Metagenomic, physicochemical, enzymatic, and greenhouse-gas datasets from rice straw management in Tolima, Colombia

Rice production is essential for food security, economic stability, and environmental sustainability. In Tolima, Colombia, post-harvest rice straw management is challenging due to high removal costs and the environmental impact of burning, highlighting the need for sustainable alternatives. This study evaluated three rice straw incorporation strategies (bioinoculant-assisted degradation for 15 and 30 days, and non-degraded straw) across three municipalities. We analyzed soil microbial diversity through metagenomics, including functional profiles and genome reconstruction (MAGs), along with physicochemical properties, enzymatic activities (cellulase, invertase, phosphatase, laccase, and peroxidase), and greenhouse gas (GHG) emissions (CO₂, CH₄, N₂O) over three cropping cycles. Results showed temporal microbial and functional shifts, with Proteobacteria dominating at 15 days, Gemmatimonadetes at 30 days, and Actinobacteria under traditional management. A total of 35 medium- and high-quality MAGs were recovered. Enzymatic activity patterns were more consistent under the 30-day treatment, which also exhibited the lowest global warming potential.This dataset provides a resource for exploring the interactions between straw management practices, soil microbial dynamics, biochemical activity, and greenhouse gas fluxes in rice agroecosystems.