Table 1.

Comparison of different target sites in rDNA and functional enzyme sequences: probes targeting the internal transcribed spacer sequences (ITS) regions of rRNA and conserved domains in functional enzymes together constitute the dual probe set (DPS). The classical GeoChip approach is also indicated.

	rDNA repeat	Functional enzymes
Structural organization	SSU/5.8/LSU	ITS1/2	conserved domains (e.g., active sites, structural determinants)	less conserved regions
Complexity of metagenomes	low	high	low	high
Amounts of molecules in total RNA	high (as mature and precursor rRNA)	low (only as precursor rRNA)	between different genes)
resolution	medium to low	high	low	high
Probe set		↳  DPS ↲	“GeoChip”