Supplementary Table S1. Phylogenetic inference of pmoA/amoA sequences from Vercelli rice fields (n = 500) (Lüke et al., 2009) and the detection by the different reverse primers A682r and mb661r . Environmental clusters were named according to representative clones and/or to the denotation of probes as used for a pmoA specific diagnostic microarray (Bodrossy et al., 2003; Lüke et al., 2009). Resulting terminal restriction fragments (TRFs) from T-RFLP analysis are shown. TRFs of methanotrophs represent genera, clusters, and species. Therefore, each TRF was handled as a methanotrophic operational taxonomic unit (OTU). TRF size was previously cross-checked by TRFLP analysis of clones.

Genus/Cluster / Type / Reverse primer / OTUs
mB661r / A682r / TRF length in bp
Methylomonas / Ia / + / + / 437
Methylobacter LW12/BB5.1 / Ia / + / - / 505, 531
Methylosarcina fibrata/lacus / Ia / + / - / 208, 241, 349, 437, 456
LP20 / Ia / - / + / 437, 505, 531
Methylocaldum / Ib / + / + / 79
Methylocaldum related / Ib / + / + / 79, 226
RPC-1 / Ib / + / + / 79
LW21 / Ib3 / + / - / 79
Methylocystis/Methylosinus / II / + / + / 244
MO3 / II / - / + / 335
pmoA-21 / II / - / + / 278
TUSC / Others3 / - / + / 335, 79
RA21 / Others3 / - / + / 58
M84-P22 / Others3 / - / + / 114, 226
M84-P105 / Others3 / - / + / 334, 79, 226,373
Ammonia oxidizers2 / AOB / - / + / 46, 114

1The pmoA2 is a second copy of the pmoA in a single genospecies; it encodes a subunit of a particulate methane monooxygenase (Dunfield et al., 2002). This enzyme possesses different oxidation kinetics (Baani and Liesack, 2008) 2The amoA of ammonium-oxidizing bacteria is homologous to pmoA and is partially covered by A682r 3 The sequences cluster between methanotroph pmoA and amoA sequences from ammonium oxidizers and lack cultivated representatives 4not detected in this analysis

Reference List

Baani M, Liesack W. (2008). Two isozymes of particulate methane monooxygenase with different methane oxidation kinetics are found in Methylocystis sp strain SC2. Proc Natl Acad Sci USA105: 10203-10208.

Bodrossy L, Stralis-Pavese N, Murrell JC, Radajewski S, Weilharter A, Sessitsch A. (2003). Development and validation of a diagnostic microbial microarray for methanotrophs. Environ. Microbiol.5: 566-582.

Dunfield PF, Yimga MT, Dedysh SN, Berger U, Liesack W, Heyer J. (2002). Isolation of a Methylocystis strain containing a novel pmoA-like gene. FEMS Microbiol Ecol41: 17-26.

Lüke C, Krause S, Cavigiolo S, Greppi D, Lupotto E, Frenzel P. (2009). Biogeography of wetland rice methanotrophs. Environ Microbiol (in press).