Low-ammonia niche of ammonia-oxidizing archaea in rotating biological contactors of a municipal wastewater treatment plant

Abstract

The first step of nitrification is catalysed by both ammonia-oxidizing bacteria (AOB) and archaea (AOA), but physicochemical controls on the relative abundance and function of these two groups are not yet fully understood, especially in freshwater environments. This study investigated ammonia-oxidizing populations in nitrifying rotating biological contactors (RBCs) from a municipal wastewater treatment plant. Individual RBC stages are arranged in series, with nitrification at each stage creating an ammonia gradient along the flowpath. This RBC system provides a valuable experimental system for testing the hypothesis that ammonia concentration determines the relative abundance of AOA and AOB. The results demonstrate that AOA increased as ammonium decreased across the RBC flowpath, as indicated by qPCR for thaumarchaeal amoA and 16S rRNA genes, and core lipid (CL) and intact polar lipid (IPL) crenarchaeol abundances. Overall, there was a negative logarithmic relationship (R(2) =0.51) between ammonium concentration and the relative abundance of AOA amoA genes. A single AOA population was detected in the RBC biofilms; this phylotype shared low amoA and 16S rRNA gene homology with existing AOA cultures and enrichments. These results provide evidence that ammonia availability influences the relative abundances of AOA and AOB, and that AOA are abundant in some municipal wastewater treatment systems.

Fig. 1

Outline of the sampling site in Guelph, Ontario. Internal medium of an RBC (A), an external view of a full RBC treatment train (B) and a schematic of the RBC arrangement in the Guelph WWTP (C).

Fig. 2

Ammonium concentrations of wastewater (A) and thaumarchaeal amoA and 16S rRNA gene abundances in associated biofilm samples (B) across RBC flowpaths. Error bars represent standard deviations based on technical duplicates; error bars that are not seen are contained within the symbols, except for ammonium concentrations in the February NE treatment train, for which duplicate measurements are not available.

Fig. 3

Ammonium concentrations of RBC-associated wastewater and relative abundance of archaeal amoA genes (as a per cent of total archaeal and bacterial amoA genes per nanogram of genomic DNA) in corresponding RBC biofilm.

Fig. 4

Lipid analysis. CL- and IPL-derived crenarchaeol abundance in biofilm across the June NE RBC flowpath (A) and core and IPL-derived crenarchaeol abundances for RBC 1 and 8 biofilm for all seasons and treatment trains (B). Letters F, J and S denote February, June and September respectively.

Fig. 5

DGGE fingerprints for bacterial and thaumarchaeal amoA and 16S rRNA genes across eight serial RBC stages. Data shown were obtained from the NE treatment train, sampled in June 2010. Data from all RBC trains are shown in Fig. S1.

Fig. 6

Phylogenetic affiliations of thaumarchaeal amoA (A) and 16S rRNA (B) gene sequences retrieved from Guelph WWTP RBCs. Both trees were inferred using the Maximum Likelihood method based on the Tamura–Nei model of sequence evolution. Bootstrap values are located above branches and are based on 500 replicates. Only bootstrap values greater than 50% are indicated on tree. The scale bars represent 5% and 2% nucleotide divergence for A and B respectively.