Metamenu

Publications

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Publications in peer reviewed journals

101 Publications found
  • In situ observation of localized, sub-mm scale changes of phosphorus biogeochemistry in the rhizosphere

    Kreuzeder A, Santner J, Scharsching V, Oburger E, Hoefer C, Hann S, Wenzel WW
    2018 - Plant and Soil, 1-17

    Abstract: 

    Aims We imaged the sub-mm distribution of labile P and pH in the rhizosphere of three plant species to localize zones and hot spots of P depletion and accumulation along individual root axes and to relate our findings to nutrient acquisition / root exudation strategies in P-limited conditions at different soil pH, and to mobilization pattern of other elements (Al, Fe, Ca, Mg, Mn) in the rhizosphere. Methods Sub-mm distributions of labile elemental patterns were sampled using diffusive gradients in thin films and analysed using laser ablation inductively coupled plasma mass spectrometry. pH images were taken using planar optodes. Results We found distinct patterns of highly localized labile P depletion and accumulation reflecting the complex interaction of plant P acquisition strategies with soil pH, fertilizer treatment, root age, and elements (Al, Fe, Ca) that are involved in P biogeochemistry in soil. We show that the plants respond to P deficiency either by acidification or alkalization, depending on initial bulk soil pH and other factors of P solubility. Conclusions P solubilization activities of roots are highly localized, typically around root apices, but may also extend towards the extension / root hair zone.

  • Environmental fate of nanopesticides: durability, sorption and photodegradation of nanoformulated clothianidin

    Melanie Kah, Helene Walch, Thilo Hofmann
    2018 - Environmental Science: Nano, 4: 882-889

    Abstract: 

    A lot of research efforts are currently dedicated to the development of nano-enabled agrochemicals. Knowledge about their environmental behaviour is however scarce, which impedes the assessment of the new risk and benefits relative to currently used agrochemicals. With the aim to advance our understanding of the fate of nanopesticides in the environment and support the development of robust exposure assessment procedures, the main objectives of the study were to (i) investigate the extent to which three nanoformulations can affect the photodegradation and sorption of the insecticide clothianidin, and (ii) evaluate various approaches to estimate durability, a key parameter for the exposure assessment of nanopesticides. The nanoformulations increased the photodegradation half-life in water by a maximum of 21% relative to the conventional formulation. Sorption to soil was investigated by two methods and over time, and results show that sorption was increased by up to 51% and 10%, relative to unformulated clothianidin and the commercial formulation, respectively. Our results generally indicate that nanoformulations may have a greater impact on the fate of pesticide active ingredients than commercial formulations. It is important to note however that differences in fate parameters were generally very moderate, including in realistic worst-case conditions (high pesticide concentration and ionic strength). Our results collectively suggest that clothianidin was rapidly released from the nanocarrier systems and that the durability of the three nanoformulations would be short in water as well as in soil environments (including under realistic soil to solution ratio). The durability of nanoformulations after their application in the environment is an essential parameter that needs to be characterised for the development as well as for the evaluation of nano-enabled agrochemicals. This study illustrates how performances of nano-enabled products can be critically benchmarked against existing products to support an objective assessment of new environmental risks and benefits. In this context, the fate of the nanocarrier system is of great interest and should be the topic of further research.

  • Mechanisms of (photo)toxicity of TiO2 nanomaterials (NM103, NM104, NM105): using high-throughput gene expression in Enchytraeus crypticus

    Susana I. L. Gomes, Carlos P. Roca, Frank von der Kammer, Janeck J. Scott-Fordsmand, Mónica J. B. Amorim
    2018 - Nanoscale, 10: 21960-21970

    Abstract: 

    Titanium dioxide (TiO2) based nanomaterials (NMs) are among the most produced NMs worldwide. When irradiated with light, particularly UV, TiO2 is photoactive, a property that is explored for several purposes. There are an increasing number of reports on the negative effects of photoactivated TiO2 on non-target organisms. We have here studied the effect of a suite of reference type TiO2 NMs (i.e. NM103, NM104, and NM105 and compared these to the bulk) with and without UV radiation to the oligochaete Enchytraeus crypticus. High-throughput gene expression was used to assess the molecular mechanisms, while also anchoring it to the known effects at the organism level (i.e., reproduction). Results showed that the photoactivity of TiO2 (UV exposed) played a major role in enhancing TiO2 toxicity, activating the transcription of oxidative stress, lysosome damage and apoptosis mechanisms. For non-UV activated TiO2, where toxicity at the organism level (reproduction) was lower, results showed potential for long-term effects (i.e., mutagenic and epigenetic). NM specific mechanisms were identified: NM103 affected transcription and translation, NM104_UV negatively affected the reproductive system/organs, and NM105_UV activated superoxide anion response. Results provided mechanistic information on UV-related phototoxicity of TiO2 materials and evidence for the potential long-term effects.

  • A bacterial pioneer produces cellulase complexes that persist through community succession

    Kolinko S, Wu YW, Tachea F, Denzel E, Hiras J, Gabriel R, Bäcker N, Chan LJG, Eichorst SA, Frey D, Chen Q, Azadi P, Adams PD, Pray TR, Tanjore D, Petzold CJ, Gladden JM, Simmons BA, Singer SW
    2018 - Nat Microbiol, 3: 99-107
  • Recognizing Patterns: Spatial Analysis of Observed Microbial Colonization on Root Surfaces

    Schmidt H, Nunan N, Höck A, Eickhorst T, Kaiser C, Woebken D, Xaynaud X
    2018 - Front Environ Sci, 6: 1-12

    Abstract: 

    Root surfaces are major sites of interactions between plants and associated microorganisms. Here, plants and microbes communicate via signaling molecules, compete for nutrients, and release substrates that may have beneficial or harmful effects on each other. Whilst the body of knowledge on the abundance and diversity of microbial communities at root-soil interfaces is now substantial, information on their spatial distribution at the microscale is still scarce.

    In this study, a standardized method for recognizing and analyzing microbial cell distributions on root surfaces is presented. Fluorescence microscopy was combined with automated image analysis and spatial statistics to explore the distribution of bacterial colonization patterns on rhizoplanes of rice roots. To test and evaluate the presented approach, a gnotobiotic experiment was performed using a potential nitrogen-fixing bacterial strain in combination with roots of wetland rice. 

    The automated analysis procedure resulted in reliable spatial data of bacterial cells colonizing the rhizoplane. Among all replicate roots, the analysis revealed an increasing density of bacterial cells from the root tip to the region of root cell maturation. Moreover, bacterial cells showed significant spatial clustering and tended to be located around plant root cell walls. The quantitative data suggest that the structure of the root surface plays a major role in bacterial colonization patterns. 

    Possible adaptations of the presented approach for future studies are discussed along with potential pitfalls such as inaccurate imaging. Our results demonstrate that standardized recognition and statistical evaluation of microbial colonization on root surfaces holds the potential to increase our understanding of microbial associations with roots and of the underlying ecological interactions.

  • Sorption of organic compounds by aged polystyrene microplastic particles

    Thorsten Hüffer, Anne-Katrin Weniger, Thilo Hofmann
    2018 - Environmental Pollution, 218-225

    Abstract: 

    Microplastics that are released into the environment undergo aging and interact with other substances such as organic contaminants. Understanding the sorption interactions between aged microplastics and organic contaminants is therefore essential for evaluating the impact of microplastics on the environment. There is little information available on how the aging of microplastics affects their sorption behavior and other properties. We have therefore investigated the effects of an accelerated UV-aging procedure on polystyrene microplastics, which are used in products such as skin cleaners and foams. Physical and chemical particle characterizations showed that aging led to significant surface oxidation and minor localized microcrack formation. Sorption coefficients of organic compounds by polystyrene microplastics following aging were up to one order of magnitude lower than for pristine particles. Sorption isotherms were experimentally determined using a diverse set of probe sorbates covering a variety of substance classes allowing an in-depth evaluation of the poly-parameter linear free-energy relationship (ppLFER) modelling used to investigate the contribution of individual molecular interactions to overall sorption. The ppLFER modelling was validated using internal cross-validation, which confirmed its robustness. This approach therefore yields improved estimates of the interactions between aged polystyrene microplastics and organic contaminants.

  • Emission and fate modelling framework for engineered nanoparticles in urban aquatic systems at high spatial and temporal resolution

    Prado Domercq, Antonia Praetorius, Alistair B. A. Boxall
    2018 - Environmental Science: Nano, 2: 533-543

    Abstract: 

    Trends in global urbanization and technology development have raised concerns about the associated increase in emissions to the environment, including novel contaminants such as engineered nanoparticles (ENPs). The assessment of these emissions in urban systems requires modelling approaches that integrate the complexity of urban environments as well as the high spatial and temporal variability of contaminant emissions. ENPs are emitted to urban surface waters through a variety of point and diffuse sources, with these emissions being driven by weather, usage patterns and population density. While the potential environmental and health impacts of ENPs are still not fully understood, understanding the spatial and temporal distribution of ENPs at the local scale will help to inform risk assessment. In this paper, we propose a novel modelling approach for estimating the exposure of ENPs in surface waters of urban systems. An integrative modelling framework combining an emission and a fate model for ENPs with high spatial and temporal resolution is presented and strategies for data gathering and the handling of knowledge gaps are discussed. Our framework is capable of identifying local emission hot spots and predicting exposure across a city, while generating information on the final speciation of the emitted ENPs (nano form, aggregates and other transformation products) within the studied environmental compartments over time.

  • Geothermally warmed soils reveal persistent increases in the respiratory costs of soil microbes contributing to substantial C losses

    Marañon-Jimenez S, Soong JL, Leblans NI, Sigurdsson B, Peñuelas J, Richter A, Asensio D, Fransen E, Janssens IA
    2018 - 138: 245-260

    Abstract: 

    Increasing temperatures can accelerate soil organic matter decomposition and release large amounts of CO2 to the atmosphere, potentially inducing positive warming feedbacks. Alterations to the temperature sensitivity and physiological functioning of soil microorganisms may play a key role in these carbon (C) losses. Geothermally active areas in Iceland provide stable and continuous soil temperature gradients to test this hypothesis, encompassing the full range of warming scenarios projected by the Intergovernmental Panel on Climate Change for the northern region. We took soils from these geothermal sites 7 years after the onset of warming and incubated them at varying temperatures and substrate availability conditions to detect persistent alterations of microbial physiology to long-term warming. Seven years of continuous warming ranging from 1.8 to 15.9 °C triggered a 8.6–58.0% decrease on the C concentrations in the topsoil (0–10 cm) of these sub-arctic silt-loam Andosols. The sensitivity of microbial respiration to temperature (Q10) was not altered. However, soil microbes showed a persistent increase in their microbial metabolic quotients (microbial respiration per unit of microbial biomass) and a subsequent diminished C retention in biomass. After an initial depletion of labile soil C upon soil warming, increasing energy costs of metabolic maintenance and resource acquisition led to a weaker capacity of C stabilization in the microbial biomass of warmer soils. This mechanism contributes to our understanding of the acclimated response of soil respiration to in situ soil warming at the ecosystem level, despite a lack of acclimation at the physiological level. Persistent increases in the respiratory costs of soil microbes in response to warming constitute a fundamental process that should be incorporated into climate change-C cycling models.

  • Resistance of soil protein depolymerization rates to eight years of elevated CO2, warming, and summer drought in a temperate heathland

    Wild B, Ambus P, Reinsch S, Richter A
    2018 - 140: 255-267

    Abstract: 

    Soil N availability for plants and microorganisms depends on the breakdown of soil polymers such as proteins into smaller, assimilable units by microbial extracellular enzymes. Changing climatic conditions are expected to alter protein depolymerization rates over the next decades, and thereby affect the potential for plant productivity. We here tested the effect of increased CO2 concentration, temperature, and drought frequency on gross rates of protein depolymerization, N mineralization, microbial amino acid and ammonium uptake using 15N pool dilution assays. Soils were sampled in fall 2013 from the multifactorial climate change experiment CLIMAITE that simulates increased CO2 concentration, temperature, and drought frequency in a fully factorial design in a temperate heathland. Eight years after treatment initiation, we found no significant effect of any climate manipulation treatment, alone or in combination, on protein depolymerization rates. Nitrogen mineralization, amino acid and ammonium uptake showed no significant individual treatment effects, but significant interactive effects of warming and drought. Combined effects of all three treatments were not significant for any of the measured parameters. Our findings therefore do not suggest an accelerated release of amino acids from soil proteins in a future climate at this site that could sustain higher plant productivity.

  • Tire wear particles in the aquatic environment - A review on generation, analysis, occurrence, fate and effects

    Wagner S, Thorsten Hüffer, Klöckner P, Wehrhahn M, Thilo Hofmann, Reemtsma T
    2018 - Water Research, 83-100

    Abstract: 

    Tire wear particles (TWP), generated from tire material during use on roads have gained increasing attention as part of organic particulate contaminants, such as microplastic, in aquatic environments. The available information on properties and generation of TWP, analytical techniques to determine TWP, emissions, occurrence and behavior and ecotoxicological effects of TWP are reviewed with a focus on surface water as a potential receptor. TWP emissions are traffic related and contribute 5–30% to non-exhaust emissions from traffic. The mass of TWP generated is estimated at 1,327,000 t/a for the European Union, 1,120,000 t/a for the United States and 133,000 t/a for Germany. For Germany, this is equivalent to four times the amount of pesticides used. The mass of TWP ultimately entering the aquatic environment strongly depends on the extent of collection and treatment of road runoff, which is highly variable. For the German highways it is estimated that up to 11,000 t/a of TWP reach surface waters. Data on TWP concentrations in the environment, including surface waters are fragmentary, which is also due to the lack of suitable analytical methods for their determination. Information on TWP properties such as density and size distribution are missing; this hampers assessing the fate of TWP in the aquatic environment. Effects in the aquatic environment may stem from TWP itself or from compounds released from TWP. It is concluded that reliable knowledge on transport mechanism to surface waters, concentrations in surface waters and sediments, effects of aging, environmental half-lives of TWP as well as effects on aquatic organisms are missing. These aspects need to be addressed to allow for the assessment of risk of TWP in an aquatic environment.

  • Comparison of Sorption to Carbon-Based Materials and Nanomaterials Using Inverse Liquid Chromatography

    Florian Metzelder, Matin Funck, Thorsten Hüffer, Torsten C. Schmidt
    2018 - Environmental Science & Technology, 1: 9731-9740

    Abstract: 

    Sorption studies of carbon-based materials and nanomaterials are typically conducted using batch experiments, but the analysis of weakly sorbing compounds may be challenging. Column chromatography represents a promising complement as higher sorbent to solution ratios can be applied. The sorbent is packed in a column, and sorption data are calculated by relating sorbate retention times to that of a nonretarded tracer. In this study, sorption of heterocyclic organic compounds (pyrazole, pyrrole, furan, and thiophene) by carbon-based materials (activated carbon, biochar, and graphite) and nanomaterials (functionalized carbon nanotubes and graphene platelets) was compared for the first time using column chromatography. D2O was used as nonretarded tracer. Sorption isotherms were nonlinear and described well by the Freundlich model. Sorption differed between the materials regarding determined Freundlich coefficients (Kf) by more than two orders of magnitude for isotherms in a similar concentration range. Normalization of Kf with the surface area of the sorbent significantly reduced but did not remove the differences between the sorbents. Overall, column chromatography represents the opportunity to study sorption of weakly sorbing compounds to diverse carbon-based sorbent materials with a single experimental approach, which is challenging in batch experiments because of the very different sorption properties of some sorbent materials.

  • Amino acid production exceeds plant nitrogen demand in Siberian tundra

    Wild B, Alves RJE, Barta J, Capek P, Gentsch N, Guggenberger G, Hugelius G, Knoltsch A, Kuhry P, Lashchinskiy N, Mikutta R, Palmtag J, Prommer J, Schnecker J, Shibistova O, Takriti M, Urich T, Richter A
    2018 - Environmental Research Letters, 13: 11

    Abstract: 

    Arctic plant productivity is often limited by low soil N availability. This has been attributed to slow breakdown of N-containing polymers in litter and soil organic matter (SOM) into smaller, available units, and to shallow plant rooting constrained by permafrost and high soil moisture. Using 15N pool dilution assays, we here quantified gross amino acid and ammonium production rates in 97 active layer samples from four sites across the Siberian Arctic. We found that amino acid production in organic layers alone exceeded literature-based estimates of maximum plant N uptake 17-fold and therefore reject the hypothesis that arctic plant N limitation results from slow SOM breakdown. High microbial N use efficiency in organic layers rather suggests strong competition of microorganisms and plants in the dominant rooting zone. Deeper horizons showed lower amino acid production rates per volume, but also lower microbial N use efficiency. Permafrost thaw together with soil drainage might facilitate deeper plant rooting and uptake of previously inaccessible subsoil N, and thereby promote plant productivity in arctic ecosystems. We conclude that changes in microbial decomposer activity, microbial N utilization and plant root density with soil depth interactively control N availability for plants in the Arctic.

  • Spatial variation of soil CO2, CH4 and N2O fluxes across topographical positions in the tropical forests of the Guiana Shield

    Courtois EA, Stahl C, Van den Berge J, Bréchet L, Van Langenhove L, Richter A, Urbina I, Soong JL, Peñuelas J, Janssens IA
    2018 - Ecosystems, 7: 1445-1458

    Abstract: 

    The spatial variation of soil greenhouse gas fluxes (GHG; carbon dioxide—CO2, methane—CH4and nitrous oxide—N2O) remains poorly understood in highly complex ecosystems such as tropical forests. We used 240 individual flux measurements of these three GHGs from different soil types, at three topographical positions and in two extreme hydric conditions in the tropical forests of the Guiana Shield (French Guiana, South America) to (1) test the effect of topographical positions on GHG fluxes and (2) identify the soil characteristics driving flux variation in these nutrient-poor tropical soils. Surprisingly, none of the three GHG flux rates differed with topographical position. CO2 effluxes covaried with soil pH, soil water content (SWC), available nitrogen and total phosphorus. The CH4 fluxes were best explained by variation in SWC, with soils acting as a sink under drier conditions and as a source under wetter conditions. Unexpectedly, our study areas were generally sinks for N2O and N2O fluxes were partly explained by total phosphorus and available nitrogen concentrations. This first study describing the spatial variation of soil fluxes of the three main GHGs measured simultaneously in forests of the Guiana Shield lays the foundation for specific studies of the processes underlying the observed patterns.

  • Microbial temperature sensitivity and biomass change explain soil carbon loss with warming

    Walker TWN, Kaiser C, Strasser F, Herbold CW, Leblans NIW, Woebken D, Janssens IA, Sigurdsson BD, Richter A
    2018 - Nature Climate Change, 9: in press

    Abstract: 

    Soil microorganisms control carbon losses from soils to the atmosphere, yet their responses to climate warming are often short-lived and unpredictable. Two mechanisms, microbial acclimation and substrate depletion, have been proposed to explain temporary warming effects on soil microbial activity. However, empirical support for either mechanism is unconvincing. Here we used geothermal temperature gradients (>50 years of field warming) and a short-term experiment to show that microbial activity (gross rates of growth, turnover, respiration and carbon uptake) is intrinsically temperature sensitive and does not acclimate to warming (+6 °C) over weeks or decades. Permanently accelerated microbial activity caused carbon loss from soil. However, soil carbon loss was temporary because substrate depletion reduced microbial biomass and constrained the influence of microbes over the ecosystem. A microbial biogeochemical model showed that these observations are reproducible through a modest, but permanent, acceleration in microbial physiology. These findings reveal a mechanism by which intrinsic microbial temperature sensitivity and substrate depletion together dictate warming effects on soil carbon loss via their control over microbial biomass. We thus provide a framework for interpreting the links between temperature, microbial activity and soil carbon loss on timescales relevant to Earth’s climate system.

  • Structure and reactivity of oxalate surface complexes on lepidocrocite derived from infrared spectroscopy, DFT-calculations, adsorption, dissolution and photochemical experiments

    Susan C. Borowski, Jagannath Biswakarma, Kyounglim Kang, Walter D.C. Schenkeveld, Janet G. Hering, James D. Kubicki, Stephan M. Kraemer, Stephan J. Hug
    2018 - Geochimica et Cosmochimica Acta, 244-262

    Abstract: 

    Oxalate, together with other ligands, plays an important role in the dissolution of iron(hdyr)oxides and the bio-availability of iron. The formation and properties of oxalate surface complexes on lepidocrocite were studied with a combination of infrared spectroscopy (IR), density functional theory (DFT) calculations, dissolution, and photochemical experiments. IR spectra measured as a function of time, concentration, and pH (50–200 µM oxalate, pH 3–7) showed that several surface complexes are formed at different rates and in different proportions. Measured spectra could be separated into three contributions described by Gaussian line shapes, with frequencies that agreed well with the theoretical frequencies of three different surface complexes: an outer-sphere complex (OS), an inner-sphere monodentate mononuclear complex (MM), and a bidentate mononuclear complex (BM) involving one O atom from each carboxylate group. At pH 6, OS was formed at the highest rate. The contribution of BM increased with decreasing pH. In dissolution experiments, lepidocrocite was dissolved at rates proportional to the surface concentration of BM, rather than to the total adsorbed concentration. Under UV-light (365 nm), BM was photolyzed at a higher rate than MM and OS. Although the comparison of measured spectra with calculated frequencies cannot exclude additional possible structures, the combined results allowed the assignment of three main structures with different reactivities consistent with experiments. The results illustrate the importance of the surface speciation of adsorbed ligands in dissolution and photochemical reactions.

  • Low Fe(II) Concentrations Catalyze the Dissolution of Various Fe(III) (hydr)oxide Minerals in the Presence of Diverse Ligands and over a Broad pH Range

    Kyounglim Kang, Walter D. C. Schenkeveld, Jagannath Biswakarma, Susan C. Borowski, Stephan J. Hug, Janet G. Hering, Stephan M. Kraemer
    2018 - Environmental Science & Technology, 1: 98-107

    Abstract: 

    Dissolution of Fe(III) (hydr)oxide minerals by siderophores (i.e., Fe-specific, biogenic ligands) is an important step in Fe acquisition in environments where Fe availability is low. The observed coexudation of reductants and ligands has raised the question of how redox reactions might affect ligand-controlled (hydr)oxide dissolution and Fe acquisition. We examined this effect in batch dissolution experiments using two structurally distinct ligands (desferrioxamine B (DFOB) and N,N′-di(2-hydroxybenzyl)ethylene-diamine-N,N′-diacetic acid (HBED)) and four Fe(III) (hydr)oxide minerals (lepidocrocite, 2-line ferrihydrite, goethite and hematite) over an environmentally relevant pH range (4–8.5). The experiments were conducted under anaerobic conditions with varying concentrations of (adsorbed) Fe(II) as the reductant. We observed a catalytic effect of Fe(II) on ligand-controlled dissolution even at submicromolar Fe(II) concentrations with up to a 13-fold increase in dissolution rate. The effect was larger for HBED than for DFOB. It was observed for all four Fe(III) (hydr)oxide minerals, but it was most pronounced for goethite in the presence of HBED. It was observed over the entire pH range with the largest effect at pH 7 and 8.5, where Fe deficiency typically occurs. The occurrence of this catalytic effect over a range of environmentally relevant conditions and at very low Fe(II) concentrations suggests that redox-catalyzed, ligand-controlled dissolution may be significant in biological Fe acquisition and in redox transition zones.

  • Significant release and microbial utilization of amino sugars and D-amino acid enantiomers from microbial cell wall decomposition in soils

    Hu Y, Zheng Q, zhang S, Noll L, Wanek W
    2018 - Soil Biology and Biochemistry, 123: 115-125

    Abstract: 

    Amino sugars and d-amino acid enantiomers are major components of bacterial and fungal cell walls (i.e. peptidoglycan and chitin) and are often used as biomarkers of microbial residue turnover in soils. However, little is known about the in situ decomposition rates of microbial cell wall residues and how soil physicochemical propertiesaffect this process. In this study, we investigated the in situ gross production and consumption rates of free amino sugars (glucosamine and muramic acid) and amino acids (meso-diaminopimelic acid, l-alanine, and d-alanine) by a novel isotope pool dilution assay using 15N-labeled amino compounds. Soils were obtained from six sites differing in land management (cropland, pasture, and forest) and bedrock (silicate and limestone) and incubated at three temperatures (5, 15, and 25 °C). Free glucosamine released during the decomposition of peptidoglycan and chitin contributed significantly to the extractable soil organic nitrogen pool. Gross production and consumption rates of glucosamine were higher than those of individual amino acids, i.e. L- and d-alanine. Muramic acid had a longer mean residence time (68 h compared to 2.7 h for glucosamine, L- and d-alanine) and made a negligible contribution to soil organic nitrogen fluxes, indicating that free muramic acid was not a major decomposition product of peptidoglycan in soils. Meso-diaminopimelic acid and d-alanine exhibited comparable gross production and consumption rates with l-alanine. These amino acids can be used as indicators to estimate the decomposition of peptidoglycan from bacterial cell wall residues. We found that chitin decomposition was greater in silicate soils, while peptidoglycan decomposition dominated in limestone soils. Glucosamine production rates were not correlated with soil total amino sugars, microbial community structure, or hydrolytic enzyme activities, but were highest in soils with low pH and high sand content, indicating that soil texture and soil pH may strongly influence the decomposition of amino sugar polymers. In contrast, mDAP, L- and d-alanine gross production and consumption rates were positively correlated with soil pH and clay content, due to greater depolymerization of peptidoglycan stem peptides in limestone soils. This isotope pool dilution approach strongly improves our understanding of the mechanisms and environmental controls on microbial cell wall decomposition in soils.

  • Transformations of Nanoenabled Copper Formulations Govern Release, Antifungal Effectiveness, and Sustainability throughout the Wood Protection Lifecycle

    Daniele Pantano, Nicole Neubauer, Jana Navratilova, Lorette Scifo, Chiara Civardi, Vicki Stone, Frank von der Kammer, Philipp Müller, Marcos Sanles Sobrido, Bernard Angeletti, Jerome Rose, Wendel Wohlleben
    2018 - Environmental Science & Technology, 3: 1128-1138

    Abstract: 

    Here we compare the standard European benchmark of wood treatment by molecularly dissolved copper amine (Cu–amine), also referred to as aqueous copper amine (ACA), against two nanoenabled formulations: copper(II)oxide nanoparticles (CuO NPs) in an acrylic paint to concentrate Cu as a barrier on the wood surface, and a suspension of micronized basic copper carbonate (CuCO3·Cu(OH)2) for wood pressure treatment. After characterizing the properties of the (nano)materials and their formulations, we assessed their effects in vitro against three fungal species: Coniophora puteana, Gloeophyllum trabeum, and Trametes versicolor, finding them to be mediated only partially by ionic transformation. To assess the use phase, we quantify both release rate and form. Cu leaching rates for the two types of impregnated wood (conventional and nanoenabled) are not significantly different at 172 ± 6 mg/m2, with Cu being released predominantly in ionic form. Various simulations of outdoor aging with release sampling by runoff, during condensation, by different levels of mechanical shear, all resulted in comparable form and rate of release from the nanoenabled or the molecular impregnated woods. Because of dissolving transformations, the nanoenabled impregnation does not introduce additional concern over and above that associated with the traditional impregnation. In contrast, Cu released from wood coated with the CuO acrylate contained particles, but the rate was at least 100-fold lower. In the same ranking, the effectiveness to protect against the wood-decaying basidiomycete Coniophora puteana was significant with both impregnation technologies but remained insignificant for untreated wood and wood coated by the acrylic CuO. Accordingly, a lifecycle-based sustainability analysis indicates that the CuO acrylic coating is less sustainable than the technological alternatives, and should not be developed into a commercial product.

  • Food supply and size class depending variations in phytodetritus intake in the benthic foraminifer Ammonia tepida

    Wukovits J, Bukenberger P, Enge AJ, Gerg M, Wanek W, Heinz P
    2018 - 4: 10

    Abstract: 

    Ammonia tepida is a common and abundant benthic foraminifer in intertidal mudflats. Benthic foraminifera are primary consumers and detritivores and act as key players in sediment nutrient fluxes. In this study, laboratory feeding experiments using isotope-labeled phytodetritus were carried out with A. tepida collected at the German Wadden Sea, to investigate the response of A. tepida to varying food supply. Feeding mode (single pulse, constant feeding; different incubation temperatures) caused strong variations in cytoplasmic carbon and nitrogen cycling, suggesting generalistic adaptations to variations in food availability. To study the influence of intraspecific size to foraminiferal carbon and nitrogen cycling, three size fractions (125-250 mu m, 250-355 mu m, >355 mu m) of A. tepida specimens were separated. Small individuals showed higher weight specific intake for phytodetritus, especially for phytodetrital nitrogen, highlighting that size distribution within foraminiferal populations is relevant to interpret foraminiferal carbon and nitrogen cycling. These results were used to extrapolate the data to natural populations of living A. tepida in sediment cores, demonstrating the impact of high abundances of small individuals on phytodetritus processing and nutrient cycling. It is estimated that at high abundances of individuals in the 125-250 mu m size fraction, Ammonia populations can account for more than 11% of phytodetritus processing in intertidal benthic communities.

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

    Thorsten Hüffer, Stephan Wagner, Thorsten Reemtsma, Thilo Hofmann
    2018 - TrAC Trends in Analytical Chemistry, 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.

  • Full 15N tracer accounting to revisit major assumptions of 15N isotope pool dilution approaches for gross nitrogen mineralization

    Braun J, Mooshammer M, Wanek W, Prommer J, Walker TWN, Rütting T, Richter A
    2018 - Soil Biology and Biochemistry, 117: 16-26
  • Metaproteogenomic profiling of microbial communities colonizing actively venting hydrothermal chimneys

    Pjevac P, Meier DV, Markert S, Hentschker C, Schweder T, Becher D, Gruber-Vodicka HR, Richter M, Bach W, Amann R, Meyerdierks A
    2018 - Front Microbiol, in press

    Abstract: 

    At hydrothermal vent sites, chimneys consisting of sulfides, sulfates, and oxides are formed upon contact of reduced hydrothermal fluids with oxygenated seawater. The walls and surfaces of these chimneys are an important habitat for vent-associated microorganisms. We used community proteogenomics to investigate and compare the composition, metabolic potential and relative in situ protein abundance of microbial communities colonizing two actively venting hydrothermal chimneys from the Manus Basin back-arc spreading center (Papua New Guinea). We identified overlaps in the in situ functional profiles of both chimneys, despite differences in microbial community composition and venting regime. Carbon fixation on both chimneys seems to have been primarily mediated through the reverse tricarboxylic acid cycle and fueled by sulfur-oxidation, while the abundant metabolic potential for hydrogen oxidation and carbon fixation via the Calvin-Benson-Bassham cycle was hardly utilized. Notably, the highly diverse microbial community colonizing the analyzed black smoker chimney had a highly redundant metabolic potential. In contrast, the considerably less diverse community colonizing the diffusely venting chimney displayed a higher metabolic versatility. An increased diversity on the phylogenetic level is thus not directly linked to an increased metabolic diversity in microbial communities that colonize hydrothermal chimneys.

  • Sulfate is transported at significant rates through the symbiosome membrane and is crucial for nitrogenase biosynthesis

    Schneider S, Schintlmeister A, Becana M, Wagner M, Woebken D, Wienkoop S
    2018 - Plant Cell Environ, in press

    Abstract: 

    Legume-rhizobia symbioses play a major role in food production for an ever growing human population. In this symbiosis, dinitrogen is reduced ('fixed') to ammonia by the rhizobial nitrogenase enzyme complex and is secreted to the plant host cells, while dicarboxylic acids derived from photosynthetically-produced sucrose are transported into the symbiosomes and serve as respiratory substrates for the bacteroids. The symbiosome membrane contains high levels of SST1 protein, a sulfate transporter. Sulfate is an essential nutrient for all living organisms, but its importance for symbiotic nitrogen fixation and nodule metabolism has long been underestimated. Using chemical imaging, we demonstrate that the bacteroids take up 20-fold more sulfate than the nodule host cells. Furthermore, we show that nitrogenase biosynthesis relies on high levels of imported sulfate, making sulfur as essential as carbon for the regulation and functioning of symbiotic nitrogen fixation. Our findings thus establish the importance of sulfate and its active transport for the plant-microbe interaction that is most relevant for agriculture and soil fertility. 

  • Effect of field site hydrogeochemical conditions on the corrosion of milled zerovalent iron particles and their dechlorination efficiency

    Milica Velimirovic, Melanie Auffan, Luca Carniato, Malfatti SE, Doris Schmid, Stephan Wagner, Daniel Borschneck, Olivier Proux, Frank von der Kammer, Thilo Hofmann
    2018 - Science of The Total Environment, 1619-1627

    Abstract: 

    Milled zerovalent iron (milled ZVI) particles have been recognized as a promising agent for groundwater remediation because of (1) their high reactivity with chlorinated aliphatic hydrocarbons, organochlorine pesticides, organic dyes, and a number of inorganic contaminants, and (2) a possible greater persistance than the more extensively investigated nanoscale zerovalent iron. We have used laboratory-scale batch degradation experiments to investigate the effect that hydrogeochemical conditions have on the corrosion of milled ZVI and on its ability to degrade trichloroethene(TCE). The observed pseudo first-order degradation rate constants indicated that the degradation of TCE by milled ZVI is affected by groundwater chemistry. The apparent corrosion rates of milled ZVI particles were of the same order of magnitude for hydrogeochemical conditions representative for two contaminated field sites (133–140 mmol kg− 1 day− 1, indicating a milled ZVI life-time of 128–135 days). Sulfate enhances milled ZVI reactivity by removing passivating iron oxides and hydroxides from the Fe0 surface, thus increasing the number of reactive sites available. The organic matter content of 1.69% in the aquifer material tends to suppress the formation of iron corrosion precipitates. Results from scanning electron microscopy, X-ray diffraction, and iron K-edge X-ray adsorption spectroscopy suggest that the corrosion mechanisms involve the partial dissolution of particles followed by the formation and surface precipitation of magnetite and/or maghemite. Numerical corrosion modeling revealed that fitting iron corrosion rates and hydrogen inhibitory terms to hydrogen and pH measurements in batch reactors can reduce the life-time of milled ZVI particles by a factor of 1.2 to 1.7.

  • Modeling Subsurface Fate of S-Metolachlor and Metolachlor Ethane Sulfonic Acid in the Westliches Leibnitzer Feld Aquifer

    Hans Kupfersberger, Gernot Klammler, Andrea Schumann, Lisa Brckner, Melanie Kah
    2018 - Vadose Zone Journal, 1: in press

    Abstract: 

    Pesticides and their metabolites have been increasingly detected in groundwater bodies in southeastern Austria in recent years. The main objective of this study was to model the fate of the herbicide S-metolachlor (2-chloro-N-(2-ethyl-6-methylphenyl)-N-[(1S)-2-methoxy-1-methylethyl]acetamide; SMET) and the main metabolite metolachlor ethane sulfonic acid (MESA) at the Westliches Leibnitzer Feld (WLF) aquifer. For this purpose, a modeling approach based on coupling the one-dimensional vadose zone model PEARL and the two-dimensional groundwater flow and solute transport model FEFLOW was developed. To calibrate the one-dimensional pesticide fate model, we used leachate concentrations of SMET and MESA from lysimeter experiments. Additionally, samples of representative soil types in the WLF aquifer were analyzed to infer SMET- and MESA-specific fate parameters (e.g., half-life DT50, Freundlich sorption coefficient Kfoc), which were used for the PEARL model. The results show that using SMET fate parameters derived from the lysimeter data considerably improved the fit of the simulation results with the field observations compared with the application of standard laboratory-derived fate parameters accounting for soil type differences. Although locally an overestimation of the monitoring data prevailed, the description of the subsurface fate of pesticides will improve the interpretation of concentration data and the design of mitigation measures.

  • Traits indicating a conservative resource strategy are weakly related to narrow range size in a group of neotropical trees

    Chacón-Madrigal E, Wanek W, Hietz P, Dullinger S
    2018 - Perspectives in Plant Ecology Evolution and Systematics, 32: 30-37

    Abstract: 

    Biological traits may co-determine differences in geographical range sizes among closely related species. In plants, trait values linked to a conservative resource-use strategy have been hypothesised to be associated with small range sizes. However, the empirical support is mixed and limited to extra-tropical species so far. Here, we analyse the relationship between range size and eight functional traits linked to the plant economics spectrum in congeneric pairs of neotropical tree species of Costa Rica with contrasting range sizes. In the lowland tropical rainforests of southern Costa Rica, we sampled 345 trees from 35 species in 14 genera and measured leaf thickness, leaf dry matter content, specific leaf area, wood specific gravity (WSG), leaf nitrogen (N), leaf phosphorus, leaf potassium and leaf N:P ratio. For each species, we estimated range size as the extent of occurrence using known localities of occurrence. We correlated range sizes with trait data scaled within-genus and with the principal components of the multivariate trait space. WSG was higher and leaf N was lower in species with small range sizes in univariate regression models, although these traits were only weakly related to range size. None of the other six traits was correlated with range size. Results were similar for a model using the principal components of the multivariate trait space, which explained 36% of the variation in species’ extent of occurrence. Again, the traits most strongly associated with the selected components were WSG and leaf N. Although high WSG and low leaf N can be interpreted as indicators of conservative resource-use, we could not detect strong relationships between the respective trait syndrome and range size in our sample of species. Traits related to conservative resource use may hence be involved in determining the range size of the species analysed, but other factors are apparently more important.

  • Soil organic matter quality exerts a stronger control than stoichiometry on microbial substrate use efficiency along a latitudinal transect

    Takriti M, Wild B, Schnecker J, Mooshammera M, Knoltsch A, Lashchinskiy N, Alves RJE, Gentsch N, Gittel A, Mikutta R, Wanek W, Richter A
    2018 - Soil Biology and Biochemistry, 121: 212-220

    Abstract: 

    A substantial portion of soil organic matter (SOM) is of microbial origin. The efficiency with which soil microorganisms can convert their substrate carbon (C) into biomass, compared to how much is lost as respiration, thus co-determines the carbon storage potential of soils. Despite increasing insight into soil microbial C cycling, empirical measurements of microbial C processing across biomes and across soil horizons remain sparse. The theory of ecological stoichiometry predicts that microbial carbon use efficiency (CUE), i.e. growth over uptake of organic C, strongly depends on the relative availability of C and nutrients, particularly N, as microorganisms will either respire excess C or conserve C while mineralising excess nutrients. Microbial CUE is thus expected to increase from high to low latitudes and from topsoil to subsoil as the soil C:N and the stoichiometric imbalance between SOM and the microbial biomass decrease. To test these hypotheses, we collected soil samples from the organic topsoil, mineral topsoil, and mineral subsoil of seven sites along a 1500-km latitudinal transect in Western Siberia. As a proxy for CUE, we measured the microbial substrate use efficiency (SUE) of added substrates by incubating soil samples with a mixture of 13C labelled sugars, amino sugarsamino acids, and organic acids and tracing 13C into microbial biomass and released CO2. In addition to soil and microbial C:N stoichiometry, we also determined the potential extracellular enzyme activities of cellobiohydrolase (CBH) and phenoloxidase (POX) and used the CBH:POX ratio as an indicator of SOM substrate quality. We found an overall decrease of SUE with latitude, corresponding to a decrease in mean annual temperature, in mineral soil horizons. SUE decreased with decreasing stoichiometric imbalance in the organic and mineral topsoil, while a relationship of SUE with soil C:N was only found in the mineral topsoil. However, contrary to our hypothesis, SUE did not increase with soil depth and mineral subsoils displayed lower average SUE than mineral topsoils. Both within individual horizons and across all horizons SUE was strongly correlated with CBH:POX ratio as well as with climate variables. Since enzyme activities likely reflect the chemical properties of SOM, our results indicate that SOM quality exerts a stronger control on SUE than SOM stoichiometry, particularly in subsoils were SOM has been turned over repeatedly and there is little variation in SOM elemental ratios.

  • Scientific rationale for the development of an OECD test guideline on engineered nanomaterial stability

    Fazel Abdolahpur Monikh, Antonia Praetorius, Andrea Schmid, Philipp Kozin, Boris Meisterjahn, Ekaterina Makarova, Thilo Hofmann, Frank von der Kammer
    2018 - NanoImpact, 42-50

    Abstract: 

    Standardized methods for assessing the behaviour of engineered nanomaterials(ENMs) under relevant environmental conditions are an important part of ENM risk assessment. Existing assays, often developed for traditional chemicals, are frequently not applicable to ENMs, which present special challenges due to their particulate nature and complex intrinsic and extrinsic properties. Here we present the development of the novel OECD test guideline (TG) No. 318 for studying the “dispersion stability of nanomaterials in simulated environmental media”. We discuss the rationalization of the test design and required simplifications to develop a test, which can be executed in standard laboratories on a routine basis at reasonable costs. The relevance of the test for capturing ENM stability in surface waters is ensured by a strategic selection of adequate test media and testing scheme. As an example, we present data of a full test performed according to the new OECD TG using NM 105 as a representative TiO2 ENM. Limitations of the test in terms of scarce kinetic information and a focus on homo- instead of heteroaggregation are discussed. The developed OECD Test No. 318 represents the first standardized assay for ENMs using an operationally defined testing scheme capable of systematically comparing different ENMs in terms of their dispersion stability under environmentally relevant conditions. It will provide crucial data to inform risk assessment and regulation and can be adapted to different types of test media if needed.

  • Proposal for a tiered dietary bioaccumulation testing strategy for engineered nanomaterials using fish

    Richard D. Handy, Jukka Ahtiainen, Jos Mara Navas, Greg Goss, Eric A. J. Bleeker, Frank von der Kammer
    2018 - Environmental Science: Nano, 9: 2030-2046

    Abstract: 

    The scientific community has invested effort into standardising methodologies for the regulatory ecotoxicity testing of engineered nanomaterials (ENMs), but the practical requirements for bioaccumulation testing of ENMs have been given less attention. A strategy for a tiered approach to bioaccumulation testing of ENMs using fish is proposed, with recommendations for its implementation by regulatory agencies. The strategy recognises that testing the many shapes, sizes and chemistries of ENMs as new substances in vivo would be an unrealistic workload. The approach therefore includes grouping/read-across methods and tools to screen out ENMs of negligible/low bioaccumulation potential. The strategy proposes reductions of animal use for in vivo testing and with greater consideration of in vitro methods. The first tier uses dissolution in water or lipids and particle settling rates as environmental chemistry triggers for ‘ENMs of concern’. The first tier also involves a weight of evidence from these tests, plus using existing data sets from selected literature that meet data quality criteria for ENMs. Tier 2 involves new data generation using in silico models now being validated for ENMs, including QSARs and systems biology tools. Tier 2 also includes using existing experimental data, and an option to collect new data. These data can be on soils/sediments, microbial degradation, and bioaccumulation studies on invertebrates or fish cell lines. In tier 3, an in chemico digestibility assay simulating the gut lumen of fish is proposed to identify the bioaccessible fractions from an oral exposure to ENMs. If the digestibility assay is positive, then in vitro gut sacs from rainbow trout can be used to confirm accumulation by the gut mucosa. Only if both these tests in tier 3 are positive would the work proceed to the final in vivo test (tier 4) which is essentially the OECD TG 305 method for dietary bioaccumulation testing using fish, with some caveats and recommendations for ENMs. These include considerations of terminology, how to prepare contaminated food for dietary exposures, the additional controls and endpoints for ENMs, measuring ENMs in food and tissues to confirm the exposure, and the limitations of any subsequent calculation of the bioaccumulation potential.

  • Significance of dark CO2 fixation in arctic soils

    Santruckova H, Kotas P, Barta J, Urich T, Capek P, Palmtag J, Alves RJE, Biasi C, Diakova K, Gentsch N, Gittel A, Guggenberger G, Hugelius G, Lashchinsky N, Martikainen PJ, Mikutta R, Schleper C, Schnecker J, Schwab C, Shibistova O, Wild B, Richter A
    2018 - Soil Biology and Biochemistry, 119: 11-21

    Abstract: 

    The occurrence of dark fixation of CO2 by heterotrophic microorganisms in soil is generally accepted, but its importance for microbial metabolism and soil organic carbon (C) sequestration is unknown, especially under Climiting conditions. To fill this knowledge gap, we measured dark 13CO2 incorporation into soil organic matter and conducted a 13C-labelling experiment to follow the 13C incorporation into phospholipid fatty acids as microbial biomass markers across soil profiles of four tundra ecosystems in the northern circumpolar region, where net primary productivity and thus soil C inputs are low. We further determined the abundance of various carboxylase genes and identified their microbial origin with metagenomics. The microbial capacity for heterotrophic CO2 fixation was determined by measuring the abundance of carboxylase genes and the incorporation of 13C into soil C following the augmentation of bioavailable C sources. We demonstrate that dark CO2 fixation occurred ubiquitously in arctic tundra soils, with increasing importance in deeper soil horizons, presumably due to increasing C limitation with soil depth. Dark CO2 fixation accounted on average for 0.4, 1.0, 1.1, and 16% of net respiration in the organic, cryoturbated organic, mineral and permafrost horizons, respectively. Genes encoding anaplerotic enzymes of heterotrophic microorganisms comprised the majority of identified carboxylase genes. The genetic potential for dark CO2 fixation was spread over a broad taxonomic range. The results suggest important regulatory function of CO2 fixation in C limited conditions. The measurements were corroborated by modeling the long-term impact of dark CO2 fixation on soil organic matter. Our results suggest that increasing relative CO2 fixation rates in deeper soil horizons play an important role for soil internal C cycling and can, at least in part, explain the isotopic enrichment with soil depth.

  • Temperature response of permafrost soil carbon is attenuated by mineral protection

    Gentsch N, Wild B, Mikutta R, Capek P, Diakova K, Schrumpf M, Turner S, Minnich C, Schaarschmidt F, Shibistova O, Schnecker J, Urich T, Gittel A, Santruckova H, Barta J, Lashchinskiy N, Fuß R, Richter A, Guggenberger G
    2018 - Global Change Biology, In press

    Abstract: 

    Climate change in Arctic ecosystems fosters permafrost thaw and makes massive amounts of ancient soil organic carbon (OC) available to microbial breakdown. However, fractions of the organic matter (OM) may be protected from rapid decomposition by their association with minerals. Little is known about the effects of mineral‐organic associations (MOA) on the microbial accessibility of OM in permafrost soils and it is not clear which factors control its temperature sensitivity. In order to investigate if and how permafrost soil OC turnover is affected by mineral controls, the heavy fraction (HF) representing mostly MOA was obtained by density fractionation from 27 permafrost soil profiles of the Siberian Arctic. In parallel laboratory incubations, the unfractionated soils (bulk) and their HF were comparatively incubated for 175 days at 5 and 15°C. The HF was equivalent to 70 ± 9% of the bulk CO2 respiration as compared to a share of 63 ± 1% of bulk OC that was stored in the HF. Significant reduction of OC mineralization was found in all treatments with increasing OC content of the HF (HF‐OC), clay‐size minerals and Fe or Al oxyhydroxides. Temperature sensitivity (Q10) decreased with increasing soil depth from 2.4 to 1.4 in the bulk soil and from 2.9 to 1.5 in the HF. A concurrent increase in the metal‐to‐HF‐OC ratios with soil depth suggests a stronger bonding of OM to minerals in the subsoil. There, the younger 14C signature in CO2 than that of the OC indicates a preferential decomposition of the more recent OM and the existence of a MOA fraction with limited access of OM to decomposers. These results indicate strong mineral controls on the decomposability of OM after permafrost thaw and on its temperature sensitivity. Thus, we here provide evidence that OM temperature sensitivity can be attenuated by MOA in permafrost soils.

  • Microbial temperature sensitivity and biomass change explain soil carbon loss with warming

    Walker TWN, Kaiser C, Strasser F, Herbold CW, Leblans NIW, Woebken D, Janssens IA, Sigurdsson BD, Richter A
    2018 - Nature Climate Change, 9: in press

    Abstract: 

    Soil microorganisms control carbon losses from soils to the atmosphere1,2,3, yet their responses to climate warming are often short-lived and unpredictable4,5,6,7. Two mechanisms, microbial acclimation and substrate depletion, have been proposed to explain temporary warming effects on soil microbial activity8,9,10. However, empirical support for either mechanism is unconvincing. Here we used geothermal temperature gradients (>50 years of field warming)11 and a short-term experiment to show that microbial activity (gross rates of growth, turnover, respiration and carbon uptake) is intrinsically temperature sensitive and does not acclimate to warming (+6 °C) over weeks or decades. Permanently accelerated microbial activity caused carbon loss from soil. However, soil carbon loss was temporary because substrate depletion reduced microbial biomass and constrained the influence of microbes over the ecosystem. A microbial biogeochemical model12,13,14 showed that these observations are reproducible through a modest, but permanent, acceleration in microbial physiology. These findings reveal a mechanism by which intrinsic microbial temperature sensitivity and substrate depletion together dictate warming effects on soil carbon loss via their control over microbial biomass. We thus provide a framework for interpreting the links between temperature, microbial activity and soil carbon loss on timescales relevant to Earth’s climate system.

  • Optimising the transport properties and reactivity of microbially-synthesised magnetite for in situ remediation

    Nimisha Joshi, Feixue Liu, Mathew Paul Watts, Heather Williams, Victoria S. Coker, Doris Schmid, Thilo Hofmann, Jonathan R. Lloyd
    2018 - Scientific Reports, 1: in press

    Abstract: 

    Engineered nanoparticles offer the potential for remediation of land and water that has been contaminated by organics and metals. Microbially synthesized nano-scale magnetite, prepared from Fe(III) oxides by subsurface Fe(III)-reducing bacteria, offers a scalable biosynthesis route to such a nano-scale remediation reagent. To underpin delivery of “bionanomagnetite” (BNM) nanomaterial during in situ treatment options, we conducted a range of batch and column experiments to assess and optimise the transport and reactivity of the particles in porous media. Collectively these experiments, which include state of the art gamma imaging of the transport of 99m Tc-labelled BNM in columns, showed that non-toxic, low cost coatings such as guar gum and salts of humic acid can be used to enhance the mobility of the nanomaterial, while maintaining reactivity against target contaminants. Furthermore, BNM reactivity can be enhanced by the addition of surface coatings of nano-Pd, extending the operational lifetime of the BNM, in the presence of a simple electron donor such as hydrogen or formate.

  • Using Silica Coated Nanoscale Zerovalent Particles for the Reduction of Chlorinated Ethylenes

    Lenka Honetschlgerov, Petra Janoukovcov, Milica Velimirovic, Martin Kubal, Leen Bastiaens
    2018 - Silicon, 6: 2593-2601

    Abstract: 

    The impact of a silica coating on the degradation potential of nanoscale zerovalent iron (nZVI) particles toward a mixture of chlorinated ethylenes is presented. The newly employed stabilization method for nZVI, based on silica deposition from saturated sodium silicate water glass, produces nZVI particles with a similar reactivity as non-stabilized particles. Moreover the removal rate constant kM of trichloroethylene (0.1740 L g−1 d−1 Fe0) and cis-dichloroethylene (0.1045 L g−1 d−1Fe0) was significantly improved (almost by a factor of 2) for stabilized nZVI. X-ray photoelectron spectroscopy (XPS) and Wavelength Dispersive X-ray Fluorescence (WDXRF) analyzes revealed a high durability of silica coating and the coating left at least half of nZVI surface silica free for reaction for more than 5 weeks. The silica coating did not affect the surface composition of silica coated nZVI which was confirmed by the very similar distribution of degradation products and corrosion products (Fe3O4, FeOOH) as was found for non-coated nanoparticles. An enhanced reactivity supplemented with a stable corrosion properties indicates that silica coated nZVI has potential as an efficient remediation agent toward chlorinated ethylenes.

  • Biodegradability standards for carrier bags and plastic films in aquatic environments: a critical review

    Harrison JP, Boardman C, O'Callaghan K, Delort A, Song J
    2018 - Royal Society Open Science, in press

    Abstract: 

    Plastic litter is encountered in aquatic ecosystems across the globe, including polar environments and the deep sea. To mitigate the adverse societal and ecological impacts of this waste, there has been debate on whether ‘biodegradable' materials should be granted exemptions from plastic bag bans and levies. However, great care must be exercised when attempting to define this term, due to the broad and complex range of physical and chemical conditions encountered within natural ecosystems. Here, we review existing international industry standards and regional test methods for evaluating the biodegradability of plastics within aquatic environments (wastewater, unmanaged freshwater and marine habitats). We argue that current standards and test methods are insufficient in their ability to realistically predict the biodegradability of carrier bags in these environments, due to several shortcomings in experimental procedures and a paucity of information in the scientific literature. Moreover, existing biodegradability standards and test methods for aquatic environments do not involve toxicity testing or account for the potentially adverse ecological impacts of carrier bags, plastic additives, polymer degradation products or small (microscopic) plastic particles that can arise via fragmentation. Successfully addressing these knowledge gaps is a key requirement for developing new biodegradability standard(s) for lightweight carrier bags.

  • Emergent Properties of Microbial Activity in Heterogeneous Soil Microenvironments: Different Research Approaches Are Slowly Converging, Yet Major Challenges Remain

    Baveye PC, Otten W, Kravchenko A, Balseiro-Romero M, Beckers É, Chalhoub M, Darnault C, Eickhorst T, Garnier P, Hapca S, Kiranyaz S, Monga O, Mueller CW, Nunan N, Pot V, Schlüter S, Schmidt H, Vogel H-J
    2018 - Frontiers in microbiology, 9: 1-48

    Abstract: 

    Over the last 60 years, soil microbiologists have accumulated a wealth of experimental data showing that the bulk, macroscopic parameters (e.g., granulometry, pH, soil organic matter, and biomass contents) commonly used to characterize soils provide insufficient information to describe quantitatively the activity of soil microorganisms and some of its outcomes, like the emission of greenhouse gasses. Clearly, new, more appropriate macroscopic parameters are needed, which reflect better the spatial heterogeneity of soils at the microscale (i.e., the pore scale) that is commensurate with the habitat of many microorganisms. For a long time, spectroscopic and microscopic tools were lacking to quantify processes at that scale, but major technological advances over the last 15 years have made suitable equipment available to researchers. In this context, the objective of the present article is to review progress achieved to date in the significant research program that has ensued. This program can be rationalized as a sequence of steps, namely the quantification and modeling of the physical-, (bio)chemical-, and microbiological properties of soils, the integration of these different perspectives into a unified theory, its upscaling to the macroscopic scale, and, eventually, the development of new approaches to measure macroscopic soil characteristics. At this stage, significant progress has been achieved on the physical front, and to a lesser extent on the (bio)chemical one as well, both in terms of experiments and modeling. With regard to the microbial aspects, although a lot of work has been devoted to the modeling of bacterial and fungal activity in soils at the pore scale, the appropriateness of model assumptions cannot be readily assessed because of the scarcity of relevant experimental data. For significant progress to be made, it is crucial to make sure that research on the microbial components of soil systems does not keep lagging behind the work on the physical and (bio)chemical characteristics. Concerning the subsequent steps in the program, very little integration of the various disciplinary perspectives has occurred so far, and, as a result, researchers have not yet been able to tackle the scaling up to the macroscopic level. Many challenges, some of them daunting, remain on the path ahead. Fortunately, a number of these challenges may be resolved by brand new measuring equipment that will become commercially available in the very near future.

  • Preservation effects on isotopic signatures in benthic foraminiferal biomass

    Enge AJ, Wanek W, Heinz P
    2018 - Marine Micropaleontology, 144: 50-59

    Abstract: 

    Foraminiferal samples for stable isotope analysis are frequently preserved after field collection or during cruises despite the lack of knowledge if and how preservation changes the elemental and stable isotope composition of the protists. Thus, the aim of this study was to investigate the effects of preservation on natural and stable isotope-enriched foraminifera. We tested the following preservation methods on specimens of the benthic foraminifer Ammonia sp. (without surrounding sediment): drying at room temperature, freezing (−25 °C in seawater), ethanol with and without Rose Bengal (RB), and formalin with and without RB. Natural specimens were preserved for 14, 90, and 240 days, while stable isotope-enriched specimens were preserved for 30 days following a pulse-chase feeding experiment. Regardless of type and length, preservation caused a significant loss of carbon (biomass) of up to 42% and lower nitrogen contents in most treatments. Already preservation for 14 days significantly affected δ13C and δ15N signatures, with the strongest shifts caused by freezing at −25 °C in seawater and formalin fixation (with RB). With longer preservation time, the gap between foraminiferal δ13C signatures and the control signal increased for all preservation methods except for 96% ethanol. The observed shifts in the δ13C signatures in the differently preserved foraminifera are in a range of shifts that are found in the signatures of natural foraminifera and are caused by the uptake of various food sources. Applying different preservation methods therefore can bias trophic interpretations based on natural isotope abundances. Preservation of stable isotope-enriched foraminifera in ethanol (with and without RB) resulted in significantly lower carbon uptake estimates, while freezing caused significantly lower nitrogen uptake estimates. Our findings suggest that, if possible, any storage or preservation should be avoided, especially in formalin or at −25 °C with seawater; otherwise storage should be kept as short as possible. Of all tested methods, drying foraminifera at room temperature was the least affecting method with comparatively low variation among replicates. Comparison of biomass, isotope signatures and uptake estimates obtained from differently preserved specimens should be considered carefully, as differences might not be caused naturally, but by alterations of the cytoplasm during preservation.

  • Environmental Impacts by Fragments Released from Nanoenabled Products: A Multiassay, Multimaterial Exploration by the SUN Approach

    Mnica J.B. Amorim, Sijie Lin, Karsten Schlich, Jos M. Navas, Andrea Brunelli, Nicole Neubauer, Klaus Vilsmeier, Anna L. Costa, Andreas Gondikas, Tian Xia, Liliana Galbis, Elena Badetti, Antonio Marcomini, Danail Hristozov, Frank von der Kammer, Kerstin Hund-Rinke, Janeck J. Scott-Fordsmand, Andr Nel, Wendel Wohlleben
    2018 - Environmental Science & Technology, 3: 1514-1524

    Abstract: 

    Nanoenabled products (NEPs) have numerous outdoor uses in construction, transportation or consumer scenarios, and there is evidence that their fragments are released in the environment at low rates. We hypothesized that the lower surface availability of NEPs fragment reduced their environmental effects with respect to pristine nanomaterials. This hypothesis was explored by testing fragments generated by intentional micronisation (“the SUN approach”; Nowack et al. Meeting the Needs for Released Nanomaterials Required for Further Testing: The SUN Approach. Environmental Science & Technology2016 (50), 2747). The NEPs were composed of four matrices (epoxy, polyolefin, polyoxymethylene, and cement) with up to 5% content of three nanomaterials (carbon nanotubes, iron oxide, and organic pigment). Regardless of the type of nanomaterial or matrix used, it was observed that nanomaterials were only partially exposed at the NEP fragment surface, indicating that mostly the intrinsic and extrinsic properties of the matrix drove the NEP fragment toxicity. Ecotoxicity in multiple assays was done covering relevant media from terrestrial to aquatic, including sewage treatment plant (biological activity), soil worms (Enchytraeus crypticus), and fish (zebrafish embryo and larvae and trout cell lines). We designed the studies to explore the possible modulation of ecotoxicity by nanomaterial additives in plastics/polymer/cement, finding none. The results support NEPs grouping by the matrix material regarding ecotoxicological effect during the use phase. Furthermore, control results on nanomaterial-free polymer fragments representing microplastic had no significant adverse effects up to the highest concentration tested.

  • pH-Dependent Bioavailability, Speciation, and Phytotoxicity of Tungsten (W) in Soil Affect Growth and Molybdoenzyme Activity of Nodulated Soybeans

    Oburger E, Cid CV, Preiner J, Hu J, Hann S, Wanek W, Richter A
    2018 - Environmental Science & Technology, 52: 6146-6156

    Abstract: 

    Increasing use of tungsten (W)-based products opened new pathways for W into environmental systems. Due to its chemical alikeness with molybdenum (Mo), W is expected to behave similarly to its “twin element”, Mo; however, our knowledge of the behavior of W in the plant−soil environment remains inadequate. The aim of this study was to investigate plant growth as well as W and nutrient uptake depending on soil chemical properties such as soil pH and texture. Soybean (Glycine max cv. Primus) was grown on two acidic soils differing in soil texture that were either kept at their natural soil pH (pH of 4.5−5) or limed (pH of ≥7) and amended with increasing concentrations of metallic W (control and 500 and 5000 mg kg−1 ). In addition, the activity of molybdoenzymes involved in N assimilation (nitrate reductase) and symbiotic N2 fixation (nitrogenase) was also investigated. Our results showed that the risk of W entering the food web was significantly greater in high-pH soils due to increased solubility of mainly monomeric W. The effect of soil texture on W solubility and phytoavailability was less pronounced compared to soil pH. Particularly at intermediate W additions (W 500 mg kg−1 ), symbiotic nitrogen fixation was able to compensate for reduced leaf nitrate reductase activity. When W soil solution concentrations became too toxic (W 5000 mg kg−1 ), nodulation was more strongly inhibited than nitrogenase activity in the few nodules formed, suggesting a more-efficient detoxification and compartmentalization mechanism in nodules than in soybean leaves. The increasing presence of polymeric W species observed in low-pH soils spiked with high W concentrations resulted in decreased W uptake. Simultaneously, polymeric W species had an overall negative effect on nutrient assimilation and plant growth, suggesting a greater phytotoxicity of W polymers. Our study demonstrates the importance of accounting for soil pH in risk assessment studies of W in the plant−soil environment, something that has been completely neglected in the past.

  • Biodegradation of synthetic polymers in soils: Tracking carbon into CO2 and microbial biomass

    Zumstein MT, Schintlmeister A, Nelson TF, Baumgartner R, Woebken D, Wagner M, Kohler H-PE, McNeill K, Sander M
    2018 - Science Advances, 4: eaas9024

    Abstract: 

    Plastic materials are widely used in agricultural applications to achieve food security for the growing world population. The use of biodegradable instead of nonbiodegradable polymers in single-use agricultural applications, including plastic mulching, promises to reduce plastic accumulation in the environment. We present a novel approach that allows tracking of carbon from biodegradable polymers into CO2 and microbial biomass. The approach is based on 13C-labeled polymers and on isotope-specific analytical methods, including nanoscale secondary ion mass spectrometry (NanoSIMS). Our results unequivocally demonstrate the biodegradability of poly(butylene adipate-co-terephthalate) (PBAT), an important polyester used in agriculture, in soil. Carbon from each monomer unit of PBAT was used by soil microorganisms, including filamentous fungi, to gain energy and to form biomass. This work advances both our conceptual understanding of polymer biodegradation and the methodological capabilities to assess this process in natural and engineered environments.

  • Minerals in the rhizosphere: overlooked mediators of soil nitrogen availability to plants and microbes

    Jilling A, Keiluweit M, Contosta AR, Frey S, Schimel J, Schnecker J, Smith RG, Tiemann L, Grandy AS
    2018 - Biogeochemistry, 2: 103-122

    Abstract: 

    Despite decades of research progress, ecologists are still debating which pools and fluxes provide nitrogen (N) to plants and soil microbes across different ecosystems. Depolymerization of soil organic N is recognized as the rate-limiting step in the production of bioavailable N, and it is generally assumed that detrital N is the main source. However, in many mineral soils, detrital polymers constitute a minor fraction of total soil organic N. The majority of organic N is associated with clay-sized particles where physicochemical interactions may limit the accessibility of N-containing compounds. Although mineral-associated organic matter (MAOM) has historically been considered a critical, but relatively passive, reservoir of soil N, a growing body of research now points to the dynamic nature of mineral-organic associations and their potential for destabilization. Here we synthesize evidence from biogeoscience and soil ecology to demonstrate how MAOM is an important, yet overlooked, mediator of bioavailable N, especially in the rhizosphere. We highlight several biochemical strategies that enable plants and microbes to disrupt mineral-organic interactions and access MAOM. In particular, root-deposited low-molecular-weight exudates may enhance the mobilization and solubilization of MAOM, increasing its bioavailability. However, the competitive balance between the possible fates of N monomers—bound to mineral surfaces versus dissolved and available for assimilation—will depend on the specific interaction between mineral properties, soil solution, mineral-bound organic matter, and microbes. Building off our emerging understanding of MAOM as a source of bioavailable N, we propose a revision of the Schimel and Bennett (Ecology 85:591–602, 2004) model (which emphasizes N depolymerization), by incorporating MAOM as a potential proximal mediator of bioavailable N.

  • Environmental transformation of natural and engineered carbon nanoparticles and implications for the fate of organic contaminants

    Gabriel Sigmund, Chuanjia Jiang, Thilo Hofmann, Wei Chen
    2018 - Environmental Science: Nano, 1: 2500-2518

    Abstract: 

    Environmental transformation of carbon nanoparticles can significantly affect their transport, fate, and effects. The last decade of environmental nano-science has often focused on understanding the behavior of well-defined engineered carbon nanoparticles (eCNPs) in the natural environment. However, more complex pyrogenic/petrogenic carbon nanoparticles (pCNPs), including those derived from soot, fossil coal, wildfire charcoal, and biochar, are more than four orders of magnitude more abundant in the environment. This paper aims to review findings from investigations into eCNPs and to consider their transferability to pCNPs, in order to improve our understanding of pCNPs and identify gaps in our knowledge. Findings from previous investigations into the chemical, physical and biological transformation of larger carbonaceous particles, as well as of eCNPs, can help us to understand the transformation of pCNPs. The transformation of soot during atmospheric transport is relatively well documented, whereas the transformation of pCNPs in soil, sediment, and aqueous systems remains poorly understood. To bridge findings on particulate transport, contaminant binding, and contaminant transformation from eCNPs to pCNPs, the complex compositions of pCNPs need to be taken into account. We therefore suggest that future research on pCNP transformation should focus on changes in intrinsic porosity and on interactions with non-carbonized phases, tar phases, and mineral phases, as well as with organo-mineral complexes in soils, sediments and water bodies.

  • Genomic insights into the Acidobacteria reveal strategies for their success in terrestrial environments

    Eichorst SA, Trojan D, Roux S, Herbold CW, Rattei T, Woebken D
    2018 - Environ Microbiol, 20: 1041-1063

    Abstract: 

    Members of the phylum Acidobacteria are abundant and ubiquitous across soils. We performed the largest (to date) comparative genome analysis spanning subdivisions 1, 3, 4, 6, 8, and 23 (n=24) with the goal to identify features to help explain their prevalence in soils and understand their ecophysiology. In contrast to earlier studies, our analysis revealed that bacteriophage integration events along with transposable and mobile elements influenced the structure and plasticity of these genomes. Low- and high-affinity respiratory oxygen reductases were detected in multiple genomes, suggesting the capacity for growing across different oxygen gradients. Amongst many genomes, the capacity to use a diverse collection of carbohydrates, as well as inorganic and organic N sources (such as extracellular peptidases), were detected – both advantageous traits in environments with fluctuating nutrient environments. We also identified multiple soil acidobacteria with the potential to scavenge atmospheric concentrations of H2, now encompassing mesophilic soil strains within the subdivision 1 and 3, in addition to a previously identified thermophilic strain in subdivision 4. This large-scale acidobacteria genome analysis reveals traits that provide genomic, physiological and metabolic versatility, presumably allowing flexibility and versatility in the challenging and fluctuating soil environment.

  • Evaluation of primers targeting the diazotroph functional gene and development of NifMAP – a bioinformatics pipeline for analyzing nifH amplicon data

    Angel R, Nepel M, Panhölzl C, Schmidt H, Herbold CW, Eichorst SA, Woebken D
    2018 - Front Microbiol, 9: 1-15

    Abstract: 

    Diazotrophic microorganisms introduce biologically available nitrogen (N) to the global N cycle through the activity of the nitrogenase enzyme. The genetically conserved dinitrogenase reductase (nifH) gene is phylogenetically distributed across four clusters (I-IV) and is widely used as a marker gene for N2 fixation, permitting investigators to study the genetic diversity of diazotrophs in nature and target potential participants in N2 fixation. To date there have been limited, standardized pipelines for the nifH functional gene, which is in stark contrast to the rRNA gene. Here we present a bioinformatics pipeline for processing nifH amplicon datasets – NifMAP (“NifH MiSeq Illumina amplicon Analysis Pipeline”), which as a novel aspect uses Hidden-Markov models to filter out homologous genes to nifH. By using this pipeline, we evaluated the broadly inclusive primer pairs (Ueda19F-R6, IGK3-DVV, F2-R6) that target the nifH gene. To evaluate any systematic biases, the nifH gene was amplified with the aforementioned primer pairs in a diverse collection of environmental samples (soils, rhizosphere and roots samples, biological soil crusts and estuarine samples), in addition to a nifH mock community consisting of six phylogenetically diverse members. We noted that all primer pairs co-amplified nifH homologs to varying degrees; up to 90% of the amplicons were nifH homologs with IGK3-DVV in some samples (rhizosphere and roots from tall oat-grass). In regards to specificity, we observed some degree of bias across the primer pairs. For example, primer pair F2-R6 discriminated against cyanobacteria (amongst others), yet captured many sequences from subclusters IIIE and IIIL-N. These aforementioned subclusters were largely missing by the primer pair IGK3-DVV, which also tended to discriminate against Alphaproteobacteria, but amplified sequences within clusters IIIC (affiliated with Clostridia) and clusters IVB and IVC. Primer pair Ueda19F-R6 exhibited the least bias and successfully captured diazotrophs in cluster I and subclusters IIIE, IIIL, IIIM and IIIN, but discriminated against Firmicutes and subcluster IIIC. Taken together, our newly established bioinformatics pipeline, NifMAP, along with our systematic evaluations of nifH primer pairs permit more robust, high-throughput investigations of diazotrophs in diverse environments. 

  • Influence of compost and biochar on microbial communities and the sorption/degradation of PAHs and NSO-substituted PAHs in contaminated soils

    Gabriel Sigmund, Caroline Poyntner, Guadalupe Piñar, Melanie Kah, Thilo Hofmann
    2018 - Journal of Hazardous Materials, 107-113

    Abstract: 

    Diffusely contaminated soils often remain untreated as classical remediation approaches would be disproportionately expensive. Adding compost can accelerate the biodegradation of organic contaminants and adding biochar can immobilize contaminants through sorption. The combined use of compost and biochar to reduce polycyclic aromatic hydrocarbon (PAH) and NSO-substituted PAH contamination has, however, not previously been systematically investigated. We have therefore investigated the processes involved (i) through sorption batch experiments, (ii) by monitoring changes in bacterial, fungal and archaeal communities using denaturing gradient gel electrophoresis, and (iii) through degradation experiments with fluorene, phenanthrene, pyrene, carbazole, dibenzothiophene, and dibenzofuran. Sorption coefficients for organic contaminants in soils increased tenfold following 10% compost addition and up to a hundredfold with further addition of 5% biochar. The rate of PAH and NSO-PAH degradation increased up to twofold following compost addition despite increased sorption, probably due to the introduction of additional microbial species into the autochthonous soil communities. In contrast, degradation of PAHs and NSO-PAHs in soil-compost-biochar mixtures slowed down up to tenfold due to the additional sorption, although some degradation still occurred. The combined use of biochar and compost may therefore provide a strategy for immobilizing PAHs and NSO-PAHs and facilitating degradation of remaining accessible contaminant fractions.

  • Sorption to soil, biochar and compost: is prediction to multicomponent mixtures possible based on single sorbent measurements?

    Melanie Kah, Gabriel Sigmund, Pedro Luis Manga Chavez, Lucie Bielská, Thilo Hofmann
    2018 - PeerJ, 673 —692

    Abstract: 

    Amendment with biochar and/or compost has been proposed as a strategy to remediate soil contaminated with low levels of polycyclic aromatic hydrocarbons. The strong sorption potential of biochar can help sequestering contaminants while the compost may promote their degradation. An improved understanding of how sorption evolves upon soil amendment is an essential step towards the implementation of the approach. The present study reports on the sorption of pyrene to two soils, four biochars and one compost. Detailed isotherm analyzes across a wide range of concentration confirmed that soil amendments can significantly increase the sorption of pyrene. Comparisons of data obtained by a classical batch and a passive sampling method suggest that dissolved organic matter did not play a significant role on the sorption of pyrene. The addition of 10% compost to soil led to a moderate increase in sorption (<2-fold), which could be well predicted based on measurements of sorption to the individual components. Hence, our result suggest that the sorption of pyrene to soil and compost can be relatively well approximated by an additive process. The addition of 5% biochar to soil (with or without compost) led to a major increase in the sorption of pyrene (2.5–4.7-fold), which was, however, much smaller than that suggested based on the sorption measured on the three individual components. Results suggest that the strong sorption to the biochar was attenuated by up to 80% in the presence of soil and compost, much likely due to surface and pore blockage. Results were very similar in the two soils considered, and collectively suggest that combined amendments with compost and biochar may be a useful approach to remediate soils with low levels of contamination. Further studies carried out in more realistic settings and over longer periods of time are the next step to evaluate the long term viability of remediation approaches based on biochar amendments.

  • Application of stable-isotope labelling techniques for the detection of active diazotrophs

    Angel R, Panhölzl C, Gabriel R, Herbold CW, Wanek W, Richter A, Eichorst SA, Woebken D
    2018 - Environmental microbiology, 20: 44-61

    Abstract: 

    Investigating active participants in the fixation of dinitrogen gas is vital as N is often a limiting factor for primary production. Biological nitrogen fixation (BNF) is performed by a diverse guild of bacteria and archaea (diazotrophs), which can be free-living or symbionts. Free-living diazotrophs are widely distributed in the environment, yet our knowledge about their identity and ecophysiology is still limited. A major challenge in investigating this guild is inferring activity from genetic data as this process is highly regulated. To address this challenge, we evaluated and improved several 15N-based methods for detecting N2 fixation activity (with a focus on soil samples) and studying active diazotrophs. We compared the acetylene reduction assay and the 15N2 tracer method and demonstrated that the latter is more sensitive in samples with low activity. Additionally, tracing 15N into microbial RNA provides much higher sensitivity compared to bulk soil analysis. Active soil diazotrophs were identified with a 15N-RNA-SIP approach optimized for environmental samples and benchmarked to 15N-DNA-SIP. Lastly, we investigated the feasibility of using SIP-Raman microspectroscopy for detecting 15N-labelled cells. Taken together, these tools allow identifying and investigating active free-living diazotrophs in a highly sensitive manner in diverse environments, from bulk to the single-cell level.

  • Is local trait variation related to total range size of tropical trees?

    Chacón-Madrigal E, Wanek W, Hietz P, Dullinger S
    2018 - PloS one, 19

    Abstract: 

    The reasons why the range size of closely related species often varies significantly have intrigued scientists for many years. Among other hypotheses, species with high trait variation were suggested to occupy more diverse environments, have more continuity in their distributions, and consequently have larger range sizes. Here, using 34 tree species of lowlands tropical rainforest in southern Costa Rica, we explored whether inherent trait variability expressed at the local scale in functional traits is related to the species’ total geographical range size. We formed 17 congeneric pairs of one narrow endemic and one widespread species, sampled 335 individuals and measured eight functional traits: leaf area, leaf thickness, leaf dry matter content, specific leaf area, leaf nitrogen content, leaf phosphorus content, leaf nitrogen to phosphorus ratio, and wood specific gravity. We tested whether there are significant differences in the locally expressed variation of individual traits or in multidimensional trait variance between the species in congeneric pairs and whether species’ range size could hence be predicted from local trait variability. However, we could not find such differences between widely distributed and narrow range species. We discuss the possible reasons for these findings including the fact that higher trait variability of widespread species may result from successive local adaptations during range expansion and may hence often be an effect rather than the cause of larger ranges.

  • Links among warming, carbon and microbial dynamics mediated by soil mineral weathering

    Doetterl S, Berhe AA, Arnold C, Bodé S, Fiener P, Finke P, Fuchslueger L, Griepentrog M, Harden JW, Nadeu E, Schnecker J, Six J, Trumbore S, Van Oost K, Vogel C, Boeckx P
    2018 - Nature Geoscience, in press

    Abstract: 

    Quantifying soil carbon dynamics is of utmost relevance in the context of global change because soils play an important role in land–atmosphere gas exchange. Our current understanding of both present and future carbon dynamics is limited because we fail to accurately represent soil processes across temporal and spatial scales, partly because of the paucity of data on the relative importance and hierarchical relationships between microbial, geochemical and climatic controls. Here, using observations from a 3,000-kyr-old soil chronosequence preserved in alluvial terrace deposits of the Merced River, California, we show how soil carbon dynamics are driven by the relationship between short-term biotic responses and long-term mineral weathering. We link temperature sensitivity of heterotrophic respiration to biogeochemical soil properties through their relationship with microbial activity and community composition. We found that soil mineralogy, and in particular changes in mineral reactivity and resulting nutrient availability, impacts the response of heterotrophic soil respiration to warming by altering carbon inputs, carbon stabilization, microbial community composition and extracellular enzyme activity. We demonstrate that biogeochemical alteration of the soil matrix (and not short-term warming) controls the composition of microbial communities and strategies to metabolize nutrients. More specifically, weathering first increases and then reduces nutrient availability and retention, as well as the potential of soils to stabilize carbon.

  • Data on sorption of organic compounds by aged polystyrene microplastic particles

    Thorsten Hüffer, Anne-Katrin Weniger, Thilo Hofmann
    2018 - Data in Brief, 474-479

    Abstract: 

    This article contains data on experimental sorption isotherms of 21 probe sorbates by aged polystyrene microplastics. The polymeric particles were subjected to an UV-induced photo-oxidation procedure using hydrogen peroxide in a custom-made aging chamber. Sorption data were obtained for aged particles. The experimental sorption data was modelled using both single- and poly-parameter linear free-energy relationships. For discussion and interpretation of the presented data, refer to the research article entitled “Sorption of organic compounds by aged polystyrene microplastic particles” (Hüffer et al., 2018) [1].

  • A critical evaluation of nanopesticides and nanofertilizers against their conventional analogues

    Melanie Kah, Rai Singh Kookana, Alexander Gogos, Thomas Daniel Bucheli
    2018 - Nature Nanotechnology, 8: 677-684

    Abstract: 

    Among a wide range of possible applications of nanotechnology in agriculture, there has been a particular interest in developing novel nanoagrochemicals. While some concerns have been expressed regarding altered risk profile of the new products, many foresee a great potential to support the necessary increase in global food production in a sustainable way. A critical evaluation of nanoagrochemicals against conventional analogues is essential to assess the associated benefits and risks. In this assessment, recent literature was critically analysed to determine the extent to which nanoagrochemicals differ from conventional products. Our analysis was based on 78 published papers and shows that median gain in efficacy relative to conventional products is about 20–30%. Environmental fate of agrochemicals can be altered by nanoformulations, but changes may not necessarily translate in a reduction of the environmental impact. Many studies lacked nano-specific quality assurance and adequate controls. Currently, there is no comprehensive study in the literature that evaluates efficacy and environmental impact of nanoagrochemicals under field conditions. This is a crucial knowledge gap and more work will thus be necessary for a sound evaluation of the benefits and new risks that nanoagrochemicals represent relative to existing products.

  • Fate of carbohydrates and lignin in north-east Siberian permafrost soils

    Dao TT, Gentsch N, Mikutta R, Sauheitl L, Shibistova O, Wild B, Schnecker J, Barta J, Capek P, Gittel A, Lashchinskiy N, Urich T, Santruckova H, Richter A, Guggenberger G
    2018 - Soil Biology and Biochemistry, 116: 311-322

    Abstract: 

    Permafrost soils preserve huge amounts of organic carbon (OC) prone to decomposition under changing climatic conditions. However, knowledge on the composition of soil organic matter (OM) and its transformation and vulnerability to decomposition in these soils is scarce. We determined neutral sugars and lignin-derived phenols, released by trifluoroacetic acid (TFA) and CuO oxidation, respectively, within plants and soil density fractions from the active layer and the upper permafrost layer at three different tundra types (shrubby grass, shrubby tussock, shrubby lichen) in the Northeast Siberian Arctic. The heavy fraction (HF; > 1.6 g mL−1 ) was characterized by a larger enrichment of microbial sugars (hexoses vs. pentoses) and more pronounced lignin degradation (acids vs. aldehydes) as compared to the light fraction (LF; < 1.6 g mL−1 ), showing the transformation from plant residue-dominated particulate OM to a largely microbial imprint in mineral-associated OM. In contrast to temperate and tropical soils, total neutral sugar contents and galactose plus mannose to arabinose plus xylose ratios (GM/AX) decreased in the HF with soil depth, which may indicate a process of effective recycling of microbial biomass rather than utilizing old plant materials. At the same time, lignin-derived phenols increased and the degree of oxidative decomposition of lignin decreased with soil depth, suggesting a selective preservation of lignin presumably due to anaerobiosis. As large parts of the plant-derived pentoses are incorporated in lignocelluloses and thereby protected against rapid decomposition, this might also explain the relative enrichment of pentoses with soil depth. Hence, our results show a relatively large contribution of plantderived OM, particularly in the buried topsoil and subsoil, which is stabilized by the current soil environmental conditions but may become available to decomposers if permafrost degradation promotes soil drainage and improves the soil oxygen supply.

  • Soil microbial CNP and respiration responses to organic matter and nutrient additions: Evidence from a tropical soil incubation

    Soong J, Marañon-Jimenez S, Cotrufo MF, Boeckx P, Bodé S, Guenet B, Peñuelas J, Richter A, Stahl C, Verbruggen E, Janssens IA
    2018 - Soil Biology and Biochemistry, 122: 141-149

    Abstract: 

    Soil nutrient availability has a strong influence on the fate of soil carbon (C) during microbial decomposition, contributing to Earth's C balance. While nutrient availability itself can impact microbial physiology and C partitioning between biomass and respiration during soil organic matter decomposition, the availability of labile C inputs may mediate the response of microorganisms to nutrient additions. As soil organic matter is decomposed, microorganisms retain or release C, nitrogen (N) or phosphorus (P) to maintain a stoichiometric balance. Although the concept of a microbial stoichiometric homeostasis has previously been proposed, microbial biomass CNP ratios are not static, and this may have very relevant implications for microbial physiological activities. Here, we tested the hypothesis that N, P and potassium (K) nutrient additions impact C cycling in a tropical soil due to microbial stoichiometric constraints to growth and respiration, and that the availability of energy-rich labile organic matter in the soil (i.e. leaf litter) mediates the response to nutrient addition. We incubated tropical soil from French Guiana with a 13C labeled leaf litter addition and with mineral nutrient additions of +K, +N, +NK, +PK and +NPK for 30 days. We found that litter additions led to a ten-fold increase in microbial respiration and a doubling of microbial biomass C, along with greater microbial N and P content. We found some evidence that P additions increased soil CO2 fluxes. Additionally, we found microbial biomass CP and NP ratios varied more widely than CN in response to nutrient and organic matter additions, with important implications for the role of microorganisms in C cycling. The addition of litter did not prime soil organic matter decomposition, except in combination with +NK fertilization, indicating possible P-mining of soil organic matter in this P-poor tropical soil. Together, these results point toward an ultimate labile organic substrate limitation of soil microorganisms in this tropical soil, but also indicate a complex interaction between C, N, P and K availability. This highlights the difference between microbial C cycling responses to N, P, or K additions in the tropics and explains why coupled C, N and P cycle modeling efforts cannot rely on strict microbial stoichiometric homeostasis as an underlying assumption.

  • Development of a versatile analytical protocol for the comprehensive determination of the elemental composition of smartphone compartments on the example of printed circuit boards

    B. Bookhagen, W. Obermaier, C. Opper, C. Koeberl, Thilo Hofmann, T. Prohaska J. Irrgeher
    2018 - Analytical Methods, 3: 3864-3871

    Abstract: 

    A versatile approach to determining the elemental content of more than 50 elements in different components of electronic devices on the example of smartphones was developed. The analytical protocol is based on accurate disassembly of smartphones, a single processing microwave-assisted acid digestion followed by ICP-OES and ICP-MS measurements. Method optimization and validation were performed using the certified reference material ERM®-EZ505 electronic scrap. Combined uncertainties revealed measurement uncertainty and sample heterogeneity as main contributors. The contents of up to 57 elements could be quantified in the certified reference material ERM®-EZ505 electronic scrap. The results of the certified elements Au, Be, Cu, In, Ni, Pd, and Pt overlapped within their uncertainties with the certified range and revealed recoveries of 100% ± 16%. Only Ag shows incomplete recoveries (75% ± 35%). The validated method was applied to all metal-containing components of selected smartphones, excluding batteries. The contents of up to 57 elements could be quantified and are presented exemplarily for printed circuit boards, which represent the most complex components in the investigated smartphones and thus limit the capability of the method. The ten most abundant elements in decreasing order are Cu, Fe, Si, Ni, Sn, Zn, Ba, Al, Cr, Ti, which comprise approx. 80% of the weight of the printed circuit boards. The method allows for the determination of metal content in various parts of modern smartphones, providing the basis for the estimation and prediction of future metal usage and thus the comprehensive investigation of recycling and circular economy aspects.

  • Mercury isotope signatures of digests and sequential extracts from industrially contaminated soils and sediments

    Andrew R.C. Grigg, Ruben Kretzschmar, Robin S. Gilli, Jan G. Wiederhold
    2018 - Science of The Total Environment, 1344-1354

    Abstract: 

    Environmental mercury (Hg) pollution is a matter of global concern. Mercury speciation controls its environmental behaviour, and stable isotope ratios can potentially trace Hg movement through environmental compartments. Here we investigated Hg in industrially contaminated soils and sediments (Visp, Valais, Switzerland) using concentration and stable isotope analysis (CV-MC-ICP-MS) of total digests, and a four-step sequential extraction procedure. The sequential extraction employed (1) water (labile Hg species), (2) NaOH or Na4P2O7 (organically-bound Hg), (3) hydroxylamine-HCl (Hg bound to Mn and Fe (oxyhydr)oxides), and (4) aqua regia (residual Hg pools). The majority of Hg was extracted in step 4 and up to 36% in step 2. Mercury bound to organic matter was the dominant source of Hg in water, NaOH and Na4P2O7 extracts. Sulfides and colloidal oxide minerals were possible additional sources of Hg in some samples. The inconsistent comparative performance of NaOH and Na4P2O7 extractions showed that these classical extractants may not extract Hg exclusively from the organically-bound pool. Samples taken at the industrial facility displayed the greatest isotopic variation (δ202Hg: −0.80‰ ± 0.14‰ to 0.25‰ ± 0.13‰, Δ199Hg: −0.10‰ ± 0.03‰ to 0.02‰ ± 0.03‰; all 2SD) whereas downstream of the facility there was much less variation around average values of δ202Hg = −0.47‰ ± 0.11‰ and Δ199Hg = −0.05‰ ± 0.03‰ (1SD, n = 19). We interpret the difference as the result of homogenisation by mixing of canal sediments containing Hg from the various sources at the industrial facility with preservation of the mixed industrial Hg signature downstream. In contrast to previous findings, Hg isotopes in the sequential extracts were largely similar to one another (2SD < 0.14‰), likely demonstrating that the Hg speciation was similar among the extracts. Our results reveal that Hg resides in relatively stable soil pools which record an averaged isotope signature of the industrial sources, potentially facilitating source tracing studies with Hg isotope signatures at larger spatial scales further downstream.

  • Transmission of fungal partners to incipient Cecropia-tree ant colonies

    Mayer VE, Nepel M, Blatrix R, Oberhauser FB, Fiedler K, Schönenberger J, Voglmayr H
    2018 - PloS one, 13: e0192207

    Abstract: 

    Ascomycete fungi in the nests of ants inhabiting plants (= myrmecophytes) are very often cultivated by the ants in small patches and used as food source. Where these fungi come from is not known yet. Two scenarios of fungus recruitment are possible: (1) random infection through spores or hyphal fragments from the environment, or (2) transmission from mother to daughter colonies by the foundress queen. It is also not known at which stage of the colony life cycle fungiculture is initiated, and whether the- symbiont fungi serve as food for the ant queen. To clarify these questions, we investigated four Azteca ant species inhabiting three different Cecropia species (CinsignisCobtusifolia, and Cpeltata). We analysed an rRNA gene fragment from 52 fungal patches produced by founding queens and compared them with those from established Azteca colonies (n = 54). The infrabuccal pockets of winged queens were dissected to investigate whether young queens carry fungi from their mother colony. Additionally, 15N labelling experiments were done to verify whether the queen feeds on the patches until she is nourished by her first worker offspring. We infer from the results that the fungi cultivated in hollow plant structures are transferred from the parental colony of the young queen. First, fungal genotypes/OTU diversity was not significantly different between foundress queen patches and established colonies, and second, hyphal parts were discovered in the infrabuccal pockets of female alates. We could show that fungiculture already starts before queens lay their eggs, and that the queens do not feed on fungal patch material but feed it to the larvae. Our findings suggest that fungiculture may be crucial for successful colony founding of arboreal ants in the tropics.

  • Sampling root exudates – Mission impossible?

    Oburger E, Jones DL
    2018 - Rhizosphere, 6: 116-133

    Abstract: 

    Accurate information about the quantity, quality and spatiotemporal dynamics of metabolite release from plant roots is vital to understanding the functional significance of root exudates in biogeochemical processes occurring at the root-microbe-soil-interface. Significant progress in analytical techniques nowadays allows us to gain a much better picture of the rich diversity of compounds that are present in root exudates, but ultimately the choice of exudation sampling strategy will determine the ecological significance of obtained exudation results. Unfortunately, in the past, little consideration has been given to the experimental strategy used to sample root exudates. To date, our knowledge on root exudation is mainly based on plants grown and sampled in nutrient solution culture (hydroponics). Despite the operational benefit of hydroponic systems, the question remains as to how ecologically relevant exudation results obtained under these artificial conditions are compared to soil environments, particularly in the context of exudate driven rhizosphere processes. The quantitative and qualitative measurement of root exudation in soil, however, is fraught with problems due to: (i) continual removal of exudates from solution by the microbial community; (ii) loss of exudates from solution due to their sorption to the solid phase; and (iii) simultaneous release of compounds from soil organic matter breakdown. While a perfect method for sampling root exudates does not exist, soil based approaches, if appropriately applied and interpreted, may still provide more realistic insights into exudation dynamics in natural soil environments. This review aims to provide an overview of different root exudation sampling approaches and their advantages and limitations to support the selection of the most suitable experimental procedure for any specific research question. We address critical methodological aspects that need to be considered in the choice of experimental approach, like growth and sampling medium (soil, hydroponic), sterility, sampling location (whole root system, individual root segments) as well as plant age, daytime, re-uptake of metabolites affecting duration and timing of the sampling event and data presentation. In addition, we summarize the main analytical approaches to analyze root exudates, ranging from liquid sample analysis to isotope tracking and imaging techniques.

  • A plant–microbe interaction framework explaining nutrient effects on primary production

    Capek P, Manzoni S, Kaštovská E, Wild B, Diakova K, Barta J, Schnecker J, Biasi C, Martikainen P, Alves R, Guggenberger G, Gentsch N, Hugelius G, Palmtag J, Mikutta R, Shibistova O, Urich T, Schleper C, Richter A, Santruckova H
    2018 - Nature Ecology & Evolution, 2: 1588-1596

    Abstract: 

    In most terrestrial ecosystems, plant growth is limited by nitrogen (N) and phosphorus (P). Adding either nutrient to soil usually affects primary production, but their effects can be positive or negative. Here we provide a general stoichiometric framework for interpreting these contrasting effects. First, we identify N and P limitations on plants and soil microorganisms using their respective N to P critical ratios. Second, we use these ratios to show how soil microorganisms mediate the response of primary production to limiting and non-limiting nutrient addition along a wide gradient of soil nutrient availability. Using a meta-analysis of 51 factorial N-P fertilization experiments conducted across multiple ecosystems, we demonstrate that the response of primary production to N and P additions is accurately predicted by our stoichiometric framework. The only pattern that could not be predicted by our original framework suggests that N has not only a structural function in growing organisms, but also a key role in promoting plant and microbial nutrient acquisition. We conclude that this stoichiometric framework offers the most parsimonious way to interpret contrasting and until now unresolved responses of primary production to nutrient addition in terrestrial ecosystems.

  • Fe(II)-Catalyzed Ligand-Controlled Dissolution of Iron(hydr)oxides

    Jagannath Biswakarma, Kyounglim Kang, Susan C. Borowski, Walter D.C. Schenkeveld, Stephan M. Kraemer, Janet G. Hering, Stephan J. Hug
    2018 - Environmental Science & Technology, 1: 88-97

    Abstract: 

    Dissolution of iron(III)phases is a key process in soils, surface waters, and the ocean. Previous studies found that traces of Fe(II) can greatly increase ligand controlled dissolution rates at acidic pH, but the extent that this also occurs at circumneutral pH and what mechanisms are involved are not known. We addressed these questions with infrared spectroscopy and 57Fe isotope exchange experiments with lepidocrocite (Lp) and 50 μM ethylenediaminetetraacetate (EDTA) at pH 6 and 7. Addition of 0.2–10 μM Fe(II) led to an acceleration of the dissolution rates by factors of 7–31. Similar effects were observed after irradiation with 365 nm UV light. The catalytic effect persisted under anoxic conditions, but decreased as soon as air or phenanthroline was introduced. Isotope exchange experiments showed that added 57Fe remained in solution, or quickly reappeared in solution when EDTA was added after 57Fe(II), suggesting that catalyzed dissolution occurred at or near the site of 57Fe incorporation at the mineral surface. Infrared spectra indicated no change in the bulk, but changes in the spectra of adsorbed EDTA after addition of Fe(II) were observed. A kinetic model shows that the catalytic effect can be explained by electron transfer to surface Fe(III) sites and rapid detachment of Fe(III)EDTA due to the weaker bonds to reduced sites. We conclude that the catalytic effect of Fe(II) on dissolution of Fe(III)(hydr)oxides is likely important under circumneutral anoxic conditions and in sunlit environments.

  • Constraints to Synergistic Fe Mobilization from Calcareous Soil by a Phytosiderophore and a Reductant

    Walter Schenkeveld, Stephan M. Kraemer
    2018 - Soil Systems, 4: 67

    Abstract: 

    Synergistic effects between ligand- and reductant-based Fe acquisition strategies can enhance the mobilization of Fe, but also of competing metals from soil. For phytosiderophores, this may alter the time and concentration window of Fe uptake during which plants can benefit from elevated Fe concentrations. We examined how the size of this window is affected by the ligand and reductant concentration and by non-simultaneous addition. To this end, a series of kinetic batch experiments was conducted with a calcareous clay soil to which the phytosiderophore 2′-deoxymugineic acid (DMA) and the reductant ascorbate were added at various concentrations, either simultaneously or with a one- or two-day lag time. Both simultaneous and non-simultaneous addition of the reductant and the phytosiderophore induced synergistic Fe mobilization. Furthermore, initial Fe mobilization rates increased with increasing reductant and phytosiderophore concentrations. However, the duration of the synergistic effect and the window of Fe uptake decreased with increasing reductant concentration due to enhanced competitive mobilization of other metals. Rate laws accurately describing synergistic mobilization of Fe and other metals from soil were parameterized. Synergistic Fe mobilization may be vital for the survival of plants and microorganisms in soils of low Fe availability. However, in order to optimally benefit from these synergistic effects, exudation of ligands and reductants in the rhizosphere need to be carefully matched.

  • Where is the nano? Analytical approaches for the detection and quantification of TiO2 engineered nanoparticles in surface waters

    Andreas Gondikas, Frank von der Kammer, Ralf Kaegi, Olga Borovinskaya, Elisabeth Neubauer, Jana Navratilova, Antonia Praetorius, Geert Cornelis, Thilo Hofmann
    2018 - Environmental Science: Nano, 2: 313-326

    Abstract: 

    Detecting and quantifying engineered nanoparticles (ENPs) in complex environmental matrices requires the distinction between natural nanoparticles (NNPs) and ENPs. The distinction of NNPs and ENPs for regulatory purposes calls for cost-efficient methods, but is hampered by similarities in intrinsic properties, such as particle composition, size, density, surface chemistry, etc. Titanium dioxide (TiO2) ENPs, for instance, are produced in very large quantities but Ti also commonly occurs naturally in nano-scale minerals. In this work, we focus on utilizing particle size and composition to identify ENPs in a system with a significant background concentration of the target metal. We have followed independent approaches involving both conventional and state-of-the-art analytical techniques to detect and quantify TiO2 ENPs released into surface waters from sunscreen products and to distinguish them from Ti-bearing NNPs. To achieve this, we applied single particle inductively coupled plasma mass spectrometry with single-element (spICPMS) and multi-element detection (time-of-flight) spICP-TOFMS, together with transmission electron microscopy (TEM), automated scanning electron microscopy (autoSEM), and bulk elemental analyses. A background concentration of Ti-bearing NPs (approximately 5 × 10particles per ml), possibly of natural origin, was consistently observed outside the bathing season. This concentration increased by up to 40% during the bathing season. Multi-element analysis of individual particles using spICP-TOFMS revealed that Al, Fe, Mn, and Pb are often present in natural Ti-bearing NPs, but no specific multi-element signatures were detected for ENPs. Our data suggests that TiO2 ENPs enter the lake water during bathing activities, eventually agglomerating and sedimenting. We found adhesion of the TiO2 ENPs to the air–water interface for short time periods, depending on wind conditions. This study demonstrates that the use of spICP-TOFMS and spICPMS in combination with other conventional analytical techniques offers significant advantages for discriminating between NNPs and ENPs. The quantitative data produced in this work can be used as input for modeling studies or as a benchmark for analysis protocols and model validations.

  • Streamlining standard bacteriophage methods for higher throughput.

    Kauffman KM, Polz MF
    2018 - MethodsX, 159-172

    Abstract: 

    A universal tool in the culture-based study of bacterial viruses (bacteriophages, or phages) is the agar overlay, which is used in the isolation of new viruses, and in their quantification and purification. Here, simple optimizations that increase efficiency and throughput in agar overlay based isolation and cultivation of virus-host systems are presented. The agar overlay is streamlined to minimize steps and materials. Serial purification of viruses from viral colonies (plaques) is optimized to eliminate steps by combining purification by serial re-streaking with the optimized agar overlay approach. Finally, recommendations are made for efficient archival and storage of virus plaques. In sum, this work presents: •Tube-free Agar Overlays: rapid plaque assays with fewer steps and materials•Molten Streaking for Singles: rapid tube-free serial purification of viruses•Archiving Plaques: saving virus purification for later.

  • Assessment of urban microbiome assemblies with the help of targeted in silico gold standards.

    Gerner SM, Rattei T, Graf AB
    2018 - Biol. Direct, 1: 22

    Abstract: 

    Microbial communities play a crucial role in our environment and may influence human health tremendously. Despite being the place where human interaction is most abundant we still know little about the urban microbiome. This is highlighted by the large amount of unclassified DNA reads found in urban metagenome samples. The only in silico approach that allows us to find unknown species, is the assembly and classification of draft genomes from a metagenomic dataset. In this study we (1) investigate the applicability of an assembly and binning approach for urban metagenome datasets, and (2) develop a new method for the generation of in silico gold standards to better understand the specific challenges of such datasets and provide a guide in the selection of available software.
    We applied combinations of three assembly (Megahit, SPAdes and MetaSPAdes) and three binning tools (MaxBin, MetaBAT and CONCOCT) to whole genome shotgun datasets from the CAMDA 2017 Challenge. Complex in silico gold standards with a simulated bacterial fraction were generated for representative samples of each surface type and city. Using these gold standards, we found the combination of SPAdes and MetaBAT to be optimal for urban metagenome datasets by providing the best trade-off between the number of high-quality genome draft bins (MIMAG standards) retrieved, the least amount of misassemblies and contamination. The assembled draft genomes included known species like Propionibacterium acnes but also novel species according to respective ANI values.
    In our work, we showed that, even for datasets with high diversity and low sequencing depth from urban environments, assembly and binning-based methods can provide high-quality genome drafts. Of vital importance to retrieve high-quality genome drafts is sequence depth but even more so a high proportion of the bacterial sequence fraction too achieve high coverage for bacterial genomes. In contrast to read-based methods relying on database knowledge, genome-centric methods as applied in this study can provide valuable information about unknown species and strains as well as functional contributions of single community members within a sample. Furthermore, we present a method for the generation of sample-specific highly complex in silico gold standards.
    This article was reviewed by Craig Herbold, Serghei Mangul and Yana Bromberg.

  • Minimum Information about an Uncultivated Virus Genome (MIUViG).

    Roux S, Adriaenssens EM, Dutilh BE, Koonin EV, Kropinski AM, Krupovic M, Kuhn JH, Lavigne R, Brister JR, Varsani A, Amid C, Aziz RK, Bordenstein SR, Bork P, Breitbart M, Cochrane GR, Daly RA, Desnues C, Duhaime MB, Emerson JB, Enault F, Fuhrman JA, Hingamp P, Hugenholtz P, Hurwitz BL, Ivanova NN, Labonté JM, Lee KB, Malmstrom RR, Martinez-Garcia M, Mizrachi IK, Ogata H, Páez-Espino D, Petit MA, Putonti C, Rattei T, Reyes A, Rodriguez-Valera F, Rosario K, Schriml L, Schulz F, Steward GF, Sullivan MB, Sunagawa S, Suttle CA, Temperton B, Tringe SG, Thurber RV, Webster NS, Whiteson KL, Wilhelm SW, Wommack KE, Woyke T, Wrighton KC, Yilmaz P, Yoshida T, Young MJ, Yutin N, Allen LZ, Kyrpides NC, Eloe-Fadrosh EA
    2018 - Nat. Biotechnol., in press

    Abstract: 

    We present an extension of the Minimum Information about any (x) Sequence (MIxS) standard for reporting sequences of uncultivated virus genomes. Minimum Information about an Uncultivated Virus Genome (MIUViG) standards were developed within the Genomic Standards Consortium framework and include virus origin, genome quality, genome annotation, taxonomic classification, biogeographic distribution and in silico host prediction. Community-wide adoption of MIUViG standards, which complement the Minimum Information about a Single Amplified Genome (MISAG) and Metagenome-Assembled Genome (MIMAG) standards for uncultivated bacteria and archaea, will improve the reporting of uncultivated virus genomes in public databases. In turn, this should enable more robust comparative studies and a systematic exploration of the global virosphere.

  • The draft genome sequence of “Nitrospira lenta” strain BS10, a nitrite oxidizing bacterium isolated from activated sludge

    Sakoula D, Nowka B, Spieck E, Daims H, Lücker S
    2018 - Stand Genomic Sci, 13: 32

    Abstract: 

    The genus Nitrospira is considered to be the most widespread and abundant group of nitrite-oxidizing bacteria in many natural and man-made ecosystems. However, the ecophysiological versatility within this phylogenetic group remains highly understudied, mainly due to the lack of pure cultures and genomic data. To further expand our understanding of this biotechnologically important genus, we analyzed the high quality draft genome of “Nitrospira lenta” strain BS10, a sublineage II Nitrospira that was isolated from a municipal wastewater treatment plant in Hamburg, Germany. The genome of “N. lenta” has a size of 3,756,190 bp and contains 3968 genomic objects, of which 3907 are predicted protein-coding sequences. Thorough genome annotation allowed the reconstruction of the “N. lenta” core metabolism for energy conservation and carbon fixation. Comparative analyses indicated that most metabolic features are shared with N. moscoviensis and “N. defluvii”, despite their ecological niche differentiation and phylogenetic distance. In conclusion, the genome of “N. lenta” provides important insights into the genomic diversity of the genus Nitrospira and provides a foundation for future comparative genomic studies that will generate a better understanding of the nitrification process.

  • Insecticidal Toxicity of Involves the Novel Enterotoxin YacT.

    Springer K, Sänger PA, Moritz C, Felsl A, Rattei T, Fuchs TM
    2018 - Front Cell Infect Microbiol, 392

    Abstract: 

    The genus comprises 19 species of which three are known as human and animal pathogens. Some species display toxicity toward invertebrates using the so-called toxin complex (TC) and/or determinants that are not yet known. Recent studies showed a remarkable variability of insecticidal activities when representatives of different species (spp.) were subcutaneously injected into the greater wax moth, . Here, we demonstrate that and are highly toxic to this insect. A member of phylogroup 1B killed larvae with injection doses of approximately 38 cells only, thus resembling the insecticidal activity of . The pathogenicity spp. displays toward the larvae was higher at 15°C than at 30°C and independent of the TC. However, upon subtraction of all genes of the low-pathogenic strain W22703 from the genomes of and , we identified a set of genes that may be responsible for the toxicity of these two species. Indeed, a mutant of lacking , a gene that encodes a protein similar to the heat-stable cytotonic enterotoxin (Ast) of , exhibited a reduced pathogenicity toward larvae and altered the morphology of hemocytes. The data suggests that the repertoire of virulence determinants present in environmental species remains to be elucidated.

  • Standardized protocols and procedures can precisely and accurately quantify non-structural carbohydrates

    Landhäuser SM, Chow PS, Dickman LT, Furze ME, Kuhlman I, Schmid S, Wiesenbauer J, Wild B, Gleixner G, Hartmann H, Hoch G, McDowell NG, Richardson AD, Richter A, Adams HD
    2018 - Tree Physiology, e-publication, 1-15

    Abstract: 

    Non-structural carbohydrates (NSCs), the stored products of photosynthesis, building blocks for growth and fuel for respiration, are central to plant metabolism, but their measurement is challenging. Differences in methods and procedures among laboratories can cause results to vary widely, limiting our ability to integrate and generalize patterns in plant carbon balance among studies. A recent assessment found that NSC concentrations measured for a common set of samples can vary by an order of magnitude, but sources for this variability were unclear. We measured a common set of nine plant material types, and two synthetic samples with known NSC concentrations, using a common protocol for sugar extraction and starch digestion, and three different sugar quantification methods (ion chromatography, enzyme, acid) in six laboratories. We also tested how sample handling, extraction solvent and centralizing parts of the procedure in one laboratory affected results. Non-structural carbohydrate concentrations measured for synthetic samples were within about 11.5% of known values for all three methods. However, differences among quantification methods were the largest source of variation in NSC measurements for natural plant samples because the three methods quantify different NSCs. The enzyme method quantified only glucose, fructose and sucrose, with ion chromatography we additionally quantified galactose, while the acid method quantified a large range of mono- and oligosaccharides. For some natural samples, sugars quantified with the acid method were two to five times higher than with other methods, demonstrating that trees allocate carbon to a range of sugar molecules. Sample handling had little effect on measurements, while ethanol sugar extraction improved accuracy over water extraction. Our results demonstrate that reasonable accuracy of NSC measurements can be achieved when different methods are used, as long as protocols are robust and standardized. Thus, we provide detailed protocols for the extraction, digestion and quantification of NSCs in plant samples, which should improve the comparability of NSC measurements among laboratories.

  • Microbial nitrogen limitation in the mammalian large intestine.

    Reese AT, Pereira FC, Schintlmeister A, Berry D, Wagner M, Hale LP, Wu A, Jiang S, Durand HK, Zhou X, Premont RT, Diehl AM, O'Connell TM, Alberts SC, Kartzinel TR, Pringle RM, Dunn RR, Wright JP, David LA
    2018 - Nat Microbiol, in press

    Abstract: 

    Resource limitation is a fundamental factor governing the composition and function of ecological communities. However, the role of resource supply in structuring the intestinal microbiome has not been established and represents a challenge for mammals that rely on microbial symbionts for digestion: too little supply might starve the microbiome while too much might starve the host. We present evidence that microbiota occupy a habitat that is limited in total nitrogen supply within the large intestines of 30 mammal species. Lowering dietary protein levels in mice reduced their faecal concentrations of bacteria. A gradient of stoichiometry along the length of the gut was consistent with the hypothesis that intestinal nitrogen limitation results from host absorption of dietary nutrients. Nitrogen availability is also likely to be shaped by host-microbe interactions: levels of host-secreted nitrogen were altered in germ-free mice and when bacterial loads were reduced via experimental antibiotic treatment. Single-cell spectrometry revealed that members of the phylum Bacteroidetes consumed nitrogen in the large intestine more readily than other commensal taxa did. Our findings support a model where nitrogen limitation arises from preferential host use of dietary nutrients. We speculate that this resource limitation could enable hosts to regulate microbial communities in the large intestine. Commensal microbiota may have adapted to nitrogen-limited settings, suggesting one reason why excess dietary protein has been associated with degraded gut-microbial ecosystems.

  • Transcriptomic and proteomic insight into the mechanism of cyclooctasulfur- versus thiosulfate-oxidation by the chemolithoautotroph Sulfurimonas denitrificans

    Götz F, Pjevac P, Markert S, McNichol J, Becher D, Schweder T, Greuter L, Sievert SM
    2018 - Environ Microbiol, in press

    Abstract: 

    Chemoautotrophic bacteria belonging to the genus Sulfurimonas (class Campylobacteria) were previously identified as key players in the turnover of zero-valence sulfur, a central intermediate in the marine sulfur cycle. S. denitrificans was further shown to be able to oxidize cyclooctasulfur (S ). However, at present the mechanism of activation and metabolism of cyclooctasulfur is not known. Here, we assessed the transcriptome and proteome of S. denitrificans grown with either thiosulfate or S as the electron donor. While the overall expression profiles under the two growth conditions were rather similar, distinct differences were observed that could be attributed to the utilization of S . This included a higher abundance of expressed genes related to surface attachment in the presence of S , and the differential regulation of the sulfur-oxidation multienzyme complex (SOX), which in S. denitrificans is encoded in two gene clusters: soxABXY Z and soxCDY Z . While the proteins of both clusters were present with thiosulfate, only proteins of the soxCDY Z were detected at significant levels with S . Based on these findings a model for the oxidation of S is proposed. Our results have implications for interpreting metatranscriptomic and -proteomic data and for the observed high level of diversification of soxY Z among sulfur-oxidizing Campylobacteria. This article is protected by copyright. All rights reserved.

  • Genomic Insights Into the Acid Adaptation of Novel Methanotrophs Enriched From Acidic Forest Soils.

    Nguyen NL, Yu WJ, Gwak JH, Kim SJ, Park SJ, Herbold CW, Kim JG, Jung MY, Rhee SK
    2018 - Front Microbiol, 1982

    Abstract: 

    Soil acidification is accelerated by anthropogenic and agricultural activities, which could significantly affect global methane cycles. However, detailed knowledge of the genomic properties of methanotrophs adapted to acidic soils remains scarce. Using metagenomic approaches, we analyzed methane-utilizing communities enriched from acidic forest soils with pH 3 and 4, and recovered near-complete genomes of proteobacterial methanotrophs. Novel methanotroph genomes designated KS32 and KS41, belonging to two representative clades of methanotrophs ( of and of ), were dominant. Comparative genomic analysis revealed diverse systems of membrane transporters for ensuring pH homeostasis and defense against toxic chemicals. Various potassium transporter systems, sodium/proton antiporters, and two copies of proton-translocating F1F0-type ATP synthase genes were identified, which might participate in the key pH homeostasis mechanisms in KS32. In addition, the V-type ATP synthase and urea assimilation genes might be used for pH homeostasis in KS41. Genes involved in the modification of membranes by incorporation of cyclopropane fatty acids and hopanoid lipids might be used for reducing proton influx into cells. The two methanotroph genomes possess genes for elaborate heavy metal efflux pumping systems, possibly owing to increased heavy metal toxicity in acidic conditions. Phylogenies of key genes involved in acid adaptation, methane oxidation, and antiviral defense in KS41 were incongruent with that of 16S rRNA. Thus, the detailed analysis of the genome sequences provides new insights into the ecology of methanotrophs responding to soil acidification.

  • Metabolic specialization of denitrifiers in permeable sediments controls NO emissions

    Marchant HK, Tegetmeyer HE, Ahmerkamp S, Holtappels M, Lavik G, Graf J, Schreiber F, Greuter L, Strous M, Kuypers MMM
    2018 - Environ Microbiol, 12: 4486-4502

    Abstract: 

    Coastal oceans receive large amounts of anthropogenic fixed nitrogen (N), most of which is denitrified in the sediment before reaching the open ocean. Sandy sediments, which are common in coastal regions, seem to play an important role in catalysing this N-loss. Permeable sediments are characterized by advective porewater transport, which supplies high fluxes of organic matter into the sediment, but also leads to fluctuations in oxygen and nitrate concentrations. Little is known about how the denitrifying communities in these sediments are adapted to such fluctuations. Our combined results indicate that denitrification in eutrophied sandy sediments from the world's largest tidal flat system, the Wadden Sea, is carried out by different groups of microorganisms. This segregation leads to the formation of NO which is advectively transported to the overlying waters and thereby emitted to the atmosphere. At the same time, the production of NO within the sediment supports a subset of Flavobacteriia which appear to be specialized on NO reduction. If the mechanisms shown here are active in other coastal zones, then denitrification in eutrophied sandy sediments may substantially contribute to current marine NO emissions.

  • Ancestral gene acquisition as the key to virulence potential in environmental Vibrio populations.

    Bruto M, Labreuche Y, James A, Piel D, Chenivesse S, Petton B, Polz MF, Le Roux F
    2018 - ISME J, 12: 2954-2966

    Abstract: 

    Diseases of marine animals caused by bacteria of the genus Vibrio are on the rise worldwide. Understanding the eco-evolutionary dynamics of these infectious agents is important for predicting and managing these diseases. Yet, compared to Vibrio infecting humans, knowledge of their role as animal pathogens is scarce. Here we ask how widespread is virulence among ecologically differentiated Vibrio populations, and what is the nature and frequency of virulence genes within these populations? We use a combination of population genomics and molecular genetics to assay hundreds of Vibrio strains for their virulence in the oyster Crassostrea gigas, a unique animal model that allows high-throughput infection assays. We show that within the diverse Splendidus clade, virulence represents an ancestral trait but has been lost from several populations. Two loci are necessary for virulence, the first being widely distributed across the Splendidus clade and consisting of an exported conserved protein (R5.7). The second is a MARTX toxin cluster, which only occurs within V. splendidus and is for the first time associated with virulence in marine invertebrates. Varying frequencies of both loci among populations indicate different selective pressures and alternative ecological roles, based on which we suggest strategies for epidemiological surveys.

  • Visualisation of the obligate hydrocarbonoclastic bacteria Polycyclovorans algicola and Algiphilus aromaticivorans in co-cultures with micro-algae by CARD-FISH.

    Thompson HF, Lesaulnier C, Pelikan C, Gutierrez T
    2018 - J. Microbiol. Methods, 73-79

    Abstract: 

    Some studies have described the isolation and 16S rRNA gene sequence-based identification of hydrocarbon-degrading bacteria living associated with marine eukaryotic phytoplankton, and thus far the direct visual observation of these bacteria on micro-algal cell surfaces ('phycosphere') has not yet been reported. Here, we developed two new 16S rRNA-targeted oligonucleotide probes, PCY223 and ALGAR209, to respectively detect and enumerate the obligate hydrocarbonoclastic bacteria Polycyclovorans algicola and Algiphilus aromaticivorans by Catalyzed Reporter Deposition Fluorescence in situ Hybridization (CARD-FISH). To enhance the hybridization specificity with the ALGAR209 probe, a competitor probe was developed. These probes were tested and optimized using pure cultures, and then used in enrichment experiments with laboratory cultures of micro-algae exposed to phenanthrene, and with coastal water enriched with crude oil. Microscopic analysis revealed these bacteria are found in culture with the micro-algal cells, some of which were found attached to algal cells, and whose abundance increased after phenanthrene or crude oil enrichment. These new probes are a valuable tool for identifying and studying the ecology of P. algicola and A. aromaticivorans in laboratory and field samples of micro-algae, as well as opening new fields of research that could harness their ability to enhance the bioremediation of contaminated sites.

  • Bacterial interactions during sequential degradation of cyanobacterial necromass in a sulfidic arctic marine sediment

    Müller AL, Pelikan C, de Rezende JR, Wasmund K, Putz M, Glombitza C, Kjeldsen KU, Jørgensen BB, Loy A
    2018 - Environ Microbiol, 20: 2927–2940

    Abstract: 

    Seafloor microorganisms impact global carbon cycling by mineralizing vast quantities of organic matter (OM) from pelagic primary production, which is predicted to increase in the Arctic because of diminishing sea ice cover. We studied microbial interspecies-carbon-flow during anaerobic OM degradation in arctic marine sediment using stable isotope probing. We supplemented sediment incubations with 13C-labeled cyanobacterial necromass (spirulina), mimicking fresh OM input, or acetate, an important OM degradation intermediate, and monitored sulfate reduction rates and concentrations of volatile fatty acids (VFAs) during substrate degradation. Sequential 16S rRNA gene and transcript amplicon sequencing and fluorescence in situ hybridization combined with Raman microspectroscopy revealed that only few bacterial species were the main degraders of 13C-spirulina necromass. Psychrilyobacter, Psychromonas, Marinifilum, Colwellia, Marinilabiaceae and Clostridiales species were likely involved in the primary hydrolysis and fermentation of spirulina. VFAs, mainly acetate, produced from spirulina degradation were mineralized by sulfate-reducing bacteria and an Arcobacter species. Cellular activity of Desulfobacteraceae and Desulfobulbaceae species during acetoclastic sulfate reduction was largely decoupled from relative 16S rRNA gene abundance shifts. Our findings provide new insights into the identities and physiological constraints that determine the population dynamics of key microorganisms during complex OM degradation in arctic marine sediments.

  • Ammonia Monooxygenase-Mediated Cometabolic Biotransformation and Hydroxylamine-Mediated Abiotic Transformation of Micropollutants in an AOB/NOB Coculture.

    Yu Y, Han P, Zhou LJ, Li Z, Wagner M, Men Y
    2018 - Environ. Sci. Technol., 16: 9196-9205

    Abstract: 

    Biotransformation of various micropollutants (MPs) has been found to be positively correlated with nitrification in activated sludge communities. To further elucidate the roles played by ammonia-oxidizing bacteria (AOB) and nitrite-oxidizing bacteria (NOB), we investigated the biotransformation capabilities of an NOB pure culture ( Nitrobacter sp.) and an AOB ( Nitrosomonas europaea)/NOB ( Nitrobacter sp.) coculture for 15 MPs, whose biotransformation was reported previously to be associated with nitrification. The NOB pure culture did not biotransform any investigated MP, whereas the AOB/NOB coculture was capable of biotransforming six MPs (i.e., asulam, bezafibrate, fenhexamid, furosemide, indomethacin, and rufinamide). Transformation products (TPs) were identified, and tentative structures were proposed. Inhibition studies with octyne, an ammonia monooxygenase (AMO) inhibitor, suggested that AMO was the responsible enzyme for MP transformation that occurred cometabolically. For the first time, hydroxylamine, a key intermediate of all aerobic ammonia oxidizers, was found to react with several MPs at concentrations typically occurring in AOB batch cultures. All of these MPs were also biotransformed by the AOB/NOB coculture. Moreover, the same asulam TPs were detected in both biotransformation and hydroxylamine-treated abiotic transformation experiments, whereas rufinamide TPs formed from biological transformation were not detected during hydroxylamine-mediated abiotic transformation, which was consistent with the inability of rufinamide abiotic transformation by hydroxylamine. Thus, in addition to cometabolism likely carried out by AMO, an abiotic transformation route indirectly mediated by AMO might also contribute to MP biotransformation by AOB.

  • Stable-Isotope Probing of Human and Animal Microbiome Function

    Berry D, Loy A
    2018 - Trends Microbiol, In press

    Abstract: 

    Humans and animals host diverse communities of microorganisms important to their physiology and health. Despite extensive sequencing-based characterization of host-associated microbiomes, there remains a dramatic lack of understanding of microbial functions. Stable-isotope probing (SIP) is a powerful strategy to elucidate the ecophysiology of microorganisms in complex host-associated microbiotas. Here, we suggest that SIP methodologies should be more frequently exploited as part of a holistic functional microbiomics approach. We provide examples of how SIP has been used to study host-associated microbes in vivo and ex vivo. We highlight recent developments in SIP technologies and discuss future directions that will facilitate deeper insights into the function of human and animal microbiomes.

  • Characterization of the first “Candidatus Nitrotoga” isolate reveals metabolic versatility and separate evolution of widespread nitrite-oxidizing bacteria

    Kitzinger K, Koch H, Lücker S, Sedlacek CJ, Herbold CW, Schwarz J, Daebeler A, Mueller AJ, Lukumbuzya M, Romano S, Leisch N, Karst SM, Kirkegaard R, Albertsen M, Nielsen PH, Wagner M, Daims H
    2018 - mBio, 9: e01186-18

    Abstract: 

    Nitrification is a key process of the biogeochemical nitrogen cycle and of biological wastewater treatment. The second step, nitrite oxidation to nitrate, is catalyzed by phylogenetically diverse, chemolithoautotrophic nitrite-oxidizing bacteria (NOB). Uncultured NOB from the genus “Candidatus Nitrotoga” are widespread in natural and engineered ecosystems. Knowledge about their biology is sparse, because no genomic information and no pure “Ca. Nitrotoga” culture was available. Here we obtained the first “Ca. Nitrotoga” isolate from activated sludge. This organism, “Candidatus Nitrotoga fabula,” prefers higher temperatures (>20°C; optimum, 24 to 28°C) than previous “Ca. Nitrotoga” enrichments, which were described as cold-adapted NOB. “Ca. Nitrotoga fabula” also showed an unusually high tolerance to nitrite (activity at 30 mM NO2) and nitrate (up to 25 mM NO3). Nitrite oxidation followed Michaelis-Menten kinetics, with an apparent Km (Km(app)) of ~89 µM nitrite and a Vmax of ~28 µmol of nitrite per mg of protein per h. Key metabolic pathways of “Ca. Nitrotoga fabula” were reconstructed from the closed genome. “Ca. Nitrotoga fabula” possesses a new type of periplasmic nitrite oxidoreductase belonging to a lineage of mostly uncharacterized proteins. This novel enzyme indicates (i) separate evolution of nitrite oxidation in “Ca. Nitrotoga” and other NOB, (ii) the possible existence of phylogenetically diverse, unrecognized NOB, and (iii) together with new metagenomic data, the potential existence of nitrite-oxidizing archaea. For carbon fixation, “Ca. Nitrotoga fabula” uses the Calvin-Benson-Bassham cycle. It also carries genes encoding complete pathways for hydrogen and sulfite oxidation, suggesting that alternative energy metabolisms enable “Ca. Nitrotoga fabula” to survive nitrite depletion and colonize new niches.

  • Corrigendum: Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea.

    Bowers RM, Kyrpides NC, Stepanauskas R, Harmon-Smith M, Doud D, Reddy TBK, Schulz F, Jarett J, Rivers AR, Eloe-Fadrosh EA, Tringe SG, Ivanova NN, Copeland A, Clum A, Becraft ED, Malmstrom RR, Birren B, Podar M, Bork P, Weinstock GM, Garrity GM, Dodsworth JA, Yooseph S, Sutton G, Glöckner FO, Gilbert JA, Nelson WC, Hallam SJ, Jungbluth SP, Ettema TJG, Tighe S, Konstantinidis KT, Liu WT, Baker BJ, Rattei T, Eisen JA, Hedlund B, McMahon KD, Fierer N, Knight R, Finn R, Cochrane G, Karsch-Mizrachi I, Tyson GW, Rinke C, Lapidus A, Meyer F, Yilmaz P, Parks DH, Eren AM, Schriml L, Banfield JF, Hugenholtz P, Woyke T
    2018 - Nat. Biotechnol., 7: 660
  • Viruses of the Nahant Collection, characterization of 251 marine Vibrionaceae viruses.

    Kauffman KM, Brown JM, Sharma RS, VanInsberghe D, Elsherbini J, Polz MF, Kelly L
    2018 - Sci Data, 180114

    Abstract: 

    Viruses are highly discriminating in their interactions with host cells and are thought to play a major role in maintaining diversity of environmental microbes. However, large-scale ecological and genomic studies of co-occurring virus-host pairs, required to characterize the mechanistic and genomic foundations of virus-host interactions, are lacking. Here, we present the largest dataset of cultivated and sequenced co-occurring virus-host pairs that captures ecologically representative fine-scale diversity. Using the ubiquitous and ecologically diverse marine Vibrionaceae as a host platform, we isolate and sequence 251 dsDNA viruses and their hosts from three time points within a 93-day time-series study. The virus collection includes representatives of the three Caudovirales tailed virus morphotypes, a novel family of nontailed viruses, and the smallest (10,046 bp) and largest (348,911 bp) Vibrio virus genomes described. We provide general characterization and annotation of the viruses and describe read-mapping protocols to standardize genome presentation. The rich ecological and genomic contextualization of hosts and viruses make the Nahant Collection a unique platform for high-resolution studies of environmental virus-host infection networks.

  • Widespread distribution of prophage-encoded virulence factors in marine Vibrio communities.

    Castillo D, Kauffman K, Hussain F, Kalatzis P, Rørbo N, Polz MF, Middelboe M
    2018 - Sci Rep, 1: 9973

    Abstract: 

    Prophages are known to encode important virulence factors in the human pathogen Vibrio cholerae. However, little is known about the occurrence and composition of prophage-encoded traits in environmental vibrios. A database of 5,674 prophage-like elements constructed from 1,874 Vibrio genome sequences, covering sixty-four species, revealed that prophage-like elements encoding possible properties such as virulence and antibiotic resistance are widely distributed among environmental vibrios, including strains classified as non-pathogenic. Moreover, we found that 45% of Vibrio species harbored a complete prophage-like element belonging to the Inoviridae family, which encode the zonula occludens toxin (Zot) previously described in the V. cholerae. Interestingly, these zot-encoding prophages were found in a variety of Vibrio strains covering both clinical and marine isolates, including strains from deep sea hydrothermal vents and deep subseafloor sediments. In addition, the observation that a spacer from the CRISPR locus in the marine fish pathogen V. anguillarum strain PF7 had 95% sequence identity with a zot gene from the Inoviridae prophage found in V. anguillarum strain PF4, suggests acquired resistance to inoviruses in this species. Altogether, our results contribute to the understanding of the role of prophages as drivers of evolution and virulence in the marine Vibrio bacteria.

  • Fluorinated Gold Nanoparticles for Nanostructure Imaging Mass Spectrometry.

    Palermo A, Forsberg EM, Warth B, Aisporna AE, Billings E, Kuang E, Benton HP, Berry D, Siuzdak G
    2018 - in press

    Abstract: 

    Nanostructure imaging mass spectrometry (NIMS) with fluorinated gold nanoparticles (f-AuNPs) is a nanoparticle assisted laser desorption/ionization approach that requires low laser energy and has demonstrated high sensitivity. Here we describe NIMS with f-AuNPs for the comprehensive analysis of metabolites in biological tissues. F-AuNPs assist in desorption/ionization by laser-induced release of the fluorocarbon chains with minimal background noise. Since the energy barrier required to release the fluorocarbons from the AuNPs is minimal, the energy of the laser is maintained in the low μJ/pulse range, thus limiting metabolite in-source fragmentation. Electron microscopy analysis of tissue samples after f-AuNP NIMS shows a distinct "raising" of the surface as compared to matrix assisted laser desorption ionization ablation, indicative of a gentle desorption mechanism aiding in the generation of intact molecular ions. Moreover, the use of perfluorohexane to distribute the f-AuNPs on the tissue creates a hydrophobic environment minimizing metabolite solubilization and spatial dislocation. The transfer of the energy from the incident laser to the analytes through the release of the fluorocarbon chains similarly enhances the desorption/ionization of metabolites of different chemical nature, resulting in heterogeneous metabolome coverage. We performed the approach in a comparative study of the colon of mice exposed to three different diets. F-AuNP NIMS allows the direct detection of carbohydrates, lipids, bile acids, sulfur metabolites, amino acids, nucleotide precursors as well as other small molecules of varied biological origins. Ultimately, the diversified molecular coverage obtained provides a broad picture of a tissue's metabolic organization.

  • Signatures of ecological processes in microbial community time series.

    Faust K, Bauchinger F, Laroche B, de Buyl S, Lahti L, Washburne AD, Gonze D, Widder S
    2018 - Microbiome, 1: 120

    Abstract: 

    Growth rates, interactions between community members, stochasticity, and immigration are important drivers of microbial community dynamics. In sequencing data analysis, such as network construction and community model parameterization, we make implicit assumptions about the nature of these drivers and thereby restrict model outcome. Despite apparent risk of methodological bias, the validity of the assumptions is rarely tested, as comprehensive procedures are lacking. Here, we propose a classification scheme to determine the processes that gave rise to the observed time series and to enable better model selection.
    We implemented a three-step classification scheme in R that first determines whether dependence between successive time steps (temporal structure) is present in the time series and then assesses with a recently developed neutrality test whether interactions between species are required for the dynamics. If the first and second tests confirm the presence of temporal structure and interactions, then parameters for interaction models are estimated. To quantify the importance of temporal structure, we compute the noise-type profile of the community, which ranges from black in case of strong dependency to white in the absence of any dependency. We applied this scheme to simulated time series generated with the Dirichlet-multinomial (DM) distribution, Hubbell's neutral model, the generalized Lotka-Volterra model and its discrete variant (the Ricker model), and a self-organized instability model, as well as to human stool microbiota time series. The noise-type profiles for all but DM data clearly indicated distinctive structures. The neutrality test correctly classified all but DM and neutral time series as non-neutral. The procedure reliably identified time series for which interaction inference was suitable. Both tests were required, as we demonstrated that all structured time series, including those generated with the neutral model, achieved a moderate to high goodness of fit to the Ricker model.
    We present a fast and robust scheme to classify community structure and to assess the prevalence of interactions directly from microbial time series data. The procedure not only serves to determine ecological drivers of microbial dynamics, but also to guide selection of appropriate community models for prediction and follow-up analysis.

  • Distinct Microbial Assemblage Structure and Archaeal Diversity in Sediments of Arctic Thermokarst Lakes Differing in Methane Sources.

    Matheus Carnevali PB, Herbold CW, Hand KP, Priscu JC, Murray AE
    2018 - Front Microbiol, 1192

    Abstract: 

    Developing a microbial ecological understanding of Arctic thermokarst lake sediments in a geochemical context is an essential first step toward comprehending the contributions of these systems to greenhouse gas emissions, and understanding how they may shift as a result of long term changes in climate. In light of this, we set out to study microbial diversity and structure in sediments from four shallow thermokarst lakes in the Arctic Coastal Plain of Alaska. Sediments from one of these lakes (Sukok) emit methane (CH) of thermogenic origin, as expected for an area with natural gas reserves. However, sediments from a lake 10 km to the North West (Siqlukaq) produce CH of biogenic origin. Sukok and Siqlukaq were chosen among the four lakes surveyed to test the hypothesis that active CH-producing organisms (methanogens) would reflect the distribution of CH gas levels in the sediments. We first examined the structure of the little known microbial community inhabiting the thaw bulb of arctic thermokarst lakes near Barrow, AK. Molecular approaches (PCR-DGGE and iTag sequencing) targeting the SSU rRNA gene and rRNA molecule were used to profile diversity, assemblage structure, and identify potentially active members of the microbial assemblages. Overall, the potentially active (rRNA dominant) fraction included taxa that have also been detected in other permafrost environments (e.g., Bacteroidetes, Actinobacteria, Nitrospirae, Chloroflexi, and others). In addition, Siqlukaq sediments were unique compared to the other sites, in that they harbored CH-cycling organisms (i.e., methanogenic Archaea and methanotrophic Bacteria), as well as bacteria potentially involved in N cycling (e.g., Nitrospirae) whereas Sukok sediments were dominated by taxa typically involved in photosynthesis and biogeochemical sulfur (S) transformations. This study revealed a high degree of archaeal phylogenetic diversity in addition to CH-producing archaea, which spanned nearly the phylogenetic extent of currently recognized Archaea phyla (e.g., Euryarchaeota, Bathyarchaeota, Thaumarchaeota, Woesearchaeota, Pacearchaeota, and others). Together these results shed light on expansive bacterial and archaeal diversity in Arctic thermokarst lakes and suggest important differences in biogeochemical potential in contrasting Arctic thermokarst lake sediment ecosystems.

  • Inter-individual variability in copepod microbiomes reveals bacterial networks linked to host physiology.

    Datta MS, Almada AA, Baumgartner MF, Mincer TJ, Tarrant AM, Polz MF
    2018 - ISME J, 9: 2103-2113

    Abstract: 

    Copepods harbor diverse bacterial communities, which collectively carry out key biogeochemical transformations in the ocean. However, bulk copepod sampling averages over the variability in their associated bacterial communities, thereby limiting our understanding of the nature and specificity of copepod-bacteria associations. Here, we characterize the bacterial communities associated with nearly 200 individual Calanus finmarchicus copepods transitioning from active growth to diapause. We find that all individual copepods sampled share a small set of "core" operational taxonomic units (OTUs), a subset of which have also been found associated with other marine copepod species in different geographic locations. However, most OTUs are patchily distributed across individual copepods, thereby driving community differences across individuals. Among patchily distributed OTUs, we identified groups of OTUs correlated with common ecological drivers. For instance, a group of OTUs positively correlated with recent copepod feeding served to differentiate largely active growing copepods from those entering diapause. Together, our results underscore the power of individual-level sampling for understanding host-microbiome relationships.

  • Detection of Chlamydiaceae and Chlamydia-like organisms on the ocular surface of children and adults from a trachoma-endemic region

    Ghasemian E, Inic-Kanada A, Collingro A, Tagini F, Stein E, Alchalabi H, Schuerer N, Keše D, Babiker BE, Borel N, Greub G, Barisani-Asenbauer T
    2018 - Sci Rep, 1: 7432

    Abstract: 

    Trachoma, the leading infectious cause of blindness, is caused by Chlamydia trachomatis (Ct), a bacterium of the phylum Chlamydiae. Recent investigations revealed the existence of additional families within the phylum Chlamydiae, also termed Chlamydia-like organisms (CLOs). In this study, the frequency of Ct and CLOs was examined in the eyes of healthy Sudanese (control) participants and those with trachoma (case). We tested 96 children (54 cases and 42 controls) and 93 adults (51 cases and 42 controls) using broad-range Chlamydiae and Ct-specific (omcB) real-time PCR. Samples positive by broad-range Chlamydiae testing were subjected to DNA sequencing. Overall Chlamydiae prevalence was 36%. Sequences corresponded to unclassified and classified Chlamydiae. Ct infection rate was significantly higher in children (31.5%) compared to adults (0%) with trachoma (p < 0.0001). In general, 21.5% of adults and 4.2% of children tested positive for CLOs (p = 0.0003). Our findings are consistent with previous investigations describing the central role of Ct in trachoma among children. This is the first study examining human eyes for the presence of CLOs. We found an age-dependent distribution of CLO DNA in human eyes with significantly higher positivity in adults. Further studies are needed to understand the impact of CLOs in trachoma pathogenicity and/or protection.

  • Long-distance electron transport in individual, living cable bacteria.

    Bjerg JT, Boschker HTS, Larsen S, Berry D, Schmid M, Millo D, Tataru P, Meysman FJR, Wagner M, Nielsen LP, Schramm A
    2018 - Proc. Natl. Acad. Sci. U.S.A., 22: 5786-5791

    Abstract: 

    Electron transport within living cells is essential for energy conservation in all respiring and photosynthetic organisms. While a few bacteria transport electrons over micrometer distances to their surroundings, filaments of cable bacteria are hypothesized to conduct electric currents over centimeter distances. We used resonance Raman microscopy to analyze cytochrome redox states in living cable bacteria. Cable-bacteria filaments were placed in microscope chambers with sulfide as electron source and oxygen as electron sink at opposite ends. Along individual filaments a gradient in cytochrome redox potential was detected, which immediately broke down upon removal of oxygen or laser cutting of the filaments. Without access to oxygen, a rapid shift toward more reduced cytochromes was observed, as electrons were no longer drained from the filament but accumulated in the cellular cytochromes. These results provide direct evidence for long-distance electron transport in living multicellular bacteria.

  • Function and functional redundancy in microbial systems.

    Louca S, Polz MF, Mazel F, Albright MBN, Huber JA, O'Connor MI, Ackermann M, Hahn AS, Srivastava DS, Crowe SA, Doebeli M, Parfrey LW
    2018 - Nat Ecol Evol, 6: 936-943

    Abstract: 

    Microbial communities often exhibit incredible taxonomic diversity, raising questions regarding the mechanisms enabling species coexistence and the role of this diversity in community functioning. On the one hand, many coexisting but taxonomically distinct microorganisms can encode the same energy-yielding metabolic functions, and this functional redundancy contrasts with the expectation that species should occupy distinct metabolic niches. On the other hand, the identity of taxa encoding each function can vary substantially across space or time with little effect on the function, and this taxonomic variability is frequently thought to result from ecological drift between equivalent organisms. Here, we synthesize the powerful paradigm emerging from these two patterns, connecting the roles of function, functional redundancy and taxonomy in microbial systems. We conclude that both patterns are unlikely to be the result of ecological drift, but are inevitable emergent properties of open microbial systems resulting mainly from biotic interactions and environmental and spatial processes.

  • Age alters uptake pattern of organic and inorganic nitrogen by rubber trees

    Liu M, Xu F, Xu X, Wanek W, Yang X
    2018 - Tree Physiology, 38: 1685-1693

    Abstract: 

    Several studies have explored plant nutrient acquisition during ecosystem succession, but it remains unclear how age affects nitrogen (N) acquisition by the same tree species. Clarifying the age effect will be beneficial to fertilization management through improving N-use efficiency and reducing the risk of environmental pollution due to NO3 leaching. To clarify the effect of age on N uptake, rubber (Hevea brasiliensis (Willd. ex A. Juss.) Muell. Arg.) plantations of five ages (7, 16, 24, 32 and 49 years) were selected in Xishuangbanna of southern China for brief 15N exposures of intact roots using field hydroponic experiments. 15Nlabeled NH4 +, NO3 or glycine were applied in this study. All targeted rubber trees uptake rates followed an order of NH4 + > glycine > NO3 . As age increased, NH4 + uptake increased first and then decreased sharply, partly consistent with the pattern of soil NH4 + concentrations. Uptake of glycine decreased first and then increased gradually, while no significant change of NO3 uptake rates existed with increasing age. Overall, rubber trees with ages from 7 to 49 years all showed a preference for NH4 + uptake. Young rubber trees (7 and 16 years) had higher NH4 + and lower glycine preferences than older trees (24, 32 and 49 years). Mycorrhizal colonization rates of rubber trees were higher in intermediately aged plantations (16, 24 and 32 years) than in plantations aged 7 and 49 years. A positive relationship was observed between arbuscular mycorrhizal colonization rates and NO3 preference. The results from this study demonstrate that rubber trees do not change their preference for NH4 + but strongly decreased their reliance on it with age. These findings indicate that the shift of N uptake patterns with age should be taken into account for rubber fertilization management to improve N-use efficiency and reduce the risk of environmental pollution during rubber production.

  • Evolution of a Vegetarian Vibrio: Metabolic Specialization of Vibrio breoganii to Macroalgal Substrates.

    Corzett CH, Elsherbini J, Chien DM, Hehemann JH, Henschel A, Preheim SP, Yu X, Alm EJ, Polz MF
    2018 - J. Bacteriol., 15: in press

    Abstract: 

    While most are considered generalists that thrive on diverse substrates, including animal-derived material, we show that has specialized for the consumption of marine macroalga-derived substrates. Genomic and physiological comparisons of with other isolates revealed the ability to degrade alginate, laminarin, and additional glycans present in algal cell walls. Moreover, the widely conserved ability to hydrolyze animal-derived polymers, including chitin and glycogen, was lost, along with the ability to efficiently grow on a variety of amino acids. Ecological data showing associations with particulate algal material but not zooplankton further support this shift in niche preference, and the loss of motility appears to reflect a sessile macroalga-associated lifestyle. Together, these findings indicate that algal polysaccharides have become a major source of carbon and energy in , and these ecophysiological adaptations may facilitate transient commensal associations with marine invertebrates that feed on algae. Vibrios are often considered animal specialists or generalists. Here, we show that has undergone massive genomic changes to become specialized on algal carbohydrates. Accompanying genomic changes include massive gene import and loss. These vibrios may help us better understand how algal biomass is degraded in the environment and may serve as a blueprint on how to optimize the conversion of algae to biofuels.

  • Microbial conservation in the Anthropocene.

    Webster NS, Wagner M, Negri AP
    2018 - Environ. Microbiol., in press
  • Microbiomes : Importance of invertebrates in understanding the natural variety of animal-microbe interactions

    Petersen JM, Osvatic J
    2018 - mSystems, 2: in press

    Abstract: 

    Animals evolved in a world teeming with microbes, which play pivotal roles in their health, development, and evolution. Although the overwhelming majority of living animals are invertebrates, the minority of "microbiome" studies focus on this group. Interest in invertebrate-microbe interactions is 2-fold-a range of immune components are conserved across almost all animal (including human) life, and their functional roles may be conserved. Thus, understanding cross talk between microbes and invertebrate animals can lead to insights of broader relevance. Invertebrates offer unique opportunities to "eavesdrop" on intricate host-microbe conversations because they tend to associate with fewer microbes. On the other hand, considering the vast diversity of form and function that has evolved in the invertebrates, they likely evolved an equally diverse range of ways to interact with beneficial microbes. We have investigated only a few of these interactions in detail; thus, there is still great potential for fundamentally new discoveries.

  • A multi-isotopic approach to investigate the influence of land use on nitrate removal in a highly saline lake-aquifer system

    Valiente N, Carrey R, Otero N, Soler A, Sanz D, Muñoz-Martín A, Jirsa F, Wanek W, Gómez-Alday JJ
    2018 - Science of The Total Environment, 631: 649-659

    Abstract: 

    Endorheic or closed drainage basins in arid and semi-arid regions are vulnerable to pollution. Nonetheless, in the freshwater-saltwater interface of endorheic saline lakes, oxidation-reduction (redox) reactions can attenuate pollutants such as nitrate (NO3-). This study traces the ways of nitrogen (N) removal in the Pétrola lake-aquifer system (central Spain), an endorheic basin contaminated with NO3- (up to 99.2mg/L in groundwater). This basin was declared vulnerable to NO3- pollution in 1998 due to the high anthropogenic pressures (mainly agriculture and wastewaters). Hydrochemical, multi-isotopic (δ18ONO3, δ15NNO3, δ13CDIC, δ18OH2O, and δ2HH2O) and geophysical techniques (electrical resistivity tomography) were applied to identify the main redox processes at the freshwater-saltwater interface. The results showed that the geometry of this interface is influenced by land use, causing spatial variability of nitrogen biogeochemical processes over the basin. In the underlying aquifer, NO3- showed an average concentration of 38.5mg/L (n=73) and was mainly derived from agricultural inputs. Natural attenuation of NO3- was observed in dryland farming areas (up to 72%) and in irrigation areas (up to 66%). In the Pétrola Lake, mineralization and organic matter degradation in lake sediment play an important role in NO3- reduction. Our findings are a major step forward in understanding freshwater-saltwater interfaces as reactive zones for NO3- attenuation. We further emphasize the importance of including a land use perspective when studying water quality-environmental relationships in hydrogeological systems dominated by density-driven circulation.

  • Cultivation and genomic analysis of “Candidatus Nitrosocaldus islandicus”, an obligately thermophilic, ammonia-oxidizing thaumarchaeon from a hot spring biofilm in Graendalur valley, Iceland

    Daebeler A, Herbold CW, Vierheilig J, Sedlacek CJ, Pjevac P, Albertsen M, Kirkegaard RH, De La Torre JR, Daims H, Wagner M
    2018 - Front Microbiol, 9: 193

    Abstract: 

    Ammonia-oxidizing archaea (AOA) within the phylum Thaumarchaeota are the only known aerobic ammonia oxidizers in geothermal environments. Although molecular data indicate the presence of phylogenetically diverse AOA from the Nitrosocaldus clade, group 1.1b and group 1.1a Thaumarchaeota in terrestrial high-temperature habitats, only one enrichment culture of an AOA thriving above 50 °C has been reported and functionally analyzed. In this study, we physiologically and genomically characterized a newly discovered thaumarchaeon from the deep-branching Nitrosocaldaceae family of which we have obtained a high (~85 %) enrichment from biofilm of an Icelandic hot spring (73 °C). This AOA, which we provisionally refer to as “Candidatus Nitrosocaldus islandicus”, is an obligately thermophilic, aerobic chemolithoautotrophic ammonia oxidizer, which stoichiometricall converts ammonia to nitrite at temperatures between 50 °C and 70 °C. “Ca. N. islandicus” encodes the expected repertoire of enzymes proposed to be required for archaeal ammonia oxidation, but unexpectedly lacks a nirK gene and also possesses no identifiable other enzyme for nitric oxide (NO) generation*. Nevertheless, ammonia oxidation by this AOA appears to be NO-dependent as “Ca. N. islandicus” is, like all other tested AOA, inhibited by the addition of an NO scavenger. Furthermore, comparative genomics revealed that “Ca. N. islandicus” has the potential for aromatic amino acid fermentation as its genome encodes an indolepyruvate oxidoreductase (iorAB) as well as a type 3b hydrogenase, which are not present in any other sequenced AOA. A further surprising genomic feature of this thermophilic ammonia oxidizer is the absence of DNA polymerase D genes – one of the predominant replicative DNA polymerases in all other ammonia-oxidizing Thaumarchaeota. Collectively, our findings suggest that metabolic versatility and DNA replication might differ substantially between obligately thermophilic and other AOA.

  • Peatland Acidobacteria with a dissimilatory sulfur metabolism

    Hausmann B, Pelikan C, Herbold CW, Köstlbacher S, Albertsen M, Eichorst SA, Glavina Del Rio T, Huemer M, Nielsen PH, Rattei T, Stingl U, Tringe SG, Trojan D, Wentrup C, Woebken D, Pester M, Loy A
    2018 - ISME J, 12: 1729-1742

    Abstract: 

    Sulfur-cycling microorganisms impact organic matter decomposition in wetlands and consequently greenhouse gas emissions from these globally relevant environments. However, their identities and physiological properties are largely unknown. By applying a functional metagenomics approach to an acidic peatland, we recovered draft genomes of seven novel Acidobacteria species with the potential for dissimilatory sulfite (dsrAB, dsrC, dsrD, dsrN, dsrT, dsrMKJOP) or sulfate respiration (sat, aprBA, qmoABC plus dsr genes). Surprisingly, the genomes also encoded DsrL, which so far was only found in sulfur-oxidizing microorganisms. Metatranscriptome analysis demonstrated expression of acidobacterial sulfur-metabolism genes in native peat soil and their upregulation in diverse anoxic microcosms. This indicated an active sulfate respiration pathway, which, however, might also operate in reverse for dissimilatory sulfur oxidation or disproportionation as proposed for the sulfur-oxidizing Desulfurivibrio alkaliphilus. Acidobacteria that only harbored genes for sulfite reduction additionally encoded enzymes that liberate sulfite from organosulfonates, which suggested organic sulfur compounds as complementary energy sources. Further metabolic potentials included polysaccharide hydrolysis and sugar utilization, aerobic respiration, several fermentative capabilities, and hydrogen oxidation. Our findings extend both, the known physiological and genetic properties of Acidobacteria and the known taxonomic diversity of microorganisms with a DsrAB-based sulfur metabolism, and highlight new fundamental niches for facultative anaerobic Acidobacteria in wetlands based on exploitation of inorganic and organic sulfur molecules for energy conservation.

  • Expanded diversity of microbial groups that shape the dissimilatory sulfur cycle

    Anantharaman K, Hausmann B, Jungbluth SP, Kantor RS, Lavy A, Warren LA, Rappé MS, Pester M, Loy A, Thomas BC, Banfield JF
    2018 - ISME J, 12: 1715-1728

    Abstract: 

    A critical step in the biogeochemical cycle of sulfur on Earth is microbial sulfate reduction, yet organisms from relatively few lineages have been implicated in this process. Previous studies using functional marker genes have detected abundant, novel dissimilatory sulfite reductases (DsrAB) that could confer the capacity for microbial sulfite/sulfate reduction but were not affiliated with known organisms. Thus, the identity of a significant fraction of sulfate/sulfite-reducing microbes has remained elusive. Here we report the discovery of the capacity for sulfate/sulfite reduction in the genomes of organisms from thirteen bacterial and archaeal phyla, thereby more than doubling the number of microbial phyla associated with this process. Eight of the thirteen newly identified groups are candidate phyla that lack isolated representatives, a finding only possible given genomes from metagenomes. Organisms from Verrucomicrobia and two candidate phyla, Candidatus Rokubacteria and Candidatus Hydrothermarchaeota, contain some of the earliest evolved dsrAB genes. The capacity for sulfite reduction has been laterally transferred in multiple events within some phyla, and a key gene potentially capable of modulating sulfur metabolism in associated cells has been acquired by putatively symbiotic bacteria. We conclude that current functional predictions based on phylogeny significantly underestimate the extent of sulfate/sulfite reduction across Earth’s ecosystems. Understanding the prevalence of this capacity is integral to interpreting the carbon cycle because sulfate reduction is often coupled to turnover of buried organic carbon. Our findings expand the diversity of microbial groups associated with sulfur transformations in the environment and motivate revision of biogeochemical process models based on microbial community composition.

  • Ecology and Biotechnological Potential of Bacteria Belonging to the Genus Pseudovibrio.

    Romano S
    2018 - 8: in press

    Abstract: 

    Members of the genus have been isolated worldwide from a great variety of marine sources as both free-living and host-associated bacteria. So far, the available data depict a group of alphaproteobacteria characterized by a versatile metabolism, which allows them to use a variety of substrates to meet their carbon, nitrogen, sulfur, and phosphorous requirements. Additionally, -related bacteria have been shown to proliferate under extreme oligotrophic conditions, tolerate high heavy-metal concentrations, and metabolize potentially toxic compounds. Considering this versatility, it is not surprising that they have been detected from temperate to tropical regions and are often the most abundant isolates obtained from marine invertebrates. Such an association is particularly recurrent with marine sponges and corals, animals that play a key role in benthic marine systems. The data so far available indicate that these bacteria are mainly beneficial to the host, and besides being involved in major nutrient cycles, they could provide the host with both vitamins/cofactors and protection from potential pathogens via the synthesis of antimicrobial secondary metabolites. In fact, the biosynthetic abilities of spp. have been emerging in recent years, and both genomic and analytic studies have underlined how these organisms promise novel natural products of biotechnological value.

  • NanoSIMS and tissue autoradiography reveal symbiont carbon fixation and organic carbon transfer to giant ciliate host.

    Volland JM, Schintlmeister A, Zambalos H, Reipert S, Mozetič P, Espada-Hinojosa S, Turk V, Wagner M, Bright M
    2018 - ISME J, 3: 714-727

    Abstract: 

    The giant colonial ciliate Zoothamnium niveum harbors a monolayer of the gammaproteobacteria Cand. Thiobios zoothamnicoli on its outer surface. Cultivation experiments revealed maximal growth and survival under steady flow of high oxygen and low sulfide concentrations. We aimed at directly demonstrating the sulfur-oxidizing, chemoautotrophic nature of the symbionts and at investigating putative carbon transfer from the symbiont to the ciliate host. We performed pulse-chase incubations with C- and C-labeled bicarbonate under varying environmental conditions. A combination of tissue autoradiography and nanoscale secondary ion mass spectrometry coupled with transmission electron microscopy was used to follow the fate of the radioactive and stable isotopes of carbon, respectively. We show that symbiont cells fix substantial amounts of inorganic carbon in the presence of sulfide, but also (to a lesser degree) in the absence of sulfide by utilizing internally stored sulfur. Isotope labeling patterns point to translocation of organic carbon to the host through both release of these compounds and digestion of symbiont cells. The latter mechanism is also supported by ultracytochemical detection of acid phosphatase in lysosomes and in food vacuoles of ciliate cells. Fluorescence in situ hybridization of freshly collected ciliates revealed that the vast majority of ingested microbial cells were ectosymbionts.

  • Coexistence of novel gammaproteobacterial and Arsenophonus symbionts in the scale insect Greenisca brachypodii (Hemiptera, Coccomorpha: Eriococcidae)

    Michalik A, Schulz F, Michalik K, Wascher F, Horn M, Szklarzewicz T
    2018 - Environ. Microbiol., in press

    Abstract: 

    Scale insects are commonly associated with obligate, intracellular microorganisms which play important roles in complementing their hosts with essential nutrients. Here we characterized the symbiotic system of Greenisca brachypodii, a member of the family Eriococcidae. Histological and ultrastructural analyses have indicated that G. brachypodii is stably associated with coccoid and rod-shaped bacteria. Phylogenetic analyses have revealed that the coccoid bacteria represent a sister group to the secondary symbiont of the mealybug Melanococcus albizziae, whereas the rod-shaped symbionts are close relatives of Arsenophonus symbionts in insects - to our knowledge, this is the first report of the presence of Arsenophonus bacterium in scale insects. As a comparison of 16S and 23S rRNA genes sequences of the G. brachypodii coccoid symbiont with other gammaprotebacterial sequences showed only low similarity (∼90%), we propose the name 'Candidatus Kotejella greeniscae' for its tentative classification. Both symbionts are transovarially transmitted from one generation to the next. The infection takes place in the neck region of the ovariole. The bacteria migrate between follicular cells, as well as through the cytoplasm of those cells to the perivitelline space, where they form a characteristic 'symbiont ball'. Our findings provide evidence for a polyphyletic origin of symbionts of Eriococcidae. This article is protected by copyright. All rights reserved.

  • A major lineage of non-tailed dsDNA viruses as unrecognized killers of marine bacteria.

    Kauffman KM, Hussain FA, Yang J, Arevalo P, Brown JM, Chang WK, VanInsberghe D, Elsherbini J, Sharma RS, Cutler MB, Kelly L, Polz MF
    2018 - Nature, 7690: 118-122

    Abstract: 

    The most abundant viruses on Earth are thought to be double-stranded DNA (dsDNA) viruses that infect bacteria. However, tailed bacterial dsDNA viruses (Caudovirales), which dominate sequence and culture collections, are not representative of the environmental diversity of viruses. In fact, non-tailed viruses often dominate ocean samples numerically, raising the fundamental question of the nature of these viruses. Here we characterize a group of marine dsDNA non-tailed viruses with short 10-kb genomes isolated during a study that quantified the diversity of viruses infecting Vibrionaceae bacteria. These viruses, which we propose to name the Autolykiviridae, represent a novel family within the ancient lineage of double jelly roll (DJR) capsid viruses. Ecologically, members of the Autolykiviridae have a broad host range, killing on average 34 hosts in four Vibrio species, in contrast to tailed viruses which kill on average only two hosts in one species. Biochemical and physical characterization of autolykiviruses reveals multiple virion features that cause systematic loss of DJR viruses in sequencing and culture-based studies, and we describe simple procedural adjustments to recover them. We identify DJR viruses in the genomes of diverse major bacterial and archaeal phyla, and in marine water column and sediment metagenomes, and find that their diversity greatly exceeds the diversity that is currently captured by the three recognized families of such viruses. Overall, these data suggest that viruses of the non-tailed dsDNA DJR lineage are important but often overlooked predators of bacteria and archaea that impose fundamentally different predation and gene transfer regimes on microbial systems than on tailed viruses, which form the basis of all environmental models of bacteria-virus interactions.

  • High resolution time series reveals cohesive but short-lived communities in coastal plankton.

    Martin-Platero AM, Cleary B, Kauffman K, Preheim SP, McGillicuddy DJ, Alm EJ, Polz MF
    2018 - Nat Commun, 1: 266

    Abstract: 

    Because microbial plankton in the ocean comprise diverse bacteria, algae, and protists that are subject to environmental forcing on multiple spatial and temporal scales, a fundamental open question is to what extent these organisms form ecologically cohesive communities. Here we show that although all taxa undergo large, near daily fluctuations in abundance, microbial plankton are organized into clearly defined communities whose turnover is rapid and sharp. We analyze a time series of 93 consecutive days of coastal plankton using a technique that allows inference of communities as modular units of interacting taxa by determining positive and negative correlations at different temporal frequencies. This approach shows both coordinated population expansions that demarcate community boundaries and high frequency of positive and negative associations among populations within communities. Our analysis thus highlights that the environmental variability of the coastal ocean is mirrored in sharp transitions of defined but ephemeral communities of organisms.

  • Evidence for H2 consumption by uncultured Desulfobacterales in coastal sediments.

    Dyksma S, Pjevac P, Ovanesov K, Greuter L
    2018 - Environ. Microbiol., In press

    Abstract: 

    Molecular hydrogen (H2 ) is the key intermediate in the anaerobic degradation of organic matter. Its removal by H2 -oxidizing microorganisms is essential to keep anaerobic degradation energetically favorable. Sulfate-reducing microorganisms (SRM) are known as the main H2 scavengers in anoxic marine sediments. Although the community of marine SRM has been extensively studied, those consuming H2 in situ are completely unknown. We combined metagenomics, PCR-based clone libraries, single-amplified genomes (SAGs) and metatranscriptomics to identify potentially H2 -consuming SRM in anoxic coastal sediments. The vast majority of SRM-related H2 ase sequences were assigned to group 1b and 1c [NiFe]-H2 ases of the deltaproteobacterial order Desulfobacterales. Surprisingly, the same sequence types were similarly highly expressed in spring and summer, suggesting that these are stable and integral members of the H2 -consuming community. Notably, one sequence cluster from the SRM group 1 consistently accounted for around half of all [NiFe]-H2 ase transcripts. Using SAGs, we could link this cluster with the 16S rRNA genes of the uncultured Sva0081-group of the family Desulfobacteraceae. Sequencing of 16S rRNA gene amplicons and H2 ase gene libraries suggested consistently high in situ abundance of the Sva0081 group also in other marine sediments. Together with other Desulfobacterales these likely are important H2 -scavengers in marine sediments. This article is protected by copyright. All rights reserved.

Book chapters and other publications

8 Publications found
  • Mangroves in Contrasting Osmotic Environments: Photosynthetic Costs of High Salinity Tolerance.

    Watzka M, Medina E
    2018 - 69-91. in Photosynthesis. (García Cañedo J.C. and López Lizárraga G.L.)
  • Microplastic-Associated Biofilms: A Comparison of Freshwater and Marine Environments

    Harrison JP, Hoellein TJ, Sapp M, Tagg AS, Ju-Nam Y, Ojeda JJ
    2018 - 181-201. in Handbook of Environmental Chemistry, vol. 58. (Barceló, Damia; Kostianoy, Andrey G.). Springer Verlag, Berlin

    Abstract: 

    Microplastics (<5 mm particles) occur within both engineered and natural freshwater ecosystems, including wastewater treatment plants, lakes, rivers, and estuaries. While a significant proportion of microplastic pollution is likely sequestered within freshwater environments, these habitats also constitute an important conduit of microscopic polymer particles to oceans worldwide. The quantity of aquatic microplastic waste is predicted to dramatically increase over the next decade, but the fate and biological implications of this pollution are still poorly understood. A growing body of research has aimed to characterize the formation, composition, and spatiotemporal distribution of microplastic-associated (“plastisphere”) microbial biofilms. Plastisphere microorganisms have been suggested to play significant roles in pathogen transfer, modulation of particle buoyancy, and biodegradation of plastic polymers and co-contaminants, yet investigation of these topics within freshwater environments is at a very early stage. Here, what is known about marine plastisphere assemblages is systematically compared with up-to-date findings from freshwater habitats. Through analysis of key differences and likely commonalities between environments, we discuss how an integrated view of these fields of research will enhance our knowledge of the complex behavior and ecological impacts of microplastic pollutants.

  • International Committee on Systematics of Prokaryotes
 - Subcommittee on the taxonomy of Chlamydiae. Meeting minutes

    Borel N, Bavoil P, Greub G, Horn M
    2018 - Int. J. Syst. Evol. Microbiol., in press
  • Nitrolancea

    Sorokin DY, Lücker S, Daims H
    2018 - in Bergey’s Manual of Systematics of Archaea and Bacteria. John Wiley & Sons

    Abstract: 

    L. n. nitrum, native soda, natron, nitrate; L. fem. n. lancea. a lance; N.L. fem. n. Nitrolancea, a nitrate (‐forming) lance‐shaped bacterium.

    Chloroflexi / Thermomicrobia / Sphaerobacterales / Sphaerobacteraceae / Nitrolancea

    The genus Nitrolancea, classified within the family Sphaerobacteriaceae, order Sphaerobacteriales, class Thermomicrobia, phylum Chloroflexi, consists of aerobic bacteria that grow chemolithoautotrophically by oxidation of nitrite to nitrate and can also oxidize formate to CO2 as an additional energy source. The electron acceptor is O2. Nitrolancea represents the first example of nitrite‐oxidizing bacteria (NOB) in the phylum Chloroflexi. The only known species of the genus is the type species, Nitrolancea hollandica. The only strain (N. hollandica LbT) has been isolated from a lab‐scale nitrifying bioreactor with a high loading rate of ammonium bicarbonate.

    DNA G + C content (mol%): 62.6 (genome).

    Type species: Nitrolancea hollandica Sorokin, Vejmelkova, Lücker, Streshinskaya, Rijpstra, Sinninghe‐Damsté, Kleerbezem, van Loosdrecht, Muyzer and Daims 2014, 1864VP.

  • Stickstoffkreisläufe in der Abwasserreinigung - neue und bewährte Wege

    Daims H
    2018 - 31-46. in Wiener Mitteilungen Wasser-Abwasser-Gewässer, vol. 247. (Krampe, J; Kreuzinger, N)

    Abstract: 

    Der klassische Weg zur Stickstoff-Eliminierung in Kläranlagen beruht auf der Kombination von Nitrifikation und Denitrifikation. In den letzten Jahren haben molekularbiologische Methoden eine Vielzahl neuer Einblicke in die Biologie der Nitrifikanten (Ammoniak- und Nitritoxidierer) ergeben. Diese Erkenntnisse beinhalten eine unerwartet hohe Diversität dieser Bakterien, alternative Stoffwechselwege sowie komplett allein nitrifizierende Mikroben (Comammox-Organismen). Das resultierende neue Bild der Nitrifikation weicht stark vom etablierten Lehrbuchwissen ab. Ein kosten- und energieeffizienterer Weg zur Stickstoff-Eliminierung nutzt die anaerobe Ammoniumoxidation (Anammox-Prozess). Dieser Ansatz nutzt extrem langsam wachsende Bakterien und erfordert die selektive Unterdrückung bestimmter Organismen (Nitritoxidierer). Aus diesen Gründen ist der Anammox-Prozess zwar vielversprechend, die praktische Implementierung ist jedoch Gegenstand aktiver Forschungs- und Optimierungsarbeiten. Ein weiterer neuer Prozess, die nitrit-abhängige anaerobe Methanoxidation (n-damo), wird großtechnisch noch nicht eingesetzt. Insbesondere in Kombination mit Anammox könnte der n-damo Prozess zur gleichzeitigen Eliminierung von restlichem Methan und von Stickstoff interessant werden.

  • Draft genome sequence of Telmatospirillum siberiense 26-4b1T, an acidotolerant peatland alphaproteobacterium potentially involved in sulfur cycling

    Hausmann B, Pjevac P, Schreck K, Herbold CW, Daims H, Wagner M, Loy A
    2018 - Genome Announc, 6: e01524-17

    Abstract: 

    The facultative anaerobic chemoorganoheterotrophic alphaproteobacterium Telmatospirillum siberiense 26-4b1T was isolated from a Siberian peatland. We report on a 6.20 Mbp near complete, high quality draft genome of T. siberiense that reveals expected and novel metabolic potential for the genus Telmatospirillum, including genes for sulfur oxidation.

  • Soil—The Hidden Part of Climate. Microbial Processes Regulating Soil–Atmosphere Exchange of Greenhouse Gases

    Zechmeister­‐Boltenstern S, Díaz-Pinés E, Spann C, Hofmann K, Schnecker J, Reinsch S
    2018 - 50. in Soil and Climate. (Lal R, Stewart BA, 1st Edition, ISBN 9781498783651). CRC Press
  • Nitrospira

    Daims H, Wagner M
    2018 - Trends Microbiol., 5: 462-463

    Abstract: 

    In this infographic, the key metabolic functions of Nitrospira and the role that these bacteria play in nitrification and other processes in the environment is shown. Nitrospira plays pivotal roles in nitrification as an aerobic chemolithoautotrophic nitrite-oxidizing bacterium. These bacteria often occur in close association with ammonia-oxidizing bacteria or archaea that convert ammonia to nitrite, which is further oxidized to nitrate by Nitrospira. However, in 'reciprocal feeding' interactions, Nitrospira can also provide ammonia oxidizers with ammonia released from urea or cyanate, which is further nitrified as described above. Recently discovered Nitrospira members even catalyze both nitrification steps alone and are therefore called complete ammonia oxidizers or 'comammox' organisms. Some strains of Nitrospira utilize alternative substrates, such as H and formate, using oxygen or nitrate as terminal electron acceptor, and can exploit these energy sources concurrently with aerobic nitrite oxidation. This metabolic versatility enables Nitrospira to colonize a broad range of habitats and to sustain shifts in environmental conditions such as changing oxygen concentrations.

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