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

BMC Genomics, Sep 2016

Background Rhizobia 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. Results In 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. Conclusions Functions 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.

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

Peralta et al. BMC Genomics Genomic studies of nitrogen-fixing rhizobial strains from Phaseolus vulgaris seeds and nodules Humberto Peralta 0 1 Alejandro Aguilar 0 1 Rafael Díaz 0 1 Yolanda Mora 0 1 Gabriel Martínez-Batallar 0 1 Emmanuel Salazar 0 1 Carmen Vargas-Lagunas 0 1 Esperanza Martínez 0 1 Sergio Encarnación 0 1 Lourdes Girard 0 1 Jaime Mora 0 1 0 Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México , Av. Universidad s/n, Chamilpa, Cuernavaca, Morelos CP 62210 , Mexico 1 Abbreviations: ANIm, Genomic average nucleotide identity; Bp, Base pairs; COG, Cluster of orthologous groups; GO, Gene ontology; Kb , Kilo base pairs; NR, Nonredundant; PAGE, Polyacrylamide gel electrophoresis; PFGE, Pulsed- field gel electrophoresis Background: Rhizobia 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. Results: In 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. Conclusions: Functions 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. Nitrogen fixation; Comparative genomics; Proteome - Background Rhizobia are saprophytic soil bacteria commonly studied for their ability to enter into nitrogen-fixing symbioses with legumes. The establishment of these symbioses by rhizobia, a collective term for strains from genera such as Rhizobium, Sinorhizobium, Mesorhizobium and Bradyrhizobium, involves the formation of organ-like structures on the legume roots (for recent reviews see references [1] and [2]). The rhizobia in the nodules are present in a metabolically differentiated form called bacteroids, which perform the reduction of atmospheric dinitrogen into ammonium. In exchange for dicarboxylic acids supplied from the plant, the bacteroids export the ammonium to the plant. Rhizobia have also been found inside legume nonnodular tissues such as roots, stems and pods [3–5]. There are also reports of endophytic rhizobia associated with Arabidopsis, wheat, maize, sugar cane, and rice [6–9]. Strains of endophytic Rhizobium were recently isolated from the tree species Populus euphratica and P. deltoides [10, 11]. Previously, we described several nitrogen-fixing rhizobial strains isolated from the interior of common bean seeds (Phaseolus vulgaris) [12]. We postulated that the vertical transmission of effective rhizobacteria in seeds expands the spectrum of their beneficial interactions with the host plants and has potential biotechnological application. Given the increasing number of endophytic rhizobial isolates, it is worth determining which genetic traits are responsible for their ability to persist in plant tissues and discover if genomic differences exist among isolates able to persist in seeds. Despite the difficulties in assigning functions to novel genes, these analyses can measure changes in cellular physiology in response to genetic or environmental adaptations [13]. The model of our previous study was to compare closely related strains with different lifestyles by analyzing their genomes in addition to other approaches (...truncated)


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Humberto Peralta, Alejandro Aguilar, Rafael Díaz, Yolanda Mora, Gabriel Martínez-Batallar, Emmanuel Salazar, Carmen Vargas-Lagunas, Esperanza Martínez, Sergio Encarnación, Lourdes Girard, Jaime Mora. Genomic studies of nitrogen-fixing rhizobial strains from Phaseolus vulgaris seeds and nodules, BMC Genomics, 2016, pp. 711, 17, DOI: 10.1186/s12864-016-3053-z