DOCSLIB.ORG

Literature Review

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Literature Review NOVEL ANAEROBIC THERMOPHILIC BACTERIA; INTRASPECIES HETEROGENEITY AND BIOGEOGRAPHY OF THERMOANAEROBACTER ISOLATES FROM THE KAMCHATKA PENINSULA, RUSSIAN FAR EAST by ISAAC DAVID WAGNER (Under the Direction of Juergen Wiegel) ABSTRACT Thermophilic anaerobic prokaryotes are of interest from basic and applied scientific perspectives. Novel anaerobic thermophilic taxa are herein described are Caldanaerovirga acetigignens gen. nov., sp. nov.; and Thermoanaerobacter uzonensis sp. nov. Novel taxa descriptions co-authored were: Thermosediminibacter oceani gen. nov., sp. nov and Thermosediminibacter litoriperuensis sp. nov; Caldicoprobacter oshimai gen. nov., sp. nov. More than 220 anaerobic thermophilic isolates were obtained from samples collected from 11 geothermal springs within the Uzon Caldera, Geyser Valley, and Mutnovsky Volcano regions of the Kamchatka Peninsula, Russian Far East. Most strains were phylogenetically related to Thermoanaerobacter uzonensis JW/IW010T, while some were phylogenetically related to Thermoanaerobacter siderophilus SR4T. Eight protein coding genes, gyrB, lepA, leuS, pyrG, recA, recG, rplB, and rpoB, were amplified and sequenced from these isolates to describe and elucidate the intraspecies heterogeneity, α- and β-diversity patterns, and the spatial and physicochemical correlations to the observed genetic variation. All protein coding genes within the T. uzonensis isolates were found to be polymorphic, although the type (i.e., synonymous/ nonsynonymous substitutions) and quantity of the variation differed between gene sequence sets. The most applicable species concept for T. uzonensis must consider metapopulation/ subpopulation dynamics and acknowledge that physiological characteristics (e.g., sporulation) likely influences the flux of genetic information between subpopulations. Spatial variation in the distribution of T. uzonensis isolates was observed. Evaluation of T. uzonensis α-diversity revealed a range of genetic variation within a single geothermal spring. β-diversity measurements revealed that while most of the molecular variance came from inter-regional comparisons, high diversity measures between populations within a region were also observed. Between geothermal springs from different regions, T. uzonensis genetic divergence was correlated with an increase in spatial separation. However, the trend was not observed when only the isolates between the geothermal springs within a region were considered. When 27 physicochemical properties from four geothermal springs in the Uzon Caldera were matched to a corresponding biological distribution pattern, high rank correlation values, calculated as Spearman's ρ, were observed. Together, these analyses suggest that the spatial variation of T. uzonensis was influenced by both environmental differences and spatial separation. INDEX WORDS: thermophiles, microbial biogeography, microbial diversity, anaerobic thermophiles, biogeochemistry NOVEL ANAEROBIC THERMOPHILIC BACTERIA; INTRASPECIES HETEROGENEITY AND BIOGEOGRAPHY OF THERMOANAEROBACTER ISOLATES FROM THE KAMCHATKA PENINSULA, RUSSIAN FAR EAST by ISAAC DAVID WAGNER B.S., Concordia University, Nebraska, 2004 A Dissertation Submitted to the Graduate Faculty of The University of Georgia in Partial Fulfillment of the Requirements for the Degree DOCTOR OF PHILOSOPHY ATHENS, GEORGIA 2010 © 2010 Isaac David Wagner All Rights Reserved NOVEL ANAEROBIC THERMOPHILIC BACTERIA; INTRASPECIES HETEROGENEITY AND BIOGEOGRAPHY OF THERMOANAEROBACTER ISOLATES FROM THE KAMCHATKA PENINSULA, RUSSIAN FAR EAST by ISAAC DAVID WAGNER Major Professor: Juergen Wiegel Committee: Mary Ann Moran Christopher S. Romanek William B. Whitman Electronic Version Approved: Maureen Grasso Dean of the Graduate School The University of Georgia May 2010 DEDICATION For their constant support and encouragement, this dissertation is dedicated to my parents, Kim and David Wagner. iv ACKNOWLEDGEMENTS Foremost, I would like to acknowledge my major professor J. Wiegel, and my committee members, M. A. Moran, C. S. Romanek, and W. B. Whitman. Thank you for your instrumental guidance and assistance. I would also like to thank my co-authors, W. Zhao, H. Yokoyama, E. A. Burgess, C. L. Zhang, M. Rohde, Y.-J. Lee, M. E. Brice, V. V. Kevbrin, G. L. Mills, and S. Ahmed. I thank D. E. Crowe for the assistance he provided concerning analyses with the physicochemical properties of the geothermal springs. I am grateful for the help provided by members of the Wiegel laboratory, including N. Mesbah, K. Bowers, M. Salameh, E. A. Burgess, Y.-J. Lee, R. Onyenwoke, B. Zhao, B. Lupa, M. Hodges, J. Fiser, F. Sarmiento, L. Varghese, and B. Pugin; C. L. Hemme for sharing unpublished sequence data; E. Yokoyama and A. Torrens for their preliminary work on the sequencing and analysis of the universally conserved protein coding genes; the participants of the Kamchatka field expeditions, including the fellow graduate students, and P. A. Schroeder, F. T. Robb, and our Russian colleagues, especially E. Bonch-Osmolovskaya and T. Sokolova; and the University of Georgia, Athens, Microbiology Department. I am also grateful to my friends and family, including A. Wagner, L. Wagner, and M. Szarke. I am especially thankful to M. Heider for the support and encouragement she has given over the years. This research was funded the National Science Foundation (NSF-MCB0238607 – Kamchatka Microbial Observatory) as well as a UGA Dissertation Completion Award. v TABLE OF CONTENTS Page ACKNOWLEDGEMENTS .............................................................................................................v LIST OF TABLES ....................................................................................................................... viii LIST OF FIGURES .......................................................................................................................xv CHAPTER 1. DISSERTATION STRUCTURE...................................................................................1 2. DIVERSITY OF THERMOPHILIC ANAEROBES ....................................................4 3. CALDANAEROVIRGA ACETIGIGNENS GEN. NOV., SP. NOV., AN ANAEROBIC, XYLANOLYTIC, ALKALITHERMOPHILIC BACTERIUM ISOLATED FROM TREGO HOT SPRING, NEVADA, USA ...........................123 4. THERMOANAEROBACTER UZONENSIS SP. NOV., AN ANAEROBIC THERMOPHILIC BACTERIUM ISOLATED FROM A HOT SPRING WITHIN THE UZON CALDERA, KAMCHATKA, FAR EAST RUSSIA .......................145 5. VARIATIONS OF EIGHT UNIVERSALLY CONSERVED PROTEIN CODING GENES AMONG 123 THERMOANAEROBACTER UZONENSIS ISOLATES FROM GEOTHERMAL SPRINGS OF KAMCHATKA, RUSSIAN FAR EAST .....................................................................................................................171 6. THE POPULATION STRUCTURE AND SPATIAL DIVERSITY OF THERMOANAEROBACTER ISOLATES FROM GEOTHERMAL SPRINGS OF KAMCHATKA, RUSSIAN FAR EAST, BASED ON ANALYSES WITH EIGHT UNIVERSALLY CONSERVED PROTEIN CODING GENES ..........................222 vi 7. SPATIAL AND PHYSICOCHEMICAL CORRELATIONS TO THE GENETIC DIVERSITY OF THERMOANAEROBACTER UZONENSIS ISOLATES FROM GEOTHERMAL SPRINGS OF THE UZON CALDERA, GEYSER VALLEY, AND MUTNOVSKY REGIONS OF KAMCHATKA, RUSSIAN FAR EAST .....................................................................................................................301 8. DISSERTATION CONCLUSION ............................................................................324 APPENDIX A. THERMOSEDIMINIBACTER OCEANI GEN. NOV., SP. NOV. AND THERMOSEDIMINIBACTER LITORIPERUENSIS SP. NOV., NEW ANAEROBIC THERMOPHILIC BACTERIA ISOLATED FROM PERU MARGIN ..............................................................................................................327 B. CALDICOPROBACTER OSHIMAI GEN. NOV., SP. NOV., AN ANAEROBIC, XYLANOLYTIC, EXTREMELY THERMOPHILIC BACTERIUM ISOLATED FROM SHEEP FAECES, AND PROPOSAL OF CALDICOPROBACTERACEAE FAM. NOV. ...........................................................................................................353 vii LIST OF TABLES Page Table 2.1: Validly described thermophilic anaerobes ........................................................................88 Table 3.1: Phospholipid fatty acid contents (%) of strains JW/SA-NV4T, JW/IW-1228PTand JW/YJL-1230-7/2T. ....................................................................................................139 Table 3.2: Morphological and physiological characteristics of strain JW/SA-NV4T and close relatives .......................................................................................................................140 Table 4.1: Phospholipid fatty acid contents (%) of strains JW/IW010T and 1501/60. ................165 Table 4.2: Characteristics of JW/IW010T, strain 1501/60, and selected members of the genus Thermoanaerobacter. ..................................................................................................166 Table 5.1: Summary of Thermoanaerobacter uzonensis isolates universally conserved protein coding gene sequence heterogeneity ...........................................................................195 Table 5.2: Comparisons of the divergence between the Thermoanaerobacter uzonensis universally conserved protein coding gene sequence sets ...........................................196 Table 5.S1: Oligonucleotide primers for the amplification of universally conserved protein coding genes from Thermoanaerobacter taxa .............................................................202 Table 5.S2: Distribution of rplB gene sequence variants
Load more

Recommended publications
  • Genome-Resolved Meta-Analysis of the Microbiome in Oil Reservoirs Worldwide
    microorganisms Article Genome-Resolved Meta-Analysis of the Microbiome in Oil Reservoirs Worldwide Kelly J. Hidalgo 1,2,* , Isabel N. Sierra-Garcia 3 , German Zafra 4 and Valéria M. de Oliveira 1 1 Microbial Resources Division, Research Center for Chemistry, Biology and Agriculture (CPQBA), University of Campinas–UNICAMP, Av. Alexandre Cazellato 999, 13148-218 Paulínia, Brazil; [email protected] 2 Graduate Program in Genetics and Molecular Biology, Institute of Biology, University of Campinas (UNICAMP), Rua Monteiro Lobato 255, Cidade Universitária, 13083-862 Campinas, Brazil 3 Biology Department & CESAM, University of Aveiro, Aveiro, Portugal, Campus de Santiago, Avenida João Jacinto de Magalhães, 3810-193 Aveiro, Portugal; [email protected] 4 Grupo de Investigación en Bioquímica y Microbiología (GIBIM), Escuela de Microbiología, Universidad Industrial de Santander, Cra 27 calle 9, 680002 Bucaramanga, Colombia; [email protected] * Correspondence: [email protected]; Tel.: +55-19981721510 Abstract: Microorganisms inhabiting subsurface petroleum reservoirs are key players in biochemical transformations. The interactions of microbial communities in these environments are highly complex and still poorly understood. This work aimed to assess publicly available metagenomes from oil reservoirs and implement a robust pipeline of genome-resolved metagenomics to decipher metabolic and taxonomic profiles of petroleum reservoirs worldwide. Analysis of 301.2 Gb of metagenomic information derived from heavily flooded petroleum reservoirs in China and Alaska to non-flooded petroleum reservoirs in Brazil enabled us to reconstruct 148 metagenome-assembled genomes (MAGs) of high and medium quality. At the phylum level, 74% of MAGs belonged to bacteria and 26% to archaea. The profiles of these MAGs were related to the physicochemical parameters and recovery management applied.
    [Show full text]
  • CUED Phd and Mphil Thesis Classes
    High-throughput Experimental and Computational Studies of Bacterial Evolution Lars Barquist Queens' College University of Cambridge A thesis submitted for the degree of Doctor of Philosophy 23 August 2013 Arrakis teaches the attitude of the knife { chopping off what's incomplete and saying: \Now it's complete because it's ended here." Collected Sayings of Muad'dib Declaration High-throughput Experimental and Computational Studies of Bacterial Evolution The work presented in this dissertation was carried out at the Wellcome Trust Sanger Institute between October 2009 and August 2013. This dissertation is the result of my own work and includes nothing which is the outcome of work done in collaboration except where specifically indicated in the text. This dissertation does not exceed the limit of 60,000 words as specified by the Faculty of Biology Degree Committee. This dissertation has been typeset in 12pt Computer Modern font using LATEX according to the specifications set by the Board of Graduate Studies and the Faculty of Biology Degree Committee. No part of this dissertation or anything substantially similar has been or is being submitted for any other qualification at any other university. Acknowledgements I have been tremendously fortunate to spend the past four years on the Wellcome Trust Genome Campus at the Sanger Institute and the European Bioinformatics Institute. I would like to thank foremost my main collaborators on the studies described in this thesis: Paul Gardner and Gemma Langridge. Their contributions and support have been invaluable. I would also like to thank my supervisor, Alex Bateman, for giving me the freedom to pursue a wide range of projects during my time in his group and for advice.
    [Show full text]
  • 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.
    [Show full text]
  • Supporting Information
    Supporting Information Lozupone et al. 10.1073/pnas.0807339105 SI Methods nococcus, and Eubacterium grouped with members of other Determining the Environmental Distribution of Sequenced Genomes. named genera with high bootstrap support (Fig. 1A). One To obtain information on the lifestyle of the isolate and its reported member of the Bacteroidetes (Bacteroides capillosus) source, we looked at descriptive information from NCBI grouped firmly within the Firmicutes. This taxonomic error was (www.ncbi.nlm.nih.gov/genomes/lproks.cgi) and other related not surprising because gut isolates have often been classified as publications. We also determined which 16S rRNA-based envi- Bacteroides based on an obligate anaerobe, Gram-negative, ronmental surveys of microbial assemblages deposited near- nonsporulating phenotype alone (6, 7). A more recent 16S identical sequences in GenBank. We first downloaded the gbenv rRNA-based analysis of the genus Clostridium defined phylo- files from the NCBI ftp site on December 31, 2007, and used genetically related clusters (4, 5), and these designations were them to create a BLAST database. These files contain GenBank supported in our phylogenetic analysis of the Clostridium species in the HGMI pipeline. We thus designated these Clostridium records for the ENV database, a component of the nonredun- species, along with the species from other named genera that dant nucleotide database (nt) where 16S rRNA environmental cluster with them in bootstrap supported nodes, as being within survey data are deposited. GenBank records for hits with Ͼ98% these clusters. sequence identity over 400 bp to the 16S rRNA sequence of each of the 67 genomes were parsed to get a list of study titles Annotation of GTs and GHs.
    [Show full text]
  • Heat Resistant Thermophilic Endospores in Cold Estuarine Sediments
    Heat resistant thermophilic endospores in cold estuarine sediments Emma Bell Thesis submitted for the degree of Doctor of Philosophy School of Civil Engineering and Geosciences Faculty of Science, Agriculture and Engineering February 2016 Abstract Microbial biogeography explores the spatial and temporal distribution of microorganisms at multiple scales and is influenced by environmental selection and passive dispersal. Understanding the relative contribution of these factors can be challenging as their effects can be difficult to differentiate. Dormant thermophilic endospores in cold sediments offer a natural model for studies focusing on passive dispersal. Understanding distributions of these endospores is not confounded by the influence of environmental selection; rather their occurrence is due exclusively to passive transport. Sediment heating experiments were designed to investigate the dispersal histories of various thermophilic spore-forming Firmicutes in the River Tyne, a tidal estuary in North East England linking inland tributaries with the North Sea. Microcosm incubations at 50-80°C were monitored for sulfate reduction and enriched bacterial populations were characterised using denaturing gradient gel electrophoresis, functional gene clone libraries and high-throughput sequencing. The distribution of thermophilic endospores among different locations along the estuary was spatially variable, indicating that dispersal vectors originating in both warm terrestrial and marine habitats contribute to microbial diversity in estuarine and marine environments. In addition to their persistence in cold sediments, some endospores displayed a remarkable heat-resistance surviving multiple rounds of autoclaving. These extremely heat-resistant endospores are genetically similar to those detected in deep subsurface environments, including geothermal groundwater investigated from a nearby terrestrial borehole drilled to >1800 m depth with bottom temperatures in excess of 70°C.
    [Show full text]
  • Full Paper Ilumatobacter Fluminis Gen. Nov., Sp. Nov., a Novel Actinobacterium Isolated from the Sediment of an Estuary
    J. Gen. Appl. Microbiol., 55, 201‒205 (2009) Full Paper Ilumatobacter fl uminis gen. nov., sp. nov., a novel actinobacterium isolated from the sediment of an estuary Atsuko Matsumoto,1 Hiroki Kasai,2 Yoshihide Matsuo,2 Satoshi Ōmura,1 Yoshikazu Shizuri,2 and Yōko Takahashi1,* 1 Kitasato Institute for Life Sciences, Kitasato University, Minato-ku, Tokyo 108‒8641, Japan 2 Marine Biotechnology Institute, Kitasato University, Kamaishi, Iwate 026‒0001, Japan (Received December 1, 2008; Accepted February 2, 2009) Bacterial strain YM22-133T was isolated from the sediment of an estuary and grew in media with an artifi cial seawater base. Strain YM22-133T was Gram-positive, aerobic, non-motile and rod shaped. The cell-wall peptidoglycan contained LL-DAP, glycine, alanine and hydroxyglutamate. The predominant menaquinone was MK-9 (H8), with MK-9 (H0), MK-9 (H2), MK-9 (H4) and MK-9 (H6) present as minor menaquinones. The G+C content of the genomic DNA from the strain was 68 mol%. Phylogenetic analysis of the 16S rRNA gene sequence showed that the strain is near- est to Acidimicrobium ferrooxidans DSM 10331T. However, the similarity is relatively low (87.1%) and the physiological characteristics are also different: Acidimicrobium ferrooxidans is thermo- tolerant and acidophilic. Therefore, strain YM22-133T can be classifi ed as a novel genus and species, Ilumatobacter fl uminis gen. nov., sp. nov. (type strain YM22-133T =DSM 18936T=MBIC 08263T). Key Words—Acidimicrobium; Actinobacteria; artifi cial sea water; Ilumatobacter fl uminis gen. nov., sp. nov. Introduction isolated as part of this study. Phylogenetic analysis on the basis of 16S rRNA gene sequence analysis showed Recently, bacteria isolated from marine environ- that the strain is most closely related to the genus Aci- ments have attracted attention due to the recognition dimicrobium (Clark and Norris, 1996).
    [Show full text]
  • 'Candidatus Phytoplasma Solani' (Quaglino Et Al., 2013)
    ‘Candidatus Phytoplasma solani’ (Quaglino et al., 2013) Synonyms Phytoplasma solani Common Name(s) Disease: Bois noir, blackwood disease of grapevine, maize redness, stolbur Phytoplasma: CaPsol, maize redness phytoplasma, potato stolbur phytoplasma, stolbur phytoplasma, tomato stolbur phytoplasma Figure 1: A ‘dornfelder’ grape cultivar Type of Pest infected with ‘Candidatus Phytoplasma Phytoplasma solani’. Courtesy of Dr. Michael Maixner, Julius Kühn-Institut (JKI). Taxonomic Position Class: Mollicutes, Order: Acholeplasmatales, Family: Acholeplasmataceae Genus: ‘Candidatus Phytoplasma’ Reason for Inclusion in Manual OPIS A pest list, CAPS community suggestion, known host range and distribution have both expanded; 2016 AHP listing. Background Information Phytoplasmas, formerly known as mycoplasma-like organisms (MLOs), are pleomorphic, cell wall-less bacteria with small genomes (530 to 1350 kbp) of low G + C content (23-29%). They belong to the class Mollicutes and are the putative causal agents of yellows diseases that affect at least 1,000 plant species worldwide (McCoy et al., 1989; Seemüller et al., 2002). These minute, endocellular prokaryotes colonize the phloem of their infected plant hosts as well as various tissues and organs of their respective insect vectors. Phytoplasmas are transmitted to plants during feeding activity by their vectors, primarily leafhoppers, planthoppers, and psyllids (IRPCM, 2004; Weintraub and Beanland, 2006). Although phytoplasmas cannot be routinely grown by laboratory culture in cell free media, they may be observed in infected plant or insect tissues by use of electron microscopy or detected by molecular assays incorporating antibodies or nucleic acids. Since biological and phenotypic properties in pure culture are unavailable as aids in their identification, analysis of 16S rRNA genes has been adopted instead as the major basis for phytoplasma taxonomy.
    [Show full text]
  • Mannoside Recognition and Degradation by Bacteria Simon Ladeveze, Elisabeth Laville, Jordane Despres, Pascale Mosoni, Gabrielle Veronese
    Mannoside recognition and degradation by bacteria Simon Ladeveze, Elisabeth Laville, Jordane Despres, Pascale Mosoni, Gabrielle Veronese To cite this version: Simon Ladeveze, Elisabeth Laville, Jordane Despres, Pascale Mosoni, Gabrielle Veronese. Mannoside recognition and degradation by bacteria. Biological Reviews, Wiley, 2016, 10.1111/brv.12316. hal- 01602393 HAL Id: hal-01602393 https://hal.archives-ouvertes.fr/hal-01602393 Submitted on 26 May 2020 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. Biol. Rev. (2016), pp. 000–000. 1 doi: 10.1111/brv.12316 Mannoside recognition and degradation by bacteria Simon Ladeveze` 1, Elisabeth Laville1, Jordane Despres2, Pascale Mosoni2 and Gabrielle Potocki-Veron´ ese` 1∗ 1LISBP, Universit´e de Toulouse, CNRS, INRA, INSA, 31077, Toulouse, France 2INRA, UR454 Microbiologie, F-63122, Saint-Gen`es Champanelle, France ABSTRACT Mannosides constitute a vast group of glycans widely distributed in nature. Produced by almost all organisms, these carbohydrates are involved in numerous cellular processes, such as cell structuration, protein maturation and signalling, mediation of protein–protein interactions and cell recognition. The ubiquitous presence of mannosides in the environment means they are a reliable source of carbon and energy for bacteria, which have developed complex strategies to harvest them.
    [Show full text]
  • Thermophilic Carboxydotrophs and Their Applications in Biotechnology Springerbriefs in Microbiology
    SPRINGER BRIEFS IN MICROBIOLOGY EXTREMOPHILIC BACTERIA Sonia M. Tiquia-Arashiro Thermophilic Carboxydotrophs and their Applications in Biotechnology SpringerBriefs in Microbiology Extremophilic Bacteria Series editors Sonia M. Tiquia-Arashiro, Dearborn, MI, USA Melanie Mormile, Rolla, MO, USA More information about this series at http://www.springer.com/series/11917 Sonia M. Tiquia-Arashiro Thermophilic Carboxydotrophs and their Applications in Biotechnology 123 Sonia M. Tiquia-Arashiro Department of Natural Sciences University of Michigan Dearborn, MI USA ISSN 2191-5385 ISSN 2191-5393 (electronic) ISBN 978-3-319-11872-7 ISBN 978-3-319-11873-4 (eBook) DOI 10.1007/978-3-319-11873-4 Library of Congress Control Number: 2014951696 Springer Cham Heidelberg New York Dordrecht London © The Author(s) 2014 This work is subject to copyright. All rights are reserved by the Publisher, whether the whole or part of the material is concerned, specifically the rights of translation, reprinting, reuse of illustrations, recitation, broadcasting, reproduction on microfilms or in any other physical way, and transmission or information storage and retrieval, electronic adaptation, computer software, or by similar or dissimilar methodology now known or hereafter developed. Exempted from this legal reservation are brief excerpts in connection with reviews or scholarly analysis or material supplied specifically for the purpose of being entered and executed on a computer system, for exclusive use by the purchaser of the work. Duplication of this publication or parts thereof is permitted only under the provisions of the Copyright Law of the Publisher’s location, in its current version, and permission for use must always be obtained from Springer.
    [Show full text]
  • Prokaryotic Biodiversity of Lonar Meteorite Crater Soda Lake Sediment and Community Dynamics During Microenvironmental Ph Homeostasis by Metagenomics
    Prokaryotic Biodiversity of Lonar Meteorite Crater Soda Lake Sediment and Community Dynamics During Microenvironmental pH Homeostasis by Metagenomics Dissertation for the award of the degree "Doctor of Philosophy" Ph.D. Division of Mathematics and Natural Sciences of the Georg-August-Universität Göttingen within the doctoral program in Biology of the Georg-August University School of Science (GAUSS) Submitted by Soumya Biswas from Ranchi (India) Göttingen, 2016 Thesis Committee Prof. Dr. Rolf Daniel Department of Genomic and Applied Microbiology, Institute of Microbiology and Genetics, Faculty of Biology and Psychology, Georg-August-Universität Göttingen, Germany PD Dr. Michael Hoppert Department of General Microbiology, Institute of Microbiology and Genetics, Faculty of Biology and Psychology, Georg-August-Universität Göttingen, Germany Members of the Examination Board Reviewer: Prof. Dr. Rolf Daniel, Department of Genomic and Applied Microbiology, Institute of Microbiology and Genetics, Faculty of Biology and Psychology, Georg-August-Universität Göttingen, Germany Second Reviewer: PD Dr. Michael Hoppert, Department of General Microbiology, Institute of Microbiology and Genetics, Faculty of Biology and Psychology, Georg-August-Universität Göttingen, Germany Further members of the Examination Board: Prof. Dr. Burkhard Morgenstern, Department of Bioinformatics, Institute of Microbiology and Genetics, Faculty of Biology and Psychology, Georg-August-Universität Göttingen, Germany PD Dr. Fabian Commichau, Department of General Microbiology,
    [Show full text]
  • A B Comea Oxaloacetate Decarboxylase, Beta Subunit C ATP
    C ATP-binding cassette, subfamily B A ComEA WP 025028831 Bacillus mannanilyticus B oxaloacetate decarboxylase, beta subunit WP 041718914 Alkaliphilus oremlandii PKM81186 Firmicutes bacterium HGW-Firmicutes-14 WP 092588843 Acidaminobacter hydrogenoformans Bacillus spp. MZQ96192 Acidaminobacter sp. Paenibacillus spp. 100% WP 088775865 Carboxydothermus islandicus WP 152967700 Oxobacter pfennigii GAV25686 Carboxydothermus islandicus WP 057983007 Virgibacillus soli 70% WP 146620656 Enterococcus florum WP 049886177 Thermacetogenium phaeum WP 064467709 Bacillus galactosidilyticus WP 126109031 Jeotgalibaca sp. H21T32 WP 090886300 Bacillus caseinilyticus Tree scale: 0.1 Peptoclostridium spp. Trichococcus spp. WP 101330798 Halalkalibacillus sp. B3227 WP 156782411 Geosporobacter ferrireducens WP 078755654 Globicatella sulfidifaciens SFQ43799 Desemzia incerta WP 110940224 Geosporobacter subterraneus WP 051258417 Atopococcus tabaci WP 047393312 Carnobacterium sp. ZWU0011 SHI93557 Geosporobacter subterraneus DSM 17957 WP 156883193 Lacticigenium naphtae WP 051237935 Lacticigenium naphtae 100% Natranaerovirga spp. WP 017470521 Amphibacillus jilinensis WP 097004362 amygdalinum Enterococcus spp. 75% HBG15709 Firmicutes bacterium WP 092653112 Isobaculum melis WP 013780596 Mahella australiensis Thermoanaerobacter spp. WP 126780365 Vagococcus salmoninarum WP 087058768 Marinilactibacillus psychrotolerans WP 084110983 Caldanaerobius fijiensis WP 072693424 Marinilactibacillus sp. 15R 2503533728 Mahella australiensis 50-1 BON Caldicellulosiruptor spp. WP 129721893
    [Show full text]
  • The Phylogenetic Composition and Structure of Soil Microbial Communities Shifts in Response to Elevated Carbon Dioxide
    View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by University of Minnesota Digital Conservancy The ISME Journal (2012) 6, 259–272 & 2012 International Society for Microbial Ecology All rights reserved 1751-7362/12 www.nature.com/ismej ORIGINAL ARTICLE The phylogenetic composition and structure of soil microbial communities shifts in response to elevated carbon dioxide Zhili He1, Yvette Piceno2, Ye Deng1, Meiying Xu1,3, Zhenmei Lu1,4, Todd DeSantis2, Gary Andersen2, Sarah E Hobbie5, Peter B Reich6 and Jizhong Zhou1,2 1Institute for Environmental Genomics, Department of Botany and Microbiology, University of Oklahoma, Norman, OK, USA; 2Ecology Department, Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA; 3Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Institute of Microbiology, Guangzhou, China; 4College of Life Sciences, Zhejiang University, Hangzhou, China; 5Department of Ecology, Evolution, and Behavior, St Paul, MN, USA and 6Department of Forest Resources, University of Minnesota, St Paul, MN, USA One of the major factors associated with global change is the ever-increasing concentration of atmospheric CO2. Although the stimulating effects of elevated CO2 (eCO2) on plant growth and primary productivity have been established, its impacts on the diversity and function of soil microbial communities are poorly understood. In this study, phylogenetic microarrays (PhyloChip) were used to comprehensively survey the richness, composition and structure of soil microbial communities in a grassland experiment subjected to two CO2 conditions (ambient, 368 p.p.m., versus elevated, 560 p.p.m.) for 10 years. The richness based on the detected number of operational taxonomic units (OTUs) significantly decreased under eCO2.
    [Show full text]