Increasing in situ bioremediation effectiveness through field-scale application of molecular biological tools

Abstract

Leveraging the capabilities of microorganisms to reduce (degrade or transform) concentrations of pollutants in soil and groundwater can be a cost-effective, natural remedial approach to manage contaminated sites. Traditional design and implementation of bioremediation strategies consist of lab-scale biodegradation studies or collection of field-scale geochemical data to infer associated biological processes. While both lab-scale biodegradation studies and field-scale geochemical data are useful for remedial decision-making, additional insights can be gained through the application of Molecular Biological Tools (MBTs) to directly measure contaminant-degrading microorganisms and associated bioremediation processes. Field-scale application of a standardized framework pairing MBTs with traditional contaminant and geochemical analyses was successfully performed at two contaminated sites. At a site with trichloroethene (TCE) impacted groundwater, framework application informed design of an enhanced bioremediation approach. Baseline abundances of 16S rRNA genes for a genus of obligate organohalide-respiring bacteria (i.e., Dehalococcoides) were measured at low abundances (101–102 cells/mL) within the TCE source and plume areas. In combination with geochemical analyses, these data suggested that intrinsic biodegradation (i.e., reductive dechlorination) may be occurring, but activities were limited by electron donor availability. The framework was utilized to support development of a full-scale enhanced bioremediation design (i.e., electron donor addition) and to monitor remedial performance. Additionally, the framework was applied at a second site with residual petroleum hydrocarbon (PHC) impacted soils and groundwater. MBTs, specifically qPCR and 16S gene amplicon rRNA sequencing, were used to characterize intrinsic bioremediation mechanisms. Functional genes associated with anaerobic biodegradation of diesel components (e.g., naphthyl-2-methyl-succinate synthase, naphthalene carboxylase, alkylsuccinate synthase, and benzoyl coenzyme A reductase) were measured to be 2–3 orders of magnitude greater than unimpacted, background samples. Intrinsic bioremediation mechanisms were determined to be sufficient to achieve groundwater remediation objectives. Nonetheless, the framework was further utilized to assess that an enhanced bioremediation could be a successful remedial alternative or complement to source area treatment. While bioremediation of chlorinated solvents, PHCs, and other contaminants has been demonstrated to successfully reduce environmental risk and reach site goals, the application of field-scale MBT data in combination with contaminant and geochemical data analyses to design, implement, and monitor a site-specific bioremediation approach can result in more consistent remedy effectiveness.

Utilization of—Omic technologies in cold climate hydrocarbon bioremediation: a text-mining approach

“…Despite these promising findings, anaerobic HC degradation mechanisms in cold climates is understudied, this gap in the literature is likely due to the utility of biopiles for the degradation of hydrocarbons in these climates; slower contaminant oxidation rates and higher O 2 saturation in many cold climate soils are all factors which highly favor aerobic processes (Delille and Coulon, 2008;Whelan et al, 2015;Martínez Álvarez et al, 2017;van Dorst et al, 2021). In contrast, anaerobic processes are better studied in warmer climates where methanogens have been observed degrading HCs through fermentative processes (Liu et al, 2019;Madison et al, 2023). Enzymes such as naphthyl-2-methylsuccinate synthase, naphthalene carboxylase, alkyl succinate synthase, and benzoyl coenzyme A have been shown to be significantly upregulated in anaerobic HC contaminated soils (Liu et al, 2019;Madison et al, 2023).…”

“…In contrast, anaerobic processes are better studied in warmer climates where methanogens have been observed degrading HCs through fermentative processes (Liu et al, 2019;Madison et al, 2023). Enzymes such as naphthyl-2-methylsuccinate synthase, naphthalene carboxylase, alkyl succinate synthase, and benzoyl coenzyme A have been shown to be significantly upregulated in anaerobic HC contaminated soils (Liu et al, 2019;Madison et al, 2023). Many of these enzymes are associated with PAH degradation, offering a potential explanation for observations that these organisms outperform aerobic bacteria in degrading larger alkanes and PAHs (Cason et al, 2019;Liu et al, 2019;Madison et al, 2023).…”