Comparison of extraction methods applicable to fungal spores in faecal samples from small mammals

Schickmann S., Kräutler K., Kohl G., Nopp-Mayr U., Krisai-Greilhuber I., Hackländer K. & Urban A. (2010) Comparison of extraction methods applicable to fungal spores in faecal samples from small mammals.

Sydowia 63(2): 237–247

Mycophagy is often underestimated as dietary strategy, but forms an important part of the webs of life, especially in forest ecosystems. The identification of consumed fungal species is crucial to gain more knowledge about food web structures. DNA based methods are the way of choice to overcome limitations of species determination by microscopic analysis. DNA extraction from fungal spores in faecal samples requires specific methodology, due to the resistance of fungal spores and due to the properties of the faecal matrix.
We tested two open source extraction buffers, as well as one widely used commercial extraction kit in combination with a mechanical disruption procedure optimised for fungal spores in faecal samples. The efficiency of the DNA extraction was assessed by comparing DNA yield after amplification by PCR with fungus-specific primers. All three protocols were successful in extracting amplifiable fungal DNA. The CTAB protocol yielded the highest amounts of DNA after PCR and gave the most constant results, but the differences among protocols were not significant. The establishment of reliable protocols for DNA extraction from small quantities of fungal spores in faecal samples paves the way for high resolution non-invasive studies in the dietary ecology of wild-living mammals.

Keywords: mycophagy, dietary ecology, DNA isolation, environmental microbiology