Department of Biology, University of Waterloo, Waterloo, Ontario, Canada.
Los Alamos National Laboratory, Los Alamos, New Mexico, USA.
Appl Environ Microbiol. 2018 Sep 17;84(19). doi: 10.1128/AEM.01430-18. Print 2018 Oct 1.
Ammonia is a metabolic waste product excreted by aquatic organisms that causes toxicity when it accumulates. Aquaria and aquaculture systems therefore use biological filters that promote the growth of nitrifiers to convert ammonia to nitrate. Ammonia-oxidizing bacteria (AOB) have been isolated from aquarium biofilters and are available as commercial supplements, but recent evidence suggests that ammonia-oxidizing archaea (AOA) are abundant in aquarium biofilters. In this study, we report the cultivation and closed genome sequence of the novel AOA representative " Nitrosotenuis aquarius," which was enriched from a freshwater aquarium biofilter. " Nitrosotenuis aquarius" oxidizes ammonia stoichiometrically to nitrite with a concomitant increase in thaumarchaeotal cells and a generation time of 34.9 h. " Nitrosotenuis aquarius" has an optimal growth temperature of 33°C, tolerates up to 3 mM NHCl, and grows optimally at 0.05% salinity. Transmission electron microscopy revealed that " Nitrosotenuis aquarius" cells are rod shaped, with a diameter of ∼0.4 μm and length ranging from 0.6 to 3.6 μm. In addition, these cells possess surface layers (S-layers) and multiple proteinaceous appendages. Phylogenetically, " Nitrosotenuis aquarius" belongs to the group I.1a , clustering with environmental sequences from freshwater aquarium biofilters, aquaculture systems, and wastewater treatment plants. The complete 1.70-Mbp genome contains genes involved in ammonia oxidation, bicarbonate assimilation, flagellum synthesis, chemotaxis, S-layer production, defense, and protein glycosylation. Incubations with differential inhibitors indicate that " Nitrosotenuis aquarius"-like AOA contribute to ammonia oxidation within the aquarium biofilter from which it originated. Nitrification is a critical process for preventing ammonia toxicity in engineered biofilter environments. This work describes the cultivation and complete genome sequence of a novel AOA representative enriched from a freshwater aquarium biofilter. In addition, despite the common belief in the aquarium industry that AOB mediate ammonia oxidation, the present study suggests an role for " Nitrosotenuis aquarius"-like AOA in freshwater aquarium biofilters.
氨是水生生物排泄的一种代谢废物产物，当其积累时会造成毒性。因此，水族馆和水产养殖系统使用生物过滤器来促进硝化菌的生长，将氨转化为硝酸盐。氨氧化细菌 (AOB) 已从水族馆生物过滤器中分离出来，并可作为商业补充剂，但最近的证据表明，氨氧化古菌 (AOA) 在水族馆生物过滤器中大量存在。在这项研究中，我们报告了从淡水水族馆生物过滤器中富集的新型 AOA 代表“Nitrosotenuis aquarius”的培养和封闭基因组序列。“Nitrosotenuis aquarius”将氨化学计量地氧化为亚硝酸盐，同时伴随着古菌细胞的增加和代时为 34.9 h。“Nitrosotenuis aquarius”的最佳生长温度为 33°C，可耐受高达 3 mM NHCl，并在 0.05%盐度下最佳生长。透射电子显微镜显示，“Nitrosotenuis aquarius”细胞呈杆状，直径约为 0.4 μm，长度从 0.6 到 3.6 μm 不等。此外，这些细胞具有表面层 (S-层) 和多个蛋白状附属物。系统发育分析表明，“Nitrosotenuis aquarius”属于 I.1a 组，与来自淡水水族馆生物过滤器、水产养殖系统和废水处理厂的环境序列聚类。完整的 1.70-Mbp 基因组包含参与氨氧化、碳酸氢盐同化、鞭毛合成、趋化性、S-层生产、防御和蛋白质糖基化的基因。用差异抑制剂孵育表明，与它起源的水族馆生物过滤器中，“Nitrosotenuis aquarius”样 AOA 有助于氨氧化。硝化作用是防止工程生物过滤器环境中氨毒性的关键过程。这项工作描述了从淡水水族馆生物过滤器中富集的新型 AOA 代表的培养和完整基因组序列。此外，尽管水族馆行业普遍认为 AOB 介导氨氧化，但本研究表明“Nitrosotenuis aquarius”-样 AOA 在淡水水族馆生物过滤器中发挥作用。
