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Gdanetz K, Dobbins MR, Villani SM, Outwater CA, Slack SM, Nesbitt D, Svircev AM, Lauwers EM, Zeng Q, Cox KD, Sundin GW. Multisite Field Evaluation of Bacteriophages for Fire Blight Management: Incorporation of Ultraviolet Radiation Protectants and Impact on the Apple Flower Microbiome. PHYTOPATHOLOGY 2024; 114:1028-1038. [PMID: 37581441 DOI: 10.1094/phyto-04-23-0145-kc] [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: 08/16/2023]
Abstract
Fire blight, a disease of pome fruits caused by the bacterium Erwinia amylovora, has become increasingly difficult to manage after the emergence of streptomycin-resistant strains. Alternative antibiotics and copper are available; however, these chemicals have use restrictions in some countries and also can carry risks of phytotoxicity. Therefore, there is growing interest in biological-based management options, with bacteriophage (phages) showing promise, as these naturally occurring pathogens of bacteria are easy to isolate and grow. However, there are several technical challenges regarding the implementation of phage biocontrol in the field, as the viral molecules suffer from ultraviolet radiation (UVR) degradation and can die off rapidly in the absence of the host bacterium. In this work, we assessed the efficacy of Erwinia phages and a commercial phage product for blossom blight control in the field across multiple locations in the eastern United States. In these tests, disease control ranged from 0.0 to 82.7%, and addition of a UVR protectant only resulted in significantly increased disease control in 2 of 12 tests. We also analyzed microbial community population changes in response to phage application. Changes in bacterial community diversity metrics over time were not detected; however, relative abundances of target taxa were temporarily reduced after phage applications, indicating that these phage applications did not have deleterious effects on the flower microbiome. We have demonstrated that biological control of fire blight with phages is achievable, but a better understanding of phage-pathogen dynamics is required to optimize disease control efficacy.
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Affiliation(s)
- Kristi Gdanetz
- Department of Plant, Soil, and Microbial Sciences, Michigan State University, East Lansing, MI 48824, U.S.A
| | - Madison R Dobbins
- Department of Plant, Soil, and Microbial Sciences, Michigan State University, East Lansing, MI 48824, U.S.A
| | - Sara M Villani
- Department of Entomology and Plant Pathology, Mountain Horticulture and Crops Research and Extension Center, North Carolina State University, Mills River, NC 28759, U.S.A
| | - Cory A Outwater
- Department of Plant, Soil, and Microbial Sciences, Michigan State University, East Lansing, MI 48824, U.S.A
| | - Suzanne M Slack
- Department of Plant, Soil, and Microbial Sciences, Michigan State University, East Lansing, MI 48824, U.S.A
- Department of Horticulture, Iowa State University, Ames, IA 50011, U.S.A
| | - Darlene Nesbitt
- London Research and Development Centre, Agriculture and Agri-Food Canada, Vineland Station, ON, Canada L0R 2E0
| | - Antonet M Svircev
- London Research and Development Centre, Agriculture and Agri-Food Canada, Vineland Station, ON, Canada L0R 2E0
| | - Erin M Lauwers
- Department of Plant, Soil, and Microbial Sciences, Michigan State University, East Lansing, MI 48824, U.S.A
- Northwest Michigan Horticulture Research Center, Michigan State University, Traverse City, MI 49694, U.S.A
| | - Quan Zeng
- Department of Plant Pathology and Ecology, CT Agricultural Experiment Station, 123 Huntington Street, New Haven, CT 06511, U.S.A
| | - Kerik D Cox
- Section of Plant Pathology and Plant-Microbe Biology, School of Integrative Plant Science, Cornell University, Cornell AgriTech, Geneva, NY 14456, U.S.A
| | - George W Sundin
- Department of Plant, Soil, and Microbial Sciences, Michigan State University, East Lansing, MI 48824, U.S.A
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2
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Ibrahim N, Nesbitt D, Guo Q(T, Lin J, Svircev A, Wang Q, Weadge JT, Anany H. Improved Viability of Spray-Dried Pantoea agglomerans for Phage-Carrier Mediated Control of Fire Blight. Viruses 2024; 16:257. [PMID: 38400033 PMCID: PMC10893313 DOI: 10.3390/v16020257] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2023] [Revised: 01/26/2024] [Accepted: 01/30/2024] [Indexed: 02/25/2024] Open
Abstract
Fire blight, caused by Erwinia amylovora, is a devastating bacterial disease that threatens apple and pear production. It is mainly controlled by using antibiotics, such as streptomycin. Due to development of E. amylovora resistant strains and the excessive agricultural use of antibiotics, there is an increased awareness of the possibility of antibiotic resistance gene transfer to other microbes. Urgent development of biocontrol agents (BCAs) is needed that can be incorporated into integrated pest management programs as antibiotic alternatives. A novel phage-carrier system (PCS) that combines an antagonistic bacterium, Pantoea agglomerans, with its ability to act as a phage-carrier bacterium for Erwinia phages has been developed. The low viability of P. agglomerans cells following spray-drying (SD) has been a challenge for the industrial-scale production of this PCS. Here, an SD protocol was developed for P. agglomerans by modifying the growth medium and bacterial cell formulation using D(+)-trehalose and maltodextrin. The developed protocol is amenable to the industrial-scale production of the BCA/PCS. The P. agglomerans viability was greater than 90% after SD and had a shelf life at 4 °C of 4 months, and reconstituted cells showed a 3 log reduction in E. amylovora counts with a pear disc assay.
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Affiliation(s)
- Nassereldin Ibrahim
- Agriculture and Agri-Food Canada (AAFC), Guelph Research and Development Centre (GRDC), 93 Stone Rd W., Guelph, ON N1G 5C9, Canada; (N.I.); (Q.G.); (Q.W.)
- Department of Biology, Wilfrid Laurier University, Waterloo, ON N2L 3C5, Canada;
- Genetic Engineering and Biotechnology Research Institute, University of Sadat City, Sadat City 32897, Egypt
| | - Darlene Nesbitt
- Agriculture and Agri-Food Canada (AAFC), Vineland Station, ON L0R 2E0, Canada; (D.N.); (A.S.)
| | - Qian (Tracy) Guo
- Agriculture and Agri-Food Canada (AAFC), Guelph Research and Development Centre (GRDC), 93 Stone Rd W., Guelph, ON N1G 5C9, Canada; (N.I.); (Q.G.); (Q.W.)
| | - Janet Lin
- National Microbiology Laboratory, National Health Agency, 110 Stone Rd. W., Guelph, ON N1G 3W4, Canada;
| | - Antonet Svircev
- Agriculture and Agri-Food Canada (AAFC), Vineland Station, ON L0R 2E0, Canada; (D.N.); (A.S.)
| | - Qi Wang
- Agriculture and Agri-Food Canada (AAFC), Guelph Research and Development Centre (GRDC), 93 Stone Rd W., Guelph, ON N1G 5C9, Canada; (N.I.); (Q.G.); (Q.W.)
| | - Joel T. Weadge
- Department of Biology, Wilfrid Laurier University, Waterloo, ON N2L 3C5, Canada;
| | - Hany Anany
- Agriculture and Agri-Food Canada (AAFC), Guelph Research and Development Centre (GRDC), 93 Stone Rd W., Guelph, ON N1G 5C9, Canada; (N.I.); (Q.G.); (Q.W.)
- Food Science Department, University of Guelph, Guelph, ON N1G 2W1, Canada
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3
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Ham H, Park DS. New Insights and Approach Toward the Genetic Diversity and Strain Typing of Erwinia pyrifoliae Based on rsxC, an Electron Transport Gene. PLANT DISEASE 2024; 108:296-301. [PMID: 37669173 DOI: 10.1094/pdis-03-23-0475-sc] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/07/2023]
Abstract
Erwinia pyrifoliae, a causal agent of black shoot blight in apple and pear trees, is a plant pathogenic bacterium first reported in South Korea. The symptoms of black shoot blight are very similar to those of the fire blight disease in apple and pear trees caused by E. amylovora, as E. pyrifoliae has a genetically very close relationship with E. amylovora. Recently, there have been reports that E. pyrifoliae causes disease in European strawberries, resulting in severe fruit loss that aroused great concern about its spread, distribution, and host range. Therefore, it is essential to establish a trustworthy approach to understanding the distribution patterns of E. pyrifoliae based on the genetic background to strengthen the barrier of potential spreading risks, although advanced methods have been provided to accurately detect E. pyrifoliae and E. amylovora. Consequently, this study discovered a noble and noteworthy gene, rsxC, capable of providing the pathogen genotype by comparing E. pyrifoliae genomic sequences in the international representative genome archive. Different numbers of 40-unit amino acid repeats in this gene among the strains induced intraspecific traits in RsxC. By comparing their repeat pattern, E. pyrifoliae isolates were divided into two main groups, branching into several clades via sequence alignment of 35 E. pyrifoliae isolates from various apple orchards from 2020 to 2021 in South Korea. The newly discovered quadraginta amino acid repeat within this gene would be a valuable genetic touchstone for determining the genotype and distribution pattern of E. pyrifoliae strains, ultimately leading to exploring their evolution. The function of amino acid repeats and the biological significance of strains need to be elucidated further.
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Affiliation(s)
- Hyeonheui Ham
- Crop Protection Division, National Institute of Agricultural Sciences, Wanju-gun 55365, Republic of Korea
| | - Dong Suk Park
- Crop Protection Division, National Institute of Agricultural Sciences, Wanju-gun 55365, Republic of Korea
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4
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Yang HW, Thapa R, Johnson K, DuPont ST, Khan A, Zhao Y. Examination of Large Chromosomal Inversions in the Genome of Erwinia amylovora Strains Reveals Worldwide Distribution and North America-Specific Types. PHYTOPATHOLOGY 2023; 113:2174-2186. [PMID: 36935376 DOI: 10.1094/phyto-01-23-0004-sa] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Erwinia amylovora is a relatively homogeneous species with low genetic diversity at the nucleotide level. However, phenotypic differences and genomic structural variations among E. amylovora strains have been documented. In this study, we identified 10 large chromosomal inversion (LCI) types in the Spiraeoideae-infecting (SI) E. amylovora strains by combining whole genome sequencing and PCR-based molecular markers. It was found that LCIs were mainly caused by homologous recombination events among seven rRNA operons (rrns) in SI E. amylovora strains. Although ribotyping results identified inter- and intra-variations in the internal transcribed spacer (ITS1 and ITS2) regions among rrns, LCIs tend to occur between rrns transcribed in the opposite directions and with the same tRNA content (tRNA-Glu or tRNA-Ile/Ala) in ITS1. Based on the LCI types, physical/estimated replichore imbalance (PRI/ERI) was examined and calculated. Among the 117 SI strains evaluated, the LCI types of Ea1189, CFBP1430, and Ea273 were the most common, with ERI values at 1.31, 7.87, and 4.47°, respectively. These three LCI types had worldwide distribution, whereas the remaining seven LCI types were restricted to North America (or certain regions of the United States). Our results indicated ongoing chromosomal recombination events in the SI E. amylovora population and showed that LCI events are mostly symmetrical, keeping the ERI less than 15°. These findings provide initial evidence about the prevalence of certain LCI types in E. amylovora strains, how LCI occurs, and its potential evolutionary advantage and history, which might help track the movement of the pathogen.
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Affiliation(s)
- Ho-Wen Yang
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61802
| | - Ranjita Thapa
- School of Integrative Plant Science Plant Pathology and Plant-Microbe Biology, Cornell University, Geneva, NY 14456
| | - Kenneth Johnson
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331
| | | | - Awais Khan
- School of Integrative Plant Science Plant Pathology and Plant-Microbe Biology, Cornell University, Geneva, NY 14456
| | - Youfu Zhao
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61802
- Department of Plant Pathology, WSU-IAREC, Prosser, WA 99350
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5
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Sun W, Gong P, Zhao Y, Ming L, Zeng Q, Liu F. Current Situation of Fire Blight in China. PHYTOPATHOLOGY 2023; 113:2143-2151. [PMID: 37505073 DOI: 10.1094/phyto-05-23-0170-rvw] [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: 07/29/2023]
Abstract
Fire blight, caused by the plant-pathogenic bacterium Erwinia amylovora, is a devastating disease that occurs on rosaceous plants, including pears and apples. E. amylovora is indigenous to North America and was spread to the Eurasian continent in the second half of the 20th century through contaminated plant materials. In 2016, fire blight was first observed in Yili, Xinjiang Province, in Northwestern China. Since then, it has spread to most pear-producing regions in Xinjiang Province and parts of Gansu Province. The disease has caused severe damage to China's pear and apple industries, including the 2017 disease epidemic in Korla, Xinjiang, which caused an overall yield reduction of 30 to about 50% in Korla and the destruction of over 1 million pear trees. Over the past few years, a combined effort of research, extension, and education by the Chinese government, scientists, and fruit growers has greatly alleviated outbreaks and epidemics in affected regions while successfully limiting the further spread of fire blight to new geographical regions. Here, we review the occurrence, spread, and damage of this disease to the Chinese fruit industry, as well as the management options used in China and their outcomes. We also discuss future perspectives for restraining the spread and alleviating the damage of fire blight in China.
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Affiliation(s)
- Weibo Sun
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base of Ministry of Science and Technology, Nanjing 210014, China
| | - Peijie Gong
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base of Ministry of Science and Technology, Nanjing 210014, China
| | - Yancun Zhao
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base of Ministry of Science and Technology, Nanjing 210014, China
| | - Liang Ming
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base of Ministry of Science and Technology, Nanjing 210014, China
| | - Quan Zeng
- Department of Plant Pathology and Ecology, The Connecticut Agricultural Experiment Station, New Haven, CT 06511, U.S.A
| | - Fengquan Liu
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base of Ministry of Science and Technology, Nanjing 210014, China
- Department of Plant Pathology/Key Laboratory of Agricultural Microbiology, College of Agriculture, Guizhou University, Guiyang 550025, China
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Sundin GW, Peng J, Brown LE, Zeng Q, Förster H, Adaskaveg JE. A Novel IncX Plasmid Mediates High-Level Oxytetracycline and Streptomycin Resistance in Erwinia amylovora from Commercial Pear Orchards in California. PHYTOPATHOLOGY 2023; 113:2165-2173. [PMID: 37565835 DOI: 10.1094/phyto-06-23-0190-sa] [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: 08/12/2023]
Abstract
Isolates of the fire blight pathogen Erwinia amylovora with high-level resistance to oxytetracycline (minimal inhibitory concentration [MIC] > 100 μg/ml) and to streptomycin (MIC > 100 μg/ml) were recovered from four commercial pear orchards in California between 2018 and 2020. The two representative oxytetracycline- and streptomycin-resistant (OxyTcR-SmR) strains 32-10 and 33-1 were as virulent as the antibiotic susceptible strain 13-1 in causing blossom blight of pear and were recovered more than 50% of the time 7 days after co-inoculation to pear flowers with strain 13-1. In the field, inoculation of strain 32-10 to pear flowers that were pretreated with oxytetracycline at 200 μg/ml did not reduce disease compared with an untreated control. Four OxyTcR-SmR strains were subjected to draft genome sequencing to identify the genetic determinants of antibiotic resistance and their location. A 43.6-kb IncX plasmid, designated pX11-7, was detected in each of the four strains, and this plasmid encoded the tetracycline-resistance gene tetB and the streptomycin-resistance gene pair strAB within a large putatively mobile genetic element consisting of the transposon Tn10 that had inserted within the streptomycin-resistance transposon Tn6082. We also determined that pX11-7 was conjugative and was transferred at a rate that was 104 to 105 higher into an E. amylovora strain isolated in California compared with an E. amylovora strain that was isolated in Michigan. The occurrence of high levels of resistance to both oxytetracycline and streptomycin in E. amylovora strains from commercial pear orchards in California significantly limits the options for blossom blight management in these locations.
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Affiliation(s)
- George W Sundin
- Department of Plant, Soil, and Microbial Sciences, Michigan State University, East Lansing, MI 48824
| | - Jingyu Peng
- Department of Plant, Soil, and Microbial Sciences, Michigan State University, East Lansing, MI 48824
| | - Lindsay E Brown
- Department of Plant, Soil, and Microbial Sciences, Michigan State University, East Lansing, MI 48824
| | - Quan Zeng
- Department of Plant Pathology and Ecology, The Connecticut Agricultural Experiment Station, New Haven, CT 06511
| | - Helga Förster
- Department of Plant Pathology and Microbiology, University of California, Riverside, CA 92521
| | - James E Adaskaveg
- Department of Plant Pathology and Microbiology, University of California, Riverside, CA 92521
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7
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García P, Tabla R, Anany H, Bastias R, Brøndsted L, Casado S, Cifuentes P, Deaton J, Denes TG, Islam MA, Lavigne R, Moreno-Switt AI, Nakayama N, Muñoz Madero C, Sulakvelidze A, Svircev AM, Wagemans J, Biosca EG, Rivera D. ECOPHAGE: Combating Antimicrobial Resistance Using Bacteriophages for Eco-Sustainable Agriculture and Food Systems. Viruses 2023; 15:2224. [PMID: 38005900 PMCID: PMC10675804 DOI: 10.3390/v15112224] [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: 10/31/2023] [Accepted: 11/02/2023] [Indexed: 11/26/2023] Open
Abstract
The focus of this meeting was to discuss the suitability of using bacteriophages as alternative antimicrobials in the agrifood sector. Following a One Health approach, the workshop explored the possibilities of implementing phage application strategies in the agriculture, animal husbandry, aquaculture, and food production sectors. Therefore, the meeting had gathered phage researchers, representatives of the agrifood industry, and policymakers to debate the advantages and potential shortcomings of using bacteriophages as alternatives to traditional antimicrobials and chemical pesticides. Industry delegates showed the latest objectives and demands from consumers. Representatives of regulatory agencies (European Medicines Agency (EMA) and Spanish Agency of Medicines and Health Products (AEMPS)) presented an update of new regulatory aspects that will impact and support the approval and implementation of phage application strategies across the different sectors.
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Affiliation(s)
- Pilar García
- Instituto de Productos Lácteos de Asturias—Consejo Superior de Investigaciones Científicas (IPLA-CSIC), 33300 Villaviciosa, Spain;
| | - Rafael Tabla
- Centro de Investigaciones Científicas y Tecnológicas de Extremadura (CICYTEX), 06071 Badajoz, Spain;
| | - Hany Anany
- Guelph Research and Development Centre, Agriculture and Agri-Food Canada, Guelph, ON N1G 5C9, Canada;
- Food Science Department, University of Guelph, Guelph, ON N1G 2W1, Canada
| | - Roberto Bastias
- Instituto de Biología, Pontificia Universidad Católica de Valparaíso, Valparaíso 2340000, Chile;
| | - Lone Brøndsted
- Department of Veterinary and Animal Sciences, University of Copenhagen, 1870 Copenhagen, Denmark;
| | - Susana Casado
- Spanish Agency of Medicines and Health Products (AEMPS), 28022 Madrid, Spain;
| | | | - John Deaton
- ADM Science & Technology, Kennesaw, GA 30152, USA;
| | - Thomas G. Denes
- Department of Food Science, University of Tennessee, Knoxville, TN 37996, USA;
| | - Mohammad Aminul Islam
- Paul G. Allen School for Global Health, Washington State University, Pullman, WA 99164, USA;
| | - Rob Lavigne
- Department of Biosystems, KU Leuven, B-3001 Leuven, Belgium; (R.L.); (J.W.)
| | - Andrea I. Moreno-Switt
- Escuela de Medicina Veterinaria, Facultad de Agronomía y Sistemas Naturales, Facultad de Ciencias Biológicas, Facultad de Medicina, Pontificia Universidad Católica de Chile, Santiago 7820435, Chile;
| | - Natsuko Nakayama
- Japan Fisheries Research and Education Agency (FRA), Hiroshima 739-0452, Japan;
| | - Cristina Muñoz Madero
- Department of Medicines for Veterinary Use, Coordinator of the National Antibiotics Plan, Spanish Agency of Medicines and Health Products (AEMPS), 28022 Madrid, Spain;
| | | | | | - Jeroen Wagemans
- Department of Biosystems, KU Leuven, B-3001 Leuven, Belgium; (R.L.); (J.W.)
| | - Elena G. Biosca
- Departamento de Microbiología y Ecología, Universitat de València (UV), 46100 Valencia, Spain
| | - Dácil Rivera
- Escuela de Medicina Veterinaria, Facultad de Ciencias de la Vida, Universidad Andrés Bello, Santiago 8320000, Chile
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Ham H, Park DS. Novel approach toward the understanding of genetic diversity based on the two types of amino acid repeats in Erwinia amylovora. Sci Rep 2023; 13:17876. [PMID: 37857695 PMCID: PMC10587187 DOI: 10.1038/s41598-023-44558-w] [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: 03/29/2023] [Accepted: 10/10/2023] [Indexed: 10/21/2023] Open
Abstract
Erwinia amylovora is a notorious plant pathogenic bacterium of global concern that has devastated the apple and pear production industry worldwide. Nevertheless, the approaches available currently to understand the genetic diversity of E. amylovora remain unsatisfactory because of the lack of a trustworthy index and data covering the globally occurring E. amylovora strains; thus, their origin and distribution pattern remains ambiguous. Therefore, there is a growing need for robust approaches for obtaining this information via the comparison of the genomic structure of Amygdaloideae-infecting strains to understand their genetic diversity and distribution. Here, the whole-genome sequences of 245 E. amylovora strains available from the NCBI database were compared to identify intraspecific genes for use as an improved index for the simple classification of E. amylovora strains regarding their distribution. Finally, we discovered two kinds of strain-typing protein-encoding genes, i.e., the SAM-dependent methyltransferase and electron transport complex subunit RsxC. Interestingly, both of these proteins carried an amino acid repeat in these strains: SAM-dependent methyltransferase comprised a single-amino-acid repeat (asparagine), whereas RsxC carried a 40-amino-acid repeat, which was differentially distributed among the strains. These noteworthy findings and approaches may enable the exploration of the genetic diversity of E. amylovora from a global perspective.
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Affiliation(s)
- Hyeonheui Ham
- Crop Protection Division, Department of Agro-Food Safety and Crop Protection, National Institute of Agricultural Sciences, Rural Development Administration, Wanju, 55365, Republic of Korea
| | - Dong Suk Park
- Crop Protection Division, Department of Agro-Food Safety and Crop Protection, National Institute of Agricultural Sciences, Rural Development Administration, Wanju, 55365, Republic of Korea.
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9
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Verhaegen M, Bergot T, Liebana E, Stancanelli G, Streissl F, Mingeot-Leclercq MP, Mahillon J, Bragard C. On the use of antibiotics to control plant pathogenic bacteria: a genetic and genomic perspective. Front Microbiol 2023; 14:1221478. [PMID: 37440885 PMCID: PMC10333595 DOI: 10.3389/fmicb.2023.1221478] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Accepted: 06/08/2023] [Indexed: 07/15/2023] Open
Abstract
Despite growing attention, antibiotics (such as streptomycin, oxytetracycline or kasugamycin) are still used worldwide for the control of major bacterial plant diseases. This raises concerns on their potential, yet unknown impact on antibiotic and multidrug resistances and the spread of their genetic determinants among bacterial pathogens. Antibiotic resistance genes (ARGs) have been identified in plant pathogenic bacteria (PPB), with streptomycin resistance genes being the most commonly reported. Therefore, the contribution of mobile genetic elements (MGEs) to their spread among PPB, as well as their ability to transfer to other bacteria, need to be further explored. The only well-documented example of ARGs vector in PPB, Tn5393 and its highly similar variants (carrying streptomycin resistance genes), is concerning because of its presence outside PPB, in Salmonella enterica and Klebsiella pneumoniae, two major human pathogens. Although its structure among PPB is still relatively simple, in human- and animal-associated bacteria, Tn5393 has evolved into complex associations with other MGEs and ARGs. This review sheds light on ARGs and MGEs associated with PPB, but also investigates the potential role of antibiotic use in resistance selection in plant-associated bacteria.
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Affiliation(s)
- Marie Verhaegen
- Laboratory of Food and Environmental Microbiology, Earth and Life Institute, Catholic University of Louvain (UCLouvain), Louvain-la-Neuve, Belgium
| | - Thomas Bergot
- Laboratory of Food and Environmental Microbiology, Earth and Life Institute, Catholic University of Louvain (UCLouvain), Louvain-la-Neuve, Belgium
| | | | | | | | - Marie-Paule Mingeot-Leclercq
- Cellular and Molecular Pharmacology Unit, Louvain Drug Research Institute, UCLouvain, Woluwe-Saint-Lambert, Belgium
| | - Jacques Mahillon
- Laboratory of Food and Environmental Microbiology, Earth and Life Institute, Catholic University of Louvain (UCLouvain), Louvain-la-Neuve, Belgium
| | - Claude Bragard
- Plant Health Laboratory, Earth and Life Institute, UCLouvain, Louvain-la-Neuve, Belgium
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Morgan T, de Rezende RR, Lima TTM, Souza FDO, Alfenas-Zerbini P. Genomic Analysis Unveils the Pervasiveness and Diversity of Prophages Infecting Erwinia Species. Pathogens 2022; 12:pathogens12010044. [PMID: 36678392 PMCID: PMC9866893 DOI: 10.3390/pathogens12010044] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 12/19/2022] [Accepted: 12/20/2022] [Indexed: 12/28/2022] Open
Abstract
Prophages are abundant elements integrated into bacterial genomes and contribute to inter-strain genetic variability and, in some cases, modulate the environmental behavior of bacteria, such as pathogen virulence. Here, we described prophage occurrence and diversity in publicly available Erwinia genome assemblies, a genus containing plant pathogens. Prophage-like sequences were identified and taxonomically classified. Sequence diversity was analyzed through intergenomic similarities. Furthermore, we searched for anti-phage defense systems in Erwinia spp., such as DISARM, BREX, and CRISPR-Cas systems, and identified the putative targets of CRISPR spacers. We identified 939 prophage-like sequences in 221 Erwinia spp. genome assemblies. Only 243 prophage-like sequences were classified, all belonging to the Caudoviricetes class. The set of putative Erwinia prophages was mostly unique since only three sequences showed more than 70% intergenomic similarities to known Erwinia phages. Overall, the number and type of CRISPR-Cas systems were conserved within Erwinia species, with many spacers directed to the putative prophages identified. This study increased the knowledge of the diversity and distribution of Erwinia prophages, contributing to the characterization of genetic and ecological factors influencing Erwinia spp. environmental fitness.
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Albanese D, Cainelli C, Gualandri V, Larger S, Pindo M, Donati C. Genome sequencing provides new insights on the distribution of Erwinia amylovora lineages in northern Italy. ENVIRONMENTAL MICROBIOLOGY REPORTS 2022; 14:584-590. [PMID: 35484918 PMCID: PMC9544390 DOI: 10.1111/1758-2229.13074] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 04/11/2022] [Accepted: 04/13/2022] [Indexed: 06/14/2023]
Abstract
Erwinia amylovora is a Gram-negative bacterium that colonizes a wide variety of plant species causing recurrent local outbreaks of fire blight in crops of the Rosaceae family. Recent genomic surveys have documented the limited genomic diversity of this species, possibly related to a recent evolutionary bottleneck and a strong correlation between geography and phylogenetic structure of the species. Despite its economic importance, little is known about the genetic variability of co-circulating strains during local outbreaks. Here, we report the genome sequences of 82 isolates of E. amylovora, collected from different host plants in a period of 16 years in Trentino, a small region in the Northeastern Italian Alps that has been characterized by recurrent outbreaks of fire blight in apple orchards. While the genome isolated before 2018 are closely related to other strains already present in Europe, we found a novel subclade composed only by isolates that were sampled starting from 2018 and demonstrate that the endemic population of this pathogen can be composed by mixture of strains.
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Affiliation(s)
- Davide Albanese
- Unit of Computational Biology, Research and Innovation Centre, Fondazione Edmund Mach, Via E. Mach 1San Michele all'Adige38010Italy
| | - Christian Cainelli
- Center for Technology Transfer, Fondazione Edmund Mach, Via E. Mach 1San Michele all'Adige38010Italy
| | - Valeria Gualandri
- Center for Technology Transfer, Fondazione Edmund Mach, Via E. Mach 1San Michele all'Adige38010Italy
- Center of Agriculture, Food and Environment (C3A)University of TrentoTrentoItaly
| | - Simone Larger
- Unit of Computational Biology, Research and Innovation Centre, Fondazione Edmund Mach, Via E. Mach 1San Michele all'Adige38010Italy
| | - Massimo Pindo
- Unit of Computational Biology, Research and Innovation Centre, Fondazione Edmund Mach, Via E. Mach 1San Michele all'Adige38010Italy
| | - Claudio Donati
- Unit of Computational Biology, Research and Innovation Centre, Fondazione Edmund Mach, Via E. Mach 1San Michele all'Adige38010Italy
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12
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Mendes RJ, Amaro C, Luz JP, Tavares F, Santos C. Variability within a clonal population of Erwinia amylovora disclosed by phenotypic analysis. PeerJ 2022; 10:e13695. [PMID: 35891645 PMCID: PMC9308965 DOI: 10.7717/peerj.13695] [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: 04/01/2022] [Accepted: 06/16/2022] [Indexed: 01/17/2023] Open
Abstract
Background Fire blight is a destructive disease of pome trees, caused by Erwinia amylovora, leading to high losses of chain-of-values fruits. Major outbreaks were registered between 2010 and 2017 in Portugal, and the first molecular epidemiological characterization of those isolates disclosed a clonal population with different levels of virulence and susceptibility to antimicrobial peptides. Methods This work aimed to further disclose the genetic characterization and unveil the phenotypic diversity of this E. amylovora population, resorting to MLSA, growth kinetics, biochemical characterization, and antibiotic susceptibility. Results While MLSA further confirmed the genetic clonality of those isolates, several phenotypic differences were recorded regarding their growth, carbon sources preferences, and chemical susceptibility to several antibiotics, disclosing a heterogeneous population. Principal component analysis regarding the phenotypic traits allows to separate the strains Ea 630 and Ea 680 from the remaining. Discussion Regardless the genetic clonality of these E. amylovora strains isolated from fire blight outbreaks, the phenotypic characterization evidenced a population diversity beyond the genotype clonality inferred by MLSA and CRISPR, suggesting that distinct sources or environmental adaptations of this pathogen may have occurred. Conclusion Attending the characteristic clonality of E. amylovora species, the data gathered here emphasizes the importance of phenotypic assessment of E. amylovora isolates to better understand their epidemiological behavior, namely by improving source tracking, make risk assessment analysis, and determine strain-specific environmental adaptations, that might ultimately lead to prevent new outbreaks.
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Affiliation(s)
- Rafael J. Mendes
- Biology Department, Faculty of Sciences, University of Porto, Porto, Portugal,LAQV-REQUIMTE, Faculty of Sciences, University of Porto, Porto, Portugal,CITAB, University of Trás-os-Montes e Alto Douro, Vila Real, Portugal,CIBIO, Research Centre in Biodiversity and Genetic Resources, InBIO, Associated Laboratory, Campus Agrário de Vairão, Faculty of Sciences, University of Porto, Vairão, Portugal,BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, Vairão, Portugal
| | - Conceição Amaro
- QRural, School of Agriculture, Polytechnic Institute of Castelo Branco, Castelo Branco, Portugal
| | - João Pedro Luz
- QRural, School of Agriculture, Polytechnic Institute of Castelo Branco, Castelo Branco, Portugal
| | - Fernando Tavares
- Biology Department, Faculty of Sciences, University of Porto, Porto, Portugal,CIBIO, Research Centre in Biodiversity and Genetic Resources, InBIO, Associated Laboratory, Campus Agrário de Vairão, Faculty of Sciences, University of Porto, Vairão, Portugal,BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, Vairão, Portugal
| | - Conceição Santos
- Biology Department, Faculty of Sciences, University of Porto, Porto, Portugal,LAQV-REQUIMTE, Faculty of Sciences, University of Porto, Porto, Portugal
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13
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Function and Application of the CRISPR-Cas System in the Plant Pathogen Erwinia amylovora. Appl Environ Microbiol 2022; 88:e0251321. [PMID: 35285707 PMCID: PMC9004355 DOI: 10.1128/aem.02513-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Phage-based biocontrol is an emerging method for managing the plant pathogen Erwinia amylovora. Control of E. amylovora in North America is achieved chiefly through the application of streptomycin and has led to the development of streptomycin resistance. Resistant E. amylovora can be tracked through the analysis of CRISPR spacer sequences. An alternative to antibiotics are bacterial viruses, known as phages, which lyse their hosts during replication to control the bacterial population. Endogenous CRISPR-Cas systems act as phage resistance mechanisms however, preliminary genomic analysis suggests this activity is limited in E. amylovora. This leaves the functionality of the CRISPR-Cas system, any clade-based differences, and the impact which this system may have on phage-based biocontrol in question. In this study, the CRISPR arrays from 127 newly available genomic sequences of E. amylovora were analyzed through a novel bioinformatic pipeline. Through this, the Eastern and Western North American clades were shown to be incompatible with the current PCR-based approaches for tracking E. amylovora given the size and composition of their CRISPR arrays. Two artificial CRISPR arrays were designed to investigate the functionality of the CRISPR-Cas system in E. amylovora. This system was capable of curing a targeted plasmid and providing phage resistance but was not the source of phage resistance observed within the controls. This suggests that while the CRISPR-Cas system is an important defense mechanism for invasive plasmids, an as yet unidentified mechanism is the primary source of phage resistance in E. amylovora. IMPORTANCE Erwinia amylovora is an economically significant agricultural pathogen found throughout the world. In North America, E. amylovora has developed streptomycin resistance and therefore alternative treatments using phages have received increased attention. In this study, we analyzed recently published genomes to determine that two significant groups of E. amylovora are poorly identified using the current, CRISPR-based tracking methods. We also showed that the CRISPR-Cas system and an unidentified mechanism work together to provide a significant degree of resistance against one of the phages proposed for phage-based biocontrol.
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Phylogenomic analysis of the Erwiniaceae supports reclassification of Kalamiella piersonii to Pantoea piersonii comb. nov. and Erwinia gerundensis to the new genus Duffyella gen. nov. as Duffyella gerundensis comb. nov. Mol Genet Genomics 2022; 297:213-225. [PMID: 34988605 DOI: 10.1007/s00438-021-01829-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Accepted: 10/27/2021] [Indexed: 01/20/2023]
Abstract
To better understand the taxonomy of Erwinia in the context of the Erwiniaceae family, we carried out a taxogenomic analysis of the Erwiniaceae, a family that was created following the taxonomic revision of the family, Enterobacteriaceae. There has been no systematic analysis of this family, including the agriculturally relevant genus, Erwinia. Our analyses focused on 80 strains of Erwinia along with 37 strains representing 7 other genera in the family. We identified 308 common proteins, generated a genome-level phylogeny and carried out Average Nucleotide Identity, Average Amino Acid Identity and Percentage of Conserved Protein analyses. We show that multiple strains of Erwinia cannot be assigned to established species groups and that both Erwinia gerundensis and "Erwinia mediterraneensis" are not members of Erwinia. We propose the creation of the genus Duffyella gen. nov. and the reclassification of Erwinia gerundensis to this genus as the type species, Duffyella gerundensis comb. nov. Furthermore, divergence between other species within Erwinia as measured by Average Amino Acid Identity is greater than the divergence between Erwinia and other genera, supporting the possible subdivision of the genus Erwinia into at least two genera. Our analyses also suggest that there is no basis for the establishment of the genus Kalamiella within the Erwiniaceae or the taxonomic revision of the Pantoea septica lineage. Therefore, we propose reclassifying Kalamiella piersonii as Pantoea piersonii comb. nov. Our study provides new insight into the diversity of the Erwiniaceae and provides a solid foundation for advancing taxonomic revision of this broadly relevant family.
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15
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Wallis A, Yannuzzi IM, Choi MW, Spafford J, Fenn M, Ramachandran P, Timme R, Pettengill JB, Cagle R, Ottesen A, Cox KD. Investigating the Distribution of Strains of Erwinia amylovora and Streptomycin Resistance in Apple Orchards in New York Using Clustered Regularly Interspaced Short Palindromic Repeat Profiles: A 6-Year Follow-Up. PLANT DISEASE 2021; 105:3554-3563. [PMID: 33599513 DOI: 10.1094/pdis-12-20-2585-re] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Fire blight, caused by the bacterium Erwinia amylovora, is one of the most important diseases of apple. The antibiotic streptomycin is routinely used in the commercial apple industries of New York (NY) and New England to manage the disease. In 2002 and again, from 2011 to 2014, outbreaks of streptomycin resistance (SmR) were reported and investigated in NY. Motivated by new grower reports of control failures, we conducted a follow-up investigation of the distribution of SmR and E. amylovora strains for major apple production regions of NY over the last 6 years (2015 to 2020). Characterization of clustered regularly interspaced short palindromic repeat (CRISPR) profiles revealed that a few "cosmopolitan" strains were widely prevalent across regions, whereas many other "resident" strains were confined to one location. In addition, we uncovered novel CRISPR profile diversity in all investigated regions. SmR E. amylovora was detected only in a small area spanning two counties from 2017 to 2020 and was always associated with one CRISPR profile (41:23:38), which matched the profile of SmR E. amylovora, discovered in 2002. This suggests the original SmR E. amylovora was never fully eradicated and went undetected because of several seasons of low disease pressure in this region. Investigation of several representative isolates under controlled greenhouse conditions indicated significant differences in aggressiveness on 'Gala' apples. Potential implications of strain differences include the propensity of strains to become distributed across wide geographic regions and associated resistance management practices. Results from this work will directly influence sustainable fire blight management recommendations for commercial apple industries in NY state and other regions.
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Affiliation(s)
- Anna Wallis
- Department of Plant Pathology and Plant-Microbe Biology, Cornell University, Geneva, NY 14456
| | - Isabella M Yannuzzi
- Department of Plant Pathology and Plant-Microbe Biology, Cornell University, Geneva, NY 14456
| | - Mei-Wah Choi
- Department of Plant Pathology and Plant-Microbe Biology, Cornell University, Geneva, NY 14456
| | - John Spafford
- Department of Plant Pathology and Plant-Microbe Biology, Cornell University, Geneva, NY 14456
| | - Matthew Fenn
- Department of Plant Pathology and Plant-Microbe Biology, Cornell University, Geneva, NY 14456
| | - Padmini Ramachandran
- Molecular Methods and Subtyping Branch, Division of Microbiology, Office of Regulatory Science, Center for Food Safety and Applied Nutrition, Food and Drug Administration, College Park, MD 20740
| | - Ruth Timme
- Molecular Methods and Subtyping Branch, Division of Microbiology, Office of Regulatory Science, Center for Food Safety and Applied Nutrition, Food and Drug Administration, College Park, MD 20740
| | - James B Pettengill
- Molecular Methods and Subtyping Branch, Division of Microbiology, Office of Regulatory Science, Center for Food Safety and Applied Nutrition, Food and Drug Administration, College Park, MD 20740
| | - Robin Cagle
- Department of Microbiology, University of Washington, Seattle, WA 98185
| | - Andrea Ottesen
- Molecular Methods and Subtyping Branch, Division of Microbiology, Office of Regulatory Science, Center for Food Safety and Applied Nutrition, Food and Drug Administration, College Park, MD 20740
| | - Kerik D Cox
- Department of Plant Pathology and Plant-Microbe Biology, Cornell University, Geneva, NY 14456
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16
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Yuan X, McGhee GC, Slack SM, Sundin GW. A Novel Signaling Pathway Connects Thiamine Biosynthesis, Bacterial Respiration, and Production of the Exopolysaccharide Amylovoran in Erwinia amylovora. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2021; 34:1193-1208. [PMID: 34081536 DOI: 10.1094/mpmi-04-21-0095-r] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Erwinia amylovora is a plant pathogen causing necrotrophic fire blight disease of apple, pear, and other rosaceous plants. This bacterium colonizes host vascular tissues via the production of exopolysaccharides (EPSs) including amylovoran. It is well-established that the nearly ubiquitous plasmid pEA29 of E. amylovora is an essential virulence factor, but the underlying mechanism remains uncharacterized. Here, we demonstrated that pEA29 was required for E. amylovora to produce amylovoran and to form a biofilm, and this regulation was dependent on the thiamine biosynthesis operon thiOSGF. We then conducted carbohydrate and genetic analyses demonstrating that the thiamine-mediated effect on amylovoran production was indirect, as cells lacking thiOSGF produced an EPS that did not contain glucuronic acid, one of the key components of amylovoran, whereas the transcriptional activity and RNA levels of the amylovoran biosynthesis genes were not altered. Alternatively, addition of exogenous thiamine restored amylovoran production in the pEA29-cured strain of E. amylovora and positively impacted amylovoran production in a dose-dependent manner. Individual deletion of several chromosomal thiamine biosynthesis genes also affected amylovoran production, implying that a complete thiamine biosynthesis pathway is required for the thiamine-mediated effect on amylovoran production in E. amylovora. Finally, we determined that an imbalanced tricarboxylic acid cycle negatively affected amylovoran production, which was restored by addition of exogenous thiamine or overexpression of the thiOSGF operon. In summary, our report revealed a novel signaling pathway that impacts E. amylovora virulence in which thiamine biosynthesis enhances bacterial respiration that provides energetic requirements for the biosynthesis of EPS amylovoran.[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)
- Xiaochen Yuan
- Department of Plant, Soil, and Microbial Sciences, Michigan State University, East Lansing, MI 48824, U.S.A
| | - Gayle C McGhee
- United States Department of Agriculture, Agriculture Research Service, Horticultural Crops Research Laboratory, Corvallis, OR 97330, U.S.A
| | - Suzanne M Slack
- Department of Plant, Soil, and Microbial Sciences, Michigan State University, East Lansing, MI 48824, U.S.A
| | - George W Sundin
- Department of Plant, Soil, and Microbial Sciences, Michigan State University, East Lansing, MI 48824, U.S.A
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Mendes RJ, Luz JP, Santos C, Tavares F. CRISPR genotyping as complementary tool for epidemiological surveillance of Erwinia amylovora outbreaks. PLoS One 2021; 16:e0250280. [PMID: 33861806 PMCID: PMC8051791 DOI: 10.1371/journal.pone.0250280] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Accepted: 04/02/2021] [Indexed: 12/12/2022] Open
Abstract
Fire blight is a destructive plant disease caused by Erwinia amylovora affecting pome fruit trees, and responsible for large yield declines, long phytosanitary confinements, and high economic losses. In Portugal, the first major fire blight outbreaks occurred in 2010 and 2011, and although later considered eradicated, the emergence of other outbreaks in recent years stressed the need to characterize the E. amylovora populations associated with these outbreaks. In this regard, CRISPR genotyping, assessment of three virulence markers, and semi-quantitative virulence bioassays, were carried out to determine the genotype, and assess the virulence of thirty-six E. amylovora isolates associated with outbreaks occurring between 2010 and 2017 and affecting apple and pear orchards located in the country central-west, known as the main producing region of pome fruits in Portugal. The data gathered reveal that 35 E. amylovora isolates belong to one of the widely-distributed CRISPR genotypes (5-24-38 / D-a-α) regardless the host species, year and region. Ea 680 was the single isolate revealing a new CRISPR genotype due to a novel CR2 spacer located closer to the leader sequence and therefore thought to be recently acquired. Regarding pathogenicity, although dot-blot hybridization assays showed the presence of key virulence factors, namely hrpL (T3SS), hrpN (T3E) and amsG from the amylovoran biosynthesis operon in all E. amylovora isolates studied, pathogenicity bioassays on immature pear slices allowed to distinguish four virulence levels, with most of the isolates revealing an intermediate to severe virulence phenotype. Regardless the clonal population structure of the E. amylovora associated to the outbreaks occurring in Portugal between 2010 and 2017, the different virulence phenotypes, suggests that E. amylovora may have been introduced at different instances into the country. This is the first study regarding E. amylovora in Portugal, and it discloses a novel CRISPR genotype for this bacterium.
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Affiliation(s)
- Rafael J. Mendes
- Faculty of Sciences of University of Porto, Porto, Portugal
- LAQV/REQUIMTE, Faculty of Sciences of University of Porto, Porto, Portugal
- CITAB—Centre for the Research and Technology of Agro-Environmental and Biological Sciences, University of Trás-os-Montes e Alto Douro, Vila Real, Portugal
- CIBIO–Research Centre in Biodiversity and Genetic Resources, InBIO, Associated Laboratory, University of Porto, Campus Agrário de Vairão, Vairão, Portugal
| | - João Pedro Luz
- QRural, Polytechnic Institute of Castelo Branco, School of Agriculture, Castelo Branco, Portugal
| | - Conceição Santos
- Faculty of Sciences of University of Porto, Porto, Portugal
- LAQV/REQUIMTE, Faculty of Sciences of University of Porto, Porto, Portugal
| | - Fernando Tavares
- Faculty of Sciences of University of Porto, Porto, Portugal
- CIBIO–Research Centre in Biodiversity and Genetic Resources, InBIO, Associated Laboratory, University of Porto, Campus Agrário de Vairão, Vairão, Portugal
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Yu M, Singh J, Khan A, Sundin GW, Zhao Y. Complete Genome Sequence of the Fire Blight Pathogen Strain Erwinia amylovora Ea1189. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2020; 33:1277-1279. [PMID: 32808873 DOI: 10.1094/mpmi-06-20-0158-a] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Erwinia amylovora causes fire blight, the most devastating bacterial disease of apples and pears in the United States and worldwide. The model strain E. amylovora Ea1189 has been extensively used to understand bacterial pathogenesis and molecular mechanisms of bacterial-plant interactions. In this work, we sequenced and assembled the de novo genome of Ea1189, using a combination of long Oxford Nanopore Technologies and short Illumina sequence reads. A complete gapless genome assembly of Ea1189 consists of a 3,797,741-bp circular chromosome and a 28,259-bp plasmid with 3,472 predicted genes, including 78 transfer RNAs, 22 ribosomal RNAs, and 20 noncoding RNAs. A comparison of the Ea1189 genome to previously sequenced E. amylovora complete genomes showed 99.94 to 99.97% sequence similarity with 314 to 946 single nucleotide polymorphisms. We believe that the availability of the complete genome sequence of strain Ea1189 will further support studies to understand evolution, diversity and structural variations of Erwinia strains, as well as the molecular basis of E. amylovora pathogenesis and its interactions with host plants, thus facilitating the development of effective management strategies for this important disease.
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Affiliation(s)
- Menghao Yu
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, IL 61801, U.S.A
| | - Jugpreet Singh
- Plant Pathology and Plant-Microbe Biology Section, Cornell University, Geneva, NY 14456, U.S.A
| | - Awais Khan
- Plant Pathology and Plant-Microbe Biology Section, Cornell University, Geneva, NY 14456, U.S.A
| | - George W Sundin
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI 48824, U.S.A
| | - Youfu Zhao
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, IL 61801, U.S.A
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