Cover cropping is considered a climate-smart strategy to regenerate low-fertility soils in arid and semi-arid regions. However, the mechanisms of soil organic carbon (SOC) storage and soil health improvement in semi-arid irrigated cropping systems are poorly understood. The main goal of this study was to evaluate cover crop effects on various physical, chemical, and biological indicators of soil health in an irrigated silage corn (Zea mays L.)–sorghum [Sorghum bicolor (L.) Moench] rotation and understanding how changes in soil health contribute to SOC storage. We evaluated various SOC and nitrogen (N) pools, and microbial community structure under cover crop mixture of grasses, brassicas, and legumes (GBL), grasses and brassicas (GB), grasses and legumes (GL), and no cover crops (NCC) control for four years. Grasses included annual ryegrass (Lolium multiflorum Lam.) and winter triticale (× Triticosecale Wittmack), brassicas included turnip (Brassica rapa subsp. rapa L.) and daikon radish (Raphanus sativus var. Longipinnatus Bailey), and legumes included pea (Pisum sativum subsp. arvense L.) and berseem clover (Trifolium alexandrinum L.). Soil C pools: SOC, potentially mineralizable C, microbial biomass C, mineral-associated organic C (MAOC), and particulate organic C (POC) were greater with cover crops than without, but the effects were not consistent in all study years. Soil organic N was also greater under cover crops than under NCC. Soil C-to-N (C:N) ratio increased over the years but was similar among treatments. Cover crops used N and soil water to grow, significantly reducing soil inorganic N content and water-filled pore spaces in the first two years. However, fungal and bacterial communities grew better under cover crops with a high fungi-to-bacteria ratio than under NCC. The soil MAOC content was related to microbial community and enzyme activity while POC was affected by soil physicochemical conditions, specifically soil pH and mineral N availability, highlighting two major pathways of SOC sequestration in semi-arid cropping systems. This study showed how cover crops enhance SOC storage and soil health in semi-arid cropping systems.
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