Transcriptomic responses of arbuscular mycorrhizal symbioses with negative growth phenotypes

Arbuscular mycorrhizal (AM) fungi can play important roles in sustainable agriculture, given that they provide multiple benefits for numerous plant species. Conversely, negative plant growth effects induced by AM fungi are also commonly observed. At present, however, comparatively little information is available regarding the effects of AM fungi at the molecular level. In this study, compared with an absence of AM fungus inoculation, tomato seedlings grown in soil inoculated with Funneliformis mosseae or Rhizophagus intraradices were characterized by reduced shoot and root growth. To gain further insights into the underlying mechanisms at the molecular level, we performed transcriptomic analyses. We accordingly identified 190 and 870 differentially expressed genes (DEGs) in the F. mosseae vs. control and R. intraradices vs. control comparisons, respectively. KEGG enrichment analysis of the former 190 DEGs revealed significant enrichment of the “Protein processing in endoplasmic reticulum,” “Flavonoid biosynthesis,” “Flavone and flavonol biosynthesis,” and “Stilbenoid, diarylheptanoid, and gingerol biosynthesis” pathways, whereas “DNA replication,” “Photosynthesis - antenna proteins,” “Cutin, suberine, and wax biosynthesis,” “Protein processing in endoplasmic reticulum,” and “Glycerophospholipid metabolism” were identified as pathways significantly enriched with the latter 870 DEGs. GO functional analysis revealed that among both groups of DEGs, many genes were assigned the “Response to stimulus” term. Moreover, we established that many of the enriched terms were associated with stimulus and stress response processes, including response to salt stress, heat, and reactive oxygen species. Collectively, our findings in this study indicate that under the experimental conditions assessed, AM fungi may trigger defense-related responses in hosts, even though the symbioses were characterized by negative growth phenotypes. These findings will contribute to advancing our current understanding of AM fungi and highlight the fact that AM fungi should not be unthinkingly applied in agricultural production without due consideration of the prevailing conditions.