Several distinct naphthalene dioxygenases have been characterized to date, which provides the opportunity to investigate the ecological significance, relative distribution, and transmission modes of the different analogs. In this study, we showed that a group of naphthalene-degrading isolates from a polycyclic aromatic hydrocarbon (PAH)-contaminated hillside soil were phenotypically and genotypically distinct from naphthalenedegrading organisms isolated from adjacent, more highly contaminated seep sediments. Mineralization of 14 C-labeled naphthalene by soil slurries suggested that the in situ seep community was more acclimated to PAHs than was the in situ hillside community. phnAc-like genes were present in diverse naphthalene-degrading isolates cultured from the hillside soil, while nahAc-like genes were found only among isolates cultured from the seep sediments. The presence of a highly conserved nahAc allele among gram-negative isolates from the coal tar-contaminated seep area provided evidence for in situ horizontal gene transfer and was reported previously (J. B. Herrick, K. G. Stuart-Keil, W. C. Ghiorse, and E. L. Madsen, Appl. Environ. Microbiol. 63:2330-2337, 1997). Natural horizontal transfer of the phnAc sequence was also suggested by a comparison of the phnAc and 16S ribosomal DNA sequences of the hillside isolates. Analysis of metabolites produced by cell suspensions and patterns of amplicons produced by PCR analysis suggested both genetic and metabolic diversity among the naphthalene-degrading isolates of the contaminated hillside. These results provide new insights into the distribution, diversity, and transfer of phnAc alleles and increase our understanding of the acclimation of microbial communities to pollutants.The biochemical, enzymatic, and genetic details of microbial naphthalene degradation have been examined extensively since the early description in 1964 of a naphthalene metabolic pathway in Pseudomonas (9). Studies of naphthalene degradation are significant for at least four reasons: (i) naphthalene's aromatic character poses unique biochemical challenges for enzymatic attack (24, 67); (ii) naphthalene is a common pollutant that serves as a chemical model for the degradation of polycyclic aromatic hydrocarbons (PAHs) (56), which are often carcinogenic (49); (iii) insights are provided into the behavior of catabolic plasmids, the lateral transfer of genetic information among bacteria, and the evolution of oxygenase genes and enzymes (19,22,51,59,60,63); and (iv) our abilities to effectively manage and treat polluted environments and to engineer novel enzymes for new technologies are increased (15,48).In all pure cultures of naphthalene-mineralizing bacteria that have been examined, the aerobic metabolism of naphthalene is initiated by a multicomponent enzyme system called naphthalene dioxygenase (NDO) (EC 1.14.12.12) (56). The NDO of Pseudomonas putida NCIB 9816-4 has been studied comprehensively and shown to be a three-component dioxygenase. Electrons from NAD(P)H are transferred via re...