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.

林木作物有助于全球农业生产，但它们通常种植在养分含量低的土壤中。据报道，覆盖作物 (CCs) 是一种可持续管理策略，可改善蔬菜系统的土壤养分可用性，但人们对其对土壤养分循环、温室气体排放 (GHG) 和树木作物土壤微生物组的影响知之甚少。与种植者标准对照（GSC ) 为期两年。与 GSC 相比，两种 CC 混合物均显着增加了行中间的土壤碳 (C) 可用性、微生物丰度和土壤呼吸。在用 LG + NL 处理的土壤中观察到土壤氮 (N) 浓度和与固氮和硝化作用相关的基因丰度显着增加。种植 LG + NL 显着增加了与 NL 和 GSC 处理相比，nosZ型反硝化剂显着减少了一氧化二氮 (N ₂ O) 的排放。两种 CC 混合物的使用降低了细菌多样性并影响了nirK和nosZ I 群落的组成。不同CC混合物的nosZ I群落组成不同，可能是由于土壤水分和碳的变化。特定的amoA氨氧化古菌、nirK和nosZ I 物种被确定为 N _{2变化的潜在指标}种植 CC 后的 O 排放。我们的研究结果表明，CCs 可以成为改善林间作物行中土壤养分循环的好策略，并且 CC 成分驱动 N 循环群落的丰度和多样性发生变化，最终影响温室气体排放。