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van Dooremalen C, Ulgezen ZN, Dall’Olio R, Godeau U, Duan X, Sousa JP, Schäfer MO, Beaurepaire A, van Gennip P, Schoonman M, Flener C, Matthijs S, Claeys Boúúaert D, Verbeke W, Freshley D, Valkenburg DJ, van den Bosch T, Schaafsma F, Peters J, Xu M, Le Conte Y, Alaux C, Dalmon A, Paxton RJ, Tehel A, Streicher T, Dezmirean DS, Giurgiu AI, Topping CJ, Williams JH, Capela N, Lopes S, Alves F, Alves J, Bica J, Simões S, Alves da Silva A, Castro S, Loureiro J, Horčičková E, Bencsik M, McVeigh A, Kumar T, Moro A, van Delden A, Ziółkowska E, Filipiak M, Mikołajczyk Ł, Leufgen K, De Smet L, de Graaf DC. Bridging the Gap between Field Experiments and Machine Learning: The EC H2020 B-GOOD Project as a Case Study towards Automated Predictive Health Monitoring of Honey Bee Colonies. Insects 2024; 15:76. [PMID: 38276825 PMCID: PMC10816039 DOI: 10.3390/insects15010076] [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: 11/25/2023] [Revised: 01/05/2024] [Accepted: 01/20/2024] [Indexed: 01/27/2024]
Abstract
Honey bee colonies have great societal and economic importance. The main challenge that beekeepers face is keeping bee colonies healthy under ever-changing environmental conditions. In the past two decades, beekeepers that manage colonies of Western honey bees (Apis mellifera) have become increasingly concerned by the presence of parasites and pathogens affecting the bees, the reduction in pollen and nectar availability, and the colonies' exposure to pesticides, among others. Hence, beekeepers need to know the health condition of their colonies and how to keep them alive and thriving, which creates a need for a new holistic data collection method to harmonize the flow of information from various sources that can be linked at the colony level for different health determinants, such as bee colony, environmental, socioeconomic, and genetic statuses. For this purpose, we have developed and implemented the B-GOOD (Giving Beekeeping Guidance by computational-assisted Decision Making) project as a case study to categorize the colony's health condition and find a Health Status Index (HSI). Using a 3-tier setup guided by work plans and standardized protocols, we have collected data from inside the colonies (amount of brood, disease load, honey harvest, etc.) and from their environment (floral resource availability). Most of the project's data was automatically collected by the BEEP Base Sensor System. This continuous stream of data served as the basis to determine and validate an algorithm to calculate the HSI using machine learning. In this article, we share our insights on this holistic methodology and also highlight the importance of using a standardized data language to increase the compatibility between different current and future studies. We argue that the combined management of big data will be an essential building block in the development of targeted guidance for beekeepers and for the future of sustainable beekeeping.
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Affiliation(s)
| | - Zeynep N. Ulgezen
- Wageningen University & Research, 6708 PB Wageningen, The Netherlands
| | | | - Ugoline Godeau
- Institut National de la Recherche pour l’Agriculture, l’Alimentation et l’Environnement, 84914 Avignon, France
| | | | - José Paulo Sousa
- Centre for Functional Ecology, Department of Life Sciences, TERRA Associated Laboratory, University of Coimbra, 3000-456 Coimbra, Portugal
| | - Marc O. Schäfer
- Friedrich-Loeffler-Institut, Bundesforschunginstitut für Tiergesundheit, 17493 Greifswald-Insel Riems, Germany
| | | | - Pim van Gennip
- Stichting BEEP, 3972 LK Driebergen-Rijsenburg, The Netherlands
| | | | - Claude Flener
- Suomen Mehiläishoitajain Liitto, 00130 Helsinki, Finland
| | | | | | | | | | | | | | - Famke Schaafsma
- Wageningen University & Research, 6708 PB Wageningen, The Netherlands
| | - Jeroen Peters
- Wageningen University & Research, 6708 PB Wageningen, The Netherlands
| | - Mang Xu
- Wageningen University & Research, 6708 PB Wageningen, The Netherlands
| | - Yves Le Conte
- Institut National de la Recherche pour l’Agriculture, l’Alimentation et l’Environnement, 84914 Avignon, France
| | - Cedric Alaux
- Institut National de la Recherche pour l’Agriculture, l’Alimentation et l’Environnement, 84914 Avignon, France
| | - Anne Dalmon
- Institut National de la Recherche pour l’Agriculture, l’Alimentation et l’Environnement, 84914 Avignon, France
| | - Robert J. Paxton
- Martin-Luther-Universitaet Halle-Wittenberg, 06120 Halle, Germany
| | - Anja Tehel
- Martin-Luther-Universitaet Halle-Wittenberg, 06120 Halle, Germany
| | - Tabea Streicher
- Martin-Luther-Universitaet Halle-Wittenberg, 06120 Halle, Germany
| | - Daniel S. Dezmirean
- Universitatea de Stiinte Agricole si Medicina Veterinara Cluj Napoca, 400372 Cluj Napoca, Romania
| | - Alexandru I. Giurgiu
- Universitatea de Stiinte Agricole si Medicina Veterinara Cluj Napoca, 400372 Cluj Napoca, Romania
| | | | | | - Nuno Capela
- Centre for Functional Ecology, Department of Life Sciences, TERRA Associated Laboratory, University of Coimbra, 3000-456 Coimbra, Portugal
| | - Sara Lopes
- Centre for Functional Ecology, Department of Life Sciences, TERRA Associated Laboratory, University of Coimbra, 3000-456 Coimbra, Portugal
| | - Fátima Alves
- Centre for Functional Ecology, Department of Life Sciences, TERRA Associated Laboratory, University of Coimbra, 3000-456 Coimbra, Portugal
| | - Joana Alves
- Centre for Functional Ecology, Department of Life Sciences, TERRA Associated Laboratory, University of Coimbra, 3000-456 Coimbra, Portugal
| | - João Bica
- Centre for Functional Ecology, Department of Life Sciences, TERRA Associated Laboratory, University of Coimbra, 3000-456 Coimbra, Portugal
| | - Sandra Simões
- Centre for Functional Ecology, Department of Life Sciences, TERRA Associated Laboratory, University of Coimbra, 3000-456 Coimbra, Portugal
| | - António Alves da Silva
- Centre for Functional Ecology, Department of Life Sciences, TERRA Associated Laboratory, University of Coimbra, 3000-456 Coimbra, Portugal
| | - Sílvia Castro
- Centre for Functional Ecology, Department of Life Sciences, TERRA Associated Laboratory, University of Coimbra, 3000-456 Coimbra, Portugal
| | - João Loureiro
- Centre for Functional Ecology, Department of Life Sciences, TERRA Associated Laboratory, University of Coimbra, 3000-456 Coimbra, Portugal
| | - Eva Horčičková
- Centre for Functional Ecology, Department of Life Sciences, TERRA Associated Laboratory, University of Coimbra, 3000-456 Coimbra, Portugal
| | - Martin Bencsik
- The Nottingham Trent University, Nottingham NG11 8NS, UK
| | - Adam McVeigh
- The Nottingham Trent University, Nottingham NG11 8NS, UK
| | - Tarun Kumar
- The Nottingham Trent University, Nottingham NG11 8NS, UK
| | - Arrigo Moro
- Institute of Bee Health, University of Bern, 3012 Bern, Switzerland
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Sánchez-Vallet A, Tian H, Rodriguez-Moreno L, Valkenburg DJ, Saleem-Batcha R, Wawra S, Kombrink A, Verhage L, de Jonge R, van Esse HP, Zuccaro A, Croll D, Mesters JR, Thomma BPHJ. A secreted LysM effector protects fungal hyphae through chitin-dependent homodimer polymerization. PLoS Pathog 2020; 16:e1008652. [PMID: 32574207 PMCID: PMC7337405 DOI: 10.1371/journal.ppat.1008652] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Revised: 07/06/2020] [Accepted: 05/25/2020] [Indexed: 12/25/2022] Open
Abstract
Plants trigger immune responses upon recognition of fungal cell wall chitin, followed by the release of various antimicrobials, including chitinase enzymes that hydrolyze chitin. In turn, many fungal pathogens secrete LysM effectors that prevent chitin recognition by the host through scavenging of chitin oligomers. We previously showed that intrachain LysM dimerization of the Cladosporium fulvum effector Ecp6 confers an ultrahigh-affinity binding groove that competitively sequesters chitin oligomers from host immune receptors. Additionally, particular LysM effectors are found to protect fungal hyphae against chitinase hydrolysis during host colonization. However, the molecular basis for the protection of fungal cell walls against hydrolysis remained unclear. Here, we determined a crystal structure of the single LysM domain-containing effector Mg1LysM of the wheat pathogen Zymoseptoria tritici and reveal that Mg1LysM is involved in the formation of two kinds of dimers; a chitin-dependent dimer as well as a chitin-independent homodimer. In this manner, Mg1LysM gains the capacity to form a supramolecular structure by chitin-induced oligomerization of chitin-independent Mg1LysM homodimers, a property that confers protection to fungal cell walls against host chitinases. Chitin plays a central role in plant-fungi interactions, since it is a major component of the fungal cell wall that is targeted by host hydrolytic enzymes to inhibit the growth of fungal pathogens on the one hand, and release chitin fragments that are recognized by host immune receptors to activate further immune responses on the other hand. In turn, many fungal pathogens secrete chitin binding LysM effectors to which currently two functions have been assigned. Most LysM effectors that were functionally characterized to date function to prevent chitin recognition by host immune receptors through chitin sequestration. Additionally, some LysM effectors were shown to protect fungal hyphae against hydrolysis by host chitinases. The crystal structure of Mg1LysM from the Septoria blotch pathogen of wheat, Zymoseptoria tritici, revealed that chitin-induced dimerization of two Mg1LysM protomers through high affinity binding is required for hyphal protection against chitinases. Since Mg1LysM also forms ligand-independent homodimers, a supramolecular structure can be formed in which chitin-induced oligomerization of Mg1LysM ligand-independent homodimers form a contiguous Mg1LysM higher ordered structure that is anchored to the chitin in the fungal cell wall to prevent hydrolysis by host chitinases.
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Affiliation(s)
- Andrea Sánchez-Vallet
- Laboratory of Phytopathology, Wageningen University& Research, Wageningen, The Netherlands
- Plant Pathology Group, Institute of Integrative Biology, ETH Zurich, Zurich, Switzerland
| | - Hui Tian
- Laboratory of Phytopathology, Wageningen University& Research, Wageningen, The Netherlands
| | - Luis Rodriguez-Moreno
- Laboratory of Phytopathology, Wageningen University& Research, Wageningen, The Netherlands
| | - Dirk-Jan Valkenburg
- Laboratory of Phytopathology, Wageningen University& Research, Wageningen, The Netherlands
| | - Raspudin Saleem-Batcha
- Institute of Biochemistry, Center for Structural and Cell Biology in Medicine, University of Lübeck, Lübeck, Germany
| | - Stephan Wawra
- University of Cologne, Institute for Plant Sciences, Cluster of Excellence on Plant Sciences (CEPLAS), Cologne, Germany
| | - Anja Kombrink
- Laboratory of Phytopathology, Wageningen University& Research, Wageningen, The Netherlands
| | - Leonie Verhage
- Laboratory of Phytopathology, Wageningen University& Research, Wageningen, The Netherlands
| | - Ronnie de Jonge
- Laboratory of Phytopathology, Wageningen University& Research, Wageningen, The Netherlands
| | - H. Peter van Esse
- Laboratory of Phytopathology, Wageningen University& Research, Wageningen, The Netherlands
| | - Alga Zuccaro
- University of Cologne, Institute for Plant Sciences, Cluster of Excellence on Plant Sciences (CEPLAS), Cologne, Germany
| | - Daniel Croll
- Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
| | - Jeroen R. Mesters
- Institute of Biochemistry, Center for Structural and Cell Biology in Medicine, University of Lübeck, Lübeck, Germany
- * E-mail: (JRM); (BPHJT)
| | - Bart P. H. J. Thomma
- Laboratory of Phytopathology, Wageningen University& Research, Wageningen, The Netherlands
- University of Cologne, Institute for Plant Sciences, Cluster of Excellence on Plant Sciences (CEPLAS), Cologne, Germany
- * E-mail: (JRM); (BPHJT)
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Yadeta KA, Valkenburg DJ, Hanemian M, Marco Y, Thomma BPHJ. The Brassicaceae-specific EWR1 gene provides resistance to vascular wilt pathogens. PLoS One 2014; 9:e88230. [PMID: 24505441 PMCID: PMC3914955 DOI: 10.1371/journal.pone.0088230] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2013] [Accepted: 01/05/2014] [Indexed: 11/19/2022] Open
Abstract
Soil-borne vascular wilt diseases caused by Verticillium spp. are among the most destructive diseases worldwide in a wide range of plant species. The most effective means of controlling Verticillium wilt diseases is the use of genetic resistance. We have previously reported the identification of four activation-tagged Arabidopsis mutants which showed enhanced resistance to Verticillium wilt. Among these, one mutant also showed enhanced resistance to Ralstonia solanacearum, a bacterial vascular wilt pathogen. Cloning of the activation tag revealed an insertion upstream of gene At3g13437, which we designated as EWR1 (for Enhancer of vascular Wilt Resistance 1) that encodes a putatively secreted protein of unknown function. The search for homologs of Arabidopsis EWR1 (AtEWR1) in public databases only identified homologs within the Brassicaceae family. We subsequently cloned the EWR1 homolog from Brassica oleracea (BoEWR1) and show that over-expression in Arabidopsis results in V. dahliae resistance. Moreover, over-expression of AtEWR1 and BoEWR1 in N. benthamiana, a member of the Solanaceae family, results in V. dahliae resistance, suggesting that EWR1 homologs can be used to engineer Verticillium wilt resistance in non-Brassicaceae crops as well.
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Affiliation(s)
- Koste A. Yadeta
- Laboratory of Phytopathology, Wageningen University, Wageningen, The Netherlands
| | - Dirk-Jan Valkenburg
- Laboratory of Phytopathology, Wageningen University, Wageningen, The Netherlands
| | - Mathieu Hanemian
- Laboratoire des Interactions Plantes Microorganismes, Centre National de la Recherche Scientifique-Institut National de la Recherche Agronomique, Castanet-Tolosan, France
| | - Yves Marco
- Laboratoire des Interactions Plantes Microorganismes, Centre National de la Recherche Scientifique-Institut National de la Recherche Agronomique, Castanet-Tolosan, France
| | - Bart P. H. J. Thomma
- Laboratory of Phytopathology, Wageningen University, Wageningen, The Netherlands
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