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Vasilyeva AA, Evseev PV, Ignatov AN, Dzhalilov FSU. Pectobacterium punjabense Causing Blackleg and Soft Rot of Potato: The First Report in the Russian Federation. PLANTS (BASEL, SWITZERLAND) 2024; 13:2144. [PMID: 39124263 PMCID: PMC11313954 DOI: 10.3390/plants13152144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2024] [Revised: 07/19/2024] [Accepted: 07/30/2024] [Indexed: 08/12/2024]
Abstract
Phytopathogenic bacteria of the genus Pectobacterium are responsible for several diseases that affect potato (Solanum tuberosum L.) production worldwide, including blackleg and tuber soft rot. These bacteria are highly diverse, with over 17 different species currently identified. However, some of the recently described species, such as Pectobacterium punjabense, are still poorly understood. In this study, we focused on P. punjabense isolates collected from diseased potato tubers in Russia in 2021. Whole-genome sequencing was used to characterise the genomic diversity of the pathogen and determine the biochemical profiles of the isolated bacteria. The ability of these isolates to cause soft rot symptoms was tested. A comparative assessment of the potential pathogenicity of the Pectobacterium isolates was conducted by infecting potato tubers and measuring the accumulation of biomass in a liquid medium during cultivation at different temperatures. A TaqMan qPCR assay was developed for the highly sensitive and specific characterisation of P. punjabense strains, which can be used in diagnostic systems. This is the first report on P. punjabense causing potato disease in the Russian Federation.
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Affiliation(s)
- Anna A. Vasilyeva
- Department of Plant Protection, Russian State Agrarian University—Moscow Timiryazev Agricultural Academy, Timiryazevskaya Str. 49, 127434 Moscow, Russia; (P.V.E.); (A.N.I.)
| | - Peter V. Evseev
- Department of Plant Protection, Russian State Agrarian University—Moscow Timiryazev Agricultural Academy, Timiryazevskaya Str. 49, 127434 Moscow, Russia; (P.V.E.); (A.N.I.)
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya Str. 16/10, 117997 Moscow, Russia
- Laboratory of Molecular Microbiology, Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, 117997 Moscow, Russia
| | - Alexandr N. Ignatov
- Department of Plant Protection, Russian State Agrarian University—Moscow Timiryazev Agricultural Academy, Timiryazevskaya Str. 49, 127434 Moscow, Russia; (P.V.E.); (A.N.I.)
- Agrobiotechnology Department, Agrarian and Technological Institute, RUDN University, Miklukho-Maklaya Str. 6, 117198 Moscow, Russia
| | - Fevzi S.-U. Dzhalilov
- Department of Plant Protection, Russian State Agrarian University—Moscow Timiryazev Agricultural Academy, Timiryazevskaya Str. 49, 127434 Moscow, Russia; (P.V.E.); (A.N.I.)
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Motyka-Pomagruk A, Babinska-Wensierska W, Sledz W, Kaczorowska AK, Lojkowska E. Phyloproteomic study by MALDI-TOF MS in view of intraspecies variation in a significant homogenous phytopathogen Dickeya solani. Sci Rep 2023; 13:18863. [PMID: 37914755 PMCID: PMC10620192 DOI: 10.1038/s41598-023-46012-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2023] [Accepted: 10/26/2023] [Indexed: 11/03/2023] Open
Abstract
Dickeya solani is an economically significant pectinolytic phytopathogen belonging to the Pectobacteriaceae family, which causes soft rot and blackleg diseases. Despite its notable impact on global potato production, there are no effective methods to control this pest. Here, we undertook a phyloproteomic study on 20 D. solani strains, of various origin and year of isolation, with matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) supported by an in-depth characterization of the strains in terms of the virulence-associated phenotype. In spite of high homogeneity in this species, we herein revealed for the first time intraspecies variation in the MALDI-TOF MS protein profiles among the studied D. solani isolates. Finally, representative mass spectra for the four delineated clades are presented. A majority of the analysed D. solani strains showed high virulence potential, while two strains stood out in their growth dynamics, virulence factors production and ability to macerate plant tissue. Nonetheless, the metabolic profiles of D. solani strains turned out to be uniform, except for gelatinase activity. Given that all D. solani isolates distinctly grouped from the other Dickeya species in the MALDI-TOF MS analysis, there is strong evidence supporting the potential routine use of this method for fast and reliable to-species identification of D. solani isolates of environmental origin.
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Affiliation(s)
- Agata Motyka-Pomagruk
- Laboratory of Plant Protection and Biotechnology, Intercollegiate Faculty of Biotechnology University of Gdansk and Medical University of Gdansk, University of Gdansk, 58 Abrahama, 80-307, Gdańsk, Poland
- Research & Development Laboratory, Intercollegiate Faculty of Biotechnology University of Gdansk and Medical University of Gdansk, University of Gdansk, 20 Podwale Przedmiejskie, 80-824, Gdańsk, Poland
| | - Weronika Babinska-Wensierska
- Laboratory of Plant Protection and Biotechnology, Intercollegiate Faculty of Biotechnology University of Gdansk and Medical University of Gdansk, University of Gdansk, 58 Abrahama, 80-307, Gdańsk, Poland
- Research & Development Laboratory, Intercollegiate Faculty of Biotechnology University of Gdansk and Medical University of Gdansk, University of Gdansk, 20 Podwale Przedmiejskie, 80-824, Gdańsk, Poland
| | - Wojciech Sledz
- Laboratory of Plant Protection and Biotechnology, Intercollegiate Faculty of Biotechnology University of Gdansk and Medical University of Gdansk, University of Gdansk, 58 Abrahama, 80-307, Gdańsk, Poland
- Research & Development Laboratory, Intercollegiate Faculty of Biotechnology University of Gdansk and Medical University of Gdansk, University of Gdansk, 20 Podwale Przedmiejskie, 80-824, Gdańsk, Poland
| | - Anna-Karina Kaczorowska
- Collection of Plasmids and Microorganisms (KPD), Faculty of Biology, University of Gdansk, 59 Wita Stwosza Street, 80-308, Gdańsk, Poland
| | - Ewa Lojkowska
- Laboratory of Plant Protection and Biotechnology, Intercollegiate Faculty of Biotechnology University of Gdansk and Medical University of Gdansk, University of Gdansk, 58 Abrahama, 80-307, Gdańsk, Poland.
- Research & Development Laboratory, Intercollegiate Faculty of Biotechnology University of Gdansk and Medical University of Gdansk, University of Gdansk, 20 Podwale Przedmiejskie, 80-824, Gdańsk, Poland.
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Ben Moussa H, Pédron J, Hugouvieux-Cotte-Pattat N, Barny MA. Two species with a peculiar evolution within the genus Pectobacterium suggest adaptation to a new environmental niche. Environ Microbiol 2023; 25:2465-2480. [PMID: 37550252 DOI: 10.1111/1462-2920.16479] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Accepted: 07/20/2023] [Indexed: 08/09/2023]
Abstract
Historically, research on Soft Rot Pectobacteriacea (SRP) has focused on economically important crops and ornamentals and knowledge of these bacteria outside the plant context remains poorly investigated. Recently, two closely related species Pectobacterium aquaticum and Pectobacterium quasiaquaticum were isolated from water and have not been isolated from any plant yet. To identify the distinctive characteristics of these two species, we performed a comparative genomic analysis of 80 genomes representing 19 Pectobacterium species and performed an evolutionary reconstruction. Both water species underwent a reduction in genome size associated with a high pseudogene content. A high gene loss was predicted at the emergence of both species. Among the 199 gene families missing from both P. aquaticum and P. quasiaquaticum genomes but present in at least 80% of other Pectobacterium genomes, COG analysis identified many genes involved in nutrient transport systems. In addition, many type II secreted proteins were also missing in both species. Phenotypic analysis revealed that both species had reduced pectinolytic activity, a biofilm formation defect, were highly motile and had reduced virulence on several plants. These genomic and phenotypic data suggest that the ecological niche of P. aquaticum and P. quasiaquaticum may differ from that of other Pectobacterium species.
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Affiliation(s)
- Hajar Ben Moussa
- Sorbonne Université, INRAE, IRD, CNRS, UPEC, UMR 7618 Institut d'Écologie et des Sciences de l'Environnement de Paris, Paris, France
| | - Jacques Pédron
- Sorbonne Université, INRAE, IRD, CNRS, UPEC, UMR 7618 Institut d'Écologie et des Sciences de l'Environnement de Paris, Paris, France
| | | | - Marie-Anne Barny
- Sorbonne Université, INRAE, IRD, CNRS, UPEC, UMR 7618 Institut d'Écologie et des Sciences de l'Environnement de Paris, Paris, France
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Han W, Wang J, Pirhonen M, Pan Y, Qin J, Zhang S, Zhu J, Yang Z. Identification and characterization of opportunistic pathogen Pectobacterium polonicum causing potato blackleg in China. FRONTIERS IN PLANT SCIENCE 2023; 14:1097741. [PMID: 36938006 PMCID: PMC10020715 DOI: 10.3389/fpls.2023.1097741] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Accepted: 01/31/2023] [Indexed: 06/18/2023]
Abstract
Blackleg and aerial stem rot of potato (Solanum tuberosum L.), caused by soft rot enterobacteria of the genera Pectobacterium and Dickeya, has recently increased years in Hebei Province, China. Field surveys were performed during the 2021 potato growing season in Hebei to identify and characterize bacterial pathogens. Sixteen potato plants showing blackleg or aerial stem rot were collected from three potato-producing areas, and ten representative pectinolytic bacteria were isolated from symptomatic plants. 16S rDNA sequencing and multilocus sequence analysis were performed to determine the taxonomic position of the bacterial isolates. The isolates belonged to the genus Pectobacterium, including Pectobacterium atrosepticum, Pectobacterium carotovorum, Pectobacterium brasiliense, and Pectobacterium parmentieri. The exceptions were isolates BY21311 and BY21312, which belonged to a new species of Pectobacterium polonicum previously found in groundwater. The taxonomy of isolate BY21311 was confirmed using whole genome-based analysis. P. polonicum has only been identified in potato plants on one farm in Baoding region in China. Isolates BY21311 and BY21312 displayed similar physiological and biochemical traits to the type strain DPMP315T. Artificial inoculation assays revealed that isolate BY21311 fulfilled Koch's postulates for potato blackleg. These findings represent the first time P. polonicum, a water-associated Pectobacterium species may be the cause of blackleg in the field. Interestingly, P. polonicum BY21311 has reduced ability to macerate potato tubers when compared to P. atrosepticum, P. brasiliense, P. versatile, and P. parvum, which is more virulent in tubers than the type strain DPMP315T. The host range of isolate BY21311 was determined by injection method, which can impregnate five plants. Although the genome of isolate BY21311 harbors gene clusters encoding a type III secretion system, it did not elicit a hypersensitive response (HR) in Nicotiana benthamiana or N. tabacum leaves. T3SS effector AvrE and T4SS effector PilN were obtained by predicting isolate BY21311 genome. P. polonicum appears to show significant variations in gene content between two genomes, and gene content varies between isolates BY21311 and DPMP315T, with strain specific-genes involved in many aspects, including lipopolysaccharide biosynthesis, substrate translocation, T4SS and T6SS among others, suggesting that isolates BY21311 and DPMP315T might represent distinct clades within the species.
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Affiliation(s)
- Wanxin Han
- College of Plant Protection, Hebei Agricultural University, Baoding, China
| | - Jinhui Wang
- College of Plant Protection, Hebei Agricultural University, Baoding, China
| | - Minna Pirhonen
- Department of Agricultural Sciences, University of Helsinki, Helsinki, Finland
| | - Yang Pan
- College of Plant Protection, Hebei Agricultural University, Baoding, China
| | - Jingxin Qin
- College of Plant Protection, Hebei Agricultural University, Baoding, China
| | - Shangqing Zhang
- Institute of Plant Protection, Tangshan Academy of Agricultural Sciences, Tangshan, China
| | - Jiehua Zhu
- College of Plant Protection, Hebei Agricultural University, Baoding, China
| | - Zhihui Yang
- College of Plant Protection, Hebei Agricultural University, Baoding, China
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Kowalczyk A, Szpakowska N, Babinska W, Motyka-Pomagruk A, Sledz W, Lojkowska E, Kaczyński Z. The structure of an abequose - containing O-polysaccharide isolated from Pectobacterium aquaticum IFB5637. Carbohydr Res 2022; 522:108696. [DOI: 10.1016/j.carres.2022.108696] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Revised: 09/25/2022] [Accepted: 09/27/2022] [Indexed: 11/02/2022]
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Ben Moussa H, Bertrand C, Rochelle-Newall E, Fiorini S, Pédron J, Barny MA. The Diversity and Abundance of Soft Rot Pectobacteriaceae Along the Durance River Stream in the Southeast of France Revealed by Multiple Seasonal Surveys. PHYTOPATHOLOGY 2022; 112:1676-1685. [PMID: 35224981 DOI: 10.1094/phyto-12-21-0515-r] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Although irrigation water is frequently assessed for the presence of plant pathogens, large spatial and temporal surveys that provide clues on the diversity and circulation of pathogens are missing. We evaluate the diversity of soft rot Pectobacteriaceae (SRP) of the genera Dickeya and Pectobacterium over 2 years in a temperate, mixed-use watershed. The abundance of isolated strains correlates with the agricultural gradient along the watershed with a positive correlation found with temperature, nitrate, and dissolved organic carbon water concentration. We characterized 582 strains by amplification and sequencing of the gapA gene. Multilocus sequence analysis, performed with three housekeeping genes for 99 strains, and core genome analysis of 38 sequenced strains, confirmed for all the strains but one, the taxonomic assignation obtained with the sole gapA sequence. Pectobacterium spp. (549 isolates) were far more abundant than Dickeya spp. (33 isolates). Dickeya spp. were only observed in the lower part of the river when water temperature was >19°C, and we experimentally confirmed a decreased fitness of several Dickeya spp. at 8°C in river water. D. oryzae dominates the Dickeya spp. and P. versatile and P. aquaticum dominate the Pectobacterium spp., but their repartition along the watershed was different, with P. versatile being the only species regularly recovered all along the watershed. Excepting P. versatile, the Dickeya and Pectobacterium spp. responsible for disease outbreak on crops were less abundant or rarely detected. This work sheds light on the various ecological behaviors of different SRP types in stream water and indicates that SRP occupation is geographically structured.
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Affiliation(s)
- Hajar Ben Moussa
- Sorbonne Université, Institut National de Recherche pour l'Agriculture, l'alimentation et l'Environnement, Institut de Recherche pour le Développement, Centre National de la Recherche Scientifique, Université Paris-Est Créteil, Institut d'Ecologie et des Sciences de l'Environnement de Paris, UMR 7618, F-75252 Paris, France
| | - Claire Bertrand
- Sorbonne Université, Institut National de Recherche pour l'Agriculture, l'alimentation et l'Environnement, Institut de Recherche pour le Développement, Centre National de la Recherche Scientifique, Université Paris-Est Créteil, Institut d'Ecologie et des Sciences de l'Environnement de Paris, UMR 7618, F-75252 Paris, France
| | - Emma Rochelle-Newall
- Sorbonne Université, Institut National de Recherche pour l'Agriculture, l'alimentation et l'Environnement, Institut de Recherche pour le Développement, Centre National de la Recherche Scientifique, Université Paris-Est Créteil, Institut d'Ecologie et des Sciences de l'Environnement de Paris, UMR 7618, F-75252 Paris, France
| | - Sarah Fiorini
- Ecole Normale Supérieure, Centre National de la Recherche Scientifique, Centre de Recherche en Écologie Expérimentale et Prédictive, Paris Sciences & Lettres Research University, UMS 3194, 77140 Saint-Pierre-lès-Nemours, France
| | - Jacques Pédron
- Sorbonne Université, Institut National de Recherche pour l'Agriculture, l'alimentation et l'Environnement, Institut de Recherche pour le Développement, Centre National de la Recherche Scientifique, Université Paris-Est Créteil, Institut d'Ecologie et des Sciences de l'Environnement de Paris, UMR 7618, F-75252 Paris, France
| | - Marie-Anne Barny
- Sorbonne Université, Institut National de Recherche pour l'Agriculture, l'alimentation et l'Environnement, Institut de Recherche pour le Développement, Centre National de la Recherche Scientifique, Université Paris-Est Créteil, Institut d'Ecologie et des Sciences de l'Environnement de Paris, UMR 7618, F-75252 Paris, France
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