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) 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.
Gene-Trac® is used by environmental professionals to:
Gene-Trac® is used by environmental professionals to make site management decisions and to demonstrate bioremediation success.
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 Hydrocarbon 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 |
| ASSAU | Alkylsuccinate Synthase (assA aka masD) | Anaerobic alkane degradation |
| ASSAP | Alkylsuccinate Synthase (assA aka masD) from paraffin degrading culture | Anaerobic alkane degradation |
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 |
| 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 |
| UREC | Urease (ureC) | Hydrolysis of urea to ammonia |
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 |
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 generation sequencing of 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.