TABLE 1.

Primer sequences used in this study for specific amplification of 18S rRNA gene sequences from environmental DNA^a

Primer set	Primer	Sequence (5′-3′)	Reference
1	EukA	AAC CTG GTT GAT CCT GCC AGT	51
	EukB	TGA TCC TTC TGC AGG TTC ACC TAC	51
2	Euk82F	GAA DCT GYG AAY GGC TC	40
	U1391R	GGG CGG TGT GTA CAA RGR	37
3	Euk360F	CGG AGA RGG MGC MTG AGA	51
	U1517R	ACG GCT ACC TTG TTA CGA CTT	66
4	18S-6-Cil-F	AAY CTG GTT GAT CCT GCC AG	28
	18S-1101-Cil-R	AGG YTR AGG TCT CGT TCG TT	28

^aMixed base sites are designated according to the IUB code. F, forward; R, reverse; Cil, ciliate specific; Euk, eukaryote specific; U, universal. The numbers refer to Escherichia coli 16S rRNA gene positions. Primer EukA is a forward primer referring to Saccharomyces cerevisiae 18S rRNA gene positions 2 to 22. Primer EukB is a reverse primer referring to S. cerevisiae 18S rRNA gene positions 1795 to 1772. In the OTU analysis of the pooled data sets only overlapping regions were considered in each case. A figure showing the fragment overlaps between the different primer sets is provided in the supplemental material.