Standardized Procedures for Use of Nucleic Acid-Based Tools
ER-1561
Objective
Current MBTs fail to differentiate field variability from sampling and analytical variability. This project will develop standardized techniques for nucleic acid-based analyses to improve site characterization, remedial design, performance monitoring, and technology validation.
The use of molecular biological tools (MBT) for detecting and quantifying biomarkers (e.g., specific nucleic acid sequences, peptides, proteins, and lipids) in environmental samples is rapidly increasing as remedial practitioners seek to improve the design, field performance, and monitoring of biologically based remediation technologies. While academic research facilities and several commercial entities have emerged in recent years to provide these MBT analyses, there are currently no standardized methods for collecting, preserving, transporting, storing, or processing environmental samples. These factors can potentially influence the results of MBT analyses significantly because biomarker integrity during the entire analytical process has not been established. A systematic evaluation of the factors affecting MBT data quality is required to improve the accuracy and reproducibility of these analyses. This evaluation will lead to the development of standardized sample collection and processing procedures to establish user confidence and widespread implementation of these powerful tools for enhanced site management.
Building on the results of ESTCP project ER-200518, the objective of this project is to obtain a fundamental understanding of the factors that affect how to optimize the quantification and interpretation of nucleic acid markers in groundwater samples and to use this information to build a foundation on which an Environmental Protection Agency (EPA) or equivalent standard method could be developed. Specific objectives include (1) elucidating the relationship between the concentration of nucleic acid-based biomarkers in environmental samples and the originating environment; (2) evaluating, quantifying, and documenting the impacts of sample collection, preservation, transport, storage, and processing on nucleic acid-based MBT analytical results; and (3) identifying surrogate biomarkers and developing internal standard approaches for the quantitative analyses of key target organisms (including Dehalococcoides).
Technical Approach
The project team will prepare an initial report that reviews the current status of nucleic acid-based MBT use and compiles and evaluates available information regarding current sample collection, handling, and processing techniques. Molecular techniques for analysis of environmental samples currently do not include surrogate standards or matrix spikes to quantify the efficiency of each analytical step. The team will identify and test suitable surrogate standards that will be used subsequently to conduct a systematic evaluation of the efficiencies of each step in the sequence of events taking place from sample collection to reporting biomarker concentrations. The team also will use a standard reference culture containing Dehalococcoides organisms along with the surrogate standards to systematically test factors that affect the quantification of Dehalococcoides (e.g., holding times, sampling methods, storage temperatures, matrix interferences, and preservation methods). The standard Dehalococcoides cultures/surrogates also will be required to address the relationship between true soil densities of Dehalococcoides and the corresponding biomarker concentrations in groundwater samples. Information will be documented and integrated from which a standard EPA or EPA equivalent methodologies for the analysis of nucleic acid biomarkers in groundwater samples can be derived.
Benefits
This project will provide a fundamental understanding necessary to create standardized techniques for collecting, handling, and processing environmental samples, and the reporting and interpreting of biomarker data. Standardized protocols will improve the accuracy and reproducibility of MBT data, build confidence in the approach, and ultimately provide the basis for science-based site management decisions that will improve the design, field performance, and monitoring of biologically based remediation technologies. In turn, this will produce cost savings for the Department of Defense. (Anticipated Project Completion – 2011)
Project Documents
Points of Contact
Principal Investigator
Ms. Carmen Lebr�n
Naval Facilities Engineering Command Engineering Service Center
Phone: 805-982-2907
Fax: 805-982-4304
Project Documents
Document Types
- Fact Sheet - Brief project summary with links to related documents and points of contact.
- Final Report - Comprehensive report for every completed SERDP and ESTCP project that contains all technical results.
- Cost & Performance Report - Overview of ESTCP demonstration activities, results, and conclusions, standardized to facilitate implementation decisions.
- Technical Report - Additional interim reports, laboratory reports, demonstration reports, and technology survey reports.
- Guidance - Instructional information on technical topics such as protocols and user’s guides.
- Workshop Report - Summary of workshop discussion and findings.
- Multimedia - On demand videos, animations, and webcasts highlighting featured initiatives or technologies.
- Model/Software - Computer programs and applications available for download.
- Database - Digitally organized collection of data available to search and access.