The genome of an endosymbiotic methanogen is very similar to those of its free‐living relatives

Abstract

The methanogenic endosymbionts of anaerobic protists represent the only known intracellular archaea, yet, almost nothing is known about genome structure and content in these lineages. Here, an almost complete genome of an intracellular Methanobacterium species was assembled from a metagenome derived from its host ciliate, a Heterometopus species. Phylogenomic analysis showed that the endosymbiont was closely related to free-living Methanobacterium isolates, and when compared with the genomes of free-living Methanobacterium, the endosymbiont did not show significant reduction in genome size or GC content. Additionally, the Methanobacterium endosymbiont genome shared the majority of its genes with its closest relative, though it did also contain unique genes possibly involved in interactions with the host via membrane-associated proteins, the removal of toxic by-products from host metabolism and the production of small signalling molecules. Though anaerobic ciliates have been shown to transmit their endosymbionts to daughter cells during division, the results presented here could suggest that the endosymbiotic Methanobacterium did not experience significant genetic isolation or drift and/or that this lineage was only recently acquired. Altogether, comparative genomic analysis identified genes potentially involved in the establishment and maintenance of the symbiosis, as well provided insight into the genomic consequences for an intracellular archaeum.

Comparative Genomics Reveals Ecological and Evolutionary Insights into Sponge-Associated Thaumarchaeota

“…Estimated genome sizes of individual sponge-associated species were also not significantly smaller than free-living ones, with “Ca. U Cenporiarchaeum stylissum” and “Ca. U Nitrosopumilus cymbastelus” having the largest of all marine genomes investigated here. This finding is consistent with recent work also noting a lack of significant reduction in genome size for archaeal endosymbionts of ciliates (45, 46).…”

Bacterial and archaeal symbioses with protists

“…The most common symbionts are Proteobacteria, especially the Alphaproteobacteria subgroup [22][23][24][25] , but Bacteroidetes 26,27 , Chlamydiae 28 , and Cyanobacteria 16 are also very common. All known symbiotic archaea are methanogens, though they are scattered through various families [29][30][31][32] . Here, sampling bias might play some role -for example, many molecular tools to detect symbionts were validated for Proteobacteria -but it is less likely to be a major factor because sampling is typically host-focused, and because many of these lineages have specifically adapted to a symbiotic lifestyle and therefore are more frequent symbionts.…”

“…Too few archaeal endosymbionts of protists are known to draw many conclusions, but current genomes range from approximately 1.7-2.0 Mbp 29,31 .…”

Methanogens: pushing the boundaries of biology

“…This is because activation of the carbon substrate to an alkyl-thiol and subsequent C-C bond breakage is thermodynamically unfavorable under standard conditions unless metabolic fluxes are coupled to favorable reduction in the terminal electron acceptor such as sulfate. While syntrophic partnerships are typically described between two or more separate organisms organized in granules or mats, it is possible that syntrophs or other organisms and methanogens could permanently combine in a single host-symbiont system [97]. Such a symbiotic system may be impossible to identify using current shotgun metagenomic approaches or could appear as a contaminated genome assembly from single-cell genomic experiments.…”