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Xi H, Fu B, Sheng Q, Luo M, Sun L. Isolation and Characterization of a Lytic Bacteriophage RH-42-1 of Erwinia amylovora from Orchard Soil in China. Viruses 2024; 16:509. [PMID: 38675852 PMCID: PMC11054837 DOI: 10.3390/v16040509] [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: 01/30/2024] [Revised: 03/14/2024] [Accepted: 03/22/2024] [Indexed: 04/28/2024] Open
Abstract
Fire blight, caused by the bacterium Erwinia amylovora, is a major threat to pear production worldwide. Bacteriophages, viruses that infect bacteria, are a promising alternative to antibiotics for controlling fire blight. In this study, we isolated a novel bacteriophage, RH-42-1, from Xinjiang, China. We characterized its biological properties, including host range, plaque morphology, infection dynamics, stability, and sensitivity to various chemicals. RH-42-1 infected several E. amylovora strains but not all. It produced clear, uniform plaques and exhibited optimal infectivity at a multiplicity of infection (MOI) of 1, reaching a high titer of 9.6 × 109 plaque-forming units (PFU)/mL. The bacteriophage had a short latent period (10 min), a burst size of 207 PFU/cell, and followed a sigmoidal one-step growth curve. It was stable at temperatures up to 60 °C but declined rapidly at higher temperatures. RH-42-1 remained viable within a pH range of 5 to 9 and was sensitive to extreme pH values. The bacteriophage demonstrates sustained activity upon exposure to ultraviolet radiation for 60 min, albeit with a marginal reduction. In our assays, it exhibited a certain level of resistance to 5% chloroform (CHCl3), 5% isopropanol (C3H8O), and 3% hydrogen peroxide (H2O2), which had little effect on its activity, whereas it showed sensitivity to 75% ethanol (C2H5OH). Electron microscopy revealed that RH-42-1 has a tadpole-shaped morphology. Its genome size is 14,942 bp with a GC content of 48.19%. Based on these characteristics, RH-42-1 was identified as a member of the Tectiviridae family, Alphatectivirus genus. This is the first report of a bacteriophage in this genus with activity against E. amylovora.
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Affiliation(s)
- Haishen Xi
- The Department of Plant Pathology, College of Agronomy at Xinjiang Agricultural University/Key Laboratory of Detection and Control of Agricultural and Forest Pests, Urumqi 830052, China; (H.X.); (B.F.)
- Ministry of Agriculture and Rural Affairs Key Laboratory for Pests and Diseases Control of Northwest Arid Oasis Agricultural Foreign Invasion Species, Urumqi 830052, China
| | - Benzhong Fu
- The Department of Plant Pathology, College of Agronomy at Xinjiang Agricultural University/Key Laboratory of Detection and Control of Agricultural and Forest Pests, Urumqi 830052, China; (H.X.); (B.F.)
- Ministry of Agriculture and Rural Affairs Key Laboratory for Pests and Diseases Control of Northwest Arid Oasis Agricultural Foreign Invasion Species, Urumqi 830052, China
| | - Qiang Sheng
- Xinjiang Bayingolin Mongolian Autonomous Prefecture Academy of Agricultural Sciences, Korla 841003, China;
| | - Ming Luo
- The Department of Plant Pathology, College of Agronomy at Xinjiang Agricultural University/Key Laboratory of Detection and Control of Agricultural and Forest Pests, Urumqi 830052, China; (H.X.); (B.F.)
- Ministry of Agriculture and Rural Affairs Key Laboratory for Pests and Diseases Control of Northwest Arid Oasis Agricultural Foreign Invasion Species, Urumqi 830052, China
| | - Liying Sun
- The Department of Plant Pathology, College of Plant Protection, Northwest A&F University, Yangling 712100, China
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2
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Jo SJ, Kim SG, Park J, Lee YM, Giri SS, Lee SB, Jung WJ, Hwang MH, Park JH, Roh E, Park SC. Optimizing the formulation of Erwinia bacteriophages for improved UV stability and adsorption on apple leaves. Heliyon 2023; 9:e22034. [PMID: 38034629 PMCID: PMC10682131 DOI: 10.1016/j.heliyon.2023.e22034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Revised: 10/30/2023] [Accepted: 11/02/2023] [Indexed: 12/02/2023] Open
Abstract
Fire blight is a bacterial disease that affects plants of the Rosaceae family and causes significant economic losses worldwide. Although antibiotics have been used to control the disease, concerns about their environmental impact and the potential to promote antibiotic resistance have arisen. Bacteriophages are being investigated as an alternative to antibiotics; however, their efficacy can be affected by environmental stresses, such as UV radiation. In this study, we optimized the formulation of Erwinia phages to enhance their stability in the field, focusing on improving their UV stability and adsorption using adjuvants. Our results confirmed that 4.5 % polysorbate 80 and kaolin improve phage stability under UV stress, resulting in an 80 % increase in PFU value and improved UV protection efficacy. Adsorption assays also demonstrated that polysorbate 80 and kaolin improved the absorption efficiency, with phages detected in plant for up to two weeks. These findings demonstrate the effectiveness of the auxiliary formulation of Erwinia bacteriophages against environmental stress.
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Affiliation(s)
- Su Jin Jo
- Laboratory of Aquatic Biomedicine, College of Veterinary Medicine and Research Institute for Veterinary Science, Seoul National University, Seoul, 08826, Republic of Korea
| | - Sang Guen Kim
- Department of Biological Sciences, Kyonggi University, Suwon, 16227, Republic of Korea
| | - Jungkum Park
- Crop Protection Division, National Institute of Agriculture Sciences, Rural Development Administration, Wanju, 55365, Republic of Korea
| | - Young Min Lee
- Laboratory of Aquatic Biomedicine, College of Veterinary Medicine and Research Institute for Veterinary Science, Seoul National University, Seoul, 08826, Republic of Korea
| | - Sib Sankar Giri
- Laboratory of Aquatic Biomedicine, College of Veterinary Medicine and Research Institute for Veterinary Science, Seoul National University, Seoul, 08826, Republic of Korea
| | - Sung Bin Lee
- Laboratory of Aquatic Biomedicine, College of Veterinary Medicine and Research Institute for Veterinary Science, Seoul National University, Seoul, 08826, Republic of Korea
| | - Won Joon Jung
- Laboratory of Aquatic Biomedicine, College of Veterinary Medicine and Research Institute for Veterinary Science, Seoul National University, Seoul, 08826, Republic of Korea
| | - Mae Hyun Hwang
- Laboratory of Aquatic Biomedicine, College of Veterinary Medicine and Research Institute for Veterinary Science, Seoul National University, Seoul, 08826, Republic of Korea
| | - Jae Hong Park
- Laboratory of Aquatic Biomedicine, College of Veterinary Medicine and Research Institute for Veterinary Science, Seoul National University, Seoul, 08826, Republic of Korea
| | - Eunjung Roh
- Crop Protection Division, National Institute of Agriculture Sciences, Rural Development Administration, Wanju, 55365, Republic of Korea
| | - Se Chang Park
- Laboratory of Aquatic Biomedicine, College of Veterinary Medicine and Research Institute for Veterinary Science, Seoul National University, Seoul, 08826, Republic of Korea
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3
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Choe J, Kim B, Park MK, Roh E. Biological and Genetic Characterizations of a Novel Lytic ΦFifi106 against Indigenous Erwinia amylovora and Evaluation of the Control of Fire Blight in Apple Plants. BIOLOGY 2023; 12:1060. [PMID: 37626946 PMCID: PMC10452218 DOI: 10.3390/biology12081060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Revised: 07/19/2023] [Accepted: 07/23/2023] [Indexed: 08/27/2023]
Abstract
Erwinia amylovora is a devastating phytobacterium causing fire blight in the Rosaceae family. In this study, ΦFifi106, isolated from pear orchard soil, was further purified and characterized, and its efficacy for the control of fire blight in apple plants was evaluated. Its genomic analysis revealed that it consisted of 84,405 bp and forty-six functional ORFs, without any genes encoding antibiotic resistance, virulence, and lysogenicity. The phage was classified into the genus Kolesnikvirus of the subfamily Ounavirinae. ΦFifi106 specifically infected indigenous E. amylovora and E. pyrifoliae. The lytic activity of ΦFifi106 was stable under temperature and pH ranges of 4-50 °C and 4-10, as well as the exposure to ultraviolet irradiation for 6 h. ΦFifi106 had a latent period of 20 min and a burst size of 310 ± 30 PFU/infected cell. ΦFifi106 efficiently inhibited E. amylovora YKB 14808 at a multiplicity of infection (MOI) of 0.1 for 16 h. Finally, the pretreatment of ΦFifi106 at an MOI of 1000 efficiently reduced disease incidence to 37.0% and disease severity to 0.4 in M9 apple plants. This study addressed the use of ΦFifi106 as a novel, safe, efficient, and effective alternative to control fire blight in apple plants.
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Affiliation(s)
- Jaein Choe
- School of Food Science and Biotechnology, Food and Bio-Industry Research Institute, Kyungpook National University, Daegu 41566, Republic of Korea;
| | - Byeori Kim
- Crop Protection Division, National Institute of Agricultural Sciences, Rural Development Administration, Wanju 55365, Republic of Korea;
| | - Mi-Kyung Park
- School of Food Science and Biotechnology, Food and Bio-Industry Research Institute, Kyungpook National University, Daegu 41566, Republic of Korea;
| | - Eunjung Roh
- Crop Protection Division, National Institute of Agricultural Sciences, Rural Development Administration, Wanju 55365, Republic of Korea;
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4
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Besarab NV, Letarova MA, Babenko VV, Belalov IS, Golomidova AK, Kulikov EE, Lagonenko AL, Evtushenkov AN, Letarov AV. The metastable associations of bacteriophages and Erwinia amylovora. Arch Microbiol 2023; 205:214. [PMID: 37129715 DOI: 10.1007/s00203-023-03550-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2023] [Revised: 04/06/2023] [Accepted: 04/13/2023] [Indexed: 05/03/2023]
Abstract
Bacteriophages are often considered as possible agents of biological control of unwanted bacterial populations in medicine, agriculture and food industry. Although the virulent phages can efficiently kill the infected host cells but at the population level phage attack not always leads to the host population collapse but may result in establishment of a more or less stable co-existence. The mechanism of the long-term stabilization of the mixed phage-host cultures is poorly understood. Here we describe bacteriophages VyarbaL and Hena2, the members of the Molineuxvirinae and the Ounavirinae subfamilies, respectively, that are able to form the pseudolysogenic associations (PA) with their host Erwinia amylovora 1/79Sm on solid media. These PAs were stable through multiple passages. The phenomenon of the PA formation between a bacterial culture and bacteriophages decreases the effectiveness of bacteriophage-mediated biological control agents based on lytic bacteriophages.
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Affiliation(s)
- Natalya V Besarab
- Department of Molecular Biology, Faculty of Biology, Belarusian State University, Nezavisimisty Ave., 4, 220030, Minsk, Belarus.
| | - Maria A Letarova
- Research Center of Biotechnology of Russian Academy of Sciences, Winogradsky Institute of Microbiology, Pr. 60-Letiya Oktyabrya 7 Bld. 2, 117312, Moscow, Russia
| | - Vladislav V Babenko
- Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia
| | - Ilya S Belalov
- Research Center of Biotechnology of Russian Academy of Sciences, Winogradsky Institute of Microbiology, Pr. 60-Letiya Oktyabrya 7 Bld. 2, 117312, Moscow, Russia
| | - Alla K Golomidova
- Research Center of Biotechnology of Russian Academy of Sciences, Winogradsky Institute of Microbiology, Pr. 60-Letiya Oktyabrya 7 Bld. 2, 117312, Moscow, Russia
| | - Eugene E Kulikov
- Research Center of Biotechnology of Russian Academy of Sciences, Winogradsky Institute of Microbiology, Pr. 60-Letiya Oktyabrya 7 Bld. 2, 117312, Moscow, Russia
| | - Alexander L Lagonenko
- Department of Molecular Biology, Faculty of Biology, Belarusian State University, Nezavisimisty Ave., 4, 220030, Minsk, Belarus
| | - Anatoly N Evtushenkov
- Department of Molecular Biology, Faculty of Biology, Belarusian State University, Nezavisimisty Ave., 4, 220030, Minsk, Belarus
| | - Andrey V Letarov
- Research Center of Biotechnology of Russian Academy of Sciences, Winogradsky Institute of Microbiology, Pr. 60-Letiya Oktyabrya 7 Bld. 2, 117312, Moscow, Russia
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5
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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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Šimoliūnienė M, Žukauskienė E, Truncaitė L, Cui L, Hutinet G, Kazlauskas D, Kaupinis A, Skapas M, de Crécy-Lagard V, Dedon PC, Valius M, Meškys R, Šimoliūnas E. Pantoea Bacteriophage vB_PagS_MED16-A Siphovirus Containing a 2'-Deoxy-7-amido-7-deazaguanosine-Modified DNA. Int J Mol Sci 2021; 22:7333. [PMID: 34298953 PMCID: PMC8306585 DOI: 10.3390/ijms22147333] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Revised: 06/30/2021] [Accepted: 07/05/2021] [Indexed: 11/16/2022] Open
Abstract
A novel siphovirus, vB_PagS_MED16 (MED16) was isolated in Lithuania using Pantoea agglomerans strain BSL for the phage propagation. The double-stranded DNA genome of MED16 (46,103 bp) contains 73 predicted open reading frames (ORFs) encoding proteins, but no tRNA. Our comparative sequence analysis revealed that 26 of these ORFs code for unique proteins that have no reliable identity when compared to database entries. Based on phylogenetic analysis, MED16 represents a new genus with siphovirus morphology. In total, 35 MED16 ORFs were given a putative functional annotation, including those coding for the proteins responsible for virion morphogenesis, phage-host interactions, and DNA metabolism. In addition, a gene encoding a preQ0 DNA deoxyribosyltransferase (DpdA) is present in the genome of MED16 and the LC-MS/MS analysis indicates 2'-deoxy-7-amido-7-deazaguanosine (dADG)-modified phage DNA, which, to our knowledge, has never been experimentally validated in genomes of Pantoea phages. Thus, the data presented in this study provide new information on Pantoea-infecting viruses and offer novel insights into the diversity of DNA modifications in bacteriophages.
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Affiliation(s)
- Monika Šimoliūnienė
- Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Life Sciences Centre, Vilnius University, Saulėtekio av. 7, LT-10257 Vilnius, Lithuania; (M.Š.); (E.Ž.); (L.T.); (R.M.)
| | - Emilija Žukauskienė
- Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Life Sciences Centre, Vilnius University, Saulėtekio av. 7, LT-10257 Vilnius, Lithuania; (M.Š.); (E.Ž.); (L.T.); (R.M.)
| | - Lidija Truncaitė
- Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Life Sciences Centre, Vilnius University, Saulėtekio av. 7, LT-10257 Vilnius, Lithuania; (M.Š.); (E.Ž.); (L.T.); (R.M.)
| | - Liang Cui
- Singapore-MIT Alliance for Research and Technology, Antimicrobial Resistance Interdisciplinary Research Group, Campus for Research Excellence and Technological Enterprise, Singapore 138602, Singapore; (L.C.); (P.C.D.)
| | - Geoffrey Hutinet
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL 32611, USA; (G.H.); (V.d.C.-L.)
| | - Darius Kazlauskas
- Department of Bioinformatics, Institute of Biotechnology, Life Sciences Centre, Vilnius University, Saulėtekio av. 7, LT-10257 Vilnius, Lithuania;
| | - Algirdas Kaupinis
- Proteomics Centre, Institute of Biochemistry, Life Sciences Centre, Vilnius University, Saulėtekio av. 7, LT-10257 Vilnius, Lithuania; (A.K.); (M.V.)
| | - Martynas Skapas
- Department of Characterisation of Materials Structure, Center for Physical Sciences and Technology, Saulėtekio av. 3, LT-10257 Vilnius, Lithuania;
| | - Valérie de Crécy-Lagard
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL 32611, USA; (G.H.); (V.d.C.-L.)
- Genetics Institute, University of Florida, Gainesville, FL 32610, USA
| | - Peter C. Dedon
- Singapore-MIT Alliance for Research and Technology, Antimicrobial Resistance Interdisciplinary Research Group, Campus for Research Excellence and Technological Enterprise, Singapore 138602, Singapore; (L.C.); (P.C.D.)
- Department of Biological Engineering and Center for Environmental Health Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Mindaugas Valius
- Proteomics Centre, Institute of Biochemistry, Life Sciences Centre, Vilnius University, Saulėtekio av. 7, LT-10257 Vilnius, Lithuania; (A.K.); (M.V.)
| | - Rolandas Meškys
- Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Life Sciences Centre, Vilnius University, Saulėtekio av. 7, LT-10257 Vilnius, Lithuania; (M.Š.); (E.Ž.); (L.T.); (R.M.)
| | - Eugenijus Šimoliūnas
- Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Life Sciences Centre, Vilnius University, Saulėtekio av. 7, LT-10257 Vilnius, Lithuania; (M.Š.); (E.Ž.); (L.T.); (R.M.)
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7
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Kim SG, Roh E, Park J, Giri SS, Kwon J, Kim SW, Kang JW, Lee SB, Jung WJ, Lee YM, Cho K, Park SC. The Bacteriophage pEp_SNUABM_08 Is a Novel Singleton Siphovirus with High Host Specificity for Erwinia pyrifoliae. Viruses 2021; 13:1231. [PMID: 34202208 PMCID: PMC8310351 DOI: 10.3390/v13071231] [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: 04/30/2021] [Revised: 06/18/2021] [Accepted: 06/24/2021] [Indexed: 01/16/2023] Open
Abstract
Species belonging to the genus Erwinia are predominantly plant pathogens. A number of bacteriophages capable of infecting Erwinia have been used for the control of plant diseases such as fire blight. Public repositories provide the complete genome information for such phages, which includes genomes ranging from 30 kb to 350 kb in size. However, limited information is available regarding bacteriophages belonging to the family Siphoviridae. A novel lytic siphophage, pEp_SNUABM_08, which specifically infects Erwinia pyrifoliae, was isolated from the soil of an affected apple orchard in South Korea. A comprehensive genome analysis was performed using the Erwinia-infecting siphophage. The whole genome of pEp_SNUABM_08 comprised 62,784 bp (GC content, 57.24%) with 79 open reading frames. The genomic characteristics confirmed that pEp_SNUABM_08 is a singleton lytic bacteriophage belonging to the family Siphoviridae, and no closely related phages have been reported thus far. Our study not only characterized a unique phage, but also provides insight into the genetic diversity of Erwinia bacteriophages.
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Affiliation(s)
- Sang Guen Kim
- Laboratory of Aquatic Biomedicine, College of Veterinary Medicine and Research Institute for Veterinary Science, Seoul National University, Seoul 08826, Korea; (S.G.K.); (S.S.G.); (J.K.); (S.W.K.); (J.W.K.); (S.B.L.); (W.J.J.); (Y.M.L.); (K.C.)
| | - Eunjung Roh
- Crop Protection Division, National Institute of Agriculture Sciences, Rural Development Administration, Wanju 55365, Korea; (E.R.); (J.P.)
| | - Jungkum Park
- Crop Protection Division, National Institute of Agriculture Sciences, Rural Development Administration, Wanju 55365, Korea; (E.R.); (J.P.)
| | - Sib Sankar Giri
- Laboratory of Aquatic Biomedicine, College of Veterinary Medicine and Research Institute for Veterinary Science, Seoul National University, Seoul 08826, Korea; (S.G.K.); (S.S.G.); (J.K.); (S.W.K.); (J.W.K.); (S.B.L.); (W.J.J.); (Y.M.L.); (K.C.)
| | - Jun Kwon
- Laboratory of Aquatic Biomedicine, College of Veterinary Medicine and Research Institute for Veterinary Science, Seoul National University, Seoul 08826, Korea; (S.G.K.); (S.S.G.); (J.K.); (S.W.K.); (J.W.K.); (S.B.L.); (W.J.J.); (Y.M.L.); (K.C.)
| | - Sang Wha Kim
- Laboratory of Aquatic Biomedicine, College of Veterinary Medicine and Research Institute for Veterinary Science, Seoul National University, Seoul 08826, Korea; (S.G.K.); (S.S.G.); (J.K.); (S.W.K.); (J.W.K.); (S.B.L.); (W.J.J.); (Y.M.L.); (K.C.)
| | - Jeong Woo Kang
- Laboratory of Aquatic Biomedicine, College of Veterinary Medicine and Research Institute for Veterinary Science, Seoul National University, Seoul 08826, Korea; (S.G.K.); (S.S.G.); (J.K.); (S.W.K.); (J.W.K.); (S.B.L.); (W.J.J.); (Y.M.L.); (K.C.)
| | - Sung Bin Lee
- Laboratory of Aquatic Biomedicine, College of Veterinary Medicine and Research Institute for Veterinary Science, Seoul National University, Seoul 08826, Korea; (S.G.K.); (S.S.G.); (J.K.); (S.W.K.); (J.W.K.); (S.B.L.); (W.J.J.); (Y.M.L.); (K.C.)
| | - Won Joon Jung
- Laboratory of Aquatic Biomedicine, College of Veterinary Medicine and Research Institute for Veterinary Science, Seoul National University, Seoul 08826, Korea; (S.G.K.); (S.S.G.); (J.K.); (S.W.K.); (J.W.K.); (S.B.L.); (W.J.J.); (Y.M.L.); (K.C.)
| | - Young Min Lee
- Laboratory of Aquatic Biomedicine, College of Veterinary Medicine and Research Institute for Veterinary Science, Seoul National University, Seoul 08826, Korea; (S.G.K.); (S.S.G.); (J.K.); (S.W.K.); (J.W.K.); (S.B.L.); (W.J.J.); (Y.M.L.); (K.C.)
| | - Kevin Cho
- Laboratory of Aquatic Biomedicine, College of Veterinary Medicine and Research Institute for Veterinary Science, Seoul National University, Seoul 08826, Korea; (S.G.K.); (S.S.G.); (J.K.); (S.W.K.); (J.W.K.); (S.B.L.); (W.J.J.); (Y.M.L.); (K.C.)
| | - Se Chang Park
- Laboratory of Aquatic Biomedicine, College of Veterinary Medicine and Research Institute for Veterinary Science, Seoul National University, Seoul 08826, Korea; (S.G.K.); (S.S.G.); (J.K.); (S.W.K.); (J.W.K.); (S.B.L.); (W.J.J.); (Y.M.L.); (K.C.)
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8
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Besarab NV, Akhremchuk AE, Zlatohurska MA, Romaniuk LV, Valentovich LN, Tovkach FI, Lagonenko AL, Evtushenkov AN. Isolation and characterization of Hena1 - a novel Erwinia amylovora bacteriophage. FEMS Microbiol Lett 2021; 367:5823740. [PMID: 32319510 DOI: 10.1093/femsle/fnaa070] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Accepted: 04/20/2020] [Indexed: 01/04/2023] Open
Abstract
Fire blight, caused by plant pathogenic bacterium Erwinia amylovora, is one of the most important diseases of Rosaceae plants. Due to the lack of effective control measures, fire blight infections pose a recurrent threat on agricultural production worldwide. Recently, bacterial viruses, or bacteriophages, have been proposed as environmentally friendly natural antimicrobial agents for fire blight control. Here, we isolated a novel bacteriophage Hena1 with activity against E. amylovora. Further analysis revealed that Hena1 is a narrow-host-range lytic phage belonging to Myoviridae family. Its genome consists of a linear 148,842 bp dsDNA (48.42% GC content) encoding 240 ORFs and 23 tRNA genes. Based on virion structure and genomic composition, Hena1 was classified as a new species of bacteriophage subfamily Vequintavirinae. The comprehensive analysis of Hena1 genome may provide further insights into evolution of bacteriophages infecting plant pathogenic bacteria.
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Affiliation(s)
- Natalya V Besarab
- Department of Molecular Biology, Faculty of Biology, Belarusian State University, 220030 Minsk, Belarus
| | - Artur E Akhremchuk
- Institute of Microbiology, National Academy of Sciences of Belarus, 220141 Minsk, Belarus
| | - Maryna A Zlatohurska
- Zabolotny Institute of Microbiology and Virology of NAS of Ukraine, D03680 Kyiv, Ukraine
| | - Liudmyla V Romaniuk
- Zabolotny Institute of Microbiology and Virology of NAS of Ukraine, D03680 Kyiv, Ukraine
| | - Leonid N Valentovich
- Department of Molecular Biology, Faculty of Biology, Belarusian State University, 220030 Minsk, Belarus.,Institute of Microbiology, National Academy of Sciences of Belarus, 220141 Minsk, Belarus
| | - Fedor I Tovkach
- Zabolotny Institute of Microbiology and Virology of NAS of Ukraine, D03680 Kyiv, Ukraine
| | - Alexander L Lagonenko
- Department of Molecular Biology, Faculty of Biology, Belarusian State University, 220030 Minsk, Belarus
| | - Anatoly N Evtushenkov
- Department of Molecular Biology, Faculty of Biology, Belarusian State University, 220030 Minsk, Belarus
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9
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Žukauskienė E, Šimoliūnienė M, Truncaitė L, Skapas M, Kaupinis A, Valius M, Meškys R, Šimoliūnas E. Pantoea Bacteriophage vB_PagS_AAS23: A Singleton of the Genus Sauletekiovirus. Microorganisms 2021; 9:668. [PMID: 33807116 PMCID: PMC8004638 DOI: 10.3390/microorganisms9030668] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Revised: 03/18/2021] [Accepted: 03/19/2021] [Indexed: 11/16/2022] Open
Abstract
A cold-adapted siphovirus, vB_PagS_AAS23 (AAS23) was isolated in Lithuania using the Pantoea agglomerans strain AUR for the phage propagation. The double-stranded DNA genome of AAS23 (51,170 bp) contains 92 probable protein encoding genes, and no genes for tRNA. A comparative sequence analysis revealed that 25 of all AAS23 open reading frames (ORFs) code for unique proteins that have no reliable identity to database entries. Based on the phylogenetic analysis, AAS23 has no close relationship to other viruses publicly available to date and represents a single species of the genus Sauletekiovirus within the family Drexlerviridae. The phage is able to form plaques in bacterial lawns even at 4 °C and demonstrates a depolymerase activity. Thus, the data presented in this study not only provides the information on Pantoea-infecting bacteriophages, but also offers novel insights into the diversity of cold-adapted viruses and their potential to be used as biocontrol agents.
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Affiliation(s)
- Emilija Žukauskienė
- Life Sciences Centre, Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Vilnius University, Saulėtekio av. 7, LT-10257 Vilnius, Lithuania; (E.Ž.); (M.Š.); (R.M.)
| | - Monika Šimoliūnienė
- Life Sciences Centre, Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Vilnius University, Saulėtekio av. 7, LT-10257 Vilnius, Lithuania; (E.Ž.); (M.Š.); (R.M.)
| | - Lidija Truncaitė
- Life Sciences Centre, Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Vilnius University, Saulėtekio av. 7, LT-10257 Vilnius, Lithuania; (E.Ž.); (M.Š.); (R.M.)
| | - Martynas Skapas
- Center for Physical Sciences and Technology, Saulėtekio av. 3, LT-10257 Vilnius, Lithuania;
| | - Algirdas Kaupinis
- Proteomics Centre, Institute of Biochemistry, Life Sciences Centre, Vilnius University, Saulėtekio av. 7, LT-10257 Vilnius, Lithuania; (A.K.); (M.V.)
| | - Mindaugas Valius
- Proteomics Centre, Institute of Biochemistry, Life Sciences Centre, Vilnius University, Saulėtekio av. 7, LT-10257 Vilnius, Lithuania; (A.K.); (M.V.)
| | - Rolandas Meškys
- Life Sciences Centre, Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Vilnius University, Saulėtekio av. 7, LT-10257 Vilnius, Lithuania; (E.Ž.); (M.Š.); (R.M.)
| | - Eugenijus Šimoliūnas
- Life Sciences Centre, Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Vilnius University, Saulėtekio av. 7, LT-10257 Vilnius, Lithuania; (E.Ž.); (M.Š.); (R.M.)
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Premaratne A, Zhang H, Wang R, Chinivasagam N, Billington C. Phage Biotechnology to Mitigate Antimicrobial Resistance in Agriculture. SUSTAINABLE AGRICULTURE REVIEWS 2021. [DOI: 10.1007/978-3-030-58259-3_9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
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11
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Akremi I, Holtappels D, Brabra W, Jlidi M, Hadj Ibrahim A, Ben Ali M, Fortuna K, Ahmed M, Meerbeek BV, Rhouma A, Lavigne R, Ben Ali M, Wagemans J. First Report of Filamentous Phages Isolated from Tunisian Orchards to Control Erwinia amylovora. Microorganisms 2020; 8:microorganisms8111762. [PMID: 33182526 PMCID: PMC7697814 DOI: 10.3390/microorganisms8111762] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2020] [Revised: 10/20/2020] [Accepted: 10/22/2020] [Indexed: 01/28/2023] Open
Abstract
Newly discovered Erwinia amylovora phages PEar1, PEar2, PEar4 and PEar6 were isolated from three different orchards in North Tunisia to study their potential as biocontrol agents. Illumina sequencing revealed that the PEar viruses carry a single-strand DNA genome between 6608 and 6801 nucleotides and belong to the Inoviridae, making them the first described filamentous phages of E. amylovora. Interestingly, phage-infected cells show a decreased swimming and swarming motility and a cocktail of the four phages can significantly reduce infection of E. amylovora in a pear bioassay, potentially making them suitable candidates for phage biocontrol.
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Affiliation(s)
- Ismahen Akremi
- Laboratory of Microbial Biotechnology, Enzymatics and Biomolecules (LBMEB), Center of Biotechnology of Sfax (CBS), University of Sfax, Road of Sidi Mansour km 6, P.O. Box 1177, Sfax 3018, Tunisia; (I.A.); (W.B.); (M.J.); (A.H.I.); (M.B.A.); (M.B.A.)
- Laboratory of Gene Technology, Department of Biosystems, KU Leuven, Kasteelpark Arenberg 21-Box 2462, 3001 Leuven, Belgium; (D.H.); (K.F.); (R.L.)
| | - Dominique Holtappels
- Laboratory of Gene Technology, Department of Biosystems, KU Leuven, Kasteelpark Arenberg 21-Box 2462, 3001 Leuven, Belgium; (D.H.); (K.F.); (R.L.)
| | - Wided Brabra
- Laboratory of Microbial Biotechnology, Enzymatics and Biomolecules (LBMEB), Center of Biotechnology of Sfax (CBS), University of Sfax, Road of Sidi Mansour km 6, P.O. Box 1177, Sfax 3018, Tunisia; (I.A.); (W.B.); (M.J.); (A.H.I.); (M.B.A.); (M.B.A.)
- Astrum Biotech, Business Incubator, Center of Biotechnology of Sfax (CBS), University of Sfax, Road of Sidi Mansour km 6, P.O. Box 1177, Sfax 3018, Tunisia
| | - Mouna Jlidi
- Laboratory of Microbial Biotechnology, Enzymatics and Biomolecules (LBMEB), Center of Biotechnology of Sfax (CBS), University of Sfax, Road of Sidi Mansour km 6, P.O. Box 1177, Sfax 3018, Tunisia; (I.A.); (W.B.); (M.J.); (A.H.I.); (M.B.A.); (M.B.A.)
| | - Adel Hadj Ibrahim
- Laboratory of Microbial Biotechnology, Enzymatics and Biomolecules (LBMEB), Center of Biotechnology of Sfax (CBS), University of Sfax, Road of Sidi Mansour km 6, P.O. Box 1177, Sfax 3018, Tunisia; (I.A.); (W.B.); (M.J.); (A.H.I.); (M.B.A.); (M.B.A.)
| | - Manel Ben Ali
- Laboratory of Microbial Biotechnology, Enzymatics and Biomolecules (LBMEB), Center of Biotechnology of Sfax (CBS), University of Sfax, Road of Sidi Mansour km 6, P.O. Box 1177, Sfax 3018, Tunisia; (I.A.); (W.B.); (M.J.); (A.H.I.); (M.B.A.); (M.B.A.)
- Astrum Biotech, Business Incubator, Center of Biotechnology of Sfax (CBS), University of Sfax, Road of Sidi Mansour km 6, P.O. Box 1177, Sfax 3018, Tunisia
| | - Kiandro Fortuna
- Laboratory of Gene Technology, Department of Biosystems, KU Leuven, Kasteelpark Arenberg 21-Box 2462, 3001 Leuven, Belgium; (D.H.); (K.F.); (R.L.)
| | - Mohammed Ahmed
- Biomaterials Research Group (BIOMAT), Department of Oral Sciences, KU Leuven, Kapucijnenvoer 7-Block A Box 7001, 3000 Leuven, Belgium; (M.A.); (B.V.M.)
- Department of Dental Biomaterials, Tanta University, Biomedical Campus, 32511 Tanta, Gharbia Governorate, Egypt
| | - Bart Van Meerbeek
- Biomaterials Research Group (BIOMAT), Department of Oral Sciences, KU Leuven, Kapucijnenvoer 7-Block A Box 7001, 3000 Leuven, Belgium; (M.A.); (B.V.M.)
| | - Ali Rhouma
- Laboratory of Integrated Olive Production, Olive Tree Institute, BP208 Marhajene City, Tunis 1082, Tunisia;
| | - Rob Lavigne
- Laboratory of Gene Technology, Department of Biosystems, KU Leuven, Kasteelpark Arenberg 21-Box 2462, 3001 Leuven, Belgium; (D.H.); (K.F.); (R.L.)
| | - Mamdouh Ben Ali
- Laboratory of Microbial Biotechnology, Enzymatics and Biomolecules (LBMEB), Center of Biotechnology of Sfax (CBS), University of Sfax, Road of Sidi Mansour km 6, P.O. Box 1177, Sfax 3018, Tunisia; (I.A.); (W.B.); (M.J.); (A.H.I.); (M.B.A.); (M.B.A.)
- Astrum Biotech, Business Incubator, Center of Biotechnology of Sfax (CBS), University of Sfax, Road of Sidi Mansour km 6, P.O. Box 1177, Sfax 3018, Tunisia
| | - Jeroen Wagemans
- Laboratory of Gene Technology, Department of Biosystems, KU Leuven, Kasteelpark Arenberg 21-Box 2462, 3001 Leuven, Belgium; (D.H.); (K.F.); (R.L.)
- Correspondence: ; Tel.: +32-1637-4622
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Host Range of Bacteriophages Against a World-Wide Collection of Erwinia amylovora Determined Using a Quantitative PCR Assay. Viruses 2019; 11:v11100910. [PMID: 31581574 PMCID: PMC6832558 DOI: 10.3390/v11100910] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Revised: 09/21/2019] [Accepted: 09/27/2019] [Indexed: 01/01/2023] Open
Abstract
Erwinia amylovora is a globally devastating pathogen of apple, pear, and other Rosaceous plants. The use of lytic bacteriophages for disease management continues to garner attention as a possible supplement or alternative to antibiotics. A quantitative productive host range was established for 10 Erwinia phages using 106 wild type global isolates of E. amylovora, and the closely related Erwinia pyrifoliae, to investigate the potential regional efficacy of these phages within a biopesticide. Each host was individually infected with each of the 10 Erwinia phages and phage production after 8 h incubation was measured using quantitative real time PCR (qPCR) in conjunction with a standardized plasmid. PCR amplicons for all phages used in the study were incorporated into a single plasmid, allowing standardized quantification of the phage genome copy number after the infection process. Nine of the tested phages exhibited a broad host range, replicating their genomes by at least one log in over 88% of tested hosts. Also, every Amygdaloideae infecting E. amylovora host was able to increase at least one phage by three logs. Bacterial hosts isolated in western North America were less susceptible to most phages, as the mean genomic titre produced dropped by nearly two logs, and this phenomenon was strongly correlated to the amount of exopolysaccharide produced by the host. This method of host range analysis is faster and requires less effort than traditional plaque assay techniques, and the resulting quantitative data highlight subtle differences in phage host preference not observable with typical plaque-based host range assays. These quantitative host range data will be useful to determine which phages should be incorporated into a phage-mediated biocontrol formulation to be tested for regional and universal control of E. amylovora.
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Dunsing V, Irmscher T, Barbirz S, Chiantia S. Purely Polysaccharide-Based Biofilm Matrix Provides Size-Selective Diffusion Barriers for Nanoparticles and Bacteriophages. Biomacromolecules 2019; 20:3842-3854. [DOI: 10.1021/acs.biomac.9b00938] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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14
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Zlatohurska M, Gorb T, Romaniuk L, Korol N, Faidiuk Y, Kropinski AM, Kushkina A, Tovkach F. Complete genome sequence analysis of temperate Erwinia bacteriophages 49 and 59. J Basic Microbiol 2019; 59:754-764. [PMID: 31099101 DOI: 10.1002/jobm.201900205] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Accepted: 05/11/2019] [Indexed: 11/09/2022]
Abstract
To date, a small number of temperate phages are known to infect members of the genus Erwinia. In this study, the genomes of temperate phages vB_EhrS_49 and vB_EhrS_59 infecting Erwinia horticola, the causative agent of beech black bacteriosis in Ukraine, were sequenced and annotated. Their genomes reveal no significant similarity to that of any previously reported viruses of Enterobacteriaceae. At the same time, phages 49 and 59 share extensive nucleotide sequence identity across the regions encoding head assembly, DNA packaging, and lysis. Despite significant homology between structural modules, the organization of distal tail morphogenesis genes is different. Furthermore, a number of putative morons and DNA methylases have been found in both phage genomes. Due to the revealed synteny as well as the structure of lysogeny module, phages 49 and 59 are suggested to be novel members of the lambdoid phage group. Conservative structural genes together with varying homology across the nonstructural region of the genomes make phages 49 and 59 highly promising objects for studying the genetic recombination and evolution of microbial viruses. The obtained data may as well be helpful for better understanding of relationships among Erwinia species.
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Affiliation(s)
- Maryna Zlatohurska
- Department of Bacteriophage Molecular Genetics, D.K. Zabolotny Institute of Microbiology and Virology of National Academy of Sciences of Ukraine, Kyiv, Ukraine
| | - Tetiana Gorb
- Department of Bacteriophage Molecular Genetics, D.K. Zabolotny Institute of Microbiology and Virology of National Academy of Sciences of Ukraine, Kyiv, Ukraine
| | - Liudmyla Romaniuk
- Department of Bacteriophage Molecular Genetics, D.K. Zabolotny Institute of Microbiology and Virology of National Academy of Sciences of Ukraine, Kyiv, Ukraine
| | - Natalia Korol
- Department of Bacteriophage Molecular Genetics, D.K. Zabolotny Institute of Microbiology and Virology of National Academy of Sciences of Ukraine, Kyiv, Ukraine
| | - Yuliia Faidiuk
- Department of Bacteriophage Molecular Genetics, D.K. Zabolotny Institute of Microbiology and Virology of National Academy of Sciences of Ukraine, Kyiv, Ukraine.,ESC "Institute of Biology and Medicine", Department of Microbiology and Immunology, Taras Shevchenko Kyiv National University, Kyiv, Ukraine
| | - Andrew M Kropinski
- Department of Food Science, University of Guelph, Guelph, Ontario, Canada.,Department of Pathobiology, University of Guelph, Guelph, Ontario, Canada
| | - Alla Kushkina
- Department of Bacteriophage Molecular Genetics, D.K. Zabolotny Institute of Microbiology and Virology of National Academy of Sciences of Ukraine, Kyiv, Ukraine
| | - Fedor Tovkach
- Department of Bacteriophage Molecular Genetics, D.K. Zabolotny Institute of Microbiology and Virology of National Academy of Sciences of Ukraine, Kyiv, Ukraine
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Šimoliūnas E, Šimoliūnienė M, Kaliniene L, Zajančkauskaitė A, Skapas M, Meškys R, Kaupinis A, Valius M, Truncaitė L. Pantoea Bacteriophage vB_PagS_Vid5: A Low-Temperature Siphovirus That Harbors a Cluster of Genes Involved in the Biosynthesis of Archaeosine. Viruses 2018; 10:v10110583. [PMID: 30366363 PMCID: PMC6266253 DOI: 10.3390/v10110583] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Revised: 10/12/2018] [Accepted: 10/23/2018] [Indexed: 12/13/2022] Open
Abstract
A novel low-temperature siphovirus, vB_PagS_Vid5 (Vid5), was isolated in Lithuania using Pantoea agglomerans isolate for the phage propagation. The 61,437 bp genome of Vid5 has a G–C content of 48.8% and contains 99 probable protein encoding genes and one gene for tRNASer. A comparative sequence analysis revealed that 46 out of 99 Vid5 open reading frames (ORFs) code for unique proteins that have no reliable identity to database entries. In total, 33 Vid5 ORFs were given a putative functional annotation, including those coding for the proteins responsible for virion morphogenesis, phage-host interactions, and DNA metabolism. In addition, a cluster of genes possibly involved in the biosynthesis of 7-deazaguanine derivatives was identified. Notably, one of these genes encodes a putative preQ0/preQ1 transporter, which has never been detected in bacteriophages to date. A proteomic analysis led to the experimental identification of 11 virion proteins, including nine that were predicted by bioinformatics approaches. Based on the phylogenetic analysis, Vid5 cannot be assigned to any genus currently recognized by ICTV, and may represent a new one within the family of Siphoviridae.
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Affiliation(s)
- Eugenijus Šimoliūnas
- Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Life Sciences Centre, Vilnius University, Saulėtekio av. 7, LT-10257 Vilnius, Lithuania.
| | - Monika Šimoliūnienė
- Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Life Sciences Centre, Vilnius University, Saulėtekio av. 7, LT-10257 Vilnius, Lithuania.
| | - Laura Kaliniene
- Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Life Sciences Centre, Vilnius University, Saulėtekio av. 7, LT-10257 Vilnius, Lithuania.
| | - Aurelija Zajančkauskaitė
- Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Life Sciences Centre, Vilnius University, Saulėtekio av. 7, LT-10257 Vilnius, Lithuania.
| | - Martynas Skapas
- Center for Physical Sciences and Technology, Saulėtekio av. 3, LT-10257 Vilnius, Lithuania.
| | - Rolandas Meškys
- Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Life Sciences Centre, Vilnius University, Saulėtekio av. 7, LT-10257 Vilnius, Lithuania.
| | - Algirdas Kaupinis
- Proteomics Centre, Institute of Biochemistry, Life Sciences Centre, Vilnius University, Saulėtekio av. 7, LT-10257 Vilnius, Lithuania.
| | - Mindaugas Valius
- Proteomics Centre, Institute of Biochemistry, Life Sciences Centre, Vilnius University, Saulėtekio av. 7, LT-10257 Vilnius, Lithuania.
| | - Lidija Truncaitė
- Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Life Sciences Centre, Vilnius University, Saulėtekio av. 7, LT-10257 Vilnius, Lithuania.
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Park J, Lee GM, Kim D, Park DH, Oh CS. Characterization of the Lytic Bacteriophage phiEaP-8 Effective against Both Erwinia amylovora and Erwinia pyrifoliae Causing Severe Diseases in Apple and Pear. THE PLANT PATHOLOGY JOURNAL 2018; 34:445-450. [PMID: 30369854 PMCID: PMC6200048 DOI: 10.5423/ppj.nt.06.2018.0100] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Revised: 07/20/2018] [Accepted: 07/25/2018] [Indexed: 05/10/2023]
Abstract
Bacteriophages, bacteria-infecting viruses, have been recently reconsidered as a biological control tool for preventing bacterial pathogens. Erwinia amylovora and E. pyrifoliae cause fire blight and black shoot blight disease in apple and pear, respectively. In this study, the bacteriophage phiEaP-8 was isolated from apple orchard soil and could efficiently and specifically kill both E. amylovora and E. pyrifoliae. This bacteriophage belongs to the Podoviridae family. Whole genome analysis revealed that phiEaP-8 carries a 75,929 bp genomic DNA with 78 coding sequences and 5 tRNA genes. Genome comparison showed that phiEaP-8 has only 85% identity to known bacteriophages at the DNA level. PhiEaP-8 retained lytic activity up to 50°C, within a pH range from 5 to 10, and under 365 nm UV light. Based on these characteristics, the bacteriophage phiEaP-8 is novel and carries potential to control both E. amylovora and E. pyrifoliae in apple and pear.
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Affiliation(s)
- Jungkum Park
- Department of Horticultural Biotechnology, College of Life Sciences, Kyung Hee University, Yongin 17104,
Korea
| | - Gyu Min Lee
- Graduate School of Biotechnology, College of Life Sciences, Kyung Hee University, Yongin 17104,
Korea
| | - Donghyuk Kim
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919,
Korea
| | - Duck Hwan Park
- Applied Biology Program, Division of Bioresource Sciences, Kangwon National University, Chuncheon 24341,
Korea
| | - Chang-Sik Oh
- Department of Horticultural Biotechnology, College of Life Sciences, Kyung Hee University, Yongin 17104,
Korea
- Corresponding author: Phone) +82-31-201-2678, FAX) +82-31-204-8116, E-mail)
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Complete Genome Sequence of Citrobacter freundii Myophage Michonne. GENOME ANNOUNCEMENTS 2015; 3:3/5/e01134-15. [PMID: 26430047 PMCID: PMC4591319 DOI: 10.1128/genomea.01134-15] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Citrobacter freundii is a Gram-negative opportunistic pathogen that causes dangerous infections such as neonatal meningitis. C. freundii also harbors antibiotic resistance, making phages infecting this host valuable tools. Here, we announce the complete genome of the C. freundii FelixO1-like myophage Michonne and describe its notable features.
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Born Y, Bosshard L, Duffy B, Loessner MJ, Fieseler L. Protection of Erwinia amylovora bacteriophage Y2 from UV-induced damage by natural compounds. BACTERIOPHAGE 2015; 5:e1074330. [PMID: 26904378 PMCID: PMC4743488 DOI: 10.1080/21597081.2015.1074330] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2015] [Revised: 06/23/2015] [Accepted: 07/14/2015] [Indexed: 10/23/2022]
Abstract
Bacteriophages have regained much attention as biocontrol agents against bacterial pathogens. However, with respect to stability, phages are biomolecules and are therefore sensitive to a number of environmental influences. UV-irradiation can readily inactivate phage infectivity, which impedes their potential application in the plant phyllosphere. Therefore, phages for control of Erwinia amylovora, the causative agent of fire blight, need to be protected from UV-damage by adequate measures. We investigated the protective effect of different light-absorbing substances on phage particles exposed to UV-light. For this, natural extracts from carrot, red pepper, and beetroot, casein and soy peptone in solution, and purified substances such as astaxanthin, aromatic amino acids, and Tween 80 were prepared and tested as natural sunscreens for phage. All compounds were found to significantly increase half-life of UV-irradiated phage particles and they did not negatively affect phage viability or infectivity. Altogether, a range of readily available, natural substances are suitable as UV-protectants to prevent phage particles from UV-light damage.
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Affiliation(s)
- Yannick Born
- Institute of Food and Beverage Innovation; Zurich University of Applied Sciences; Wädenswil, Switzerland
- Agroscope Wädenswil; Swiss National Competence Center for Fire Blight; Wädenswil, Switzerland
- Institute of Food; Nutrition and Health; ETH Zurich; Zürich, Switzerland
| | - Lars Bosshard
- Institute of Food; Nutrition and Health; ETH Zurich; Zürich, Switzerland
| | - Brion Duffy
- Agroscope Wädenswil; Swiss National Competence Center for Fire Blight; Wädenswil, Switzerland
- Institute of Natural Resource Sciences; Zurich University of Applied Sciences; Wädenswil, Switzerland
| | - Martin J. Loessner
- Institute of Food; Nutrition and Health; ETH Zurich; Zürich, Switzerland
| | - Lars Fieseler
- Institute of Food and Beverage Innovation; Zurich University of Applied Sciences; Wädenswil, Switzerland
- Institute of Food; Nutrition and Health; ETH Zurich; Zürich, Switzerland
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19
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Roach DR, Sjaarda DR, Sjaarda CP, Ayala CJ, Howcroft B, Castle AJ, Svircev AM. Absence of lysogeny in wild populations of Erwinia amylovora and Pantoea agglomerans. Microb Biotechnol 2015; 8:510-8. [PMID: 25678125 PMCID: PMC4408183 DOI: 10.1111/1751-7915.12253] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2014] [Revised: 11/04/2014] [Accepted: 11/08/2014] [Indexed: 12/03/2022] Open
Abstract
Lytic bacteriophages are in development as biological control agents for the prevention of fire blight disease caused by Erwinia amylovora. Temperate phages should be excluded as biologicals since lysogeny produces the dual risks of host resistance to phage attack and the transduction of virulence determinants between bacteria. The extent of lysogeny was estimated in wild populations of E. amylovora and Pantoea agglomerans with real-time polymerase chain reaction primers developed to detect E. amylovora phages belonging to the Myoviridae and Podoviridae families. Pantoea agglomerans, an orchard epiphyte, is easily infected by Erwinia spp. phages, and it serves as a carrier in the development of the phage-mediated biological control agent. Screening of 161 E. amylovora isolates from 16 distinct geographical areas in North America, Europe, North Africa and New Zealand and 82 P. agglomerans isolates from southern Ontario, Canada showed that none possessed prophage. Unstable phage resistant clones or lysogens were produced under laboratory conditions. Additionally, a stable lysogen was recovered from infection of bacterial isolate Ea110R with Podoviridae phage ΦEa35-20. These laboratory observations suggested that while lysogeny is possible in E. amylovora, it is rare or absent in natural populations, and there is a minimal risk associated with lysogenic conversion and transduction by Erwinia spp. phages.
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Affiliation(s)
- Dwayne R Roach
- Department of Biological Science, Brock University500 Glenridge Avenue, St. Catharines, ON, L2S 3A1, Canada
- Agriculture and Agri-Food Canada4902 Victoria Ave. North, P.O. Box 6000, Vineland Station, ON, L0R 2E0, Canada
| | - David R Sjaarda
- Department of Biological Science, Brock University500 Glenridge Avenue, St. Catharines, ON, L2S 3A1, Canada
- Agriculture and Agri-Food Canada4902 Victoria Ave. North, P.O. Box 6000, Vineland Station, ON, L0R 2E0, Canada
| | - Calvin P Sjaarda
- Department of Biological Science, Brock University500 Glenridge Avenue, St. Catharines, ON, L2S 3A1, Canada
- Agriculture and Agri-Food Canada4902 Victoria Ave. North, P.O. Box 6000, Vineland Station, ON, L0R 2E0, Canada
| | - Carlos Juarez Ayala
- Agriculture and Agri-Food Canada4902 Victoria Ave. North, P.O. Box 6000, Vineland Station, ON, L0R 2E0, Canada
| | - Brittany Howcroft
- Department of Biological Science, Brock University500 Glenridge Avenue, St. Catharines, ON, L2S 3A1, Canada
- Agriculture and Agri-Food Canada4902 Victoria Ave. North, P.O. Box 6000, Vineland Station, ON, L0R 2E0, Canada
| | - Alan J Castle
- Department of Biological Science, Brock University500 Glenridge Avenue, St. Catharines, ON, L2S 3A1, Canada
| | - Antonet M Svircev
- Agriculture and Agri-Food Canada4902 Victoria Ave. North, P.O. Box 6000, Vineland Station, ON, L0R 2E0, Canada
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Born Y, Fieseler L, Klumpp J, Eugster MR, Zurfluh K, Duffy B, Loessner MJ. The tail-associated depolymerase ofErwinia amylovoraphage L1 mediates host cell adsorption and enzymatic capsule removal, which can enhance infection by other phage. Environ Microbiol 2013; 16:2168-80. [DOI: 10.1111/1462-2920.12212] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2013] [Revised: 07/05/2013] [Accepted: 07/10/2013] [Indexed: 01/21/2023]
Affiliation(s)
- Yannick Born
- Institute of Food, Nutrition and Health; ETH Zurich; Zürich CH-8092 Switzerland
- Phytopathology; Research Station Agroscope Changins-Wädenswil ACW; Wädenswil CH-8820 Switzerland
| | - Lars Fieseler
- Institute of Food, Nutrition and Health; ETH Zurich; Zürich CH-8092 Switzerland
| | - Jochen Klumpp
- Institute of Food, Nutrition and Health; ETH Zurich; Zürich CH-8092 Switzerland
| | - Marcel R. Eugster
- Institute of Food, Nutrition and Health; ETH Zurich; Zürich CH-8092 Switzerland
| | - Katrin Zurfluh
- Institute of Food, Nutrition and Health; ETH Zurich; Zürich CH-8092 Switzerland
| | - Brion Duffy
- Phytopathology; Research Station Agroscope Changins-Wädenswil ACW; Wädenswil CH-8820 Switzerland
| | - Martin J. Loessner
- Institute of Food, Nutrition and Health; ETH Zurich; Zürich CH-8092 Switzerland
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Jock S, Wensing A, Pulawska J, Drenova N, Dreo T, Geider K. Molecular analyses of Erwinia amylovora strains isolated in Russia, Poland, Slovenia and Austria describing further spread of fire blight in Europe. Microbiol Res 2013; 168:447-54. [PMID: 23570971 DOI: 10.1016/j.micres.2013.01.008] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2012] [Revised: 01/23/2013] [Accepted: 01/25/2013] [Indexed: 11/27/2022]
Abstract
Fire blight, a bacteriosis of apple and pear, was assayed with molecular tools to associate its origin in Russia, Slovenia and south-eastern Austria with neighboring countries. The identification of all investigated strains was confirmed by MALDI-TOF mass spectroscopy except one. Independent isolation was verified by the level of amylovoran synthesis and by the number of short sequence DNA repeats in plasmid pEA29. DNA of gently lysed E. amylovora strains from Russia, Slovenia, Austria, Hungary, Italy, Spain, Croatia, Poland, Central Europe and Iran was treated with restriction enzymes XbaI and SpeI to create typical banding patterns for PFGE analysis. The pattern Pt2 indicated that most Russian E. amylovora strains were related to strains from Turkey and Iran. Strains from Slovenia exhibited patterns Pt3 and Pt2, both present in the neighboring countries. Strains were also probed for the recently described plasmid pEI70 detected in Pt1 strains from Poland and in Pt3 strains from other countries. The distribution of pattern Pt3 suggests distribution of fire blight from Belgium and the Netherlands to Central Spain and Northern Italy and then north to Carinthia. The PFGE patterns indicate that trade of plants may have introduced fire blight into southern parts of Europe proceeded by sequential spread.
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Affiliation(s)
- Susanne Jock
- Julius Kuehn Institute, Institute for Plant Protection in Fruit Crops and Viticulture, Schwabenheimer Str. 101, D-69221 Dossenheim, Germany
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Bühlmann A, Pothier JF, Rezzonico F, Smits THM, Andreou M, Boonham N, Duffy B, Frey JE. Erwinia amylovora loop-mediated isothermal amplification (LAMP) assay for rapid pathogen detection and on-site diagnosis of fire blight. J Microbiol Methods 2012; 92:332-9. [PMID: 23275135 DOI: 10.1016/j.mimet.2012.12.017] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2012] [Revised: 12/17/2012] [Accepted: 12/20/2012] [Indexed: 11/16/2022]
Abstract
Several molecular methods have been developed for the detection of Erwinia amylovora, the causal agent of fire blight in pear and apple, but none are truly applicable for on-site use in the field. We developed a fast, reliable and field applicable detection method using a novel target on the E. amylovora chromosome that we identified by applying a comparative genomic pipeline. The target coding sequences (CDSs) are both uniquely specific for and all-inclusive of E. amylovora genotypes. This avoids potential false negatives that can occur with most commonly used methods based on amplification of plasmid gene targets, which can vary among strains. Loop-mediated isothermal AMPlification (LAMP) with OptiGene Genie II chemistry and instrumentation proved to be an exceptionally rapid (under 15 min) and robust method for detecting E. amylovora in orchards, as well as simple to use in the plant diagnostic laboratory. Comparative validation results using plant samples from inoculated greenhouse trials and from natural field infections (of regional and temporal diverse origin) showed that our LAMP had an equivalent or greater performance regarding sensitivity, specificity, speed and simplicity than real-time PCR (TaqMan), other LAMP assays, immunoassays and plating, demonstrating its utility for routine testing.
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Affiliation(s)
- Andreas Bühlmann
- Agroscope Changins-Wädenswil Research Station ACW, Plant Protection Division, CH-8820 Wädenswil, Switzerland
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Müller I, Lurz R, Geider K. Tasmancin and lysogenic bacteriophages induced from Erwinia tasmaniensis strains. Microbiol Res 2012; 167:381-7. [PMID: 22381912 DOI: 10.1016/j.micres.2012.01.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2011] [Revised: 01/16/2012] [Accepted: 01/22/2012] [Indexed: 11/29/2022]
Abstract
Mitomycin C treatment of Erwinia tasmaniensis strains from Australia induced prophages and the expression of bacteriocins. The bacteriocin named tasmancin inhibited E. tasmaniensis strains from South Africa and Germany. A gene cluster with a klebicin-related operon and an immunity protein was detected on plasmid pET46 from E. tasmaniensis strain Et1/99. PCR reactions using primers directed to this region produced signals for several strains originating from Australia, but not for strains isolated in South Africa and Germany. The latter isolates lacked plasmid pET46. Bacteriophages were induced from E. tasmaniensis strains Et88 and Et14/99, both isolates from South-Eastern Australia. These phages formed plaques on several other strains from this region, as well as on E. tasmaniensis strains from South Africa and Germany. Sequencing revealed similarity of phages ϕEt88 and ϕEt14, which shared the host range on E. tasmaniensis strains. Bacteriophages and tasmancin may interfere with the viability of several related E. tasmaniensis strains in the environment of carrier strains.
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Affiliation(s)
- Ina Müller
- Julius Kühn-Institut, Institut für Pflanzenschutz in Obst- und Weinbau, Schwabenheimer Str. 101, 69221 Dossenheim, Germany
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Schollmeyer M, Langlotz C, Huber A, Coplin DL, Geider K. Variations in the molecular masses of the capsular exopolysaccharides amylovoran, pyrifolan and stewartan. Int J Biol Macromol 2012; 50:518-22. [PMID: 22266385 DOI: 10.1016/j.ijbiomac.2012.01.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2011] [Revised: 12/30/2011] [Accepted: 01/07/2012] [Indexed: 11/19/2022]
Abstract
Erwinia amylovora, causing fire blight of apple, pear and some ornamentals, Erwinia pyrifoliae, causing Asian pear blight, and Pantoea stewartii, causing Stewart's wilt of sweet maize, synthesize capsular extracellular polysaccharides (EPSs) with a high molecular mass. The EPSs are virulence factors and form viscous aggregates, which participate in clogging vessels of infected plants and causing wilting. The sizes of EPSs produced under different environmental growth conditions were determined by analysis with large pore HPLC columns. Their molecular mass of ca. 5 MDa, when isolated from agar plates, decreases to ca. 1 MDa for E. amylovora amylovoran from freeze-dried supernatants from liquid cultures and to 2 MDa for freeze-dried preparations of P. stewartii stewartan. Size changes were also found following growth in various other media and for different strains. Stewartan, amylovoran and E. pyrifoliae pyrifolan were also shown to be completely degraded by a bacteriophage EPS depolymerase.
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