1887

Abstract

Phylogenetic analyses of the genus were performed using the sequences of the 16S rRNA gene and the GyrB protein to establish its taxonomic status. The results indicated a consistent clustering of the genus into two clades, with significant bootstrap values, with all the phylogenetic methods employed. Clade 1 was represented by seven species, , , , , , and , while clade 2 consisted of only three species, , and . Evolutionary distances between species of clades 1 and 2, based on 16S rRNA gene and GyrB protein sequences, ranged from 93.0 to 95.0 % and 69.0 to 73.0 %, respectively. In addition, clades 1 and 2 possessed 18 unique signature nucleotides, at positions 132, 184 : 193, 185 : 192, 230, 616 : 624, 631, 632, 633, 738, 829, 1257, 1265, 1281, 1356 and 1366, in the 16S rRNA gene sequence and can be differentiated by the occurrence of a 15 nt signature motif 5′-CAAATCAGAATGTTG at positions 1354–1368 in members of clade 2. Robust clustering of the genus into two clades based on analysis of 16S rRNA gene and GyrB protein sequences, 16S rRNA gene sequence similarity of ≤95.0 % and the occurrence of signature nucleotides and signature motifs in the 16S rRNA gene suggested that the genus should be split into two genera. The genus gen. nov. is therefore created to accommodate the seven species of clade 1, while the name is retained to represent species of clade 2. The species of clade 1 are transferred to the genus as comb. nov. (type strain DSM 15026 = KMM 241), comb. nov. (type strain NO2 = KCTC 12755 = LMG 23762), comb. nov. (type strain GGW-M5 = KCTC 32108 = CCUG 62918), comb. nov. (type strain BSs20135 = CCTCC AB 209161 = KACC 14537), comb. nov. (type strain E3 = CGMCC 1.7001 = JCM 15139), comb. nov. (type strain ARK 150 = CIP 108324 = LMG 21857) and comb. nov. (type strain 170 = CGMCC1.6130 = JCM 13954). The type species of the genus is . An emended description of the genus is provided. In addition, a novel strain, 162Z-12, was isolated from seawater collected as part of an iron fertilization experiment (LOHAFEX) conducted in the Southern Ocean in 2009 and was subjected to polyphasic taxonomic characterization. Cells of 162Z-12 were Gram-negative, aerobic, motile, ovoid to short rod-shaped, obligatorily halophilic and possessed all the characteristics of the genus . Strain 162Z-12 shared the highest 16S rRNA gene sequence similarity with the type strains of (99.7 %), (99.7 %), (98.5 %) and (98.3 %). However, it exhibited DNA–DNA relatedness of less than 70.0 % with its nearest phylogenetic relatives, well below the threshold value for species delineation. Further, strain 162Z-12 differed from the nearest species in several phenotypic characteristics, in addition to the occurrence of unique nucleotides G, T, T and T at positions 1194, 1269, 1270 and 1271 of the 16S rRNA gene. Based on the cumulative differences it exhibited from its nearest phylogenetic neighbours, strain 162Z-12 was identified as a novel member of the genus and assigned to the novel species sp. nov. The type strain of is 162Z-12 ( = KCTC 32337 = LMG 27453).

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2014-09-01
2019-11-22
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References

  1. Altschul S. F., Gish W., Miller W., Myers E. W., Lipman D. J.. ( 1990;). Basic local alignment search tool. . J Mol Biol 215:, 403–410. [CrossRef][PubMed]
    [Google Scholar]
  2. Anzai Y., Kim H., Park J. Y., Wakabayashi H., Oyaizu H.. ( 2000;). Phylogenetic affiliation of the pseudomonads based on 16S rRNA sequence. . Int J Syst Evol Microbiol 50:, 1563–1589. [CrossRef][PubMed]
    [Google Scholar]
  3. Ash C., Farrow J. A. E., Wallbanks S., Collins M. D.. ( 1991;). Phylogenetic heterogeneity of the genus Bacillus revealed by comparative analysis of small subunit ribosomal RNA sequences. . Lett Appl Microbiol 13:, 202–206. [CrossRef]
    [Google Scholar]
  4. Atlas R. M., Parks L. C.. ( 1993;). Handbook of Microbiological Media. London:: CRC Press;.
    [Google Scholar]
  5. Baik K. S., Park Y. D., Seong C. N., Kim E. M., Bae K. S., Chun J.. ( 2006;). Glaciecola nitratireducens sp. nov., isolated from seawater. . Int J Syst Evol Microbiol 56:, 2185–2188. [CrossRef][PubMed]
    [Google Scholar]
  6. Bailey T. L., Williams N., Misleh C., Li W. W.. ( 2006;). meme: discovering and analyzing DNA and protein sequence motifs. . Nucleic Acids Res 34: (Web Server issue), W369–W373. [CrossRef][PubMed]
    [Google Scholar]
  7. Baumann P., Gauthier M., Baumann L.. ( 1984;). Genus Alteromonas Baumann, Baumann, Mandel and Allen 1972, 418AL. . In Bergey’s Manual of Systematic Bacteriology, vol. 1, pp. 343–352. Edited by Krieg N. R., Holt J. G... Baltimore:: Williams & Wilkins;.
    [Google Scholar]
  8. Bertani G.. ( 1951;). Studies on lysogenesis. I. The mode of phage liberation by lysogenic Escherichia coli. . J Bacteriol 62:, 293–300.[PubMed]
    [Google Scholar]
  9. Bowman J. P., McCammon S. A., Brown J. L., McMeekin T. A.. ( 1998;). Glaciecola punicea gen. nov., sp. nov. and Glaciecola pallidula gen. nov., sp. nov.: psychrophilic bacteria from Antarctic sea-ice habitats. . Int J Syst Bacteriol 48:, 1213–1222. [CrossRef]
    [Google Scholar]
  10. Chen L. P., Xu H. Y., Fu S.-Z., Fan H. X., Liu Y. H., Liu S. J., Liu Z. P.. ( 2009;). Glaciecola lipolytica sp. nov., isolated from seawater near Tianjin city, China. . Int J Syst Evol Microbiol 59:, 73–76. [CrossRef][PubMed]
    [Google Scholar]
  11. Chun J., Lee J. H., Jung Y., Kim M., Kim S., Kim B. K., Lim Y. W.. ( 2007;). EzTaxon: a web-based tool for the identification of prokaryotes based on 16S ribosomal RNA gene sequences. . Int J Syst Evol Microbiol 57:, 2259–2261. [CrossRef][PubMed]
    [Google Scholar]
  12. Colwell R. R.. ( 1970;). Polyphasic taxonomy of the genus Vibrio: numerical taxonomy of Vibrio cholerae, Vibrio parahaemolyticus, and related Vibrio species. . J Bacteriol 104:, 410–433.[PubMed]
    [Google Scholar]
  13. Cowan S. T., Steel K. J.. ( 1965;). Manual for the Identification of Medical Bacteria. London:: Cambridge University Press;.
    [Google Scholar]
  14. Dai X., Wang Y. N., Wang B. J., Liu S. J., Zhou Y. G.. ( 2005;). Planomicrobium chinense sp. nov., isolated from coastal sediment, and transfer of Planococcus psychrophilus and Planococcus alkanoclasticus to Planomicrobium as Planomicrobium psychrophilum comb. nov. and Planomicrobium alkanoclasticum comb. nov.. Int J Syst Evol Microbiol 55:, 699–702. [CrossRef][PubMed]
    [Google Scholar]
  15. Davis B. D.. ( 1949;). The isolation of biochemically deficient mutants of bacteria by means of penicillin. . Proc Natl Acad Sci U S A 35:, 1–10. [CrossRef][PubMed]
    [Google Scholar]
  16. Deming J. W., Somers L. K., Straube W. L., Swartz D. G., Macdonell M. T.. ( 1988;). Isolation of an obligately barophilic bacterium and description of a new genus, Colwellia gen. nov.. Syst Appl Microbiol 10:, 152–160. [CrossRef]
    [Google Scholar]
  17. Gauthier G., Gauthier M., Christen R.. ( 1995;). Phylogenetic analysis of the genera Alteromonas, Shewanella, and Moritella using genes coding for small-subunit rRNA sequences and division of the genus Alteromonas into two genera, Alteromonas (emended) and Pseudoalteromonas gen. nov., and proposal of twelve new species combinations. . Int J Syst Bacteriol 45:, 755–761. [CrossRef][PubMed]
    [Google Scholar]
  18. Gügi B., Orange N., Hellio F., Burini J. F., Guillou C., Leriche F., Guespin-Michel J. F.. ( 1991;). Effect of growth temperature on several exported enzyme activities in the psychrotrophic bacterium Pseudomonas fluorescens. . J Bacteriol 173:, 3814–3820.[PubMed]
    [Google Scholar]
  19. Ivanova E. P., Flavier S., Christen R.. ( 2004;). Phylogenetic relationships among marine Alteromonas-like proteobacteria: emended description of the family Alteromonadaceae and proposal of Pseudoalteromonadaceae fam. nov., Colwelliaceae fam. nov., Shewanellaceae fam. nov., Moritellaceae fam. nov., Ferrimonadaceae fam. nov., Idiomarinaceae fam. nov. and Psychromonadaceae fam. nov.. Int J Syst Evol Microbiol 54:, 1773–1788. [CrossRef][PubMed]
    [Google Scholar]
  20. Jean W. D., Hsu C. Y., Huang S. P., Chen J. S., Lin S., Su M. H., Shieh W. Y.. ( 2013;). Reclassification of [Glaciecola] lipolytica and [Aestuariibacter] litoralis in Aliiglaciecola gen. nov., as Aliiglaciecola lipolytica comb. nov. and Aliiglaciecola litoralis comb. nov., respectively. . Int J Syst Evol Microbiol 63:, 2859–2864. [CrossRef][PubMed]
    [Google Scholar]
  21. Justice S. S., Hunstad D. A., Cegelski L., Hultgren S. J.. ( 2008;). Morphological plasticity as a bacterial survival strategy. . Nat Rev Microbiol 6:, 162–168. [CrossRef][PubMed]
    [Google Scholar]
  22. Kimura M.. ( 1980;). A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. . J Mol Evol 16:, 111–120. [CrossRef][PubMed]
    [Google Scholar]
  23. Komagata K., Suzuki K.. ( 1987;). Lipid and cell-wall analysis in bacterial systematics. . Methods Microbiol 19:, 161–207. [CrossRef]
    [Google Scholar]
  24. Lányi B.. ( 1987;). Classical and rapid identification methods for medically important bacteria. . Methods Microbiol 19:, 1–67. [CrossRef]
    [Google Scholar]
  25. Ludwig W., Strunk O., Klugbauer S., Klugbauer N., Weizenegger M., Neumaier J., Bachleitner M., Schleifer K. H.. ( 1998;). Bacterial phylogeny based on comparative sequence analysis. . Electrophoresis 19:, 554–568. [CrossRef][PubMed]
    [Google Scholar]
  26. Lyman J., Fleming R. H.. ( 1940;). Composition of sea water. . J Mar Res 3:, 134–146.
    [Google Scholar]
  27. MacDonell M. T., Colwell R. R.. ( 1985;). Phylogeny of the Vibrionaceae, and recommendation for two new genera, Listonella and Shewanella. . Syst Appl Microbiol 6:, 171–182. [CrossRef]
    [Google Scholar]
  28. MacFaddin J. F.. ( 1985;). Media for Isolation, Cultivation, Identification, Maintenance of Medical Bacteria, vol. 1. Baltimore:: Williams & Wilkins;.
    [Google Scholar]
  29. Marmur J.. ( 1961;). Procedure for the isolation of deoxyribonucleic acid from microorganisms. . J Mol Biol 3:, 208–218. [CrossRef]
    [Google Scholar]
  30. Maruyama T., Park H. D., Ozawa K., Tanaka Y., Sumino T., Hamana K., Hiraishi A., Kato K.. ( 2006;). Sphingosinicella microcystinivorans gen. nov., sp. nov., a microcystin-degrading bacterium. . Int J Syst Evol Microbiol 56:, 85–89. [CrossRef][PubMed]
    [Google Scholar]
  31. Matsuyama H., Hirabayashi T., Kasahara H., Minami H., Hoshino T., Yumoto I.. ( 2006;). Glaciecola chathamensis sp. nov., a novel marine polysaccharide-producing bacterium. . Int J Syst Evol Microbiol 56:, 2883–2886. [CrossRef][PubMed]
    [Google Scholar]
  32. Murray R. G. E., Brenner D. J., Colwell R. R., De Vos P., Goodfellow M., Grimont P. A. D., Pfennig N., Stackebrandt E., Zavarzin G. A.. ( 1990;). Report of the ad hoc committee on approaches to taxonomy within the Proteobacteria. . Int J Syst Bacteriol 40:, 213–215. [CrossRef]
    [Google Scholar]
  33. Pandey K. K., Mayilraj S., Chakrabarti T.. ( 2002;). Pseudomonas indica sp. nov., a novel butane-utilizing species. . Int J Syst Evol Microbiol 52:, 1559–1567. [CrossRef][PubMed]
    [Google Scholar]
  34. Park S., Yoon J. H.. ( 2013;). Glaciecola aquimarina sp. nov., a gammaproteobacterium isolated from coastal seawater. . Antonie van Leeuwenhoek 103:, 1141–1148. [CrossRef][PubMed]
    [Google Scholar]
  35. Reddy G. S. N.. ( 2013;). Phylogenetic analyses of the genus Hymenobacter and description of Siccationidurans gen. nov., and Parahymenobacter gen. nov.. J Phylogenet Evol Biol 1:, 122. [CrossRef]
    [Google Scholar]
  36. Reddy G. S. N., Garcia-Pichel F.. ( 2005;). Dyadobacter crusticola sp. nov., from biological soil crusts in the Colorado Plateau, USA, and an emended description of the genus Dyadobacter Chelius and Triplett 2000. . Int J Syst Evol Microbiol 55:, 1295–1299. [CrossRef][PubMed]
    [Google Scholar]
  37. Reddy G. S. N., Garcia-Pichel F.. ( 2009;). Description of Patulibacter americanus sp. nov., isolated from biological soil crusts, emended description of the genus Patulibacter Takahashi et al. 2006 and proposal of Solirubrobacterales ord. nov. and Thermoleophilales ord. nov.. Int J Syst Evol Microbiol 59:, 87–94. [CrossRef][PubMed]
    [Google Scholar]
  38. Reddy G. S. N., Aggarwal R. K., Matsumoto G. I., Shivaji S.. ( 2000;). Arthrobacter flavus sp. nov., a psychrophilic bacterium isolated from a pond in McMurdo Dry Valley, Antarctica. . Int J Syst Evol Microbiol 50:, 1553–1561. [CrossRef][PubMed]
    [Google Scholar]
  39. Reddy G. S. N., Uttam A., Shivaji S.. ( 2008;). Bacillus cecembensis sp. nov., isolated from the Pindari glacier of the Indian Himalayas. . Int J Syst Evol Microbiol 58:, 2330–2335. [CrossRef][PubMed]
    [Google Scholar]
  40. Reddy G. S. N., Pradhan S., Manorama R., Shivaji S.. ( 2010;). Cryobacterium roopkundense sp. nov., a psychrophilic bacterium isolated from glacial soil. . Int J Syst Evol Microbiol 60:, 866–870. [CrossRef][PubMed]
    [Google Scholar]
  41. Reddy G. S. N., Manasa B. P., Singh S. K., Shivaji S.. ( 2013;). Paenisporosarcina indica sp. nov., a psychrophilic bacterium from a glacier, and reclassification of Sporosarcina antarctica Yu et al. 2008 as Paenisporosarcina antarctica comb. nov. and emended description of the genus Paenisporosarcina. . Int J Syst Evol Microbiol 63:, 2927–2933. [CrossRef][PubMed]
    [Google Scholar]
  42. Romanenko L. A., Zhukova N. V., Rohde M., Lysenko A. M., Mikhailov V. V., Stackebrandt E.. ( 2003;). Glaciecola mesophila sp. nov., a novel marine agar-digesting bacterium. . Int J Syst Evol Microbiol 53:, 647–651. [CrossRef][PubMed]
    [Google Scholar]
  43. Rosselló-Mora R., Ludwig W., Kämpfer P., Amann R., Schleifer K. H.. ( 1995;). Ferrimonas balearica gen. nov., sp. nov., a new marine facultative Fe(III)-reducing bacterium. . Syst Appl Microbiol 18:, 196–202. [CrossRef]
    [Google Scholar]
  44. Scherer C., Müller K. D., Rath P. M., Ansorg R. A.. ( 2003;). Influence of culture conditions on the fatty acid profiles of laboratory-adapted and freshly isolated strains of Helicobacter pylori. . J Clin Microbiol 41:, 1114–1117. [CrossRef][PubMed]
    [Google Scholar]
  45. Shivaji S., Rao N. S., Saisree I., Sheth V., Reddy G. S. N., Bhargava P. M.. ( 1988;). Isolation and identification of Micrococcus roseus and Planococcus sp. from Schirmacher oasis, Antarctica. . J Biosci 13:, 409–414. [CrossRef]
    [Google Scholar]
  46. Shivaji S., Srinivas T. N. R., Reddy G. S. N.. ( 2013;). Family Planococcaceae. . In The Prokaryotes, , 4th edn.. Edited by Rosenberg E., DeLong E. F., Thompson F., Lory S., Stackebrandt E... New York:: Springer;.
    [Google Scholar]
  47. Smibert R. M., Krieg N. R.. ( 1994;). Phenotypic characterization. . In Methods for General and Molecular Bacteriology, pp. 607–654. Edited by Gerhardt P., Murray R. G. E., Wood W. A., Krieg N. R... Washington, DC:: American Society for Microbiology;.
    [Google Scholar]
  48. Sousa A. M., Machado I., Pereira M. O.. ( 2011;). Phenotypic switching: an opportunity to bacteria thrive. . In Science against Microbial Pathogens: Communicating Current Research and Technological Advances, vol. 1, pp. 252–262. Edited by Méndez-Vilas A... Badajoz, Spain:: Formatexa;.
    [Google Scholar]
  49. Stackebrandt E., Goebel B. M.. ( 1994;). Taxonomic note: a place for DNA-DNA reassociation and 16S rRNA sequence analysis in the present species definition in bacteriology. . Int J Syst Bacteriol 44:, 846–849. [CrossRef]
    [Google Scholar]
  50. Stackebrandt E., Rainey F. A., Ward-Rainey N.. ( 1997;). Proposal for a new hierarchic classification system, Actinobacteria classis nov.. Int J Syst Bacteriol 47:, 479–491. [CrossRef]
    [Google Scholar]
  51. Stackebrandt E., Frederiksen W., Garrity G. M., Grimont P. A., Kämpfer P., Maiden M. C., Nesme X., Rosselló-Mora R., Swings J.. & other authors ( 2002;). Report of the ad hoc committee for the re-evaluation of the species definition in bacteriology. . Int J Syst Evol Microbiol 52:, 1043–1047. [CrossRef][PubMed]
    [Google Scholar]
  52. Swofford D. L., Waddell P. J., Huelsenbeck J. P., Foster P. G., Lewis P. O., Rogers J. S.. ( 2001;). Bias in phylogenetic estimation and its relevance to the choice between parsimony and likelihood methods. . Syst Biol 50:, 525–539. [CrossRef][PubMed]
    [Google Scholar]
  53. Tamaoka J., Katayama-Fujimura Y., Kuraishi H.. ( 1983;). Analysis of bacterial menaquinone mixtures by high-performance liquid chromatography. . J Appl Bacteriol 54:, 31–36. [CrossRef]
    [Google Scholar]
  54. Tamura K., Peterson D., Peterson N., Stecher G., Nei M., Kumar S.. ( 2011;). mega5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. . Mol Biol Evol 28:, 2731–2739. [CrossRef][PubMed]
    [Google Scholar]
  55. Thiele S., Fuchs B. M., Ramaiah N., Amann R.. ( 2012;). Microbial community response during the iron fertilization experiment LOHAFEX. . Appl Environ Microbiol 78:, 8803–8812. [CrossRef][PubMed]
    [Google Scholar]
  56. Thompson J. D., Gibson T. J., Plewniak F., Jeanmougin F., Higgins D. G.. ( 1997;). The clustal_x windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. . Nucleic Acids Res 25:, 4876–4882. [CrossRef][PubMed]
    [Google Scholar]
  57. Van Trappen S., Tan T. L., Yang J., Mergaert J., Swings J.. ( 2004;). Glaciecola polaris sp. nov., a novel budding and prosthecate bacterium from the Arctic Ocean, and emended description of the genus Glaciecola. . Int J Syst Evol Microbiol 54:, 1765–1771. [CrossRef][PubMed]
    [Google Scholar]
  58. Vandamme P., Pot B., Gillis M., de Vos P., Kersters K., Swings J.. ( 1996;). Polyphasic taxonomy, a consensus approach to bacterial systematics. . Microbiol Rev 60:, 407–438.[PubMed]
    [Google Scholar]
  59. Woese C. R.. ( 1985;). Why study evolutionary relationships among bacteria?. In Evolution of Prokaryotes, pp. 1–30. Edited by Schleifer K. H., Stackebrandt E... London:: Academic Press;.
    [Google Scholar]
  60. Woese C. R., Fox G. E.. ( 1977;). Phylogenetic structure of the prokaryotic domain: the primary kingdoms. . Proc Natl Acad Sci U S A 74:, 5088–5090. [CrossRef][PubMed]
    [Google Scholar]
  61. Yi H., Bae K. S., Chun J.. ( 2004;). Aestuariibacter salexigens gen. nov., sp. nov. and Aestuariibacter halophilus sp. nov., isolated from tidal flat sediment, and emended description of Alteromonas macleodii. . Int J Syst Evol Microbiol 54:, 571–576. [CrossRef][PubMed]
    [Google Scholar]
  62. Yong J. J., Park S. J., Kim H. J., Rhee S. K.. ( 2007;). Glaciecola agarilytica sp. nov., an agar-digesting marine bacterium from the East Sea, Korea. . Int J Syst Evol Microbiol 57:, 951–953. [CrossRef][PubMed]
    [Google Scholar]
  63. Young K. D.. ( 2006;). The selective value of bacterial shape. . Microbiol Mol Biol Rev 70:, 660–703. [CrossRef][PubMed]
    [Google Scholar]
  64. Young K. D.. ( 2007;). Bacterial morphology: why have different shapes?. Curr Opin Microbiol 10:, 596–600. [CrossRef][PubMed]
    [Google Scholar]
  65. Zhang D. C., Yu Y., Chen B., Wang H. X., Liu H. C., Dong X. Z., Zhou P. J.. ( 2006;). Glaciecola psychrophila sp. nov., a novel psychrophilic bacterium isolated from the Arctic. . Int J Syst Evol Microbiol 56:, 2867–2869. [CrossRef][PubMed]
    [Google Scholar]
  66. Zhang Y. J., Zhang X. Y., Mi Z. H., Chen C. X., Gao Z. M., Chen X. L., Yu Y., Chen B., Zhang Y. Z.. ( 2011;). Glaciecola arctica sp. nov., isolated from Arctic marine sediment. . Int J Syst Evol Microbiol 61:, 2338–2341. [CrossRef][PubMed]
    [Google Scholar]
  67. ZoBell C. E.. ( 1941;). Studies on marine bacteria. I. The cultural requirements of heterotrophic aerobes. . J Mar Res 4:, 42–75.
    [Google Scholar]
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