Population genomic insights into syntrophic symbioses between marine anaerobic ciliates and intracellular methanogens

Symbiotic interactions are an ecologically and evolutionary significant phenomenon pertaining to virtually every organism on Earth. For eukaryotes inhabiting extreme environments, syntrophic symbioses with microbes may be key to successfully colonizing new niches, such as globally expanding oxygen-depleted habitats. Multi-domain symbioses between microbial eukaryotes and intracellular methanogenic archaea are crucial to understanding the origins and mechanisms of eukaryotic anaerobiosis. Nearly all anaerobic ciliates, ecologically important protists found in diverse oxygen-depleted environments, host methanogenic endosymbionts, sometimes alongside bacterial partners, that facilitate their anaerobic metabolism. Although vertical symbiont transmission necessarily occurs during ciliate cell division, symbionts might occasionally be acquired horizontally. However, patterns of host-symbiont specificity and intraspecific variability remain poorly understood. Here, we present the first intra-specific genomic analysis of both host and symbionts in such partnerships, providing key insights into the fidelity of eukaryotic-prokaryotic liaisons in anoxia. We assessed the symbiont-host co-diversification and genetic variation across eleven populations of a single undescribed Metopus species hosting Methanocorpusculum cultured from intertidal sediment locations separated by meters to 1000s of kilometers. Our results show incongruency in host mitochondrial and symbiont phylogenies, indicating a mixed transmission mode. On a genomic level, both host and symbiont populations formed distinct location-specific clusters exhibiting no signs of isolation-by-distance. Instead, ecological factors appear to have driven population genomic divergence at least partly and likely led to differences in metabolic traits. Symbiont comparative and population genomics enable us to further comprehend the complex nature of these multi-partner syntrophic symbioses, crucial to interpreting cell-cell interactions across the domains of life.