Genetic diversity of dioxygenase genes in polycyclic aromatic hydrocarbon-degrading bacteria isolated from mangrove sediments

Abstract

To investigate the diversity of dioxygenase genes involved in polycyclic aromatic hydrocarbon (PAH)-degradation, a total of 32 bacterial strains were isolated from surface mangrove sediments, from the genera Mycobacterium, Sphingomonas, Terrabacter, Sphingopyxis, Sphingobium and Rhodococcus. Two sets of PCR primers were constructed to detect the nidA-like and nahAc-like sequences of the alpha subunit of the PAH ring-hydroxylating dioxygenase. PCR amplified the DNA fragments from all Gram-positive bacteria by using nidA-like primers and from all Gram-negative bacteria, except two, by using nahAc-like primers. The nidA-like primers showed three subtypes of nidA-like gene: (i) fadA1, clustering with nidA3 from M. vanbaalenii PYR-1, (ii) nidA, clustering with nidA from PYR-1, and (iii) fadA2 clustering with dioxygenase from Arthrobacter sp. FB24. The amplicons detected by nahAc-like primers had high sequence homologies to phnA1a from Sphingomonas sp. CHY-1 and were amplifiable from 8 of the 16 Gram-negative isolates. The primer also generated amplicons that had a 32-36% similarity to phnA1a and 53-93% identity to p-cumate dioxygenase. These results suggest that the nidA-like and nahAc-like genes are prevalent in the PAH-degrading bacteria and that they are useful for determining the presence of PAH-dioxygenase genes in environmental samples.

Dynamics of the Linuron HydrolaselibAGene Pool Size in Response to Linuron Application and Environmental Perturbations in Agricultural Soil and On-Farm Biopurification Systems

“…Alternative qPCR techniques, such as a TaqMan-based approach, do not result in a lower detection limit (3). Examples of catabolic functional gene detection in environmental samples by PCR are manifold (13,16,29,30), but qPCR approaches have only been reported for a few of them (2,3,11,15,27). The target genes are often involved in the degradation of aromatic hydrocarbons.…”

Comparison of the Specificities and Efficacies of Primers for Aromatic Dioxygenase Gene Analysis of Environmental Samples

“…The first class (class A) covers all five reference subclades. (DP2 or Rieske_f [17] and Nah-for [26] primers showed especially high coverage of more than 100 genes [see Fig. S1 in the supplemental material].…”

Comparison of the Levels of Bacterial Diversity in Freshwater, Intertidal Wetland, and Marine Sediments by Using Millions of Illumina Tags

“…For instance, rhizospheric and sediment microbes are thought to be the major biological components that contribute to the productivity of intertidal mangrove ecosystems. Meanwhile, our group and others have isolated a large number of xenobiotic-degrading bacteria from intertidal wetland sediments (33,35). Nevertheless, microbial ecology studies mainly focus on sulfate-reducing bacteria from Deltaproteobacteria or other limited groups in intertidal sediments (1,21).…”