Metamenu

Publications

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Publications in peer reviewed journals

32 Publications found
  • Combination of techniques to quantify the distribution of bacteria in their soil microhabitats at different spatial scales

    Juyal A, Otten W, Falconer R, Hapca S, Schmidt H, Baveye PC, Eickhorst T
    2019 - Geoderma, 334: 165-174

    Abstract: 

    To address a number of issues of great societal concern at the moment, like the sequestration of carbon, information is direly needed about interactions between soil architecture and microbial dynamics. Unfortunately, soils are extremely complex, heterogeneous systems comprising highly variable and dynamic micro-habitats that have significant impacts on the growth and activity of inhabiting microbiota. Data remain scarce on the influence of soil physical parameters characterizing the pore space on the distribution and diversity of bacteria. In this context, the objective of the research described in this article was to develop a method where X-ray microtomography, to characterize the soil architecture, is combined with fluorescence microscopy to visualize and quantify bacterial distributions in resin-impregnated soil sections. The influence of pore geometry (at a resolution of 13.4 μm) on the distribution of Pseudomonas fluorescens was analysed at macro- (5.2 mm × 5.2 mm), meso- (1 mm × 1 mm) and microscales (0.2 mm × 0.2 mm) based on an experimental setup simulating different soil architectures. The cell density of P. fluorescenswas 5.59 x 107(SE 2.6 x 106) cells g−1 soil in 1–2 mm and 5.84 x 107(SE 2.4 x 106) cells g−1 in 2–4 mm size aggregates soil. Solid-pore interfaces influenced bacterial distribution at micro- and macroscale, whereas the effect of soil porosity on bacterial distribution varied according to three observation scales in different soil architectures. The influence of soil porosity on the distribution of bacteria in different soil architectures was observed mainly at the macroscale, relative to micro- and mesoscales. Experimental data suggest that the effect of pore geometry on the distribution of bacteria varied with the spatial scale, thus highlighting the need to consider an “appropriate spatial scale” to understand the factors that regulate the distribution of microbial communities in soils. The results obtained to date also indicate that the proposed method is a significant step towards a full mechanistic understanding of microbial dynamics in structured soils.

  • Synthesis and biological evaluation of biotin-conjugated anticancer thiosemicarbazones and their iron(III) and copper(II) complexes

    Sebastian Kallus, Lukas Uhlik, Sushilla van Schoonhoven, Karla Pelivan, Walter Berger, Éva A. Enyedy, Thilo Hofmann, Petra Heffeter, Christian R. Kowol and Bernhard K. Keppler
    2019 - Journal of Inorganic Biochemistry, 85-97
  • The Effect of pH and biogenic ligands on the weathering of chrysotile asbestos: The pivotal role of tetrahedral Fe in dissolution kinetics and radical formation

    Martin Walter, Walter D. C. Schenkeveld, Michael Reissner, Lars Gille and Stephan M. Kraemer
    2019 - Chemistry A European Journal, in press
  • Low yield and abiotic origin of N2O formed by the complete nitrifier Nitrospira inopinata

    Kits KD, Jung M-Y, Vierheilig J, Pjevac P, Sedlacek CJ, Liu S, Herbold CW, Stein LY, Richter A, Wissel H, Brüggemann N, Wagner M, Daims H
    2019 - Nat Commun, in press
    Nitrous oxide comammox

    Abstract: 

    Nitrous oxide (N2O) and nitric oxide (NO) are atmospheric trace gases that contribute to climate change and affect stratospheric and ground-level ozone concentrations. Ammonia oxidizing bacteria (AOB) and archaea (AOA) are key players in the nitrogen cycle and major producers of N2O and NO globally. However, nothing is known about N2O and NO production by the recently discovered and widely distributed complete ammonia oxidizers (comammox). Here, we show that the comammox bacterium Nitrospira inopinata is sensitive to inhibition by an NO scavenger, cannot denitrify to N2O, and emits N2O at levels that are comparable to AOA but much lower than AOB. Furthermore, we demonstrate that N2O formed by N.  inopinata formed under varying oxygen regimes originates from abiotic conversion of hydroxylamine. Ourfindings indicate that comammox microbes may produce less N2O during nitrification than AOB.

  • Rapid transfer of plant photosynthates to soil bacteria via ectomycorrhizal hyphae and its interaction with nitrogen availability

    Gorka S, Dietrich M, Mayerhofer W, Gabriel R, Wiesenbauer J, Martin V, Zheng Q, Imai B, Prommer J, Weidinger M, Schweiger P, Eichorst SA, Wagner M, Richter A, Schintlmeister A, Woebken D, Kaiser C
    2019 - Frontiers Microbioly, 10: Article 168

    Abstract: 

    Plant roots release recent photosynthates into the rhizosphere, accelerating decomposition of organic matter by saprotrophic soil microbes (’rhizosphere priming effect’) which consequently increases nutrient availability for plants. However, about 90% of all higher plant species are mycorrhizal, transferring a significant fraction of their photosynthates directly to their fungal partners. Whether mycorrhizal fungi pass on plant-derived carbon (C) to bacteria in root-distant soil areas, i.e. incite a ‘hyphosphere priming effect’, is not known. Experimental evidence for C transfer from mycorrhizal hyphae to soil bacteria is limited, especially for ectomycorrhizal systems. As ectomycorrhizal fungi possess enzymatic capabilities to degrade organic matter themselves, it remains unclear whether they cooperate with soil bacteria by providing photosynthates, or compete for available nutrients.

    To investigate a possible C transfer from ectomycorrhizal hyphae to soil bacteria, and its response to changing nutrient availability, we planted young beech trees (Fagus sylvatica) into ‘split-root’ boxes, dividing their root systems into two disconnected soil compartments. Each of these compartments was separated from a litter compartment by a mesh penetrable for fungal hyphae, but not for roots. Plants were exposed to a 13C-CO2–labeled atmosphere, while 15N-labeled ammonium and amino acids were added to one side of the split-root system.

    We found a rapid transfer of recent photosynthates via ectomycorrhizal hyphae to bacteria in root-distant soil areas. Fungal and bacterial phospholipid fatty acid (PLFA) biomarkers were significantly enriched in hyphae-exclusive compartments 24 h after 13C-CO2–labeling. Isotope imaging with nanometer-scale secondary ion mass spectrometry (NanoSIMS) allowed for the first time in situ visualization of plant-derived C and N taken up by extraradical fungal hyphae, and in microbial cells thriving on hyphal surfaces. When N was added to the litter compartments, bacterial biomass and the amount of incorporated 13C strongly declined. Interestingly, this effect was also observed in adjacent soil compartments where added N was only available for bacteria through hyphal transport, indicating that ectomycorrhizal fungi were acting on soil bacteria. Together, our results demonstrate that (i) ectomycorrhizal hyphae rapidly transfer plant-derived C to bacterial communities in root-distant areas, and (ii) this transfer promptly responds to changing soil nutrient conditions.

  • Variation in rhizosphere priming and microbial growth and carbon use efficiency caused by wheat genotypes and temperatures

    Yin L, Corneo PE, Richter A, Wang P, Cheng W, Dijkstra FA
    2019 - Soil Biology and Biochemistry, 134: 54-61

    Abstract: 

    Living roots can influence microbial decomposition of soil organic matter, which has been referred to as the rhizosphere priming effect (RPE). Both microbial carbon efficiency (CUE) and microbial growth and turnover rates are associated with microbial decomposition and respiration of soil-derived C, but their linkage to the RPE remains poorly understood. Here we used a natural 13C tracer method to determine the RPE in soils planted with two wheat genotypes (249 or IAW2013) grown at high (30/24 °C during day/night) and low temperature (25/17 °C during day/night). We also determined microbial CUE, growth and biomassturnover rate using a substrate-independent H218O labeling method. The RPE varied from −2 to +455%, with significant effects of genotype, sampling date and their interaction with temperature. Compared to the unplanted control, microbial biomass C and growth/turnover rate were both enhanced in planted pots, with an average increase of 17% and 70%, respectively. Microbial CUE was lowest in pots planted with IAW2013 at low temperature, but there were no significant main effects of planting and temperature. Microbial biomass growth/turnover rate together with CUE accounted for 83% of the variation in soil-derived CO2, with a relatively larger contribution of microbial biomass growth/turnover rate (52%) than CUE (31%). Furthermore, using linear regression, we demonstrated that the RPE was significantly positively related to microbial biomass growth/turnover rate. No net soil organic C (SOC) loss or gain was detected, indicating that any increase in SOC due to increased microbial growth/turnover was counteracted by C loss caused by a higher RPE during the relatively short time of planting. These findings suggest that microbial biomass turnover associated with growth could control the loss of SOC with planting. We highlight the importance of plant-induced changes in microbial CUE and biomass growth/turnover for long-term soil C dynamics.

  • Vertical Redistribution of Soil Organic Carbon Pools After Twenty Years of Nitrogen Addition in Two Temperate Coniferous Forests

    Forstner, SJ, Wechselberger V, Müller S, Keiblinger KM, Díaz-Pinés E, Wanek W, Scheppi P, Hagedorn F, Gundersen P, Tatzber M, Gerzabek MH, Zechmeister-Boltenstern S
    2019 - Ecosystems, 22: 379-400

    Abstract: 

    Nitrogen (N) inputs from atmospheric deposition can increase soil organic carbon (SOC) storage in temperate and boreal forests, thereby mitigating the adverse effects of anthropogenic CO2 emissions on global climate. However, direct evidence of N-induced SOC sequestration from low-dose, long-term N addition experiments (that is, addition of < 50 kg N ha−1 y−1 for > 10 years) is scarce worldwide and virtually absent for European temperate forests. Here, we examine how tree growth, fine roots, physicochemical soil properties as well as pools of SOC and soil total N responded to 20 years of regular, low-dose N addition in two European coniferous forests in Switzerland and Denmark. At the Swiss site, the addition of 22 kg N ha−1 y−1 (or 1.3 times throughfall deposition) stimulated tree growth, but decreased soil pH and exchangeable calcium. At the Danish site, the addition of 35 kg N ha−1 y−1 (1.5 times throughfall deposition) impaired tree growth, increased fine root biomass and led to an accumulation of N in several belowground pools. At both sites, elevated N inputs increased SOC pools in the moderately decomposed organic horizons, but decreased them in the mineral topsoil. Hence, long-term N addition led to a vertical redistribution of SOC pools, whereas overall SOC storage within 30 cm depth was unaffected. Our results imply that an N-induced shift of SOC from older, mineral-associated pools to younger, unprotected pools might foster the vulnerability of SOC in temperate coniferous forest soils.

  • Models for assessing engineered nanomaterial fate and behaviour in the aquatic environment

    Richard J Williams, Samuel Harrison, Virginie Keller, Jeroen Kuenen, Stephen Lofts, Antonia Praetorius, Claus Svendsen, Lucie C Vermeulen and Jikke van Wijnen
    2019 - Current Opinion in Environmental Sustainability, 105-115
  • Growth explains microbial carbon use efficiency across soils differing in land use and geology

    Zheng Q, Hu Y, zhang S, Noll L, Boeckle T, Richter A, Wanek W
    2019 - Soil Biology and Biochemistry, 128: 45-55

    Abstract: 

    The ratio of carbon (C) that is invested into microbial growth to organic C taken up is known as microbial carbon use efficiency (CUE), which is influenced by environmental factors such as soil temperature and soil moisture. How microbes will physiologically react to short-term environmental changes is not well understood, primarily due to methodological restrictions. Here we report on two independent laboratory experiments to explore short-term temperature and soil moisture effects on soil microbial physiology(i.e. respiration, growth, CUE, and microbial biomass turnover): (i) a temperature experiment with 1-day pre-incubation at 5, 15 and 25 °C at 60% water holding capacity (WHC), and (ii) a soil moisture/oxygen (O2) experiment with 7-day pre-incubation at 20 °C at 30%, 60% WHC (both at 21% O2) and 90% WHC at 1% O2. Experiments were conducted with soils from arable, pasture and forest sites derived from both silicate and limestone bedrocks. We found that microbial CUE responded heterogeneously though overall positively to short-term temperature changes, and decreased significantly under high moisture level (90% WHC)/suboxic conditions due to strong decreases in microbial growth. Microbial biomass turnover time decreased dramatically with increasing temperature, and increased significantly at high moisture level (90% WHC)/suboxic conditions. Our findings reveal that the responses of microbial CUE and microbial biomass turnover to short-term temperature and moisture/O2 changes depended mainly on microbial growth responses and less on respiration responses to the environmental cues, which were consistent across soils differing in land use and geology.

  • Characterization of sorption properties of high-density polyethylene using the poly-parameter linearfree-energy relationships

    Tobias H. Uber, Thorsten Hüffer, Sibylle Planitz and Torsten C. Schmidt
    2019 - Environmental Pollution, 312-319
  • Emerging contaminants in sediment core from the Iron Gate I reservoir on the Danube River

    Ivana Matić Bujagić, Svetlana Grujić, Mila Laušević, Thilo Hofmann and Vesna Micić
    2019 - Science of The Total Environment, 77-87
  • The cooling tower water microbiota: Seasonal dynamics and co-occurrence of bacterial and protist phylotypes

    Tsao HF, Scheikl U, Herbold CW, Indra A, Walochnik J, Horn M
    2019 - Water Res., in press

    Abstract: 

    Cooling towers for heating, ventilation and air conditioning are ubiquitous in the built environment. Often located on rooftops, their semi-open water basins provide a suitable environment for microbial growth. They are recognized as a potential source of bacterial pathogens and have been associated with disease outbreaks such as Legionnaires’ disease. While measures to minimize public health risks are in place, the general microbial and protist community structure and dynamics in these systems remain largely elusive. In this study, we analysed the microbiome of the bulk water from the basins of three cooling towers by 16S and 18S rRNA gene amplicon sequencing over the course of one year. Bacterial diversity in all three towers was broadly comparable to other freshwater systems, yet less diverse than natural environments; the most abundant taxa are also frequently found in freshwater or drinking water. While each cooling tower had a pronounced site-specific microbial community, taxa shared among all locations mainly included groups generally associated with biofilm formation. We also detected several groups related to known opportunistic pathogens, such as Legionella, Mycobacterium, and Pseudomonasspecies, albeit at generally low abundance. Although cooling towers represent a rather stable environment, microbial community composition was highly dynamic and subject to seasonal change. Protists are important members of the cooling tower water microbiome and known reservoirs for bacterial pathogens. Co-occurrence analysis of bacteria and protist taxa successfully captured known interactions between amoeba-associated bacteria and their hosts, and predicted a large number of additional relationships involving ciliates and other protists. Together, this study provides an unbiased and comprehensive overview of microbial diversity of cooling tower water basins, establishing a framework for investigating and assessing public health risks associated with these man-made freshwater environments.

  • Coupled carbon and nitrogen losses in response to seven years of chronic warming in subarctic soils

    Marañon-Jimenez S, Peñuelas J, Richter A, Sigurdsson BD, Fuchslueger L, Leblans NIW, Janssens IA
    2019 - Soil Biology and Biochemistry, 134: 152-161

    Abstract: 

    Increasing temperatures may alter the stoichiometric demands of soil microbes and impair their capacity to stabilize carbon (C) and retain nitrogen (N), with critical consequences for the soil C and N storage at high latitude soils. Geothermally active areas in Iceland provided wide, continuous and stable gradients of soil temperatures to test this hypothesis. In order to characterize the stoichiometric demands of microbes from these subarctic soils, we incubated soils from ambient temperatures after the factorial addition of C, N and P substrates separately and in combination. In a second experiment, soils that had been exposed to different in situ warming intensities (+0, +0.5, +1.8, +3.4, +8.7, +15.9 °C above ambient) for seven years were incubated after the combined addition of C, N and P to evaluate the capacity of soil microbes to store and immobilize C and N at the different warming scenarios. The seven years of chronic soil warming triggered large and proportional soil C and N losses (4.1 ± 0.5% °C−1 of the stocks in unwarmed soils) from the upper 10 cm of soil, with a predominant depletion of the physically accessible organic substrates that were weakly sorbed in soil minerals up to 8.7 °C warming. Soil microbes met the increasing respiratory demands under conditions of low C accessibility at the expenses of a reduction of the standing biomass in warmer soils. This together with the strict microbial C:N stoichiometric demands also constrained their capacity of N retention, and increased the vulnerability of soil to N losses. Our findings suggest a strong control of microbial physiology and C:N stoichiometric needs on the retention of soil N and on the resilience of soil C stocks from high-latitudes to warming, particularly during periods of vegetation dormancy and low C inputs.

  • Wide-spread limitation of soil organic nitrogen transformations by substrate availability and not by extracellular enzyme content

    Noll L, zhang S, Zheng Q, Hu Y, Wanek W
    2019 - Soil Biology and Biochemistry, 133: 37-49

    Abstract: 

    Proteins constitute the single largest soil organic nitrogen (SON) reservoir and its decomposition drives terrestrial N availability. Protein cleavage by extracellular enzymes is the rate limiting step in the soil organic N cycle and can be controlled by extracellular enzyme production or protein availability/stabilization in soil. Both controls can be affected by geology and land use, as well as be vulnerable to changes in soil temperature and moisture/O2. To explore major controls of soil gross protein depolymerization we sampled six soils from two soil parent materials (calcareous and silicate), where each soil type included three land uses (cropland, pasture and forest). Soil samples were subjected to three temperature treatments (5, 15, 25 °C at 60% water-holding capacity (WHC) and aerobic conditions) or three soil moisture/O2 treatments (30 and 60% WHC at 21% O2, 90% WHC at 1% O2, at 20 °C) in short-term experiments. Samples were incubated for one day in the temperature experiment and for one week in the moisture/O2experiment. Gross protein depolymerization rates were measured by a novel 15N isotope pool dilution approach. The low temperature sensitivity of gross protein depolymerization, the lack of relationship with protease activity and strong effects of soil texture and pHdemonstrate that this process is constrained by organo-mineral associations and not by soil enzyme content. This also became apparent from the inverse effects in calcareous and silicate soils caused by water saturation/O2 limitation. We highlight that the specific soil mineralogy influenced the response of gross depolymerization rates to water saturation/O2 limitation, causing (I) increasing gross depolymerization rates due to release of adsorbed proteins by reductive dissolution of Fe- and Mn-oxyhydroxides in calcareous soils and (II) decreasing gross depolymerization rates due to mobilization of coagulating and toxic Al3+compounds in silicate soils.

  • Determination of nanoparticle heteroaggregation attachment efficiencies and rates in presence of natural organic matter monomers. Monte Carlo modelling

    Arnaud Clavier, Antonia Praetorius and Serge Stoll
    2019 - Science of The Total Environment, 530-540
  • Polyethylene microplastics influence the transport of organic contaminants in soil

    Thorsten Hüffer, Florian Metzelder, Gabriel Sigmund, Sophie Slawek, Torsten C. Schmidt, Thilo Hofmann
    2019 - Science of The Total Environment, 242-247
  • Root exudation of primary metabolites: mechanisms and their roles in plant responses to environmental stimuli

    Canarini A, Wanek W, Merchant A, Richter A, Kaiser C
    2019 - Frontiers in Plant Science, 10: Article 157

    Abstract: 

    Root exudation is an important process determining plant interactions with the soil environment. Many studies have linked this process to soil nutrient mobilization. Yet, it remains unresolved how exudation is controlled and how exactly and under what circumstances plants benefit from exudation. The majority of root exudates include primary metabolites (sugars, amino acids and organic acids) believed to be passively lost from the root and used by rhizosphere-dwelling microbes. In this review, we synthetize recent advances in ecology and plant biology to explain and propose mechanisms by which root exudation of primary metabolites is controlled, and what role their exudation plays in plant nutrient acquisition strategies. Specifically, we propose a novel conceptual framework for root exudates. This framework is built upon two main concepts: (i) root exudation of primary metabolites is driven by diffusion, with plants and microbes both modulating concentration gradients and therefore diffusion rates to soil depending on their nutritional status; (ii) exuded metabolite concentrations can be sensed at the root tip and signals are translated to modify root architecture. The flux of primary metabolites through root exudation is mostly located at the root tip, where the lack of cell differentiation favors diffusion of metabolites to the soil. We show examples of how the root tip senses concentration changes of exuded metabolites and translate that into signals to modify root growth. Plants can modify the concentration of metabolites either by controlling source/sink processes or by expressing and regulating efflux carriers, therefore challenging the idea of root exudation as a purely unregulated passive process. Through root exudate flux, plants can locally enhance concentrations of many common metabolites which can serve as sensors and integrators of the plant nutritional status and of the nutrient availability in the surrounding environment. Plant-associated micro-organisms also constitute a strong sink for plant carbon thereby increasing concentration gradients of metabolites and affecting root exudation. Understanding the mechanisms of, and the effects that, environmental stimuli have on the magnitude and type of root exudation will ultimately improve our knowledge of processes determining soil CO2 emissions, ecosystem functioning and how to improve the sustainability of agricultural production.

  • Sorption of organic substances to tire wear materials: Similarities and differences with other types of microplastic

    Thorsten Hüffer, Stephan Wagner, Thorsten Reemtsma and Thilo Hofmann
    2019 - Trends in Analytical Chemistry, 113: 392-401

    Abstract: 

    Tire materials are a significant proportion of the (micro)plastics in the environment that until today have been clearly overlooked. These materials are released into the environment, either unintentionally as an abrasion product from tire wear, that reaches the environment via road runoff, or intentionally as, for example, shredded “tire crumble rubber” used as filling material for playgrounds. Although there are a few estimates available the amount of tire-wear material to be found in aquatic environments, investigations on the fate tire materials and especially their interaction with organic substances are missing. Although the sorption processes associated with the complex constituents of tires are an important aspect of any environmental risk assessment for tire-wear materials, they have yet to be thoroughly investigated. In this review we elucidate the sorption properties of the polymeric rubbers and carbon black that form the main components of tires, within the context of current microplastic research.

  • Beta diversity and oligarchic dominance in the tropical forests of Southern Costa Rica

    Morera-Beita A, Sánchez D, Wanek W, Hofhansl F, Huber W, Chacón-Madrigal E, Montero-Munoz JL, Silla F
    2019 - Biotropica, 51: 117-128

    Abstract: 

    Recent studies have reported a consistent pattern of strong dominance of a small subset of tree species in neotropical forests. These species have been called “hyperdominant” at large geographical scales and “oligarchs” at regional‐landscape scales when being abundant and frequent. Forest community assembly is shaped by environmental factors and stochastic processes, but so far the contribution of oligarchic species to the variation of community composition (i.e., beta diversity) remains poorly known. To that end, we established 20.1‐ha plots, that is, five sites with four forest types (ridge, slope and ravine primary forest, and secondary forest) per site, in humid lowland tropical forests of southwestern Costa Rica to (a) investigate how community composition responds to differences in topography, successional stage, and distance among plots for different groups of species (all, oligarch, common and rare/very rare species) and (b) identify oligarch species characterizing changes in community composition among forest types. From a total of 485 species of trees, lianas and palms recorded in this study only 27 species (i.e., 6%) were nominated as oligarch species. Oligarch species accounted for 37% of all recorded individuals and were present in at least half of the plots. Plant community composition significantly differed among forest types, thus contributing to beta diversity at the landscape scale. Oligarch species was the component best explained by geographical and topographic variables, allowing a confident characterization of the beta diversity among tropical lowland forest stands.

  • Novel high-throughput approach to determine key processes of soil organic nitrogen cycling: Gross protein depolymerization and microbial amino acid uptake

    Noll L, zhang S, Wanek W
    2019 - Soil Biology and Biochemistry, 130: 73-81

    Abstract: 

    Proteins comprise the largest soil N reservoir but cannot be taken up directly by microorganisms and plants due to size constraints and stabilization of proteins in organo-mineral associations. Therefore the cleavage of this high molecular weight organic N to smaller soluble compounds as amino acids is a key step in the terrestrial N cycle. In the last years two isotope pool dilution approaches have been successfully established to measure gross rates of protein depolymerization and microbial amino acid uptake in soils. However, both require laborious sample preparation and analyses, which limits sample throughput. Therefore, we here present a novel isotope pool dilution approach based on the addition of 15N-labeled amino acids to soils and subsequent concentration and 15N analysis by the oxidation of α-amino groups to NO2 and further reduction to N2O, followed by purge-and-trap isotope ratio mass spectrometry (PT-IRMS). We applied this method in mesocosm experiments with forest and meadow soils as well as with a cropland soil amended with either organic C (cellulose) or organic N (bovine serum albumin). To measure direct organic N mineralization to NH4+, the latter was captured in acid traps and analyzed by an elemental analyzer coupled to an isotope ratio mass spectrometer (EA-IRMS). Our results demonstrate that the proposed method provides fast and precise measurements of at%15N even at low amino acid concentrations, allows high sample throughput and enables parallel estimations of instantaneous organic N mineralization rates.

  • Are We Speaking the Same Language? Recommendations for a Definition and Categorization Framework for Plastic Debris

    Nanna B. Hartmann, Thorsten Hüffer, Richard C. Thompson, Martin Hassellöv, Anja Verschoor, Anders E. Daugaard, Sinja Rist, Therese Karlsson, Nicole Brennholt, Matthew Cole, Maria P. Herrling, Maren C. Hess, Natalia P. Ivleva, Amy L. Lusher and Martin Wagner
    2019 - Environmental Science & Technology, 3: 1039-1047
  • Mucispirillum schaedleri antagonizes Salmonella virulence to protect mice against colitis

    Herp S, Brugiroux S, Garzetti D, Ring D, Jochum LM, Beutler M, Eberl C, Hussain S, Walter S, Gerlach RG, Ruscheweyh HJ, Huson D, Sellin ME, Slack E, Hanson B, Loy A, Baines JF, Rausch P, Basic M, Bleich A, Berry D, Stecher B
    2019 - Cell Host Microbe, In press

    Abstract: 

    The microbiota and the gastrointestinal mucus layer play a pivotal role in protection against non-typhoidal Salmonellaenterica serovar Typhimurium (S. Tm) colitis. Here, we analyzed the course of Salmonella colitis in mice lacking a functional mucus layer in the gut. Unexpectedly, in contrast to mucus-proficient littermates, genetically deficient mice were protected against Salmonella-induced gut inflammation in the streptomycin colitis model. This correlated with microbiota alterations and enrichment of the bacterial phylum Deferribacteres. Using gnotobiotic mice associated with defined bacterial consortia, we causally linked Mucispirillum schaedleri, currently the sole known representative of Deferribacteres present in the mammalian microbiota, to host protection against S. Tm colitis. Inhibition by M. schaedleri involves interference with S. Tm invasion gene expression, partly by competing for anaerobic electron acceptors. In conclusion, this study establishes M. schaedleri, a core member of the murine gut microbiota, as a key antagonist of S. Tm virulence in the gut.

  • Widespread soil bacterium that oxidizes atmospheric methane.

    Tveit AT, Hestnes AG, Robinson SL, Schintlmeister A, Dedysh SN, Jehmlich N, von Bergen M, Herbold CW, Wagner M, Richter A, Svenning MM
    2019 - Proc. Natl. Acad. Sci. U.S.A., in press

    Abstract: 

    The global atmospheric level of methane (CH), the second most important greenhouse gas, is currently increasing by ∼10 million tons per year. Microbial oxidation in unsaturated soils is the only known biological process that removes CH from the atmosphere, but so far, bacteria that can grow on atmospheric CH have eluded all cultivation efforts. In this study, we have isolated a pure culture of a bacterium, strain MG08 that grows on air at atmospheric concentrations of CH [1.86 parts per million volume (p.p.m.v.)]. This organism, named , is globally distributed in soils and closely related to uncultured members of the upland soil cluster α. CH oxidation experiments and C-single cell isotope analyses demonstrated that it oxidizes atmospheric CH aerobically and assimilates carbon from both CH and CO Its estimated specific affinity for CH (a) is the highest for any cultivated methanotroph. However, growth on ambient air was also confirmed for and , close relatives with a lower specific affinity for CH, suggesting that the ability to utilize atmospheric CH for growth is more widespread than previously believed. The closed genome of MG08 encodes a single particulate methane monooxygenase, the serine cycle for assimilation of carbon from CH and CO, and CO fixation via the recently postulated reductive glycine pathway. It also fixes dinitrogen and expresses the genes for a high-affinity hydrogenase and carbon monoxide dehydrogenase, suggesting that atmospheric CH oxidizers harvest additional energy from oxidation of the atmospheric trace gases carbon monoxide (0.2 p.p.m.v.) and hydrogen (0.5 p.p.m.v.).

  • Resolving the individual contribution of key microbial populations to enhanced biological phosphorus removal with Raman-FISH.

    Fernando EY, McIlroy SJ, Nierychlo M, Herbst FA, Petriglieri F, Schmid MC, Wagner M, Nielsen JL, Nielsen PH
    2019 - ISME J, in press

    Abstract: 

    Enhanced biological phosphorus removal (EBPR) is a globally important biotechnological process and relies on the massive accumulation of phosphate within special microorganisms. Candidatus Accumulibacter conform to the classical physiology model for polyphosphate accumulating organisms and are widely believed to be the most important player for the process in full-scale EBPR systems. However, it was impossible till now to quantify the contribution of specific microbial clades to EBPR. In this study, we have developed a new tool to directly link the identity of microbial cells to the absolute quantification of intracellular poly-P and other polymers under in situ conditions, and applied it to eight full-scale EBPR plants. Besides Ca. Accumulibacter, members of the genus Tetrasphaera were found to be important microbes for P accumulation, and in six plants they were the most important. As these Tetrasphaera cells did not exhibit the classical phenotype of poly-P accumulating microbes, our entire understanding of the microbiology of the EBPR process has to be revised. Furthermore, our new single-cell approach can now also be applied to quantify storage polymer dynamics in individual populations in situ in other ecosystems and might become a valuable tool for many environmental microbiologists.

  • An automated Raman-based platform for the sorting of live cells by functional properties.

    Lee KS, Palatinszky M, Pereira FC, Nguyen J, Fernandez VI, Mueller AJ, Menolascina F, Daims H, Berry D, Wagner M, Stocker R
    2019 - Nat Microbiol, in press

    Abstract: 

    Stable-isotope probing is widely used to study the function of microbial taxa in their natural environment, but sorting of isotopically labelled microbial cells from complex samples for subsequent genomic analysis or cultivation is still in its early infancy. Here, we introduce an optofluidic platform for automated sorting of stable-isotope-probing-labelled microbial cells, combining microfluidics, optical tweezing and Raman microspectroscopy, which yields live cells suitable for subsequent single-cell genomics, mini-metagenomics or cultivation. We describe the design and optimization of this Raman-activated cell-sorting approach, illustrate its operation with four model bacteria (two intestinal, one soil and one marine) and demonstrate its high sorting accuracy (98.3 ± 1.7%), throughput (200-500 cells h; 3.3-8.3 cells min) and compatibility with cultivation. Application of this sorting approach for the metagenomic characterization of bacteria involved in mucin degradation in the mouse colon revealed a diverse consortium of bacteria, including several members of the underexplored family Muribaculaceae, highlighting both the complexity of this niche and the potential of Raman-activated cell sorting for identifying key players in targeted processes.

  • Historical Factors Associated With Past Environments Influence the Biogeography of Thermophilic Endospores in Arctic Marine Sediments.

    Hanson CA, Müller AL, Loy A, Dona C, Appel R, Jørgensen BB, Hubert CRJ
    2019 - Front Microbiol, 245

    Abstract: 

    Selection by the local, contemporary environment plays a prominent role in shaping the biogeography of microbes. However, the importance of historical factors in microbial biogeography is more debatable. Historical factors include past ecological and evolutionary circumstances that may have influenced present-day microbial diversity, such as dispersal and past environmental conditions. Diverse thermophilic sulfate-reducing are present as dormant endospores in marine sediments worldwide where temperatures are too low to support their growth. Therefore, they are dispersed to here from elsewhere, presumably a hot, anoxic habitat. While dispersal through ocean currents must influence their distribution in cold marine sediments, it is not clear whether even earlier historical factors, related to the source habitat where these organisms were once active, also have an effect. We investigated whether these historical factors may have influenced the diversity and distribution of thermophilic endospores by comparing their diversity in 10 Arctic fjord surface sediments. Although community composition varied spatially, clear biogeographic patterns were only evident at a high level of taxonomic resolution (>97% sequence similarity of the 16S rRNA gene) achieved with oligotyping. In particular, the diversity and distribution of oligotypes differed for the two most prominent OTUs (defined using a standard 97% similarity cutoff). One OTU was dominated by a single ubiquitous oligotype, while the other OTU consisted of ten more spatially localized oligotypes that decreased in compositional similarity with geographic distance. These patterns are consistent with differences in historical factors that occurred when and where the taxa were once active, prior to sporulation. Further, the influence of history on biogeographic patterns was only revealed by analyzing microdiversity within OTUs, suggesting that populations within standard OTU-level groupings do not necessarily share a common ecological and evolutionary history.

  • Rapid Transfer of Plant Photosynthates to Soil Bacteria via Ectomycorrhizal Hyphae and Its Interaction With Nitrogen Availability.

    Gorka S, Dietrich M, Mayerhofer W, Gabriel R, Wiesenbauer J, Martin V, Zheng Q, Imai B, Prommer J, Weidinger M, Schweiger P, Eichorst SA, Wagner M, Richter A, Schintlmeister A, Woebken D, Kaiser C
    2019 - Front Microbiol, 168

    Abstract: 

    Plant roots release recent photosynthates into the rhizosphere, accelerating decomposition of organic matter by saprotrophic soil microbes ("rhizosphere priming effect") which consequently increases nutrient availability for plants. However, about 90% of all higher plant species are mycorrhizal, transferring a significant fraction of their photosynthates directly to their fungal partners. Whether mycorrhizal fungi pass on plant-derived carbon (C) to bacteria in root-distant soil areas, i.e., incite a "hyphosphere priming effect," is not known. Experimental evidence for C transfer from mycorrhizal hyphae to soil bacteria is limited, especially for ectomycorrhizal systems. As ectomycorrhizal fungi possess enzymatic capabilities to degrade organic matter themselves, it remains unclear whether they cooperate with soil bacteria by providing photosynthates, or compete for available nutrients. To investigate a possible C transfer from ectomycorrhizal hyphae to soil bacteria, and its response to changing nutrient availability, we planted young beech trees () into "split-root" boxes, dividing their root systems into two disconnected soil compartments. Each of these compartments was separated from a litter compartment by a mesh penetrable for fungal hyphae, but not for roots. Plants were exposed to a C-CO-labeled atmosphere, while N-labeled ammonium and amino acids were added to one side of the split-root system. We found a rapid transfer of recent photosynthates via ectomycorrhizal hyphae to bacteria in root-distant soil areas. Fungal and bacterial phospholipid fatty acid (PLFA) biomarkers were significantly enriched in hyphae-exclusive compartments 24 h after C-CO-labeling. Isotope imaging with nanometer-scale secondary ion mass spectrometry (NanoSIMS) allowed for the first time visualization of plant-derived C and N taken up by an extraradical fungal hypha, and in microbial cells thriving on hyphal surfaces. When N was added to the litter compartments, bacterial biomass, and the amount of incorporated C strongly declined. Interestingly, this effect was also observed in adjacent soil compartments where added N was only available for bacteria through hyphal transport, indicating that ectomycorrhizal fungi were acting on soil bacteria. Together, our results demonstrate that (i) ectomycorrhizal hyphae rapidly transfer plant-derived C to bacterial communities in root-distant areas, and (ii) this transfer promptly responds to changing soil nutrient conditions.

  • Long-term transcriptional activity at zero growth by a cosmopolitan rare biosphere member

    Hausmann B, Pelikan C, Rattei T, Loy A, Pester M
    2019 - mBio, 10: e02189-18

    Abstract: 

    Microbial diversity in the environment is mainly concealed within the rare biosphere (all species with <0.1% relative abundance). While dormancy explains a low-abundance state very well, the mechanisms leading to rare but active microorganisms remain elusive. We used environmental systems biology to genomically and transcriptionally characterise Candidatus Desulfosporosinus infrequens, a low-abundance sulfate-reducing microorganism cosmopolitan to freshwater wetlands, where it contributes to cryptic sulfur cycling. We obtained its near-complete genome by metagenomics of acidic peat soil. In addition, we analyzed anoxic peat soil incubated under in situ-like conditions for 50 days by Desulfosporosinus-targeted qPCR and metatranscriptomics. The Desulfosporosinus population stayed at a constant low abundance under all incubation conditions, averaging 1.2 × 10⁶ 16S rRNA gene copies per cm³ soil. In contrast, transcriptional activity of Ca.D. infrequens increased at day 36 by 56- to 188-fold when minor amendments of acetate, propionate, lactate, or butyrate were provided with sulfate, as compared to the no-substrate-control. Overall transcriptional activity was driven by expression of genes encoding ribosomal proteins, energy metabolism and stress response but not by expression of genes encoding cell growth-associated processes. Since our results did not support growth of these highly active microorganisms in terms of biomass increase or cell division, they had to invest their sole energy for maintenance, most likely counterbalancing acidic pH conditions. This finding explains how a rare biosphere member can contribute to a biogeochemically relevant process while remaining in a zero growth state over a period of 50 days.

  • Plasmid DNA contaminant in molecular reagents.

    Wally N, Schneider M, Thannesberger J, Kastner MT, Bakonyi T, Indik S, Rattei T, Bedarf J, Hildebrand F, Law J, Jovel J, Steininger C
    2019 - Sci Rep, 1: 1652

    Abstract: 

    Background noise in metagenomic studies is often of high importance and its removal requires extensive post-analytic, bioinformatics filtering. This is relevant as significant signals may be lost due to a low signal-to-noise ratio. The presence of plasmid residues, that are frequently present in reagents as contaminants, has not been investigated so far, but may pose a substantial bias. Here we show that plasmid sequences from different sources are omnipresent in molecular biology reagents. Using a metagenomic approach, we identified the presence of the (pol) of equine infectious anemia virus in human samples and traced it back to the expression plasmid used for generation of a commercial reverse transcriptase. We found fragments of multiple other expression plasmids in human samples as well as commercial polymerase preparations. Plasmid contamination sources included production chain of molecular biology reagents as well as contamination of reagents from environment or human handling of samples and reagents. Retrospective analyses of published metagenomic studies revealed an inaccurate signal-to-noise differentiation. Hence, the plasmid sequences that seem to be omnipresent in molecular biology reagents may misguide conclusions derived from genomic/metagenomics datasets and thus also clinical interpretations. Critical appraisal of metagenomic data sets for the possibility of plasmid background noise is required to identify reliable and significant signals.

  • Dark aerobic sulfide oxidation by anoxygenic phototrophs in anoxic waters.

    Berg JS, Pjevac P, Sommer T, Buckner CRT, Philippi M, Hach PF, Liebeke M, Holtappels M, Danza F, Tonolla M, Sengupta A, Schubert CJ, Milucka J, Kuypers MMM
    2019 - Environ. Microbiol., in press

    Abstract: 

    Anoxygenic phototrophic sulfide oxidation by green and purple sulfur bacteria (PSB) plays a key role in sulfide removal from anoxic shallow sediments and stratified waters. Although some PSB can also oxidize sulfide with nitrate and oxygen, little is known about the prevalence of this chemolithotrophic lifestyle in the environment. In this study, we investigated the role of these phototrophs in light-independent sulfide removal in the chemocline of Lake Cadagno. Our temporally resolved, high-resolution chemical profiles indicated that dark sulfide oxidation was coupled to high oxygen consumption rates of ~9 μM O ·h . Single-cell analyses of lake water incubated with CO in the dark revealed that Chromatium okenii was to a large extent responsible for aerobic sulfide oxidation and it accounted for up to 40 % of total dark carbon fixation. The genome of Chr. okenii reconstructed from the Lake Cadagno metagenome confirms its capacity for microaerophilic growth and provides further insights into its metabolic capabilities. Moreover, our genomic and single-cell data indicated that other PSB grow microaerobically in these apparently anoxic waters. Altogether, our observations suggest that aerobic respiration may not only play an underappreciated role in anoxic environments, but also that organisms typically considered strict anaerobes may be involved. This article is protected by copyright. All rights reserved.

  • Surface-enhanced Raman spectroscopy of microorganisms: limitations and applicability on the single-cell level.

    Weiss R, Palatinszky M, Wagner M, Niessner R, Elsner M, Seidel M, Ivleva NP
    2019 - Analyst, 3: 943-953
    Raman single cell isotope imaging

    Abstract: 

    Detection and characterization of microorganisms is essential for both clinical diagnostics and environmental studies. An emerging technique to analyse microbes at single-cell resolution is surface-enhanced Raman spectroscopy (surface-enhanced Raman scattering: SERS). Optimised SERS procedures enable fast analytical read-outs with specific molecular information, providing insight into the chemical composition of microbiological samples. Knowledge about the origin of microbial SERS signals and parameter(s) affecting their occurrence, intensity and/or reproducibility is crucial for reliable SERS-based analyses. In this work, we explore the feasibility and limitations of the SERS approach for characterizing microbial cells and investigate the applicability of SERS for single-cell sorting as well as for three-dimensional visualization of microbial communities. Analyses of six different microbial species (an archaeon, two Gram-positive bacteria, three Gram-negative bacteria) showed that for several of these organisms distinct features in their SERS spectra were lacking. As additional confounding factor, the physiological conditions of the cells (as influenced by e.g., storage conditions or deuterium-labelling) were systematically addressed, for which we conclude that the respective SERS signal at the single-cell level is strongly influenced by the metabolic activity of the analysed cells. While this finding complicates the interpretation of SERS data, it may on the other hand enable probing of the metabolic state of individual cells within microbial populations of interest.

  • Cyanate and urea are substrates for nitrification by Thaumarchaeota in the marine environment.

    Kitzinger K, Padilla CC, Marchant HK, Hach PF, Herbold CW, Kidane AT, Könneke M, Littmann S, Mooshammer M, Niggemann J, Petrov S, Richter A, Stewart FJ, Wagner M, Kuypers MMM, Bristow LA
    2019 - Nat Microbiol, 2: 234-243
    Cyanate use by thaumarchaeota

    Abstract: 

    Ammonia-oxidizing archaea of the phylum Thaumarchaeota are among the most abundant marine microorganisms. These organisms thrive in the oceans despite ammonium being present at low nanomolar concentrations. Some Thaumarchaeota isolates have been shown to utilize urea and cyanate as energy and N sources through intracellular conversion to ammonium. Yet, it is unclear whether patterns observed in culture extend to marine Thaumarchaeota, and whether Thaumarchaeota in the ocean directly utilize urea and cyanate or rely on co-occurring microorganisms to break these substrates down to ammonium. Urea utilization has been reported for marine ammonia-oxidizing communities, but no evidence of cyanate utilization exists for marine ammonia oxidizers. Here, we demonstrate that in the Gulf of Mexico, Thaumarchaeota use urea and cyanate both directly and indirectly as energy and N sources. We observed substantial and linear rates of nitrite production from urea and cyanate additions, which often persisted even when ammonium was added to micromolar concentrations. Furthermore, single-cell analysis revealed that the Thaumarchaeota incorporated ammonium-, urea- and cyanate-derived N at significantly higher rates than most other microorganisms. Yet, no cyanases were detected in thaumarchaeal genomic data from the Gulf of Mexico. Therefore, we tested cyanate utilization in Nitrosopumilus maritimus, which also lacks a canonical cyanase, and showed that cyanate was oxidized to nitrite. Our findings demonstrate that marine Thaumarchaeota can use urea and cyanate as both an energy and N source. On the basis of these results, we hypothesize that urea and cyanate are substrates for ammonia-oxidizing Thaumarchaeota throughout the ocean.

Book chapters and other publications

2 Publications found
  • Mikrobiome – Wissensstand und Perspektiven

    Wagner M
    2019 - 17-29. in Die unbekannte 
Welt der Mikrobiome; Rundgespräche Forum Ökologie Bd. 47. (Bauer J & von Mutius E). Bayerische Akademie der Wissenschaften; Verlag Dr. Friedrich Pfeil
  • Up-close-and-personal with the human microbiome

    Berry D
    2019 - Environ Microbiol Rep, 1: 17-19
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