Short-term effects of cover crops on soil properties and the abundance of N-cycling genes in citrus agroecosystems

Abstract

Limited information is available on the influence of cover crops (CCs) on soil nutrient cycling and the abundance of bacterial and archaeal communities, nitrogen (N)-fixers, nitrifiers, and denitrifiers in tree crops. We examined the effect of replacing the traditional weedy inter-row middle of a commercial citrus orchard in Florida with two different mixtures of CCs: legumes and non-legumes (LG + NL) and non-legumes only (NL). A no-treatment/grower standard was used as a control (GSC). After one year of CCs, the use of NL and LG + NL CCs significantly increased soil carbon (C) availability in the row middles compared to GSC as shown by increases in permanganate oxidizable C, and to a lesser extent, soil organic matter. Treatment with LG + NL significantly increased soil ammonium content compared to the NL and GSC treatments. Improved C cycling in soils treated with CCs was related to increased abundance of bacteria and archaea. Changes in the size of the soil N pool were accompanied by increases in the abundance of N-fixation (nifH) and nitrification (amoA) genes in soils treated with LG + NL, likely due to greater N-mineralization and N-fixation by legumes. The use of CCs significantly altered the abundance of the nirK, nirS, norB, nosZI, and nosZII denitrification genes after one year compared to the GSC treatment. Changes of the ratio between genes involved in nitrous oxide (N2O) production and reduction showed a greater abundance of N2O producers in soils treated with NL compared to the GSC and the LG + NL treatments. Nitrous oxide fluxes determined over a 1-month period after one year of CCs were also significantly higher in NL than in LG + NL and GSC soils. The lower N2O fluxes from soils treated with LG + NL were accompanied by significantly greater abundances of genes involved in N2O reduction (nosZI and nosZII). Overall, our data suggest enhanced soil nutrient cycling and nutrient availability and associated nitrogen-cycling microorganisms in Florida citrus orchards after only one year of CC treatments. These impacts depended on the composition of the CC mixture and appear to be accelerated in sandy soils under warm humid climate such as in Florida.