Expanding the Indicator Bacteria Concept: A Novel Approach to Assess Ecosystem Risk in Impaired Waters


Many studies report the relationship between coliform indicator bacteria levels and the overall quality of environmental water for public use. This study, an outgrowth of a long-term water-monitoring program within the upper Appomattox River (Virginia) watershed, employs a zebrafish model to examine the relationship between impaired stream water and aquatic vertebrate development. We report results that suggest an expansion of the indicator bacteria concept, showing a possible relationship between waters containing high levels of the indicator bacterium, Escherichia coli (E. coli), with developmental defects upon zebrafish embryos. These effects are not directly attributable to bacterial presence, as filtered test waters void of bacteria produce the same results in embryos, indicating these developmental defects are due to the presence of other toxins or contaminants. Fish embryos exposed to the test waters show reduced survivorship and altered brain and heart development. Furthermore, fish surviving to adulthood exhibit altered gonads and skewed sex ratios. We suggest that this broadly focused approach examining the complex interactions (biotic and abiotic) within raw water sources could be used in conjunction with traditional chemical assays and/or dose-response studies on vertebrate models for a more complete analysis of stream water quality conditions.

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Carrara, N. , Settell, K. , Andrews, B. , Buckalew, D. and Znosko, W. (2015) Expanding the Indicator Bacteria Concept: A Novel Approach to Assess Ecosystem Risk in Impaired Waters. Journal of Water Resource and Protection, 7, 938-955. doi: 10.4236/jwarp.2015.712077.

Conflicts of Interest

The authors declare no conflicts of interest.


[1] Escherich, T. (1885) Die Darmbakterien des Neugeborenen und Sauglings. Fortschritte der Medizin, 3, 515-522.
[2] Cabelli, V., Dufour, A., Levin, M., McCabe, L. and Haberman, P. (1979) Relationship of Microbial Indicators to Health Effects at Marine Bathing Beaches. American Journal of Public Health, 69, 690-696.
[3] Dufour, A. (1984) Bacterial Indicators of Recreational Water Quality. Canadian Journal of Public Health, 75, 49-56.
[4] Leclerc, H., Mossel, D., Edberg, S. and Struijk, C. (2001) Advances in the Bacteriology of the Coliform Group: Their Suitability as Markers of Microbial Water Safety. Annual Review of Microbiology, 55, 201-234.
[5] Wade, T., Calderon R., Sams, E., Beach, M., Brenner, K., Williams, A. and Dufour, A. (2006) Rapidly Measured Indicators of Recreational Water Quality Are Predictive of Swimming-Associated Gastrointestinal Illness. Environmental Health Perspectives, 114, 24-28.
[6] Wade, T., Calderon, R., Brenner, K., Sams, E., Beach, M., Haugland, R., Wymer, L. and Dufour, A. (2008) High Sensitivity of Children to Swimming-Associated Gastrointestinal Illness: Results Using a Rapid Assay of Recreational Water Quality. Epidemiology, 19, 375-383.
[7] Heaney, C., Sams, E., Wing, S., Marshall, S., Brenner, K., Dufour, A. and Wade, T. (2009) Contact with Beach Sand among Beachgoers and Risk of Illness. American Journal of Epidemiology, 170, 164-172.
[8] Wu, C., Sercu, B., Van de Werfhorst, L., Wong, J., DeSantis, T., Brodie, E., Hazen, T., Holden, P. and Andersen, G. (2010) Characterization of Coastal Urban Watershed Bacterial Communities Leads to Alternative Community-Based Indicators. PLoS ONE, 5, e11285.
[9] Abraham, W.-R. (2011) Megacities as Sources for Pathogenic Bacteria in Rivers and Their Fate Downstream. International Journal of Microbiology, 2011, Article ID: 798292.
[10] United States Environmental Protection Agency (2012) Water Monitoring and Assessment Report: 5.11 Fecal Bacteria. US EPA, Washington DC.
[11] Cabral, J. (2010) Water Microbiology: Bacterial Pathogens and Water. International Journal of Environmental Research and Public Health, 7, 3657-3703.
[12] American Public Health Association (APHA), American Water Works Association (AWWA) and Water Environment Federation (WEF) (2012) Standard Methods for the Examination of Water and Wastewater. 22nd Edition, American Public Health Association, Washington DC.
[13] Wilkes, G., Edge, T., Gannon, V., Jokinen, C., Lyautey, E., Neumann, N., Ruecker, N., Scott, A., Sunohara, M., Topp, E. and Lapen, D. (2011) Associations among Pathogenic Bacteria, Parasites, and Environmental and Land Use Factors in Multiple Mixed-Use Watersheds. Water Research, 45, 5807-5825.
[14] Williamson, K., Harris, J., Green, J., Rahman F. and Chambers, R. (2014) Stormwater Runoff Drives Viral Community Composition Changes in Inland Freshwaters. Frontiers in Microbiology, 5, 105.
[15] Walsh, C. (2000) Urban Impacts on the Ecology of Receiving Waters: A Framework for Assessment, Conservation, and Restoration. Hydrobiologia, 431, 107-114.
[16] United States Environmental Protection Agency (2014) Impaired Waters and Total Maximum Daily Loads (303d) Report. US EPA, Washington DC.
[17] Staley, Z., Senkbeil, J., Rohr, J. and Harwood, V. (2012) Lack of Direct Effects of Agrochemicals on Zoonotic Pathogens and Fecal Indicator Bacteria. Applied and Environmental Microbiology, 78, 8146-8150.
[18] Staley, Z., Rohr, J., Senkbeil, J. and Harwood, V. (2014) Agrochemicals Indirectly Increase Survival of E. coli O157:H7 and Indicator Bacteria by Reducing Ecosystem Services. Ecological Applications, 24, 1945-1953.
[19] Carriger, J., Hoang, T., Rand, G., Gardinali, P. and Castro, J. (2011) Acute Toxicity and Effects Analysis of Endosulfan Sulfate to Freshwater Fish Species. Archives of Environmental Contamination and Toxicology, 60, 281-289.
[20] Carmichael, N., Enzmann, H., Pate, I. and Waechter, F. (1997) The Significance of Mouse Liver Tumor Formation for Carcinogenic Risk Assessment: Results and Conclusions from a Survey of Ten Years of Testing by Agrochemical Industry. Environmental Health Perspectives, 105, 1196-1203.
[21] Pereira, J., Antunes, S., Castro, B., Marques, C., Goncalves, A., Goncalves F. and Pereira, R. (2009) Toxicity Evaluation of Three Pesticides on Non-Target Aquatic and Soil Organisms: Commercial Formulation versus Active Ingredient. Ecotoxicology, 18, 455-463.
[22] Pogacean, M. and Gavrilescu, M. (2009) Plant Protection Products and Their Sustainable and Environmentally Friendly use. Environmental Engineering and Management Journal, 8, 607-627.
[23] Abe, T., Saito, H., Niikura, Y., Shigeoka, T. and Nakano, Y. (2001) Embryonic Development Assay with Daphnia magna: Application to Toxicity of Aniline Derivatives. Chemosphere, 45, 487-495.
[24] Palma, P., Palma, V., Fernandes, R., Bohn, A., Soares, A. and Barbosa, I. (2009) Embryo-Toxic Effects of Environmental Concentrations of Chlorpyrifos on the Crustacean Daphnia magna. Ecotoxicology and Environmental Safety, 72, 1714-1718.
[25] Traunspurger, W., Haitzer, M., Hoss, S., Beier, S., Ahlf, W. and Steinberg, C. (1997) Ecotoxicological Assessment of Aquatic Sediments with Caenorhabditis elegans (Nematode)—A Method for Testing in Liquid Medium and Whole Sediment Samples. Environmental Toxicology and Chemistry, 16, 245-250.
[26] Strmac, M. and Braunbeck, T. (1999) Effects of Triphenyltin Acetate on Survival, Hatching Success, and Liver Ultrastructure of Early Life Stages of Zebrafish (Danio rerio). Ecotoxicology and Environmental Safety, 44, 25-39.
[27] Osterauer, R. and Kohler, H. (2008) Temperature-Dependent Effect of the Pesticides Thiacloprid and Diazinon on the Embryonic Development of the Zebrafish (Danio rerio). Aquatic Toxicology, 86, 485-494.
[28] Villalobos, S., Hamm, K., The, S. and Hinton, D. (2000) Thiobencarb-Induced Embryotoxicity in Medaka (Oryzias latipes): Stage-Specific Toxicity and the Protective Role of the Chorion. Aquatic Toxicology, 48, 309-326.
[29] Werner, I., Geist, J., Okihiro, M., Rosenkranz, P. and Hinton, D. (2002) Effects of Dietary Exposure to the Pyrethroid Pesticide Esfenvalerate on Medaka (Oryzias latipes). Marine Environmental Research, 54, 609-614.
[30] Hayes, T., Case, P., Chui, S., Chung, D., Haeffele, C., Haston, K., Lee, M., Mai, V., Marjuoa, Y., Parker, J. and Tsui, M. (2006) Pesticide Mixtures, Endocrine Disruption, and Amphibian Declines: Are We Underestimating the Impact? Environmental Health Perspectives, 114, 40-50.
[31] Bacchetta, R., Mantecca, P., Andrioletti, M., Vismara, C. and Vailati, G. (2008) Axial-Skeletal Defects Caused by Carbaryl in Xenopus laevis Embryos. Science of the Total Environment, 392, 110-118.
[32] Robles-Mendoza, C., Garcia-Basilio, C., Cram-Heydrich, S., Hernandez-Quiroz, M. and Vanegas-Perez, C. (2009) Organophosphorus Pesticides Effect on Early Stages of the Axolotl Ambystoma mexicanum (Amphibia: Caudata). Chemosphere, 74, 703-710.
[33] Lele, Z. and Krone, P.H. (1996) The Zebrafish as a Model System in Developmental, Toxicological and Transgenic Research. Biotechnology Advances, 14, 57-72.
[34] Hill, A.J., Teraoka, H., Heideman, W. and Peterson, R.E. (2005) Zebrafish as a Model Vertebrate for Investigating Chemical Toxicity. Toxicological Sciences, 86, 6-19.
[35] Yang, L., Ho, N.Y., Alshut, R., Legradi, J., Weiss, C., Reischl, M., Mikut, R., Liebel, U., Muller, F. and Strahle, U. (2009) Zebrafish Embryos as Models for Embryotoxic and Teratological Effects of Chemicals. Reproductive Toxicology, 28, 245-253.
[36] Sipes, N.S., Padilla S. and Knudsen, T.B. (2011) Zebrafish as an Integrative Model for Twenty-First Century Toxicity Testing. Birth Defects Research Part C: Embryo Today, 93, 256-267.
[37] Goolish, E.M., Okutake, K. and Johnson, P. (2000) The Behavioral Response of Zebrafish to Hypergravity Conditions. Journal of Gravitational Physiology, 7, 99-100.
[38] Mizell, M. and Romig, E.S. (1997) The Aquatic Vertebrate Embryo as a Sentinel for Toxins: Zebrafish Embryo Dechorionation and Perivitelline Space Microinjection. International Journal of Developmental Biology, 41, 411-423.
[39] Murk, A.J., Leglar, J., Denison, M.S., Giesy, J.P., van de Guchte, C. and Brouwer, A. (1996) Chemical Activated Luciferase Gene Expression (CALUX): A Novel in Vitro Bioassay for Ah Receptor Active Compounds in Sediments and Pore Water. Fundamental and Applied Toxicology, 33, 149-160.
[40] Erbe, M., Ramsdorf, W., Vicari, T. and Cestari, M. (2011) Toxicity Evaluation of Water Samples Collected near a Hospital Waste Landfill through Bioassays of Genotoxicity Piscine Micronucleus Gest and Comet Assay in Fish Astyanax and Ecotoxiticy Vibrio fischeri and Daphnia magna. Ecotoxicology, 20, 320-328.
[41] Buckalew, D., Hartman, L., Grimsley, G., Martin, A. and Register, K. (2006) A Long-Term Study Comparing Membrane Filtration with Colilert Defined Substrates in Detecting Fecal Coliforms and Escherichia coli in Natural Waters. Journal of Environmental Management, 80, 191-197.
[42] Virginia Department of Environmental Quality (VA DEQ) (2012) Final 2012 305(b)/303(d) Water Quality Assessment Integrated Report.
[43] Kudoh, T., Tsang, M., Hukriede, N., Chen, X., Dedekian, M., Clarke, C., Kiang, A., Schultz, S., Epstein, J., Toyama, R. and Dawid, I. (2001) A Gene Expression Screen in Zebrafish Embryogenesis. Genome Research, 11, 1979-1987.
[44] Reifers, F., Bohli, H., Walsh, E., Crossley, P., Stainier, D. and Brand, M. (1998) Fgf8 Is Mutated in Zebrafish acerebellar (ace) Mutants and Is Required for Maintenance of Midbrain-Hindbrain Boundary Development and Somitogenesis. Development, 125, 2381-2395.
[45] Yelon, D., Horne, S. and Stainier, D. (1999) Restricted Expression of Cardiac Myosin Genes Reveals Regulated Aspects of Heart Tube Assembly in Zebrafish. Developmental Biology, 214, 23-37.
[46] Gupta, T. and Mullins, M.C. (2010) Dissection of Organs from the Adult Zebrafish. Journal of Visualized Experiments, 37, Article ID: e1717.
[47] Parichy, D., Elizondo, M., Mills, M., Gordon, T. and Engeszer, R. (2009) Normal Table of Postembryonic Zebrafish Development: Staging by Externally Visible Anatomy of the Living Fish. Developmental Dynamics, 238, 2975-3015.
[48] Kimmel, C., Ballard, W., Kimmel, S., Ullmann, B. and Schilling, T. (1995) Stages of Embryonic Development of the Zebrafish. Developmental Dynamics, 203, 253-310.
[49] Picker, A., Brennan, C., Reifers, F., Clarke, J., Holder, N. and Brand, M. (1999) Requirement for the Zebrafish Mid-Hindbrain Boundary in Midbrain Polarization, Mapping and Confinement of the Retinotectal Projection. Development, 126, 2967-2978.
[50] Chen, J., van Eeden, F., Warren, K., Chin, A., Nusslein-Volhard, C., Haffter, P. and Fishman, M. (1997) Left-Right Pattern of Cardiac BMP4 May Drive Asymmetry of the Heart in Zebrafish. Development, 124, 4373-4382.
[51] Chin, A., Tsang, M. and Weinberg, E. (2000) Heart and Gut Chiralities Are Controlled Independently from Initial Heart Position in the Developing Zebrafish. Developmental Biology, 227, 403-421.
[52] Gercken, J. and Sordyl, H. (2002) Intersex in Feral Marine and Freshwater Fish from Northeastern Germany. Marine Environmental Research, 54, 651-655.
[53] Segner, H., Navas, J.M., Schafers, C. and Wenzel, A. (2003) Potencies of Estrogenic Compounds in Vitro Screening Assays and in Life Cycle Test with Zebrafish in Vivo. Ecotoxicology and Environmental Safety, 54, 315-322.
[54] Antibus, R. and Linkins, A. (1989) Microbial and Rhizosphere Markers of Air Pollution Induced Stress. In: Biologic Markers of Air-Pollution Stress and Damage in Forests, National Academy Press, Washington DC, 233-244.
[55] Adamus, P. (1996) Bioindicators for Assessing Ecological Integrity of Prairie Wetlands. EPA/600/R-96/082, US EPA Environmental Research Laboratory, Corvallis.
[56] Sims, A., Zhang, Y., Gajaraj, S., Brown, P. and Hu, Z. (2013) Toward the Development of Microbial Indicators for Wetland Assessment. Water Research, 47, 1711-1725.
[57] Paerl, H., Dyble, J., Moisander, P., Noble, R., Piehler, M., Pinckney, J., Steppe, T., Twomey, L. and Valdes, L. (2003) Microbial Indicators of Aquatic Ecosystem Change: Current Applications to Eutrophication Studies. FEMS Microbial Ecology, 46, 233-246.
[58] United States Environmental Protection Agency (2008) Ecological Condition Report: 6.6 What Are the Trends in Biomarkers of Exposure to Common Environmental Contaminants in Plants and Animals? US EPA, Washington DC.
[59] Haendel, M., Tilton, F., Bailey, G. and Tanguay, R. (2004) Developmental Toxicity of the Dithiocarbamate Pesticide Sodium Metam in Zebrafish. Toxicological Sciences, 81, 390-400.
[60] Koprucu, K. and Aydin, R. (2004) The Toxic Effects of Pyrethroid Deltamethrin on Common Carp (Cyprinus carpio L.) Embryos and Larvae. Pesticide Biochemistry and Physiology, 80, 47-53.
[61] Tilton, F., La Du, J. and Tanguay, R. (2008) Sulfhydryl Systems Are a Critical Factor in the Zebrafish Developmental Toxicity of the Dithiocarbamate Sodium Metam (NaM). Aquatic Toxicology, 90, 121-127.
[62] DeMicco, A., Cooper, K., Richardson, J. and White, L. (2010) Developmental Neurotoxicity of Pyrethroid Insecticides in Zebrafish Embryos. Toxicological Sciences, 113, 177-186.
[63] Hamm, J. and Hinton, D. (2000) The Role of Development and Duration of Exposure to the Embryotoxicity of Diazinon. Aquatic Toxicology, 48, 403-418.
[64] Lin, C., Hui, M. and Cheng, S. (2007) Toxicity and Cardiac Effects of Carbaryl in Early Developing Zebrafish (Danio rerio) Embryos. Toxicology and Applied Pharmacology, 222, 159-168.
[65] Honrubia, M., Paz Herraez, M. and Alvarez, R. (1993) The Carbamate Insecticide ZZ-Aphox Induced Structural Changes of Gills, Liver, Gall-Bladder, Heart, and Notochord of Rana perezi Tadpoles. Archives of Environmental Contamination and Toxicology, 25, 184-191.
[66] Degitz, S., Durhan, E., Tietge, J., Kosian, P., Holcombe, G. and Ankley, G. (2003) Developmental Toxicity of Methoprene and Several Degradation Products in Xenopus laevis. Aquatic Toxicology, 64, 97-105.
[67] Falconer, I.R., Chapman, H.F., Moore, M.R. and Ranmuthugala, G. (2006) Endocrine Disrupting Compounds: A Review of Their Challenge to Sustainable and Safe Water Supply and Water Reuse. Environmental Toxicology, 21, 181-191.
[68] Kolpin, D.W., Furlong, E.T., Meyer, M.T., Thurman, E.M., Zaugg, S.D., Barber, L.B. and Buxton, H.T. (2002) Pharmaceuticals, Hormones, and Other Organic Wastewater Contaminants in US Streams, 1999-2000: A National Reconnaissance. Environmental Science and Technology, 36, 1202-1211.
[69] Metcalfe, C.D., Metcalfe, T.L., Kiparissis, Y., Koening, B.G., Khan, C., Hughes, R.J., Croley, T.R., March, R.E. and Potter, T. (2001) Estrogenic Potency of Chemicals Detected in Sewage Treatment Plant Effluents as Determined by in Vivo Assays with Japanese Medaka (Oryzias latipes). Environmental Toxicology and Chemistry, 20, 297-308.
[70] Ashfield, L.A., Pottinger, T.G. and Sumpter, J.P. (1998) Exposure of Female Juvenile Rainbow Trout to Alkylphenolic Compounds Results in Modifications to Growth and Ovosomatic Index. Environmental Toxicology and Chemistry, 17, 679-686.
[71] Gray, M.A. and Metcalfe, C.D. (1997) Induction of Testis-Ova in Japanese Medaka (Oryzias latipes) Exposed to p-Nonylphenol. Environmental Toxicology and Chemistry, 16, 1082-1086.
[72] Jobling, S., Sheahan, D., Osborne, J.A., Matthiessen, P. and Sumpter, J.P. (1996) Inhibition of Testicular Growth in Rainbow Trout (Oncorhynchus mykiss) Exposed to Estrogenic Alkyl-Phenolic Chemicals. Environmental Toxicology and Chemistry, 15, 194-202.
[73] Silva, P., Rocha, M.J., Cruzeiro, C., Malhao, F., Reis, B., Urbatzka, R., Monteiro, R.A.F. and Rocha, E. (2012) Testing the Effects of Ethinylestradiol and of an Environmentally Relevant Mixture of Xenoestrogens as Found in the Douro River (Portugal) on the Maturation of Fish Gonads—A Stereological Study Using the Zebrafish (Danio rerio) as a Model. Aquatic Toxicology, 124-125, 1-10.
[74] Wang, M., Chen, J., Lin, K., Chen, Y., Hu, W., Tanguay, R.L., Huang, C. and Dong, Q. (2011) Chronic Zebrafish PFOS Exposure Alters Sex Ratio and Maternal Related Effects in F1 Offspring. Environmental Toxicology and Chemistry, 30, 2073-2080.

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