16S rRNA gene sequencing data of soil bacterial communities from four agroecological cropping systems in the CA-SYS experiment (2018–2021)

This dataset provides soil bacterial community data obtained by 16S rRNA gene sequencing from samples collected between 2018 and 2021 within the CA-SYS experimental platform. The dataset includes an OTU count table, sample metadata, phyloseq objects (raw and filtered), and HTML vignettes (with R code) illustrating the data structure, data preprocessing steps and basic diversity analyses. Samples originate from four agroecological cropping systems: SD1 (permanent no-till), SD2 (non-permanent no-till), TS1 (tillage with exogenous nitrogen input), and TS2 (tillage without exogenous nitrogen input), all managed without pesticide use.