Analysis of microbial utilization of rice straw in paddy soil using a DNA‐SIP approach

Abstract

AbstractConsidering the close connection between soil microorganisms with carbon (C) cycling, the aim of this study was to identify the specific bacterial and fungal microbes that assimilate 13C from incorporated rice straw and explore their dynamics and characteristics during straw decomposition in paddy soil. Soil microcosms based on 12/13C‐labeled rice straw were incubated with the determination of CO2 production at 1, 3, 7, 14, 28, 56 and 90 days after straw incorporation. Meanwhile, the targeted soil bacterial and fungal communities were characterized using a DNA‐based stable isotope probing (DNA‐SIP) approach combined with Illumina MiSeq sequencing. Rice straw decomposed rapidly in the first 2 weeks, coupled with a large turnover of soil native organic matter. During this process, Actinobacteria including the orders Streptomycetales, Caternulisporales and Corynebacteriales dominated the community utilizing rice straw‐derived C with a succession from Streptomyces, to Kitasatospora, to Catenulispora. At Days 56 to 90, the dominant orders assimilating rice straw‐derived 13C were Micrococcales, Sphingobacteriia, Gammaproteobacteria from phyla Actinobacteria, Bacteroidetes and Proteobacteria, respectively. The fungal orders Onygenales, Capnodiales, Sordariales and Pleosporales showed stronger ability of 13C utilization at late decomposition stage. Taken together, along with stimulation of soil organic matter mineralization after rice straw addition, dynamics of 13C‐assimilating bacterial and fungal groups with various characteristics were identified.