Ecological intensification strategies increase abundance of denitrifying functional genes in a greenhouse agricultural soil

Understanding the denitrification process in agriculture is key to preventing nitrogen (N) losses and reducing emissions of the greenhouse gas nitrous oxide (N2O) to the atmosphere. Since the type of fertilization influences this process, in this study we evaluated the comparative effect of conventional (CON) versus ecological intensification (EI) soil management under greenhouse conditions on the abundance and expression of the denitrifying functional genes nitrite reductase (nirK, nirS) and nitrous oxide reductase (nosZ). For this purpose, quantitative PCR (qPCR) was performed in three phenological stages of eggplant (Solanum melongena L var. Telma). The results showed that the addition of organic amendments tripled the copies of nirK DNA, doubled the copies of nosZ DNA and increased the copies of nirS, albeit by 2 %, compared to conventionally managed soils. The abundance of mRNA transcripts also increased for all three genes studied: nirK increased 15-fold, followed by nirS, which tripled its expression, and nosZ, which doubled its expression. Ammonium ion (NH4-N) correlated positively with the three genes analyzed, total organic carbon (TOC) with nirK and nosZ, and pH correlated negatively with nirK and nosZ. Regardless of the type of fertilization (CON or EI), a decreasing trend in gene abundance was observed from the initial growth phase of the crop (t0) until the crop was removed and crop residues incorporated into the soil (t2). The results suggest that the dynamics and composition of the denitrifying community varied in response to the type of fertilization and the phenological stage of the crop. Further studies based on metagenomics and transcriptomics, including N2O flux measurements, are needed to better understand the denitrification process in these soils.