Community dynamics and activity of ammonia-oxidizing prokaryotes in intertidal sediments of the Yangtze estuary

Abstract

Diversity, abundance, and activity of ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) were investigated using the ammonia monooxygenase α subunit (amoA) in the intertidal sediments of the Yangtze Estuary. Generally, AOB had a lower diversity of amoA genes than did AOA in this study. Clone library analysis revealed great spatial variations in both AOB and AOA communities along the estuary. The UniFrac distance matrix showed that all the AOB communities and 6 out of 7 AOA communities in the Yangtze Estuary were statistically indistinguishable between summer and winter. The studied AOB and AOA community structures were observed to correlate with environmental parameters, of which salinity, pH, ammonium, total phosphorus, and organic carbon had significant correlations with the composition and distribution of both communities. Also, the AOA communities were significantly correlated with sediment clay content. Quantitative PCR (qPCR) results indicated that the abundance of AOB amoA genes was greater than that of AOA amoA genes in 10 of the 14 samples analyzed in this study. Potential nitrification rates were significantly greater in summer than in winter and had a significant negative correlation with salinity. In addition, potential nitrification rates were correlated strongly only with archaeal amoA gene abundance and not with bacterial amoA gene abundance. However, no significant differences were observed between rates measured with and without ampicillin (AOB inhibitor). These results implied that archaea might play a more important role in mediating the oxidation of ammonia to nitrite in the Yangtze estuarine sediments.

FIG 1

Neighbor-joining phylogenetic tree of bacterial amoA genes. The phylogeny is based on nucleotide sequences. Bootstrap values greater than 50% of 1,000 resamplings are shown near nodes. The scale indicates the number of nucleotide substitutions per site. GenBank accession numbers are shown for sequences from other studies. Numbers in parentheses following each cluster indicate the number of sequences recovered from each sampling site in summer (red) and winter (blue). The asterisk indicates the Nitrosospira clusters based on the nomenclature of Avrahami and Conrad (53). Representative accession numbers for each cluster and the relative abundance of clones from each site in each of the clusters are shown in Table S3 in the supplemental material.

FIG 2

Neighbor-joining phylogenetic tree of archaeal amoA genes. The phylogeny is based on nucleotide sequences. Bootstrap values greater than 50% of 1,000 resamplings are shown near nodes. The scale indicates the number of nucleotide substitutions per site. GenBank accession numbers are shown for sequences from other studies. Numbers in parentheses following each cluster indicate the number of sequences recovered from each sampling site in summer (red) and winter (blue). Representative accession numbers for each cluster and the relative abundance of clones from each site in each of the clusters are shown in Table S3 in the supplemental material.

FIG 3

The UniFrac distance matrix of bacterial (a) and archaeal (b) amoA gene clone libraries. The summer samples are in red font, while the winter samples are in blue. The values show the UniFrac distances between each pair of clone libraries. Boldface values indicate that the libraries are drawn from significantly different communities (red background, P < 0.01; pink background, P < 0.05). All P values have been corrected for multiple comparisons by multiplying the calculated P value by the number of comparisons made (Bonferroni correction). The dendrograms represent clustering of the 14 clone libraries based on the distance matrix.

FIG 4

Bacterial and archaeal amoA gene copy numbers. The mean values of amoA copy numbers were obtained from triplicate real-time quantitative PCR assays.

FIG 5

CCA ordination plots for the first two principal dimensions of the relationship between the AOB (a) and AOA (b) community compositions with the environmental parameters. The red circles represent the sampling stations in summer, and the blue circles represent the sampling stations in winter. The size of the circles corresponds to the Shannon diversity index in individual samples. TP, Temp, OC, NH4-N, NO3-N, and NO2-N represent total phosphorus, temperature, organic carbon, ammonium, nitrate, and nitrite, respectively.

FIG 6

Potential nitrification rates (PNR) in the intertidal sediments of the Yangtze Estuary incubated with and without ampicillin. The error bars are standard deviations of triplicate incubations. Ampicillin at 1 g liter⁻¹ was used as an antibiotic to inhibit ammonia-oxidizing bacteria.