Long-term conversion from rice-wheat to rice-vegetable rotations drives variation in soil microbial communities and shifts in nitrogen-cycling through soil profiles

Abstract Land-use change (LUC) caused by agricultural intensification has aggravated soil reactive nitrogen (Nr) pollution in global rice agroecosystems. Microorganisms mediate Nr transformation; however, the structural and functional responses of the microbial community to LUC and soil Nr loading have yet to be synthesized. Simultaneously, rice–wheat (RW) rotations in China have been subjected to high rates of LUC, primarily to intensive rice-vegetable (RV) rotations. Here, 16S rRNA gene sequencing coupled with Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt2) was performed to assess the influence of conversion from RW to RV on soil Nr fractions, microbial communities, and N-cycling genes, especially over longer time scales and at deeper soil depths. Compared to RW, bacterial alpha-diversity increased in the 10-year RV, whereas archaeal alpha-diversity decreased with increasing years under RV rotations. Microbial beta-diversity significantly decreased after the conversion from RW to RV rotations, resulting in reduced heterogeneity in community structure (composition and abundance) across 0–40 cm soil profiles in RV rotations. Redundancy analysis suggested that this homogenization was driven by increased concentrations of nitrate N and decreased soil pH and soluble organic N concentrations in the RV. At 0–20 cm, RV decreased the abundance of Geobacter spp., Candidatus_Nitrosotalea spp., and their related N-fixation genes, whereas it increased the abundance of Streptomyces spp. and their related nitrification genes. Moreover, the 20-year RV significantly increased the potential denitrification and N2O emissions from soil at 0–40 cm by decreasing the abundance of bacterial nosZ genes (encoding nitrous-oxide reductase) and increasing archaeal nirK, nirS (nitrite reductase) genes, and bacterial norB and norC genes (nitric-oxide reductase). Collectively, RW-to-RV conversion decreased soil microbial diversity and increased the size of denitrification/N2O-producing communities, this homogenization of microbiomes in long-term RV system may be a potential source of N2O.