Structural and functional metagenomic analyses of a tropical agricultural soil

Abstract

Understanding the intricate link between the soil microbiota and their metabolic functions is important for agricultural and ecological processes and could be used as a biomarker of soil health. To understand the relationship between soil microbial community structure and functions, a soil microcosm designated 2S (agricultural soil) was set up. Metagenomic DNA was extracted from the soil microcosm and sequenced using Miseq Illumina next generation sequencing and analysed for their structural and functional properties. Structural analysis of the soil microcosm by MG-RAST revealed 40 phyla, 78 classes, 157 orders, 273 families and 750 genera. Actinobacteria (54.0%) and Proteobacteria (17.5%) are the dominant phyla while Conexibacter (8.38%), Thermoleophilum (7.40%), and Streptomyces (4.14%) are the dominant genera. Further assignment of the metagenomics using Cluster of Orthologous Groups (COG), Kyoto Encyclopedia of Genes and Genomes (KEGG), GhostKOALA, and NCBI’s CDD revealed diverse metabolic pathways utilized by the microbial community for the metabolism of carbohydrates, amino acids, lipids, biosynthesis of secondary metabolites and resistance to antibiotics. Taxonomic analysis of the annotated genes also revealed the preponderance of members of Actinobacteria and Proteobacteria. This study has established that members of the phyla Actinobacteria and Proteobacteria are the key drivers of the majority of important metabolic activities in the soil ecosystem and are thus an integral part of the soil microbial community.