Absence of genome reduction in diverse, facultative endohyphal bacteria

Abstract

Fungi interact closely with bacteria, both on the surfaces of the hyphae and within their living tissues (i.e. endohyphal bacteria, EHB). These EHB can be obligate or facultative symbionts and can mediate diverse phenotypic traits in their hosts. Although EHB have been observed in many lineages of fungi, it remains unclear how widespread and general these associations are, and whether there are unifying ecological and genomic features can be found across EHB strains as a whole. We cultured 11 bacterial strains after they emerged from the hyphae of diverse Ascomycota that were isolated as foliar endophytes of cupressaceous trees, and generated nearly complete genome sequences for all. Unlike the genomes of largely obligate EHB, the genomes of these facultative EHB resembled those of closely related strains isolated from environmental sources. Although all analysed genomes encoded structures that could be used to interact with eukaryotic hosts, pathways previously implicated in maintenance and establishment of EHB symbiosis were not universally present across all strains. Independent isolation of two nearly identical pairs of strains from different classes of fungi, coupled with recent experimental evidence, suggests horizontal transfer of EHB across endophytic hosts. Given the potential for EHB to influence fungal phenotypes, these genomes could shed light on the mechanisms of plant growth promotion or stress mitigation by fungal endophytes during the symbiotic phase, as well as degradation of plant material during the saprotrophic phase. As such, these findings contribute to the illumination of a new dimension of functional biodiversity in fungi.

Horizontal gene transfer and silver nanoparticles production in a new Marinomonas strain isolated from the Antarctic psychrophilic ciliate Euplotes focardii

“…Genome reduction is seen as a hallmark for obligate endosymbiosis 53 and it is considered the result of the coevolution between endosymbiont and host or the bottleneck of a small population size 54 . Limited signs of genome reduction were also reported for facultative endohyphal bacteria of diverse Ascomycota 55 . Considering that the symbiotic relationship between Marinomonas sp.…”

Complete Genome Sequence of Luteibacter pinisoli MAH-14

“…Strains classified within the genus Luteibacter ( Gammaproteobacteria ) are yellow-pigmented members of microbiomes found in close association with plants (1–4). A subset of strains have also been characterized as endohyphal bacteria within a diverse set of ascomycete fungi (5–8). These bacterial/fungal complexes modulate diverse fungal phenotypes, including the potential for some fungi to act as plant growth promoters (5–8).…”

The fungal holobiont: Evidence from early diverging fungi

“…Remarkably, all genome sequencing projects of endobacteria inhabiting early diverging fungi have revealed small, reduced genomes (Lackner et al, 2011a;Ghignone et al, 2012;Fujimura et al, 2014;Naito et al, 2015;Torres-Cort es et al, 2015;Uehling et al, 2017), while genomes of facultative endosymbionts of Piriformospora indica and of diverse foliar fungal endophytes of the Ascomycota do not show signs of genome reduction (Glaeser et al, 2016;Baltrus et al, 2017).…”