Interdisciplinary Graduate Program in Advance Convergence Technology and Science, Jeju National University, Jeju, South Korea.
Division of Microbial Ecology, Centre for Microbiology and Environmental System Science, University of Vienna, Vienna, Austria.
mBio. 2024 Nov 13;15(11):e0216924. doi: 10.1128/mbio.02169-24. Epub 2024 Oct 3.
Nitrification is a core process in the global nitrogen (N) cycle mediated by ammonia-oxidizing microorganisms, including ammonia-oxidizing archaea (AOA) as a key player. Although much is known about AOA abundance and diversity across environments, the genetic drivers of the ecophysiological adaptations of the AOA are often less clearly defined. This is especially true for AOA within the genus , which have several unique physiological traits (e.g., high substrate tolerance, low substrate affinity, and large cell size). To better understand what separates the physiology of AOA, we performed comparative genomics with genomes from 39 cultured AOA, including five AOA. The absence of a canonical high-affinity type ammonium transporter and typical S-layer structural genes was found to be conserved across all AOA. In agreement, cryo-electron tomography confirmed the absence of a visible outermost S-layer structure, which has been observed in other AOA. In contrast to other AOA, the cryo-electron tomography highlighted the possibility that AOA may possess a glycoprotein or glycolipid-based glycocalyx cell covering outer layer. Together, the genomic, physiological, and metabolic properties revealed in this study provide insight into niche adaptation mechanisms and the overall ecophysiology of members of the clade in various terrestrial ecosystems.
Nitrification is a vital process within the global biogeochemical nitrogen cycle but plays a significant role in the eutrophication of aquatic ecosystems and the production of the greenhouse gas nitrous oxide (NO) from industrial agriculture ecosystems. While various types of ammonia-oxidizing microorganisms play a critical role in the N cycle, ammonia-oxidizing archaea (AOA) are often the most abundant nitrifiers in natural environments. Members of the genus are one of the prevalent AOA groups detected in undisturbed terrestrial ecosystems and have previously been reported to possess a range of physiological characteristics that set their physiology apart from other AOA species. This study provides significant progress in understanding these unique physiological traits and their genetic drivers. Our results highlight how physiological studies based on comparative genomics-driven hypotheses can contribute to understanding the unique niche of AOA.
硝化作用是全球氮（N）循环中的核心过程，由氨氧化微生物介导，包括氨氧化古菌（AOA）作为关键参与者。尽管人们对环境中 AOA 的丰度和多样性有了很多了解，但 AOA 的生态生理适应的遗传驱动因素往往定义不明确。这在属内的 AOA 中尤其如此，它们具有几个独特的生理特征（例如，高基质耐受性、低基质亲和力和大细胞尺寸）。为了更好地了解将 AOA 的生理学分开的原因，我们对来自 39 种培养的 AOA 的基因组进行了比较基因组学研究，其中包括 5 种 。发现所有 AOA 都保守地缺乏典型的高亲和力铵转运体和典型的 S-层结构基因。冷冻电子断层扫描证实了在其他 AOA 中观察到的可见最外层 S-层结构的缺失。与其他 AOA 不同，冷冻电子断层扫描突出了一种可能性，即 AOA 可能具有糖蛋白或糖脂基糖萼细胞覆盖外层。总之，本研究中揭示的基因组、生理和代谢特性为各种陆地生态系统中 属成员的生态位适应机制和整体生态生理学提供了见解。
硝化作用是全球生物地球化学氮循环中的一个重要过程，但在水生生态系统的富营养化和工业农业生态系统中产生温室气体氧化亚氮（NO）方面起着重要作用。虽然各种类型的氨氧化微生物在氮循环中起着关键作用，但氨氧化古菌（AOA）通常是自然环境中最丰富的硝化生物。属的成员是在未受干扰的陆地生态系统中检测到的最普遍的 AOA 群体之一，先前已报道它们具有一系列使它们的生理学与其他 AOA 物种不同的生理特征。本研究在理解这些独特的生理特征及其遗传驱动因素方面取得了重大进展。我们的研究结果强调了基于比较基因组学驱动假设的生理研究如何有助于理解 AOA 的独特生态位。
