Population genomics of the legume plant host specific selection of rhizobial genotypes

Rhizobium leguminosarum bv. viciae (Rlv) establish effective symbioses with four legume genera: Pisum, Lens, Lathyrus and Vicia. Classic studies using trap plants provided evidence that, given a choice, specific hosts select specific genotypes of rhizobia which are, apparently, particularly adapted to that host (Mutch & Young, 2004; Louvrier et al, 1996). OBJETIVE Pooled DNA samples from Rlv nodule isolates obtained from different legume plant hosts used as rhizobial traps should allow a test of the hypothesis that different plant hosts select specific subpopulations of rhizobia from the available population present in a given soil. MATERIALS AND METHODS We have applied a Pool-Seq approach (Kofler et al, 2011), to study plant host selection of genotypes from the available rhizobial genomic diversity present in a well-characterized agricultural soil (INRA Bretennieres). Plants of P. sativum, L. culinaris, V. sativa and V. faba were employed as traps. We pooled 100 nodule isolates from each host, and the pooled DNAs were sequenced (BGI-Hong Kong; Illumina Hi-Seq 2000, 180 bp PE libraries, 100 bp reads, 12 Mreads). Reads were quality filtered with Trimmomatic, mapped with Bowtie2 using Rlv 3841 as reference genome. Single Nucleotide Polymorphisms (SNPs) were called with VarScan. Results were visualized with SeqMonk and IGV. RESULTS Our results confirm, at the genomic level, previous observations regarding plant selection of specific genotypes. We expect that further, ongoing comparative studies on differential Pool-Seq sequences will identify specific gene components of the plant-selected genotypes. CONCLUSIONS Since rhizobial populations are a minor fraction of the soil microbiota, any attempt to approach the genomic structure of such populations will necessarily require a preliminary enrichment through the use of legume host trap plants, thus potentially introducing a host-mediated bias. Our work discussed here provides genomic evidence that specific hosts select specific genotypes from the available variability present in the soil