SZU-HKUST Joint Ph.D. Program in Marine Environmental Science, Shenzhen University, Shenzhen, China.
Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, China.
Appl Environ Microbiol. 2020 Sep 1;86(18). doi: 10.1128/AEM.00736-20.
Ammonia-oxidizing archaea (AOA) are ubiquitous in diverse ecosystems and play a pivotal role in global nitrogen and carbon cycling. Although AOA diversity and distribution are widely studied, mainly based on the (alpha subunit of ammonia monooxygenase) genotypes, only limited investigations have addressed the relationship between AOA genetic adaptation, metabolic features, and ecological niches, especially in estuaries. Here, we describe the AOA communities along the Jiulong River estuary in southern China. Nine high-quality AOA metagenome-assembled genomes (MAGs) were obtained by metagenomics. Five of the MAGs are proposed to constitute a new species, " Nitrosopumilus aestuariumsis" sp. nov., based on the phylogenies of the 16S and 23S rRNA genes and concatenated ribosomal proteins, as well as the average amino acid identity. Comparative genomic analysis revealed unique features of the new species, including a high number of genes related to diverse carbohydrate-active enzymes, phosphatases, heavy-metal transport systems, flagellation, and chemotaxis. These genes may be crucial for AOA adaptation to the eutrophic and heavy-metal-contaminated Jiulong River estuary. The uncovered detailed genomic characteristics of the new estuarine AOA species highlight AOA contributions to ammonia oxidation in the Jiulong River estuary. In this study, AOA communities along a river in southern China were characterized, and metagenome-assembled genomes (MAGs) of a novel AOA clade were also obtained. Based on the characterization of AOA genomes, the study suggests adaptation of the novel AOAs to estuarine environments, providing new information on the ecology of estuarine AOA and the nitrogen cycle in contaminated estuarine environments.
氨氧化古菌（AOA）广泛存在于各种生态系统中，在全球氮碳循环中起着关键作用。尽管 AOA 的多样性和分布已得到广泛研究，主要基于氨单加氧酶（alpha 亚基）基因型，但仅有有限的研究涉及 AOA 的遗传适应、代谢特征和生态位之间的关系，特别是在河口。在这里，我们描述了中国南方九龙江河口的 AOA 群落。通过宏基因组学获得了 9 个高质量的 AOA 宏基因组组装基因组（MAG）。基于 16S 和 23S rRNA 基因以及串联核糖体蛋白的系统发育以及平均氨基酸同一性，其中 5 个 MAG 被提议构成一个新的物种，即“Nitrosopumilus aestuariumsis”sp. nov.。比较基因组分析揭示了新物种的独特特征，包括与多种碳水化合物活性酶、磷酸酶、重金属转运系统、鞭毛和趋化性相关的基因数量众多。这些基因可能对 AOA 适应富营养化和重金属污染的九龙江河口至关重要。新发现的河口 AOA 物种的详细基因组特征揭示了 AOA 对九龙江河口氨氧化的贡献。在本研究中，对中国南方一条河流的 AOA 群落进行了特征描述，并获得了新型 AOA 分支的宏基因组组装基因组（MAG）。基于 AOA 基因组的特征，该研究表明新型 AOAs 适应河口环境，为河口 AOA 的生态学和受污染河口环境中的氮循环提供了新信息。
