Enhanced near-surface soil labile carbon and microbial indicators under cover crops and crop diversification in long-term no-till systems

• Cover cropping improved SOC, microbial biomass C& N, and enzyme activities. • Both 4-year rotation & cover crops promoted TN, water extractable C& N, and POXC. • Cover cropping increased microbial abundance especially under 4-year rotation. • 4-year rotation promoted bacterial and total PLFA in the fall in corn phase. • 4-year rotation increased AM fungi in the spring when cover crops were integrated. No-till systems improve soil functions and are widely adopted in South Dakota cropping systems. However, these cropping systems have become increasingly simplified due to reduced small grain adoption, potentially reducing carbon inputs and microbial diversity. Therefore, this study aimed to (i) quantify the effects of crop rotations and cover cropping on soil organic carbon (SOC), total nitrogen (TN), and their labile fractions across the 0–80 cm soil profile, and (ii) assess how these management practices affect microbial properties in the topsoil (0–7.5 cm), using a long-term no-till (>30 years) field experiment in South Dakota. Main treatments included a corn ( Zea mays L.)–soybean [ Glycine max L. (Merr)]–oat (Avena sativa L.)–rye ( Secale cereale L.) rotation (CSOR) and a corn–soybean rotation (CS) in a randomized complete block design with four replicates. Each rotation plot was split into cover crops (CC) and no cover crops (NCC). Near-surface SOC concentrations, microbial biomass carbon, and enzyme activities were increased by CC but showed little response to rotations. Both CSOR and CC increased TN, water-extractable carbon and nitrogen, and permanganate-oxidizable carbon in the topsoil. The CSOR promoted bacterial and total microbial phospholipid fatty acid abundance during the corn phase in fall and promoted arbuscular mycorrhiza fungi in spring under CC. In the fall, CC increased all microbial groups in both rotations, with greater benefits under CSOR in spring. Overall, at this long-term no-till site, cover crops and, to a lesser extent diversified rotations, can improve near-surface SOC concentrations, labile carbon, and microbial indicators.