Synergism and symbioses: Unpacking complex mutualistic species interactions using transcriptomic approaches

Damian Hernandez, Kasey N. Kiesewetter, Sathvik Palakurty, John R. Stinchcombe, Michelle E. Afkhami

Research output: Chapter in Book/Report/Conference proceedingChapter

1 Scopus citations


Many legumes form beneficial symbioses with nitrogen‐fixing bacteria and arbuscular mycorrhizal fungi that can have important effects on the structure of natural communities, ecosystem functions, and agricultural yields. Pairwise studies of these mutualisms (i.e. plant–fungi or plant–rhizobia) have provided important insight into the mechanistic basis of their effects on plant nutrition and fitness. However, a mechanistic understanding of how plants coordinate responses to concurrent associations with these mutualists has remained enigmatic, despite many plants interacting with both mutualists simultaneously in natural and agroecosystems. Here, we review lessons garnered from Afkhami and Stinchcombe (2016), which used factorial experiments to embark on the first examination of the tripartite effects of these symbioses at a genome‐wide transcriptomic level. Co‐inoculation of the model legume Medicago truncatula with Rhizophagus irregularis (arbuscular mycorrhizal fungus) and Ensifer meliloti (rhizobium) demonstrated: (i) the tripartite mutualism had synergistic effects on plant, bacterial, and fungal performance; (ii) genome‐wide expression of M. truncatula roots showed pervasive shifts in response to mutualisms, including subtle synergistic shifts in expression of mycorrhizal fungi‐responding plant genes in the presence of multispecies mutualism; (iii) expression of most host plant genes was regulated by a single mutualistic partner, but ∼10% of the differentially expressed genes were regulated by both mutualists; and (iv) mycorrhizal fungi had a greater effect on the gene expression in the common symbiosis pathway (utilized to establish these symbioses) than rhizobia, including unexpected fungal effects on bacterial‐specific components upstream and downstream of the pathway. These findings illustrate the complexity underlying multispecies mutualistic interactions and the need for additional research. We conclude this chapter with suggested future directions that will provide further insight into this important tripartite interaction.

Original languageEnglish (US)
Title of host publicationThe Model Legume Medicago truncatula
PublisherTaylor and Francis
Number of pages10
ISBN (Electronic)9781119409144
ISBN (Print)9781119409151
StatePublished - Dec 13 2019
Externally publishedYes


  • Arbuscular mycorrhizal fungi
  • Expression
  • Legumes
  • Multispecies mutualism
  • Rhizobia
  • Symbiosis
  • Transcriptomics

ASJC Scopus subject areas

  • Immunology and Microbiology(all)


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