Matching population diversity of rhizobial nodA and legume NFR5 genes in plant–microbe symbiosis

Abstract

We hypothesized that population diversities of partners in nitrogen‐fixing rhizobium–legume symbiosis can be matched for “interplaying” genes. We tested this hypothesis using data on nucleotide polymorphism of symbiotic genes encoding two components of the plant–bacteria signaling system: (a) the rhizobial nodA acyltransferase involved in the fatty acid tail decoration of the Nod factor (signaling molecule); (b) the plant NFR5 receptor required for Nod factor binding. We collected three wild‐growing legume species together with soil samples adjacent to the roots 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 and further sequencing: the plant pool (30 plant indiv.), the nodule pool (90 nodules), and the soil pool (30 samples). We observed the following statistically significant conclusions: (a) a monotonic relationship between the diversity in the plant NFR5 gene pools and the nodule rhizobial nodA gene pools; (b) higher topological similarity of the NFR5 gene tree with the nodA gene tree of the nodule pool, than with the nodA gene tree of the soil pool. Both nonsynonymous diversity and Tajima's D were increased in the nodule pools compared with the soil pools, consistent with relaxation of negative selection and/or admixture of balancing selection. We propose that the observed genetic concordance between NFR5 gene pools and nodule nodA gene pools arises from the selection of particular genotypes of the nodA gene by the host plant.

Influence of Peanut, Sorghum, and Soil Salinity on Microbial Community Composition in Interspecific Interaction Zone

“…Rhizobiales (Alpha subclass of the Proteobacteria) was the core taxon in IP, and Burkholderiales (Delta subclass of the Proteobacteria) is the core taxon in IS ( Figure 7A ). The observed results corroborated those of a previous study, which showed population diversities of partners in N−fixing rhizobium-legume symbiosis to be matched ( Igolkina et al, 2019 ). These results indicated that even in the same microorganism library, plants can still actively recruit plant-associated microorganisms from the soil to construct specific microbial communities.…”

Towards Understanding Afghanistan Pea Symbiotic Phenotype Through the Molecular Modeling of the Interaction Between LykX-Sym10 Receptor Heterodimer and Nod Factors

“…Therefore, any structural variability in the NF tail (i.e., chain length or double bond positions) can potentially have an impact on NF-dimer specificity. This conclusion is in line with previous results, where the correspondence between population diversities of the rhizobial nodA gene (coding for the acyltransferase involved in the fatty acid tail decoration of the NF) and plant heterodimeric receptor genes was demonstrated (Igolkina et al, 2019). Plausible mechanisms of this linkage, namely coordinated variability of amino acids in contact with the surface of the receptor dimer adjacent to the NF fatty tail, were proposed (Igolkina et al, 2018).…”

Function identification of MdTIR1 in apple root growth benefited from the predicted MdPPI network

“…Previous studies have implicated PPIs in plant–microbe interactions. For example, membrane‐bound receptor flagellin‐sensing 2 detects and binds bacterial flagellin (flg22) to trigger PAMP‐triggered immunity and confer resistance to bacteria (Sun et al, 2013); and the legume NFR5 receptor can recognize rhizobial nodA acyltransferase to regulate the Nod‐factor signaling pathway (Igolkina et al, 2019). Thus, the construction of plant–microbe interaction networks can contribute to the understanding of interspecies interactions and elucidate the cross‐linking mechanism among different species from another perspective.…”