Cover crop composition drives changes in the abundance and diversity of nitrifiers and denitrifiers in citrus orchards with critical effects on N2O emissions

Tree crops contribute to global agriculture production, but they are usually cultivated in soils with low nutrient availability. Cover crops (CCs) have been reported as a sustainable management strategy to improve soil nutrient availability for vegetable systems, but less is known about their influence on soil nutrient cycling, greenhouse gas emissions (GHG), and the soil microbiome in tree crops. We examined the effect of replacing the traditional weedy row middles of a commercial Florida citrus orchard with two different mixtures of CCs (legumes and non-legumes, LG + NL; and non-legumes only, NL) compared to a grower standard control (GSC) over a period of two years. Both CC mixtures significantly increased soil carbon (C) availability, microbial abundance, and soil respiration in the row middles compared to the GSC. Significant increases in soil nitrogen (N) concentrations and abundance of genes associated with N-fixation and nitrification were observed in soils treated with LG + NL. Planting LG + NL significantly increased the abundance of nosZ-type denitrifiers compared to NL and the GSC treatments, and significantly reduced nitrous oxide (N₂O) emissions. The use of both CC mixtures reduced bacterial diversity and affected the composition of nirK and nosZI communities. The composition of nosZI communities differed between CC mixtures, possibly due to changes in soil moisture and carbon. Specific amoA ammonia-oxidizing archaea, nirK, and nosZI species were identified as potential indicators for changes in N₂O emissions after planting CCs. Our results show that CCs can be a good strategy to improve soil nutrient cycling in the row middles of tree crops and that CC composition drives changes in the abundance and diversity of N-cycling communities which ultimately impact GHG emissions.