Cover cropping differentially shapes soil fungal and bacterial communities in citrus orchards

The role of cover crops in promoting the abundance of beneficial soil microbes is increasingly gaining attention in tree crops. However, soil fungi remain comparatively understudied despite their roles in nutrient cycling and soil organic matter turnover, functions that are directly influenced by cover crops and may, in turn, affect the cash crop. This study compared the effects of cover crop mixtures to a weedy control on soil bacterial and fungal communities in young (< 10 years) and old (> 20 years) citrus orchards-with different lengths of cover cropping-across three soil depths over 2 years. Soil fungi responded to cover crops, whereas soil bacteria showed minimal changes in both orchards. In the young orchard, non-legume cover crop mixtures altered soil fungal communities three months after planting and after 2 years, both cover crop mixtures resulted in distinct community shifts relative to the control. In the old orchard, soil depth shaped fungal communities, with the strongest cover crop effects in the topsoil and subsurface soil. In both orchards, cover crops enriched potentially plant-beneficial microbial taxa, including arbuscular mycorrhizal fungi, highlighting the importance of cover crops as a management tool for driving fungal-mediated ecological processes and soil health benefits in orchard systems.