Abstract
BackgroundThe purpose of this study is to decipher the diverse carbohydrate metabolism pathways in a spent engine oil-perturbed agricultural soil, enunciate the carbohydrate-active enzymes and genes involved in the process, taxonomically classify the annotated enzymes and genes, and highlight the importance of the study for ecological and biotechnological processes.ResultsFunctional analysis of the metagenome of spent engine oil (SEO)-contaminated agricultural soil (AB1) using the Kyoto Encyclopedia of Genes and Genomes (KEGG) GhostKOALA, Cluster of Orthologous Groups (COG) of proteins, the Carbohydrate-Active Enzymes (CAZy) database, and the NCBI’s conserved domain database (CDD) revealed extensive metabolism of carbohydrates via diverse carbohydrate-active enzymes and genes. Enzymes and genes annotated for glycolysis/gluconeogenesis pathway, citric acid (TCA) cycle, pentose phosphate pathway, and pyruvate metabolism, among others, were detected, and these were not detected in the original agricultural soil (1S). Analysis of carbohydrate-active enzymes, using the CAZy database, showed 45 CAZy families with preponderance of glycoside hydrolases (GHs, 46.7%), glycosyltransferases (GTs, 24.4%), and carbohydrate-binding modules (CBMs, 15.5%). Taxonomic classification of the annotated enzymes and genes for carbohydrate metabolism using the GhostKOALA and CAZy databases revealed the predominance of the phylum Proteobacteria with the representative genera Pseudomonas (18%), Sphingobium (13.5%), and Sphingomonas (4.5%), respectively. Biotechnologically important enzymes such as xylanases, endoglucanases, α- and β-glucosidases and glycogen debranching enzymes were also retrieved from the metagenome.ConclusionsThis study revealed the presence of diverse carbohydrate-active enzymes and genes mediating various carbohydrate metabolism pathways in the SEO-perturbed soil metagenome. It also reveals the detection of biotechnologically important enzymes with potentials for industrial use.
Highlights
The purpose of this study is to decipher the diverse carbohydrate metabolism pathways in a spent engine oil-perturbed agricultural soil, enunciate the carbohydrate-active enzymes and genes involved in the process, taxonomically classify the annotated enzymes and genes, and highlight the importance of the study for ecological and biotechnological processes
Complex carbohydrates found in nature are catalyzed by a range of enzymes involved in their assembly and their breakdown, collectively called carbohydrate-active enzymes (CAZymes)
Functional analyses of AB1 metagenome using GhostKOALA, Cluster of Orthologous Groups (COG), Carbohydrate-Active Enzymes (CAZy), and NCBI conserved domain database (CDD) databases revealed the presence of various carbohydrate metabolism pathways such as glycolysis/gluconeogenesis, citric acid (TCA) cycle, pentose phosphate pathway, and several others as well as carbohydrate-active enzymes (Table 1 and Table 2)
Summary
The purpose of this study is to decipher the diverse carbohydrate metabolism pathways in a spent engine oil-perturbed agricultural soil, enunciate the carbohydrate-active enzymes and genes involved in the process, taxonomically classify the annotated enzymes and genes, and highlight the importance of the study for ecological and biotechnological processes. Hydrolysis of carbohydrates by microorganisms is a combination of diverse biochemical processes responsible for their formation, degradation, and transformation. The carbohydrate-binding modules (CBMs) assist in hydrolysis of polysaccharides by bringing the biocatalyst into close contact with its recalcitrant substrate (Lombard et al 2014). Glycoside hydrolases (GHs) are enzymes that cleave glycosidic bonds in glycosides, glucan, and glycoconjugates.
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