Data and R code for reproducible analysis of herbicide-induced microbiota reorganization in a rice–barnyardgrass co-cultivation system

This record contains data, R code, and output files for reproducible analyses associated with a study on herbicide-induced ecological responses in a rice–barnyardgrass co-cultivation system. The study examined how sublethal doses of propanil and cyhalofop-butyl affected plant performance and microbiota dynamics in a coupled crop–weed context. The package includes analysis workflows for (1) bacterial–fungal co-occurrence network construction and export, and (2) phylogenetic turnover analysis based on beta nearest taxon index (bNTI). These workflows were used to characterize herbicide-associated changes in microbial diversity, community composition, assembly processes, and interkingdom network structure in rice-associated microbiota. The archive contains input data, R scripts, exported result tables, README files, and session information to facilitate reproducibility. The analyses support the interpretation that herbicide application in paddy fields acts not only on individual plant hosts, but also as an external disturbance to the coupled rice–barnyardgrass system, with microbiota reorganization representing an important component of the ecological response.