DOCSLIB.ORG

Molecular Characterisation of Microbial Communities Involved In

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Molecular Characterisation of Microbial Communities Involved In Molecular characterisation of microbial communities involved in nitrate-driven anaerobic oxidation of methane Mohamed Fauzi Haroon BBiotech (Hons I), University of Queensland A thesis submitted for the degree of Doctor of Philosophy at The University of Queensland in 2014 School of Chemistry and Molecular Biosciences, Australian Centre for Ecogenomics Abstract Methane is a potent greenhouse gas, approximately 30 times more effective in trapping heat than carbon dioxide, and contributes significantly to global warming. In nature, methane can be produced and consumed by microbes. One of the most important methane sinks is anaerobic oxidation of methane (AOM), which is responsible for substantial consumption of methane from anoxic environments by coupling its oxidation to various electron acceptors. This thesis aims to understand the microorganisms associated with AOM coupled to nitrate reduction, a process that is of increasing environmental relevance as water bodies become eutrophied through endemic use of fertilisers for agriculture. The first report of a consortium capable of AOM coupled to denitrification was reported in 2006, comprised of an anaerobic methanotrophic (ANME) archaea belonging to the family ANME-2d, now known as Candidatus Methanoperedens nitroreducens, and a bacterial member Candidatus Methlomirabilis oxyfera. However, long-term incubations demonstrate that the M. nitroreducens can be absent from the process and that M. oxyfera is capable of performing AOM alone by coupling to nitrite reduction. The disappearance of M. nitroreducens brought into question its role in the initial consortium. Here, microbial community profiling of nitrate-driven AOM reactors showed that M. nitroreducens dominated the community. In Chapter Two, a novel method that modified the conventional fluorescence in situ hybridisation (FISH) by removing the fixation-step and separated cells of interest using fluorescence activated cell sorting (FACS), was developed with the goal of sequencing single-cells of M. nitroreducens. This fixation-free method was believed to eliminate the crosslinking of protein and nucleic acid by fixatives, thus increasing the nucleic acid yield for sequencing. As a proof of concept, the fixation- free FISH-FACS method was successfully applied to populations of monoderm and diderm cells. Using an optimised approach, single cells and populations of M. nitroreducens were separated away from other community members for genome sequencing. These results are presented as a published book chapter. To further elucidate the role of M. nitroreducens in nitrate-driven AOM, detailed analysis of metagenomic, single-cell genomics and metatranscriptomics data was undertaken in Chapter Three. Results showed that M. nitroreducens was capable of independent AOM through reverse methanogenesis using nitrate as the terminal electron acceptor. Comparative analyses revealed that the genes for nitrate reduction appear to be laterally transferred from a bacterial donor, suggesting selection for this novel process within M. nitroreducens. Nitrite produced by M. nitroreducens was reduced to dinitrogen gas through a syntrophic relationship with an anaerobic ammonium-oxidizing bacterium. These results are presented as a published manuscript. ii In Chapter Four, eight reactor communities fed with different combinations of methane, nitrate, nitrite and ammonium were characterised using 16S ribosomal RNA gene amplicon sequencing and validated using FISH. Results showed that core populations (Methanoperedeneceae, Kuenenia and Methylomirabilis) were stable across reactors but present at different abundances suggestive of competitive and cooperative interactions between populations. Deep amplicon sequencing revealed a diverse community including three previously unrecognized bacterial populations; Ignavibacteriales (belonging to the phylum Chlorobi), Phycisphaerales (belonging to the phylum Planctomycetes) and Anaerolineae (belonging to the phylum Chloroflexi). Ignavibacteriales abundance correlated with high nitrite consumption rates suggesting its role in nitrite reduction. Phycisphaerales had an inverse relationship with Kuenenia and Ignavibacteriales suggesting that there may be competitive interactions and that Phycisphaerales may also have a similar role in nitrite reduction. The ubiquity of Anaerolineae in most reactors indicated that it may be a generalist. These results are presented as a draft manuscript. Genomic evidence indicates that M. nitroreducens is not only able to reduce nitrate to nitrite but also nitrite to ammonium, in a process called dissimilatory nitrate reduction to ammonium (DNRA). DNRA is a major part of the nitrogen cycle and catalysed by the cytochrome c nitrite reductases (nrfA). M. nitroreducens has three copies of nrfA, making this the first report of nrfA in an archaeon. Chapter Five applied meta-omic approaches, coupled to stable isotope labelling tests, to characterise a reactor community performing AOM coupled to DNRA. Stable isotope labelling tests showed accumulation of 15N-labelled ammonium in batch reactor with high carbon to nitrogen ratio. Metagenomics showed similar members of the community as described in Chapter Four and were consistently dominated by M. nitroreducens. Using a differential coverage binning approach, 20 near-complete population genomes were extracted. Gene-centric analysis indicated that a number of the populations had the genes for nitrate reduction (napA and narG) and nitrite ammonification (nrfA), but only two known methanotrophs (M. nitroreducens and Candidatus Methylomirabilis oxyfera) harboured key genes for methane oxidation (mcrA and pmoA), respectively. However, most of M. nitroreducens’ expressed genes were in the top 5% of absolute transcript counts, showing that M. nitroreducens is the most active population in the reactor. The M. nitroreducens’ mcr complex was differentially expressed but its nrfAs were not significantly expressed in the AOM-DNRA batch reactor and several other members of the community also demonstrated low levels of nrfA expression. These results may suggest that 1) DNRA may have already been occurring in the nitrate-driven AOM batch reactor, 2) other bacterial populations together with M. nitroreducens may collectively be carrying out DNRA or 3) the gene expression of nrfA may not iii correlate to the cytochrome c nitrite reductase protein abundance. Future metaproteomics will be required to confirm this finding. The findings presented in this thesis have provided new insight into the structure of microbial communities in nitrate-driven AOM and the highlighted potential interplay between specific populations. iv Declaration by author This thesis is composed of my original work, and contains no material previously published or written by another person except where due reference has been made in the text. I have clearly stated the contribution by others to jointly-authored works that I have included in my thesis. I have clearly stated the contribution of others to my thesis as a whole, including statistical assistance, survey design, data analysis, significant technical procedures, professional editorial advice, and any other original research work used or reported in my thesis. The content of my thesis is the result of work I have carried out since the commencement of my research higher degree candidature and does not include a substantial part of work that has been submitted to qualify for the award of any other degree or diploma in any university or other tertiary institution. I have clearly stated which parts of my thesis, if any, have been submitted to qualify for another award. I acknowledge that an electronic copy of my thesis must be lodged with the University Library and, subject to the policy and procedures of The University of Queensland, the thesis be made available for research and study in accordance with the Copyright Act 1968 unless a period of embargo has been approved by the Dean of the Graduate School. I acknowledge that copyright of all material contained in my thesis resides with the copyright holder(s) of that material. Where appropriate I have obtained copyright permission from the copyright holder to reproduce material in this thesis. v Publications during candidature Haroon MF, Hu S, Shi Y, Imelfort M, Keller J, Hugenholtz P, Yuan Z, Tyson GW. 2013. Anaerobic oxidation of methane coupled to nitrate reduction in a novel archaeal lineage. Nature 500:567-570. Haroon MF, Skennerton CT, Steen JA, Lachner N, Hugenholtz P, Tyson GW. 2013. Chapter One - In-solution fluorescence in situ hybridization and fluorescence-activated cell sorting for single cell and population genome recovery, p. 3-19. In Edward FD (ed.), Methods in Enzymology, vol. Volume 531. Academic Press. Hu S, Zeng RJ, Haroon MF, Keller J, Lant PA, Tyson GW, Yuan Z. Submitted. A laboratory investigation of interactions between denitrifying anaerobic methane oxidation (DAMO) and anammox processes in anoxic environments. Scientific Reports. Publications included in this thesis - Haroon MF, Skennerton CT, Steen JA, Lachner N, Hugenholtz P, Tyson GW. 2013. Chapter One - In-solution fluorescence in situ hybridization and fluorescence-activated cell sorting for single cell and population genome recovery, p. 3-19. In Edward FD (ed.), Methods in Enzymology, vol. Volume 531. Academic Press. (Incorporated as Chapter 2) Contributor Statement of contribution Haroon, MF (Candidate) Designed experiments (35%) Performed experiments (45%) Wrote the initial draft (80%) Prepared figures
Load more

Recommended publications
  • Comparison of Community Structures of Candidatus Methylomirabilis Oxyfera-Like Bacteria of NC10 Phylum in Different Freshwater Habitats
    www.nature.com/scientificreports OPEN Comparison of community structures of Candidatus Methylomirabilis oxyfera-like Received: 09 March 2016 Accepted: 20 April 2016 bacteria of NC10 phylum in Published: 09 May 2016 different freshwater habitats Li-dong Shen1,2, Hong-sheng Wu1,2, Zhi-qiu Gao3,4, Xu Liu2 & Ji Li2 Methane oxidation coupled to nitrite reduction is mediated by ‘Candidatus Methylomirabilis oxyfera’ (M. oxyfera), which belongs to the NC10 phylum. In this study, the community composition and diversity of M. oxyfera-like bacteria of NC10 phylum were examined and compared in four different freshwater habitats, including reservoir sediments (RS), pond sediments (PS), wetland sediments (WS) and paddy soils (PAS), by using Illumina-based 16S rRNA gene sequencing. The recovered NC10-related sequences accounted for 0.4–2.5% of the 16S rRNA pool in the examined habitats, and the highest percentage was found in WS. The diversity of NC10 bacteria were the highest in RS, medium in WS, and lowest in PS and PAS. The observed number of OTUs (operational taxonomic unit; at 3% cut-off) were 97, 46, 61 and 40, respectively, in RS, PS, WS and PAS. A heterogeneous distribution of NC10 bacterial communities was observed in the examined habitats, though group B members were the dominant bacteria in each habitat. The copy numbers of NC10 bacterial 16S rRNA genes ranged between 5.8 × 106 and 3.2 × 107 copies g−1 sediment/soil in the examined habitats. These results are helpful for a systematic understanding of NC10 bacterial communities in different types of freshwater habitats. Methane (CH4) is the most important greenhouse gas after carbon dioxide, and responsible for ~20% of the current greenhouse effect1.
    [Show full text]
  • Comparative Genomics of Candidatus Methylomirabilis Species and Description of Ca. Methylomirabilis Lanthanidiphila
    Delft University of Technology Comparative genomics of Candidatus Methylomirabilis species and description of Ca. Methylomirabilis lanthanidiphila Versantvoort, Wouter; Guerrero-Cruz, Simon; Speth, Daan R.; Frank, Hans; Gambelli, Lavinia; Cremers, Geert; van Alen, Theo; Jetten, Mike S.M.; Kartal, Boran; Op den Camp, Huub J.M. DOI 10.3389/fmicb.2018.01672 Publication date 2018 Document Version Final published version Published in Frontiers in Microbiology Citation (APA) Versantvoort, W., Guerrero-Cruz, S., Speth, D. R., Frank, J., Gambelli, L., Cremers, G., ... Reimann, J. (2018). Comparative genomics of Candidatus Methylomirabilis species and description of Ca. Methylomirabilis lanthanidiphila. Frontiers in Microbiology, 9(July), [1672]. https://doi.org/10.3389/fmicb.2018.01672 Important note To cite this publication, please use the final published version (if applicable). Please check the document version above. Copyright Other than for strictly personal use, it is not permitted to download, forward or distribute the text or part of it, without the consent of the author(s) and/or copyright holder(s), unless the work is under an open content license such as Creative Commons. Takedown policy Please contact us and provide details if you believe this document breaches copyrights. We will remove access to the work immediately and investigate your claim. This work is downloaded from Delft University of Technology. For technical reasons the number of authors shown on this cover page is limited to a maximum of 10. fmicb-09-01672 July 24, 2018 Time: 12:49 # 1 ORIGINAL RESEARCH published: 24 July 2018 doi: 10.3389/fmicb.2018.01672 Comparative Genomics of Candidatus Methylomirabilis Species and Description of Ca.
    [Show full text]
  • Bacterial Oxygen Production in the Dark
    HYPOTHESIS AND THEORY ARTICLE published: 07 August 2012 doi: 10.3389/fmicb.2012.00273 Bacterial oxygen production in the dark Katharina F. Ettwig*, Daan R. Speth, Joachim Reimann, Ming L. Wu, Mike S. M. Jetten and JanT. Keltjens Department of Microbiology, Institute for Water and Wetland Research, Radboud University Nijmegen, Nijmegen, Netherlands Edited by: Nitric oxide (NO) and nitrous oxide (N2O) are among nature’s most powerful electron Boran Kartal, Radboud University, acceptors. In recent years it became clear that microorganisms can take advantage of Netherlands the oxidizing power of these compounds to degrade aliphatic and aromatic hydrocar- Reviewed by: bons. For two unrelated bacterial species, the “NC10” phylum bacterium “Candidatus Natalia Ivanova, Lawrence Berkeley National Laboratory, USA Methylomirabilis oxyfera” and the γ-proteobacterial strain HdN1 it has been suggested Carl James Yeoman, Montana State that under anoxic conditions with nitrate and/or nitrite, monooxygenases are used for University, USA methane and hexadecane oxidation, respectively. No degradation was observed with *Correspondence: nitrous oxide only. Similarly, “aerobic” pathways for hydrocarbon degradation are employed − Katharina F.Ettwig, Department of by (per)chlorate-reducing bacteria, which are known to produce oxygen from chlorite (ClO ). Microbiology, Institute for Water and 2 Wetland Research, Radboud In the anaerobic methanotroph M. oxyfera, which lacks identifiable enzymes for nitrogen University Nijmegen, formation, substrate activation in the presence of nitrite was directly associated with both Heyendaalseweg 135, 6525 AJ oxygen and nitrogen formation. These findings strongly argue for the role of NO, or an Nijmegen, Netherlands. e-mail: [email protected] oxygen species derived from it, in the activation reaction of methane.
    [Show full text]
  • Article Is Available On- a Freshwater Meromictic Lake, FEMS Microbiol
    Biogeosciences, 18, 3087–3101, 2021 https://doi.org/10.5194/bg-18-3087-2021 © Author(s) 2021. This work is distributed under the Creative Commons Attribution 4.0 License. Methane oxidation in the waters of a humic-rich boreal lake stimulated by photosynthesis, nitrite, Fe.III/ and humics Sigrid van Grinsven1;, Kirsten Oswald1,2;, Bernhard Wehrli1,2, Corinne Jegge1,3, Jakob Zopfi4, Moritz F. Lehmann4, and Carsten J. Schubert1,2 1Department of Surface Waters – Research and Management, Eawag, Swiss Federal Institute of Aquatic Science and Technology, Kastanienbaum, Switzerland 2Institute of Biogeochemistry and Pollutant Dynamics, ETH Zurich, Swiss Federal Institute of Technology, Zurich, Switzerland 3School of Architecture, Civil and Environmental Engineering, EPFL, Swiss Federal Institute of Technology, Lausanne, Switzerland 4Department of Environmental Sciences, Aquatic and Stable Isotope Biogeochemistry, University of Basel, Basel, Switzerland These authors contributed equally to this work. Correspondence: Sigrid van Grinsven ([email protected]) and Carsten J. Schubert ([email protected]) Received: 11 January 2021 – Discussion started: 28 January 2021 Revised: 7 April 2021 – Accepted: 22 April 2021 – Published: 20 May 2021 Abstract. Small boreal lakes are known to contribute sig- cess in CH4 removal in the water column of humic, turbid nificantly to global CH4 emissions. Lake Lovojärvi is a eu- lakes, thereby limiting diffusive CH4 emissions from boreal trophic lake in southern Finland with bottom water CH4 con- lakes. Yet, it also highlights the potential importance of a centrations up to 2 mM. However, the surface water concen- whole suite of alternative electron acceptors, including hu- tration, and thus the diffusive emission potential, was low mics, in these freshwater environments in the absence of light (< 0.5 µM).
    [Show full text]
  • Comparative Genomics of Candidatus Methylomirabilis Species and Description of Ca. Methylomirabilis Lanthanidiphila
    fmicb-09-01672 July 24, 2018 Time: 12:49 # 1 ORIGINAL RESEARCH published: 24 July 2018 doi: 10.3389/fmicb.2018.01672 Comparative Genomics of Candidatus Methylomirabilis Species and Description of Ca. Methylomirabilis Lanthanidiphila Edited by: Iain Sutcliffe, Wouter Versantvoort1†, Simon Guerrero-Cruz1†, Daan R. Speth1‡, Jeroen Frank1,2, Northumbria University, Lavinia Gambelli1, Geert Cremers1, Theo van Alen1, Mike S. M. Jetten1,2,3, Boran Kartal4, United Kingdom Huub J. M. Op den Camp1* and Joachim Reimann1* Reviewed by: Monali C. Rahalkar, 1 Department of Microbiology, Institute for Water and Wetland Research, Radboud University Nijmegen, Nijmegen, Agharkar Research Institute, India Netherlands, 2 Department of Biotechnology, Delft University of Technology, Delft, Netherlands, 3 Soehngen Institute Lidong Shen, of Anaerobic Microbiology, Nijmegen, Netherlands, 4 Microbial Physiology Group, Max Planck Institute for Marine Nanjing University of Information Microbiology, Bremen, Germany Science and Technology, China *Correspondence: Methane is a potent greenhouse gas, which can be converted by microorganism at the Huub J. M. Op den Camp [email protected] expense of oxygen, nitrate, nitrite, metal-oxides or sulfate. The bacterium ‘Candidatus Joachim Reimann Methylomirabilis oxyfera,’ a member of the NC10 phylum, is capable of nitrite-dependent [email protected] anaerobic methane oxidation. Prolonged enrichment of ‘Ca. M. oxyfera’ with cerium † These authors have contributed added as trace element and without nitrate resulted in the shift of the dominant equally to this work. species. Here, we present a high quality draft genome of the new species ‘Candidatus ‡Present address: Daan R. Speth, Methylomirabilis lanthanidiphila’ and use comparative genomics to analyze its metabolic Division of Geological and Planetary potential in both nitrogen and carbon cycling.
    [Show full text]
  • Current Advances in Molecular Methods for Detection of Nitrite-Dependent Anaerobic Methane Oxidizing Bacteria in Natural Environments
    Original citation: Chen, Jing, Dick, Richard, Lin, Jih-Gaw and Gu, Ji-Dong. (2016) Current advances in molecular methods for detection of nitrite-dependent anaerobic methane oxidizing bacteria in natural environments. Applied Microbiology and Biotechnology, 100 (23). pp. 9845-9860. Permanent WRAP URL: http://wrap.warwick.ac.uk/86286 Copyright and reuse: The Warwick Research Archive Portal (WRAP) makes this work by researchers of the University of Warwick available open access under the following conditions. Copyright © and all moral rights to the version of the paper presented here belong to the individual author(s) and/or other copyright owners. To the extent reasonable and practicable the material made available in WRAP has been checked for eligibility before being made available. Copies of full items can be used for personal research or study, educational, or not-for profit purposes without prior permission or charge. Provided that the authors, title and full bibliographic details are credited, a hyperlink and/or URL is given for the original metadata page and the content is not changed in any way. Publisher’s statement: The final publication is available at Springer via http://dx.doi.org/10.1007/s00253-016-7853- 5 A note on versions: The version presented here may differ from the published version or, version of record, if you wish to cite this item you are advised to consult the publisher’s version. Please see the ‘permanent WRAP url’ above for details on accessing the published version and note that access may require a subscription. For more information, please contact the WRAP Team at: [email protected] warwick.ac.uk/lib-publications 1 Current Advances in Molecular Methods for Detection of 2 Nitrite-dependent Anaerobic Methane Oxidizing Bacteria in Natural 3 Environments 4 5 Jing Chen1,2, Richard Dick3, Jih-Gaw Lin4, and Ji-Dong Gu1* 6 7 1 Laboratory of Environmental Microbiology and Toxicology, School of Biological 8 Sciences, Faculty of Science, The University of Hong Kong, Pokfulam Road, Hong Kong 9 SAR, P.R.
    [Show full text]
  • Diversity of Methane-Cycling Microorganisms in Soils and Their Relation to Oxygen
    Diversity of Methane-cycling Microorganisms in Soils and Their Relation to Oxygen Claudia Knief* Institute of Crop Science and Resource Conservation – Molecular Biology of the Rhizosphere, University of Bonn, Bonn, Germany. *Correspondence: [email protected] htps://doi.org/10.21775/cimb.033.023 Abstract Introduction Microorganisms are important players in the Methane cycling microorganisms are of interest global methane cycle. Anaerobic methanogenic for microbiologists since more than a century. archaea are largely responsible for methane pro- Research on these microorganisms was initially duction, while aerobic methanotrophic bacteria, largely driven by the curiosity to understand their as well as anaerobic methanotrophic bacteria particular physiology that leads to the production and archaea, are involved in methane oxidation. or consumption of methane. While this interest is In anoxic wetland soils, methanogens produce still a driver, the importance of methane as green- methane, while methanotrophs act as a flter house gas has become another important factor, and reduce methane emissions. In the predomi- promoting further research on methanogenic and nantly oxic upland soils, aerobic methanotrophs methanotrophic microorganisms. Tis leads to a oxidize atmospheric methane. Tis review gives continuously beter understanding of their physi- an overview of the diversity of methanogenic ology and ecology, and it becomes evident that and methanotrophic microorganisms, highlights the processes of microbial methane production recent discoveries and provides information and consumption are mediated by more com- concerning their occurrence in soils. Recent plex functional guilds than initially thought. Te fndings indicate that the methanogenic and improved understanding is not only due to the con- methanotrophic lifestyles are more widespread stantly increasing diversity of methanogenic and in microorganisms than previously thought, and methanotrophic microorganisms (e.g.
    [Show full text]
  • Anaerobic Oxidization of Methane in a Minerotrophic Peatland: Enrichment of Nitrite-Dependent Methane-Oxidizing Bacteria
    Anaerobic Oxidization of Methane in a Minerotrophic Peatland: Enrichment of Nitrite-Dependent Methane-Oxidizing Bacteria Baoli Zhu,a Gijs van Dijk,b,c Christian Fritz,b Alfons J. P. Smolders,b,c Arjan Pol,a Mike S. M. Jetten,a and Katharina F. Ettwiga Downloaded from Department of Microbiology, Institute for Water and Wetland Research, Radboud University, Nijmegen, The Netherlandsa; Department of Aquatic Ecology and Environmental Biology, Institute for Water and Wetland Research, Radboud University, Nijmegen, The Netherlandsb; and B-WARE Research Centre, Radboud University, Nijmegen, The Netherlandsc The importance of anaerobic oxidation of methane (AOM) as a methane sink in freshwater systems is largely unexplored, partic- ularly in peat ecosystems. Nitrite-dependent anaerobic methane oxidation (n-damo) was recently discovered and reported to be catalyzed by the bacterium “Candidatus Methylomirabilis oxyfera,” which is affiliated with the NC10 phylum. So far, several “Ca. Methylomirabilis oxyfera” enrichment cultures have been obtained using a limited number of freshwater sediments or http://aem.asm.org/ wastewater treatment sludge as the inoculum. In this study, using stable isotope measurements and porewater profiles, we inves- tigated the potential of n-damo in a minerotrophic peatland in the south of the Netherlands that is infiltrated by nitrate-rich ground water. Methane and nitrate profiles suggested that all methane produced was oxidized before reaching the oxic layer, and NC10 bacteria could be active in the transition zone where countergradients of methane and nitrate occur. Quantitative PCR showed high NC10 bacterial cell numbers at this methane-nitrate transition zone. This soil section was used to enrich the preva- lent NC10 bacteria in a continuous culture supplied with methane and nitrite at an in situ pH of 6.2.
    [Show full text]
  • Rare Bacteriohopanepolyols As Markers for an Autotrophic, Intra-Aerobic Methanotroph
    Accepted Manuscript Rare bacteriohopanepolyols as markers for an autotrophic, intra-aerobic meth- anotroph Dorien M. Kool, Helen M. Talbot, Darci Rush, Katharina Ettwig, Jaap S. Sinninghe Damsté PII: S0016-7037(14)00224-5 DOI: http://dx.doi.org/10.1016/j.gca.2014.04.002 Reference: GCA 8752 To appear in: Geochimica et Cosmochimica Acta Received Date: 5 February 2014 Accepted Date: 2 April 2014 Please cite this article as: Kool, D.M., Talbot, H.M., Rush, D., Ettwig, K., Sinninghe Damsté, J.S., Rare bacteriohopanepolyols as markers for an autotrophic, intra-aerobic methanotroph, Geochimica et Cosmochimica Acta (2014), doi: http://dx.doi.org/10.1016/j.gca.2014.04.002 This is a PDF file of an unedited manuscript that has been accepted for publication. As a service to our customers we are providing this early version of the manuscript. The manuscript will undergo copyediting, typesetting, and review of the resulting proof before it is published in its final form. Please note that during the production process errors may be discovered which could affect the content, and all legal disclaimers that apply to the journal pertain. Rare bacteriohopanepolyols as markers for an autotrophic, intra-aerobic methanotroph Dorien M. Kool1, Helen M. Talbot2, Darci Rush2, Katharina Ettwig3, Jaap S. Sinninghe Damsté1# 1NIOZ Royal Netherlands Institute for Sea Research, Department of Marine Organic Biogeochemistry, PO Box 59, 1790 AB Den Burg, Texel, the Netherlands; 2Newcastle University, School of Civil Engineering and Geosciences, Drummond Building, Newcastle upon Tyne NE1 7RU, UK; 3Radboud University Nijmegen, Institute of Water and Wetland Research, Department of Microbiology, PO Box 9010, 6500 GL Nijmegen, the Netherlands.
    [Show full text]
  • Nitrogen Cycle &Nitrogen Contamination
    Ecological Perspective on New Connectivity between Nitrogen and Carbon Cycle Ananda S. Bhattacharjee, Sachiyo T. Mukherji, Shaikha Abedin* and Ramesh Goel Urban Riparian Symposium February 13th 2015 1 Introduction: Nitrogen Cycle &Nitrogen Contamination Nitrogen contamination is one of the 14 grand challenges prioritized by the National Academy of Engineering. The innovative and effective N transformations through prokaryotic mediated pathways have been well received. Example: Ananerobic ammonia oxidation was included in the overall N cycle after its inception in mid 1990’s. Denitrification is an important component of the overall nitrogen cycle. • Heterotrophic process organic carbon • Autotrophic process hydrogen and reduced sulfur compounds. 2 Introduction: Recent Developments In N Cycle: Methane Coupled Denitrification Denitrification with anoxic methane oxidation (DAMO) is a very recent development P P: 3CH + 8NO - + 8H+ 3CO + 4N + 10H O Q 4 2 2 2 2 - Q: CH4 + 4NO3 CO2 + 4NO2 + 2H2O Adapted from Galloway et al., 2008 3 Introduction: Connectivity Between C & N Cycle : Methane oxidation coupled to NO2 4 DAMO Process in Sediments Water Column Dissolved Nutrients Dissolved Methanogen nutrients - - CH4 NO2 / NO3 Methane DAMO process produced Sediments - + P: 3CH4 + 8NO2 + 8H 3CO2 + 4N2 + 10H2O - Q: CH4 + 4NO3 CO2 + 4NO2 + 2H2O Bed Rocks 5 Introduction: Denitrifying Anaerobic Methane Oxidizing (DAMO) Prokaryotes Bacteria Archaea - (NO2 ) (NO3- ) • Candidatus ’ Methylomirabilis • Candidatus ’ Methanoperedens oxyfera only known bacteria
    [Show full text]
  • Archaea Catalyze Iron-Dependent Anaerobic Oxidation of Methane
    Archaea catalyze iron-dependent anaerobic oxidation of methane Katharina F. Ettwiga,1,2, Baoli Zhua,1,3, Daan Spetha,4, Jan T. Keltjensa, Mike S. M. Jettena, and Boran Kartala,2,5 aDepartment of Microbiology, Institute for Water and Wetland Research, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands Edited by Donald E. Canfield, Institute of Biology and Nordic Center for Earth Evolution, University of Southern Denmark, Odense M, Denmark, and approved September 16, 2016 (received for review June 13, 2016) Anaerobic oxidation of methane (AOM) is crucial for controlling analogous to aerobic methanotrophs (6). In addition, archaea of a the emission of this potent greenhouse gas to the atmosphere. new group within Methanosarcinales [termed AOM-associated ar- Nitrite-, nitrate-, and sulfate-dependent methane oxidation is well- chaea (AAA) (2), sometimes also referred to as ANME-2d], orig- documented, but AOM coupled to the reduction of oxidized metals inally coenriched together with M. oxyfera (7), were recently found has so far been demonstrated only in environmental samples. Here, to couple the oxidation of methane to the reduction of nitrate to using a freshwater enrichment culture, we show that archaea of the nitrite (5). In reaching these insights, laboratory enrichment cultures order Methanosarcinales, related to “Candidatus Methanoperedens of the responsible microorganisms were of crucial importance. nitroreducens,” couple the reduction of environmentally relevant Even though rock weathering supplies ample amounts of iron, + + forms of Fe3 and Mn4 to the oxidation of methane. We obtained manganese, and other metal oxides suitable as electron acceptors an enrichment culture of these archaea under anaerobic, nitrate- to freshwater bodies (8), and eventually oceans, evidence for the reducing conditions with a continuous supply of methane.
    [Show full text]
  • Buckner, C. Imaging Anaerobic Methane Oxidation at Environs Near Woods Hole
    Imaging anaerobic methane oxidation at environs near Woods Hole Caroline Buckner Microbial Diversity Course 2013 Abstract CARD-FISH was performed to determine the presence of S-DAMO and N- DAMO in the Cape Cod Area. Samples were taken from marine sediments at Trunk River and Great Sippewissett Salt Marsh for S-DAMO studies, while freshwater samples were collected from Cedar Swamp and the Cape Cod Aquifer for N-DAMO. Comparisons of the epifluorescence micrographs found at the marine sites indicate that ANME/SRB consortia are more prevalent at Great Sippewissett Salt Marsh and more free-living members of the ANME clades are found at Trunk River. On comparing Cedar Swamp and the Cape Cod Aquifer, it seems that the M. oxyfera at the Cape Cod Aquifer are in consortia with methanogenic archaea, and that those at Cedar Swamp are primarily free-living. Introduction The process of anaerobic methane oxidation (AMO) was first discovered over 35 years ago [3, 18, 25] in the marine environment. Early in vitro activity assays, radiotracer experiments, and stable carbon isotope analysis led to the hypothesis that AMO is mediated by methanogenic archaea conducting reverse methanogenesis and sulfate-reducting bacteria [1, 10, 30]. Evidence for this hypothesis was found in 1999 with in situ detection of isotopic biomarkers [8]. Lipid biomarkers that are commonly characteristic of archaea were strongly depleted in 13C. Therefore, the archaea that contain these lipids must use CH4 as a carbon source, not as its metabolic product. With the advent of fluorescence in situ hybridization (FISH), a structured consortium of archaea and sulfate-reducing bacteria (SRB) [4] was discovered.
    [Show full text]