Expanded metabolic versatility of ubiquitous nitrite-oxidizing bacteria from the genus Nitrospira
Expanded metabolic versatility of ubiquitous nitrite-oxidizing bacteria from the genus Nitrospira
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DOI：
10.1073/pnas.1506533112
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发表时间：
2015-09-08
影响因子：
11.1
通讯作者：
Daims, Holger
中科院分区：
文献类型：
--
作者：
Koch, Hanna;Luecker, Sebastian;Daims, Holger
硝化螺菌是一类多样化的亚硝酸盐氧化细菌，也是环境中最广泛分布的硝化菌之一。然而，他们仍然很少被研究，而且大多没有被培养。根据代表普遍存在的 Nitrospira 谱系 II 的莫斯科 Nitrospira moscoviensis 的基因组和实验数据，我们确定了有助于 Nitrospira 生态成功的生态生理特征。出乎意料的是，莫斯科新丝虫拥有编码脲酶的基因，并将尿素裂解为氨和二氧化碳。在亚硝酸盐氧化剂中尚未观察到尿素分解，这使得莫斯科新孢子虫能够向缺乏脲酶的氨氧化剂提供来自尿素的氨，而尿素被该菌群通过相互喂养而完全硝化。活性污泥中的慢硝化螺菌、土壤和淡水栖息地的宏基因组中以及海洋亚硝酸盐氧化剂中的其他脲酶中存在高度相似的脲酶基因，这表明氨和亚硝酸盐氧化剂之间的这种扩展相互作用广泛分布，这使得亚硝酸盐氧化细菌能够间接利用尿素作为能量来源。可溶性甲酸脱氢酶提供了额外的生态生理灵活性，并允许莫斯科小蚊使用甲酸，无论是否伴随亚硝酸盐氧化，使用氧、硝酸盐或两种化合物作为末端电子受体。与谱系 I 的 Nitrospira defluvii 相比，N. moscoviensis 具有 Nitrospira 核心代谢，但显示出显着的基因组差异，包括适应高氧浓度的基因。相互摄食和代谢多样性，包括参与不同的氮循环过程，可能是自然和工程生态系统中 Nitrospira 的生态位划分、普遍性和高度多样性的关键因素。
Nitrospira are a diverse group of nitrite-oxidizing bacteria and among the environmentally most widespread nitrifiers. However, they remain scarcely studied and mostly uncultured. Based on genomic and experimental data from Nitrospira moscoviensis representing the ubiquitous Nitrospira lineage II, we identified ecophysiological traits that contribute to the ecological success of Nitrospira. Unexpectedly, N. moscoviensis possesses genes coding for a urease and cleaves urea to ammonia and CO2. Ureolysis was not observed yet in nitrite oxidizers and enables N. moscoviensis to supply ammonia oxidizers lacking urease with ammonia from urea, which is fully nitrified by this consortium through reciprocal feeding. The presence of highly similar urease genes in Nitrospira lenta from activated sludge, in metagenomes from soils and freshwater habitats, and of other ureases in marine nitrite oxidizers, suggests a wide distribution of this extended interaction between ammonia and nitrite oxidizers, which enables nitrite-oxidizing bacteria to indirectly use urea as a source of energy. A soluble formate dehydrogenase lends additional ecophysiological flexibility and allows N. moscoviensis to use formate, with or without concomitant nitrite oxidation, using oxygen, nitrate, or both compounds as terminal electron acceptors. Compared with Nitrospira defluvii from lineage I, N. moscoviensis shares the Nitrospira core metabolism but shows substantial genomic dissimilarity including genes for adaptations to elevated oxygen concentrations. Reciprocal feeding and metabolic versatility, including the participation in different nitrogen cycling processes, likely are key factors for the niche partitioning, the ubiquity, and the high diversity of Nitrospira in natural and engineered ecosystems.