Publications

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Publications in peer reviewed journals

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

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

    Abstract: 

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

  • Amino acid production exceeds plant nitrogen demand in Siberian tundra

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

    Abstract: 

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

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

    Oburger E, Cid CV, Preiner J, Hu J, Hann S, Wanek W, Richter A
    2018 - Environmental Science & Technology, in press

    Abstract: 

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

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

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

    Abstract: 

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

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

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

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

    Abstract: 

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

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

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

    Abstract: 

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

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

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

    Abstract: 

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

  • Sampling root exudates – Mission impossible?

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

    Abstract: 

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

  • Significance of dark CO2 fixation in arctic soils

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

    Abstract: 

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

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

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

    Abstract: 

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

  • Recognizing Patterns: Spatial Analysis of Observed Microbial Colonization on Root Surfaces

    Schmidt H, Nunan N, Höck A, Eickhorst T, Kaiser C, Woebken D, Xaynaud X
    2018 - Front Environ Sci, in press

    Abstract: 

    Root surfaces are major sites of interactions between plants and associated microorganisms. Here, plants and microbes communicate via signaling molecules, compete for nutrients, and release substrates that may have beneficial or harmful effects on each other. Whilst the body of knowledge on the abundance and diversity of microbial communities at root-soil interfaces is now substantial, information on their spatial distribution at the microscale is still scarce.
    In this study, a standardized method for recognizing and analyzing microbial cell distributions on root surfaces is presented. Fluorescence microscopy was combined with automated image analysis and spatial statistics to explore the distribution of bacterial colonization patterns on rhizoplanes of rice roots. To test and evaluate the presented approach, a gnotobiotic experiment was performed using a potential nitrogen-fixing bacterial strain in combination with roots of wetland rice. 
    The automated analysis procedure resulted in reliable spatial data of bacterial cells colonizing the rhizoplane. Among all replicate roots, the analysis revealed an increasing density of bacterial cells from the root tip to the region of root cell maturation. Moreover, bacterial cells showed significant spatial clustering and tended to be located around plant root cell walls. The quantitative data suggest that the structure of the root surface plays a major role in bacterial colonization patterns. 
    Possible adaptations of the presented approach for future studies are discussed along with potential pitfalls such as inaccurate imaging. Our results demonstrate that standardized recognition and statistical evaluation of microbial colonization on root surfaces holds the potential to increase our understanding of microbial associations with roots and of the underlying ecological interactions.

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

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

    Abstract: 

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

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

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

    Abstract: 

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

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

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

    Abstract: 

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

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

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

    Abstract: 

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

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

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

    Abstract: 

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

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

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

    Abstract: 

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

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

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

    Abstract: 

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

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

    Müller AL, Pelikan C, de Rezende JR, Wasmund K, Putz M, Glombitza C, Kjeldsen KU, Jørgensen BB, Loy A
    2018 - Environ Microbiol, In press

    Abstract: 

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

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

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

    Abstract: 

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

  • Ammonia monooxygenase-mediated cometabolic biotransformation and hydroxylamine-mediated abiotic transformation of micropollutants in an AOB/NOB co-culture

    Yu Y, Han P, Zhou L-J, Li Z, Wagner M, Men Y
    2018 - Environ Sci Technol, in press

    Abstract: 

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

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

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

    Abstract: 

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

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

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

    Abstract: 

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

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

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

    Abstract: 

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

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

    Kolinko S, Wu YW, Tachea F, Denzel E, Hiras J, Gabriel R, Bäcker N, Chan LJG, Eichorst SA, Frey D, Chen Q, Azadi P, Adams PD, Pray TR, Tanjore D, Petzold CJ, Gladden JM, Simmons BA, Singer SW
    2018 - Nat Microbiol, 3: 99-107
  • Temperature response of permafrost soil carbon is attenuated by mineral protection

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

    Abstract: 

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

  • Fluorinated Gold Nanoparticles for Nanostructure Imaging Mass Spectrometry.

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

    Abstract: 

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

  • Signatures of ecological processes in microbial community time series.

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

    Abstract: 

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

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

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

    Abstract: 

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

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

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

    Abstract: 

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

  • Microbial conservation in the Anthropocene.

    Webster NS, Wagner M, Negri AP
    2018 - Environ. Microbiol., in press
  • Reef Invertebrate Viromics: Diversity, Host-Specificity & Functional Capacity.

    Laffy PW, Wood-Charlson EM, Turaev D, Jutz S, Pascelli C, Botté ES, Bell SC, Peirce T, Weynberg KD, van Oppen MJH, Rattei T, Webster NS
    2018 - Environ. Microbiol., in press

    Abstract: 

    Recent metagenomic analyses have revealed a high diversity of viruses in the pelagic ocean and uncovered clear habitat-specific viral distribution patterns. Conversely, similar insights into the composition, host-specificity and function of viruses associated with marine organisms have been limited by challenges associated with sampling and computational analysis. Here we performed targeted viromic analysis of six coral reef invertebrate species and their surrounding seawater to deliver taxonomic and functional profiles of viruses associated with reef organisms. Sponges and corals host species-specific viral assemblages with low sequence identity to known viral genomes. While core viral genes involved in capsid formation, tail structure and infection mechanisms were observed across all reef samples, auxiliary genes including those involved in herbicide resistance and viral pathogenesis pathways such as host immune suppression were differentially enriched in reef hosts. Utilising a novel OTU based assessment, we also show a prevalence of dsDNA viruses belonging to the Mimiviridae, Caudovirales and Phycodnaviridae in reef environments and further highlight the abundance of ssDNA viruses belonging to the Circoviridae, Parvoviridae, Bidnaviridae and Microviridae in reef invertebrates. These insights into coral reef viruses provide an important framework for future research into how viruses contribute to the health and evolution of reef organisms. This article is protected by copyright. All rights reserved.

  • Microbiomes : Importance of invertebrates in understanding the natural variety of animal-microbe interactions

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

    Abstract: 

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

  • Great Cause-Small Effect: Undeclared Genetically Engineered Orange Petunias Harbor an Inefficient Dihydroflavonol 4-Reductase.

    Haselmair-Gosch C, Miosic S, Nitarska D, Roth BL, Walliser B, Paltram R, Lucaciu RC, Eidenberger L, Rattei T, Olbricht K, Stich K, Halbwirth H
    2018 - Front Plant Sci, 149

    Abstract: 

    A recall campaign for commercial, orange flowering petunia varieties in spring 2017 caused economic losses worldwide. The orange varieties were identified as undeclared genetically engineered (GE)-plants, harboring a maize dihydroflavonol 4-reductase (), which was used in former scientific transgenic breeding attempts to enable formation of orange pelargonidin derivatives from the precursor dihydrokaempferol (DHK) in petunia. How and when the cDNA entered the commercial breeding process is unclear. We provide an in-depth analysis of three orange petunia varieties, released by breeders from three countries, with respect to their transgenic construct, transcriptomes, anthocyanin composition, and flavonoid metabolism at the level of selected enzymes and genes. The two possible sources of the cDNA in the undeclared GE-petunia can be discriminated by PCR. A special version of the gene, the type 2 allele, is present, which includes, at the 3'-end, an additional 144 bp segment from the non-viral transposable sequence, which does not add any functional advantage with respect to DFR activity. This unequivocally points at the first scientific GE-petunia from the 1980s as the source, which is further underpinned e.g., by the presence of specific restriction sites, parts of the untranslated sequences, and the same arrangement of the building blocks of the transformation plasmid used. Surprisingly, however, the GE-petunia cannot be distinguished from native red and blue varieties by their ability to convert DHK in common enzyme assays, as DHK is an inadequate substrate for both the petunia and maize DFR. Recombinant maize DFR underpins the low DHK acceptance, and, thus, the strikingly limited suitability of the protein for a transgenic approach for breeding pelargonidin-based flower color. The effect of single amino acid mutations on the substrate specificity of DFRs is demonstrated. Expression of the gene is generally lower than the petunia expression despite being under the control of the strong, constitutive p promoter. We show that a rare constellation in flavonoid metabolism-absence or strongly reduced activity of both flavonol synthase and B-ring hydroxylating enzymes-allows pelargonidin formation in the presence of DFRs with poor DHK acceptance.

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

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

    Abstract: 

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

  • Peatland Acidobacteria with a dissimilatory sulfur metabolism

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

    Abstract: 

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

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

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

    Abstract: 

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

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

    Romano S
    2018 - Appl. Environ. Microbiol., 8: in press

    Abstract: 

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

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

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

    Abstract: 

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

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

    Bowers RM, Kyrpides NC, Stepanauskas R, Harmon-Smith M, Doud D, Reddy TBK, Schulz F, Jarett J, Rivers AR, Eloe-Fadrosh EA, Tringe SG, Ivanova NN, Copeland A, Clum A, Becraft ED, Malmstrom RR, Birren B, Podar M, Bork P, Weinstock GM, Garrity GM, Dodsworth JA, Yooseph S, Sutton G, Glöckner FO, Gilbert JA, Nelson WC, Hallam SJ, Jungbluth SP, Ettema TJG, Tighe S, Konstantinidis KT, Liu WT, Baker BJ, Rattei T, Eisen JA, Hedlund B, McMahon KD, Fierer N, Knight R, Finn R, Cochrane G, Karsch-Mizrachi I, Tyson GW, Rinke C, Lapidus A, Meyer F, Yilmaz P, Parks DH, Eren AM, Schriml L, Banfield JF, Hugenholtz P, Woyke T
    2018 - Nat. Biotechnol., 2: 196
  • Coexistence of novel gammaproteobacterial and Arsenophonus symbionts in the scale insect Greenisca brachypodii (Hemiptera, Coccomorpha: Eriococcidae)

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

    Abstract: 

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

  • Asian horses deepen the MSY phylogeny.

    Felkel S, Vogl C, Rigler D, Jagannathan V, Leeb T, Fries R, Neuditschko M, Rieder S, Velie B, Lindgren G, Rubin CJ, Schlötterer C, Rattei T, Brem G, Wallner B
    2018 - Anim. Genet., 1: 90-93

    Abstract: 

    Humans have shaped the population history of the horse ever since domestication about 5500 years ago. Comparative analyses of the Y chromosome can illuminate the paternal origin of modern horse breeds. This may also reveal different breeding strategies that led to the formation of extant breeds. Recently, a horse Y-chromosomal phylogeny of modern horses based on 1.46 Mb of the male-specific Y (MSY) was generated. We extended this dataset with 52 samples from five European, two American and seven Asian breeds. As in the previous study, almost all modern European horses fall into a crown group, connected via a few autochthonous Northern European lineages to the outgroup, the Przewalski's Horse. In total, we now distinguish 42 MSY haplotypes determined by 158 variants within domestic horses. Asian horses show much higher diversity than previously found in European breeds. The Asian breeds also introduce a deep split to the phylogeny, preliminarily dated to 5527 ± 872 years. We conclude that the deep splitting Asian Y haplotypes are remnants of a far more diverse ancient horse population, whose haplotypes were lost in other lineages.

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

    Eichorst SA, Trojan D, Roux S, Herbold C, Rattei T, Woebken D
    2018 - Environ. Microbiol., 3: 1041-1063

    Abstract: 

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

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

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

    Abstract: 

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

Book chapters and other publications

4 Publications found
  • Microplastic-Associated Biofilms: A Comparison of Freshwater and Marine Environments

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

    Abstract: 

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

  • Stickstoffkreisläufe in der Abwasserreinigung - neue und bewährte Wege

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

    Abstract: 

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

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

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

    Abstract: 

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

  • Nitrospira.

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

    Abstract: 

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

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