Evolution of Substrate Specificity in Lichens

Lichens are widely reported to be strictly autotrophic symbiotic systems in which carbohydrate production is entirely covered by the photosynthesizing partner, typically an alga, and substrate plays no role in carbohydrate metabolisms. Ecological data reconcile poorly with this paradigm: in fact, obligate substrate specificity characterizes many species that are apparently unable to colonize adjacent substrates despite efficient dispersal. It is unknown what mechanism enforces substrate specificity, but recent molecular and physiological results suggest that facultative saprobism and lichenization can occur in one and the same fungal species. We hypothesize that lichen substrate specificity, and by extension a key part of the ecological indicator value of lichens, evolved through the sequential loss of the ability of early trophic generalists to metabolize various naturally occurring environmental polymers. We will test this hypothesis with two complementary methods: one, by mapping the used substrate spectrum over a robust molecular phylogeny of a model system with mixed substrate-specific and generalist lineages; and second, by genome sequencing to compare patterns of genome evolution and genetic inventory in related specialist and generalist genomes.

The aim of the project Evolution of substrate specificity in lichens was to understand evolutionary implications and consequences of long-lasting substrate associations of trapelioid lichen-forming fungi from the order Baeomycetales which exhibit intimate substrate contact. We substantially expanded the understanding of lichen substrate associations on various levels, while producing thousands of single gene sequences from hundreds of specimens and six de-novo sequenced fungal genomes and transcriptomes. We provided the most comprehensive phylogenetic analyses to date of multiple species groups in four interlinked studies. Thereby we discovered several novel fungal species, a new fungal genus and resolved long-standing questions about the higher-level relationships in the studied group of fungi. We showed that lichen-substrate relationships are distinct and evolutionarily well conserved in otherwise closely related fungal genera. Some species groups are highly specialized to single substrates while others maintain greater flexibility and switches between substrates occur more frequently on certain substrate types than on others. We concluded that substrate associations, although manifold, are factors influencing long-term evolutionary success of trapelioid fungi. They may thus represent constraints to the symbiotic outcome of the lichens they are part of. To deepen the understanding of the evolutionary imprint substrate association leave on lichen fungi we compiled a large comparative genomic dataset including six de-novo sequenced, assembled and annotated genomes of lichen-forming fungi from different substrates and with degrees of substrate specialization. While overall genome sizes and genetic repertoires of the sequenced species were similar to those of previously sequenced lichen genomes we found that our studied species have a reduced set of genes to access and potentially utilize long chained carbohydrates such as cellulose. Functional genomic analyses further revealed enriched protein domains potentially involved in adaptations to long-lasting substrate associations. Our phylogenetic comparative and genome studies provide new and strong inferential evidence for substrate related selection in the studied group of fungi. The generated data and results not only provide the first comprehensive insights into an important aspect of lichen symbioses but they also serve as a baseline for the development of experimental approaches and hypotheses about environmental interactions, evolutionary biology and taxonomy of lichen-forming fungi.