Spatial distribution and factors shaping the niche segregation of ammonia-oxidizing microorganisms in the Qiantang River, China

Abstract

Ammonia oxidation is performed by both ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB). However, the current knowledge of the distribution, diversity, and relative abundance of these two microbial groups in freshwater sediments is insufficient. We examined the spatial distribution and analyzed the possible factors leading to the niche segregation of AOA and AOB in the sediments of the Qiantang River, using clone library construction and quantitative PCR for both archaeal and bacterial amoA genes. pH and NH4(+)-N content had a significant effect on AOA abundance and AOA operational taxonomy unit (OTU) numbers. pH and organic carbon content influenced the ratio of AOA/AOB OTU numbers significantly. The influence of these factors showed an obvious spatial trend along the Qiantang River. This result suggested that AOA may contribute more than AOB to the upstream reaches of the Qiantang River, where the pH is lower and the organic carbon and NH4(+)-N contents are higher, but AOB were the principal driver of nitrification downstream, where the opposite environmental conditions were present.

Fig 1

Study area and sediment sampling sites in the Qiantang River (Reprinted from reference with permission from the Society for Applied Microbiology and Blackwell Publishing Ltd.).

Fig 2

Quantitative analysis of AOA and AOB at seven sampling sites along the Qiantang River. The ratio of AOA to AOB gene copy numbers is shown above the histogram.

Fig 3

Neighbor-joining phylogenetic tree showing the phylogenetic affiliations of AOA amoA gene sequences recovered from the Qiantang River. The numbers at the nodes are percentages that indicate the levels of bootstrap support (1,000 replicates). The scale bar represents 0.1 nucleic acid substitution per nucleotide position.

Fig 4

Neighbor-joining phylogenetic tree showing the phylogenetic affiliations of AOB amoA gene sequences recovered from the Qiantang River. The numbers at the nodes are percentages that indicate the levels of bootstrap support (1,000 replicates). The scale bar represents 0.05 nucleic acid substitution per nucleotide position.

Fig 5

RDA ordination plots for the first dimension to show the relationship between the AOA (a) and AOB (b) communities and environmental factors. Correlations between environmental factors and RDA axes are represented by the length and angle of arrows.