Department of Environmental Geosciences, Centre for Microbiology and Environmental Systems Science, University of Vienna, Althanstrasse 14, UZA2, 1090, Vienna, Austria.
Department of Functional and Evolutionary Ecology, Archaea Biology and Ecogenomics Unit, University of Vienna, Althanstrasse 14, UZA1, 1090, Vienna, Austria.
ISME J. 2020 Nov;14(11):2659-2674. doi: 10.1038/s41396-020-0715-2. Epub 2020 Jul 14.
Ammonia-oxidizing archaea (AOA) are widespread in nature and are involved in nitrification, an essential process in the global nitrogen cycle. The enzymes for ammonia oxidation and electron transport rely heavily on copper (Cu), which can be limited in nature. In this study the model soil archaeon Nitrososphaera viennensis was investigated via transcriptomic analysis to gain insight regarding possible Cu uptake mechanisms and compensation strategies when Cu becomes limiting. Upon Cu limitation, N. viennensis exhibited impaired nitrite production and thus growth, which was paralleled by downregulation of ammonia oxidation, electron transport, carbon fixation, nucleotide, and lipid biosynthesis pathway genes. Under Cu-limitation, 1547 out of 3180 detected genes were differentially expressed, with 784 genes upregulated and 763 downregulated. The most highly upregulated genes encoded proteins with a possible role in Cu binding and uptake, such as the Cu chelator and transporter CopC/D, disulfide bond oxidoreductase D (dsbD), and multicopper oxidases. While this response differs from the marine strain Nitrosopumilus maritimus, conserved sequence motifs in some of the Cu-responsive genes suggest conserved transcriptional regulation in terrestrial AOA. This study provides possible gene regulation and energy conservation mechanisms linked to Cu bioavailability and presents the first model for Cu uptake by a soil AOA.
氨氧化古菌（AOA）广泛存在于自然界中，参与硝化作用，这是全球氮循环的一个重要过程。氨氧化和电子传递的酶严重依赖于铜（Cu），而铜在自然界中可能是有限的。在这项研究中，通过转录组分析研究了模式土壤古菌硝化螺旋菌，以深入了解在铜变得有限时可能的铜摄取机制和补偿策略。在铜限制下，N. viennensis 的亚硝酸盐产生和生长受到损害，这与氨氧化、电子传递、碳固定、核苷酸和脂质生物合成途径基因的下调相一致。在铜限制下，3180 个检测到的基因中有 1547 个差异表达，其中 784 个基因上调，763 个基因下调。上调最显著的基因编码的蛋白质可能具有铜结合和摄取的作用，如铜螯合剂和转运蛋白 CopC/D、二硫键氧化还原酶 D（dsbD）和多铜氧化酶。虽然这种反应与海洋菌株 Nitrosopumilus maritimus 不同，但一些铜响应基因中的保守序列基序表明陆地 AOA 中存在保守的转录调控。这项研究提供了与铜生物利用性相关的可能的基因调控和能量守恒机制，并提出了土壤 AOA 摄取铜的第一个模型。
