Uncovering the dominant role of root metabolism in shaping rhizosphere metabolome under drought in tropical rainforest plants

Gina A. Hildebrand, Linnea K. Honeker, Viviana Freire-Zapata, Christian Ayala-Ortiz, Sumudu Rajakaruna, Jane Fudyma, L. Erik Daber, Roya AminiTabrizi, Rosalie L. Chu, Jason Toyoda, Sarah E. Flowers, David W. Hoyt, Rasha Hamdan, Juliana Gil-Loaiza, Lingling Shi, Michaela A. Dippold, S. Nemiah Ladd, Christiane Werner, Laura K. Meredith, Malak M. Tfaily

Research output: Contribution to journalArticlepeer-review


Plant-soil-microbe interactions are crucial for driving rhizosphere processes that contribute to metabolite turnover and nutrient cycling. With the increasing frequency and severity of water scarcity due to climate warming, understanding how plant-mediated processes, such as root exudation, influence soil organic matter turnover in the rhizosphere is essential. In this study, we used 16S rRNA gene amplicon sequencing, rhizosphere metabolomics, and position-specific 13C-pyruvate labeling to examine the effects of three different plant species (Piper auritum, Hibiscus rosa sinensis, and Clitoria fairchildiana) and their associated microbial communities on soil organic carbon turnover in the rhizosphere. Our findings indicate that in these tropical plants, the rhizosphere metabolome is primarily shaped by the response of roots to drought rather than direct shifts in the rhizosphere bacterial community composition. Specifically, the reduced exudation of plant roots had a notable effect on the metabolome of the rhizosphere of P. auritum, with less reliance on neighboring microbes. Contrary to P. auritum, H. rosa sinensis and C. fairchildiana experienced changes in their exudate composition during drought, causing alterations to the bacterial communities in the rhizosphere. This, in turn, had a collective impact on the rhizosphere's metabolome. Furthermore, the exclusion of phylogenetically distant microbes from the rhizosphere led to shifts in its metabolome. Additionally, C. fairchildiana appeared to be associated with only a subset of symbiotic bacteria under drought conditions. These results indicate that plant species-specific microbial interactions systematically change with the root metabolome. As roots respond to drought, their associated microbial communities adapt, potentially reinforcing the drought tolerance strategies of plant roots. These findings have significant implications for maintaining plant health and preference during drought stress and improving plant performance under climate change.

Original languageEnglish (US)
Article number165689
JournalScience of the Total Environment
StatePublished - Nov 15 2023


  • Drought
  • Primary and secondary metabolites
  • Pyruvate
  • Rhizosphere
  • Roots
  • Tropical rainforest

ASJC Scopus subject areas

  • Environmental Engineering
  • Environmental Chemistry
  • Waste Management and Disposal
  • Pollution


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