Detection of carbohydrate-active enzymes and genes in a spent engine oil-perturbed agricultural soil
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Date
2018-08
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Bulletin of the National Research Centre
Abstract
Background: 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.
Results: Functional 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.
Conclusions: This 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.
Description
Staff Publication
Keywords
Spent engine oil,, Agricultural soil,, Soil microcosm,, Illumina sequencing,, Carbohydrate metabolism,, Carbohydrate-active enzymes,, Microbial enzymes and genes
Citation
Salam, L. B. (2018). Detection of carbohydrate-active enzymes and genes in a spent engine oil-perturbed agricultural soil. Bulletin of the National Research Centre, 42(1). doi:10.1186/s42269-018-0013-6