Molecular Genetic Testing

Gene-Trac® testing uses quantitative polymerase chain reaction (qPCR) 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) 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.

0 Years
Leading in environmental molecular genetic testing
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

Test ID

Gene Target

Target Activity/Relevanc


Dehalococcoides 16S rRNA

Dechlorination of PCE, TCE, all DCE isomers, VC


Dehalococcoides Vinyl Chloride Reductase A (vcrA)

Dechlorination of cDCE and VC to ethene


Dehalococcoides BAV1 Vinyl Chloride Reductase A (bvcA)

Dechlorination of cDCE and VC to ethene


Dehalococcoides Trichloroethene Reductase A (tceA)

Dechlorination of PCE and TCE to cDCE and VC


Dehalococcoides PCE reductase (pceA)

Dechlorination of PCE & TCE also 2,3-dichlorophenol


trans-DCE reductase (tdrA)

 Dechlorination of tDCE to ethene


Dehalobacter 16S rRNA

Dechlorination of PCE and TCE to cDCE


Desulfuromonas 16S rRNA

Dechlorination of PCE and TCE to cDCE


Desulfitobacterium 16S rRNA

Dechlorination of PCE and TCE to cDCE


Geobacter 16S rRNA

Dechlorination of PCE to cDCE, biogeochemical  pathways


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

Aerobic Metabolism and Co-Metabolism of Chlorinated Solvents

Test ID Gene-Target Relevance
PRMS Polaromonas JS666 isocitrate lyase Aerobic degradation of cDCE
ETN Alkene monooxygenase (etnE) Aerobic degradation of VC and ethene by Myocobacterium and Nocardioides
Alkene monooxygenase (etnC)
DHLA Haloalkane dehalogenase (dhlA) Aerobic dechlorination of 1,2-DCA by Xanthobacter
PMMO Particulate methane monooxygenase Co-oxidation of 1,4-dioxane and TCE in presence of methane
SMMO Soluble methane monooxygenase Co-metabolism of chlorinated compounds by methanotrophs
PMO Propane monooxygenase Co-metabolism of chlorinated compounds by propanotrophs
CBDO Chlorobenzene dioxygenase Aerobic degradation of chlorobenzenes with fewer than four chlorines
TCBA Chlorinated benzene terminal dioxygenase (tcbAa) Aerobic chlorinated benzene degradation


  • DCE – Dichloroethene (C2H2Cl4)
  • VC – Vinyl chloride (C2H3Cl)
  • DCA – Dichloroethane (C2H4Cl2)
  • TCE – Trichloroethene (C2HCl3)

Anaerobic and Aerobic Hydrocarbon Degradation

Test ID Gene Target Relevance
Anaerobic Hydrocarbon Degradation
BNVX Candidatus Benzivorax ORM-2 16S rRNA Anaerobic benzene degrader under SO4/CH4 reducing conditions -benzene degrader in DGG-Plus culture
ABCA Benzene carboxylase (abcA) Anaerobic benzene degradation under nitrate reducing conditions
BSSA Benzylsuccinate synthase (bssA) Anaerobic toluene biodegradation
DSP-DGGT Desulfosporosinus 16S rRNA gene in DGG-T Culture Important in anaerobic toluene biodegradation, present in DGG-Plus culture
BSS-DGG-T Benzylsuccinate synthase (bssA) gene in DGG-T Culture Anaerobic toluene degradation, present in DGG-Plus bioaugmentation culture
PEP-DGG-X Peptococcaceae 16S rRNA in DGG-X Culture 16S rRNA gene of Peptococcaceae in Bioaugmentation culture DGG-X responsible for anaerobic xylene degradation
BSS-DGG-X Benzylsuccinate synthase (bssA) gene in DGG-X culture Anaerobic xylene/toluene degradation, present in DGG-Plus culture
SRB Sulfate reducing bacteria (SRB) dissimilatory sulfite reductase (dsrA) SRB are, syntrophic partners in anaerobic benzene degradation, anaerobic hydrocarbon degraders including BTEX, PAHs and alkanes and alkenes
MCRA Methyl-coenzyme M reductase (mcrA) in methanogenic Archaea Syntrophic partners in anaerobic benzene degradation and for hydrocarbon fermenters generally
GEO Geobacter 16S rRNA BTEX degraders under iron reducing conditions
Aerobic Hydrocarbon /MTBE Degradation
TMO Toluene monooxygenase Aerobic oxidation of toluene
TDO Toluene dioxygenase Degrades toluene and benzene by incorporating two oxygen molecules into the aromatic ring
PHMO Phenol monooxygenase Hydroxylates phenol to catechol which is subject to further degradation under aerobic and anaerobic conditions
XMO Xylene monooxygenase Degrades xylene and toluene by oxidizing methyl groups
NDO Naphthalene dioxygenase (nahAc) Catalyzes the first step in aerobic degradation of naphthalene, activity for other polycyclic compounds with less than three rings
MTBE Methylibium petroleiphilum strain PM1 16S rRNA Aerobic MTBE/TBA degrading microorganism
Tert-butyl alcohol hydroxylase (mdpJ) Aerobic MTBE degradation pathway


  • MTBE – Methyl tert-butyl ether (CH3)3COCH3
  • TBA – tert-Butyl alcohol (CH3)3COCH
  • 2-HIBA – 2-Hydroxyisobutyric acid (CH3)2CCO2H

1,4-Dioxane Metabolism and Co-metabolism

Gene-Trac Test ID Gene-Target Relevance
PMMO Particulate methane monooxygenase (pMMO) Aerobic co-oxidation of 1,4-dioxane in the presence of methane
1,4-Dioxane Dioxane monooxygenase (dxmb) Aerobic energy yielding
1,4-dioxane degradation
Aldehyde dehydrogenase (ALDH)


Nitrogen Compounds

Test ID Gene-Target Relevance
Denitrification Nitrous oxide reductase (nosZ) Denitrification anaerobically converts nitrate to inert dinitrogen gas
Nitrite reductase (nirS)
Nitrite reductase (nirK)
Nitrification Bacteria ammonia monooxygenase (amoA) Nitrification converts ammonium to nitrate under aerobic conditions-then subject to denitrification
Archaea ammonia monooxygenase (amoA)
Nitrobacter 16S rRNA
Anammox 16S rRNA of the 5 major genera of anammox bacteria Anaerobic process that converts ammonium and nitrite to dinitrogen gas
DNRA Nitrite reductase (nrfA) active in dissimilatory nitrate reduction to ammonium (DNRA) DNRA is anaerobic conversion of ammonium to nitrate, occurs preferentially over denitrification under nitrate limiting conditions


(See NitroGen Analytical Suite for our full range of analyses for remediation and monitoring of nitrogen compounds)

Metals and Mining

Test ID Gene-Target Relevance
Perchlorate Perchlorate reductases (pcrA) of Dechloromonas agitata Reduces perchlorate to chlorate and chlorite-diagnostic for perchlorate degrading bacteria
Perchlorate reductases (pcrA) of Dechloromonas aromatica
SERA Selenate reductase (serA) of
Thauera selenatis
Detection of selenate reductases indicate increased likelihood of selenium precipitation with reduced aqueous solubility
SRDA Selenate reductase (srdA) of
Bacillus selenatarsenatis
Mercury Mercuric ion reductase (merA) merA converts Hg2+ to Hg0 reducing toxicity, important in bacterial mercury resistance
Organomercurial lyase (merB) merB converts methylmercury to less toxic elemental mercury, important in bacterial mercury resistance
GEO Geobacter 16S rRNA Geobacter reduce uranium and hexavalent chromium lowering aqueous solubility, can increase arsenic solubility
SRB Sulfate reducing bacteria (SRB) via dissimilatory sulfite reductase (dsrA) H2S produced by SRB are known to precipitate metals in acid mine drainage
SOXB Sulfur-oxidizing bacteria (SOB) via sox enzyme system (soxB) SOB produce sulfuric acid and are important in acid mine drainage

Microbial Groups

Test ID Target Relevance
PROK Bacteria and Archaea 16S rRNA using universal Primers Quantifies most Bacteria and Archaea to measure total prokaryotic biomass
SRB Sulfate Reducing bacteria (dsrA) SRB are important in hydrocarbon degradation, acid mine drainage and biogeochemical treatment of chlorinated solvents
Methanogens Methanogens via Methyl coenzyme reductase (mcrA) highly conserved gene among this group Measure potential for methane production, methanogens have syntrophic relationships with hydrocarbon degraders and dechlorinators
SOXB Sulfur-oxidizing bacteria (SOB) via sox enzyme system (soxB) SOB produce sulfuric acid, important in acid mine drainage and in microbially influenced corrosion (MIC)
NGS 16S rRNA gene of Bacteria and Archaea via Gene-Trac® NGS Characterize entire microbial communities to determine metabolic functions and response to changing conditions

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.