Table 2.

Frequencies of the 16S rRNA genes of “Ca. Nitrospira defluvii” and other bacteria in clone libraries established with and without preceding treatment by LNAzymes^e

Treatmenta	No. of distinct RFLP patterns (no. of singletons)d	No. of clones assigned to “Ca. Nitrospira defluvii”	No. of clones assigned to other bacteria	Frequency of “Ca. Nitrospira defluvii” (%)	Good's coverage (%)	Simpson diversity index
Untreated DNA 907R	4 (2)	40	11	78.4	96.1	0.36
DNA 907Rb	12 (5)	3	39	7.1	88.1	0.8
RNA 907Rc	14 (9)	9	35	20.5	79.6	0.76
RNA 1492Rc	14 (9)	1	45	2.2	80.4	0.84

^aDNA, DNA was used as the initial template; RNA, RNA was used as the initial template. 907R and 1492R are the reverse primers used for 16S rRNA gene-specific PCR.

^bTreatment by LNAzyme Ntspa668 prior to cloning.

^cTreatment by LNAzyme Ntspa665 prior to cloning.

^dSingletons are RFLP patterns that occurred only once.

^eAssignments of cloned genes to “Ca. Nitrospira defluvii” or other bacteria were based on RFLP band patterns, exploiting the fact that “Ca. Nitrospira defluvii” has a characteristic RFLP pattern after digestion of its 16S rRNA gene amplicon with the endonuclease MspI (this was confirmed by sequencing of selected clones showing this RFLP pattern).