BACKGROUND Thaumarchaeota are abundant in the Amazon River, where they are the only ammonia-oxidizing archaea. Despite the importance of Thaumarchaeota, little is known about their physiology, mainly because few isolates are available for study. Therefore, information about Thaumarchaeota was obtained primarily from genomic studies. The aim of this study was to investigate the ecological roles of Thaumarchaeota in the Amazon River and the Amazon River plume. RESULTS The archaeal community of the shallow in Amazon River and its plume is dominated by Thaumarchaeota lineages from group 1.1a, which are mainly affiliated to Candidatus Nitrosotenuis uzonensis, members of order Nitrosopumilales, Candidatus Nitrosoarchaeum, and Candidatus Nitrosopelagicus sp. While Thaumarchaeota sequences have decreased their relative abundance in the plume, Candidatus Nitrosopelagicus has increased. One genome was recovered from metagenomic data of the Amazon River (ThauR71 [1.05 Mpb]), and two from metagenomic data of the Amazon River plume (ThauP25 [0.94 Mpb] and ThauP41 [1.26 Mpb]). Phylogenetic analysis placed all three Amazon genome bins in Thaumarchaeota Group 1.1a. The annotation revealed that most genes are assigned to the COG subcategory coenzyme transport and metabolism. All three genomes contain genes involved in the hydroxypropionate/hydroxybutyrate cycle, glycolysis, tricarboxylic acid cycle, oxidative phosphorylation. However, ammonia-monooxygenase genes were detected only in ThauP41 and ThauR71. Glycoside hydrolases and auxiliary activities genes were detected only in ThauP25. CONCLUSIONS Our data indicate that Amazon River is a source of Thaumarchaeota, where these organisms are important for primary production, vitamin production, and nitrification.

中文翻译：

---

通过基因组解析的宏基因组学分析，可以深入了解Thaumarchaeota在亚马逊河及其羽流中的生态作用。

背景技术伞形藻在亚马逊河中丰富，是唯一的氨氧化古细菌。尽管Thaumarchaeota的重要性，但对其生理机制知之甚少，主要是因为很少有分离株可用于研究。因此，有关Thaumarchaeota的信息主要来自基因组研究。这项研究的目的是调查Thaumarchaeota在亚马逊河和亚马逊河羽流中的生态作用。结果亚马孙河及其羽状流中的古细菌群落主要由1.1a族的伞形藻属谱系支配，这些谱系主要与乌氏念珠菌，亚硝化伞菌，尼古拉菌念珠菌和尼古拉菌藻属有关。尽管Thaumarchaeota序列降低了羽流中的相对丰度，Nitrosopelagicus念珠菌有所增加。从亚马孙河的宏基因组学数据（ThauR71 [1.05 Mpb]）中恢复了一个基因组，从亚马孙河羽流的宏基因组学数据（ThauP25 [0.94 Mpb]和ThauP41 [1.26 Mpb]）中恢复了两个基因组。系统发育分析将所有三个亚马逊基因组箱都放入了Thaumarchaeota Group 1.1a。注释表明，大多数基因被分配给COG子类别辅酶运输和代谢。这三个基因组均包含参与羟基丙酸酯/羟基丁酸酯循环，糖酵解，三羧酸循环，氧化磷酸化的基因。但是，仅在ThauP41和ThauR71中检测到氨单加氧酶基因。仅在ThauP25中检测到糖苷水解酶和辅助活性基因。结论我们的数据表明，亚马逊河是Thaumarchaeota的来源，