Table_1_Increasing in situ bioremediation effectiveness through field-scale application of molecular biological tools.DOCX

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.利用微生物的功能以降低（降解或转化）土壤与地下水中污染物的浓度，是一种兼具成本效益的自然修复手段，可用于管控受污染场地。传统生物修复策略的设计与实施，通常依托实验室规模的生物降解研究，或采集现场尺度的地球化学数据以推断相关生物过程。尽管实验室生物降解研究与现场地球化学数据均有助于修复决策，但借助分子生物学工具（Molecular Biological Tools, MBTs）直接检测污染物降解微生物及相关生物修复过程，可获得额外的关键见解。 一套将分子生物学工具与传统污染物及地球化学分析相结合的标准化框架，已在两处受污染场地成功完成现场尺度应用。在一处受三氯乙烯（trichloroethene, TCE）污染的地下水流场中，该框架的应用为强化生物修复方案的设计提供了依据。在三氯乙烯污染源头及羽流区域内，专性卤代呼吸细菌属（脱卤球菌属Dehalococcoides）的16S核糖体RNA基因（16S rRNA genes）的基线丰度处于较低水平（10¹–10² 细胞/毫升）。结合地球化学分析结果，这些数据表明可能存在原位生物降解（即还原性脱氯）过程，但电子供体的可用性限制了该过程的活性。该框架被用于支撑大规模强化生物修复方案的开发（即添加电子供体），并用于监测修复效果。 此外，该框架还应用于另一处受残留石油烃（petroleum hydrocarbon, PHC）污染的土壤与地下水场地。研究采用实时定量PCR（quantitative real-time PCR, qPCR）与16S核糖体RNA基因扩增子测序技术，表征了原位生物修复机制。针对柴油组分厌氧降解相关的功能基因（如萘基-2-甲基琥珀酸合酶、萘羧酸化酶、烷基琥珀酸合酶及苯甲酰辅酶A还原酶）的检测结果显示，其丰度较未受污染的背景样本高出2–3个数量级。经判定，原位生物修复机制足以满足地下水体修复目标。尽管如此，该框架仍被进一步用于评估强化生物修复可作为污染源头治理的有效替代方案或补充手段。 尽管针对氯化溶剂、石油烃及其他污染物的生物修复已被证实可有效降低环境风险并达成场地修复目标，但将现场尺度的分子生物学工具数据与污染物及地球化学数据分析相结合，用于设计、实施并监测针对特定场地的生物修复方案，可进一步提升修复效果的一致性。