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Dia NC, Van Vaerenbergh J, Van Malderghem C, Blom J, Smits THM, Cottyn B, Pothier JF. Xanthomonas hydrangeae sp. nov., a novel plant pathogen isolated from Hydrangea arborescens. Int J Syst Evol Microbiol 2021; 71. [PMID: 34913859 DOI: 10.1099/ijsem.0.005163] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
This paper describes a novel species isolated in 2011 and 2012 from nursery-grown Hydrangea arborescens cultivars in Flanders, Belgium. After 4 days at 28 °C, the strains yielded yellow, round, convex and mucoid colonies. Pathogenicity of the strains was confirmed on its isolation host, as well as on Hydrangea quercifolia. Analysis using MALDI-TOF MS identified the Hydrangea strains as belonging to the genus Xanthomonas but excluded them from the species Xanthomonas hortorum. A phylogenetic tree based on gyrB confirmed the close relation to X. hortorum. Three fatty acids were dominant in the Hydrangea isolates: anteiso-C15 : 0, iso-C15 : 0 and summed feature 3 (C16 : 1 ω7c/C16 : 1 ω6c). Unlike X. hortorum pathovars, the Hydrangea strains were unable to grow in the presence of lithium chloride and could only weakly utilize d-fructose-6-PO4 and glucuronamide. Phylogenetic characterization based on multilocus sequence analysis and phylogenomic characterization revealed that the strains are close to, yet distinct from, X. hortorum. The genome sequences of the strains had average nucleotide identity values ranging from 94.35-95.19 % and in silico DNA-DNA hybridization values ranging from 55.70 to 59.40 % to genomes of the X. hortorum pathovars. A genomics-based loop-mediated isothermal amplification assay was developed which was specific to the Hydrangea strains for its early detection. A novel species, Xanthomonas hydrangeae sp. nov., is proposed with strain LMG 31884T (=CCOS 1956T) as the type strain.
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Affiliation(s)
- Nay C Dia
- Environmental Genomics and Systems Biology Research Group, Institute for Natural Resource Sciences, Zurich University of Applied Sciences (ZHAW), Wädenswil, Switzerland.,Molecular Plant Breeding, Institute of Agricultural Sciences, ETH Zurich, Zurich, Switzerland
| | - Johan Van Vaerenbergh
- Plant Sciences Unit, Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Merelbeke, Belgium
| | - Cinzia Van Malderghem
- Plant Sciences Unit, Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Merelbeke, Belgium
| | - Jochen Blom
- Bioinformatics and Systems Biology, Justus-Liebig University Giessen, Giessen, Germany
| | - Theo H M Smits
- Environmental Genomics and Systems Biology Research Group, Institute for Natural Resource Sciences, Zurich University of Applied Sciences (ZHAW), Wädenswil, Switzerland
| | - Bart Cottyn
- Plant Sciences Unit, Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Merelbeke, Belgium
| | - Joël F Pothier
- Environmental Genomics and Systems Biology Research Group, Institute for Natural Resource Sciences, Zurich University of Applied Sciences (ZHAW), Wädenswil, Switzerland
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Debode J, De Tender C, Soltaninejad S, Van Malderghem C, Haegeman A, Van der Linden I, Cottyn B, Heyndrickx M, Maes M. Chitin Mixed in Potting Soil Alters Lettuce Growth, the Survival of Zoonotic Bacteria on the Leaves and Associated Rhizosphere Microbiology. Front Microbiol 2016; 7:565. [PMID: 27148242 PMCID: PMC4838818 DOI: 10.3389/fmicb.2016.00565] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [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: 01/09/2016] [Accepted: 04/04/2016] [Indexed: 11/13/2022] Open
Abstract
Chitin is a promising soil amendment for improving soil quality, plant growth, and plant resilience. The objectives of this study were twofold. First, to study the effect of chitin mixed in potting soil on lettuce growth and on the survival of two zoonotic bacterial pathogens, Escherichia coli O157:H7 and Salmonella enterica on the lettuce leaves. Second, to assess the related changes in the microbial lettuce rhizosphere, using phospholipid fatty acid (PLFA) analysis and amplicon sequencing of a bacterial 16S rRNA gene fragment and the fungal ITS2. As a result of chitin addition, lettuce fresh yield weight was significantly increased. S. enterica survival in the lettuce phyllosphere was significantly reduced. The E. coli O157:H7 survival was also lowered, but not significantly. Moreover, significant changes were observed in the bacterial and fungal community of the lettuce rhizosphere. PLFA analysis showed a significant increase in fungal and bacterial biomass. Amplicon sequencing showed no increase in fungal and bacterial biodiversity, but relative abundances of the bacterial phyla Acidobacteria, Verrucomicrobia, Actinobacteria, Bacteroidetes, and Proteobacteria and the fungal phyla Ascomycota, Basidiomycota, and Zygomycota were significantly changed. More specifically, a more than 10-fold increase was observed for operational taxonomic units belonging to the bacterial genera Cellvibrio, Pedobacter, Dyadobacter, and Streptomyces and to the fungal genera Lecanicillium and Mortierella. These genera include several species previously reported to be involved in biocontrol, plant growth promotion, the nitrogen cycle and chitin degradation. These results enhance the understanding of the response of the rhizosphere microbiome to chitin amendment. Moreover, this is the first study to investigate the use of soil amendments to control the survival of S. enterica on plant leaves.
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Affiliation(s)
- Jane Debode
- Plant Sciences Unit, Institute for Agricultural and Fisheries ResearchMerelbeke, Belgium
| | - Caroline De Tender
- Plant Sciences Unit, Institute for Agricultural and Fisheries ResearchMerelbeke, Belgium
| | - Saman Soltaninejad
- Plant Sciences Unit, Institute for Agricultural and Fisheries ResearchMerelbeke, Belgium
- Technology and Food Science Unit, Institute for Agricultural and Fisheries ResearchMelle, Belgium
| | - Cinzia Van Malderghem
- Plant Sciences Unit, Institute for Agricultural and Fisheries ResearchMerelbeke, Belgium
| | - Annelies Haegeman
- Plant Sciences Unit, Institute for Agricultural and Fisheries ResearchMerelbeke, Belgium
| | - Inge Van der Linden
- Technology and Food Science Unit, Institute for Agricultural and Fisheries ResearchMelle, Belgium
- Department of Food Safety and Food Quality, Ghent UniversityGhent, Belgium
| | - Bart Cottyn
- Plant Sciences Unit, Institute for Agricultural and Fisheries ResearchMerelbeke, Belgium
| | - Marc Heyndrickx
- Technology and Food Science Unit, Institute for Agricultural and Fisheries ResearchMelle, Belgium
- Department of Pathology, Bacteriology, and Poultry Diseases, Faculty of Veterinary Sciences, Ghent UniversityMerelbeke, Belgium
| | - Martine Maes
- Plant Sciences Unit, Institute for Agricultural and Fisheries ResearchMerelbeke, Belgium
- Department of Biochemistry and Microbiology, Ghent UniversityGhent, Belgium
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Rombouts S, Volckaert A, Venneman S, Declercq B, Vandenheuvel D, Allonsius CN, Van Malderghem C, Jang HB, Briers Y, Noben JP, Klumpp J, Van Vaerenbergh J, Maes M, Lavigne R. Characterization of Novel Bacteriophages for Biocontrol of Bacterial Blight in Leek Caused by Pseudomonas syringae pv. porri. Front Microbiol 2016; 7:279. [PMID: 27014204 PMCID: PMC4791379 DOI: 10.3389/fmicb.2016.00279] [Citation(s) in RCA: 65] [Impact Index Per Article: 8.1] [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: 11/17/2015] [Accepted: 02/22/2016] [Indexed: 01/29/2023] Open
Abstract
Pseudomonas syringae pv. porri, the causative agent of bacterial blight in leek (Allium porrum), is increasingly frequent causing problems in leek cultivation. Because of the current lack of control measures, novel bacteriophages were isolated to control this pathogen using phage therapy. Five novel phages were isolated from infected fields in Flanders (vB_PsyM_KIL1, vB_PsyM_KIL2, vB_PsyM_KIL3, vB_PsyM_KIL4, and vB_PsyM_KIL5), and were complemented with one selected host range mutant phage (vB_PsyM_KIL3b). Genome analysis of the phages revealed genome sizes between 90 and 94 kb and an average GC-content of 44.8%. Phylogenomic networking classified them into a novel clade, named the "KIL-like viruses," related to the Felixounalikevirus genus, together with phage phiPsa374 from P. syringae pv. actinidiae. In vitro characterization demonstrated the stability and lytic potential of these phages. Host range analysis confirmed heterogeneity within P. syringae pv. porri, leading to the development of a phage cocktail with a range that covers the entire set of 41 strains tested. Specific bio-assays demonstrated the in planta efficacy of phages vB_PsyM_KIL1, vB_PsyM_KIL2, vB_PsyM_KIL3, and vB_PsyM_KIL3b. In addition, two parallel field trial experiments on three locations using a phage cocktail of the six phages showed variable results. In one trial, symptom development was attenuated. These data suggest some potential for phage therapy in controlling bacterial blight of leek, pending optimization of formulation and application methods.
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Affiliation(s)
- Sofie Rombouts
- Laboratory of Gene Technology, Department of Biosystems, KU LeuvenLeuven, Belgium
- Unit Plant— Crop Protection, Institute for Agricultural and Fisheries ResearchMerelbeke, Belgium
| | | | - Sofie Venneman
- Research Station for Vegetable ProductionSint-Katelijne-Waver, Belgium
| | | | - Dieter Vandenheuvel
- Laboratory of Applied Microbiology and Biotechnology, Department of Bioscience Engineering, University of AntwerpAntwerpen, Belgium
| | - Camille N. Allonsius
- Laboratory of Applied Microbiology and Biotechnology, Department of Bioscience Engineering, University of AntwerpAntwerpen, Belgium
| | - Cinzia Van Malderghem
- Unit Plant— Crop Protection, Institute for Agricultural and Fisheries ResearchMerelbeke, Belgium
| | - Ho B. Jang
- Laboratory of Gene Technology, Department of Biosystems, KU LeuvenLeuven, Belgium
| | - Yves Briers
- Laboratory of Gene Technology, Department of Biosystems, KU LeuvenLeuven, Belgium
- Laboratory of Applied Biotechnology, Department of Applied Biosciences, Ghent UniversityGhent, Belgium
| | - Jean P. Noben
- School of Life Sciences, Biomedical Research Institute and Transnational University Limburg, Hasselt UniversityDiepenbeek, Belgium
| | - Jochen Klumpp
- Institute of Food, Nutrition and Health, ETH ZurichZurich, Switzerland
| | - Johan Van Vaerenbergh
- Unit Plant— Crop Protection, Institute for Agricultural and Fisheries ResearchMerelbeke, Belgium
| | - Martine Maes
- Unit Plant— Crop Protection, Institute for Agricultural and Fisheries ResearchMerelbeke, Belgium
- Lab. of Microbiology, Department of Biochemistry and Microbiology, Ghent UniversityGent, Belgium
| | - Rob Lavigne
- Laboratory of Gene Technology, Department of Biosystems, KU LeuvenLeuven, Belgium
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