Molecular Genetic Testing

Gene-Trac® testing uses quantitative polymerase chain reaction (qPCR) or digital polymerase chain reaction (dPCR) to enumerate specific microbes or functional gene targets at your site.

Available Gene-Trac® Tests

SiREM offers a growing number of Gene-Trac® tests for a wide range of contaminants and remediation strategies. We regularly add new tests to provide our customers the tools they need for effective site characterization. See below for further information on available Gene-Trac® options for specific microbial processes and contaminant classes.

Gene-Trac® is a tool used by site managers to assess, optimize and monitor bioremediation and other microbial processes. To effectively understand biodegradation of contaminants such as chlorinated solvents, petroleum hydrocarbons, 1,4-dioxane, nitrogen compounds, and metals, it is critical to know which microorganisms and functional genes are present.

Gene-Trac® uses quantitative polymerase chain reaction (qPCR) or digital polymerase chain reaction (dPCR) to accurately enumerate critical microbial targets in many matrices including soil, sediment, groundwater, mine tailings, and wastewater. Gene-Trac® testing gives environmental professionals the confidence they need to make critical site management decisions and provides compelling evidence of bioremediation success.

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Leading in environmental molecular genetic testing
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Samples tested by SiREM from sites globally

Gene-Trac® is used by environmental professionals to:

  • Provide an important line of evidence for monitored natural attenuation (MNA) remedies
  • Understand how microbial communities vary across a site and over time.
  • Assess the need for enhanced in-situ bioremediation including biostimulation and bioaugmentation.
  • Optimize remediation by tracking the growth and spread of indigenous, or bioaugmented microbes, and making decisions based on that information.
  • Diagnose and address upset conditions in the subsurface that can hinder bioremediation performance.

Gene-Trac® is used by environmental professionals to make site management decisions and to demonstrate bioremediation success.

The Gene-Trac® Advantage:

  • Testing accredited to ISO/IEC 17025:2017 standard.

  • Clear and comprehensive reports that include detailed quality assurance data.
  • Electronic data deliverables available in various formats.
  • USA, Canadian, and European sample reception locations.
  • Field-filter protocols that reduce shipping costs and are ideal for use in remote locations.
  • Unparalleled technical support for planning, data analysis, and interpretation.

Ready to get started?

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

Available Gene-Trac® Tests

Chlorinated Ethenes Reductive Dechlorination

Gene-Trac®
Test ID
Gene Target Target Activity/Relevance
DHC Dehalococcoides 16S rRNA Dechlorination of PCE, TCE, all DCE isomers, VC
FGA-VCRA Dehalococcoides Vinyl Chloride Reductase A (vcrA) Dechlorination of cDCE and VC to ethene
FGA-BVCA Dehalococcoides BAV1 Vinyl Chloride Reductase A (bvcA) Dechlorination of cDCE and VC to ethene
FGA-TCEA Dehalococcoides Trichloroethene Reductase A (tceA) Dechlorination of PCE and TCE to cDCE and VC
DPCE Dehalococcoides PCE reductase (pceA) Dechlorination of PCE & TCE also 2,3-dichlorophenol
TDRA trans-DCE reductase (tdrA)  Dechlorination of tDCE to ethene
DHB Dehalobacter 16S rRNA Dechlorination of PCE and TCE to cDCE
DSM Desulfuromonas 16S rRNA Dechlorination of PCE and TCE to cDCE
DSB Desulfitobacterium 16S rRNA Dechlorination of PCE and TCE to cDCE
GEO Geobacter 16S rRNA Dechlorination of PCE to cDCE, biogeochemical  pathways
GPCE Geobacter PCE Reductive Dehalogenase (pceA) Dechlorination of PCE and TCE to cDCE, enhanced DNAPL dissolution
SSP Sulfurospirillum 16S rRNA Dechlorination of PCE to cDCE
DHGM Dehalogenimonas 16S rRNA Dechlorination of tDCE to VC and VC to ethene
CERA Dehalogenimonas Vinyl Chloride Reductase (cerA) Dechlorination of VC to ethene
MBRA Reductive Dehalogenase (mbrA) Dechlorination of PCE, TCE to tDCE & cDCE

Legend:

  • DCE – Dichloroethene
  • DNAPL – Dense nonaqueous phase liquid
  • PCE – Tetrachloroethene
  • TCE – Trichloroethene, c-cis, t-trans
  • VC – Vinyl chloride

Chlorinated Ethanes Reductive Dechlorination

Gene-Trac®
Test ID
Gene Target Target Activity/Relevance
DHB Dehalobacter 16S rRNA Dechlorination of CF to DCM and fermentation of DCM to VFAs
DCA 1,2-DCA reductase (dcaA) Dechlorination of 1,2-DCA to ethene
DCRA 1,1-DCA Reductase (dcrA) Dechlorination of 1,1-DCA to chloroethane
CFRA/DCRA CF Reductase (cfrA) and Dichloroethane Dehalogenase (dcrA) Dechlorination of 1,1,1-TCA and 1,1-DCA to chloroethane

Legend:

  • CF – Chloroform
  • DCA – Dichloroethane
  • TCA – Trichloroethane

Chlorinated Methanes Degradation

Gene-Trac®
Test ID
Gene Target Target Activity/Relevance
DHB Dehalobacter 16S rRNA Dechlorination of CF to DCM and fermentation of DCM to VFAs
CFRA/DCRA Chloroform Reductase (cfrA) Dechlorination of CF to DCM
MECE Methylene chloride catabolism cassette (mecE) Fermentation of DCM to VFAs

Legend:

  • CF – Chloroform
  • DCM – Dichloromethane
  • VFAs – Volatile fatty acids

Chlorinated Benzenes Degradation

Gene-Trac®
Test ID
Gene Target Target Activity/Relevance
CBRA Chlorobenzene reductase (cbrA) Dechlorination of tri/tetrachlorobenzenes
TCBA  Tetra/Trichlorobenzene Reductase (tcbA/pceA) Dechlorination of chlorobenzenes
TCBAB Trichlorobenzene Dioxygenase (tcbAb) Aerobic CB degradation (<4 chlorines) e.g., 1,2,4,5-TetraCB /1,2,4-TCB
DHB Dehalobacter 16S rRNA Dechlorination of 1,2,4,5-Tetra, 1,2,4-TCB, 1,2-DCB, and MCB
DHBM Dehalobium chlorocoercia 16S rRNA Dechlorination of hexachlorobenzene

Legend:

  • CB – Chlorobenzene
  • DCB – Dichlorobenzene
  • MCB – Monochlorobenzene
  • TCB – Trichlorobenzene

PCBs Reductive Dechlorination 

Gene-Trac®
Test ID
Gene Target Target Activity/Relevance
DHC Dehalococcoides 16S rRNA  Dhc PCB dechlorination includes Penta and Tetra PCBs
DHBM Dehalobium chlorocoercia 16S rRNA Dechlorination of hexachlorobenzene and PCBs
MBRA Reductive Dehalogenase (mbrA) Cometabolic dechlorination of Aroclor 1260 and 1254 

Legend:

  • PCB – Polychlorinated biphenyls

Chlorinated Propanes Reductive Dechlorination

Gene-Trac®
Test ID
Gene Target Target Activity/Relevance
DHGM Dehalogenimonas 16S rRNA  Dechlorination of 1,2,3-TCP to allyl chloride
DCPA Chloropropane reductase (dcpA) Dechlorination of 1,2-DCP to propene
DHC Dehalococcoides 16S rRNA Dechlorination of 1,2-DCP to propene

Legend:

  • DCP – Dichloropropane
  • TCP – Trichloropropane

Aerobic and Cometabolic Degradation of Chlorinated Compounds

Gene-Trac®
Test ID
Gene Target Target Activity/Relevance
PRMS Polaromonas JS666 Isocitrate Lyase Gene Dechlorination of cDCE
ETNE Epoxyalkane Transferase (etnE) Degradation of VC
ETNC Alkene Monooxygenase Alpha Subunit (etnC) Degradation of VC
DHLA Haloalkane Dehalogenase (dhlA) Dechlorination of 1,2-DCA by Xanthobacter
PMMO Particulate Methane Monooxygenase (pMMO) Co-oxidation of TCE in presence of methane
SMMO Soluble Methane Monooxygenase (sMMO) Co-metabolism of 1,1,1-TCA and 1,2-DCA by methanotrophs
PMO Propane Monooxygenase Co-metabolism of chloroethanes by propane utilizing bacteria

Legend:

  • DCA – Dichloroethane
  • DCE – Dichloroethene
  • TCA – Trichloroethane
  • TCE – Trichloroethene
  • VC – Vinyl chloride

Anaerobic BTEX Degradation

Gene-Trac®
Test ID
Gene Target Target Activity/Relevance
BNVX Candidatus Benzenivorax ORM2 16S rRNA Degradation of benzene: sulfate reducing/methanogenic conditions
Pepto-Ben Peptococcaceae 16S rRNA Degradation of benzene: nitrate reducing conditions
ABCA Benzene Carboxylase (abcA) Functional gene involved in benzene ring cleavage
BSSA Benzylsuccinate Synthase (bssA) Toluene biodegradation
BSS-DGG-T Benzylsuccinate Synthase (bssA) in DGG-T Culture Degradation of toluene /DGG-T bioaugmentation tracking
BSS-DGG-X Benzylsuccinate Synthase (bssA) in DGG-X Culture Degradation of xylene & toluene /DGG-X bioaugmentation tracking
DSP-DGG-T Desulfosporosinus 16S rRNA in DGG-T Culture Degradation of Toluene /DGG-T bioaugmentation tracking
PEP-DGG-X Peptococcaceae 16S rRNA in DGG-X Culture  Degradation of Xylene /DGG-X bioaugmentation tracking

 

Aerobic Hydrocarbon Degradation

Gene-Trac®
Test ID

Gene Target

Target Activity/Relevance

TMO

Toluene Monooxygenase

 Toluene oxidation

TDO

Toluene Dioxygenase (tobD)

 Toluene and benzene oxidation 

PHE

Phenol Monooxygenase

 Phenol hydroxylation to catechol

XMO

Xylene Monooxygenase

 Xylene and toluene oxidation

NDO

Naphthalene Dioxygenase (nahAc)

Naphthalene/other polycyclics degradation (< 3 rings)

CDO

Catechol 2,3-dioxygenase (C230)

Catechol central to BTX, phenol, and naphthalene metabolism

ASSA

Alkylsuccinate Synthase

Anaerobic alkane degradation

MTBE-PM1 Methylibium petroleiphilum strain PM1 16S rRNA Degradation of MTBE/TBA by M. petroleiphilum PM1
MTBE-HIBA HIBA Mutase (hcmA) Active on 2-HIBA in aerobic MTBE degradation pathway
MTBE-MDJP Tert-Butyl Alcohol (TBA) Hydroxylase (mdpJ) Oxidizes TBA-breakdown product of MTBE

Legend:

  • BTX – Benzene, toluene, and xylene
  • HIBA – Hydroxyisobutyryl-CoA
  • MTBE – Methyl tert-butyl ether
  • TBA – Tertiary butyl alcohol

1,4-Dioxane Aerobic Metabolic/Cometabolic Degradation 

Gene-Trac®
Test ID
Gene Target Target Activity/Relevance
14D-ALDH Aldehyde Dehydrogenase (ALDH) Energy-yielding degradation of 1,4-dioxane
14D-DXMB Dioxane Monooxygenase (dxmB) Energy-yielding degradation of 1,4-dioxane
SMMO Soluble Methane Monooxygenase (sMMO) Co-oxidation of 1,4-dioxane with methane
PMO Propane Monooxygenase Co-metabolism of 1,4-dioxane with propane

 

Nitrogen Compound Metabolism

Gene-Trac®
Test ID

Gene Target

Target Activity/Relevance

NIRK

Nitrite Reductase (nirK)

Denitrification of nitrite to nitric oxide

NIRS

Nitrite Reductase (nirS)

Denitrification of nitrite to nitric oxide

NOSZ

Nitrous Oxide Reductase (nosZ)

Denitrification of nitrous oxide to dinitrogen gas

DNRA

Nitrite Reductase (nrfA)

Dissimilatory nitrate reduction to ammonium

AMOA

Archaeal Ammonia Monooxygenase (amoA)

 Aerobic oxidation of ammonium to nitrate by archaea

AMOB

Bacterial Ammonia Monooxygenase (amoA)

 Aerobic oxidation of ammonium to nitrate by bacteria

NIBAC

Nitrobacter 16S rRNA

Aerobic oxidation of nitrite to nitrate

AMOX ANAMMOX Bacteria 16S rRNA Detects 5 genera of ANAMMOX bacteria
NIFD Dehalococcoides Nitrogenase (nifD) Fixation of nitrogen by some Dehalococcoides

Legend:

  • ANAMMOX – anaerobic ammonia oxidizing

Perchlorate Reduction

Gene-Trac®
Test ID
Gene Target Target Activity/Relevance
PCRA-AG Dechloromonas agitata Perchlorate Reductase (pcrA) Reduction of perchlorate to chlorate and chlorite
PCRA-AR Dechloromonas aromatica Perchlorate Reductase (pcrA) Reduction of perchlorate to chlorate and chlorite

Legend:

  • ANAMMOX – anaerobic ammonia oxidizing

Metals Metabolism

Gene-Trac®
Test ID
Gene Target Target Activity/Relevance
SERA Thauera selenatis Selenate Reductase (serA)  Reduction of selenate
SRDA Bacillus selenatarsenatis Selenate Reductase (srdA)  Reduction of selenate
YNFE Escherichia coli Selenate Reductase (ynfE) Reduction of selenate to selenium by Escherichia coli
SELDE Escherichia coli Selenophosphate Synthetase (selD) Signals selenium utilization by Escherichia coli
SELD Selenophosphate Synthetase Signals selenium utilization
HG-MERA Mercuric Reductase (merA) Conversion of Hg2+ to Hg0
GEO Geobacter 16S rRNA Iron Reduction Fe3+ to Fe2+

 

Legend:

  • Hg – Mercury
  • Fe – Iron

Sulfolane Degradation

Gene-Trac®
Test ID
Gene Target Target Activity/Relevance
SAR Sulfolane associated Rhodococcus 16S rRNA Degradation of sulfolane (or byproducts) by Rhodococcus

 

Microbial Groups

Gene-Trac®
Test ID
Gene Target Target Activity/Relevance
PROK Bacteria and Archaea 16S rRNA using Universal Primers Quantification of Bacteria and Archaea, measure of total biomass
ARC Archaea 16S rRNA Quantification of Archaea biomass
SRB  Sulfate Reducing Bacteria (dsrA) Chlorinated solvents biogeochemical pathways, hydrocarbon degradation
MCRA Methyl Coenzyme M Reductase (mcrA) Gene critical to final step in methanogenesis
SOXB Sulfur Oxidizing Bacteria (soxB) Important in acid mine drainage/microbially induced corrosion (MIC)
NGS Next gen.sequencing- Bacteria & Archaea 16S rRNA genes In depth characterization of microbial communities

 

If your target microbe or functional gene is not on our list of available tests, that’s no problem.
Gene-Trac® NGS provides non-targeted comprehensive microbial community characterization that is applicable to almost any microbial system. Also, SiREM routinely develops custom qPCR tests on request. See Custom Scientific Solutions or contact SiREM to learn about affordable custom test development options.

Ready to get started?

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