The Evolutionary Moulding in plant-microbial symbiosis: matching population diversity of rhizobial nodA and legume NFR5 genes

Abstract

We propose the Evolutionary Moulding hypothesis that population diversities of partners in nitrogen-fixing rhizobium-legume symbiosis are matched, and tested it in nucleotide polymorphism of symbiotic genes encoding two components of the plant-bacteria signalling system. The first component is the rhizobial nodA acyltransferase involved in the fatty acid tail decoration of Nod factor (rhizobia signalling molecule). The second component is the plant NFR5 receptor, putatively required for Nod-factor binding.\n\nWe collected three wild growing legume species together with soil samples adjacent to the roots (soil pool) from one large 25-year fallow: Vicia sativa, Lathyrus pratensis and Trifolium hybridum nodulated by one of the two Rhizobium leguminosarum biovars (viciae and trifolii). For each plant species we prepared three pools for DNA extraction: the plant pool (30 plant indiv.), the nodule pool (90 nodules) and the soil pool (30 samples). NFR5 gene libraries from the plant pool and nodA gene libraries from nodule and soil pools were sequenced by Sanger technology and High-throughput pyrosequencing, respectively. Analysis of the data demonstrated concordance in population diversities of one symbiotic partner (rhizobia) the second partner (legume host), in line with the Evolutionary Moulding hypothesis. This effect was evinced by the following observations for each plant species: (1) significantly increased diversity in the nodule nodA popset (set of gene sequences derived from the nodule population) compared to the soil popset; (2) a monotonic relationship between the diversity in the plant NFR5 gene popset and the nodule rhizobial nodA gene popset; and (3) higher topological similarity of the NFR5 gene tree with the nodA gene tree of the nodule popset, than with the nodA gene tree of the soil popset. Both nonsynonymous diversity and Tajimas D were increased in the nodule popsets compared to the soil popsets, consistent with relaxation of negative selection and/or admixture of balancing selection underlying the Evolutionary Moulding effect. We propose that the observed genetic concordance arises from the selection of particular characteristics of the nodule nodA genes by the host plant.