Cultivation and Genomic Analysis of "Candidatus Nitrosocaldus islandicus," an Obligately Thermophilic, Ammonia-Oxidizing Thaumarchaeon from a Hot Spring Biofilm in Graendalur Valley, Iceland.
Cultivation and Genomic Analysis of "Candidatus Nitrosocaldus islandicus," an Obligately Thermophilic, Ammonia-Oxidizing Thaumarchaeon from a Hot Spring Biofilm in Graendalur Valley, Iceland.
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DOI：
10.3389/fmicb.2018.00193
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发表时间：
2018
影响因子：
5.2
通讯作者：
Wagner M
中科院分区：
文献类型：
--
作者：
Daebeler A;Herbold CW;Vierheilig J;Sedlacek CJ;Pjevac P;Albertsen M;Kirkegaard RH;de la Torre JR;Daims H;Wagner M
氨氧化古菌（AOA）是古菌门中唯一已知的地热环境中的好氧氨氧化菌。虽然分子数据表明在陆地高温生境中存在来自亚寒热菌分支、1.1b组和1.1a组Thaumarchaeota的遗传多样性AOA，但只有一种AOA在50°C以上茁壮成长的富集培养物被报道和功能分析。在这项研究中，我们从生理学和基因组学上表征了一种新发现的来自深分支亚硝化热菌科的thaumarchaeon，我们已经从冰岛温泉（73°C）的生物膜中获得了高（约85%）的富集。这种AOA，我们暂时称之为“Islandicus Nitrosocaldus”，是一种专性嗜热、有氧化能自养氨氧化剂，在50至70°C的温度下将氨化学计量转化为亚硝酸盐。“Ca. N. islandicus”编码古细菌氨氧化所需的预期酶库，但出乎意料地缺乏nirK基因，也没有可识别的其他一氧化氮（NO）生成酶§。尽管如此，氨氧化的AOA似乎是NO依赖性的“钙。N. islandicus”与所有其它测试的AOA一样，通过添加NO清除剂来抑制。此外，比较基因组学显示，“Ca。N. islandicus”具有芳香族氨基酸发酵的潜力，因为其基因组编码吲哚丙酮酸氧化还原酶（iorAB）以及3b型氢化酶，这在任何其它测序的AOA中不存在。这种嗜热氨氧化菌的另一个令人惊讶的基因组特征是不存在DNA聚合酶D基因，该基因是所有其他氨氧化Thaumarchaeota中的主要复制DNA聚合酶之一。总的来说，我们的研究结果表明，代谢的多样性和DNA复制可能有很大的不同专性嗜热和其他AOA。
Ammonia-oxidizing archaea (AOA) within the phylum Thaumarchaeota are the only known aerobic ammonia oxidizers in geothermal environments. Although molecular data indicate the presence of phylogenetically diverse AOA from the Nitrosocaldus clade, group 1.1b and group 1.1a Thaumarchaeota in terrestrial high-temperature habitats, only one§ enrichment culture of an AOA thriving above 50°C has been reported and functionally analyzed. In this study, we physiologically and genomically characterized a newly discovered thaumarchaeon from the deep-branching Nitrosocaldaceae family of which we have obtained a high (∼85%) enrichment from biofilm of an Icelandic hot spring (73°C). This AOA, which we provisionally refer to as “Candidatus Nitrosocaldus islandicus,” is an obligately thermophilic, aerobic chemolithoautotrophic ammonia oxidizer, which stoichiometrically converts ammonia to nitrite at temperatures between 50 and 70°C. “Ca. N. islandicus” encodes the expected repertoire of enzymes proposed to be required for archaeal ammonia oxidation, but unexpectedly lacks a nirK gene and also possesses no identifiable other enzyme for nitric oxide (NO) generation§. Nevertheless, ammonia oxidation by this AOA appears to be NO-dependent as “Ca. N. islandicus” is, like all other tested AOA, inhibited by the addition of an NO scavenger. Furthermore, comparative genomics revealed that “Ca. N. islandicus” has the potential for aromatic amino acid fermentation as its genome encodes an indolepyruvate oxidoreductase (iorAB) as well as a type 3b hydrogenase, which are not present in any other sequenced AOA. A further surprising genomic feature of this thermophilic ammonia oxidizer is the absence of DNA polymerase D genes§ – one of the predominant replicative DNA polymerases in all other ammonia-oxidizing Thaumarchaeota. Collectively, our findings suggest that metabolic versatility and DNA replication might differ substantially between obligately thermophilic and other AOA.