The genome sequence of Rhizobium sp. LPU83, a peculiar rhizobia able to nodulate alfalfa, common bean and Leucaena

TORRES TEJERIZO, G. A.; WIBBERG, D.; DEL PAPA, M.F.; DRAGHI, W. O.; LOZANO, M. J.; GIUSTI, M. A.; MARTINI, C; SALAS, M, E.; SZCZEPANOWSKI, R.; WEIDNER, S.; SCHLÜTER, A.; PÜHLER, A.; LAGARES, A.; PISTORIO, M.

Bielefeld, Alemania.

Simposio; 5th CeBiTec Symposium "New Frontiers in Microbial Genome Research"; 2010

CeBiTec, Universidad de Bielefeld

Alfalfa is the main forage used in several countries for cattle and animal feeding. Only in Argentina there are over 6 million ha cultivated with alfalfa, where the symbiosis with eficient rhizobia represents a central point to assure the entry of fixed nirogen to agricultural soils. In addition to the association of alfalfa with its N2-fixing symbionts Sinorhizobium meliloti and S. Medicae (both completely sequenced), the legume is able to associate with a much less characterizad type of rhizobia represented by strains related to the Rhizobium sp. Or191 initially isolated in the USA (Eardly, et al., 1985) and Rhizobium sp. LPU83 isolated in Argentina (Del Papa, et al., 1999). These rhizobia are acid tolerant, have an extended host range (nodulate several legumes), are very competitive for the nodulation of alfalfa in acids soils and are inefficient for nitrogen-fixation in association with alfalfa. All these features point the Oregon-like rhizobia as a factor of risk in agricultural soils where they co-exist and compete with the efficient symbiont S. meliloti. In addition, the collected genetic evidence revealed that the genome structure of the Or191-like isolates is a complex chimera in terms of its similarity to those of the other sequence rhizobia. A matter that has made difficult the assignment of a clear phylogenetic position of these bacteria.Because of their peculiar phenotypic and taxonomic characteristics, Or191-like rhizobia have attracted the attention of rhizobiologists ever since their original isolation by Eardly et al. (1985). The accumulated evidence strongly supports the concept that these rhizobia are related to bean/pea/clover-nodulating rhizobia, and Medicago-nodulating rhizobia. Thus, the Or191-like isolates provide a valuable sourse of germoplasm to explore and understand the underlying mechanisms of rhizobial diversification and evolution.        The genome of the R. sp. LPU83 consist of a single chromosome and three extrachromosomal replicons, designated as pLPU83a, pLPU83b (pSym) and pLPU83c, with 59.66 guanine-cytosine (GC) overall. Currently, the chromosome (4,15 Mbp) has been closed and represent 57% of the genome. The genome comprises 7569 potential coding genes, 2 sets of rRNA genes and 45 tRNA genes. 68% of the potential protein genes showed sequence similarity to genes of known function, 18% to hypothetical genes reported in other organisms, and the remaining 14% had no apparent similarity to any reported genes. The predicted translation products were classified into different Clusters of Orthologous Groups (COG) according to Tatusov et al.(1997). As observed in S. meliloti and R. etli, in Rhizobium sp. LPU83, several COG categories are overrepresented, namely carbohydrate transport and metabolism, amino acid transport and metabolism, and transcription (COGs G, E, and K, respectively).        To unravel similarities and differences among different sequenced rhizobia we performed a phylogenetic analysis with the complete set of chromosomal genes. The resulting tree confirmed a close chromosomal relationship of Rhizobium sp. LPU83 with R. legumnosarum and R.etli. However, the analysis of the nodulation (nod) cluster from plasmid pLPU83b demonstrated a very strong synteny with the alfalfa nodulating rhizobia S. meliloti and S. medicae. If we extend this analysis to nod sequences of not fully sequenced rhizobia, nod genes from LPU83 map at the same branch that the type strain R. mongolense 1844. A more extended similarity between Or191-like rhizobia and R. mongolense is supported by the close relationship between the 16S rDNA of these two bacteria.        To get a deeper insight on how the so closely related symbiotic clusters present in S.meliloti, S. medicae, R. mongolense, and in the Or191-like rhizobia evolved to give place to their specific symbioses will require classical experiments cross-combining specific pSym determinants in different genomic backgrounds.References[1] Del Papa MF, Balague LJ, Sowinski SC, et al. (1999) Isolation and characterization of alfalfa-nodulating rhizobia present in acidic soils of central argentina and uruguay. Appl Environ Microbiol 65: 1420-1427.[2] Eardly BD, Hannaway DB & Bottomley PJ (1985) Characterization of Rhizobia from Ineffective Alfalfa Nodules: Ability to Nodulate Bean Plants [Phaseolus vulgaris (L.) Savi.]. Appl Environ Microbiol 50: 1422-1427.[3] Tatusov RL, Koonin EV & Lipman DJ (1997) A genomic perspective on protein families. Science 278: 631-637.