Mycobiome and metatranscriptomic analysis of asymptomatic and symptomatic Norway spruce trees naturally infected by the conifer pathogen Heterobasidion spp

Microorganisms are ubiquitous residents of forest tree tissues living in close symbiosis with their hosts. An important role of plant microbiome in maintaining the host fitness is supported by numerous studies. Despite significant progress achieved in our understanding of the factors affecting the composition of microbial communities associated with trees, very little is known about the effect of plant pathogens on their structure. Similarly not much is known on the effect of beneficial fungal biota on the disease dynamics and progression. We investigated the effect of Heterobasidion root and butt rot disease on fungal communities associated with Norway spruce. The sequenced ITS2 data were analyzed using the mothur standard operation pipeline. Canonical analysis of principle coordinate (CAP) and principal coordinates analysis (PCoA) were used to visualize the fungal community structure. To identify differentially secreted host transcripts and in-planta expressed pathogen genes, the processed RNA-seq data were mapped against genome assembly of Norway spruce and Heterobasidion annosum respectively. Our results demonstrate that diseased and asymptomatic trees significantly differed in the structure of the fungal communities residing in their sapwood, but not in other anatomic regions. Each of the investigated tissues (sapwood, bark, needles and suberized roots) harbored a unique fungal community. Heterobasidion infected trees were also more susceptible to co-infection by other saprotrophic wood degrading fungi. Furthermore, inspite of considerable overlap in the number of shared mycobiomes, metatranscriptomic analysis revealed pronounced differences in gene expression pattern among the individual symptomatic and asymptomatic trees. The distance-based linear model analysis showed that expression levels of several genes with a predicted role in host defense (e.g. NBS-LRR disease resistance protein) were significantly correlated with the abundance of in planta expressed gene transcripts of Heterobasidion spp. Our results indicate that plant pathogens may cause significant changes in the structure of microbial communities associated with trees.