The genome of the widespread Mycoplasma-related endobacteria colonizing arbuscular mycorrhizal fungi reveals transkingdom horizontal gene transfer and extreme dependence on the fungal host

For more than 400 million years, arbuscular mycorrhizal fungi (AMF) have formed symbiotic associations with most land plants. The obligate plant-symbiotic AMF hosts the uncultivable Mollicutes-related endobacteria (MRE). Mollicutes-related endobacteria could be detected in all major evolutionary AMF lineages studied, but their function in arbuscular mycorrhiza (AM) is unknown. 16S rRNA gene sequences of MRE fall in a monophyletic clade in the Mollicutes and are highly polymorphic within a single AMF spore. Thus, MRE represent an unnamed, diverse, but monophyletic higher bacterial taxon. They probably evolved endosymbiotically for more than 400 million years. To uncover putative roles of these widespread MRE and to shed light on MRE evolution, we sequenced the genome of the MRE living in Dentiscutata heterogama called DhMRE. Multilocus phylogenetic analyses showed that DhMRE belong to a previously unknown lineage that is sister to a Mycoplasma clade. In addition, the draft annotation indicated an extremely reduced metabolic capacity, a strict dependency on the fungal host, and a large number of unique proteins. Strikingly, several DhMRE proteins show similarity to nuclear encoded proteins of AMF, indicating trans-kingdom gene transfer between MRE and AMF. The DhMRE genome encodes many proteins with domains predominantly described for eukaryotic proteins involved in bacteria-host interactions. Moreover, we found evidence for gene transfer of MRE with fungi of the Mucuromycotina, raising new questions about the role of MRE in the early evolution of fungus-plant associations and the AM symbiosis.