1887

Abstract

Three novel bacterial strains, designated Vu-144, Vu-7 and Vu-35, were isolated on minimal medium from rhizosphere soil of field-grown cowpea and subjected to a taxonomic study using a polyphasic approach. Cells of the strains were Gram-stain-negative, non-motile, non-spore-forming, coccoid rods, and formed non-pigmented colonies. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain Vu-144 was affiliated with an uncultivated lineage of the phylum . Its closest phylogenetic neighbour was the recently described species , a member of the family , with just 90.7 % sequence similarity to the type strain. The only isoprenoid quinone detected was menaquinone 7 (MK-7). The fatty acid profiles showed large amounts of iso-C, iso-C 3-OH and iso-C G and minor amounts of summed feature 3 (Cω7 and/or iso-C 2-OH), C and other fatty acids, allowing the differentiation of the strains from other genera. The G+C content of the genomic DNA of the three strains ranged from 43.1 to 44.3 mol%. In addition to phosphatidylethanolamine, the major polar lipids were three unidentified aminophospholipids (APL1–APL3), two unidentified phospholipids (PL1, PL2) and three unidentified lipids (UL1–UL3). Biochemical test patterns also differed from those of and members of other genera. All three isolates showed plant-growth-promoting properties, e.g. the ability to produce indole-3-acetic acid and NH and to solubilize phosphate, utilized 1-aminocyclopropane 1-carboxylate (ACC) as a sole source of nitrogen and possessed the ACC deaminase enzyme. The novel isolates readily colonized roots and stimulated growth of tomato and cowpea under glasshouse conditions. Inoculated plants showed a 45–60 % increase in dry matter weight with respect to uninoculated controls. On the basis of the evidence from our polyphasic study, isolate Vu-144 represents a novel genus and species in the family , for which the name gen. nov., sp. nov. is proposed. The type strain of is Vu-144 ( = KCTC 22378 = NCIMB 14473).

Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijs.0.069377-0
2015-02-01
2019-10-18
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/65/2/578.html?itemId=/content/journal/ijsem/10.1099/ijs.0.069377-0&mimeType=html&fmt=ahah

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. [CrossRef][PubMed]
    [Google Scholar]
  2. An D.-S., Lee H.-G., Im W.-T., Liu Q.-M., Lee S.-T.. ( 2007;). Segetibacter koreensis gen. nov., sp. nov., a novel member of the phylum Bacteroidetes, isolated from the soil of a ginseng field in South Korea. . Int J Syst Evol Microbiol 57:, 1828–1833. [CrossRef][PubMed]
    [Google Scholar]
  3. Andro T., Chambost J. P., Kotoujansky A., Cattaneo J., Bertheau Y., Barras F., Van Gijsegem F., Coleno A.. ( 1984;). Mutants of Erwinia chrysanthemi defective in secretion of pectinase and cellulase. . J Bacteriol 160:, 1199–1203.[PubMed]
    [Google Scholar]
  4. Baik K. S., Kim M. S., Lee J. H., Lee S. S., Im W. T., Seong C. N.. ( 2014;). Flavisolibacter rigui sp. nov., isolated from the freshwater of artificial reservoir and emended description of the genus Flavisolibacter. . Int J Syst Evol Microbiol (in press). [CrossRef][PubMed]
    [Google Scholar]
  5. Bozzola J. J., Russell L. D.. ( 1998;). Electron Microscopy, , 2nd edn.. Sudbury, MS:: Jones & Bartlett;.
    [Google Scholar]
  6. Cappuccino J. C., Sherman N.. ( 1992;). In Microbiology: A Laboratory Manual, , 3rd edn., pp. 125–179. New York:: Benjamin Cummings;.
    [Google Scholar]
  7. Choi D. H., Zhang G. I., Noh J. H., Kim W. S., Cho B. C.. ( 2009;). Gracilimonas tropica gen. nov., sp. nov., isolated from a Synechococcus culture. . Int J Syst Evol Microbiol 59:, 1167–1172. [CrossRef][PubMed]
    [Google Scholar]
  8. Chung E. J., Park T. S., Jeon C. O., Chung Y. R.. ( 2012;). Chitinophaga oryziterrae sp. nov., isolated from the rhizosphere soil of rice (Oryza sativa L.). . Int J Syst Evol Microbiol 62:, 3030–3035. [CrossRef][PubMed]
    [Google Scholar]
  9. DeLong E. F.. ( 1992;). Archaea in coastal marine environments. . Proc Natl Acad Sci U S A 89:, 5685–5689. [CrossRef][PubMed]
    [Google Scholar]
  10. Dworkin M., Foster J. W.. ( 1958;). Experiments with some microorganisms which utilize ethane and hydrogen. . J Bacteriol 75:, 592–603.[PubMed]
    [Google Scholar]
  11. Fautz E., Reichenbach H.. ( 1980;). A simple test for flexirubin-type pigments. . FEMS Microbiol Lett 8:, 87–91. [CrossRef]
    [Google Scholar]
  12. Felsenstein J.. ( 1981;). Evolutionary trees from DNA sequences: a maximum likelihood approach. . J Mol Evol 17:, 368–376. [CrossRef][PubMed]
    [Google Scholar]
  13. Felsenstein J.. ( 1985;). Confidence limits on phylogenies: an approach using the bootstrap. . Evolution 39:, 783–791. [CrossRef]
    [Google Scholar]
  14. Fitch W. M.. ( 1971;). Toward defining the course of evolution: minimum change for a specific tree topology. . Syst Zool 20:, 406–416. [CrossRef]
    [Google Scholar]
  15. Garrity G. M., Holt J. G.. ( 2001;). Phylum BVI Chloroflexi phy. nov.. In Bergey’s Manual of Systematic Bacteriology, , 2nd edn., vol. 1, pp. 427–446. Edited by Boone D. R., Castenholz R. W., Garrity G. M... New York:: Springer;. [CrossRef]
    [Google Scholar]
  16. Ghosh S., Penterman J. N., Little R. D., Chavez R., Glick B. R.. ( 2003;). Three newly isolated plant growth-promoting bacilli facilitate the seedling growth of canola, Brassica campestris. . Plant Physiol Biochem 41:, 277–281. [CrossRef]
    [Google Scholar]
  17. Glaeser S. P., Galatis H., Martin K., Kämpfer P.. ( 2013;). Niabella hirudinis and Niabella drilacis sp. nov., isolated from the medicinal leech Hirudo verbana. . Int J Syst Evol Microbiol 63:, 3487–3493. [CrossRef][PubMed]
    [Google Scholar]
  18. Honma M., Shimomura T.. ( 1978;). Metabolism of 1-aminocyclopropane-1-carboxylic acid. . Agric Biol Chem 42:, 1825–1831. [CrossRef]
    [Google Scholar]
  19. Jackson M. L.. ( 1973;). Soil Chemical Analysis. New Delhi:: Prentice Hall of India;.
    [Google Scholar]
  20. Jin D., Wang P., Bai Z., Jin B., Yu Z., Wang X., Zhuang G., Zhang H.. ( 2013;). Terrimonas pekingensis sp. nov., isolated from bulking sludge, and emended descriptions of the genus Terrimonas, Terrimonas ferruginea, Terrimonas lutea and Terrimonas aquatica. . Int J Syst Evol Microbiol 63:, 1658–1664. [CrossRef][PubMed]
    [Google Scholar]
  21. Kämpfer P., Young C. C., Sridhar K. R., Arun A. B., Lai W. A., Shen F. T., Rekha P. D.. ( 2006;). Transfer of [Flexibacter] sancti, [Flexibacter] filiformis, [Flexibacter] japonensis and [Cytophaga] arvensicola to the genus Chitinophaga and description of Chitinophaga skermanii sp. nov.. Int J Syst Evol Microbiol 56:, 2223–2228. [CrossRef][PubMed]
    [Google Scholar]
  22. Kämpfer P., Lodders N., Falsen E.. ( 2011;). Hydrotalea flava gen. nov., sp. nov., a new member of the phylum Bacteroidetes and allocation of the genera Chitinophaga, Sediminibacterium, Lacibacter, Flavihumibacter, Flavisolibacter, Niabella, Niastella, Segetibacter, Parasegetibacter, Terrimonas, Ferruginibacter, Filimonas and Hydrotalea to the family Chitinophagaceae fam. nov.. Int J Syst Evol Microbiol 61:, 518–523. [CrossRef][PubMed]
    [Google Scholar]
  23. Kang H., Kim H., Lee B. I., Joung Y., Joh K.. ( 2014;). Sediminibacterium goheungense sp. nov., isolated from a freshwater reservoir. . Int J Syst Evol Microbiol 64:, 1328–1333. [CrossRef][PubMed]
    [Google Scholar]
  24. Kim B. Y., Weon H. Y., Yoo S. H., Hong S. B., Kwon S. W., Stackebrandt E., Go S. J.. ( 2007;). Niabella aurantiaca gen. nov., sp. nov., isolated from a greenhouse soil in Korea. . Int J Syst Evol Microbiol 57:, 538–541. [CrossRef][PubMed]
    [Google Scholar]
  25. 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. [CrossRef][PubMed]
    [Google Scholar]
  26. Kim Y. J., Nguyen N. L., Weon H. Y., Yang D. C.. ( 2013;). Sediminibacterium ginsengisoli sp. nov., isolated from soil of a ginseng field, and emended descriptions of the genus Sediminibacterium and of Sediminibacterium salmoneum. . Int J Syst Evol Microbiol 63:, 905–912. [CrossRef][PubMed]
    [Google Scholar]
  27. 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]
  28. Kirchman D. L.. ( 2002;). The ecology of Cytophaga-Flavobacteria in aquatic environments. . FEMS Microbiol Ecol 39:, 91–100.[PubMed]
    [Google Scholar]
  29. Komagata K., Suzuki K.. ( 1987;). Lipid and cell-wall analysis in bacterial systematics. . Methods Microbiol 19:, 161–207. [CrossRef]
    [Google Scholar]
  30. Kumar S., Tamura K., Nei M.. ( 2004;). mega3: integrated software for molecular evolutionary genetics analysis and sequence alignment. . Brief Bioinform 5:, 150–163. [CrossRef][PubMed]
    [Google Scholar]
  31. Lee H. G., An D. S., Im W. T., Liu Q. M., Na J. R., Cho D. H., Jin C. W., Lee S. T., Yang D. C.. ( 2007;). Chitinophaga ginsengisegetis sp. nov. and Chitinophaga ginsengisoli sp. nov., isolated from soil of a ginseng field in South Korea. . Int J Syst Evol Microbiol 57:, 1396–1401. [CrossRef][PubMed]
    [Google Scholar]
  32. Lee D.-G., Park J.-M., Kang H., Hong S.-Y., Lee K.-R., Chang H.-B., Trujillo M. E.. ( 2013;). Asinibacterium lactis gen. nov., sp. nov., a member of the family Chitinophagaceae, isolated from donkey (Equus asinus) milk. . Int J Syst Evol Microbiol 63:, 3180–3185. [CrossRef][PubMed]
    [Google Scholar]
  33. Li J., Ovakim D. H., Charles T. C., Glick B. R.. ( 2000;). An ACC deaminase minus mutant of Enterobacter cloacae UW4 no longer promotes root elongation. . Curr Microbiol 41:, 101–105. [CrossRef][PubMed]
    [Google Scholar]
  34. Li L., Sun L., Shi N., Liu L., Guo H., Xu A., Zhang X., Yao N.. ( 2013;). Chitinophaga cymbidii sp. nov., isolated from Cymbidium goeringii roots. . Int J Syst Evol Microbiol 63:, 1800–1804. [CrossRef][PubMed]
    [Google Scholar]
  35. Lim J. H., Baek S.-H., Lee S.-T.. ( 2009;). Ferruginibacter alkalilentus gen. nov., sp. nov. and Ferruginibacter lapsinanis sp. nov., novel members of the family ‘Chitinophagaceae’ in the phylum Bacteroidetes, isolated from freshwater sediment. . Int J Syst Evol Microbiol 59:, 2394–2399. [CrossRef][PubMed]
    [Google Scholar]
  36. Lin S. Y., Hameed A., Liu Y. C., Hsu Y. H., Lai W. A., Huang H. I., Young C. C.. ( 2014;). Chitinophaga taiwanensis sp. nov., isolated from the rhizosphere of Arabidopsis thaliana. . Int J Syst Evol Microbiol 64:, 426–430. [CrossRef][PubMed]
    [Google Scholar]
  37. Madhaiyan M., Poonguzhali S.. ( 2014;). Methylobacterium pseudosasicola sp. nov. and Methylobacterium phyllostachyos sp. nov., isolated from bamboo leaf surfaces. . Int J Syst Evol Microbiol 64:, 2376–2384. [CrossRef][PubMed]
    [Google Scholar]
  38. Madhaiyan M., Poonguzhali S., Ryu J.-H., Sa T.-M.. ( 2006;). Regulation of ethylene levels in canola (Brassica campestris) by 1-aminocyclopropane-1-carboxylate deaminase-containing Methylobacterium fujisawaense. . Planta 224:, 268–278. [CrossRef][PubMed]
    [Google Scholar]
  39. Madhaiyan M., Kim B.-Y., Poonguzhali S., Kwon S.-W., Song M.-H., Ryu J.-H., Go S.-J., Koo B.-S., Sa T.-M.. ( 2007;). Methylobacterium oryzae sp. nov., an aerobic, pink-pigmented, facultatively methylotrophic, 1-aminocyclopropane-1-carboxylate deaminase-producing bacterium isolated from rice. . Int J Syst Evol Microbiol 57:, 326–331. [CrossRef][PubMed]
    [Google Scholar]
  40. 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. [CrossRef]
    [Google Scholar]
  41. Minnikin D. E., O’Donnell A. G., Goodfellow M., Alderson G., Athalye M., Schaal A., Parlett J. H.. ( 1984;). An integrated procedure for the extraction of bacterial isoprenoid quinones and polar lipids. . J Microbiol Methods 2:, 233–241. [CrossRef]
    [Google Scholar]
  42. Myers E. W., Miller W.. ( 1988;). Optimal alignments in linear space. . Comput Appl Biosci 4:, 11–17.[PubMed]
    [Google Scholar]
  43. Olsen G. J., Matsuda H., Hagstrom R., Overbeek R.. ( 1994;). fastDNAmL: a tool for construction of phylogenetic trees of DNA sequences using maximum likelihood. . Comput Appl Biosci 10:, 41–48.[PubMed]
    [Google Scholar]
  44. Penrose D. M., Glick B. R.. ( 2003;). Methods for isolating and characterizing ACC deaminase-containing plant growth-promoting rhizobacteria. . Physiol Plant 118:, 10–15. [CrossRef][PubMed]
    [Google Scholar]
  45. Pikovskaya R. I.. ( 1948;). [Mobilization of phosphorus in soil in connection with vital activity of some microbial species]. . Mikrobiologiia 17:, 362–370 (in Russian).
    [Google Scholar]
  46. Plazinski J., Rolfe B. G.. ( 1985;). Analysis of the pectolytic activity of Rhizobium and Azospirillium strains isolated from Trifolium repens. . J Plant Physiol 120:, 181–187. [CrossRef]
    [Google Scholar]
  47. Proença D. N., Nobre M. F., Morais P. V.. ( 2014;). Chitinophaga costaii sp. nov., an endophyte of Pinus pinaster, and emended description of Chitinophaga niabensis. . Int J Syst Evol Microbiol 64:, 1237–1243. [CrossRef][PubMed]
    [Google Scholar]
  48. Qu J.-H., Yuan H.-L.. ( 2008;). Sediminibacterium salmoneum gen. nov., sp. nov., a member of the phylum Bacteroidetes isolated from sediment of a eutrophic reservoir. . Int J Syst Evol Microbiol 58:, 2191–2194. [CrossRef][PubMed]
    [Google Scholar]
  49. Qu J. H., Yuan H. L., Yang J. S., Li H. F., Chen N.. ( 2009;). Lacibacter cauensis gen. nov., sp. nov., a novel member of the phylum Bacteroidetes isolated from sediment of a eutrophic lake. . Int J Syst Evol Microbiol 59:, 1153–1157. [CrossRef][PubMed]
    [Google Scholar]
  50. 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]
  51. Sangkhobol V., Skerman V. B. D.. ( 1981;). Chitinophaga, a new genus of chitinolytic myxobacteria. . Int J Syst Bacteriol 31:, 285–293. [CrossRef]
    [Google Scholar]
  52. Sasser M.. ( 1990;). Identification of bacteria through fatty acid analysis. . In Methods in Phytobacteriology, pp. 199–204. Edited by Klement S., Rudolf K., Sands D... Budapest:: Akademiai Kiado;.
    [Google Scholar]
  53. Schwyn B., Neilands J. B.. ( 1987;). Universal chemical assay for the detection and determination of siderophores. . Anal Biochem 160:, 47–56. [CrossRef][PubMed]
    [Google Scholar]
  54. 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:, 151–154. [CrossRef]
    [Google Scholar]
  55. Shah S., Li J., Moffatt B. A., Glick B. R.. ( 1998;). Isolation and characterization of ACC deaminase genes from two different plant growth-promoting rhizobacteria. . Can J Microbiol 44:, 833–843. [CrossRef][PubMed]
    [Google Scholar]
  56. Shiratori H., Tagami Y., Morishita T., Kamihara Y., Beppu T., Ueda K.. ( 2009;). Filimonas lacunae gen. nov., sp. nov., a member of the phylum Bacteroidetes isolated from fresh water. . Int J Syst Evol Microbiol 59:, 1137–1142. [CrossRef][PubMed]
    [Google Scholar]
  57. 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]
  58. Urios L., Agogué H., Lesongeur F., Stackebrandt E., Lebaron P.. ( 2006;). Balneola vulgaris gen. nov., sp. nov., a member of the phylum Bacteroidetes from the north-western Mediterranean Sea. . Int J Syst Evol Microbiol 56:, 1883–1887. [CrossRef][PubMed]
    [Google Scholar]
  59. Urios L., Intertaglia L., Lesongeur F., Lebaron P.. ( 2008;). Balneola alkaliphila sp. nov., a marine bacterium isolated from the Mediterranean Sea. . Int J Syst Evol Microbiol 58:, 1288–1291. [CrossRef][PubMed]
    [Google Scholar]
  60. Wang H., Zhang Y. Z., Man C. X., Chen W. F., Sui X. H., Li Y., Zhang X. X., Chen W. X.. ( 2009;). Niabella yanshanensis sp. nov., isolated from the soybean rhizosphere. . Int J Syst Evol Microbiol 59:, 2854–2856. [CrossRef][PubMed]
    [Google Scholar]
  61. Wang Y., Cai F., Tang Y., Dai J., Qi H., Rahman E., Peng F., Fang C.. ( 2011;). Flavitalea populi gen. nov., sp. nov., isolated from soil of a Euphrates poplar (Populus euphratica) forest. . Int J Syst Evol Microbiol 61:, 1554–1560. [CrossRef][PubMed]
    [Google Scholar]
  62. Wang Q., Cheng C., He L. Y., Huang Z., Sheng X. F.. ( 2014;). Chitinophaga jiangningensis sp. nov., a mineral-weathering bacterium. . Int J Syst Evol Microbiol 64:, 260–265. [CrossRef][PubMed]
    [Google Scholar]
  63. Weon H. Y., Kim B. Y., Yoo S. H., Lee S. Y., Kwon S. W., Go S. J., Stackebrandt E.. ( 2006;). Niastella koreensis gen. nov., sp. nov. and Niastella yeongjuensis sp. nov., novel members of the phylum Bacteroidetes, isolated from soil cultivated with Korean ginseng. . Int J Syst Evol Microbiol 56:, 1777–1782. [CrossRef][PubMed]
    [Google Scholar]
  64. Weon H. Y., Kwon S. W., Son J. A., Kim S. J., Kim Y. S., Kim B. Y., Ka J. O.. ( 2010;). Adhaeribacter aerophilus sp. nov., Adhaeribacter aerolatus sp. nov. and Segetibacter aerophilus sp. nov., isolated from air samples. . Int J Syst Evol Microbiol 60:, 2424–2429. [CrossRef][PubMed]
    [Google Scholar]
  65. Whittenbury R., Phillips K. C., Wilkinson J. F.. ( 1970;). Enrichment, isolation and some properties of methane-utilizing bacteria. . J Gen Microbiol 61:, 205–218. [CrossRef][PubMed]
    [Google Scholar]
  66. Xie C.-H., Yokota A.. ( 2006;). Reclassification of [Flavobacterium] ferrugineum as Terrimonas ferruginea gen. nov., comb. nov., and description of Terrimonas lutea sp. nov., isolated from soil. . Int J Syst Evol Microbiol 56:, 1117–1121. [CrossRef][PubMed]
    [Google Scholar]
  67. Yasir M., Chung E. J., Song G. C., Bibi F., Jeon C. O., Chung Y. R.. ( 2011;). Chitinophaga eiseniae sp. nov., isolated from vermicompost. . Int J Syst Evol Microbiol 61:, 2373–2378. [CrossRef][PubMed]
    [Google Scholar]
  68. Yoon M.-H., Im W.-T.. ( 2007;). Flavisolibacter ginsengiterrae gen. nov., sp. nov. and Flavisolibacter ginsengisoli sp. nov., isolated from ginseng cultivating soil. . Int J Syst Evol Microbiol 57:, 1834–1839. [CrossRef][PubMed]
    [Google Scholar]
  69. Zhang K., Tang Y., Zhang L., Dai J., Wang Y., Luo X., Liu M., Luo G., Fang C.. ( 2009;). Parasegetibacter luojiensis gen. nov., sp. nov., a member of the phylum Bacteroidetes isolated from a forest soil. . Int J Syst Evol Microbiol 59:, 3058–3062. [CrossRef][PubMed]
    [Google Scholar]
  70. Zhang N. N., Qu J.-H., Yuan H.-L., Sun Y. M., Yang J.-S.. ( 2010;). Flavihumibacter petaseus gen. nov., sp. nov., isolated from soil of a subtropical rainforest. . Int J Syst Evol Microbiol 60:, 1609–1612. [CrossRef][PubMed]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijs.0.069377-0
Loading
/content/journal/ijsem/10.1099/ijs.0.069377-0
Loading

Data & Media loading...

Supplements

Supplementary Data



PDF

Most Cited This Month

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