A new bacterial strain that is capable of in situ biodegradation of the major environmental pollutant naphthalene has been identified.

Biogeochemical cycling, the cycling of elements from the Earth's surface to the atmosphere and back again, is driven by microorganisms. However, the complex nature of natural environments means that the identification of the specific microorganisms responsible for a particular biogeochemical process in situ is extremely problematic. Now, Eugene Madsen and colleagues have carried out the first contaminated-field-based trials of a technique known as stable isotope probing (SIP), which enables researchers to follow the flow of labelled carbon atoms from a substrate — in this case naphthalene — into the DNA of naturally occurring microbial populations.

At a coal-tar waste disposal site that was contaminated with naphthalene and other aromatic hydrocarbons 40 years ago, 13C-labelled naphthalene was released into surface sediments and the presence of naphthalene-degrading bacteria was confirmed by monitoring the generation of 13C-labelled CO2. The DNA was extracted from the treated sediment and the 13C-labelled DNA fraction was isolated using a CsCl gradient and was then used to create a 16S ribosomal RNA (rRNA) clone library. Phylogenetic analysis of the library showed that most of the clones isolated from the sediment were clustered in a group containing β-proteobacterial species, including Acidovorax and Variovorax.

Of the 92 rRNA clones isolated from the contaminated soil, 46 were identical. Serial dilutions of the contaminated soil were grown on a mineral salts medium in the presence and absence of naphthalene vapours. The naphthalene-degrading bacterium was identified as a new strain, Polaromonas naphthalenivorans strain CJ2. Genetic analysis revealed that strain CJ2 contains the 16S rRNA gene that was identified in the clone library. It also revealed that strain CJ2 contains a novel naphthalene dioxygenase gene that had been identified in environmental samples, but for which the bacterial 'host' has been unknown until now.

This work proves that SIP can be used in the field to detect the in situ metabolism of environmental pollutants. Researchers hope that the same technique can be applied to identify other useful bacteria in contaminated sediments, such as those that metabolize the carcinogenic derivatives of naphthalene, the polycyclic aromatic hydrocarbons.