Genomic studies of nitrogen-fixing rhizobial strains from Phaseolus vulgaris seeds and nodules

Abstract

BackgroundRhizobia are soil bacteria that establish symbiotic relationships with legumes and fix nitrogen in root nodules. We recently reported that several nitrogen-fixing rhizobial strains, belonging to Rhizobium phaseoli, R. trifolii, R. grahamii and Sinorhizobium americanum, were able to colonize Phaseolus vulgaris (common bean) seeds. To gain further insight into the traits that support this ability, we analyzed the genomic sequences and proteomes of R. phaseoli (CCGM1) and S. americanum (CCGM7) strains from seeds and compared them with those of the closely related strains CIAT652 and CFNEI73, respectively, isolated only from nodules.ResultsIn a fine structural study of the S. americanum genomes, the chromosomes, megaplasmids and symbiotic plasmids were highly conserved and syntenic, with the exception of the smaller plasmid, which appeared unrelated. The symbiotic tract of CCGM7 appeared more disperse, possibly due to the action of transposases. The chromosomes of seed strains had less transposases and strain-specific genes. The seed strains CCGM1 and CCGM7 shared about half of their genomes with their closest strains (3353 and 3472 orthologs respectively), but a large fraction of the rest also had homology with other rhizobia. They contained 315 and 204 strain-specific genes, respectively, particularly abundant in the functions of transcription, motility, energy generation and cofactor biosynthesis. The proteomes of seed and nodule strains were obtained and showed a particular profile for each of the strains. About 82 % of the proteins in the comparisons appeared similar. Forty of the most abundant proteins in each strain were identified; these proteins in seed strains were involved in stress responses and coenzyme and cofactor biosynthesis and in the nodule strains mainly in central processes. Only 3 % of the abundant proteins had hypothetical functions.ConclusionsFunctions that were enriched in the genomes and proteomes of seed strains possibly participate in the successful occupancy of the new niche. The genome of the strains had features possibly related to their presence in the seeds. This study helps to understand traits of rhizobia involved in seed adaptation.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-3053-z) contains supplementary material, which is available to authorized users.

Functional and taxonomic classification of a greenhouse water drain metagenome

“…2 ). This result was in agreement with reports in which rhizobial bacteria associated with the nodules and seed of plants has many genes for these molecular functions in their genomes [ 34 ].

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Formulation of a Highly Effective Inoculant for Common Bean Based on an Autochthonous Elite Strain of Rhizobium leguminosarum bv. phaseoli, and Genomic-Based Insights Into Its Agronomic Performance

“…Similarly, five nodD reiterations were found in R. tropici CIAT899, necessary to engage the symbiont in nodulation with different legume species (Del Cerro et al, 2015). These nodD reiterations were also present in various different N-fixing rhizobial strains from P. vulgaris, suggesting a potential role in host range (Peralta et al, 2016). Sequence heterogeneity within p42d already suggested extensive genomic rearrangements, recombination rates, lateral transfer, and relaxation or intensification of selective pressures (González et al, 2003).…”

La diversidad de rizobios nativos de México a la luz de la genómica

“…Hemos descrito nuevas especies de rizobios con capacidad de nodular diversas leguminosas, R. grahamii (Althabegoiti et al, 2014;Peralta et al, 2016), R. mesoamericanum (López-López et al, 2012), R. mayense, R. jaguaris y R. calliandrae (Rincón-Rosales et al, 2013) y una especie que no nodula, pero se encuentra dentro de las semillas de frijol, R. endophyticum (López-López, . También hay rizobios simbióticos que se encuentran sobre la superficie de semillas de Phaseolus vulgaris (Pérez-Ramírez et al, 1998).…”

“…Las bacterias en semillas contribuirían con su dispersión fuera de su sitio de origen (Cao et al, 2014). Se han reportado R. grahamii, R. trifolii, R. phaseoli y Sinorhizobium americanum en semillas del frijol (Peralta et al, 2016).…”