Host‐specific competitiveness to form nodules in Rhizobium leguminosarum symbiovar viciae

Abstract

Summary Fabeae legumes such as pea and faba bean form symbiotic nodules with a large diversity of soil Rhizobium leguminosarum symbiovar viciae (Rlv) bacteria. However, bacteria competitive to form root nodules (CFN) are generally not the most efficient to fix dinitrogen, resulting in a decrease in legume crop yields. Here, we investigate differential selection by host plants on the diversity of Rlv. A large collection of Rlv was collected by nodule trapping with pea and faba bean from soils at five European sites. Representative genomes were sequenced. In parallel, diversity and abundance of Rlv were estimated directly in these soils using metabarcoding. The CFN of isolates was measured with both legume hosts. Pea/faba bean CFN were associated to Rlv genomic regions. Variations of bacterial pea and/or faba bean CFN explained the differential abundance of Rlv genotypes in pea and faba bean nodules. No evidence was found for genetic association between CFN and variations in the core genome, but variations in specific regions of the nod locus, as well as in other plasmid loci, were associated with differences in CFN. These findings shed light on the genetic control of CFN in Rlv and emphasise the importance of host plants in controlling Rhizobium diversity.

MAUI-seq: Metabarcoding using amplicons with unique molecular identifiers to improve error correction

“…For the samples studied here, with abundant template DNA, the proofreading enzyme was clearly superior in performance, although more costly. On the other hand, this enzyme may provide less robust amplification when the template is weak, as we have observed in another project aimed at rhizobial DNA in soil [32]. The use of UMIs introduces other design considerations.…”

Amplicons and isolates:Rhizobiumdiversity in fields under conventional and organic management

“…Rhizobia are harboured in specialised root structures, known as nodules. To confidently establish the level of diversity within nodule populations, the most common assessment method uses cultured bacteria isolated from nodules (Sbabou et al, 2016;Efrose et al, 2018;Stefan et al, 2018;Boivin et al, 2020;Cavassim et al, 2020). Isolate-based approaches rely on the culturability of the microbes and become very labour intensive if the desired number of isolates per site is high, though they have the advantage that isolates are available for evaluation as potential inoculants.…”

“…For soil microbiome diversity studies, where many of the organisms cannot be cultured using traditional methods, high throughput amplicon sequencing (HTAS) is used to amplify sequences that distinguish microbial communities at different levels of resolution from environmental DNA samples in a cultivation-independent manner (Smalla et al, 2001;Costa et al, 2006). This method can be adapted for Rhizobium nodule or soil populations using multiplexed amplicons with unique molecular identifiers (MAUI-seq), as has been shown in recent publications (Fields et al, 2019;Boivin et al, 2020). How well diversity estimates from traditional isolate-based approaches compare to HTAS in evaluating the rhizobial diversity has not been explored in detail.…”

“…White clover (Trifolium repens L.) is an important agricultural crop in temperate climates used by both conventional and organic farmers primarily to improve forage quality by raising protein content in perennial grass pastures. Its symbiotic partner, Rhizobium leguminosarum (Rl), is a species complex comprising at least seven genetically distinct genospecies (gs) with limited gene flow between them (Kumar et al, 2015;Boivin et al, 2020;Cavassim et al, 2020). Rl can nodulate several legume species, and its specificity is determined by a group of symbiosis genes located on mobile plasmids.…”

“…While isolates potentially provide the full genome information and allow assessment of whole genome differences between strains, sample sizes are necessarily limited. In recent studies, the numbers of isolates ranged from 73 to 212 ( (Efrose et al, 2018) n=73; (Stefan et al, 2018) n=86; (Cavassim et al, 2020) n=196; (Boivin et al, 2020) n=210; (Sbabou et al, 2016) n=212). Our previous study characterised isolates from 196 nodules in detail and facilitated in-depth population genomics analysis and the discovery of movement of symbiosis genes between genospecies on a promiscuous plasmid (Cavassim et al, 2020).…”