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Bricout A, Morris CE, Chandeysson C, Duban M, Boistel C, Chataigné G, Lecouturier D, Jacques P, Leclère V, Rochex A. The Diversity of Lipopeptides in the Pseudomonas syringae Complex Parallels Phylogeny and Sheds Light on Structural Diversification during Evolutionary History. Microbiol Spectr 2022; 10:e0145622. [PMID: 36287007 PMCID: PMC9769872 DOI: 10.1128/spectrum.01456-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Accepted: 08/12/2022] [Indexed: 01/05/2023] Open
Abstract
Pseudomonas spp. colonize diverse aquatic and terrestrial habitats and produce a wide variety of secondary metabolites, including lipopeptides. However, previous studies have often examined a limited number of lipopeptide-producing strains. In this study, we performed a systematic analysis of lipopeptide production across a wide data set of strains of the Pseudomonas syringae complex (724) by using a combined bioinformatics, mass spectrometry, and phylogenetics approach. The large P. syringae complex, which is composed of 13 phylogroups, is known to produce factins (including syringafactin-like lipopeptides), mycins (including syringomycin-like lipopeptides), and peptins (such as syringopeptins). We found that 80.8% of P. syringae strains produced lipopeptides and that factins were the most frequently produced (by 96% of the producing strains). P. syringae strains were either factin monoproducers or factin, mycin, and peptin coproducers or lipopeptide nonproducers in relation to their phylogenetic group. Our analyses led to the discovery of 42 new lipopeptides, bringing the number of lipopeptides identified in the P. syringae complex to 75. We also highlighted that factins have high structural resemblance and are widely distributed among the P. syringae complex, while mycins and peptins are highly structurally diverse and patchily distributed. IMPORTANCE This study provides an insight into the P. syringae metabolome that emphasizes the high diversity of lipopeptides produced within the P. syringae complex. The production profiles of strains are closely related to their phylogenetic classification, indicating that structural diversification of lipopeptides parallels the phylogeny of this bacterial complex, thereby further illustrating the inherent importance of lipopeptides in the ecology of this group of bacteria throughout its evolutionary history. Furthermore, this overview of P. syringae lipopeptides led us to propose a refined classification that could be extended to the lipopeptides produced by other bacterial groups.
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Affiliation(s)
- Alexandre Bricout
- Université de Lille, Université de Liège, UMRt BioEcoAgro 1158-INRAE, Métabolites Secondaires d’Origine Microbienne, Charles Viollette Institute, Lille, France
- Agence de la transition écologique (ADEME), Angers, France
| | | | | | - Matthieu Duban
- Université de Lille, Université de Liège, UMRt BioEcoAgro 1158-INRAE, Métabolites Secondaires d’Origine Microbienne, Charles Viollette Institute, Lille, France
| | - Corinne Boistel
- Université de Lille, Université de Liège, UMRt BioEcoAgro 1158-INRAE, Métabolites Secondaires d’Origine Microbienne, Charles Viollette Institute, Lille, France
| | - Gabrielle Chataigné
- Université de Lille, Université de Liège, UMRt BioEcoAgro 1158-INRAE, Métabolites Secondaires d’Origine Microbienne, Charles Viollette Institute, Lille, France
| | - Didier Lecouturier
- Université de Lille, Université de Liège, UMRt BioEcoAgro 1158-INRAE, Métabolites Secondaires d’Origine Microbienne, Charles Viollette Institute, Lille, France
| | - Philippe Jacques
- Université de Liège, Université de Lille, UMRt BioEcoAgro 1158-INRAE, Métabolites Secondaires d’Origine Microbienne, TERRA Teaching and Research Centre, Gembloux Agro-Bio Tech, Gembloux, Belgium
| | - Valérie Leclère
- Université de Lille, Université de Liège, UMRt BioEcoAgro 1158-INRAE, Métabolites Secondaires d’Origine Microbienne, Charles Viollette Institute, Lille, France
| | - Alice Rochex
- Université de Lille, Université de Liège, UMRt BioEcoAgro 1158-INRAE, Métabolites Secondaires d’Origine Microbienne, Charles Viollette Institute, Lille, France
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Morris CE, Ramirez N, Berge O, Lacroix C, Monteil C, Chandeysson C, Guilbaud C, Blischke A, Sigurbjörnsdóttir MA, Vilhelmsson OÞ. Pseudomonas syringae on Plants in Iceland Has Likely Evolved for Several Million Years Outside the Reach of Processes That Mix This Bacterial Complex across Earth’s Temperate Zones. Pathogens 2022; 11:pathogens11030357. [PMID: 35335680 PMCID: PMC8951587 DOI: 10.3390/pathogens11030357] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Revised: 03/03/2022] [Accepted: 03/08/2022] [Indexed: 12/04/2022] Open
Abstract
Here we report, for the first time, the occurrence of the bacteria from the species complex Pseudomonas syringae in Iceland. We isolated this bacterium from 35 of the 38 samples of angiosperms, moss, ferns and leaf litter collected across the island from five habitat categories (boreal heath, forest, subalpine and glacial scrub, grazed pasture, lava field). The culturable populations of P. syringae on these plants varied in size across 6 orders of magnitude, were as dense as 107 cfu g−1 and were composed of strains in phylogroups 1, 2, 4, 6, 7, 10 and 13. P. syringae densities were significantly greatest on monocots compared to those on dicots and mosses and were about two orders of magnitude greater in grazed pastures compared to all other habitats. The phylogenetic diversity of 609 strains of P. syringae from Iceland was compared to that of 933 reference strains of P. syringae from crops and environmental reservoirs collected from 27 other countries based on a 343 bp sequence of the citrate synthase (cts) housekeeping gene. Whereas there were examples of identical cts sequences across multiple countries and continents among the reference strains indicating mixing among these countries and continents, the Icelandic strains grouped into monophyletic lineages that were unique compared to all of the reference strains. Based on estimates of the time of divergence of the Icelandic genetic lineages of P. syringae, the geological, botanical and land use history of Iceland, and atmospheric circulation patterns, we propose scenarios whereby it would be feasible for P. syringae to have evolved outside the reach of processes that tend to mix this bacterial complex across the planet elsewhere.
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Affiliation(s)
- Cindy E. Morris
- INRAE, Pathologie Végétale, F-84140 Montfavet, France; (O.B.); (C.L.); (C.M.); (C.C.); (C.G.)
- Correspondence:
| | - Natalia Ramirez
- Faculty of Natural Resource Sciences, University of Akureyri, 600 Akureyri, Iceland; (N.R.); (M.A.S.); (O.Þ.V.)
| | - Odile Berge
- INRAE, Pathologie Végétale, F-84140 Montfavet, France; (O.B.); (C.L.); (C.M.); (C.C.); (C.G.)
| | - Christelle Lacroix
- INRAE, Pathologie Végétale, F-84140 Montfavet, France; (O.B.); (C.L.); (C.M.); (C.C.); (C.G.)
| | - Cécile Monteil
- INRAE, Pathologie Végétale, F-84140 Montfavet, France; (O.B.); (C.L.); (C.M.); (C.C.); (C.G.)
| | - Charlotte Chandeysson
- INRAE, Pathologie Végétale, F-84140 Montfavet, France; (O.B.); (C.L.); (C.M.); (C.C.); (C.G.)
| | - Caroline Guilbaud
- INRAE, Pathologie Végétale, F-84140 Montfavet, France; (O.B.); (C.L.); (C.M.); (C.C.); (C.G.)
| | - Anett Blischke
- ÍSOR, Iceland GeoSurvey, Rangárvöllum við Hlíðarfjallsveg, 600 Akureyri, Iceland;
| | | | - Oddur Þ. Vilhelmsson
- Faculty of Natural Resource Sciences, University of Akureyri, 600 Akureyri, Iceland; (N.R.); (M.A.S.); (O.Þ.V.)
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Oueslati M, Mulet M, Zouaoui M, Chandeysson C, Lalucat J, Hajlaoui MR, Berge O, García-Valdés E, Sadfi-Zouaoui N. Diversity of pathogenic Pseudomonas isolated from citrus in Tunisia. AMB Express 2020; 10:198. [PMID: 33130970 PMCID: PMC7604283 DOI: 10.1186/s13568-020-01134-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2020] [Accepted: 10/21/2020] [Indexed: 11/12/2022] Open
Abstract
The damages observed in Tunisian citrus orchards have prompted studies on the Pseudomonas spp. responsible for blast and black pit. Prospective orchards between 2015 and 2017 showed that the diseases rapidly spread geographically and to new cultivars. A screening of Pseudomonas spp. isolated from symptomatic trees revealed their wide diversity according to phylogenetic analysis of their housekeeping rpoD and cts genes. The majority of strains were affiliated to Pseudomonas syringae pv. syringae (Phylogroup PG02b), previously described in Tunisia. However, they exhibited various BOX-PCR fingerprints and were not clonal. This work demonstrated, for the first time in Tunisia, the involvement of Pseudomonas cerasi (PG02a) and Pseudomonas congelans (PG02c). The latter did not show significant pathogenicity on citrus, but was pathogenic on cantaloupe and active for ice nucleation that could play a role in the disease. A comparative phylogenetic study of citrus pathogens from Iran, Montenegro and Tunisia revealed that P. syringae (PG02b) strains are closely related but again not clonal. Interestingly P. cerasi (PG02a) was isolated in two countries and seems to outspread. However, its role in the diseases is not fully understood and it should be monitored in future studies. The diversity of pathogenic Pseudomonas spp. and the extension of the diseases highlight that they have become complex and synergistic. It opens questions about which factors favor diseases and how to fight against them efficiently and with sustainable means.
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Pédron J, Guyon L, Lecomte A, Blottière L, Chandeysson C, Rochelle-Newall E, Raynaud X, Berge O, Barny MA. Comparison of Environmental and Culture-Derived Bacterial Communities through 16S Metabarcoding: A Powerful Tool to Assess Media Selectivity and Detect Rare Taxa. Microorganisms 2020; 8:microorganisms8081129. [PMID: 32727027 PMCID: PMC7464939 DOI: 10.3390/microorganisms8081129] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Revised: 07/16/2020] [Accepted: 07/23/2020] [Indexed: 12/19/2022] Open
Abstract
To compare environmental and culture-derived microbial communities, we performed 16S metabarcoding of uncultured samples and their culture-derived bacterial lawns. Microbial communities were obtained from freshwater river samples representative of an anthropization gradient along a river stream. Their culture-derived bacterial lawns were obtained by growing aliquots of the samples on a broad range medium and on two different semi-selective media. The V3–V4 16S rRNA region was amplified and sequenced. The bacterial diversity of water samples decreased from the upper to lower stream sampling sites and, as expected, these differences were mostly suppressed by the culture step. Overall, the diversity of cultured-derived bacterial communities reflected selectivity of each tested medium. Comparison of treatments indicated that the culture selected both detected and rare undetected environmental species. Accurate detection of rare environmental bacteria of the Pectobacterium genus by 16S metabarcoding of the culture lawn was demonstrated. Interestingly, for abundant taxa, such as those of the Pseudomonas genus, the culture/environment ratio varied between sampled sites, indicating the difficulty of comparing cultured-derived taxa abundance between environmental sites. Finally, our study also highlighted media specificity and complementarity: bacterial communities grown on the two selective media, while selecting a small set of specific species, were mostly a subset of the bacterial community observed on the broad range medium.
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Affiliation(s)
- Jacques Pédron
- INRAE, IRD, Institute of Ecology and Environmental Sciences-Paris, Sorbonne Université, IEES-Paris, F-75231 Paris, France; (J.P.); (L.G.); (A.L.); (L.B.); (E.R.-N.); (X.R.)
| | - Léa Guyon
- INRAE, IRD, Institute of Ecology and Environmental Sciences-Paris, Sorbonne Université, IEES-Paris, F-75231 Paris, France; (J.P.); (L.G.); (A.L.); (L.B.); (E.R.-N.); (X.R.)
| | - Amandine Lecomte
- INRAE, IRD, Institute of Ecology and Environmental Sciences-Paris, Sorbonne Université, IEES-Paris, F-75231 Paris, France; (J.P.); (L.G.); (A.L.); (L.B.); (E.R.-N.); (X.R.)
| | - Lydie Blottière
- INRAE, IRD, Institute of Ecology and Environmental Sciences-Paris, Sorbonne Université, IEES-Paris, F-75231 Paris, France; (J.P.); (L.G.); (A.L.); (L.B.); (E.R.-N.); (X.R.)
| | | | - Emma Rochelle-Newall
- INRAE, IRD, Institute of Ecology and Environmental Sciences-Paris, Sorbonne Université, IEES-Paris, F-75231 Paris, France; (J.P.); (L.G.); (A.L.); (L.B.); (E.R.-N.); (X.R.)
| | - Xavier Raynaud
- INRAE, IRD, Institute of Ecology and Environmental Sciences-Paris, Sorbonne Université, IEES-Paris, F-75231 Paris, France; (J.P.); (L.G.); (A.L.); (L.B.); (E.R.-N.); (X.R.)
| | - Odile Berge
- INRAE, Pathologie Végétale, F-84143 Montfavet, France; (C.C.); (O.B.)
| | - Marie-Anne Barny
- INRAE, IRD, Institute of Ecology and Environmental Sciences-Paris, Sorbonne Université, IEES-Paris, F-75231 Paris, France; (J.P.); (L.G.); (A.L.); (L.B.); (E.R.-N.); (X.R.)
- Correspondence:
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Borschinger B, Bartoli C, Chandeysson C, Guilbaud C, Parisi L, Bourgeay JF, Buisson E, Morris CE. A set of PCRs for rapid identification and characterization of Pseudomonas syringae phylogroups. J Appl Microbiol 2016; 121:903. [PMID: 27528015 DOI: 10.1111/jam.13219] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- B Borschinger
- INRA, Unité de Pathologie Végétale, Domaine de St Maurice, BP 94, 84140, Montfavet, France.,IMBE, Université d'Avignon et des Pays de Vaucluse, UMR CNRS IRD Aix Marseille Université, Site Agroparc BP 61207, 84911, Avignon, France
| | - C Bartoli
- INRA, Laboratoire des Interactions Plantes-Microorganismes (LIPM), UMR441, F-31326, Castanet-Tolosan, France.,CNRS, Laboratoire des Interactions Plantes-Microorganismes (LIPM), UMR2594, F-31326, Castanet-Tolosan, France
| | - C Chandeysson
- INRA, Unité de Pathologie Végétale, Domaine de St Maurice, BP 94, 84140, Montfavet, France
| | - C Guilbaud
- INRA, Unité de Pathologie Végétale, Domaine de St Maurice, BP 94, 84140, Montfavet, France
| | - L Parisi
- INRA, Unité de Pathologie Végétale, Domaine de St Maurice, BP 94, 84140, Montfavet, France
| | - J F Bourgeay
- INRA, Unité de Pathologie Végétale, Domaine de St Maurice, BP 94, 84140, Montfavet, France
| | - E Buisson
- IMBE, Université d'Avignon et des Pays de Vaucluse, UMR CNRS IRD Aix Marseille Université, Site Agroparc BP 61207, 84911, Avignon, France
| | - C E Morris
- INRA, Unité de Pathologie Végétale, Domaine de St Maurice, BP 94, 84140, Montfavet, France
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Borschinger B, Bartoli C, Chandeysson C, Guilbaud C, Parisi L, Bourgeay JF, Buisson E, Morris CE. A set of PCRs for rapid identification and characterization of Pseudomonas syringae phylogroups. J Appl Microbiol 2016; 120:714-23. [PMID: 26661140 DOI: 10.1111/jam.13017] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2015] [Revised: 10/29/2015] [Accepted: 11/26/2015] [Indexed: 12/13/2022]
Abstract
AIMS The aim of this study was to develop a rapid PCR-based method for the specific detection of individual phylogroups of the Pseudomonas syringae complex. METHODS AND RESULTS Seven primer pairs were developed by analysing whole genomes of 54 Ps. syringae strains. The specificity and sensitivity of these primer pairs were assessed on 236 strains from a large and comprehensive Ps. syringae collection. The method was also validated by characterizing the phylogenetic diversity of 174 putative Ps. syringae isolates from kiwifruit and apricot orchards of southeastern France. CONCLUSION Our PCR-based method allows for the detection and characterization of nine of the 13 Ps. syringae phylogroups (phylogroups 1, 2, 3, 4, 7, 8, 9, 10 and 13). SIGNIFICANCE AND IMPACT OF THE STUDY To date, phylogenetic affiliation within the Ps. syringae complex was only possible by sequencing housekeeping genes. Here, we propose a rapid PCR-based method for the detection of specific phylogroups of the Ps. syringae complex. Furthermore, for the first time we reveal the presence of Ps. syringae strains belonging to phylogroups 10 and 13 as epiphytes on plants, whereas they had previously only been observed in aquatic habitats.
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Affiliation(s)
- B Borschinger
- Unité de Pathologie Végétale, INRA, Montfavet, France.,IMBE, Université d'Avignon et des Pays de Vaucluse, UMR CNRS IRD Aix Marseille Université, Avignon, France
| | - C Bartoli
- Laboratoire des Interactions Plantes-Microorganismes (LIPM), INRA, Castanet-Tolosan, France.,Laboratoire des Interactions Plantes-Microorganismes (LIPM), CNRS, Castanet-Tolosan, France
| | - C Chandeysson
- Unité de Pathologie Végétale, INRA, Montfavet, France
| | - C Guilbaud
- Unité de Pathologie Végétale, INRA, Montfavet, France
| | - L Parisi
- Unité de Pathologie Végétale, INRA, Montfavet, France
| | - J F Bourgeay
- Unité de Pathologie Végétale, INRA, Montfavet, France
| | - E Buisson
- IMBE, Université d'Avignon et des Pays de Vaucluse, UMR CNRS IRD Aix Marseille Université, Avignon, France
| | - C E Morris
- Unité de Pathologie Végétale, INRA, Montfavet, France
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Desbiez C, Chandeysson C, Lecoq H. A short motif in the N-terminal part of the coat protein is a host-specific determinant of systemic infectivity for two potyviruses. Mol Plant Pathol 2014; 15:217-21. [PMID: 24118745 PMCID: PMC6638817 DOI: 10.1111/mpp.12076] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Although the biological variability of Watermelon mosaic virus is limited, isolates from the three main molecular groups differ in their ability to infect systemically Chenopodium quinoa. Mutations were introduced in a motif of three or five amino acids located in the N-terminal part of the coat protein, and differing in isolates from group 1 (motif: lysine-glutamic acid-alanine (Lys-Glu-Ala) or KEA, systemic on C. quinoa), group 2 (Lys-Glu-Thr or KET, not systemic on C. quinoa) and group 3 (KEKET, not systemic on C. quinoa). Mutagenesis of KEKET in an isolate from group 3 to KEA or KEKEA was sufficient to make the virus systemic on C. quinoa, whereas mutagenesis to KET had no effect. Introduction of a KEA motif in Zucchini yellow mosaic virus coat protein also resulted in systemic infection on C. quinoa. These mutations had no obvious effect on the disorder profile or potential post-translational modifications of the coat protein as determined in silico.
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Affiliation(s)
- Cecile Desbiez
- UR0407 Pathologie Végétale, INRA, F-84140, Montfavet, France
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Desbiez C, Chandeysson C, Lecoq H, Moury B. A simple, rapid and efficient way to obtain infectious clones of potyviruses. J Virol Methods 2012; 183:94-7. [DOI: 10.1016/j.jviromet.2012.03.035] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2012] [Revised: 03/23/2012] [Accepted: 03/28/2012] [Indexed: 11/29/2022]
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Lecoq H, Fabre F, Joannon B, Wipf-Scheibel C, Chandeysson C, Schoeny A, Desbiez C. Search for factors involved in the rapid shift in Watermelon mosaic virus (WMV) populations in South-eastern France. Virus Res 2011; 159:115-23. [PMID: 21605606 DOI: 10.1016/j.virusres.2011.05.004] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2011] [Accepted: 04/12/2011] [Indexed: 10/18/2022]
Abstract
Watermelon mosaic virus (WMV, genus Potyvirus, family Potyviridae) was reported for the first time in France in 1974, and it is now the most prevalent virus in cucurbit crops. In 2000, new strains referred as 'emerging' (EM) strains were detected in South-eastern France. EM strains are generally more severe and phylogenetically distinct from those previously reported in this country and referred as 'classic' (CL) strains. Since 2000, EM strains have been progressively replacing CL strains in several areas where they co-exist. In order to explain this rapid shift in virus populations, the biological properties of a set of 17 CL and EM WMV isolates were compared. No major differences were observed when comparing a limited host range including 48 different plant species or cultivars. Only two species were differential; Chenopodium quinoa was systemically infected by CL and not by EM isolates whereas Ranunculus sardous was systemically infected by EM and not by CL isolates. A considerable variability was observed in aphid transmission efficiencies but this could not be correlated to the CL or EM types. Two subsets of five isolates of each group were used to compare aphid transmission efficiencies from single and double (CL-EM) infections using six different cucurbit and non-cucurbit hosts. EM isolates were generally better transmitted from mixed CL-EM infections than CL isolates and CL transmission rates were significantly lower from double than from single infections. Cross-protection was only partial between CL and EM strains leading to frequent double infections, and only a slight asymmetry was observed in cross-protection efficiencies. Since double infections occur very commonly in fields, the preferential transmission of EM from mixed CL-EM infections could be one of the factors leading to the displacement of CL isolates by EM isolates.
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Affiliation(s)
- H Lecoq
- INRA, UR407, Station de Pathologie Végétale, Domaine Saint Maurice, 84140 Montfavet, France.
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10
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Desbiez C, Joannon B, Wipf-Scheibel C, Chandeysson C, Lecoq H. Recombination in natural populations of watermelon mosaic virus: new agronomic threat or damp squib? J Gen Virol 2011; 92:1939-1948. [PMID: 21471312 DOI: 10.1099/vir.0.031401-0] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Since their introduction in south-eastern France around 1999, new, 'emerging' (EM) strains of watermelon mosaic virus (WMV) coexist with the 'classic' (CL) strains present for more than 40 years. This situation constitutes a unique opportunity to estimate the frequency of recombinants appearing in the few years following introduction of new strains of a plant RNA virus. Molecular analyses performed on more than 1000 isolates from epidemiological surveys (2004-2008) and from experimental plots (2009-2010), and targeting only recombinants that became predominant in at least one plant, revealed at least seven independent CL/EM or EM/EM recombination events. The frequency of recombinants involving at least one EM parent in the natural populations tested was on the order of 1 %. No new recombinant was detected for more than 1 year, and none but one in more than one location. In tests comparing host range and aphid transmissibility, the new recombinants did not display a better fitness than their 'parental' isolates. No recombinant was detected from artificial mixed infections of CL and EM isolates of various hosts after testing more than 1500 subcultures obtained after single-aphid transmission. These results constitute one of the first estimations of the frequency of recombinants in natural conditions for a plant RNA virus. This suggests that although viable recombinants of WMV are not rare, and although recombination may potentially lead to new highly damaging strains, the new recombinants observed so far had a lower fitness than the parental strains and did not emerge durably in the populations.
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Affiliation(s)
- C Desbiez
- INRA, Unité de Pathologie Végétale UR407, F-84140 Montfavet, France
| | - B Joannon
- INRA, Unité de Pathologie Végétale UR407, F-84140 Montfavet, France
| | - C Wipf-Scheibel
- INRA, Unité de Pathologie Végétale UR407, F-84140 Montfavet, France
| | - C Chandeysson
- INRA, Unité de Pathologie Végétale UR407, F-84140 Montfavet, France
| | - H Lecoq
- INRA, Unité de Pathologie Végétale UR407, F-84140 Montfavet, France
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Koné D, Aké S, Abo K, Soro S, N'Guessan CA, Wipf-Scheibel C, Chandeysson C, Desbiez C, Lecoq H. First Report of Zucchini yellow mosaic virus in Cucurbits in Ivory Coast. Plant Dis 2010; 94:1378. [PMID: 30743639 DOI: 10.1094/pdis-06-10-0416] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
During a field survey conducted in December 2008 and January 2009 in southern Ivory Coast, zucchini squash (Cucurbita pepo L.) and cucumber (Cucumis sativus L.) plants were observed showing severe symptoms of leaf mosaic and distortions, filiformism, and fruit deformations. Nine samples were collected from symptomatic plants in four locations (Adzopé, Songon, Ayamé, and Gagnoa) and dried over CaCl2. Double-antibody sandwich (DAS)-ELISA tests were performed directly on dried samples with antisera against nine cucurbit-infecting viruses: Zucchini yellow mosaic virus (ZYMV, Potyvirus); Papaya ringspot virus (PRSV, Potyvirus); Watermelon mosaic virus (WMV, Potyvirus); Moroccan watermelon mosaic virus (MWMV, Potyvirus); Cucumber vein yellowing virus (CVYV, Ipomovirus); Cucumber mosaic virus (CMV, Cucumovirus); Cucurbit aphid borne yellows virus (CABYV, Polerovirus); Squash mosaic virus (SqMV, Comovirus); and Cucumber green mottle mosaic virus (CGMMV, Tobamovirus). ZYMV was detected alone in four of six zucchini squash samples and in mixed infection with CMV and PRSV in two of three cucumber samples. A cucumber sample (CI09-09) collected at Songon and infected by ZYMV, CMV, and PRSV was inoculated to zucchini squash. ZYMV was separated from CMV and PRSV by inoculating zucchini squash plantlets with one Myzus persicae Sulzer per plant with 2-min acquisition and 2-h inoculation access periods. Plants infected by ZYMV only developed typical symptoms of severe mosaic, distortion, and filiformism on leaves. Total RNA was extracted from the original dried sample of CI09-09 using TRI-Reagent (Molecular Research Center Inc., Cincinnati, OH) (2). One-step reverse transcription (RT)-PCR was performed with our standard protocol and specific primers (2), yielding a 605-bp fragment corresponding to part of the polymerase (NIb) and coat protein (CP) coding regions. The nucleotide sequence of the NIb-CP fragment of Ivory Coast ZYMV isolate CI09-09 (GenBank No. HM450303) shared 98.5, 92.7, 80.5, and 75.7% identity with ZYMV isolates from France (isolate E9, HM641798), Florida (D13914), Singapore (AF014811), and Vietnam (DQ925449), respectively. Sequence comparison indicated that CI09-09 belongs to the phylogenetic cluster 1 of group A of ZYMV (2). ZYMV, first described in 1981, is now one of the most damaging viruses in cucurbit crops worldwide and is characterized by an important biological and molecular diversity (1,3). ZYMV has already been reported in several African countries, mostly in the northern and southern parts of the continent (1), but to our knowledge, this is the first report of ZYMV in Ivory Coast. Among African isolates, CI09-09 shared 97.5% identity with isolate Su06-22 from Sudan (HM641799) belonging to the phylogenetic cluster 1 of group A of ZYMV, 94 to 95% identity with isolates from neighboring Mali (HM005307-HM005312) belonging to cluster 2 of group A, and 79.6% identity with the divergent isolate R5A from Réunion Island (L29569) belonging to phylogenetic group B of ZYMV. The presence of ZYMV in four distant locations in southern Ivory Coast suggests that this virus constitutes a serious threat to cucurbit production in this country. References: (1) C. Desbiez and H. Lecoq. Plant Pathol. 46:809, 1997, (2) C. Desbiez et al. Virus Res. 85:5, 2002, (3) H. Lecoq et al. Virus Res. 141:190, 2009.
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Affiliation(s)
- D Koné
- Laboratoire de Physiologie Végétale, UFR Biosciences, Université de Cocody-Abidjan, 22 BP 582 Abidjan 22, Côte d'Ivoire
| | - S Aké
- Laboratoire de Physiologie Végétale, UFR Biosciences, Université de Cocody-Abidjan, 22 BP 582 Abidjan 22, Côte d'Ivoire
| | - K Abo
- ENSA, Départment Agriculture et Ressources Animales, INP-HB, BP 1313 Yamoussoukro, Côte-d'Ivoire
| | - S Soro
- ENSA, Départment Agriculture et Ressources Animales, INP-HB, BP 1313 Yamoussoukro, Côte-d'Ivoire
| | - C A N'Guessan
- ENSA, Départment Agriculture et Ressources Animales, INP-HB, BP 1313 Yamoussoukro, Côte-d'Ivoire
| | - C Wipf-Scheibel
- INRA, UR407, Station de Pathologie Végétale, Domaine Saint Maurice, BP 94, 84140 Montfavet cedex, France
| | - C Chandeysson
- INRA, UR407, Station de Pathologie Végétale, Domaine Saint Maurice, BP 94, 84140 Montfavet cedex, France
| | - C Desbiez
- INRA, UR407, Station de Pathologie Végétale, Domaine Saint Maurice, BP 94, 84140 Montfavet cedex, France
| | - H Lecoq
- INRA, UR407, Station de Pathologie Végétale, Domaine Saint Maurice, BP 94, 84140 Montfavet cedex, France
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Lecoq H, Wipf-Scheibel C, Chandeysson C, Lê Van A, Fabre F, Desbiez C. Molecular epidemiology of Zucchini yellow mosaic virus in France: An historical overview. Virus Res 2009; 141:190-200. [DOI: 10.1016/j.virusres.2008.11.020] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/21/2008] [Indexed: 10/21/2022]
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Desbiez C, Joannon B, Wipf-Scheibel C, Chandeysson C, Lecoq H. Emergence of new strains of Watermelon mosaic virus in South-eastern France: evidence for limited spread but rapid local population shift. Virus Res 2009; 141:201-8. [PMID: 19152813 DOI: 10.1016/j.virusres.2008.08.018] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/16/2008] [Indexed: 11/18/2022]
Abstract
Severe symptoms caused by Watermelon mosaic virus (WMV) in zucchini squash leaves and fruits have been observed since 1999 in South-eastern (SE) France. Their appearance correlates with the introduction of new, "emerging" (EM) isolates distant at the molecular level from the "classic" (CL) isolates present for more than 30 years. To understand the origin and spread of EM isolates, a survey was performed between 2004 and 2007. WMV isolates collected were characterized by sequencing part of the polymerase and coat protein coding regions. This revealed the presence of EM isolates in SE France only, whereas CL isolates were widespread throughout the country. Besides, four subgroups of EM isolates were observed in SE France, suggesting multiple introductions. Recombinants between CL and EM groups, which probably arose locally, were observed during the survey. A strong geographic structure that remained stable during the 4 years was observed between different EM isolates. Our results showed that EM isolates did not spread over long distances, but rapidly replaced the pre-existing CL isolates in all sites where both groups occurred.
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Affiliation(s)
- C Desbiez
- INRA, UR 407, Unité de Pathologie Végétale, Domaine Saint Maurice, Montfavet, France.
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