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The amendment of crop residues produced under elevated CO 2  (eCO 2 ) may alter soil microbial community structure and their functions on residue decomposition and carbon (C) cycling in soil. The key to understanding this process is to elucidate the structure of prokaryotic communities that metabolize crop residues derived from eCO 2 . A soil incubation experiment was conducted to explore the response of soil microbial community to the amendment of  13 C-labeled soybean residues produced under ambient CO 2  (aCO 2 ) and eCO 2  .  The residues were applied to a Mollisol, followed by  13 C-DNA stable isotope probing (SIP) and Illumina sequencing on soil prokaryotic community over time. The structure of residue-metabolizing community differed in response to the amendment of eCO 2 - and aCO 2 -derived residues after 28 days of incubation. In particular, genera  Actinomadura ,  Nocardia ,  Non-omuraea , and  Shimazuella  were the dominant members of the residue-metabolizing bacteria, which contributed to this difference. The relative abundances of genera  Actinomadura ,  Nocardia  and  Shimazuella  were 118–144%, 71–113%, and 2–4-fold higher in the Mollisol amended with aCO 2 -derived than eCO 2 -derived residue. In contrast, the relative abundance of  Non-omuraea  was 87–90% greater in the eCO 2 -residue treatment. However, during the incubation period, there was no difference between the two residue treatments in the community structure as a whole without SIP. These results implied that a pioneering prokaryotic community metabolized the residue initially prior to the entire community. Those bacteria genera being inhibited with the amendment of the eCO 2 -derived residue, compared to aCO 2 -derived residue, were likely preferential to metabolize recalcitrant C, which might be associated with changes of chemical composition of the residue under eCO 2 .

13C-DNA-SIP Distinguishes the Prokaryotic Community That Metabolizes Soybean Residues Produced Under Different CO2 Concentrations