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Fig. S1. Maximum-likelihood phylogenetic tree for the 16S rRNA gene of all SAGMAGC-1 sequences found in NCBI (search Nov 2012). GenBank accession numbers are shown for each sequence. Scale bar, 10% estimated divergence.

Fig. S2. Agarose gel electrophoresis analysis of SAGMGC-1 16S rRNA and amoA genes amplified using different combinations of the newly designed specific primers in lakes Bergús, Granotes and Redon, and in clones containing the target sequences. Electrophoresis was carried out at 110 V for 45 min, and the gels were stained with ethidium bromide (2 mg ml−1).

Fig. S3. Agarose gel electrophoresis analysis of amoA gene amplification after different combinations of the newly designed specific primers and different clones containing target and non-target sequences. Negative results were obtained in all the combinations with non-target clones. Electrophoresis was carried out at 110 V for 45 min, and the gels were stained with ethidium bromide (2 mg ml−1).

Table S1. Accession numbers for the 16S rRNA and amoA genes sequences used for designing specific primers targeting SAGMGC-1 and AOA ecotypes.

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