Table 2. Potential susceptibility of current methods to biases and other limitations for assessing protist community composition in environmental samples.

	PCR clones/454 tags	Metagenomics	qPCR	FISH	SAGs
Sources of potential biases
Cell permeability	+	+	+	+	+
Gene copy number	++	++	++	−	−
Primers and probes	++	−	++	++	+
Cloning efficiency	+/−	+	−	−	−
Ribosome number	−	−	−	+	−
Inadequate controls (false positives)	−	−	++	++	−
Other limitations
Low phylogenetic resolution	+/++	+	−	+	−
High cost per sample	−	+	+	++	+
Specialized equipment needed	−/+	+	+	−	++

Abbreviations: FISH, fluorescence in situ hybridization; qPCR, quantitative real-time; SAG, single amplified genome.

The susceptibility is designated as high (++), moderate (+) or absent (−).