The semiarid Texas Southern High Plains (TSHP) and Texas Rolling Plains (TRP) produce 95% of the nation’s organic cotton and 90% of organic peanuts. Organic farmers cite weeds and soil health as their greatest challenges, yet they hesitate to grow cover crops or diversify rotations because of limited moisture. Field trials in Vernon (TRP) and Lamesa (TSHP) evaluated impacts of different cover crops, rotations, and subsurface versus broadcast manure compost on soil moisture, soil organic carbon (SOC), nutrient cycling, greenhouse gas emissions, microbial biomass, weeds, crop yields, and net economic returns in organic cotton and peanuts under deficit irrigation (60% of ET). Systems included continuous cotton, cotton/peanut, cotton/mungbean, cotton/sesame, and cotton/wheat/sorghum-sudangrass forage, with or without a cover crops of fall-planted rye.

Weeds such as palmer amaranth overwhelmed cash crops even when trials were clean-tilled and replanted, showing that organic transition should be undertaken in “well managed, weed-free fields.” Severe drought caused multiple crop failures at both sites, and poor seed quality caused cotton failures in 2023 and a peanut failure in 2022. Organic yields were similar to conventional, and weed control costs hurt net returns during organic transition.

Despite low plant biomass, integrating rotation, compost, and cover crops boosted SOC by 14-43% and enhanced soil aggregation, microbial biomass, and arbuscular mycorrhizal fungi at both sites. Compost + cover crops enhanced microbial biomass, community structure, and enzyme activities by the second year in the cotton-peanut rotation. The cotton-wheat-forage rotation with compost increased CO2 emissions but rotation, cover crop, and compost had no effect on N2O or CH4 emissions. Cover crops did not reduce soil moisture reserves (surface to 140 cm) and crop rotations, especially cotton-wheat-forage and cotton-sesame, conserved moisture.