Genomic analysis of Sinorhizobium meliloti LPU63, an acid-tolerant and symbiotically efficient alfalfa-nodulating rhizobia

CAFIERO, JUAN HILARIO; SALVETTI CASASCO, MARÍA; LOZANO, MAURICIO JAVIER; VACCA, CAROLINA; LÓPEZ GARCÍA, SILVINA LAURA; DRAGHI, WALTER OMAR; LAGARES, ANTONIO; DEL PAPA, MARÍA FLORENCIA

Frontiers in Agronomy

Frontiers

Año: 2023 vol. 5

The growth and persistence of alfalfa (Medicago sativa), a perennial legumecapable of producing high yields of high-quality forage, is reduced in moderatelyacidic soils. The low performance of alfalfa at low pH is due to numerous factorsthat affect the host plant, their rhizobia, and the symbiotic interaction.Sinorhizobium meliloti LPU63 was isolated from acid topsoil (in Argentina) andshowed to be a highly competitive and efficient N2-fixing rhizobium under bothneutral and moderately acidic soil conditions. In this study, we obtained a draft ofthe LPU63 genome sequence using Illumina HiSeq4000. The whole genomephylogenetic analysis confirmed the taxonomic position of LPU63 as a S. melilotistrain and the multilocus sequence analysis confirmed that LPU63 is not relatedto the strains used in Argentina in bioformulations. The genomic analysis showedthat beyond the canonical chromosome, pSymA, and pSymB, LPU63 strain hasan accessory plasmid that codes for a repABC origin of replication and aconjugative T4SS, suggesting that this plasmid could be self-transmissible. Inaddition, the complete denitrification pathway (i.e., the gene clusters nap, nir,nor, and nos), including napC and nosZ, which could be used as an alternativerespiration route under hypoxic conditions with moderate N2O emissions wasfound. Also, genes associated with plant growth-promoting activities (PGPR) andthe degradation of phenylacetic acid (PAA) were identified. LPU63 is a highlymelanogenic strain, a property that could enhance its survival under soilconditions, and the genome data showed a particular arrangement of thegenes involved in melanin production. The information regarding LPU63activities compatible with plant-growth promotion phenotypes, together withother characteristics mentioned here (melanin production, potential moderateN2O emissions), constitute the basis of future experiments toward the rationaldesign of a novel bioinoculant for the environmentally sustainable productionof alfalfa.