Genetic diversity of Mimosa pudica rhizobial symbionts in soils of French Guiana: investigating the origin and diversity of Burkholderia phymatum and other beta-rhizobia

Abstract

The genetic diversity of 221 Mimosa pudica bacterial symbionts trapped from eight soils from diverse environments in French Guiana was assessed by 16S rRNA PCR-RFLP, REP-PCR fingerprints, as well as by phylogenies of their 16S rRNA and recA housekeeping genes, and by their nifH, nodA and nodC symbiotic genes. Interestingly, we found a large diversity of beta-rhizobia, with Burkholderia phymatum and Burkholderia tuberum being the most frequent and diverse symbiotic species. Other species were also found, such as Burkholderia mimosarum, an unnamed Burkholderia species and, for the first time in South America, Cupriavidus taiwanensis. The sampling site had a strong influence on the diversity of the symbionts sampled, and the specific distributions of symbiotic populations between the soils were related to soil composition in some cases. Some alpha-rhizobial strains taxonomically close to Rhizobium endophyticum were also trapped in one soil, and these carried two copies of the nodA gene, a feature not previously reported. Phylogenies of nodA, nodC and nifH genes showed a monophyly of symbiotic genes for beta-rhizobia isolated from Mimosa spp., indicative of a long history of interaction between beta-rhizobia and Mimosa species. Based on their symbiotic gene phylogenies and legume hosts, B. tuberum was shown to contain two large biovars: one specific to the mimosoid genus Mimosa and one to South African papilionoid legumes.

The Structure and Evolution of Beta-Rhizobial Symbiotic Genes Deduced from Their Complete Genomes

“…Interestingly, Sinorhizobium and two Burkholderia strains also shared the nodH and nodQ genes, which may be linked with the fact that Sinorhizobium strains nodulate some Indian and Mexican Mimosa spp. [31,37]. We also found that nodH was located on the Methylobacterium symbiosis island, which may be significant in terms of recent studies showing that related genera in the Crotalariae (Aspalathus, Rafnia and Lebeckia spp.)…”

“…Although it is widely reported [58], some reports have indicated that horizontal gene transfer (HGT) has not been common even within Alpharhizobia, as revealed by the nodA and nodC phylogenies of some Ensifer and Rhizobium symbionts [8,31]. This lack of clarity as to the origin and evolution of symbiotic genes (nodulation and nitrogen fixation genes) in rhizobium sensu lato means that their origin/evolution in the Beta-rhizobia are still a subject of much debate.…”

“…In addition, R. leguminosarum has two nodT genes, which it shares with three Burkholderia strains, which is interesting in consideration that Rhizobium strains are often isolated from Mimosa pudica e.g. R. etli, R. tropici, R. leucaenae, R. mesoamericanum and R. altiplani [31,35,59,73,74]. Moreover, the Mimosa-nodulating R. etli sv.…”

“…With regard to the origins of Beta-rhizobial symbiosis-related genes, Mimosa-(and other Mimsoideae)-nodulating Burkholderia strains are somewhat separate from Cupriavidus strains, such as C. taiwanensis and C. necator-like strains in their nodA and nodC phylogenies, but are still clearly related to them, and both are very different from Alpharhizobia, including those which can nodulate Mimosa [31,35,37,38]. However, B. tuberum STM678 T and related South African strains which nodulate papilionoid legumes and which cannot nodulate Mimosa, appear to be more closely-related to Alpha-rhizobia and are distant from other beta-rhizobia in terms of their nod genes [5,[12][13][14][15][16]41].…”

Novel Burkholderia bacteria isolated from Lebeckia ambigua – A perennial suffrutescent legume of the fynbos

“…a Originally reported as isolated from Machaerium lunatum but not authenticated on this host, effectively nodulates Mimosa ( Elliott et al, 2007b;Mishra et al, 2012). …”