The paper in Nature Ecology & Evolution is here: http://go.nature.com/2A0CJp3
The emergence of complex multicellularity is a fascinating transition in evolution, that involves a drastic reprogramming of growth patterns and functioning of ancestral organisms. It is thus not surprising that it has evolved in no more than five lineages across the tree of life. Fungi is one of these, and is particularly notable because complex multicellularity comes in many flavors, fruiting bodies being the best known. The vegetative, nutritionally active life stage of fungi is the vegetative mycelium, which, shows little differentiation and, following recent definitions, is better regarded as simple multicellular. Our lab focuses on fungi as a model system for understanding the genetic mechanisms that underlie the emergence of complex multicellularity.
In a particular group of fungi, called Armillaria, complex multicellularity comes in two distinct forms, fruiting bodies (‘mushrooms’) and rhizomorphs, shoestring-like structures of clonal dispersal. Fruiting bodies of these species are known as the delicious honey mushrooms. They appear in massive clusters on and around trees in infected areas. However, this comes at a hefty price for trees: Armillaria spp are aggressive pathogens that can spread from tree to tree under the soil surface to harvest their materials for food.
Clusters of fruiting bodies emerge on and around trees in Armillaria-infected areas in the fall. Photo courtesy of Virág Tomity.
They spread in the soil via rhizomorphs, another type of complex multicellular structure. The unique role of rhizomorphs in the life of these fungi made us interested in how they and how their development relates to that of fruiting bodies. We reasoned that the comparison of the genes involved in fruiting body and rhizomorph development should yield insights into the general principles of the genetics of complex multicellularity in fungi. We started the work as a collaboration with György Sipos at the University of West-Hungary, whose team had sequenced the genomes of two Armillaria species, including the conifer pathogen A. ostoyae. We then performed phylogenomic, comparative genomic and transcriptomic analyses to understand both the evolution of gene copy numbers and expression patterns in fruiting bodies and rhizomorphs. Fortunately, many analyses worked out quite fast, which is to a large extent due to the painstaking effort Arun Prasanna (a postdoc in the lab at the time) has taken.
Rhizomorphs of Armillaria mellea grown on a plate. Courtesy of Zsolt Merényi.
We wanted to answer how rhizomorphs originate developmentally and, if the data allows, evolutionarily, and how they enable Armillaria to invade plants and grow their immense colonies. The first challenge we faced was to get A. ostoyae to fruit. Although there are many fruiting protocols for saprotrophic fungi, species with complex life cycles and ecological demands can be challenging. In A. ostoyae, this should mimic the transition from summer to fall, with higher to lower temperatures, changing light intensities and altering dark/light cycles in a growth chamber. To our surprise, our fruiting protocol, which we designed following a protocol for a different Armillaria species, worked like a dream from the beginning. After completing the transcriptomic and proteomic analyses, the most exciting moment for me was to find a number of genes with concomitant upregulation in various developmental stages of the stipe and in rhizomorphs, but low expression in other developmental stages (see Figure 3 in the paper). This suggested that rhizomorphs have a lot in common with stipes, so we started speculating whether they evolved via the modification of a stipe developmental program? We further identified several candidate genes for understanding what governs the complex development of mushroom-forming fungi. I anticipate that across-species comparisons of transcriptomes in the near future will help to further generalize these findings and highlight the fundamental principles of fruiting body development.
This work also gave us some interesting insights into how wood-decaying fungi can pick up the ability to damage living trees. In their saprotrophic phase, Armillaria feed on dead wood by using powerful extracellular enzyme systems. In rotting wood, competition among bacteria, fungi and other microbes must be fierce, which creates a pressure on species to find ways for gaining access to nutrients in the least competitive environment. This might drive the evolution of necrotrophic pathogens, like Armillaria, which, by damaging living trees gains the upper hand in colonizing wood compared to saprotrophs that feed on already dead wood. A future challenge will be to understand how Armillaria bypasses the plant’s defense systems, although the genomes of Armillaria gave some clues. Several pathogenicity-related gene families are expanded in Armillaria species and/or expressed in rhizomorphs, including ones involved in evading detection by the plant immune system (e.g. by masking chitin residues of the fungal cell wall) and cellular detoxification. I expect that future research will unravel the exact mechanisms by which Armillaria species infect and damage trees, and will lead to the development of strategies to control their spread in forest ecosystems.