Role for urea in nitrification by polar marine Archaea

Abstract

Despite the high abundance of Archaea in the global ocean, their metabolism and biogeochemical roles remain largely unresolved. We investigated the population dynamics and metabolic activity of Thaumarchaeota in polar environments, where these microorganisms are particularly abundant and exhibit seasonal growth. Thaumarchaeota were more abundant in deep Arctic and Antarctic waters and grew throughout the winter at surface and deeper Arctic halocline waters. However, in situ single-cell activity measurements revealed a low activity of this group in the uptake of both leucine and bicarbonate (<5% Thaumarchaeota cells active), which is inconsistent with known heterotrophic and autotrophic thaumarchaeal lifestyles. These results suggested the existence of alternative sources of carbon and energy. Our analysis of an environmental metagenome from the Arctic winter revealed that Thaumarchaeota had pathways for ammonia oxidation and, unexpectedly, an abundance of genes involved in urea transport and degradation. Quantitative PCR analysis confirmed that most polar Thaumarchaeota had the potential to oxidize ammonia, and a large fraction of them had urease genes, enabling the use of urea to fuel nitrification. Thaumarchaeota from Arctic deep waters had a higher abundance of urease genes than those near the surface suggesting genetic differences between closely related archaeal populations. In situ measurements of urea uptake and concentration in Arctic waters showed that small-sized prokaryotes incorporated the carbon from urea, and the availability of urea was often higher than that of ammonium. Therefore, the degradation of urea may be a relevant pathway for Thaumarchaeota and other microorganisms exposed to the low-energy conditions of dark polar waters.

Fig. 1.

Marine Group I (MGI) archaeal in situ abundance and metabolic activity in Arctic waters as analyzed by CARD-FISH and MAR-FISH. (A) Abundance of MGI Archaea expressed as percentage of total prokaryotes (bars) and number of cells in surface waters (line). The star symbol indicates the date at which the Arctic metagenome was retrieved. (B) Single-cell activity of Bacteria and MGI Archaea in the uptake of leucine (Upper) and bicarbonate (Lower). Individual dots represent replicate measurements carried out in some samples. Dark and light gray bars represent samples collected in Arctic surface and halocline waters, respectively.

Fig. 2.

MGI archaeal in situ abundance and metabolic activity in Antarctic waters as analyzed by CARD-FISH and MAR-FISH. (A) Abundance of MGI Archaea in waters of the Ross and Amundsen seas expressed as percentage of total prokaryotes (bars in Upper) and number of cells (box plots in Lower). Data in Upper are shown as averages ± SD, and n ranges from 4 to 18. (B) Single-cell activity of Bacteria (hatched bars) and MGI Archaea (open bars) in the uptake of leucine (Upper) and bicarbonate (Lower). n ranges from 4 to 5. AASW, Antarctic Surface Waters; CDW, Circumpolar Deep Waters; SW, Shelf Waters; THE, thermocline.

Fig. 3.

Comparative genomic analysis between the Arctic thaumarchaeal metagenome and the three sequenced MGI Archaea to date. Nitrosopumilus maritimus SCM1, Candidatus N. limnia SFB1, and Candidatus C. symbiosum A were used to build OGs specific to Thaumarchaeota and, thereafter, the genes identified in Arctic Thaumarchaeota metagenome were assigned to these OGs. The numbers in parentheses represent the total number of OGs for the genomes or regions in the Venn. The large numbers in each region of the Venn represent OGs with functional annotation from eggNOG v2. OGs that did not occur in the Arctic thaumarchaeal metagenome and were shared among only two other genomes are hidden. Some OGs of interest have been highlighted in boxes. 3OHP/4OHB, 3 hydroxyproprionate/4 Hydroxybutyrate.

Fig. 4.

Proposed pathway used by Arctic Thaumarchaeota to obtain carbon and energy from the degradation of urea. The pie charts show the phylogenetic affiliation of reads assigned to the orthologous groups COG0804 (urease) and NOG67450 (ammonia monooxygenase) within the Arctic metagenome. Plots at Right show the abundance of ureC genes (upper plot) and amoA genes (lower plot) versus the abundance of MGI Archaea 16S rRNA genes in Arctic and Antarctic waters, as analyzed by qPCR. Two samples from AASW did not show detectable amplification of ureC genes and were not included in the upper plot. Uptake measurements of ¹⁴C-labeled urea in surface Arctic samples of different size fractions (>0.2 and >0.6 μm) under light and dark conditions are shown on the bottom left side. AASW, Antarctic Surface Waters; CDW, Circumpolar Deep Waters; haloc, halocline; n.d, nondetected; surf, surface; SW, Shelf Waters; THE, thermocline.