DOCSLIB.ORG

Appl. Environ. Microbiol. 62:1171–1177

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Appl. Environ. Microbiol. 62:1171–1177 16S rRNA Phylogenetic Investigation of the Candidate Division "Korarchaeota" The Harvard community has made this article openly available. Please share how this access benefits you. Your story matters Citation Auchtung, T. A., C. D. Takacs-Vesbach, and C. M. Cavanaugh. 2006. “16S rRNA Phylogenetic Investigation of the Candidate Division ‘Korarchaeota.’” Applied and Environmental Microbiology 72 (7) (July 1): 5077–5082. doi:10.1128/aem.00052-06. Published Version doi:10.1128/AEM.00052-06 Citable link http://nrs.harvard.edu/urn-3:HUL.InstRepos:14368993 Terms of Use This article was downloaded from Harvard University’s DASH repository, and is made available under the terms and conditions applicable to Other Posted Material, as set forth at http:// nrs.harvard.edu/urn-3:HUL.InstRepos:dash.current.terms-of- use#LAA APPLIED AND ENVIRONMENTAL MICROBIOLOGY, July 2006, p. 5077–5082 Vol. 72, No. 7 0099-2240/06/$08.00ϩ0 doi:10.1128/AEM.00052-06 Copyright © 2006, American Society for Microbiology. All Rights Reserved. 16S rRNA Phylogenetic Investigation of the Candidate Division “Korarchaeota” Thomas A. Auchtung,1 Cristina D. Takacs-Vesbach,2 and Colleen M. Cavanaugh1* Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts 02138,1 and Department of Biology, University of New Mexico, Albuquerque, New Mexico 871312 Received 9 January 2006/Accepted 15 April 2006 The environmental distribution and phylogeny of “Korarchaeota,” a proposed ancient archaeal division, was investigated by using the 16S rRNA gene framework. Korarchaeota-specific primers were designed based on previously published sequences and used to screen a variety of environments. Korarchaeota 16S rRNA genes were amplified exclusively from high temperature Yellowstone National Park hot springs and a 9°N East Pacific Downloaded from Rise deep-sea hydrothermal vent. Phylogenetic analyses of these and all available sequences suggest that Korarchaeota exhibit a high level of endemicity. In 1994, 16S rRNA gene sequences PCR amplified from for Korarchaeota. Samples, collected from the 9°N East Pacific Yellowstone National Park hot spring Obsidian Pool were Rise (EPR) 2,500-m-deep hydrothermal field in December reported (3). These sequences were hypothesized to belong to 2002 using DSV Alvin on R/V Atlantis cruise AT-07, Leg 26, an ancient division, the “Korarchaeota,” that diverged from the were from the following environments: the dark red surface of http://aem.asm.org/ Archaea lineage before the separation of Crenarchaeota and a black smoker sulfide chimney through which 370°C fluid Euryarchaeota (2). Other deeply branching clades have since flowed (P-vent; Dive 3851), a basalt settlement piece (FRIE been proposed, including the Nanoarchaeota and “Ancient Ar- 16.2) left by an active sulfide chimney for 1 week (Tica vent; chaeal Group,” although phylogenetic support for any group Dives 3843 and 3849), and a 0.45-␮m-pore-size, 142-mm-diam- having a basal position is not strong (2, 4, 29). What little is eter mixed cellulose ester filter (Millipore) and a 1-␮m-pore-size, known about Korarchaeota comes from detection of their 16S 142-mm-diameter Petex prefilter (Sefar) through which 200 liters rRNA genes during environmental diversity surveys that used of water 1 m peripheral to a hydrothermal vent was filtered by “universal” Archaea primers. Nineteen such sequences which using a McLane Research Laboratories, Inc., pump in situ were believed to be in the Korarchaeota clade have been pub- (Tica vent). On board ship, sulfide chimney surfaces were on March 14, 2015 by guest lished (3, 12, 15, 17, 19, 22–24, 28, 31, 32). These genes were scraped into 2-ml freezer tubes and dropped in liquid nitrogen, PCR amplified from fluid, sediment, sulfide chimneys, or mi- basalt pieces were placed in 50-ml polypropylene tubes, and crobial mats of high-temperature hot springs or submarine filters were wrapped in aluminum foil. Samples were stored on vents. Although attempts to grow Korarchaeota in pure culture board at Ϫ70°C, transported on dry ice, and then stored at have not been successful, Korarchaeota cells of the pJP27 phylo- Ϫ80°C until use. To extract DNA from sulfide chimney sam- type originally detected in Obsidian Pool have now been highly ples, the Bio 101 FastDNA SPIN kit for soil was used accord- enriched, and their (meta)genome is being sequenced (K. O. ing to the manufacturer’s instructions. DNA was extracted Stetter, J. G. Elkins, M. Keller, and the JGI-DOE [http://www.jgi from basalt and filters (in 50-ml polypropylene tubes) by the .doe.gov/sequencing/why/CSP2006/korarchaeota.html]). addition of sucrose-lysis buffer (10 ml), lysozyme, proteinase K, To further assess their diversity and distribution, we de- signed Korarchaeota-specific primers based on published se- sodium dodecyl sulfate, and phenol-chloroform according to quences and used them to PCR amplify 16S rRNA genes from the method of Gordon and Giovannoni (11) and then ethanol deep-sea hydrothermal vents, various Yellowstone National precipitated (20) and resuspended in water. Park hydrothermal features, and a number of nonhydrother- A number of hydrothermal features in Yellowstone National mal environments. PCR amplification products were cloned Park were also screened for Korarchaeota. Samples were col- and sequenced, and the phylogeny of these 16S rRNA genes, lected from 19 sites in summer 2003 and 17 sites in summer as well as those previously named Korarchaeota or sharing 2004 as part of a microbial inventory being conducted of Yel- identity to those previously named as such, was inferred. The lowstone thermal features. Sediment, sinter, mud, and micro- relationships among Korarchaeota were compared to the prop- bial mats were mixed 1:1 in sucrose-lysis buffer, and hydrother- erties of the environments from which they were amplified to mal fluid was mixed 2:1 with RNAlater (Ambion) on site and gain insights into basic physiological properties of this enig- then stored at Ϫ80°C as soon as possible. DNA was extracted matic group. from sediment, sinter, and mud by using a Bio 101 FastDNA Diverse deep-sea hydrothermal vent niches were screened SPIN kit for soil. For extracting microbial mat DNA, 50 ␮lof thawed sample was mixed with 100 ␮l of CTAB buffer (1% cetyltrimethylammonium bromide, 0.75 M NaCl, 50 mM Tris * Corresponding author. Mailing address: Harvard University, Bio- [pH 8], 10 mM EDTA) and then processed like the deep-sea logical Laboratories 4083, 16 Divinity Ave., Cambridge, MA 02138. Phone: (617) 495-2177. Fax: (617) 496-6933. E-mail: cavanaug@fas hydrothermal vent basalt and filters. For fluid samples, 2-ml .harvard.edu. portions were centrifuged 10 min at 16,000 ϫ g, all but 50 ␮lof 5077 5078 AUCHTUNG ET AL. APPL.ENVIRON.MICROBIOL. supernatant was removed, and then the samples were pro- (Bac27F [26]-Univ1492R) primers yielded at least one cor- cessed as described for microbial mat samples. rectly sized band for all samples, suggesting that samples that Since Korarchaeota-specific primers had not previously been did not yield products in Korarchaeota-specific PCR did not fail used to screen natural samples, a range of readily available, due to inhibition or lack of DNA. As additional positive con- primarily nonhydrothermal environmental samples were also trols, KorY38 plasmid (described below) was added to, and DNA collected and tested for Korarchaeota 16S rRNA genes. These was successfully amplified from, replicates of the Kor236F- included compost (with temperatures measured up to 60°C), Kor1236R reaction of nonhydrothermal samples and a rep- plant leaves, flower petals, tree bark, human saliva, biofilms on licate of each Korarchaeota-specific PCR for Yellowstone computer mice, a mosquito, soil (5- to 10-cm-deep Harvard 2004 samples. Forest, Petersham, MA, and surface soil of Cambridge, MA), PCR mixtures contained 0.625 U of Taq,1ϫ buffer (QIAGEN), 2 sand (Harvard University campus), river water and sediment mM deoxynucleoside triphosphates, 4 mM MgCl2, 200 nM con- (Charles River, Cambridge, MA), lake water (oxic-anoxic in- centrations of each primer, and 0.04% bovine serum albumin. terface of Lake Mishawum, Woburn, MA), seawater (coast of After an initial denaturation of 94°C for 2 min, there were 35 Nahant, MA), 32°C spring water (Chena, AK), 57°C tap water cycles of 94°C for 45 s, 55°C (Kor236F-Univ1492R) or 62°C (Cambridge, MA), and 60 and 90°C steam exhaust biofilms (Arc26F-Kor1236R and Kor236F-Kor1236R) for 45 s, and 72°C Downloaded from (campus of Massachusetts Institute of Technology, Cambridge, for 2 min, followed by 72°C for 2 min. A portion of each Korar- MA). Except the DNA of sediment, soil, and sand that was chaeota-specific PCR-amplified sample was visualized on a 1% extracted by using a Bio 101 FastDNA SPIN kit for soil, DNA agarose gel. When a band of the appropriate size was observed, was extracted as for Yellowstone microbial mat samples. DNA in the remaining reaction volumes was purified by using a For primer design, fifteen sequences of variable size identi- PCR purification kit (QIAGEN), cloned into pCR2.1 (Invitro- fied as belonging to the Korarchaeota (3, 12, 15, 17, 19, 22, 23, gen) or pDrive (QIAGEN) and then transformed into TOP10 E. 31, 32) were manually aligned in BioEdit (http://www.mbio coli (20). The resulting colonies were screened by PCR with the .ncsu.edu/BioEdit/bioedit.html) with a number of Euryarcha- primers M13F and M13R under the same conditions as for the http://aem.asm.org/ eota, Crenarchaeota, and Nanoarchaeota sequences. Two Kor236F-Univ1492R reactions to identify clones that contained “Korarchaeota” sequences (FZ2bA214 and pOWA133 [22, inserts of the appropriate size. At least one clone per reaction was 31]) that shared very little identity with the other 13 were sequenced by using the primer M13F with an ABI BigDye ter- excluded for the design of the Korarchaeota-specific primers minator v3.1 cycle sequencing kit on an ABI Prism 3100 genetic Kor236F (GCT GAG GCC CCA GGR TGG GAC CG) and analyzer.
Load more

Recommended publications
  • 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]
  • 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.
    [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]
  • 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]
  • Coral-Associated Archaea
    MARINE ECOLOGY PROGRESS SERIES Vol. 273: 89–96, 2004 Published June 8 Mar Ecol Prog Ser Coral-associated Archaea Linda Wegley1, Yanan Yu1, Mya Breitbart1, Veronica Casas1, David I. Kline1, 2, 3, Forest Rohwer1, 4,* 1Department of Biology, LS316, San Diego State University, 5500 Campanile Dr, San Diego, California 92182-4614, USA 2University of California, San Diego, Scripps Institution of Oceanography, La Jolla, California 92093-0202, USA 3Smithsonian Tropical Research Institute, Apartado 2072, Balboa, Panama 4Center for Microbial Sciences, San Diego State University, 5500 Campanile Dr, San Diego, California 92182, USA ABSTRACT: The coral holobiont includes the coral, zooxanthellae, fungi, endolithic algae, and >30 species of Bacteria. Using culture-independent techniques, we now show that Archaea are also abun- dant and widespread on corals. Sequence analyses of Archaea on 3 species of Caribbean corals revealed that coral-associated Archaea are novel, diverse, and include representatives from both the Crenarchaeota and Euryarchaeota. Unlike zooxanthellae and Bacteria, the Archaea do not appear to form species-specific associations with reef-building corals. Fluorescent in situ hybridizations with peptide nucleic acid (PNA) probes showed that Archaea were present at >107 cells cm–2 on Porites astreoides, comprising nearly half of the prokaryotic community. This study and one by Kellogg (Mar Ecol Prog Ser 273:81–88) show that Archaea are abundant, diverse, and potentially important com- ponents of the coral holobiont. KEY WORDS: Coral · Archaea · 16S rDNA · Fluorescent in situ hybridization · FISH · Peptide nucleic acid probe · PNA Resale or republication not permitted without written consent of the publisher INTRODUCTION 1994, Murray et al. 1998, 1999).
    [Show full text]
  • Variations in the Two Last Steps of the Purine Biosynthetic Pathway in Prokaryotes
    GBE Different Ways of Doing the Same: Variations in the Two Last Steps of the Purine Biosynthetic Pathway in Prokaryotes Dennifier Costa Brandao~ Cruz1, Lenon Lima Santana1, Alexandre Siqueira Guedes2, Jorge Teodoro de Souza3,*, and Phellippe Arthur Santos Marbach1,* 1CCAAB, Biological Sciences, Recoˆ ncavo da Bahia Federal University, Cruz das Almas, Bahia, Brazil 2Agronomy School, Federal University of Goias, Goiania,^ Goias, Brazil 3 Department of Phytopathology, Federal University of Lavras, Minas Gerais, Brazil Downloaded from https://academic.oup.com/gbe/article/11/4/1235/5345563 by guest on 27 September 2021 *Corresponding authors: E-mails: [email protected]fla.br; [email protected]. Accepted: February 16, 2019 Abstract The last two steps of the purine biosynthetic pathway may be catalyzed by different enzymes in prokaryotes. The genes that encode these enzymes include homologs of purH, purP, purO and those encoding the AICARFT and IMPCH domains of PurH, here named purV and purJ, respectively. In Bacteria, these reactions are mainly catalyzed by the domains AICARFT and IMPCH of PurH. In Archaea, these reactions may be carried out by PurH and also by PurP and PurO, both considered signatures of this domain and analogous to the AICARFT and IMPCH domains of PurH, respectively. These genes were searched for in 1,403 completely sequenced prokaryotic genomes publicly available. Our analyses revealed taxonomic patterns for the distribution of these genes and anticorrelations in their occurrence. The analyses of bacterial genomes revealed the existence of genes coding for PurV, PurJ, and PurO, which may no longer be considered signatures of the domain Archaea. Although highly divergent, the PurOs of Archaea and Bacteria show a high level of conservation in the amino acids of the active sites of the protein, allowing us to infer that these enzymes are analogs.
    [Show full text]
  • Systema Naturae. the Classification of Living Organisms
    Systema Naturae. The classification of living organisms. c Alexey B. Shipunov v. 5.601 (June 26, 2007) Preface Most of researches agree that kingdom-level classification of living things needs the special rules and principles. Two approaches are possible: (a) tree- based, Hennigian approach will look for main dichotomies inside so-called “Tree of Life”; and (b) space-based, Linnaean approach will look for the key differences inside “Natural System” multidimensional “cloud”. Despite of clear advantages of tree-like approach (easy to develop rules and algorithms; trees are self-explaining), in many cases the space-based approach is still prefer- able, because it let us to summarize any kinds of taxonomically related da- ta and to compare different classifications quite easily. This approach also lead us to four-kingdom classification, but with different groups: Monera, Protista, Vegetabilia and Animalia, which represent different steps of in- creased complexity of living things, from simple prokaryotic cell to compound Nature Precedings : doi:10.1038/npre.2007.241.2 Posted 16 Aug 2007 eukaryotic cell and further to tissue/organ cell systems. The classification Only recent taxa. Viruses are not included. Abbreviations: incertae sedis (i.s.); pro parte (p.p.); sensu lato (s.l.); sedis mutabilis (sed.m.); sedis possi- bilis (sed.poss.); sensu stricto (s.str.); status mutabilis (stat.m.); quotes for “environmental” groups; asterisk for paraphyletic* taxa. 1 Regnum Monera Superphylum Archebacteria Phylum 1. Archebacteria Classis 1(1). Euryarcheota 1 2(2). Nanoarchaeota 3(3). Crenarchaeota 2 Superphylum Bacteria 3 Phylum 2. Firmicutes 4 Classis 1(4). Thermotogae sed.m. 2(5).
    [Show full text]
  • A Higher Level Classification of All Living Organisms
    RESEARCH ARTICLE A Higher Level Classification of All Living Organisms Michael A. Ruggiero1*, Dennis P. Gordon2, Thomas M. Orrell1, Nicolas Bailly3, Thierry Bourgoin4, Richard C. Brusca5, Thomas Cavalier-Smith6, Michael D. Guiry7, Paul M. Kirk8 1 Integrated Taxonomic Information System, National Museum of Natural History, Smithsonian Institution, Washington, District of Columbia, United States of America, 2 National Institute of Water & Atmospheric Research, Wellington, New Zealand, 3 WorldFish—FIN, Los Baños, Philippines, 4 Institut Systématique, Evolution, Biodiversité (ISYEB), UMR 7205 MNHN-CNRS-UPMC-EPHE, Sorbonne Universités, Museum National d'Histoire Naturelle, 57, rue Cuvier, CP 50, F-75005, Paris, France, 5 Department of Ecology & Evolutionary Biology, University of Arizona, Tucson, Arizona, United States of America, 6 Department of Zoology, University of Oxford, Oxford, United Kingdom, 7 The AlgaeBase Foundation & Irish Seaweed Research Group, Ryan Institute, National University of Ireland, Galway, Ireland, 8 Mycology Section, Royal Botanic Gardens, Kew, London, United Kingdom * [email protected] Abstract We present a consensus classification of life to embrace the more than 1.6 million species already provided by more than 3,000 taxonomists’ expert opinions in a unified and coherent, OPEN ACCESS hierarchically ranked system known as the Catalogue of Life (CoL). The intent of this collab- orative effort is to provide a hierarchical classification serving not only the needs of the Citation: Ruggiero MA, Gordon DP, Orrell TM, Bailly CoL’s database providers but also the diverse public-domain user community, most of N, Bourgoin T, Brusca RC, et al. (2015) A Higher Level Classification of All Living Organisms. PLoS whom are familiar with the Linnaean conceptual system of ordering taxon relationships.
    [Show full text]
  • Mean and SD Archaea Bacteria Genome Size (Mb)
    Distributions for kingdom level Primer score mean and SD Genomic GC (%) mean and SD 60 3 2 50 1 Primer score 40 0 Genomic GC (%) Bacteria Bacteria Archaea Archaea kingdom kingdom 16S GC (%) mean and SD Genome size (Mb) mean and SD 65 5 60 4 55 3 16S GC (%) 2 Genome size (Mb) Genome size 50 Bacteria Bacteria Archaea Archaea kingdom kingdom 16S GC (%) Primer score 45 50 55 60 65 0 1 2 3 4 Acidobacteria Acidobacteria Actinobacteria Actinobacteria Aquificae Aquificae Bacteroidetes Bacteroidetes Caldiserica Caldiserica Chlamydiae Chlamydiae Chlorobi Primer scoremeanandSD Chlorobi 16S GC(%)meanandSD Chloroflexi Chloroflexi Chrysiogenetes Chrysiogenetes Crenarchaeota Crenarchaeota Cyanobacteria Cyanobacteria Deferribacteres Deferribacteres Deinococcus−Thermus Deinococcus−Thermus Dictyoglomi Dictyoglomi Elusimicrobia Elusimicrobia phylum phylum Euryarchaeota Euryarchaeota Fibrobacteres Fibrobacteres Firmicutes Firmicutes Fusobacteria Fusobacteria Gemmatimonadetes Gemmatimonadetes Ignavibacteria Ignavibacteria Ignavibacteriae Ignavibacteriae Korarchaeota Korarchaeota Lentisphaerae Lentisphaerae Nanoarchaeota Nanoarchaeota Nitrospirae Nitrospirae Planctomycetes Planctomycetes level phylum for Distributions Proteobacteria Proteobacteria Spirochaetes Spirochaetes Synergistetes Synergistetes Tenericutes Tenericutes Thaumarchaeota Thaumarchaeota Thermodesulfobacteria Thermodesulfobacteria Thermotogae Thermotogae unclassified unclassified Verrucomicrobia Verrucomicrobia Genome size (Mb) Genomic GC (%) 10.0 30 40 50 60 70 2.5 5.0 7.5 Acidobacteria Acidobacteria
    [Show full text]
  • And Iron-Reducing Thaumarchaeote from a Terrestrial Acidic Hot Spring
    The ISME Journal (2019) 13:2465–2474 https://doi.org/10.1038/s41396-019-0447-3 ARTICLE Isolation and characterization of a thermophilic sulfur- and iron- reducing thaumarchaeote from a terrestrial acidic hot spring 1,2 1 1 1,3 1,3 4 Shingo Kato ● Takashi Itoh ● Masahiro Yuki ● Mai Nagamori ● Masafumi Ohnishi ● Katsuyuki Uematsu ● 2 3 1 Katsuhiko Suzuki ● Tomonori Takashina ● Moriya Ohkuma Received: 10 September 2018 / Revised: 18 April 2019 / Accepted: 3 May 2019 / Published online: 6 June 2019 © International Society for Microbial Ecology 2019 Abstract A deep-branching clade of Thaumarchaeota, conventionally called Terrestrial hot spring creanarchaeotic group (THSCG), is a missing link between thaumarchaeotic ammonia oxidizers and the deeper-branching non-ammonia oxidizers, such as Crenarchaeota and Candidatus Korarchaeota. Here, we report isolation of the first cultivated representative from the THSCG, named as NAS-02. Physiological characterization demonstrated that the isolate was a thermoacidophilic, sulfur- and iron-reducing organoheterotroph, which was supported by gene contents encoded in its complete genome. There was no evidence for ammonia oxidation by the isolate. Members in THSCG are likely thermophiles, and may play roles in 1234567890();,: 1234567890();,: degrading cell debris as a scavenger and in biogeochemical cycling of sulfur and iron in the hot environments, as suggested by the physiological characteristics of the isolate and the geographical distribution of the 16S rRNA gene sequences of THSCG in terrestrial hot springs and marine hydrothermal fields. Phylogenetic analysis suggests that the THSCG lineage represented by NAS-02 has gained the ability of sulfur reduction via horizontal gene transfer. Based on the phylogeny and physiology, we propose the name Conexivisphaera calidus gen.
    [Show full text]
  • Community Analysis of Plant Biomass-Degrading Microorganisms from Obsidian Pool, Yellowstone National Park
    Microb Ecol DOI 10.1007/s00248-014-0500-8 ENVIRONMENTAL MICROBIOLOGY Community Analysis of Plant Biomass-Degrading Microorganisms from Obsidian Pool, Yellowstone National Park Tatiana A. Vishnivetskaya & Scott D. Hamilton-Brehm & Mircea Podar & Jennifer J. Mosher & Anthony V. Palumbo & Tommy J. Phelps & Martin Keller & James G. Elkins Received: 12 May 2014 /Accepted: 16 September 2014 # Springer Science+Business Media New York (outside the USA) 2014 Abstract The conversion of lignocellulosic biomass into (OBP), was examined for potential biomass-active microorgan- biofuels can potentially be improved by employing robust mi- isms using cultivation-independent and enrichment techniques. croorganisms and enzymes that efficiently deconstruct plant Analysis of 33,684 archaeal and 43,784 bacterial quality-filtered polysaccharides at elevated temperatures. Many of the geother- 16S rRNA gene pyrosequences revealed that archaeal diversity mal features of Yellowstone National Park (YNP) are surrounded in the main pool was higher than bacterial; however, in the by vegetation providing a source of allochthonic material to vegetated area, overall bacterial diversity was significantly support heterotrophic microbial communities adapted to utilize higher. Of notable interest was a flooded depression adjacent to plant biomass as a primary carbon and energy source. In this OBP supporting a stand of Juncus tweedyi, a heat-tolerant rush study, a well-known hot spring environment, Obsidian Pool commonly found growing near geothermal features in YNP. The microbial community from heated sediments surrounding the The submitted manuscript has been authored by a contractor of the U.S. plants was enriched in members of the Firmicutes including Government under contract DE-AC05-00OR22725. Accordingly, the potentially (hemi)cellulolytic bacteria from the genera U.S.
    [Show full text]