1887

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY logo

Volume 63, Issue Pt_8

sp. nov., a phototrophic bacterium isolated from rhizosphere soil of paddy Free

Abstract

A reddish-brown bacterium, designated strain JA318, was purified from a photoheterotrophic enrichment culture obtained from the rhizosphere soil of paddy. Cells of strain JA318 are spiral shaped, Gram-stain-negative and motile by means of amphitrichous flagella. Strain JA318 has no NaCl requirement for growth but can tolerate up to 1.5 % (w/v) NaCl. Internal photosynthetic membranes are present as lamellar stacks. Photoorganoheterotrophy is the only growth mode observed. Strain JA318 contains bacteriochlorophyll , lycopene and rhodopin as major carotenoids. Thiamine, niacin and -aminobenzoic acid (PABA) are required as growth factors. Major fatty acids are Cω7 and C. Ubiquinone-8 and rhodoquinone-8 are the observed quinones. Diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and an unidentified aminolipid are the major polar lipids in strain JA318. Phylogenetic analysis based on 16S rRNA gene sequences showed that the strain JA318 clustered with species of the genus which belongs to the class . The highest sequence similarity of strain JA318 was found with JA143 (99.9 %). The DNA–DNA reassociation values of strain JA318 with JA143 and DSM 122 were 52±2 % and 45±1 %, respectively. The genomic DNA G+C content of strain JA318 was 60.2 mol%. Based on the morphological, physiological, chemotaxonomical and molecular evidence, strain JA318 is significantly different from the type strains of species of the genus , of the family , and it is proposed that the strain be classified as a representative of a novel species for which the name sp. nov. is proposed. The type strain is JA318 ( = KCTC 5960 = NBRC 107573).

  • Published Online:
Funding
This study was supported by the:
  • Council of Scientific and Industrial Research CSIR
© 2013 IUMS
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijs.0.049023-0
2013-08-01
2024-04-25
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/63/8/3050.html?itemId=/content/journal/ijsem/10.1099/ijs.0.049023-0&mimeType=html&fmt=ahah

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.[PubMed] [CrossRef]
    [Google Scholar]
  2. Anil Kumar P., Aparna P., Srinivas T. N. R., Sasikala Ch., Ramana Ch. V. ( 2008 ). Rhodospirillum sulfurexigens sp. nov., a phototrophic alphaproteobacterium requiring a reduced sulfur source for growth. . Int J Syst Evol Microbiol 58, 2917–2920. [View Article] [PubMed]
    [Google Scholar]
  3. Brosius J., Palmer M. L., Kennedy P. J., Noller H. F. ( 1978 ). Complete nucleotide sequence of a 16S ribosomal RNA gene from Escherichia coli . . Proc Natl Acad Sci U S A 75, 4801–4805. [View Article] [PubMed]
    [Google Scholar]
  4. Hanada S., Takaichi S., Matsuura K., Nakamura K. ( 2002 ). Roseiflexus castenholzii gen. nov., sp. nov., a thermophilic, filamentous, photosynthetic bacterium that lacks chlorosomes. . Int J Syst Evol Microbiol 52, 187–193.[PubMed] [CrossRef]
    [Google Scholar]
  5. Hiraishi A., Hoshino Y. ( 1984 ). Distribution of rhodoquinone in Rhodospirillaceae and its taxonomic implications. . J Gen Appl Microbiol 30, 435–448. [View Article]
    [Google Scholar]
  6. Hiraishi A., Hoshino Y., Kitamura H. ( 1984 ). Isoprenoid quinone composition in the classification of Rhodospirillaceae . . J Gen Appl Microbiol 30, 197–210. [View Article]
    [Google Scholar]
  7. Imhoff J. F. ( 1984 ). Quinones of phototrophic purple bacteria. . FEMS Microbiol Lett 25, 85–89. [View Article]
    [Google Scholar]
  8. Imhoff J. F. ( 2005 ). Genus I. . Rhodospirillum Molisch 1907, 24AL emend. Imhoff, Petri and Süling 1998, 796. . In Bergey’s Mannual of Systematic Bacteriololgy , , 2nd edn., vol. 2, Part C, pp. 1–6. Edited by Brenner D. J., Krieg N. R., Staley J. T., Garrity G. M. . New York:: Springer;. [View Article]
    [Google Scholar]
  9. Imhoff J. F., Pfennig N. ( 2001 ). Thioflavicoccus mobilis gen. nov., sp. nov., a novel purple sulfur bacterium with bacteriochlorophyll b. . Int J Syst Evol Microbiol 51, 105–110.[PubMed]
    [Google Scholar]
  10. Imhoff J. F., Süling J., Petri R. ( 1998a ). 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., Rhodothalassium gen. nov. and Roseospira gen. nov. as well as transfer of Rhodospirillum fulvum to Phaeospirillum fulvum comb. nov., of Rhodospirillum molischianum to Phaeospirillum molischianum 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 Bacteriol 48, 793–798. [View Article] [PubMed]
    [Google Scholar]
  11. Imhoff J. F., Süling J., Petri R. ( 1998b ). Phylogenetic relationships among the Chromatiaceae, their taxonomic reclassification and description of the new genera Allochromatium, Halochromatium, Isochromatium, Marichromatium, Thiococcus, Thiohalocapsa and Thermochromatium . . Int J Syst Bacteriol 48, 1129–1143. [View Article] [PubMed]
    [Google Scholar]
  12. Kates M. ( 1972 ). Techniques of lipidology. . In Laboratory Techniques in Biochemistry and Molecular Biology, vol. 3, pp. 355–356. Edited by Work T. S., Work E. . New York:: Elsevier;.
     [Google Scholar]
  13. Kates M. ( 1986 ). Techniques of lipidology: isolation, analysis and identification of lipids. . In Laboratory Techniques in Biochemistry and Molecular Biology, vol. 3, pp. 100–112. Edited by Burdon R. H., van Knippenberg P. H. . Amsterdam:: Elsevier;.
     [Google Scholar]
  14. Kim O. S., Cho Y. J., Lee K., Yoon S. H., Kim M., Na H., Park S. C., Jeon Y. S., Lee J. H. & other authors ( 2012 ). Introducing EzTaxon-e: a prokaryotic 16S rRNA gene sequence database with phylotypes that represent uncultured species. . Int J Syst Evol Microbiol 62, 716–721. [View Article] [PubMed]
    [Google Scholar]
  15. 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. [View Article] [PubMed]
    [Google Scholar]
  16. Lakshmi K. V. N. S., Sasikala Ch., Ashok Kumar G. V., Chandrasekaran R., Ramana Ch. V. ( 2011a ). Phaeovibrio sulfidiphilus gen. nov., sp. nov., phototrophic alphaproteobacteria isolated from brackish water. . Int J Syst Evol Microbiol 61, 828–833. [View Article] [PubMed]
    [Google Scholar]
  17. Lakshmi K. V. N. S., Sasikala Ch., Takaichi S., Ramana Ch. V. ( 2011b ). Phaeospirillum oryzae sp. nov., a spheroplast-forming, phototrophic alphaproteobacterium from a paddy soil. . Int J Syst Evol Microbiol 61, 1656–1661. [View Article] [PubMed]
    [Google Scholar]
  18. Lane D. J., Pace B., Olsen G. J., Stahl D. A., Sogin M. L., Pace N. R. ( 1985 ). Rapid determination of 16S ribosomal RNA sequences for phylogenetic analyses. . Proc Natl Acad Sci U S A 82, 6955–6959. [View Article] [PubMed]
    [Google Scholar]
  19. Marmur J. ( 1961 ). A procedure for the isolation of deoxyribonucleic acid from microorganisms. . J Mol Biol 3, 208–218. [View Article]
    [Google Scholar]
  20. Mesbah M., Premachandran U., Whitman W. B. ( 1989 ). Precise measurement of the G+C content of deoxyribonucleic acid by high performance liquid chromatography. . Int J Syst Bacteriol 39, 159–167. [View Article]
    [Google Scholar]
  21. Oren A., Duker S., Ritter S. ( 1996 ). The polar lipid composition of Walsby’s square bacterium. . FEMS Microbiol Lett 138, 135–140. [View Article]
    [Google Scholar]
  22. Sanger F., Nicklen S., Coulson A. R. ( 1977 ). DNA sequencing with chain-terminating inhibitors. . Proc Natl Acad Sci U S A 74, 5463–5467. [View Article] [PubMed]
    [Google Scholar]
  23. Sasikala K., Ramana Ch. V., Raghuveer Rao P., Subrahmanyam M. ( 1990 ). Photoproduction of hydrogen, nitrogenase and hydrogenase activities of free and immobilized whole cells of Rhodobacter sphaeroides OU001. . FEMS Microbiol Lett 72, 23–28. [View Article]
    [Google Scholar]
  24. Sasser M. ( 1990 ). Identification of bacteria by gas chromatography of cellular fatty acids, MIDI Technical Note 101. . Newark, DE:: MIDI Inc;.
     [Google Scholar]
  25. Stackebrandt E., Ebers J. ( 2006 ). Taxonomic parameters revisited: tarnished gold standards. . Microbiol Today 3, 152–155.
     [Google Scholar]
  26. Stackebrandt E., Goebel B. M. ( 1994 ). 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. [View Article]
    [Google Scholar]
  27. Tamura K., Dudley J., Nei M., Kumar S. ( 2007 ). mega4: molecular evolutionary genetics analysis (mega) software version 4.0. . Mol Biol Evol 24, 1596–1599. [View Article] [PubMed]
    [Google Scholar]
  28. Tindall B. J. ( 1990a ). Lipid composition of Halobacterium lacusprofundi . . FEMS Microbiol Lett 66, 199–202. [View Article]
    [Google Scholar]
  29. Tindall B. J. ( 1990b ). A comparative study of the lipid composition of Halobacterium saccharovorum from various sources. . Syst Appl Microbiol 13, 128–130. [View Article]
    [Google Scholar]
  30. Tourova T. P., Antonov A. S. ( 1988 ). Identification of microorganisms by rapid DNA-DNA hybridization. . Methods Microbiol 19, 333–355. [View Article]
    [Google Scholar]
  31. Trüper H. G., Pfennig N. ( 1981 ). Characterization and identification of the anoxygenic phototrophic bacteria. . In The Prokaryotes: A Handbook on Habitats, Isolation, and Identification of Bacteria, vol. 1, pp. 298–312. Edited by Starr M. P., Stolp H., Trüper H. G., Balows A., Schlegel H. G. . New York:: Springer;.
     [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijs.0.049023-0
Loading
Rhodospirillumoryzae sp. nov., a phototrophic bacterium isolated from rhizosphere soil of paddy
Int J Syst Evol Microbiol 63, 3050 (2013); https://doi.org/10.1099/ijs.0.049023-0
/content/journal/ijsem/10.1099/ijs.0.049023-0
/content/journal/ijsem/10.1099/ijs.0.049023-0
Loading

Data & Media loading...

Supplements

Supplementary material 1

PDF

Most cited Most Cited RSS feed

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