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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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Tang WC, Wang LH, Chan JJ, Goh RP, Wu YF, Chu CC. Inter- and Intra-Specific Variations in Phenotypic Traits of Pectobacterium Strains Isolated from Diverse Eudicots and Monocots in Taiwan. PLANT DISEASE 2024; 108:2410-2421. [PMID: 38506909 DOI: 10.1094/pdis-10-23-2130-re] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/21/2024]
Abstract
Pectobacterium spp. are phytopathogenic bacteria whose phylogeny has been continuously revised throughout the years. Previous studies on Pectobacterium's phenotypic diversity often analyzed strains obtained from specific crops or adopted outdated Pectobacterium classification systems. Therefore, a current perspective on trait variations in Pectobacterium species or strains infecting more diverse plant species is limited. This study conducted phylogenetic and phenotypic analyses on strains isolated from eight eudicot and four monocot families in Taiwan. Phylogenetic analysis on 78 strains identified six recognized species, namely, P. brasiliense, P. aroidearum, P. actinidiae, P. colocasium, P. carotovorum, and P. versatile. Among these, the first two were the most predominant species. Patterns suggesting varying host preferences among bacterial species were detected; most P. aroidearum strains were isolated from monocots, whereas P. brasiliense and P. actinidiae tended to exhibit preferences for eudicots. Physiological tests and Biolog analyses conducted on representative strains of each species revealed great within-species phenotypic variations. Despite these strain-level variations, a combination of indole production and phosphatase activity tests was capable of distinguishing all representative strains of P. brasiliense from those of other identified species. Inoculation assays on potato, bok choy, calla lily, and onion showed inter- and intra-specific heterogeneities in the tested strains' maceration potentials. Virulence patterns across Pectobacterium species and strains differed depending on the inoculated host. Altogether, the findings from this work expand the understanding of Pectobacterium's phenotypic diversity and provide implications for pathogen identification and management.
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Affiliation(s)
- Wen-Chien Tang
- Department of Plant Pathology, National Chung Hsing University, Taichung City 40227, Taiwan
| | - Liang-Hsuan Wang
- Department of Plant Pathology, National Chung Hsing University, Taichung City 40227, Taiwan
| | - Jiun-Jie Chan
- Department of Plant Pathology, National Chung Hsing University, Taichung City 40227, Taiwan
| | - Reun-Ping Goh
- Department of Plant Pathology, National Chung Hsing University, Taichung City 40227, Taiwan
| | - Yea-Fang Wu
- Tainan District Agricultural Research and Extension Station, Ministry of Agriculture, Tainan 71246, Taiwan
| | - Chia-Ching Chu
- Department of Plant Pathology, National Chung Hsing University, Taichung City 40227, Taiwan
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Hugouvieux-Cotte-Pattat N, Flandrois JP, Briolay J, Reverchon S, Brochier-Armanet C. Description of a new genus of the Pectobacteriaceae family isolated from water in coastal brackish wetlands of the French Camargue region, Prodigiosinella gen. nov., including the new species Prodigiosinella aquatilis sp. nov. Syst Appl Microbiol 2024; 47:126497. [PMID: 38402653 DOI: 10.1016/j.syapm.2024.126497] [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: 11/06/2023] [Revised: 02/14/2024] [Accepted: 02/15/2024] [Indexed: 02/27/2024]
Abstract
The Pectobacteriaceae family comprises plant pathogens able to provoke diverse diseases, including plant maceration due to the production of pectinases disrupting the plant cell wall. To better understand their diversity, a survey of pectinolytic bacteria was performed in brackish lakes of the French region La Camargue near the Mediterranean Sea. The genome of six atypical isolates was sequenced; their size is around 4.8 to 5.0 Mb, including a plasmid of 59 to 61 kb; their G+C values range from 49.1 to 49.3 mol%. Phylogenetic analyses indicated that the novel strains form a new clade of Pectobacteriaceae that branches at the basis of the group encompassing the genera Lonsdalea, Musicola, and Dickeya. Based on phenotypic, genomic and phylogenetic characteristics, we propose the creation of a new genus with the name Prodigiosinella gen. nov. Both the phenotypic and phylogenetic analyses separated the strains into two distinct subgroups, G1 and G2. The type strain LS101T (CFBP 8826T = LMG 32072T) and strain CE70 (CFBP 9054 = LMG 32867) are representative G1 and G2 members, respectively. Three genomic methods were used to analyze DNA-DNA relatedness: digital DNA-DNA hybridization (isDDH), average nucleotide identity (ANI), and genome alignment fraction (AF). They revealed a close relationship between genomes of the two groups, supporting their appurtenance to a same species for which we propose the name Prodigiosinella aquatilis sp. nov. Four strains previously designated as Serratia sp. (ATCC 39006), Brenneria "ulupoensis" (K61) or Erwinia sp. (MK01 and MK09) belong to the new genus Prodigiosinella.
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Affiliation(s)
- Nicole Hugouvieux-Cotte-Pattat
- Université de Lyon, CNRS UMR 5240, INSA de Lyon, Université Claude Bernard Lyon 1, Microbiologie Adaptation et Pathogénie, F-69621 Villeurbanne, France.
| | - Jean-Pierre Flandrois
- Université Claude Bernard Lyon 1, LBBE, UMR 5558, CNRS, VAS, Villeurbanne F-69621, France.
| | - Jérôme Briolay
- Université Claude Bernard Lyon 1, CNRS FR 3728 BioEEnViS, plateforme DTAMB, F-69621 Villeurbanne, France.
| | - Sylvie Reverchon
- Université de Lyon, CNRS UMR 5240, INSA de Lyon, Université Claude Bernard Lyon 1, Microbiologie Adaptation et Pathogénie, F-69621 Villeurbanne, France.
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Sawada H, Someya N, Morohoshi T, Ono M, Satou M. Pectobacterium araliae sp. nov., a pathogen causing bacterial soft rot of Japanese angelica tree in Japan. Int J Syst Evol Microbiol 2024; 74. [PMID: 38625720 DOI: 10.1099/ijsem.0.006326] [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] [Indexed: 04/17/2024] Open
Abstract
Phytopathogenic bacteria (MAFF 302110T and MAFF 302107) were isolated from lesions on Japanese angelica trees affected by bacterial soft rot in Yamanashi Prefecture, Japan. The strains were Gram-reaction-negative, facultatively anaerobic, motile with peritrichous flagella, rod-shaped, and non-spore-forming. The genomic DNA G+C content was 51.1 mol % and the predominant cellular fatty acids included summed feature 3 (C16 : 1 ω7c and/or C16 : 1 ω6c), C16 : 0, summed feature 8 (C18 : 1 ω7c and/or C18 : 1 ω6c), summed feature 2 (comprising any combination of C12 : 0 aldehyde, an unknown fatty acid with an equivalent chain length of 10.928, C16 : 1 iso I, and C14 : 0 3OH), and C12 : 0. Phylogenetic analyses based on 16S rRNA and gyrB gene sequences, along with phylogenomic analysis utilizing whole-genome sequences, consistently placed these strains within the genus Pectobacterium. However, their phylogenetic positions did not align with any known species within the genus. Comparative studies involving average nucleotide identity and digital DNA-DNA hybridization with the closely related species indicated values below the thresholds employed for the prokaryotic species delineation (95-96 % and 70 %, respectively), with the highest values observed for Pectobacterium polonicum DPMP315T (92.10 and 47.1 %, respectively). Phenotypic characteristics, cellular fatty acid composition, and a repertoire of secretion systems could differentiate the strains from their closest relatives. The phenotypic, chemotaxonomic, and genotypic data obtained in this study show that MAFF 302110T/MAFF 302107 represent a novel species of the genus Pectobacterium, for which we propose the name Pectobacterium araliae sp. nov., designating MAFF 302110T (=ICMP 25161T) as the type strain.
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Affiliation(s)
- Hiroyuki Sawada
- Research Center of Genetic Resources, National Agriculture and Food Research Organization (NARO), 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602, Japan
| | - Nobutaka Someya
- Institute for Plant Protection, NARO, 2-1-18 Kannondai, Tsukuba, Ibaraki 305-8666, Japan
| | - Tomohiro Morohoshi
- Graduate School of Regional Development and Creativity, Utsunomiya University, 7-1-2 Yoto, Utsunomiya, Tochigi 321-8585, Japan
| | - Mitsuaki Ono
- Yamanashi Agritechnology Center (retired), 1100 Shimoimai, Kai, Yamanashi 400-0105, Japan
| | - Mamoru Satou
- Research Center of Genetic Resources, National Agriculture and Food Research Organization (NARO), 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602, Japan
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Mainello-Land AM, Bibi S, Gugino B, Bull CT. Multilocus sequence and phenotypic analysis of Pectobacterium and Dickeya type strains for identification of soft rot Pectobacteriaceae from symptomatic potato stems and tubers in Pennsylvania. Syst Appl Microbiol 2024; 47:126476. [PMID: 38113702 DOI: 10.1016/j.syapm.2023.126476] [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: 09/08/2023] [Revised: 11/13/2023] [Accepted: 11/24/2023] [Indexed: 12/21/2023]
Abstract
Outbreaks of potato blackleg and soft rot caused by Pectobacterium species and more recently Dickeya species across the U.S. mid-Atlantic region have caused yield loss due to poor emergence as well as losses from stem and tuber rot. To develop management strategies for soft rot diseases, we must first identify which members of the soft rot Pectobacteriaceae are present in regional potato plantings. However, the rapidly expanding number of soft rot Pectobacteriaceae species and the lack of readily available comparative data for type strains of Pectobacterium and Dickeya hinder quick identification. This manuscript provides a comparative analysis of soft rot Pectobacteriaceae and a comprehensive comparison of type strains from this group using rep-PCR, MLSA and 16S sequence analysis, as well as phenotypic and physiological analyses using Biolog GEN III plates. These data were used to identify isolates cultured from symptomatic potato stems collected between 2016 and 2018. The isolates were characterized for phenotypic traits and by sequence analysis to identify the bacteria from potatoes with blackleg and soft rot symptoms in Pennsylvania potato fields. In this survey, P. actinidiae, P. brasiliense, P. polonicum, P. polaris, P. punjabense, P. parmentieri, and P. versatile were identified from Pennsylvania for the first time. Importantly, the presence of P. actinidiae in Pennsylvania represents the first report of this organism in the U.S. As expected, P. carotorvorum and D. dianthicola were also isolated. In addition to a resource for future work studying the Dickeya and Pectobacterium associated with potato blackleg and soft rot, we provide recommendations for future surveys to monitor for quarantine or emerging soft rot Pectobacteriace regionally.
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Affiliation(s)
- Amanda M Mainello-Land
- Department of Plant Pathology and Environmental Microbiology, The Pennsylvania State University, University Park, PA 16802, USA
| | - Shaheen Bibi
- Department of Plant Pathology and Environmental Microbiology, The Pennsylvania State University, University Park, PA 16802, USA
| | - Beth Gugino
- Department of Plant Pathology and Environmental Microbiology, The Pennsylvania State University, University Park, PA 16802, USA
| | - Carolee T Bull
- Department of Plant Pathology and Environmental Microbiology, The Pennsylvania State University, University Park, PA 16802, USA; Department of Plant and Soil Sciences, Faculty of Natural and Agricultural Sciences, University of Pretoria, Pretoria, South Africa.
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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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Aleid GM, Alshammari AS, Alomari AD, Ahmad A, Alaysuy O, Ibrahim MNM. Biomass and domestic waste: a potential resource combination for bioenergy generation and water treatment via benthic microbial fuel cell. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023:10.1007/s11356-023-29430-8. [PMID: 37632620 DOI: 10.1007/s11356-023-29430-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Accepted: 08/17/2023] [Indexed: 08/28/2023]
Abstract
The benthic microbial fuel cell (BMFC) is one of the most efficient types of bioelectrochemical fuel cell systems. Modern bioelectrochemical fuel cells have several drawbacks, including an unstable organic substrate and a microorganism-unfriendly atmosphere. The recent literature to encounter such issues is one of the emerging talks. Researchers are focusing on the utilization of biomass and waste to encounter such challenges and make the technique more feasible at the pilot scale. This study investigated the combination of local bakery waste as an organic substrate with lignocellulosic biomass material. The whole experiment was conducted for 45 days. At an external resistance of 1000 ῼ and an internal resistance of 677 ῼ, the power density was found to be 3.51 mW/m2. Similarly, for Pb2+, Cd2+, Cr3+, Ni2+, and Co2+, the degradation efficiency was 84.40%, 81.21%, 80%, 89.50%, and 86.0%, respectively. The bacterial identification results showed that Liquorilactobacillus nagelii, Proteus mirabilis, Pectobacterium punjabense, and Xenorhabdus thuongxuanensis are the most prominent species found on anode biofilm. The method of electron generation in this study, which includes the degradation of metal ions, is also well described. Lastly, optimising the parameters showed that pH 7 provides a feasible environment for operation. A few future suggestions for practical steps are enclosed for the research community.
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Affiliation(s)
- Ghada Mohamed Aleid
- Department, Preparatory Year College, University of Ha'il, Hail, Saudi Arabia
| | - Anoud Saud Alshammari
- Department of Physics and Chemistry, Northern Border University, Rafha, Saudi Arabia
| | - Asma D Alomari
- Chemistry Department, Al-Qunfudah University College, Umm Al-Qura University, 1109, Al-7 Qunfudah, Saudi Arabia
| | - Akil Ahmad
- Department of Chemistry, College of Science and Humanities in Al-Kharj, Prince Sattam Bin Abdulaziz University, 11942, Al-Kharj, Saudi Arabia.
| | - Omaymah Alaysuy
- Department of Chemistry, College of Science, University of Tabuk, 71474, Tabuk, Saudi Arabia
| | - Mohamad Nasir Mohamad Ibrahim
- Materials Technology Research Group (MaTRec), School of Chemical Sciences, Universiti Sains Malaysia, 11800, Penang, Malaysia
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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: 2] [Impact Index Per Article: 2.0] [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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Loc M, Milošević D, Ivanović Ž, Ignjatov M, Budakov D, Grahovac J, Grahovac M. Genetic Diversity of Pectobacterium spp. on Potato in Serbia. Microorganisms 2022; 10:microorganisms10091840. [PMID: 36144442 PMCID: PMC9503840 DOI: 10.3390/microorganisms10091840] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Revised: 08/28/2022] [Accepted: 09/07/2022] [Indexed: 11/17/2022] Open
Abstract
Pectobacterium is a diverse genus which comprises of multiple destructive bacterial species which cause soft rot/blackleg/wilt disease complex in a wide variety of crops by employing high levels of virulence factors. During the 2018, 2019 and 2020 potato growing seasons, numerous outbreaks of bacterial wilt, stem blackleg and tuber soft rot were recorded, and symptomatic plant samples from ten localities in the Province of Vojvodina (Serbia) were collected and analysed. Bacterial soft-rot pathogens were detected in 63 samples using genus and species-specific primers. Through 16S rRNA Sanger sequencing of 19 representative isolates, the identity of P. brasiliense (73.7%), P. punjabense (15.8%), and P. carotovorum (10.5%) species were revealed. To further validate the identification, genotypic profiling of Pectobacterium strains using rep-PCR (ERIC, BOX, REP) was conducted for 25 selected isolates and the phylogenetic assessment based on four selected housekeeping genes (gyrA, recA, rpoA, and rpoS). Physiological and biochemical properties were analysed using basic microbiological tests and VITEK® 2 GN card, and pathogenicity was confirmed on cv. VR808 and cv. Desiree potato tubers and plants. This study confirmed the distinctiveness of the newly described P. punjabense in Serbia as well as the high diversity of Pectobacterium brasiliense and Pectobacterium carotovorum species in Serbia.
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Affiliation(s)
- Marta Loc
- Department of Plant and Environmental Protection, Faculty of Agriculture, University of Novi Sad, Trg Dositeja Obradovića 8, 21000 Novi Sad, Serbia
| | - Dragana Milošević
- Laboratory for Seed Testing, Institute of Field and Vegetable Crops, Maksima Gorkog 30, 21101 Novi Sad, Serbia
| | - Žarko Ivanović
- Department of Plant Diseases, Institute for Plant Protection and Environment, Teodora Drajzera 9, 11040 Belgrade, Serbia
| | - Maja Ignjatov
- Laboratory for Seed Testing, Institute of Field and Vegetable Crops, Maksima Gorkog 30, 21101 Novi Sad, Serbia
| | - Dragana Budakov
- Department of Plant and Environmental Protection, Faculty of Agriculture, University of Novi Sad, Trg Dositeja Obradovića 8, 21000 Novi Sad, Serbia
| | - Jovana Grahovac
- Department of Biotechnology and Pharmaceutical Engineering, Faculty of Technology, University of Novi Sad, Bulevar cara Lazara 1, 21102 Novi Sad, Serbia
| | - Mila Grahovac
- Department of Plant and Environmental Protection, Faculty of Agriculture, University of Novi Sad, Trg Dositeja Obradovića 8, 21000 Novi Sad, Serbia
- Correspondence:
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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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11
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Smoktunowicz M, Jonca J, Stachowska A, May M, Waleron MM, Waleron M, Waleron K. The International Trade of Ware Vegetables and Orna-Mental Plants—An Underestimated Risk of Accelerated Spreading of Phytopathogenic Bacteria in the Era of Globalisation and Ongoing Climatic Changes. Pathogens 2022; 11:pathogens11070728. [PMID: 35889973 PMCID: PMC9319320 DOI: 10.3390/pathogens11070728] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Revised: 06/18/2022] [Accepted: 06/22/2022] [Indexed: 11/17/2022] Open
Abstract
Bacteria of the genus Pectobacterium are globally occurring pathogens that infect a broad spectrum of plants. The plant cell wall degrading enzymes allow them to cause diseases like soft rot and blackleg. Worldwide trade and exchange of plant material together with the accompanying microorganisms contributed to the rapid spread and consequently the acquisition of new traits by bacteria. The 161 pectinolytic strains were isolated from symptomless vegetables and ornamental plants acquired from Polish and foreign local food markets. All strains except four Dickeya isolates were identified as belonging to the Pectobacterium genus by PCR with species-specific primers and recA gene sequencing. The newly isolated bacteria were assigned to eight species, P. versatile (50 strains), P. carotovorum (33), P. brasiliense (27), P. atrosepticum (19), P. parmentieri (12), P. polaris (11), P. parvum (3) and P. odoriferum (2). ERIC PCR and phenotypic characteristics revealed high heterogeneity among P. carotovorum, P. brasiliense and P. versatile isolates. Moreover, a subset of the newly isolated strains was characterised by high tolerance to changing environmental conditions such as salinity, pH and water availability. These bacteria can effectively macerate the tissues of various plants, including potato, chicory and orchid. Our results indicate that Pectobacterium strains isolated from internationally traded, symptomless vegetables and ornamental plants have high potential for adaptation to adverse environmental conditions and to infect various host plants. These features may contribute to the success of the genus Pectobacterium in spreading between different climatic zones and facilitate the colonisation of different ecological niches.
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Affiliation(s)
- Magdalena Smoktunowicz
- Department of Pharmaceutical Microbiology, Faculty of Pharmacy, Medical University of Gdansk, 80-416 Gdansk, Poland;
| | - Joanna Jonca
- Laboratory of Plant Protection and Biotechnology, Intercollegiate Faculty of Biotechnology of the University of Gdansk and the Medical University of Gdansk, 80-307 Gdansk, Poland; (J.J.); (A.S.); (M.M.); (M.M.W.)
| | - Aneta Stachowska
- Laboratory of Plant Protection and Biotechnology, Intercollegiate Faculty of Biotechnology of the University of Gdansk and the Medical University of Gdansk, 80-307 Gdansk, Poland; (J.J.); (A.S.); (M.M.); (M.M.W.)
| | - Michal May
- Laboratory of Plant Protection and Biotechnology, Intercollegiate Faculty of Biotechnology of the University of Gdansk and the Medical University of Gdansk, 80-307 Gdansk, Poland; (J.J.); (A.S.); (M.M.); (M.M.W.)
| | - Michal Mateusz Waleron
- Laboratory of Plant Protection and Biotechnology, Intercollegiate Faculty of Biotechnology of the University of Gdansk and the Medical University of Gdansk, 80-307 Gdansk, Poland; (J.J.); (A.S.); (M.M.); (M.M.W.)
| | - Malgorzata Waleron
- Laboratory of Plant Protection and Biotechnology, Intercollegiate Faculty of Biotechnology of the University of Gdansk and the Medical University of Gdansk, 80-307 Gdansk, Poland; (J.J.); (A.S.); (M.M.); (M.M.W.)
- Correspondence: (M.W.); (K.W.)
| | - Krzysztof Waleron
- Department of Pharmaceutical Microbiology, Faculty of Pharmacy, Medical University of Gdansk, 80-416 Gdansk, Poland;
- Correspondence: (M.W.); (K.W.)
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12
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Insights into complex infection by two Pectobacterium species causing potato blackleg and soft rot. Microbiol Res 2022; 261:127072. [DOI: 10.1016/j.micres.2022.127072] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 04/02/2022] [Accepted: 05/11/2022] [Indexed: 11/19/2022]
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13
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Arizala D, Dobhal S, Babler B, Crockford AB, Rioux RA, Alvarez AM, Arif M. Development of a multiplex TaqMan qPCR targeting unique genomic regions for the specific and sensitive detection of Pectobacterium species and P. parmentieri. J Appl Microbiol 2022; 132:3089-3110. [PMID: 35026058 DOI: 10.1111/jam.15447] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Revised: 12/13/2021] [Accepted: 01/06/2022] [Indexed: 11/26/2022]
Abstract
AIM The newly defined species P. parmentieri has emerged as an aggressive pathogen that causes soft rot and blackleg diseases on potato and has been widely disseminated across the globe, jeopardizing the productivity and potato food safety. The implementation of a fast and accurate detection tool is imperative to control, monitor and prevent further spread of these pathogens. The objective of this work was to develop a specific and sensitive multiplex TaqMan qPCR to detect P. parmentieri and distinguish it from all known Pectobacterium species. A universal internal control (UIC) was included to enhance the reliability of the assay. METHODS AND RESULTS A comparative genomics approach was used to identify O-acetyltransferase and the XRE family transcriptional regulator as specific targets for primers/probe design for the detection of the Pectobacterium genus and P. parmentieri, respectively. Specificity was assessed with 35 and 25 strains included inclusivity and exclusivity panels, respectively, isolated from different geographic locations and sources. The assay specifically detected all 35 strains of Pectobacterium sp. and all 15 P. parmentieri strains. No cross-reactivity was detected during assay validation. Our assay detected up to 10 fg genomic DNA and 1 CFU ml-1 bacterial culture. No change in the detection threshold (1 CFU ml-1 ) was observed in spiked assays after adding host tissue to the reactions. The assay was validated with naturally and artificially infected host tissues and soil rhizosphere samples. All infected plant samples containing the target pathogens were accurately amplified. CONCLUSION The presented multiplex TaqMan qPCR diagnostic assay is highly specific, sensitive, reliable for the detection of Pectobacterium species and P. parmentieri with no false positives or false negatives. SIGNIFICANCE AND IMPACT The developed assay can be adopted for multiple purposes such as seed certification programs, surveillance, biosecurity, microbial forensics, quarantine, border protection, inspections, and epidemiology.
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Affiliation(s)
- Dario Arizala
- Department of Plant and Environmental Protection Sciences, University of Hawaii at Manoa, Honolulu
| | - Shefali Dobhal
- Department of Plant and Environmental Protection Sciences, University of Hawaii at Manoa, Honolulu
| | - Brooke Babler
- Department of Plant Pathology, University of Wisconsin-Madison
| | | | - Renee A Rioux
- Department of Plant Pathology, University of Wisconsin-Madison
| | - Anne M Alvarez
- Department of Plant and Environmental Protection Sciences, University of Hawaii at Manoa, Honolulu
| | - Mohammad Arif
- Department of Plant and Environmental Protection Sciences, University of Hawaii at Manoa, Honolulu
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14
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Ben Moussa H, Pédron J, Bertrand C, Hecquet A, Barny MA. Pectobacterium quasiaquaticum sp. nov., isolated from waterways. Int J Syst Evol Microbiol 2021; 71. [PMID: 34633924 DOI: 10.1099/ijsem.0.005042] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Through this study, we established the taxonomic status of seven strains belonging to the genus Pectobacterium (A477-S1-J17T, A398-S21-F17, A535-S3-A17, A411-S4-F17, A113-S21-F16, FL63-S17 and FL60-S17) collected from four different river streams and an artificial lake in south-east France between 2016 and 2017. Ecological surveys in rivers and lakes pointed out different repartition of strains belonging to this clade compared to the closest species, Pectobacterium aquaticum. The main phenotypic difference observed between these strains and the P. aquaticum type strain was strongly impaired growth with rhamnose as the sole carbon source. This correlates with three different forms of pseudogenization of the l-rhamnose/proton symporter gene rhaT in the genomes of strains belonging to this clade. Phylogenetic analysis using gapA gene sequences and multi locus sequence analysis of the core genome showed that these strains formed a distinct clade within the genus Pectobacterium closely related to P. aquaticum. Digital DNA-DNA hybridization (dDDH) and average nucleotide identity (ANI) values showed a clear discontinuity between the new clade and P. aquaticum. However, the calculated values are potentially consistent with either splitting or merging of this new clade with P. aquaticum. In support of the split, ANI coverages were higher within this new clade than between this new clade and P. aquaticum. The split is also consistent with the range of observed ANI or dDDH values that currently separate several accepted species within the genus Pectobacterium. On the basis of these data,strains A477-S1-J17T, A398-S21-F17, A535-S3-A17, A411-S4-F17, A113-S21-F16, FL63-S17 and FL60-S17 represent a novel species of the genus Pectobacterium, for which the name Pectobacterium quasiaquaticum sp. nov. is proposed. The type strain is A477-S1-J17T (=CFBP 8805T=LMG 32181T).
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Affiliation(s)
- Hajar Ben Moussa
- Sorbonne Université, INRAE, Institute of Ecology and Environmental Sciences-Paris, 4 place 7 Jussieu, F-75 252 Paris, France
| | - Jacques Pédron
- Sorbonne Université, INRAE, Institute of Ecology and Environmental Sciences-Paris, 4 place 7 Jussieu, F-75 252 Paris, France
| | - Claire Bertrand
- Sorbonne Université, INRAE, Institute of Ecology and Environmental Sciences-Paris, 4 place 7 Jussieu, F-75 252 Paris, France
| | - Amandine Hecquet
- Sorbonne Université, INRAE, Institute of Ecology and Environmental Sciences-Paris, 4 place 7 Jussieu, F-75 252 Paris, France
| | - Marie-Anne Barny
- Sorbonne Université, INRAE, Institute of Ecology and Environmental Sciences-Paris, 4 place 7 Jussieu, F-75 252 Paris, France
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15
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Quantitative Real-Time PCR Assay for the Detection of Pectobacterium parmentieri, a Causal Agent of Potato Soft Rot. PLANTS 2021; 10:plants10091880. [PMID: 34579412 PMCID: PMC8468878 DOI: 10.3390/plants10091880] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Accepted: 09/08/2021] [Indexed: 11/17/2022]
Abstract
Pectobacterium parmentieri is a plant-pathogenic bacterium, recently attributed as a separate species, which infects potatoes, causing soft rot in tubers. The distribution of P. parmentieri seems to be global, although the bacterium tends to be accommodated to moderate climates. Fast and accurate detection systems for this pathogen are needed to study its biology and to identify latent infection in potatoes and other plant hosts. The current paper reports on the development of a specific and sensitive detection protocol based on a real-time PCR with a TaqMan probe for P. parmentieri, and its evaluation. In sensitivity assays, the detection threshold of this protocol was 102 cfu/mL on pure bacterial cultures and 102–103 cfu/mL on plant material. The specificity of the protocol was evaluated against P. parmentieri and more than 100 strains of potato-associated species of Pectobacterium and Dickeya. No cross-reaction with the non-target bacterial species, or loss of sensitivity, was observed. This specific and sensitive diagnostic tool may reveal a wider distribution and host range for P. parmentieri and will expand knowledge of the life cycle and environmental preferences of this pathogen.
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16
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Species of Dickeya and Pectobacterium Isolated during an Outbreak of Blackleg and Soft Rot of Potato in Northeastern and North Central United States. Microorganisms 2021; 9:microorganisms9081733. [PMID: 34442812 PMCID: PMC8401272 DOI: 10.3390/microorganisms9081733] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Revised: 08/09/2021] [Accepted: 08/11/2021] [Indexed: 12/04/2022] Open
Abstract
An outbreak of bacterial soft rot and blackleg of potato has occurred since 2014 with the epicenter being in the northeastern region of the United States. Multiple species of Pectobacterium and Dickeya are causal agents, resulting in losses to commercial and seed potato production over the past decade in the Northeastern and North Central United States. To clarify the pathogen present at the outset of the epidemic in 2015 and 2016, a phylogenetic study was made of 121 pectolytic soft rot bacteria isolated from symptomatic potato; also included were 27 type strains of Dickeya and Pectobacterium species, and 47 historic reference strains. Phylogenetic trees constructed based on multilocus sequence alignments of concatenated dnaJ, dnaX and gyrB fragments revealed the epidemic isolates to cluster with type strains of D. chrysanthemi, D. dianthicola, D. dadantii, P. atrosepticum, P. brasiliense, P. carotovorum, P. parmentieri, P. polaris, P. punjabense, and P. versatile. Genetic diversity within D. dianthicola strains was low, with one sequence type (ST1) identified in 17 of 19 strains. Pectobacterium parmentieri was more diverse, with ten sequence types detected among 37 of the 2015–2016 strains. This study can aid in monitoring future shifts in potato soft rot pathogens within the U.S. and inform strategies for disease management.
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17
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Genome-Wide Analyses of the Temperature-Responsive Genetic Loci of the Pectinolytic Plant Pathogenic Pectobacterium atrosepticum. Int J Mol Sci 2021; 22:ijms22094839. [PMID: 34063632 PMCID: PMC8125463 DOI: 10.3390/ijms22094839] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 04/23/2021] [Accepted: 04/27/2021] [Indexed: 12/12/2022] Open
Abstract
Temperature is one of the critical factors affecting gene expression in bacteria. Despite the general interest in the link between bacterial phenotypes and environmental temperature, little is known about temperature-dependent gene expression in plant pathogenic Pectobacterium atrosepticum, a causative agent of potato blackleg and tuber soft rot worldwide. In this study, twenty-nine P. atrosepticum SCRI1043 thermoregulated genes were identified using Tn5-based transposon mutagenesis coupled with an inducible promotorless gusA gene as a reporter. From the pool of 29 genes, 14 were up-regulated at 18 °C, whereas 15 other genes were up-regulated at 28 °C. Among the thermoregulated loci, genes involved in primary bacterial metabolism, membrane-related proteins, fitness-corresponding factors, and several hypothetical proteins were found. The Tn5 mutants were tested for their pathogenicity in planta and for features that are likely to remain important for the pathogen to succeed in the (plant) environment. Five Tn5 mutants expressed visible phenotypes differentiating these mutants from the phenotype of the SCRI1043 wild-type strain. The gene disruptions in the Tn5 transposon mutants caused alterations in bacterial generation time, ability to form a biofilm, production of lipopolysaccharides, and virulence on potato tuber slices. The consequences of environmental temperature on the ability of P. atrosepticum to cause disease symptoms in potato are discussed.
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18
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Lu Q, Yan F, Liu Y, Li Q, Yang M, Liu P. Comparative Genomic Analyses Reveal Functional Insights Into Key Determinants of the Pathogenesis of Pectobacterium actinidiae in Kiwifruit. PHYTOPATHOLOGY 2021; 111:789-798. [PMID: 33245255 DOI: 10.1094/phyto-07-20-0287-r] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
The Gram-negative bacterial species Pectobacterium actinidiae causes summer canker in kiwifruit plants. However, little is known about its virulence factors and mechanisms of genetic adaptation. We aimed to identify the key determinants that control the virulence of P. actinidiae in kiwifruit by genomic and functional analyses. Analysis of four P. actinidiae isolates indicated low genetic variability with an average of 98.7% genome-level sequence similarity and 82% shared protein-coding gene content. Phylogenetic analysis, based on both bulk single nucleotide polymorphisms (SNPs) and single-copy genes, revealed that P. actinidiae strains cluster into a single clade, which is closely related to the clades of P. odoriferum (species with a completely different host range). Through comparison between these two clades of strains, 746 unique core orthologs/genes were clustered in the clades of P. actinidiae, especially key virulence determinants involved in the biosynthesis of secretion systems (type III, IV, and VI), iron, flagellar structure, and the quorum-sensing system. Our results provide insights into the pathogenomics underlying the genetic diversification and evolution of pathogenicity in P. actinidiae species.
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Affiliation(s)
- Qi Lu
- School of Horticulture, Anhui Agricultural University, Hefei 230036, People's Republic of China
| | - Fuhua Yan
- Lishui Academy of Agricultural and Forestry Sciences, Lishui 323000, People's Republic of China
| | - Yuanyuan Liu
- School of Horticulture, Anhui Agricultural University, Hefei 230036, People's Republic of China
| | - Qiaohong Li
- Kiwifruit Breeding and Utilization Key Laboratory, Sichuan Provincial Academy of Natural Resource Sciences, Chengdu 610015, People's Republic of China
| | - Meng Yang
- School of Horticulture, Hebei Agricultural University, Baoding 071001, People's Republic of China
| | - Pu Liu
- School of Horticulture, Anhui Agricultural University, Hefei 230036, People's Republic of China
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19
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European Population of Pectobacterium punjabense: Genomic Diversity, Tuber Maceration Capacity and a Detection Tool for This Rarely Occurring Potato Pathogen. Microorganisms 2021; 9:microorganisms9040781. [PMID: 33917923 PMCID: PMC8068253 DOI: 10.3390/microorganisms9040781] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Revised: 04/02/2021] [Accepted: 04/06/2021] [Indexed: 11/16/2022] Open
Abstract
Enterobacteria belonging to the Pectobacterium and Dickeya genera are responsible for soft rot and blackleg diseases occurring in many crops around the world. Since 2016, the number of described species has more than doubled. However, some new species, such as Pectobacterium punjabense, are often poorly characterized, and little is known about their genomic and phenotypic variation. Here, we explored several European culture collections and identified seven strains of P. punjabense. All were collected from potato blackleg symptoms, sometimes from a long time ago, i.e., the IFB5596 strain isolated almost 25 years ago. We showed that this species remains rare, with less than 0.24% of P. punjabense strains identified among pectinolytic bacteria present in the surveyed collections. The analysis of the genomic diversity revealed the non-clonal character of P. punjabense species. Furthermore, the strains showed aggressiveness differences. Finally, a qPCR Taqman assay was developed for rapid and specific strain characterization and for use in diagnostic programs.
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20
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Bourigault Y, Chane A, Barbey C, Jafra S, Czajkowski R, Latour X. Biosensors Used for Epifluorescence and Confocal Laser Scanning Microscopies to Study Dickeya and Pectobacterium Virulence and Biocontrol. Microorganisms 2021; 9:microorganisms9020295. [PMID: 33535657 PMCID: PMC7912877 DOI: 10.3390/microorganisms9020295] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 01/22/2021] [Accepted: 01/27/2021] [Indexed: 12/31/2022] Open
Abstract
Promoter-probe vectors carrying fluorescent protein-reporter genes are powerful tools used to study microbial ecology, epidemiology, and etiology. In addition, they provide direct visual evidence of molecular interactions related to cell physiology and metabolism. Knowledge and advances carried out thanks to the construction of soft-rot Pectobacteriaceae biosensors, often inoculated in potato Solanum tuberosum, are discussed in this review. Under epifluorescence and confocal laser scanning microscopies, Dickeya and Pectobacterium-tagged strains managed to monitor in situ bacterial viability, microcolony and biofilm formation, and colonization of infected plant organs, as well as disease symptoms, such as cell-wall lysis and their suppression by biocontrol antagonists. The use of dual-colored reporters encoding the first fluorophore expressed from a constitutive promoter as a cell tag, while a second was used as a regulator-based reporter system, was also used to simultaneously visualize bacterial spread and activity. This revealed the chronology of events leading to tuber maceration and quorum-sensing communication, in addition to the disruption of the latter by biocontrol agents. The promising potential of these fluorescent biosensors should make it possible to apprehend other activities, such as subcellular localization of key proteins involved in bacterial virulence in planta, in the near future.
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Affiliation(s)
- Yvann Bourigault
- Laboratory of Microbiology Signals and Microenvironment (LMSM EA 4312), University of Rouen Normandy, 55 rue Saint-Germain, F-27000 Evreux, France; (Y.B.); (A.C.); (C.B.)
- Research Federations NORVEGE Fed4277 & NORSEVE, Normandy University, F-76821 Mont-Saint-Aignan, France
| | - Andrea Chane
- Laboratory of Microbiology Signals and Microenvironment (LMSM EA 4312), University of Rouen Normandy, 55 rue Saint-Germain, F-27000 Evreux, France; (Y.B.); (A.C.); (C.B.)
| | - Corinne Barbey
- Laboratory of Microbiology Signals and Microenvironment (LMSM EA 4312), University of Rouen Normandy, 55 rue Saint-Germain, F-27000 Evreux, France; (Y.B.); (A.C.); (C.B.)
- Research Federations NORVEGE Fed4277 & NORSEVE, Normandy University, F-76821 Mont-Saint-Aignan, France
| | - Sylwia Jafra
- Division of Biological Plant Protection, Intercollegiate Faculty of Biotechnology UG and MUG, University of Gdansk, ul. A. Abrahama 58, 80-307 Gdansk, Poland;
| | - Robert Czajkowski
- Division of Biologically Active Compounds, Intercollegiate Faculty of Biotechnology UG and MUG, University of Gdansk, ul. A. Abrahama 58, 80-307 Gdansk, Poland
- Correspondence: (R.C.); (X.L.); Tel.: +48-58-523-63-33 (R.C.); +33-235-146-000 (X.L.)
| | - Xavier Latour
- Laboratory of Microbiology Signals and Microenvironment (LMSM EA 4312), University of Rouen Normandy, 55 rue Saint-Germain, F-27000 Evreux, France; (Y.B.); (A.C.); (C.B.)
- Research Federations NORVEGE Fed4277 & NORSEVE, Normandy University, F-76821 Mont-Saint-Aignan, France
- Correspondence: (R.C.); (X.L.); Tel.: +48-58-523-63-33 (R.C.); +33-235-146-000 (X.L.)
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Oulghazi S, Sarfraz S, Zaczek-Moczydłowska MA, Khayi S, Ed-Dra A, Lekbach Y, Campbell K, Novungayo Moleleki L, O’Hanlon R, Faure D. Pectobacterium brasiliense: Genomics, Host Range and Disease Management. Microorganisms 2021; 9:E106. [PMID: 33466309 PMCID: PMC7824751 DOI: 10.3390/microorganisms9010106] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Revised: 12/29/2020] [Accepted: 12/30/2020] [Indexed: 12/13/2022] Open
Abstract
Pectobacterium brasiliense (Pbr) is considered as one of the most virulent species among the Pectobacteriaceae. This species has a broad host range within horticulture crops and is well distributed elsewhere. It has been found to be pathogenic not only in the field causing blackleg and soft rot of potato, but it is also transmitted via storage causing soft rot of other vegetables. Genomic analysis and other cost-effective molecular detection methods such as a quantitative polymerase chain reaction (qPCR) are essential to investigate the ecology and pathogenesis of the Pbr. The lack of fast, field deployable point-of-care testing (POCT) methods, specific control strategies and current limited genomic knowledge make management of this species difficult. Thus far, no comprehensive review exists about Pbr, however there is an intense need to research the biology, detection, pathogenicity and management of Pbr, not only because of its fast distribution across Europe and other countries but also due to its increased survival to various climatic conditions. This review outlines the information available in peer-reviewed literature regarding host range, detection methods, genomics, geographical distribution, nomenclature and taxonomical evolution along with some of the possible management and control strategies. In summary, the conclusions and a further directions highlight the management of this species.
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Affiliation(s)
- Said Oulghazi
- Department of Biology, Faculty of Sciences, Moulay Ismaïl University, BP.11201, Zitoune Meknes 50000, Morocco; (S.O.); (A.E.-D.)
- Institute for Integrative Biology of the Cell (I2BC), CEA CNRS University Paris-Saclay, 91190 Gif-sur-Yvette, France
| | - Sohaib Sarfraz
- Department of Plant Pathology, Faculty of Agriculture, University of Agriculture Faisalabad, Faisalabad 38040, Pakistan;
| | - Maja A. Zaczek-Moczydłowska
- Institute for Global Food Security, School of Biological Sciences, Queen’s University, Belfast BT9 5DL, UK; (M.A.Z.-M.); (K.C.)
| | - Slimane Khayi
- Biotechnology Research Unit, CRRA-Rabat, National Institute for Agricultural Research (INRA), Rabat 10101, Morocco;
| | - Abdelaziz Ed-Dra
- Department of Biology, Faculty of Sciences, Moulay Ismaïl University, BP.11201, Zitoune Meknes 50000, Morocco; (S.O.); (A.E.-D.)
| | - Yassir Lekbach
- Shenyang National Laboratory for Materials Science, Northeastern University, Shenyang 110819, China;
| | - Katrina Campbell
- Institute for Global Food Security, School of Biological Sciences, Queen’s University, Belfast BT9 5DL, UK; (M.A.Z.-M.); (K.C.)
| | - Lucy Novungayo Moleleki
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria 0002, South Africa;
| | - Richard O’Hanlon
- Agri-Food and Biosciences Institute, 18a Newforge Lane, Belfast BT9 5PX, UK;
- Department of Agriculture, Food and the Marine, D02 WK12 Dublin 2, Ireland
| | - Denis Faure
- Institute for Integrative Biology of the Cell (I2BC), CEA CNRS University Paris-Saclay, 91190 Gif-sur-Yvette, France
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Host Specificity and Differential Pathogenicity of Pectobacterium Strains from Dicot and Monocot Hosts. Microorganisms 2020; 8:microorganisms8101479. [PMID: 32993160 PMCID: PMC7599833 DOI: 10.3390/microorganisms8101479] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Revised: 09/18/2020] [Accepted: 09/24/2020] [Indexed: 01/28/2023] Open
Abstract
Recent phylogenetic studies have transferred certain isolates from monocot plants previously included in the heterogeneous group of Pectobacteriumcarotovorum (Pc) to a species level termed Pectobacterium aroidearum. The specificity of Pectobacterium associated infections had received less attention, and may be of high scientific and economic importance. Here, we have characterized differential responses of Pectobacterium isolates from potato (WPP14) and calla lily (PC16) on two typical hosts: Brassica oleracea var. capitata (cabbage) a dicot host; and Zantedeschia aethiopica (calla lily) a monocot host. The results revealed clear host specific responses following infection with the two bacterial strains. This was demonstrated by differential production of volatile organic compounds (VOCs) and the expression of plant defense-related genes (pal, PR-1, lox2, ast). A related pattern was observed in bacterial responses to each of the host’s extract, with differential expression of virulence-related determinants and genes associated with quorum-sensing and plant cell wall-degrading enzymes. The differences were associated with each strain’s competence on its respective host.
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23
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Portier P, Pédron J, Taghouti G, Dutrieux C, Barny MA. Updated Taxonomy of Pectobacterium Genus in the CIRM-CFBP Bacterial Collection: When Newly Described Species Reveal "Old" Endemic Population. Microorganisms 2020; 8:microorganisms8091441. [PMID: 32962307 PMCID: PMC7565848 DOI: 10.3390/microorganisms8091441] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Revised: 09/16/2020] [Accepted: 09/17/2020] [Indexed: 11/16/2022] Open
Abstract
Bacterial collections are invaluable tools for microbiologists. However, their practical use is compromised by imprecise taxonomical assignation of bacterial strains. This is particularly true for soft rotting plant pathogens of the Pectobacterium genus. We analysed the taxonomic status of 265 Pectobacterium strains deposited at CIRM-CFBP collection from 1944 to 2020. This collection gathered Pectobacterium strains isolated in 27 countries from 32 plant species representing 17 botanical families or from nonhost environments. The MLSA approach completed by genomic analysis of 15 strains was performed to update the taxonomic status of these 265 strains. The results showed that the CIRM-CFBP Pectobacterium collection harboured at least one strain of each species, with the exception of P. polonicum. Yet, seven strains could not be assigned to any of the described species and may represent at least two new species. Surprisingly, P. versatile, recently described in 2019, is the most prevalent species among CIRM-CFBP strains. An analysis of P. versatile strains revealed that this species is pandemic and isolated from various host plants and environments. At the opposite, other species gathered strains isolated from only one botanical family or exclusively from a freshwater environment. Our work also revealed new host plants for several Pectobacterium spp.
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Affiliation(s)
- Perrine Portier
- IRHS-UMR1345, CIRM-CFBP, Institut Agro, INRAE, Université d’Angers, SFR 4207 QuaSav, 49071 Beaucouzé, France; (P.P.); (G.T.); (C.D.)
| | - Jacques Pédron
- Sorbonne Université, INRAE, Institute of Ecology and Environmental Sciences-Paris, 4 place Jussieu, F-75 252 Paris, France;
| | - Géraldine Taghouti
- IRHS-UMR1345, CIRM-CFBP, Institut Agro, INRAE, Université d’Angers, SFR 4207 QuaSav, 49071 Beaucouzé, France; (P.P.); (G.T.); (C.D.)
| | - Cécile Dutrieux
- IRHS-UMR1345, CIRM-CFBP, Institut Agro, INRAE, Université d’Angers, SFR 4207 QuaSav, 49071 Beaucouzé, France; (P.P.); (G.T.); (C.D.)
| | - Marie-Anne Barny
- Sorbonne Université, INRAE, Institute of Ecology and Environmental Sciences-Paris, 4 place Jussieu, F-75 252 Paris, France;
- Correspondence:
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Pasanen M, Waleron M, Schott T, Cleenwerck I, Misztak A, Waleron K, Pritchard L, Bakr R, Degefu Y, van der Wolf J, Vandamme P, Pirhonen M. Pectobacterium parvum sp. nov., having a Salmonella SPI-1-like Type III secretion system and low virulence. Int J Syst Evol Microbiol 2020; 70:2440-2448. [PMID: 32100697 PMCID: PMC7395620 DOI: 10.1099/ijsem.0.004057] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Revised: 01/27/2020] [Accepted: 01/30/2020] [Indexed: 11/25/2022] Open
Abstract
Pectobacterium strains isolated from potato stems in Finland, Poland and the Netherlands were subjected to polyphasic analyses to characterize their genomic and phenotypic features. Phylogenetic analysis based on 382 core proteins showed that the isolates clustered closest to Pectobacterium polaris but could be divided into two clades. Average nucleotide identity (ANI) analysis revealed that the isolates in one of the clades included the P. polaris type strain, whereas the second clade was at the border of the species P. polaris with a 96 % ANI value. In silico genome-to-genome comparisons between the isolates revealed values below 70%, patristic distances based on 1294 core proteins were at the level observed between closely related Pectobacterium species, and the two groups of bacteria differed in genome size, G+C content and results of amplified fragment length polymorphism and Biolog analyses. Comparisons between the genomes revealed that the isolates of the atypical group contained SPI-1-type Type III secretion island and genes coding for proteins known for toxic effects on nematodes or insects, and lacked many genes coding for previously characterized virulence determinants affecting rotting of plant tissue by soft rot bacteria. Furthermore, the atypical isolates could be differentiated from P. polaris by their low virulence, production of antibacterial metabolites and a citrate-negative phenotype. Based on the results of a polyphasic approach including genome-to-genome comparisons, biochemical and virulence assays, presented in this report, we propose delineation of the atypical isolates as a novel species Pectobacterium parvum, for which the isolate s0421T (CFBP 8630T=LMG 30828T) is suggested as a type strain.
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Affiliation(s)
- Miia Pasanen
- Department of Agricultural Sciences, University of Helsinki, Helsinki, Finland
| | - Malgorzata Waleron
- Department of Biotechnology, Intercollegiate Faculty of Biotechnology, University of Gdansk and Medical University of Gdansk, Gdansk, Poland
| | | | - Ilse Cleenwerck
- Ghent University, BCCM/LMG Bacteria Collection, Ghent, Belgium
| | - Agnieszka Misztak
- Department of Biotechnology, Intercollegiate Faculty of Biotechnology, University of Gdansk and Medical University of Gdansk, Gdansk, Poland
| | - Krzysztof Waleron
- Department of Pharmaceutical Microbiology, Medical University of Gdansk, Gdańsk, Poland
| | - Leighton Pritchard
- Information and Computational Sciences, The James Hutton Institute, Dundee, Scotland, UK
- Present address: Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow, UK
| | - Ramadan Bakr
- Department of Agricultural Sciences, University of Helsinki, Helsinki, Finland
- Present address: Department of Agricultural Botany, Faculty of Agriculture, Menoufia University, Shibin Elkom, Egypt
| | | | - Jan van der Wolf
- Wageningen University and Research, Bio-interactions and Plant Health, Wageningen, The Netherlands
| | - Peter Vandamme
- Ghent University, BCCM/LMG Bacteria Collection, Ghent, Belgium
| | - Minna Pirhonen
- Department of Agricultural Sciences, University of Helsinki, Helsinki, Finland
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25
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Portier P, Pédron J, Taghouti G, Fischer-Le Saux M, Caullireau E, Bertrand C, Laurent A, Chawki K, Oulgazi S, Moumni M, Andrivon D, Dutrieux C, Faure D, Hélias V, Barny MA. Elevation of Pectobacterium carotovorum subsp. odoriferum to species level as Pectobacterium odoriferum sp. nov., proposal of Pectobacterium brasiliense sp. nov. and Pectobacterium actinidiae sp. nov., emended description of Pectobacterium carotovorum and description of Pectobacterium versatile sp. nov., isolated from streams and symptoms on diverse plants. Int J Syst Evol Microbiol 2019; 69:3207-3216. [PMID: 31343401 DOI: 10.1099/ijsem.0.003611] [Citation(s) in RCA: 84] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
The Pectobacteriumcarotovorum species corresponds to a complex, including two subspecies with validly published names, two proposed subspecies and two new species, Pectobacterium polaris and Pectobacterium aquaticum. Recent studies suggested that this complex needed revision. We examined the taxonomic status of 144 Pectobacterium strains isolated from a wide range of plant species, various geographical origins and waterways. Sequences of the leuS, dnaX and recA housekeeping genes clustered 114 of these Pectobacterium strains together within a not yet described clade. We sequenced eight strains of this clade and analysed them together with the 102 Pectobacterium genomes available in the NCBI database. Phylogenetic analysis, average nucleotide identity calculation and in silico DNA-DNA hybridization allowed us to differentiate seven clades. This led us to propose the elevation of Pectobacterium carotovorumsubsp. odoriferum to species level as Pectobacteriumodoriferum sp. nov. (type strain CFBP 1878T=LMG 5863T=NCPPB 3839T=ICMP 11533T), the proposal of Pectobacteriumactinidiae sp. nov. (type strain KKH3=LMG 26003 T=KCTC 23131T) and Pectobacteriumbrasiliense sp. nov. (type strain CFBP 6617T= LMG 21371T=NCPPB 4609T), to emend the description of Pectobacterium carotovorum (type strain CFBP 2046T=LMG 2404T=NCPPB 312T=ICMP 5702T), and to propose a novel species, Pectobacterium versatile sp. nov (type strain CFBP6051T= NCPPB 3387T=ICMP 9168T) which includes the strains previously described as 'Candidatus Pectobacterium maceratum'. Phenotypic analysis performed using Biolog GENIII plates on eight strains of P. versatile sp. nov. and related strains completed our analysis.
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Affiliation(s)
- Perrine Portier
- IRHS, CIRM-CFBP, Agrocampus-Ouest, INRA, Université d'Angers, SFR 4207 QuaSaV, 49071, Beaucouzé, France
| | - Jacques Pédron
- Sorbonne Université, INRA, Institute of Ecology and Environmental sciences-Paris, 4 place Jussieu, F-75 252 Paris, France
| | - Géraldine Taghouti
- IRHS, CIRM-CFBP, Agrocampus-Ouest, INRA, Université d'Angers, SFR 4207 QuaSaV, 49071, Beaucouzé, France
| | - Marion Fischer-Le Saux
- IRHS, CIRM-CFBP, Agrocampus-Ouest, INRA, Université d'Angers, SFR 4207 QuaSaV, 49071, Beaucouzé, France
| | - Emma Caullireau
- IRHS, CIRM-CFBP, Agrocampus-Ouest, INRA, Université d'Angers, SFR 4207 QuaSaV, 49071, Beaucouzé, France
| | - Claire Bertrand
- Sorbonne Université, INRA, Institute of Ecology and Environmental sciences-Paris, 4 place Jussieu, F-75 252 Paris, France
| | - Angélique Laurent
- FN3PT/RD3PT, French Federation of Seed Potato Growers, 75008, Paris, France
| | - Khaoula Chawki
- FN3PT/RD3PT, French Federation of Seed Potato Growers, 75008, Paris, France
| | - Saïd Oulgazi
- Institute for Integrative Biology of the Cell (I2BC), CEA CNRS Univ. Paris-Sud, University Paris-Saclay, 91198 Gif-sur-Yvette, France.,Department of Biology, Faculty of Sciences, Moulay Ismaïl University, BP11201 Zitoune, 50 000, Meknes, Morocco
| | - Mohedine Moumni
- Department of Biology, Faculty of Sciences, Moulay Ismaïl University, BP11201 Zitoune, 50 000, Meknes, Morocco
| | - Didier Andrivon
- IGEPP, Agrocampus Ouest, INRA, University Rennes 1, 35653 Le Rheu Cedex, France
| | - Cécile Dutrieux
- IRHS, CIRM-CFBP, Agrocampus-Ouest, INRA, Université d'Angers, SFR 4207 QuaSaV, 49071, Beaucouzé, France
| | - Denis Faure
- Institute for Integrative Biology of the Cell (I2BC), CEA CNRS Univ. Paris-Sud, University Paris-Saclay, 91198 Gif-sur-Yvette, France
| | - Valérie Hélias
- FN3PT/RD3PT, French Federation of Seed Potato Growers, 75008, Paris, France
| | - Marie-Anne Barny
- Sorbonne Université, INRA, Institute of Ecology and Environmental sciences-Paris, 4 place Jussieu, F-75 252 Paris, France
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