qPCR Complete Pack List

Phenol monooxygenase (PMO), catalyze the hydroxylation of phenol by incorporating a single oxygen atom from molecular oxygen into the organic substrate, converting phenol into its o-diol derivatives, like catechol.

GP-PAH-RHDs are key enzymes in Gram-positive bacteria that start the degradation of polycyclic aromatic hydrocarbons (PAHs) such as naphthalene, phenanthrene, and benzo[a]pyrene. They serve as functional markers for identifying and studying PAH-degrading bacteria.

Biphenyl dioxygenase (bhpA) is an essential enzyme that initiates the degradation of biphenyl and structurally related compounds such as polychlorinated biphenyls (PCBs). Biphenyl dioxygenase belongs to the family of aromatic ring-hydroxylating dioxygenases (ARHDs), which catalyse the activation of aromatic rings through hydroxylation, enabling further breakdown of these persistent pollutants.

Alkane monooxygenase (AlmA) is an enzyme that catalyzes the initial oxidation of long-chain n-alkanes in bacteria like Acinetobacter and Alcanivorax. This process converts alkanes into primary alcohols, which are then further metabolised into fatty acids, making them available for use as an energy source. AlmA is crucial for the degradation of specific long-chain alkanes (C26-C38), as shown by the inability of bacteria to grow on these substrates when the almA gene is not present.

Biphenyl dioxygenase genes (BphA) are abundant in BTEXN contaminated environment and postively correlated with BTEXN concentrations.

GN-PAH-RHDs are key enzymes in Gram-negative bacteria that start the degradation of polycyclic aromatic hydrocarbons (PAHs) such as naphthalene, phenanthrene, and benzo[a]pyrene. They serve as functional markers for identifying and studying PAH-degrading bacteria.

Toluene monooxygenase (TMO) functions by hydroxylating toluene, using molecular oxygen (O2) and NADH to oxidize it to an alcohol or cresol.

Naphthalene dioxygenase is a multicomponent bacterial enzyme system that catalyzes the initial oxidation of aromatic compounds like naphthalene. Naphthalene dioxygenase (NDO) is a multi-component bacterial enzyme that catalyzes the conversion of naphthalene and other aromatic compounds into cis-dihydrodiols by adding both atoms of molecular oxygen to the substrate. This reaction is the first step in the metabolic degradation of naphthalene by bacterian.

Encodes alkane 1-monooxygenases, which initiate hydroxylation of medium-chain alkanes (C6-C22). These genes are widespread in Pseudomonas, Rhodococcus and other aerobes.

Toluene dioxygenase is an enzyme system, notably found in Pseudomonas putida, that converts toluene and other aromatic hydrocarbons to cis-dihydrodiols by adding two atoms of oxygen to the aromatic ring.

Catechol 2,3-dioxygenases are involved in the biodegradation of benzene, toluene, xylenes, phenol, and naphthalene through at least one catabolic pathway, and therefore play a key role in the metabolism of these compounds

Benzylsuccinate synthase (bssA) is the key enzyme that attacks methyl groups on aromatic rings.  It is therefore a key enzyme for anaerobic oxidation of toluene, ethylbenzene and xylene, but not benzene.  

bssA is utilized by a variety of bacteria, including:

• Denitrifiers (Nitrate-Reducing Bacteria) such as Azoarcus and Thauera species.

• Iron-Reducing Bacteria (IRB): such as Geobacter spp.

• Sulfate-Reducing Bacteria (SRB): such as Desulfatibacillum and Desulfoglaeba.

Micronovo's BSS target uses a complex primer design that measures bssA abundance across this wide variety of bacteria utilising anaerobic-oxidising pathways for toluene, ethylbenzene and xylene degradation. 

Alkylsuccinate synthase is a complex enzyme that catalyses the initial step of anaerobic alkane degradation, where it adds an alkane to the double bond of fumarate. This process yields a (1-methylalkyl)succinate, which can then be further metabolised under anaerobic conditions by bacteria or methanogens. These enzymes, which use a glycyl radical, are found in various microorganisms, including nitrate- and sulfate-reducing bacteria, and play a crucial role in bioremediation of petroleum hydrocarbons.

Benzene is difficult to break down without oxygen. The presence and transcription of Anaerobic benzene carboxylase (abcAD) proves that the microbial community has the specific machinery to "attack" the benzene ring.  

Anaerobic benzene carboxylase (abcAD) indicates that benzene is remediated (as opposed to other aromatics such as phenol or benzoate).

The abcAD gene is typically associated with strict anaerobes, particularly members of the sulphate-reducing family Peptococcaceae.  The abcAD gene has also been identified amongst benzene degrading iron-reducers.

Bacteria of the Peptococcaceae family have been shown to play an important role in anaerobic petroleum hydrocarbon degradation under denitrifying, iron-reducing, and sulfate-reducing conditions.  Whilst Peptococcaceae are strictly anaerobic, they often form syntrophic partnerships with denitrifiers, eg. Peptococcaceae "crack" the benzene ring and pass the intermediate products to the nitrate-reducing partner.

The Peptococcaceae family are highly versatile and act as iron, sulfate and manganese reducers to degrade alkanes, BTEX and PAHs.

The bacteria will express different genes depending upon the type of hydrocarbon they are degrading, ie:

• assA for alkanes

• abcAD for benzene

• bssA for toluene and xylene

Ring-cleaving hydrolase (bamA) is a crucial enzyme for anaerobic aromatic hydrocarbon biodegradation as it is used to break the cyclic ring, converting cyclohexadienes to aliphatic hydrocarbons.

This bamA ring-cleaving hydrolase is highly conserved across both Class I and Class II benzoyl-CoA pathways.  Therefore, bamA is a biomarker for aromatic degradation by denitrifiers, iron-reducers and sulphate-reducers.

In the absence of oxygen (anaerobic conditions), bacteria cannot use oxygenases to break down aromatic rings. Instead, they activate aromatic compounds to benzoyl-CoA.

Because the benzene ring is highly stable, it must be reduced (dearomatised) first. Benzoyl-CoA is the substrate for benzoyl-CoA reductase (BCR), which uses electrons and adenosine triphosphate (ATP) to reduce the ring, forming a non-aromatic cyclohexadiene ring.  This unlocks the door for further bioremediation.

This Benzoyl-CoA qPCR gene target is used by denitrifiers for this key step.

Nitrate reductase (napA) is a key denitrifying enzyme produced by heterotrophic denitrifying bacteria that catalyses the reduction of nitrate to nitrite. The napA gene serves as a reliable molecular target for quantifying the abundance of functional denitrifiers in environmental samples, helping assess the capacity and activity of denitrifying microbial communities relevant to bioremediation

Ammonia monooxygenase (AMO) enzymes (particularly the amoA subunit) are among the most reliable molecular markers for identifying and quantifying ammonia-oxidising archaea (AOA) in environmental samples. Ammonia oxidation is the first and rate-limiting step in nitrification, where AOB convert ammonia (NH3) into nitrite (NO2-) via hydroxylamine. This process is catalysed by ammonia monooxygenase (AMO). Hence, AOB quantification is a robust indicator of nitrification potential rather than general microbial presence. Note, the same amoA subunit is targeted to quantify Bacterial ammonia monooxygenase (AOB).

Ammonia monooxygenase (AMO) enzymes (particularly the amoA subunit) are among the most reliable molecular markers for identifying and quantifying ammonia-oxidising bacteria (AOB) in environmental samples. Ammonia oxidation is the first and rate-limiting step in nitrification, where AOB convert ammonia (NH3) into nitrite (NO2-) via hydroxylamine. This process is catalyzed by ammonia monooxygenase (AMO). Hence, AOB quantification is a robust indicator of nitrification potential rather than general microbial presence. Note, the same amoA subunit is targeted to quantify Archael ammonia monooxygenase (AOA).

bvcA is a functional gene of Dehalococcoides mccartyi strains with enzymes that catalyse reductive dechlorination of DCE and VC to ethene.  Dehalococcoides mccartyi in Micronovo's AusPCE culture mix carry the bvcA functional gene, enabling complete dechlorination of DCE and VC, ensuring bioremediation of PCE or TCE doesn't stall at DCE or VC.

Chloroform reductase (tmrA) gene copies for reductive dechlorination of chloroform to dichloromethane (DCM) and then acetate.

Chloroform reductase, encoded by the tmrA gene, is a specialized enzyme found in certain organohalide-respiring bacteria. It catalyses the reductive dechlorination of chloroform to dichloromethane (DCM), followed by further conversion to acetate under anaerobic conditions. Quantifying tmrA gene copies in environmental samples enables sensitive monitoring of key chloroform-degrading bacteria, helping assess bioremediation progress and optimize conditions for complete detoxification of chloroform and its breakdown products.

Micronovo's high performance AusCF Chloroform degrading culture utilises Chloroform reductase.

Micronovo’s AusCF high performance organo-halide respiring bacteria culture mix contains  Dehalobacter UNSWDHB that carry the tmrA gene. 

tceA is a functional gene carried by organohalide respiring bacteria with enzymes that catalyse reductive dechlorination of TCE to VC. Dehalococcoides mccartyi in Micronovo's AusPCE culture mix carry the tceA functional gene.

vcrA is a functional gene of Dehalococcoides mccartyi strains with enzymes that catalyses reductive dechlorination of VC to ethene.

Dehalococcoides mccartyi in Micronovo's AusPCE culture mix carry the vcrA functional gene, enabling complete dechlorination of VC and ensuring bioremediation of PCE or TCE doesn't stall at VC (a contaminant more toxic than the initial PCE and TCE contaminants).

1,2-dichloroethane reductive dehalogenase is the key enzyme that catalyzes the organohalide‑respiring step of converting 1,2‑dichloroethane (1,2‑DCA) to ethene under anaerobic conditions.  

As this enzyme performs the key detoxification step from chlorinated ethane to a non‑chlorinated end product, dcaA functions as a substrate‑specific functional biomarker for active reductive dechlorination of 1,2‑DCA in groundwater systems.

The gene is found in strains of Desulfitobacterium and/or Dehalobacter enriched from 1,2‑DCA‑contaminated aquifers. Micronovo's AusDCA contains Desulfitobacterium with this gene.

Note, 1,2-dichloroethane is also known as 1,2-DCA, DCA and ethylene dichloride or EDC in Australia.

Reductive Dehalogenase A (RdhA) enzyme, is the catalytic subunit of reductive dehalogenases (RDases) responsible for PCB reductive dechlorination. These enzymes use a cobalamin (vitamin B12) cofactor and iron-sulfur clusters to remove chlorine atoms from highly chlorinated PCBs, converting them into less chlorinated forms under anaerobic conditions. AusPCE culture mix expresses RdhA to dechlorinate PCBs under anaerobic conditions.