Metagenomic insights of microbial functions under conventional and conservation agriculture.

Abstract

Agricultural practices such as conventional (CN) and conservation agriculture (CA) influence the composition and structure of soil microorganisms. We used short reads and genome-resolved metagenomic-based dual sequencing approaches to create a profile of bacterial and archaeal communities in hyperthermic Typic Haplustepts soil after seven years of CA and CN. The most differences in the physico-chemical and biological properties of soil were higher pH, organics carbon, available nitrogen and microbial biomass contents, activities of dehydrogenase, β-glucosidase, and arylsulfatase, found in CA soil. The dominant bacterial taxa under both management types were Pseudomonadota (46-48%), Acidobacteriota (12-13%), Planctomycetota (8-10%), Bacteroidota (7-8%), and Actinomycetota (6-7%). Nitrososphaerota (1.1-1.5%) was the predominant archaeal phyla in CA and CN soils. The alpha diversity was 1.5 times higher in CA compared to CN soils. Fourteen high-quality (HQ) metagenomic-assembled genomes (MAGs) were recovered from both groups. Four HQ metagenome-assembled genomes (MAGs) from the Pseudomonadota phylum were exclusively recovered from the CA soil. The dominance of this phylum in the CA soil might be correlated with its nutrient richness, as certain classes of Pseudomonadota, such as Alpha, Beta-, Gamma-, and Deltaproteobacteria, are known to be copiotrophic. Copiotrophic organisms thrive in nutrient-rich environments, which could explain their prevalence in the CA soil. CAZyme gene analysis showed that Glycoside Hydrolases (GH) and GlycosylTransferases (GT) classes are dominant in the CA group, possibly due to higher substrate availability from the application of crop residues, which provide a rich source of complex carbohydrates. Several biogeochemical gene families related to C1 compounds, hydrogen, oxygen, and sulfur metabolism were enriched in CA soils, suggesting these practices may contribute to a soil environment with increased organic matter content, microbial diversity, and nutrient availability. Overall, CA practices seemed to improve soil health by supporting soil microbial communities abundance.