HARNESSING THE WHOLE PLANT MICROBIOME FOR PLANT HEALTH AND NOVEL DISEASE CONTROL METHODS

• Sponsoring Institution: National Institute of Food and Agriculture
• Project Status: ACTIVE
• Funding Source: HATCH
• Reporting Frequency: Annual
• Accession No.: 1025628
• Project Start Date: Mar 26, 2021
• Project End Date: Jan 11, 2026
• Program Code: [(N/A)]- (N/A)

Recipient Organization
AUBURN UNIVERSITY
108 M. WHITE SMITH HALL
AUBURN,AL 36849

Performing Department
Plant Pathology

Non Technical Summary
Agricultural management strategies in the U.S. and worldwide contribute to changes in the crop's associated microbiota. It is now more apparent than ever that the microbiota associated with a plant, known as the microbiome, is important for maintaining a healthy plant through preventing diseases and resiliency to stress. This project aims to understand how the microbiome responds to different management strategies from the seed to seedling level combined with stressors like fungicide application and pathogens. More specifically, we will study the microbiome at an early but critical plant growth stage (the spermosphere) to restrict invasion from plant pathogens causing damping-off, an ever-growing threat to Alabama field crops. Additionally, we will study the non-target effects of fungicide application to develop strategies to mitigate the non-target effects while maintaining efficacy against pathogens. Modern molecular ecology techniques will be used to understand how the microbiome forms and functions. These molecular datasets will be used to form hypotheses about how microbial communities restrict plant pathogens and tested in the laboratory. Understanding how microbial communities form and function will help develop sustainable crop management practices in the face of pathogen pressure. This project's long-term goal will be to harness the microbiome to build agricultural ecosystems resilient to both biotic and abiotic stressors.

Animal Health Component

80%

Research Effort Categories

Basic

15%

Applied

80%

Developmental

5%

Classification

Knowledge Area (KA)	Subject of Investigation (SOI)	Field of Science (FOS)	Percent
212	1820	1102	30%
212	1710	1102	50%
212	1510	1102	20%

Knowledge Area
212 - Pathogens and Nematodes Affecting Plants;

Subject Of Investigation
1510 - Corn; 1820 - Soybean; 1710 - Upland cotton;

Field Of Science
1102 - Mycology;

Keywords

microbiome

fungi

oomycetes

bacteria

spermosphere

fungicide

ecology

phyllosphere

Goals / Objectives
The plant microbiome is a new frontier for understanding plant health in Alabama and around the globe. Understanding the microbiome's assembly process is a critical step to mitigating losses due to plant diseases and improving plant health. However, one of the most vital stages of a plant's growth and development (i.e., the spermosphere) has not received the research attention needed to harness the microbiome's full potential. It is well documented that agricultural management strategies, like fungicide use and no-till agriculture, can alter the microbiome's composition. Agricultural production will continue to use these strategies, and strategies must be developed to mitigate crop losses due to pathogens while building microbiomes that are resilient to perturbations. The soilborne pathogens listed here are important pathogens for Alabama field crops and occur worldwide, and research will have broad-reaching impacts. Information acquired during this research and collaborations at Auburn University will serve as a foundation for new insights into microbial ecology, plant health, and plant disease protection. The specific objectives for this HATCH project are to 1) Understand the effects of crop management practices on the plant microbiome, 2) understand spermosphere microbial ecology for improved seedling disease management, 3) use novel microbial consortia to control seedling pathogens of Alabama field crops

Project Methods
1.Understanding the effects of crop management practices on the plant microbiome.To understand how crop management practices influence the microbiome, we will take advantage of the long-term field experiments at Auburn University, such as the Old Rotation, Cullars Rotation, or other long-term plots in Alabama to isolate microbes from different plant organs and sequence the whole plant (root, leaves, soil) microbiome over space and time as described previously (Gdanetz et al. 2017; Gdanetz et al. 2020; Longley et al. 2020). The Old Rotation started irrigating one-half of the plots in 2003, so the effect of irrigation within a cotton-corn-soybean rotation on pathogen abundance and drought tolerating microbes within the microbiome will be investigated. Additionally, the impact of fungicides on non-target organisms will be assessed with and without pathogen pressure. Fungicides will be applied as either seed treatments to see disturbance to the spermosphere microbiome assembly or used as a foliar application against fungal diseases important for Alabama field crop or specialty crop production such as Cercospora sojina or Corynespora casiicola. Additionally, since fungicides are applied to many crops, including specialty crops such as blueberry or peaches, the opportunity exists to study fungicide perturbation within an annual system and a perennial cropping system.2.Understanding spermosphere microbial ecology for improved seedling disease managementExperiments utilizing amplicon sequencing, metagenomics, and transcriptomics will be used to study the composition, and gene repertoires of the microbiome or gene expression of associated microbiota within the spermosphere, with and without pathogen pressure. Corresponding isolations of bacteria and fungi will also be conducted to study the pathogens' interactions with competing fungi and bacteria. For this objective, we will focus on restricting pathogen abundance that causes pre- and post-emergence damping-off that are important to Alabama cotton, soybean, and corn industry, like Rhizoctonia solani, Fusarium oxysporum vasinfectum, and Pythium species.3.Use novel combinations of microbes to control seedling pathogens and promote microbiome resiliency within Alabama field crops.Sequence data from objectives 1 and 2 will generate hypotheses of which microbes to combine from culture collections established in my laboratory or existing in collaborators laboratories. Microbes will be selected based on positions in co-occurrence networks, deviation from neutral expectations in abundance-occupancy models, and performance in bioassays against pathogens or other plant health measures. Microbes will be inoculated onto expanded clay pellets, encapsulated into alginate, and inoculated into the soil near a germinating seed to determine plant health effects on cotton, corn, or soybean. Using this inoculation method also has great potential to eventually be used in the field or used for potential industry collaborations and product development for agricultural innovation within Alabama and across the United States.

Progress 03/26/21 to 09/30/21

Outputs
Target Audience:This project's target audience is Alabama crop producers, scientists, students, and the general public. Changes/Problems:There are no new changes. However, certain impacts due to COVID19 have been noticeable. Documenting impact fromvirtual presentationsis difficult and several opportunities to present research have been canceled in 2021 due to COVID19. Cancelations and virtual presence can impact the professional development of students,can impair the ability to recruit students, and form new meaningful collaborations. What opportunities for training and professional development has the project provided?This project has so far supported two graduate students and three undergraduate students. Each of these students has one-on-one mentoring sessions. The undergraduate students have each presented at university research symposia. The graduate students have each presented at University Research Symposia and the American Phytopathological Society meeting. Other presentations were given at the Mycological Society of America. One graduate student gave a departmental seminar. In total, fifteen research presentations were given by personnel supported by this project, and half of which were given by students. One undergraduate student was awarded a summer internship with Hudson Alpha Genomics Institute, and the other was accepted and moved on to advanced degrees. All graduate students and undergraduate students were trained in the basic handling of microbial cultures and molecular identification using sequencing low and high-throughput sequencing. Graduate students received training in bioinformatics, statistics, microbiology, and plant pathology. Presentations Oral - Online Alam, J., McInroy, J.A., Liles, M.R., Noel, Z.A., Goodwin, D.C. 2021. Bacillus Secondary Metabolites as Potential Biocontrol Agents against Plant Pathogenic Oomycetes. American Phytopathological Society Annual Meeting 2021 Noel, Z.A., Longley, R., Benucci, GMN, Trail, F., Chilvers, M.I., Bonito, G., 2021. Non-target fungicidal effects in the corn (Zea mays) and soybean (Glycine max) microbiome. American Phytopathological Society Annual Meeting 2021 Noel, Z.A., Longley, R., Benucci, GMN, Trail, F., Chilvers, M.I., Bonito, G., 2021. Non-target fungicidal effects in the corn (Zea mays) and soybean (Glycine max) microbiome. Mycological Society of America Annual Meeting 2021 Noel, Z.A., Roze, L., Breunig, M., Trail, F., 2021. Wheat fungal endophytes protect against Fusarium graminearum infection and reduce mycotoxins. American Phytopathological Society Annual Meeting 2021 Munroe, E., Noel, Z.A. 2021. Diversity of phyllosphere yeasts from southern magnolia (Magnolia grandiflora) in Auburn Alabama. Mycological Society of America Annual Meeting 2021 Olofintila, O.E., Moen, F.S., Liles, M.R., Noel, Z.A., 2021. The diversity and virulence of oomycetes associated with cotton seedlings in Alabama and options for biocontrol. American Phytopathological Society Annual Meeting 2021 Trail, F., Noel, Z.A., 2021. Influence of spore traits on the microbiome composition of plant organs. American Phytopathological Society Annual Meeting 2021. Trail, F., Noel, Z.A., 2021. Influence of spore traits on the microbiome composition of plant organs. Mycological Society Annual Meeting 2021. Oral presentations posters Rodríguez, L.R., Harrison, C., Bowen, K., Noel, Z.A., 2021. Composition and salt tolerance of fungi isolated from non-irrigated soils of The Old Rotation. Auburn University 2021 Research Symposium Olofintila, O.E., Moen, F.S., Liles, M.R., Noel, Z.A., 2021. The diversity and virulence of oomycetes associated with cotton seedlings in Alabama and options for biocontrol. Auburn University 2021 Research Symposium Harrison, C., Olofintila, O.E., Noel, Z.A., 2021. Comparison of soybean spermosphere microbiomes in long-term irrigated versus non-irrigated soil form the Old Rotation. Spring 2021 Undergraduate Research Symposium Harrison, C., Noel, Z.A., 2021. Potential of Chromobacterium spp. as a biocontrol for Pythium ultimum. Fall 2021 Undergraduate Research Symposium Munroe, E., Noel, Z.A., 2021. Evidence of non-antagonistic interactions between yeast and bacteria on plants in the Auburn Arboretum. Spring 2021 Undergraduate Research Symposium Munroe, E., Noel, Z.A., 2021. Evidence of positive interactions between yeast and bacteria isolated from the plant phyllosphere. Fall 2021 Undergraduate Research Symposium Warner, D.L., Moen, F., Dyal, H., Noel, Z.A., Liles, M., 2021. Biocontrol of plant pathogens using a combination of Bacillus strains and pectin-rich orange peel. Spring 2021 Undergraduate Research Symposium. Invited seminar online Noel, Z.A., Crop microbiomes for practical disease control. Invited Cornell Seminar. Spring 2021. Invited talk How have the results been disseminated to communities of interest?The results of this project have been communicated through annual scientific meetings, presentations to commodity crop organizations, and through the public. For research presentations, it is estimated that results from this project reached several hundreds of individuals.In terms of public engagement, personnel supported by this project held a mushroom foray event in a university-supported forest aimed to document the diversity of macrofungi. The event reached 25 individuals and allowed students to engage in an outreach event. The event attracted individuals that learned the identification of fungi found in forest ecosystems. The event impacts the preservation, conservation, and appreciation of fungi in natural areas. What do you plan to do during the next reporting period to accomplish the goals?In the next reporting period, the primary focus will be to attract more students to the program to generate more research output. To accomplish this goal, research will need to generate enough preliminary data to leverage for larger extramural grants. Several proposals are already planned. In addition, we anticipate at least two new graduate students in 2022. We plan to generate millions of unique sequences from microbial collections. We also plan to continue outreach events to document fungal diversity in Alabama. Additionally, we plan to present research to domestic and international universities through seminars. Students also plan to travel to regional plant pathology and grower-sponsored meetings to present research findings.

Impacts
What was accomplished under these goals? Agricultural management strategies in the U.S. and worldwide contribute to the crop's associated microbiota changes. It is now more apparent than ever that the microbiota associated with a plant, known as the microbiome, is essential for maintaining a healthy plant through preventing diseases and resiliency to stress. This project's long-term goal will be to harness the microbiome to build agricultural ecosystems resilient to biotic and abiotic stressors. We have designed a protocol to efficiently sample the microbiome and generated culture collections of fungi and bacteria from the spermosphere that can be used for plant protection in the future. We have also investigated the use of novel commercially relevantBacillusstrains for protection from fungal and oomycetes that could be used as seed treatments to reduce chemical inputs over the next five years. We have also surveyed Alabama cotton roots for fungal and oomycete pathogens, which several previously unreported pathogenic species. Identification of unreported pathogens will result in better management of crop loss due to seedling pathogens, and that could result in hundreds of thousands of dollars saved each year. Specific accomplishments include the identification of 30 novelBacillusstrains able to protect soybean seeds against oomycete infection. We have worked with companies to make the next steps toward getting these strains onto soybean seed treatments. We sequenced the genomes of these 30 strains and are now able to search through the genomes of novel strains for novel properties, which could lead to new biologically based chemical products for protection against soilborne oomycete and fungal pathogens, which will be helpful for the development of new seed treatment products for soybean and cotton growers. We will incorporate these strains into microbiome studies of the spermosphere. Therefore, we developed a new efficient sampling design that enabled us to sample the microbial communities in soils directly surrounding a germinating seed. We have also been active in different microbial collections. We have made a collection of about 150 yeasts and inoculated soybean seeds. Seeds inoculated with some yeast strains could decrease the time to soybean germination. Some of these yeasts have never been described before and may have novel properties. We have surveyed Alabama cotton for fungal and oomycete pathogens. This survey resulted in 26 oomycete species, of which 14 were pathogenic toward cotton seeds. At least 10 of these species are newly reported as pathogenic to cotton in Alabama.

Publications

• Type: Conference Papers and Presentations Status: Accepted Year Published: 2021 Citation: Alam, J., McInroy, J.A., Liles, M.R., Noel, Z.A., Goodwin, D.C. 2021. Bacillus Secondary Metabolites as Potential Biocontrol Agents against Plant Pathogenic Oomycetes. American Phytopathological Society Annual Meeting 2021
• Type: Conference Papers and Presentations Status: Accepted Year Published: 2021 Citation: Noel, Z.A., Longley, R., Benucci, GMN, Trail, F., Chilvers, M.I., Bonito, G., 2021. Non-target fungicidal effects in the corn (Zea mays) and soybean (Glycine max) microbiome. American Phytopathological Society Annual Meeting 2021
• Type: Conference Papers and Presentations Status: Accepted Year Published: 2021 Citation: Noel, Z.A., Longley, R., Benucci, GMN, Trail, F., Chilvers, M.I., Bonito, G., 2021. Non-target fungicidal effects in the corn (Zea mays) and soybean (Glycine max) microbiome. Mycological Society of America Annual Meeting 2021
• Type: Conference Papers and Presentations Status: Accepted Year Published: 2021 Citation: Noel, Z.A., Roze, L., Breunig, M., Trail, F., 2021. Wheat fungal endophytes protect against Fusarium graminearum infection and reduce mycotoxins. American Phytopathological Society Annual Meeting 2021
• Type: Conference Papers and Presentations Status: Accepted Year Published: 2021 Citation: Munroe, E., Noel, Z.A. 2021. Diversity of phyllosphere yeasts from southern magnolia (Magnolia grandiflora) in Auburn Alabama. Mycological Society of America Annual Meeting 2021
• Type: Journal Articles Status: Accepted Year Published: 2021 Citation: Olofintila, O.E., Moen, F.S., Liles, M.R., Noel, Z.A., 2021. The diversity and virulence of oomycetes associated with cotton seedlings in Alabama and options for biocontrol. American Phytopathological Society Annual Meeting 2021
• Type: Conference Papers and Presentations Status: Accepted Year Published: 2021 Citation: Trail, F., Noel, Z.A., 2021. Influence of spore traits on the microbiome composition of plant organs. American Phytopathological Society Annual Meeting 2021.
• Type: Conference Papers and Presentations Status: Accepted Year Published: 2021 Citation: Trail, F., Noel, Z.A., 2021. Influence of spore traits on the microbiome composition of plant organs. Mycological Society Annual Meeting 2021.
• Type: Conference Papers and Presentations Status: Accepted Year Published: 2021 Citation: Rodr�guez, L.R., Harrison, C., Bowen, K., Noel, Z.A., 2021. Composition and salt tolerance of fungi isolated from non-irrigated soils of The Old Rotation. Auburn University 2021 Research Symposium
• Type: Conference Papers and Presentations Status: Accepted Year Published: 2021 Citation: Olofintila, O.E., Moen, F.S., Liles, M.R., Noel, Z.A., 2021. The diversity and virulence of oomycetes associated with cotton seedlings in Alabama and options for biocontrol. Auburn University 2021 Research Symposium
• Type: Conference Papers and Presentations Status: Accepted Year Published: 2021 Citation: Harrison, C., Olofintila, O.E., Noel, Z.A., 2021. Comparison of soybean spermosphere microbiomes in long-term irrigated versus non-irrigated soil form the Old Rotation. Spring 2021 Undergraduate Research Symposium
• Type: Conference Papers and Presentations Status: Accepted Year Published: 2021 Citation: Harrison, C., Noel, Z.A., 2021. Potential of Chromobacterium spp. as a biocontrol for Pythium ultimum. Fall 2021 Undergraduate Research Symposium
• Type: Conference Papers and Presentations Status: Accepted Year Published: 2021 Citation: Munroe, E., Noel, Z.A., 2021. Evidence of non-antagonistic interactions between yeast and bacteria on plants in the Auburn Arboretum. Spring 2021 Undergraduate Research Symposium
• Type: Conference Papers and Presentations Status: Accepted Year Published: 2021 Citation: Munroe, E., Noel, Z.A., 2021. Evidence of positive interactions between yeast and bacteria isolated from the plant phyllosphere. Fall 2021 Undergraduate Research Symposium.
• Type: Conference Papers and Presentations Status: Accepted Year Published: 2021 Citation: Warner, D.L., Moen, F., Dyal, H., Noel, Z.A., Liles, M., 2021. Biocontrol of plant pathogens using a combination of Bacillus strains and pectin-rich orange peel. Spring 2021 Undergraduate Research Symposium.
• Type: Journal Articles Status: Under Review Year Published: 2021 Citation: Noel, Z.A., Longley, R., Chilvers, M.I., Trail, F., Bonito, G. 2021. Fungicide pulse disturbance changes phyllosphere microbiome complexity and architecture in corn and soybean. https://www.biorxiv.org/content/10.1101/2021.09.20.461135v1
• Type: Journal Articles Status: Accepted Year Published: 2021 Citation: Noel, Z.A., Roze L.V., Breunig, M., Trail, F. 2021. Endophytic fungi as a promising biocontrol agent to protect wheat from F. graminearum head blight. Plant Disease. https://doi.org/10.1094/PDIS-06-21-1253-RE
• Type: Journal Articles Status: Accepted Year Published: 2021 Citation: McCoy, A.G., Noel, Z.A., Jacobs, J.L., Clouse, K.M., Chilvers, M.I. 2021. Phytophthora sojae pathotype distribution and fugnicide sensitivity in Michigan. Plant Disease. https://doi.org/10.1094/PDIS-03-21-0443-RE
• Type: Journal Articles Status: Accepted Year Published: 2021 Citation: Chang, H.X., Noel, Z.A., Chilvers, M.I., 2021. A �-lactamase gene of Fusarium oxysporum alters rhizosphere microbiota of soybean. The plant journal. doi: 10.1111/tpj.15257
• Type: Journal Articles Status: Accepted Year Published: 2021 Citation: Gdanetz, K., Noel, Z.A., Trail, F. 2021. The phytobiomes of a three-crop rotation: Influence of land management, host, and plant organ on microbial diversity. Phytobiomes. https://doi.org/10.1094/PBIOMES-08-19-0045-R
• Type: Journal Articles Status: Accepted Year Published: 2021 Citation: Noel, Z.A. McDuffee, D., and Chilvers M.I. 2021. Influence of soybean tissue and oomicide seed treatments on oomycete isolation. Plant Disease. https://doi.org/10.1094/PDIS-03-20-0642-RE