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emi12194-sup-0001-si.tif92K

Fig. S1. Rank-abundance distribution of amplicon data sets from the three different depths screened for ciliate phylotype diversity in Piburgersee in March 2011. The distribution follows a long-tail distribution, typically for large environmental amplicon data sets.

emi12194-sup-0002-si.tif68K

Fig. S2. Log-regression of relative abundances of amplicon ciliate genera and morphotype ciliate genera. Abundance distributions are incongruent and do not correlate, suggesting that amplicon read abundances do not reflect morphotaxon (organismic) abundances.

emi12194-sup-0003-si.docx38K

Table S1. ‘Candidatus ciliate genera’ that were detected through V4 SSU rDNA amplicons in data sets from the three different depths screened for ciliate phylotype diversity in Piburgersee in March 2011. Amplicons were assigned to a ‘candidatus genus’ status when the maximum sequence similarity to a reference sequence database of described ciliate morphotypes did not exceed 95%.

Table S2. Ciliate genera and number of species (in brackets) detected in Piburgersee on 1 March, 2011 in order of relative frequency (mean abundance in ind. l−1 over the three sampling depths) and abundance in the respective depth. n = 6 (0 m, 9 m), n = 3 (21 m), n.d., not detected.

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