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The Hydrocarbon Biodegradation Potential of Faroe-Shetland Channel Bacterioplankton
THE HYDROCARBON BIODEGRADATION POTENTIAL OF FAROE-SHETLAND CHANNEL BACTERIOPLANKTON Angelina G. Angelova Submitted for the degree of Doctor of Philosophy Heriot Watt University School of Engineering and Physical Sciences July 2017 The copyright in this thesis is owned by the author. Any quotation from the thesis or use of any of the information contained in it must acknowledge this thesis as the source of the quotation or information. ABSTRACT The Faroe-Shetland Channel (FSC) is an important gateway for dynamic water exchange between the North Atlantic Ocean and the Nordic Seas. In recent years it has also become a frontier for deep-water oil exploration and petroleum production, which has raised the risk of oil pollution to local ecosystems and adjacent waterways. In order to better understand the factors that influence the biodegradation of spilled petroleum, a prerequisite has been recognized to elucidate the complex dynamics of microbial communities and their relationships to their ecosystem. This research project was a pioneering attempt to investigate the FSC’s microbial community composition, its response and potential to degrade crude oil hydrocarbons under the prevailing regional temperature conditions. Three strategies were used to investigate this. Firstly, high throughput sequencing and 16S rRNA gene-based community profiling techniques were utilized to explore the spatiotemporal patterns of the FSC bacterioplankton. Monitoring proceeded over a period of 2 years and interrogated the multiple water masses flowing through the region producing 2 contrasting water cores: Atlantic (surface) and Nordic (subsurface). Results revealed microbial profiles more distinguishable based on water cores (rather than individual water masses) and seasonal variability patterns within each core. -
Table 1. Overview of Reactions Examined in This Study. ΔG Values Were Obtained from Thauer Et Al., 1977
Supplemental Information: Table 1. Overview of reactions examined in this study. ΔG values were obtained from Thauer et al., 1977. No. Equation ∆G°' (kJ/reaction)* Acetogenic reactions – – – + 1 Propionate + 3 H2O → Acetate + HCO3 + 3 H2 + H +76.1 Sulfate-reducing reactions – 2– – – – + 2 Propionate + 0.75 SO4 → Acetate + 0.75 HS + HCO3 + 0.25 H –37.8 2– + – 3 4 H2 + SO4 + H → HS + 4 H2O –151.9 – 2– – – 4 Acetate + SO4 → 2 HCO3 + HS –47.6 Methanogenic reactions – – + 5 4 H2 + HCO3 + H → CH4 + 3 H2O –135.6 – – 6 Acetate + H2O → CH4 + HCO3 –31.0 Syntrophic propionate conversion – – – + 1+5 Propionate + 0.75 H2O → Acetate + 0.75 CH4 + 0.25 HCO3 + 0.25 H –25.6 Complete propionate conversion by SRB – 2– – – + 2+4 Propionate + 1.75 SO4 → 1.75 HS + 3 HCO3 + 0.25 H –85.4 Complete propionate conversion by syntrophs and methanogens 1+5+6 Propionate– + 1.75 H O → 1.75 CH + 1.25 HCO – + 0.25 H+ –56.6 2 4 3 1 Table S2. Overview of all enrichment slurries fed with propionate and the total amounts of the reactants consumed and products formed during the enrichment period. The enrichment slurries consisted of sediment from either the sulfate zone (SZ), sulfate-methane transition zone (SMTZ) or methane zone (MZ) and were incubated at 25°C or 10°C, with 3 mM, 20 mM or without (-) sulfate amendments along the study. The slurries P1/P2, P3/P4, P5/P6, P7/P8 from each sediment zone are biological replicates. Slurries with * are presented in the propionate conversion graphs and used for molecular analysis. -
Bacterial Epibiotic Communities of Ubiquitous and Abundant Marine Diatoms Are Distinct in Short- and Long-Term Associations
fmicb-09-02879 December 1, 2018 Time: 14:0 # 1 ORIGINAL RESEARCH published: 04 December 2018 doi: 10.3389/fmicb.2018.02879 Bacterial Epibiotic Communities of Ubiquitous and Abundant Marine Diatoms Are Distinct in Short- and Long-Term Associations Klervi Crenn, Delphine Duffieux and Christian Jeanthon* CNRS, Sorbonne Université, Station Biologique de Roscoff, Adaptation et Diversité en Milieu Marin, Roscoff, France Interactions between phytoplankton and bacteria play a central role in mediating biogeochemical cycling and food web structure in the ocean. The cosmopolitan diatoms Thalassiosira and Chaetoceros often dominate phytoplankton communities in marine systems. Past studies of diatom-bacterial associations have employed community- level methods and culture-based or natural diatom populations. Although bacterial assemblages attached to individual diatoms represents tight associations little is known on their makeup or interactions. Here, we examined the epibiotic bacteria of 436 Thalassiosira and 329 Chaetoceros single cells isolated from natural samples and Edited by: collection cultures, regarded here as short- and long-term associations, respectively. Matthias Wietz, Epibiotic microbiota of single diatom hosts was analyzed by cultivation and by cloning- Alfred Wegener Institut, Germany sequencing of 16S rRNA genes obtained from whole-genome amplification products. Reviewed by: The prevalence of epibiotic bacteria was higher in cultures and dependent of the host Lydia Jeanne Baker, Cornell University, United States species. Culture approaches demonstrated that both diatoms carry distinct bacterial Bryndan Paige Durham, communities in short- and long-term associations. Bacterial epibonts, commonly University of Washington, United States associated with phytoplankton, were repeatedly isolated from cells of diatom collection *Correspondence: cultures but were not recovered from environmental cells. -
Bacterium That Produces Antifouling Agents
International Journal of Systematic Bacteriology (1998), 48, 1205-1 21 2 Printed in Great Britain ~- Pseudoalteromonas tunicata sp. now, a bacterium that produces antifouling agents Carola Holmstromfl Sally James,’ Brett A. Neilan,’ David C. White’ and Staffan Kjellebergl Author for correspondence : Carola Holmstrom. Tel: + 61 2 9385 260 1. Fax: + 6 1 2 9385 159 1. e-mail: c.holmstrom(cx unsw.edu.au 1 School of Microbiology A dark-green-pigmented marine bacterium, previously designated D2, which and Immunology, The produces components that are inhibitory to common marine fouling organisms University of New South Wales, Sydney 2052, has been characterized and assessed for taxonomic assignment. Based on Australia direct double-stranded sequencing of the 16s rRNA gene, D2Twas found to show the highest similarity to members of the genus 2 Center for Environmental (93%) B iotechnology, Un iversity Pseudoalteromonas. The G+C content of DZT is 42 molo/o, and it is a of Tennessee, 10515 facultatively anaerobic rod and oxidase-positive. DZT is motile by a sheathed research Drive, Suite 300, Knoxville, TN 37932, USA polar flagellum, exhibited non-fermentative metabolism and required sodium ions for growth. The strain was not capable of using citrate, fructose, sucrose, sorbitol and glycerol but it utilizes mannose and maltose and hydrolyses gelatin. The molecular evidence, together with phenotypic characteristics, showed that this bacterium which produces an antifouling agent constitutes a new species of the genus Pseudoalteromonas.The name Pseudoalteromonas tunicata is proposed for this bacterium, and the type strain is DZT (= CCUG 2 6 7 5 7T). 1 Kevwords: PseudoalttJvomonas tunicata, pigment, antifouling bacterium, marine, 16s I rRNA sequence .__ , INTRODUCTION results suggested that the genus Alteromonas should be separated into two genera. -
Supplementary Figure S2. Taxonomic Composition in Individual Microcosm Treatments Across a 14-Week Experiment
100. 0 f Viruses|g Viruses|s Sulfitobacter phage pCB2047 C f Viruses|g Viruses|s Sulfitobacter phage pCB2047 A f Sinobacteraceae|g Sinobacteraceae f Vibrionaceae|g Vibrio|s Vibrio splendidus f Vibrionaceae|g Vibrio|s Vibrio kanaloae f Piscirickettsiaceae|g Methylophaga|s Methylophaga 90.0 f Piscirickettsiaceae|g Cycloclasticus|s Cycloclasticus pugetii f Pseudomonadaceae|g Pseudomonas|s Pseudomonas stutzeri f Pseudomonadaceae|g Pseudomonas|s Pseudomonas sp S9 f Pseudomonadaceae|g Pseudomonas|s Pseudomonas pelagia f Pseudomonadaceae|g Pseudomonas|s Pseudomonas f Pseudomonadaceae|g Cellvibrio|s Cellvibrio 80.0 f Moraxellaceae|g Psychrobacter|s Psychrobacter cryohalolentis f Moraxellaceae|g Acinetobacter|s Acinetobacter f Oceanospirillaceae|g Marinomonas|s Marinomonas sp MWYL1 f Oceanospirillaceae|g Marinomonas|s Marinomonas f Halomonadaceae|g Halomonas|s Halomonas titanicae 70.0 f Halomonadaceae|g Halomonas|s Halomonas f Alcanivoracaceae|g Alcanivorax|s Alcanivorax f Gammaproteobacteria|g Gammaproteobacteria|s gammaproteobacterium HIMB55 f Enterobacteriaceae|g Buchnera|s Buchnera aphidicola f Shewanellaceae|g Shewanella|s Shewanella frigidimarina f Shewanellaceae|g Shewanella|s Shewanella baltica 60.0 f Shewanellaceae|g Shewanella|s Shewanella f Pseudoalteromonadaceae|g Pseudoalteromonas|s Pseudoalteromonas undina f Pseudoalteromonadaceae|g Pseudoalteromonas|s Pseudoalteromonas haloplanktis f Pseudoalteromonadaceae|g Pseudoalteromonas|s Pseudoalteromonas arctica f Pseudoalteromonadaceae|g Pseudoalteromonas|s Pseudoalteromonas agarivorans -
Centro De Investigación Científica Y De Educación Superior De Ensenada, Baja California
Centro de Investigación Científica y de Educación Superior de Ensenada, Baja California Maestría en Ciencias en Acuicultura Calidad bacteriológica del agua en sistemas de mantenimiento de reproductores de Seriola lalandi Tesis para cubrir parcialmente los requisitos necesarios para obtener el grado de Maestro en Ciencias Presenta: Miriam Esther Garcia Mendoza Ensenada, Baja California, México 2017 Tesis defendida por Miriam Esther Garcia Mendoza y aprobada por el siguiente Comité Dr. Jorge Abelardo Cáceres Martínez Director de tesis Dra. Rebeca Vásquez Yeomans Dra. Beatriz Cordero Esquivel Dr. Pierrick Gerard Jean Fournier Dr. Jorge Abelardo Cáceres Martínez Coordinador del Posgrado en Acuicultura Dra. Rufina Hernández Martínez Directora de Estudios de Posgrado Miriam Esther Garcia Mendoza © 2017 Queda prohibida la reproducción parcial o total de esta obra sin el permiso formal y explícito del autor y director de la tesis. ii Resumen de la tesis que presenta Miriam Esther Garcia Mendoza como requisito parcial para la obtención del grado de Maestro en Ciencias en Acuicultura. Calidad bacteriológica del agua en sistemas de mantenimiento de reproductores de Seriola lalandi Resumen aprobado por: __ ____________________________ Dr. Jorge Abelardo Cáceres Martínez Director de tesis Con la expansión e intensificación de la piscicultura, los brotes de enfermedades infecciosas se han incrementado y reconocido como una limitante para su desarrollo. Entre éstas, se encuentran las causadas por bacterias, que ocasionan uno de los efectos más negativos. La industria japonesa de cultivo de Seriola spp. pierde anualmente $200 millones de USD debido a estas enfermedades. Una medida recomendada para evitar su ocurrencia, es conocer la carga y diversidad de comunidades bacterianas a las que están expuestas los peces. -
Arthrocnemum Macrostachyum Y Su Microbioma Como Herramienta Para La Recuperación De Suelos Degradados
Arthrocnemum macrostachyum y su microbioma como herramienta para la recuperación de suelos degradados TESIS DOCTORAL Salvadora Navarro de la Torre Sevilla, 2017 DEPARTAMENTO DE MICROBIOLOGÍA Y PARASITOLOGÍA FACULTAD DE FARMACIA UNIVERSIDAD DE SEVILLA ARTHROCNEMUM MACROSTACHYUM Y SU MICROBIOMA COMO HERRAMIENTA PARA LA RECUPERACIÓN DE SUELOS DEGRADADOS SALVADORA NAVARRO DE LA TORRE SEVILLA, 2017 La Tesis Doctoral titulada “Arthrocnemum macrostachyum y su microbioma como herramienta para la recuperación de suelos degradados”, realizada por la Licenciada en Biología Dña. Salvadora Navarro de la Torre para optar al grado de Doctor en Biología Molecular y Biomedicina con Mención Internacional por la Universidad de Sevilla, se presenta con la aprobación de los Directores y el Departamento de Microbiología y Parasitología de la Universidad de Sevilla. Los directores, Fdo. Dr. Ignacio D. Rodríguez Llorente Fdo. Dra. Eloísa Pajuelo Domínguez El Director del Departamento, La doctoranda, Fdo. Dr. Miguel Ángel Caviedes Formento Fdo. Salvadora Navarro de la Torre A todas las personas que han formado parte de esta etapa de aprendizaje “Sin prisa, pero sin descanso” Johann W. Goethe “Una sucesión de pequeñas voluntades consigue un gran resultado” Charles Baudelaire AGRADECIMIENTOS Todos los que me conocéis sabréis como soy, y por ello sabréis que esta parte de la Tesis puede que haya sido la más difícil de escribir, por lo que intentaré que no quede muy sosa. Siempre me gustó el Conocimiento del Medio en el colegio, y conforme esta asignatura fue avanzando durante el instituto, me fue gustando cada vez más, sobre todo “esa parte” de las bacterias y las células (desde pequeña iba para bióloga de bata). -
Thalassomonas Agarivorans Sp. Nov., a Marine Agarolytic Bacterium Isolated from Shallow Coastal Water of An-Ping Harbour, Taiwan
International Journal of Systematic and Evolutionary Microbiology (2006), 56, 1245–1250 DOI 10.1099/ijs.0.64130-0 Thalassomonas agarivorans sp. nov., a marine agarolytic bacterium isolated from shallow coastal water of An-Ping Harbour, Taiwan, and emended description of the genus Thalassomonas Wen Dar Jean,1 Wung Yang Shieh2 and Tung Yen Liu2 Correspondence 1Center for General Education, Leader University, No. 188, Sec. 5, An-Chung Rd, Tainan, Wung Yang Shieh Taiwan [email protected] 2Institute of Oceanography, National Taiwan University, PO Box 23-13, Taipei, Taiwan A marine agarolytic bacterium, designated strain TMA1T, was isolated from a seawater sample collected in a shallow-water region of An-Ping Harbour, Taiwan. It was non-fermentative and Gram-negative. Cells grown in broth cultures were straight or curved rods, non-motile and non-flagellated. The isolate required NaCl for growth and exhibited optimal growth at 25 6C and 3 % NaCl. It grew aerobically and was incapable of anaerobic growth by fermenting glucose or other carbohydrates. Predominant cellular fatty acids were C16 : 0 (17?5 %), C17 : 1v8c (12?8 %), C17 : 0 (11?1 %), C15 : 0 iso 2-OH/C16 : 1v7c (8?6 %) and C13 : 0 (7?3 %). The DNA G+C content was 41?0 mol%. Phylogenetic, phenotypic and chemotaxonomic data accumulated in this study revealed that the isolate could be classified in a novel species of the genus Thalassomonas in the family Colwelliaceae. The name Thalassomonas agarivorans sp. nov. is proposed for the novel species, with TMA1T (=BCRC 17492T=JCM 13379T) as the type strain. Alteromonas-like bacteria in the class Gammaproteobacteria however, they are not exclusively autochthonous in the comprise a large group of marine, heterotrophic, polar- marine environment, since some reports have shown that flagellated, Gram-negative rods that are mainly non- they also occur in freshwater, sewage and soil (Agbo & Moss, fermentative aerobes. -
Changes in Bacterial Community Metabolism and Composition During
Changes in bacterial community metabolism and composition during the degradation of dissolved organic matter from the jellyfish Aurelia aurita in a Mediterranean coastal lagoon Marine Blanchet 1,2 , Olivier Pringault 3, Marc Bouvy 3, Philippe Catala 1,2 , Louise Oriol 1,2 , Jocelyne Caparros 1,2 , Eva Ortega-Retuerta 1,2,4 , Laurent Intertaglia 5,6 , Nyree West 5,6 , Martin Agis 3, Patrice Got 3, Fabien Joux 1,2* 1Sorbonne Universités, UPMC Univ Paris 06, UMR 7621, Laboratoire dOcéanographie Microbienne, Observatoire Océanologique, F-66650 Banyuls/mer, France 2 CNRS, UMR 7621, Laboratoire dOcéanographie Microbienne, Observatoire Océanologique, F- 66650 Banyuls/mer, France 3UMR5119 Ecologie des systèmes marins côtiers (ECOSYM), CNRS, IRD, UM2, UM1; Université Montpellier 2. Case 093, F-34095 Montpellier Cedex 5, France 4Institut de Ciències del Mar, CSIC, Barcelona, Spain 5Sorbonne Universités UPMC Univ Paris 06, UMS 2348, Observatoire Océanologique, F-66650 Banyuls/Mer, France 6CNRS, UMS 2348, Observatoire Océanologique, F-66650 Banyuls/Mer, France *corresponding author: Email: [email protected], Phone: 33(0)4 6888 7342, Fax: 33(0)4 6888 7395 Abstract Spatial increases and temporal shifts in outbreaks of gelatinous plankton have been observed over the past several decades in many estuarine and coastal ecosystems. The effects of these blooms on marine ecosystem functioning, and particularly on the dynamics of the heterotrophic bacteria are still unclear. The response of the bacterial community from a Mediterranean coastal lagoon to th e addition of dissolved organic matter (DOM) from the jellyfish Aurelia aurita, corresponding to an enrichment of dissolved organic carbon (DOC) by 1.4, was assessed during 22 days in microcosms (8 liters). -
Bacterial Diversity and Biogeography of the Cold-Water Gorgonian Primnoa Resedaeformis in Norfolk and Baltimore Canyons Christina A
617 Bacterial diversity and biogeography of the cold-water gorgonian Primnoa resedaeformis in Norfolk and Baltimore canyons Christina A. Kellogg* and Michael A. Gray U.S. Geological Survey, St. Petersburg Coastal and Marine Science Center, St. Petersburg, Florida 33701, USA Abstract Much attention has been paid to the bacterial associates of the cold-water reef- forming scleractinian coral, Lophelia pertusa. However, many other cold-water coral species remain microbiological terra incognita, including the locally abundant, habitat-forming Atlantic octocoral Primnoa resedaeformis. During research cruises in 2012 and 2013, we collected samples from 10 individual coral colonies in each of Baltimore and Norfolk Canyons in the western Atlantic Ocean. DNA was extracted from each sample and the V4-V5 variable regions of the 16S ribosomal RNA gene were amplified and then subjected to 454 pyrosequencing. Samples were dominated by Proteobacteria followed by smaller amounts of Firmicutes, Planctomycetes, Bacteroidetes and Actinobacteria. Bacterial community sequences were found to cluster based on submarine canyon of origin. Norfolk Canyon bacterial communities had much higher representation of Gammaproteobacteria, particularly the family Moraxellaceae, compared to Baltimore Canyon communities that were dominated by Alphaproteobacteria, particularly the family Kiloniellaceae. These data provide a first Figure 2. Primnoa resedaeformis, a cold-water octocoral Figure 3. A non-metric multidimensional scaling (NMDS) plot comparing the look at the biogeographic structuring of the bacterial associates of P. resedaeformis bacterial communities of Primnoa resedaeformis from Baltimore and Norfolk likely caused by physical barriers to dispersal imposed by submarine canyons. Canyons to those of P. pacifica collected in the Gulf of Alaska (Pacific Ocean). -
Life in the Cold Biosphere: the Ecology of Psychrophile
Life in the cold biosphere: The ecology of psychrophile communities, genomes, and genes Jeff Shovlowsky Bowman A dissertation submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy University of Washington 2014 Reading Committee: Jody W. Deming, Chair John A. Baross Virginia E. Armbrust Program Authorized to Offer Degree: School of Oceanography i © Copyright 2014 Jeff Shovlowsky Bowman ii Statement of Work This thesis includes previously published and submitted work (Chapters 2−4, Appendix 1). The concept for Chapter 3 and Appendix 1 came from a proposal by JWD to NSF PLR (0908724). The remaining chapters and appendices were conceived and designed by JSB. JSB performed the analysis and writing for all chapters with guidance and editing from JWD and co- authors as listed in the citation for each chapter (see individual chapters). iii Acknowledgements First and foremost I would like to thank Jody Deming for her patience and guidance through the many ups and downs of this dissertation, and all the opportunities for fieldwork and collaboration. The members of my committee, Drs. John Baross, Ginger Armbrust, Bob Morris, Seelye Martin, Julian Sachs, and Dale Winebrenner provided valuable additional guidance. The fieldwork described in Chapters 2, 3, and 4, and Appendices 1 and 2 would not have been possible without the help of dedicated guides and support staff. In particular I would like to thank Nok Asker and Lewis Brower for giving me a sample of their vast knowledge of sea ice and the polar environment, and the crew of the icebreaker Oden for a safe and fascinating voyage to the North Pole. -
Three Manganese Oxide-Rich Marine Sediments Harbor Similar Communities of Acetate-Oxidizing Manganese-Reducing Bacteria
CORE Metadata, citation and similar papers at core.ac.uk Provided by University of Southern Denmark Research Output The ISME Journal (2012) 6, 2078–2090 & 2012 International Society for Microbial Ecology All rights reserved 1751-7362/12 www.nature.com/ismej ORIGINAL ARTICLE Three manganese oxide-rich marine sediments harbor similar communities of acetate-oxidizing manganese-reducing bacteria Verona Vandieken1,5 , Michael Pester2, Niko Finke1,6, Jung-Ho Hyun3, Michael W Friedrich4, Alexander Loy2 and Bo Thamdrup1 1Nordic Center for Earth Evolution, University of Southern Denmark, Odense, Denmark; 2Department of Microbial Ecology, Faculty of Life Sciences, University of Vienna, Vienna, Austria; 3Department of Environmental Marine Sciences, Hanyang University, Ansan, South Korea and 4Department of Microbial Ecophysiology, University of Bremen, Bremen, Germany Dissimilatory manganese reduction dominates anaerobic carbon oxidation in marine sediments with high manganese oxide concentrations, but the microorganisms responsible for this process are largely unknown. In this study, the acetate-utilizing manganese-reducing microbiota in geographi- cally well-separated, manganese oxide-rich sediments from Gullmar Fjord (Sweden), Skagerrak (Norway) and Ulleung Basin (Korea) were analyzed by 16S rRNA-stable isotope probing (SIP). Manganese reduction was the prevailing terminal electron-accepting process in anoxic incubations of surface sediments, and even the addition of acetate stimulated neither iron nor sulfate reduction. The three geographically distinct sediments harbored surprisingly similar communities of acetate- utilizing manganese-reducing bacteria: 16S rRNA of members of the genera Colwellia and Arcobacter and of novel genera within the Oceanospirillaceae and Alteromonadales were detected in heavy RNA-SIP fractions from these three sediments. Most probable number (MPN) analysis yielded up to 106 acetate-utilizing manganese-reducing cells cm À 3 in Gullmar Fjord sediment.