RNA-Seq for investigation of adaptations to extremes of soil pH, incorporating natural host-microbiome interactions

  • Poster Presentation
  • Poster 30 (Flash Talk: 11 Jun 2018 17:19)
  • Foyer, UCD Agriculture and food science Centre
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Ellen Young*
Queen's University Belfast, Institute for Global Food Security

Manus Carey
Queen's University Belfast, Institute for Global Food Security

Andrew A Meharg
Queen's University Belfast, Institute for Global Food Security

Caroline Meharg
Queen's University Belfast, Institute for Global Food Security

*Presenting Author

Plants can adapt to soil stress using controlled gene expression responses, incorporating associations with microorganisms. These can be studied using RNA sequencing, although complex, natural plant-microbiome studies are limited. We address this knowledge gap using a novel meta-transcriptome functional analysis approach, incorporating the grass Holcus lanatus and associated natural eukaryotic microbiome. Plant ecotypes from two contrasting natural habitats, acid bog and limestone quarry soil, were used in a reciprocal soil transplant experiment.

Roots in acid soil, particularly acid ecotype, were dominated by the putatively beneficial Ascomycete Phialocephala. However, limestone ecotype showed greater expression of other Ascomycete and Oomycete genera in acid soil, including those identified by RNA-Seq as pathogens (Phytophthora), corresponding with reduced induction of pathogen defence processes in limestone ecotype in acid soil. This suggests greater defence capability in the acid ecotype, in response to stresses characteristic of acid bog soils.

AM fungal (Rhizophagus) colonisation was greater in roots on limestone soil, where P availability is low, and coincided with upregulation of plant genes involved in AM symbiosis initiation and AM-based P acquisition, indicating plant-fungal communication to permit beneficial infection and nutrient exchange.

Thus this novel approach identified patterns of fungal infection between soils and ecotypes, with RNA-Seq providing putative identification of fungal genera, plus information about their functional roles. Coupled with information about the plant gene expression response provided by RNA-Seq, we demonstrate that this novel meta-transcriptome based functional analysis is a powerful tool for the study of natural plant-microbiome interactions, and their role in plant stress adaptation.

Young et al. Microbiome. 2018;6:48