Biodegradation of DDT by Stenotrophomonas sp. DDT-1: Characterization and genome functional analysis

Abstract

A novel bacterium capable of utilizing 1,1,1-trichloro-2,2-bis(p-chlorophenyl)ethane (DDT) as the sole carbon and energy source was isolated from a contaminated soil which was identified as Stenotrophomonas sp. DDT-1 based on morphological characteristics, BIOLOG GN2 microplate profile, and 16S rDNA phylogeny. Genome sequencing and functional annotation of the isolate DDT-1 showed a 4,514,569 bp genome size, 66.92% GC content, 4,033 protein-coding genes, and 76 RNA genes including 8 rRNA genes. Totally, 2,807 protein-coding genes were assigned to Clusters of Orthologous Groups (COGs), and 1,601 protein-coding genes were mapped to Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway. The degradation half-lives of DDT increased with substrate concentration from 0.1 to 10.0 mg/l, whereas decreased with temperature from 15 °C to 35 °C. Neutral condition was the most favorable for DDT biodegradation. Based on genome annotation of DDT degradation genes and the metabolites detected by GC-MS, a mineralization pathway was proposed for DDT biodegradation in which it was orderly converted into DDE/DDD, DDMU, DDOH, and DDA via dechlorination, hydroxylation, and carboxylation, and ultimately mineralized to carbon dioxide. The results indicate that the isolate DDT-1 is a promising bacterial resource for the removal or detoxification of DDT residues in the environment.

GET_PHYLOMARKERS, a software package to select optimal orthologous clusters for phylogenomics and inferring pan-genome phylogenies, used for a critical geno-taxonomic revision of the genusStenotrophomonas

“…It groups the Brazilian rhizosphere-colonizing isolate JV3, the Chinese highly metal tolerant strain TD3 (Ge and Ge, 2016) and strain As1, isolated from the Asian malaria vector Anopheles stephensi (Hughes et al, 2016). The lineage Sm3 holds eight isolates of contrasting origin, including the Chinese soil isolate DDT-1, capable of using DDT as the sole source of carbon and energy (Pan et al, 2016), as well as clinical isolates like 1162_SMAL (Roach et al, 2015) and AU12-09, isolated from a vascular catheter (Zhang et al, 2013), and environmental isolates like SmF22, Sm32COP and SmSOFb1, isolated from different manures in France (Bodilis et al, 2016). Cluster Sm2 groups the S. pavanii strains, including the type strain DSM_25135 T , isolated from the stems of sugar cane in Brazil (Ramos et al, 2011), together with the clinical isolates ISMMS6 and ISMMS7, that carry mutations conferring quinolone resistance and causing bacteremia (Pak et al, 2015), and strain C11, recovered from pediatric cystic fibrosis patients (Ormerod et al, 2015).…”

Phytoremediation and Bioremediation of Pesticide-Contaminated Soil

“…The insecticide 1,1,1-trichloro-2,2-bis(p-chlorophenyl) ethane (DDT) is known to be persistent in the environment, and its use is banned in many locations [289]. However, it is still in use in Africa and India.…”

“…However, it is still in use in Africa and India. It has very low solubility in water, about 0.001 mg/L and is more soluble in lipids [289,290]. The log of the octanol/water partition coefficient is 7.48 [292].…”

“…DDT can be removed from soil and transported into alfalfa, rye grass and tall fescue also [139]. Pan et al [289] have reported their research to isolate a bacterium that biodegrades DDT and uses DDT as a carbon and energy source. The mineralization pathway is reported [289].…”

“…Pan et al [289] have reported their research to isolate a bacterium that biodegrades DDT and uses DDT as a carbon and energy source. The mineralization pathway is reported [289]. Nano-scale zero valent iron has been found to enhance the biodegradation rate of DDT [290].…”