A comparative analysis of genomic characters of reference sinorhizobium meliloti strains, the alfalfa symbionts: (Review)

Abstract

Plant-microbial symbiotic interaction is a unique highly specific biological system for fixing atmospheric nitrogen and its transformation into compounds accessible to living organisms. A fundamentally new approach may be the creation of a system for genetic monitoring of the stability of economically valuable strains in microbioms of agroecosystems. By comparison of the genomic characteristics of symbiotically active strains functionally significant marker sequences could be identified and the basis for genetic monitoring system will be created. In the review, we compared genomic characteristics of the symbiotic active strains obtained on the basis of Sinorhizobium meliloti 425a and SU47 strains, used for production of biologicals. Strain 425a was isolated from alfalfa nodules in the mid-1970s in the Almaty region (Kazakhstan), which is a part of the Central Asian primary center of cultivated plant origin designated by N.I. Vavilov. Strain SU47 was isolated from alfalfa nodules in the late 1930s in Australia, which is the secondary center of the diversity of cultivated plants. Strains CXM1-105 (CXM1) and Rm1021 (Rm2011) are widely applied as a reference strain as they have been used to develop or adapt a wide range of symbiogenetics methods. Genomes of both the original strains and their derivatives consist of a chromosome (SMc) and two megaplasmids (SMa, SMb), and do not contain cryptic plasmids. However CXM1-105 genome, unlike Rm1021 genome, did not contains 508 protein encoding ORFs (open reading frames) of which 242 are located on SMa, 121 are on SMb and 145 are on SM, as it was found using DNA biochips. This indicates significant differences in the structure of all three replicons in the reference strains CXM1-105 and Rm1021. Chromosome of CXM1-105 (CXM1), as well as of 425a did not contain sequences of phage origin (the genomic islands) described in Rm1021. It was found that 62 ORFs of genomic islands are similar or homologous to those of the members of the same species or genus, as well as of phylogenetically distant bacterial classes. However, in the CXM1-105 chromosome there are sites for the integration of genomic islands (EU196757, EU196758 and EU196759), which are 99-100 % homologous to appropriate sequences of Rm1021 (Rm2011). We studied the occurrence of S. meliloti strains harboring type SMcRm1021 or SMcCXM1-105 chromosome (presence or absence of genomic islands, respectively) in native populations. The significant prevalence of strains inherited SMcRm1021 was shown for the area, belonging to the Middle-Asian gene center of cultivated plants, while strains harboring the chromosomal type SMcCXM1-105 were dominant in the area of extremely saline soils next to Aral Sea area (P < 0.05). Consequently, the presence of additional foreign sequences, which could participate in horizontal gene transfer, is typical of native S. meliloti isolates abundant in the primary center of the diversity of their host plants whereas those sequences are lost under an abiotic stress (salinity) impact. In addition, strains harboring different chromosome types, according to structural differences in the intergenic sequence of rrn-rrl operons, can be referred to divergent clonal lineages. According to the discussed data, it was suggested to consider strain 425a and its derivatives as the model S. meliloti strains to create a system for genetic monitoring of practically valuable strains in agrocenoses.