Bai Xin, Hu Xiaojing, Liu Junjie, Gu Haidong, Jin Jian, Liu Xiaobing, Wang Guanghua
Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, China.
University of Chinese Academy of Sciences, Beijing, China.
Front Microbiol. 2022 Jul 26;13:944373. doi: 10.3389/fmicb.2022.944373. eCollection 2022.
Comammox, as a newly discovered ammonia oxidizer, urgently needs highly efficient and specific primers to detect its community structure and diversity. In this study, the performance of widely used primer set Ntsp-amoA 162F/359R and newly designed primer sets comamoA F/R, CA377f/C576r, and CB377f/C576r were evaluated, for high-throughput sequencing of comammox genes in natural and arable soils sampled from two locations in the black soil region of northeast China. Results showed that, compared with the primer set comamoA F/R, primers Ntsp-amoA 162F/359R had more advantages in detecting comammox operational taxonomic unit (OTU) numbers, diversity, and community structure. The primer sets CA377f/C576r and CB377f/C576r had an advantage in detecting comammox sequences with low relative abundance. In addition, the results of the phylogenetic tree and the relative abundance of dominant OTUs showed that the comammox in the black soils of northeast China was dominated by Clade B. Furthermore, our study found that long-term land use reduced the alpha diversity of the comammox community, but lead to the convergent evolution of community structure. The Mantel test and canonical correspondence analysis indicated that soil NO -N content was the most important factor affecting the community structure of comammox. Our study provided experience accumulation for the selection of comammox primers for high-throughput sequencing in the black soil of northeast China.
完整氨氧化微生物（Comammox）作为一种新发现的氨氧化菌，迫切需要高效且特异的引物来检测其群落结构和多样性。本研究对广泛使用的引物组Ntsp-amoA 162F/359R以及新设计的引物组comamoA F/R、CA377f/C576r和CB377f/C576r进行了性能评估，用于对采自中国东北黑土区两个地点的天然土壤和耕地土壤中的完整氨氧化微生物基因进行高通量测序。结果表明，与引物组comamoA F/R相比，引物Ntsp-amoA 162F/359R在检测完整氨氧化微生物的可操作分类单元（OTU）数量、多样性和群落结构方面具有更多优势。引物组CA377f/C576r和CB377f/C576r在检测相对丰度较低的完整氨氧化微生物序列方面具有优势。此外，系统发育树和优势OTU相对丰度的结果表明，中国东北黑土中的完整氨氧化微生物以进化枝B为主。此外，我们的研究发现，长期土地利用降低了完整氨氧化微生物群落的α多样性，但导致了群落结构的趋同进化。Mantel检验和典范对应分析表明，土壤硝态氮含量是影响完整氨氧化微生物群落结构的最重要因素。我们的研究为中国东北黑土高通量测序中完整氨氧化微生物引物的选择提供了经验积累。
