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Suprun EV, Khmeleva SA, Duskaev IF, Ptitsyn KG, Kurbatov LK, Shershov VE, Kuznetsova VE, Lapa SA, Chudinov AV, Radko SP. Combining recombinase polymerase amplification with tyrosine modified 2'-deoxyuridine-5'-triphosphate for direct voltammetric detection of double-stranded DNA: Application to potato pathogen Dickeya solani. Talanta 2024; 273:125841. [PMID: 38460421 DOI: 10.1016/j.talanta.2024.125841] [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: 11/09/2023] [Revised: 02/22/2024] [Accepted: 02/26/2024] [Indexed: 03/11/2024]
Abstract
The approach based on a combination of isothermal recombinase polymerase amplification (RPA), 2'-deoxyuridine-5'-triphosphate modified with tyrosine aromatic group (dUTP-Y1), and direct voltammetric detection of RPA product carrying electroactive labels was successfully applied to the potato pathogen Dickeya solani. The artificial nucleotide dUTP-Y1 demonstrated a good compatibility with RPA, enabling by targeting a section of D. solani genome with a unique sequence to produce the full-size modified products at high levels of substitution of dTTP by dUTP-Y1 (up to 80-90 %) in the reaction mixture. The optimized procedure of square wave voltammetry allowed to reliably detect the product generated by RPA at 80 % substitution of dTTP by dUTP-Y1 (dsDNA-Y1) in microliter sample volumes on the surface of disposable carbon screen printed electrodes at the potential of about 0.6 V. The calibration curve for the amplicon detection was linear in coordinates 'Ip, A vs. Log (c, M)' within the 0.05-1 μM concentration range. The limit of detection for dsDNA-Y1 was estimated as 8 nM. The sensitivity of the established electrochemical approach allowed to detect amplicons generated in a single standard 50 μL RPA reaction after their purification with silica-coated magnetic beads. The overall detectability of D. solani with the suggested combination of RPA and voltammetric registration of dsDNA-Y1 can be as low as a few copies of bacterial genome per standard reaction. In total, amplification, purification, and electrochemical detection take about 120-150 min. Considering the potential of direct electrochemical analysis for miniaturization, as well as compliance with low-cost and low-power requirements, the findings provide grounds for future development of microfluidic devices integrating isothermal amplification, amplicon purification and detection based on the tyrosine modified nucleotide for the purpose of 'on-site' detection of various pathogens.
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Affiliation(s)
- Elena V Suprun
- Chemistry Faculty of M.V. Lomonosov Moscow State University, Lenin Hills, 1/3, Moscow, 119991, Russia; Institute of Biomedical Chemistry, Pogodinskaya Street, 10/8, Moscow, 119121, Russia.
| | - Svetlana A Khmeleva
- Institute of Biomedical Chemistry, Pogodinskaya Street, 10/8, Moscow, 119121, Russia
| | - Insaf F Duskaev
- Chemistry Faculty of M.V. Lomonosov Moscow State University, Lenin Hills, 1/3, Moscow, 119991, Russia; Institute of Biomedical Chemistry, Pogodinskaya Street, 10/8, Moscow, 119121, Russia
| | - Konstantin G Ptitsyn
- Institute of Biomedical Chemistry, Pogodinskaya Street, 10/8, Moscow, 119121, Russia
| | - Leonid K Kurbatov
- Institute of Biomedical Chemistry, Pogodinskaya Street, 10/8, Moscow, 119121, Russia
| | - Valeriy E Shershov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov Street, 32, Moscow, 119991, Russia
| | - Viktoriya E Kuznetsova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov Street, 32, Moscow, 119991, Russia
| | - Sergey A Lapa
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov Street, 32, Moscow, 119991, Russia
| | - Alexander V Chudinov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov Street, 32, Moscow, 119991, Russia
| | - Sergey P Radko
- Institute of Biomedical Chemistry, Pogodinskaya Street, 10/8, Moscow, 119121, Russia
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Hugouvieux-Cotte-Pattat N, Pédron J, Van Gijsegem F. Insight into biodiversity of the recently rearranged genus Dickeya. FRONTIERS IN PLANT SCIENCE 2023; 14:1168480. [PMID: 37409305 PMCID: PMC10319131 DOI: 10.3389/fpls.2023.1168480] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Accepted: 05/22/2023] [Indexed: 07/07/2023]
Abstract
The genus Dickeya includes plant pathogenic bacteria attacking a wide range of crops and ornamentals as well as a few environmental isolates from water. Defined on the basis of six species in 2005, this genus now includes 12 recognized species. Despite the description of several new species in recent years, the diversity of the genus Dickeya is not yet fully explored. Many strains have been analyzed for species causing diseases on economically important crops, such as for the potato pathogens D. dianthicola and D. solani. In contrast, only a few strains have been characterized for species of environmental origin or isolated from plants in understudied countries. To gain insights in the Dickeya diversity, recent extensive analyzes were performed on environmental isolates and poorly characterized strains from old collections. Phylogenetic and phenotypic analyzes led to the reclassification of D. paradisiaca (containing strains from tropical or subtropical regions) in the new genus, Musicola, the identification of three water species D. aquatica, D. lacustris and D. undicola, the description of a new species D. poaceaphila including Australian strains isolated from grasses, and the characterization of the new species D. oryzae and D. parazeae, resulting from the subdivision of the species D. zeae. Traits distinguishing each new species were identified from genomic and phenotypic comparisons. The high heterogeneity observed in some species, notably for D. zeae, indicates that additional species still need to be defined. The objective of this study was to clarify the present taxonomy of the genus Dickeya and to reassign the correct species to several Dickeya strains isolated before the current classification.
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Affiliation(s)
| | - Jacques Pédron
- Institute of Ecology and Environmental Sciences, Sorbonne University, CNRS, INRAE, Paris, France
| | - Frédérique Van Gijsegem
- Institute of Ecology and Environmental Sciences, Sorbonne University, CNRS, INRAE, Paris, France
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3
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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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Ivanov AV, Safenkova IV, Drenova NV, Zherdev AV, Dzantiev BB. Development of lateral flow assay combined with recombinase polymerase amplification for highly sensitive detection of Dickeya solani. Mol Cell Probes 2020; 53:101622. [PMID: 32569728 DOI: 10.1016/j.mcp.2020.101622] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Revised: 06/15/2020] [Accepted: 06/18/2020] [Indexed: 02/07/2023]
Abstract
Dickeya solani, one of the most significant bacterial pathogens, infects potato plants, resulting in severe economic damage. In this study, a lateral flow assay (LFA) combined with isothermal DNA amplification was developed for rapid, specific, and sensitive diagnosis of the potato blackleg disease caused by D. solani. Recombinase polymerase amplification (RPA) was chosen for this purpose. Five primer pairs specific to different regions of the D. solani genome were designed and screened. A primer pair providing correct recognition of the target sequence was aligned with the SOL-C region specific to D. solani and flanked by fluorescein (forward primer) and biotin (reverse primer). Lateral flow test strips were constructed to detect DNA amplicons. The RPA-LFA demonstrated a detection limit equal to 14,000 D. solani colony-forming units per gram of potato tuber. This assay provided sensitivity corresponding to the polymerase chain reaction (PCR) but was implemented at a fixed temperature (39 °C) over 30 min. No unspecific reactions with Pectobacterium, Clavibacter, and other Dickeya species were observed. Detection of latent infection of D. solani in the potato tubers by the developed RPA-LFA was verified by PCR. The obtained results confirmed that RPA-LFA has great potential for highly sensitive detection of latent infection.
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Affiliation(s)
- Aleksandr V Ivanov
- A.N. Bach Institute of Biochemistry, Research Centre of Biotechnology of the Russian Academy of Sciences, Leninsky Prospect 33, Moscow, 119071, Russia
| | - Irina V Safenkova
- A.N. Bach Institute of Biochemistry, Research Centre of Biotechnology of the Russian Academy of Sciences, Leninsky Prospect 33, Moscow, 119071, Russia
| | - Natalia V Drenova
- All-Russian Plant Quarantine Centre, Pogranichnaya Street, 32, Bykovo-2, Moscow Region, 140150, Russia
| | - Anatoly V Zherdev
- A.N. Bach Institute of Biochemistry, Research Centre of Biotechnology of the Russian Academy of Sciences, Leninsky Prospect 33, Moscow, 119071, Russia
| | - Boris B Dzantiev
- A.N. Bach Institute of Biochemistry, Research Centre of Biotechnology of the Russian Academy of Sciences, Leninsky Prospect 33, Moscow, 119071, Russia.
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Dobhal S, Boluk G, Babler B, Stulberg MJ, Rascoe J, Nakhla MK, Chapman TA, Crockford AB, Melzer MJ, Alvarez AM, Arif M. Comparative genomics reveals signature regions used to develop a robust and sensitive multiplex TaqMan real-time qPCR assay to detect the genus Dickeya and Dickeya dianthicola. J Appl Microbiol 2020; 128:1703-1719. [PMID: 31950553 DOI: 10.1111/jam.14579] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 12/16/2019] [Accepted: 01/07/2020] [Indexed: 11/30/2022]
Abstract
AIMS Dickeya species are high consequence plant pathogenic bacteria; associated with potato disease outbreaks and subsequent economic losses worldwide. Early, accurate and reliable detection of Dickeya spp. is needed to prevent establishment and further dissemination of this pathogen. Therefore, a multiplex TaqMan qPCR was developed for sensitive detection of Dickeya spp. and specifically, Dickeya dianthicola. METHODS AND RESULTS A signature genomic region for the genus Dickeya (mglA/mglC) and unique genomic region for D. dianthicola (alcohol dehydrogenase) were identified using a whole genome-based comparative genomics approach. The developed multiplex TaqMan qPCR was validated using extensive inclusivity and exclusivity panels, and naturally/artificially infected samples to confirm broad range detection capability and specificity. Both sensitivity and spiked assays showed a detection limit of 10 fg DNA. CONCLUSION The developed multiplex assay is sensitive and reliable to detect Dickeya spp. and D. dianthicola with no false positives or false negatives. It was able to detect mixed infection from naturally and artificially infected plant materials. SIGNIFICANCE AND IMPACT OF THE STUDY The developed assay will serve as a practical tool for screening of propagative material, monitoring the presence and distribution, and quantification of target pathogens in a breeding programme. The assay also has applications in routine diagnostics, biosecurity and microbial forensics.
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Affiliation(s)
- S Dobhal
- Department of Plant and Environmental Protection Sciences, University of Hawaii at Manoa, Honolulu, HI, USA
| | - G Boluk
- Department of Plant and Environmental Protection Sciences, University of Hawaii at Manoa, Honolulu, HI, USA
| | - B Babler
- Department of Plant Pathology, Wisconsin Seed Potato Lab, University of Wisconsin, Madison, WI, USA
| | - M J Stulberg
- Science and Technology, Plant Protection and Quarantine, Animal and Health Inspection Service, United States Department of Agriculture, Beltsville, MD, USA
| | - J Rascoe
- Science and Technology, Plant Protection and Quarantine, Animal and Health Inspection Service, United States Department of Agriculture, Beltsville, MD, USA
| | - M K Nakhla
- Science and Technology, Plant Protection and Quarantine, Animal and Health Inspection Service, United States Department of Agriculture, Beltsville, MD, USA
| | - T A Chapman
- Biosecurity and Food Safety, NSW Department of Primary Industries, Elizabeth Macarthur Agricultural Institute, Menangle, NSW, Australia
| | - A B Crockford
- Department of Plant Pathology, Wisconsin Seed Potato Lab, University of Wisconsin, Madison, WI, USA
| | - M J Melzer
- Department of Plant and Environmental Protection Sciences, University of Hawaii at Manoa, Honolulu, HI, USA
| | - A M Alvarez
- Department of Plant and Environmental Protection Sciences, University of Hawaii at Manoa, Honolulu, HI, USA
| | - M Arif
- Department of Plant and Environmental Protection Sciences, University of Hawaii at Manoa, Honolulu, HI, USA
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Kabanova AP, Shneider MM, Korzhenkov AA, Bugaeva EN, Miroshnikov KK, Zdorovenko EL, Kulikov EE, Toschakov SV, Ignatov AN, Knirel YA, Miroshnikov KA. Host Specificity of the Dickeya Bacteriophage PP35 Is Directed by a Tail Spike Interaction With Bacterial O-Antigen, Enabling the Infection of Alternative Non-pathogenic Bacterial Host. Front Microbiol 2019; 9:3288. [PMID: 30687274 PMCID: PMC6336734 DOI: 10.3389/fmicb.2018.03288] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Accepted: 12/18/2018] [Indexed: 11/13/2022] Open
Abstract
Dickeya solani is a recently emerged virulent bacterial potato pathogen that poses a major threat to world agriculture. Because of increasing antibiotic resistance and growing limitations in antibiotic use, alternative antibacterials such as bacteriophages are being developed. Myoviridae bacteriophages recently re-ranked as a separate Ackermannviridae family, such as phage PP35 described in this work, are the attractive candidates for this bacterial biocontrol. PP35 has a very specific host range due to the presence of tail spike protein PP35 gp156, which can depolymerize the O-polysaccharide (OPS) of D. solani. The D. solani OPS structure, →2)-β-D-6-deoxy-D-altrose-(1→, is so far unique among soft-rot Pectobacteriaceae, though it may exist in non-virulent environmental Enterobacteriaceae. The phage tail spike depolymerase degrades the shielding polysaccharide, and launches the cell infection process. We hypothesize that non-pathogenic commensal bacteria may maintain the population of the phage in soil environment.
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Affiliation(s)
- Anastasia P Kabanova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia.,Research Center "PhytoEngineering" Ltd., Rogachevo, Russia
| | - Mikhail M Shneider
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | | | | | - Kirill K Miroshnikov
- Winogradsky Institute of Microbiology, Federal Research Center "Fundamentals of Biotechnology", Russian Academy of Sciences, Moscow, Russia
| | - Evelina L Zdorovenko
- Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Eugene E Kulikov
- Winogradsky Institute of Microbiology, Federal Research Center "Fundamentals of Biotechnology", Russian Academy of Sciences, Moscow, Russia
| | - Stepan V Toschakov
- Immanuel Kant Baltic Federal University, Kaliningrad, Russia.,Winogradsky Institute of Microbiology, Federal Research Center "Fundamentals of Biotechnology", Russian Academy of Sciences, Moscow, Russia
| | | | - Yuriy A Knirel
- Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Konstantin A Miroshnikov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia.,Research Center "PhytoEngineering" Ltd., Rogachevo, Russia
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7
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Zhang J, Hu J, Shen H, Zhang Y, Sun D, Pu X, Yang Q, Fan Q, Lin B. Genomic analysis of the Phalaenopsis pathogen Dickeya sp. PA1, representing the emerging species Dickeya fangzhongdai. BMC Genomics 2018; 19:782. [PMID: 30373513 PMCID: PMC6206727 DOI: 10.1186/s12864-018-5154-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Accepted: 10/09/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Dickeya sp. strain PA1 is the causal agent of bacterial soft rot in Phalaenopsis, an important indoor orchid in China. PA1 and a few other strains were grouped into a novel species, Dickeya fangzhongdai, and only the orchid-associated strains have been shown to cause soft rot symptoms. METHODS We constructed the complete PA1 genome sequence and used comparative genomics to explore the differences in genomic features between D. fangzhongdai and other Dickeya species. RESULTS PA1 has a 4,979,223-bp circular genome with 4269 predicted protein-coding genes. D. fangzhongdai was phylogenetically similar to Dickeya solani and Dickeya dadantii. The type I to type VI secretion systems (T1SS-T6SS), except for the stt-type T2SS, were identified in D. fangzhongdai. The three phylogenetically similar species varied significantly in terms of their T5SSs and T6SSs, as did the different D. fangzhongdai strains. Genomic island (GI) prediction and synteny analysis (compared to D. fangzhongdai strains) of PA1 also indicated the presence of T5SSs and T6SSs in strain-specific regions. Two typical CRISPR arrays were identified in D. fangzhongdai and in most other Dickeya species, except for D. solani. CRISPR-1 was present in all of these Dickeya species, while the presence of CRISPR-2 varied due to species differentiation. A large polyketide/nonribosomal peptide (PK/NRP) cluster, similar to the zeamine biosynthetic gene cluster in Dickeya zeae rice strains, was discovered in D. fangzhongdai and D. solani. The D. fangzhongdai and D. solani strains might recently have acquired this gene cluster by horizontal gene transfer (HGT). CONCLUSIONS Orchid-associated strains are the typical members of D. fangzhongdai. Genomic analysis of PA1 suggested that this strain presents the genomic characteristics of this novel species. Considering the absence of the stt-type T2SS, the presence of CRISPR loci and the zeamine biosynthetic gene cluster, D. fangzhongdai is likely a transitional form between D. dadantii and D. solani. This is supported by the later acquisition of the zeamine cluster and the loss of CRISPR arrays by D. solani. Comparisons of phylogenetic positions and virulence determinants could be helpful for the effective quarantine and control of this emerging species.
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Affiliation(s)
- Jingxin Zhang
- Key Laboratory of New Techniques for Plant Protection in Guangdong, Institute of Plant Protection, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640 China
| | - John Hu
- Department of Plant and Environmental Protection Sciences, College of Tropical Agriculture and Human Resources, University of Hawaii, Honolulu, HI 96822 USA
| | - Huifang Shen
- Key Laboratory of New Techniques for Plant Protection in Guangdong, Institute of Plant Protection, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640 China
| | - Yucheng Zhang
- Department of Plant Pathology, University of Florida, Gainesville, FL 32611 USA
| | - Dayuan Sun
- Key Laboratory of New Techniques for Plant Protection in Guangdong, Institute of Plant Protection, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640 China
| | - Xiaoming Pu
- Key Laboratory of New Techniques for Plant Protection in Guangdong, Institute of Plant Protection, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640 China
| | - Qiyun Yang
- Key Laboratory of New Techniques for Plant Protection in Guangdong, Institute of Plant Protection, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640 China
| | - Qiurong Fan
- Department of Plant Pathology, University of Florida, Gainesville, FL 32611 USA
| | - Birun Lin
- Key Laboratory of New Techniques for Plant Protection in Guangdong, Institute of Plant Protection, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640 China
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Yasuhara-Bell J, Marrero G, Arif M, de Silva A, Alvarez AM. Development of a Loop-Mediated Isothermal Amplification Assay for the Detection of Dickeya spp. PHYTOPATHOLOGY 2017; 107:1339-1345. [PMID: 28697662 DOI: 10.1094/phyto-04-17-0160-r] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Dickeya and Pectobacterium spp. are responsible for soft-rotting diseases of several plant species, some with overlapping host range. On potato, symptoms caused by these pathogens cannot be clearly differentiated. Disease results in the downgrading and rejection of potato seed, thus requiring additional phytosanitary restrictions across Northern Europe and other parts of the world. In an effort to provide a more timely and accurate diagnostic to distinguish these two groups of pathogens, a method for detecting Dickeya spp. using loop-mediated isothermal amplification (LAMP) was developed. The LAMP assay can be used to test crude extracts prepared directly from symptomatic lesions. The entire test can be completed in less than 30 min, making it faster than the current diagnostic standard, the pelADE conventional polymerase chain reaction. Additionally, the LAMP assay was able to detect Dickeya DNA in samples spiked with varying amounts of Pectobacterium DNA, thus demonstrating the highly specific and sensitive nature of the assay, which can be applied on survey samples with mixed soft-rotting bacterial populations.
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Affiliation(s)
- Jarred Yasuhara-Bell
- First author: Department of Molecular Biosciences and Bioengineering, and second, third, fourth, and fifth authors: Department of Plant and Environmental Protection Sciences, University of Hawai'i at Mānoa, Honolulu 96822
| | - Glorimar Marrero
- First author: Department of Molecular Biosciences and Bioengineering, and second, third, fourth, and fifth authors: Department of Plant and Environmental Protection Sciences, University of Hawai'i at Mānoa, Honolulu 96822
| | - Mohammad Arif
- First author: Department of Molecular Biosciences and Bioengineering, and second, third, fourth, and fifth authors: Department of Plant and Environmental Protection Sciences, University of Hawai'i at Mānoa, Honolulu 96822
| | - Asoka de Silva
- First author: Department of Molecular Biosciences and Bioengineering, and second, third, fourth, and fifth authors: Department of Plant and Environmental Protection Sciences, University of Hawai'i at Mānoa, Honolulu 96822
| | - Anne M Alvarez
- First author: Department of Molecular Biosciences and Bioengineering, and second, third, fourth, and fifth authors: Department of Plant and Environmental Protection Sciences, University of Hawai'i at Mānoa, Honolulu 96822
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9
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Alič Š, Naglič T, Tušek-Žnidarič M, Ravnikar M, Rački N, Peterka M, Dreo T. Newly Isolated Bacteriophages from the Podoviridae, Siphoviridae, and Myoviridae Families Have Variable Effects on Putative Novel Dickeya spp. Front Microbiol 2017; 8:1870. [PMID: 29033917 PMCID: PMC5626979 DOI: 10.3389/fmicb.2017.01870] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2017] [Accepted: 09/13/2017] [Indexed: 11/13/2022] Open
Abstract
Soft rot pathogenic bacteria from the genus Dickeya cause severe economic losses in orchid nurseries worldwide, and there is no effective control currently available. In the last decade, the genus Dickeya has undergone multiple changes as multiple new taxa have been described, and just recently a new putative Dickeya species was reported. This study reports the isolation of three bacteriophages active against putative novel Dickeya spp. isolates from commercially produced infected orchids that show variable host-range profiles. Bacteriophages were isolated through enrichment from Dickeya-infected orchid tissue. Convective interaction media monolith chromatography was used to isolate bacteriophages from wastewaters, demonstrating its suitability for the isolation of infective bacteriophages from natural sources. Based on bacteriophage morphology, all isolated bacteriophages were classified as being in the order Caudovirales, belonging to three different families, Podoviridae, Myoviridae, and Siphoviridae. The presence of three different groups of bacteriophages was confirmed by analyzing the bacteriophage specificity of bacterial hosts, restriction fragment length polymorphism and plaque morphology. Bacteriophage BF25/12, the first reported Podoviridae bacteriophage effective against Dickeya spp., was selected for further characterization. Its genome sequence determined by next-generation sequencing showed limited similarity to other characterized Podoviridae bacteriophages. Interactions among the bacteriophages and Dickeya spp. were examined using transmission electron microscopy, which revealed degradation of electron-dense granules in response to bacteriophage infection in some Dickeya strains. The temperature stability of the chosen Podoviridae bacteriophage monitored over 1 year showed a substantial decrease in the survival of bacteriophages stored at -20°C over longer periods. It showed susceptibility to low pH and UV radiation but was stable in neutral and alkaline pH. Furthermore, the stability of the tested bacteriophage was also connected to the incubation medium and bacteriophage concentration at certain pH values. Finally, the emergence of bacteriophage-resistant bacterial colonies is highly connected to the concentration of bacteriophages in the bacterial environment. This is the first report on bacteriophages against Dickeya from the Podoviridae family to expand on potential bacteriophages to include in bacteriophage cocktails as biocontrol agents. Some of these bacteriophage isolates also showed activity against Dickeya solani, an aggressive strain that causes the soft rot of potatoes, which indicates their broad potential as biocontrol agents.
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Affiliation(s)
- Špela Alič
- Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, Slovenia.,Jožef Stefan International Postgraduate School, Ljubljana, Slovenia
| | - Tina Naglič
- Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, Slovenia.,Laboratory for Bioanalytics (LBA), Centre of Excellence for Biosensors, Instrumentation and Process Control (COBIK), Ajdovščina, Slovenia
| | - Magda Tušek-Žnidarič
- Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, Slovenia
| | - Maja Ravnikar
- Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, Slovenia.,Laboratory for Bioanalytics (LBA), Centre of Excellence for Biosensors, Instrumentation and Process Control (COBIK), Ajdovščina, Slovenia
| | - Nejc Rački
- Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, Slovenia
| | - Matjaž Peterka
- Laboratory for Bioanalytics (LBA), Centre of Excellence for Biosensors, Instrumentation and Process Control (COBIK), Ajdovščina, Slovenia
| | - Tanja Dreo
- Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, Slovenia.,Laboratory for Bioanalytics (LBA), Centre of Excellence for Biosensors, Instrumentation and Process Control (COBIK), Ajdovščina, Slovenia
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10
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Motyka A, Zoledowska S, Sledz W, Lojkowska E. Molecular methods as tools to control plant diseases caused by Dickeya and Pectobacterium spp: A minireview. N Biotechnol 2017; 39:181-189. [PMID: 28847714 DOI: 10.1016/j.nbt.2017.08.010] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2016] [Revised: 08/19/2017] [Accepted: 08/21/2017] [Indexed: 12/19/2022]
Abstract
Dickeya spp. and Pectobacterium spp. are etiological agents of soft rot on crops, vegetables, and ornamentals. They also cause blackleg on potato. These pectinolytic phytopathogens are responsible for significant economic losses, mostly within the potato production sector. Importantly, there are no methods to eradicate these microorganisms once they have infected plant material. Solely preventive measures remain, including early detection and identification of the pathogens, monitoring of their spread in addition to planting certified seed material tested for latent infections. As proper identification of the causative agent allows for efficient limitation of disease spread, numerous detection and differentiation methods have been developed. Most commonly followed procedures involve: isolation of viable bacterial cells (alternatively post-enrichment) on semi-selective media, identification to species level by PCR (single, multiplex, Real time), serology or fatty acids profiling. Differentiation of the isolates is often accomplished by sequencing the housekeeping genes or molecular fingerprinting. In view of lowering total costs of next-generation sequencing (NGS), a huge amount of generated data reveals subtle differences between strains that have proven to be potentially useful for the establishment of specific novel detection pipelines. Successful implementation of molecular diagnostic methods is exemplified by 20-year studies on the populations of pectinolytic bacteria on potatoes in Poland. The presented work aims to gather the characteristics of Dickeya spp. and Pectobacterium spp. important for the identification process in addition to providing an overview of modern and newly developed specific, rapid, high-throughput and cost-effective screening methods for the detection and identification of these phytopathogens.
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Affiliation(s)
- Agata Motyka
- Department of Biotechnology, Intercollegiate Faculty of Biotechnology University of Gdansk and Medical University of Gdansk, Abrahama 58, 80-307 Gdansk, Poland
| | - Sabina Zoledowska
- Department of Biotechnology, Intercollegiate Faculty of Biotechnology University of Gdansk and Medical University of Gdansk, Abrahama 58, 80-307 Gdansk, Poland
| | - Wojciech Sledz
- Department of Biotechnology, Intercollegiate Faculty of Biotechnology University of Gdansk and Medical University of Gdansk, Abrahama 58, 80-307 Gdansk, Poland
| | - Ewa Lojkowska
- Department of Biotechnology, Intercollegiate Faculty of Biotechnology University of Gdansk and Medical University of Gdansk, Abrahama 58, 80-307 Gdansk, Poland.
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11
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Cigna J, Dewaegeneire P, Beury A, Gobert V, Faure D. A gapA PCR-sequencing Assay for Identifying the Dickeya and Pectobacterium Potato Pathogens. PLANT DISEASE 2017; 101:1278-1282. [PMID: 30682965 DOI: 10.1094/pdis-12-16-1810-re] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Several pectinolytic Pectobacterium and Dickeya species and subspecies are causative agents of blackleg and soft rot diseases on potato plants and tubers. Rapid and accurate identification of these taxa is a crucial issue for the production and international trade of potato seed-tubers. Here, we developed a PCR-sequencing tool to easily characterize the different Pectobacterium and Dickeya taxa. The gapA gene sequences from 53 published genomes were aligned and a phylogeny tree was constructed. A set of 35 signature nucleotides was discovered to distinguish the Pectobacterium and Dickeya genera, species, and subspecies. Then, a PCR-primer couple was designed for amplifying the gapA gene in pectinolytic enterobacteria. The primers were tested on 22 isolates recovered from blackleg symptoms in several potato fields. Amplicons were sequenced and signature-nucleotides were analyzed. A phylogeny that includes gapA sequence specimens confirmed the taxonomical identification of these environmental isolates.
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Affiliation(s)
- Jérémy Cigna
- Seed Innovation Protection Research Environment, Comité Nord-SIPRE, 62217 Achicourt, France; and Institute for Integrative Biology of the Cell, CNRS CEA Univ. Paris-Sud, Université Paris-Saclay, 91198 Gif-sur-Yvette, France
| | - Pauline Dewaegeneire
- Seed Innovation Protection Research Environment, Comité Nord-SIPRE, 62217 Achicourt, France
| | - Amélie Beury
- Seed Innovation Protection Research Environment, Comité Nord-SIPRE, 62217 Achicourt, France
| | - Virginie Gobert
- Seed Innovation Protection Research Environment, Comité Nord-SIPRE, 62217 Achicourt, France
| | - Denis Faure
- Institute for Integrative Biology of the Cell, CNRS CEA Univ. Paris-Sud, Université Paris-Saclay, 91198 Gif-sur-Yvette, France
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12
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Khayi S, Blin P, Pédron J, Chong TM, Chan KG, Moumni M, Hélias V, Van Gijsegem F, Faure D. Population genomics reveals additive and replacing horizontal gene transfers in the emerging pathogen Dickeya solani. BMC Genomics 2015; 16:788. [PMID: 26467299 PMCID: PMC4607151 DOI: 10.1186/s12864-015-1997-z] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2015] [Accepted: 10/03/2015] [Indexed: 11/17/2022] Open
Abstract
BACKGROUND Dickeya solani is an emerging pathogen that causes soft rot and blackleg diseases in several crops including Solanum tuberosum, but little is known about its genomic diversity and evolution. RESULTS We combined Illumina and PacBio technologies to complete the genome sequence of D. solani strain 3337 that was used as a reference to compare with 19 other genomes (including that of the type strain IPO2222(T)) which were generated by Illumina technology. This population genomic analysis highlighted an unexpected variability among D. solani isolates since it led to the characterization of two distinct sub-groups within the D. solani species. This approach also revealed different types of variations such as scattered SNP/InDel variations as well as replacing and additive horizontal gene transfers (HGT). Infra-species (between the two D. solani sub-groups) and inter-species (between D. solani and D. dianthicola) replacing HGTs were observed. Finally, this work pointed that genetic and functional variation in the motility trait could contribute to aggressiveness variability in D. solani. CONCLUSIONS This work revealed that D. solani genomic variability may be caused by SNPs/InDels as well as replacing and additive HGT events, including plasmid acquisition; hence the D. solani genomes are more dynamic than that were previously proposed. This work alerts on precautions in molecular diagnosis of this emerging pathogen.
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Affiliation(s)
- Slimane Khayi
- Institute for Integrative Biology of the Cell (I2BC), CNRS CEA Univ. Paris-Sud, Université Paris-Saclay, Saclay Plant Sciences, Avenue de la Terrasse, 91198, Gif-sur-Yvette cedex, France.
- Université Moulay Ismaïl, Faculté des Sciences, Département de Biologie, Meknès, Morocco.
| | - Pauline Blin
- Institute for Integrative Biology of the Cell (I2BC), CNRS CEA Univ. Paris-Sud, Université Paris-Saclay, Saclay Plant Sciences, Avenue de la Terrasse, 91198, Gif-sur-Yvette cedex, France.
| | - Jacques Pédron
- UPMC Univ Paris 06, UMR 7618, IEES Paris (Institute of Ecology and Environmental Sciences), 7 Quai Saint bernard, 75005, Paris, France.
| | - Teik-Min Chong
- Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603, Kuala Lumpur, Malaysia.
| | - Kok-Gan Chan
- Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603, Kuala Lumpur, Malaysia.
| | - Mohieddine Moumni
- Université Moulay Ismaïl, Faculté des Sciences, Département de Biologie, Meknès, Morocco.
| | - Valérie Hélias
- Fédération Nationale des Producteurs de Plants de Pomme de Terre-Recherche développement Promotion du Plant de Pomme de Terre (FN3PT-RD3PT), 75008, Paris, France.
- UMR 1349 IGEPP INRA - Agrocampus Ouest Rennes, 35653, LeRheu, France.
| | - Frédérique Van Gijsegem
- INRA, UMR 1392, IEES Paris (Institute of Ecology and Environmental Sciences), 7 Quai Saint Bernard, 75005, Paris, France.
| | - Denis Faure
- Institute for Integrative Biology of the Cell (I2BC), CNRS CEA Univ. Paris-Sud, Université Paris-Saclay, Saclay Plant Sciences, Avenue de la Terrasse, 91198, Gif-sur-Yvette cedex, France.
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13
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Draft Genome Sequences of Dickeya sp. Isolates B16 (NIB Z 2098) and S1 (NIB Z 2099) Causing Soft Rot of Phalaenopsis Orchids. GENOME ANNOUNCEMENTS 2015; 3:3/5/e00973-15. [PMID: 26358590 PMCID: PMC4566172 DOI: 10.1128/genomea.00973-15] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The genus Dickeya contains bacteria causing soft rot of economically important crops and ornamental plants. Here, we report the draft genome sequences of two Dickeya sp. isolates from rotted leaves of Phalaenopsis orchids.
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14
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Czajkowski R, Pérombelon MCM, Jafra S, Lojkowska E, Potrykus M, van der Wolf JM, Sledz W. Detection, identification and differentiation of Pectobacterium and Dickeya species causing potato blackleg and tuber soft rot: a review. THE ANNALS OF APPLIED BIOLOGY 2015; 166:18-38. [PMID: 25684775 PMCID: PMC4320782 DOI: 10.1111/aab.12166] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2014] [Accepted: 08/05/2014] [Indexed: 05/10/2023]
Abstract
The soft rot Enterobacteriaceae (SRE) Pectobacterium and Dickeya species (formerly classified as pectinolytic Erwinia spp.) cause important diseases on potato and other arable and horticultural crops. They may affect the growing potato plant causing blackleg and are responsible for tuber soft rot in storage thereby reducing yield and quality. Efficient and cost-effective detection and identification methods are essential to investigate the ecology and pathogenesis of the SRE as well as in seed certification programmes. The aim of this review was to collect all existing information on methods available for SRE detection. The review reports on the sampling and preparation of plant material for testing and on over thirty methods to detect, identify and differentiate the soft rot and blackleg causing bacteria to species and subspecies level. These include methods based on biochemical characters, serology, molecular techniques which rely on DNA sequence amplification as well as several less-investigated ones.
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Affiliation(s)
- R Czajkowski
- Department of Biotechnology, Intercollegiate Faculty of Biotechnology, University of Gdansk and Medical University of GdanskGdansk, Poland
| | | | - S Jafra
- Department of Biotechnology, Intercollegiate Faculty of Biotechnology, University of Gdansk and Medical University of GdanskGdansk, Poland
| | - E Lojkowska
- Department of Biotechnology, Intercollegiate Faculty of Biotechnology, University of Gdansk and Medical University of GdanskGdansk, Poland
| | - M Potrykus
- Department of Biotechnology, Intercollegiate Faculty of Biotechnology, University of Gdansk and Medical University of GdanskGdansk, Poland
| | | | - W Sledz
- Department of Biotechnology, Intercollegiate Faculty of Biotechnology, University of Gdansk and Medical University of GdanskGdansk, Poland
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15
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Marrero G, Schneider KL, Jenkins DM, Alvarez AM. Phylogeny and classification of Dickeya based on multilocus sequence analysis. Int J Syst Evol Microbiol 2014; 63:3524-3539. [PMID: 24003072 DOI: 10.1099/ijs.0.046490-0] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Bacterial heart rot of pineapple reported in Hawaii in 2003 and reoccurring in 2006 was caused by an undetermined species of Dickeya. Classification of the bacterial strains isolated from infected pineapple to one of the recognized Dickeya species and their phylogenetic relationships with Dickeya were determined by a multilocus sequence analysis (MLSA), based on the partial gene sequences of dnaA, dnaJ, dnaX, gyrB and recN. Individual and concatenated gene phylogenies revealed that the strains form a clade with reference Dickeya sp. isolated from pineapple in Malaysia and are closely related to D. zeae; however, previous DNA-DNA reassociation values suggest that these strains do not meet the genomic threshold for consideration in D. zeae, and require further taxonomic analysis. An analysis of the markers used in this MLSA determined that recN was the best overall marker for resolution of species within Dickeya. Differential intraspecies resolution was observed with the other markers, suggesting that marker selection is important for defining relationships within a clade. Phylogenies produced with gene sequences from the sequenced genomes of strains D. dadantii Ech586, D. dadantii Ech703 and D. zeae Ech1591 did not place the sequenced strains with members of other well-characterized members of their respective species. The average nucleotide identity (ANI) and tetranucleotide frequencies determined for the sequenced strains corroborated the results of the MLSA that D. dadantii Ech586 and D. dadantii Ech703 should be reclassified as Dickeya zeae Ech586 and Dickeya paradisiaca Ech703, respectively, whereas D. zeae Ech1591 should be reclassified as Dickeya chrysanthemi Ech1591.
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Affiliation(s)
- Glorimar Marrero
- Department of Molecular Biosciences and Bioengineering, University of Hawaii at Manoa, Honolulu, HI 96822, USA
| | - Kevin L Schneider
- Department of Molecular Biosciences and Bioengineering, University of Hawaii at Manoa, Honolulu, HI 96822, USA
| | - Daniel M Jenkins
- Department of Molecular Biosciences and Bioengineering, University of Hawaii at Manoa, Honolulu, HI 96822, USA
| | - Anne M Alvarez
- Department of Plant and Environmental Protection Sciences, University of Hawaii at Manoa, Honolulu, HI 96822, USA
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16
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Pédron J, Mondy S, des Essarts YR, Van Gijsegem F, Faure D. Genomic and metabolic comparison with Dickeya dadantii 3937 reveals the emerging Dickeya solani potato pathogen to display distinctive metabolic activities and T5SS/T6SS-related toxin repertoire. BMC Genomics 2014; 15:283. [PMID: 24735398 PMCID: PMC4028081 DOI: 10.1186/1471-2164-15-283] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2013] [Accepted: 04/04/2014] [Indexed: 11/28/2022] Open
Abstract
Background The pectinolytic enterobacteria of the Pectobacterium and Dickeya genera are causative agents of maceration-associated diseases affecting a wide variety of crops and ornamentals. For the past decade, the emergence of a novel species D. solani was observed in potato fields in Europe and the Mediterranean basin. The purpose of this study is to search by comparative genomics the genetic traits that could be distinctive to other Dickeya species and be involved in D. solani adaptation to the potato plant host. Results D. solani 3337 exhibits a 4.9 Mb circular genome that is characterized by a low content in mobile elements with the identification of only two full length insertion sequences. A genomic comparison with the deeply-annotated model D. dadantii 3937 strain was performed. While a large majority of Dickeya virulence genes are shared by both strains, a few hundreds genes of D. solani 3337, mostly regrouped in 25 genomic regions, are distinctive to D. dadantii 3937. These genomic regions are present in the other available draft genomes of D. solani strains and interestingly some of them were not found in the sequenced genomes of the other Dickeya species. These genomic regions regroup metabolic genes and are often accompanied by genes involved in transport systems. A metabolic analysis correlated some metabolic genes with distinctive functional traits of both D. solani 3337 and D. dadantii 3937. Three identified D. solani genomic regions also regroup NRPS/PKS encoding genes. In addition, D. solani encodes a distinctive arsenal of T5SS and T6SS-related toxin-antitoxin systems. These genes may contribute to bacteria-bacteria interactions and to the fitness of D. solani to the plant environment. Conclusions This study highlights the genomic specific traits of the emerging pathogen D. solani and will provide the basis for studying those that are involved in the successful adaptation of this emerging pathogen to the potato plant host.
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Affiliation(s)
| | | | | | - Frédérique Van Gijsegem
- UPMC Univ Paris 06, UMR 1392, IEES Paris (Institute of Ecology and Environmental Sciences), 46 rue d'Ulm, F-75005 Paris, France.
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Naushad HS, Lee B, Gupta RS. Conserved signature indels and signature proteins as novel tools for understanding microbial phylogeny and systematics: identification of molecular signatures that are specific for the phytopathogenic genera Dickeya, Pectobacterium and Brenneria. Int J Syst Evol Microbiol 2014; 64:366-383. [DOI: 10.1099/ijs.0.054213-0] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Genome sequences are enabling applications of different approaches to more clearly understand microbial phylogeny and systematics. Two of these approaches involve identification of conserved signature indels (CSIs) and conserved signature proteins (CSPs) that are specific for different lineages. These molecular markers provide novel and more definitive means for demarcation of prokaryotic taxa and for identification of species from these groups. Genome sequences are also enabling determination of phylogenetic relationships among species based upon sequences for multiple proteins. In this work, we have used all of these approaches for studying the phytopathogenic bacteria belonging to the genera
Dickeya
,
Pectobacterium
and
Brenneria
. Members of these genera, which cause numerous diseases in important food crops and ornamental plants, are presently distinguished mainly on the basis of their branching in phylogenetic trees. No biochemical or molecular characteristic is known that is uniquely shared by species from these genera. Hence, detailed studies using the above approaches were carried out on proteins from the genomes of these bacteria to identify molecular markers that are specific for them. In phylogenetic trees based upon concatenated sequences for 23 conserved proteins, members of the genera
Dickeya
,
Pectobacterium
and
Brenneria
formed a strongly supported clade within the other
Enterobacteriales
. Comparative analysis of protein sequences from the
Dickeya
,
Pectobacterium
and
Brenneria
genomes has identified 10 CSIs and five CSPs that are either uniquely or largely found in all genome-sequenced species from these genera, but not present in any other bacteria in the database. In addition, our analyses have identified 10 CSIs and 17 CSPs that are specifically present in either all or most sequenced
Dickeya
species/strains, and six CSIs and 19 CSPs that are uniquely found in the sequenced
Pectobacterium
genomes. Finally, our analysis also identified three CSIs and one CSP that are specifically shared by members of the genera
Pectobacterium
and
Brenneria
, but absent in species of the genus
Dickeya
, indicating that the former two genera shared a common ancestor exclusive of
Dickeya
. The identified CSIs and CSPs provide novel tools for identification of members of the genera
Dickeya
and
Pectobacterium
and for delimiting these taxa in molecular terms. Descriptions of the genera
Dickeya
and
Pectobacterium
have been revised to provide information for these molecular markers. Biochemical studies on these CSIs and CSPs, which are specific for these genera, may lead to discovery of novel properties that are unique to these bacteria and which could be targeted to develop antibacterial agents that are specific for these plant-pathogenic bacteria.
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Affiliation(s)
- Hafiz Sohail Naushad
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada L8N 3Z5
| | - Brian Lee
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada L8N 3Z5
| | - Radhey S. Gupta
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada L8N 3Z5
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18
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Scientific Opinion on the risk ofDickeya dianthicolafor the EU territory with identification and evaluation of risk reduction options. EFSA J 2013. [DOI: 10.2903/j.efsa.2013.3072] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
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