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Bringing Remediation into Focus

Gene-Trac® Digital Arrays use state-of-the-art digital polymerase chain reaction (dPCR) to co-quantify multiple microbes or functional gene targets at your site.

Available Gene-Trac® Digital Arrays

Gene-Trac® Digital Arrays quantify a wide range of microorganisms providing valuable insights for developing and optimizing remediation strategies. See below for information on available Gene-Trac Digital Arrays and the specific microbial processes that are targeted.

Clip of a draw to a QuantStudio Absolute Q Digital PCR System opening

Digital PCR: The Evolution of Gene-Trac® Testing

Gene-Trac® Digital Arrays use a new technology called digital polymerase chain reaction (dPCR), to enumerate numerous microbial targets in many matrices including soil, sediment, groundwater, mine tailings, and wastewater. Gene-Trac® Digital Arrays give environmental professionals the confidence they need to make critical site management decisions and provides compelling evidence of bioremediation success.

SiREM worker testing samples in the lab.

  • Even greater accuracy and precision

    Because dPCR does not calibrate to external standards, it provides more accurate, absolute quantification. Also, dPCR’s high precision makes it easier to detect quantitative changes in microbial communities.

  • Greater resistance to PCR inhibition

    A small percentage of environmental samples impart matrix interference that can low-bias qPCR results. Because the potential for matrix interference is reduced with dPCR, more accurate results for these samples can be obtained.

  • Increased Value for Money

    With dPCR, more tests can be performed on a single extraction, and multiple gene targets can be analyzed per reaction, providing more data at a lower cost per test.

Ready to get started?

Contact SiREM for a quote or to order Gene-Trac® sampling supplies.

Documentation

KB-1 Trac Cut Sheet

Dechlor Array Cut Sheet

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KB-1 Trac

Multi-target Monitoring for KB-1® Bioaugmented Sites

Bioaugmentation with the KB-1® culture promotes complete biodegradation of chlorinated ethenes to non-toxic ethene. Leveraging leading-edge digital PCR technology KB-1 Trac, is an 8-target Gene-Trac® Digital Array used to evaluate and optimize KB-1® bioaugmentation by quantifying multiple KB-1® microbes and functional genes. KB-1 Trac increases the practitioner’s ability to monitor and manage bioaugmented systems.

KB-1 Trac is also a useful tool for general purpose monitoring of reductive dechlorination sites, as the targeted microbes and functional genes can be naturally present, even without bioaugmentation.

Use KB-1 Trac to:

  • Confirm bioaugmentation success, track the introduction and colonization of multiple KB-1® microbes;

  • Differentiate Dehalococcoides (Dhc) strains with unique dechlorination capabilities which may be dominant at different stages of remediation;

  • Quantify dechlorinating Geobacter that enhances DNAPL dissolution when growing in PCE and TCE source areas;

  • Quantify the potential for the Dhc population to fix nitrogen to assess impacts of nutrient limitations and if nitrogen amendment could enhance dechlorination rates;

  • Quantify Acetobacterium, a Dhc partner that produces vitamin B12, an essential nutrient for Dhc growth;

  • Quantify total microbial biomass to assess the impact of biostimulation and overall microbial growth.
KB-1 Trac data demonstrating quantification of key microbes and functional genes in the KB-1 culture

KB-1 Trac Targets

Test ID Gene Target Relevance
DHCD Dehalococcoides (Dhc) 16S rRNA PCE, TCE, DCE, VC, & 1,2-DCA, chlorobenzenes, PCBs
TCEAD Trichloroethene reductase (tceA) TCE, cDCE, 1,1-DCE to VC
VCRAD VC reductase (vcrA) cDCE 1,1-DCE & VC to ethene
BVCAD VC reductase (bvcA) cDCE, 1,1-DCE, tDCE, VC & 1,2-DCA to ethene
DPCE Dhc tetrachloroethene reductase (pceA) PCE & TCE, 2,3-dichlorophenol
GPCE Geobacter pceA reductase PCE and TCE to cDCE, enhanced DNAPL dissolution
AB12 Acetobacterium KB-1 16S rRNA Produces vitamin B12, essential for Dhc growth
NIFD Nitrogenase (nifD) Nitrogen fixation
PROK Bacteria and Archaea 16S rRNA Measure of total microbial biomass

Dechlor-Array

Multi-target Monitoring for Sites with Chlorinated Compounds

A 32-target Gene-Trac® Digital Array, Dechlor-Array quantifies biodegradation pathways for a wide range of chlorinated compounds. Dechlor-Array uses digital PCR to accurately and sensitively quantify microbes and functional genes that are critical in reductive, aerobic, and biogeochemical dechlorination. Compared to testing platforms providing fewer targets, Dechlor-Array provides site managers with the data they need to make better-informed decisions and optimize remediation strategies at chlorinated solvent sites.

Use Dechlor Array to:

  • Quantify aerobic and anaerobic biodegradation potential for multiple contaminant classes, including chlorinated ethenes, ethanes, methanes, benzenes, propanes, and PCBs plus 1,4-dioxane.
  • Characterize biogeochemical, cometabolic, and other pathways impacting dechlorination, including sulfate reduction, methanogenesis, iron reduction, and nitrogen fixation.
  • Assess multiple pathways as a line of evidence for monitored natural attenuation and understand microbial community shifts caused by enhanced bioremediation or other changes at a site.
Dechlorination-Array pathways graph

Dechlor-Array pathways graph provides an easy-to-interpret summary of dechlorination potential for a range of contaminants and biodegradation pathways.

Dechlor-Array Targets

Reductive Dechlorination

Test ID Gene Target Relevance/Compounds Dechlorinated
DHCD Dehalococcoides (Dhc) 16S rRNA PCE, TCE, DCE, VC, & 1,2-DCA, chlorobenzenes, PCBs
DPCE Dhc tetrachloroethene reductase (pceA) PCE & TCE, 2,3-dichlorophenol
TCEAD Trichloroethene reductase (tceA) TCE, cDCE, 1,1-DCE to VC
VCRAD VC reductase (vcrA) cDCE 1,1-DCE & VC to ethene
BVCAD VC reductase (bvcA) cDCE, 1,1-DCE, tDCE, VC & 1,2-DCA to ethene
CBRA Chlorobenzene reductase (cbrA) Tri/tetrachlorobenzenes
MBRA Reductive dehalogenase (mbrA) PCE, TCE to tDCE, cDCE/some PCBs
NIFD Nitrogenase (nifD) Nitrogen fixation
DHGD Dehalogenimonas 16S rRNA Chloropropanes, Chloroethenes, 1,2 DCA
TDRA trans-DCE reductase (tdrA) tDCE to ethene
CERAD VC reductase (cerA) VC to ethene
DHBD Dehalobacter 16S rRNA Chlorinated ethenes, ethanes, methanes
CFRAD Chloroform reductase (cfrA) 1,1,1-TCA to 1,1-DCA and CF to DCM
TCBA Tetra/Trichlorobenzene reductase (tcbA/pceA) Chlorobenzenes also PCE to cDCE
DCA 1,2-DCA reductase (dcaA) 1,2-DCA to ethene
DCRA 1,1-DCA reductase (dcrA) 1,1-DCA to chloroethane
DSBD Desulfitobacterium 16S rRNA PCE and TCE to cDCE, some chlorophenols
DSMD Desulfuromonas 16S rRNA PCE and TCE to cDCE
SSPD Sulfurospirillum 16S rRNA PCE to cDCE, enhanced DNAPL dissolution
GEOD Geobacterales 16S rRNA PCE and TCE, FeS biogeochemical pathways, enhanced DNAPL dissolution
GPCE Geobacter pceA reductase PCE and TCE to cDCE, enhanced DNAPL dissolution
DHBMD Dehalobium 16S rRNA PCBs, Chlorobenzenes
MECE Methylene chloride catabolism cassette (mecE) DCM fermentation to VFAs
DCPA Chloropropane reductase (dcpA) 1,2-DCP to propene

Aerobic Degradation

Test ID Gene Target Relevance/Compounds Dechlorinated
POLD Polaromonas JS666 Isocitrate lyase Aerobic cDCE degradation
ETNCD Alkene monooxygenase (etnC) Aerobic degradation of VC & ethene
ETNED Epoxyalkane:Coenzyme M Transferase (etnE) Aerobic degradation of VC & ethene
DHLAD Haloalkane dehalogenase (dhlA) Aerobic 1,2-DCA degradation
TCBAB Trichlorobenzene dioxygenase (tcbAB) Aerobic CB (<4 chlorines), including 1,2,4,5 tetra and 1,2,4-TCB
DXMBD 1,4-dioxane monooxygenase (dxmB) Aerobic degradation of 1,4-dioxane

Microbial Groups

Test ID Gene Target Relevance
SRBD Sulfate reducing bacteria (dsrA) Sulfate reduction, FeS biogeochemical pathways for chlorinated solvents
MTHD Methanogens 16S rRNA Methane production, anaerobic cometabolic pathways for TCE
PROK Bacteria and Archaea 16S rRNA Measure of total microbial biomass

Ready to get started?

Contact SiREM for a quote or to order Gene-Trac® sampling supplies.

Documentation

KB-1 Trac Cut Sheet

Dechlor Array Cut Sheet

SiREM worker testing samples in the lab.