Patchy-distributed ciliate (Protozoa) diversity of eight polar communities as determined by 454 amplicon pyrosequencing

To determine ciliate diversity and community structure in the polar ecosystem efficiently, we applied the pyrosequencing technique to the polar samples. To select the appropriate sequencing depth using a ciliate-specific primer, we evaluated different pyrosequencing depths, ranging 4149–112,306 reads. At a 3% distance cutoff for clustering, 750 operational taxonomic units (OTUs) were identified, and 332 were composed of a single read (singletons). The singletons showed a 1.8-fold increase in OTU richness, although their beta diversity showed no significant changes. The ratio of singletons in each sequencing depth was sharply decreased after reaching the sequencing depth of approximately 10,000 reads, and the singletons did not completely disappear even at 73,435 qualified reads. The data set without singletons showed saturated trends in rarefaction curves. In addition, we built a normalized data set without the singletons (1227 reads × eight samples). Among the samples, one brackish water having a broad r...