Analysis of salt-sensitive and salt-tolerant sinorhizobium meliloti strains using dna microarray, phenotype microarray and genome mining techniques

Nodule bacteria increase the resistance of host plants to abiotic stress factors; however, the role of the genetic potential of rhizobia in the formation of productive salt-tolerant plant-microbial symbiosis remains underestimated. The aim of the study was to evaluate the pool of genes responsible for the salt tolerance of the alfalfa microsymbiont, Sinorhizobium meliloti, using the DNA microarray technique, phenotype microarray (PM), NGS and NNGS-technologies and genome mining (antismash 5.0). As a result of the analysis of the genomes of strains contrastingly different in salt tolerance, it was found that nucleotide changes in genes in salt-sensitive strains occurred significantly more often in genomic islands located on the chromosome. The genome of the salttolerant strain contained at least 25 genes involved in the DNA replication and repair and metabolism of nucleotides (1 KEGG group), amino acids (8 KEGG groups), lipids (2 KEGG groups), and carbohydrates (4 KEGG groups). Genomic analysis of the saltsensitive strain revealed 2 unique secondary metabolite biosynthesis gene clusters on pSymB (NAGGN) and on the cryptic plasmid (phosphonate and ectoine), while both gene clusters are involved in the synthesis of substances that involved in osmotic stress response. In the genomes of salt-tolerant phenotype strains, changes occurred in a smaller number of genes belonging to other KEGG groups. Two unique clusters of antibiotic synthesis, the class of macrolides (conglobactin) and aminoglycosides (2- deoxystreptamine), as well as an additional cluster of synthesis of thioamitide RiPPs, were identified on the chromosome of a salt-tolerant strain using genome mining. The use of the PM technique made it possible to show that the salt-tolerant strain is resistant to 10 beta-lactam antibiotics, 7 cephalosporins, 9 aminoglycoside antibiotics, 5 tetracyclines, polymyxin E, and 16 antibiotics that block the synthesis of DNA, RNA, enzymes and proteins, while the salt-sensitive strain grew up on alternative sources of organic sulfur and carbon. The revealed characteristics of strains that contrastingly differ in stress tolerance are promising for their use in agrobiotechnology.