Vertical and horizontal shifts in the microbial community structure of paddy soil under long-term fertilization regimes

Knowledge remains limited on how the structure of microbial community in paddy soils changes in relation to different types of fertilizers with same amount of nutrients. Thus, here, soil samples were collected at 0–10, 10–20, 20–30, and 30–40 cm depths from a paddy field subjected to four long-term fertilization treatments (no fertilization, mineral fertilization, mineral fertilization combined with rice straw, and chicken manure) and analyzed for microbial biomass and community composition. In unfertilized soils, microbial biomass decreased from 0 to 40 cm (with actinomycetes < gram-positive (G+) bacteria < gram-negative (G−) bacteria < fungi). This ordering was retained after fertilization, but the decline with depth was less pronounced. Both mineral and mineral plus organic fertilization increased the biomass of G+ bacteria compared to G− bacteria (22.7–56.2% increase) and actinomycetes (14.8–52.5% increase). Thus, over the long term, G+ bacteria benefited the most from mineral fertilizer than the other microbial groups. The partial replacement of mineral fertilizer with manure primarily enhanced the abundance of G+ bacteria at 0–30 cm soil depth, whereas replacement with straw enhanced the abundance of fungi at 10–20 cm soil depth. Our findings demonstrate that the structure of the microbial community is strongly impacted by long-term fertilization, independent of fertilizer type.