Molecular characterization of autochthonous hydrocarbon utilizing bacteria in oil-polluted sites at Bodo Community, Ogoni land, Niger Delta, Nigeria

Abstract

Hydrocarbon utilizing bacteria in water, soil and sediment samples collected from crude oil-impacted sites at Bodo community, Ogoniland in the Niger Delta were isolated using Bushnell-Haas agar. Bacterial genera tentatively characterized were Bacillus, Corynebacterium, Enterobacter, Flavobacterium, Klebsiella, Micrococcus, Proteus, Pseudomonas and Serratia. A portion of the 16S ribosomal ribonucleic acid (16S rRNA) gene of the genomic DNA extracted from each bacterial isolate was amplified with polymerase chain reaction (PCR) using the universal primer set 27F: GAGTTTGATCCTGGCTCAG and 1492R: GGTTACCTTGTTACGACT. The PCR products (ca.1500bp) were cleaned up and sequenced with the ABI Big Dye version 3.1 kit on ABI 3730XL genetic analyzer. Electropherograms were inspected with Chromas Lite 2.01 while sequence identification was performed using GenBank’s BLAST algorithm. Sequence analysis revealed the presence of distinct known hydrocarbon degrading bacteria like Acinetobacter radioresistens strain Philippines-11, Alcaligenes sp. PAH- 43, Bacillus sp. UR2, Bacillus subtilis strain B7, Bacterium NLAE-zl-H221, Bacterium NLAE-zl-H156, Bacterium NLAE-zl-H231, Bacterium NLAE-zl-H84, Cedecea davisae isolate PSB5, Pantoea agglomerans strain T224 (formerly Enterobacter agglomerans), Proteus mirabilis strain SNB5, Proteus mirabilis strain NBRC 13300, Proteus mirabilis strain ALK418, Proteus penneri strain YCY34, Proteus mirabilis strain TL14C1, Proteus mirabilis strain 73, Proteus mirabilis strain SZH18, Proteus mirabilis strain CIFR1, Proteus hauseri strain ZMd44, Proteus vulgaris strain Knp3, Proteus mirabilis strain D27, Pseudomonas sp. G4 (2013) and Pseudomonas aeruginosa strain XM1. It is highly recommended that16S rRNA-gene-based techniques be used when studying the bacterial community diversity and dynamics in oil-polluted ecosystems in order to fully describe the active microorganisms involved in hydrocarbon degradation.

Keywords: Hydrocarbon utilizing bacteria; Bodo Ogoniland; 16S rRNA gene; PCR; GenBank.