Succession of bacterial communities during petroleum degradation in bark compost as detected by small subunit ribosomal RNA gene profiles

Abstract

Bioremediation of crude oil was tested by hot bark composting, and the changes in microbial assemblages in the compost were monitored by polymerase chain reaction (PCR) and denaturing gradient gel electrophoresis of small subunit ribosomal RNA gene (16S rDNA) sequences. Most of the analyzed 16S rDNA sequences were unrelated to any cultured and known uncultured microorganisms. Only two compost-derived 16S rDNA sequences from a total of 16 were related to known sequences at similarities higher than 97%, viz., a species-level criterion. One sequence related to an uncultured soil bacterium, which was affiliated with the Cytophaga-Flavobacterium-Bacteroides group, was found throughout petroleum degradation; and the other sequence related to Chryseobacterium indoltheticum, a Cytophaga-Flavobacterium-Bacteroides species, was only found in association with the petroleum degradation. Despite relatively low similarities (< 97%), the rest of the compost-derived 16S rDNA sequences were mostly ascribed to CFB and spore-forming Firmicutes. In particular, four 16S rDNA sequences (out of a total of five) specific to petroleum degradation were affiliated with the Cytophaga-Flavobacterium-Bacteroides group, with the other one related to an uncultured bacterium from a deep aquifer. Many species of the Cytophaga-Flavobacterium-Bacteroides group are known for their ability to degrade diverse refractory substrates. Therefore, isolation and characterization of these compost-derived bacteria may facilitate bioremediation of oil spill in soil as well as aquatic environments.