Genome-resolved metagenomics reveals site-specific diversity of episymbiotic CPR bacteria and DPANN archaea in groundwater ecosystems

Jillian F. Banfield,Michael L. Whittaker,Jennifer A. Doudna,Ibrahim F. Farag,Christine He,Ray Keren,Jamie H. D. Cate

doi:10.1038/s41564-020-00840-5

Abstract

Candidate phyla radiation (CPR) bacteria and DPANN archaea are unisolated, small-celled symbionts that are often detected in groundwater. The effects of groundwater geochemistry on the abundance, distribution, taxonomic diversity and host association of CPR bacteria and DPANN archaea has not been studied. Here, we performed genome-resolved metagenomic analysis of one agricultural and seven pristine groundwater microbial communities and recovered 746 CPR and DPANN genomes in total. The pristine sites, which serve as local sources of drinking water, contained up to 31% CPR bacteria and 4% DPANN archaea. We observed little species-level overlap of metagenome-assembled genomes (MAGs) across the groundwater sites, indicating that CPR and DPANN communities may be differentiated according to physicochemical conditions and host populations. Cryogenic transmission electron microscopy imaging and genomic analyses enabled us to identify CPR and DPANN lineages that reproducibly attach to host cells and showed that the growth of CPR bacteria seems to be stimulated by attachment to host-cell surfaces. Our analysis reveals site-specific diversity of CPR bacteria and DPANN archaea that coexist with diverse hosts in groundwater aquifers. Given that CPR and DPANN organisms have been identified in human microbiomes and their presence is correlated with diseases such as periodontitis, our findings are relevant to considerations of drinking water quality and human health.

Highlights

Metagenome-enabled phylogenomic analyses have led to the classification of two groups of organisms that lack pure culture representatives—the Candidate phyla radiation (CPR) bacteria and DPANN archaea1–4
We recovered a total of 746 draft quality CPR and DPANN genomes that derive from most of the major lineages within both radiations and from two apparently new phylum-level lineages within the CPR, hereafter named ‘Candidatus Genascibacteria’ and ‘Candidatus Montesolbacteria’
Our findings suggest that characterization of microbiomes of additional groundwater sites— using 0.1 μm filters rather than 0.22 μm filters and binning of metagenome-assembled genomes (MAGs) to capture maximum CPR/DPANN diversity—is likely to reveal further diversity in the CPR and DPANN radiations

Summary

Introduction

Metagenome-enabled phylogenomic analyses have led to the classification of two groups of organisms that lack pure culture representatives—the CPR bacteria and DPANN archaea. The variation in the abundance and distribution of CPR and DPANN organisms in groundwater environments, their roles and their relationships with host organisms are not well characterized. Subsurface environments such as groundwater are difficult to sample and are poorly characterized compared with surface environments, despite harbouring an estimated 90% of all bacterial biomass. Most of the available near-complete CPR and DPANN genomes are from just two aquifers. Most of the available near-complete CPR and DPANN genomes are from just two aquifers2,19,22 In this Article, to investigate the roles that CPR and DPANN organisms may have in groundwater ecosystems, we applied genome-resolved metagenomics to analyse eight groundwater communities in Northern California, and cryogenic transmission electron microscopy (cryo-TEM) to image the community with the highest abundance of CPR/DPANN organisms

Methods

Results

Conclusion