title: Multilocus sequence analysis for assessment of the biogeography and evolutionary genetics of four Bradyrhizobium species that nodulate soybeans on the asiatic continent.
abstract: A highly supported maximum-likelihood species phylogeny for the genus Bradyrhizobium was inferred from a supermatrix obtained from the concatenation of partial atpD, recA, glnII, and rpoB sequences corresponding to 33 reference strains and 76 bradyrhizobia isolated from the nodules of Glycine max (soybean) trap plants inoculated with soil samples from Myanmar, India, Nepal, and Vietnam. The power of the multigene approach using multiple strains per species was evaluated in terms of overall tree resolution and phylogenetic congruence, representing a practical and portable option for bacterial molecular systematics. Potential pitfalls of the approach are highlighted. Seventy-five of the isolates could be classified as B. japonicum type Ia (USDA110/USDA122-like), B. liaoningense, B. yuanmingense, or B. elkanii, whereas one represented a novel Bradyrhizobium lineage. Most Nepalese B. japonicum Ia isolates belong to a highly epidemic clone closely related to strain USDA110. Significant phylogenetic evidence against the monophyly of the of B. japonicum I and Ia lineages was found. Analysis of their DNA polymorphisms revealed high population distances, significant genetic differentiation, and contrasting population genetic structures, suggesting that the strains in the Ia lineage are misclassified as B. japonicum. The DNA polymorphism patterns of all species conformed to the expectations of the neutral mutation and population equilibrium models and, excluding the B. japonicum Ia lineage, were consistent with intermediate recombination levels. All species displayed epidemic clones and had broad geographic and environmental distribution ranges, as revealed by mapping climate types and geographic origins of the isolates on the species tree.
authors.affiliation: Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México UNAM, Cuernavaca CP 62210, Morelos, México. vinuesa@ccg.unam.mx
authors.forename: Pablo
authors.initials: P
authors.lastname: Vinuesa
authors.forename: Keilor
authors.initials: K
authors.lastname: Rojas-Jiménez
authors.forename: Bruno
authors.initials: B
authors.lastname: Contreras-Moreira
authors.forename: Suresh K
authors.initials: SK
authors.lastname: Mahna
authors.forename: Braj Nandan
authors.initials: BN
authors.lastname: Prasad
authors.forename: Hla
authors.initials: H
authors.lastname: Moe
authors.forename: Suresh Babu
authors.initials: SB
authors.lastname: Selvaraju
authors.forename: Heidemarie
authors.initials: H
authors.lastname: Thierfelder
authors.forename: Dietrich
authors.initials: D
authors.lastname: Werner
mesh_terms: D001208:Asia; D001426:Bacterial Proteins / Q000235:genetics; D015373:Bacterial Typing Techniques; D020369:Bradyrhizobium / Q000145:classification* / Q000235:genetics / Q000302:isolation & purification*; D002980:Climate; D016000:Cluster Analysis; D004269:DNA, Bacterial / Q000737:chemistry / Q000235:genetics; D005838:Genotype; D005843:Geography; D008969:Molecular Sequence Data; D010802:Phylogeny; D018517:Plant Roots / Q000382:microbiology; D011110:Polymorphism, Genetic; D017421:Sequence Analysis; D013025:Glycine max / Q000382:microbiology*
chemical_list: D001426:Bacterial Proteins; D004269:DNA, Bacterial
references.citation: Mol Phylogenet Evol. 2008 Sep;48(3):1131-44
references.pmid: 18539053
references.citation: Microb Ecol. 2007 Feb;53(2):197-207
references.pmid: 17106806
references.citation: PLoS One. 2007 Mar 07;2(3):e277
references.pmid: 17356689
references.citation: Syst Appl Microbiol. 2004 May;27(3):334-42
references.pmid: 15214639
references.citation: Can J Microbiol. 2006 Jan;52(1):31-46
references.pmid: 16541157
references.citation: Syst Biol. 2007 Feb;56(1):17-24
references.pmid: 17366134
references.citation: Appl Environ Microbiol. 2003 Feb;69(2):884-93
references.pmid: 12571008
references.citation: Mol Biol Evol. 2002 Dec;19(12):2092-100
references.pmid: 12446801
references.citation: Genetics. 1985 Sep;111(1):147-64
references.pmid: 4029609
references.citation: Mol Ecol. 1998 Jul;7(7):889-95
references.pmid: 9691490
references.citation: Bioinformatics. 1998;14(9):817-8
references.pmid: 9918953
references.citation: Int J Syst Bacteriol. 1997 Jul;47(3):874-9
references.pmid: 9226921
references.citation: Nat Rev Microbiol. 2005 Sep;3(9):733-9
references.pmid: 16138101
references.citation: Mol Ecol. 2005 Nov;14(13):4033-50
references.pmid: 16262857
references.citation: Can J Microbiol. 1999 Aug;45(8):639-45
references.pmid: 10528395
references.citation: Appl Environ Microbiol. 2001 May;67(5):2076-82
references.pmid: 11319084
references.citation: Appl Environ Microbiol. 1995 Apr;61(4):1599-609
references.pmid: 7538280
references.citation: Syst Biol. 2004 Oct;53(5):793-808
references.pmid: 15545256
references.citation: Mol Biol Evol. 1992 Jan;9(1):138-51
references.pmid: 1552836
references.citation: Int J Syst Evol Microbiol. 2002 Nov;52(Pt 6):2219-2230
references.pmid: 12508891
references.citation: Theor Popul Biol. 1975 Apr;7(2):256-76
references.pmid: 1145509
references.citation: Genet Res. 1987 Dec;50(3):245-50
references.pmid: 3443297
references.citation: Syst Appl Microbiol. 2006 Apr;29(3):253-62
references.pmid: 16564961
references.citation: Genetics. 1997 Oct;147(2):915-25
references.pmid: 9335623
references.citation: Int J Syst Evol Microbiol. 2005 Mar;55(Pt 2):569-575
references.pmid: 15774626
references.citation: J Bacteriol. 2003 May;185(10):2988-98
references.pmid: 12730157
references.citation: Appl Environ Microbiol. 2008 Oct;74(19):5991-6
references.pmid: 18676699
references.citation: Microb Ecol. 2008 May;55(4):662-72
references.pmid: 17828570
references.citation: Int J Syst Bacteriol. 1994 Jul;44(3):392-403
references.pmid: 7520731
references.citation: Int J Syst Evol Microbiol. 2000 Nov;50 Pt 6:2165-2172
references.pmid: 11155993
references.citation: Int J Syst Bacteriol. 1995 Oct;45(4):706-11
references.pmid: 7547289
references.citation: Bioinformatics. 2003 Dec 12;19(18):2496-7
references.pmid: 14668244
references.citation: Nat Rev Microbiol. 2006 Feb;4(2):102-12
references.pmid: 16415926
references.citation: Syst Biol. 2001 Aug;50(4):580-601
references.pmid: 12116655
references.citation: Syst Appl Microbiol. 1999 Sep;22(3):378-86
references.pmid: 10553290
references.citation: Syst Biol. 2003 Oct;52(5):696-704
references.pmid: 14530136
references.citation: Appl Environ Microbiol. 2002 Apr;68(4):2044-8
references.pmid: 11916730
references.citation: Genetics. 1992 Oct;132(2):583-9
references.pmid: 1427045
references.citation: BMC Bioinformatics. 2004 Aug 19;5:113
references.pmid: 15318951
references.citation: Appl Environ Microbiol. 2003 Nov;69(11):6740-9
references.pmid: 14602635
references.citation: Syst Appl Microbiol. 2003 Nov;26(4):611-23
references.pmid: 14666990
references.citation: FEMS Microbiol Lett. 2008 Aug;285(2):146-54
references.pmid: 18564340
references.citation: Trends Ecol Evol. 2001 Jul 1;16(7):358-364
references.pmid: 11403868
references.citation: Appl Environ Microbiol. 2007 May;73(10):3254-64
references.pmid: 17400786
references.citation: Proc Natl Acad Sci U S A. 1993 May 15;90(10):4384-8
references.pmid: 8506277
references.citation: Mol Phylogenet Evol. 2005 Jan;34(1):29-54
references.pmid: 15579380
references.citation: Appl Environ Microbiol. 2005 Nov;71(11):7041-52
references.pmid: 16269740
references.citation: Theor Popul Biol. 2002 Mar;61(2):225-47
references.pmid: 11969392
references.citation: Syst Biol. 2006 Feb;55(1):21-30
references.pmid: 16507521
references.citation: PLoS Genet. 2006 May;2(5):e68
references.pmid: 16733550
references.citation: Int J Syst Evol Microbiol. 2004 Jul;54(Pt 4):1271-1275
references.pmid: 15280302
references.citation: Genetics. 1989 Nov;123(3):585-95
references.pmid: 2513255
references.citation: Syst Appl Microbiol. 2005 Oct;28(8):702-16
references.pmid: 16261860
references.citation: Int J Syst Evol Microbiol. 2001 Jan;51(Pt 1):111-7
references.pmid: 11211247
references.citation: Syst Biol. 2006 Aug;55(4):539-52
references.pmid: 16785212
references.citation: Appl Environ Microbiol. 1998 Jun;64(6):2096-104
references.pmid: 9603820
references.citation: Genetics. 1993 Mar;133(3):693-709
references.pmid: 8454210
references.citation: Int J Syst Evol Microbiol. 2002 Mar;52(Pt 2):457-462
references.pmid: 11931157