Soil Bacteriome Shifts along a Cultivation Gradient in Southwestern Spanish Wetlands

Understanding how long-term agricultural practices affect soil bacteriome is essential for sustainable land management. In the Guadalquivir Marshes of southwestern Spain, which encompass both Doñana National Park and one of Europe's most productive rice cultivation areas, decades of rice farmin...

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Autores: González-Pimentel, José Luis, Cuecas, Alba, Álvarez, Consolación, Mariscal, Vicente
Tipo de documento: artigo
Estado:Versão publicada
Data de publicação:2026
País:España
Recursos:Consejo Superior de Investigaciones Científicas (CSIC)
Repositório:DIGITAL.CSIC. Repositorio Institucional del CSIC
OAI Identifier:oai:digital.csic.es:10261/418715
Acesso em linha:http://hdl.handle.net/10261/418715
https://api.elsevier.com/content/abstract/scopus_id/105027028491
Access Level:Acceso aberto
Palavra-chave:16S rRNA gene sequencing
Denitrification
Rice paddies
Soil bacteriome
Wetland soils
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spelling Soil Bacteriome Shifts along a Cultivation Gradient in Southwestern Spanish WetlandsGonzález-Pimentel, José LuisCuecas, AlbaÁlvarez, ConsolaciónMariscal, Vicente16S rRNA gene sequencingDenitrificationRice paddiesSoil bacteriomeWetland soilsUnderstanding how long-term agricultural practices affect soil bacteriome is essential for sustainable land management. In the Guadalquivir Marshes of southwestern Spain, which encompass both Doñana National Park and one of Europe's most productive rice cultivation areas, decades of rice farming have transformed natural wetlands into artificial agroecosystems. Although bacterial degradation in cultivated soils has been previously suggested, comparative analyses between rice paddies and adjacent natural wetlands remain scarce.Here, we characterized the soil bacteriome across a cultivation gradient by comparing undisturbed natural marshes, within Doñana National Park, with rice fields cultivated for 25 years (Cantarita) and 80 years (Mínima 2). Using full 16S rRNA gene via long-read metabarcoding and standardized soil physicochemical assays, we analysed taxonomic composition, environmental associations, and predicted functional profiles.Our results reveal a progressive restructuring of bacterial communities with increased cultivation time, notably a significant enrichment of Chloroflexota (especially Anaerolineae) and a decline in Actinomycetota and Planctomycetota in paddy soils. Functional predictions indicated a higher potential for denitrification in cultivated soils-likely involving Chloroflexota taxa-compared to more diverse nitrogen pathways in natural sites. These shifts were strongly associated with changes in pH, electrical conductivity, calcium carbonate, and nitrate levels. Remarkably, most bacterial differences were already evident within the first 25 years of cultivation, underscoring the rapid ecological impact of intensive rice cultivation.Notably, we identified specific bacterial groups (Anaerolineae and Nocardioides in paddy soils; Euzebya, Rubrobacter, and Planctomycetota in natural wetlands), whose enrichment was associated with soil type. This approach highlights the value of integrating bacterial-based assessments into sustainable wetland management strategies.Open Access funding provided thanks to the CRUE-CSIC agreement with Springer Nature.Peer reviewedSpringerConferencia de Rectores de las Universidades EspañolasConsejo Superior de Investigaciones Científicas (España)González-Pimentel, José Luis [0000-0002-9687-3134]Cuecas, Alba [0000-0001-7567-4964]Álvarez, Consolación [0000-0002-2893-3545]Mariscal, Vicente [0000-0002-3490-3713]Consejo Superior de Investigaciones Científicas [https://ror.org/02gfc7t72]202620262026info:eu-repo/semantics/articlehttp://purl.org/coar/resource_type/c_6501Publisher's versioninfo:eu-repo/semantics/publishedVersionapplication/pdfhttp://hdl.handle.net/10261/418715https://api.elsevier.com/content/abstract/scopus_id/105027028491reponame:DIGITAL.CSIC. Repositorio Institucional del CSICinstname:Consejo Superior de Investigaciones Científicas (CSIC)InglésThe underlying dataset has been published as supplementary material of the article in the publisher platform at DOI http://dx.doi.org/10.1007/s00248-025-02660-8http://dx.doi.org/10.1007/s00248-025-02660-8Síinfo:eu-repo/semantics/openAccessoai:digital.csic.es:10261/4187152026-05-22T06:33:51Z
dc.title.none.fl_str_mv Soil Bacteriome Shifts along a Cultivation Gradient in Southwestern Spanish Wetlands
title Soil Bacteriome Shifts along a Cultivation Gradient in Southwestern Spanish Wetlands
spellingShingle Soil Bacteriome Shifts along a Cultivation Gradient in Southwestern Spanish Wetlands
González-Pimentel, José Luis
16S rRNA gene sequencing
Denitrification
Rice paddies
Soil bacteriome
Wetland soils
title_short Soil Bacteriome Shifts along a Cultivation Gradient in Southwestern Spanish Wetlands
title_full Soil Bacteriome Shifts along a Cultivation Gradient in Southwestern Spanish Wetlands
title_fullStr Soil Bacteriome Shifts along a Cultivation Gradient in Southwestern Spanish Wetlands
title_full_unstemmed Soil Bacteriome Shifts along a Cultivation Gradient in Southwestern Spanish Wetlands
title_sort Soil Bacteriome Shifts along a Cultivation Gradient in Southwestern Spanish Wetlands
dc.creator.none.fl_str_mv González-Pimentel, José Luis
Cuecas, Alba
Álvarez, Consolación
Mariscal, Vicente
author González-Pimentel, José Luis
author_facet González-Pimentel, José Luis
Cuecas, Alba
Álvarez, Consolación
Mariscal, Vicente
author_role author
author2 Cuecas, Alba
Álvarez, Consolación
Mariscal, Vicente
author2_role author
author
author
dc.contributor.none.fl_str_mv Conferencia de Rectores de las Universidades Españolas
Consejo Superior de Investigaciones Científicas (España)
González-Pimentel, José Luis [0000-0002-9687-3134]
Cuecas, Alba [0000-0001-7567-4964]
Álvarez, Consolación [0000-0002-2893-3545]
Mariscal, Vicente [0000-0002-3490-3713]
Consejo Superior de Investigaciones Científicas [https://ror.org/02gfc7t72]
dc.subject.none.fl_str_mv 16S rRNA gene sequencing
Denitrification
Rice paddies
Soil bacteriome
Wetland soils
topic 16S rRNA gene sequencing
Denitrification
Rice paddies
Soil bacteriome
Wetland soils
description Understanding how long-term agricultural practices affect soil bacteriome is essential for sustainable land management. In the Guadalquivir Marshes of southwestern Spain, which encompass both Doñana National Park and one of Europe's most productive rice cultivation areas, decades of rice farming have transformed natural wetlands into artificial agroecosystems. Although bacterial degradation in cultivated soils has been previously suggested, comparative analyses between rice paddies and adjacent natural wetlands remain scarce.Here, we characterized the soil bacteriome across a cultivation gradient by comparing undisturbed natural marshes, within Doñana National Park, with rice fields cultivated for 25 years (Cantarita) and 80 years (Mínima 2). Using full 16S rRNA gene via long-read metabarcoding and standardized soil physicochemical assays, we analysed taxonomic composition, environmental associations, and predicted functional profiles.Our results reveal a progressive restructuring of bacterial communities with increased cultivation time, notably a significant enrichment of Chloroflexota (especially Anaerolineae) and a decline in Actinomycetota and Planctomycetota in paddy soils. Functional predictions indicated a higher potential for denitrification in cultivated soils-likely involving Chloroflexota taxa-compared to more diverse nitrogen pathways in natural sites. These shifts were strongly associated with changes in pH, electrical conductivity, calcium carbonate, and nitrate levels. Remarkably, most bacterial differences were already evident within the first 25 years of cultivation, underscoring the rapid ecological impact of intensive rice cultivation.Notably, we identified specific bacterial groups (Anaerolineae and Nocardioides in paddy soils; Euzebya, Rubrobacter, and Planctomycetota in natural wetlands), whose enrichment was associated with soil type. This approach highlights the value of integrating bacterial-based assessments into sustainable wetland management strategies.
publishDate 2026
dc.date.none.fl_str_mv 2026
2026
2026
dc.type.none.fl_str_mv info:eu-repo/semantics/article
http://purl.org/coar/resource_type/c_6501
Publisher's version
info:eu-repo/semantics/publishedVersion
format article
status_str publishedVersion
dc.identifier.none.fl_str_mv http://hdl.handle.net/10261/418715
https://api.elsevier.com/content/abstract/scopus_id/105027028491
url http://hdl.handle.net/10261/418715
https://api.elsevier.com/content/abstract/scopus_id/105027028491
dc.language.none.fl_str_mv Inglés
language_invalid_str_mv Inglés
dc.relation.none.fl_str_mv The underlying dataset has been published as supplementary material of the article in the publisher platform at DOI http://dx.doi.org/10.1007/s00248-025-02660-8
http://dx.doi.org/10.1007/s00248-025-02660-8
Sí
dc.rights.none.fl_str_mv info:eu-repo/semantics/openAccess
eu_rights_str_mv openAccess
dc.format.none.fl_str_mv application/pdf
dc.publisher.none.fl_str_mv Springer
publisher.none.fl_str_mv Springer
dc.source.none.fl_str_mv reponame:DIGITAL.CSIC. Repositorio Institucional del CSIC
instname:Consejo Superior de Investigaciones Científicas (CSIC)
instname_str Consejo Superior de Investigaciones Científicas (CSIC)
reponame_str DIGITAL.CSIC. Repositorio Institucional del CSIC
collection DIGITAL.CSIC. Repositorio Institucional del CSIC
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