Horizontal ‘gene drives’ harness indigenous bacteria for bioremediation

Abstract

Engineering bacteria to clean-up oil spills is rapidly advancing but faces regulatory hurdles and environmental concerns. Here, we develop a new technology to harness indigenous soil microbial communities for bioremediation by flooding local populations with catabolic genes for petroleum hydrocarbon degradation. Overexpressing three enzymes (almA, xylE, p450cam) in Escherichia coli led to degradation of 60–99% of target hydrocarbon substrates. Mating experiments, fluorescence microscopy and TEM revealed indigenous bacteria could obtain these vectors from E. coli through several mechanisms of horizontal gene transfer (HGT), including conjugation and cytoplasmic exchange through nanotubes. Inoculating petroleum-polluted sediments with E. coli carrying the vector pSF-OXB15-p450camfusion showed that the E. coli cells died after five days but a variety of bacteria received and carried the vector for over 60 days after inoculation. Within 60 days, the total petroleum hydrocarbon content of the polluted soil was reduced by 46%. Pilot experiments show that vectors only persist in indigenous populations when under selection pressure, disappearing when this carbon source is removed. This approach to remediation could prime indigenous bacteria for degrading pollutants while providing minimal ecosystem disturbance.

Recent Advanced Technologies for the Characterization of Xenobiotic-Degrading Microorganisms and Microbial Communities

“…Moreover, microbial plasmids believed to be responsible for the continuous progression, evolution, and distribution of novel biodegradable genes/enzymes (Zhang et al, 2016 ; Jeffries et al, 2019 ). These novel genes/enzymes have endowed microorganism's biodegradation capability to remove or detoxify a wide variety of environmental pollutants due to their inheritance horizontal gene transfer property (Singh V. et al, 2018 ; Jaiswal et al, 2019 ; Li et al, 2019 ; Phale et al, 2019 ; French et al, 2020 ). The microbial remediation process can be further improved via successful application of genome editing and biochemical techniques that modify existing strains and result in the development of a genetically modified organism capable of simultaneously degrading several xenobiotics (Shanker et al, 2011 ; Zhang et al, 2016 ; Hussain et al, 2018 ; Janssen and Stucki, 2020 ).…”

Microbial Biocontainment Systems for Clinical, Agricultural, and Industrial Applications

“…Nonetheless, some studies have shown that bacterial vectors can be used for the delivery of plasmids to the microbiota found in contaminated soil; this enhances the rate at which plasmidencoded enzymes can digest petroleum hydrocarbons. Once the carbon source is removed, the plasmids disappear, most likely because they no longer provide a selective advantage (French et al, 2020). This represents a promising strategy for removing contaminants with minimal disturbance to the environment.…”

Laccases—Versatile Enzymes Used to Reduce Environmental Pollution

“…Although they are efficient, there are some factors such as the ecological characteristics that can influence the degradation process outcome. Additionally, bioremediation studies presented the potential for and capability of microorganism biodegradability when having to deal with a large number of environmental contaminants, all because of the mutagenesis processes [113][114][115][116]. In Figure 12, the chemical structures of various xenobiotic compounds are presented.…”