Mapping Soil Microbiome Shifts During Pythium Disease Development in Soybean Seeds and Seedlings Under Different Management and Soil Conditions

Project Overview

Project Type: Graduate Student
Funds awarded in 2020: $14,986.00
Projected End Date: 12/31/2022
Grant Recipient: The Pennsylvania State University
Region: Northeast
State: Pennsylvania
Graduate Student:
Faculty Advisor:
Paul Esker
The Pennsylvania State University


  • Agronomic: soybeans


  • Pest Management: prevention
  • Soil Management: soil microbiology, soil quality/health

    Proposal abstract:

    Seedling diseases are one of the top five most destructive soybean diseases in the Northern United States with an estimated 500,000 bushels lost in Pennsylvania in 2018 (Crop 2020). Pythium spp. is one important soilborne pathogen that can be suppressed by soil organisms like Trichoderma or increase in severity in the presence of other soilborne pathogens. This study’s objective is to further elucidate the microbiome’s role in Pythium disease development by assessing how microbiome composition shifts in bacterial and fungal abundance and diversity during Pythium disease development is predictive of disease severity in soybean. This interaction will be assessed under common management practices and soil conditions including fungicide seed treatments, liming, fertilizer, flooding, and soil sand/silt/clay content using a novel rhizobox design for non-destructive daily rhizosphere sampling in greenhouse and field experiments. Pythium qPCR, 16S-rRNA bacterial gene sequencing and ITS fungal gene sequencing using MiSeq will be used to visualize the abundances and diversity of fungal and bacterial microbiome members.

    Mixed analyses including principal coordinates analysis, linear discriminant analysis, and correlation network analysis will identify treatment variations and relate microbiomes to disease severity. I hypothesize that certain management practices support a suppressive microbiome and that potential biocontrol organisms will be identified that can support sustainable agriculture. Results will be published in a peer-reviewed scientific journal, presented at professional and farmer meetings, and compiled with videos and photos from the experiments for public dissemination as factsheets, online educational resources, and extension teaching materials to promote adoption of sustainable management practices.

    Project objectives from proposal:

    Objective 1: Determine how common PA soybean production management practices and field conditions such as fungicide seed treatments, liming, fertilizer, flooding, and soil sand/silt/clay content impact shifts in bacterial and fungal composition and diversity during pre- and post-emergence Pythium disease in soybeans up to two weeks after planting using both greenhouse and PA research field experiments.

    Objective 2: Determine how shifts in soil microbiome fungal and bacterial diversity and abundance during Pythium disease development relate to the severity of disease after two weeks from planting.

    Objective 3: Identify key fungal and bacterial taxa in the soil microbiome involved in synergism with or inhibition of Pythium disease development under the different management and soil conditions, supporting future studies delving into the pathogen-interaction mechanisms that can be developed into viable sustainable management options such as biocontrols.

    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.