Microscopic and metatranscriptomic analyses revealed unique cross-domain parasitism between phylum Patescibacteria/candidate phyla radiation and methanogenic archaea in anaerobic ecosystems.

To verify whether members of the phylum Patescibacteria parasitize archaea, we applied cultivation, microscopy, metatranscriptomic, and protein structure prediction analyses on the Patescibacteria-enriched cultures derived from a methanogenic bioreactor. Amendment of cultures with exogenous methanogenic archaea, acetate, amino acids, and nucleoside monophosphates increased the relative abundance of . Patescibacteria. The predominant . Patescibacteria were families . Yanofskyibacteriaceae and . Minisyncoccaceae, and the former showed positive linear relationships ( ≥ 0.70) in their relative abundances, suggesting related growth patterns. and cells with attached . Yanofskyibacteriaceae and . Minisyncoccaceae, respectively, had significantly lower cellular activity than those of the methanogens without . Patescibacteria, as extrapolated from fluorescence hybridization-based fluorescence. We also observed that parasitized methanogens often had cell surface deformations. Some -like filamentous cells were dented where the submicron cells were attached. . Yanofskyibacteriaceae and . Minisyncoccaceae highly expressed extracellular enzymes, and based on structural predictions, some contained peptidoglycan-binding domains with potential involvement in host cell attachment. Collectively, we propose that the interactions of . Yanofskyibacteriaceae and . Minisyncoccaceae with methanogenic archaea are parasitisms.IMPORTANCECulture-independent DNA sequencing approaches have explored diverse yet-to-be-cultured microorganisms and have significantly expanded the tree of life in recent years. One major lineage of the domain Bacteria, . Patescibacteria (also known as candidate phyla radiation), is widely distributed in natural and engineered ecosystems and has been thought to be dependent on host bacteria due to the lack of several biosynthetic pathways and small cell/genome size. Although bacteria-parasitizing or bacteria-preying . Patescibacteria have been described, our recent studies revealed that some lineages can specifically interact with archaea. In this study, we provide strong evidence that the relationship is parasitic, shedding light on overlooked roles of . Patescibacteria in anaerobic habitats.