The Importance of DNA Quality and Primers in Comparative Soil Faunal Community Structure Analyses.

Molecular techniques significantly advance our ability to understand the biodiversity of soil fungi and animals.  Commonly encountered problems in amplifying soil faunal DNA is the lack of efficiency of DNA extraction and the suitability of that DNA for PCR amplification.  Using CTAB combined with a column purification method, we obtained soil DNA that successfully amplifies soil faunal 18S rDNA.  Another limitation is a suitable primer set amplifying a broad range of soil animal without amplifying other eukaryotes.  We developed primers (11b, 11c, 11d and 11e) to amplify the 18S rRNA gene from a broad array of animals.  We also tested the ability of the primers in amplifying eukaryotes including arthropods, nematodes, rotifers, tardigrades and algae.  The soil animal specific primers will provide new tools to increase our understanding of soil animal biodiversity.