Metabolic gene analysis of newly isolated Pseudochrobactrum sp. BJQ-1 and BJQ-2 reveals global dissemination of the chlorothalonil hydrolytic dehalogenase chd gene

Abstract

Chlorothalonil (TPN; 2,4,5,6-tetrachloroisophthalonitrile) is a globally used, persistent chlorinated fungicide. Its bacterial detoxification is driven mainly by the hydrolytic dehalogenase Chd. Although the chd gene and its association with mobile genetic elements have been reported, the extent to which identical chd modules have spread across distinct hosts on a global scale remains unclear. Here we isolated two chlorothalonil-degrading strains, BJQ-1 and BJQ-2, from geographically distinct sites. Both were identified as Pseudochrobactrum spp. by 16S rRNA phylogeny. Shotgun cloning and sequence comparison revealed that both strains harbor a chd ORF essentially identical (≥99.7% nucleotide identity) to those of Pseudomonas sp. CTN series, Paracoccus sp. XF-3 and Ochrobactrum lupini TP-D1. The same chd gene is embedded in three distinct mobile-element configurations, an IS 21 -like composite transposon in CTN series, an IS 6 -family transposase TnpA plus Pin recombinase in BJQ-1, and a λ Rac-like invertase in BJQ-2, a pattern incompatible with vertical inheritance. Upstream spacer analysis showed that a conserved IS 21 -like fusion promoter, composed of an IRR-borne −35 box fused to the native −10 element of chd gene, and the 179-bp istB–chd intergenic spacer (100% identical between the BJQ isolates and the CTN series) are preserved. Mining of the Prokaryotic Genome dataset retrieved chd -like sequences from diverse prokaryotic genomes spanning soil, aquatic and plant-associated habitats, confirming a broad phylogeography of the cassette. The recovery of an identical, transposon-associated chd module from two distantly sampled Pseudochrobactrum strains, together with its global genomic distribution, indicates that the chd detoxification cassette has disseminated worldwide, providing a general mechanism for the rapid recruitment of TPN biodegradation capacity in microbial communities.