Long-term residue removal under tillage decreases amoA-nitrifiers and stimulates nirS-denitrifier groups in the soil

No-till in continuous corn (Zea mays L.) production helps to keep an important volume of residues on the soil surface, creating management challenges that could be alleviated by residue removal for bioenergy or animal use. Crop residues, however, are essential to stimulate microbial nutrient cycling in agroecosystems. Thus, both residue removal and tillage options need to be fully evaluated for their impacts on ecosystem services related to soil health, including microbial N cycling. We explored the main steps of the microbial N cycle in relation to soil properties by using targeted gene abundance as a proxy following over a decade of residue removal in continuous corn systems either under no-till or chisel tillage. We used real-time quantitative polymerase chain reaction (qPCR) for the quantification of phylogenetic groups and functional gene screening of the soil microbial communities, including genes encoding critical enzymes of the microbial N cycle: nifH (N₂ fixation), amoA (nitrification – ammonia oxidation), nirK and nirS (denitrification – nitrite reduction), and nosZ (denitrification – nitrous oxide reduction). Our results showed that long-term residue removal and tillage decreased soil organic matter (SOM), water aggregate stability (WAS), and the relative abundance (RA) of ammonia-oxidizing bacteria (AOB) carrying nitrifying amoA genes. Denitrifiers carrying nirS genes decreased under no-till as crop residue was removed. In addition, our results evidenced strong correlations among soil properties and phylogenetic groups of bacteria, archaea, and fungi. Overall, this study demonstrated limited but definite impacts of residue management and tillage on the soil environment, which could be exacerbated under less resilient conditions.