Management impacts rhizosphere composition and gene expression in vineyards

This study examined rhizosphere soil samples from vineyards located in Sannio area, (Campania, Italy) with different management practices to assess the microbiota's functionality through a metatranscriptomic analysis. The analysis provided a comprehensive taxonomic characterization, gene expression insights, and predictive functional analyses. The experiment included 18 samples from three management-based groups (green manure, periodic hoeing, burying pruning) each with six biological replicates from two vineyards, yielding 316 Gb of data (17.5 Gb/sample). In the vineyards in which a green manure mix of Brassicaceae and Fabaceae was practised, the predominant bacterial phyla are Actinomycetota (with predominant families Conexibacteraceae and Nocardioidaceae), and Pseudomonadota (predominantly Nitrobacteraceae and Methylobacteriaceae). As regards the phylum Streptophyta, as expected, there is a greater abundance of transcripts from Vitaceae and Brassicaceae. About fungi, the most abundant phylum Ascomycota has predominantly Pyronemataceae and Pleosporaceae. Of particular interest related to this type of managment is the abundance of viral transcripts, with the most abundant phylum Pisuviricota and the families Secoviridae and Dicistroviridae. The most significantly up-regulated genes in these vineyards belonged to GO classes involved in viral infections and plant stress responses. In vineyards where regular tilling is carried out, a similar pattern but higher percentages of Actinobacteria and Lenarviricota were observed. In these samples, genes involved in phytohormone pathways (Jasmonic acid, Gibberellin, Salicylic acid) and root system development were up-expressed. Vineyards with a discordant taxonomic profile were those where pruning waste was routinely buried. This management practice was correlated with a marked increase in Nematoda transcripts. Gene expression and pathway enrichment analyses identified significant metabolic and signal transduction pathways associated with differentially expressed genes, highlighting how the rhizosphere is influenced by agricultural practices. • Different management induced a taxonomic change in the rhizosphere. • A higher abundance of viral transcripts was found in vineyards where green manure is practised. • Higher abundance of nematode transcripts was found in vineyards where pruning residues are buried. • BP increase abundance of bacteria involved in the nitrogen biogeochemical cycle.