Species, Abundance and Function of Ammonia-oxidizing Archaea in Inland Waters across China

Abstract

Ammonia oxidation is the first step in nitrification and was thought to be performed solely by specialized bacteria. The discovery of ammonia-oxidizing archaea (AOA) changed this view. We examined the large scale and spatio-temporal occurrence, abundance and role of AOA throughout Chinese inland waters (n = 28). Molecular survey showed that AOA was ubiquitous in inland waters. The existence of AOA in extreme acidic, alkaline, hot, cold, eutrophic and oligotrophic environments expanded the tolerance limits of AOA, especially their known temperature tolerance to -25 °C, and substrate load to 42.04 mM. There were spatio-temporal divergences of AOA community structure in inland waters, and the diversity of AOA in inland water ecosystems was high with 34 observed species-level operational taxonomic units (OTUs; based on a 15% cutoff) distributed widely in group I.1b, I.1a, and I.1a-associated. The abundance of AOA was quite high (8.5 × 10(4) to 8.5 × 10(9) copies g(-1)), and AOA outnumbered ammonia-oxidizing bacteria (AOB) in the inland waters where little human activities were involved. On the whole AOB predominate the ammonia oxidation rate over AOA in inland water ecosystems, and AOA play an indispensable role in global nitrogen cycle considering that AOA occupy a broader habitat range than AOB, especially in extreme environments.

Figure 1. Biogeographical distribution of sampling sites in Chinese inland water ecosystems.

Sites 1 to 14 were in order of longitude and sites 15 to 28 were in order of latitude as listed in Table 1. Different colors represent different types of inland waters as shown in the legend. The map were come from web of “Data Sharing Infrastructure of Earth System Science” http://www.geodata.cn. All of the maps used in the manuscript are free.

Figure 2. Phylogenetic tree showing the spatial divergences of AOA community structure among various inland waters.

Phylogenetic trees were constructed with the neighbor-joining method using Maximum Composite Likelihood with 1000 bootstraps. The scale bar represents 5% of the sequence divergence. Pie charts for each species-level OTU show the composition of sequences from different origins with the colors corresponding to the legend.

Figure 3. Phylogenetic tree showing the temporal divergences of AOA community structure in the Pearl River.

Phylogenetic trees were constructed with the neighbor-joining method using Maximum Composite Likelihood with 1000 bootstraps. The scale bar represents 5% of the sequence divergence. Numbers in the parentheses after each species in red give the numbers of sequences obtained in summer, and blue give those in winter.

Figure 4

(A) The abundance of archaeal & bacterial amoA genes and potential nitrification rate (PNR) in various Chinese inland water ecosystems. (B) The abundance of archaeal & bacterial amoA genes in different types of inland waters. Boxes give the 25^th and 75^th percentiles; whiskers show the range from 1^th to 99^th percentiles; horizontal lines in and out the boxes represent the medians and maximum/minimum values respectively; little squares give the averages.

Figure 5. The spatio-temporal variation of AOA & AOB abundance, PNR and AOA populations in four sites on the Tiaoxi River.

(A) Phylogenetic tree of the archaeal amoA gene sequences from sediments in the Tiaoxi River. The letters ABCD in the sequence names are used to distinguish sequences from different sites, marked by circles with different colors. The phylogenetic tree was constructed with the neighbor-joining method using Maximum Composite Likelihood with 1000 bootstraps. The scale bar represents 5% of the sequence divergence. (B)The seasonal variance in archaeal & bacterial amoA gene abundance and PNR in sediments from the Tiaoxi River. The ratios of archaeal amoA gene abundance to bacterial are listed above the diagrams. Error bars indicate standard deviation (n = 3).