Genotypic and phenotypic diversity of rhizobia isolated from Lathyrus japonicus indigenous to Japan

Systematic and Applied Microbiology

Volumn 33, Issue 7, 2010, Pages 383-397

  Aoki, Seishiro ^a   Kondo, Tetsuya ^b   Prévost, Danielle ^c   Nakata, Sayuri ^d   Kajita, Tadashi ^d   Ito, Motomi ^a  

^a UNIVERSITY OF TOKYO   (Japan)

^b HOKKAIDO UNIVERSITY   (Japan)

^c AGRICULTURE AND AGRI FOOD CANADA   (Canada)

^d CHIBA UNIVERSITY   (Japan)

Author keywords

Dispersing plants; Horizontal gene transfer; Lathyrus japonicus; Nod genes; Rhizobium leguminorasum; Rhizobium pisi

Indexed keywords

ARTICLE; BACTERIAL STRAIN; CANADA; GENE SEQUENCE; GENETIC VARIABILITY; GENOTYPE; JAPAN; LATHYRUS; LATHYRUS JAPONICUS; LEGUME; NATIVE SPECIES; NONHUMAN; NUCLEOTIDE SEQUENCE; PHENOTYPE; PHYLOGENY; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; RANDOM AMPLIFIED POLYMORPHIC DNA; RECA GENE; RESTRICTION FRAGMENT LENGTH POLYMORPHISM; RHIZOBIACEAE; RHIZOBIUM LEGUMINOSARUM; RHIZOBIUM PISI; SEASHORE; SYMBIOSIS;

AMIDOHYDROLASES; BACTERIAL PROTEINS; BACTERIAL TYPING TECHNIQUES; BASE SEQUENCE; CANADA; DNA FINGERPRINTING; DNA, BACTERIAL; DNA, INTERGENIC; GENE TRANSFER, HORIZONTAL; GENOTYPE; HOST SPECIFICITY; JAPAN; LATHYRUS; MOLECULAR SEQUENCE DATA; N-ACETYLGLUCOSAMINYLTRANSFERASES; PHENOTYPE; PHYLOGENY; POLYMERASE CHAIN REACTION; REC A RECOMBINASES; RHIZOBIUM; RNA, RIBOSOMAL, 16S; SALT-TOLERANCE; SEQUENCE ANALYSIS, DNA; SYMBIOSIS;

LATHYRUS; LATHYRUS JAPONICUS; RHIZOBIUM; RHIZOBIUM ETLI; RHIZOBIUM LEGUMINOSARUM; RHIZOBIUM PHASEOLI;

EID: 78249281344     PISSN: 07232020     EISSN: 16180984     Source Type: Journal    
DOI: 10.1016/j.syapm.2010.07.001     Document Type: Article

References (59)

1. Alvarez-Martinez E.R., Valverde A., Ramirez-Bahena M.H., Garcia-Fraile P., Tejedor C., Mateos P.F., Santillana N., Zuniga D., Peix A., Velazquez E. The analysis of core and symbiotic genes of rhizobia nodulating Vicia from different continents reveals their common phylogenetic origin and suggests the distribution of Rhizobium leguminosarum strains together with Vicia seeds. Arch. Microbiol. 2009, 191:659-668.
2. Binde D.R., Menna P., Bangel E.V., Barcellos F.G., Hungria M. rep-PCR fingerprinting and taxonomy based on the sequencing of the 16S rRNA gene of 54 elite commercial rhizobial strains. Appl. Microbiol. Biotechnol. 2009, 83:897-908.
3. Brightmore D., White P.H. Lathyrus japonicus Willd. J. Ecol. 1963, 3:795-801.
4. Cannone J.J., Subramanian S., Schnare M.N., Collett J.R., D'Souza L.M., Du Y., Feng B., Lin N., Madabusi L.V., Muller K.M., Pande N., Shang Z., Yu N., Gutell R.R. The comparative RNA web (CRW) site: an online database of comparative sequence and structure information for ribosomal, intron, and other RNAs. BMC Bioinform. 2002, 3:2.
5. Clark I.M., Mendum T.A., Hirsch P.R. The influence of the symbiotic plasmid pRL1JI on the distribution of GM rhizobia in soil and crop rhizospheres, and implications for gene flow. Antonie Van Leeuwenhoek 2002, 81:607-616.
6. Dobert R.C., Breil B.T., Triplet E.W. DNA sequence of the common nodulation genes of Bradyrhizobium elkanii and their phylogenetic relationship to those of other nodulating bacteria. Mol. Plant Microbe Interact. 1994, 7:564-572.
7. Dresler-Nurmi A., Fewer D.P., Rasanen L.A., Lindstrom K. The diversity and evolution of rhizobia. Microbiol. Monogr. 2009, 8:3-41.
8. Drouin P., Provost D., Antoun H. Classification of bacteria nodulating Lathyrus japonicus and Lathyrus pratensis in northern Quebec as strains of Rhizobium leguminosarum biovar viciae. Int. J. Syst. Bacteriol. 1996, 46:1016-1024.
9. Elbanna K., Elbadry M., Gamal-Eldin H. Genotypic and phenotypic characterization of rhizobia that nodulate snap bean (Phaseolus vulgaris L.) in Egyptian soils. Syst. Appl. Microbiol. 2009, 32:522-530.
10. Faith D.P., Cranston P.S. Could a cladogram this short have arisen by chance alone? On permutation tests for cladistic structure. Cladistics 1991, 7:1-28.
11. Felsenstein J. PHYLIP (Phylogeny Inference Package) Version 3.67 2007, Department of Genome Sciences, University of Washington, Seattle, USA, (Distributed by the author).
12. Guindon S., Gascuel O. A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst. Biol. 2003, 52:696-704.
13. Hagen M.J., Hamrick J.L. A hierarchical analysis of population genetic structure in Rhizobium leguminosarum bv. trifolii. Mol. Ecol. 1996, 5:177-186.
14. Han T.X., Tian C.F., Wang E.T., Chen W.X. Associations among rhizobial chromosomal background, nod genes, and host plants based on the analysis of symbiosis of indigenous rhizobia and wild legumes native to Xinjiang. Microb. Ecol. 2009, (online first).
15. Han T.X., Wang E.T., Han L.L., Chen W.F., Sui X.H., Chen W.X. Molecular diversity and phylogeny of rhizobia associated with wild legumes native to Xinjiang, China. Syst. Appl. Microbiol. 2008, 31:287-301.
16. Han T.X., Wang E.T., Wu L.J., Chen W.F., Gu J.G., Gu C.T., Tian C.F., Chen W.X. Rhizobium multihospitium sp. nov., isolated from multiple legume species native of Xinjiang, China. Int. J. Syst. Evol. Microbiol. 2008, 58:1693-1699.
17. Houle G. No evidence for interspecific interactions between plants in the first stage of succession on coastal dunes in subarctic Quebec, Canada. Can. J. Bot. 1997, 75:902-915.
18. Imbert É., Houle G. Persistence of colonizing plant species along an inferred successional sequence on a subarctic coastal dune (Quebec, Canada). Écoscience 2000, 7:370-378.
19. Janczarek M., Kalita M., Skorupska A.M. New taxonomic markers for identification of Rhizobium leguminosarum and discrimination between closely related species. Arch. Microbiol. 2009, 191:207-219.
20. Jaspers E., Overmann J. Ecological significance of microdiversity: identical 16S rRNA gene sequences can be found in bacteria with highly divergent genomes and ecophysiologies. Appl. Environ. Microbiol. 2004, 70:4831-4839.
21. Kenicer G. An introduction to the genus Lathyrus L. Curtis's Bot. Mag. 2008, 25:286-295.
22. Kiers E.T., Rousseau R.A., West S.A., Denison R.F. Host sanctions and the legume-rhizobium mutualism. Nature 2003, 425:78-81.
23. Kondo T., Yamaguchi M. Germination characteristics of Lathyrus japonicus Willd. for landscaping and vegetation restoration in seacoast. J. Jpn. Inst. Landscape Architect. 1999, 62:507-510. (in Japanese).
24. Lafay B., Burdon J.J. Molecular diversity of rhizobia nodulating the invasive legume Cytisus scoparius in Australia. J. Appl. Microbol. 2006, 100:1228-1238.
25. Mantelin S., Saux M.F., Zakhia F., Bena G., Bonneau S., Jeder H., de Lajudie P., Cleyet-Marel J.C. Emended description of the genus Phyllobacterium and description of four novel species associated with plant roots: Phyllobacterium bourgognense sp. nov., Phyllobacterium ifriqiyense sp. nov., Phyllobacterium leguminum sp. nov. and Phyllobacterium brassicacearum sp. nov. Int. J. Syst. Evol. Microbiol. 2006, 56:827-839.
26. Moschetti G., Peluso A., Protopapa A., Anastasio M., Pepe O., Defez R. Use of nodulation pattern, stress tolerance, nodC gene amplification, RAPD-PCR and RFLP-16S rDNA analysis to discriminate genotypes of Rhizobium leguminosarum biovar viciae. Syst. Appl. Microbiol. 2005, 28:619-631.
27. Mutch L.A., Young J.P. Diversity and specificity of Rhizobium leguminosarum biovar viciae on wild and cultivated legumes. Mol. Ecol. 2004, 13:2435-2444.
28. Nei M., Li W.H. Mathematical model for studying genetic variation in terms of restriction endonucleases. Proc. Natl. Acad. Sci. U.S.A. 1979, 76. 5269-5267.
29. Nekrutenko A., Makova K.D., Baker R.J. Isolation of binary species-specific PCR-based markers and their value for diagnostic applications. Gene 2000, 249:47-51.
30. Nichols R. Gene trees and species trees are not the same. Trends Ecol. Evol. 2001, 16:358-364.
31. Nylander J.A.A. MrModeltest v2. Program distributed by the author 2004, Evolutionary Biology Centre, Uppsala University, Sweden.
32. Parker M.A. Mutualism as a constraint on invasion success for legumes and rhizobia. Divers. Distrib. 2001, 7:125-136.
33. Parker M.A., Malek W., Parker I.M. Growth of an invasive legume is symbiont limited in newly occupied habitats. Divers. Distrib. 2006, 12:563-571.
34. Parker M.A., Wurtz A.K., Paynter Q. Nodule symbiosis of invasive Mimosa pigra in Australia and in ancestral habitats: a comparative analysis. Biol. Invas. 2007, 9:127-138.
35. Posada D., Crandall K.A. MODELTEST: testing the model of DNA substitution. Bioinformatics 1998, 14:817-818.
36. T (5NCIMB 11478) as Rhizobium pisi sp. nov. Int. J. Syst. Evol. Microbiol. 2008, 58:2484-2490.
37. Reinhart K.O., Callaway R.M. Soil biota and invasive plants. New Phytol. 2006, 170:445-457.
38. Rivas R., Peix A., Mateos P.F., Trujillo M.E., Marti{dotless}nez-Molina E., Velazquez E. Biodiversity of populations of phosphate solubilizing rhizobia that nodulate chickpea in different Spanish soils. Plant Soil 2006, 287:23-33.
39. Rodriguez-Echeverria S., Crisostomo J.A., Freitas H. Genetic diversity of rhizobia associated with Acacia longifolia in two stages of invasion of coastal sand dunes. J. Environ. Micorbiol. 2007, 73:5066-5070.
40. Ronquist F., Huelsenbeck J.P. MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 2003, 19:1572-1574.
41. Santillana N., Ramirez-Bahena M.H., Garcia-Fraile P., Velazquez E., Zuniga D. Phylogenetic diversity based on rrs, atpD, recA genes and 16S-23S intergenic sequence analyses of rhizobial strains isolated from Vicia faba and Pisum sativum in Peru. Arch. Microbiol. 2008, 189:239-247.
42. Sanchez-Contreras M., Lloret J., Martin M., Villacieros M., Bonilla I., Rivilla R. PCR use of highly conserved DNA regions for identification of Sinorhizobium meliloti. Appl. Environ. Microbiol. 2000, 66:3621-3623.
43. Sawada H., Kuykendall L.D., Young J.M. Changing concepts in the systematics of bacterial nitrogen-fixing legume symbionts. J. Gen. Appl. Microbiol. 2003, 49:155-179.
44. Schoniger M., von Haeseler A. A stochastic model for the evolution of autocorrelated DNA sequences. Mol. Phylogenet. Evol. 1994, 3:240-247.
45. Schwendiman J.L. Coastal sand dune stabilization in the pacific northwest. Int. J. Biometeorol. 1977, 21:281-289.
46. Simms E.L., Taylor D.L., Povich J., Shefferson R.P., Sachs J.L., Urbina M., Tausczik Y. An empirical test of partner choice mechanisms in a wild legume-rhizobium interaction. Proc. Biol. Sci. 2006, 273:77-81.
47. Silva C., Eguiarte E., Souza V. Reticulated and epidemic population genetic structure of Rhizobium etli biovar phaseoli in a traditionally managed locality in Mexico. Mol. Ecol. 1999, 8:277-287.
48. Sui X., Han L., Wang E., Jiang F., Liu Y., Chen W. Novel associations between rhizobial populations and legume species within the genera Lathyrus and Oxytropis grown in the temperate region of China. Sci. China C Life Sci. 2009, 52:182-192.
49. Suominen L., Roos C., Lortet G., Paulin L., Lindstroem K. Identification and structure of the Rhizobium galegae common nodulation genes: evidence for horizontal gene transfer. Mol. Biol. Evol. 2001, 18:907-916.
50. Swofford D.L. PAUP*: Phylogenetic Analysis Using Parsimony (*and other methods) 2003, Sinauer Associates, Sunderland, MA.
51. Ueda T., Suga Y., Yahiro N., Matsuguchi T. Phylogeny of Sym plasmids of rhizobia by PCR-based sequencing of a nodC segment. J. Bacteriol. 1995, 177:468-472.
52. Valverde A., Igual J.M., Peix A., Cervantes E., Velazquez E. Rhizobium lusitanum sp. nov. a bacterium that nodulates Phaseolus vulgaris. Int. J. Syst. Evol. Microbiol. 2006, 56:2631-2637.
53. Vinuesa P., Silva C., Werner D., Martinez-Romero E. Population genetics and phylogenetic inference in bacterial molecular systematics: the roles of migration and recombination in Bradyrhizobium species cohesion and delineation. Mol. Phylogenet. Evol. 2005, 34:29-54.
54. Walmsley C.A., Davy A.J. Germination characteristics of shingle beach species, effects of seed ageing and their implications for vegetation restoration. J. Appl. Ecol. 1997, 34:131-142.
55. Walmsley C.A., Davy A.J. The restoration of coastal shingle vegetation: effect of substrate composition on the establishment of seedlings. J. Appl. Ecol. 1997, 34:143-153.
56. Walmsley C.A., Davy A.J. The restoration of coastal shingle vegetation: effect of substrate composition on the establishment of container-grown plants. J. Appl. Ecol. 1997, 34:154-165.
57. Weir B.S., Turner S.J., Silvester W.B., Park D.C., Young J.M. Unexpectedly diverse Mesorhizobium strains and Rhizobium leguminosarum nodulate native legume genera of New Zealand, while introduced legume weeds are nodulated by Bradyrhizobium species. Appl. Environ. Microbiol. 2004, 70:5980-5987.
58. Wernegreen J.J., Riley M.A. Comparison of the evolutionary dynamics of symbiotic and housekeeping loci: a case for the genetic coherence of rhizobial lineages. Mol. Biol. Evol. 1999, 16:98-113.
59. Young J.M., Kuykendall L.D., Martinez-Romero E., Kerr A., Sawada H. A revision of Rhizobium Frank 1889, with an emended description of the genus, and the inclusion of all species of Agrobacterium Conn 1942 and Allorhizobium undicola de Lajudie et al. 1998 as new combinations: Rhizobium radiobacter, R. rhizogenes, R. rubi, R. undicola and R. vitis. Int. J. Syst. Evol. Microbiol. 2001, 51:89-103.