Ammonia-oxidizing archaea of the phylum Thaumarchaeota are among the most abundant marine microorganisms1. These organisms thrive in the oceans despite ammonium being present at low nanomolar concentrations2,3. Some Thaumarchaeota isolates have been shown to utilize urea and cyanate as energy and N sources through intracellular conversion to ammonium4,5,6. Yet, it is unclear whether patterns observed in culture extend to marine Thaumarchaeota, and whether Thaumarchaeota in the ocean directly utilize urea and cyanate or rely on co-occurring microorganisms to break these substrates down to ammonium. Urea utilization has been reported for marine ammonia-oxidizing communities7,8,9,10, but no evidence of cyanate utilization exists for marine ammonia oxidizers. Here, we demonstrate that in the Gulf of Mexico, Thaumarchaeota use urea and cyanate both directly and indirectly as energy and N sources. We observed substantial and linear rates of nitrite production from urea and cyanate additions, which often persisted even when ammonium was added to micromolar concentrations. Furthermore, single-cell analysis revealed that the Thaumarchaeota incorporated ammonium-, urea- and cyanate-derived N at significantly higher rates than most other microorganisms. Yet, no cyanases were detected in thaumarchaeal genomic data from the Gulf of Mexico. Therefore, we tested cyanate utilization in Nitrosopumilus maritimus, which also lacks a canonical cyanase, and showed that cyanate was oxidized to nitrite. Our findings demonstrate that marine Thaumarchaeota can use urea and cyanate as both an energy and N source. On the basis of these results, we hypothesize that urea and cyanate are substrates for ammonia-oxidizing Thaumarchaeota throughout the ocean.
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All sequence data and thaumarchaeal MAGs generated in this study are deposited in NCBI under BioProject number: PRJNA397176. Metatranscriptomes are deposited under BioSample numbers SAMN07461123–SAMN07461125; 16S amplicon sequencing under SAMN07461114–SAMN07461122; metagenomes under SAMN10227777–SAMN10227781 and MAGs under SAMN10233969–SAMN10233974. Accession numbers of sequences used for tree calculations (16S rRNA gene, amoA, UreC, CynS, and genome sequences) are given in Supplementary Table 9. CTD data, measured nutrient concentrations, process rates, Thaumarchaeota relative abundance based on 16S rRNA gene amplicon sequencing and Thaumarchaeota-specific CARD-FISH counts are given in Supplementary Table 10.
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The authors thank the captain and crew of the R/V Pelican PE17-02 cruise. The authors are grateful to G. Klockgether, D. Tienken, I. Ulber, L. Seidl, W. Neweshy, N. Alrubeay, M. Philippi and D. J. Parris for technical support; G. Lavik, J. Milucka, W. Mohr, N. Lehnen and S. Ahmerkamp for fruitful discussions. This research was funded by the Max-Planck-Society, the European Research Council Advanced Grant project NITRICARE 294343 (to M.W.) and the National Science Foundation grants 1558916 and 1564559 (to F.J.S.)
The authors declare no competing interests.
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Statistics for rate calculations at all stations and depths (one-tailed t-test).
Accession numbers of sequences used for 16S rRNA gene tree, amoA, CynS, UreC and genome trees.
CTD data, measured nutrient concentrations, process rates, relative abundance of Thaumarchaeota based on 16S rRNA gene amplicon sequencing and Thaumarchaeota-specific CARD-FISH counts.
UreC tree with bootstrap values (PDF).
UreC tree with bootstrap values (tree).
UreC tree with node labels (PDF).
UreC tree with node labels (tree).
UreC tree annotation.
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Kitzinger, K., Padilla, C.C., Marchant, H.K. et al. Cyanate and urea are substrates for nitrification by Thaumarchaeota in the marine environment. Nat Microbiol 4, 234–243 (2019). https://doi.org/10.1038/s41564-018-0316-2
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