Microbial utilization of rice root residue‐derived carbon explored by DNA stable‐isotope probing

Abstract Despite the vast carbon (C) stock of crop root residues in arable ecosystems, the microbial assimilation mechanism of crop root derived‐C is poorly understood. In this study, a DNA‐based stable isotope probing (DNA‐SIP) approach was used to explore and characterize the diversity of the soil bacterial community assimilating C derived from 13 C‐labelled rice root residues during a 90‐day incubation. Overall, 13 C‐assimilating bacterial groups with various characteristics were identified with the occurrence of strong priming effects on soil native C. Significant increases of Actinobacteria, Proteobacteria and Bacteroidetes abundances within the 13 C‐assimilating bacterial community were observed. Generally, Streptomyces were the predominant utilizers of 13 C derived from rice root residues within a 28‐day incubation. The 13 C‐labelling of Pseudomonas , which was continuously detected during incubation, indicated stronger effects at the later decomposition stage. The role of genera Kitasatospora , Catenulispora , Nocardioides , Flavisolibacter and Niastella in 13 C‐labelled rice root residues assimilation was also observed. Meanwhile, incorporation of rice root residues stimulated the growth of certain bacterial groups that incorporated unlabelled native soil C, including Chloroflexi, Acidobacteria, Planctomycetes, Verrumicrobia and Nitrospirae. Highlights The microbial mechanism of the utilization of crop root residues is largely neglected. We explored the diversity of bacterial communities assimilating rice root residues with DNA‐SIP Actinobacteria, Proteobacteria and Bacteroidetes were dominant decomposers of root residues Streptomyces and Pseudomonas were consistently detected as key assimilators during decomposition