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Elsherbiny AS, Galal A, Ghoneem KM, Salahuddin NA. Graphene oxide-based nanocomposites for outstanding eco-friendly antifungal potential against tomato phytopathogens. BIOMATERIALS ADVANCES 2024; 160:213863. [PMID: 38642516 DOI: 10.1016/j.bioadv.2024.213863] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Revised: 04/01/2024] [Accepted: 04/15/2024] [Indexed: 04/22/2024]
Abstract
To obtain the collaborative antifungal potential of nanocomposites conjugated with graphene oxide (GO), a combination of GO with chitosan (CS/GO) and GO with chitosan (CS) and polyaniline (PANI/CS/GO) was carried out. The synthesized GO-nanocomposites were recognized by several techniques. Vanillin (Van.) and cinnamaldehyde (Cinn.) were loaded on the prepared nanocomposites as antioxidants through a batch adsorption process. In vitro release study of Van. and Cinn. from the nanocomposites was accomplished at pH 7 and 25°C. The antimicrobial activity of GO, CS/GO, and PANI/CS/GO was studied against tomato Fusarium oxysporum (FOL) and Pythium debaryanum (PYD) pathogens. The loaded ternary composite PANI/CS/GO exhibited the best percent of reduction against the two pathogens in vitro studies. The Greenhouse experiment revealed that seedlings' treatment by CS/GO/Van. and PANI/CS/GO/Van significantly lowered both disease index and disease incidence. The loaded CS/GO and PANI/CS/GO nanocomposites had a positive effect on lengthening shoots. Additionally, when CS/GO/Cinn., CS/GO/Van. and PANI/CS/GO/Van. were used, tomato seedlings' photosynthetic pigments dramatically increased as compared to infected control. The results show that these bio-nanocomposites can be an efficient, sustainable, nontoxic, eco-friendly, and residue-free approach for fighting fungal pathogens and improving plant growth.
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Affiliation(s)
- Abeer S Elsherbiny
- Department of Chemistry, Faculty of Science, Tanta University, Tanta 31527, Egypt.
| | - Alyaa Galal
- Department of Chemistry, Faculty of Science, Tanta University, Tanta 31527, Egypt
| | - Khalid M Ghoneem
- Seed Pathology Research Department, Plant Pathology Research Institute, Agricultural Research Center (ID: 60019332), Giza 12112, Egypt
| | - Nehal A Salahuddin
- Department of Chemistry, Faculty of Science, Tanta University, Tanta 31527, Egypt
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Das Laha S, Kundu A, Podder S. Impact of biotic stresses on the Brassicaceae family and opportunities for crop improvement by exploiting genotyping traits. PLANTA 2024; 259:97. [PMID: 38520529 DOI: 10.1007/s00425-024-04379-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Accepted: 03/07/2024] [Indexed: 03/25/2024]
Abstract
MAIN CONCLUSION Utilizing RNAi, miRNA, siRNA, lncRNA and exploiting genotyping traits can help safeguard the food supply from illnesses and pest damage to Brassicas, as well as reduce yield losses caused by plant pathogens and insect pests. In the natural environment, plants face significant challenges in the form of biotic stress, due to various living organisms, leading to biological stress and a sharp decline in crop yields. To cope with these effects, plants have evolved specialized mechanisms to mitigate these challenges. Plant stress tolerance and resistance are influenced by genes associated with stress-responsive pathogens that interact with various stress-related signaling pathway components. Plants employ diverse strategies and mechanisms to combat biological stress, involving a complex network of transcription factors that interact with specific cis-elements to regulate gene expression. Understanding both plant developmental and pathogenic disease resistance mechanisms can allow us to develop stress-tolerant and -resistant crops. Brassica genus includes commercially important crops, e.g., broccoli, cabbage, cauliflower, kale, and rapeseed, cultivated worldwide, with several applications, e.g., oil production, consumption, condiments, fodder, as well as medicinal ones. Indeed, in 2020, global production of vegetable Brassica reached 96.4 million tones, a 10.6% rise from the previous decade. Taking into account their commercial importance, coupled to the impact that pathogens can have in Brassica productivity, yield losses up to 60%, this work complies the major diseases caused due to fungal, bacterial, viral, and insects in Brassica species. The review is structured into three parts. In the first part, an overview is provided of the various pathogens affecting Brassica species, including fungi, bacteria, viruses, and insects. The second part delves into the exploration of defense mechanisms that Brassica plants encounter against these pathogens including secondary metabolites, duplicated genes, RNA interference (RNAi), miRNA (micro-RNA), siRNA (small interfering RNA), and lncRNA (long non-coding RNA). The final part comprehensively outlines the current applications of CRISPR/Cas9 technology aimed at enhancing crop quality. Taken collectively, this review will contribute to our enhanced understanding of these mechanisms and their role in the development of resistance in Brassica plants, thus supporting strategies to protect this crucial crop.
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Affiliation(s)
- Shayani Das Laha
- Computational and Systems Biology Laboratory, Department of Microbiology, Raiganj University, Raiganj, West Bengal, India
- Department of Genetics and Plant Breeding, Uttar Banga Krishi Viswavidyalaya, Coochbehar, West Bengal, India
| | - Avijit Kundu
- Department of Genetics and Plant Breeding, Uttar Banga Krishi Viswavidyalaya, Coochbehar, West Bengal, India
| | - Soumita Podder
- Computational and Systems Biology Laboratory, Department of Microbiology, Raiganj University, Raiganj, West Bengal, India.
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3
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Greer SF, Surendran A, Grant M, Lillywhite R. The current status, challenges, and future perspectives for managing diseases of brassicas. Front Microbiol 2023; 14:1209258. [PMID: 37533829 PMCID: PMC10392840 DOI: 10.3389/fmicb.2023.1209258] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Accepted: 06/23/2023] [Indexed: 08/04/2023] Open
Abstract
The Brassica genus comprises the greatest diversity of agriculturally important crops. Several species from this genus are grown as vegetable and oil crops for food, animal feed and industrial purposes. In particular, B. oleracea has been extensively bred to give rise to several familiar vegetables (cabbage, broccoli, cauliflower, kale and Brussels Sprouts, etc.) that are grouped under seven major cultivars. In 2020, 96.4 million tonnes of vegetable brassicas were produced globally with a 10.6% increase over the past decade. Yet, like other crops, the production of brassicas is challenged by diseases among which, black rot, clubroot, downy mildew and turnip yellows virus have been identified by growers as the most damaging to UK production. In some cases, yield losses can reach 90% depending upon the geographic location of cultivation. This review aims to provide an overview of the key diseases of brassicas and their management practices, with respect to the biology and lifecycle of the causal pathogens. In addition, the existing controls on the market as well as those that are currently in the research and development phases were critically reviewed. There is not one specific control method that is effective against all the diseases. Generally, cultural practices prevent disease rather than reduce or eliminate disease. Chemical controls are limited, have broad-spectrum activity, are damaging to the environment and are rapidly becoming ineffective due to the evolution of resistance mechanisms by the pathogens. It is therefore important to develop integrated pest management (IPM) strategies that are tailored to geographic locations. Several knowledge gaps have been identified and listed in this review along with the future recommendations to control these four major diseases of brassicas. As such, this review paper will act as a guide to sustainably tackle pre-harvest diseases in Brassica crops to reduce food loss.
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Affiliation(s)
- Shannon F. Greer
- School of Life Sciences, University of Warwick, Coventry, United Kingdom
| | - Arthy Surendran
- School of Life Sciences, University of Warwick, Coventry, United Kingdom
- Carbon, Crop and Soils Group, SRUC, Edinburgh, United Kingdom
| | - Murray Grant
- School of Life Sciences, University of Warwick, Coventry, United Kingdom
| | - Robert Lillywhite
- School of Life Sciences, University of Warwick, Coventry, United Kingdom
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Fondevilla S, Arias-Giraldo LF, García-León FJ, Landa BB. Molecular Characterization of Peronospora variabilis Isolates Infecting Chenopodium quinoa and Chenopodium album in Spain. PLANT DISEASE 2023; 107:999-1004. [PMID: 36190302 DOI: 10.1094/pdis-05-22-1198-sc] [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: 06/16/2023]
Abstract
Quinoa is an expanding crop in southern Spain. Downy mildew, caused by Peronospora variabilis, is the most important quinoa disease in Spain and worldwide. In Spain, this disease has also been observed on the weed Chenopodium album. The objectives of this study were to unravel the origin of the P. variabilis isolates currently infecting quinoa in southern Spain and to study their genetic diversity. We hypothesized that P. variabilis isolates infecting quinoa in Spain could have been introduced through the seeds of the quinoa varieties currently grown in the country or, alternatively, that these isolates are endemic isolates, originally infecting C. album, that jumped to quinoa. In order to test these hypotheses, we sequenced the internal transcribed spacer (ITS), cytochrome c oxidase subunit 1 (cox1), and cox2 regions of 33 P. variabilis isolates infecting C. quinoa and C. album in southern Spain and analyzed their phylogenetic relationship with isolates present in other countries infecting Chenopodium spp. cox1 gene sequences from all of the Spanish P. variabilis isolates were identical and exhibited nine single-nucleotide polymorphisms (SNPs) compared with a single P. variabilis cox1 sequence found at GenBank. Phylogenetic analyses based on the ITS ribosomal DNA region were not suitable to differentiate isolates according to their geographical origin or host. The cox2 sequences from P. variabilis Spanish isolates collected from C. quinoa and C. album were all identical and had a distinctive SNP in the last of four polymorphic sites that distinguished Spanish isolates from isolates from other countries. These results suggest that P. variabilis infecting quinoa in southern Spain could be native isolates that originally infected C. album.[Formula: see text] Copyright © 2023 The Author(s). This is an open access article distributed under the CC BY 4.0 International license.
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Affiliation(s)
- Sara Fondevilla
- Institute for Sustainable Agriculture, CSIC, Av. Menendez Pidal s/n, Córdoba 14004, Spain
| | - Luis F Arias-Giraldo
- Institute for Sustainable Agriculture, CSIC, Av. Menendez Pidal s/n, Córdoba 14004, Spain
| | | | - Blanca B Landa
- Institute for Sustainable Agriculture, CSIC, Av. Menendez Pidal s/n, Córdoba 14004, Spain
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Liu Y, Vaghefi N, Ades PK, Idnurm A, Ahmed A, Taylor PWJ. Globisporangium and Pythium Species Associated with Yield Decline of Pyrethrum ( Tanacetum cinerariifolium) in Australia. PLANTS (BASEL, SWITZERLAND) 2023; 12:1361. [PMID: 36987047 PMCID: PMC10051369 DOI: 10.3390/plants12061361] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 03/13/2023] [Accepted: 03/13/2023] [Indexed: 06/19/2023]
Abstract
Pyrethrum (Tanacetum cinerariifolium) cultivation in Australia, which accounts for the majority of global production of natural insecticidal pyrethrins, is affected by a persistent yield decline which in part is caused by a complex of pathogens. Globisporangium and Pythium species were isolated from crown and roots of pyrethrum plants showing stunting and brown discoloration of crown tissue, and from soil adjacent to diseased plants from yield-decline-affected sites in Tasmania and Victoria, Australia. Ten known Globisporangium species (Globisporangium attrantheridium, G. erinaceum, G. intermedium, G. irregulare, G. macrosporum, G. recalcitrans, G. rostratifingens, G. sylvaticum, G. terrestris and G. ultimum var. ultimum), two new Globisporangium species (Globisporangium capense sp. nov. and Globisporangium commune sp. nov.) and three Pythium species (Pythium diclinum/lutarium, P. tracheiphilum and P. vanterpoolii) were identified through morphological studies and multigene phylogenetic analyses using ITS and Cox1 sequences. Globisporangium ultimum var. ultimum, G. sylvaticum, G. commune sp. nov. and G. irregulare were most abundant. Globisporangium attrantheridium, G. macrosporum and G. terrestris were reported for the first time in Australia. Seven Globisporangium species were pathogenic on both pyrethrum seeds (in vitro assays) and seedlings (glasshouse bioassays), while two Globisporangium species and three Pythium species only caused significant symptoms on pyrethrum seeds. Globisporangium irregulare and G. ultimum var. ultimum were the most aggressive species, causing pyrethrum seed rot, seedling damping-off and significant plant biomass reduction. This is the first report of Globisporangium and Pythium species causing disease in pyrethrum globally and suggests that oomycete species in the family Pythiaceae may have an important role in the yield decline of pyrethrum in Australia.
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Affiliation(s)
- Yuzhu Liu
- School of Agriculture and Food, Faculty of Science, University of Melbourne, Parkville, VIC 3010, Australia
| | - Niloofar Vaghefi
- School of Agriculture and Food, Faculty of Science, University of Melbourne, Parkville, VIC 3010, Australia
| | - Peter K. Ades
- School of Ecosystem and Forest Sciences, Faculty of Science, University of Melbourne, Parkville, VIC 3010, Australia
| | - Alexander Idnurm
- School of BioSciences, Faculty of Science, University of Melbourne, Parkville, VIC 3010, Australia
| | - Aabroo Ahmed
- Department of Plant Sciences, University of Saskatchewan, Saskatoon, SK S7N2R6, Canada
| | - Paul W. J. Taylor
- School of Agriculture and Food, Faculty of Science, University of Melbourne, Parkville, VIC 3010, Australia
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Mourou M, Raimondo ML, Lops F, Carlucci A. Brassicaceae Fungi and Chromista Diseases: Molecular Detection and Host–Plant Interaction. PLANTS (BASEL, SWITZERLAND) 2023; 12:1033. [PMID: 36903895 PMCID: PMC10005080 DOI: 10.3390/plants12051033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Revised: 02/20/2023] [Accepted: 02/21/2023] [Indexed: 06/18/2023]
Abstract
Brassicaceae plants cover a large number of species with great economic and nutritional importance around the world. The production of Brassica spp. is limited due to phytopathogenic fungal species causing enormous yield losses. In this scenario, precise and rapid detection and identification of plant-infecting fungi are essential to facilitate the effective management of diseases. DNA-based molecular methods have become popular methods for accurate plant disease diagnostics and have been used to detect Brassicaceae fungal pathogens. Polymerase chain reaction (PCR) assays including nested, multiplex, quantitative post, and isothermal amplification methods represent a powerful weapon for early detection of fungal pathogens and preventively counteract diseases on brassicas with the aim to drastically reduce the fungicides as inputs. It is noteworthy also that Brassicaceae plants can establish a wide variety of relationships with fungi, ranging from harmful interactions with pathogens to beneficial associations with endophytic fungi. Thus, understanding host and pathogen interaction in brassica crops prompts better disease management. The present review reports the main fungal diseases of Brassicaceae, molecular methods used for their detection, review studies on the interaction between fungi and brassicas plants, and the various mechanisms involved including the application of omics technologies.
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Affiliation(s)
- Marwa Mourou
- Department of Agricultural Sciences, Food, Natural Resources and Engineering, University of Foggia, Via Napoli 25, 71122 Foggia, Italy
| | | | | | - Antonia Carlucci
- Department of Agricultural Sciences, Food, Natural Resources and Engineering, University of Foggia, Via Napoli 25, 71122 Foggia, Italy
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7
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Grosse C, Brandt N, Van Antwerpen P, Wintjens R, Matthijs S. Two new siderophores produced by Pseudomonas sp. NCIMB 10586: The anti-oomycete non-ribosomal peptide synthetase-dependent mupirochelin and the NRPS-independent triabactin. Front Microbiol 2023; 14:1143861. [PMID: 37032897 PMCID: PMC10080011 DOI: 10.3389/fmicb.2023.1143861] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Accepted: 03/02/2023] [Indexed: 04/11/2023] Open
Abstract
Introduction Globisporangium ultimum is an oomycetal pathogen causing damping-off on over 300 different plant hosts. Currently, as for many phytopathogens, its control relies in the use of chemicals with negative impact on health and ecosystems. Therefore, many biocontrol strategies are under investigation to reduce the use of fungicides. Results In this study, the soil bacterium Pseudomonas sp. NCIMB 10586 demonstrates a strong iron-repressed in vitro antagonism against G. ultimum MUCL 38045. This antagonism does not depend on the secretion of the broad-range antibiotic mupirocin or of the siderophore pyoverdine by the bacterial strain. The inhibitor molecule was identified as a novel non-ribosomal peptide synthetase (NRPS) siderophore named mupirochelin. Its putative structure bears similarities to other siderophores and bioactive compounds. The transcription of its gene cluster is affected by the biosynthesis of pyoverdine, the major known siderophore of the strain. Besides mupirochelin, we observed the production of a third and novel NRPS-independent siderophore (NIS), here termed triabactin. The iron-responsive transcriptional repression of the two newly identified siderophore gene clusters corroborates their role as iron scavengers. However, their respective contributions to the strain fitness are dissimilar. Bacterial growth in iron-deprived conditions is greatly supported by pyoverdine production and, to a lesser extent, by triabactin. On the contrary, mupirochelin does not contribute to the strain fitness under the studied conditions. Conclusion Altogether, we have demonstrated here that besides pyoverdine, Pseudomonas sp. NCIMB 10586 produces two newly identified siderophores, namely mupirochelin, a weak siderophore with strong antagonism activity against G. ultimum, and the potent siderophore triabactin.
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Affiliation(s)
- Camille Grosse
- Unité de Recherche NaturaMonas, Institut de Recherche LABIRIS, Brussels, Belgium
| | - Nathalie Brandt
- Unité de Recherche NaturaMonas, Institut de Recherche LABIRIS, Brussels, Belgium
| | - Pierre Van Antwerpen
- RD3 – Pharmacognosy, Bioanalysis and Drug Discovery and Analytical Platform of the Faculty of Pharmacy, Université Libre de Bruxelles, Brussels, Belgium
| | - René Wintjens
- Unité Microbiologie, Chimie Bioorganique et Macromoléculaire, Department of Research in Drug Development (RD3), Faculty of Pharmacy, Université Libre de Bruxelles, Brussels, Belgium
| | - Sandra Matthijs
- Unité de Recherche NaturaMonas, Institut de Recherche LABIRIS, Brussels, Belgium
- *Correspondence: Sandra Matthijs,
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Wohor OZ, Rispail N, Ojiewo CO, Rubiales D. Pea Breeding for Resistance to Rhizospheric Pathogens. PLANTS (BASEL, SWITZERLAND) 2022; 11:2664. [PMID: 36235530 PMCID: PMC9572552 DOI: 10.3390/plants11192664] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 09/30/2022] [Accepted: 10/06/2022] [Indexed: 06/16/2023]
Abstract
Pea (Pisum sativum L.) is a grain legume widely cultivated in temperate climates. It is important in the race for food security owing to its multipurpose low-input requirement and environmental promoting traits. Pea is key in nitrogen fixation, biodiversity preservation, and nutritional functions as food and feed. Unfortunately, like most crops, pea production is constrained by several pests and diseases, of which rhizosphere disease dwellers are the most critical due to their long-term persistence in the soil and difficulty to manage. Understanding the rhizosphere environment can improve host plant root microbial association to increase yield stability and facilitate improved crop performance through breeding. Thus, the use of various germplasm and genomic resources combined with scientific collaborative efforts has contributed to improving pea resistance/cultivation against rhizospheric diseases. This improvement has been achieved through robust phenotyping, genotyping, agronomic practices, and resistance breeding. Nonetheless, resistance to rhizospheric diseases is still limited, while biological and chemical-based control strategies are unrealistic and unfavourable to the environment, respectively. Hence, there is a need to consistently scout for host plant resistance to resolve these bottlenecks. Herein, in view of these challenges, we reflect on pea breeding for resistance to diseases caused by rhizospheric pathogens, including fusarium wilt, root rots, nematode complex, and parasitic broomrape. Here, we will attempt to appraise and harmonise historical and contemporary knowledge that contributes to pea resistance breeding for soilborne disease management and discuss the way forward.
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Affiliation(s)
- Osman Z. Wohor
- Instituto de Agricultura Sostenible, CSIC, Avenida Menéndez Pidal s/n, 14004 Córdoba, Spain
- Savanna Agriculture Research Institute, CSIR, Nyankpala, Tamale Post TL52, Ghana
| | - Nicolas Rispail
- Instituto de Agricultura Sostenible, CSIC, Avenida Menéndez Pidal s/n, 14004 Córdoba, Spain
| | - Chris O. Ojiewo
- International Maize and Wheat Improvement Center (CIMMYT), ICRAF House, United Nations Avenue—Gigiri, Nairobi P.O. Box 1041-00621, Kenya
| | - Diego Rubiales
- Instituto de Agricultura Sostenible, CSIC, Avenida Menéndez Pidal s/n, 14004 Córdoba, Spain
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Espindola AS, Cardwell K, Martin FN, Hoyt PR, Marek SM, Schneider W, Garzon CD. A Step Towards Validation of High-Throughput Sequencing for the Identification of Plant Pathogenic Oomycetes. PHYTOPATHOLOGY 2022; 112:1859-1866. [PMID: 35345904 DOI: 10.1094/phyto-11-21-0454-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: 06/14/2023]
Abstract
The advancement in high-throughput sequencing (HTS) technology allows the detection of pathogens without the need for isolation or template amplification. Plant regulatory agencies worldwide are adopting HTS as a prescreening tool for plant pathogens in imported plant germplasm. The technique is a multipronged process and, often, the bioinformatic analysis complicates detection. Previously, we developed E-probe diagnostic nucleic acid analysis (EDNA), a bioinformatic tool that detects pathogens in HTS data. EDNA uses custom databases of signature nucleic acid sequences (e-probes) to reduce computational effort and subjectivity when determining pathogen presence in a sample. E-probes of Pythium ultimum and Phytophthora ramorum were previously validated only using simulated HTS data. However, HTS samples generated from infected hosts or pure culture may vary in pathogen concentration, sequencing bias, and data quality, suggesting that each pathosystem requires further validation. Here, we used metagenomic and genomic HTS data generated from infected hosts and pure culture, respectively, to further validate and curate e-probes of Pythium ultimum and Phytophthora ramorum. E-probe length was found to be a determinant of diagnostic sensitivity and specificity; 80-nucleotide e-probes increased the diagnostic specificity to 100%. Curating e-probes to increase specificity affected diagnostic sensitivity only for 80-nucleotide Pythium ultimum e-probes. Comparing e-probes with alternative databases and bioinformatic tools in their speed and ability to find Pythium ultimum and Phytophthora ramorum demonstrated that, although pathogen sequence reads were detected by other methods, they were less specific and slower when compared with e-probes.
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Affiliation(s)
- Andres S Espindola
- Department of Entomology and Plant Pathology, Oklahoma State University, Stillwater, OK 74078
| | - Kitty Cardwell
- Department of Entomology and Plant Pathology, Oklahoma State University, Stillwater, OK 74078
| | - Frank N Martin
- U.S. Department of Agriculture-Agriculture Research Service, Salinas, CA
| | - Peter R Hoyt
- Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, OK 74078
| | - Stephen M Marek
- Department of Entomology and Plant Pathology, Oklahoma State University, Stillwater, OK 74078
| | | | - Carla D Garzon
- Department of Entomology and Plant Pathology, Oklahoma State University, Stillwater, OK 74078
- Department of Plant Science and Landscape Architecture, Delaware Valley University, Doylestown, PA 18901
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Chen S, Daly P, Zhou D, Li J, Wang X, Deng S, Feng H, Wang C, Sheikh TMM, Chen Y, Xue T, Cai F, Kubicek CP, Wei L, Druzhinina IS. The use of mutant and engineered microbial agents for biological control of plant diseases caused by Pythium: Achievements versus challenges. FUNGAL BIOL REV 2022. [DOI: 10.1016/j.fbr.2022.03.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
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11
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Barboza E, Cabral C, Rossato M, Martins F, Reis A. Pythium
and
Phytopythium
species associated with weeds collected in vegetable production fields in Brazil. Lett Appl Microbiol 2022; 74:796-808. [DOI: 10.1111/lam.13666] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Revised: 01/31/2022] [Accepted: 02/01/2022] [Indexed: 11/29/2022]
Affiliation(s)
- E.A. Barboza
- Dept. of Plant Pathology Universidade de Brasília (UnB) Brazil
| | | | - M. Rossato
- Dept. of Plant Pathology Universidade de Brasília (UnB) Brazil
| | | | - A. Reis
- CNPH/Embrapa Hortaliças Brazil
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Feng H, Ye W, Liu Z, Wang Y, Chen J, Wang Y, Zheng X. Development of LAMP Assays Using a Novel Target Gene for Specific Detection of Pythium terrestris, Pythium spinosum, and ' Candidatus Pythium huanghuaiense'. PLANT DISEASE 2021; 105:2888-2897. [PMID: 33823611 DOI: 10.1094/pdis-01-21-0068-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: 06/12/2023]
Abstract
Pythium terrestris, Pythium spinosum, and 'Candidatus Pythium huanghuaiense' are closely related species and important pathogens of soybean that cause root rot. However, the sequences of commonly used molecular markers, such as rDNA internal transcribed spacer 2 and cytochrome oxidase 1 gene, are similar among these species, making it difficult to design species-specific primers for loop-mediated isothermal amplification (LAMP) assays. The genome sequences of these species are also currently unavailable. Based on a comparative genomic analysis and de novo RNA-sequencing transcript assemblies, we identified and cloned the sequences of the M90 gene, a conserved but highly polymorphic single-copy gene encoding a Puf family RNA-binding protein among oomycetes. After primer design and screening, three LAMP assays were developed that specifically amplified the targeted DNA sequences in P. terrestris and P. spinosum at 62°C for 70 min and in 'Ca. Pythium huanghuaiense' at 62°C for 60 min. After adding SYBR Green I, a positive yellow-green color (under natural light) or intense green fluorescence (under ultraviolet light) was observed by the naked eye only in the presence of the target species. The minimum concentration of target DNA detected in all three LAMP assays was 100 pg·μl-1. The assays also successfully detected the target Pythium spp. with high accuracy and sensitivity from inoculated soybean seedlings and soils collected from soybean fields. This study provides a method for identification and cloning of candidate detection targets without a reference genome sequence and identified M90 as a novel specific target for molecular detection of three Pythium species causing soybean root rot.
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Affiliation(s)
- Hui Feng
- Department of Plant Pathology and The Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
- The Key Laboratory of Integrated Management of Crop Diseases and Pests (Ministry of Education), Nanjing, Jiangsu 210095, China
| | - Wenwu Ye
- Department of Plant Pathology and The Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
- The Key Laboratory of Integrated Management of Crop Diseases and Pests (Ministry of Education), Nanjing, Jiangsu 210095, China
| | - Zhuoyuan Liu
- Department of Plant Pathology and The Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
- The Key Laboratory of Integrated Management of Crop Diseases and Pests (Ministry of Education), Nanjing, Jiangsu 210095, China
| | - Yang Wang
- Department of Plant Pathology and The Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
- The Key Laboratory of Integrated Management of Crop Diseases and Pests (Ministry of Education), Nanjing, Jiangsu 210095, China
| | - Jiajia Chen
- Department of Plant Pathology and The Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
- College of Landscape Architecture, Jiangsu Vocational College of Agriculture and Forestry, Zhenjiang 212400, China
| | - Yuanchao Wang
- Department of Plant Pathology and The Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
- The Key Laboratory of Integrated Management of Crop Diseases and Pests (Ministry of Education), Nanjing, Jiangsu 210095, China
| | - Xiaobo Zheng
- Department of Plant Pathology and The Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
- The Key Laboratory of Integrated Management of Crop Diseases and Pests (Ministry of Education), Nanjing, Jiangsu 210095, China
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13
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Wang T, Ji H, Yu Y, Wang X, Cheng Y, Li Z, Chen J, Guo L, Xu J, Gao C. Development of a Loop-Mediated Isothermal Amplification Method for the Rapid Detection of Phytopythium vexans. Front Microbiol 2021; 12:720485. [PMID: 34552572 PMCID: PMC8450588 DOI: 10.3389/fmicb.2021.720485] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Accepted: 08/06/2021] [Indexed: 11/13/2022] Open
Abstract
Brown root rot caused by Phytopythium vexans is a new destructive root disease on many plants such as Gingko, Citrus, kiwifruit, and ramie. The establishment of loop-mediated isothermal amplification (LAMP) technology for detecting P. vexans can help monitor and control brown root rot quickly, efficiently, and accurately. LAMP technology is known for its simplicity, sensitivity, and speed; and it does not require any specialized equipment – a water bath or a thermoblock is sufficient for isothermal amplifications. LAMP products can be visualized by using hydroxy naphthol blue (HNB) dye or agarose gel electrophoresis. In this study, by searching and comparing the internal transcribed spacer (ITS) sequences of P. vexans and the related species in oomycete genera Pythium, Phytopythium, and Phytophthora, we designed specific primers targeting the ITS gene region of P. vexans. Using HNB dye, we established a LAMP technique for rapid detection of P. vexans by visible color change. In addition, we optimized the protocol to enhance both sensitivity and specificity for P. vexans detection. Under the optimized condition, our protocol based on LAMP technology could detect as low as 24 copies of the P. vexans genomic DNA, which is ∼100 times more sensitive than conventional PCR. This method can successfully detect P. vexans using cell suspensions from P. vexans – infected ramie root tissues.
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Affiliation(s)
- Tuhong Wang
- Institute of Bast Fiber Crops and Center of Southern Economic Crops, Chinese Academy of Agricultural Sciences, Changsha, China
| | - Haojun Ji
- Institute of Bast Fiber Crops and Center of Southern Economic Crops, Chinese Academy of Agricultural Sciences, Changsha, China.,State Key Laboratory of Crop Stress Biology for Arid Areas, College of Life Sciences, Northwest A&F University, Yangling, China
| | - Yongting Yu
- Institute of Bast Fiber Crops and Center of Southern Economic Crops, Chinese Academy of Agricultural Sciences, Changsha, China
| | - Xiaojie Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Life Sciences, Northwest A&F University, Yangling, China
| | - Yi Cheng
- Institute of Bast Fiber Crops and Center of Southern Economic Crops, Chinese Academy of Agricultural Sciences, Changsha, China
| | - Zhimin Li
- Institute of Bast Fiber Crops and Center of Southern Economic Crops, Chinese Academy of Agricultural Sciences, Changsha, China
| | - Jia Chen
- Institute of Bast Fiber Crops and Center of Southern Economic Crops, Chinese Academy of Agricultural Sciences, Changsha, China
| | - Litao Guo
- Institute of Bast Fiber Crops and Center of Southern Economic Crops, Chinese Academy of Agricultural Sciences, Changsha, China
| | - Jianping Xu
- Institute of Bast Fiber Crops and Center of Southern Economic Crops, Chinese Academy of Agricultural Sciences, Changsha, China.,Department of Biology, McMaster University, Hamilton, ON, Canada
| | - Chunsheng Gao
- Institute of Bast Fiber Crops and Center of Southern Economic Crops, Chinese Academy of Agricultural Sciences, Changsha, China
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14
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Wang M, Van Vleet S, McGee R, Paulitz T, Porter L, Schroeder K, Vandemark G, Chen W. Chickpea Seed Rot and Damping-Off Caused by Metalaxyl-Resistant Pythium ultimum and Its Management with Ethaboxam. PLANT DISEASE 2021; 105:1728-1737. [PMID: 33118871 DOI: 10.1094/pdis-08-20-1659-re] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Metalaxyl and its isomer mefenoxam have been the primary fungicides used as seed treatments in managing Pythium seed rot and damping-off of chickpea (Cicer arietinum). However, outbreaks of seed rot and damping-off of metalaxyl-treated chickpea seeds were found in the dryland agriculture regions of southeastern Washington and northern Idaho. Pythium spp. isolated from rotten seeds and associated soils showed high levels of resistance to metalaxyl. Large proportions (31 to 91%) of Pythium isolates resistant to metalaxyl were detected in areas where severe chickpea damping-off occurred and were observed in commercial chickpea fields over several years. All metalaxyl-resistant (MR) isolates were identified as Pythium ultimum var. ultimum. The metalaxyl resistance trait measured by EC50 values was stable over 10 generations in the absence of metalaxyl, and no observable fitness costs were associated with metalaxyl resistance. Under controlled conditions, metalaxyl treatments failed to protect chickpea seeds from seed rot and damping-off after inoculation with MR Pythium isolates. In culture, ethaboxam inhibited mycelial growth of both MR and metalaxyl-sensitive isolates. Greenhouse and field tests showed that ethaboxam is effective in managing MR Pythium. Ethaboxam in combination with metalaxyl is commonly applied as seed treatments in commercial chickpea production.
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Affiliation(s)
- Moying Wang
- Washington State University, Pullman, WA 99164
| | | | - Rebecca McGee
- Washington State University, Pullman, WA 99164
- U.S. Department of Agriculture-Agricultural Research Service and Washington State University, Pullman, WA 99164
| | - Timothy Paulitz
- Washington State University, Pullman, WA 99164
- U.S. Department of Agriculture-Agricultural Research Service and Washington State University, Pullman, WA 99164
| | - Lyndon Porter
- Washington State University, Pullman, WA 99164
- U.S. Department of Agriculture-Agricultural Research Service and Washington State University, Prosser, WA 99350
| | | | - George Vandemark
- Washington State University, Pullman, WA 99164
- U.S. Department of Agriculture-Agricultural Research Service and Washington State University, Pullman, WA 99164
| | - Weidong Chen
- Washington State University, Pullman, WA 99164
- U.S. Department of Agriculture-Agricultural Research Service and Washington State University, Pullman, WA 99164
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15
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Arora H, Sharma A, Sharma S, Haron FF, Gafur A, Sayyed RZ, Datta R. Pythium Damping-Off and Root Rot of Capsicum annuum L.: Impacts, Diagnosis, and Management. Microorganisms 2021; 9:microorganisms9040823. [PMID: 33924471 PMCID: PMC8069622 DOI: 10.3390/microorganisms9040823] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2021] [Revised: 04/07/2021] [Accepted: 04/09/2021] [Indexed: 11/16/2022] Open
Abstract
Capsicum annuum L. is a significant horticulture crop known for its pungent varieties and used as a spice. The pungent character in the plant, known as capsaicinoid, has been discovered to have various health benefits. However, its production has been affected due to various exogenous stresses, including diseases caused by a soil-borne pathogen, Pythium spp. predominantly affecting the Capsicum plant in younger stages and causing damping-off, this pathogen can incite root rot in later plant growth stages. Due to the involvement of multiple Pythium spp. and their capability to disperse through various routes, their detection and diagnosis have become crucial. However, the quest for a point-of-care technology is still far from over. The use of an integrated approach with cultural and biological techniques for the management of Pythium spp. can be the best and most sustainable alternative to the traditionally used and hazardous chemical approach. The lack of race-specific resistance genes against Pythium spp. can be compensated with the candidate quantitative trait loci (QTL) genes in C. annuum L. This review will focus on the epidemiological factors playing a major role in disease spread, the currently available diagnostics in species identification, and the management strategies with a special emphasis on Pythium spp. causing damping-off and root rot in different cultivars of C. annuum L.
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Affiliation(s)
- Himanshu Arora
- Centre for Rural Development and Technology, Indian Institute of Technology, New Delhi 110016, India; (H.A.); (S.S.)
| | - Abhishek Sharma
- Amity Food and Agriculture Foundation, Amity University, Noida 201313, Uttar Pradesh, India
- Correspondence: (A.S.); (R.Z.S.); (R.D.)
| | - Satyawati Sharma
- Amity Food and Agriculture Foundation, Amity University, Noida 201313, Uttar Pradesh, India
| | - Farah Farhanah Haron
- Pest and Disease Management Program, Horticulture Research Center, Malaysian Agriculture Research and Development Institute (MARDI), Persiaran MARDI-UPM, Serdang 43400, Selangor, Malaysia;
| | - Abdul Gafur
- Sinarmas Forestry Corporate Research and Development, Perawang 28772, Indonesia;
| | - R. Z. Sayyed
- Department of Microbiology, PSGVP Mandal’s Arts, Science, Commerce College, Shahada 425409, Maharashtra, India
- Correspondence: (A.S.); (R.Z.S.); (R.D.)
| | - Rahul Datta
- Department of Geology and Pedology, Mendel University in Brno, 613 00 Brno-sever-Černá Pole, Czech Republic
- Correspondence: (A.S.); (R.Z.S.); (R.D.)
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16
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Fantastic Downy Mildew Pathogens and How to Find Them: Advances in Detection and Diagnostics. PLANTS 2021; 10:plants10030435. [PMID: 33668762 PMCID: PMC7996204 DOI: 10.3390/plants10030435] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 02/11/2021] [Accepted: 02/15/2021] [Indexed: 12/26/2022]
Abstract
Downy mildews affect important crops and cause severe losses in production worldwide. Accurate identification and monitoring of these plant pathogens, especially at early stages of the disease, is fundamental in achieving effective disease control. The rapid development of molecular methods for diagnosis has provided more specific, fast, reliable, sensitive, and portable alternatives for plant pathogen detection and quantification than traditional approaches. In this review, we provide information on the use of molecular markers, serological techniques, and nucleic acid amplification technologies for downy mildew diagnosis, highlighting the benefits and disadvantages of the technologies and target selection. We emphasize the importance of incorporating information on pathogen variability in virulence and fungicide resistance for disease management and how the development and application of diagnostic assays based on standard and promising technologies, including high-throughput sequencing and genomics, are revolutionizing the development of species-specific assays suitable for in-field diagnosis. Our review provides an overview of molecular detection technologies and a practical guide for selecting the best approaches for diagnosis.
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17
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Feasibility of Volatile Biomarker-Based Detection of Pythium Leak in Postharvest Stored Potato Tubers Using Field Asymmetric Ion Mobility Spectrometry. SENSORS 2020; 20:s20247350. [PMID: 33371462 PMCID: PMC7767497 DOI: 10.3390/s20247350] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Revised: 12/17/2020] [Accepted: 12/17/2020] [Indexed: 11/17/2022]
Abstract
The study evaluates the suitability of a field asymmetric ion mobility spectrometry (FAIMS) system for early detection of the Pythium leak disease in potato tubers simulating bulk storage conditions. Tubers of Ranger Russet (RR) and Russet Burbank (RB) cultivars were inoculated with Pythium ultimum, the causal agent of Pythium leak (with negative control samples as well) and placed in glass jars. The headspace in sampling jars was scanned using the FAIMS system at regular intervals (in days up to 14 and 31 days for the tubers stored at 25 °C and 4 °C, respectively) to acquire ion mobility current profiles representing the volatile organic compounds (VOCs). Principal component analysis plots revealed that VOCs ion peak profiles specific to Pythium ultimum were detected for the cultivars as early as one day after inoculation (DAI) at room temperature storage condition, while delayed detection was observed for tubers stored at 4 °C (RR: 5th DAI and RB: 10th DAI), possibly due to a slower disease progression at a lower temperature. There was also some overlap between control and inoculated samples at a lower temperature, which could be because of the limited volatile release. Additionally, data suggested that the RB cultivar might be less susceptible to Pythium ultimum under reduced temperature storage conditions. Disease symptom-specific critical compensation voltage (CV) and dispersion field (DF) from FAIMS responses were in the ranges of −0.58 to −2.97 V and 30–84% for the tubers stored at room temperature, and −0.31 to −2.97 V and 28–90% for reduced temperature, respectively. The ion current intensities at −1.31 V CV and 74% DF showed distinctive temporal progression associated with healthy control and infected tuber samples.
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18
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Van der Heyden H, Bilodeau GJ, Carisse O, Charron JB. Monitoring of Peronospora destructor Primary and Secondary Inoculum by Real-Time qPCR. PLANT DISEASE 2020; 104:3183-3191. [PMID: 33044917 DOI: 10.1094/pdis-03-20-0687-re] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Onion downy mildew (ODM), caused by Peronospora destructor, is a serious threat for onion growers worldwide. In southwestern Québec, Canada, a steady increase in occurrence of ODM has been observed since the mid-2000s. On onion, P. destructor can develop local and systemic infections producing numerous sporangia which act as initial inoculum locally and also for neighboring areas. It also produces oospores capable of surviving in soils and tissues for a prolonged period of time. A recent study showed that ODM epidemics are strongly associated with weather conditions related to production and survival of overwintering inoculum, stressing the need to understand the role of primary (initial) and secondary inoculum. However, P. destructor is an obligate biotrophic pathogen, which complicates the study of inoculum sources. This study aimed at developing a molecular assay specific to P. destructor, allowing its quantification in environmental samples. In this study, a reliable and sensitive hydrolysis probe-based assay multiplexed with an internal control was developed on the internal transcribed spacer (ITS) region to quantify soil- and airborne inoculum of P. destructor. The assay specificity was tested against 17 isolates of P. destructor obtained from different locations worldwide, other members of the order Peronosporales, and various onion pathogens. Validation with artificially inoculated soil and air samples suggested a sensitivity of less than 10 sporangia g-1 of dry soil and 1 sporangium m-3 of air. Validation with environmental air samples shows a linear relationship between microscopic and real-time quantitative PCR counts. In naturally infested soils, inoculum ranged from 0 to 162 sporangia equivalent g-1 of dry soil, which supported the hypothesis of overwintering under northern climates. This assay will be useful for primary and secondary inoculum monitoring to help characterize ODM epidemiology and could be used for daily tactical and short-term strategic decision-making.
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Affiliation(s)
- Hervé Van der Heyden
- Cie de Recherche Phytodata, 291 rue de la coopérative, Sherrington, QC, Canada
- Department of Plant Science, McGill University, Macdonald Campus, 21,111 Lakeshore Road, Ste-Anne-de-Bellevue, QC, Canada
| | | | - Odile Carisse
- Agriculture and Agri-Food Canada, 430 Boulevard Gouin, St-Jean-sur-Richelieu, QC, Canada
| | - Jean-Benoit Charron
- Department of Plant Science, McGill University, Macdonald Campus, 21,111 Lakeshore Road, Ste-Anne-de-Bellevue, QC, Canada
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19
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Toporek SM, Keinath AP. Characterization of Pythium Species Collected from a Multiple Time-Point Sampling of Cucurbits in South Carolina. PLANT DISEASE 2020; 104:2832-2842. [PMID: 32946348 DOI: 10.1094/pdis-04-20-0728-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
Species of Pythium cause root and stem rot in cucurbits, but no formal surveys have been conducted in the United States to identify which species are responsible. The cucurbit hosts bottle gourd, cucumber, Hubbard squash, and watermelon were transplanted in May, July, September, and November into sentinel plots in four and five different fields in 2017 and 2018, respectively, in South Carolina. Eight of the nine fields were replanted in March 2019. Isolates (600) were collected and identified by sequencing DNA of the mitochondrial cytochrome oxidase I region. The four most common species were P. spinosum (45.6% of all isolates), P. myriotylum (20.0%), P. irregulare (15.3%), and P. aphanidermatum (12.8%). P. myriotylum and P. aphanidermatum were predominantly isolated in May, July, and September, whereas P. spinosum and P. irregulare were predominantly isolated in November and March. Isolates of P. ultimum, P. irregulare, and P. spinosum were more virulent than isolates of P. myriotylum and P. aphanidermatum at 25°C. Representative isolates were screened in vitro for sensitivity to three fungicides: mefenoxam, propamocarb, and oxathiapiprolin. All isolates were sensitive to mefenoxam and propamocarb, but these same isolates were insensitive to oxathiapiprolin, except those classified taxonomically in Pythium clade I.
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Affiliation(s)
- Sean M Toporek
- Department of Plant and Environmental Sciences, Clemson University, Coastal Research and Education Center, Charleston, SC 29414
| | - Anthony P Keinath
- Department of Plant and Environmental Sciences, Clemson University, Coastal Research and Education Center, Charleston, SC 29414
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20
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Badali F, Abrinbana M, Abdollahzadeh J. Morphological and Molecular Taxonomy of Pythium monoclinum Abrinbana, Abdollahz. & Badali, Sp. Nov., and P. iranense, Sp. Nov., from Iran. CRYPTOGAMIE MYCOL 2020. [DOI: 10.5252/cryptogamie-mycologie2020v41a11] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Farzaneh Badali
- Department of Plant Protection, Faculty of Agriculture and Natural Resources, Urmia University, P.O. Box 165, Urmia (Iran)
| | - Masoud Abrinbana
- Department of Plant Protection, Faculty of Agriculture and Natural Resources, Urmia University, P.O. Box 165, Urmia (Iran)
| | - Jafar Abdollahzadeh
- Department of Plant Protection, Faculty of Agriculture, University of Kurdistan, P.O. Box 416, Sanandaj (Iran)
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21
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Oni FE, Geudens N, Adiobo A, Omoboye OO, Enow EA, Onyeka JT, Salami AE, De Mot R, Martins JC, Höfte M. Biosynthesis and Antimicrobial Activity of Pseudodesmin and Viscosinamide Cyclic Lipopeptides Produced by Pseudomonads Associated with the Cocoyam Rhizosphere. Microorganisms 2020; 8:microorganisms8071079. [PMID: 32698413 PMCID: PMC7409209 DOI: 10.3390/microorganisms8071079] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2020] [Revised: 07/13/2020] [Accepted: 07/15/2020] [Indexed: 01/26/2023] Open
Abstract
Pseudomonas cyclic lipopeptides (CLPs) are encoded non-ribosomally by biosynthetic gene clusters (BGCs) and possess diverse biological activities. In this study, we conducted chemical structure and BGC analyses with antimicrobial activity assays for two CLPs produced by Pseudomonas strains isolated from the cocoyam rhizosphere in Cameroon and Nigeria. LC-MS and NMR analyses showed that the Pseudomonas sp. COR52 and A2W4.9 produce pseudodesmin and viscosinamide, respectively. These CLPs belong to the Viscosin group characterized by a nonapeptidic moiety with a 7-membered macrocycle. Similar to other Viscosin-group CLPs, the initiatory non-ribosomal peptide synthetase (NRPS) gene of the viscosinamide BGC is situated remotely from the other two NRPS genes. In contrast, the pseudodesmin genes are all clustered in a single genomic locus. Nano- to micromolar levels of pseudodesmin and viscosinamide led to the hyphal distortion and/or disintegration of Rhizoctonia solani AG2-2 and Pythium myriotylum CMR1, whereas similar levels of White Line-Inducing Principle (WLIP), another member of the Viscosin group, resulted in complete lysis of both soil-borne phytopathogens. In addition to the identification of the biosynthetic genes of these two CLPs and the demonstration of their interaction with soil-borne pathogens, this study provides further insights regarding evolutionary divergence within the Viscosin group.
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Affiliation(s)
- Feyisara E. Oni
- Laboratory of Phytopathology, Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, B-9000 Ghent, Belgium; (F.E.O.); (O.O.O.); (E.A.E.)
- Unit for Environmental Sciences and Management, Faculty of Natural and Agricultural Sciences, North-West University, 2520 Potchefstroom, South Africa
| | - Niels Geudens
- NMR and Structure Analysis Unit, Department of Organic and Macromolecular Chemistry, Faculty of Science, Ghent University, Krijgslaan 281, B-9000 Gent, Belgium; (N.G.); (J.C.M.)
| | - Amayana Adiobo
- Jay PJ Biotechnology Laboratory, Institute of Agricultural Research for Development (IRAD), Ekona, P. M. B 25 Buea, Cameroon;
| | - Olumide O. Omoboye
- Laboratory of Phytopathology, Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, B-9000 Ghent, Belgium; (F.E.O.); (O.O.O.); (E.A.E.)
- Department of Microbiology, Obafemi Awolowo University, 220005 Ile-Ife, Osun State, Nigeria
| | - Elsie A. Enow
- Laboratory of Phytopathology, Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, B-9000 Ghent, Belgium; (F.E.O.); (O.O.O.); (E.A.E.)
| | - Joseph T. Onyeka
- Plant Pathology Unit, National Root Crops Research Institute (NRCRI), 440001 Umudike, Abia State, Nigeria;
| | - Ayodeji E. Salami
- Faculty of Agriculture, Department of Crop, Horticulture and Landscape Design, Ekiti State University (EKSU), 360211 Ado-Ekiti, Nigeria;
| | - René De Mot
- Centre of Microbial and Plant Genetics, Faculty of Bioscience Engineering, KU Leuven, 3001 Heverlee, Belgium;
| | - José C. Martins
- NMR and Structure Analysis Unit, Department of Organic and Macromolecular Chemistry, Faculty of Science, Ghent University, Krijgslaan 281, B-9000 Gent, Belgium; (N.G.); (J.C.M.)
| | - Monica Höfte
- Laboratory of Phytopathology, Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, B-9000 Ghent, Belgium; (F.E.O.); (O.O.O.); (E.A.E.)
- Correspondence: ; Tel.: +32-9-264-6017
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Wang T, Gao C, Cheng Y, Li Z, Chen J, Guo L, Xu J. Molecular Diagnostics and Detection of Oomycetes on Fiber Crops. PLANTS (BASEL, SWITZERLAND) 2020; 9:E769. [PMID: 32575466 PMCID: PMC7355704 DOI: 10.3390/plants9060769] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 06/12/2020] [Accepted: 06/15/2020] [Indexed: 11/16/2022]
Abstract
Fiber crops are an important group of economic plants. Traditionally cultivated for fiber, fiber crops have also become sources of other materials such as food, animal feed, cosmetics and medicine. Asia and America are the two main production areas of fiber crops in the world. However, oomycete diseases have become an important factor limiting their yield and quality, causing devastating consequences for the production of fiber crops in many regions. To effectively control oomycete pathogens and reduce their negative impacts on these crops, it is very important to have fast and accurate detection systems, especially in the early stages of infection. With the rapid development of molecular biology, the diagnosis of plant pathogens has progressed from relying on traditional morphological features to the increasing use of molecular methods. The objective of this paper was to review the current status of research on molecular diagnosis of oomycete pathogens on fiber crops. Our search of PubMed identified nearly 30 species or subspecies of oomycetes on fiber crops, among which the top three species were Phytophthora boehmeriae, Phytophthora nicotianae and Pythium ultimum. The gene regions that have been used for molecular identifications of these pathogens include the internal transcribed spacer (ITS) regions of the nuclear ribosomal RNA gene cluster, and genes coding for translation elongation factor 1α (EF-1α) and mitochondrial cytochrome c oxidase subunits I and II (Cox 1, Cox 2), etc. We summarize the molecular assays that have been used to identify these pathogens and discuss potential areas of future development for fast, specific, and accurate diagnosis of oomycetes on fiber crops.
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Affiliation(s)
- Tuhong Wang
- Institute of Bast Fiber Crops and Center of Southern Economic Crops, Chinese Academy of Agricultural Sciences, Changsha 410205, China; (T.W.); (C.G.); (Y.C.); (Z.L.); (J.C.); (L.G.)
| | - Chunsheng Gao
- Institute of Bast Fiber Crops and Center of Southern Economic Crops, Chinese Academy of Agricultural Sciences, Changsha 410205, China; (T.W.); (C.G.); (Y.C.); (Z.L.); (J.C.); (L.G.)
| | - Yi Cheng
- Institute of Bast Fiber Crops and Center of Southern Economic Crops, Chinese Academy of Agricultural Sciences, Changsha 410205, China; (T.W.); (C.G.); (Y.C.); (Z.L.); (J.C.); (L.G.)
| | - Zhimin Li
- Institute of Bast Fiber Crops and Center of Southern Economic Crops, Chinese Academy of Agricultural Sciences, Changsha 410205, China; (T.W.); (C.G.); (Y.C.); (Z.L.); (J.C.); (L.G.)
| | - Jia Chen
- Institute of Bast Fiber Crops and Center of Southern Economic Crops, Chinese Academy of Agricultural Sciences, Changsha 410205, China; (T.W.); (C.G.); (Y.C.); (Z.L.); (J.C.); (L.G.)
| | - Litao Guo
- Institute of Bast Fiber Crops and Center of Southern Economic Crops, Chinese Academy of Agricultural Sciences, Changsha 410205, China; (T.W.); (C.G.); (Y.C.); (Z.L.); (J.C.); (L.G.)
| | - Jianping Xu
- Institute of Bast Fiber Crops and Center of Southern Economic Crops, Chinese Academy of Agricultural Sciences, Changsha 410205, China; (T.W.); (C.G.); (Y.C.); (Z.L.); (J.C.); (L.G.)
- Department of Biology, McMaster University, Hamilton, ON L8S 4K1, Canada
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23
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Scott K, Eyre M, McDuffee D, Dorrance AE. The Efficacy of Ethaboxam as a Soybean Seed Treatment Toward Phytophthora, Phytopythium, and Pythium in Ohio. PLANT DISEASE 2020; 104:1421-1432. [PMID: 32191161 DOI: 10.1094/pdis-09-19-1818-re] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Phytophthora, Phytopythium, and Pythium species that cause early-season seed decay and pre-emergence and post-emergence damping off of soybean are most commonly managed with seed treatments. The phenylamide fungicides metalaxyl and mefenoxam, and ethaboxam are effective toward some but not all species. The primary objective of this study was to evaluate the efficacy of ethaboxam in fungicide mixtures and compare those with other fungicides as seed treatments to protect soybean against Pythium, Phytopythium, and Phytophthora species in both high-disease field environments and laboratory seed plate assays. The second objective was to evaluate these seed treatment mixtures on cultivars that have varying levels and combinations of resistance to these soilborne pathogens. Five of eight environments received adequate precipitation in the 14 days after planting for high levels of seedling disease development and treatment evaluations. Three environments had significantly greater stands, and three had significantly greater yield when ethaboxam was used in the seed treatment mixture compared with treatments containing metalaxyl or mefenoxam alone. Three fungicide formulations significantly reduced disease severity compared with nontreated in the seed plate assay for 17 species. However, the combination of ethaboxam plus metalaxyl in a mixture was more effective than either fungicide alone against some Pythium and Phytopythium species. Overall, our results indicate that the addition of ethaboxam to a fungicide seed treatment is effective in reducing seed rot caused by these pathogens commonly isolated from soybean in Ohio but that these effects can be masked when cultivars with resistance are planted.
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Affiliation(s)
- Kelsey Scott
- Department of Plant Pathology, The Ohio State University, Wooster, OH 44691
| | - Meredith Eyre
- Department of Plant Pathology, The Ohio State University, Wooster, OH 44691
| | | | - Anne E Dorrance
- Department of Plant Pathology, The Ohio State University, Wooster, OH 44691
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Inderbitzin P, Robbertse B, Schoch CL. Species Identification in Plant-Associated Prokaryotes and Fungi Using DNA. PHYTOBIOMES JOURNAL 2020; 4:103-114. [PMID: 35265781 PMCID: PMC8903201 DOI: 10.1094/pbiomes-12-19-0067-rvw] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Species names are fundamental to managing biological information. The surge of interest in microbial diversity has resulted in an increase in the number of microbes that need to be identified and assigned a species name. This article provides an introduction to the principles of DNA-based identification of Archaea and Bacteria traditionally known as prokaryotes, and Fungi, the Oomycetes and other protists, collectively referred to as fungi. The prokaryotes and fungi are the most commonly studied microbes from plants, and we introduce the most relevant concepts of prokaryote and fungal taxonomy and nomenclature. We first explain how prokaryote and fungal species are defined, delimited, and named, and then summarize the criteria and methods used to identify prokaryote and fungal organisms to species.
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Affiliation(s)
| | - Barbara Robbertse
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 45 Center Drive, Bethesda, MD 20892
| | - Conrad L. Schoch
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 45 Center Drive, Bethesda, MD 20892
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Philosoph AM, Dombrovsky A, Elad Y, Koren A, Frenkel O. Insight Into Late Wilting Disease of Cucumber Demonstrates the Complexity of the Phenomenon in Fluctuating Environments. PLANT DISEASE 2019; 103:2877-2883. [PMID: 31490089 DOI: 10.1094/pdis-12-18-2141-re] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Some diseases are caused by coinfection of several pathogens in the same plant. However, studies on the complexity of these coinfection events under different environmental conditions are scarce. Our ongoing research involves late wilting disease of cucumber caused by coinfection of Cucumber green mottle mosaic virus (CGMMV) and Pythium spp. We specifically investigated the role of various temperatures (18, 25, 32°C) on the coinfection by CGMMV and two predominant Pythium species occurring in cucumber greenhouses under Middle Eastern climatic conditions. During the summer months, Pythium aphanidermatum was most common, whereas P. spinosum predominated during the winter-spring period. P. aphanidermatum preferred higher temperatures while P. spinosum preferred low temperatures and caused very low levels of disease at 32°C when the 6-day-old seedlings were infected with P. spinosum alone. Nevertheless, after applying a later coinfection with CGMMV on the 14-day-old plants, a synergistic effect was detected for both Pythium species at optimal and suboptimal temperatures, with P. spinosum causing high mortality incidence even at 32°C. The symptoms caused by CGMMV infection appeared earlier as the temperature increased. However, within each temperature, no significant influence of the combined infection was detected. Our results demonstrate the complexity of coinfection in changing environmental conditions and indicate its involvement in disease development and severity as compared with infection by each of the pathogens alone.
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Affiliation(s)
- Amit M Philosoph
- Department of Plant Pathology and Weed Sciences, Agricultural Research Organization, The Volcani Center, Rishon Lezion 7528809, Israel
- The Robert H. Smith Faculty of Agriculture, Food and Environment, The Levi Eshkol School of Agriculture, The Hebrew University of Jerusalem, Rehovot 761001, Israel
| | - Aviv Dombrovsky
- Department of Plant Pathology and Weed Sciences, Agricultural Research Organization, The Volcani Center, Rishon Lezion 7528809, Israel
| | - Yigal Elad
- Department of Plant Pathology and Weed Sciences, Agricultural Research Organization, The Volcani Center, Rishon Lezion 7528809, Israel
| | | | - Omer Frenkel
- Department of Plant Pathology and Weed Sciences, Agricultural Research Organization, The Volcani Center, Rishon Lezion 7528809, Israel
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Del Castillo Múnera J, Quesada-Ocampo LM, Rojas A, Chilvers MI, Hausbeck MK. Population Structure of Pythium ultimum from Greenhouse Floral Crops in Michigan. PLANT DISEASE 2019; 103:859-867. [PMID: 30908944 DOI: 10.1094/pdis-03-18-0394-re] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Pythium ultimum causes seedling damping-off and root and crown rot in greenhouse ornamental plants. To understand the population dynamics and assess population structure of P. ultimum in Michigan floriculture crops, simple sequence repeats (SSRs) were developed using the previously published P. ultimum predicted transcriptome. A total of 166 isolates sampled from 2011 to 2013 from five, one, and three greenhouses in Kalamazoo, Kent, and Wayne Counties, respectively, were analyzed using six polymorphic and fluorescently labeled SSR markers. The average unbiased Simpson's index (λu, 0.95), evenness (E5, 0.56), and recovery of 12 major clones out of the 65 multilocus genotypes obtained, suggests that P. ultimum is not a recent introduction into Michigan greenhouses. Analyses revealed a clonal population, with limited differentiation among seasons, hosts, and counties sampled. Results also indicated the presence of common genotypes among years, suggesting that sanitation measures should be enhanced to eradicate resident P. ultimum populations. Finally, the presence of common genotypes among counties suggests that there is an exchange of infected plant material among greenhouse facilities, or that there is a common source of inoculum coming to the region. Continued monitoring of pathogen populations will enhance our understanding of population dynamics of P. ultimum in Michigan and facilitate improvement of control strategies.
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Affiliation(s)
| | | | - Alejandro Rojas
- 3 Department of Plant Pathology, University of Arkansas, Fayetteville, AR 72701
| | - Martin I Chilvers
- 4 Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, 48824
| | - Mary K Hausbeck
- 4 Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, 48824
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27
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Molecular identification of oomycete species affecting aquaculture in Bangladesh. AQUACULTURE AND FISHERIES 2019. [DOI: 10.1016/j.aaf.2018.12.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Van der Heyden H, Wallon T, Lévesque CA, Carisse O. Detection and Quantification of Pythium tracheiphilum in Soil by Multiplex Real-Time qPCR. PLANT DISEASE 2019; 103:475-483. [PMID: 30657427 DOI: 10.1094/pdis-03-18-0419-re] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
In Canada, head lettuce (Lactuca sativa capitata) is extensively produced in the muck soils of southwestern Québec. However, yields are increasingly affected by various soilborne pathogens, including Pythium spp., which cause wilt and damping off. In a survey conducted in Québec muck soils in 2010 and 2011, Pythium tracheiphilum Matta was identified as the predominant Pythium sp. in the root of head lettuce showing Pythium stunt symptoms. Therefore, to improve risk assessment and help further understanding of disease epidemiology, a specific and sensitive real-time quantitative polymerase chain reaction (qPCR) assay based on TaqMan-minor groove binder (MGB) technology was developed for P. tracheiphilum. The PCR primers along with a TaqMan-MGB probe were designed from the ribosomal internal transcribed spacer 2 region. A 100-bp product was amplified by PCR from all P. tracheiphilum isolates tested while no PCR product was obtained from 38 other Pythium spp. or from a selection of additional lettuce pathogens tested. In addition to P. tracheiphilum, the assay was multiplexed with an internal control allowing for the individual validation of each PCR. In artificially infested soils, the sensitivity of the qPCR assay was established as 10 oospores/g of dry soil. P. tracheiphilum was not detected in soils in which lettuce has never been grown; however, inoculum ranged from 0 to more than 200,000 oospores/g of dry soil in commercial lettuce fields. Also, disease incidence was positively correlated with inoculum concentration (r = 0.764). The results suggest that inoculum concentration should be considered when making Pythium stunt management decisions. The developed qPCR assay will facilitate reliable detection and quantification of P. tracheiphilum from field soil.
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Affiliation(s)
| | - Thérèse Wallon
- 1 Compagnie de recherche Phytodata, Sherrington, QC J0L 2N0, Canada
| | - C André Lévesque
- 2 Ottawa Research and Development Research Centre, Agriculture and Agri-Food Canada, Ottawa, ON K1A 0C6, Canada; and
| | - Odile Carisse
- 3 Saint-Jean-sur-Richelieu Research and Development Centre, Agriculture and Agri-Food Canada, Saint-Jean-sur-Richelieu, QC J3B 3E6, Canada
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Matić S, Gilardi G, Gisi U, Gullino ML, Garibaldi A. Differentiation of Pythium spp. from vegetable crops with molecular markers and sensitivity to azoxystrobin and mefenoxam. PEST MANAGEMENT SCIENCE 2019; 75:356-365. [PMID: 29888848 DOI: 10.1002/ps.5119] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2018] [Revised: 05/11/2018] [Accepted: 06/01/2018] [Indexed: 06/08/2023]
Abstract
BACKGROUND Pythium species attack various vegetable crops causing seed, stem and root rot, and 'damping-off' after germination. Pythium diseases are prevalently controlled by two classes of fungicides, QoIs with azoxystrobin and phenlyamides with mefenoxam as representatives. The present study aimed to test the sensitivity of six Pythium species from different vegetable crops to azoxystrobin and mefenoxam and differentiating species based on ITS, cytochrome b and RNA polymerase I gene sequences. RESULTS The inter- and intra-species sensitivity to azoxystrobin was found to be stable, with the exception of one Pythium paroecandrum isolate, which showed reduced sensitivity and two cytochrome b amino acid changes. For mefenoxam, the inter-species sensitivity was quite variable and many resistant isolates were found in all six Pythium species, but no RNA polymerase I amino acid changes were observed in them. ITS and cytochrome b phylogenetic analyses permitted a clear separation of Pythium species corresponding to globose- and filamentous-sporangia clusters. CONCLUSION The results document the necessity of well-defined chemical control strategies adapted to different Pythium species. Since the intrinsic activity of azoxystrobin among species was stable and no resistant isolates were found, it may be applied without species differentiation, provided it is used preventatively to also control highly aggressive isolates. For a reliable use of mefenoxam, precise identification and sensitivity tests of Pythium species are crucial because its intrinsic activity is variable and resistant isolates may exist. Appropriate mixtures and/or alternation of products may help to further delay resistance development. © 2018 Society of Chemical Industry.
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Affiliation(s)
- Slavica Matić
- AGROINNOVA - Centre of Competence for the Innovation in the Agro-environmental Sector, Università di Torino, Grugliasco (TO), Italy
| | - Giovanna Gilardi
- AGROINNOVA - Centre of Competence for the Innovation in the Agro-environmental Sector, Università di Torino, Grugliasco (TO), Italy
| | - Ulrich Gisi
- AGROINNOVA - Centre of Competence for the Innovation in the Agro-environmental Sector, Università di Torino, Grugliasco (TO), Italy
| | - Maria Lodovica Gullino
- AGROINNOVA - Centre of Competence for the Innovation in the Agro-environmental Sector, Università di Torino, Grugliasco (TO), Italy
- Department of Agricultural, Forestry and Food Sciences (DISAFA), Università di Torino, Grugliasco (TO), Italy
| | - Angelo Garibaldi
- AGROINNOVA - Centre of Competence for the Innovation in the Agro-environmental Sector, Università di Torino, Grugliasco (TO), Italy
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Geisen S, Mitchell EAD, Adl S, Bonkowski M, Dunthorn M, Ekelund F, Fernández LD, Jousset A, Krashevska V, Singer D, Spiegel FW, Walochnik J, Lara E. Soil protists: a fertile frontier in soil biology research. FEMS Microbiol Rev 2018; 42:293-323. [DOI: 10.1093/femsre/fuy006] [Citation(s) in RCA: 212] [Impact Index Per Article: 35.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2017] [Accepted: 02/12/2018] [Indexed: 12/27/2022] Open
Affiliation(s)
- Stefan Geisen
- Department of Terrestrial Ecology, Netherlands Institute of Ecology, 6708 PB Wageningen, The Netherlands
- Laboratory of Nematology, Wageningen University, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
| | - Edward A D Mitchell
- Laboratory of Soil Biodiversity, University of Neuchâtel, Rue Emile-Argand 11, Neuchâtel 2000, Switzerland
- Jardin Botanique de Neuchâtel, Chemin du Perthuis-du-Sault 58, Neuchâtel 2000, Switzerland
| | - Sina Adl
- Department of Soil Sciences, College of Agriculture and Bioresources, University of Saskatchewan, 51 Campus Drive, Saskatoon, Canada
| | - Michael Bonkowski
- Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne, Institute of Zoology, Terrestrial Ecology, Zülpicher Straße 47b, 50674 Köln, Germany
| | - Micah Dunthorn
- Department of Ecology, University of Kaiserslautern, Erwin-Schrödinger Straße, 67663 Kaiserslautern, Germany
| | - Flemming Ekelund
- Department of Biology, University of Copenhagen, Universitetsparken 15, 2100 Copenhagen, Denmark
| | - Leonardo D Fernández
- Centro de Investigación en Recursos Naturales y Sustentabilidad (CIRENYS), Universidad Bernardo O’Higgins, Avenida Viel 1497, Santiago, Chile
| | - Alexandre Jousset
- Department of Ecology and Biodiversity, Utrecht University, 3584 CH Utrecht, The Netherlands
| | - Valentyna Krashevska
- University of Göttingen, J.F. Blumenbach Institute of Zoology and Anthropology, Untere Karspüle 2, 37073 Göttingen, Germany
| | - David Singer
- Laboratory of Soil Biodiversity, University of Neuchâtel, Rue Emile-Argand 11, Neuchâtel 2000, Switzerland
| | - Frederick W Spiegel
- Department of Biological Sciences, University of Arkansas, Fayetteville, AR, 72701, United States of America
| | - Julia Walochnik
- Molecular Parasitology, Institute of Tropical Medicine, Medical University, 1090 Vienna, Austria
| | - Enrique Lara
- Laboratory of Soil Biodiversity, University of Neuchâtel, Rue Emile-Argand 11, Neuchâtel 2000, Switzerland
- Real Jardín Botánico, CSIC, Plaza de Murillo 2, 28014 Madrid, Spain
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Crandall SG, Rahman A, Quesada-Ocampo LM, Martin FN, Bilodeau GJ, Miles TD. Advances in Diagnostics of Downy Mildews: Lessons Learned from Other Oomycetes and Future Challenges. PLANT DISEASE 2018; 102:265-275. [PMID: 30673522 DOI: 10.1094/pdis-09-17-1455-fe] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Downy mildews are plant pathogens that damage crop quality and yield worldwide. Among the most severe and notorious crop epidemics of downy mildew occurred on grapes in the mid-1880s, which almost destroyed the wine industry in France. Since then, there have been multiple outbreaks on sorghum and millet in Africa, tobacco in Europe, and recent widespread epidemics on lettuce, basil, cucurbits, and spinach throughout North America. In the mid-1970s, loss of corn to downy mildew in the Philippines was estimated at US$23 million. Today, crops that are susceptible to downy mildews are worth at least $7.5 billion of the United States' economy. Although downy mildews cause devastating economic losses in the United States and globally, this pathogen group remains understudied because they are difficult to culture and accurately identify. Early detection of downy mildews in the environment is critical to establish pathogen presence and identity, determine fungicide resistance, and understand how pathogen populations disperse. Knowing when and where pathogens emerge is also important for identifying critical control points to restrict movement and to contain populations. Reducing the spread of pathogens also decreases the likelihood of sexual recombination events and discourages the emergence of novel virulent strains. A major challenge in detecting downy mildews is that they are obligate pathogens and thus cannot be cultured in artificial media to identify and maintain specimens. However, advances in molecular detection techniques hold promise for rapid and in some cases, relatively inexpensive diagnosis. In this article, we discuss recent advances in diagnostic tools that can be used to detect downy mildews. First, we briefly describe downy mildew taxonomy and genetic loci used for detection. Next, we review issues encountered when identifying loci and compare various traditional and novel platforms for diagnostics. We discuss diagnosis of downy mildew traits and issues to consider when detecting this group of organisms in different environments. We conclude with challenges and future directions for successful downy mildew detection.
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Affiliation(s)
- Sharifa G Crandall
- California State University Monterey Bay, School of Natural Sciences, Seaside, CA, 93955
| | - Alamgir Rahman
- North Carolina State University, Department of Plant Pathology, Raleigh, NC, 27695
| | | | - Frank N Martin
- USDA-ARS, Crop Improvement and Protection Research Unit, Salinas, CA, 93905
| | | | - Timothy D Miles
- California State University Monterey Bay, School of Natural Sciences, Seaside, CA, 93955
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Sapp M, Ploch S, Fiore-Donno AM, Bonkowski M, Rose LE. Protists are an integral part of the Arabidopsis thaliana
microbiome. Environ Microbiol 2017; 20:30-43. [DOI: 10.1111/1462-2920.13941] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2017] [Revised: 09/19/2017] [Accepted: 09/21/2017] [Indexed: 11/29/2022]
Affiliation(s)
- Melanie Sapp
- Institute of Population Genetics, Universitätstrasse 1; Cluster of Excellence on Plant Sciences (CEPLAS), Heinrich Heine University; Universitätstrasse 40225 Düsseldorf Germany
- Institute of Zoology, Department of Terrestrial Ecology, Zülpicher Str 47b; Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne; Zülpicher Strasse 50674 Köln Germany
| | - Sebastian Ploch
- Institute of Population Genetics, Universitätstrasse 1; Cluster of Excellence on Plant Sciences (CEPLAS), Heinrich Heine University; Universitätstrasse 40225 Düsseldorf Germany
- Biodiversity and Climate Research Centre, Senckenberg Gesellschaft für Naturforschung, Senckenberganlage 25; 60325 Frankfurt am Main Germany
| | - Anna M. Fiore-Donno
- Institute of Zoology, Department of Terrestrial Ecology, Zülpicher Str 47b; Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne; Zülpicher Strasse 50674 Köln Germany
| | - Michael Bonkowski
- Institute of Zoology, Department of Terrestrial Ecology, Zülpicher Str 47b; Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne; Zülpicher Strasse 50674 Köln Germany
| | - Laura E. Rose
- Institute of Population Genetics, Universitätstrasse 1; Cluster of Excellence on Plant Sciences (CEPLAS), Heinrich Heine University; Universitätstrasse 40225 Düsseldorf Germany
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Berg LE, Miller SS, Dornbusch MR, Samac DA. Seed Rot and Damping-off of Alfalfa in Minnesota Caused by Pythium and Fusarium Species. PLANT DISEASE 2017; 101:1860-1867. [PMID: 30677318 DOI: 10.1094/pdis-02-17-0185-re] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Globally, 15 Pythium species have been found to cause damping-off and seed rot of alfalfa, although surveys of species causing disease on alfalfa in the midwestern United States are lacking. Pathogens were isolated by a seedling baiting technique from soil samples of five alfalfa fields in Minnesota with high levels of damping-off. Of the 149 organisms isolated, 93 (62%) were identified as Pythium spp. and 43 (29%) were identified as Fusarium species. Pythium sylvaticum, P. irregulare, and P. ultimum var. ultimum were aggressive pathogens on germinating alfalfa seedlings. Strains of seven Pythium spp. pathogenic on soybean and corn were also pathogenic on alfalfa. The majority of the Fusarium isolates were identified as F. solani and F. oxysporum with a low number of F. redolens and F. incarnatum-equiseti. The F. oxysporum and F. incarnatum-equiseti strains were the most aggressive in causing seed and root rot. Pythium strains were sensitive to Apron XL (mefenoxam) and pyraclostrobin in vitro but efficacy varied when the fungicides were applied as a seed treatment. Seed treatments with Apron XL were more effective than treatments with Stamina against Pythium. The presence of aggressive, broad-host-range pathogens causing seed rot and damping-off suggests that new strategies are needed for managing this disease in alfalfa production systems.
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Affiliation(s)
- Laurine E Berg
- College of Biological Sciences, University of Minnesota, St. Paul 55108
| | - Susan S Miller
- United States Department of Agriculture-Agricultural Research Service, Plant Science Research Unit, St. Paul, MN 55108
| | - Melinda R Dornbusch
- United States Department of Agriculture-Agricultural Research Service, Plant Science Research Unit, St. Paul, MN 55108
| | - Deborah A Samac
- United States Department of Agriculture-Agricultural Research Service, Plant Science Research Unit, and Department of Plant Pathology, University of Minnesota, St. Paul 55108
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Rossman DR, Rojas A, Jacobs JL, Mukankusi C, Kelly JD, Chilvers MI. Pathogenicity and Virulence of Soilborne Oomycetes on Phaseolus vulgaris. PLANT DISEASE 2017; 101:1851-1859. [PMID: 30677317 DOI: 10.1094/pdis-02-17-0178-re] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Dry bean (Phaseolus vulgaris L.) is a globally important leguminous food crop. Yields can be reduced by high incidence of soilborne oomycetes that cause seedling disease. Breeders have attempted to develop Pythium root rot-resistant bean varieties; however, relationships between dry bean and most soilborne oomycete species remain uncharacterized. Oomycete species (n = 28), including Pythium spp. and Phytopythium spp., were tested in a growth chamber seedling assay at 20°C and an in vitro seed assay at 20°C and 26°C to evaluate their pathogenicity and virulence on 'Red Hawk' dark red kidney bean and 'Zorro' black bean. Root size or disease severity was significantly impacted by 14 oomycete species, though results varied by bean variety, temperature, and assay. Of these 14 pathogenic oomycete species, 11 species exhibited significant differences in DSI due to temperature on at least one bean variety. Pythium aphanidermatum, P. myriotylum, P. ultimum, P. ultimum var. sporangiiferium, and P. ultimum var. ultimum were the most virulent species in both assays, causing seed rot and pre-emergence damping-off of dry bean. Oomycete species were clustered into three groups based on symptom development: seed rot pathogens, root rot pathogens, or nonpathogens. Intraspecific variability in virulence was observed for eight of the 14 pathogenic oomycete species. Improved understanding of Pythium and Phytopythium interactions with dry bean may enable breeders and pathologists to more effectively evaluate strategies for oomycete seedling disease management.
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Affiliation(s)
- D R Rossman
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing
| | - A Rojas
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing
| | - J L Jacobs
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing
| | - C Mukankusi
- International Center for Tropical Agriculture, Kawanda Agricultural Research Institute, Kampala, Uganda
| | - J D Kelly
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing
| | - M I Chilvers
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing
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Xiong W, Jousset A, Guo S, Karlsson I, Zhao Q, Wu H, Kowalchuk GA, Shen Q, Li R, Geisen S. Soil protist communities form a dynamic hub in the soil microbiome. ISME JOURNAL 2017; 12:634-638. [PMID: 29028001 PMCID: PMC5776453 DOI: 10.1038/ismej.2017.171] [Citation(s) in RCA: 88] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Revised: 08/28/2017] [Accepted: 09/05/2017] [Indexed: 11/09/2022]
Abstract
Soil microbes are essential for soil fertility. However, most studies focus on bacterial and/or fungal communities, while the top-down drivers of this microbiome composition, protists, remain poorly understood. Here, we investigated how soil amendments affect protist communities and inferred potential interactions with bacteria and fungi. Specific fertilization treatments impacted both the structure and function of protist communities. Organic fertilizer amendment strongly reduced the relative abundance of plant pathogenic protists and increased bacterivorous and omnivorous protists. The addition of individual biocontrol bacteria and fungi further altered the soil protist community composition, and eventually function. Network analysis integrating protist, bacterial and fungal community data, placed protists as a central hub in the soil microbiome, linking diverse bacterial and fungal populations. Given their dynamic response to soil management practices and key position in linking soil microbial networks, protists may provide the leverage between soil management and the enhancement of bacterial and fungal microbiota at the service of improved soil health.
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Affiliation(s)
- Wu Xiong
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic-based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, China.,Ecology and Biodiversity Group, Department of Biology, Institute of Environmental Biology, Utrecht University, Utrecht, Netherlands.,Spice and Beverage Research Institute, Chinese Academy of Tropical Agricultural Science, Wanning, Hainan, China
| | - Alexandre Jousset
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic-based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, China.,Ecology and Biodiversity Group, Department of Biology, Institute of Environmental Biology, Utrecht University, Utrecht, Netherlands
| | - Sai Guo
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic-based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, China
| | - Ida Karlsson
- Ecology and Biodiversity Group, Department of Biology, Institute of Environmental Biology, Utrecht University, Utrecht, Netherlands.,Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Qingyun Zhao
- Spice and Beverage Research Institute, Chinese Academy of Tropical Agricultural Science, Wanning, Hainan, China
| | - Huasong Wu
- Spice and Beverage Research Institute, Chinese Academy of Tropical Agricultural Science, Wanning, Hainan, China
| | - George A Kowalchuk
- Ecology and Biodiversity Group, Department of Biology, Institute of Environmental Biology, Utrecht University, Utrecht, Netherlands
| | - Qirong Shen
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic-based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, China
| | - Rong Li
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic-based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, China
| | - Stefan Geisen
- Department of Terrestrial Ecology, Netherlands Institute for Ecology (NIOO-KNAW), Wageningen, Netherlands.,Laboratory of Nematology, Wageningen University, Wageningen, Netherlands
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36
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Bennett RM, de Cock AWAM, Lévesque CA, Thines M. Calycofera gen. nov., an estuarine sister taxon to Phytopythium, Peronosporaceae. Mycol Prog 2017. [DOI: 10.1007/s11557-017-1326-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
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Miles TD, Martin FN, Robideau GP, Bilodeau GJ, Coffey MD. Systematic Development of Phytophthora Species-Specific Mitochondrial Diagnostic Markers for Economically Important Members of the Genus. PLANT DISEASE 2017; 101:1162-1170. [PMID: 30682972 DOI: 10.1094/pdis-09-16-1224-re] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
The genus Phytophthora contains many invasive species to the U.S.A. that have the potential to cause significant damage to agriculture and native ecosystems. A genus and species-specific diagnostic assay was previously reported based on mitochondrial gene order differences that allowed for the systematic development of 14 species-specific TaqMan probes for pathogen detection ( Bilodeau et al. 2014 ). In this study, an additional 32 species-specific TaqMan probes for detection of primarily invasive species have been validated against 145 Phytophthora taxa as well as a range of Pythium and plant DNA samples. All validated probes were found to be species-specific and could be multiplexed with a genus-specific probe. The lower limit of linear detection using purified genomic DNA ranged from 1 to 100 fg in all assays. In addition, 124 unique TaqMan probes for Phytophthora spp. developed in silico are presented, which, if testing confirms they are species-specific, will provide diagnostic capabilities for approximately 89% of the genus. To enhance sensitivity of detection for several species that contained a single nucleotide polymorphism (SNP) in the reverse primer, a second primer was developed that is added in a small amount to the master mix. Furthermore, a PCR-RFLP system was developed that could be used to identify individual species when multiple species are present in a sample, without requiring cloning or sequencing. Several experiments were also conducted to compare various qPCR thermal cyclers and independent validation experiments with another research laboratory to identify possible limitations when the assays are used on a range of equipment in different labs. This system represents a comprehensive, hierarchal approach to increase the detection capability and provide tools to help prevent the introduction of invasive Phytophthora species.
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Affiliation(s)
- Timothy D Miles
- School of Natural Sciences, California State University Monterey Bay, Seaside, CA
| | - Frank N Martin
- Crop Improvement and Protection Research Unit, USDA-ARS, Salinas, CA
| | | | | | - Michael D Coffey
- Department of Plant Pathology and Microbiology, University of California, Riverside
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Rojas JA, Jacobs JL, Napieralski S, Karaj B, Bradley CA, Chase T, Esker PD, Giesler LJ, Jardine DJ, Malvick DK, Markell SG, Nelson BD, Robertson AE, Rupe JC, Smith DL, Sweets LE, Tenuta AU, Wise KA, Chilvers MI. Oomycete Species Associated with Soybean Seedlings in North America-Part II: Diversity and Ecology in Relation to Environmental and Edaphic Factors. PHYTOPATHOLOGY 2017; 107:293-304. [PMID: 27841963 DOI: 10.1094/phyto-04-16-0176-r] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Soybean (Glycine max (L.) Merr.) is produced across a vast swath of North America, with the greatest concentration in the Midwest. Root rot diseases and damping-off are a major concern for production, and the primary causal agents include oomycetes and fungi. In this study, we focused on examination of oomycete species distribution in this soybean production system and how environmental and soil (edaphic) factors correlate with oomycete community composition at early plant growth stages. Using a culture-based approach, 3,418 oomycete isolates were collected from 11 major soybean-producing states and most were identified to genus and species using the internal transcribed spacer region of the ribosomal DNA. Pythium was the predominant genus isolated and investigated in this study. An ecology approach was taken to understand the diversity and distribution of oomycete species across geographical locations of soybean production. Metadata associated with field sample locations were collected using geographical information systems. Operational taxonomic units (OTU) were used in this study to investigate diversity by location, with OTU being defined as isolate sequences with 97% identity to one another. The mean number of OTU ranged from 2.5 to 14 per field at the state level. Most OTU in this study, classified as Pythium clades, were present in each field in every state; however, major differences were observed in the relative abundance of each clade, which resulted in clustering of states in close proximity. Because there was similar community composition (presence or absence) but differences in OTU abundance by state, the ordination analysis did not show strong patterns of aggregation. Incorporation of 37 environmental and edaphic factors using vector-fitting and Mantel tests identified 15 factors that correlate with the community composition in this survey. Further investigation using redundancy analysis identified latitude, longitude, precipitation, and temperature as factors that contribute to the variability observed in community composition. Soil parameters such as clay content and electrical conductivity also affected distribution of oomycete species. The present study suggests that oomycete species composition across geographical locations of soybean production is affected by a combination of environmental and edaphic conditions. This knowledge provides the basis to understand the ecology and distribution of oomycete species, especially those able to cause diseases in soybean, providing cues to develop management strategies.
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Affiliation(s)
- J Alejandro Rojas
- First, second, third, fourth, and nineteenth authors: Department of Plant, Soil and Microbial Sciences, and first and nineteenth authors: Program in Ecology, Evolutionary Biology and Behavior, Michigan State University, East Lansing 48824; fifth author; Department of Crop Sciences, University of Illinois, Urbana 61801; sixth author: Department of Plant Science, South Dakota State University, Brookings 57007; seventh and fifteenth authors: Department of Plant Pathology, University of Wisconsin-Madison 53706; eighth author: Department of Plant Pathology, University of Nebraska-Lincoln 68583; ninth author: Department of Plant Pathology, Kansas State University, Manhattan 66506; tenth author: Department of Plant Pathology, University of Minnesota, St. Paul 55108; eleventh and twelfth authors: Department of Plant Pathology, North Dakota State University, Fargo 58105; thirteenth author: Department of Plant Pathology and Microbiology, Iowa State University, Ames 50011; fourteenth author: Department of Plant Pathology, University of Arkansas, Fayetteville 72701; sixteenth author: Division of Plant Sciences, University of Missouri, Columbia 65211; seventeenth author: Ontario Ministry of Agriculture, Food & Rural Affairs, Ridgetown, ON N0P2C0, Canada; and eighteenth author: Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN 47907
| | - Janette L Jacobs
- First, second, third, fourth, and nineteenth authors: Department of Plant, Soil and Microbial Sciences, and first and nineteenth authors: Program in Ecology, Evolutionary Biology and Behavior, Michigan State University, East Lansing 48824; fifth author; Department of Crop Sciences, University of Illinois, Urbana 61801; sixth author: Department of Plant Science, South Dakota State University, Brookings 57007; seventh and fifteenth authors: Department of Plant Pathology, University of Wisconsin-Madison 53706; eighth author: Department of Plant Pathology, University of Nebraska-Lincoln 68583; ninth author: Department of Plant Pathology, Kansas State University, Manhattan 66506; tenth author: Department of Plant Pathology, University of Minnesota, St. Paul 55108; eleventh and twelfth authors: Department of Plant Pathology, North Dakota State University, Fargo 58105; thirteenth author: Department of Plant Pathology and Microbiology, Iowa State University, Ames 50011; fourteenth author: Department of Plant Pathology, University of Arkansas, Fayetteville 72701; sixteenth author: Division of Plant Sciences, University of Missouri, Columbia 65211; seventeenth author: Ontario Ministry of Agriculture, Food & Rural Affairs, Ridgetown, ON N0P2C0, Canada; and eighteenth author: Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN 47907
| | - Stephanie Napieralski
- First, second, third, fourth, and nineteenth authors: Department of Plant, Soil and Microbial Sciences, and first and nineteenth authors: Program in Ecology, Evolutionary Biology and Behavior, Michigan State University, East Lansing 48824; fifth author; Department of Crop Sciences, University of Illinois, Urbana 61801; sixth author: Department of Plant Science, South Dakota State University, Brookings 57007; seventh and fifteenth authors: Department of Plant Pathology, University of Wisconsin-Madison 53706; eighth author: Department of Plant Pathology, University of Nebraska-Lincoln 68583; ninth author: Department of Plant Pathology, Kansas State University, Manhattan 66506; tenth author: Department of Plant Pathology, University of Minnesota, St. Paul 55108; eleventh and twelfth authors: Department of Plant Pathology, North Dakota State University, Fargo 58105; thirteenth author: Department of Plant Pathology and Microbiology, Iowa State University, Ames 50011; fourteenth author: Department of Plant Pathology, University of Arkansas, Fayetteville 72701; sixteenth author: Division of Plant Sciences, University of Missouri, Columbia 65211; seventeenth author: Ontario Ministry of Agriculture, Food & Rural Affairs, Ridgetown, ON N0P2C0, Canada; and eighteenth author: Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN 47907
| | - Behirda Karaj
- First, second, third, fourth, and nineteenth authors: Department of Plant, Soil and Microbial Sciences, and first and nineteenth authors: Program in Ecology, Evolutionary Biology and Behavior, Michigan State University, East Lansing 48824; fifth author; Department of Crop Sciences, University of Illinois, Urbana 61801; sixth author: Department of Plant Science, South Dakota State University, Brookings 57007; seventh and fifteenth authors: Department of Plant Pathology, University of Wisconsin-Madison 53706; eighth author: Department of Plant Pathology, University of Nebraska-Lincoln 68583; ninth author: Department of Plant Pathology, Kansas State University, Manhattan 66506; tenth author: Department of Plant Pathology, University of Minnesota, St. Paul 55108; eleventh and twelfth authors: Department of Plant Pathology, North Dakota State University, Fargo 58105; thirteenth author: Department of Plant Pathology and Microbiology, Iowa State University, Ames 50011; fourteenth author: Department of Plant Pathology, University of Arkansas, Fayetteville 72701; sixteenth author: Division of Plant Sciences, University of Missouri, Columbia 65211; seventeenth author: Ontario Ministry of Agriculture, Food & Rural Affairs, Ridgetown, ON N0P2C0, Canada; and eighteenth author: Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN 47907
| | - Carl A Bradley
- First, second, third, fourth, and nineteenth authors: Department of Plant, Soil and Microbial Sciences, and first and nineteenth authors: Program in Ecology, Evolutionary Biology and Behavior, Michigan State University, East Lansing 48824; fifth author; Department of Crop Sciences, University of Illinois, Urbana 61801; sixth author: Department of Plant Science, South Dakota State University, Brookings 57007; seventh and fifteenth authors: Department of Plant Pathology, University of Wisconsin-Madison 53706; eighth author: Department of Plant Pathology, University of Nebraska-Lincoln 68583; ninth author: Department of Plant Pathology, Kansas State University, Manhattan 66506; tenth author: Department of Plant Pathology, University of Minnesota, St. Paul 55108; eleventh and twelfth authors: Department of Plant Pathology, North Dakota State University, Fargo 58105; thirteenth author: Department of Plant Pathology and Microbiology, Iowa State University, Ames 50011; fourteenth author: Department of Plant Pathology, University of Arkansas, Fayetteville 72701; sixteenth author: Division of Plant Sciences, University of Missouri, Columbia 65211; seventeenth author: Ontario Ministry of Agriculture, Food & Rural Affairs, Ridgetown, ON N0P2C0, Canada; and eighteenth author: Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN 47907
| | - Thomas Chase
- First, second, third, fourth, and nineteenth authors: Department of Plant, Soil and Microbial Sciences, and first and nineteenth authors: Program in Ecology, Evolutionary Biology and Behavior, Michigan State University, East Lansing 48824; fifth author; Department of Crop Sciences, University of Illinois, Urbana 61801; sixth author: Department of Plant Science, South Dakota State University, Brookings 57007; seventh and fifteenth authors: Department of Plant Pathology, University of Wisconsin-Madison 53706; eighth author: Department of Plant Pathology, University of Nebraska-Lincoln 68583; ninth author: Department of Plant Pathology, Kansas State University, Manhattan 66506; tenth author: Department of Plant Pathology, University of Minnesota, St. Paul 55108; eleventh and twelfth authors: Department of Plant Pathology, North Dakota State University, Fargo 58105; thirteenth author: Department of Plant Pathology and Microbiology, Iowa State University, Ames 50011; fourteenth author: Department of Plant Pathology, University of Arkansas, Fayetteville 72701; sixteenth author: Division of Plant Sciences, University of Missouri, Columbia 65211; seventeenth author: Ontario Ministry of Agriculture, Food & Rural Affairs, Ridgetown, ON N0P2C0, Canada; and eighteenth author: Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN 47907
| | - Paul D Esker
- First, second, third, fourth, and nineteenth authors: Department of Plant, Soil and Microbial Sciences, and first and nineteenth authors: Program in Ecology, Evolutionary Biology and Behavior, Michigan State University, East Lansing 48824; fifth author; Department of Crop Sciences, University of Illinois, Urbana 61801; sixth author: Department of Plant Science, South Dakota State University, Brookings 57007; seventh and fifteenth authors: Department of Plant Pathology, University of Wisconsin-Madison 53706; eighth author: Department of Plant Pathology, University of Nebraska-Lincoln 68583; ninth author: Department of Plant Pathology, Kansas State University, Manhattan 66506; tenth author: Department of Plant Pathology, University of Minnesota, St. Paul 55108; eleventh and twelfth authors: Department of Plant Pathology, North Dakota State University, Fargo 58105; thirteenth author: Department of Plant Pathology and Microbiology, Iowa State University, Ames 50011; fourteenth author: Department of Plant Pathology, University of Arkansas, Fayetteville 72701; sixteenth author: Division of Plant Sciences, University of Missouri, Columbia 65211; seventeenth author: Ontario Ministry of Agriculture, Food & Rural Affairs, Ridgetown, ON N0P2C0, Canada; and eighteenth author: Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN 47907
| | - Loren J Giesler
- First, second, third, fourth, and nineteenth authors: Department of Plant, Soil and Microbial Sciences, and first and nineteenth authors: Program in Ecology, Evolutionary Biology and Behavior, Michigan State University, East Lansing 48824; fifth author; Department of Crop Sciences, University of Illinois, Urbana 61801; sixth author: Department of Plant Science, South Dakota State University, Brookings 57007; seventh and fifteenth authors: Department of Plant Pathology, University of Wisconsin-Madison 53706; eighth author: Department of Plant Pathology, University of Nebraska-Lincoln 68583; ninth author: Department of Plant Pathology, Kansas State University, Manhattan 66506; tenth author: Department of Plant Pathology, University of Minnesota, St. Paul 55108; eleventh and twelfth authors: Department of Plant Pathology, North Dakota State University, Fargo 58105; thirteenth author: Department of Plant Pathology and Microbiology, Iowa State University, Ames 50011; fourteenth author: Department of Plant Pathology, University of Arkansas, Fayetteville 72701; sixteenth author: Division of Plant Sciences, University of Missouri, Columbia 65211; seventeenth author: Ontario Ministry of Agriculture, Food & Rural Affairs, Ridgetown, ON N0P2C0, Canada; and eighteenth author: Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN 47907
| | - Doug J Jardine
- First, second, third, fourth, and nineteenth authors: Department of Plant, Soil and Microbial Sciences, and first and nineteenth authors: Program in Ecology, Evolutionary Biology and Behavior, Michigan State University, East Lansing 48824; fifth author; Department of Crop Sciences, University of Illinois, Urbana 61801; sixth author: Department of Plant Science, South Dakota State University, Brookings 57007; seventh and fifteenth authors: Department of Plant Pathology, University of Wisconsin-Madison 53706; eighth author: Department of Plant Pathology, University of Nebraska-Lincoln 68583; ninth author: Department of Plant Pathology, Kansas State University, Manhattan 66506; tenth author: Department of Plant Pathology, University of Minnesota, St. Paul 55108; eleventh and twelfth authors: Department of Plant Pathology, North Dakota State University, Fargo 58105; thirteenth author: Department of Plant Pathology and Microbiology, Iowa State University, Ames 50011; fourteenth author: Department of Plant Pathology, University of Arkansas, Fayetteville 72701; sixteenth author: Division of Plant Sciences, University of Missouri, Columbia 65211; seventeenth author: Ontario Ministry of Agriculture, Food & Rural Affairs, Ridgetown, ON N0P2C0, Canada; and eighteenth author: Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN 47907
| | - Dean K Malvick
- First, second, third, fourth, and nineteenth authors: Department of Plant, Soil and Microbial Sciences, and first and nineteenth authors: Program in Ecology, Evolutionary Biology and Behavior, Michigan State University, East Lansing 48824; fifth author; Department of Crop Sciences, University of Illinois, Urbana 61801; sixth author: Department of Plant Science, South Dakota State University, Brookings 57007; seventh and fifteenth authors: Department of Plant Pathology, University of Wisconsin-Madison 53706; eighth author: Department of Plant Pathology, University of Nebraska-Lincoln 68583; ninth author: Department of Plant Pathology, Kansas State University, Manhattan 66506; tenth author: Department of Plant Pathology, University of Minnesota, St. Paul 55108; eleventh and twelfth authors: Department of Plant Pathology, North Dakota State University, Fargo 58105; thirteenth author: Department of Plant Pathology and Microbiology, Iowa State University, Ames 50011; fourteenth author: Department of Plant Pathology, University of Arkansas, Fayetteville 72701; sixteenth author: Division of Plant Sciences, University of Missouri, Columbia 65211; seventeenth author: Ontario Ministry of Agriculture, Food & Rural Affairs, Ridgetown, ON N0P2C0, Canada; and eighteenth author: Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN 47907
| | - Samuel G Markell
- First, second, third, fourth, and nineteenth authors: Department of Plant, Soil and Microbial Sciences, and first and nineteenth authors: Program in Ecology, Evolutionary Biology and Behavior, Michigan State University, East Lansing 48824; fifth author; Department of Crop Sciences, University of Illinois, Urbana 61801; sixth author: Department of Plant Science, South Dakota State University, Brookings 57007; seventh and fifteenth authors: Department of Plant Pathology, University of Wisconsin-Madison 53706; eighth author: Department of Plant Pathology, University of Nebraska-Lincoln 68583; ninth author: Department of Plant Pathology, Kansas State University, Manhattan 66506; tenth author: Department of Plant Pathology, University of Minnesota, St. Paul 55108; eleventh and twelfth authors: Department of Plant Pathology, North Dakota State University, Fargo 58105; thirteenth author: Department of Plant Pathology and Microbiology, Iowa State University, Ames 50011; fourteenth author: Department of Plant Pathology, University of Arkansas, Fayetteville 72701; sixteenth author: Division of Plant Sciences, University of Missouri, Columbia 65211; seventeenth author: Ontario Ministry of Agriculture, Food & Rural Affairs, Ridgetown, ON N0P2C0, Canada; and eighteenth author: Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN 47907
| | - Berlin D Nelson
- First, second, third, fourth, and nineteenth authors: Department of Plant, Soil and Microbial Sciences, and first and nineteenth authors: Program in Ecology, Evolutionary Biology and Behavior, Michigan State University, East Lansing 48824; fifth author; Department of Crop Sciences, University of Illinois, Urbana 61801; sixth author: Department of Plant Science, South Dakota State University, Brookings 57007; seventh and fifteenth authors: Department of Plant Pathology, University of Wisconsin-Madison 53706; eighth author: Department of Plant Pathology, University of Nebraska-Lincoln 68583; ninth author: Department of Plant Pathology, Kansas State University, Manhattan 66506; tenth author: Department of Plant Pathology, University of Minnesota, St. Paul 55108; eleventh and twelfth authors: Department of Plant Pathology, North Dakota State University, Fargo 58105; thirteenth author: Department of Plant Pathology and Microbiology, Iowa State University, Ames 50011; fourteenth author: Department of Plant Pathology, University of Arkansas, Fayetteville 72701; sixteenth author: Division of Plant Sciences, University of Missouri, Columbia 65211; seventeenth author: Ontario Ministry of Agriculture, Food & Rural Affairs, Ridgetown, ON N0P2C0, Canada; and eighteenth author: Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN 47907
| | - Alison E Robertson
- First, second, third, fourth, and nineteenth authors: Department of Plant, Soil and Microbial Sciences, and first and nineteenth authors: Program in Ecology, Evolutionary Biology and Behavior, Michigan State University, East Lansing 48824; fifth author; Department of Crop Sciences, University of Illinois, Urbana 61801; sixth author: Department of Plant Science, South Dakota State University, Brookings 57007; seventh and fifteenth authors: Department of Plant Pathology, University of Wisconsin-Madison 53706; eighth author: Department of Plant Pathology, University of Nebraska-Lincoln 68583; ninth author: Department of Plant Pathology, Kansas State University, Manhattan 66506; tenth author: Department of Plant Pathology, University of Minnesota, St. Paul 55108; eleventh and twelfth authors: Department of Plant Pathology, North Dakota State University, Fargo 58105; thirteenth author: Department of Plant Pathology and Microbiology, Iowa State University, Ames 50011; fourteenth author: Department of Plant Pathology, University of Arkansas, Fayetteville 72701; sixteenth author: Division of Plant Sciences, University of Missouri, Columbia 65211; seventeenth author: Ontario Ministry of Agriculture, Food & Rural Affairs, Ridgetown, ON N0P2C0, Canada; and eighteenth author: Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN 47907
| | - John C Rupe
- First, second, third, fourth, and nineteenth authors: Department of Plant, Soil and Microbial Sciences, and first and nineteenth authors: Program in Ecology, Evolutionary Biology and Behavior, Michigan State University, East Lansing 48824; fifth author; Department of Crop Sciences, University of Illinois, Urbana 61801; sixth author: Department of Plant Science, South Dakota State University, Brookings 57007; seventh and fifteenth authors: Department of Plant Pathology, University of Wisconsin-Madison 53706; eighth author: Department of Plant Pathology, University of Nebraska-Lincoln 68583; ninth author: Department of Plant Pathology, Kansas State University, Manhattan 66506; tenth author: Department of Plant Pathology, University of Minnesota, St. Paul 55108; eleventh and twelfth authors: Department of Plant Pathology, North Dakota State University, Fargo 58105; thirteenth author: Department of Plant Pathology and Microbiology, Iowa State University, Ames 50011; fourteenth author: Department of Plant Pathology, University of Arkansas, Fayetteville 72701; sixteenth author: Division of Plant Sciences, University of Missouri, Columbia 65211; seventeenth author: Ontario Ministry of Agriculture, Food & Rural Affairs, Ridgetown, ON N0P2C0, Canada; and eighteenth author: Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN 47907
| | - Damon L Smith
- First, second, third, fourth, and nineteenth authors: Department of Plant, Soil and Microbial Sciences, and first and nineteenth authors: Program in Ecology, Evolutionary Biology and Behavior, Michigan State University, East Lansing 48824; fifth author; Department of Crop Sciences, University of Illinois, Urbana 61801; sixth author: Department of Plant Science, South Dakota State University, Brookings 57007; seventh and fifteenth authors: Department of Plant Pathology, University of Wisconsin-Madison 53706; eighth author: Department of Plant Pathology, University of Nebraska-Lincoln 68583; ninth author: Department of Plant Pathology, Kansas State University, Manhattan 66506; tenth author: Department of Plant Pathology, University of Minnesota, St. Paul 55108; eleventh and twelfth authors: Department of Plant Pathology, North Dakota State University, Fargo 58105; thirteenth author: Department of Plant Pathology and Microbiology, Iowa State University, Ames 50011; fourteenth author: Department of Plant Pathology, University of Arkansas, Fayetteville 72701; sixteenth author: Division of Plant Sciences, University of Missouri, Columbia 65211; seventeenth author: Ontario Ministry of Agriculture, Food & Rural Affairs, Ridgetown, ON N0P2C0, Canada; and eighteenth author: Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN 47907
| | - Laura E Sweets
- First, second, third, fourth, and nineteenth authors: Department of Plant, Soil and Microbial Sciences, and first and nineteenth authors: Program in Ecology, Evolutionary Biology and Behavior, Michigan State University, East Lansing 48824; fifth author; Department of Crop Sciences, University of Illinois, Urbana 61801; sixth author: Department of Plant Science, South Dakota State University, Brookings 57007; seventh and fifteenth authors: Department of Plant Pathology, University of Wisconsin-Madison 53706; eighth author: Department of Plant Pathology, University of Nebraska-Lincoln 68583; ninth author: Department of Plant Pathology, Kansas State University, Manhattan 66506; tenth author: Department of Plant Pathology, University of Minnesota, St. Paul 55108; eleventh and twelfth authors: Department of Plant Pathology, North Dakota State University, Fargo 58105; thirteenth author: Department of Plant Pathology and Microbiology, Iowa State University, Ames 50011; fourteenth author: Department of Plant Pathology, University of Arkansas, Fayetteville 72701; sixteenth author: Division of Plant Sciences, University of Missouri, Columbia 65211; seventeenth author: Ontario Ministry of Agriculture, Food & Rural Affairs, Ridgetown, ON N0P2C0, Canada; and eighteenth author: Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN 47907
| | - Albert U Tenuta
- First, second, third, fourth, and nineteenth authors: Department of Plant, Soil and Microbial Sciences, and first and nineteenth authors: Program in Ecology, Evolutionary Biology and Behavior, Michigan State University, East Lansing 48824; fifth author; Department of Crop Sciences, University of Illinois, Urbana 61801; sixth author: Department of Plant Science, South Dakota State University, Brookings 57007; seventh and fifteenth authors: Department of Plant Pathology, University of Wisconsin-Madison 53706; eighth author: Department of Plant Pathology, University of Nebraska-Lincoln 68583; ninth author: Department of Plant Pathology, Kansas State University, Manhattan 66506; tenth author: Department of Plant Pathology, University of Minnesota, St. Paul 55108; eleventh and twelfth authors: Department of Plant Pathology, North Dakota State University, Fargo 58105; thirteenth author: Department of Plant Pathology and Microbiology, Iowa State University, Ames 50011; fourteenth author: Department of Plant Pathology, University of Arkansas, Fayetteville 72701; sixteenth author: Division of Plant Sciences, University of Missouri, Columbia 65211; seventeenth author: Ontario Ministry of Agriculture, Food & Rural Affairs, Ridgetown, ON N0P2C0, Canada; and eighteenth author: Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN 47907
| | - Kiersten A Wise
- First, second, third, fourth, and nineteenth authors: Department of Plant, Soil and Microbial Sciences, and first and nineteenth authors: Program in Ecology, Evolutionary Biology and Behavior, Michigan State University, East Lansing 48824; fifth author; Department of Crop Sciences, University of Illinois, Urbana 61801; sixth author: Department of Plant Science, South Dakota State University, Brookings 57007; seventh and fifteenth authors: Department of Plant Pathology, University of Wisconsin-Madison 53706; eighth author: Department of Plant Pathology, University of Nebraska-Lincoln 68583; ninth author: Department of Plant Pathology, Kansas State University, Manhattan 66506; tenth author: Department of Plant Pathology, University of Minnesota, St. Paul 55108; eleventh and twelfth authors: Department of Plant Pathology, North Dakota State University, Fargo 58105; thirteenth author: Department of Plant Pathology and Microbiology, Iowa State University, Ames 50011; fourteenth author: Department of Plant Pathology, University of Arkansas, Fayetteville 72701; sixteenth author: Division of Plant Sciences, University of Missouri, Columbia 65211; seventeenth author: Ontario Ministry of Agriculture, Food & Rural Affairs, Ridgetown, ON N0P2C0, Canada; and eighteenth author: Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN 47907
| | - Martin I Chilvers
- First, second, third, fourth, and nineteenth authors: Department of Plant, Soil and Microbial Sciences, and first and nineteenth authors: Program in Ecology, Evolutionary Biology and Behavior, Michigan State University, East Lansing 48824; fifth author; Department of Crop Sciences, University of Illinois, Urbana 61801; sixth author: Department of Plant Science, South Dakota State University, Brookings 57007; seventh and fifteenth authors: Department of Plant Pathology, University of Wisconsin-Madison 53706; eighth author: Department of Plant Pathology, University of Nebraska-Lincoln 68583; ninth author: Department of Plant Pathology, Kansas State University, Manhattan 66506; tenth author: Department of Plant Pathology, University of Minnesota, St. Paul 55108; eleventh and twelfth authors: Department of Plant Pathology, North Dakota State University, Fargo 58105; thirteenth author: Department of Plant Pathology and Microbiology, Iowa State University, Ames 50011; fourteenth author: Department of Plant Pathology, University of Arkansas, Fayetteville 72701; sixteenth author: Division of Plant Sciences, University of Missouri, Columbia 65211; seventeenth author: Ontario Ministry of Agriculture, Food & Rural Affairs, Ridgetown, ON N0P2C0, Canada; and eighteenth author: Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN 47907
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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.
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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
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Coffua LS, Veterano ST, Clipman SJ, Mena-Ali JI, Blair JE. Characterization of Pythium spp. Associated with Asymptomatic Soybean in Southeastern Pennsylvania. PLANT DISEASE 2016; 100:1870-1879. [PMID: 30682988 DOI: 10.1094/pdis-11-15-1355-re] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Soybean production in Pennsylvania has increased substantially over the past 20 years and is a highly valued field crop, together with corn. Soilborne pathogens such as Pythium spp. can contribute to soybean stand establishment issues, particularly under the conservation tillage practices that are common in the state. In this study, we collected soil samples from eight asymptomatic soybean-corn rotation fields across six counties in southeastern Pennsylvania between May and June 2012. Pythium spp. were isolated via baiting, and tested for aggressiveness on both soybean and corn using laboratory assays. In addition to our culture-based survey, we also assessed the use of cytochrome oxidase subunit 1 pyrosequencing as a culture-independent method for measuring Pythium spp. diversity from environmental samples. Diversity estimates were consistent between the culture-based and pyrosequencing datasets; however, important methodological biases inherent to culture-independent methods may have led to some differences. Our results show that several Pythium spp. previously characterized as soybean or corn pathogens are present in southeastern Pennsylvania, including Pythium irregulare, P. sylvaticum, and P. ultimum var. sporangiiferum, with isolates showing aggressive phenotypes in lab assays.
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Affiliation(s)
- Lauren S Coffua
- Department of Biology, Franklin & Marshall College, Lancaster, PA 17603
| | - S Tyler Veterano
- Department of Biology, Franklin & Marshall College, Lancaster, PA 17603
| | - Steven J Clipman
- Department of Biology, Franklin & Marshall College, Lancaster, PA 17603
| | - Jorge I Mena-Ali
- Department of Biology, Franklin & Marshall College, Lancaster, PA 17603
| | - Jaime E Blair
- Department of Biology, Franklin & Marshall College, Lancaster, PA 17603
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41
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Falade MO, Opene AJ, Benson O. DNA barcoding of Clarias gariepinus, Coptodon zillii and Sarotherodon melanotheron from Southwestern Nigeria. F1000Res 2016; 5:1268. [PMID: 27990256 PMCID: PMC5133684 DOI: 10.12688/f1000research.7895.1] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 06/01/2016] [Indexed: 11/20/2022] Open
Abstract
DNA barcoding has been adopted as a gold standard rapid, precise and unifying identification system for animal species and provides a database of genetic sequences that can be used as a tool for universal species identification. In this study, we employed mitochondrial genes 16S rRNA (16S) and cytochrome oxidase subunit I (COI) for the identification of some Nigerian freshwater catfish and Tilapia species. Approximately 655 bp were amplified from the 5' region of the mitochondrial cytochrome C oxidase subunit I (COI) gene whereas 570 bp were amplified for the 16S rRNA gene. Nucleotide divergences among sequences were estimated based on Kimura 2-parameter distances and the genetic relationships were assessed by constructing phylogenetic trees using the neighbour-joining (NJ) and maximum likelihood (ML) methods. Analyses of consensus barcode sequences for each species, and alignment of individual sequences from within a given species revealed highly consistent barcodes (99% similarity on average), which could be compared with deposited sequences in public databases. The nucleotide distance between species belonging to different genera based on COI ranged from 0.17% between Sarotherodonmelanotheron and Coptodon zillii to 0.49% between Clarias gariepinus and C. zillii, indicating that S. melanotheron and C. zillii are closely related. Based on the data obtained, the utility of COI gene was confirmed in accurate identification of three fish species from Southwest Nigeria.
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Affiliation(s)
- Mofolusho O. Falade
- Cellular Parasitology Programme, Cell Biology and Genetics Unit, Department of Zoology, University of Ibadan, Ibadan, Nigeria
| | - Anthony J. Opene
- Cellular Parasitology Programme, Cell Biology and Genetics Unit, Department of Zoology, University of Ibadan, Ibadan, Nigeria
| | - Otarigho Benson
- Cellular Parasitology Programme, Cell Biology and Genetics Unit, Department of Zoology, University of Ibadan, Ibadan, Nigeria
- Department of Biological Science, Edo University, Iyamho, Edo State, Nigeria
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42
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Foo E, Blake SN, Fisher BJ, Smith JA, Reid JB. The role of strigolactones during plant interactions with the pathogenic fungus Fusarium oxysporum. PLANTA 2016; 243:1387-96. [PMID: 26725046 DOI: 10.1007/s00425-015-2449-3] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2015] [Accepted: 12/14/2015] [Indexed: 05/28/2023]
Abstract
MAIN CONCLUSION Strigolactones (SLs) do not influence spore germination or hyphal growth of Fusarium oxysporum. Mutant studies revealed no role for SLs but a role for ethylene signalling in defence against this pathogen in pea. Strigolactones (SLs) play important roles both inside the plant as a hormone and outside the plant as a rhizosphere signal in interactions with mycorrhizal fungi and parasitic weeds. What is less well understood is any potential role SLs may play in interactions with disease causing microbes such as pathogenic fungi. In this paper we investigate the influence of SLs on the hemibiotrophic pathogen Fusarium oxysporum f.sp. pisi both directly via their effects on fungal growth and inside the plant through the use of a mutant deficient in SL. Given that various stereoisomers of synthetic and naturally occuring SLs can display different biological activities, we used (+)-GR24, (-)-GR24 and the naturally occurring SL, (+)-strigol, as well as a racemic mixture of 5-deoxystrigol. As a positive control, we examined the influence of a plant mutant with altered ethylene signalling, ein2, on disease development. We found no evidence that SLs influence spore germination or hyphal growth of Fusarium oxysporum and that, while ethylene signalling influences pea susceptibility to this pathogen, SLs do not.
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Affiliation(s)
- Eloise Foo
- School of Biological Sciences, University of Tasmania, Private Bag 55, Hobart, TAS, 7001, Australia.
| | - Sara N Blake
- School of Biological Sciences, University of Tasmania, Private Bag 55, Hobart, TAS, 7001, Australia
| | - Brendan J Fisher
- School of Physical Sciences, University of Tasmania, Private Bag 75, Hobart, TAS, 7001, Australia
| | - Jason A Smith
- School of Physical Sciences, University of Tasmania, Private Bag 75, Hobart, TAS, 7001, Australia
| | - James B Reid
- School of Biological Sciences, University of Tasmania, Private Bag 55, Hobart, TAS, 7001, Australia
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43
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Blake SN, Barry KM, Gill WM, Reid JB, Foo E. The role of strigolactones and ethylene in disease caused by Pythium irregulare. MOLECULAR PLANT PATHOLOGY 2016; 17:680-90. [PMID: 26377026 PMCID: PMC6638477 DOI: 10.1111/mpp.12320] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Plant hormones play key roles in defence against pathogen attack. Recent work has begun to extend this role to encompass not just the traditional disease/stress hormones, such as ethylene, but also growth-promoting hormones. Strigolactones (SLs) are the most recently defined group of plant hormones with important roles in plant-microbe interactions, as well as aspects of plant growth and development, although the knowledge of their role in plant-pathogen interactions is extremely limited. The oomycete Pythium irregulare is a poorly controlled pathogen of many crops. Previous work has indicated an important role for ethylene in defence against this oomycete. We examined the role of ethylene and SLs in response to this pathogen in pea (Pisum sativum L.) at the molecular and whole-plant levels using a set of well-characterized hormone mutants, including an ethylene-insensitive ein2 mutant and SL-deficient and insensitive mutants. We identified a key role for ethylene signalling in specific cell types that reduces pathogen invasion, extending the work carried out in other species. However, we found no evidence that SL biosynthesis or response influences the interaction of pea with P. irregulare or that synthetic SL influences the growth or hyphal branching of the oomycete in vitro. Future work should seek to extend our understanding of the role of SLs in other plant interactions, including with other fungal, bacterial and viral pathogens, nematodes and insect pests.
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Affiliation(s)
- Sara N Blake
- School of Biological Sciences, University of Tasmania, Private Bag 55, Hobart, Tasmania, 7001, Australia
| | - Karen M Barry
- Tasmanian Institute of Agriculture & School of Land and Food, University of Tasmania, Private Bag 98, Hobart, Tasmania, 7001, Australia
| | - Warwick M Gill
- Tasmanian Institute of Agriculture & School of Land and Food, University of Tasmania, Private Bag 98, Hobart, Tasmania, 7001, Australia
| | - James B Reid
- School of Biological Sciences, University of Tasmania, Private Bag 55, Hobart, Tasmania, 7001, Australia
| | - Eloise Foo
- School of Biological Sciences, University of Tasmania, Private Bag 55, Hobart, Tasmania, 7001, Australia
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Del Castillo Múnera J, Hausbeck MK. Characterization of Pythium Species Associated With Greenhouse Floriculture Crops in Michigan. PLANT DISEASE 2016; 100:569-576. [PMID: 30688597 DOI: 10.1094/pdis-03-15-0296-re] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Michigan ranks third in the United States for the wholesale value of floriculture products, with an estimated value of $375.7 million. Seedling damping-off and root and crown rot are commonly caused by Pythium spp. and are important problems for greenhouse growers. Pythium spp. associated with Michigan's floriculture crops were characterized as a means to improve current management strategies. During 2011 and 2012, potted poinsettias with root rot symptoms were sampled from nine greenhouses located in Kent, Kalamazoo, and Wayne counties. In 2013, from the same three counties, symptomatic geranium and snapdragon bedding plants were sampled from 12 greenhouses. Additionally, symptomatic hibiscus and lantana plants were sampled at one greenhouse facility. Isolates were confirmed to be Pythium spp. via morphology and sequencing of the ITS region. A total of 287 Pythium spp. isolates were obtained from poinsettias and 726 isolates from geranium, snapdragon, hibiscus, and lantana. Seven Pythium spp., and a group of isolates determined as Pythium sp. 1 were identified. The most prevalent species were P. irregulare, P. ultimum, and P. aphanidermatum. A subset of isolates was chosen for pathogenicity and mefenoxam sensitivity testing. Six of the species were virulent to germinating geranium seeds. Most P. ultimum and P. cylindrosporum isolates tested were intermediate to highly resistant to mefenoxam, whereas most P. aphanidermatum isolates were sensitive. This study suggests that Pythium spp. recovered from Michigan greenhouses may vary depending on the host, and that mefenoxam may not be effective to control P. ultimum or P. cylindrosporum.
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Affiliation(s)
| | - Mary K Hausbeck
- Professor, Department of Plant, Soil, and Microbial Sciences, Michigan State University, East Lansing 48824
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Lookabaugh EC, Ivors KL, Shew BB. Mefenoxam Sensitivity, Aggressiveness, and Identification of Pythium Species Causing Root Rot on Floriculture Crops in North Carolina. PLANT DISEASE 2015; 99:1550-1558. [PMID: 30695958 DOI: 10.1094/pdis-02-15-0232-re] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Herbaceous ornamental plants exhibiting symptoms of Pythium root rot were collected from 26 greenhouses in 21 counties in North Carolina (NC) from 2010 to 2012. Plant symptoms ranged from mild stunting to severe wilting, root rot, and death. Roots were plated on selective media, and 356 isolates of Pythium were recovered from 34 host species. Selected isolates were identified by sequencing of the internal transcribed spacer (ITS) rDNA gene region. Seventeen Pythium species were identified, with P. aphanidermatum, P. irregulare, and P. myriotylum comprising 75% of the 320 isolates sequenced. Twelve of the 26 greenhouses had more than one species present. Mefenoxam sensitivity was tested in vitro by growing isolates in wells of microtiter plates containing clarified V8 agar amended with 100 µg a.i./ml mefenoxam. Colonization was scored after 24 to 48 h using a scale of 0 (no growth) to 5 (entire well colonized). Fifty-two percent of the isolates were resistant to mefenoxam (mean score ≥4). All 32 isolates of P. myriotylum were sensitive, whereas sensitivity varied among isolates of P. aphanidermatum and P. irregulare. Resistant and sensitive isolates of the same species were found within the same greenhouses. The aggressiveness of P. aphanidermatum and P. irregulare isolates was evaluated on poinsettia, Gerbera daisy, and petunia. P. aphanidermatum was more aggressive than P. irregulare on poinsettia and petunia; symptoms were mild and no differences in aggressiveness were observed on Gerbera daisy. Sensitivity to mefenoxam was not related to aggressiveness.
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Affiliation(s)
- E C Lookabaugh
- Department of Plant Pathology, North Carolina State University, Raleigh, NC 27695
| | - K L Ivors
- Department of Horticulture and Crop Science, California Polytechnic University, San Luis Obispo, CA
| | - B B Shew
- Department of Plant Pathology, North Carolina State University, Raleigh, NC 27695
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46
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Choi YJ, Beakes G, Glockling S, Kruse J, Nam B, Nigrelli L, Ploch S, Shin HD, Shivas RG, Telle S, Voglmayr H, Thines M. Towards a universal barcode of oomycetes--a comparison of the cox1 and cox2 loci. Mol Ecol Resour 2015; 15:1275-88. [PMID: 25728598 PMCID: PMC5736100 DOI: 10.1111/1755-0998.12398] [Citation(s) in RCA: 108] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2014] [Revised: 01/28/2015] [Accepted: 02/02/2015] [Indexed: 11/30/2022]
Abstract
Oomycetes are a diverse group of eukaryotes in terrestrial, limnic and marine habitats worldwide and include several devastating plant pathogens, for example Phytophthora infestans (potato late blight). The cytochrome c oxidase subunit 2 gene (cox2) has been widely used for identification, taxonomy and phylogeny of various oomycete groups. However, recently the cox1 gene was proposed as a DNA barcode marker instead, together with ITS rDNA. The cox1 locus has been used in some studies of Pythium and Phytophthora, but has rarely been used for other oomycetes, as amplification success of cox1 varies with different lineages and sample ages. To determine which out of cox1 or cox2 is best suited as a universal oomycete barcode, we compared these two genes in terms of (i) PCR efficiency for 31 representative genera, as well as for historic herbarium specimens, and (ii) sequence polymorphism, intra- and interspecific divergence. The primer sets for cox2 successfully amplified all oomycete genera tested, while cox1 failed to amplify three genera. In addition, cox2 exhibited higher PCR efficiency for historic herbarium specimens, providing easier access to barcoding-type material. Sequence data for several historic type specimens exist for cox2, but there are none for cox1. In addition, cox2 yielded higher species identification success, with higher interspecific and lower intraspecific divergences than cox1. Therefore, cox2 is suggested as a partner DNA barcode along with ITS rDNA instead of cox1. The cox2-1 spacer could be a useful marker below species level. Improved protocols and universal primers are presented for all genes to facilitate future barcoding efforts.
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Affiliation(s)
- Young-Joon Choi
- Institute of Ecology, Evolution and Diversity, Faculty of Biosciences, Goethe University Frankfurt am Main, Max-von-Laue-Str. 9, D-60438 Frankfurt am Main, Germany
- Biodiversity and Climate Research Centre (BiK-F), Senckenberganlage 25, D-60325 Frankfurt am Main, Germany
| | - Gordon Beakes
- Division of Biology, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
| | | | - Julia Kruse
- Institute of Ecology, Evolution and Diversity, Faculty of Biosciences, Goethe University Frankfurt am Main, Max-von-Laue-Str. 9, D-60438 Frankfurt am Main, Germany
- Biodiversity and Climate Research Centre (BiK-F), Senckenberganlage 25, D-60325 Frankfurt am Main, Germany
| | - Bora Nam
- Institute of Ecology, Evolution and Diversity, Faculty of Biosciences, Goethe University Frankfurt am Main, Max-von-Laue-Str. 9, D-60438 Frankfurt am Main, Germany
- Biodiversity and Climate Research Centre (BiK-F), Senckenberganlage 25, D-60325 Frankfurt am Main, Germany
| | - Lisa Nigrelli
- Institute of Ecology, Evolution and Diversity, Faculty of Biosciences, Goethe University Frankfurt am Main, Max-von-Laue-Str. 9, D-60438 Frankfurt am Main, Germany
- Biodiversity and Climate Research Centre (BiK-F), Senckenberganlage 25, D-60325 Frankfurt am Main, Germany
| | - Sebastian Ploch
- Biodiversity and Climate Research Centre (BiK-F), Senckenberganlage 25, D-60325 Frankfurt am Main, Germany
- Cluster of Excellence on Plant Sciences (CEPLAS), Institute of Population Genetics,University of Duesseldorf, Universtitätsstr. 1, D-40225 Duesseldorf, Germany
| | - Hyeon-Dong Shin
- Division of Environmental Science and Ecological Engineering, Korea University, 136-701 Seoul, South Korea
| | - Roger G. Shivas
- Plant Pathology Herbarium, Biosecurity Queensland, Ecosciences Precinct, GPO Box 267, Brisbane, 4001 Queensland, Australia
| | - Sabine Telle
- Institute of Ecology, Evolution and Diversity, Faculty of Biosciences, Goethe University Frankfurt am Main, Max-von-Laue-Str. 9, D-60438 Frankfurt am Main, Germany
- Biodiversity and Climate Research Centre (BiK-F), Senckenberganlage 25, D-60325 Frankfurt am Main, Germany
| | - Hermann Voglmayr
- Division of Systematic and Evolutionary Botany, Department of Botany and Biodiversity Research, University of Vienna, Rennweg 14, 1030 Wien, Austria
- Department of Forest and Soil Sciences, Institute of Forest Entomology, Forest Pathology and Forest Protection, BOKU-University of Natural Resources and Life Sciences, Peter Jordan-Straße 82, 1190 Wien, Austria
| | - Marco Thines
- Institute of Ecology, Evolution and Diversity, Faculty of Biosciences, Goethe University Frankfurt am Main, Max-von-Laue-Str. 9, D-60438 Frankfurt am Main, Germany
- Biodiversity and Climate Research Centre (BiK-F), Senckenberganlage 25, D-60325 Frankfurt am Main, Germany
- Integrative Fungal Research Cluster (IPF), Georg-Voigt-Str. 14-16, D-60325 Frankfurt am Main, Germany
- Senckenberg Gesellschaft für Naturforschung, Senckenberganlage 25, D-60325 Frankfurt am Main, Germany
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47
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Feng W, Ishiguro Y, Hotta K, Watanabe H, Suga H, Kageyama K. Simple detection of Pythium irregulare using loop-mediated isothermal amplification assay. FEMS Microbiol Lett 2015; 362:fnv174. [PMID: 26394643 DOI: 10.1093/femsle/fnv174] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/19/2015] [Indexed: 11/14/2022] Open
Abstract
Pythium irregulare is an important soil-borne pathogen that causes seed, stem and root rot, and seedling damping-off in various crops. Here, we have developed a rapid and reliable approach for detecting the pathogen using loop-mediated isothermal amplification (LAMP) in combination with primers designed from the sequences of the P. irregulare ribosomal DNA internal transcribed spacer region. The specificity of the primers for P. irregulare was tested using 50 isolates of 40 Pythium species, 11 Phytophthora isolates and 8 isolates of 7 other soil-borne pathogens. The assay showed that the limit of sensitivity of the LAMP method was 100 fg of pure DNA, a similar level to that of a polymerase chain reaction. LAMP detected P. irregulare from the supernatant after mixing culture medium (template DNA source) with distilled water. Similarly, positive results were obtained using a 'Plant-LAMP' method applied to a suspension rotted roots in water. A 'Bait-LAMP' method using the supernatant of autoclaved perilla seeds incubated in a soil/water mixture for 1 week at 25°C successfully detected P. irregulare from the soil. The LAMP assay described in this study is therefore a simple and effective way for practical detection of P. irregulare.
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Affiliation(s)
- Wenzhuo Feng
- Graduate School of Applied Biological Sciences, Gifu University, 1-1 Yanagido, Gifu 501-1193, Japan
| | - Yasushi Ishiguro
- River Basin Research Center, Gifu University, 1-1 Yanagido, Gifu 501-1193, Japan
| | - Keisuke Hotta
- River Basin Research Center, Gifu University, 1-1 Yanagido, Gifu 501-1193, Japan
| | - Hideki Watanabe
- Gifu Prefectural Agricultural Technology Center, Matamaru, Gifu 501-1152, Japan
| | - Haruhisa Suga
- Life Science Research Center, Gifu University, 1-1 Yanagido, Gifu 501-1193, Japan
| | - Koji Kageyama
- River Basin Research Center, Gifu University, 1-1 Yanagido, Gifu 501-1193, Japan
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48
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Li M, Ishiguro Y, Kageyama K, Zhu Z. A simple method for normalization of DNA extraction to improve the quantitative detection of soil-borne plant pathogenic oomycetes by real-time PCR. Lett Appl Microbiol 2015; 61:179-85. [PMID: 25970140 DOI: 10.1111/lam.12441] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2014] [Revised: 05/04/2015] [Accepted: 05/06/2015] [Indexed: 11/28/2022]
Abstract
UNLABELLED Most of the current research into the quantification of soil-borne pathogenic oomycetes lacks determination of DNA extraction efficiency, probably leading to an incorrect estimation of DNA quantity. In this study, we developed a convenient method by using a 100 bp artificially synthesized DNA sequence derived from the mitochondrion NADH dehydrogenase subunit 2 gene of Thunnus thynnus as a control to determine the DNA extraction efficiency. The control DNA was added to soils and then co-extracted along with soil genomic DNA. DNA extraction efficiency was determined by the control DNA. Two different DNA extraction methods were compared and evaluated using different types of soils, and the commercial kit was proved to give more consistent results. We used the control DNA combined with real-time PCR to quantify the oomycete DNAs from 12 naturally infested soils. Detectable target DNA concentrations were three to five times higher after normalization. Our tests also showed that the extraction efficiencies varied on a sample-to-sample basis and were <50%. Therefore, the method introduced here is simple and useful for the accurate quantification of soil-borne pathogenic oomycetes. SIGNIFICANCE AND IMPACT OF THE STUDY Oomycetes include many important plant pathogens. Accurate quantification of these pathogens is essential in the management of diseases. This study reports an easy method utilizing an external DNA control for the normalization of DNA extraction by real-time PCR. By combining two different efficient soil DNA extraction methods, the developed quantification method dramatically improved the results. This study also proves that the developed normalization method is necessary and useful for the accurate quantification of soil-borne plant pathogenic oomycetes.
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Affiliation(s)
- M Li
- College of Life Sciences, Shaanxi Normal University, Xi'an, China
| | - Y Ishiguro
- River Basin Research Center, Gifu University, Gifu, Japan
| | - K Kageyama
- River Basin Research Center, Gifu University, Gifu, Japan
| | - Z Zhu
- College of Life Sciences, Shaanxi Normal University, Xi'an, China
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49
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Rahman MZ, Abdelzaher HMA, Mingzhu L, Motohashi K, Suga H, Kageyama K. Pythium rishiriense sp. nov. from water and P. alternatum sp. nov. from soil, two new species from Japan. FEMS Microbiol Lett 2015; 362:fnv086. [PMID: 26062753 DOI: 10.1093/femsle/fnv086] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/25/2015] [Indexed: 11/14/2022] Open
Abstract
In an investigation of Pythium species in natural ecosystems of Rishiri Island in Northern Japan, two new species, Pythium rishiriense and P. alternatum, were identified based on morphological and molecular analyses. Pythium rishiriense differed morphologically from other Pythium species by its characteristic oogonial formation which occasionally arranged in chains. Pythium alternatum differed morphologically from other Pythium species by its distinguishing sexual organs where oogonia occasionally arranged alternately with antheridia in chains. Pythium rishiriense is a fast growing, high-temperature loving species, while P. alternatum is a slow growing species. Phylogenetic analyses based on the internal transcribed spacer region and cytochrome c oxidase 1 gene sequences showed that these two species are clearly separate from morphologically similar species.
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Affiliation(s)
| | | | - Li Mingzhu
- River Basin Research Center, Gifu University, 1-1 Yanagido, Gifu 501-1193, Japan
| | - Keiichi Motohashi
- Faculty of Regional Environment Science, Tokyo University of Agriculture, Tokyo 156-8502, Japan
| | - Haruhisa Suga
- Life Science Research Center, Gifu University, 1-1 Yanagido, Gifu 501-1193, Japan
| | - Koji Kageyama
- River Basin Research Center, Gifu University, 1-1 Yanagido, Gifu 501-1193, Japan
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50
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Weiland JE, Garrido P, Kamvar ZN, Espíndola AS, Marek SM, Grünwald NJ, Garzón CD. Population Structure of Pythium irregulare, P. ultimum, and P. sylvaticum in Forest Nursery Soils of Oregon and Washington. PHYTOPATHOLOGY 2015; 105:684-694. [PMID: 25607720 DOI: 10.1094/phyto-05-14-0147-r] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Pythium species are important soilborne pathogens occurring in the forest nursery industry of the Pacific Northwest. However, little is known about their genetic diversity or population structure and it is suspected that isolates are moved among forest nurseries on seedling stock and shared field equipment. In order to address these concerns, a total of 115 isolates of three Pythium species (P. irregulare, P. sylvaticum, and P. ultimum) were examined at three forest nurseries using simple sequence repeat (SSR) and amplified fragment length polymorphism (AFLP) markers. Analyses revealed distinct patterns of intraspecific variation for the three species. P. sylvaticum exhibited the most diversity, followed by P. irregulare, while substantial clonality was found in P. ultimum. For both P. irregulare and P. sylvaticum, but not P. ultimum, there was evidence for significant variation among nurseries. However, all three species also exhibited at least two distinct lineages not associated with the nursery of origin. Finally, evidence was found that certain lineages and clonal genotypes, including fungicide-resistant isolates, are shared among nurseries, indicating that pathogen movement has occurred.
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Affiliation(s)
- Jerry E Weiland
- First and sixth authors: U.S. Department of Agriculture-Agriculture Research Service, Horticultural Crops Research Laboratory, and Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331; second, fourth, fifth, and seventh authors: Department of Entomology and Plant Pathology, Oklahoma State University, Stillwater, OK 74074; and third author: Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331
| | - Patricia Garrido
- First and sixth authors: U.S. Department of Agriculture-Agriculture Research Service, Horticultural Crops Research Laboratory, and Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331; second, fourth, fifth, and seventh authors: Department of Entomology and Plant Pathology, Oklahoma State University, Stillwater, OK 74074; and third author: Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331
| | - Zhian N Kamvar
- First and sixth authors: U.S. Department of Agriculture-Agriculture Research Service, Horticultural Crops Research Laboratory, and Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331; second, fourth, fifth, and seventh authors: Department of Entomology and Plant Pathology, Oklahoma State University, Stillwater, OK 74074; and third author: Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331
| | - Andrés S Espíndola
- First and sixth authors: U.S. Department of Agriculture-Agriculture Research Service, Horticultural Crops Research Laboratory, and Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331; second, fourth, fifth, and seventh authors: Department of Entomology and Plant Pathology, Oklahoma State University, Stillwater, OK 74074; and third author: Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331
| | - Stephen M Marek
- First and sixth authors: U.S. Department of Agriculture-Agriculture Research Service, Horticultural Crops Research Laboratory, and Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331; second, fourth, fifth, and seventh authors: Department of Entomology and Plant Pathology, Oklahoma State University, Stillwater, OK 74074; and third author: Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331
| | - Niklaus J Grünwald
- First and sixth authors: U.S. Department of Agriculture-Agriculture Research Service, Horticultural Crops Research Laboratory, and Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331; second, fourth, fifth, and seventh authors: Department of Entomology and Plant Pathology, Oklahoma State University, Stillwater, OK 74074; and third author: Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331
| | - Carla D Garzón
- First and sixth authors: U.S. Department of Agriculture-Agriculture Research Service, Horticultural Crops Research Laboratory, and Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331; second, fourth, fifth, and seventh authors: Department of Entomology and Plant Pathology, Oklahoma State University, Stillwater, OK 74074; and third author: Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331
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