Taxonomic and functional characterization of the rhizobiome under different edaphic conditions within a vineyard plot.
Grapevine, mainly Vitis vinifera, occupies an elite position among agricultural crops worldwide. Plant rhizosphere microbiome with fungi and bacteria are among primary promoters for plant growth and health status. Although plant root system can select for microbial community through roots exudates, soil physicochemical parameters influence structure and composition of the microbial community. In this work we characterize the taxonomic composition and potential functional microbiome in combination to a large set of physicochemical parameters from the same soil samples collected at short distance (250 m) within a conventionally managed commercial vineyard plot in Alentejo (Portugal). Metabarcoding and metagenome analysis, using amplicon and shotgun sequencing, allowed to explore the structure and composition of the microbiome and their functional activity. Although mild phenotypical difference between locations, diversity of rhizosphere microbial structure and functionality differed strongly across the considered locations. Of 17 physicochemical parameters measured, seven resulted to be significantly different across the two locations, albeit ranging between safe concentrations. Elevation, boron, and sodium showed high correlation with the sample distribution of microbial community and functional genes suggesting they could affect directly microbial community and their interaction with grapevine roots. Elevation variable, which includes a set of stochastic and deterministic factors, could have exacerbated further the differences in the microbial community and functionality. As a result, Burkholderia-Caballeronia-Paraburkholderia, Pseudomonas, Pseudoxanthomonas, and Streptomyces genera, which were described to effectively improve plant growth and resistance to abiotic stresses, were significantly more abundant in location B at lower levels of boron, zinc and active limestone and higher level of sodium (within safe ranges). Microbial activity points out for higher positive plant interactions in the same location registering upregulation of genes regulating biofilm formation and quorum sensing pathways together with lipopolysaccharide biosynthesis and membrane transport. Mild phenotypic changes in grapevines, within the same vineyard, could hide significant changes in soil physicochemical properties and microbial communities, suggesting the importance of such studies to better understand complex systems such as plant rhizosphere.