Abstract
Bacteroides–Prevotella group is one of the most promising targets for detecting fecal contamination in water environments, principally due to its host-specific distributions and high concentrations in feces of warm-blooded animals. We developed real-time PCR assays for quantifying chicken/duck-, chicken-, and duck-associated Bacteroides–Prevotella 16S rRNA genetic markers (Chicken/Duck-Bac, Chicken-Bac, and Duck-Bac). A reference collection of DNA extracts from 143 individual fecal samples and wastewater treatment plant influent was tested by the newly established markers. The quantification limits of Chicken/Duck-Bac, Chicken-Bac, and Duck-Bac markers in environmental water were 54, 57, and 12 copies/reaction, respectively. It was possible to detect possible fecal contaminations from wild ducks in environmental water with the constructed genetic marker assays, even though the density of total coliforms in the identical water samples was below the detection limit. Chicken/Duck-Bac marker was amplified from feces of wild duck and chicken with the positive ratio of 96 and 61 %, respectively, and no cross-reaction was observed for the other animal feces. Chicken-Bac marker was detected from 70 % of chicken feces, while detected from 39 % of cow feces, 8.3 % of pig feces, and 12 % of swan feces. Duck-Bac marker was detected from 85 % of wild duck feces and cross-reacted with 31 % of cow feces. These levels of detection specificity are common in avian-associated genetic markers previously proposed, which implies that there is a practical limitation in the independent application of avian-associated Bacteroides–Prevotella 16S rRNA genetic markers and a combination with other fecal contamination markers is preferable for detecting fecal contamination in water environments.
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References
Altschul SF, Warren G, Webb M, Eugene WM, David JL (1990) Basic local alignment search tool. J Mol Biol 215:403–410
Bernhard AE, Field KG (2000a) Identification of nonpoint sources of fecal pollution in coastal waters by using host-specific 16S rDNA markers from decal anaerobes. Appl Environ Microbiol 66:1587–1594
Bernhard AE, Field KG (2000b) A PCR assay to discriminate human and ruminant feces on the basis of host differences in Bacteroides–Prevotella genes encoding 16S rRNA. Appl Environ Microbiol 66:4571–4574
Blanch AR, Belanche-Munoz L, Bonjoch X, Ebdon J, Gantzer C, Lucena F, Ottoson J, Kourtis C, Iversen A, Kuhn I, Moce L, Muniesa M, Schwartzbrod J, Skraber S, Papageorgiou GT, Taylor H, Wallis J, Jofre J (2006) Integrated analysis of established and novel microbial and chemical methods for microbial source tracking. Appl Environ Microbiol 72:5915–5926
Champagne J, Diarra MS, Rempel H, Topp E, Greer CW, Harel J, Masson L (2011) Development of a DNA microarray for Enterococcal species, virulence, and antibiotic resistance gene determinations among isolates from poultry. Appl Environ Microbiol 77:2625–2633
Cho JC, Kim SJ (2000) Increase in bacterial community diversity in subsurface aquifers receiving livestock wastewater input. Appl Environ Microbiol 66:956–965
Devane ML, Robson B, Nourozi F, Scholes P, Gilpin BJ (2007) A PCR marker for detection in surface waters of faecal pollution derived from ducks. Water Res 41:3553–3560
Dick LK, Field KG (2004) Rapid estimation of numbers of fecal Bacteroidetes by use of a quantitative PCR assay for 16S rRNA genes. Appl Environ Microbiol 70:5695–5697
Dick LK, Bernhard AE, Brodeur TJ, Santo Domingo JW, Simpson JM, Walters SP, Field KG (2005) Host distributions of uncultivated fecal Bacteroidales bacteria reveal genetic markers for fecal source identification. Appl Environ Microbiol 71:3184–3191
Field KG, Samadpour M (2007) Fecal source tracking, the indicator paradigm, and managing water quality. Water Res 41:3517–3538
Fogarty LR, Voytek MA (2005) Comparison of Bacteroides-Prevotella 16S rRNA genetic markers for fecal samples from different animal species. Appl Environ Microbiol 71:5999–6007
Fogarty LR, Haack SK, Wolcott MJ, Whitman RL (2003) Abundance and charateristics of the recreational water quality indicator bacteria Escherichia coli and enterococci in gull faeces. J Appl Microbiol 94:865–878
Fremaux B, Boa T, Yost CK (2010) Quantitative real-time PCR assays for sensitive detection of Canada goose-specific fecal pollution in water sources. Appl Environ Microbiol 76:4886–4889
Hamilton MJ, Yan T, Sadowsky MJ (2006) Development of goose- and duck specific DNA markers to determine sources of Escherichia coli in waterways. Appl Environ Microbiol 72:4012–4019
Harwood VJ, Levine AD, Scott TM, Chivukula V, Lukasik J, Farrah SR, Rose JB (2005) Validity of the indicator organism paradigm for pathogen reduction in reclaimed water and public health protection. Appl Environ Microbiol 71:3163–3170
Himathongkham S, Riemann H (1999) Destruction of Salmonella typhimurium, Escherichia coli O157, H7 and Listeria monocytogenes in chicken manure by drying and/or gassing with ammonia. FEMS Microbiol Lett 171:179–182
Ishii S, Hansen DL, Hicks RE, Sadowsky MJ (2007) Beach sand and sediments are temporal sinks and sources of Escherichia coli in Lake Superior. Environ Sci Tech 41:2203–2209
Kassa H, Harrington B, Bisesi MS (2001) Risk of occupational exposure to Cryptosporidium, Giardia, and Campylobacter associated with the feces of giant Canada geese. Appl Occup Environ Hyg 16(9):905–909
Khawaja JZ, Naeem K, Ahmed Z, Ahmad S (2005) Surveillance of avian influenza viruses in wild birds in areas adjacent to epicenter of an outbreak in federal capital territory of Pakistan. Int J Poult Sci 4:39–43
Kildare BJ, Leutenegger CM, McSwain BS, Bambic DG, Rajal VB, Wuertz S (2007) 16S rRNA-based assays for quantitative detection of universal, human-, cow-, and dog-specific fecal Bacteroidales, a Bayesian approach. Water Res 41:3701–3715
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. Appl Environ Microbiol 72:4214–4224
Loy A, Arnold R, Tischler P, Rattei T, Wagner M, Horn M (2008) probeCheck - a central resource for evaluating oligonucleotide probe coverage and specificity. Environ Microbiol 10: 2894–2896
Lu J, Santo Domingo JW, Lamendella R, Edge T, Hill S (2008) Phylogenetic diversity and molecular detection of gull feces. Appl Environ Microbiol 74:3969–3976
Maidak BL, Olsen GJ, Larsen N, Overbeek R, McCaughey MJ, Woese CR (1997) The RDP (Ribosomal Database Project). Nucleic Acids Res 25:109–110
Mieszkin S, Yala J-F, Joubrel R, Gourmelon M (2009) Phylogenetic analysis of Bacteroidales 16S rRNA gene sequences from human and animal effluents and assessment of ruminant faecal pollution by real-time PCR. J Appl Microbiol 108:974–984
Okabe S, Shimazu Y (2007) Persistence of host-specific Bacteroides-Prevotella 16S rRNA genetic markers in environmental waters: effects of temperature and salinity. Appl Microbiol Biotechnol 76:935–944
Okabe S, Okayama N, Savichtcheva O, Ito T (2007) Quantification of host-specific Bacteroides- Prevotella 16S rRNA genetic markers for assessment of fecal pollution in freshwater. Appl Microbiol Biotechnol 74:890–901
Pei AY, Oberdorf WE, Nossa CW, Agarwal A, Chokshi P, Gerz EA, Jin Z, Lee P, Yang L, Poles M, Brown SM, Sotero S, Desantis T, Brodie E, Nelson K, Pei Z (2010) Diversity of 16S rRNA genes within individual prokaryotic genomes. Appl Environ Microbiol 76:3886–3897
Ryu H, Lu J, Vogel J, Elk M, Chavez-Ramirez F, Ashbolt N, Santo Domingo J (2012) Development and evaluation of a quantitative PCR assay targeting Sandhill Crene (Grus canadensis) fecal pollution. Appl Environ Micobiol 78:4338–4345
Saito N, Nei M (1987) The neighbor joining method: a new method for constructing phylogenetic trees. Mol Biol Evol 4:406–425
Savichtcheva O, Okabe S (2006) Alternative indicators of fecal pollution: relations with pathogens and conventional indicators, current methodologies for direct pathogen monitoring and future application perspectives. Water Res 40:2463–2476
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 Res 41:3615–3628
Scott TM, Rose JB, Jenkins TM, Farrah SR, Lukasik J (2002) Microbial source tracking: current methodology and future directions. Appl Environ Microbiol 68:5796–5803
Seurinck S, Defoirdt T, Verstraete W, Siciliano SD (2005) Detection and quantification of the human-specific HF183 Bacteroides 16S rRNA genetic marker with real-time PCR for assessment of human faecal pollution in freshwater. Environ Microbiol 7:249–259
Shanks OC, Kelty CA, Sivaganesan M, Varma M, Haugland RA (2009) Quantitative PCR for genetic markers of human fecal pollution. Appl Environ Microbiol 75:5507–5513
Simpson JM, Santo-Domingo JW, Reasoner DJ (2002) Microbial source tracking: state of the science. Environ Sci Technol 36:5279–5288
Stephen AB, Vladimir B, Jeremy AG, Jan H, Jim H, Mikael K, Reinhold M, Tania N, Michael WP, Gregory LS, Jo V, Carl TW (2009) The MIQE guidelines: minimum information for publication of quantitative real-time pcr experiments. Clin Chem 55:611–622
Stoeckel DM, Stelzer EA, Dick LK (2009) Evaluation of two spike-and-recovery controls for assessment of extraction efficiency in microbial source tracking studies. Water Res 43:4820–4827
Thompson JD, Higgins DG, Gibson T (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties, and weight matrix choice. Nucleic Acids Res 22:4673–4680
Unno T, Jang J, Han D, Kim JH, Sadowsky MJ, Kim OS, Chun J, Hur HG (2010) Use of barcoded pyrosequencing and shared OTUs to determine sources of fecal bacteria in watersheds. Environ Sci Technol 44:7777–7782
Weidhaas JL, Macbeth TW, Olsen RL, Harwood VJ (2011) Correlation of quantitative PCR for a poultry-specific Brevibacterium marker gene with bacterial and chemical indicators of water pollution in a watershed impacted by land application of poultry litter. Appl Environ Microbiol 77:2094–2102
WHO Scientific group (2011) Guidelines for drinking water quality, 4th edn. World Health Organization, Geneva
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This work was funded by Core Research for Evolutional Science and Technology (CREST) from Japan Science and Technology Agency (JST) and Grant-in Aid for Scientific Research A (23246094) from Japan Society for the Promotion of Science (JSPS).
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Kobayashi, A., Sano, D., Hatori, J. et al. Chicken- and duck-associated Bacteroides–Prevotella genetic markers for detecting fecal contamination in environmental water. Appl Microbiol Biotechnol 97, 7427–7437 (2013). https://doi.org/10.1007/s00253-012-4469-2
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DOI: https://doi.org/10.1007/s00253-012-4469-2