1
|
Check JC, Harkness RJ, Heger L, Chilvers MI, Mahaffee WF, Sakalidis ML, Miles TD. It's a Trap! Part II: An Approachable Guide to Constructing and Using Rotating-Arm Air Samplers. PLANT DISEASE 2024; 108:1923-1936. [PMID: 38537138 DOI: 10.1094/pdis-01-24-0131-sr] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/06/2024]
Abstract
An increasing number of researchers are looking to understand the factors affecting microbial dispersion but are often limited by the costs of commercially available air samplers. Some have reduced these costs by designing self-made versions; however, there are no published sampler designs, and there is limited information provided on the actual construction process. Lack of appropriate reference material limits the use of these self-made samplers by many researchers. This manuscript provides a guide to designing and constructing rotating-arm impaction air samplers by covering (i) environmental considerations, (ii) construction materials and equipment, (iii) the construction process, and (iv) air sampler deployment. Information regarding how to calculate rotational velocity, motor speed, and power supply requirements and to troubleshoot common issues is presented in an approachable format for individuals without experience in electronics or machining. Although many of the components discussed in this guide may change in their availability or be updated over time, this document is intended to serve as a "builder's guide" for future research into air sampling technology for phytopathology research.
Collapse
Affiliation(s)
- Jill C Check
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI 48824, U.S.A
| | - Rebecca J Harkness
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI 48824, U.S.A
| | - Lexi Heger
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI 48824, U.S.A
| | - Martin I Chilvers
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI 48824, U.S.A
| | - Walter F Mahaffee
- U.S. Department of Agriculture, Agricultural Research Service, Horticulture Crops Disease and Pest Management Research Unit, Corvallis, OR 97330, U.S.A
| | - Monique L Sakalidis
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI 48824, U.S.A
- Department of Forestry, Michigan State University, East Lansing, MI 48824, U.S.A
- Department of Industries and Regional Development, Perth, WA, Australia
| | - Timothy D Miles
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI 48824, U.S.A
| |
Collapse
|
2
|
Check JC, Harkness RJ, Heger L, Sakalidis ML, Chilvers MI, Mahaffee WF, Miles TD. It's a Trap! Part I: Exploring the Applications of Rotating-Arm Impaction Samplers in Plant Pathology. PLANT DISEASE 2024; 108:1910-1922. [PMID: 38411610 DOI: 10.1094/pdis-10-23-2096-fe] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/28/2024]
Abstract
Although improved knowledge on the movement of airborne plant pathogens is likely to benefit plant health management, generating this knowledge is often far more complicated than anticipated. This complexity is driven by the dynamic nature of environmental variables, diversity among pathosystems that are targeted, and the unique needs of each research group. When using a rotating-arm impaction sampler, particle collection is dependent on the pathogen, environment, research objectives, and limitations (monetary, environmental, or labor). Consequently, no design will result in 100% collection efficiency. Fortunately, it is likely that multiple approaches can succeed despite these constraints. Choices made during design and implementation of samplers can influence the results, and recognizing this influence is crucial for researchers. This article is for beginners in the art and science of using rotating-arm impaction samplers; it provides a foundation for designing a project, from planning the experiment to processing samples. We present a relatively nontechnical discussion of the factors influencing pathogen dispersal and how placement of the rotating-arm air samplers alters propagule capture. We include a discussion of applications of rotating-arm air samplers to demonstrate their versatility and potential in plant pathology research as well as their limitations.
Collapse
Affiliation(s)
- Jill C Check
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI 48824, U.S.A
| | - Rebecca J Harkness
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI 48824, U.S.A
| | - Lexi Heger
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI 48824, U.S.A
| | - Monique L Sakalidis
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI 48824, U.S.A
- Department of Forestry, Michigan State University, East Lansing, MI 48824, U.S.A
- Department of Industries and Regional Development, South Perth, WA 6151, Australia
| | - Martin I Chilvers
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI 48824, U.S.A
| | - Walter F Mahaffee
- USDA Agricultural Research Service, Horticulture Crops Disease and Pest Management Research Unit, Corvallis, OR 97330, U.S.A
| | - Timothy D Miles
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI 48824, U.S.A
| |
Collapse
|
3
|
Lowder SR, Neill TM, Peetz AB, Miles TD, Moyer MM, Oliver C, Stergiopoulos I, Ding S, Mahaffee WF. A Rapid Glove-Based Inoculum Sampling Technique to Monitor Erysiphe necator in Commercial Vineyards. PLANT DISEASE 2023; 107:3096-3105. [PMID: 37079020 DOI: 10.1094/pdis-02-23-0216-re] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Information on the presence and severity of grape powdery mildew (GPM), caused by Erysiphe necator, has long been used to guide management decisions. While recent advances in the available molecular diagnostic assays and particle samplers have made monitoring easier, there is still a need for more efficient field collection of E. necator. The use of vineyard worker gloves worn during canopy manipulation as a sampler (glove swab) of E. necator was compared with samples identified by visual assessment with subsequent molecular confirmation (leaf swabs) and airborne spore samples collected by rotating-arm impaction traps (impaction traps). Samples from United States commercial vineyards in Oregon, Washington, and California were analyzed using two TaqMan qPCR assays targeting the internal transcribed spacer regions or cytochrome b gene of E. necator. Based on qPCR assays, visual disease assessments misidentified GPM up to 59% of the time with a higher frequency of misidentification occurring earlier in the growing season. Comparison of the aggregated leaf swab results for a row (n = 915) to the row's corresponding glove swab had 60% agreement. The latent class analysis (LCA) indicated that glove swabs were more sensitive than leaf swabs in detecting E. necator presence. The impaction trap results had 77% agreement to glove swabs (n = 206) taken from the same blocks. The LCAs estimated that the glove swabs and impaction trap samplers varied each year in which was more sensitive for detection. This likely indicates that these methods have similar levels of uncertainty and provide equivalent information. Additionally, all samplers, once E. necator was detected, were similarly sensitive and specific for detection of the A-143 resistance allele. Together, these results suggest that glove swabs are an effective sampling method for monitoring the presence of E. necator and, subsequently, the G143A amino acid substitution associated with resistance to quinone outside inhibitor fungicides in vineyards. Glove swabs could reduce sampling costs due to the lack of need for specialized equipment and time required for swab collection and processing.
Collapse
Affiliation(s)
- Sarah R Lowder
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331
| | - Tara M Neill
- USDA-ARS Horticultural Crops Disease and Pest Management Research Unit, Corvallis, OR 97330
| | - Amy B Peetz
- Revolution Crop Consultants, LLC, Albany, OR 97321
| | - Timothy D Miles
- Department of Plant, Soil, and Microbial Science, Michigan State University, East Lansing, MI 48824
| | - Michelle M Moyer
- Department of Viticulture and Enology, Washington State University, Prosser, WA 99350
| | | | | | - Shunping Ding
- Department of Wine and Viticulture, California Polytechnic State University, San Luis Obispo, CA 93407
| | - Walter F Mahaffee
- USDA-ARS Horticultural Crops Disease and Pest Management Research Unit, Corvallis, OR 97330
| |
Collapse
|
4
|
Hou J, Fujiyoshi S, Perera IU, Nishiuchi Y, Nakajima M, Ogura D, Yarimizu K, Maruyama F. Perspectives on Sampling and New Generation Sequencing Methods for Low-Biomass Bioaerosols in Atmospheric Environments. J Indian Inst Sci 2023; 103:1-11. [PMID: 37362849 PMCID: PMC10176311 DOI: 10.1007/s41745-023-00380-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Accepted: 03/13/2023] [Indexed: 06/28/2023]
Abstract
Bioaerosols play essential roles in the atmospheric environment and can affect human health. With a few exceptions (e.g., farm or rainforest environments), bioaerosol samples from wide-ranging environments typically have a low biomass, including bioaerosols from indoor environments (e.g., residential homes, offices, or hospitals), outdoor environments (e.g., urban or rural air). Some specialized environments (e.g., clean rooms, the Earth's upper atmosphere, or the international space station) have an ultra-low-biomass. This review discusses the primary sources of bioaerosols and influencing factors, the recent advances in air sampling techniques and the new generation sequencing (NGS) methods used for the characterization of low-biomass bioaerosol communities, and challenges in terms of the bias introduced by different air samplers when samples are subjected to NGS analysis with a focus on ultra-low biomass. High-volume filter-based or liquid-based air samplers compatible with NGS analysis are required to improve the bioaerosol detection limits for microorganisms. A thorough understanding of the performance and outcomes of bioaerosol sampling using NGS methods and a robust protocol for aerosol sample treatment for NGS analysis are needed. Advances in NGS techniques and bioinformatic tools will contribute toward the precise high-throughput identification of the taxonomic profiles of bioaerosol communities and the determination of their functional and ecological attributes in the atmospheric environment. In particular, long-read amplicon sequencing, viability PCR, and meta-transcriptomics are promising techniques for discriminating and detecting pathogenic microorganisms that may be active and infectious in bioaerosols and, therefore, pose a threat to human health. Supplementary Information The online version contains supplementary material available at 10.1007/s41745-023-00380-x.
Collapse
Affiliation(s)
- Jianjian Hou
- Microbial Genomics and Ecology, Center for the Planetary Health and Innovation Science (PHIS), The IDEC Institute, Hiroshima University, Hiroshima, 739-0046 Japan
| | - So Fujiyoshi
- Microbial Genomics and Ecology, Center for the Planetary Health and Innovation Science (PHIS), The IDEC Institute, Hiroshima University, Hiroshima, 739-0046 Japan
- Center for Holobiome and Built Environment (CHOBE), Hiroshima University, Hiroshima, 739-0046 Japan
| | - Ishara Uhanie Perera
- Microbial Genomics and Ecology, Center for the Planetary Health and Innovation Science (PHIS), The IDEC Institute, Hiroshima University, Hiroshima, 739-0046 Japan
| | - Yukiko Nishiuchi
- Microbial Genomics and Ecology, Center for the Planetary Health and Innovation Science (PHIS), The IDEC Institute, Hiroshima University, Hiroshima, 739-0046 Japan
| | - Makiko Nakajima
- Center for Holobiome and Built Environment (CHOBE), Hiroshima University, Hiroshima, 739-0046 Japan
- Department of Architectural Engineering, Faculty of Engineering, Hiroshima Institute of Technology, Hiroshima, 731-5193 Japan
| | - Daisuke Ogura
- Center for Holobiome and Built Environment (CHOBE), Hiroshima University, Hiroshima, 739-0046 Japan
- Department of Architecture and Architectural Engineering, Graduate School of Engineering, Kyoto University, Kyoto, 615-8540 Japan
| | - Kyoko Yarimizu
- Microbial Genomics and Ecology, Center for the Planetary Health and Innovation Science (PHIS), The IDEC Institute, Hiroshima University, Hiroshima, 739-0046 Japan
| | - Fumito Maruyama
- Microbial Genomics and Ecology, Center for the Planetary Health and Innovation Science (PHIS), The IDEC Institute, Hiroshima University, Hiroshima, 739-0046 Japan
- Center for Holobiome and Built Environment (CHOBE), Hiroshima University, Hiroshima, 739-0046 Japan
| |
Collapse
|
5
|
Métris KL, Métris J. Aircraft surveys for air eDNA: probing biodiversity in the sky. PeerJ 2023; 11:e15171. [PMID: 37077310 PMCID: PMC10108859 DOI: 10.7717/peerj.15171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Accepted: 03/13/2023] [Indexed: 04/21/2023] Open
Abstract
Air is a medium for dispersal of environmental DNA (eDNA) carried in bioaerosols, yet the atmosphere is mostly unexplored as a source of genetic material encompassing all domains of life. In this study, we designed and deployed a robust, sterilizable hardware system for airborne nucleic acid capture featuring active filtration of a quantifiable, controllable volume of air and a high-integrity chamber to protect the sample from loss or contamination. We used our hardware system on an aircraft across multiple height transects over major aerosolization sources to collect air eDNA, coupled with high-throughput amplicon sequencing using multiple DNA metabarcoding markers targeting bacteria, plants, and vertebrates to test the hypothesis of large-scale genetic presence of these bioaerosols throughout the planetary boundary layer in the lower troposphere. Here, we demonstrate that the multi-taxa DNA assemblages inventoried up to 2,500 m using our airplane-mounted hardware system are reflective of major aerosolization sources in the survey area and show previously unreported airborne species detections (i.e., Allium sativum L). We also pioneer an aerial survey flight grid standardized for atmospheric sampling of genetic material and aeroallergens using a light aircraft and limited resources. Our results show that air eDNA from terrestrial bacteria, plants, and vertebrates is detectable up to high altitude using our airborne air sampler and demonstrate the usefulness of light aircraft in monitoring campaigns. However, our work also underscores the need for improved marker choices and reference databases for species in the air column, particularly eukaryotes. Taken together, our findings reveal strong connectivity or mixing of terrestrial-associated eDNA from ground level aerosolization sources and the atmosphere, and we recommend that parameters and indices considering lifting action, atmospheric instability, and potential for convection be incorporated in future surveys for air eDNA. Overall, this work establishes a foundation for light aircraft campaigns to comprehensively and economically inventory bioaerosol emissions and impacts at scale, enabling transformative future opportunities in airborne DNA technology.
Collapse
Affiliation(s)
- Kimberly L. Métris
- Department of Genetics and Biochemistry, Clemson University, Clemson, SC, United States
- Airborne Science LLC, Clemson, SC, United States
| | | |
Collapse
|
6
|
Mahaffee WF, Margairaz F, Ulmer L, Bailey BN, Stoll R. Catching Spores: Linking Epidemiology, Pathogen Biology, and Physics to Ground-Based Airborne Inoculum Monitoring. PLANT DISEASE 2023; 107:13-33. [PMID: 35679849 DOI: 10.1094/pdis-11-21-2570-fe] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Monitoring airborne inoculum is gaining interest as a potential means of giving growers an earlier warning of disease risk in a management unit or region. This information is sought by growers to aid in adapting to changes in the management tools at their disposal and the market-driven need to reduce the use of fungicides and cost of production. To effectively use inoculum monitoring as a decision aid, there is an increasing need to understand the physics of particle transport in managed and natural plant canopies to effectively deploy and use near-ground aerial inoculum data. This understanding, combined with the nuances of pathogen-specific biology and disease epidemiology, can serve as a guide to designing improved monitoring approaches. The complexity of any pathosystem and local environment are such that there is not a generalized approach to near-ground air sampler placement, but there is a conceptual framework to arrive at a "semi-optimal" solution based on available resources. This review is intended as a brief synopsis of the linkages among pathogen biology, disease epidemiology, and the physics of the aerial dispersion of pathogen inoculum and what to consider when deciding where to locate ground-based air samplers. We leverage prior work in developing airborne monitoring tools for hops, grapes, spinach, and turf, and research into the fluid mechanics governing particle transport in sparse canopies and urban and forest environments. We present simulation studies to demonstrate how particles move in the complex environments of agricultural fields and to illustrate the limited sampling area of common air samplers.
Collapse
Affiliation(s)
- Walter F Mahaffee
- United States Department of Agriculture, Agricultural Research Service (USDA-ARS), Corvallis, OR 97330
| | - Fabien Margairaz
- Department of Mechanical Engineering, University of Utah, Salt Lake City, UT 84112
| | - Lucas Ulmer
- Department of Mechanical Engineering, University of Utah, Salt Lake City, UT 84112
| | - Brian N Bailey
- Department of Plant Sciences, University of California, Davis, Davis, CA 95616
| | - Rob Stoll
- Department of Mechanical Engineering, University of Utah, Salt Lake City, UT 84112
| |
Collapse
|
7
|
Higgins DS, Miles TD, Byrne JM, Hausbeck MK. Optimizing Molecular Detection for the Hop Downy Mildew Pathogen Pseudoperonospora humuli in Plant Tissue. PHYTOPATHOLOGY 2022; 112:2426-2439. [PMID: 35722890 DOI: 10.1094/phyto-01-22-0013-r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Downy mildew-free hop plantlets and rhizomes are essential to limit the introduction of this destructive pathogen, Pseudoperonospora humuli, into hopyards. The objective of this research was to determine which DNA-based diagnostic tools are optimal for P. humuli detection in plant tissue. Quantitative real-time PCR (qPCR) assays with TaqMan probes for nuclear (c125015.3e1) and mitochondrial (orf359) DNA loci were developed and tested side by side. A recombinase polymerase amplification (RPA) assay was designed based on the orf359 DNA locus. The mitochondrial qPCR assay had a 10-fold lower limit of detection (100 fg of genomic DNA) and was 60% more effective in detecting P. humuli in asymptomatic stems than the nuclear-based assay. Both qPCR assays had linear standard curves (R2 > 0.99) but lacked the quantitative precision to differentiate leaf infections beyond 1 day postinoculation. A wide range of Cq values (≥4.9) in standardized tests was observed among isolates, suggesting that the number of mitochondria and nuclear DNA targets can vary. The absence of P. humuli DNA in symptomatic rhizomes was explained, in part, by the detection of Phytophthora DNA. However, the Phytophthora-specific atp9-nad9 assay cross-reacted with P. humuli, leading to false positive amplification. Sensitivity in the RPA assay was reduced by crude plant DNA extract. Improvements to the objectivity of calling positive amplifications and determining the onset of amplification from RPA fluorescence data were realized by applying the first and second derivatives, respectively. The orf359 qPCR assay is specific and sensitive, making it well suited for P. humuli diagnostics in plant tissue.
Collapse
Affiliation(s)
- Douglas S Higgins
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI 48824
| | - Timothy D Miles
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI 48824
| | - Jan M Byrne
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI 48824
| | - Mary K Hausbeck
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI 48824
| |
Collapse
|
8
|
Bello JC, Higgins DS, Sakalidis ML, Quesada-Ocampo LM, Martin F, Hausbeck MK. Clade-Specific Monitoring of Airborne Pseudoperonospora spp. Sporangia Using Mitochondrial DNA Markers for Disease Management of Cucurbit Downy Mildew. PHYTOPATHOLOGY 2022; 112:2110-2125. [PMID: 35585721 DOI: 10.1094/phyto-12-21-0500-r] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Management of cucurbit downy mildew (CDM) caused by Pseudoperonospora cubensis, relies on an intensive fungicide program. In Michigan, CDM occurs annually due to an influx of airborne sporangia and timely alerts of airborne inoculum can assist growers in assessing the need to initiate fungicide sprays. This research aimed to improve the specific detection of airborne P. cubensis sporangia by adapting quantitative real-time polymerase chain reaction (qPCR) assays to distinguish among P. cubensis clades I and II and P. humuli in spore trap samples from commercial production sites and research plots. We also evaluated the suitability of impaction spore traps compared with Burkard traps for detection of airborne sporangia. A multiplex qPCR assay improved the specificity of P. cubensis clade II detection accelerating the assessment of field spore trap samples. After 2 years of monitoring, P. cubensis clade II DNA was detected in spore trap samples before CDM symptoms were first observed in cucumber fields (July and August), while P. cubensis clade I DNA was not detected in air samples before or after the disease onset. In some commercial cucumber fields, P. humuli DNA was detected throughout the growing season. The Burkard spore trap appeared to be better suited for recovery of sporangia at low concentrations than the impaction spore trap. This improved methodology for the monitoring of airborne Pseudoperonospora spp. sporangia could be used as part of a CDM risk advisory system to time fungicide applications that protect cucurbit crops in Michigan.
Collapse
Affiliation(s)
- Julian C Bello
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI 48824
| | - Douglas S Higgins
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI 48824
| | - Monique L Sakalidis
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI 48824
- Department of Forestry, Michigan State University, East Lansing, MI 48824
| | - Lina M Quesada-Ocampo
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC 27695-7613
| | - Frank Martin
- U.S. Department of Agriculture-Agriculture Research Service, Salinas, CA 93905
| | - Mary K Hausbeck
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI 48824
| |
Collapse
|
9
|
Possamai T, Wiedemann-Merdinoglu S. Phenotyping for QTL identification: A case study of resistance to Plasmopara viticola and Erysiphe necator in grapevine. FRONTIERS IN PLANT SCIENCE 2022; 13:930954. [PMID: 36035702 PMCID: PMC9403010 DOI: 10.3389/fpls.2022.930954] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Accepted: 06/27/2022] [Indexed: 06/01/2023]
Abstract
Vitis vinifera is the most widely cultivated grapevine species. It is highly susceptible to Plasmopara viticola and Erysiphe necator, the causal agents of downy mildew (DM) and powdery mildew (PM), respectively. Current strategies to control DM and PM mainly rely on agrochemical applications that are potentially harmful to humans and the environment. Breeding for resistance to DM and PM in wine grape cultivars by introgressing resistance loci from wild Vitis spp. is a complementary and more sustainable solution to manage these two diseases. During the last two decades, 33 loci of resistance to P. viticola (Rpv) and 15 loci of resistance to E. necator (Ren and Run) have been identified. Phenotyping is salient for QTL characterization and understanding the genetic basis of resistant traits. However, phenotyping remains a major bottleneck for research on Rpv and Ren/Run loci and disease resistance evaluation. A thorough analysis of the literature on phenotyping methods used for DM and PM resistance evaluation highlighted phenotyping performed in the vineyard, greenhouse or laboratory with major sources of variation, such as environmental conditions, plant material (organ physiology and age), pathogen inoculum (genetic and origin), pathogen inoculation (natural or controlled), and disease assessment method (date, frequency, and method of scoring). All these factors affect resistance assessment and the quality of phenotyping data. We argue that the use of new technologies for disease symptom assessment, and the production and adoption of standardized experimental guidelines should enhance the accuracy and reliability of phenotyping data. This should contribute to a better replicability of resistance evaluation outputs, facilitate QTL identification, and contribute to streamline disease resistance breeding programs.
Collapse
Affiliation(s)
- Tyrone Possamai
- CREA—Research Centre for Viticulture and Enology, Conegliano, Italy
| | | |
Collapse
|
10
|
Arocha Rosete Y, To H, Evans M, White K, Saleh M, Trueman C, Tomecek J, Van Dyk D, Summerbell RC, Scott JA. Assessing the Use of DNA Detection Platforms Combined with Passive Wind-Powered Spore Traps for Early Surveillance of Potato and Tomato Late Blight in Canada. PLANT DISEASE 2021; 105:3610-3622. [PMID: 34743538 DOI: 10.1094/pdis-12-20-2695-re] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Quantitative PCR (qPCR), loop-mediated amplification (LAMP), and lateral flow strip-based recombinase polymerase amplification (RPA-LFS) assays were assessed for early detection of Phytophthora infestans, the global causal agent of potato and tomato late blight, on passive wind-powered spore traps known as Spornados. Spore traps were deployed in potato and tomato fields during the 2018, 2019, and 2020 growing seasons in the provinces of Alberta, British Columbia, Manitoba, Prince Edward Island, and Ontario. All assays used DNA extracts from Spornado cassette membranes targeting the P. infestans nuclear ribosomal internal transcribed spacer. A total of 1,003 Spornado samples were qPCR tested, yielding 115 positive samples for P. infestans spores. In further assessment of these samples, LAMP detected P. infestans in 108 (93.9%) of 115 qPCR positive samples, and RPA-LFS detected it in 103 (89.6%). None of the assays showed cross-reaction with other Phytophthora species or pathogenic fungi known to infect potato and tomato. The qPCR detected ≤1 fg of P. infestans DNA, and LAMP and RPA-LFS amplified 10 fg in as little as 10 min. All assays detected P. infestans before the first report of late blight symptoms in commercial potato or tomato fields within each region or province. The combination of Spornado passive samplers with qPCR, LAMP, or RPA-LFS proved a valuable spore trapping system for early surveillance of late blight in potato and tomato. Both LAMP and RPA-LFS showed potential as alternative approaches to qPCR for in-field monitoring of P. infestans.
Collapse
Affiliation(s)
| | - Henry To
- Sporometrics Inc., Toronto, Ontario M6K 3J1, Canada
| | - Martin Evans
- Sporometrics Inc., Toronto, Ontario M6K 3J1, Canada
| | | | | | - Cheryl Trueman
- Department of Plant Agriculture, University of Guelph, Ridgetown, Ontario N0P 2C0, Canada
| | - Joseph Tomecek
- Department of Plant Agriculture, University of Guelph, Ridgetown, Ontario N0P 2C0, Canada
| | - Dennis Van Dyk
- Ontario Ministry of Agriculture, Food and Rural Affairs, Guelph, Ontario, Canada
| | - Richard C Summerbell
- Sporometrics Inc., Toronto, Ontario M6K 3J1, Canada
- Occupational and Environmental Health, Dalla Lana School of Public Health, University of Toronto, Toronto, Ontario M5T 1R4, Canada
| | - James A Scott
- Occupational and Environmental Health, Dalla Lana School of Public Health, University of Toronto, Toronto, Ontario M5T 1R4, Canada
| |
Collapse
|
11
|
Tummon F, Arboledas LA, Bonini M, Guinot B, Hicke M, Jacob C, Kendrovski V, McCairns W, Petermann E, Peuch VH, Pfaar O, Sicard M, Sikoparija B, Clot B. The need for Pan-European automatic pollen and fungal spore monitoring: A stakeholder workshop position paper. Clin Transl Allergy 2021; 11:e12015. [PMID: 33934521 PMCID: PMC8120382 DOI: 10.1002/clt2.12015] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Accepted: 02/21/2021] [Indexed: 01/21/2023] Open
Abstract
Background Information about airborne pollen concentrations is required by a range of end users, particularly from the health sector who use both observations and forecasts to diagnose and treat allergic patients. Manual methods are the standard for such measurements but, despite the range of pollen taxa that can be identified, these techniques suffer from a range of drawbacks. This includes being available at low temporal resolution (usually daily averages) and with a delay (usually 3–9 days from the measurement). Recent technological developments have made possible automatic pollen measurements, which are available at high temporal resolution and in real time, although currently only scattered in a few locations across Europe. Materials & Methods To promote the development of an extensive network across Europe and to ensure that this network will respond to end user needs, a stakeholder workshop was organised under the auspices of the EUMETNET AutoPollen Programme. Participants discussed requirements for the groups they represented, ranging from the need for information at various spatial scales, at high temporal resolution, and for targeted services to be developed. Results The provision of real‐time information is likely to lead to a notable decrease in the direct and indirect health costs associated with allergy in Europe, currently estimated between €50–150 billion/year.1 Discussion & Conclusion A European measurement network to meet end user requirements would thus more than pay for itself in terms of potential annual savings and provide significant impetus to research across a range of disciplines from climate science and public health to agriculture and environmental management.
Collapse
Affiliation(s)
- Fiona Tummon
- Federal Office of Meteorology and Climatology MeteoSwiss, Payerne, Switzerland
| | | | - Maira Bonini
- Agency for Health Protection of Metropolitan Area of Milan (ATS), Milan, Italy
| | - Benjamin Guinot
- Laboratoire d'Aérologie, CNRS, UPS-Université Toulouse III, Toulouse, France.,Réseau National de Surveillance Aérobiologique, Brussieu, France
| | - Martin Hicke
- Bavarian State Ministry of Health and Care, Munich, Germany
| | | | | | | | | | - Vincent-Henri Peuch
- Copernicus Atmospheric Monitoring Services, European Centre for Medium-Range Weather Forecasts, Reading, UK
| | - Oliver Pfaar
- Department of Otorhinolaryngology, Head and Neck Surgery, Section of Rhinology and Allergy, University Hospital Marburg, Philipps-Universität Marburg, Marburg, Germany
| | - Michaël Sicard
- CommSensLab, Department of Signal Theory and Communications, Universitat Politècnica de Catalunya, Barcelona, Spain.,Ciències i Tecnologies de l'Espai-Centre de Recerca de l'Aeronàutica i de l'Espai/Institut d'Estudis Epacials de Catalunya (CTE-CRAE/IEEC), Universitat Politècnica de Catalunya, Barcelona, Spain
| | - Branko Sikoparija
- BioSensе Institute-Research Institute for Information Technologies in Biosystems, University of Novi Sad, Serbia
| | - Bernard Clot
- Federal Office of Meteorology and Climatology MeteoSwiss, Payerne, Switzerland
| |
Collapse
|
12
|
Griggs RG, Steenwerth KL, Mills DA, Cantu D, Bokulich NA. Sources and Assembly of Microbial Communities in Vineyards as a Functional Component of Winegrowing. Front Microbiol 2021; 12:673810. [PMID: 33927711 PMCID: PMC8076609 DOI: 10.3389/fmicb.2021.673810] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Accepted: 03/22/2021] [Indexed: 01/05/2023] Open
Abstract
Microbiomes are integral to viticulture and winemaking – collectively termed winegrowing – where diverse fungi and bacteria can exert positive and negative effects on grape health and wine quality. Wine is a fermented natural product, and the vineyard serves as a key point of entry for quality-modulating microbiota, particularly in wine fermentations that are conducted without the addition of exogenous yeasts. Thus, the sources and persistence of wine-relevant microbiota in vineyards critically impact its quality. Site-specific variations in microbiota within and between vineyards may contribute to regional wine characteristics. This includes distinctions in microbiomes and microbiota at the strain level, which can contribute to wine flavor and aroma, supporting the role of microbes in the accepted notion of terroir as a biological phenomenon. Little is known about the factors driving microbial biodiversity within and between vineyards, or those that influence annual assembly of the fruit microbiome. Fruit is a seasonally ephemeral, yet annually recurrent product of vineyards, and as such, understanding the sources of microbiota in vineyards is critical to the assessment of whether or not microbial terroir persists with inter-annual stability, and is a key factor in regional wine character, as stable as the geographic distances between vineyards. This review examines the potential sources and vectors of microbiota within vineyards, general rules governing plant microbiome assembly, and how these factors combine to influence plant-microbe interactions relevant to winemaking.
Collapse
Affiliation(s)
- Reid G Griggs
- Department of Viticulture and Enology, Robert Mondavi Institute for Wine and Food Science, University of California, Davis, Davis, CA, United States
| | - Kerri L Steenwerth
- USDA-ARS, Crops Pathology and Genetics Research Unit, Department of Land, Air and Water Resources, University of California, Davis, Davis, CA, United States
| | - David A Mills
- Department of Viticulture and Enology, Robert Mondavi Institute for Wine and Food Science, University of California, Davis, Davis, CA, United States.,Department of Food Science and Technology, Robert Mondavi Institute for Wine and Food Science, University of California, Davis, Davis, CA, United States.,Foods for Health Institute, University of California, Davis, Davis, CA, United States
| | - Dario Cantu
- Department of Viticulture and Enology, Robert Mondavi Institute for Wine and Food Science, University of California, Davis, Davis, CA, United States
| | - Nicholas A Bokulich
- Laboratory of Food Systems Biotechnology, Institute of Food, Nutrition and Health, ETH Zurich, Zurich, Switzerland
| |
Collapse
|
13
|
Block M, Knaus BJ, Wiseman MS, Grünwald NJ, Gent DH. Development of a Diagnostic Assay for Race Differentiation of Podosphaera macularis. PLANT DISEASE 2021; 105:965-971. [PMID: 32915117 DOI: 10.1094/pdis-06-20-1289-re] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Hop powdery mildew (caused by Podosphaera macularis) was confirmed in the Pacific Northwest in 1996. Before 2012, the most common race of P. macularis was able to infect plants that possessed powdery mildew resistance based on the R-genes Rb, R3, and R5. After 2012, two additional races of P. macularis were discovered that can overcome the resistance gene R6 and the partial resistance found in the cultivar Cascade. These three races now occur throughout the region, which can complicate management and research efforts because of uncertainty on which race(s) may be present in the region and able to infect susceptible hop genotypes. Current methods for determining the races of P. macularis are labor intensive, costly, and typically require more than 14 days to obtain results. We sought to develop a molecular assay to differentiate races of the fungus possessing virulence on plants with R6, referred to as V6-virulent, from other races. The transcriptomes of 46 isolates of P. macularis were sequenced to identify loci and variants unique to V6 isolates. Fourteen primer pairs were designed for 10 candidate loci that contained single nucleotide polymorphisms (SNP) and short insertion-deletion polymorphisms. Two differentially labeled locked nucleic acid probes were designed for a contig that contained a conserved SNP associated with V6-virulence. The resulting duplexed real-time PCR assay was validated against 46 V6 and 54 non-V6 P. macularis isolates collected from the United States and Europe. The assay had perfect discrimination of V6-virulence among isolates of P. macularis originating from the western U.S. but failed to predict V6-virulence in three isolates collected from Europe. The specificity of the assay was tested with different species of powdery mildew fungi and other microorganisms associated with hop. Weak nonspecific amplification occurred with powdery mildew fungi collected from Vitis vinifera, Fragaria sp., and Zinnia sp.; however, nonspecification amplification is not a concern when differentiating pathogen race from colonies on hop. The assay has practical applications in hop breeding, epidemiological studies, and other settings where rapid confirmation of pathogen race is needed.
Collapse
Affiliation(s)
- Mary Block
- Oregon State University, Department of Crop and Soil Science, Corvallis, OR 97331
| | - Brian J Knaus
- Oregon State University, Department of Horticulture, Corvallis, OR 97331
| | - Michele S Wiseman
- Oregon State University, Department of Botany and Plant Pathology, Corvallis, OR 97331
| | - Niklaus J Grünwald
- U.S. Department of Agriculture-Agricultural Research Service, Horticultural Crops Research Unit, Corvallis, OR 97330
| | - David H Gent
- Oregon State University, Department of Botany and Plant Pathology, Corvallis, OR 97331
- U.S. Department of Agriculture-Agricultural Research Service, Forage Seed and Cereal Research Unit, Corvallis, OR 97331
| |
Collapse
|
14
|
Miles TD, Neill TM, Colle M, Warneke B, Robinson G, Stergiopoulos I, Mahaffee WF. Allele-Specific Detection Methods for QoI Fungicide-Resistant Erysiphe necator in Vineyards. PLANT DISEASE 2021; 105:175-182. [PMID: 33186075 DOI: 10.1094/pdis-11-19-2395-re] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Grapevine powdery mildew (GPM), caused by the fungus Erysiphe necator, is a constant threat to worldwide production of grape berries, requiring repeated use of fungicides for management. The frequent fungicide applications have resulted in resistance to commonly used quinone outside inhibitor (QoI) fungicides and the resistance is associated with single-nucleotide polymorphisms (SNPs) in the mitochondrial cytochrome b gene (cytb). In this study, we attempted to detect the most common SNP causing a glycine to alanine substitution at amino acid position 143 (i.e., G143A) in the cytb protein, to track this resistance using allele-specific TaqMan probe and digital-droplet PCR-based assays. Specificity and sensitivity of these assays showed that these two assays could discriminate SNPs and were effective on mixed samples. These diagnostic assays were implemented to survey E. necator samples collected from leaf and air samples from California and Oregon grape-growing regions. Sequencing of PCR amplicons and phenotyping of isolates also revealed that these assays accurately detected each allele (100% agreement), and there was an absolute agreement between the presence or absence of the G143A mutation and resistance to QoIs in the E. necator sampled. These results indicate that the developed diagnostic tools will help growers make informed decisions about fungicide selections and applications which, in turn, will facilitate GPM disease management and improve grape production systems.
Collapse
Affiliation(s)
- Timothy D Miles
- Michigan State University, Department of Plant, Soil and Microbial Sciences, East Lansing, MI 48824
| | - Tara M Neill
- United States Department of Agriculture-Agricultural Research Service, Corvallis, OR 97330
| | - Marivi Colle
- Michigan State University, Department of Plant, Soil and Microbial Sciences, East Lansing, MI 48824
| | - Brent Warneke
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97330
| | - Guy Robinson
- Department of Plant Pathology, University of California-Davis, Davis, CA 95616
| | | | - Walter F Mahaffee
- United States Department of Agriculture-Agricultural Research Service, Corvallis, OR 97330
| |
Collapse
|
15
|
Early Detection of Airborne Inoculum of Nothopassalora personata in Spore Trap Samples from Peanut Fields Using Quantitative PCR. PLANTS 2020; 9:plants9101327. [PMID: 33050299 PMCID: PMC7650562 DOI: 10.3390/plants9101327] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 10/05/2020] [Accepted: 10/07/2020] [Indexed: 01/11/2023]
Abstract
A quantitative PCR (qPCR)-assay was developed to detect airborne inoculum of Nothopassalora personata, causal agent of late leaf spot (LLS) on peanut, collected with a modified impaction spore trap. The qPCR assay was able to consistently detect as few as 10 spores with purified DNA and 25 spores based on crude DNA extraction from rods. In 2019, two spore traps were placed in two peanut fields with a history of LLS. Sampling units were replaced every 2 to 4 days and tested with the developed qPCR assay, while plots were monitored for symptom development. The system detected inoculum 35 to 56 days before visual symptoms developed in the field, with detection related to environmental parameters affecting pathogen life-cycle and disease development. This study develops the framework of the qPCR spore trap system and represents the initial steps towards validation of the performance of the system for use as a decision support tool to complement integrated management of LLS.
Collapse
|
16
|
Brischetto C, Bove F, Languasco L, Rossi V. Can Spore Sampler Data Be Used to Predict Plasmopara viticola Infection in Vineyards? FRONTIERS IN PLANT SCIENCE 2020; 11:1187. [PMID: 32903587 PMCID: PMC7438544 DOI: 10.3389/fpls.2020.01187] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Accepted: 07/22/2020] [Indexed: 06/02/2023]
Abstract
Grapevine downy mildew (DM) is caused by the dimorphic oomycete Plasmopara viticola, which incites epidemics through primary and secondary infection cycles that occur throughout the season. The secondary infection cycles are caused by the sporangia produced on DM lesions. The current research examined the relationship between numbers of airborne sporangia and DM development on grape leaves to determine whether spore sampler data can be useful to predict the potential for secondary infections of P. viticola. Three years (2015-2017) of spore sampler data confirmed that sporangia are a common component of the airborne microflora in a DM-infested vineyard and that their numbers depend on weather conditions. For a total of 108 days, leaf samples were collected from the vineyard at 2- to 3-day intervals and incubated under optimal conditions for P. viticola infection. The numbers of airborne sporangia sampled on 1 to 7 days before leaf sampling were significantly correlated with the numbers of DM lesions on the leaves. The best correlation (r=0.59), however, was found for the numbers of viable airborne sporangia (SPV), which were assessed by using equations driven by the vapour pressure deficit. In Bayesian and ROC curve analyses, SPV was found to be a good predictor of P. viticola infection of grape leaves, with AUROC=0.821 and false positive predictions mainly occurring at low SPV. A binary logistic regression showed that a threshold of 2.52 viable sporangia m-3 air day-1 enables a prediction of no infection with a posterior probability of 0.870, which was higher than the prior probability of 0.574. Numbers of viable sporangia in the vineyard air is therefore a useful predictor of infection and especially of no infection. The predictor missed some observed infections, but these infections were not severe (they accounted for only 31 of 374 DM lesions).
Collapse
|
17
|
Dynamic changes in bacterial communities in the recirculating nutrient solution of cucumber plug seedlings cultivated in an ebb-and-flow subirrigation system. PLoS One 2020; 15:e0232446. [PMID: 32353053 PMCID: PMC7192414 DOI: 10.1371/journal.pone.0232446] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Accepted: 04/14/2020] [Indexed: 12/04/2022] Open
Abstract
Ebb-and-flow subirrigation systems are highly efficient, water-saving and environmentally friendly. However, one concern with these recirculating systems is the possible transmission of plant pathogens. Here, through 16S rRNA-targeted Illumina sequencing, the bacterial dynamics in a recirculating nutrient solution were characterized for cucumber plug seedlings cultivated in an ebb-and-flow system in summer and winter. Both the bacterial number and diversity in the nutrient solution increased immediately after the first irrigation cycle; then, these values were gradually stable with recirculating irrigation. In summer and winter, different bacterial compositions and changing patterns were observed. In summer, the predominant genera in the nutrient solution included Comamonas, Pseudomonas, Acinetobacter, Reyranella, Sphingobium, Bradyrhizobium, Sphingomonas, and Acidovorax. Of those genera, during recirculating irrigation, the relative abundance of Bradyrhizobium gradually decreased, whereas those of Pseudomonas, Reyranella, Sphingobium, Sphingomonas, and Acidovorax gradually increased. In winter, the bacterial communities were mainly composed of Nevskia, Bosea, Sphingobium, Acidovorax, Pseudomonas, and Hydrocarboniphaga. Of those genera, the relative abundance of Bosea, Sphingobium, and Acidovorax showed an increasing trend, whereas those of Nevskia and Hydrocarboniphaga decreased overall. Furthermore, in both summer and winter, no plant pathogenic bacteria on cucumber could be detected; however, some potentially beneficial bacteria, including Comamonas testosteroni, Acinetobacter baumannii, Pseudomonas aeruginosa, P. koreensis and Sphingobium yanoikuyae, colonized the nutrient solution and exhibited increased relative abundances during irrigation. The colonization of these bacteria might facilitate the plant growth promotion. Inoculation of the microbes from the effluent nutrient solution also promoted the growth of cucumber seedlings, but did not lead to any disease. The present data elucidate the bacterial dynamics in a cucumber cultivation ebb-and-flow system and provide useful information for biological control during cucumber seedling production.
Collapse
|
18
|
Dhar N, Mamo BE, Subbarao KV, Koike ST, Fox A, Anchieta A, Klosterman SJ. Measurements of Aerial Spore Load by qPCR Facilitates Lettuce Downy Mildew Risk Advisement. PLANT DISEASE 2020; 104:82-93. [PMID: 31738689 DOI: 10.1094/pdis-03-19-0441-re] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The lettuce downy mildew pathogen, Bremia lactucae, is an obligate oomycete that causes extensive produce losses. Initial chlorotic symptoms that severely reduce the market value of the produce are followed by the appearance of white, downy sporulation on the abaxial side of the leaves. These spores become airborne and disseminate the pathogen. Controlling lettuce downy mildew has relied on repeated fungicide applications to prevent outbreaks. However, in addition to direct economic costs, heterogeneity and rapid adaptation of this pathogen to repeatedly applied fungicides has led to the development of fungicide-insensitivity in the pathogen. We deployed a quantitative PCR assay-based detection method using a species-specific DNA target for B. lactucae coupled with a spore trap system to measure airborne B. lactucae spore loads within three commercial fields that each contained experimental plots, designated EXP1 to EXP3. Based upon these measurements, when the spore load in the air reached a critical level (8.548 sporangia per m3 air), we advised whether or not to apply fungicides on a weekly basis within EXP1 to EXP3. This approach saved three sprays in EXP1, and one spray each in EXP2 and EXP3 without a significant increase in disease incidence. The reduction in fungicide applications to manage downy mildew can decrease lettuce production costs while slowing the development of fungicide resistance in B. lactucae by eliminating unnecessary fungicide applications.
Collapse
Affiliation(s)
- Nikhilesh Dhar
- Department of Plant Pathology, University of California, Davis, c/o USDA, Agricultural Research Service Station, Salinas, CA 93905
| | - Bullo Erena Mamo
- Department of Plant Pathology, University of California, Davis, c/o USDA, Agricultural Research Service Station, Salinas, CA 93905
| | - Krishna V Subbarao
- Department of Plant Pathology, University of California, Davis, c/o USDA, Agricultural Research Service Station, Salinas, CA 93905
| | | | - Alan Fox
- Fox Weather, LLC, Fortuna, CA 95540
| | | | | |
Collapse
|
19
|
Kilin V, Pini V, Kasparian J, Gros S, Wolf JP. Real-time and spatially resolved assessment of pathogens in crops for site-specific pesticide reduction strategies. BIO WEB OF CONFERENCES 2019. [DOI: 10.1051/bioconf/20191501019] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We deploy a network of autonomous stations measuring meteorological and soil parameters, as well as the airborne particle size distribution with a focus on the size ofPlasmapora Viticola(PV). They provide early warning and detection of PV spore outbursts with high spatial and temporal resolution. We evidence the high spatial inhomogeneity of this pathogen, potentially allowing to limit treatments to the specific times and locations where infection risk is detected.
Collapse
|
20
|
Sherman J, Burke JM, Gent DH. Cooperation and Coordination in Plant Disease Management. PHYTOPATHOLOGY 2019; 109:1720-1731. [PMID: 31148511 DOI: 10.1094/phyto-01-19-0010-r] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Scaling of management efforts beyond the boundaries of individual farms may require that individuals act collectively. Such approaches have been suggested several times in plant pathology contexts but rarely have been implemented, in part because the institutional structures that enable successful collective action are poorly understood. In this research, we conducted in-depth interviews with hop producers in Oregon and Washington State to identify their motivations for and barriers to collective action regarding communication of disease levels, coordination of management practices, and sharing of best management practices and other data for powdery mildew (caused by Podosphaera macularis). Growers were generally open to and engaged in communication with neighbors and others on disease status in their hop yards and some evidence of higher levels of information sharing on management practices was found. However, growers who had developed extensive knowledge and databases were reluctant to share information viewed as proprietary. Relationships, trust, and reciprocity were facilitating factors for communication and information sharing, whereas lack of these factors and social norms of independence and pride in portions of the grower community were identified as impediments. Given the heterogeneity of trust, lack of confidence in reciprocity, and weak shared norms, communication of disease risk and coordinated management may be most successful if directed at a smaller scale as a series of neighborhood-based partnerships of growers and their immediate neighbors. Developing a disease reporting system and coordinated disease management efforts with more producers and at larger spatial extents would require formalized structures and rules that would provide assurance that there is consistency in disease data collection and reporting, reciprocation, and sanctions for those who use the information for marketing purposes against other growers. Given the analyses presented here, we believe there is potential for collective action in disease management but with limitations on the scope and nature of the actions.
Collapse
Affiliation(s)
- Jennifer Sherman
- Department of Sociology, Washington State University, Pullman, WA
| | - Jordan M Burke
- Department of Sociology, Washington State University, Pullman, WA
| | - David H Gent
- Forage Seed and Cereal Research Unit, U.S. Department of Agriculture Agricultural Research Service, Corvallis, OR
| |
Collapse
|
21
|
Moral J, Morgan D, Trapero A, Michailides TJ. Ecology and Epidemiology of Diseases of Nut Crops and Olives Caused by Botryosphaeriaceae Fungi in California and Spain. PLANT DISEASE 2019; 103:1809-1827. [PMID: 31232653 DOI: 10.1094/pdis-03-19-0622-fe] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
In recent decades, the cultivated area and production of nuts and olives have increased, driven by an increasing consumer interest in healthier food. Diseases of almond, pistachio, olive, and walnut crops caused by species belonging to the Botryosphaeriaceae family have caused concern worldwide. Although considerable progress has been made in elucidating the etiology of these diseases, scientific knowledge of other aspects of these diseases is more limited. In this article, we present an overview of the most important diseases caused by Botryosphaeriaceae fungi affecting almond, pistachio, olive, and walnut crops by focusing on ecology and epidemiology, primarily in California and Spain.
Collapse
Affiliation(s)
- Juan Moral
- 1Department of Plant Pathology, University of California, Davis, Kearney Agricultural Research and Extension Center, Parlier, CA 93648, U.S.A
- 2Departamento de Agronomía, ETSIAM, Universidad de Córdoba, Campus de Rabanales, Edif. C4, 14071 Córdoba, Spain
| | - David Morgan
- 1Department of Plant Pathology, University of California, Davis, Kearney Agricultural Research and Extension Center, Parlier, CA 93648, U.S.A
| | - Antonio Trapero
- 2Departamento de Agronomía, ETSIAM, Universidad de Córdoba, Campus de Rabanales, Edif. C4, 14071 Córdoba, Spain
| | - Themis J Michailides
- 1Department of Plant Pathology, University of California, Davis, Kearney Agricultural Research and Extension Center, Parlier, CA 93648, U.S.A
| |
Collapse
|
22
|
Grosdidier M, Ioos R, Husson C, Cael O, Scordia T, Marçais B. Tracking the invasion: dispersal of Hymenoscyphus fraxineus airborne inoculum at different scales. FEMS Microbiol Ecol 2019; 94:4950393. [PMID: 29668932 DOI: 10.1093/femsec/fiy049] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2017] [Accepted: 03/20/2018] [Indexed: 12/26/2022] Open
Abstract
Ash dieback is caused by an invasive pathogen Hymenoscyphus fraxineus, which emerged in Europe in the 1990s and jeopardizes the management of ash stands. Although the biological cycle of the pathogen is well understood, its dispersal patterns via airborne spores remain poorly described. We investigated the seasonal and spatial patterns of dispersal in France using both a passive spore-trapping method coupled with a real-time PCR assay and reports of ash dieback based on symptom observations. Spores detection varies from year to year with a detection ability of 30-47% depending on meteorological conditions, which affect both production of inoculum and efficiency of the trapping. Nevertheless, our results are consistent and we showed that the sporulation peak occurred from June to August and that spores were detected up to 50-100 km ahead of the disease front, proving the presence of the pathogen before any observation of symptoms. The spore dispersal gradient was steep, most of inoculum remaining within 50 m of infected ashes. Two dispersal kernels were fitted using Bayesian methods to estimate the mean dispersal distance of H. fraxineus from inoculum sources. The estimated mean distances of dispersal, either local or regional scale, were 1.4 km and 2.6 km, respectively, the best fitting kernel being the inverse power-law. This information may help to design disease management strategies.
Collapse
Affiliation(s)
- M Grosdidier
- Université de Lorraine, Inra, IAM, F-54000 Nancy, France.,ANSES Laboratoire de la Santé des Végétaux, Unité de Mycologie, Domaine de Pixérécourt, Bâtiment E, F-54220 Malzéville, France
| | - R Ioos
- ANSES Laboratoire de la Santé des Végétaux, Unité de Mycologie, Domaine de Pixérécourt, Bâtiment E, F-54220 Malzéville, France
| | - C Husson
- Université de Lorraine, Inra, IAM, F-54000 Nancy, France
| | - O Cael
- Université de Lorraine, Inra, IAM, F-54000 Nancy, France
| | - T Scordia
- Département de la Santé des Forêts Auvergne-Rhône-Alpes, Ministère de l'agriculture et de l'alimentation DGAL-SDQPV, 251 rue de Vaugirard, F-75732, Paris cedex 15, France
| | - B Marçais
- Université de Lorraine, Inra, IAM, F-54000 Nancy, France
| |
Collapse
|
23
|
Dung JKS, Scott JC, Cheng Q, Alderman SC, Kaur N, Walenta DL, Frost KE, Hamm PB. Detection and Quantification of Airborne Claviceps purpurea sensu lato Ascospores from Hirst-Type Spore Traps using Real-Time Quantitative PCR. PLANT DISEASE 2018; 102:2487-2493. [PMID: 30256180 DOI: 10.1094/pdis-02-18-0310-re] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
The U.S. Pacific Northwest states of Oregon and Washington are major producers of cool-season grass seed. Ergot, caused by fungi in the Claviceps purpurea sensu lato group, is an important seed replacement disease of grass worldwide. Microscopic methods that are currently used to quantify airborne Claviceps ascospores captured by spore traps are not currently rapid enough to allow for detecting and reporting of spore numbers in a timely manner, hindering growers from using this information to help manage ergot. We developed a SYBR Green real-time quantitative polymerase chain reaction (qPCR)-based assay for fast and efficient detection and quantification of C. purpurea sensu lato ascospores from Hirst-type spore traps. Species-specificity of the qPCR assay was confirmed against 41 C. purpurea sensu lato isolates collected from six hosts and six other Claviceps spp. Significant relationships were observed between cycle threshold (Ct) values and standard curves of serial dilutions of DNA ranging from 1 pg to 10 ng (R2 = -0.99; P = 0.0002) and DNA extracted from a conidial suspension representing 8 to 80,000 conidia (R2 = -0.99; P = 0.0004). Ct values from qPCR were significantly correlated with results from microscopic examination of spore trap samples from the field (r = -0.68; P < 0.0001) and the procedure was able to detect a single ascospore from spore trap tape samples. The qPCR procedure developed in this study provided a means for quantifying airborne Claviceps ascospores that was highly specific and useful over a wide range of spore densities, and could be performed in a matter of hours instead of days. The qPCR assay developed in this study could be part of an integrated pest management approach to help grass seed growers make risk-based fungicide application decisions for ergot management in grass grown for seed.
Collapse
Affiliation(s)
- Jeremiah K S Dung
- Department of Botany and Plant Pathology, Central Oregon Agricultural Research Center, Oregon State University, Madras
| | - Jeness C Scott
- Department of Botany and Plant Pathology, Central Oregon Agricultural Research Center, Oregon State University, Madras
| | - Qunkang Cheng
- Department of Botany and Plant Pathology, Central Oregon Agricultural Research Center, Oregon State University, Madras
| | - Stephen C Alderman
- National Forage Seed Production Research Center, United States Department of Agriculture-Agricultural Research Service, Corvallis, OR
| | - Navneet Kaur
- Department of Botany and Plant Pathology, Hermiston Agricultural Research and Extension Center, Oregon State University, Hermiston
| | - Darrin L Walenta
- Union County Extension Service, Oregon State University, La Grande
| | - Kenneth E Frost
- Department of Botany and Plant Pathology, Hermiston Agricultural Research and Extension Center, Oregon State University, Hermiston
| | - Philip B Hamm
- Department of Botany and Plant Pathology, Hermiston Agricultural Research and Extension Center, Oregon State University, Hermiston
| |
Collapse
|
24
|
Smith DJ, Ravichandar JD, Jain S, Griffin DW, Yu H, Tan Q, Thissen J, Lusby T, Nicoll P, Shedler S, Martinez P, Osorio A, Lechniak J, Choi S, Sabino K, Iverson K, Chan L, Jaing C, McGrath J. Airborne Bacteria in Earth's Lower Stratosphere Resemble Taxa Detected in the Troposphere: Results From a New NASA Aircraft Bioaerosol Collector (ABC). Front Microbiol 2018; 9:1752. [PMID: 30154759 PMCID: PMC6102410 DOI: 10.3389/fmicb.2018.01752] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Accepted: 07/13/2018] [Indexed: 01/26/2023] Open
Abstract
Airborne microorganisms in the upper troposphere and lower stratosphere remain elusive due to a lack of reliable sample collection systems. To address this problem, we designed, installed, and flight-validated a novel Aircraft Bioaerosol Collector (ABC) for NASA's C-20A that can make collections for microbiological research investigations up to altitudes of 13.7 km. Herein we report results from the first set of science flights-four consecutive missions flown over the United States (US) from 30 October to 2 November, 2017. To ascertain how the concentration of airborne bacteria changed across the tropopause, we collected air during aircraft Ascent/Descent (0.3 to 11 km), as well as sustained Cruise altitudes in the lower stratosphere (~12 km). Bioaerosols were captured on DNA-treated gelatinous filters inside a cascade air sampler, then analyzed with molecular and culture-based characterization. Several viable bacterial isolates were recovered from flight altitudes, including Bacillus sp., Micrococcus sp., Arthrobacter sp., and Staphylococcus sp. from Cruise samples and Brachybacterium sp. from Ascent/Descent samples. Using 16S V4 sequencing methods for a culture-independent analysis of bacteria, the average number of total OTUs was 305 for Cruise samples and 276 for Ascent/Descent samples. Some taxa were more abundant in the flight samples than the ground samples, including OTUs from families Lachnospiraceae, Ruminococcaceae and Erysipelotrichaceae as well as the following genera: Clostridium, Mogibacterium, Corynebacterium, Bacteroides, Prevotella, Pseudomonas, and Parabacteroides. Surprisingly, our results revealed a homogeneous distribution of bacteria in the atmosphere up to 12 km. The observation could be due to atmospheric conditions producing similar background aerosols across the western US, as suggested by modeled back trajectories and satellite measurements. However, the influence of aircraft-associated bacterial contaminants could not be fully eliminated and that background signal was reported throughout our dataset. Considering the tremendous engineering challenge of collecting biomass at extreme altitudes where contamination from flight hardware remains an ever-present issue, we note the utility of using the stratosphere as a proving ground for planned life detection missions across the solar system.
Collapse
Affiliation(s)
- David J. Smith
- NASA Ames Research Center, Space Biosciences DivisionMoffett Field, CA, United States
| | | | - Sunit Jain
- Second Genome Inc.South San Francisco, CA, United States
| | - Dale W. Griffin
- United States Geological Survey, Environmental HealthSt. Petersburg, FL, United States
| | - Hongbin Yu
- Climate and Radiation Laboratory, NASA Goddard Space Flight CenterGreenbelt, MD, United States
| | - Qian Tan
- Earth Science Division, Bay Area Environmental Research InstituteMoffett Field, CA, United States
| | - James Thissen
- Lawrence Livermore National LaboratoryLivermore, CA, United States
| | - Terry Lusby
- NASA Ames Research Center, Space Biosciences DivisionMoffett Field, CA, United States
| | - Patrick Nicoll
- Space Biosciences Division, Blue Marble Space Institute of ScienceMoffett Field, CA, United States
| | - Sarah Shedler
- Biological Oceanography Department, University of South Florida, College of Marine SciencesSt. Petersburg, FL, United States
| | - Paul Martinez
- NASA Armstrong Flight Research CenterPalmdale, CA, United States
| | - Alejandro Osorio
- Jacobs Technology Inc., NASA Armstrong Flight Research CenterPalmdale, CA, United States
| | - Jason Lechniak
- NASA Armstrong Flight Research CenterPalmdale, CA, United States
| | - Samuel Choi
- Jacobs Technology Inc., NASA Armstrong Flight Research CenterPalmdale, CA, United States
| | - Kayleen Sabino
- Second Genome Inc.South San Francisco, CA, United States
| | | | - Luisa Chan
- Second Genome Inc.South San Francisco, CA, United States
| | - Crystal Jaing
- Lawrence Livermore National LaboratoryLivermore, CA, United States
| | - John McGrath
- NASA Armstrong Flight Research CenterPalmdale, CA, United States
| |
Collapse
|
25
|
Behzad H, Mineta K, Gojobori T. Global Ramifications of Dust and Sandstorm Microbiota. Genome Biol Evol 2018; 10:1970-1987. [PMID: 29961874 PMCID: PMC6097598 DOI: 10.1093/gbe/evy134] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/28/2018] [Indexed: 12/17/2022] Open
Abstract
Dust and sandstorm events inject substantial quantities of foreign microorganisms into global ecosystems, with the ability to impact distant environments. The majority of these microorganisms originate from deserts and drylands where the soil is laden with highly stress-resistant microbes capable of thriving under extreme environmental conditions, and a substantial portion of them survive long journeys through the atmosphere. This large-scale transmission of highly resilient alien microbial contaminants raises concerns with regards to the invasion of sensitive and/or pristine sink environments, and to human health-concerns exacerbated by increases in the rate of desertification. Further increases in the transport of dust-associated microbiota could extend the spread of foreign microbes to new ecosystems, increase their load in present sink environments, disrupt ecosystem balance, and potentially introduce new pathogens. Our present understanding of these microorganisms, their phylogenic affiliations and functional significance, is insufficient to determine their impact. The purpose of this review is to provide an overview of available data regarding dust and sandstorm microbiota and their potential ramifications on human and ecosystem health. We conclude by discussing current gaps in dust and sandstorm microbiota research, and the need for collaborative studies involving high-resolution meta-omic approaches in conjunction with extensive ecological time-series studies to advance the field towards an improved and sufficient understanding of these invisible atmospheric travelers and their global ramifications.
Collapse
Affiliation(s)
- Hayedeh Behzad
- King Abdullah University of Science and Technology (KAUST), Computational Bioscience Research Center (CBRC), Thuwal, Saudi Arabia
- King Abdullah University of Science and Technology (KAUST), Biological and Environmental Sciences and Engineering Division (BESE), Thuwal, Saudi Arabia
| | - Katsuhiko Mineta
- King Abdullah University of Science and Technology (KAUST), Computational Bioscience Research Center (CBRC), Thuwal, Saudi Arabia
- King Abdullah University of Science and Technology (KAUST), Computer, Electrical and Mathematical Sciences and Engineering Division (CEMSE), Thuwal, Saudi Arabia
| | - Takashi Gojobori
- King Abdullah University of Science and Technology (KAUST), Computational Bioscience Research Center (CBRC), Thuwal, Saudi Arabia
- King Abdullah University of Science and Technology (KAUST), Biological and Environmental Sciences and Engineering Division (BESE), Thuwal, Saudi Arabia
| |
Collapse
|
26
|
Aguayo J, Fourrier-Jeandel C, Husson C, Ioos R. Assessment of Passive Traps Combined with High-Throughput Sequencing To Study Airborne Fungal Communities. Appl Environ Microbiol 2018; 84:e02637-17. [PMID: 29572213 PMCID: PMC5960964 DOI: 10.1128/aem.02637-17] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2017] [Accepted: 03/19/2018] [Indexed: 11/20/2022] Open
Abstract
Techniques based on high-throughput sequencing (HTS) of environmental DNA have provided a new way of studying fungal diversity. However, these techniques suffer from a number of methodological biases which may appear at any of the steps involved in a metabarcoding study. Air is one of the most important environments where fungi can be found, because it is the primary medium of dispersal for many species. Looking ahead to future developments, it was decided to test 20 protocols, including different passive spore traps, spore recovery procedures, DNA extraction kits, and barcode loci. HTS was performed with the Illumina MiSeq platform targeting two subloci of the fungal internal transcribed spacer. Multivariate analysis and generalized linear models showed that the type of passive spore trap, the spore recovery procedure, and the barcode all impact the description of fungal communities in terms of richness and diversity when assessed by HTS metabarcoding. In contrast, DNA extraction kits did not significantly impact these results. Although passive traps may be used to describe airborne fungal communities, a study using specific real-time PCR and a mock community showed that these kinds of traps are affected by environmental conditions that may induce losses of biological material, impacting diversity and community composition results.IMPORTANCE The advent of high-throughput sequencing (HTS) methods, such as those offered by next-generation sequencing (NGS) techniques, has opened a new era in the study of fungal diversity in different environmental substrates. In this study, we show that an assessment of the diversity of airborne fungal communities can reliably be achieved by the use of simple and robust passive spore traps. However, a comparison of sample processing protocols showed that several methodological biases may impact the results of fungal diversity when assessed by metabarcoding. Our data suggest that identifying these biases is of paramount importance to enable a correct identification and relative quantification of community members.
Collapse
Affiliation(s)
- Jaime Aguayo
- ANSES, Laboratoire de la Santé des Végétaux-LSV, Unité de Mycologie. Domaine de Pixérécourt, Malzéville, France
| | - Céline Fourrier-Jeandel
- ANSES, Laboratoire de la Santé des Végétaux-LSV, Unité de Mycologie. Domaine de Pixérécourt, Malzéville, France
| | - Claude Husson
- UMR IAM, INRA, Université de Lorraine, Nancy, France
| | - Renaud Ioos
- ANSES, Laboratoire de la Santé des Végétaux-LSV, Unité de Mycologie. Domaine de Pixérécourt, Malzéville, France
| |
Collapse
|
27
|
Thiessen LD, Neill TM, Mahaffee WF. Development of a quantitative loop-mediated isothermal amplification assay for the field detection of Erysiphe necator. PeerJ 2018; 6:e4639. [PMID: 29692952 PMCID: PMC5912203 DOI: 10.7717/peerj.4639] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2017] [Accepted: 03/28/2018] [Indexed: 11/21/2022] Open
Abstract
Plant pathogen detection systems have been useful tools to monitor inoculum presence and initiate management schedules. More recently, a loop-mediated isothermal amplification (LAMP) assay was successfully designed for field use in the grape powdery mildew pathosystem; however, false negatives or false positives were prevalent in grower-conducted assays due to the difficulty in perceiving the magnesium pyrophosphate precipitate at low DNA concentrations. A quantitative LAMP (qLAMP) assay using a fluorescence resonance energy transfer-based probe was assessed by grape growers in the Willamette Valley of Oregon. Custom impaction spore samplers were placed at a research vineyard and six commercial vineyard locations, and were tested bi-weekly by the lab and by growers. Grower-conducted qLAMP assays used a beta-version of the Smart-DART handheld LAMP reaction devices (Diagenetix, Inc., Honolulu, HI, USA), connected to Android 4.4 enabled, Bluetooth-capable Nexus 7 tablets for output. Quantification by a quantitative PCR assay was assumed correct to compare the lab and grower qLAMP assay quantification. Growers were able to conduct and interpret qLAMP results; however, the Erysiphe necator inoculum quantification was unreliable using the beta-Smart-DART devices. The qLAMP assay developed was sensitive to one spore in early testing of the assay, but decreased to >20 spores by the end of the trial. The qLAMP assay is not likely a suitable management tool for grape powdery mildew due to losses in sensitivity and decreasing costs and portability for other, more reliable molecular tools.
Collapse
Affiliation(s)
- Lindsey D Thiessen
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, USA
| | - Tara M Neill
- Agricultural Research Service, United States Department of Agriculture, Corvallis, OR, USA
| | - Walter F Mahaffee
- Agricultural Research Service, United States Department of Agriculture, Corvallis, OR, USA
| |
Collapse
|
28
|
Fall ML, Boyse JF, Wang D, Willbur JF, Smith DL, Chilvers MI. Case Study of an Epidemiological Approach Dissecting Historical Soybean Sclerotinia Stem Rot Observations and Identifying Environmental Predictors of Epidemics and Yield Loss. PHYTOPATHOLOGY 2018; 108:469-478. [PMID: 29231778 DOI: 10.1094/phyto-12-16-0446-r] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Sclerotinia sclerotiorum is a significant threat to soybean production worldwide. In this study, an epidemiological approach was used to examine 11 years of historical data from a soybean management performance trial in order to advance our understanding of Sclerotinia stem rot (SSR) development and to identify environmental predictors of SSR epidemics and associated yield losses. Recursive partitioning analysis suggested that average air temperature and total precipitation in July were the most significant variables associated with disease severity. High levels of SSR disease severity index were observed when the average temperature in July was below 19.5°C and total precipitation in July was moderate, between 20 and 108.5 mm. A biphasic sigmoidal curve accurately described the relationship between SSR disease severity index (DSI) and yield, with a DSI threshold of 22, below which minimal yield loss was observed. A 10% increase in the DSI, from 22.0 to 24.2, led to an 11% decrease in yield, from 3,308.14 to 2,951.29 kg/ha. Also, a yield threshold (3,353 kg/ha) that was higher than the annual U.S. average soybean yield (3,039.7 kg/ha) was suggested as an expected yield under low or no SSR pressure in the U.S. Midwest. These thresholds can allow soybean stakeholders to assess the value of disease control and establish an SSR baseline for cost-effective management to protect yields. Because S. sclerotiorum has more than 400 plant host species, and because having quantitative information concerning crop losses is crucial for decision making, this study shows the usefulness of historical data on SSR and, hence, can serve as a model in other SSR pathosystems (canola, dry bean, potato, pea, and so on).
Collapse
Affiliation(s)
- Mamadou L Fall
- First, second, third, and sixth authors: Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing; and fourth and fifth authors: Department of Plant Pathology, University of Wisconsin-Madison, Madison
| | - John F Boyse
- First, second, third, and sixth authors: Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing; and fourth and fifth authors: Department of Plant Pathology, University of Wisconsin-Madison, Madison
| | - Dechun Wang
- First, second, third, and sixth authors: Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing; and fourth and fifth authors: Department of Plant Pathology, University of Wisconsin-Madison, Madison
| | - Jaime F Willbur
- First, second, third, and sixth authors: Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing; and fourth and fifth authors: Department of Plant Pathology, University of Wisconsin-Madison, Madison
| | - Damon L Smith
- First, second, third, and sixth authors: Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing; and fourth and fifth authors: Department of Plant Pathology, University of Wisconsin-Madison, Madison
| | - Martin I Chilvers
- First, second, third, and sixth authors: Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing; and fourth and fifth authors: Department of Plant Pathology, University of Wisconsin-Madison, Madison
| |
Collapse
|
29
|
Thiessen LD, Neill TM, Mahaffee WF. Timing Fungicide Application Intervals Based on Airborne Erysiphe necator Concentrations. PLANT DISEASE 2017; 101:1246-1252. [PMID: 30682951 DOI: 10.1094/pdis-12-16-1727-re] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Management of grape powdery mildew (Erysiphe necator) and other polycyclic diseases relies on numerous fungicide applications that follow calendar or model-based application intervals, both of which assume that inoculum is always present. Quantitative molecular assays have been previously developed to initiate fungicide applications, and could be used to optimize fungicide application intervals throughout the growing season based on inoculum concentration. Airborne inoculum samplers were placed at one research and six commercial vineyards in the Willamette Valley of Oregon. Fungicide applications in all plots were initiated at the first detection of E. necator inoculum, and all subsequent fungicide application intervals were made based the grower' standard calendar program or based on inoculum concentration. In adjusted-interval plots, fungicides were applied at the shortest labeled application interval when >10 spores were detected and the longest labeled application interval when <10 spores were detected. Fungicide applications in control plots consisted of the growers' standard management practice. An average of 2.3 fewer fungicide applications in 2013 and 1.6 fewer fungicide applications in 2014 were used in the adjusted fungicide application intervals treatment in grower fields without significant differences in berry or leaf disease incidence between treatments.
Collapse
Affiliation(s)
- L D Thiessen
- Oregon State University, Department of Botany and Plant Pathology, Corvallis, OR 97331
| | - T M Neill
- U.S. Department of Agriculture-Agricultural Research Service (USDA-ARS), Horticultural Crops Research Laboratory, Corvallis, OR 97331
| | - W F Mahaffee
- U.S. Department of Agriculture-Agricultural Research Service (USDA-ARS), Horticultural Crops Research Laboratory, Corvallis, OR 97331
| |
Collapse
|
30
|
Villari C, Mahaffee WF, Mitchell TK, Pedley KF, Pieck ML, Hand FP. Early Detection of Airborne Inoculum of Magnaporthe oryzae in Turfgrass Fields Using a Quantitative LAMP Assay. PLANT DISEASE 2017; 101:170-177. [PMID: 30682295 DOI: 10.1094/pdis-06-16-0834-re] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Gray leaf spot (GLS) is a destructive disease of perennial ryegrass caused by a host specific pathotype of the ascomycete Magnaporthe oryzae. Early diagnosis is crucial for effective disease management and the implementation of Integrated Pest Management practices. However, a rapid protocol for the detection of low levels of airborne inoculum is still missing. We developed a pathogen-specific quantitative loop-mediated isothermal amplification (qLAMP) assay coupled with a spore trap system for rapid detection and quantification of airborne inoculum of the M. oryzae perennial ryegrass pathotype, and tested its suitability for implementation in GLS-infected turfgrass fields. In summer 2015, two perennial ryegrass plots were artificially inoculated with the pathogen, with four continuously running custom impaction spore traps placed in each plot. Sampling units were replaced daily and tested with the developed qLAMP assay, while plots were monitored for symptom development. Results confirmed that the qLAMP assay-trap system was able to detect as few as 10 conidia up to 12 days before symptoms developed in the field. LAMP technology is particularly appropriate for field implementation by nontechnical users, and has the potential to be a powerful decision support tool to guide timing of fungicide applications for GLS management.
Collapse
Affiliation(s)
- Caterina Villari
- Department of Plant Pathology, The Ohio State University, Columbus 43210
| | - Walter F Mahaffee
- Horticultural Crops Research Laboratory, United States Department of Agriculture-Agricultural Research Service (USDA-ARS), Corvallis, OR 97330
| | | | - Kerry F Pedley
- Foreign Disease-Weed Science Research Unit, USDA-ARS, Fort Detrick, MD 21702
| | - Michael L Pieck
- Foreign Disease-Weed Science Research Unit, USDA-ARS, Fort Detrick, MD 21702
| | | |
Collapse
|
31
|
Kunjeti SG, Anchieta A, Martin FN, Choi YJ, Thines M, Michelmore RW, Koike ST, Tsuchida C, Mahaffee W, Subbarao KV, Klosterman SJ. Detection and Quantification of Bremia lactucae by Spore Trapping and Quantitative PCR. PHYTOPATHOLOGY 2016; 106:1426-1437. [PMID: 27392175 DOI: 10.1094/phyto-03-16-0143-r] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Bremia lactucae is an obligate, oomycete pathogen of lettuce that causes leaf chlorosis and necrosis and adversely affects marketability. The disease has been managed with a combination of host resistance and fungicide applications with success over the years. Fungicide applications are routinely made under the assumption that inoculum is always present during favorable environmental conditions. This approach often leads to fungicide resistance in B. lactucae populations. Detection and quantification of airborne B. lactucae near lettuce crops provides an estimation of the inoculum load, enabling more judicious timing of fungicide applications. We developed a quantitative polymerase chain reaction (qPCR)-based assay using a target sequence in mitochondrial DNA for specific detection of B. lactucae. Validation using amplicon sequencing of DNA from 83 geographically diverse isolates, representing 14 Bremia spp., confirmed that the primers developed for the TaqMan assays are species specific and only amplify templates from B. lactucae. DNA from a single sporangium could be detected at a quantification cycle (Cq) value of 32, and Cq values >35 were considered to be nonspecific. The coefficient of determination (R2) for regression between sporangial density derived from flow cytometry and Cq values derived from the qPCR was 0.86. The assay was deployed using spore traps in the Salinas Valley, where nearly half of U.S. lettuce is produced. The deployment of this sensitive B. lactucae-specific assay resulted in the detection of the pathogen during the 2-week lettuce-free period as well as during the cropping season. These results demonstrate that this assay will be useful for quantifying inoculum load in and around the lettuce fields for the purpose of timing fungicide applications based on inoculum load.
Collapse
Affiliation(s)
- Sridhara G Kunjeti
- First and tenth authors: Department of Plant Pathology, University of California-Davis, 1636 E. Alisal St. Salinas 93901; second, third, and eleventh authors: United States Department of Agriculture-Agricultural Research Service (USDA-ARS), 1636 E. Alisal St., Salinas, CA 93905; fourth author: Kunsan National University, Department of Biology, Gunsan 54150, Republic of Korea; fourth and fifth authors: Biodiversity and Climate Research Center (BiK-F) Senckenberg Gesellscharft für Naturforschung, D-60325 Frankfurt am Main, and Goethe University, Department of Biological Sciences, Institute of Ecology, Evolution and Diversity, D-60325 Frankfurt am Main, Germany; sixth author: The Genome Center and Department of Plant Sciences, University of California, Davis 95616; seventh author: University of California Cooperative Extension, Monterey County, Salinas; eighth author: The Genome Center and Department of Plant Pathology, University of California, Davis; and ninth author: USDA-ARS, Corvallis, OR
| | - Amy Anchieta
- First and tenth authors: Department of Plant Pathology, University of California-Davis, 1636 E. Alisal St. Salinas 93901; second, third, and eleventh authors: United States Department of Agriculture-Agricultural Research Service (USDA-ARS), 1636 E. Alisal St., Salinas, CA 93905; fourth author: Kunsan National University, Department of Biology, Gunsan 54150, Republic of Korea; fourth and fifth authors: Biodiversity and Climate Research Center (BiK-F) Senckenberg Gesellscharft für Naturforschung, D-60325 Frankfurt am Main, and Goethe University, Department of Biological Sciences, Institute of Ecology, Evolution and Diversity, D-60325 Frankfurt am Main, Germany; sixth author: The Genome Center and Department of Plant Sciences, University of California, Davis 95616; seventh author: University of California Cooperative Extension, Monterey County, Salinas; eighth author: The Genome Center and Department of Plant Pathology, University of California, Davis; and ninth author: USDA-ARS, Corvallis, OR
| | - Frank N Martin
- First and tenth authors: Department of Plant Pathology, University of California-Davis, 1636 E. Alisal St. Salinas 93901; second, third, and eleventh authors: United States Department of Agriculture-Agricultural Research Service (USDA-ARS), 1636 E. Alisal St., Salinas, CA 93905; fourth author: Kunsan National University, Department of Biology, Gunsan 54150, Republic of Korea; fourth and fifth authors: Biodiversity and Climate Research Center (BiK-F) Senckenberg Gesellscharft für Naturforschung, D-60325 Frankfurt am Main, and Goethe University, Department of Biological Sciences, Institute of Ecology, Evolution and Diversity, D-60325 Frankfurt am Main, Germany; sixth author: The Genome Center and Department of Plant Sciences, University of California, Davis 95616; seventh author: University of California Cooperative Extension, Monterey County, Salinas; eighth author: The Genome Center and Department of Plant Pathology, University of California, Davis; and ninth author: USDA-ARS, Corvallis, OR
| | - Young-Joon Choi
- First and tenth authors: Department of Plant Pathology, University of California-Davis, 1636 E. Alisal St. Salinas 93901; second, third, and eleventh authors: United States Department of Agriculture-Agricultural Research Service (USDA-ARS), 1636 E. Alisal St., Salinas, CA 93905; fourth author: Kunsan National University, Department of Biology, Gunsan 54150, Republic of Korea; fourth and fifth authors: Biodiversity and Climate Research Center (BiK-F) Senckenberg Gesellscharft für Naturforschung, D-60325 Frankfurt am Main, and Goethe University, Department of Biological Sciences, Institute of Ecology, Evolution and Diversity, D-60325 Frankfurt am Main, Germany; sixth author: The Genome Center and Department of Plant Sciences, University of California, Davis 95616; seventh author: University of California Cooperative Extension, Monterey County, Salinas; eighth author: The Genome Center and Department of Plant Pathology, University of California, Davis; and ninth author: USDA-ARS, Corvallis, OR
| | - Marco Thines
- First and tenth authors: Department of Plant Pathology, University of California-Davis, 1636 E. Alisal St. Salinas 93901; second, third, and eleventh authors: United States Department of Agriculture-Agricultural Research Service (USDA-ARS), 1636 E. Alisal St., Salinas, CA 93905; fourth author: Kunsan National University, Department of Biology, Gunsan 54150, Republic of Korea; fourth and fifth authors: Biodiversity and Climate Research Center (BiK-F) Senckenberg Gesellscharft für Naturforschung, D-60325 Frankfurt am Main, and Goethe University, Department of Biological Sciences, Institute of Ecology, Evolution and Diversity, D-60325 Frankfurt am Main, Germany; sixth author: The Genome Center and Department of Plant Sciences, University of California, Davis 95616; seventh author: University of California Cooperative Extension, Monterey County, Salinas; eighth author: The Genome Center and Department of Plant Pathology, University of California, Davis; and ninth author: USDA-ARS, Corvallis, OR
| | - Richard W Michelmore
- First and tenth authors: Department of Plant Pathology, University of California-Davis, 1636 E. Alisal St. Salinas 93901; second, third, and eleventh authors: United States Department of Agriculture-Agricultural Research Service (USDA-ARS), 1636 E. Alisal St., Salinas, CA 93905; fourth author: Kunsan National University, Department of Biology, Gunsan 54150, Republic of Korea; fourth and fifth authors: Biodiversity and Climate Research Center (BiK-F) Senckenberg Gesellscharft für Naturforschung, D-60325 Frankfurt am Main, and Goethe University, Department of Biological Sciences, Institute of Ecology, Evolution and Diversity, D-60325 Frankfurt am Main, Germany; sixth author: The Genome Center and Department of Plant Sciences, University of California, Davis 95616; seventh author: University of California Cooperative Extension, Monterey County, Salinas; eighth author: The Genome Center and Department of Plant Pathology, University of California, Davis; and ninth author: USDA-ARS, Corvallis, OR
| | - Steven T Koike
- First and tenth authors: Department of Plant Pathology, University of California-Davis, 1636 E. Alisal St. Salinas 93901; second, third, and eleventh authors: United States Department of Agriculture-Agricultural Research Service (USDA-ARS), 1636 E. Alisal St., Salinas, CA 93905; fourth author: Kunsan National University, Department of Biology, Gunsan 54150, Republic of Korea; fourth and fifth authors: Biodiversity and Climate Research Center (BiK-F) Senckenberg Gesellscharft für Naturforschung, D-60325 Frankfurt am Main, and Goethe University, Department of Biological Sciences, Institute of Ecology, Evolution and Diversity, D-60325 Frankfurt am Main, Germany; sixth author: The Genome Center and Department of Plant Sciences, University of California, Davis 95616; seventh author: University of California Cooperative Extension, Monterey County, Salinas; eighth author: The Genome Center and Department of Plant Pathology, University of California, Davis; and ninth author: USDA-ARS, Corvallis, OR
| | - Cayla Tsuchida
- First and tenth authors: Department of Plant Pathology, University of California-Davis, 1636 E. Alisal St. Salinas 93901; second, third, and eleventh authors: United States Department of Agriculture-Agricultural Research Service (USDA-ARS), 1636 E. Alisal St., Salinas, CA 93905; fourth author: Kunsan National University, Department of Biology, Gunsan 54150, Republic of Korea; fourth and fifth authors: Biodiversity and Climate Research Center (BiK-F) Senckenberg Gesellscharft für Naturforschung, D-60325 Frankfurt am Main, and Goethe University, Department of Biological Sciences, Institute of Ecology, Evolution and Diversity, D-60325 Frankfurt am Main, Germany; sixth author: The Genome Center and Department of Plant Sciences, University of California, Davis 95616; seventh author: University of California Cooperative Extension, Monterey County, Salinas; eighth author: The Genome Center and Department of Plant Pathology, University of California, Davis; and ninth author: USDA-ARS, Corvallis, OR
| | - Walt Mahaffee
- First and tenth authors: Department of Plant Pathology, University of California-Davis, 1636 E. Alisal St. Salinas 93901; second, third, and eleventh authors: United States Department of Agriculture-Agricultural Research Service (USDA-ARS), 1636 E. Alisal St., Salinas, CA 93905; fourth author: Kunsan National University, Department of Biology, Gunsan 54150, Republic of Korea; fourth and fifth authors: Biodiversity and Climate Research Center (BiK-F) Senckenberg Gesellscharft für Naturforschung, D-60325 Frankfurt am Main, and Goethe University, Department of Biological Sciences, Institute of Ecology, Evolution and Diversity, D-60325 Frankfurt am Main, Germany; sixth author: The Genome Center and Department of Plant Sciences, University of California, Davis 95616; seventh author: University of California Cooperative Extension, Monterey County, Salinas; eighth author: The Genome Center and Department of Plant Pathology, University of California, Davis; and ninth author: USDA-ARS, Corvallis, OR
| | - Krishna V Subbarao
- First and tenth authors: Department of Plant Pathology, University of California-Davis, 1636 E. Alisal St. Salinas 93901; second, third, and eleventh authors: United States Department of Agriculture-Agricultural Research Service (USDA-ARS), 1636 E. Alisal St., Salinas, CA 93905; fourth author: Kunsan National University, Department of Biology, Gunsan 54150, Republic of Korea; fourth and fifth authors: Biodiversity and Climate Research Center (BiK-F) Senckenberg Gesellscharft für Naturforschung, D-60325 Frankfurt am Main, and Goethe University, Department of Biological Sciences, Institute of Ecology, Evolution and Diversity, D-60325 Frankfurt am Main, Germany; sixth author: The Genome Center and Department of Plant Sciences, University of California, Davis 95616; seventh author: University of California Cooperative Extension, Monterey County, Salinas; eighth author: The Genome Center and Department of Plant Pathology, University of California, Davis; and ninth author: USDA-ARS, Corvallis, OR
| | - Steven J Klosterman
- First and tenth authors: Department of Plant Pathology, University of California-Davis, 1636 E. Alisal St. Salinas 93901; second, third, and eleventh authors: United States Department of Agriculture-Agricultural Research Service (USDA-ARS), 1636 E. Alisal St., Salinas, CA 93905; fourth author: Kunsan National University, Department of Biology, Gunsan 54150, Republic of Korea; fourth and fifth authors: Biodiversity and Climate Research Center (BiK-F) Senckenberg Gesellscharft für Naturforschung, D-60325 Frankfurt am Main, and Goethe University, Department of Biological Sciences, Institute of Ecology, Evolution and Diversity, D-60325 Frankfurt am Main, Germany; sixth author: The Genome Center and Department of Plant Sciences, University of California, Davis 95616; seventh author: University of California Cooperative Extension, Monterey County, Salinas; eighth author: The Genome Center and Department of Plant Pathology, University of California, Davis; and ninth author: USDA-ARS, Corvallis, OR
| |
Collapse
|