Li Jiyun, Hua Zheng-Shuang, Liu Tao, Wang Chengwen, Li Jie, Bai Ge, Lücker Sebastian, Jetten Mike S M, Zheng Min, Guo Jianhua
School of Environment, Tsinghua University, Beijing, China.
Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei, People's Republic of China.
ISME Commun. 2021 Mar 25;1(1):7. doi: 10.1038/s43705-021-00005-3.
The discovery of complete ammonia-oxidizing (comammox) Nitrospira has added an important new process to the microbial nitrogen cycle. While comammox Nitrospira have been detected in various ecosystems, only few studies have achieved their enrichment over other canonical nitrifiers. Here, we obtained a selective enrichment of comammox Nitrospira in a urine-fed membrane bioreactor in less than 200 days. By using 16S rRNA gene amplicon sequencing and quantitative PCR of the functional marker gene amoA, we observed a dominance (up to 30% relative abundance) of comammox Nitrospira over ammonia-oxidizing bacteria and archaea. Furthermore, the complete genomes of three new clade A comammox Nitrospira were recovered by metagenomics. These three strains were divergent from previously reported comammox species according to comparative genome and amoA-based analyses. In addition to the key genes for ammonia and nitrite oxidation, the three recovered genomes contained a complete urea utilization pathway. Our findings suggest that the urea present in the urine media played a significant role in the selective enrichment of these novel comammox Nitrospira, and support the diversity and versatility of their metabolism.
完全氨氧化（comammox）硝化螺旋菌的发现为微生物氮循环增添了一个重要的新过程。虽然在各种生态系统中都检测到了comammox硝化螺旋菌，但只有少数研究实现了其相对于其他典型硝化菌的富集。在此，我们在以尿液为进料的膜生物反应器中不到200天就实现了comammox硝化螺旋菌的选择性富集。通过使用16S rRNA基因扩增子测序和功能标记基因amoA的定量PCR，我们观察到comammox硝化螺旋菌相对于氨氧化细菌和古菌占主导地位（相对丰度高达30%）。此外，通过宏基因组学获得了三个新的A类comammox硝化螺旋菌的完整基因组。根据比较基因组和基于amoA的分析，这三个菌株与先前报道的comammox物种不同。除了氨和亚硝酸盐氧化的关键基因外，这三个获得的基因组还包含完整的尿素利用途径。我们的研究结果表明，尿液培养基中存在的尿素在这些新型comammox硝化螺旋菌的选择性富集中发挥了重要作用，并支持了它们代谢的多样性和多功能性。
