DOCSLIB.ORG

Physiological and Genomic Characterization of Thermophilic Methanotrophic Archaea and Their Partner-Bacteria

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Physiological and Genomic Characterization of Thermophilic Methanotrophic Archaea and Their Partner-Bacteria Physiological and genomic characterization of thermophilic methanotrophic archaea and their partner-bacteria Dissertation zur Erlangung des Doktorgrades der Naturwissenschaften - Dr. rer. nat. - dem Fachbereich Biologie/Chemie der Universität Bremen vorgelegt von Viola Krukenberg Bremen, November 2015 Die vorliegende Arbeit wurde in der Zeit von Januar 2012 bis November 2015 am Max-Planck-Institut für Marine Mikrobiologie angefertigt. 1. Gutachterin: Prof. Dr. Antje Boetius 2. Gutachter: Prof. Dr. Ulrich Fischer 1. Prüfer: Prof. Dr. Jens Harder 2. Prüfer: Dr. Gunter Wegener Tag des Promotionskolloquiums: 11.12.2015 Table of contents Summary .................................................................................................................................... 1 Zusammenfassung ...................................................................................................................... 3 Abbreviations ............................................................................................................................. 5 Chapter I Introduction ........................................................................................................... 7 1.1. Relevance of microbial processes in the global methane budget ................. 8 1.2. Anaerobic mineralization of organic matter ................................................. 9 1.3. Microbial syntrophy ................................................................................... 12 1.4. Anaerobic oxidation of methane ................................................................ 16 1.5. Research outline and objectives ................................................................. 29 1.6. Material and methods ................................................................................. 31 1.7. Overview of enclosed manuscripts ............................................................. 45 Chapter II Intercellular wiring enables electron transfer between methanotrophic archaea and bacteria ......................................................................................................... 47 Chapter III Candidatus Desulfofervidus auxilii, a hydrogenotrophic sulfate-reducing bacterium involved in the thermophilic anaerobic oxidation of methane ........... 79 Chapter IV Comparative analysis of the metabolic potential of different subgroups of anaerobic methanotrophic archaea of clade 1 ................................................... 127 Chapter V Metabolic capabilities of microorganisms involved in and associated with the anaerobic oxidation of methane ........................................................................ 165 Chapter VI Discussion and perspectives .............................................................................. 207 6.1. Physiology and interspecies interaction in thermophilic AOM................ 208 6.2. Physiology and genomic profile of the bacterial partner HotSeep-1 ....... 210 6.3. Metabolic potential of ANME-1 .............................................................. 211 6.4. Metabolic capabilities of organisms in AOM enrichments ...................... 213 6.5. Perspectives for future research on AOM ................................................ 215 6.6. Concluding remarks .................................................................................. 217 Bibliography ........................................................................................................................... 219 Acknowledgements ................................................................................................................ 233 Appendix ................................................................................................................................ 235 Summary Methane is a potent greenhouse gas and its atmospheric concentration is strongly influenced by microbial processes. In anoxic marine environments 80% of the methane is oxidized by anaerobic microorganisms leading to reduced oceanic methane emissions. This anaerobic oxidation of methane (AOM) is coupled to sulfate reduction and is mediated by microbial consortia of anaerobic methane-oxidizing archaea and partner bacteria. The physiology of the consortia is incompletely understood but is thought to base on a metabolic interdependency of the partners, a syntrophy. The research presented in this PhD thesis focused on the physiology and genomic profile of AOM consortia, in particular on the microorganisms that are active at elevated temperatures (thermophiles). The thermophilic AOM is performed by a unique consortium of ANME-1 archaea and HotSeep-1 bacteria. In Chapter II we describe physiological studies and gene expression experiments with thermophilic AOM consortia and propose a syntrophy of AOM via direct exchange of reducing equivalents. In support of this hypothesis we visualized cell-to-cell connections in these consortia that we suggest to function as conductive nanowires in interspecies electron transfer. For the thermophilic bacterial partner, HotSeep-1 we obtained an ANME-1-free enrichment culture using hydrogen as alternative energy source, and by physiological and genomic investigation we show in Chapter III that this bacterial partner grows as chemolithoautotrophic sulfate reducer. Based on phylogenetic analysis we propose that HotSeep-1 presents a novel species, Candidatus Desulfofervidus auxilii. ANME-1, the archaeon participating in thermophilic AOM, belongs to a large group of uncultured organisms, which are known to have reversed the methanogenesis pathway to metabolize methane. The metabolic diversity among members of the ANME-1 group is still widely unexplored. In a comparative genome analysis of different ANME-1 in Chapter IV we show central aspects of their metabolism including a modified reverse methanogenesis pathway and abundant cytochromes possibly relevant for electron transfer. Environments of AOM activity and in vitro AOM enrichments are dominated by AOM consortia, but other microorganisms sustain as low abundant community whose function is not well understood. In Chapter V we show the cultivation of methanogens and sulfur-disproportionating bacteria from AOM enrichments. In conclusion the work of this PhD thesis has advanced our understanding of the functioning of thermophilic AOM, while further detailed comparative approaches are necessary to comprehend AOM syntrophy in all its detail and diversity. 1 2 Zusammenfassung Methan ist ein wichtiges Klimagas, dessen atmosphärische Konzentration stark von mikrobiellen Prozessen beeinflusst ist. In sauerstofffreien marinen Sedimenten wird 80% des Methans durch Mikroorganismen verbraucht, was zu verminderter Methanemission der Ozeane beiträgt. Diese anaerobe Oxidation von Methan (AOM) ist gekoppelt mit Sulfatreduktion und findet in Konsortien aus anaerob methan-oxidierenden Archaeen (ANME) und Partnerbakterien statt. Die Physiologie dieser Konsortien ist unvollständig verstanden, aber basiert vermutlich auf metabolischer Abhängigkeit der Partner, einer Syntrophie. Diese Doktorarbeit behandelt die Physiologie und die genomischen Eigenschaften von AOM Konsortien, speziell solcher die bei erhöhter Temperatur leben (thermophile). Thermophile AOM wird von einem einzigartigen Konsortium aus ANME-1 Archaeen und HotSeep-1 Bakterien durchgeführt. In Kapitel II beschreiben wir physiologische Studien und Genexpressions-Experimente und schlagen vor, dass die Syntrophie von ANME-1 und HotSeep-1 auf dem direkten Austausch von Elektronen beruht. Diese Hypothese unterstützend weisen wir Zell-zu-Zell Verbindungen nach, die wir als mikrobielle Drähte (‚nanowires‘) beschreiben und für den Austausch von Elektronen vorschlagen. Den bakteriellen Partner HotSeep-1 konnten wir ohne ANME, mit Wasserstoff als alternativem Wachstumssubstrat, anreichern und zeigen in Kapitel III in physiologischen und genomischen Untersuchung, dass HotSeep-1 chemolithoautotroph als Sulfatreduzierer wächst. Zusammen mit phylogenetischen Analysen schlagen wir vor, dass HotSeep-1 eine neue Art darstellt: Candidatus Desulfofervidus auxilii. Das Archaeum, beteiligt an thermophiler AOM, gehört zu einer großen Gruppe unkultivierter Organismen, von denen bekannt ist, dass sie den methanogenen Stoffwechselweg umkehren um Methan zu oxidieren. Die metabolische Diversität innerhalb der ANME-1 Gruppe ist noch weitgehend unerforscht. In Kapitel IV zeigen wir mithilfe von vergleichender Genomanalyse zentrale metabolische Aspekte von ANME-1, u.a. eine modifizierte reverse Methanogenese und häufige Cytochrome, welche vermutlich relevant für den Elektronentransfer sind. Standorte natürlicher AOM Aktivität und in vitro AOM Anreicherungen sind dominiert von AOM Konsortien, dennoch überleben auch andere Mikroorganismen langfristig, deren Funktion kaum verstanden ist. In Kapitel V zeigen wir, dass aus AOM Anreicherungen Methanogene und Schwefeldisproportionierer kultivert werden können. Zusammenfassend hat diese Doktorarbeit unser Verständnis der Physiologie der thermophilen AOM vorangebracht, während weitere vergleichende Analysen nötig sind, um die AOM Syntrophie im Detail und in aller Diversität zu verstehen. 3 4 Abbreviations AFM Atomic Force Microscopy ANME ANaerobe MEthane-oxidizing archaea AOM Anaerobic Oxidation of Methane AQDS AnthraQuinone-2,6-DiSulfonate APS Adenosine-5'-PhosphoSulfate ATP Adenosine TriPhosphate CARD-FISH CAtalyzed Reporter Deposition Fluorescence In Situ Hybridization CFE Carbon Fixation Efficiencies DAPI 4,6-DiAmidino-2-PhenylIndole COG Cluster of Orthologous Groups DBB
Load more

Recommended publications
  • Hydrocarbon-Degrading Sulfate-Reducing Bacteria in Marine Hydrocarbon Seep Sediments
    Hydrocarbon-degrading sulfate-reducing bacteria in marine hydrocarbon seep sediments Sara Kleindienst Cover: 13 C-mass images of alkane-degrading SRB from Amon Mud Volcano or Guaymas Basin marine seep sediments as determined by NanoSIMS analysis. Hydrocarbon-degrading sulfate-reducing bacteria in marine hydrocarbon seep sediments Dissertation zur Erlangung des Grades eines Doktors der Naturwissenschaften - Dr. rer. nat. - Dem Fachbereich Biologie/Chemie der Universität Bremen vorgelegt von Sara Kleindienst Bremen April 2012 Die vorliegende Arbeit wurde in der Zeit von September 2008 bis April 2012 im Rahmen der „International Max Planck Research School of Marine Microbiology (MarMic)“ in der Abteilung Molekulare Ökologie am Max-Planck-Institut für marine Mikrobiologie in Bremen angefertigt. 1. Gutachter: Prof. Dr. Rudolf Amann 2. Gutachter: Prof. Dr. Heribert Cypionka Tag des Promotionskolloquiums: 24. Mai 2012 Table of Contents Table of Contents Summary................................................................................................................................ III Zusammenfassung..................................................................................................................IV List of Abbreviations............................................................................................................... V Chapter I ................................................................................................................................... 1 General Introduction ..........................................................................................................
    [Show full text]
  • Fermentation and Anaerobic Decomposition in a Hot Spring
    Fermentation and anaerobic decomposition in a hot spring microbial mat by Karen Leigh Anderson A thesis submitted in partial fulfillment of requirements for the degree of Master of Science in Microbiology Montana State University © Copyright by Karen Leigh Anderson (1984) Abstract: Fermentation was investigated in a low sulfate hot spring microbial mat (Octopus Spring) according to current models on anaerobic decomposition. The mat was studied to determine what fermentation products accumulated, where in the mat they accumulated, and what factors affected their accumulation. Mat samples were incubated under dark anaerobic conditions to measure accumulation of fermentation products. Acetate and propionate (ca. 3:1) were the major products to accumulate in a 55&deg,C mat. Other products accumulated to a much lesser extent. Incubation of mat samples of varying thickness showed that fermentation occurred in the top 4mm of the mat. This has interesting implications for fermentative organisms in the mat due to the diurnal changes in mat oxygen concentrations. Fermentation measured in mat samples collected at various temperatures (50&deg,-70°C) showed acetate and propionate to be the major accumulation products. According to the interspecies hydrogen transfer model, the hydrogen concentration in a system affects the types of fermentation products produced. At a 65° C site, with natural high hydrogen levels, and at a 55°C site, with active methanogenesis, fermentation product accumulation was compared. There was a greater ratio of reduced fermentation products to acetate, with the exception of propionate, at 65°C. Ethanol accumulated at the 65°C site, as did lactate, though to a lesser extent.
    [Show full text]
  • Exploring the Nutritional Values of Hydrogenotrophic Bacteria As Space Food
    ISSN: 2455-2631 © December 2018 IJSDR | Volume 3, Issue 12 Exploring the Nutritional Values of Hydrogenotrophic Bacteria as Space Food 1M.GIRISH, 2S.ABIRAMI, 3Dr.V.MAHALAKSHMI 1,2Research scholar, 3Professor 1,3Madras Christian College, 2V.R.R Institute of Biomedical Sciences. Abstract: Hydrogenotrophs are organisms that are capable of metabolizing molecular hydrogen as source of energy and hence hydrogenotrophy is performed by carbon dioxide reducing organism to produce methane. Methanogens are diverse group of strict anaerobes where methanogenesis is a major route in the anaerobic mineralization of organic matter. They have very unique enzyme and cofactors involved in this metabolic pathway. The anaerobic chamber provides a convenient culture system for large-scale studies of strictly anaerobic and/or facultative anaerobic bacteria. In this study, the Hydrogenotrophic organism isolated was characterized as Methanosarcina sp. Though these hydrogenotrophs utilise carbon dioxide and grow in a minimal growth requirement, they were found to be rich in carbohydrates and protein content. Therefore, Hydrogenotroph being a good food source, can be used for future space travel where the astronauts could carry them aboard and synthesis their own food. The by-products produced by these organisms can be used to produce a protein rich meal. This system can be incorporated on to space craft where this works as a closed loop between astronauts and hydrogenotrophs, where carbon dioxide released by astronauts can be captured and filtered through a system and supplied for the growth of these microbes which in turn synthesis carbohydrates. Keywords: Hydrogenotrophs, space food, anaerobes. I. INTRODUCTION Hydrogenotrophs are organisms that are capable of metabolizing molecular hydrogen as source of energy.
    [Show full text]
  • Tree Scale: 1 D Bacteria P Desulfobacterota C Jdfr-97 O Jdfr-97 F Jdfr-97 G Jdfr-97 S Jdfr-97 Sp002010915 WGS ID MTPG01
    d Bacteria p Desulfobacterota c Thermodesulfobacteria o Thermodesulfobacteriales f Thermodesulfobacteriaceae g Thermodesulfobacterium s Thermodesulfobacterium commune WGS ID JQLF01 d Bacteria p Desulfobacterota c Thermodesulfobacteria o Thermodesulfobacteriales f Thermodesulfobacteriaceae g Thermosulfurimonas s Thermosulfurimonas dismutans WGS ID LWLG01 d Bacteria p Desulfobacterota c Desulfofervidia o Desulfofervidales f DG-60 g DG-60 s DG-60 sp001304365 WGS ID LJNA01 ID WGS sp001304365 DG-60 s DG-60 g DG-60 f Desulfofervidales o Desulfofervidia c Desulfobacterota p Bacteria d d Bacteria p Desulfobacterota c Desulfofervidia o Desulfofervidales f Desulfofervidaceae g Desulfofervidus s Desulfofervidus auxilii RS GCF 001577525 1 001577525 GCF RS auxilii Desulfofervidus s Desulfofervidus g Desulfofervidaceae f Desulfofervidales o Desulfofervidia c Desulfobacterota p Bacteria d d Bacteria p Desulfobacterota c Thermodesulfobacteria o Thermodesulfobacteriales f Thermodesulfatatoraceae g Thermodesulfatator s Thermodesulfatator atlanticus WGS ID ATXH01 d Bacteria p Desulfobacterota c Desulfobacteria o Desulfatiglandales f NaphS2 g 4484-190-2 s 4484-190-2 sp002050025 WGS ID MVDB01 ID WGS sp002050025 4484-190-2 s 4484-190-2 g NaphS2 f Desulfatiglandales o Desulfobacteria c Desulfobacterota p Bacteria d d Bacteria p Desulfobacterota c Thermodesulfobacteria o Thermodesulfobacteriales f Thermodesulfobacteriaceae g QOAM01 s QOAM01 sp003978075 WGS ID QOAM01 d Bacteria p Desulfobacterota c BSN033 o UBA8473 f UBA8473 g UBA8473 s UBA8473 sp002782605 WGS
    [Show full text]
  • Conversion of Amazon Rainforest to Agriculture Alters Community Traits of Methane-Cycling Organisms
    Conversion of Amazon rainforest to agriculture alters community traits of methane-cycling organisms Kyle M. Meyer1***, Ann M. Klein1**, Jorge L.M. Rodrigues2*, Klaus Nüsslein3, Susannah Tringe4, Babur Mirza5, James M. Tiedje6, Titus Brown7 and Brendan J.M. Bohannan1* 1. Institute of Ecology and Evolution, Department of Biology, University of Oregon, Eugene, OR 2. Department of Land, Air and Water Resources, University of California, Davis, CA 3. Department of Microbiology, University of Massachusetts, Amherst, MA 4. Joint Genome Institute, United States Department of Energy, Walnut Creek, CA 5. 6. Department of Plant, Soil, and Microbial Sciences, Michigan State University, East Lansing, MI 7. Department of Population Health and Reproduction, University of California, Davis, CA * Corresponding authors ([email protected], [email protected], [email protected]) **These authors contributed equally to this work. ABSTRACT Land use change is one of the greatest environmental threats worldwide, especially to tropical forests. The Amazon rainforest has been subject to particularly high rates of land use change, primarily to cattle pasture. A commonly observed response to cattle pasture establishment in the Amazon is the conversion of soil from a methane sink in rainforest, to a methane source in pasture. However, it is not known how the microorganisms that mediate methane flux are altered by land use change. Here we use the deepest metagenomic sequencing of Amazonian soil to date to investigate differences in methane-cycling microorganisms and their traits across rainforest and cattle pasture soils. We found that methane-cycling microorganisms responded to land use change, with the strongest responses exhibited by methane- consuming, rather than methane-producing, microorganisms.
    [Show full text]
  • Microbial Sulfur Transformations in Sediments from Subglacial Lake Whillans
    ORIGINAL RESEARCH ARTICLE published: 19 November 2014 doi: 10.3389/fmicb.2014.00594 Microbial sulfur transformations in sediments from Subglacial Lake Whillans Alicia M. Purcell 1, Jill A. Mikucki 1*, Amanda M. Achberger 2 , Irina A. Alekhina 3 , Carlo Barbante 4 , Brent C. Christner 2 , Dhritiman Ghosh1, Alexander B. Michaud 5 , Andrew C. Mitchell 6 , John C. Priscu 5 , Reed Scherer 7 , Mark L. Skidmore8 , Trista J. Vick-Majors 5 and the WISSARD Science Team 1 Department of Microbiology, University of Tennessee, Knoxville, TN, USA 2 Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, USA 3 Climate and Environmental Research Laboratory, Arctic and Antarctic Research Institute, St. Petersburg, Russia 4 Institute for the Dynamics of Environmental Processes – Consiglio Nazionale delle Ricerche and Department of Environmental Sciences, Informatics and Statistics, Ca’ Foscari University of Venice, Venice, Italy 5 Department of Land Resources and Environmental Sciences, Montana State University, Bozeman, MT, USA 6 Geography and Earth Sciences, Aberystwyth University, Ceredigion, UK 7 Department of Geological and Environmental Sciences, Northern Illinois University, DeKalb, IL, USA 8 Department of Earth Sciences, Montana State University, Bozeman, MT, USA Edited by: Diverse microbial assemblages inhabit subglacial aquatic environments.While few of these Andreas Teske, University of North environments have been sampled, data reveal that subglacial organisms gain energy for Carolina at Chapel Hill, USA growth from reduced minerals containing nitrogen, iron, and sulfur. Here we investigate Reviewed by: the role of microbially mediated sulfur transformations in sediments from Subglacial Aharon Oren, The Hebrew University of Jerusalem, Israel Lake Whillans (SLW), Antarctica, by examining key genes involved in dissimilatory sulfur John B.
    [Show full text]
  • Microbial Diversity and Cellulosic Capacity in Municipal Waste Sites By
    Microbial diversity and cellulosic capacity in municipal waste sites by Rebecca Co A thesis presented to the University of Waterloo in fulfilment of the thesis requirement for the degree of Master of Science in Biology Waterloo, Ontario, Canada, 2019 © Rebecca Co 2019 Author’s Declaration This thesis consists of material all of which I authored or co-authored: see Statement of Contributions included in the thesis. This is a true copy of the thesis, including any required final revisions, as accepted by my examiners. I understand that my thesis may be made electronically available to the public. ii Statement of Contributions In Chapter 2, the sampling and DNA extraction and sequencing of samples (Section 2.2.1 - 2.2.2) were carried out by Dr. Aneisha Collins-Fairclough and Dr. Melessa Ellis. The work described in Section 2.2.3 Metagenomic pipeline and onwards was done by the thesis’s author. Sections 2.2.1 Sample collection – 2.2.4 16S rRNA gene community profile were previously published in Widespread antibiotic, biocide, and metal resistance in microbial communities inhabiting a municipal waste environment and anthropogenically impacted river by Aneisha M. Collins- Fairclough, Rebecca Co, Melessa C. Ellis, and Laura A. Hug. 2018. mSphere: e00346-18. The writing and analyses incorporated into this chapter are by the thesis's author. iii Abstract Cellulose is the most abundant organic compound found on earth. Cellulose’s recalcitrance to hydrolysis is a major limitation to improving the efficiency of industrial applications. The biofuel, pulp and paper, agriculture, and textile industries employ mechanical and chemical methods of breaking down cellulose.
    [Show full text]
  • Variations in the Two Last Steps of the Purine Biosynthetic Pathway in Prokaryotes
    GBE Different Ways of Doing the Same: Variations in the Two Last Steps of the Purine Biosynthetic Pathway in Prokaryotes Dennifier Costa Brandao~ Cruz1, Lenon Lima Santana1, Alexandre Siqueira Guedes2, Jorge Teodoro de Souza3,*, and Phellippe Arthur Santos Marbach1,* 1CCAAB, Biological Sciences, Recoˆ ncavo da Bahia Federal University, Cruz das Almas, Bahia, Brazil 2Agronomy School, Federal University of Goias, Goiania,^ Goias, Brazil 3 Department of Phytopathology, Federal University of Lavras, Minas Gerais, Brazil Downloaded from https://academic.oup.com/gbe/article/11/4/1235/5345563 by guest on 27 September 2021 *Corresponding authors: E-mails: [email protected]fla.br; [email protected]. Accepted: February 16, 2019 Abstract The last two steps of the purine biosynthetic pathway may be catalyzed by different enzymes in prokaryotes. The genes that encode these enzymes include homologs of purH, purP, purO and those encoding the AICARFT and IMPCH domains of PurH, here named purV and purJ, respectively. In Bacteria, these reactions are mainly catalyzed by the domains AICARFT and IMPCH of PurH. In Archaea, these reactions may be carried out by PurH and also by PurP and PurO, both considered signatures of this domain and analogous to the AICARFT and IMPCH domains of PurH, respectively. These genes were searched for in 1,403 completely sequenced prokaryotic genomes publicly available. Our analyses revealed taxonomic patterns for the distribution of these genes and anticorrelations in their occurrence. The analyses of bacterial genomes revealed the existence of genes coding for PurV, PurJ, and PurO, which may no longer be considered signatures of the domain Archaea. Although highly divergent, the PurOs of Archaea and Bacteria show a high level of conservation in the amino acids of the active sites of the protein, allowing us to infer that these enzymes are analogs.
    [Show full text]
  • Bacterial Involvements in Ulcerative Colitis: Molecular and Microbiological Studies
    BACTERIAL INVOLVEMENTS IN ULCERATIVE COLITIS: MOLECULAR AND MICROBIOLOGICAL STUDIES Samia Alkhalil A thesis submitted in partial fulfilment of the requirements for the award of the degree of Doctor of Philosophy of the University of Portsmouth Institute of Biomedical and biomolecular Sciences School of Pharmacy and Biomedical Sciences October 2017 AUTHORS’ DECLARATION I declare that whilst registered as a candidate for the degree of Doctor of Philosophy at University of Portsmouth, I have not been registered as a candidate for any other research award. The results and conclusions embodied in this thesis are the work of the named candidate and have not been submitted for any other academic award. Samia Alkhalil I ABSTRACT Inflammatory bowel disease (IBD) is a series of disorders characterised by chronic intestinal inflammation, with the principal examples being Crohn’s Disease (CD) and ulcerative colitis (UC). A paradigm of these disorders is that the composition of the colon microbiota changes, with increases in bacterial numbers and a reduction in diversity, particularly within the Firmicutes. Sulfate reducing bacteria (SRB) are believed to be involved in the etiology of these disorders, because they produce hydrogen sulfide which may be a causative agent of epithelial inflammation, although little supportive evidence exists for this possibility. The purpose of this study was (1) to detect and compare the relative levels of gut bacterial populations among patients suffering from ulcerative colitis and healthy individuals using PCR-DGGE, sequence analysis and biochip technology; (2) develop a rapid detection method for SRBs and (3) determine the susceptibility of Desulfovibrio indonesiensis in biofilms to Manuka honey with and without antibiotic treatment.
    [Show full text]
  • Geochemical, Biological and Clumped Isotopologue Evidence For
    Geochemical, biological and clumped isotopologue evidence for substantial microbial methane production under carbon limitation in serpentinites of the Samail Ophiolite, Oman Daniel Nothaft, Alexis Templeton, Jeemin Rhim, David Wang, Jabrane Labidi, Hannah Miller, Eric Boyd, Juerg Matter, Shuhei Ono, Edward Young, et al. To cite this version: Daniel Nothaft, Alexis Templeton, Jeemin Rhim, David Wang, Jabrane Labidi, et al.. Geochemical, biological and clumped isotopologue evidence for substantial microbial methane production under carbon limitation in serpentinites of the Samail Ophiolite, Oman. Journal of Geophysical Research: Biogeosciences, American Geophysical Union, In press, 10.1029/2020JG006025. hal-03325162 HAL Id: hal-03325162 https://hal.archives-ouvertes.fr/hal-03325162 Submitted on 24 Aug 2021 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. manuscript submitted to JGR: Biogeosciences 1 Geochemical, biological and clumped isotopologue 2 evidence for substantial microbial methane production 3 under carbon limitation in serpentinites of the Samail 4 Ophiolite, Oman 1 1 2 2∗ 5 Daniel B. Nothaft , Alexis S. Templeton , Jeemin H. Rhim , David T. Wang 3 1y 4 5 6 , Jabrane Labidi , Hannah M. Miller , Eric S. Boyd , Juerg M. Matter , 2 3 1 6 7 Shuhei Ono , Edward D.
    [Show full text]
  • Abstract Tracing Hydrocarbon
    ABSTRACT TRACING HYDROCARBON CONTAMINATION THROUGH HYPERALKALINE ENVIRONMENTS IN THE CALUMET REGION OF SOUTHEASTERN CHICAGO Kathryn Quesnell, MS Department of Geology and Environmental Geosciences Northern Illinois University, 2016 Melissa Lenczewski, Director The Calumet region of Southeastern Chicago was once known for industrialization, which left pollution as its legacy. Disposal of slag and other industrial wastes occurred in nearby wetlands in attempt to create areas suitable for future development. The waste creates an unpredictable, heterogeneous geology and a unique hyperalkaline environment. Upgradient to the field site is a former coking facility, where coke, creosote, and coal weather openly on the ground. Hydrocarbons weather into characteristic polycyclic aromatic hydrocarbons (PAHs), which can be used to create a fingerprint and correlate them to their original parent compound. This investigation identified PAHs present in the nearby surface and groundwaters through use of gas chromatography/mass spectrometry (GC/MS), as well as investigated the relationship between the alkaline environment and the organic contamination. PAH ratio analysis suggests that the organic contamination is not mobile in the groundwater, and instead originated from the air. 16S rDNA profiling suggests that some microbial communities are influenced more by pH, and some are influenced more by the hydrocarbon pollution. BIOLOG Ecoplates revealed that most communities have the ability to metabolize ring structures similar to the shape of PAHs. Analysis with bioinformatics using PICRUSt demonstrates that each community has microbes thought to be capable of hydrocarbon utilization. The field site, as well as nearby areas, are targets for habitat remediation and recreational development. In order for these remediation efforts to be successful, it is vital to understand the geochemistry, weathering, microbiology, and distribution of known contaminants.
    [Show full text]
  • Arsenic Metabolism in High Altitude Modern Stromatolites Revealed by Metagenomic Analysis Received: 25 November 2016 Daniel Kurth 1, Ariel Amadio2, Omar F
    www.nature.com/scientificreports OPEN Arsenic metabolism in high altitude modern stromatolites revealed by metagenomic analysis Received: 25 November 2016 Daniel Kurth 1, Ariel Amadio2, Omar F. Ordoñez1, Virginia H. Albarracín1,3, Wolfgang Accepted: 16 March 2017 Gärtner4 & María E. Farías1 Published: xx xx xxxx Modern stromatolites thrive only in selected locations in the world. Socompa Lake, located in the Andean plateau at 3570 masl, is one of the numerous extreme Andean microbial ecosystems described over recent years. Extreme environmental conditions include hypersalinity, high UV incidence, and high arsenic content, among others. After Socompa’s stromatolite microbial communities were analysed by metagenomic DNA sequencing, taxonomic classification showed dominance of Proteobacteria, Bacteroidetes and Firmicutes, and a remarkably high number of unclassified sequences. A functional analysis indicated that carbon fixation might occur not only by the Calvin-Benson cycle, but also through alternative pathways such as the reverse TCA cycle, and the reductive acetyl-CoA pathway. Deltaproteobacteria were involved both in sulfate reduction and nitrogen fixation. Significant differences were found when comparing the Socompa stromatolite metagenome to the Shark Bay (Australia) smooth mat metagenome: namely, those involving stress related processes, particularly, arsenic resistance. An in-depth analysis revealed a surprisingly diverse metabolism comprising all known types of As resistance and energy generating pathways. While the ars operon was the main mechanism, an important abundance of arsM genes was observed in selected phyla. The data resulting from this work will prove a cornerstone for further studies on this rare microbial community. Arsenic is not only a natural component in the Earth crust and in various minerals, but it is also a major con- taminant of aquatic ecosystems worldwide1.
    [Show full text]