Biofilms are indispensable ecological habitats for microbes that have garnered global attention and play a potential role in influencing the biogeochemical cycling of nitrogen. However, the biogeochemical significance of biofilms and the mechanisms by which they regulate nitrogen cycling remain elusive. In this study, we utilized DNA-stable isotope probing (DNA-SIP) labelling techniques in conjunction with metagenomics to reveal a nitrifying ecological niche in biofilms taken from the Yangtze Estuary, with those from sediment and water samples for comparison. Quantitative analysis showed that the amoA gene abundance of comammox Nitrospira (2.3 × 10³ copies ng⁻¹ DNA) was significantly higher than that of ammonia-oxidizing archaea (AOA-amoA, 62.4 copies ng⁻¹ DNA) and ammonia-oxidizing bacteria (AOB-amoA, 218.1 copies ng⁻¹ DNA) in biofilms, and the average abundance of comammox Nitrospira showed the following order: water > biofilm > sediment. Moreover, the NOB nxrB gene was more abundant than the amoA gene of ammonia oxidizers in all three media. DNA-SIP further revealed that the active comammox Nitrospira clade A mediates the nitrification process in biofilms with peak abundance at a buoyant density of 1.715 g mL⁻¹. Active nitrifying bacteria exhibit metabolic diversity in both biofilms and sediments, and occupy unique nitrifying ecological niches. Additionally, the co-occurrence network showed that chlorophyll a, NO₃⁻ and salinity emerged as the predominant physicochemical factors affecting the nitrogen transformation genes in biofilms. Taken together, this study indicates that biofilms constitute an emerging nitrifying ecological niche in estuarine environments and deepens our understanding of the mechanisms by which biofilms function in marine biogeochemistry.

中文翻译：

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Comammox Nitrospira 是长江口生物膜中的主要氨氧化剂


生物膜是微生物不可或缺的生态栖息地，引起了全球的关注，并在影响氮的生物地球化学循环方面发挥着潜在作用。然而，生物膜的生物地球化学意义及其调节氮循环的机制仍然难以捉摸。在这项研究中，我们利用 DNA 稳定同位素探测 （DNA-SIP） 标记技术与宏基因组学相结合，揭示了从长江口采集的生物膜中的硝化生态位，与来自沉积物和水样的生物膜进行比较。定量分析表明，生物膜中 comammox Nitrospira 的 amoA 基因丰度（2.3 × 10³ 拷贝 ^ng-1 DNA）显著高于氨氧化古细菌（AOA-amo A，62.4 拷贝 ^ng-1 DNA）和氨氧化细菌（AOB-amo A，218.1 拷贝 ^ng-1 DNA），并且 comammox Nitrospira 的平均丰度显示以下顺序： 水 > 生物膜 > 沉积物。此外，在所有三种培养基中，氨氧化剂的 NOB nxrB 基因都比 amoA 基因高。DNA-SIP 进一步揭示，活性共聚氨氧化 Nitrospira 分支 A 介导生物膜中的硝化过程，在 1.715 g ^mL-1 的浮力密度下具有峰值丰度。活性硝化细菌在生物膜和沉积物中都表现出代谢多样性，并占据独特的硝化生态位。此外，共生网络显示叶绿素 a、NO₃⁻ 和盐度成为影响生物膜中氮转化基因的主要理化因子。 综上所述，这项研究表明，生物膜在河口环境中构成了一个新兴的硝化生态位，并加深了我们对生物膜在海洋生物地球化学中发挥作用机制的理解。