Analysis of catabolic genes for naphthalene and phenanthrene degradation in contaminated New Zealand soils

Abstract

Culture-dependent and culture-independent methods were used to investigate the diversity of three polycyclic aromatic hydrocarbon (PAH) catabolic genes in contaminated soils. PAH-degrading bacteria were isolated based on growth at the expense of naphthalene (44 isolates) or phenanthrene (35 isolates). Of these 79 PAH-degraders, 53% (42 isolates) failed to hybridise with three gene probes specific for PAH degradation. The gene for the naphthalene dioxygenase iron–sulfur protein (<it>nahAc</it>) from <it>Pseudomonas putida</it> G7 hybridised to 45% (20/44) of the culturable naphthalene-degrading bacteria of the ‘classical’<it>nah</it>-type, whilst analogues of the bacterial glutathione <it>S</it>-transferase (GST) encoding gene of <it>Sphingomonas paucimobilis</it> EPA505 were associated with culturable phenanthrene-degrading isolates and hybridised to 29% (10/35) of these isolates. Apart from the host strain <it>Burkholderia</it> RP007, we were not able to detect the <it>phnAc</it> gene amongst cultured isolates by hybridisation or PCR, though could directly amplify this gene from contaminated soils.