Open AccessDiversity of tfd C genes: distribution and polymorphism among 2,4‐dichlorophenoxyacetic acid degrading soil bacteria
Author(s) -
Cavalca Lucia,
Hartmann Alain,
Rouard Nadine,
Soulas Guy
Publication year - 1999
Publication title -
fems microbiology ecology
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.377
H-Index - 155
eISSN - 1574-6941
pISSN - 0168-6496
DOI - 10.1111/j.1574-6941.1999.tb00597.x
Subject(s) - biology , plasmid , genetics , ralstonia , gene , restriction fragment length polymorphism , genomic dna , sequence analysis , amplified ribosomal dna restriction analysis , phylogenetic tree , microbiology and biotechnology , polymerase chain reaction , ribosomal dna
Abstract The aim of the present work was to study the occurrence, distribution and diversity of 1,2‐dichlorocatechol dioxygenase genes among 2,4‐dichlorophenoxyacetic acid degrading bacteria. Phylogenetic relationships between the 31 strains or isolates were evaluated by amplified ribosomal DNA restriction analysis of the 16S rDNA gene. All the strains could be assigned to the β or γ subdivisions of the Proteobacteria. tfd C genes were detected by PCR amplification using degenerated primers. Two specific probes were produced from Ralstonia eutropha strain JMP134 and from a soil isolate strain PLAE6 which was grouped with Variovorax paradoxus . Sequence analysis of the probes revealed that they were homologous to the tfd C genes of JMP134 located on plasmid pJP4 and to the tfd C gene of Pseudomonas putida strain PaW85 located on plasmid pEST4011. The localization and the copy number of tfd C genes were determined by hybridization of plasmid profiles and genomic DNA restriction fragment length polymorphism profiles with the two probes. Most of the strains were found to bear tfd C genes on plasmids ranging from 78 to 532 kb; two strains without any plasmids were also found to hybridize with the probes, revealing a chromosomal localization of catabolic genes. Sequence analysis of the PCR products from different strains confirmed that four different classes of chlorocatechol 1,2‐dioxygenase genes were present in the strains and isolates studied.