Isolation and Comparative Genomics of Mycoavidus sp. B2-EB Reveals Minimal Genomic Features Required by cultivable Burkholderiaceae-related Endofungal Bacterium.

Obligate bacterial endosymbionts are critical to the existence of many eukaryotes. Such endobacteria are usually characterized by reduced genomes and metabolic dependence on the host, which may cause difficulty in isolating them in pure cultures. Family Burkholderiaceae-related endofungal bacteria affiliated with the Mycoavidus-Glomeribacter clade can be associated with the fungal subphyla Mortierellomycotina and Glomeromycotina. In this study, a cultivable endosymbiotic bacterium, Mycoavidus sp. B2-EB, present in the fungal host Mortierella parvispora, was obtained successfully. The B2-EB genome (1.88 Mb) represents the smallest genome among the endofungal bacteria Mycoavidus cysteinexigens (2.64–2.80 Mb) of Mortierella elongata and uncultured endosymbionts ‘Candidatus Glomeribacter gigasporarum’ (1.37–2.36 Mb) of arbuscular mycorrhizal fungi. Despite a reduction in genome size, strain B2-EB displays a high genome completeness suggesting a nondegenerative reduction in the B2-EB genome. Compared with a large proportion of transposable elements (TEs) in other known Mycoavidus genomes (7.2–11.5% of total genome length), TEs accounted for only 2.4% of the B2-EB genome. This pattern, together with a high proportion of single-copy genes in the B2-EB genome, suggests that the B2-EB genome reached a state of relative evolutionary stability. These results represented the most streamlined structure among the cultivable endofungal bacteria and suggested the minimal genome features required by both an endofungal lifestyle and artificial culture. This study allowed us to understand the genome evolution of Burkholderiaceae-related endosymbionts and to elucidate microbiological interactions. Importance This study attempts the isolation of a novel endobacterium, Mycoavidus sp. B2-EB (= JCM 33615), harbored in the fungal host Mortierella parvispora E1425 (= JCM 39028). We report the complete genome sequence of this strain, which possesses a reduced genome size with relatively high genome completeness and a streamlined genome structure. The information indicates the minimal genomic features required by both endofungal lifestyle and artificial cultivation, which furthers our understanding of genome reduction in fungal endosymbionts and extends the culture resources for biotechnological development on engineering synthetic microbiomes.