title: Cultivation and characterization of Candidatus Nitrosocosmicus exaquare, an ammonia-oxidizing archaeon from a municipal wastewater treatment system.
abstract: Thaumarchaeota have been detected in several industrial and municipal wastewater treatment plants (WWTPs), despite the fact that ammonia-oxidizing archaea (AOA) are thought to be adapted to low ammonia environments. However, the activity, physiology and metabolism of WWTP-associated AOA remain poorly understood. We report the cultivation and complete genome sequence of Candidatus Nitrosocosmicus exaquare, a novel AOA representative from a municipal WWTP in Guelph, Ontario (Canada). In enrichment culture, Ca. N. exaquare oxidizes ammonia to nitrite stoichiometrically, is mesophilic, and tolerates at least 15 mm of ammonium chloride or sodium nitrite. Microautoradiography (MAR) for enrichment cultures demonstrates that Ca. N. exaquare assimilates bicarbonate in association with ammonia oxidation. However, despite using inorganic carbon, the ammonia-oxidizing activity of Ca. N. exaquare is greatly stimulated in enrichment culture by the addition of organic compounds, especially malate and succinate. Ca. N. exaquare cells are coccoid with a diameter of ~1-2 μm. Phylogenetically, Ca. N. exaquare belongs to the Nitrososphaera sister cluster within the Group I.1b Thaumarchaeota, a lineage which includes most other reported AOA sequences from municipal and industrial WWTPs. The 2.99 Mbp genome of Ca. N. exaquare encodes pathways for ammonia oxidation, bicarbonate fixation, and urea transport and breakdown. In addition, this genome encodes several key genes for dealing with oxidative stress, including peroxidase and catalase. Incubations of WWTP biofilm demonstrate partial inhibition of ammonia-oxidizing activity by 2-phenyl-4,4,5,5-tetramethylimidazoline-1-oxyl 3-oxide (PTIO), suggesting that Ca. N. exaquare-like AOA may contribute to nitrification in situ. However, CARD-FISH-MAR showed no incorporation of bicarbonate by detected Thaumarchaeaota, suggesting that detected AOA may incorporate non-bicarbonate carbon sources or rely on an alternative and yet unknown metabolism.
authors.affiliation: Department of Biology, University of Waterloo, Waterloo, Ontario, Canada.
authors.forename: Laura A
authors.initials: LA
authors.lastname: Sauder
authors.affiliation: Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark.
authors.forename: Mads
authors.initials: M
authors.lastname: Albertsen
authors.affiliation: Department of Biology, University of Waterloo, Waterloo, Ontario, Canada.
authors.forename: Katja
authors.initials: K
authors.lastname: Engel
authors.affiliation: Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, Research Network 'Chemistry meets Microbiology', University of Vienna, Vienna, Austria.
authors.forename: Jasmin
authors.initials: J
authors.lastname: Schwarz
authors.affiliation: Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark.
authors.forename: Per H
authors.initials: PH
authors.lastname: Nielsen
authors.affiliation: Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, Research Network 'Chemistry meets Microbiology', University of Vienna, Vienna, Austria.
authors.forename: Michael
authors.initials: M
authors.lastname: Wagner
authors.affiliation: Department of Biology, University of Waterloo, Waterloo, Ontario, Canada.
authors.forename: Josh D
authors.initials: JD
authors.lastname: Neufeld
mesh_terms: D000641:Ammonia / Q000378:metabolism*; D001105:Archaea / Q000145:classification / Q000235:genetics / Q000302:isolation & purification / Q000378:metabolism*; D002244:Carbon / Q000378:metabolism; D020745:Genome, Archaeal; D058465:Nitrification; D009573:Nitrites / Q000378:metabolism; D010084:Oxidation-Reduction; D010802:Phylogeny; D062065:Wastewater / Q000382:microbiology*
chemical_list: D000641:Ammonia; D002244:Carbon; D009573:Nitrites; D062065:Wastewater