# Patent

## Title
Nanoliter qPCR platform for parallel quantitative assessment of reductive dehalogenase genes

## Abstract

Combinations of reductive dehalogenase (rdh) genes are a distinguishing genomic feature of closely-related organohalogen-respiring bacteria. This feature can be used to deconvolute the population structure of organohalogen-respiring bacteria in complex environments and to identify relevant subpopulations, which is important for tracking interspecies dynamics needed for successful site remediation. The present disclosure encompasses embodiments of a nanoliter qPCR platform to identify organohalogen-respiring bacteria by quantitatively identifying major orthologous reductive dehalogenase gene groups.

## Background
CROSS-REFERENCE TO RELATED APPLICATION
This application claims priority to U.S. Provisional Application No. 61/968,578, entitled “A NANOLITER QPCR PLATFORM FOR PARALLEL, QUANTITATIVE ASSESSMENT OF REDUCTIVE DEHALOGENASE GENES AND POPULATIONS OF DEHALOGENATING MICROORGANISMS IN COMPLEX ENVIRONMENTS” filed on Mar. 21, 2014, the entirety of which is herein incorporated by reference.


STATEMENT REGARDING FEDERALLY SPONSORED RESEARCH OR DEVELOPMENT
This invention was made with government support under Grant No. MCB-1330832 awarded by the National Science Foundation. The government has certain rights in the invention.


FIELD OF THE DISCLOSURE
The present disclosure relates to methods of identifying reductive dehalogenase genes and populations of dehalogenating microorganisms in complex environments.
SEQUENCE LISTING
The present disclosure includes a sequence listing incorporated herein by reference in its entirety.
BACKGROUND
The bioremediation of groundwater aquifers and sediments contaminated with chlorinated aliphatic hydrocarbons (CAHs) depends on the activities of reductive dehalogenases that are present in some anaerobic microorganisms (Bouwer et al., (1983) Appl. Environ. Microbiol. 45: 1286-1294; DiStefano et al., (1991) Appl. Environ. Microbiol. 57: 2287-2292). Of particular importance are organohalogen-respiring bacteria, such as Dehalococcoides or Dehalogenimonas sp., because reductive dehalogenation is the only known mode of metabolic energy conservation in these microorganisms, and each group can carry up to 36 different non-redundant rdh genes (Seshadri et al., (2005) Science 307: 105-108; McMurdie et al., (2009) PLoS Genet. 5, e1000714; Moe et al., (2009) Int. J. Syst. Evol. Microbiol. 59: 2692-2697).
While organohalogen-respiring bacteria have been key for decontaminating polluted sites via biostimulation and bioaugmentation (bioremediation), there are many instances where such treatments have been hindered by the absence of key microorganisms and genes, enzymatic inhibition, hydrological complications, or incomplete management of microbial competition and associated biogeochemistry. Remediation of common groundwater contaminants such as tetrachloroethene (PCE), trichloroethene (TCE), 1,1,2-trichloroethane (1,1,2-TCA), and 1,2-dichloroethane (1,2-DCA) poses additional challenges since an appropriate assemblage of organohalogen-respiring bacteria, plus their supporting microbial communities, is required for complete dechlorination of these compounds to a harmless end product. Furthermore, it is unclear whether faithful representatives of the well-studied laboratory isolates are dominant organohalogen-respiring bacteria in sediments and groundwater, and to what extent their laboratory-studied phenotypes are relevant in the field.
Given this uncertainty, managing bioremediation of CAHs requires (i) gauging the structure of the microbial community, in particular the organohalogen-respiring bacteria; and (ii) being able to identify and differentiate between closely related but functionally distinct subpopulations. Such information is crucial for predicting and controlling the ecological responses of the microbial communities to natural or engineered perturbations during bioremediation. To be useful for both lab and field applications, any such molecular diagnostic for comprehensively quantifying organohalogen-respiring microorganisms and their complex rdh gene inventories should be simple, cost-effective, and require the minimum possible biological input material (Ziv-El et al., (2012) Biotechnol. Bioeng. 109: 2200-2210; Maphosa et al., (2010) Trends Biotechnol. 28: 308-316).
Metagenomics (Hug et al., (2012) BMC Genomics 13, 327), transcriptomics (Lee et al., (2012) Appl. Environ. Microbiol. 78: 1424-1436), proteomics (Rowe et al., (2012) Environ. Sci. & Technol. 46: 9388-9397), pan-genome-microarrays (Hug et al., (2011) Appl. Environ. Microbiol. 77, 5361-5369; Men et al., (2013) Appl. Microbiol. Biotechnol. 97: 6439-6450) and functional-gene tiling microarrays (Marshall et al., (2012) ISME J. 6: 814-826; Marshall et al., (2014) FEMS Microbiol Ecol. 86: 428-440) have been used to study the eco-physiology of organohalogen-respiring bacteria. However, these approaches have not been widely applied as tools in full-scale field studies due to the requirement of large amounts of DNA as input, bioinformatic complexity, cost constraints, and inadequate sensitivity of the assay primer pairs for detecting low-abundance genes in complex genomic backgrounds. A number of single quantitative PCR (qPCR) assay primer pairs targeting a few of the best understood rdh genes have been shown capable of overcoming these obstacles and are employed regularly in the remediation industry.
SUMMARY
Combinations of reductive dehalogenase (rdh) genes are a distinguishing genomic feature of closely-related organohalogen-respiring bacteria. This feature can be used to deconvolute the population structure of organohalogen-respiring bacteria in complex environments and to identify relevant subpopulations, which is important for tracking interspecies dynamics needed for successful site remediation. The present disclosure encompasses embodiments of a nanoliter qPCR platform to identify organohalogen-respiring bacteria by quantitatively identifying major orthologous reductive dehalogenase gene groups.
One aspect of the disclosure encompasses embodiments of a method for identifying a dechlorinating microbial organism, or a plurality of said microbial organisms, in a sample comprising: (a) obtaining a sample suspected of having a population of at least one microbial strain having at least one species of a reductive dehalogenase enzyme; (b) isolating nucleic acid from the sample; (c) applying the isolated nucleic acid to a microfluidic device configured for quantitative real-time PCR and comprising a panel of reductive dehalogenase (rdh)-specific PCR primer pairs, wherein each primer pair of the panel is selected to allow amplification of a specific target nucleotide sequence under a common PCR protocol; (d) simultaneously performing quantitative real-time PCR on the isolated nucleic acid in the microfluidic device with each rdh-specific PCR primer pair of said panel and under conditions wherein the presence of a microbial reductive dehalogenase (rdh)-related nucleic acid sequence results in at least one detectable amplicon encoding a region of a reductive dehalogenase (rdh); (e) detecting the at least one amplicon of step (d); (f) identifying the reductive dehalogenase enzyme encoded by the at least one amplicon; and (g) identifying the microbial strain or strains in the sample of step (a) that has at least one reductive dehalogenase enzyme.
In embodiments of this aspect of the disclosure, the method can further comprise the step of quantitatively determining the population(s) of microbial strains in the sample of step (a) that have a reductive dehalogenase enzyme.
In embodiments of this aspect of the disclosure, the method can further comprise the step of classifying the identified reductive dehalogenase enzyme(s) encoded by the at least one amplified PCR product according to their respective reductive dehalogenase (rdh) orthologous groups.
Another aspect of the disclosure encompasses embodiments of a microfluidic nanoliter-quantitative PCR device configured for quantitative real-time PCR and comprising a panel of reductive dehalogenase (rdh)-specific PCR primer pairs.



BRIEF DESCRIPTION OF THE DRAWINGS
Many aspects of the disclosure can be better understood with reference to the following drawings.
FIG. 1 is a graph illustrating the assay calibration results across two chips with DNA standards applied in a ten-fold dilution series show sensitivity of the assays. Proximity to the 45-degree line reflects replicability across duplicate chips. The addition of genomic bait from 8 non-organohalogen respiring bacteria at 10 to 100 times the copy ratio of the target did not cause a loss of sensitivity.
FIGS. 2A-2D are graphs illustrating the heterogeneity in RD-OG composition and biostimulation response in contaminated pore-water.
FIGS. 2A-2C are graphs illustrating 1,2-dichloroethane concentrations in replicate pore waters. Pore-water samples from wells BPR011, PC008, and PC031 amended with 2 mM mineral salt control (∇), sodium-lactate (X), sodium-formate (+), or sodium-acetate (♦).
FIG. 2D illustrates the measured abundance of 16S rRNA gene, hupL and reductive dehalogenase orthologue groups (RD-OG). In some cases, roughly stoichiometric increases between a 16S marker genes and RD-OG estimates suggest a potential linkage between genes to a specific genus.
FIGS. 3A and 3B illustrate reductive dehalogenase types detected in a TCE-fed reactor over a 5-year time course.
FIG. 3A illustrates the hierarchical clustering of RD-OG and rdh based on time-series correlation.
FIG. 3B illustrates the median gene counts for each RD-OG and rdh at each sampled time point. Lines represent unique RD-OG, rdh, or hupL sequence types, with colors indicating assignment to a hypothesized strain based on hierarchical clustering. Unique shapes in the figure legend emphasize hupL types and biochemically characterized RD-OG.
FIG. 3C illustrates 16S level gene count estimates for Dehalococcoides and Geobacter compared with mean gene abundance estimates of hypothesized vinyl-chloride respiring strains: Ev2 containing vinyl-chloride reductase (vcrA) and Ev3 containing putative vinyl-chloride reductase (bvcA).
FIG. 3D illustrates chloroethene/ethene/hydrogen concentrations in the EV2L reactor.
FIGS. 4A and 4B illustrate reductive dehalogenase nl-qPCR suite validation.
FIG. 4A illustrates a network displaying sequences in Dehalogenase Pfam PF13486 v26.0 as nodes. Edges represent pairwise percent identity greater than 90% spanning at least half the length of the shorter sequence.
FIG. 4B illustrates accuracy and quantitative estimates achieved when amplifying rdh genes from four isolates representing the three major Dehalococcoides mccartyi subgroups: Victoria (VS), Cornell (195), and Pinellas (CBDB1, GT). Classification of results as true positive (TP), true negative (TN), false positive (FP), and false negative (FN) were based on the majority result for all assays associated with each target group.
FIG. 5 is a graph illustrating the Ct difference between technical duplicates. Solid points are mean Ct difference between technical duplicates at 20, 200, 2000, and 20000 starting copies (n=116). Solid line shows the expected difference due to Poisson noise.
FIG. 6 is a histogram of the Ct errors between the observed result at 20 copies per reaction and the predicted Ct by linear regression from a 3-point calibration curve. A strong bias in the errors was not seen.



DETAILED DESCRIPTION
Before the present disclosure is described in greater detail, it is to be understood that this disclosure is not limited to particular embodiments described, and as such may, of course, vary. It is also to be understood that the terminology used herein is for the purpose of describing particular embodiments only, and is not intended to be limiting, since the scope of the present disclosure will be limited only by the appended claims.
Where a range of values is provided, it is understood that each intervening value, to the tenth of the unit of the lower limit unless the context clearly dictates otherwise, between the upper and lower limit of that range and any other stated or intervening value in that stated range, is encompassed within the disclosure. The upper and lower limits of these smaller ranges may independently be included in the smaller ranges and are also encompassed within the disclosure, subject to any specifically excluded limit in the stated range. Where the stated range includes one or both of the limits, ranges excluding either or both of those included limits are also included in the disclosure.
Unless defined otherwise, all technical and scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art to which this disclosure belongs. Although any methods and materials similar or equivalent to those described herein can also be used in the practice or testing of the present disclosure, the preferred methods and materials are now described.
All publications and patents cited in this specification are herein incorporated by reference as if each individual publication or patent were specifically and individually indicated to be incorporated by reference and are incorporated herein by reference to disclose and describe the methods and/or materials in connection with which the publications are cited. The citation of any publication is for its disclosure prior to the filing date and should not be construed as an admission that the present disclosure is not entitled to antedate such publication by virtue of prior disclosure. Further, the dates of publication provided could be different from the actual publication dates that may need to be independently confirmed.
As will be apparent to those of skill in the art upon reading this disclosure, each of the individual embodiments described and illustrated herein has discrete components and features which may be readily separated from or combined with the features of any of the other several embodiments without departing from the scope or spirit of the present disclosure. Any recited method can be carried out in the order of events recited or in any other order that is logically possible.
Embodiments of the present disclosure will employ, unless otherwise indicated, techniques of medicine, organic chemistry, biochemistry, molecular biology, pharmacology, and the like, which are within the skill of the art. Such techniques are explained fully in the literature.
It must be noted that, as used in the specification and the appended claims, the singular forms “a,” “an,” and “the” include plural referents unless the context clearly dictates otherwise. Thus, for example, reference to “a support” includes a plurality of supports. In this specification and in the claims that follow, reference will be made to a number of terms that shall be defined to have the following meanings unless a contrary intention is apparent.
As used herein, the following terms have the meanings ascribed to them unless specified otherwise. In this disclosure, “comprises,” “comprising,” “containing” and “having” and the like can have the meaning ascribed to them in U.S. Patent law and can mean “includes,” “including,” and the like; “consisting essentially of” or “consists essentially” or the like, when applied to methods and compositions encompassed by the present disclosure refers to compositions like those disclosed herein, but which may contain additional structural groups, composition components or method steps (or analogs or derivatives thereof as discussed above). Such additional structural groups, composition components or method steps, etc., however, do not materially affect the basic and novel characteristic(s) of the compositions or methods, compared to those of the corresponding compositions or methods disclosed herein. “Consisting essentially of” or “consists essentially” or the like, when applied to methods and compositions encompassed by the present disclosure have the meaning ascribed in U.S. Patent law and the term is open-ended, allowing for the presence of more than that which is recited so long as basic or novel characteristics of that which is recited is not changed by the presence of more than that which is recited, but excludes prior art embodiments.
Prior to describing the various embodiments, the following definitions are provided and should be used unless otherwise indicated.
Abbreviations
CAH, Chlorinated Aliphatic Hydrocarbon; hupL, gene name abbreviation for nickel-containing uptake hydrogenase; NCBI, National Center for Biotechnology Information; HRB, Organohalogen-Respiring Bacteria; PCR, Polymerase Chain Reaction; PID, Percent Pairwise Identity between aligned sequences; Rdh, reductive dehalogenase enzyme; rdh, reductive dehalogenase gene; RD-OG, Reductive Dehalogenase Orthologue Group; 16S rRNA, 16S small subunit ribosomal ribonucleic acid
Definitions
In describing and claiming the disclosed subject matter, the following terminology will be used in accordance with the definitions set forth below.
The term “sample” as used herein refers to any water-based sample that may be obtained from an environmental source including, but not limited to, rivers, pools, drainage, sewage, standing puddles, industrial effluent, and the like. A sample may further refer to a water-based extract derived from a solid such as soil.
The term “isolating nucleic acid from a sample” as used herein refers to any method known to one of skill in the art that results in an aqueous solution of microbial nucleic acid. for example, but not intended to be limiting, the microbial population of a collected sample may be concentrated by centrifugation or filtration, the microbial organisms may be resuspended in a suitable aqueous medium, lysed by such as sonication or enzyme, the nucleic acid precipitated by ethanol, dried and resuspended in an aqueous medium for application to a microfluidic device of the disclosure. It is contemplated that the nucleic acid of a microbial population is so isolated that each reaction chamber of the microfluidic device receives an identical aliquot of the isolated nucleic acid, thereby allowing comparisons between the amounts amplification products of each chamber.
The term “common PCR protocol” as used herein refers to each reaction site of a microfluidic device according to the disclosure being exposed to the same PCR conditions of buffer, nucleotide concentrations, enzyme amounts, etc. to allow comparisons between the amounts of the amplification products of each chamber.
The term “orthologs” as used herein refers to genes in different species that evolved from a common ancestral gene by specification. Normally, orthologs retain the same function in the course of evolution.
The terms “digital PCR” and “quantitative PCR (qPCR)” as used herein refer to a method of quantifying the amount of specific nucleic acids in a sample by counting amplification from a number of single molecules. Digital PCR (polymerase chain reaction) is achieved by capturing or isolating each individual nucleic acid molecule present in a sample within many separate chambers, zones or regions that are able to localize and concentrate the amplification product to detectable levels. After PCR amplification, a count of chambers, zones or regions containing PCR end product is a direct measure of the absolute nucleic acids quantity.
The term “microfluidic digital PCR” as used herein refers to a method of digital (quantitative) PCR that uses a microfluidic system. A microfluidic system comprises a number of fluidic elements, such as passages, chambers, conduit, valves, etc. configured to carry out or permit fluid handling and treatment operations, such as introduction of reagents, heating, cooling, etc. The system will generally have an internal cross-sectional dimension, e.g., depth or width, of between about 10 nm and 500 μm. Microfluidic digital PCR devices can typically include a number of microscale channels, and preferably from at least 50 to the order of hundreds of separate reaction chambers for individual PCR reactions to be carried out in parallel. The body structure of the microfluidic device may comprise a single component, or an aggregation of separate parts, e.g., capillaries, joints, chambers, layers, etc., which when appropriately mated or joined together, form the microfluidic device. It is contemplated that any microfluidic device known to one of skill in the art that allows the simultaneous PCR detection of the amplicon products using the primer pairs of the disclosure under a common PCR protocol may be suitably adapted for use in the methods herein disclosed.
Microfluidic devices advantageous for use in the methods of the disclosure can comprise, but are not limited to, a top portion, a bottom portion, and an interior portion, wherein the interior portion substantially defines the channels and chambers of the device. The bottom portion can comprise a solid substrate that is substantially planar in structure, and which has at least one substantially flat upper surface, although one or more of these surfaces is generally provided with valve and other deformable structures. A variety of substrate materials may be employed. The substrate materials will generally be selected based upon their compatibility with known microfabrication techniques, e.g., photolithography, wet chemical etching, laser ablation, air abrasion techniques, injection molding, embossing, and other techniques. The substrate materials are also generally selected for their compatibility with the full range of conditions to which the microfluidic devices may be exposed, including extremes of pH, temperature, salt concentration, and other reaction conditions needed for the amplification of a single nucleic acid. In some embodiments, the substrate material may include materials normally associated with the semiconductor industry in which such microfabrication techniques are regularly employed, including, e.g., silica based substrates such as glass, quartz, silicon or polysilicon, as well as other substrate materials, such as gallium arsenide and the like. In the case of semiconductive materials, it will often be advantageous to provide an insulating coating or layer, e.g., silicon oxide, over the substrate material. Details on the construction of suitable microfluidic device for use in the methods of the disclosure, while not intending to be limiting, may be found, for example, in U.S. Pat. No. 6,899,137, U.S. Pat. No. 6,911,345, U.S. Pat. No. 7,118,910, and U.S. Pat. No. 7,833,709.
The term “quantitative real-Time PCR” as used herein, used interchangeably with the term “quantitative PCR” (abbreviated “qPCR”), refers to a method for simultaneous amplification, detection, and quantification of a target polynucleotide using double dye-labeled fluorogenic oligodeoxyribonucleotide probes during PCR and includes such methods as TaqMan, SYBR Green assays, and the like.
The term “propene” as used herein refers to H2C═CH—CH3.
The term “1,2-dichloropropane” as used herein refers to CH3—ClCH—CH2Cl.
The term “reductive dechlorination” as used herein refers to a subset of dehalorespiration. Reductive dechlorination refers to the process in which a chloro-organic compound as terminal electron acceptor and a chloride atom is removed from a chloro-organic compound. “Dehalorespiration” is a process whereby an organism uses a halo-organic compound as an electron acceptor for energy and growth. More specifically, hydrogen is used as the electron donor, the halo-organic compound is the electron acceptor, and hydrogen halide (i.e., HBr, HCl or HF) is produced. Several anaerobic bacteria are able to reductively dechlorinate chlorinated hydrocarbons and to gain energy from this dehalorespiration process.
The term “reductive dehalogenase” (abbreviated as “rdh”) as used herein refers to an enzyme system that is capable of dehalogenating a halogenated straight chain (aliphatic)—or ring (aromatic or cycloaliphatic)—containing organic compound that contains at least one halogen atom. Examples of halogenated organic compounds that may be dehalogenated by a reductive dehalogenase include, but are not limited to, 1,2-dichloropropane, perchloroethylene (Cl2C═CCl2), trichloroethylene (Cl2C═CH—Cl), dichloroethylene (Cl—HC═CH—Cl) and vinyl chloride (H2C═CH—Cl).
The term “dechlorinating bacteria” refers to a bacterial species or organism population that has the ability to remove at least one chlorine atom from a chlorinated organic compound. Examples of dechlorinating bacteria include, but are not limited to, strains of Dehalococcoides mccartyi, Dehalogenimonas lycanthroporepellens, Dehalobacter restrictus, Sulfurospirillum multivorans, Desulfitobacterium dehalogenans, Geobacter lovleyi, Desulfuromonas chioroethenica, and Desulfuromonas michiganensis. The methods and compositions of the disclosure are most advantageously applied to members of the Dehalococcoides, Dehalogenimonas, and Dehalobacter genera, and most advantageously to the Dehalococcoides genus.
The term “sequence similarity” as used herein refers to the extent to which nucleotide or protein sequences are related. The extent of similarity between two sequences can be based on percent sequence identity and/or conservation. With regard to proteins, “sequence identity” is a comparison of exact amino acid matches, whereas sequence similarity refers to amino acids at a position that have the same physical-chemical properties (i.e. charge, hydrophobicity). Amino acids other than those indicated as conserved may differ in a protein or enzyme so that the percent protein or amino acid sequence similarity between any two proteins of similar function may vary.
With regard to polynucleotides, “sequence identity” is a quantitative comparison of exact nucleotide matches. The sequence identity is at least 80%, at least 85%, at least 90%, at least 95%, at least 97%, and at least 99%, as determined by an alignment scheme.
The term “sequence alignment” as used herein refers to the process of lining up two or more sequences to achieve maximal levels of sequence identity (and, in the case of amino acid sequences, conservation), e.g., for the purpose of assessing the degree of sequence similarity or the degree of sequence identity. Methods for aligning sequences and assessing similarity and/or identity are well known in the art. Such methods include for example, the MEGALIGN software Clustal Method, wherein similarity is based on the MEGALIGN Clustal algorithm, ClustalW and ClustaIX (Thompson et al. (1997) Nucleic Acid Res. 25: 4876-4882) as well as BLASTN, BLASTP, and FASTA (Pearson et al. (1988) Proc. Natl. Acad. Sci. USA. 85: 2444-2448). When using these programs, the preferred settings are those that result in the highest sequence similarity or identity.
The term “primer” as used herein refers to an oligonucleotide complementary to a DNA segment to be amplified or replicated. Typically primers are used in PCR. A primer hybridizes with (or “anneals” to) the template DNA and is used by the polymerase enzyme as the starting point for the replication/amplification process. By “complementary” it is meant that the primer sequence can form a stable hydrogen bond complex with the template.
The term “detectably labeled” as used herein refers to an oligonucleotide labeled with a fluorophore, or other molecular species that elicits a physical or chemical response that can be detected by eye or by an instrument.
The term “fluorophore” as used herein refers to any reporter group whose presence can be detected by its light emitting properties.
The term “dye” as used herein refers to any reporter group whose presence can be detected by its light absorbing or light emitting properties. For example, Cy5 is a reactive water-soluble fluorescent dye of the cyanine dye family. Cy5 is fluorescent in the red region (about 650 to about 670 nm). It may be synthesized with reactive groups on either one or both of the nitrogen side chains so that they can be chemically linked to either nucleic acids or protein molecules. Labeling is done for visualization and quantification purposes. Cy5 is excited maximally at about 649 nm and emits maximally at about 670 nm, in the far red part of the spectrum; quantum yield is 0.28. FW=792. Suitable fluorophores(chromes) for the primers of the disclosure may be selected from, but not intended to be limited to, fluorescein isothiocyanate (FITC, green), cyanine dyes Cy2, Cy3, Cy3.5, Cy5, Cy5.5 Cy7, Cy7.5 (ranging from green to near-infrared), Texas Red, and the like. Derivatives of these dyes for use in the embodiments of the disclosure may be, but are not limited to, Cy dyes (Amersham Bioscience), Alexa Fluors (Molecular Probes Inc.,), HiLyteTM Fluors (AnaSpec), and DyLiteTM Fluors (Pierce, Inc).
The term “DNA” as used herein refers to the polymeric form of deoxyribonucleotides (adenine, guanine, thymine, or cytosine) in a single or double-stranded state and includes linear or circular DNA molecules. In discussing DNA molecules, sequences may be described by the convention of giving only the sequence in the 5′ to 3′ direction.
The term “DNA amplification” as used herein refers to any process that increases the number of copies of a specific DNA sequence by enzymatically amplifying the nucleic acid sequence. A variety of processes are known. One of the most commonly used is the polymerase chain reaction (PCR), which is defined and described in later sections below. The PCR process of Mullis is described in U.S. Pat. Nos. 4,683,195 and 4,683,202. PCR involves the use of a thermostable DNA polymerase, known sequences as primers, and heating cycles, which separate the replicating deoxyribonucleic acid (DNA) strands and exponentially amplify a gene of interest. Any type of PCR, such as quantitative PCR, RT-PCR, hot start PCR, LAPCR, multiplex PCR, touchdown PCR, etc., may be used. Advantageously, real-time PCR is used. In general, the PCR amplification process involves an enzymatic chain reaction for preparing exponential quantities of a specific nucleic acid sequence. It requires a small amount of a sequence to initiate the chain reaction and oligonucleotide primers that will hybridize to the sequence. In PCR the primers are annealed to denatured nucleic acid followed by extension with an inducing agent (enzyme) and nucleotides. This results in newly synthesized extension products. Since these newly synthesized sequences become templates for the primers, repeated cycles of denaturing, primer annealing, and extension results in exponential accumulation of the specific sequence being amplified. The extension product of the chain reaction will be a discrete nucleic acid duplex with a termini corresponding to the ends of the specific primers employed.
The term “amplification product” and “amplicon” as used herein simultaneously refer to portions of nucleic acid fragments that are produced during a primer directed amplification reaction. A typical method of primer directed amplification includes polymerase chain reaction (PCR). In PCR, the replication composition would include for example, nucleotide triphosphates, two primers with appropriate sequences, DNA or RNA polymerase and proteins. These reagents and details describing procedures for their use in amplifying nucleic acids are provided in U.S. Pat. No. 4,683,202 (1987, Mullis, et al.) and U.S. Pat. No. 4,683,195 (1986, Mullis, et al.), the contents of which are hereby incorporated by reference herein.
The terms “enzymatically amplify” or “amplify” as used herein refer to DNA amplification. Currently the most common method is the polymerase chain reaction (PCR). Other amplification methods include LCR (ligase chain reaction), strand displacement amplification (SDA); Qβ replicase amplification (QβRA); self-sustained replication (3SR); and NASBA (nucleic acid sequence-based amplification), which can be performed on both RNA and DNA.
The terms “nucleic acid,” “nucleic acid sequence,” or “oligonucleotide” that also encompass a polynucleotide, refers to a linear chain of nucleotides connected by a phosphodiester linkage between the 3′-hydroxyl group of one nucleoside and the 5′-hydroxyl group of a second nucleoside which in turn is linked through its 3′-hydroxyl group to the 5′-hydroxyl group of a third nucleoside and so on to form a polymer comprised of nucleosides linked by a phosphodiester backbone.
The term “oligonucleotide” as used herein refers to a series of linked nucleotide residues, which oligonucleotide has a sufficient number of nucleotide bases to be used in a PCR reaction. A short oligonucleotide sequence may be based on, or designed from, a genomic or cDNA sequence and is used to amplify, confirm, or reveal the presence of an identical, similar or complementary DNA or RNA in a particular cell or tissue. Oligonucleotides may be chemically synthesized and may be used as primers or probes. Oligonucleotide means any nucleotide of more than 3 bases in length used to facilitate detection or identification of a target nucleic acid, including probes and primers.
The term “polymerase” as used herein refers to an enzyme that catalyzes the sequential addition of monomeric units to a polymeric chain. In advantageous embodiments of this disclosure, the “polymerase” will work by adding monomeric units whose identity is determined by a complementary template of a specific sequence. DNA polymerases such as DNA pol 1 and Taq polymerase add deoxyribonucleotides to the 3′ end of a polynucleotide chain in a template-dependent manner, thereby synthesizing a complementary nucleic acid. Polymerases may extend a primer once or may repetitively amplify two complementary strands using two primers.
The term “polynucleotide” as used herein refers to any polyribonucleotide or polydeoxribonucleotide, which may be unmodified RNA or DNA or modified RNA or DNA. Thus, for instance, polynucleotides as used herein refers to, among others, single- and double-stranded DNA, DNA that is a mixture of single- and double-stranded regions, single- and double-stranded RNA, and RNA that is a mixture of single- and double-stranded regions, hybrid molecules comprising DNA and RNA that may be single-stranded or, more typically, double-stranded or a mixture of single- and double-stranded regions. The terms “nucleic acid,” “nucleic acid sequence,” or “oligonucleotide” also encompass a polynucleotide as defined above.
DESCRIPTION
PCR Based Detection of Dechlorinating Bacteria:
The oligonucleotides having the sequences SEQ ID NO: 1-336 of the present invention may be used as primers in primer-directed nucleic acid amplification, i.e., PCR or qPCR, to detect the presence of the target gene(s) in dechlorinating wild-type or cultured bacterial strains. Methods of PCR primer design are well known in the art (see, e.g., Sambrook, et al. 2001; Herndon, Va. and Rychlik, W. (1993 In White, B. A. (ed.), Methods in Molecular Biology, Vol. 15, pp 31-39, PCR Protocols: Current Methods and Applications. Humania Press, Inc., Totowa, N.J.; see also, U.S. Pat. Nos. 4,683,195; 4,683,202; 4,965,188; and 4,800,159, which are hereby incorporated by reference). Methods for selecting the oligonucleotides of the present disclosure are herein fully disclosed.
Detection of dechlorinating bacteria, such as Dehalococcoides strains including Dehalococcoides (Dhc) mccartyi strains using PCR involves the amplification of DNA obtained from a sample suspected of having microbial dechlorinating activity. The isolated DNA is amplified using a pair, or pairs, of oligonucleotide primers, wherein one primer (a forward primer) binds to the coding strand of the template and the other primer (a reverse primer) binds to the complementary strand of the template, thus creating two copies of the target region in each PCR cycle. A primer refers to an oligonucleotide that can be extended with a DNA polymerase using monodeoxyribonucleoside triphosphates and a nucleic acid that is used as a template. This primer preferably has a 3′ hydroxyl group on an end that is facing the 5′ end of the template nucleic acid when it is hybridized with the template.
A set of primers refers to a combination or mixture of at least a first (forward) and a second (reverse) primer. The first primer can be extended using the template nucleic acid while forming an extension product in such a way that the second primer can hybridize with this extension product in a region of the extension product that lies in the 3′ direction of the extendable end of the first primer. The extendable end of the second primer points in the 5′ direction of the extension product of the first primer. Primer pairs that are suitable for performing the polymerase chain reactions (PCR) and identifying the species or strain of dehalogenating bacteria by the methods of the disclosure are provided in Table 2, wherein odd numbered SEQ ID NO: designations refer to forward primers and even SEQ ID NO: designations refer to reverse primers. Typical amplicons (i.e. the DNA product of a PCR reaction) range in size from 300 by to about 800 base pairs.
The primers of the present disclosure are designed to be specific to regions of the rdh genes identified herein and to allow amplification of rdh-specific sequences under a common PCR condition applied to the microfluidic device used in the analysis. Advantageous primers include, but are not limited to, those having the nucleotide sequence according to SEQ ID NOS: 1-336. Primer pairs suitable for a PCR reaction can be SEQ ID NOs: 1 and 2, 3 and 4, 5 and 6, etc. as disclosed in Table 3.
Quantitative Real-Time PCR Based Enumeration of Dechlorinating Bacteria:
The present disclosure encompasses embodiments of a method of detecting and enumerating dechlorinating bacteria using Quantitative Real-Time PCR (“qPCR”). Quantitative Real-Time PCR allows contemporaneous quantification of a sample of interest, for example a bacteria population having a polynucleotide sequence of interest.
In qPCR, a fluorogenically-labeled oligonucleotide probe can be used in addition to the primer sets which are employed in standard PCR. In qPCR, the probe anneals to a sequence on the target DNA found between a first (forward, 5′ primer) and second (reverse, 3′ primer) PCR primer binding sites and consists of an oligonucleotide with a 5′-reporter dye (e.g., FAM, 6-carboxyfluorescein) and a quencher dye [e.g., TAMRA, 6-carboxytetramethylrhodamine, black hole quencher (BHQ)] which quenches the emission spectra of the reporter dye as long as both dyes are attached to the probe. The probe signals the formation of PCR amplicons by a process involving the polymerase-induced nucleolytic degradation of the double-labeled fluorogenic probe that anneals to the target template at a site between the two primer recognition sequences (see, e.g., U.S. Pat. No. 6,387,652).
The measurement of the released fluorescent emission following each round of PCR amplification (Heid et al., (1996) Genome Res. 6: 986-994) thus forms the basis for quantifying the amount of target nucleic acid present in a sample at the initiation of the PCR reaction. Since the exponential accumulation of the fluorescent signal directly reflects the exponential accumulation of the PCR amplification product, this reaction is monitored in real time. From the output data of the qPCR, quantification from a reliable back calculation to the input target DNA sequence is possible using standard curves generated with known amounts of template DNA.
Quantitative Real-Time PCR may be used to identify and quantify a population of dechlorinating bacteria having a polynucleotide sequence of interest by first isolating DNA from a sample suspected of having dechlorinating activity using any one of the methods known in the art (see e.g., He et al. (2003) Appl. Environ. Microbiol. 65: 485-495) or otherwise herein disclosed. The isolated DNA may be amplified using qPCR by contacting the sample with any one of the primer pairs described above. The isolated DNA sample is subjected to qPCR using any one of the qPCR protocols known in the art or as herein disclosed. During the course of PCR the fluorescent signal generated by the reaction may be continuously monitored using detection hardware known in the art.
The amount of dechlorinating bacteria containing the rdh-specific nucleotide sequence of interest and present in the sample may be determined, using qPCR, by comparing the results of the qPCR assay to a calibration curve. A calibration curve (log DNA concentration versus arbitrarily set cycle threshold value, CT) may be obtained using serial dilutions of DNA of known concentration or gene copy numbers. The CT values obtained for each sample may be compared with the standard curve to determine the abundance of such as Dehalococcoides gene targets.
Idiosyncratic combinations of reductive dehalogenase (rdh) genes are a distinguishing genomic feature of closely related organohalogen-respiring bacteria. This feature can be used to deconvolute the population structure of organohalogen-respiring bacteria in complex environments and to identify relevant subpopulations, which is important for tracking interspecies dynamics needed for successful site remediation. The present disclosure encompasses embodiments of a nanoliter qPCR platform to identify organohalogen-respiring bacteria by quantifying major orthologous reductive dehalogenase gene groups. The qPCR assay primer pairs of the disclosure have been selected as particularly advantageous for use at a single annealing temperature and buffer condition and can be operated in parallel within, for example, a 5184-well nl-qPCR chip. A robust bioinformatics approach was developed to select from thousands of computationally-designed primer pairs those that are specific to individual rdh gene groups and compatible with a single PCR assay condition. The most selective qPCR assay primer pairs were validated and their performance examined in two pilot applications: (i) the quantitative analysis of biostimulated aquifer pore water microcosms from a 1,2-dichloroethane-contaminated site and (ii) a trichloroethene-degrading bioreactor. Both revealed sub-population abundance shifts and unexpected community dynamics.
The number of uncharacterized rdh genes continues to expand rapidly (Hug et al., (2013) Philo. Trans. Roy. Soc. B: Biol. Sci. 368: 20120322-20120322). More than 690 non-redundant Rdh protein sequences are currently in the NCBI database. Given the constraints of existing molecular tools, a microfluidics-based, massively parallel qPCR approach was explored for targeting known rdh orthologue groups to: quantitatively track sub-populations of organohalide-respiring microorganisms, identify geographically-specific bacterial taxons, and observe interspecies population dynamics. The usefulness of this parallel nl-qPCR platform was demonstrated as a tool for the quantitative analysis of rdh gene repertoires and microbial communities, which collectively dehalogenate CAHs. It has now been shown that (i) with a biostimulated aquifer pore-water from a contaminated site and (ii) with a lab-scale bioreactor that the embodiments of the platform of the disclosure translates well to engineering applications. Quantitative data is achieved economically and rapidly from very modest DNA input quantities without bias introduced by DNA pre-amplification.
Reductive dehalogenases (Rdh) enzymes contain two 4Fe-4S clusters and one corrinoid co-factor per catalytic subunit (Müller et al., (2004) Appl. Environ. Microbiol. 70: 4880-4888). Rdhs are identified by the presence of amino acid sequence motifs for binding these cofactors as well as by pairwise amino acid sequence identity to biochemically characterized Rdh enzymes. A sequence-identity-based naming system for Rdhs exists wherein the protein family is divided into orthologue groups (Hug et al., (2013) Philo. Trans. Roy. Soc. B: Biol. Sci. 368: 20120322-20120322). ‘Reductive Dehalogenase Orthologue Groups’ (RD-OGs) are sets of two or more distinct Rdh sequences where all members share at least 90% amino acid identity with another member. RD-OG membership is limited to sequences in known microorganisms. RD-OG sequence similarity does not guarantee shared substrate specificity, however, and members of distinct orthologue groups can have a biochemical activity for a common substrate.
A suite of novel qPCR primers was designed as suitable for the detection of, and distinguishing between, different orthologue groups of reductive dehalogenase (rdh) genes in the Dehalogenase protein family (Pfam) PF13486 (Hug et al., (2013) Philo. Trans. Roy. Soc. B: Biol. Sci. 368: 20120322-20120322). The Pfam database included sequences obtained from both microbial isolates and environmental samples, which were incorporated into the RD-OG framework. Because qPCR primers cannot accommodate degenerate base positions, it was sometimes found necessary to rely on multiple primer sets to encompass an RD-OG.
Assay primer pairs were initially designed for the detection of 54 primary rdh references sequences, where each assay was complementary to at least two additional sequences sharing high percentage pairwise identity (>90%) to the reference. A computational pipeline for the automated primer selection was developed because nl-qPCR requires running PCR reactions with many distinct primer pairs at a single stringent annealing temperature and buffer composition. Unique assay primer pairs were further designed for those rdh genes in Dehalococcoides mccartyi sp. that are not assigned to an orthologue group but have been identified by previous tiling-microarrays.21 The computational pipeline also enabled the design of primers that could differentiate among three closely-related nucleotide sequence types of the important HupL uptake hydrogenase (hupL) in Dehalococcoides mccartyi sp. Assay Specificity: Given high sequence similarity among rdh homologues (Hug et al., (2013) Philo. Trans. Roy. Soc. B: Biol. Sci. 368: 20120322-20120322) it was necessary to test whether the candidate assay primer pairs were specific to their intended target. This specificity was predicted via a bioinformatics search for conserved nucleic acid signatures that were distinguishable among groups of closely-related rdh genes.
Experimentally, assay primer pair specificity were tested in two ways. First, assay primer pair specificity was tested by attempting to amplify dilute linear rdh gene standards in the presence of a concentrated mixture of total genomic DNA isolated from eight non-target anaerobic archaea and bacteria. Genes for rdh are absent in these eight anaerobic microorganisms, but these microbes contain iron-sulfur-cluster and corrinoid-containing enzymes that share motifs similar to regions conserved in Rdh proteins. Second, assay primer pairs were tested against four distinct Dehalococcoides mccartyi cultures for which there was a priori knowledge of their rdh and hupL gene composition. DNA from Dehalococcoides strains isolated from contaminated and wastewater treatment sites was used: VS (Victoria, Tex., USA), ethenogenes 195 (Ithaca, N.Y.), GT (Cottage Grove, Wis., USA), and CBDB1 (Jena, Germany). The isolates (Seshadri et al., (2005) Science 307: 105-108; McMurdie et al., (2009) PLoS Genet. 5, e1000714; Kube et al., (2005) Nat Biotechnol. 23: 1269-1273) represent all three known Dehalococcoides subgroups as defined by 16S rRNA differences: Cornell, Victoria, and Pinellas (Hendrickson et al., (2002) Appl. Environ. Microbiol. 68: 485-495).
Amplification was observed across target DNA concentrations ranging from 25 pg to 0.1 pg per 100 nL reaction. The assay primer pairs were sensitive at the lowest target-DNA inputs tested. In the presence of more concentrated non-target genomic DNA (50 pg per well) from 8 non-organohalogen-respiring anaerobic bacteria, selectivity and sensitivity remained.
For PCR assay primer pairs selected to be included in the final nl-qPCR platform, each assay had to (i) amplify its target with a PCR efficiency greater than 85% (most were >90%), (ii) not amplify negative control DNA prior to thermal cycle 28, and (iii) not exhibit self-dimerization as evidenced by a melt curve analysis. Of 600 candidate rdh assay primer pairs tested, 168 fulfilled these criteria, and absence/presence classification was >93% accurate against the four Dehalococcoides isolates tested (as shown in FIG. 4B).
False-positive amplification could arise from permissive primer binding conditions. There were instances in which an individual assay produced a false-positive result, usually manifested as a delayed amplification for an orthologue group not expected in a given Dehalococcoides isolate. The resulting gene count estimates were 2 to 3 orders of magnitude lower than the gene count estimates for the true-positives, suggesting that partial complementarity between primer and non-target sequences carries the risk of producing a delayed Ct. A delayed amplification could not be distinguished as a false positive by the slope of the amplification curve alone; however, the partial redundancy we designed in the form of multiple assay primer pairs targeting different nucleotide positions on each target reference rdh sequence allowed us to improve detection accuracy.
Across the isolates tested, 15 of the 168 assay primer pairs produced delayed Ct false positive results. In 66% of these cases, the other assay primer pairs for the same target sequence yielded a correct negative result. FIG. 4B reveals these individual false-positive events, as well as the majority result from multiple assay primer pairs to improve the classification of true negatives vs. false positives at the target level. Absence/presence classification accuracy on the target is recorded rather than the individual assay level.
Assay primer pairs for every known RD-OG were not developed but it is contemplated that the primer selection method may be usefully employed to similarly identify new and useful primers for incorporation into the microfluidic devices of the disclosure for the quantitative detection of other bacterial strains later identified. Space on the nl-qPCR chip was selected for those assay primer pairs with support from three or more unique sequences in the database. For some orthologue groups, none of the candidate assay primer pairs passed all the above-mentioned quality control requirements and thus were not included. One particularly useful assay suite, while not intended to be limiting, encompassed 30 orthologue groups, 12 reductive dehalogenase types not-yet assigned an orthologue group, and 3 hydrogenase gene types found in Dehalococcoides mccartyi. It is, however, contemplated that other primer pairs may be devised and selected by the methods of the disclosure to detect rdh gene variants as and when identified. To those assay primer pairs developed here, were added four 16S rRNA marker gene assay primer pairs developed in previous studies32-34 that tested compatible with our nl-qPCR reaction conditions.
Sensitivity:
The sensitivities of the qPCR assay primer pairs were tested against linear DNA standards in ten-fold dilution series. FIG. 1 shows the technical replicates across two separate chips at four dilutions, spanning approximately 20,000, 2,000, 200, and 20 linear gene copies per 100 nl-reaction volume. Proximity to the 45-degree line reflects replicability across chips. The dynamic range of most nl-qPCR assay primer pairs spanned over six orders of magnitude, as has been shown in another study of the technology (Morrison et al., (2006) Nucl. Acids Res. 34: e123-e123).
The sensitivity of the assay primer pairs of the disclosure against low starting gene copy numbers likely to be found in mixed microbial populations were tested. When the assay primer pairs were calibrated against DNA standards, the amplification Ct values were reproducible across duplicate chips at 20,000, 2000 and 200 starting copies per reaction. At higher dilution, the technical variability increased, and at 20 copies per reaction the mean absolute Ct difference between cross-chip replicate samples was 0.73, compared to 0.33, 0.16, and 0.13 at the respective higher concentrations (FIG. 1). The statistically unbiased nature of the errors, as well as results from counting simulations, indicated that an increased Ct difference at low copy numbers was to be expected, as shown in FIGS. 5 and 6.
Accuracy:
Typically, a single qPCR assay can be used to estimate the abundance of a target gene. Despite strong technical reproducibility, such estimates are not necessarily accurate in environmental samples when an unanticipated mismatch between target and primers causes systematic and reproducible shifts in measured Ct. With the large number of parallel reaction wells available to the nl-qPCR approach, it is possible to estimate the abundance of a target gene based on the combined results of multiple unique assays. While the measurement variability from such an approach will be greater than that for an estimate based on a single set of primers, it is a potentially more robust option for probing previously unsequenced bacterial communities.
This multi-assay-per-target approach was explored with well-characterized samples by examining the mean rdh gene counts in Dehalococcoides mccartyi. The median gene count from multiple distinct assay primer pairs targeting the same reference group was calculated. The mean value of these group counts was used to estimate the mean number of rdh copies per sample, which likely had come from a near-clonal Dehalococcoides mccartyi population. For example, when DNA from Dehalococcoides mccartyi CBDB1 was supplied at 1 pg, 10 pg, and 25 pg per well, the mean estimates—and 95% confidence intervals—of rdh gene abundance were 960+/−200, 9800+/−1800, and 22000+/−4600, respectively. These estimates are consistent with theoretical expectations for single copy genes in an organism with a 1.39 Mb genome (approximately 670 copies per pg DNA).
The range of estimates for individual rdh genes within a single Dehalococcoides strains were unexpected, with some estimates greater than double the median estimate possible due to gene duplications, a common evolutionary process in bacteria. Within a near-clonal population, duplicated genes exist in some portion of the population, resulting in total population level DNA that may contain some genes in higher copy numbers than others. In the genome of Dehalococcoides mccartyi VS, there are two instances of near identical rdh genes. Dehalococcoides cultures are maintained through years of serial transfer, whereupon gene duplication may occur.
Another likely cause for the range of estimates in rdh gene abundance is the lack of perfect complementarity between the primers and intended target sequences. All primers were based on the reference nucleic acid sequences published in the NCBI database, as shown in Table 1.







TABLE 1







NCBI Accession numbers, NCBI Description, Source Organism, and Associated


RD-OG of Reference Sequences Used for nL-qPCR Primer Suite Design










NCBI Protein





Accession No.
NCBI Description
Genome
RD-OG













AAC60788.1
tetrachloroethene reductive
Sulfurospirillum multivorans
1



dehalogenase catalytically



active subunit


AAD44542.1
ortho-chlorophenol reductive
Desulfitobacterium dehalogenans
2



dehalogenase catalytically
ATCC51507



active subunit precursor


ACL18777.1
reductive dehalogenase
Desulfitobacterium hafniense DCB-2
4


AAW39060.1
trichloroethene reductive
Dehalococcoides mccartyi 195
5



dehalogenase


ACH87594.1
putative 1,2-dichloroethane
Dehalobacter sp. WL
6.1



reductive dehalogenase


CAJ75430.1
dichloroethane reductive
Desulfitobacterium dichloroeliminans
6.2



dehalogenase
LMG P-21439


CAD28790.2
tetrachloroethene reductive
Dehalobacter restrictus
6.3



dehalogenase


BAE84628.1
tetrachloroethene
Desulfitobacterium hafniense Y51
6.4



dehalogenase


CAR57931.1
reductive dehalogenase
uncultured bacterium
6.5



subunit A


ACH87598.1
putative reductive
Dehalobacter sp. MS
6.6



dehalogenase RdhA1


ACZ62391.1
vinyl chloride reductive
Dehalococcoides mccartyi VS
8



dehalogenase


AAQ54585.2
3,5-dichlorophenol reductive
Desulfitobacterium hafniense
9



dehalogenase


ACZ62520.1
reductive dehalogenase
Dehalococcoides mccartyi VS
10


ACZ62501.1
reductive dehalogenase
Dehalococcoides mccartyi VS
11


ACF24861.1
putative reductive
Dehalococcoides sp. MB
12.1



dehalogenase


ABY28312.1
putative reductive
Dehalococcoides sp. enrichment
12.2



dehalogenase
culture clone KS22(KSRdA03)


AAW39229.1
putative reductive
Dehalococcoides mccartyi 195
13



dehalogenase


ACZ62529.1
reductive dehalogenase
Dehalococcoides mccartyi VS
13.1


BAG72170.1
reductive dehalogenase
uncultured bacterium
14



homolog


ACZ62535.1
reductive dehalogenase
Dehalococcoides mccartyi VS
15


ACZ62362.1
reductive dehalogenase
Dehalococcoides mccartyi VS
17


ACZ62482.1
reductive dehalogenase
Dehalococcoides mccartyi VS
19


ABQ16695.1
reductive dehalogenase
Dehalococcoides mccartyi BAV1
20


ABQ16703.1
reductive dehalogenase
Dehalococcoides mccartyi BAV1
21


ACZ61341.1
reductive dehalogenase
Dehalococcoides mccartyi VS
23


ACZ61277.1
reductive dehalogenase
Dehalococcoides mccartyi VS
24


ACZ61272.1
reductive dehalogenase
Dehalococcoides mccartyi VS
25


ACZ61261.1
reductive dehalogenase
Dehalococcoides mccartyi VS
27


AAT64888.1
putative vinyl chloride
Dehalococcoides mccartyi BAV1
28



reductive dehalogenase



bvcA


ACZ62492.1
reductive dehalogenase
Dehalococcoides mccartyi VS
30


ACZ62459.1
reductive dehalogenase
Dehalococcoides mccartyi VS
31


ADC74655.1
reductive dehalogenase
Dehalococcoides mccartyi GT
32.1


AAW39273.1
putative reductive
Dehalococcoides mccartyi 195
32.2



dehalogenase


AAW39262.1
putative reductive
Dehalococcoides mccartyi 195
33



dehalogenase


AAW39240.1
putative reductive
Dehalococcoides mccartyi 195
34



dehalogenase


AAW39215.1
putative reductive
Dehalococcoides mccartyi 195
35



dehalogenase


CAI83519.1
putative reductive
Dehalococcoides mccartyi CBDB1
36



dehalogenase


ADC74627.1
reductive dehalogenase
Dehalococcoides mccartyi GT
37


ACZ62477.1
reductive dehalogenase
Dehalococcoides mccartyi VS
38


ACZ62486.1
putative reductive
Dehalococcoides mccartyi VS
39



dehalogenase


AAR24308.1
reductive dehalogenase
Dehalococcoides mccartyi CBDB1
40



homologous protein RdhA7


AAT48554.1
putative reductive
Dehalococcoides mccartyi BAV1
NA



dehalogenase


AAW39256.1
putative reductive
Dehalococcoides mccartyi 195
NA



dehalogenase


AAW39843.1
putative reductive
Dehalococcoides mccartyi 195
NA



dehalogenase


AAW40589.1
putative reductive
Dehalococcoides mccartyi 195
NA



dehalogenase


ACZ62413.1
reductive dehalogenase
Dehalococcoides mccartyi VS
NA


ACZ62419.1
reductive dehalogenase
Dehalococcoides mccartyi VS
NA


ACZ62441.1
reductive dehalogenase
Dehalococcoides mccartyi VS
NA


ACZ62470.1
reductive dehalogenase
Dehalococcoides mccartyi VS
NA


BAF34982.1
trichloroethene reductive
uncultured Dehalococcoides sp.
NA



dehalogenase


BAI47830.1
putative reductive
uncultured bacterium
NA



dehalogenase


BAI70453.1
reductive dehalogenase
uncultured bacterium
NA


CAI83531.1
putative reductive
Dehalococcoides mccartyi CBDB1
NA



dehalogenase


CAI83566.1
putative reductive
Dehalococcoides mccartyi CBDB1
NA



dehalogenase





NA: Sequences not having designated RD-OG






Even for these sequenced isolates, recently accumulated mutations that may be present in the DNA retrieved for this study could produce mismatches that result in systematic downward Ct shifts. The likelihood of Ct shifts increases when primers are applied to previously unsequenced populations. In this context, heightened variability among gene counts can be expected.
Pilot Applications:
After establishing the sensitivity and selectivity of the assay primer pairs in a controlled experimental context, evaluation of performance of the newly established nl-qPCR platform in applications directly relevant to bioremediation was undertaken. Pilot applications were performed to quantitatively (i) evaluate the biostimulation potential of different sections of a contaminated aquifer and (ii) determine sub-population-level responses of dehalogenating microbes to electron donor limitation in a continuously-fed TCE bioreactor.
Biostimulation Potential in a Contaminated Field Site:
In virtually all field environments, hydrological and geochemical conditions are heterogeneous and levels of contaminants vary spatially. For successful in situ bioremediation of CAHs, engineers often need to gauge the potential effectiveness of the remediation technology in different areas of the site that might respond to the intervention according to variable biological and geochemical characteristics. Accordingly, in one study, focusing on three observation wells, 100-500 horizontal meters apart and representative of diverse areas throughout the site, it was endeavored to assess the level of spatial heterogeneity in rdh gene abundance and biochemical potential for the transformation of 1,2-dichloroethane (1,2-DCA).
Several types of organohalogen-respiring bacteria are known to dechlorinate 1,2-DCA. Two distinct dcaA genes have been found to be associated with 1,2-DCA dihaloelimination to ethene in laboratory cultures. Both discovered dcaA genes are members of RD-OG 6, but they share only 88% pairwise identity at the amino acid level by blastp. The first dcaA (hereafter dcaA type I) was identified in Desulfitobacterium dichloroeliminans (Marzorati et al., (2007) Appl. Environ. Microbiol. 73: 2990-2999; De Wildeman et al., (2003) Appl. Environ. Microbiol. 69: 5643-5647). A second type of dcaA (hereafter dceA type II) was found in a Dehalobacter sp. (Grostern et al., (2009) Appl. Environ. Microbiol. 75: 2684-2693). Certain strains of Dehalococcoides mccartyi and Dehalogenimonas sp. have also been shown to be capable of growth-linked dechlorination of 1,2-DCA, but the responsible enzymes have not yet been identified. It remains unclear which of these enzymes is most relevant for degrading 1,2-DCA in the field, and under what conditions.
Aquifer pore water contaminated with 1,2-DCA was collected from observation wells at an industrial site in Italy. The microbiology of the site had not been previously characterized. Thus, it was possible to evaluate whether assay primer pairs of the disclosure designed to be complementary to conserved DNA signatures among database sequences would be effective at amplifying genes in an environment where there was no a priori sequence information. Replicate pore water samples from each well were placed in serum vials and amended with 2 mM sodium lactate, sodium formate, sodium acetate, or a mineral salt control.
The quantification of rdh and 16S rRNA marker genes (targeting Dehalococcoides, Geobacter and Desulfitobacterium genera) combined with chemical time-point measurements from the pore water samples revealed a high degree of heterogeneity in biostimulation response and resident OHRB community structure at each sampling well. The effect of the biostimulants on the fate of 1,2-DCA varied and no single biostimulant consistently facilitated dechlorination across all three pore waters (FIG. 2A). The Geobacter 16S rRNA gene was detected at all three wells and was abundant in samples from wells BPR03 and PC008, but was less abundant in PC031. The enrichment of Geobacter in BPR03 and PC008 pore waters under lactate stimulation occurred in a roughly stoichiometric fashion with the enrichment of a dcaA type I gene. The type II dcaA gene was not detected in the BPR03 nor PC008 pore water, regardless of stimulant condition.
Previous studies of rdh-containing Geobacter lovleyi showed the bacterium's capacity for growth-linked dehalogenation of PCE but not for 1,2-DCA (Sung et al., (2006) Appl. Environ. Microbiol. 72: 2775-2782). However, the role of Geobacter in this environment and the limitations on its activity are not straightforward. Concomitant enrichment of the Geobacter 16S rRNA gene and the type I dcaA was neither necessary nor sufficient for 1,2-DCA transformations across all treatments. While 1,2-DCA transformation was observed for lactate amended BPR03 pore water, no similar 1,2-DCA transformation was observed in lactate-amended PC008 pore water, despite equal or greater enrichment of Geobacter 16S rRNA and the putative dcaA type I gene (FIG. 2B). It is possible that the enriched well BPR03 Geobacter population may contain this type I dcaA gene and is capable of growth with 1,2-DCA as a terminal electron acceptor.
Pore water from well PC031 appeared to have a markedly different organohalogen-respiring community structure than that in either BPR03 or PC008, with Dehalococcoides sp. in equivalent or greater abundance than Geobacter sp. and Desulfitobacterium sp. When stimulated with lactate, a large number of reductive dehalogenase orthologue groups were detected at varying abundances, suggesting the presence of multiple distinct Dehalococcoides sub-populations. This is consistent with the significant Dehalococcoides sp. diversity found in this area: all three hupL gene groups (Cornell, Victoria, and Pinellas) were detected in both lactate and formate-amended PC031 pore water (as shown in FIG. 2B). The dehalogenation of 1,2-DCA with lactate, but not the formate, suggests that the putative type I dcaA gene enriched in both cases may not be a driver for the observed 1,2-DCA dechlorination.
Determining Composition of Organohalgen-Respiring Bacteria in a Continuous Bioreactor:
In a separate study, the nl-qPCR platform according to the disclosure was used to investigate the effect of electron donor limitation on the population structure of organohalogen-respiring bacteria in a continuous-flow bioreactor inoculated with aquifer material from the Evanite contaminated site in Corvallis, Oreg., USA. The EV2L reactor was operated as a chemostat with influent TCE at 10 mM. After 168 days of the reactor's 5 year operation, the influent formate concentration was reduced from 45 mM to 25 mM.
The high degree of sequence similarity at the 16S rRNA gene level among Dehalococcoides mccartyi strains has complicated the tracking of distinct Dehalococcoides sub-populations via conventional qPCR or 16S short-amplicon sequencing. However, the relative stoichiometry of different subtypes of Dehalococcoides is important for modeling the degradation kinetics and partitioning of TCE, cDCE, and VC electron acceptors among closely related bacterial strains.
DNA samples from the reactor's five-year operation were brought to a standard concentration of 10 ng/μl. 20 ng of DNA was applied to duplicate nl-qPCR chips, resulting in a final input of 25 pg of total community DNA per reaction well. The most likely population structure of organohalogen-respiring bacteria in the reactor was inferred using a correlation-based clustering method similar to that described by Marshall et al. Briefly, gene abundance profiles were hierarchically clustered by their time-series correlation, as shown in FIG. 3A. Correlated genes were grouped into clusters representing hypothesized strains if they were at similar absolute abundance.
Operationally Identified Strains:
The clustering pattern of rdh and hupL gene counts suggests the presence of at least four distinct organohalogen-respiring sub-populations within the EV2L reactor (FIG. 3A). These operational strains are designated as Ev1, Ev2, Ev3, and Ev4. Throughout the reactor's operation, Ev1 appears to be most numerous (FIG. 3B). Multiple lines of evidence suggested that Ev1 is a Dehalococcoides-like-bacterium: Ev1 links at least four orthologue groups (5, 10, 13, and 23), which have so far only been found in Dehalococcoides isolates or environmental samples. Group 5 is the best understood, since it contains the characterized trichloroethene reductase tceA first discovered in Dehalococcoides mccartyi strain ethenogenes 195 (He et al., (2003) Nature 424: 62-65).
The rdh gene clustering supports the assignment of a detected vinyl chloride reductase vcrA gene to the numerically less abundant Ev2, a second Dehalococcoides-like operational strain. In addition to vcrA, Ev2 is predicted to contain at least 9 other orthologue groups (10, 11, 13, 15, 17, 20, 21, 30, 32). In contrast to Ev1, Ev2 declined precipitously in the final 500 days of the time course. At day 168, prior to the introduction of formate-limiting conditions, the mean estimate of rdh gene count in Ev2 was 1500+/−600 copies per 25 pg of total community DNA. By the end of experiment, the mean estimate of Ev2 was 90+/−60 copies. Moreover, the decline in Ev2 correlates with changes in reactor's chemical performance, where the percentage of TCE converted fully to ethene dropped from 90% to 30% (FIG. 3C). At day 600, Ev2 was estimated to constitute more than 1/10th of the total Dehalococcoides population, but by the end, it constituted less than 1/200th. Because the dominant tceA-containing strain Ev1 remained in far greater abundance, the dramatic decline in the vcrA-containing-population was not obvious from 16S rRNA-based qPCR measurements alone (FIG. 3D).
Ev3, a third operationally defined Dehalococcoides-like strain containing RD-OG 1, 12, 28, 38, 40, and 48 was even rarer. This strain appears to have gained a modest presence by day 900, reaching an estimated mean of 40+/−20 copies per 25 pg of total community DNA. This strain was near the limit of detection at the experiment's onset and was no longer detected in the last 300 days of the time-course. The detection of this strain at such low absolute copy numbers highlights the sensitivity of this nl-qPCR platform for tracking rare populations in mixed bacterial ecosystems. This rare Dehalococcoides-like strain was not detected when similar samples were studied using a less sensitive tiling DNA-DNA hybridization microarray approach.
Ev4, a fourth-operational non-Dehalococcoides-like strain, was also detected. It is predicted to contain genes from orthologue groups 6 and 9. The known substrate range of orthologue group 6 members, so far found in Dehalobacter and Desulfitobacterium isolates, includes PCE as well as 1,2-DCA (Marzorati et al., (2007) Appl. Environ. Microbiol. 73: 2990-2999; De Wildeman et al., (2003) Appl. Environ. Microbiol. 69: 5643-5647; Suyama et al., (2002) J. Bacteriol. 184: 3419-3425), so this strain's precise role in a TCE-fed reactor is uncertain. Nevertheless, a niche for this strain was apparently stably maintained.
Linkage of rdh to hupL Genes:
The correlation among hupL and rdh gene counts allowed for the inference of linkages between functional genes. For instance, the genome of vcrA-containing operational strain Ev2 appears to contain a Pinellas-type HupL hydrogenase. Similarly, the gene abundance profile of the Cornell type HupL hydrogenase indicates that it is present in the numerically dominant tceA-containing population Ev1 (FIG. 3B). If applied to more systems, this approach can reveal whether particular rdh and hupL genes are in linkage disequilibrium. If hydrogenases have different kinetic characteristics that are phenotypically relevant, consistent linkage between particular rdh and specific hupL types can delineate niche boundaries between sub-populations. This ecological information may prove useful as a design lever for managing community structure during bioremediation, since the ratio of Dehalococcoides types influences the kinetics of different degradation steps.
Diametric Ev2 and Geobacter Population Shifts:
One strain's expansion consistently co-occurred with the recession of another strain and vice-versa (FIG. 3B). These shifts in a constantly fed mixed reactor are suggestive of fine-scale niche boundaries determining the outcome of direct competition. Despite automation, subtle shifts in chemical composition in a reactor can be sufficient to shift population. Diametric shifts can also reflect density-dependent fitness dynamics observed during phage-predation on a sub-population (Rodriguez-Valera et al., (2009) Nat. Rev. Microbiol. 7: 828-836). The stability of the dominant Dehalococcoides-type suggests that predation was not the dominant ecological process in these systems, although the frequency of sampling was inadequate to rule it out completely. The modest DNA input requirements associated with the nl-qPCR technique of the present disclosure do advantageously allow more frequent sampling regimes in experiments.
There was an diametric relationship between the vcrA-containing Ev2 population and the 16S rRNA marker gene for Geobacter (FIG. 3C). Geobacter is most often studied as an iron-respiring bacterium (Lovley et al., (1993) Arch. Microbiol. 159: 336-344; Caccavo et al., (1994) Appl. Environ. Microbiol. 60: 3752-3759). One species of Geobacter has been shown to carry rdh genes and the capacity for growth-linked PCE-reduction (Sung et al., (2006) Appl. Environ. Microbiol. 72: 2775-2782; Wagner et al., (2012) BMC Genomics. 13: 200). The negative correlation between a presumed Geobacter strain and Ev2 is consistent with competition for a shared resource, such as hydrogen, acetate, or a CAH electron acceptor, although other explanations for the diametric relations cannot be excluded. The two-order of magnitude predicted increase in Geobacter population between days 1281 and 1347 coincided with a decline in the vcrA-type Ev2, but no decline was detected in the tceA-containing Ev1 strain. Hydrogen concentrations gradually decreased from 5 nM to 1-2 nM over the period of 600 to 1731 days, corresponding to the decrease of Ev2 strain. Competition for hydrogen might be a factor for this decrease, since previous studies of different VC-respiring Dehalococcoides strains reported hydrogen thresholds near 1 nM (Cupples & Spormann (2004) Environ. Sci. & Technol. 38: 1102-1107; Sung et al., (2006) Appl. Environ. Microbiol. 72: 1980-1987).
Since increases in Geobacter 16S gene copies were observed after two sampling events, these events may have influenced the selective conditions within the reactor. For instance, an introduction of trace oxygen or a change in reactor pH could tip the ecological balance in the Geobacter-like organism's favor. The reactor appeared to return to Dehalococcoides-favorable equilibrium between days 981-1281, but a similar re-equilibration did not occur after the subsequent Geobacter increase at day 1347, indicating a new stable state was reached (FIGS. 3C and 3D).
Geobacter and multiple Dehalococcoides-like strains often co-inhabit contaminated sediment environments. It has now been shown that rdh gene profiling by nl-qPCR using the methods of the disclosure can be useful for monitoring competition among closely related strains. Characterization of the biochemical potential, population stoichiometry, and perturbation-response-phenotypes of relevant organohalogen-respiring strains is a prerequisite for accurate modeling.
One aspect of the disclosure encompasses embodiments of a method for identifying a dechlorinating microbial organism, or a plurality of said microbial organisms, in a sample comprising: (a) obtaining a sample suspected of having a population of at least one microbial strain having at least one species of a reductive dehalogenase enzyme; (b) isolating nucleic acid from the sample; (c) applying the isolated nucleic acid to a microfluidic device configured for quantitative real-time PCR and comprising a panel of reductive dehalogenase (rdh)-specific PCR primer pairs, wherein each primer pair of the panel is selected to allow amplification of a specific target nucleotide sequence under a common PCR protocol; (d) simultaneously performing quantitative real-time PCR on the isolated nucleic acid in the microfluidic device with each rdh-specific PCR primer pair of said panel and under conditions wherein the presence of a microbial reductive dehalogenase (rdh)-related nucleic acid sequence results in at least one detectable amplicon encoding a region of a reductive dehalogenase (rdh); (e) detecting the at least one amplicon of step (d); (f) identifying the reductive dehalogenase enzyme encoded by the at least one amplicon; and (g) identifying the microbial strain or strains in the sample of step (a) that has at least one reductive dehalogenase enzyme.
In embodiments of this aspect of the disclosure, the sample can react with a primer pair in a total reaction volume of between about 3 nanoliters and about 500 nanoliters.
In embodiments of this aspect of the disclosure, the at least one primer of each primer pair can have a detectable label attached thereto.
In embodiments of this aspect of the disclosure, the detectable label is a fluorescent dye.
In embodiments of this aspect of the disclosure, the panel of reductive dehalogenase (rdh)-specific PCR primer pairs comprises at least one PCR primer pair selected from the group of PCR primer pairs according to Table 3.
In embodiments of this aspect of the disclosure, the method can further comprise the step of quantitatively determining the population of microbial strains in the sample of step (a) that have a reductive dehalogenase enzyme.
In embodiments of this aspect of the disclosure, the sample can be a sample obtained from a location suspected of comprising at least one microbial strain having a reductive dehalogenase (rdh) enzyme.
In embodiments of this aspect of the disclosure, the method can further comprise the step of obtaining an aqueous sample from a non-aqueous sample.
In embodiments of this aspect of the disclosure, the method can further comprise the step of classifying the identified reductive dehalogenase enzyme(s) encoded by the at least one amplified PCR product according to their respective reductive dehalogenase (rdh) orthologous groups.
In embodiments of this aspect of the disclosure, the panel of reductive dehalogenase (rdh)-specific PCR primer pairs consists essentially of at least one PCR primer pair selected from the group of PCR primer pairs according to Table 3.
In embodiments of this aspect of the disclosure, the panel of reductive dehalogenase (rdh)-specific PCR primer pairs consists of at least one PCR primer pair selected from the group of PCR primer pairs according to Table 3.
Another aspect of the disclosure encompasses embodiments of a microfluidic nanoliter-quantitative PCR device configured for quantitative real-time PCR and comprising a panel of reductive dehalogenase (rdh)-specific PCR primer pairs.
In some embodiments of this aspect of the disclosure, the panel of reductive dehalogenase (rdh)-specific PCR primer pairs comprises at least one PCR primer pair selected from the group of PCR primer pairs according to Table 3.
In some embodiments of this aspect of the disclosure, the panel of reductive dehalogenase (rdh)-specific PCR primer pairs consists essentially of at least one PCR primer pair selected from the group of PCR primer pairs according to Table 3.
In some embodiments of this aspect of the disclosure, the panel of reductive dehalogenase (rdh)-specific PCR primer pairs consists of the PCR primer pairs according to Table 3.
The specific examples below are to be construed as merely illustrative, and not limitative of the remainder of the disclosure in any way whatsoever. Without further elaboration, it is believed that one skilled in the art can, based on the description herein, utilize the present disclosure to its fullest extent. All publications recited herein are hereby incorporated by reference in their entirety.
It should be emphasized that the embodiments of the present disclosure, particularly, any “preferred” embodiments, are merely possible examples of the implementations, merely set forth for a clear understanding of the principles of the disclosure. Many variations and modifications may be made to the above-described embodiment(s) of the disclosure without departing substantially from the spirit and principles of the disclosure. All such modifications and variations are intended to be included herein within the scope of this disclosure, and the present disclosure and protected by the following claims.
The following examples are put forth so as to provide those of ordinary skill in the art with a complete disclosure and description of how to perform the methods and use the compositions and compounds disclosed and claimed herein. Efforts have been made to ensure accuracy with respect to numbers (e.g., amounts, temperature, etc.), but some errors and deviations should be accounted for. Unless indicated otherwise, parts are parts by weight, temperature is in ° C., and pressure is at or near atmospheric. Standard temperature and pressure are defined as 20° C. and 1 atmosphere.
EXAMPLES
Example 1
Development of a rdh qPCR Assay Suite:
A suite of novel qPCR primer pairs was designed to detect and distinguish between full-length and near-full-length reductive dehalogenase (rdh) gene groups. The Dehalogenase protein family (Pfam v 26.0) PF13486 (Punta et al., (2012) Nucl. Acids Res. 40: D290-D301) as a database of non-redundant Rdh protein sequences was used and consideration was limited to sequences 350-700 amino acids in length. Corresponding rdh nucleotide sequences were downloaded from NCBI (Accession numbers are given in Table 1).
Pfam sequences were clustered based on percent pairwise identity (PID) using blastp as described in Altschul et al., (1990) J. Mol. Biol. 215: 403-410, incorporated herein in its entirety by reference). Assay primer pairs were designed for 54 references sequences, most with at least one known high-PID homologue (>90% amino acid level). A Python script directed the software primer3 (Rozen & Skaletsky (2000) Methods Mol. Biol. 132: 365-386, incorporated herein by reference in its entirety) to generate thousands of candidate primer pairs that were ranked based on oligonucleotide complementarity to high-PID sequences with the primary reference sequence. Where possible, two assay types for each reference sequence were selected. The first was ‘specific’ to a reference sequence and those homologues with high PID values. The second ‘extended’ the number of sequences matched by the primers to include the reference sequence as well as many homologue sequences as possible.
Example 2
Initial Screening of Candidate Assays:
Primer performance data were collected using a SMARTCHIP MYDESIGN® (Wafergen Biosystems, Fremont, Calif.) platform. Chips were prepared by robotically dispensing oligonucleotide primers (Integrated DNA Technology) at a final concentration of 1 μM into 100 nL wells. Assay primer pairs were tested using both (20 sample×248 Assay) and (12 Sample×384 Assay) formats. For each sample, data were collected from two separate chip runs using a standard WaferGen protocol: 95° C. for 3 min, then 40 cycles of 95° C. for 60 sec and 60° C. for 70 sec.
Candidate assay primer pairs were physically tested against a collection of 500 bp synthesized linear DNA standards (Integrated DNA Technology) diluted to concentrations of 20,000, 2000, 200, and 20 copies per 100 nL reaction well. Assay primer pairs at 5 copies per reaction well were also tested.
Candidate assay primer pairs that failed to amplify standards at 5 copies per well or reproducibly amplified the negative control before cycle 28 were excluded from further consideration. Candidate assay primer pairs with PCR efficiencies less than 85% were also excluded, thereby providing 168 assay primer pairs (i.e. primer pairs) that met these requirements. The primers (forward and reverse primers) are listed in Table 2. Primer pairs selected for use in the methods of the disclosure are given in Table 3.







TABLE 2





Primers

















SEQ ID NO: 1
AAC60788.1_378_ext_F_1302
TGGATTCATGATGGCGTTGA


SEQ ID NO: 2
AAC60788.1_378_ext_R_1391
ACCATAGCCCAATGCATCAT


 


SEQ ID NO: 3
AAC60788.1_624_ext_F_1302
TGGATTCATGATGGCGTTGA


SEQ ID NO: 4
AAC60788.1_624_ext_R_1384
CCCAATGCATCATCCATACCA


 


SEQ ID NO: 5
AAD44542.1_105_ext_F_984
TTCTGCCGGGTATGCAAAAA


SEQ ID NO: 6
AAD44542.1_105_ext_R_1086
CACTGTTCCAACGCAGGTAT


 


SEQ ID NO: 7
AAD44542.1_11_spec_F_1016
TTGTCCAAACGACGCGATTA


SEQ ID NO: 8
AAD44542.1_11_spec_R_1091
AAAGTCACTGTTCCAACGCA


 


SEQ ID NO: 9
AAD44542.1_1304_ext_F_1067
ATACCTGCGTTGGAACAGTG


SEQ ID NO: 10
AAD44542.1_1304_ext_R_1201
CCTGCTTTATGGAACCAGGA


 


SEQ ID NO: 11
AAD44542.1_14_spec_F_742
GCTGCATTGCCGTCATTATG


SEQ ID NO: 12
AAD44542.1_14_spec_R_868
GACAATTCTCCCAGACCTGC


 


SEQ ID NO: 13
AAD44542.1_43_ext_F_849
GCAGGTCTGGGAGAATTGTC


SEQ ID NO: 14
AAD44542.1_43_ext_R_934
GTCGTTACTGCGGCTACTTT


 


SEQ ID NO: 15
AAD44542.1_7_spec_F_572
TACAGTCGGACTCATGAGCA


SEQ ID NO: 16
AAD44542.1_7_spec_R_766
TTGGCCATAATGACGGCAAT


 


SEQ ID NO: 17
AAQ54585.2_1_spec_F_576
GTGTTTCTGGCGGGAATGTA


SEQ ID NO: 18
AAQ54585.2_1_spec_R_748
GTCCAGCGATCGTCATAAGG


 


SEQ ID NO: 19
AAQ54585.2_1053_ext_F_1446
TGCTCCTGGAACAAAATCGA


SEQ ID NO: 20
AAQ54585.2_1053_ext_R_1544
CCACTCATCGAACTTACGGG


 


SEQ ID NO: 21
AAQ54585.2_1536_ext_F_1292
GGCGATCTCCCATGTGAAAG


SEQ ID NO: 22
AAQ54585.2_1536_ext_R_1474
TGCCAGGCATCGATTTTGTT


 


SEQ ID NO: 23
AAQ54585.2_3115_ext_F_1203
TTGGAACTTGTTCCGGACAA


SEQ ID NO: 24
AAQ54585.2_3115_ext_R_1316
GGGGTCTTTCACATGGGAGA


 


SEQ ID NO: 25
AAR24308.1_0_spec_F_235
GCAAAACAGAAAGCAGACCG


SEQ ID NO: 26
AAR24308.1_0_spec_R_352
CATGTGAAAAACCTGCCTGC


 


SEQ ID NO: 27
AAR24308.1_4_spec_F_183
TCAAGTTGCGTATGCCAGTT


SEQ ID NO: 28
AAR24308.1_4_spec_R_352
CATGTGAAAAACCTGCCTGC


 


SEQ ID NO: 29
AAR24308.1_9_spec_F_918
CACAGATTTGCCATTGGTGC


SEQ ID NO: 30
AAR24308.1_9_spec_R_1042
AGGAAGGAACATCATCCGGA


 


SEQ ID NO: 31
AAT64888.1_1_spec_F_983
TAATGGAGGCCGAGTTCAGA


SEQ ID NO: 32
AAT64888.1_1_spec_R_1106
ACGACCTTGTTCGGAAAGAC


 


SEQ ID NO: 33
AAT64888.1_18_spec_F_922
AACGTTCTCTAGGGTGGTCA


SEQ ID NO: 34
AAT64888.1_18_spec_R_1002
TCTGAACTCGGCCTCCATTA


 


SEQ ID NO: 35
AAW39060.1_1596_spec_F_1129
GAGTTGAAGCTTGGGGTCC


SEQ ID NO: 36
AAW39060.1_1596_spec_R_1293
CGGCATCTATAGGCTTGGTG


 


SEQ ID NO: 37
AAW39060.1_1629_spec_F_1025
ACCTATGGACCCATGCTCTT


SEQ ID NO: 38
AAW39060.1_1629_spec_R_1146
GACCCCAAGCTTCAACTCC


 


SEQ ID NO: 39
AAW39060.1_2131_spec_F_1129
GAGTTGAAGCTTGGGGTCC


SEQ ID NO: 40
AAW39060.1_2131_spec_R_1289
ATCTATAGGCTTGGTGGGGG


 


SEQ ID NO: 41
AAW39215.1_0_spec_F_793
TAGCACAGTGGCGTTTACAG


SEQ ID NO: 42
AAW39215.1_0_spec_R_898
CCAGACATAACACCCCAACC


 


SEQ ID NO: 43
AAW39215.1_10_spec_F_879
GGTTGGGGTGTTATGTCTGG


SEQ ID NO: 44
AAW39215.1_10_spec_R_1034
ACAAAACTTTCTGGCACCGA


 


SEQ ID NO: 45
AAW39215.1_15_spec_F_801
TGGCGTTTACAGGCATTTCT


SEQ ID NO: 46
AAW39215.1_15_spec_R_898
CCAGACATAACACCCCAACC


 


SEQ ID NO: 47
AAW39215.1_7_spec_F_1052
TGCTGATCTTTGCCCTTCTG


SEQ ID NO: 48
AAW39215.1_7_spec_R_1229
AACGCCGCAATAGGTATCTG


 


SEQ ID NO: 49
AAW39229.1_204_spec_F_1257
TGTACCGGCGTTTGTGTATT


SEQ ID NO: 50
AAW39229.1_204_spec_R_1419
GGTCAAGATCCCACCATTCG


 


SEQ ID NO: 51
AAW39240.1_1121_spec_F_889
AAAGATTCCCCTTTGTCGGG


SEQ ID NO: 52
AAW39240.1_1121_spec_R_1081
ATTACCCACATAGCCCGGTT


 


SEQ ID NO: 53
AAW39240.1_1506_spec_F_666
GGTGCTCAGGAAATGGATTCA


SEQ ID NO: 54
AAW39240.1_1506_spec_R_819
GGGCAGTCCACTGGAGTATA


 


SEQ ID NO: 55
AAW39240.1_2398_spec_F_946
CTGCGGTTTCCACCCATATG


SEQ ID NO: 56
AAW39240.1_2398_spec_R_1081
ATTACCCACATAGCCCGGTT


 


SEQ ID NO: 57
AAW39240.1_4451_spec_F_801
ATACTCCAGTGGACTGCCC


SEQ ID NO: 58
AAW39240.1_4451_spec_R_961
TGGGTGGAAACCGCAGTATA


 


SEQ ID NO: 59
AAW39256.1_76_spec_F_1109
CGGTTCACATCTTAGAGGACAG


SEQ ID NO: 60
AAW39256.1_76_spec_R_1192
CGTTCCATACCGGCATCTAT


 


SEQ ID NO: 61
AAW39256.1_95_spec_F_1109
CGGTTCACATCTTAGAGGACAG


SEQ ID NO: 62
AAW39256.1_95_spec_R_1183
CCGGCATCTATGGGTTTGG


 


SEQ ID NO: 63
AAW39256.1_96_spec_F_1109
CGGTTCACATCTTAGAGGACAG


SEQ ID NO: 64
AAW39256.1_96_spec_R_1198
CAGAAGCGTTCCATACCGG


 


SEQ ID NO: 65
AAW39262.1_2442_spec_F_1050
ATGTCTTCCCCTGCCATTCA


SEQ ID NO: 66
AAW39262.1_2442_spec_R_1200
AGGCATCAGCACAAATACCG


 


SEQ ID NO: 67
AAW39273.1_1218_spec_F_1259
CAACCTGTTCAGCTGTGCAT


SEQ ID NO: 68
AAW39273.1_1218_spec_R_1416
CACCCTCCATGCTGGTAAAG


 


SEQ ID NO: 69
AAW39273.1_2015_ext_F_1101
TGCGGTATCTGTGCTGAAAC


SEQ ID NO: 70
AAW39273.1_2015_ext_R_1183
TGGCCGCAATTATTATCCCA


 


SEQ ID NO: 71
AAW39843.1_0_spec_F_1212
GAATTTGGCTCAGTTTGCGG


SEQ ID NO: 72
AAW39843.1_0_spec_R_1324
GCGCATTTACGGCAAGTATG


 


SEQ ID NO: 73
AAW39843.1_13_spec_F_1169
TATAGCAGAGATGGGACGCA


SEQ ID NO: 74
AAW39843.1_13_spec_R_1300
AAACGGAATATCCCAGCGTC


 


SEQ ID NO: 75
AAW39843.1_19_spec_F_1249
CTGACTTGCCTCTAATGCCA


SEQ ID NO: 76
AAW39843.1_19_spec_R_1324
GCGCATTTACGGCAAGTATG


 


SEQ ID NO: 77
AAW40581.1_4941_spec_F_202
GCACTACCGCCGCTTTAAA


SEQ ID NO: 78
AAW40581.1_4941_spec_R_276
GGAGTATCCGCCCGTTATTC


 


SEQ ID NO: 79
AAW40581.1_91_spec_F_957
CTGAACGAGGTAACCGAACC


SEQ ID NO: 80
AAW40581.1_91_spec_R_1046
TACTTCGTAGGGAGTGCCAT


 


SEQ ID NO: 81
AAW40581.1_96_spec_F_1027
ATGGCACTCCCTACGAAGTA


SEQ ID NO: 82
AAW40581.1_96_spec_R_1216
ACCATTTCGTCAGCCACAAT


 


SEQ ID NO: 83
AAW40581.1_98_spec_F_886
CCTTTGACCCCAGCAAGATT


SEQ ID NO: 84
AAW40581.1_98_spec_R_1046
TACTTCGTAGGGAGTGCCAT


 


SEQ ID NO: 85
AAW40589.1_12_spec_F_1218
GGCAGTGTTCACGGCTATTT


SEQ ID NO: 86
AAW40589.1_12_spec_R_1344
ATTTGGCAGGGCATTCATCA


 


SEQ ID NO: 87
AAW40589.1_5_spec_F_1186
GCAACTCAAACGTCTGCATC


SEQ ID NO: 88
AAW40589.1_5_spec_R_1312
CAGGTATGGCAGAAACGGAA


 


SEQ ID NO: 89
ABQ16695.1_3523_spec_F_1205
TGCTAATTCCAATCCCACCAA


SEQ ID NO: 90
ABQ16695.1_3523_spec_R_1302
CCCAGAAATTGTGACAGGCA


 


SEQ ID NO: 91
ABQ16695.1_627_spec_F_1209
AATTCCAATCCCACCAAGCT


SEQ ID NO: 92
ABQ16695.1_627_spec_R_1302
CCCAGAAATTGTGACAGGCA


 


SEQ ID NO: 93
ABQ16703.1_2_spec_F_1242
TCACGGTGGAGTGGAGTATT


SEQ ID NO: 94
ABQ16703.1_2_spec_R_1331
GGTGGGAGCTAAAGGCAAAT


 


SEQ ID NO: 95
ABQ16703.1_54_spec_F_1312
ATTTGCCTTTAGCTCCCACC


SEQ ID NO: 96
ABQ16703.1_54_spec_R_1393
CAAGCATCGGCACAAATACC


 


SEQ ID NO: 97
ABY28312.1_3639_spec_F_842
CGCTCACTTGGCTATACCTG


SEQ ID NO: 98
ABY28312.1_3639_spec_R_942
CGGTTTCCTTCCGTAATACCG


 


SEQ ID NO: 99
ACF24861.1_1091_spec_F_1344
TGGCAGGCGGATAAATTCTT


SEQ ID NO: 100
ACF24861.1_1091_spec_R_1437
CGGCACTGTCAAACCCATAA


 


SEQ ID NO: 101
ACF24861.1_1415_ext_F_1342
TGTGGCAGGCGGATAAATTC


SEQ ID NO: 102
ACF24861.1_1415_ext_R_1430
GTCAAACCCATAAACCGGCA


 


SEQ ID NO: 103
ACH87594.1_2227_ext_F_161
CAAGGTGGATGCAAAGTACCA


SEQ ID NO: 104
ACH87594.1_2227_ext_R_340
TTGATCCCAAGTCTTTCCGC


 


SEQ ID NO: 105
ACH87594.1_2865_ext_F_161
CAAGGTGGATGCAAAGTACCA


SEQ ID NO: 106
ACH87594.1_2865_ext_R_299
CCCCGTATCTTTCTTGCCTG


 


SEQ ID NO: 107
ACH87594.1_437_pr_F_407
AACCCAGCGCCATAATGAAA


SEQ ID NO: 108
ACH87594.1_437_pr_R_516
GACCACCACTTACGCAGTTA


 


SEQ ID NO: 109
ACH87594.1_4754_ext_F_138
ACGGAAACCTCAGAATTTCCA


SEQ ID NO: 110
ACH87594.1_4754_ext_R_299
CCCCGTATCTTTCTTGCCTG


 


SEQ ID NO: 111
ACH87594.1_522_pr_F_353
GACAAATGCAGAAACAGGCG


SEQ ID NO: 112
ACH87594.1_522_pr_R_516
GACCACCACTTACGCAGTTA


 


SEQ ID NO: 113
ACH87594.1_646_pr_F_401
CATGTTAACCCAGCGCCATA


SEQ ID NO: 114
ACH87594.1_646_pr_R_516
GACCACCACTTACGCAGTTA


 


SEQ ID NO: 115
ACH87598.1_3654_ext_F_690
TTTTCTGAGGAAGCTTGGCT


SEQ ID NO: 116
ACH87598.1_3654_ext_R_873
CTTGTCCGGAGCAAGTTCC


 


SEQ ID NO: 117
ACL18777.1_2120_ext_F_1011
GATTTCTGCCGGGTATGCAA


SEQ ID NO: 118
ACL18777.1_2120_ext_R_1117
TCACTGTTCCAGCGCAGATA


 


SEQ ID NO: 119
ACL18777.1_2126_ext_F_1016
CTGCCGGGTATGCAAGAAAT


SEQ ID NO: 120
ACL18777.1_2126_ext_R_1117
TCACTGTTCCAGCGCAGATA


 


SEQ ID NO: 121
ACL18777.1_38_spec_F_248
TAATGATCAGTGGCTGGGGA


SEQ ID NO: 122
ACL18777.1_38_spec_R_421
AAAATACCCAGCGCTCCATC


 


SEQ ID NO: 123
ACL18777.1_77_spec_F_355
CACAGGTTGCCATGTACCAT


SEQ ID NO: 124
ACL18777.1_77_spec_R_485
TATGGGCAGTTTCTCCTGGT


 


SEQ ID NO: 125
ACZ61261.1_113_spec_F_456
TCTGCTTTACCGGTTGAACC


SEQ ID NO: 126
ACZ61261.1_113_spec_R_568
ACCTGAGGCGTACCGAAATA


 


SEQ ID NO: 127
ACZ61261.1_36_spec_F_398
CACCTCTTCGTCATGGATGG


SEQ ID NO: 128
ACZ61261.1_36_spec_R_475
GGTTCAACCGGTAAAGCAGA


 


SEQ ID NO: 129
ACZ61261.1_94_spec_F_409
CATGGATGGGGCTTGATGTT


SEQ ID NO: 130
ACZ61261.1_94_spec_R_568
ACCTGAGGCGTACCGAAATA


 


SEQ ID NO: 131
ACZ61261.1_98_spec_F_692
TCCGGTTGGTTTTCAGGATG


SEQ ID NO: 132
ACZ61261.1_98_spec_R_785
CAGTGCATTTTCTTTGGCGG


 


SEQ ID NO: 133
ACZ61272.1_0_spec_F_1075
CCGGTTTGTGTGAATCAGGA


SEQ ID NO: 134
ACZ61272.1_0_spec_R_1175
GGCTAGAGGAAGGTCAGTGA


 


SEQ ID NO: 135
ACZ61272.1_4_spec_F_1085
TGAATCAGGACGTACCACCT


SEQ ID NO: 136
ACZ61272.1_4_spec_R_1175
GGCTAGAGGAAGGTCAGTGA


 


SEQ ID NO: 137
ACZ61272.1_8_spec_F_1156
TCACTGACCTTCCTCTAGCC


SEQ ID NO: 138
ACZ61272.1_8_spec_R_1261
CTGATTGTGTTGGAAGGGCA


 


SEQ ID NO: 139
ACZ61277.1_0_spec_F_741
GAAAAGCTGGTGATTCCGGA


SEQ ID NO: 140
ACZ61277.1_0_spec_R_886
GTTTGCCAAACAGATGCCAG


 


SEQ ID NO: 141
ACZ61277.1_1673_ext_F_1317
GGTATCTGCATGGGTTCCTG


SEQ ID NO: 142
ACZ61277.1_1673_ext_R_1445
ACCAAAGAACTTGTCAGCCT


 


SEQ ID NO: 143
ACZ61277.1_2882_ext_F_1317
GGTATCTGCATGGGTTCCTG


SEQ ID NO: 144
ACZ61277.1_2882_ext_R_1446
AACCAAAGAACTTGTCAGCCT


 


SEQ ID NO: 145
ACZ61277.1_3_spec_F_741
GAAAAGCTGGTGATTCCGGA


SEQ ID NO: 146
ACZ61277.1_3_spec_R_841
ACTCTCAAATTGCCGCTACC


 


SEQ ID NO: 147
ACZ61277.1_7_spec_F_1244
TCCGGGCAAAAAGGTTTTCT


SEQ ID NO: 148
ACZ61277.1_7_spec_R_1357
GCATTGTCCACGTTGAACAC


 


SEQ ID NO: 149
ACZ61293.1_101_spec_F_876
AAACTCCGCACCTTTGATCC


SEQ ID NO: 150
ACZ61293.1_101_spec_R_993
CCGGCTTGGTAAATTCAGGT


 


SEQ ID NO: 151
ACZ61293.1_61_spec_F_931
TCAGCGGTGAAACCAATGAA


SEQ ID NO: 152
ACZ61293.1_61_spec_R_1038
AGGGGGTATTCTCGTATCGG


 


SEQ ID NO: 153
ACZ61293.1_764_spec_F_955
CCCTGAACGAAGTAACCGAA


SEQ ID NO: 154
ACZ61293.1_764_spec_R_1038
AGGGGGTATTCTCGTATCGG


 


SEQ ID NO: 155
ACZ61341.1_1883_spec_F_437
GGACAGGTGGCATATTACCC


SEQ ID NO: 156
ACZ61341.1_1883_spec_R_517
TCGGGAGAAAGCTCAACCTT


 


SEQ ID NO: 157
ACZ61341.1_2104_spec_F_270
TTTTCCCAGATAGTCAGGCG


SEQ ID NO: 158
ACZ61341.1_2104_spec_R_456
GGGTAATATGCCACCTGTCC


 


SEQ ID NO: 159
ACZ61341.1_4924_spec_F_258
CGCGAACATGGTTTTTCCC


SEQ ID NO: 160
ACZ61341.1_4924_spec_R_456
GGGTAATATGCCACCTGTCC


 


SEQ ID NO: 161
ACZ61341.1_589_spec_F_259
GCGAACATGGTTTTTCCCAG


SEQ ID NO: 162
ACZ61341.1_589_spec_R_456
GGGTAATATGCCACCTGTCC


 


SEQ ID NO: 163
ACZ62362.1_1266_ext_F_957
TTTATCCGCGGTTTGGGTTA


SEQ ID NO: 164
ACZ62362.1_1266_ext_R_1097
GTTGGTTGTGCCGTATTTGG


 


SEQ ID NO: 165
ACZ62362.1_137_spec_F_178
TTAACAAGAACCCGTGGTGG


SEQ ID NO: 166
ACZ62362.1_137_spec_R_304
AAGTCAGCTACAGTGGGTCT


 


SEQ ID NO: 167
ACZ62362.1_3471_ext_F_957
TTTATCCGCGGTTTGGGTTA


SEQ ID NO: 168
ACZ62362.1_3471_ext_R_1063
GAAGACATACGCCCGTGTTC


 


SEQ ID NO: 169
ACZ62362.1_361_spec_F_48
TTTCATTCCACACTCTCGCG


SEQ ID NO: 170
ACZ62362.1_361_spec_R_197
CCACCACGGGTTCTTGTTAA


 


SEQ ID NO: 171
ACZ62362.1_37_spec_F_105
GGTTTAGGGACTATGAGCGC


SEQ ID NO: 172
ACZ62362.1_37_spec_R_197
CCACCACGGGTTCTTGTTAA


 


SEQ ID NO: 173
ACZ62362.1_389_spec_F_94
TAGTCGGAGCAGGTTTAGGG


SEQ ID NO: 174
ACZ62362.1_389_spec_R_197
CCACCACGGGTTCTTGTTAA


 


SEQ ID NO: 175
ACZ62362.1_67_spec_F_178
TTAACAAGAACCCGTGGTGG


SEQ ID NO: 176
ACZ62362.1_67_spec_R_358
ATTTCGGGGGTTTCAAGGTC


 


SEQ ID NO: 177
ACZ62391.1_11_ext_F_550
ATGGGAGCGTACCAAAATGG


SEQ ID NO: 178
ACZ62391.1_11_ext_R_707
TAGAGTCATCGGCTGAGCTT


 


SEQ ID NO: 179
ACZ62391.1_13_ext_F_550
ATGGGAGCGTACCAAAATGG


SEQ ID NO: 180
ACZ62391.1_13_ext_R_703
GTCATCGGCTGAGCTTTCTT


 


SEQ ID NO: 181
ACZ62391.1_3_ext_F_550
ATGGGAGCGTACCAAAATGG


SEQ ID NO: 182
ACZ62391.1_3_ext_R_667
CATTTGGGATCTGCCAGGTT


 


SEQ ID NO: 183
ACZ62391.1_6_ext_F_479
TCCTGATCAACCCGGTAAGT


SEQ ID NO: 184
ACZ62391.1_6_ext_R_667
CATTTGGGATCTGCCAGGTT


 


SEQ ID NO: 185
ACZ62413.1_0_spec_F_1196
ACCCACCACGCCTATAGATT


SEQ ID NO: 186
ACZ62413.1_0_spec_R_1274
CTGAGTCGGACAGGTTTGAG


 


SEQ ID NO: 187
ACZ62419.1_0_spec_F_1235
TCTTCCTCTAGCGCCTACTC


SEQ ID NO: 188
ACZ62419.1_0_spec_R_1312
GCTTCGGCACATATACCACA


 


SEQ ID NO: 189
ACZ62419.1_30_spec_F_1150
TAGGTGAGCACAGCCGTAT


SEQ ID NO: 190
ACZ62419.1_30_spec_R_1254
GAGTAGGCGCTAGAGGAAGA


 


SEQ ID NO: 191
ACZ62419.1_5_spec_F_1208
GCGGACTCATGCTGTCTTTT


SEQ ID NO: 192
ACZ62419.1_5_spec_R_1308
CGGCACATATACCACAGGTC


 


SEQ ID NO: 193
ACZ62441.1_2_spec_F_1111
GGGCTGCCATGACTATTGAG


SEQ ID NO: 194
ACZ62441.1_2_spec_R_1237
CAGTTGTGACAAAAGCGACG


 


SEQ ID NO: 195
ACZ62459.1_179_spec_F_1518
GGTGTTTACGAACCTCCGAA


SEQ ID NO: 196
ACZ62459.1_179_spec_R_1594
TTCACCCCCATCGGAGTATT


 


SEQ ID NO: 197
ACZ62459.1_430_spec_F_112
CATTCTCCATGCAGGGTCAG


SEQ ID NO: 198
ACZ62459.1_430_spec_R_206
TTCCCAGCTGAAAGGGGTAA


 


SEQ ID NO: 199
ACZ62477.1_52_ext_F_809
TGCCATACCCAACAAATGCA


SEQ ID NO: 200
ACZ62477.1_52_ext_R_913
TACCAGACCGCAAAACCTTC


 


SEQ ID NO: 201
ACZ62477.1_760_ext_F_809
TGCCATACCCAACAAATGCA


SEQ ID NO: 202
ACZ62477.1_760_ext_R_927
AGCGGGCATAAGAATACCAG


 


SEQ ID NO: 203
ACZ62477.1_782_spec_F_809
TGCCATACCCAACAAATGCA


SEQ ID NO: 204
ACZ62477.1_782_spec_R_914
ATACCAGACCGCAAAACCTT


 


SEQ ID NO: 205
ACZ62486.1_0_ext_F_1024
GCGGTGTTATGACTCCCAAA


SEQ ID NO: 206
ACZ62486.1_0_ext_R_1187
CTTGCTGATAGCTCCCATCG


 


SEQ ID NO: 207
ACZ62486.1_1038_spec_F_926
GGGTCTGGGATATATCTCGCT


SEQ ID NO: 208
ACZ62486.1_1038_spec_R_1071
CGTGCATTACCCGTACAGAG


 


SEQ ID NO: 209
ACZ62486.1_319_spec_F_920
CCTGTGGGGTCTGGGATATA


SEQ ID NO: 210
ACZ62486.1_319_spec_R_1071
CGTGCATTACCCGTACAGAG


 


SEQ ID NO: 211
ACZ62486.1_47_spec_F_1024
GCGGTGTTATGACTCCCAAA


SEQ ID NO: 212
ACZ62486.1_47_spec_R_1195
GGCTCATCCTTGCTGATAGC


 


SEQ ID NO: 213
ACZ62486.1_970_ext_F_931
TGGGATATATCTCGCTGGACA


SEQ ID NO: 214
ACZ62486.1_970_ext_R_1043
TTTGGGAGTCATAACACCGC


 


SEQ ID NO: 215
ACZ62486.1_983_spec_F_113
TGAAATGGCTTCAGCACCC


SEQ ID NO: 216
ACZ62486.1_983_spec_R_245
CATAGGGGGAGGGCCTTTAT


 


SEQ ID NO: 217
ACZ62492.1_147_spec_F_814
GGACTATGCGTCAGCCATAC


SEQ ID NO: 218
ACZ62492.1_147_spec_R_916
TGGGCTTTGGTATTGTAGGC


 


SEQ ID NO: 219
ACZ62492.1_799_spec_F_814
GGACTATGCGTCAGCCATAC


SEQ ID NO: 220
ACZ62492.1_799_spec_R_923
CTGGAAGTGGGCTTTGGTAT


 


SEQ ID NO: 221
ACZ62501.1_1067_spec_F_1077
ATGTGGCGTTTCTGCCATAC


SEQ ID NO: 222
ACZ62501.1_1067_spec_R_1219
AACTGTTTCTTGCCGGGTAC


 


SEQ ID NO: 223
ACZ62501.1_2033_spec_F_1084
GTTTCTGCCATACCTGCACC


SEQ ID NO: 224
ACZ62501.1_2033_spec_R_1219
AACTGTTTCTTGCCGGGTAC


 


SEQ ID NO: 225
ACZ62520.1_209_spec_F_874
CTGCTACCCTTACCGGTTTG


SEQ ID NO: 226
ACZ62520.1_209_spec_R_1013
CATACCGGCATCAATGGGAG


 


SEQ ID NO: 227
ACZ62520.1_3576_ext_F_994
CTCCCATTGATGCCGGTATG


SEQ ID NO: 228
ACZ62520.1_3576_ext_R_1095
CCCAGGTTGGTTCATGCTC


 


SEQ ID NO: 229
ACZ62520.1_3979_ext_F_882
CTTACCGGTTTGGGTGAGG


SEQ ID NO: 230
ACZ62520.1_3979_ext_R_1006
GCATCAATGGGAGGTGTAGG


 


SEQ ID NO: 231
ACZ62520.1_768_spec_F_866
CATTGCCACTGCTACCCTTA


SEQ ID NO: 232
ACZ62520.1_768_spec_R_1006
GCATCAATGGGAGGTGTAGG


 


SEQ ID NO: 233
ACZ62529.1_1422_spec_F_1329
ACCACCGGCATTTTCAACA


SEQ ID NO: 234
ACZ62529.1_1422_spec_R_1418
GTCAAGATCCCACCATTCGG


 


SEQ ID NO: 235
ACZ62529.1_1912_spec_F_1073
TTTCCGCTTCTGCCATAGC


SEQ ID NO: 236
ACZ62529.1_1912_spec_R_1223
CAGCTTGCACTCAGGTTCAT


 


SEQ ID NO: 237
ACZ62529.1_3935_ext_F_1257
TGTACCGGCGTTTGTGTATT


SEQ ID NO: 238
ACZ62529.1_3935_ext_R_1416
CAAGATCCCACCATTCGGC


 


SEQ ID NO: 239
ACZ62529.1_746_spec_F_796
GTGTTTGTTATGCCGCCAAT


SEQ ID NO: 240
ACZ62529.1_746_spec_R_901
GCAGACTGCAAACCCTGATA


 


SEQ ID NO: 241
ACZ62535.1_2901_spec_F_978
CGTTATGTGGGTTCCGAGG


SEQ ID NO: 242
ACZ62535.1_2901_spec_R_1152
AGAAACGGTAAATGCCTGCA


 


SEQ ID NO: 243
ACZ62535.1_2902_spec_F_977
CCGTTATGTGGGTTCCGAG


SEQ ID NO: 244
ACZ62535.1_2902_spec_R_1152
AGAAACGGTAAATGCCTGCA


 


SEQ ID NO: 245
ACZ62535.1_325_spec_F_1133
TGCAGGCATTTACCGTTTCT


SEQ ID NO: 246
ACZ62535.1_325_spec_R_1323
TTTCGTTGGAATACTGGCGG


 


SEQ ID NO: 247
ACZ62535.1_4389_spec_F_1133
TGCAGGCATTTACCGTTTCT


SEQ ID NO: 248
ACZ62535.1_4389_spec_R_1315
GAATACTGGCGGCAGAGAG


 


SEQ ID NO: 249
ADC73508.1_197_ext_F_106
TGTTCCGCGGCTTTGAAATA


SEQ ID NO: 250
ADC73508.1_197_ext_R_275
GAGTATCCGCCCGTTATTCG


 


SEQ ID NO: 251
ADC73508.1_20_spec_F_1019
CCGCTATGAAAACACCCCTT


SEQ ID NO: 252
ADC73508.1_20_spec_R_1205
AGCCACAATCTTGCATTCCA


 


SEQ ID NO: 253
ADC73508.1_202_spec_F_916
TCAAGTACGGCTGGTTCAAG


SEQ ID NO: 254
ADC73508.1_202_spec_R_1038
AAGGGGTGTTTTCATAGCGG


 


SEQ ID NO: 255
ADC73508.1_3_spec_F_877
CACTCCACACCTTTGATCCC


SEQ ID NO: 256
ADC73508.1_3_spec_R_1038
AAGGGGTGTTTTCATAGCGG


 


SEQ ID NO: 257
ADC73508.1_338_ext_F_49
AAATCGAAGCCACCGTAGAC


SEQ ID NO: 258
ADC73508.1_338_ext_R_125
TATTTCAAAGCCGCGGAACA


 


SEQ ID NO: 259
ADC74627.1_1_spec_F_757
CGGCAGTAAATCCCACCAAT


SEQ ID NO: 260
ADC74627.1_1_spec_R_876
GTGCAGCGTTCTGAGTAGTT


 


SEQ ID NO: 261
ADC74627.1_2_spec_F_757
CGGCAGTAAATCCCACCAAT


SEQ ID NO: 262
ADC74627.1_2_spec_R_875
TGCAGCGTTCTGAGTAGTTG


 


SEQ ID NO: 263
ADC74627.1_9_spec_F_741
GATTTTGTATGCACACCGGC


SEQ ID NO: 264
ADC74627.1_9_spec_R_876
GTGCAGCGTTCTGAGTAGTT


 


SEQ ID NO: 265
ADC74655.1_1033_spec_F_656
ATCCGTTCCAGGCAATAAGC


SEQ ID NO: 266
ADC74655.1_1033_spec_R_792
GCAGAAACCCGTCACATGAA


 


SEQ ID NO: 267
ADC74655.1_1058_spec_F_656
ATCCGTTCCAGGCAATAAGC


SEQ ID NO: 268
ADC74655.1_1058_spec_R_749
CTTTTGCGAAGTGGGGATGT


 


SEQ ID NO: 269
ADC74655.1_161_ext_F_876
CAGTTTATCCGCGGGTTAGG


SEQ ID NO: 270
ADC74655.1_161_ext_R_983
CTGACCCATACGGCAATGTT


 


SEQ ID NO: 271
ADC74655.1_166_ext_F_876
CAGTTTATCCGCGGGTTAGG


SEQ ID NO: 272
ADC74655.1_166_ext_R_982
TGACCCATACGGCAATGTTC


 


SEQ ID NO: 273
ADC74655.1_2926_ext_F_950
GAGCGGTGTTGGTGAACATT


SEQ ID NO: 274
ADC74655.1_2926_ext_R_1120
GTTTCAGCACAGATACCGCA


 


SEQ ID NO: 275
BAE84628.1_1113_spec_F_317
AAATGCGGAAAGACTTGGGA


SEQ ID NO: 276
BAE84628.1_1113_spec_R_411
GGGTTAACATGGCACCCAAA


 


SEQ ID NO: 277
BAE84628.1_3406_ext_F_1459
GGAACAAAGTCGAGACCTGG


SEQ ID NO: 278
BAE84628.1_3406_ext_R_1546
TCATCAAACTTGCGGGCTG


 


SEQ ID NO: 279
BAE84628.1_400_spec_F_317
AAATGCGGAAAGACTTGGGA


SEQ ID NO: 280
BAE84628.1_400_spec_R_405
ACATGGCACCCAAATGTTGA


 


SEQ ID NO: 281
BAE84628.1_4184_ext_F_1102
GTGTTCCTATGGCCGTTCAG


SEQ ID NO: 282
BAE84628.1_4184_ext_R_1229
CTTGTCCGGAGCAAGTTCC


 


SEQ ID NO: 283
BAF34982.1_9_spec_F_1138
GGGAACAATCACGCGTATCA


SEQ ID NO: 284
BAF34982.1_9_spec_R_1251
CGGCATCTATAGGCTTGGTG


 


SEQ ID NO: 285
BAG72170.1_2661_spec_F_1104
CCTGCAAGAAGTGTGCAGAT


SEQ ID NO: 286
BAG72170.1_2661_spec_R_1200
ACTCTGGGTTTGCCGTCTA


 


SEQ ID NO: 287
BAG72170.1_2758_spec_F_1001
ACTCCTGAAACCGGTCCTAA


SEQ ID NO: 288
BAG72170.1_2758_spec_R_1111
CTTGCAGGAGTGGCAGAAG


 


SEQ ID NO: 289
BAG72170.1_283_spec_F_1001
ACTCCTGAAACCGGTCCTAA


SEQ ID NO: 290
BAG72170.1_283_spec_R_1123
ATCTGCACACTTCTTGCAGG


 


SEQ ID NO: 291
BAG72170.1_866_spec_F_1029
CCTTTACCATGCTGACCGAT


SEQ ID NO: 292
BAG72170.1_866_spec_R_1123
ATCTGCACACTTCTTGCAGG


 


SEQ ID NO: 293
BAI47830.1_259_spec_F_251
AGTGAGCGGCATTTACAAGG


SEQ ID NO: 294
BAI47830.1_259_spec_R_348
GTAGAGCCATAGTTGCCACC


 


SEQ ID NO: 295
BAI47830.1_561_spec_F_193
AATGCCTGGTTTCCGTGAAG


SEQ ID NO: 296
BAI47830.1_561_spec_R_348
GTAGAGCCATAGTTGCCACC


 


SEQ ID NO: 297
BAI70453.1_0_spec_F_309
TCTTGGTTGGGTCCTCAGAA


SEQ ID NO: 298
BAI70453.1_0_spec_R_459
CGTTTTCATCCAGCTCCAGT


 


SEQ ID NO: 299
BAI70453.1_10_spec_F_718
TGGGTTATCAGGCTATGGCT


SEQ ID NO: 300
BAI70453.1_10_spec_R_908
ACCGGCATCAATAGGTTTGG


 


SEQ ID NO: 301
BAI70453.1_14_spec_F_182
ACAGAAAATTGCGGCGGATA


SEQ ID NO: 302
BAI70453.1_14_spec_R_342
CGGGGGTAGGAGATTTCTGA


 


SEQ ID NO: 303
BAI70453.1_28_ext_F_1104
GCCTGTGTGTACACCAAGAA


SEQ ID NO: 304
BAI70453.1_28_ext_R_1289
CCAGAAATCTTCGGCACCTT


 


SEQ ID NO: 305
BAI70453.1_44_ext_F_1046
GGTGAAATGCCAGAGTACCC


SEQ ID NO: 306
BAI70453.1_44_ext_R_1241
GTCAGGCCCGAATTCAGTAC


 


SEQ ID NO: 307
BAI70453.1_45_ext_F_927
GACTGCGCTAAATGCTCTGA


SEQ ID NO: 308
BAI70453.1_45_ext_R_1065
GGGTACTCTGGCATTTCACC


 


SEQ ID NO: 309
BAI70453.1_6_spec_F_16
TGATAACTTCTGGTGCTGCG


SEQ ID NO: 310
BAI70453.1_6_spec_R_126
TAACCTTACGGGCGTCAAAC


 


SEQ ID NO: 311
CAD28790.2_81_pr_F_209
TGAAAAGACTTTCGACCCGG


SEQ ID NO: 312
CAD28790.2_81_pr_R_403
ATGGCACCCAAATGTTGAGT


 


SEQ ID NO: 313
CAD28790.2_953_pr_F_385
CTCAACATTTGGGTGCCATG


SEQ ID NO: 314
CAD28790.2_953_pr_R_484
TCAAATTCTACAGCCCAGGC


 


SEQ ID NO: 315
CAI83519.1_2479_spec_F_141
AACAAAAGGCCATGGTGGG


SEQ ID NO: 316
CAI83519.1_2479_spec_R_252
GAGCAGTCATGGGATAAGCC


 


SEQ ID NO: 317
CAI83531.1_104_spec_F_1181
CACCGATTTACCTCTCTCGC


SEQ ID NO: 318
CAI83531.1_104_spec_R_1267
CAAGCCTCGGCACAGATAC


 


SEQ ID NO: 319
CAI83566.1_1_spec_F_314
ACAACGCATGCAAGATGGTA


SEQ ID NO: 320
CAI83566.1_1_spec_R_464
GGGAAGTCCTTGTTCTTCGG


 


SEQ ID NO: 321
CAI83566.1_10_spec_F_444
CCCGAAGAACAAGGACTTCC


SEQ ID NO: 322
CAI83566.1_10_spec_R_539
TACTTGCCCTGCACCAAAAA


 


SEQ ID NO: 323
CAI83566.1_14_spec_F_1161
CCTGGACACAAGGCATTCTT


SEQ ID NO: 324
CAI83566.1_14_spec_R_1247
CATACAGATACCGCAGCCTG


 


SEQ ID NO: 325
CAI83566.1_4_spec_F_1134
AAATGGGATTGTGCGCCTTA


SEQ ID NO: 326
CAI83566.1_4_spec_R_1247
CATACAGATACCGCAGCCTG


 


SEQ ID NO: 327
CAI83566.1_6_spec_F_445
CCGAAGAACAAGGACTTCCC


SEQ ID NO: 328
CAI83566.1_6_spec_R_640
CAAGATGAGCCGTACGTACC


 


SEQ ID NO: 329
CAJ75430.1_2099_pr_F_321
GCGGAAAGACTTGGGATCAA


SEQ ID NO: 330
CAJ75430.1_2099_pr_R_408
GTGGCATGACACCCGTATG


 


SEQ ID NO: 331
CAJ75430.1_2693_pr_F_280
CAGGCAAGAAAGATACGGGG


SEQ ID NO: 332
CAJ75430.1_2693_pr_R_408
GTGGCATGACACCCGTATG


 


SEQ ID NO: 333
CAR57931.1_1638_pr_F_298
GGAAAGACCTGCCCATACTT


SEQ ID NO: 334
CAR57931.1_1638_pr_R_372
CGCCTGTTTCTGCATTTGTC


 


SEQ ID NO: 335
CAR57931.1_2137_pr_F_298
GGAAAGACCTGCCCATACTT


SEQ ID NO: 336
CAR57931.1_2137_pr_R_376
AGAACGCCTGTTTCTGCATT
















TABLE 3





qPCR primer pairs (assays)-SEQ ID NOs.




















1 and 2
3 and 4
5 and 6
7 and 8
9 and 10
11 and 12


13 and 14
15 and 16
17 and 18
19 and 20
21 and 22
23 and 24


25 and 26
27 and 28
29 and 30
31 and 32
33 and 34
35 and 36


37 and 38
39 and 40
41 and 42
43 and 44
45 and 46
47 and 48


49 and 50
51 and 52
53 and 54
55 and 56
57 and 58
59 and 60


61 and 62
63 and 64
65 and 66
67 and 68
69 and 70
71 and 72


73 and 74
75 and 76
77 and 78
79 and 80
81 and 82
83 and 84


85 and 86
87 and 88
89 and 90
91 and 92
93 and 94
95 and 96


97 and 98
 99 and 100
101 and 102
103 and 104
105 and 106
107 and 108


109 and 110
111 and 112
113 and 114
115 and 116
117 and 118
119 and 120


121 and 122
123 and 124
125 and 126
127 and 128
129 and 130
131 and 132


133 and 134
135 and 136
137 and 138
139 and 140
141 and 142
143 and 144


145 and 146
147 and 148
149 and 150
151 and 152
153 and 154
155 and 156


157 and 158
159 and 160
161 and 162
163 and 164
165 and 166
167 and 168


169 and 170
171 and 172
173 and 174
175 and 176
177 and 178
179 and 180


181 and 182
183 and 184
185 and 186
187 and 188
189 and 190
191 and 192


193 and 194
195 and 196
197 and 198
199 and 200
201 and 202
203 and 204


205 and 206
207 and 208
209 and 210
211 and 212
213 and 214
215 and 216


217 and 218
219 and 220
221 and 222
223 and 224
225 and 226
227 and 228


229 and 230
231 and 232
233 and 234
235 and 236
237 and 238
239 and 240


241 and 242
243 and 244
245 and 246
247 and 248
249 and 250
251 and 252


253 and 254
255 and 256
257 and 258
259 and 260
261 and 262
263 and 264


265 and 266
267 and 268
269 and 270
271 and 272
273 and 274
275 and 276


277 and 278
279 and 280
281 and 282
283 and 284
285 and 286
287 and 288


289 and 290
291 and 292
293 and 294
295 and 296
297 and 298
299 and 300


301 and 302
303 and 304
305 and 306
307 and 308
309 and 310
311 and 312


313 and 314
315 and 316
317 and 318
319 and 320
321 and 322
323 and 324


325 and 326
327 and 328
329 and 330
331 and 332
333 and 334
335 and 336









The results from these serial dilution experiments at the three highest dilutions were used to construct assay specific standard curves.
A set of three Mus musculus genes were spiked into the master mix of both calibration and experimental chips to test for PCR inhibitors and ensure roughly similar amplification performance.
Negative controls consisted of a complex genomic mixture absent reductive dehalogenases. The mixture was constructed from DNA isolated from the following archaea and bacteria: Methanococcus maripaludis 109, Methanothermococcus thermolithotrophicus DSM 2095, Sporomusa ovata DSM 2662, Shewanella oneidensis MR-1, Geobacter metallireducens GS-15, Clostridium sporogenes, Sinorhizobium meliloti, and Bacteroides thetaiotaomicron. 
Example 3
Assay Specificity Tests:
To validate the selectivity of newly-designed assay primer pairs to distinguish among rdh groups, total DNA was isolated by a POWERSOIL® kit (MoBio Laboratories, Inc, Carlsbad, Calif.) or by methods such as described in Behrens et al., (2008) Appl. Environ. Microbiol. 74: 5695-5703 from cultures highly enriched for Dehalococcoides mccartyi VS, GT, CBDB1, and ethenogenes 195. Samples were prepared at various bulk concentrations varying from 10 to 0.01 ng/μl. These were further diluted in LIGHTCYCLER® 480 SYBR Green I Master Mix (Roche Applied Science, Inc) to final concentrations of 25 to 0.1 pg per well. Additionally, a separate sample was amended with the above-mentioned genomic negative control mixture (50 pg) such that the Dehalococcoides DNA represented a minority fraction of total complex DNA mixture in each reaction.
The systems of the disclosure were then examining for consistent amplification of high PID homologs across Dehalococcoides isolates, while also measuring the frequency of false positives due to off-target amplifications. It was predicted that primer sets containing three or more cumulative mismatches with a target gene would not amplify efficiently. If it did, it was classified as a false positive. By comparing this expectation with the amplification result, each assay/isolate combination was designated as true-positive, true-negative, false-positive, or false-negative if confirmed by duplicate chip results.
The final rdh PCR suite of primers included multiple pairs for each reference group. Individual assay primer pair results were aggregated in concordance with the recently developed Reductive Dehalogenase Orthologue Group naming system Hug et al., (2013) Philo. Trans. Roy. Soc. B: Biol. Sci. 368: 20120322-20120322). Each group presence/absence classification (true-positive, false-positive, false-negative, or true-negative) was determined by the majority result of all assay primer pairs targeting that group. If an equal number of assay primer pairs returned estimates above and below 1 copy per reaction, the group was considered absent.
Example 4
Pore Water Biostimulation:
Pore waters extracted from sampling wells from an Italian industrial site were transferred in an anoxic glove box into nitrogen-filled serum vials. The vials were sparged to remove volatile organic chloroethenes. 1,2-DCA remained in concentrations ranging from 1.5 to 6 mM, reflecting differential contamination at each observation well. 2 mM lactate, acetate, or formate was supplied as an electron donor in replicate vials of each pore water. As a control, a fourth replicate vial received salts in lieu of an electron donor. AH vials were amended with a vitamin solution (Table 4).







TABLE 4





Vitamin Mix (final concentration of each


component in the stimulated pore water)



















Vitamin B12
100
μg/L



p-aminobenzoic acid
80
μg/L



D(+)-biotin
20
μg/L



Nicotinic acid
200
μg/L



Calcium pantothenate
100
μg/L



Pyridoxine hydrochioride
300
μg/L



Thiamine-HCl × 2H2O
200
μg/L










Chemical degradation was measured by gas chromatography at 7, 18 and 23 days. After day 23, DNA was isolated from 8 ml of pore water with the MP SOIL® DNA (MP Biomedicals) bead-beating protocol.
Recovered DNA, ranging in concentration from 0.1 ng to 30 ng/μl, was applied to the nl-qPCR chip containing the validated assay suite of primers shown in Table 2. Gene target estimates ranged from 4×103 to 4.6×108 copies per ml pore water. 4×103 copies per ml pore water was the practical limit of detection given constraints introduced by the DNA isolation method used on-site.
Example 5
Sampling of the Continuous Bioreactor:
Operation and sampling procedure for the Evanite two-liter (EV2L) TCE-degrading continuously-fed reactor has been previously described (Berggren et al., (2013) Environ. Sci. & Technol. 47: 1879-1886). Briefly, cells were grown at a mean-cell residence time of 50 days and fed formate as an electron donor. Reactor liquid (50 ml) was spun by centrifuge (8000 RCF) for 30 min with solids transferred to a MOBIO POWERSOIL® bead-beating tube followed by isolation with Phenol:Chloroform:Isoamyl Alcohol saturated with Tris-HCl pH 8.05. The resulting DNA per sample was diluted to 10 ng/μl, corresponding to 25 pg DNA per 100 nL qPCR reaction.
Example 6
Detection of Rare Community Members:
In practice, the limits of detection in environmental samples depend not only on assay quality, but also on the quantity of nucleic acid template and the fraction of target DNA within a mixed community. Assuming modest 20 ng DNA recovered from an environment dominated by bacteria and archaea, a nL-qPCR platform was developed that enabled detection of rdh genes in rare population members that constitute on the order of 10-3 of the total microbial population.
This estimate was based on the following calculations where the volume of DNA applied to a sample mastermix can range from 1-10 μL ( 1/40th to 1⁄8th of the total mastermix volume) per sample depending on the demands of the experiment.














F
[%]
Minimum Fraction of Community Detectable


CpW
[copies]
Copies needed for detection


CINPUT
[ng/μl]
Sample Concentration


VINPUT
[μL]
Sample Input Volume


VMM
[μL]
Master Mix Volume


VWELL
[μL]
Reaction Well Volume


G
[bp]
Average Bacterial Genome Size









One can calculate the DNA mass per well by:




  
    DNA
    MASSng
  
  =
  
    
      (
      
        
          
            C
            INPUT
          
          ⁢
          
            V
            INPUT
          
        
        
          V
          MIX
        
      
      )
    
    ⁢
    
      (
      
        
          V
          WELL
        
        1
      
      )
    
  




One can convert DNA mass to genomic copies assuming a dsDNA bp=650 Daltons by




  
    Number
    ⁢
    
      
    
    ⁢
    of
    ⁢
    
      
    
    ⁢
    Copies
  
  =
  
    
      
        DNA
        
          MASS
          ng
        
      
      G
    
    *
    
      (
      
        
          6.022
          *
          
            10
            23
          
        
        
          
            10
            9
          
          *
          650
        
      
      )
    
  




by substituting from above:




  
    Number
    ⁢
    
      
    
    ⁢
    of
    ⁢
    
      
    
    ⁢
    Copies
  
  =
  
    
      (
      
        
          
            C
            INPUT
          
          ⁢
          
            V
            INPUT
          
        
        
          V
          MIX
        
      
      )
    
    ⁢
    
      (
      
        
          V
          WELL
        
        1
      
      )
    
    *
    
      1
      G
    
    *
    
      (
      
        
          6.022
          *
          
            10
            23
          
        
        
          
            10
            9
          
          *
          650
        
      
      )
    
  




Assuming 1 to 10 copies of the target organism's DNA are needed for detection we can estimate the minimum fraction of the community detectable.



  
    F
    =
    
      
        (
        
          
            (
            
              1
              CpW
            
            )
          
          ⁢
          
            (
            
              
                
                  C
                  INPUT
                
                ⁢
                
                  V
                  INPUT
                
              
              
                V
                MIX
              
            
            )
          
          ⁢
          
            (
            
              
                V
                WELL
              
              1
            
            )
          
          *
          
            1
            G
          
          *
          
            (
            
              
                6.022
                *
                
                  10
                  23
                
              
              
                
                  10
                  9
                
                *
                650
              
            
            )
          
        
        )
      
      
        -
        1
      
    
  




  
    
      F
      ⁡
      
        (
        
          
            CpW
            =
            10
          
          ,
          
            
              V
              I
            
            =
            2
          
          ,
          
            
              C
              INPUT
            
            =
            10
          
          ,
          
            G
            =
            
              3.5
              ⁢
              
                E
                6
              
            
          
        
        )
      
    
    =
    
      1.5
      ⁢
      
        E
        
          -
          3
        
      
    
  




  
    
      F
      ⁡
      
        (
        
          
            CpW
            =
            1
          
          ,
          
            
              V
              INPUT
            
            =
            2
          
          ,
          
            
              C
              INPUT
            
            =
            10
          
          ,
          
            G
            =
            
              3.5
              ⁢
              
                E
                6
              
            
          
        
        )
      
    
    =
    
      1.5
      ⁢
      
        E
        
          -
          4
        
      
    
  



(These estimates assume no contaminating eukaryotic or viral DNA which may be considerable in some sample types).
Poisson Noise at Low Copy Numbers:
To investigate the sensitivity of the nl-qPCR assays, each primer pair was tested against a dilution series of linear 500 bp DNA standards. The Ct difference between two replicate reactions increased as the number of starting gene copies per reaction well decreased. Simulation, run using the statistical software environment R, indicated increasing Ct difference should be expected from stochastic processes associated with small-number statistics (“Poisson noise”). In the simulation, it was assumed drawing pairs of observations from an underlying Poisson distribution with varying parameter mean from 1 to 20,000.
FIG. 5 shows the expected Poisson noise and observed difference in replicate Ct of the assays (n=116) at 20,000, 2000, 200, and 20 starting copies per reaction. Because of the observed variability at 20 starting copy numbers, 3-point standard curves were generated with the more concentrated standards (200, 2000, 20000 starting copies). The nature of the errors were examined, defined as the difference between the observed Ct at 20 starting copies and the value predicted by the linear regression from the 3-point calibration ordinary least squares line.
A systematic loss in sensitivity at low copy numbers was not seen. Strong bias in the errors would have suggested diminished assay performance against dilute targets, whereas the relatively unbiased errors observed here suggest the result of stochastic processes (where an over or under estimate are equally likely). Given the random nature of errors, the errors due to Poisson noise could likely be overcome and improved calibration accuracy achieved by increasing the number of technical replicates at low starting copies per reaction.
Because of the observed variability at the dilution of 20 copies per reaction 3-point standard curves were generated with the more concentrated standards (200, 2000, 20000 starting copies). The nature of the errors were examined, defined as the difference between the observed Ct at 20 starting copies and the value predicted by the linear regression from the 3-point calibration, based on ordinary least squares (see FIG. 6). A systematic loss in sensitivity at low copy numbers was not observed. Strong bias in the errors would have suggested diminished assay performance against dilute targets, whereas the relatively unbiased errors observed here suggest the result of stochastic processes (where an over or under estimate are equally likely).
Example 7
Specific Parameters and Programs for Primer Selection:
The “Primer3 www primer tool” (University of Massachusetts Medical School) is software for the design of oligonucleotide PCR primers. The command-line version 2.3.4 of Primer3 was used with the following parameters to design thousands of assay primer pairs for each rdh or hupL reference sequence. By using standard WAFERGEN® validated assays known to perform well within a standard WAFERGEN® thermocycler program, the input parameters of Primer3 were tuned to produce assays with similar predicted thermodynamic binding properties. The parameters used in the control file were:

    
    
        PRIMER_NUM_RETURN=2500
        PRIMER_MIN_TM=59
        PRIMER_OPT_TM=60
        PRIMER_MAX_TM=61
        PRIMER_MIN_SIZE=15
        PRIMER_MAX_SIZE=28
        PRIMER_NUM_NS_ACCEPTED=1
        PRIMER_PRODUCT_SIZE_RANGE=75-200
        PRIMER_GC_CLAMP=0
        PRIMER_FILE_FLAG=1
        PRIMER_EXPLAIN_FLAG=1
        PRIMER_TM_FORMULA=1
        PRIMER_SALT_CORRECTIONS=1
        PRIMER_THERMODYNAMIC_ALIGNMENT=1
        PRIMER_SALT_DIVALENT=3
        PRIMER_DNTP_CONC=0.6
        PRIMER_LIB_AMBIGUITY_CODES_CONSENSUS=0
    
    


These parameters produced many high efficiency assays when run at a 60° C. annealing temperature in the ROCHE LIGHTCYCLER® SYBR Green I Master Mix. Use of an alternative master mix or annealing temperatures will necessitate retuning of these parameters to account for the change in PCR reaction conditions.
The freely available Emboss program “fuzznuc” (as described by Rice et al., (2000) EMBOSS: The European Molecular Biology Open Software Suite in Trends in Genetics 16: 276-277, incorporated herein by reference in its entirety) was used to perform fuzzy matching between each candidate assay primer pair and the relevant reductive dehalogenase genes. This permitted determination of how many gene sequences were complementary to a given primer.

    
    
        The fuzznuc pattern file used was:
        pat1 <mismatch=4>
        forward primer sequence
        >pat2 <mismatch=4>
        reverse primer sequence
    
    


This input allowed for match detection of sequences with up to 4 mismatches per primer, and was produced for each candidate assay as follows.
Example 8
Detection of Rare Community Members:
The limits of detection in environmental samples depend not only on assay quality, but also on the quantity of nucleic acid template and the fractional enrichment the target DNA within a mixed community. With about 20 ng DNA recovered from an environment dominated by bacteria and archaea, an nl-qPCR platform was developed that enabled detection of rdh genes in rare population members that constitute on the order of 10−3 of the total microbial population.
This estimate was based on the following calculations where the volume of DNA applied to a sample mastermix can range from 2-10 μl (0.025 to about 0.125 of the total mastermix volume) per sample depending on the demands of the experiment.














F
[%]
Minimum Fraction of Community Detectable


CpW
[copies]
Copies needed for detection


CINPUT
[ng/μl]
Sample Concentration


VINPUT
[μl]
Sample Input Volume


VMM
[μl]
Master Mix Volume


VWELL
[μl]
Reaction Well Volume


G
[bp]
Average Bacterial Genome Size









The DNA mass per well is given by:





  
    DNA
    
      MASS
      ng
    
  
  =
  
    
      (
      
        
          
            C
            INPUT
          
          ⁢
          
            V
            INPUT
          
        
        
          V
          MIX
        
      
      )
    
    ⁢
    
      (
      
        
          V
          WELL
        
        1
      
      )
    
  




and converted to genomic copies, assuming a dsDNA bp=650 Daltons, by





  
    Number
    ⁢
    
      
    
    ⁢
    of
    ⁢
    
      
    
    ⁢
    Copies
  
  =
  
    
      
        DNA
        
          MASS
          ng
        
      
      G
    
    *
    
      (
      
        
          6.022
          *
          
            10
            23
          
        
        
          
            10
            9
          
          *
          650
        
      
      )
    
  




by substituting from above:





  
    Number
    ⁢
    
      
    
    ⁢
    of
    ⁢
    
      
    
    ⁢
    Copies
  
  =
  
    
      (
      
        
          
            C
            INPUT
          
          ⁢
          
            V
            INPUT
          
        
        
          V
          MIX
        
      
      )
    
    ⁢
    
      (
      
        
          V
          WELL
        
        1
      
      )
    
    *
    
      1
      G
    
    *
    
      (
      
        
          6.022
          *
          
            10
            23
          
        
        
          
            10
            9
          
          *
          650
        
      
      )
    
  




Assuming 1 to 10 copies of the target organism's DNA are needed for detection, the minimum fraction of the community detectable is given by:



  
    F
    =
    
      
        (
        
          
            (
            
              1
              CpW
            
            )
          
          ⁢
          
            (
            
              
                
                  C
                  INPUT
                
                ⁢
                
                  V
                  INPUT
                
              
              
                V
                MIX
              
            
            )
          
          ⁢
          
            (
            
              
                V
                WELL
              
              1
            
            )
          
          *
          
            1
            G
          
          *
          
            (
            
              
                6.022
                *
                
                  10
                  23
                
              
              
                
                  10
                  9
                
                *
                650
              
            
            )
          
        
        )
      
      
        -
        1
      
    
  




  
    
      F
      ⁡
      
        (
        
          
            CpW
            =
            10
          
          ,
          
            
              V
              INPUT
            
            =
            2
          
          ,
          
            
              C
              INPUT
            
            =
            10
          
          ,
          
            G
            =
            
              3.5
              ⁢
              
                E
                6
              
            
          
        
        )
      
    
    =
    
      1.5
      ⁢
      
        E
        
          -
          3
        
      
    
  




  
    
      F
      ⁡
      
        (
        
          
            CpW
            =
            1
          
          ,
          
            
              V
              INPUT
            
            =
            2
          
          ,
          
            
              C
              INPUT
            
            =
            10
          
          ,
          
            G
            =
            
              3.5
              ⁢
              
                E
                6
              
            
          
        
        )
      
    
    =
    
      1.5
      ⁢
      
        E
        
          -
          4
        
      
    
  



*These estimates assume no contaminating eukaryotic or viral DNA which may be considerable in some sample types.

Example 9
Calculating Copies Per mL from Counts Per 0.1 μl Reaction Well:














Nwell

Copies per well estimated from observed Ct




and standard curve.


Cmm

Copies per μl once diluted into the MasterMix


CDNA

Copies per μl of eluted isolated DNA


CS

Copies per μl of original water sample


VWELL
[μl]
Reaction Well Volume 0.1 μL


VMM
[μl]
Total Volume of the Master Mix


VINPUT
[μl]
Total volume of DNA applied to the chip


VDNA
[μl]
Volume of DNA eluent following DNA isolation




protocol (Usually varies between 20 and 100 μl)


VS
[ml]
Volume of original liquid sample




(Usually varies between 1 ml-1000 ml)









The concentration of gene copies in the original sample is related to the concentration in the isolated DNA (assuming 100% DNA isolation efficiency) by:




  
    C
    S
  
  =
  
    
      (
      
        
          V
          DNA
        
        
          V
          S
        
      
      )
    
    ⁢
    
      C
      DNA
    
  




The concentration of gene copies in the isolated DNA concentrate is related to that in the sample mastermix:




  
    C
    DNA
  
  =
  
    
      (
      
        
          V
          MM
        
        
          V
          Input
        
      
      )
    
    ⁢
    
      C
      MM
    
  




The concentration in the master mix is related to the number of copies in each nl-qPCR reaction well:




  
    C
    MM
  
  =
  
    
      N
      well
    
    
      V
      well
    
  




Combining these relations, the copies in the original water sample from the number of copies found in an individual nl-qPCR reaction well is calculated:




  
    C
    
      S
      ,
      
        μ
        ⁢
        
          
        
        ⁢
        l
      
    
  
  =
  
    
      
        (
        
          
            V
            DNA
          
          
            V
            s
          
        
        )
      
      ⁢
      
        (
        
          
            V
            MM
          
          
            V
            input
          
        
        )
      
      ⁢
      
        
          N
          well
        
        
          V
          well
        
      
    
    =
    
      
        
          (
          
            
              80
              ⁢
              
                
              
              ⁢
              μl
            
            
              8
              ,
              000
              ⁢
              
                
              
              ⁢
              μl
            
          
          )
        
        ⁢
        
          (
          
            
              80
              ⁢
              
                
              
              ⁢
              μl
            
            
              2
              ⁢
              
                
              
              ⁢
              μl
            
          
          )
        
        ⁢
        
          
            N
            well
          
          
            0.1
            ⁢
            
              
            
            ⁢
            μl
          
        
      
      =
      
        4
        ⁢
        
          
            N
            well
          
          ⁡
          
            [
            
              1
              μl
            
            ]
          
        
      
    
  




Converting to copies per mL pore water.




  
    C
    
      S
      ,
      
        m
        ⁢
        
          
        
        ⁢
        l
      
    
  
  =
  
    
      4
      ⁢
      
        
      
      ⁢
      
        
          N
          well
        
        ⁡
        
          [
          
            1
            μl
          
          ]
        
      
      *
      
        [
        
          
            1000
            ⁢
            
              
            
            ⁢
            μl
          
          
            1
            ⁢
            
              
            
            ⁢
            ml
          
        
        ]
      
    
    =
    
      4000
      ⁢
      
        
      
      ⁢
      
        
          N
          well
        
        ⁡
        
          [
          
            1
            ml
          
          ]
        
      
    
  




Example 10
Practical Pore Water Detection Limits:
4×103 copies per ml pore water was the practical limit of detection given constraints introduced by the DNA isolation method used on-site; however, a strategy to further concentrate isolated DNA could lower the detection limit to 200 copies per ml pore water.
Assuming almost 100% DNA extraction efficiency, the practical detection limit (PDL) can be calculated from the following parameters.
Vs [ml] Vol. of original liquid sample about 0.5 ml to about 1000 ml)
VDNA [μl] Vol. of DNA eluent following Isolation Protocol about 10 to about 100 μl
VINPUT [μl] Vol. of DNA applied to the chip (between about 2 to about 10 μl)
VWELL [μl] Vol. qPCR reaction well
MDL [copies] Machine Detection Limit




  PDL
  =
  
    
      MDL
      *
      
        (
        
          
            V
            DNA
          
          
            V
            s
          
        
        )
      
      *
      
        (
        
          
            V
            MM
          
          
            V
            INPUT
          
        
        )
      
      *
      
        (
        
          1
          
            V
            well
          
        
        )
      
      *
      
        (
        
          
            1000
            ⁢
            
              
            
            ⁢
            μl
          
          
            1
            ⁢
            
              
            
            ⁢
            ml
          
        
        )
      
    
    =
    
      PDL
      =
      
        
          
            MDL
            *
            
              (
              
                80
                8000
              
              )
            
          
          +
          
            
              (
              
                80
                2
              
              )
            
            *
            
              (
              
                1
                0.1
              
              )
            
            *
            
              (
              
                
                  1000
                  ⁢
                  
                    
                  
                  ⁢
                  μl
                
                
                  1
                  ⁢
                  
                    
                  
                  ⁢
                  ml
                
              
              )
            
          
        
        =
        
          4000
          ⁢
          
            
          
          ⁢
          copies
          ⁢
          
            
          
          ⁢
          per
          ⁢
          
            
          
          ⁢
          ml
          ⁢
          
            
          
          ⁢
          original
          ⁢
          
            
          
          ⁢
          sample
        
      
    
  




If a lower detection limits is required, the following protocol can be employed:
VS [8 ml]
VDNA [20 μl] from use of a DNA CLEAN & CONCENTRATOR®-5, Qiagen Mini-elute or Rotary Evaporation
VCHIP [10 μl] Use all of sample for two replicates
MDL [1 copy]




  PDL
  =
  
    
      MDL
      *
      
        (
        
          20
          8000
        
        )
      
      *
      
        (
        
          80
          10
        
        )
      
      *
      
        (
        
          1
          0.1
        
        )
      
      *
      
        (
        
          
            1000
            ⁢
            
              
            
            ⁢
            μl
          
          
            1
            ⁢
            
              
            
            ⁢
            ml
          
        
        )
      
    
    =
    
      200
      ⁢
      
        
      
      ⁢
      copies
      ⁢
      
        
      
      ⁢
      per
      ⁢
      
        
      
      ⁢
      ml
      ⁢
      
        
      
      ⁢
      original
      ⁢
      
        
      
      ⁢
      sample
    
  




Still lower detection limits can be achieved by filtering a large volume of pore water from which to perform the DNA extraction.
Example 11
Evaluation of Known 16SrRNA Gene Primers for Parallel Use with the rdhA Primer Suite:
Determining the relative stoichiometry among specific functional genes and phylogenetically informative 16S rRNA marker genes is desirable. Designing and validating selective 16S rRNA gene primers is a challenge due to the high level of conservation in the ribosomal gene. Which 16S rRNA qPCR primers for organohalogen-respiring genera would be compatible with the nL-qPCR conditions of the methods of the disclosure were determined.
Table 5 illustrates those primers selected from the literature given the major genera thought to be involved in dehalogenating chloroethenes and chloroethanes. Recommended PCR conditions varied significantly for these primers, but most had an annealing temperature between 55° C. and 63° C. All were tested only at the Wafergen standard nL-qPCR conditions used for the rdh primer validation their performance was evaluated in that context against linear DNA standards of 16S rRNA gene fragments from Dehalococcoides mccartyi strain 195, Geobacter metallireducens, Desulfitobacterium hafniense Y51, Dehalogenimonas lykanthroporepellens, and Dehalobacter sp. WL. The primers that performed suitably under our standard nL-qPCR conditions are indicated in Table 5.







TABLE 5





Evaluation of known 16S rRNA primers for use with rdhA primer suite



















Genus
Forward Primer Sequence
Reverse Primer Sequence





1
Dehalobacter
GTTAGGGAAGAACGGCATCTGT
CCTCTCCTGTCCTCAAGCC




(SEQ ID NO: 337)
ATA (SEQ ID NO: 338)


 


2
Dehalococcoides/
GAGGCAGCAGCAAGGAA
GGCGGGACACTTAAAGCG



Dehaligenimonas
(SEQ ID NO: 339)
(SEQ ID NO: 340)


 


3
Dehalobacter
GCACAAGCGGTGGAGCATGTGG
ACAATCCGAACTGAGAACG




(SEQ ID NO: 341)
(SEQ ID NO: 342)


 


4
Dehalobacter
GATTGACGGTACCTAACGAGG
TACAGTTTCCAATGCTTTAC




(SEQ ID NO: 343)
GG (SEQ ID NO: 344)


 


5
Dehalococcoides
GGCGTAAAGTGAGCGTAG
GACAACCTAGAAAACCGC




(SEQ ID NO: 345)
(SEQ ID NO: 346)


 


6
Dehalococcoides
GATGAACGCTAGCGGCG
CAGACCAGCTACCGATCGA




(SEQ ID NO: 347)
A (SEQ ID NO: 348)


 


7
Dehalococcoides
GAAGTAGTGAACCGAAAGG
TCTGTCCATTGTAGCGTG




(SEQ ID NO: 349)
(SEQ ID NO: 350)


 


8
Dehalococcoides
AAGGCGGTTTTCTAGGTTGTCAC
CTTCATGCATGTCAAAT




(SEQ ID NO: 351)
(SEQ ID NO: 352)


 


9
Dehalogenimonas
GGTCATCTGATACTGTTGGACTT
ACCCAGTGTTTAGGGCGTG




GA (SEQ ID NO: 353)
GACTA (SEQ ID NO: 354)


 


10
Desulfitobacterium
GTACGACGAAGGCCTTCGGGT
CCCAGGGTTGAGCCCTAGG




(SEQ ID NO: 355)
T (SEQ ID NO: 356)


 


11
Desulfitobacteriam
GCACAAGCGGTGGAGCATGTGG
TATCTAGAGTGCTCRACC




(SEQ ID NO: 357)
(SEQ ID NO: 358)


 


12
Eubacteria
CCTACGGGAGGCAGCAG
ATTACCGCGGCTGCTGGC




(SEQ ID NO: 359)
(SEQ ID NO: 360)


 


13
Geobacter
AAGCGTTGTTCGGAWTTAT
GGCACTGCAGGGGTCAATA




(SEQ ID NO: 361)
(SEQ ID NO: 362)


 


14
Geobacter
AGGAAGCACCGGCTAACTCC
TACCCGCRACACCTAGT




(SEQ ID NO: 363)
(SEQ ID NO: 364)


 


15
Dehalococcoides
GGGAGTATCGACCCTCTC
GGATTAGCTCCAGTTCACA




(SEQ ID NO: 365)
CT (SEQ ID NO: 366)














Amplicon





(bp)
Primer reference
Rejection Criteria





1
226
Smits et al., (2004) Microbiol. Methods
Low Selectivity




57: 369-378



 


2
512
Fagervold et al., (2005) Appl. Environ. Microbiol. 71:
Low Efficiency




8085-8090



 


3
380
Marzorati et al., (2007) Appl. Environ. Microbiol. 73:
Amplified Negative




2990-2999
Control


 


4
169
Groestern et al., (2006) Appl. Environ. Microbiol. 72:
Amplified




428-436
Desulfitobacterium


 


5
181
Behrens et al., (20008) Appl. Environ.
Poor Efficiency




Microbiol. 74: 5695-5703



 


6
265
Duhamel et al., (2006 FEMS Microbiol. Ecol.
Low Efficiency




58: 538-549



 


7
235
Schaefer et al., (2009) Chemosphere 75: 141-148. S34



 


8
278
Smits et al., (2004) Microbiol. Methods 57: 369-378



 


9
193
Yan et al., (2009) Environ. Microbiol. 11: 833-843
Low Efficiency,





Amplified Dhc


 


10
224
Smits et al., (2004) Microbiol. Methods 57: 369-378



 


11
225
Marzorati et al., (2007) Appl. Environ. Microbiol.
Multi-Product




73: 2990-2999
Amplification


 


12
193
Muyzer et al., (1993) Appl. Environ.
Inconsistent




Microbiol. 59: 695-700
Amplification


 


13
312
Cummings et al., (2003) Microb. Ecol. 46: 257-269



 


14
346
Bond et al., (2002) Science 295: 483-485
Low Efficiency


 


15
446
Hendrickson et al., (2002) Appl. Environ.
Low Efficiency




Microbiol. 68:









Example 12
Quantification of Genes from nL1qPCR Results-Method of Estimating Starting Copies:
Quantifying genes by nL-qPCR was performed by methods of quantification similar to those used for μL-PCR. A standard curve was produced for each assay by use of synthesized linear DNA standards (Integrated DNA Technology). In this study, assays were run over a serial dilution range of 20,000, 2,000, and 200 starting copies per reaction. Data from each set of standards was duplicated on two separate chips. A cycle number (Ct) is determined at which the amplification passes through a critical threshold value determined by the default parameter of the Wafergen qPCR gene expression analysis software. A linear regression best-fit line was constructed based on Ct values and log 10 (input concentrations), determining an assay specific slope and intercept parameter

Ct=slope*log 10[DNA copies]+intercept

For each assay the PCR efficiency is directly related to the slope parameter and was calculated as follows:




  efficiency
  =
  
    
      10
      
        (
        
          -
          
            1
            slope
          
        
        )
      
    
    -
    1
  




For each experimental sample a Ct value was related to an estimate of starting copies per
reaction as follows:

[DNA copies]=10ct-intercept/slope 

Example 13
Quantitative estimates of starting gene copies are frequently made by the inclusion of standard DNA fragments at a known concentration run alongside experimental samples. Running a calibration with every plate or chip is desirable since it can account for chip-specific or master-mix variability, which might otherwise bias the results. However, when running a few samples against many different assays (e.g. 20 samples×384 assays), dedicating chip capacity to calibration can greatly increase the cost of a project. For instance, conducting a 3-point calibration curve in duplicate would consume 25% the capacity of 24 sample×216 assay chip. A 5-point calibration curve would consume 40% of the chip capacity. Moreover if some assays target multiple templates, these templates must be run as separate calibration samples. As a result, the number of samples that must be dedicated to calibration can quickly consume the full capacity of a single chip.
For the assays of the disclosure, for low sample:assay chip ratios, it can be advantageous to use previously generated standard curves made with the same lot of master-mix and rely on an exogenous DNA spike-in to ensure similar performance across-multiple chips. Some known nL-qPCR studies abandon the use of standards and adopt a statistical approach to Ct interpretation. Even when using the standard curve library approach, as used in developing the assays of the disclosure, the lack of standard curves on each chip potentially reduced the absolute accuracy of nL estimates compared with traditional lower throughput uL-qPCR. All results were duplicated on at least two separate chips and found only modest chip-to-chip variation. However, if a new lot of master mix (polymerase enzyme and buffer) was used, new standard curves would be generated as reagent quality could contribute to significant bias. Accordingly, where absolute accuracy is paramount, it can be advantageous to first screen samples at a low samples:assays format and then select a subset of assays to be run against the same samples and a comprehensive set of calibration standards at a high sample:assay format (e.g. 96:54 samples:assays).

## Claims

1. A method for identifying a dechlorinating microbial organism, or a plurality of said microbial organisms, in a sample comprising:
(a) obtaining a sample suspected of having a population of at least one dechlorinating microbial strain having at least one species of a reductive dehalogenase enzyme;
(b) isolating nucleic acid from the sample;
(c) applying the isolated nucleic acid to a microfluidic device configured for quantitative real-time PCR and comprising a panel of reductive dehalogenase (rdh)-specific PCR primer pairs selected to allow amplification of a specific target nucleotide sequence under a common PCR protocol, said panel comprising at least five reductive dehalogenase (rdh)-specific PCR primer pairs selected from the group consisting of SEQ ID NOs: 1 and 2, 3 and 4, 5 and 6, 7 and 8, 9 and 10, 11 and 12, 13 and 14, 15 and 16, 17 and 18, 19 and 20, 21 and 22, 23 and 24, 25 and 26, 27 and 28, 29 and 30, 31 and 32, 33 and 34, 35 and 36, 37 and 38, 39 and 40, 41 and 42, 43 and 44, 45 and 46, 47 and 48, 49 and 50, 51 and 52, 53 and 54, 55 and 56, 57 and 58, 59 and 60, 61 and 62, 63 and 64, 65 and 66, 67 and 68, 69 and 70, 71 and 72, 73 and 74, 75 and 76, 77 and 78, 79 and 80, 81 and 82, 83 and 84, 85 and 86, 87 and 88, 89 and 90, 91 and 92, 93 and 94, 95 and 96, 97 and 98, 99 and 100, 101 and 102, 103 and 104, 105 and 106, 107 and 108, 109 and 110, 111 and 112, 113 and 114, 115 and 116, 117 and 118, 119 and 120, 121 and 122, 123 and 124, 125 and 126, 127 and 128, 129 and 130, 131 and 132, 133 and 134, 135 and 136, 137 and 138, 139 and 140, 141 and 142, 143 and 144, 145 and 146, 147 and 148, 149 and 150, 151 and 152, 153 and 154, 155 and 156, 157 and 158, 159 and 160, 161 and 162, 163 and 164, 165 and 166, 167 and 168, 169 and 170, 171 and 172, 173 and 174, 175 and 176, 177 and 178, 179 and 180, 181 and 182, 183 and 184, 185 and 186, 187 and 188, 189 and 190, 191 and 192, 193 and 194, 195 and 196, 197 and 198, 199 and 200, 201 and 202, 203 and 204, 205 and 206, 207 and 208, 209 and 210, 211 and 212, 213 and 214, 215 and 216, 217 and 218, 219 and 220, 221 and 222, 223 and 224, 225 and 226, 227 and 228, 229 and 230, 231 and 232, 233 and 234, 235 and 236, 237 and 238, 239 and 240, 241 and 242, 243 and 244, 245 and 246, 247 and 248, 249 and 250, 251 and 252, 253 and 254, 255 and 256, 257 and 258, 259 and 260, 261 and 262, 263 and 264, 265 and 266, 267 and 268, 269 and 270, 271 and 272, 273 and 274, 275 and 276, 277 and 278, 279 and 280, 281 and 282, 283 and 284, 285 and 286, 287 and 288, 289 and 290, 291 and 292, 293 and 294, 295 and 296, 297 and 298, 299 and 300, 301 and 302, 303 and 304, 305 and 306, 307 and 308, 309 and 310, 311 and 312, 313 and 314, 315 and 316, 317 and 318 319 and 320, 321 and 322, 323 and 324, 325 and 326, 327 and 328, 329 and 330, 331 and 332, 333 and 334, and 335 and 336;
(d) performing quantitative real-time PCR on the isolated nucleic acid in the microfluidic device with each rdh-specific PCR primer pair of said panel and under conditions wherein the presence of a microbial reductive dehalogenase (rdh)-related nucleic acid sequence results in at least one detectable amplicon encoding a region of a reductive dehalogenase (rdh);
(e) detecting the at least one amplicon of step (d);
(f) identifying the reductive dehalogenase enzyme encoded by the at least one amplicon; and
(g) identifying the dechlorinating microbial strain or strains in the sample of step (a) that has at least one reductive dehalogenase enzyme.

2. The method of claim 1, wherein the sample reacts with each primer pair in a total reaction volume of between about 3 nanoliters and about 500 nanoliters.

3. The method of claim 1, wherein at least one primer of each primer pair has a detectable label attached thereto.

4. The method of claim 3, wherein the detectable label is a fluorescent dye.

5. The method of claim 1, wherein the method further comprises the step of quantitatively identifying the population of dechlorinating microbial strains in the sample of step (a) that have a reductive dehalogenase enzyme.

6. The method of claim 1, wherein the method further comprises the step of classifying the identified reductive dehalogenase enzyme(s) encoded by the at least one amplified PCR product according to their respective reductive dehalogenase (rdh) orthologous groups.

7. The method of claim 1, wherein the sample is obtained from a location suspected of having at least one dechlorinating microbial strain having a reductive dehalogenase (rdh) enzyme.

8. The method of claim 1, wherein the method further comprises the step of obtaining the aqueous sample from a non-aqueous sample.

9. The method of claim 1, wherein the panel of reductive dehalogenase (rdh)-specific PCR primer pairs consists essentially of at least five of the PCR primer pairs SEQ ID NOs: 1 and 2, 3 and 4, 5 and 6, 7 and 8, 9 and 10, 11 and 12, 13 and 14, 15 and 16, 17 and 18, 19 and 20, 21 and 22, 23 and 24, 25 and 26, 27 and 28, 29 and 30, 31 and 32, 33 and 34, 35 and 36, 37 and 38, 39 and 40, 41 and 42, 43 and 44, 45 and 46, 47 and 48, 49 and 50, 51 and 52, 53 and 54, 55 and 56, 57 and 58, 59 and 60, 61 and 62, 63 and 64, 65 and 66, 67 and 68, 69 and 70, 71 and 72, 73 and 74, 75 and 76, 77 and 78, 79 and 80, 81 and 82, 83 and 84, 85 and 86, 87 and 88, 89 and 90, 91 and 92, 93 and 94, 95 and 96, 97 and 98, 99 and 100, 101 and 102, 103 and 104, 105 and 106, 107 and 108, 109 and 110, 111 and 112, 113 and 114, 115 and 116, 117 and 118, 119 and 120, 121 and 122, 123 and 124, 125 and 126, 127 and 128, 129 and 130, 131 and 132, 133 and 134, 135 and 136, 137 and 138, 139 and 140, 141 and 142, 143 and 144, 145 and 146, 147 and 148, 149 and 150, 151 and 152, 153 and 154, 155 and 156, 157 and 158, 159 and 160, 161 and 162, 163 and 164, 165 and 166, 167 and 168, 169 and 170, 171 and 172, 173 and 174, 175 and 176, 177 and 178, 179 and 180, 181 and 182, 183 and 184, 185 and 186, 187 and 188, 189 and 190, 191 and 192, 193 and 194, 195 and 196, 197 and 198, 199 and 200, 201 and 202, 203 and 204, 205 and 206, 207 and 208, 209 and 210, 211 and 212, 213 and 214, 215 and 216, 217 and 218, 219 and 220, 221 and 222, 223 and 224, 225 and 226, 227 and 228, 229 and 230, 231 and 232, 233 and 234, 235 and 236, 237 and 238, 239 and 240, 241 and 242, 243 and 244, 245 and 246, 247 and 248, 249 and 250, 251 and 252, 253 and 254, 255 and 256, 257 and 258, 259 and 260, 261 and 262, 263 and 264, 265 and 266, 267 and 268, 269 and 270, 271 and 272, 273 and 274, 275 and 276, 277 and 278, 279 and 280, 281 and 282, 283 and 284, 285 and 286, 287 and 288, 289 and 290, 291 and 292, 293 and 294, 295 and 296, 297 and 298, 299 and 300, 301 and 302, 303 and 304, 305 and 306, 307 and 308, 309 and 310, 311 and 312, 313 and 314, 315 and 316, 317 and 318, 319 and 320, 321 and 322, 323 and 324, 325 and 326, 327 and 328, 329 and 330, 331 and 332, 333 and 334, and 335 and 336.

10. The method of claim 1, wherein the panel of reductive dehalogenase (rdh)-specific PCR primer pairs consists of at least five of the PCR primer pairs SEQ ID NOs: 1 and 2, 3 and 4, 5 and 6, 7 and 8, 9 and 10, 11 and 12, 13 and 14, 15 and 16, 17 and 18, 19 and 20, 21 and 22, 23 and 24, 25 and 26, 27 and 28, 29 and 30, 31 and 32, 33 and 34, 35 and 36, 37 and 38, 39 and 40, 41 and 42, 43 and 44, 45 and 46, 47 and 48, 49 and 50, 51 and 52, 53 and 54, 55 and 56, 57 and 58, 59 and 60, 61 and 62, 63 and 64, 65 and 66, 67 and 68, 69 and 70, 71 and 72, 73 and 74, 75 and 76, 77 and 78, 79 and 80, 81 and 82, 83 and 84, 85 and 86, 87 and 88, 89 and 90, 91 and 92, 93 and 94, 95 and 96, 97 and 98, 99 and 100, 101 and 102, 103 and 104, 105 and 106, 107 and 108, 109 and 110, 111 and 112, 113 and 114, 115 and 116, 117 and 118, 119 and 120, 121 and 122, 123 and 124, 125 and 126, 127 and 128, 129 and 130, 131 and 132, 133 and 134, 135 and 136, 137 and 138, 139 and 140, 141 and 142, 143 and 144, 145 and 146, 147 and 148, 149 and 150, 151 and 152, 153 and 154, 155 and 156, 157 and 158, 159 and 160, 161 and 162, 163 and 164, 165 and 166, 167 and 168, 169 and 170, 171 and 172, 173 and 174, 175 and 176, 177 and 178, 179 and 180, 181 and 182, 183 and 184, 185 and 186, 187 and 188, 189 and 190, 191 and 192, 193 and 194, 195 and 196, 197 and 198, 199 and 200, 201 and 202, 203 and 204, 205 and 206, 207 and 208, 209 and 210, 211 and 212, 213 and 214, 215 and 216, 217 and 218, 219 and 220, 221 and 222, 223 and 224, 225 and 226, 227 and 228, 229 and 230, 231 and 232, 233 and 234, 235 and 236, 237 and 238, 239 and 240, 241 and 242, 243 and 244, 245 and 246, 247 and 248, 249 and 250, 251 and 252, 253 and 254, 255 and 256, 257 and 258, 259 and 260, 261 and 262, 263 and 264, 265 and 266, 267 and 268, 269 and 270, 271 and 272, 273 and 274, 275 and 276, 277 and 278, 279 and 280, 281 and 282, 283 and 284, 285 and 286, 287 and 288, 289 and 290, 291 and 292, 293 and 294, 295 and 296, 297 and 298, 299 and 300, 301 and 302, 303 and 304, 305 and 306, 307 and 308, 309 and 310, 311 and 312, 313 and 314, 315 and 316, 317 and 318, 319 and 320, 321 and 322, 323 and 324, 325 and 326, 327 and 328, 329 and 330, 331 and 332, 333 and 334, and 335 and 336.

11. A microfluidic nanoliter quantitative PCR device configured for a plurality of quantitative real-time PCR reactions and comprising a panel of reductive dehalogenase (rdh)-specific PCR primer pairs, wherein the panel of reductive dehalogenase (rdh)-specific PCR primer pairs comprises at least five of the PCR primer pairs SEQ ID NOs: 1 and 2, 3 and 4, 5 and 6, 7 and 8, 9 and 10, 11 and 12, 13 and 14, 15 and 16, 17 and 18, 19 and 20, 21 and 22, 23 and 24, 25 and 26, 27 and 28, 29 and 30, 31 and 32, 33 and 34, 35 and 36, 37 and 38, 39 and 40, 41 and 42, 43 and 44, 45 and 46, 47 and 48, 49 and 50, 51 and 52, 53 and 54, 55 and 56, 57 and 58, 59 and 60, 61 and 62, 63 and 64, 65 and 66, 67 and 68, 69 and 70, 71 and 72, 73 and 74, 75 and 76, 77 and 78, 79 and 80, 81 and 82, 83 and 84, 85 and 86, 87 and 88, 89 and 90, 91 and 92, 93 and 94, 95 and 96, 97 and 98, 99 and 100, 101 and 102, 103 and 104, 105 and 106, 107 and 108, 109 and 110, 111 and 112, 113 and 114, 115 and 116, 117 and 118, 119 and 120, 121 and 122, 123 and 124, 125 and 126, 127 and 128, 129 and 130, 131 and 132, 133 and 134, 135 and 136, 137 and 138, 139 and 140, 141 and 142, 143 and 144, 145 and 146, 147 and 148, 149 and 150, 151 and 152, 153 and 154, 155 and 156, 157 and 158, 159 and 160, 161 and 162, 163 and 164, 165 and 166, 167 and 168, 169 and 170, 171 and 172, 173 and 174, 175 and 176, 177 and 178, 179 and 180, 181 and 182, 183 and 184, 185 and 186, 187 and 188, 189 and 190, 191 and 192, 193 and 194, 195 and 196, 197 and 198, 199 and 200, 201 and 202, 203 and 204, 205 and 206, 207 and 208, 209 and 210, 211 and 212, 213 and 214, 215 and 216, 217 and 218, 219 and 220, 221 and 222, 223 and 224, 225 and 226, 227 and 228, 229 and 230, 231 and 232, 233 and 234, 235 and 236, 237 and 238, 239 and 240, 241 and 242, 243 and 244, 245 and 246, 247 and 248, 249 and 250, 251 and 252, 253 and 254, 255 and 256, 257 and 258, 259 and 260, 261 and 262, 263 and 264, 265 and 266, 267 and 268, 269 and 270, 271 and 272, 273 and 274, 275 and 276, 277 and 278, 279 and 280, 281 and 282, 283 and 284, 285 and 286, 287 and 288, 289 and 290, 291 and 292, 293 and 294, 295 and 296, 297 and 298, 299 and 300, 301 and 302, 303 and 304, 305 and 306, 307 and 308, 309 and 310, 311 and 312, 313 and 314, 315 and 316, 317 and 318, 319 and 320, 321 and 322, 323 and 324, 325 and 326, 327 and 328, 329 and 330, 331 and 332, 333 and 334, and 335 and 336.

12. The microfluidic device of claim 11, wherein the panel of reductive dehalogenase (rdh)-specific PCR primer pairs consists essentially of at least five of the PCR primer pairs SEQ ID NOs: 1 and 2, 3 and 4, 5 and 6, 7 and 8, 9 and 10, 11 and 12, 13 and 14, 15 and 16, 17 and 18, 19 and 20, 21 and 22, 23 and 24, 25 and 26, 27 and 28, 29 and 30, 31 and 32, 33 and 34, 35 and 36, 37 and 38, 39 and 40, 41 and 42, 43 and 44, 45 and 46, 47 and 48, 49 and 50, 51 and 52, 53 and 54, 55 and 56, 57 and 58, 59 and 60, 61 and 62, 63 and 64, 65 and 66, 67 and 68, 69 and 70, 71 and 72, 73 and 74, 75 and 76, 77 and 78, 79 and 80, 81 and 82, 83 and 84, 85 and 86, 87 and 88, 89 and 90, 91 and 92, 93 and 94, 95 and 96, 97 and 98, 99 and 100, 101 and 102, 103 and 104, 105 and 106, 107 and 108, 109 and 110, 111 and 112, 113 and 114, 115 and 116, 117 and 118, 119 and 120, 121 and 122, 123 and 124, 125 and 126, 127 and 128, 129 and 130, 131 and 132, 133 and 134, 135 and 136, 137 and 138, 139 and 140, 141 and 142, 143 and 144, 145 and 146, 147 and 148, 149 and 150, 151 and 152, 153 and 154, 155 and 156, 157 and 158, 159 and 160, 161 and 162, 163 and 164, 165 and 166, 167 and 168, 169 and 170, 171 and 172, 173 and 174, 175 and 176, 177 and 178, 179 and 180, 181 and 182, 183 and 184, 185 and 186, 187 and 188, 189 and 190, 191 and 192, 193 and 194, 195 and 196, 197 and 198, 199 and 200, 201 and 202, 203 and 204, 205 and 206, 207 and 208, 209 and 210, 211 and 212, 213 and 214, 215 and 216, 217 and 218, 219 and 220, 221 and 222, 223 and 224, 225 and 226, 227 and 228, 229 and 230, 231 and 232, 233 and 234, 235 and 236, 237 and 238, 239 and 240, 241 and 242, 243 and 244, 245 and 246, 247 and 248, 249 and 250, 251 and 252, 253 and 254, 255 and 256, 257 and 258, 259 and 260, 261 and 262, 263 and 264, 265 and 266, 267 and 268, 269 and 270, 271 and 272, 273 and 274, 275 and 276, 277 and 278, 279 and 280, 281 and 282, 283 and 284, 285 and 286, 287 and 288, 289 and 290, 291 and 292, 293 and 294, 295 and 296, 297 and 298, 299 and 300, 301 and 302, 303 and 304, 305 and 306, 307 and 308, 309 and 310, 311 and 312, 313 and 314, 315 and 316, 317 and 318, 319 and 320, 321 and 322, 323 and 324, 325 and 326, 327 and 328, 329 and 330, 331 and 332, 333 and 334, and 335 and 336.

13. The microfluidic device of claim 11, wherein the panel of reductive dehalogenase (rdh)-specific PCR primer pairs consists of at least five of the PCR primer pairs SEQ ID NOs: 1 and 2, 3 and 4, 5 and 6, 7 and 8, 9 and 10, 11 and 12, 13 and 14, 15 and 16, 17 and 18, 19 and 20, 21 and 22, 23 and 24, 25 and 26, 27 and 28, 29 and 30, 31 and 32, 33 and 34, 35 and 36, 37 and 38, 39 and 40, 41 and 42, 43 and 44, 45 and 46, 47 and 48, 49 and 50, 51 and 52, 53 and 54, 55 and 56, 57 and 58, 59 and 60, 61 and 62, 63 and 64, 65 and 66, 67 and 68, 69 and 70, 71 and 72, 73 and 74, 75 and 76, 77 and 78, 79 and 80, 81 and 82, 83 and 84, 85 and 86, 87 and 88, 89 and 90, 91 and 92, 93 and 94, 95 and 96, 97 and 98, 99 and 100, 101 and 102, 103 and 104, 105 and 106, 107 and 108, 109 and 110, 111 and 112, 113 and 114, 115 and 116, 117 and 118, 119 and 120, 121 and 122, 123 and 124, 125 and 126, 127 and 128, 129 and 130, 131 and 132, 133 and 134, 135 and 136, 137 and 138, 139 and 140, 141 and 142, 143 and 144, 145 and 146, 147 and 148, 149 and 150, 151 and 152, 153 and 154, 155 and 156, 157 and 158, 159 and 160, 161 and 162, 163 and 164, 165 and 166, 167 and 168, 169 and 170, 171 and 172, 173 and 174, 175 and 176, 177 and 178, 179 and 180, 181 and 182, 183 and 184, 185 and 186, 187 and 188, 189 and 190, 191 and 192, 193 and 194, 195 and 196, 197 and 198, 199 and 200, 201 and 202, 203 and 204, 205 and 206, 207 and 208, 209 and 210, 211 and 212, 213 and 214, 215 and 216, 217 and 218, 219 and 220, 221 and 222, 223 and 224, 225 and 226, 227 and 228, 229 and 230, 231 and 232, 233 and 234, 235 and 236, 237 and 238, 239 and 240, 241 and 242, 243 and 244, 245 and 246, 247 and 248, 249 and 250, 251 and 252, 253 and 254, 255 and 256, 257 and 258, 259 and 260, 261 and 262, 263 and 264, 265 and 266, 267 and 268, 269 and 270, 271 and 272, 273 and 274, 275 and 276, 277 and 278, 279 and 280, 281 and 282, 283 and 284, 285 and 286, 287 and 288, 289 and 290, 291 and 292, 293 and 294, 295 and 296, 297 and 298, 299 and 300, 301 and 302, 303 and 304, 305 and 306, 307 and 308, 309 and 310, 311 and 312, 313 and 314, 315 and 316, 317 and 318, 319 and 320, 321 and 322, 323 and 324, 325 and 326, 327 and 328, 329 and 330, 331 and 332, 333 and 334, and 335 and 336.