Appendix F: Additional Resources

F.1 CSIA Methods

Brown, R. A., J. T. Wilson and M. L. Ferrey. 2007. Monitored Natural Attenuation Forum: The Case for Abiotic MNA.” Remediation. Spring.

Coleman, D.D., C. L. Liu,K. C. Hackley and L. J. Benson. 1993. “Identification of Landfill Methane Using Carbon and Hydrogen Isotope Analysis.” Presented at The Sixteenth Annual Madison Waste Conference.

Commission on Isotopic Abundances and Atomic Weights, www.ciaaw.org.

Cox, E. 2010 “Elucidation of the Mechanisms and Environmental Relevance of cis-Dichloroethene and Vinyl Chloride Biodegradation”.  SERDP Project #ER-1557.

Dijk, J.A., J.M. de Bont, X. Lu, P.M. Becker, T. Bosma, H. Rijnaarts, and J. Gerritse, 2000. “Anaerobic Oxidation of (Chlorinated) Hydrocarbons”. Proceedings of the Second International In-Situ and On-Site Bioremediation Symposium, Monterey, California. Vol. 4:63-70.

ER-201029 “Integrated Stable Isotope-Reactive Transport Model Approach for Assessment of Chlorinated Solvent Degradation.” www.serdp-estcp.org.

Ferrey, M. L., R. T. Wilkin, R. G. Ford and J. T. Wilson. 2004. “Nonbiological removal of cis-Dichloroethylene and 1,1-Dichloroethylene in Aquifer Sediment Containing Magnetite. Environmental Science & Technology, 38, 1746-1752.

IAEA 2000. Environmental Isotopes in the Hydrological Cycle: Principles and Applications, Volume 1, Vienna, March.

Liu, C. Q., Li, S-L., Lang, Y-C., Xiao, H-Y. 2006. Using Ϫ15N- and Ϫ18O-Values to Identify Nitrate Sources in Karst Ground Water, Guiyang, Southwest China. Environ. Sci. Technol. 40: 6928-6933.

Meckenstock, R. U., B. Morasch, R. Warthmann, B. Schink, E. Annweiler, W. Michelis, and H.H. Richnow, “ 13C / 12C isotope fractionation of aromatic hydrocarbons during microbial degradation”. Environmental Microbiology 1, 409 - 414, 1999.

NELAC (http://www.nelac-institute.org/index.php), web site accessed 2011.

Petrisor, I.G., Wells, J. 2008a. Tracking Chlorinated Solvents in the Environment. In: Issues in Environmental Science and Technology, Vol. 26: Environmental Forensics. Edited by R.E. Hester and R.M. Harrison, RSC Publishing, Royal Society of Chemistry 2008, pp: 130-152.

Petrisor, I.G., Wells, J. 2008b. Perchlorate – Is Nature the Main Manufacturer? In: Issues in Environmental Science and Technology, Vol. 26: Environmental Forensics. Ed. by R.E. Hester and R.M. Harrison, RSC Publishing, Royal Society of Chemistry 2008, pp: 105-129.

Silva, S.R., Ging, P., Lee, R.W., Ebbert, J.C., Tesoriero, A.J., Inkpen, E.L. 2002. Forensic Applications of Nitrogen and Oxygen Isotopes in Tracing Nitrate Sources in Urban Environments. Environmental Forensics 3: 125-130.

Sueker, J.K. 2001. Isotope Applications in Environmental Investigations: Theory and Use in Chlorinated Solvent and Petroleum Hydrocarbon Studies. Remediation/Winter, John Wiley & Sons, Inc., 5-24.

Sueker, J.K. 2003. Isotope Applications in Environmental Investigations Part II: Groundwater Age Dating and Recharge Processes, and Provenance of Sulfur and Methane. Remediation/Spring 2003, Wiley Periodicals, Inc., 71-90.

F.2 PCR and qPCR Methods

http://www.gene-quantification.de/movie.html

http://www.cnpg.com/video/flatfiles/539/

http://www.youtube.com/watch?v=eEcy9k_KsDI&NR=1

http://www.gene-quantification.info/

http://www.bio-rad.com/webroot/web/movies/lsr/support/qPCR_Hallmarks.htm

http://www.appliedbiosystems.com/absite/us/en/home/support/tutorials.html

Baldwin, B.R., C.H. Nakatsu, L. Nies. 2008. Enumeration of aromatic oxygenase genes to evaluate monitored natural attenuation at gasoline-contaminated sites.  Water Research 42 (3): 723-31. www.ncbi.nlm.nih.gov/pubmed/17707876.

Beller, H.R., S.R. Kane, T.C. Legler and P.J. Alvarez. 2002. A Real-Time Polymerase Chain Reaction Method for Monitoring Anaerobic, Hydrocarbon-Degrading Bacteria Based on a Catabolic Gene.  Environmental Science and Technology. 36:3977-3984. www.ncbi.nlm.nih.gov/pubmed/12269751.

Correa P.A., L. Lin, C.L. Just, D. Hu, K.C. Hornbuckle, J.L. Schnoor, and B. Van Aken. 2010.  The effects of individual PCB congeners on the soil bacterial community structure and the abundance of biphenyl dioxygenase genes.  Environ Int. 36(8):901-906. www.ncbi.nlm.nih.gov/pubmed/19716603.

DeBruyn, J.M., C.S. Chewning, and G.S. Sayler.  2007.  Comparative Quantitative Prevalence of Mycobacteria and Functionally Abundant nidA, nahAc, and nagAc Dioxygenase Genes in Coal Tar Contaminated Sediments. Environmental Science and Technology. 41(15): 5426-5432. PMID: 17822112.  www.ncbi.nlm.nih.gov/pubmed/17822112.

Dominguez R.F., M.L. daSilva, T.M. McGuire, D. Adamson, C.J. Newell and P.J. Alvarez. 2008. Aerobic Bioremediation of Chlorobenzene Source-Zone Soil in Flow-through Columns: Performance Assessment Using Quantitative PCR. Biodegradation 19(4):545-553. www.ncbi.nlm.nih.gov/pubmed/17960485.

Hamann C., J. Hegemann, and A. Hildebrandt.  1999.  Detection of polycyclic aromatic hydrocarbon degradation genes in different soil bacteria by polymerase chain reaction and DNA hybridization. FEMS Microbiol Lett. 173(1):255-63. www.ncbi.nlm.nih.gov/pubmed/10220903.

Hatt, J.K., Ritalahti, K. M., F. E. Löffler, N. Barros, D. Major, E. Petrovskis, G. Davis, D. Ogles, P. Dennis, X. Druar, J. Wilkinson, M. Duhamel, E. Edwards, A. Perez-de-Mora, C. A. Lebron, and C. Yaeger. 2011. “Verification of Laboratory and Field Procedures to Reduce Variability in Quantitative PCR Testing of Groundwater.”Presented at the International Symposium on In Situ and On-Site Bioremediation, Reno, NV, June 27-30, 2011.

He, J., K.M. Ritalahti, M.R. Aiello and F. E. Löffler. 2002. Complete Detoxification of Vinyl Chloride by an Anaerobic Enrichment Culture and Identification of the Reductively Dechlorinating Population as a Dehalococcoides Species.  Applied and Environmental Microbiology. 69. 996-1003.

He, J., Ritalahti, K.M., Yang, K.L., Koenigsberg, S.S., Löffler, F.E., 2003. Detoxification of vinyl chloride to ethene coupled to growth of an anaerobic bacterium. Nature 424, 62–65.

He, J., Sung, Y., Krajmalnik-Brown, R., Ritalahti, K.M., Löffler, F.E., 2005. Isolation and characterization of Dehalococcoides sp. Strain FL2, a trichloroethene (TCE)-and 1,2-dichloroethene-respiring anaerobe. Environmental Microbiology 7 (9), 1442–1450.

Hendrickson, E.R., J. Payne, R.M. Young, M.G. Starr, M.P. Perry, S. Fahnesock, E.E. Ellis, and R.C. Ebersole.  2002. Molecular Analysis of Dehalococcoides 16S Ribosomal DNA from Chloroethene-Contaminated Sites throughout North America and Europe. Applied and Environmental Microbiology.  68(2): 485-495.  PMID:  11823182.  www.ncbi.nlm.nih.gov/pubmed/11823182.

Hendrickx, B., H. Junca, J. Vosahlova, A. Lindner, I. Ruegg, M. Bucheli-Witschel, F. Faber, T. Egli, M. Mau, M. Schlomann, M. Brennerova, V. Brenner, D.H. Pieper, E.M. Top, W. Dejonghe, L. Bastiaens, and D. Springael. 2006. Alternative primer sets for PCR detection of genotypes involved in bacterial aerobic BTEX degradation: distribution of the genes in BTEX degrading isolates and in subsurface soils of a BTEX contaminated industrial site. Journal of Microbiological Methods. 64(2):250-65. www.ncbi.nlm.nih.gov/pubmed/15949858.

Hristova, K., B. Gebreyesus, D. Mackay, and K.M. Scow.  2003.  Naturally Occurring Bacteria Similar to the Methyl tertiary-butyl ether (MTBE)-Degrading Strain PM1 Are Present in MTBE-Contaminanted Groundwater.  Applied and Environmental Microbiology. 69(5): 2616-2623. PMID: 12732529.  www.ncbi.nlm.nih.gov/pubmed/12732529.

Indest KJ, FH Crocker, and R Athow. 2007.  A TaqMan polymerase chain reaction method for monitoring RDX-degrading bacteria based on the xplA functional gene. Journal of Microbiological Methods 68:267-274.

Kolb S., C. Knief, S. Stubner, and R. Conrad.  2003.  Quantitative Detection of Methanotrophs in Soil by Novel pmoA-Targeted Real Time PCR Assays.  Applied and Environmental Microbiology. 69(5):2423-2429.

Krajmalnik-Brown R, T. Hölscher, I.N. Thomson, F.M. Saunders, K.M. Ritalahti, and F. E. Löffler. 2004. Genetic Identification of a Putative Vinyl Chloride Reductase in Dehalococcoides sp. Strain BAV1. Applied and Environmental Microbiology. 70(10): 6347-6351.

Lu, X., Wilson, J.T., Kampbell D.H. 2006. Relationship between Dehalococcoides DNA in groundwater and rates of reductive dechlorination at field scale. Water Res. 40 (16), 3131-3140.PMID: 16889813.

Lyew D., and S. Guiot. 2003.  Effects of aeration and organic loading rates on degradation of trichloroethylene in  a methanogenic-methanotrophic coupled reactor.  Appl Microbiol Biotechnol. 61:206-213.

Marzorati M., Balloi A., DeFerra F., Daffonchio D. 2010. Identification of Molecular Markers to Follow Up the Bioremediation of Sites Contaminated with Chlorinated Compounds.  Methods Mol Biol. 668:219-34. PMID: 20830567.

Petric I., D. Hrsak, S. Fingler, N. Udikovic, D. Bru, and F. Martin-Laurent. 2010. Insight in the PCB-Degrading Functional Community in Long-Term Contaminated Soil under Bioremediation. Journal of Soils and Sediments. 11(2): 290-300.

Petrisor, I.G., Parkinson, R.A., Horsewell, J., Waters, J.M., Burgoyne, L.A., Catchside, D.E.A., DeJonghe, W., Leys, N., VanBroekhoven, K., Pattnaik, P., Graves, D. 2005. Microbial Forensics. In: Environmental Forensics – Contaminants specific Approaches, Eds. Robert D. Morrison and Brian L. Murphy, Elsevier, 227-257.

Sanford, R. A., J. R. Cole, and J. M. Tiedje. 2002. Characterization and description of Anaeromyxobacter dehalogenans gen. nov., sp. nov., an aryl halorespiring facultative anaerobic myxobacterium. Appl. Environ. Microbiol. 68:893–900. PMID: 11823233.

Smits T.H., C. Devenoges, K. Szynalski, J. Maillard, C. Holliger. 2004. Development of a real-time PCR method for quantification of the three genera Dehalobacter, Dehalococcoides, and Desulfitobacterium in microbial communities.  Journal of Microbiological Methods. 57:369-378.

Sung, Y., Ritalahti, K.M., Apkarian, R.P., Löffler, F.E., 2006. Quantitative PCR confirms purity of strain GT, a novel trichloroethene-to-ethene-respiring Dehalococcoides isolate. Applied and Environmental Microbiology 72 (3), 1980–1987.

Tani, K., M. Muneta, K. Nakamura, K. Shibuya, and M. Nasu. 2002. Monitoring of Ralstonia eutropha KT1 in Groundwater in an Experimental Bioaugmentation Field by In Situ PCR. Appl. Environ. Microbiol. 68:412-416.

Thomas, S. H., E. Padilla-Crespo, P. M. Jardine, R. A. Sanford, and F. E. Löffler. 2009. Diversity and distribution of Anaeromyxobacter strains in a uranium-contaminated subsurface environment with nonuniform flow. Appl. Environ. Microbiol. 75:3679-3687. PMID: 19346346.

van der Zaan B, F Hannes, N Hoekstra, H Rijnaarts, WM de Vos, H Smidt, and J Gerritse. 2010. Correlation of Dehalococcoides 16S rRNA and chloroethene- reductive dehalogenase genes to different geochemcial conditions in chloroethene-contaminated groundwater. Applied and Environmental Microbiology. 76:843-850.

Wu, Q., R. A. Sanford, and F. E. Löffler. 2006. Uranium(VI) reduction by Anaeromyxobacter dehalogenans strain 2CP-C. Appl. Environ. Microbiol. 72:3608-3614. PMID: 16672509.

F.3 Fingerprinting Methods

Frostegård, Å, A. Tunlid,and E. Bååth. 1996. Changes in microbial community structure during long-term incubation in two soils experimentally contaminated with metals. Soil Biology & Biochemistry 28, 55-63.

Frostegard, A., A. Tunlid, and E. Baath. 2011. The use and misuse of PLFA measurements in soils. Soil Biology & Biochemistry, 43: 1621-1625.

Fischer, J., F. Schauer, and H.J. Heipieper. 2010. The trans/cis ratio of unsaturated fatty acids is not applicable as biomarker for environmental stress in case of long-term contaminated habitats. Appl. Microbiol. Biotechnol. 87: 365-371.

Hendrickx, B., W. Dejonghe, W. Boenne, M. Brennerova, M. Cernik, T. Lederer, M. Bucheli-Witschel, L. Bastiaens, W. Verstraete, E.M. Top, L. Diels, and D. Springael. 2005. Dynamics of an oligotrophic bacterial aquifer community during contact with a groundwater plume contaminated with benzene, toluene, ethylbenzene, and xylenes: an in situ mesocosm study.  Applied and Environmental Microbiology. 71(7): 3815-25. www.ncbi.nlm.nih.gov/pubmed/16000793.

Huang. L.N., H. De Wever, and L. Diels. 2008. Diverse and distinct bacterial communities induced biofilm fouling in membrane bioreactors operated under different conditions. Environmental Science and Technology 42: 8360-8366. PMID:19068818.  www.ncbi.nlm.nih.gov/pubmed/19068818.

Zhou, H. W., A. H. Y. Wong, R. M. K. Yu, Y. D. Park, Y. S. Wong, and N. F. Y. Tam. 2009. Polycyclic aromatic hydrocarbon-induced structural shift of bacterial communities in mangrove sediment. Microbial Ecology 58: 153-160.PMID:18958515.  www.ncbi.nlm.nih.gov/pubmed/18958515.

F.4 Microarrays

Lee, P. K.H., Warnecke F., Brodie E., Macbeth T.W., Conrad M.E., Andersen G., and L. Alvarez-Cohen. 2012. “ Phylogenetic Microarray Analysis of a Microbial Community Performing Reductive Dechlorination at a TCE-Contaminated Site.” Environ. Sci. Technol. 46(2):1044-1054.

Rastogi G, S. Osman , P.A. Vaishampayan, G.L. Andersen, L.D. Stetler, and R.K. Sani. 2010.  Microbial diversity in uranium mining-impacted soils as revealed by high-density 16S microarray and clone library. Microb Ecol. 2010 Jan: 59(1):94-108. PMID: 19888627 www.ncbi.nlm.nih.gov/pubmed/19888627.

Shalon, D., Smith, S. J. and Brown, P. O. 2011. A DNA microarray system for analyzing complex DNA samples using two-color fluorescent probe hybridization. Genome Res. 6: 639-645.

Wu C.H., B. Sercu, L. C. Van De Werfhorst, J. Wong, T. Z. DeSantis, E. L. Brodie, T. C. Hazen, P. A. Holden, and G. L. Andersen, 2010. Characterization of coastal urban watershed bacterial communities leads to alternative community based indicators. PLoS One. 2010, Jun;5(6):11285. www.plosone.org

F.5 SIP Methods

Table 1 in the SIP Fact Sheet includes examples of recent applications of SIP to important contaminants.

F.6 EAP Methods

Battin, T.J. 1997. Assessment of fluorescein diacetate hydrolysis as a measure of total esterase activity in natural stream sediment biofilms. Science of The Total Environment. 198, 51-60.

Ensley, B., Ratzkin, B., Osslund, T., Simon, M., Wackett, L., and Gibson, D. 1983. Expression of naphthalene oxidation genes in Escherichia coli results in the biosynthesis of indigo. Science 222, 167-169.

Field, J.A., Reed, R.L., Istok, J.D., Semprini, L., Bennett, P., and Buscheck, T.E. 2005. Trichlorofluoroethene: A reactive tracer for evaluating reductive dechlorination in large-diameter permeable columns. Ground Water Monitoring & Remediation 25, 68-77.

Fontvieille, D.A., Outaguerouine, A., and Thevenot, D.R. 1992. Fluorescein diacetate hydrolysis as a measure of microbial activity in aquatic systems: Application to activated sludges. Environmental Technology 13, 531 - 540.

Gu, A.Z., Stensel, H.D., Pietari, J.M.H., and Strand, S.E. 2003. Vinyl Bromide as a Surrogate for Determining Vinyl Chloride Reductive Dechlorination Potential. Environmental Science & Technology 37, 4410-4416. PMID 14572093.

Hageman, K.J., Field, J.A., Istok, J.D., and Semprini, L. 2004. Quantifying the effects of fumarate on in situ reductive dechlorination rates. Journal of Contaminant Hydrology 75, 281-296. PMID 15610903.

Jones, K.H., and Senft, J.A. 1985. An improved method to determine cell viability by simultaneous staining with fluorescein diacetate-propidium iodide. Journal of Histochemistry & Cytochemistry 33, 77-79.

Kauffman, M.E., Keener, W.K., Clingenpeel, S.R., Watwood, M.E., Reed, D.W., Fujita, Y., and Lehman, R.M. 2003. Use of 3-hydroxyphenylacetylene for activity-dependent, fluorescent labeling of bacteria that degrade toluene via 3-methylcatechol. Journal of Microbiological Methods 55, 801-805. PMID 14607424.

Schnurer, J., and Rosswall, T. 1982. Fluorescein Diacetate Hydrolysis as a Measure of Total Microbial Activity in Soil and Litter. Appl. Environ. Microbiol. 43, 1256-1261. PMID 16346026.

Watwood, M.E., Keener, W.K., and Smith, W.A. 2002. Characterization of microbial isolates from the Idaho National Engineering and Environmental Laboratory Teat Area North aquifer: identifying potential enzymatic pathways for toluene oxidation. In Geology, Hydrogeology, and Environmental Remediation: Idaho National Engineering and Environmental Laboratory, Eastern Snake River Plain, Idaho, P.K. Link, and L.L Mink, ed. (Geologic Society of America).

F.7 FISH methods

SILVA rRNA database project: http://www.arb-silva.de/fish-probes/

probeBase: www.microbial-ecology.net/probebase/

Amann, R.I, B. Binder, R. Olson, S. Chisholm, R. Devereux, and D. Stahl. 1990. Combination of 16S rRNA-targeted oligonucleotide probes with flow cytometry for analyzing mixed microbial populations. Applied and Environmental Microbiology 56:1919-1925.

Grenni, P., A. Gibello, A. Barra Caracciolo, C. Fajardo, M. Nande, R. Vargas, M. L. Saccà, M. J. Martinez-Iñigo, R. Ciccoli, and M. Martín. 2009. A new fluorescent oligonucleotide probe for in situ detection of s-triazine-degrading Rhodococcus wratislaviensis in contaminated groundwater and soil samples. Water Research 43:2999-3008.

Rowe, A., B. Lazar, R. Morris, and R. Richardson. 2008. Characterization of the Community Structure of a dechlorinating mixed culture and comparisons of gene expression in planktonic and biofloc-associated Dehalococcoides and Methanospirillum species. Applied and Environmental Microbiology 74:6709-6719.

Shepard, J. R., R. M. Addison, B. D. Alexander, P. Della-Latta, M. Gherna, G. Haase, G. Hall, J. K. Johnson, W. G. Merz, H. Peltroche-Llacsahuanga, H. Stender, R. A. Venezia, D. Wilson, G. W. Procop, F. Wu, and M. J. Fiandaca. 2008. Multicenter Evaluation of the Candida albicans/Candida glabrata Peptide Nucleic Acid Fluorescent In Situ Hybridization Method for Simultaneous Dual-Color Identification of C. albicans and C. glabrata Directly from Blood Culture Bottles. J. Clin. Microbiol. 46:50-55.

F.8 Data Quality and Sampling

Davis, G., D. Ogles, B. Baldwin, D. McElroy, S. Lewis, R. Pirkle, P. McLoughlin, and K. Sublette. 2008. Demonstrating monitored natural attenuation using Bio-Trap® samplers. In: Poster presented at the Proceedings of the Sixth International Conference on Remediation of Chlorinated and Recalcitrant Compounds, Monterey, CA. Ed. B. M. Sass. Abstract B-025. Columbus, Ohio: Battelle Press.

Schafer, C.E., C.W. Condee, , S. Vainburg, and R. J. Steffan. 2008. Bioaugmentation for chlorinated ethenes using Dehalococcoides sp.: Comparison between batch and column experiments. Chemosphere 75: 141-148. PMID: 19171368.

F.9 Additional Resources, General

Adrian, L., Szewzyk, U., Wecke, J., Görisch, H., 2000. Bacterial dehalorespiration with chlorinated benzenes. Nature 408 (6812), 580–583.

DaSilva M.L.B., and P.J.J. Alvarez. 2004.  Enhanced Anaerobic Biodegradation of Benzene-Toluene-Ethylbenzene-Xylene-Ethanol Mixtures in Bioaugmented Aquifer Columns. Applied and Environmental Microbiology. 70(8): 4720-4726.

Deeb R, J Nyman, E Hawley, M Kavanaugh, and R O’Laskey. 2012. Advanced Diagnostic Tools.  Chapter 8 in Kueper B, HF Stroo and CH Ward (eds.).  Chlorinated Solvent Source Zone Remediation.  Springer, New York, NY.  (In preparation).

ESTCP Web Site: http://www.serdp-estcp.org/Featured-Initiatives/Cleanup-Initiatives/Molecular-Biological-Tools

Harvey, R. G. 1997. Polycyclic aromatic hydrocarbons. Wiley-VCH, New York.

Madigan, M. T., J. M. Martinko, P. V. Dunlap, and D. P. Clark. 2008. Brock Biology of Microorganisms, 12th ed. San Francisco, CA: Pearson/Benjamin Cummings.

Petrovskis, E. A., W. Amber, and C. Walker. 2013. “Microbial Monitoring during Bioaugmentation with Dehalococcoides.” In Leeson A, H. Stroo and CH Ward (eds), Bioaugmentation for Groundwater Remediation, Springer, New York, NY.

Stahl, D., and R. Amann. 1991. Development and application of nucleic acid probes, p. 205-248. In E. Stackebrandt and M. Goodfellow (ed.), Nucleic acid techniques in bacterial systematics. John Wiley & Sons Ltd., Chichester, England.

Stroo HF, A Leeson, and CH Ward, Eds. 2013. Bioaugmentation for Groundwater Remediation. Springer, New York, NY. 389 p.

USEPA 1998. “Technical Protocol for Evaluating Natural Attenuation Of Chlorinated Solvents In Ground Water.” EPA/600/R-98/128.

 


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