title: An acid-tolerant ammonia-oxidizing γ-proteobacterium from soil.
abstract: Nitrification, the microbial oxidation of ammonia to nitrate via nitrite, occurs in a wide range of acidic soils. However, the ammonia-oxidizing bacteria (AOB) that have been isolated from soil to date are acid-sensitive. Here we report the isolation and characterization of an acid-adapted AOB from an acidic agricultural soil. The isolated AOB, strain TAO100, is classified within the Gammaproteobacteria based on phylogenetic characteristics. TAO100 can grow in the pH range of 5-7.5 and survive in highly acidic conditions until pH 2 by forming cell aggregates. Whereas all known gammaproteobacterial AOB (γ-AOB) species, which have been isolated from marine and saline aquatic environments, are halophiles, TAO100 is not phenotypically halophilic. Thus, TAO100 represents the first soil-originated and non-halophilic γ-AOB. The TAO100 genome is considerably smaller than those of other γ-AOB and lacks several genes associated with salt tolerance which are unnecessary for survival in soil. The ammonia monooxygenase subunit A gene of TAO100 and its transcript are higher in abundance than those of ammonia-oxidizing archaea and betaproteobacterial AOB in the strongly acidic soil. These results indicate that TAO100 plays an important role in the nitrification of acidic soils. Based on these results, we propose TAO100 as a novel species of a new genus, Candidatus Nitrosoglobus terrae.
authors.affiliation: Institute of Agro-Environmental Science, National Agriculture and Food Research Organization (NARO), Tsukuba, Ibaraki, Japan.
authors.forename: Masahito
authors.initials: M
authors.lastname: Hayatsu
authors.affiliation: Institute of Agro-Environmental Science, National Agriculture and Food Research Organization (NARO), Tsukuba, Ibaraki, Japan.
authors.forename: Kanako
authors.initials: K
authors.lastname: Tago
authors.affiliation: National Institute for Basic Biology, Okazaki, Aichi, Japan.
authors.forename: Ikuo
authors.initials: I
authors.lastname: Uchiyama
authors.affiliation: Center for Information Biology, National Institute of Genetics, Mishima, Shizuoka, Japan.
authors.forename: Atsushi
authors.initials: A
authors.lastname: Toyoda
authors.affiliation: Institute of Agro-Environmental Science, National Agriculture and Food Research Organization (NARO), Tsukuba, Ibaraki, Japan.
authors.forename: Yong
authors.initials: Y
authors.lastname: Wang
authors.affiliation: Institute of Agro-Environmental Science, National Agriculture and Food Research Organization (NARO), Tsukuba, Ibaraki, Japan.
authors.forename: Yumi
authors.initials: Y
authors.lastname: Shimomura
authors.affiliation: Institute of Agro-Environmental Science, National Agriculture and Food Research Organization (NARO), Tsukuba, Ibaraki, Japan.
authors.forename: Takashi
authors.initials: T
authors.lastname: Okubo
authors.affiliation: Research Center for Water Environment Technology, Graduate School of Engineering, The University of Tokyo, Tokyo, Japan.
authors.forename: Futoshi
authors.initials: F
authors.lastname: Kurisu
authors.affiliation: Institute of Fruit Tree and Tea Science, NARO, Shimada, Shizuoka, Japan.
authors.forename: Yuhei
authors.initials: Y
authors.lastname: Hirono
authors.affiliation: Institute of Fruit Tree and Tea Science, NARO, Shimada, Shizuoka, Japan.
authors.forename: Kunihiko
authors.initials: K
authors.lastname: Nonaka
authors.affiliation: Institute of Agro-Environmental Science, National Agriculture and Food Research Organization (NARO), Tsukuba, Ibaraki, Japan.
authors.forename: Hiroko
authors.initials: H
authors.lastname: Akiyama
authors.affiliation: Graduate School of Bioscience and Biotechnology,Tokyo Institute of Technology, Meguro-ku, Tokyo, Japan.
authors.forename: Takehiko
authors.initials: T
authors.lastname: Itoh
authors.affiliation: Yokohama Institute, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokohama, Kanagawa, Japan.
authors.forename: Hideto
authors.initials: H
authors.lastname: Takami
mesh_terms: D000222:Adaptation, Physiological; D000383:Agriculture; D000641:Ammonia / Q000378:metabolism*; D001105:Archaea / Q000235:genetics; D020562:Betaproteobacteria / Q000235:genetics; D020563:Gammaproteobacteria / Q000145:classification / Q000302:isolation & purification / Q000378:metabolism*; D016680:Genome, Bacterial; D006863:Hydrogen-Ion Concentration; D058465:Nitrification; D010084:Oxidation-Reduction; D010088:Oxidoreductases / Q000235:genetics; D010802:Phylogeny; D012987:Soil / Q000737:chemistry; D012988:Soil Microbiology
chemical_list: D012987:Soil; D000641:Ammonia; D010088:Oxidoreductases; C045582:ammonia monooxygenase