Shifts in Soil Microbial Communities Under Cover Cropping in Citrus Orchards

Cover crops are increasingly used by growers in the United States as an effective approach to enhance soil health. The interactions between cover crops and soil microbiomes have been studied extensively; however, research evaluating the impact of cover crops on rhizosphere microbial communities in tree crop systems, particularly under nutrient-limited field soils in Florida, remains limited. To address these knowledge gaps, a three-year field study was conducted to evaluate the effects of cover crop mixtures on soil bacterial and fungal communities in orchards of different citrus species and cultivars across seasons. The trial included ‘Star Ruby’ grapefruit trees grafted on ‘US-942’, ‘Bearss’ lemon trees grafted on ‘Sour Orange’, and ‘OLL-8’ sweet orange trees grafted on ‘US-942’ rootstock in a randomized complete block design comparing conventional management (no cover crop-control) with cover crop treatments. Bacterial community composition showed consistent taxonomic patterns across cultivars and treatments, with Proteobacteria consistently the most abundant phylum across grapefruit, lemon, and orange orchards, followed by Actinobacteriota, Acidobacteriota, and Firmicutes. Despite this overall stability, cultivar was the strongest determinant of bacterial community structure. Additionally, functional analysis revealed significant treatment-associated shifts in predicted guilds related to nitrogen transformations, carbon metabolism, sulfur oxidation, and manganese oxidation. In contrast, fungal community composition and predicted functional profiles were primarily structured by season, with limited effects of cultivar and cover cropping. Fungal communities were consistently dominated by Ascomycota across orchards, sampling dates, and treatments.