The association between anaerobic ciliates and methanogenic archaea has been recognized for over a century. Nevertheless, knowledge of these associations is limited to a few ciliate species, and so the identification of patterns of host-symbiont specificity has been largely speculative. In this study, we integrated microscopy and genetic identification to survey the methanogenic symbionts of 32 free-living anaerobic ciliate species, mainly from the order Metopida. Based on Sanger and Illumina sequencing of the 16S rRNA gene, our results show that a single methanogenic symbiont population, belonging to Methanobacterium, Methanoregula, or Methanocorpusculum, is dominant in each host strain. Moreover, the host's taxonomy (genus and above) and environment (i.e. endobiotic, marine/brackish, or freshwater) are linked with the methanogen identity at the genus level, demonstrating a strong specificity and fidelity in the association. We also established cultures containing artificially co-occurring anaerobic ciliate species harboring different methanogenic symbionts. This revealed that the host-methanogen relationship is stable over short timescales in cultures without evidence of methanogenic symbiont exchanges, although our intraspecific survey indicated that metopids also tend to replace their methanogens over longer evolutionary timescales. Therefore, anaerobic ciliates have adapted a mixed transmission mode to maintain and replace their methanogenic symbionts, allowing them to thrive in oxygen-depleted environments.

• Keywords
• anaerobiosis, archaea, endosymbionts, methane, symbiosis, syntrophy, transmission mode,
• MeSH
• Anaerobiosis MeSH
• Ciliophora * classification   genetics   physiology   MeSH
• DNA, Archaeal genetics   MeSH
• Ecosystem * MeSH
• Phylogeny * MeSH
• Methane * metabolism   MeSH
• RNA, Ribosomal, 16S * genetics   MeSH
• Sequence Analysis, DNA MeSH
• Symbiosis * MeSH
• Publication type
• Journal Article MeSH
• Names of Substances
• DNA, Archaeal MeSH
• Methane * MeSH
• RNA, Ribosomal, 16S * MeSH

Ciliates are a diverse group of protists known for their ability to establish various partnerships and thrive in a wide variety of oxygen-depleted environments. Most anaerobic ciliates harbor methanogens, one of the few known archaea living intracellularly. These methanogens increase the metabolic efficiency of host fermentation via syntrophic use of host end-product in methanogenesis. Despite the ubiquity of these symbioses in anoxic habitats, patterns of symbiont specificity and fidelity are not well known. We surveyed two unrelated, commonly found groups of anaerobic ciliates, the Plagiopylea and Metopida, isolated from anoxic marine sediments. We sequenced host 18S rRNA and symbiont 16S rRNA marker genes as well as the symbiont internal transcribed spacer region from our cultured ciliates to identify hosts and their associated methanogenic symbionts. We found that marine ciliates from both of these co-occurring, divergent groups harbor closely related yet distinct intracellular archaea within the Methanocorpusculum genus. The symbionts appear to be stable at the host species level, but at higher taxonomic levels, there is evidence that symbiont replacements have occurred. Gaining insight into this unique association will deepen our understanding of the complex transmission modes of marine microbial symbionts, and the mutualistic microbial interactions occurring across domains of life.

• Keywords
• Metopida, Plagiopylea, anaerobic protists, anoxic sediments, archaea, methanogens, symbiosis, syntrophy,
• MeSH
• Anaerobiosis MeSH
• Ciliophora * classification   genetics   physiology   MeSH
• DNA, Archaeal genetics   chemistry   MeSH
• Phylogeny * MeSH
• Geologic Sediments * microbiology   MeSH
• Seawater microbiology   parasitology   MeSH
• RNA, Ribosomal, 16S * genetics   MeSH
• RNA, Ribosomal, 18S genetics   MeSH
• Sequence Analysis, DNA MeSH
• Symbiosis * MeSH
• Publication type
• Journal Article MeSH
• Names of Substances
• DNA, Archaeal MeSH
• RNA, Ribosomal, 16S * MeSH
• RNA, Ribosomal, 18S MeSH