Difference between revisions of "User:Admin/sandbox"

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Proteomics is the analysis of proteins present in a sample. Proteogenomics is the combined use of proteomics with genomics and transcriptomics to support protein identifications and analyses. As tools, proteomics and proteogenomics allow researchers and practitioners to understand the functional gene products and relevant microbial metabolisms in a system, which in turn can lead to informed decision-making in remediation situations.

Introduction

Proteomics is the comprehensive analysis of the proteins produced by single organisms or by microbial community (e.g., “meta”-proteomics). In this regard, proteomics represents the identification of functional gene products, providing information and insight into structural proteins and the molecular machinery produced and utilized by organisms to sustain the metabolic processes. While proteomics data can be analyzed in a de novo manner by comparing to global protein sequence databases, from a systems biology perspective, the ideal starting point for all considerations and the key enabling information is the (meta)genome of the sample under study.

Proteogenomics combines proteomics with (meta)genomics and/or transcriptomics to better analyze and identify proteins^[2]. For environmental applications, proteomics can be applied to soil, groundwater, sediment, or other environmental samples. Proteomics allows for functional characterization of a sample, enabling investigators to infer what relevant metabolisms may be active in a system (e.g., hydrocarbon degradation, reductive dechlorination). The large-scale characterization of any given proteome is accomplished by comparing measured peptide spectra with predicted protein or peptide data derived from (meta)genomic information. Thus, it is vital to have complete (meta)genome sequence information for the system being studied ^[3].This has led to the term proteogenomics to describe the strong linkage between genomics and proteomics. As implied, the quality of the proteomic measurements is inextricably linked to the quality of the genomic or metagenomic sequence data. Proteogenomics is an inherently more uncertain technique when compared to nucleic acid sequencing or qPCR technologies, yet it provides unparalleled global insights into biological structure and function.

DNA-based methods such as shotgun metagenomics and 16S rRNA amplicon sequencing provide important information and guidance for potential function of microbial communities. Like shotgun proteomics, both methods also provide relative abundances of many features. On the other hand, quantitative real time PCR (qPCR) provides absolute quantities of few features with greater sensitivity (at least 1 order of magnitude) than metagenomics approaches^[4].As with all nucleic-acid-based (eg. DNA or RNA) methods, qPCR only informs potential activity, not actual activity. By detecting gene expression rather than simply genes, RNA-based methods such as metatranscriptomics provide insight into which genes are active^[5], but at the cost of additional challenges posed by increased difficulty with RNA isolation and instability. Proteomics provides the actual catalytic activity by detection and quantification of proteins of interest.

Advantages

The two main advantages of the application of metaproteomics are:

the ability to directly measure microbial enzymes (not just potential for enzyme synthesis), and
the ability to generate detailed information on hundreds of microorganisms and proteins in one assay.

The process of obtaining the information does not require culturing of microorganisms or performance of any molecular assays. To measure features that are directly correlated to microbial activity, metaproteomics can be used to identify and relatively quantify proteins^[6]^[7]^[8]. These proteins provide important information about community activities, such as which microbial organisms are most active and what proteins are present (including proteins catalyzing reactions involved in bioremediation)^[1]^[9].

Limitations

Limitations associated with this technology are related to composition of the proteome to be analyzed, mainly concerning protein expression levels and limitations of the analytical equipment. Limitations are summarized as follows:

Sample preparation - the vast diversity of protein molecular sizes, charge states, conformational states, post-translational modifications etc., make it unfeasible to use a single sample preparation protocol that captures the entire proteome for a given microbial community. Thus, use of a protocol that allows isolation of protein content from a biological sample and eliminates non-specific contaminants (e.g., keratins, fatty acids, plastic polymers, nucleic acids and salt clusters) should be developed and tested prior to sample analysis^[10]^[11]
Proteins are not expressed in equal amounts and there may be large differences in protein levels in proteomes in samples collected from the same site. A proteomic analysis must employ proper technologies for the detection of all proteins or proteins of interest. In a small sample volume that is usually used in a proteomic analysis, a large percentage of the expressed proteins occur at low abundance levels and cannot be readily detected in the analysis due to high-abundance proteins effectively monopolizing the “sampling effort”. These rare proteins may be of particular interest in environmental samples because proteins associated with contaminant degradation are often a very small fraction of the total expressed proteins. The practical protein detection limit for Liquid Chromatography-Tandem Mass Spectrometry-Time-of-Flight (LC-MS/MS-TOF) analysis lies in the femtomol (10-15 [fmol]) range. However, due to losses during protein extraction and sample clean up and dilution, the sufficient protein concentration for detection is more realistically in the low picomol (10-12 [pmol]) to high fmol range. This limitation can be addressed by collecting a greater volume of groundwater for analysis; however, this may not be possible at all sampling locations.
Detection of proteins at low concentrations (low abundance) may be limited by other proteins present in high concentrations (high abundance). The successful search for low-abundance proteins may be mitigated by use of chromatography for separation of high-abundance proteins and precipitation for elution of proteins of interest prior to analytical detection. However, complete removal of high-abundance proteins may not be recommended because they may trap the low-abundance proteins along with their associated fragments and peptides, which will be lost and not detected. An alternative approach relies on 2-dimensional chromatography coupled with tandem mass spectrometry.
Success in the identification of proteins may vary with the sensitivity of the mass spectrometer. Proper analytic equipment can be costly. Of the most sensitive mass spectrometers, electrospray ionization and laser desorption ionization-based instruments can detect peptides with low detection limits.
Not all biological variation can be accounted for. Despite great improvements in the costs of genomic sequencing and gene prediction, there remain some aspects of biology that cannot be accurately or consistently predicted. For example, the presence and variety of post-translational modifications remains problematic and, if present and not accounted for during analysis, such modified proteins will not be efficiently detected.
Selection of the appropriate analytical method determines the success of the study. Depending on the study goals and context, some methodological adjustments should be considered, including pre-enrichment of key low-abundance proteins, adjustment of protein extraction methods or tuning of the analytical equipment. A single methodological approach is not suitable for all purposes.

Assessing Changes in Microbial Community Composition and Dynamics – Common Applications

Environmental metaproteomics is used in applied in research areas such as:

Bioenergy – characterization of feedstock conversion into energy e.g., cellulose or lignin degradation to biofuels^[12]
Human health – characterization of microbial involvement in impact/control of disease vs health in human bodies^[13]^[14]
Bioremediation – characterization of degradation of contaminants in sediments, soils, and groundwater by microorganisms^[15]^[16]^[17]^[18]^[19]^[20]
Carbon cycling – characterization of a role of microorganisms in carbon flow in an ecosystem.
Agricultural metabolism – characterization of microbial interactions with plants^[21]

Targeted vs Shotgun Proteomics

Proteomics techniques can be broadly classified into two categories:

Untargeted or shotgun proteomics, aimed at comprehensively identifying and characterizing relative abundances of the totality of proteins in a sample.
Targeted proteomics, focused on identifying and absolutely quantifying one protein.

Shotgun proteomics refers to digestion of the total proteome and subjecting all resulting peptides to separation, mass-spectroscopy, and identification based on a reference protein database (ideally derived from in silico translation of the (meta)genome). Notably, shotgun proteomics generates only an approximated relative abundance for identified proteins. On the other hand, targeted proteomics allows for absolute quantification of a single protein within a complex sample, which in turn allows for analysis of any potential correlation to a degradation rate. Prediction of degradation rates based on enzyme concentration is a crucial step towards better understanding of the molecular events underlying metabolic processes. By measuring key biomarkers, proteomic studies present an opportunity to gain profound into ecosystem health, degradation of recalcitrant compounds, and bioremediation. Quantitative proteomics can also guide regulatory agencies to make better site management decisions, thereby minimizing radiation costs and chemically induced adverse effects. Targeted Proteomics targets peptides of a specific protein in a complex mixture of other peptides and determines their presence (if they are above the detection limit) and quantity in one sample or across multiple samples (Figure 1). This analysis usually utilizes a triple quadrupole mass spectrometer (QqQ-MS), an instrument which has traditionally been used to quantify small molecules. Only recently has it been utilized for peptides. Parallel Reaction Monitoring (PRM) and data independent analysis are alternative options that can be far cheaper than developing a method for a QqQ-MS. Each targeted proteomics assay must be carefully developed. The assay specifically “targets” peptides enzymatically digested from the target protein, necessitating careful selection of peptides and method. Development of a new assay also requires preliminary analyses to ensure the method is robust. Once a method is developed and verified, it can be applied to an unlimited number of samples.

Figure 1. Targeted proteomic workflow

^[22]

Bottom-Up Proteomics

Bottom-up proteomics (Figure 2) begins by analyzing of mass spectrum fragmentation patterns of peptides, which are generated after proteolytic digestion of proteins^[22]. Spectra are identified by comparison to a database of reference proteins which are digested in silico. The creation or selection of this database is one of the most crucial steps in the analysis; ideally, the database consists of proteins encoded by the genome or metagenome of the organisms present in the sample under study. While the rapidly decreasing cost of DNA sequencing and emergence of standard assembly and annotation pipelines make obtaining (meta)genomes increasingly cost-effective, it remains an option to use global reference protein databases, such as UniProt (see [1]). However, making peptide-spectrum matches (a.k.a. PSMs) is a statistically uncertain process, as the alignment of mass fragmentation pattern of the peptide to the database is seldom perfect. Several algorithms have been developed to tackle this problem (Comet, X! Tandem, MyriMatch, OMSSA, Tide, etc.). PSM matching must carefully consider factors such as what enzyme was used to digest the proteome and how specific and complete digestion was. Additionally, peptide modifications, chemical modification of amino acids which lead to differences in mass and fragmentation pattern, are a wide-spread complication that must be accounted for. Some are intentional, for example carbiodomethylation of cysteine residues, which is applied to protect sulfur residues from becoming oxidized. Other modifications occur unintentionally during sample preparation, such as oxidation of methionine residues. PSMs are inherently statistically uncertain. A given shotgun proteome may involve hundreds of thousands of PSMs, which leads to the danger of false discovery. Traditionally, a formal false discovery rate (FDR) is applied; this is an adjustment of the threshold for statistical significance based on the number of tests performed, i.e. the more PSMs, the more stringent the testing must be. The risk is greatly exacerbated by using reference protein databases that do not reflect the sample. Use of the (meta)genome correlating to the sample under study makes this danger of false identification much less risky when compared to traditional approaches. It is generally acknowledged that rigid adherence to FDR thresholds is a serious impediment to thorough PSM assignment^[23] but is generally advisable when analyzing a proteome without any pre-existing knowledge on sample composition. Following PSM assignment, whether by use of a global reference protein database with application of FDR or by comparison to a sample-specific reference (meta)genome, peptides are matched to proteins. This step acts as a second statistical filtering step and can employ several criteria such as whether the peptide identified is unique in the database, how many peptides match a given protein, and what score was assigned to the PSMs by the PSM algorithm. A metaproteome protein identification might, for example, require three or six matching PSMs. Software for making PSMs and protein identifications can be obtained as individual packages, but several convenient open-source packages are available, some of which include several PSM algorithms (SearchGUI) and even pipelines for making further sample comparisons (PatternLab for Proteomics) or functional interpretations (MetaProteomeAnalyzer). Many of these features are also available in commercial software packages, such as Progenesis QI (Waters) and ProteinPilot (SCIEX). Global bottom-up shotgun proteomics data analysis remains an actively evolving discipline.

Figure 2. Bottom- up shotgun proteomics

Selecting Sample Locations

Below are a few guidelines for selecting sampling locations to aid in drawing conclusions from metaproteomics data. • Background: Samples from non-impacted background area can be compared with results from impacted areas to examine the impact of contamination on composition of microbial proteomes that reflect the ongoing metabolical processes. • Baseline: These samples are collected and analyzed prior to treatment as a baseline for evaluating changes in the microbial metabolism in response to the remediation. • Plume: These samples are collected from distinct zones within the source area or contaminant plume to reflect variations in contaminant concentrations, geochemical conditions, and other site-specific criteria.

Sample Collection, Preservation, and Shipping

Sampling procedures for proteomics analyses are straightforward and readily integrated into existing monitoring programs. Almost any type of sample matrix (soil, sediment, groundwater), filters (on-site filtration) can be analyzed. All samples should be shipped to the laboratory on ice or dry ice (-20 °C) using an overnight carrier to minimize the potential for changes in the microbial community between collection and analysis and keep integrity of proteins. Groundwater samples (typically 1 L) can be shipped directly to the laboratory or filtered in the field. For on-site filtration, groundwater is pumped through a Sterivex^® or Bio-Flo^® filter using standard low flow sampling techniques. The groundwater may then be discarded appropriately. As with other sample types, filters should be shipped on ice (4 °C) using an overnight carrier.

References

^ ^1.0 ^1.1 Arsène-Ploetze, F., Bertin, P.N., and Carapito, C., 2015. Proteomic tools to decipher microbial community structure and functioning. Environmental Science and Pollution Research, 22, pp. 13599-13612. DOI: 10.1007/s11356-014-3898-0 Article
^ Helbling, D.E., Ackermann, M., Fenner, K., Kohler, H.P., and Johnson, D.R., 2012. The activity level of a microbial community function can be predicted from its metatranscriptome. The ISME Journal, 6(4), pp. 902-904. DOI: 10.1038/ismej.2011.158 Article
^ Ansong C., Purvine, S.O., Adkins, J.N., Lipton, M.S., and Smith, R.D., 2008. Proteogenomics: needs and roles to be filled by proteomics in genome annotation. Briefings in Functional Genomics, 7(1), pp. 50-62. DOI: 10.1093/bfgp/eln010 Article
^ Clark K., Taggart, D.M., Baldwin, B.R., Ritalahti, K.M., Murdoch, R.W., Hatt, J.K., and Löffler, F.E., 2018. Normalized Quantitative PCR Measurements as Predictors for Ethene Formation at Sites Impacted with Chlorinated Ethenes. Environmental Science & Technology, 52(22), pp. 13410-13420. DOI: 10.1021/acs.est.8b04373
^ Czaplicki, L.M. and Gunsch, C.K., 2016. Reflection on Molecular Approaches Influencing State-of-the-Art Bioremediation Design: Culturing to Microbial Community Fingerprinting to Omics. Journal of Environmental Engineering, 142(10), pp. 1-13. DOI: 10.1061/(ASCE)EE.1943-7870.0001141
^ Hettich, R.L., Pan, C., Chourey, K., and Giannone, R.J., 2013. Metaproteomics: Harnessing the Power of High Performance Mass Spectrometry to Identify the Suite of Proteins That Control Metabolic Activities in Microbial Communities. Analytical Chemistry, 85(9), pp. 4203-4214. DOI: 10.1021/ac303053e Article
^ Keller, M. and Hettich, R.L., 2009. Environmental Proteomics: a Paradigm Shift in Characterizing Microbial Activities at the Molecular Level. Microbiology and Molecular Biology Reviews, 73(1), pp. 62-70. DOI: 10.1128/MMBR.00028-08 Article
^ Schneider, T. and Riedel, K., 2010. Environmental proteomics: Analysis of structure and function of microbial communities. Proteomics, 10(4), pp. 785-98. DOI: 10.1002/pmic.200900450
^ Johnson, D.R., Helbling, D.E., Men, Y., and Fenner, K., 2015. Can meta-omics help to establish causality between contaminant biotransformations and genes or gene products? Environmental Science: Water Research & Technology, 1, pp. 272-278. DOI: 10.1039/C5EW00016E Article
^ Chourey, K., Jansson, J., VerBerkmoes, N., Shah, M., Chavarria, K.L., Tom, L.M., Brodie, E.L., and Hettich, R.L., 2010. Direct Cellular Lysis/Protein Extraction Protocol for Soil Metaproteomics. Journal of Proteome Research, 9(12), pp. 6615-6622. DOI: 10.1021/pr100787q
^ Qian, C. and Hettich, R.L., 2017. Optimized Extraction Method To Remove Humic Acid Interferences from Soil Samples Prior to Microbial Proteome Measurements. Journal of Proteome Research, 16(7), pp. 2537-2546. DOI: 10.1021/acs.jproteome.7b00103
^ Ndimba, B.K., Ndimba, R.J., Johnson, T.S., Waditee-Sirisattha, R., Baba, M., Sirisattha, S., Shiraiwa, Y., Agrawal, G.K., and Rakwal, R, 2013. Biofuels as a sustainable energy source: an update of the applications of proteomics in bioenergy crops and algae Journal of Proteomics, 20(93), pp. 234-244. DOI: 10.1016/j.jprot.2013.05.041
^ Brooks, B., Mueller, R.S., Young, J.C., Morowitz, M.J., Hettich, R.L., and Banfield, J.F., 2015. Strain-resolved microbial community proteomics reveals simultaneous aerobic and anaerobic function during gastrointestinal tract colonization of a preterm infant. Frontiers in Microbiology, 1(6) pp. 654. DOI: 10.3389/fmicb.2015.00654 Article
^ Carr, S.A., Abbatiello, S.E., Ackermann, B.L., Borchers, C., Domon, B., Deutsch, E.W.,, Grant, R.P., Hoofnagle, A.N., Hüttenhain, R., Koomen, J.M., Liebler, D.C., Liu, T., MacLean, B., Mani, D.R., Mansfield, E., Neubert, H., Paulovich, A.G., Reiter, L., Vitek, O., Aebersold, R., Anderson, L., Bethem, R., Blonder, J., Boja, E., Botelho, J., Boyne, M., Bradshaw, R.A., Burlingame, A.L., Chan, D., Keshishian, H., Kuhn, E., Kinsinger, C., Lee, J.S., Lee, S.W., Moritz, R., Oses-Prieto, J., Rifai, N., Ritchie, J., Rodriguez, H., Srinivas, P.R., Townsend, R.R., Van Eyk, J., Whiteley, G., Wiita, A., and Weintraub, S., 2014. Targeted peptide measurements in biology and medicine: best practices for mass spectrometry-based assay development using a fit-for-purpose approach. Molecular and Cellular Proteomics, 13(3), pp. 907-917. DOI: 10.1074/mcp.M113.036095] Article
^ Bansal, R., Deobald, L.A., Crawford, R.L., Paszczynski, A.J., 2009. Proteomic detection of proteins involved in perchlorate and chlorate metabolism. Biodegradation, 20(5), pp.603-620. DOI: 10.1007/s10532-009-9248-0
^ Fuller, M. E., van Groos, P. G. K., Jarrett, M., Kucharzyk, K. H., Minard-Smith, A., Heraty, L. J., and Sturchio, N. C., 2020. Application of a multiple lines of evidence approach to document natural attenuation of hexahydro-1, 3, 5-trinitro-1, 3, 5-triazine (RDX) in groundwater. Chemosphere. 250, pp. 126210. DOI: 10.1016/j.chemosphere.2020.126210
^ Kucharzyk, K. H., Meisel, J. E., Kara-Murdoch, F., Murdoch, R. W., Higgins, S. A., Vainberg, S., and Löffler, F. E., 2020. Metagenome-guided proteomic quantification of reductive dehalogenases in the Dehalococcoides mccartyi-containing consortium SDC-9. Journal of Proteome Research, 9(4), pp. 1812-1823. DOI: 10.1021/acs.jproteome.0c00072
^ Kucharzyk, K.H., Rectanus, H.V., Bartling, C., Chang, P., Rosansky. S., Neil, K., and Chaudhry, T., 2018. Assessment of post remediation performance of a biobarrier oxygen injection system at a methyl tert-butyl ether (MTBE)-contaminated site, Marine Corps Base Camp Pendleton San Diego, California. Environmental Security Technology Certification Program, Alexandria, VA. ER-201588 Report
^ Michalsen, M. M., Kucharzyk, K. H., Bartling, C., Meisel, J. E., Hatzinger, P., Wilson, J., Istok, J., and Loffler, F, 2020. Validation of advanced molecular biological tools to monitor chlorinated solvent bioremediation and estimate cVOC degradation rates. Environmental Security Technology Certification Program, Alexandria, VA. ER201726. Report
^ Michalsen, M. M., King, A. S., Istok, J. D., Crocker, F. H., Fuller, M. E., Kucharzyk, K. H., and Gander, M. J., 2020. Spatially distinct redox conditions and degradation rates following field-scale bioaugmentation for RDX-contaminated groundwater remediation. Journal of Hazardous Materials, 387, 121529. DOI: 10.1016/j.jhazmat.2019.121529
^ Tan, B.C, Lim, Y.S., and Lau, S.E., 2017. Proteomics in commercial crops: An overview. Journal of Proteomics, 169, pp. 176-188. DOI:10.1016/j.jprot.2017.05.018
^ ^22.0 ^22.1 Zhang, Y., Fonslow, B.R, Shan, B., Baek, M.C., and Yates, J.R. III., 2013. Protein analysis by shotgun/bottom-up proteomics. Chemical Reviews, 113(4), pp 2343-94. DOI:10.1021/cr3003533
^ Heyer, R., Schallert, K., Zoun, R., Becher, B., Saake, G., and Benndorf, D., 2017. Challenges and perspectives of metaproteomic data analysis. Journal of Biotechnology, 261, pp. 24–36. DOI: 10.1016/j.jbiotec.2017.06.1201 Article

Difference between revisions of "User:Admin/sandbox"

Revision as of 23:47, 29 November 2021

Contents

Introduction

Advantages

Limitations

Assessing Changes in Microbial Community Composition and Dynamics – Common Applications

Targeted vs Shotgun Proteomics

Selecting Sample Locations

Sample Collection, Preservation, and Shipping

References

See Also

Navigation menu

Personal tools

Namespaces

Variants

Views

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Search

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Tools

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@@ Line 1: / Line 1: @@
 I have installed SandboxLink extension that provides each user their own sandbox accessible through their personal menu bar (top right)
-Simple table
+Proteomics is the analysis of proteins present in a sample. Proteogenomics is the combined use of proteomics with genomics and transcriptomics to support protein identifications and analyses. As tools, proteomics and proteogenomics allow researchers and practitioners to understand the functional gene products and relevant microbial metabolisms in a system, which in turn can lead to informed decision-making in remediation situations.
-{| class="wikitable" style="float:right; margin-left: 10px;"
-| See Also
-|-
-|
-*text
-*more text
-|}
-TABLE Edits below this line
-<!-- class="wikitable" -->
-{| class="mw-collapsible mw-collapsed wikitable" style="margin: auto; color:black; background-color:white; width: 80%;"
-|+Table 1. Nomenclature and Structure of Most Widely Used Chlorinated Solvents <ref name="CS 2010">Cwiertny, D. M. and M.M. Scherer, 2010. Chapter 2, Chlorinated Solvent Chemistry: Structures, Nomenclature and Properties. In: HF Stroo and CH.Ward (eds.). In Situ Remediation of Chlorinated Solvent Plumes.  Springer, pp. 29-37. ISBN: 978-0-387-23036-8/e-ISBN: 978-0-387-23079-5, DOI: 10.1007/0-387-23079-3_32</ref>
-|- style="color:white; background-color:#006699; text-align:center;"
-| IUPAC Name
-| Common Name
-| Acronym
-| Molecular Formula
-| Chemical Structure
-| Formula Weight
-| Density (ρ)(g/mL)
-| Solubility (mg/L)
-| Vapor Pressure (ρ<sup>0</sup>)(kPa)
-| Henry's Law Constant    (K<sub>H</sub>)(x10<sup>-3</sup>atm・m<sup>3</sup>/mol)
-| Log K<sub>ow</sub>
-| MCL<sup>c</sup> (μg/L)
-|-
-| colspan="12" style="color:black; background-color:#99C2D6;"|Chlorinated Methanes
-|-
-| style="color:black; background-color:#E6F0F5;"|tetrachloromethane
-| style="text-align:center;"|carbon tetrachloride
-| style="text-align:center;"| CT
-| style="text-align:center;"|CCl<sub>4</sub>
-|
-[[File:Tetrachloromethane.png|center|70px|frameless]]
-| style="text-align:center;"|153.8
-| style="text-align:center;"|1.59
-| style="text-align:center;"|800
-| style="text-align:center;"|20.5
-| style="text-align:center;"|28.9
-| style="text-align:center;"|2.64
-| style="text-align:center;"|0.005
-|-
-| style="color:black; background-color:#E6F0F5;"|trichloromethane
-| style="text-align:center;"|chloroform
-| style="text-align:center;"|CF
-| style="text-align:center;"|CHCl<sub>3</sub>
-|
-[[File:Trichloromethane.png|center|70px|frameless]]
-| style="text-align:center;"|119.4
-| style="text-align:center;"|1.49
-| style="text-align:center;"|8,200
-| style="text-align:center;"|26.2
-| style="text-align:center;"|3.8
-| style="text-align:center;"|1.97
-| style="text-align:center;"|0.080<sup>d</sup>
-|-
-| style="color:black; background-color:#E6F0F5;"|dichloromethane
-| style="text-align:center;"|methylene chloride
-| style="text-align:center;"|DCM
-| style="text-align:center;"|CH<sub>2</sub>Cl<sub>2</sub>
-|
-[[File:Dichloromethane.png|center|70px|frameless]]
-| style="text-align:center;"|84.9
-| style="text-align:center;"|1.33
-| style="text-align:center;"|13,200
-| style="text-align:center;"|55.3
-| style="text-align:center;"|1.7
-| style="text-align:center;"|1.25
-| style="text-align:center;"|0.005
-|-
-| style="color:black; background-color:#E6F0F5;"|chloromethane
-| style="text-align:center;"|methyl chloride
-| style="text-align:center;"|CM
-| style="text-align:center;"|CH<sub>3</sub>Cl
-|
-[[File:Chloromethane.png|center|70px|frameless]]
-| style="text-align:center;"|50.5
-| style="text-align:center;"|0.92
-| style="text-align:center;"|5,235
-| style="text-align:center;"|570
-| style="text-align:center;"|9.6
-| style="text-align:center;"|0.91
-| style="text-align:center;"|NR<sup>e</sup>
-|-
-| colspan="12" style="color:black; background-color:#99C2D6;"|Chlorinated Ethanes
-|-
-| style="color:black; background-color:#E6F0F5;"|hexachloroethane
-| style="text-align:center;"|perchloroethane
-| style="text-align:center;"|HCA
-| style="text-align:center;"|C<sub>2</sub>Cl<sub>6</sub>
-|
-[[File:hexachloroethane.png|center|70px|frameless]]
-| style="text-align:center;"|236.7
-| style="text-align:center;"|2.09
-| style="text-align:center;"|50
-| style="text-align:center;"|0.05<sup>f</sup>
-| style="text-align:center;"|-
-| style="text-align:center;"|3.93
-| style="text-align:center;"|NR
-|-
-| style="color:black; background-color:#E6F0F5;"|pentachloroethane
-| style="text-align:center;"|-
-| style="text-align:center;"|PCA
-| style="text-align:center;"|C<sub>2</sub>HCl<sub>5</sub>
-|
-[[File:pentachloroethane.png|center|70px|frameless]]
-| style="text-align:center;"|202.3
-| style="text-align:center;"|1.68
-| style="text-align:center;"|500
-| style="text-align:center;"|0.6
-| style="text-align:center;"|2.5
-| style="text-align:center;"|2.89
-| style="text-align:center;"|NR
-|-
-| style="color:black; background-color:#E6F0F5;"|1,1,1,2-tetrachloroethane
-| style="text-align:center;"|-
-| style="text-align:center;"|1,1,1,2-TeCA
-| style="text-align:center;"|C<sub>2</sub>H<sub>2</sub>Cl<sub>4</sub>
-|
-[[File:1,1,1,2-Tetrachloroethane.png|72px|frameless|center]]
-| style="text-align:center;"|167.9
-| style="text-align:center;"|1.54
-| style="text-align:center;"|1,100
-| style="text-align:center;"|1.6
-| style="text-align:center;"|2.4
-| style="text-align:center;"|-
-| style="text-align:center;"|NR
-|-
-| style="color:black; background-color:#E6F0F5;"|1,1,2,2-tetrachloroethane
-| style="text-align:center;"|-
-| style="text-align:center;"|1,1,2,2-TeCA
-| style="text-align:center;"|C<sub>2</sub>H<sub>2</sub>Cl<sub>4</sub>
-|
-[[File:1,1,2,2-Tetrachloroethane.png|72px|frameless|center]]
-| style="text-align:center;"|167.9
-| style="text-align:center;"|1.60
-| style="text-align:center;"|2,962
-| style="text-align:center;"|0.8
-| style="text-align:center;"|0.44
-| style="text-align:center;"|2.39
-| style="text-align:center;"|NR
-|-
-| style="color:black; background-color:#E6F0F5;"|1,1,2-trichloroethane
-| style="text-align:center;"|-
-| style="text-align:center;"|1,1,2-TCA
-| style="text-align:center;"|C<sub>2</sub>H<sub>3</sub>Cl<sub>3</sub>
-|
-[[File:1,1,2-Trichloroethane.svg.png|72px|frameless|center]]
-| style="text-align:center;"|133.4
-| style="text-align:center;"|1.44
-| style="text-align:center;"|4,394
-| style="text-align:center;"|3.22
-| style="text-align:center;"|0.96
-| style="text-align:center;"|2.38
-| style="text-align:center;"|0.005
-|-
-| style="color:black; background-color:#E6F0F5;"|1,1,1-trichloroethane
-| style="text-align:center;"|methyl chloroform
-| style="text-align:center;"|1,1,1-TCA
-| style="text-align:center;"|C<sub>2</sub>H<sub>3</sub>Cl<sub>3</sub>
-|
-[[File:1,1,1-trichloroethane.png|center|70px|frameless]]
-| style="text-align:center;"|133.4
-| style="text-align:center;"|1.35
-| style="text-align:center;"|1,495
-| style="text-align:center;"|16.5
-| style="text-align:center;"|14.5
-| style="text-align:center;"|2.49
-| style="text-align:center;"|0.20
-|-
-| style="color:black; background-color:#E6F0F5;"|1,2-dichloroethane
-| style="text-align:center;"|-
-| style="text-align:center;"|1,2-DCA
-| style="text-align:center;"|C<sub>2</sub>H<sub>4</sub>Cl<sub>2</sub>
-|
-[[File:1,2-dichloroethane.png|center|70px|frameless]]
-| style="text-align:center;"|99.0
-| style="text-align:center;"|1.25
-| style="text-align:center;"|8,606
-| style="text-align:center;"|10.5
-| style="text-align:center;"|1.2
-| style="text-align:center;"|1.48
-| style="text-align:center;"|0.005
-|-
-| style="color:black; background-color:#E6F0F5;"|1,1-dichloroethane
-| style="text-align:center;"|-
-| style="text-align:center;"|1,1-DCA
-| style="text-align:center;"|C<sub>2</sub>H<sub>4</sub>Cl<sub>2</sub>
-|
-[[File:1,1-Dichloroethane 2.svg.png|72px|frameless|center]]
-| style="text-align:center;"|99.0
-| style="text-align:center;"|1.17
-| style="text-align:center;"|4,676
-| style="text-align:center;"|30.3
-| style="text-align:center;"|6.2
-| style="text-align:center;"|1.79
-| style="text-align:center;"|NR
-|-
-| style="color:black; background-color:#E6F0F5;"|chloroethane
-| style="text-align:center;"|-
-| style="text-align:center;"|CA
-| style="text-align:center;"|C<sub>2</sub>H<sub>5</sub>Cl
-|
-[[File:Chloroethane.png|center|70px|frameless]]
-| style="text-align:center;"|64.5
-| style="text-align:center;"|0.92
-| style="text-align:center;"|5,700
-| style="text-align:center;"|16.0
-| style="text-align:center;"|1.8
-| style="text-align:center;"|1.43
-| style="text-align:center;"|NR
-|-
-| colspan="12" style="color:black; background-color:#99C2D6;"|Chlorinated Ethenes
-|-
-| style="color:black; background-color:#E6F0F5;"|tetrachloroethene
-| style="text-align:center;"|perchloroethene
-| style="text-align:center;"|PCE
-| style="text-align:center;"|C<sub>2</sub>Cl<sub>4</sub>
-|
-[[File:Tetrachloroethene.png|center|70px|frameless]]
-| style="text-align:center;"|165.8
-| style="text-align:center;"|1.63
-| style="text-align:center;"|150
-| style="text-align:center;"|2.4
-| style="text-align:center;"|26.3
-| style="text-align:center;"|2.88
-| style="text-align:center;"|0.005
-|-
-| style="color:black; background-color:#E6F0F5;"|trichloroethene
-| style="text-align:center;"|-
-| style="text-align:center;"|TCE
-| style="text-align:center;"|C<sub>2</sub>HCl<sub>3</sub>
-|
-[[File:Trichloroethene.png|72px|frameless|center]]
-| style="text-align:center;"|131.4
-| style="text-align:center;"|1.46
-| style="text-align:center;"|1,100
-| style="text-align:center;"|9.9
-| style="text-align:center;"|11.7
-| style="text-align:center;"|2.53
-| style="text-align:center;"|0.005
-|-
-| style="color:black; background-color:#E6F0F5;"|<i>cis</i>-1,2-dichloroethene
-| style="text-align:center;"|<i>cis</i>-dichloroethene
-| style="text-align:center;"|<i>cis</i>-DCE
-| style="text-align:center;"|C<sub>2</sub>H<sub>2</sub>Cl<sub>2</sub>
-|
-[[File:Cis-1,2-dichloroethene.png|center|70px|frameless]]
-| style="text-align:center;"|96.9
-| style="text-align:center;"|1.28
-| style="text-align:center;"|3,500
-| style="text-align:center;"|27.1
-| style="text-align:center;"|7.4
-| style="text-align:center;"|1.86
-| style="text-align:center;"|0.07
-|-
-| style="color:black; background-color:#E6F0F5;"|<i>trans</i>-1,2-dichloroethene
-| style="text-align:center;"|<i>trans</i>-dichloroethene
-| style="text-align:center;"|<i>trans</i>-DCE
-| style="text-align:center;"|C<sub>2</sub>H<sub>2</sub>Cl<sub>2</sub>
-|
-[[File:Trans-1,2-dichloroethene.png|72px|frameless|center]]
-| style="text-align:center;"|96.9
-| style="text-align:center;"|1.26
-| style="text-align:center;"|6,260
-| style="text-align:center;"|44.4
-| style="text-align:center;"|6.8
-| style="text-align:center;"|1.93
-| style="text-align:center;"|0.1
-|-
-| style="color:black; background-color:#E6F0F5;"|1,1-dichloroethene
-| style="text-align:center;"|vinylidene chloride
-| style="text-align:center;"|1,1-DCE
-| style="text-align:center;"|C<sub>2</sub>H<sub>2</sub>Cl<sub>2</sub>
-|
-[[File:1,1-Dichloroethene.svg.png|72px|frameless|center]]
-| style="text-align:center;"|96.9
-| style="text-align:center;"|1.22
-| style="text-align:center;"|3,344
-| style="text-align:center;"|80.5
-| style="text-align:center;"|23.0
-| style="text-align:center;"|2.13
-| style="text-align:center;"|0.007
-|-
-| style="color:black; background-color:#E6F0F5;"|chloroethene
-| style="text-align:center;"|vinyl chloride
-| style="text-align:center;"|VC
-| style="text-align:center;"|C<sub>2</sub>H<sub>3</sub>Cl
-|
-[[File:Chloroethene.png|center|70px|frameless]]
-| style="text-align:center;"|62.5
-| style="text-align:center;"|0.91
-| style="text-align:center;"|2,763
-| style="text-align:center;"|355
-| style="text-align:center;"|79.2
-| style="text-align:center;"|1.38
-| style="text-align:center;"|0.002
-|}
-The chlorinated solvents and many of their transformation products are colorless liquids at room temperature. They are heavier than water with densities greater than 1 gram per cubic centimeter (g/cm<sub>3</sub>) which means they can penetrate deeply into an aquifer. Some physical and chemical properties of most widely used chlorinated solvents are listed in Table 2.
-{| class="mw-collapsible mw-collapsed wikitable" style="float:left; margin-right: 40px; color:black; background-color:white; width: 60%;"
-|+Table 2. Physical and Chemical Properties of Most Widely Used Chlorinated Solvents at 25°C. Unless otherwise noted, all values have been taken from Mackay et al. (1993) <ref name="CS 2010" />
-|- style="color:white; background-color:#006699; text-align:center;"
-| Species
-| Formula Weight
-| Density (ρ)(g/mL)
-| Solubility (mg/L)
-| Vapor Pressure (ρ<sup>0</sup>)(kPa)
-| Henry's Law Constant (K<sub>H</sub>)(x10<sup>-3</sup>atm・m<sup>3</sup>/mol)
-| Log K<sub>ow</sub>
-| MCL<sup>c</sup> (μg/L)
-|-
-| colspan="8" style="color:black; background-color:#99C2D6;"|Chlorinated Methanes
-|-
-| style="color:black; background-color:#E6F0F5;"|tetrachloromethane
-| style="text-align:center;"|153.8
-| style="text-align:center;"|1.59
-| style="text-align:center;"|800
-| style="text-align:center;"|20.5
-| style="text-align:center;"|28.9
-| style="text-align:center;"|2.64
-| style="text-align:center;"|0.005
-|-
-| style="color:black; background-color:#E6F0F5;"|trichloromethane
-| style="text-align:center;"|119.4
-| style="text-align:center;"|1.49
-| style="text-align:center;"|8,200
-| style="text-align:center;"|26.2
-| style="text-align:center;"|3.8
-| style="text-align:center;"|1.97
-| style="text-align:center;"|0.080<sup>d</sup>
-|-
-| style="color:black; background-color:#E6F0F5;"|dichloromethane
-| style="text-align:center;"|84.9
-| style="text-align:center;"|1.33
-| style="text-align:center;"|13,200
-| style="text-align:center;"|55.3
-| style="text-align:center;"|1.7
-| style="text-align:center;"|1.25
-| style="text-align:center;"|0.005
-|-
-| style="color:black; background-color:#E6F0F5;"|chloromethane
-| style="text-align:center;"|50.5
-| style="text-align:center;"|0.92
-| style="text-align:center;"|5,235
-| style="text-align:center;"|570
-| style="text-align:center;"|9.6
-| style="text-align:center;"|0.91
-| style="text-align:center;"|NR<sup>e</sup>
-|-
-| colspan="8" style="color:black; background-color:#99C2D6;"|Chlorinated Ethanes
-|-
-| style="color:black; background-color:#E6F0F5;"|hexachloroethane
-| style="text-align:center;"|236.7
-| style="text-align:center;"|2.09
-| style="text-align:center;"|50
-| style="text-align:center;"|0.05<sup>f</sup>
-| style="text-align:center;"|-
-| style="text-align:center;"|3.93
-| style="text-align:center;"|NR
-|-
-| style="color:black; background-color:#E6F0F5;"|pentachloroethane
-| style="text-align:center;"|202.3
-| style="text-align:center;"|1.68
-| style="text-align:center;"|500
-| style="text-align:center;"|0.6
-| style="text-align:center;"|2.5
-| style="text-align:center;"|2.89
-| style="text-align:center;"|NR
-|-
-| style="color:black; background-color:#E6F0F5;"|1,1,1,2-tetrachloroethane
-| style="text-align:center;"|167.9
-| style="text-align:center;"|1.54
-| style="text-align:center;"|1,100
-| style="text-align:center;"|1.6
-| style="text-align:center;"|2.4
-| style="text-align:center;"|-
-| style="text-align:center;"|NR
-|-
-| style="color:black; background-color:#E6F0F5;"|1,1,2,2-tetrachloroethane
-| style="text-align:center;"|167.9
-| style="text-align:center;"|1.60
-| style="text-align:center;"|2,962
-| style="text-align:center;"|0.8
-| style="text-align:center;"|0.44
-| style="text-align:center;"|2.39
-| style="text-align:center;"|NR
-|-
-| style="color:black; background-color:#E6F0F5;"|1,1,2-trichloroethane
-| style="text-align:center;"|133.4
-| style="text-align:center;"|1.44
-| style="text-align:center;"|4,394
-| style="text-align:center;"|3.22
-| style="text-align:center;"|0.96
-| style="text-align:center;"|2.38
-| style="text-align:center;"|0.005
-|-
-| style="color:black; background-color:#E6F0F5;"|1,1,1-trichloroethane
-| style="text-align:center;"|133.4
-| style="text-align:center;"|1.35
-| style="text-align:center;"|1,495
-| style="text-align:center;"|16.5
-| style="text-align:center;"|14.5
-| style="text-align:center;"|2.49
-| style="text-align:center;"|0.20
-|-
-| style="color:black; background-color:#E6F0F5;"|1,2-dichloroethane
-| style="text-align:center;"|99.0
-| style="text-align:center;"|1.25
-| style="text-align:center;"|8,606
-| style="text-align:center;"|10.5
-| style="text-align:center;"|1.2
-| style="text-align:center;"|1.48
-| style="text-align:center;"|0.005
-|-
-| style="color:black; background-color:#E6F0F5;"|1,1-dichloroethane
-| style="text-align:center;"|99.0
-| style="text-align:center;"|1.17
-| style="text-align:center;"|4,676
-| style="text-align:center;"|30.3
-| style="text-align:center;"|6.2
-| style="text-align:center;"|1.79
-| style="text-align:center;"|NR
-|-
-| style="color:black; background-color:#E6F0F5;"|chloroethane
-| style="text-align:center;"|64.5
-| style="text-align:center;"|0.92
-| style="text-align:center;"|5,700
-| style="text-align:center;"|16.0
-| style="text-align:center;"|1.8
-| style="text-align:center;"|1.43
-| style="text-align:center;"|NR
-|-
-| colspan="8" style="color:black; background-color:#99C2D6;"|Chlorinated Ethenes
-|-
-| style="color:black; background-color:#E6F0F5;"|tetrachloroethene
-| style="text-align:center;"|165.8
-| style="text-align:center;"|1.63
-| style="text-align:center;"|150
-| style="text-align:center;"|2.4
-| style="text-align:center;"|26.3
-| style="text-align:center;"|2.88
-| style="text-align:center;"|0.005
-|-
-| style="color:black; background-color:#E6F0F5;"|trichloroethene
-| style="text-align:center;"|131.4
-| style="text-align:center;"|1.46
-| style="text-align:center;"|1,100
-| style="text-align:center;"|9.9
-| style="text-align:center;"|11.7
-| style="text-align:center;"|2.53
-| style="text-align:center;"|0.005
-|-
-| style="color:black; background-color:#E6F0F5;"|<i>cis</i>-1,2-dichloroethene
-| style="text-align:center;"|96.9
-| style="text-align:center;"|1.28
-| style="text-align:center;"|3,500
-| style="text-align:center;"|27.1
-| style="text-align:center;"|7.4
-| style="text-align:center;"|1.86
-| style="text-align:center;"|0.07
-|-
-| style="color:black; background-color:#E6F0F5;"|<i>trans</i>-1,2-dichloroethene
-| style="text-align:center;"|96.9
-| style="text-align:center;"|1.26
-| style="text-align:center;"|6,260
-| style="text-align:center;"|44.4
-| style="text-align:center;"|6.8
-| style="text-align:center;"|1.93
-| style="text-align:center;"|0.1
-|-
-| style="color:black; background-color:#E6F0F5;"|1,1-dichloroethene
-| style="text-align:center;"|96.9
-| style="text-align:center;"|1.22
-| style="text-align:center;"|3,344
-| style="text-align:center;"|80.5
-| style="text-align:center;"|23.0
-| style="text-align:center;"|2.13
-| style="text-align:center;"|0.007
-|-
-| style="color:black; background-color:#E6F0F5;"|chloroethene
-| style="text-align:center;"|62.5
-| style="text-align:center;"|0.91
-| style="text-align:center;"|2,763
-| style="text-align:center;"|355
-| style="text-align:center;"|79.2
-| style="text-align:center;"|1.38
-| style="text-align:center;"|0.002
-|-
-|}
-TABLE Edits above this line
-<!-- class="wikitable" -->
-{| class="mw-collapsible mw-collapsed wikitable" style="float:left; margin-right: 40px; color:black; background-color:white; width: 60%;"
-|+Table 1. Nomenclature and Structure of Most Widely Used Chlorinated Solvents <ref name="CS 2010">Cwiertny, D. M. and M.M. Scherer, 2010. Chapter 2, Chlorinated Solvent Chemistry: Structures, Nomenclature and Properties. In: HF Stroo and CH.Ward (eds.). In Situ Remediation of Chlorinated Solvent Plumes.  Springer, pp. 29-37. ISBN: 978-0-387-23036-8/e-ISBN: 978-0-387-23079-5, DOI: 10.1007/0-387-23079-3_32</ref>
-|- style="color:white; background-color:#006699; text-align:center;"
-| IUPAC Name
-| Common Name
-| Acronym
-| Molecular Formula
-| Chemical Structure
-|-
-| colspan="5" style="color:black; background-color:#99C2D6;"|Chlorinated Methanes
-|-
-| style="color:black; background-color:#E6F0F5;"|tetrachloromethane
-| style="text-align:center;"|carbon tetrachloride
-| style="text-align:center;"| CT
-| style="text-align:center;"|CCl<sub>4</sub>
-|
-[[File:Tetrachloromethane.png|center|70px|frameless]]
-|-
-| style="color:black; background-color:#E6F0F5;"|trichloromethane
-| style="text-align:center;"|chloroform
-| style="text-align:center;"|CF
-| style="text-align:center;"|CHCl<sub>3</sub>
-|
-[[File:Trichloromethane.png|center|70px|frameless]]
-|-
-| style="color:black; background-color:#E6F0F5;"|dichloromethane
-| style="text-align:center;"|methylene chloride
-| style="text-align:center;"|DCM
-| style="text-align:center;"|CH<sub>2</sub>Cl<sub>2</sub>
-|
-[[File:Dichloromethane.png|center|70px|frameless]]
-|-
-| style="color:black; background-color:#E6F0F5;"|chloromethane
-| style="text-align:center;"|methyl chloride
-| style="text-align:center;"|CM
-| style="text-align:center;"|CH<sub>3</sub>Cl
-|
-[[File:Chloromethane.png|center|70px|frameless]]
-|-
-| colspan="5" style="color:black; background-color:#99C2D6;"|Chlorinated Ethanes
-|-
-| style="color:black; background-color:#E6F0F5;"|hexachloroethane
-| style="text-align:center;"|perchloroethane
-| style="text-align:center;"|HCA
-| style="text-align:center;"|C<sub>2</sub>Cl<sub>6</sub>
-|
-[[File:hexachloroethane.png|center|70px|frameless]]
-|-
-| style="color:black; background-color:#E6F0F5;"|pentachloroethane
-| style="text-align:center;"|-
-| style="text-align:center;"|PCA
-| style="text-align:center;"|C<sub>2</sub>HCl<sub>5</sub>
-|
-[[File:pentachloroethane.png|center|70px|frameless]]
-|-
-| style="color:black; background-color:#E6F0F5;"|1,1,1,2-tetrachloroethane
-| style="text-align:center;"|-
-| style="text-align:center;"|1,1,1,2-TeCA
-| style="text-align:center;"|C<sub>2</sub>H<sub>2</sub>Cl<sub>4</sub>
-|
-[[File:1,1,1,2-Tetrachloroethane.png|72px|frameless|center]]
-|-
-| style="color:black; background-color:#E6F0F5;"|1,1,2,2-tetrachloroethane
-| style="text-align:center;"|-
-| style="text-align:center;"|1,1,2,2-TeCA
-| style="text-align:center;"|C<sub>2</sub>H<sub>2</sub>Cl<sub>4</sub>
-|
-[[File:1,1,2,2-Tetrachloroethane.png|72px|frameless|center]]
-|-
-| style="color:black; background-color:#E6F0F5;"|1,1,2-trichloroethane
-| style="text-align:center;"|-
-| style="text-align:center;"|1,1,2-TCA
-| style="text-align:center;"|C<sub>2</sub>H<sub>3</sub>Cl<sub>3</sub>
-|
-[[File:1,1,2-Trichloroethane.svg.png|72px|frameless|center]]
-|-
-| style="color:black; background-color:#E6F0F5;"|1,1,1-trichloroethane
-| style="text-align:center;"|methyl chloroform
-| style="text-align:center;"|1,1,1-TCA
-| style="text-align:center;"|C<sub>2</sub>H<sub>3</sub>Cl<sub>3</sub>
-|
-[[File:1,1,1-trichloroethane.png|center|70px|frameless]]
-|-
-| style="color:black; background-color:#E6F0F5;"|1,2-dichloroethane
-| style="text-align:center;"|-
-| style="text-align:center;"|1,2-DCA
-| style="text-align:center;"|C<sub>2</sub>H<sub>4</sub>Cl<sub>2</sub>
-|
-[[File:1,2-dichloroethane.png|center|70px|frameless]]
-|-
-| style="color:black; background-color:#E6F0F5;"|1,1-dichloroethane
-| style="text-align:center;"|-
-| style="text-align:center;"|1,1-DCA
-| style="text-align:center;"|C<sub>2</sub>H<sub>4</sub>Cl<sub>2</sub>
-|
-[[File:1,1-Dichloroethane 2.svg.png|72px|frameless|center]]
-|-
-| style="color:black; background-color:#E6F0F5;"|chloroethane
-| style="text-align:center;"|-
-| style="text-align:center;"|CA
-| style="text-align:center;"|C<sub>2</sub>H<sub>5</sub>Cl
-|
-[[File:Chloroethane.png|center|70px|frameless]]
-|-
-| colspan="5" style="color:black; background-color:#99C2D6;"|Chlorinated Ethenes
-|-
-| style="color:black; background-color:#E6F0F5;"|tetrachloroethene
-| style="text-align:center;"|perchloroethene
-| style="text-align:center;"|PCE
-| style="text-align:center;"|C<sub>2</sub>Cl<sub>4</sub>
-|
-[[File:Tetrachloroethene.png|center|70px|frameless]]
-|-
-| style="color:black; background-color:#E6F0F5;"|trichloroethene
-| style="text-align:center;"|-
-| style="text-align:center;"|TCE
-| style="text-align:center;"|C<sub>2</sub>HCl<sub>3</sub>
-|
-[[File:Trichloroethene.png|72px|frameless|center]]
-|-
-| style="color:black; background-color:#E6F0F5;"|<i>cis</i>-1,2-dichloroethene
-| style="text-align:center;"|<i>cis</i>-dichloroethene
-| style="text-align:center;"|<i>cis</i>-DCE
-| style="text-align:center;"|C<sub>2</sub>H<sub>2</sub>Cl<sub>2</sub>
-|
-[[File:Cis-1,2-dichloroethene.png|center|70px|frameless]]
-|-
-| style="color:black; background-color:#E6F0F5;"|<i>trans</i>-1,2-dichloroethene
-| style="text-align:center;"|<i>trans</i>-dichloroethene
-| style="text-align:center;"|<i>trans</i>-DCE
-| style="text-align:center;"|C<sub>2</sub>H<sub>2</sub>Cl<sub>2</sub>
-|
-[[File:Trans-1,2-dichloroethene.png|72px|frameless|center]]
-|-
-| style="color:black; background-color:#E6F0F5;"|1,1-dichloroethene
-| style="text-align:center;"|vinylidene chloride
-| style="text-align:center;"|1,1-DCE
-| style="text-align:center;"|C<sub>2</sub>H<sub>2</sub>Cl<sub>2</sub>
-|
-[[File:1,1-Dichloroethene.svg.png|72px|frameless|center]]
-|-
-| style="color:black; background-color:#E6F0F5;"|chloroethene
-| style="text-align:center;"|vinyl chloride
-| style="text-align:center;"|VC
-| style="text-align:center;"|C<sub>2</sub>H<sub>3</sub>Cl
-|
-[[File:Chloroethene.png|center|70px|frameless]]
-|}
-The chlorinated solvents and many of their transformation products are colorless liquids at room temperature. They are heavier than water with densities greater than 1 gram per cubic centimeter (g/cm<sub>3</sub>) which means they can penetrate deeply into an aquifer. Some physical and chemical properties of most widely used chlorinated solvents are listed in Table 2.
-{| class="mw-collapsible mw-collapsed wikitable" style="float:left; margin-right: 40px; color:black; background-color:white; width: 60%;"
-|+Table 2. Physical and Chemical Properties of Most Widely Used Chlorinated Solvents at 25°C. Unless otherwise noted, all values have been taken from Mackay et al. (1993) <ref name="CS 2010" />
-|- style="color:white; background-color:#006699; text-align:center;"
-| Species
-| Formula Weight
-| Density (ρ)(g/mL)
-| Solubility (mg/L)
-| Vapor Pressure (ρ<sup>0</sup>)(kPa)
-| Henry's Law Constant (K<sub>H</sub>)(x10<sup>-3</sup>atm・m<sup>3</sup>/mol)
-| Log K<sub>ow</sub>
-| MCL<sup>c</sup> (μg/L)
-|-
-| colspan="8" style="color:black; background-color:#99C2D6;"|Chlorinated Methanes
-|-
-| style="color:black; background-color:#E6F0F5;"|tetrachloromethane
-| style="text-align:center;"|153.8
-| style="text-align:center;"|1.59
-| style="text-align:center;"|800
-| style="text-align:center;"|20.5
-| style="text-align:center;"|28.9
-| style="text-align:center;"|2.64
-| style="text-align:center;"|0.005
-|-
-| style="color:black; background-color:#E6F0F5;"|trichloromethane
-| style="text-align:center;"|119.4
-| style="text-align:center;"|1.49
-| style="text-align:center;"|8,200
-| style="text-align:center;"|26.2
-| style="text-align:center;"|3.8
-| style="text-align:center;"|1.97
-| style="text-align:center;"|0.080<sup>d</sup>
-|-
-| style="color:black; background-color:#E6F0F5;"|dichloromethane
-| style="text-align:center;"|84.9
-| style="text-align:center;"|1.33
-| style="text-align:center;"|13,200
-| style="text-align:center;"|55.3
-| style="text-align:center;"|1.7
-| style="text-align:center;"|1.25
-| style="text-align:center;"|0.005
-|-
-| style="color:black; background-color:#E6F0F5;"|chloromethane
-| style="text-align:center;"|50.5
-| style="text-align:center;"|0.92
-| style="text-align:center;"|5,235
-| style="text-align:center;"|570
-| style="text-align:center;"|9.6
-| style="text-align:center;"|0.91
-| style="text-align:center;"|NR<sup>e</sup>
-|-
-| colspan="8" style="color:black; background-color:#99C2D6;"|Chlorinated Ethanes
-|-
-| style="color:black; background-color:#E6F0F5;"|hexachloroethane
-| style="text-align:center;"|236.7
-| style="text-align:center;"|2.09
-| style="text-align:center;"|50
-| style="text-align:center;"|0.05<sup>f</sup>
-| style="text-align:center;"|-
-| style="text-align:center;"|3.93
-| style="text-align:center;"|NR
-|-
-| style="color:black; background-color:#E6F0F5;"|pentachloroethane
-| style="text-align:center;"|202.3
-| style="text-align:center;"|1.68
-| style="text-align:center;"|500
-| style="text-align:center;"|0.6
-| style="text-align:center;"|2.5
-| style="text-align:center;"|2.89
-| style="text-align:center;"|NR
-|-
-| style="color:black; background-color:#E6F0F5;"|1,1,1,2-tetrachloroethane
-| style="text-align:center;"|167.9
-| style="text-align:center;"|1.54
-| style="text-align:center;"|1,100
-| style="text-align:center;"|1.6
-| style="text-align:center;"|2.4
-| style="text-align:center;"|-
-| style="text-align:center;"|NR
-|-
-| style="color:black; background-color:#E6F0F5;"|1,1,2,2-tetrachloroethane
-| style="text-align:center;"|167.9
-| style="text-align:center;"|1.60
-| style="text-align:center;"|2,962
-| style="text-align:center;"|0.8
-| style="text-align:center;"|0.44
-| style="text-align:center;"|2.39
-| style="text-align:center;"|NR
-|-
-| style="color:black; background-color:#E6F0F5;"|1,1,2-trichloroethane
-| style="text-align:center;"|133.4
-| style="text-align:center;"|1.44
-| style="text-align:center;"|4,394
-| style="text-align:center;"|3.22
-| style="text-align:center;"|0.96
-| style="text-align:center;"|2.38
-| style="text-align:center;"|0.005
-|-
-| style="color:black; background-color:#E6F0F5;"|1,1,1-trichloroethane
-| style="text-align:center;"|133.4
-| style="text-align:center;"|1.35
-| style="text-align:center;"|1,495
-| style="text-align:center;"|16.5
-| style="text-align:center;"|14.5
-| style="text-align:center;"|2.49
-| style="text-align:center;"|0.20
-|-
-| style="color:black; background-color:#E6F0F5;"|1,2-dichloroethane
-| style="text-align:center;"|99.0
-| style="text-align:center;"|1.25
-| style="text-align:center;"|8,606
-| style="text-align:center;"|10.5
-| style="text-align:center;"|1.2
-| style="text-align:center;"|1.48
-| style="text-align:center;"|0.005
-|-
-| style="color:black; background-color:#E6F0F5;"|1,1-dichloroethane
-| style="text-align:center;"|99.0
-| style="text-align:center;"|1.17
-| style="text-align:center;"|4,676
-| style="text-align:center;"|30.3
-| style="text-align:center;"|6.2
-| style="text-align:center;"|1.79
-| style="text-align:center;"|NR
-|-
-| style="color:black; background-color:#E6F0F5;"|chloroethane
-| style="text-align:center;"|64.5
-| style="text-align:center;"|0.92
-| style="text-align:center;"|5,700
-| style="text-align:center;"|16.0
-| style="text-align:center;"|1.8
-| style="text-align:center;"|1.43
-| style="text-align:center;"|NR
-|-
-| colspan="8" style="color:black; background-color:#99C2D6;"|Chlorinated Ethenes
-|-
-| style="color:black; background-color:#E6F0F5;"|tetrachloroethene
-| style="text-align:center;"|165.8
-| style="text-align:center;"|1.63
-| style="text-align:center;"|150
-| style="text-align:center;"|2.4
-| style="text-align:center;"|26.3
-| style="text-align:center;"|2.88
-| style="text-align:center;"|0.005
-|-
-| style="color:black; background-color:#E6F0F5;"|trichloroethene
-| style="text-align:center;"|131.4
-| style="text-align:center;"|1.46
-| style="text-align:center;"|1,100
-| style="text-align:center;"|9.9
-| style="text-align:center;"|11.7
-| style="text-align:center;"|2.53
-| style="text-align:center;"|0.005
-|-
-| style="color:black; background-color:#E6F0F5;"|<i>cis</i>-1,2-dichloroethene
-| style="text-align:center;"|96.9
-| style="text-align:center;"|1.28
-| style="text-align:center;"|3,500
-| style="text-align:center;"|27.1
-| style="text-align:center;"|7.4
-| style="text-align:center;"|1.86
-| style="text-align:center;"|0.07
-|-
-| style="color:black; background-color:#E6F0F5;"|<i>trans</i>-1,2-dichloroethene
-| style="text-align:center;"|96.9
-| style="text-align:center;"|1.26
-| style="text-align:center;"|6,260
-| style="text-align:center;"|44.4
-| style="text-align:center;"|6.8
-| style="text-align:center;"|1.93
-| style="text-align:center;"|0.1
-|-
-| style="color:black; background-color:#E6F0F5;"|1,1-dichloroethene
-| style="text-align:center;"|96.9
-| style="text-align:center;"|1.22
-| style="text-align:center;"|3,344
-| style="text-align:center;"|80.5
-| style="text-align:center;"|23.0
-| style="text-align:center;"|2.13
-| style="text-align:center;"|0.007
-|-
-| style="color:black; background-color:#E6F0F5;"|chloroethene
-| style="text-align:center;"|62.5
-| style="text-align:center;"|0.91
-| style="text-align:center;"|2,763
-| style="text-align:center;"|355
-| style="text-align:center;"|79.2
-| style="text-align:center;"|1.38
-| style="text-align:center;"|0.002
-|-
-|}
-Review these links later:
-http://www.navfac.navy.mil/navfac_worldwide/specialty_centers/exwc/products_and_services/ev/erb/tech/t2.html#hdbks
-http://www.navfac.navy.mil/navfac_worldwide/specialty_centers/exwc/products_and_services/ev/erb/tech/t2.html#hdbks
-<div class="toccolours mw-collapsible mw-collapsed" style="width:80%">
-Table 2. Physical and Chemical Properties of Most Widely Used Chlorinated Solvents at 25°C.<br>Unless otherwise noted, all values have been taken from Mackay et al. (1993) <ref name="CS 2010">Cwiertny, D. M. and M.M. Scherer, 2010. Chapter 2, Chlorinated Solvent Chemistry: Structures, Nomenclature and Properties. In: HF Stroo and CH.Ward (eds.). In Situ Remediation of Chlorinated Solvent Plumes.  Springer, pp. 29-37. ISBN: 978-0-387-23036-8/e-ISBN: 978-0-387-23079-5, DOI: 10.1007/0-387-23079-3_32</ref>
-<div class="mw-collapsible-content">
-[[File:Table 2 Chlorinated Solvents.JPG|frameless|center|800px|TABLE 2]]
-</div>
-</div>
-<!-- This div allows the TOC to float right -->
 <div style="float:right;margin:0 0 2em 2em;">__TOC__</div>
+'''Related Article(s):'''
+*[[Molecular Biological Tools - MBTs]]
+*[[Metagenomics]]
-CONTRIBUTOR(S):
+'''Contributor(s):''' Kate H. Kucharzyk, Ph.D., Morgan V. Evans, Ph.D., Robert W. Murdoch, Ph.D., Fadime Kara Murdoch, Ph.D.
-*[[Dr. Bilgen Yuncu, P.E.]]
-*[[M. Tony Lieberman]]
-==INTRODUCTION==
-Chlorinated solvents&nbsp;are a large family of organic solvents that contain&nbsp;chlorine chlorine atoms in their molecular structure.&nbsp;They were first produced in Germany in the 1800s, and widespread use in the United States (U.S.) began after World War II. In the period of 1940-1980, the U.S. produced about 2 billion pounds of chlorinated solvents each year <ref name="PC 1996"> Pankow, J.F. and Cherry, J.A., 1996. Dense Chlorinated Solvents and Other DNAPLs in Groundwater, Waterloo Press, Portland, OR.  ISBN-10: 0964801418/ISBN-13: 978-0964801417 </ref>. Chlorinated solvents, including [[wikipedia:Carbon_tetrachloride|carbon tetrachloride (CT)]], [[wikipedia:1,1,1-Trichloroethane|1,1,1-trichloroethane (TCA)]], [[wikipedia:Tetrachloroethylene|perchloroethene or tetrachloroethene (PCE)]] and [[wikipedia:Trichloroethylene|trichloroethene (TCE)]] have been among the most widely used cleaning and degreasing solvents in the U.S <ref> Doherty RE 2000. A history of the production and use of carbon tetrachloride, tetrachloroethylene, trichloroethylene and 1,1,1-trichloroethane in the United States: Part 1. Historical background; carbon tetrachloride and tetrachloroethylene. J Environ Forensics1:69–81</ref>.  They also have been used in a wide variety of other purposes such as adhesives, chemical intermediates, clothes, pharmaceuticals, pesticides, and textile processing.
-==PHYSICAL and CHEMICAL PROPERTIES==
-Chlorinated solvents are organic compounds generally constructed of a simple hydrocarbon chain (typically one to three carbon atoms in length). They can be divided into three categories based on their structural characteristics: chlorinated methanes, chlorinated ethanes and chlorinated ethenes.
-Chlorinated methanes represent the most structurally simple solvent class and consist of a single carbon center (known as a methyl carbon) to which as many as four chlorine atoms are bonded. From the perspective of groundwater contamination, perhaps the most well-known chlorinated methanes are [[wikipedia:carbon tetrachloride|carbon tetrachloride (CT)]] or [[wikipedia:tetrachloromethane|tetrachloromethane]], [[wikipedia:trichloromethane|trichloromethane]] (commonly known as [[wikipedia:chloroform|chloroform [CF])]], [[wikipedia:dichloromethane|dichloromethane (DCM)]], or [[wikipedia:methylene chloride|methylene chloride (MC)]] and [[wikipedia:chloromethane|chloromethane (CM)]], or [[wikipedia:methyl chloride|methyl chloride]].
-Chlorinated ethanes consist of two carbon centers joined by a single covalent bond. The most frequently encountered groundwater pollutants of this class include [[wikipedia:1,1,1-trichloroethane|1,1,1-trichloroethane (1,1,1-TCA)]] and [[wikipedia:1,2-dichloroethane|1,2-dichloroethane]].
-Chlorinated ethenes (also referred to as chlorinated ethylenes) also possess two carbon centers, but unlike chlorinated ethanes, these carbon atoms are joined by a carbon-carbon double bond. Chlorinated ethenes that are important groundwater contaminants include [[wikipedia:tetrachloroethene|tetrachloroethene]], or [[wikipedia:perchloroethene|perchloroethene (PCE)]],  [[wikipedia:trichloroethene|trichloroethene (TCE)]], [[wikipedia:dichloroethene|dichloroethene (DCE)]]) (DCE, mainly two geometric isomers cis-1,2-dichloroethene and trans-1,2-dichloroethene), and [[wikipedia:vinyl chloride|vinyl chloride (VC)]]. Nomenclature and structure of selected compounds from each solvent class are shown in Table 1.
-{| class="wikitable" style="float:left; margin-right: 40px; color:black; background-color:white; width: 60%;"
-|+Table 1. Nomenclature and Structure of Most Widely Used Chlorinated Solvents <ref name="CS 2010">Cwiertny, D. M. and M.M. Scherer, 2010. Chapter 2, Chlorinated Solvent Chemistry: Structures, Nomenclature and Properties. In: HF Stroo and CH.Ward (eds.). In Situ Remediation of Chlorinated Solvent Plumes.  Springer, pp. 29-37. ISBN: 978-0-387-23036-8/e-ISBN: 978-0-387-23079-5, DOI: 10.1007/0-387-23079-3_32</ref>
-|- style="color:white; background-color:#006699; text-align:center;"
-| IUPAC Name
-| Common Name
-| Abbreviation/Acronym
-| CAS Registry Number
-| Molecular Formula
-| Chemical Structure
-|-
-| colspan="6" style="color:black; background-color:#99C2D6;"|Chlorinated Methanes
-|-
-| style="color:black; background-color:#E6F0F5;"|tetrachloromethane
-| style="text-align:center;"|carbon tetrachloride
-| style="text-align:center;"| CT
-| style="text-align:center;"| 56-23-5
-| style="text-align:center;"|CCl<sub>4</sub>
-|
-[[File:Tetrachloromethane.png|center|70px|frameless]]
-|-
-| style="color:black; background-color:#E6F0F5;"|trichloromethane
-| style="text-align:center;"|chloroform
-| style="text-align:center;"|CF
-| style="text-align:center;"| 67-66-3
-| style="text-align:center;"|CHCl<sub>3</sub>
-|
-[[File:Trichloromethane.png|center|70px|frameless]]
-|-
-| style="color:black; background-color:#E6F0F5;"|dichloromethane
-| style="text-align:center;"|methylene chloride
-| style="text-align:center;"|DCM
-| style="text-alighn:center;"|75-09-2
-| style="text-align:center;"|CH<sub>2</sub>Cl<sub>2</sub>
-|
-[[File:Dichloromethane.png|center|70px|frameless]]
-|-
-| style="color:black; background-color:#E6F0F5;"|chloromethane
-| style="text-align:center;"|methyl chloride
-| style="text-align:center;"|CM
-| style="text-align:center;"|74-87-3
-| style="text-align:center;"|CH<sub>3</sub>Cl
-|
-[[File:Chloromethane.png|center|70px|frameless]]
-|-
-| colspan="6" style="color:black; background-color:#99C2D6;"|Chlorinated Ethanes
-|-
-| style="color:black; background-color:#E6F0F5;"|hexachloroethane
-| style="text-align:center;"|perchloroethane
-| style="text-align:center;"|HCA
-| style="text-align:center;"|67-72-1
-| style="text-align:center;"|C<sub>2</sub>Cl<sub>6</sub>
-|
-[[File:hexachloroethane.png|center|70px|frameless]]
-|-
-| style="color:black; background-color:#E6F0F5;"|pentachloroethane
-| style="text-align:center;"|-
-| style="text-align:center;"|PCA
-| style="text-align:center;"|76-01-7
-| style="text-align:center;"|C<sub>2</sub>HCl<sub>5</sub>
-|
-[[File:pentachloroethane.png|center|70px|frameless]]
-|-
-| style="color:black; background-color:#E6F0F5;"|1,1,1,2-tetrachloroethane
-| style="text-align:center;"|-
-| style="text-align:center;"|1,1,1,2-TeCA
-| style="text-align:center;"|630-20-6
-| style="text-align:center;"|C<sub>2</sub>H<sub>2</sub>Cl<sub>4</sub>
-|
-[[File:1,1,1,2-Tetrachloroethane.png|72px|frameless|center]]
-|-
-| style="color:black; background-color:#E6F0F5;"|1,1,2,2-tetrachloroethane
-| style="text-align:center;"|-
-| style="text-align:center;"|1,1,2,2-TeCA
-| style="text-align:center;"|79-34-5
-| style="text-align:center;"|C<sub>2</sub>H<sub>2</sub>Cl<sub>4</sub>
-|
-[[File:1,1,2,2-Tetrachloroethane.png|72px|frameless|center]]
-|-
-| style="color:black; background-color:#E6F0F5;"|1,1,2-trichloroethane
-| style="text-align:center;"|-
-| style="text-align:center;"|1,1,2-TCA
-| style="text-align:center;"|79-00-5
-| style="text-align:center;"|C<sub>2</sub>H<sub>3</sub>Cl<sub>3</sub>
-|
-[[File:1,1,2-Trichloroethane.svg.png|72px|frameless|center]]
-|-
-| style="color:black; background-color:#E6F0F5;"|1,1,1-trichloroethane
-| style="text-align:center;"|methyl chloroform
-| style="text-align:center;"|1,1,1-TCA
-| style="text-align:center;"|71-55-6
-| style="text-align:center;"|C<sub>2</sub>H<sub>3</sub>Cl<sub>3</sub>
-|
-[[File:1,1,1-trichloroethane.png|center|70px|frameless]]
-|-
-| style="color:black; background-color:#E6F0F5;"|1,2-dichloroethane
-| style="text-align:center;"|-
-| style="text-align:center;"|1,2-DCA
-| style="text-align:center;"|107-06-2
-| style="text-align:center;"|C<sub>2</sub>H<sub>4</sub>Cl<sub>2</sub>
-|
-[[File:1,2-dichloroethane.png|center|70px|frameless]]
-|-
-| style="color:black; background-color:#E6F0F5;"|1,1-dichloroethane
-| style="text-align:center;"|-
-| style="text-align:center;"|1,1-DCA
-| style="text-align:center;"|75-34-3
-| style="text-align:center;"|C<sub>2</sub>H<sub>4</sub>Cl<sub>2</sub>
-|
-[[File:1,1-Dichloroethane 2.svg.png|72px|frameless|center]]
-|-
-| style="color:black; background-color:#E6F0F5;"|chloroethane
-| style="text-align:center;"|-
-| style="text-align:center;"|CA
-| style="text-align:center;"|75-00-3
-| style="text-align:center;"|C<sub>2</sub>H<sub>5</sub>Cl
-|
-[[File:Chloroethane.png|center|70px|frameless]]
-|-
-| colspan="6" style="color:black; background-color:#99C2D6;"|Chlorinated Ethenes
-|-
-| style="color:black; background-color:#E6F0F5;"|tetrachloroethene
-| style="text-align:center;"|perchloroethene
-| style="text-align:center;"|PCE
-| style="text-align:center:"|127-18-4
-| style="text-align:center;"|C<sub>2</sub>Cl<sub>4</sub>
-|
-[[File:Tetrachloroethene.png|center|70px|frameless]]
-|-
-| style="color:black; background-color:#E6F0F5;"|trichloroethene
-| style="text-align:center;"|-
-| style="text-align:center;"|TCE
-| style="text-align:center;"|79-01-6
-| style="text-align:center;"|C<sub>2</sub>HCl<sub>3</sub>
-|
-[[File:Trichloroethene.png|72px|frameless|center]]
-|-
-| style="color:black; background-color:#E6F0F5;"|<i>cis</i>-1,2-dichloroethene
-| style="text-align:center;"|<i>cis</i>-dichloroethene
-| style="text-align:center;"|<i>cis</i>-DCE
-| style="text-align:center;"|156-59-2
-| style="text-align:center;"|C<sub>2</sub>H<sub>2</sub>Cl<sub>2</sub>
-|
-[[File:Cis-1,2-dichloroethene.png|center|70px|frameless]]
-|-
-| style="color:black; background-color:#E6F0F5;"|<i>trans</i>-1,2-dichloroethene
-| style="text-align:center;"|<i>trans</i>-dichloroethene
-| style="text-align:center;"|<i>trans</i>-DCE
-| style="text-align:center;"|156-60-5
-| style="text-align:center;"|C<sub>2</sub>H<sub>2</sub>Cl<sub>2</sub>
-|
-[[File:Trans-1,2-dichloroethene.png|72px|frameless|center]]
-|-
-| style="color:black; background-color:#E6F0F5;"|1,1-dichloroethene
-| style="text-align:center;"|vinylidene chloride
-| style="text-align:center;"|1,1-DCE
-| style+"text-alighn:center;"|75-35-4
-| style="text-align:center;"|C<sub>2</sub>H<sub>2</sub>Cl<sub>2</sub>
-|
-[[File:1,1-Dichloroethene.svg.png|72px|frameless|center]]
-|-
-| style="color:black; background-color:#E6F0F5;"|chloroethene
-| style="text-align:center;"|vinyl chloride
-| style="text-align:center;"|VC
-| style="text-align:center;"|75-01-4
-| style="text-align:center;"|C<sub>2</sub>H<sub>3</sub>Cl
-|
-[[File:Chloroethene.png|center|70px|frameless]]
-|}
-The chlorinated solvents and many of their transformation products are colorless liquids at room temperature. They are heavier than water with densities greater than 1 gram per cubic centimeter (g/cm<sub>3</sub>) which means they can penetrate deeply into an aquifer. Some physical and chemical properties of most widely used chlorinated solvents are listed in Table 2.
-{| class="wikitable" style="float:left; margin-right: 40px; color:black; background-color:white; width: 60%;"
-|+Table 2. Physical and Chemical Properties of Most Widely Used Chlorinated Solvents at 25°C. Unless otherwise noted, all values have been taken from Mackay et al. (1993) <ref name="CS 2010">Cwiertny, D. M. and M.M. Scherer, 2010. Chapter 2, Chlorinated Solvent Chemistry: Structures, Nomenclature and Properties. In: HF Stroo and CH.Ward (eds.). In Situ Remediation of Chlorinated Solvent Plumes.  Springer, pp. 29-37. ISBN: 978-0-387-23036-8/e-ISBN: 978-0-387-23079-5, DOI: 10.1007/0-387-23079-3_32</ref>
-|- style="color:white; background-color:#006699; text-align:center;"
-| Species
-| Formula Weight
-| Carbon Oxidation State<sup>a</sup>
-| Density (ρ)(g/mL)
-| Solubility (mg/L)
-| Vapor Pressure (ρ<sup>0</sup>)(kPa)
-| Henry's Law Constant (K<sub>H</sub>)(x10<sup>-3</sup>
-| Log K<sub>ow</sub>
-| Log K<sub>oc</sub><sup>b</sup>
-| MCL<sup>c</sup> (μg/L)
-|-
-| colspan="10" style="color:black; background-color:#99C2D6;"|Chlorinated Methanes
-|-
-| style="color:black; background-color:#E6F0F5;"|tetrachloromethane
-| style="text-align:center;"|153.8
-| style="text-align:center;"|+IV
-| style="text-align:center;"|1.59
-| style="text-align:center;"|800
-| style="text-align:center;"|20.5
-| style="text-align:center;"|28.9
-| style="text-align:center;"|2.64
-| style="text-align:center;"|1.9
-| style="text-align:center;"|0.005
-|-
-| style="color:black; background-color:#E6F0F5;"|trichloromethane
-| style="text-align:center;"|119.4
-| style="text-align:center;"|+III
-| style="text-align:center;"|1.49
-| style="text-align:center;"|8,200
-| style="text-align:center;"|26.2
-| style="text-align:center;"|3.8
-| style="text-align:center;"|1.97
-| style="text-align:center;"|1.52
-| style="text-align:center;"|0.080<sup>d</sup>
-|-
-| style="color:black; background-color:#E6F0F5;"|dichloromethane
-| style="text-align:center;"|84.9
-| style="text-align:center;"|+II
-| style="text-align:center;"|1.33
-| style="text-align:center;"|13,200
-| style="text-align:center;"|55.3
-| style="text-align:center;"|1.7
-| style="text-align:center;"|1.25
-| style="text-align:center;"|-
-| style="text-align:center;"|0.005
-|-
-| style="color:black; background-color:#E6F0F5;"|chloromethane
-| style="text-align:center;"|50.5
-| style="text-align:center;"|+I
-| style="text-align:center;"|0.92
-| style="text-align:center;"|5,235
-| style="text-align:center;"|570
-| style="text-align:center;"|9.6
-| style="text-align:center;"|0.91
-| style="text-align:center;"|-
-| style="text-align:center;"|NR<sup>e</sup>
-|-
-| colspan="10" style="color:black; background-color:#99C2D6;"|Chlorinated Ethanes
-|-
-| style="color:black; background-color:#E6F0F5;"|hexachloroethane
-| style="text-align:center;"|236.7
-| style="text-align:center;"|+III
-| style="text-align:center;"|2.09
-| style="text-align:center;"|50
-| style="text-align:center;"|0.05<sup>f</sup>
-| style="text-align:center;"|-
-| style="text-align:center;"|3.93
-| style="text-align:center;"|-
-| style="text-align:center;"|NR
-|-
-| style="color:black; background-color:#E6F0F5;"|pentachloroethane
-| style="text-align:center;"|202.3
-| style="text-align:center;"|+III
-| style="text-align:center;"|1.68
-| style="text-align:center;"|500
-| style="text-align:center;"|0.6
-| style="text-align:center;"|2.5
-| style="text-align:center;"|2.89
-| style="text-align:center;"|-
-| style="text-align:center;"|NR
-|-
-| style="color:black; background-color:#E6F0F5;"|1,1,1,2-tetrachloroethane
-| style="text-align:center;"|167.9
-| style="text-align:center;"|+I
-| style="text-align:center;"|1.54
-| style="text-align:center;"|1,100
-| style="text-align:center;"|1.6
-| style="text-align:center;"|2.4
-| style="text-align:center;"|-
-| style="text-align:center;"|-
-| style="text-align:center;"|NR
-|-
-| style="color:black; background-color:#E6F0F5;"|1,1,2,2-tetrachloroethane
-| style="text-align:center;"|167.9
-| style="text-align:center;"|+I
-| style="text-align:center;"|1.60
-| style="text-align:center;"|2,962
-| style="text-align:center;"|0.8
-| style="text-align:center;"|0.44
-| style="text-align:center;"|2.39
-| style="text-align:center;"|1.9
-| style="text-align:center;"|NR
-|-
-| style="color:black; background-color:#E6F0F5;"|1,1,2-trichloroethane
-| style="text-align:center;"|133.4
-| style="text-align:center;"|0
-| style="text-align:center;"|1.44
-| style="text-align:center;"|4,394
-| style="text-align:center;"|3.22
-| style="text-align:center;"|0.96
-| style="text-align:center;"|2.38
-| style="text-align:center;"|-
-| style="text-align:center;"|0.005
-|-
-| style="color:black; background-color:#E6F0F5;"|1,1,1-trichloroethane
-| style="text-align:center;"|133.4
-| style="text-align:center;"|0
-| style="text-align:center;"|1.35
-| style="text-align:center;"|1,495
-| style="text-align:center;"|16.5
-| style="text-align:center;"|14.5
-| style="text-align:center;"|2.49
-| style="text-align:center;"|2.25
-| style="text-align:center;"|0.20
-|-
-| style="color:black; background-color:#E6F0F5;"|1,2-dichloroethane
-| style="text-align:center;"|99.0
-| style="text-align:center;"|-I
-| style="text-align:center;"|1.25
-| style="text-align:center;"|8,606
-| style="text-align:center;"|10.5
-| style="text-align:center;"|1.2
-| style="text-align:center;"|1.48
-| style="text-align:center;"|1.52
-| style="text-align:center;"|0.005
-|-
-| style="color:black; background-color:#E6F0F5;"|1,1-dichloroethane
-| style="text-align:center;"|99.0
-| style="text-align:center;"|-I
-| style="text-align:center;"|1.17
-| style="text-align:center;"|4,676
-| style="text-align:center;"|30.3
-| style="text-align:center;"|6.2
-| style="text-align:center;"|1.79
-| style="text-align:center;"|-
-| style="text-align:center;"|NR
-|-
-| style="color:black; background-color:#E6F0F5;"|chloroethane
-| style="text-align:center;"|64.5
-| style="text-align:center;"|-II
-| style="text-align:center;"|0.92
-| style="text-align:center;"|5,700
-| style="text-align:center;"|16.0
-| style="text-align:center;"|1.8
-| style="text-align:center;"|1.43
-| style="text-align:center;"|-
-| style="text-align:center;"|NR
-|-
-| colspan="10" style="color:black; background-color:#99C2D6;"|Chlorinated Ethenes
-|-
-| style="color:black; background-color:#E6F0F5;"|tetrachloroethene
-| style="text-align:center;"|165.8
-| style="text-align:center;"|+II
-| style="text-align:center;"|1.63
-| style="text-align:center;"|150
-| style="text-align:center;"|2.4
-| style="text-align:center;"|26.3
-| style="text-align:center;"|2.88
-| style="text-align:center;"|2.29
-| style="text-align:center;"|0.005
-|-
-| style="color:black; background-color:#E6F0F5;"|trichloroethene
-| style="text-align:center;"|131.4
-| style="text-align:center;"|+I
-| style="text-align:center;"|1.46
-| style="text-align:center;"|1,100
-| style="text-align:center;"|9.9
-| style="text-align:center;"|11.7
-| style="text-align:center;"|2.53
-| style="text-align:center;"|1.53
-| style="text-align:center;"|0.005
-|-
-| style="color:black; background-color:#E6F0F5;"|<i>cis</i>-1,2-dichloroethene
-| style="text-align:center;"|96.9
-| style="text-align:center;"|0
-| style="text-align:center;"|1.28
-| style="text-align:center;"|3,500
-| style="text-align:center;"|27.1
-| style="text-align:center;"|7.4
-| style="text-align:center;"|1.86
-| style="text-align:center;"|-
-| style="text-align:center;"|0.07
-|-
-| style="color:black; background-color:#E6F0F5;"|<i>trans</i>-1,2-dichloroethene
-| style="text-align:center;"|96.9
-| style="text-align:center;"|0
-| style="text-align:center;"|1.26
-| style="text-align:center;"|6,260
-| style="text-align:center;"|44.4
-| style="text-align:center;"|6.8
-| style="text-align:center;"|1.93
-| style="text-align:center;"|-
-| style="text-align:center;"|0.1
-|-
-| style="color:black; background-color:#E6F0F5;"|1,1-dichloroethene
-| style="text-align:center;"|96.9
-| style="text-align:center;"|0
-| style="text-align:center;"|1.22
-| style="text-align:center;"|3,344
-| style="text-align:center;"|80.5
-| style="text-align:center;"|23.0
-| style="text-align:center;"|2.13
-| style="text-align:center;"|-
-| style="text-align:center;"|0.007
-|-
-| style="color:black; background-color:#E6F0F5;"|chloroethene
-| style="text-align:center;"|62.5
-| style="text-align:center;"|-I
-| style="text-align:center;"|0.91
-| style="text-align:center;"|2,763
-| style="text-align:center;"|355
-| style="text-align:center;"|79.2
-| style="text-align:center;"|1.38
-| style="text-align:center;"|-
-| style="text-align:center;"|0.002
-|-
-|}
-They are relatively volatile compounds with relatively high [[wikipedia:Henry’s Law|Henry’s Law]] constants(K<sub>H</sub>, a measure of the strength of partitioning from water into air). Generally, when K<sub>H</sub> for a compound exceeds 0.2 atmosphere/mole fraction (atm/M), they can readily be removed from water by air stripping it. Most chlorinated solvents can be classified as sparingly soluble in water, with aqueous solubilities generally on the order of 10s to 100s of mg/L (Table 2). As the number of chlorine atoms on a compound increases, the solubility decreases. Because of their relatively low solubilities, chlorinated solvents dissolve slowly in groundwater. Another consequence of their limited solubility is their tendency to occur in the subsurface as a separate immiscible liquid phase which, because of its density compared to water, tends to sink in groundwater.  Under these conditions, these are referred to as [[wikipedia:DNAPL|dense non-aqueous phase liquid (DNAPL)]]. Although chlorinated solvents are not very soluble in water, their solubility is typically orders of magnitude greater than their established [http://water.epa.gov/drink/contaminants/#Organic drinking water standards].
-Chlorinated solvents can be considered moderately hydrophobic which can be determined by their [[wikipedia:Partition coefficient|octanol-water partition coefficient]]s (K<sub>ow</sub>, a measure of the tendency of a substance to prefer an organic or oily phase rather than an aqueous phase). Log K<sub>ow</sub> values less than 3 indicate that the compound does not sorb strongly to aquifer solids, but can be removed readily by activated carbon. On the other hand, compounds with log K<sub>ow</sub> less than 2, such as VC, generally are not removed well by activated carbon either.  <ref name="CS 2010">Cwiertny, D. M. and M.M. Scherer, 2010. Chapter 2, Chlorinated Solvent Chemistry: Structures, Nomenclature and Properties. In: HF Stroo and CH.Ward (eds.). In Situ Remediation of Chlorinated Solvent Plumes.  Springer, pp. 29-37. ISBN: 978-0-387-23036-8/e-ISBN: 978-0-387-23079-5, DOI: 10.1007/0-387-23079-3_32</ref>
-==ENVIRONMENTAL CONCERN==
-For decades, widespread use and improper storage/disposal practices of these solvents has impacted underlying soils and groundwater, creating a significant environmental problem and human health risk. This problem became most evident following the passage in the United States of the [http://www.epa.gov/superfund/policy/cercla.htm Comprehensive Environmental Response, Compensation and Liability Act (CERCLA)], or Superfund legislation, in 1980 and the subsequent evaluation of chemical contamination of groundwater. Over 5,000 Department of Defense (DoD), Department of Energy (DOE), and [http://www.epa.gov/superfund/sites/npl/ Superfund National Priorities List (NPL)] sites are contaminated with chlorinated solvents <ref>U.S. Environmental Protection Agency (USEPA). 1996. A Citizen’s Guide to Treatment Walls. Office of Solid Waste and Emergency Response, Washington, DC, EPA 542-F-96-016, September 1996</ref> , with TCE being the most frequently detected contaminant (''e.g.,'' &gt;60% of NPL sites).<ref>Agency for Toxic Substance and Disease Registry (ATSDR). 2003. Trichloroethylene CAS# 79-01-6, Division of Toxicology ToxFAQs™, July 2003.</ref>. Additionally, there are approximately 36,000 active drycleaner sites across the United States; 75% of these facilities are suspected to have soil and/or groundwater contamination from solvent releases<ref>U.S. Department of Health and Human Services. 2011. Report on Carcinogens, Twelfth Edition. National Toxicology Program. June 10, 2011.</ref>. According to the USEPA Toxic Release Inventory, an average of 11 million pounds of TCE and 3 million pounds of PCE were released between 1998 and 2001<ref>U.S. Environmental Protection Agency (USEPA). 2003. 2001 Toxics release inventory public data release report. Office of Environmental Information, Washington, D.C., USEPA 260–R–03–001, July 2003.</ref>.
-The USEPA characterized TCE as “carcinogenic in humans by all routes of exposure” <ref>U.S. Environmental Protection Agency (USEPA). 2011. Toxicological Review of Trichloroethylene. National Center for Environmental Assessment, Washington, DC, EPA 635-R-09-011F, September 2011.</ref> and classified PCE as “likely to be carcinogenic to humans”.<ref>U.S. Environmental Protection Agency (USEPA). 2012. Toxicological Review of Tetrachloroethylene (Perchloroethylene). National Center for Environmental Assessment, Washington, DC, EPA 635-R-08-011F, February 2012.</ref> Exposure to TCE and PCE has been linked to an increased risk of kidney cancer in humans <ref name="ATSDR 2013"> Agency for Toxic Substance and Disease Registry (ATSDR). 2013. [http://www.atsdr.cdc.gov/spl/ 2013 Comprehensive Environmental Response, Compensation, and Liability Act (CERCLA) Priority List of Hazardous Substances].</ref> and has caused liver, kidney, lung, and testicular tumors in mice and rat studies. <ref>U.S. Department of Health and Human Services. 2011. Report on Carcinogens, Twelfth Edition. National Toxicology Program. June 10, 2011.</ref> Furthermore, TCE and PCE are ranked sixteenth and thirty-third, respectively, on the ''2013 Comprehensive Environmental Response, Compensation, and Liability Act (CERCLA) Priority List of Hazardous Substances'' based on their toxicity, frequency of occurrence at NPL sites, and potential for human exposure.<ref name="ATSDR 2013"> Agency for Toxic Substance and Disease Registry (ATSDR). 2013. [http://www.atsdr.cdc.gov/spl/ 2013 Comprehensive Environmental Response, Compensation, and Liability Act (CERCLA) Priority List of Hazardous Substances].</ref> The close proximity of chlorinated solvent sites (''e.g.,'' drycleaners, NPL, industrial) to urban areas has led to numerous impacts to public and private water supply wells;<ref>U.S. Environmental Protection Agency (USEPA). 2011. State Coalition for Remediation of Drycleaners – Website Resources Brochure. Office of Solid Waste and Emergency Response, Washington, DC, EPA 542-F-11-009, May 2011.</ref> between 9% and 34% of drinking water supply sources have some level of TCE contamination.<ref>U.S. Environmental Protection Agency (USEPA). 2001. Trichloroethylene Health Risk Assessment: Synthesis and Characterization, National Center for Environmental Assessment, Office of Research and Development, Washington, DC, EPA 600-P-01-002A, August 2001.</ref>
-Since most of the commonly used chlorinated solvents are classified as “known” or “potential” carcinogens; they are regulated with strict drinking water standards (also referred as [http://water.epa.gov/drink/contaminants/#Organic maximum contaminant levels [MCLs<nowiki>]</nowiki>]]).  Many chlorinated solvents are considered to present health risks if ingested in drinking water at concentrations greater than 5 micrograms per liter (µg/L) (5 parts per billion<nowiki> [ppb]</nowiki>). Also, due to their relatively high volatility, vapors from groundwater plumes can also pose unacceptable risks at some sites. When the MCL is compared to concentrations of hundreds or thousands of ppb that are commonly observed in groundwater at chlorinated solvent sites, it becomes apparent that even a small release can lead to a significant environmental problem. Today, it is recognized that there are thousands of public and private sites with chlorinated solvent related groundwater contamination problems. The groundwater plumes we see today were largely caused by releases that occurred in the 1960s, 1970s, and 1980s, illustrating the persistent long-term aspects of the chlorinated solvent problem .<ref name="Sale et al 2008">Sale T., Newell C., Stroo H., Hinchee R., and Johnson P. 2008. [http://cms.serdp-estcp.org/projects/tools/er-200530/faq/content/index.html Frequently Asked Questions Regarding Management of Chlorinated Solvents in Soil and Groundwater].</ref>
-===Fate and Transport===
-The physical, chemical and biological properties of chlorinated solvents and the nature of the subsurface media through which the compounds are migrating affect their fate and transport in the environment and potential remediation strategies. Figure 1 illustrates a typical distribution of chlorinated solvents discharged into subsurface. The solvent migrates down through the [[wikipedia:Vadose zone|unsaturated (vadose) zone]], probably leaving some residual solvent behind as it follows the path of least resistance. Eventually, it may encounter groundwater that forms the aquifer of a potential groundwater supply. Since the chlorinated solvents are denser than water, the downward movement continues within the subsurface via gravity along a permeable pathway, potentially spreading laterally or changing directions as less permeable material is encountered.  Soils and aquifer solids containing sand and gravel material that is relatively large in diameter and relatively porous, allows good passage of both water and chlorinated solvent liquids through them. <ref name="M 2010">McCarty P.L. 2010. Chapter 1, Gorundwater Contamination by Chlorinated Solvents: History, Remediation Technologies and Strategies. In: HF Stroo and CH.Ward (eds.). In Situ Remediation of Chlorinated Solvent Plumes.  Springer, pp. 29-37. ISBN: 978-0-387-23036-8/e-ISBN: 978-0-387-23079-5, DOI: 10.1007/0-387-23079-3_32</ref>
-[[File:Figure1 sale 2008.png|framed|right|Figure 1. Typical distribution of chlorinated solvents (modified from Sale et al., 2008) <ref name="Sale et al 2008">Sale T., Newell C., Stroo H., Hinchee R., and Johnson P. 2008. [http://cms.serdp-estcp.org/projects/tools/er-200530/faq/content/index.html Frequently Asked Questions Regarding Management of Chlorinated Solvents in Soil and Groundwater].</ref>]]
-Other subsurface materials such as silts and clays are very fine and may be relatively impervious to water and solvents. Chlorinated solvents migrating vertically downward are subject to a variety of influences including capillary forces imposed by the various types of subsurface soils that are encountered, and organic carbon content in soils.  When chlorinated solvents meet clay layers in their downward migration, they may pool on top of the clay, sorb into the clays, and/or seek a downward passage around the clay layer. Even when chlorinated solvents encounter more permeable sand and gravel layers, they may be diverted into one or the other because of these influences.
-The liquid solvent (or DNAPL) present in soil, subsurface solids and groundwater represents the “source” of groundwater contamination. DNAPLs have very low aqueous solubilities that may exceed regulatory criteria by as much as five orders of magnitude <ref name="PC 1996"> Pankow, J.F. and Cherry, J.A., 1996. Dense Chlorinated Solvents and Other DNAPLs in Groundwater, Waterloo Press, Portland, OR.  ISBN-10: 0964801418/ISBN-13: 978-0964801417 </ref>; as a result, these compounds only slowly dissolve in groundwater and act as long-term sources of groundwater contamination. Over time, constituents in DNAPL dissolve in water and/or volatilize into soil gas. This process leads to plume formation in transmissive zones where there is flow. At the same time, high concentrations of dissolved contaminants in transmissive zones drive contaminants into low permeability zones via diffusion. Within low permeability zones, contaminants are stored as a dissolved phase in water and as a sorbed phase on or in solids. The process of contaminants moving into low permeability layers via diffusion is referred to as matrix diffusion. The significance of contaminants in low permeability layers is that they can sustain dissolved plumes in transmissive zones long after the DNAPL source is gone.<ref>Air Force Center for Engineering and the Environment (AFCEE). 2007. AFCEE Source Zone Initiative, Contributing Authors: T. Sale, B. Twitchell, F. Marinelli—Colorado State University; T. Illangasekare, B. Wilking, and D. Rodriguez—Colorado School of Mines. </ref><ref>Chapman, S.W. and Parker, B.L., 2005. Plume Persistence Due to Aquitard Back Diffusion Following Dense Non-aqueous Phase Liquid Removal or Isolation, Water Resource Research, Vol. 41, No. 12, W12411. DOI: 10.1029/2005WR004224</ref>
-Chlorinated solvents can also be transformed by both abiotic and biotic processes at normal groundwater temperatures, leading to the production of many intermediate chlorinated compounds in groundwater that were also of health concern. <ref> Vogel TM, Criddle CS, McCarty PL. 1987. Transformations of halogenated aliphatic compounds. Environ Sci Technol 21:722–736.</ref> PCE was first reported to be biologically reduced under anaerobic conditions to form TCE,<ref> Bouwer EJ, Rittmann BE, McCarty PL. 1981. Anaerobic degradation of halogenated 1- and 2-carbon organic compounds. Environ Sci Technol 15:596–599.</ref> and later TCE was also found to be biologically reduced to form cis-1,2-dichloroethene (cis-DCE) and VC which is called [[wikipedia:reductive dechlorination|reductive dechlorination]].<ref> Parsons F, Lage BG. 1985. Chlorinated organics in simulated groundwater environments. J Am Water Works Assoc 77:52–59.</ref> <ref>Vogel TM, McCarty PL. 1985. Biotransformation of tetrachloroethylene to trichloroethylene, dichloroethylene, vinyl chloride, and carbon dioxide under methanogenic conditions. Appl Environ Microbiol 49:1080–1083</ref> VC was of even greater concern than the parent compounds as it was a known human carcinogen. However, in 1989 VC was also found to be capable of biological reduction, forming ethene.<ref>Freedman DL, Gossett JM. 1989. Biological reductive dechlorination of tetrachloroethylene and trichloroethylene to ethylene under methanogenic conditions. Appl Environ Microbiol 55:2144–2151.</ref> In order for biological reduction to occur, other organic compounds must be present to serve as electron donors for the bacteria. When this occurs, transformation of PCE or TCE to intermediate and end products is frequently found, leading to natural attenuation.
-Transformations of TCA have been found to be even more complex as both abiotic and biotic processes are operable in its transformation.<ref>Vogel TM, McCarty PL. 1987. Abiotically 1,1,1-trichloroethane Environ Sci Technol 21:1208–1213.</ref> Abiotically, TCA can be transformed into 1,1-dichloroethene (1,1-DCE) by removal of one chlorine atom and one hydrogen atom (dehydrohalogenation), or into acetic acid through hydrolysis reactions. The rate of transformation to acetic acid is about four times that of 1,1-DCE. Formation of 1,1-DCE is harmful as this compound is much more toxic than TCA itself, while formation of acetic acid is beneficial as this is a normal compound in the human diet and readily degraded biologically. The half-life for TCA transformation to the two different products is on the order of two years, a relatively short time when compared to the residence time of groundwater contaminants. Thus, 1,1-DCE is generally found in groundwater contaminated with TCA. TCA can also be transformed biologically by reductive dehalogenation to form 1,1-dichloroethane (1,1-DCA), which can be further reduced to chloroethane. Chloroethane can be further reduced biologically to form ethane, although chemical hydrolysis to form ethanol is generally faster. <ref name="M 2010">McCarty, 2010. Chapter 1, Gorundwater Contamination by Chlorinated Solvents: History, Remediation Technologies and Strategies. In: HF Stroo and CH.Ward (eds.). In Situ Remediation of Chlorinated Solvent Plumes.  Springer, pp. 29-37. ISBN: 978-0-387-23036-8/e-ISBN: 978-0-387-23079-5, DOI: 10.1007/0-387-23079-3_32</ref>
-CT also can be transformed by both abiotic and biotic processes, primarily through free radical processes that lead to a variety of possible end products.<ref>Criddle CS, McCarty PL. 1991. Electrolytic model system for reductive dehalogenation in aqueous enviroments. Environ Sci Technol 25:973–978.</ref> The abiotic processes, however, generally require the presence of a reducing agent of some type, and thus abiotic transformations do not often occur spontaneously as with TCA. Many of the CT transformation intermediates are unstable and do not last long. The main compound of concern found present from CT transformation, either abiotic or biotic, is chloroform. This too can be transformed by both abiotic and biotic processes, although generally much slower than CT.<ref name="M 2010">McCarty, 2010. Chapter 1, Gorundwater Contamination by Chlorinated Solvents: History, Remediation Technologies and Strategies. In: HF Stroo and CH.Ward (eds.). In Situ Remediation of Chlorinated Solvent Plumes.  Springer, pp. 29-37. ISBN: 978-0-387-23036-8/e-ISBN: 978-0-387-23079-5, DOI: 10.1007/0-387-23079-3_32</ref>
-== APPLICABLE REMEDIATION TECHNOLOGIES ==
-Because of their physico-chemical properties, most chlorinated solvents are relatively recalcitrant in the subsurface, posing challenges for remediation.   Fortunately, a number of ex situ and in situ approaches can be used are available to address chlorinated solvent contamination.  However, the choice of which technology to implement is very site specific.  It is important to thoroughly characterize the site to make a thorough evaluation and comparison of the remediation options and select an appropriate approach with a high probability of success. At a minimum, site characterization should provide information on: 1) the target chlorinated solvent(s); 2) the expected fate and transport of these contaminants based on their chemical properties;  3) the current sitewide biogeochemistry; 4) the sitewide hydrogeology and its influence on both the lateral and vertical extent of the contamination; 5) the remedial goals and objectives of the cleanup; 6) the schedule constraints; and 7) the available budget.   Knowing this information, one can choose from the following list of technologies.
-<embedvideo service="youtube" dimensions=480 alignment="right" description="Biogeochemical Transformation of Chlorinated Solvents by Dr. Pat Evans" container="frame">https://youtu.be/wRuQSChkrDk</embedvideo>
-===For Soil===
-====Ex Situ Treatment Technologies for Soil====
-*Excavation and Off-site Disposal.  Applicable to vadose zone (unsataturated) soils.  Vertical and lateral access to the contaminated material by excavators is key for this removal approach.
-*Excavation and On-site Mobile Steam Distillation.  Applicable to vadose zone and saturated soils.  Vertical and lateral access to the contaminated material by excavators is key for this removal approach.  Soils are heated to above the boiling point of the contaminants, then contaminants are then removed through condensation, leaving the soil solvent-free.  Soils can then be returned to the excavation.
-====In Situ Treatment Technologies for Soil====
-*VOS (Vadose Oil Substrate).  VOS® is a technology that helps microbes breakdown chlorinated solvents in the vadose zone before they reach groundwater.  VOS technology is based on emulsified oil technology used for treating groundwater, but in this approach, VOS is injected into the unsaturated soil to create a long-lasting treatment zone that promotes anaerobic reductive dechlorination. *Soil Vacuum Extraction (SVE).  Applicable to vadose zone soil with moderate to high permeability.  Relies on a compound’s ability to partition from where it is adsorbed to the soil into to soil gas where it can be vacuum extracted under pressure and discharged or treated before discharge.
-*Vitrification.  Involves applying and electrical current to the contaminated soil matrix to solidify the matrix and bind the contamination in place.
-===For Groundwater===
-====Ex Situ Treatment Technologies for Groundwater====
-*Aggressive Fluid Vacuum Recovery (AFVR).  Applicable to localized areas of groundwater containing elevated concentrations of chlorinated solvents including DNAPL.  Involves short-term mechanical removal of groundwater by vacuum extraction.  Contaminated groundwater is disposed off site.
-*Pump and Treat (P&T) with Discharge, Air Stripping (AS) or Carbon Adsorption (CA). Typically applied where hydraulic control of contaminant migration is desirable along with contaminant removal.  Discharging contaminated water or treated water to a receiving feature (e.g., stream, wasterwater treatment plant) may require a permit.  Air stripping may require off-gas treatment; carbon adsorption cells must be monitored for breakthrough and replacement.
-====In Situ Treatment Technologies for Groundwater====
-*Physical Approaches (Thermal).  Thermal treatment involves inserting heating probes into the contaminated aquifer with the intent of raising the temperature above the boiling point of the contaminant to drive the contamination from the aqueous phase into the vapor phase.  As the contaminated vapor migration upward into the overlying unsaturated soil, it is then captured by SVE for removal.
-*Chemical Approaches (In Situ Chemical Oxidation [ISCO], In Situ Chemical Reduction [ISCR]).  ISCO uses strong chemical oxidizers (e.g., potassium permanganate, sodium persulfate, Fenton’s Reagent, or ozone) to destroy the contaminants in place.  ISCR is the combination of abiotic chemical reduction using zero valent iron (ZVI) and/or reduced minerals coupled with anerobic bioremediation to treat chlorinated solvent contamination in groundwater.
-*Biological (Enhanced Reductive Dechlorination [ERD], Co-metabolism, Monitored Natural Attenuation [MNA]).  Biological approaches serve to stimulate specific native or inoculated microbial communities in the metabolic removal of chlorine from the solvent yielding non-toxic end-products.
-==REFERENCES==
-<references/>
-==SEE ALSO==
+'''Key Resources(s):'''
-Add Related Pages from within this Wiki here
+*Proteomic tools to decipher microbial community structure and functioning<ref name="Arsène-Ploetze2015">Arsène-Ploetze, F., Bertin, P.N., and Carapito, C., 2015.  Proteomic tools to decipher microbial community structure and functioning. Environmental Science and Pollution Research, 22, pp. 13599-13612. [https://doi.org/10.1007/s11356-014-3898-0 DOI: 10.1007/s11356-014-3898-0] [[Media: Arsene-Ploetze2015.pdf | Article]]</ref>.
-<!-- [[Category:Common Groundwater Contaminants]] -->
+==Introduction==
+'''Proteomics''' is the comprehensive analysis of the proteins produced by single organisms or by microbial community (e.g., “meta”-proteomics). In this regard, proteomics represents the identification of functional gene products, providing information and insight into structural proteins and the molecular machinery produced and utilized by organisms to sustain the metabolic processes. While proteomics data can be analyzed in a de novo manner by comparing to global protein sequence databases, from a systems biology perspective, the ideal starting point for all considerations and the key enabling information is the (meta)genome of the sample under study.
-----
+'''Proteogenomics''' combines proteomics with (meta)genomics and/or transcriptomics to better analyze and identify proteins<ref name="Helbling2012">Helbling, D.E., Ackermann, M., Fenner, K., Kohler, H.P., and Johnson, D.R., 2012.  The activity level of a microbial community function can be predicted from its metatranscriptome. The ISME Journal, 6(4), pp. 902-904. [https://doi.org/10.1038/ismej.2011.158 DOI: 10.1038/ismej.2011.158] [[Media: Helbling2012.pdf | Article]]</ref>. For environmental applications, proteomics can be applied to soil, groundwater, sediment, or other environmental samples. Proteomics allows for functional characterization of a sample, enabling investigators to infer what relevant metabolisms may be active in a system (e.g., hydrocarbon degradation, reductive dechlorination). The large-scale characterization of any given proteome is accomplished by comparing measured peptide spectra with predicted protein or peptide data derived from (meta)genomic information. Thus, it is vital to have complete (meta)genome sequence information for the system being studied <ref name="Ansong2008">Ansong C., Purvine, S.O., Adkins, J.N., Lipton, M.S., and Smith, R.D., 2008.  Proteogenomics: needs and roles to be filled by proteomics in genome annotation. Briefings in Functional Genomics, 7(1), pp. 50-62. [https://doi.org/10.1093/bfgp/eln010 DOI: 10.1093/bfgp/eln010] [[Media: Ansong2008.pdf | Article]]</ref>.This has led to the term proteogenomics to describe the strong linkage between genomics and proteomics. As implied, the quality of the proteomic measurements is inextricably linked to the quality of the genomic or metagenomic sequence data. Proteogenomics is an inherently more uncertain technique when compared to nucleic acid sequencing or qPCR technologies, yet it provides unparalleled global insights into biological structure and function.
-{| class="mw-collapsible mw-collapsed wikitable" style="float:left; margin-right: 40px; color:black; background-color:white; width: 60%; "
+DNA-based methods such as shotgun metagenomics and 16S rRNA amplicon sequencing provide important information and guidance for potential function of microbial communities. Like shotgun proteomics, both methods also provide <u>relative abundances of many features</u>. On the other hand, quantitative real time PCR (qPCR) provides <u>absolute quantities of few features</u> with greater sensitivity (at least 1 order of magnitude) than metagenomics approaches<ref name="Clark2018">Clark K., Taggart, D.M., Baldwin, B.R., Ritalahti, K.M., Murdoch, R.W., Hatt, J.K., and Löffler, F.E., 2018.  Normalized Quantitative PCR Measurements as Predictors for Ethene Formation at Sites Impacted with Chlorinated Ethenes. Environmental Science & Technology, 52(22), pp. 13410-13420. [https://doi.org/10.1021/acs.est.8b04373 DOI: 10.1021/acs.est.8b04373]</ref>.As with all nucleic-acid-based (eg. DNA or RNA) methods, qPCR only informs potential activity, not actual activity. By detecting gene expression rather than simply genes, RNA-based methods such as metatranscriptomics provide insight into which genes are active<ref name="Czaplicki2016">Czaplicki, L.M. and Gunsch, C.K., 2016.  Reflection on Molecular Approaches Influencing State-of-the-Art Bioremediation Design: Culturing to Microbial Community Fingerprinting to Omics. Journal of Environmental Engineering, 142(10), pp. 1-13. [https://doi.org/10.1061/(ASCE)EE.1943-7870.0001141 DOI: 10.1061/(ASCE)EE.1943-7870.0001141]</ref>, but at the cost of additional challenges posed by increased difficulty with RNA isolation and instability. Proteomics provides the actual catalytic activity by detection and quantification of proteins of interest.
-|+Table 2. Physical and Chemical Properties of Most Widely Used Chlorinated Solvents at 25°C.<br> Unless otherwise noted, all values have been taken from Mackay et al. (1993) <ref name="CS 2010">Cwiertny, D. M. and M.M. Scherer, 2010. Chapter 2, Chlorinated Solvent Chemistry: Structures, Nomenclature and Properties. In: HF Stroo and CH.Ward (eds.). In Situ Remediation of Chlorinated Solvent Plumes.  Springer, pp. 29-37. ISBN: 978-0-387-23036-8/e-ISBN: 978-0-387-23079-5, DOI: 10.1007/0-387-23079-3_32</ref>
-|- style="color:white; background-color:#006699; text-align:center;"
-| Species
-| Formula Weight
-| Carbon Oxidation State<sup>a</sup>
-| Density (ρ)(g/mL)
-| Solubility (mg/L)
-| Vapor Pressure (ρ<sup>0</sup>)(kPa)
-| Henry's Law Constant (K<sub>H</sub>)(x10<sup>-3</sup>
-| Log K<sub>ow</sub>
-| Log K<sub>oc</sub><sup>b</sup>
-| MCL<sup>c</sup> (μg/L)
-|-
-| colspan="10" style="color:black; background-color:#99C2D6;"|Chlorinated Methanes
-|-
-| style="color:black; background-color:#E6F0F5;"|tetrachloromethane
-| style="text-align:center;"|x
-| style="text-align:center;"|x
-| style="text-align:center;"|x
-| style="text-align:center;"|x
-| style="text-align:center;"|x
-| style="text-align:center;"|x
-| style="text-align:center;"|x
-| style="text-align:center;"|x
-| style="text-align:center;"|x
-|-
-| style="color:black; background-color:#E6F0F5;"|trichloromethane
-| style="text-align:center;"|x
-| style="text-align:center;"|x
-| style="text-align:center;"|x
-| style="text-align:center;"|x
-| style="text-align:center;"|x
-| style="text-align:center;"|x
-| style="text-align:center;"|x
-| style="text-align:center;"|x
-| style="text-align:center;"|x
-|-
-| style="color:black; background-color:#E6F0F5;"|dichloromethane
-| style="text-align:center;"|x
-| style="text-align:center;"|x
-| style="text-align:center;"|x
-| style="text-align:center;"|x
-| style="text-align:center;"|x
-| style="text-align:center;"|x
-| style="text-align:center;"|x
-| style="text-align:center;"|x
-| style="text-align:center;"|x
-|-
-| style="color:black; background-color:#E6F0F5;"|chloromethane
-| style="text-align:center;"|x
-| style="text-align:center;"|x
-| style="text-align:center;"|x
-| style="text-align:center;"|x
-| style="text-align:center;"|x
-| style="text-align:center;"|x
-| style="text-align:center;"|x
-| style="text-align:center;"|x
-| style="text-align:center;"|x
-|-
-| colspan="10" style="color:black; background-color:#99C2D6;"|Chlorinated Ethanes
-|-
-| style="color:black; background-color:#E6F0F5;"|hexachloroethane
-| style="text-align:center;"|x
-| style="text-align:center;"|x
-| style="text-align:center;"|x
-| style="text-align:center;"|x
-| style="text-align:center;"|x
-| style="text-align:center;"|x
-| style="text-align:center;"|x
-| style="text-align:center;"|x
-| style="text-align:center;"|x
-|-
-| style="color:black; background-color:#E6F0F5;"|pentachloroethane
-| style="text-align:center;"|x
-| style="text-align:center;"|x
-| style="text-align:center;"|x
-| style="text-align:center;"|x
-| style="text-align:center;"|x
-| style="text-align:center;"|x
-| style="text-align:center;"|x
-| style="text-align:center;"|x
-| style="text-align:center;"|x
-|-
-| style="color:black; background-color:#E6F0F5;"|1,1,1,2-tetrachloroethane
-| style="text-align:center;"|x
-| style="text-align:center;"|x
-| style="text-align:center;"|x
-| style="text-align:center;"|x
-| style="text-align:center;"|x
-| style="text-align:center;"|x
-| style="text-align:center;"|x
-| style="text-align:center;"|x
-| style="text-align:center;"|x
-|-
-| style="color:black; background-color:#E6F0F5;"|1,1,2,2-tetrachloroethane
-| style="text-align:center;"|x
-| style="text-align:center;"|x
-| style="text-align:center;"|x
-| style="text-align:center;"|x
-| style="text-align:center;"|x
-| style="text-align:center;"|x
-| style="text-align:center;"|x
-| style="text-align:center;"|x
-| style="text-align:center;"|x
-|-
-| style="color:black; background-color:#E6F0F5;"|1,1,2-trichloroethane
-| style="text-align:center;"|x
-| style="text-align:center;"|x
-| style="text-align:center;"|x
-| style="text-align:center;"|x
-| style="text-align:center;"|x
-| style="text-align:center;"|x
-| style="text-align:center;"|x
-| style="text-align:center;"|x
-| style="text-align:center;"|x
-|-
-| style="color:black; background-color:#E6F0F5;"|1,1,1-trichloroethane
-| style="text-align:center;"|x
-| style="text-align:center;"|x
-| style="text-align:center;"|x
-| style="text-align:center;"|x
-| style="text-align:center;"|x
-| style="text-align:center;"|x
-| style="text-align:center;"|x
-| style="text-align:center;"|x
-| style="text-align:center;"|x
-|-
-| style="color:black; background-color:#E6F0F5;"|1,2-dichloroethane
-| style="text-align:center;"|x
-| style="text-align:center;"|x
-| style="text-align:center;"|x
-| style="text-align:center;"|x
-| style="text-align:center;"|x
-| style="text-align:center;"|x
-| style="text-align:center;"|x
-| style="text-align:center;"|x
-| style="text-align:center;"|x
-|-
-| style="color:black; background-color:#E6F0F5;"|1,1-dichloroethane
-| style="text-align:center;"|x
-| style="text-align:center;"|x
-| style="text-align:center;"|x
-| style="text-align:center;"|x
-| style="text-align:center;"|x
-| style="text-align:center;"|x
-| style="text-align:center;"|x
-| style="text-align:center;"|x
-| style="text-align:center;"|x
-|-
-| style="color:black; background-color:#E6F0F5;"|chloroethane
-| style="text-align:center;"|x
-| style="text-align:center;"|x
-| style="text-align:center;"|x
-| style="text-align:center;"|x
-| style="text-align:center;"|x
-| style="text-align:center;"|x
-| style="text-align:center;"|x
-| style="text-align:center;"|x
-| style="text-align:center;"|x
-|-
-| colspan="10" style="color:black; background-color:#99C2D6;"|Chlorinated Ethenes
-|-
-| style="color:black; background-color:#E6F0F5;"|tetrachloroethene
-| style="text-align:center;"|x
-| style="text-align:center;"|x
-| style="text-align:center;"|x
-| style="text-align:center;"|x
-| style="text-align:center;"|x
-| style="text-align:center;"|x
-| style="text-align:center;"|x
-| style="text-align:center;"|x
-| style="text-align:center;"|x
-|-
-| style="color:black; background-color:#E6F0F5;"|trichloroethene
-| style="text-align:center;"|x
-| style="text-align:center;"|x
-| style="text-align:center;"|x
-| style="text-align:center;"|x
-| style="text-align:center;"|x
-| style="text-align:center;"|x
-| style="text-align:center;"|x
-| style="text-align:center;"|x
-| style="text-align:center;"|x
-|-
-| style="color:black; background-color:#E6F0F5;"|<i>cis</i>-1,2-dichloroethene
-| style="text-align:center;"|x
-| style="text-align:center;"|x
-| style="text-align:center;"|x
-| style="text-align:center;"|x
-| style="text-align:center;"|x
-| style="text-align:center;"|x
-| style="text-align:center;"|x
-| style="text-align:center;"|x
-| style="text-align:center;"|x
-|-
-| style="color:black; background-color:#E6F0F5;"|<i>trans</i>-1,2-dichloroethene
-| style="text-align:center;"|x
-| style="text-align:center;"|x
-| style="text-align:center;"|x
-| style="text-align:center;"|x
-| style="text-align:center;"|x
-| style="text-align:center;"|x
-| style="text-align:center;"|x
-| style="text-align:center;"|x
-| style="text-align:center;"|x
-|-
-| style="color:black; background-color:#E6F0F5;"|1,1-dichloroethene
-| style="text-align:center;"|x
-| style="text-align:center;"|x
-| style="text-align:center;"|x
-| style="text-align:center;"|x
-| style="text-align:center;"|x
-| style="text-align:center;"|x
-| style="text-align:center;"|x
-| style="text-align:center;"|x
-| style="text-align:center;"|x
-|-
-| style="color:black; background-color:#E6F0F5;"|chloroethene
-| style="text-align:center;"|x
-| style="text-align:center;"|x
-| style="text-align:center;"|x
-| style="text-align:center;"|x
-| style="text-align:center;"|x
-| style="text-align:center;"|x
-| style="text-align:center;"|x
-| style="text-align:center;"|x
-| style="text-align:center;"|x
-|-
-|}
-<!-- We are making changes to Contributor pages, so I have copied Bilgen's previous version here in case we need it -->
+==Advantages==
-==Qualification Summary==
-Dr. Yuncu specializes in the application of physico-chemical treatment processes and bioremediation of hazardous compounds in soil and groundwater. She serves as a project manager and lead engineer on many of Solutions-IES’ in situ bioremediation projects. She is an author of several publications and an active presenter of in situ remediation technologies at international conferences.
-==Education/Training==
+The two main advantages of the application of metaproteomics are:
-Ph.D. - Civil, Construction & Environmental Engineering, NC State University, December 2010
+#the ability to directly measure microbial enzymes (not just potential for enzyme synthesis), and
-M.S. - Environmental Engineering, Middle East Technical University, September 2003
+#the ability to generate detailed information on hundreds of microorganisms and proteins in one assay.
-B.S. - Environmental Engineering, Middle East Technical University, June 2000
-==Registrations/Certifications/Licenses ==
+The process of obtaining the information does not require culturing of microorganisms or performance of any molecular assays. To measure features that are directly correlated to microbial activity, metaproteomics can be used to identify and relatively quantify proteins<ref name="Hettich2013">Hettich, R.L., Pan, C., Chourey, K., and Giannone, R.J., 2013.  Metaproteomics: Harnessing the Power of High Performance Mass Spectrometry to Identify the Suite of Proteins That Control Metabolic Activities in Microbial Communities. Analytical Chemistry, 85(9), pp. 4203-4214. [https://doi.org/10.1021/ac303053e DOI: 10.1021/ac303053e] [[Media: Hettich2013.pdf | Article]]</ref><ref name="Keller2009">Keller, M. and Hettich, R.L., 2009.  Environmental Proteomics: a Paradigm Shift in Characterizing Microbial Activities at the Molecular Level. Microbiology and Molecular Biology Reviews, 73(1), pp. 62-70. [https://doi.org/10.1128/MMBR.00028-08 DOI: 10.1128/MMBR.00028-08] [[Media: Keller2009.pdf | Article]]</ref><ref name="Schneider2010">Schneider, T. and Riedel, K., 2010.  Environmental proteomics: Analysis of structure and function of microbial communities. Proteomics, 10(4), pp. 785-98. [https://doi.org/10.1002/pmic.200900450 DOI: 10.1002/pmic.200900450]</ref>. These proteins provide important information about community activities, such as which microbial organisms are most active and what proteins are present (including proteins catalyzing reactions involved in bioremediation)<ref name="Arsène-Ploetze2015"/><ref name="Johnson2015">Johnson, D.R., Helbling, D.E., Men, Y., and Fenner, K., 2015.  Can meta-omics help to establish causality between contaminant biotransformations and genes or gene products? Environmental Science: Water Research & Technology, 1, pp. 272-278. [https://doi.org/10.1039/C5EW00016E DOI: 10.1039/C5EW00016E] [[Media: Johnson2015.pdf | Article]]</ref>.
-Professional Engineer, North Carolina, 2014
-==Representative Projects==
+==Limitations==
-Quantifying Mobile-Immobile Mass Transfer using Direct Push Tools – Strategic Environmental Research and Development Program, Department of Defense
+Limitations associated with this technology are related to composition of the proteome to be analyzed, mainly concerning protein expression levels and limitations of the analytical equipment. Limitations are summarized as follows:
-Project Manager - The overall objective of this project is to develop methods to better characterize and model the mass transfer of contaminants between higher and lower mobility zones and its impact on the long-term release of contaminants in groundwater (Funded – project will start in May 2015).
-Novel Substrate Application for Bioremediation of Comingled 1,4-Dioxane and Chlorinated Solvent Plumes - Air Force Civil Engineer Center
+*'''''Sample preparation''''' - the vast diversity of protein molecular sizes, charge states, conformational states, post-translational modifications etc., make it unfeasible to use a single sample preparation protocol that captures the entire proteome for a given microbial community. Thus, use of a protocol that allows isolation of protein content from a biological sample and eliminates non-specific contaminants (e.g., keratins, fatty acids, plastic polymers, nucleic acids and salt clusters) should be developed and tested prior to sample analysis<ref name="Chourey2010">Chourey, K., Jansson, J., VerBerkmoes, N., Shah, M., Chavarria, K.L., Tom, L.M., Brodie, E.L., and Hettich, R.L., 2010. Direct Cellular Lysis/Protein Extraction Protocol for Soil Metaproteomics. Journal of Proteome Research, 9(12), pp. 6615-6622. [https://doi.org/10.1021/pr100787q DOI: 10.1021/pr100787q]</ref><ref name="Qian2017">Qian, C. and Hettich, R.L., 2017. Optimized Extraction Method To Remove Humic Acid Interferences from Soil Samples Prior to Microbial Proteome Measurements. Journal of Proteome Research, 16(7), pp. 2537-2546. [https://doi.org/10.1021/acs.jproteome.7b00103 DOI: 10.1021/acs.jproteome.7b00103]</ref>
-Principal Investigator - The overall objective of this project is to demonstrate (proof of concept) a simple, low-cost approach for enhancing the in situ cometabolic biodegradation of 1,4-dioxane and TCE using two-barrier system to create distinct geochemical zones (anaerobic/aerobic) within a comingled plume.
+*'''''Proteins are not expressed in equal amounts''''' and there may be large differences in protein levels in proteomes in samples collected from the same site. A proteomic analysis must employ proper technologies for the detection of all proteins or proteins of interest. In a small sample volume that is usually used in a proteomic analysis, a large percentage of the expressed proteins occur at low abundance levels and cannot be readily detected in the analysis due to high-abundance proteins effectively monopolizing the “sampling effort”. These rare proteins may be of particular interest in environmental samples because proteins associated with contaminant degradation are often a very small fraction of the total expressed proteins. The practical protein detection limit for Liquid Chromatography-Tandem Mass Spectrometry-Time-of-Flight (LC-MS/MS-TOF) analysis lies in the femtomol (10-15 [fmol]) range. However, due to losses during protein extraction and sample clean up and dilution, the sufficient protein concentration for detection is more realistically in the low picomol (10-12 [pmol]) to high fmol range. This limitation can be addressed by collecting a greater volume of groundwater for analysis; however, this may not be possible at all sampling locations.
+*'''''Detection of proteins at low concentrations''''' (low abundance) may be limited by other proteins present in high concentrations (high abundance). The successful search for low-abundance proteins may be mitigated by use of chromatography for separation of high-abundance proteins and precipitation for elution of proteins of interest prior to analytical detection. However, complete removal of high-abundance proteins may not be recommended because they may trap the low-abundance proteins along with their associated fragments and peptides, which will be lost and not detected. An alternative approach relies on 2-dimensional chromatography coupled with tandem mass spectrometry.
+*'''''Success in the identification of proteins may vary with the sensitivity of the mass spectrometer.''''' Proper analytic equipment can be costly. Of the most sensitive mass spectrometers, electrospray ionization and laser desorption ionization-based instruments can detect peptides with low detection limits.
+*'''''Not all biological variation can be accounted for.''''' Despite great improvements in the costs of genomic sequencing and gene prediction, there remain some aspects of biology that cannot be accurately or consistently predicted.  For example, the presence and variety of post-translational modifications remains problematic and, if present and not accounted for during analysis, such modified proteins will not be efficiently detected.
+*'''''Selection of the appropriate analytical method determines the success of the study.''''' Depending on the study goals and context, some methodological adjustments should be considered, including pre-enrichment of key low-abundance proteins, adjustment of protein extraction methods or tuning of the analytical equipment.  A single methodological approach is not suitable for all purposes.
+==Assessing Changes in Microbial Community Composition and Dynamics – Common Applications==
-Generation of Biodegradation - Sorption Barriers for Munitions Constituents - Environmental Security Technology Certification Program, Department of Defense
+Environmental metaproteomics is used in applied in research areas such as:
-Project Engineer - The overall objective of this project is to develop and demonstrate a process to enhance the sorption and/or degradation of explosives and perchlorate in soils by spray application of an organic amendment solution, followed by irrigation to carry the amendments deeper into the soil profile.
+#'''Bioenergy''' – characterization of feedstock conversion into energy e.g., cellulose or lignin degradation to biofuels<ref name="Ndimba2013"> Ndimba, B.K., Ndimba, R.J., Johnson, T.S., Waditee-Sirisattha, R., Baba, M., Sirisattha, S., Shiraiwa, Y., Agrawal, G.K., and Rakwal, R, 2013. Biofuels as a sustainable energy source: an update of the applications of proteomics in bioenergy crops and algae Journal of Proteomics, 20(93), pp. 234-244. [https://doi.org/10.1016/j.jprot.2013.05.041 DOI: 10.1016/j.jprot.2013.05.041]</ref>
+#'''Human health''' – characterization of microbial involvement in impact/control of disease vs health in human bodies<ref name="Brooks2015">Brooks, B., Mueller, R.S., Young, J.C., Morowitz, M.J., Hettich, R.L., and Banfield, J.F., 2015. Strain-resolved microbial community proteomics reveals simultaneous aerobic and anaerobic function during gastrointestinal tract colonization of a preterm infant. Frontiers in Microbiology, 1(6) pp. 654. [https://doi.org/10.3389/fmicb.2015.00654 DOI: 10.3389/fmicb.2015.00654] [[Media: Brooks2015.pdf | Article]]</ref><ref name="Carr2014">Carr, S.A., Abbatiello, S.E., Ackermann, B.L., Borchers, C., Domon, B., Deutsch, E.W.,, Grant, R.P., Hoofnagle, A.N., Hüttenhain, R., Koomen, J.M., Liebler, D.C., Liu, T., MacLean, B., Mani, D.R., Mansfield, E., Neubert, H., Paulovich, A.G., Reiter, L., Vitek, O., Aebersold, R., Anderson, L., Bethem, R., Blonder, J., Boja, E., Botelho, J., Boyne, M., Bradshaw, R.A., Burlingame, A.L., Chan, D., Keshishian, H., Kuhn, E., Kinsinger, C., Lee, J.S., Lee, S.W., Moritz, R., Oses-Prieto, J., Rifai, N., Ritchie, J., Rodriguez, H., Srinivas, P.R., Townsend, R.R., Van Eyk, J., Whiteley, G., Wiita, A., and Weintraub, S., 2014.  Targeted peptide measurements in biology and medicine: best practices for mass spectrometry-based assay development using a fit-for-purpose approach. Molecular and Cellular Proteomics, 13(3), pp. 907-917. [https://doi.org/10.1074/mcp.M113.036095 DOI: 10.1074/mcp.M113.036095]] [[Media: Carr2014.pdf | Article]]</ref>
+#'''Bioremediation''' – characterization of degradation of contaminants in sediments, soils, and groundwater by microorganisms<ref name="Bansal2009">Bansal, R., Deobald, L.A., Crawford, R.L., Paszczynski, A.J., 2009. Proteomic detection of proteins involved in perchlorate and chlorate metabolism. Biodegradation, 20(5), pp.603-620. [https://doi.org/10.1007/s10532-009-9248-0 DOI: 10.1007/s10532-009-9248-0]</ref><ref name="Fuller2020">Fuller, M. E., van Groos, P. G. K., Jarrett, M., Kucharzyk, K. H., Minard-Smith, A., Heraty, L. J., and Sturchio, N. C., 2020. Application of a multiple lines of evidence approach to document natural attenuation of hexahydro-1, 3, 5-trinitro-1, 3, 5-triazine (RDX) in groundwater. Chemosphere. 250, pp. 126210. [https://doi.org/10.1016/j.chemosphere.2020.126210 DOI: 10.1016/j.chemosphere.2020.126210]</ref><ref name="Kucharzyk2020">Kucharzyk, K. H., Meisel, J. E., Kara-Murdoch, F., Murdoch, R. W., Higgins, S. A., Vainberg, S., and Löffler, F. E., 2020. Metagenome-guided proteomic quantification of reductive dehalogenases in the Dehalococcoides mccartyi-containing consortium SDC-9. Journal of Proteome Research, 9(4), pp. 1812-1823. [https://doi.org/10.1021/acs.jproteome.0c00072 DOI: 10.1021/acs.jproteome.0c00072]</ref><ref name="Kucharzyk2018">Kucharzyk, K.H., Rectanus, H.V., Bartling, C., Chang, P., Rosansky. S., Neil, K., and Chaudhry, T., 2018. Assessment of post remediation performance of a biobarrier oxygen injection system at a methyl tert-butyl ether (MTBE)-contaminated site, Marine Corps Base Camp Pendleton San Diego, California. Environmental Security Technology Certification Program, Alexandria, VA. ER-201588 [[Media: Kucharzyk2018.pdf | Report]]</ref><ref name="Michalsen2020a"> Michalsen, M. M., Kucharzyk, K. H., Bartling, C., Meisel, J. E., Hatzinger, P., Wilson, J., Istok, J., and Loffler, F, 2020. Validation of advanced molecular biological tools to monitor chlorinated solvent bioremediation and estimate cVOC degradation rates. Environmental Security Technology Certification Program, Alexandria, VA. ER201726. [[Media: Michalsen2020a.pdf | Report]]</ref><ref name="Michalsen2020b">Michalsen, M. M., King, A. S., Istok, J. D., Crocker, F. H., Fuller, M. E., Kucharzyk, K. H., and Gander, M. J., 2020. Spatially distinct redox conditions and degradation rates following field-scale bioaugmentation for RDX-contaminated groundwater remediation. Journal of Hazardous Materials, 387, 121529. [https://doi.org/10.1016/j.jhazmat.2019.121529 DOI: 10.1016/j.jhazmat.2019.121529]</ref>
+#'''Carbon cycling''' – characterization of a role of microorganisms in carbon flow in an ecosystem.
+#'''Agricultural metabolism''' – characterization of microbial interactions with plants<ref name="Tan2017">Tan, B.C, Lim, Y.S., and Lau, S.E., 2017. Proteomics in commercial crops: An overview. Journal of Proteomics, 169, pp. 176-188. [https://doi.org/10.1016/j.jprot.2017.05.018 DOI:10.1016/j.jprot.2017.05.018]</ref>
+==Targeted vs Shotgun Proteomics==
+Proteomics techniques can be broadly classified into two categories:
+#'''Untargeted or shotgun proteomics,''' aimed at comprehensively identifying and characterizing relative abundances of the totality of proteins in a sample.
+#'''Targeted proteomics,''' focused on identifying and absolutely quantifying one protein.
+''Shotgun proteomics'' refers to digestion of the total proteome and subjecting all resulting peptides to separation, mass-spectroscopy, and identification based on a reference protein database (ideally derived from in silico translation of the (meta)genome).
+Notably, shotgun proteomics generates only an approximated ''relative abundance'' for identified proteins. On the other hand, ''targeted proteomics'' allows for ''absolute quantification'' of a single protein within a complex sample, which in turn allows for analysis of any potential correlation to a degradation rate. Prediction of degradation rates based on enzyme concentration is a crucial step towards better understanding of the molecular events underlying metabolic processes. By measuring key biomarkers, proteomic studies present an opportunity to gain profound into ecosystem health, degradation of recalcitrant compounds, and bioremediation. Quantitative proteomics can also guide regulatory agencies to make better site management decisions, thereby minimizing radiation costs and chemically induced adverse effects.
+''Targeted Proteomics'' targets peptides of a specific protein in a complex mixture of other peptides and determines their presence (if they are above the detection limit) and quantity in one sample or across multiple samples (Figure 1). This analysis usually utilizes a triple quadrupole mass spectrometer (QqQ-MS), an instrument which has traditionally been used to quantify small molecules. Only recently has it been utilized for peptides. Parallel Reaction Monitoring (PRM) and data independent analysis are alternative options that can be far cheaper than developing a method for a QqQ-MS.
+Each targeted proteomics assay must be carefully developed.  The assay specifically “targets” peptides enzymatically digested from the target protein, necessitating careful selection of peptides and method. Development of a new assay also requires preliminary analyses to ensure the method is robust. Once a method is developed and verified, it can be applied to an unlimited number of samples.
+[[File: ProteomicsFig1.png|thumb|625px|left | Figure 1. Targeted proteomic workflow]]<ref name="Zhang2013"> Zhang, Y., Fonslow, B.R, Shan, B., Baek, M.C., and Yates, J.R. III., 2013. Protein analysis by shotgun/bottom-up proteomics. Chemical Reviews, 113(4), pp 2343-94. [https://doi.org/10.1021/cr3003533 DOI:10.1021/cr3003533]</ref>
-Anaerobic Bioremediation of DNAPLs - Air Force Civil Engineer Center
+'''Bottom-Up Proteomics'''
-Project Engineer - The overall objective is to demonstrate enhanced dissolution and biodegradation of a chlorinated solvent DNAPL using an emulsified oil technology formulated with a slow-release pH buffer and a bioaugmentation culture.
-Groundwater MNA and Landfill Monitoring, Ceiba, Puerto Rico – Naval Facilities Engineering Command Southeast
+''Bottom-up proteomics'' (Figure 2) begins by analyzing of mass spectrum fragmentation patterns of peptides, which are generated after proteolytic digestion of proteins<ref name="Zhang2013"/>. Spectra are identified by comparison to a database of reference proteins which are digested ''in silico''.  The creation or selection of this database is one of the most crucial steps in the analysis; ideally, the database consists of proteins encoded by the genome or metagenome of the organisms present in the sample under study.  While the rapidly decreasing cost of DNA sequencing and emergence of standard assembly and annotation pipelines make obtaining (meta)genomes increasingly cost-effective, it remains an option to use global reference protein databases, such as UniProt (see [https://unipept.ugent.be/]). However, making peptide-spectrum matches (a.k.a. PSMs) is a statistically uncertain process, as the alignment of mass fragmentation pattern of the peptide to the database is seldom perfect. Several algorithms have been developed to tackle this problem (Comet, X! Tandem, MyriMatch, OMSSA, Tide, etc.). PSM matching must carefully consider factors such as what enzyme was used to digest the proteome and how specific and complete digestion was.  Additionally, peptide modifications, chemical modification of amino acids which lead to differences in mass and fragmentation pattern, are a wide-spread complication that must be accounted for. Some are intentional, for example carbiodomethylation of cysteine residues, which is applied to protect sulfur residues from becoming oxidized. Other modifications occur unintentionally during sample preparation, such as oxidation of methionine residues.
-Task Manager responsible for reviewing and evaluating analytical data and report preparation - The project is a reoccurring large scale sampling event that includes the collection of groundwater, landfill gas, soil, and ambient gas samples.
+PSMs are inherently statistically uncertain. A given shotgun proteome may involve hundreds of thousands of PSMs, which leads to the danger of false discovery. Traditionally, a formal false discovery rate (FDR) is applied; this is an adjustment of the threshold for statistical significance based on the number of tests performed, i.e. the more PSMs, the more stringent the testing must be.  The risk is greatly exacerbated by using reference protein databases that do not reflect the sample. Use of the (meta)genome correlating to the sample under study makes this danger of false identification much less risky when compared to traditional approaches.  It is generally acknowledged that rigid adherence to FDR thresholds is a serious impediment to thorough PSM assignment<ref name="Heyer2017"> Heyer, R., Schallert, K., Zoun, R., Becher, B., Saake, G., and Benndorf, D., 2017. Challenges and perspectives of metaproteomic data analysis. Journal of Biotechnology, 261, pp. 24–36. [https://doi.org/10.1016/j.jbiotec.2017.06.1201 DOI: 10.1016/j.jbiotec.2017.06.1201] [[Media: Heyer2017.pdf | Article]]</ref> but is generally advisable when analyzing a proteome without any pre-existing knowledge on sample composition.
+Following PSM assignment, whether by use of a global reference protein database with application of FDR or by comparison to a sample-specific reference (meta)genome, peptides are matched to proteins. This step acts as a second statistical filtering step and can employ several criteria such as whether the peptide identified is unique in the database, how many peptides match a given protein, and what score was assigned to the PSMs by the PSM algorithm. A metaproteome protein identification might, for example, require three or six matching PSMs.
+Software for making PSMs and protein identifications can be obtained as individual packages, but several convenient open-source packages are available, some of which include several PSM algorithms (SearchGUI) and even pipelines for making further sample comparisons (PatternLab for Proteomics) or functional interpretations (MetaProteomeAnalyzer). Many of these features are also available in commercial software packages, such as Progenesis QI (Waters) and ProteinPilot (SCIEX).  Global bottom-up shotgun proteomics data analysis remains an actively evolving discipline.
+[[File: ProteomicsFig2.png|thumb|630px|Figure 2. Bottom- up shotgun proteomics]]
+==Selecting Sample Locations==
+Below are a few guidelines for selecting sampling locations to aid in drawing conclusions from metaproteomics data.
+•	Background: Samples from non-impacted background area can be compared with results from impacted areas to examine the impact of contamination on composition of microbial proteomes that reflect the ongoing metabolical processes.
+•	Baseline: These samples are collected and analyzed prior to treatment as a baseline for evaluating changes in the microbial metabolism in response to the remediation.
+•	Plume: These samples are collected from distinct zones within the source area or contaminant plume to reflect variations in contaminant concentrations, geochemical conditions, and other site-specific criteria.
+==Sample Collection, Preservation, and Shipping==
+Sampling procedures for proteomics analyses are straightforward and readily integrated into existing monitoring programs. Almost any type of sample matrix (soil, sediment, groundwater), filters (on-site filtration) can be analyzed. All samples should be shipped to the laboratory on ice or dry ice (-20 °C) using an overnight carrier to minimize the potential for changes in the microbial community between collection and analysis and keep integrity of proteins.
+Groundwater samples (typically 1 L) can be shipped directly to the laboratory or filtered in the field. For on-site filtration, groundwater is pumped through a Sterivex<sup>&reg;</sup> or Bio-Flo<sup>&reg;</sup> filter using standard low flow sampling techniques. The groundwater may then be discarded appropriately. As with other sample types, filters should be shipped on ice (4 °C) using an overnight carrier.
+==References==
+<references />
+==See Also==
+*[https://www.serdp-estcp.org/Program-Areas/Environmental-Restoration/Contaminants-on-Ranges/Protecting-Groundwater-Resources/ER-1374  Environmental Fate and Exposure Assessment for Arsenic in Groundwater]
+*[[Media: Cantarel2011.pdf | Strategies for Metagenomic-Guided Whole-Community Proteomics of Complex Microbial Environments]]
+*[https://www.nature.com/articles/nbt.1661  Options and considerations when selecting a quantitative proteomics strategy]
+*[[Media: Ge2013.pdf | Environmental OMICS: Current Status and Future Directions]]
+*[https://pubs.acs.org/doi/abs/10.1021/acs.jproteome.6b00239  An Alignment-Free “Metapeptide” Strategy for Metaproteomic Characterization of Microbiome Samples Using Shotgun Metagenomic Sequencing]
+*[https://www.sciencedirect.com/science/article/abs/pii/S0038071713003799  Environmental proteomics: A long march in the pedosphere]
+*[https://www.sciencedirect.com/science/article/abs/pii/S0038071713003799  Proteome profile and proteogenomics of the organohalide-respiring bacterium Dehalococcoides mccartyi strain CBDB1 grown on hexachlorobenzene as electron acceptor]
+*[https://pubs.acs.org/doi/10.1021/acs.jproteome.8b00716  Unipept 4.0: Functional Analysis of Metaproteome Data]
+*[https://www.nature.com/articles/nbt0808-860  Guidelines for reporting the use of mass spectrometry in proteomics]
+*[https://www.nature.com/articles/nbt1329  The minimum information about a proteomics experiment (MIAPE)]
+*[https://pubs.acs.org/doi/10.1021/es501673s  Next-Generation Proteomics: Toward Customized Biomarkers for Environmental Biomonitoring]
+*[[Media: Wilmes2015.pdf | A decade of metaproteomics: Where we stand and what the future holds]]