Archaeal nitrification in the ocean

Abstract

Marine Crenarchaeota are the most abundant single group of prokaryotes in the ocean, but their physiology and role in marine biogeochemical cycles are unknown. Recently, a member of this clade was isolated from a sea aquarium and shown to be capable of nitrification, tentatively suggesting that Crenarchaeota may play a role in the oceanic nitrogen cycle. We enriched a crenarchaeote from North Sea water and showed that its abundance, and not that of bacteria, correlates with ammonium oxidation to nitrite. A time series study in the North Sea revealed that the abundance of the gene encoding for the archaeal ammonia monooxygenase alfa subunit (amoA) is correlated with a decline in ammonium concentrations and with the abundance of Crenarchaeota. Remarkably, the archaeal amoA abundance was 1-2 orders of magnitude higher than those of bacterial nitrifiers, which are commonly thought to mediate the oxidation of ammonium to nitrite in marine environments. Analysis of Atlantic waters of the upper 1,000 m, where most of the ammonium regeneration and oxidation takes place, showed that crenarchaeotal amoA copy numbers are also 1-3 orders of magnitude higher than those of bacterial amoA. Our data thus suggest a major role for Archaea in oceanic nitrification.

Fig. 1.

Archaeal nitrification in an enrichment culture of a crenarchaeote from the North Sea. (Upper) Nutrient concentrations (micromolar) in the course of the experiment. (Lower) Crenarchaeotal, eubacterial, and β- and γ-proteobacterial cell numbers (cells per milliliter) as determined by CARD-FISH (18). Aged seawater from a large mesocosm experiment (see text and Materials and Methods) with added inorganic nutrients was incubated at two different temperatures in the dark. The data shown are those obtained at 25°C. The crenarchaeotal population in our enrichment culture was shown to consist of a single species, phylogenetically closely related to North Sea Crenarchaeota (Figs. 3–5).

Fig. 2.

Phylogenetic analyses of archaeal amoA recovered from the enrichment culture (red), the North Sea (blue), and the Atlantic Ocean (green). Neighbor-joining bootstrap tree of 594-bp-long amoA-like nucleotide sequences published by Francis et al. (14) and Könneke et al. (10) to which we added our partial sequences (217 bp) using the ARB parsimony tool. The amoA gene recovered from the incubation experiment is closely related (91% nucleotide identity) to that of Candidatus “N. maritimus” (10) and of the Sargasso Sea environmental sequences (20) (up to 90% nucleotide identity). The amoA recovered from the North Sea time series is also closely related to that of Candidatus “N. maritimus” (91% nucleotide identity) and some Sargasso Sea environmental sequences (98% nucleotide identity).

Fig. 3.

Crenarchaeotal abundance in the North Sea between August 2002 and July 2003 as a response to changing nutrient concentrations. (Top) Nutrient concentrations (micromolar). (Middle) Cell abundances (cells per milliliter) of Crenarchaeota as determined by CARD-FISH (18) and abundances of 16S rDNA copies of Crenarchaeota as determined by QPCR (see Materials and Methods). (Bottom) Abundances of archaeal and β-proteobacterial amoA copy numbers as determined by QPCR. The sharp increases in crenarchaeotal cell numbers and archaeal amoA copy numbers in November and January co-occur with the transformation of ammonia to nitrate. In contrast, a far less pronounced increase in amoA copy numbers of β-proteobacterial ammonia oxidizers was observed in this period (≈1.0 × 10⁴) compared with the rest of the year (≈2.3 × 10³).