title: 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.
authors.affiliation: Department of Ecology and Genetics, Limnology, Uppsala University, 75236 Uppsala, Sweden. laura.alonso@gi.ieo.es
authors.forename: Laura
authors.initials: L
authors.lastname: Alonso-Sáez
authors.forename: Alison S
authors.initials: AS
authors.lastname: Waller
authors.forename: Daniel R
authors.initials: DR
authors.lastname: Mende
authors.forename: Kevin
authors.initials: K
authors.lastname: Bakker
authors.forename: Hanna
authors.initials: H
authors.lastname: Farnelid
authors.forename: Patricia L
authors.initials: PL
authors.lastname: Yager
authors.forename: Connie
authors.initials: C
authors.lastname: Lovejoy
authors.forename: Jean-Éric
authors.initials: JÉ
authors.lastname: Tremblay
authors.forename: Marianne
authors.initials: M
authors.lastname: Potvin
authors.forename: Friederike
authors.initials: F
authors.lastname: Heinrich
authors.forename: Marta
authors.initials: M
authors.lastname: Estrada
authors.forename: Lasse
authors.initials: L
authors.lastname: Riemann
authors.forename: Peer
authors.initials: P
authors.lastname: Bork
authors.forename: Carlos
authors.initials: C
authors.lastname: Pedrós-Alió
authors.forename: Stefan
authors.initials: S
authors.lastname: Bertilsson
mesh_terms: D001105:Archaea / Q000378:metabolism*; D017404:In Situ Hybridization, Fluorescence; D008386:Marine Biology; D056186:Metagenomics; D008969:Molecular Sequence Data; D058465:Nitrification; D016133:Polymerase Chain Reaction; D014508:Urea / Q000378:metabolism*
chemical_list: D014508:Urea