Unraveling the secrets of microbiome reengineering for highly efficient bioremediation by artificial intelligence and metagenomics

  • Publication Date: 2021-02-10
Application Dept. Dept. of Environmental Engineering
Principal Investigator A.P. Shu-Chi Chang
Project Title Unraveling the secrets of microbiome reengineering for highly efficient bioremediation by artificial intelligence and metagenomics
Co-Principal Investigator
Co-Investigator
Abstract Trichloroethylene (TCE) was a widely-applied industrial solvents but now a notorious contaminant in groundwater. Due to the wave of green remediation, anaerobic reductive dechlorination was considered as a more sustainable remediation strategy for TCE-contaminated aquifer. However, the accumulation of toxic intermediates, cis-1,2-dichloroethene (cis-1,2-DCE) and vinyl chloride (VC), and longer remediation time are of high concerns. To accelerate the bioremediation, biostimulation and bioaugmentation have been developed for decades. The former may not be effective and the latter may introduce foreign genes. Here, we have developed a new approach, microbiome reengineering (MBRE), by heat selection of indigenous cultures and has achieved more than 70-folds improvement in TCE biodegradation rate. However, other major environmental variables have not been tested yet. Thus, in this study, we tested heat, pH, salinity, and desiccation by using Taguchi method. A full-length sequencing technology was applied to the 16S ribosomal RNA (rRNA) genes of all samples. The results showed that the optimum selecting conditions were 50ºC, pH 9, 100% sea water salinity, and 60% water content. In the batch test, group 7 (G7) and original culture (OC) performed best, and these two groups were selected to proceed a re-spike test. In this re-spike test, G7 have finished the complete conversion of TCE to ethene in three days, the fastest in the literature. In the 16S rRNA sequencing data, a new association was found of Dehalococcoides mccartyi with Desulfuromonas michiganensis and Cloacibacillus porcorum. Four environmental variables can enhance or inhibit different functions of the microbial community based on FAPROTAX function prediction and redundancy analysis also confirmed that all variables showed different directions that they can modify the structure of the community. These results suggested that MBRE could be an ideal approach for rapid bioremediation of TCE-contaminated aquifers.