Rhizobial Microsymbionts of Kamchatka Oxytropis Species Possess Genes of the Type III and VI Secretion Systems, Which Can Affect the Development of Symbiosis

Abstract

A collection of rhizobial strains isolated from root nodules of the narrowly endemic legume species Oxytropis erecta, O. anadyrensis, O. kamtschatica and O. pumilio originated from the Kamchatka Peninsula (Russian Federation) was obtained. Analysis of the 16S rRNA gene sequence showed a significant diversity of isolates belonging to families Rhizobiaceae (genus Rhizobium), Phyllobacteriaceae (genera Mesorhizobium, Phyllobacterium) and Bradyrhizobiaceae (genera Bosea, Tardiphaga). Plant nodulation assay showed that only strains belonging to the genus Mesorhizobium could form nitrogen-fixing nodules on Oxytropis plants. The strains M. loti 582 and M. huakuii 583, in addition to symbiotic clusters, possessed genes of the T3SS and T6SS secretion systems, which can influence the host specificity of strains. These strains formed nodules of two types (elongated and rounded) on O. kamtschatica roots. We suggest this phenomenon may result from Nod-factor dependent and independent nodulation strategies. The obtained strains are of interest for further study of the T3SS and T6SS gene function and their role in the development of rhizobium-legume symbiosis. The prospects of using rhizobia having both gene systems related to symbiotic and non-symbiotic nodulation strategies to enhance the efficiency of plant-microbe interactions by expanding the host specificity and increasing nodulation efficiency are discussed.

Whole genome sequencing of three mesorhizobia isolated from northern Canada to identify genomic adaptations promoting nodulation in cold climates

“…This contrasts with the majority of mesorhizobia that more often carry these genes within a symbiotic island on the chromosome; of the 50 Mesorhizobium genomes downloaded from NCBI carrying nifH, nifD, nifK, nodA, nodB, and nodC, only five had these genes on a plasmid. Interestingly, the only other strains in our dataset isolated from Oxytropis (M. loti 582 and M. huakuii 583, isolated from the Kamchatka Peninsula, Russia) or Astragalus plants (M. huakuii 7653R, isolated from Nanjing, China) also contained these six genes on a megaplasmid (Wang et al 2014;Safronova et al 2020). Thus, although symbiotic megaplasmids are uncommon in the genus Mesorhizobium, they appear to be the dominant source of the symbiotic genes in microsymbionts of the subtribe Astragalinae.…”

“…Interestingly, the only other strains in our dataset isolated from Oxytropis ( M. loti 582 and M. huakuii 583, isolated from the Kamchatka Peninsula, Russia) or Astragalus plants ( M . huakuii 7653R, isolated from Nanjing, China) also contained these six genes on a megaplasmid (Wang et al 2014; Safronova et al 2020). Thus, although symbiotic megaplasmids are uncommon in the genus Mesorhizobium , they appear to be the dominant source of the symbiotic genes in microsymbionts of the subtribe Astragalinae.…”

“…This pangenome of 97 strains was then used as input for a pangenome-wide association study using Scoary, in which the following five strains were marked as isolated from northern sites: the three newly isolated strains (M. spp. AR02, AR07, and AR10), as well as M. loti 582 and M. huakuii 583 that were isolated from O. kamtschatica in the Kamchatka Peninsula (Russia) (Safronova et al 2020). A total of 25 genes were identified as putatively associated with mesorhizobia isolated from northern sites (Benjamini-Hochberg adjusted p-value ≤ 0.01; Table 3).…”

Increasing the Legume–Rhizobia Symbiotic Efficiency Due to the Synergy between Commercial Strains and Strains Isolated from Relict Symbiotic Systems

“…The presence of these genes in M. kowhaii Ach-343 apparently caused a significant increase in biomass of alfalfa plants with a decrease in the number of root nodules (Table 6). The influence of secretion systems on the formation of plant-microbial relationships was previously shown on the example of two strains (M. loti 582 and M. huakuii 583) isolated from the endemic of Kamchatka Oxytropis kamtschatica [16]. These strains possessed the T3SS and T6SS genes and formed two types of nodules (typical elongated and abnormal rounded) on roots of the host plant after mono-inoculations.…”

“…The level of acetylene reduction activity per one nodule in a tube was calculated. Strains were re-isolated from the obtained nodules (5 nodules from different tubes for each co-inoculation variant) and identified by 16S rDNA sequencing as described earlier [16]. Pictures of roots and nodules were performed by the stereo microscope Stemi 508 (Carl Zeiss, Oberkochen, Germany).…”