Association of Microbiome Diversity with Disease Symptoms in Brassica oleracea Leaves

Cabbage (Brassica oleracea), a crop of major economic importance worldwide, is affected by numerous diseases, which are caused by a wide range of microorganisms, including fungi, oomycetes, bacteria, and viruses, which lead to important losses in yield and quality. The increasing availability of ref...

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Detalles Bibliográficos
Autores: Martín-Cardoso, Héctor, González, Víctor M., Soler-López, Luis, Campo, Sonia, San Segundo, Blanca
Tipo de recurso: artículo
Estado:Versión publicada
Fecha de publicación:2024
País:España
Institución:Consejo Superior de Investigaciones Científicas (CSIC)
Repositorio:DIGITAL.CSIC. Repositorio Institucional del CSIC
OAI Identifier:oai:digital.csic.es:10261/372291
Acceso en línea:http://hdl.handle.net/10261/372291
https://api.elsevier.com/content/abstract/scopus_id/85199773694
Access Level:acceso abierto
Palabra clave:Bacterial diversity
Cabbage
Leaf
Fungal diversity
Microbiome
Shotgun metagenomics
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network_acronym_str ES
network_name_str España
repository_id_str
dc.title.none.fl_str_mv Association of Microbiome Diversity with Disease Symptoms in Brassica oleracea Leaves
title Association of Microbiome Diversity with Disease Symptoms in Brassica oleracea Leaves
spellingShingle Association of Microbiome Diversity with Disease Symptoms in Brassica oleracea Leaves
Martín-Cardoso, Héctor
Bacterial diversity
Cabbage
Leaf
Fungal diversity
Microbiome
Shotgun metagenomics
title_short Association of Microbiome Diversity with Disease Symptoms in Brassica oleracea Leaves
title_full Association of Microbiome Diversity with Disease Symptoms in Brassica oleracea Leaves
title_fullStr Association of Microbiome Diversity with Disease Symptoms in Brassica oleracea Leaves
title_full_unstemmed Association of Microbiome Diversity with Disease Symptoms in Brassica oleracea Leaves
title_sort Association of Microbiome Diversity with Disease Symptoms in Brassica oleracea Leaves
dc.creator.none.fl_str_mv Martín-Cardoso, Héctor
González, Víctor M.
Soler-López, Luis
Campo, Sonia
San Segundo, Blanca
author Martín-Cardoso, Héctor
author_facet Martín-Cardoso, Héctor
González, Víctor M.
Soler-López, Luis
Campo, Sonia
San Segundo, Blanca
author_role author
author2 González, Víctor M.
Soler-López, Luis
Campo, Sonia
San Segundo, Blanca
author2_role author
author
author
author
dc.contributor.none.fl_str_mv Ministerio de Ciencia e Innovación (España)
Agencia Estatal de Investigación (España)
Generalitat de Catalunya
European Commission
Martín-Cardoso, Héctor [0000-0002-0002-9001]
González, Víctor M. [0009-0006-8963-4588]
Soler-López, Luis [0009-0004-9608-1286]
San Segundo, Blanca [0000-0001-7409-3172]
Consejo Superior de Investigaciones Científicas [https://ror.org/02gfc7t72]
dc.subject.none.fl_str_mv Bacterial diversity
Cabbage
Leaf
Fungal diversity
Microbiome
Shotgun metagenomics
topic Bacterial diversity
Cabbage
Leaf
Fungal diversity
Microbiome
Shotgun metagenomics
description Cabbage (Brassica oleracea), a crop of major economic importance worldwide, is affected by numerous diseases, which are caused by a wide range of microorganisms, including fungi, oomycetes, bacteria, and viruses, which lead to important losses in yield and quality. The increasing availability of reference genomes of plant-associated microbes together with recent advances in metagenomic approaches provide new opportunities to identify microbes linked to distinct symptomatology in Brassica leaves. In this study, shotgun metagenomics was used to investigate the microbial community in leaves of B. oleracea plants from agricultural farmlands. Compared with conventional techniques based on culture-based methods, whole-genome shotgun sequencing allows the reliable identification of the microbial population inhabiting a plant tissue at the species level. Asymptomatic and symptomatic leaves showing different disease symptoms were examined. In the asymptomatic leaves, Xanthomonas species were the most abundant taxa. The relative abundance of bacterial and fungal communities varied depending on disease symptoms on the leaf. The microbiome of the leaves showing mild to severe levels of disease was enriched in bacterial populations (Sphingomonas, Methylobacterium, Paracoccus) and to a lesser degree in some fungal taxa, such as Alternaria and Colletotrichum (e.g., in leaves with high levels of necrotic lesions). Sclerotinia species were highly abundant in severely damaged leaves (S. sclerotium, S. trifolium, S. bolearis), followed by Botrytis species. The common and specific bacterial and fungal species associated to disease symptoms were identified. Finally, the analysis of the gene functions in the metagenomic data revealed enrichment in carbohydrate-active enzymes potentially involved in pathogenicity, whose distribution also varied among disease severity groups. Understanding the B. oleracea leaf microbiome in agricultural ecosystems will pave the way for the efficient management of diseases in this crop.
publishDate 2024
dc.date.none.fl_str_mv 2024
2024
2024
dc.type.none.fl_str_mv info:eu-repo/semantics/article
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dc.identifier.none.fl_str_mv http://hdl.handle.net/10261/372291
https://api.elsevier.com/content/abstract/scopus_id/85199773694
url http://hdl.handle.net/10261/372291
https://api.elsevier.com/content/abstract/scopus_id/85199773694
dc.language.none.fl_str_mv Inglés
language_invalid_str_mv Inglés
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Horticulturae
The underlying dataset has been published as supplementary material of the article in the publisher platform at DOI https://doi.org/10.3390/horticulturae10070765
https://doi.org/10.3390/horticulturae10070765
Sí
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dc.publisher.none.fl_str_mv Multidisciplinary Digital Publishing Institute
publisher.none.fl_str_mv Multidisciplinary Digital Publishing Institute
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spelling Association of Microbiome Diversity with Disease Symptoms in Brassica oleracea LeavesMartín-Cardoso, HéctorGonzález, Víctor M.Soler-López, LuisCampo, SoniaSan Segundo, BlancaBacterial diversityCabbageLeafFungal diversityMicrobiomeShotgun metagenomicsCabbage (Brassica oleracea), a crop of major economic importance worldwide, is affected by numerous diseases, which are caused by a wide range of microorganisms, including fungi, oomycetes, bacteria, and viruses, which lead to important losses in yield and quality. The increasing availability of reference genomes of plant-associated microbes together with recent advances in metagenomic approaches provide new opportunities to identify microbes linked to distinct symptomatology in Brassica leaves. In this study, shotgun metagenomics was used to investigate the microbial community in leaves of B. oleracea plants from agricultural farmlands. Compared with conventional techniques based on culture-based methods, whole-genome shotgun sequencing allows the reliable identification of the microbial population inhabiting a plant tissue at the species level. Asymptomatic and symptomatic leaves showing different disease symptoms were examined. In the asymptomatic leaves, Xanthomonas species were the most abundant taxa. The relative abundance of bacterial and fungal communities varied depending on disease symptoms on the leaf. The microbiome of the leaves showing mild to severe levels of disease was enriched in bacterial populations (Sphingomonas, Methylobacterium, Paracoccus) and to a lesser degree in some fungal taxa, such as Alternaria and Colletotrichum (e.g., in leaves with high levels of necrotic lesions). Sclerotinia species were highly abundant in severely damaged leaves (S. sclerotium, S. trifolium, S. bolearis), followed by Botrytis species. The common and specific bacterial and fungal species associated to disease symptoms were identified. Finally, the analysis of the gene functions in the metagenomic data revealed enrichment in carbohydrate-active enzymes potentially involved in pathogenicity, whose distribution also varied among disease severity groups. Understanding the B. oleracea leaf microbiome in agricultural ecosystems will pave the way for the efficient management of diseases in this crop.This research was supported by the “Severo Ochoa Program for Centres of Excellence in R&D” CEX2019-000902-S, funded by MCIN/AEI/10.13039/501100011033; the CERCA Program/“Generalitat de Catalunya”; and by grant PID2021-128825OB-I00 from the MCIN/AEI/10.13039/501100011033 and by “ERDF A way of making Europe” to BSS. We also acknowledge financial support from grant 2021 SGR 00875 from the Generalitat de Catalunya.With funding from the Spanish government through the ‘Severo Ochoa Centre of Excellence’ accreditation (CEX2019-000902-S)Peer reviewedMultidisciplinary Digital Publishing InstituteMinisterio de Ciencia e Innovación (España)Agencia Estatal de Investigación (España)Generalitat de CatalunyaEuropean CommissionMartín-Cardoso, Héctor [0000-0002-0002-9001]González, Víctor M. [0009-0006-8963-4588]Soler-López, Luis [0009-0004-9608-1286]San Segundo, Blanca [0000-0001-7409-3172]Consejo Superior de Investigaciones Científicas [https://ror.org/02gfc7t72]202420242024info:eu-repo/semantics/articlehttp://purl.org/coar/resource_type/c_6501Publisher's versioninfo:eu-repo/semantics/publishedVersionapplication/pdfhttp://hdl.handle.net/10261/372291https://api.elsevier.com/content/abstract/scopus_id/85199773694reponame:DIGITAL.CSIC. Repositorio Institucional del CSICinstname:Consejo Superior de Investigaciones Científicas (CSIC)Inglés#PLACEHOLDER_PARENT_METADATA_VALUE##PLACEHOLDER_PARENT_METADATA_VALUE#info:eu-repo/grantAgreement/AEI//CEX2019-000902-Sinfo:eu-repo/grantAgreement/AEI/Plan Estatal de Investigación Científica y Técnica y de Innovación 2021-2023/PID2021-128825OB-I00HorticulturaeThe underlying dataset has been published as supplementary material of the article in the publisher platform at DOI https://doi.org/10.3390/horticulturae10070765https://doi.org/10.3390/horticulturae10070765Síinfo:eu-repo/semantics/openAccessoai:digital.csic.es:10261/3722912026-05-22T06:33:51Z
score 15.812429

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