DOCSLIB.ORG

Molecular Characterization of Methanotrophic and Chemoautotrophic Communities at Cold Seeps

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Molecular Characterization of Methanotrophic and Chemoautotrophic Communities at Cold Seeps Molecular Characterization of Methanotrophic and Chemoautotrophic Communities at Cold Seeps Dissertation zur Erlangung des Grades eines Doktors der Naturwissenschaften - Dr. rer. nat. - dem Fachbereich Biologie/Chemie der Universität Bremen vorgelegt von Tina Lösekann Bremen März 2006 Die Untersuchungen zur vorliegenden Doktorarbeit wurden in der Zeit von September 2002 bis März 2006 am Max-Planck-Institut für Marine Mikrobiologie in Bremen durchgeführt. 1. Gutachterin: Prof. Dr. A. Boetius 2. Gutachter: Prof. Dr. R. Amann Weitere Prüfer: Prof. Dr. U. Fischer Dr. K. Knittel Tag des Promotionskolloquiums: 30. März 2006 Table of Contents Summary ................................................................................................................................... 1 Zusammenfassung..................................................................................................................... 2 Part I: Combined Presentation of Results A Introduction .............................................................................................................. 5 1 Reducing Habitats in the Ocean............................................................................. 6 1.1 Oxygen Minimum Zones............................................................................. 7 1.2 Large Organic Falls..................................................................................... 7 1.3 Hydrothermal Vents..................................................................................... 8 1.4 Cold Seeps................................................................................................... 8 2 Key Biogeochemical Processes in Reducing Habitats .......................................... 10 2.1 Methanogenesis ........................................................................................... 10 2.2 Anaerobic Oxidation of Methane................................................................. 11 2.3 Sulfate Reduction......................................................................................... 14 2.4 Oxidation of Sulfide..................................................................................... 14 2.5 Aerobic Oxidation of Methane .................................................................... 16 2.6 Oxidation of Other Reduced Elements ........................................................ 18 3 Key Players in Reducing Habitats ......................................................................... 18 3.1 Anaerobic Methane-Oxidizing Archaea...................................................... 18 3.2 Sulfate-Reducing Bacteria........................................................................... 21 3.3 Sulfide-Oxidizing Bacteria.......................................................................... 22 3.4 Aerobic Methane-Oxidizing Bacteria.......................................................... 23 3.5 Symbiont-Bearing Marine Invertebrates...................................................... 24 4 Cultivation-Independent Methods for the Identification of Microorganisms........ 27 4.1 The Full Cycle rRNA Approach.................................................................. 27 4.2 Lipid Biomarkers ......................................................................................... 28 4.3 Metagenomics.............................................................................................. 28 5 Thesis Outline........................................................................................................ 29 B Results and Discussion............................................................................................. 31 1 Haakon Mosby Mud Volcano (Barents Sea) ......................................................... 31 1.1 Methanotrophic Communities in Surface Sediments .................................. 31 1.2 Microbial Communities in Subsurface Sediments....................................... 35 1.3 Microbial Communities in Mats of Sulfur-Oxidizing Bacteria ................... 36 1.4 Symbioses between Bacteria and Siboglinid Tubeworms ........................... 38 1.5 Diversity of mcrA Genes.............................................................................. 39 2 Cascadia Margin (Hydrate Ridge, coast off Oregon) ............................................ 41 2.1 Detection and Quantification of ANME-2 Subgroups in Surface Sediments........................................................................................ 42 2.2 Detection of ANME-3 in Surface Sediments............................................... 43 2.3 Methanotrophic Communities in Shallow Subsurface Sediments and Gas Hydrates................................................................................................ 43 3 Final Discussion..................................................................................................... 44 3.1 Key Microbial Players and Their Distribution............................................. 44 3.2 Difference between Surface and Subsurface Communities......................... 47 3.3 Interspecies Associations............................................................................. 48 3.4 Environmental Selection of ANME Groups................................................ 49 3.5 Outlook ........................................................................................................ 53 C References ................................................................................................................. 55 Part II: Publications A List of Publications................................................................................................... 65 B Publications............................................................................................................... 69 1 Fluid Flow Controls Distribution of Methanotrophic Microorganisms at Submarine Cold Seeps....................................................................................... 69 2 Novel Clusters of Aerobic and Anaerobic Methane Oxidizers at an Arctic Cold Seep (Haakon Mosby Mud Volcano, Barents Sea)....................... 87 3 Endosymbioses between Bacteria and Deep-Sea Siboglinid Tubeworms from an Arctic Cold Seep (Haakon Mosby Mud Volcano, Barents Sea).............. 117 4 Microbial Diversity and Community Composition in Gas Hydrates and Hydrate-Bearing Sediments of the Cascadia Margin (Hydrate Ridge) ................. 145 5 Diversity and Distribution of Methanotrophic Archaea at Cold Seeps............................................................................................................. 177 Part III: Appendix A List of Clones ............................................................................................................ 191 Acknowledgement..................................................................................................................... 197 Summary Summary Cold seeps are complex ecosystems based on chemosynthesis. Sulfide and methane are available in high concentrations and support a variety of highly adapted microorganisms and symbiont-bearing invertebrates. The anaerobic oxidation of methane (AOM) is a key biogeochemical process at cold seeps and is assumed to be mediated by a consortium of anaerobic methanotrophic archaea (ANME) and sulfate-reducing bacteria. In this thesis I used 16S rRNA-based molecular methods to identify and quantify methanotrophic and chemoautotrophic, sulfur-oxidizing communities at two cold seeps and collaborated with scientists from other disciplines to correlate the molecular results with biogeochemical, geological, and physical data sets. Two types of cold seeps were studied, the Arctic Haakon Mosby Mud Volcano (HMMV; 1250 m water depth) and the Hydrate Ridge at the Cascadia Margin (700 m water depth) off the coast of Oregon. The actively methane-seeping HMMV hosts novel clades of aerobic and anaerobic methanotrophs. The distribution of the methanotrophic guilds is controlled by fluid flow and bioirrigation activities of marine invertebrates. The center of the volcano is characterized by high upward fluid flow. High numbers of novel aerobic methanotrophs were detected in the upper millimeters of the sediment. These dominated the microbial community in surface sediments of HMMV. At sites with decreased upward fluid flow, a new group of ANME archaea (ANME-3) was identified, dominating the zone of AOM in 1-4 cm sediment depth. In this zone, the microbial biomass was almost entirely comprised by ANME-3 archaea which form consortia with sulfate-reducing bacteria of the Desulfobulbus branch. In bioirrigated sediments populated by siboglinid tubeworms, sulfate is transported deeper into the sediment and here the AOM consortia were found at the base of the tubeworm roots. The symbioses between bacteria and the tubeworms at HMMV were characterized. Two species of tubeworms coexist at the same site and represent the dominant megafauna at HMMV. The symbionts of Sclerolinum contortum were identified as chemoautotrophic sulfur oxidizers and are closely related to symbionts of vestimentiferan tubeworms. The symbionts of Oligobrachia haakonmosbiensis represent a novel symbiont lineage. The molecular results in combination with stable carbon isotope analysis suggest that this species may harbor both chemoautotrophic sulfur-oxidizing and methane-oxidizing symbionts. Another focus of the thesis was to compare microbial communities in gas hydrate bearing shallow subsurface sediments with surface communities at Hydrate Ridge. The microbial diversity in these
Load more

Recommended publications
  • Chemotaxonomic Characterization of the Thaumarchaeal Lipidome
    View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Aberdeen University Research Archive Chemotaxonomic characterization of the thaumarchaeal lipidome Running title: Comparative analysis of the thaumarchaeal lipidome Felix J. Elling1+, Martin Könneke1,2#, Graeme W. Nicol3, Michaela Stieglmeier4, Barbara Bayer5, Eva Spieck6, José R. de la Torre7, Kevin W. Becker1†, Michael Thomm8, James I. Prosser9, Gerhard J. Herndl5,10, Christa Schleper4, Kai-Uwe Hinrichs1 1 Organic Geochemistry Group, MARUM - Center for Marine Environmental Sciences & Department of Geosciences, University of Bremen, 28359 Bremen, Germany. 2 Marine Archaea Group, MARUM Center for Marine Environmental Sciences & Department of Geosciences, University of Bremen, 28359 Bremen, Germany. 3 Environmental Microbial Genomics, Laboratoire Ampère, École Centrale de Lyon, Université de Lyon, 69134 Ecully, France 4 Department of Ecogenomics and Systems Biology, Center of Ecology, University of Vienna, 1090 Vienna, Austria. 5 Department of Limnology and BioOceanography, Center of Ecology, University of Vienna, 1090 Vienna, Austria. 6 Biocenter Klein Flottbek, Department of Microbiology and Biotechnology, University of Hamburg, 22609 Hamburg, Germany. 7 Department of Biology, San Francisco State University, San Francisco, CA, USA. 8 Lehrstuhl für Mikrobiologie und Archaeenzentrum, Universität Regensburg, 93053 Regensburg, Germany. 9 Institute of Biological and Environmental Sciences, University of Aberdeen, Cruickshank Building, Aberdeen, AB24 3UU, United Kingdom. 10 Department of Marine Microbiology and Biogeochemistry, Royal Netherlands Institute for Sea Research, Utrecht University, 1790 AB Den Burg, Texel, The Netherlands #Corresponding author. Tel.: + 49 421 218 65747. Fax: +49 421 218 65715. E-mail: [email protected] +present address: Department of Earth and Planetary Sciences, Harvard University, Cambridge, MA 02138, USA.
    [Show full text]
  • Phylogenetics of Archaeal Lipids Amy Kelly 9/27/2006 Outline
    Phylogenetics of Archaeal Lipids Amy Kelly 9/27/2006 Outline • Phlogenetics of Archaea • Phlogenetics of archaeal lipids • Papers Phyla • Two? main phyla – Euryarchaeota • Methanogens • Extreme halophiles • Extreme thermophiles • Sulfate-reducing – Crenarchaeota • Extreme thermophiles – Korarchaeota? • Hyperthermophiles • indicated only by environmental DNA sequences – Nanoarchaeum? • N. equitans a fast evolving euryarchaeal lineage, not novel, early diverging archaeal phylum – Ancient archael group? • In deepest brances of Crenarchaea? Euryarchaea? Archaeal Lipids • Methanogens – Di- and tetra-ethers of glycerol and isoprenoid alcohols – Core mostly archaeol or caldarchaeol – Core sometimes sn-2- or Images removed due to sn-3-hydroxyarchaeol or copyright considerations. macrocyclic archaeol –PMI • Halophiles – Similar to methanogens – Exclusively synthesize bacterioruberin • Marine Crenarchaea Depositional Archaeal Lipids Biological Origin Environment Crocetane methanotrophs? methane seeps? methanogens, PMI (2,6,10,15,19-pentamethylicosane) methanotrophs hypersaline, anoxic Squalane hypersaline? C31-C40 head-to-head isoprenoids Smit & Mushegian • “Lost” enzymes of MVA pathway must exist – Phosphomevalonate kinase (PMK) – Diphosphomevalonate decarboxylase – Isopentenyl diphosphate isomerase (IPPI) Kaneda et al. 2001 Rohdich et al. 2001 Boucher et al. • Isoprenoid biosynthesis of archaea evolved through a combination of processes – Co-option of ancestral enzymes – Modification of enzymatic specificity – Orthologous and non-orthologous gene
    [Show full text]
  • Doctoral Dissertation Template
    UNIVERSITY OF OKLAHOMA GRADUATE COLLEGE METAGENOMIC INSIGHTS INTO MICROBIAL COMMUNITY RESPONSES TO LONG-TERM ELEVATED CO2 A DISSERTATION SUBMITTED TO THE GRADUATE FACULTY in partial fulfillment of the requirements for the Degree of DOCTOR OF PHILOSOPHY By QICHAO TU Norman, Oklahoma 2014 METAGENOMIC INSIGHTS INTO MICROBIAL COMMUNITY RESPONSES TO LONG-TERM ELEVATED CO2 A DISSERTATION APPROVED FOR THE DEPARTMENT OF MICROBIOLOGY AND PLANT BIOLOGY BY ______________________________ Dr. Jizhong Zhou, Chair ______________________________ Dr. Meijun Zhu ______________________________ Dr. Fengxia (Felicia) Qi ______________________________ Dr. Michael McInerney ______________________________ Dr. Bradley Stevenson © Copyright by QICHAO TU 2014 All Rights Reserved. Acknowledgements At this special moment approaching the last stage for this degree, I would like to express my gratitude to all the people who encouraged me and helped me out through the past years. Dr. Jizhong Zhou, my advisor, is no doubt the most influential and helpful person in pursuing my academic goals. In addition to continuous financial support for the past six years, he is the person who led me into the field of environmental microbiology, from a background of bioinformatics and plant molecular biology. I really appreciated the vast training I received from the many interesting projects I got involved in, without which I would hardly develop my broad experienced background from pure culture microbial genomics to complex metagenomics. Dr. Zhili He, who played a role as my second advisor, is also the person I would like to thank most. Without his help, I could be still struggling working on those manuscripts lying in my hard drive. I definitely learned a lot from him in organizing massed results into logical scientific work—skills that will benefit me for life.
    [Show full text]
  • Methylamine As a Nitrogen Source for Microorganisms from a Coastal Marine
    Methylamine as a Nitrogen Source for Microorganisms from a Coastal Marine Environment Martin Tauberta,b, Carolina Grobb, Alexandra M. Howatb, Oliver J. Burnsc, Jennifer Pratscherb, Nico Jehmlichd, Martin von Bergend,e,f, Hans H. Richnowg, Yin Chenh,1, J. Colin Murrellb,1 aAquatic Geomicrobiology, Institute of Ecology, Friedrich Schiller University Jena, Dornburger Str. 159, 07743 Jena, Germany bSchool of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK cSchool of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK dDepartment of Molecular Systems Biology, Helmholtz Centre for Environmental Research – UFZ, Leipzig, Germany eInstitute of Biochemistry, Faculty of Biosciences, Pharmacy and Psychology, University of Leipzig, Brüderstraße 32, 04103 Leipzig, Germany fDepartment of Chemistry and Bioscience, University of Aalborg, Fredrik Bajers Vej 7H, 9220 Aalborg East, Denmark. gDepartment of Isotope Biogeochemistry, Helmholtz-Centre for Environmental Research – UFZ, Permoserstrasse 15, 04318 Leipzig, Germany hSchool of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK 1To whom correspondence should be addressed. J. Colin Murrell, Phone: +44 (0)1603 59 2959, Email: [email protected], and Yin Chen, Phone: +44 (0)24 76528976, Email: [email protected] Keywords: marine methylotrophs, 15N stable isotope probing, methylamine, metagenomics, metaproteomics Classification: BIOLOGICAL SCIENCES/Microbiology Short title: Methylamine as a Nitrogen Source for Marine Microbes This article has been accepted for publication and undergone full peer review but has not been through the copyediting, typesetting, pagination and proofreading process which may lead to differences between this version and the Version of Record. Please cite this article as an ‘Accepted Article’, doi: 10.1111/1462-2920.13709 This article is protected by copyright.
    [Show full text]
  • Diversity and Activity of Sulfate-Reducing Bacteria In
    Diversity and Activity of Sulfate- reducing bacteria in Sulfidogenic Wastewater Treatment Reactors If we knew what we are doing, it would not be called research would it? Albert Einstien ii Diversity and Activity of Sulfate- reducing bacteria in Sulfidogenic Wastewater Treatment Reactors Proefschrift ter verkrijging van de graad van doctor aan de Technische Universiteit Delft, op gezag van de Rector Magnificus Prof. dr. ir. J. T. Fokkema, voorzitter van het College voor Promoties, in het openbaar te verdedigen op vrijdag 19 oktober 2007 om 10.00 uur door Shabir Ahmad DAR Master in Science of Bioprocess Technology, Asian Institute of Technology (AIT), Thailand geboren te Srinagar, J&K, India iii Dit proefschrift is goedgekeurd door de promotor: Prof. dr. J. G. Kuenen Toegevoegd promotor Dr. G. Muyzer Samenstelling promotie commissie: Rector Magnificus Voorzitter Prof. dr. J.G. Kuenen Delft University of Technology, Promotor Dr. G. Muyzer Delft University of Technology, Toegevoegd promotor Prof. dr. F. Widdel Max-Planck-Institute for Marine Microbiology, Bremen, Germany Prof. dr. ir. M.C.M. van Loosdrecht Delft University of Technology Prof. dr. H.J. Laanbroek Utrecht University Prof. dr. ir.A.J.M. Stams Wageningen University Prof. dr. ir. P.N.L. Lens Wageningen University This study was carried out in the Environmental Biotechnology group of the Department of Biotechnology at Delft University of Technology, Delft, the Netherlands. This research was financially supported by The Netherlands Organization for Scientific Research – (NWO Earth
    [Show full text]
  • High Density of Diploria Strigosa Increases
    HIGH DENSITY OF DIPLORIA STRIGOSA INCREASES PREVALENCE OF BLACK BAND DISEASE IN CORAL REEFS OF NORTHERN BERMUDA Sarah Carpenter Department of Biology, Clark University, Worcester, MA 01610 ([email protected]) Abstract Black Band Disease (BBD) is one of the most widespread and destructive coral infectious diseases. The disease moves down the infected coral leaving complete coral tissue degradation in its wake. This coral disease is caused by a group of coexisting bacteria; however, the main causative agent is Phormidium corallyticum. The objective of this study was to determine how BBD prominence is affected by the density of D. strigosa, a common reef building coral found along Bermuda coasts. Quadrats were randomly placed on the reefs at Whalebone Bay and Tobacco Bay and then density and percent infection were recorded and calculated. The results from the observations showed a significant, positive correlation between coral density and percent infection by BBD. This provides evidence that BBD is a water borne infection and that transmission can occur at distances up to 1m. Information about BBD is still scant, but in order to prevent future damage, details pertaining to transmission methods and patterns will be necessary. Key Words: Black Band Disease, Diploria strigosa, density Introduction Coral pathogens are a relatively new area of study, with the first reports and descriptions made in the 1970’s. Today, more than thirty coral diseases have been reported, each threatening the resilience of coral communities (Green and Bruckner 2000). The earliest identified infection was characterized by a dark band, which separated the healthy coral from the dead coral.
    [Show full text]
  • Miniaturized Biosignature Analysis Reveals Implications for the Formation of Cold Seep Carbonates at Hydrate Ridge (Off Oregon, USA) T
    Miniaturized biosignature analysis reveals implications for the formation of cold seep carbonates at Hydrate Ridge (off Oregon, USA) T. Leefmann, J. Bauermeister, A. Kronz, V. Liebetrau, J. Reitner, V. Thiel To cite this version: T. Leefmann, J. Bauermeister, A. Kronz, V. Liebetrau, J. Reitner, et al.. Miniaturized biosignature analysis reveals implications for the formation of cold seep carbonates at Hydrate Ridge (off Oregon, USA). Biogeosciences Discussions, European Geosciences Union, 2007, 4 (6), pp.4443-4458. hal- 00297947 HAL Id: hal-00297947 https://hal.archives-ouvertes.fr/hal-00297947 Submitted on 28 Nov 2007 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. Biogeosciences Discuss., 4, 4443–4458, 2007 Biogeosciences www.biogeosciences-discuss.net/4/4443/2007/ Discussions BGD © Author(s) 2007. This work is licensed 4, 4443–4458, 2007 under a Creative Commons License. Biogeosciences Discussions is the access reviewed discussion forum of Biogeosciences Biosignature analysis of cold seep carbonates T. Leefmann et al. Miniaturized biosignature analysis reveals Title Page implications for the formation of cold Abstract Introduction seep carbonates at Hydrate Ridge Conclusions References (off Oregon, USA) Tables Figures T. Leefmann1, J. Bauermeister1, A. Kronz1, V.
    [Show full text]
  • Cas Du Modèle Symbiotique Rimicaris Exoculata
    THÈSE / UNIVERSITÉ DE BRETAGNE OCCIDENTALE présentée par sous le sceau de l’Université Bretagne Loire pour obtenir le titre de Simon Le Bloa DOCTEUR DE L’UNIVERSITÉ DE BRETAGNE OCCIDENTALE Préparée à l'UMR 6197, Ifremer-CNRS-UBO Mention : Ecologie Microbienne Etablissement de rattachement : Ifremer, Centre de Brest École Doctorale des Sciences de la Mer Laboratoire de Microbiologie des Environnements Extrêmes Thèse soutenue le 15 décembre 2016 devant le jury composé de : Sébastien Duperron (Rapporteur) Maître de Conférences, Université Pierre et Marie Curie (Paris VI) Mode de reconnaissance Abdelazis Heddi (Rapporteur) Professeur, Directeur du Laboratoire Biologie Fonctionnelle Insectes et Intéractions - INSA lyon hôte -symbionte en milieux Christine Paillard (Examinatrice) Directeur de Recherche, Laboratoire des Sciences de extrêmes: cas du modèle l'Environnement Marin symbiotique, la crevette Mohamed Jebbar (Examinateur) Directeur du Laboratoire de Microbiologie des Environnements Extrêmes, Professeur Université de Bretagne Occidentale Rimicaris exoculata Aurélie Tasiemski (Examinatrice) Maitre de Conférences, Université de Lille I Alexis Bazire (Co-Directeur de thèse) Maitre de Conférences, Université de Bretagne Sud Marie-Anne Cambon-Bonavita (Directrice de thèse) Chercheur, Laboratoire de Microbiologie des Environnements Extrêmes Remerciements Après 3 ans à voguer sur les flots de la thèse, parfois mouvementés, parfois placides, me voilà arrivé à bon port. Je n’ai vraiment pas vu le temps passer. Ma première navigation dans la recherche ne s’est évidemment pas faite toute seule. Il est temps de remercier les membres d’équipages, les personnes et les organismes qui ont contribué à mener à bien ce projet. Ce travail de thèse a été réalisé au sein du Laboratoire de Microbiologie des Environnements Extrêmes (LM2E), UMR6197 (Ifremer/UBO/CNRS), à l’Ifremer de Brest ; au Laboratoire de Biotechnologie et Chimie Marine (LBCM), EA3884 (UBS) à Lorient et au Laboratoire de Génétique et Evolution des Végétaux (GEPV), UMR 8198, (CNRS/Université de Lille1).
    [Show full text]
  • Which Organisms Are Used for Anti-Biofouling Studies
    Table S1. Semi-systematic review raw data answering: Which organisms are used for anti-biofouling studies? Antifoulant Method Organism(s) Model Bacteria Type of Biofilm Source (Y if mentioned) Detection Method composite membranes E. coli ATCC25922 Y LIVE/DEAD baclight [1] stain S. aureus ATCC255923 composite membranes E. coli ATCC25922 Y colony counting [2] S. aureus RSKK 1009 graphene oxide Saccharomycetes colony counting [3] methyl p-hydroxybenzoate L. monocytogenes [4] potassium sorbate P. putida Y. enterocolitica A. hydrophila composite membranes E. coli Y FESEM [5] (unspecified/unique sample type) S. aureus (unspecified/unique sample type) K. pneumonia ATCC13883 P. aeruginosa BAA-1744 composite membranes E. coli Y SEM [6] (unspecified/unique sample type) S. aureus (unspecified/unique sample type) graphene oxide E. coli ATCC25922 Y colony counting [7] S. aureus ATCC9144 P. aeruginosa ATCCPAO1 composite membranes E. coli Y measuring flux [8] (unspecified/unique sample type) graphene oxide E. coli Y colony counting [9] (unspecified/unique SEM sample type) LIVE/DEAD baclight S. aureus stain (unspecified/unique sample type) modified membrane P. aeruginosa P60 Y DAPI [10] Bacillus sp. G-84 LIVE/DEAD baclight stain bacteriophages E. coli (K12) Y measuring flux [11] ATCC11303-B4 quorum quenching P. aeruginosa KCTC LIVE/DEAD baclight [12] 2513 stain modified membrane E. coli colony counting [13] (unspecified/unique colony counting sample type) measuring flux S. aureus (unspecified/unique sample type) modified membrane E. coli BW26437 Y measuring flux [14] graphene oxide Klebsiella colony counting [15] (unspecified/unique sample type) P. aeruginosa (unspecified/unique sample type) graphene oxide P. aeruginosa measuring flux [16] (unspecified/unique sample type) composite membranes E.
    [Show full text]
  • Hmelo Thesis.Pdf (3.770Mb)
    MICROBIAL INTERACTIONS ASSOCIATED WITH BIOFILMS ATTACHED TO TRICHODESMIUM SPP. AND DETRITAL PARTICLES IN THE OCEAN By Laura Robin Hmelo B.A., Carleton College, 2002 Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy at the MASSACHUSETTS INSTITUTE OF TECHNOLOGY and the WOODS HOLE OCEANOGRAPHIC INSTITUTION June 2010 © 2010 Laura R. Hmelo. All rights reserved. The author hereby grants to MIT and WHOI permission to reproduce and distribute publicly paper and electronic copies of this thesis document in whole or in part in any medium now known or hereafter created. Author ________________________________________________________________________ Joint Program in Oceanography/Applied Ocean Science and Engineering Massachusetts Institute of Technology And Woods Hole Oceanographic Institution May 11, 2010 Certified by ________________________________________________________________________ Dr. Benjamin A.S. Van Mooy Associate Scientist of Marine Chemistry and Geochemistry, WHOI Thesis Supervisor Accepted by ________________________________________________________________________ Prof. Roger E. Summons Professor of Earth, Atmospheric, and Planetary Sciences, MIT Chair, Joint Committee for Chemical Oceanography Woods Hole Oceanographic Institution 2 MICROBIAL INTERACTIONS ASSOCIATED WITH BIOFILMS ATTACHED TO TRICHODESMIUM SPP. AND DETRITAL PARTICLES IN THE OCEAN By Laura R. Hmelo Submitted to the MIT/WHOI Joint Program in Oceanography in partial fulfillment of the requirements for the degree of Doctor of Philosophy in the field of Chemical Oceanography THESIS ABSTRACT Quorum sensing (QS) via acylated homoserine lactones (AHLs) was discovered in the ocean, yet little is known about its role in the ocean beyond its involvement in certain symbiotic interactions. The objectives of this thesis were to constrain the chemical stability of AHLs in seawater, explore the production of AHLs in marine particulate environments, and probe selected behaviors which might be controlled by AHL-QS.
    [Show full text]
  • Versatile Cyanobacteria Control the Timing and Extent of Sulfide
    The ISME Journal (2020) 14:3024–3037 https://doi.org/10.1038/s41396-020-0734-z ARTICLE Versatile cyanobacteria control the timing and extent of sulfide production in a Proterozoic analog microbial mat 1 2,9 1,10 2 3 Judith M. Klatt ● Gonzalo V. Gomez-Saez ● Steffi Meyer ● Petra Pop Ristova ● Pelin Yilmaz ● 4,5,11 6 7 1,8 2 Michael S. Granitsiotis ● Jennifer L. Macalady ● Gaute Lavik ● Lubos Polerecky ● Solveig I. Bühring Received: 28 February 2020 / Revised: 16 July 2020 / Accepted: 28 July 2020 / Published online: 7 August 2020 © The Author(s) 2020. This article is published with open access Abstract Cyanobacterial mats were hotspots of biogeochemical cycling during the Precambrian. However, mechanisms that controlled O2 release by these ecosystems are poorly understood. In an analog to Proterozoic coastal ecosystems, the Frasassi sulfidic springs mats, we studied the regulation of oxygenic and sulfide-driven anoxygenic photosynthesis (OP and AP) in versatile cyanobacteria, and interactions with sulfur reducing bacteria (SRB). Using microsensors and stable isotope probing we found that dissolved organic carbon (DOC) released by OP fuels sulfide production, likely by a specialized SRB population. Increased sulfide fluxes were only stimulated after the cyanobacteria switched from AP to OP. O2 production 1234567890();,: 1234567890();,: triggered migration of large sulfur-oxidizing bacteria from the surface to underneath the cyanobacterial layer. The resultant sulfide shield tempered AP and allowed OP to occur for a longer duration over a diel cycle. The lack of cyanobacterial DOC supply to SRB during AP therefore maximized O2 export. This mechanism is unique to benthic ecosystems because transitions between metabolisms occur on the same time scale as solute transport to functionally distinct layers, with the rearrangement of the system by migration of microorganisms exaggerating the effect.
    [Show full text]
  • Biogeochemical and Microbiological Evidence for Methane-Related
    Biogeosciences Discuss., https://doi.org/10.5194/bg-2018-91-SC5, 2018 © Author(s) 2018. This work is distributed under the Creative Commons Attribution 4.0 License. Interactive comment on “Biogeochemical and microbiological evidence for methane-related archaeal communities at active submarine mud volcanoes on the Canadian Beaufort Sea slope” by Dong-Hun Lee et al. J.-H. Kim [email protected] Received and published: 7 June 2018 Short comment #1: Manuscript ID: bg-2018-91 Biogeochemical and microbiological evidence for methane-related archaeal communities at active submarine mud volca- noes on the Canadian Beaufort Sea slope This paper reports the occurrence of AOM in the active mud volcanos on the continental slope of the Canadian Beaufort Sea, based on the analysis of lipid biomarker and 16S rRNA gene in three sediment cores. The authors state that archaea of the ANME- C1 2c and ANME-3 clades participated in the process of methane consumption, by the relative high ratio of sn-2-hydroxyarchaeol to archaeol and the phylogenetic identities. They then speculate that the difference in distribution of ANME-2c and ANME-3 in these mud volcanos is under the control of methane flux changes. The results of this study can further help us to understand the biogeochemical cycling of methane in the seafloor mud volcano environments. Generally, it is a very interesting study, especially the detection of extreme depleted δ13C value of sn-2- and sn-3-hydroxyarchaeol. The approach is scientifically valid and the conclusions are reasonably sound. Reply: We are thankfull for the positive assessment about our manuscript.
    [Show full text]