1887

Abstract

A novel basophilic bacterial strain, designated as SCSIO 08040, was recovered from a deep-sea sediment sample collected from the Indian Ocean. The strain was Gram-stain-negative, vibrioid or spiral, light pink, 0.6–1.0 µm wide and 1.0–2.5 µm long. Growth occurred at 20–45 °C, pH 7–11 and <5 % (w/v) NaCl, with optimum growth at 28–37 °C, pH 7 and 0–3 % (w/v) NaCl. Catalase-, oxidase and urease-positive, nitrate reduction-negative. Analysis of 16S rRNA gene sequencing revealed that strain SCSIO 08040 had the highest similarity of 95.3 % to Rhodocista pekingensis 3-p. Phylogenetic analysis based on nearly complete 16S rRNA gene sequences showed that the novel isolate formed a distinct phylogenetic lineage in the family Rhodospirillaceae . The whole-cell hydrolysate contained meso–diaminopimelic acid, galactose, mannose and xylose. The total cellular fatty acid profile was dominated by C18:1ω7c and C19:0cycloω8c. Q-10 was the predominant ubiquinone. The major phospholipids were diphosphatidylglycerol, phosphatidylcholine and phosphatidylethanolamine. The DNA G+C content of strain SCSIO 08040 was 66.82 mol%. Based on these polyphasic data, a new genus, Indioceanicola gen. nov., is proposed in the family Rhodospirillaceae with the type species Indioceanicola profundi sp. nov. and the type strain SCSIO 08040 (=DSM 105146=CGMCC 1.15812).

Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.003016
2018-10-11
2024-03-28
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/68/12/3707.html?itemId=/content/journal/ijsem/10.1099/ijsem.0.003016&mimeType=html&fmt=ahah

References

  1. Pfennig N, Truper HG. Higher taxa of the phototrophic bacteria. Int J Syst Evol Microbiol 1971; 21:17–18
    [Google Scholar]
  2. Molisch H. Die Purpurbakterien nach neuen untersuchungen: eine mikrobiologische studie. Fischer 1907
    [Google Scholar]
  3. Park S, Park JM, Kang CH, Yoon JH. Aestuariispira insulae gen. nov., sp. nov., a lipolytic bacterium isolated from a tidal flat. Int J Syst Evol Microbiol 2014; 64:1841–1846 [View Article][PubMed]
    [Google Scholar]
  4. Yamada K, Fukuda W, Kondo Y, Miyoshi Y, Atomi H et al. Constrictibacter antarcticus gen. nov., sp. nov., a cryptoendolithic micro-organism from Antarctic white rock. Int J Syst Evol Microbiol 2011; 61:1973–1980 [View Article][PubMed]
    [Google Scholar]
  5. Kawasaki H, Hoshino Y, Kuraishi H, Yamasato K. Rhodocista centenaria gen. nov., sp. nov., a cyst-forming anoxygenic photosynthetic bacterium and its phylogenetic position in the Proteobacteria alpha group. J Gen Appl Microbiol 1992; 38:541–551 [View Article]
    [Google Scholar]
  6. Imhoff JF, Petri R, Suling J. Reclassification of species of the spiral-shaped phototrophic purple non-sulfur bacteria of the α-Proteobacteria: description of the new genera Phaeospirillum gen. nov., Rhodovibrio gen. nov., Rhodothalussium gen. nov. and Roseospira gen. nov. as well as transfer of Rhodospirillum fulvum to Phaeospirillum fulvum comb. nov., of Rhodospirillum molischianum to Phaeospirillum molischianuvn comb. nov., of Rhodospirillum salinarum to Rhodovibrio salinarum comb. nov., of Rhodospirillum sodomense to Rhodovibrio sodomensis comb. nov., of Rhodospirillum salexigens to Rhodothalassium salexigens comb. nov., and of Rhodospirillum mediosalinum to Roseospira mediosalina comb. nov. Int J Syst Evol Microbiol 1998; 48:793–798
    [Google Scholar]
  7. Williams TJ, Lefèvre CT, Zhao WD, Beveridge TJ, Bazylinski DA. Magnetospira thiophila gen. nov., sp. nov., a marine magnetotactic bacterium that represents a novel lineage within the Rhodospirillaceae (Alphaproteobacteria). Int J Syst Evol Microbiol 2012; 62:2443–2450 [View Article][PubMed]
    [Google Scholar]
  8. Bazylinski DA, Williams TJ, Lefèvre CT, Trubitsyn D, Fang JS et al. Magnetovibrio blakemorei gen. nov., sp. nov., a magnetotactic bacterium (Alphaproteobacteria: Rhodospirillaceae) isolated from a salt marsh. Int J Syst Evol Microbiol 2013; 63:1824–1833 [View Article][PubMed]
    [Google Scholar]
  9. Sizova MV, Panikov NS, Spiridonova EM, Slobodova NV, Tourova TP. Novel facultative anaerobic acidotolerant Telmatospirillum siberiense gen. nov. sp. nov. isolated from mesotrophic fen. Syst Appl Microbiol 2007; 30:213–220 [View Article][PubMed]
    [Google Scholar]
  10. Patwardhan S, Vetriani C. Varunaivibrio sulfuroxidans gen. nov., sp. nov., a facultatively chemolithoautotrophic, mesophilic alphaproteobacterium from a shallow-water gas vent at Tor Caldara, Tyrrhenian Sea. Int J Syst Evol Microbiol 2016; 66:3579–3584 [View Article][PubMed]
    [Google Scholar]
  11. Lakshmi K, Sasikala C, Ashok Kumar GV, Chandrasekaran R, Ramana CV. Phaeovibrio sulfidiphilus gen. nov., sp. nov., phototrophic alphaproteobacteria isolated from brackish water. Int J Syst Evol Microbiol 2011; 61:828–833 [View Article][PubMed]
    [Google Scholar]
  12. Lakshmi KV, Divyasree B, Ramprasad EV, Sasikala C, Ramana C. Reclassification of Rhodospirillum photometricum Molisch 1907, Rhodospirillum sulfurexigens Anil Kumar et al. 2008 and Rhodospirillum oryzae Lakshmi et al. 2013 in a new genus, Pararhodospirillum gen. nov., as Pararhodospirillum photometricum comb. nov., Pararhodospirillum sulfurexigens comb. nov. and Pararhodospirillum oryzae comb. nov., respectively, and emended description of the genus Rhodospirillum. Int J Syst Evol Microbiol 2014; 64:1154–1159 [View Article][PubMed]
    [Google Scholar]
  13. Brandl H, Knee EJ, Fuller RC, Gross RA, Lenz RW. Ability of the phototrophic bacterium Rhodospirillum rubrum to produce various poly (beta-hydroxyalkanoates): potential sources for biodegradable polyesters. Int J Biol Macromol 1989; 11:49–55 [View Article][PubMed]
    [Google Scholar]
  14. Pfennig N, Lünsdorf H, Süling J, Imhoff JF. Rhodospira trueperi gen. nov., spec. nov., a new phototrophic Proteobacterium of the alpha group. Arch Microbiol 1997; 168:39–45 [View Article][PubMed]
    [Google Scholar]
  15. Steenhoudt O, Vanderleyden J. Azospirillum, a free-living nitrogen-fixing bacterium closely associated with grasses: genetic, biochemical and ecological aspects. FEMS Microbiol Rev 2000; 24:487–506 [View Article][PubMed]
    [Google Scholar]
  16. Ostle AG, Holt JG. Nile blue A as a fluorescent stain for poly-beta-hydroxybutyrate. Appl Environ Microbiol 1982; 44:238–241[PubMed]
    [Google Scholar]
  17. Smibert RM, Krieg NR. Phenotypic characterization. In Gerhardt P, Murray RGE, Wood WA, Krieg NR. (editors) Methods for General and Molecular Microbiology Washington, DC, USA: American Society for Microbiology; 1994 pp. 611–654
    [Google Scholar]
  18. Xu XW, Ren PG, Liu SJ, Wu M, Zhou PJ. Natrinema altunense sp. nov., an extremely halophilic archaeon isolated from a salt lake in Altun Mountain in Xinjiang, China. Int J Syst Evol Microbiol 2005; 55:1311–1314 [View Article][PubMed]
    [Google Scholar]
  19. Li WJ, Xu P, Schumann P, Zhang YQ, Pukall R et al. Georgenia ruanii sp. nov., a novel actinobacterium isolated from forest soil in Yunnan (China), and emended description of the genus Georgenia. Int J Syst Evol Microbiol 2007; 57:1424–1428 [View Article][PubMed]
    [Google Scholar]
  20. Gordon RE, Barnett DA, Handerhan JE, Pang CH. Nocardia coeliaca, Nocardia autotrophica, and the nocardin strain. Int J Syst Evol Microbiol 1974; 24:54–63
    [Google Scholar]
  21. Williams ST, Goodfellow M, Alderson G. Genus Streptomyces Waksman and Henrici 1943, 339AL. In Williams ST, Sharpe ME, Holt JG. (editors) Bergey’s Manual of Determinative Bacteriology vol. 4 Baltimore: Williams & Willkins; 1989 pp. 2453–2492
    [Google Scholar]
  22. Kovacs N. Identification of Pseudomonas pyocyanea by the oxidase reaction. Nature 1956; 178:703 [View Article][PubMed]
    [Google Scholar]
  23. Gonzalez C, Gutierrez C, Ramirez C. Halobacterium vallismortis sp. nov. an amylolytic and carbohydrate-metabolizing, extremely halophilic bacterium. Can J Microbiol 1978; 24:710–715 [View Article][PubMed]
    [Google Scholar]
  24. Tindall BJ, Sikorski J, Smibert RA, Krieg NR. Phenotypic characterization and the principles of comparative systematics. In Reddy CA, Beveridge TJ, Breznak JA, Marzluf GA, Schmidt TM et al. (editors) Methods for General and Molecular Microbiology Washington, DC, USA: American Society for Microbiology; 2007 pp. 330–393
    [Google Scholar]
  25. Bauer AW, Kirby WM, Sherris JC, Turck M. Antibiotic susceptibility testing by a standardized single disk method. Am J Clin Pathol 1966; 45:493–496 [View Article][PubMed]
    [Google Scholar]
  26. Cohen-Bazire G, Sistrom WR, Stanier RY. Kinetic studies of pigment synthesis by non-sulfur purple bacteria. J Cell Comp Physiol 1957; 49:25–68 [View Article][PubMed]
    [Google Scholar]
  27. Hasegawa T, Takizawa M, Tanida S. A rapid analysis for chemical grouping of aerobic actinomycetes. J Gen Appl Microbiol 1983; 29:319–322 [View Article]
    [Google Scholar]
  28. Staneck JL, Roberts GD. Simplified approach to identification of aerobic actinomycetes by thin-layer chromatography. Appl Microbiol 1974; 28:226–231[PubMed]
    [Google Scholar]
  29. Lechevalier MP, Lechevalier HA. The chemotaxonomy of actinomycetes. In Dietz A, Thayer DW. (editors) Actinomycete Taxonomy Arlington, VA: Society for Industrial Microbiology; 1980 pp. 227–291
    [Google Scholar]
  30. Minnikin DE, Collins MD, Goodfellow M. Fatty acid and polar lipid composition in the classification of Cellulomonas, Oerskovia and related taxa. J Appl Microbiol 1979; 47:87–95
    [Google Scholar]
  31. Collins MD. Isoprenoid quinone analysis in bacterial classification and identification. In Goodfellow M, Minnikin DE. (editors) Chemical Methods in Bacterial Systematics London: Academic Press; 1985 pp. 267–287
    [Google Scholar]
  32. Wu C, Lu X, Qin M, Ruan J. Analysis of quinone in cells of microorganisms by HPLC method. Microbiology 1989; 16:176–178
    [Google Scholar]
  33. Sasser M. Identification of bacteria by gas chromatography of cellular fatty acids. USFCC Newsl 1990; 20:1–6
    [Google Scholar]
  34. Mesbah M, Premachandran U, Whitman WB. Precise measurement of the G+C content of deoxyribonucleic acid by high-performance liquid chromatography. Int J Syst Evol Microbiol 1989; 39:159–167
    [Google Scholar]
  35. Rainey FA, Ward-Rainey N, Kroppenstedt RM, Stackebrandt E. The genus Nocardiopsis represents a phylogenetically coherent taxon and a distinct actinomycete lineage: proposal of Nocardiopsaceae fam. nov. Int J Syst Evol Microbiol 1996; 46:1088–1092
    [Google Scholar]
  36. Hall TA. BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucl Acids Symp Ser 1999; 41:95–98
    [Google Scholar]
  37. Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG. The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 1997; 25:4876–4882 [View Article][PubMed]
    [Google Scholar]
  38. Kimura M. A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 1980; 16:111–120 [View Article][PubMed]
    [Google Scholar]
  39. Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 1987; 4:406–425 [View Article][PubMed]
    [Google Scholar]
  40. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article][PubMed]
    [Google Scholar]
  41. Rzhetsky A, Nei M. A simple method for estimating and testing minimum-evolution trees; 1992945–967
  42. Kumar S, Stecher G, Tamura K. MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol 2016; 3:1870–1874
    [Google Scholar]
  43. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:783–791 [View Article][PubMed]
    [Google Scholar]
  44. Magalhães FM, Baldani JL, Souto SM, Kuykendall JR, Döbereiner J. A new acid-tolerant Azospirillum species. An Acad Bras Cien 1983; 55:417–430
    [Google Scholar]
  45. Young CC, Hupfer H, Siering C, Ho MJ, Arun AB et al. Azospirillum rugosum sp. nov., isolated from oil-contaminated soil. Int J Syst Evol Microbiol 2008; 58:959–963 [View Article][PubMed]
    [Google Scholar]
  46. Lin SY, Hameed A, Shen FT, Liu YC, Hsu YH et al. Description of Niveispirillum fermenti gen. nov., sp. nov., isolated from a fermentor in Taiwan, transfer of Azospirillum irakense (1989) as Niveispirillum irakense comb. nov., and reclassification of Azospirillum amazonense (1983) as Nitrospirillum amazonense gen. nov. Antonie van Leeuwenhoek 2014; 105:1149–1162 [View Article][PubMed]
    [Google Scholar]
  47. Zhang D, Yang H, Zhang W, Huang Z, Liu SJ. Rhodocista pekingensis sp. nov., a cyst-forming phototrophic bacterium from a municipal wastewater treatment plant. Int J Syst Evol Microbiol 2003; 53:1111–1114 [View Article][PubMed]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.003016
Loading
/content/journal/ijsem/10.1099/ijsem.0.003016
Loading

Data & Media loading...

Supplements

Supplementary File 1

PDF
This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error