Jong-Geol Kima, Soo-Je Parkb, Jaap S. Sinninghe Damstec,d, Stefan Schoutenc,d, W. Irene C. Rijpstrac, Man-Young Junga, So-Jeong Kima, Joo-Han Gwaka, Heeji Honga, Ok-Ja Sia, SangHoon Leee, Eugene L. Madsenf, and Sung-Keun Rheea,1
aDepartment of Microbiology, Chungbuk National University, Cheongju 361-763, South Korea;
bDepartment of Biology, Jeju National University, Jeju 690-756, South Korea;
cDepartment of Marine Microbiology and Biogeochemistry, Royal Netherlands Institute for Sea Research (NIOZ) and Utrecht University, 1790 AB Den Burg, Texel, The Netherlands;
dFaculty of Geosciences, Department of Earth Sciences, Geochemistry, Utrecht University, 3584 CD Utrecht, The Netherlands;
eDivision of Polar Climate Research, Korea Polar Research Institute, Incheon 406-840, South Korea;
fDepartment of Microbiology, Cornell University, Ithaca, NY 14853-8101
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.
H2O2 detoxification, mixotrophy, α-keto acid, ammonia-oxidizing archaea
1To whom correspondence should be addressed.
Author contributions: J.-G.K. and S.-K.R. designed research; J.-G.K., M.-Y.J., S.-J.K., H.H., S.L., and S.-K.R. performed research; J.-G.K., S.-J.P., J.S.S.D., S.S., W.I.C.R., M.-Y.J., S.-J.K., J.-H.G., O.-J.S., and S.-K.R. analyzed data; and J.-G.K., J.S.S.D., E.L.M., and S.-K.R. wrote the paper.