1887

Abstract

A Gram-negative, rod-shaped, motile, aerobic bacterial strain, W3, was isolated from hexachlorocyclohexane (HCH)-contaminated groundwater from Lucknow, India, and its taxonomic position was determined using a polyphasic approach. Strain W3 shared highest 16S rRNA gene sequence similarity of 97.8 % with B1, followed by L61 (97.7 %), ATCC 19358 (97.5 %) and IFAM 1003 (97.2 %). Strain W3 formed a monophyletic clade with IFAM 1003 ( = DSM 1111) in the cluster of species of the genus . Phylogenetic analyses of strain W3 using and gene sequences confirmed the phylogenetic arrangements obtained by using 16S rRNA gene sequences. Hence, the taxonomic characterization of DSM 1111 was also undertaken. Strains W3 and DSM 1111 contained summed feature 8 (18 : 1ω7 and/or 18 : 1ω6; 65.4 and 70.8 %, respectively) as the major fatty acid, characteristic of the genus . DNA–DNA relatedness of strain W3 with LMG 24075, DSM 17795, DSM 30147 and DSM 1111 was 42, 34, 30 and 34 %, respectively. The DNA G+C contents of strain W3 and DSM 1111 were 62.3 and 62.7 mol%, respectively. A gene encoding dinitrogenase reductase was detected in strain W3 but not in DSM 1111. Based on the results obtained by phylogenetic and chemotaxonomic analyses, phenotypic characterization and DNA–DNA hybridization, it is concluded that strain W3 represents a novel species of the genus , for which the name sp. nov. is proposed (type strain W3  = CCM 7583  = MTCC 9454). It is also proposed that Hirsch and Müller 1986 be transferred to the genus as comb. nov. (type strain IFAM 1003  = DSM 1111  = ATCC 43293).

Funding
This study was supported by the:
  • Department of Biotechnology (DBT)
  • National Bureau of Agricultural Important Microorganisms (NBAIM), Government of India
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2011-05-01
2024-12-12
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References

  1. Altschul S. F., Madden T. L., Schäffer A. A., Zhang J., Zhang Z., Miller W., Lipman D. J. 1997; Gapped blast and psi-blast: a new generation of protein database search programs. Nucleic Acids Res 25:3389–3402 [View Article][PubMed]
    [Google Scholar]
  2. Arden Jones M. P., McCarthy A. J., Cross T. 1979; Taxonomic and serological studies on Micropolyspora faeni and Micropolyspora strains from soil bearing the specific epithet rectivirgula . J Gen Microbiol 115:343–344 [CrossRef]
    [Google Scholar]
  3. Bala S., Khanna R., Dadhwal M., Prabagaran S. R., Shivaji S., Cullum J., Lal R. 2004; Reclassification of Amycolatopsis mediterranei DSM 46095 as Amycolatopsis rifamycinica sp. nov.. Int J Syst Evol Microbiol 54:1145–1149 [View Article][PubMed]
    [Google Scholar]
  4. Balachandar D., Raja P., Kumar K., Sundaram S. P. 2007; Non-rhizobial nodulation in legumes. Biotechnol Mol Biol Rev 2:49–57
    [Google Scholar]
  5. Christensen W. B. 1946; Urea decomposition as a means of differentiating Proteus and Paracolon cultures from each other and from Salmonella and Shigella types. J Bacteriol 52:461–466
    [Google Scholar]
  6. Cowan S. T., Steel K. J. 1965 Manual for the Identification of Medical Bacteria London: Cambridge University Press;
    [Google Scholar]
  7. Cubo M. T., Buendia-Claveria A. M., Beringer J. E., Ruiz-Sainz J. E. 1988; Melanin production by Rhizobium strains. Appl Environ Microbiol 54:1812–1817[PubMed]
    [Google Scholar]
  8. Doronina N. V., Trotsenko Y. A. 2003; Reclassification of ‘Blastobacter viscosus’ 7d and ‘Blastobacter aminooxidans’ 14a as Xanthobacter viscosus sp. nov. and Xanthobacter aminoxidans sp. nov.. Int J Syst Evol Microbiol 53:179–182 [CrossRef]
    [Google Scholar]
  9. Farmer J. J. III 1999; Enterobacteriaceae: introduction and identification. In Manual of Clinical Microbiology, 7th edn. pp. 442–458 Edited by Murray P. R., Baron E. J., Pfaller M. A., Tenover F. C., Yolken R. H. Washington, DC: American Society for Microbiology;
    [Google Scholar]
  10. Felsenstein, J. (1993). phylip (phylogeny inference package), version 3.5c. Department of Genome Sciences, University of Washington, Seattle, USA.
  11. Frank B. 1889; Über die Pilzsymbiose der Leguminosen. Ber Dtsch Bot Ges 7:332–346 (in German)
    [Google Scholar]
  12. Gao J. L., Sun J. G., Li Y., Wang E. T., Chen W. X. 1994; Numerical taxonomy and DNA relatedness of tropical rhizobia isolated from Hainan Province, China. Int J Syst Bacteriol 44:151–158 [View Article]
    [Google Scholar]
  13. García-Fraile P., Rivas R., Willems A., Peix A., Martens M., Martínez-Molina E., Mateos P. F., Velázquez E. 2007; Rhizobium cellulosilyticum sp. nov., isolated from sawdust of Populus alba . Int J Syst Evol Microbiol 57:844–848 [View Article][PubMed]
    [Google Scholar]
  14. Gaunt M. W., Turner S. L., Rigottier-Gois L., Lloyd-Macgilp S. A., Young J. P. 2001; Phylogenies of atpD and recA support the small subunit rRNA-based classification of rhizobia. Int J Syst Evol Microbiol 51:2037–2048[PubMed] [CrossRef]
    [Google Scholar]
  15. Gonzalez J. M., Saiz-Jimenez C. 2002; A fluorimetric method for the estimation of G+C mol% content in microorganisms by thermal denaturation temperature. Environ Microbiol 4:770–773 [View Article][PubMed]
    [Google Scholar]
  16. Haukka K., Lindström K., Young J. P. W. 1998; Three phylogenetic groups of nodA and nifH genes in Sinorhizobium and Mesorhizobium isolates from leguminous trees growing in Africa and Latin America. Appl Environ Microbiol 64:419–426[PubMed]
    [Google Scholar]
  17. Hirsch P., Müller M. 1985; Blastobacter aggregatus sp. nov., Blastobacter capsulatus sp. nov., and Blastobacter denitrificans sp. nov., new budding bacteria from freshwater habitats. Syst Appl Microbiol 6:281–286 [CrossRef]
    [Google Scholar]
  18. Hugenholtz P., Stackebrandt E., Fuerst J. A. 1994; A phylogenetic analysis of the genus Blastobacter with a view to its future reclassification. Syst Appl Microbiol 17:51–57 [CrossRef]
    [Google Scholar]
  19. Hunter W. J., Kuykendall L. D., Manter D. K. 2007; Rhizobium selenireducens sp. nov.: a selenite-reducing alpha-Proteobacteria isolated from a bioreactor. Curr Microbiol 55:455–460 [View Article][PubMed]
    [Google Scholar]
  20. Jordan D. C. 1984; Family III. Rhizobiaceae Conn 1938, 321AL . In Bergey’s Manual of Systematic Bacteriology vol. 1 pp. 234–242 Edited by Krieg N. R., Holt J. G. Baltimore: Williams & Wilkins;
    [Google Scholar]
  21. Jukes T. H., Cantor C. R. 1969; Evolution of protein molecules. In Mammalian Protein Metabolism vol. 3 pp. 21–132 Edited by Munro H. N. New York: Academic Press;
    [Google Scholar]
  22. Kumar M., Verma M., Lal R. 2008; Devosia chinhatensis sp. nov., isolated from a hexachlorocyclohexane (HCH) dump site in India. Int J Syst Evol Microbiol 58:861–865 [View Article][PubMed]
    [Google Scholar]
  23. Kuykendall L. D., Roy M. A., O’Neill J. J., Devine T. E. 1988; Fatty acids, antibiotic resistance, and deoxyribonucleic acid homology groups of Bradyrhizobium japonicum . Int J Syst Bacteriol 38:358–361 [View Article]
    [Google Scholar]
  24. Laguerre G., Nour S. M., Macheret V., Sanjuan J., Drouin P., Amarger N. 2001; Classification of rhizobia based on nodC and nifH gene analysis reveals a close phylogenetic relationship among Phaseolus vulgaris symbionts. Microbiology 147:981–993[PubMed]
    [Google Scholar]
  25. McCarthy A. J., Cross T. 1984; A taxonomic study of Thermomonospora and other monosporic actinomycetes. J Gen Microbiol 130:5–25
    [Google Scholar]
  26. Miller L. T. 1982; Single derivatization method for routine analysis of bacterial whole-cell fatty acid methyl esters, including hydroxy acids. J Clin Microbiol 16:584–586[PubMed]
    [Google Scholar]
  27. Peng G., Yuan Q., Li H., Zhang W., Tan Z. 2008; Rhizobium oryzae sp. nov., isolated from the wild rice Oryza alta . Int J Syst Evol Microbiol 58:2158–2163 [View Article][PubMed]
    [Google Scholar]
  28. Poly F., Monrozier L. J., Bally R. 2001; Improvement in the RFLP procedure for studying the diversity of nifH genes in communities of nitrogen fixers in soil. Res Microbiol 152:95–103 [View Article][PubMed]
    [Google Scholar]
  29. Prakash O., Kumari K., Lal R. 2007; Pseudomonas delhiensis sp. nov., from a fly ash dumping site of a thermal power plant. Int J Syst Evol Microbiol 57:527–531 [View Article][PubMed]
    [Google Scholar]
  30. Quan Z. X., Bae H. S., Baek J. H., Chen W. F., Im W. T., Lee S. T. 2005; Rhizobium daejeonense sp. nov. isolated from a cyanide treatment bioreactor. Int J Syst Evol Microbiol 55:2543–2549 [View Article][PubMed]
    [Google Scholar]
  31. Rivas R., Velázquez E., Willems A., Vizcaíno N., Subba-Rao N. S., Mateos P. F., Gillis M., Dazzo F. B., Martínez-Molina E. 2002; A new species of Devosia that forms a unique nitrogen-fixing root-nodule symbiosis with the aquatic legume Neptunia natans (L.f.) Druce. Appl Environ Microbiol 68:5217–5222 [View Article][PubMed]
    [Google Scholar]
  32. Rothe B., Fischer A., Hirsch P., Sittig M., Stackebrandt E. 1987; The phylogenetic position of the budding bacteria Blastobacter aggregatus and Gemmobacter aquatilis gen. nov. sp. nov.. Arch Microbiol 147:92–99 [View Article]
    [Google Scholar]
  33. Saitou N., Nei M. 1987; The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406–425[PubMed]
    [Google Scholar]
  34. Sambrook J., Fritsch E. F., Maniatis T. 1989 Molecular Cloning: a Laboratory Manual, 2nd edn. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory;
    [Google Scholar]
  35. Sawada H., Ieki H., Oyaizu H., Matsumoto S. 1993; Proposal for rejection of Agrobacterium tumefaciens and revised descriptions for the genus Agrobacterium and for Agrobacterium radiobacter and Agrobacterium rhizogenes . Int J Syst Bacteriol 43:694–702 [View Article][PubMed]
    [Google Scholar]
  36. Simmons J. S. 1926; A culture medium for differentiating organisms of typhoid-colon aerogenes groups and for isolating of certain fungi. J Infect Dis 39:209–241 [CrossRef]
    [Google Scholar]
  37. Sittig M., Hirsch P. 1992; Chemotaxonomic investigation of budding and hyphal bacteria. Syst Appl Microbiol 15:209–222 [CrossRef]
    [Google Scholar]
  38. Sly L. I. 1985; Emendation of the genus Blastobacter Zavarzin 1961 and description of Blastobacter natatorius sp. nov.. Int J Syst Bacteriol 35:40–45 [View Article]
    [Google Scholar]
  39. Sly L. I., Cahill M. M. 1997; Transfer of Blastobacter natatorius (Sly 1985) to the genus Blastomonas gen. nov. as Blastomonas natatoria comb. nov.. Int J Syst Bacteriol 47:566–568 [View Article][PubMed]
    [Google Scholar]
  40. Sly L. I., Hugenholtz P. 2005; Genus IV. Blastobacter Zavarzin 1961, 962AL emend. Sly 1985, 44. In Bergey’s Manual of Systematic Bacteriology, 2nd edn. vol. 2C pp. 452–459 Edited by Boone D. R., Castenholtz R. W., Bergey D. H., Garrity G. M., Staley J. T. New York: Springer;
    [Google Scholar]
  41. 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]
  42. 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 [View Article]
    [Google Scholar]
  43. 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 [View Article][PubMed]
    [Google Scholar]
  44. Tighe S. W., de Lajudie P., Dipietro K., Lindström K., Nick G., Jarvis B. D. 2000; Analysis of cellular fatty acids and phenotypic relationships of Agrobacterium, Bradyrhizobium, Mesorhizobium, Rhizobium and Sinorhizobium species using the Sherlock Microbial Identification System. Int J Syst Evol Microbiol 50:787–801[PubMed] [CrossRef]
    [Google Scholar]
  45. Tourova T. P., Antonov A. S. 1987; Identification of microorganisms by rapid DNA-DNA hybridization. Methods Microbiol 19:333–355 [View Article]
    [Google Scholar]
  46. Trotsenko Y. A., Doronina N. V., Hirsch P. 1989; Genus Blastobacter . In Bergey’s Manual of Systematic Bacteriology vol. 3 pp. 1963–1968 Edited by Staley J. T., Bryant M. P., Pfennig N., Holt J. G. Baltimore: Williams & Wilkins;
    [Google Scholar]
  47. van Berkum P., Leibold J. M., Eardly B. D. 2006; Proposal for combining Bradyrhizobium spp. (Aeschynomene indica) with Blastobacter denitrificans and to transfer Blastobacter denitrificans (Hirsch and Muller, 1985) to the genus Bradyrhizobium as Bradyrhizobium denitrificans (comb. nov.). Syst Appl Microbiol 29:207–215 [View Article][PubMed]
    [Google Scholar]
  48. Van de Peer Y., De Wachter R. 1994; treecon for Windows: a software package for the construction and drawing of evolutionary trees for the Microsoft Windows environment. Comput Appl Biosci 10:569–570[PubMed]
    [Google Scholar]
  49. Wayne L. G., Brenner D. J., Colwell R. R., Grimont P. A. D., Kandler O., Krichevsky M. I., Moore L. H., Moore W. E. C., Murray R. G. E. et al. 1987; International Committee on Systematic Bacteriology. Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. Int J Syst Bacteriol 37:463–464 [View Article]
    [Google Scholar]
  50. Willems A., Collins M. D. 1992; Evidence for a close genealogical relationship between Afipia (the causal organism of cat scratch disease), Bradyrhizobium japonicum and Blastobacter denitrificans . FEMS Microbiol Lett 96:241–246 [View Article][PubMed]
    [Google Scholar]
  51. Zavarzin G. A. 1961; [Budding bacteria]. Mikrobiologiia 30:952–975 (in Russian) [PubMed]
    [Google Scholar]
  52. Zurdo-Piñeiro J. L., Velázquez E., Lorite M. J., Brelles-Mariño G., Schröder E. C., Bedmar E. J., Mateos P. F., Martínez-Molina E. 2004; Identification of fast-growing rhizobia nodulating tropical legumes from Puerto Rico as Rhizobium gallicum and Rhizobium tropici . Syst Appl Microbiol 27:469–477 [View Article][PubMed]
    [Google Scholar]
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