An Interactive, Online Web Map Resource of Global Fusarium oxysporum ff. spp. Diversity and Distribution.

HomePlant DiseaseVol. 107, No. 2An Interactive, Online Web Map Resource of Global Fusarium oxysporum ff. spp. Diversity and Distribution PreviousNext RESOURCE ANNOUNCEMENT OPENOpen Access licenseAn Interactive, Online Web Map Resource of Global Fusarium oxysporum ff. spp. Diversity and DistributionRocío Calderón, Jaclyn A. Eller, Hannah K. Brodsky, Andrew D. Miles, Sharifa G. Crandall, Natalie Mahowald, Ryan Pavlick, and Kaitlin M. GoldRocío Calderón†Corresponding author: R. Calderón; E-mail Address: [email protected]https://orcid.org/0000-0002-7639-1795Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Sciences, Cornell AgriTech, Cornell University, Geneva, NY 14456Search for more papers by this author, Jaclyn A. EllerPlant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Sciences, Cornell AgriTech, Cornell University, Geneva, NY 14456Search for more papers by this author, Hannah K. BrodskyDepartment of Earth and Atmospheric Sciences, Atkinson Center for a Sustainable Future, Cornell University, Ithaca, NY 14853Search for more papers by this author, Andrew D. MilesDepartment of Plant Pathology and Environmental Microbiology, Pennsylvania State University, University Park, PA 16802Search for more papers by this author, Sharifa G. Crandallhttps://orcid.org/0000-0003-3392-5627Department of Plant Pathology and Environmental Microbiology, Pennsylvania State University, University Park, PA 16802Search for more papers by this author, Natalie MahowaldDepartment of Earth and Atmospheric Sciences, Atkinson Center for a Sustainable Future, Cornell University, Ithaca, NY 14853Search for more papers by this author, Ryan PavlickJet Propulsion Laboratory, California Institute of Technology, Pasadena, CA 91109Search for more papers by this author, and Kaitlin M. GoldPlant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Sciences, Cornell AgriTech, Cornell University, Geneva, NY 14456Search for more papers by this authorAffiliationsAuthors and Affiliations Rocío Calderón1 † Jaclyn A. Eller1 Hannah K. Brodsky2 Andrew D. Miles3 Sharifa G. Crandall3 Natalie Mahowald2 Ryan Pavlick4 Kaitlin M. Gold1 1Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Sciences, Cornell AgriTech, Cornell University, Geneva, NY 14456 2Department of Earth and Atmospheric Sciences, Atkinson Center for a Sustainable Future, Cornell University, Ithaca, NY 14853 3Department of Plant Pathology and Environmental Microbiology, Pennsylvania State University, University Park, PA 16802 4Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA 91109 Published Online:31 Dec 2022https://doi.org/10.1094/PDIS-04-22-0789-AAboutSectionsPDF ToolsAdd to favoritesDownload CitationsTrack Citations ShareShare onFacebookTwitterLinked InRedditEmailWechat Fusarium oxysporum species complex (FOSC) is a ubiquitous group of soilborne fungal pathogens that cause significant disease in agricultural and natural agroecosystems and can also impact human and animal health (Baayen et al. 2000; O’Donnell et al. 2009). This fungal complex possesses a high level of phylogenetic diversity with cryptic morphologies, hence making it difficult to identify and manage in the field. Plant pathogenic F. oxysporum strains in particular rank among the top 10 most damaging plant fungal pathogens worldwide (Dean et al. 2012) and are responsible for causing diseases such as Fusarium vascular wilt (FW), rot, and damping-off, typically of host seedlings. This leads to food insecurity and devastating crop and economic losses in a wide variety of crops, including staple food crops (e.g., chickpea [Cicer arietinum] and banana [Musa spp.]), economically important market crops (e.g., tomato [Solanum lycopersicum] and melon [Cucumis melo]), ornamental crops (e.g., carnation [Dianthus caryophyllus] and pineapple palm [Phoenix canariensis]), and one commoditized crop (cotton [Gossypium spp.]). Although FOSC has a very wide host range, individual plant pathogenic strains of F. oxysporum have a narrow pathogenic specificity to host species, upon which basis such strains are classified into more than 100 formae speciales (ff. spp.), with each forma specialis (f. sp.) grouping strains with the same host range (Edel-Hermann and Lecomte 2019). Additionally, some formae speciales are further divided into subgroups and/or races indicating cultivar-level specialization, such as the notable F. oxysporum f. sp. cubense race TR-4 impacting the “Cavendish” banana.F. oxysporum is almost impossible to eradicate once established due to its capacity to survive in the soil for over 20 years (Stover 1962) and its ability to colonize and survive on symptomless plant hosts (Gordon 1989). National authorities, such as the European Food Safety Authority (EFSA 2008), have adopted a set of tools and recommendations aimed at ensuring pathogen exclusion, containment, eradication, suppression, and surveillance to avoid or delay pathogen dispersal and reduce the intensity of emerging novel F. oxysporum strains as well as local outbreaks of endemic diseases. However, uncertainties about key aspects of FW epidemiology and incomplete spatial information on disease presence impact the success of these endeavors. For example, little is known about how anthropogenic and environmental factors drive the diversity and distribution of F. oxysporum at the global scale (Delgado-Baquerizo et al. 2020; Hulme et al. 2008) or the role of aerial dispersal in the FW disease cycle, an aspect that has been long speculated upon but never established due to a lack of scalable and practical methodology (Dita et al. 2018).Foundational to pursuing the above outlined research frontiers is a better understanding of where the pathogen currently is, and where it is anticipated to disperse because of a changing climate. While it is well documented that F. oxysporum is endemic to all six crop-producing continents, more detailed georeferenced records are limited, even more so at the forma specialis level. In 2020, we received a NASA ROSES Interdisciplinary Sciences grant (#80NSSC20K1533) to use remote sensing, aerosol transport modeling, and comparative genomics to assess the ability of F. oxysporum spores and inoculum to survive in aerosolized agricultural soil and transit on long-range dust currents. As a foundation for our global FW susceptibility assessment, we have compiled a sorely needed database of published data on the presence of the 40 most important F. oxysporum ff. spp. at the country and subcountry level across the world to better facilitate our own and other interdisciplinary, mixed-method, and global-scale research on this critically important disease. We turned this geodatabase and accompanying metadata into a publicly available, interactive web map that depicts instances of F. oxysporum occurrence. This web map is available at https://blogs.cornell.edu/goldlab/fusarium-oxysporum-webmap/. The simple user interface allows users to search for F. oxysporum epidemiological parameters in three major ways: (1) explore the distribution of F. oxysporum incidence reports at the country and subcountry level; (2) download essential metadata; and (3) submit data from future studies to constantly update the web map and, in this way, to serve as a long-term resource to the global FW research community, policymakers, and stakeholders.The process for building and uploading our web map involved the following steps: (1) an extensive literature search to identify and select the pertinent references; (2) extraction of the relevant metadata information from the selected references; and (3) uploading online through a web map. The literature search that was conducted in 2021 identified 1,174 references from research articles, technical reports, public repositories, and government announcements. From these sources, a total 3,980 occurrences were gathered, validated, and added to the final geodatabase of F. oxysporum ff. spp. For all occurrences, we collected metadata covering the f. sp. found, the host plant where the pathogen was detected, year of detection, location of the infected plants at country and first administrative division level, identification method (e.g., visual inspection of disease symptoms, culture-based morphological identification, pathogenicity test, vegetative compatibility group [VCG] analyses, PCR-based methods, and genome sequencing), and the publication reference. Where no temporal occurrence data were available, we recorded the available publication date of the document or the website. Where location was solely given at the country level, subcountry level occurrence was determined by searching the main host growing areas within the country on historical national official statistics and technical reports from the governments’ agricultural services. To convert our geodatabase into an interactive web map, a global base map, including country and first administrative level divisions, was downloaded as vector data from Natural Earth (version 4.1.0). First, each layer corresponding to a specific forma specialis was manually inputted using Microsoft Excel (i.e., country, subdivision, host, how many occurrences were found, year of most recent detection, and references). An additional layer representing all the F. oxysporum ff. spp. together was created to show the number found at the country and subcountry levels. These tables were then uploaded in ArcGIS Pro (version 2.6, Esri Inc., Redlands, CA) and joined with the global base vector data. Finally, each layer map was shared to ArcGIS Online (Esri Inc.) to showcase the global geodatabase of F. oxysporum. ArcGIS Experience Builder (Esri Inc.) was used to create the interactive web map.The web map interface consists of a multipage app where the homepage shows the global distribution of F. oxysporum ff. spp. and the remaining 40 pages show the individual global distribution of 40 formae speciales. The user can access the different pages of the app through the left menu foldable sidebar (Fig. 1). The map widget allows the user to interact with layers displaying both the country and subcountry level distribution. Pop-up windows are displayed when clicking on a country and/or subcountry feature. These windows show relevant metadata related to the pathogen found, host, country, subdivision, most recent year of occurrence, number of occurrences, and references. Relevant important metadata pertaining to the map is shown in a table on the bottom foldable sidebar, where the user can download the complete dataset and the references. Furthermore, a fact sheet for each F. oxysporum f. sp. is shown on the right foldable sidebar. The “contact” button allows the user to inform us about peer-reviewed incidence reports that should be included on the web map and to send questions and/or suggestions.Fig. 1. Web map interface for global Fusarium oxysporum ff. spp. diversity and distribution.Download as PowerPointGlobal plant pathogen distribution maps are scarce, with the Global Biodiversity Information Facility (GBIF; https://www.gbif.org/) and CABI Distribution Maps of Plant Pests and Plant Diseases (Pasiecznik et al. 2005) representing the most extensive and reliable resources (Shabani et al. 2014; Shaw and Osborne 2011). These databases provide a large collection of plant pathogens’ occurrences, but their reports of F. oxysporum have limitations. While both are generally kept up to date, they do not always contain the historical and latest occurrence records available in the literature. These maps usually show coarse distributional data typically at the country level and rarely include specifics about how the occurrence data were derived. Our web map improves on these resources by providing historical and current F. oxysporum occurrences at finer resolution with detailed and revised metadata that include the source from which the occurrence was derived. However, occurrence reports described by our web map, as well as by GBIF and CABI distribution maps, suffer from taxonomic and geographical biases (Pyšek et al. 2008). Some F. oxysporum ff. spp. (such as cubense and lycopersici) have a higher amount of occurrence reports because they are more intensively studied and surveyed due to their socio-economic impact. For diseases of less interest, the reported incidence is likely to depend on where specialists work and on whether the disease currently matters. Geographic bias may be a result of differing amounts of financial resources available for study and survey in different regions of the world, translated into research and technical scouting intensity. Scientific and technical capacity is lower for developing countries, resulting in under-reporting F. oxysporum occurrences. Thus, if a disease is not reported in a country/subcountry, it is unknown if this is a true absence or an unreported presence.An improved understanding of current FW disease distribution, of which pathogen incidence is foundational, is essential for research that seeks to assess future disease spread, untangle uncertainties about the epidemiology of emerging F. oxysporum strains, or develop early detection methods at the global scale. Our web map will support research on identifying future areas suitable for F. oxysporum growth under various climate change scenarios and international, national, and regional spread pathways that could prove essential to disentangling the host and ecosystem traits responsible for the emergence of resistance-breaking races, in addition to both predicting future trends and guiding management responses. Recent work has demonstrated that the number of regions suitable to FW development is expected to expand greatly in the Mediterranean basin and the Middle East under various climate change scenarios using different global pathogen distribution databases as a basis (Shabani et al. 2014). Moreover, epidemiological models have been widely used to inform decision making in the form of optimized surveillance programs, disease control strategies, and quarantine assessments (Parnell et al. 2017). These models and research can benefit from the improved understanding of underlying disease distribution that our web map provides. Parameterization of these models is in turn informed by genomic and bioinformatic disciplines, which could use both archival and present geospatial information on the presence of F. oxysporum to track movement of plant pathogens by elucidating the origins, evolution, and migration routes of past outbreak strains and identifying where the highest and greatest threats to crop populations may exist (Bieker and Martin 2018; Ristaino 2020). Furthermore, the detection of global hot spots of emerging diseases along with genotyping and race information will be useful to guide breeding efforts to deploy resistant varieties and to effectively implement quarantine measures and other eradication methods at landscape level.The author(s) declare no conflict of interest.Literature CitedBaayen, R. P., O’Donnell, K., Bonants, P. J. M., Cigelnik, E., Kroon, L. P. N. 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The Commonwealth Mycological Institute, Kew, U.K. Google ScholarFunding: This work is supported by the NASA-ROSES Interdisciplinary Sciences Grant #80NSSC20K1533.The author(s) declare no conflict of interest.DetailsFiguresLiterature CitedRelated Vol. 107, No. 2 February 2023SubscribeISSN:0191-2917e-ISSN:1943-7692 Download Metrics Article History Issue Date: 28 Feb 2023Published: 31 Dec 2022Accepted: 7 Jul 2022 Pages: 538-541 Information© 2022 The American Phytopathological SocietyFundingNASA-ROSESGrant/Award Number: 80NSSC20K1533Keywordsforma specialisFusarium oxysporumglobal distributionweb mapThe author(s) declare no conflict of interest.PDF download