Culture- and genome-based characterization of a tripartite interaction between patescibacterial epibionts, methylotrophic proteobacteria, and a jumbo phage in freshwater ecosystems

Patescibacteria form a very diverse and widely distributed phylum of small bacteria that are inferred to have an episymbiotic lifestyle. However, our knowledge about the prevalence of this lifestyle within the phylum and the specificity of the hosts they interact with remains very limited due to the scarcity of cultured patescibacterial representatives. Thanks to enrichment cultures, we describe here a new tripartite interaction in freshwater ecosystems between a patescibacterium, a gammaproteobacterial host, and a phage. The patescibacterium, Strigamonas methylophilicida, belongs to a new genus within the family Absconditicoccaceae. It grows associated with species of the proteobacterial family Methylophilaceae, so far unknown to host patescibacterial epibionts. Strigamonas cells are closely attached to the host, sometimes forming stacks that connect two host cells. Despite having a surprisingly larger genome (1,9 Mb) than those of many other Patescibacteria, S. methylophilicida does not encode many essential biosynthetic pathways. This is the case of the complete biosynthesis of phospholipids, amino acids, and nucleic acids, suggesting a dependence on the host to obtain these molecules. The third player in this trio, a jumbo phage, was identified through a CRISPR spacer match in the patescibacterial genome. It has a very large genome (230 kb) that contains a wide repertoire of genes, including many that probably modify the metabolism and the cell surface of S. methylophilicida and impact the interaction with its methylotrophic host. Our results confirm a prevalent episymbiotic lifestyle in the Absconditicoccaceae and the selectivity to interact with gammaproteobacterial hosts, supporting a clade-specific adaptation of Patescibacteria to particular hosts.