QuantArray®-BGC: qPCR Testing for Biogeochemical Processes

Comprehensive Microbial Analysis for Biogeochemical Cycles

Microbial communities have diverse metabolic capabilities, and the selective pressure of environmental conditions (e.g., dissolved oxygen, pH, temperature, availability of electron donors and acceptors, etc.) influences which metabolic processes will be predominant. Inferring microbial processes from chemical and geochemical data alone can result in an oversimplified view of the microbial activity occurring at a site or in a system. The QuantArray^®-BGC analysis provides direct microbial evidence to determine if an in situ community has metabolic capabilities of interest.

QuantArray^®-BGC quantifies a wide range of microorganisms and genes involved in biogeochemical processes, including sulfate reduction, sulfur oxidation, iron reduction, metal oxidation, the nitrogen cycle, fermentation, acetogenesis, and methanogenesis. This broad view of microbial community dynamics can enhance site assessment and empower decision-makers across industries to make more informed choices.

QUANTARRAY^®-BGC ADVANTAGES:

ACCURATE

Direct analysis of sample DNA removes the need to grow the bacteria, thus eliminating biases associated with traditional approaches (e.g., plate counts and MPNs).

QUANTITATIVE

Absolute quantification of the concentrations of specific microorganisms and functional genes encoding enzymes responsible for contaminant biodegradation gives site managers a direct line of evidence to evaluate remediation options and monitor remedy performance. Results reported as cells/mL, cells/g, etc.

COST EFFECTIVE

In a single analysis, QuantArray^®-BGC quantifies a broad spectrum of microbial groups and functional genes involved in biogeochemical processes. QuantArray^® provides the same accuracy as CENSUS^® qPCR, but is more comprehensive and cost-effective.

INFORMATIVE

Is that a low, medium or high concentration of contaminant degraders? With the MI Database, clients can retrieve percentile rankings of their QuantArray^® results to answer that question based on the tens of thousands of samples MI has received from sites around the world.

SENSITIVE

The Method Detection Limit (MDL) is 10 cells/sample and the Practical Quantification Limit (PQL) is 250 cells/sample.

SPECIFIC

Target specific microbial groups (e.g., sulfate reducing bacteria and archaea, nitrite oxidizing bacteria, acetogens) and functional genes (e.g., acetylene hydratase) involved in biogeochemical processes.

FLEXIBLE

Analysis can be performed on almost any type of sample (water, soil, sediments, Bio-Traps^®, and others).

HOW TO USE QUANTARRAY^®-BGC:

Since the metabolic processes QuantArray^®-BGC targets are broadly applicable, QuantArray^®-BGC testing can be beneficial to practitioners across a variety of fields. To highlight the range of applications, here are a few examples of questions QuantArray^®-BGC can be used to answer.

Environmental Remediation: Are biogeochemical processes related to abiotic chlorinated solvent degradation occurring at my site?

In the combined biotic/abiotic treatment of chlorinated solvents, sulfate reducing bacteria are desirable for the formation of reactive iron sulfides which drive long-term abiotic contaminant degradation. Additionally, acetylene, an intermediate of abiotic chlorinated solvent degradation, is readily biodegraded and may not appreciably accumulate in groundwater. Quantification of acetylene hydratase genes may be used as an alternative indicator of acetylene production.

Landfills: Is a biogas or leachate issue linked to inhibited methanogenesis?

Inhibited methanogenesis can adversely impact biogas production and increase leachate strength. Use QuantArray^®– BGC as a line of evidence to determine if methanogen concentrations are substantially lower in the impacted area compared to an unimpacted location.

Mining: Are microorganisms beneficial for the reclamation of mine water present?

QuantArray^®– BGC includes gene targets related to sulfur, nitrogen, and metal cycles. Sulfate reducing bacteria contribute to the removal of sulfate, the neutralization of acidity, and the immobilization of dissolved iron as sulfide. Denitrifiers decrease nitrate levels in mine waters, reducing the overall environmental impact and lowering the risk of associated liabilities. Metal reducing bacteria can reduce metals, including iron, manganese, and in certain instances, uranium.

Biofouling: Did the fouling mitigation strategy effectively reduce microorganisms in the system?

Microbial biofouling can have negative effects at many different points in industrial processes. For example, biofouling can restrict fluid flow in pipes, reduce process efficiency, and lead to microbiologically influenced corrosion of tanks and equipment. Once a mitigation solution has been selected, collect multiple lines of evidence, including microbial data, to evaluate and optimize its efficacy. QuantArray^®– BGC results indicating a post-treatment decrease in microbial groups like slime forming bacteria in areas of concern can be a useful indicator of the success of a fouling control program.

GENE TARGETS INCLUDED IN A SINGLE QUANTARRAY^®-BGC qPCR ANALYSIS

TARGET	CODE	RELEVANCE / DATA INTERPRETATION
Total Eubacteria	EBAC	Index of total bacterial biomass
Total Archaea	ARC	Index of total archaeal biomass
Sulfate Reducing Bacteria	APS	Quantification of sulfate reducing bacteria provides an additional line of evidence when evaluating redox conditions and terminal electron accepting processes.
Sulfate Reducing Archaea	SRA	Sulfate reducing archaea consume hydrogen and produce hydrogen sulfide.
Iron Reducing Bacteria - Other	IRB	Iron reducing bacteria (IRB) are capable of reducing insoluble iron oxides to soluble ferrous iron. Some IRB can also reduce insoluble manganese oxides to soluble manganese.
Iron Reducing Geobacter	IRG	Many Geobacter spp. are capable of reducing insoluble iron and manganese oxides to soluble forms.
Iron Reducing Shewanella	IRS	Many Shewanella spp. are capable of reducing insoluble iron and manganese oxides to soluble forms.
Iron Oxidizing Bacteria	FEOB	Iron oxidizing bacteria are a group of microorganisms commonly implicated in metal deposition.
Manganese Oxidizing Bacteria	MnOB	Although the physiological function of manganese oxidation remains unclear, functional genes encoding proteins related to multicopper oxidases have been linked to manganese oxidation. Manganese oxidation leads to the formation of insoluble manganese oxides.
Sulfur Oxidizing Bacteria	SOB	Often aerobic bacteria oxidize sulfide or elemental sulfur producing sulfuric acid.
Ammonia Oxidizing Bacteria	AMO	The AMO assay targets the ammonia monooxygenase gene (amoA) that encodes the enzyme responsible for the initial oxidation of ammonia in the nitrification process.
Ammonia Oxidizing Archaea	AOA	Taxonomic gene for archaea that can oxidize ammonia to nitrite.
Anaerobic Ammonia Oxidizers	AMXIRK, AMXNIRS	Targets nitrite reductase genes involved in converting nitrite to nitric oxide.
Nitrite Oxidizing Bacteria	NOR	Targets the gene encoding the enzyme responsible for the last step in nitrification.
Nitrogen Fixing Bacteria	NIF	Nitrogen fixation converts nitrogen gas into ammonia which can be assimilated by organisms. Nitrogen fixation may become increasingly important in mature biofilms.
Denitrifying Bacteria	nirK, nirS	Denitrifying bacteria are involved in the reduction of nitrate to nitrogen gas (denitrification).
Denitrifying Archaea	ANIRK, ANIRS	Quantifies the two types of nitrite reductase genes (nirS and nirK) found in archaeal organisms.
Acetogens	AGN	Acetogens can utilize hydrogen and carbon dioxide produced during the anaerobic degradation of hydrocarbons to produce acetate.
Fermenters	FER	Some fermenters in anaerobic LNAPL zones are capable of biodegrading hydrocarbons to form dissolved hydrogen and/or acetate which can be utilized by methanogens to form methane.
Methanogens	MGN	Methanogens utilize the hydrogen, acetate, and other substrates that are produced by fermenters and other hydrocarbon degraders as byproducts during the anaerobic biodegradation of hydrocarbons.
Acetylene Hydratase	AHY	Targets acetylene hydratase genes encoding the enzyme that mediates anaerobic acetylene biodegradation may suggest acetylene production even if dissolved acetylene has not been detected.
Burkholderia cepacian exopolysaccharide	BCE	Targets a functional gene involved in exopolysaccharide (EPS) production by slime-forming Burhkholderia cepacia.
Deinococcus spp.	DCS	Deinococcus spp., most notably Deinococcus geothermalis, are considered eﬀicient primary biofilm formers.
Meiothermus spp.	MTS	Along with Deinococcus, Meiothermus are considered primary biofilm formers functioning as an adhesion platform for secondary biofilm bacteria.

FREQUENTLY ASKED QUESTIONS

How soon can I expect to receive the QuantArray®-BGC results?

The turnaround time to receive a QuantArray^®-BGC report is 10-14 calendar days.

If both provide a broad picture of the microbial community, should I choose QuantArray®-BGC or next generation sequencing?

QuantArray^®results are quantitative, providing concentrations of the targeted microbial groups and functional genes, which can be easily compared across locations and sampling events. QuantArray^®-BGC is most appropriate for answering targeted questions relating to biogeochemical processes.

Next generation sequencing is a qualitative analysis that allows identification of the dominant organisms to the genus level but cannot quantify specific organisms or microbial functions.

How do I know if a change in biomass is significant?

As a general rule, gene target concentrations that increase or decrease by at least an order of magnitude are considered to be significant. However, concentration changes of less than an order of magnitude may still show a trend.

How is QuantArray® different from CENSUS® qPCR and multiplex qPCR?

In many respects, QuantArray® is the same as conventional qPCR, so you can expect the same level of accuracy and precision. Other methods like multiplex qPCR have been described that achieve some level of parallel quantification. However, there is a fundamental difference between the QuantArray® and multiplex qPCR. For multiplex qPCR, multiple primer sets are added to a reaction mixture to quantify multiple gene targets whereas QuantArray® employs discrete through-holes for individual qPCR reactions ensuring that reaction kinetics are not compromised. Download our “CENSUS® versus QuantArray®” white paper for further information.