DOCSLIB.ORG

Tree Scale: 1

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Tree Scale: 1 5 /1-396 5 1-396 bchX LYXE d Bacteria bchX GCA 000152145. bchX ADVR d Bacteria us aggregans DSM 948 DSM aggregans us us aurantiacus J-10-fl / p Chloroflexota c Chlor xus sp. Y-400-fl /1-396 bchX NQWI d Bacteria us islandicus 1/1-396 1 ASM15214v1 protein p Chloroflexota c Chlo loroflexus s 1/1-396 s loroflexus in subunit X Chloroflex X subunit in loroflexus s 1/1-396 in subunit X Chloroflex ein subunit X Chlorofle bchX GCA 000012485. oflexia o Chloroflexales bchX GCA 000016085. p Chloroflexota c Chlo hloroflexus s Chloroflex bchX GCA 000012585. EFO79826.1 chloroph roflexia o Chloroflexale bchX DCSM d Bacteria f Chloroflexaceae g Ch g Chloroflexaceae f de reductase iron prote iron reductase de f Chloroflexaceae g Ch ide reductase iron prote 1 ASM1248v1 protein A 1 ASM1608v1 protein A lide reductase iron prot bchX GCA 000020505. f Chloroflexaceae g Ch roflexia o Chloroflexale 1 ASM1258v1 protein A s f Chloroflexaceae g C yllide reductase iron pr bchX GCA 000006985. p Chloroflexota c Chlo s f Chloroflexaceae g O bchX GCA 000168715. flexia o Chloroflexales CL25985.1 chlorophylli CL25985.1 oflexia o Chloroflexales o oflexia BB24282.1 Chlorophyl BY33667.1 chlorophyll 1 ASM2050v1 protein A BP37253.1 chlorophyll bchX GCA 000020645. CM51883.1 chlorophyl bchX Viridilinea medios loroploca s Chloroploca bchX Chloroploca asia BB27673.1 Chlorophyl s f Chloroflexaceae g C roflexia o Chloroflexale 1 ASM16871v1 protein 1 ASM698v1 protein AA bchX Chloroploca asia roflexia o Chloroflexale otein subunit X Oscilloc bchX GCA 000015125. scillochloris s Oscilloch bchX GCA 000020465. bchX OHK Co dastool lide reductase iron prot CF11158.1 chlorophylli ide reductase iron prote Chloroflexota c Chloro 396/1-396 p Chloroflexota c Chlor c Chloroflexota p egans/1-396 egans 1/1-396 egans 1 ASM2064v1 protein A A protein ASM2194v1 1 96 ntiacus 1/1-396 1ASM1886v1 proteinA bchX OHK UC 40.cont bchX RYFF01 1/1-394 dicus isl2 1/1-396 bchX OHK Co maxb.04 lide reductase iron prot ntiacus/1-396 1 ASM2218v1 protein A dicus isl2/1-396 EAT58209.1 chlorophy bchX NQWI01/1-395 alina Kir153F/1-395 bchX RSAS01 1/1-392 tica B79 1/1-394 asiatica 1/1-394 hloroploca s 1/1-395 6 1 ASM1512v1 protein A M72651.1 chlorophyllid bchX RYFE01 1/1-395 1 ASM2046v1 protein A p Chloroflexota c Chlo 400/1-396 bchX GCA 000020625. s f Chloroflexaceae g U tica B79/1-394 hloris trichoides DG6 /1 /1-383 bchX Oscillochloris/1-3 loris trichoides 1/1-391 de reductase iron prote metabat 40/1-395 1/1-383 CF43263.1 chlorophyll ein subunit X Chlorobiu in subunit X Chlorobium bchX RYFD01 1/1-391 bchX Chlorothrix 1/1-42 bchX AZXV d Bacteria Bacteria d AZXV bchX bchX Chloroflexus spY bchX chloroflexus aggr chloroflexus bchX bchX JPIM d Bacteria p bchX chloroflexus aggr chloroflexus bchX bchX JPIM01/1-396 bchX GCA 000021945. GCA bchX bchX chloroflexus aura bchX PNIQ01 1/1-396 PNIQ01 bchX bchX GCA 000020545. ein subunit X Chlorobiu bchX Nak metab 64/1-3 igs 1/1-395 bchX GCA 000018865. BL65809.1 chlorophylli llide reductase iron pro bchX TC 147/1-384 bchX DOPW01 1/1-396 bchX RFHF01 1/1-396 bchX Chlorothrix/1-420 3/1-395 bchX Chloroflexus islan 1 ASM2062v1 protein A CD89976.1 chlorophyll e reductase BchX subu bchX chloroflexus aura bchX GCA 000022185. 83 bchX Chloroflexus islan bchX Pelodictyon luteo bchX J043 1/1-396 bchX J metab 161/1-39 bchX DCSM01/1-389 83 ide reductase iron prote BA1466 s 1/1-389 bchX LWQS d Bacteria in subunit X Chlorobac bchX Chloroflexus sp Y -391 91 bchX Anaerolinea YNP bchX TC 160/1-392 m luteolum DSM 273 /1 bchX Anaerolinea YNP 63 1/1-383 phaeovibrioides DSM 1 ASM2054v1 protein A bchX NP1 C 2 1/1-383 bchX TC 63/1-306 bchX RFGY01 1/1-383 s sp. RS-1 /1-388 de reductase iron prote bchX Chlorobaculum li tein subunit X Chlorobi bchX JP3 C 13 1/1-383 CF46555.1 chlorophyll m chlorochromatii CaD 41 /1-388 ide reductase iron prote bchX JP3 Bin7 1/1-383 bchX SJPA01 1/1-326 0 nit Chlorobium tepidum bchX J036 1/1-383 -383 bchX PGTN01 1/1-383 lum/1-284 bchX Nak metab 36/1-3 in subunit X Pelodictyo bchX Chlorobaculum p ulum parvum NCIB 832 bchX Nak UC 36 1/1-3 CE03882.1 chlorophyll bchX J CC 140 1/1-383 in subunit X Roseiflexu bchX Pelodictyon phae bchX J UC mh maxb.2 s castenholzii DSM 139 bchX GCA 000020525. ide reductase iron prote in subunit X Chlorobium 265 /1-283 -284 um ferrooxidans DSM 1 mnaeum/1-297 0.3 bchX N CC 20 1/1-383 in subunit X Chlorobium bchX NP3 C 7 1/1-383 3 /1-301 1.0 1.0 0.9 bchX J UC 75 1/1-383 TLS /1-283 1.0 n phaeoclathratiforme B bchX MPJE01/1-286 bchX Nak metab 36 1/1 ide reductase iron prote 1.0 Tree scale: 1 arvulum/1-283 bchX J metab 75/1-383 1 ASM2052v1 protein A bchX Prosthecochloris 7 /1-283 1.0 ide reductase iron prote in subunit X Roseiflexu 1.0 1.0 1.0 bchX TC 71 1/1-388 0.1 0.3 0.9 0.9 1.0 90 in subunit X Prostheco 1.0 oclathratiforme/1-284 1.0 0.8 phaeobacteroides DSM 0.4 1.0 0.7 bchX TC 71/1-388 1.0 1.0 0.3 1.0 0.9 3031 /1-286 0.3 0.9 1.0 0.20.0 390 limicola DSM 245 /1-2 0.1 0.80.0 bchX TC 152/1-390 1.0 0.0 0.0 bchX Prosthecochloris 0.0 0.7 bchX TC 152 1/1-390 4/1-390 1.0 0.9 CF15169.1 chlorophyll in subunit X Chlorobium 1.0 0.5 bchX TC 22 1/1-323 U-1 /1-284 1.0 0.4 metabat 10/1-390 BQ91621.1 chlorophyll ide reductase iron prote aestuarii DSM271/1-28 0.9 1.0 1.0 0.3 bchX TC 22/1-323 90 chloris aestuarii DSM 2 0.2 1.0 bchX OHK UC 10 1/1-3 266 /1-287 0.9 0.2 igs 1/1-390 86 bchX OHK C C 18 1/1- ide reductase iron prote 0.4 1.0 0.1 1-388 aestuarii/1-282 0.7 bchX OHK Co maxb.09 0.1 BU59786.1 chlorophyll phaeobacteroidesbchX PDNY02 BS1 1/1-322 0.9 0.6 0.6 1.0 bchX OHK Co dastool 1 ASM1666v1 protein A 2 0.5 1.0 71 /1-282 1.0 1.0 1.0 bchX OHK CC 13 1/1-3 388 bchX PDNZ01 1/1-291 0.9 in subunit X Chloroherp bchX OHK UC 10.cont 1.0 1.0 bchX Roseiflexus sp 1/ bchX NSLH01/1-267 /1-287 0.8 1 ASM1780v1 protein A bchX Chloroherpeton t 0.6 1.0 bchX GCA 000016665. bchX Nak bchXmaxb PHFL01/1-267 085/1- 1.0 387 0.9 1.0 0.8 bchX Roseiflexus sp/1- eton thalassium ATCC 0.7 0.5 metabat 108/1-371 0.9 0.9 bchX PNIR01 1/1-388 bchX MGTX d Bacteria 0.6 0.4 7/1-371 bchX GCA 000017805. halassium/1-267 1.0 0.5 267 1.0 1.0 bchX Nak concoct 8/1- nholzii/1-387 35110 /1-267 p Elusimicrobiota c Elu bchX OHK Co dastool nholzii 1/1-387 bchX WPS2 29 1 1.0 bchX OHK Co maxb.09 bchX WPS2 33 1 0.9 1.0 1.0 1.0 0.3 bchX roseiflexus caste tigs 1/1-388 simicrobia o UBA1565 bchX roseiflexus caste 1.0 1.0 5/1-388 1.0 bchX kouleothrix/1-260 1.0 1.0 metabat 106/1-388 f UBA9628 g GWA2-66 1.0 bchX OHK UC 106.con 4/1-387 BA965 s 1/1-390 1.0 1.0 0.91.0 bchX OHK Co maxb.00 1.0 0.6 bchX OHK Co dastool igs 1/1-387 -18 s 2/1-297 0.9 s f Roseiflexaceae g U 0.4 bchX OHK Co maxb.00 metabat 77/1-387 0.7 e1 /1-278 bchX OHK UC 77.cont roflexia o Chloroflexale 0.8 bchX OHK Co dastool rium modesticaldum Ic bchX FOPK d Bacteria 1.00.3 1.0 bchX QWQZ01 1/1-390 p Chloroflexota c Chlo in subunit x Heliobacte p Proteobacteria c Alp bchX LGEI d Bacteria p bchX QWQY01 1/1-390 0.8 de reductase iron prote Proteobacteria c Alpha haproteobacteria o Rhi 1.0 bchX DBCF d Bacteria 0.3 0 ilum B /1-246 proteobacteria o Rhizo zobiales f Beijerinckiac bchX DBCF01/1-390 BZ83893.1 chlorophylli bchX FPBW d Bacteria odesticaldum/1-278 dobacterium thermoph 0.9 1.0 bchX QWQO01 1/1-39 p Proteobacteria c Alp biales f Beijerinckiacea 1.0 eae g Methylobacterium 1 ASM1916v1 protein A tein subunit X Chloraci 1.0 bchX Heliobacterium m ovibrio sp. 970 /1-289 bchX GCA 000272495. haproteobacteria o Rhi e g Methylobacterium s s Methylobacterium ph 1.0 246 6 llide reductase iron pro bchX GCA 000019165. tein subunit X Thiorhod 1 ASM27249v1 protein bchX FOQW d Bacteria zobiales f Beijerinckiac Methylobacterium purp 0.3 yllosphaerae 1/1-289 bchX Nak maxb 100/1- ium thermophilum/1-24 AEP11691.1 chlorophy llide reductase iron pro -289 p Proteobacteria c Alp EIZ84117.1 chlorophyl eae g Methylobacterium urogeneiscleroticus 1/1 1 ASM22629v1 protein icoccus mobilis 8321 /1 bchX FOTK d Bacteria haproteobacteria o Rhi lide reductase iron prot bchX Chloracidobacter EIC20041.1 chlorophy s Methylobacterium or p Proteobacteria c Alp -289 otein subunit X Thioflav zobiales f Beijerinckiac ein subunit X Methylob bchX GCA 000226295.
Load more

Recommended publications
  • Feasibility of Bacterial Probiotics for Mitigating Coral Bleaching
    Feasibility of bacterial probiotics for mitigating coral bleaching Ashley M. Dungan ORCID: 0000-0003-0958-2177 Thesis submitted in total fulfilment of the requirements of the degree of Doctor of Philosophy September 2020 School of BioSciences The University of Melbourne Declaration This is to certify that: 1. This thesis comprises only of my original work towards the PhD, except where indicated in the preface. 2. Due acknowledgements have been made in the text to all other material used. 3. The thesis is under 100,000 words, exclusive of tables, bibliographies, and appendices. Signed: Date: 11 September 2020 ii General abstract Given the increasing frequency of climate change driven coral mass bleaching and mass mortality events, intervention strategies aimed at enhancing coral thermal tolerance (assisted evolution) are urgently needed in addition to strong action to reduce carbon emissions. Without such interventions, coral reefs will not survive. The seven chapters in my thesis explore the feasibility of using a host-sourced bacterial probiotic to mitigate bleaching starting with a history of reactive oxygen species (ROS) as a biological explanation for bleaching (Chapter 1). In part because of the difficulty to experimentally manipulate corals post-bleaching, I use Great Barrier Reef (GBR)-sourced Exaiptasia diaphana as a model organism for this system, which I describe in Chapter 2. The comparatively high levels of physiological and genetic variability among GBR anemone genotypes make these animals representatives of global E. diaphana diversity and thus excellent model organisms. The ‘oxidative stress theory for coral bleaching’ provides rationale for the development of a probiotic with a high free radical scavenging ability.
    [Show full text]
  • Unlocking the Genomic Taxonomy of the Prochlorococcus Collective
    bioRxiv preprint doi: https://doi.org/10.1101/2020.03.09.980698; this version posted March 11, 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 4.0 International license. Unlocking the genomic taxonomy of the Prochlorococcus collective Diogo Tschoeke1#, Livia Vidal1#, Mariana Campeão1, Vinícius W. Salazar1, Jean Swings1,2, Fabiano Thompson1*, Cristiane Thompson1* 1Laboratory of Microbiology. SAGE-COPPE and Institute of Biology. Federal University of Rio de Janeiro. Rio de Janeiro. Brazil. Av. Carlos Chagas Fo 373, CEP 21941-902, RJ, Brazil. 2Laboratory of Microbiology, Ghent University, Gent, Belgium. *Corresponding authors: E-mail: [email protected] , [email protected] Phone no.: +5521981041035, +552139386567 #These authors contributed equally. ABSTRACT 1 bioRxiv preprint doi: https://doi.org/10.1101/2020.03.09.980698; this version posted March 11, 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 4.0 International license. Prochlorococcus is the most abundant photosynthetic prokaryote on our planet. The extensive ecological literature on the Prochlorococcus collective (PC) is based on the assumption that it comprises one single genus comprising the species Prochlorococcus marinus, containing itself a collective of ecotypes. Ecologists adopt the distributed genome hypothesis of an open pan-genome to explain the observed genomic diversity and evolution patterns of the ecotypes within PC.
    [Show full text]
  • Article-Associated Bac- Teria and Colony Isolation in Soft Agar Medium for Bacteria Unable to Grow at the Air-Water Interface
    Biogeosciences, 8, 1955–1970, 2011 www.biogeosciences.net/8/1955/2011/ Biogeosciences doi:10.5194/bg-8-1955-2011 © Author(s) 2011. CC Attribution 3.0 License. Diversity of cultivated and metabolically active aerobic anoxygenic phototrophic bacteria along an oligotrophic gradient in the Mediterranean Sea C. Jeanthon1,2, D. Boeuf1,2, O. Dahan1,2, F. Le Gall1,2, L. Garczarek1,2, E. M. Bendif1,2, and A.-C. Lehours3 1Observatoire Oceanologique´ de Roscoff, UMR7144, INSU-CNRS – Groupe Plancton Oceanique,´ 29680 Roscoff, France 2UPMC Univ Paris 06, UMR7144, Adaptation et Diversite´ en Milieu Marin, Station Biologique de Roscoff, 29680 Roscoff, France 3CNRS, UMR6023, Microorganismes: Genome´ et Environnement, Universite´ Blaise Pascal, 63177 Aubiere` Cedex, France Received: 21 April 2011 – Published in Biogeosciences Discuss.: 5 May 2011 Revised: 7 July 2011 – Accepted: 8 July 2011 – Published: 20 July 2011 Abstract. Aerobic anoxygenic phototrophic (AAP) bac- detected in the eastern basin, reflecting the highest diver- teria play significant roles in the bacterioplankton produc- sity of pufM transcripts observed in this ultra-oligotrophic tivity and biogeochemical cycles of the surface ocean. In region. To our knowledge, this is the first study to document this study, we applied both cultivation and mRNA-based extensively the diversity of AAP isolates and to unveil the ac- molecular methods to explore the diversity of AAP bacte- tive AAP community in an oligotrophic marine environment. ria along an oligotrophic gradient in the Mediterranean Sea By pointing out the discrepancies between culture-based and in early summer 2008. Colony-forming units obtained on molecular methods, this study highlights the existing gaps in three different agar media were screened for the production the understanding of the AAP bacteria ecology, especially in of bacteriochlorophyll-a (BChl-a), the light-harvesting pig- the Mediterranean Sea and likely globally.
    [Show full text]
  • Diversity of Cultivated and Metabolically Active Aerobic Anoxygenic Phototrophic Bacteria Along an Oligotrophic Gradientthe in Mediterranean Sea C
    Discussion Paper | Discussion Paper | Discussion Paper | Discussion Paper | Biogeosciences Discuss., 8, 4421–4457, 2011 Biogeosciences www.biogeosciences-discuss.net/8/4421/2011/ Discussions doi:10.5194/bgd-8-4421-2011 © Author(s) 2011. CC Attribution 3.0 License. This discussion paper is/has been under review for the journal Biogeosciences (BG). Please refer to the corresponding final paper in BG if available. Diversity of cultivated and metabolically active aerobic anoxygenic phototrophic bacteria along an oligotrophic gradient in the Mediterranean Sea C. Jeanthon1,2, D. Boeuf1,2, O. Dahan1,2, F. Le Gall1,2, L. Garczarek1,2, E. M. Bendif1,2, and A.-C. Lehours3 1INSU-CNRS, UMR 7144, Observatoire Oceanologique´ de Roscoff, Groupe Plancton Oceanique,´ 29680 Roscoff, France 2UPMC Univ Paris 06, UMR 7144, Adaptation et Diversite´ en Milieu Marin, Station Biologique de Roscoff, 29680 Roscoff, France 3CNRS, UMR 6023, Microorganismes: Genome´ et Environnement, Universite´ Blaise Pascal, 63177 Aubiere` Cedex, France Received: 21 April 2011 – Accepted: 29 April 2011 – Published: 5 May 2011 Correspondence to: C. Jeanthon (jeanthon@sb-roscoff.fr) Published by Copernicus Publications on behalf of the European Geosciences Union. 4421 Discussion Paper | Discussion Paper | Discussion Paper | Discussion Paper | Abstract Aerobic anoxygenic phototrophic (AAP) bacteria play significant roles in the bacterio- plankton productivity and biogeochemical cycles of the surface ocean. In this study, we applied both cultivation and mRNA-based molecular methods to explore the diversity of 5 AAP bacteria along an oligotrophic gradient in the Mediterranean Sea in early summer 2008. Colony-forming units obtained on three different agar media were screened for the production of bacteriochlorophyll-a (BChl-a), the light-harvesting pigment of AAP bacteria.
    [Show full text]
  • Bismis-2016 Abstract Book
    BISMiS-2016 Abstract Book Third Meeting of Bergey's International Society for Microbial Systematics on Microbial Systematics and Metagenomics September 12-15, 2016 | Pune, INDIA PUNE UNIT Abstracts - Opening Address - Keynotes Abstract Book | BISMiS-2016 | Pune, India Opening Address TAXONOMY OF PROKARYOTES - NEW CHALLENGES IN A GLOBAL WORLD Peter Kämpfer* Justus-Liebig-University Giessen, HESSEN, Germany Email: [email protected] Systematics can be considered as a comprehensive science, because in science it is an essential aspect in comparing any two or more elements, whether they are genes or genomes, proteins or proteomes, biochemical pathways or metabolomes (just to list a few examples), or whole organisms. The development of high throughput sequencing techniques has led to an enormous amount of data (genomic and other “omic” data) and has also revealed an extensive diversity behind these data. These data are more and more used also in systematics and there is a strong trend to classify and name the taxonomic units in prokaryotic systematics preferably on the basis of sequence data. Unfortunately, the knowledge of the meaning behind the sequence data does not keep up with the tremendous increase of generated sequences. The extent of the accessory genome in any given cell, and perhaps the infinite extent of the pan-genome (as an aggregate of all the accessory genomes) is fascinating but it is an open question if and how these data should be used in systematics. Traditionally the polyphasic approach in bacterial systematics considers methods including both phenotype and genotype. And it is the phenotype that is (also) playing an essential role in driving the evolution.
    [Show full text]
  • An Updated Genome Annotation for the Model Marine Bacterium Ruegeria Pomeroyi DSS-3 Adam R Rivers, Christa B Smith and Mary Ann Moran*
    Rivers et al. Standards in Genomic Sciences 2014, 9:11 http://www.standardsingenomics.com/content/9/1/11 SHORT GENOME REPORT Open Access An Updated genome annotation for the model marine bacterium Ruegeria pomeroyi DSS-3 Adam R Rivers, Christa B Smith and Mary Ann Moran* Abstract When the genome of Ruegeria pomeroyi DSS-3 was published in 2004, it represented the first sequence from a heterotrophic marine bacterium. Over the last ten years, the strain has become a valuable model for understanding the cycling of sulfur and carbon in the ocean. To ensure that this genome remains useful, we have updated 69 genes to incorporate functional annotations based on new experimental data, and improved the identification of 120 protein-coding regions based on proteomic and transcriptomic data. We review the progress made in understanding the biology of R. pomeroyi DSS-3 and list the changes made to the genome. Keywords: Roseobacter,DMSP Introduction Genome properties Ruegeria pomeroyi DSS-3 is an important model organ- The R. pomeroyi DSS-3 genome contains a 4,109,437 bp ism in studies of the physiology and ecology of marine circular chromosome (5 bp shorter than previously re- bacteria [1]. It is a genetically tractable strain that has ported [1]) and a 491,611 bp circular megaplasmid, with been essential for elucidating bacterial roles in the mar- a G + C content of 64.1 (Table 3). A detailed description ine sulfur and carbon cycles [2,3] and the biology and of the genome is found in the original article [1]. genomics of the marine Roseobacter clade [4], a group that makes up 5–20% of bacteria in ocean surface waters [5,6].
    [Show full text]
  • Trna Signatures Reveal a Polyphyletic Origin of SAR11 Strains Among Alphaproteobacteria
    tRNA Signatures Reveal a Polyphyletic Origin of SAR11 Strains among Alphaproteobacteria Katherine C. H. Amrine, Wesley D. Swingley¤, David H. Ardell* Program in Quantitative and Systems Biology, University of California, Merced, Merced, California, United States of America Abstract Molecular phylogenetics and phylogenomics are subject to noise from horizontal gene transfer (HGT) and bias from convergence in macromolecular compositions. Extensive variation in size, structure and base composition of alphaproteobacterial genomes has complicated their phylogenomics, sparking controversy over the origins and closest relatives of the SAR11 strains. SAR11 are highly abundant, cosmopolitan aquatic Alphaproteobacteria with streamlined, A+T- biased genomes. A dominant view holds that SAR11 are monophyletic and related to both Rickettsiales and the ancestor of mitochondria. Other studies dispute this, finding evidence of a polyphyletic origin of SAR11 with most strains distantly related to Rickettsiales. Although careful evolutionary modeling can reduce bias and noise in phylogenomic inference, entirely different approaches may be useful to extract robust phylogenetic signals from genomes. Here we develop simple phyloclassifiers from bioinformatically derived tRNA Class-Informative Features (CIFs), features predicted to target tRNAs for specific interactions within the tRNA interaction network. Our tRNA CIF-based model robustly and accurately classifies alphaproteobacterial genomes into one of seven undisputed monophyletic orders or families, despite great variability in tRNA gene complement sizes and base compositions. Our model robustly rejects monophyly of SAR11, classifying all but one strain as Rhizobiales with strong statistical support. Yet remarkably, conventional phylogenetic analysis of tRNAs classifies all SAR11 strains identically as Rickettsiales. We attribute this discrepancy to convergence of SAR11 and Rickettsiales tRNA base compositions.
    [Show full text]
  • Roseovarius Azorensis Sp. Nov., Isolated from Seawater At
    Author version: Antonie van Leeuwenhoek, vol.105(3); 2014; 571-578 Roseovarius azorensis sp. nov., isolated from seawater at Espalamaca, Azores Raju Rajasabapathy • Chellandi Mohandass • Syed Gulam Dastager • Qing Liu • Thi-Nhan Khieu • Chu Ky Son • Wen-Jun Li • Ana Colaco Raju Rajasabapathy · Chellandi Mohandass* Biological Oceanography Division, CSIR-National Institute of Oceanography, Dona Paula, Goa 403 004, India. E-mail: [email protected] Syed Gulam Dastager NCIM Resource Center, CSIR-National Chemical Laboratory, Dr. Homi Bhabha road, Pune 411 008, India Qing Liu · Thi-Nhan Khieu · Wen-Jun Li Yunnan Institute of Microbiology, Yunnan University, Kunming, Yunnan 650091, P.R. China Thi-Nhan Khieu · Chu Ky Son School of Biotechnology and Food Technology, Hanoi University of Science and Technology, Vietnam Ana Colaco IMAR-Department of Oceanography and Fisheries, University Açores, Cais de Sta Cruz, 9901-862, Horta, Portugal Abstract A Gram-negative, motile, non-spore forming, rod shaped aerobic bacterium, designated strain SSW084T, was isolated from a surface seawater sample collected at Espalamaca (38°33’N; 28°39’W), Azores. Growth was found to occur from 15 – 40 °C (optimum 30 °C), at pH 7.0 – 9.0 (optimum pH 7.0) and with 25 to 100 % seawater or 0.5 – 7.0 % NaCl in the presence of Mg2+ and Ca2+; no growth was found with NaCl alone. Colonies on seawater nutrient agar (SWNA) were observed to be punctiform, white, convex, circular, smooth, and translucent. Strain SSW084T did not grow on Zobell Marine Agar (ZMA) and tryptic soy agar (TSA) even when seawater supplemented. The major respiratory quinone was found to be Q-10 and the G+C content was determined to be 61.9 mol%.
    [Show full text]
  • Intrahepatic Bacterial Metataxonomic Signature in Non-Alcoholic Fatty Liver
    Hepatology ORIGINAL RESEARCH Intrahepatic bacterial metataxonomic signature in Gut: first published as 10.1136/gutjnl-2019-318811 on 2 January 2020. Downloaded from non- alcoholic fatty liver disease Silvia Sookoian ,1,2 Adrian Salatino,1,3 Gustavo Osvaldo Castaño,4 Maria Silvia Landa,1,3 Cinthia Fijalkowky,1,3 Martin Garaycoechea,5 Carlos Jose Pirola 1,3 ► Additional material is ABSTRact published online only. To view Objective We aimed to characterise the liver tissue Significance of this study please visit the journal online bacterial metataxonomic signature in two independent (http:// dx. doi. org/ 10. 1136/ What is already known on this subject? gutjnl- 2019- 318811). cohorts of patients with biopsy- proven non- alcoholic fatty liver disease (NAFLD) diagnosis, as differences in ► The natural history of non- alcoholic fatty liver For numbered affiliations see disease (NAFLD) is modulated by genetic and end of article. the host phenotypic features—from moderate to severe obesity—may be associated with significant changes in environmental factors. ► Recent discoveries revealed the role of the Correspondence to the microbial DNA profile. Dr Silvia Sookoian, Institute Design and methods Liver tissue samples from 116 gut microbiota in human health and disease, of Medical Research A Lanari, individuals, comprising of 47 NAFLD overweight or including NAFLD. However, the impact of the University of Buenos Aires moderately obese patients, 50 NAFLD morbidly obese liver tissue microbial DNA profiling on the Faculty of Medicine, Buenos disease biology remains unknown. Aires, 10109 CABA, Argentina; patients elected for bariatric surgery and 19 controls, ssookoian@ intramed. net were analysed using high- throughput 16S rRNA gene What are the new findings? Dr Carlos Jose Pirola; sequencing.
    [Show full text]
  • Assessment of the Dynamics of Microbial Community Associated with Tetraselmis Suecica Culture Under Different LED Lights Using N
    J. Microbiol. Biotechnol. (2019), 29(12), 1957–1968 https://doi.org/10.4014/jmb.1910.10046 Research Article Review jmb Assessment of the Dynamics of Microbial Community Associated with Tetraselmis suecica Culture under Different LED Lights Using Next-Generation Sequencing Su-Jeong Yang1†, Hyun-Woo Kim1†, Seok-Gwan Choi2, Sangdeok Chung2, Seok Jin Oh3, Shweta Borkar4, and Hak Jun Kim4* 1Interdisciplinary Program of Biomedical, Mechanical and Electrical Engineering, Pukyong National University, Busan 48513, Republic of Korea 2National Institute of Fisheries Science (NIFS), Busan 46083, Republic of Korea 3Department of Oceanography, Pukyong National University, Busan 48513, Republic of Korea 4Department of Chemistry, Pukyong National University, Busan 48513, Republic of Korea Received: October 21, 2019 Revised: November 11, 2019 Tetraselmis is a green algal genus, some of whose species are important in aquaculture as well Accepted: November 14, 2019 as biotechnology. In algal culture, fluorescent lamps, traditional light source for culturing First published online: algae, are now being replaced by a cost-effective light-emitting diodes (LEDs). In this study, November 18, 2019 we investigated the effect of LED light of different wavelengths (white, red, yellow, and blue) *Corresponding author on the growth of Tetraselmis suecica and its associated microbial community structures using Phone: +82-51-629-5926 the next-generation sequencing (NGS). The fastest growth rate of T. suecica was shown in the Fax: +82-51-629-5930 Email: [email protected] red light, whereas the slowest was in yellow. The highest OTUs (3426) were identified on day 0, whereas the lowest ones (308) were found on day 15 under red light.
    [Show full text]
  • Bacterial Diversity Associated with the Coccolithophorid Algae Emiliania Huxleyi and Coccolithus Pelagicus F
    Hindawi Publishing Corporation BioMed Research International Volume 2015, Article ID 194540, 15 pages http://dx.doi.org/10.1155/2015/194540 Research Article Bacterial Diversity Associated with the Coccolithophorid Algae Emiliania huxleyi and Coccolithus pelagicus f. braarudii David H. Green,1 Virginia Echavarri-Bravo,1,2 Debra Brennan,1 and Mark C. Hart1 1 Microbial & Molecular Biology, Scottish Association for Marine Science, Oban, Argyll PA37 1QA, UK 2School of Life Science, Heriot-Watt University, Edinburgh EH14 4AS, UK Correspondence should be addressed to David H. Green; [email protected] Received 28 August 2014; Accepted 30 January 2015 Academic Editor: Ameur Cherif Copyright © 2015 David H. Green et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Coccolithophores are unicellular calcifying marine phytoplankton that can form large and conspicuous blooms in the oceans and make significant contributions to oceanic carbon cycling and atmospheric CO2 regulation. Despite their importance, the bacterial diversity associated with these algae has not been explored for ecological or biotechnological reasons. Bacterial membership of Emiliania huxleyi and Coccolithus pelagicus f. braarudii cultures was assessed using cultivation and cultivation-independent methods. The communities were species rich compared to other phytoplankton cultures. Community analysis identified specific taxa which cooccur in all cultures (Marinobacter and Marivita). Hydrocarbon-degrading bacteria were found in all cultures. The presence of Acidobacteria, Acidimicrobidae, Schlegelella,andThermomonas was unprecedented but were potentially explained by calcification associated with coccolith production. One strain of Acidobacteria was cultivated and is closely related toa marine Acidobacteria isolated from a sponge.
    [Show full text]
  • Taxonomic Hierarchy of the Phylum Proteobacteria and Korean Indigenous Novel Proteobacteria Species
    Journal of Species Research 8(2):197-214, 2019 Taxonomic hierarchy of the phylum Proteobacteria and Korean indigenous novel Proteobacteria species Chi Nam Seong1,*, Mi Sun Kim1, Joo Won Kang1 and Hee-Moon Park2 1Department of Biology, College of Life Science and Natural Resources, Sunchon National University, Suncheon 57922, Republic of Korea 2Department of Microbiology & Molecular Biology, College of Bioscience and Biotechnology, Chungnam National University, Daejeon 34134, Republic of Korea *Correspondent: [email protected] The taxonomic hierarchy of the phylum Proteobacteria was assessed, after which the isolation and classification state of Proteobacteria species with valid names for Korean indigenous isolates were studied. The hierarchical taxonomic system of the phylum Proteobacteria began in 1809 when the genus Polyangium was first reported and has been generally adopted from 2001 based on the road map of Bergey’s Manual of Systematic Bacteriology. Until February 2018, the phylum Proteobacteria consisted of eight classes, 44 orders, 120 families, and more than 1,000 genera. Proteobacteria species isolated from various environments in Korea have been reported since 1999, and 644 species have been approved as of February 2018. In this study, all novel Proteobacteria species from Korean environments were affiliated with four classes, 25 orders, 65 families, and 261 genera. A total of 304 species belonged to the class Alphaproteobacteria, 257 species to the class Gammaproteobacteria, 82 species to the class Betaproteobacteria, and one species to the class Epsilonproteobacteria. The predominant orders were Rhodobacterales, Sphingomonadales, Burkholderiales, Lysobacterales and Alteromonadales. The most diverse and greatest number of novel Proteobacteria species were isolated from marine environments. Proteobacteria species were isolated from the whole territory of Korea, with especially large numbers from the regions of Chungnam/Daejeon, Gyeonggi/Seoul/Incheon, and Jeonnam/Gwangju.
    [Show full text]