Figure 1.
Sampling sites for Lake Superior (A) and Lake Erie (B) sediments.
Table 1.
Environmental data from the sediment samples and the overlaying water.
Figure 2.
Abundance (amoA gene copy number) of AOA and AOB in the sediment of Lake Erie and Superior (mean ± SD, n = 3; different letters above the columns indicate significant differences between samples determined by one-way ANOVA followed by Tukey test; p<0.05).
Figure 3.
Alpha-diversity at 98% identity and singletons removed of the AOA and AOB amoA sequence libraries.
(mean ± SD, n = 100 rarefactions; different letters in figure A above the columns indicate significant differences between samples determined by one-way ANOVA followed by Tukey test; p<0.05; data for AOA and AOB were tested separately).
Table 2.
Pearson correlations of AOA and AOB abundances with environmental and alpha diversity data.
Figure 4.
Relative frequency [%] of the AOA in the different phylogenetic groups.
Representative sequences were picked based on 98% identity, aligned in ARB to the AOA tree published by Pester et al. (2012) and assigned to different phylogenetic groups. Cultivated members of the AOA can be found in Nitrosopumilus cluster 1.1: Nitrosopumilus maritimus, Candidatus Nitrosoarchaeum limnia, Candidatus Nitrosoarchaeum korensis MY1 and Enrichment AOA-AC2; Nitrosopumilus cluster 5: Enrichments AOA-AC1, AOA-AC5 and AOA-DW. Most cultivated strains are integrated in Figure S3.
Figure 5.
Relative frequency [%] of the AOB in the different phylogenetic groups.
Representative sequences were picked based on 98% identity, aligned in ARB and assigned to phylogenetic groups.
Figure 6.
UPGMA clustering of Weighted Unifrac distances (A) and Jaccard abundances (B) of AOA in the sediment of Lake Erie and Superior at 98% similarity.
Numbers at the nodes represent statistical analysis of 100 rarefactions.
Figure 7.
Canonical correspondence analysis (CCA) triplot (arrows: environmental variables; circles: samples; triangles: species) for quantitative data as presented in Fig. 3 of the AOA amoA sequence libraries in Lake Erie and Superior (Eigenvalues: Axis 1: 0.5865, Axis 2: 0.0421, Axis 3: 0.0073).
Explanatory value of the environmental factors was determined using forward selection: AOA_log explained 47%; ammonium concentration 18.3% and nitrate concentration 0.8% of the variation. (Abbreviations: Npum11: Nitrosopumilus subcluster 1.1; Npum51: Nitrosopumilus subcluster 5.1; Npum15: Nitrosopumilus subcluster 15; Nspae21: Nitrososphaera subcluster 2.1; Nspae32: Nitrososphaera subcluster 3.2; Nspae41: Nitrososphaera subcluster 4.1; Nspae51: Nitrososphaera subcluster 5.1; Nspae7: Nitrososphaera subcluster 7; Nspae81: Nitrososphaera subcluster 8.1; Nspae9: Nitrososphaera subcluster 9; Nspae11: Nitrososphaera subcluster 11; NspaeX: Nitrososphaera subcluster diverse; Ntalea: Nitrosotalea subcluster 2)