Large scale transcriptome analysis reveals interplay between development of forest trees and a beneficial mycorrhiza helper bacterium

Abstract

Background: Pedunculate oak, Quercus robur is an abundant forest tree species that hosts a large and diverse community of beneficial ectomycorrhizal fungi (EMFs), whereby ectomycorrhiza (EM) formation is stimulated by mycorrhiza helper bacteria such as Streptomyces sp. AcH 505. Oaks typically grow rhythmically, with alternating root flushes (RFs) and shoot flushes (SFs). We explored the poorly understood mechanisms by which oaks integrate signals induced by their beneficial microbes and endogenous rhythmic growth at the level of gene expression. To this end, we compared transcript profiles of oak microcuttings at RF and SF during interactions with AcH 505 alone and in combination with the basidiomycetous EMF Piloderma croceum.

Results: The local root and distal leaf responses to the microorganisms differed substantially. More genes involved in the recognition of bacteria and fungi, defence and cell wall remodelling related transcription factors (TFs) were differentially expressed in the roots than in the leaves of oaks. In addition, interaction with AcH 505 and P. croceum affected the expression of a higher number of genes during SF than during RF, including AcH 505 elicited defence response, which was attenuated by co-inoculation with P. croceum in the roots during SF. Genes encoding leucine-rich receptor-like kinases (LRR-RLKs) and proteins (LRR-RLPs), LRR containing defence response regulators, TFs from bZIP, ERF and WRKY families, xyloglucan cell wall transglycolases/hydrolases and exordium proteins were differentially expressed in both roots and leaves of plants treated with AcH 505. Only few genes, including specific RLKs and TFs, were induced in both AcH 505 and co-inoculation treatments.

Conclusion: Treatment with AcH 505 induces and maintains the expression levels of signalling genes encoding candidate receptor protein kinases and TFs and leads to differential expression of cell wall modification related genes in pedunculate oak microcuttings. Local gene expression response to AcH 505 alone and in combination with P. croceum are more pronounced when roots are in resting stages, possibly due to the fact that non growing roots re-direct their activity towards plant defence rather than growth.

Fig. 1

Pedunculate oak microcuttings with interacting microorganisms. Streptomyces sp. AcH 505 on soil particles in the microcosm (a) Piloderma croceum – oak ectomycorrhizas (b) and a pedunculate oak Quercus robur microcutting (c)

Fig. 2

Venn-diagrams illustrating numbers of DECs (Benjamini-Hochberg adjusted, p ≤ 0.01). The comparisons depicted are for the following pairs of roots and leaves of microcuttings during RF and SF: Control versus AcH 505 inoculated (Co-Ac) and Control- versus AcH 505- and P. croceum-inoculated (Co-AcPi)

Fig. 3

Protein family (Pfam) terms enriched for up- and down-regulated contigs, in roots and leaves harvested from plants during RF and SF, treated with AcH 505 (Co-Ac) and both microorganisms (Co-AcPi). Putative function categories “perception and signalling”, “plant cell wall proteins”, “oxidases and reductases” and “primary metabolism and photosynthesis” are given. Orange colour indicates up-regulated and blue down-regulated enriched Pfam terms. Significance levels are marked by asterisks in the boxes (*** :p ≤ 0.001; **: 0.001 < p ≤ 0.01; *: 0.01 < p ≤ 0.05). The p-value cut-off was set at p ≤ 0.05

Fig. 4

Enriched plant defence-related GO terms in pedunculate oak roots, showing terms enriched for up-regulated contigs after AcH 505 inoculation specifically during SF and partially depleted in co-inoculated plants. GO enrichment analysis was implemented by GOseq. Orange colour indicates up-regulated and blue down-regulated enriched Pfam terms. Significance levels are marked by asterisks in the boxes. (*** :p ≤ 0.001; **: 0.001 < p ≤ 0.01; *: 0.01 < p ≤ 0.05). The p-value cut-off was set at p ≤ 0.05