Abstract
Fecal pollution from human and natural sources enters soil or watercourses, mixes, then reemerges as a nuisance of unknown origin. Before remediation is attempted, the sources and identities of pollution must be identified. Previous microbial source tracking studies have relied on traditional methods of microbiology such as selective media and biochemical characteristics to quantify fecal bacteria in water samples. This is successful when single sources are responsible for pollution. However, when multiple sources are present, numbers must be subdivided into categories of pollution to define relative importance and select appropriate methods of remediation which are very different for examples such as humans and avifauna pollution. Rather than depending on a single method, we recommend a tiered approach which takes advantage of ecological parameters and conventional microbiology to provide context for more precise DNA data and related statistics.
This is a preview of subscription content, log in via an institution to check access.
Similar content being viewed by others
References
Altschul, S. F., Madden, T. L., Schaffer, A. A., Zhang, J., Zhang, Z., Miller, W., et al. (1997). Gapped BLAST and PSI-BLAST: A new generation of protein database search programs. Nucleic Acids Research, 25(17), 3389–3402. doi:10.1093/nar/25.17.3389.
Amann, R. I., Ludwig, W., & Schleifer, K. H. (1995). Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiological Reviews, 59, 143–169.
Atherholt, T. (2005). Microbial source tracking; library based methods technology critique. Trenton: New Jersey Department of Environmental Protection, Division of Science, Research and Technology.
Bejarano, E. R., Khashoggi, A. M., Witty, M., & Lichtenstein, C. P. (1994). Discovery of ancient recombination between geminiviral DNA and the nuclear genome of Nicotiana sp. Proceedings of the National Academy of Science, 93, 759–764.
Chenna, R., Sugawara, H., Koike, T., Lopez, R., Gibson, T. J., Higgins, D. G., et al. (2003). Multiple sequence alignment with the Clustal series of programs. Nucleic Acids Research, 31(13), 3497–3500. doi:10.1093/nar/gkg500.
Clesceri, L. S., Greenberg, A. E., & Eaton, A. D. (1998). Standard methods for the examination of water and wastewater (20th ed.). Washington DC: American Public Health Association. ISBN:0 87553 235 7.
Figuerola, E. L., & Erijman, L. (2007). Bacterial taxa abundance pattern in an industrial wastewater treatment system determined by the full rRNA cycle approach. Environmental Microbiology, 9(7), 1780–1789. doi:10.1111/j.1462-2920.2007.01298.x.
Fiksdal, L., Maki, J. S., La, S., Croix, S. J., & Staley, J. T. (1985). Survival and detection of Bacteroides spp., prospective indicator bacteria. Applied and Environmental Microbiology, 49(1), 148–150.
Fonty, G., Gouet, P., Jouany, J. P., & Senaud, J. (1987). Establishment of the microflora and anaerobic fungi in the rumen of lambs. Journal of General Microbiology, 133(7), 1835–1843.
Guarner, F., & Malagelada, J. (2003). Gut flora in health and disease. Lancet, 361(9356), 512–519. doi:10.1016/S0140-6736(03)12489-0.
Harmsen, H. J. M., Wildeboer-Veloo, A. C. M., Raangs, G. C., Wagendorp, A. A., Klijn, N., Bindels, J. G., et al. (2000). Analysis of intestinal flora development in breast-fed and formula-fed infants by using molecular identification and detection methods. Journal of Pediatric Gastroenterology and Nutrition, 30(1), 61–67. doi:10.1097/00005176-200001000-00019.
Holt, J. G. (1994). Bergey’s manual of determinative bacteriology (9th ed.). Baltimore: Williams & Wilkins. ISBN:0-683-00603-7.
Hughes, J. B., Hellmann, J. J., Ricketts, T. H., & Bohannan, B. J. (2001). Counting the uncountable: Statistical approaches to estimating microbial diversity. Applied and Environmental Microbiology, 67(10), 4399–4406 Erratum in: Applied and Environmental Microbiology 2002 68 1:448 doi:10.1128/AEM.67.10.4399-4406.2001.
Lahr, M. L., & Lodhi, P. (2006). Economic impact analysis of hosting breeders’ cup. Center for Urban Planning Research, Rutgers University. http://policy.rutgers.edu/cupr/recon/report061201.pdf.
Layton, A., McKay, L., Williams, D., Garrett, V., Gentry, R., & Sayler, G. (2006). Development of Bacteroides 16S rRNA gene TaqMan-based real-time PCR assays for estimation of total, human, and bovine fecal pollution in water. Applied and Environmental Microbiology, 72(6), 4214–4224.
Malinowski, K. (2007). New Jersey equine industry. New Brunswick: Rutgers Equine Science Center http://www.hallnj.org/cm/streamer.jsp?dId=1000297&fId=560, http://esc.rutgers.edu/news_more/PDF_Files/2007_Equine_Economic_Impact_Study_Report.pdf.
Mallin, M. A., McIver, M. R., Wells, H. A., Parsons, D. C., & Johnson, V. L. (2005). Reversal of eutrophication following sewage treatment upgrades in the New River Estuary, North Carolina. Journal Estuaries and Coasts, 28(5), 750–760. doi:10.1007/BF02732912.
Martín, R., Langa, S., Reviriego, C., Jimínez, E., Marín, M. L., Xaus, J., et al. (2003). Human milk is a source of lactic acid bacteria for the infant gut. The Journal of Pediatrics, 143(6), 754–758. doi:10.1016/j.jpeds.2003.09.028.
McFall-Ngai, M. (2006). Vertebrate guts shape their microbiota. Cell, 127(2), 247–249. doi:10.1016/j.cell.2006.10.005.
MCHD (2007). Branch Port Creek sampling stations. Freehold: Monmouth County Health Department http://co.monmouth.nj.us/documents/121/MonParkWebsiteLarge.pdf.
McLellan, S. L., & Salmore, A. K. (2003). Evidence for localized bacterial loading as the cause of chronic beach closings in a freshwater marina. Water Research, 37(11), 2700–2708. doi:10.1016/S0043-1354(03)00068-X.
Moore, W. E., & Moore, L. H. (1995). Intestinal floras of populations that have a high risk of colon cancer. Applied and Environmental Microbiology, 61, 3202–3207.
NJWC. (2008). New Jersey weather and climate network. http://climate.rutgers.edu/njwxnet/ and Point Pleasant data.
Obiso, R. J., Lyerly, D. M., van Tassell, R. L., & Wilkins, T. D. (1995). Proteolytic activity of the Bacteroides fragilis enterotoxin causes fluid secretion and intestinal damage in vivo. Infection and Immunity, 63(10), 3820–3826.
O’Hara, A. M., & Shanahan, F. (2006). The gut flora as a forgotten organ. EMBO Reports, 7(7), 688–693. doi:10.1038/sj.embor.7400731.
Pietzak, M. (2004). Bacterial colonization of the neonatal gut. Journal of Pediatric Gastroenterology and Nutrition, 38, 389–391. doi:10.1097/00005176-200404000-00005.
Rawls, J. F., Samuel, B. S., & Gordon, J. I. (2004). Gnotobiotic zebra fish reveal evolutionarily conserved responses to the gut microbiota. Proceedings of the National Academy of Science, 101(13), 4596–4601. doi:10.1073/pnas.0400706101.
Rawls, J. F., Mahowald, M. A., Ley, R. E., & Gordon, J. I. (2006). Reciprocal gut microbiota transplants from zebra fish and mice to germ-free recipients reveal host habitat selection. Cell, 127(2), 423–433. doi:10.1016/j.cell.2006.08.043.
Reid, C. A., Avery, S. M., Warriss, P., & Buncic, S. (2002). The effect of feed withdrawal on Escherichia coli shedding in beef cattle. Food Control, 13(6-7), 393–398. doi:10.1016/S0956-7135(01)00096-2.
Rhodes, M. W., & Kator, H. (1988). Survival of Escherichia coli and Salmonella spp. in estuarine environments. Applied and Environmental Microbiology, 54(12), 2902–2907.
Ryan, J. R. (2008). Past pandemics and their outcome. Chapter 1. In J. R. Ryan (Ed.), Pandemic influenza, emergency planning and community awareness. Boca Raton: CRC http://books.google.com/books?hl=en&lr=&id=t13C_eWhOX4C&oi=fnd&pg=PA3&dq=+%22second+cholera+pandemic%22&ots=zVatDXLgK8&sig=FU6M0ynqcUFClM-Ht7XNvVVDi4g ISBN:1420060872.
Santoro, A. E., & Boehm, A. B. (2007). Frequent occurrence of the human-specific Bacteroides fecal marker at an open coast marine beach: Relationship to waves, tides and traditional indicators. Environmental Microbiology, 9(8), 2038–2049. doi:10.1111/j.1462-2920.2007.01319.x.
Savichtcheva, O., Okayama, N., & Okabe, S. (2007). Relationships between Bacteroides 16S rRNA genetic markers and presence of bacterial enteric pathogens and conventional fecal indicators. Water Research, 41(16), 3615–3628. doi:10.1016/j.watres.2007.03.028.
Schloss, P. D., & Handelsman, J. (2005). Introducing DOTUR, a computer program for defining operational taxonomic units and estimating species richness. Applied and Environmental Microbiology, 71(3), 1501–1506. doi:10.1128/AEM.71.3.1501-1506.2005.
Schloss, P. D., & Handelsman, J. (2008). A statistical toolbox for metagenomics: Assessing functional diversity in microbial communities. BMC Bioinformatics, 9, 34. doi:10.1186/1471-2105-9-34.
Schloss, P. D., Larget, B. R., & Handelsman, (2004). Integration of microbial ecology and statistics: A test to compare gene libraries. Applied and Environmental Microbiology, 70, 5485–5492 http://www.plantpath.wisc.edu/fac/joh/S-libshuff/documentation.html.
Singleton, D. R., Furlong, M. A., Rathbun, S. L., & Whitman, W. B. (2001). Quantitative comparisons of 16S rRNA gene sequence libraries from environmental samples. Applied and Environmental Microbiology, 67, 4374–4376 http://www.plantpath.wisc.edu/fac/joh/S-libshuff/documentation.html doi:10.1128/AEM.67.9.4374-4376.2001.
Smith, P. B., Tomfohrde, K. M., Rhoden, D. L., & Balows, A. (1972). API System: A multitube micromethod for identification of enterobacteriaceae. Applied and Environmental Microbiology, 24(3), 449–452.
Snow, J. (1855). On the mode of communication of cholera. London: Churchill http://www.ph.ucla.edu/epi/snow/broadstreetpump.html, http://www.ph.ucla.edu/epi/snow/snowbook.html.
Stoeckel, D. M., & Harwood, V. J. (2007). Performance, design, and analysis in microbial source tracking studies. Applied and Environmental Microbiology, 73(8), 2405–2415. doi:10.1128/AEM.02473-06.
Suau, A., Bonnet, R., Sutren, M., Godon, J. J., Gibson, G. R., Collins, M. D., et al. (1999). Direct analysis of genes encoding 16S rRNA from complex communities reveals many novel molecular species within the human gut. Applied and Environmental Microbiology, 6(11), 4799–4807.
USEPA (2005). Microbial source tracking guide document. Cincinnati: US Environmental Protection Agency, Office of Research and Development EPA Publication No. EPA/600-R-05-064.
van der Wal, R., & Loonen, M. J. J. E. (1998). Goose droppings as food for reindeer. Canadian Journal of Zoology, 76(6), 1117–1122. doi:10.1139/cjz-76-6-1117.
Witty, M. (1990). Preprothaumatin II is processed to biological activity in Solanum tuberosum. Biotechnology Letters, 12, 131–136. doi:10.1007/BF01022429.
Xu, J., & Gordon, J. I. (2003). Honor thy symbionts. Proceedings of the National Academy of Science, 100(18), 10452–10459. doi:10.1073/pnas.1734063100.
Author information
Authors and Affiliations
Corresponding author
Rights and permissions
About this article
Cite this article
Witty, M., Nickels, J., Lisa, J. et al. Ecology, DNA, and the Future of Microbial Source Tracking. Water Air Soil Pollut 201, 219–232 (2009). https://doi.org/10.1007/s11270-008-9939-x
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s11270-008-9939-x