Population structure and migration of the Tobacco Blue Mold Pathogen, Peronospora tabacina, into North America and Europe

Recent developments in plant-downy mildew interactions

Downy mildews are obligate oomycete pathogens that attack a wide range of plants and can cause significant economic impacts on commercial crops and ornamental plants. Traditionally, downy mildew disease control relied on an integrated strategies, that incorporate cultural practices, deployment of resistant cultivars, crop rotation, application of contact and systemic pesticides, and biopesticides. Recent advances in genomics provided data that significantly advanced understanding of downy mildew evolution, taxonomy and classification. In addition, downy mildew genomics also revealed that these obligate oomycetes have reduced numbers of virulence factor genes in comparison to hemibiotrophic and necrotrophic oomycetes. However, downy mildews do deploy significant arrays of virulence proteins, including so-called RXLR proteins that promote virulence or are recognized as avirulence factors. Pathogenomics are being applied to downy mildew population studies to determine the genetic diversity within the downy mildew populations and manage disease by selection of appropriate varieties and management strategies. Genome editing technologies have been used to manipulate host disease susceptibility genes in different plants including grapevine and sweet basil and thereby provide new soucres of resistance genes against downy mildews. Previously, it has proved difficult to transform and manipulate downy mildews because of their obligate lifestyle. However, recent exploitation of RNA interference machinery through Host-Induced Gene Silencing (HIGS) and Spray-Induced Gene Silencing (SIGS) indicate that functional genomics in downy mildews is now possible. Altogether, these breakthrough technologies and attendant fundamental understanding will advance our ability to mitigate downy mildew diseases.

Genotyping by sequencing suggests overwintering of Peronospora destructor in southwestern Québec, Canada

Several Peronospora species are carried by wind over short and long distances, from warmer climates where they survive on living plants to cooler climates. In eastern Canada, this annual flow of sporangia was thought to be the main source of Peronospora destructor responsible for onion downy mildew. However, the results of a recent study showed that the increasing frequency of onion downy mildew epidemics in eastern Canada is associated with warmer autumns, milder winters, and previous year disease severity, suggesting overwintering of the inoculum in an area where the pathogen is not known to be endogenous. In this study, genotyping by sequencing was used to investigate the population structure of P. destructor at the landscape scale. The study focused on a particular region of southwestern Québec-Les Jardins de Napierville-to determine if the populations were clonal and regionally differentiated. The data were characterized by a high level of linkage disequilibrium, characteristic of clonal organisms. Consequently, the null hypothesis of random mating was rejected when tested on predefined or nonpredefined populations, indicating that linkage disequilibrium was not a function of population structure and suggesting a mixed reproduction mode. Discriminant analysis of principal components performed with predefined population assignment allowed grouping P. destructor isolates by geographical regions, while analysis of molecular variance confirmed that this genetic differentiation was significant at the regional level. Without using a priori population assignment, isolates were clustered into four genetic clusters. These results represent a baseline estimate of the genetic diversity and population structure of P. destructor.

Microsatellite Markers from Peronospora tabacina, the Cause of Blue Mold of Tobacco, Reveal Species Origin, Population Structure, and High Gene Flow

Peronospora tabacina is an obligate parasite that causes blue mold of tobacco. The pathogen reproduces primarily by sporangia, whereas the sexual oospores are rarely observed. A collection of 122 isolates of P. tabacina was genotyped using nine microsatellites to assess the population structure of individuals from subpopulations collected from central, southern, and western Europe; the Middle East; Central America; North America; and Australia. Genetic variations among the six subpopulations accounted for ∼8% of the total variation, including moderate levels of genetic differentiation, high gene flow among these subpopulations, and a positive correlation between geographic and genetic distance (r = 0.225; P < 0.001). Evidence of linkage disequilibrium (P < 0.001) showed that populations contained partially clonal subpopulations but that subpopulations from Australia and Mediterranean Europe did not. High genetic variation and population structure among samples could be explained by continuous gene flow across continents via infected transplant exchange and/or long-distance dispersal of sporangia via wind currents. This study analyzed the most numerous P. tabacina collection and allowed conclusions regarding the migration, mutation, and evolutionary history of this obligate biotrophic oomycete. The evidence pointed to the species origin in Australia and identified intracontinental and intercontinental migration patterns of this important pathogen.[Formula: see text] Copyright © 2022 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.

Deciphering the Bacillus amyloliquefaciens B9601-Y2 as a Potential Antagonist of Tobacco Leaf Mildew Pathogen During Flue-Curing

Tobacco leaf mildew caused by Rhizopus oryzae (Mucorales, Zygomycota) is an important and devastating post-harvest disease during flue-cured tobacco period, and also is known to cause diseases of fruits and vegetables. In this study, assessment of several candidate biological control agents were first tested in vitro to determine their antifungal activities and potential strains were further applied to tobacco leaves to prevent pathogen colonization during the tobacco-curing process. In vitro screening of 36 bacteria and the isolates of one fungus were performed for their antifungal activities against R. oryzae using dual culture method. Potential five isolates viz. Bacillus amyloliquefaciens B9601-Y2 (Y2), B. amyloliquefaciens YN201728 (YN28), Pseudomonas sp. (Pb), and B. amyloliquefaciens YN201732 (YN32) and T. harzianum B (Th-B) from total screened isolates have shown remarkable results for controlling the mycelial growth of R. oryzae. Finally, out of these five isolates, B. amyloliquefaciens B9601-Y2 potentially reduced the mycelial growth of fungal pathogen with great inhibitory effect. In order to get a better understanding of the biocontrol effect of B9601-Y2 in a flue-curing barn, various suspension density tests with two application methods involving spraying and soaking were examined. Two application methods of B. amyloliquefaciens B9601-Y2 had 98.60 and 98.15% control effects, respectively. In curing barn, the incidence in the treatment group was significantly reduced and tobacco leaves did not get mildew. Altogether, the study demonstrated that candidate bacterial strain B. amyloliquefaciens B9601-Y2 is a potential antagonist for the management of tobacco leaf mildew during flue-curing.

Multi-Scale Airborne Infectious Disease Transmission

Airborne disease transmission is central to many scientific disciplines including agriculture, veterinary biosafety, medicine, and public health. Legal and regulatory standards are in place to prevent agricultural, nosocomial, and community airborne disease transmission. However, the overall importance of the airborne pathway is underappreciated, e.g.,, US National Library of Medicine's Medical Subjects Headings (MESH) thesaurus lacks an airborne disease transmission indexing term. This has practical consequences as airborne precautions to control epidemic disease spread may not be taken when airborne transmission is important, but unrecognized. Publishing clearer practical methodological guidelines for surveillance studies and disease outbreak evaluations could help address this situation.To inform future work, this paper highlights selected, well-established airborne transmission events - largely cases replicated in multiple, independently conducted scientific studies. Methodologies include field experiments, modeling, epidemiology studies, disease outbreak investigations and mitigation studies. Collectively, this literature demonstrates that airborne viruses, bacteria, and fungal pathogens have the capability to cause disease in plants, animals, and humans over multiple distances - from near range (< 5 m) to continental (> 500 km) in scale. The plausibility and implications of undetected airborne disease transmission are discussed, including the notable underreporting of disease burden for several airborne transmitted diseases.

T-BAS Version 2.1: Tree-Based Alignment Selector Toolkit for Evolutionary Placement of DNA Sequences and Viewing Alignments and Specimen Metadata on Curated and Custom Trees

The Tree-Based Alignment Selector (T-BAS) toolkit combines phylogenetic-based placement of DNA sequences with alignment and specimen metadata visualization tools in an integrative pipeline for analyzing microbial biodiversity. The release of T-BAS version 2.1 makes available reference phylogenies, supports multilocus sequence placements and permits uploading and downloading trees, alignments, and specimen metadata.

The Tree-Based Alignment Selector (T-BAS) toolkit combines phylogenetic-based placement of DNA sequences with alignment and specimen metadata visualization tools in an integrative pipeline for analyzing microbial biodiversity. The release of T-BAS version 2.1 makes available reference phylogenies, supports multilocus sequence placements and permits uploading and downloading trees, alignments, and specimen metadata.