Soil Autotrophic Bacterial Community Structure and Carbon Utilization Are Regulated by Soil Disturbance—The Case of a 19-Year Field Study

Abstract

The roles of bacterial communities in the health of soil microenvironments can be more adequately defined through longer-term soil management options. Carbon dioxide (CO2) fixation by autotrophic bacteria is a principal factor in soil carbon cycles. However, the information is limited to how conservation tillage practices alter soil physiochemical properties, autotrophic bacterial communities, and microbial catabolic diversity. In this study, we determined the changes in autotrophic bacterial communities and carbon substrate utilization in response to different soil management practices. A replicated field study was established in 2001, with the following soil treatments arranged in a randomized complete block: conventional tillage with crop residue removed (T), conventional tillage with residue incorporated into the soil (TS), no tillage with crop residue removed (NT), and no tillage with residue remaining on the soil surface (NTS). Soils were sampled in 2019 and microbial DNA was analyzed using high-throughput sequencing. After the 19-year (2001–2019) treatments, the soils with conservation tillage (NTS and NT) increased the soil’s microbial biomass carbon by 13%, organic carbon by 5%, and total nitrogen by 16% compared to conventional tillage (T and TS). The NTS treatment increased the abundance of the cbbL gene by 53% in the soil compared with the other soil treatments. The cbbL-carrying bacterial community was mainly affiliated with the phylum Proteobacteria and Actinobacteria, accounting for 56–85% of the community. Retaining crop residue in the field (NTS and TS) enhanced community-level physiological profiles by 31% and carbon substrate utilization by 32% compared to those without residue retention (T and NT). The 19 years of soil management lead to the conclusion that minimal soil disturbance, coupled with crop residue retention, shaped autotrophic bacterial phylogenetics, modified soil physicochemical properties, and created a microenvironment that favored CO2-fixing activity and increased soil productivity.