First author

About 85% of all plant species, most notably trees, depend on partnerships with soil fungi to thrive. The resulting mycorrhizal fungi scavenge hard-to-access nutrients and pass them on to the trees in exchange for the plants' store of carbon-rich sugar. On page 88, a team of international researchers reports some of the secrets of the genome of the mycorrhizal Laccaria bicolor. Francis Martin, a microbiologist at the French National Institute of Agricultural Research in Nancy tells Nature how the genome sequence reveals an underground molecular dialogue that controls important ecosystem functions.

Was it difficult to get funding to sequence the genome of a mycorrhizal fungus?

I've worked with mycorrhizae for 25 years, but I wouldn't have bet a penny that we could get the E5-million worth of funding needed to sequence this genome. I worked on a collaborative effort, funded by the California-based Joint Genome Institute (JGI), to sequence the poplar tree's genome. After that, we were able to convince the JGI that sequencing Laccaria would provide a better understanding of ecosystem function.

Was this your first choice of species?

Yes. We wanted an ecologically relevant species that interacts with seedlings as well as mature trees found in Europe and North America. There were only a handful of such species with the minimal set of genetic resources required for sequencing, such as cDNA libraries. Laccaria is also economically relevant because it is used to promote the growth of conifer seedlings in nurseries.

Did the genome generate new hypotheses?

Many. For example, the genome has some features that are common to saprotrophs — organisms that consume dead organic matter — as well as genes required for symbiotic interactions, so we speculate that Laccaria may be an ancestral species of both groups. We also found genes encoding hundreds of small peptides, which we suspect the fungi may use to manipulate plant gene expression.

Are there any other mycorrhizal genome sequences on the horizon?

Yes, we are sequencing the genome of the black truffle mushroom, another mycorrhizal fungus. There are two main evolutionary branches of fungi, and the black truffle and Laccaria belong to different ones. By comparing the two genome sequences, we can see whether the two fungal kingdoms used the same tools to develop mycorrhizal symbioses with trees during evolution. We hope to get that paper out before Christmas — when truffles will reach the market.