Ammonia-oxidizing Bacteria of the Nitrosospira cluster 1 dominate over ammonia-oxidizing Archaea in oligotrophic surface sediments near the South Atlantic Gyre

Abstract

Sediments across the Namibian continental margin feature a strong microbial activity gradient at their surface. This is reflected in ammonium concentrations of < 10 μM in oligotrophic abyssal plain sediments near the South Atlantic Gyre compared with ammonium concentrations of > 700 μM in upwelling areas near the coast. Here we address changes in apparent abundance and structure of ammonia-oxidizing archaeal and bacterial communities (AOA and AOB) along a transect of seven sediment stations across the Namibian shelf by analysing their respective ammonia monooxygenase genes (amoA). The relative abundance of archaeal and bacterial amoA (g(-1) DNA) decreased with increasing ammonium concentrations, and bacterial amoA frequently outnumbered archaeal amoA at the sediment-water interface [0-1 cm below seafloor (cmbsf)]. In contrast, AOA were apparently as abundant as AOB or dominated in several deeper (> 10 cmbsf), anoxic sediment layers. Phylogenetic analyses showed a change within the AOA community along the transect, from two clusters without cultured representatives at the gyre to Nitrososphaera and Nitrosopumilus clusters in the upwelling region. AOB almost exclusively belonged to the Nitrosospira cluster 1. Our results suggest that this predominantly marine AOB lineage without cultured representatives can thrive at low ammonium concentrations and is active in the marine nitrogen cycle.

Figure 1

Bathymetric map of the Benguela upwelling system. Sampling sites on a cross‐slope transect. Organic‐rich surface sediments (total organic carbon content higher than 10%) are indicated by shading (data from Inthorn et al., 2006). Modified from Goldhammer and colleagues (2011). Representative bottom water temperatures (from Mohrholz et al., 2008) are given at the respective sites. Oceanographically, the stations represent the abyssal plain (GeoB12815), the continental rise (GeoB12808, GeoB12811), the continental slope (GeoB12803, GeoB12802), the shelf break (GeoB12807) and the shelf (GeoB12806). Surface sediments were recovered by gravity and multi‐coring. Sediment samples were transported on dry ice to Aarhus University, Denmark, where they were stored at −80°C until processed further.

Figure 2

Sediment pore water concentrations of ammonium, estimated rates of organic matter re‐mineralization, and abundance of prokaryotes and ammonia oxidizers. A. Sediment pore water concentrations of ammonium (NH ₄ ⁺). White data points represent ammonium concentrations below the detection limit (see Appendix S1). Smooth pore water profiles (grey lines), ammonium fluxes and volumetric rates of ammonium production were calculated by fitting transport‐reaction models to the measured pore water profiles according to Berg and colleagues (1998). Ammonium fluxes (μmol m⁻² day⁻¹) to the top 1 cm are shown in grey‐shaded boxes. Grey‐shaded data points were excluded from model fitting. The predicted O ₂ penetration depth (Table S1) is indicated by the hatching pattern. Ammonium values were analysed onshore (for detailed methods, see Goldhammer et al., 2011). B. Sum of archaeal and bacterial 16S rRNA gene copy numbers g⁻¹ of sediment. Overlaid grey and black bars represent the relative abundance of bacterial (grey) and archaeal (black) 16S rRNA gene copies (in %, not log scale). Gene copy numbers were determined by qPCR on DNA extracted after removal of extracellular DNA (see Appendix S1). Primer sets were 806F (Takai and Horikoshi, 2000)/958R (DeLong, 1992) for Archaea, and Bac8F (Reysenbach et al., 1994)/Bac338Rabc (Daims et al., 1999) for Bacteria. Quantitative PCR was performed in technical triplicates, which were averaged. C. Abundance of archaeal (black lines and symbols) and bacterial (grey lines and symbols) amoA gene copy numbers g⁻¹ of sediment. Averages of technical qPCR triplicates are depicted as symbols. Different symbols of the same colour represent results from replicate DNA extractions, i.e. a black square and a black triangle at the same depth represent archaeal amoA gene copy numbers from two different DNA extracts. Lines connect the average values for each depth. The ratios between bacterial and archaeal amoA gene copy numbers are shown for each depth in grey‐shaded boxes. Primers Arch‐amoAF and Arch‐amoAR (Francis et al., 2005) and amoA‐1F and amoA‐2R (Rotthauwe et al., 1997) were used for archaeal and bacterial amoA gene quantification respectively.

Figure 3

Relative abundance of amoA along the transect. Gene copy numbers of bacterial (grey circles) and archaeal (black triangles) amoA (g⁻¹ DNA) as determined by qPCR (for exact values, see Table S3). Data points for a given water depth and station represent the different sediment depths analysed at that station. The lines connect the average values across sediment depths for bacterial (grey) and archaeal (black) amoA copy numbers.