Using genetic microbial source tracking (MST) markers to identify fecal pollution sources in spring water of a large alpine karst catchment

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Rita Linke (Vienna University of Technology Institute of Chemical Engineering)Andreas Farnleitner (TU Wien, Karl Landsteiner University )



  • Apply MST markers as E. coli does not provide information on fecal pollution sources
  • Support water resource management (SDG 6.5) by genetic MST marker detection
  • Identified animals instead of suspected human sewage disposal as emission sources
  • Demonstrate how to generate robust MST information at head water catchments
  • Tiered MST approach as interface between E. coli diagnostics and QMRA

Management objective

Fecal pollution analysis still relies on cultivation-based E. coli and intestinal Enterococci (FIB) standard methods. However, these approaches do not give information on the kind of pollution sources. This study demonstrates how to identify pollution sources based on the application of genetic microbial source tracking (MST) markers at alpine spring water to guide target-oriented catchment protection and management.

Location and description of the system

The study site is located in the Northern Calcareous Alps (Austria) and drains a large Triassic limestone aquifer between 820 and 1828 m (catchment approx. 70 km2). Vegetation comprises summer pastures, natural calcareous alpine swards with open krummholz and forests. Potential fecal pollution sources include humans, livestock (cattle) and wild life. During base-flow conditions the observed spring has excellent water quality. In contrast, heavy rain events can result in high FIB concentrations.

Description of the method

The integrated multi-tiered approach covers, i) pollution source profiling using information from catchment survey activities, ii) hypothesis formulation on the potentially important fecal pollution sources and MST assay selection, and finally iii) hypothesis testing at the spring using hydrology-driven sampling and data stratification with concurrent analysis of FIB and genetic MST markers.

Outcome and recommendations

  • FIB could be traced back to animal fecal pollution sources (ruminants). Despite of being initially suspected, human sewage was not identified as the source of contamination.
  • Results verified catchment protection measures and also guided further hazard and risk assessment activities.
  • The tiered approach proved very valuable for MST. It is also suitable for the application in other complex headwater catchments, since the used parameters and methods can be adapted to the specific situation.


This paper was supported by Vienna Water (MA31) and the Austrian Science Fund (FWF) P23900-B22. This is a joint study effort of the ICC Water & Health (