Examining microbial mediation of disease resistance, pollinator attraction, and crop yield in apple crops

The composition of microbial communities can have dramatic, but often unappreciated, impacts on crop production. In apple crops, surveys indicate that numerous microbe species colonize flowers and nectar, which can in turn mediate floral and nectar traits and pollinator behavior. Microbial communities also affect the susceptibility of trees to pathogens such as the bacterium Erwinia amylovora, the causal agent of fire blight. For example, Blossom Protect is an organic-approved pesticide that inoculates apples with a yeast (Aureobasidium pullulans) that may limit subsequent infection by Erwinia through competition. However, our prior research suggests that management of Erwinia with Blossom Protect or other microbial-based strategies, including the use of antibiotics, could indirectly impact pollination in apples. This is because microbes are susceptible to many pesticides used in apples, and pollinators are sensitive to the presence of these same microbes. Yet, the extent by which microbes affect nectar traits, pollinator behavior, and resulting apple production remain untested. Moreover, the role of disease management on nectar microbe communities, and resulting impacts on pollination services, are relatively unknown. To address these knowledge gaps, we conducted a series of objectives to examine: (1) how apple management practices influence the flower microbiome, (2) the role of different microbes on limiting infection of apples with Erwinia, and (3) the indirect effects of microbial communities and pathogen management on pollination services and apple production. Our project broadly explored linkages between sustainable pathogen and pollination management by identifying new microbial strains that could serve as both antagonists for Erwinia and promoters of pollinator foraging behavior. These objectives align with WSU’s Sustainable Resources Grand Challenge by identifying optimal management schemes to promote production of a key agricultural crop in WA.

Grant Information

  • Project ID: 168
  • Project Status: Complete


  • Principal Investigator(s): Crowder, D.
  • Investigator(s): Schaeffer, R.
  • Grant Amount: $39,931



Schaeffer R, Crowder D, Fukami T, and Vannette R. In prep. Niche-based priority effects mediate microbial inhibition or facilitation of a destructive plant pathogen.

Schaeffer R, Beck J, Vannette R, Crowder D. In submission. How do orchard management practices affect floral microbiome structure, assembly, and function? Journal of Applied Ecology

Schaeffer R, Fukami T, Vannette R, Crowder D. In submission. Can microbial traits predict Erwinia suppression?  Molecular Plant-Insect Interactions.

Additional Funds Leveraged

Applied for, but unsecured: Development of improved antagonists for control of fire blight in apple and pear (PI: R Vannette, co-PIs: D Crowder, J Beck, K Johnson, Cooperating personnel: R Schaeffer ($325,000) California Department of Food and Agriculture, Specialty Crop Multi-State Program

Applied for, and secured: Screening potential antagonists for fire blight control (PI: R Vannette; Cooperating personnel: R Schaeffer, J Beck, S Lindow) ($9972) California Pear Commission

Applied for, pending: Sustainability of organic, mixed crop-livestock, and conventional agricultural production systems (PI: D Crowder) ($500K). USDA Foundational Program.



Short-Term:  (1) Determined how orchard management practices, including organic/conventional production and pesticide-use intensity affect microbial colonists of apple flowers and nectar; (2) Assessed effects of variation in microbe communities on resistance to Erwinia in the laboratory and field; (3) Evaluated how variation in microbial community structure affects pollination services and apple yields; (4) Delivered results to growers through field days and incorporation in the WSU Decision Aid System; (5) Trained two PhD students in bioinformatics and sequencing; (6) Wrote and submitted research proposals to conduct broader investigations of microbial mediation of tree fruit production.

Intermediate-Term: (1) Incorporation of putative Erwinia-antagonists into field trials for fire blight, in an ongoing effort to identify novel and cost-effective control options for organic and conventional growers; (2) Increased use of microbial “biological controls” for fire blight control on at least 25% of apple and pear orchards; (3) Documented decreases in applications of antibiotics or synthetic chemicals for fire blight control; (4) More complete integration of results into the WSU DAS system (Decision Aid System for Tree Fruit Growers), whereby growers can query the system to determine the impacts of different microbial strains on Erwinia resistance and pollination services.

Long-Term: (1) Widespread adoption (> 50% of orchards) of biologicals incorporating microbes for Erwinia resistance and pollinators in apple orchards; (2) Expansion of research into other crops affected by fire blight, such as pears; (3) Phasing out of antibiotics for fire blight control in conventional apple orchards by replacing them with more environmentally-friendly options; (4) Commercialization of new products to diversify management options for growers; (5) Establishment of WSU as a leader in the use of microbes for integrated control of diseases and pollinators.