Enhanced plant-microbe remediation of PCBs in soil using enzyme modification technique combined with molecular docking and molecular dynamics

Abstract

The study on the enhanced mechanisms of the enzymes involved in plant absorption, plant degradation, and microbial mineralization in the remediation of soils contaminated with polychlorinated biphenyls (PCBs) is of great significance for the application of plant-microbe combined remediation technique in PCB-contaminated soils. The present study first used a combination of molecular docking and molecular dynamics methods to calculate the effects of the plant absorption enzyme, plant degradation enzyme, and microbial mineralization enzyme on the PCBs in the soil environment. A multifunctional plant degradation enzyme was constructed with three functional roles of absorption, degradation, and mineralization using amino acid sequence recombination and site-directed mutagenesis to modify the template of plant degradation enzyme. Finally, using the Taguchi experimental design-assisted molecular dynamics simulation method, the suitable external environmental conditions of plant-microbe combined remediation of the PCB-contaminated soil were determined. In total, six multifunctional plant degradation enzymes were designed, which exhibited a significantly improved efficiency of PCB degradation. In comparison to the complex of plant absorption enzyme, plant degradation enzyme, and microorganism mineralization enzyme (6QIM-3GZX-1B85), the six multifunctional plant degradation enzymes exhibited significantly higher efficiency (2.10–2.38 times) in degrading the PCBs, with a maximum of 2.69 times under suitable external environmental conditions.

Compositional, genetic and functional characterization of soil culturable microbial communities in polychlorinated dibenzo-p-dioxins/furans contaminated soil

“…Although the total N content of soil samples did not correlate with their level of contamination with dioxins, it is well worth noting that the highest polluted soil samples with PCDD/Fs had also the highest content of total nitrogen. This statement could be possibly supported by the high affinity of dioxin towards soil organic materials (Huyen et al, 2015;Li et al, 2021;Yuan et al, 2021).…”

“…Dioxins are extremely potent environmental toxins with proven toxicological effects in humans, animals, plants and microorganisms (Wu et al, 2002;Kong et al, 2018;Hanano et al, 2019a;Hanano et al, 2019b;González and Domingo, 2021;Hanano et al, 2021;Li et al, 2021;Sun et al, 2021). Nowadays, it is well known that the main pathway by which mammalians are exposed to dioxins is occurring via the consuming of dioxin-contaminated food, thus it is worth to avoid, as downstream as possible, these contaminants to go into the food chain.…”