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. <em>Actinobacteria</em> (54.0%) and <em>Proteobacteria </em>(17.5%) are the dominant phyla while <em>Conexibacter</em> (8.38%), <em>Thermoleophilum</em> (7.40%), and <em>Streptomyces</em> (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 <em>Actinobacteria</em> and <em>Proteobacteria</em>. This study has established that members of the phyla <em>Actinobacteria</em> and <em>Proteobacteria</em> 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.
Highlights
Microorganisms found in natural environments are responsible for most of the biological transformations that lead to formation of soil nutrients (Asadu et al 2015; Costa et al 2015)
The physicochemical properties of 2S soil microcosm showed that the pH was slightly above neutral (7.20 ± 0.01) while the organic matter content was 1.10%
The pH value (7.2) of the soil is close to neutral, which is considered favourable for most microorganisms, bacteria that are essential for soil fertility and health (Lauber et al 2009)
Summary
Microorganisms found in natural environments are responsible for most of the biological transformations that lead to formation of soil nutrients (Asadu et al 2015; Costa et al 2015) The role these organisms play in driving various biogeochemical cycles of elements, fixing carbon and nitrogen, mineralizing dead organic matter and protection of plants from biotic and abiotic stresses is replete in the literature. They play a very important role in the health and ecological balance of these environments. Shifts in microbial community structure and function could be used as biomarkers of soil ecological health
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