Abstract
BackgroundRhizobium grahamii belongs to a new phylogenetic group of rhizobia together with Rhizobium mesoamericanum and other species. R. grahamii has a broad-host-range that includes Leucaena leucocephala and Phaseolus vulgaris, although it is a poor competitor for P. vulgaris nodulation in the presence of Rhizobium etli or Rhizobium phaseoli strains. This work analyzed the genome sequence and transfer properties of R. grahamii plasmids.ResultsGenome sequence was obtained from R. grahamii CCGE502 type strain isolated from Dalea leporina in Mexico. The CCGE502 genome comprises one chromosome and two extrachromosomal replicons (ERs), pRgrCCGE502a and pRgrCCGE502b. Additionally, a plasmid integrated in the CCGE502 chromosome was found. The genomic comparison of ERs from this group showed that gene content is more variable than average nucleotide identity (ANI). Well conserved nod and nif genes were found in R. grahamii and R. mesoamericanum with some differences. R. phaseoli Ch24-10 genes expressed in bacterial cells in roots were found to be conserved in pRgrCCGE502b. Regarding conjugative transfer we were unable to transfer the R. grahamii CCGE502 symbiotic plasmid and its megaplasmid to other rhizobial hosts but we could transfer the symbiotic plasmid to Agrobacterium tumefaciens with transfer dependent on homoserine lactones.ConclusionVariable degrees of nucleotide identity and gene content conservation were found among the different R. grahamii CCGE502 replicons in comparison to R. mesoamericanum genomes. The extrachromosomal replicons from R. grahamii were more similar to those found in phylogenetically related Rhizobium species. However, limited similarities of R. grahamii CCGE502 symbiotic plasmid and megaplasmid were observed in other more distant Rhizobium species. The set of conserved genes in R. grahamii comprises some of those that are highly expressed in R. phaseoli on plant roots, suggesting that they play an important role in root colonization.
Highlights
Rhizobium grahamii belongs to a new phylogenetic group of rhizobia together with Rhizobium mesoamericanum and other species
The genome of R. grahamii CCGE502 consists of three circular replicons, one chromosome and two extrachromosomal replicons (ERs): one megaplasmid and a symbiotic plasmid
It is interesting to note that the location of the homologous genes in other bacteria is variable, they may be in plasmids or chromosomes
Summary
Rhizobium grahamii belongs to a new phylogenetic group of rhizobia together with Rhizobium mesoamericanum and other species. R. grahamii has a broad-host-range that includes Leucaena leucocephala and Phaseolus vulgaris, it is a poor competitor for P. vulgaris nodulation in the presence of Rhizobium etli or Rhizobium phaseoli strains. Two types of ERs have been recognized, chromids [3] and plasmids. The term chromid have been found respectively in rhizobia nodulating Phaseolus vulgaris corresponding to symbiovars (sv) tropici or phaseoli [6,7], and we wondered if conserved pSyms are a rule or an exception in rhizobia [8]. An “acaciella” symbiotic plasmid seems to be contained in the related Ensifer ( named Sinorhizobium) species, E. mexicanum and E. chiapanecum [9]. Symbiovar mimosae is found in the related species Rhizobium etli and Rhizobium phaseoli and symbiovar meliloti is the most widespread found in several Ensifer or Mesorhizobium species [5]
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