Microbial Community Analysis Offers Insight into the Complex Origins of Plant Disease in a Smallholder Farm Context
Classical approaches to plant disease diagnosis assume a single pathogen/single disease paradigm. Here, we revisit the presumed role of Fusarium oxysporum as the causal agent of wilting and yellowing of chickpea plants on smallholder farms in Ethiopia. Contrary to expectations, detection of Fusarium...
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| Language: | English |
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The American Phytopathological Society
2024-11-01
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| Series: | Phytobiomes Journal |
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| Online Access: | https://apsjournals.apsnet.org/doi/10.1094/PBIOMES-02-24-0023-R |
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| author | Betsy A. Alford Dagnachew Bekele Sultan M. Yimer Amna Fayyaz Noelia Carrasquilla-Garcia Peter L. Chang Calen Badger Anandkumar Surendrarao Eric J. B. von Wettberg M. Farooq H. Munis Kassahun Tesfaye Asnake Fikre Douglas R. Cook |
| author_facet | Betsy A. Alford Dagnachew Bekele Sultan M. Yimer Amna Fayyaz Noelia Carrasquilla-Garcia Peter L. Chang Calen Badger Anandkumar Surendrarao Eric J. B. von Wettberg M. Farooq H. Munis Kassahun Tesfaye Asnake Fikre Douglas R. Cook |
| author_sort | Betsy A. Alford |
| collection | DOAJ |
| description | Classical approaches to plant disease diagnosis assume a single pathogen/single disease paradigm. Here, we revisit the presumed role of Fusarium oxysporum as the causal agent of wilting and yellowing of chickpea plants on smallholder farms in Ethiopia. Contrary to expectations, detection of Fusarium DNA using conserved PCR primers failed to associate the pathogen with symptomatic plants. Instead, culture-independent sequencing of microbial communities nominated unexpected pathogens and revealed patchiness in the assembly of common microbial consortia. Surprisingly, tests of differential enrichment identified Phytophthora as the most common disease-associated taxon. More generally, across all field sites, multilevel pattern analysis identified indicator taxa whose patterns of co-occurrence demarcate discrete microbial communities and are consistent with a range of specific interactions, including mutualism and antagonism. Taken together, these data indicate that soilborne chickpea disease in Ethiopia has heterogeneous origins and that despite decades of emphasis and disease resistance breeding, the role of Fusarium as the frequent agent of chickpea disease in Ethiopia remains enigmatic. |
| format | Article |
| id | doaj-art-a676f61c4dfa4e9186f14c4cedd15fa5 |
| institution | Kabale University |
| issn | 2471-2906 |
| language | English |
| publishDate | 2024-11-01 |
| publisher | The American Phytopathological Society |
| record_format | Article |
| series | Phytobiomes Journal |
| spelling | doaj-art-a676f61c4dfa4e9186f14c4cedd15fa52024-11-23T17:01:49ZengThe American Phytopathological SocietyPhytobiomes Journal2471-29062024-11-018445646810.1094/PBIOMES-02-24-0023-RMicrobial Community Analysis Offers Insight into the Complex Origins of Plant Disease in a Smallholder Farm ContextBetsy A. Alford0Dagnachew Bekele1Sultan M. Yimer2Amna Fayyaz3Noelia Carrasquilla-Garcia4Peter L. Chang5Calen Badger6Anandkumar Surendrarao7Eric J. B. von Wettberg8M. Farooq H. Munis9Kassahun Tesfaye10Asnake Fikre11Douglas R. Cook12Department of Plant Pathology, University of California, One Shields Ave., Davis, CA 95616-8680, U.S.A.Ethiopian Institute of Agricultural Research, Debre Zeit Research Center, Addis Ababa, EthiopiaWoldia University, Woldia, EthiopiaDepartment of Plant Pathology, University of California, One Shields Ave., Davis, CA 95616-8680, U.S.A.Department of Plant Pathology, University of California, One Shields Ave., Davis, CA 95616-8680, U.S.A.Department of Plant Pathology, University of California, One Shields Ave., Davis, CA 95616-8680, U.S.A.Integrative Genetics and Genomics Graduate Group, University of California, One Shields Ave., Davis, CA 95616-8680, U.S.A.Plant Biology Graduate Group, University of California, One Shields Ave., Davis, CA 95616-8680, U.S.A.Department of Agriculture, Landscape, and Environment, University of Vermont, Burlington, VT 05405, U.S.A.Department of Plant Sciences, Quaid-i-Azam University, Islamabad, 45320, PakistanInstitute of Biotechnology, Addis Ababa University, Addis Ababa, EthiopiaEthiopian Institute of Agricultural Research, Debre Zeit Research Center, Addis Ababa, EthiopiaDepartment of Plant Pathology, University of California, One Shields Ave., Davis, CA 95616-8680, U.S.A.Classical approaches to plant disease diagnosis assume a single pathogen/single disease paradigm. Here, we revisit the presumed role of Fusarium oxysporum as the causal agent of wilting and yellowing of chickpea plants on smallholder farms in Ethiopia. Contrary to expectations, detection of Fusarium DNA using conserved PCR primers failed to associate the pathogen with symptomatic plants. Instead, culture-independent sequencing of microbial communities nominated unexpected pathogens and revealed patchiness in the assembly of common microbial consortia. Surprisingly, tests of differential enrichment identified Phytophthora as the most common disease-associated taxon. More generally, across all field sites, multilevel pattern analysis identified indicator taxa whose patterns of co-occurrence demarcate discrete microbial communities and are consistent with a range of specific interactions, including mutualism and antagonism. Taken together, these data indicate that soilborne chickpea disease in Ethiopia has heterogeneous origins and that despite decades of emphasis and disease resistance breeding, the role of Fusarium as the frequent agent of chickpea disease in Ethiopia remains enigmatic.https://apsjournals.apsnet.org/doi/10.1094/PBIOMES-02-24-0023-R18S sequencingchickpeaFusarium oxysporumhierarchical clusteringindicator analysismicrobiome |
| spellingShingle | Betsy A. Alford Dagnachew Bekele Sultan M. Yimer Amna Fayyaz Noelia Carrasquilla-Garcia Peter L. Chang Calen Badger Anandkumar Surendrarao Eric J. B. von Wettberg M. Farooq H. Munis Kassahun Tesfaye Asnake Fikre Douglas R. Cook Microbial Community Analysis Offers Insight into the Complex Origins of Plant Disease in a Smallholder Farm Context Phytobiomes Journal 18S sequencing chickpea Fusarium oxysporum hierarchical clustering indicator analysis microbiome |
| title | Microbial Community Analysis Offers Insight into the Complex Origins of Plant Disease in a Smallholder Farm Context |
| title_full | Microbial Community Analysis Offers Insight into the Complex Origins of Plant Disease in a Smallholder Farm Context |
| title_fullStr | Microbial Community Analysis Offers Insight into the Complex Origins of Plant Disease in a Smallholder Farm Context |
| title_full_unstemmed | Microbial Community Analysis Offers Insight into the Complex Origins of Plant Disease in a Smallholder Farm Context |
| title_short | Microbial Community Analysis Offers Insight into the Complex Origins of Plant Disease in a Smallholder Farm Context |
| title_sort | microbial community analysis offers insight into the complex origins of plant disease in a smallholder farm context |
| topic | 18S sequencing chickpea Fusarium oxysporum hierarchical clustering indicator analysis microbiome |
| url | https://apsjournals.apsnet.org/doi/10.1094/PBIOMES-02-24-0023-R |
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