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Isolation and phylogenetic characterization of non-symbiotic Ensifer (Sinorhizobium) directly isolated from soil

Research Areas
  • Microbiology,
  • Ecology,
  • Agriculture

Members of the genus Ensifer (Sinorhizobium) establish important endosymbioses with legumes such as Glycine max, Medicago sativa (alfalfa) or the model plant Medicago truncatula (1). In this symbiosis, as in all rhizobial symbioses, legumes are able to feed from the nitrogen fixed by the bacteria, which makes them independent from any external fixed nitrogen supply. Their symbiotic capability relies on nod, nif and fix genes (50-100 genes). These genes are grouped in symbiotic islands within the symbiotic plasmids (pSyms) (2). Symbiotic islands can be lost or transferred in the soil/rhizosphere environment (3). For the isolation of symbiotic rhizobia (those containing the symbiotic genes) ?plant traps? have traditionally been used. However, non-symbiotic populations have seldom been studied due to the absence of a methodology for their isolation. To this end, we developed a strategy, the Ensifer sp. direct isolation method, consisting of a combination of semi-selective media already described, with the use of a chromosomal genus marker developed in our laboratory (4). We describe the characterisation of Ensifer sp. populations isolated from two different soils using our strategy. Non-symbiotic populations were generally much larger and more diverse than the symbiotic populations. Two representative isolates from the same soil, one symbiotic and one non-symbiotic, that appeared to be very closely related (16SrRNA, recA and glnII phylogenies) were genome sequenced to high quality draft. The genomes of MMN_5 (a nodule isolate from Medicago sativa) and M_4_45 (a soil non-symbiotic isolate). showed very similar GC% content, 62.18 and 62.36, respectively. The genome size of the non-symbiotic isolate M_4_45 is slightly smaller (6.34 Mb) than that of the nodule isolate (6.63 Mb), consistent with the absence of symbiotic genes. Very high Average Nucleotide Identities (ANI) between strains indicate a high similarity between the aligned portions of the genome sequences. Genome sequence alignment revealed highly syntenic chromosomes, in contrast to pSym plasmids. (1) Sugawara, M et al. (2013) Genome Biol. 14, R17-R17. (2) Lagares, A et al (2014) Microbiol Spectr. 2(5):PLAS-0005-2013. (3) Finan, T. M (2002) J Bacteriol. 184(11): 2855?2856. (4) Wu, D. Y et al. (2013) Plos one. 8(10): e77033. We gratefully acknowledge Drs. Francisco Perea, Francisco Temprano, and Dulce Rodríguez (IFAPA Las Torres-Tomejil) for their help and support for soil sampling. Supported by CSB2009-00006 and CBGL2011-26932, MINECO, Spain.
20th. International Congress on Nitrogen Fixation
Granada, España
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Isolation and phylogenetic characterization of non-symbiotic Ensifer (Sinorhizobium) directly isolated from soil

Research Group, Departaments and Institutes related
  • Creador: Grupo de Investigación: BIOLOGÍA MOLECULAR Y COMPUTACIONAL
  • Centro o Instituto I+D+i: Centro de Biotecnología y Genómica de Plantas, CBGP