Exploring the use of Anaerobic Soil Disinfestation for the control of soilborne pathogens in specialty cut flower production systems

Cut flowers are produced in diverse systems, ranging from crates, raised and in-ground beds in high tunnels and greenhouses, to open fields. When crops are cultivated in soil, they are constantly challenged by soilborne plant pathogens, which can have a major impact on cut flower plantings. 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, due to increased concerns for human and environmental health, an increasing number of growers is choosing to adopt more sustainable farming practices.

This project aims to explore the use of a non-pesticide-based soil disinfestation 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 (Rosskopf et al. 2015). Toxic byproducts generated during the anaerobic breakdown of the organic matter by soil microbes, along with changes occurring in the soil biochemical composition, affect soilborne pathogen survival.


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. Current research aims to identify the relationship between fruit physiology and D. ilicicola, which allow for the pathogen to remain quiescent within immature Ilex fruits and colonize the infected tissues in the fall. Research questions for this project aim to identify differences in chemical compositions between immature and mature fruits which may account for differences in susceptibility to rot, as well as the mechanisms used by the fungus to infect and colonize the fruit tissues of Ilex plants.


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).