Short-term effect of manure and straw application on bacterial and fungal community compositions and abundances in an acidic paddy soil

The application of organic fertilizers such as crop straw and manure is a feasible practice to alleviate the adverse effects caused by chemical fertilizers, and such alleviation is reflected mainly on soil microorganisms. However, our understanding of the short-term impacts of different organic materials combined with chemical fertilizer on soil fertility, bacterial and fungal abundances, and community compositions is limited. An acidic paddy field experiment in South China under three short-term fertilization regimes with equal amounts of inorganic fertilizers: chemical fertilizer (NPK), chemical fertilizer combined with cattle manure (NPKM), and chemical fertilizer combined with rice straw (NPKS) were investigated. Soil chemical properties were measured to analyze the effects of fertilization regimes on soil nutrients. Real-time quantitative PCR and MiSeq sequencing based on bacterial 16S rRNA gene and fungal internal transcribed spacer (ITS) sequence were employed to compare the bacterial and fungal abundances and community compositions under different fertilization regimes. The NPKM treatment significantly increased soil organic matter, nitrogen, and phosphorus contents compared with the NPK treatment. Also, manure application stimulated bacterial and fungal growth and distinctly shaped bacterial and fungal communities compared with chemical fertilizer alone. However, the incorporation of rice straw into soil had minor effects on soil nutrients, microbial abundance, and community composition. Redundancy analysis and variation partitioning analysis indicated that soil nutrients (e.g., SOM, available N, and P) and salinity (e.g., calcium and magnesium ions) together influenced soil bacterial and fungal communities. These results implicated a more prominent role of manure than rice straw in increasing soil fertility, bacterial and fungal abundances, and shaping microbial community distributions in this acidic paddy soil under short-term fertilization.