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Image by Wolfgang Hasselmann

Pyroaeromycoses: fundamental discovery and modeling in an unexplored phenomenon.


Our team will be the first to quantify the relationship between wildfire smoke and emerging mycotic diseases such as Valley Fever, focusing on California and neighboring regions with high population densities and accelerating wildfire frequency and severity. Existing research navigating the nexus of wildfire smoke and human health—including respiratory, cardiovascular, and reproductive functions—has focused primarily on the context of fine particulate matter and various chemical species. Recent studies have revealed that living microbes, notably fungi, also comprise a significant portion of particulate matter from wildfires. Habitats in the western U.S. where wildfires burn harbor fungal species that can act as human pathogens and aeroallergens, including Cryptococcus gattii (found in decayed trees and causes cryptococcal meningitis), Coccidioides spp. (found in soils and causes Valley Fever), and mold species like the fungicide-resistant Aspergillus fumigatus (causal agent of invasive aspergillosis) that appears to have origins in quasi-agricultural landscapes.  However, the mechanisms of how these fungi migrate from the realm of humus to humans is not understood. Our approach capitalizes on our multidisciplinary team’s expertise to link a series of threats, beginning with the source, to combustion-aerosolization and transport, to exposure, and finally to pathogenicity of microbes in smoke using a combination of analytical, modeling, and experimental techniques. These data will be integrated using advanced machine-learning analysis to develop epidemiological models for smoke-borne pathogens and will create a fully translatable methodology for predicting the consequences of additional point-source pollutants on human health. Results will have immediate relevance for epidemiology and global health. 


Funding Provided By: W.M. Keck Foundation 


Collaborators: Dr. Leda Kobziar (University of Idaho), Dr. Stephen VanDenEeden (Kaiser Permanente), Dr. Borna Mehrad (UF College of Medicine), Dr. Karen Garrett (UF Emerging Pathogens Institute).


Target-SNAP: Development of a High Priority Pathogen Surveillance System for Southern Pines.


During the past 5 years our team has developed a low-cost spore trap designed for disease monitoring, that allows for deployment of multiple traps per site to allow for surveys, epidemiological studies and research. Initially the traps have been used in climate change and pitch canker (a top disease of commercial pines) studies. More recently, we have improved the design through use of 3D printing and biological engineering (use of membranes compatible with DNA extraction and microscopy) to avoid the use of petroleum jelly and now have a novel system that allows for repeatable, sensitive, systematic surveillance for Fusarium circinatum in the field. Our goal for this Farm Bill suggestion is to develop a pine disease surveillance system that focuses on the 5 most threatening pathogens of southern pine in the US: Fusarium circinatum, Heterobasidion annosum, Phytophthora pinifolia, Cronartium flaccidum & Lecanosticta tecunumannii. The first two are well known, established and important pathogens of pines. Phytophthora pinifolia and C. flaccidum are not known yet in North America, yet threaten the resource and southern pines are thought to be susceptible. Lecanosticta tecunumannii is associated with an ongoing needlecast epidemic affecting commercial loblolly pine in multiple states and the PI is collaborating with several other researchers to better to understand the etiology and epidemiology of this potentially highly devastating exotic pathogen that has only very recently been identified. The work will involve lab testing to develop a multiplex molecular panel for the target pathogens to confirm that diagnostic testing on the spore trap surface works properly (when spiked with positive control samples in a BSL II containment facility, this will be done in collaboration with Dr. Carrie Harmon, Plant Diagnostic Lab, University of Florida). We will deploy traps (using a network of existing collaborators) to sites in the region to survey &  test efficacy and examine trap quality, diagnostic capacity and identify issues that were not identified through previous R & D. The results will allow us to provide a novel tool that will allow cooperators in industry and agencies to rapidly protect (in a greatly more efficient and cost-effective manner) the pine resource in the region.


Funding Provided By: USDA-APHIS/PPQ (Farm Bill)


Collaborators: Dr. Carrie Harmon, UF Plant Diagnostic Center, Rayonier Inc., Dr. Caterina Villari, University of Georgia

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Ironwood and hophornbeam leaf rust (IHLR): A new major threat to North American hardwood forests


Foliar rusts of hardwoods are typically of little consequence where native in natural forests, being problematic in forestry plantations and ornamental plantings where defoliation can reduce productivity, reduce vigor and decrease aesthetic value (Helfer, 2014). When these fungi encounter new (non-coevolved) hosts, due to introductions into exotic locations, they can have devastating impacts on hosts, where resistance can be limited or nonexisistent. Some examples include the introduction of myrtle rust (Austropuccinia psidii) into multiple locations worldwide, poplar leaf rusts (Melampsora spp.) into Australia and New Zealand and cereal rusts worldwide (Puccinia spp.) (Helfer 2014; Uchida et al., 2006).


Of utmost importance to biosecurity and effective management of rust diseases is a complete understanding of their biology in order to reduce widescale spread and potential jumps to additional hosts. Due to their often complex life cycles (heteroecious – i.e. alternate hosts), multiple spore stages, overwintering capacities, long distance and rapid spore dispersal, early elucidation of these features are critical when a new rust is discovered in a new location.


In the late fall of 2018, foliar rust (Figure 1) was discovered in Alachua, Levy, Marion and Gilchrist Counties, Florida on ironwood/eastern hornbeam (Carpinus caroliniana) and hophornbeam (Ostrya virginiana) – here referred to as Ironwood/Hophornbeam Leaf Rust (IHLR), both members of the Betulaceae family. Uredinia were observed on leaves of both species at numerous locations on trees of all age classes with estimated incidence rates at locations ranging from 30-100% on each species. Due to the phenology of the trees, it was difficult to assess severity and impact, however it was apparent that some heavily impacted trees were being defoliated by the pathogen.


Samples from both hosts were collected in the field and brought back to the laboratory for identification. Light microscopy revealed that the spores were echinulated and fit the general description of urediniospores of Melampsoridium. DNA was extracted from several samples and ITS rDNA sequences were generated and compared in GenBank. The sequences for the samples were identical and did not have any perfect matches in the database, with the best matches being Puccinianstrum coryli (96% identity), Melampsoridium alni (94% identity), and M. hiratsukanum (94% identity). These results suggest our discovery represents a taxon not currently in GenBank (Figure 2) and possibly a rust belonging to a different genus than represented by these matches. Clearly, further taxonomic work is needed to identify the pathogen and determine its origin – and ultimately, its risk to North American forests.


Only two rusts have been reported on these host Genera previously: Melampsoridium asiaticum on Carpinus and Ostrya in Asia,  Melampsoridium carpini in Europe on Carpinus betulus and M. carpini on Ostrya virginiana in New York (only a single report). Several other rusts occur on alder and birch throughout the northern hemisphere, including North America, however, these have never been known to affect Carpinus or Ostrya. There has never been any report of any rust disease on ironwood ever in North America.


We propose to carry out a set of studies to: (1) determine the identity of the pathogen causing IHLR & attempt to identify an origin & (2) Carry out a National survey during the field season to identify the current extent of the introduction on potential hosts.

Specific Objectives:

Objective 1: Determine identity of pathogen causing IHLR and identify potential geographic origin.

Objective 2: Examine the geographic range of IHLR in the U.S. during the 2019 &2020 field seasons and determine host range.


Funding Provided by: UF Forest Pathology Foundation funding

Collaborators: Dr. Robert Blanchette (University of Minnesota), Dr. Ben Held (University of Minnesota), Dr. Cathie Aime (Purdue University), Dr. Yoshitaka Ono
(Ibaraki University), Fernando Tobar (El Salvador)

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Investigating the spread and impact of a new non-native needle cast species on loblolly pine


An increase in needle cast and/or blight outbreaks on loblolly pine has been observed since at least 2013 in five southern U.S. states (AR, AL, FL, GA and MS) (Pandit et al. 2020), and industrial forest managers had reported extensive economic losses due to reduction in radial growth, early harvesting to prevent disease spread, and changes in stand management at high cost, with impacts to nearly all stand age classes and property sizes. Given that commercial pine plantations cover millions of acres in the southeastern U.S., and are a fundamental component of the regional economy, the possible spread of an invasive pathogen affecting productivity poses a great risk.


This project aims to examine the etiology of this disease and determine the causal agent(s) responsible through carrying out repeated isolations, pathogen recovery, identifications, next-generation sequencing and pathogenicity testing to test Koch’s Postulates.



Funding: USDA-Forest Service (R8)


Collaborators: Dr. Caterina Villari (University of Georgia), Dr. Rabiu Olatinwo (USDA-Forest Service), Dr. Jaesoon Hwang (USDA-Forest Service).


A comprehensive survey and species delimitation of decay fungi affecting urban trees in Florida.


The overall goal of this project is to provide tools for arborists to improve their ability to identify hazardous trees in the landscape. In particular, trees with evidence of fungal decay create a conundrum. Conventional wisdom has led professionals to make decisions based on a range of non-empirical data sources, knowledge of fungal species not necessarily specific to Florida and a lack of information in general about the decay fungi present in the state. To provide data that will allow for Florida-specific hazard tree assessments to be made, the following objectives are proposed:


1.) Survey the urban forests of 3 cities in Florida (1 south,1 central and 1 north) for decay fungi affecting trees. The survey will be completed using urban tree inventories to assure the survey represents the relative tree diversity present.


2.) Samples will be identified and if necessary, used in taxonomy studies (with new species descriptions made). Fruiting bodies will be carefully photographed and catalogued.


3.) Prominent fungi found on hosts will be used in "wood block" decay studies in the lab to test their relative decay capacities.


4.) Examine the decay present in trees found in Obj. 1 affected by the fungi with the greatest decay rates in Obj. 3. We will use several standard methods including visual inspections, resistograph and possibly sonic tomography (if available).  The results from this objective will allow us to create two categories for the fungi found in the study: 1) The aggressive decayers and 2.) "Everything else". This will allow us to improve training for arborists and simplify hazard tree assessments.


Funding: Florida Chapter ISA Research Fund


Collaborators: Dr. Matt Smith (Department of Plant Pathology), Dr. Andrew Loyd (Bartlett Inc.)

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ROTKEY: A Guide to the Most Significant Decay Fungi Affecting Florida Trees


Preventing tree failure due to fungal decay can save millions of dollars and many lives each year. This prevention must be balanced with many other issues including aesthetics, removal costs, jurisdictional issues, legal issues and public attitudes. Thus, prevention strategies must rely on the most efficient and accurate methods of assessment to insure success. Current methods range from high tech and non-destructive such as magnetic resonance imaging (MRI) to simple, such as visual observations of decay and fungal fruiting bodies and destructive sampling (e.g. drilling). The high tech methods require much less destructive sampling, but require expensive equipment and user expertise. Thus, arborists face the greatest challenge from balancing cost effectiveness and time constraints with accuracy and risk. Therefore, utilization of rapid, cost-effective standard protocols for assessment of hazard trees is a primary need for arborists nationwide.


One of the most utilized approaches to assessment of decay has been visual inspection for fungal fruiting bodies (a.k.a. “conks”) produced primarily by Basidiomycete fungi. The general rule of thumb has been that when a conk is observed, extensive colonization and decay can be expected. Thus, trees with conks present are often marked as hazardous and removed.


Although the presence of conks can often indicate extensive decay, this is variable. Sometimes little to no decay is present in trees with conks present. This may be due to differences in inherent decay capacity between fungal species. In reality, although there are dozens of species that arborists are likely to encounter on trees in urban and suburban landscapes in Florida, only a subset of these are known to cause significant decay in living trees leading to risk for failures.


This project will develop an identification guide for arborists to allow for rapid, in situ separation of between the “significant rotters” and “everything else”.

Funding: Florida Chapter ISA Research Fund


Collaborators: Dr. Ed Barnard (Retired), Dr. Matt Smith (Department of Plant Pathology, University of Florida), Dr. Andrew Loyd (Bartlett Inc.).

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Developing tools for development of disease-resistant Florida torreya


Florida torreya (Torreya taxifolia), known locally as “Stinking cedar” or “Gopherwood” , is critically endangered and North America’s most endangered conifer. Decline began in the 1930s (when there were about 900,000 healthy adult trees), intensified during the 1950s, by the 1990s adult population was estimated to be less than 2500, by 2012, the total population was estimated to be around 850 or so. The cause has been determined to be fungal pathogen, Fusarium torreyae, a new species, likely introduced from China.


Over 90% of current population is infected, and the average height of the trees is less than 3 feet and diameter about 1”  - these are just root sprouts from dead adult trees. Adult healthy trees once grew to 70’ tall or more. This is a similar situation to American Chestnut and chestnut blight.It is estimated that in 25 years or so the wild population will go extinct without intervention.


Objective 1:  Screen vegetatively propagated canker-free genotypes  ‘Madison 1’ and ‘ABG 8003’ against F. torreyae to confirm tolerance to canker.


Rationale – Two ‘canker-free’ T. taxifolia have been observed (one in the wild and one cultivated near wild populations). These have been propagated, but whether they are escapes or disease-tolerant is still unknown. Identifying genotypes that differentially respond to the pathogen will be key to developing disease-tolerant germplasm for future restoration efforts.


Objective 2: Assess putative toxin role in canker development in T. taxifolia through  inoculations with secondary metabolites and dead fungal inoculum.


Rationale – Fusarium canker pathogens (necrotrophs) commonly produce toxins as they infect their hosts and invade host-tissues. These toxins are specific, can be identified and used to identify potential resistance genes in the host. Genetically modified chestnut-blight resistant American chestnut were developed through insertion of a toxin-resistance gene, for example. Preliminary studies indicate that F. torreyae produces a toxin and this toxin is important in canker development. We aim to identify this toxin and use this information to identify potential disease resistance strategies.


Funding: USDA-Forest Service (R8)


Collaborators: Dr. Emily Coffey (Atlanta Botanical Garden), Dr. Kerry O’Donnell, (USDA-ARS (Peoria)), Dr. Tyler Dreaden (USDA-Forest Service Forest Health Center, Lexington, KY)


Ahead of the threat: In-field early detection of Fusarium circinatum using LAMP


Pitch canker, caused by Fusarium circinatum, is an aggressive disease affecting several species of pine, and is currently considered one of the most serious diseases of pines worldwide, especially in nurseries and intensively managed plantations. Not surprisingly, control of this pathogen is one of the top forest health priorities of the forestry industry in the southern US region, as well as in other countries. Unfortunately, chemical control has limited applicability in natural forests, nor is considered a viable option in plantations and nurseries, hence, prevention is one the few currently available options to limit its impact.


The goal of this project is to develop and deliver to forestry industry stakeholders an affordable system and portable tool for the early detection of F. circinatum spores in the air and infected plants, and to familiarize them with the technique. Our objectives are to (i) design and validate a pathogen-specific loop mediated isothermal amplification (LAMP) assay; (ii) Identify the best low-cost spore trap and sampling strategy/in-field DNA extraction method to be coupled with the field-portable LAMP assay; (iii) Provide training to commercial pine stakeholders for the use of the portable device and the implementation of the integrated detection system.


The implementation of LAMP technology can be a game-changer in the early detection of F. circinatum, and will allow for successful management of pitch canker. Moreover, this assay would be crucial to monitor the presence of this quarantine pathogen during international trades of seeds and seedlings and prevent its further spread worldwide.


Funding: USDA-NIFA


Collaborators: Dr. Caterina Villari (University of Georgia)

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