Table 2. Comparison of methanotroph genera detected in three samples based on three methods.

	Methanotroph reads	Methylocaldum/Methylococcus	Methylomonas	Methylobacter/Methylosoma/other type 1A	Methylosinus	Methylocystis
Pond B 07/10/10 16S pyrotag	76	85.4	1.6	8.0	0	0
Pond B 07/10/10 pmoA pyrotag	2523	98.0	0.24	1.6	0.078	0.039
Pond B 07/10/10 microarray		++	++	++	++	+
Pond A 07/10/10 16S pyrotag	496	94.4	1.9	4.6	0	0
Pond A 07/10/10 pmoA pyrotag	5279	99.8	0.038	0	0.11	0
Pond A 07/10/10 microarray		++	++	++	−	−
Pond A 23/11/10 16S pyrotag	488	65.5	23.0	8.4	0	0
Pond A 23/11/10 microarray		++	++	++	+	−

The ‘Methanotroph reads' column refers to the number of methanotrophs in the total pyrotag sequence data sets (that is, only 16S rRNA gene sequences belonging to methanotroph clusters or only pmoA rather than amoA genes). Numbers under the genera columns refer to percentage of the reads belonging to each genus. For microarray data,+represents a weak positive signal and ++ a strong positive signal (Supplementary Figure S2).