. difficile was undetectable. Given that short shedding events were often linked to gastrointestinal disturbances, our results help explain why C. difficile is frequently detected as a co-infecting pathogen in patients with diarrhoea. To directly test the impact of diarrhoea on susceptibility to colonization, we developed a mouse model of variable disturbance intensity, which allowed us to monitor colonization in the absence of disease. As mice exposed to avirulent C. difficile spores ingested increasing quantities of laxatives, more individuals experienced C. difficile blooms. Our results indicate that the likelihood of colonization is highest in the days immediately following acute disturbances, suggesting that this could be an important window during which transmission could be interrupted and the incidence of infection lowered.

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

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

      Abstract: 

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

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

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

      Abstract: 

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

    • Culture-independent tracking of Vibrio cholerae lineages reveals complex spatiotemporal dynamics in a natural population.

      Kirchberger PC, Orata FD, Nasreen T, Kauffman KM, Tarr CL, Case RJ, Polz MF, Boucher YF
      2020 - Environ. Microbiol., in press

      Abstract: 

      Populations of the bacterium Vibrio cholerae consist of dozens of distinct lineages, with primarily (but not exclusively) members of the pandemic generating lineage capable of causing the diarrhoeal disease cholera. Assessing the composition and temporal dynamics of such populations requires extensive isolation efforts and thus only rarely covers large geographic areas or timeframes exhaustively. We developed a culture-independent amplicon sequencing strategy based on the protein-coding gene viuB (vibriobactin utilization) to study the structure of a V. cholerae population over the course of a summer. We show that the 26 co-occurring V. cholerae lineages continuously compete for limited space on nutrient-rich particles where only a few of them can grow to large numbers. Differential abundance of lineages between locations and size-fractions associated with a particle-attached or free-swimming lifestyle could reflect adaptation to various environmental niches. In particular, a major V. cholerae lineage occasionally grows to large numbers on particles but remain undetectable using isolation-based methods, indicating selective culturability for some members of the species. We thus demonstrate that isolation-based studies may not accurately reflect the structure and complex dynamics of V. cholerae populations and provide a scalable high-throughput method for both epidemiological and ecological approaches to studying this species.

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

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

      Abstract: 

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

    • The role of gut microbiota, butyrate and proton pump inhibitors in amyotrophic lateral sclerosis: a systematic review.

      Erber AC, Cetin H, Berry D, Schernhammer ES
      2020 - Int. J. Neurosci., 7: 727-735

      Abstract: 

      We conducted a systematic review on existing literature in humans and animals, linking the gut microbiome with amyotrophic lateral sclerosis (ALS). Additionally, we sought to explore the role of the bacterially produced metabolite butyrate as well as of proton pump inhibitors (PPIs) in these associations. Following PRISMA guidelines for systematic literature reviews, four databases (Medline, Scopus, Embase and Web of Science) were searched and screened by two independent reviewers against defined inclusion criteria. Six studies in humans and six animal studies were identified, summarized and reviewed. Overall, the evidence accrued to date is supportive of changes in the gut microbiome being associated with ALS risk, and potentially progression, though observational studies are small (describing a total of 145 patients with ALS across all published studies), and not entirely conclusive. With emerging studies beginning to apply metagenome sequencing, more clarity regarding the importance and promise of the gut microbiome in ALS can be expected. Future studies may also help establish the therapeutic potential of butyrate, and the role of PPIs in these associations.

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

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

      Abstract: 

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

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

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

      Abstract: 

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

    Book chapters and other publications

    7 Publications found
    • Comment on Predicting Aqueous Adsorption of Organic Compounds onto Biochars, Carbon Nanotubes, Granular Activated Carbons, And Resins with Machine Learning

      Gabriel Sigmund, Mehdi Gharasoo, Thorsten Hüffer, Thilo Hofmann
      2020 - Environmental Science & Technology, A-B
    • One complete and seven draft genome sequences of subdivision 1 and 3 Acidobacteria from soil

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

      Abstract: 

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

    • STILLLEBEN with Symbionts

      Athanassakis I, Berry D
      2020 - Performance Research, 25: 83-87

      Abstract: 

      STILLLEBEN. Becoming Symbionts’ proposes to value milk and its microbial constituents as primordial assets and currencies - along with cells, sperm, blood, water, and oxygen. The latest scientific research, which has suggested that there is an intimate unseen interplay between mothers and their babies via the transfer of breast milk and microbes, which actually increases the value of the currency with each exchange. The co-operation of Irini Athanassakis and David Berry is an invitation to perceive the transfer of milk not only as an interaction visible to the naked eye, but also on the microscopic level of cells and bacteria. In order to challenge us with this unseen perspective, Athanassakis encourages us to step forward and take a performative and procreative role in expanding our perception. As we are home to billions of microscopic entities, we continuously cast this part of ourselves into our surroundings, impacting and interacting with everything around us. We leave a microbial trace, a lingering residue of cells on the objects, rooms, and people that we encounter. Breast milk and formula are part of such an exchange process. If we look at the logic of microbial exchange in nursing as ‘giving’ and knowledge about symbionts for a future holo-economy based on co-operation and mutualism for collective survival.

    • Is too much fertilizer a problem?

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

      Abstract: 

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

    • Thinking outside the Chlamydia box

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

      Abstract: 

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

    • A genomic catalog of Earth's microbiomes

      Nayfach S, Roux S, Seshadri R, Udwary D, Varghese N, Schulz F, Wu D, Páez-Espino D, Chen IM, Huntemann M, Palaniappan K, Ladau J, Mukherjee S, Reddy TBK, Nielsen T, Kirton E, Faria JP, Edirisinghe JN, Henry CS, Jungbluth SP, Chivian D, Dehal P, Wood-Charlson EM, Arkin AP, Tringe SG, Visel A, IMG/M Data Consortium, Woyke T, Mouncey NJ, Ivanova NN, Kyrpides NC, Eloe-Fadrosh EA
      2020 - Nat Biotechnol, In press

      Abstract: 

      The reconstruction of bacterial and archaeal genomes from shotgun metagenomes has enabled insights into the ecology and evolution of environmental and host-associated microbiomes. Here we applied this approach to >10,000 metagenomes collected from diverse habitats covering all of Earth's continents and oceans, including metagenomes from human and animal hosts, engineered environments, and natural and agricultural soils, to capture extant microbial, metabolic and functional potential. This comprehensive catalog includes 52,515 metagenome-assembled genomes representing 12,556 novel candidate species-level operational taxonomic units spanning 135 phyla. The catalog expands the known phylogenetic diversity of bacteria and archaea by 44% and is broadly available for streamlined comparative analyses, interactive exploration, metabolic modeling and bulk download. We demonstrate the utility of this collection for understanding secondary-metabolite biosynthetic potential and for resolving thousands of new host linkages to uncultivated viruses. This resource underscores the value of genome-centric approaches for revealing genomic properties of uncultivated microorganisms that affect ecosystem processes.

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

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

      Abstract: 

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

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