Table 1.
Diversity, phylogenetic affiliation and relative abundance of AOA and AOB clones from three sites along the BUS transect
| GeoB12815 | GeoB12811 | GeoB12807 | |||
|---|---|---|---|---|---|
| Ammonia‐oxidizing Archaea (amoA a) | Diversity measures | Simpson's index of diversity | 0.75 | 0.7 | 0.61 |
| Shannon‐Wiener index | 1.6 | 1.35 | 1.15 | ||
| Richness | 9 | 6 | 7 | ||
| Chao1 | 13 | 6 | 11 | ||
| Phylogeny | Nitrosopumilus cluster | 5% | 16% | 50% | |
| Nitrososphaera cluster | 10% | 6% | 37% | ||
| Cluster A | 49% | 29% | 0% | ||
| Cluster B | 0% | 0% | 6% | ||
| Cluster C | 1% | 0% | 3% | ||
| Cluster D | 28% | 44% | 3% | ||
| Cluster E | 7% | 4% | 0% | ||
| Total number of clones (n) | 87 | 93 | 78 | ||
| Ammonia‐oxidizing Bacteria (amoA b) | Diversity measures | Simpson's index of diversity | 0.22 | 0 | 0.59 |
| Shannon‐Wiener index | 0.68 | 0 | 1.14 | ||
| Richness | 3 | 1 | 5 | ||
| Chao1 | 3 | 1 | 5 | ||
| Phylogeny | Sister cluster of Nitrosospira cluster | 100% | 100% | 100% | |
| Total number of clones (n) | 88 | 96 | 80 | ||
| Ammonia‐oxidizing Bacteria (16S rRNAc) | Diversity measures | Simpson's index of diversity | 0.55 | 0.16 | 0.52 |
| Shannon‐Wiener index | 0.89 | 0.44 | 0.95 | ||
| Richness | 4 | 7 | 7 | ||
| Chao1 | 4 | 19 | 15 | ||
| Phylogeny | Nitrosospira cluster 1 | 100% | 100% | 99% | |
| Total number of clones (n) | 91 | 83 | 88 |
Based on 635 bp archaeal amoA gene fragment obtained with the primer set Arch‐amoAF and Arch‐amoAR (Francis et al., 2005).
Based on 491 bp bacterial amoA gene fragment obtained with the primer set amoA‐1F/amoA‐2R (Rotthauwe et al., 1997).
Based on 510–514 bp betaproteobacterial AOB 16S rRNA gene fragment obtained with primer set CTO189fA‐B‐C/CTO654r (Kowalchuk and Stephen, 2001).
Diversity measures were calculated based on OTU clustering using a 13% sequence divergence cut‐off for archaeal amoA (Pester et al., 2012), an 8% cut‐off for bacterial amoA (this study; Fig. S1) and a 1% cut‐off for 16S rRNA genes (Ebers and Stackebrandt, 2006). Chao1 analysis was performed using EstimateS 9.1.0 (Colwell, 2013). Phylogenetic affiliation of amoA and 16S rRNA gene clones is based on consensus phylogeny of maximum likelihood (RAxML version 7.4.2; Stamatakis et al., 2008), maximum parsimony, and neighbour joining (both phylip 3.69; Felsenstein, 2005) analyses (Figs S2–S4). Sequences are available under European Nucleotide Archive Accession Numbers LK055903‐LK056644 and LK392634‐LK392675.