Metamenu

Publications

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Publications in peer reviewed journals

90 Publications found
  • Retention of phytosiderophores by the soil solid phase adsorption and desorption

    M. Walter, E. Oburger, Y. Schindlegger, S. Hann, M. Puschenreiter, Stephan M. Kraemer, W. D. C. Schenkeveld
    2016 - Plant and Soil, 1: 85-97

    Abstract: 

    Background and aims

    Graminaceous plants exude phytosiderophores (PS) for acquiring Fe. Adsorption of PS and its metal complexes to the soil solid phase reduces the FePS solution concentration and hence Fe uptake. In this study we aimed to quantify adsorption, and to determine to what extent adsorption depends on the complexed metal and on soil properties. Furthermore, we examined if adsorption is a reversible process.

    Methods

    Adsorption and desorption of PS and metal-PS complexes were examined in batch experiments in which the PS 2′-deoxymugineic acid (DMA) and its metal-complexes (FeDMA, CuDMA, NiDMA and ZnDMA) interacted with several calcareous soils.

    Results

    Adsorption of DMA ligand (0–1000 μM) and metal-DMA complexes (0–100 μM) was linear in the concentration range examined. Adsorption varied by a factor ≈2 depending on the complexed metal and by up to a factor 3.5 depending on the soil. Under field-like conditions (50 % water holding capacity), 50–84 % of the DMA was predicted to be retained to the soil solid phase. Alike adsorption, desorption of metal-DMA complexes is fast (approximate equilibrium within 1 hour). However, only a small fraction of the adsorbed FeDMA (28–35 %) could be desorbed.

    Conclusions

    Despite this small fraction, the desorbed FeDMA still exceeded the amount in solution, indicating that desorption of FeDMA from soil reactive compounds can be an important process buffering the solution concentration.

  • Macromolecular Pt(IV) Prodrugs from Poly(organo)phosphazenes

    Helena Henke, Kushtrim Kryeziu, Jelena Banfić, Sarah Theiner, Proc. Natl. Acad. Sci. USA, Oliver Brüggemann, Walter Berger, Bernhard K. Keppler, Petra Heffeter, Ian Teasdale
    2016 - Macromolecular Bioscience, 8: 1239-1249

    Abstract: 

    The preparation of novel macromolecular prodrugs via the conjugation of two platinum(IV) complexes to suitably functionalized poly(organo)phosphazenes is presented. The inorganic/organic polymers provide carriers with controlled dimensions due to the use of living cationic polymerization and allow the preparation of conjugates with excellent aqueous solubility but long‐term hydrolytic degradability. The macromolecular Pt(IV) prodrugs are designed to undergo intracellular reduction and simultaneous release from the macromolecular carrier to present the active Pt(II) drug derivatives. In vitro investigations show a significantly enhanced intracellular uptake of Pt for the macromolecular prodrugs when compared to small molecule Pt complexes, which is also reflected in an increase in cytotoxicity. Interestingly, drug‐resistant sublines also show a significantly smaller resistance against the conjugates compared to clinically established platinum drugs, indicating that an alternative uptake route of the Pt(IV) conjugates might also be able to overcome acquired resistance against Pt(II) drugs. In vivo studies of a selected conjugate show improved tumor shrinkage compared to the respective Pt(IV) complex.

  • Refining the phylum Chlorobi by resolving the phylogeny and metabolic potential of the representative of a deeply branching, uncultivated lineage

    Hiras J, Wu YW, Eichorst SA, Simmons BA, Singer SW
    2016 - ISME Journal, 10: 833-845
  • Silver and gold nanoparticle separation using asymmetrical flow-field flow fractionation: Influence of run conditions and of particle and membrane charges

    Boris Meisterjahn, Stephan Wagner, Frank von der Kammer, Dieter Hennecke, Thilo Hofmann
    2016 - Journal of Chromatography A, 150-159

    Abstract: 

    Flow-Field Flow Fractionation (Flow-FFF), coupled with online detection systems is one of the most promising tools available for the separation and quantification of engineered nanoparticles (ENPs) in complex matrices. To correctly relate the retention of nanoparticles in the Flow-FFF-channel to the particle size, ideal separation conditions must be met. This requires optimization of the parameters that influence the separation behavior. The aim of this study was therefore to systematically investigate and evaluate the influence of parameters such as the carrier liquid, the cross flow, and the membrane material, on the separation behavior of two metallic ENPs. For this purpose the retention, recovery, and separation efficiency of sterically stabilized silver nanoparticles (AgNPs) and electrostatically stabilized gold nanoparticles (AuNPs), which represent two materials widely used in investigations on environmental fate and ecotoxicology, were investigated against a parameter matrix of three different cross-flow densities, four representative carrier solutions, and two membrane materials.

    The use of a complex mixture of buffers, ionic and non-ionic surfactants (FL-70 solution) together with a medium cross-flow density provided an acceptable compromise in peak quality and recovery for both types of ENPs. However, these separation conditions do not represent a perfect match for both particle types at the same time (maximized recovery at maximized retention).

    It could be shown that the behavior of particles within Flow-FFF channels cannot be predicted or explained purely in terms of electrostatic interactions. Particles were irreversibly lost under conditions where the measured zeta potentials suggested that there should have been sufficient electrostatic repulsion to ensure stabilization of the particles in the Flow-FFF channel resulting in good recoveries.

    The wide variations that we observed in ENP behavior under different conditions, together with the different behavior that has been reported in published literature for the same NPs under similar conditions, indicate a need for improvement in the membrane materials used for Flow-FFF analysis of NPs.

    This research has shown that careful adjustment of separation conditions can result in acceptable, but not ideal, separation conditions for two fundamentally different stabilized materials, and that it may not be possible to separate a set of different particles under ideal conditions for each particle type. This therefore needs to be taking into account in method development and when interpreting FFF results from complex samples.

  • Soil microbial carbon use efficiency and biomass turnover in a long-term fertilization experiment in a temperate grassland

    Spohn M, Pötsch EM, Eichorst SA, Woebken D, Wanek W, Richter A
    2016 - Soil Biology and Biochemistry, 97: 168-175

    Abstract: 

    Soil microbial carbon use efficiency (CUE), defined as the ratio of organic C allocated to growth over organic C taken up, strongly affects soil carbon (C) cycling. Despite the importance of the microbial CUE for the terrestrial C cycle, very little is known about how it is affected by nutrient availability. Therefore, we studied microbial CUE and microbial biomass turnover time in soils of a long-term fertilization experiment in a temperate grassland comprising five treatments (control, PK, NK, NP, NPK). Microbial CUE and the turnover of microbial biomass were determined using a novel substrate-independent method based on incorporation of 18O from labeled water into microbial DNA. Microbial respiration was 28–37% smaller in all three N treatments (NK, NP, and NPK) compared to the control, whereas the PK treatment did not affect microbial respiration. N-fertilization decreased microbial C uptake, while the microbial growth rate was not affected. Microbial CUE ranged between 0.31 and 0.45, and was 1.3- to 1.4-fold higher in the N-fertilized soils than in the control. The turnover time ranged between 80 and 113 days and was not significantly affected by fertilization. Net primary production (NPP) and the abundance of legumes differed strongly across the treatments, and the fungal:bacterial ratio was very low in all treatments. Structural equation modeling revealed that microbial CUE was exclusively controlled by N fertilization and that neither the abundance of legumes (as a proxy for the quality of the organic matter inputs) nor NPP (as a proxy for C inputs) had an effect on microbial CUE. Our results show that N fertilization did not only decrease microbial respiration, but also microbial C uptake, indicating that less C was intracellularly processed in the N fertilized soils. The reason for reduced C uptake and increased CUE in the N-fertilization treatments is likely an inhibition of oxidative enzymes involved in the degradation of aromatic compounds by N in combination with a reduced energy requirement for microbial N acquisition in the fertilized soils. In conclusion, the study shows that N availability can control soil C cycling by affecting microbial CUE, while plant community-mediated changes in organic matter inputs and P and K availability played no important role for C partitioning of the microbial community in this temperate grassland.

  • Sorption of non-polar organic compounds by micro-sized plastic particles in aqueous solution

    Thorsten Hüffer, Thilo Hofmann
    2016 - Environmental Pollution, 194-201

    Abstract: 

    The presence of microscale polymer particles (i.e., microplastics) in the environment has become a major concern in recent years. Sorption of organic compounds by microplastics may affect the phase distribution within both sediments and aqueous phases. To investigate this process, isotherms were determined for the sorption of seven aliphatic and aromatic organic probe sorbates by four polymers with different physico-chemical properties. Sorption increased in the order polyamide < polyethylene < polyvinylchloride < polystyrene. This order does not reflect the particle sizes of the investigated microplastics within the aqueous dispersions, indicating the influence of additional factors (e.g., π-π-interactions) on the sorption of aromatic compounds by polystyrene. Linear isotherms by polyethylene suggested that sorbate uptake was due to absorption into the bulk polymer. In contrast, non-linear isotherms for sorption by PS, PA, and PVC suggest a predominance of adsorption onto the polymer surface, which is supported by the best fit of these isotherms using the Polanyi-Manes model. A strong relationship between the sorption coefficients of the microplastics and the hydrophobicity of the sorbates suggests that hydrophobic interactions are of major importance.

  • Functional leaf traits of vascular epiphytes: vertical trends within the forest, intra- and interspecific trait variability, and taxonomic signals

    Petter G, Wagner K, Wanek W, Delago EJS, Zotz G, Cabral JS, Kreft H
    2016 - Functional Ecology, 30: 188-198

    Abstract: 

    Summary

    1. Analysing functional traits along environmental gradients can improve our understanding of the mechanisms structuring plant communities. Within forests, vertical gradients in light intensity, temperature and humidity are often pronounced. Vascular epiphytes are particularly suitable for studying the influence of these vertical gradients on functional traits because they lack contact with the soil and thus individual plants are entirely exposed to different environmental conditions, from the dark and humid understorey to the sunny and dry outer canopy.
    2. In this study, we analysed multiple aspects of the trait-based ecology of vascular epiphytes: shifts in trait values with height above ground (as a proxy for vertical environmental gradients) at community and species level, the importance of intra- vs. interspecific trait variability, and trait differences among taxonomic groups. We assessed ten leaf traits for 1151 individuals belonging to 83 epiphyte species of all major taxonomic groups co-occurring in a Panamanian lowland forest.
    3. Community mean trait values of many leaf traits were strongly correlated with height and particularly specific leaf area and chlorophyll concentration showed nonlinear, negative trends.
    4. Intraspecific trait variability was pronounced and accounted for one-third of total observed trait variance. Intraspecific trait adjustments along the vertical gradient were common and seventy per cent of all species showed significant trait–height relationships. In addition, intraspecific trait variability was positively correlated with the vertical range occupied by species.
    5. We observed significant trait differences between major taxonomic groups (orchids, ferns, aroids, bromeliads). In ferns, for instance, leaf dry matter content was almost twofold higher than in the other taxonomic groups. This indicates that some leaf traits are taxonomically conserved.
    6. Our study demonstrates that vertical environmental gradients strongly influence functional traits of vascular epiphytes. In order to understand community composition along such gradients, it is central to study several aspects of trait-based ecology, including both community and intraspecific trends of multiple traits.
  • Agar agar-stabilized milled zerovalent iron particles for in situ groundwater remediation

    Milica Velimirovic, Doris Schmid, Stephan Wagner, Malfatti SE, Frank von der Kammer, Thilo Hofmann
    2016 - Science of The Total Environment, 713-723

    Abstract: 

    Submicron-scale milled zerovalent iron (milled ZVI) particles produced by grinding macroscopic raw materials could provide a cost-effective alternative to nanoscale zerovalent iron (nZVI) particles for in situ degradation of chlorinated aliphatic hydrocarbons in groundwater. However, the aggregation and settling of bare milled ZVI particles from suspension presents a significant obstacle to their in situ application for groundwater remediation. In our investigations we reduced the rapid aggregation and settling rate of bare milled ZVI particles from suspension by stabilization with a “green” agar agar polymer. The transport potential of stabilized milled ZVI particle suspensions in a diverse array of natural heterogeneous porous media was evaluated in a series of well-controlled laboratory column experiments. The impact of agar agar on trichloroethene (TCE) removal by milled ZVI particles was assessed in laboratory-scale batch reactors. The use of agar agar significantly enhanced the transport of milled ZVI particles in all of the investigated porous media. Reactivity tests showed that the agar agar-stabilized milled ZVI particles were reactive towards TCE, but that their reactivity was an order of magnitude less than that of bare, non-stabilized milled ZVI particles. Our results suggest that milled ZVI particles could be used as an alternative to nZVI particles as their potential for emplacement into contaminated zone, their reactivity, and expected longevity are beneficial for in situ groundwater remediation.

  • Mycorrhizas across scales: a journey between genomics, global patterns of biodiversity and biogeochemistry

    Chagnon P, Rineau F, Kaiser C
    2016 - New Phytologist, 209: 913-916

    Abstract: 

    Mycorrhizal fungi are found in almost all ecosystems of the planet.
    They interact with a majority of plant species, and it seems that
    every single aspect of the life history of a plant individual is affected
    by the presence of mycorrhizal fungal symbion ts in its roots (van der
    Heijden et al., 2015). Mycorrhizal fungi are also known to affect
    plant population-level and community-level dynamics. Yet, classic
    800-page plant ecology textbooks typically devote only one to two
    pages to mycorrhizal symbioses. Is it time to put mycorrhizal
    ecologists on the editorial boards of these textbooks? Meetings like
    the International Conference on Mycorrhizas (ICOM) tend to
    suggest that this might not be a bad idea.
    On August 37, 2015, mycorrhizal researchers from around the
    world shared their thoughts and empirical results on these globally
    widespread symbioses at a comfortable elevation of 2135 m in
    Flagstaff, Arizona, surrounded by beautiful landscapes, like
    widespread Ponderosa Pine forests, the San Francisco Peaks area,
    and the impressive Grand Canyon. New Phytologist was present
    as a sponsor, continuing its ongoing support of mycorrhizal
    research (Selosse & Martin, 2013; Dickie et al., 2015). Through
    talks and posters, mycorrhizal researchers literally took us on a
    journey across all scales of observation of this symbiosis: from the
    intracellular environment to global patterns of mycorrhizal
    fungal diversity and biogeochemical cycles (Fig. 1).

    Mycorrhizal fungi are found in almost all ecosystems of the planet.

    They interact with a majority of plant species, and it seems that
    every single aspect of the life history of a plant individual is affected
    by the presence of mycorrhizal fungal symbion ts in its roots (van der
    Heijden et al., 2015). Mycorrhizal fungi are also known to affect
    plant population-level and community-level dynamics. Yet, classic
    800-page plant ecology textbooks typically devote only one to two
    pages to mycorrhizal symbioses. Is it time to put mycorrhizal
    ecologists on the editorial boards of these textbooks? Meetings like
    the International Conference on Mycorrhizas (ICOM) tend to
    suggest that this might not be a bad idea.
    On August 37, 2015, mycorrhizal researchers from around the
    world shared their thoughts and empirical results on these globally
    widespread symbioses at a comfortable elevation of 2135 m in
    Flagstaff, Arizona, surrounded by beautiful landscapes, like
    widespread Ponderosa Pine forests, the San Francisco Peaks area,
    and the impressive Grand Canyon. New Phytologist was present
    as a sponsor, continuing its ongoing support of mycorrhizal
    research (Selosse & Martin, 2013; Dickie et al., 2015). Through
    talks and posters, mycorrhizal researchers literally took us on a
    journey across all scales of observation of this symbiosis: from the
    intracellular environment to global patterns of mycorrhizal
    fungal diversity and biogeochemical cycles (Fig. 1).
  • Drought history affects grassland plant and microbial carbon turnover during and after a subsequent drought event

    Fuchslueger L, Bahn M, Hasibeder R, Kienzl S, Fritz K, Schmitt M, Watzka M, Richter A
    2016 - Journal of Ecology, 104: 1453-1465

    Abstract: 

    Summary

    1. Drought periods are projected to become more severe and more frequent in many European regions. While effects of single strong droughts on plant and microbial carbon (C) dynamics have been studied in some detail, impacts of recurrent drought events are still little understood.
    2. We tested whether the legacy of extreme experimental drought affects responses of plant and microbial C and nitrogen (N) turnover to further drought and rewetting. In a mountain grassland, we conducted a 13C pulse-chase experiment during a naturally occurring drought and rewetting event in plots previously exposed to experimental droughts and in ambient controls (AC). After labelling, we traced 13C below-ground allocation and incorporation into soil microbes using phospholipid fatty acid biomarkers.
    3. Drought history (DH) had no effects on the standing shoot and fine root plant biomass. However, plants with experimental DH displayed decreased shoot N concentrations and increased fine root N concentrations relative to those in AC. During the natural drought, plants with DH assimilated and allocated less 13C below-ground; moreover, fine root respiration was reduced and not fuelled by fresh C compared to plants in AC.
    4. Regardless of DH, microbial biomass remained stable during natural drought and rewetting. Although microbial communities initially differed in their composition between soils with and without DH, they responded to the natural drought and rewetting in a similar way: gram-positive bacteria increased, while fungal and gram-negative bacteria remained stable. In soils with DH, a strongly reduced uptake of recent plant-derived 13C in microbial biomarkers was observed during the natural drought, pointing to a smaller fraction of active microbes or to a microbial community that is less dependent on plant C.
    5. Synthesis. Drought history can induce changes in above- vs. below-ground plant N concentrations and affect the response of plant C turnover to further droughts and rewetting by decreasing plant C uptake and below-ground allocation. DH does not affect the responses of the microbial community to further droughts and rewetting, but alters microbial functioning, particularly the turnover of recent plant-derived carbon, during and after further drought periods.
  • Anthropogenic gadolinium as a transient tracer for investigating river bank filtration

    Robert Brünjes, Andrea Bichler, Philipp Hoehn, Frank Thomas Lange, Heinz-Juergen Brauch, Thilo Hofmann
    2016 - Science of The Total Environment, 1432-1440

    Abstract: 

    The growing use of gadolinium-based contrast agents in magnetic resonance imaging (MRI) leads to an increasing input of anthropogenic gadolinium (Gdanth) into natural environments. Conventional sewage treatment is unable to remove Gdanth and since MRI facilities are mainly used on weekdays the Gdanth inputs to sewage treatment plants are generally higher between Monday and Friday. This transient signal has been traced in both surface water and groundwater through 12-h composite samples collected at high spatial resolutions using depth-discrete rhizon samplers. Propagation of the Gdanth signal from surface water to groundwater was used to calibrate lumped parameter models. Transit time distributions derived for each sampling site revealed mean transit times of between 0.5 and 10 days. Other metrics, such as peak transit time, were shown to correlate better with observed time lags between peak Gdanth concentrations in stream water and groundwater. The relatively stable artificial sweetener acesulfame was investigated as a possible additional sewage indicator, but decreasing concentrations along the flow path indicated its attenuation. We have demonstrated that the ideal tracer Gdanth occurs transiently and can be used to derive groundwater transit times.

  • Stable isotope signatures reflect dietary diversity in European forest moths

    Adams MO, Seifert CL, Lehner L, Truxa C, Wanek W, Fiedler K
    2016 - Frontiers in Zoology, 13: 1-10

    Abstract: 

    Background: Information on larval diet of many holometabolous insects remains incomplete. Carbon (C) and nitrogen (N) stable isotope analysis in adult wing tissue can provide an efficient tool to infer such trophic relationships. The present study examines whether moth feeding guild affiliations taken from literature are reflected in isotopic signatures. Results: Non-metric multidimensional scaling and permutational analysis of variance indicate that centroids of dietary groups differ significantly. In particular, species whose larvae feed on mosses or aquatic plants deviated from those that consumed vascular land plants. Moth δ15N signatures spanned a broader range, and were less dependent on species identity than δ13C values. Comparison between moth samples and ostensible food sources revealed heterogeneity in the lichenivorous guild, indicating only Lithosia quadra as an obligate lichen feeder. Among root-feeding Agrotis segetum, some specimens appear to have developed on crop plants in forest-adjacent farm land. Reed-feeding stem-borers may partially rely on intermediary trophic levels such as fungal or bacterial growth. Conclusion: Diagnostic partitioning of moth dietary guilds based on isotopic signatures alone could not be achieved, but hypotheses on trophic relationships based on often vague literature records could be assessed with high resolution. Hence, the approach is well suited for basic categorization of moths where diet is unknown or notoriously difficult to observe (i.e. Microlepidoptera, lichen-feeders). Keywords: δ13C, δ15N, Larval diet, Trophic position Abbreviations: C, Chemical symbol for carbon; IAEA-CH-6, Reference standard for 13C/12C ratios derived from sucrose and provided by the international atomic energy agency (IAEA); IAEA-CH-7, Reference standard for 13C/12C ratios derived from polyethylene and provided by the international atomic energy agency (IAEA); IAEA-N-1, Reference standard for 15N/ 14N ratios derived from ammonium sulfate and provided by the international atomic energy agency (IAEA); IAEA-N- 2, Reference standard for 15N/14N ratios derived from ammonium sulfate and provided by the international atomic energy agency (IAEA); IAEA-NO-3, Reference standard for 15N/14N ratios derived from potassium nitrate and provided by the international atomic energy agency (IAEA); MMDS, Metric multi-dimensional scaling; N, Chemical symbol for nitrogen; NMDS, Non-metric multi-dimensional scaling; SD, Standard deviation; TLE, Trophic level enrichment; δ 13C, Shift in the 13C/12C ratio of the sample relative to the reference standard (i.e. Pee Dee Belemnite); δ 15N, Shift in the 15N/14N ratio of the sample relative to the reference standard (i.e. atmospheric nitrogen)

  • Microbial decomposition of 13C- labeled phytosiderophores in the rhizosphere of wheat: Mineralization dynamics and key microbial groups involved

    Eva Oburger, Barbara Gruber, Wolfgang Wanek, Andrea Watzinger, Christian Stanetty, Yvonne Schindlegger, Stephan Hann, Walter D.C. Schenkeveld, Stephan M. Kraemer, Markus Puschenreiter
    2016 - Soil Biology and Biochemistry, 196-207

    Abstract: 

    Being low molecular weight carbon (LMW-C) compounds, phytosiderophores (PS) released by strategy II plants are highly susceptible to microbial decomposition. However, to date very little is known about the fate of PS in soil. Using in-house synthesized 13C4-2′-deoxymugineic acid (DMA), the main PS released by wheat, we investigated DMA mineralization dynamics, including microbial incorporation into phospholipid fatty acids (PLFA), in the wheat rhizosphere and bulk soil of two alkaline and one acidic soil. Half-lives of the intact DMA molecule (3–8 h) as well as of DMA-derived C-compounds (8–38 days) were in the same order of magnitude as those published for other LMW-C compounds like sugars, amino acids and organic acids. Combining mineralization with PLFA data showed that between 40 and 65% of the added DMA was either respired or incorporated into soil microbial biomass after 24 h, with the largest part of total incorporated DMA-13C being recovered in gram negative bacteria. Considering root growth dynamics and that PS are mainly exuded from root tips, the significantly slower mineralization of DMA in bulk soil is of high ecological importance to enhance the Fe scavenging efficiency of PS released into the soil.

  • Chronic arsenic trioxide exposure leads to enhanced aggressiveness via Met oncogene addiction in cancer cells

    Kushtrim Kryeziu, Christine Pirker, Bernhard Englinger, Sushilla van Schoonhoven, Melanie Spitzwieser, Thomas Mohr, Proc. Natl. Acad. Sci. USA, Regina Weinmüllner, Koray Tav, Johannes Grillari, Margit Cichna-Markl, Walter Berger, Petra Heffeter
    2016 - Oncotarget, 1: 27379-27393

    Abstract: 

    As an environmental poison, arsenic is responsible for many cancer deaths. Paradoxically, arsenic trioxide (ATO) presents also a powerful therapy used to treat refractory acute promyelocytic leukemia (APL) and is intensively investigated for treatment of other cancer types. Noteworthy, cancer therapy is frequently hampered by drug resistance, which is also often associated with enhancement of tumor aggressiveness.

    In this study, we analyzed ATO-selected cancer cells (A2780ATO) for the mechanisms underlying their enhanced tumorigenicity and aggressiveness. These cells were characterized by enhanced proliferation and spheroid growth as well as increased tumorigenicity of xenografts in SCID mice. Noteworthy, subsequent studies revealed that overexpression of Met receptor was the underlying oncogenic driver of these effects, as A2780ATO cells were characterized by collateral sensitivity against Met inhibitors. This finding was also confirmed by array comparative genomic hybridization (array CGH) and whole genome gene expression arrays, which revealed that Met overexpression by chronic ATO exposure was based on the transcriptional regulation via activation of AP-1. Finally, it was shown that treatment with the Met inhibitor crizotinib was also effective against A2780ATO cell xenografts in vivo, indicating that targeting of Met presents a promising strategy for the treatment of Met-overexpressing tumors after either arsenic exposure or failure to ATO treatment.

  • Exploring the metabolic potential of microbial communities in ultra-basic, reducing springs at The Cedars, CA, USA: Experimental evidence of microbial methanogenesis and heterotrophic acetogenesis

    Kohl L, Cumming E, Cox A, Rietze A, Morrissey L, Lang SQ, Richter A, Suzuki S, Nealson KH, Morrill PL
    2016 - Journal of Geophysical Research Biogeosciences, 4: 1203-1220

    Abstract: 

    Present-day serpentinization generates groundwaters with conditions (pH > 11, Eh < −550 mV) favorable for the microbial and abiotic production of organic compounds from inorganic precursors. Elevated concentrations of methane, C2-C6 alkanes, acetate, and formate have been detected at these sites, but the microbial or abiotic origin of these compounds remains unclear. While geochemical data indicate that methane at most sites of present-day serpentinization is abiogenic, the stable carbon, hydrogen, and clumped isotope data as well as the hydrocarbon gas composition from The Cedars, CA, USA, are consistent with a microbial origin for methane. However, there is no direct evidence of methanogenesis at this site of serpentinization. We report on laboratory experiments in which the microbial communities in fluids and sediments from The Cedars were incubated with 13C labeled substrates. Increasing methane concentrations and the incorporation of 13C into methane in live experiments, but not in killed controls, demonstrated that methanogens converted methanol, formate, acetate (methyl group), and bicarbonate to methane. The apparent fractionation between methane and potential substrates (α13CCH4-CO2(g) = 1.059 to 1.105, α13CCH4-acetate = 1.042 to 1.119) indicated that methanogenesis was dominated by the carbonate reduction pathway. Increasing concentrations of volatile organic acid anions indicated microbial acetogenesis. α13CCO2(g)-acetate values (0.999 to 1.000), however, were inconsistent with autotrophic acetogenesis, thus suggesting that acetate was produced through fermentation. This is the first study to show direct evidence of microbial methanogenesis and acetogenesis by the native microbial community at a site of present-day serpentinization.

  • Permanent draft genome of strain ESFC-1: ecological genomics of a newly discovered lineage of filamentous diazotrophic cyanobacteria

    Everroad RC, Stuart RK, Bebout BM, Detweiler AM, Lee JZ, Woebken D, Prufert-Bebout L, Pett-Ridge J
    2016 - Standards in Genomic Sciences, 11: 1-8

    Abstract: 

    The nonheterocystous filamentous cyanobacterium, strain ESFC-1, is a recently described member of the order Oscillatoriales within the Cyanobacteria. ESFC-1 has been shown to be a major diazotroph in the intertidal microbial mat system at Elkhorn Slough, CA, USA. Based on phylogenetic analyses of the 16S RNA gene, ESFC-1 appears to belong to a unique, genus-level divergence; the draft genome sequence of this strain has now been determined. Here we report features of this genome as they relate to the ecological functions and capabilities of strain ESFC-1. The 5,632,035 bp genome sequence encodes 4914 protein-coding genes and 92 RNA genes. One striking feature of this cyanobacterium is the apparent lack of either uptake or bi-directional hydrogenases typically expected within a diazotroph. Additionally, a large genomic island is found that contains numerous low GC-content genes and genes related to extracellular polysaccharide production and cell wall synthesis and maintenance.

  • Meeting the Needs for Released Nanomaterials Required for Further Testing-The SUN Approach

    Bernd Nowack, Alessio Boldrin, Alejandro Caballero, Steffen Foss Hansen, Fadri Gottschalk, Laura Heggelund, Michael Hennig, Aiga Mackevica, Hanna Maes, Jana Navratilova, Nicole Neubauer, Ruud Peters, Jerome Rose, Andreas Schäffer, Lorette Scifo, Stefan van Leeuwen, Frank von der Kammer, Wendel Wohlleben, Anne Wyrwoll, Danail Hristozov
    2016 - Environmental Science & Technology, 6: 2747-2753

    Abstract: 

    The analysis of the potential risks of engineered nanomaterials (ENM) has so far been almost exclusively focused on the pristine, as-produced particles. However, when considering a life-cycle perspective, it is clear that ENM released from genuine products during manufacturing, use, and disposal is far more relevant. Research on the release of materials from nanoproducts is growing and the next necessary step is to investigate the behavior and effects of these released materials in the environment and on humans. Therefore, sufficient amounts of released materials need to be available for further testing. In addition, ENM-free reference materials are needed since many processes not only release ENM but also nanosized fragments from the ENM-containing matrix that may interfere with further tests. The SUN consortium (Project on “Sustainable Nanotechnologies”, EU seventh Framework funding) uses methods to characterize and quantify nanomaterials released from composite samples that are exposed to environmental stressors. Here we describe an approach to provide materials in hundreds of gram quantities mimicking actual released materials from coatings and polymer nanocomposites by producing what is called “fragmented products” (FP). These FP can further be exposed to environmental conditions (e.g., humidity, light) to produce “weathered fragmented products” (WFP) or can be subjected to a further size fractionation to isolate “sieved fragmented products” (SFP) that are representative for inhalation studies. In this perspective we describe the approach, and the used methods to obtain released materials in amounts large enough to be suitable for further fate and (eco)toxicity testing. We present a case study (nanoparticulate organic pigment in polypropylene) to show exemplarily the procedures used to produce the FP. We present some characterization data of the FP and discuss critically the further potential and the usefulness of the approach we developed.

  • Vulnerability of drinking water supplies to engineered nanoparticles

    Martin Troester, Heinz-Juergen Brauch, Thilo Hofmann
    2016 - Water Research, 255-279

    Abstract: 

    The production and use of engineered nanoparticles (ENPs) inevitably leads to their release into aquatic environments, with the quantities involved expected to increase significantly in the future. Concerns therefore arise over the possibility that ENPs might pose a threat to drinking water supplies. Investigations into the vulnerability of drinking water supplies to ENPs are hampered by the absence of suitable analytical methods that are capable of detecting and quantifiying ENPs in complex aqueous matrices. Analytical data concerning the presence of ENPs in drinking water supplies is therefore scarce. The eventual fate of ENPs in the natural environment and in processes that are important for drinking water production are currently being investigated through laboratory based-experiments and modelling.

    Although the information obtained from these studies may not, as yet, be sufficient to allow comprehensive assessment of the complete life-cycle of ENPs, it does provide a valuable starting point for predicting the significance of ENPs to drinking water supplies.

    This review therefore addresses the vulnerability of drinking water supplies to ENPs. The risk of ENPs entering drinking water is discussed and predicted for drinking water produced from groundwater and from surface water. Our evaluation is based on reviewing published data concerning ENP production amounts and release patterns, the occurrence and behavior of ENPs in aquatic systems relevant for drinking water supply and ENP removability in drinking water purification processes. Quantitative predictions are made based on realistic high-input case scenarios. The results of our synthesis of current knowledge suggest that the risk probability of ENPs being present in surface water resources is generally limited, but that particular local conditions may increase the probability of raw water contamination by ENPs. Drinking water extracted from porous media aquifers are not generally considered to be prone to ENP contamination. In karstic aquifers, however, there is an increased probability that if any ENPs enter the groundwater system they will reach the extraction point of a drinking water treatment plant (DWTP).

    The ability to remove ENPs during water treatment depends on the specific design of the treatment process. In conventional DWTPs with no flocculation step a proportion of ENPs, if present in the raw water, may reach the final drinking water. The use of ultrafiltration techniques improves drinking water safety with respect to ENP contamination.

  • Microbial decomposition of 13C- labeled phytosiderophores in the rhizosphere of wheat: Mineralization dynamics and key microbial groups involved

    Oburger E, Gruber B, Wanek W, Watzinger A, Stanetty C, Schindlegger Y, Hann S., Schenkeveld WDC, Kraemer SM, Puschenteiter M
    2016 - Soil Biology and Biochemistry, 98: 196-207

    Abstract: 

    Being low molecular weight carbon (LMW-C) compounds, phytosiderophores (PS) released by strategy II plants are highly susceptible to microbial decomposition. However, to date very little is known about the fate of PS in soil. Using in-house synthesized 13C4-2′-deoxymugineic acid (DMA), the main PS released by wheat, we investigated DMA mineralization dynamics, including microbial incorporation into phospholipid fatty acids (PLFA), in the wheat rhizosphere and bulk soil of two alkaline and one acidic soil. Half-lives of the intact DMA molecule (3–8 h) as well as of DMA-derived C-compounds (8–38 days) were in the same order of magnitude as those published for other LMW-C compounds like sugars, amino acids and organic acids. Combining mineralization with PLFA data showed that between 40 and 65% of the added DMA was either respired or incorporated into soil microbial biomass after 24 h, with the largest part of total incorporated DMA-13C being recovered in gram negative bacteria. Considering root growth dynamics and that PS are mainly exuded from root tips, the significantly slower mineralization of DMA in bulk soil is of high ecological importance to enhance the Fe scavenging efficiency of PS released into the soil.

  • Physicochemical characterization of titanium dioxide pigments using various techniques for size determination and asymmetric flow field flow fractionation hyphenated with inductively coupled plasma mass spectrometry

    Johannes P. F. G. Helsper, Ruud J. B. Peters, Margaretha E. M. van Bemmel, Zahira E. Herrera Rivera, Stephan Wagner, Frank von der Kammer, Peter C. Tromp, Thilo Hofmann, Stefan Weigel
    2016 - Analytical and Bioanalytical Chemistry, 2: 6679-6691

    Abstract: 

    Seven commercial titanium dioxide pigments and two other well-defined TiO2 materials (TiMs) were physicochemically characterised using asymmetric flow field flow fractionation (aF4) for separation, various techniques to determine size distribution and inductively coupled plasma mass spectrometry (ICPMS) for chemical characterization. The aF4-ICPMS conditions were optimised and validated for linearity, limit of detection, recovery, repeatability and reproducibility, all indicating good performance. Multi-element detection with aF4-ICPMS showed that some commercial pigments contained zirconium co-eluting with titanium in aF4. The other two TiMs, NM103 and NM104, contained aluminium as integral part of the titanium peak eluting in aF4. The materials were characterised using various size determination techniques: retention time in aF4, aF4 hyphenated with multi-angle laser light spectrometry (MALS), single particle ICPMS (spICPMS), scanning electron microscopy (SEM) and particle tracking analysis (PTA). PTA appeared inappropriate. For the other techniques, size distribution patterns were quite similar, i.e. high polydispersity with diameters from 20 to >700 nm, a modal peak between 200 and 500 nm and a shoulder at 600 nm. Number-based size distribution techniques as spICPMS and SEM showed smaller modal diameters than aF4-UV, from which mass-based diameters are calculated. With aF4-MALS calculated, light-scattering-based “diameters of gyration” (Øg) are similar to hydrodynamic diameters (Øh) from aF4-UV analyses and diameters observed with SEM, but much larger than with spICPMS. A Øg/Øh ratio of about 1 indicates that the TiMs are oblate spheres or fractal aggregates. SEM observations confirm the latter structure. The rationale for differences in modal peak diameter is discussed.

  • Environmental and landscape controls of soil organic carbon storage in continuous permafrost terrain of the Taymyr Peninsula (N Siberia, Russia)

    Palmtag J, Ramage J, Hugelius G, Gentsch N, Lashchinskiy N, Richter A, Kuhry P
    2016 - European Journal of Soil Science, 67: 478-491

    Abstract: 

    Summary

    This research examined soil organic carbon (SOC), total nitrogen (TN) and aboveground phytomass carbon (PhC) stocks in two areas of the Taymyr Peninsula, northern Siberia. We combined field sampling, chemical and 14C radiocarbon dating analyses with land cover classifications for landscape-level assessments. The estimated mean for the 0–100-cm depth SOC stocks was 14.8 and 20.8 kg C m−2 in Ary-Mas and Logata, respectively. The corresponding values for TN were 1.0 and 1.3 kg N m−2. On average, about 2% only (range 0–12%) of the total ecosystem C is stored in PhC. In both study areas about 34% of the SOC at 0–100 cm is stored in cryoturbated pockets, which have formed since at least the early Holocene. The larger carbon/nitrogen (C/N) ratio of this cryoturbated material indicates that it consists of relatively undecomposed soil organic matter (SOM). There are substantial differences in SOC stocks and SOM properties within and between the two study areas, which emphasizes the need to consider both geomorphology and soil texture in the assessment of landscape-level and regional SOC stocks.

    Highlights

    • This research addresses landscape-scale and regional variation in SOC stocks.
    • Landform and soil texture are taken into account in the analysis.
    • The contribution of phytomass to total ecosystem C stored is limited.
    • Large SOC stocks are susceptible to decomposition following permafrost thaw.

  • Budget of primary production and dinitrogen fixation in a highly seasonal Red Sea coral reef

    Cardini U, Bednarz VN, van Hoytema N, Rovere A, Naumann MS, Al-Rshaidat MMD, Wild C
    2016 - Ecosystems, 5: 771-785

    Abstract: 

    Biological dinitrogen (N2) fixation (diazotrophy, BNF) relieves marine primary producers of nitrogen (N) limitation in a large part of the world oceans. N concentrations are particularly low in tropical regions where coral reefs are located, and N is therefore a key limiting nutrient for these productive ecosystems. In this context, the importance of diazotrophy for reef productivity is still not resolved, with studies up to now lacking organismal and seasonal resolution. Here, we present a budget of gross primary production (GPP) and BNF for a highly seasonal Red Sea fringing reef, based on ecophysiological and benthic cover measurements combined with geospatial analyses. Benthic GPP varied from 215 to 262 mmol C m−2 reef d−1, with hard corals making the largest contribution (41–76%). Diazotrophy was omnipresent in space and time, and benthic BNF varied from 0.16 to 0.92 mmol N m−2 reef d−1. Planktonic GPP and BNF rates were respectively approximately 60- and 20-fold lower than those of the benthos, emphasizing the importance of the benthic compartment in reef biogeochemical cycling. BNF showed higher sensitivity to seasonality than GPP, implying greater climatic control on reef BNF. Up to about 20% of net reef primary production could be supported by BNF during summer, suggesting a strong biogeochemical coupling between diazotrophy and the reef carbon cycle.

  • Nano electrospray gas-phase electrophoretic mobility molecular analysis (nES GEMMA) of liposomes: applicability of the technique for nano vesicle batch control

    Victor U. Weiss, Carlos Urey, Andreas Gondikas, Monika Golesne, Gernot Friedbacher, Frank von der Kammer, Thilo Hofmann, Roland Andersson, György Marko-Varga, Martina Marchetti-Deschmann, Günter Allmaier
    2016 - Analyst, 2: 6042-6050

    Abstract: 

    Liposomes are biodegradable nanoparticle vesicles consisting of a lipid bilayer encapsulating an aqueous core. Entrapped cargo material is shielded from the extra-vesicular medium and sustained release of encapsulated material can be achieved. However, application of liposomes as nano-carriers demands their characterization concerning size and size distribution, particle-number concentration, occurrence of vesicle building blocks in solution and determination of the resulting vesicle encapsulation capacity. These questions can be targeted via gas-phase electrophoretic mobility molecular analysis (GEMMA) based on a nano electrospray (nES) charge-reduction source. This instrument separates single-charged nanoparticles in the gas-phase according to size in a high-laminar sheath-flow by means of an orthogonal, tunable electric field. nES GEMMA analysis enables to confirm liposome integrity after passage through the instrument (in combination with atomic force microscopy) as well as to exclude vesicle aggregation. Additionally, nanoparticle diameters at peak apexes and size distribution data are obtained. Differences of hydrodynamic and dry particle diameter values, as well as the effect of number- and mass-based concentration data analysis on obtained liposome diameters are shown. Furthermore, the repeatability of liposome preparation is studied, especially upon incorporation of PEGylated lipids in the bilayer. Finally, the instruments applicability to monitor mechanical stress applied to vesicles is demonstrated.

  • Microbial carbon use efficiency and biomass turnover times depending on soil depth - Implications for carbon cycling.

    Spohn M, Klaus K, Wanek W, Richter A
    2016 - Soil Biology and Biochemistry, 96: 74-81

    Abstract: 

    Processing of organic carbon (C) by soil microorganisms is a key process of terrestrial C cycling. For this reason we studied (i) microbial carbon use efficiency (CUE) defined as C allocated to growth over organic C taken up by the microbial community, and (ii) the turnover time of microbial biomass in a pasture and in two forest soils. We hypothesized that microbial CUE decreases in mineral soils with depth from the topsoil to the subsoil, while the turnover time of the microbial biomass increases due to energetic constrains. We determined microbial CUE and turnover of microbial biomass C using a novel substrate-independent method based on incorporation of 18O from labeled water into microbial DNA with concurrent measurements of basal respiration. Microorganisms showed decreasing C uptake rates with decreasing C contents in the deeper soil layers. In the forest soils, no adaptation of microbial CUE with soil depth took place, i.e., microbes in the forest topsoil used C at the same efficiency as microbes in the subsoil. However, in the pasture soil, microbial CUE decreased in the lower soil layers compared to the topsoil, indicating that microorganisms in the deeper soil layers allocated relatively more C to respiration. In the organic soil layer, microorganisms respired more per unit microbial biomass C than in the subsoil, but had a similar CUE despite the high C-to-nitrogen and C-to-phosphorus ratios of the litter layers. The turnover time of microbial biomass increased with soil depth in the two forest soils. Thus, in the forest soils, a lower microbial C uptake rate in the deeper soil layers was partially compensated by a longer turnover time of microbial biomass C. In conclusion, our findings emphasize that in addition to microbial CUE, the turnover time of the microbial biomass strongly affects soil C cycling.

    Keywords

    • Soil microbial carbon use efficiency
    • Growth efficiency
    • Organic matter decomposition;
    • Microbial metabolism
    • Stoichiometry
    • Microbial biomass carbon turnover
  • Synergistic Effects between Biogenic Ligands and a Reductant in Fe Acquisition from Calcareous Soil

    Walter D. C. Schenkeveld, Zimeng Wang, Daniel E. Giammar, Stephan M. Kraemer
    2016 - Environmental Science & Technology, 1: 6381-6388

    Abstract: 

    Organisms have developed different strategies to cope with environmental conditions of low Fe availability based on the exudation of reducing, ligating, and acidifying compounds. In the context of Fe acquisition from soil, the effects of these reactive compounds have generally been considered independent and additive. However, highly efficient Fe acquisition strategies may rely on synergistic effects between reactive exudates. In the present study, we demonstrate that synergistic effects between biogenic ligands and a reductant (ascorbate) can occur in Fe mobilization from soil. Synergistic Fe mobilization was found for all ligands examined (desferrioxamine B (DFOB), 2′-deoxymugineic acid (DMA), esculetin, and citrate). The size and duration of the synergistic effect on Fe mobilization varied with ligand: larger effects were observed for the sideorphores compared to esculetin and citrate. For DFOB, the synergistic effect lasted for the 168 h duration of the experiment; for DMA, an initial synergistic effect turned into an antagonistic effect after 4 h because of enhanced mobilization of competing metals; and for esculetin and citrate, the synergistic effect was temporary (less than 24 h). Our results demonstrate that synergistic effects greatly enhance the reactivity of mixtures of compounds known to be exuded in response to Fe limitation. These synergistic effects could be decisive for the survival of plants and microorganisms under conditions of low Fe availability.

  • Bacterial communities potentially involved in iron-cycling in Baltic Sea and North Sea sediments revealed by pyrosequencing

    Carolina Reyes, Olaf Dellwig, Kirstin Dähnke, Matthias Gehre, Beatriz E. Noriega-Ortega, Michael E. Böttcher, Patrick Meister, Michael W. Friedrich, Tillmann Lueders
    2016 - FEMS microbiology ecology, 4: fiw054

    Abstract: 

    To gain insight into the bacterial communities involved in iron-(Fe) cycling under marine conditions, we analysed sediments with Fe-contents (0.5–1.5 wt %) from the suboxic zone at a marine site in the Skagerrak (SK) and a brackish site in the Bothnian Bay (BB) using 16S rRNA gene pyrosequencing. Several bacterial families, including Desulfobulbaceae, Desulfuromonadaceae and Pelobacteraceae and genera, including Desulfobacter and Geobacter, known to reduce Fe were detected and showed highest abundance near the Fe(III)/Fe(II) redox boundary. Additional genera with microorganisms capable of coupling fermentation to Fe-reduction, including Clostridium and Bacillus, were observed. Also, the Fe-oxidizing families Mariprofundaceae and Gallionellaceae occurred at the SK and BB sites, respectively, supporting Fe-cycling. In contrast, the sulphate (SO42−) reducing bacteria Desulfococcus and Desulfobacterium were more abundant at greater depths concurring with a decrease in Fe-reducing activity. The communities revealed by pyrosequencing, thus, match the redox stratification indicated by the geochemistry, with the known Fe-reducers coinciding with the zone of Fe-reduction. Not the intensely studied model organisms, such as Geobacter spp., but rather versatile microorganisms, including sulphate reducers and possibly unknown groups appear to be important for Fe-reduction in these marine suboxic sediments.

  • Biophysical and Population Genetic Models Predict the Presence of “Phantom” Stepping Stones Connecting Mid-Atlantic Ridge Vent Ecosystems

    Breusing C, Biastoch A, Drews A, Metaxas A, Jollivet D, Vrijenhoek RC, Bayer T, Melzner F, Sayavedra L, Petersen JM, Dubilier N, Schilhabel MB, Rosenstiel P, Reusch TBH
    2016 - Current Biology, 26: 1 - 11

    Abstract: 

    Deep-sea hydrothermal vents are patchily distributed ecosystems inhabited by specialized animal populations that are textbook meta-populations. Many vent-associated species have free-swimming, dispersive larvae that can establish connections between remote populations. However, connectivity patterns among hydrothermal vents are still poorly understood because the deep sea is undersampled, the molecular tools used to date are of limited resolution, and larval dispersal is difficult to measure directly. A better knowledge of connectivity is urgently needed to develop sound environmental management plans for deep-sea mining. Here, we investigated larval dispersal and contemporary connectivity of ecologically important vent mussels (Bathymodiolus spp.) from the Mid-Atlantic Ridge by using high-resolution ocean modeling and population genetic methods. Even when assuming a long pelagic larval duration, our physical model of larval drift suggested that arrival at localities more than 150 km from the source site is unlikely and that dispersal between populations requires intermediate habitats (“phantom” stepping stones). Dispersal patterns showed strong spatiotemporal variability, making predictions of population connectivity challenging. The assumption that mussel populations are only connected via additional stepping stones was supported by contemporary migration rates based on neutral genetic markers. Analyses of population structure confirmed the presence of two southern and two hybridizing northern mussel lineages that exhibited a substantial, though incomplete, genetic differentiation. Our study provides insights into how vent animals can disperse between widely separated vent habitats and shows that recolonization of perturbed vent sites will be subject to chance events, unless connectivity is explicitly considered in the selection of conservation areas.

  • Stress-induced changes in carbon allocation among metabolite pools influence isotope-based predictions of water use efficiency in Phaseolus vulgaris

    Lockhart R, Wild B, Richter A, Simonin K, Merchant A
    2016 - Functional Plant Biology, 1149-1158

    Abstract: 

    Understanding how major food crops respond to environmental stress will expand our capacity to improve food production with growing populations and a changing climate. This study uses chemical and physiological adaptations to heat, water deficit and elevated light stresses in Phaseolus vulgaris L. to identify changes in carbon (C) allocation that, combined with post-photosynthetic fractionation of C isotopes, influences water use efficiency (WUE) predictions. The chemical stress response was explored through changes in C allocation to the carbohydrate and cyclitol pools using GC–triple quadrupole MS. Carbon allocation to the sucrose pool fluctuated significantly among treatments, and the putative osmolytes and osmoprotectants (myo-inositol and D-ononitol) accumulated under stress. Significant osmotic adjustment (P < 0.05), quantified via pressure–volume curve analysis, was detected between control and stress treatments, although this was not attributable to active accumulation of the metabolites. Compound-specific 13C isotope abundance was measured using liquid chromatography isotope ratio MS to predict intrinsic WUE. In contrast to other metabolites measured, the δ13C of the sucrose pool fluctuated according to treatment and was proportional to predicted values based upon modelled Δ13C from gas exchange data. The results suggest that the accuracy and precision of predicting WUE may be enhanced by compound-specific analysis of Δ13C and that changes in the allocation of C among metabolite pools may influence WUE predictions based upon analysis of total soluble C. Overall, the plants appeared to use a range of mechanisms to cope with adverse conditions that could be utilised to improve plant breeding and management strategies.

  • Fate assessment of engineered nanoparticles in solids dominated media – Current insights and the way forward

    W. Peijnenburg, A. Praetorius, J. Scott-Fordsmand, G. Cornelis
    2016 - Environmental Pollution, 1365-1369

    Abstract: 

    Exposure assessment of engineered nanoparticles (ENPs) in soil and sediment is severely hampered by a lack of understanding of the underlying processes and of the impact of matrix constituents on the fate of ENPs in natural systems, including porewater properties like pH, ionic strength, and presence of naturally occurring (nano)particles. Additional issues such as lack of proper methods for in-situ assessment of ENP speciation, ENP ageing, and agglomeration state, hinder proper exposure assessment. Let alone that the lack does not allow for development of predictive methods for endpoints like transformation and agglomeration potential. This paper discusses current approaches for fate assessment of ENPs in solids dominated media and addresses the most prominent knowledge gaps and how these may be addressed. It is concluded that the key issue to be dealt with, are the attachment and deposition processes that are characteristic for ENPs as opposed to equilibrium-driven partitioning processes of non-particulate organic and inorganic contaminants.

  • Mapping limits to life on Earth

    Freeman K, Harrison J, Dobinson L, Cockell C, McKenzie R, Wyllie D, Nixon SL
    2016 - 2: 15-17

    Abstract: 

    Kenneth Freeman and colleagues take a look at extremophiles and ask how their biology fits them for life on and off planet Earth.

  • Predicting the Sorption of Aromatic Acids to Noncarbonized and Carbonized Sorbents

    Gabriel Sigmund, Huichao Sun, Thilo Hofmann, Melanie Kah
    2016 - Environmental Science & Technology, 7: 3641-3648

    Abstract: 

    Approaches based on the octanol–water partition coefficient are commonly used to describe sorption of neutral organic compounds in environmental systems, but they are not suitable for organic acids, which can dissociate to form anions. We here investigate the applicability of an alternative approach based on the pH-dependent distribution ratio (DOW) to describe sorption of aromatic acids to sorbents representing different degrees of carbonization. Sorption isotherms for four structurally similar acids ((2,4-dichlorophenoxy)acetic acid (2,4-D), 4-chloro-2-15 methylphenoxy)acetic acid (MCPA), 4-(2,4-dichlorophenoxy)butanoic16 acid (2,4-DB), and 5-chloro-2-(2,4-dichlorophenoxy)phenol (triclosan)) were measured for 15 sorbents: fresh and carbonized wood shavings, pig manure, sewage sludge, carbon nanotubes, and activated carbon. Dissociation greatly affected the sorption of all acids. Sorption coefficients measured in the high pH range indicated that sorption of the anions ranged over several orders of magnitude and should not be neglected. Sorption trends for all sorbates and carbonized sorbents could be very well described by a single regression equation that included DOW of the sorbate and the specific surface area of the sorbent (R2 > 0.89).

  • Moss δ13C: Implications for subantarctic palaeohydrological reconstructions

    Bramley-Alves J, Wanek W, Robinson SA
    2016 - Palaeogeography, 453: 20-29

    Abstract: 

    Southern Ocean Islands, despite their equitable oceanic climates, have recently experienced a number of pronounced climate variations. Shifts in water availability in this region are of concern; however, methods of measuring water availability are currently inadequate. Recent advances using stable carbon isotopes (δ13C) in Antarctic mosses to record long-term variations in water availability suggest that this technique might be applicable in other locations where conditions are cold enough to produce meaningful moss growth for reconstructions. Verification of this technique at each new location is essential, however, due to disparity between species and climates. Here, variations in δ13CBULK with growth water availability were measured in three moss species on subantarctic Macquarie Island. We found these subantarctic mosses showed no difference in δ13CBULK signatures between growth water environments and displayed more negative δ13CBULK ranges than those from East Antarctica, suggesting that climatic differences override the microclimate signal. Despite significant differences in leaf cell morphology there was no variation in δ13CBULK between these subantarctic species. It may be that these species are unsuitable as biological proxies due to their growth form being less dense than the turf forming Antarctic species. This underlines the need to carryout preliminary research into moss carbon isotope fractionation for each new region, and for each species, where palaeohydrological reconstructions are planned – a step that is often not given appropriate consideration in palaeo-research.

  • Little effects on soil organic matter chemistry of density fractions after seven years of forest soil warming

    Schnecker J, Borken W, Schindlbacher A, Wanek W
    2016 - Soil Biology and Biochemistry, 103: 300-307

    Abstract: 

    Rising temperatures enhance microbial decomposition of soil organic matter (SOM) and thereby increase the soil CO2 efflux. Elevated decomposition rates might differently affect distinct SOM pools, depending on their stability and accessibility. Soil fractions derived from density fractionation have been suggested to represent SOM pools with different turnover times and stability against microbial decomposition.

    To investigate the effect of soil warming on functionally different soil organic matter pools, we here investigated the chemical and isotopic composition of bulk soil and three density fractions (free particulate organic matter, fPOM; occluded particulate organic matter, oPOM; and mineral associated organic matter, MaOM) of a C-rich soil from a long-term warming experiment in a spruce forest in the Austrian Alps. At the time of sampling, the soil in this experiment had been warmed during the snow-free period for seven consecutive years. During that time no thermal adaptation of the microbial community could be identified and CO2 release from the soil continued to be elevated by the warming treatment. Our results, which included organic carbon content, total nitrogen content, δ13C, Δ14C, δ15N and the chemical composition, identified by pyrolysis-GC/MS, showed no significant differences in bulk soil between warming treatment and control. Surprisingly, the differences in the three density fractions were mostly small and the direction of warming induced change was variable with fraction and soil depth. Warming led to reduced N content in topsoil oPOM and subsoil fPOM and to reduced relative abundance of N-bearing compounds in subsoil MaOM. Further, warming increased the δ13C of MaOM at both sampling depths, reduced the relative abundance of carbohydrates while it increased the relative abundance of lignins in subsoil oPOM. As the size of the functionally different SOM pools did not significantly change, we assume that the few and small modifications in SOM chemistry result from an interplay of enhanced microbial decomposition of SOM and increased root litter input in the warmed plots. Overall, stable functional SOM pool sizes indicate that soil warming had similarly affected easily decomposable and stabilized SOM of this C-rich forest soil.

     
  • Pyrolysis of waste materials: Characterization and prediction of sorption potential across a wide range of mineral contents and pyrolysis temperatures

    Melanie Kah, Huichao Sun, Gabriel Sigmund, Thorsten Hüffer, Thilo Hofmann
    2016 - Bioresource Technology, 225-233

    Abstract: 

    Sewage sludge (50% mineral), manure (29%) and wood (<1%) were pyrolyzed at 200, 350 and 500 °C with the aim to study the characteristics and sorption potential of materials undergoing pyrolysis across a wide range of mineral contents. A commercial plant-derived biochar (41% mineral) was also considered. The materials were extensively characterized and tested for their sorption towards the model sorbates benzene, naphthalene and pyrene. Plant-derived materials, regardless of their mineral content, developed micropores causing size exclusion of pyrene. Changes in properties and sorption behavior upon pyrolysis were generally consistent for the manure and wood series. A single regression equation developed on our data (including the sorbate hydrophobicity and sorbent polarity) provided excellent prediction of previously reported changes in sorption upon pyrolysis across a wide range of mineral content (up to 500 °C). The sewage sludge series, however, followed a particular behavior, possibly due to very high mineral content (up to 67%).

  • Multi-scale imaging of anticancer platinum(IV) compounds in murine tumor and kidney

    Legin AA, Theiner S, Schintlmeister A, Reipert S, Heffeter P, Jakupec MA, Varbanov HP, Kowol CR, Galanski, Berger MW, Wagner M, Keppler BK
    2016 - Chemical Science, 7: 3052-3061

    Abstract: 

    Nano-scale secondary ion mass spectrometry (NanoSIMS) enables trace element and isotope analyses with high spatial resolution. This unique capability has recently been exploited in several studies analyzing the subcellular distribution of Au and Pt anticancer compounds. However, these studies were restricted to cell culture systems. To explore the applicability to the in vivo setting, we developed a combined imaging approach consisting of laser ablation inductively coupled plasma mass spectrometry (LA-ICP-MS), NanoSIMS and transmission electron microscopy (TEM) suitable for multi-scale detection of the platinum distribution in tissues. Applying this approach to murine tumor and kidney samples upon administration of selected platinum(IV) anticancer prodrugs revealed uneven platinum distributions on both the organ and subcellular scales. Spatial platinum accumulation patterns by LA-ICP-MS were quantitatively assessed in histologically heterogeneous organs (e.g., higher platinum accumulation in kidney cortex than in medulla) and used to select regions of interest for subcellular scale imaging with NanoSIMS. These analyses revealed cytoplasmic sulfur-rich organelles to accumulate platinum in both kidney and malignant cells. Those in the tumor were subsequently identified as organelles of lysosomal origin, demonstrating the potential of the combinatorial approach for investigating therapeutically relevant drug concentrations on a submicrometer scale.

  • Metabolism of mineral-sorbed organic matter and microbial lifestyles in fluvial ecosystems

    Hunter WR, Niederdorfer R, Gernand A, Veuger B, Prommer J, Mooshammer M, Wanek W, Battin TJ
    2016 - Geophysical Research Letters, 43: 1582-1588

    Abstract: 

    In fluvial ecosystems mineral erosion, carbon (C), and nitrogen (N) fluxes are linked via organomineral complexation, where dissolved organic molecules bind to mineral surfaces. Biofilms and suspended aggregates represent major aquatic microbial lifestyles whose relative importance changes predictably through fluvial networks. We tested how organomineral sorption affects aquatic microbial metabolism, using organomineral particles containing a mix of 13C, 15N-labeled amino acids. We traced 13C and 15N retention within biofilm and suspended aggregate biomass and its mineralization. Organomineral complexation restricted C and N retention within biofilms and aggregates and also their mineralization. This reduced the efficiency with which biofilms mineralize C and N by 30% and 6%. By contrast, organominerals reduced the C and N mineralization efficiency of suspended aggregates by 41% and 93%. Our findings show how organomineral complexation affects microbial C:N stoichiometry, potentially altering the biogeochemical fate of C and N within fluvial ecosystems.

  • Impacts of (Nano)formulations on the Fate of an Insecticide in Soil and Consequences for Environmental Exposure Assessment

    Melanie Kah, Anne-Kathrin Weniger, Thilo Hofmann
    2016 - Environmental Science & Technology, 2: 10960-10967

    Abstract: 

    The development of nanopesticides has recently received an increased level of attention. However, there are very few data about the environmental fate of these new products, and it is not known whether nanoformulations can be evaluated within the current pesticide regulatory framework. Sorption and degradation parameters of the insecticide bifenthrin were measured in two soils for (i) the pure active ingredient, (ii) three nanoformulations, and (iii) a commercially available formulation. In most cases, fate parameters derived for the nanopesticides were significantly different from those derived for the pure active ingredient (factors of up to 10 for sorption and 1.8 for degradation), but discrepancies were not easy to relate to the characteristics of the nanocarriers. In some cases, differences were also observed between the commercial formulation and the pure active ingredient (factors of up to 1.4 for sorption and 1.7 for degradation). In the regulatory context, the common assumption that formulations do not influence the environmental fate of pesticide active ingredients after application seems therefore not always adequate. In the absence of direct measurement, an inverse modeling approach was successfully applied to evaluate the durability of the formulations in soil (release half-life ranged between 11 and 74 days). Predicted groundwater concentrations very much depended on the modeling approach adopted but overall suggest that the nanoformulations studied could reduce losses to groundwater.

  • Synergistic effects of diffusion and microbial physiology reproduce the Birch effect in a micro-scale model

    Evans S, Dieckmann U, Franklin O, Kaiser C
    2016 - Soil Biology and Biochemistry, 93: 28-37

    Abstract: 

    Large rainfall events following drought cause pulses of CO2 flux that are higher than models predict. This phenomenon, named the “Birch effect” after its discoverer, has been observed for decades, and will influence carbon-climate feedbacks as drying–rewetting (DRW) cycles become more common under intensified climates. Yet, the many interacting factors that determine how soil DRW cycles affect C balance have been difficult to separate empirically. Here we use a spatially explicit biogeochemical–microbial model to examine the mechanisms underlying CO2 dynamics under DRW. We independently model physiological activity and diffusion based on how they vary with (constant) moisture levels in nature, and subject the model to DRW to test the importance of different mechanisms in models with one or two microbial functional groups (cheaters and producers). Our model reproduces respiration patterns similar to empirical observations of the Birch effect when we include mechanisms that link water content to microbial growth and to diffusion rate, whereas inclusion of either mechanism alone produces significantly lower pulses upon rewetting. Diffusion limitation under drought increases substrate availability under rewetting, a process mediated by biogeochemical hotspots and continued enzyme activity under drought. At the same time, high microbial growth under rewetting is needed to replenish enzyme pools and to sustain the biomass required to generate respiration pulses under repeated DRW. Inclusion of cheaters in the model dampens the size of the rewetting pulse and the cumulative amount of CO2release, as cheaters outcompete producers and reduce overall biomass. Our results provide several novel hypotheses regarding the microbial, biogeochemical, and spatial processes that mediate the Birch effect, which will contribute to a better mechanistic understanding of this important deviation from model predictions.

    Keywords

    • Dry/wet cycles
    • Birch effect
    • Microbial communities
    • Spatial dynamics
    • Individual-based model
    • Carbon cycling
    • Rainfall timing
  • Combining gas-phase electrophoretic mobility molecular analysis (GEMMA), light scattering, field flow fractionation and cryo electron microscopy in a multidimensional approach to characterize liposomal carrier vesicles

    Carlos Urey, Victor U. Weiss, Andreas Gondikas, Frank von der Kammer, Thilo Hofmann, Martina Marchetti-Deschmann, Günter Allmaier, György Marko-Varga, Roland Andersson
    2016 - International Journal of Pharmaceutics, 1: 309-318

    Abstract: 

    For drug delivery, characterization of liposomes regarding size, particle number concentrations, occurrence of low-sized liposome artefacts and drug encapsulation are of importance to understand their pharmacodynamic properties. In our study, we aimed to demonstrate the applicability of nano Electrospray Gas-Phase Electrophoretic Mobility Molecular Analyser (nES GEMMA) as a suitable technique for analyzing these parameters. We measured number-based particle concentrations, identified differences in size between nominally identical liposomal samples, and detected the presence of low-diameter material which yielded bimodal particle size distributions. Subsequently, we compared these findings to dynamic light scattering(DLS) data and results from light scattering experiments coupled to Asymmetric Flow-Field Flow Fractionation (AF4), the latter improving the detectability of smaller particles in polydisperse samples due to a size separation step prior detection. However, the bimodal size distribution could not be detected due to method inherent limitations. In contrast, cryo transmission electron microscopy corroborated nES GEMMA results. Hence, gas-phase electrophoresis proved to be a versatile tool for liposome characterization as it could analyze both vesicle size and size distribution. Finally, a correlation of nES GEMMA results with cell viability experiments was carried out to demonstrate the importance of liposome batch-to-batch control as low-sized sample components possibly impact cell viability.

  • Kunststoffe in aquatischen Umweltsystemen - Vorstellung einer neuen Fachausschusses

    Thorsten Hüffer, Nicole, B., Heß, M., Ivleva, N., Klein, S., Laforsch, C., Wagner M.
    2016 - Vom Wasser - das Journal, 26: in press
  • Geothermal ecosystems as natural climate change experiments: The ForHot research site in Iceland as a case study

    Sigurdsson BD, Leblans NIW, Dauwe S, Guðmundsdóttir E, Gundersen P, Gunnarsdóttir GE, Holmstrup M, Ilieva-Makulec K, Kätterer T, Marteinsdóttir B, Maljanen M, Oddsdóttir ES, Ostonen I, Peñuelas J, Poeplau C, Richter A, Sigurðsson P, Van Bodegom P, Wallander H, Weedon J, Janssens I
    2016 - Icelandic Agricultural Sciences (IAS), 29: 53-71

    Abstract: 

    This article describes how natural geothermal soil temperature gradients in Iceland have been used to study terrestrial ecosystem responses to soil warming. The experimental approach was evaluated at three study sites in southern Iceland; one grassland site that has been warm for at least 50 years (GO), and another comparable grassland site (GN) and a Sitka spruce plantation (FN) site that have both been warmed since an earthquake took place in 2008. Within each site type, five ca. 50 m long transects, with six permanent study plots each, were established across the soil warming gradients, spanning from unwarmed control conditions to gradually warmer soils. It was attempted to select the plots so the annual warming levels would be ca. +1, +3, +5, +10 and +20 °C within each transect. Results of continuous measurements of soil temperature (Ts) from 2013-2015 revealed that the soil warming was relatively constant and followed the seasonal Ts cycle of the unwarmed control plots. Volumetric water content in the top 5 cm of soil was repeatedly surveyed during 2013-2016. The grassland soils were wetter than the FN soils, but they had sometimes some significant warming-induced drying in the surface layer of the warmest plots, in contrast to FN. Soil chemistry did not show any indications that geothermal water had reached the root zone, but soil pH did increase somewhat with warming, which was probably linked to vegetation changes. As expected, the potential decomposition rate of organic matter increased significantly with warming. It was concluded that the natural geothermal gradients at the ForHot sites in Iceland offered realistic conditions for studying terrestrial ecosystem responses to warming with minimal artefacts. 

  • Ecology and Fisheries: Dark Carbon on Your Dinner Plate.

    Petersen JM
    2016 - Curr. Biol., 24: R1277-R1279

    Abstract: 

    Chemosynthetic primary production by symbiotic microbes powers entire ecosystems in the remote deep sea. New research shows that in shallow waters chemosynthetic symbioses can contribute substantially to a vital economic resource - lobster fisheries in the Caribbean Sea.

  • Environmental enteric dysfunction and growth failure/stunting in global child health

    Owino V, Ahmed T, Freemark M, Kelly P, Loy A, Manary M, Loechl C
    2016 - Pediatrics, 138: e20160641

    Abstract: 

    Approximately 25% of the world’s children under age 5 years have stunted growth, which is associated with increased mortality, cognitive dysfunction, and loss of productivity. Reducing by 40% the number of stunted children is a global target for 2030. The pathogenesis of stunting is poorly understood. Pre- and post-natal nutritional deficits and enteric and systemic infections clearly contribute, but recent findings implicate a central role for environmental enteric dysfunction (EED), a generalized disturbance of small intestinal structure and function found at high prevalence in children living under unsanitary conditions. Mechanisms contributing to growth failure in EED include intestinal leakiness and heightened permeability, gut inflammation, dysbiosis and bacterial translocation, systemic inflammation, and nutrient malabsorption. Since EED has multiple causal pathways, approaches to manage it need to be multi-faceted. Potential interventions to tackle EED include: a) reduction of exposure to feces and contact with animals through programs like improved water, sanitation and hygiene (WASH); b) breastfeeding and enhanced dietary diversity; c) probiotics and prebiotics; d) nutrient supplements including zinc, polyunsaturated fatty acids, and amino acids; e) anti-inflammatory agents such as 5-aminosalicyclic acid; and f) antibiotics in the context of acute malnutrition and infection. Better understanding of the underlying causes of EED, and development of non-invasive, practical, simple, and affordable point of care diagnostic tools remain key gaps. ‘Omics’ technologies (genomics, epigenomics, transcriptomics, proteomics, and metabolomics) and stable isotope techniques (e.g., 13Carbon breath tests) targeted at children and their intestinal microbiota will enhance our ability to successfully identify, manage, and prevent the disorder.

  • Fenton's reagent for the rapid and efficient isolation of microplastics from wastewater.

    Tagg AS, Harrison JP, Ju-Nam Y, Sapp M, Bradley EL, Sinclair CJ, Ojeda JJ
    2016 - 2: 372-375

    Abstract: 

    Fenton's reagent was used to isolate microplastics from organic-rich wastewater. The catalytic reaction did not affect microplastic chemistry or size, enabling its use as a pre-treatment method for focal plane array-based micro-FT-IR imaging. Compared with previously described microplastic treatment methods, Fenton's reagent offers a considerable reduction in sample preparation times.

  • Evidence for Ecological Flexibility in the Cosmopolitan Genus Curtobacterium.

    Chase AB, Arevalo P, Polz MF, Berlemont R, Martiny JB
    2016 - Front Microbiol, 1874

    Abstract: 

    Assigning ecological roles to bacterial taxa remains imperative to understanding how microbial communities will respond to changing environmental conditions. Here we analyze the genus , as it was found to be the most abundant taxon in a leaf litter community in southern California. Traditional characterization of this taxon predominantly associates it as the causal pathogen in the agricultural crops of dry beans. Therefore, we sought to investigate whether the abundance of this genus was because of its role as a plant pathogen or another ecological role. By collating >24,000 16S rRNA sequences with 120 genomes across the Microbacteriaceae family, we show that has a global distribution with a predominant presence in soil ecosystems. Moreover, this genus harbors a high diversity of genomic potential for the degradation of carbohydrates, specifically with regards to structural polysaccharides. We conclude that may be responsible for the degradation of organic matter within litter communities.

  • Genome-guided design of a novel defined mouse microbiota that confers colonization resistance against Salmonella enterica serovar Typhimurium

    Brugiroux S, Beutler M, Pfann C, Garzetti D, Ruscheweyh H-J, Ring D, Diehl M, Herp S, Lötscher Y, Hussain S, Bunk B, Pukall R, Huson DH, Münch PC, McHardy AC, McCoy KD, Macpherson AJ, Loy A, Clavel T, Berry D, Stecher B
    2016 - Nature Microbiol, 2: 16215

    Abstract: 

    Protection against enteric infections, also termed colonization resistance, results from mutualistic interactions of the host and its indigenous microbes. The gut microbiota of humans and mice is highly diverse and it is therefore challenging to assign specific properties to its individual members. Here, we have used a collection of murine bacterial strains and a modular design approach to create a minimal bacterial community that, once established in germ-free mice, provided colonization resistance against the human enteric pathogen Salmonella enterica serovar Typhimurium (S. Tm). Initially, a community of 12 strains, termed Oligo-Mouse Microbiota (Oligo-MM12), representing members of the major bacterial phyla in the murine gut, was selected. This community was stable over consecutive mouse generations and provided colonization resistance against S. Tm infection, albeit not to the degree of a conventional complex microbiota. Comparative (meta)genome analyses identified functions represented in a conventional microbiome but absent from the Oligo-MM12. By genome-informed design, we created an improved version of the Oligo-MM community harbouring three facultative anaerobic bacteria from the Mouse Intestinal Bacterial Collection (miBC) that provided conventional-like colonization resistance. In conclusion, we have established a highly versatile experimental system that showed efficacy in an enteric infection model. Thus, in combination with exhaustive bacterial strain collections and systems-based approaches, genomeguided design can be used to generate insights into microbe–microbe and microbe–host interactions for the investigation of ecological and disease-relevant mechanisms in the intestine.

  • Bacterial evolution: Genomics of metabolic trade-offs.

    Polz MF, Cordero OX
    2016 - Nat Microbiol, 11: 16181

    Abstract: 

    The number of ribosomal operons in bacterial genomes correlates with both growth rate and carbon use efficiency, likely via proteome allocation trade-offs, providing clues into how microbial communities are structured to make best use of available nutrients.

  • Chemosynthetic symbionts of marine invertebrate animals are capable of nitrogen fixation.

    Petersen JM, Kemper A, Gruber-Vodicka H, Cardini U, van der Geest M, Kleiner M, Bulgheresi S, Mussmann M, Herbold C, Seah BK, Antony CP, Liu D, Belitz A, Weber M
    2016 - Nat Microbiol, 2: 16195

    Abstract: 

    Chemosynthetic symbioses are partnerships between invertebrate animals and chemosynthetic bacteria. The latter are the primary producers, providing most of the organic carbon needed for the animal host's nutrition. We sequenced genomes of the chemosynthetic symbionts from the lucinid bivalve Loripes lucinalis and the stilbonematid nematode Laxus oneistus. The symbionts of both host species encoded nitrogen fixation genes. This is remarkable as no marine chemosynthetic symbiont was previously known to be capable of nitrogen fixation. We detected nitrogenase expression by the symbionts of lucinid clams at the transcriptomic and proteomic level. Mean stable nitrogen isotope values of Loripes lucinalis were within the range expected for fixed atmospheric nitrogen, further suggesting active nitrogen fixation by the symbionts. The ability to fix nitrogen may be widespread among chemosynthetic symbioses in oligotrophic habitats, where nitrogen availability often limits primary productivity.

  • Intensive cryptic microbial iron cycling in the low iron water column of the meromictic Lake Cadagno.

    Berg JS, Michellod D, Pjevac P, Martinez-Perez C, Buckner CR, Hach PF, Schubert CJ, Milucka J, Kuypers MM
    2016 - Environ. Microbiol., 12: 5288-5302

    Abstract: 

    Iron redox reactions play an important role in carbon remineralization, supporting large microbial communities in iron-rich terrestrial and aquatic sediments. Stratified water columns with comparably low iron concentrations are globally widespread, but microbial iron cycling in these systems has largely been ignored. We found evidence for unexpectedly high iron turnover rates in the low (1-2 µmol·l(-1) ) iron waters of Lake Cadagno. Light-dependent, biological iron oxidation rates (1.4-13.8 µmol·l(-1) ·d(-1) ) were even higher than in ferruginous lakes with well-studied microbial iron cycles. This photoferrotrophic iron oxidation may account for up to 10% of total primary production in the chemocline. Iron oxides could not be detected and were presumably reduced immediately by iron-reducing microorganisms. Sequences of putative iron oxidizers and reducers were retrieved from in situ 16S rRNA gene amplicon libraries and some of these bacteria were identified in our enrichment cultures supplemented with Fe(II) and FeS. Based on our results, we propose a model in which iron is oxidized by photoferrotrophs and microaerophiles, and iron oxides are immediately reduced by heterotrophic iron reducers, resulting in a cryptic iron cycle. We hypothesize that microbial iron cycling may be more prevalent in water column redoxclines, especially those within the photic zone, than previously believed.

  • IMNGS: A comprehensive open resource of processed 16S rRNA microbial profiles for ecology and diversity studies.

    Lagkouvardos I, Joseph D, Kapfhammer M, Giritli S, Horn M, Haller D, Clavel T
    2016 - Sci Rep, 33721

    Abstract: 

    The SRA (Sequence Read Archive) serves as primary depository for massive amounts of Next Generation Sequencing data, and currently host over 100,000 16S rRNA gene amplicon-based microbial profiles from various host habitats and environments. This number is increasing rapidly and there is a dire need for approaches to utilize this pool of knowledge. Here we created IMNGS (Integrated Microbial Next Generation Sequencing), an innovative platform that uniformly and systematically screens for and processes all prokaryotic 16S rRNA gene amplicon datasets available in SRA and uses them to build sample-specific sequence databases and OTU-based profiles. Via a web interface, this integrative sequence resource can easily be queried by users. We show examples of how the approach allows testing the ecological importance of specific microorganisms in different hosts or ecosystems, and performing targeted diversity studies for selected taxonomic groups. The platform also offers a complete workflow for de novo analysis of users' own raw 16S rRNA gene amplicon datasets for the sake of comparison with existing data. IMNGS can be accessed at www.imngs.org.

  • Ecogenomics and potential biogeochemical impacts of globally abundant ocean viruses

    Roux S, Brum JR, Dutilh BE, Sunagawa S, Duhaime MB, Loy A, Poulos BT, Solonenko N, Lara E, Poulain J, Pesant S, Kandels-Lewis S, Dimier C, Picheral M, Searson S, Cruaud C, Alberti A, Duarte CM, Gasol JM, Vaque D, Tara Oceans Coordinators, Bork P, Acinas SG, Wincker P, Sullivan MB
    2016 - Nature, 537: 689–693

    Abstract: 

    Ocean microbes drive biogeochemical cycling on a global scale1. However, this cycling is constrained by viruses that affect community composition, metabolic activity, and evolutionary trajectories23. Owing to challenges with the sampling and cultivation of viruses, genome-level viral diversity remains poorly described and grossly understudied, with less than 1% of observed surface-ocean viruses known4. Here we assemble complete genomes and large genomic fragments from both surface- and deep-ocean viruses sampled during the Tara Oceans and Malaspina research expeditions56, and analyse the resulting ‘global ocean virome’ dataset to present a global map of abundant, double-stranded DNA viruses complete with genomic and ecological contexts. A total of 15,222 epipelagic and mesopelagic viral populations were identified, comprising 867 viral clusters (defined as approximately genus-level groups78). This roughly triples the number of known ocean viral populations4 and doubles the number of candidate bacterial and archaeal virus genera8, providing a near-complete sampling of epipelagic communities at both the population and viral-cluster level. We found that 38 of the 867 viral clusters were locally or globally abundant, together accounting for nearly half of the viral populations in any global ocean virome sample. While two-thirds of these clusters represent newly described viruses lacking any cultivated representative, most could be computationally linked to dominant, ecologically relevant microbial hosts. Moreover, we identified 243 viral-encoded auxiliary metabolic genes, of which only 95 were previously known. Deeper analyses of four of these auxiliary metabolic genes (dsrC, soxYZ, P-II (also known as glnB) and amoC) revealed that abundant viruses may directly manipulate sulfur and nitrogen cycling throughout the epipelagic ocean. This viral catalog and functional analyses provide a necessary foundation for the meaningful integration of viruses into ecosystem models where they act as key players in nutrient cycling and trophic networks.

  • Adaptive radiation by waves of gene transfer leads to fine-scale resource partitioning in marine microbes.

    Hehemann JH, Arevalo P, Datta MS, Yu X, Corzett CH, Henschel A, Preheim SP, Timberlake S, Alm EJ, Polz MF
    2016 - Nat Commun, 12860

    Abstract: 

    Adaptive radiations are important drivers of niche filling, since they rapidly adapt a single clade of organisms to ecological opportunities. Although thought to be common for animals and plants, adaptive radiations have remained difficult to document for microbes in the wild. Here we describe a recent adaptive radiation leading to fine-scale ecophysiological differentiation in the degradation of an algal glycan in a clade of closely related marine bacteria. Horizontal gene transfer is the primary driver in the diversification of the pathway leading to several ecophysiologically differentiated Vibrionaceae populations adapted to different physical forms of alginate. Pathway architecture is predictive of function and ecology, underscoring that horizontal gene transfer without extensive regulatory changes can rapidly assemble fully functional pathways in microbes.

  • Nitrogen isotope fractionation during N uptake via arbuscular mycorrhizal and ectomycorrhizal fungi into grey alder

    Schweiger P
    2016 - Journal of Plant Physiology, 205: 84-92

    Abstract: 

    Arbuscular mycorrhizal (AM) and ectomycorrhizal (ECM) fungi affect plant nitrogen (N) dynamics. Plant
    N isotope patterns have been used to characterise the contribution of ECM fungi to plant N uptake. By
    quantifying and comparing the effects of an AM and an ECM fungus on growth, N uptake and isotopic
    composition of one host plant grown at different relative N supply levels, the aim of this study was to
    improve the mechanistic understanding of natural 15N abundance patterns in mycorrhizal plants and
    their underlying causes.
    Grey alders were inoculated with one ECM fungus or one AM fungus or left non-mycorrhizal. Plants
    were grown under semi-hydroponic conditions and were supplied with three rates of relative N supply
    ranging from deficient to luxurious.
    Neither mycorrhizal fungus increased plant growth or N uptake. AM root colonisation had no effect
    on whole plant 15N and decreased foliar 15N only under N deficiency. The roots of these plants were
    15N-enriched. ECM root colonisation consistently decreased foliar and whole plant 15N.
    It is concluded, that both mycorrhizal fungi contributed to plant N uptake into the shoot. Nitrogen
    isotope fractionation during N assimilation and transformations in fungal mycelia is suggested to have
    resulted in plants receiving 15N-depleted N via the mycorrhizal uptake pathways. Negative mycorrhizal
    growth effects are explained by symbiotic resource trade on carbon and N and decreased direct plant N
    uptake.
    © 2016 Elsevier GmbH. All rights reserved.

  • Bacterial nutrient foraging in a mouse model of enteral nutrient deprivation: Insight into the gut origin of sepsis

    Ralls MW, Demehri FR, Feng Y, Raskind S, Ruan C, Schintlmeister A, Loy A, Hanson B, Berry D, Burant CF, Teitelbaum DH
    2016 - 311: G734-G743

    Abstract: 

    Total parenteral nutrition (TPN) leads to a shift in small intestinal microbiota with a characteristic dominance of Proteobacteria. This study examined how metabolomic changes within the small bowel support an altered microbial community in enterally deprived mice.
    C57BL/6 mice were given TPN or enteral chow. Metabolomic analysis of jejunal contents was performed by liquid chromatography/mass spectrometry (LC/MS). In some experiments, leucine in TPN was partly substituted with (13)C-leucine. Additionally, jejunal contents from TPN dependent and enterally fed mice were gavaged into germ-free mice to reveal if the TPN phenotype was transferrable.
    Small bowel contents of TPN mice maintained an amino acid composition similar to that of the TPN solution. Mass spectrometry analysis of small bowel contents of TPN dependent mice showed increased concentration of (13)C compared to fed mice receiving saline enriched with (13)C-leucine. (13)C-leucine added to the serosal side of Ussing chambers showed rapid permeation across TPN-dependent jejunum, suggesting increased transmucosal passage. Single-cell analysis by fluorescence in situ hybridization (FISH) - NanoSIMS demonstrated uptake of (13)C-leucine by TPN-associated bacteria, with preferential uptake by Enterobacteriaceae. Gavage of small bowel effluent from TPN mice into germ-free, fed mice resulted in a trend toward the pro-inflammatory TPN-phenotype with loss of epithelial barrier function.
    TPN-dependence leads to increased permeation of TPN-derived nutrients into the small intestinal lumen, where they are predominately utilized by Enterobacteriaceae. The altered metabolomic composition of the intestinal lumen during TPN promotes dysbiosis.

  • A specific and widespread association between deep-sea Bathymodiolus mussels and a novel family of Epsilonproteobacteria.

    Assié A, Borowski C, van der Heijden K, Raggi L, Geier B, Leisch N, Schimak MP, Dubilier N, Petersen JM
    2016 - Environ Microbiol Rep, 8: 805-813

    Abstract: 

    Bathymodiolus mussels dominate animal communities at many hydrothermal vents and cold seeps. Essential to the mussels' ecological and evolutionary success is their association with symbiotic methane- and sulfur-oxidizing gammaproteobacteria, which provide them with nutrition. In addition to these well-known gammaproteobacterial endosymbionts, we found epsilonproteobacterial sequences in metatranscriptomes, metagenomes and 16S rRNA clone libraries as well as by polymerase chain reaction screening of Bathymodiolus species sampled from vents and seeps around the world. These epsilonproteobacterial sequences were closely related, indicating that the association is highly specific. The Bathymodiolus-associated epsilonproteobacterial 16S rRNA sequences were at most 87.6% identical to the closest cultured relative, and 91.2% identical to the closest sequences in public databases. This clade therefore represents a novel family within the Epsilonproteobacteria. Fluorescence in situ hybridization and transmission electron microscopy showed that the bacteria are filamentous epibionts associated with the gill epithelia in two Bathymodiolus species. In animals that host highly specific symbioses with one or a few types of endosymbionts, other less-abundant members of the microbiota can be easily overlooked. Our work highlights how widespread and specific associations with less-abundant microbes can be. Possibly, these microbes play an important role in the survival and health of their animal hosts.

  • A Small Number of Phylogenetically Distinct Clonal Complexes Dominate a Coastal Vibrio cholerae Population.

    Kirchberger PC, Orata FD, Barlow EJ, Kauffman KM, Case RJ, Polz MF, Boucher Y
    2016 - Appl. Environ. Microbiol., 18: 5576-86

    Abstract: 

    Vibrio cholerae is a ubiquitous aquatic microbe in temperate and tropical coastal areas. It is a diverse species, with many isolates that are harmless to humans, while others are highly pathogenic. Most notable among them are strains belonging to the pandemic O1/O139 serogroup lineage, which contains the causative agents of cholera. The environmental selective regimes that led to this diversity are key to understanding how pathogens evolve in environmental reservoirs. A local population of V. cholerae and its close relative Vibrio metoecus from a coastal pond and lagoon system was extensively sampled during two consecutive months across four size fractions (480 isolates). In stark contrast to previous studies, the observed population was highly clonal, with 60% of V. cholerae isolates falling into one of five clonal complexes, which varied in abundance in the short temporal scale sampled. V. cholerae clonal complexes had significantly different distributions across size fractions and the two environments sampled, the pond and the lagoon. Sequencing the genomes of 20 isolates representing these five V. cholerae clonal complexes revealed different evolutionary trajectories, with considerable variations in gene content with potential ecological significance. Showing genotypic differentiation and differential spatial distribution, the dominant clonal complexes are likely ecologically divergent. Temporal variation in the relative abundance of these complexes suggests that transient blooms of specific clones could dominate local diversity.
    Vibrio cholerae is commonly found in coastal areas worldwide, with only a single group of this bacterium capable of causing severe cholera outbreaks. However, the potential to evolve the ability to cause disease exists in many strains of this species in its aquatic reservoir. Understanding how pathogenic bacteria evolve requires the study of their natural environments. By extensive sampling in a geographically restricted location in the United States, we found that most cells of a V. cholerae population belong to only a small number of strains. Analysis of their genome composition and spatial distribution indicates differential environmental adaptations between these strains. Other strains exist in smaller numbers, and the population was found to be temporally varied. This suggests frequent bloom and collapse cycles on a time scale of weeks. These population dynamics make it possible that more virulent strains could stochastically rise to large numbers, allowing for infection to occur.

  • Carbon isotope composition of carbohydrates and polyols in leaf and phloem sap of Phaseolus vulgaris L. influences predictions of plant water use efficiency

    Smith M, Wild B, Richter A, Simonin K, Merchant A
    2016 - Plant and Cell Physiology, 57: 1756-1766

    Abstract: 

    The use of carbon isotope abundance (δ13C) to assess plant carbon acquisition and water use has significant potential for use in crop management and plant improvement programs. Utilising Phaseolus vulgaris L. as a model system, this study demonstrates the occurrence and sensitivity of carbon isotope fractionation during the onset of abiotic stresses between leaf and phloem carbon pools. In addition to gas exchange data; compound-specific measures of carbon isotope abundance and concentrations of soluble components of phloem sap were compared to major carbohydrate and sugar alcohol pools in leaf tissue. Differences in both δ13C and concentration of metabolites were found in leaf and phloem tissues, the magnitude of which responded to changing environmental conditions. These changes have inplications for the modelling of leaf level gas exchange based upon δ13C natural abundance. While estimates of δ13C of low molecular weight carbohydrates and polyols increased the precision of predictions of water use efficiency compared to those based on bulk soluble carbon. The use of this technique requires consideration of the dynamics of the δ13C pool under investigation. Understanding the dynamics of changes in δ13C during movement and incorporation into heterotrophic tissues is vital for the continued development of tools that provide information on plant physiological performance relating to water use.

  • Population genomics of the symbiotic plasmids of sympatric nitrogen-fixing Rhizobium species associated with Phaseolus vulgaris.

    Pérez Carrascal OM, VanInsberghe D, Juárez S, Polz MF, Vinuesa P, González V
    2016 - Environ. Microbiol., 8: 2660-76

    Abstract: 

    Cultivated common beans are the primary protein source for millions of people around the world who subsist on low-input agriculture, enabled by the symbiotic N2 -fixation these legumes perform in association with rhizobia. Within a single agricultural plot, multiple Rhizobium species can nodulate bean roots, but it is unclear how genetically isolated these species remain in sympatry. To better understand this issue, we sequenced and compared the genomes of 33 strains isolated from the rhizosphere and root nodules of a particular bean variety grown in the same agricultural plot. We found that the Rhizobium species we observed coexist with low genetic recombination across their core genomes. Accessory plasmids thought to be necessary for the saprophytic lifestyle in soil show similar levels of genetic isolation, but with higher rates of recombination than the chromosomes. However, the symbiotic plasmids are extremely similar, with high rates of recombination and do not appear to have co-evolved with the chromosome or accessory plasmids. Therefore, while Rhizobium species are genetically isolated units within the microbial community, a common symbiotic plasmid allows all Rhizobium species to engage in symbiosis with the same host in a single agricultural plot.

  • Microbial interactions lead to rapid micro-scale successions on model marine particles.

    Datta MS, Sliwerska E, Gore J, Polz MF, Cordero OX
    2016 - Nat Commun, 11965

    Abstract: 

    In the ocean, organic particles harbour diverse bacterial communities, which collectively digest and recycle essential nutrients. Traits like motility and exo-enzyme production allow individual taxa to colonize and exploit particle resources, but it remains unclear how community dynamics emerge from these individual traits. Here we track the taxon and trait dynamics of bacteria attached to model marine particles and demonstrate that particle-attached communities undergo rapid, reproducible successions driven by ecological interactions. Motile, particle-degrading taxa are selected for during early successional stages. However, this selective pressure is later relaxed when secondary consumers invade, which are unable to use the particle resource but, instead, rely on carbon from primary degraders. This creates a trophic chain that shifts community metabolism away from the particle substrate. These results suggest that primary successions may shape particle-attached bacterial communities in the ocean and that rapid community-wide metabolic shifts could limit rates of marine particle degradation.

  • A New Perspective on Microbes Formerly Known as Nitrite-Oxidizing Bacteria.

    Daims H, Lücker S, Wagner M
    2016 - Trends Microbiol., 9: 699-712

    Abstract: 

    Nitrite-oxidizing bacteria (NOB) catalyze the second step of nitrification, nitrite oxidation to nitrate, which is an important process of the biogeochemical nitrogen cycle. NOB were traditionally perceived as physiologically restricted organisms and were less intensively studied than other nitrogen-cycling microorganisms. This picture is in contrast to new discoveries of an unexpected high diversity of mostly uncultured NOB and a great physiological versatility, which includes complex microbe-microbe interactions and lifestyles outside the nitrogen cycle. Most surprisingly, close relatives to NOB perform complete nitrification (ammonia oxidation to nitrate) and this finding will have far-reaching implications for nitrification research. We review recent work that has changed our perspective on NOB and provides a new basis for future studies on these enigmatic organisms.

  • The root-associated microbial community of the world's highest growing vascular plants

    Angel R, Conrad R, Dvorsky M, Kopecky M, Kotilínek M, Hiiesalu I, Schweingruber F, Doležal J
    2016 - Microbial ecology, 72: 394-406

    Abstract: 

    Upward migration of plants to barren subnival areas is occurring worldwide due to raising ambient temperatures and glacial recession. In summer 2012, the presence of six vascular plants, growing in a single patch, was recorded at an unprecedented elevation of 6150 m.a.s.l. close to the summit of Mount Shukule II in the Western Himalayas (Ladakh, India). Whilst showing multiple signs of stress, all plants have managed to establish stable growth and persist for several years. To learn about the role of microbes in the process of plant upward migration, we analysed the root-associated microbial community of the plants (three individuals from each) using microscopy and tagged amplicon sequencing. No mycorrhizae were found on the roots, implying they are of little importance to the establishment and early growth of the plants. However, all roots were associated with a complex bacterial community, with richness and diversity estimates similar or even higher than the surrounding bare soil. Both soil and root-associated communities were dominated by members of the orders Sphingomonadales and Sphingobacteriales, which are typical for hot desert soils, but were different from communities of temperate subnival soils and typical rhizosphere communities. Despite taxonomic similarity on the order level, the plants harboured a unique set of highly dominant operational taxonomic units which were not found in the bare soil. These bacteria have been likely transported with the dispersing seeds and became part of the root-associated community following germination. The results indicate that developing soils act not only as a source of inoculation to plant roots but also possibly as a sink for plant-associated bacteria.

  • Microbial dinitrogen fixation in coral holobionts exposed to thermal stress and bleaching.

    Cardini U, van Hoytema N, Bednarz VN, Rix L, Foster RA, Al-Rshaidat MM, Wild C
    2016 - Environ. Microbiol., 8: 2620-33

    Abstract: 

    Coral holobionts (i.e., coral-algal-prokaryote symbioses) exhibit dissimilar thermal sensitivities that may determine which coral species will adapt to global warming. Nonetheless, studies simultaneously investigating the effects of warming on all holobiont members are lacking. Here we show that exposure to increased temperature affects key physiological traits of all members (herein: animal host, zooxanthellae and diazotrophs) of both Stylophora pistillata and Acropora hemprichii during and after thermal stress. S. pistillata experienced severe loss of zooxanthellae (i.e., bleaching) with no net photosynthesis at the end of the experiment. Conversely, A. hemprichii was more resilient to thermal stress. Exposure to increased temperature (+ 6°C) resulted in a drastic increase in daylight dinitrogen (N2 ) fixation, particularly in A. hemprichii (threefold compared with controls). After the temperature was reduced again to in situ levels, diazotrophs exhibited a reversed diel pattern of activity, with increased N2 fixation rates recorded only in the dark, particularly in bleached S. pistillata (twofold compared to controls). Concurrently, both animal hosts, but particularly bleached S. pistillata, reduced both organic matter release and heterotrophic feeding on picoplankton. Our findings indicate that physiological plasticity by coral-associated diazotrophs may play an important role in determining the response of coral holobionts to ocean warming.

  • Free-living amoebae and their associated bacteria in Austrian cooling towers: a 1-year routine screening

    Scheikl U, Tsao HF, Horn M, Indra A, Walochnik J
    2016 - Parasitol Res, 115: 3365-74

    Abstract: 

    Free-living amoebae (FLA) are widely spread in the environment and known to cause rare but often serious infections. Besides this, FLA may serve as vehicles for bacterial pathogens. In particular, Legionella pneumophila is known to replicate within FLA thereby also gaining enhanced infectivity. Cooling towers have been the source of outbreaks of Legionnaires' disease in the past and are thus usually screened for legionellae on a routine basis, not considering, however, FLA and their vehicle function. The aim of this study was to incorporate a screening system for host amoebae into a Legionella routine screening. A new real-time PCR-based screening system for various groups of FLA was established. Three cooling towers were screened every 2 weeks over the period of 1 year for FLA and Legionella spp., by culture and molecular methods in parallel. Altogether, 83.3 % of the cooling tower samples were positive for FLA, Acanthamoeba being the dominating genus. Interestingly, 69.7 % of the cooling tower samples were not suitable for the standard Legionella screening due to their high organic burden. In the remaining samples, positivity for Legionella spp. was 25 % by culture, but overall positivity was 50 % by molecular methods. Several amoebal isolates revealed intracellular bacteria.

  • Plant-derived compounds stimulate the decomposition of organic matter in arctic permafrost soils

    Wild B, Gentsch N, Capek P, Diakova K, Alves RJ, Barta J, Gittel A, Hugelius G, Knoltsch A, Kuhry P, Lashchinskiy N, Mikutta R, Palmtag J, Schleper C, Schnecker J, Shibistova O, Takriti M, Torsvik VL, Urich T, Watzka M, Santruckova H, Guggenberger G, Richter A
    2016 - Scientific Reports, 6: 11

    Abstract: 

    Arctic ecosystems are warming rapidly, which is expected to promote soil organic matter (SOM) decomposition. In addition to the direct warming effect, decomposition can also be indirectly stimulated via increased plant productivity and plant-soil C allocation, and this so called “priming effect” might significantly alter the ecosystem C balance. In this study, we provide first mechanistic insights into the susceptibility of SOM decomposition in arctic permafrost soils to priming. By comparing 119 soils from four locations across the Siberian Arctic that cover all horizons of active layer and upper permafrost, we found that an increased availability of plant-derived organic C particularly stimulated decomposition in subsoil horizons where most of the arctic soil carbon is located. Considering the 1,035 Pg of arctic soil carbon, such an additional stimulation of decomposition beyond the direct temperature effect can accelerate net ecosystem C losses, and amplify the positive feedback to global warming.

  • Single cell stable isotope probing in microbiology using Raman microspectroscopy

    Yun Wang Y, Huang WE, Cui L, Wagner M
    2016 - Curr Opin Biotechnol, 41:34-42
    Single Cell Stable Isotope Probing in Microbiology using Raman Microspectroscopy

    Abstract: 

    Microbial communities are essential for most ecosystem processes and interact in highly complex ways with virtually all eukaryotes. Thus, a detailed understanding of the function of such communities is a fundamental prerequisite for microbial ecologists, applied microbiologists and microbiome researchers. Using single cell Raman microspectroscopy, biochemical fingerprints of individual microbial cells can be obtained in a fast and nondestructive manner. If combined with stable isotope probing (SIP), Raman spectroscopy can directly reveal functions of single microorganisms in their natural habitat. This review provides an update on various SIP-approaches suitable for combination with different Raman scattering techniques and illustrates how single cell Raman SIP can be directly combined with the omics-centric analysis pipelines generally applied to investigate microbial communities. 

  • Single cell genome and group-specific dsrAB sequencing implicate members of the class Dehalococcoidia (phylum Chloroflexi) in sulfur cycling

    Wasmund K, Cooper M, Schreiber L, Lloyd KG, Baker B, Petersen DG, Jørgensen BB, Stepanauskas R, Reinhardt R, Schramm A, Loy A, Adrian L
    2016 - mBio, 7: e00266-16

    Abstract: 

    The marine subsurface sediment biosphere is widely inhabited by bacteria affiliated with the class Dehalococcoidia (DEH), phylum Chloroflexi, yet little is known regarding their metabolisms. In this report, genomic content from a single DEH cell (‘DEH-C11’) with a 16S rRNA gene that affiliated with a diverse cluster of 16S rRNA gene sequences prevalent in marine sediments, was obtained from sediments of Aarhus Bay, Denmark. The distinctive gene content of this cell suggests metabolic characteristics that differ from those of known DEH and Chloroflexi. Genes encoding dissimilatory sulfite reductase (Dsr) suggest DEH could respire oxidized sulfur compounds, although Chloroflexi have never been implicated in this mode of sulfur cycling. Using long-range PCR assays targeting DEH dsr-loci, dsrAB were amplified and sequenced from various marine sediments. Many of the amplified dsrAB sequences affiliated with the DEH Dsr-clade, which we propose equates to a family-level clade. This provides supporting evidence for the potential for sulfite reduction by diverse DEH. DEH-C11 also harboured genes encoding reductases for arsenate, dimethyl sulfoxide and halogenated organics. The reductive dehalogenase homolog (RdhA) forms a monophyletic clade along with RdhA sequences from various DEH-derived contigs retrieved from available metagenomes. Multiple facts indicate this RdhA may not be a terminal reductase. Other genes indicated nutrients and energy may be derived from the oxidation of substituted homocyclic and heterocyclic aromatic compounds. Together, these results suggest that marine DEH play a previously unrecognised role in sulfur cycling, and reveal potential for expanded catabolic and respiratory functions among subsurface DEH.

  • A genomic comparison of 13 symbiotic Vibrio fischeri isolates from the perspective of their host source and colonization behavior.

    Bongrand C, Koch EJ, Moriano-Gutierrez S, Cordero OX, McFall-Ngai M, Polz MF, Ruby EG
    2016 - ISME J, 12: 2907-2917

    Abstract: 

    Newly hatched Euprymna scolopes squid obtain their specific light-organ symbionts from an array of Vibrio (Allivibrio) fischeri strains present in their environment. Two genetically distinct populations of this squid species have been identified, one in Kaneohe Bay (KB), and another in Maunaloa Bay (MB), Oahu. We asked whether symbionts isolated from squid in each of these populations outcompete isolates from the other population in mixed-infection experiments. No relationship was found between a strain's host source (KB or MB) and its ability to competitively colonize KB or MB juveniles in a mixed inoculum. Instead, two colonization behaviors were identified among the 11 KB and MB strains tested: a 'dominant' outcome, in which one strain outcompetes the other for colonization, and a 'sharing' outcome, in which two strains co-colonize the squid. A genome-level comparison of these and other V. fischeri strains suggested that the core genomic structure of this species is both syntenous and highly conserved over time and geographical distance. We also identified ~250 Kb of sequence, encoding 194 dispersed orfs, that was specific to those strains that expressed the dominant colonization behavior. Taken together, the results indicate a link between the genome content of V. fischeri strains and their colonization behavior when initiating a light-organ symbiosis.

  • L-System model for the growth of arbuscular mycorrhizal fungi, both within and outside of their host roots

    Schnepf A, Leitner D, Schweiger P, Scholl P, Jansa J
    2016 - Journal of the Royal Society Interface, 117: 11

    Abstract: 

    Development of arbuscular mycorrhizal fungal colonization of roots and the surrounding soil is the central process of mycorrhizal symbiosis, important for ecosystem functioning and commercial inoculum applications. To improve mechanistic understanding of this highly spatially and temporarily dynamic process, we developed a three-dimensional model taking into account growth of the roots and hyphae. It is for the first time that infection within the root system is simulated dynamically and in a spatially resolved way. Comparison between data measured in a calibration experiment and simulated results showed a good fit. Our simulations showed that the position of the fungal inoculum affects the sensitivity of hyphal growth parameters. Variation in speed of secondary infection and hyphal lifetime had a different effect on root infection and hyphal length, respectively, depending on whether the inoculum was concentrated or dispersed. For other parameters (branching rate, distance between entry points), the relative effect was the same independent of inoculum placement. The model also indicated that maximum root colonization levels well below 100%, often observed experimentally, may be a result of differential spread of roots and hyphae, besides intrinsic plant control, particularly upon localized placement of inoculum and slow secondary infection.

  • Genomics of a phototrophic nitrite oxidizer: insights into the evolution of photosynthesis and nitrification.

    Hemp J, Lücker S, Schott J, Pace LA, Johnson JE, Schink B, Daims H, Fischer WW
    2016 - ISME J, 11: 2669-2678

    Abstract: 

    Oxygenic photosynthesis evolved from anoxygenic ancestors before the rise of oxygen ~2.32 billion years ago; however, little is known about this transition. A high redox potential reaction center is a prerequisite for the evolution of the water-oxidizing complex of photosystem II. Therefore, it is likely that high-potential phototrophy originally evolved to oxidize alternative electron donors that utilized simpler redox chemistry, such as nitrite or Mn. To determine whether nitrite could have had a role in the transition to high-potential phototrophy, we sequenced and analyzed the genome of Thiocapsa KS1, a Gammaproteobacteria capable of anoxygenic phototrophic nitrite oxidation. The genome revealed a high metabolic flexibility, which likely allows Thiocapsa KS1 to colonize a great variety of habitats and to persist under fluctuating environmental conditions. We demonstrate that Thiocapsa KS1 does not utilize a high-potential reaction center for phototrophic nitrite oxidation, which suggests that this type of phototrophic nitrite oxidation did not drive the evolution of high-potential phototrophy. In addition, phylogenetic and biochemical analyses of the nitrite oxidoreductase (NXR) from Thiocapsa KS1 illuminate a complex evolutionary history of nitrite oxidation. Our results indicate that the NXR in Thiocapsa originates from a different nitrate reductase clade than the NXRs in chemolithotrophic nitrite oxidizers, suggesting that multiple evolutionary trajectories led to modern nitrite-oxidizing bacteria.

  • Biotransformation of Two Pharmaceuticals by the Ammonia-Oxidizing Archaeon Nitrososphaera gargensis.

    Men Y, Han P, Helbling DE, Jehmlich N, Herbold C, Gulde R, Onnis-Hayden A, Gu AZ, Johnson DR, Wagner M, Fenner K
    2016 - Environ Sci Technol, 9: 4682-92
    Nitrososphaera gargensis

    Abstract: 

    The biotransformation of some micropollutants has previously been observed to be positively associated with ammonia oxidation activities and the transcript abundance of the archaeal ammonia monooxygenase gene (amoA) in nitrifying activated sludge. Given the increasing interest in and potential importance of ammonia-oxidizing archaea (AOA), we investigated the capabilities of an AOA pure culture, Nitrososphaera gargensis, to biotransform ten micropollutants belonging to three structurally similar groups (i.e., phenylureas, tertiary amides, and tertiary amines). N. gargensis was able to biotransform two of the tertiary amines, mianserin (MIA) and ranitidine (RAN), exhibiting similar compound specificity as two ammonia-oxidizing bacteria (AOB) strains that were tested for comparison. The same MIA and RAN biotransformation reactions were carried out by both the AOA and AOB strains. The major transformation product (TP) of MIA, α-oxo MIA was likely formed via a two-step oxidation reaction. The first hydroxylation step is typically catalyzed by monooxygenases. Three RAN TP candidates were identified from nontarget analysis. Their tentative structures and possible biotransformation pathways were proposed. The biotransformation of MIA and RAN only occurred when ammonia oxidation was active, suggesting cometabolic transformations. Consistently, a comparative proteomic analysis revealed no significant differential expression of any protein-encoding gene in N. gargensis grown on ammonium with MIA or RAN compared with standard cultivation on ammonium only. Taken together, this study provides first important insights regarding the roles played by AOA in micropollutant biotransformation.

  • Oysters and Vibrios as a Model for Disease Dynamics in Wild Animals.

    Le Roux F, Wegner KM, Polz MF
    2016 - Trends Microbiol., 7: 568-580

    Abstract: 

    Disease dynamics in the wild are influenced by a number of ecological and evolutionary factors not addressed by traditional laboratory-based characterization of pathogens. Here we propose the oyster, Crassostrea gigas, as a model for studying the interaction of the environment, bacterial pathogens, and the host in disease dynamics. We show that an important first step is to ask whether the functional unit of pathogenesis is a bacterial clone, a population, or a consortium in order to assess triggers of disease outbreaks and devise appropriate monitoring tools. Moreover, the development of specific-pathogen-free (SPF) oysters has enabled assessment of the infection process under natural conditions. Finally, recent results show the importance of microbial interactions and host genetics in determining oyster health and disease.

  • Consortia of low-abundance bacteria drive sulfate reduction-dependent degradation of fermentation products in peat soil microcosms

    Hausmann B, Knorr K-H, Schreck K, Tringe SG, del Rio TG, Loy A, Pester M
    2016 - ISME J, 10: 2365-75

    Abstract: 

    Dissimilatory sulfate reduction in peatlands is sustained by a cryptic sulfur cycle and effectively competes with methanogenic degradation pathways. In a series of peat soil microcosms incubated over 50 days, we identified bacterial consortia that responded to small, periodic additions of individual fermentation products (formate, acetate, propionate, lactate or butyrate) in the presence or absence of sulfate. Under sulfate supplementation, net sulfate turnover (ST) steadily increased to 16-174 nmol cm-3 per day and almost completely blocked methanogenesis. 16S rRNA gene and cDNA amplicon sequencing identified microorganisms whose increases in ribosome numbers strongly correlated to ST. Natively abundant (⩾0.1% estimated genome abundance) species-level operational taxonomic units (OTUs) showed no significant response to sulfate. In contrast, low-abundance OTUs responded significantly to sulfate in incubations with propionate, lactate and butyrate. These OTUs included members of recognized sulfate-reducing taxa (Desulfosporosinus, Desulfopila, Desulfomonile, Desulfovibrio) and also members of taxa that are either yet unknown sulfate reducers or metabolic interaction partners thereof. Most responsive OTUs markedly increased their ribosome content but only weakly increased in abundance. Responsive Desulfosporosinus OTUs even maintained a constantly low population size throughout 50 days, which suggests a novel strategy of rare biosphere members to display activity. Interestingly, two OTUs of the non-sulfate-reducing genus Telmatospirillum (Alphaproteobacteria) showed strongly contrasting preferences towards sulfate in butyrate-amended microcosms, corroborating that closely related microorganisms are not necessarily ecologically coherent. We show that diverse consortia of low-abundance microorganisms can perform peat soil sulfate reduction, a process that exerts control on methane production in these climate-relevant ecosystems.

  • AstRoMap European Astrobiology Roadmap.

    Horneck G, Walter N, Westall F, Grenfell JL, Martin WF, Gomez F, Leuko S, Lee N, Onofri S, Tsiganis K, Saladino R, Pilat-Lohinger E, Palomba E, Harrison J, Rull F, Muller C, Strazzulla G, Brucato JR, Rettberg P, Capria MT
    2016 - 3: 201-43

    Abstract: 

    The European AstRoMap project (supported by the European Commission Seventh Framework Programme) surveyed the state of the art of astrobiology in Europe and beyond and produced the first European roadmap for astrobiology research. In the context of this roadmap, astrobiology is understood as the study of the origin, evolution, and distribution of life in the context of cosmic evolution; this includes habitability in the Solar System and beyond. The AstRoMap Roadmap identifies five research topics, specifies several key scientific objectives for each topic, and suggests ways to achieve all the objectives. The five AstRoMap Research Topics are • Research Topic 1: Origin and Evolution of Planetary Systems • Research Topic 2: Origins of Organic Compounds in Space • Research Topic 3: Rock-Water-Carbon Interactions, Organic Synthesis on Earth, and Steps to Life • Research Topic 4: Life and Habitability • Research Topic 5: Biosignatures as Facilitating Life Detection It is strongly recommended that steps be taken towards the definition and implementation of a European Astrobiology Platform (or Institute) to streamline and optimize the scientific return by using a coordinated infrastructure and funding system.

  • Microbes as engines of ecosystem function: when does community structure enhance predictions of ecosystem processes?

    Graham EB, Knelman JE, Schindlbacher A, Siciliano S, Breulmann M, Yannarell A, Beman JM, Abell G, Philippot L, Prosser J, Foulquier A, Yuste JC, Glanville HC, Jones DL, Angel R, Salminen J, Newton RJ, Bürgmann H, Ingram LJ, Hamer U, Siljanen HM, Peltoniemi K, Potthast K, Bañeras L, Hartmann M, Banerjee S, Yu RQ, Nogaro G, Richter A, Koranda M, Castle SC, Goberna M, Song B, Chatterjee A, Nunes OC, Lopes AR, Cao Y, Kaisermann A, Hallin S, Strickland MS, Garcia-Pausas J, Barba J, Kang H, Isobe K, Papaspyrou S, Pastorelli R, Lagomarsino A, Lindström ES, Basiliko N, Nemergut DR
    2016 - Frontiers in microbiology, 7: 214

    Abstract: 

    Microorganisms are vital in mediating the earth's biogeochemical cycles; yet, despite our rapidly increasing ability to explore complex environmental microbial communities, the relationship between microbial community structure and ecosystem processes remains poorly understood. Here, we address a fundamental and unanswered question in microbial ecology: 'When do we need to understand microbial community structure to accurately predict function?' We present a statistical analysis investigating the value of environmental data and microbial community structure independently and in combination for explaining rates of carbon and nitrogen cycling processes within 82 global datasets. Environmental variables were the strongest predictors of process rates but left 44% of variation unexplained on average, suggesting the potential for microbial data to increase model accuracy. Although only 29% of our datasets were significantly improved by adding information on microbial community structure, we observed improvement in models of processes mediated by narrow phylogenetic guilds via functional gene data, and conversely, improvement in models of facultative microbial processes via community diversity metrics. Our results also suggest that microbial diversity can strengthen predictions of respiration rates beyond microbial biomass parameters, as 53% of models were improved by incorporating both sets of predictors compared to 35% by microbial biomass alone. Our analysis represents the first comprehensive analysis of research examining links between microbial communitystructure and ecosystem function. Taken together, our results indicate that a greater understanding of microbial communities informed by ecological principles may enhance our ability to predict ecosystem process rates relative to assessments based on environmental variables and microbial physiology.

  • Microbes as Engines of Ecosystem Function: When Does Community Structure Enhance Predictions of Ecosystem Processes?

    Graham EB, Knelman JE, Schindlbacher A, Siciliano S, Breulmann M, Yannarell A, Beman JM, Abell G, Philippot L, Prosser J, Foulquier A, Yuste JC, Glanville HC, Jones DL, Angel R, Salminen J, Newton RJ, Bürgmann H, Ingram LJ, Hamer U, Siljanen HMP, Peltoniemi K, Potthast K, Bañeras L, Hartmann M, Banerjee S, Yu R-Q, Nogaro G, Richter A, Koranda M, Castle SC, Goberna M, Song B, Chatterjee A, Nunes OC, Lopes AR, Cao Y, Kaisermann A, Hallin S, Strickland MS, Garcia-Pausas J, Barba J, Kang H, Isobe K, Papaspyrou S, Pastorelli R, Lagomarsino A, Lindström ES, Basiliko N, and Nemergut DR
    2016 - Front Microbiol, 7: 214

    Abstract: 

    Microorganisms are vital in mediating the earth's biogeochemical cycles; yet, despite our rapidly increasing ability to explore complex environmental microbial communities, the relationship between microbial community structure and ecosystem processes remains poorly understood. Here, we address a fundamental and unanswered question in microbial ecology: 'When do we need to understand microbial community structure to accurately predict function?' We present a statistical analysis investigating the value of environmental data and microbial community structure independently and in combination for explaining rates of carbon and nitrogen cycling processes within 82 global datasets. Environmental variables were the strongest predictors of process rates but left 44% of variation unexplained on average, suggesting the potential for microbial data to increase model accuracy. Although only 29% of our datasets were significantly improved by adding information on microbial community structure, we observed improvement in models of processes mediated by narrow phylogenetic guilds via functional gene data, and conversely, improvement in models of facultative microbial processes via community diversity metrics. Our results also suggest that microbial diversity can strengthen predictions of respiration rates beyond microbial biomass parameters, as 53% of models were improved by incorporating both sets of predictors compared to 35% by microbial biomass alone. Our analysis represents the first comprehensive analysis of research examining links between microbial community structure and ecosystem function. Taken together, our results indicate that a greater understanding of microbial communities informed by ecological principles may enhance our ability to predict ecosystem process rates relative to assessments based on environmental variables and microbial physiology.

  • Back to the Future of Soil Metagenomics.

    Nesme J, Achouak W, Agathos SN, Bailey M, Baldrian P, Brunel D, Frostegård A, Heulin T, Jansson JK, Jurkevitch E, Kruus KL, Kowalchuk GA, Lagares A, Lappin-Scott HM, Lemanceau P, Le Paslier D, Mandic-Mulec I, Murrell JC, Myrold DD, Nalin R, Nannipieri P, Neufeld JD, O'Gara F, Parnell JJ, Pühler A, Pylro V, Ramos JL, Roesch LF, Schloter M, Schleper C, Sczyrba A, Sessitsch A, Sjöling S, Sørensen J, Sørensen SJ, Tebbe CC, Topp E, Tsiamis G, van Elsas JD, van Keulen G, Widmer F, Wagner M, Zhang T, Zhang X, Zhao L, Zhu YG, Vogel TM, Simonet P
    2016 - Front Microbiol, 73
  • Carbon and Nitrogen Uptake of Calcareous Benthic Foraminifera along a Depth-Related Oxygen Gradient in the OMZ of the Arabian Sea

    Enge AJ, Wukovits J, Wanek W, Watzka M, Witte UFM, Hunter WR, Heinz P
    2016 - Frontiers in microbiology, 7: 71

    Abstract: 

    Foraminifera are an important faunal element of the benthos in oxygen-depleted settings such as Oxygen Minimum Zones (OMZs) where they can play a relevant role in the processing of phytodetritus. We investigated the uptake of phytodetritus (labeled with 13C and 15N) by calcareous foraminifera in the 0–1 cm sediment horizon under different oxygen concentrations within the OMZ in the eastern Arabian Sea. The in situ tracer experiments were carried out along a depth transect on the Indian margin over a period of 4 to 10 days. The uptake of phytodetrital carbon within 4 days by all investigated species shows that phytodetritus is a relevant food source for foraminifera in OMZ sediments. The decrease of total carbon uptake from 540 to 1100 m suggests a higher demand for carbon by species in the low-oxygen core region of the OMZ or less food competition with macrofauna. Especially Uvigerinids showed high uptake of phytodetrital carbon at the lowest oxygenated site. Variation in the ratio of phytodetrital carbon to nitrogen between species and sites indicates that foraminiferal carbon and nitrogen use can be decoupled and different nutritional demands are found between species. Lower ratio of phytodetrital carbon and nitrogen at 540 m could hint for greater demand or storage of food-based nitrogen, ingestion, or hosting of bacteria under almost anoxic conditions. Shifts in the foraminiferal assemblage structure (controlled by oxygen or food availability) and in the presence of other benthic organisms are likely to account for observed changes in the processing of phytodetritus in the different OMZ habitats. Foraminifera dominate the short-term processing of phytodetritus in the OMZ core but are less important in the lower OMZ boundary region of the Indian margin as biological interactions and species distribution of foraminifera change with depth and oxygen levels.

  • Behavior of platinum(iv) complexes in models of tumor hypoxia: cytotoxicity, compound distribution and accumulation

    Schreiber-Brynzak E, Pichler V, Heffeter P, Hanson B, Theiner S, Lichtscheidl-Schultz I, Kornauth C, Bamonti L, Dhery V, Groza D, Berry D, Berger W, Galanski M, Jakupec MA, Keppler BK
    2016 - Metallomics, 4: 422-33

    Abstract: 

    Hypoxia in solid tumors remains a challenge for conventional cancer therapeutics. As a source for resistance, metastasis development and drug bioprocessing, it influences treatment results and disease outcome. Bioreductive platinum(iv) prodrugs might be advantageous over conventional metal-based therapeutics, as biotransformation in a reductive milieu, such as under hypoxia, is required for drug activation. This study deals with a two-step screening of experimental platinum(iv) prodrugs with different rates of reduction and lipophilicity with the aim of identifying the most appropriate compounds for further investigations. In the first step, the cytotoxicity of all compounds was compared in hypoxic multicellular spheroids and monolayer culture using a set of cancer cell lines with different sensitivities to platinum(ii) compounds. Secondly, two selected compounds were tested in hypoxic xenografts in SCID mouse models in comparison to satraplatin, and, additionally, (LA)-ICP-MS-based accumulation and distribution studies were performed for these compounds in hypoxic spheroids and xenografts. Our findings suggest that, while cellular uptake and cytotoxicity strongly correlate with lipophilicity, cytotoxicity under hypoxia compared to non-hypoxic conditions and antitumor activity of platinum(iv) prodrugs are dependent on their rate of reduction.

  • New methods to unravel rhizosphere processes

    Oburger E, Schmidt H
    2016 - Trends Plant Sci., 3: 243-55

    Abstract: 

    Root-triggered processes (growth, uptake and release of solutes) vary in space and time, and interact with heterogeneous soil microenvironments that provide habitats for (micro)biota on various scales. Despite tremendous progress in method development in the past decades, finding a suitable experimental set-up to investigate processes occurring at the dynamic conjunction of biosphere, hydrosphere, and pedosphere in the close vicinity of active plant roots still represents a major challenge. We discuss recent methodological developments in rhizosphere research with a focus on imaging techniques. We further review established concepts that have been updated with novel techniques, highlighting the need for combinatorial approaches to disentangle rhizosphere processes on relevant scales.

  • Relative Abundance of Nitrotoga spp. in a Biofilter of a Cold-Freshwater Aquaculture Plant Appears To Be Stimulated by Slightly Acidic pH.

    Hüpeden J, Wegen S, Off S, Lücker S, Bedarf Y, Daims H, Kühn C, Spieck E
    2016 - 6: 1838-45

    Abstract: 

    The functioning of recirculation aquaculture systems (RAS) is essential to maintain water quality for fish health, and one crucial process here is nitrification. The investigated RAS was connected to a rainbow trout production system and operated at an average temperature of 13°C and pH 6.8. Community analyses of the nitrifying biofilm revealed a coexistence of Nitrospira and Nitrotoga, and it is hypothesized that a slightly acidic pH in combination with lower temperatures favors the growth of the latter. Modification of the standard cultivation approach toward lower pH values of 5.7 to 6.0 resulted in the successful enrichment (99% purity) of Nitrotoga sp. strain HW29, which had a 16S rRNA sequence similarity of 99.0% to Nitrotoga arctica. Reference cultures of Nitrospira defluvii and the novel Nitrotoga sp. HW29 were used to confirm differentiation of these nitrite oxidizers in distinct ecological niches. Nitrotoga sp. HW29 revealed pH and temperature optima of 6.8 and 22°C, respectively, whereas Nitrospira defluvii displayed the highest nitrite oxidation rate at pH 7.3 and 32°C. We report here the occurrence of Nitrotoga as one of the main nitrite-oxidizing bacteria in freshwater aquaculture systems and indicate that a slightly acidic pH, in addition to temperatures below 20°C, can be applied as a selective isolation criterion for this microorganism.

  • Trophosome of the deep-sea tubeworm Riftia pachyptila inhibits bacterial growth

    Klose J, Aistleitner K, Horn M, Krenn L, Dirsch V, Zehl M, Bright M
    2016 - PloS one, 11: e0146446

    Abstract: 

    The giant tubeworm Riftia pachyptila lives in symbiosis with the chemoautotrophic gammaproteobacterium Cand. Endoriftia persephone. Symbionts are released back into the environment upon host death in high-pressure experiments, while microbial fouling is not involved in trophosome degradation. Therefore, we examined the antimicrobial effect of the tubeworm's trophosome and skin. The growth of all four tested Gram-positive, but only of one of the tested Gram-negative bacterial strains was inhibited by freshly fixed and degrading trophosome (incubated up to ten days at either warm or cold temperature), while no effect on Saccharomyces cerevisiae was observed. The skin did not show antimicrobial effects. A liquid chromatography-mass spectrometric analysis of the ethanol supernatant of fixed trophosomes lead to the tentative identification of the phospholipids 1-palmitoleyl-2-lyso-phosphatidylethanolamine, 2-palmitoleyl-1-lyso-phosphatidylethanolamine and the free fatty acids palmitoleic, palmitic and oleic acid, which are known to have an antimicrobial effect. As a result of tissue autolysis, the abundance of the free fatty acids increased with longer incubation time of trophosome samples. This correlated with an increasing growth inhibition of Bacillus subtilis and Listeria welshimeri, but not of the other bacterial strains. Therefore, the free fatty acids produced upon host degradation could be the cause of inhibition of at least these two bacterial strains.

  • Diversity analysis of sulfite- and sulfate-reducing microorganisms by multiplex dsrA and dsrB amplicon sequencing using new primers and mock community-optimized bioinformatics

    Pelikan C, Herbold CW, Hausmann B, Müller AL, Pester M, Loy A
    2016 - Environ Microbiol, 18: 2994-3009

    Abstract: 

    Genes encoding dissimilatory sulfite reductase (DsrAB) are commonly used as diagnostic markers in ecological studies of sulfite- and sulfate-reducing microorganisms. Here, we developed new high-coverage primer sets for generation of reductive bacterial-type dsrA and dsrB PCR products for highly parallel amplicon sequencing and a bioinformatics workflow for processing and taxonomic classification of short dsrA and dsrB reads. We employed two diverse mock communities that consisted of 45 or 90 known dsrAB sequences derived from environmental clones to precisely evaluate the performance of individual steps of our amplicon sequencing approach on the Illumina MiSeq platform. Although PCR cycle number, gene-specific primer mismatches, and stringent filtering for high-quality sequences had notable effects on the observed dsrA and dsrB community structures, recovery of most mock community sequences was generally proportional to their relative input abundances. Successful dsrA and dsrB diversity analysis in selected environmental samples further proved that the multiplex amplicon sequencing approach is adequate for monitoring spatial distribution and temporal abundance dynamics of dsrAB-containing microorganisms. While tested for reductive bacterial-type dsrAB, this method is readily applicable for oxidative-type dsrAB of sulfur-oxidizing bacteria and also provides guidance for processing short amplicon reads of other functional genes.

  • Phylogenetic and genomic analysis of Methanomassiliicoccales in wetlands and animal intestinal tracts reveals clade-specific habitat preferences

    Söllinger A, Schwab C, Weinmaier T, Loy A, Tveit AT, Schleper C, Urich T
    2016 - FEMS Microbiol Ecol, 92: fiv149

    Abstract: 

    Methanogenic Thermoplasmata of the novel order Methanomassiliicoccales were recently discovered in human and animal gastro-intestinal tracts (GITs). However their distribution in other methanogenic environments has not been addressed systematically. Here we surveyed Methanomassiliicoccales presence in wetland soils, a globally important source of methane emissions to the atmosphere, and in the GITs of different animals by PCR targeting their 16S rRNA and methyl:coenzyme M reductase (α-subunit) genes. We detected Methanomassiliicoccales in all 16 peat soils investigated, indicating their wide distribution in these habitats. Additionally, we detected their genes in various animal feces. Methanomassiliicoccales were subdivided in two broad phylogenetic clades designated 'environmental' and 'GIT' clades based on differential, although non-exclusive, habitat preferences of their members. A well-supported cluster within the environmental clade comprised more than 80% of all wetland 16S rRNA gene sequences. Metagenome assembly from bovine rumen fluid enrichments resulted in two almost complete genomes of both Methanomassiliicoccales clades. Comparative genomics revealed that members of the environmental clade contain larger genomes and a higher number of genes encoding anti-oxidative enzymes than animal GIT clade representatives. This study highlights the wide distribution of Methanomassiliicoccales in wetlands, which suggests that they contribute to methane emissions from these climate-relevant ecosystems.

  • probeBase - an online resource for rRNA-targeted oligonucleotide probes and primers: new features 2016

    Greuter D, Loy A, Horn M, Rattei T
    2016 - Nucleic Acids Res, 44: D586-D589

    Abstract: 

    probeBase http://www.probebase.net is a manually maintained and curated database of rRNA-targeted oligonucleotide probes and primers. Contextual information and multiple options for evaluating in silico hybridization performance against the most recent rRNA sequence databases are provided for each oligonucleotide entry, which makes probeBase an important and frequently used resource for microbiology research and diagnostics. Here we present a major update of probeBase, which was last featured in the NAR Database Issue 2007. This update describes a complete remodeling of the database architecture and environment to accommodate computationally efficient access. Improved search functions, sequence match tools, and data output now extend the opportunities for finding suitable hierarchical probe sets that target an organism or taxon at different taxonomic levels. To facilitate the identification of complementary probe sets for organisms represented by short rRNA sequence reads generated by amplicon sequencing or metagenomic analysis with next generation sequencing technologies such as Illumina and IonTorrent, we introduce a novel tool that recovers surrogate near full-length rRNA sequences for short query sequences and finds matching oligonucleotides in probeBase.

  • Chlamydial seasonal dynamics and isolation of 'Candidatus Neptunochlamydia vexilliferae' from a Tyrrhenian coastal lake.

    Pizzetti I, Schulz F, Tyml T, Fuchs BM, Amann R, Horn M, Fazi S
    2016 - Environ. Microbiol., 8: 2405-17

    Abstract: 

    The Chlamydiae are a phylum of obligate intracellular bacteria comprising important human and animal pathogens, yet their occurrence in the environment, their phylogenetic diversity and their host range has been largely underestimated. We investigated the seasonality of environmental chlamydiae in a Tyrrhenian coastal lake. By catalysed reporter deposition fluorescence in situ hybridization, we quantified the small planktonic cells and detected a peak in the abundance of environmental chlamydiae in early autumn with up to 5.9 × 10(4) cells ml(-1) . Super-resolution microscopy improved the visualization and quantification of these bacteria and enabled the detection of pleomorphic chlamydial cells in their protist host directly in an environmental sample. To isolate environmental chlamydiae together with their host, we applied a high-throughput limited dilution approach and successfully recovered a Vexillifera sp., strain harbouring chlamydiae (93% 16S rRNA sequence identity to Simkania negevensis), tentatively named 'Candidatus Neptunochlamydia vexilliferae'. Transmission electron microscopy in combination with fluorescence in situ hybridization was used to prove the intracellular location of these bacteria representing the first strain of marine chlamydiae stably maintained alongside with their host in a laboratory culture. Taken together, this study contributes to a better understanding of the distribution and diversity of environmental chlamydiae in previously neglected marine environments.

  • Rock geochemistry induces stress and starvation responses in the bacterial proteome.

    Bryce CC, Le Bihan T, Martin SF, Harrison JP, Bush T, Spears B, Moore A, Leys N, Byloos B, Cockell CS
    2016 - Environ. Microbiol., 4: 1110-21

    Abstract: 

    Interactions between microorganisms and rocks play an important role in Earth system processes. However, little is known about the molecular capabilities microorganisms require to live in rocky environments. Using a quantitative label-free proteomics approach, we show that a model bacterium (Cupriavidus metallidurans CH34) can use volcanic rock to satisfy some elemental requirements, resulting in increased rates of cell division in both magnesium- and iron-limited media. However, the rocks also introduced multiple new stresses via chemical changes associated with pH, elemental leaching and surface adsorption of nutrients that were reflected in the proteome. For example, the loss of bioavailable phosphorus was observed and resulted in the upregulation of diverse phosphate limitation proteins, which facilitate increase phosphate uptake and scavenging within the cell. Our results revealed that despite the provision of essential elements, rock chemistry drives complex metabolic reorganization within rock-dwelling organisms, requiring tight regulation of cellular processes at the protein level. This study advances our ability to identify key microbial responses that enable life to persist in rock environments.

  • Activity and community structures of sulfate-reducing microorganisms in polar, temperate and tropical marine sediments

    Robador A, Müller AL, Sawicka JE, Berry D, Hubert CRJ, Loy A, Jørgensen BB, Brüchert V
    2016 - ISME J, 10: 796–809

    Abstract: 

    Temperature has a fundamental impact on the metabolic rates of microorganisms and strongly influences microbial ecology and biogeochemical cycling in the environment. In this study, we examined the catabolic temperature response of natural communities of sulfate-reducing microorganisms (SRM) in polar, temperate, and tropical marine sediments. In short-term sediment incubation experiments with 35S-sulfate, we demonstrated how the cardinal temperatures for sulfate reduction correlate with mean annual sediment temperatures, indicating specific thermal adaptations of the dominant SRM in each of the investigated ecosystems. The community structure of putative SRM in the sediments, as revealed by pyrosequencing of bacterial 16S rRNA gene amplicons and phylogenetic assignment to known SRM taxa, consistently correlated with in situ temperatures, but not with sediment organic carbon concentrations or C:N ratios of organic matter. Additionally, several species-level SRM phylotypes of the class Deltaproteobacteria tended to co-occur at sites with similar mean annual temperatures, regardless of geographic distance. The observed temperature adaptations of SRM imply that environmental temperature is a major controlling variable for physiological selection and ecological and evolutionary differentiation of microbial communities.

  • Response of the bacterial community associated with a cosmopolitan marine diatom to crude oil shows a preference for the biodegradation of aromatic hydrocarbons.

    Mishamandani S, Gutierrez T, Berry D, Aitken MD
    2016 - Environ. Microbiol., 6: 1817-33

    Abstract: 

    Emerging evidence shows that hydrocarbonoclastic bacteria (HCB) may be commonly found associated with phytoplankton in the ocean, but the ecology of these bacteria and how they respond to crude oil remains poorly understood. Here, we used a natural diatom-bacterial assemblage to investigate the diversity and response of HCB associated with a cosmopolitan marine diatom, Skeletonema costatum, to crude oil. Pyrosequencing analysis and qPCR revealed a dramatic transition in the diatom-associated bacterial community, defined initially by a short-lived bloom of Methylophaga (putative oil degraders) that was subsequently succeeded by distinct groups of HCB (Marinobacter, Polycyclovorans, Arenibacter, Parvibaculum, Roseobacter clade), including putative novel phyla, as well as other groups with previously unqualified oil-degrading potential. Interestingly, these oil-enriched organisms contributed to the apparent and exclusive biodegradation of substituted and non-substituted polycyclic aromatic hydrocarbons (PAHs), thereby suggesting that the HCB community associated with the diatom is tuned to specializing in the degradation of PAHs. Furthermore, the formation of marine oil snow (MOS) in oil-amended incubations was consistent with its formation during the Deepwater Horizon oil spill. This work highlights the phycosphere of phytoplankton as an underexplored biotope in the ocean where HCB may contribute importantly to the biodegradation of hydrocarbon contaminants in marine surface waters.

  • Ecophysiology of an uncultivated lineage of Aigarchaeota from an oxic, hot spring filamentous 'streamer' community.

    Beam JP, Jay ZJ, Schmid MC, Rusch DB, Romine MF, M Jennings Rd, Kozubal MA, Tringe SG, Wagner M, Inskeep WP
    2016 - ISME J, 1: 210-224

    Abstract: 

    The candidate archaeal phylum 'Aigarchaeota' contains microorganisms from terrestrial and subsurface geothermal ecosystems. The phylogeny and metabolic potential of Aigarchaeota has been deduced from several recent single-cell amplified genomes; however, a detailed description of their metabolic potential and in situ transcriptional activity is absent. Here, we report a comprehensive metatranscriptome-based reconstruction of the in situ metabolism of Aigarchaeota in an oxic, hot spring filamentous 'streamer' community. Fluorescence in situ hybridization showed that these newly discovered Aigarchaeota are filamentous, which is consistent with the presence and transcription of an actin-encoding gene. Aigarchaeota filaments are intricately associated with other community members, which include both bacteria (for example, filamentous Thermocrinis spp.) and archaea. Metabolic reconstruction of genomic and metatranscriptomic data suggests that this aigarchaeon is an aerobic, chemoorganoheterotroph with autotrophic potential. A heme copper oxidase complex was identified in the environmental genome assembly and highly transcribed in situ. Potential electron donors include acetate, fatty acids, amino acids, sugars and aromatic compounds, which may originate from extracellular polymeric substances produced by other microorganisms shown to exist in close proximity and/or autochthonous dissolved organic carbon (OC). Transcripts related to genes specific to each of these potential electron donors were identified, indicating that this aigarchaeon likely utilizes several OC substrates. Characterized members of this lineage cannot synthesize heme, and other cofactors and vitamins de novo, which suggests auxotrophy. We propose the name Candidatus 'Calditenuis aerorheumensis' for this aigarchaeon, which describes its filamentous morphology and its primary electron acceptor, oxygen.

  • Gypsum amendment to rice paddy soil stimulated bacteria involved in sulfur cycling but largely preserved the phylogenetic composition of the total bacterial community

    Wörner S, Zecchin S, Dan J, Hristova Todorova N, Loy A, Conrad R, Pester M
    2016 - Environ Microbiol Rep, 8: 413-23

    Abstract: 

    Rice paddies are indispensable for human food supply but emit large amounts of the greenhouse gas methane. Sulfur cycling occurs at high rates in these water-submerged soils and controls methane production, an effect that is increased by sulfate-containing fertilizers or soil amendments. We grew rice plants until their late vegetative phase with and without gypsum (CaSO4 ·2H2 O) amendment and identified responsive bacteria by 16S rRNA gene amplicon sequencing. Gypsum amendment decreased methane emissions by up to 99% but had no major impact on the general phylogenetic composition of the bacterial community. It rather selectively stimulated or repressed a small number of 129 and 27 species-level operational taxonomic units (OTUs) (out of 1,883-2,287 observed) in the rhizosphere and bulk soil, respectively. Gypsum-stimulated OTUs were affiliated with several potential sulfate-reducing (Syntrophobacter, Desulfovibrio, unclassified Desulfobulbaceae, unclassified Desulfobacteraceae) and sulfur-oxidizing taxa (Thiobacillus, unclassified Rhodocyclaceae), while gypsum-repressed OTUs were dominated by aerobic methanotrophs (Methylococcaceae). Abundance correlation networks suggested that two abundant (>1%) OTUs (Desulfobulbaceae, Rhodocyclaceae) were central to the reductive and oxidative parts of the sulfur cycle.

Book chapters and other publications

5 Publications found
  • Candidatus Nitrosotenuis

    Herbold CW, Lebedeva E, Palatinszky M, Wagner M
    2016 - 1-9. in Bergey’s Manual of Systematics of Archaea and Bacteria. (William B. Whitman). John Wiley & Sons, Chichester, England
    Nitrosotenuis

    Abstract: 

    Candidatus Nitrosotenuis is a genus of Thaumarchaeota that can be found widely distributed in soils, freshwater, hot springs, the subsurface, and activated sludge. They may be rods or spheres and may or may not have flagella. Like other known and described Thaumarchaeota, Ca. Nitrosotenuis are aerobic chemolithautotrophs that use energy gained from the oxidation of ammonia to nitrite to fix carbon via modified 3-hydroxypropionate/4-hydroxybutyrate carbon fixation pathway. At this time, no pure culture of Ca. Nitrosotenuis exists, but some of the six available enrichments with members of the genus are almost pure. It remains to be  demonstrated whether the remaining bacterial contaminants provide essential compounds to Ca. Nitrosotenuis. Enrichments of Ca. Nitrosotenuis are intolerant to high salinity (>0.3%), although they are phylogenetically related to the Group I.1a Thaumarchaeota (Nitrosopumilaceae), which includes taxa that are widely distributed in the ocean.

    1.  

  • Stability, Mobility, Delivery and Fate of optimized NPs under Field Relevant Conditions

    Malfatti SE, Thilo Hofmann
    2016 - in press
  • Candidatus Nitrosotenuaceae

    Herbold CW, Lebedeva E, Palatinszky M, Wagner M
    2016 - 1-5. in Bergey’s Manual of Systematics of Archaea and Bacteria. (William B. Whitman)). John Wiley & Sons, Chichester, England

    Abstract: 

    Candidatus Nitrosotenuaceae is a family of Thaumarchaeota that consists of a single genus, Ca. Nitrosotenuis, which can be found widely distributed in soils, freshwater, hot springs, the subsurface, and activated sludge. They may be rods or spheres and may or may not have flagella. Similar to other known and described Thaumarchaeota, Ca. Nitrosotenuaceae are aerobic chemolithautotrophs that use energy gained from the oxidation of ammonia to nitrite to fix carbon via modified 3-hydroxypropionate/4 –hydroxybutyrate carbon fixation pathway. At this time, no pure culture of Ca. Nitrosotenuaceae exists, but some of the six available enrichments with members of the genus are almost pure. It remains to be demonstrated whether the remaining bacterial contaminants provide essential compounds to Ca. Nitrosotenuaceae. Enrichments of Ca. Nitrosotenuaceae are intolerant to high salinity (>0.3%), although they are phylogenetically related to the Group I.1a Thaumarchaeota (Ca. Nitrosopumilaceae), which includes taxa that are widely distributed in the ocean.

  • Making It Stick: A Compelling Case for Precision Microbiome Reconstitution

    Berry D
    2016 - 20: 415-417

    Abstract: 

    Modification of the intestinal microbiome is an emerging target to improve health and prevent or treat a number of diseases. In this issue of Cell Host & Microbe, Maldonado-Gomez et al. (2016) uncover the basic principles that govern the successful establishment and persistence of an exogenously introduced gut bacterium.

  • The emerging view of Firmicutes as key fibre degraders in the human gut

    Berry D
    2016 - Environ. Microbiol., 7: 2081-3
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