1887

Abstract

Two strains (JA575 and JA576) of orange- to pink-pigmented, rod-shaped, motile and budding phototrophic bacteria were isolated from paddy soils. Both strains contained bacteriochlorophyll and carotenoids of spirilloxanthin series. Both strains had Cω7 as the major cellular fatty acid, ubiquinone-10 (Q) as the main quinone, and diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and phosphatidylcholine as polar lipids. Phylogenetic analysis on the basis of 16S rRNA gene sequences showed that both strains clustered with species of the genus in the class . Strains JA575 and JA576 were genotypically (<35 % DNA–DNA relatedness) and phenotypically distinct from each other. Further, both strains showed less than 48 % DNA–DNA relatedness with the type strains of all recognized species of the genus The molecular evidence is supported by phenotypic evidence. It is proposed that strains JA575 and JA576 be classified as representing two novel species of the genus with the species names sp. nov. and sp. nov., respectively. The type strains of the proposed novel species are JA575 ( = NBRC 108862 = KCTC15143) and JA576 ( = NBRC 108863 = KCTC 15144), respectively.

Funding
This study was supported by the:
  • Ministry of Earth Sciences, Government of India
  • CSIR, Government of India
  • JNTU Hyderabad
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijs.0.038620-0
2013-01-01
2024-03-28
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/63/1/200.html?itemId=/content/journal/ijsem/10.1099/ijs.0.038620-0&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, 403410.[PubMed] [CrossRef]
    [Google Scholar]
  2. 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, 48014805. [View Article] [PubMed]
    [Google Scholar]
  3. 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, 22592261. [View Article] [PubMed]
    [Google Scholar]
  4. Guindon S., Lethiec F., Duroux P., Gascuel O. ( 2005 ). PHYML Online–a web server for fast maximum likelihood-based phylogenetic inference. . Nucleic Acids Res 33 (Web Server issue), W557W559. [View Article] [PubMed]
    [Google Scholar]
  5. Hall T. A. ( 1999 ). BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. . Nucleic Acids Symp Ser 41, 9598.
    [Google Scholar]
  6. 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, 187193.[PubMed] [CrossRef]
    [Google Scholar]
  7. Hiraishi A., Hoshino Y. ( 1984 ). Distribution of rhodoquinone in Rhodospirillaceae and its taxonomic implications. . J Gen Appl Microbiol 30, 435448. [View Article]
    [Google Scholar]
  8. Hiraishi A., Hoshino Y., Kitamura H. ( 1984 ). Isoprenoid quinone composition in the classification of Rhodospirillaceae . . J Gen Appl Microbiol 30, 197210. [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, 105110.[PubMed]
    [Google Scholar]
  10. Imhoff J. F., Süling J., Petri R. ( 1998 ). 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, 11291143. [View Article] [PubMed]
    [Google Scholar]
  11. Kämpfer P., Rosselló-Mora R., Scholz H. C., Welinder-Olsson C., Falsen E., Busse H.-J. ( 2006 ). Description of Pseudochrobactrum gen. nov., with the two species Pseudochrobactrum asaccharolyticum sp. nov. and Pseudochrobactrum saccharolyticum sp. nov.. Int J Syst Evol Microbiol 56, 18231829. [View Article] [PubMed]
    [Google Scholar]
  12. Kates M. ( 1972 ). Techniques of Lipidology. New York:: Elsevier;.
    [Google Scholar]
  13. Kates M. ( 1986 ). Techniques of Lipidology: Isolation, Analysis, and Identification of Lipids. Amsterdam:: Elsevier;.
    [Google Scholar]
  14. Kimura M. ( 1980 ). A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. . J Mol Evol 16, 111120. [View Article] [PubMed]
    [Google Scholar]
  15. Lakshmi K. V. N. S., Sasikala Ch., Ramana Ch. V. ( 2009 ). Rhodoplanes pokkaliisoli sp. nov., a phototrophic alphaproteobacterium isolated from a waterlogged brackish paddy soil. . Int J Syst Evol Microbiol 59, 21532157. [View Article] [PubMed]
    [Google Scholar]
  16. Lanave C., Preparata G., Sacone C., Serio G. ( 1984 ). A new method for calculating evolutionary substitution rates. . J Mol Evol 20, 8693. [View Article] [PubMed]
    [Google Scholar]
  17. 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, 69556959. [View Article] [PubMed]
    [Google Scholar]
  18. Marmur J. ( 1961 ). A procedure for the isolation of deoxyribonucleic acid from microorganisms. . J Mol Biol 3, 208218. [View Article]
    [Google Scholar]
  19. 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, 159167. [View Article]
    [Google Scholar]
  20. Neunlist S., Holst O., Rohmer M. ( 1985 ). Prokaryotic triterpenoids. The hopanoids of the purple non-sulphur bacterium Rhodomicrobium vannielii: an aminotriol and its aminoacyl derivatives, N-tryptophanyl and N-ornithinyl aminotriol. . Eur J Biochem 147, 561568. [View Article] [PubMed]
    [Google Scholar]
  21. Okamura K., Takata K., Hiraishi A. ( 2009 ). Intrageneric relationships of members of the genus Rhodopseudomonas . . J Gen Appl Microbiol 55, 469478. [View Article] [PubMed]
    [Google Scholar]
  22. Oren A., Duker S., Ritter S. ( 1996 ). The polar lipid composition of Walsby’s square bacterium. . FEMS Microbiol Lett 138, 135140. [View Article]
    [Google Scholar]
  23. Sanger F., Nicklen S., Coulson A. R. ( 1977 ). DNA sequencing with chain-terminating inhibitors. . Proc Natl Acad Sci U S A 74, 54635467. [View Article] [PubMed]
    [Google Scholar]
  24. Sasser M. ( 1990 ). Identification of bacteria by gas chromatography of cellular fatty acids, MIDI Technical Note 101. . Newark, DE:: MIDI Inc.;
  25. Seldin L., Dubnau D. ( 1985 ). Deoxyribonucleic acid homology among Bacillus polymyxa, Bacillus macerans, Bacillus azotofixans and other nitrogen-fixing Bacillus strains. . Int J Syst Bacteriol 35, 151154. [View Article]
    [Google Scholar]
  26. Srinivas T. N. R., Kumar P. A., Sasikala Ch., Ramana ChV. ( 2007 ). Rhodovulum imhoffii sp. nov.. Int J Syst Evol Microbiol 57, 228232. [View Article] [PubMed]
    [Google Scholar]
  27. Stackebrandt E., Ebers J. ( 2006 ). Taxonomic parameters revisited: tarnished gold standards. . Microbiol Today 33, 152155.
    [Google Scholar]
  28. 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, 846849. [View Article]
    [Google Scholar]
  29. Tamura K., Dudley J., Nei M., Kumar S. ( 2007 ). mega4: molecular evolutionary genetics analysis (mega) software version 4.0. . Mol Biol Evol 24, 15961599. [View Article] [PubMed]
    [Google Scholar]
  30. 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, 48764882. [View Article] [PubMed]
    [Google Scholar]
  31. Tindall B. J. ( 1990a ). Lipid composition of Halobacterium lacusprofundi . . FEMS Microbiol Lett 66, 199202. [View Article]
    [Google Scholar]
  32. Tindall B. J. ( 1990b ). A comparative study of the lipid composition of Halobacterium saccharovorum from various sources. . Syst Appl Microbiol 13, 128130. [View Article]
    [Google Scholar]
  33. Tindall B. J., Rosselló-Móra R., Busse H.-J., Ludwig W., Kämpfer P. ( 2010 ). Notes on the characterization of prokaryote strains for taxonomic purposes. . Int J Syst Evol Microbiol 60, 249266. [View Article] [PubMed]
    [Google Scholar]
  34. Tourova T. P., Antonov A. S. ( 1988 ). Identification of microorganisms by rapid DNA-DNA hybridization. . Methods Microbiol 19, 333355. [View Article] [PubMed]
    [Google Scholar]
  35. Trüper H. G., Pfennig N. ( 1981 ). Isolation of members of the families Chromatiaceae and Chlorobiaceae . . In The Prokaryotes: a Handbook on Habitats, Isolation, and Identification of Bacteria, pp. 279289. Edited by Starr M. P., Stolp H., Trüper H. G., Balows A., Schlegel H. G. . Berlin:: Springer;.
    [Google Scholar]
  36. Venkata Ramana V., Chakravarthy K. S., Shalem P. R., Vinay K. B., Shobha E., Ramaprasad E. V. V., Sasikala C., Ramana C. V. ( 2012 ). Description of Rhodopseudomonas parapalustris sp. nov., Rhodopseudomonas harwoodiae sp. nov., Rhodopseudomonas pseudopalustris sp. nov. and emended description of Rhodopseudomonas palustris . . Int J Syst Evol Microbiol 62, 17901798. [View Article] [PubMed]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijs.0.038620-0
Loading
/content/journal/ijsem/10.1099/ijs.0.038620-0
Loading

Data & Media loading...

Supplements

Supplementary material 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