Agricultural and Rural Watersheds

  • Andreas H. Farnleitner
  • Georg H. Reischer
  • Hermann Stadler
  • Denny Kollanur
  • Regina Sommer
  • Wolfgang Zerobin
  • Günter Blöschl
  • Karina M. Barrella
  • Joy A. Truesdale
  • Elizabeth A. Casarez
  • George D. Di Giovanni


Identifying all relevant human and animal fecal sources is a basic requirement for target-oriented water resource management in agricultural and rural watersheds (ARW). As outlined, microbial source tracking (MST) is most suitably applied in concert with other methods within a broader conceptual framework of fecal pollution analysis. Two case studies – covering surface and karstic ground­water resources within ARW – are presented with the following features in common: public importance, problem formulation based on catchment-based pollution source profiling or modeling, and integrated use of several methods and parameters for fecal source characterization and identification at the water resource level. Possibilities and limitations of currently available MST tools, as well as fundamental requirements for their successful application and combination with other ­methods, are discussed. The use of multiple tools helps overcome specific limitations of individual methods, increases the robustness of the study, improves confidence in the results, or can help identify issues for further investigation.


Water quality Fecal pollution Microbial source tracking Human vs. animal pollution ground and surface water Library dependent and independent methods 



The Austrian part of the work was supported by the Vienna Water Works and the Austrian Science Fund (FWF) translational research project No. L414-B03 and DK plus W 1219-N22 (Vienna Doctoral Programme on Water Resource Systems) granted to A.H.F. The US Environmental Protection Agency Clean Water Act 319(h) program provided funding to G.D.D. for the Lake Granbury study through the Brazos River Authority and Texas Commission on Environmental Quality (Project 582-6-77030), and through the Texas Soil and Water Conservation Board for the Buck Creek study (Project 06–11).


  1. Bernhard, A. E. and K. G. Field (2000a). Identification of nonpoint sources of fecal pollution in coastal waters by using host-specific 16S ribosomal DNA genetic markers from fecal anaerobes. Appl Environ Microbiol 66(4): 1587–1594.PubMedCrossRefGoogle Scholar
  2. Bernhard, A. E. and K. G. Field (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(10): 4571–4574.PubMedCrossRefGoogle Scholar
  3. Besner, M. C., R. Broseus, et al. (2010). Pressure monitoring and characterization of external sources of contamination at the site of the Payment drinking water epidemiological studies. Environ Sci Technol 44(1): 269–277.PubMedCrossRefGoogle Scholar
  4. BrazosRiverAuthority (2006). Lake Granbury Watershed Protection Plan In: Retrieved January 21 2010.
  5. BrazosRiverAuthority (2008). Lake Granbury Water Quality Modeling In: Retrieved January 21 2010.
  6. Casarez, E. A., S. D. Pillai, et al. (2007). Direct comparison of four bacterial source tracking methods and a novel use of composite data sets. J Appl Microbiol 103(2): 350–364.PubMedCrossRefGoogle Scholar
  7. Cotruvo, J. A., A. Dufour, et al., (eds) (2004). Waterborn Zoonoses. IWA Publishing, London.Google Scholar
  8. Dick, L. K., A. E. Bernhard, et al. (2005). Host distributions of uncultivated fecal Bacteroidales bacteria reveal genetic markers for fecal source identification. Appl Environ Microbiol 71(6): 3184–3191.PubMedCrossRefGoogle Scholar
  9. Farnleitner, A. H., H. Stadler, et al. (2008). Methods and strategies for alpine karstic water resource management: opening pollution microbiology’s “black box”. World Water Conference and Exhibition, Vienna, IWA.Google Scholar
  10. Farnleitner, A. H., G. Ryzinska-Paier, et al. (2010). Escherichia coli and enterococci are sensitive and reliable indicators for human, livestock, and wild life faecal pollution in alpine mountainous water resources. J Appl Microbiol. 109(5): 1599–1608.PubMedGoogle Scholar
  11. Farnleitner, A. H., I. Wilhartitz, et al. (2005). Bacterial dynamics in spring water of two contrasting alpine karst aquifers indicate autochthounous microbial endokarst communities. Environmental Microbiology 7: 1248–1259.PubMedCrossRefGoogle Scholar
  12. Fewtrell, L. and J. Bartram, (eds) (2002). Water Quality: Guidlines, Standards and Health. IWA Publishing, Padstone.Google Scholar
  13. Field, K. G., E. C. Chern, et al. (2003). A comparative study of culture-independent, library-independent genotypic methods of fecal source tracking. J Water Health 1(4): 181–94.PubMedGoogle Scholar
  14. Ford, D. C. and P. Williams (2007). Karst hydrogeology and geomorphology. Wiley, New York.Google Scholar
  15. Fujioka, R. S. (2001). Monitoring coastal marine waters for spore-forming bacteria of faecal and soil origin to determine point from non-point source pollution. Water Sci Technol 44: 181–188.PubMedGoogle Scholar
  16. Geldreich, E. E. (1978). Bacterial populations and indicator concepts in feces, sewage, stormwater and solid wastes. In: G. Berg, (ed) Indicators of viruses in water and food Ann Arbor, MI: Ann Arbor Science Publishers, Inc. pp. 51–97.Google Scholar
  17. Grayson, R., P. Kay, et al. (2008). The use of GIS and multi-criteria evaluation (MCE) to identify agricultural land management practices which cause surface water pollution in drinking water supply catchments. Water Sci Technol 59(9): 1797–802.Google Scholar
  18. Griffiths, R. I., A. S. Whiteley, et al. (2000). Rapid method for coextraction of DNA and RNA from natural environments for analysis of ribosomal DNA- and rRNA-based microbial community composition. Appl Environ Microbiol 66(12): 5488–91.PubMedCrossRefGoogle Scholar
  19. Ishii, S. and M. J. Sadowsky (2008). Escherichia coli in the environment: implications for water quality and human health. Microbes and Environments 23: 101–108.Google Scholar
  20. ISO (2000). Water Quality – Detection and Enumeration of Escherichia coli and Coliform Bacteria – Part 1: Membrane Filtration Method (ISO 9308-1: 2000). In: International Organization of Standardization Geneva, Switzerland.Google Scholar
  21. ISO (2000). Water Quality – Detection and Enumeration of Intestinal Enterococci – Part 2: Membrane Filtration Method (ISO 7899-2: 2000). International Organization of Standardization, Geneva.Google Scholar
  22. ISO (2002). Water Quality – Detection and Enumeration of Clostridium perfringens – Part 2: Method by Membrane filtration (ISO/CD 6461-2). International Organization of Standardization, Geneva.Google Scholar
  23. Kollanur, D., Reischer, G.H., Sommer, R., Wehrspaun, C., Stadler, H, Mach, R.L., Zerobin. W. and A. H. Farnleitner (submitted) Quantitative Assessment of Faecal Pollution Sources in Alpine Spring Catchments as a Basis for Microbial Hazard – and Risk Assessment. Water Science and Technology. Google Scholar
  24. Lamendella, R., J. W. Domingo, et al. (2007). Assessment of fecal pollution sources in a small northern-plains watershed using PCR and phylogenetic analyses of Bacteroidetes 16S rRNA gene. FEMS Microbiol Ecol 59(3): 651–60.PubMedCrossRefGoogle Scholar
  25. Lamendella, R., J. W. Santo Domingo, et al. (2009). Evaluation of swine-specific PCR assays used for fecal source tracking and analysis of molecular diversity of Bacteriodales-swine specific populations. Appl Environ Microbiol 75(18): 5507–5513.CrossRefGoogle Scholar
  26. McQuaig, S. M., T. M. Scott, et al. (2009). Quantification of human polyomaviruses JC Virus and BK Virus by TaqMan quantitative PCR and comparison to other water quality indicators in water and fecal samples. Appl Environ Microbiol 75(11): 3379–88.PubMedCrossRefGoogle Scholar
  27. Medema, G. J., S. Shaw, et al. (2003). Catchment characterisation and source water quality In: A. Dufour, M. Snozzi, W. Koster, et al., (ed) Assessing microbial safety of drinking water, IWA Publishing, London.Google Scholar
  28. Reischer, G. H., J. M. Haider, et al. (2008). Quantitative microbial faecal source tracking with sampling guided by hydrological catchment dynamics. Environ Microbiol 10: 2598–2608.PubMedCrossRefGoogle Scholar
  29. Reischer, G. H., D. C. Kasper, et al. (2007). A quantitative real-time PCR assay for the highly sensitive and specific detection of human faecal influence in spring water from a large alpine catchment. Lett Appl Microbiol 44: 351–356.PubMedCrossRefGoogle Scholar
  30. Reischer, G. H., D. C. Kasper, et al. (2006). Quantitative PCR method for sensitive detection of ruminant faecal pollution in freshwater and evaluation of this method in alpine karstic regions. Appl Environ Microbiol 72: 5610–5614.PubMedCrossRefGoogle Scholar
  31. Reischer, G. H., D. Kollanur, et al. (2011). A hypothesis-driven approach for the identification of fecal pollution sources in water resources. Environ Sci Technol 45(9): 4038–4045.Google Scholar
  32. Soller, J. A., M. E. Schoen, et al. (2010). Estimated human health risks from exposure to recreational waters impacted by human and non-human sources of faecal contamination. Water Research 44(16): 4674–4691.Google Scholar
  33. Stadler, H., P. Skritek, et al. (2008). Microbiological monitoring and automated event sampling at karst springs using LEO-satellites. Water Sci Technol 58(4): 899–909.PubMedCrossRefGoogle Scholar
  34. Stadler, H., Klock, E., Skritek, P., Mach, R.L., Zerobin, W. and Farnleitner, A.H. (2010). The spectral absorbance coefficient at 254nm as a near real time early warning proxy for detecting faecal pollution events at alpine karst water resources. Water Sci Technol 62(8): 1898–1906.PubMedCrossRefGoogle Scholar
  35. Teague, A., R. Karthikeyan, et al. (2009). Spatially explicit load enrichment calculation tool to identify potential E. coli sources in watersheds. Transactions of the ASABE 52(4): 1109–1120.Google Scholar
  36. TexasA&MAgriLifeResearch (2006). Watershed Protection Plan Development for Buck Creek, TSSWCB Project # 06-11, Quality Assurance Project Plan. In: Retrieved January 21 2010.
  37. Ufnar, J. A., S. Y. Wang, et al. (2006). Detection of the nifH gene of Methanobrevibacter smithii: a potential tool to identify sewage pollution in recreational waters. J Appl Microbiol 101(1): 44–52.PubMedCrossRefGoogle Scholar
  38. USEPA (2005). Microbial Source Tracking Guide Document. Office of Research and Development, Cincinnati.Google Scholar
  39. USEPA (2006). Method 1603: Escherichia coli (E. coli) in water by membrane filtration using modified membrane-thermotolerant Escherichia coli agar (Modified mTEC). Office of Research and Development, Government Printing Office, Washington.Google Scholar
  40. Versalovic, J., M. Schneider, et al. (1994). Genomic fingerprinting of bacteria using repetitive sequence-based polymerase chain reaction. Methods Mol Cell Biol 5: 25–40.Google Scholar
  41. Vogel, J. R., D. M. Stoeckel, et al. (2007). Identifying fecal sources in a selected catchment reach using multiple source-tracking tools. J Environ Qual 36(3): 718–729.PubMedCrossRefGoogle Scholar
  42. WHO (2004). Guidlines for drinking-water quality. World Health Organisation, Geneva.Google Scholar
  43. Wilhartitz, I., A. K. T. Kirschner, et al. (2009). Prokaryotic production in karstic alpine spring aquifers and their ecological implications. FEMS Microbiol Ecol 68(3): 287–299.PubMedCrossRefGoogle Scholar
  44. Winter, C., T. Hein, et al. (2007). Longitudinal Changes In The Bacterial Community Composition Of The Danube River: A Whole River Approach. Appl Environ Microbiol 73: 421–431.PubMedCrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media, LLC 2011

Authors and Affiliations

  • Andreas H. Farnleitner
    • 1
    • 2
  • Georg H. Reischer
  • Hermann Stadler
  • Denny Kollanur
  • Regina Sommer
  • Wolfgang Zerobin
  • Günter Blöschl
  • Karina M. Barrella
  • Joy A. Truesdale
  • Elizabeth A. Casarez
  • George D. Di Giovanni
  1. 1.Institute of Chemical Engineering, Research Area Applied Biochemistry and Gene Technology, Research Group Environmental Microbiology and Molecular EcologyVienna University of TechnologyViennaAustria
  2. 2.InterUniversitary Cooperation Centre for Water and Health (ICC Water & Health)Vienna University of TechnologyViennaAustria

Personalised recommendations