Soil salinity determines the assembly of endophytic bacterial communities in the roots but not leaves of halophytes in a river delta ecosystem

Abstract

Although soil and rhizosphere microbiomes in highly saline environments have been well-studied, the role of soil salinity in the ecological processes affecting endophyte colonization and persistence remain largely unclear in halophytic plants. The present study sampled young and mature plants of the halophyte Suaeda salsa from 42 sites in the Yellow River Delta, China that varied in soil salinity. Soil physicochemical properties, root and leaf microbiomes, phylogenetic variation among plant ecotypes, and leaf metabolites were analysed. In the roots of both young and mature plants, soil salinity significantly influenced the composition of the endophytic microbiota (r = 0.29 ∼ 0.45, P < 0.001), and negatively correlated with endophyte alpha-diversity (r = -0.75 ∼ -0.78, P < 0.001). Leaf microbiome dissimilarity increased with geographic distance (r = 0.17 ∼ 0.26, P < 0.001), based on a distance-decay model, and was associated with plant phylogenetic variation (r = 0.15, P = 0.015 for young plants only). Additionally, leaf microbiome diversity and composition were correlated with soil age, pH, P content, and certain leaf metabolite compounds, but not with soil salinity. The dominant genera observed in young roots were Mesorhizobium spp. and Rhodomicrobium spp., while Pelagibius spp. was dominant in mature roots, and Pseudomonas spp. and Kushneria spp. were dominant in leaves. Soil salinity exerted a strong deterministic effect on the diversity and composition of the root endophyte community, while the acquisition and assembly of the leaf microbiome was affected by the dispersal effects, and the leaf metabolism of the host halophyte.