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In the Niger Delta region of Nigeria, the major anthropogenic source of xenobiotics is petroleum based hydrocarbons. Studies suggest that hydrocarbon degradation genes with potential for bioremediation have a greater abundance at equatorial biomes. Therefore, the primary aim of this study was to establish the distribution of hydrocarbon utilizing genes and metabolic activities in different ecosystems in Eastern Obolo in the Niger Delta and correlate same with total petroleum hydrocarbons contents of these ecosystems. Samples were designated as 1 to 5 (two soil samples: 1 and 2), epipellic and benthic sediment samples (3 and 4), and estuary water (5) samples). Sample collection, determination of total petroleum hydrocarbon (TPH) contents and molecular analyses were all done using standard methods. Extracted DNAs from the various samples were then subjected to next generation sequencing on Miseq Illumina platform.
Gene calling was then performed on the assembled sequence reads using Frag Gene Scan to predict open reading frames (ORFs). The ORFS were then functionally annotated to various taxonomic groups using the Kyoto Encyclopedia of Genes and Genomes (KEGG) and Ghost KOALA databases. A total of 10 xenobiotics metabolisms were detected and these were amino benzoate and steroid degradation, phenylalanine metabolism, synthesis and degradation of ketones, fatty acid degradation, caprolactam, ethylbenezene, chloroalkane and chloroalkene, geraniol, and limonene and pinene degradations. Mean values of TPH (mg/L) ranged from 1.58 to 23.48 in the samples. Furthermore, sample 1 with the least TPH had no xenobiotics metabolism while sample 2 with the highest TPH had the highest number of xenobiotic metabolisms. Dioxygenase, monoxygenase, dehydrogenase and acyltransferase enzymes were the most commonly annotated genes in our samples. Annotated bacteria classes in decreasing order were Alphaproteobacteria > Firmicutes > Gammaproteobacteria > Betaproteobacteria. Correlation analysis between levels of TPH and various annotated metabolisms gave a significant (p < 0.05) and strong positive R2 value (> 0.90). The findings in this study indicate that TPH coupled with metagenomic assessment of xenobiotics metabolic activities is a better way of monitoring biodegradation capacity of an impacted ecosystem.