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Volume 63, Issue Pt_5

sp. nov., sp. nov. and sp. nov., isolated from root nodules of different agroforestry legume trees Free

Abstract

A total of 18 strains, representing members of the genus , obtained from root nodules of woody legumes growing in Ethiopia, have been previously shown, by multilocus sequence analysis (MLSA) of five housekeeping genes, to form three novel genospecies. In the present study, the phylogenetic relationship between representative strains of these three genospecies and the type strains of their closest phylogenetic neighbours , and was further evaluated using a polyphasic taxonomic approach. In line with our earlier MLSA of other housekeeping genes, the phylogenetic trees derived from the and genes grouped the test strains into three well-supported, distinct lineages that exclude all defined species of the genus . The DNA–DNA relatedness between the representative strains of genospecies I–III and the type strains of their closest phylogenetic neighbours was low (≤59 %). They differed from each other and from their closest phylogenetic neighbours by the presence/absence of several fatty acids, or by large differences in the relative amounts of particular fatty acids. While showing distinctive features, they were generally able to utilize a wide range of substrates as sole carbon and nitrogen sources. The strains belonging to genospecies I, II and III therefore represent novel species for which we propose the names sp. nov., sp. nov. and sp. nov. The isolates AC39a ( = LMG 26966 = HAMBI 3295), AC99b ( = LMG 26968 = HAMBI 3301) and AC98c ( = LMG 26967 = HAMBI 3306) are proposed as type strains for the respective novel species.

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Funding
This study was supported by the:
  • Norwegian Programme for Development, Research and Education (NUFU)
© 2013 IUMS
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2013-05-01
2024-04-18
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References

  1. Amarger N., Macheret V., Laguerre G. ( 1997 ). Rhizobium gallicum sp. nov. and Rhizobium giardinii sp. nov., from Phaseolus vulgaris nodules. . Int J Syst Bacteriol 47, 996–1006. [View Article] [PubMed]
    [Google Scholar]
  2. Anyango B., Wilson K. J., Beynon J. L., Giller K. E. ( 1995 ). Diversity of rhizobia nodulating Phaseolus vulgaris L. in two Kenyan soils with contrasting PHs. . Appl Environ Microbiol 61, 4016–4021.[PubMed]
    [Google Scholar]
  3. Ba S., Willems A., de Lajudie P., Roche P., Jeder H., Quatrini P., Neyra M., Ferro M., Promé J.-C. & other authors ( 2002 ). Symbiotic and taxonomic diversity of rhizobia isolated from Acacia tortilis subsp. raddiana in Africa. . Syst Appl Microbiol 25, 130–145. [View Article] [PubMed]
    [Google Scholar]
  4. Cleenwerck I., Vandemeulebroecke K., Janssens D., Swings J. ( 2002 ). Re-examination of the genus Acetobacter, with description of Acetobacter cerevisiae sp. nov. and Acetobacter malorum sp. nov.. Int J Syst Evol Microbiol 52, 1551–1558. [View Article] [PubMed]
    [Google Scholar]
  5. de Lajudie P., Willems A., Pot B., Dewettinck D., Maestrojuan G., Neyra M., Collins M. D., Dreyfus B., Kersters K., Gillis M. ( 1994 ). Polyphasic taxonomy of rhizobia: emendation of the genus Sinorhizobium and description of Sinorhizobium meliloti comb. nov., Sinorhizobium saheli sp. nov., and Sinorhizobium terangae sp. nov.. Int J Syst Bacteriol 44, 715–733. [View Article]
    [Google Scholar]
  6. de Lajudie P., Laurent-Fulele E., Willems A., Torck U., Coopman R., Collins M. D., Kersters K., Dreyfus B., Gillis M. ( 1998a ). Allorhizobium undicola gen. nov., sp. nov., nitrogen-fixing bacteria that efficiently nodulate Neptunia natans in Senegal. . Int J Syst Bacteriol 48, 1277–1290. [View Article] [PubMed]
    [Google Scholar]
  7. de Lajudie P., Willems A., Nick G., Moreira F., Molouba F., Hoste B., Torck U., Neyra M., Collins M. D. & other authors ( 1998b ). Characterization of tropical tree rhizobia and description of Mesorhizobium plurifarium sp. nov.. Int J Syst Bacteriol 48, 369–382. [View Article] [PubMed]
    [Google Scholar]
  8. Degefu T., Wolde-meskel E., Frostegård Å. ( 2011 ). Multilocus sequence analyses reveal several unnamed Mesorhizobium genospecies nodulating Acacia species and Sesbania sesban trees in Southern regions of Ethiopia. . Syst Appl Microbiol 34, 216–226. [View Article] [PubMed]
    [Google Scholar]
  9. Degefu T., Wolde-meskel E., Frostegård Å. ( 2012 ). Phylogenetic multilocus sequence analysis identifies seven novel Ensifer genospecies isolated from a less-well-explored biogeographical region in East Africa. . Int J Syst Evol Microbiol 62, 2286–2295. [View Article] [PubMed]
    [Google Scholar]
  10. Dreyfus B., Garcia J. L., Gillis M. ( 1988 ). Characterization of Azorhizobium caulinodans gen.nov. sp.nov., a stem-nodulating nitrogen-fixing bacterium isolated from Sesbania rostrata . . Int J Syst Bacteriol 38, 89–98. [View Article]
    [Google Scholar]
  11. Ezaki T., Hashimoto Y., Yabuuchi E. ( 1989 ). Fluorometric deoxyribonucleic acid– deoxyribonucleic acid hybridization in microdilution wells as an alternative to membrane filter hybridization in which radioisotopes are used to determine genetic relatedness among bacterial strains. . Int J Syst Bacteriol 39, 224–229. [View Article]
    [Google Scholar]
  12. Gaunt M. W., Turner S. L., Rigottier-Gois L., Lloyd-Macgilp S. A., Young J. P. W. ( 2001 ). Phylogenies of atpD and recA support the small subunit rRNA-based classification of rhizobia. . Int J Syst Evol Microbiol 51, 2037–2048. [View Article] [PubMed]
    [Google Scholar]
  13. Goris J., Suzuki K., De Vos P., Nakase T., Kersters K. ( 1998 ). Evaluation of a microplate DNA–DNA hybridization method compared with the initial renaturation method. . Can J Microbiol 44, 1148–1153. [View Article]
    [Google Scholar]
  14. Graham P. H., Sadowsky M. J., Keyser H. H., Barnet Y. M., Bradley R. S., Cooper J. E., Deley D. J., Jarvis B. D. W., Roslycky E. B. & other authors ( 1991 ). Proposed minimal standards for the description of new genera and species of root and stem-nodulating bacteria. . Int J Syst Bacteriol 41, 582–587. [View Article]
    [Google Scholar]
  15. Hanage W. P., Fraser C., Spratt B. G. ( 2005 ). Fuzzy species among recombinogenic bacteria. . BMC Biol 3, 6. [View Article] [PubMed]
    [Google Scholar]
  16. Hanage W. P., Fraser C., Spratt B. G. ( 2006 ). Sequences, sequence clusters and bacterial species. . Philos Trans R Soc Lond B Biol Sci 361, 1917–1927. [View Article] [PubMed]
    [Google Scholar]
  17. Haukka K., Lindström K. ( 1994 ). Pulsed-field gel electrophoresis for genotypic comparison of Rhizobium bacteria that nodulate leguminous trees. . FEMS Microbiol Lett 119, 215–220. [View Article]
    [Google Scholar]
  18. Haukka K., Lindström K., Peter J., Young W. ( 1996 ). Diversity of partial 16S rRNA sequences among and within strains of African rhizobia isolated from Acacia and Prosopis . . Syst Appl Microbiol 19, 352–359. [View Article]
    [Google Scholar]
  19. Islam M. S., Kawasaki H., Muramatsu Y., Nakagawa Y., Seki T. ( 2008 ). Bradyrhizobium iriomotense sp. nov., isolated from a tumor-like root of the legume Entada koshunensis from Iriomote Island in Japan. . Biosci Biotechnol Biochem 72, 1416–1429. [View Article] [PubMed]
    [Google Scholar]
  20. Jarvis B. D. W., Pankhurst C. E., Patel J. J. ( 1982 ). Rhizobium loti, a new species of legume root nodule bacteria. . Int J Syst Bacteriol 32, 378–380. [View Article]
    [Google Scholar]
  21. Jarvis B. D. W., Sivakumaran S., Tighe S. W., Gillis M. ( 1996 ). Identification of Agrobacterium and Rhizobium species based on cellular fatty acid composition. . Plant Soil 184, 143–158. [View Article]
    [Google Scholar]
  22. Jarvis B. D. W., van Berkum P., Chen W. X., Nour S. M., Fernandez M. P., Cleyet-Marel J. C., Gillis M. ( 1997 ). Transfer of Rhizobium loti, Rhizobium huakuii, Rhizobium ciceri, Rhizobium mediterraneum, and Rhizobium tianshanense to Mesorhizobium gen. nov.. Int J Syst Bacteriol 47, 895–898. [View Article]
    [Google Scholar]
  23. Khbaya B., Neyra M., Normand P., Zerhari K., Filali-Maltouf A. ( 1998 ). Genetic diversity and phylogeny of rhizobia that nodulate Acacia spp. in morocco assessed by analysis of rRNA genes. . Appl Environ Microbiol 64, 4912–4917.[PubMed]
    [Google Scholar]
  24. Martens M., Delaere M., Coopman R., De Vos P., Gillis M., Willems A. ( 2007 ). Multilocus sequence analysis of Ensifer and related taxa. . Int J Syst Evol Microbiol 57, 489–503. [View Article] [PubMed]
    [Google Scholar]
  25. Martens M., Dawyndt P., Coopman R., Gillis M., De Vos P., Willems A. ( 2008 ). Advantages of multilocus sequence analysis for taxonomic studies: a case study using 10 housekeeping genes in the genus Ensifer (including former Sinorhizobium). . Int J Syst Evol Microbiol 58, 200–214. [View Article] [PubMed]
    [Google Scholar]
  26. McInroy S. G., Campbell C. D., Haukka K. E., Odee D. W., Sprent J. I., Wang W. J., Young J. P. W., Sutherland J. M. ( 1999 ). Characterisation of rhizobia from African acacias and other tropical woody legumes using Biolog and partial 16S rRNA sequencing. . FEMS Microbiol Lett 170, 111–117.[PubMed]
    [Google Scholar]
  27. Merabet C., Martens M., Mahdhi M., Zakhia F., Sy A., Le Roux C., Domergue O., Coopman R., Bekki A. & other authors ( 2010 ). Multilocus sequence analysis of root nodule isolates from Lotus arabicus (Senegal), Lotus creticus, Argyrolobium uniflorum and Medicago sativa (Tunisia) and description of Ensifer numidicus sp. nov. and Ensifer garamanticus sp. nov.. Int J Syst Evol Microbiol 60, 664–674. [View Article] [PubMed]
    [Google Scholar]
  28. 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]
  29. Mhamdi R., Laguerre G., Aouani M. E., Mars M., Amarger N. ( 2002 ). Different species and symbiotic genotypes of field rhizobia can nodulate Phaseolus vulgaris in Tunisian soils. . FEMS Microbiol Ecol 41, 77–84. [View Article] [PubMed]
    [Google Scholar]
  30. Nandasena K. G., O’Hara G. W., Tiwari R. P., Willems A., Howieson J. G. ( 2009 ). Mesorhizobium australicum sp. nov. and Mesorhizobium opportunistum sp. nov., isolated from Biserrula pelecinus L. in Australia. . Int J Syst Evol Microbiol 59, 2140–2147. [View Article] [PubMed]
    [Google Scholar]
  31. Naser S. M., Thompson F. L., Hoste B., Gevers D., Dawyndt P., Vancanneyt M., Swings J. ( 2005 ). Application of multilocus sequence analysis (MLSA) for rapid identification of Enterococcus species based on rpoA and pheS genes. . Microbiology 151, 2141–2150. [View Article] [PubMed]
    [Google Scholar]
  32. Nick G., de Lajudie P., Eardly B. D., Suomalainen S., Paulin L., Zhang X., Gillis M., Lindström K. ( 1999a ). Sinorhizobium arboris sp. nov., and Sinorhizobium kostiense sp. nov., isolated from leguminous trees in Sudan and Kenya. . Int J Syst Bacteriol 49, 1359–1368. [View Article] [PubMed]
    [Google Scholar]
  33. Nick G., Jussila M., Hoste B., Niemi M., Kaijalainen S., de Lajudie P., Gillis M., de Bruijn F. J., Lindström K. ( 1999b ). Rhizobia isolated from root nodules of tropical leguminous trees characterized using DNA-DNA dot-blot hybridisation and rep-PCR genomic fingerprinting. . Syst Appl Microbiol 22, 287–299. [View Article]
    [Google Scholar]
  34. Nour S. M., Fernandez M. P., Normand P., Cleyet-Marel J. C. ( 1994 ). Rhizobium ciceri sp. nov., consisting of strains that nodulate chickpeas (Cicer arietinum L.). . Int J Syst Bacteriol 44, 511–522. [View Article] [PubMed]
    [Google Scholar]
  35. Odee D. W., Sutherland J. M., Kimiti J. M., Sprent J. I. ( 1995 ). Natural rhizobial populations and nodulation status of woody legumes growing in diverse Kenyan conditions. . Plant Soil 173, 211–224. [View Article]
    [Google Scholar]
  36. Odee D. W., Sutherland J. M., Makatiani E. T., McInroy S. G., Sprent J. I. ( 1997 ). Phenotypic characteristics and composition of rhizobia associated with woody legumes growing in diverse Kenyan conditions. . Plant Soil 188, 65–75. [View Article]
    [Google Scholar]
  37. Odee D. W., Haukka K., McInroy S. G., Sprent J. I., Sutherland J. M., Young J. P. W. ( 2002 ). Genetic and symbiotic characterization of rhizobia isolated from tree and herbaceous legumes grown in soils from ecologically diverse sites in Kenya. . Soil Biol Biochem 34, 801–811. [View Article]
    [Google Scholar]
  38. Ratledge C., Wilkinson S. G. ( 1988 ). Microbial lipids. London:: Academic Press;.
     [Google Scholar]
  39. Sawada H., Kuykendall L. D., Young J. M. ( 2003 ). Changing concepts in the systematics of bacterial nitrogen-fixing legume symbionts. . J Gen Appl Microbiol 49, 155–179. [View Article] [PubMed]
    [Google Scholar]
  40. Stackebrandt E., Frederiksen W., Garrity G. M., Grimont P. A., Kämpfer P., Maiden M. C., Nesme X., Rosselló-Mora R., Swings J. & other authors ( 2002 ). Report of the ad hoc committee for the re-evaluation of the species definition in bacteriology. . Int J Syst Evol Microbiol 52, 1043–1047. [View Article] [PubMed]
    [Google Scholar]
  41. Sy A., Giraud E., Jourand P., Garcia N., Willems A., de Lajudie P., Prin Y., Neyra M., Gillis M. & other authors ( 2001 ). Methylotrophic Methylobacterium bacteria nodulate and fix nitrogen in symbiosis with legumes. . J Bacteriol 183, 214–220. [View Article] [PubMed]
    [Google Scholar]
  42. 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. [View Article] [PubMed]
    [Google Scholar]
  43. Tighe S. W., de Lajudie P., Dipietro K., Lindström K., Nick G., Jarvis B. D. W. ( 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. [View Article] [PubMed]
    [Google Scholar]
  44. Turner S. L., Young J. P. W. ( 2000 ). The glutamine synthetases of rhizobia: phylogenetics and evolutionary implications. . Mol Biol Evol 17, 309–319. [View Article] [PubMed]
    [Google Scholar]
  45. Vinuesa P., León-Barrios M., Silva C., Willems A., Jarabo-Lorenzo A., Pérez-Galdona R., Werner D., Martínez-Romero E. ( 2005 ). Bradyrhizobium canariense sp. nov., an acid-tolerant endosymbiont that nodulates endemic genistoid legumes (Papilionoideae: Genisteae) from the Canary Islands, along with Bradyrhizobium japonicum bv. genistearum, Bradyrhizobium genospecies alpha and Bradyrhizobium genospecies beta. . Int J Syst Evol Microbiol 55, 569–575. [View Article] [PubMed]
    [Google Scholar]
  46. Wang F. Q., Wang E. T., Liu J., Chen Q., Sui X. H., Chen W. F., Chen W. X. ( 2007 ). Mesorhizobium albiziae sp. nov., a novel bacterium that nodulates Albizia kalkora in a subtropical region of China. . Int J Syst Evol Microbiol 57, 1192–1199. [View Article] [PubMed]
    [Google Scholar]
  47. 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. & other authors ( 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]
  48. Wilson K. ( 1987 ). Preparation of genomic DNA from bacteria. . In Current protocols in molecular biology, pp. 241–245. Edited by Ausubel F. M., Brent R., Kingston R. E., Moore D. D., Seidman J. G., Smith J. A., Struhl K. . New York:: Green Publishing and Wiley-Interscience;.
     [Google Scholar]
  49. Wolde-meskel E., Terefework Z., Lindström K., Frostegård Å. ( 2004 ). Metabolic and genomic diversity of rhizobia isolated from field standing native and exotic woody legumes in southern Ethiopia. . Syst Appl Microbiol 27, 603–611. [View Article] [PubMed]
    [Google Scholar]
  50. Wolde-meskel E., Terefework Z., Frostegård Å., Lindström K. ( 2005 ). Genetic diversity and phylogeny of rhizobia isolated from agroforestry legume species in southern Ethiopia. . Int J Syst Evol Microbiol 55, 1439–1452. [View Article] [PubMed]
    [Google Scholar]
  51. Zhang X. P., Harper R., Karsisto M., Lindström K. ( 1991 ). Diversity of Rhizobium bacteria isolated from the root nodules of leguminous trees. . Int J Syst Bacteriol 41, 104–113. [View Article]
    [Google Scholar]
  52. Zhang J. J., Liu T. Y., Chen W. F., Wang E. T., Sui X. H., Zhang X. X., Li Y., Li Y., Chen W. X. ( 2012 ). Mesorhizobium muleiense sp. nov., nodulating with Cicer arietinum L.. Int J Syst Evol Microbiol 62, 2737–2742. [View Article] [PubMed]
    [Google Scholar]
  53. Zhao C. T., Wang E. T., Zhang Y. M., Chen W. F., Sui X. H., Chen W. X., Liu H. C., Zhang X. X. ( 2012 ). Mesorhizobium silamurunense sp. nov., isolated from root nodules of Astragalus species. . Int J Syst Evol Microbiol 62, 2180–2186. [View Article] [PubMed]
    [Google Scholar]
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Mesorhizobium shonense sp. nov., Mesorhizobium hawassense sp. nov. and Mesorhizobium abyssinicae sp. nov., isolated from root nodules of different agroforestry legume trees
Int J Syst Evol Microbiol 63, 1746 (2013); https://doi.org/10.1099/ijs.0.044032-0
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