Phylogenetic analyses of symbiotic nodulation genes support vertical and lateral gene co-transfer within the Bradyrhizobium genus

Moulin, Lionel; Béna, Gilles; Boivin-Masson, Catherine; Stępkowski, Tomasz

doi:10.1016/s1055-7903(03)00255-0

Cited by 190 publications

(187 citation statements)

References 69 publications

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“…The majority of the investigated nodules contained Bacillus (17.9%), Paenibacillus (12.5%) and Pseudomonas (15.9%) NRE species, together with small numbers of other NRE bacterial genera from the classes Actinobacteria, Alpha-and Betaproteobacteria. Nodulation and nitrogen fixation capacity are characters usually studied in rhizobia research, since they give an indication of the host specificity and nitrogen fixing ability (Perret et al, 2000;Moulin et al, 2004;Diouf et al, 2010). No nodC or nifH gene sequences could be detected among the isolates, indicating an endophytic lifestyle rather than a rhizobial lifestyle.…”

Section: Discussionmentioning

confidence: 99%

A large diversity of non-rhizobial endophytes found in legume root nodules in Flanders (Belgium)

Meyer

Beuf

Vekeman

et al. 2015

Soil Biology and Biochemistry

120

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Statistical analysis grouped the investigated plant species into six clusters according to the presence of particular NRE. However, no correlations could be found within these six clusters towards plant tribes or ecoregions the plants had been sampled from. Cluster analysis of the ecoregions according to the presence of NRE, revealed correlations between bacterial genera and those areas. However, groups present in the ecoregions did not correlate with the groups present in the different plant clusters. When combining our previous study on rhizobial diversity recovered from the same sampling campaign (De Meyer et al., 2011) with the current study, 84.1% of the isolates belonged to the traditional rhizobia groups and only 15.9% were NRE. The Loamy ecoregion yielded the lowest number of culturable NRE (8.04%) and the Campine ecoregion the highest number (24.19%). The present study highlights the frequent presence of these NRE in root nodules. The occurrence of certain rhizobia was correlated with the presence of particular NRE, suggesting their presence may not be accidental, however their functions remain unclear at this point.

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Section: Discussionmentioning

confidence: 99%

A large diversity of non-rhizobial endophytes found in legume root nodules in Flanders (Belgium)

Meyer

Beuf

Vekeman

et al. 2015

Soil Biology and Biochemistry

120

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“…The nodA gene is a key gene for the establishment of symbiosis; it is present as a single copy and has a size of 590-660 bp (Moulin et al, 2004). Except for some photosynthetic species of the genus Bradyrhizobia (Giraud et al, 2007), all bacteria described thus far as being capable of establishing a symbiosis with legumes harbour nodulation (nod) and nitrogen fixation (nif, fix) genes.…”

Section: Discussionmentioning

confidence: 99%

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.

Merabet

Martens

Mahdhi

et al. 2010

International Journal of Systematic and Evolutionary Microbiology

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Nine isolates from Argyrolobium uniflorum, Lotus creticus, Medicago sativa (Tunisia) and Lotus arabicus (Senegal) were analysed by multilocus sequence analysis (MLSA) of five housekeeping genes (recA, atpD, glnA, gltA and thrC), the 16S rRNA gene and the nodulation gene nodA. Analysis of the individual and concatenated gene sequences demonstrated that the nine new strains constituted three stable, well-supported (bootstrap and gene sequence similarity values) monophyletic clusters, A, B and C, all belonging to the branch of the genus Ensifer, regardless of the phylogenetic reconstruction method used (maximum likelihood, maximum-parsimony, neighbour-joining). The three groups were further characterized by API 100 auxanographic tests, host specificity and nodA gene sequence analysis. On the basis of these data, clusters A and C are suggested as representing two novel species within the genus Ensifer, for which the names Ensifer numidicus sp. nov. (type strain ORS 1407T=LMG 24690T=CIP 109850T) and Ensifer garamanticus sp. nov. (type strain ORS 1400T=LMG 24692T=CIP 109916T) are proposed. The cluster B strains were assigned to Ensifer adhaerens genomovar A.

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“…Hosts given the same inoculated strains either all became nodulated or were all lacking nodules. The remaining 342 root surface isolates were classified as symbiotic or non-symbiotic based on success or failure of PCR amplification of at least one symbiosis island locus (nifD, nodD-A, nodZ, and nolL) [22,24,45]. Earlier analyses showed that successful amplification of these loci, giving a band of the correct size, is a reliable indicator of presence of the symbiosis island [24].…”

Section: Symbiotic Capacity Assessmentmentioning

confidence: 99%

“…Rhizobial genomes are subdivided into genome regions specific for their life stages, with chromosomal loci expressed during free-living phases in the soil and symbiosis loci expressed inside of host cells [13,14]. Symbiosis loci required for host nodulation and nitrogen fixation are clustered onto large plasmids or genomic islands [15][16][17][18][19], that can be transferred among lineages, presumably via conjugation [20][21][22]. Non-nodulating rhizobia are also common [23,24], and these strains often lack some or all of the characterized symbiosis loci [23][24][25][26][27][28].…”

Section: Introductionmentioning

confidence: 99%

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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Phylogenetic analyses of symbiotic nodulation genes support vertical and lateral gene co-transfer within the Bradyrhizobium genus

Cited by 190 publications

References 69 publications

A large diversity of non-rhizobial endophytes found in legume root nodules in Flanders (Belgium)

A large diversity of non-rhizobial endophytes found in legume root nodules in Flanders (Belgium)

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.

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

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