Determining the Impact Changing Host Metabolism has on Leaf Associated Microbiomes for Improved Efficacy of Foliar Biopesticides

Project Overview

Project Type: Graduate Student
Funds awarded in 2022: $14,997.00
Projected End Date: 12/31/2023
Grant Recipient: The Pennsylvania State University
Region: Northeast
State: Pennsylvania
Graduate Student:
Faculty Advisor:
Kevin Hockett
The Pennsylvania State University

Information Products


  • Vegetables: tomatoes


  • Crop Production: biological inoculants, plant breeding and genetics
  • Pest Management: biological control, genetic resistance

    Proposal abstract:

    The use of conventional agricultural methods (e.g. pesticides) to increase crop yield has previously allowed generations to break through established yield plateaus. However overuse of these methods jeopardizes the ability of future generations to meet their food needs. Sustainable alternatives to pesticides include biological control agents (BCA), cultivars with resistance genes, and cultivars with horizontal resistance packages. BCA have limited success in field application, resistance genes select for resistant pathogens, and horizontal resistance packages simply reduce disease incidence. An alternative is to utilize horizontal resistance packages that bolster the persistence of applied biological control agents via specialized metabolites.  

    Specialized metabolites act as a carbon source on leaf surfaces and have antimicrobial properties. However, specialized metabolites are a function of plant metabolism which is influenced by the plant stress response. Changes in specialized metabolite profiles during stress responses has already been linked to changes in microbiomes within the rhizosphere (plant roots) but this has not been explored in the phyllosphere (leaf surface). The purpose of this work is to examine the influence of altered metabolite expression via induced stress on phyllosphere bacterial colonization. By pairing untargeted metabolomic techniques with metagenomics, this work will tease apart the influence host stress responses have on the leaf surface metabolic profile (LSMP) and the subsequent effect this has on the associated microbiome. If LSMP’s are mutable, this can lead to breeding packages that favor BCA during plant stress responses by providing specialized metabolites preferentially utilized by BCA and disrupting  established microbiomes for increased BCA persistence.

    Project objectives from proposal:

    Objective 1: Characterizing the influence of biotic stress on leaf surface metabolite profiles. Plant defense responses to pathogens are dynamic, multifaceted, and occur at multiple spatial scales. The well-established host-pathogen model system, tomato (Solanum lycopersicon) and Pseudomonas syringae pv. tomato DC3000 (DC3K; bacterial speck), will be used to investigate the relationship between induction of plant defense responses and its subsequent effects on leaf surface metabolite profiles. Considering the differential responses elicited by different defense pathways, utilizing DC3K, a jasmonic acid defense pathway (JA) elicitor, and DC3K mutants capable of eliciting the salicylic acid defense pathway (SA), will effectively characterize any differences in metabolite profiles that may be generated. Furthermore, comparing pathogen elicitation of JA and SA responses against treatments with pure salicylic acid and jasmonic acid  will determine the extent of pathogen influence on LSMP. Defining LSMP changes on leaves directly affected by the treatments, as well as leaves that have not been treated but are on the same plant will give a better understanding of the influence of host stress response on the entire plant. Quantification of LSMP will be done utilizing nuclear magnetic resonance and ultrahigh performance liquid chromatography.  

    Object 2: Investigating biotic stress influence on phyllosphere bacterial assemblage establishment. Metabolites accessible to phylloplane colonizing bacteria influence assemblage diversity [16-18]. However, work has not characterized how induced plant defense responses, which directly alters the host metabolite expression, influence associated phyllosphere communities. To address this, bacterial establishment on the tomato phyllosphere post defense induction will be observed. This aim will resolve patterns of bacterial establishment on leaves of tomato that have been stressed with DC3K.  Characterization of changes in colonization will be done by relating leaf surface metabolites across differential defense responses (SA vs JA) induced by DC3K and associated mutants and distance from the site of infection (inoculated vs youngest uninoculated mature leaf) to changes in the diversity of the applied microbiome. Changes in species composition associated with patterns of defense elicitation and spatial distance from the initial site of infection will be examined via metagenomic sequencing and diversity analysis (richness and evenness). I aim to disentangle the relationship between plant defense and associated phyllosphere bacterial assemblages from the perspective of altered LSMP. 

    Any opinions, findings, conclusions, or recommendations expressed in this publication are those of the author(s) and do not necessarily reflect the view of the U.S. Department of Agriculture or SARE.