Publications

Publications in peer reviewed journals

28 Publications found
  • 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
    2017 - Environmental Microbiology, in press

    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.

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

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

    Abstract: 

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

  • Advancements in the application of NanoSIMS and Raman microspectroscopy to investigate the activity of microbial cells in soils

    Eichorst SA, Strasser F, Woyke T, Schintlmeister A, Wagner M, Woebken D
    2015 - FEMS Microbiology Ecology - *Editor's Choice Article*, in press

    Abstract: 

    The combined approach of incubating environmental samples with stable isotope-labeled substrates followed by single-cell analyses through high-resolution secondary ion mass spectrometry (NanoSIMS) or Raman microspectroscopy provides insights into the in situ function of microorganisms. This approach has found limited application in soils presumably due to the dispersal of microbial cells in a large background of particles. We developed a pipeline for the efficient preparation of cell extracts from soils for subsequent single-cell methods by combining cell detachment with separation of cells and soil particles followed by cell concentration. The procedure was evaluated by examining its influence on cell recoveries and microbial community composition across two soils. This approach generated a cell fraction with considerably reduced soil particle load and of sufficient small size to allow single-cell analysis by NanoSIMS, as shown when detecting active N2-fixing and cellulose-responsive microorganisms via 15N2 and 13C-UL-cellulose incubations, respectively. The same procedure was also applicable for Raman microspectroscopic analyses of soil microorganisms, assessed via microcosm incubations with a 13C-labeled carbon source and deuterium oxide (D2O, a general activity marker). The described sample preparation procedure enables single-cell analysis of soil microorganisms using NanoSIMS and Raman microspectroscopy, but should also facilitate single-cell sorting and sequencing.

  • Tracking heavy water (D2O) incorporation for identifying and sorting active microbial cells

    Berry D, Mader E, Lee TK, Woebken D, Wang Y, Zhu D, Palatinszky M, Schintlmeister A, Schmid MC, Hanson BT, Shterzer N, Mizrahi I, Rauch I, Decker T, Bocklitz T, Popp J, Gibson CM, Fowler PW, Huang WE, Wagner M
    2015 - Proc Natl Acad Sci USA, 112: E194-203

    Abstract: 

    Microbial communities are essential to the function of virtually all ecosystems and eukaryotes, including humans. However, it is still a major challenge to identify microbial cells active under natural conditions in complex systems. In this study, we developed a new method to identify and sort active microbes on the single-cell level in complex samples using stable isotope probing with heavy water (D2O) combined with Raman microspectroscopy. Incorporation of D2O-derived D into the biomass of autotrophic and heterotrophic bacteria and archaea could be unambiguously detected via C-D signature peaks in single-cell Raman spectra, and the obtained labeling pattern was confirmed by nanoscale-resolution secondary ion MS. In fast-growing Escherichia coli cells, label detection was already possible after 20 min. For functional analyses of microbial communities, the detection of D incorporation from D2O in individual microbial cells via Raman microspectroscopy can be directly combined with FISH for the identification of active microbes. Applying this approach to mouse cecal microbiota revealed that the host-compound foragers Akkermansia muciniphila and Bacteroides acidifaciens exhibited distinctive response patterns to amendments of mucin and sugars. By Raman-based cell sortingof active (deuterated) cells with optical tweezers and subsequent multiple displacement amplification and DNA sequencing, novel cecal microbes stimulated by mucin and/or glucosamine were identified, demonstrating the potential of the nondestructive D2O-Raman approach for targeted sortingof microbial cells with defined functional properties for single-cell genomics.

  • Revisiting N₂ fixation in Guerrero Negro intertidal microbial mats with a functional single-cell approach

    Woebken D, Burow L, Behnam F, Mayali X, Schintlmeister A, Fleming E, Prufert-Bebout L, Singer S, López Cortés A, Hoehler T, Pett-Ridge J, Spormann A, Wagner M, Weber P, Bebout B
    2015 - ISME J, 9: 485-96

    Abstract: 

    Photosynthetic microbial mats are complex, stratified ecosystems in which high rates of primary production create a demand for nitrogen, met partially by N₂ fixation. Dinitrogenase reductase (nifH) genes and transcripts from Cyanobacteria and heterotrophic bacteria (for example, Deltaproteobacteria) were detected in these mats, yet their contribution to N2 fixation is poorly understood. We used a combined approach of manipulation experiments with inhibitors, nifH sequencing and single-cell isotope analysis to investigate the active diazotrophic community inintertidal microbial mats at Laguna Ojo de Liebre near Guerrero Negro, Mexico. Acetylene reduction assays with specific metabolic inhibitors suggested that both sulfate reducers and members of the Cyanobacteria contributed to N₂ fixation, whereas (15)N₂ tracer experiments at the bulk level only supported a contribution of Cyanobacteria. Cyanobacterial and nifH Cluster III (including deltaproteobacterial sulfate reducers) sequences dominated the nifH gene pool, whereas the nifH transcript pool was dominated by sequences related to Lyngbya spp. Single-cell isotope analysis of (15)N₂-incubated mat samples via high-resolution secondary ion mass spectrometry (NanoSIMS) revealed that Cyanobacteria were enriched in (15)N, with the highest enrichment being detected in Lyngbya spp. filaments (on average 4.4 at% (15)N), whereas the Deltaproteobacteria (identified by CARD-FISH) were not significantly enriched. We investigated the potential dilution effect from CARD-FISH on the isotopic composition and concluded that the dilution bias was not substantial enough to influence our conclusions. Our combined data provide evidence that members of the Cyanobacteria, especially Lyngbya spp., actively contributed to N₂ fixation in the intertidal mats, whereas support for significant N₂ fixation activity of the targeted deltaproteobacterial sulfate reducers could not be found.

  • Bacteria from diverse habitats colonize and compete in the mouse gut

    Seedorf H, Griffin NW, Ridaura VK, Reyes A, Cheng J, Rey FE, Smith MI, Simon GM, Scheffrahn RH, Woebken D, Spormann AM, Van Treuren W, Ursell LK, Pirrung M, Robbins-Pianka A, Cantarel BL, Lombard V, Henrissat B, Knight R, Gordon JI.
    2014 - Cell, 159: 253-266
  • Identification of Desulfobacterales as primary hydrogenotrophs in a complex microbial mat community

    Burow LC, Woebken D, Bebout BM, Marshall IPG, Singer SW, Pett-Ridge J, Prufert-Bebout L, Spormann AM, Weber PK, Hoehler TM
    2014 - Geobiology, 12: 221-230

    Abstract: 

    Hypersaline microbial mats have been shown to produce significant quantities of H2 under dark, anoxic conditions via cyanobacterial fermentation. This flux of a widely accessible microbial substrate has potential to significantly influence the ecology of the mat, and any consumption will affect the net efflux of H2 that might otherwise be captured as a resource. Here, we focus on H2 consumption in a microbial mat from Elkhorn Slough, California, USA, for which H2 production has been previously characterized. Active biologic H2 consumption in this mat is indicated by a significant time-dependent decrease in added H2 compared with a killed control. Inhibition of sulfate reduction, as indicated by a decrease in hydrogen sulfide production relative to controls, resulted in a significant increase in H2 efflux, suggesting that sulfate-reducing bacteria (SRB) are important hydrogenotrophs. Low methane efflux under these same conditions indicated that methanogens are likely not important hydrogenotrophs. Analyses of genes and transcripts that encode for rRNA or dissimilatory sulfite reductase, using both PCR-dependent and PCR-independent metatranscriptomic sequencing methods, demonstrated that Desulfobacterales are the dominant, active SRB in the upper, H2-producing layer of the mat (0-2 mm). This hypothesis was further supported by the identification of transcripts encoding hydrogenases derived from Desulfobacterales capable of H2 oxidation. Analysis of molecular data provided no evidence for the activity of hydrogenotrophic methanogens. The combined biogeochemical and molecular data strongly indicate that SRB belonging to the Desulfobacterales are the quantitatively important hydrogenotrophs in the Elkhorn Slough mat.

  • Fermentation couples Chloroflexi and sulfate-reducing bacteria to Cyanobacteria in hypersaline microbial mats

    Lee JZ, Burow LC, Woebken D, Everroad RC, Kubo MD, Spormann AM, Weber PK, Pett-Ridge J, Bebout BM, Hoehler TM
    2014 - Front Microbiol., 5:61

    Abstract: 

    Past studies of hydrogen cycling in hypersaline microbial mats have shown an active nighttime cycle, with production largely from Cyanobacteriaand consumption from sulfate-reducing bacteria (SRB). However, the mechanisms and magnitude of hydrogen cycling have not been extensively studied. Two mats types near Guerrero Negro, Mexico-permanently submerged Microcoleus microbial mat (GN-S), and intertidal Lyngbya microbialmat (GN-I)-were used in microcosm diel manipulation experiments with 3-(3,4-dichlorophenyl)-1,1-dimethylurea (DCMU), molybdate, ammonium addition, and physical disruption to understand the processes responsible for hydrogen cycling between mat microbes. Across microcosms, H2 production occurred under dark anoxic conditions with simultaneous production of a suite of organic acids. H2 production was not significantly affected by inhibition of nitrogen fixation, but rather appears to result from constitutive fermentation of photosynthetic storage products by oxygenic phototrophs. Comparison to accumulated glycogen and to CO2 flux indicated that, in the GN-I mat, fermentation released almost all of the carbon fixed via photosynthesis during the preceding day, primarily as organic acids. Across mats, although oxygenic and anoxygenic phototrophs were detected, cyanobacterial [NiFe]-hydrogenase transcripts predominated. Molybdate inhibition experiments indicated that SRBs from a wide distribution of DsrA phylotypes were responsible for H2 consumption. Incubation with (13)C-acetate and NanoSIMS (secondary ion mass-spectrometry) indicated higher uptake in both Chloroflexi and SRBs relative to other filamentous bacteria. These manipulations and diel incubations confirm thatCyanobacteria were the main fermenters in Guerrero Negro mats and that the net flux of nighttime fermentation byproducts (not only hydrogen) was largely regulated by the interplay between Cyanobacteria, SRBs, and Chloroflexi.

  • Draft genome sequence of an oscillatorian cyanobacterium, strain ESFC-1

    Everroad RC, Woebken D, Singer SW, Burow LC, Kyrpides N, Woyke T, Goodwin L, Detweiler A, Prufert-Bebout L, Pett-Ridge J
    2013 - Genome Announc., 1: e00527-13

    Abstract: 

    The nonheterocystous filamentous cyanobacterium strain ESFC-1 has recently been isolated from a marine microbial mat system, where it was identified as belonging to a recently discovered lineage of active nitrogen-fixing microorganisms. Here, we report the draft genome sequence of this isolate. The assembly consists of 3 scaffolds and contains 5,632,035 bp with a GC content of 46.5%.

  • Anoxic carbon flux in photosynthetic microbial mats as revealed by metatranscriptomics and NanoSIMS

    Burow LC, Woebken D, Marshall IPG, Lindquist EA, Bebout BM, Prufert-Bebout L, Hoehler TM, Tringe SG, Pett-Ridge J, Weber PK, Spormann AM, Singer SW
    2013 - The ISME Journal, 7: 817-829

    Abstract: 

    Photosynthetic microbial mats possess extraordinary phylogenetic and functional diversity that makes linking specific pathways with individual microbial populations a daunting task. Close metabolic and spatial relationships between Cyanobacteria and Chloroflexi have previously been observed in diverse microbial mats. Here, we report that an expressed metabolic pathway for the anoxic catabolism of photosynthate involving Cyanobacteria and Chloroflexi in microbial mats can be reconstructed through metatranscriptomic sequencing of mats collected at Elkhorn Slough, Monterey Bay, CA, USA. In this reconstruction, Microcoleus spp., the most abundant cyanobacterial group in the mats, ferment photosynthate to organic acids, CO2 and H2 through multiple pathways, and an uncultivated lineage of the Chloroflexi take up these organic acids to store carbon as polyhydroxyalkanoates. The metabolic reconstruction is consistent with metabolite measurements and single cell microbial imaging with fluorescence in situ hybridization and NanoSIMS.

  • The metagenome of the marine anammox bacterium ‘Candidatus Scalindua profunda’ illustrates the versatility of this globally important nitrogen cycle bacterium

    van de Vossenberg J, Woebken D, Maalcke WJ, Wessels HJCT, Dutilh BE, Kartal B, Janssen-Megens EM, Roeselers G, Yan J, Speth D, Gloerich J, Geerts W, van der Biezen E, Pluk W, Francoijs K-J, Russ L, Lam P, Malfatti SA, Tringe SG, Haaijer SCM, op den Camp HJM, Stunnenberg HG, Amann R, Kuypers MMM, Jetten MSM
    2013 - Environmental Microbiology, 15: 1275-1289

    Abstract: 

    Anaerobic ammonium-oxidizing (anammoxbacteria are responsible for a significant portion of the loss of fixed nitrogen from the oceans, making them important players in the global nitrogen cycle. To date, marine anammox bacteria found in marine water columns and sediments worldwide belong almost exclusively to the 'Candidatus Scalindua' species, but the molecular basis of their metabolism and competitive fitness is presently unknown. We applied community sequencing of a marine anammoxenrichment culture dominated by 'Candidatus Scalindua profunda' to construct a genome assembly, which was subsequently used to analyse the most abundant gene transcripts and proteins. In the S. profunda assembly, 4756 genes were annotated, and only about half of them showed the highest identity to the only other anammox bacterium of which a metagenome assembly had been constructed so far, the freshwater 'Candidatus Kuenenia stuttgartiensis'. In total, 2016 genes of S. profunda could not be matched to the K. stuttgartiensis metagenome assembly at all, and a similar number of genes in K.stuttgartiensis could not be found in S. profunda. Most of these genes did not have a known function but 98 expressed genes could be attributed to oligopeptide transport, amino acid metabolism, use of organic acids and electron transport. On the basis of the S. profunda metagenome, and environmental metagenome data, we observed pronounced differences in the gene organization and expression of importantanammox enzymes, such as hydrazine synthase (HzsAB), nitrite reductase (NirS) and inorganic nitrogen transport proteins. Adaptations of Scalindua to the substrate limitation of the ocean may include highly expressed ammonium, nitrite and oligopeptide transport systems and pathways for the transport, oxidation, and assimilation of small organic compounds that may allow a more versatile lifestyle contributing to the competitive fitness of Scalindua in the marine realm.

  • Identification of a novel cyanobacterial group as active diazotrophs in a coastal microbial mat using NanoSIMS analysis

    Woebken D, Burow LC, Prufert-Bebout L, Bebout BM, Hoehler TM, Pett-Ridge J, Singer SW§, Spormann AM, Weber PK
    2012 - The ISME Journal, 6: 1427-1439

    Abstract: 

    N(2) fixation is a key process in photosynthetic microbial mats to support the nitrogen demands associated with primary production. Despite its importance, groups that actively fix N(2) and contribute to the input of organic N in these ecosystems still remain largely unclear. To investigate the active diazotrophic community in microbial mats from the Elkhorn Slough estuary, Monterey Bay, CA, USA, we conducted an extensive combined approach, including biogeochemical, molecular and high-resolution secondary ion mass spectrometry (NanoSIMS) analyses. Detailed analysis of dinitrogenase reductase (nifH) transcript clone libraries from mat samples that fixed N(2) at night indicated that cyanobacterial nifH transcripts were abundant and formed a novel monophyletic lineage. Independent NanoSIMS analysis of (15)N(2)-incubated samples revealed significant incorporation of (15)N into small, non-heterocystous cyanobacterial filaments. Mat-derived enrichment cultures yielded a unicyanobacterial culture with similar filaments (named Elkhorn Slough Filamentous Cyanobacterium-1 (ESFC-1)) that contained nifH gene sequences grouping with the novel cyanobacterial lineage identified in the transcript clone libraries, displaying up to 100% amino-acid sequence identity. The 16S rRNA gene sequence recovered from this enrichment allowed for the identification of related sequences from Elkhorn Slough mats and revealed great sequence diversity in this cluster. Furthermore, by combining (15)N(2) tracer experiments, fluorescence in situ hybridization and NanoSIMS, in situ N(2) fixation activity by the novel ESFC-1 group was demonstrated, suggesting that this group may be the most active cyanobacterial diazotroph in the Elkhorn Slough mat. Pyrotag sequences affiliated with ESFC-1 were recovered from mat samples throughout 2009, demonstrating the prevalence of this group. This work illustrates that combining standard and single-cell analyses can link phylogeny and function to identify previously unknown key functional groups in complex ecosystems.

  • Hydrogen production in photosynthetic microbial mats in the Elkhorn Slough estuary, Monterey Bay

    Burow LC, Woebken D, Bebout BM, McMurdie PJ, Singer SW, Pett-Ridge J, Prufert-Bebout L, Spormann AM, Weber PK, Hoehler TM
    2012 - The ISME Journal, 6: 863-874

    Abstract: 

    Hydrogen (H(2)) release from photosynthetic microbial mats has contributed to the chemical evolution of Earth and could potentially be a source of renewable H(2) in the future. However, the taxonomy of H(2)-producing microorganisms (hydrogenogens) in these mats has not been previously determined. With combined biogeochemical and molecular studies of microbial mats collected from Elkhorn SloughMonterey Bay, California, we characterized the mechanisms of H(2) production and identified a dominant hydrogenogen. Net production of H(2) was observed within the upper photosynthetic layer (0-2 mm) of the mats under dark and anoxic conditions. Pyrosequencing of rRNA gene libraries generated from this layer demonstrated the presence of 64 phyla, with Bacteriodetes, Cyanobacteria and Proteobacteria dominating the sequences. Sequencing of rRNA transcripts obtained from this layer demonstrated that Cyanobacteria dominated rRNA transcript pyrotag libraries. An OTU affiliated to Microcoleus spp. was the most abundant OTU in both rRNA gene and transcript libraries. Depriving mats of sunlight resulted in an order of magnitude decrease in subsequent nighttime H(2) production, suggesting that newly fixed carbon is critical to H(2) production. Suppression of nitrogen (N(2))-fixation in the mats did not suppress H(2) production, which indicates that co-metabolic production of H(2) during N(2)-fixation is not an important contributor to H(2) production. Concomitant production of organic acids is consistent with fermentation of recently produced photosynthate as the dominant mode of H(2) production. Analysis of rRNA % transcript:% gene ratios and H(2)-evolving bidirectional [NiFe] hydrogenase % transcript:% gene ratios indicated that Microcoelus spp. are dominant hydrogenogens in the Elkhorn Slough mats.

  • Microbial nitrate-dependent cyclohexane degradation coupled with anaerobic ammonium oxidation

    Musat F, Wilkes H, Behrends A, Woebken D, Widdel F. 2010
    2010 - The ISME Journal, 4: 1290-1301
  • Anammox bacteria and the anaerobic oxidation of ammonium in the oxygen minimum zone off northern Chile

    Galan A, Molina V, Thamdrup B, Woebken D, Lavik G, Kuypers MMM, Ulloa O
    2009 - Deep-Sea Research II, 56: 1021-1031
  • Complex nitrogen cycling in the sponge Geodia barretti

    Hoffmann F, Radax R, Woebken D, Holtappels M, Lavik G, Rapp HT, Schläppy M-L, Schleper C, Kuypers MMM
    2009 - Environmental Microbiology, 11: 2228-2243
  • Water column anammox and denitrification in a temperate permanently-stratified lake (Lake Rassnitzer, Germany)

    Hamersley MR, Woebken D, Boehrer B, Schulze M, Lavik G, Kuypers MMM
    2009 - Systematic and Applied Microbiology, 32: 571-582
  • Revising the nitrogen cycle in the Peruvian oxygen minimum zone

    Lam P, Lavik G, Jensen MM, van de Vossenberg J, Schmid M, Woebken D, Gutiérrez D, Amann R, Jetten MSM, Kuypers MMM
    2008 - Proc. Natl. Acad. Sci. U.S.A., 106: 4752-4757

    Abstract: 

    The oxygen minimum zone (OMZ) of the Eastern Tropical South Pacific (ETSP) is 1 of the 3 major regions in the world where oceanic nitrogen is lost in the pelagic realm. The recent identification of anammox, instead of denitrification, as the likely prevalent pathway for nitrogen loss in this OMZ raises strong questions about our understanding of nitrogen cycling and organic matter remineralization in these waters. Without detectable denitrification, it is unclear how NH(4)(+) is remineralized from organic matter and sustains anammox or how secondary NO(2)(-) maxima arise within the OMZ. Here we show that in the ETSP-OMZ, anammox obtains 67% or more of NO(2)(-) from nitrate reduction, and 33% or less from aerobic ammonia oxidation, based on stable-isotope pairing experiments corroborated by functional gene expression analyses. Dissimilatory nitrate reduction to ammonium was detected in an open-ocean setting. It occurred throughout the OMZ and could satisfy a substantial part of the NH(4)(+) requirement for anammox. The remaining NH(4)(+) came from remineralization via nitrate reduction and probably from microaerobic respiration. Altogether, deep-sea NO(3)(-) accounted for only approximately 50% of the nitrogen loss in the ETSP, rather than 100% as commonly assumed. Because oceanic OMZs seem to be expanding because of global climate change, it is increasingly imperative to incorporate the correct nitrogen-loss pathways in global biogeochemical models to predict more accurately how the nitrogen cycle in our future ocean may respond.

  • Environmental detection of octahaem cytochrome chydroxylamine/hydrazine oxidoreductase genes of aerobic and anaerobic ammonium-oxidizing bacteria

    Schmid MC, Hooper AB, Klotz MG, Woebken D, Lam P, Kuypers MMM, Pommerening-Roeser A, op den Camp HJM, Jetten MSM
    2008 - Environmental Microbiology, 10: 3140-3149
  • Microdiversity study of marine anammox bacteria reveals a novel Candidatus Scalindua phylotype in marine oxygen minimum zones

    Woebken D, Lam P, Fuchs BM, Kuypers MMM, Naqvi SWA, Kartal B, Strous M, Jetten MSM, Amann R
    2008 - Environmental Microbiology, 10: 3106-3119

    Abstract: 

    The anaerobic oxidation of ammonium (anammox) contributes significantly to the global loss of fixed nitrogen and is carried out by a deep branching monophyletic group of bacteria within the phylum Planctomycetes. Various studies have implicated anammox to be the most important process responsible for the nitrogen loss in the marine oxygen minimum zones (OMZs) with a low diversity of marine anammox bacteria. This comprehensive study investigated the anammox bacteria in the suboxic zone of the Black Sea and in three major OMZs (off Namibia, Peru and in the Arabian Sea). The diversity and population composition of anammoxbacteria were investigated by both, the 16S rRNA gene sequences and the 16S-23S rRNA internal transcribed spacer (ITS). Our results showed that the anammox bacterial sequences of the investigated samples were all closely related to the CandidatusScalindua genus. However, a greater microdiversity of marine anammox bacteria than previously assumed was observed. Both phylogenetic markers supported the classification of all sequences in two distinct anammox bacterial phylotypesCandidatusScalindua clades 1 and 2. Scalindua 1 could be further divided into four distinct clusters, all comprised of sequences from either the Namibian or the Peruvian OMZ. Scalindua 2 consisted of sequences from the Arabian Sea and the Peruvian OMZ and included one previously published 16S rRNA gene sequence from Lake Tanganyika and one from South China Sea sediment (97.9-99.4% sequence identity). This cluster showed only <or= 97% sequence identity to other known Candidatus Scalinduaspecies. Based on 16S rRNA gene and ITS sequences we propose that the anammox bacteria of Scalindua clade 2 represent a novel anammox bacterial species, for which the name Candidatus Scalindua arabica is proposed. As sequences of this new cluster were found in the Arabian Sea, the Peruvian OMZ, in Lake Tanganyika and in South China sediment, we assume a global distribution of Candidatus Scalindua arabica as it is observed for Candidatus Scalindua sorokinii/brodae (or Scalindua clade 1).

  • Anaerobic ammonium oxidation in the Peruvian oxygen minimum zone

    Hamersley MR, Lavik G, Woebken D, Rattray JE, Lam P, Hopmans EC, Sinninghe Damsté JS, Krüger S, Graco M, Gutiérrez D, Kuypers MMM
    2007 - Limnology and Oceanography, 52: 923-933
  • Microbial ecology of the stratified water column of the Black Sea as revealed by a comprehensive biomarker study

    Wakeham SG, Amann R, Freeman KH, Hopmans EC, Jørgensen BB, Putnam IF, Schouten S, Sinninghe Damsté JS, Talbot HM, Woebken D
    2007 - Organic Geochemistry, 38: 2070-2097
  • Shift from denitrification to anammox after inflow events in the central Baltic Sea

    Hannig M, Lavik G, Kuypers MMM, Woebken D, Martens-Habbena W, Jürgens K
    2007 - Limnology and Oceanography, 52: 1336-1345
  • Fosmids of novel marine Planctomycetes from the Namibian and Oregon coast upwelling systems and their cross-comparison with planctomycete genomes

    Woebken D, Teeling H, Dumitriu A, Kostadinov I, Amann R, Glöckner FO
    2007 - The ISME Journal, 1: 419-435

    Abstract: 

    Planctomycetes are widely distributed in marine environments, where they supposedly play a role in carbon recycling. To deepen our understanding about the ecology of this sparsely studied phylum six planctomycete fosmids from two marine upwellingsystems were investigated and compared with all available planctomycete genomic sequences including the as yet unpublished near-complete genomes of Blastopirellula marina DSM 3645(T) and Planctomyces maris DSM 8797(T). High numbers of sulfatase genes (41-109) were found on all marine planctomycete genomes and on two fosmids (2). Furthermore, C1 metabolism genes otherwise only known from methanogenic Archaea and methylotrophic Proteobacteria were found on two fosmids and all planctomycete genomes, except for 'Candidatus Kuenenia stuttgartiensis'. Codon usage analysis indicated high expression levels for some of these genes. In addition, novel large families of planctomycete-specific paralogs with as yet unknown functions were identified, which are notably absent from the genome of 'Candidatus Kuenenia stuttgartiensis'. The high numbers of sulfatases in marine planctomycetes characterizes them as specialists for the initial breakdown of sulfatated heteropolysaccharides and indicate their importance for recycling carbon from these compounds. The almost ubiquitous presence of C1 metabolism genes among Planctomycetes together with codon usage analysis and information from the genomes suggest a general importance of these genes for Planctomycetes other than formaldehyde detoxification. The notable absence of these genes in Candidatus K. stuttgartiensis plus the surprising lack of almost any planctomycete-specific gene within this organism reveals an unexpected distinctiveness of anammox bacteria from all other Planctomycetes.

  • Potential interactions of particle-associated anammox bacteria with bacterial and archaeal partners in the Namibian upwelling system

    Woebken D, Fuchs BM, Kuypers MMM, Amann R
    2007 - Applied and Environmental Microbiology, 73: 4648-4657

    Abstract: 

    Recent studies have shown that the anaerobic oxidation of ammonium by anammox bacteria plays an important role in catalyzing the loss of nitrogen from marine oxygen minimum zones (OMZ). However, in situ oxygen concentrations of up to 25 microM and ammonium concentrations close to or below the detection limit in the layer of anammox activity are hard to reconcile with the current knowledge of the physiology of anammox bacteria. We therefore investigated samples from the Namibian OMZ by comparative 16S rRNA gene analysis and fluorescence in situ hybridization. Our results showed that "Candidatus Scalindua" spp., the typical marine anammox bacteria, colonized microscopic particles that were likely the remains of either macroscopic marine snow particles or resuspended particles. These particles were slightly but significantly (P < 0.01) enriched in Gammaproteobacteria (11.8% +/- 5.0%) compared to the free-water phase (8.1% +/- 1.8%). No preference for the attachment to particles could be observed for members of the Alphaproteobacteria and Bacteroidetes, which were abundant (12 to 17%) in both habitats. The alphaproteobacterial SAR11 clade, the Euryarchaeota, and group I Crenarchaeota, were all significantly depleted in particles compared to their presence in the free-water phase (16.5% +/- 3.5% versus 2.6% +/- 1.7%, 2.7% +/- 1.9% versus <1%, and 14.9% +/- 4.6% versus 2.2% +/- 1.8%, respectively, all P < 0.001). Sequence analysis of the crenarchaeotal 16S rRNA genes showed a 99% sequence identity to the nitrifying "Nitrosopumilus maritimus." Even though we could not observe conspicuous consortium-like structures of anammox bacteria with particle-enriched bacterioplankton groups, we hypothesize that members of Gammaproteobacteria, Alphaproteobacteria, and Bacteroidetes play a critical role in extending the anammox reaction to nutrient-depleted suboxic water layers in the Namibian upwelling system by creating anoxic, nutrient-enriched microniches.

  • Whole genome analysis of the marine Bacteroidetes Gramella forsetii reveals adaptations to degradation of polymeric organic matter

    Bauer M, Kube M, Teeling H, Richter M, Lombardot T, Allers E, Wurdemann CA, Quast C, Kuhl H, Knaust F, Woebken D, Bischof K, Mussmann M, Choudhuri JV, Meyer F, Reinhardt R, Amann R, FO Glöckne
    2006 - Environmental Microbiology, 8: 2201-2213
  • Molecular identification of picoplankton populations in contrasting waters of the Arabian Sea

    Fuchs BM, Woebken D, Zubkov MV, Burkhill P, Amann R
    2005 - Aquat. Microb. Ecol., 39: 145-157
  • Massive nitrogen loss from the Benguela upwelling system through anaerobic ammonium oxidation

    Kuypers MMM, Lavik G, Woebken D, Schmid M, Fuchs BM, Amann R, Jorgensen BB, Jetten MSM
    2005 - Proc Natl Acad Sci USA, 102: 6478-6483

Book chapters and other publications

2 Publications found
  • Genus Terriglobus

    2017 - in press. in Bergey’s Manual of Systematics of Archaea and Bacteria. (William B. Whitman). John Wiley & Sons, Chichester, England

    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%.

  • Investigation of microorganisms at the single-cell level using Raman Microspectroscopy and Nanometer-scale Secondary Ion Mass Spectrometry.

    2014 - pp. 203-211. in Molecular Methods and Applications in Microbiology. (Skovhus TL, Caffrey S, Hubert CRJ). Caister Academic Press, Norfolk, UK

    Abstract: 

    The field of single-cell ecophysiology has taken an exciting turn with the introduction of two powerful techniques, nanometer-scale secondary ion mass spectrometry (NanoSIMS) and Raman microspectroscopy. These techniques allow the investigation of microorganisms and their associated activity at the single-cell level. When combined with stable isotope tracers and/or identification of the targeted cell using fluorescence in situ hybridization (FISH), they have the potential to link the identity of a microorganism with its in situ activity. Raman microspectroscopy detects the scattering of light due to interaction with chemical bonds of cell constituents thereby providing compound specific information, which can also be used for bacterial identification. NanoSIMS permits highly sensitive analysis of multiple elements or isotopes with sub-micrometer spatial resolution, allowing the measurements of microbial activity when used in stable-isotope tracer experiments. In this chapter we present the principle for each technique, discuss their strengths and weaknesses, and document their applicability with particular emphasis on microbial ecology research. The integration of these single-cell techniques in the field of microbial ecology will improve our understanding of the ecophysiology of (novel) microorganisms across a multitude of environments.