Soil metagenomics reveals reduced tillage improves soil functional profiles of carbon, nitrogen, and phosphorus cycling in bulk and rhizosphere soils

Conservation tillage practices (CAT) are known to benefit soil health and soil ecosystem functions relative to conventional tillage (CVT); however, much uncertainty remains concerning microbial functional traits and their subsequent effects on soil nutrients under different tillage practices. We analyzed the functional profiles of the C, N, and P cycles in response to CAT of no-tillage (NT), reduced tillage (RT), and CVT of moldboard plowing (MP) in bulk and rhizosphere soils using shotgun sequencing. CAT induced distinct microbial functional patterns relative to CVT, and these differences were generally more evident in rhizosphere soils than in bulk soils. CAT promotes multiple metabolic pathways such as C and N decomposition, fermentation, CO oxidation, N fixation, nitrate reduction and inorganic-P and organic-P transformations in bulk and/or rhizosphere soils. Variations in these metabolic pathways were mainly driven by Bradyrhizobium, Mesorhizobium, Nitrososphaera, Phenylobacterium, Rhizobium which are affiliated with Proteobacteria, Actinobacteria, Acidobacteria, Bacteroidota and Thaumarchaeota. Furthermore, 24 high-quality metagenome-assembled genomes (MAGs) were reconstructed, of which three novel MAGs (TL100, TL46, and TL57) harbored functional genes regulating all metabolic pathways. In particular, NT-enriched MAGs (such as Sphingomonas) promote fermentation, resulting in the reduction of soil total carbon (TC) relative to MP in bulk soils. RT retained the contents of soil TC and total nitrogen (TN) well and up-regulated the phoR gene carried by Streptomyces, which promoted the regulation of P-starvation concomitantly with the increase in the contents of total phosphorous (TP) and available phosphorous (AP) in bulk soil. Additionally, assimilatory nitrate reduction coupled with organic-P mineralization was facilitated by CAT in rhizosphere soil, leading to the mitigation of N loss and the activation of soil organic-P for crop uptake. Overall, our results revealed that CAT significantly accelerated multiple metabolic potentials, and RT could sustain soil nutrient contents better than NT.