Genomic characterization of Sinorhizobium meliloti AK21, a wild isolate from the Aral Sea Region

Abstract

The symbiotic, nitrogen-fixing bacterium Sinorhizobium meliloti has been widely studied due to its ability to improve crop yields through direct interactions with leguminous plants. S. meliloti AK21 is a wild type strain that forms nodules on Medicago plants in saline and drought conditions in the Aral Sea Region. The aim of this work was to establish the genetic similarities and differences between S. meliloti AK21 and the reference strain S. meliloti 1021. Comparative genome hybridization with the model reference strain S. meliloti 1021 yielded 365 variable genes, grouped into 11 regions in the three main replicons in S. meliloti AK21. The most extensive regions of variability were found in the symbiotic plasmid pSymA, which also contained the largest number of orthologous and polymorphic sequences identified by suppression subtractive hybridization. This procedure identified a large number of divergent sequences and others without homology in the databases, the further investigation of which could provide new insight into the alternative metabolic pathways present in S. meliloti AK21. We identified a plasmid replication module from the repABC replicon family, together with plasmid mobilization-related genes (traG and a VirB9-like protein), which suggest that this indigenous isolate harbors an accessory plasmid. Furthermore, the transcriptomic profiles reflected differences in gene content and regulation between S. meliloti AK21 and S. meliloti 1021 (ExpR and PhoB regulons), but provided evidence for an as yet unknown, alternative mechanism involving activation of the cbb3 terminal oxidase. Finally, phenotypic microarrays characterization revealed a greater versatility of substrate use and chemical degradation than for S. meliloti 1021.Electronic supplementary materialThe online version of this article (doi:10.1186/s40064-015-1062-z) contains supplementary material, which is available to authorized users.

Divergent genes in potential inoculant Sinorhizobium strains are related to DNA replication, recombination, and repair

“…Contrary to the wild‐type S. meliloti strains, the genes of HAMBI 1552 variable to the salt stress affected genes of Rm1021 included equal number of multiplied and divergent genes, among others, three divergent rhizobactin genes and two multiplied iron uptake genes. The rhizobactin operon is missing from the genomes of Aral sea isolates S. meliloti AK 21 and AK83 , implying that the wild type strains have alternative, possibly more stress tolerant, systems for iron uptake.…”

Characterization of symbiotic and nitrogen fixing bacteria

“…The technology is increasingly being adopted in classifying nitrogen-fixing and related bacteria (Uelze et al 2020 ). So far complete genome sequences of Rhizobium , Sinorhizobium , Mesorhizobium , Bradyrhizobium and Azorhizobium among others have been sequenced and available for public use (Molina-Sánchez et al 2015 ; Sugawara et al 2013 ). The technique provides complete genetic variation and the sequence data can be used for identification and taxonomy of organisms.…”

Deciphering the Symbiotic Plant Microbiome: Translating the Most Recent Discoveries on Rhizobia for the Improvement of Agricultural Practices in Metal-Contaminated and High Saline Lands

“…Examples include: Rhizobium sp. LCM 4573 (a salt-tolerant rhizobium from Senegalese soil [94]), R. leucaenae (a stress-tolerant species nodulating plants in tropical acid soils [95]), S. meliloti AK21 (from the Aral Sea Region that experiences saline and drought conditions [96]) and Ensifer aridi (isolated from arid soils of diverse deserts [97]). Transcriptomic and proteomic studies have been instrumental in highlighting how rhizobia respond to environmental stresses (a detailed list is provided elsewhere [98]).…”