The recent discovery of comammox Nitrospira as complete nitrifiers has fundamentally renewed perceptions of nitrogen cycling in natural and engineered systems, yet little is known about the environmental controls on these newly recognized bacteria. Based on improved phylogenetic resolution through successful assembly of ten novel genomes (71–96% completeness), we provided the first biogeographic patterns for planktonic and benthic comammox Nitrospira in the Yangtze River over a 6030 km continuum. Our study revealed the widespread distributions and relative abundance of comammox Nitrospira in this large freshwater system, constituting 30 and 46% of ammonia-oxidizing prokaryotes (AOPs) and displaying 30.4- and 17.9-fold greater abundances than canonical Nitrospira representatives in water and sediments, respectively. Comammox Nitrospira contributed more to nitrifier abundances (34–87% of AOPs) in typical oligotrophic environments with a higher pH and lower temperature, particularly in the plateau (clade B), mountain and foothill (clade A) areas of the upper reach. The dominant position of planktonic comammox Nitrospira was replaced by canonical Nitrospira sublineages I/II and ammonia-oxidizing bacteria from the plateau to downstream plain due to environmental selection, while the dissimilarity of benthic comammox Nitrospira was moderately associated with geographic distance. A substantial decrease (83%) in benthic comammox Nitrospira abundance occurred immediately downstream of the Three Gorges Dam, consistent with a similarly considerable decrease in overall sediment bacterial taxa. Together, this study highlights the previously unrecognized dominance of comammox Nitrospira in major river systems and underlines the importance of revisiting the distributions of and controls on nitrification processes within global freshwater environments.

最近发现comammox Nitrospira作为完全硝化菌，从根本上更新了人们对自然和工程系统中氮循环的认识，但人们对这些新认识的细菌的环境控制知之甚少。基于通过成功组装十个新基因组（完整性为 71-96%）而提高的系统发育分辨率，我们提供了长江流域 6030 公里连续体中浮游和底栖 comammox Nitrospira的第一个生物地理模式。我们的研究揭示了comammox Nitrospira在这个大型淡水系统中的广泛分布和相对丰度，占氨氧化原核生物（AOP）的30％和46％，并且丰度比水和沉积物中典型的Nitrospira代表高30.4倍和17.9倍，分别。在pH值较高、温度较低的典型贫营养环境中，Comammox Nitrospira对硝化菌丰度（AOP的34-87%）贡献较大，特别是在上游的高原（B分支）、山地和山麓（A分支）地区。由于环境选择，浮游comammox Nitrospira的优势地位被典型的Nitrospira亚系I/II和氨氧化细菌从高原向下游平原所取代，而底栖comammox Nitrospira的差异性与地理距离呈中度相关。三峡大坝下游的底栖comammox Nitrospira丰度大幅下降（83%），这与沉积物总体细菌类群的类似大幅下降一致。 总之，这项研究强调了以前未被认识到的comammox Nitrospira在主要河流系统中的主导地位，并强调了重新审视全球淡水环境中硝化过程的分布和控制的重要性。