Cover crops enhance resource availability for soil microorganisms in a pecan orchard

Currently, there are substantial knowledge gaps on the impacts of cover crops on soil resources in tree cropping systems, wherein they are typically planted in interrow alleys and maintained for multiple years. While cover crops uptake soil nutrients and water, they can also prevent soil water evaporative losses and return nutrients to soils via decomposition of plant residues and stimulation of microbial nutrient cycling. This field sampling study examined variances in soil conditions across 5- and 7-year-old, cover cropped pecan orchards. We collected soil beneath cover crops and beneath adjacent trees, where soil was kept bare, to evaluate impacts of cover on the soil biota, nutrients, carbon, and their dynamics across a production season. We employed routine soil chemical analyses, phospholipid fatty acid (PLFA) analysis, and high throughput sequencing of 16 S rRNA genes and ITS regions for soils collected at four time points. We revealed that the cover cropped alley soils contained higher relative abundances of microbes that use labile soil substrates in resource rich conditions than did the tree row soils. Soil chemical analyses provided additional evidence that the cover crops did not deplete soil nutrients and reduce soil moisture, but rather, enhanced soil nutrient and moisture contents during many of the sampling time points. Notably, cover crop plant species correlated with soil nutrients and plant beneficial microbes, which may warrant consideration when selecting cover crop species. The tree row and cover cropped alley soils had different proportions of plant-beneficial mycorrhizal fungi. The tree rows supported higher numbers of ectomycorrhizal (ECM) fungi and alleys had higher relative abundances of arbuscular mycorrhizal (AM) fungi, suggesting potential benefits for tree species like pecan, which support dual colonization by AM and ECM Fungi. Altogether, the cover crops enhanced soil carbon, nutrients, and microbial populations in a pecan orchard and these impacts were frequently larger in a 7-year-old versus 5-year-old orchard. • Alley cover crops in pecan orchards promote distinct soil conditions. • Cover crop soils had higher carbon, nitrogen, and moisture than soil under trees. • Soil microbial biomass and copiotroph oligotroph ratios were enhanced under cover crops. • AM and ECM fungi were differentially abundant under cover or trees. • Some cover crop plant species correlated with soil health indicators.