Graduate students receive grants from Northeast SARE

UNIVERSITY PARK, Pa. – The Northeast Sustainable Agriculture Research & Education (SARE) program selected proposals of four plant pathology graduate students for the 2020 Graduate Student Grant Awards. SARE offers competitive grants to projects that explore and address key issues affecting the sustainability and future economic viability of agriculture.

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

This project, funded from August 2020 to September 2022, is designed to identify shifts in soil bacterial and fungal abundance and diversity during Pythium disease development in soybean plants grown in rhizoboxes to determine if these shifts or keystone organisms are predictive of seedling disease severity. Ultimately, this research can help identify disease suppressive soils and management practices, as well as highlight potential biocontrol candidates for further study, all of which can enhance future sustainable management of Pythium in U.S. soybean agriculture. This role of the microbiome will be assessed over a two-week period using non-destructive daily sampling of soil under different field scenarios including silty versus sandy soil, high and low pH, saturated and unsaturated soil, and fungicide-treated versus non-treated seeds. This project involves a greenhouse trial to be conducted in Spring 2021, immediately duplicated in field trials at the Russell E. Larson Agricultural Research Center at Rock Springs. Samples will undergo genetic sequencing and statistical analysis to visualize the abundances and diversity of fungi and bacteria in the soil microbiome through time and in association with Pythium disease severity. Results and educational resources will be provided to various stakeholders including farmers, extension specialists and other researchers to improve scientific understanding of the microbiome's role in seedling disease development, guide soybean production management decisions and serve as a basis for future agricultural sustainability studies.

Emma Wallace
Understanding Emergence of Vegetable Vascular Wilt Disease from an Ecological Perspective

Emerging fungal plant diseases such as Fusarium wilt of tomato cause significant losses for growers in the northeast United States. Although some members of the Fusarium oxysporum Species Complex (FOSC) are responsible for this plant disease on over 100 crops, most isolates live in the soil or inhabit plants without causing disease. In fact, because of the complex evolutionary history of this group and the multiple modes of genetic exchange available, the isolates that cause Fusarium wilt can be very closely related to isolates that do not. As these isolates occupy the same ecological niche in agroecosystems, it is important to understand how these isolates relate to and impact one another. Improving this understanding helps researchers understand risks related to pathogen emergence and aid in developing better diagnostic tools. Therefore, it is crucial that we understand the evolutionary and ecological context from which pathogenicity emerges. This necessitates characterizing host adaptation among nonpathogenic isolates. Therefore, we propose to conduct a systematic sampling of FOSC isolated from specific parts of asymptomatic tomato plants and agricultural and non-agricultural soil. This sampling will allow meaningful comparisons to evaluate the genetic diversity of nonpathogenic FOSC in Pennsylvania tomato production, and identify factors that may be influencing population structure, and adaptation to tomato. Specifically, we will assess agricultural production, crop history, time, and host variety. We will also assess current diagnostic approaches for Fusarium-associated diseases. We will identify educational needs of diagnosticians for Fusarium identification and provide resources to address those needs.

Mary Smith
Using bacteriocin repertoires to uncover competitive microbial interactions that mediate bacterial speck of tomato

Pseudomonas syringae pv. tomato (pto), the causal agent of bacterial speck of tomato, is an increasing problem in the Northeast and Mid-Atlantic region that can cause devastating crop losses. With the wide-spread emergence of chemical resistance in bacteria coupled with increasing severe weather events that favor the disease development, there is a need to find reliable long-term management strategies. One potential solution is the use of bacteriocins. Bacteriocins are proteinaceous antimicrobial compounds bacteria use to kill closely related bacteria and are considered promising and safe potential agricultural bactericides and biological control agents. Current biological control strategies ignore complex community interactions, and therefore fail to produce reliable outcomes. They often only assess the effects of one individual bacteriocin on a population, when many bacteria including pto carry as many as 5 bacteriocins in their genome that can also influence the outcome of competition within a microbial community. In order to understand the role bacteriocins play in the development of bacterial speck of tomato, the competitive interactions that correlate to increased disease development due to individual and combinations of bacteriocins in pto will be assessed. First, the targets of pto's bacteriocin repertoire will be identified to determine susceptible community members. Then two ecological strategies (invasion & defending) will be evaluated for each bacteriocin repertoire by performing microbiome transplant experiments, enumerating pathogen populations inside and on the surface of the leaf, and assessing disease severity of each treatment. This will pinpoint when during the disease cycle (e.g. colonization and epiphytic survival) and where (inside the leaf or on the surface) bacteriocins are most beneficial to the pathogen. This data can then be applied to determine how and when to manipulate the foliar microbial community to effectively control the pto during critical points of its disease cycle to develop more robust and sustainable microbial biocontrol strategies for future tomato production in both conventional and organic systems.

Chad Fautt
Development of a PCR-based assay for identifying members of the Pseudomonas syringae species complex from environmental samples

Many closely related bacteria are capable of causing similar diseases in crops. In many cases, it can be difficult to discriminate between related pathogens, which makes disease control more difficult. In tomato alone, at least five distinct groups (pathovars) of Pseudomonas syringae have been shown to cause disease, and we have seen a considerable shift in abundance among these lineages over the last century. Moreover, surveys of environmental strains show they contain multiple virulence factors not yet present in pathogenic lineages and might be a source of future emerging pathogens.

Using a technique to detect a specific genomic locus (PCR) that is present in nearly all P. syringae strains, we will be testing the efficacy of an assay for detection and identification of members of this species. Our assay will allow for more robust screening of common sources of disease transmission in agricultural fields and easier monitoring of the population dynamics occurring among current and emerging pathogenic lineages.