Seed health in ornamental crops

Seed health is the cornerstone of plant health.  Xanthomonas campestris (Xc) is a seedborne bacterial pathogen that threatens seed health and causes destruction among a wide variety of hosts, including most prominently vegetable and ornamental Brassica species. It is also known to infect non Brassicaceae such as tomato (Solanaceae) and zinnia (Asteraceae). Xc pv. incanae (Xci) causes bacterial blight on stock (Matthiola incana) while Xc pv. zinniae (Xcz) causes bacterial spot on zinnia (Zinnia elegans), two economically important cut flower species. One of our current research objectives in the seed health space is to investigate the pathways of Xcc and Xcz transmission to the seeds of M. incana and Z. elegans, respectively. This will be achieved through a series of inoculation experiments where vascular, floral, and seed-to-seed will be tested as potential pathways of transmission.

One largely contributing factor to seed health is the microbiome, or the complexity of organisms present on and within the seed. Additional research goals are to investigate whether there is an association between the microorganisms present within the seed and the presence or absence of Xanthomonas campestris pathovars focusing specifically on the seeds of stock (Matthiola incana), ornamental kale (Brassica oleracea), and zinnia (Zinnia elegans). This will be achieved using both a metagenomic lens and cultural methods. This project at its core has a wide scope of impact that will help provide knowledge and more informed disease management strategies to growers, seed producers, and those managing bacterial diseases that associate with seeds.

Exploring the use of anaerobic soil disinfestation (ASD) for the control of soilborne pathogens in specialty cut flower production 

Cut flowers are produced in diverse systems, ranging from crates, raised and in-ground beds in high tunnels and greenhouses, to open fields. Commercial growers have historically relied on soil fumigants to manage soilborne diseases, but the global phase-out of methyl bromide has left them with limited chemical options. At the same time, growers are increasingly choosing to adopt more sustainable farming practices.To help growers achieve their sustainable farming goals, we are exploring the use of a non-pesticide-based technique, known as anaerobic soil disinfestation (ASD), for its potential to reduce soilborne disease damage in cut flower production. ASD is a three-step process in which soil is first amended with easily decomposable, carbon-rich, organic substrates, then irrigated to saturation, and finally covered with a plastic film for several weeks to prevent the resupply of oxygen. Toxic byproducts generated during the anaerobic digestion of the organic matter by soil microbes, along with changes in the soil biochemical composition, affect soilborne pathogen survival.

Our preliminary studies have shown that ASD has the potential to be deployed successfully for the control of Rhizoctonia stem rot in in both soilless and soil-based substrates commonly used in specialty cut flower production (Gutierrez Yanez et al. 2023). Ongoing research is aimed at further our understanding of how the diversity of factors involved in ASD influence its efficacy in suppressing soilborne pathogens and its effects on plant growth. We are also assessing if ASD can be effective at specific inoculum thresholds, and evaluating more carbon sources and carbon amendment rates. Finally, we are interested in comparing the efficacy of ASD and soil steaming in suppressing soilborne pathogens in naturally infested soils in high tunnel cut flower production to assess if ASD can result in significant and broader disease reduction and have lower impact on beneficial soil microorganisms compared to soil steaming.

Understanding pathogen-host interactions in the fruit rot disease of deciduous holly (winterberry)

Deciduous holly (Ilex spp.) is an ornamental shrub with branches bearing brightly colored fruits, that are cut and sold during the fall and winter holiday seasons. In the last few years, an emerging fruit rot disease caused by a complex of fungi, including the newly described species Diaporthe ilicicola (Lin et al. 2018), has been threatening holly production in the Northeastern and Midwestern U.S., leading, in some cases, to complete crop loss. Symptoms of the disease include early plant defoliation and fruits that fail to turn red, loose their gloss, and become necrotic. While D. ilicicola infects the fruit at flower anthesis (Lin & Peduto Hand 2019), symptoms only emerge several months later, approximately two weeks prior to crop harvest, progressing rapidly following onset and making prevention the only means of control.

The late onset of disease symptoms suggests that D. ilicicola undergoes a period of quiescence, or metabolic dormancy, within infected fruits. In recent research, we used a combination of classic microbiology, metabolomics, and genomics approaches to investigate host-pathogen interactions and advance our understanding of pathogen biology and host physiological factors that contribute to disease development. We identified environmental factors and significant changes in fruit chemistry during maturation that are correlated with disease onset and tested them in vitro and ex vivo to determine whether they could affect the growth of D. ilicicola (Emanuel et al. 2023a); we screened germplasm and identified resistant cultivars to provide growers with recommendations when establishing new plantings (Emanuel et al. 2023b); and finally discovered metabolites in the fruit associated with natural disease resistance (Emanuel et al. 2024), which could inform breeding programs, chemical management programs, and novel antifungal compound development pipelines.

 

Using bioassays and genomic tools to study host resistance in the Phlox-powdery mildew pathosystem

The genus Phlox consists of approximately 65 species that include some of the most prevalent ornamental plants in the temperate zone. These popular ornamentals are extremely susceptible to powdery mildew (PM) caused by the biotrophic fungi Golovinomyces magnicellulatus and Podosphaera sp. Due to difficulties in growing PM fungi under axenic conditions, little is known regarding the genetic and evolutionary bases of their lifestyles. Over the last few years we successfully developed two laboratory bioassays and optimized the experimental conditions to use these tools to study PM pathogens of Phlox in vitro (Farinas et al. 2019a), and we used them to to evaluate host resistance in perennial Phlox germplasm (Farinas et al. 2020). We also used multilocus sequence typing (MLST) analysis and whole-genome analysis to gain insights into the genetic diversity of Phlox PM pathogen (Golovinomyces magnicellulatus and Podosphaera sp.) isolates collected from the eastern U.S. and relate it to the ability to overcome host resistance (Farinas et al. 2019b; Farinas et al. 2020).