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Vlková-Žlebková M, Yuen FW, McCann HC. Evolving Archetypes: Learning from Pathogen Emergence on a Nonmodel Host. ANNUAL REVIEW OF PHYTOPATHOLOGY 2024; 62:49-68. [PMID: 38885452 DOI: 10.1146/annurev-phyto-021622-095110] [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: 06/20/2024]
Abstract
Research initiatives undertaken in response to disease outbreaks accelerate our understanding of microbial evolution, mechanisms of virulence and resistance, and plant-pathogen coevolutionary interactions. The emergence and global spread of Pseudomonas syringae pv. actinidiae (Psa) on kiwifruit (Actinidia chinensis) showed that there are parallel paths to host adaptation and antimicrobial resistance evolution, accelerated by the movement of mobile elements. Significant progress has been made in identifying type 3 effectors required for virulence and recognition in A. chinensis and Actinidia arguta, broadening our understanding of how host-mediated selection shapes virulence. The rapid development of Actinidia genomics after the Psa3 pandemic began has also generated new insight into molecular mechanisms of immunity and resistance gene evolution in this recently domesticated, nonmodel host. These findings include the presence of close homologs of known resistance genes RPM1 and RPS2 as well as the novel expansion of CCG10-NLRs (nucleotide-binding leucine-rich repeats) in Actinidia spp. The advances and approaches developed during the pandemic response can be applied to new pathosystems and new outbreak events.
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Affiliation(s)
| | - Fang Wei Yuen
- Max Planck Institute for Biology, Tübingen, Germany;
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2
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Liu YH, Wang FL, Ren XL, Li CK, Jin LH, Zhou X. Synthesis, Structural Characterization, and Biological Activities of 1,3,4- Thiadiazole Derivatives Containing Sulfonylpiperazine Structures. Chem Biodivers 2024; 21:e202400408. [PMID: 38441384 DOI: 10.1002/cbdv.202400408] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2024] [Accepted: 03/05/2024] [Indexed: 06/19/2024]
Abstract
To develop novel bacterial biofilm inhibiting agents, a series of 1,3,4-thiadiazole derivatives containing sulfonylpiperazine structures were designed, synthesized, and characterized using 1H nuclear magnetic resonance (1H NMR), 13C nuclear magnetic resonance (13C NMR), and high-resolution mass spectrometry. Meanwhile, their biological activities were evaluated, and the ensuing structure-activity relationships were discussed. The bioassay results showed the substantial antimicrobial efficacy exhibited by most of the compounds. Among them, compound A24 demonstrated a strong efficacy with an EC50 value of 7.8 μg/mL in vitro against the Xanthomonas oryzae pv. oryzicola (Xoc) pathogen, surpassing commercial agents thiodiazole copper (31.8 μg/mL) and bismerthiazol (43.3 μg/mL). Mechanistic investigations into its anti-Xoc properties revealed that compound A24 operates by increasing the permeability of bacterial cell membranes, inhibiting biofilm formation and cell motility, and inducing morphological changes in bacterial cells. Importantly, in vivo tests showed its excellent protective and curative effects on rice bacterial leaf streak. Besides, molecular docking showed that the hydrophobic effect and hydrogen-bond interactions are key factors between the binding of A24 and AvrRxo1-ORF1. Therefore, these results suggest the utilization of 1,3,4-thiadiazole derivatives containing sulfonylpiperazine structures as a bacterial biofilm inhibiting agent, warranting further exploration in the realm of agrochemical development.
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Affiliation(s)
- You-Hua Liu
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals of Guizhou University, Guiyang, 550025, China
| | - Fa-Li Wang
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals of Guizhou University, Guiyang, 550025, China
| | - Xiao-Li Ren
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals of Guizhou University, Guiyang, 550025, China
| | - Chang-Kun Li
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals of Guizhou University, Guiyang, 550025, China
| | - Lin-Hong Jin
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals of Guizhou University, Guiyang, 550025, China
| | - Xia Zhou
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals of Guizhou University, Guiyang, 550025, China
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3
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Colombi E, Bertels F, Doulcier G, McConnell E, Pichugina T, Sohn KH, Straub C, McCann HC, Rainey PB. Rapid dissemination of host metabolism-manipulating genes via integrative and conjugative elements. Proc Natl Acad Sci U S A 2024; 121:e2309263121. [PMID: 38457521 PMCID: PMC10945833 DOI: 10.1073/pnas.2309263121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Accepted: 01/08/2024] [Indexed: 03/10/2024] Open
Abstract
Integrative and conjugative elements (ICEs) are self-transmissible mobile elements that transfer functional genetic units across broad phylogenetic distances. Accessory genes shuttled by ICEs can make significant contributions to bacterial fitness. Most ICEs characterized to date encode readily observable phenotypes contributing to symbiosis, pathogenicity, and antimicrobial resistance, yet the majority of ICEs carry genes of unknown function. Recent observations of rapid acquisition of ICEs in a pandemic lineage of Pseudomonas syringae pv. actinidae led to investigation of the structural and functional diversity of these elements. Fifty-three unique ICE types were identified across the P. syringae species complex. Together they form a distinct family of ICEs (PsICEs) that share a distant relationship to ICEs found in Pseudomonas aeruginosa. PsICEs are defined by conserved backbone genes punctuated by an array of accessory cargo genes, are highly recombinogenic, and display distinct evolutionary histories compared to their bacterial hosts. The most common cargo is a recently disseminated 16-kb mobile genetic element designated Tn6212. Deletion of Tn6212 did not alter pathogen growth in planta, but mutants displayed fitness defects when grown on tricarboxylic acid (TCA) cycle intermediates. RNA-seq analysis of a set of nested deletion mutants showed that a Tn6212-encoded LysR regulator has global effects on chromosomal gene expression. We show that Tn6212 responds to preferred carbon sources and manipulates bacterial metabolism to maximize growth.
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Affiliation(s)
- Elena Colombi
- School of Agriculture, Food and Ecosystem Sciences, Faculty of Science, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Frederic Bertels
- Department of Microbial Population Biology, Max Planck Institute for Evolutionary Biology, Plön 24306, Germany
| | - Guilhem Doulcier
- Laboratoire Biophysique et Évolution, Institut Chemie Biologie Innovation, École Supérieure de Physique et de Chemie Industrielles de la Ville de Paris, Université Paris Science et Lettres, Centre National de al Reserche Scientifique, Paris 75005, France
| | - Ellen McConnell
- Department of Microbial Population Biology, Max Planck Institute for Evolutionary Biology, Plön 24306, Germany
| | - Tatyana Pichugina
- Department of Microbial Population Biology, Max Planck Institute for Evolutionary Biology, Plön 24306, Germany
| | - Kee Hoon Sohn
- Plant Immunity Research Center, Seoul National University, Seoul 08826, Republic of Korea
- Department of Agricultural Biotechnology, Seoul National University, Seoul 08826, Republic of Korea
- Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Republic of Korea
- Plant Genomics and Breeding Institute, Seoul National University, Seoul 08826, Republic of Korea
| | - Christina Straub
- Health and Environment, Institute of Environmental Science and Research, Auckland 1025, New Zealand
- Division of Microbial Ecology, Center for Microbiology and Environmental Systems Science, University of Vienna, Vienna 1030, Austria
| | - Honour C McCann
- Plant Pathogen Evolution Research Group, Max Planck Institute for Biology, Tübingen 72076, Germany
| | - Paul B Rainey
- Department of Microbial Population Biology, Max Planck Institute for Evolutionary Biology, Plön 24306, Germany
- Laboratoire Biophysique et Évolution, Institut Chemie Biologie Innovation, École Supérieure de Physique et de Chemie Industrielles de la Ville de Paris, Université Paris Science et Lettres, Centre National de al Reserche Scientifique, Paris 75005, France
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González AJ, Díaz D, Ciordia M, Landeras E. Occurrence of Pseudomonas syringae pvs. actinidiae, actinidifoliorum and Other P. syringae Strains on Kiwifruit in Northern Spain. Life (Basel) 2024; 14:208. [PMID: 38398717 PMCID: PMC10890144 DOI: 10.3390/life14020208] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Revised: 01/24/2024] [Accepted: 01/29/2024] [Indexed: 02/25/2024] Open
Abstract
Pseudomonas syringae pv. actinidiae (Psa), the agent causing bacterial canker of kiwifruit, has been present in the Principality of Asturias (PA), Northern Spain, since 2013, although with restricted distribution. In this study, 53 strains collected in kiwifruit orchards in PA during the period 2014-2020 were characterized by a polyphasic approach including biochemical and phylogenetic analysis. Thirty-three strains, previously identified by PCR as Psa, have been found to be a homogeneous group in phylogenetic analysis, which seems to indicate that there have been few introductions of the pathogen into the region. Two strains were confirmed as P. syringae pv. actinidifoliorum (Pfm), so this is the first report of Pfm in the PA. The remaining 18 strains were found to be close to P. avellanae and P. syringae pv. antirrhini or to strains described as Pfm look-alikes. Pathogenicity tests carried out on peppers with a selection of strains have shown that both Psa and Pfm caused clear damage, while the 18 atypical strains caused variable lesions. It would be necessary to carry out pathogenicity testing of atypical strains on kiwifruit plants to study the role of these strains in the kiwifruit pathosystem to evaluate their pathogenic potential in this crop.
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Affiliation(s)
- Ana J. González
- Servicio Regional de Investigación y Desarrollo Agroalimentario (SERIDA), Ctra. AS-267, PK 19, 33300 Villaviciosa, Spain; (D.D.); (M.C.)
| | - David Díaz
- Servicio Regional de Investigación y Desarrollo Agroalimentario (SERIDA), Ctra. AS-267, PK 19, 33300 Villaviciosa, Spain; (D.D.); (M.C.)
| | - Marta Ciordia
- Servicio Regional de Investigación y Desarrollo Agroalimentario (SERIDA), Ctra. AS-267, PK 19, 33300 Villaviciosa, Spain; (D.D.); (M.C.)
| | - Elena Landeras
- Laboratorio de Sanidad Vegetal del Principado de Asturias, C/Lucas Rodríguez Pire, 4-Bajo, 33011 Oviedo, Spain;
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Santos MG, Nunes da Silva M, Vasconcelos MW, Carvalho SMP. Scientific and technological advances in the development of sustainable disease management tools: a case study on kiwifruit bacterial canker. FRONTIERS IN PLANT SCIENCE 2024; 14:1306420. [PMID: 38273947 PMCID: PMC10808555 DOI: 10.3389/fpls.2023.1306420] [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: 10/03/2023] [Accepted: 12/21/2023] [Indexed: 01/27/2024]
Abstract
Plant disease outbreaks are increasing in a world facing climate change and globalized markets, representing a serious threat to food security. Kiwifruit Bacterial Canker (KBC), caused by the bacterium Pseudomonas syringae pv. actinidiae (Psa), was selected as a case study for being an example of a pandemic disease that severely impacted crop production, leading to huge economic losses, and for the effort that has been made to control this disease. This review provides an in-depth and critical analysis on the scientific progress made for developing alternative tools for sustainable KBC management. Their status in terms of technological maturity is discussed and a set of opportunities and threats are also presented. The gradual replacement of susceptible kiwifruit cultivars, with more tolerant ones, significantly reduced KBC incidence and was a major milestone for Psa containment - which highlights the importance of plant breeding. Nonetheless, this is a very laborious process. Moreover, the potential threat of Psa evolving to more virulent biovars, or resistant lineages to existing control methods, strengthens the need of keep on exploring effective and more environmentally friendly tools for KBC management. Currently, plant elicitors and beneficial fungi and bacteria are already being used in the field with some degree of success. Precision agriculture technologies, for improving early disease detection and preventing pathogen dispersal, are also being developed and optimized. These include hyperspectral technologies and forecast models for Psa risk assessment, with the latter being slightly more advanced in terms of technological maturity. Additionally, plant protection products based on innovative formulations with molecules with antibacterial activity against Psa (e.g., essential oils, phages and antimicrobial peptides) have been validated primarily in laboratory trials and with few compounds already reaching field application. The lessons learned with this pandemic disease, and the acquired scientific and technological knowledge, can be of importance for sustainably managing other plant diseases and handling future pandemic outbreaks.
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Affiliation(s)
- Miguel G. Santos
- GreenUPorto—Sustainable Agrifood Production Research Centre/Inov4Agro, DGAOT, Faculty of Sciences of the University of Porto, Vairão, Portugal
| | - Marta Nunes da Silva
- GreenUPorto—Sustainable Agrifood Production Research Centre/Inov4Agro, DGAOT, Faculty of Sciences of the University of Porto, Vairão, Portugal
- Universidade Católica Portuguesa, CBQF – Centro de Biotecnologia e Química Fina – Laboratório Associado, Escola Superior de Biotecnologia, Porto, Portugal
| | - Marta W. Vasconcelos
- Universidade Católica Portuguesa, CBQF – Centro de Biotecnologia e Química Fina – Laboratório Associado, Escola Superior de Biotecnologia, Porto, Portugal
| | - Susana M. P. Carvalho
- GreenUPorto—Sustainable Agrifood Production Research Centre/Inov4Agro, DGAOT, Faculty of Sciences of the University of Porto, Vairão, Portugal
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Subedi A, Barrera LBTDL, Ivey ML, Egel DS, Kebede M, Kara S, Aysan Y, Minsavage GV, Roberts PD, Jones JB, Goss EM. Population Genomics Reveals an Emerging Lineage of Xanthomonas perforans on Pepper. PHYTOPATHOLOGY 2024; 114:241-250. [PMID: 37432099 DOI: 10.1094/phyto-04-23-0128-r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/12/2023]
Abstract
Xanthomonas perforans-the dominant causal agent of bacterial leaf spot of tomato-is an emerging pathogen of pepper, indicative of a potential host expansion across the southeastern United States. However, studies of the genetic diversity and evolution of X. perforans from pepper remain limited. In this study, the whole-genome sequences of 35 X. perforans strains isolated from pepper from four fields and two transplant facilities across southwest Florida between 2019 and 2021 were used to compare genomic divergence, evolution, and variation in type III secreted effectors. Phylogenetic analysis based on core genes revealed that all 35 X. perforans strains formed one genetic cluster with pepper and tomato strains from Alabama and Turkey and were closely related to strains isolated from tomato in Indiana, Mexico, and Louisiana. The in planta population growth of tomato strains isolated from Indiana, Mexico, Louisiana, and Turkey in pepper leaf mesophyll was on par with pepper X. perforans and X. euvesicatoria strains. Molecular clock analysis of the 35 Florida strains dated their emergence to approximately 2017. While strains varied in copper tolerance, all sequenced strains harbored the avrHah1 transcription activation-like effector located on a conjugative plasmid, not previously reported in Florida. Our findings suggest that there is a geographically distributed lineage of X. perforans strains on tomato that has the genetic background to cause disease on pepper. Moreover, this study clarifies potential adaptive variants of X. perforans on pepper that could help forecast the emergence of such strains and enable immediate or preemptive intervention.
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Affiliation(s)
- Aastha Subedi
- Department of Plant Pathology, University of Florida, Gainesville, FL, U.S.A
| | | | - Melanie Lewis Ivey
- Department of Plant Pathology, The Ohio State University, Wooster, OH, U.S.A
| | - Daniel S Egel
- Botany and Plant Pathology Department, Purdue University, West Lafayette, IN, U.S.A
| | - Misrak Kebede
- Biotechnology Department, Collage of Biological and Chemical Engineering, Addis Ababa Science and Technology University, Addis Ababa, Ethiopia
| | - Serhat Kara
- Alata Horticulture Research Institute, Mersin, Turkey
| | - Yesim Aysan
- Department of Plant Protection, Cukurova University, Adana, Turkey
| | - Gerald V Minsavage
- Department of Plant Pathology, University of Florida, Gainesville, FL, U.S.A
| | - Pamela D Roberts
- Southwest Florida Research & Education Center, University of Florida, Immokalee, FL, U.S.A
| | - Jeffrey B Jones
- Department of Plant Pathology, University of Florida, Gainesville, FL, U.S.A
| | - Erica M Goss
- Department of Plant Pathology, University of Florida, Gainesville, FL, U.S.A
- Emerging Pathogens Institute, University of Florida, Gainesville, FL, U.S.A
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7
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Pei Y, Ma L, Zheng X, Yao K, Fu X, Chen H, Chang X, Zhang M, Gong G. Identification and Genetic Characterization of Pseudomonas syringae pv. actinidiae from Kiwifruit in Sichuan, China. PLANT DISEASE 2023; 107:3248-3258. [PMID: 37005505 DOI: 10.1094/pdis-01-23-0005-re] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
Pseudomonas syringae pv. actinidiae causes kiwifruit bacterial canker and poses a major threat to the kiwifruit industry. This study aimed to investigate the genetic characteristics of the P. syringae pv. actinidiae population from kiwifruit in Sichuan, China. Sixty-seven isolates obtained from diseased plants were characterized using morphological features, multiplex-PCR, and multilocus sequence analysis (MLSA). The isolates exhibited the typical colony morphology of P. syringae pv. actinidiae. Multiplex PCR amplification identified every isolate as P. syringae pv. actinidiae biovar 3. MLSA of the three housekeeping genes gapA, gyrB, and pfk, revealed that the reference strains of the five described biovars were clearly distinguished by a combined phylogenetic tree, and all of the tested isolates clustered with the reference strains of P. syringae pv. actinidiae biovar 3. Through a phylogenetic tree constructed from a single gene, it was found that pkf gene alone could distinguish biovar 3 from the other biovars. Furthermore, all P. syringae pv. actinidiae isolates analyzed by BOX-A1R-based repetitive extragenic palindromic (BOX)-PCR and enterobacterial repetitive intergenic consensus (ERIC)-PCR clustered into four groups. The clustering results of BOX- and ERIC-PCR indicated that group III had the largest number of isolates, accounting for 56.72 and 61.19% of all 67 isolates, respectively, and the two characterization methods were similar and complementary. The results of this study revealed that the genomes of P. syringae pv. actinidiae isolates from Sichuan had rich genetic diversity but no obvious correlation was found between clustering and geographical region. This research provides novel methodologies for rapidly detecting kiwifruit bacterial canker pathogen and a molecular differentiation at genetic level of P. syringae pv. actinidiae biovar diversity in China.
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Affiliation(s)
- Yangang Pei
- Department of Plant Pathology, Sichuan Agricultural University, Chengdu 611130, P.R. China
| | - Li Ma
- Department of Plant Pathology, Sichuan Agricultural University, Chengdu 611130, P.R. China
- Plant Protection Station, Sichuan Provincial Department of Agriculture and Rural Affairs, Chengdu 610041, P.R. China
| | - Xiaojuan Zheng
- Department of Plant Pathology, Sichuan Agricultural University, Chengdu 611130, P.R. China
| | - Kaikai Yao
- Department of Plant Pathology, Sichuan Agricultural University, Chengdu 611130, P.R. China
| | - Xiangru Fu
- Department of Plant Pathology, Sichuan Agricultural University, Chengdu 611130, P.R. China
| | - Huabao Chen
- Department of Plant Pathology, Sichuan Agricultural University, Chengdu 611130, P.R. China
| | - Xiaoli Chang
- Department of Plant Pathology, Sichuan Agricultural University, Chengdu 611130, P.R. China
| | - Ming Zhang
- Department of Plant Pathology, Sichuan Agricultural University, Chengdu 611130, P.R. China
| | - Guoshu Gong
- Department of Plant Pathology, Sichuan Agricultural University, Chengdu 611130, P.R. China
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Hulme PE, Beggs JR, Binny RN, Bray JP, Cogger N, Dhami MK, Finlay-Smits SC, French NP, Grant A, Hewitt CL, Jones EE, Lester PJ, Lockhart PJ. Emerging advances in biosecurity to underpin human, animal, plant, and ecosystem health. iScience 2023; 26:107462. [PMID: 37636074 PMCID: PMC10450416 DOI: 10.1016/j.isci.2023.107462] [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] [Indexed: 08/29/2023] Open
Abstract
One Biosecurity is an interdisciplinary approach to policy and research that builds on the interconnections between human, animal, plant, and ecosystem health to effectively prevent and mitigate the impacts of invasive alien species. To support this approach requires that key cross-sectoral research innovations be identified and prioritized. Following an interdisciplinary horizon scan for emerging research that underpins One Biosecurity, four major interlinked advances were identified: implementation of new surveillance technologies adopting state-of-the-art sensors connected to the Internet of Things, deployable handheld molecular and genomic tracing tools, the incorporation of wellbeing and diverse human values into biosecurity decision-making, and sophisticated socio-environmental models and data capture. The relevance and applicability of these innovations to address threats from pathogens, pests, and weeds in both terrestrial and aquatic ecosystems emphasize the opportunity to build critical mass around interdisciplinary teams at a global scale that can rapidly advance science solutions targeting biosecurity threats.
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Affiliation(s)
- Philip E. Hulme
- The Centre for One Biosecurity Research, Analysis and Synthesis, Lincoln University, PO Box 85084, Lincoln, Christchurch 7648, New Zealand
- Department of Pest Management and Conservation, Lincoln University, PO Box 85084, Lincoln, Christchurch 7648, New Zealand
| | - Jacqueline R. Beggs
- Centre for Biodiversity and Biosecurity, School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland 1142, New Zealand
| | - Rachelle N. Binny
- Manaaki Whenua - Landcare Research, PO Box 69040, Lincoln, New Zealand
| | - Jonathan P. Bray
- The Centre for One Biosecurity Research, Analysis and Synthesis, Lincoln University, PO Box 85084, Lincoln, Christchurch 7648, New Zealand
- Department of Pest Management and Conservation, Lincoln University, PO Box 85084, Lincoln, Christchurch 7648, New Zealand
| | - Naomi Cogger
- Tāwharau Ora, School of Veterinary Science, Massey University, Palmerston North 4472, New Zealand
| | - Manpreet K. Dhami
- Manaaki Whenua - Landcare Research, PO Box 69040, Lincoln, New Zealand
| | | | - Nigel P. French
- Tāwharau Ora, School of Veterinary Science, Massey University, Palmerston North 4472, New Zealand
| | - Andrea Grant
- Scion, 10 Kyle Street, Riccarton, Christchurch 8011, New Zealand
| | - Chad L. Hewitt
- The Centre for One Biosecurity Research, Analysis and Synthesis, Lincoln University, PO Box 85084, Lincoln, Christchurch 7648, New Zealand
| | - Eirian E. Jones
- The Centre for One Biosecurity Research, Analysis and Synthesis, Lincoln University, PO Box 85084, Lincoln, Christchurch 7648, New Zealand
- Department of Pest Management and Conservation, Lincoln University, PO Box 85084, Lincoln, Christchurch 7648, New Zealand
| | - Phil J. Lester
- School of Biological Sciences, Victoria University of Wellington, PO Box 600, Wellington, New Zealand
| | - Peter J. Lockhart
- School of Natural Sciences, Massey University, Palmerston North 4472, New Zealand
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Lin L, Li L, Tao M, Wu Q, Zhou L, Wang B, Wang L, Shao X, Zhong C, Qian G. Assembly of an active microbial consortium by engineering compatible combinations containing foreign and native biocontrol bacteria of kiwifruit. Comput Struct Biotechnol J 2023; 21:3672-3679. [PMID: 37576746 PMCID: PMC10412838 DOI: 10.1016/j.csbj.2023.07.021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 07/12/2023] [Accepted: 07/19/2023] [Indexed: 08/15/2023] Open
Abstract
Assembling functional bacterial biocontrol consortia is expected to expand the scope and efficiency of biocontrol agents. Generally, bacterial interspecies interactions lead to incompatibility events, as bacteria can produce antibacterial compounds and/or assemble contact-dependent killing (CDK) devices. Here, we aimed to assemble a bacterial consortium comprising Lysobacter enzymogenes OH11 and Bacillus safensis ZK-1 for the synergistic control of bacterial and fungal diseases of kiwifruit. ZK-1, a native kiwifruit biocontrol bacterium, is effective against Pseudomonas syringae pv. actinidiae (Psa) that causes bacterial kiwifruit canker, but has weak antifungal activity. OH11 is a foreign kiwifruit biocontrol agent with strong antifungal activity. While OH11 was unable to produce anti-Gram-negative metabolites, this strain could utilize type IV secretion system as an antibacterial CDK weapon. We first observed that OH11 could inhibit growth of ZK-1 by generating diffusible anti-Gram-positive antibiotic WAP-8294A2, whereas ZK-1 failed to generate diffusible antibacterial compound to inhibit growth of OH11. To disrupt this interspecies incompatibility, we generated a transgenic OH11-derived strain, OH11W, by deleting the WAP-8294A2 biosynthetic gene and found that OH11W did not kill ZK-1. We further observed that when OH11W and ZK-1 were co-inoculated on agar plates, no CDK effect was observed between them, whereas co-culture of OH11W or ZK-1 with Psa on agar plates resulted in Psa killing, suggesting L. enzymogenes and B. safensis assemble antibacterial CDK weapons against bacterial pathogens, and these CDK weapons did not affect the compatibility between OH11W and ZK-1. Based on these findings, we assembled an OH11W/ZK-1 dependent consortium that was shown to be functional in controlling bacterial canker and several representative fungal diseases of kiwifruit.
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Affiliation(s)
- Long Lin
- Key Laboratory of Biological interactions and Crop Health, Key Laboratory of Integrated Management of Crop Diseases and Pests, College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Li Li
- CAS Engineering Laboratory for Kiwifruit Industrial Technology, CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei Province 430074, China
| | - Min Tao
- Key Laboratory of Biological interactions and Crop Health, Key Laboratory of Integrated Management of Crop Diseases and Pests, College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Qianhua Wu
- Key Laboratory of Biological interactions and Crop Health, Key Laboratory of Integrated Management of Crop Diseases and Pests, College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Longteng Zhou
- Key Laboratory of Biological interactions and Crop Health, Key Laboratory of Integrated Management of Crop Diseases and Pests, College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Bozhen Wang
- Key Laboratory of Biological interactions and Crop Health, Key Laboratory of Integrated Management of Crop Diseases and Pests, College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Limin Wang
- Key Laboratory of Biological interactions and Crop Health, Key Laboratory of Integrated Management of Crop Diseases and Pests, College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Xiaolong Shao
- Key Laboratory of Biological interactions and Crop Health, Key Laboratory of Integrated Management of Crop Diseases and Pests, College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Caihong Zhong
- CAS Engineering Laboratory for Kiwifruit Industrial Technology, CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei Province 430074, China
| | - Guoliang Qian
- Key Laboratory of Biological interactions and Crop Health, Key Laboratory of Integrated Management of Crop Diseases and Pests, College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, PR China
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10
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Iruegas-Bocardo F, Weisberg AJ, Riutta ER, Kilday K, Bonkowski JC, Creswell T, Daughtrey ML, Rane K, Grünwald NJ, Chang JH, Putnam ML. Whole Genome Sequencing-Based Tracing of a 2022 Introduction and Outbreak of Xanthomonas hortorum pv. pelargonii. PHYTOPATHOLOGY 2023; 113:975-984. [PMID: 36515656 DOI: 10.1094/phyto-09-22-0321-r] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Globalization has made agricultural commodities more accessible, available, and affordable. However, their global movement increases the potential for invasion by pathogens and necessitates development and implementation of sensitive, rapid, and scalable surveillance methods. Here, we used 35 strains, isolated by multiple diagnostic laboratories, as a case study for using whole genome sequence data in a plant disease diagnostic setting. Twenty-seven of the strains were isolated in 2022 and identified as Xanthomonas hortorum pv. pelargonii. Eighteen of these strains originated from material sold by a plant breeding company that had notified clients following a release of infected geranium cuttings. Analyses of whole genome sequences revealed epidemiological links among the 27 strains from different growers that confirmed a common source of the outbreak and uncovered likely secondary spread events within facilities that housed plants originating from different plant breeding companies. Whole genome sequencing data were also analyzed to reveal how preparatory and analytical methods can impact conclusions on outbreaks of clonal pathogenic strains. The results demonstrate the potential power of using whole genome sequencing among a network of diagnostic labs and highlight how sharing such data can help shorten response times to mitigate outbreaks more expediently and precisely than standard methods.
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Affiliation(s)
| | - Alexandra J Weisberg
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331
| | - Elizabeth R Riutta
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331
| | - Kameron Kilday
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331
| | - John C Bonkowski
- Botany and Plant Pathology, Purdue University, West Lafayette, IN 47907
| | - Tom Creswell
- Botany and Plant Pathology, Purdue University, West Lafayette, IN 47907
| | - Margery L Daughtrey
- Long Island Horticultural Research and Extension Center, Cornell University, Riverhead, NY 11901
| | - Karen Rane
- Department of Entomology, University of Maryland, College Park, MD 20742
| | - Niklaus J Grünwald
- Horticultural Crops Research Laboratory, U.S. Department of Agriculture-Agricultural Research Service, Corvallis, OR 97331
| | - Jeff H Chang
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331
| | - Melodie L Putnam
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331
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11
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Jayaraman J, Yoon M, Hemara LM, Bohne D, Tahir J, Chen RKY, Brendolise C, Rikkerink EHA, Templeton MD. Contrasting effector profiles between bacterial colonisers of kiwifruit reveal redundant roles converging on PTI-suppression and RIN4. THE NEW PHYTOLOGIST 2023; 238:1605-1619. [PMID: 36856342 DOI: 10.1111/nph.18848] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Accepted: 02/14/2023] [Indexed: 06/18/2023]
Abstract
Testing effector knockout strains of the Pseudomonas syringae pv. actinidiae biovar 3 (Psa3) for reduced in planta growth in their native kiwifruit host revealed a number of nonredundant effectors that contribute to Psa3 virulence. Conversely, complementation in the weak kiwifruit pathogen P. syringae pv. actinidifoliorum (Pfm) for increased growth identified redundant Psa3 effectors. Psa3 effectors hopAZ1a and HopS2b and the entire exchangeable effector locus (ΔEEL; 10 effectors) were significant contributors to bacterial colonisation of the host and were additive in their effects on virulence. Four of the EEL effectors (HopD1a, AvrB2b, HopAW1a and HopD2a) redundantly contribute to virulence through suppression of pattern-triggered immunity (PTI). Important Psa3 effectors include several redundantly required effectors early in the infection process (HopZ5a, HopH1a, AvrPto1b, AvrRpm1a and HopF1e). These largely target the plant immunity hub, RIN4. This comprehensive effector profiling revealed that Psa3 carries robust effector redundancy for a large portion of its effectors, covering a few functions critical to disease.
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Affiliation(s)
- Jay Jayaraman
- The New Zealand Institute for Plant and Food Research Ltd, Mt. Albert Research Centre, Auckland, 1025, New Zealand
| | - Minsoo Yoon
- The New Zealand Institute for Plant and Food Research Ltd, Mt. Albert Research Centre, Auckland, 1025, New Zealand
| | - Lauren M Hemara
- The New Zealand Institute for Plant and Food Research Ltd, Mt. Albert Research Centre, Auckland, 1025, New Zealand
- School of Biological Sciences, University of Auckland, Auckland, 1010, New Zealand
| | - Deborah Bohne
- The New Zealand Institute for Plant and Food Research Ltd, Mt. Albert Research Centre, Auckland, 1025, New Zealand
| | - Jibran Tahir
- The New Zealand Institute for Plant and Food Research Ltd, Mt. Albert Research Centre, Auckland, 1025, New Zealand
| | - Ronan K Y Chen
- The New Zealand Institute for Plant and Food Research Ltd, Food Industry Science Centre, Palmerston North, 4472, New Zealand
| | - Cyril Brendolise
- The New Zealand Institute for Plant and Food Research Ltd, Mt. Albert Research Centre, Auckland, 1025, New Zealand
| | - Erik H A Rikkerink
- The New Zealand Institute for Plant and Food Research Ltd, Mt. Albert Research Centre, Auckland, 1025, New Zealand
| | - Matthew D Templeton
- The New Zealand Institute for Plant and Food Research Ltd, Mt. Albert Research Centre, Auckland, 1025, New Zealand
- School of Biological Sciences, University of Auckland, Auckland, 1010, New Zealand
- Bioprotection Aotearoa, Lincoln, 7647, New Zealand
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12
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Xie T, Wu X, Luo L, Qu Y, Fan R, Wu S, Long Y, Zhao Z. Natural variation in the hrpL promoter renders the phytopathogen Pseudomonas syringae pv. actinidiae nonpathogenic. MOLECULAR PLANT PATHOLOGY 2023; 24:262-271. [PMID: 36600466 PMCID: PMC9923390 DOI: 10.1111/mpp.13289] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 11/22/2022] [Accepted: 12/09/2022] [Indexed: 05/14/2023]
Abstract
The genetic basis underlying loss-of-virulence mutations that arise among natural phytopathogen populations is not well documented. In this study, we examined the virulence of 377 isolates of Pseudomonas syringae pv. actinidiae biovar 3 (Psa3) that were isolated from 76 kiwifruit orchards suffering from bacterial canker disease. Eighty-four nonpathogenic isolates were identified in 40 orchards. A nonpathogenic isolate G166 was found to be defective in hrpL transcription and the downstream type III secretion system (T3SS)-dependent phenotypes. Comparative genomics and complementary expression assay revealed that a single-base "G" insertion in the hrpL promoter blocks gene transcription by reducing promoter activity. The electrophoretic mobility shift assay showed that the genetic variation impairs σ54 /promoter binding during gene transcription under hrp-inducing conditions, resulting in lower expression of hrpL. A PCR-restriction fragment length polymorphism assay was performed to trace the evolutionary history of this mutation, which revealed the independent onset of genetic variations in natural Psa3 populations. We also found that nonpathogenic variants outperformed virulent Psa3 bacteria for both epiphytic and apoplast colonization of kiwifruit leaves in mixed inoculations. Our study highlights a novel mechanism for loss of virulence in Psa3 and provides insight into bacterial adaptive evolution under natural settings.
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Affiliation(s)
- Ting Xie
- Department of Plant Pathology, College of AgricultureGuizhou UniversityGuiyangChina
| | - Xiujiao Wu
- Department of Plant Pathology, College of AgricultureGuizhou UniversityGuiyangChina
| | - Le Luo
- Department of Plant Pathology, College of AgricultureGuizhou UniversityGuiyangChina
| | - Yuan Qu
- Department of Plant Pathology, College of AgricultureGuizhou UniversityGuiyangChina
| | - Rong Fan
- Kiwifruit Engineering & Technology Research CenterGuizhou UniversityGuiyangChina
| | - Shiping Wu
- Institute of Plant ProtectionGuizhou Academy of Agricultural SciencesGuiyangChina
| | - Youhua Long
- Kiwifruit Engineering & Technology Research CenterGuizhou UniversityGuiyangChina
| | - Zhibo Zhao
- Department of Plant Pathology, College of AgricultureGuizhou UniversityGuiyangChina
- Kiwifruit Engineering & Technology Research CenterGuizhou UniversityGuiyangChina
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13
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Hulin MT, Rabiey M, Zeng Z, Vadillo Dieguez A, Bellamy S, Swift P, Mansfield JW, Jackson RW, Harrison RJ. Genomic and functional analysis of phage-mediated horizontal gene transfer in Pseudomonas syringae on the plant surface. THE NEW PHYTOLOGIST 2023; 237:959-973. [PMID: 36285389 PMCID: PMC10107160 DOI: 10.1111/nph.18573] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Accepted: 10/19/2022] [Indexed: 06/16/2023]
Abstract
Many strains of Pseudomonas colonise plant surfaces, including the cherry canker pathogens, Pseudomonas syringae pathovars syringae and morsprunorum. We have examined the genomic diversity of P. syringae in the cherry phyllosphere and focused on the role of prophages in transfer of genes encoding Type 3 secreted effector (T3SE) proteins contributing to the evolution of virulence. Phylogenomic analysis was carried out on epiphytic pseudomonads in the UK orchards. Significant differences in epiphytic populations occurred between regions. Nonpathogenic strains were found to contain reservoirs of T3SE genes. Members of P. syringae phylogroups 4 and 10 were identified for the first time from Prunus. Using bioinformatics, we explored the presence of the gene encoding T3SE HopAR1 within related prophage sequences in diverse P. syringae strains including cherry epiphytes and pathogens. Results indicated that horizontal gene transfer (HGT) of this effector between phylogroups may have involved phage. Prophages containing hopAR1 were demonstrated to excise, circularise and transfer the gene on the leaf surface. The phyllosphere provides a dynamic environment for prophage-mediated gene exchange and the potential for the emergence of new more virulent pathotypes. Our results suggest that genome-based epidemiological surveillance of environmental populations will allow the timely application of control measures to prevent damaging diseases.
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Affiliation(s)
- Michelle T. Hulin
- NIABLawrence Weaver RoadCambridgeCB3 0LEUK
- The Sainsbury LaboratoryNorwichNR4 7UHUK
| | - Mojgan Rabiey
- School of Biosciences and the Birmingham Institute of Forest ResearchUniversity of BirminghamBirminghamB15 2TTUK
| | - Ziyue Zeng
- NIABLawrence Weaver RoadCambridgeCB3 0LEUK
| | | | | | - Phoebe Swift
- School of Biosciences and the Birmingham Institute of Forest ResearchUniversity of BirminghamBirminghamB15 2TTUK
| | | | - Robert W. Jackson
- School of Biosciences and the Birmingham Institute of Forest ResearchUniversity of BirminghamBirminghamB15 2TTUK
| | - Richard J. Harrison
- NIABLawrence Weaver RoadCambridgeCB3 0LEUK
- Present address:
Plant Science GroupWageningen University and ResearchWageningen6708WBthe Netherlands
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14
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Luo J, Dai D, Lv L, Ahmed T, Chen L, Wang Y, An Q, Sun G, Li B. Advancements in the Use of Bacteriophages to Combat the Kiwifruit Canker Phytopathogen Pseudomonas syringae pv. actinidiae. Viruses 2022; 14:2704. [PMID: 36560706 PMCID: PMC9785728 DOI: 10.3390/v14122704] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2022] [Revised: 11/27/2022] [Accepted: 11/29/2022] [Indexed: 12/05/2022] Open
Abstract
Over the last several decades, kiwifruit production has been severely damaged by the bacterial plant pathogen Pseudomonas syringae pv. actinidiae (Psa), resulting in severe economic losses worldwide. Currently, copper bactericides and antibiotics are the main tools used to control this bacterial disease. However, their use is becoming increasingly ineffective due to the emergence of antibiotic resistance. In addition, environmental issues and the changes in the composition of soil bacterial communities are also concerning when using these substances. Although biocontrol methods have shown promising antibacterial effects on Psa infection under in vitro conditions, the efficiency of antagonistic bacteria and fungi when deployed under field conditions remains unclear. Therefore, it is crucial to develop a phage-based biocontrol strategy for this bacterial pathogen. Due to the specificity of the target bacteria and for the benefit of the environment, bacteriophages (phages) have been widely regarded as promising biological agents to control plant, animal, and human bacterial diseases. An increasing number of studies focus on the use of phages for the control of plant diseases, including the kiwifruit bacterial canker. In this review, we first introduce the characteristics of the Psa-induced kiwifruit canker, followed by a description of the diversity and virulence of Psa strains. The main focus of the review is the description of recent advances in the isolation of Psa phages and their characterization, including morphology, host range, lytic activity, genome characterization, and lysis mechanism, but we also describe the biocontrol strategies together with potential challenges introduced by abiotic factors, such as high temperature, extreme pH, and UV irradiation in kiwifruit orchards. The information presented in this review highlights the potential role of phages in controlling Psa infection to ensure plant protection.
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Affiliation(s)
- Jinyan Luo
- Department of Plant Quarantine, Shanghai Extension and Service Center of Agriculture Technology, Shanghai 201103, China
| | - Dejiang Dai
- Station for the Plant Protection & Quarantine and Control of Agrochemicals Zhejiang Province, Hangzhou 310004, China
| | - Luqiong Lv
- State Key Laboratory of Rice Biology, Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Temoor Ahmed
- State Key Laboratory of Rice Biology, Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Lei Chen
- Department of Plant Quarantine, Shanghai Extension and Service Center of Agriculture Technology, Shanghai 201103, China
| | - Yanli Wang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Qianli An
- State Key Laboratory of Rice Biology, Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Guochang Sun
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Bin Li
- State Key Laboratory of Rice Biology, Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China
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15
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The OmpR-like Transcription Factor as a Negative Regulator of hrpR/S in Pseudomonas syringae pv. actinidiae. Int J Mol Sci 2022; 23:ijms232012306. [PMID: 36293158 PMCID: PMC9602974 DOI: 10.3390/ijms232012306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2022] [Revised: 09/28/2022] [Accepted: 10/10/2022] [Indexed: 11/05/2022] Open
Abstract
Bacterial canker of kiwifruit is a devastating disease caused by Pseudomonas syringae pv. actinidiae (Psa). The type III secretion system (T3SS), which translocates effectors into plant cells to subvert plant immunity and promote extracellular bacterial growth, is required for Psa virulence. Despite that the “HrpR/S-HrpL” cascade that sophisticatedly regulates the expression of T3SS and effectors has been well documented, the transcriptional regulators of hrpR/S remain to be determined. In this study, the OmpR-like transcription factor, previously identified by DNA pull-down assay, was found to be involved in the regulation of hrpR/S genes, and its regulatory mechanisms and other functions in Psa were explored through techniques including gene knockout and overexpression, ChIP-seq, and RNA-seq. The OmpR-like transcription factor had binding sites in the promoter region of the hrpR/S, and the transcriptional level of the hrpR/S increased after the deletion of OmpR-like and decreased upon its overexpression in an OmpR-like deletion background. Additionally, OmpR-like overexpression reduced the strain’s capacity to form biofilms and lipopolysaccharides, led to its slow growth in King’s B medium, and reduced its swimming ability, although there was no significant effect on its pathogenicity against kiwifruit hosts. Our results indicated that OmpR-like directly and negatively regulates the transcription of hrpR/S and may be involved in the regulation of multiple biological processes in Psa. Our results provide a basis for further understanding the transcriptional regulation mechanism of hrpR/S in Psa.
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16
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Yu JJ, Wei WK, Zhang Y, Cox RJ, He J, Liu JK, Feng T. Terpenoids from Kiwi endophytic fungus Bipolaris sp. and their antibacterial activity against Pseudomonas syringae pv. actinidiae. Front Chem 2022; 10:990734. [PMID: 36118317 PMCID: PMC9475172 DOI: 10.3389/fchem.2022.990734] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2022] [Accepted: 08/08/2022] [Indexed: 11/13/2022] Open
Abstract
A chemical investigation on the kiwi endophytic fungus Bipolaris sp. Resulted in the isolation of eight new terpenoids (1–8) and five known analogues (9–13). Compounds 1–5 are novel sativene sesquiterpenoids containing three additional skeletal carbons, while compounds 4 and 5 are rare dimers. Compounds 6–8 and 13 are sesterterpenoids that have been identified from this species for the first time. Compounds 4 and 5 showed antibacterial activity against kiwifruit canker pathogen Pseudomonas syringae pv. Actinidiae (Psa) with MIC values of 32 and 64 μg/ml, respectively.
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Affiliation(s)
- Jun-Jie Yu
- School of Pharmaceutical Sciences, South-Central Minzu University, Wuhan, China
| | - Wen-Ke Wei
- School of Pharmaceutical Sciences, South-Central Minzu University, Wuhan, China
| | - Yu Zhang
- State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Russell J. Cox
- Institute for Organic Chemistry and Biomolekulares Wirkstoffzentrum (BMWZ), Hannover, Germany
| | - Juan He
- School of Pharmaceutical Sciences, South-Central Minzu University, Wuhan, China
- *Correspondence: Juan He, ; Ji-Kai Liu, ; Tao Feng,
| | - Ji-Kai Liu
- School of Pharmaceutical Sciences, South-Central Minzu University, Wuhan, China
- *Correspondence: Juan He, ; Ji-Kai Liu, ; Tao Feng,
| | - Tao Feng
- School of Pharmaceutical Sciences, South-Central Minzu University, Wuhan, China
- *Correspondence: Juan He, ; Ji-Kai Liu, ; Tao Feng,
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17
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Genomic Variation and Host Interaction among Pseudomonas syringae pv. actinidiae Strains in Actinidia chinensis ‘Hongyang’. Int J Mol Sci 2022; 23:ijms23179743. [PMID: 36077140 PMCID: PMC9456109 DOI: 10.3390/ijms23179743] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 08/24/2022] [Accepted: 08/24/2022] [Indexed: 11/17/2022] Open
Abstract
Kiwifruit bacterial canker is a recent epidemic disease caused by Pseudomonas syringae pv. actinidiae (Psa), which has undergone worldwide expansion in a short time and resulted in significant economic losses. ‘Hongyang’ (Actinidia chinensis), a widely grown cultivar because of its health-beneficial nutrients and appreciated red-centered inner pericarp, is highly sensitive to Psa. In this work, ten Psa strains were isolated from ‘Hongyang’ and sequenced for genome analysis. The results indicated divergences in pathogenicity and pathogenic-related genes among the Psa strains. Significantly, the interruption at the 596 bp of HrpR in two low-pathogenicity strains reemphasized this gene, expressing a transcriptional regulator for the effector secretion system, as an important pathogenicity-associated locus of Psa. The transcriptome analysis of ‘Hongyang’ infected with different Psa strains was performed by RNA-seq of stem tissues locally (at the inoculation site) and systemically. Psa infection re-programmed the host genes expression, and the susceptibility to Psa might be attributed to the down-regulation of several genes involved in plant-pathogen interactions, especially calcium signaling transduction, as well as fatty acid elongation. This suppression was found in both low- and high-pathogenicity Psa inoculated tissues, but the effect was stronger with more virulent strains. Taken together, the divergences of P. syringae pv. actinidiae in pathogenicity, genome, and resulting transcriptomic response of A. chinensis provide insights into unraveling the molecular mechanism of Psa-kiwifruit interactions and resistance improvement in the kiwifruit crop.
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18
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Zhi T, Liu Q, Xie T, Ding Y, Hu R, Sun Y, Fan R, Long Y, Zhao Z. Identification of Genetic and Chemical Factors Affecting Type III Secretion System Expression in Pseudomonas syringae pv. actinidiae Biovar 3 Using a Luciferase Reporter Construct. PHYTOPATHOLOGY 2022; 112:1610-1619. [PMID: 35240868 DOI: 10.1094/phyto-09-21-0404-r] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
The type III secretion system (T3SS) is a key factor in the pathogenesis of Pseudomonas syringae pv. actinidiae biovar 3 (Psa3), the causal agent of a global kiwifruit bacterial canker pandemic. To monitor the T3SS expression levels in Psa3, we constructed a luciferase reporter plasmid-expressing HrpAPsa3-NLuc fusion protein. The expression of HrpA-NLuc was induced in hrp-inducing conditions whereas the level of luciferase activity correlated with the expression of hrp/hrc genes in Psa3 confirmed the reliability of the reporter construct. Based on the readout of the NLuc reporter construct, three small molecule compounds 4-methoxy-cinnamic acid, sulforaphane, and ferulic acid were determined as T3SS inhibitors in Psa3, whereas sodium acetate was determined to be a T3SS inducer. Moreover, the aqueous extract of fruit inhibited the accumulation of HrpA-NLuc in Psa3 in medium and in planta. Additionally, the T3SS inhibitors suppress Psa3 virulence, whereas the T3SS inducer promotes Psa3 virulence on kiwifruit. Thus, our findings may provide clues to why the fruit is not infected by Psa3, and the Psa3 T3SS inhibitors have potential as alternatives to current nonspecific antimicrobials for disease management.
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Affiliation(s)
- Taihui Zhi
- Department of Plant Pathology, College of Agriculture, Guizhou University, Guiyang 550025, People's Republic of China
| | - Quanhong Liu
- Department of Plant Pathology, College of Agriculture, Guizhou University, Guiyang 550025, People's Republic of China
| | - Ting Xie
- Department of Plant Pathology, College of Agriculture, Guizhou University, Guiyang 550025, People's Republic of China
| | - Yue Ding
- Department of Plant Pathology, College of Agriculture, Guizhou University, Guiyang 550025, People's Republic of China
| | - Renjian Hu
- Department of Plant Pathology, College of Agriculture, Guizhou University, Guiyang 550025, People's Republic of China
| | - Yu Sun
- Department of Plant Pathology, College of Agriculture, Guizhou University, Guiyang 550025, People's Republic of China
| | - Rong Fan
- Kiwifruit Engineering and Technology Research Center, College of Agriculture, Guizhou University, Guiyang 550025, People's Republic of China
| | - Youhua Long
- Kiwifruit Engineering and Technology Research Center, College of Agriculture, Guizhou University, Guiyang 550025, People's Republic of China
| | - Zhibo Zhao
- Department of Plant Pathology, College of Agriculture, Guizhou University, Guiyang 550025, People's Republic of China
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19
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Mariz-Ponte N, Gimranov E, Rego R, Moura L, Santos C, Tavares F. Distinct phenotypic behaviours within a clonal population of Pseudomonas syringae pv. actinidiae. PLoS One 2022; 17:e0269343. [PMID: 35679321 PMCID: PMC9182710 DOI: 10.1371/journal.pone.0269343] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Accepted: 05/18/2022] [Indexed: 11/18/2022] Open
Abstract
Bacterial canker of the kiwifruit caused by the etiological agent Pseudomonas syringae pv. actinidiae is the most severe disease in kiwifruit production. Since 2008 a hypervirulent Psa biovar 3 has spread rapidly worldwide. Different genomic and phenotypic approaches have been used to understand the origin of the dissemination and geographical evolution of populations associated with this pandemic. This study aimed to characterize the genetic and phenotypic diversity of 22 Psa isolates collected in different regions of Portugal between 2013 and 2017. Genotypic and phenotypic characterization was based on Multi-Locus Sequence Analysis (MLSA), motility, IAA production, Biolog GEN III, and copper sensitivity. No polymorphisms were detected for the concatenated sequence (1950 bp) of the housekeeping genes gltA, gapA, gyrB, and rpoD. Results support the analysed Portuguese Psa isolates (2013–2017) belonging to Psa3, and MLSA indicates high genetic clonality and stability of these populations. The phenotypic analysis through Biolog revealed a heterogeneous pattern in the Psa collection and its position in the Pseudomonas complex. This heterogeneity reflects a genomic diversity that may reflect distinct adaptive trends associated with the environmental conditions and widespread. The Portuguese Psa collection showed no resistance to copper. This information is relevant to kiwi producers that predominantly use Cu-treatments to control kiwifruit bacterial canker.
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Affiliation(s)
- Nuno Mariz-Ponte
- Biology Department, Faculty of Sciences, University of Porto (FCUP), Porto, Portugal
- LAQV-REQUIMTE, Biology Department, Faculty of Sciences, University of Porto (FCUP), Porto, Portugal
- CIBIO-Research Centre in Biodiversity and Genetic Resources, In-BIO-Associate Laboratory, Campus de Vairão, University of Porto, Vairão, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, Vairão, Portugal
- * E-mail:
| | - Emil Gimranov
- Biology Department, Faculty of Sciences, University of Porto (FCUP), Porto, Portugal
- LAQV-REQUIMTE, Biology Department, Faculty of Sciences, University of Porto (FCUP), Porto, Portugal
| | - Rute Rego
- CISAS—Centre for Research and Development in Agrifood Systems and Sustainability, Instituto Politécnico de Viana do Castelo, Viana do Castelo, Portugal
| | - Luísa Moura
- CISAS—Centre for Research and Development in Agrifood Systems and Sustainability, Instituto Politécnico de Viana do Castelo, Viana do Castelo, Portugal
| | - Conceição Santos
- Biology Department, Faculty of Sciences, University of Porto (FCUP), Porto, Portugal
- LAQV-REQUIMTE, Biology Department, Faculty of Sciences, University of Porto (FCUP), Porto, Portugal
| | - Fernando Tavares
- Biology Department, Faculty of Sciences, University of Porto (FCUP), Porto, Portugal
- CIBIO-Research Centre in Biodiversity and Genetic Resources, In-BIO-Associate Laboratory, Campus de Vairão, University of Porto, Vairão, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, Vairão, Portugal
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20
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Bertaccini A. Plants and Phytoplasmas: When Bacteria Modify Plants. PLANTS (BASEL, SWITZERLAND) 2022; 11:plants11111425. [PMID: 35684198 PMCID: PMC9182842 DOI: 10.3390/plants11111425] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Revised: 05/18/2022] [Accepted: 05/24/2022] [Indexed: 05/14/2023]
Abstract
Plant pathogen presence is very dangerous for agricultural ecosystems and causes huge economic losses. Phytoplasmas are insect-transmitted wall-less bacteria living in plants, only in the phloem tissues and in the emolymph of their insect vectors. They are able to manipulate several metabolic pathways of their hosts, very often without impairing their life. The molecular diversity described (49 'Candidatus Phytoplasma' species and about 300 ribosomal subgroups) is only in some cases related to their associated symptomatology. As for the other plant pathogens, it is necessary to verify their identity and recognize the symptoms associated with their presence to appropriately manage the diseases. However, the never-ending mechanism of patho-adaptation and the copresence of other pathogens makes this management difficult. Reducing the huge impact of phytoplasma-associated diseases in all the main crops and wild species is, however, relevant, in order to reduce their effects that are jeopardizing plant biodiversity.
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Affiliation(s)
- Assunta Bertaccini
- Department of Agricultural and Food Sciences, Alma Mater Studiorum-University of Bologna, 40127 Bologna, Italy
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21
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Hemara LM, Jayaraman J, Sutherland PW, Montefiori M, Arshed S, Chatterjee A, Chen R, Andersen MT, Mesarich CH, van der Linden O, Yoon M, Schipper MM, Vanneste JL, Brendolise C, Templeton MD. Effector loss drives adaptation of Pseudomonas syringae pv. actinidiae biovar 3 to Actinidia arguta. PLoS Pathog 2022; 18:e1010542. [PMID: 35622878 PMCID: PMC9182610 DOI: 10.1371/journal.ppat.1010542] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Revised: 06/09/2022] [Accepted: 04/21/2022] [Indexed: 11/18/2022] Open
Abstract
A pandemic isolate of Pseudomonas syringae pv. actinidiae biovar 3 (Psa3) has devastated kiwifruit orchards growing cultivars of Actinidia chinensis. In contrast, A. arguta (kiwiberry) is not a host of Psa3. Resistance is mediated via effector-triggered immunity, as demonstrated by induction of the hypersensitive response in infected A. arguta leaves, observed by microscopy and quantified by ion-leakage assays. Isolates of Psa3 that cause disease in A. arguta have been isolated and analyzed, revealing a 51 kb deletion in the exchangeable effector locus (EEL). This natural EEL-mutant isolate and strains with synthetic knockouts of the EEL were more virulent in A. arguta plantlets than wild-type Psa3. Screening of a complete library of Psa3 effector knockout strains identified increased growth in planta for knockouts of four effectors–AvrRpm1a, HopF1c, HopZ5a, and the EEL effector HopAW1a –suggesting a resistance response in A. arguta. Hypersensitive response (HR) assays indicate that three of these effectors trigger a host species-specific HR. A Psa3 strain with all four effectors knocked out escaped host recognition, but a cumulative increase in bacterial pathogenicity and virulence was not observed. These avirulence effectors can be used in turn to identify the first cognate resistance genes in Actinidia for breeding durable resistance into future kiwifruit cultivars. Clonally propagated monoculture crop plants facilitate the emergence and spread of new diseases. Plant pathogens cause disease by the secretion of effectors that function by repressing the host defense response. While the last few decades have seen a huge increase in our understanding of the role effectors play in mediating plant-pathogen interactions, the combinations of effectors required for the establishment of plant disease and that account for host specificity are less well understood. Breeding genetic resistance is often used to protect plants from disease but it is frequently evaded by rapidly evolving pathogens. Pseudomonas syringae pv. actinidiae (Psa) which causes bacterial canker disease of kiwifruit has spread rapidly throughout the world’s kiwifruit orchards, particularly those growing cultivars of Actinidia chinensis. Other Actinidia species including A. arguta display strong resistance conferred by recognition of effectors delivered by Psa. We explore the depth and dynamics of Psa effector recognition by A. arguta and show that there is a trade-off between losses of effector recognition by A. arguta versus the retention of pathogenicity. Our findings should aid in the understanding of how to breed durable resistance into perennial plants challenged by swiftly evolving pathogens.
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Affiliation(s)
- Lauren M. Hemara
- The New Zealand Institute for Plant and Food Research Limited, Mt. Albert Research Centre, Auckland, New Zealand
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
- Bioprotection Aoteoroa, New Zealand
| | - Jay Jayaraman
- The New Zealand Institute for Plant and Food Research Limited, Mt. Albert Research Centre, Auckland, New Zealand
- Bioprotection Aoteoroa, New Zealand
| | - Paul W. Sutherland
- The New Zealand Institute for Plant and Food Research Limited, Mt. Albert Research Centre, Auckland, New Zealand
| | - Mirco Montefiori
- The New Zealand Institute for Plant and Food Research Limited, Mt. Albert Research Centre, Auckland, New Zealand
| | - Saadiah Arshed
- The New Zealand Institute for Plant and Food Research Limited, Mt. Albert Research Centre, Auckland, New Zealand
| | - Abhishek Chatterjee
- The New Zealand Institute for Plant and Food Research Limited, Mt. Albert Research Centre, Auckland, New Zealand
| | - Ronan Chen
- The New Zealand Institute for Plant and Food Research Limited, Food Industry Science Centre, Palmerston North, New Zealand
| | - Mark T. Andersen
- The New Zealand Institute for Plant and Food Research Limited, Mt. Albert Research Centre, Auckland, New Zealand
| | - Carl H. Mesarich
- Bioprotection Aoteoroa, New Zealand
- School of Agriculture and Environment, Massey University, Palmerston North, New Zealand
| | - Otto van der Linden
- The New Zealand Institute for Plant and Food Research Limited, Mt. Albert Research Centre, Auckland, New Zealand
| | - Minsoo Yoon
- The New Zealand Institute for Plant and Food Research Limited, Mt. Albert Research Centre, Auckland, New Zealand
| | - Magan M. Schipper
- The New Zealand Institute for Plant and Food Research Limited, Ruakura Campus, Hamilton, New Zealand
| | - Joel L. Vanneste
- The New Zealand Institute for Plant and Food Research Limited, Ruakura Campus, Hamilton, New Zealand
| | - Cyril Brendolise
- The New Zealand Institute for Plant and Food Research Limited, Mt. Albert Research Centre, Auckland, New Zealand
| | - Matthew D. Templeton
- The New Zealand Institute for Plant and Food Research Limited, Mt. Albert Research Centre, Auckland, New Zealand
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
- Bioprotection Aoteoroa, New Zealand
- * E-mail: ,
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22
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Baltrus DA, Feng Q, Kvitko BH. Genome Context Influences Evolutionary Flexibility of Nearly Identical Type III Effectors in Two Phytopathogenic Pseudomonads. Front Microbiol 2022; 13:826365. [PMID: 35250942 PMCID: PMC8895235 DOI: 10.3389/fmicb.2022.826365] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Accepted: 01/19/2022] [Indexed: 12/02/2022] Open
Abstract
Integrative Conjugative Elements (ICEs) are replicons that can insert and excise from chromosomal locations in a site-specific manner, can conjugate across strains, and which often carry a variety of genes useful for bacterial growth and survival under specific conditions. Although ICEs have been identified and vetted within certain clades of the agricultural pathogen Pseudomonas syringae, the impact of ICE carriage and transfer across the entire P. syringae species complex remains underexplored. Here we identify and vet an ICE (PmaICE-DQ) from P. syringae pv. maculicola ES4326, a strain commonly used for laboratory virulence experiments, demonstrate that this element can excise and conjugate across strains, and highlight that this element contains loci encoding multiple type III effector proteins. Moreover, genome context suggests that another ICE (PmaICE-AOAB) is highly similar in comparison with and found immediately adjacent to PmaICE-DQ within the chromosome of strain ES4326, and also contains multiple type III effectors. Lastly, we present passage data from in planta experiments that suggests that genomic plasticity associated with ICEs may enable strains to more rapidly lose type III effectors that trigger R-gene mediated resistance in comparison to strains where nearly isogenic effectors are not present in active ICEs. Taken together, our study sheds light on a set of ICE elements from P. syringae pv. maculicola ES4326 and suggests how genomic context may lead to different evolutionary dynamics for shared virulence genes between strains.
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Affiliation(s)
- David A. Baltrus
- School of Plant Sciences, University of Arizona, Tucson, AZ, United States
- School of Animal and Comparative Biomedical Sciences, University of Arizona, Tucson, AZ, United States
- *Correspondence: David A. Baltrus,
| | - Qian Feng
- Institute of Plant Breeding, Genetics and Genomics, University of Georgia, Athens, GA, United States
| | - Brian H. Kvitko
- Department of Plant Pathology, University of Georgia, Athens, GA, United States
- Brian H. Kvitko,
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23
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Djitro N, Roach R, Mann R, Rodoni B, Gambley C. Characterization of Pseudomonas syringae Isolated from Systemic Infection of Zucchini in Australia. PLANT DISEASE 2022; 106:541-548. [PMID: 34645305 DOI: 10.1094/pdis-05-21-1039-re] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Zucchini plants with symptoms including twisted petioles, necrotic leaves, crown rot, and internal fruit rot were found in Bundaberg, Australia, at a commercial field for the first time during late autumn 2016, resulting in direct yield losses of 70 to 80%. Three Pseudomonas syringae strains isolated from symptomatic leaf (KL004-k1), crown (77-4C), and fruit (KFR003-1) were characterized and their pathogenicity evaluated on pumpkin, rockmelon, squash, and zucchini. Biochemical assays showed typical results for P. syringae. The three isolates differed, however, in that two produced fluorescent pigment (KFR003-1 and 77-4C) whereas the third, KL004-k1, was nonfluorescent. Multilocus sequence analysis classified the isolates to phylogroup 2b. The single-nucleotide polymorphism analysis of core genome from the Australian and closely related international isolates of P. syringae showed two separate clusters. The Australian isolates were clustered based on fluorescent phenotype. Pathogenicity tests demonstrated that all three isolates moved systemically within the inoculated plants and induced necrotic leaf symptoms in zucchini plants. Their identities were confirmed with specific PCR assays for P. syringae and phylogroup 2. Pathogenicity experiments also showed that the Eva variety of zucchini was more susceptible than the Rosa variety for all three isolates. Isolate KL004-k1 was more virulent than 77-4C on pumpkin, rockmelon, squash, and zucchini. This study expands the knowledge of P. syringae isolates that infect cucurbits and provides useful information for growers about the relative susceptibility of a range of cucurbit species.
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Affiliation(s)
- Noel Djitro
- School of Applied Systems Biology, La Trobe University, Bundoora, Victoria 3086, Australia
| | - Rebecca Roach
- Department of Agriculture and Fisheries, Ecosciences Precinct, Dutton Park, Queensland 4102, Australia
| | - Rachel Mann
- Agriculture Victoria Research, Department of Jobs, Precincts and Regions, AgriBio, Bundoora, Victoria 3083, Australia
| | - Brendan Rodoni
- School of Applied Systems Biology, La Trobe University, Bundoora, Victoria 3086, Australia
- Agriculture Victoria Research, Department of Jobs, Precincts and Regions, AgriBio, Bundoora, Victoria 3083, Australia
| | - Cherie Gambley
- Department of Agriculture and Fisheries, Maroochy Research Facility, Nambour, Queensland 4560, Australia
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24
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Klein-Gordon JM, Timilsina S, Xing Y, Abrahamian P, Garrett KA, Jones JB, Vallad GE, Goss EM. Whole genome sequences reveal the Xanthomonas perforans population is shaped by the tomato production system. THE ISME JOURNAL 2022; 16:591-601. [PMID: 34489540 PMCID: PMC8776747 DOI: 10.1038/s41396-021-01104-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/23/2021] [Revised: 08/11/2021] [Accepted: 08/23/2021] [Indexed: 02/08/2023]
Abstract
Modern agricultural practices increase the potential for plant pathogen spread, while the advent of affordable whole genome sequencing enables in-depth studies of pathogen movement. Population genomic studies may decipher pathogen movement and population structure as a result of complex agricultural production systems. We used whole genome sequences of 281 Xanthomonas perforans strains collected within one tomato production season across Florida and southern Georgia fields to test for population genetic structure associated with tomato production system variables. We identified six clusters of X. perforans from core gene SNPs that corresponded with phylogenetic lineages. Using whole genome SNPs, we found genetic structure among farms, transplant facilities, cultivars, seed producers, grower operations, regions, and counties. Overall, grower operations that produced their own transplants were associated with genetically distinct and less diverse populations of strains compared to grower operations that received transplants from multiple sources. The degree of genetic differentiation among components of Florida's tomato production system varied between clusters, suggesting differential dispersal of the strains, such as through seed or contaminated transplants versus local movement within farms. Overall, we showed that the genetic variation of a bacterial plant pathogen is shaped by the structure of the plant production system.
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Affiliation(s)
- Jeannie M Klein-Gordon
- Department of Plant Pathology, IFAS, University of Florida, Gainesville, FL, USA
- Emerging Pathogens Institute, University of Florida, Gainesville, FL, USA
| | - Sujan Timilsina
- Department of Plant Pathology, IFAS, University of Florida, Gainesville, FL, USA
| | - Yanru Xing
- Department of Plant Pathology, IFAS, University of Florida, Gainesville, FL, USA
- Emerging Pathogens Institute, University of Florida, Gainesville, FL, USA
- Food Systems Institute, University of Florida, Gainesville, FL, USA
| | - Peter Abrahamian
- Department of Plant Pathology, IFAS, University of Florida, Gainesville, FL, USA
- Gulf Coast Research and Education Center, IFAS, University of Florida, Balm, FL, USA
- USDA-ARS, Beltsville Agricultural Research Center, Molecular Plant Pathology Laboratory, Beltsville, MD, USA
| | - Karen A Garrett
- Department of Plant Pathology, IFAS, University of Florida, Gainesville, FL, USA
- Emerging Pathogens Institute, University of Florida, Gainesville, FL, USA
- Food Systems Institute, University of Florida, Gainesville, FL, USA
| | - Jeffrey B Jones
- Department of Plant Pathology, IFAS, University of Florida, Gainesville, FL, USA
| | - Gary E Vallad
- Department of Plant Pathology, IFAS, University of Florida, Gainesville, FL, USA.
- Gulf Coast Research and Education Center, IFAS, University of Florida, Balm, FL, USA.
| | - Erica M Goss
- Department of Plant Pathology, IFAS, University of Florida, Gainesville, FL, USA.
- Emerging Pathogens Institute, University of Florida, Gainesville, FL, USA.
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25
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Yu JJ, Jin YX, Huang SS, He J. Sesquiterpenoids and Xanthones from the Kiwifruit-Associated Fungus Bipolaris sp. and Their Anti-Pathogenic Microorganism Activity. J Fungi (Basel) 2021; 8:9. [PMID: 35049949 PMCID: PMC8781276 DOI: 10.3390/jof8010009] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 12/21/2021] [Accepted: 12/21/2021] [Indexed: 01/08/2023] Open
Abstract
Nine previously undescribed sesquiterpenoids, bipolarisorokins A-I (1-9); two new xanthones, bipolarithones A and B (10 and 11); two novel sativene-xanthone adducts, bipolarithones C and D (12 and 13); as well as five known compounds (14-18) were characterized from the kiwifruit-associated fungus Bipolaris sp. Their structures were elucidated by extensive spectroscopic methods, electronic circular dichroism (ECD), 13C NMR calculations, DP4+ probability analyses, and single crystal X-ray diffractions. Many compounds exhibited anti-pathogenic microorganism activity against the bacterium Pseudomonas syringae pv. actinidiae and four pathogenic microorganisms.
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Affiliation(s)
| | | | | | - Juan He
- National Demonstration Center for Experimental Ethnopharmacology Education, School of Pharmaceutical Sciences, South-Central University for Nationalities, Wuhan 430074, China; (J.-J.Y.); (Y.-X.J.); (S.-S.H.)
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26
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Wang Z, Zhong C. Cas12c-DETECTOR: A specific and sensitive Cas12c-based DNA detection platform. Int J Biol Macromol 2021; 193:441-449. [PMID: 34715203 DOI: 10.1016/j.ijbiomac.2021.10.167] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 10/21/2021] [Accepted: 10/22/2021] [Indexed: 12/26/2022]
Abstract
The robust and precise nucleic acid detection platform enormously influences the clinical diagnosis of human and plant pathogens, drastically affecting disease pandemic control. CRISPR-based nucleic acid detection tools have been successfully applied for rapid and sensitive nucleic acid detection. However, the T-rich protospacer adjacent motif (PAM), specificity, and sensitivity of the CRISPR-based nucleic acid detection tools limited its wide application. We first developed a new Cas12c-based nucleic acid detection platform (Cas12c-DETECTOR), recognizing a 5'-TG PAM and showing high sensitivity and specificity on examined targets. Our results indicate that Cas12c-DETECTOR coupling with the optimized single-guide RNA (sgRNA) can be applied to specifically identity single nucleotide polymorphism (SNP). Moreover, combined with pre-amplification and lateral flow strips or the visual fluorescence detection method, Cas12c-DETECTOR can be used to diagnose human and plant pathogens in practice. Therefore, our findings illustrated that Cas12c-DETECTOR is a robust, sensitive, precise, and practiced nucleic acid detection platform.
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Affiliation(s)
- Zupeng Wang
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China; Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China; Engineering Laboratory for Kiwifruit Industrial Technology, Chinese Academy of Sciences, Wuhan 430074, China.
| | - Caihong Zhong
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China; Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China; Engineering Laboratory for Kiwifruit Industrial Technology, Chinese Academy of Sciences, Wuhan 430074, China.
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27
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Liu Y, Liu M, Hu R, Bai J, He X, Jin Y. Isolation of the Novel Phage PHB09 and Its Potential Use against the Plant Pathogen Pseudomonas syringae pv. actinidiae. Viruses 2021; 13:v13112275. [PMID: 34835081 PMCID: PMC8622976 DOI: 10.3390/v13112275] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Revised: 11/11/2021] [Accepted: 11/12/2021] [Indexed: 12/26/2022] Open
Abstract
Bacteriophages are viruses that specifically infect target bacteria. Recently, bacteriophages have been considered potential biological control agents for bacterial pathogens due to their host specificity. Pseudomonas syringae pv. actinidiae (Psa) is a reemerging pathogen that causes bacterial canker of kiwifruit (Actinidia sp.). The economic impact of this pest and the development of resistance to antibiotics and copper sprays in Psa and other pathovars have led to investigation of alternative management strategies. Phage therapy may be a useful alternative to conventional treatments for controlling Psa infections. Although the efficacy of bacteriophage φ6 was evaluated for the control of Psa, the characteristics of other DNA bacteriophages infecting Psa remain unclear. In this study, the PHB09 lytic bacteriophage specific to Psa was isolated from kiwifruit orchard soil. Extensive host range testing using Psa isolated from kiwifruit orchards and other Pseudomonas strains showed PHB09 has a narrow host range. It remained stable over a wide range of temperatures (4-50 °C) and pH values (pH 3-11) and maintained stability for 50 min under ultraviolet irradiation. Complete genome sequence analysis indicated PHB09 might belong to a new myovirus genus in Caudoviricetes. Its genome contains a total of 94,844 bp and 186 predicted genes associated with phage structure, packaging, host lysis, DNA manipulation, transcription, and additional functions. The isolation and identification of PHB09 enrich the research on Pseudomonas phages and provide a promising biocontrol agent against kiwifruit bacterial canker.
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28
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Martino G, Holtappels D, Vallino M, Chiapello M, Turina M, Lavigne R, Wagemans J, Ciuffo M. Molecular Characterization and Taxonomic Assignment of Three Phage Isolates from a Collection Infecting Pseudomonas syringae pv. actinidiae and P. syringae pv. phaseolicola from Northern Italy. Viruses 2021; 13:2083. [PMID: 34696512 PMCID: PMC8537276 DOI: 10.3390/v13102083] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2021] [Revised: 10/08/2021] [Accepted: 10/11/2021] [Indexed: 12/27/2022] Open
Abstract
Bacterial kiwifruit vine disease (Pseudomonas syringae pv. actinidiae, Psa) and halo blight of bean (P. syringae pv. phaseolicola, Pph) are routinely treated with copper, leading to environmental pollution and bacterial copper resistance. An alternative sustainable control method could be based on bacteriophages, as phage biocontrol offers high specificity and does not result in the spread of toxic residues into the environment or the food chain. In this research, specific phages suitable for phage-based biocontrol strategies effective against Psa and Pph were isolated and characterized. In total, sixteen lytic Pph phage isolates and seven lytic Psa phage isolates were isolated from soil in Piedmont and Veneto in northern Italy. Genome characterization of fifteen selected phages revealed that the isolated Pph phages were highly similar and could be considered as isolates of a novel species, whereas the isolated Psa phages grouped into four distinct clades, two of which represent putative novel species. No lysogeny-, virulence- or toxin-related genes were found in four phages, making them suitable for potential biocontrol purposes. A partial biological characterization including a host range analysis was performed on a representative subset of these isolates. This analysis was a prerequisite to assess their efficacy in greenhouse and in field trials, using different delivery strategies.
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Affiliation(s)
- Gabriele Martino
- Institute for Sustainable Plant Protection, National Research Council of Italy, I-10135 Torino, Italy; (G.M.); (M.V.); (M.C.); (M.T.)
| | - Dominique Holtappels
- Laboratory of Gene Technology, Department of Biosystems, Katholieke Universiteit Leuven, 3001 Leuven, Belgium; (D.H.); (R.L.); (J.W.)
| | - Marta Vallino
- Institute for Sustainable Plant Protection, National Research Council of Italy, I-10135 Torino, Italy; (G.M.); (M.V.); (M.C.); (M.T.)
| | - Marco Chiapello
- Institute for Sustainable Plant Protection, National Research Council of Italy, I-10135 Torino, Italy; (G.M.); (M.V.); (M.C.); (M.T.)
| | - Massimo Turina
- Institute for Sustainable Plant Protection, National Research Council of Italy, I-10135 Torino, Italy; (G.M.); (M.V.); (M.C.); (M.T.)
| | - Rob Lavigne
- Laboratory of Gene Technology, Department of Biosystems, Katholieke Universiteit Leuven, 3001 Leuven, Belgium; (D.H.); (R.L.); (J.W.)
| | - Jeroen Wagemans
- Laboratory of Gene Technology, Department of Biosystems, Katholieke Universiteit Leuven, 3001 Leuven, Belgium; (D.H.); (R.L.); (J.W.)
| | - Marina Ciuffo
- Institute for Sustainable Plant Protection, National Research Council of Italy, I-10135 Torino, Italy; (G.M.); (M.V.); (M.C.); (M.T.)
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29
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Lee YS, Kim GH, Koh YJ, Jung JS. Identification of strA-strB Genes in Streptomycin-Resistant Pseudomonas syringae pv. actinidiae Biovar 2 Strains Isolated in Korea. THE PLANT PATHOLOGY JOURNAL 2021; 37:489-493. [PMID: 34847635 PMCID: PMC8632614 DOI: 10.5423/ppj.nt.05.2021.0078] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 07/23/2021] [Accepted: 08/25/2021] [Indexed: 06/13/2023]
Abstract
Bacterial canker is a devastating disease of kiwifruit caused by the bacterium Pseudomonas syringe pv. actinidiae. Canker disease of kiwifruit in Korea has been controlled using streptomycin for more than two decades. Four streptomycin-resistant strains, belonging to biovar 2, which are found only in Korea, were collected between 2013 and 2014 from different orchards located in Jeju, Korea. The genetic background for streptomycin resistance among P. syringe pv. actinidiae strains were determined by examining the presence of strA-strB or aadA, which are genes frequently found in streptomycin-resistant bacteria, and a point mutation at codon 43 in the rpsL gene. All four streptomycin-resistant strains of P. syringe pv. actinidiae investigated in this study contained strA-strB as a resistant determinant. The presence of the aadA gene and a mutation in codon 43 of the rpsL gene was not identified.
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Affiliation(s)
- Young Sun Lee
- Department of Biology, Sunchon National University, Suncheon 57922, Korea
| | - Gyoung Hee Kim
- Department of Plant Medicine, Sunchon National University, Suncheon 57922, Korea
| | - Young Jin Koh
- Department of Plant Medicine, Sunchon National University, Suncheon 57922, Korea
| | - Jae Sung Jung
- Department of Biology, Sunchon National University, Suncheon 57922, Korea
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30
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Weisberg AJ, Grünwald NJ, Savory EA, Putnam ML, Chang JH. Genomic Approaches to Plant-Pathogen Epidemiology and Diagnostics. ANNUAL REVIEW OF PHYTOPATHOLOGY 2021; 59:311-332. [PMID: 34030448 DOI: 10.1146/annurev-phyto-020620-121736] [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
Diseases have a significant cost to agriculture. Findings from analyses of whole-genome sequences show great promise for informing strategies to mitigate risks from diseases caused by phytopathogens. Genomic approaches can be used to dramatically shorten response times to outbreaks and inform disease management in novel ways. However, the use of these approaches requires expertise in working with big, complex data sets and an understanding of their pitfalls and limitations to infer well-supported conclusions. We suggest using an evolutionary framework to guide the use of genomic approaches in epidemiology and diagnostics of plant pathogens. We also describe steps that are necessary for realizing these as standard approaches in disease surveillance.
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Affiliation(s)
- Alexandra J Weisberg
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon 97331, USA;
| | - Niklaus J Grünwald
- Horticultural Crops Research Laboratory, USDA Agricultural Research Service, Corvallis, Oregon 97331, USA
| | | | - Melodie L Putnam
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon 97331, USA;
| | - Jeff H Chang
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon 97331, USA;
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31
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Martel A, Ruiz-Bedoya T, Breit-McNally C, Laflamme B, Desveaux D, Guttman DS. The ETS-ETI cycle: evolutionary processes and metapopulation dynamics driving the diversification of pathogen effectors and host immune factors. CURRENT OPINION IN PLANT BIOLOGY 2021; 62:102011. [PMID: 33677388 DOI: 10.1016/j.pbi.2021.102011] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Revised: 01/21/2021] [Accepted: 01/24/2021] [Indexed: 05/13/2023]
Abstract
The natural diversity of pathogen effectors and host immune components represents a snapshot of the underlying evolutionary processes driving the host-pathogen arms race. In plants, this arms race is manifested by an ongoing cycle of disease and resistance driven by pathogenic effectors that promote disease (effector-triggered susceptibility; ETS) and plant resistance proteins that recognize effector activity to trigger immunity (effector-triggered immunity; ETI). Here we discuss how this ongoing ETS-ETI cycle has shaped the natural diversity of both plant resistance proteins and pathogen effectors. We focus on the evolutionary forces that drive the diversification of the molecules that determine the outcome of plant-pathogen interactions and introduce the concept of metapopulation dynamics (i.e., the introduction of genetic variation from conspecific organisms in different populations) as an alternative mechanism that can introduce and maintain diversity in both host and pathogen populations.
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Affiliation(s)
- Alexandre Martel
- Department of Cell & Systems Biology, University of Toronto, Toronto, Ontario M6S2Y1, Canada
| | - Tatiana Ruiz-Bedoya
- Department of Cell & Systems Biology, University of Toronto, Toronto, Ontario M6S2Y1, Canada
| | - Clare Breit-McNally
- Department of Cell & Systems Biology, University of Toronto, Toronto, Ontario M6S2Y1, Canada
| | - Bradley Laflamme
- Department of Cell & Systems Biology, University of Toronto, Toronto, Ontario M6S2Y1, Canada
| | - Darrell Desveaux
- Department of Cell & Systems Biology, University of Toronto, Toronto, Ontario M6S2Y1, Canada; Centre for the Analysis of Genome Evolution & Function, University of Toronto, Toronto, Ontario M6S2Y1, Canada.
| | - David S Guttman
- Department of Cell & Systems Biology, University of Toronto, Toronto, Ontario M6S2Y1, Canada; Centre for the Analysis of Genome Evolution & Function, University of Toronto, Toronto, Ontario M6S2Y1, Canada.
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Jayaraman J, Chatterjee A, Hunter S, Chen R, Stroud EA, Saei H, Hoyte S, Deroles S, Tahir J, Templeton MD, Brendolise C. Rapid Methodologies for Assessing Pseudomonas syringae pv. actinidiae Colonization and Effector-Mediated Hypersensitive Response in Kiwifruit. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2021; 34:880-890. [PMID: 33834857 DOI: 10.1094/mpmi-02-21-0043-r] [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: 06/12/2023]
Abstract
The infection of Pseudomonas syringae pv. actinidiae in kiwifruit is currently assessed by numerous methodologies, each with their own limitations. Most studies are based on either a laborious method of growth quantification of the pathogen or qualitative assessments by visual scoring following stem or cutting inoculation. Additionally, when assessing for resistance against specific pathogen effectors, confounding interactions between multiple genes in the pathogen can make mapping resistance phenotypes nearly impossible. Here, we present robust alternative methods to quantify pathogen load based on rapid bacterial DNA quantification by PCR, the use of Pseudomonas fluorescens, and a transient reporter eclipse assay for assessing resistance conferred by isolated bacterial avirulence genes. These assays compare well with bacterial plate counts to assess bacterial colonization as a result of plant resistance activation. The DNA-based quantification, when coupled with the P. fluorescens and reporter eclipse assays to independently identify bacterial avirulence genes, is rapid, highly reproducible, and scalable for high-throughput screens of multiple cultivars or genotypes. Application of these methodologies will allow rapid and high-throughput identification of resistant cultivars and the bacterial avirulence genes they recognize, facilitating resistance gene discovery for plant breeding programs.[Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
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Affiliation(s)
- Jay Jayaraman
- The New Zealand Institute for Plant and Food Research Limited, Auckland, New Zealand
- Bio-Protection Research Centre, Lincoln, New Zealand
| | - Abhishek Chatterjee
- The New Zealand Institute for Plant and Food Research Limited, Auckland, New Zealand
| | - Shannon Hunter
- The New Zealand Institute for Plant and Food Research Limited, Auckland, New Zealand
| | - Ronan Chen
- The New Zealand Institute for Plant and Food Research Limited, Palmerston North, New Zealand
| | - Erin A Stroud
- The New Zealand Institute for Plant and Food Research Limited, Auckland, New Zealand
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Hassan Saei
- The New Zealand Institute for Plant and Food Research Limited, Palmerston North, New Zealand
| | - Stephen Hoyte
- The New Zealand Institute for Plant and Food Research Limited, Ruakura Research Centre, Hamilton, New Zealand
| | - Simon Deroles
- The New Zealand Institute for Plant and Food Research Limited, Palmerston North, New Zealand
| | - Jibran Tahir
- The New Zealand Institute for Plant and Food Research Limited, Auckland, New Zealand
| | - Matthew D Templeton
- The New Zealand Institute for Plant and Food Research Limited, Auckland, New Zealand
- Bio-Protection Research Centre, Lincoln, New Zealand
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Cyril Brendolise
- The New Zealand Institute for Plant and Food Research Limited, Auckland, New Zealand
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Dillon MM, Ruiz-Bedoya T, Bundalovic-Torma C, Guttman KM, Kwak H, Middleton MA, Wang PW, Horuz S, Aysan Y, Guttman DS. Comparative genomic insights into the epidemiology and virulence of plant pathogenic pseudomonads from Turkey. Microb Genom 2021; 7:000585. [PMID: 34227931 PMCID: PMC8477409 DOI: 10.1099/mgen.0.000585] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2020] [Accepted: 04/16/2021] [Indexed: 12/31/2022] Open
Abstract
Pseudomonas is a highly diverse genus that includes species that cause disease in both plants and animals. Recently, pathogenic pseudomonads from the Pseudomonas syringae and Pseudomonas fluorescens species complexes have caused significant outbreaks in several agronomically important crops in Turkey, including tomato, citrus, artichoke and melon. We characterized 169 pathogenic Pseudomonas strains associated with recent outbreaks in Turkey via multilocus sequence analysis and whole-genome sequencing, then used comparative and evolutionary genomics to characterize putative virulence mechanisms. Most of the isolates are closely related to other plant pathogens distributed among the primary phylogroups of P. syringae, although there are significant numbers of P. fluorescens isolates, which is a species better known as a rhizosphere-inhabiting plant-growth promoter. We found that all 39 citrus blast pathogens cluster in P. syringae phylogroup 2, although strains isolated from the same host do not cluster monophyletically, with lemon, mandarin orange and sweet orange isolates all being intermixed throughout the phylogroup. In contrast, 20 tomato pith pathogens are found in two independent lineages: one in the P. syringae secondary phylogroups, and the other from the P. fluorescens species complex. These divergent pith necrosis strains lack characteristic virulence factors like the canonical tripartite type III secretion system, large effector repertoires and the ability to synthesize multiple bacterial phytotoxins, suggesting they have alternative molecular mechanisms to cause disease. These findings highlight the complex nature of host specificity among plant pathogenic pseudomonads.
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Affiliation(s)
- Marcus M. Dillon
- Department of Cell and Systems Biology, University of Toronto, Toronto, Ontario, Canada
- Present address: Department of Biology, University of Toronto at Mississauga, Mississauga, Ontario, Canada
| | - Tatiana Ruiz-Bedoya
- Department of Cell and Systems Biology, University of Toronto, Toronto, Ontario, Canada
| | | | - Kevin M. Guttman
- Department of Cell and Systems Biology, University of Toronto, Toronto, Ontario, Canada
| | - Haejin Kwak
- Department of Cell and Systems Biology, University of Toronto, Toronto, Ontario, Canada
| | - Maggie A. Middleton
- Department of Cell and Systems Biology, University of Toronto, Toronto, Ontario, Canada
- Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, Ontario, Canada
| | - Pauline W. Wang
- Department of Cell and Systems Biology, University of Toronto, Toronto, Ontario, Canada
- Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, Ontario, Canada
| | - Sumer Horuz
- Department of Plant Protection, Erciyes University, Kayseri, Turkey
| | - Yesim Aysan
- Department of Plant Protection, University of Çukurova, Adana, Turkey
| | - David S. Guttman
- Department of Cell and Systems Biology, University of Toronto, Toronto, Ontario, Canada
- Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, Ontario, Canada
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Scortichini M, Loreti S, Pucci N, Scala V, Tatulli G, Verweire D, Oehl M, Widmer U, Codina JM, Hertl P, Cesari G, De Caroli M, Angilè F, Migoni D, Del Coco L, Girelli CR, Dalessandro G, Fanizzi FP. Progress towards Sustainable Control of Xylella fastidiosa subsp. pauca in Olive Groves of Salento (Apulia, Italy). Pathogens 2021; 10:668. [PMID: 34072394 PMCID: PMC8228964 DOI: 10.3390/pathogens10060668] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Revised: 05/19/2021] [Accepted: 05/26/2021] [Indexed: 11/16/2022] Open
Abstract
Xylella fastidiosa subsp. pauca is the causal agent of "olive quick decline syndrome" in Salento (Apulia, Italy). On April 2015, we started interdisciplinary studies to provide a sustainable control strategy for this pathogen that threatens the multi-millennial olive agroecosystem of Salento. Confocal laser scanning microscopy and fluorescence quantification showed that a zinc-copper-citric acid biocomplex-Dentamet®-reached the olive xylem tissue either after the spraying of the canopy or injection into the trunk, demonstrating its effective systemicity. The biocomplex showed in vitro bactericidal activity towards all X. fastidiosa subspecies. A mid-term evaluation of the control strategy performed in some olive groves of Salento indicated that this biocomplex significantly reduced both the symptoms and X. f. subsp. pauca cell concentration within the leaves of the local cultivars Ogliarola salentina and Cellina di Nardò. The treated trees started again to yield. A 1H-NMR metabolomic approach revealed, upon the treatments, a consistent increase in malic acid and γ-aminobutyrate for Ogliarola salentina and Cellina di Nardò trees, respectively. A novel endotherapy technique allowed injection of Dentamet® at low pressure directly into the vascular system of the tree and is currently under study for the promotion of resprouting in severely attacked trees. There are currently more than 700 ha of olive groves in Salento where this strategy is being applied to control X. f. subsp. pauca. These results collectively demonstrate an efficient, simple, low-cost, and environmentally sustainable strategy to control this pathogen in Salento.
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Affiliation(s)
- Marco Scortichini
- Research Centre for Olive, Fruit Trees and Citrus Crops, Council for Agricultural Research and Economics (CREA), 00134 Roma, Italy
| | - Stefania Loreti
- Research Centre for Plant Protection and Certification, Council for Agricultural Research and Economics (CREA), 00156 Roma, Italy; (S.L.); (N.P.); (V.S.); (G.T.)
| | - Nicoletta Pucci
- Research Centre for Plant Protection and Certification, Council for Agricultural Research and Economics (CREA), 00156 Roma, Italy; (S.L.); (N.P.); (V.S.); (G.T.)
| | - Valeria Scala
- Research Centre for Plant Protection and Certification, Council for Agricultural Research and Economics (CREA), 00156 Roma, Italy; (S.L.); (N.P.); (V.S.); (G.T.)
| | - Giuseppe Tatulli
- Research Centre for Plant Protection and Certification, Council for Agricultural Research and Economics (CREA), 00156 Roma, Italy; (S.L.); (N.P.); (V.S.); (G.T.)
| | - Dimitri Verweire
- Invaio Sciences, Cambridge, MA 02138, USA; (D.V.); (M.O.); (U.W.); (J.M.C.); (P.H.)
| | - Michael Oehl
- Invaio Sciences, Cambridge, MA 02138, USA; (D.V.); (M.O.); (U.W.); (J.M.C.); (P.H.)
| | - Urs Widmer
- Invaio Sciences, Cambridge, MA 02138, USA; (D.V.); (M.O.); (U.W.); (J.M.C.); (P.H.)
| | - Josep Massana Codina
- Invaio Sciences, Cambridge, MA 02138, USA; (D.V.); (M.O.); (U.W.); (J.M.C.); (P.H.)
| | - Peter Hertl
- Invaio Sciences, Cambridge, MA 02138, USA; (D.V.); (M.O.); (U.W.); (J.M.C.); (P.H.)
| | | | - Monica De Caroli
- Department of Biological and Environmental Sciences and Technologies, University of Salento, 73100 Monteroni-Lecce, Italy; (M.D.C.); (F.A.); (D.M.); (L.D.C.); (C.R.G.); (G.D.); (F.P.F.)
| | - Federica Angilè
- Department of Biological and Environmental Sciences and Technologies, University of Salento, 73100 Monteroni-Lecce, Italy; (M.D.C.); (F.A.); (D.M.); (L.D.C.); (C.R.G.); (G.D.); (F.P.F.)
| | - Danilo Migoni
- Department of Biological and Environmental Sciences and Technologies, University of Salento, 73100 Monteroni-Lecce, Italy; (M.D.C.); (F.A.); (D.M.); (L.D.C.); (C.R.G.); (G.D.); (F.P.F.)
| | - Laura Del Coco
- Department of Biological and Environmental Sciences and Technologies, University of Salento, 73100 Monteroni-Lecce, Italy; (M.D.C.); (F.A.); (D.M.); (L.D.C.); (C.R.G.); (G.D.); (F.P.F.)
| | - Chiara Roberta Girelli
- Department of Biological and Environmental Sciences and Technologies, University of Salento, 73100 Monteroni-Lecce, Italy; (M.D.C.); (F.A.); (D.M.); (L.D.C.); (C.R.G.); (G.D.); (F.P.F.)
| | - Giuseppe Dalessandro
- Department of Biological and Environmental Sciences and Technologies, University of Salento, 73100 Monteroni-Lecce, Italy; (M.D.C.); (F.A.); (D.M.); (L.D.C.); (C.R.G.); (G.D.); (F.P.F.)
| | - Francesco Paolo Fanizzi
- Department of Biological and Environmental Sciences and Technologies, University of Salento, 73100 Monteroni-Lecce, Italy; (M.D.C.); (F.A.); (D.M.); (L.D.C.); (C.R.G.); (G.D.); (F.P.F.)
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Song YR, Vu NT, Park J, Hwang IS, Jeong HJ, Cho YS, Oh CS. Phage PPPL-1, A New Biological Agent to Control Bacterial Canker Caused by Pseudomonas syringae pv. actinidiae in Kiwifruit. Antibiotics (Basel) 2021; 10:antibiotics10050554. [PMID: 34068711 PMCID: PMC8150970 DOI: 10.3390/antibiotics10050554] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Revised: 05/06/2021] [Accepted: 05/07/2021] [Indexed: 11/16/2022] Open
Abstract
Pseudomonas syringae pv. actinidiae (Psa) is a Gram-negative bacterium that causes bacterial canker disease in kiwifruit. Copper or antibiotics have been used in orchards to control this disease, but the recent emergence of antibiotic-resistant Psa has called for the development of a new control agent. We previously reported that the bacteriophage (or phage) PPPL-1 showed antibacterial activity for both biovar 2 and 3 of Psa. To investigate the possibility of PPPL-1 to control bacterial canker in kiwifruit, we further tested the efficacy of PPPL-1 and its phage cocktail with two other phages on suppressing disease development under greenhouse conditions using 6 weeks old kiwifruit plants. Our results showed that the disease control efficacy of PPPL-1 treatment was statistically similar to those of phage cocktail treatment or AgrimycinTM, which contains streptomycin and oxytetracycline antibiotics as active ingredients. Moreover, PPPL-1 could successfully kill streptomycin-resistant Psa isolates, of which the treatment of BuramycinTM carrying only streptomycin as an active ingredient had no effect in vitro. The phage PPPL-1 was further characterized, and stability assays showed that the phage was stable in the field soil and at low temperature of 0 ± 2 °C. In addition, the phage could be scaled up quickly up to 1010 pfu/mL at 12 h later from initial multiplicity of infection of 0.000005. Our results indicate that PPPL-1 phage is a useful candidate as a biocontrol agent and could be a tool to control the bacterial canker in kiwifruit by Psa infection in the field conditions.
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Affiliation(s)
- Yu-Rim Song
- Department of Horticultural Biotechnology, College of Life Science, Kyung Hee University, Yongin 17104, Korea; (Y.-R.S.); (N.T.V.); (J.P.); (I.S.H.)
| | - Nguyen Trung Vu
- Department of Horticultural Biotechnology, College of Life Science, Kyung Hee University, Yongin 17104, Korea; (Y.-R.S.); (N.T.V.); (J.P.); (I.S.H.)
| | - Jungkum Park
- Department of Horticultural Biotechnology, College of Life Science, Kyung Hee University, Yongin 17104, Korea; (Y.-R.S.); (N.T.V.); (J.P.); (I.S.H.)
| | - In Sun Hwang
- Department of Horticultural Biotechnology, College of Life Science, Kyung Hee University, Yongin 17104, Korea; (Y.-R.S.); (N.T.V.); (J.P.); (I.S.H.)
| | - Hyeon-Ju Jeong
- Fruit Research Institute, Jeollanamdo Agricultural Research and Extension Services, Haenam-gun 59021, Korea; (H.-J.J.); (Y.-S.C.)
| | - Youn-Sup Cho
- Fruit Research Institute, Jeollanamdo Agricultural Research and Extension Services, Haenam-gun 59021, Korea; (H.-J.J.); (Y.-S.C.)
| | - Chang-Sik Oh
- Department of Horticultural Biotechnology, College of Life Science, Kyung Hee University, Yongin 17104, Korea; (Y.-R.S.); (N.T.V.); (J.P.); (I.S.H.)
- Graduate School of Biotechnology, Kyung Hee University, Yongin 17104, Korea
- Correspondence: ; Tel.: +82-31-201-2678
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Ni P, Wang L, Deng B, Jiu S, Ma C, Zhang C, Almeida A, Wang D, Xu W, Wang S. Characterization of a Lytic Bacteriophage against Pseudomonas syringae pv. actinidiae and Its Endolysin. Viruses 2021; 13:631. [PMID: 33917076 PMCID: PMC8067700 DOI: 10.3390/v13040631] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Revised: 03/14/2021] [Accepted: 03/15/2021] [Indexed: 12/14/2022] Open
Abstract
Pseudomonas syringae pv. actinidiae (Psa) is a phytopathogen that causes canker in kiwifruit. Few conventional control methods are effective against this bacterium. Therefore, alternative approaches, such as phage therapy are warranted. In this study, a lytic bacteriophage (PN09) of Psa was isolated from surface water collected from a river in Hangzhou, China in 2019. Morphologically, PN09 was classified into the Myoviridae family, and could lyse all 29 Psa biovar 3 strains. The optimal temperature and pH ranges for PN09 activity were determined as 25 to 35 ∘C and 6.0 to 9.0, respectively. The complete genome of PN09 was found to be composed of a linear 99,229 bp double-stranded DNA genome with a GC content of 48.16%. The PN09 endolysin (LysPN09) was expressed in vitro and characterized. LysPN09 was predicted to belong to the Muraidase superfamily domain and showed lytic activity against the outer-membrane-permeabilized Psa strains. The lytic activity of LysPN09 was optimal over temperature and pH ranges of 25 to 40 ∘C and 6.0 to 8.0, respectively. When recombinant endolysin LysPN09 was combined with EDTA, Psa strains were effectively damaged. All these characteristics demonstrate that the phage PN09 and its endolysin, LysPN09, are potential candidates for biocontrol of Psa in the kiwifruit industry.
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Affiliation(s)
- Peien Ni
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China; (P.N.); (L.W.); (B.D.); (S.J.); (C.M.); (C.Z.); (D.W.); (S.W.)
| | - Lei Wang
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China; (P.N.); (L.W.); (B.D.); (S.J.); (C.M.); (C.Z.); (D.W.); (S.W.)
| | - Bohan Deng
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China; (P.N.); (L.W.); (B.D.); (S.J.); (C.M.); (C.Z.); (D.W.); (S.W.)
| | - Songtao Jiu
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China; (P.N.); (L.W.); (B.D.); (S.J.); (C.M.); (C.Z.); (D.W.); (S.W.)
| | - Chao Ma
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China; (P.N.); (L.W.); (B.D.); (S.J.); (C.M.); (C.Z.); (D.W.); (S.W.)
| | - Caixi Zhang
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China; (P.N.); (L.W.); (B.D.); (S.J.); (C.M.); (C.Z.); (D.W.); (S.W.)
| | - Adelaide Almeida
- Department of Biology and CESAM, University of Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal
| | - Dapeng Wang
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China; (P.N.); (L.W.); (B.D.); (S.J.); (C.M.); (C.Z.); (D.W.); (S.W.)
| | - Wenping Xu
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China; (P.N.); (L.W.); (B.D.); (S.J.); (C.M.); (C.Z.); (D.W.); (S.W.)
| | - Shiping Wang
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China; (P.N.); (L.W.); (B.D.); (S.J.); (C.M.); (C.Z.); (D.W.); (S.W.)
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Li Y, Zhu Q, Zhi T, Fan R, Xie T, Zhao Z, Long Y, Li Z. Genetic Causes of Non-pathogenic Pseudomonas syringae pv. actinidiae Isolates in Kiwifruit Orchards. Front Microbiol 2021; 12:650099. [PMID: 33841374 PMCID: PMC8027508 DOI: 10.3389/fmicb.2021.650099] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Accepted: 03/08/2021] [Indexed: 11/13/2022] Open
Abstract
Bacterial canker disease has become the largest threat to kiwifruit cultivation and production. A monomorphic subpopulation of Pseudomonas syringae pv. actinidiae biovar 3 (Psa3) is responsible for the pandemic worldwide. Diversity in pathogenicity has been found in the pandemic subpopulation and in other Psa3 subpopulations causing epidemics in China. However, the genetic bases have not yet been elucidated. In this study, 117 Psa3 isolates were identified by Psa- and Psa3-specific primers, and evaluated for pathogenicity. Three isolates G4, G40, and S2 are not pathogenic to kiwifruit and do not elicit hypersensitivity responses (HRs) in non-host Nicotiana benthamiana leaves. Two isolates, G25 and G35, exhibited attenuated HR-eliciting activity in non-host N. benthamiana, but they exhibited greatly and slightly reduced pathogenicity in host plants, respectively. The genomes of the five isolates were sequenced and compared with closely related isolates revealed by MLVA and whole-genome typing methods. The candidate genetic loci responsible for the changes in pathogenicity and HR elicitation, were further evaluated by allele replacement experiments. We found that the three non-pathogenic isolates were formed due to the independent, identical insertion events of ISPsy36 transposon in the hrpR gene, encoding a key regulator of type III secretion system (T3SS) and type III effectors (T3Es). In the symptomatic sample from which G4 was isolated, 27% HR negative isolates were detected. In isolate G25, transposon insertion of ISPsy32 at the non-coding sequence upstream of the hrpR gene was detected, similar to a previously reported low-virulent Psa3 strain M227. In isolate G35, we detected disruptions of T3Es hopBB1-1 and hopBB1-2, which induce HR in N. benthamiana leaves revealed by Agrobacterium tumefaciens infiltration. These phenotype-changed isolates were formed at low frequencies during the course of pathogen infection in host plants, supported by the binding assay of ISPsy32 and the non-coding DNA sequences upstream of the hrpR gene, the co-isolation of the virulent isolates belonging to the same MLVA clade, and the low levels of transcription of the transposon genes. Taken together, in terms of short-term field evolution, transposon insertions in the T3SS-related genes resulted in the formation of non-pathogenic and low-virulent Psa3 isolates.
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Affiliation(s)
- Yue Li
- Department of Plant Pathology, College of Agriculture, Guizhou University, Guiyang, China
| | - Qiaomei Zhu
- Department of Plant Pathology, College of Agriculture, Guizhou University, Guiyang, China
| | - Taihui Zhi
- Department of Plant Pathology, College of Agriculture, Guizhou University, Guiyang, China
| | - Rong Fan
- Kiwifruit Engineering and Technology Research Center, Guizhou University, Guiyang, China
| | - Ting Xie
- Department of Plant Pathology, College of Agriculture, Guizhou University, Guiyang, China
| | - Zhibo Zhao
- Department of Plant Pathology, College of Agriculture, Guizhou University, Guiyang, China.,Kiwifruit Engineering and Technology Research Center, Guizhou University, Guiyang, China
| | - Youhua Long
- Kiwifruit Engineering and Technology Research Center, Guizhou University, Guiyang, China
| | - Zhong Li
- Department of Plant Pathology, College of Agriculture, Guizhou University, Guiyang, China
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Pereira C, Costa P, Pinheiro L, Balcão VM, Almeida A. Kiwifruit bacterial canker: an integrative view focused on biocontrol strategies. PLANTA 2021; 253:49. [PMID: 33502587 DOI: 10.1007/s00425-020-03549-1] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Accepted: 12/22/2020] [Indexed: 06/12/2023]
Abstract
Phage-based biocontrol strategies can be an effective alternative to control Psa-induced bacterial canker of kiwifruit. The global production of kiwifruit has been seriously affected by Pseudomonas syringae pv. actinidiae (Psa) over the last decade. Psa damages both Actinidia chinensis var. deliciosa (green kiwifruit) but specially the susceptible Actinidia chinensis var. chinensis (gold kiwifruit), resulting in severe economic losses. Treatments for Psa infections currently available are scarce, involving frequent spraying of the kiwifruit plant orchards with copper products. However, copper products should be avoided since they are highly toxic and lead to the development of bacterial resistance to this metal. Antibiotics are also used in some countries, but bacterial resistance to antibiotics is a serious worldwide problem. Therefore, it is essential to develop new approaches for sustainable agriculture production, avoiding the emergence of resistant Psa bacterial strains. Attempts to develop and establish highly accurate approaches to combat and prevent the occurrence of bacterial canker in kiwifruit plants are currently under study, using specific viruses of bacteria (bacteriophages, or phages) to eliminate the Psa. This review discusses the characteristics of Psa-induced kiwifruit canker, Psa transmission pathways, prevention and control, phage-based biocontrol strategies as a new approach to control Psa in kiwifruit orchards and its advantages over other therapies, together with potential ways to bypass phage inactivation by abiotic factors.
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Affiliation(s)
- Carla Pereira
- Department of Biology and CESAM, University of Aveiro, Campus de Santiago, 3810-193, Aveiro, Portugal
| | - Pedro Costa
- Department of Biology and CESAM, University of Aveiro, Campus de Santiago, 3810-193, Aveiro, Portugal
| | - Larindja Pinheiro
- Department of Biology and CESAM, University of Aveiro, Campus de Santiago, 3810-193, Aveiro, Portugal
| | - Victor M Balcão
- Department of Biology and CESAM, University of Aveiro, Campus de Santiago, 3810-193, Aveiro, Portugal.
- PhageLab - Laboratory of Biofilms and Bacteriophages, University of Sorocaba, Sorocaba, SP, CEP 18023-000, Brazil.
| | - Adelaide Almeida
- Department of Biology and CESAM, University of Aveiro, Campus de Santiago, 3810-193, Aveiro, Portugal.
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Abstract
Population genomics is transforming our understanding of pathogen biology and evolution, and contributing to the prevention and management of disease in diverse crops. We provide an overview of key methods in bacterial population genomics and describe recent work focusing on three topics of critical importance to plant pathology: (i) resolving pathogen origins and transmission pathways during outbreak events, (ii) identifying the genetic basis of host specificity and virulence, and (iii) understanding how pathogens evolve in response to changing agricultural practices.[Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
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Affiliation(s)
- Christina Straub
- Institute of Environmental Science and Research, Health and Environment, Auckland, New Zealand
- Genomics Aotearoa, New Zealand
| | - Elena Colombi
- Curtin Health Innovation Research Institute (CHIRI), Curtin University, Perth, Western Australia, Australia
- School of Pharmacy and Biomedical Sciences, Curtin University, Perth, Western Australia, Australia
| | - Honour C McCann
- New Zealand Institute for Advanced Study, Massey University, Albany, New Zealand
- Max Planck Institute for Developmental Biology, Tübingen, Germany
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Jayaraman J, Jones WT, Harvey D, Hemara LM, McCann HC, Yoon M, Warring SL, Fineran PC, Mesarich CH, Templeton MD. Variation at the common polysaccharide antigen locus drives lipopolysaccharide diversity within the Pseudomonas syringae species complex. Environ Microbiol 2020; 22:5356-5372. [PMID: 32985740 PMCID: PMC7820976 DOI: 10.1111/1462-2920.15250] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 09/22/2020] [Accepted: 09/22/2020] [Indexed: 12/19/2022]
Abstract
The common polysaccharide antigen (CPA) of the lipopolysaccharide (LPS) from Pseudomonas syringae is highly variable, but the genetic basis for this is poorly understood. We have characterized the CPA locus from P. syringae pv. actinidiae (Psa). This locus has genes for l- and d-rhamnose biosynthesis and an operon coding for ABC transporter subunits, a bifunctional glycosyltransferase and an o-methyltransferase. This operon is predicted to have a role in the transport, elongation and termination of the CPA oligosaccharide and is referred to as the TET operon. Two alleles of the TET operon were present in different biovars (BV) of Psa and lineages of the closely related pathovar P. syringae pv. actinidifoliorum. This allelic variation was reflected in the electrophoretic properties of purified LPS from the different isolates. Gene knockout of the TET operon allele from BV1 and replacement with that from BV3, demonstrated the link between the genetic locus and the biochemical properties of the LPS molecules in Psa. Sequence analysis of the TET operon from a range of P. syringae and P. viridiflava isolates displayed a phylogenetic history incongruent with core gene phylogeny but correlates with previously reported tailocin sensitivity, suggesting a functional relationship between LPS structure and tailocin susceptibility.
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Affiliation(s)
- Jay Jayaraman
- Bioprotection TechnologiesThe New Zealand Institute for Plant and Food Research LimitedAucklandNew Zealand
- Bioprotection Centre for Research ExcellenceNew Zealand
| | - William T. Jones
- Bioprotection TechnologiesThe New Zealand Institute for Plant and Food Research LimitedPalmerston NorthNew Zealand
| | - Dawn Harvey
- Bioprotection TechnologiesThe New Zealand Institute for Plant and Food Research LimitedPalmerston NorthNew Zealand
| | - Lauren M. Hemara
- Bioprotection TechnologiesThe New Zealand Institute for Plant and Food Research LimitedAucklandNew Zealand
- Bioprotection Centre for Research ExcellenceNew Zealand
- School of Biological SciencesUniversity of AucklandNew Zealand
| | - Honour C. McCann
- Institute of Advanced StudiesMassey UniversityAucklandNew Zealand
| | - Minsoo Yoon
- Bioprotection TechnologiesThe New Zealand Institute for Plant and Food Research LimitedAucklandNew Zealand
| | - Suzanne L. Warring
- Department of Microbiology and ImmunologyUniversity of OtagoDunedinNew Zealand
| | - Peter C. Fineran
- Bioprotection Centre for Research ExcellenceNew Zealand
- Department of Microbiology and ImmunologyUniversity of OtagoDunedinNew Zealand
| | - Carl H. Mesarich
- Bioprotection Centre for Research ExcellenceNew Zealand
- School of Agriculture and EnvironmentMassey UniversityPalmerston NorthNew Zealand
| | - Matthew D. Templeton
- Bioprotection TechnologiesThe New Zealand Institute for Plant and Food Research LimitedAucklandNew Zealand
- Bioprotection Centre for Research ExcellenceNew Zealand
- School of Biological SciencesUniversity of AucklandNew Zealand
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41
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Draft Genome Sequences of Nine Japanese Strains of the Kiwifruit Bacterial Canker Pathogen Pseudomonas syringae pv. actinidiae Biovar 3. Microbiol Resour Announc 2020; 9:9/45/e01007-20. [PMID: 33154006 PMCID: PMC7645661 DOI: 10.1128/mra.01007-20] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Pseudomonas syringae pv. actinidiae is the pathogen that causes kiwifruit bacterial canker and is categorized into several groups (biovars). In Japan, biovar 3, known as the pandemic group, was first discovered in 2014. Here, we sequenced the genomes of nine Japanese biovar 3 strains. Pseudomonas syringae pv. actinidiae is the pathogen that causes kiwifruit bacterial canker and is categorized into several groups (biovars). In Japan, biovar 3, known as the pandemic group, was first discovered in 2014. Here, we sequenced the genomes of nine Japanese biovar 3 strains.
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Jayaraman J, Yoon M, Applegate ER, Stroud EA, Templeton MD. AvrE1 and HopR1 from Pseudomonas syringae pv. actinidiae are additively required for full virulence on kiwifruit. MOLECULAR PLANT PATHOLOGY 2020; 21:1467-1480. [PMID: 32969167 PMCID: PMC7548996 DOI: 10.1111/mpp.12989] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 08/14/2020] [Accepted: 08/14/2020] [Indexed: 06/01/2023]
Abstract
Pseudomonas syringae pv. actinidiae ICMP 18884 biovar 3 (Psa3) produces necrotic lesions during infection of its kiwifruit host. Bacterial growth in planta and lesion formation are dependent upon a functional type III secretion system (T3S), which translocates multiple effector proteins into host cells. Associated with the T3S locus is the conserved effector locus (CEL), which has been characterized and shown to be essential for the full virulence in other P. syringae pathovars. Two effectors at the CEL, hopM1 and avrE1, as well as an avrE1-related non-CEL effector, hopR1, have been shown to be redundant in the model pathogen P. syringae pv. tomato DC3000 (Pto), a close relative of Psa. However, it is not known whether CEL-related effectors are required for Psa pathogenicity. The Psa3 allele of hopM1, and its associated chaperone, shcM, have diverged significantly from their orthologs in Pto. Furthermore, the CEL effector hopAA1-1, as well as a related non-CEL effector, hopAA1-2, have both been pseudogenized. We have shown that HopM1 does not contribute to Psa3 virulence due to a truncation in shcM, a truncation conserved in the Psa lineage, probably due to the need to evade HopM1-triggered immunity in kiwifruit. We characterized the virulence contribution of CEL and related effectors in Psa3 and found that only avrE1 and hopR1, additively, are required for in planta growth and lesion production. This is unlike the redundancy described for these effectors in Pto and indicates that these two Psa3 genes are key determinants essential for kiwifruit bacterial canker disease.
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Affiliation(s)
- Jay Jayaraman
- The New Zealand Institute for Plant and Food Research LimitedAucklandNew Zealand
- Bio‐Protection Research CentreLincolnNew Zealand
| | - Minsoo Yoon
- The New Zealand Institute for Plant and Food Research LimitedAucklandNew Zealand
| | - Emma R. Applegate
- The New Zealand Institute for Plant and Food Research LimitedAucklandNew Zealand
- School of Biological SciencesUniversity of AucklandAucklandNew Zealand
- Present address:
AgResearch Ltd., Grasslands Research CentrePalmerston NorthNew Zealand
| | - Erin A. Stroud
- The New Zealand Institute for Plant and Food Research LimitedAucklandNew Zealand
- School of Biological SciencesUniversity of AucklandAucklandNew Zealand
| | - Matthew D. Templeton
- The New Zealand Institute for Plant and Food Research LimitedAucklandNew Zealand
- Bio‐Protection Research CentreLincolnNew Zealand
- School of Biological SciencesUniversity of AucklandAucklandNew Zealand
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43
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Li L, Pan H, Deng L, Feng D, Zhong C. First Report of Bacterial Leaf Spot Disease of Broussonetia papyrifera Caused by Pseudomonas syringae pv. actinidiae in China. PLANT DISEASE 2020; 105:696-696. [PMID: 33044141 DOI: 10.1094/pdis-07-20-1527-pdn] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Broussonetia papyrifera (paper mulberry) is a deciduous tree with a number of uses and is native to northeastern Asia. Because of its fast-growing nature and high tolerance to dust, smoke, and high temperatures, paper mulberry is regarded as an important and economically-valuable component of a biologically diverse community and is used extensively in several areas including medicine, animal husbandry, paper making, weaving, afforestation and light industry (Mei et al. 2016). From June to August of 2019, symptoms on paper mulberry trees were observed in Shiniushan village, Sanhua town, Xishui County, Hubei province of China. Typical symptoms on leaves included small, angular, brown spots surrounded by yellow haloes. These spots coalesced into necrotic areas. The incidence was around 30%, which threatened the survival and reduced the yield of paper mulberry. In order to identify the causal pathogenic organism, leaf samples from 10 different infected trees were collected every two weeks and isolations made over three months. Several circular, flat, granulated colonies with entire margins were isolated on King's B medium (KB). The biochemical and physiological characteristics of thirty typical strains were tested and listed as following: gram negative, aerobic, rod shaped, and non-fluorescent on King's B medium; positive for carbohydrate utilization (sucrose, glucose, fructose and arabinose), levan production, hypersensitive on tobacco, potato and tomato; and negative for oxidase, arginine dehydrolase, tyrosinase and urease activity, gelatin liquefaction, and reduction of nitrate. Psa pathovar-specific primers PsaF1/PsaR2 (280bp product ) identified two representative strains as Psa (Rees-George et al. 2010). BLAST analysis further confirmed that the 16S rDNA region amplified by primers 27F/1492R (NCBI accession nos. MT472100 and MT472101) shared 99.84% and 99.77% identity with the Psa type strain ICMP 18884 (CP011972) respectively (Weisburg et al. 1991). For ten typical strains, pathogenicity was confirmed by spraying a bacterial suspension (108 cfu/mL) onto fifty one-year seedlings of B. papyrifera, five seedlings repetitions for each strain. Symptoms of infection similar to those observed initially in the field were detected within 7 days after incubation at 25°C with 80-85% humidity. No symptoms were observed on control plants. The pathogen was re-isolated from symptomatic leaves and re-identified as Psa by morphological characteristics and sequencing. To our knowledge, this is the first report of Psa causing bacterial leaf spot disease on B. papyrifera, China. Psa has been reported as a pathogen causing bacterial canker of kiwifruit worldwide, resulting in severe economic losses to kiwifruit growers (McCann & Li, 2017). As a host of Psa, B. papyrifera may be a source of inoculum for nearby kiwifruit orchards, and consequently effective control measures should be taken to manage this disease. Funding: This study was supported by the National Natural Science Foundation of China (31701974; 31901980), Science and technology program funded by Wuhan Science and Technology Bureau (2018020401011307). References: Mei et al. 2016. Eur J Plant Pathol. 145: 203. McCann & Li et al. 2017. Genome Biol Evol. 9: 932. Rees-George et al. 2010. Plant Pathol. 59: 453 Weisburg et al. 1991. J Bacteriol. 173: 697.
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Affiliation(s)
- Li Li
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanic Garden, Chinese Academy of Sciences, Hubei Province, Wuhan, Lumo 1, Wuhan, China, 430074;
| | - Hui Pan
- Key laboratory of Plant Germplasm Enhancement and Specialty Agricμlture, Wuhan Botanic Garden, Chinese Academy of Sciences, Wuhan, China;
| | - Lei Deng
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China, Wuhan, China;
| | - Dandan Feng
- Key laboratory of Plant Germplasm Enhancement and Specialty Agricμlture, Wuhan Botanic Garden, Chinese Academy of Sciences, Wuhan, China;
| | - Caihong Zhong
- Key laboratory of Plant Germplasm Enhancement and Specialty Agricμlture, Wuhan Botanic Garden, Chinese Academy of Sciences, Key laboratory of Plant Germplasm Enhancement and Specialty Agricμlture, Wuhan Botanic Garden, Chinese Academy of Sciences, Wuhan 430074, China, Wuhan, China, 430074;
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44
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Plant–microbiome interactions: from community assembly to plant health. Nat Rev Microbiol 2020; 18:607-621. [DOI: 10.1038/s41579-020-0412-1] [Citation(s) in RCA: 597] [Impact Index Per Article: 149.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/18/2020] [Indexed: 01/17/2023]
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45
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Hulin MT, Jackson RW, Harrison RJ, Mansfield JW. Cherry picking by pseudomonads: After a century of research on canker, genomics provides insights into the evolution of pathogenicity towards stone fruits. PLANT PATHOLOGY 2020; 69:962-978. [PMID: 32742023 PMCID: PMC7386918 DOI: 10.1111/ppa.13189] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Revised: 03/09/2020] [Accepted: 03/23/2020] [Indexed: 05/10/2023]
Abstract
Bacterial canker disease is a major limiting factor in the growing of cherry and other Prunus species worldwide. At least five distinct clades within the bacterial species complex Pseudomonas syringae are known to be causal agents of the disease. The different pathogens commonly coexist in the field. Reducing canker is a challenging prospect as the efficacy of chemical controls and host resistance may vary against each of the diverse clades involved. Genomic analysis has revealed that the pathogens use a variable repertoire of virulence factors to cause the disease. Significantly, strains of P. syringae pv. syringae possess more genes for toxin biosynthesis and fewer encoding type III effector proteins. There is also a shared pool of key effector genes present on mobile elements such as plasmids and prophages that may have roles in virulence. By contrast, there is evidence that absence or truncation of certain effector genes, such as hopAB, is characteristic of cherry pathogens. Here we highlight how recent research, underpinned by the earlier epidemiological studies, is allowing significant progress in our understanding of the canker pathogens. This fundamental knowledge, combined with emerging insights into host genetics, provides the groundwork for development of precise control measures and informed approaches to breed for disease resistance.
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Affiliation(s)
| | - Robert W. Jackson
- Birmingham Institute of Forest Research (BIFoR), University of BirminghamBirminghamUK
- School of Biosciences, University of BirminghamBirminghamUK
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46
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McCann HC. Skirmish or war: the emergence of agricultural plant pathogens. CURRENT OPINION IN PLANT BIOLOGY 2020; 56:147-152. [PMID: 32712539 DOI: 10.1016/j.pbi.2020.06.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Revised: 06/12/2020] [Accepted: 06/16/2020] [Indexed: 06/11/2023]
Abstract
Understanding the ecological and evolutionary processes underlying the emergence of infectious disease is critically important in guiding prevention, management and breeding strategies. Novel pathogen lineages may arise within agricultural environments, wild hosts or from non-host associated disease reservoirs. Although the source of most disease outbreaks remains unknown, environmental and zoonotic origins are frequently identified in mammalian pathosystems and expanded sampling of plant pathosystems reveals important links with wild populations. This review describes key ecological and evolutionary processes underlying disease emergence, with particular emphasis on shifts from wild reservoirs to cultivated hosts and genetic mechanisms driving host adaption subsequent to emergence.
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Affiliation(s)
- Honour C McCann
- New Zealand Institute for Advanced Study, Massey University, Albany, New Zealand; Max Planck Institute for Developmental Biology, Tübingen, Germany.
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47
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Baltrus DA. Bacterial dispersal and biogeography as underappreciated influences on phytobiomes. CURRENT OPINION IN PLANT BIOLOGY 2020; 56:37-46. [PMID: 32278259 DOI: 10.1016/j.pbi.2020.02.010] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Revised: 02/14/2020] [Accepted: 02/25/2020] [Indexed: 06/11/2023]
Abstract
Bacterial strains are not distributed evenly throughout the environment. Here I explore how differential distribution and dispersal patterns of bacteria could affect interactions and coevolutionary dynamics with plants, and highlight ways that variation could be taken advantage of to develop robust and effective microbial consortia to inoculate crops. Questions about biogeographical patterns in viruses, fungi, and other eukaryotes are equally as prevalent and important for agriculture, and are in some cases more thoroughly explored. For simplicity as well as to bring attention to bacterial biogeography and dispersal in the context of plant interactions, I focus solely on bacterial patterns and questions for this article. The next few years will no doubt bring great advances in our understanding of dispersal capabilities and population dynamics for many plant-associated bacteria, and one of the next looming challenges will be learning to harvest this diversity in ways that can benefit agriculture.
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Affiliation(s)
- David A Baltrus
- School of Plant Sciences, University of Arizona, Tucson AZ, USA; School of Animal and Comparative Biomedical Sciences, University of Arizona, Tucson AZ, USA.
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48
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Characterization of Bacteriophages against Pseudomonas Syringae pv. Actinidiae with Potential Use as Natural Antimicrobials in Kiwifruit Plants. Microorganisms 2020; 8:microorganisms8070974. [PMID: 32610695 PMCID: PMC7409275 DOI: 10.3390/microorganisms8070974] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 06/09/2020] [Accepted: 06/12/2020] [Indexed: 02/06/2023] Open
Abstract
Pseudomonas syringae pv. actinidiae (Psa) is the causal agent of a bacterial canker in kiwifruit plants and has caused economic losses worldwide. Currently, the primary strategies to control this pathogen include the use of copper-based compounds and even antibiotics. However, the emergence of isolates of Psa that are resistant to these agrochemicals has raised the need for new alternatives to control this pathogen. Bacteriophages have been proposed as an alternative to control bacterial infections in agriculture, including Psa. Here, we show the isolation and characterization of 13 phages with the potential to control Psa infections in kiwifruit plants. The phages were characterized according to their host range and restriction fragment length polymorphism (RFLP) pattern. Four phages were selected according to their lytic effect on the bacteria and their tolerance to different environmental conditions of pH (4–7), temperature (4–37 °C), and solar radiation exposure (30 and 60 min). The selected phages (CHF1, CHF7, CHF19, and CHF21) were sequenced, revealing a high identity with the podophage of Psa phiPSA2. In vitro assays with kiwifruit leaf samples demonstrated that the mixture of phages reduced the Psa bacterial load within three hours post-application and was able to reduce the damage index in 50% of cases. Similarly, assays with kiwifruit plants maintained in greenhouse conditions showed that these phages were able to reduce the Psa bacterial load in more than 50% of cases and produced a significant decrease in the damage index of treated plants after 30 days. Finally, none of the selected phages were able to infect the other bacteria present in the natural microbiota of kiwifruit plants. These results show that bacteriophages are an attractive alternative to control Psa infections in kiwifruit plants.
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49
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Figueira D, Garcia E, Ares A, Tiago I, Veríssimo A, Costa J. Genetic Diversity of Pseudomonas syringae pv. actinidiae: Seasonal and Spatial Population Dynamics. Microorganisms 2020; 8:E931. [PMID: 32575724 PMCID: PMC7357126 DOI: 10.3390/microorganisms8060931] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Revised: 06/01/2020] [Accepted: 06/16/2020] [Indexed: 11/21/2022] Open
Abstract
Pseudomonassyringae pv. actinidiae (Psa) is a gram-negative bacterium responsible for the bacterial canker in Actinidia chinensis var. deliciosa and A. chinensis var. chinensis, a quarantine organism threatening the kiwifruit industry sustainability. The present study aimed to determine the genetic structure of the endophytic and epiphytic populations of Psa isolated from four different Portuguese orchards with distinct abiotic conditions in two consecutive seasons. The results identified several coexisting and highly heterogeneous Psa populations. Moreover, evident changes in population structure occurred between the epiphytic and endophytic populations, and between seasons with a notable decrease in Psa diversity in autumn. This work provided solid evidence that the initial clonal expansion of Psa in Europe was followed by a wide genomic diversification. This perspective is important for the understanding of kiwifruit bacterial canker disease occurrence and Psa evolution, namely when adopting strategies for management of epidemics.
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Affiliation(s)
- Daniela Figueira
- Department of Life Sciences, Centre for Functional Ecology, University of Coimbra, Calçada Martim de Freitas, 3000-456 Coimbra, Portugal; (D.F.); (E.G.); (A.A.); (I.T.); (A.V.)
- FitoLab, Laboratory for Phytopathology, Instituto Pedro Nunes, 3030-199 Coimbra, Portugal
| | - Eva Garcia
- Department of Life Sciences, Centre for Functional Ecology, University of Coimbra, Calçada Martim de Freitas, 3000-456 Coimbra, Portugal; (D.F.); (E.G.); (A.A.); (I.T.); (A.V.)
- FitoLab, Laboratory for Phytopathology, Instituto Pedro Nunes, 3030-199 Coimbra, Portugal
| | - Aitana Ares
- Department of Life Sciences, Centre for Functional Ecology, University of Coimbra, Calçada Martim de Freitas, 3000-456 Coimbra, Portugal; (D.F.); (E.G.); (A.A.); (I.T.); (A.V.)
- FitoLab, Laboratory for Phytopathology, Instituto Pedro Nunes, 3030-199 Coimbra, Portugal
| | - Igor Tiago
- Department of Life Sciences, Centre for Functional Ecology, University of Coimbra, Calçada Martim de Freitas, 3000-456 Coimbra, Portugal; (D.F.); (E.G.); (A.A.); (I.T.); (A.V.)
| | - António Veríssimo
- Department of Life Sciences, Centre for Functional Ecology, University of Coimbra, Calçada Martim de Freitas, 3000-456 Coimbra, Portugal; (D.F.); (E.G.); (A.A.); (I.T.); (A.V.)
| | - Joana Costa
- Department of Life Sciences, Centre for Functional Ecology, University of Coimbra, Calçada Martim de Freitas, 3000-456 Coimbra, Portugal; (D.F.); (E.G.); (A.A.); (I.T.); (A.V.)
- FitoLab, Laboratory for Phytopathology, Instituto Pedro Nunes, 3030-199 Coimbra, Portugal
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50
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Zhang X, Ritchie SR, Chang H, Arnold DL, Jackson RW, Rainey PB. Genotypic and phenotypic analyses reveal distinct population structures and ecotypes for sugar beet-associated Pseudomonas in Oxford and Auckland. Ecol Evol 2020; 10:5963-5975. [PMID: 32607204 PMCID: PMC7319117 DOI: 10.1002/ece3.6334] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Revised: 04/09/2020] [Accepted: 04/14/2020] [Indexed: 01/02/2023] Open
Abstract
Fluorescent pseudomonads represent one of the largest groups of bacteria inhabiting the surfaces of plants, but their genetic composition in planta is poorly understood. Here, we examined the population structure and diversity of fluorescent pseudomonads isolated from sugar beet grown at two geographic locations (Oxford, United Kingdom and Auckland, New Zealand). To seek evidence for niche adaptation, bacteria were sampled from three types of leaves (immature, mature, and senescent) and then characterized using a combination of genotypic and phenotypic analysis. We first performed multilocus sequence analysis (MLSA) of three housekeeping genes (gapA, gltA, and acnB) in a total of 152 isolates (96 from Oxford, 56 from Auckland). The concatenated sequences were grouped into 81 sequence types and 22 distinct operational taxonomic units (OTUs). Significant levels of recombination were detected, particularly for the Oxford isolates (rate of recombination to mutation (r/m) = 5.23 for the whole population). Subsequent ancestral analysis performed in STRUCTURE found evidence of six ancestral populations, and their distributions significantly differed between Oxford and Auckland. Next, their ability to grow on 95 carbon sources was assessed using the Biolog™ GN2 microtiter plates. A distance matrix was generated from the raw growth data (A 660) and subjected to multidimensional scaling (MDS) analysis. There was a significant correlation between substrate utilization profiles and MLSA genotypes. Both phenotypic and genotypic analyses indicated presence of a geographic structure for strains from Oxford and Auckland. Significant differences were also detected for MLSA genotypes between strains isolated from immature versus mature/senescent leaves. The fluorescent pseudomonads thus showed an ecotypic population structure, suggestive of adaptation to both geographic conditions and local plant niches.
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Affiliation(s)
- Xue‐Xian Zhang
- New Zealand Institute for Advanced StudyMassey UniversityAucklandNew Zealand
- School of Natural and Computational SciencesMassey UniversityAucklandNew Zealand
| | - Stephen R. Ritchie
- New Zealand Institute for Advanced StudyMassey UniversityAucklandNew Zealand
- Faculty of Medical and Health SciencesUniversity of AucklandAucklandNew Zealand
| | - Hao Chang
- New Zealand Institute for Advanced StudyMassey UniversityAucklandNew Zealand
| | - Dawn L. Arnold
- Centre for Research in BioscienceUniversity of the West of EnglandBristolUK
| | - Robert W. Jackson
- School of Biosciences and Birmingham Institute of Forest ResearchUniversity of BirminghamBirminghamUK
| | - Paul B. Rainey
- New Zealand Institute for Advanced StudyMassey UniversityAucklandNew Zealand
- Department of Microbial Population BiologyMax Planck Institute for Evolutionary BiologyPlönGermany
- Laboratoire de Génétique de l'Evolution, Chemistry, Biology and Innovation (CBI)UMR8231ESPCI ParisCNRSPSL Research UniversityParisFrance
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