Using next generation transcriptome sequencing to predict an ectomycorrhizal metabolome

Abstract

BackgroundMycorrhizae, symbiotic interactions between soil fungi and tree roots, are ubiquitous in terrestrial ecosystems. The fungi contribute phosphorous, nitrogen and mobilized nutrients from organic matter in the soil and in return the fungus receives photosynthetically-derived carbohydrates. This union of plant and fungal metabolisms is the mycorrhizal metabolome. Understanding this symbiotic relationship at a molecular level provides important contributions to the understanding of forest ecosystems and global carbon cycling.ResultsWe generated next generation short-read transcriptomic sequencing data from fully-formed ectomycorrhizae between Laccaria bicolor and aspen (Populus tremuloides) roots. The transcriptomic data was used to identify statistically significantly expressed gene models using a bootstrap-style approach, and these expressed genes were mapped to specific metabolic pathways. Integration of expressed genes that code for metabolic enzymes and the set of expressed membrane transporters generates a predictive model of the ectomycorrhizal metabolome. The generated model of mycorrhizal metabolome predicts that the specific compounds glycine, glutamate, and allantoin are synthesized by L. bicolor and that these compounds or their metabolites may be used for the benefit of aspen in exchange for the photosynthetically-derived sugars fructose and glucose.ConclusionsThe analysis illustrates an approach to generate testable biological hypotheses to investigate the complex molecular interactions that drive ectomycorrhizal symbiosis. These models are consistent with experimental environmental data and provide insight into the molecular exchange processes for organisms in this complex ecosystem. The method used here for predicting metabolomic models of mycorrhizal systems from deep RNA sequencing data can be generalized and is broadly applicable to transcriptomic data derived from complex systems.

Oak Root Response to Ectomycorrhizal Symbiosis Establishment: RNA-Seq Derived Transcript Identification and Expression Profiling

“…An activation of genes involved in vesicle trafficking was also reported for ECM roots of P. trichocarpa [5]. In the context of ECM development an activation of genes involved in the secretory pathway is consistent with the alterations in expression of transcripts encoding proteins involved in cell wall remodeling, defense, and signaling events by secreted plant receptors (see below), observed in this and others studies [5], [10], [35], [48]. Interestingly, we also observed induction of a transcript encoding glutamate decarboxylase, the enzyme that catalyses decarboxylation of glutamate to γ -aminobutyric acid (GABA).…”

The effect of elevated carbon dioxide on the interaction betweenEucalyptus grandisand diverse isolates ofPisolithussp. is associated with a complex shift in the root transcriptome

“…New Phytologist of hormone-related genes induced in the core E. grandis transcriptomic response to P. microcarpus as compared with other host plants to mycorrhizal fungi (Heller et al, 2008;Martin et al, 2008;Felten et al, 2009;Larsen et al, 2010Larsen et al, , 2011Plett et al, 2014). These differences include a reduction in the number of auxin-and ethylene-related genes in the roots of E. grandis undergoing colonization, while GA-regulated genes feature more prominently.…”

Exploring the Transcriptome of Mycorrhizal Interactions

“…Therefore, another huge advantage of sequencing compared to microarrays for plant-microbe interaction studies is the possibility to monitor the transcriptome of both partners in the same sample. Next-generation transcriptome sequencing was first used by Larsen et al (2011) for mycorrhizal interactions, in order to predict the ectomycorrhizal metabolome of poplar and Laccaria bicolor. Matsumura et al, 2003, sequenced tags >25 bp from defined positions of cDNAs by using type III restriction enzyme EcoP15I, so-called SuperSAGE, to study rice and Magnaporthe grisea simultaneously in infected leaves.…”

“…The expression of one of these ammonium transporters, AMT2.2, is highly upregulated in ectomycorrhiza, showing an increased nitrogen uptake potential in L. bicolor that is probably related to its symbiotic lifestyle (Lucic et al, 2008;Martin et al, 2008). In addition, RNA-Seq data from fully formed ectomycorrhiza between L. bicolor and poplar roots were used to predict the ectomycorrhizal metabolome (Larsen et al, 2011). CAZymes) were highly increased in differentiating tissues of L. bicolor as ectomycorrhizal root tips or fruiting bodies.…”