The ecology and evolution of symbiosis
Symbiosis, as we use the word, is not restricted to mutualism. It covers commensal and antagonistic associations as well. We follow the three questions below across the study systems listed here.
A lichen is a lichen-forming fungus together with a photosynthetic partner, behaving as a single organism. Other microbes, including endolichenic fungi, live within the thallus as well.
We isolate and culture endolichenic fungi to describe what is present, and have described a new Trichoderma species along with several previously unrecorded species from Korean lichens. We have also surveyed how endolichenic fungal communities are distributed across hosts and localities on Jeju Island.
We also study population structure in the foliicolous lichen genus Strigula: how populations are genetically partitioned and how they spread.
Matsutake forms ectomycorrhizae with pine and is notoriously difficult to cultivate. Part of the reason is that it does not associate with pine alone: soil, roots and fruiting bodies carry microbial communities that the fungus lives among. Where matsutake grows, a fairy ring develops, and microbial communities differ sharply inside and outside it.
We isolated bacteria and fungi from fairy ring soil, pine roots and fruiting bodies, and co-cultured them with matsutake. Some bacteria promoted mycelial growth; others, including Trichoderma and various microfungi, suppressed it.
Ongoing work. We are using genomic, transcriptomic and metabolomic analyses to identify the genes and metabolites behind the promotion and suppression observed in culture, and testing whether the same mechanisms hold in pine forests.
Symbiosis research starts with knowing what is there. Ecological and evolutionary interpretation is hard to support if the organisms involved are not clearly identified.
We survey mycorrhizal and forest fungal communities, describe new and previously unrecorded species, revise existing taxa, and sequence genomes and mitochondrial genomes to build reference data.
We have shown that profiles of root mycorrhizal communities can differ depending on the sequencing platform used, and have taken part in international efforts to re-examine the taxonomic annotation of publicly deposited fungal sequences.
Fungal community research has centred on plants and soil. Fungi associated with animal hosts remain comparatively little known, as do the microbial communities of environments built and managed by people.
In terrestrial isopods, habitat explained more of the variation in mycobiome structure than host sex did. We have also surveyed fungi associated with the Joro spider and reported Metarhizium viridulum from a cicada for the first time in Korea.
Aquaculture systems allow husbandry method and water quality to be controlled cleanly. We have examined how biofloc technology restructures the water microbiome of Japanese eel culture, how freshwater microbial diversity changes as nitrification establishes, and how fungal communities turn over in FLOCponics.
METHODS
Our work usually begins in the field. We collect from forests, coasts, tidal flats and aquaculture facilities, and isolate and culture the microbes we need. Microbial communities are surveyed by metabarcoding and metagenomics; function and interaction are examined through genomic, transcriptomic and metabolomic analyses.
Phylogenetics and population genetics let us follow how organisms diverged and spread. New organisms are formally described, and the phylogeny and species boundaries of existing taxa are re-examined.