Hayatsu Masahito, Tago Kanako, Uchiyama Ikuo, Toyoda Atsushi, Wang Yong, Shimomura Yumi, Okubo Takashi, Kurisu Futoshi, Hirono Yuhei, Nonaka Kunihiko, Akiyama Hiroko, Itoh Takehiko, Takami Hideto
Institute of Agro-Environmental Science, National Agriculture and Food Research Organization (NARO), Tsukuba, Ibaraki, Japan.
National Institute for Basic Biology, Okazaki, Aichi, Japan.
ISME J. 2017 May;11(5):1130-1141. doi: 10.1038/ismej.2016.191. Epub 2017 Jan 10.
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.
硝化作用，即微生物将氨通过亚硝酸盐氧化为硝酸盐的过程，发生在多种酸性土壤中。然而，迄今为止从土壤中分离出的氨氧化细菌（AOB）对酸敏感。在此，我们报告了从酸性农业土壤中分离出一种适应酸性环境的AOB及其特性。基于系统发育特征，分离出的AOB菌株TAO100属于γ-变形菌纲。TAO100能在pH值为5至7.5的范围内生长，并通过形成细胞聚集体在pH值低至2的高酸性条件下存活。虽然所有已知的从海洋和咸水水生环境中分离出的γ-变形菌纲AOB（γ-AOB）物种都是嗜盐菌，但TAO100在表型上并非嗜盐菌。因此，TAO100代表了首个源自土壤的非嗜盐γ-AOB。TAO100的基因组比其他γ-AOB的基因组小得多，并且缺乏几个与耐盐性相关的基因，而这些基因对于在土壤中生存并非必需。在强酸性土壤中，TAO100的氨单加氧酶亚基A基因及其转录本的丰度高于氨氧化古菌和β-变形菌纲AOB。这些结果表明，TAO100在酸性土壤的硝化作用中起重要作用。基于这些结果，我们提议将TAO100作为一个新属“新硝化土球菌（Candidatus Nitrosoglobus terrae）”的一个新物种。
