Assessing <scp>BTEX</scp> Biodegradation Potential at a Refinery Using Molecular Biological Tools

Key, Katherine C.; Sublette, Kerry L.; Johannes, Tyler W.; Ogles, Dora; Baldwin, Brett R.; Biernacki, Anita

doi:10.1111/gwmr.12037

Cited by 8 publications

(5 citation statements)

References 55 publications

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“…DNA extraction from Bio-Sep beads (~160 beads per depth) was performed by Microbial Insights using established procedures. 28 Published primer sets and PCR conditions were used to amplify total bacterial, 29 Dhc, 30 Dhb, 31 Dehalogenimonas, 22 and Geobacter lovleyi strain SZ 32 16S rRNA genes, and dcpA encoding a 1,2-dichloropropane-to-propene RDase. 33 For increased sensitivity of detection, a nested PCR approach was applied 34 (see the Supporting Information for details).…”

Section: Methodsmentioning

confidence: 99%

“…DNA was extracted from 0.25 g of wet sediment using the MoBio PowerSoil DNA Isolation Kit (MO BIO, Carlsbad, CA). DNA extraction from Bio-Sep beads (∼160 beads per depth) was performed by Microbial Insights using established procedures . Published primer sets and PCR conditions were used to amplify total bacterial, Dhc , Dhb , Dehalogenimonas , and Geobacter lovleyi strain SZ 16S rRNA genes, and dcpA encoding a 1,2-dichloropropane-to-propene RDase .…”

Section: Methodsmentioning

confidence: 99%

See 1 more Smart Citation

Natural Attenuation in Streambed Sediment Receiving Chlorinated Solvents from Underlying Fracture Networks

Şimşir¹,

Yan

et al. 2017

Environ. Sci. Technol.

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Contaminant discharge from fractured bedrock formations remains a remediation challenge. We applied an integrated approach to assess the natural attenuation potential of sediment that forms the transition zone between upwelling groundwater from a chlorinated solvent-contaminated fractured bedrock aquifer and the receiving surface water. In situ measurements demonstrated that reductive dechlorination in the sediment attenuated chlorinated compounds before reaching the water column. Microcosms established with creek sediment or in situ incubated Bio-Sep beads degraded C-C chlorinated solvents to less-chlorinated or innocuous products. Quantitative PCR and 16S rRNA gene amplicon sequencing revealed the abundance and spatial distribution of known dechlorinator biomarker genes within the creek sediment and demonstrated that multiple dechlorinator populations degrading chlorinated C-C alkanes and alkenes co-inhabit the sediment. Phylogenetic classification of bacterial and archaeal sequences indicated a relatively uniform distribution over spatial (300 m horizontally) scale, but Dehalococcoides and Dehalobacter were more abundant in deeper sediment, where 5.7 ± 0.4 × 10 and 5.4 ± 0.9 × 10 16S rRNA gene copies per g of sediment, respectively, were measured. The microbiological and hydrogeological characterization demonstrated that microbial processes at the fractured bedrock-sediment interface were crucial for preventing contaminants reaching the water column, emphasizing the relevance of this critical zone environment for contaminant attenuation.

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Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Natural Attenuation in Streambed Sediment Receiving Chlorinated Solvents from Underlying Fracture Networks

Şimşir¹,

Yan

et al. 2017

Environ. Sci. Technol.

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“…RT-qPCR is a variation of qPCR, which can be used to quantify gene expression [i.e., messenger ribonucleic acids (mRNA)] indicative of biological activity. The occurrence of mRNA expressed from genes linked to biodegradation indicates that the associated contaminant-degrading microorganisms are metabolically active and carrying out biodegradation processes ( Wilson et al, 1999 ; Winderl et al, 2007 ; Bombach et al, 2010 ; Key et al, 2014 ; Bouchard et al, 2018 ; Lawson et al, 2019 ). While positive detections of mRNA transcripts in environmental samples can provide strong evidence of biodegradation occurrence, the absence of specific mRNA transcripts should not be interpreted to indicate that biodegradation activities are not occurring.…”

Section: Molecular Biological Tools To Assess Bioremediationmentioning

confidence: 99%

Framework for field-scale application of molecular biological tools to support natural and enhanced bioremediation

et al. 2022

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Microorganisms naturally present at environmental contaminated sites are capable of biodegrading, biotransforming, or removing contaminants in soil and groundwater through bioremediation processes. Cleanup strategies and goals for site remediation can be effectively achieved by bioremediation leveraging the capabilities of microorganisms to biotransform contaminants into lesser or non-toxic end products; however, reproducible success can be limited by inadequate design or performance monitoring. A group of biological analyses collectively termed molecular biological tools (MBTs) can be used to assess the contaminant-degrading capabilities and activities of microorganisms present in the environment and appropriately implement bioremediation approaches. While successful bioremediation has been demonstrated through previously described lab-scale studies and field-scale implementation for a variety of environmental contaminants, design and performance monitoring of bioremediation has often been limited to inferring biodegradation potential, occurrence, and pathways based on site geochemistry or lab-scale studies. Potential field-scale application of MBTs presents the opportunity to more precisely design and monitor site-specific bioremediation approaches. To promote standardization and successful implementation of bioremediation, a framework for field-scale application of MBTs within a multiple lines of evidence (MLOE) approach is presented. The framework consists of three stages: (i) “Assessment” to evaluate naturally occurring biogeochemical conditions and screen for potential applicability of bioremediation, (ii) “Design” to define a site-specific bioremediation approach and inform amendment selection, and (iii) “Performance Monitoring” to generate data to measure or infer bioremediation progress following implementation. This framework is introduced to synthesize the complexities of environmental microbiology and guide field-scale application of MBTs to assess bioremediation potential and inform site decision-making.

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“…Traditional design and implementation of bioremediation strategies, including enhanced bioremediation treatment technologies or monitored natural attenuation (MNA) strategies, rely on contaminant concentrations and spatiotemporal trends, field-scale geochemical data, and/or lab-scale biodegradation studies. While useful for remedial decision-making, these evaluations are largely indirect indicators of in situ microbial activity and bioremediation potential (Wiedemeier et al, 1999;Rittmann and McCarty, 2001;Key et al, 2014;Lawson et al, 2019). Additional insights can be gained through the fieldscale application of Molecular Biological Tools (MBTs) to analyze field samples and directly measure biomarkers (e.g., genes) associated with contaminant-degrading or transforming microorganisms and associated enzymes, which can vary spatially and temporally (Interstate Technology and Regulatory Council, 2013;Taggart and Clark, 2021).…”

Section: Introductionmentioning

confidence: 99%

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

et al. 2023

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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.

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Assessing BTEX Biodegradation Potential at a Refinery Using Molecular Biological Tools

Cited by 8 publications

References 55 publications

Natural Attenuation in Streambed Sediment Receiving Chlorinated Solvents from Underlying Fracture Networks

Natural Attenuation in Streambed Sediment Receiving Chlorinated Solvents from Underlying Fracture Networks

Framework for field-scale application of molecular biological tools to support natural and enhanced bioremediation

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

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