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Ancestry and Adaptive Radiation of Bacteroidetes As Assessed by Comparative Genomics
1 Ancestry and adaptive radiation of Bacteroidetes as assessed by comparative genomics 2 3 Raul Munoza,b,*, Hanno Teelinga, Rudolf Amanna and Ramon Rosselló-Mórab,* 4 5 a Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, D-28359 6 Bremen, Germany. 7 b Marine Microbiology Group, Department of Ecology and Marine Resources, Institut Mediterrani 8 d’Estudis Avançats (CSIC-UIB), E-07190 Esporles, Balearic Islands, Spain. 9 10 * Corresponding authors: 11 Raul Munoz, Marine Microbiology Group, Carrer Miquel Marquès 21, 07190 Esporles, Illes 12 Balears, Spain. e-mail: [email protected] 13 Ramon Rosselló-Móra, Marine Microbiology Group, Carrer Miquel Marquès 21, 07190 Esporles, 14 Illes Balears, Spain. e-mail: [email protected] 15 16 17 18 Keywords + 19 Bacteroidetes, Na -NQR, alternative complex III, caa3 cytochrome oxidase, gliding, T9SS. 20 21 Abbreviations 22 m.s.i.: median sequence identity. 23 24 25 26 27 ABSTRACT 28 As of this writing, the phylum Bacteroidetes comprises more than 1,500 described species with 29 diverse ecological roles. However, there is little understanding of archetypal Bacteroidetes traits on 30 a genomic level. We compiled a representative set of 89 Bacteroidetes genomes and used pairwise 31 reciprocal best match gene comparisons and gene syntenies to identify common traits that allow to 32 trace Bacteroidetes’ evolution and adaptive radiation. Highly conserved among all studied 33 Bacteroidetes was the type IX secretion system (T9SS). Class-level comparisons furthermore 34 suggested that the ACIII-caa3COX super-complex evolved in the ancestral aerobic bacteroidetal 35 lineage, and was secondarily lost in extant anaerobic Bacteroidetes. -
Halophilic Bacteroidetes As an Example on How Their Genomes Interact with the Environment
DOCTORAL THESIS 2020 PHYLOGENOMICS OF BACTEROIDETES; HALOPHILIC BACTEROIDETES AS AN EXAMPLE ON HOW THEIR GENOMES INTERACT WITH THE ENVIRONMENT Raúl Muñoz Jiménez DOCTORAL THESIS 2020 Doctoral Programme of Environmental and Biomedical Microbiology PHYLOGENOMICS OF BACTEROIDETES; HALOPHILIC BACTEROIDETES AS AN EXAMPLE ON HOW THEIR GENOMES INTERACT WITH THE ENVIRONMENT Raúl Muñoz Jiménez Thesis Supervisor: Ramon Rosselló Móra Thesis Supervisor: Rudolf Amann Thesis tutor: Elena I. García-Valdés Pukkits Doctor by the Universitat de les Illes Balears Publications resulted from this thesis Munoz, R., Rosselló-Móra, R., & Amann, R. (2016). Revised phylogeny of Bacteroidetes and proposal of sixteen new taxa and two new combinations including Rhodothermaeota phyl. nov. Systematic and Applied Microbiology, 39(5), 281–296 Munoz, R., Rosselló-Móra, R., & Amann, R. (2016). Corrigendum to “Revised phylogeny of Bacteroidetes and proposal of sixteen new taxa and two new combinations including Rhodothermaeota phyl. nov.” [Syst. Appl. Microbiol. 39 (5) (2016) 281–296]. Systematic and Applied Microbiology, 39, 491–492. Munoz, R., Amann, R., & Rosselló-Móra, R. (2019). Ancestry and adaptive radiation of Bacteroidetes as assessed by comparative genomics. Systematic and Applied Microbiology, 43(2), 126065. Dr. Ramon Rosselló Móra, of the Institut Mediterrani d’Estudis Avançats, Esporles and Dr. Rudolf Amann, of the Max-Planck-Institute für Marine Mikrobiologie, Bremen WE DECLARE: That the thesis titled Phylogenomics of Bacteroidetes; halophilic Bacteroidetes as an example on how their genomes interact with the environment, presented by Raúl Muñoz Jiménez to obtain a doctoral degree, has been completed under our supervision and meets the requirements to opt for an International Doctorate. For all intents and purposes, we hereby sign this document. -
View and Research Objectives
University of Alberta Carotenoid diversity in novel Hymenobacter strains isolated from Victoria Upper Glacier, Antarctica, and implications for the evolution of microbial carotenoid biosynthesis by Jonathan Lee Klassen A thesis submitted to the Faculty of Graduate Studies and Research in partial fulfillment of the requirements for the degree of Doctor of Philosophy in Microbiology and Cell Biotechnology Department of Biological Sciences ©Jonathan Lee Klassen Fall 2009 Edmonton, Alberta Permission is hereby granted to the University of Alberta Libraries to reproduce single copies of this thesis and to lend or sell such copies for private, scholarly or scientific research purposes only. Where the thesis is converted to, or otherwise made available in digital form, the University of Alberta will advise potential users of the thesis of these terms. The author reserves all other publication and other rights in association with the copyright in the thesis and, except as herein before provided, neither the thesis nor any substantial portion thereof may be printed or otherwise reproduced in any material form whatsoever without the author's prior written permission. Examining Committee Dr. Julia Foght, Department of Biological Science Dr. Phillip Fedorak, Department of Biological Sciences Dr. Brenda Leskiw, Department of Biological Sciences Dr. David Bressler, Department of Agriculture, Food and Nutritional Science Dr. Jeffrey Lawrence, Department of Biological Sciences, University of Pittsburgh Abstract Many diverse microbes have been detected in or isolated from glaciers, including novel taxa exhibiting previously unrecognized physiological properties with significant biotechnological potential. Of 29 unique phylotypes isolated from Victoria Upper Glacier, Antarctica (VUG), 12 were related to the poorly studied bacterial genus Hymenobacter including several only distantly related to previously described taxa. -
Appendix 1. New and Emended Taxa Described Since Publication of Volume One, Second Edition of the Systematics
188 THE REVISED ROAD MAP TO THE MANUAL Appendix 1. New and emended taxa described since publication of Volume One, Second Edition of the Systematics Acrocarpospora corrugata (Williams and Sharples 1976) Tamura et Basonyms and synonyms1 al. 2000a, 1170VP Bacillus thermodenitrificans (ex Klaushofer and Hollaus 1970) Man- Actinocorallia aurantiaca (Lavrova and Preobrazhenskaya 1975) achini et al. 2000, 1336VP Zhang et al. 2001, 381VP Blastomonas ursincola (Yurkov et al. 1997) Hiraishi et al. 2000a, VP 1117VP Actinocorallia glomerata (Itoh et al. 1996) Zhang et al. 2001, 381 Actinocorallia libanotica (Meyer 1981) Zhang et al. 2001, 381VP Cellulophaga uliginosa (ZoBell and Upham 1944) Bowman 2000, VP 1867VP Actinocorallia longicatena (Itoh et al. 1996) Zhang et al. 2001, 381 Dehalospirillum Scholz-Muramatsu et al. 2002, 1915VP (Effective Actinomadura viridilutea (Agre and Guzeva 1975) Zhang et al. VP publication: Scholz-Muramatsu et al., 1995) 2001, 381 Dehalospirillum multivorans Scholz-Muramatsu et al. 2002, 1915VP Agreia pratensis (Behrendt et al. 2002) Schumann et al. 2003, VP (Effective publication: Scholz-Muramatsu et al., 1995) 2043 Desulfotomaculum auripigmentum Newman et al. 2000, 1415VP (Ef- Alcanivorax jadensis (Bruns and Berthe-Corti 1999) Ferna´ndez- VP fective publication: Newman et al., 1997) Martı´nez et al. 2003, 337 Enterococcus porcinusVP Teixeira et al. 2001 pro synon. Enterococcus Alistipes putredinis (Weinberg et al. 1937) Rautio et al. 2003b, VP villorum Vancanneyt et al. 2001b, 1742VP De Graef et al., 2003 1701 (Effective publication: Rautio et al., 2003a) Hongia koreensis Lee et al. 2000d, 197VP Anaerococcus hydrogenalis (Ezaki et al. 1990) Ezaki et al. 2001, VP Mycobacterium bovis subsp. caprae (Aranaz et al. -
Genome-Based Taxonomic Classification Of
ORIGINAL RESEARCH published: 20 December 2016 doi: 10.3389/fmicb.2016.02003 Genome-Based Taxonomic Classification of Bacteroidetes Richard L. Hahnke 1 †, Jan P. Meier-Kolthoff 1 †, Marina García-López 1, Supratim Mukherjee 2, Marcel Huntemann 2, Natalia N. Ivanova 2, Tanja Woyke 2, Nikos C. Kyrpides 2, 3, Hans-Peter Klenk 4 and Markus Göker 1* 1 Department of Microorganisms, Leibniz Institute DSMZ–German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany, 2 Department of Energy Joint Genome Institute (DOE JGI), Walnut Creek, CA, USA, 3 Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia, 4 School of Biology, Newcastle University, Newcastle upon Tyne, UK The bacterial phylum Bacteroidetes, characterized by a distinct gliding motility, occurs in a broad variety of ecosystems, habitats, life styles, and physiologies. Accordingly, taxonomic classification of the phylum, based on a limited number of features, proved difficult and controversial in the past, for example, when decisions were based on unresolved phylogenetic trees of the 16S rRNA gene sequence. Here we use a large collection of type-strain genomes from Bacteroidetes and closely related phyla for Edited by: assessing their taxonomy based on the principles of phylogenetic classification and Martin G. Klotz, Queens College, City University of trees inferred from genome-scale data. No significant conflict between 16S rRNA gene New York, USA and whole-genome phylogenetic analysis is found, whereas many but not all of the Reviewed by: involved taxa are supported as monophyletic groups, particularly in the genome-scale Eddie Cytryn, trees. Phenotypic and phylogenomic features support the separation of Balneolaceae Agricultural Research Organization, Israel as new phylum Balneolaeota from Rhodothermaeota and of Saprospiraceae as new John Phillip Bowman, class Saprospiria from Chitinophagia. -
1587715368 865 4.Pdf
Systematic and Applied Microbiology 42 (2019) 284–290 Contents lists available at ScienceDirect Systematic and Applied Microbiology jou rnal homepage: http://www.elsevier.com/locate/syapm Hymenobacter amundsenii sp. nov. resistant to ultraviolet radiation, ଝ,ଝଝ, isolated from regoliths in Antarctica a,∗,1 b,1 a b Ivo Sedlácekˇ , Roman Pantu˚ cekˇ , Stanislava Králová , Ivana Maslaˇ novᡠ, a a a,b a c Pavla Holochová , Eva Stankovᡠ, Veronika Vrbovská , Pavel Svecˇ , Hans-Jürgen Busse a Czech Collection of Microorganisms, Department of Experimental Biology, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic b Section of Molecular Biology, Department of Experimental Biology, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic c Institut für Mikrobiologie, Veterinärmedizinische Universität Wien, Veterinärplatz 1, A-1210 Wien, Austria a r a t i b s c l e i n f o t r a c t Article history: A group of thirteen bacterial strains was isolated from rock samples collected in a deglaciated northern Received 28 February 2018 part of James Ross Island, Antarctica. The cells were rod-shaped, Gram-stain-negative, non-motile, cata- Received in revised form lase positive, and produced moderately slimy, ultraviolet light (UVC)-irradiation-resistant and red–pink 27 November 2018 pigmented colonies on R2A agar. A polyphasic taxonomic approach based on 16S rRNA gene sequencing, Accepted 9 December 2018 extensive biotyping, fatty acid profile, chemotaxonomy analyses, and whole genome sequencing were applied in order to clarify the taxonomic position of these isolates. Phylogenetic analysis based on the 16S Keywords: rRNA gene indicated that all isolates constituted a coherent group belonging to the genus Hymenobacter. -
University of Florida Thesis Or Dissertation
BIOPRECIPITATION: THE CONNECTION BETWEEN MICROBIOLOGY AND METEOROLOGY By RACHEL ELAINE JOYCE A DISSERTATION PRESENTED TO THE GRADUATE SCHOOL OF THE UNIVERSITY OF FLORIDA IN PARTIAL FULFILLMENT OF THE REQUIREMENTS FOR THE DEGREE OF DOCTOR OF PHILOSOPHY UNIVERSITY OF FLORIDA 2020 © 2020 Rachel Joyce To Mom and Dad ACKNOWLEDGMENTS I want to first and foremost thank my advisor, Dr. Brent Christner, who has made this research possible. His mentorship and support gave me the confidence to carry out my dissertation research. Without a doubt, I would not be the scientist that I am today, with such an unwavering passion for scientific research, if I had not gotten the encouragement that I received from Dr. Christner, and for that I am incredibly grateful. I would also like to thank all of my committee members for agreeing to oversee my PhD and offering me guidance and advice: Dr. Bryan Kolaczkowski, Dr. Ana Conesa, and Dr. Corene Matyas. I want to acknowledge the friends who proved to be an incredible support system over the last six years: To James Ramsden, who has worked with me in the lab for over a year and is always willing to go above and beyond to get work done; To Christina Davis, who was my first friend and confidant at UF; and Rachel Moore, whose sheer excitement about bioaerosols and microbiology is enough to keep me going even on my worst days; To the ladies of LSU--Heather Lavender, Dr. Noelle Bryan, and Dr. Amanda Achberger—who even after four years of moving apart, are always there to offer me a shoulder to lean on; To my two biggest role models, my mom and dad, who showed me how far hard work and dedication can get you in life; To all three of my siblings, Alex, Chris, and Luke, because I love them more than anything; And to my rock, Christopher Wilson, who has kept me grounded and sane and smiling even through the toughest of times. -
Microbial Ecology, Biogeochemistry, and Signatures of Life at Low Temperature in Arctic Thermokarst Lake Sediments and High Sierra Snow Fields
University of Nevada, Reno Microbial Ecology, Biogeochemistry, and Signatures of Life at Low Temperature in Arctic Thermokarst Lake Sediments and High Sierra Snow Fields A dissertation submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy in Biochemistry by Paula B. Matheus Carnevali Dr. Alison Murray/Dissertation Advisor May, 2015 Copyright by Paula B. Matheus Carnevali 2015 All Rights Reserved THE GRADUATE SCHOOL We recommend that the dissertation prepared under our supervision by PAULA B. MATHEUS CARNEVALI Entitled Microbial Ecology, Biogeochemistry, And Signatures Of Life At Low Temperature In Arctic Thermokarst Lake Sediments And High Sierra Snow Fields be accepted in partial fulfillment of the requirements for the degree of DOCTOR OF PHILOSOPHY Alison E. Murray, Ph.D., Advisor Gary Blomquist, Ph.D., Committee Member David Shintani, Ph.D., Committee Member Henry Sun, Ph.D., Committee Member Kevin Hand, Ph.D., Committee Member Jerry Qualls, Ph.D., Graduate School Representative David W. Zeh, Ph. D., Dean, Graduate School May, 2015 i Abstract The subjects of biological methane (CH4) production and microbial community diversity and structure in extreme cold environments were at the core of this dissertation. CH4 is a potent greenhouse gas that contributes to the warming of the planet and has chemical properties that allow its detection by instruments that can go into space. In this sense, CH4 is also a biosignature, because its presence could be indicative of the presence of life. Mechanisms that lead to the formation of this gas on Earth include reactions mediated by biological enzymes that evolved early in life’s evolutionary time. -
Identificación Molecular De Bacterias Asociadas a La Filosfera De Plantas De Arroz (Oryza Sativa L), Mediante Técnicas De Cultivo Microbiano
Manglar 12(1): 25 - 36 Revista de Investigación Científica Universidad Nacional de Tumbes, Perú Identificación molecular de bacterias asociadas a la filosfera de plantas de arroz (Oryza sativa L), mediante técnicas de cultivo microbiano. Molecular identification of bacteria associated with the phyllosphere of rice plants (Oryza sativa L), through microbial culture techniques. Carlos Deza N.1, Dicson. Sánchez A2, Jean Silva A3, Ramón García1, Eric Mialhe2. Resumen Las plantas albergan una gran diversidad de microorganismos, como hongos, bacterias, etc., que interactúan con ella y tienen una funcionalidad que va desde la patogenicidad, hasta la protección de la misma. Se ha estudiado parte de esta diversidad microbiana a nivel de la filosfera en plantas de Oryza sativa (L) “arroz”; mediante microbiología molecular se ha caracterizado siete especies bacterianas entre las cuales sobresalieron especies Uncultured, es decir no cultivadas, además de Bacillus amyloliquefafaciens, Enterobacter asburiae, Klebsiella pneumoniae y Pantoea sp., todas ellas con un alto porcentaje de identidad; asimismo, mediante metagenómica dirigida se caracterizó trecientos ochenta y cinco especies bacterianas, de las que sobresalen pertenecen a los generos Bacillus, Rhizobium, Pseudomonas, Mycobacterium, Nocardioides, Clostridium, Methylobacterium y Pantoea. Las faamilias que más destacan son Enterobacteriaceae, Rhizobiaceae, Microbacteriaceae, Bacillaceae, Flavobacteriaceae, Pseudomonadaceae, Nocardiaceae, Mycobacteriaceae, Clostridiaceae y Methylobacteriaceae; no -
Pontibacter Indicus Sp. Nov., Isolated from Hexachlorocyclohexane-Contaminated Soil
International Journal of Systematic and Evolutionary Microbiology (2014), 64, 254–259 DOI 10.1099/ijs.0.055319-0 Pontibacter indicus sp. nov., isolated from hexachlorocyclohexane-contaminated soil Amit Kumar Singh,1 Nidhi Garg,1 Pushp Lata,1 Roshan Kumar,1 Vivek Negi,1 Surendra Vikram2 and Rup Lal1 Correspondence 1Molecular Biology Laboratory, Department of Zoology, University of Delhi, Delhi-110007, India Rup Lal 2IMTECH-Institute of Microbial Technology, Sector-39A, Chandigarh-160036, India [email protected] An orange-pigmented bacterial strain, designated LP100T, was isolated from hexachlorocyclohexane-contaminated soil (Lucknow, India). A neighbour-joining tree based on 16S rRNA gene sequences showed that strain LP100T occupied a distinct phylogenetic position in the Pontibacter species cluster, showing highest similarity with Pontibacter lucknowensis DM9T (97.4 %). Levels of similarity to strains of other Pontibacter species ranged between 94.0 and 96.8 %. Strain LP100T contained MK-7 as the predominant menaquinone and sym- homospermidine was the major polyamine in the cell. The major cellular fatty acids of strain T T LP100 were anteiso-C17 : 0 A, iso-C15 : 0 and iso-C18 : 1 H. The polar lipid profile of strain LP100 showed the presence of phosphatidylethanolamine, an unidentified aminophospholipid, three unknown aminolipids and two unknown polar lipids. The G+C content of strain LP100T was 58.2 mol%. The results of DNA–DNA hybridization, biochemical and physiological tests clearly distinguish the novel strain from closely related species of the genus Pontibacter. Therefore, strain LP100T represents a novel species of the genus Pontibacter for which the name Pontibacter indicus is proposed. The type strain is LP100T (5CCM8435T5MCC2027T). -
Genome-Based Taxonomic Classification of Bacteroidetes
Lawrence Berkeley National Laboratory Recent Work Title Genome-Based Taxonomic Classification of Bacteroidetes. Permalink https://escholarship.org/uc/item/2fs841cf Journal Frontiers in microbiology, 7(DEC) ISSN 1664-302X Authors Hahnke, Richard L Meier-Kolthoff, Jan P García-López, Marina et al. Publication Date 2016 DOI 10.3389/fmicb.2016.02003 Peer reviewed eScholarship.org Powered by the California Digital Library University of California ORIGINAL RESEARCH published: 20 December 2016 doi: 10.3389/fmicb.2016.02003 Genome-Based Taxonomic Classification of Bacteroidetes Richard L. Hahnke 1 †, Jan P. Meier-Kolthoff 1 †, Marina García-López 1, Supratim Mukherjee 2, Marcel Huntemann 2, Natalia N. Ivanova 2, Tanja Woyke 2, Nikos C. Kyrpides 2, 3, Hans-Peter Klenk 4 and Markus Göker 1* 1 Department of Microorganisms, Leibniz Institute DSMZ–German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany, 2 Department of Energy Joint Genome Institute (DOE JGI), Walnut Creek, CA, USA, 3 Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia, 4 School of Biology, Newcastle University, Newcastle upon Tyne, UK The bacterial phylum Bacteroidetes, characterized by a distinct gliding motility, occurs in a broad variety of ecosystems, habitats, life styles, and physiologies. Accordingly, taxonomic classification of the phylum, based on a limited number of features, proved difficult and controversial in the past, for example, when decisions were based on unresolved phylogenetic trees of the 16S rRNA gene sequence. Here we use a large collection of type-strain genomes from Bacteroidetes and closely related phyla for Edited by: assessing their taxonomy based on the principles of phylogenetic classification and Martin G. -
The Effect of Environmental Perturbations on the Plant Phyllosphere Microbiome
University of Mississippi eGrove Electronic Theses and Dissertations Graduate School 1-1-2018 The Effect of Environmental Perturbations on the Plant Phyllosphere Microbiome Bram W. Stone University of Mississippi Follow this and additional works at: https://egrove.olemiss.edu/etd Part of the Ecology and Evolutionary Biology Commons Recommended Citation Stone, Bram W., "The Effect of Environmental Perturbations on the Plant Phyllosphere Microbiome" (2018). Electronic Theses and Dissertations. 1356. https://egrove.olemiss.edu/etd/1356 This Dissertation is brought to you for free and open access by the Graduate School at eGrove. It has been accepted for inclusion in Electronic Theses and Dissertations by an authorized administrator of eGrove. For more information, please contact [email protected]. THE EFFECT OF ENVIRONMENTAL PERTURBATIONS ON THE PLANT PHYLLOSPHERE MICROBIOME A Dissertation Presented for the Degree of Doctor of Philosophy In the Department of Biology The University of Mississippi Bram Stone May 2018 Copyright © 2018 by Bram Stone All rights reserved ABSTRACT Applying ecological concepts to microbial communities has proved to be challenging, often revolving around the relative importance of stochastic and deterministic processes applied heterogeneously across the habitat in time or space. The phyllosphere is the aboveground surface of plants on which microbial communities, composed primarily of Bacteria, but also including Archaea and microbial eukaryotes, exist and is characterized by stochastic immigration balanced with strong selective forces. Variation in bacterial community composition was characterized across space and time, with special attention given to the exposure of phyllosphere communities to rain as a plausible mechanism of ecological disturbance. Bacterial communities were characterized through targeted Illumina sequencing of the 16S rRNA taxonomic marker gene.