Microbial community responses to alternative management regulate soil organic carbon storage in agroecosystems experiencing irrigation retirement

Authors: SHARMA, BARSHA - New Mexico State University; FRENE, JUAN - New Mexico State University; Acosta Martinez, Veronica; LI, XIUFEN - New Mexico State University; GHIMIRE, RAJAN - New Mexico State University

Submitted to: Agriculture, Ecosystems & Environment
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 11/13/2025
Publication Date: 11/22/2025
Citation: Sharma, B., Frene, J., Acosta Martinez, V., Li, X., Ghimire, R. 2025. Microbial community responses to alternative management regulate soil organic carbon storage in agroecosystems experiencing irrigation retirement. Agriculture, Ecosystems & Environment. 398. https://doi.org/10.1016/j.agee.2025.110098.
DOI: https://doi.org/10.1016/j.agee.2025.110098

Interpretive Summary: Water limitations in the Southern High Plains are driving some producers to stop irrigation practices therefore prompting research to evaluate drought resistant cover crops and perennial systems that reduce fallow periods, improve soil health, and maintain productivity. We evaluated changes in soil carbon, nitrogen and microbial responses as indicators of soil health under irrigated compared to new dryland systems within the first two years of irrigation cutoff. In irrigated conditions, treatments were mixed (grass, brassica, legume) and grass-only cover crops with residue left on the field after termination and mixed cover crops with residue removed after termination. Perennial wheatgrass replaced grass-only cover crop treatment in land that faced irrigation retirement (new dryland). In irrigation retired systems with cover crops, we found an increase in mineral-associated organic C, particulate organic C, potentially mineralizable C, and microbial biomass C by 17, 11, 80, 81 and 35%, respectively. Cover cropping and perennial wheatgrass also enhanced the abundance of certain bacteria (Actinobacteriota) and fungi (Ascomycota) that are beneficial to soil organic matter formation. We also identified microbes (Mortierrellomycota and Bacteroidetes) that play an important role in soil C storage. These types of cover crops and perennial grasses suggested for the Southern High Plains showed to be beneficial for microbial communities involved in soil C storage within the first few years of dryland agriculture.

Technical Abstract: Diminishing water availability in arid and semi-arid regions can cause a rapid shift in the soil microbial community, resulting in changes in soil biogeochemical cycling, carbon (C) storage, and soil health. However, the magnitude of change and mechanisms of soil organic carbon (SOC) storage and soil health during the transition from irrigated crop production to dryland farming have not been well studied, specifically in arid and semi-arid regions. This study examined soil health, specifically, soil C and nitrogen (N) indicators and microbial community responses to various silage corn (Zea mays) production systems under irrigation and within the first two years of irrigation retirement under semi-arid conditions. In irrigated conditions, treatments were mixed (CCM; grass, brassica, legume) and grass-only (CCG) cover crops with residue left on the field after termination and mixed cover crops with residue removed after termination (CCM-Rem). Perennial wheatgrass (PG) replaced CCG in fields facing irrigation retirement. Compared to fallow, cover crops and PG facilitated storage of more soil organic carbon (SOC), mineral-associated organic C (MAOC), particulate organic C (POC), potentially mineralizable C (PMC), and microbial biomass C (MBC) by 17%, 11%, 80%, 81%, and 35%, respectively. Cover cropping and PG also enhanced the abundance of Actinobacteriota and Ascomycota, plant-associated microbes, while lowering the abundance of Chloroflexi. Ascomycota, Mortierrellomycota, and Bacteroidetes were linked to C storage among various groups due to their ability to rapidly accumulate microbial biomass. Cover crops and perennial grasses are critical tools for enhancing soil health during the first years of transition from irrigation to dryland agriculture in semi-arid regions.