Conjugation-dependent "gene drives" harness indigenous bacteria for bioremediation

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 E.coli led to degradation rates of 60-99% of target hydrocarbon substrates. Mating experiments, fluorescence microscopy and TEM revealed indigenous bacteria could obtain these vectors from E.coli through conjugation. Inoculating petroleum-polluted sediments from a former refinery with engineered E.coli showed that the E.coli die after five days but a variety of bacteria received and carried the vector for over 120 days after inoculation. This approach could prime indigenous bacteria for degrading pollutants while providing minimal ecosystem disturbance.