DOCSLIB.ORG

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

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
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 30, 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
Load more

Recommended publications
  • 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]
  • 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]
  • Within-Arctic Horizontal Gene Transfer As a Driver of Convergent Evolution in Distantly Related 2 Microalgae
    bioRxiv preprint doi: https://doi.org/10.1101/2021.07.31.454568; this version posted August 2, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. 1 Within-Arctic horizontal gene transfer as a driver of convergent evolution in distantly related 2 microalgae 3 Richard G. Dorrell*+1,2, Alan Kuo3*, Zoltan Füssy4, Elisabeth Richardson5,6, Asaf Salamov3, Nikola 4 Zarevski,1,2,7 Nastasia J. Freyria8, Federico M. Ibarbalz1,2,9, Jerry Jenkins3,10, Juan Jose Pierella 5 Karlusich1,2, Andrei Stecca Steindorff3, Robyn E. Edgar8, Lori Handley10, Kathleen Lail3, Anna Lipzen3, 6 Vincent Lombard11, John McFarlane5, Charlotte Nef1,2, Anna M.G. Novák Vanclová1,2, Yi Peng3, Chris 7 Plott10, Marianne Potvin8, Fabio Rocha Jimenez Vieira1,2, Kerrie Barry3, Joel B. Dacks5, Colomban de 8 Vargas2,12, Bernard Henrissat11,13, Eric Pelletier2,14, Jeremy Schmutz3,10, Patrick Wincker2,14, Chris 9 Bowler1,2, Igor V. Grigoriev3,15, and Connie Lovejoy+8 10 11 1 Institut de Biologie de l'ENS (IBENS), Département de Biologie, École Normale Supérieure, CNRS, 12 INSERM, Université PSL, 75005 Paris, France 13 2CNRS Research Federation for the study of Global Ocean Systems Ecology and Evolution, 14 FR2022/Tara Oceans GOSEE, 3 rue Michel-Ange, 75016 Paris, France 15 3 US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, 1 16 Cyclotron Road, Berkeley,
    [Show full text]
  • A Korarchaeal Genome Reveals Insights Into the Evolution of the Archaea
    A korarchaeal genome reveals insights into the evolution of the Archaea James G. Elkinsa,b, Mircea Podarc, David E. Grahamd, Kira S. Makarovae, Yuri Wolfe, Lennart Randauf, Brian P. Hedlundg, Ce´ line Brochier-Armaneth, Victor Kunini, Iain Andersoni, Alla Lapidusi, Eugene Goltsmani, Kerrie Barryi, Eugene V. Koonine, Phil Hugenholtzi, Nikos Kyrpidesi, Gerhard Wannerj, Paul Richardsoni, Martin Kellerc, and Karl O. Stettera,k,l aLehrstuhl fu¨r Mikrobiologie und Archaeenzentrum, Universita¨t Regensburg, D-93053 Regensburg, Germany; cBiosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831; dDepartment of Chemistry and Biochemistry, University of Texas, Austin, TX 78712; eNational Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894; fDepartment of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520; gSchool of Life Sciences, University of Nevada, Las Vegas, NV 89154; hLaboratoire de Chimie Bacte´rienne, Unite´ Propre de Recherche 9043, Centre National de la Recherche Scientifique, Universite´de Provence Aix-Marseille I, 13331 Marseille Cedex 3, France; iU.S. Department of Energy Joint Genome Institute, Walnut Creek, CA 94598; jInstitute of Botany, Ludwig Maximilians University of Munich, D-80638 Munich, Germany; and kInstitute of Geophysics and Planetary Physics, University of California, Los Angeles, CA 90095 Communicated by Carl R. Woese, University of Illinois at Urbana–Champaign, Urbana, IL, April 2, 2008 (received for review January 7, 2008) The candidate division Korarchaeota comprises a group of uncul- and sediment samples from Obsidian Pool as an inoculum. The tivated microorganisms that, by their small subunit rRNA phylog- cultivation system supported the stable growth of a mixed commu- eny, may have diverged early from the major archaeal phyla nity of hyperthermophilic bacteria and archaea including an or- Crenarchaeota and Euryarchaeota.
    [Show full text]
  • Archaea and the Origin of Eukaryotes
    REVIEWS Archaea and the origin of eukaryotes Laura Eme, Anja Spang, Jonathan Lombard, Courtney W. Stairs and Thijs J. G. Ettema Abstract | Woese and Fox’s 1977 paper on the discovery of the Archaea triggered a revolution in the field of evolutionary biology by showing that life was divided into not only prokaryotes and eukaryotes. Rather, they revealed that prokaryotes comprise two distinct types of organisms, the Bacteria and the Archaea. In subsequent years, molecular phylogenetic analyses indicated that eukaryotes and the Archaea represent sister groups in the tree of life. During the genomic era, it became evident that eukaryotic cells possess a mixture of archaeal and bacterial features in addition to eukaryotic-specific features. Although it has been generally accepted for some time that mitochondria descend from endosymbiotic alphaproteobacteria, the precise evolutionary relationship between eukaryotes and archaea has continued to be a subject of debate. In this Review, we outline a brief history of the changing shape of the tree of life and examine how the recent discovery of a myriad of diverse archaeal lineages has changed our understanding of the evolutionary relationships between the three domains of life and the origin of eukaryotes. Furthermore, we revisit central questions regarding the process of eukaryogenesis and discuss what can currently be inferred about the evolutionary transition from the first to the last eukaryotic common ancestor. Sister groups Two descendants that split The pioneering work by Carl Woese and colleagues In this Review, we discuss how culture- independent from the same node; the revealed that all cellular life could be divided into three genomics has transformed our understanding of descendants are each other’s major evolutionary lines (also called domains): the archaeal diversity and how this has influenced our closest relative.
    [Show full text]
  • Life in Extreme Heat
    THERMOPHILES Thermophiles, or heat-loving microscopic organisms, are nourished by the extreme habitat at hydrothermal features in Yellowstone National Park. They also color hydrothermal features shown here at Clepsydra Geyser. Life in Extreme Heat The hydrothermal features of Yellowstone are enough to blister your skin. Some create layers that magnificent evidence of Earth’s volcanic activity. look like molten wax on the surface of steaming Amazingly, they are also habitats in which micro- alkaline pools. Still others, apparent to us through scopic organisms called thermophiles—“thermo” for the odors they create, exist only in murky, sulfuric heat, “phile” for lover—survive and thrive. caldrons that stink worse than rotten eggs. Grand Prismatic Spring at Midway Geyser Basin Today, many scientists study Yellowstone’s ther- is an outstanding example of this dual characteristic. mophiles. Some of these microbes are similar to the Visitors marvel at its size and brilliant colors. The boardwalk crosses a vast habitat for thermophiles. Nourished by energy and chemical building blocks Words to Know available in the hot springs, microbes construct Extremophile: A microorganism living in extreme vividly colored communities. Living with these conditions such as heat and acid, that cannot survive without these conditions. microscopic life forms are larger examples of life in extreme environments, such as mites, flies, spiders, Thermophile: Heat-loving extremophile. and plants. Microorganism: Single- or multi-celled organism of microscopic or submicroscopic size. Also called a microbe. For thousands of years, people have likely won- dered about these extreme habitats. The color of Microbes in Yellowstone: In addition to the thermophilic microorganisms, millions of other microbes thrive in Yellowstone’s superheated environments certainly Yellowstone’s soils, streams, rivers, lakes, vegetation, and caused geologist Walter Harvey Weed to pause, think, animals.
    [Show full text]
  • Across Bacterial Phyla, Distantly-Related Genomes with Similar Genomic GC Content Have Similar Patterns of Amino Acid Usage
    University of South Carolina Scholar Commons Faculty Publications Biological Sciences, Department of 3-10-2011 Across Bacterial Phyla, Distantly-Related Genomes with Similar Genomic GC Content Have Similar Patterns of Amino Acid Usage John Lightfield Noah R. Fram Bert Ely University of South Carolina - Columbia, [email protected] Follow this and additional works at: https://scholarcommons.sc.edu/biol_facpub Part of the Biology Commons Publication Info Published in PLoS ONE, Volume 6, Issue 3, 2011, pages e17677-. © 2011 Lightfield et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. This Article is brought to you by the Biological Sciences, Department of at Scholar Commons. It has been accepted for inclusion in Faculty Publications by an authorized administrator of Scholar Commons. For more information, please contact [email protected]. Across Bacterial Phyla, Distantly-Related Genomes with Similar Genomic GC Content Have Similar Patterns of Amino Acid Usage John Lightfield¤a, Noah R. Fram¤b, Bert Ely* Department of Biological Sciences, University of South Carolina, Columbia, South Carolina, United States of America Abstract The GC content of bacterial genomes ranges from 16% to 75% and wide ranges of genomic GC content are observed within many bacterial phyla, including both Gram negative and Gram positive phyla. Thus, divergent genomic GC content has evolved repeatedly in widely separated bacterial taxa. Since genomic GC content influences codon usage, we examined codon usage patterns and predicted protein amino acid content as a function of genomic GC content within eight different phyla or classes of bacteria.
    [Show full text]
  • Comparative Analyses of Whole-Genome Protein Sequences
    www.nature.com/scientificreports OPEN Comparative analyses of whole- genome protein sequences from multiple organisms Received: 7 June 2017 Makio Yokono 1,2, Soichirou Satoh3 & Ayumi Tanaka1 Accepted: 16 April 2018 Phylogenies based on entire genomes are a powerful tool for reconstructing the Tree of Life. Several Published: xx xx xxxx methods have been proposed, most of which employ an alignment-free strategy. Average sequence similarity methods are diferent than most other whole-genome methods, because they are based on local alignments. However, previous average similarity methods fail to reconstruct a correct phylogeny when compared against other whole-genome trees. In this study, we developed a novel average sequence similarity method. Our method correctly reconstructs the phylogenetic tree of in silico evolved E. coli proteomes. We applied the method to reconstruct a whole-proteome phylogeny of 1,087 species from all three domains of life, Bacteria, Archaea, and Eucarya. Our tree was automatically reconstructed without any human decisions, such as the selection of organisms. The tree exhibits a concentric circle-like structure, indicating that all the organisms have similar total branch lengths from their common ancestor. Branching patterns of the members of each phylum of Bacteria and Archaea are largely consistent with previous reports. The topologies are largely consistent with those reconstructed by other methods. These results strongly suggest that this approach has sufcient taxonomic resolution and reliability to infer phylogeny, from phylum to strain, of a wide range of organisms. Te reconstruction of phylogenetic trees is a powerful tool for understanding organismal evolutionary processes. Molecular phylogenetic analysis using ribosomal RNA (rRNA) clarifed the phylogenetic relationship of the three domains, bacterial, archaeal, and eukaryotic1.
    [Show full text]
  • Antibus Revised Thesis 11-16 For
    Molecular and Cultivation-based Characterization of Ancient Algal Mats from the McMurdo Dry Valleys, Antarctica A thesis submitted to Kent State University in partial fulfillment of the requirements for the degree of Master of Science by Doug Antibus December, 2009 Thesis written by Doug Antibus B.S., Kent State University, 2007 M.S., Kent State University, 2009 Approved by Dr. Christopher B. Blackwood Advisor Dr. James L. Blank Chair, Department of Biological Sciences Dr. Timothy Moerland Dean, College of Arts and Sciences iii TABLE OF CONTENTS LIST OF TABLES………………………………………………………………………..iv LIST OF FIGURES ……………………………………………………………………...vi ACKNOWLEDGEMENTS…………………………………………………………......viii CHAPTER I: General Introduction……………………………………………………….1 CHAPTER II: Molecular Characterization of Ancient Algal Mats from the McMurdo Dry Valleys, Antarctica: A Legacy of Genetic Diversity Introduction……………………………………………………………....22 Results and Discussion……………………………………………..……27 Methods…………………………………………………………………..51 Literature Cited…………………………………………………………..59 CHAPTER III: Recovery of Viable Bacteria from Ancient Algal Mats from the McMurdo Dry Valleys, Antarctica Introduction………………………………………………..……………..78 Methods…………………………………………………………………..80 Results……………………………………………………………...…….88 Discussion…………………………………………………………...….106 Literature Cited………………………………………………………....109 CHAPTER IV: General Discussion…………………………………………………….120 iii LIST OF TABLES Chapter II: Molecular Characterization of Ancient Algal Mats from the McMurdo Dry Valleys, Antarctica: A Legacy of Genetic Diversity
    [Show full text]
  • Kineococcus Vitellinus Sp. Nov., Kineococcus Indalonis Sp
    microorganisms Article Kineococcus vitellinus sp. nov., Kineococcus indalonis sp. nov. and Kineococcus siccus sp. nov., Isolated Nearby the Tabernas Desert (Almería, Spain) Esther Molina-Menor 1, Helena Gimeno-Valero 2, Javier Pascual 2 , Juli Peretó 1,2,3 and Manuel Porcar 1,2,* 1 Institute for Integrative Systems Biology I2SysBio (Universitat de València-CSIC), Calle del Catedràtic Agustin Escardino Benlloch 9, 46980 Paterna, Spain; [email protected] (E.M.-M.); [email protected] (J.P.) 2 Darwin Bioprospecting Excellence SL. Parc Científic Universitat de València, Calle del Catedràtic Agustin Escardino Benlloch 9, 46980 Paterna, Spain; [email protected] (H.G.-V.); [email protected] (J.P.) 3 Departament de Bioquimica i Biologia Molecular, Universitat de València, Calle del Dr. Moliner 50, 46100 Burjassot, Spain * Correspondence: [email protected] Received: 31 August 2020; Accepted: 2 October 2020; Published: 7 October 2020 Abstract: Three novel Gram-positive, aerobic, chemoheterotrophic, motile, non-endospore-forming, orange-pigmented bacteria designated strains T13T, T90T and R8T were isolated from the Tabernas Desert biocrust (Almería, Spain). Cells of the three strains were coccus-shaped and occurred singly, in pairs or clusters. The three strains were oxidase-negative and catalase-positive, and showed a mesophilic, neutrophilic and non-halophilic metabolism. Based on the 16S rRNA gene sequences, the closest neighbours of strains T13T, T90T and R8T were Kineococcus aurantiacus IFO 15268T, Kineococcus gypseus YIM 121300T and Kineococcus radiotolerans SRS 30216T (98.5%, 97.1% and 97.9% gene sequence similarity, respectively). The genomes were sequenced, and have been deposited in the GenBank/EMBL/DDBJ databases under the accession numbers JAAALL000000000, JAAALM000000000 and JAAALN000000000, respectively, for strains T13T, T90T and R8T.
    [Show full text]
  • Human Milk Microbiota Profiles in Relation to Birthing Method, Gestation and Infant Gender Camilla Urbaniak1,2, Michelle Angelini3, Gregory B
    Urbaniak et al. Microbiome (2016) 4:1 DOI 10.1186/s40168-015-0145-y RESEARCH Open Access Human milk microbiota profiles in relation to birthing method, gestation and infant gender Camilla Urbaniak1,2, Michelle Angelini3, Gregory B. Gloor4 and Gregor Reid1,2* Abstract Background: Human milk is an important source of bacteria for the developing infant and has been shown to influence the bacterial composition of the neonate, which in turn can affect disease risk later in life. Very little is known about what factors shape the human milk microbiome. The goal of the present study was to examine the milk microbiota from a range of women who delivered vaginally or by caesarean (C) section, who gave birth to males or females, at term or preterm. Methods: Milk was collected from 39 Caucasian Canadian women, and microbial profiles were analyzed by 16S ribosomal RNA (rRNA) sequencing using the Illumina platform. Results: A diverse community of milk bacteria was found with the most dominant phyla being Proteobacteria and Firmicutes and at the genus level, Staphylococcus, Pseudomonas, Streptococcus and Lactobacillus. Comparison of bacterial profiles between preterm and term births, C section (elective and non-elective) and vaginal deliveries, and male and female infants showed no statistically significant differences. Conclusions: The study revealed the diverse bacterial types transferred to newborns. We postulate that there may be a fail-safe mechanism whereby the mother is “ready” to pass along her bacterial imprint irrespective of when and how the baby is born. Keywords: Human milk, Milk microbiota, Factors affecting the milk microbiota Background levels of Bifidobacterium in human milk correlate with With the incidence of various non-infectious diseases on low levels of Bifidobacterium in the neonatal gut [3], the rise, there is much interest in the developmental ori- allowing for higher than normal levels of Bacteroides to gins of health and disease and the potential role of early be established [4].
    [Show full text]
  • Chapter 4: PROKARYOTIC DIVERSITY
    Chapter 4: PROKARYOTIC DIVERSITY 1. Prokaryote Habitats, Relationships & Biomes 2. Proteobacteria 3. Gram-negative and Phototropic Non-Proteobacteria 4. Gram-Positive Bacteria 5. Deeply Branching Bacteria 6. Archaea 1. Prokaryote Habitats, Relationships & Biomes Important Metabolic Terminology Oxygen tolerance/usage: aerobic – requires or can use oxygen (O2) anaerobic – does not require or cannot tolerate O2 Energy usage: phototroph – uses light as an energy source • all photosynthetic organisms chemotroph – acquires energy from organic or inorganic molecules • organotrophs – get energy from organic molecules • lithotrophs – get energy from inorganic molecules …more Important Terminology Carbon Source: autotroph – uses CO2 as a carbon source • e.g., photoautotrophs or chemoautotrophs heterotroph – requires an organic carbon source • e.g., chemoheterotroph – gets energy & carbon from organic molecules Oligotrophs require few nutrients, the opposite of eutrophs or copiotrophs Facultative vs Obligate (or Strict): facultative – “able to, but not requiring” • e.g., facultative anaerobes can survive w/ or w/o O2 obligate – “absolutely requires” • e.g., obligate anaerobes cannot survive in O2 Symbiotic Relationships Symbiotic relationships (close, direct interactions) between different organisms in nature are of several types: • e.g., humans have beneficial bacteria in their digestive tracts that also benefit from the food we eat (mutualism) Microbiomes All the microorganisms that inhabit a particular organism or environment (e.g., human or
    [Show full text]