Nitrification, the oxidation of ammonia to nitrate via nitrite, is an important process in municipal wastewater treatment plants (WWTPs). Members of the Nitrospira genus that contribute to complete ammonia oxidation (comammox) have only recently been discovered and their relevance to engineered water treatment systems is poorly understood. This study investigated distributions of Nitrospira, ammonia-oxidizing archaea (AOA), and ammonia-oxidizing bacteria (AOB) in biofilm samples collected from tertiary rotating biological contactors (RBCs) of a municipal WWTP in Guelph, Ontario, Canada. Using quantitative PCR (qPCR), 16S rRNA gene sequencing, and metagenomics, our results demonstrate that Nitrospira species strongly dominate RBC biofilm samples and that comammox Nitrospira outnumber all other nitrifiers. Genome bins recovered from assembled metagenomes reveal multiple populations of comammox Nitrospira with distinct spatial and temporal distributions, including several taxa that are distinct from previously characterized Nitrospira members. Diverse functional profiles imply a high level of niche heterogeneity among comammox Nitrospira, in contrast to the sole detected AOA representative that was previously cultivated and characterized from the same RBC biofilm. Our metagenome bins also reveal two cyanase-encoding populations of comammox Nitrospira, suggesting an ability to degrade cyanate, which has only been shown previously for several Nitrospira representatives that are strict nitrite oxidizers. This study demonstrates the importance of RBCs as model systems for continued investigation of environmental factors that control the distributions and activities of AOB, AOA, comammox Nitrospira, and other nitrite oxidizers.

中文翻译：

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在城市污水处理厂的旋转生物接触器微生物群落中占主导地位的 Nitrospira 种群具有高度功能多样性。


硝化，即氨通过亚硝酸盐氧化成硝酸盐，是城市污水处理厂 (WWTP) 中的一个重要过程。有助于氨完全氧化（comammox）的 Nitrospira 属成员最近才被发现，并且人们对它们与工程水处理系统的相关性知之甚少。本研究调查了从加拿大安大略省圭尔夫市污水处理厂的三级旋转生物接触器 (RBC) 收集的生物膜样品中硝化螺菌、氨氧化古菌 (AOA) 和氨氧化细菌 (AOB) 的分布。使用定量 PCR (qPCR)、16S rRNA 基因测序和宏基因组学，我们的结果表明 Nitrospira 物种在红细胞生物膜样本中占据主导地位，并且 comammox Nitrospira 的数量超过所有其他硝化菌。从组装的宏基因组中恢复的基因组箱揭示了具有不同空间和时间分布的多个comammox Nitrospira种群，包括与先前表征的Nitrospira成员不同的几个分类单元。不同的功能特征意味着comammox Nitrospira 之间存在高度的生态位异质性，这与之前从同一红细胞生物膜中培养和表征的唯一检测到的AOA 代表形成鲜明对比。我们的宏基因组箱还揭示了两个编码氰酶的comammox Nitrospira群体，表明其具有降解氰酸盐的能力，此前仅在几种严格亚硝酸盐氧化剂的Nitrospira代表中显示出这种能力。这项研究证明了红细胞作为模型系统的重要性，用于继续研究控制 AOB、AOA、comammox Nitrospira 和其他亚硝酸盐氧化剂的分布和活性的环境因素。