Additional file 1: of The application of high-throughput sequencing technology to analysis of amoA phylogeny and environmental niche specialisation of terrestrial bacterial ammonia-oxidisers

Figure S1. Full amoA (A) and 16S rRNA (B) gene trees for the bacterial ammonia oxidiser reference sequences. Figure S2. Congruence of amoA and 16S rRNA gene phylogenetic trees for the bacterial ammonia oxidiser reference sequences. Shades of blue indicate similarity between the most common nodes between the two trees. Figure S3. Full bacterial amoA gene tree including the environmental sequences (assembled using the MiSeq ‘Assembly’ pipeline) and the reference sequences. Figure S4. Congruence between two phylogenetic trees of 370 archaeal amoA sequences (see Gubry-Rangin et al., 2015) with (A) or without (B) the sequence gap corresponding to the MiSeq AOA gap pipeline. Branch colour corresponds to congruence between the two trees. Table S1. Identification of sequences of the 56 terrestrial Nitrosospira AOB strains used in this study. For strains with > 1 copy, only the sequences used in this study presented. n.a. – not applicable. Table S2. Statistical results of the canonical correspondence and permutation analyses performed on the AOB amoA communities clustered at different identity cut-offs. Table S3. Number of sequences and richness of AOA and AOB amoA sequences retrieved in each Craibstone soil sample with different sequencing technologies, with or without rarefaction to the smallest number of sequences obtained in one of the two technologies. Table S4. Characteristics of the 33 UK soils (26 CEH followed by 7 Craibstone soils) used in the multivariate statistics analysis. (DOCX 1560 kb)