Functional ecology of soilborne pathogens
Soilborne microbes vary greatly in their ecological response to the environment. These responses are governed by functional traits, a suite of morphological, physiological, or genomic characteristics that affect fitness, performance and survival in a given location. Spores, for example, are critical for the reproduction and dispersal of fungal pathogens. These structures possess numerous traits (e.g., size, shape, pigmentation, desiccation tolerance) that may be conserved across evolutionary time.
Current projects on Fusarium: We are quantifying fungal traits within the Fusarium oxysporum soilborne pathogen complex (Foc). Together with our collaborators, we are interested in the long-distance dispersal potential of Fusarium and other soilborne pathogens both intra-and intercontinentally. A major contributor to spore dispersal are large atmospheric dust storm events that carry spores from sub-Saharan Africa to the Americas. This interdisciplinary initiative seeks to model spore dispersal and in particular, the probability of spore deposition and potential viability across various crop growing regions. Moreover, using a trait-based morphological and genomic approach to explore shared pathogenicity functional gene regions. Our ultimate goal is to resolve fungal traits such as: life history traits, morphological traits, and physiological, or functional traits to fit our spore dispersal model.
Funding / Collaborators: NASA – ROSES, “Soilborne plant pathogen dispersal and assessment: Building a remote sensing-based global surveillance system for plant disease.” – K.M. Gold (PI), S.G. Crandall (Co-PI) – Pennsylvania State University, N. Mahowald (Co-PI) – Cornell University; R. Pavlick (Co-PI) Jet Propulsion Laboratory / CA Institute of Technology, F. Shabani (Collaborator), Flinders University, S. Mohammed (Collaborator), Woldia University, M. Dita (Collaborator), CGIAR).
Disease dynamics of the soil, seed, and root microbiome
Microbial community abundance, composition, and functionality changes dramatically based on location, time of year, meteorological variables, and in response to plant stress. Abiotic and biotic stressors can alter the composition and structure of microbial communities within seeds and roots and the rhizosphere. We are interested in the understanding how ecological gradients drive the mechanisms behind microbial diversity, structure, and function of fungal and oomycete microbiomes at the scale of the root. Understanding these dynamics can help us better understand the mechanisms behind soilborne disease suppression. We are currently developing these questions in specialty crops such as grape, strawberry, and potato.
Current project on Trichoderma: The fungus Trichoderma harizanum shows promise as a sustainable management option for eliminating soilborne plant pathogens. Others have shown that T. harizanum can successfully suppress oomycete pathogens such as Phytophthora sp. and in particular, P. ramorum, the cause of sudden oak death in forests. However, the soil microbiome diversity, structure, function, and soil chemistry pre/post treatment using Trichoderma is still a mystery. This project harnesses an -omics approach using metagenomics and metatranscriptomics to experimentally explore the underlying functional mechanisms for biocontrol and how it shapes the soil microbiome. Results should provide baseline data for future experiments as well as information for growers on how to amend the soil post-treatment.
Funding / Collaborators: College of Agriculture – The Pennsylvania State University, National Ornamentals Research Site at Dominican (NORS-DUC) – S.G. Crandall (PI), The Pennsylvania State University, in collaboration with W. Schweigkofler, V. Hoffman, NORS-DUC.
Current project on legume rhizosphere microbiome: To effectively manage for plant health in agro-ecosystems, it is important to understand the ecological drivers of plant-soil-microbial interactions. Soil provides the physical matrix and chemical environment for plant roots to establish. Roots in turn, locally modify soil properties in their vicinity. As roots grow, they disturb the soil structure and produce exudates, organic compounds that are released by root cells, and are responsible for the rhizosphere effect. It is unclear how this effect, or the growth of microorganisms within this spatial zone, shapes ecological interactions at the soil-plant interface, especially in legumes that are used as cover crops on many farms.
Funding / Collaborators: Flower Grant for Ecological Research, The Ecology Institute, The Pennsylvania State University. E. Couradeau (PI), S.G. Crandall (Co-PI), L. Burghardt (Co-PI) – The Pennsylvania State University.
Cluster rot disease dynamics
Current project on microbiome assembly of the sour rot pathogen complex on grape: Sour rot of grapevine is a disease that costs the grape industry millions of dollars annually. This disease complex is the product of the interaction between acetic acid bacteria, yeasts, insects and the grape host. Our research explores: (1) The potential for certain grape cultivars to become less susceptible to sour rot by reducing cluster compactness in field experiments using sustainable practices such as plant hormone sprays. (2) The impact of microclimate on sour rot disease ecology will be found by placing small temperature & relative humidity sensors into developing grape clusters during the growing season in sites across the growing regions of grapevine in the US (PA, NY, MI, and CA). (3) Which microbes cause disease within the sour rot complex using high throughput culturing and bioassay experiments in the lab. A grower friendly risk model will be created based on these data to help predict sour rot for cultivars of interest. Understanding when and where rots occur can help growers plan for management and promote sustainable management practices. This project part of Jamie Spychalla’s dissertation research (NSF-GRFP; ASEV).
Funding / Collaborators: National Science Foundation, American Society for Enology and Viticulture, Lake Erie Regional Grape Research and Extension Center (Penn State/Cornell), USDA/Cornell Geneva Research Station in New York, Small Fruit Pathology Lab (T. Miles) Michigan State University, Cal Poly Technic, Wine and Viticulture (S. Ding).
Soil health
The role of disturbance on the functional diversity of soil and plant microbial communities: Environmental disturbance can affect the fertility of soils. Abiotic stressors such as storms, droughts, fires and farm management practices can affect which biota can persist in soil and their functions. Other biotic stressors, such as pathogens or pests can also influence soil and plant health. The recovery of soil microbiomes after disturbance in agricultural systems has been understudied, especially within the context of phytosanitary measures to suppress soilborne diseases. We examine the resiliency of soils after disturbance. Tools we employ: metabarcoding, metagenomics and other -omics tools. This project is part of Dr. Eric Larson’s post-doctoral research.
Project on sustainable soil management: Quantifying how and why different farms are making decisions about their management practices can help us understand which farms might be disproportionately affected by the COVID-19 pandemic and the potential downstream effect on the environment. Our goal is to quantify the extent to which the impact of the pandemic has affected and will continue to influence the capacity of Pennsylvania farmers to implement best soil management practices and maintain soil health.
Funding / Collaborators: Institute for Sustainable Agricultural, Food, and Environmental Science (SAFES), The Pennsylvania State University: “Quantifying the impacts of COVID-19 on farmers’ decisions to manage for soil health in Pennsylvania,” S.G. Crandall (PI), L. Burghardt (Co-PI), E. Couradeau (Co-PI), F. Di Gioia (Co-PI), F. Dini-Andreote (Co-PI), B. Gugino (Co-PI), S. Windon (Co-PI), The Pennsylvania State University, F. Egan (Collaborator) – Pennsylvania Association for Sustainable Agriculture (PASA).
Current project on developing molecular diagnostic tools for Verticillium dahliae: Verticillium wilt is a devastating disease on potato and growers are interested in early and accurate pathogen detection. Currently, diagnostic markers that differentiate clonal lineages of 4A and 4B of Verticillium dahliae are not available. Assigning an isolate to a clonal lineage still involves testing vegetative compatibility groups (VCGs) via nit mutants or sequencing, which requires extensive time, isolation, and culturing of V. dahliae isolates. Methods of V. dahliae detection and quantification exist, but these assays cannot differentiate lineages intra-species. Moreover, lineage 4A is geographically constrained to North America but it is highly host-adapted and very aggressive on potato, often resulting in more severe disease symptoms than 4B. Lineage 4B has a wider geographic range spanning multiple countries but it is relatively less aggressive when it causes disease on potatoes. Other studies have found that 4B can colonize hosts other than potato without causing any symptoms, this is known as endophytic colonization. Through controlled experiments, we are researching the extent to which these two lineages can live endophytically on common weeds that grow within and near potato fields in PA. These weeds may act as reservoir plant hosts for V. dahliae. This project is part of Uma Crouch’s thesis research.
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