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Niem JM, Billones-Baaijens R, Stodart BJ, Reveglia P, Savocchia S. Biocontrol Potential of an Endophytic Pseudomonas poae Strain against the Grapevine Trunk Disease Pathogen Neofusicoccum luteum and Its Mechanism of Action. Plants (Basel) 2023; 12:plants12112132. [PMID: 37299111 DOI: 10.3390/plants12112132] [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] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 05/11/2023] [Accepted: 05/21/2023] [Indexed: 06/12/2023]
Abstract
Grapevine trunk diseases (GTDs) impact the sustainability of vineyards worldwide and management options are currently limited. Biological control agents (BCAs) may offer a viable alternative for disease control. With an aim to develop an effective biocontrol strategy against the GTD pathogen Neofusicoccum luteum, this study investigated the following: (1) the efficacy of the strains in suppressing the BD pathogen N. luteum in detached canes and potted vines; (2) the ability of a strain of Pseudomonas poae (BCA17) to colonize and persist within grapevine tissues; and (3) the mode of action of BCA17 to antagonize N. luteum. Co-inoculations of the antagonistic bacterial strains with N. luteum revealed that one strain of P. poae (BCA17) suppressed infection by 100% and 80% in detached canes and potted vines, respectively. Stem inoculations of a laboratory-generated rifampicin-resistant strain of BCA17 in potted vines (cv. Shiraz) indicated the bacterial strain could colonize and persist in the grapevine tissues, potentially providing some protection against GTDs for up to 6 months. The bioactive diffusible compounds secreted by BCA17 significantly reduced the spore germination and fungal biomass of N. luteum and the other representative GTD pathogens. Complementary analysis via MALDI-TOF revealed the presence of an unknown cyclic lipopeptide in the bioactive diffusible compounds, which was absent in a non-antagonistic strain of P. poae (JMN13), suggesting this novel lipopeptide may be responsible for the biocontrol activity of the BCA17. Our study provided evidence that P. poae BCA17 is a potential BCA to combat N. luteum, with a potential novel mode of action.
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Affiliation(s)
- Jennifer Millera Niem
- Gulbali Institute, Charles Sturt University, Locked Bag 588, Wagga Wagga, NSW 2678, Australia
- Faculty of Science and Health, School of Agricultural, Environmental and Veterinary Sciences, Charles Sturt University, Locked Bag 588, Wagga Wagga, NSW 2678, Australia
- UPLB Museum of Natural History, University of the Philippines Los Baños, College, Los Baños 4031, Laguna, Philippines
- Institute of Weed Science, Entomology, and Plant Pathology, College of Agriculture and Food Science, University of the Philippines Los Baños, College, Los Baños 4031, Laguna, Philippines
| | | | - Benjamin J Stodart
- Gulbali Institute, Charles Sturt University, Locked Bag 588, Wagga Wagga, NSW 2678, Australia
- Faculty of Science and Health, School of Agricultural, Environmental and Veterinary Sciences, Charles Sturt University, Locked Bag 588, Wagga Wagga, NSW 2678, Australia
| | - Pierluigi Reveglia
- Gulbali Institute, Charles Sturt University, Locked Bag 588, Wagga Wagga, NSW 2678, Australia
- Faculty of Science and Health, School of Agricultural, Environmental and Veterinary Sciences, Charles Sturt University, Locked Bag 588, Wagga Wagga, NSW 2678, Australia
- Institute for Sustainable Agriculture, CSIC, 14004 Córdoba, Spain
| | - Sandra Savocchia
- Gulbali Institute, Charles Sturt University, Locked Bag 588, Wagga Wagga, NSW 2678, Australia
- Faculty of Science and Health, School of Agricultural, Environmental and Veterinary Sciences, Charles Sturt University, Locked Bag 588, Wagga Wagga, NSW 2678, Australia
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Chowdhury IF, Rohan M, Stodart BJ, Chen C, Wu H, Doran GS. Persistence of atrazine and trifluralin in a clay loam soil undergoing different temperature and moisture conditions. Environ Pollut 2021; 276:116687. [PMID: 33621732 DOI: 10.1016/j.envpol.2021.116687] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Revised: 01/18/2021] [Accepted: 02/04/2021] [Indexed: 05/21/2023]
Abstract
Dissipation kinetics of atrazine and trifluralin in a clay loam soil was investigated in a laboratory incubation experiment under different temperature and moisture conditions. The soil was spiked with diluted atrazine and trifluralin concentrations at 4.50 and 4.25 mg/kg soil, respectively, the moisture content adjusted to 40, 70, and 100% of field capacity (FC) and then incubated in three climatic chambers at 10, 20, and 30 °C. For each of the herbicides, soil samples were collected at 0, 7, 21, 42, 70, and 105 days and analysed by Gas Chromatography-Electron Capture Detector (GC-ECD). A stochastic gamma model was used to model the dissipation of herbicides from the clay loam soil by incorporating environmental factors as covariates to determine half-life and days to complete dissipation. Results showed that temperature played a greater role on atrazine persistence than soil moisture; while the interaction effect of temperature and moisture was significant on the persistence of trifluralin over time. Atrazine dissipated more rapidly at 30 °C compared to 10 and 20 °C, with a half-life of 7.50 days and 326.23 days to reach complete dissipation. Rapid loss of trifluralin was observed at 70% moisture content when incubated at 30 °C, with a half-life of 5.80 days and 182.01 days to complete dissipation. It was observed that the half-life of both herbicides tended to double with every 10 °C decreases of temperature over the range tested. The model indicated that both atrazine and trifluralin have the potential to persist in clay loam soil for several years at temperature ≤20 °C; which could potentially affect following crops in rotation.
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Affiliation(s)
- Imtiaz Faruk Chowdhury
- School of Agricultural and Wine Sciences, Charles Sturt University, Wagga Wagga, NSW 2678, Australia; Graham Centre for Agricultural Innovation, Charles Sturt University, Locked Bag 588, Wagga Wagga, NSW 2678, Australia; Department of Agronomy, Faculty of Agriculture, Sher-e-Bangla Agricultural University, Dhaka 1207, Bangladesh.
| | - Maheswaran Rohan
- NSW Department of Primary Industries, Wagga Wagga Agricultural Institute, Wagga Wagga, NSW 2650, Australia
| | - Benjamin J Stodart
- School of Agricultural and Wine Sciences, Charles Sturt University, Wagga Wagga, NSW 2678, Australia; Graham Centre for Agricultural Innovation, Charles Sturt University, Locked Bag 588, Wagga Wagga, NSW 2678, Australia
| | - Chengrong Chen
- Australian Rivers Institute and School of Environment and Science, Griffith University, Nathan, Queensland 4111, Australia
| | - Hanwen Wu
- Graham Centre for Agricultural Innovation, Charles Sturt University, Locked Bag 588, Wagga Wagga, NSW 2678, Australia; NSW Department of Primary Industries, Wagga Wagga Agricultural Institute, Wagga Wagga, NSW 2650, Australia
| | - Gregory S Doran
- School of Agricultural and Wine Sciences, Charles Sturt University, Wagga Wagga, NSW 2678, Australia; Graham Centre for Agricultural Innovation, Charles Sturt University, Locked Bag 588, Wagga Wagga, NSW 2678, Australia.
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Weeraratne N, Stodart BJ, Venturi V, Hofte M, Hua GKH, Ongena M, Savocchia S, Steel CC, Ash GJ. Syringopeptin Contributes to the Virulence of Pseudomonas fuscovaginae, Based on sypA Biosynthesis Mutant Analysis. Phytopathology 2020; 110:780-789. [PMID: 31804903 DOI: 10.1094/phyto-07-19-0235-r] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Pseudomonas fuscovaginae, first reported from Japan in 1976, is now present in many agroecological regions around the world; it causes sheath brown rot of rice and is reported as a pathogen of a broad range of hosts. The pathogen can infect rice plants at all stages of growth and is known to cause significant losses due to grain discoloration, poor spike emergence and panicle sterility. Limited information is available on the virulence and mechanisms of pathogenicity for P. fuscovaginae. To address this, an analysis of genomes was conducted, which identified the presence of a gene showing homology to one of the genes contributing to syringopeptin synthetase (sypA) of P. syringae pv. syringae. To study the potential role of this gene in the virulence and pathogenicity of P. fuscovaginae, a site-specific mutation was created. Following inoculation of seeds and plantlets of rice and wheat with P. fuscovaginae wild types and their respective mutants, we demonstrated that the mutation significantly reduced virulence. This was evident on rice and wheat inoculated with mutants causing a significantly higher number of roots, length of roots and seedling height compared with their respective wild types. Characteristic disease symptoms of necrotic lesions were significantly less in rice seedlings infected with bacterial suspensions of mutants indicating a reduction in virulence. Chromatography analysis of bacterial exudates showed suppression of synthesis of metabolites analogous to syringopeptin in the mutants. These data demonstrate that the protein encoded by this sypA homolog gene is a major virulence determinant of P. fuscovaginae.
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Affiliation(s)
- Nirodha Weeraratne
- Graham Centre for Agricultural Innovation, School of Agricultural and Wine Sciences, Charles Sturt University, Locked Bag 588, Wagga Wagga, NSW 2678, Australia
- Centre for Crop Health, Institute for Life Sciences and the Environment, University of Southern Queensland, West Street, Toowoomba, QLD 4350, Australia
| | - Benjamin J Stodart
- Graham Centre for Agricultural Innovation, School of Agricultural and Wine Sciences, Charles Sturt University, Locked Bag 588, Wagga Wagga, NSW 2678, Australia
| | - Vittorio Venturi
- International Centre for Genetic Engineering and Biotechnology, Padriciano 99, 34149 Trieste, Italy
| | - Monica Hofte
- Department of Plants and Crops, Laboratory of Phytopathology, Ghent University, Coupure, Links 653, 9000 Ghent, Belgium
| | - Gia Khuong Hoang Hua
- Department of Plants and Crops, Laboratory of Phytopathology, Ghent University, Coupure, Links 653, 9000 Ghent, Belgium
| | - Marc Ongena
- Microbial Processes and Interactions (MiPI) Research Unit, Gembloux Agro-Bio Tech, University of Liège, B-5030 Gembloux, Belgium
| | - Sandra Savocchia
- National Wine and Grape Industry Centre, School of Agricultural and Wine Sciences, Charles Sturt University, Locked Bag 588, Wagga Wagga, NSW 2678, Australia
| | - Christopher C Steel
- National Wine and Grape Industry Centre, School of Agricultural and Wine Sciences, Charles Sturt University, Locked Bag 588, Wagga Wagga, NSW 2678, Australia
| | - Gavin J Ash
- Graham Centre for Agricultural Innovation, School of Agricultural and Wine Sciences, Charles Sturt University, Locked Bag 588, Wagga Wagga, NSW 2678, Australia
- Centre for Crop Health, Institute for Life Sciences and the Environment, University of Southern Queensland, West Street, Toowoomba, QLD 4350, Australia
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Ash GJ, Lang JM, Triplett LR, Stodart BJ, Verdier V, Cruz CV, Rott P, Leach JE. Development of a Genomics-Based LAMP (Loop-Mediated Isothermal Amplification) Assay for Detection of Pseudomonas fuscovaginae from Rice. Plant Dis 2014; 98:909-915. [PMID: 30708849 DOI: 10.1094/pdis-09-13-0957-re] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [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
The vast amount of data available through next-generation sequencing technology is facilitating the design of diagnostic marker systems. This study reports the use of draft genome sequences from the bacterial plant pathogen Pseudomonas fuscovaginae, the cause of sheath brown rot of rice, to describe the genetic diversity within a worldwide collection of strains representing the species. Based on a comparative analysis with the draft sequences, primers for a loop-mediated isothermal amplification (LAMP) assay were developed to identify P. fuscovaginae. The assay reported here reliably differentiated strains of P. fuscovaginae isolated from rice from a range of other bacteria that are commonly isolated from rice and other plants using a primer combination designated Pf8. The LAMP assay identified P. fuscovaginae purified DNA, live or heat-killed cells from pure cultures, and detected the bacterium in extracts or exudates from infected host plant material. The P. fuscovaginae LAMP assay is a suitable diagnostic tool for the glasshouse and laboratory and could be further developed for in-field surveys.
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Affiliation(s)
- Gavin J Ash
- Graham Centre for Agricultural Innovation (an alliance between Charles Sturt University and NSW DPI), School of Agricultural and Wine Sciences, Charles Sturt University, Wagga Wagga 2678, NSW, Australia
| | - Jillian M Lang
- Colorado State University, Department of Bioagricultural Sciences & Pest Management, Fort Collins 80523-1177
| | - Lindsay R Triplett
- Colorado State University, Department of Bioagricultural Sciences & Pest Management, Fort Collins 80523-1177
| | | | - Valérie Verdier
- Institut de Recherche pour le Développement, UMR Résistance des Plantes aux Bioagresseurs, IRD-CIRAD-UM2, 34394 Montpellier Cedex 5, France
| | - Casiana Vera Cruz
- International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines
| | | | - Jan E Leach
- Colorado State University, Department of Bioagricultural Science & Pest Management
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Raman H, Ryan PR, Raman R, Stodart BJ, Zhang K, Martin P, Wood R, Sasaki T, Yamamoto Y, Mackay M, Hebb DM, Delhaize E. Analysis of TaALMT1 traces the transmission of aluminum resistance in cultivated common wheat (Triticum aestivum L.). Theor Appl Genet 2008; 116:343-54. [PMID: 18046532 DOI: 10.1007/s00122-007-0672-4] [Citation(s) in RCA: 32] [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] [Subscribe] [Scholar Register] [Received: 09/06/2006] [Revised: 08/08/2007] [Accepted: 10/28/2007] [Indexed: 05/24/2023]
Abstract
Allele diversities of four markers specific to intron three, exon four and promoter regions of the aluminum (Al) resistance gene of wheat (Triticum aestivum L.) TaALMT1 were compared in 179 common wheat cultivars used in international wheat breeding programs. In wheat cultivars released during the last 93 years, six different promoter types were identified on the basis of allele size. A previous study showed that Al resistance was not associated with a particular coding allele for TaALMT1 but was correlated with blocks of repeated sequence upstream of the coding sequence. We verified the linkage between these promoter alleles and Al resistance in three doubled haploid and one intercross populations segregating for Al resistance. Molecular and pedigree analysis suggest that Al resistance in modern wheat germplasm is derived from several independent sources. Analysis of a population of 278 landraces and subspecies of wheat showed that most of the promoter alleles associated with Al resistance pre-existed in Europe, the Middle East and Asia prior to dispersal of cultivated germplasm around the world. Furthermore, several new promoter alleles were identified among the landraces surveyed. The TaALMT1 promoter alleles found within the spelt wheats were consistent with the hypothesis that these spelts arose on several independent occasions from hybridisations between non-free-threshing tetraploid wheats and Al-resistant hexaploid bread wheats. The strong correlation between Al resistance and Al-stimulated malate efflux from the root apices of 49 diverse wheat genotypes examined was consistent with the previous finding that Al resistance in wheat is conditioned primarily by malate efflux. These results demonstrate that the markers based on intron, exon and promoter regions of TaALMT1 can trace the inheritance of the Al resistance locus within wheat pedigrees and track Al resistance in breeding programmes.
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Affiliation(s)
- Harsh Raman
- NSW Department of Primary Industries and NSW Agricultural Genomics Centre, Wagga Wagga Agricultural Institute, Pine Gully Road, Wagga Wagga, NSW, 2650, Australia.
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Stodart BJ, Harvey PR, Neate SM, Melanson DL, Scott ES. Genetic variation and pathogenicity of anastomosis group 2 isolates of Rhizoctonia solani in Australia. ACTA ACUST UNITED AC 2007; 111:891-900. [PMID: 17707626 DOI: 10.1016/j.mycres.2007.05.008] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2006] [Revised: 04/13/2007] [Accepted: 05/22/2007] [Indexed: 11/18/2022]
Abstract
A collection of isolates of Rhizoctonia solani anastomosis group (AG) 2 was examined for genetic diversity and pathogenicity. Anastomosis reactions classified the majority of isolates into the known subgroups of AG 2-1 and AG 2-2 but the classification of several isolates was ambiguous. Morphological characters were consistent with the species, with no discriminating characters existing between subgroups. Vertical PAGE of pectic enzymes enabled the separation of zymogram group (ZG) 5 and 6 within AG 2-1, but not the separation of ZG 4 and 10 within AG 2-2. PCR analysis using inter-simple sequence repeats (ISSR) and the intron-splice junction (ISJ) region supported the separation of ZG 5 and 6, while the AG 2-2 isolates were separated by geographic region. A comparison of distance matrices produced by the zymogram analysis and PCR indicated a strong correlation between the marker types. Pathogenicity studies suggested canola (Brassica napus) cultivars were most severely affected by AG 2-1, while cultivars of two species of medic (Medicago truncatula cv. Caliph and M. littoralis cv. Herald) were susceptible to both AG 2-1 and 2-2. The results indicate that AG 2 is a polyphyletic group in which the classification of subtypes is sometimes difficult. Further investigation of the population structure within Australia is required to determine the extent and origin of the observed diversity.
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Affiliation(s)
- Benjamin J Stodart
- School of Agriculture, Food and Wine, The University of Adelaide, PMB 1, Glen Osmond, South Australia 5064, Australia.
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Balali GR, Neate SM, Kasalkheh AM, Stodart BJ, Melanson DL, Scott ES. Intraspecific variation of Rhizoctonia solani AG 3 isolates recovered from potato fields in Central Iran and South Australia. Mycopathologia 2007; 163:105-15. [PMID: 17245557 DOI: 10.1007/s11046-006-0089-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2006] [Accepted: 12/28/2006] [Indexed: 11/28/2022]
Abstract
Pectic zymogram, RFLP and PCR analyses were used to characterize Rhizoctonia solani AG 3 isolates collected from diseased potatoes in South Australia. The pectic zymogram data were compared with those obtained for isolates collected from central Iran. Analyses of bands corresponding to pectin esterase and polygalacturonase revealed three zymogram subgroups (ZG) in AG 3. In addition to the previously reported ZG7 (here renamed ZG7-1), two new zymogram subgroups, ZG7-2 and ZG7-3, were identified. Of the 446 isolates tested, 50% of the South Australian and 46% of the Iranian isolates were ZG7-1. The majority of the isolates originating from stem and root cankers were ZG7-1, whereas most of the isolates designated ZG7-2 and ZG7-3 originated from tuber-borne sclerotia. Pathogenicity tests revealed that ZG7-1 generally produced fewer sclerotia and more severe cankers of underground parts of the potato plants than the other two ZGs. Two random DNA clones, one originating from an AG 3 isolate and the other from an AG 4 isolate, were used as probes for RFLP analyses of Australian isolates. The AG 3 probe, previously identified to be specific to this group, detected a high level of genetic diversity, with 11 genotypes identified amongst 50 isolates analysed. The low-copy AG 4 probe resolved three genotypes amongst 24 isolates. For 23 isolates analysed with both markers, the combined data distinguished a total of six genotypes and similarity analysis resolved the isolates into two main groups with 50% homology. PCR, using primers for the plant intron splice junction region (R1), also revealed variation. No obvious relationship among pectic zymogram groups, RFLP and PCR genotypes was observed.
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Affiliation(s)
- G R Balali
- Department of Biology, The University of Isfahan, Isfahan, Iran.
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