Table 2. Abundances of the 22 operational taxonomic units (OUTs) with a maximum intra-group distance of 5% (AA) in the clone library.

OTU	Affiliation	TRF	Start, DNA	Control, mRNA	CH3F 3.85%, mRNA
1	Msarc	139	15	40	42
2	Mcell	139	6	0	0
3	Mcell	138	6	0	0
4	Mcell	139	1	0	0
5	Mcell	139	5	0	0
6	Mbac	760	10	0	0
7	Mbac	131	3	0	0
8	Mbac	760	3	0	0
9	Mbac	666	1	0	0
10	Mbac	666	1	0	0
11	Mcell	138	10	3	0
12	NN	139	1	0	2
13	Msaeta	131	2	0	0
14	Fen	139	1	0	0
15	Msarc	139	1	0	0
16	Mbac	733	1	0	0
17	Mbac	760	1	0	0
18	Mcell	138	1	0	0
19	Mcell	138	0	1	0
20	Msarc-like	139	0	2	0
21	Mcell	139	0	0	1
χ2 test,simulated p-values				Control, mRNA	CH3F, mRNA
Start, DNA				0.0001	0.0001
Control, mRNA					0.05

Clones were derived from samples taken before (‘start’, based on DNA) and after (‘control’ and 3.85% CH₃F, based on transcripts) anoxic incubation for 14 days. OTU number and affiliation to families are given as in Figure 4. Msarc: Methanosarcinaceae, Mcell: Methanocellales, Mbac: Methanobacteriales, Msaeta = Methanosaetaceae, Fen = Fen cluster, Msarc-like = uncertain affiliation, but nearest to Methanosarcinaceae; NN = unknown cluster. Simulated p-values are from a Monte-Carlo simulation with 9999 replicates.