ER1561 MBT Literature Search Text Final
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ER1561 MBT Literature Search Text Final
Strategic Environmental Research and Development Program (SERDP)AN OVERVIEW OF CURRENT APPROACHES AND METHODOLOGIES TO IMPROVE ACCURACY, DATA QUALITY ER1561 MBT Literature Search Text Final AND STANDARDIZATION OF ENVIRONMENTAL MICROBIAL QUANTITATIVE PCR METHODSProject ER-1561Prepared by:©SRNL UNAfEACỐS REMGeosyntec*•*consultants(••ding ỉo»nc*.l»ttaaq Sokrtkae*I KáentMt I30 January 2008 Version 1GeosyntecpconsultantsEXECUTIVE SUMMARYGroundwater and soil samples are frequently analyzed ER1561 MBT Literature Search Text Finalby academic and commercial organizations using molecular biological tools (MBTs) to detect unique genetic biomarkers associated with Deholococcoides (ER1561 MBT Literature Search Text Final
Dhc) and other environmentally relevant microorganisms. The results of these analyses are increasingly used by site owners, consultants and regulatorsStrategic Environmental Research and Development Program (SERDP)AN OVERVIEW OF CURRENT APPROACHES AND METHODOLOGIES TO IMPROVE ACCURACY, DATA QUALITY ER1561 MBT Literature Search Text Finalno standardized methods for collecting, preserving, transporting, storing, or processing groundwater samples for analysis. More importantly, the lack of standardized reference materials: a) prevents comparison of MBT results between laboratories and over time, b) makes confident assessment of the re ER1561 MBT Literature Search Text Finallationship between biodegradative microorganisms, such as Dhc, and remediation success a challenge, and c) obscures the impacts of sampling methodologER1561 MBT Literature Search Text Final
ies, detection of procedural errors, and other biases that affect the accuracy, precision and reproducibility of MBT analysis. Currently, there is litStrategic Environmental Research and Development Program (SERDP)AN OVERVIEW OF CURRENT APPROACHES AND METHODOLOGIES TO IMPROVE ACCURACY, DATA QUALITY ER1561 MBT Literature Search Text Final affecting MBT data quality is required to improve the accuracy and reproducibility of these analyses. This evaluation will lead to recommendations for standardization of sample collection and processing and analysis/reporting procedures to establish user confidence with the goal of increasing imple ER1561 MBT Literature Search Text Finalmentation of these powerful tools to enhance site management.The primary focus of SERDP Project number ER-1561 is the development of standardized procER1561 MBT Literature Search Text Final
edures for use in nucleic acid-based MBTs. Prior to embarking on developing these procedures, a literature review of the state-of-the-art of quantitatStrategic Environmental Research and Development Program (SERDP)AN OVERVIEW OF CURRENT APPROACHES AND METHODOLOGIES TO IMPROVE ACCURACY, DATA QUALITY ER1561 MBT Literature Search Text Finalojects team’s strategy and approach, and to identify additional promising approaches and technologies that could be incorporated as part of the research effort. Of particular interest was the evaluation of:i.Methods that are currently available and/or emeiging:ii.Quality assurance.'quality control ( ER1561 MBT Literature Search Text FinalQA/QC) procedures associated with these methods, specifically internal and reference standards;iii.Factors that affect sensitivity of the analysis, anER1561 MBT Literature Search Text Final
d the variability within/between methods;iv.The impact of field heterogeneity on MBT results and data interpretation; andV. Groundwater/soil sampling Strategic Environmental Research and Development Program (SERDP)AN OVERVIEW OF CURRENT APPROACHES AND METHODOLOGIES TO IMPROVE ACCURACY, DATA QUALITY ER1561 MBT Literature Search Text Finalher disciplines utilizing qPCR including theER1561iGeosyntec^consultantsmedical, agricultural/food, forensics, and environmental fields. In addition, ancillary topics such as sampling and biomass concentration from groundwater samples were reviewed. Methods and practices of the major commercial enti ER1561 MBT Literature Search Text Finalties providing qPCR testing of biorcmediation samples, specifically SiREM (www.siremlab.com) and Microbial Insights (www.microbc.com) were also reviewER1561 MBT Literature Search Text Final
ed.The review identified that unique challenges are associated with environmental remediation samples, with a locus on groundwaler, including lhe (X)lStrategic Environmental Research and Development Program (SERDP)AN OVERVIEW OF CURRENT APPROACHES AND METHODOLOGIES TO IMPROVE ACCURACY, DATA QUALITY ER1561 MBT Literature Search Text Finalce leading to 1’CR inhibition. Recommendations for assessing and addressing these challenges are provided and include the development of Dhc reference standards and internal microbial controls (i.e., microbial surrogates) Io: a) assess current approaches to sampling, shipping, storage, biomass conce ER1561 MBT Literature Search Text Finalntration, nucleic acid extraction, and data analysis/intcrprctation, and b) identify promising areas where methodological improvements may be requiredER1561 MBT Literature Search Text Final
. The following are highlights of the key findings, additional findings and further details are provided in the spec ific sections devoted to these toStrategic Environmental Research and Development Program (SERDP)AN OVERVIEW OF CURRENT APPROACHES AND METHODOLOGIES TO IMPROVE ACCURACY, DATA QUALITY ER1561 MBT Literature Search Text Finalo qPCR testing are well developed in disciplines such as pathogen detection, medical testing and forensics, but that the methods have not been fully applied to environmental testing.Specifically a certified Dhc reference culture is a prerequisite for:•Method validation and optimization;•Assessment o ER1561 MBT Literature Search Text Finalf inter laboratory variation;•Assessment of laboratory personnel; and•Assessing Dhc specific matrix effects.The review also indicated that the environER1561 MBT Literature Search Text Final
mental industry will benefit from the use of internal controls and microbial surrogates. Internal controls arc standards that arc added directly in knStrategic Environmental Research and Development Program (SERDP)AN OVERVIEW OF CURRENT APPROACHES AND METHODOLOGIES TO IMPROVE ACCURACY, DATA QUALITY ER1561 MBT Literature Search Text Finalnce. Microbial surrogates are whole cell internal process controls that are co-quantilied with the lest target (Dhc) and func tion to assess losses throughout the processing and analysis steps including:•incomplete biomass recovery; ER1561 MBT Literature Search Text FinalStrategic Environmental Research and Development Program (SERDP)AN OVERVIEW OF CURRENT APPROACHES AND METHODOLOGIES TO IMPROVE ACCURACY, DATA QUALITYGọi ngay
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