DOCSLIB.ORG

Description of Algoriphagus Aquimarinus Sp. Nov., Algoriphagus Chordae Sp

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Description of Algoriphagus Aquimarinus Sp. Nov., Algoriphagus Chordae Sp International Journal of Systematic and Evolutionary Microbiology (2004), 54, 1757–1764 DOI 10.1099/ijs.0.02915-0 Description of Algoriphagus aquimarinus sp. nov., Algoriphagus chordae sp. nov. and Algoriphagus winogradskyi sp. nov., from sea water and algae, transfer of Hongiella halophila Yi and Chun 2004 to the genus Algoriphagus as Algoriphagus halophilus comb. nov. and emended descriptions of the genera Algoriphagus Bowman et al. 2003 and Hongiella Yi and Chun 2004 Olga I. Nedashkovskaya,1 Marc Vancanneyt,2 Stefanie Van Trappen,3 Katrien Vandemeulebroecke,2 Anatoly M. Lysenko,4 Manfred Rohde,5 Enevold Falsen,6 Galina M. Frolova,1 Valery V. Mikhailov1 and Jean Swings2,3 Correspondence 1Pacific Institute of Bioorganic Chemistry of the Far-Eastern Branch of the Russian Academy Olga I. Nedashkovskaya of Sciences, Pr. 100 Let Vladivostoku 159, 690022, Vladivostok, Russia [email protected] 2,3BCCM/LMG Bacteria Collection2 and Laboratory of Microbiology3, Ghent University, or Ledeganckstraat 35, B-9000 Ghent, Belgium [email protected] 4Institute of Microbiology of the Russian Academy of Sciences, Pr. 60 Let October 7/2, Moscow, 117811, Russia 5Bereich Mikrobiologie, Abt. Mikrobielle Pathogenitat und Impfstoffforschung, GBF – Gesellschaft fu¨r Biotechnologische Forschung, Mascheroder Weg 1, D-38124 Braunschweig, Germany 6Culture Collection, Department of Clinical Bacteriology, University of Go¨teborg, Guldhedsgatan 10, S-413 46 Go¨teborg, Sweden Four marine heterotrophic, aerobic, pink-pigmented and non-motile bacterial strains were isolated from sea water and algae collected in the Sea of Japan. In a polyphasic taxonomic study, 16S rRNA gene sequence analysis indicated that the strains were phylogenetically highly related to Algoriphagus ratkowskyi LMG 21435T, a member of the phylum Bacteroidetes. Further phenotypic, chemotaxonomic and genomic analyses revealed that the strains represent three novel species of the genus Algoriphagus, for which the following names are proposed: Algoriphagus aquimarinus sp. nov., Algoriphagus chordae sp. nov. and Algoriphagus winogradskyi sp. nov., with type strains KMM 3958T (=LMG 21971T=CCUG 47101T), KMM 3957T (=LMG 21970T=CCUG 47095T) and KMM 3956T (=LMG 21969T=CCUG 47094T), respectively. The species Hongiella halophila Yi and Chun 2004 is transferred to the genus Algoriphagus as Algoriphagus halophilus comb. nov. because of its close phylogenetic relatedness to Algoriphagus species and analogous phenotypic and chemotaxonomic properties. The above-mentioned novel species descriptions and species reclassification justify emended descriptions of the genera Algoriphagus and Hongiella. Published online ahead of print on 13 April 2004 as DOI 10.1099/ijs.0.02915-0. The GenBank/EMBL/DDBJ accession numbers for the 16S rRNA gene sequences of strains KMM 3956T, KMM 3958T, KMM 3957T, LMG 13164T and LMG 21435T are AJ575263, AJ575264, AJ575265, AJ575266 and AJ608641, respectively. A scanning electron micrograph of cells of strain KMM 3956T is available as supplementary material in IJSEM Online. Downloaded from www.microbiologyresearch.org by 02915 G 2004 IUMS Printed in Great Britain 1757 IP: 193.191.134.1 On: Fri, 21 Oct 2016 10:33:24 O. I. Nedashkovskaya and others The genus Algoriphagus was proposed by Bowman et al. according to the manufacturer’s instructions. Purified PCR (2003) for heterotrophic, Gram-negative, non-motile, products were sequenced using the ABI Prism Big Dye strictly aerobic, saccharolytic, rod-like, pink-pigmented Terminator cycle sequencing ready reaction kit and an and cold-adapted strains isolated from sea ice and from Applied Biosystems 3100 DNA sequencer, using the saline lake cyanobacterial mats collected in Antarctica. The protocols of the manufacturer (Applied Biosystems). The genus is phylogenetically distantly related to the genus eight sequencing primers used are listed in Coenye et al. Cyclobacterium of the phylum Bacteroidetes and was repre- (1999). Sequence assembly was performed using the sented by a single species Algoriphagus ratkowskyi with type program AUTOASSEMBLER (Applied Biosystems). strain IC025T. A novel genus, Hongiella, closely related to the genus Algoriphagus, was recognized by Yi & Chun (2004) The 16S rRNA gene sequences (continuous stretches of T T T and comprised three species of pink–orange-pigmented, 1473 bp for KMM 3956 , KMM 3957 and KMM 3958 , T aerobic, non-motile, heterotrophic and mesophilic bacteria 1436 bp for A. ratkowskyi LMG 21435 and 1476 bp for C. from marine sediments of the Sea of Japan. In the present marinum LMG 13164T) and sequences of strains retrieved paper, the taxonomic position of four novel bacteria was from EMBL were aligned and a phylogenetic tree was studied, which were obtained from sea water and algae from constructed by the neighbour-joining method using the the Sea of Japan and which were related to the genera BIONUMERICS software package, version 3.50 (Applied Algoriphagus and Hongiella. Maths). Unknown bases were discarded from the calcula- tions. Phylogenetic analysis of nearly complete 16S rRNA T T Strains KMM 3956 , KMM 3977 and KMM 3957 were gene sequences of strains KMM 3956T, KMM 3957T and isolated in Troitsa Bay (Gulf of Peter the Great, Sea of KMM 3958T revealed sequence similarities of 98?2–98?9%. Japan), the former two from the green alga Acrosiphonia The marine isolates represent part of the phylum Bac- sonderi and the latter from the brown alga Chorda filum. ? ? T teroidetes. Highest sequence similarities (98 0–99 1 %) were KMM 3958 was isolated in Amursky Bay (Gulf of Peter the obtained with the sequence of A. ratkowskyi LMG 21435T, Great) from a sea-water sample. All samples were collected determined in the present study. The latter sequence was in June 2000. For isolation, 0?1 ml algal homogenates or significantly different from the originally deposited 0?1 ml sea water was transferred on marine agar 2216 sequence of A. ratkowskyi IC025T (GenBank/EMBL acces- (Difco) at 28 uC, and the isolates were purified and sion no. U85891), in which multiple errors were found cultivated for further experiments under the same condi- (confirmed by J. Bowman, personal communication). Other tions and stored at 280 uC in marine broth (Difco) closest phylogenetic neighbours were the genera Hongiella, supplemented with 20 % (v/v) glycerol. Cyclobacterium and Belliella (Yi & Chun, 2004; Raj & Maloy, Gram-staining reaction was performed as described by 1990; Brettar et al., 2004; Fig. 1). Among these and the Gerhardt et al. (1994). Cell morphology was observed by marine isolates, significantly high sequence similarities scanning electron microscopy according to the method were obtained with the species Hongiella halophila (96?8– described by Bruns et al. (2001). Strains isolated in this 97?5 %), whereas Hongiella mannitolivorans and Hongiella study were Gram-negative, chemo-organotrophic, aerobic, ornithinivorans were more distantly related (93?7–94?0 and non-motile organisms with short rod-shaped cells, 0?4– 94?3–94?6 %, respectively). Sequence similarities with the 0?6 mm in diameter and 1?2–1?5 mm in length (an image of genera Cyclobacterium and Belliella were in the range cells of strain KMM 3956T is available as supplementary 92?8–93?5%. material in IJSEM Online). On marine agar, colonies formed DNA G+C contents were determined for the three marine by strains KMM 3956T, KMM 3977 and KMM 3957T were isolates KMM 3956T, KMM 3957T and KMM 3958T, A. round, convex, 2–3 mm in diameter, bright-pink coloured ratkowskyi LMG 21435T and H. halophila DSM 15292T. and grew into the agar. Colonies of strain KMM 3958T were DNA was extracted from strains KMM 3956T, KMM 3957T a pale-pink colour and grew on the agar surface. and KMM 3958T using the protocol described by Marmur The phylogenetic position of three novel isolates, KMM (1961) for determination of DNA G+C contents by the 3956T, KMM 3957T and KMM 3958T, and the reference thermal denaturation method of Marmur & Doty (1962). strains A. ratkowskyi LMG 21435T and Cyclobacterium DNA base contents of the latter isolates, A. ratkowskyi T T marinum LMG 13164T was determined by complete 16S LMG 21435 and H. halophila DSM 15292 were also rRNA gene sequence analysis. Genomic DNA was prepared determined by HPLC (Mesbah et al., 1989) with DNA according to the protocol of Niemann et al. (1997). 16S extracts prepared using the protocol described by Pitcher rRNA genes were amplified using oligonucleotide primers et al. (1989), modified for large-scale preparation. For complementary to highly conserved regions of bacterial 16S the HPLC experiments, the nucleoside mixture was rRNA genes. The forward primer was 59-AGAGTTT- separated by using a Waters SymmetryShield C8 column GATCCTGGCTCAG-39 (hybridizing at positions 8–27, maintained at a temperature of 37 uC. The solvent was according to the Escherichia coli numbering system) and 0?02 M NH4H2PO4 (pH 4?0) with 1?5 % acetonitrile. Non- the reverse primer was 59-AAGGAGGTGATCCAGCCGCA- methylated l-phage DNA (Sigma) was used as the 39 (hybridizing at positions 1541–1522). PCR products were calibration reference. The DNA G+C contents of the purified using a QIAquick PCR purification kit (Qiagen), three marine strains KMM 3956T, KMM 3957T and KMM Downloaded from www.microbiologyresearch.org by 1758 International Journal of Systematic and Evolutionary Microbiology 54 IP: 193.191.134.1 On: Fri, 21 Oct 2016 10:33:24 Description of three novel Algoriphagus species Fig. 1. Distance matrix tree showing the phylogenetic relationships of the genus
Load more

Recommended publications
  • Runella Slithyformis Type Strain (LSU 4(T))
    Lawrence Berkeley National Laboratory Recent Work Title Complete genome sequence of the aquatic bacterium Runella slithyformis type strain (LSU 4(T)). Permalink https://escholarship.org/uc/item/52p6k8qb Journal Standards in genomic sciences, 6(2) ISSN 1944-3277 Authors Copeland, Alex Zhang, Xiaojing Misra, Monica et al. Publication Date 2012-05-04 DOI 10.4056/sigs.2475579 Peer reviewed eScholarship.org Powered by the California Digital Library University of California Standards in Genomic Sciences (2012) 6:145-154 DOI:10.4056/sigs.2485911 Complete genome sequence of the aquatic bacterium T Runella slithyformis type strain (LSU 4 ) Alex Copeland1, Xiaojing Zhang1,2, Monica Misra1,2, Alla Lapidus1, Matt Nolan1, Susan Lucas1, Shweta Deshpande1, Jan-Fang Cheng1, Roxanne Tapia1,2, Lynne A. Goodwin1,2, Sam Pitluck1, Konstantinos Liolios1, Ioanna Pagani1, Natalia Ivanova1, Natalia Mikhailova1, Amrita Pati1, Amy Chen3, Krishna Palaniappan3, Miriam Land1,4, Loren Hauser1,4, Chongle Pan1,4, Cynthia D. Jeffries1,4, John C. Detter1, Evelyne-Marie Brambilla5, Manfred Rohde6, Olivier D. Ngatchou Djao6, Markus Göker5, Johannes Sikorski5, Brian J. Tindall5, Tanja Woyke1, James Bristow1, Jonathan A. Eisen1,7, Victor Markowitz3, Philip Hugenholtz1,8, Nikos C. Kyrpides1, Hans-Peter Klenk5*, and Konstantinos Mavromatis1 1 DOE Joint Genome Institute, Walnut Creek, California, USA 2 Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA 3 Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, Berkeley,
    [Show full text]
  • A Report of Nine Unrecorded Bacterial Species in the Phylum Bacteroidetes Collected from Freshwater Environments in Korea
    Journal of Species Research 7(3):187-192, 2018 A report of nine unrecorded bacterial species in the phylum Bacteroidetes collected from freshwater environments in Korea Sanghwa Park, Kiwoon Beak, Ji-Hye Han, Yoon-Jong Nam and Mi-Hwa Lee* Bacterial Resources Research Division, Freshwater Bioresources Research Bureau, Nakdonggang National Institute of Biological Resources (NNIBR), Sangju, Gyengsangbuk-do 37242, Republic of Korea *Correspondent: [email protected] During a comprehensive study of indigenous prokaryotic species in South Korea, nine bacterial species in the phylum Bacteroidetes were isolated from freshwater environmental samples that were collected from three major rivers in the Republic of Korea. High 16S rRNA gene sequence similarity (≥98.7%) and robust phylogenetic clades with the closely related species suggest that each strain was correctly assigned to an independent and predefined bacterial species. There were no previous reports of these nine species in Korea. Within the phylum Bacteroidetes, four species were assigned to the genus Flavobacterium, order Flavobac- teriales, and five species to three genera of two families in the order Cytophagales. Gram reaction, colony and cell morphology, basic biochemical characteristics, isolation source, and strain IDs are described in the species description section. Keywords: ‌16S rRNA gene, Bacteroidetes, Flavobacteriales, Cytophagales, unrecorded species Ⓒ 2018 National Institute of Biological Resources DOI:10.12651/JSR.2018.7.3.187 INTRODUCTION MATERIALS AND METHODS The phylum Bacteroidetes (Ludwig and Klenk, 2001), Samples of freshwater, brackish water, and sediment also known as the Bacteroides-Cytophaga-Flexibacter were collected from the Han River, Nakdong River, and group, are widely distributed over a diverse range of eco- Seomjin River.
    [Show full text]
  • 1 Detection of Horizontal Gene Transfer in the Genome of the Choanoflagellate Salpingoeca
    bioRxiv preprint doi: https://doi.org/10.1101/2020.06.28.176636; this version posted June 29, 2020. 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 Detection of Horizontal Gene Transfer in the Genome of the Choanoflagellate Salpingoeca 2 rosetta 3 4 Danielle M. Matriano1, Rosanna A. Alegado2, and Cecilia Conaco1 5 6 1 Marine Science Institute, University of the Philippines, Diliman 7 2 Department of Oceanography, Hawaiʻi Sea Grant, Daniel K. Inouye Center for Microbial 8 Oceanography: Research and Education, University of Hawai`i at Manoa 9 10 Corresponding author: 11 Cecilia Conaco, [email protected] 12 13 Author email addresses: 14 Danielle M. Matriano, [email protected] 15 Rosanna A. Alegado, [email protected] 16 Cecilia Conaco, [email protected] 17 18 19 20 21 22 1 bioRxiv preprint doi: https://doi.org/10.1101/2020.06.28.176636; this version posted June 29, 2020. 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. 23 Abstract 24 25 Horizontal gene transfer (HGT), the movement of heritable materials between distantly related 26 organisms, is crucial in eukaryotic evolution. However, the scale of HGT in choanoflagellates, the 27 closest unicellular relatives of metazoans, and its possible roles in the evolution of animal 28 multicellularity remains unexplored.
    [Show full text]
  • Life in the Cold Biosphere: the Ecology of Psychrophile
    Life in the cold biosphere: The ecology of psychrophile communities, genomes, and genes Jeff Shovlowsky Bowman A dissertation submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy University of Washington 2014 Reading Committee: Jody W. Deming, Chair John A. Baross Virginia E. Armbrust Program Authorized to Offer Degree: School of Oceanography i © Copyright 2014 Jeff Shovlowsky Bowman ii Statement of Work This thesis includes previously published and submitted work (Chapters 2−4, Appendix 1). The concept for Chapter 3 and Appendix 1 came from a proposal by JWD to NSF PLR (0908724). The remaining chapters and appendices were conceived and designed by JSB. JSB performed the analysis and writing for all chapters with guidance and editing from JWD and co- authors as listed in the citation for each chapter (see individual chapters). iii Acknowledgements First and foremost I would like to thank Jody Deming for her patience and guidance through the many ups and downs of this dissertation, and all the opportunities for fieldwork and collaboration. The members of my committee, Drs. John Baross, Ginger Armbrust, Bob Morris, Seelye Martin, Julian Sachs, and Dale Winebrenner provided valuable additional guidance. The fieldwork described in Chapters 2, 3, and 4, and Appendices 1 and 2 would not have been possible without the help of dedicated guides and support staff. In particular I would like to thank Nok Asker and Lewis Brower for giving me a sample of their vast knowledge of sea ice and the polar environment, and the crew of the icebreaker Oden for a safe and fascinating voyage to the North Pole.
    [Show full text]
  • David López Escardó
    Unveiling new molecular Opisthokonta diversity: A perspective from evolutionary genomics David López Escardó TESI DOCTORAL UPF / ANY 2017 DIRECTOR DE LA TESI Dr. Iñaki Ruiz Trillo DEPARTAMENT DE CIÈNCIES EXPERIMENTALS I DE LA SALUT ii Acknowledgements: Aquesta tesi va començar el dia que, mirant grups on poguer fer el projecte de màster, vaig trobar la web d'un grup de recerca que treballaven amb uns microorganismes, desconeguts per mi en aquell moment, per entendre l'origen dels animals. Tres o quatre assignatures de micro a la carrera, i cap d'elles tractava a fons amb protistes i menys els parents unicel·lulars dels animals. En fi, "Bitxos" raros, origen dels animals... em va semblar interessant. Així que em vaig presentar al despatx del Iñaki vestit amb el tratge de comercial de Tecnocasa, per veure si podia fer les pràctiques del Màster amb ells. El primer que vaig volguer remarcar durant l'entrevista és que no pretenia anar amb tratge a la feina, que no es pensés que jo de normal vaig tan seriós... Sigui com sigui, després de rumiar-s'ho, em va dir que endavant i em va emplaçar a fer una posterior entrevista amb els diferents membres del lab perquè tries un projecte de màster. Per tant, aquí el meu primer agraïment i molt gran, al Iñaki, per permetre'm, no només fer el màster, sinó també permetre'm fer aquesta tesis al seu laboratori. També per la llibertat alhora de triar projectes i per donar-li al MCG un ambient cordial on hi dóna gust treballar. Gràcies, doncs, per deixar-me entrar al món científic per la porta de la protistologia, la genòmica i l'evolució, que de ben segur m'acompanyaran sempre.
    [Show full text]
  • Choanoflagellate Models — Monosiga Brevicollis and Salpingoeca Rosetta
    Available online at www.sciencedirect.com ScienceDirect Choanoflagellate models — Monosiga brevicollis and Salpingoeca rosetta 1,2 1 Tarja T Hoffmeyer and Pawel Burkhardt Choanoflagellates are the closest single-celled relatives of choanoflagellate cells are highly polarized [1 ,6]. Choano- animals and provide fascinating insights into developmental flagellates possess a single posterior flagellum that is processes in animals. Two species, the choanoflagellates enclosed by a collar composed of microvilli (Figure 1b). Monosiga brevicollis and Salpingoeca rosetta are emerging The movement of the flagellum serves two main functions: as promising model organisms to reveal the evolutionary origin to allow motile cells to swim and to create water currents of key animal innovations. In this review, we highlight how which trap bacteria to the collar to allow phagocytosis [7,8]. choanoflagellates are used to study the origin of multicellularity Phagocytosed bacteria are digested in anterior localized in animals. The newly available genomic resources and food vacuoles (Figure 1b). The Golgi apparatus with many functional techniques provide important insights into the associated vesicles is positioned posterior to the prominent function of choanoflagellate pre- and postsynaptic proteins, nucleus. Moreover, many choanoflagellates possess anteri- cell–cell adhesion and signaling molecules and the evolution or filopodia (Figure 1b), which allow for substratum attach- of animal filopodia and thus underscore the relevance of ment of the cells [1 ,9]. choanoflagellate models for evolutionary biology, neurobiology and cell biology research. In this review, we highlight recent advances in choano- Addresses flagellate phylogeny and critically discuss the latest pro- 1 Marine Biological Association, The Laboratory, Citadel Hill, Plymouth gresses made on the establishment of choanoflagellates as PL1 2PB, UK 2 model organisms to understand the origin of multicellulari- Department of Biosciences, University of Exeter, Exeter EX4 4QD, UK ty in animals.
    [Show full text]
  • 7Th International Choanoflagellates & Friends Meeting 24Th-27Th May 2019
    7th International Choanoflagellates & Friends Meeting 24th-27th May 2019 ~ Barcelona Organizing Committee Omaya Dudin Andrej Ondacka Postdoctoral Researcher Postdoctoral Researcher [email protected] [email protected] Daniel J. Richter Núria Ros i Rocher Postdoctoral Researcher Postdoctoral Researcher [email protected] [email protected] Acknowledgements for organizational support Administration & Communication Services - Institute of Evolutionary Biology (CSIC-UPF) The King Lab – UC Berkeley Sponsors Book of Abstracts 7th International Choanoflagellates & Friends Meeting 24th-27th May 2019 ~ Barcelona Book of Abstracts Friday, 24th May 2019 The evolutionary origin of animal cell differentiation and synaptic signalling machinery Pawel Burkhardt Sars International Centre for Marine Molecular Biology, University of Bergen, Norway Choanoflagellates, the closest unicellular relatives of animals, express many genes previously thought to be animal specific. Strikingly, these tiny protists can alternate between unicellular and multicellular states, making choanoflagellates powerful models to investigate the origin of animal multicellularity, the mechanisms underlying cell differentiation and the ancestry of synaptic protein machinery. We used electron microscopy to reconstruct in three dimensions the total subcellular composition of unicellular and multicellular choanoflagellates as well as the collar cells from a marine sponge. We found differences between single and multicellular choanoflagellates in structures associated with cellular energetics, membrane trafficking and cell morphology and identified a putative novel cell type within rosette colonies. These findings are an important step forward in reconstructing the biology of last common ancestor of the animals and suggests that both, temporal and spatial cell type differentiation was present in the stem lineage leading to animals. In the second part of my talk, I will present our recent discoveries on synaptic protein homologs found in choanoflagellates.
    [Show full text]
  • Bacterial Composition and Diversity in Deep-Sea Sediments from the Southern Colombian Caribbean Sea
    diversity Article Bacterial Composition and Diversity in Deep-Sea Sediments from the Southern Colombian Caribbean Sea Nelson Rivera Franco 1 , Miguel Ángel Giraldo 1,2, Diana López-Alvarez 1,* , Jenny Johana Gallo-Franco 3, Luisa F. Dueñas 4,5 , Vladimir Puentes 4 and Andrés Castillo 1,2,* 1 TAO-Lab, Centre for Bioinformatics and Photonics-CIBioFi, Universidad del Valle, Calle 13 # 100-00, Edif. E20, No. 1069, Cali 760032, Colombia; [email protected] (N.R.F.); [email protected] (M.Á.G.) 2 Department of Biology, Universidad del Valle, Calle 13 No 100-00, Edif. E20, Cali 760032, Colombia 3 Natural Sciences and Mathematics Department, Pontificia Universidad Javeriana-Cali, Cali 760032, Colombia; [email protected] 4 Anadarko Colombia Company-HSE, Calle 113 No. 7-80 Piso 11, Bogotá D.C. 110111, Colombia; [email protected] (L.F.D.); [email protected] (V.P.) 5 Department of Biology, Universidad Nacional de Colombia, Sede Bogotá, Carrera 45 No. 26-85, Bogotá D.C. 111321, Colombia * Correspondence: [email protected] (D.L.-A.); [email protected] (A.C.) Abstract: Deep-sea sediments are considered an extreme environment due to high atmospheric pressure and low temperatures, harboring novel microorganisms. To explore marine bacterial diversity in the southern Colombian Caribbean Sea, this study used 16S ribosomal RNA (rRNA) gene sequencing to estimate bacterial composition and diversity of six samples collected at different depths (1681 to 2409 m) in two localities (CCS_A and CCS_B). We found 1842 operational taxonomic units (OTUs) assigned to bacteria.
    [Show full text]
  • Coral Reef Biodiversity in the Face of Climatic Changes Stéphane La Barre
    Coral Reef Biodiversity in the Face of Climatic Changes Stéphane La Barre To cite this version: Stéphane La Barre. Coral Reef Biodiversity in the Face of Climatic Changes. Biodiversity Loss in a Changing Planet, Intech, pp.75, 2011, SBN 978-953-307-707-9. 10.5772/1832. hal-00698924 HAL Id: hal-00698924 https://hal.archives-ouvertes.fr/hal-00698924 Submitted on 18 May 2012 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. 4 Coral Reef Biodiversity in the Face of Climatic Changes Stéphane La Barre Université Pierre et Marie Curie-Paris 6, UMR 7139 Végétaux marins et Biomolécules, Station Biologique F-29682, Roscoff CNRS, UMR 7139 Végétaux marins et Biomolécules, Station Biologique F-29682, Roscoff France 1. Introduction Loss of marine biodiversity seems inevitable in the 21st century. In benthic marine systems, survivors will have to acclimatize to seawater constantly increasing in temperature and evolving chemically, while also needing to out-compete new opportunistic neighbors and possibly facing increased predation pressure. Last but not the least, with a metabolism already pushed to its limits, survivors will have to fight against emerging diseases. Recent studies have shown that thermal stresses on coral reef scleractinians (Vega Thurber et al., 2009), sponges (Webster et al., 2008) and coralline algae (Webster et al., 2010a) induce changes from a balanced, functional associated microflora to a pathogen-dominated one, causing disease before the physiological tolerance limits of the hosts are reached.
    [Show full text]
  • Genome-Based Taxonomic Classification Of
    ORIGINAL RESEARCH published: 20 December 2016 doi: 10.3389/fmicb.2016.02003 Genome-Based Taxonomic Classification of Bacteroidetes Richard L. Hahnke 1 †, Jan P. Meier-Kolthoff 1 †, Marina García-López 1, Supratim Mukherjee 2, Marcel Huntemann 2, Natalia N. Ivanova 2, Tanja Woyke 2, Nikos C. Kyrpides 2, 3, Hans-Peter Klenk 4 and Markus Göker 1* 1 Department of Microorganisms, Leibniz Institute DSMZ–German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany, 2 Department of Energy Joint Genome Institute (DOE JGI), Walnut Creek, CA, USA, 3 Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia, 4 School of Biology, Newcastle University, Newcastle upon Tyne, UK The bacterial phylum Bacteroidetes, characterized by a distinct gliding motility, occurs in a broad variety of ecosystems, habitats, life styles, and physiologies. Accordingly, taxonomic classification of the phylum, based on a limited number of features, proved difficult and controversial in the past, for example, when decisions were based on unresolved phylogenetic trees of the 16S rRNA gene sequence. Here we use a large collection of type-strain genomes from Bacteroidetes and closely related phyla for Edited by: assessing their taxonomy based on the principles of phylogenetic classification and Martin G. Klotz, Queens College, City University of trees inferred from genome-scale data. No significant conflict between 16S rRNA gene New York, USA and whole-genome phylogenetic analysis is found, whereas many but not all of the Reviewed by: involved taxa are supported as monophyletic groups, particularly in the genome-scale Eddie Cytryn, trees. Phenotypic and phylogenomic features support the separation of Balneolaceae Agricultural Research Organization, Israel as new phylum Balneolaeota from Rhodothermaeota and of Saprospiraceae as new John Phillip Bowman, class Saprospiria from Chitinophagia.
    [Show full text]
  • Diversity and Distribution of Unicellular Opisthokonts Along the European Coast Analyzed Using High-Throughput Sequencing
    Diversity and distribution of unicellular opisthokonts along the European coast analyzed using high-throughput sequencing Javier del Campo 1,2,* , Diego Mallo 3, Ramon Massana 4, Colomban de Vargas 5,6 , Thomas A. Richards 7,8 , and Iñaki Ruiz-Trillo 1,9,10 1Institut de Biologia Evolutiva (CSIC-UPF), Passeig Marítim de la Barceloneta 37-49, 08003 Barcelona, Catalonia, Spain. 3Department of Biochemistry, Genetics and Immunology, University of Vigo, Vigo, Galicia, Spain 4Department of Marine Biology and Oceanography, Institut de Ciències del Mar (CSIC), Barcelona, Catalonia, Spain 5CNRS, UMR 7144, Adaptation et Diversité en Milieu Marin, Station Biologique de Roscoff, Roscoff, France 6UPMC Univ. Paris 06, UMR 7144, Station Biologique de Roscoff, Roscoff, France 7Geoffrey Pope Building, Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter, UK 8Canadian Institute for Advanced Research, CIFAR Program in Integrated Microbial Biodiversity 9Departament de Genètica, Universitat de Barcelona, Barcelona, Catalonia, Spain 10 Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Catalonia, Spain Summary The opisthokonts are one of the major super-groups of eukaryotes. It comprises two major clades: 1) the Metazoa and their unicellular relatives and 2) the Fungi and their unicellular relatives. There is, however, little knowledge of the role of opisthokont microbes in many natural environments, especially among non-metazoan and non-fungal opisthokonts. Here we begin to address this gap by analyzing high throughput 18S rDNA and 18S rRNA sequencing data from different European coastal sites, sampled at different size fractions and depths. In particular, we analyze the diversity and abundance of choanoflagellates, filastereans, ichthyosporeans, nucleariids, corallochytreans and their related lineages.
    [Show full text]
  • Algoriphagus Machipongonensis Sp. Nov., Co- Isolated with a Colonial Choanoflagellate
    Algoriphagus machipongonensis sp. nov., co- isolated with a colonial choanoflagellate The MIT Faculty has made this article openly available. Please share how this access benefits you. Your story matters. Citation Alegado, R. A., J. D. Grabenstatter, R. Zuzow, A. Morris, S. Y. Huang, R. E. Summons, and N. King. “Algoriphagus Machipongonensis Sp. Nov., Co-Isolated with a Colonial Choanoflagellate.”International Journal of Systematic and Evolutionary Microbiology 63, no. Pt 1 (January 1, 2013): 163–168. As Published http://dx.doi.org/10.1099/ijs.0.038646-0 Publisher Society for General Microbiology Version Final published version Citable link http://hdl.handle.net/1721.1/85932 Terms of Use Article is available under a Creative Commons license; see publisher's site for details. Detailed Terms http://creativecommons.org/ International Journal of Systematic and Evolutionary Microbiology (2013), 63, 163–168 DOI 10.1099/ijs.0.038646-0 Algoriphagus machipongonensis sp. nov., co-isolated with a colonial choanoflagellate Rosanna A. Alegado,1 Jonathan D. Grabenstatter,2 Richard Zuzow,13 Andrea Morris,14 Sherri Y. Huang,1 Roger E. Summons2 and Nicole King1 Correspondence 1Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA 94720, Nicole King USA [email protected] 2Department of Earth, Atmospheric, and Planetary Sciences, Massachusetts Institute of Rosanna A. Alegado Technology, Cambridge, MA 02139, USA [email protected] A Gram-negative, non-motile, non-spore-forming bacterial strain, PR1T, was isolated from a mud core sample containing colonial choanoflagellates near Hog Island, Virginia, USA. Strain PR1T grew optimally at 30 6C and with 3 % (w/v) NaCl.
    [Show full text]