title: Enrichment and characterization of an autotrophic ammonia-oxidizing archaeon of mesophilic crenarchaeal group I.1a from an agricultural soil.
abstract: Soil nitrification is an important process for agricultural productivity and environmental pollution. Though one cultivated representative of ammonia-oxidizing Archaea from soil has been described, additional representatives warrant characterization. We describe an ammonia-oxidizing archaeon (strain MY1) in a highly enriched culture derived from agricultural soil. Fluorescence in situ hybridization microscopy showed that, after 2 years of enrichment, the culture was composed of >90% archaeal cells. Clone libraries of both 16S rRNA and archaeal amoA genes featured a single sequence each. No bacterial amoA genes could be detected by PCR. A [¹³C]bicarbonate assimilation assay showed stoichiometric incorporation of ¹³C into Archaea-specific glycerol dialkyl glycerol tetraethers. Strain MY1 falls phylogenetically within crenarchaeal group I.1a; sequence comparisons to "Candidatus Nitrosopumilus maritimus" revealed 96.9% 16S rRNA and 89.2% amoA gene similarities. Completed growth assays showed strain MY1 to be chemoautotrophic, mesophilic (optimum at 25°C), neutrophilic (optimum at pH 6.5 to 7.0), and nonhalophilic (optimum at 0.2 to 0.4% salinity). Kinetic respirometry assays showed that strain MY1's affinities for ammonia and oxygen were much higher than those of ammonia-oxidizing bacteria (AOB). The yield of the greenhouse gas N₂O in the strain MY1 culture was lower but comparable to that of soil AOB. We propose that this new soil ammonia-oxidizing archaeon be designated "Candidatus Nitrosoarchaeum koreensis."
authors: Department of Microbiology, Chungbuk National University, 12 Gaeshin-dong, Heungduk-gu, Cheongju 361-763, South Korea.
authors: Man-Young
authors: MY
authors: Jung
authors: Soo-Je
authors: SJ
authors: Park
authors: Deullae
authors: D
authors: Min
authors: Jin-Seog
authors: JS
authors: Kim
authors: W Irene C
authors: WI
authors: Rijpstra
authors: Jaap S
authors: JS
authors: Sinninghe Damsté
authors: Geun-Joong
authors: GJ
authors: Kim
authors: Eugene L
authors: EL
authors: Madsen
authors: Sung-Keun
authors: SK
authors: Rhee
mesh_terms: D000641:Ammonia / Q000378:metabolism*; D001105:Archaea / Q000145:classification / Q000235:genetics / Q000302:isolation & purification* / Q000378:metabolism*; D016000:Cluster Analysis; D019641:DNA, Archaeal / Q000737:chemistry / Q000235:genetics; D004275:DNA, Ribosomal / Q000737:chemistry / Q000235:genetics; D020459:Genes, rRNA; D006863:Hydrogen-Ion Concentration; D017404:In Situ Hybridization, Fluorescence; D008969:Molecular Sequence Data; D009609:Nitrous Oxide / Q000378:metabolism; D010084:Oxidation-Reduction; D010088:Oxidoreductases / Q000235:genetics; D010802:Phylogeny; D019642:RNA, Archaeal / Q000235:genetics; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D017422:Sequence Analysis, DNA; D012689:Sequence Homology, Nucleic Acid; D012988:Soil Microbiology; D013696:Temperature
chemical_list: D019641:DNA, Archaeal; D004275:DNA, Ribosomal; D019642:RNA, Archaeal; D012336:RNA, Ribosomal, 16S; D000641:Ammonia; D010088:Oxidoreductases; C045582:ammonia monooxygenase; D009609:Nitrous Oxide