A study of different agricultural practices over a dozen years: Influence on soil CO2 fixation rates and soil autotrophic microbial communities

Human activities, including agricultural practice, have a significant effect on soil biodiversity and function. However, little is known about the influence of agricultural practice on the microbial CO2 fixation potential. We applied stable isotope, quantitative polymerase chain reaction, and high-throughput sequencing to study the atmospheric CO2 fixation rates and the composition of autotrophic cbbL-gene-harboring bacterial and accA-gene-harboring archaeal communities in response to a dozen years of agricultural practice (including rice-upland rotation, fertilization, and tillage). Fertilizer additions significantly increased CO2 fixation rates by 14.9–40.5%, with the highest rates found for combined nitrogen and manure treatments. Rice-fallow increased soil CO2 fixation rates by 26.8% and 15.6% compared with rice-wheat and rice-Chinese milk vetch rotation, respectively, while no-tillage treatments increased it by 24.7% than traditional tillage treatments. Different agricultural practices significantly affected the cbbL-harboring bacterial diversity but not accA-harboring archaeal diversity, suggesting that cbbL-harboring bacteria are more sensitive to agricultural practices than are the accA-harboring archaea. The principal coordinated analysis revealed that agricultural practices affected both cbbL-harboring bacterial and accA-harboring archaeal communities. Partial least squares path models further revealed that the modified cbbL-harboring bacterial communities and accA-harboring archaeal communities directly or indirectly affected the CO2 fixation rate. Both random forest and correlation analyses revealed that CO2 fixation potential was attributed to Rhodobacteraceae, Oscillochloridaceae, and Dokdonella, and that soil available phosphorus was the most important factor shaping autotrophic microbial composition. Our study shows that a dozen years of agricultural practice modifies soil microbial CO2 fixation and the composition of autotrophic microorganisms. It also highlights the role of no-tillage and rice-fallow treatments in increasing soil organic carbon sequestration.