Increasing livestock wastewater application in alternate-furrow irrigation reduces nitrification gene abundance but not nitrification rate in rhizosphere

In water-scarce regions, alternate-furrow irrigation (AFI)—alternately wetting half of the plant roots—has proven to be an effective water-saving approach without compromising yield. However, the extent to which AFI with wastewater affects N cycling genes remains poorly studied. We aimed to investigate changes in main N transformation processes, bacterial and fungal community composition, as well as relative abundance of N cycle-associated genes in soil receiving AFI with swine wastewater. The experimental plan included three irrigation rates, irrigating pepper plants with 50%, 65%, and 80% of the amount of water required under conventional furrow irrigation to prevent the crop suffering water stress. Each treatment had a groundwater irrigation control. We measured edaphic factors, microbial community composition, and relative abundance of genes in rhizosphere and bulk soils. Altering water use in AFI did not exert a significant effect on bacterial and fungal communities. By increasing the irrigation rate of wastewater, relative abundances of nifH , bacterial and archaeal amoA and nosZ genes decreased, whereas those of nirK and nirS genes increased in the rhizosphere soil; nitrification rate did not decrease and the denitrification rate remained unchanged in both rhizosphere and bulk soil, implying that appropriate increase of wastewater use by AFI can improve N use efficiency.