Genetic diversity of dioxygenase genes in polycyclic aromatic hydrocarbon-degrading bacteria isolated from mangrove sediments.
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.
Zhou
Hong Wei
HW
Department of Biology and Chemistry, City University of Hong Kong, Hong Kong SAR, China.
Guo
Chu Ling
CL
Wong
Yuk Shan
YS
Tam
Nora Fung Yee
NF
D001419:Bacteria / Q000145:classification / Q000201:enzymology / Q000235:genetics* / Q000302:isolation & purification*; D001673:Biodegradation, Environmental; D004275:DNA, Ribosomal / Q000235:genetics; D049308:Dioxygenases / Q000235:genetics*; D017753:Ecosystem; D014644:Genetic Variation; D019015:Geologic Sediments / Q000382:microbiology*; D008969:Molecular Sequence Data; D010802:Phylogeny; D011084:Polycyclic Aromatic Hydrocarbons / Q000378:metabolism*; D016133:Polymerase Chain Reaction / Q000379:methods; D012336:RNA, Ribosomal, 16S / Q000235:genetics
D004275:DNA, Ribosomal; D011084:Polycyclic Aromatic Hydrocarbons; D012336:RNA, Ribosomal, 16S; D049308:Dioxygenases