呼和浩特市周边地下水CPR和DPANN类群的检测及多样性分析

Diversity of CPR and DPANN in groundwater around Hohhot City

摘要:

【背景】候选门级辐射类群(candidate phyla radiation, CPR)和DPANN是与绝大多数已知细菌和古菌具有显著差异的独特类群，因发现较晚，人们对其认识还非常有限。已知二者类群庞大、存在广泛，但在不同生境中的多样性研究还较少，生态功能尚属未知。【目的】分析不同地下水中CPR和DPANN的多样性，探讨不同方法对CPR和DPANN检出及富集的影响。【方法】采用0.1 μm滤膜收集菌体和宏基因组测序的方法分析呼和浩特市周边4个不同地下水中CPR和DPANN的多样性。比较宏基因组测序与16S rRNA基因扩增子测序对CPR和DPANN检出的影响，以及不同过滤方式和不同滤膜组合对CPR和DPANN富集的作用。【结果】4个地下水样品CPR类群检出33−64个菌门，相对丰度在0.17%−1.67%之间；DPANN检出1−7个菌门，相对丰度在0.000 93%−0.071 00%之间。对于CPR和DPANN，16S rRNA基因V3−V4区扩增子测序仅检出了纳古菌门(Nanoarchaeota)。1.2 μm与0.1 μm滤膜组合具有最好的CPR和DPANN富集效果，在及时更换滤膜的过滤方式下相对丰度分别提高到13.33%和0.58%。【结论】地下水中存在种类丰富但相对丰度较低的CPR和DPANN物种资源，且不同地下水中的CPR和DPANN存在一定的差异。16S rRNA基因V3−V4区扩增子测序会遗漏地下水中CPR和DPANN物种信息。在及时更换滤膜的过滤方式下采用不同孔径滤膜组合过滤会显著提高CPR和DPANN的相对丰度，达到富集效果。本研究为后续CPR和DPANN物种资源、基因资源和天然产物资源的挖掘，以及该类菌株的可培养工作奠定了基础。

Abstract:

[Background] Candidate phyla radiation (CPR) and DPANN are unique groups that are significantly different from most known bacteria and archaea, and the knowledge about them is limited due to the late discovery. The two groups are known to be large and widespread, while their diversity and ecological roles in different habitats remain to be studied. [Objective] To analyze the diversity of CPR and DPANN in different groundwater samples and the influences of different methods on the detection and enrichment of CPR and DPANN. [Methods] Metagenomic sequencing was employed to determine the diversity of CPR and DPANN in four different groundwater samples around Hohhot after filtration through a 0.1 μm membrane. Metagenomic sequencing was compared with 16S rRNA gene amplicon sequencing regarding the detection of CPR and DPANN, and the effects of different filtration methods and membrane combinations on the enrichment of CPR and DPANN were compared. [Results] From the 4 groundwater samples, 33-64 phyla of CPR with the relative abundance of 0.17%-1.67% and 1-7 phyla of DPANN with the relative abundance of 0.000 93%-0.071% were detected. For CPR and DPANN, only Nanoarchaeota was detected by 16S rRNA gene V3-V4 amplicon sequencing. The combination of 1.2μm and 0.1 μm filters showed the best enrichment effect on CPR and DPANN, and the relative abundance increased to 13.33% and 0.58%, respectively, by timely replacement of filters. [Conclusion] There were abundant resources of CPR and DPANN with low relative abundance in groundwater, and the distribution of CPR and DPANN varied in different groundwater samples. The 16S rRNA gene V3-V4 amplicon sequencing missed the information of CPR and DPANN in groundwater. The enrichment effect on CPR and DPANN can be significantly improved by the combination of filters with different pore sizes and the timely replacement of filters. The findings underpin the further exploration of species, gene, and natural product resources and the strain culture of CPR and DPANN.