DOCSLIB.ORG

Microbial Community Diversity Associated with Carbon and Nitrogen Cycling in Permeable Marine Sediments Evan M

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Microbial Community Diversity Associated with Carbon and Nitrogen Cycling in Permeable Marine Sediments Evan M Florida State University Libraries Electronic Theses, Treatises and Dissertations The Graduate School 2006 Microbial Community Diversity Associated with Carbon and Nitrogen Cycling in Permeable Marine Sediments Evan M. Hunter Follow this and additional works at the FSU Digital Library. For more information, please contact [email protected] THE FLORIDA STATE UNIVERSITY COLLEGE OF ARTS AND SCIENCES MICROBIAL COMMUNITY DIVERSITY ASSOCIATED WITH CARBON AND NITROGEN CYCLING IN PERMEABLE MARINE SEDIMENTS By EVAN M. HUNTER A Thesis submitted to the Department of Oceanography in partial fulfillment of the requirements for the degree of Master of Science Degree Awarded: Spring Semester, 2006 The members of the Committee approve the thesis of Evan Hunter on March 20th, 2006. _________________________ Joel Kostka Professor Directing Thesis _________________________ Heath Mills Committee Member _________________________ Markus Huettel Committee Member _________________________ Lee Kerkhof Committee Member Approved: _____________________________________________ William K. Dewar, Chair, Department of Oceanography The Office of Graduate Studies has verified and approved the above named committee members. ii TABLE OF CONTENTS List of Tables iv List of Figures v Abstract vii INTRODUCTION 1 1. CHARACTERIZATION OF MICROBIAL DIVERSITY IN PERMEABLE MARINE SEDIMENTS OF THE SOUTH ATLANTIC BIGHT 8 2. PROFILING OF THE OVERALL, NITRIFYING, AND DENITRIFYING MICROBIAL COMMUNITY DIVERSITY IN PERMEABLE MARINE SEDIMENTS OF THE NORTHEASTERN GULF OF MEXICO 46 CONCLUSIONS 86 REFERENCES 89 BIOGRAPHICAL SKETCH 101 iii LIST OF TABLES 1.1 Summary of dissolved gases and nutrient concentrations in column experiments. 16 1.2 Statistical analyses of SSU rRNA, nosZ, and amoA gene clone libraries using standard ecological and molecular estimates of sequence diversity. 18 1.3 Summary of SSU rRNA gene sequences from SC#1, SC#3, LC#1, LC#3 and SAB clone libraries. 22 1.4 Summary of nosZ gene sequences from SC#1, SC#3, LC#1, LC#3 and SAB clone libraries. 33 1.5 Summary of amoA gene sequences from SC#1, SC#3, LC#1, LC#3 and SAB clone libraries. 37 2.1 Summary of amoA gene sequences from 3B02, 3B1820, 3G02, 3G1820, and Total clone libraries. 55 2.2 Statistical analyses of SSU rRNA and nosZ gene clone libraries using standard ecological and molecular estimates of sequence diversity. 58 2.3 Summary of SSU rRNA gene sequences from 3B02, 3B1820, 3G02, 3G1820, and Total clone libraries. 59 2.4 Summary of nosZ gene sequences from 3B02, 3B1820, 3G02, 3G1820, and Total clone libraries. 78 iv LIST OF FIGURES 1.1 The South Atlantic Bight sampling site (W27) located at 31o29’N, 80o26’W (Google Earth, 2006). 11 1.2 Experimental design of column incubations. 12 1.3 Rarefaction curves determined for the different RFLP patterns of SSU rRNA (A), nosZ (B), and amoA (C) gene clones from total, SC#1, SC#3, LC#1, LC#3 and SAB samples. 20 1.4 Frequencies of bacterial phylogenetic lineages detected in SSU rRNA gene clone libraries derived from SC#1, SC#3, LC#1, LC#3 and SAB samples. 25 1.5 Phylum Proteobacteria neighbor-joining phylogenetic tree, incorporating a Jukes-Cantor distance correction, of SSU rRNA gene from SC#1, SC#3, LC#1, LC#3 and SAB samples. 27 1.6 Non-Proteobacteria neighbor-joining phylogenetic tree, incorporating a Jukes-Cantor distance correction, of SSU rRNA gene from SC#1, SC#3, LC#1, LC#3 and SAB samples. 30 1.7 Neighbor-joining phylogenetic tree, incorporating a Jukes- Cantor distance correction, of nosZ gene from SC#1, SC#3, LC#1, LC#3 and SAB samples. 36 1.8 Neighbor-joining phylogenetic tree, incorporating a Jukes- Cantor distance correction, of amoA gene from SC#1, SC#3, LC#1, LC#3 and SAB samples 39 2.1 The St. George Island sampling sites located at 29o 44.885 N, 84o 42.594 W (Gulf site) and 29o 45.034 N, 84o 42.719 W (Bay site) (Google Earth, 2006). 49 v 2.2 Rarefaction curves determined for the different RFLP patterns of SSU rRNA (A), nosZ (B), and amoA (C) gene clones from total, 3B02, 3B1820, 3G02, and 3G1820 samples. 57 2.3 Frequencies of bacterial phylogenetic lineages detected in SSU rRNA gene clone libraries derived from 3B02, 3B1820, 3G02, 3G1820, and Total samples. 62 2.4 Phylum Proteobacteria neighbor-joining phylogenetic tree, incorporating a Jukes-Cantor distance correction, of SSU rRNA gene from 3B02, 3B1820, 3G02, and 3G1820 samples. 65 2.5 Non-Proteobacteria neighbor-joining phylogenetic tree, incorporating a Jukes-Cantor distance correction, of SSU rRNA gene from 3B02, 3B1820, 3G02, and 3G1820 samples. 67 2.6 T-RFLP fingerprints of March Bay 0-2 cm, Bay 2-4 cm, and Gulf 0-2 cm samples. 72 2.7 Sorensen’s based index dendrograms of SSU rRNA gene (A) and nosZ gene (B). 75 2.8 Neighbor-joining phylogenetic tree, incorporating a Jukes- Cantor distance correction, of nosZ gene from 3B02, 3B1820, 3G02, and 3G1820 samples. 77 vi ABSTRACT Though a large fraction of primary production and organic matter cycling in the oceans occurs on continental shelves dominated by sandy deposits, the microbial communities associated with permeable shelf sediments remain poorly characterized. Therefore, the primary objective of this study was to provide the first detailed characterization of microbial diversity in representative marine sands of the South Atlantic Bight (SAB) and the northeastern Gulf of Mexico (NEGOM) through analyses of SSU rRNA gene (Bacteria), nosZ (denitrifying bacteria), and amoA (ammonia- oxidizing bacteria) sequences. Communities were analyzed by DNA extraction, clone library construction, and terminal restriction fragment length polymorphism (T-RFLP) community fingerprinting. Sediment characteristics, geochemical parameters, and rate measurements were obtained in parallel with microbial community analysis. Microbiological and biogeochemical approaches were coupled, allowing the structure- function relationships of key microbial groups involved in carbon and nitrogen cycling in continental shelf sediments to be examined. In the SAB study (Ch. 1), clone libraries were constructed from both sediment core material and manipulated sediment within column experiments. Rapid organic matter degradation and coupled nitrification-denitrification were observed in column experiments at flow rates and oxygen concentrations resembling in situ conditions. Numerous SSU rRNA gene phylotypes were affiliated with the phyla Proteobacteria (classes α-, δ-, and γ-Proteobacteria), Planctomycetes, Cyanobacteria, Chloroflexi and Bacteroidetes. Detectable sequence diversity of nosZ and SSU rRNA genes increased in stratified redox-stabilized columns compared to in situ sediments, with the α- Proteobacteria comprising the most frequently detected group. Alternatively, nitrifier communities showed a relatively low and stable diversity that did not co-vary with the other gene targets. In the NEGOM study (Ch. 2), high throughput techniques were developed and applied to extensively profile overall and denitrifying microbial communities in a large vii number of sediment samples over various sediment depth intervals, contrasting sites, and sampling periods. Cloning/sequencing and community fingerprinting (T-RFLP) approaches were applied in parallel to characterize microbial diversity and phylogenetic composition. Statistical estimators including species richness, Shannon-Weiner and 1/D indices, nucleotide diversity, gene diversity, evenness, and θ (π) indicated little difference between four clone libraries constructed from selected depth intervals (0-2 cm, 18-20 cm) at each site in March. In contrast, T-RFLP profiles and robust phylogenetic analysis showed distinct trends in diversity according to site, depth, and time period sampled. The results elucidate predominant phylotypes that are likely to catalyze carbon and nitrogen cycling in marine sands. Several microbial groups (δ-Proteobacteria, γ- Proteobacteria, Planctomycetes) were confirmed as significant contributors to the microbial communities of permeable marine sediments in agreement with previous work. However, the robust sequence database of this study expanded current knowledge to reveal a large overall community diversity including additional groups (α- Proteobacteria, Bacteriodetes/Chlorobi, and Cyanobacteria) that had not been previously recognized using cultivation-independent methods with inherently lower resolution. The α-Proteobacteria, in particular, were shown to be relatively abundant in the overall and denitrifying communities at both SAB and NEGOM sites. Although overall diversity increased in response to redox stabilization and stratification in column experiments, the major phylotypes remained the same, indicating that the columns sufficiently mimic in situ conditions. While SSU rRNA gene phylotypes detected by clonal analysis were similar at the phylum level at all sites, the NEGOM site showed much higher species richness in comparison to SAB. At NEGOM, T-RFLP showed distinct differences in community diversity according to site, depth, and time. The sequence database from this thesis will facilitate the development of improved probes and primer sets to be used in quantifying the metabolically active members of permeable sand communities. Rapid community fingerprinting methods developed here should allow for more extensive comparisons across environmental gradients in order to better understand the factors controlling microbial diversity in permeable sediments viii INTRODUCTION THE PERMEABLE CONTINENTAL SHELF ENVIRONMENT AND IT’S SIGNIFICANCE TO ORGANIC MATTER CYCLING Approximately one-third of oceanic primary
Load more

Recommended publications
  • Organic Electron Donors and Terminal Electron Acceptors Structure
    bioRxiv preprint doi: https://doi.org/10.1101/2021.02.16.431432; this version posted February 16, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-ND 4.0 International license. 1 Organic electron donors and terminal electron acceptors structure 2 anaerobic microbial communities and interactions in a permanently 3 stratified sulfidic lake 4 Connie A. Rojas1,2, Ana De Santiago Torio3, Serry Park1, Tanja Bosak3*, Vanja Klepac- 5 Ceraj1* 6 1Department of Biological Sciences, Wellesley College, Wellesley, MA, USA. 7 2Ecology, Evolution, and Behavior, Michigan State University, East Lansing, MI, USA. 8 3Department of Earth, Atmospheric, and Planetary Sciences, Massachusetts Institute of Technology, 9 Cambridge, MA, USA. 10 11 * Correspondence: 12 Tanja Bosak [email protected] 13 Vanja Klepac-Ceraj [email protected] 14 15 Keywords: meromictic lake, microbial community assembly, generalists, enrichment cultures, 16 nutrient cycling, sulfur cycle, carbon cycle, organic electron donors, terminal electron acceptors 17 18 ABstract 19 The extent to which nutrients structure microbial communities in permanently stratified lakes is not 20 well understood. This study characterizeD microbial communities from the anoxic layers of the 21 meromictic and sulfidic Fayetteville Green Lake (FGL), NY, and investigated the roles of organic 22 electron donors and terminal electron acceptors in shaping microbial community structure and 23 interactions. Bacterial communities from the permanently stratified layer below the chemocline 24 (monimolimnion) and from enrichment cultures inoculated by lake sediments were analyzed using 25 16S rRNA gene sequencing.
    [Show full text]
  • Bibliography
    Bibliography Abella, C.A., X.P. Cristina, A. Martinez, I. Pibernat and X. Vila. 1998. on moderate concentrations of acetate: production of single cells. Two new motile phototrophic consortia: "Chlorochromatium lunatum" Appl. Microbiol. Biotechnol. 35: 686-689. and "Pelochromatium selenoides". Arch. Microbiol. 169: 452-459. Ahring, B.K, P. Westermann and RA. Mah. 1991b. Hydrogen inhibition Abella, C.A and LJ. Garcia-Gil. 1992. Microbial ecology of planktonic of acetate metabolism and kinetics of hydrogen consumption by Me­ filamentous phototrophic bacteria in holomictic freshwater lakes. Hy­ thanosarcina thermophila TM-I. Arch. Microbiol. 157: 38-42. drobiologia 243-244: 79-86. Ainsworth, G.C. and P.H.A Sheath. 1962. Microbial Classification: Ap­ Acca, M., M. Bocchetta, E. Ceccarelli, R Creti, KO. Stetter and P. Cam­ pendix I. Symp. Soc. Gen. Microbiol. 12: 456-463. marano. 1994. Updating mass and composition of archaeal and bac­ Alam, M. and D. Oesterhelt. 1984. Morphology, function and isolation terial ribosomes. Archaeal-like features of ribosomes from the deep­ of halobacterial flagella. ]. Mol. Biol. 176: 459-476. branching bacterium Aquifex pyrophilus. Syst. Appl. Microbiol. 16: 629- Albertano, P. and L. Kovacik. 1994. Is the genus LeptolynglYya (Cyano­ 637. phyte) a homogeneous taxon? Arch. Hydrobiol. Suppl. 105: 37-51. Achenbach-Richter, L., R Gupta, KO. Stetter and C.R Woese. 1987. Were Aldrich, H.C., D.B. Beimborn and P. Schönheit. 1987. Creation of arti­ the original eubacteria thermophiles? Syst. Appl. Microbiol. 9: 34- factual internal membranes during fixation of Methanobacterium ther­ 39. moautotrophicum. Can.]. Microbiol. 33: 844-849. Adams, D.G., D. Ashworth and B.
    [Show full text]
  • Microbial and Mineralogical Characterizations of Soils Collected from the Deep Biosphere of the Former Homestake Gold Mine, South Dakota
    University of Nebraska - Lincoln DigitalCommons@University of Nebraska - Lincoln US Department of Energy Publications U.S. Department of Energy 2010 Microbial and Mineralogical Characterizations of Soils Collected from the Deep Biosphere of the Former Homestake Gold Mine, South Dakota Gurdeep Rastogi South Dakota School of Mines and Technology Shariff Osman Lawrence Berkeley National Laboratory Ravi K. Kukkadapu Pacific Northwest National Laboratory, [email protected] Mark Engelhard Pacific Northwest National Laboratory Parag A. Vaishampayan California Institute of Technology See next page for additional authors Follow this and additional works at: https://digitalcommons.unl.edu/usdoepub Part of the Bioresource and Agricultural Engineering Commons Rastogi, Gurdeep; Osman, Shariff; Kukkadapu, Ravi K.; Engelhard, Mark; Vaishampayan, Parag A.; Andersen, Gary L.; and Sani, Rajesh K., "Microbial and Mineralogical Characterizations of Soils Collected from the Deep Biosphere of the Former Homestake Gold Mine, South Dakota" (2010). US Department of Energy Publications. 170. https://digitalcommons.unl.edu/usdoepub/170 This Article is brought to you for free and open access by the U.S. Department of Energy at DigitalCommons@University of Nebraska - Lincoln. It has been accepted for inclusion in US Department of Energy Publications by an authorized administrator of DigitalCommons@University of Nebraska - Lincoln. Authors Gurdeep Rastogi, Shariff Osman, Ravi K. Kukkadapu, Mark Engelhard, Parag A. Vaishampayan, Gary L. Andersen, and Rajesh K. Sani This article is available at DigitalCommons@University of Nebraska - Lincoln: https://digitalcommons.unl.edu/ usdoepub/170 Microb Ecol (2010) 60:539–550 DOI 10.1007/s00248-010-9657-y SOIL MICROBIOLOGY Microbial and Mineralogical Characterizations of Soils Collected from the Deep Biosphere of the Former Homestake Gold Mine, South Dakota Gurdeep Rastogi & Shariff Osman & Ravi Kukkadapu & Mark Engelhard & Parag A.
    [Show full text]
  • Microbial Degradation of Organic Micropollutants in Hyporheic Zone Sediments
    Microbial degradation of organic micropollutants in hyporheic zone sediments Dissertation To obtain the Academic Degree Doctor rerum naturalium (Dr. rer. nat.) Submitted to the Faculty of Biology, Chemistry, and Geosciences of the University of Bayreuth by Cyrus Rutere Bayreuth, May 2020 This doctoral thesis was prepared at the Department of Ecological Microbiology – University of Bayreuth and AG Horn – Institute of Microbiology, Leibniz University Hannover, from August 2015 until April 2020, and was supervised by Prof. Dr. Marcus. A. Horn. This is a full reprint of the dissertation submitted to obtain the academic degree of Doctor of Natural Sciences (Dr. rer. nat.) and approved by the Faculty of Biology, Chemistry, and Geosciences of the University of Bayreuth. Date of submission: 11. May 2020 Date of defense: 23. July 2020 Acting dean: Prof. Dr. Matthias Breuning Doctoral committee: Prof. Dr. Marcus. A. Horn (reviewer) Prof. Harold L. Drake, PhD (reviewer) Prof. Dr. Gerhard Rambold (chairman) Prof. Dr. Stefan Peiffer In the battle between the stream and the rock, the stream always wins, not through strength but by perseverance. Harriett Jackson Brown Jr. CONTENTS CONTENTS CONTENTS ............................................................................................................................ i FIGURES.............................................................................................................................. vi TABLES ..............................................................................................................................
    [Show full text]
  • Effects of Alternate Precipitation Patterns on Soil Microbial
    EFFECTS OF ALTERNATE PRECIPITATION PATTERNS ON SOIL MICROBIAL COMMUNITIES IN A CALIFORNIA GRASSLAND by Karelyn Cruz Martínez A dissertation submitted in partial satisfaction of the requirements for the degree of Doctor of Philosophy in Microbiology in the Graduate Division of the University of California, Berkeley Committee in charge: Professor Jillian F. Banfield, Chair Professor Mary K. Firestone Professor Mary E. Power Spring 2010 EFFECTS OF ALTERNATE PRECIPITATION PATTERNS ON SOIL MICROBIAL COMMUNITIES IN A CALIFORNIA GRASSLAND © 2010 by Karelyn Cruz Martínez Abstract EFFECTS OF ALTERNATE PRECIPITATION PATTERNS ON SOIL MICROBIAL COMMUNITIES IN A CALIFORNIA GRASSLAND by Karelyn Cruz Martínez Doctor of Philosophy in Microbiology University of California, Berkeley Professor Jillian F. Banfield, Chair Anthropogenic changes in climatic conditions, such as the timing and amount of rainfall, can have profound biotic and abiotic consequences on grassland ecosystems. Grassland‘s plant and animal phenology are adapted to the ecosystem‘s wet and cold winters and hot and dry summers and changes to this pattern will have profound consequences in aboveground community structure. Changes in climatic conditions and aboveground communities will also affect the soil biogeochemistry and microbial communities. Soil microbes are an essential component in ecosystem functioning, as they are the key players in nutrient cycling. This thesis investigated the direct and indirect effects of climate change on the structure, composition and abundance of grassland soil microbial communities. The research used the high-throughput technique of 16S rRNA microarrays (Phylochip) to detect changes in the abundances and activities of soil bacterial and archaeal taxa in response to changes in precipitation patterns, aboveground plant communities, and soil environmental conditions.
    [Show full text]
  • WO 2015/100432 A2 2 July 2015 (02.07.2015) P O P CT
    (12) INTERNATIONAL APPLICATION PUBLISHED UNDER THE PATENT COOPERATION TREATY (PCT) (19) World Intellectual Property Organization International Bureau (10) International Publication Number (43) International Publication Date WO 2015/100432 A2 2 July 2015 (02.07.2015) P O P CT (51) International Patent Classification: Gerardo, V.; C/o Symbiota, Inc., 1 Memorial Drive, 7th A 63/02 (2006.01) Floor, Cambridge, MA 0242 1 (US). DJONOVIC, Slavica; C/o Symbiota, Inc., 1 Memorial Drive, 7th Floor, Cam (21) International Application Number: bridge, MA 02421 (US). MARQUEZ, Luis, Miguel; C/o PCT/US20 14/072400 Symbiota, Inc., 1 Memorial Drive, 7th Floor, Cambridge, (22) International Filing Date: MA 02421 (US). JOHNSTON, David, Morris; C/o Sym 24 December 2014 (24. 12.2014) biota, Inc., 1 Memorial Drive, 7th Floor, Cambridge, MA 02421 (US). MILLET, Yves, Alain; C/o Symbiota, Inc., 1 (25) Filing Language: English Memorial Drive, 7th Floor, Cambridge, MA 02421 (US). (26) Publication Language: English LYFORD, Jeffrey; C/o Symbiota, Inc., 1 Memorial Drive, 7th Floor, Cambridge, MA 02421 (US). LEFF, Jonathan, (30) Priority Data: W.; C/o Symbiota, Inc., 1 Memorial Drive, 7th Floor, 61/920,560 24 December 201 3 (24. 12.2013) US Cambrdige, MA 02421 (US). SAMAYOA, Philip; C/o 62/017,816 26 June 2014 (26.06.2014) US Symbiota, Inc., 1 Memorial Drive, 7th Floor, Cambridge, 62/017,809 26 June 2014 (26.06.2014) us MA 02421 (US). SADOWSKI, Craig; C/o Symbiota, Inc., PCT/US20 14/044427 26 June 2014 (26.06.2014) us 1 Memorial Drive, 7th Floor, Cambridge, MA 02421 (US).
    [Show full text]
  • Kaksonen.Pdf
    Julkaisu 489 Publication 489 Anna Kaksonen The Performance, Kinetics and Microbiology of Sulfidogenic Fluidized-Bed Reactors Treating Acidic Metal- and Sulfate-Containing Wastewater Tampere 2004 Tampereen teknillinen yliopisto. Julkaisu 489 Tampere University of Technology. Publication 489 Anna Kaksonen The Performance, Kinetics and Microbiology of Sulfidogenic Fluidized-Bed Reactors Treating Acidic Metal- and Sulfate-Containing Wastewater Thesis for the degree of Doctor of Technology to be presented with due permission for public examination and criticism in Festia Building, Small Auditorium 1, at Tampere University of Technology, on the 17th of September 2004, at 12 noon. Tampereen teknillinen yliopisto - Tampere University of Technology Tampere 2004 ISBN 952-15-1234-2 (printed) ISBN 952-15-1404-3 (PDF) ISSN 1459-2045 Anna Kaksonen The performance, kinetics and microbiology of sulfidogenic fluidized-bed reactors treating acidic metal- and sulfate-containing wastewater ERRATA Summary 2- - Page 50, equation 14: “HCO3 “should read “HCO3 “ Pages 56-59, Tables 18 and 19, 1st column 1st row: “rector” should read “reactor” Paper I: Page 255, abstract, line 3, “250 and 350” should read 350 and 250” Page 257, Figure 2, part A, legend, “yeast extractt” should read “yeast extract” Page 258, right paragraph, 2nd last row of paragraph 3.1, “FBR3” should read “FBR2” Page 260, Figure 3, part D, “Fe load an precipitation” should read “Fe load and precipitation” Page 261, 1st paragraph, line 4: “79-87%” should read “79-86%” Page 261, 1st paragraph,
    [Show full text]
  • Assessing the Genetic Potential of Uncultivated Sulfate Reducing Bacteria
    Assessing the Genetic Potential of Uncultivated Sulfate Reducing Bacteria Dissertation zur Erlangung des Grades eines Doktors der Naturwissenschaften - Dr. rer. nat. - Dem Fachbereich Biologie/Chemie der Universität Bremen vorgelegt von Lars Schreiber Bremen August 2010 Die vorliegende Arbeit wurde in der Zeit von April 2007 bis Juli 2010 im Rahmen des Programms „The 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. Antje Boetius Tag des Promotionskolloquiums: 1. September 2010 When asked to move a mountain, do not look upon its size. Merely move the first rock. - David Gemmell Table of Contents ZUSAMMENFASSUNG 1 ABSTRACT 3 ABBREVIATIONS 5 I. INTRODUCTION 1. Methane in marine systems 7 2. Cold seeps 8 3. Sulfate-reduction pathway 9 4. Sulfate-reducing prokaryotes 11 5. Ecology and physiology of sulfate-reducing prokaryotes 14 6. Sulfate-reducing prokaryotes and the anaerobic oxidation of 15 methane 7. Metagenomics and single-cell techniques 20 8. Aims of this work 23 9. References 25 II. IDENTIFICATION OF THE DOMINANT SULFATE-REDUCING 31 BACTERIAL PARTNER OF ANAEROBIC METHANOTROPHS OF THE ANME-2 CLADE Introduction 33 Results and Discussion 34 Conclusion 42 Experimental Procedures 42 References 44 Appendix / Supporting Information 47 III. DIVERSITY OF ADENOSINE-5’-PHOSPHOSULFATE REDUCTASE 56 AND DISSIMILATORY SULFITE REDUCTASE IN MICROBIAL COMMUNITIES MEDIATING THE ANAEROBIC OXIDATION OF METHANE Abstract 59 Introduction 60 Results 63 Discussion 74 Conclusion 80 Experimental Procedures 81 References 88 Appendix / Supporting Information 93 IV. METAGENOMIC ANALYSIS OF THE DOMINATING SULFATE- 103 REDUCING BACTERIA IN ANME2-DOMINATED ENRICHMENTS CATALYZING THE ANAEROBIC OXIDATION OF METHANE Abstract 106 Introduction 107 Results and Discussion 109 Conclusion 122 Experimental Procedures 123 References 126 Appendix / Supporting Information 129 V.
    [Show full text]
  • Survey of Microbial Diversity in Flood Areas During Thailand 2011 Flood Crisis Using High-Throughput Tagged Amplicon Pyrosequencing
    RESEARCH ARTICLE Survey of Microbial Diversity in Flood Areas during Thailand 2011 Flood Crisis Using High-Throughput Tagged Amplicon Pyrosequencing Wuttichai Mhuantong1, Sarunyou Wongwilaiwalin1, Thanaporn Laothanachareon1, Lily Eurwilaichitr1, Sithichoke Tangphatsornruang2, Benjaporn Boonchayaanant3,4, Tawan Limpiyakorn3,4, Kobchai Pattaragulwanit5, Thantip Punmatharith4, John McEvoy6, Eakalak Khan7, Manaskorn Rachakornkij3,4, Verawat Champreda1* 1 Enzyme Technology Laboratory, National Center for Genetic Engineering and Biotechnology, 113 Thailand Science Park, Phahonyothin Road, Khlong Luang, Pathum Thani 12120, Thailand, 2 Genome Institute, National Center for Genetic Engineering and Biotechnology, Thailand Science Park, Khlong Luang, Pathum Thani 12120, Thailand, 3 Department of Environmental Engineering, Faculty of Engineering, Chulalongkorn University, Phayatai, Bangkok 10330, Thailand, 4 Center of Excellence on Hazardous Substance Management (HSM), Chulalongkorn University, Phayatai, Bangkok 10330, Thailand, OPEN ACCESS 5 Department of Microbiology, Faculty of Science, Chulalongkorn University, Phayatai, Bangkok 10330, Thailand, 6 Department of Veterinary and Microbiological Sciences, North Dakota State University, Fargo, Citation: Mhuantong W, Wongwilaiwalin S, ND 58108, United States of America, 7 Department of Civil and Environmental Engineering, North Dakota Laothanachareon T, Eurwilaichitr L, State University, Fargo, ND 58108, United States of America Tangphatsornruang S, Boonchayaanant B, et al. * [email protected] (2015)
    [Show full text]
  • Effects of Alternate Precipitation Patterns on Soil Microbial Communities in a California Grassland
    UC Berkeley UC Berkeley Electronic Theses and Dissertations Title EFFECTS OF ALTERNATE PRECIPITATION PATTERNS ON SOIL MICROBIAL COMMUNITIES IN A CALIFORNIA GRASSLAND Permalink https://escholarship.org/uc/item/2pg7k9w1 Author Cruz Martinez, Karelyn Publication Date 2010 Peer reviewed|Thesis/dissertation eScholarship.org Powered by the California Digital Library University of California EFFECTS OF ALTERNATE PRECIPITATION PATTERNS ON SOIL MICROBIAL COMMUNITIES IN A CALIFORNIA GRASSLAND by Karelyn Cruz Martínez A dissertation submitted in partial satisfaction of the requirements for the degree of Doctor of Philosophy in Microbiology in the Graduate Division of the University of California, Berkeley Committee in charge: Professor Jillian F. Banfield, Chair Professor Mary K. Firestone Professor Mary E. Power Spring 2010 EFFECTS OF ALTERNATE PRECIPITATION PATTERNS ON SOIL MICROBIAL COMMUNITIES IN A CALIFORNIA GRASSLAND © 2010 by Karelyn Cruz Martínez Abstract EFFECTS OF ALTERNATE PRECIPITATION PATTERNS ON SOIL MICROBIAL COMMUNITIES IN A CALIFORNIA GRASSLAND by Karelyn Cruz Martínez Doctor of Philosophy in Microbiology University of California, Berkeley Professor Jillian F. Banfield, Chair Anthropogenic changes in climatic conditions, such as the timing and amount of rainfall, can have profound biotic and abiotic consequences on grassland ecosystems. Grassland‘s plant and animal phenology are adapted to the ecosystem‘s wet and cold winters and hot and dry summers and changes to this pattern will have profound consequences in aboveground community structure. Changes in climatic conditions and aboveground communities will also affect the soil biogeochemistry and microbial communities. Soil microbes are an essential component in ecosystem functioning, as they are the key players in nutrient cycling. This thesis investigated the direct and indirect effects of climate change on the structure, composition and abundance of grassland soil microbial communities.
    [Show full text]