Characterization of PAHs-degrading bacterium Porphyrobacter sp. D22F and its ecological niche in oil-degrading consortium D22-1

Abstract

In order to explore the diversity of microbial resources which could degrade polycyclic aromatic hydrocarbons (PAHs), and dominant species in oil-degrading consortium, the PAHs-degrading capability of strain D22F isolated from the sediment of South China Sea and its ecological niche in the oil-degrading consortium D22-1 were studied. Strain D22F was identified by 16S rRNA gene sequences homology analysis and transmission electron micrograph (TEM). The sphere and rate of PAHs degradation by stain D22F were determined by cultivation experiments and gas chromatography-mass spectrometry (GC-MS), respectively. The phnAc gene encoding the large subunit of PAHs dioxygenase was obtained by PCR amplification with degenerate primers and then analysed phylogenetically. Besides, the dominant species of oil-degrading consortium D22-1 was determined by denatured gradient gel electrophoresis (DGGE) analysis. The results indicated that strain D22F was closely related to type strain Porphyrobacter tepidarius DSM10594 T (AF465839), with 98.55% 16S rRNA gene similarity. It could degrade naphthalene, methylnaphthalene, acenaphthene, dibenzothiophene, phenanthrene and anthracene. Strain D22F was used to degrade phenanthrene (0.2 g/L) and the degradation efficiency was above 90% after ten days of incubation. The phnAc gene cloned from genome of strain D22F exhibited 99.41% similarity with the gene bphA //located on plasmid pNLl (CP000676) of Novosphingobium aromaticivorans DSM12444. Furthermore, DGGE analysis indicated that strain D22F was one of the three dominant species of oil-degrading consortium D22-1 and its abundance kept stable in the sequential subcultures. These research results suggested that strain D22F played an important role in ecological niche of oil-degrading consortium D22-1.