Figure 1.
Relative gene abundances of Bacteria and Thaumarchaetoa in aquaria.
Relative 16S rRNA (A) and amoA (B) gene abundances for bacteria and thaumarchaea in saltwater (SW1–SW8) and freshwater (FW1–F27) aquaria and in aquarium supplements (SP1, SP2). These data were calculated from duplicate qPCR amplifications.
Figure 2.
Freshwater aquaria ammonium concentrations and relative thaumarchaeal amoA gene abundances.
AOA amoA gene copies are expressed as a percentage of the total amoA gene copies (per ng DNA). The coefficient of determination (R2) for the linear regression is 0.7249. The associated Pearson correlation coefficient (r) is −0.8518, with an associated p-value of <0.001. See Table S1 for all sample data.
Figure 3.
Denaturing gradient gel electrophoresis of thaumarchaeal amoA gene amplicons.
Saltwater (A) and freshwater (B) fingerprints have been normalized and aligned. Bands chosen for sequencing are indicated with triangles: white triangles correspond to bands appearing in Figure 4. Black triangles represent failed sequencing reactions. Clustering of freshwater and saltwater fingerprints (C) is based on nonmetric multidimensional scaling (NMDS) using Pearson correlations of background-subtracted densitometric curves.
Figure 4.
NMDS ordination of translated thaumarchaeal amoA gene sequences.
Sequences were obtained from clone libraries and DGGE bands derived from freshwater and saltwater aquarium filter samples. The inset panel provides a summary of the number of freshwater and saltwater clone library sequences contained within each cluster. Sequences obtained from DGGE bands correspond to the white triangles in Figure 3, and are labelled with sample and band numbers. Selected Genbank sequences from uncultivated clones and reference strains are included for comparison. The sampling environment and Genbank accession numbers for all reference sequences are included within parentheses.