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Djuikem C, Grognard F, Touzeau S. Impact of ontogenic changes on the dynamics of a fungal crop disease model motivated by coffee leaf rust. J Math Biol 2024; 88:30. [PMID: 38400915 DOI: 10.1007/s00285-024-02053-4] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 01/19/2024] [Accepted: 01/21/2024] [Indexed: 02/26/2024]
Abstract
Ontogenic resistance has been described for many plant-pathogen systems. Conversely, coffee leaf rust, a major fungal disease that drastically reduces coffee production, exhibits a form of ontogenic susceptibility, with a higher infection risk for mature leaves. To take into account stage-dependent crop response to phytopathogenic fungi, we developed an SEIR-U epidemiological model, where U stands for spores, which differentiates between young and mature leaves. Based on this model, we also explored the impact of ontogenic resistance on the sporulation rate. We computed the basic reproduction number [Formula: see text], which classically determines the stability of the disease-free equilibrium. We identified forward and backward bifurcation cases. The backward bifurcation is generated by the high sporulation of young leaves compared to mature ones. In this case, when the basic reproduction number is less than one, the disease can persist. These results provide useful insights on the disease dynamics and its control. In particular, ontogenic resistance may require higher control efforts to eradicate the disease.
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Affiliation(s)
- Clotilde Djuikem
- Université Côte d'Azur, Inria, INRAE, CNRS, MACBES, Nice, France.
| | | | - Suzanne Touzeau
- Université Côte d'Azur, Inria, INRAE, CNRS, MACBES, Nice, France
- Université Côte d'Azur, INRAE, ISA, Nice, France
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Djuikem C, Grognard F, Touzeau S. Impulsive modelling of rust dynamics and predator releases for biocontrol. Math Biosci 2023; 356:108968. [PMID: 36693588 DOI: 10.1016/j.mbs.2023.108968] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Revised: 01/16/2023] [Accepted: 01/16/2023] [Indexed: 01/22/2023]
Abstract
Fungal diseases cause serious damages in crop worldwide. In particular, coffee leaf rust (CLR), caused by fungus Hemileia vastatrix attacks coffee leaves and reduces coffee yield. This paper presents a multi-seasonal model of the CLR development in the coffee plantation with continuous dynamics during the rainy season and a discrete event to represent the simpler dynamics during the dry season. Biological control using predators through one or more discrete introduction events over the year is then added. Analytical and semi-numerical studies are performed to identify how much and how frequently predators need to be introduced through the definition of a threshold value, as a function of various parameters. We show that the best strategy to efficiently control the disease depends on the predator mortality: low mortality parasites need be released only once a year, while high mortality parasites should be released more frequently to ensure their persistence in the plantation. This work hence provides qualitative and quantitative bases for the deployment of predator-based biocontrol, a promising alternative to fungicides for rust control.
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da Silva UP, Ferreira BW, de Sousa BL, Barreto RW, Martins FT, de A Neto JH, Vaz BG, da Silva RR, Martins TVF, de Oliveira Mendes TA, Varejão EVV. Synthesis of bis(ylidene) cyclohexanones and their antifungal activity against selected plant pathogenic fungi. Mol Divers 2023; 27:281-297. [PMID: 35441971 DOI: 10.1007/s11030-022-10431-7] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Accepted: 03/31/2022] [Indexed: 02/08/2023]
Abstract
Botrytis cinerea, Rhizoctonia solani and Hemileia vastatrix are three species of phytopathogenic fungi behind major crop losses worldwide. These have been selected as target models for testing the fungicide potential of a series of bis(ylidene) cyclohexanones. Although some compounds of this chemical class are known to have inhibitory activity against human pathogens, they have never been explored for the control of phytopathogens until now. In the present work, bis(ylidene) cyclohexanones were synthesized through simple, fast and low-cost base- or acid-catalyzed aldol condensation reaction and tested in vitro against B. cinerea, R. solani and H. vastatrix. bis(pyridylmethylene) cyclohexanones showed the highest activity against the target fungi. When tested at 200 nmol per mycelial plug against R. solani., these compounds completely inhibited the mycelial growth, and the most active bis(pyridylmethylene) cyclohexanone compound had an IC50 of 155.5 nmol plug-1. Additionally, bis(pyridylmethylene) cyclohexanones completely inhibited urediniospore germination of H. vastatrix, at 125 μmol L-1. The most active bis(pyridylmethylene) cyclohexanone had an IC50 value of 4.8 µmol L-1, which was estimated as approximately 2.6 times lower than that found for the copper oxychloride-based fungicide, used as control. Additionally, these substances had a low cytotoxicity against the mammalian Vero cell line. Finally, in silico calculations indicated that these compounds present physicochemical parameters regarded as suitable for agrochemicals. Bis(ylidene) cyclohexanones may constitute promising candidates for the development of novel antifungal agents for the control of relevant fungal diseases in agriculture.
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Affiliation(s)
- Ueveton Pimentel da Silva
- Department of Chemistry, Universidade Federal de Viçosa, Av PH Rolfs sn, Viçosa, Minas Gerais, 36.570-900, Brazil
| | - Bruno Wesley Ferreira
- Department of Phytopathology, Universidade Federal de Viçosa, Av PH Rolfs sn, Viçosa, Minas Gerais, 36.570-900, Brazil
| | - Bianca Lana de Sousa
- Department of Chemistry, Universidade Federal de Viçosa, Av PH Rolfs sn, Viçosa, Minas Gerais, 36.570-900, Brazil
| | - Robert Weingart Barreto
- Department of Phytopathology, Universidade Federal de Viçosa, Av PH Rolfs sn, Viçosa, Minas Gerais, 36.570-900, Brazil
| | - Felipe Terra Martins
- Institute of Chemistry, Universidade Federal de Goiás, Av Esperança, sn, Samambaia, Goiânia, 74.690-900, Brazil
| | - João Honorato de A Neto
- Department of Chemistry, Universidade Federal de São Carlos, Rodovia Washington Luís s/n Km 235, Sao Carlos, SP, 74.690-900, Brazil
| | - Boniek Gontijo Vaz
- Institute of Chemistry, Universidade Federal de Goiás, Av Esperança, sn, Samambaia, Goiânia, 74.690-900, Brazil
| | - Rodolfo Rodrigues da Silva
- Institute of Chemistry, Universidade Federal de Goiás, Av Esperança, sn, Samambaia, Goiânia, 74.690-900, Brazil
| | - Thaís Viana Fialho Martins
- Department of Biochemistry and Molecular Biology, Universidade Federal de Viçosa, Av PH Rolfs sn, Viçosa, Minas Gerais, 36.570-900, Brazil
| | - Tiago Antônio de Oliveira Mendes
- Department of Biochemistry and Molecular Biology, Universidade Federal de Viçosa, Av PH Rolfs sn, Viçosa, Minas Gerais, 36.570-900, Brazil
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Harvey CA, Pritts AA, Zwetsloot MJ, Jansen K, Pulleman MM, Armbrecht I, Avelino J, Barrera JF, Bunn C, García JH, Isaza C, Munoz-Ucros J, Pérez-Alemán CJ, Rahn E, Robiglio V, Somarriba E, Valencia V. Transformation of coffee-growing landscapes across Latin America. A review. Agron Sustain Dev 2021; 41:62. [PMID: 34484434 PMCID: PMC8406019 DOI: 10.1007/s13593-021-00712-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 06/28/2021] [Indexed: 06/01/2023]
Abstract
UNLABELLED In Latin America, the cultivation of Arabica coffee (Coffea arabica) plays a critical role in rural livelihoods, biodiversity conservation, and sustainable development. Over the last 20 years, coffee farms and landscapes across the region have undergone rapid and profound biophysical changes in response to low coffee prices, changing climatic conditions, severe plant pathogen outbreaks, and other drivers. Although these biophysical transformations are pervasive and affect millions of rural livelihoods, there is limited information on the types, location, and extent of landscape changes and their socioeconomic and ecological consequences. Here we review the state of knowledge on the ongoing biophysical changes in coffee-growing regions, explore the potential socioeconomic and ecological impacts of these changes, and highlight key research gaps. We identify seven major land-use trends which are affecting the sustainability of coffee-growing regions across Latin America in different ways. These trends include (1) the widespread shift to disease-resistant cultivars, (2) the conventional intensification of coffee management with greater planting densities, greater use of agrochemicals and less shade, (3) the conversion of coffee to other agricultural land uses, (4) the introduction of Robusta coffee (Coffea canephora) into areas not previously cultivated with coffee, (5) the expansion of coffee into forested areas, (6) the urbanization of coffee landscapes, and (7) the increase in the area of coffee produced under voluntary sustainability standards. Our review highlights the incomplete and scattered information on the drivers, patterns, and outcomes of biophysical changes in coffee landscapes, and lays out a detailed research agenda to address these research gaps and elucidate the effects of different landscape trajectories on rural livelihoods, biodiversity conservation, and other aspects of sustainable development. A better understanding of the drivers, patterns, and consequences of changes in coffee landscapes is vital for informing the design of policies, programs, and incentives for sustainable coffee production. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s13593-021-00712-0.
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Affiliation(s)
- Celia A. Harvey
- Monteverde Institute, Apdo.69-5655, Monteverde, Puntarenas, Costa Rica
| | - Alyssa A. Pritts
- Farming Systems Ecology Group, Wageningen University & Research, P.O. Box 430, 6700 AK Wageningen, The Netherlands
| | - Marie J. Zwetsloot
- Soil Biology Group, Wageningen University & Research, P.O. Box 47, 6700 AA Wageningen, The Netherlands
| | - Kees Jansen
- Rural Sociology Group, Wageningen University & Research, Hollandseweg 1, 6706 KN Wageningen, The Netherlands
| | - Mirjam M. Pulleman
- Soil Biology Group, Wageningen University & Research, P.O. Box 47, 6700 AA Wageningen, The Netherlands
- The International Center for Tropical Agriculture (CIAT), Km 17 Recta Cali-Palmira, AA 6713, 763537 Cali, Colombia
| | - Inge Armbrecht
- Departamento de Biología, Universidad del Valle, Calle 13 # 100-00 ed, 320 Cali, Colombia
| | - Jacques Avelino
- CIRAD, UMR PHIM, San José, Costa Rica
- PHIM, Univ Montpellier, CIRAD, INRAE, Institut Agro, IRD, Montpellier, France
- Program of Agriculture, Livestock and Agroforestry, CATIE, Turrialba, 7170 Costa Rica
- IICA, 2200 Coronado, San José, AP 55 Costa Rica
| | - Juan F. Barrera
- Arthropod Ecology and Pest Management Group, Department of Agriculture, Society and Environment, El Colegio de la Frontera Sur, Carretera Antiguo Aeropuerto km 2.5, 30700 Tapachula, Chiapas Mexico
| | - Christian Bunn
- The International Center for Tropical Agriculture (CIAT), Km 17 Recta Cali-Palmira, AA 6713, 763537 Cali, Colombia
- University of Göttingen, Platz der Göttinger Sieben 5, 37073 Göttingen, Germany
| | - Javier Hoyos García
- Parque Tecnológico de Innovación TECNiCAFÉ, Cra 17 # 48 N 18 Casa 53 Conjunto Cerrado Entrepinos, Popayán, Cauca Colombia
| | - Carlos Isaza
- Programa de Café para Solidaridad en Colombia, Solidaridad, Calle 43 N, °23-78 Manizales, Colombia
| | - Juana Munoz-Ucros
- School of Integrative Plant Science, Cornell University, 236 Tower Rd, Ithaca, NY USA
| | - Carlos J. Pérez-Alemán
- Fundación Solidaridad Latinoamericana, Calle Evelio Lara No. 131-B, Ciudad del Saber, Ciudad de Panamá, Panamá
| | - Eric Rahn
- The International Center for Tropical Agriculture (CIAT), Km 17 Recta Cali-Palmira, AA 6713, 763537 Cali, Colombia
| | - Valentina Robiglio
- World Agroforestry Centre (ICRAF), c/o CIP, Av. La Molina 1895, P.O Box 1558, 12 Lima, Peru
| | - Eduardo Somarriba
- Program of Agriculture, Livestock and Agroforestry, CATIE, Turrialba, 7170 Costa Rica
| | - Vivian Valencia
- Farming Systems Ecology Group, Wageningen University & Research, P.O. Box 430, 6700 AK Wageningen, The Netherlands
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Parraga-Alava J, Cusme K, Loor A, Santander E. RoCoLe: A robusta coffee leaf images dataset for evaluation of machine learning based methods in plant diseases recognition. Data Brief 2019; 25:104414. [PMID: 31516934 PMCID: PMC6727496 DOI: 10.1016/j.dib.2019.104414] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [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: 05/17/2019] [Revised: 08/02/2019] [Accepted: 08/12/2019] [Indexed: 11/28/2022] Open
Abstract
In this article we introduce a robusta coffee leaf images dataset called RoCoLe. The dataset contains 1560 leaf images with visible red mites and spots (denoting coffee leaf rust presence) for infection cases and images without such structures for healthy cases. In addition, the data set includes annotations regarding objects (leaves), state (healthy and unhealthy) and the severity of disease (leaf area with spots). Images were all obtained in real-world conditions in the same coffee plants field using a smartphone camera. RoCoLe data set facilitates the evaluation of the performance of machine learning algorithms used in image segmentation and classification problems related to plant diseases recognition. The current dataset is freely and publicly available at https://doi.org/10.17632/c5yvn32dzg.2.
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Affiliation(s)
- Jorge Parraga-Alava
- Escuela Superior Politécnica Agropecuaria de Manabí Manuel Félix López, Calceta, Ecuador.,Universidad de Santiago de Chile, Santiago, Chile
| | - Kevin Cusme
- Escuela Superior Politécnica Agropecuaria de Manabí Manuel Félix López, Calceta, Ecuador
| | - Angélica Loor
- Escuela Superior Politécnica Agropecuaria de Manabí Manuel Félix López, Calceta, Ecuador
| | - Esneider Santander
- Escuela Superior Politécnica Agropecuaria de Manabí Manuel Félix López, Calceta, Ecuador
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Vacacela Ajila HE, Ferreira JAM, Colares F, Oliveira CM, Bernardo AMG, Venzon M, Pallini A. Ricoseius loxocheles (Acari: Phytoseiidae) is not a predator of false spider mite on coffee crops: What does it eat? Exp Appl Acarol 2018; 74:1-11. [PMID: 29383531 DOI: 10.1007/s10493-018-0211-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [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: 08/03/2017] [Accepted: 01/23/2018] [Indexed: 06/07/2023]
Abstract
Ricoseius loxocheles (De Leon) (Acari: Phytoseiidae) is often found in coffee crops and is known to feed on coffee leaf rust, Hemileia vastatrix Berkeley and Broome (Uredinales). As the occurrence of coffee leaf rust is limited primarily to the rainy season, the mite may use other food sources to survive during the periods of low pathogen prevalence. It is well known that phytoseiid mites can survive on a variety of food sources, such as herbivorous mites, fungi and pollen. We evaluated the ability of R. loxocheles to survive and reproduce on a diet of Brevipalpus phoenicis Geijskes (Acari: Tenuipalpidae), cattail pollen (Typha spp.), clover rust (Puccinia oxalidis), bee pollen (Santa Bárbara® dehydrated pollen, Santa Bárbara, MG, Brazil) and coffee leaf rust. Ricoseius loxocheles did not survive or reproduce on any B. phoenicis stages tested (egg, larva, adult). The survival and oviposition of R. loxocheles were directly affected by the presence of coffee rust urediniospores, but not by the presence of the prey. Survival and oviposition of the phytoseiid were similar when fed cattail pollen, clover rust and coffee leaf rust but was lower when fed bee pollen. Our results show that R. loxocheles is not a predator of B. phoenicis but it is able to utilize other resources besides coffee leaf rust.
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Affiliation(s)
- Henry E Vacacela Ajila
- Department of Entomology, Section Acarology, Federal University of Viçosa, Viçosa, MG, Brazil.
| | - João A M Ferreira
- Department of Entomology, Section Acarology, Federal University of Viçosa, Viçosa, MG, Brazil
| | - Felipe Colares
- Department of Entomology, Section Acarology, Federal University of Viçosa, Viçosa, MG, Brazil
| | - Cleber M Oliveira
- Department of Entomology, Section Acarology, Federal University of Viçosa, Viçosa, MG, Brazil
| | - Ana Maria G Bernardo
- Department of Entomology, Section Acarology, Federal University of Viçosa, Viçosa, MG, Brazil
| | - Madelaine Venzon
- Agriculture and Livestock Research Enterprise of Minas Gerais (EPAMIG), Vila Gianetti 46, Viçosa, MG, 36570-000, Brazil
| | - Angelo Pallini
- Department of Entomology, Section Acarology, Federal University of Viçosa, Viçosa, MG, Brazil
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Loureiro A, Azinheira HG, Silva MDC, Talhinhas P. A method for obtaining RNA from Hemileia vastatrix appressoria produced in planta, suitable for transcriptomic analyses. Fungal Biol 2015; 119:1093-1099. [PMID: 26466882 DOI: 10.1016/j.funbio.2015.08.008] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2015] [Revised: 08/10/2015] [Accepted: 08/11/2015] [Indexed: 11/20/2022]
Abstract
Appressoria are the first infection structures developed by rust fungi and require specific topographic signals from the host for their differentiation. The ease in obtaining appressoria in vitro for these biotrophic fungi led to studies concerning gene expression and gene discovery at appressorial level, avoiding the need to distinguish plant and fungal transcripts. However, in some pathosystems, it was observed that gene expression in appressoria seems to be influenced by host-derived signals, suggesting that transcriptomic analyses performed from in planta differentiated appressoria would be potentially more informative than those from in vitro differentiated appressoria. Nevertheless analysing appressorial RNA obtained from in planta samples is often hampered by an excessive dilution of fungal RNA within plant RNA, besides uncertainty regarding the fungal or plant origin of RNA from highly conserved genes. To circumvent these difficulties, we have recovered Hemileia vastatrix appressoria from Arabica coffee leaf surface using a film of nitrocellulose dissolved in butyl and ethyl acetates (nail polish), and extracted fungal RNA from the polish peel. RNA thus obtained is of good quality and usable for cDNA synthesis and transcriptomic (quantitative PCR) studies. This method could provide the means to investigate specific host-induced appressoria-related fungal pathogenicity factors.
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Affiliation(s)
- Andreia Loureiro
- (CIFC) Centro de Investigação das Ferrugens do Cafeeiro, Instituto Superior de Agronomia, Universidade de Lisboa, Quinta do Marquês, 2784-505 Oeiras, Portugal; (LEAF) Linking Landscape, Environment, Agriculture and Food, Instituto Superior de Agronomia, Universidade de Lisboa, 1349-017 Lisboa, Portugal
| | - Helena Gil Azinheira
- (CIFC) Centro de Investigação das Ferrugens do Cafeeiro, Instituto Superior de Agronomia, Universidade de Lisboa, Quinta do Marquês, 2784-505 Oeiras, Portugal; (LEAF) Linking Landscape, Environment, Agriculture and Food, Instituto Superior de Agronomia, Universidade de Lisboa, 1349-017 Lisboa, Portugal.
| | - Maria do Céu Silva
- (CIFC) Centro de Investigação das Ferrugens do Cafeeiro, Instituto Superior de Agronomia, Universidade de Lisboa, Quinta do Marquês, 2784-505 Oeiras, Portugal; (LEAF) Linking Landscape, Environment, Agriculture and Food, Instituto Superior de Agronomia, Universidade de Lisboa, 1349-017 Lisboa, Portugal
| | - Pedro Talhinhas
- (CIFC) Centro de Investigação das Ferrugens do Cafeeiro, Instituto Superior de Agronomia, Universidade de Lisboa, Quinta do Marquês, 2784-505 Oeiras, Portugal; (LEAF) Linking Landscape, Environment, Agriculture and Food, Instituto Superior de Agronomia, Universidade de Lisboa, 1349-017 Lisboa, Portugal
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