Marine archaea take a short cut in the nitrogen cycle.

S eeing “nitrification” and “Archaea” in the title of the paper in PNAS by Alonso-Sáez et al. (1) will not surprise anyone following the story about the role of these microbes in an important pathway of the nitrogen cycle. What will puzzle, if not surprise, everyone is the other key word, “urea.” That nitrogenous compound never comes up in discussions of nitrification and Archaea, and even other organic nitrogen forms figure into the story only indirectly. Thus, it is a surprise to see the evidence from Alonso-Sáez et al. (1) indicating that a group of Archaea uses urea to fuel a key step in nitrification in the Arctic Ocean and Antarctic seas. Their study suggests a previously undescribed, shorter pathway in the nitrogen cycle and may help to explain the relatively high abundance of Archaea in some ecosystems. Once thought to be relegated to extreme environments, Archaea are now known to be everywhere. They are particularly common in the deep ocean, where Archaea rival bacteria in abundance, although both prokaryotic groups are about 100-fold less abundant than in surface waters (2). Originally classified as being in the Crenarchaeota phylum, many of these oceanic Archaea have been put into a new phylum, the Thaumarchaeota, because of differences with thermophilic relatives. Hints about the biogeochemical role of these Archaea first came from the Sargasso Sea metagenomic study of Venter et al. (3), which was soon followed up by several surveys of the abundance of a key functional gene in marine as well as terrestrial systems (4). The defining feature of these microbes seemed to be nailed down by studies of Nitrosopumilus maritimus, an archaeon originally isolated from a saltwater aquarium (5). This isolate remains the only one representing the marine Thaumarchaeota, although genomes of a few Archaea in consortia have been deduced by metagenomic sequencing. The pure culture work, metagenomic data, and biogeochemical studies all indicated that marine Thaumarchaeota are ammonia oxidizers, mediating the first, rate-limiting step in nitrification. The energy gained from ammonia oxidation is used to fuel reduction of carbon dioxide, making these microbes chemoautotrophs or to use their full name, chemoautolithotrophs (Fig. 1A). Previous to these discoveries over the past 10 y, chemoautotrophic ammonia oxidation was thought to be carried out mainly by Betaproteobacteria in a reaction first suggested by Pasteur in 1861 (6). The recent findings helped to explain the success of Archaea in the deep ocean and other environments. Still, they did not change our ideas about nitrification. Ammonia oxidation seemed to be the same as in Pasteur’s time, just carried out by a different group of microbes. Alonso-Sáez et al. (1) knew all this as they began their studies in the Beaufort Sea, north of Canada. They also knew of previous work showing a fairly high abundance of Archaea even in surface waters of polar seas, especially in winter. It was no surprise then when they found Archaea to be abundant in the Beaufort Sea and Antarctic seas. Using a type of FISH, a microscopic approach to identify microbes without cultivation, Alonso-Sáez et al. (1) discovered that Archaea made up 6% of total microbial abundance in the Beaufort Sea in January 2008. It was more of a surprise to see these Archaea increase in abundance to 18% by March of the same year. These investigators then ran into their first puzzle. They did microautoradiography assays to examine whether these Archaea are chemoautotrophs, and thus use C-CO2, or are heterotrophs, and thus take up H-leucine. To the investigators’ chagrin, the Beaufort Sea Archaea took up neither compound, even though bacteria were active in taking up both, especially leucine. Some of the Archaea undoubtedly were inactive, but many had to be doing something to account for the threefold increase in abundance in the Beaufort Sea. Metagenomics provided a possible answer. Alonso-Sáez et al. (1) analyzed sequence data collected in March from 65 m deep in the water column, where nitrite concentrations, and possibly nitrification, were highest. They found ammonia oxidation genes (amoA) as well as 16S rRNA genes most similar to genes from N. maritimus and other marine Thaumarchaeota. The abundance of the two genes suggested that most of the Archaea in these waters are ammonia oxidizers. More revealing, they found several genes (ureA, ureB, and ureC) for urease (urea amidohydrolase), Fig. 1. Pathways linking urea and nitrification. (A) Current pathway, featuring an autotroph, such as an alga, that takes up and degrades urea using urease (ureC). The resulting CO2 is fixed by ribulose bisphosphate carboxylase oxygenase (rbc) in the Calvin–Benson–Bassham (CBB) cycle. The resulting ammonium is taken up by a chemolithotrophic bacterium that oxidizes ammonia to nitrite using ammonia monooxygenase (amoA). The second step in nitrification, the oxidation of nitrite to nitrate, is carried out by other microbes. (B) Shorter pathway suggested Alonso-Sáez et al. (1). Instead of one microbe degrading urea and another oxidizing ammonia, the authors suggest that some marine Archaea combine the reactions. Rather than the CBB cycle, these Archaea use the 3-hydroxypropionate-4-hydroxybutyrate pathway (3-HP/4-HB) for inorganic carbon fixation.