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Molecular MIC Diagnoses from ATP Field Test: Streamlined Workflow from Field to 16S Results

The ability to bundle the ATP MIC diagnostic assay with DNA acquisition for metagenomics would reduce the cost and labor intensity of DNA extraction, and alleviate complex sample storage and handling logistics - thus to substantially improve resultant molecular assay accuracy and accessibility. 

 

Product Number: 51317--9420-SG
ISBN: 9420 2017 CP
Author: Marc Demeter
Publication Date: 2017
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$20.00
$20.00

Microbiologically influenced corrosion (MIC) is a term used to describe corrosive damage to metals caused by microbes including bacteria archaea and fungi. MIC affects many industries such as power generation oil production transportation and water storage and distribution. The costs inferred by corrosion across all industrial sectors are staggering. As such monitoring for and diagnosing MIC as part of a complete corrosion mitigation strategy is of paramount importance.While culture based growth tests are the traditional means of assessing MIC their accuracy and reliability suffers greatly as a result of the inability to culture most microbes. Numerous culture-independent biochemical and genetics-based assays have been developed; one of which is the adenosine triphosphate (ATP)-based assay. Since ATP is present in all living cells extraction and quantification of ATP directly from an environmental sample allows for indirect enumeration of living microbes. ATP in dead cells rapidly decomposes. Although a valuable assay as it can be performed easily in the field the ATP-assay does not divulge which microbes are present.16S based DNA molecular assays are the preferred method for characterizing the microbial populations; however molecular assays have not yet been widely adopted as an MIC standard due to prohibitive costs and complex workflows that are not feasible in the field. Costs are decreasing as sequencer technologies improve however the need to minimize sample handling in the workflow is increasingly evident. Microbial communities including those from corrosion products are highly sensitive to changes in their environment and will undesirably change in composition as a result of sample storage transport and handling ultimately diminishing the quality of the knowledge gained from the molecular analysis of the community. Thus MIC diagnostic best-practices rely on field over laboratory testing when allowable; currently much of a 16S rDNA workflow must be performed in a laboratory by a trained professional including DNA extraction from environmental samples.Recently the presence of microbial DNA in various physical elements of the ATP assay were found. This observation led us to hypothesize that the ATP assay may hold added value as a method to acquire DNA for downstream molecular analyses. The ability to bundle the ATP MIC diagnostic assay with DNA acquisition for 16S profiling would be of great value to industry as it would reduce the costs and streamline the workflow associated with enumerating and identifying the microbes associated with corrosion products. Moreover as the ATP assay can be conducted in the field DNA for molecular analysis could in theory be collected in the field as well which would minimize handling and storage related sample deterioration – once extracted DNA is relatively stable. This paper presents work done on combining both ATP and 16S molecular strategies into a single product/workflow.

Key words: MIC, ATP, 16S rRNA, gene sequencing, culture media, workflow, field metagenomics.

Microbiologically influenced corrosion (MIC) is a term used to describe corrosive damage to metals caused by microbes including bacteria archaea and fungi. MIC affects many industries such as power generation oil production transportation and water storage and distribution. The costs inferred by corrosion across all industrial sectors are staggering. As such monitoring for and diagnosing MIC as part of a complete corrosion mitigation strategy is of paramount importance.While culture based growth tests are the traditional means of assessing MIC their accuracy and reliability suffers greatly as a result of the inability to culture most microbes. Numerous culture-independent biochemical and genetics-based assays have been developed; one of which is the adenosine triphosphate (ATP)-based assay. Since ATP is present in all living cells extraction and quantification of ATP directly from an environmental sample allows for indirect enumeration of living microbes. ATP in dead cells rapidly decomposes. Although a valuable assay as it can be performed easily in the field the ATP-assay does not divulge which microbes are present.16S based DNA molecular assays are the preferred method for characterizing the microbial populations; however molecular assays have not yet been widely adopted as an MIC standard due to prohibitive costs and complex workflows that are not feasible in the field. Costs are decreasing as sequencer technologies improve however the need to minimize sample handling in the workflow is increasingly evident. Microbial communities including those from corrosion products are highly sensitive to changes in their environment and will undesirably change in composition as a result of sample storage transport and handling ultimately diminishing the quality of the knowledge gained from the molecular analysis of the community. Thus MIC diagnostic best-practices rely on field over laboratory testing when allowable; currently much of a 16S rDNA workflow must be performed in a laboratory by a trained professional including DNA extraction from environmental samples.Recently the presence of microbial DNA in various physical elements of the ATP assay were found. This observation led us to hypothesize that the ATP assay may hold added value as a method to acquire DNA for downstream molecular analyses. The ability to bundle the ATP MIC diagnostic assay with DNA acquisition for 16S profiling would be of great value to industry as it would reduce the costs and streamline the workflow associated with enumerating and identifying the microbes associated with corrosion products. Moreover as the ATP assay can be conducted in the field DNA for molecular analysis could in theory be collected in the field as well which would minimize handling and storage related sample deterioration – once extracted DNA is relatively stable. This paper presents work done on combining both ATP and 16S molecular strategies into a single product/workflow.

Key words: MIC, ATP, 16S rRNA, gene sequencing, culture media, workflow, field metagenomics.

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