Population genetics and phylogenetic inference in bacterial molecular systematics: the roles of migration and recombination in Bradyrhizobium species cohesion and delineation

Vinuesa, Pablo; Silva, Claudia; Werner, Dietrich; Martı́nez-Romero, Esperanza

doi:10.1016/j.ympev.2004.08.020

Cited by 316 publications

(274 citation statements)

References 140 publications

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“…Partial sequences from two chromosomal loci, glutamine synthetase (glnII) and recombinase (recA), totaling~1 kb were PCR amplified and sequenced at the Institute for Integrative Genome Biology of UC Riverside using published protocols [34]. Only sequences with unambiguous bases were utilized leading to a total of 1292 sequenced isolates.…”

Section: Sequencing and Haplotype Analysismentioning

confidence: 99%

“…Bradyrhizobium is the most cosmopolitan rhizobial lineage and is found free-living in soils and in aquatic environments as well as in symbiotic association with plant and animal hosts, including humans [29][30][31][32][33][34][35][36][37]. Recent work suggests that there are~19 species of Bradyrhizobium that form symbiotic associations with legumes [36], although non-symbiotic strains are also common in soils [37].…”

Section: Introductionmentioning

confidence: 99%

“…(e.g., BTAi1 and ORS278) lack a symbiosis island and use a different mechanism to nodulate hosts [41]. Previous studies have revealed that Bradyrhizobium populations can exhibit patterns consistent with epidemics such as a few genotypes existing at high frequency at a single site [33] or genotypes isolated at multiple locations [34,35,37]. But these patterns remain poorly understood, and it is unclear what role the symbiosis island might play as a driver of increased abundance and epidemic spread.…”

Section: Introductionmentioning

confidence: 99%

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Epidemic Spread of Symbiotic and Non-Symbiotic Bradyrhizobium Genotypes Across California

et al. 2015

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The patterns and drivers of bacterial strain dominance remain poorly understood in natural populations. Here, we cultured 1292 Bradyrhizobium isolates from symbiotic root nodules and the soil root interface of the host plant Acmispon strigosus across a >840-km transect in California. To investigate epidemiology and the potential role of accessory loci as epidemic drivers, isolates were genotyped at two chromosomal loci and were assayed for presence or absence of accessory Bsymbiosis island^loci that encode capacity to form nodules on hosts. We found that Bradyrhizobium populations were very diverse but dominated by few haplotypeswith a single Bepidemic^haplotype constituting nearly 30 % of collected isolates and spreading nearly statewide. In many Bradyrhizobium lineages, we inferred presence and absence of the symbiosis island suggesting recurrent evolutionary gain and or loss of symbiotic capacity. We did not find statistical phylogenetic evidence that the symbiosis island acquisition promotes strain dominance and both symbiotic and nonsymbiotic strains exhibited population dominance and spatial spread. Our dataset reveals that a strikingly few Bradyrhizobium genotypes can rapidly spread to dominate a landscape and suggests that these epidemics are not driven by the acquisition of accessory loci as occurs in key human pathogens.

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Section: Sequencing and Haplotype Analysismentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Epidemic Spread of Symbiotic and Non-Symbiotic Bradyrhizobium Genotypes Across California

et al. 2015

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“…Therefore, multi locus sequence analysis (MLSA) was performed with glnII (537 bp), recA (415 bp) and rpoB (429 bp) following previous reports (Vinuesa et al, 2005;Martens et al, 2008, Menna et al, 2009. Before concatenating the sequences obtained, congruence tests (tree topology observation) and partition-homogeneity tests using PAUP software (Farris et al, 1994;Swofford, 1997) were performed.…”

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confidence: 99%

Bradyrhizobium manausense sp. nov., isolated from effective nodules of Vigna unguiculata grown in Brazilian Amazonian rainforest soils

Silva

Meyer

Simões‐Araújo³

et al. 2014

International Journal of Systematic and Evolutionary Microbiology

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Root nodule bacteria were trapped within cowpea (Vigna unguiculata) in soils with different cultivation histories collected from the Amazonian rainforest in northern Brazil. Analysis of the 16S rRNA gene sequences of six strains (BR 3351 T , BR 3307, BR 3310, BR 3315, BR 3323 BR and BR 3361) isolated from cowpea nodules showed that they formed a distinct group within the genus Bradyrhizobium, which was separate from previously identified type strains. Phylogenetic analyses of three housekeeping genes (glnII, recA and rpoB) revealed that Bradyrhizobium huanghuaihaiense CCBAU 23303 T was the most closely related type strain (96 % sequence similarity or lower). Chemotaxonomic data, including fatty acid profiles (predominant fatty acids being C 16 : 0 and summed feature 8), the slow growth rate and carbon compound utilization patterns supported the assignment of the strains to the genus Bradyrhizobium. The results of DNA-DNA hybridizations, antibiotic resistance and physiological tests differentiated these novel strains from the most closely related species of the genus Bradyrhizobium with validly published names. Symbiosis-related genes for nodulation (nodC) and nitrogen fixation (nifH) grouped the novel strains of the genus Bradyrhizobium together with Bradyrhizobium iriomotense strain EK05 T , with 94 % and 96 % sequence similarity, respectively. Based on these data, these six strains represent a novel species for which the name Brabyrhizobium manausense sp. nov. (BR 3351 T 5HAMBI 3596 T ), is proposed.The family Leguminosae is one of the most abundant plant families in the Amazonian rainforest (AR) with more than 1240 species and 140 genera of all three subfamilies (Caesalpinioideae, Mimosoideae and Papilionoideae) catalogued (Ducke, 1949;Silva et al., 1988). This family is ecologically and economically important to the biome, because it contains pioneer species that revegetate bare soils, species that produce grain for food and species used for timber production. Many legume species are capable of forming root (or sometimes stem) nodules, which contain nitrogen-fixing bacterial symbionts, collectively known as 'rhizobia ' (Sprent, 1995). The capacity to nodulate appears to be the rule for leguminous plants within the AR, since more than 80 % of species of the subfamilies Papilionoideae and Mimosoideae do it; however, only about 20 % of the Caesalpinioideae are capable of forming nodules (de Faria, et al., 1989(de Faria, et al., , 2010Moreira, et al., 1993). Legumes contribute significantly to the AR N-balance, with more than 1006 10 8 kg of nitrogen being fixed annually (Salati et al., 1982;Martinelli et al., 1992;Gehring, et al., 2005).Bacteria of the genus Bradyrhizobium have been reported to comprise the majority of root nodule bacteria isolated from The GenBank/EMBL/DDBJ accession number for the 16S rRNA, glnII, recA, rpoB, dnaK, gyrB, nodC and nifH gene sequences of BR3351 T are HQ641226, KF785986, KF785992, KF785998, KF786000, KF786001, KF786002 and KF786003, respectively. Abbreviation: AR, Amazonian ra...

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“…Due to this limitation, analysis of the IGS region has become a useful tool for determining relatedness among closely related bacteria, including bradyrhizobial strains (Willems et al, 2001(Willems et al, , 2003. In addition to the IGS region, several other phylogenetic markers, such as the atpD, recA and glnII genes, have been proposed for species and genospecies descriptions within the genus Bradyrhizobium (Vinuesa et al, 2005). In accordance with previous studies and the RFLP results in the present study, three strains (CCBAU 23086 T , CCBAU 23160 and CCBAU 61434) representing different BOX types and different host origins were chosen for sequence analyses of the IGS and 16S rRNA, atpD, recA, glnII, nodC and nifH genes, as well as for DNA-DNA hybridization.…”

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confidence: 99%

Bradyrhizobium lablabi sp. nov., isolated from effective nodules of Lablab purpureus and Arachis hypogaea

Chang

Wang

et al. 2011

International Journal of Systematic and Evolutionary Microbiology

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Five strains isolated from root nodules of Lablab purpureus and Arachis hypogaea grown in the Anhui and Sichuan provinces of China were classified as members of the genus Bradyrhizobium. These strains had identical 16S rRNA gene sequences which shared 99.48 %, 99.48 % and 99.22 % similarity with the most closely related strains of Bradyrhizobium jicamae PAC68 T , Bradyrhizobium pachyrhizi PAC48 T and Bradyrhizobium elkanii USDA 76 T , respectively. A study using a polyphasic approach, including 16S rRNA gene RFLP, IGS-RFLP, BOX-PCR, comparative sequence analysis of the 16S-23S rRNA intergenic spacer (IGS) and the recA, atpD and glnII genes, DNA-DNA hybridization and phenotypic tests, showed that the five strains clustered into a coherent group that differentiated them from all recognized species of the genus Bradyrhizobium. Sequencing of nifH and nodC genes and cross-nodulation tests showed that the representative strains CCBAU 23086 T , CCBAU 23160 and CCBAU 61434, isolated from different plants, had identical nifH and nodC gene sequences and were all able to nodulate Lablab purpureus, Arachis hypogaea and Vigna unguiculata. Based upon these results, the name Bradyrhizobium lablabi sp. nov. is proposed for this novel species and strain CCBAU 23086 T (5LMG 25572 T 5HAMBI 3052 T ) is designated as the type strain. The DNA G+C mol% is 60.14 (T m ).

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Population genetics and phylogenetic inference in bacterial molecular systematics: the roles of migration and recombination in Bradyrhizobium species cohesion and delineation

Cited by 316 publications

References 140 publications

Epidemic Spread of Symbiotic and Non-Symbiotic Bradyrhizobium Genotypes Across California

Epidemic Spread of Symbiotic and Non-Symbiotic Bradyrhizobium Genotypes Across California

Bradyrhizobium manausense sp. nov., isolated from effective nodules of Vigna unguiculata grown in Brazilian Amazonian rainforest soils

Bradyrhizobium lablabi sp. nov., isolated from effective nodules of Lablab purpureus and Arachis hypogaea

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