An anaerobic Legionellales symbiont in Anaeramoeba pumila

Anaeramoeba pumila is a free-living anaerobic amoeba and the smallest known member of the Anaeramoebae, a phylum characterized by elaborate membrane-bound symbiosomes housing sulfate-reducing bacterial symbionts. Here, we report a draft nuclear genome assembly of A. pumila LANTAAN and describe the discovery, genomic characterization, and metabolic reconstruction of Candidatus Centrionella anaeramoebae gen. nov., sp. nov., an obligate intracellular symbiont of A. pumila belonging to the order Legionellales. Ca. Centrionella is a rare anaerobic member of Legionellales, a lineage otherwise comprising aerobic intracellular pathogens. Its genome (1.52 Mbp, 1,249 genes) is highly reduced and encodes an entirely anaerobic metabolism centered on substrate-level phosphorylation, arginine fermentation, and hydrogen oxidation via a bidirectional [NiFe]-hydrogenase -- metabolic strategies that parallel those independently evolved in the distantly related Anoxychlamydiales. The complete Dot/Icm type IVB secretion system is retained and likely mediates ongoing host manipulation, including via a large repertoire of predicted effector proteins. Strikingly, Ca. Centrionella has acquired eukaryotic Rac1-like GTPase genes from its host through horizontal gene transfer, with subsequent domain shuffling and duplication, that it may use to manipulate the cytoskeleton of its host. Unlike other Anaeramoeba symbionts, Centrionella localizes to the host microtubule-organizing center rather than a symbiosome, a localization consistent with cytoskeletal anchoring strategies described in other endosymbionts. The symbiosome, present in other Anaeramoeba species, appears to have been secondarily lost in A. pumila. A co-occurring Desulfobacter sp. LANTAAN, related to symbionts of other Anaeramoebidae, likely forms a tripartite syntrophic consortium by consuming hydrogenosomal fermentation end-products and supplying vitamin B12. Together, these findings illuminate the evolutionary transition in Legionellales from aerobic pathogenesis to anaerobic mutualism, providing a new model for the origins of intracellular symbiosis.