Interkingdom communication between fungi and plants: induction of a novel silent secondary metabolite cluster required for root colonization

The interaction between soil fungi and plant roots crucially depends on proper recognition and communication by both partners. However, the precise determinants of this communication remain to be identified, both in terms of chemical communication and the underlying gene regulation upon recognition and response. Additionally, the beneficial interaction of fungi and plants often depends on the characteristics of the surrounding soil as well as on the variety of plant species, although the molecular basis of this phenomenon is largely unknown.

Trichoderma harzianum is a filamentous ascomycete frequently applied as plant beneficial agent in agriculture. While mycoparasitism and antagonism of Trichoderma spp. against fungal pathogens is well known, early responses of the fungus to the presence of a plant await broader investigation. In this study we analyzed these early stages of plant- fungus communication at the molecular level. We show that T. harzianum B97 is an efficient colonizer of plants. Analysis of chemotropic responses of B97 germlings to a plant extract showed directed hyphal growth. Patterns of secreted secondary metabolites revealed that the fungus chemically responds to the presence of the plant and that the plant secrets a fungus specific metabolite as well. Hence we developed a strategy for omics analysis to simulate the conditions of the early plant recognition eliciting a chemotropic response in the fungus. We found only 102 genes to be regulated, reflecting a very early stage of response, which revealed a general decrease in secondary metabolism upon recognition. In contrast, among these genes, a so far uncharacterized, presumably silent gene cluster was strongly induced upon recognition of the plant. Gene deletion of two genes of this Plant Communication Associated (PCA) cluster showed that they are essential for colonization of soy been roots. Moreover, for part of the gene cluster a DNA motif with palindromic sequence was detected. Phylogenetic analysis indicated that the PCA cluster is only present in the Harzianum clade of Trichoderma and closely related to from Metarhizium spp. Analysis of horizontal gene transfer (HGT) of the cluster genes, revealed that plants likely acquired a subset of the core genes of the cluster from fungi.

We conclude that the plant recognition specific PCA cluster mediates early chemical communication between plant and fungus and is potentially responsible for the high potential of T. harzianum sensu stricto and closely related species for biocontrol applications. Due to the requirement of this cluster for successful plant interaction (i.e. root colonization) we propose regulation of the PCA cluster as a diagnostic feature to delineate soil characteristics and plant genomic features blocking or facilitating beneficial fungal plant interaction and hence plant protection.