Methylamine As a Nitrogen Source for Microorganisms from a Coastal Marine
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Metagenomics and Metatranscriptomics of the Leaf-And Root-Associated Microbiomes of Zostera Marina and Zostera Japonica
1 Metagenomics and metatranscriptomics of the leaf- and root-associated microbiomes of Zostera marina and Zostera japonica by John Michael Adrian Wojahn A THESIS submitted to Oregon State University Honors College in partial fulfillment of the requirements for the degree of Honors Baccalaureate of Science in Microbiology and Biology (Honors BS) Presented May 10, 2016 Commencement June 2016 2 3 AN ABSTRACT OF THE THESIS OF John M. A. Wojahn for the degree of Honors Baccalaureate of Science in Microbiology and Biology presented on May 10, 2016. Title: Metagenomics and Metatranscriptomics of the leaf- and root-associated microbiomes of Zostera marina and Zostera japonica . Abstract approved: _____________________________________________ Byron C. Crump A great deal of research has been focused on the microbiomes of terrestrial angiosperms (flowering plants), but much less research has been performed on the microbiomes of aquatic angiosperms (Turner et al. 2013). Eelgrass beds are extremely productive ecosystems that provide habitat for many marine organisms, such as fish, shelfish, crabs, and algae (Smith et al. 1988). Eelgrass beds contribute to storm surge damping (Spalding et al. 2009), nutrient cycling (Smith et al. 1988), and water clarification (Orth et al. 2006). We examined the metagenomics and metatranscriptomics of the leaf- and root- associated microbiomes of Zostera marina and Zostera japonica. In our study, the phylogenetic composition of plant-associated bacterial communities was not significantly different between plant species for leaf communities (ANOSIM P<0.199) and for root communities (ANOSIM P<0.091). However, leaf-, root-, and water column associated bacterial communities were significantly different from one another (ANOSIM, P<0.001). -
Alpine Soil Bacterial Community and Environmental Filters Bahar Shahnavaz
Alpine soil bacterial community and environmental filters Bahar Shahnavaz To cite this version: Bahar Shahnavaz. Alpine soil bacterial community and environmental filters. Other [q-bio.OT]. Université Joseph-Fourier - Grenoble I, 2009. English. tel-00515414 HAL Id: tel-00515414 https://tel.archives-ouvertes.fr/tel-00515414 Submitted on 6 Sep 2010 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. THÈSE Pour l’obtention du titre de l'Université Joseph-Fourier - Grenoble 1 École Doctorale : Chimie et Sciences du Vivant Spécialité : Biodiversité, Écologie, Environnement Communautés bactériennes de sols alpins et filtres environnementaux Par Bahar SHAHNAVAZ Soutenue devant jury le 25 Septembre 2009 Composition du jury Dr. Thierry HEULIN Rapporteur Dr. Christian JEANTHON Rapporteur Dr. Sylvie NAZARET Examinateur Dr. Jean MARTIN Examinateur Dr. Yves JOUANNEAU Président du jury Dr. Roberto GEREMIA Directeur de thèse Thèse préparée au sien du Laboratoire d’Ecologie Alpine (LECA, UMR UJF- CNRS 5553) THÈSE Pour l’obtention du titre de Docteur de l’Université de Grenoble École Doctorale : Chimie et Sciences du Vivant Spécialité : Biodiversité, Écologie, Environnement Communautés bactériennes de sols alpins et filtres environnementaux Bahar SHAHNAVAZ Directeur : Roberto GEREMIA Soutenue devant jury le 25 Septembre 2009 Composition du jury Dr. -
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). -
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. -
The Gut Microbiome of the Sea Urchin, Lytechinus Variegatus, from Its Natural Habitat Demonstrates Selective Attributes of Micro
FEMS Microbiology Ecology, 92, 2016, fiw146 doi: 10.1093/femsec/fiw146 Advance Access Publication Date: 1 July 2016 Research Article RESEARCH ARTICLE The gut microbiome of the sea urchin, Lytechinus variegatus, from its natural habitat demonstrates selective attributes of microbial taxa and predictive metabolic profiles Joseph A. Hakim1,†, Hyunmin Koo1,†, Ranjit Kumar2, Elliot J. Lefkowitz2,3, Casey D. Morrow4, Mickie L. Powell1, Stephen A. Watts1,∗ and Asim K. Bej1,∗ 1Department of Biology, University of Alabama at Birmingham, 1300 University Blvd, Birmingham, AL 35294, USA, 2Center for Clinical and Translational Sciences, University of Alabama at Birmingham, Birmingham, AL 35294, USA, 3Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL 35294, USA and 4Department of Cell, Developmental and Integrative Biology, University of Alabama at Birmingham, 1918 University Blvd., Birmingham, AL 35294, USA ∗Corresponding authors: Department of Biology, University of Alabama at Birmingham, 1300 University Blvd, CH464, Birmingham, AL 35294-1170, USA. Tel: +1-(205)-934-8308; Fax: +1-(205)-975-6097; E-mail: [email protected]; [email protected] †These authors contributed equally to this work. One sentence summary: This study describes the distribution of microbiota, and their predicted functional attributes, in the gut ecosystem of sea urchin, Lytechinus variegatus, from its natural habitat of Gulf of Mexico. Editor: Julian Marchesi ABSTRACT In this paper, we describe the microbial composition and their predictive metabolic profile in the sea urchin Lytechinus variegatus gut ecosystem along with samples from its habitat by using NextGen amplicon sequencing and downstream bioinformatics analyses. The microbial communities of the gut tissue revealed a near-exclusive abundance of Campylobacteraceae, whereas the pharynx tissue consisted of Tenericutes, followed by Gamma-, Alpha- and Epsilonproteobacteria at approximately equal capacities. -
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. -
Stable-Isotope Probing Implicates Methylophaga Spp and Novel Gammaproteobacteria in Marine Methanol and Methylamine Metabolism
The ISME Journal (2007) 1, 480–491 & 2007 International Society for Microbial Ecology All rights reserved 1751-7362/07 $30.00 www.nature.com/ismej ORIGINAL ARTICLE Stable-isotope probing implicates Methylophaga spp and novel Gammaproteobacteria in marine methanol and methylamine metabolism Josh D Neufeld1, Hendrik Scha¨fer, Michael J Cox2, Rich Boden, Ian R McDonald3 and J Colin Murrell Department of Biological Sciences, University of Warwick, Coventry, UK The metabolism of one-carbon (C1) compounds in the marine environment affects global warming, seawater ecology and atmospheric chemistry. Despite their global significance, marine micro- organisms that consume C1 compounds in situ remain poorly characterized. Stable-isotope probing (SIP) is an ideal tool for linking the function and phylogeny of methylotrophic organisms by the metabolism and incorporation of stable-isotope-labelled substrates into nucleic acids. By combining DNA-SIP and time-series sampling, we characterized the organisms involved in the assimilation of methanol and methylamine in coastal sea water (Plymouth, UK). Labelled nucleic acids were analysed by denaturing gradient gel electrophoresis (DGGE) and clone libraries of 16S rRNA genes. In addition, we characterized the functional gene complement of labelled nucleic acids with an improved primer set targeting methanol dehydrogenase (mxaF) and newly designed primers for methylamine dehydrogenase (mauA). Predominant DGGE phylotypes, 16S rRNA, methanol and methylamine dehydrogenase gene sequences, and cultured isolates all implicated Methylophaga spp, moderately halophilic marine methylotrophs, in the consumption of both methanol and methylamine. Additionally, an mxaF sequence obtained from DNA extracted from sea water clustered with those detected in 13C-DNA, suggesting a predominance of Methylophaga spp among marine methylotrophs. -
SIP Metagenomics Identifies Uncultivated Methylophilaceae As Dimethylsulphide Degrading Bacteria in Soil and Lake Sediment
The ISME Journal (2015) 9, 2336–2348 © 2015 International Society for Microbial Ecology All rights reserved 1751-7362/15 OPEN www.nature.com/ismej ORIGINAL ARTICLE SIP metagenomics identifies uncultivated Methylophilaceae as dimethylsulphide degrading bacteria in soil and lake sediment Özge Eyice1, Motonobu Namura2, Yin Chen1, Andrew Mead1,3, Siva Samavedam1 and Hendrik Schäfer1 1School of Life Sciences, University of Warwick, Coventry, UK and 2MOAC Doctoral Training Centre, University of Warwick, Coventry, UK Dimethylsulphide (DMS) has an important role in the global sulphur cycle and atmospheric chemistry. Microorganisms using DMS as sole carbon, sulphur or energy source, contribute to the cycling of DMS in a wide variety of ecosystems. The diversity of microbial populations degrading DMS in terrestrial environments is poorly understood. Based on cultivation studies, a wide range of bacteria isolated from terrestrial ecosystems were shown to be able to degrade DMS, yet it remains unknown whether any of these have important roles in situ. In this study, we identified bacteria using DMS as a carbon and energy source in terrestrial environments, an agricultural soil and a lake sediment, by DNA stable isotope probing (SIP). Microbial communities involved in DMS degradation were analysed by denaturing gradient gel electrophoresis, high-throughput sequencing of SIP gradient fractions and metagenomic sequencing of phi29-amplified community DNA. Labelling patterns of time course SIP experiments identified members of the Methylophilaceae family, not previously implicated in DMS degradation, as dominant DMS-degrading populations in soil and lake sediment. Thiobacillus spp. were also detected in 13C-DNA from SIP incubations. Metagenomic sequencing also suggested involvement of Methylophilaceae in DMS degradation and further indicated shifts in the functional profile of the DMS-assimilating communities in line with methylotrophy and oxidation of inorganic sulphur compounds. -
Experimental Horizontal Gene Transfer of Methylamine
Experimental Horizontal Gene Transfer of Methylamine Dehydrogenase Mimics Prevalent Exchange in Nature and Overcomes the Methylamine Growth Constraints Posed by the Sub- Optimal N-Methylglutamate Pathway The Harvard community has made this article openly available. Please share how this access benefits you. Your story matters Citation Nayak, Dipti D., and Christopher J. Marx. 2015. “Experimental Horizontal Gene Transfer of Methylamine Dehydrogenase Mimics Prevalent Exchange in Nature and Overcomes the Methylamine Growth Constraints Posed by the Sub-Optimal N-Methylglutamate Pathway.” Microorganisms 3 (1): 60-79. doi:10.3390/microorganisms3010060. http://dx.doi.org/10.3390/ microorganisms3010060. Published Version doi:10.3390/microorganisms3010060 Citable link http://nrs.harvard.edu/urn-3:HUL.InstRepos:29407840 Terms of Use This article was downloaded from Harvard University’s DASH repository, and is made available under the terms and conditions applicable to Other Posted Material, as set forth at http:// nrs.harvard.edu/urn-3:HUL.InstRepos:dash.current.terms-of- use#LAA Microorganisms 2015, 3, 60-79; doi:10.3390/microorganisms3010060 OPEN ACCESS microorganisms ISSN 2076-2607 www.mdpi.com/journal/microorganisms Article Experimental Horizontal Gene Transfer of Methylamine Dehydrogenase Mimics Prevalent Exchange in Nature and Overcomes the Methylamine Growth Constraints Posed by the Sub-Optimal N-Methylglutamate Pathway Dipti D. Nayak 1,2,† and Christopher J. Marx 1,2,3,4,* 1 Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA; E-Mail: [email protected] 2 Biological Sciences, University of Idaho, Moscow, ID 83844, USA 3 Faculty of Arts and Sciences Center for Systems Biology, Harvard University, Cambridge, MA 02138, USA 4 Institute for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, ID 83844, USA † Present Address: Institute for Genomic Biology, University of Illinois, Urbana, IL 61801, USA. -
Linking Activity and Function to Ecosystem Dynamics in a Coastal Bacterioplankton Community
Linking activity and function to ecosystem dynamics in a coastal bacterioplankton community The MIT Faculty has made this article openly available. Please share how this access benefits you. Your story matters. Citation Gifford, Scott M., Shalabh Sharma, and Mary Ann Moran. “Linking Activity and Function to Ecosystem Dynamics in a Coastal Bacterioplankton Community.” Frontiers in Microbiology 5 (April 24, 2014). As Published http://dx.doi.org/10.3389/fmicb.2014.00185 Publisher Frontiers Research Foundation Version Final published version Citable link http://hdl.handle.net/1721.1/88031 Terms of Use Article is made available in accordance with the publisher's policy and may be subject to US copyright law. Please refer to the publisher's site for terms of use. ORIGINAL RESEARCH ARTICLE published: 24 April 2014 doi: 10.3389/fmicb.2014.00185 Linking activity and function to ecosystem dynamics in a coastal bacterioplankton community Scott M. Gifford †, Shalabh Sharma and Mary Ann Moran* Department of Marine Sciences, University of Georgia, Athens, GA, USA Edited by: For bacterial communities containing hundreds to thousands of distinct populations, Anton F.Post, Marine Biological connecting functional processes and environmental dynamics at high taxonomic Laboratory, USA resolution has remained challenging. Here we use the expression of ribosomal proteins Reviewed by: (%RP) as a proxy for in situ activity of 200 taxa within 20 metatranscriptomic samples in Gerhard Josef Herndl, University of Vienna, Austria a coastal ocean time series encompassing both seasonal variability and diel dynamics. Frank Stewart, Georgia Institute of %RP patterns grouped the taxa into seven activity clusters with distinct profiles in Technology, USA functional gene expression and correlations with environmental gradients. -
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Manuscript version: Author’s Accepted Manuscript The version presented in WRAP is the author’s accepted manuscript and may differ from the published version or, Version of Record. Persistent WRAP URL: http://wrap.warwick.ac.uk/117505 How to cite: Please refer to published version for the most recent bibliographic citation information. If a published version is known of, the repository item page linked to above, will contain details on accessing it. Copyright and reuse: The Warwick Research Archive Portal (WRAP) makes this work of researchers of the University of Warwick available open access under the following conditions. This article is made available under the Creative Commons Attribution 4.0 International license (CC BY 4.0) and may be reused according to the conditions of the license. For more details see: http://creativecommons.org/licenses/by/4.0/. Publisher’s statement: Please refer to the repository item page, publisher’s statement section, for further information. For more information, please contact the WRAP Team at: [email protected]. warwick.ac.uk/lib-publications 1 Identification of proteins and genes expressed by Methylophaga thiooxydans during 2 growth on dimethylsulfide and their presence in other members of the genus 3 4 5 6 Eileen Kröber1,2, Hendrik Schäfer1* 7 8 9 10 1 School of Life Sciences, Gibbet Hill Campus, University of Warwick, Coventry, CV4 7AL, 11 United Kingdom 12 2 Current address: Microbial Biogeochemistry, RA Landscape Functioning, ZALF Leibniz 13 Centre for Agricultural Landscape Research, Müncheberg, Germany 14 15 16 17 *Correspondence to 18 H Schäfer, School of Life Sciences, Gibbet Hill Campus, University of Warwick, Coventry, 19 CV4 7AL, United Kingdom 1 20 Abstract 21 Dimethylsulfide is a volatile organic sulfur compound that provides the largest input of biogenic 22 sulfur from the oceans to the atmosphere, and thence back to land, constituting an important 23 link in the global sulfur cycle. -
Production of Indigo and Indirubin Using Recombinant Escherichia Coli Harboring a Novel Flavin-Containing Monooxygenase Gene
August 2012 Ph.D. Dissertation Production of indigo and indirubin using recombinant Escherichia coli harboring a novel flavin-containing monooxygenase gene Graduate School of Chosun University Department of Environmental Engineering Gui Hwan Han Production of indigo and indirubin using recombinant Escherichia coli harboring a novel flavin-containing monooxygenase gene Methylophaga aminisulfidivorans MPT 유래 flavin-containing monooxygenase 유전자를 내포시킨 재조합 대장균을 이용한 인디고 및 인디루빈의 생산 August 24 2012 Graduate School of Chosun University Department of Environmental Engineering Gui Hwan Han Production of indigo and indirubin using recombinant Escherichia coli harboring a novel flavin-containing monooxygenase gene Supervisor : Prof. Si Wouk Kim A dissertation submitted to the Department of Environmental Engineering and the Graduate School of Chosun University in fulfillment of the requirements for the degree of Doctor of Philosophy April 2012 Graduate School of Chosun University Department of Environmental Engineering Gui Hwan Han This certifies that the degree of Doctor of Philosophy of Gui Hwan Han is approved by Heon Man Lim Chair of committee Il Soo Bang Committee member Hyung Joon Cha Committee member Jintae Lee Committee member Si Wouk Kim Committee member June 2012 Graduate School of Chosun University Contents Contents ······································································································································ i List of tables ····························································································································