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Sun Y, Utpal H, Wu Y, Sun Q, Feng Z, Shen Y, Zhang R, Zhou X, Wu J. Comparative genomic and transcriptome analyses of two Pectobacterium brasiliense strains revealed distinct virulence determinants and phenotypic features. Front Microbiol 2024; 15:1362283. [PMID: 38800750 PMCID: PMC11116658 DOI: 10.3389/fmicb.2024.1362283] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Accepted: 04/26/2024] [Indexed: 05/29/2024] Open
Abstract
Potato soft rot caused by Pectobacterium spp. are devastating diseases of potato which cause severe economic losses worldwide. Pectobacterium brasiliense is considered as one of the most virulent species. However, the virulence mechanisms and pathogenicity factors of this strain have not been fully elucidated. Here, through pathogenicity screening, we identified two Pectobacterium brasiliense isolates, SM and DQ, with distinct pathogenicity levels. SM exhibits higher virulence compared to DQ in inducing aerial stem rot, blackleg and tuber soft rot. Our genomic and transcriptomic analyses revealed that SM encodes strain specific genes with regard to plant cell wall degradation and express higher level of genes associated with bacterial motility and secretion systems. Our plate assays verified higher pectinase, cellulase, and protease activities, as well as fast swimming and swarming motility in SM. Importantly, a unique endoglucanase S specific to SM was identified. Expression of this cellulase in DQ greatly enhances its virulence compared to wild type strain. Our study sheds light on possible determinants causing different pathogenicity of Pectobacterium brasiliense species with close evolutionary distance and provides new insight into the direction of genome evolution in response to host variation and environmental stimuli.
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Affiliation(s)
- Yue Sun
- Potato Engineering and Technology Research Center, Inner Mongolia University, Hohhot, Inner Mongolia, China
| | - Handique Utpal
- Potato Engineering and Technology Research Center, Inner Mongolia University, Hohhot, Inner Mongolia, China
| | - Yajuan Wu
- Potato Engineering and Technology Research Center, Inner Mongolia University, Hohhot, Inner Mongolia, China
| | - Qinghua Sun
- Potato Engineering and Technology Research Center, Inner Mongolia University, Hohhot, Inner Mongolia, China
| | - Zhiwen Feng
- Potato Engineering and Technology Research Center, Inner Mongolia University, Hohhot, Inner Mongolia, China
| | | | - Ruofang Zhang
- Potato Engineering and Technology Research Center, Inner Mongolia University, Hohhot, Inner Mongolia, China
| | - Xiaofeng Zhou
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, School of Agriculture and Biotechnology, Sun Yat-sen University, Shenzhen, China
| | - Jian Wu
- Potato Engineering and Technology Research Center, Inner Mongolia University, Hohhot, Inner Mongolia, China
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2
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Van Gijsegem F, Portier P, Taghouti G, Pédron J. Clonality and Diversity in the Soft Rot Dickeya solani Phytopathogen. Int J Mol Sci 2023; 24:17553. [PMID: 38139383 PMCID: PMC10743776 DOI: 10.3390/ijms242417553] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Revised: 12/05/2023] [Accepted: 12/06/2023] [Indexed: 12/24/2023] Open
Abstract
Bacterial diversity analyses often suffer from a bias due to sampling only from a limited number of hosts or narrow geographic locations. This was the case for the phytopathogenic species Dickeya solani, whose members were mainly isolated from a few hosts-potato and ornamentals-and from the same geographical area-Europe and Israel, which are connected by seed trade. Most D. solani members were clonal with the notable exception of the potato isolate RNS05.1.2A and two related strains that are clearly distinct from other D. solani genomes. To investigate if D. solani genomic diversity might be broadened by analysis of strains isolated from other environments, we analysed new strains isolated from ornamentals and from river water as well as strain CFBP 5647 isolated from tomato in the Caribbean island Guadeloupe. While water strains were clonal to RNS05.1.2A, the Caribbean tomato strain formed a third clade. The genomes of the three clades are highly syntenic; they shared almost 3900 protein families, and clade-specific genes were mainly included in genomic islands of extrachromosomal origin. Our study thus revealed both broader D. solani diversity with the characterisation of a third clade isolated in Latin America and a very high genomic conservation between clade members.
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Affiliation(s)
- Frédérique Van Gijsegem
- Institute of Ecology and Environmental Sciences-Paris, Sorbonne Université, INRAE, 4 Place Jussieu, F-75252 Paris, France;
| | - Perrine Portier
- Univ Angers, Institut Agro, INRAE, IRHS, SFR QUASAV, CIRM-CFBP, F-49000 Angers, France; (P.P.); (G.T.)
| | - Géraldine Taghouti
- Univ Angers, Institut Agro, INRAE, IRHS, SFR QUASAV, CIRM-CFBP, F-49000 Angers, France; (P.P.); (G.T.)
| | - Jacques Pédron
- Institute of Ecology and Environmental Sciences-Paris, Sorbonne Université, INRAE, 4 Place Jussieu, F-75252 Paris, France;
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3
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Motyka-Pomagruk A, Babinska-Wensierska W, Sledz W, Kaczorowska AK, Lojkowska E. Phyloproteomic study by MALDI-TOF MS in view of intraspecies variation in a significant homogenous phytopathogen Dickeya solani. Sci Rep 2023; 13:18863. [PMID: 37914755 PMCID: PMC10620192 DOI: 10.1038/s41598-023-46012-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2023] [Accepted: 10/26/2023] [Indexed: 11/03/2023] Open
Abstract
Dickeya solani is an economically significant pectinolytic phytopathogen belonging to the Pectobacteriaceae family, which causes soft rot and blackleg diseases. Despite its notable impact on global potato production, there are no effective methods to control this pest. Here, we undertook a phyloproteomic study on 20 D. solani strains, of various origin and year of isolation, with matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) supported by an in-depth characterization of the strains in terms of the virulence-associated phenotype. In spite of high homogeneity in this species, we herein revealed for the first time intraspecies variation in the MALDI-TOF MS protein profiles among the studied D. solani isolates. Finally, representative mass spectra for the four delineated clades are presented. A majority of the analysed D. solani strains showed high virulence potential, while two strains stood out in their growth dynamics, virulence factors production and ability to macerate plant tissue. Nonetheless, the metabolic profiles of D. solani strains turned out to be uniform, except for gelatinase activity. Given that all D. solani isolates distinctly grouped from the other Dickeya species in the MALDI-TOF MS analysis, there is strong evidence supporting the potential routine use of this method for fast and reliable to-species identification of D. solani isolates of environmental origin.
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Affiliation(s)
- Agata Motyka-Pomagruk
- Laboratory of Plant Protection and Biotechnology, Intercollegiate Faculty of Biotechnology University of Gdansk and Medical University of Gdansk, University of Gdansk, 58 Abrahama, 80-307, Gdańsk, Poland
- Research & Development Laboratory, Intercollegiate Faculty of Biotechnology University of Gdansk and Medical University of Gdansk, University of Gdansk, 20 Podwale Przedmiejskie, 80-824, Gdańsk, Poland
| | - Weronika Babinska-Wensierska
- Laboratory of Plant Protection and Biotechnology, Intercollegiate Faculty of Biotechnology University of Gdansk and Medical University of Gdansk, University of Gdansk, 58 Abrahama, 80-307, Gdańsk, Poland
- Research & Development Laboratory, Intercollegiate Faculty of Biotechnology University of Gdansk and Medical University of Gdansk, University of Gdansk, 20 Podwale Przedmiejskie, 80-824, Gdańsk, Poland
| | - Wojciech Sledz
- Laboratory of Plant Protection and Biotechnology, Intercollegiate Faculty of Biotechnology University of Gdansk and Medical University of Gdansk, University of Gdansk, 58 Abrahama, 80-307, Gdańsk, Poland
- Research & Development Laboratory, Intercollegiate Faculty of Biotechnology University of Gdansk and Medical University of Gdansk, University of Gdansk, 20 Podwale Przedmiejskie, 80-824, Gdańsk, Poland
| | - Anna-Karina Kaczorowska
- Collection of Plasmids and Microorganisms (KPD), Faculty of Biology, University of Gdansk, 59 Wita Stwosza Street, 80-308, Gdańsk, Poland
| | - Ewa Lojkowska
- Laboratory of Plant Protection and Biotechnology, Intercollegiate Faculty of Biotechnology University of Gdansk and Medical University of Gdansk, University of Gdansk, 58 Abrahama, 80-307, Gdańsk, Poland.
- Research & Development Laboratory, Intercollegiate Faculty of Biotechnology University of Gdansk and Medical University of Gdansk, University of Gdansk, 20 Podwale Przedmiejskie, 80-824, Gdańsk, Poland.
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Balasubramaniam HM, Tze Yan F, Michelle JiaMin L, Parimannan S, Mutusamy P, Jaya Jothi S, Rajandas H. Genome characterization of Dickeya solani bacteriophage W2B. Microbiol Resour Announc 2023; 12:e0045223. [PMID: 37540022 PMCID: PMC10508119 DOI: 10.1128/mra.00452-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Accepted: 07/02/2023] [Indexed: 08/05/2023] Open
Abstract
We have successfully characterized the complete genome sequence of the lytic Dickeya solani bacteriophage W2B, isolated from the Bunus Sewage Treatment Plant. The lytic phage from the Ningirsuvirus family has a 40,385-bp linear double-stranded DNA genome containing 51 coding sequences (CDSs).
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Affiliation(s)
| | - Fong Tze Yan
- Center of Excellence for Omics-Driven Computational Biodiscovery, AIMST University, Bedong, Kedah, Malaysia
| | - Loh Michelle JiaMin
- Center of Excellence for Omics-Driven Computational Biodiscovery, AIMST University, Bedong, Kedah, Malaysia
| | - Sivachandran Parimannan
- Center of Excellence for Omics-Driven Computational Biodiscovery, AIMST University, Bedong, Kedah, Malaysia
- Center for Evolutionary Hologenomics, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Prasanna Mutusamy
- Center of Excellence for Omics-Driven Computational Biodiscovery, AIMST University, Bedong, Kedah, Malaysia
| | | | - Heera Rajandas
- Center of Excellence for Omics-Driven Computational Biodiscovery, AIMST University, Bedong, Kedah, Malaysia
- Center for Evolutionary Hologenomics, Globe Institute, University of Copenhagen, Copenhagen, Denmark
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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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6
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Robic K, Munier E, Effantin G, Lachat J, Naquin D, Gueguen E, Faure D. Dissimilar gene repertoires of Dickeya solani involved in the colonization of lesions and roots of Solanum tuberosum. FRONTIERS IN PLANT SCIENCE 2023; 14:1154110. [PMID: 37223796 PMCID: PMC10202176 DOI: 10.3389/fpls.2023.1154110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Accepted: 04/12/2023] [Indexed: 05/25/2023]
Abstract
Dickeya and Pectobacterium species are necrotrophic pathogens that macerate stems (blackleg disease) and tubers (soft rot disease) of Solanum tuberosum. They proliferate by exploiting plant cell remains. They also colonize roots, even if no symptoms are observed. The genes involved in pre-symptomatic root colonization are poorly understood. Here, transposon-sequencing (Tn-seq) analysis of Dickeya solani living in macerated tissues revealed 126 genes important for competitive colonization of tuber lesions and 207 for stem lesions, including 96 genes common to both conditions. Common genes included acr genes involved in the detoxification of plant defense phytoalexins and kduD, kduI, eda (=kdgA), gudD, garK, garL, and garR genes involved in the assimilation of pectin and galactarate. In root colonization, Tn-seq highlighted 83 genes, all different from those in stem and tuber lesion conditions. They encode the exploitation of organic and mineral nutrients (dpp, ddp, dctA, and pst) including glucuronate (kdgK and yeiQ) and synthesis of metabolites: cellulose (celY and bcs), aryl polyene (ape), and oocydin (ooc). We constructed in-frame deletion mutants of bcsA, ddpA, apeH, and pstA genes. All mutants were virulent in stem infection assays, but they were impaired in the competitive colonization of roots. In addition, the ΔpstA mutant was impaired in its capacity to colonize progeny tubers. Overall, this work distinguished two metabolic networks supporting either an oligotrophic lifestyle on roots or a copiotrophic lifestyle in lesions. This work revealed novel traits and pathways important for understanding how the D. solani pathogen efficiently survives on roots, persists in the environment, and colonizes progeny tubers.
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Affiliation(s)
- Kévin Robic
- French Federation of Seed Potato Growers (FN3PT/inov3PT), Paris, France
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Euphrasie Munier
- French Federation of Seed Potato Growers (FN3PT/inov3PT), Paris, France
| | - Géraldine Effantin
- Univ Lyon, Université Claude Bernard Lyon1, CNRS, INSA Lyon, UMR5240 MAP, Lyon, France
| | - Joy Lachat
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Delphine Naquin
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Erwan Gueguen
- Univ Lyon, Université Claude Bernard Lyon1, CNRS, INSA Lyon, UMR5240 MAP, Lyon, France
| | - Denis Faure
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
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Pan-Genomics of Escherichia albertii for Antibiotic Resistance Profiling in Different Genome Fractions and Natural Product Mediated Intervention: In Silico Approach. Life (Basel) 2023; 13:life13020541. [PMID: 36836896 PMCID: PMC9962377 DOI: 10.3390/life13020541] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Accepted: 02/09/2023] [Indexed: 02/17/2023] Open
Abstract
Escherichia albertii is an emerging, enteric pathogen of significance. It was first isolated in 2003 from a pediatric diarrheal sample from Bangladesh. In this study, a comprehensive in silico strategy was followed to first list out antibiotic-resistant genes from core, accessory and unique genome fractions of 95 available genomes of E. albertii. Then, 56 drug targets were identified from the core essential genome. Finally, ZipA, an essential cell division protein that stabilizes the FtsZ protofilaments by cross-linking them and serves as a cytoplasmic membrane anchor for the Z ring, was selected for further downstream processing. It was computationally modeled using a threading approach, followed by virtual screening of two phytochemical libraries, Ayurvedic (n = 2103 compounds) and Traditional Chinese Medicine (n = 36,043 compounds). ADMET profiling, followed by PBPK modeling in the central body compartment, in a population of 250 non-diseased, 250 cirrhotic and 250 renally impaired people was attempted. ZINC85624912 from Chinese medicinal library showed the highest bioavailability and plasma retention. This is the first attempt to simulate the fate of natural products in the body through PBPK. Dynamics simulation of 20 ns for the top three compounds from both libraries was also performed to validate the stability of the compounds. The obtained information from the current study could aid wet-lab scientists to work on the scaffold of screened drug-like compounds from natural resources and could be useful in our quest for therapy against antibiotic-resistant E. albertii.
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Khayi S, Chan KG, Faure D. Patterns of Genomic Variations in the Plant Pathogen Dickeya solani. Microorganisms 2022; 10:2254. [PMID: 36422324 PMCID: PMC9699125 DOI: 10.3390/microorganisms10112254] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 11/07/2022] [Accepted: 11/08/2022] [Indexed: 01/14/2024] Open
Abstract
The plant pathogen Dickeya solani causes soft rot and blackleg diseases in several crops including Solanum tuberosum. Unveiling the patterns of its diversity contributes to understanding the emergence and virulence of this pathogen in potato agro-systems. In this study, we analyzed the genome of several D. solani strains exhibiting an atypically high number of genetic variations. Variant calling and phylogenomics support the evidence that the strains RNS10-105-1A, A623S-20A-17 and RNS05.1.2A belong to a divergent sub-group of D. solani for which we proposed RNS05.1.2A as a reference strain. In addition, we showed that the variations (1253 to 1278 snp/indels) in strains RNS13-30-1A, RNS13-31-1A and RNS13-48-1A were caused by a horizontal gene transfer event from a donor belonging to the D. solani RNS05.1.2A subgroup. The overall results highlight the patterns driving the diversification in D. solani species. This work contributes to understanding patterns and causes of diversity in the emerging pathogen D. solani.
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Affiliation(s)
- Slimane Khayi
- Biotechnology Research Unit, Regional Center of Agricultural Research of Rabat, National Institute of Agricultural Research (INRA), Avenue Ennasr, BP 415 Rabat Principale, Rabat 10090, Morocco
| | - Kok-Gan Chan
- Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur 50603, Malaysia
- International Genome Centre, Jiangsu University, Zhenjiang 212100, China
| | - Denis Faure
- University of Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91190 Gif-sur-Yvette, France
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Zhang J, Arif M, Shen H, Sun D, Pu X, Hu J, Lin B, Yang Q. Genomic Comparisons and Phenotypic Diversity of Dickeya zeae Strains Causing Bacterial Soft Rot of Banana in China. FRONTIERS IN PLANT SCIENCE 2022; 13:822829. [PMID: 35222482 PMCID: PMC8864124 DOI: 10.3389/fpls.2022.822829] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Accepted: 01/19/2022] [Indexed: 06/14/2023]
Abstract
Bacterial soft rot of banana, caused by Dickeya zeae, is spreading rapidly in important banana growing areas in China and seriously threatens banana production. In this study, we sequenced the high-quality complete genomes of three typical banana strains, MS1 (size: 4,831,702-bp; genome coverages: 538x), MS_2014 (size: 4,740,000-bp; genome coverages: 586x) and MS_2018 (size: 4,787,201-bp; genome coverages: 583x), isolated in 2009, 2014, and 2018, respectively. To determine their genomic and phenotypic diversity with respect to their hosts of origin, they were compared with other D. zeae strains, including another representative banana strain MS2 from China. The sequenced strains were similar in utilization of carbon source and chemical substrates, and general genomic features of GC content, and tRNA and rRNA regions. They were also conserved in most virulence determinants, including gene-encoding secretion systems, plant cell wall degrading enzymes, and exopolysaccharides. We further explored their genomic diversity in the predicted genomic islands (GIs). These GIs were rich in integrases and transposases, where some genomic dissimilarity was observed in the flagellar gene cluster and several secondary metabolite gene clusters. Different constituents of core biosynthetic modules were found within the bacteriocin and aryl polyene (APE) pigment gene clusters, and the strains from banana showed different phenotypes with respect to antibiosis effects and colony pigmentation. Additionally, clustered regularly interspaced short palindromic repeat (CRISPR) and prophage elements, such as type I-F and III-A CRISPR arrays and an intact prophage of MS1-P5, contributed to bacterial diversity. Phylogenetic tree analysis and genome-genome nucleotide comparison confirmed the genomic divergence among the strains isolated from banana. Considering these characteristics, MS2 and MS_2014 probably diverged later than MS1, while MS_2018 was different and more similar to foreign strains isolated from other hosts in several characteristics. Strain MS_2018 caused severe symptoms on banana varieties previously considered moderately resistant or moderately susceptible, including varieties of Cavendish (Musa AAA) and Plantain (Musa ABB). Our study of genomic and phenotypic diversity raises public attention to the risk of spreading new pathogenic variants within banana growing regions and supports development of predictive strategies for disease control.
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Affiliation(s)
- Jingxin Zhang
- Key Laboratory of New Technique for Plant Protection in Guangdong, Institute of Plant Protection, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Mohammad Arif
- Department of Plant and Environmental Protection Sciences, College of Tropical Agriculture and Human Resources, University of Hawai’i at Mānoa, Honolulu, HI, United States
| | - Huifang Shen
- Key Laboratory of New Technique for Plant Protection in Guangdong, Institute of Plant Protection, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Dayuan Sun
- Key Laboratory of New Technique for Plant Protection in Guangdong, Institute of Plant Protection, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Xiaoming Pu
- Key Laboratory of New Technique for Plant Protection in Guangdong, Institute of Plant Protection, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - John Hu
- Department of Plant and Environmental Protection Sciences, College of Tropical Agriculture and Human Resources, University of Hawai’i at Mānoa, Honolulu, HI, United States
| | - Birun Lin
- Key Laboratory of New Technique for Plant Protection in Guangdong, Institute of Plant Protection, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Qiyun Yang
- Key Laboratory of New Technique for Plant Protection in Guangdong, Institute of Plant Protection, Guangdong Academy of Agricultural Sciences, Guangzhou, China
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Helmann TC, Filiatrault MJ, Stodghill PV. Genome-Wide Identification of Genes Important for Growth of Dickeya dadantii and Dickeya dianthicola in Potato (Solanum tuberosum) Tubers. Front Microbiol 2022; 13:778927. [PMID: 35145503 PMCID: PMC8821946 DOI: 10.3389/fmicb.2022.778927] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Accepted: 01/10/2022] [Indexed: 11/18/2022] Open
Abstract
Dickeya species are causal agents of soft rot diseases in many economically important crops, including soft rot disease of potato (Solanum tuberosum). Using random barcode transposon-site sequencing (RB-TnSeq), we generated genome-wide mutant fitness profiles of Dickeya dadantii 3937, Dickeya dianthicola ME23, and Dickeya dianthicola 67-19 isolates collected after passage through several in vitro and in vivo conditions. Though all three strains are pathogenic on potato, D. dadantii 3937 is a well-characterized model while D. dianthicola strains ME23 and 67-19 are recent isolates. Strain ME23 specifically was identified as a representative strain from a 2014 outbreak on potato. This study generated comparable gene fitness measurements across ecologically relevant conditions for both model and non-model strains. Tubers from the potato cultivars “Atlantic,” “Dark Red Norland,” and “Upstate Abundance” provided highly similar conditions for bacterial growth. Using the homolog detection software PyParanoid, we matched fitness values for orthologous genes in the three bacterial strains. Direct comparison of fitness among the strains highlighted shared and variable traits important for growth. Bacterial growth in minimal medium required many metabolic traits that were also essential for competitive growth in planta, such as amino acid, carbohydrate, and nucleotide biosynthesis. Growth in tubers specifically required the pectin degradation gene kduD. Disruption in three putative DNA-binding proteins had strain-specific effects on competitive fitness in tubers. Though the Soft Rot Pectobacteriaceae can cause disease with little host specificity, it remains to be seen the extent to which strain-level variation impacts virulence.
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Affiliation(s)
- Tyler C. Helmann
- Emerging Pests and Pathogens Research Unit, Agricultural Research Service, United States Department of Agriculture, Robert W. Holley Center for Agriculture and Health, Ithaca, NY, United States
| | - Melanie J. Filiatrault
- Emerging Pests and Pathogens Research Unit, Agricultural Research Service, United States Department of Agriculture, Robert W. Holley Center for Agriculture and Health, Ithaca, NY, United States
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, United States
| | - Paul V. Stodghill
- Emerging Pests and Pathogens Research Unit, Agricultural Research Service, United States Department of Agriculture, Robert W. Holley Center for Agriculture and Health, Ithaca, NY, United States
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, United States
- *Correspondence: Paul V. Stodghill,
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Ge T, Jiang H, Tan EH, Johnson SB, Larkin RP, Charkowski AO, Secor G, Hao J. Pangenomic Analysis of Dickeya dianthicola Strains Related to the Outbreak of Blackleg and Soft Rot of Potato in the United States. PLANT DISEASE 2021; 105:3946-3955. [PMID: 34213964 DOI: 10.1094/pdis-03-21-0587-re] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Dickeya dianthicola has caused an outbreak of blackleg and soft rot of potato in the eastern half of the United States since 2015. To investigate genetic diversity of the pathogen, a comparative analysis was conducted on genomes of D. dianthicola strains. Whole genomes of 16 strains from the United States outbreak were assembled and compared with 16 previously sequenced genomes of D. dianthicola isolated from potato or carnation. Among the 32 strains, eight distinct clades were distinguished based on phylogenomic analysis. The outbreak strains were grouped into three clades, with the majority of the strains in clade I. Clade I strains were unique and homogeneous, suggesting a recent incursion of this strain into potato production from alternative hosts or environmental sources. The pangenome of the 32 strains contained 6,693 genes, 3,377 of which were core genes. By screening primary protein subunits associated with virulence from all U.S. strains, we found that many virulence-related gene clusters, such as plant cell wall degrading enzyme genes, flagellar and chemotaxis related genes, two-component regulatory genes, and type I/II/III secretion system genes, were highly conserved but that type IV and type VI secretion system genes varied. The clade I strains encoded two clusters of type IV secretion systems, whereas the clade II and III strains encoded only one cluster. Clade I and II strains encoded one more VgrG/PAAR spike protein than did clade III. Thus, we predicted that the presence of additional virulence-related genes may have enabled the unique clade I strain to become predominant in the U.S. outbreak.
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Affiliation(s)
- Tongling Ge
- School of Food and Agriculture, University of Maine, Orono, ME 04469
| | - He Jiang
- School of Food and Agriculture, University of Maine, Orono, ME 04469
| | - Ek Han Tan
- School of Biology and Ecology, University of Maine, Orono, ME 04469
| | | | - Robert P Larkin
- USDA-ARS, New England Plant, Soil, and Water Laboratory, University of Maine, Orono, ME 04469
| | - Amy O Charkowski
- Department of Agricultural Biology, Colorado State University, Fort Collins, CO 80523
| | - Gary Secor
- Department of Plant Pathology, North Dakota State University, Fargo, ND58108
| | - Jianjun Hao
- School of Food and Agriculture, University of Maine, Orono, ME 04469
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12
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Miroshnikov KA, Evseev PV, Lukianova AA, Ignatov AN. Tailed Lytic Bacteriophages of Soft Rot Pectobacteriaceae. Microorganisms 2021; 9:1819. [PMID: 34576713 PMCID: PMC8472413 DOI: 10.3390/microorganisms9091819] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 08/23/2021] [Accepted: 08/24/2021] [Indexed: 02/07/2023] Open
Abstract
The study of the ecological and evolutionary traits of Soft Rot Pectobacteriaceae (SRP) comprising genera Pectobacterium and Dickeya often involves bacterial viruses (bacteriophages). Bacteriophages are considered to be a prospective tool for the ecologically safe and highly specific protection of plants and harvests from bacterial diseases. Information concerning bacteriophages has been growing rapidly in recent years, and this has included new genomics-based principles of taxonomic distribution. In this review, we summarise the data on phages infecting Pectobacterium and Dickeya that are available in publications and genomic databases. The analysis highlights not only major genomic properties that assign phages to taxonomic families and genera, but also the features that make them potentially suitable for phage control applications. Specifically, there is a discussion of the molecular mechanisms of receptor recognition by the phages and problems concerning the evolution of phage-resistant mutants.
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Affiliation(s)
- Konstantin A Miroshnikov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya Str., 16/10, 117997 Moscow, Russia
- Timiryazev Agricultural Academy, Russian State Agrarian University, Timiryazevskaya Str., 49, 127434 Moscow, Russia
| | - Peter V Evseev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya Str., 16/10, 117997 Moscow, Russia
| | - Anna A Lukianova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya Str., 16/10, 117997 Moscow, Russia
- Timiryazev Agricultural Academy, Russian State Agrarian University, Timiryazevskaya Str., 49, 127434 Moscow, Russia
- Department of Biology, Lomonosov Moscow State University, Leninskie Gory, 1, bldg. 12, 119234 Moscow, Russia
| | - Alexander N Ignatov
- Timiryazev Agricultural Academy, Russian State Agrarian University, Timiryazevskaya Str., 49, 127434 Moscow, Russia
- Agrobiotechnology Department, Agrarian and Technological Institute, RUDN University, Miklukho-Maklaya Str., 6, 117198 Moscow, Russia
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13
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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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14
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Perkowska I, Potrykus M, Siwinska J, Siudem D, Lojkowska E, Ihnatowicz A. Interplay between Coumarin Accumulation, Iron Deficiency and Plant Resistance to Dickeya spp. Int J Mol Sci 2021; 22:ijms22126449. [PMID: 34208600 PMCID: PMC8235353 DOI: 10.3390/ijms22126449] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 06/04/2021] [Accepted: 06/09/2021] [Indexed: 01/17/2023] Open
Abstract
Coumarins belong to a group of secondary metabolites well known for their high biological activities including antibacterial and antifungal properties. Recently, an important role of coumarins in plant resistance to pathogens and their release into the rhizosphere upon pathogen infection was discovered. It is also well documented that coumarins play a crucial role in the Arabidopsis thaliana growth under Fe-limited conditions. However, the mechanisms underlying interplay between plant resistance, accumulation of coumarins and Fe status, remain largely unknown. In this work, we investigated the effect of both mentioned factors on the disease severity using the model system of Arabidopsis/Dickeya spp. molecular interactions. We evaluated the disease symptoms in Arabidopsis plants, wild-type Col-0 and its mutants defective in coumarin accumulation, grown in hydroponic cultures with contrasting Fe regimes and in soil mixes. Under all tested conditions, Arabidopsis plants inoculated with Dickeya solani IFB0099 strain developed more severe disease symptoms compared to lines inoculated with Dickeya dadantii 3937. We also showed that the expression of genes encoding plant stress markers were strongly affected by D. solani IFB0099 infection. Interestingly, the response of plants to D. dadantii 3937 infection was genotype-dependent in Fe-deficient hydroponic solution.
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Affiliation(s)
- Izabela Perkowska
- Laboratory of Plant Protection and Biotechnology, Intercollegiate Faculty of Biotechnology of University of Gdansk and Medical University of Gdansk, University of Gdansk, Abrahama 58, 80-307 Gdansk, Poland; (I.P.); (M.P.); (J.S.); (D.S.); (E.L.)
| | - Marta Potrykus
- Laboratory of Plant Protection and Biotechnology, Intercollegiate Faculty of Biotechnology of University of Gdansk and Medical University of Gdansk, University of Gdansk, Abrahama 58, 80-307 Gdansk, Poland; (I.P.); (M.P.); (J.S.); (D.S.); (E.L.)
- Department of Environmental Toxicology, Faculty of Health Sciences with Institute of Maritime and Tropical Medicine, Medical University of Gdansk, Debowa 23 A, 80-204 Gdansk, Poland
| | - Joanna Siwinska
- Laboratory of Plant Protection and Biotechnology, Intercollegiate Faculty of Biotechnology of University of Gdansk and Medical University of Gdansk, University of Gdansk, Abrahama 58, 80-307 Gdansk, Poland; (I.P.); (M.P.); (J.S.); (D.S.); (E.L.)
| | - Dominika Siudem
- Laboratory of Plant Protection and Biotechnology, Intercollegiate Faculty of Biotechnology of University of Gdansk and Medical University of Gdansk, University of Gdansk, Abrahama 58, 80-307 Gdansk, Poland; (I.P.); (M.P.); (J.S.); (D.S.); (E.L.)
| | - Ewa Lojkowska
- Laboratory of Plant Protection and Biotechnology, Intercollegiate Faculty of Biotechnology of University of Gdansk and Medical University of Gdansk, University of Gdansk, Abrahama 58, 80-307 Gdansk, Poland; (I.P.); (M.P.); (J.S.); (D.S.); (E.L.)
| | - Anna Ihnatowicz
- Laboratory of Plant Protection and Biotechnology, Intercollegiate Faculty of Biotechnology of University of Gdansk and Medical University of Gdansk, University of Gdansk, Abrahama 58, 80-307 Gdansk, Poland; (I.P.); (M.P.); (J.S.); (D.S.); (E.L.)
- Correspondence: ; Tel.: +48-58-5236330
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15
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Pédron J, Schaerer S, Kellenberger I, Van Gijsegem F. Early Emergence of Dickeya solani Revealed by Analysis of Dickeya Diversity of Potato Blackleg and Soft Rot Causing Pathogens in Switzerland. Microorganisms 2021; 9:microorganisms9061187. [PMID: 34072830 PMCID: PMC8226965 DOI: 10.3390/microorganisms9061187] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 05/14/2021] [Accepted: 05/21/2021] [Indexed: 11/16/2022] Open
Abstract
Blackleg and soft rot in potato caused by Pectobacterium and Dickeya enterobacteral genera are among the most destructive bacterial diseases in this crop worldwide. In Europe, over the last century, Pectobacterium spp. were the predominant causal agents of these diseases. As for Dickeya, before the large outbreak caused by D. solani in the 2000s, only D. dianthicola was isolated in Europe. The population dynamics of potato blackleg causing soft rot Pectobacteriaceae was, however, different in Switzerland as compared to that in other European countries with a high incidence (60 up to 90%) of Dickeya species (at the time called Erwinia chrysanthemi) already in the 1980s. To pinpoint what may underlie this Swiss peculiarity, we analysed the diversity present in the E. chrysanthemi Agroscope collection gathering potato isolates from 1985 to 2000s. Like elsewhere in Europe during this period, the majority of Swiss isolates belonged to D. dianthicola. However, we also identified a few isolates, such as D. chrysanthemi and D. oryzeae, two species that have not yet been reported in potatoes in Europe. Interestingly, this study allowed the characterisation of two "early" D. solani isolated in the 1990s. Genomic comparison between these early D. solani strains and strains isolated later during the large outbreak in the 2000s in Europe revealed only a few SNP and gene content differences, none of them affecting genes known to be important for virulence.
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Affiliation(s)
- Jacques Pédron
- Institute of Ecology and Environmental Sciences-Paris, Sorbonne Université, INRAE, 4 Place Jussieu, F-75252 Paris, France;
| | - Santiago Schaerer
- Agroscope Changins, Domaine de Recherche Protection des Végétaux, CH-1260 Nyon, Switzerland; (S.S.); (I.K.)
| | - Isabelle Kellenberger
- Agroscope Changins, Domaine de Recherche Protection des Végétaux, CH-1260 Nyon, Switzerland; (S.S.); (I.K.)
| | - Frédérique Van Gijsegem
- Institute of Ecology and Environmental Sciences-Paris, Sorbonne Université, INRAE, 4 Place Jussieu, F-75252 Paris, France;
- Correspondence:
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16
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Dzimitrowicz A, Jamroz P, Pohl P, Babinska W, Terefinko D, Sledz W, Motyka-Pomagruk A. Multivariate Optimization of the FLC-dc-APGD-Based Reaction-Discharge System for Continuous Production of a Plasma-Activated Liquid of Defined Physicochemical and Anti-Phytopathogenic Properties. Int J Mol Sci 2021; 22:ijms22094813. [PMID: 34062832 PMCID: PMC8124219 DOI: 10.3390/ijms22094813] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 04/23/2021] [Accepted: 04/27/2021] [Indexed: 01/09/2023] Open
Abstract
To the present day, no efficient plant protection method against economically important bacterial phytopathogens from the Pectobacteriaceae family has been implemented into agricultural practice. In this view, we have performed a multivariate optimization of the operating parameters of the reaction-discharge system, employing direct current atmospheric pressure glow discharge, generated in contact with a flowing liquid cathode (FLC-dc-APGD), for the production of a plasma-activated liquid (PAL) of defined physicochemical and anti-phytopathogenic properties. As a result, the effect of the operating parameters on the conductivity of PAL acquired under these conditions was assessed. The revealed optimal operating conditions, under which the PAL of the highest conductivity was obtained, were as follows: flow rate of the solution equaled 2.0 mL min-1, the discharge current was 30 mA, and the inorganic salt concentration (ammonium nitrate, NH4NO3) in the solution turned out to be 0.50% (m/w). The developed PAL exhibited bacteriostatic and bactericidal properties toward Dickeya solani IFB0099 and Pectobacterium atrosepticum IFB5103 strains, with minimal inhibitory and minimal bactericidal concentrations equaling 25%. After 24 h exposure to 25% PAL, 100% (1-2 × 106) of D. solani and P. atrosepticum cells lost viability. We attributed the antibacterial properties of PAL to the presence of deeply penetrating, reactive oxygen and nitrogen species (RONS), which were, in this case, OH, O, O3, H2O2, HO2, NH, N2, N2+, NO2-, NO3-, and NH4+. Putatively, the generated low-cost, eco-friendly, easy-to-store, and transport PAL, exhibiting the required antibacterial and physicochemical properties, may find numerous applications in the plant protection sector.
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Affiliation(s)
- Anna Dzimitrowicz
- Department of Analytical Chemistry and Chemical Metallurgy, Wroclaw University of Science and Technology, 27 Wybrzeze St. Wyspianskiego, 50-370 Wroclaw, Poland; (P.J.); (P.P.); (D.T.)
- Correspondence: (A.D.); (A.M.-P.); Tel.: +48-71-320-2815 (A.D.); +48-58-523-6330 (A.M.-P.)
| | - Piotr Jamroz
- Department of Analytical Chemistry and Chemical Metallurgy, Wroclaw University of Science and Technology, 27 Wybrzeze St. Wyspianskiego, 50-370 Wroclaw, Poland; (P.J.); (P.P.); (D.T.)
| | - Pawel Pohl
- Department of Analytical Chemistry and Chemical Metallurgy, Wroclaw University of Science and Technology, 27 Wybrzeze St. Wyspianskiego, 50-370 Wroclaw, Poland; (P.J.); (P.P.); (D.T.)
| | - Weronika Babinska
- Laboratory of Plant Protection and Biotechnology, Intercollegiate Faculty of Biotechnology University of Gdansk and Medical University of Gdansk, University of Gdansk, 58 Abrahama, 80-307 Gdansk, Poland; (W.B.); (W.S.)
| | - Dominik Terefinko
- Department of Analytical Chemistry and Chemical Metallurgy, Wroclaw University of Science and Technology, 27 Wybrzeze St. Wyspianskiego, 50-370 Wroclaw, Poland; (P.J.); (P.P.); (D.T.)
| | - Wojciech Sledz
- Laboratory of Plant Protection and Biotechnology, Intercollegiate Faculty of Biotechnology University of Gdansk and Medical University of Gdansk, University of Gdansk, 58 Abrahama, 80-307 Gdansk, Poland; (W.B.); (W.S.)
| | - Agata Motyka-Pomagruk
- Laboratory of Plant Protection and Biotechnology, Intercollegiate Faculty of Biotechnology University of Gdansk and Medical University of Gdansk, University of Gdansk, 58 Abrahama, 80-307 Gdansk, Poland; (W.B.); (W.S.)
- Correspondence: (A.D.); (A.M.-P.); Tel.: +48-71-320-2815 (A.D.); +48-58-523-6330 (A.M.-P.)
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17
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Zoledowska S, Motyka-Pomagruk A, Misztak A, Lojkowska E. Comparative Genomics, from the Annotated Genome to Valuable Biological Information: A Case Study. Methods Mol Biol 2021; 2242:91-112. [PMID: 33961220 DOI: 10.1007/978-1-0716-1099-2_7] [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: 06/12/2023]
Abstract
High availability of fast, cheap, and high-throughput next generation sequencing techniques resulted in acquisition of numerous de novo sequenced and assembled bacterial genomes. It rapidly became clear that digging out useful biological information from such a huge amount of data presents a considerable challenge. In this chapter we share our experience with utilization of several handy open source comparative genomic tools. All of them were applied in the studies focused on revealing inter- and intraspecies variation in pectinolytic plant pathogenic bacteria classified to Dickeya solani and Pectobacterium parmentieri. As the described software performed well on the species within the Pectobacteriaceae family, it presumably may be readily utilized on some closely related taxa from the Enterobacteriaceae family. First of all, implementation of various annotation software is discussed and compared. Then, tools computing whole genome comparisons including generation of circular juxtapositions of multiple sequences, revealing the order of synteny blocks or calculation of ANI or Tetra values are presented. Besides, web servers intended either for functional annotation of the genes of interest or for detection of genomic islands, plasmids, prophages, CRISPR/Cas are described. Last but not least, utilization of the software designed for pangenome studies and the further downstream analyses is explained. The presented work not only summarizes broad possibilities assured by the comparative genomic approach but also provides a user-friendly guide that might be easily followed by nonbioinformaticians interested in undertaking similar studies.
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Affiliation(s)
- Sabina Zoledowska
- Department of Plant Protection and Biotechnology, Intercollegiate Faculty of Biotechnology University of Gdansk & Medical University of Gdansk, University of Gdansk, Gdansk, 58 Abrahama, Poland
- Institute of Biotechnology and Molecular Medicine, Gdansk, 3 Trzy Lipy, Poland
| | - Agata Motyka-Pomagruk
- Department of Plant Protection and Biotechnology, Intercollegiate Faculty of Biotechnology University of Gdansk & Medical University of Gdansk, University of Gdansk, Gdansk, 58 Abrahama, Poland
| | - Agnieszka Misztak
- Department of Plant Protection and Biotechnology, Intercollegiate Faculty of Biotechnology University of Gdansk & Medical University of Gdansk, University of Gdansk, Gdansk, 58 Abrahama, Poland
| | - Ewa Lojkowska
- Department of Plant Protection and Biotechnology, Intercollegiate Faculty of Biotechnology University of Gdansk & Medical University of Gdansk, University of Gdansk, Gdansk, 58 Abrahama, Poland.
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18
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Motyka-Pomagruk A, Zoledowska S, Kabza M, Lojkowska E. PacBio-Based Protocol for Bacterial Genome Assembly. Methods Mol Biol 2021; 2242:3-14. [PMID: 33961214 DOI: 10.1007/978-1-0716-1099-2_1] [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: 06/12/2023]
Abstract
Acquisition of high-quality bacterial genomes is fundamental, while having in mind investigation of subtitle intraspecies variation in addition to development of sensitive species-specific tools for detection and identification of the pathogens. In this view, Pacific Biosciences technology seems highly tempting taking into consideration over 10,000 bp length of the generated reads. In this work, we describe a bacterial genome assembly pipeline based on open-source software that might be handled also by non-bioinformaticians interested in transformation of sequencing data into reliable biological information. With the use of this method, we successfully closed six Dickeya solani genomes, while the assembly process was run just on a slightly improved desktop computer.
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Affiliation(s)
- Agata Motyka-Pomagruk
- Department of Plant Protection and Biotechnology, Intercollegiate Faculty of Biotechnology, University of Gdansk & Medical University of Gdansk, University of Gdansk, Gdansk, Poland
| | - Sabina Zoledowska
- Department of Plant Protection and Biotechnology, Intercollegiate Faculty of Biotechnology, University of Gdansk & Medical University of Gdansk, University of Gdansk, Gdansk, Poland
- Institute of Biotechnology and Molecular Medicine, Gdansk, Poland
| | - Michal Kabza
- Department of Integrative Genomics, Faculty of Biology, Adam Mickiewicz University, Poznan, Poland
| | - Ewa Lojkowska
- Department of Plant Protection and Biotechnology, Intercollegiate Faculty of Biotechnology, University of Gdansk & Medical University of Gdansk, University of Gdansk, Gdansk, Poland.
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19
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Blin P, Robic K, Khayi S, Cigna J, Munier E, Dewaegeneire P, Laurent A, Jaszczyszyn Y, Hong KW, Chan KG, Beury A, Reverchon S, Giraud T, Hélias V, Faure D. Pattern and causes of the establishment of the invasive bacterial potato pathogen Dickeya solani and of the maintenance of the resident pathogen D. dianthicola. Mol Ecol 2020; 30:608-624. [PMID: 33226678 DOI: 10.1111/mec.15751] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 11/09/2020] [Accepted: 11/18/2020] [Indexed: 11/29/2022]
Abstract
Invasive pathogens can be a threat when they affect human health, food production or ecosystem services, by displacing resident species, and we need to understand the cause of their establishment. We studied the patterns and causes of the establishment of the pathogen Dickeya solani that recently invaded potato agrosystems in Europe by assessing its invasion dynamics and its competitive ability against the closely related resident D. dianthicola species. Epidemiological records over one decade in France revealed the establishment of D. solani and the maintenance of the resident D. dianthicola in potato fields exhibiting blackleg symptoms. Using experimentations, we showed that D. dianthicola caused a higher symptom incidence on aerial parts of potato plants than D. solani, while D. solani was more aggressive on tubers (i.e. with more severe symptoms). In co-infection assays, D. dianthicola outcompeted D. solani in aerial parts, while the two species co-existed in tubers. A comparison of 76 D. solani genomes (56 of which have been sequenced here) revealed balanced frequencies of two previously uncharacterized alleles, VfmBPro and VfmBSer , at the vfmB virulence gene. Experimental inoculations showed that the VfmBSer population was more aggressive on tubers, while the VfmBPro population outcompeted the VfmBSer population in stem lesions, suggesting an important role of the vfmB virulence gene in the ecology of the pathogens. This study thus brings novel insights allowing a better understanding of the pattern and causes of the D.solani invasion into potato production agrosystems, and the reasons why the endemic D. dianthicola nevertheless persisted.
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Affiliation(s)
- Pauline Blin
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Paris-Saclay University, Gif-sur-Yvette, France
| | - Kévin Robic
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Paris-Saclay University, Gif-sur-Yvette, France.,French Federation of Seed Potato Growers (FN3PT/inov3PT), Paris, France
| | - Slimane Khayi
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Paris-Saclay University, Gif-sur-Yvette, France.,Biotechnology Research Unit, National Institute for Agronomic Research (INRA), Rabat, Morocco
| | - Jérémy Cigna
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Paris-Saclay University, Gif-sur-Yvette, France.,French Federation of Seed Potato Growers (FN3PT/inov3PT), Paris, France
| | - Euphrasie Munier
- French Federation of Seed Potato Growers (FN3PT/inov3PT), Paris, France
| | | | - Angélique Laurent
- French Federation of Seed Potato Growers (FN3PT/inov3PT), Paris, France
| | - Yan Jaszczyszyn
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Paris-Saclay University, Gif-sur-Yvette, France
| | - Kar-Wai Hong
- International Genome Centre, Jiangsu University, Zhenjiang, China
| | - Kok-Gan Chan
- International Genome Centre, Jiangsu University, Zhenjiang, China.,Division of Genetics and Molecular Biology, Institute of Biological Sciences, University of Malaya, Kuala Lumpur, Malaysia
| | - Amélie Beury
- French Federation of Seed Potato Growers (FN3PT/inov3PT), Paris, France
| | - Sylvie Reverchon
- Microbiologie Adaptation et Pathogénie (MAP), UMR5240, CNRS, INSA-Lyon, Univ. Lyon, Université Claude Bernard, Lyon 1, Villeurbanne, France
| | - Tatiana Giraud
- Ecologie Systématique et Evolution, CNRS, AgroParisTech, Université Paris-Saclay, Orsay, France
| | - Valérie Hélias
- French Federation of Seed Potato Growers (FN3PT/inov3PT), Paris, France
| | - Denis Faure
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Paris-Saclay University, Gif-sur-Yvette, France
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20
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Czajkowski R, Fikowicz-Krosko J, Maciag T, Rabalski L, Czaplewska P, Jafra S, Richert M, Krychowiak-Maśnicka M, Hugouvieux-Cotte-Pattat N. Genome-Wide Identification of Dickeya solani Transcriptional Units Up-Regulated in Response to Plant Tissues From a Crop-Host Solanum tuberosum and a Weed-Host Solanum dulcamara. FRONTIERS IN PLANT SCIENCE 2020; 11:580330. [PMID: 32983224 PMCID: PMC7492773 DOI: 10.3389/fpls.2020.580330] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2020] [Accepted: 08/18/2020] [Indexed: 05/25/2023]
Abstract
Dickeya solani is a Gram-negative bacterium able to cause disease symptoms on a variety of crop and ornamental plants worldwide. Weeds including Solanum dulcamara (bittersweet nightshade) growing near agricultural fields have been reported to support populations of soft rot bacteria in natural settings. However, little is known about the specific interaction of D. solani with such weed plants that may contribute to its success as an agricultural pathogen. The aim of this work was to assess the interaction of D. solani with its crop plant (Solanum tuberosum) and an alternative (S. dulcamara) host plant. From a collection of 10,000 Tn5 transposon mutants of D. solani IPO2222 carrying an inducible, promotorless gusA reporter gene, 210 were identified that exhibited plant tissue-dependent expression of the gene/operon into which the Tn5 insertion had occurred. Thirteen Tn5 mutants exhibiting the greatest plant tissue induction of such transcriptional units in S. tuberosum or S. dulcamara as measured by qRT-PCR were assessed for plant host colonization, virulence, and ability to macerate plant tissue, as well as phenotypes likely to contribute to the ecological fitness of D. solani, including growth rate, carbon and nitrogen source utilization, motility, chemotaxis toward plant extracts, biofilm formation, growth under anaerobic conditions and quorum sensing. These 13 transcriptional units encode proteins involved in bacterial interactions with plants, with functions linked to cell envelope structure, chemotaxis and carbon metabolism. The selected 13 genes/operons were differentially expressed in, and thus contributed preferentially to D. solani fitness in potato and/or S. dulcamara stem, leaf, and root tissues.
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Affiliation(s)
- Robert Czajkowski
- Division of Biologically Active Compounds, Intercollegiate Faculty of Biotechnology UG and MUG, University of Gdansk, Gdansk, Poland
| | - Jakub Fikowicz-Krosko
- Division of Biologically Active Compounds, Intercollegiate Faculty of Biotechnology UG and MUG, University of Gdansk, Gdansk, Poland
| | - Tomasz Maciag
- Division of Biological Plant Protection, Intercollegiate Faculty of Biotechnology UG and MUG, University of Gdansk, Gdansk, Poland
| | - Lukasz Rabalski
- Division of Recombinant Vaccines, Intercollegiate Faculty of Biotechnology UG and MUG, University of Gdansk, Gdansk, Poland
| | - Paulina Czaplewska
- Laboratory of Mass Spectrometry - Core Facility Laboratories, Intercollegiate Faculty of Biotechnology UG and MUG, University of Gdansk, Gdansk, Poland
| | - Sylwia Jafra
- Division of Biological Plant Protection, Intercollegiate Faculty of Biotechnology UG and MUG, University of Gdansk, Gdansk, Poland
| | - Malwina Richert
- Laboratory of Electron Microscopy, Faculty of Biology, University of Gdansk, Gdansk, Poland
| | - Marta Krychowiak-Maśnicka
- Division of Biologically Active Compounds, Intercollegiate Faculty of Biotechnology UG and MUG, University of Gdansk, Gdansk, Poland
| | - Nicole Hugouvieux-Cotte-Pattat
- Microbiology Adaptation and Pathogenesis, CNRS UMR5240, University of Lyon, University Claude Bernard Lyon 1, INSA Lyon, Villeurbanne, France
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Comparative genomics and pangenome-oriented studies reveal high homogeneity of the agronomically relevant enterobacterial plant pathogen Dickeya solani. BMC Genomics 2020; 21:449. [PMID: 32600255 PMCID: PMC7325237 DOI: 10.1186/s12864-020-06863-w] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Accepted: 06/22/2020] [Indexed: 11/11/2022] Open
Abstract
Background Dickeya solani is an important plant pathogenic bacterium causing severe losses in European potato production. This species draws a lot of attention due to its remarkable virulence, great devastating potential and easier spread in contrast to other Dickeya spp. In view of a high need for extensive studies on economically important soft rot Pectobacteriaceae, we performed a comparative genomics analysis on D. solani strains to search for genetic foundations that would explain the differences in the observed virulence levels within the D. solani population. Results High quality assemblies of 8 de novo sequenced D. solani genomes have been obtained. Whole-sequence comparison, ANIb, ANIm, Tetra and pangenome-oriented analyses performed on these genomes and the sequences of 14 additional strains revealed an exceptionally high level of homogeneity among the studied genetic material of D. solani strains. With the use of 22 genomes, the pangenome of D. solani, comprising 84.7% core, 7.2% accessory and 8.1% unique genes, has been almost completely determined, suggesting the presence of a nearly closed pangenome structure. Attribution of the genes included in the D. solani pangenome fractions to functional COG categories showed that higher percentages of accessory and unique pangenome parts in contrast to the core section are encountered in phage/mobile elements- and transcription- associated groups with the genome of RNS 05.1.2A strain having the most significant impact. Also, the first D. solani large-scale genome-wide phylogeny computed on concatenated core gene alignments is herein reported. Conclusions The almost closed status of D. solani pangenome achieved in this work points to the fact that the unique gene pool of this species should no longer expand. Such a feature is characteristic of taxa whose representatives either occupy isolated ecological niches or lack efficient mechanisms for gene exchange and recombination, which seems rational concerning a strictly pathogenic species with clonal population structure. Finally, no obvious correlations between the geographical origin of D. solani strains and their phylogeny were found, which might reflect the specificity of the international seed potato market.
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Zoledowska S, Motyka-Pomagruk A, Sledz W, Mengoni A, Lojkowska E. High genomic variability in the plant pathogenic bacterium Pectobacterium parmentieri deciphered from de novo assembled complete genomes. BMC Genomics 2018; 19:751. [PMID: 30326842 PMCID: PMC6192338 DOI: 10.1186/s12864-018-5140-9] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2018] [Accepted: 10/03/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Pectobacterium parmentieri is a newly established species within the plant pathogenic family Pectobacteriaceae. Bacteria belonging to this species are causative agents of diseases in economically important crops (e.g. potato) in a wide range of different environmental conditions, encountered in Europe, North America, Africa, and New Zealand. Severe disease symptoms result from the activity of P. parmentieri virulence factors, such as plant cell wall degrading enzymes. Interestingly, we observe significant phenotypic differences among P. parmentieri isolates regarding virulence factors production and the abilities to macerate plants. To establish the possible genomic basis of these differences, we sequenced 12 genomes of P. parmentieri strains (10 isolated in Poland, 2 in Belgium) with the combined use of Illumina and PacBio approaches. De novo genome assembly was performed with the use of SPAdes software, while annotation was conducted by NCBI Prokaryotic Genome Annotation Pipeline. RESULTS The pan-genome study was performed on 15 genomes (12 de novo assembled and three reference strains: P. parmentieri CFBP 8475T, P. parmentieri SCC3193, P. parmentieri WPP163). The pan-genome includes 3706 core genes, a high number of accessory (1468) genes, and numerous unique (1847) genes. We identified the presence of well-known genes encoding virulence factors in the core genome fraction, but some of them were located in the dispensable genome. A significant fraction of horizontally transferred genes, virulence-related gene duplications, as well as different CRISPR arrays were found, which can explain the observed phenotypic differences. Finally, we found also, for the first time, the presence of a plasmid in one of the tested P. parmentieri strains isolated in Poland. CONCLUSIONS We can hypothesize that a large number of the genes in the dispensable genome and significant genomic variation among P. parmentieri strains could be the basis of the potential wide host range and widespread diffusion of P. parmentieri. The obtained data on the structure and gene content of P. parmentieri strains enabled us to speculate on the importance of high genomic plasticity for P. parmentieri adaptation to different environments.
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Affiliation(s)
- S Zoledowska
- Department of Biotechnology, Intercollegiate Faculty of Biotechnology, University of Gdansk and Medical University of Gdansk, Gdansk, Poland
| | - A Motyka-Pomagruk
- Department of Biotechnology, Intercollegiate Faculty of Biotechnology, University of Gdansk and Medical University of Gdansk, Gdansk, Poland
| | - W Sledz
- Department of Biotechnology, Intercollegiate Faculty of Biotechnology, University of Gdansk and Medical University of Gdansk, Gdansk, Poland
| | - A Mengoni
- Department of Biology, University of Florence, Sesto Fiorentino, Florence, Italy
| | - E Lojkowska
- Department of Biotechnology, Intercollegiate Faculty of Biotechnology, University of Gdansk and Medical University of Gdansk, Gdansk, Poland.
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