The Two-Domain Tree of Life Is Linked to a New Root for the Archaea

Total Page:16

File Type:pdf, Size:1020Kb

The Two-Domain Tree of Life Is Linked to a New Root for the Archaea The two-domain tree of life is linked to a new root for the Archaea Kasie Raymanna, Céline Brochier-Armanetb, and Simonetta Gribaldoa,1 aInstitut Pasteur, Department of Microbiology, Unit Biologie Moléculaire du Gène chez les Extrêmophiles, 75015 Paris, France; and bUniversité de Lyon, Université Lyon 1, CNRS, UMR5558, Laboratoire de Biométrie et Biologie Evolutive, 69622 Villeurbanne, France Edited by W. Ford Doolittle, Dalhousie University, Halifax, NS, Canada, and approved April 17, 2015 (received for review November 02, 2014) One of the most fundamental questions in evolutionary biology is restricted taxonomic sampling, notably for the outgroup, may also the origin of the lineage leading to eukaryotes. Recent phyloge- generate or mask potential tree reconstruction artifacts (16). All nomic analyses have indicated an emergence of eukaryotes from these considerations emphasize that we have not yet found a way within the radiation of modern Archaea and specifically from a group out of the phylogenomic impasse caused by the use of universal comprising Thaumarchaeota/“Aigarchaeota” (candidate phylum)/ trees to investigate the relationships among Archaea and eu- Crenarchaeota/Korarchaeota (TACK). Despite their major im- karyotes (12). plications, these studies were all based on the reconstruction of Here, we have applied an original two-step strategy that we universal trees and left the exact placement of eukaryotes with re- proposed a few years ago which involves separately analyzing the spect to the TACK lineage unclear. Here we have applied an original markers shared between Archaea and eukaryotes and between two-step approach that involves the separate analysis of markers Archaea and Bacteria (12). This strategy allowed us to use a larger shared between Archaea and eukaryotes and between Archaea and taxonomic sampling, more markers and thus more positions, have Bacteria. This strategy allowed us to use a larger number of markers higher-quality alignments, and detect potential tree reconstruction and greater taxonomic coverage, obtain high-quality alignments, and artifacts more easily. With respect to previous analyses, we obtained alleviate tree reconstruction artifacts potentially introduced when phylogenies that are fully resolved and consistent between datasets analyzing the three domains simultaneously. Our results robustly in- and with the systematics of each domain, demonstrating the rele- dicate a sister relationship of eukaryotes with the TACK superphylum vance of our approach. Comparison of the results obtained from that is strongly associated with a distinct root of the Archaea that lies the Archaea/eukaryote (A/E) and the Archaea/Bacteria (A/B) within the Euryarchaeota, challenging the traditional topology of the datasets robustly indicates that eukaryotes are sister to the TACK archaeal tree. Therefore, if we are to embrace an archaeal origin for superphylum but also that this topology is strongly linked to a root eukaryotes, our view of the evolution of the third domain of life will for the tree of the Archaea lying within the Euryarchaeota. have to be profoundly reconsidered, as will many areas of investiga- This topology is in contrast to the traditional root between tion aimed at inferring ancestral characteristics of early life and Earth. Euryarchaeota and the TACK superphylum (17, 18), which we demonstrate as likely being the product of an artifact resulting methanogenesis | Tree of Life | ancient evolution | site-heterogeneous from the combination of noise introduced by fast-evolving posi- model | archaeal phylogeny tions and the use of an overly simplistic evolutionary model. s was suggested by a few early phylogenetic analyses (1–3), Results Aover the past five years a number of universal trees of life A/E Dataset. Universal trees obtained in previous analyses have rooted on the branch leading to Bacteria have supported an left the precise relationship of eukaryotes to the TACK superphylum emergence of eukaryotes from within the radiation of modern unclear (10). We sought to clarify this placement by assembling Archaea (4–11), with a specific link to a group comprising a large supermatrix of 72 markers shared between Archaea and Thaumarchaeota/“Aigarchaeota” (candidate phylum)/Cren- eukaryotes—the A/E dataset—totaling 17,892 amino acid positions archaeota/Korarchaeota (the TACK superphylum) (5). This finding has very important consequences, because it clearly defines Significance that an organism endowed with characteristics of a modern archaeon was the starting point for the process of eukaryogenesis An archaeal origin for eukaryotes is an exciting recent finding. (12, 13). Although these analyses used sophisticated approaches, Nevertheless, it has been based largely on the reconstruction of they were all based on the reconstruction of universal trees of universal trees. The use of an alternative strategy based on life and a restricted taxonomic sampling, in particular for the markers shared between Archaea and eukaryotes and Archaea bacterial outgroup. Moreover, these studies have left the and Bacteria bypasses potential problems linked to the analysis precise relationship of eukaryotes with the TACK lineages of the three domains simultaneously. Comparison of the unclear (10) and showed intradomain phylogenies that were phylogenies obtained by these two complementary sets of only partially resolved and often inconsistent between differ- markers supports a sister relationship between eukaryotes and ent analyses and with well-established relationships. In fact, the Thaumarchaeota/“Aigarchaeota” (candidate phylum)/Cren- analyzing the three domains at once reduces the number of archaeota/Korarchaeota lineage but also robustly indicates a markers and unambiguously aligned positions that can be used root of the tree of Archaea that challenges the traditional to- for phylogenetic reconstruction and may produce artifacts pology of this domain. This sensibly changes our perspective of because of the very large interdomain distances (14). Fur- the ancient evolution of the Archaea, early life, and Earth. thermore, the inclusion of very fast-evolving lineages may distort the phylogeny within each domain and bias the in- Author contributions: C.B.-A. and S.G. designed research; K.R. performed research; K.R., ference of interdomain relationships. Such is the case, for C.B.-A., and S.G. analyzed data; and K.R., C.B.-A., and S.G. wrote the paper. example, of the recently proposed archaeal superphylum The authors declare no conflict of interest. DPANN (Diapherotrites, Parvarchaeota, Aenigmarchaeota, This article is a PNAS Direct Submission. Nanohaloarchaeota, and Nanoarchaeota) (15), which has 1To whom correspondence should be addressed. Email: [email protected]. shown conflicting placements in recent universal trees (9, 11), This article contains supporting information online at www.pnas.org/lookup/suppl/doi:10. and may not even be monophyletic. Finally, the use of very 1073/pnas.1420858112/-/DCSupplemental. 6670–6675 | PNAS | May 26, 2015 | vol. 112 | no. 21 www.pnas.org/cgi/doi/10.1073/pnas.1420858112 Downloaded by guest on September 26, 2021 Candidatus Korarchaeum cryptofilum OPF8 KOR Physcomitrella patens Desulfurococcus kamchatkensis 1221n 1 1 Pyrolobus fumarii 1A Selaginella moellendorffii 1 Desulfurococcales VIRIDIPLANTAE Arabidopsis thaliana 1 1 Ignicoccus hospitalis KIN4_I 1 Metallosphaera sedula DSM 5348 Chlamydomonas reinhardtii 1 1 Sulfolobales Micromonas pusilla 1 1 Sulfolobus tokodaii str. 7 Dictyostelium discoideum 1 Thermofilum pendens Hrk 5 CREN Vulcanisaeta moutnovskia 768-28 AMOEBOZOA Monosiga brevicollis 1 1 1 Homo sapiens 1 Caldivirga maquilingensis IC-167 Thermoproteales 1 1 1 Thermoproteus tenax Kra 1 OPISTHOKONTA Saccharomyces cerevisiae 1 1 Pyrobaculum aerophilum str. IM2 Batrachochytrium dendrobatidis 0.98 Thalassiosira pseudonana Candidatus Caldiarchaeum subterraneum ‘AIG’ Phaeodactylum tricornutum 1 Candidatus Nitrosoarchaeum limnia SFB1 ALVEOLATA 1 1 1 Aureococcus anophagefferens 1 Nitrosopumilus maritimus SCM1 Nitrosopumilales STRAMENOPILES Paramecium tetraurelia 1 1 1 Cenarchaeum symbiosum A Cenarchaeales THAUM Tetrahymena thermophila 1 Candidatus Nitrososphaera gargensis Ga9.2 Thermococcus litoralis DSM 5473 Leishmania major 2.09 1 EUGLENOZOA 1 Thermococcus barophilus MP Trypanosoma brucei 1 1 Thermococcales Naegleria gruberi Pyrococcus yayanosil CH1 HETEROLOBOSEA 1 Pyrococcus abyssi GE5 Methanotorris igneus Kol 5 1 Methanococcus vannielii SB Methanococcales 1 Methanocaldococcus infernus ME 1 1 1 Methanocaldococcus jannaschii DSM 2661 Methanothermus fervidus DSM 2088 1 Methanobacterium sp. SWAN-1 1 Methanobrevibacter smithii ATCC 35061 Methanobacteriales 1 Methanothermobacter thermautotrophicus str. Delta H 1 Aciduliprofundum boonei T469 DHEV2 1 Ferroplasma acidarmanus fer1 1 Thermoplasmatales uncultured marine group II euryarchaeote Marine Group II 0.93 Candidatus Methanomethylophilus alvus Mx1201 EURY 1 Methanomassiliicoccus luminyensis Methanomassiliicoccales Ferroglobus placidus DSM 10642 1 1 Archaeoglobus veneficus SNP6 Archaeoglobales 1 Archaeoglobus profundus DSM 5631 1 Archaeoglobus fulgidus DSM 4304 Methanocorpusculum labreanum Z 1 Methanoregula boonei 6A8 Methanomicrobiales 1 1 1 Methanoculleus marisnigri JR1 Haloferax volcanii DS2 1 Natrialba magadii ATCC 43099 Halobacteriales 1 1 Haloarcula marismortui ATCC 43049 Methanococcoides burtonii DSM 6242 1 1 Methanosarcina mazei Go1 Methanosarcinales Methanosaeta harundinacea 6Ac 1 Methanocella arvoryzae MRE50
Recommended publications
  • Structural Characterization of Helicobacter Pylori Proteins Contributing to Stomach Colonization
    Università degli Studi di Padova Dipartimento di Biologia Scuola di Dottorato di Ricerca in Bioscienze e Biotecnologie Indirizzo: Biotecnologie Ciclo XXVIII STRUCTURAL CHARACTERIZATION OF HELICOBACTER PYLORI PROTEINS CONTRIBUTING TO STOMACH COLONIZATION Direttore della Scuola: Ch.mo Prof. Paolo Bernardi Coordinatore di Indirizzo: Ch.ma Prof.ssa Fiorella Lo Schiavo Supervisore: Ch.mo Prof. Giuseppe Zanotti Dottorando: Maria Elena Compostella 31 Gennaio 2016 Università degli Studi di Padova Department of Biology School of Biosciences and Biotechnology Curriculum: Biotechnology XXVIII Cycle STRUCTURAL CHARACTERIZATION OF HELICOBACTER PYLORI PROTEINS CONTRIBUTING TO STOMACH COLONIZATION Director of the Ph.D. School: Ch.mo Prof. Paolo Bernardi Coordinator of the Curriculum: Ch.ma Prof.ssa Fiorella Lo Schiavo Supervisor: Ch.mo Prof. Giuseppe Zanotti Ph.D. Candidate: Maria Elena Compostella 31 January 2016 Contents ABBREVIATIONS AND SYMBOLS IV SUMMARY 9 SOMMARIO 15 1. INTRODUCTION 21 1.1 HELICOBACTER PYLORI 23 1.2 GENETIC VARIABILITY 26 1.2.1 GENOME COMPARISON 26 1.2.1.1 HELICOBACTER PYLORI 26695 26 1.2.1.2 HELICOBACTER PYLORI J99 28 1.2.2 CORE GENOME 30 1.2.3 MECHANISMS GENERATING GENETIC VARIABILITY 31 1.2.3.1 MUTAGENESIS 32 1.2.3.2 RECOMBINATION 35 1.2.4 HELICOBACTER PYLORI AS A “QUASI SPECIES” 37 1.2.5 CLASSIFICATION OF HELICOBACTER PYLORI STRAINS 38 1.3 EPIDEMIOLOGY 40 1.3.1 INCIDENCE AND PREVALENCE OF HELICOBACTER PYLORI INFECTION 40 1.3.2 SOURCE AND TRANSMISSION 42 1.4 ADAPTATION AND GASTRIC COLONIZATION 47 1.4.1 ACID ADAPTATION 49 1.4.2 MOTILITY AND CHEMIOTAXIS 60 1.4.3 ADHESION 65 1.5 PATHOGENESIS AND VIRULENCE FACTORS 72 1.5.1 VACUOLATING CYTOTOXIN A 78 1.5.2 CAG PATHOGENICITY ISLAND AND CYTOTOXIN-ASSOCIATED GENE A 83 1.5.3 NEUTROPHIL-ACTIVATING PROTEIN 90 1.6 HELICOBACTER PYLORI AND GASTRODUODENAL DISEASES 92 1.7 ERADICATION AND POTENTIAL BENEFITS 97 2.
    [Show full text]
  • Leaf-Associated Shifts in Bacterial and Fungal Communities in Response to Chicken Rearing Under Moso Bamboo Forests in Subtropical China
    Article Leaf-Associated Shifts in Bacterial and Fungal Communities in Response to Chicken Rearing Under Moso Bamboo Forests in Subtropical China Xiaoping Zhang 1, Zheke Zhong 1,*, Xu Gai 1, Jiafu Ying 2, Weifen Li 2, Xuhua Du 1, Fangyuan Bian 1 and Chuanbao Yang 1 1 China National Bamboo Research Center, Key Laboratory of Resources and Utilization of Bamboo of State Forestry Administration, Hangzhou 310012, China; [email protected] (X.Z.); [email protected] (X.G.); [email protected] (X.D.); [email protected] (F.B.); [email protected] (C.Y.) 2 College of Animal Sciences, Zhejiang University, Hangzhou 310058, China; [email protected] (J.Y.); wfl[email protected] (W.L.) * Correspondence: [email protected]; Tel.: +86-0571-88860734 Received: 25 January 2019; Accepted: 25 February 2019; Published: 1 March 2019 Abstract: Integrated bamboo-chicken farming (BCF) systems are a traditional agroforestry pattern with large economic benefits in subtropical China. However, little is known regarding the effect of this integration on the bamboo leaf-associated microbiome, which can be very important for disease control and nutrient turnover. In the present study, we compared the leaf-associated bacterial and fungal communities of moso bamboo (Phyllostachys edulis) in a BCF system and an adjacent moso bamboo forest (MBF). The results showed that Cyanobacteria and Ascomycota were the predominant microbial phyla associated with bamboo leaves. Chicken farming under the bamboo forest significantly increased the bacterial and fungal alpha diversity (observed operational taxonomic units (OTUs) and Simpson’s index) associated with bamboo leaves. Principal components analysis (PCoA) further confirmed the shifts in the bacterial and fungal communities caused by chicken farming.
    [Show full text]
  • Genomics 98 (2011) 370–375
    Genomics 98 (2011) 370–375 Contents lists available at ScienceDirect Genomics journal homepage: www.elsevier.com/locate/ygeno Whole-genome comparison clarifies close phylogenetic relationships between the phyla Dictyoglomi and Thermotogae Hiromi Nishida a,⁎, Teruhiko Beppu b, Kenji Ueda b a Agricultural Bioinformatics Research Unit, Graduate School of Agricultural and Life Sciences, University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan b Life Science Research Center, College of Bioresource Sciences, Nihon University, Fujisawa, Japan article info abstract Article history: The anaerobic thermophilic bacterial genus Dictyoglomus is characterized by the ability to produce useful Received 2 June 2011 enzymes such as amylase, mannanase, and xylanase. Despite the significance, the phylogenetic position of Accepted 1 August 2011 Dictyoglomus has not yet been clarified, since it exhibits ambiguous phylogenetic positions in a single gene Available online 7 August 2011 sequence comparison-based analysis. The number of substitutions at the diverging point of Dictyoglomus is insufficient to show the relationships in a single gene comparison-based analysis. Hence, we studied its Keywords: evolutionary trait based on whole-genome comparison. Both gene content and orthologous protein sequence Whole-genome comparison Dictyoglomus comparisons indicated that Dictyoglomus is most closely related to the phylum Thermotogae and it forms a Bacterial systematics monophyletic group with Coprothermobacter proteolyticus (a constituent of the phylum Firmicutes) and Coprothermobacter proteolyticus Thermotogae. Our findings indicate that C. proteolyticus does not belong to the phylum Firmicutes and that the Thermotogae phylum Dictyoglomi is not closely related to either the phylum Firmicutes or Synergistetes but to the phylum Thermotogae. © 2011 Elsevier Inc.
    [Show full text]
  • Diversity of Understudied Archaeal and Bacterial Populations of Yellowstone National Park: from Genes to Genomes Daniel Colman
    University of New Mexico UNM Digital Repository Biology ETDs Electronic Theses and Dissertations 7-1-2015 Diversity of understudied archaeal and bacterial populations of Yellowstone National Park: from genes to genomes Daniel Colman Follow this and additional works at: https://digitalrepository.unm.edu/biol_etds Recommended Citation Colman, Daniel. "Diversity of understudied archaeal and bacterial populations of Yellowstone National Park: from genes to genomes." (2015). https://digitalrepository.unm.edu/biol_etds/18 This Dissertation is brought to you for free and open access by the Electronic Theses and Dissertations at UNM Digital Repository. It has been accepted for inclusion in Biology ETDs by an authorized administrator of UNM Digital Repository. For more information, please contact [email protected]. Daniel Robert Colman Candidate Biology Department This dissertation is approved, and it is acceptable in quality and form for publication: Approved by the Dissertation Committee: Cristina Takacs-Vesbach , Chairperson Robert Sinsabaugh Laura Crossey Diana Northup i Diversity of understudied archaeal and bacterial populations from Yellowstone National Park: from genes to genomes by Daniel Robert Colman B.S. Biology, University of New Mexico, 2009 DISSERTATION Submitted in Partial Fulfillment of the Requirements for the Degree of Doctor of Philosophy Biology The University of New Mexico Albuquerque, New Mexico July 2015 ii DEDICATION I would like to dedicate this dissertation to my late grandfather, Kenneth Leo Colman, associate professor of Animal Science in the Wool laboratory at Montana State University, who even very near the end of his earthly tenure, thought it pertinent to quiz my knowledge of oxidized nitrogen compounds. He was a man of great curiosity about the natural world, and to whom I owe an acknowledgement for his legacy of intellectual (and actual) wanderlust.
    [Show full text]
  • A Dicarboxylate/4-Hydroxybutyrate Autotrophic Carbon Assimilation Cycle in the Hyperthermophilic Archaeum Ignicoccus Hospitalis
    A dicarboxylate/4-hydroxybutyrate autotrophic carbon assimilation cycle in the hyperthermophilic Archaeum Ignicoccus hospitalis Harald Huber*†, Martin Gallenberger*, Ulrike Jahn*, Eva Eylert‡, Ivan A. Berg§, Daniel Kockelkorn§, Wolfgang Eisenreich‡, and Georg Fuchs§ *Lehrstuhl fu¨r Mikrobiologie und Archaeenzentrum, Universita¨t Regensburg, Universitaetsstrasse 31, D-93053 Regensburg, Germany; ‡Lehrstuhl fu¨r Biochemie, Department Chemie, Technische Universita¨t Mu¨ nchen, Lichtenbergstrasse 4, D-85748 Garching, Germany; and §Lehrstuhl fu¨r Mikrobiologie, Universita¨t Freiburg, Scha¨nzlestrasse 1, D-79104 Freiburg, Germany Edited by Dieter So¨ll, Yale University, New Haven, CT, and approved April 1, 2008 (received for review February 1, 2008) Ignicoccus hospitalis is an anaerobic, autotrophic, hyperthermophilic starting from acetyl-CoA (4). On the basis of these data, pyruvate Archaeum that serves as a host for the symbiotic/parasitic Archaeum synthase and phosphoenolpyruvate (PEP) carboxylase were pos- Nanoarchaeum equitans. It uses a yet unsolved autotrophic CO2 tulated as CO2 fixing enzymes, with PEP carboxylase serving as the fixation pathway that starts from acetyl-CoA (CoA), which is reduc- only enzyme used for oxaloacetate synthesis. In addition, the tively carboxylated to pyruvate. Pyruvate is converted to phosphoe- operation of an incomplete ‘‘horseshoe-type’’ citric acid cycle, in nol-pyruvate (PEP), from which glucogenesis as well as oxaloacetate which 2-oxoglutarate oxidation does not take place, was demon- formation branch off. Here, we present the complete metabolic cycle strated. Enzyme and labeling data indicated a conventional glu- by which the primary CO2 acceptor molecule acetyl-CoA is regener- coneogenesis, but with some enzymes unrelated to those of the ated. Oxaloacetate is reduced to succinyl-CoA by an incomplete classical pathway.
    [Show full text]
  • In Silico Evolutionary Analysis of Helicobacter Pylori Outer Membrane Phospholipase a (OMPLA) Hilde S Vollan1*, Tone Tannæs1, Yoshio Yamaoka2 and Geir Bukholm3,4
    Vollan et al. BMC Microbiology 2012, 12:206 http://www.biomedcentral.com/1471-2180/12/206 RESEARCH ARTICLE Open Access In silico evolutionary analysis of Helicobacter pylori outer membrane phospholipase A (OMPLA) Hilde S Vollan1*, Tone Tannæs1, Yoshio Yamaoka2 and Geir Bukholm3,4 Abstract Background: In the past decade, researchers have proposed that the pldA gene for outer membrane phospholipase A (OMPLA) is important for bacterial colonization of the human gastric ventricle. Several conserved Helicobacter pylori genes have distinct genotypes in different parts of the world, biogeographic patterns that can be analyzed through phylogenetic trees. The current study will shed light on the importance of the pldA gene in H. pylori. In silico sequence analysis will be used to investigate whether the bacteria are in the process of preserving, optimizing, or rejecting the pldA gene. The pldA gene will be phylogenetically compared to other housekeeping (HK) genes, and a possible origin via horizontal gene transfer (HGT) will be evaluated through both intra- and inter- species evolutionary analyses. Results: In this study, pldA gene sequences were phylogenetically analyzed and compared with a large reference set of concatenated HK gene sequences. A total of 246 pldA nucleotide sequences were used; 207 were from Norwegian isolates, 20 were from Korean isolates, and 19 were from the NCBI database. Best-fit evolutionary models were determined with MEGA5 ModelTest for the pldA (K80 + I + G) and HK (GTR + I + G) sequences, and maximum likelihood trees were constructed. Both HK and pldA genes showed biogeographic clustering. Horizontal gene transfer was inferred based on significantly different GC contents, the codon adaptation index, and a phylogenetic conflict between a tree of OMPLA protein sequences representing 171 species and a tree of the AtpA HK protein for 169 species.
    [Show full text]
  • Bacterial Community Structure in High-Arctic Snow and Freshwater As Revealed by Pyrosequencing of 16S Rrna Genes and Cultivation Annette K
    RESEARCH/REVIEW ARTICLE Bacterial community structure in High-Arctic snow and freshwater as revealed by pyrosequencing of 16S rRNA genes and cultivation Annette K. Møller,1 Ditte A. Søborg,1 Waleed Abu Al-Soud,2 Søren J. Sørensen2 & Niels Kroer1 1 Department of Environmental Science, Aarhus University, Frederiksborgvej 399, DK-4000 Roskilde, Denmark 2 Department of Biology, University of Copenhagen, Sølvgade 83H, DK-1307 K Copenhagen, Denmark Keywords Abstract Taxonomic diversity; microbial assemblages; bacterial density; DOC. The bacterial community structures in High-Arctic snow over sea ice and an ice-covered freshwater lake were examined by pyrosequencing of 16S rRNA Correspondence genes and 16S rRNA gene sequencing of cultivated isolates. Both the Niels Kroer, pyrosequence and cultivation data indicated that the phylogenetic composition Department of Environmental Science, of the microbial assemblages was different within the snow layers and between Aarhus University, snow and freshwater. The highest diversity was seen in snow. In the middle Frederiksborgvej 399, and top snow layers, , and dominated, DK-4000 Roskilde, Denmark. Proteobacteria Bacteroidetes Cyanobacteria E-mail: [email protected] although Actinobacteria and Firmicutes were relatively abundant also. High numbers of chloroplasts were also observed. In the deepest snow layer, large percentages of Firmicutes and Fusobacteria were seen. In freshwater, Bacter- oidetes, Actinobacteria and Verrucomicrobia were the most abundant phyla while relatively few Proteobacteria and Cyanobacteria were present. Possibly, light intensity controlled the distribution of the Cyanobacteria and algae in the snow while carbon and nitrogen fixed by these autotrophs in turn fed the heterotrophic bacteria. In the lake, a probable lower light input relative to snow resulted in low numbers of Cyanobacteria and chloroplasts and, hence, limited input of organic carbon and nitrogen to the heterotrophic bacteria.
    [Show full text]
  • Evolution Génomique Chez Les Bactéries Du Super Phylum Planctomycetes-Verrucomicrobiae-Chlamydia
    AIX-MARSEILLE UNIVERSITE FACULTE DE MEDECINE DE MARSEILLE ECOLE DOCTORALE : SCIENCE DE LA VIE ET DE LA SANTE THESE Présentée et publiquement soutenue devant LA FACULTE DE MEDECINE DE MARSEILLE Le 15 janvier 2016 Par Mme Sandrine PINOS Née à Saint-Gaudens le 09 octobre 1989 TITRE DE LA THESE: Evolution génomique chez les bactéries du super phylum Planctomycetes-Verrucomicrobiae-Chlamydia Pour obtenir le grade de DOCTORAT d'AIX-MARSEILLE UNIVERSITE Spécialité : Génomique et Bioinformatique Membres du jury de la Thèse: Pr Didier RAOULT .................................................................................Directeur de thèse Dr Pierre PONTAROTTI ....................................................................Co-directeur de thèse Pr Gilbert GREUB .............................................................................................Rapporteur Dr Pascal SIMONET............................................................................................Rapporteur Laboratoires d’accueil Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes – UMR CNRS 6236, IRD 198 I2M - UMR CNRS 7373 - EBM 1 Avant propos Le format de présentation de cette thèse correspond à une recommandation de la spécialité Maladies Infectieuses et Microbiologie, à l’intérieur du Master de Sciences de la Vie et de la Santé qui dépend de l’Ecole Doctorale des Sciences de la Vie de Marseille. Le candidat est amené à respecter des règles qui lui sont imposées et qui comportent un format de thèse utilisé dans le Nord de l’Europe permettant un meilleur rangement que les thèses traditionnelles. Par ailleurs, la partie introduction et bibliographie est remplacée par une revue envoyée dans un journal afin de permettre une évaluation extérieure de la qualité de la revue et de permettre à l’étudiant de le commencer le plus tôt possible une bibliographie exhaustive sur le domaine de cette thèse. Par ailleurs, la thèse est présentée sur article publié, accepté ou soumis associé d’un bref commentaire donnant le sens général du travail.
    [Show full text]
  • Table S4. Phylogenetic Distribution of Bacterial and Archaea Genomes in Groups A, B, C, D, and X
    Table S4. Phylogenetic distribution of bacterial and archaea genomes in groups A, B, C, D, and X. Group A a: Total number of genomes in the taxon b: Number of group A genomes in the taxon c: Percentage of group A genomes in the taxon a b c cellular organisms 5007 2974 59.4 |__ Bacteria 4769 2935 61.5 | |__ Proteobacteria 1854 1570 84.7 | | |__ Gammaproteobacteria 711 631 88.7 | | | |__ Enterobacterales 112 97 86.6 | | | | |__ Enterobacteriaceae 41 32 78.0 | | | | | |__ unclassified Enterobacteriaceae 13 7 53.8 | | | | |__ Erwiniaceae 30 28 93.3 | | | | | |__ Erwinia 10 10 100.0 | | | | | |__ Buchnera 8 8 100.0 | | | | | | |__ Buchnera aphidicola 8 8 100.0 | | | | | |__ Pantoea 8 8 100.0 | | | | |__ Yersiniaceae 14 14 100.0 | | | | | |__ Serratia 8 8 100.0 | | | | |__ Morganellaceae 13 10 76.9 | | | | |__ Pectobacteriaceae 8 8 100.0 | | | |__ Alteromonadales 94 94 100.0 | | | | |__ Alteromonadaceae 34 34 100.0 | | | | | |__ Marinobacter 12 12 100.0 | | | | |__ Shewanellaceae 17 17 100.0 | | | | | |__ Shewanella 17 17 100.0 | | | | |__ Pseudoalteromonadaceae 16 16 100.0 | | | | | |__ Pseudoalteromonas 15 15 100.0 | | | | |__ Idiomarinaceae 9 9 100.0 | | | | | |__ Idiomarina 9 9 100.0 | | | | |__ Colwelliaceae 6 6 100.0 | | | |__ Pseudomonadales 81 81 100.0 | | | | |__ Moraxellaceae 41 41 100.0 | | | | | |__ Acinetobacter 25 25 100.0 | | | | | |__ Psychrobacter 8 8 100.0 | | | | | |__ Moraxella 6 6 100.0 | | | | |__ Pseudomonadaceae 40 40 100.0 | | | | | |__ Pseudomonas 38 38 100.0 | | | |__ Oceanospirillales 73 72 98.6 | | | | |__ Oceanospirillaceae
    [Show full text]
  • Supplemental Material S1.Pdf
    Phylogeny of Selenophosphate synthetases (SPS) Supplementary Material S1 ! SelD in prokaryotes! ! ! SelD gene finding in sequenced prokaryotes! We downloaded a total of 8263 prokaryotic genomes from NCBI (see Supplementary Material S7). We scanned them with the program selenoprofiles (Mariotti 2010, http:// big.crg.cat/services/selenoprofiles) using two SPS-family profiles, one prokaryotic (seld) and one mixed eukaryotic-prokaryotic (SPS). Selenoprofiles removes overlapping predictions from different profiles, keeping only the prediction from the profile that seems closer to the candidate sequence. As expected, the great majority of output predictions in prokaryotic genomes were from the seld profile. We will refer to the prokaryotic SPS/SelD !genes as SelD, following the most common nomenclature in literature.! To be able to inspect results by hand, and also to focus on good-quality genomes, we considered a reduced set of species. We took the prok_reference_genomes.txt list from ftp://ftp.ncbi.nlm.nih.gov/genomes/GENOME_REPORTS/, which NCBI claims to be a "small curated subset of really good and scientifically important prokaryotic genomes". We named this the prokaryotic reference set (223 species - see Supplementary Material S8). We manually curated most of the analysis in this set, while we kept automatized the !analysis on the full set.! We detected SelD proteins in 58 genomes (26.0%) in the prokaryotic reference set (figure 1 in main paper), which become 2805 (33.9%) when considering the prokaryotic full set (figure SM1.1). The difference in proportion between the two sets is due largely to the presence of genomes of very close strains in the full set, which we consider redundant.
    [Show full text]
  • Deinococcus Antarcticus Sp. Nov., Isolated from Soil
    International Journal of Systematic and Evolutionary Microbiology (2015), 65, 331–335 DOI 10.1099/ijs.0.066324-0 Deinococcus antarcticus sp. nov., isolated from soil Ning Dong,1,2 Hui-Rong Li,1 Meng Yuan,1,2 Xiao-Hua Zhang2 and Yong Yu1 Correspondence 1SOA Key Laboratory for Polar Science, Polar Research Institute of China, Shanghai 200136, Yong Yu PR China [email protected] 2College of Marine Life Sciences, Ocean University of China, Qingdao 266003, PR China A pink-pigmented, non-motile, coccoid bacterial strain, designated G3-6-20T, was isolated from a soil sample collected in the Grove Mountains, East Antarctica. This strain was resistant to UV irradiation (810 J m”2) and slightly more sensitive to desiccation as compared with Deinococcus radiodurans. Phylogenetic analyses based on the 16S rRNA gene sequence of the isolate indicated that the organism belongs to the genus Deinococcus. Highest sequence similarities were with Deinococcus ficus CC-FR2-10T (93.5 %), Deinococcus xinjiangensis X-82T (92.8 %), Deinococcus indicus Wt/1aT (92.5 %), Deinococcus daejeonensis MJ27T (92.3 %), Deinococcus wulumuqiensis R-12T (92.3 %), Deinococcus aquaticus PB314T (92.2 %) and T Deinococcus radiodurans DSM 20539 (92.2 %). Major fatty acids were C18 : 1v7c, summed feature 3 (C16 : 1v7c and/or C16 : 1v6c), anteiso-C15 : 0 and C16 : 0. The G+C content of the genomic DNA of strain G3-6-20T was 63.1 mol%. Menaquinone 8 (MK-8) was the predominant respiratory quinone. Based on its phylogenetic position, and chemotaxonomic and phenotypic characteristics, strain G3-6-20T represents a novel species of the genus Deinococcus, for which the name Deinococcus antarcticus sp.
    [Show full text]
  • Novel Insights Into the Thaumarchaeota in the Deepest Oceans: Their Metabolism and Potential Adaptation Mechanisms
    Zhong et al. Microbiome (2020) 8:78 https://doi.org/10.1186/s40168-020-00849-2 RESEARCH Open Access Novel insights into the Thaumarchaeota in the deepest oceans: their metabolism and potential adaptation mechanisms Haohui Zhong1,2, Laura Lehtovirta-Morley3, Jiwen Liu1,2, Yanfen Zheng1, Heyu Lin1, Delei Song1, Jonathan D. Todd3, Jiwei Tian4 and Xiao-Hua Zhang1,2,5* Abstract Background: Marine Group I (MGI) Thaumarchaeota, which play key roles in the global biogeochemical cycling of nitrogen and carbon (ammonia oxidizers), thrive in the aphotic deep sea with massive populations. Recent studies have revealed that MGI Thaumarchaeota were present in the deepest part of oceans—the hadal zone (depth > 6000 m, consisting almost entirely of trenches), with the predominant phylotype being distinct from that in the “shallower” deep sea. However, little is known about the metabolism and distribution of these ammonia oxidizers in the hadal water. Results: In this study, metagenomic data were obtained from 0–10,500 m deep seawater samples from the Mariana Trench. The distribution patterns of Thaumarchaeota derived from metagenomics and 16S rRNA gene sequencing were in line with that reported in previous studies: abundance of Thaumarchaeota peaked in bathypelagic zone (depth 1000–4000 m) and the predominant clade shifted in the hadal zone. Several metagenome-assembled thaumarchaeotal genomes were recovered, including a near-complete one representing the dominant hadal phylotype of MGI. Using comparative genomics, we predict that unexpected genes involved in bioenergetics, including two distinct ATP synthase genes (predicted to be coupled with H+ and Na+ respectively), and genes horizontally transferred from other extremophiles, such as those encoding putative di-myo-inositol-phosphate (DIP) synthases, might significantly contribute to the success of this hadal clade under the extreme condition.
    [Show full text]