Formatted Title
Advancing a Novel Next-Generation, Sequencing-Based Metric for Optimizing Bioremediation Performance: Microbial Community Structure Index (MCSI)
Background/Objectives
While bioremediation is a proven technology for addressing halogenated volatile organic compounds (HVOCs), opportunities remain for further optimizing performance of both in situ and ex situ treatment technologies. The role of entire microbial ecosystems in remediation success is an underrecognized factor. Dehalococcoides are well known organohalide-respiring bacteria (OHRB) responsible for directly transforming contaminants. However, these OHRB grow in syntrophic relationships and require the support of other microbial community members to generate usable carbon sources (hydrogen and acetate), and produce cofactors and corrinoids. Recent advances in next generation gene sequencing present an opportunity to track entire microbial communities in situ and in bioreactors, and thus, gain an understanding regarding the health of microbial ecosystems. However, to date simple, useful metrics based on next generation sequencing data have been lacking to provide guidance for optimization of biodegradation performance.
Approach/Activities
Herein a novel metric termed Microbial Community Structure Index (MCSI) is advanced, which allows next generation sequencing data to be converted to a single MSCI ratio. The MSCI value is a summed relative abundance of all relevant microbial community members known, or found, to support OHRB activity, as a percent of the total microbial population. A list of relevant microbial community members, including 37 genera, were identified via literature and further refinement through examination of performance data at several field sites. Samples were collected for microbial analysis from groundwater wells with decreasing HVOC concentrations within background locations (i.e., native, unamended aquifer conditions where natural attenuation is monitored), emulsified vegetable oil (EVO) injection sites, and biogeochemical reactor (BGR) sites. DNA was extracted and 16S rRNA gene amplicon sequencing was conducted using Illumina by Microbial Insights. First-order biodegradation rates were computed using data originating from eight dissolved-phase HVOC plumes, including 27 groundwater wells, as well as multiple ex situ biogeochemical reactors. Rates were compared to standard quantitative Polymerase Chain Reaction (qPCR) assays targeting OHRB and specific enzyme-encoding genes (e.g., Dehalobacter and Desulfitobacterium, DCA reductase, soluble methane monooxygenase, and ethene monooxygenase genes) and to MSCI values.
Results/Lessons Learned
First-order degradation rate constants for the in situ locations ranged from 0.04 to 7.2 y-1, with an average of 0.81 y-1, while calculated first-order rate constants for the BGRs range from 37 and 581 y-1, with an average of 267 y-1. First-order degradation rates were found to not correlate with the relative abundance of OHRB. By contrast, there was a clear correlation (R2=0.58, p=9.2x10-9) between increasing MSCI metric and first-order degradation rates for in situ locations. For ex situ locations, MSCI values always exceeded 5%, and correlations were not observed, suggesting a threshold exists above which rates will not improve as key supporting microbial community members are not limiting. A case study at an emulsified vegetable oil injection pilot, demonstrated use of MSCI to correctly, and cost-effectively, troubleshoot a bioremediation stall, leading to a successful pilot.