Bayer Barbara, Vojvoda Jana, Offre Pierre, Alves Ricardo J E, Elisabeth Nathalie H, Garcia Juan Al, Volland Jean-Marie, Srivastava Abhishek, Schleper Christa, Herndl Gerhard J
Department of Limnology and Bio-Oceanography, University of Vienna, Vienna, Austria.
National Institute of Biology, Fornace 41, Piran, Slovenia.
ISME J. 2016 May;10(5):1051-63. doi: 10.1038/ismej.2015.200. Epub 2015 Nov 3.
Ammonia-oxidizing Archaea (AOA) are ubiquitous throughout the oceanic water column; however, our knowledge on their physiological and ecological diversity in different oceanic regions is rather limited. Here, we report the cultivation and characterization of two novel Nitrosopumilus strains, originating from coastal surface waters of the Northern Adriatic Sea. The combined physiological and genomic information revealed that each strain exhibits different metabolic and functional traits, potentially reflecting contrasting life modes. Strain NF5 contains many chemotaxis-related genes and is able to express archaella, suggesting that it can sense and actively seek favorable microenvironments such as nutrient-rich particles. In contrast, strain D3C is non-motile and shows higher versatility in substrate utilization, being able to use urea as an alternative substrate in addition to ammonia. Furthermore, it encodes a divergent, second copy of the AmoB subunit of the key enzyme ammonia monooxygenase, which might have an additional catalytic function and suggests further metabolic versatility. However, the role of this gene requires further investigation. Our results provide evidence for functional diversity and metabolic versatility among phylogenetically closely related thaumarchaeal strains, and point toward adaptations to free-living versus particle-associated life styles and possible niche differentiation among AOA in marine ecosystems.
氨氧化古菌（AOA）在整个海洋水柱中普遍存在；然而，我们对其在不同海洋区域的生理和生态多样性的了解相当有限。在此，我们报告了源自亚得里亚海北部沿海水域的两株新型亚硝化侏儒菌（Nitrosopumilus）菌株的培养和特性。综合的生理和基因组信息表明，每株菌株都表现出不同的代谢和功能特征，这可能反映了不同的生活方式。NF5菌株包含许多与趋化作用相关的基因，并且能够表达古菌鞭毛，这表明它能够感知并积极寻找有利的微环境，如富含营养的颗粒。相比之下，D3C菌株不能运动，在底物利用方面表现出更高的多样性，除了氨之外还能够利用尿素作为替代底物。此外，它编码关键酶氨单加氧酶的AmoB亚基的一个不同的第二拷贝，这可能具有额外的催化功能，并表明其具有进一步的代谢多样性。然而，该基因的作用需要进一步研究。我们的结果为系统发育密切相关的奇古菌门（Thaumarchaeota）菌株之间的功能多样性和代谢多功能性提供了证据，并表明了它们对自由生活与颗粒附着生活方式的适应性以及海洋生态系统中AOA之间可能的生态位分化。
