Abstract:

Denitrifying anaerobic methane oxidation (DAMO) is a key process for reducing methane emissions from the natural environment. In recent years, it has been found that nitrite-dependent anaerobic methane oxidation (n-damo) bacteria exhibit different distribution characteristics and community patterns in lakes, rivers, rice fields and bioreactors. However, previous environmental investigations have mainly focused on a single ecological environment or sample type; thus, the overall role and distribution characteristics of n-damo bacteria in the global environment remain unknown. In addition, the specific preference of 16S rRNA and pmoA genes in characterizing the diversity of n-damo bacteria in different ecological environments is unclear. Therefore, to fill this research gap, this study evaluated the diversity characteristics of n-damo bacteria in different ecosystems through bioinformatics analysis based on two key genes of n-damo bacteria, 16S rRNA and pmoA. Differences were found between the genetic diversity and potential functions of n-damo bacteria, as revealed by the 16S rRNA and pmoA genes. The most conserved 16S rRNA gene had the highest diversity in the wetland environment, and the lowest diversity in the artificial enrichment environment. The pmoA gene showed the highest diversity in the freshwater environment but also showed the lowest diversity in the artificial enrichment environment. Heatmaps and Venn diagrams illustrated that the similarity of n-damo bacteria was highest in freshwater and wetland environments; however, n-damo bacteria in artificial enrichment and saltwater environments were significantly different from those in other environments. In addition, phylogenetic analysis revealed that the 16S rRNA and pmoA genes had different homology patterns, with 16S rRNA having higher homology due to its high conservation, whereas the pmoA gene showed more cluster differentiation. These results provide important insights into the contribution of DAMO microorganisms to methane emission reduction and the carbon/nitrogen biogeochemical cycles in different ecosystems. Future environmental investigations of n-damo bacteria should simultaneously analyze the 16S rRNA and pmoA genes, to obtain a more scientific and comprehensive evaluation of the distribution and function of n-damo bacteria.

Key words: Denitrifying anaerobic methane oxidation (DAMO), nitrite-dependent anaerobic methane oxidation (n-damo) bacteria, 16S rRNA gene, pmoAgene, bioinformatics analysis, genetic diversity

摘要：

反硝化厌氧甲烷氧化（DAMO）是自然环境中减少甲烷排放的关键过程。近年来研究发现，亚硝酸盐依赖型厌氧甲烷氧化（n-damo）细菌在湖泊、河流、稻田和生物反应器等环境中表现出不同的分布特征和群落格局。然而，以往的环境调研主要集中在单一生态环境或样本类型，使得n-damo细菌在全球生态格局中的总体作用和分布特征仍然存在一定的未知。此外，在描述不同生态环境中n-damo细菌多样性时，16S rRNA和pmoA基因之间的具体区别或偏好性尚不清楚。因此，为了填补这一研究空白，基于n-damo细菌的两个关键基因，即16S rRNA和pmoA，通过生物信息学分析来评估不同生态系统中n-damo细菌的多样性特征。研究发现，16S rRNA和pmoA基因所揭示的n-damo细菌遗传多样性和潜在功能存在差异。保守性更高的16S rRNA基因在湿地环境中多样性最高，而在人工富集环境中多样性最低。pmoA基因则在淡水环境中表现出最高的多样性，但也同样在人工富集环境中表现出最低的多样性。热图和韦恩图显示，淡水环境和湿地环境中n-damo细菌的相似性最高，但人工富集和咸水环境下的n-damo细菌与其他环境差异显著。此外，系统发育分析显示，16S rRNA与pmoA基因具有不同的同源模式，16S rRNA因其保守性而具有较高的同源性，而pmoA基因则表现出更多的簇族分化。这些结果为了解DAMO微生物对不同生态系统中甲烷减排和碳氮生物地球化学循环的贡献提供了重要见解。此外，未来n-damo细菌的环境调研工作应同时分析16S rRNA和pmoA基因，从而对n-damo细菌的分布和功能进行更加科学地综合评价。

关键词: 反硝化厌氧甲烷氧化（DAMO）, 亚硝酸盐依赖型厌氧甲烷氧化细菌（n-damo细菌）, 16S rRNA基因, pmoA基因, 生物信息学分析, 遗传多样性