Metamenu

Publications

The fulltext of publications might not be freely accessible but require subscription. Please contact the authors to request reprints.

Publications in peer reviewed journals

87 Publications found
  • The Effect of pH and biogenic ligands on the weathering of chrysotile asbestos: The pivotal role of tetrahedral Fe in dissolution kinetics and radical formation

    Martin Walter, Walter D. C. Schenkeveld, Michael Reissner, Lars Gille, Stephan M. Kraemer
    2019 - Chemistry A European Journal, 13: 3286-3300

    Abstract: 

    Chrysotile asbestos is a soil pollutant in many countries. It is a carcinogenic mineral, partly due to its surface chemistry. In chrysotile, FeII and FeIII substitute Mg octahedra (Fe[6]), and FeIII substitutes Si tetrahedra (Fe[4]). Fe on fiber surfaces can generate hydroxyl radicals (HO.) in Fenton reactions, which damage biomolecules. To better understand chrysotile weathering in soils, net Mg and Si dissolution rates over the pH range 3.0–11.5 were determined in the presence and absence of biogenic ligands. Also, HO. generation and Fe bulk speciation of pristine and weathered fibers were examined by EPR and Mössbauer spectroscopy. Dissolution rates were increased by ligands and inversely related to pH with complete inhibition at cement pH (11.5). Surface‐exposed Mg layers readily dissolved at low pH, but only after days at neutral pH. On longer timescales, the slow dissolution of Si layers became rate‐determining. In the absence of ligands, Fe[6] precipitated as Fenton‐inactive Fe phases, whereas Fe[4] (7 % of bulk Fe) remained redox‐active throughout two‐week experiments and at pH 7.5 generated 50±10 % of the HO. yield of Fe[6] at pristine fiber surfaces. Ligand‐promoted dissolution of Fe[4] (and potentially Al[4]) labilized exposed Si layers. This increased Si and Mg dissolution rates and lowered HO. generation to near‐background level. It is concluded that Fe[4] surface species control long‐term HO. generation and dissolution rates of chrysotile at natural soil pH.

  • Substrate quality and concentration control decomposition and microbial strategies in a model soil system

    Schnecker J, Bowles T, Hobbie EA, Smith RG, Grandy AS
    2019 - Biogeochemistry, 144: 47-59

    Abstract: 

    Soil carbon models typically scale decomposition linearly with soil carbon (C) concentration, but this linear relationship has not been experimentally verified. Here we investigated the underlying biogeochemical mechanisms controlling the relationships between soil C concentration and decomposition rates. We incubated a soil/sand mixture with increasing amounts of finely ground plant residue in the laboratory at constant temperature and moisture for 63 days. The plant residues were rye (Secale cereale, C/N ratio of 23) and wheat straw (Triticum spp., C/N ratio of 109) at seven soil C concentrations ranging from 0.38 to 2.99%. We measured soil respiration, dissolved organic carbon (DOC) concentrations, microbial biomass, and potential enzyme activities over the course of the incubation. Rye, which had higher N and DOC contents, lost 6 to 8 times more C as CO2 compared to wheat residue. Under rye and wheat amendment, absolute C losses as CO2 (calculated per g dry soil) increased linearly with C concentration while relative C losses as CO2 (expressed as percent of initial C) increased with C concentration following a quadratic function. In low C concentration treatments (0.38–0.79% OC), DOC decreased gradually from day 3 to day 63, microbial C increased towards the end in the rye treatment or decreased only slightly with straw amendment, and microbes invested in general enzymes such as proteases and oxidative enzymes. At increasing C levels, enzyme activity shifted to degrading cellulose after 15 days and degrading microbial necromass (e.g. chitin) after 63 days. At the highest C concentrations (2.99% OC), microbial biomass peaked early in the incubation and remained high in the rye treatment and decreased only slightly in the wheat treatment. While wheat lost C as CO2 constantly at all C concentrations, respiration dynamics in the rye treatment strongly depended on C concentration. Our results indicate that litter quality and C concentration regulate enzyme activities, DOC concentrations, and microbial respiration. The potential for non-linear relationships between soil C concentration and decomposition may need to be considered in soil C models and soil C sequestration management approaches.

  • On the evolution and physiology of cable bacteria

    Kjeldsen KU, Schreiber L, Thorup CA, Boesen T, Bjerg JT, Yang T, Dueholm MS, Larsen S, Risgaard-Petersen N, Nierychlof M, Schmid M, Bøggildd A, van de Vossenbergh J, Geelhoedi JS, Meysman FJR, Wagner M, Nielsen PH, Nielsen LP, Schramm A
    2019 - Proc Natl Acad Sci U S A, PNAS Latest Articles
    Metabolic model for cable bacteria

    Abstract: 

    Cable bacteria of the family Desulfobulbaceae form centimeter- long filaments comprising thousands of cells. They occur world-wide in the surface of aquatic sediments, where they connect sulfide oxidation with oxygen or nitrate reduction via long-distance electron transport. In the absence of pure cultures, we used single-filament genomics and metagenomics to retrieve draft genomes of 3 marine Candidatus Electrothrix and 1 freshwater Ca. Electronema species. These genomes contain >50% unknown genes but still share their core genomic makeup with sulfate- reducing and sulfur-disproportionating Desulfobulbaceae, with few core genes lost and 212 unique genes (from 197 gene families) conserved among cable bacteria. Last common ancestor analysis indicates gene divergence and lateral gene transfer as equally important origins of these unique genes. With support from meta-proteomics of a Ca. Electronema enrichment, the genomes suggest that cable bacteria oxidize sulfide by reversing the canonical sulfate reduction pathway and fix CO2 using the Wood–Ljungdahl pathway. Cable bacteria show limited organotrophic potential, may assimilate smaller organic acids and alcohols, fix N2, and synthesize polyphosphates and polyglucose as storage compounds; several of these traits were confirmed by cell-level experimental analyses. We propose a model for electron flow from sulfide to oxygen that involves periplasmic cytochromes, yet-unidentified conductive periplasmic fibers, and periplasmic oxygen reduction. This model proposes that an active cable bacterium gains energy in the anodic, sulfide-oxidizing cells, whereas cells in the oxic zone flare off electrons through intense cathodic oxygen respiration without energy conservation; this peculiar form of multicellularity seems unparalleled in the microbial world.

  • Glacial runoff promotes deep burial of sulfur cycling-associated microorganisms in marine sediments

    Pelikan C, Jaussi M, Wasmund K, Seidenkrantz MS, Pearce C, Kuzyk ZZA, Herbold CW, Røy H, Kjeldsen KU, Loy A
    2019 - Front Microbiol, 10: 2558

    Abstract: 

    Marine fjords with active glacier outlets are hot spots for organic matter burial in the sediments and subsequent microbial mineralization. Here, we investigated controls on microbial community assembly in sub-arctic glacier-influenced (GI) and non-glacier-influenced (NGI) marine sediments in the Godthåbsfjord region, south-western Greenland. We used a correlative approach integrating 16S rRNA gene and dissimilatory sulfite reductase (dsrB) amplicon sequence data over six meters of depth with biogeochemistry, sulfur-cycling activities, and sediment ages. GI sediments were characterized by comparably high sedimentation rates and had ‘young’ sediment ages of <500 years even at 6 m sediment depth. In contrast, NGI stations reached ages of approximately 10,000 years at these depths. Sediment age-depth relationships, sulfate reduction rates, and C/N ratios were strongly correlated with differences in microbial community composition between GI and NGI sediments, indicating that age and diagenetic state were key drivers of microbial community assembly in subsurface sediments. Similar bacterial and archaeal communities were present in the surface sediments of all stations, whereas only in GI sediments were many surface taxa also abundant through the whole sediment core. The relative abundance of these taxa, including diverse Desulfobacteraceae members, correlated positively with sulfate reduction rates, indicating their active contributions to sulfur-cycling processes. In contrast, other surface community members, such as Desulfatiglans, Atribacteria and Chloroflexi, survived the slow sediment burial at NGI stations and dominated in the deepest sediment layers. These taxa are typical for the energy-limited marine deep biosphere and their relative abundances correlated positively with sediment age. In conclusion, our data suggests that high rates of sediment accumulation caused by glacier runoff and associated changes in biogeochemistry, promote persistence of sulfur-cycling activity and burial of a larger fraction of the surface microbial community into the deep subsurface.

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

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

    Abstract: 

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

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

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

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

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

    Abstract: 

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

  • Mineralogy and weathering of realgar-rich tailings at a former As-Sb-Cr mine at Lojane, North Macedonia

    Tamara Dordevic, Uwe Kolitsch, Todor Serafimovski, Goran Tasev, Nathalie Tepe, Michael Stger-Pollach, Thilo Hofmann, Blazo Boev
    2019 - The Canadian Mineralogist, 57: 1-21

    Abstract: 

    In the Lojane area (North Macedonia) ores of Sb (stibnite), As (realgar), and Cr (chromite) were mined and processed in a metallurgical plant until 1979. Over one million tons of flotation tailings containing As, Sb, and other hazardous substances are located in an open dump site for flotation waste created by the mine. The tailings site is completely unprotected, and its orange color reflects a very high concentration of arsenic (fine-grained realgar superficially altered to pararealgar). In order to better understand the weathering behavior of these tailings, which is necessary to evaluate the environmental risks (mainly from the mobilization of As-Sb-Cr), solid waste material was sampled and studied from the chemical and mineralogical point of view. The material was characterized by inductively coupled plasma-mass spectrometry (ICP-MS), inductively coupled plasmaoptical emission spectrometry (ICP-OES), X-ray diffraction analysis (both single crystal and powder), scanning electron microscopy (SEM) with energy-dispersive microanalysis (EDX), Raman spectroscopy, and transmission electron microscopy (TEM) with selected area electron diffraction (SAED), energy-dispersive X-ray analysis (EDX), and electron energy loss spectrometry (EELS). The studied tailings material is comprised mostly of well-crystallized realgar, gypsum, and quartz, and minor amounts of stibnite, pararealgar, chromite, and sulfur. Very minor pyrite is found within quartz aggregates. The most abundant secondary phase, which forms thin coatings around realgar and stibnite grains, is an As-Sb-Fe-Ca-(Ni)-oxide/hydroxide in which the As:Sb ratio varies from ca. 2:1 to 1:2.2 and Fe contents are variable. Antimony-dominant variants of this oxide also form larger homogeneous grains up to 500 lm in size, characterized by broad dehydration cracks suggesting original formation as a gel. Both As-rich and -poor variants were identified as members of the rom´eite group. EELS showed that all the Fe is ferric. Further secondary phases originated from the weathering of realgar, stibnite, and other primary phases are As-bearing sulfur, scorodite (often slightly Sb-bearing, locally common), arsenolite, ‘‘limonite’’, pickeringite (Ni- and Febearing), alunogen, and annabergite. The weathering of primary sulfides in the flotation tailings at Lojane proceeded under mostly oxidizing, acidic, and temporarily wet conditions. Highly acidic conditions on the surface of the tailings dump imply dissolution of arsenolite and scorodite, thus causing contamination of the environment and high mobility of arsenic.

  • Chemosymbiotic bivalves contribute to the nitrogen budget of seagrass ecosystems

    Ulisse Cardini, Marco Bartoli, Sebastian Lücker, Maria Mooshammer, Julia Polzin, Raymond W. Lee, Vesna Micić, Thilo Hofmann, Miriam Weber, Jillian M. Petersen
    2019 - The ISME journal, in press

    Abstract: 

    In many seagrass sediments, lucinid bivalves and their sulfur-oxidizing symbionts are thought to underpin key ecosystem functions, but little is known about their role in nutrient cycles, particularly nitrogen. We used natural stable isotopes, elemental analyses, and stable isotope probing to study the ecological stoichiometry of a lucinid symbiosis in spring and fall. Chemoautotrophy appeared to dominate in fall, when chemoautotrophic carbon fixation rates were up to one order of magnitude higher as compared with the spring, suggesting a flexible nutritional mutualism. In fall, an isotope pool dilution experiment revealed carbon limitation of the symbiosis and ammonium excretion rates up to tenfold higher compared with fluxes reported for nonsymbiotic marine bivalves. These results provide evidence that lucinid bivalves can contribute substantial amounts of ammonium to the ecosystem. Given the preference of seagrasses for this nitrogen source, lucinid bivalves’ contribution may boost productivity of these important blue carbon ecosystems.
  • Life at 0 °C: the biology of the alpine snowbed plant Soldanella pus

    Körner C, Riedl S, Keplinger T, Richter A, Wiesenbauer J, Schweingruber F, Hiltbrunner E
    2019 - Alpine Botany, 129: 63-80

    Abstract: 

    All plant species reach a low temperature range limit when either low temperature extremes exceed their freezing tolerance
    or when their metabolism becomes too restricted. In this study, we explore the ultimate thermal limit of plant tissue formation
    exemplified by a plant species that seemingly grows through snow. By a combination of studies in alpine snowbeds and
    under controlled environmental conditions, we demonstrate and quantify that the clonal herb Soldanella pusilla (Primulaceae)
    does indeed grow its entire flowering shoot at 0 °C. We show that plants resume growth under 2–3 m of snow in mid-winter,
    following an internal clock, with the remaining period under snow until snow melt (mostly in July) sufficient to produce a
    flowering shoot that is ready for pollination. When snow pack gets thin, the flowering shoot intercepts and re-radiates longwave
    solar radiation, so that snow and ice gently melt around the fragile shoot and the flowers emerge without any mechanical
    interaction. We evidence bud preformation in the previous season and enormous non-structural carbohydrate reserves
    in tissues (mainly below ground) in the form of soluble sugars (largely stachyose) that would support basic metabolism for
    more than 2 entire years under snow. However, cell-wall formation at 0 °C appears to lack unknown strengthening factors,
    including lignification (assessed by confocal Raman spectroscopy imaging) that require between a few hours or a day of
    warmth after snow melt to complete tissue strengthening. Complemented with a suite of anatomical data, the work opens a
    window towards understanding low temperature limits of plant growth in general, with potential relevance for winter crops
    and trees at the natural climatic treeline.

  • Legal and practical challenges in classifying nanomaterials according to regulatory definitions

    Martin Miernicki, Thilo Hofmann, Iris Eisenberger, Frank von der Kammer, Antonia Praetorius
    2019 - Nature Nanotechnology, 14: 208–216

    Abstract: 

    The European Union (EU) has adopted nano-specific provisions for cosmetics, food and biocides, among others, which include binding definitions of the term “nanomaterial”. Here we take an interdisciplinary approach to analyse the respective definitions from a legal and practical perspective. Our assessment reveals that the definitions contain several ill-defined terms such as “insoluble” or “characteristic properties” and/or are missing thresholds. Furthermore, the definitions pose major and so far unsolved analytical challenges that, in practice, make it nearly impossible to classify nanomaterials according to EU regulatory requirements. An important purpose of the regulations, the protection of human health and the environment, may remain unfulfilled and the development of innovative applications of nanomaterials may be facing a path full of (legal) uncertainties. Based on our findings, we provide five recommendations for a more coherent and practical approach towards the regulation of nanomaterials.

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

    Richard J Williams, Samuel Harrison, Virginie Keller, Jeroen Kuenen, Stephen Lofts, Antonia Praetorius, Claus Svendsen, Lucie C Vermeulen, Jikke van Wijnen
    2019 - Current Opinion in Environmental Sustainability, 105-115

    Abstract: 

    Engineered nanomaterials (ENMs, material containing particles with at least one dimension less than 100 nm) are present in a range of consumer products and could be released into the environment from these products during their production, use or end-of-life. The high surface to volume ratio of nanomaterials imparts a high reactivity, which is of interest for novel applications but may raise concern for the environment. In the absence of measurement methods, there is a need for modelling to assess likely concentrations and fate arising from current and future releases. To assess the capability that exists to do such modelling, progress in modelling ENM fate since 2011 is reviewed. ENM-specific processes represented in models are mainly limited to aggregation and, in some instances, dissolution. Transformation processes (e.g. sulphidation), the role of the manufactured coatings, particle size distribution and particle form and state are still usually excluded. Progress is also being made in modelling ENMs at larger scales. Currently, models can give a reasonable assessment of the fate of ENMs in the environment, but a full understanding will likely require fuller inclusion of these ENM-specific processes.

  • Soil multifunctionality is affected by the soil environment and by microbial community composition and diversity

    Zheng Q, Hu Y, zhang S, Noll L, Böckle T, Dietrich M, Herbold CW, Eichhorst SA, Woebken D, Richter A, Wanek W
    2019 - Soil Biology and Biochemistry, 136: Article 107521

    Abstract: 

    Microorganisms are critical in mediating carbon (C) and nitrogen (N) cycling processes in soils. Yet, it has long been debated whether the processes underlying biogeochemical cycles are affected by the composition and diversity of the soil microbial community or not. The composition and diversity of soil microbial communities can be influenced by various environmental factors, which in turn are known to impact biogeochemical processes. The objectives of this study were to test effects of multiple edaphic drivers individually and represented as the multivariate soil environment interacting with microbial community composition and diversity, and concomitantly on multiple soil functions (i.e. soil enzyme activities, soil C and N processes). We employed high-throughput sequencing (Illumina MiSeq) to analyze bacterial/archaeal and fungal community composition by targeting the 16S rRNA gene and the ITS1 region of soils collected from three land uses (cropland, grassland and forest) deriving from two bedrock forms (silicate and limestone). Based on this data set we explored single and combined effects of edaphic variables on soil microbial community structure and diversity, as well as on soil enzyme activities and several soil C and N processes. We found that both bacterial/archaeal and fungal communities were shaped by the same edaphic factors, with most single edaphic variables and the combined soil environment representation exerting stronger effects on bacterial/archaeal communities than on fungal communities, as demonstrated by (partial) Mantel tests. We also found similar edaphic controls on the bacterial/archaeal/fungal richness and diversity. Soil C processes were only directly affected by the soil environment but not affected by microbial community composition. In contrast, soil N processes were significantly related to bacterial/archaeal community composition and bacterial/archaeal/fungal richness/diversity but not directly affected by the soil environment. This indicates direct control of the soil environment on soil C processes and indirect control of the soil environment on soil N processes by structuring the microbial communities. The study further highlights the importance of edaphic drivers and microbial communities (i.e. composition and diversity) on important soil C and N processes.

  • Nitrogen and phosphorus constrain the CO2 fertilization of global plant biomass

    Terrer C, Jackson RB, Prentice IC, Keenan TF, Kaiser C, Vicca S, Fisher JB, Reich PB, Stocker BD, Hungate BA, Peñuelas J, McCallum I, Soudzilovskaia NA, Cernusak LA, Talhelm AF, Van Sundert K, Piao S, Newton PCD, Hoveden MJ, Blumenthal DM, Liu YY, Muller C, Winter K, Field CB, Viechtbauer W, Van Lissa CJ, Hoosbeek MR, Watanabe M, Kolke T, Leshyk VO, Polley HW, Franklin O
    2019 - Nature Climate Change, 9: 684-689

    Abstract: 

    Elevated CO2 (eCO2) experiments provide critical information
    to quantify the effects of rising CO2 on vegetation1–6.
    Many eCO2 experiments suggest that nutrient limitations
    modulate the local magnitude of the eCO2 effect on plant
    biomass1,3,5, but the global extent of these limitations has
    not been empirically quantified, complicating projections of
    the capacity of plants to take up CO2
    7,8. Here, we present a
    data-driven global quantification of the eCO2 effect on biomass
    based on 138 eCO2 experiments. The strength of CO2
    fertilization is primarily driven by nitrogen (N) in ~65% of
    global vegetation and by phosphorus (P) in ~25% of global
    vegetation, with N- or P-limitation modulated by mycorrhizal
    association. Our approach suggests that CO2 levels expected
    by 2100 can potentially enhance plant biomass by 12 ± 3%
    above current values, equivalent to 59 ± 13 PgC. The globalscale
    response to eCO2 we derive from experiments is similar
    to past changes in greenness9 and biomass10 with rising CO2,
    suggesting that CO2 will continue to stimulate plant biomass
    in the future despite the constraining effect of soil nutrients.
    Our research reconciles conflicting evidence on CO2 fertilization
    across scales and provides an empirical estimate of
    the biomass sensitivity to eCO2 that may help to constrain
    climate projections.

  • Growth explains microbial carbon use efficiency across soils differing in land use and geology

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

    Abstract: 

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

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

    Tobias H. Uber, Thorsten Hüffer, Sibylle Planitz, Torsten C. Schmidt
    2019 - Environmental Pollution, 312-319

    Abstract: 

    High-density polyethylene (HDPE) is a known sorbent for non-ionic organic compounds in technical applications. Nevertheless, there is little information available describing sorption to industrial HDPE for a broad range of compounds. With a better understanding of the sorption properties of synthetic polymers, environmental risk assessment would achieve a higher degree of accuracy, especially for microplastic interactions with organic substances. Therefore, a robust methodology for the determination of sorbent properties for non-ionic organic compounds by HDPE is relevant for the understanding of molecular interactions for both technical use and environmental risk assessment.

    In this work, sorption properties of HDPE material used for water pipes were characterized using a poly-parameter linear free-energy relationship (ppLFER) approach. Sorption batch experiments with selected probe sorbates were carried out in a three-phase system (air/HDPE/water) covering an aqueous concentration range of at least three orders of magnitude. Sorption in the concentration range below 10−2 of the aqueous solubility was found to be non-linear and the Freundlich model was used to account for this non-linearity. Multiple regression analysis (MRA) using the determined distribution coefficients and literature-tabulated sorbate descriptors was performed to obtain the ppLFER phase descriptors for HDPE. Sorption properties of HDPE were then derived from the ppLFER model and statistical analysis of its robustness was conducted. The derived ppLFER model described sorption more accurately than commonly used single-parameter predictions, based i.e., on log Ko/w. The ppLFER predicted distribution data with an error 0.5 log units smaller than the spLFERs. The ppLFER was used for a priori prediction of sorption by the characterized sorbent material. The prediction was then compared to experimental data from literature and this work and demonstrated the strength of the ppLFER, based on the training set over several orders of magnitude.

  • Proteomic response of three marine ammonia-oxidizing archaea to hydrogen peroxide and their metabolic interactions with a heterotrophic alphaproteobacterium

    Bayer B, Pelikan C, Bittner MJ, Reinthaler T, Könneke M, Herndl GJ, Offre P
    2019 - mSystems, 4: e00181-1

    Abstract: 

    Ammonia-oxidizing archaea (AOA) play an important role in the nitrogen cycle and account for a considerable fraction of the prokaryotic plankton in the ocean. Most AOA lack the hydrogen peroxide (H2O2)-detoxifying enzyme catalase, and some AOA have been shown to grow poorly under conditions of exposure to H2O2. However, differences in the degrees of H2O2 sensitivity of different AOA strains, the physiological status of AOA cells exposed to H2O2, and their molecular response to H2O2 remain poorly characterized. Further, AOA might rely on heterotrophic bacteria to detoxify H2O2, and yet the extent and variety of costs and benefits involved in these interactions remain unclear. Here, we used a proteomics approach to compare the protein profiles of three Nitrosopumilus strains grown in the presence and absence of catalase and in coculture with the heterotrophic alphaproteobacterium Oceanicaulis alexandrii. We observed that most proteins detected at a higher relative abundance in H2O2-exposed Nitrosopumilus cells had no known function in oxidative stress defense. Instead, these proteins were putatively involved in the remodeling of the extracellular matrix, which we hypothesize to be a strategy limiting the influx of H2O2 into the cells. Using RNA-stable isotope probing, we confirmed that O. alexandrii cells growing in coculture with the Nitrosopumilus strains assimilated Nitrosopumilus-derived organic carbon, suggesting that AOA could recruit H2O2-detoxifying bacteria through the release of labile organic matter. Our results contribute new insights into the response of AOA to H2O2 and highlight the potential ecological importance of their interactions with heterotrophic free-living bacteria in marine environments.

  • Biochar particle aggregation in soil pore water: the influence of ionic strength and interactions with pyrene

    Stephanie Castan, Gabriel Sigmund, Thorsten Hüffer, Thilo Hofmann
    2019 - Environmental Science: Processes & Impacts, 21: 1722-1728

    Abstract: 

    The beneficial properties of biochar have led to its increasing application to soils for environmental management. Despite its stability in soil, biochar can physically disintegrate into smaller particles, which can then be relocated from the application area. Biochar transport is strongly dependent on the biochar particle size and aggregation, with the extent of aggregation depending on the chemistry of the soil pore water. Biochar has a strong sorption affinity for polyaromatic hydrocarbons (PAHs) such as pyrene, which can also affect its transport. We therefore investigated biochar particle aggregation in solutions of different ionic strengths (ultrapure water, 0.01 M CaCl2, and 0.1 M CaCl2) with suspensions of biochar particles, and with suspensions of biochar particles loaded with pyrene (0.2 and 3.6 g kg−1). Increasing the pyrene concentration in ultrapure water resulted in an increase in the biochar particle size, an effect that was more pronounced following equilibration for 28 days than following equilibration for only 24 hours. Biochar particle aggregation in solutions containing both pyrene and 0.01 M CaCl2 was greatly enhanced compared to aggregation in similar solutions with no pyrene. However, the influence of pyrene became negligible at high CaCl2 concentrations (0.1 M CaCl2). To determine the fate of biochar in soil, both the presence of PAHs and the influence of the pore water's ionic strength therefore need to be taken into account.

  • Emerging contaminants in sediment core from the Iron Gate I reservoir on the Danube River

    Ivana Mati Bujagi, Svetlana Gruji, Mila Lauevi, Thilo Hofmann, Vesna Micić
    2019 - Science of The Total Environment, 77-87

    Abstract: 

    The Iron Gate I Reservoir is the largest impoundment on the Danube River. It retains >50% of the incoming total suspended solids load and the associated organic contaminants. In the sediment core of the Iron Gate I Reservoir we report the presence and fate of four classes of emerging contaminants (pharmaceuticals, pesticides, steroids and perfluorinated compounds), predominantly not covered by the EU monitoring programs, but considered as future candidates. Based on contaminant's partitioning behavior in the water/sediment system and the suspected ecotoxicological potential asserted from the literature data, the risk of recorded concentrations for sediment-dwelling organisms was discussed. The high anticipated risk was associated with antibiotics sulfamethoxazole and erythromycin, and pesticides linuron and carbendazim (banned in the EU, but still approved for use in the investigated area) and malathion. This indicated the need for better control of release of these compounds into the river, and implied their inclusion in future regular monitoring. Higher concentrations of pharmaceuticals and most pesticides and sterols were recorded in the fragment of allochthonous coarser sediment, assumed to have entered the reservoir during a high discharge event. Only one perfluorinated compound was recorded in the upper part of the sediment core. The vertical concentration profiles of pesticides propazine and malathion indicated their uniform source, most likely atmospheric transport and deposition of particles deriving from agricultural land.

  • The cooling tower water microbiota: Seasonal dynamics and co-occurrence of bacterial and protist phylotypes

    Tsao HF, Scheikl U, Herbold CW, Indra A, Walochnik J, Horn M
    2019 - Water Res., 159: 464-479

    Abstract: 

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

  • A novel isotope pool dilution approach to quantify gross rates of key abiotic and biological processes in the soil phosphorus cycle

    Wanek W, Zezula D, Wasner D, Mooshammer M, Prommer J
    2019 - Biogeosciences, 16: 3047-3068

    Abstract: 

    Efforts to understand and model the current and future behavior of the global phosphorus (P) cycle are limited by the availability of global data on rates of soil P processes, as well as their environmental controls. Here, we present a novel isotope pool dilution approach using 33Plabeling of live and sterile soils, which allows for high-quality data on gross fluxes of soil inorganic P (Pi) sorption and desorption, as well as of gross fluxes of organic P mineralization and microbial Pi uptake to be obtained. At the same time, net immobilization of 33Pi by soil microbes and abiotic sorption can be easily derived and partitioned. Compared with other approaches, we used short incubation times (up to 48 h), avoiding tracer remineralization, which was confirmed by the separation of organic P and Pi using isobutanol fractionation. This approach is also suitable for strongly weathered and P-impoverished soils, as the sensitivity is increased by the extraction of exchangeable bioavailable Pi(Olsen Pi; 0.5 M NaHCO3) followed by Pi measurement using the malachite green assay. Biotic processes were corrected for desorption/sorption processes using adequate sterile abiotic controls that exhibited negligible microbial and extracellular phosphatase activities. Gross rates were calculated using analytical solutions of tracer kinetics, which also allowed for the study of gross soil P dynamics under non-steady-state conditions. Finally, we present major environmental controls of gross P-cycle processes that were measured for three P-poor tropical forest and three P-rich temperate grassland soils.

  • A Bioinformatics Guide to Plant Microbiome Analysis

    Lucaciu R, Pelikan C, Gerner SM, Zioutis C, Köstlbacher S, Marx H, Herbold CW, Schmidt H, Rattei T
    2019 - Frontiers in Plant Science, 10: Article 1313

    Abstract: 

    Recent evidence for intimate relationship of plants with their microbiota shows that plants host individual and diverse microbial communities that are essential for their survival. Understanding their relatedness using genome-based and high-throughput techniques remains a hot topic in microbiome research. Molecular analysis of the plant holobiont necessitates the application of specific sampling and preparatory steps that also consider sources of unwanted information, such as soil, co-amplified plant organelles, human DNA, and other contaminations. Here, we review state-of-the-art and present practical guidelines regarding experimental and computational aspects to be considered in molecular plant–microbiome studies. We discuss sequencing and “omics” techniques with a focus on the requirements needed to adapt these methods to individual research approaches. The choice of primers and sequence databases is of utmost importance for amplicon sequencing, while the assembly and binning of shotgun metagenomic sequences is crucial to obtain quality data. We discuss specific bioinformatic workflows to overcome the limitation of genome database resources and for covering large eukaryotic genomes such as fungi. In transcriptomics, it is necessary to account for the separation of host mRNA or dual-RNAseq data. Metaproteomics approaches provide a snapshot of the protein abundances within a plant tissue which requires the knowledge of complete and well-annotated plant genomes, as well as microbial genomes. Metabolomics offers a powerful tool to detect and quantify small molecules and molecular changes at the plant– bacteria interface if the necessary requirements with regard to (secondary) metabolite databases are considered. We highlight data integration and complementarity which should help to widen our understanding of the interactions among individual players of the plant holobiont in the future.

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

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

    Abstract: 

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

  • Environmental effects on soil microbial nitrogen use efficiency are controlled by allocation of organic nitrogen to microbial growth and regulate gross N mineralization

    zhang S, Zheng Q, Noll L, Hu Y, Wanek W
    2019 - Soil Biology and Biochemistry, 135: 304-315

    Abstract: 

    Microbial nitrogen use efficiency (NUE) is the efficiency by which microbes allocate organic N acquired to biomass formation relative to the N in excess of microbial demand released through N mineralization. Microbial NUE thus is critical to estimate the capacity of soil microbes to retain N in soils and thereby affects inorganic N availability to plants and ecosystem N losses. However, how soil temperature and soil moisture/O2 affect microbial NUE to date is not clear. Therefore, two independent incubation experiments were conducted with soils from three land uses (cropland, grassland and forest) on two bedrocks (silicate and limestone). Soils were exposed to 5, 15 and 25 °C overnight at 60% water holding capacity (WHC) or acclimated to 30 and 60% WHC at 21% O2 and to 90% WHC at 1% O2 over one week at 20 °C. Microbial NUE was measured as microbial growth over microbial organic N uptake (the sum of growth N demand and gross N mineralization). Microbial NUE responded positively to temperature increases with Q10 values ranging from 1.30 ± 0.11 to 2.48 ± 0.67. This was due to exponentially increasing microbial growth rates with incubation temperature while gross N mineralization rates were relatively insensitive to temperature increases (Q10 values 0.66 ± 0.30 to 1.63 ± 0.15). Under oxic conditions (21% O2), microbial NUE as well as gross N mineralization were not stimulated by the increase in soil moisture from 30 to 60% WHC. Under suboxic conditions (90% WHC and 1% O2), microbial NUE markedly declined as microbial growth rates were strongly negatively affected due to increasing microbial energy limitation. In contrast, gross N mineralization rates increased strongly as organic N uptake became in excess of microbial growth N demand. Therefore, in the moisture/O2 experiment microbial NUE was mainly regulated by the shift in O2 status (to suboxic conditions) and less affected by increasing water availability per se. These temperature and moisture/O2 effects on microbial organic N metabolism were consistent across the soils differing in bedrock and land use. Overall it has been demonstrated that microbial NUE was controlled by microbial growth, and that NUE controlled gross N mineralization as an overflow metabolism when energy (C) became limiting or N in excess in soils. This study thereby greatly contributes to the understanding of short-term environmental responses of microbial community N metabolism and the regulation of microbial organic-inorganic N transformations in soils.

  • The membrane lipid composition of the moderately thermophilic ammonia-oxidizing archaeon Ca. Nitrosotenuis uzonensis at different growth temperatures

    Bale NJ, Palatinszky M, Rijpstra WIC, Herbold CW, Wagner M, Damste JSS
    2019 - Appl Environ Microbiol, in press
    AOA N. uzonensis lipids

    Abstract: 

    Ca. Nitrosotenuis uzonensis is the only cultured moderately thermophilic member of the thaumarchaeotal order Nitrosopumilales (NP) that contains many mesophilic marine strains. We examined its membrane lipid composition at different growth temperatures (37, 46 and 50 °C). Its lipids were all membrane-spanning glycerol dialkyl glycerol tetraethers (GDGTs), with 0 to 4 cyclopentane moieties. Crenarchaeol (cren), the characteristic thaumarchaeotal GDGT, and its isomer (crenʹ) were present in high abundance (30-70 %). The GDGT polar headgroups were mono-, di- and trihexoses and hexose/phosphohexose. The ratio of glycolipid to phospholipid GDGTs was highest in the cultures grown at 50 °C. With increasing growth temperature, the relative contribution of cren and crenʹ increased, while GDGT-0 to GDGT-4 (including isomers) decreased. TEX86 (tetraether index of tetraethers consisting of 86 carbons)-derived temperatures were much lower than the actual growth temperatures, further demonstrating that TEX86 does not accurately reflect the membrane lipid adaptation of thermophilic Thaumarchaeota. As temperature increased, specific GDGTs changed relative to their isomers, possibly representing temperature adaption-induced changes in cyclopentane ring stereochemistry. Comparison of a wide range of thaumarcheotal core lipid compositions revealed the Ca. N. uzonensis cultures clustered separately fromother members of the NP order and the Nitrososphaerales (NS) order. While phylogeny generally seems to have a strong influence on GDGT distribution, our analysis of Ca. Nitrosotenuis uzonensis demonstrates that its terrestrial, higher temperature niche has led to a lipid composition that clearly differentiates it from other NP members and that this difference is mostly driven by its high crenʹ content.

  • A fiber-deprived diet disturbs the fine-scale spatial architecture of the murine colon microbiome

    Riva A, Kuzyk O, Forsberg E, Siuzdak G, Pfann C, Herbold CW, Daims H, Loy A, Warth B, Berry D
    2019 - Nat Commun, 10: 4366

    Abstract: 

    Compartmentalization of the gut microbiota is thought to be important to system function, but the extent of spatial organization in the gut ecosystem remains poorly understood. Here, we profile the murine colonic microbiota along longitudinal and lateral axes using laser capture microdissection. We found fine-scale spatial structuring of the microbiota marked by gradients in composition and diversity along the length of the colon. Privation of fiber reduces the diversity of the microbiota and disrupts longitudinal and lateral gradients in microbiota composition. Both mucus-adjacent and luminal communities are influenced by the absence of dietary fiber, with the loss of a characteristic distal colon microbiota and a reduction in the mucosa-adjacent community, concomitant with depletion of the mucus layer. These results indicate that diet has not only global but also local effects on the composition of the gut microbiota, which may affect function and resilience differently depending on location.

  • Microbial carbon and nitrogen cycling responses to drought and temperature in differently managed mountain grasslands

    Fuchslueger L, Wild B, Mooshammer M, Takriti M, Kienzl S, Knoltsch A, Hofhansl F, Bahn M, Richter A
    2019 - Soil Biology and Biochemistry, 135: 144-153

    Abstract: 

    Grassland management can modify soil microbial carbon (C) and nitrogen (N) cycling, affecting the resistance to extreme weather events, which are predicted to increase in frequency and magnitude in the near future. However, effects of grassland management on microbial C and N cycling and their responses to extreme weather events, such as droughts and heatwaves, have rarely been tested in a combined approach. We therefore investigated whether grassland management affects microbial C and N cycling responses to drought and temperature manipulation. We collected soils from in situdrought experiments conducted in an extensively managed and an abandoned mountain grassland and incubated them at two temperature levels. We measured microbial respiration and substrate incorporation, as well as gross rates of organic and inorganic N cycling to estimate microbial C and N use efficiencies (CUE and NUE). The managed grassland was characterized by lower microbial biomass, lower fungi to bacteria ratio, and higher microbial CUE, but only slightly different microbial NUE. At both sites drought induced a shift in microbial community composition driven by an increase in Gram-positive bacterial abundance. Drought significantly reduced C substrate respiration and incorporation by microbes at both sites, while microbial CUE remained constant. In contrast, drought increased gross rates of N mineralization at both sites, whereas gross amino acid uptake rates only marginally changed. We observed a significant direct, as well as interactive effect between land management and drought on microbial NUE. Increased temperatures significantly stimulated microbial respiration and reduced microbial CUE independent of drought or land management. Although microbial N processing rates showed no clear response, microbial NUE significantly decreased at higher temperatures. In summary in our study, microbial CUE, in particular respiration, is more responsive to temperature changes. Although N processing rates were stronger responding to drought than to temperature microbial NUE was affected by both drought and temperature increase. We conclude that direct effects of drought and heatwaves can induce different responses in soil microbial C and N cycling similarly in the studied land management systems.

  • In situ remediation of subsurface contamination: opportunities and challenges for nanotechnology and advanced materials

    Tong Zhang, Gregory V. Lowry, Natalie L. Capiro, Jianmin Chen, Wei Chen, Yongsheng Chen, Dionysios D. Dionysiou, Daniel W. Elliott, Subhasis Ghoshal, Thilo Hofmann, Heileen Hsu-Kim, Joseph Hughes, Chuanjia Jiang, Guibin Jiang, Chuanyong Jing, Michael Kavanaugh, Qilin Li, Sijin Liu, Jie Ma, Bingcai Pan, Tanapon Phenrat, Xiaolei Qu, Xie Quan, Navid Saleh, Peter J. Vikesland, Qiuquan Wang, Paul Westerhoff, Michael S. Wong, Tian Xia, Baoshan Xing, Bing Yan, Lunliang Zhang, Dongmei Zhouaa, Pedro J. J. Alvarez
    2019 - Environmental Science: Nano, 5: 1283-1302

    Abstract: 

    Complex subsurface contamination domains and limited efficacy of existing treatment approaches pose significant challenges to site remediation and underscore the need for technological innovation to develop cost-effective remedies. Here, we discuss opportunities for nanotechnology-enabled in situ remediation technologies to address soil and groundwater contamination. The discussion covers candidate nanomaterials, applications of nanomaterials to complement existing remediation approaches and address emerging contaminants, as well as the potential barriers for implementation and strategies and research needs to overcome these barriers. Promising nanomaterials in subsurface remediation include multi-functional nanocomposites for synergistic contaminant sequestration and degradation, selective adsorbents and catalysts, nano-tracers for subsurface contaminant delineation, and slow-release reagents enabled by stimuli-responsive nanomaterials. Limitations on mixing and transport of nanomaterials in the subsurface are severe constraints for in situ applications of these materials. Mixing enhancements are needed to overcome transport limitations in laminar flow environments. Reactive nanomaterials may be generated in situ to remediate contamination in low hydraulic conductivity zones. Overall, nano-enabled remediation technologies may improve remediation performance for a broad range of legacy and emerging contaminants. These technologies should continue to be developed and tested to discern theoretical hypotheses from feasible opportunities, and to establish realistic performance expectations for in situ remediation techniques using engineered nanomaterials alone or in combination with other technologies.

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

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

    Abstract: 

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

  • Mitigating anticipated effects of systematic errors supports sister-group relationship between Xenacoelomorpha and Ambulacraria

    Philippe H, Poustka AJ, Chiodin M, Hoff KJ, Dessimoz C, Tomiczek B, Schiffer PH, Müller S, Domman D, Horn M, Kuhl H, Timmermann B, Satoh N, Hikosaka-Katayama T, Nakano H, Rowe ML, Elphick MR, Thomas-Chollier M, Hankeln T, Mertes F, Wallberg A, Rast JP, Copley RR, Martinez P, Telford MJ
    2019 - Curr. Biol., in press
     Xenoturbella japonica

    Abstract: 

    Xenoturbella and the acoelomorph worms (Xenacoelomorpha) are simple marine animals with controversial affinities. They have been placed as the sister group of all other bilaterian animals (Nephrozoa hypothesis), implying their simplicity is an ancient characteristic; alternatively, they have been linked to the complex Ambulacraria (echinoderms and hemichordates) in a clade called the Xenambulacraria, suggesting their simplicity evolved by reduction from a complex ancestor. The difficulty resolving this problem implies the phylogenetic signal supporting the correct solution is weak and affected by inadequate modeling, creating a misleading non-phylogenetic signal. The idea that the Nephrozoa hypothesis might be an artifact is prompted by the faster molecular evolutionary rate observed within the Acoelomorpha. Unequal rates of evolution are known to result in the systematic artifact of long branch attraction, which would be predicted to result in an attraction between long-branch acoelomorphs and the outgroup, pulling them toward the root. Other biases inadequately accommodated by the models used can also have strong effects, exacerbated in the context of short internal branches and long terminal branches. We have assembled a large and informative dataset to address this problem. Analyses designed to reduce or to emphasize misleading signals show the Nephrozoa hypothesis is supported under conditions expected to exacerbate errors, and the Xenambulacraria hypothesis is preferred in conditions designed to reduce errors. Our reanalyses of two other recently published datasets produce the same result. We conclude that the Xenacoelomorpha are simplified relatives of the Ambulacraria.

  • Editorial: Rhizosphere Functioning and Structural Development as Complex Interplay Between Plants, Microorganisms and Soil Minerals

    Mueller CW, Carminati A, Kaiser C, Subke JA, Gutjahr C
    2019 - Frontiers in Environmental Science, 7: Article 130
  • Determination of nanoparticle heteroaggregation attachment efficiencies and rates in presence of natural organic matter monomers. Monte Carlo modelling

    Arnaud Clavier, Antonia Praetorius, Serge Stoll
    2019 - Science of The Total Environment, 530-540

    Abstract: 

    Understanding the transformation and transport of manufactured nanoparticles (NPs) in aquatic systems remains an important issue due to their potential hazard. Once released in aquatic systems, NPs will interact with natural compounds such as suspended inorganic particles and/or natural organic matter (NOM) and heteroaggregation will control their ultimate fate. Unfortunately, systematic experimental methods to study heteroaggregation are not straightforward and still scarce. In addition, the description of heteroaggregation rate constants and attachment efficiencies is still a matter of debate since no clear definition exists.

    In this work, an original cluster-cluster Monte Carlo model is developed to get an insight into heteroaggregation process descriptions. A two-component system composed of NPs and NOM fulvic acid monomers is investigated by considering several water models to cover a range of (relevant) conditions from fresh to marine waters. For that purpose, homo- and hetero- individual attachment efficiencies between NPs and NOM units are adjusted (NP-NP, NOM-NOM and NP-NOM). The influence of NP/NOM ratio, NOM-NOM homoaggregation versus heteroaggregation, and surface coating effects is studied systematically. From a quantitative point of view, aggregation rate constants as well as attachment efficiencies are calculated as a function of physical time so as to characterize the individual influence of each parameter and to allow future comparison with experimental data. Heteroaggregation processes and global attachment efficiencies corresponding to several mechanisms and depending on the evolution of heteroaggregate structures all along the simulations are defined. The calculation of attachment efficiency values is found dependent on NP/NOM concentration ratios via coating effects, by the initial set of elementary attachment efficiencies and influence of homoaggregation.

    Marine water represents a specific case of aggregation where all particle contacts are effective. On the other hand, in “ultrapure” and “fresh waters”, a competition between homo- and heteroaggregation occurs depending on the initial attachment efficiencies therefore indicating that a subtle change in the NP surface properties as well as in the water chemistry have a significant impact on heteroaggregation processes.

  • NO2 and natural organic matter affect both soot aggregation behavior and sorption of S-metolachlor

    Gabriel Sigmund, Stephanie Castan, Christopher Wabnitz, Rani Bakkour, Thorsten Hüffer, Thilo Hofmann, Martin Elsner
    2019 - Environmental Science: Processes & Impacts, 21: 1729-1735

    Abstract: 

    Soot is an important carbonaceous nanoparticle (CNP) frequently found in natural environments. Its entry into surface waters can occur directly via surface runoff or infiltration, as well as via atmospheric deposition. Pristine soot is likely to rapidly undergo aggregation and subsequent sedimentation in aquatic environments. Further, soot can sorb a variety of organic contaminants, such as S-metolachlor (log KD = 3.25 ± 0.12). During atmospheric transport, soot can be chemically transformed by reactive oxygen species including NO2. The presence of natural organic matter (NOM) in surface waters can further affect the aquatic fate of soot. To better understand the processes driving the fate of soot and its interactions with contaminants, pristine and NO2-transformed model soot suspensions were investigated in the presence and absence of NOM. NO2-oxidized soot showed a smaller particle size, a higher number of particles remaining in suspension, and a decreased sorption of S-metolachlor (log KD = 2.47 ± 0.40). In agreement with findings for other CNPs, soot stability against aggregation was increased for both pristine and NO2 transformed soot in the presence of NOM.

  • Improved extraction efficiency of natural nanomaterials in soils to facilitate their characterization using a multimethod approach

    Frédéric Loosli, Zebang Yi, Jingjing Wang, Mohammed Baalousha
    2019 - Science of The Total Environment, 677: 34-46

    Abstract: 

    Characterization of natural nanomaterial (NNM) physicochemical properties – such as size, size distribution, elemental composition and elemental ratios - is often hindered by lack of methods to disperse NNMs from environmental samples. This study evaluates the effect of extractant composition, pH, and ionic strength on soil NNM extraction in term of recovery and release of primary particles/small aggregate sizes (i.e., <200 nm). The extracted NNMs were characterized for hydrodynamic diameter and zeta potential by dynamic light scattering and laser Doppler electrophoresis, natural organic matter desorption by UV–Vis spectroscopy, element composition by inductively coupled plasma-mass spectroscopy (ICP-MS), size based elemental distribution by field flow fractionation coupled to ICP-MS, and morphology by transmission electron microscopy. The extracted NNM concentrations increased following the order of NaOH ≤ Na2CO3 < Na2C2O4 < Na4P2O7. Na4P2O7 was the most efficient extractant and results in 2–12 folds higher NNM extraction than other extractants. The Na4P2O7 extracted NNMs exhibited narrower size distribution with smaller modal size relative to NaOH, Na2CO3, Na2C2O4 extracted NNMs. Thus, Na4P2O7 enhances the extraction of primary NNMs and/or smaller NNM aggregates (i.e., size <200 nm). Na4P2O7 promote soil microaggregates breakup and release of NNMs by reducing free multivalent cation concentration in soil pore water by forming metal-phosphate complexes and by enhancing NNM surface charge via phosphate sorption on NNM surfaces. Additionally, the extracted NNM concentrations increased with the increase in extractant concentration and pH, except at 100 mM where the high ionic strength might have induced NNM aggregation. The improved NNM-extraction will improve the overall understanding of the physicochemical properties of NNMs in environmental systems. This study presents the key properties of NNMs that can be used as background information to differentiate engineered nanomaterials (ENMs) from NNMs in complex environmental media.

  • Polyethylene microplastics influence the transport of organic contaminants in soil

    Thorsten Hüffer, Florian Metzelder, Gabriel Sigmund, Sophie Slawek, Torsten C. Schmidt, Thilo Hofmann
    2019 - Science of The Total Environment, 242-247

    Abstract: 

    Plastics are now found in all natural environments including soil. The effects of microplastics in terrestrial systems, however, remain largely unexplored. Polyethylene is one of the mass-manufactured polymers found in terrestrial environments. It is used in many different sectors, for example in agricultural mulches, composite materials, and packaging. The presence of microplastics in soil, including polyethylene, can affect the transport of hydrophobic organic pollutants including pesticides. The objective of this study was to investigate the influence of polyethylene microplastics (<250 μm) on the transport of two selected organic plant-protection agents (atrazine and 4-(2,4-dichlorophenoxy) butyric acid) in soil under different aqueous conditions, using inverse liquid chromatography. The distribution coefficients for the sorbates that were sorbed to pure polyethylene microplastic were found to be significantly smaller than those for the sorbates sorbed to pure soil. The addition of 10% (w/w) polyethylene to the soil therefore led to an overall reduction in sorption, but the sorption trends due to variations in pH and ionic strength were not affected. The results imply that the presence of polyethylene microplastics in soil may therefore increase the mobility of organic contaminants by reducing the sorption capacity of natural soils, which must be validated by further research.

  • How to disentangle microbially functional complexity: an insight from the network analysis of C, N, P and S cycling genes

    Zheng BX, Zhao Y, Bi QF, Zhou GW, Wang HJ, Hao XL, Ding K
    2019 - Science Bulletin, 64: 1129-1131

    Abstract: 

    A complete ecosystem is also a complex network in which mul-tifarious species interact with each other to achieve system-levelfunctions, such as nutrient biogeochemistry[1]. Microbial commu-nity is commonly considered as the primary driving force ofecosystem nutrient mobilization and metabolism, especially car-bon (C), nitrogen (N), phosphorus (P), sulfur (S) and methane cou-pling process[2]. The rise of metagenomics and high-throughputarray (e.g. PhyloChip, GeoChip, etc.) technologies enable acquiringthe detailed information on microbial community functional geneabundance and diversity[3,4]; however, there has been far lessattention focusing on the direct and indirect interactions betweennutrient cycling genes coexisting in environmental samples. Docu-menting these interactions between functional genes acrossdiverse microbial communities may help to clarify the functionalroles and even environmental niches in different contexts[5]. Withthe increasing accumulation of functional gene data from modernhigh-throughput technologies, we are facing the challenge of thoseinteraction explorations, and to extend analyses beyond sole abun-dance and diversity comparisons.

  • The composition of bacterial communities associated with plastic biofilms differs between different polymers and stages of biofilm succession

    Maria Pinto, Teresa M. Langer, Thorsten Hüffer, Thilo Hofmann, Gerhard J. Herndl
    2019 - PloS one, 14: 1-20

    Abstract: 

    Once in the ocean, plastics are rapidly colonized by complex microbial communities. Factors affecting the development and composition of these communities are still poorly understood. Additionally, whether there are plastic-type specific communities developing on different plastics remains enigmatic. We determined the development and succession of bacterial communities on different plastics under ambient and dim light conditions in the coastal Northern Adriatic over the course of two months using scanning electron microscopy and 16S rRNA gene analyses. Plastics used were low- and high-density polyethylene (LDPE and HDPE, respectively), polypropylene (PP) and polyvinyl chloride with two typical additives (PVC DEHP and PVC DINP). The bacterial communities developing on the plastics clustered in two groups; one group was found on PVC and the other group on all the other plastics and on glass, which was used as an inert control. Specific bacterial taxa were found on specific surfaces in essentially all stages of biofilm development and in both ambient and dim light conditions. Differences in bacterial community composition between the different plastics and light exposures were stronger after an incubation period of one week than at the later stages of the incubation. Under both ambient and dim light conditions, one part of the bacterial community was common on all plastic types, especially in later stages of the biofilm development, with families such as Flavobacteriaceae, Rhodobacteraceae, Planctomycetaceae and Phyllobacteriaceae presenting relatively high relative abundances on all surfaces. Another part of the bacterial community was plastic-type specific. The plastic-type specific fraction was variable among the different plastic types and was more abundant after one week of incubation than at later stages of the succession.

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

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

    Abstract: 

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

  • Sorption of non-ionic organic compounds by polystyrene in water

    Tobias H. Uber, Thorsten Hüffer, Sibylle Planitz, Thorsten C. Schmidt
    2019 - Science of The Total Environment, 682: 348-355

    Abstract: 

    Polystyrene (PS) is a plastic material that is well known for its use in many different applications, e.g. as shock sensitive packaging.With its prevalence across society, PS contributes significantly to the overall plastic load in aqueous systems. Sorption of organic compounds by the plastics, especiallymicrometer-sized particles, in the environment has become a concern in the past years. The aim of this study was to improve the understanding of sorption properties of PS, one of the major plastic pollutants in the aqueous environment. Batch experiments with PS film (29 μmthickness)were performed for 4 days using a diverse set of 24 sorbates to account for varying molecular properties like polarity or molecular volume. Isotherms were evaluated using different sorption models to elucidate the sorption process of PS. Sorption to PS film was non-linear and absorption into the bulk materialwas the dominant sorption mode. A clear discrimination between the specific and non-specific interactions in the aqueous environment could be shown. The non-linear sorption to PS was shown to be controlled by themolar volume but also by the polarizability/dipolarity parameter (S) of the ppLFER model. The latter is influenced
    by the aromaticπ-π-interactions of PSwith the sorbate. Similar to other plastics like polyethylene, sorption to PS is driven by hydrophobic interactions but phase descriptors of pristine PS were significantly different than descriptors for other environmental relevant plastics.

  • Mercury Isotope Fractionation in the Subsurface of a Hg(II) Chloride-Contaminated Industrial Legacy Site

    Flora M. Brocza, Harald Biester, Jan-Helge Richard, Stephan M. Kraemer, Jan G. Wiederhold
    2019 - Environmental Science & Technology, 13: 7296-7305

    Abstract: 

    To understand the transformations of mercury (Hg) species in the subsurface of a HgCl2-contaminated former industrial site in southwest Germany, Hg isotope analysis was combined with an investigation of Hg forms by a four-step sequential extraction protocol (SEP) and pyrolytic thermodesorption. Data from two soil cores revealed that the initial HgCl2was partly reduced to metallic Hg(0) and that Hg forms of different mobility and oxidation state coexist in the subsurface. The most contaminated sample (K2-8, 802 mg kg–1 Hg) had a bulk δ202Hg value of around −0.43 ± 0.06‰ (2SD), similar to published average values for industrial Hg sources. Other sample signatures varied significantly with depth and between SEP pools. The most Hg-rich samples contained mixtures of Hg(0) and Hg(II) phases, and the water-extractable, mobile Hg pool exhibited heavy δ202Hg values of up to +0.18‰. Sequential water extracts revealed slow dissolution kinetics of mobile Hg pools, continuously releasing isotopically heavy Hg into solution. This was further corroborated by heavy δ202Hg values of groundwater samples. Our results demonstrate that the Hg isotope signature of an industrial contamination source can be significantly altered during the transformations of Hg species in the subsurface, which complicates source tracing applications but offers the possibility of using Hg isotopes as process tracers in contaminated subsurface systems.

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

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

    Abstract: 

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

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

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

    Abstract: 

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

  • Are we speaking the same language? Recommendations for a definition and categorisation framework for plastic debris

    Nanna B. Hartmann, Thorsten Hüffer, Richard C. Thompson, Martin Hassellv, Anja Verschoor, Anders E. Daugaard, Sinja Rist, Therese Karlsson, Nicole Brennholt, Matthew Cole, Maria P. Herrling, Maren C. Hess, Natalia P. Ivleva, Amy L. Lusher, Martin Wagner
    2019 - Environmental Science & Technology, 3: 1039-1047

    Abstract: 

    The accumulation of plastic litter in natural environments is a global issue. Concerns over potential negative impacts on the economy, wildlife, and human health provide strong incentives for improving the sustainable use of plastics. Despite the many voices raised on the issue, we lack a consensus on how to define and categorize plastic debris. This is evident for microplastics, where inconsistent size classes are used and where the materials to be included are under debate. While this is inherent in an emerging research field, an ambiguous terminology results in confusion and miscommunication that may compromise progress in research and mitigation measures. Therefore, we need to be explicit on what exactly we consider plastic debris. Thus, we critically discuss the advantages and disadvantages of a unified terminology, propose a definition and categorization framework, and highlight areas of uncertainty. Going beyond size classes, our framework includes physicochemical properties (polymer composition, solid state, solubility) as defining criteria and size, shape, color, and origin as classifiers for categorization. Acknowledging the rapid evolution of our knowledge on plastic pollution, our framework will promote consensus building within the scientific and regulatory community based on a solid scientific foundation.

  • Complex-conductivity monitoring to delineate aquifer pore clogging during nanoparticles injection

    Flores Orozco Adrián, Vesna Micić, Matthias Bücker, Jakob Gallistl, Thilo Hofmann, Frederic Nguyen
    2019 - Geophysical Journal International, 3: 1838-1852

    Abstract: 

    Laboratory and field studies have demonstrated the applicability of nanoparticles (NP) for accelerated contaminant degradation. Beside other limitations (e.g. costs, delivery, longevity, non-target specific reactions), concerns of regulators arose regarding toxicity of injected NP and particles delivered off-target (i.e. renegade particles). Renegade particles also significantly reduce the efficiency of the remediation. The delivery of particles off-target is caused, mainly, by unintended fracking, where the fractures act then as preferential flow paths changing the trajectory of the particles. Hence, the real-time monitoring of particle injection is of major importance to verify correct particle delivery and thus help to optimize the remediation strategy. However, to date NP monitoring techniques rely on the analysis of soil and water samples, which cannot provide information about clogging or the formation of fractures away of the sampling points. To overcome these limitations, in this study we investigate the applicability of complex-conductivity imaging (CCI), a geophysical electrical method, to characterize possible pore clogging and fracking during NP injections. We hypothesize that both processes are related to different electrical footprints, considering the loss of porosity during clogging and the accumulation of NP in areas away of the target after fracking. Here, we present CCI results for data collected before and during the injection of Nano-Goethite particles (NGP) applied to enhance biodegradation of a BTEX (benzene, toluene, ethylbenzene and xylene) contaminant plume. Imaging results for background data revealed consistency with the known lithology, while overall high electrical conductivity values and a negligible induced-polarization magnitude correspond with the expected response of a mature hydrocarbon plume. Monitoring images revealed a general increase (∼15 per cent) in the electrical conductivity due to the injected NGP suspension in agreement with geochemical data. Furthermore, abrupt changes in this trend, shortly before daylighting events, show the sensitivity of the method to pore clogging. Such interpretation is in line with the larger variations in CCI resolved in the unsaturated zone, clearly indicating the accumulation of renegade NGP close to the surface due to fracking. Our results demonstrate the applicability of the CCI method for the assessment of pore clogging accompanying particles injection.

  • Opportunities for examining the natural nanogeochemical environment using recent advances in nanoparticle analysis

    Manuel D. Montaño, Frank von der Kammer, Chad W. Cuss, James F. Ranville
    2019 - Journal of Analytical Atomic Spectrometry, 34: 1768-1772

    Abstract: 

    The characterization of engineered nanoparticles (ENPs) has been a main pillar in the advancement of nanotechnology in recent decades. Because the properties of ENPs are closely linked to their size, shape, morphology, and surface coatings, development of nanoanalysis methods capable of assessing these parameters was necessary. Many advanced instruments and data analysis tools have now been established for analysis of ENPs in complex matrices, providing a comprehensive assessment of not only their intended virtues, but also the unintended consequences of their manufacture, use, and disposal. Current generation electron microscopy enables atom-scale imaging. Hyphenated (FFF-ICP-MS), and single particle (spICP-MS) techniques now possess the requisite sensitivity and elemental selectivity to quantify and characterize inorganic ENPs. These tools also provide a means to examine processes involving naturally-occurring nanoparticles (NNPs) to a degree not previously attainable. Though colloids and nanominerals have been investigated for decades, modern nanoanalysis offers a wealth of opportunities to improve our understanding of the natural nanogeochemical environment. Applying nanoanalysis on a single particle basis may lead to a more mechanistic understanding of particle formation and reactivity, global biogeochemical cycling, quantifying nanoparticle transport and impacts as they relate to hydrochemical and geochemical factors, and possibly differentiating ENPs from NNPs.

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

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

    Abstract: 

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

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

    Sebastian Kallus, Lukas Uhlik, Sushilla van Schoonhoven, Karla Pelivan, Walter Berger, va A. Enyedy, Thilo Hofmann, Petra Heffeter, Christian R. Kowol, Bernhard K. Keppler
    2019 - Journal of Inorganic Biochemistry, 85-97

    Abstract: 

    Triapine, the most prominent anticancer drug candidate from the substance class of thiosemicarbazones, was investigated in >30 clinical phase I and II studies. However, the results were rather disappointing against solid tumors, which can be explained (at least partially) due to inefficient delivery to the tumor site. Hence, we synthesized the first biotin-functionalized thiosemicarbazone derivatives in order to increase tumor specificity and accumulation. Additionally, for Triapine and one biotin conjugate the iron(III) and copper(II) complexes were prepared. Subsequently, the novel compounds were biologically evaluated on a cell line panel with different biotin uptake. The metal-free biotin-conjugated ligands showed comparable activity to the reference compound Triapine. However, astonishingly, the metal complexes of the biotinylated derivative showed strikingly decreased anticancer activity. To further analyze possible differences between the metal complexes, detailed physico- and electrochemical experiments were performed. However, neither lipophilicity or complex solution stability, nor the reduction potential or behavior in the presence of biologically relevant reducing agents showed strong variations between the biotinylated and non-biotinylated derivatives (only some differences in the reduction kinetics were observed). Nonetheless, the metal-free biotin-conjugate of Triapine revealed distinct activity in a colon cancer mouse model upon oral application comparable to Triapine. Therefore, this type of biotin-conjugated thiosemicarbazone is of interest for further synthetic strategies and biological studies.

  • A multicolor fluorescence in situ hybridization approach using an extended set of fluorophores to visualize microorganisms

    Lukumbuzya M, Schmid M, Pjevac P, Daims H
    2019 - Front Microbiol, 10: 1383

    Abstract: 

    Fluorescence in situ hybridization (FISH) with rRNA-targeted oligonucleotide probes is a key method for the detection of (uncultured) microorganisms in environmental and medical samples. A major limitation of standard FISH protocols, however, is the small number of phylogenetically distinct target organisms that can be detected simultaneously. In this study, we introduce a multicolor FISH approach that uses eight fluorophores with distinct spectral properties, which can unambiguously be distinguished by confocal laser scanning microscopy combined with white light laser technology. Hybridization of rRNA-targeted DNA oligonucleotide probes, which were mono-labeled with these fluorophores, to Escherichia coli cultures confirmed that the fluorophores did not affect probe melting behavior. Application of the new multicolor FISH method enabled the differentiation of seven (potentially up to eight) phylogenetically distinct microbial populations in an artificial community of mixed pure cultures (five bacteria, one archaeon, and one yeast strain) and in activated sludge from a full-scale wastewater treatment plant. In contrast to previously published multicolor FISH approaches, this method does not rely on combinatorial labeling of the same microorganisms with different fluorophores, which is prone to biases. Furthermore, images acquired by this method do not require elaborate post-processing prior to analysis. We also demonstrate that the newly developed multicolor FISH method is compatible with an improved cell fixation protocol for FISH targeting Gram-negative bacterial populations. This fixation approach uses agarose embedding during formaldehyde fixation to better preserve the three-dimensional structure of spatially complex samples such as biofilms and activated sludge flocs. The new multicolor FISH approach should be highly suitable for studying structural and functional aspects of microbial communities in virtually all types of samples that can be analyzed by conventional FISH methods.

  • A Bioinformatics Guide to Plant Microbiome Analysis.

    Lucaciu R, Pelikan C, Gerner SM, Zioutis C, Köstlbacher S, Marx H, Herbold CW, Schmidt H, Rattei T
    2019 - Front Plant Sci, 1313

    Abstract: 

    Recent evidence for intimate relationship of plants with their microbiota shows that plants host individual and diverse microbial communities that are essential for their survival. Understanding their relatedness using genome-based and high-throughput techniques remains a hot topic in microbiome research. Molecular analysis of the plant holobiont necessitates the application of specific sampling and preparatory steps that also consider sources of unwanted information, such as soil, co-amplified plant organelles, human DNA, and other contaminations. Here, we review state-of-the-art and present practical guidelines regarding experimental and computational aspects to be considered in molecular plant-microbiome studies. We discuss sequencing and "omics" techniques with a focus on the requirements needed to adapt these methods to individual research approaches. The choice of primers and sequence databases is of utmost importance for amplicon sequencing, while the assembly and binning of shotgun metagenomic sequences is crucial to obtain quality data. We discuss specific bioinformatic workflows to overcome the limitation of genome database resources and for covering large eukaryotic genomes such as fungi. In transcriptomics, it is necessary to account for the separation of host mRNA or dual-RNAseq data. Metaproteomics approaches provide a snapshot of the protein abundances within a plant tissue which requires the knowledge of complete and well-annotated plant genomes, as well as microbial genomes. Metabolomics offers a powerful tool to detect and quantify small molecules and molecular changes at the plant-bacteria interface if the necessary requirements with regard to (secondary) metabolite databases are considered. We highlight data integration and complementarity which should help to widen our understanding of the interactions among individual players of the plant holobiont in the future.

  • Berry-enriched diet in salt-sensitive hypertensive rats: metabolic fate of (poly)phenols and the role of gut microbiota.

    Gomes A, Oudot C, Macià A, Foito A, Carregosa D, Stewart D, Van de Wiele T, Berry D, Motilva MJ, Brenner C, Dos Santos CN
    2019 - Nutrients, 11: in press

    Abstract: 

    Diets rich in (poly)phenols are associated with a reduced reduction in the incidence of cardiovascular disorders. While the absorption and metabolism of (poly)phenols has been described, it is not clear how their metabolic fate is affected under pathological conditions. This study evaluated the metabolic fate of berry (poly)phenols in an in vivo model of hypertension as well as the associated microbiota response. Dahl salt-sensitive rats were fed either a low-salt diet (0.26% NaCl) or a high-salt diet (8% NaCl), with or without a berry mixture (blueberries, blackberries, raspberries, Portuguese crowberry and strawberry tree fruit) for 9 weeks. The salt-enriched diet promoted an increase in the urinary excretion of berry (poly)phenol metabolites, while the abundance of these metabolites decreased in faeces, as revealed by UPLC-MS/MS. Moreover, salt and berries modulated gut microbiota composition as demonstrated by 16S rRNA analysis. Some changes in the microbiota composition were associated with the high-salt diet and revealed an expansion of the families and . However, this effect was mitigated by the dietary supplementation with berries. Alterations in the metabolic fate of (poly)phenols occur in parallel with the modulation of gut microbiota in hypertensive rats. Thus, beneficial effects of (poly)phenols could be related with these interlinked modifications, between metabolites and microbiota environments.

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

    Gwak JH, Jung MY, Hong H, Kim JG, Quan ZX, Reinfelder JR, Spasov E, Neufeld JD, Wagner M, Rhee SK
    2019 - ISME J, in press

    Abstract: 

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

  • The Prevotella copri Complex Comprises Four Distinct Clades Underrepresented in Westernized Populations.

    Tett A, Huang KD, Asnicar F, Fehlner-Peach H, Pasolli E, Karcher N, Armanini F, Manghi P, Bonham K, Zolfo M, De Filippis F, Magnabosco C, Bonneau R, Lusingu J, Amuasi J, Reinhard K, Rattei T, Boulund F, Engstrand L, Zink A, Collado MC, Littman DR, Eibach D, Ercolini D, Rota-Stabelli O, Huttenhower C, Maixner F, Segata N
    2019 - Cell Host Microbe, in press

    Abstract: 

    Prevotella copri is a common human gut microbe that has been both positively and negatively associated with host health. In a cross-continent meta-analysis exploiting >6,500 metagenomes, we obtained >1,000 genomes and explored the genetic and population structure of P. copri. P. copri encompasses four distinct clades (>10% inter-clade genetic divergence) that we propose constitute the P. copri complex, and all clades were confirmed by isolate sequencing. These clades are nearly ubiquitous and co-present in non-Westernized populations. Genomic analysis showed substantial functional diversity in the complex with notable differences in carbohydrate metabolism, suggesting that multi-generational dietary modifications may be driving reduced prevalence in Westernized populations. Analysis of ancient metagenomes highlighted patterns of P. copri presence consistent with modern non-Westernized populations and a clade delineation time pre-dating human migratory waves out of Africa. These findings reveal that P. copri exhibits a high diversity that is underrepresented in Western-lifestyle populations.

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

    Assié A, Leisch N, Meier DV, Gruber-Vodicka H, Tegetmeyer HE, Meyerdierks A, Kleiner M, Hinzke T, Joye S, Saxton M, Dubilier N, Petersen JM
    2019 - ISME J, in press

    Abstract: 

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

  • Plant roots increase both decomposition and stable organic matter formation in boreal forest soil

    Adamczyk B, Sietiö OM, Straková P, Prommer J, Wild B, Hagner M, Pihlatie M, Fritze H, Richter A, Heinonsalo J
    2019 - Nature communications, 10: Article 3982
  • Expansion of Thaumarchaeota habitat range is correlated with horizontal transfer of ATPase operons.

    Wang B, Qin W, Ren Y, Zhou X, Jung MY, Han P, Eloe-Fadrosh EA, Li M, Zheng Y, Lu L, Yan X, Ji J, Liu Y, Liu L, Heiner C, Hall R, Martens-Habbena W, Herbold CW, Rhee SK, Bartlett DH, Huang L, Ingalls AE, Wagner M, Stahl DA, Jia Z
    2019 - ISME J, in press
    Phylogenetic ATPase tree of Thaumarchaeota

    Abstract: 

    Thaumarchaeota are responsible for a significant fraction of ammonia oxidation in the oceans and in soils that range from alkaline to acidic. However, the adaptive mechanisms underpinning their habitat expansion remain poorly understood. Here we show that expansion into acidic soils and the high pressures of the hadopelagic zone of the oceans is tightly linked to the acquisition of a variant of the energy-yielding ATPases via horizontal transfer. Whereas the ATPase genealogy of neutrophilic Thaumarchaeota is congruent with their organismal genealogy inferred from concatenated conserved proteins, a common clade of V-type ATPases unites phylogenetically distinct clades of acidophilic/acid-tolerant and piezophilic/piezotolerant species. A presumptive function of pumping cytoplasmic protons at low pH is consistent with the experimentally observed increased expression of the V-ATPase in an acid-tolerant thaumarchaeote at low pH. Consistently, heterologous expression of the thaumarchaeotal V-ATPase significantly increased the growth rate of E. coli at low pH. Its adaptive significance to growth in ocean trenches may relate to pressure-related changes in membrane structure in which this complex molecular machine must function. Together, our findings reveal that the habitat expansion of Thaumarchaeota is tightly correlated with extensive horizontal transfer of atp operons.

  • Chemosymbiotic bivalves contribute to the nitrogen budget of seagrass ecosystems.

    Cardini U, Bartoli M, Lücker S, Mooshammer M, Polzin J, Lee RW, Micić V, Hofmann T, Weber M, Petersen JM
    2019 - ISME J, in press

    Abstract: 

    In many seagrass sediments, lucinid bivalves and their sulfur-oxidizing symbionts are thought to underpin key ecosystem functions, but little is known about their role in nutrient cycles, particularly nitrogen. We used natural stable isotopes, elemental analyses, and stable isotope probing to study the ecological stoichiometry of a lucinid symbiosis in spring and fall. Chemoautotrophy appeared to dominate in fall, when chemoautotrophic carbon fixation rates were up to one order of magnitude higher as compared with the spring, suggesting a flexible nutritional mutualism. In fall, an isotope pool dilution experiment revealed carbon limitation of the symbiosis and ammonium excretion rates up to tenfold higher compared with fluxes reported for nonsymbiotic marine bivalves. These results provide evidence that lucinid bivalves can contribute substantial amounts of ammonium to the ecosystem. Given the preference of seagrasses for this nitrogen source, lucinid bivalves' contribution may boost productivity of these important blue carbon ecosystems.

  • Horizontally transmitted symbiont populations in deep-sea mussels are genetically isolated.

    Romero Picazo D, Dagan T, Ansorge R, Petersen JM, Dubilier N, Kupczok A
    2019 - ISME J, in press

    Abstract: 

    Eukaryotes are habitats for bacterial organisms where the host colonization and dispersal among individual hosts have consequences for the bacterial ecology and evolution. Vertical symbiont transmission leads to geographic isolation of the microbial population and consequently to genetic isolation of microbiotas from individual hosts. In contrast, the extent of geographic and genetic isolation of horizontally transmitted microbiota is poorly characterized. Here we show that chemosynthetic symbionts of individual Bathymodiolus brooksi mussels constitute genetically isolated subpopulations. The reconstruction of core genome-wide strains from high-resolution metagenomes revealed distinct phylogenetic clades. Nucleotide diversity and strain composition vary along the mussel life span and individual hosts show a high degree of genetic isolation. Our results suggest that the uptake of environmental bacteria is a restricted process in B. brooksi, where self-infection of the gill tissue results in serial founder effects during symbiont evolution. We conclude that bacterial colonization dynamics over the host life cycle is thus an important determinant of population structure and genome evolution of horizontally transmitted symbionts.

  • Diversity decoupled from sulfur isotope fractionation in a sulfate reducing microbial community

    Colangelo J, Pelikan C, Herbold CW, Altshuler I, Loy A, Whyte LG, Wing BA
    2019 - Geobiology, 17: 660-67

    Abstract: 

    The extent of fractionation of sulfur isotopes by sulfate-reducing microbes is dictated by genomic and environmental factors. A greater understanding of species-specific fractionations may better inform interpretation of sulfur isotopes preserved in the rock record. To examine whether gene diversity influences net isotopic fractionation in situ, we assessed environmental chemistry, sulfate reduction rates, diversity of putative sulfur-metabolizing organisms by 16S rRNA and dissimilatory sulfite reductase (dsrB) gene amplicon sequencing, and net fractionation of sulfur isotopes along a sediment transect of a hypersaline Arctic spring. In situ sulfate reduction rates yielded minimum cell-specific sulfate reduction rates < 0.3 × 10-15 moles cell-1  day-1 . Neither 16S rRNA nor dsrB diversity indices correlated with relatively constant (38‰-45‰) net isotope fractionation (ε34 Ssulfide-sulfate ). Measured ε34 S values could be reproduced in a mechanistic fractionation model if 1%-2% of the microbial community (10%-60% of Deltaproteobacteria) were engaged in sulfate respiration, indicating heterogeneous respiratory activity within sulfate-reducing populations. This model indicated enzymatic kinetic diversity of Apr was more likely to correlate with sulfur fractionation than DsrB. We propose that, above a threshold Shannon diversity value of 0.8 for dsrB, the influence of the specific composition of the microbial community responsible for generating an isotope signal is overprinted by the control exerted by environmental variables on microbial physiology.

  • In situ abundance and carbon fixation activity of distinct anoxygenic phototrophs in the stratified seawater lake Rogoznica.

    Pjevac P, Dyksma S, Goldhammer T, Mujakić I, Koblížek M, Mussmann M, Amann R, Orlić S
    2019 - Environ. Microbiol., 10: 3896-3908

    Abstract: 

    Sulphide-driven anoxygenic photosynthesis is an ancient microbial metabolism that contributes significantly to inorganic carbon fixation in stratified, sulphidic water bodies. Methods commonly applied to quantify inorganic carbon fixation by anoxygenic phototrophs, however, cannot resolve the contributions of distinct microbial populations to the overall process. We implemented a straightforward workflow, consisting of radioisotope labelling and flow cytometric cell sorting based on the distinct autofluorescence of bacterial photopigments, to discriminate and quantify contributions of co-occurring anoxygenic phototrophic populations to in situ inorganic carbon fixation in environmental samples. This allowed us to assign 89.3% ± 7.6% of daytime inorganic carbon fixation by anoxygenic phototrophs in Lake Rogoznica (Croatia) to an abundant chemocline-dwelling population of green sulphur bacteria (dominated by Chlorobium phaeobacteroides), whereas the co-occurring purple sulphur bacteria (Halochromatium sp.) contributed only 1.8% ± 1.4%. Furthermore, we obtained two metagenome assembled genomes of green sulphur bacteria and one of a purple sulphur bacterium which provides the first genomic insights into the genus Halochromatium, confirming its high metabolic flexibility and physiological potential for mixo- and heterotrophic growth.

  • Highly variable mRNA half-life time within marine bacterial taxa and functional genes.

    Steiner PA, De Corte D, Geijo J, Mena C, Yokokawa T, Rattei T, Herndl GJ, Sintes E
    2019 - Environ. Microbiol., in press

    Abstract: 

    Messenger RNA can provide valuable insights into the variability of metabolic processes of microorganisms. However, due to uncertainties that include the stability of RNA, its application for activity profiling of environmental samples is questionable. We explored different factors affecting the decay rate of transcripts of three marine bacterial isolates using qPCR and determined mRNA half-life time of specific bacterial taxa and of functional genes by metatranscriptomics of a coastal environmental prokaryotic community. The half-life time of transcripts from 11 genes from bacterial isolates ranged from 1 to 46 min. About 80% of the analysed transcripts exhibited half-live times shorter than 10 min. Significant differences were found in the half-life time between mRNA and rRNA. The half-life time of mRNA obtained from a coastal metatranscriptome ranged from 9 to 400 min. The shortest half-life times of the metatranscriptome corresponded to transcripts from the same clusters of orthologous groups (COGs) in all bacterial classes. The prevalence of short mRNA half-life time in genes related to defence mechanisms and motility indicate a tight connection of RNA decay rate to environmental stressors. The short half-life time of RNA and its high variability needs to be considered when assessing metatranscriptomes especially in environmental samples.

  • Specific micropollutant biotransformation pattern by the comammox bacterium Nitrospira inopinata

    Han P, Yu Y, Zhou L, Tian Z, Li Z, Hou L, Liu M, Wu Q, Wagner M, Men Y
    2019 - Environ. Sci. Technol., 15: 8695-8705
    Comammox biodegradation graphical abstract

    Abstract: 

    The recently discovered complete ammonia-oxidizing (comammox) bacteria occur in various environments, including wastewater treatment plants. To better understand their role in micropollutant biotransformation in comparison with ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA), we investigated the biotransformation capability of (the only comammox isolate) for 17 micropollutants. Asulam, fenhexamid, mianserin, and ranitidine were biotransformed by , (AOA), and Nm90 (AOB). More distinctively, carbendazim, a benzimidazole fungicide, was exclusively biotransformed by . The biotransformation of carbendazim only occurred when was supplied with ammonia but not nitrite as the energy source. The exclusive biotransformation of carbendazim by was likely enabled by an enhanced substrate promiscuity of its unique AMO and its much higher substrate (for ammonia) affinity compared with the other two ammonia oxidizers. One major plausible transformation product (TP) of carbendazim is a hydroxylated form at the aromatic ring, which is consistent with the function of AMO. These findings provide fundamental knowledge on the micropollutant degradation potential of a comammox bacterium to better understand the fate of micropollutants in nitrifying environments.

  • Thermal stress modifies the marine sponge virome.

    Laffy PW, Botté ES, Wood-Charlson EM, Weynberg KD, Rattei T, Webster NS
    2019 - Environ Microbiol Rep, in press

    Abstract: 

    Marine sponges can form stable partnerships with a wide diversity of microbes and viruses, and this high intraspecies symbiont specificity makes them ideal models for exploring how host-associated viromes respond to changing environmental conditions. Here we exposed the abundant Great Barrier Reef sponge Rhopaloiedes odorabile to elevated seawater temperature for 48 h and utilised a metaviromic approach to assess the response of the associated viral community. An increase in endogenous retro-transcribing viruses within the Caulimorviridae and Retroviridae families was detected within the first 12 h of exposure to 32 °C, and a 30-fold increase in retro-transcribing viruses was evident after 48 h at 32 °C. Thermally stressed sponges also exhibited a complete loss of ssDNA viruses which were prevalent in field samples and sponges from the control temperature treatment. Despite these viromic changes, functional analysis failed to detect any loss or gain of auxiliary metabolic genes, indicating that viral communities are not providing a direct competitive advantage to their host under thermal stress. In contrast, endogenous sponge retro-transcribing viruses appear to be replicating under thermal stress, and consistent with retroviral infections in other organisms, may be contributing to the previously described rapid decline in host health evident at elevated temperature.

  • Characterization of a thaumarchaeal symbiont that drives incomplete nitrification in the tropical sponge Ianthella basta.

    Moeller FU, Webster NS, Herbold CW, Behnam F, Domman D, Albertsen M, Mooshammer M, Markert S, Turaev D, Becher D, Rattei T, Schweder T, Richter A, Watzka M, Nielsen PH, Wagner M
    2019 - Environ. Microbiol., in press
    Metabolic scheme of the AOA symbiont in I. basta

    Abstract: 

    Marine sponges represent one of the few eukaryotic groups that frequently harbour symbiotic members of the Thaumarchaeota, which are important chemoautotrophic ammonia-oxidizers in many environments. However, in most studies, direct demonstration of ammonia-oxidation by these archaea within sponges is lacking, and little is known about sponge-specific adaptations of ammonia-oxidizing archaea (AOA). Here, we characterized the thaumarchaeal symbiont of the marine sponge Ianthella basta using metaproteogenomics, fluorescence in situ hybridization, qPCR and isotope-based functional assays. 'Candidatus Nitrosospongia ianthellae' is only distantly related to cultured AOA. It is an abundant symbiont that is solely responsible for nitrite formation from ammonia in I. basta that surprisingly does not harbour nitrite-oxidizing microbes. Furthermore, this AOA is equipped with an expanded set of extracellular subtilisin-like proteases, a metalloprotease unique among archaea, as well as a putative branched-chain amino acid ABC transporter. This repertoire is strongly indicative of a mixotrophic lifestyle and is (with slight variations) also found in other sponge-associated, but not in free-living AOA. We predict that this feature as well as an expanded and unique set of secreted serpins (protease inhibitors), a unique array of eukaryotic-like proteins, and a DNA-phosporothioation system, represent important adaptations of AOA to life within these ancient filter-feeding animals.

  • A proteotranscriptomic study of silk-producing glands from the orb-weaving spiders.

    Dos Santos-Pinto JRA, Esteves FG, Sialana FJ, Ferro M, Smidak R, Rares LC, Nussbaumer T, Rattei T, Bilban M, Bacci Júnior M, Palma MS, Lubec G
    2019 - Mol Omics, 4: 256-270

    Abstract: 

    Orb-weaving spiders can produce different silk fibers, which constitute outstanding materials characterized by their high strength and elasticity. Researchers have tried to reproduce the fibers of these proteins synthetically and/or by using recombinant DNA technology, but only a few of the natural physicochemical and biophysical properties have been obtained to date. Female orb-web-spiders present seven silk-glands, which synthesize the spidroins and a series of other proteins, which interact with the spidroins, resulting in silk fibers with notable physicochemical properties. Despite the recognized importance of the silk-glands for understanding how the fibers are produced and processed, the investigation of these glands is at a nascent stage. In the current study we present the assembled transcriptome of silk-producing glands from the orb-weaving spider Nephila clavipes, as well as develop a large-scale proteomic approach for in-depth analyses of silk-producing glands. The present investigation revealed an extensive repertoire of hitherto undescribed proteins involved in silk secretion and processing, such as prevention of degradation during the silk spinning process, transportation, protection against proteolytic autolysis and against oxidative stress, molecular folding and stabilization, and post-translational modifications. Comparative phylogenomic-level evolutionary analyses revealed orthologous genes among three groups of silk-producing organisms - (i) Araneomorphae spiders, (ii) Mygalomorphae spiders, and (iii) silk-producing insects. A common orthologous gene, which was annotated as silk gland factor-3 is present among all species analysed. This protein belongs to a transcription factor family, that is important and related to the development of the silk apparatus synthesis in the silk glands of silk-producing arthropods.

  • Indications for enzymatic denitrification to NO at low pH in an ammonia-oxidizing archaeon.

    Jung MY, Gwak JH, Rohe L, Giesemann A, Kim JG, Well R, Madsen EL, Herbold CW, Wagner M, Rhee SK
    2019 - ISME J, in press
    P450 NOR in AOA

    Abstract: 

    Nitrous oxide (NO) is a key climate change gas and nitrifying microbes living in terrestrial ecosystems contribute significantly to its formation. Many soils are acidic and global change will cause acidification of aquatic and terrestrial ecosystems, but the effect of decreasing pH on NO formation by nitrifiers is poorly understood. Here, we used isotope-ratio mass spectrometry to investigate the effect of acidification on production of NO by pure cultures of two ammonia-oxidizing archaea (AOA; Nitrosocosmicus oleophilus and Nitrosotenuis chungbukensis) and an ammonia-oxidizing bacterium (AOB; Nitrosomonas europaea). For all three strains acidification led to increased emission of NO. However, changes of N site preference (SP) values within the NO molecule (as indicators of pathways for NO formation), caused by decreasing pH, were highly different between the tested AOA and AOB. While acidification decreased the SP value in the AOB strain, SP values increased to a maximum value of 29‰ in N. oleophilus. In addition, N-nitrite tracer experiments showed that acidification boosted nitrite transformation into NO in all strains, but the incorporation rate was different for each ammonia oxidizer. Unexpectedly, for N. oleophilus more than 50% of the NO produced at pH 5.5 had both nitrogen atoms from nitrite and we demonstrated that under these conditions expression of a putative cytochrome P450 NO reductase is strongly upregulated. Collectively, our results indicate that N. oleophilus might be able to enzymatically denitrify nitrite to NO at low pH.

  • Cometabolic biotransformation and microbial-mediated abiotic transformation of sulfonamides by three ammonia oxidizers.

    Zhou LJ, Han P, Yu Y, Wang B, Men Y, Wagner M, Wu QL
    2019 - Water Res., 444-453

    Abstract: 

    The abilities of three phylogenetically distant ammonia oxidizers, Nitrososphaera gargensis, an ammonia-oxidizing archaeon (AOA); Nitrosomomas nitrosa Nm90, an ammonia-oxidizing bacterium (AOB); and Nitrospira inopinata, the only complete ammonia oxidizer (comammox) available as a pure culture, to biotransform seven sulfonamides (SAs) were investigated. The removals and protein-normalized biotransformation rate constants indicated that the AOA strain N. gargensis exhibited the highest SA biotransformation rates, followed by N. inopinata and N. nitrosa Nm90. The transformation products (TPs) of sulfadiazine (SDZ), sulfamethazine (SMZ) and sulfamethoxazole (SMX) and the biotransformation mechanisms were evaluated. Based on the analysis of the TP formulas and approximate structures, it was found that during biotransformation, i) the AOA strain carried out SA deamination, hydroxylation, and nitration; ii) the AOB strain mainly performed SA deamination; and iii) the comammox isolate participated only in deamination reactions. It is proposed that deamination was catalyzed by deaminases while hydroxylation and nitration were mediated by nonspecific activities of the ammonia monooxygenase (AMO). Additionally, it was demonstrated that among the three ammonia oxidizers, only AOB contributed to the formation of pterin-SA conjugates. The biotransformation of SDZ, SMZ and SMX occurred only when ammonia oxidation was active, suggesting a cometabolic transformation mechanism. Interestingly, SAs could also be transformed by hydroxylamine, an intermediate of ammonia oxidation, suggesting that in addition to enzymatic conversions, a microbially induced abiotic mechanism contributes to SA transformation during ammonia oxidation. Overall, using experiments with pure cultures, this study provides important insights into the roles played by ammonia oxidizers in SA biotransformation.

  • Proteome Changes Paralleling the Olfactory Conditioning in the Forager Honey Bee and Provision of a Brain Proteomics Dataset.

    Sialana FJ, Menegasso ARS, Smidak R, Hussein AM, Zavadil M, Rattei T, Lubec G, Palma MS, Lubec J
    2019 - Proteomics, e1900094

    Abstract: 

    The olfactory conditioning of the bee proboscis extension reflex (PER) has been extensively used as a paradigm in associative learning of invertebrates but with limited molecular investigations. To investigate which protein changes are linked to olfactory conditioning, we applied a non-sophisticated conditioning model using the PER in the honeybee (Apis mellifera). Foraging honeybees were assigned into three groups based on the reflex behaviour and training: conditioned using 2-octanone (PER-conditioned), and sucrose and water controls. Thereafter, the brain synaptosomal proteins were isolated and analyzed by quantitative proteomics using stable isotope labeling (TMT). Additionally, the complex proteome dataset of the bee brain was generated with a total number of 5411 protein groups, including key players in neurotransmitter signalling. The most significant categories affected during olfactory conditioning were associated with "SNARE interactions in vesicular transport" (BET1 and VAMP7), ABC transporters, and fatty acid degradation pathways. This article is protected by copyright. All rights reserved.

  • Symbiont-mediated defense against Legionella pneumophila in amoebae

    König L, Wentrup C, Schulz F, Wascher F, Escola S, Swanson MS, Buchrieser C, Horn M
    2019 - mBio, 10: e00333-19

    Abstract: 

    Legionella pneumophila is an important opportunistic pathogen for which environmental reservoirs are crucial for the infection of humans. In the environment, free-living amoebae represent key hosts providing nutrients and shelter for highly efficient intracellular proliferation of L. pneumophila, which eventually leads to lysis of the protist. However, the significance of other bacterial players for L. pneumophila ecology is poorly understood. In this study, we used a ubiquitous amoeba and bacterial endosymbiont to investigate the impact of this common association on L. pneumophilainfection. We demonstrate that L. pneumophila proliferation was severely suppressed in Acanthamoeba castellanii harboring the chlamydial symbiont Protochlamydia amoebophila. The amoebae survived the infection and were able to resume growth. Different environmental amoeba isolates containing the symbiont were equally well protected as different L. pneumophila isolates were diminished, suggesting ecological relevance of this symbiont-mediated defense. Furthermore, protection was not mediated by impaired L. pneumophila uptake. Instead, we observed reduced virulence of L. pneumophila released from symbiont-containing amoebae. Pronounced gene expression changes in the presence of the symbiont indicate that interference with the transition to the transmissive phase impedes the L. pneumophila infection. Finally, our data show that the defensive response of amoebae harboring P. amoebophila leaves the amoebae with superior fitness reminiscent of immunological memory. Given that mutualistic associations between bacteria and amoebae are widely distributed, P. amoebophila and potentially other amoeba endosymbionts could be key in shaping environmental survival, abundance, and virulence of this important pathogen, thereby affecting the frequency of human infection.

  • Antioxidative activity and health benefits of anthocyanin-rich fruit juice in healthy volunteers.

    Bakuradze T, Tausend A, Galan J, Maria Groh IA, Berry D, Tur JA, Marko D, Richling E
    2019 - Free Radic. Res., 1-11

    Abstract: 

    Oxidative cell damage has been linked to the pathogenesis of numerous diseases such as atherosclerosis, type 2 diabetes, and cancer. The consumption of foods rich in polyphenols (e.g. anthocyanins) has been shown to exert preventive effects against such diseases. We investigated the biological effects of anthocyanin-rich fruit juice in a 9-week, placebo-controlled intervention study with 57 healthy male volunteers. The study design encompassed an initial 1 week of wash-out, followed by 8 weeks of intervention period with anthocyanin-rich fruit juice or placebo. The anthocyanin-rich fruit juice demonstrated DNA-protective and antioxidant effects; however, the placebo beverage, rich in vitamin C, showed similar effects based on the tested biomarkers. A significant reduction in background and total DNA strand breaks was observed in both groups within 24 h as well as after 8 weeks of intervention. Only anthocyanin-rich fruit juice consumption provided a significant reduction in body fat and an increase in fat-free mass. The activity of superoxide dismutase (SOD) was significantly elevated after consumption of anthocyanin-rich fruit juice. Both groups showed decreased levels of LDL and total cholesterol (TC) within the first week of the intervention. Similar results in both groups could be explained by the relatively high vitamin C contents of both beverages (>500 mg/L), which may have masked the effects of anthocyanins and other antioxidants in the studied juice. Taken together, anthocyanin-rich fruit juice as well as the placebo drink, both of which had high vitamin C content, can improve DNA integrity and might influence lipid metabolism in humans.

  • Global diversity and biogeography of bacterial communities in wastewater treatment plants.

    Wu L, Ning D, Zhang B, Li Y, Zhang P, Shan X, Zhang Q, Brown M, Li Z, Van Nostrand JD, Ling F, Xiao N, Zhang Y, Vierheilig J, Wells GF, Yang Y, Deng Y, Tu Q, Wang A, Zhang T, He Z, Keller J, Nielsen PH, Alvarez PJJ, Criddle CS, Wagner M, Tiedje JM, He Q, Curtis TP, Stahl DA, Alvarez-Cohen L, Rittmann BE, Wen X, Zhou J
    2019 - Nat Microbiol, 7: 1183-1195
    Sources of microbes in activated sludge

    Abstract: 

    Microorganisms in wastewater treatment plants (WWTPs) are essential for water purification to protect public and environmental health. However, the diversity of microorganisms and the factors that control it are poorly understood. Using a systematic global-sampling effort, we analysed the 16S ribosomal RNA gene sequences from ~1,200 activated sludge samples taken from 269 WWTPs in 23 countries on 6 continents. Our analyses revealed that the global activated sludge bacterial communities contain ~1 billion bacterial phylotypes with a Poisson lognormal diversity distribution. Despite this high diversity, activated sludge has a small, global core bacterial community (n = 28 operational taxonomic units) that is strongly linked to activated sludge performance. Meta-analyses with global datasets associate the activated sludge microbiomes most closely to freshwater populations. In contrast to macroorganism diversity, activated sludge bacterial communities show no latitudinal gradient. Furthermore, their spatial turnover is scale-dependent and appears to be largely driven by stochastic processes (dispersal and drift), although deterministic factors (temperature and organic input) are also important. Our findings enhance our mechanistic understanding of the global diversity and biogeography of activated sludge bacterial communities within a theoretical ecology framework and have important implications for microbial ecology and wastewater treatment processes.

  • Conserved Secondary Structures in Viral mRNAs.

    Kiening M, Ochsenreiter R, Hellinger HJ, Rattei T, Hofacker I, Frishman D
    2019 - Viruses, 5: in press

    Abstract: 

    RNA secondary structure in untranslated and protein coding regions has been shown to play an important role in regulatory processes and the viral replication cycle. While structures in non-coding regions have been investigated extensively, a thorough overview of the structural repertoire of protein coding mRNAs, especially for viruses, is lacking. Secondary structure prediction of large molecules, such as long mRNAs remains a challenging task, as the contingent of structures a sequence can theoretically fold into grows exponentially with sequence length. We applied a structure prediction pipeline to Viral Orthologous Groups that first identifies the local boundaries of potentially structured regions and subsequently predicts their functional importance. Using this procedure, the orthologous groups were split into structurally homogenous subgroups, which we call subVOGs. This is the first compilation of potentially functional conserved RNA structures in viral coding regions, covering the complete RefSeq viral database. We were able to recover structural elements from previous studies and discovered a variety of novel structured regions. The subVOGs are available through our web resource RNASIV (RNA structure in viruses; http://rnasiv.bio.wzw.tum.de).

  • Low yield and abiotic origin of NO formed by the complete nitrifier Nitrospira inopinata.

    Kits KD, Jung MY, Vierheilig J, Pjevac P, Sedlacek CJ, Liu S, Herbold CW, Stein LY, Richter A, Wissel H, Brüggemann N, Wagner M, Daims H
    2019 - Nat Commun, 1: 1836
    Nitrous oxide comammox

    Abstract: 

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

  • Mucispirillum schaedleri antagonizes Salmonella virulence to protect mice against colitis

    Herp S, Brugiroux S, Garzetti D, Ring D, Jochum LM, Beutler M, Eberl C, Hussain S, Walter S, Gerlach RG, Ruscheweyh HJ, Huson D, Sellin ME, Slack E, Hanson B, Loy A, Baines JF, Rausch P, Basic M, Bleich A, Berry D, Stecher B
    2019 - Cell Host Microbe, 25: 681-694

    Abstract: 

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

  • The horse Y chromosome as an informative marker for tracing sire lines.

    Felkel S, Vogl C, Rigler D, Dobretsberger V, Chowdhary BP, Distl O, Fries R, Jagannathan V, Janečka JE, Leeb T, Lindgren G, McCue M, Metzger J, Neuditschko M, Rattei T, Raudsepp T, Rieder S, Rubin CJ, Schaefer R, Schlötterer C, Thaller G, Tetens J, Velie B, Brem G, Wallner B
    2019 - Sci Rep, 1: 6095

    Abstract: 

    Analysis of the Y chromosome is the best-established way to reconstruct paternal family history in humans. Here, we applied fine-scaled Y-chromosomal haplotyping in horses with biallelic markers and demonstrate the potential of our approach to address the ancestry of sire lines. We de novo assembled a draft reference of the male-specific region of the Y chromosome from Illumina short reads and then screened 5.8 million basepairs for variants in 130 specimens from intensively selected and rural breeds and nine Przewalski's horses. Among domestic horses we confirmed the predominance of a young'crown haplogroup' in Central European and North American breeds. Within the crown, we distinguished 58 haplotypes based on 211 variants, forming three major haplogroups. In addition to two previously characterised haplogroups, one observed in Arabian/Coldblooded and the other in Turkoman/Thoroughbred horses, we uncovered a third haplogroup containing Iberian lines and a North African Barb Horse. In a genealogical showcase, we distinguished the patrilines of the three English Thoroughbred founder stallions and resolved a historic controversy over the parentage of the horse 'Galopin', born in 1872. We observed two nearly instantaneous radiations in the history of Central and Northern European Y-chromosomal lineages that both occurred after domestication 5,500 years ago.

  • Widespread soil bacterium that oxidizes atmospheric methane.

    Tveit AT, Hestnes AG, Robinson SL, Schintlmeister A, Dedysh SN, Jehmlich N, von Bergen M, Herbold CW, Wagner M, Richter A, Svenning MM
    2019 - Proc. Natl. Acad. Sci. U.S.A., 17: 8515-8524
    air eating microbe

    Abstract: 

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

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

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

    Abstract: 

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

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

    Fernando EY, McIlroy SJ, Nierychlo M, Herbst FA, Petriglieri F, Schmid MC, Wagner M, Nielsen JL, Nielsen PH
    2019 - ISME J, 8: 1933-1946

    Abstract: 

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

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

    Lee KS, Palatinszky M, Pereira FC, Nguyen J, Fernandez VI, Mueller AJ, Menolascina F, Daims H, Berry D, Wagner M, Stocker R
    2019 - Nat Microbiol, 6: 1035-1048

    Abstract: 

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

  • Root exudation of primary metabolites: mechanisms and their roles in plant responses to environmental stimuli

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

    Abstract: 

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

  • Historical factors associated with past environments influence the biogeography of thermophilic endospores in Arctic marine sediments

    Hanson CA, Müller AL, Loy A, Dona C, Appel R, Jørgensen BB, Hubert CRJ
    2019 - Front Microbiol, 10: 245

    Abstract: 

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

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

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

    Abstract: 

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

  • Man-made microbial resistances in built environments.

    Mahnert A, Moissl-Eichinger C, Zojer M, Bogumil D, Mizrahi I, Rattei T, Martinez JL, Berg G
    2019 - Nat Commun, 1: 968

    Abstract: 

    Antimicrobial resistance is a serious threat to global public health, but little is known about the effects of microbial control on the microbiota and its associated resistome. Here we compare the microbiota present on surfaces of clinical settings with other built environments. Using state-of-the-art metagenomics approaches and genome and plasmid reconstruction, we show that increased confinement and cleaning is associated with a loss of microbial diversity and a shift from Gram-positive bacteria, such as Actinobacteria and Firmicutes, to Gram-negative such as Proteobacteria. Moreover, the microbiome of highly maintained built environments has a different resistome when compared to other built environments, as well as a higher diversity in resistance genes. Our results highlight that the loss of microbial diversity correlates with an increase in resistance, and the need for implementing strategies to restore bacterial diversity in certain built environments.

  • Increased risk of phosphorus and metal leaching from paddy soils after excessive manure application: Insights from a mesocosm study

    Liu XP, Bi QF, Qiu LL, Li KJ, Yang XR, Lin XY
    2019 - Science of The Total Environment, 666: 778-785

    Abstract: 

    Livestock manure has gradually become an alternative fertilizer for maintaining soil fertility, whereas excessive application of manure leads to the release of phosphorus (P) and toxic metals that may cause complex environmental risks. To investigate the accumulation and migration of P within soil profiles, a mesocosm experiment was conducted to analyze the content and leaching of soil P, metals, and dissolved organic carbon after different fertilization treatments, including control (no fertilizer, CK), chemical fertilizer (CF), chemical fertilizer combined low (CF + LPM) and high (CF + HPM) rate of manure application. Results showed that a high rate of manure application significantly enhanced the accumulation of total soil P (by ~14%) and P availability (easily-available P, by ~24%; Olsen-P, by ~20%) in topsoil, and also increased the content of easily-available organic P (EA-Po) in both topsoil and subsoil compared to the CK treatment. The migration of dissolved inorganic and organic P (DIP and DOP) in leachate within soil profiles was strengthened by manure application. Moreover, significant positive correlations between P, metals, and dissolved organic carbon (DOC) in leachate indicated that downward co-migration occurred within the soil profiles, and also suggested that excessive manure application can intensify the risk of P loss by increasing the migration of manure-derived DOC. Overall, our findings provide insights into P accumulation and migration within soil profiles after excessive manure application, which is useful for predicting the potential risk of P and metal leaching from paddy soils.

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

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

    Abstract: 

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

  • Plasmid DNA contaminant in molecular reagents.

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

    Abstract: 

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

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

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

    Abstract: 

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

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

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

    Abstract: 

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

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

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

    Abstract: 

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

Book chapters and other publications

6 Publications found
  • Response to the Letter to the Editor Regarding Our Feature “Are We Speaking the Same Language? Recommendations for a Definition and Categorization Framework for Plastic Debris”

    Nanna B. Hartmann, Thorsten Hüffer, Richard C. Thompson, Gaul T, Anja Verschoor, Anders E. Daugaard, Sinja Rist, Therese Karlsson, Nicole Brennholt, Matthew Cole, Maria P. Herrling, Maren C. Hess, Natalia P. Ivleva, Amy L. Lusher, Martin Wagner
    2019 - Environmental Science & Technology, 53: 4678−4679
  • Mikrobiome – Wissensstand und Perspektiven

    Wagner M
    2019 - 17-29. in Die unbekannte 
Welt der Mikrobiome; Rundgespräche Forum Ökologie Bd. 47. (Bauer J & von Mutius E). Bayerische Akademie der Wissenschaften; Verlag Dr. Friedrich Pfeil
  • International Committee on Systematics of Prokaryotes (ICSP) Subcommittee on the taxonomy of Chlamydiae. Minutes of the closed meeting, 20 March 2019, Seattle, WA, USA.

    Borel N, Horn M, Greub G
    2019 - Int. J. Syst. Evol. Microbiol., 69: 3654-3656
  • Draft Genome Sequence of Desulfosporosinus fructosivorans Strain 63.6F, Isolated from Marine Sediment in the Baltic Sea

    Hausmann B, Vandieken V, Pjevac P, Schreck K, Herbold CW, Loy A
    2019 - Microbiology Resource Announcements, 8: e00427-1

    Abstract: 

    Desulfosporosinus fructosivorans strain 63.6FT is a strictly anaerobic, spore-forming, sulfate-reducing bacterium isolated from marine sediment in the Baltic Sea. Here, we report the draft genome sequence of D. fructosivorans 63.6FT.

  • Draft Genome Sequence of Desulfosporosinus sp. Strain Sb-LF, Isolated from an acidic peatland in Germany

    Hausmann B, Pjevac P, Huemer M, Herbold CW, Pester M, Loy A
    2019 - Microbiology Resource Announcements, 8: e00428-1

    Abstract: 

    Desulfosporosinus sp. strain Sb-LF was isolated from an acidic peatland in Bavaria, Germany. Here, we report the draft genome sequence of the sulfate-reducing and lactate-utilizing strain Sb-LF.

  • Up-close-and-personal with the human microbiome

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