title: Hydrogen peroxide detoxification is a key mechanism for growth of ammonia-oxidizing archaea.
abstract: Ammonia-oxidizing archaea (AOA), that is, members of the Thaumarchaeota phylum, occur ubiquitously in the environment and are of major significance for global nitrogen cycling. However, controls on cell growth and organic carbon assimilation by AOA are poorly understood. We isolated an ammonia-oxidizing archaeon (designated strain DDS1) from seawater and used this organism to study the physiology of ammonia oxidation. These findings were confirmed using four additional Thaumarchaeota strains from both marine and terrestrial habitats. Ammonia oxidation by strain DDS1 was enhanced in coculture with other bacteria, as well as in artificial seawater media supplemented with α-keto acids (e.g., pyruvate, oxaloacetate). α-Keto acid-enhanced activity of AOA has previously been interpreted as evidence of mixotrophy. However, assays for heterotrophic growth indicated that incorporation of pyruvate into archaeal membrane lipids was negligible. Lipid carbon atoms were, instead, derived from dissolved inorganic carbon, indicating strict autotrophic growth. α-Keto acids spontaneously detoxify H2O2 via a nonenzymatic decarboxylation reaction, suggesting a role of α-keto acids as H2O2 scavengers. Indeed, agents that also scavenge H2O2, such as dimethylthiourea and catalase, replaced the α-keto acid requirement, enhancing growth of strain DDS1. In fact, in the absence of α-keto acids, strain DDS1 and other AOA isolates were shown to endogenously produce H2O2 (up to ∼4.5 μM), which was inhibitory to growth. Genomic analyses indicated catalase genes are largely absent in the AOA. Our results indicate that AOA broadly feature strict autotrophic nutrition and implicate H2O2 as an important factor determining the activity, evolution, and community ecology of AOA ecotypes.
authors.affiliation: Department of Microbiology, Chungbuk National University, Cheongju 361-763, South Korea;
authors.forename: Jong-Geol
authors.initials: JG
authors.lastname: Kim
authors.affiliation: Department of Biology, Jeju National University, Jeju 690-756, South Korea;
authors.forename: Soo-Je
authors.initials: SJ
authors.lastname: Park
authors.affiliation: Department of Marine Microbiology and Biogeochemistry, Royal Netherlands Institute for Sea Research (NIOZ) and Utrecht University, 1790 AB Den Burg, Texel, The Netherlands; Faculty of Geosciences, Department of Earth Sciences, Geochemistry, Utrecht University, 3584 CD Utrecht, The Netherlands;
authors.forename: Jaap S
authors.initials: JS
authors.lastname: Sinninghe Damsté
authors.affiliation: Department of Marine Microbiology and Biogeochemistry, Royal Netherlands Institute for Sea Research (NIOZ) and Utrecht University, 1790 AB Den Burg, Texel, The Netherlands; Faculty of Geosciences, Department of Earth Sciences, Geochemistry, Utrecht University, 3584 CD Utrecht, The Netherlands;
authors.forename: Stefan
authors.initials: S
authors.lastname: Schouten
authors.affiliation: Department of Marine Microbiology and Biogeochemistry, Royal Netherlands Institute for Sea Research (NIOZ) and Utrecht University, 1790 AB Den Burg, Texel, The Netherlands;
authors.forename: W Irene C
authors.initials: WI
authors.lastname: Rijpstra
authors.affiliation: Department of Microbiology, Chungbuk National University, Cheongju 361-763, South Korea;
authors.forename: Man-Young
authors.initials: MY
authors.lastname: Jung
authors.affiliation: Department of Microbiology, Chungbuk National University, Cheongju 361-763, South Korea;
authors.forename: So-Jeong
authors.initials: SJ
authors.lastname: Kim
authors.affiliation: Department of Microbiology, Chungbuk National University, Cheongju 361-763, South Korea;
authors.forename: Joo-Han
authors.initials: JH
authors.lastname: Gwak
authors.affiliation: Department of Microbiology, Chungbuk National University, Cheongju 361-763, South Korea;
authors.forename: Heeji
authors.initials: H
authors.lastname: Hong
authors.affiliation: Department of Microbiology, Chungbuk National University, Cheongju 361-763, South Korea;
authors.forename: Ok-Ja
authors.initials: OJ
authors.lastname: Si
authors.affiliation: Division of Polar Climate Research, Korea Polar Research Institute, Incheon 406-840, South Korea;
authors.forename: SangHoon
authors.initials: S
authors.lastname: Lee
authors.affiliation: Department of Microbiology, Cornell University, Ithaca, NY 14853-8101.
authors.forename: Eugene L
authors.initials: EL
authors.lastname: Madsen
authors.affiliation: Department of Microbiology, Chungbuk National University, Cheongju 361-763, South Korea; rhees@chungbuk.ac.kr.
authors.forename: Sung-Keun
authors.initials: SK
authors.lastname: Rhee
mesh_terms: D000641:Ammonia / Q000378:metabolism*; D001105:Archaea / Q000302:isolation & purification / Q000502:physiology*; D016680:Genome, Bacterial; D006861:Hydrogen Peroxide / Q000378:metabolism*; D058465:Nitrification; D010084:Oxidation-Reduction; D009195:Peroxidase / Q000378:metabolism
chemical_list: D000641:Ammonia; D006861:Hydrogen Peroxide; D009195:Peroxidase
keywords: H2O2 detoxification; ammonia-oxidizing archaea; mixotrophy; α-keto acid