Archaeal amoA and ureC genes and their transcriptional activity in the Arctic Ocean

Abstract

Thaumarchaeota and the gene encoding for a subunit of ammonia monooxygenase (amoA) are ubiquitous in Polar Seas, and some Thaumarchaeota also have a gene coding for ureC, diagnostic for urease. Using quantitative PCR we investigated the occurrence of genes and transcripts of ureC and amoA in Arctic samples from winter, spring and summer. AmoA genes, ureC genes and amoA transcripts were always present, but ureC transcripts were rarely detected. Over a 48 h light manipulation experiment amoA transcripts persisted under light and dark conditions, but not ureC transcripts. In addition, maxima for amoA transcript were nearer the surface compared to amoA genes. Clone libraries using DNA template recovered shallow and deep amoA clades but only the shallow clade was recovered from cDNA (from RNA). These results imply environmental control of amoA expression with direct or indirect light effects, and rare ureC expression despite its widespread occurrence in the Arctic Ocean.

Figure 1. Number of MG1 rRNA, ureC and amoA transcripts from winter Amundsen Gulf waters.

Standard errors of triplicates were smaller than the size of the symbols. The abbreviation for the month is followed by relative depth of collection: surface (S) or halocline (H).

Figure 2. Number of MG1 rRNA and amoA transcripts in the light manipulation experiment from Lancaster Sound samples, which were collected at 25 m (25% surface irradiance) and 80 m (1% surface irradiance).

Light treatment (L, open symbols), dark treatment (D, closed symbols).

Figure 3. Depth profiles of Northern Baffin Bay Stations 129, 123 and 109.

Density (sigma theta) is indicated by the solid black line, circles embedded in these lines show sample depths for DNA and RNA (open circles) and for DNA only (filled circles). In situ chlorophyll fluorescence (relative units) is shown by the green line and oxygen concentrations (μmol kg ⁻¹) by the dotted line.

Figure 4. Nitrate (solid lines with open circles) and nitrite (dotted line with open triangles) concentrations down the water column (μmol L⁻¹), note log scale for depth.

Bars indicate copies mL⁻¹ of amoA from cDNA.

Figure 5

Panel (a) Northern Baffin Bay, qPCR copies mL⁻¹ of MGI, amoA and ureC genes (DNA template). Station number and depth of sampling are indicated along the X axis. Panel (b) Log-log plots of gene copies of ureC (open circles) and amoA (closed circles) compared the 16S rRNA genes of MGI. Lines indicate significant linear regressions of the log transformed data; the dashed line is ureC versus MG1 (r² = 0.76, p < 0.001), the solid line is amoA versus MGI (r² = 0.78, p < 0.001). Standard errors of triplicates and standards were smaller than the size of the symbols.

Figure 6. Distance tree of the amoA gene from the Northern Baffin Bay.

Major clades A and B from (Francis et al. 2005) are indicated; A.a coincides with A in Kalanetra et al. (2009). All reference sequences except N. maritimus were from open water (Francis et al. 2005). Sequence names in this study consist of station number and sample depth followed by d for DNA or r for RNA (from cDNA).