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      Draft Genome Sequence of Thermophilic Exiguobacterium sp. Strain JLM-2, Isolated from Deep-Sea Ferromanganese Nodules

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          Abstract

          Exiguobacterium sp. strain JLM-2 is a thermophilic bacterium isolated from deep-sea ferromanganese (FeMn) nodules. The estimated genome of this strain is 2.9 Mb, with a G+C content of 48.32%. It has a novel circular 15,570-bp plasmid. The draft genome sequence may provide useful information about Mn-microbe interactions and the genetic basis for tolerance to environment stresses.

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          The Exiguobacterium genus: biodiversity and biogeography.

          Tatiana A Vishnivetskaya, Sophia Kathariou, James Tiedje (2009)
          Bacteria of the genus Exiguobacterium are low G + C, Gram-positive facultative anaerobes that have been repeatedly isolated from ancient Siberian permafrost. In addition, Exiguobacterium spp. have been isolated from markedly diverse sources, including Greenland glacial ice, hot springs at Yellowstone National Park, the rhizosphere of plants, and the environment of food processing plants. Strains of this hereto little known bacterium that have been retrieved from such different (and often extreme) environments are worthy of attention as they are likely to be specifically adapted to such environments and to carry variations in the genome which may correspond to psychrophilic and thermophilic adaptations. However, comparative genomic investigations of Exiguobacterium spp. from different sources have been limited. In this study, we employed different molecular approaches for the comparative analysis of 24 isolates from markedly diverse environments including ancient Siberian permafrost and hot springs at Yellowstone National Park. Pulsed-field gel electrophoresis (PFGE) with I-CeuI (an intron-encoded endonuclease), AscI and NotI were optimized for the determination of genomic fingerprints of nuclease-producing isolates. The application of a DNA macroarray for 82 putative stress-response genes yielded strain-specific hybridization profiles. Cluster analyses of 16S rRNA gene sequence data, PFGE I-CeuI restriction patterns and hybridization profiles suggested that Exiguobacterium strains formed two distinct divisions that generally agreed with temperature ranges for growth. With few exceptions (e.g., Greenland ice isolate GIC31), psychrotrophic and thermophilic isolates belonged to different divisions.
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            Characterization of Exiguobacterium isolates from the Siberian permafrost. Description of Exiguobacterium sibiricum sp. nov.

            Debora Frigi Rodrigues, Johan Goris, Tatiana Vishnivetskaya … (2006)
            Three Gram-positive bacterial strains, 7-3, 255-15 and 190-11, previously isolated from Siberian permafrost, were characterized and taxonomically classified. These microorganisms are rod-shaped, facultative aerobic, motile with peritrichous flagella and their growth ranges are from -2.5 to 40 degrees C. The chemotaxonomic markers indicated that the three strains belong to the genus Exiguobacterium. Their peptidoglycan type was A3alpha L-Lys-Gly. The predominant menaquinone detected in all three strains was MK7. The polar lipids present were phosphatidyl-glycerol, diphosphatidyl-glycerol and phosphatidyl-ethanolamine. The major fatty acids were iso-C13:0, anteiso-C13:0, iso-C15:0, C16:0 and iso-C17:0. Phylogenetic analysis based on 16S rRNA and six diverse genes, gyrB (gyrase subunit B), rpoB (DNA-directed RNA polymerase beta subunit), recA (homologous recombination), csp (cold shock protein), hsp70 (ClassI-heat shock protein-chaperonin) and citC (isocitrate dehydrogenase), indicated that the strains were closely related to Exiguobacterium undae (DSM 14481(T)) and Exiguobacterium antarcticum (DSM 14480(T)). On the basis of the phenotypic characteristics, phylogenetic data and DNA-DNA reassociation data, strain 190-11 was classified as E. undae, while the other two isolates, 7-3 and 255-15, comprise a novel species, for which the name Exiguobacterium sibiricum sp. nov. is proposed.
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              Exiguobacterium indicum sp. nov., a psychrophilic bacterium from the Hamta glacier of the Himalayan mountain ranges of India.

              Preeti Chaturvedi, S. Shivaji (2006)
              Strain HHS 31(T), a Gram-positive, motile, rod-shaped, non-spore-forming, alkaliphilic bacterium, was isolated from the melt water of a glacier. Phenotypic and chemotaxonomic characteristics indicate that strain HHS 31(T) is related to species of the genus Exiguobacterium. The 16S rRNA gene sequence similarities between HHS 31(T) and strains of known species confirm that it is closely related to members of the genus Exiguobacterium (93-99 %) and that it exhibits >97 % similarity with Exiguobacterium acetylicum DSM 20416(T) (98.9 %), Exiguobacterium antarcticum DSM 14480(T) (98.0 %), Exiguobacterium oxidotolerans JCM 12280(T) (97.9 %) and Exiguobacterium undae DSM 14481(T) (97.4 %). Phylogenetic analysis based on the 16S rRNA gene sequence further confirms the affiliation of HHS 31(T) with the genus Exiguobacterium. However, the levels of DNA-DNA relatedness between HHS 31(T) and E. oxidotolerans JCM 12280(T), E. acetylicum DSM 20416(T), E. undae DSM 14481(T) and E. antarcticum DSM 14480(T) are 50, 63, 67 and 28 %, respectively. Strain HHS 31(T) also differs from these four closely related species in terms of a number of phenotypic traits. The phenotypic, chemotaxonomic and phylogenetic data suggest that HHS 31(T) merits the status of a novel species, for which the name Exiguobacterium indicum sp. nov. is proposed. The type strain is HHS 31(T) (=LMG 23471(T)=IAM 15368(T)).
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                Author and article information

                Journal
                Journal ID (nlm-ta): Genome Announc
                Journal ID (iso-abbrev): Genome Announc
                Journal ID (hwp): ga
                Journal ID (pmc): ga
                Journal ID (publisher-id): GA
                Title: Genome Announcements
                Publisher: American Society for Microbiology (1752 N St., N.W., Washington, DC )
                ISSN (Electronic): 2169-8287
                Publication date (Electronic): 23 July 2015
                Publication date Collection: Jul-Aug 2015
                Volume: 3
                Issue: 4
                Electronic Location Identifier: e00794-15
                Affiliations
                [a ]Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
                [b ]Laboratory of Marine Ecosystem and Biogeochemistry, Second Institute of Oceanography, State Oceanic Administration, Hangzhou, China
                Author notes
                Address correspondence to Xin-Zheng Li, lixzh@ 123456qdio.ac.cn .
                Article
                Publisher ID: genomeA00794-15
                DOI: 10.1128/genomeA.00794-15
                PMC ID: 4513150
                PubMed ID: 26205856
                SO-VID: 5ac4e3a8-76b6-4e79-9bd0-0a74ebfcd101
                Copyright © Copyright © 2015 Zhang et al.
                License:

                This is an open-access article distributed under the terms of the Creative Commons Attribution 3.0 Unported license.

                History
                Date received : 9 June 2015
                Date accepted : 16 June 2015
                Page count
                Figures: 0, Tables: 0, Equations: 0, References: 9, Pages: 1, Words: 841
                Categories
                Subject: Prokaryotes
                Custom metadata
                cover-date July/August 2015
                access-type free

                ScienceOpen disciplines: Genetics
                Data availability:
                ScienceOpen disciplines: Genetics

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