Symbiotic relationships between eukaryotes and prokaryotes played pivotal roles in the evolution of life and drove the emergence of specialized symbiotic structures in animals, plants and fungi. The host-evolved symbiotic structures of microbial eukaryotes - the vast majority of such hosts in nature - remain largely unstudied. Here we describe highly structured symbiosomes within three free-living anaerobic protists (Anaeramoeba spp.). We dissect this symbiosis using complete genome sequencing and transcriptomics of host and symbiont cells coupled with fluorescence in situ hybridization, and 3D reconstruction using focused-ion-beam scanning electron microscopy. The emergence of the symbiosome is underpinned by expansion of gene families encoding regulators of membrane trafficking and phagosomal maturation and extensive bacteria-to-eukaryote lateral transfer. The symbionts reside deep within a symbiosomal membrane network that enables metabolic syntrophy by precisely positioning sulfate-reducing bacteria alongside host hydrogenosomes. Importantly, the symbionts maintain connections to the Anaeramoeba plasma membrane, blurring traditional boundaries between ecto- and endosymbiosis.

Centre for Life's Origin and Evolution Department of Genetics Evolution and Environment University College London UK

Department of Biochemistry University of Cambridge Cambridge UK

Department of Biology Lund University Lund Sweden

Department of Cell and Molecular Biology Uppsala Universitet Uppsala Sweden

Department of Parasitology Faculty of Science Charles University BIOCEV Vestec Czechia

Department of Zoology Faculty of Science Charles University Prague Czechia

Division of Infectious Diseases Department of Medicine Faculty of Medicine and Dentistry and Department of Biological Sciences University of Alberta Edmonton AB Canada

Institute for Comparative Genomics Department of Biochemistry and Molecular Biology Dalhousie University Halifax NS Canada

Institute of Parasitology Biology Centre Czech Academy of Sciences České Budějovice Czechia

Life Science Research Centre Department of Biology and Ecology Faculty of Science University of Ostrava Ostrava Czechia

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