Structural and functional metagenomic analyses of a tropical agricultural soil
Loading...
Date
2019-01-21
Journal Title
Journal ISSN
Volume Title
Publisher
Spanish Journal of Soil Science
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.
Description
Staff Publication
Keywords
Illumina next generation sequencing,, microbial community structure,, shotgun metagenomics,, Actinobacteria,, Proteobacteria.