Wang Xinxin, Lu Lu, Zhou Xue, Tang Xiufeng, Kuang Lu, Chen Junhui, Shan Jun, Lu Huijie, Qin Hua, Adams Jonathan, Wang Baozhan
College of Environmental Science and Engineering, China West Normal University, Nanchong, China.
Department of Environmental Engineering, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, China.
Front Microbiol. 2021 Jan 14;11:618287. doi: 10.3389/fmicb.2020.618287. eCollection 2020.
The discovery of complete ammonia oxidation (comammox), oxidizing ammonia to nitrate via nitrite in a single organism, has redefined the traditional recognition of the two-step nitrification driven by two functional groups (ammonia-oxidizing and nitrite-oxidizing microorganisms). However, the understanding of the distribution and niche differentiation of comammox in the estuarine mudflats and their reclaimed agricultural soils is still limited. Here, we investigated the abundance, diversity and community structures of comammox in the mudflats and the reclaimed agricultural soils in the northern Yangtze River estuary. Quantitative PCR showed the abundances of genes of comammox were lower than that of ammonia-oxidizing bacteria (AOB) in nearly all samples. Amplicon sequencing of genes revealed that the community structures of comammox were significantly ( < 0.001) different between the original mudflats and the reclaimed agricultural soils, indicating niche differentiation among comammox clades (clade A.1, clade A.2, and clade B). The clade A.1 was the dominant group of comammox in the mudflats, while clade B predominated in the agricultural soils. However, the members of clade A.2 could be clearly divided into two groups, the mudflat-preferred and agricultural soil-preferred groups, suggesting more complicated ecological preferences within this sub-clade. Furthermore, it was demonstrated that salinity, organic matter (OM) and NO -N had a significantly influence on the distribution of comammox in the estuarine environment. Clade A.1 and nearly half members of clade A.2 were positively correlated with salinity, and negatively correlated with the concentrations of OM and NO -N. In contrast, the clade B and the other half members of clade A.2 showed the exact opposite pattern: a negative correlation with salinity and positive correlation with OM and NO -N. The co-occurrence network demonstrated that the operational taxonomic units (OTUs) within the same (sub-)clade were mostly positively correlated, indicating the similar niche preferences among the members from the same (sub-)clade of comammox . Taken together, our results revealed the niche differentiation of comammox in estuarine ecosystems where salinity and OM were the primary factors responsible for the distinct ecological distribution patterns.
全程氨氧化（comammox）的发现，即单个生物体可将氨经亚硝酸盐氧化为硝酸盐，这重新定义了传统上对由两个功能菌群（氨氧化微生物和亚硝酸盐氧化微生物）驱动的两步硝化作用的认识。然而，对于河口潮滩及其围垦农田土壤中全程氨氧化细菌的分布和生态位分化的了解仍然有限。在此，我们调查了长江口北部潮滩及围垦农田土壤中全程氨氧化细菌的丰度、多样性和群落结构。定量PCR结果显示，几乎在所有样本中，全程氨氧化细菌的基因丰度均低于氨氧化细菌（AOB）。对基因的扩增子测序表明，原始潮滩和围垦农田土壤中全程氨氧化细菌的群落结构存在显著差异（P<0.001），这表明全程氨氧化细菌进化枝（进化枝A.1、进化枝A.2和进化枝B）之间存在生态位分化。进化枝A.1是潮滩中全程氨氧化细菌的优势菌群，而进化枝B在农田土壤中占主导地位。然而，进化枝A.2的成员可明显分为两组，即偏好潮滩的组和偏好农田土壤的组，这表明该亚进化枝内存在更复杂的生态偏好。此外，研究表明盐度、有机质（OM）和NO₃-N对河口环境中全程氨氧化细菌的分布有显著影响。进化枝A.1和近一半的进化枝A.2成员与盐度呈正相关，与OM和NO₃-N浓度呈负相关。相反，进化枝B和另一半进化枝A.2成员呈现出相反的模式：与盐度呈负相关，与OM和NO₃-N呈正相关。共现网络表明，同一（亚）进化枝内的可操作分类单元（OTU）大多呈正相关，这表明来自全程氨氧化细菌同一（亚）进化枝的成员具有相似的生态位偏好。综上所述，我们的研究结果揭示了河口生态系统中全程氨氧化细菌的生态位分化，其中盐度和OM是导致不同生态分布模式的主要因素。
