Metamenu

Publications

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Publications in peer reviewed journals

90 Publications found
  • Phytosiderophore-induced mobilization and uptake of Cd, Cu, Fe, Ni, Pb and Zn by wheat plants grown on metal-enriched soils

    Puschenreiter M, Gruber B, Wenzel WW, Schindlegger Y, Hann S, Spangl B, Schenkeveld WDC, Kraemer SM, Oburger E
    2017 - Environmental and Experimental Botany, 138: 67-76

    Abstract: 

    We investigated to which extent phytosiderophores (PS), released by grasses for the acquisition of iron, solubilize other metals in contaminated soils, and how this affects metal mobilization and uptake in wheat plants. A plant-based bioassay (‘RHIZOtest’) and batch extraction scheme were carried out for assessing metal mobilisation in soil, PS exudation and metal accumulation in wheat. Increased PS exudation was observed in Fe-deficient wheat, leading to enhanced Zn, Cu, Mn and Ni concentrations in wheat shoots on some soils. In contrast, plant Cd and Pb concentrations were not affected. Likewise, in the batch experiment, strongly increased extractable Cu, Ni and Zn concentrations were observed, in particular when 100 or 1000 μM PS were added. Our results suggest that Fe deficiency can enhance the accumulation of some metals in shoots of grass species. Although our results indicate that the risk of enhanced accumulation of Cd and Pb in Fe deficient wheat shoots is rather small, further experiments conducted on soil for the complete vegetation period would be needed to confirm this observation.

  • Single-particle multi-element fingerprinting (spMEF) using inductively-coupled plasma time-of-flight mass spectrometry (ICP-TOFMS) to identify engineered nanoparticles against the elevated natural background in soils

    Antonia Praetorius, Alexander Gundlach-Graham, Eli Goldberg, Willi Fabienke, Jana Navratilova, Andreas Gondikas, Ralf Kaegi, Detlef Günther, Thilo Hofmann, Frank von der Kammer
    2017 - Environmental Science: Nano, 2: 307-314

    Abstract: 

    The discrimination of engineered nanoparticles (ENPs) from the natural geogenic background is one of the preeminent challenges for assessing their potential implications. At low ENP concentrations, most conventional analytical techniques are not able to take advantage of inherent differences (e.g. in terms of composition, isotopic signatures, element ratios, structure, shape or surface characteristics) between ENPs and naturally occurring nanoscale particles (NNPs) of similar composition. Here, we present a groundbreaking approach to overcome these limitations and enable the discrimination of man-made ENPs from NNPs through simultaneous detection of multiple elements on an individual particle level. This new analytical approach is accessible by an inductively-coupled plasma time-of-flight mass spectrometer (ICP-TOFMS) operated in single-particle mode. Machine learning is employed to classify ENPs and NNPs based on their unique elemental fingerprints and quantify their concentrations. We demonstrate the applicability of this single-particle multi-element fingerprinting (spMEF) method by distinguishing engineered cerium oxide nanoparticles (CeO2 ENPs) from natural Ce-containing nanoparticles (Ce-NNPs) in soils at environmentally relevant ENP concentrations, orders of magnitude below the natural background.

  • Effect of boron on reactivity and apparent corrosion rate of microscale zerovalent irons

    Milica Velimirovic, Per-Olof Larsson, Queenie Simons, Leen Bastiaens
    2017 - Journal of Environmental Chemical Engineering, 5: 1892-1898

    Abstract: 

    The reactivity and apparent corrosion rate of newly produced boron-alloyed microscale zerovalent iron (mZVI) particles toward a variety of chlorinated aliphatic hydrocarbons (CAHs) were assessed in laboratory-scale batch reactors. For comparison, commercially available nanoscale zerovalent irons (nZVIs) were also included in the study. Based on mass normalized (kM) pseudo first-order degradation rate constants, the reactivity of boron-alloyed mZVIs appeared to be one order of magnitude lower than most reactive nZVI. However, specific surface area normalized reaction rate constants (kSA) were 1–2 orders of magnitude higher than for nZVIs showing that boron-alloyed mZVIs can compete with nZVIs. The high reactivity of boron-alloyed mZVIs was attributed to (1) the prevented iron surface passivation during anaerobic corrosion due to the simultaneous iron and boron dissolution kinetics preventing the formation of insoluble oxidized iron species, (2) the involvement of boron in facilitating electron transfer by inducing β-elimination followed by hydrogenation to ethane and/or (3) involvement of boron in improved particle size reduction during milling process leading to increased active surface areas of the particles. Results of this study suggest that boron-alloyed mZVIs could be an efficient alternative to nZVIs for in situ groundwater remediation of different CAHs in terms of their reactivity and apparent corrosion rate.

  • Mineral-Associated Soil Carbon is Resistant to Drought but Sensitive to Legumes and Microbial Biomass in an Australian Grassland

    Canarini A, Mariotte P, Ingram L, Merchant A, Dijkstra FA
    2017 - Ecosystems, e-publication, 1-15

    Abstract: 

    Drought is predicted to increase in many areas of the world with consequences for soil carbon (C) dynamics. Plant litter, root exudates and microbial biomass can be used as C substrates to form organo-mineral complexes. Drought effects on plants and microbes could potentially compromise these relative stable soil C pools, by reducing plant C inputs and/or microbial activity. We conducted a 2-year drought experiment using rainout shelters in a semi-natural grassland. We measured aboveground biomass and C and nitrogen (N) in particulate organic matter (Pom), the organo-mineral fraction (Omin), and microbial biomass within the first 15 cm of soil. Aboveground plant biomass was reduced by 50% under drought in both years, but only the dominant C4 grasses were significantly affected. Soil C pools were not affected by drought, but were significantly higher in the relatively wet second year compared to the first year. Omin-C was positively related to microbial C during the first year, and positively related to clay and silt content in the second year. Increases in Omin-C in the second year were explained by increases in legume biomass and its effect on Pom-N and microbial biomass N (MBN) through structural equation modeling. In conclusion, soil C pools were unaffected by the drought treatment. Drought resistant legumes enhanced formation of organo-mineral complexes through increasing Pom-N and MBN. Our findings also indicate the importance of microbes for the formation of Omin-C as long as soil minerals have not reached their maximum capacity to bind with C (that is, saturation).

  • Biochar total surface area and total pore volume determined by N2 and CO2 physisorption are strongly influenced by degassing temperature

    Gabriel Sigmund, Thorsten Hüffer, Thilo Hofmann, Melanie Kah
    2017 - Science of The Total Environment, 770-775

    Abstract: 

    The surface area and pore volume of carbonaceous materials, which are commonly determined by N2 and/or CO2 gas-physisorption, are important parameters when describing environmental processes such as adsorption. Their measurement requires prior degassing of samples, which can change the nature of the material. Current guidelines for biochar characterization recommend different degassing temperatures. To investigate how degassing temperatures affect gas-physisorption we systematically degassed a range of materials (four biochars, carbon nanotubes, and Al2O3 reference material) at different temperatures (105, 150, 200, 250 and 300 °C; for ≥ 14 h each). Degassing temperatures had no effect on Al2O3 or carbon nanotubes but the measured surface areas and pore volumes of biochars increased by up to 300% with degassing temperature. An equation is presented for predicting surface area obtained at different degassing temperatures. Elemental analysis and results from sorption batch experiments suggest that surface area and pore volume may increase as biochar components volatilize during degassing. Our results showed that degassing temperatures change material properties and influence gas-physisorption measurements, and therefore need to be standardized. These results may also apply to the characterization of other complex materials, including carbon nanotubes coated with natural organic matter and fouled activated carbon.

  • Nitrogen Metabolism Genes from Temperate Marine Sediments

    Carolina Reyes, Dominik Schneider, Marko Lipka, Andrea Thürmer, Michael E. Böttcher, Michael W. Friedrich
    2017 - Marine Biotechnology, 2: 175-190

    Abstract: 

    In this study, we analysed metagenomes along with biogeochemical profiles from Skagerrak (SK) and Bothnian Bay (BB) sediments, to trace the prevailing nitrogen pathways. NO3  was present in the top 5 cm below the sediment-water interface at both sites. NH4 + increased with depth below 5 cm where it overlapped with the NO3  zone. Steady-state modelling of NO3 and NH4 + porewater profiles indicates zones of net nitrogen species transformations. Bacterial protease and hydratase genes appeared to make up the bulk of total ammonification genes. Genes involved in ammonia oxidation (amohao), denitrification (nirnor), dissimilatory NO3  reduction to NH4 + (nfr and otr) and in both of the latter two pathways (narnap) were also present. Results show ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) are similarly abundant in both sediments. Also, denitrification genes appeared more abundant than DNRA genes. 16S rRNA gene analysis showed that the relative abundance of the nitrifying group Nitrosopumilales and other groups involved in nitrification and denitrification (NitrobacterNitrosomonasNitrospiraNitrosococcus and Nitrosomonas) appeared less abundant in SK sediments compared to BB sediments. Beggiatoa and Thiothrix 16S rRNA genes were also present, suggesting chemolithoautotrophic NO3  reduction to NO2  or NH4 + as a possible pathway. Our results show the metabolic potential for ammonification, nitrification, DNRA and denitrification activities in North Sea and Baltic Sea sediments.

  • Astrobiology as a framework for investigating antibiotic susceptibility: a study of Halomonas hydrothermalis

    Harrison JP, Angel R, Cockell CS
    2017 - J R Soc Interface, 126: online only

    Abstract: 

    Physical and chemical boundaries for microbial multiplication on Earth are strongly influenced by interactions between environmental extremes. However, little is known about how interactions between multiple stress parameters affect the sensitivity of microorganisms to antibiotics. Here, we assessed how 12 distinct permutations of salinity, availability of an essential nutrient (iron) and atmospheric composition (aerobic or microaerobic) affect the susceptibility of a polyextremotolerant bacterium, Halomonas hydrothermalis, to ampicillin, kanamycin and ofloxacin. While salinity had a significant impact on sensitivity to all three antibiotics (as shown by turbidimetric analyses), the nature of this impact was modified by iron availability and the ambient gas composition, with differing effects observed for each compound. These two parameters were found to be of particular importance when considered in combination and, in the case of ampicillin, had a stronger combined influence on antibiotic tolerance than salinity. Our data show how investigating microbial responses to multiple extremes, which are more representative of natural habitats than single extremes, can improve our understanding of the effects of antimicrobial compounds and suggest how studies of habitability, motivated by the desire to map the limits of life, can be used to systematically assess the effectiveness of antibiotics.

  • Post photosynthetic carbon partitioning to sugar alcohols and consequences for plant growth

    Dumschott K, Richter A, Loescher W, Merchant A
    2017 - Phytochemistry, 144: 243-252

    Abstract: 

    The occurrence of sugar alcohols is ubiquitous among plants. Physiochemical properties of sugar alcohols suggest numerous primary and secondary functions in plant tissues and are often well documented. In addition to functions arising from physiochemical properties, the synthesis of sugar alcohols may have significant influence over photosynthetic, respiratory, and developmental processes owing to their function as a large sink for photosynthates. Sink strength is demonstrated by the high concentrations of sugar alcohols found in plant tissues and their ability to be readily transported. The plant scale distribution and physiochemical function of these compounds renders them strong candidates for functioning as stress metabolites. Despite this, several aspects of sugar alcohol biosynthesis and function are poorly characterised namely: 1) the quantitative characterisation of carbon flux into the sugar alcohol pool; 2) the molecular control governing sugar alcohol biosynthesis on a quantitative basis; 3) the role of sugar alcohols in plant growth and ecology; and 4) consequences of sugar alcohol synthesis for yield production and yield quality. We highlight the need to adopt new approaches to investigating sugar alcohol biosynthesis using modern technologies in gene expression, metabolic flux analysis and agronomy. Combined, these approaches will elucidate the impact of sugar alcohol biosynthesis on growth, stress tolerance, yield and yield quality.

  • TiO2 nanomaterial detection in calcium rich matrices by spICPMS. A matter of resolution and treatment

    Mickaël Tharaud, Andreas P. Gondikas, Marc F. Benedetti, Frank von der Kammer, Thilo Hofmann, Geert Cornelis
    2017 - Journal of Analytical Atomic Spectrometry, 7: 1400-1411

    Abstract: 

    High Ca concentrations in complex matrices such as river waters often hamper the detection of titanium nanomaterials (TiO2 NPs) by single particle inductively coupled plasma mass spectrometry (spICPMS), because of isobaric interference of 48Ca on the most abundant Ti isotope (48Ti). Several approaches were used to reduce this interference while measuring TiO2 in solutions with different Ca concentrations up to 100 mg L−1. ICP-MS/MS was used with ammonia as the reaction cell gas and high resolution (HR) ICP-MS was used under different resolution settings. These approaches were compared by measuring different Ti isotopes (47Ti and 49Ti). spICPMS data were then treated with a deconvolution method to filter out dissolved signals and identify the best approach to detect the lowest possible corresponding spherical size of TiO2 NPs (Dmin). ICP-MS/MS allowed for an important decrease of the theoretical Dmin compared to standard quadrupole ICP-MS, down to 64 nm in ultrapure water; however the sensitivity was reduced by the reaction gas and increasing Ca concentrations also increased the Dmin. The comparably higher sensitivity of HR-ICP-MS allowed for theoretically measuring a Dmin of 10 nm in ultrapure water. Combined with the deconvolution analysis, the highest resolution mode in HR-ICP-MS leads to the lowest Dmin at high Ca concentrations, even though significant broadening of the measured mass distributions occurred for TiO2 NPs at Ca concentrations up to 100 mg L−1.

  • The effect of pH, electrolytes and temperature on the rhizosphere geochemistry of phytosiderophores

    M. Walter, Stephan M. Kraemer, W. D. C. Schenkeveld
    2017 - Plant and Soil, 1: 5-23
  • Bioavailability and toxicity of pyrene in soils upon biochar and compost addition

    Lucie Bielská, Melanie Kah, Gabriel Sigmund, Thilo Hofmann, Sebastian Höss
    2017 - Science of The Total Environment, 132-140

    Abstract: 

    The study investigates the role of biochar and/or compost in mitigating the toxic effects of pyrene in soils using reproduction of nematodes and porewater concentration as measures of pyrene toxicity and bioavailability, respectively. Two soils were spiked with increasing levels of pyrene to achieve a concentration-response relationship for the reproduction of Caenorhabditis elegans. The observed EC50 values (pyrene concentration causing 50% inhibition of reproduction) were 14 mg/kg and 31 mg/kg (dry mass) for these soils, corresponding to equilibrium porewater concentrations of 37 μg/L and 47 μg/L, respectively. Differences in organic carbon content were not sufficient to explain the variability in toxicity between the different soils. Soils causing a significant inhibition of reproduction were further amended with 10%-compost, 5%-biochar, or both, and the effects on reproduction and porewater concentration determined. Combined addition of compost and biochar was identified as the most effective strategy in reducing pyrene concentration in soil porewater, which was also partly reflected in soil toxicity. However, porewater concentrations predicted only 52% of pyrene toxicity to nematodes, pointing to particle-bound or dietary exposure pathways.

    Capsule: Amending pyrene-spiked soil with biochar and compost effectively reduced pyrene porewater concentrations and toxicity to nematodes, which were significantly related.

  • Fish as bioindicators for trace element pollution from two contrasting lakes in the Eastern Rift Valley, Kenya: spatial and temporal aspects

    Christof Plessl, Elick O. Otachi, Proc. Natl. Acad. Sci. USA, Annemariè Avenant-Oldewage, Franz Jirsa
    2017 - Environmental Science and Pollution Research, 2: 19767-19776

    Abstract: 

    Lake Turkana and Lake Naivasha are two freshwater lakes in the Kenyan Rift Valley that differ significantly in water chemistry and anthropogenic influence: Lake Turkana is believed to be rather pristine and unpolluted, but a previous study has shown rather high levels of Li, Zn, and Cd in the migratory fish species Hydrocynus forskahlii, questioning this pristine status. Lake Naivasha is heavily influenced by agricultural activity in its catchment area and by direct water use, and high levels of metal pollutants have been reported in fish. This study presents the distribution of nine important trace elements in liver and muscle of the nonmigratory red belly tilapia Tilapia zillii from Lake Turkana and from Lake Naivasha (before and after a significant rise in water level due to as yet not fully understood reasons). In addition, trace element levels in the common carp Cyprinus carpio from Lake Naivasha are presented. Metal concentrations measured in the liver and muscle of T. zillii collected in Lake Turkana confirm the pristine status of the study site, but contrast with the results obtained for the migratory H. forskahlii. Comparing T. zillii from the two lakes reveals a clear difference in accumulation patterns between essential and nonessential trace elements: physiologically regulated essential elements are present in a very similar range in fish from both lakes, while levels of nonessential metals reflect short- or long-term exposure to those elements. The comparison of trace element concentrations in the fish samples from Lake Naivasha showed lower levels of most trace elements after the significant increase of the water level. This study demonstrates that fish are valuable bioindicators for evaluating trace element pollution even in contrasting lakes as long as the way-of-life habits of the species are taken into account.

  • Decoupling of microbial carbon, nitrogen, and phosphorus cycling in response to extreme temperature events

    Mooshammer M, Hofhansl F, Frank AH, Wanek W, Hämmerle I, Leitner S, Schnecker J, Wild B, Watzka M, Keiblinger KM, Zechmeister­‐Boltenstern S, Richter A
    2017 - Science Advances, 3: 13

    Abstract: 

    Predicted changes in the intensity and frequency of climate extremes urge a better mechanistic understanding of the
    stress response of microbially mediated carbon (C) and nutrient cycling processes. We analyzed the resistance and
    resilience of microbial C, nitrogen (N), and phosphorus (P) cycling processes and microbial community composition
    in decomposing plant litter to transient, but severe, temperature disturbances, namely, freeze-thaw and heat. Disturbances
    led temporarily to a more rapid cycling of C and N but caused a down-regulation of P cycling. In contrast to the
    fast recovery of the initially stimulated C and N processes, we found a slow recovery of P mineralization rates, which
    was not accompanied by significant changes in community composition. The functional and structural responses to
    the two distinct temperature disturbances were markedly similar, suggesting that direct negative physical effects and
    costs associated with the stress response were comparable. Moreover, the stress response of extracellular enzyme
    activities, but not that of intracellular microbial processes (for example, respiration or N mineralization), was
    dependent on the nutrient content of the resource through its effect on microbial physiology and community
    composition. Our laboratory study provides novel insights into the mechanisms of microbial functional stress responses
    that can serve as a basis for field studies and, in particular, illustrates the need for a closer integration of
    microbial C-N-P interactions into climate extremes research.

  • Phytosiderophore-induced mobilization and uptake of Cd, Cu, Fe, Ni, Pb and Zn by wheat plants grown on metal-enriched soils

    Markus Puschenreiter, Barbara Gruber, Walter W. Wenzel, Yvonne Schindlegger, Stephan Hann, Bernhard Spangl, Walter D.C. Schenkeveld, Stephan M. Kraemer, Eva Oburger
    2017 - Environmental and Experimental Botany, 67-76

    Abstract: 

    We investigated to which extent phytosiderophores (PS), released by grasses for the acquisition of iron, solubilize other metals in contaminated soils, and how this affects metal mobilization and uptake in wheat plants. A plant-based bioassay (‘RHIZOtest’) and batch extraction scheme were carried out for assessing metal mobilisation in soil, PS exudation and metal accumulation in wheat. Increased PS exudation was observed in Fe-deficient wheat, leading to enhanced Zn, Cu, Mn and Ni concentrations in wheat shoots on some soils. In contrast, plant Cd and Pb concentrations were not affected. Likewise, in the batch experiment, strongly increased extractable Cu, Ni and Zn concentrations were observed, in particular when 100 or 1000 μM PS were added. Our results suggest that Fe deficiency can enhance the accumulation of some metals in shoots of grass species. Although our results indicate that the risk of enhanced accumulation of Cd and Pb in Fe deficient wheat shoots is rather small, further experiments conducted on soil for the complete vegetation period would be needed to confirm this observation.

  • Novel Multi-isotope Tracer Approach To Test ZnO Nanoparticle and Soluble Zn Bioavailability in Joint Soil Exposures

    Adam Laycock, Ana Romero-Freire, Jens Najorka, Claus Svendsen, Cornelis A. M. van Gestel, Mark Rehkämper
    2017 - Environmental Science & Technology, 2: 12756-12763

    Abstract: 

    Here we use two enriched stable isotopes, 68Znen and 64Znen (>99%), to prepare 68ZnO nanoparticles (NPs) and soluble 64ZnCl2. The standard LUFA 2.2 test soil was dosed with 68ZnO NPs and soluble 64ZnCl2 to 5 mg kg–1 each, plus between 0 and 95 mg kg–1 of soluble ZnCl2 with a natural isotope composition. After 0, 1, 3, 6, and 12 months of soil incubation, earthworms (Eisenia andrei) were introduced for 72 h exposures. Analyses of soils, pore waters, and earthworm tissues using multiple collector inductively coupled plasma mass spectrometry allowed the simultaneous measurement of the diagnostic 68Zn/66Zn, 64Zn/66Zn, and 68Zn/64Zn ratios, from which the three different isotopic forms of Zn were quantified. Eisenia andrei was able to regulate Zn body concentrations with no difference observed between the different total dosing concentrations. The accumulation of labeled Zn by the earthworms showed a direct relationship with the proportion of labeled to total Zn in the pore water, which increased with longer soil incubation times and decreasing soil pH. The 68Znen/64Znen ratios determined for earthworms (1.09 ± 0.04), soils (1.09 ± 0.02), and pore waters (1.08 ± 0.02) indicate indistinguishable environmental distribution and uptake of the Zn forms, most likely due to rapid dissolution of the ZnO NPs.

  • Magnitude and Mechanism of Siderophore-Mediated Competition at Low Iron Solubility in the Pseudomonas aeruginosa Pyochelin System

    Konstanze T. Schiessl, Elisabeth M.-L. Janssen, Stephan M. Kraemer, Kristopher McNeill, Martin Ackermann
    2017 - Frontiers in microbiology, 8: 1964

    Abstract: 

    A central question in microbial ecology is whether microbial interactions are predominantly cooperative or competitive. The secretion of siderophores, microbial iron chelators, is a model system for cooperative interactions. However, siderophores have also been shown to mediate competition by sequestering available iron and making it unavailable to competitors. The details of how siderophores mediate competition are not well understood, especially considering the complex distribution of iron phases in the environment. One pertinent question is whether sequestering iron through siderophores can indeed be effective in natural conditions; many natural environments are characterized by large pools of precipitated iron, and it is conceivable that any soluble iron that is sequestered by siderophores is replenished by the dissolution of these precipitated iron sources. Our goal here was to address this issue, and investigate the magnitude and mechanism of siderophore-mediated competition in the presence of precipitated iron. We combined experimental work with thermodynamic modeling, using Pseudomonas aeruginosa as a model system and ferrihydrite precipitates as the iron source with low solubility. Our experiments show that competitive growth inhibition by the siderophore pyochelin is indeed efficient, and that inhibition of a competitor can even have a stronger growth-promoting effect than solubilization of precipitated iron. Based on the results of our thermodynamic models we conclude that the observed inhibition of a competitor is effective because sequestered iron is only very slowly replenished by the dissolution of precipitated iron. Our research highlights the importance of competitive benefits mediated by siderophores, and underlines that the dynamics of siderophore production and uptake in environmental communities could be a signature of competitive, not just cooperative, dynamics.

  • Nanoscale Coloristic Pigments: Upper Limits on Releases from Pigmented Plastic during Environmental Aging, In Food Contact, and by Leaching

    Nicole Neubauer, Lorette Scifo, Jana Navratilova, Andreas Gondikas, Aiga Mackevica, Daniel Borschneck, Perrine Chaurand, Vladimir Vidal, Jerome Rose, Frank von der Kammer, Wendel Wohlleben
    2017 - Environmental Science & Technology, 2: 11669-11680

    Abstract: 

    The life cycle of nanoscale pigments in plastics may cause environmental or human exposure by various release scenarios. We investigated spontaneous and induced release with mechanical stress during/after simulated sunlight and rain degradation of polyethylene (PE) with organic and inorganic pigments. Additionally, primary leaching in food contact and secondary leaching from nanocomposite fragments with an increased surface into environmental media was examined. Standardized protocols/methods for release sampling, detection, and characterization of release rate and form were applied: Transformation of the bulk material was analyzed by Scanning Electron Microscopy (SEM), X-ray-tomography and Fourier-Transform Infrared spectroscopy (FTIR); releases were quantified by Inductively Coupled Plasma Mass Spectrometry (ICP-MS), single-particle-ICP-MS (sp-ICP-MS), Transmission Electron Microscopy (TEM), Analytical Ultracentrifugation (AUC), and UV/Vis spectroscopy. In all scenarios, the detectable particulate releases were attributed primarily to contaminations from handling and machining of the plastics, and were not identified with the pigments, although the contamination of 4 mg/kg (Fe) was dwarfed by the intentional content of 5800 mg/kg (Fe as Fe2O3 pigment). We observed modulations (which were at least partially preventable by UV stabilizers) when comparing as-produced and aged nanocomposites, but no significant increase of releases. Release of pigments was negligible within the experimental error for all investigated scenarios, with upper limits of 10 mg/m2 or 1600 particles/mL. This is the first holistic confirmation that pigment nanomaterials remain strongly contained in a plastic that has low diffusion and high persistence such as the polyolefin High Density Polyethylene (HDPE).

  • Interactions between aromatic hydrocarbons and functionalized C60 fullerenes insights from experimental data and molecular modelling

    Thorsten Hüffer, Huichao Sun, James D. Kubicki, Thilo Hofmann, Melanie Kah
    2017 - Environmental Science: Nano, 5: 1045-1053

    Abstract: 

    Understanding molecular interactions between organic compounds and carbon-based nanomaterials is crucial to the interpretation of phase transfer processes, both in technical applications and within the environment. There is, however, little information available on the interactions between organic compounds and C60 fullerenes, in particular regarding the effects of functionalization. Experimental sorption isotherms and molecular modelling have therefore been used to systematically investigate how these interactions are affected by functionalization of the sorbate (using one, two and four ring aromatics, with –OH or –NH2functional groups) and the sorbent (i.e., C60 and C60-OH). Functionalization of the sorbent, as well as hydroxyl- and amino-functionalization of the sorbate, had a significant effect on sorption. The enhanced sorption of hydroxyl- and amino-functionalized sorbates by C60 may be due to an increased contribution from π–π electron donor–acceptor interactions. Additional hydrogen bond interactions with C60-OH also appear to play an important role. Our results emphasize that the surface chemistry of C60 is of critical importance to their interactions with organic compounds. The ageing of C60 in technical applications, or in the environment, is therefore likely to significantly affect the molecular interactions, and hence sorption strength, for polar and non-polar organic compounds.

  • Potentially Active Iron, Sulfur, and Sulfate Reducing Bacteria in Skagerrak and Bothnian Bay Sediments

    Carolina Reyes, Dominik Schneider, Andrea Thürmer, Ajinkya Kulkarni, Marko Lipka, Saar Y. Sztejrenszus, Michael E. Böttcher, Rolf Daniel, Michael W. Friedrich
    2017 - Geomicrobiology Journal, 1: 840-850

    Abstract: 

    In many marine surface sediments, the reduction of manganese (Mn) and iron (Fe) oxides is obscured by sulfate reduction, which is regarded as the predominant anaerobic microbial respiration process. However, many dissimilatory sulfate and sulfur reducing microorganisms are known to utilize alternative electron acceptors such as metal oxides. In this study, we tested whether sulfate and sulfur reducing bacteria are linked to metal oxide reduction based on biogeochemical modeling of porewater concentration profiles of Mn2+ and Fe2+ in Bothnian Bay (BB) and Skagerrak (SK) sediments. Steady-state modeling of Fe2+ and Mn2+ porewater profiles revealed zones of net Fe (0–9 cm BB; ∼10 and 20 cm SK) and Mn (0–5 cm BB; 2–8 cm SK) species transformations. 16S rRNA pyrosequencing analysis of the in-situcommunity showed that Desulfobacteraceae, Desulfuromonadaceae and Desulfobulbaceae were present in the zone of Fe-reduction of both sediments. Rhodobacteraceae were also detected at high relative abundance in both sediments. BB sediments appeared to harbor a greater diversity of potential Fe-reducers compared to SK. Additionally, when the upper 10 cm of sediment from the SK was incubated with lepidocrocite and acetate, Desulfuromonas was the dominant bacteria. Real-time quantitative polymerase chain reaction (qPCR) results showed decreasing dsrA gene copy numbers with depth coincided with decreased Fe-reduction activity. Our results support the idea that sulfur and sulfate reducing bacteria contribute to Fe-reduction in the upper centimeters of both sediments.

  • Short-term carbon input increases microbial nitrogen demand, but not microbial nitrogen mining, in a set of boreal forest soils

    Wild B, Alaei S, Bengston P, Bodé S, Boeckx P, Schnecker J, Mayerhofer W, Rütting T
    2017 - 136: 261-278

    Abstract: 

    Abstract Rising carbon dioxide (CO2) concentrations and temperatures are expected to stimulate plant productivity and ecosystem C sequestration, but these effects require a concurrent increase in N availability for plants. Plants might indirectly promote N availability as they release organic C into the soil (e.g., by root exudation) that can increase microbial soil organic matter (SOM) decomposition (‘‘priming effect’’), and possibly the enzymatic breakdown of N-rich polymers, such as proteins, into bio-available units (‘‘N mining’’). We tested the adjustment of protein depolymerization to changing soil C and N availability in a laboratory experiment. We added easily available C or N sources to six boreal forest soils, and determined soil organic C mineralization, gross protein depolymerization and gross ammonification rates (using 15N pool dilution assays), and potential extracellular enzyme activities after 1 week of incubation. Added C sources were 13C-labelled to distinguish substrate from soil derived C mineralization. Observed effects reflect short-term adaptations of non-symbiotic soil microorganisms to increased C or N availability. Although C input promoted microbial growth and N demand, we did not find indicators of increased N mobilization from SOM polymers, given that none of the soils showed a significant increase in
    protein depolymerization, and only one soil showed a significant increase in N-targeting enzymes. Instead, our findings suggest that microorganisms immobilized 
    the already available N more efficiently, as indicated by decreased ammonification and inorganic N concentrations.
    Likewise, although N input stimulated ammonification, we found no significant effect on protein depolymerization. Although our findings do not rule out in general that higher plant-soil C allocation can promote microbial N mining, they suggest that such an effect can be counteracted, at least in the short term, by increased microbial N immobilization, further aggravating plant N limitation.
     

  • Effect of ageing on the properties and polycyclic aromatic hydrocarbon composition of biochar

    Gabriel Sigmund, Thomas D. Bucheli, Isabel Hilber, Malfatti SE, Melanie Kah, Thilo Hofmann
    2017 - Environmental Science: Processes & Impacts, 5: 768-774

    Abstract: 

    The influence of ageing on biochar properties has been investigated by comparing three fresh biochars with biochars artificially aged by either H2O2 thermal oxidation or horseradish peroxidase enzymatic oxidation. In addition, a field-aged counterpart for one of the biochars was recovered from an agricultural field site, four years after application. Biochar properties, including surface areas and pore volumes (derived by N2 and CO2 physisorption) and elemental compositions, showed only minor changes following both artificial and field ageing, indicating high biochar stability. Concentrations of the 16 US EPA PAHs were measured in all of the biochars and a contaminant trap was used to investigate the effect of ageing on their bioaccessibility. The concentrations of total and bioaccessible PAHs ranged from 4.4 to 22.6 mg kg−1 and 0.0 to 9.7 mg kg−1, respectively. Concentrations of the 16 US EPA PAHs decreased following field ageing, but the proportion of low molecular weight PAHs increased. The observed changes in PAH composition with field ageing can be explained by uptake from the surrounding soil and intra-biochar transfer processes. To better understand changes in PAH composition with ageing, an additional broad range of alkylated PAHs was also analyzed in selected samples. Our results show that the tested artificial ageing protocols are unable to approximate the changes in PAH composition resulting from field ageing. Nevertheless, total and bioaccessible PAH concentrations decreased for both artificially and field-aged biochars, indicating that biochars release PAHs when they are freshly produced and that the risk of PAH release decreases with ageing.

  • Mechanism of ascaridole activation in Leishmania

    Gerald Geroldinger, Matthias Tonner, Hubert Hettegger, Markus Bacher, Lianet Monzote, Martin Walter, Katrin Staniek, Thomas Rosenau, Lars Gille
    2017 - Biochemical Pharmacology, 48-62

    Abstract: 

    Endoperoxides (EP) are an emerging class of drugs which have potential in antiparasitic therapy, but also in other fields. For malaria therapy the EP artemisinin (Art) and its derivatives are successfully used. We have shown in the past that the EP ascaridole (Asc) is useful for the treatment of cutaneous leishmaniasis in a mouse model. Biomimetic experiments suggested that these drugs need activation in the respective target pathogens to exert their function. In spite of this idea, direct activation of EP to radicals inside cells has never been demonstrated. Therefore, this study was initiated to explore the activation of Asc in biomimetic systems and inside Leishmania in comparison to Art. Using electron paramagnetic resonance spectroscopy (EPR) in combination with spin-trapping we identified the secondary alkyl radical intermediates arising from reduction by Fe2+ in cell-free systems. Combined GC/NMR analysis confirmed the loss of isopropyl residues from Asc during this process as intermediates. This activation of Asc was stimulated by low molecular Fe2+ complexes or alternatively by hemin in conjunction with thiol reductants, such as cysteine (Cys). In Leishmania tarentolae promastigotes (LtP) as model for pathogenic forms of Leishmania carbon-centered radicals were identified in the presence of Asc by EPR spin-trapping. Both Asc and Art inhibited the viability in LtP with IC50 values in the low micromolar range while IC50values for J774 macrophages were considerably higher. A similar structure without EP bridge (1,4-cineole) resulted in no detectable radicals and possessed much less cytotoxicity in LtP and no selectivity for LtP compared to J774 cells. The Asc-derived radical formation in LtP was inhibited by the iron chelator deferoxamine (DFO), and stimulated by Cys (a suitable reductant for hemin). The IC50 values for LtP viability in the presence of Asc or Art were increased significantly by the spin trap DMPO, while Cys and DFO increased only IC50 values for Art. In a heme association assay Asc demonstrated a lower binding affinity to heme than Art. ICP-OES measurements revealed that in LtP the total iron concentrations were twice as high as values in J774 macrophages. Since low molecular iron was important in Asc activation we studied the influence of Asc on the labile iron pool (LIP) in LtP. Low temperature EPR experiments demonstrated that Asc shifts the redox balance of iron in the LIP to its oxidized state. These data demonstrate that univalent cleavage of Asc/Art in LtP is an essential part of their pharmacological mechanism. The structure of the EP determines whether activation by low molecular iron or heme is favored and the availability of these intracellular activators modulates their cytotoxicity. These findings may be helpful for synthesis of new Asc derivatives and understanding the action of EP in other cell types.

  • Sedimentary sulfides

    David Rickard, Marc Mussmann, and Jeffrey A. Steadman
    2017 - Elements, 13: 117–122.
    Phylogeny of sulfide producing organisms

    Abstract: 

    Sedimentary sulfides constitute over 95% of the sulfide on the surface

    of the planet, and their formation, preservation and destruction largely

    determines the surface environment. The sulfide in sediments is mainly

    derived from the products of sulfate-reducing bacteria, which are currently

    responsible for oxidizing over half the organic matter flux reaching sediments.

    Pyrite is the mineral overwhelmingly produced. The geochemistry of pyrite,

    both in terms of its isotopic composition and its trace-element loading, has

    varied dramatically over geologic time. As such, it is a major source of our

    current understanding about the nature of the early Earth and of the Earth’s

    subsequent geochemical and biological evolution.

  • Sensitivity towards the GRP78 inhibitor KP1339/IT-139 is characterized by apoptosis induction via caspase 8 upon disruption of ER homeostasis

    Beatrix Schoenhacker-Alte, Thomas Mohr, Christine Pirker, Kushtrim Kryeziu, Paul-Steffen Kuhn, Alicia Buck, Thilo Hofmann, Christopher Gerner, Gerrit Hermann, Gunda Koellensperger, Bernhard K. Keppler, Walter Berger, Petra Heffeter
    2017 - Cancer Letters, 79-88

    Abstract: 

    The ruthenium drug and GRP78 inhibitor KP1339/IT-139 has already demonstrated promising anticancer activity in a phase I clinical trial. This study aimed to identify mechanisms underlying increased sensitivity to KP1339 treatment. Based on a screen utilizing 23 cell lines, a small panel was selected to compare KP1339-sensitive and low-responsive models. KP1339 sensitivity was neither based on differences in ruthenium accumulation, nor sensitivity to oxidative stress or constituents of KP1339 (ruthenium chloride and indazole). Subsequently, the biochemical response to KP1339 was analyzed using whole genome expression arrays indicating that, while sensitive cell lines were characterized by “response to chemical stimuli” and “regulation of cell death”, low-responsive cells preferentially activated pathways controlling cell cycle, DNA repair, and metabolism. Cell culture experiments confirmed that, while low-responsive cells executed cell cycle arrest in G2 phase, pronounced apoptosis induction via activation of caspase 8 was found in sensitive cells. Cell death induction is based on a unique disruption of the ER homeostasis by depletion of key cellular chaperones including GRP78 in combination with enhanced KP1339-mediated protein damage.

  • Sorbent material characterization using in-tube extraction needles as inverse gas chromatography column

    Xochitli L. Osorio Barajas, Maik A. Jochmann, Thorsten Hüffer, Beat Schilling, Torsten C. Schmidt
    2017 - Journal of Separation Science, 1: 2390-2397

    Abstract: 

    In‐tube extraction is a full automated enrichment technique that consists of a stainless‐steel needle, packed with sorbent material for the extraction of volatile and semivolatile compounds. In principle, all particulate sorbents used for enrichment in air or headspace analysis can be used. However, the selection of the sorbents is merely based on empirical considerations rather than on experimental data, which is caused by a lack of knowledge about the relevant physicochemical properties of the sorbent. Especially, the knowledge of hydrostatic, advective, diffusive, and dispersion mechanisms in addition to sorption enthalpies are important for combined transport and sorption models. To provide these missing parameters, we developed and evaluated a method in which an ordinary in‐tube extraction needle was employed directly as column for sorbent characterization by inverse gas chromatography. As probe compounds, benzene, ethyl acetate, and 3‐methyl‐1‐butanol were used to determine thermodynamic parameters such as sorption enthalpy, partitioning constant between the solid and gas phase, and kinetic parameters such as the diffusion coefficient, dispersion coefficient, and apparent permeability, exemplarily. As sorbent, three commercially available phases were characterized to demonstrate the applicability of the method.

  • Global patterns of phosphatase activity in natural soils

    Margalef O, Sardans J, Fernández-Martínez M, Molowny-Horas R, Janssens IA, Ciais P, Richter A, Obersteiner M, Asenio D, Peñuelas J
    2017 - Scientific Reports, 7: 13

    Abstract: 

    Soil phosphatase levels strongly control the biotic pathways of phosphorus (P), an essential element for
    life, which is often limiting in terrestrial ecosystems. We investigated the influence of climatic and soil
    traits on phosphatase activity in terrestrial systems using metadata analysis from published studies.
    This is the first analysis of global measurements of phosphatase in natural soils. Our results suggest
    that organic P (Porg), rather than available P, is the most important P fraction in predicting phosphatase
    activity. Structural equation modeling using soil total nitrogen (TN), mean annual precipitation, mean
    annual temperature, thermal amplitude and total soil carbon as most available predictor variables
    explained up to 50% of the spatial variance in phosphatase activity. In this analysis, Porg could not be
    tested and among the rest of available variables, TN was the most important factor explaining the
    observed spatial gradients in phosphatase activity. On the other hand, phosphatase activity was also
    found to be associated with climatic conditions and soil type across different biomes worldwide. The
    close association among different predictors like Porg, TN and precipitation suggest that P recycling is
    driven by a broad scale pattern of ecosystem productivity capacity.

  • Experimental considerations in metal mobilization from soil by chelating ligands: The influence of soil-solution ratio and pre-equilibration A case study on Fe acquisition by phytosiderophores

    W.D.C. Schenkeveld, R.L. Kimber, M. Walter, E. Oburger, M. Puschenreiter, Stephan M. Kraemer
    2017 - Science of The Total Environment, 1831-1842

    Abstract: 

    The efficiency of chelating ligands in mobilizing metals from soils and sediments is generally examined under conditions remote from those under which they are exuded or applied in the field. This may lead to incorrect estimations of the mobilizing efficiency. The aim of this study was to establish the influence of the soil solution ratio (SSR) and pre-equilibration with electrolyte solution on metal mobilization and metal displacement. For this purpose a series of interaction experiments with a calcareous clay soil and a biogenic chelating agent, the phytosiderophore 2′-deoxymugineic acid (DMA) were carried out.

    For a fixed ligand concentration, the SSR had a strong influence on metal mobilization and displacement. Metal complexation was faster at higher SSR. Reactive pools of metals that were predominantly mobilized at SSR 6 (in this case Cu), became depleted at SSR 0.1, whereas metals that were marginally mobilized at SSR 6, were dominantly mobilized at SSR 0.1 (in this case Fe), because of large soil reactive pools. For a fixed “amount of ligand”-to-“amount of soil”-ratio, metal complexation scaled linearly with the SSR. The efficiency of ligands in mobilizing metals under field conditions can be predicted with batch experiments, as long as the ligand-to-soil-ratio is matched. In most previously reported studies this criterion was not met. Equivalent metal-complex concentrations under field conditions can be back-calculated using adsorption isotherms for the respective metal-complexes.

    Drying and dry storage created labile pools of Fe, Cu and Zn, which were rapidly mobilized upon addition of DMA solution to dry soil. Pre-equilibration decreased these labile pools, leading to smaller concentrations of these metals during initial mobilization, but did not reduce the lag time between ligand addition and onset of microbial degradation of the metal-complexes. Hence SSR and pre-equilibration should be carefully considered when testing the metal mobilizing efficiency of chelating ligands.

  • Magnitude and Mechanism of Siderophore-Mediated Competition at Low Iron Solubility in the Pseudomonas aeruginosa Pyochelin System

    Konstanze T. Schiessl, Elisabeth M.-L. Janssen, Stephan M. Kraemer, Kristopher McNeill, Martin Ackermann
    2017 - Frontiers in microbiology, in press
  • Increased temperature causes different carbon and nitrogen processing patterns in two common intertidal foraminifera (Ammonia tepida and Haynesina germanica)

    Wukovits J, Enge AJ, Wanek W, Watzka M, Heinz P
    2017 - 11: 2815-2829

    Abstract: 

    Benthic foraminifera are highly abundant heterotrophic protists in marine sediments, but future environmental changes will challenge the tolerance limits of intertidal species. Metabolic rates and physiological processes in foraminifera are strongly dependent on environmental temperatures. Temperature-related stress could therefore impact foraminiferal food source processing efficiency and might result in altered nutrient fluxes through the intertidal food web. In this study, we performed a laboratory feeding experiment on Ammonia tepida and Haynesina germanica, two dominant foraminiferal species of the German Wadden Sea/Friedrichskoog, to test the effect of temperature on phytodetritus retention. The specimens were fed with C-13 and N-15 labelled freeze-dried Dunaliella tertiolecta (green algae) at the start of the experiment and were incubated at 20, 25 and 30 degrees C respectively. Dual labelling was applied to observe potential temperature effects on the relation of phytodetrital carbon and nitrogen retention. Samples were taken over a period of 2 weeks. Foraminiferal cytoplasm was isotopically analysed to investigate differences in carbon and nitrogen uptake derived from the food source. Both species showed a positive response to the provided food source, but carbon uptake rates of A. tepida were 10-fold higher compared to those of H. germanica. Increased temperatures had a far stronger impact on the carbon uptake of H. germanica than on A. tepida. A distinct increase in the levels of phytodetrital-derived nitrogen (compared to more steady carbon levels) could be observed over the course of the experiment in both species. The results suggest that higher temperatures have a significant negative effect on the carbon exploitation of H. germanica. For A. tepida, higher carbon uptake rates and the enhanced tolerance range for higher temperatures could outline an advantage in warmer periods if the main food source consists of chlorophyte phytodetritus. These conditions are likely to impact nutrient fluxes in A. tepida/H. germanica associations.

  • The effect of pH, electrolytes and temperature on the rhizosphere geochemistry of phytosiderophores

    M. Walter, Stephan M. Kraemer, W. D. C. Schenkeveld
    2017 - Plant and Soil, 1: 5-23

    Abstract: 

    Background and aims

    Graminaceous plants are grown worldwide as staple crops under a variety of climatic and soil conditions. They release phytosiderophores for Fe acquisition (Strategy II). Aim of the present study was to uncover how the rhizosphere pH, background electrolyte and temperature affect the mobilization of Fe and other metals from soil by phytosiderophores.

    Methods

    For this purpose a series of kinetic batch interaction experiments with the phytosiderophore 2′-deoxymugineic acid (DMA), a calcareous clay soil and a mildly acidic sandy soil were performed. The temperature, electrolyte concentration and applied electrolyte cation were varied. The effect of pH was examined by applying two levels of lime and Cu to the acidic soil.

    Results

    Fe mobilization by DMA increased by lime application, and was negatively affected by Cu amendment. Mobilization of Fe and other metals decreased with increasing ionic strength, and was lower for divalent than for monovalent electrolyte cations at equal ionic strength, due to higher adsorption of metal-DMA complexes to the soil. Metal mobilization rates increased with increasing temperature leading to a faster onset of competition; Fe was mobilized faster, but also became depleted faster at higher temperature. Temperature also affected biodegradation rates of metal-DMA complexes.

    Conclusion

    Rhizosphere pH, electrolyte type and concentration and temperature can have a pronounced effect on Strategy II Fe acquisition by affecting the time and concentration ‘window of Fe uptake’ in which plants can benefit from phytosiderophore-mediated Fe uptake.

  • Release of TiO2 – (Nano) particles from construction and demolition landfills

    Ralf Kaegi, Alexander Englert, Andreas Gondikas, Brian Sinnet, Frank von der Kammer, Michael Burkhardt
    2017 - NanoImpact, 73-79

    Abstract: 

    A large fraction of engineered nanomaterials (ENM) will be deposited in landfills and it is assumed that ENM are securely locked in landfill sites and cannot leach into the environment (e.g. surface waters). However, experimental evidence supporting this assumption is lacking, as current production volumes of ENM are still too small and/or analytical techniques not sensitive enough to allow for the detection and quantification of ENM in landfill leachates. TiO2 particles are currently used in large quantities, for example in construction materials such as paints and renders as white pigments and their sizes extend into the nano-size range. We, therefore, selected TiO2 particles as a surrogate to assess the potential release of ENM from construction and demolition (C&D) landfill sites. We collected leachate samples from a landfill over one year and used complementary analytical techniques, including inductively coupled plasma (ICP) – optical emission spectroscopy (OES), automated scanning electron microscopy (auto SEM), transmission electron microscopy (TEM) and single particle ICP - mass spectrometry (spICPMS) to quantify TiO2 particles in landfill leachates. Total elemental Ti contents were mostly around a few tens of μg L− 1 and were strongly correlated with total suspended solids. Based on the volumetric discharge of the landfill leachate water from the landfill, we estimate a total amount of ~ 0.5 kg of TiO2 particles that are released annually from the landfill. Ti concentrations derived from ICP-OES measurements were in good agreement with quantifications based on TiO2 particles detected by auto SEM analyses. spICPMS measurements indicated a number concentration of Ti-containing particles in the order of 105 mL− 1 and TEM analyses dominantly revealed nanoscale TiO2 particles with a spherical shape typically observed for TiO2 particles used as white pigments. In addition, angular TiO2 particles with a well-defined crystal habitus were detected, suggesting that also natural TiO2 particles of comparable sizes are present in the landfill leachates.

    The results from this study indicate that (nanoscale) TiO2 particles are released from C&D landfill sites (~ 5 g/year). Although the amount of TiO2 particles released from C&D landfill sites may still be rather low, these particles may serve as proxy for assessing the future release of ENM from C&D landfill sites, which may become relevant as an increasing use of ENM is predicted for construction materials in general.

  • Optimal metabolic regulation along resource stoichiometry gradients

    Manzoni S, Capek P, Mooshammer M, Lindahl BD, Richter A, Santruckova H
    2017 - Ecology Letters, 20: 1182-1191

    Abstract: 

    Most heterotrophic organisms feed on substrates that are poor in nutrients compared to their
    demand, leading to elemental imbalances that may constrain their growth and function. Flexible
    carbon (C)-use efficiency (CUE, C used for growth over C taken up) can represent a strategy to
    reduce elemental imbalances. Here, we argue that metabolic regulation has evolved to maximise
    the organism growth rate along gradients of nutrient availability and translated this assumption
    into an optimality model that links CUE to substrate and organism stoichiometry. The optimal
    CUE is predicted to decrease with increasing substrate C-to-nutrient ratio, and increase with
    nutrient amendment. These predictions are generally confirmed by empirical evidence from a new
    database of c. 2200 CUE estimates, lending support to the hypothesis that CUE is optimised
    across levels of organisation (microorganisms and animals), in aquatic and terrestrial systems, and
    when considering nitrogen or phosphorus as limiting nutrients.

  • Cytotoxicity of Biochar: A Workplace Safety Concern?

    Gabriel Sigmund, Daniela Huber, Thomas D. Bucheli, Martina Baumann, Nicole Borth, Georg M. Guebitz, Thilo Hofmann
    2017 - Environmental Science & Technology Letters, 9: 362-366

    Abstract: 

    Biochar has a number of environmental applications, including soil amendment for agriculture, remediation of contaminated soils and sediments, and climate change mitigation. Dust formed during its production and field application may pose a health risk, but the cytotoxicity of biochar has, to the best of our knowledge, not previously been investigated. Therefore, we measured the concentration-dependent cytotoxicity of biochar on an NIH 3T3 mouse fibroblast cell line. We used a contaminant trap experiment to measure the total and nondesorbable polycyclic aromatic hydrocarbon (PAH) fractions of the biochar. PAH release was found to be negligible because of the biochar’s strong PAH sorption potential. The biochar was nevertheless observed to have a cytotoxic effect on the fibroblast cells; the EC10 values were 49.6 and 18.8 μg/mL after incubation for 24 and 48 h, respectively. This cytotoxic effect is likely to relate to the particulate nature and size distribution of the biochar; the biochar had particles similar in size to atmospheric particulate matter (PM2.5) that bound to the fibroblast cell surface. To minimize the risk of exposure, practitioners should wear respiratory protective equipment during biochar production. During field application, biochar should be applied in slurries and should always be mixed with a soil matrix to avoid secondary dust formation.

  • Mikroplastik: Lernen aus den Fehlern der Vergangenheit

    Thilo Hofmann
    2017 - Vom Wasser - das Journal, 115: 1
  • Soil carbon loss regulated by drought intensity and available substrate: A meta-analysis

    Canarini A, Kiær LP, Dijkstra FA
    2017 - Soil Biology and Biochemistry, 112: 90-99

    Abstract: 

    Drought is one of the most important climate change factors, but its effects on ecosystems are little
    understood. While known to influence soil carbon (C) cycling, it remains unresolved if altered rainfall
    patterns induced by climate change will stimulate positive feedbacks of CO2 into the atmosphere. Using a
    meta-analysis frame-work including 1495 observations from 60 studies encompassing a variety of
    ecosystems and soil types, we investigated drought effects on respiration rates, cumulative respiration
    during drying-rewetting cycles, metabolic quotient (qCO2), dissolved organic C (DOC), microbial biomass
    and fungi to bacteria (F:B) ratios from laboratory and field experiments. We show that C-rich soils (>2%
    organic carbon) increase CO2 release into the atmosphere after intense droughts, but that C-poor soils
    show a net decline in C losses. We explain this self-reinforcing mechanism of climate change in C-rich
    soils by: (i) high substrate availability that magnify bursts of CO2 release after drought events and (ii) a
    shift in microbial community with increased loss of C per unit of biomass. These findings shed light on
    important responses of soil CO2 emissions to drought, which could either offset or facilitate positive
    feedbacks to global warming. Our results should be considered in global climate models, as even small
    changes in soil CO2 emission have large repercussions for global warming.

  • Microplastic Exposure Assessment in Aquatic Environments: Learning from Similarities and Differences to Engineered Nanoparticles

    Thorsten Hüffer, Antonia Praetorius, Stephan Wagner, Frank von der Kammer, Thilo Hofmann
    2017 - Environmental Science & Technology, 5: 2499-2507

    Abstract: 

    Microplastics (MPs) have been identified as contaminants of emerging concern in aquatic environments and research into their behavior and fate has been sharply increasing in recent years. Nevertheless, significant gaps remain in our understanding of several crucial aspects of MP exposure and risk assessment, including the quantification of emissions, dominant fate processes, types of analytical tools required for characterization and monitoring, and adequate laboratory protocols for analysis and hazard testing. This Feature aims at identifying transferrable knowledge and experience from engineered nanoparticle (ENP) exposure assessment. This is achieved by comparing ENP and MPs based on their similarities as particulate contaminants, whereas critically discussing specific differences. We also highlight the most pressing research priorities to support an efficient development of tools and methods for MPs environmental risk assessment.

  • Loss of CUL4A expression is underlying cisplatin hypersensitivity in colorectal carcinoma cells with acquired trabectedin resistance

    B Englinger, M Mair, W Miklos, C Pirker, T Mohr, S van Schoonhoven, D Lötsch, W Körner, F Ferk, S Knasmüller, P Heffeter, B K Keppler, M Grusch, W Berger
    2017 - British Journal of Cancer, 4: 489-500

    Abstract: 

    Background:

    Colorectal carcinoma (CRC) is the third most common cancer worldwide. Platinum-based anticancer compounds still constitute one mainstay of systemic CRC treatment despite limitations due to adverse effects and resistance development. Trabectedin has shown promising antitumor effects in CRC, however, again resistance development may occur. In this study, we aimed to develop strategies to circumvent or even exploit acquired trabectedin resistance in novel CRC treatment regimens.

    Methods:

    Human HCT116 CRC cells were selected for acquired trabectedin resistance in vitro and characterised by cell biological as well as bioinformatic approaches. In vivo xenograft experiments were conducted.

    Results:

    Selection of HCT116 cells for trabectedin resistance resulted in p53-independent hypersensitivity of the selected subline against cisplatin. Bioinformatic analyses of mRNA microarray data suggested deregulation of nucleotide excision repair and particularly loss of the ubiquitin ligase CUL4A in trabectedin-selected cells. Indeed, transient knockdown of CUL4A sensitised parental HCT116 cells towards cisplatin. Trabectedin selected but not parental HCT116 xenografts were significantly responsive towards cisplatin treatment.

    Conclusions:

    Trabectedin selection-mediated CUL4A loss generates an Achilles heel in CRC cancer cells enabling effective cisplatin treatment. Hence, inclusion of trabectedin in cisplatin-containing cancer treatment regimens might cause profound synergism based on reciprocal resistance prevention.

  • Microbial utilization of mineral-associated nitrogen in soils

    Turner S, Meyer-Stüve S, Schippers A, Guggenberger G, Schaarschmidt F, Wild B, Richter A, Dohrmann R, Mikutta R
    2017 - Soil Biology and Biochemistry, 104: 185-196

    Abstract: 

    In soils, a large portion of organic nitrogen (ON) is associated with minerals and thus, possibly stabilized against biological decay. We therefore tested if mineral-associated N is an important N source for soil microorganisms, and which soil parameters control its bioavailability. Microcosm experiments with mineral-associated organic matter, obtained as heavy fraction (HF) via density fractionation, and bulk soil from mineral topsoil of the Franz Josef chronosequence were conducted for 125 days. We examined the effects of O2 status, soil age (differences in mineralogical properties), as well as cellulose and phosphate additions on the turnover of mineral-associated N. Using a combination of activity measurements and quantitative PCR, microbial N transformation rates and abundances of N-related functional genes (amoAnarGchiA) were determined. Similar or higher values for microbial N cycling rates and N-related functional abundances in the HF compared to bulk soil indicated that mineral-associated N provides an important bioavailable N source for soil microorganism. The turnover of mineral-associated N was mainly controlled by the O2 status. Besides, soil mineralogical properties significantly affected microbial N cycling and related gene abundances with the effect depending on the N substrate type (ON, NH4+ or NO3). In contrast, cellulose or phosphate addition hardly enhanced microbial utilization of mineral-associated N. The results of our microcosm study indicate that mineral-associated N is highly bioavailable in mineral topsoils, but effects of the mineral phase differ between N cycling processes.

  • Organic and inorganic nitrogen uptake by 21 dominant tree species in temperate and tropical forests

    Liu M, Li C, Xu X, Wanek W, Jiang N, Wang H, Yang X
    2017 - Tree Physiology, 11: 1515-1526

    Abstract: 

    Evidence shows that many tree species can take up organic nitrogen (N) in the form of free amino acids from soils, but few studies have been conducted to compare organic and inorganic N uptake patterns in temperate and tropical tree species in relation to mycorrhizal status and successional state. We labeled intact tree roots by brief 15N exposures using field hydroponic experiments in a temperate forest and a tropical forest in China. A total of 21 dominant tree species were investigated, 8 in the temperate forest and 13 in the tropical forest. All investigated tree species showed highest uptake rates for NH4+ (ammonium), followed by glycine and NO3− (nitrate). Uptake of NH4+ by temperate trees averaged 12.8 μg N g−1 dry weight (d.w.) root h−1, while those by tropical trees averaged 6.8 μg N g−1 d.w. root h−1. Glycine uptake rates averaged 3.1 μg N g−1 d.w. root h−1 for temperate trees and 2.4 μg N g−1 d.w. root h−1 for tropical trees. NO3− uptake was the lowest (averaging 0.8 μg N g−1 d.w. root h−1 for temperate trees and 1.2 μg N g−1 d.w. root h−1 for tropical trees). Uptake of NH4+ accounted for 76% of the total uptake of all three N forms in the temperate forest and 64% in the tropical forest. Temperate tree species had similar glycine uptake rates as tropical trees, with the contribution being slightly lower (20% in the temperate forest and 23% in the tropical forest). All tree species investigated in the temperate forest were ectomycorrhizal and all species but one in the tropical forest were arbuscular mycorrhizal (AM). Ectomycorrhizal trees showed significantly higher NH4+ and lower NO3− uptake rates than AM trees. Mycorrhizal colonization rates significantly affected uptake rates and contributions of NO3− or NH4+, but depended on forest types. We conclude that tree species in both temperate and tropical forests preferred to take up NH4+, with organic N as the second most important N source. These findings suggest that temperate and tropical forests demonstrate similar N uptake patterns although they differ in physiology of trees and soil biogeochemical processes.

  • Impact of Sodium Humate Coating on Collector Surfaces on Deposition of Polymer-Coated Nanoiron Particles

    Malfatti SE, Doris Schmid, Nathan Bossa, Andreas Gondikas, Milica Velimirovic, Frank von der Kammer, Mark R. Wiesner, Thilo Hofmann
    2017 - Environmental Science & Technology, 1: 9202-9209

    Abstract: 

    The affinity between nanoscale zerovalent iron (nano-ZVI) and mineral surfaces hinders its mobility, and hence its delivery into contaminated aquifers. We have tested the hypothesis that the attachment of poly(acrylic acid)-coated nano-ZVI (PAA-nano-ZVI) to mineral surfaces could be limited by coating such surfaces with sodium (Na) humate prior to PAA-nano-ZVI injection. Na humate was expected to form a coating over favorable sites for PAA-nano-ZVI attachment and hence reduce the affinity of PAA-nano-ZVI for the collector surfaces through electrosteric repulsion between the two interpenetrating charged polymers. Column experiments demonstrated that a low concentration (10 mg/L) Na humate solution in synthetic water significantly improved the mobility of PAA-nano-ZVI within a standard sand medium. This effect was, however, reduced in more heterogeneous natural collector media from contaminated sites, as not an adequate amount of the collector sites favorable for PAA-nano-ZVI attachment within these media appear to have been screened by the Na humate. Na humate did not interact with the surfaces of acid-washed glass beads or standard Ottawa sand, which presented less surface heterogeneity. Important factors influencing the effectiveness of Na humate application in improving PAA-nano-ZVI mobility include the solution chemistry, the Na humate concentration, and the collector properties.

  • Investigation of carbon-based nanomaterials as sorbents for headspace in-tube extraction of polycyclic aromatic hydrocarbons

    Xochitli L. Osorio Barajas, Thorsten Hüffer, Pascal Mettig, Beat Schilling, Maik A. Jochmann, Torsten C. Schmidt
    2017 - Analytical and Bioanalytical Chemistry, 1: 3861-3870

    Abstract: 

    Carbon-based nanomaterials (CNM) represent promising materials for the application as sorbents in micro- and other extraction devices. In this work, we investigate the applicability of five different CNM (multi-walled carbon nanotubes (MWCNTs), fullerenes, carboxylic acid functionalized multi-walled carbon nanotubes (MWCNTs-COOH), graphene platelets, and carbon nanohorns) for their performance on PAH extraction from the aqueous phase by headspace in-tube extraction (HS-ITEX). Optimal extraction parameters for HS-ITEX were determined using a Box-Behnken experimental design. From the extraction yield response, central point analysis, fullerenes showed the best extraction properties for the eight selected headspace compatible PAHs (naphthalene, acenaphthylene, acenaphthene, fluorene, phenanthrene, anthracene, fluoranthene, and pyrene). Fullerenes were used for a further method validation including the linear range, limit of detection, precision, as well as recovery. Finally, extraction yields were compared to a commercial material (Tenax GR), demonstrating that fullerene represents a better option as sorbent in ITEX for PAH analysis. Method detection limits for the PAH on fullerene ranged from 10 to 300 ng L−1, with recoveries between 45 and 103%.

  • Rhizospheric microbial community of Caesalpinia spinosa (Mol.) Kuntze in conserved and deforested zones of the Atiquipa fog forest in Peru

    Cordero I, Ruiz-Diez B, Balaguer L, Richter A, Pueyo JJ, Rincon A
    2017 - 114: 132-141

    Abstract: 

    Caesalpinia spinosa, tara, is the predominant fog catcher tree in the fog forest of Atiquipa, a biodiversity hotspot ecosystem within the coastal Peruvian desert highly threatened by intense land use over time. We investigated the impact of deforestation, as well as potential effects of the tree age (juveniles vs adults) and the type of tree (recruited vs planted), on the rhizospheric microbial communities of tara growing in contrasting landscapes (conserved vs deforested) of the Atiquipa forest.

    We used a phospholipid fatty acids analysis approach to study the microbial community associated with tara. Additionally, we isolated and sought for native rhizospheric bacteria with plant growth promoting (PGPR) traits to be used as potential inoculants for restoration projects.

    Deforestation profoundly altered the chemical and biological fertility of soils. All rhizospheric microorganisms were clearly reduced in abundance by deforestation, while the age or the type of trees had no effects. Both, deforestation and tree age influenced the assemblage of microbial communities, which tightly correlated with soil pH and organic matter among other soil properties. Adult trees harboured similar microbial communities in conserved and deforested soils being potential reservoirs of native microorganisms in the degraded areas. Some selected bacterial strains showed high plant growth promoting abilities, and PGPR traits were related with the isolation source of bacteria. The knowledge about key factors structuring the rhizospheric microbiota of tara and the identification of high-performing PGPR strains, provide a solid framework to formulate inocula for their use in restoration programmes in the Atiquipa fog forest.

  • Flux Analysis of Free Amino Sugars and Amino Acids in Soils by Isotope Tracing with a Novel Liquid Chromatography/High Resolution Mass Spectrometry Platform

    Hu Y, Zheng Q, Wanek W
    2017 - 17: 9192-9200

    Abstract: 

    Soil fluxomics analysis can provide pivotal information for understanding soil biochemical pathways and their regulation, but direct measurement methods are rare. Here, we describe an approach to measure soil extracellular metabolite (amino sugar and amino acid) concentrations and fluxes based on a 15N isotope pool dilution technique via liquid chromatography and high-resolution mass spectrometry. We produced commercially unavailable 15N and 13C labeled amino sugars and amino acids by hydrolyzing peptidoglycan isolated from isotopically labeled bacterial biomass and used them as tracers (15N) and internal standards (13C). High-resolution (Orbitrap Exactive) MS with a resolution of 50 000 allowed us to separate different stable isotope labeled analogues across a large range of metabolites. The utilization of 13C internal standards greatly improved the accuracy and reliability of absolute quantification. We successfully applied this method to two types of soils and quantified the extracellular gross fluxes of 2 amino sugars, 18 amino acids, and 4 amino acid enantiomers. Compared to the influx and efflux rates of most amino acids, similar ones were found for glucosamine, indicating that this amino sugar is released through peptidoglycan and chitin decomposition and serves as an important nitrogen source for soil microorganisms. d-Alanine and d-glutamic acid derived from peptidoglycan decomposition exhibited similar turnover rates as their l-enantiomers. This novel approach offers new strategies to advance our understanding of the production and transformation pathways of soil organic N metabolites, including the unknown contributions of peptidoglycan and chitin decomposition to soil organic N cycling.

  • Sorption of ionizable and ionic organic compounds to biochar, activated carbon and other carbonaceous materials

    Melanie Kah, Gabriel Sigmund, Feng Xiao, Thilo Hofmann
    2017 - Water Research, 673-692

    Abstract: 

    The sorption of ionic and ionizable organic compounds (IOCs) (e.g., pharmaceuticals and pesticides) on carbonaceous materials plays an important role in governing the fate, transport and bioavailability of IOCs. The paradigms previously established for the sorption of neutral organic compounds do not always apply to IOCs and the importance of accounting for the particular sorption behavior of IOCs is being increasingly recognized. This review presents the current state of knowledge and summarizes the recent advances on the sorption of IOCs to carbonaceous sorbents. A broad range of sorbents were considered to evaluate the possibility to read across between fields of research that are often considered in isolation (e.g., carbon nanotubes, graphene, biochar, and activated carbon). Mechanisms relevant to IOCs sorption on carbonaceous sorbents are discussed and critically evaluated, with special attention being given to emerging sorption mechanisms including low-barrier, charge-assisted hydrogen bonds and cation-π assisted π–π interactions. The key role played by some environmental factors is also discussed, with a particular focus on pH and ionic strength.

    Overall the review reveals significant advances in our understanding of the interactions between IOCs and carbonaceous sorbents. In addition, knowledge gaps are identified and priorities for future research are suggested.

  • Source tracing of natural organic matter bound mercury in boreal forest runoff with mercury stable isotopes

    Martin Jiskra, Jan G. Wiederhold, Ulf Skyllberg, Rose-Marie Kronberg, Ruben Kretzschmar
    2017 - Environmental Science: Processes & Impacts, 1: 1235-1248

    Abstract: 

    Terrestrial runoff represents a major source of mercury (Hg) to aquatic ecosystems. In boreal forest catchments, such as the one in northern Sweden studied here, mercury bound to natural organic matter (NOM) represents a large fraction of mercury in the runoff. We present a method to measure Hg stable isotope signatures of colloidal Hg, mainly complexed by high molecular weight or colloidal natural organic matter (NOM) in natural waters based on pre-enrichment by ultrafiltration, followed by freeze-drying and combustion. We report that Hg associated with high molecular weight NOM in the boreal forest runoff has very similar Hg isotope signatures as compared to the organic soil horizons of the catchment area. The mass-independent fractionation (MIF) signatures (Δ199Hg and Δ200Hg) measured in soils and runoff were in agreement with typical values reported for atmospheric gaseous elemental mercury (Hg0) and distinctly different from reported Hg isotope signatures in precipitation. We therefore suggest that most Hg in the boreal terrestrial ecosystem originated from the deposition of Hg0 through foliar uptake rather than precipitation. Using a mixing model we calculated the contribution of soil horizons to the Hg in the runoff. At moderate to high flow runoff conditions, that prevailed during sampling, the uppermost part of the organic horizon (Oe/He) contributed 50–70% of the Hg in the runoff, while the underlying more humified organic Oa/Ha and the mineral soil horizons displayed a lower mobility of Hg. The good agreement of the Hg isotope results with other source tracing approaches using radiocarbon signatures and Hg : C ratios provides additional support for the strong coupling between Hg and NOM. The exploratory results from this study illustrate the potential of Hg stable isotopes to trace the source of Hg from atmospheric deposition through the terrestrial ecosystem to soil runoff, and provide a basis for more in-depth studies investigating the mobility of Hg in terrestrial ecosystems using Hg isotope signatures.

  • A density functional theory investigation of oxalate and Fe(II) adsorption onto the (010) goethite surface with implications for ligand- and reduction-promoted dissolution

    James D. Kubicki, Daniel Tunega, Stephan M. Kraemer
    2017 - Chemical Geology, 14-22

    Abstract: 

    Oxalic acid is an important, biologically-produced species in the natural environment. The deprotonated form, oxalate, is dominant in aqueous solutions under circumneutral pH conditions and is a strong ligand for Fe(III). The high affinity of oxalate for Fe(III) means that Fe(III)-oxalate surface and aqueous complexes are common and can lead to ligand-enhanced dissolution. Fe(II) adsorption onto goethite (α-FeOOH) has been shown to enhance dissolution-recrystallization reactions. The goethite (010) face is one of the more common and reactive surfaces on this environmentally critical Fe-hydroxide phase. Hence, this study models both separate and coordinated adsorption of oxalate and Fe(II) onto the (010) face of goethite in order to test for synergistic effects of ligand-promoted and reductive dissolution. Periodic and cluster density functional theory (DFT) energy minimizations were performed to determine the structure, vibrational frequencies and energies of various configurations. The adsorption mechanism of oxalate is verified via comparison to observed IR spectra. The potential roles of oxalate and Fe(II) in ligand-enhanced reductive dissolution of goethite are discussed.

  • Ecological Risk Assessment of Nano-enabled Pesticides: A Perspective on Problem Formulation

    Glen W. Walker, Rai S. Kookana, Natalie E. Smith, Melanie Kah, Casey L. Doolette, Philip T. Reeves, Wess Lovell, Darren J. Anderson, Terence W. Turney, Divina A. Navarro
    2017 - Journal of Agricultural and Food Chemistry, 2: 6480-6486

    Abstract: 

    Plant protection products containing nanomaterials that alter the functionality or risk profile of active ingredients (nano-enabled pesticides) promise many benefits over conventional pesticide products. These benefits may include improved formulation characteristics, easier application, better targeting of pest species, increased efficacy, lower application rates, and enhanced environmental safety. After many years of research and development, nano-enabled pesticides are starting to make their way into the market. The introduction of this technology raises a number of issues for regulators, including how does the ecological risk assessment of nano-enabled pesticide products differ from that of conventional plant protection products? In this paper, a group drawn from regulatory agencies, academia, research, and the agrochemicals industry offers a perspective on relevant considerations pertaining to the problem formulation phase of the ecological risk assessment of nano-enabled pesticides.

  • Adaptability as the key to success for the ubiquitous marine nitrite oxidizer Nitrococcus

    Füssel J, Lücker S, Yilmaz P, Nowka B, van Kessel MAHJ, Bourceau P, Hach PF, Littmann S, Berg J, Spieck E, Daims H, Kuypers MMM, Lam P
    2017 - Sci Adv, 3: e1700807

    Abstract: 

    Nitrite-oxidizing bacteria (NOB) have conventionally been regarded as a highly specialized functional group responsible for the production of nitrate in the environment. However, recent culture-based studies suggest that they have the capacity to lead alternative lifestyles, but direct environmental evidence for the contribution of marine nitrite oxidizers to other processes has been lacking to date. We report on the alternative biogeochemical functions, worldwide distribution, and sometimes high abundance of the marine NOB Nitrococcus. These largely overlooked bacteria are capable of not only oxidizing nitrite but also reducing nitrate and producing nitrous oxide, an ozone-depleting agent and greenhouse gas. Furthermore, Nitrococcus can aerobically oxidize sulfide, thereby also engaging in the sulfur cycle. In the currently fast-changing global oceans, these findings highlight the potential functional switches these ubiquitous bacteria can perform in various biogeochemical cycles, each with distinct or even contrasting consequences.

  • Vitamin and Amino Acid Auxotrophy in Anaerobic Consortia Operating under Methanogenic Conditions.

    Hubalek V, Buck M, Tan B, Foght J, Wendeberg A, Berry D, Bertilsson S, Eiler A
    2017 - mSystems, 5: e00038-17

    Abstract: 

    Syntrophy among Archaea and Bacteria facilitates the anaerobic degradation of organic compounds to CH4 and CO2. Particularly during aliphatic and aromatic hydrocarbon mineralization, as in the case of crude oil reservoirs and petroleum-contaminated sediments, metabolic interactions between obligate mutualistic microbial partners are of central importance. Using micromanipulation combined with shotgun metagenomic approaches, we describe the genomes of complex consortia within short-chain alkane-degrading cultures operating under methanogenic conditions. Metabolic reconstruction revealed that only a small fraction of genes in the metagenome-assembled genomes encode the capacity for fermentation of alkanes facilitated by energy conservation linked to H2 metabolism. Instead, the presence of inferred lifestyles based on scavenging anabolic products and intermediate fermentation products derived from detrital biomass was a common feature. Additionally, inferred auxotrophy for vitamins and amino acids suggests that the hydrocarbon-degrading microbial assemblages are structured and maintained by multiple interactions beyond the canonical H2-producing and syntrophic alkane degrader-methanogen partnership. Compared to previous work, our report points to a higher order of complexity in microbial consortia engaged in anaerobic hydrocarbon transformation. IMPORTANCE Microbial interactions between Archaea and Bacteria mediate many important chemical transformations in the biosphere from degrading abundant polymers to synthesis of toxic compounds. Two of the most pressing issues in microbial interactions are how consortia are established and how we can modulate these microbial communities to express desirable functions. Here, we propose that public goods (i.e., metabolites of high energy demand in biosynthesis) facilitate energy conservation for life under energy-limited conditions and determine the assembly and function of the consortia. Our report suggests that an understanding of public good dynamics could result in new ways to improve microbial pollutant degradation in anaerobic systems.

  • Ammonia-oxidising archaea living at low pH: Insights from comparative genomics.

    Herbold CW, Lehtovirta-Morley LE, Jung MY, Jehmlich N, Hausmann B, Han P, Loy A, Pester M, Sayavedra-Soto LA, Rhee SK, Prosser JI, Nicol GW, Wagner M, Gubry-Rangin C
    2017 - Environ. Microbiol., 12: 4939-4952

    Abstract: 

    Obligate acidophilic members of the thaumarchaeotal genus Candidatus Nitrosotalea play an important role in nitrification in acidic soils, but their evolutionary and physiological adaptations to acidic environments are still poorly understood, with only a single member of this genus (Ca. N. devanaterra) having its genome sequenced. In this study, we sequenced the genomes of two additional cultured Ca. Nitrosotalea strains, extracted an almost complete Ca. Nitrosotalea metagenome-assembled genome from an acidic fen, and performed comparative genomics of the four Ca. Nitrosotalea genomes with 19 other archaeal ammonia oxidiser genomes. Average nucleotide and amino acid identities revealed that the four Ca. Nitrosotalea strains represent separate species within the genus. The four Ca. Nitrosotalea genomes contained a core set of 103 orthologous gene families absent from all other ammonia-oxidizing archaea and, for most of these gene families, expression could be demonstrated in laboratory culture or the environment via proteomic or metatranscriptomic analyses respectively. Phylogenetic analyses indicated that four of these core gene families were acquired by the Ca. Nitrosotalea common ancestor via horizontal gene transfer from acidophilic representatives of Euryarchaeota. We hypothesize that gene exchange with these acidophiles contributed to the competitive success of the Ca. Nitrosotalea lineage in acidic environments.

  • Abiotic Conversion of Extracellular NH2OH Contributes to N2O Emission during Ammonia Oxidation.

    Liu S, Han P, Hink L, Prosser JI, Wagner M, Brüggemann N
    2017 - Environ. Sci. Technol., 22: 13122-13132

    Abstract: 

    Abiotic processes involving the reactive ammonia-oxidation intermediates nitric oxide (NO) or hydroxylamine (NH2OH) for N2O production have been indicated recently. The latter process would require the availability of substantial amounts of free NH2OH for chemical reactions during ammonia (NH3) oxidation, but little is known about extracellular NH2OH formation by the different clades of ammonia-oxidizing microbes. Here we determined extracellular NH2OH concentrations in culture media of several ammonia-oxidizing bacteria (AOB) and archaea (AOA), as well as one complete ammonia oxidizer (comammox) enrichment (Ca. Nitrospira inopinata) during incubation under standard cultivation conditions. NH2OH was measurable in the incubation media of Nitrosomonas europaea, Nitrosospira multiformis, Nitrososphaera gargensis, and Ca. Nitrosotenuis uzonensis, but not in media of the other tested AOB and AOA. NH2OH was also formed by the comammox enrichment during NH3 oxidation. This enrichment exhibited the largest NH2OH:final product ratio (1.92%), followed by N. multiformis (0.56%) and N. gargensis (0.46%). The maximum proportions of NH4+ converted to N2O via extracellular NH2OH during incubation, estimated on the basis of NH2OH abiotic conversion rates, were 0.12%, 0.08%, and 0.14% for AOB, AOA, and Ca. Nitrospira inopinata, respectively, and were consistent with published NH4+:N2O conversion ratios for AOB and AOA.

  • Depth distribution and assembly of sulfate-reducing microbial communities in marine sediments of Aarhus Bay

    Jochum LM, Chena X, Lever MA, Loy A, Jørgensen BB, Schramm A, Kjeldsen KU
    2017 - 83: e01547-17

    Abstract: 

    Most sulfate-reducing microorganisms (SRM) present in subsurface marine sediments belong to uncultured groups only distantly related to known SRM and it remains unclear how changing geochemical zones and sediment depth influence their community structure. We mapped the community composition and abundance of SRM by amplicon-sequencing and quantifying dsrB, which encodes dissimilatory sulfite reductase subunit beta, in sediment samples covering different vertical geochemical zones ranging from the surface sediment to the deep sulfate-depleted subsurface at four locations in Aarhus Bay, Denmark. SRM were present in all geochemical zones including sulfate-depleted methanogenic sediment. The biggest shift in SRM community composition and abundance occurring across the transition from bioturbated surface sediments into non-bioturbated sediments below, where redox fluctuations and input of fresh organic matter due to macrofaunal activity are absent. SRM abundance correlated with sulfate reduction rates determined for the same sediments. Sulfate availability showed weaker correlation with SRM abundances and no significant correlation with the composition of the SRM community. The overall SRM species diversity decreased with depth, yet we identified a subset of highly abundant community members that persists across all vertical geochemical zones of all stations. We conclude that subsurface SRM communities assemble by persistence of members of the surface community and that the transition from the bioturbated surface sediment to the unmixed sediment below is a main site of assembly of the subsurface SRM community.

  • Bottled aqua incognita: Microbiota assembly and dissolved organic matter diversity in natural mineral waters

    Lesaulnier CC, Herbold CW, Pelikan C, Gérard C, Le Coz X, Gagnot S, Berry D, Niggemann J, Dittmar T, Singer GA, Loy A
    2017 - Microbiome, 5: 126

    Abstract: 

    Background: Non-carbonated natural mineral waters contain microorganisms that regularly grow after bottling despite low concentrations of dissolved organic matter (DOM). Yet, the compositions of bottled water microbiota and organic substrates that fuel microbial activity, and how both change after bottling, are still largely unknown.

    Results: We performed a multifaceted analysis of microbiota and DOM diversity in twelve natural mineral waters from six European countries. 16S rRNA gene-based analyses showed that less than ten species-level operational taxonomic units (OTUs) dominated the bacterial communities in the water phase and associated with the bottle wall after a short phase of post-bottling growth. Members of the betaproteobacterial genera Curvibacter, Aquabacterium, and Polaromonas (Comamonadaceae) grew in most waters and represent ubiquitous, mesophilic, heterotrophic aerobes in bottled waters. Ultrahigh-resolution mass spectrometry of DOM in bottled waters and their corresponding source waters identified thousands of molecular formulae characteristic of mostly refractory, soil-derived DOM.

    Conclusions. The bottle environment, including source water physicochemistry, selected for growth of a similar low-diversity microbiota across various bottled waters. Relative abundance changes of hundreds of multi-carbon molecules were related to growth of less than ten abundant OTUs. We thus speculate that individual bacteria cope with oligotrophic conditions by simultaneously consuming diverse DOM molecules.

  • Identification of secondary metabolite gene clusters in the Pseudovibrio genus reveals encouraging biosynthetic potential toward the production of novel bioactive compounds

    Naughton LM, Romano S, O'Gara F, Dobson ADW
    2017 - Front Microbiol, 8: 1494

    Abstract: 

    Increased incidences of antimicrobial resistance and the emergence of pan-resistant 'superbugs' have provoked an extreme sense of urgency amongst researchers focusing on the discovery of potentially novel antimicrobial compounds. A strategic shift in focus from the terrestrial to the marine environment has resulted in the discovery of a wide variety of structurally and functionally diverse bioactive compounds from numerous marine sources, including sponges. Bacteria found in close association with sponges and other marine invertebrates have recently gained much attention as potential sources of many of these novel bioactive compounds. Members of the genus Pseudovibrio are one such group of organisms. In this study, we interrogate the genomes of 21 Pseudovibrio strains isolated from a variety of marine sources, for the presence, diversity and distribution of biosynthetic gene clusters (BGCs). We expand on results obtained from antiSMASH analysis to demonstrate the similarity between the Pseudovibrio-related BGCs and those characterized in other bacteria and corroborate our findings with phylogenetic analysis. We assess how domain organization of the most abundant type of BGCs present among the isolates (Non-ribosomal peptide synthetases and Polyketide synthases) may influence the diversity of compounds produced by these organisms and highlight for the first time the potential for novel compound production from this genus of bacteria, using a genome guided approach.

  • Kinetic analysis of a complete nitrifier reveals an oligotrophic lifestyle.

    Kits KD, Sedlacek CJ, Lebedeva EV, Han P, Bulaev A, Pjevac P, Daebeler A, Romano S, Albertsen M, Stein LY, Daims H, Wagner M
    2017 - Nature, 549: 269-272

    Abstract: 

    Nitrification, the oxidation of ammonia (NH3) via nitrite (NO2(-)) to nitrate (NO3(-)), is a key process of the biogeochemical nitrogen cycle. For decades, ammonia and nitrite oxidation were thought to be separately catalysed by ammonia-oxidizing bacteria (AOB) and archaea (AOA), and by nitrite-oxidizing bacteria (NOB). The recent discovery of complete ammonia oxidizers (comammox) in the NOB genus Nitrospira, which alone convert ammonia to nitrate, raised questions about the ecological niches in which comammox Nitrospira successfully compete with canonical nitrifiers. Here we isolate a pure culture of a comammox bacterium, Nitrospira inopinata, and show that it is adapted to slow growth in oligotrophic and dynamic habitats on the basis of a high affinity for ammonia, low maximum rate of ammonia oxidation, high growth yield compared to canonical nitrifiers, and genomic potential for alternative metabolisms. The nitrification kinetics of four AOA from soil and hot springs were determined for comparison. Their surprisingly poor substrate affinities and lower growth yields reveal that, in contrast to earlier assumptions, AOA are not necessarily the most competitive ammonia oxidizers present in strongly oligotrophic environments and that N. inopinata has the highest substrate affinity of all analysed ammonia oxidizer isolates except the marine AOA Nitrosopumilus maritimus SCM1 (ref. 3). These results suggest a role for comammox organisms in nitrification under oligotrophic and dynamic conditions.

  • AmoA-targeted polymerase chain reaction primers for the specific detection and quantification of comammox Nitrospira in the environment

    Pjevac P, Schauberger C, Poghosyan L, Herbold CW, van Kessel MAHJ, Daebeler A, Steinberger M, Jetten MSM, Luecker S, Wagner M, Daims H
    2017 - Front Microbiol, 8:1508
    Comammox PCR primers

    Abstract: 

    Nitrification, the oxidation of ammonia via nitrite to nitrate, has always been considered to be catalyzed by the concerted activity of ammonia- and nitrite-oxidizing microorganisms. Only recently, complete ammonia oxidizers (‘comammox’), which oxidize ammonia to nitrate on their own, were identified in the bacterial genus Nitrospira, previously assumed to contain only canonical nitrite oxidizers. Nitrospira are widespread in nature, but for assessments of the distribution and functional importance of comammox Nitrospira in ecosystems, cultivation-independent tools to distinguish comammox from strictly nitrite oxidizing Nitrospira are required. Here we developed new PCR primer sets that specifically target the amoA genes coding for subunit A of the distinct ammonia monooxygenase of comammox Nitrospira. While existing primers capture only a fraction of the known comammox amoA diversity, the new primer sets cover as much as 95% of the comammox amoA clade A and 92% of the clade B sequences in a reference database containing 326 comammox amoA genes with sequence information at the primer binding sites. Application of the primers to 13 samples from engineered systems (a groundwater well, drinking water treatment and wastewater treatment plants) and other habitats (rice paddy and forest soils, rice rhizosphere, brackish lake sediment and freshwater biofilm) detected comammox Nitrospira in all samples and revealed a considerable diversity of comammox in most habitats. Excellent primer specificity for comammox amoA was achieved by avoiding the use of highly degenerate primer preparations and by using equimolar mixtures of oligonucleotides that match existing comammox amoA genes. Quantitative PCR with these equimolar primer mixtures was highly sensitive and specific, and enabled the efficient quantification of clade A and clade B comammox amoA gene copy numbers in environmental samples. The measured relative abundances of comammox Nitrospira, compared to canonical ammonia oxidizers, were highly variable across environments. The new comammox amoA-targeted primers enable more encompassing future studies of nitrifying microorganisms in diverse habitats. For example, they may be used to monitor the population dynamics of uncultured comammox organisms under changing environmental conditions and in response to altered treatments in engineered and agricultural ecosystems.

  • In situ architecture, function, and evolution of a contractile injection system.

    Böck D, Medeiros JM, Tsao HF, Penz T, Weiss GL, Aistleitner K, Horn M, Pilhofer M
    2017 - Science, 6352: 713-717

    Abstract: 

    Contractile injection systems mediate bacterial cell-cell interactions by a bacteriophage tail-like structure. In contrast to extracellular systems, the type 6 secretion system (T6SS) is defined by intracellular localization and attachment to the cytoplasmic membrane. Here we used cryo-focused ion beam milling, electron cryotomography, and functional assays to study a T6SS in Amoebophilus asiaticus The in situ architecture revealed three modules, including a contractile sheath-tube, a baseplate, and an anchor. All modules showed conformational changes upon firing. Lateral baseplate interactions coordinated T6SSs in hexagonal arrays. The system mediated interactions with host membranes and may participate in phagosome escape. Evolutionary sequence analyses predicted that T6SSs are more widespread than previously thought. Our insights form the basis for understanding T6SS key concepts and exploring T6SS diversity.

  • Allspice and Clove As Source of Triterpene Acids Activating the G Protein-Coupled Bile Acid Receptor TGR5.

    Ladurner A, Zehl M, Grienke U, Hofstadler C, Faur N, Pereira FC, Berry D, Dirsch VM, Rollinger JM
    2017 - Front Pharmacol, 8: 468

    Abstract: 

    Worldwide, metabolic diseases such as obesity and type 2 diabetes have reached epidemic proportions. A major regulator of metabolic processes that gained interest in recent years is the bile acid receptor TGR5 (Takeda G protein-coupled receptor 5). This G protein-coupled membrane receptor can be found predominantly in the intestine, where it is mainly responsible for the secretion of the incretins glucagon-like peptide 1 (GLP-1) and peptide YY (PYY). The aim of this study was (i) to identify plant extracts with TGR5-activating potential, (ii) to narrow down their activity to the responsible constituents, and (iii) to assess whether the intestinal microbiota produces transformed metabolites with a different activity profile. Chenodeoxycholic acid (CDCA) served as positive control for both, the applied cell-based luciferase reporter gene assay for TGR5 activity and the biotransformation assay using mouse fecal slurry. The suitability of the workflow was demonstrated by the biotransformation of CDCA to lithocholic acid resulting in a distinct increase in TGR5 activity. Based on a traditional Tibetan formula, 19 plant extracts were selected and investigated for TGR5 activation. Extracts from the commonly used spices Syzygium aromaticum (SaroE, clove), Pimenta dioica (PdioE, allspice), and Kaempferia galanga (KgalE, aromatic ginger) significantly increased TGR5 activity. After biotransformation, only KgalE showed significant differences in its metabolite profile, which, however, did not alter its TGR5 activity compared to non-transformed KgalE. UHPLC-HRMS (high-resolution mass spectrometry) analysis revealed triterpene acids (TTAs) as the main constituents of the extracts SaroE and PdioE. Identification and quantification of TTAs in these two extracts as well as comparison of their TGR5 activity with reconstituted TTA mixtures allowed the attribution of the TGR5 activity to TTAs. EC50s were determined for the main TTAs, i.e., oleanolic acid (2.2 ± 1.6 μM), ursolic acid (1.1 ± 0.2 μM), as well as for the hitherto unknown TGR5 activators corosolic acid (0.5 ± 1.0 μM) and maslinic acid (3.7 ± 0.7 μM). In conclusion, extracts of clove, allspice, and aromatic ginger activate TGR5, which might play a pivotal role in their therapeutic use for the treatment of metabolic diseases. Moreover, the TGR5 activation of SaroE and PdioE could be pinpointed solely to TTAs.

  • Unexpected genomic features in widespread intracellular bacteria: evidence for motility of marine chlamydiae.

    Collingro A, Köstlbacher S, Greuter L, Stepanauskas R, Hallam SJ, Horn M
    2017 - ISME J, 10: 2334-2344

    Abstract: 

    Chlamydiae are obligate intracellular bacteria comprising important human pathogens and symbionts of protists. Molecular evidence indicates a tremendous diversity of chlamydiae particularly in marine environments, yet our current knowledge is based mainly on terrestrial representatives. Here we provide first insights into the biology of marine chlamydiae representing three divergent clades. Our analysis of single-cell amplified genomes revealed hallmarks of the chlamydial lifestyle, supporting the ancient origin of their characteristic developmental cycle and major virulence mechanisms. Surprisingly, these chlamydial genomes encode a complete flagellar apparatus, a previously unreported feature. We show that flagella are an ancient trait that was subject to differential gene loss among extant chlamydiae. Together with a chemotaxis system, these marine chlamydiae are likely motile, with flagella potentially playing a role during host cell infection. This study broadens our view on chlamydial biology and indicates a largely underestimated potential to adapt to different hosts and environments.

  • 'Candidatus Cochliophilus cryoturris' (Coxiellaceae), a symbiont of the testate amoeba Cochliopodium minus.

    Tsao HF, Scheikl U, Volland JM, Köhsler M, Bright M, Walochnik J, Horn M
    2017 - Sci Rep, 1: 3394

    Abstract: 

    Free-living amoebae are well known for their role in controlling microbial community composition through grazing, but some groups, namely Acanthamoeba species, also frequently serve as hosts for bacterial symbionts. Here we report the first identification of a bacterial symbiont in the testate amoeba Cochliopodium. The amoeba was isolated from a cooling tower water sample and identified as C. minus. Fluorescence in situ hybridization and transmission electron microscopy revealed intracellular symbionts located in vacuoles. 16S rRNA-based phylogenetic analysis identified the endosymbiont as member of a monophyletic group within the family Coxiellaceae (Gammaprotebacteria; Legionellales), only moderately related to known amoeba symbionts. We propose to tentatively classify these bacteria as 'Candidatus Cochliophilus cryoturris'. Our findings add both, a novel group of amoeba and a novel group of symbionts, to the growing list of bacteria-amoeba relationships.

  • Biphasic Metabolism and Host Interaction of a Chlamydial Symbiont.

    König L, Siegl A, Penz T, Haider S, Wentrup C, Polzin J, Mann E, Schmitz-Esser S, Domman D, Horn M
    2017 - mSystems, 2: e00202-16

    Abstract: 

    Chlamydiae are obligate intracellular bacteria comprising well-known human pathogens and ubiquitous symbionts of protists, which are characterized by a unique developmental cycle. Here we comprehensively analyzed gene expression dynamics of Protochlamydia amoebophila during infection of its Acanthamoeba host by RNA sequencing. This revealed a highly dynamic transcriptional landscape, where major transcriptional shifts are conserved among chlamydial symbionts and pathogens. Our data served to propose a time-resolved model for type III protein secretion during the developmental cycle, and we provide evidence for a biphasic metabolism of P. amoebophila during infection, which involves energy parasitism and amino acids as the carbon source during initial stages and a postreplicative switch to endogenous glucose-based ATP production. This fits well with major transcriptional changes in the amoeba host, where upregulation of complex sugar breakdown precedes the P. amoebophila metabolic switch. The biphasic chlamydial metabolism represents a unique adaptation to exploit eukaryotic host cells, which likely contributed to the evolutionary success of this group of microbes. IMPORTANCE Chlamydiae are known as major bacterial pathogens of humans, causing the ancient disease trachoma, but they are also frequently found in the environment where they infect ubiquitous protists such as amoebae. All known chlamydiae require a eukaryotic host cell to thrive. Using the environmental chlamydia Protochlamydia amoebophila within its natural host, Acanthamoeba castellanii, we investigated gene expression dynamics in vivo and throughout the complete chlamydial developmental cycle for the first time. This allowed us to infer how a major virulence mechanism, the type III secretion system, is regulated and employed, and we show that the physiology of chlamydiae undergoes a complete shift regarding carbon metabolism and energy generation. This study provides comprehensive insights into the infection strategy of chlamydiae and reveals a unique adaptation to life within a eukaryotic host cell.

  • Exploiting fine-scale genetic and physiological variation of closely related microbes to reveal unknown enzyme functions.

    Badur AH, Plutz MJ, Yalamanchili G, Jagtap SS, Schweder T, Unfried F, Markert S, Polz MF, Hehemann JH, Rao CV
    2017 - J. Biol. Chem., 31: 13056-13067

    Abstract: 

    Polysaccharide degradation by marine microbes represents one of the largest and most rapid heterotrophic transformations of organic matter in the environment. Microbes employ systems of complementary carbohydrate-specific enzymes to deconstruct algal or plant polysaccharides (glycans) into monosaccharides. Because of the high diversity of glycan substrates, the functions of these enzymes are often difficult to establish. One solution to this problem may lie within naturally occurring microdiversity; varying numbers of enzymes, due to gene loss, duplication, or transfer, among closely related environmental microbes create metabolic differences akin to those generated by knock-out strains engineered in the laboratory used to establish the functions of unknown genes. Inspired by this natural fine-scale microbial diversity, we show here that it can be used to develop hypotheses guiding biochemical experiments for establishing the role of these enzymes in nature. In this work, we investigated alginate degradation among closely related strains of the marine bacterium One strain, 13B01, exhibited high extracellular alginate lyase activity compared with other strains. To identify the enzymes responsible for this high extracellular activity, we compared 13B01 with the previously characterized 12B01, which has low extracellular activity and lacks two alginate lyase genes present in 13B01. Using a combination of genomics, proteomics, biochemical, and functional screening, we identified a polysaccharide lyase family 7 enzyme that is unique to 13B01, secreted, and responsible for the rapid digestion of extracellular alginate. These results demonstrate the value of querying the enzymatic repertoires of closely related microbes to rapidly pinpoint key proteins with beneficial functions.

  • Crenothrix are major methane consumers in stratified lakes.

    Oswald K, Graf JS, Littmann S, Tienken D, Brand A, Wehrli B, Albertsen M, Daims H, Wagner M, Kuypers MM, Schubert CJ, Milucka J
    2017 - ISME J, 9: 2124-2140
    Crenothrix

    Abstract: 

    Methane-oxidizing bacteria represent a major biological sink for methane and are thus Earth's natural protection against this potent greenhouse gas. Here we show that in two stratified freshwater lakes a substantial part of upward-diffusing methane was oxidized by filamentous gamma-proteobacteria related to Crenothrix polyspora. These filamentous bacteria have been known as contaminants of drinking water supplies since 1870, but their role in the environmental methane removal has remained unclear. While oxidizing methane, these organisms were assigned an 'unusual' methane monooxygenase (MMO), which was only distantly related to 'classical' MMO of gamma-proteobacterial methanotrophs. We now correct this assignment and show that Crenothrix encode a typical gamma-proteobacterial PmoA. Stable isotope labeling in combination swith single-cell imaging mass spectrometry revealed methane-dependent growth of the lacustrine Crenothrix with oxygen as well as under oxygen-deficient conditions. Crenothrix genomes encoded pathways for the respiration of oxygen as well as for the reduction of nitrate to N2O. The observed abundance and planktonic growth of Crenothrix suggest that these methanotrophs can act as a relevant biological sink for methane in stratified lakes and should be considered in the context of environmental removal of methane.

  • Capturing the genetic makeup of the active microbiome in situ.

    Singer E, Wagner M, Woyke T
    2017 - ISME J, 9: 1949-1963

    Abstract: 

    More than any other technology, nucleic acid sequencing has enabled microbial ecology studies to be complemented with the data volumes necessary to capture the extent of microbial diversity and dynamics in a wide range of environments. In order to truly understand and predict environmental processes, however, the distinction between active, inactive and dead microbial cells is critical. Also, experimental designs need to be sensitive toward varying population complexity and activity, and temporal as well as spatial scales of process rates. There are a number of approaches, including single-cell techniques, which were designed to study in situ microbial activity and that have been successively coupled to nucleic acid sequencing. The exciting new discoveries regarding in situ microbial activity provide evidence that future microbial ecology studies will indispensably rely on techniques that specifically capture members of the microbiome active in the environment. Herein, we review those currently used activity-based approaches that can be directly linked to shotgun nucleic acid sequencing, evaluate their relevance to ecology studies, and discuss future directions.

  • Evaluating the Detection of Hydrocarbon-Degrading Bacteria in 16S rRNA Gene Sequencing Surveys.

    Berry D, Gutierrez T
    2017 - Front Microbiol, 8: 2460

    Abstract: 

    Hydrocarbonoclastic bacteria (HCB) play a key role in the biodegradation of oil hydrocarbons in marine and other environments. A small number of taxa have been identified as obligate HCB, notably the Gammaproteobacterial genera Alcanivorax, Cycloclasticus, Marinobacter, Neptumonas, Oleiphilus, Oleispira, and Thalassolituus, as well as the Alphaproteobacterial genus Thalassospira. Detection of HCB in amplicon-based sequencing surveys relies on high coverage by PCR primers and accurate taxonomic classification. In this study, we performed a phylogenetic analysis to identify 16S rRNA gene sequence regions that represent the breadth of sequence diversity within these taxa. Using validated sequences, we evaluated 449 universal 16S rRNA gene-targeted bacterial PCR primer pairs for their coverage of these taxa. The results of this analysis provide a practical framework for selection of suitable primer sets for optimal detection of HCB in sequencing surveys.

  • Vibrational Spectroscopy for Imaging Single Microbial Cells in Complex Biological Samples.

    Harrison JP, Berry D
    2017 - Front Microbiol, 8: 675

    Abstract: 

    Vibrational spectroscopy is increasingly used for the rapid and non-destructive imaging of environmental and medical samples. Both Raman and Fourier-transform infrared (FT-IR) imaging have been applied to obtain detailed information on the chemical composition of biological materials, ranging from single microbial cells to tissues. Due to its compatibility with methods such as stable isotope labeling for the monitoring of cellular activities, vibrational spectroscopy also holds considerable power as a tool in microbial ecology. Chemical imaging of undisturbed biological systems (such as live cells in their native habitats) presents unique challenges due to the physical and chemical complexity of the samples, potential for spectral interference, and frequent need for real-time measurements. This Mini Review provides a critical synthesis of recent applications of Raman and FT-IR spectroscopy for characterizing complex biological samples, with a focus on developments in single-cell imaging. We also discuss how new spectroscopic methods could be used to overcome current limitations of single-cell analyses. Given the inherent complementarity of Raman and FT-IR spectroscopic methods, we discuss how combining these approaches could enable us to obtain new insights into biological activities either in situ or under conditions that simulate selected properties of the natural environment.

  • HuR small-molecule inhibitor elicits differential effects in adenomatosis polyposis and colorectal carcinogenesis

    Lang M, Berry D, Passecker K, Mesteri I, Bhuju S, Ebner F, Sedlyarov V, Evstatiev R, Dammann K, Loy A, Kuzyk O, Kovarik P, Khare V, Beibel M, Roma G, Meisner-Kober N, Gasche C
    2017 - 77: 2424-2438

    Abstract: 

    HuR is an RNA-binding protein implicated in immune homeostasis and various cancers, including colorectal cancer. HuR binding to AU-rich elements within the 3' untranslated region of mRNAs encoding oncogenes, growth factors, and various cytokines leads message stability and translation. In this study, we evaluated HuR as a small-molecule target for preventing colorectal cancer in high-risk groups such as those with familial adenomatosis polyposis (FAP) or inflammatory bowel disease (IBD). In human specimens, levels of cytoplasmic HuR were increased in colonic epithelial cells from patients with IBD, IBD-cancer, FAP-adenoma, and colorectal cancer, but not in patients with IBD-dysplasia. Intraperitoneal injection of the HuR small-molecule inhibitor MS-444 in AOM/DSS mice, a model of IBD and inflammatory colon cancer, augmented DSS-induced weight loss and increased tumor multiplicity, size, and invasiveness. MS-444 treatment also abrogated tumor cell apoptosis and depleted tumor-associated eosinophils, accompanied by a decrease in IL18 and eotaxin-1. In contrast, HuR inhibition in APCMin mice, a model of FAP and colon cancer, diminished the number of small intestinal tumors generated. In this setting, fecal microbiota, evaluated by 16S rRNA gene amplicon sequencing, shifted to a state of reduced bacterial diversity, with an increased representation of Prevotella, Akkermansia, and Lachnospiraceae Taken together, our results indicate that HuR activation is an early event in FAP-adenoma but is not present in IBD-dysplasia. Furthermore, our results offer a preclinical proof of concept for HuR inhibition as an effective means of FAP chemoprevention, with caution advised in the setting of IBD.

  • Natural resource landscapes of a marine bacterium reveal distinct fitness-determining genes across the genome.

    Takemura AF, Corzett CH, Hussain F, Arevalo P, Datta M, Yu X, Le Roux F, Polz MF
    2017 - Environ. Microbiol., 6: 2422-2433

    Abstract: 

    Heterotrophic bacteria exploit diverse microhabitats in the ocean, from particles to transient gradients. Yet the degree to which genes and pathways can contribute to an organism's fitness on such complex and variable natural resource landscapes remains poorly understood. Here, we determine the gene-by-gene fitness of a generalist saprophytic marine bacterium (Vibrio sp. F13 9CS106) on complex resources derived from its natural habitats - copepods (Apocyclops royi) and brown algae (Fucus vesiculosus) - and as reference substrates, glucose and the polysaccharide alginate, derived from brown algal cell walls. We find that resource complexity strongly buffers fitness costs of mutations, and that anabolic rather than catabolic pathways are more stringently required, likely due to functional redundancy in the latter. Moreover, while carbohydrate-rich algae requires several synthesis pathways, protein-rich Apocyclops does not, suggesting this ancestral habitat for Vibrios is a replete medium with metabolically redundant substrates. We also identify a candidate fitness trade-off for algal colonization: deletion of mshA increases mutant fitness. Our results demonstrate that gene fitness depends on habitat composition, and suggest that this generalist uses distinct resources in different natural habitats. The results further indicate that substrate replete conditions may lead to relatively relaxed selection on catabolic genes.

  • The life sulfuric: microbial ecology of sulfur cycling in marine sediments.

    Wasmund K, Greuter L, Loy A
    2017 - Environ Microbiol Rep, 4: 323-344

    Abstract: 

    Almost the entire seafloor is covered with sediments that can be more than 10 000 m thick and represent a vast microbial ecosystem that is a major component of Earth's element and energy cycles. Notably, a significant proportion of microbial life in marine sediments can exploit energy conserved during transformations of sulfur compounds among different redox states. Sulfur cycling, which is primarily driven by sulfate reduction, is tightly interwoven with other important element cycles (carbon, nitrogen, iron, manganese) and therefore has profound implications for both cellular- and ecosystem-level processes. Sulfur-transforming microorganisms have evolved diverse genetic, metabolic, and in some cases, peculiar phenotypic features to fill an array of ecological niches in marine sediments. Here, we review recent and selected findings on the microbial guilds that are involved in the transformation of different sulfur compounds in marine sediments and emphasise how these are interlinked and have a major influence on ecology and biogeochemistry in the seafloor. Extraordinary discoveries have increased our knowledge on microbial sulfur cycling, mainly in sulfate-rich surface sediments, yet many questions remain regarding how sulfur redox processes may sustain the deep-subsurface biosphere and the impact of organic sulfur compounds on the marine sulfur cycle.

  • The life sulfuric: Microbial ecology of sulfur cycling in marine sediments.

    Wasmund K, Mussmann M, Loy A
    2017 - Environ Microbiol Rep, 9: 323-344

    Abstract: 

    Almost the entire seafloor is covered with sediments that can be more than 10,000 m thick and represent a vast microbial ecosystem that is a major component of Earth's element and energy cycles. Notably, a significant proportion of microbial life in marine sediments can exploit energy conserved during transformations of sulfur compounds among different redox states. Sulfur cycling, which is primarily driven by sulfate reduction, is tightly interwoven with other important element cycles (carbon, nitrogen, iron, manganese) and therefore has profound implications for both cellular- and ecosystem-level processes. Sulfur-transforming microorganisms have evolved diverse genetic, metabolic, and in some cases, peculiar phenotypic features to fill an array of ecological niches in marine sediments. Here, we review recent and selected findings on the microbial guilds that are involved in the transformation of different sulfur compounds in marine sediments and emphasize how these are interlinked and have a major influence on ecology and biogeochemistry in the seafloor. Extraordinary discoveries have increased our knowledge on microbial sulfur cycling, mainly in sulfate-rich surface sediments, yet many questions remain regarding how sulfur redox processes may sustain the deep-subsurface biosphere and the impact of organic sulfur compounds on the marine sulfur cycle. This article is protected by copyright. All rights reserved.

  • Giant viruses with an expanded complement of translation system components.

    Schulz F, Yutin N, Ivanova NN, Ortega DR, Lee TK, Vierheilig J, Daims H, Horn M, Wagner M, Jensen GJ, Kyrpides NC, Koonin EV, Woyke T
    2017 - Science, 6333: 82-85
    Klosneuvirus

    Abstract: 

    The discovery of giant viruses blurred the sharp division between viruses and cellular life. Giant virus genomes encode proteins considered as signatures of cellular organisms, particularly translation system components, prompting hypotheses that these viruses derived from a fourth domain of cellular life. Here we report the discovery of a group of giant viruses (Klosneuviruses) in metagenomic data. Compared with other giant viruses, the Klosneuviruses encode an expanded translation machinery, including aminoacyl transfer RNA synthetases with specificities for all 20 amino acids. Notwithstanding the prevalence of translation system components, comprehensive phylogenomic analysis of these genes indicates that Klosneuviruses did not evolve from a cellular ancestor but rather are derived from a much smaller virus through extensive gain of host genes.

  • Members of the Oral Microbiota Are Associated with IL-8 Release by Gingival Epithelial Cells in Healthy Individuals.

    Schueller K, Riva A, Pfeiffer S, Berry D, Somoza V
    2017 - Front Microbiol, 8: 416

    Abstract: 

    The triggers for the onset of oral diseases are still poorly understood. The aim of this study was to characterize the oral bacterial community in healthy humans and its association with nutrition, oral hygiene habits, and the release of the inflammatory marker IL-8 from gingival epithelial cells (GECs) with and without stimulation by bacterial endotoxins to identify possible indicator operational taxonomic units (OTUs) associated with inflammatory marker status. GECs from 21 healthy participants (13 females, 8 males) were incubated with or without addition of bacterial lipopolysaccharides (LPSs), and the oral microbiota was profiled using 16S rRNA gene-targeted sequencing. The basal IL-8 release after 6 h was between 9.9 and 98.2 pg/ml, and bacterial communities were characteristic for healthy oral microbiota. The composition of the oral microbiota was associated with basal IL-8 levels, the intake of meat, tea, white wine, sweets and the use of chewing gum, as well as flossing habits, allergies, gender and body mass index. Additionally, eight OTUs were associated with high basal levels of IL-8 and GEC response to LPS, with high basal levels of IL-8, and 1 with low basal levels of IL8. The identification of indicator bacteria in healthy subjects with high levels of IL-8 release is of importance as they may be promising early warning indicators for the possible onset of oral diseases.

  • Microbial community assembly and evolution in subseafloor sediment.

    Starnawski P, Bataillon T, Ettema TJ, Jochum LM, Schreiber L, Chen X, Lever MA, Polz MF, Jørgensen BB, Schramm A, Kjeldsen KU
    2017 - Proc. Natl. Acad. Sci. U.S.A., 11: 2940-2945

    Abstract: 

    Bacterial and archaeal communities inhabiting the subsurface seabed live under strong energy limitation and have growth rates that are orders of magnitude slower than laboratory-grown cultures. It is not understood how subsurface microbial communities are assembled and whether populations undergo adaptive evolution or accumulate mutations as a result of impaired DNA repair under such energy-limited conditions. Here we use amplicon sequencing to explore changes of microbial communities during burial and isolation from the surface to the >5,000-y-old subsurface of marine sediment and identify a small core set of mostly uncultured bacteria and archaea that is present throughout the sediment column. These persisting populations constitute a small fraction of the entire community at the surface but become predominant in the subsurface. We followed patterns of genome diversity with depth in four dominant lineages of the persisting populations by mapping metagenomic sequence reads onto single-cell genomes. Nucleotide sequence diversity was uniformly low and did not change with age and depth of the sediment. Likewise, there was no detectable change in mutation rates and efficacy of selection. Our results indicate that subsurface microbial communities predominantly assemble by selective survival of taxa able to persist under extreme energy limitation.

  • Variant profiling of evolving prokaryotic populations.

    Zojer M, Schuster LN, Schulz F, Pfundner A, Horn M, Rattei T
    2017 - PeerJ, e2997

    Abstract: 

    Genomic heterogeneity of bacterial species is observed and studied in experimental evolution experiments and clinical diagnostics, and occurs as micro-diversity of natural habitats. The challenge for genome research is to accurately capture this heterogeneity with the currently used short sequencing reads. Recent advances in NGS technologies improved the speed and coverage and thus allowed for deep sequencing of bacterial populations. This facilitates the quantitative assessment of genomic heterogeneity, including low frequency alleles or haplotypes. However, false positive variant predictions due to sequencing errors and mapping artifacts of short reads need to be prevented. We therefore created VarCap, a workflow for the reliable prediction of different types of variants even at low frequencies. In order to predict SNPs, InDels and structural variations, we evaluated the sensitivity and accuracy of different software tools using synthetic read data. The results suggested that the best sensitivity could be reached by a union of different tools, however at the price of increased false positives. We identified possible reasons for false predictions and used this knowledge to improve the accuracy by post-filtering the predicted variants according to properties such as frequency, coverage, genomic environment/localization and co-localization with other variants. We observed that best precision was achieved by using an intersection of at least two tools per variant. This resulted in the reliable prediction of variants above a minimum relative abundance of 2%. VarCap is designed for being routinely used within experimental evolution experiments or for clinical diagnostics. The detected variants are reported as frequencies within a VCF file and as a graphical overview of the distribution of the different variant/allele/haplotype frequencies. The source code of VarCap is available at https://github.com/ma2o/VarCap. In order to provide this workflow to a broad community, we implemeted VarCap on a Galaxy webserver, which is accessible at http://galaxy.csb.univie.ac.at.

  • Accurate Quantification of Laminarin in Marine Organic Matter with Enzymes from Marine Microbes.

    Becker S, Scheffel A, Polz MF, Hehemann JH
    2017 - Appl. Environ. Microbiol., 9: in press

    Abstract: 

    Marine algae produce a variety of glycans, which fulfill diverse biological functions and fuel the carbon and energy demands of heterotrophic microbes. A common approach to analysis of marine organic matter uses acid to hydrolyze the glycans into measurable monosaccharides. The monosaccharides may be derived from different glycans that are built with the same monosaccharides, however, and this approach does not distinguish between glycans in natural samples. Here we use enzymes to digest selectively and thereby quantify laminarin in particulate organic matter. Environmental metaproteome data revealed carbohydrate-active enzymes from marine flavobacteria as tools for selective hydrolysis of the algal β-glucan laminarin. The enzymes digested laminarin into glucose and oligosaccharides, which we measured with standard methods to establish the amounts of laminarin in the samples. We cloned, expressed, purified, and characterized three new glycoside hydrolases (GHs) of bacteria: two are endo-β-1,3-glucanases, of the GH16 and GH17 families, and the other is a GH30 exo-β-1,6-glucanase. sp. nov strain Hel1_33_131 GH30 (FbGH30) removed the β-1,6-glucose side chains, and GH17A (FaGH17A) and FaGH16A hydrolyzed the β-1,3-glucose backbone of laminarin. Specificity profiling with a library of glucan oligosaccharides and polysaccharides revealed that FaGH17A and FbGH30 were highly specific enzymes, while FaGH16A also hydrolyzed mixed-linked glucans with β-1,4-glucose. Therefore, we chose the more specific FaGH17A and FbGH30 to quantify laminarin in two cultured diatoms, namely, and , and in seawater samples from the North Sea and the Arctic Ocean. Combined, these results demonstrate the potential of enzymes for faster, stereospecific, and sequence-specific analysis of select glycans in marine organic matter. Marine algae synthesize substantial amounts of the glucose polymer laminarin for energy and carbon storage. Its concentrations, rates of production by autotrophic organisms, and rates of digestion by heterotrophic organisms remain unknown. Here we present a method based on enzymes that hydrolyze laminarin and enable its quantification even in crude substrate mixtures, without purification. Compared to the commonly used acid hydrolysis, the enzymatic method presented here is faster and stereospecific and selectively cleaves laminarin in mixtures of glycans, releasing only glucose and oligosaccharides, which can be easily quantified with reducing sugar assays.

  • Cultivation and characterization of Candidatus Nitrosocosmicus exaquare, an ammonia-oxidizing archaeon from a municipal wastewater treatment system.

    Sauder LA, Albertsen M, Engel K, Schwarz J, Nielsen PH, Wagner M, Neufeld JD
    2017 - ISME J, 5: 1142-1157
    Nitrosocosmicus

    Abstract: 

    Thaumarchaeota have been detected in several industrial and municipal wastewater treatment plants (WWTPs), despite the fact that ammonia-oxidizing archaea (AOA) are thought to be adapted to low ammonia environments. However, the activity, physiology and metabolism of WWTP-associated AOA remain poorly understood. We report the cultivation and complete genome sequence of Candidatus Nitrosocosmicus exaquare, a novel AOA representative from a municipal WWTP in Guelph, Ontario (Canada). In enrichment culture, Ca. N. exaquare oxidizes ammonia to nitrite stoichiometrically, is mesophilic, and tolerates at least 15 mm of ammonium chloride or sodium nitrite. Microautoradiography (MAR) for enrichment cultures demonstrates that Ca. N. exaquare assimilates bicarbonate in association with ammonia oxidation. However, despite using inorganic carbon, the ammonia-oxidizing activity of Ca. N. exaquare is greatly stimulated in enrichment culture by the addition of organic compounds, especially malate and succinate. Ca. N. exaquare cells are coccoid with a diameter of ~1-2 μm. Phylogenetically, Ca. N. exaquare belongs to the Nitrososphaera sister cluster within the Group I.1b Thaumarchaeota, a lineage which includes most other reported AOA sequences from municipal and industrial WWTPs. The 2.99 Mbp genome of Ca. N. exaquare encodes pathways for ammonia oxidation, bicarbonate fixation, and urea transport and breakdown. In addition, this genome encodes several key genes for dealing with oxidative stress, including peroxidase and catalase. Incubations of WWTP biofilm demonstrate partial inhibition of ammonia-oxidizing activity by 2-phenyl-4,4,5,5-tetramethylimidazoline-1-oxyl 3-oxide (PTIO), suggesting that Ca. N. exaquare-like AOA may contribute to nitrification in situ. However, CARD-FISH-MAR showed no incorporation of bicarbonate by detected Thaumarchaeaota, suggesting that detected AOA may incorporate non-bicarbonate carbon sources or rely on an alternative and yet unknown metabolism.

  • A Mobile Element in mutS Drives Hypermutation in a Marine Vibrio.

    Chu ND, Clarke SA, Timberlake S, Polz MF, Grossman AD, Alm EJ
    2017 - mBio, 1: in press

    Abstract: 

    Bacteria face a trade-off between genetic fidelity, which reduces deleterious mistakes in the genome, and genetic innovation, which allows organisms to adapt. Evidence suggests that many bacteria balance this trade-off by modulating their mutation rates, but few mechanisms have been described for such modulation. Following experimental evolution and whole-genome resequencing of the marine bacterium Vibrio splendidus 12B01, we discovered one such mechanism, which allows this bacterium to switch to an elevated mutation rate. This switch is driven by the excision of a mobile element residing in mutS, which encodes a DNA mismatch repair protein. When integrated within the bacterial genome, the mobile element provides independent promoter and translation start sequences for mutS-different from the bacterium's original mutS promoter region-which allow the bacterium to make a functional mutS gene product. Excision of this mobile element rejoins the mutS gene with host promoter and translation start sequences but leaves a 2-bp deletion in the mutS sequence, resulting in a frameshift and a hypermutator phenotype. We further identified hundreds of clinical and environmental bacteria across Betaproteobacteria and Gammaproteobacteria that possess putative mobile elements within the same amino acid motif in mutS In a subset of these bacteria, we detected excision of the element but not a frameshift mutation; the mobile elements leave an intact mutS coding sequence after excision. Our findings reveal a novel mechanism by which one bacterium alters its mutation rate and hint at a possible evolutionary role for mobile elements within mutS in other bacteria.
    DNA mutations are a double-edged sword. Most mutations are harmful; they can scramble precise genetic sequences honed over thousands of generations. However, in rare cases, mutations also produce beneficial new traits that allow populations to adapt to changing environments. Recent evidence suggests that some bacteria balance this trade-off by altering their mutation rates to suit their environment. To date, however, we know of few mechanisms that allow bacteria to change their mutation rates. We describe one such mechanism, driven by the action of a mobile element, in the marine bacterium Vibrio splendidus 12B01. We also found similar mobile genetic sequences in the mutS genes of many different bacteria, including clinical and agricultural pathogens. These mobile elements might play an as yet unknown role in the evolution of these important bacteria.

  • Lifestyle and horizontal gene transfer-mediated evolution of Mucispirillum schaedleri, a core member of the murine gut microbiota

    Loy A, Pfann C, Steinberger M, Hanson B, Herp S, Brugiroux S, Gomes Neto JC, Boekschoten MV, Schwab C, Urich T, Ramer-Tait AE, Rattei T, Stecher B, Berry D
    2017 - mSystems, 2: e00171-16

    Abstract: 

    Mucispirillum schaedleri is an abundant inhabitant of the intestinal mucus layer of rodents and other animals and has been suggested to be a pathobiont, a commensal that plays a role in disease. In order to gain insights into its lifestyle, we analyzed the genome and transcriptome of M. schaedleri ASF 457 and performed physiological experiments to test traits predicted by its genome. Although described as a mucus inhabitant, M. schaedleri has limited capacity for degrading host-derived mucosal glycans and other complex polysaccharides. Additionally, M. schaedleri reduces nitrate and expresses systems for scavenging oxygen and reactive oxygen species in vivo, which may account for its localization close to the mucosal tissue and expansion during inflammation. Also of note, M. schaedleri harbors a type VI secretion system and putative effector proteins and can modify gene expression in mucosal tissue, suggesting intimate interactions with its host and a possible role in inflammation. The M. schaedleri genome has been shaped by extensive horizontal gene transfer, primarily from intestinal Epsilon- and Deltaproteobacteria, indicating that horizontal gene transfer has played a key role in defining its niche in the gut ecosystem.

  • Physiological and gene expression responses to nitrogen regimes and temperatures in Mastigocladus sp. strain CHP1, a predominant thermotolerant cyanobacterium of hot springs.

    Alcamán ME, Alcorta J, Bergman B, Vásquez M, Polz MF, Díez B
    2017 - Syst. Appl. Microbiol., 2: 102-113

    Abstract: 

    Cyanobacteria are widely distributed primary producers with significant implications for the global biogeochemical cycles of carbon and nitrogen. Diazotrophic cyanobacteria of subsection V (Order Stigonematales) are particularly ubiquitous in photoautotrophic microbial mats of hot springs. The Stigonematal cyanobacterium strain CHP1 isolated from the Porcelana hot spring (Chile) was one of the major contributors of the new nitrogen through nitrogen fixation. Further morphological and genetic characterization verified that the strain CHP1 belongs to Stigonematales, and it formed a separate clade together with other thermophiles of the genera Fischerella and Mastigocladus. Strain CHP1 fixed maximum N in the light, independent of the temperature range. At 50°C nifH gene transcripts showed high expression during the light period, whereas the nifH gene expression at 45°C was arrhythmic. The strain displayed a high affinity for nitrate and a low tolerance for high ammonium concentrations, whereas the narB and glnA genes showed higher expression in light and at the beginning of the dark phase. It is proposed that Mastigocladus sp. strain CHP1 would represent a good model for the study of subsection V thermophilic cyanobacteria, and for understanding the adaptations of these photoautotrophic organisms inhabiting microbial mats in hot springs globally.

  • Genomic repertoire of the Woeseiaceae/JTB255, cosmopolitan and abundant core members of microbial communities in marine sediments.

    Mussmann M, Pjevac P, Krüger K, Dyksma S
    2017 - ISME J, 5: 1276-1281

    Abstract: 

    To date, very little is known about the bacterial core community of marine sediments. Here we study the environmental distribution, abundance and ecogenomics of the gammaproteobacterial Woeseiaceae/JTB255 marine benthic group. A meta-analysis of published work shows that the Woeseiaceae/JTB255 are ubiquitous and consistently rank among the most abundant 16S rRNA gene sequences in diverse marine sediments. They account for up to 22% of bacterial amplicons and 6% of total cell counts in European and Australian coastal sediments. The analysis of a single-cell genome, metagenomic bins and the genome of the next cultured relative Woeseia oceani indicated a broad physiological range, including heterotrophy and facultative autotrophy. All tested (meta)genomes encode a truncated denitrification pathway to nitrous oxide. The broad range of energy-yielding metabolisms possibly explains the ubiquity and high abundance of Woeseiaceae/JTB255 in marine sediments, where they carry out diverse, but yet unknown ecological functions.

  • Endemicity of the cosmopolitan mesophilic chemolithoautotroph Sulfurimonas at deep-sea hydrothermal vents.

    Mino S, Nakagawa S, Makita H, Toki T, Miyazaki J, Sievert SM, Polz MF, Inagaki F, Godfroy A, Kato S, Watanabe H, Nunoura T, Nakamura K, Imachi H, Watsuji TO, Kojima S, Takai K, Sawabe T
    2017 - ISME J, 4: 909-919

    Abstract: 

    Rich animal and microbial communities have been found at deep-sea hydrothermal vents. Although the biogeography of vent macrofauna is well understood, the corresponding knowledge about vent microbial biogeography is lacking. Here, we apply the multilocus sequence analysis (MLSA) to assess the genetic variation of 109 Sulfurimonas strains with ⩾98% 16S rRNA gene sequence similarity, which were isolated from four different geographical regions (Okinawa Trough (OT), Mariana Volcanic Arc and Trough (MVAT), Central Indian Ridge (CIR) and Mid-Atlantic Ridge (MAR)). Sequence typing based on 11 protein-coding genes revealed high genetic variation, including some allele types that are widespread within regions, resulting in 102 nucleotide sequence types (STs). This genetic variation was predominantly due to mutation rather than recombination. Phylogenetic analysis of the 11 concatenated genes showed a clear geographical isolation corresponding to the hydrothermal regions they originated from, suggesting limited dispersal. Genetic differentiation among Sulfurimonas populations was primarily influenced by geographical distance rather than gas composition of vent fluid or habitat, although in situ environmental conditions of each microhabitat could not be examined. Nevertheless, Sulfurimonas may possess a higher dispersal capability compared with deep-sea hydrothermal vent thermophiles. This is the first report on MLSA of deep-sea hydrothermal vent Epsilonproteobacteria, which is indicative of allopatric speciation.

  • Microbial nutrient niches in the gut.

    Pereira FC, Berry D
    2017 - Environ. Microbiol., 4: 1366-1378

    Abstract: 

    The composition and function of the mammalian gut microbiota has been the subject of much research in recent years, but the principles underlying the assembly and structure of this complex community remain incompletely understood. Processes that shape the gut microbiota are thought to be mostly niche-driven, with environmental factors such as the composition of available nutrients largely determining whether or not an organism can establish. The concept that the nutrient landscape dictates which organisms can successfully colonize and persist in the gut was first proposed in Rolf Freter's nutrient niche theory. In a situation where nutrients are perfectly mixed and there is balanced microbial growth, Freter postulated that an organism can only survive if it is able to utilize one or a few limiting nutrients more efficiently than its competitors. Recent experimental work indicates, however, that nutrients in the gut vary in space and time. We propose that in such a scenario, Freter's nutrient niche theory must be expanded to account for the co-existence of microorganisms utilizing the same nutrients but in distinct sites or at different times, and that metabolic flexibility and mixed-substrate utilization are common strategies for survival in the face of ever-present nutrient fluctuations.

  • A 12-week intervention with nonivamide, a TRPV1 agonist, prevents a dietary-induced body fat gain and increases peripheral serotonin in moderately overweight subjects.

    Hochkogler CM, Lieder B, Rust P, Berry D, Meier SM, Pignitter M, Riva A, Leitinger A, Bruk A, Wagner S, Hans J, Widder S, Ley JP, Krammer GE, Somoza V
    2017 - Mol Nutr Food Res, 5: 1600731

    Abstract: 

    A bolus administration of 0.15 mg nonivamide has previously been demonstrated to reduce energy intake in moderately overweight men. This 12-week intervention investigated whether a daily consumption of nonivamide in a protein-based product formulation promotes a reduction in body weight in healthy overweight subjects and affects outcome measures associated with mechanisms regulating food intake, e.g. plasma concentrations of (an)orexigenic hormones, energy substrates as well as changes in fecal microbiota.
    Nineteen overweight subjects were randomly assigned to either a control (C) or a nonivamide (NV) group. Changes in the body composition and plasma concentrations of satiating hormones were determined at fasting and 15, 30, 60, 90, and 120 min after a glucose load. Participants were instructed to consume 0.15 mg nonivamide per day in 450 mL of a milk shake additionally to their habitual diet. After treatment, a group difference in body fat mass change (-0.61 ± 0.36% in NV and +1.36 ± 0.38% in C) and an increase in postprandial plasma serotonin were demonstrated. Plasma metabolome and fecal microbiome read outs were not affected.
    A daily intake of 0.15 mg nonivamide helps to support to maintain a healthy body composition.

  • Convergent patterns in the evolution of mealybug symbioses involving different intrabacterial symbionts.

    Szabó G, Schulz F, Toenshoff ER, Volland JM, Finkel OM, Belkin S, Horn M
    2017 - ISME J, 3: 715-726
    Mealybugs (Trabutina mannipara) enveloped in a wax cover feeding on Tamarix twig

    Abstract: 

    Mealybugs (Insecta: Hemiptera: Pseudococcidae) maintain obligatory relationships with bacterial symbionts, which provide essential nutrients to their insect hosts. Most pseudococcinae mealybugs harbor a unique symbiosis setup with enlarged betaproteobacterial symbionts ('Candidatus Tremblaya princeps'), which themselves contain gammaproteobacterial symbionts. Here we investigated the symbiosis of the manna mealybug, Trabutina mannipara, using a metagenomic approach. Phylogenetic analyses revealed that the intrabacterial symbiont of T. mannipara represents a novel lineage within the Gammaproteobacteria, for which we propose the tentative name 'Candidatus Trabutinella endobia'. Combining our results with previous data available for the nested symbiosis of the citrus mealybug Planococcus citri, we show that synthesis of essential amino acids and vitamins and translation-related functions partition between the symbiotic partners in a highly similar manner in the two systems, despite the distinct evolutionary origin of the intrabacterial symbionts. Bacterial genes found in both mealybug genomes and complementing missing functions in both symbioses were likely integrated in ancestral mealybugs before T. mannipara and P. citri diversified. The high level of correspondence between the two mealybug systems and their highly intertwined metabolic pathways are unprecedented. Our work contributes to a better understanding of the only known intracellular symbiosis between two bacteria and suggests that the evolution of this unique symbiosis included the replacement of intrabacterial symbionts in ancestral mealybugs.

  • Vibrio crassostreae, a benign oyster colonizer turned into a pathogen after plasmid acquisition.

    Bruto M, James A, Petton B, Labreuche Y, Chenivesse S, Alunno-Bruscia M, Polz MF, Le Roux F
    2017 - ISME J, 4: 1043-1052

    Abstract: 

    Vibrios are frequently associated with oyster mortality; however whether they are the primary causative agent or secondary opportunistic colonizers is not well understood. Here we combine analysis of natural infection dynamics, population genomics and molecular genetics to ask (i) to what extent oysters are passively colonized by Vibrio population present in the surrounding water, (ii) how populations turn over during pathogenicity events and (iii) what genetic factors are responsible for pathogenicity. We identified several populations of Vibrio preferentially associated with oyster tissues. Among these, Vibrio crassostreae is particularly abundant in diseased animals while nearly absent in the surrounding water, and its pathogenicity is correlated with the presence of a large mobilizable plasmid. We further demonstrate that the plasmid is essential for killing but not necessary for survival in tissues of oysters. Our results suggest that V. crassostreae first differentiated into a benign oyster colonizer that was secondarily turned into a pathogen by introgression of a virulence plasmid into the population, possibly facilitated by elevated host density in farming areas.

  • Direct single-cell biomass estimates for marine bacteria via Archimedes' principle.

    Cermak N, Becker JW, Knudsen SM, Chisholm SW, Manalis SR, Polz MF
    2017 - ISME J, 3: 825-828

    Abstract: 

    Microbes are an essential component of marine food webs and biogeochemical cycles, and therefore precise estimates of their biomass are of significant value. Here, we measured single-cell biomass distributions of isolates from several numerically abundant marine bacterial groups, including Pelagibacter (SAR11), Prochlorococcus and Vibrio using a microfluidic mass sensor known as a suspended microchannel resonator (SMR). We show that the SMR can provide biomass (dry mass) measurements for cells spanning more than two orders of magnitude and that these estimates are consistent with other independent measures. We find that Pelagibacterales strain HTCC1062 has a median biomass of 11.9±0.7 fg per cell, which is five- to twelve-fold smaller than the median Prochlorococcus cell's biomass (depending upon strain) and nearly 100-fold lower than that of rapidly growing V. splendidus strain 13B01. Knowing the biomass contributions from various taxonomic groups will provide more precise estimates of total marine biomass, aiding models of nutrient flux in the ocean.

  • Happens in the best of subfamilies: establishment and repeated replacements of co-obligate secondary endosymbionts within Lachninae aphids.

    Manzano-Marín A, Szabó G, Simon JC, Horn M, Latorre A
    2017 - Environ. Microbiol., 1: 393-408

    Abstract: 

    Virtually all aphids maintain an obligate mutualistic symbiosis with bacteria from the Buchnera genus, which produce essential nutrients for their aphid hosts. Most aphids from the Lachninae subfamily have been consistently found to house additional endosymbionts, mainly Serratia symbiotica. This apparent dependence on secondary endosymbionts was proposed to have been triggered by the loss of the riboflavin biosynthetic capability by Buchnera in the Lachninae last common ancestor. However, an integral large-scale analysis of secondary endosymbionts in the Lachninae is still missing, hampering the interpretation of the evolutionary and genomic analyses of these endosymbionts. Here, we analysed the endosymbionts of selected representatives from seven different Lachninae genera and nineteen species, spanning four tribes, both by FISH (exploring the symbionts' morphology and tissue tropism) and 16S rRNA gene sequencing. We demonstrate that all analysed aphids possess dual symbiotic systems, and while most harbour S. symbiotica, some have undergone symbiont replacement by other phylogenetically-distinct bacterial taxa. We found that these secondary associates display contrasting cell shapes and tissue tropism, and some appear to be lineage-specific. We propose a scenario for symbiont establishment in the Lachninae, followed by changes in the symbiont's tissue tropism and symbiont replacement events, thereby highlighting the extraordinary versatility of host-symbiont interactions.

  • Metabolic and physiological interdependencies in the Bathymodiolus azoricus symbiosis.

    Ponnudurai R, Kleiner M, Sayavedra L, Petersen JM, Moche M, Otto A, Becher D, Takeuchi T, Satoh N, Dubilier N, Schweder T, Markert S
    2017 - ISME J, 11: 463–477

    Abstract: 

    The hydrothermal vent mussel Bathymodiolus azoricus lives in an intimate symbiosis with two types of chemosynthetic Gammaproteobacteria in its gills: a sulfur oxidizer and a methane oxidizer. Despite numerous investigations over the last decades, the degree of interdependence between the three symbiotic partners, their individual metabolic contributions, as well as the mechanism of carbon transfer from the symbionts to the host are poorly understood. We used a combination of proteomics and genomics to investigate the physiology and metabolism of the individual symbiotic partners. Our study revealed that key metabolic functions are most likely accomplished jointly by B. azoricus and its symbionts: (1) CO2 is pre-concentrated by the host for carbon fixation by the sulfur-oxidizing symbiont, and (2) the host replenishes essential biosynthetic TCA cycle intermediates for the sulfur-oxidizing symbiont. In return (3), the sulfur oxidizer may compensate for the host's putative deficiency in amino acid and cofactor biosynthesis. We also identified numerous 'symbiosis-specific' host proteins by comparing symbiont-containing and symbiont-free host tissues and symbiont fractions. These proteins included a large complement of host digestive enzymes in the gill that are likely involved in symbiont digestion and carbon transfer from the symbionts to the host.The ISME Journal advance online publication, 1 November 2016; doi:10.1038/ismej.2016.124.

  • Stable isotope techniques for the assessment of host and microbiota response during gastrointestinal dysfunction

    Butler RN, Kosek M, Krebs N, Loechl C, Loy A, Owino V, Zimmermann M, and Morrison DJ
    2017 - J Pediatr Gastroenterol Nutr, 64: 8-14

    Abstract: 

    The International Atomic Energy Agency convened a technical meeting on environmental enteric dysfunction (EED) in Vienna (28th – 30th October 2015; https://nucleus.iaea.org/HHW/Nutrition/EED_Technical_Meeting/index.html) to bring together international experts in the fields of EED, nutrition and stable isotope technologies. Advances in stable isotope labelling techniques open up new possibilities to improve our understanding of gastrointestinal dysfunction and the role of the microbiota in host health. In the context of EED, little is known about the role gut dysfunction may play in macro- and micronutrient bioavailability and requirements and what the consequences may be for nutritional status and linear growth. Stable isotope labelling techniques have been used to assess intestinal mucosal injury and barrier function, carbohydrate digestion and fermentation, protein derived amino acid bioavailability and requirements, micronutrient bioavailability and to track microbe-microbe and microbe-host interactions at the single cell level. The non-invasive nature of stable isotope technologies potentially allows for low-hazard, field deployable tests of gut dysfunction that are applicable across all age-groups. The purpose of this review is to assess the state-of-the-art in the use of stable isotope technologies and to provide a perspective on where these technologies can be exploited to further our understanding of gut dysfunction in EED.

  • Pediatric obesity is associated with an altered gut microbiota and discordant shifts in Firmicutes populations

    Riva A, Borgo F, Lassandro C, Verduci E, Morace G, Borghi E, Berry D
    2017 - Environ. Microbiol., 1: 95-105

    Abstract: 

    An altered gut microbiota has been linked to obesity in adulthood, although little is known about childhood obesity. The aim of this study was to characterize the composition of the gut microbiota in obese (n = 42) and normal-weight (n = 36) children aged 6 to 16. Using 16S rRNA gene-targeted sequencing, we evaluated taxa with differential abundance according to age- and sex-normalized body mass index (BMI z-score). Obesity was associated with an altered gut microbiota characterized by elevated levels of Firmicutes and depleted levels of Bacteroidetes. Correlation network analysis revealed that the gut microbiota of obese children also had increased correlation density and clustering of operational taxonomic units (OTUs). Members of the Bacteroidetes were generally better predictors of BMI z-score and obesity than Firmicutes, which was likely due to discordant responses of Firmicutes OTUs. In accordance with these observations, the main metabolites produced by gut bacteria, short chain fatty acids (SCFAs), were higher in obese children, suggesting elevated substrate utilisation. Multiple taxa were correlated with SCFA levels, reinforcing the tight link between the microbiota, SCFAs and obesity. Our results suggest that gut microbiota dysbiosis and elevated fermentation activity may be involved in the etiology of childhood obesity.

Book chapters and other publications

5 Publications found
  • Generalized Guideline for Application of Nanoremediation

    Braun J., Malfatti SE, Thilo Hofmann, et all
    2017 - in press
  • Hidden potential: Diet-driven changes in redox level shape the rumen microbiome

    Berry D
    2017 - Environmental microbiology, 1: 19-20
  • The unexpected versatility of the cellulosome

    Berry D
    2017 - Environmental microbiology, 1: 13-14
  • Terriglobus

    Eichorst SA, Trojan D, Woebken D
    2017 - in Bergey's Manual of Systematics of Archaea and Bacteria.. (Whitman WB, Rainey F, Kämpfer P, Trujillo M, Chun J, DeVos P, Hedlund B, Dedysh S)

    Abstract: 

    Terriglobus is a genus in the phylum Acidobacteria in the family Acidobacteriaceae, order Acidobacteriales, class Acidobacteriia, subdivision 1. It currently comprises five species - Terriglobus roseus, Terriglobus saanensis, Terriglobus tenax, Terriglobus aquaticus, and Terriglobus albidus. Members of the genus are widely distributed in soils including rhizosphere soils and the phyllosphere, but is also found in freshwater and in association with insects. This genus encompasses bacteria that are chemo-organotrophs and have obligatory aerobic metabolism with an optimal growth in mildly acidic (pH ~5 to 6) and mesophilic (ca. 25 to 30°C) conditions. Colonies of Terriglobus are typically circular in form with a convex elevation and can be with or without pink pigmentation. These bacteria can use a range of different carbon sources, and nitrogen is attained by exogenous amino acids or ammonium chloride. Cells are non-motile, Gram-stain-negative with a length and width ranging from 0.8 to 2.5 µm and 0.4 to 0.9 µm, respectively. Some strains produce extracellular material, which can be visualized by microscopy or in liquid culture, generating a floc/clumping phenotype. The dominant fatty acids are iso-C15:0 and C16:1 ω7c/ C16:1 ω6c. The DNA G+C content (mol%) ranges from 57.3 to 63.2%.

  • Principles of Systems Biology, No. 13 - A pathogen-resistant designer microbiota

    Stecher B, Clavel T, Loy A, Berry D
    2017 - 4: 3-6
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