Diversity of CPR and DPANN in groundwater around Hohhot City

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.