Exploring the soil-associated bacterial microbiome of coffee plantations in different regions of Colombia: a metabarcoding approach = Exploración del microbioma bacteriano asociado al suelo de plantaciones de café en diferentes regiones de Colombia: un enfoque de metabarcoding
Introduction: Coffee is one of the leading tropical crops produced worldwide. Colombia ranks third in coffee production in the world. Microorganisms associated with coffee plants can have many biotechnological applications, such as plant growth promotion and biological control. Objective: To describ...
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| Format: | info:ar-repo/semantics/artículo |
| Language: | Inglés |
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Universidad Autónoma de Yucatán
2025
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| Online Access: | http://hdl.handle.net/20.500.12123/21385 https://www.revista.ccba.uady.mx/ojs/index.php/TSA/article/view/5196 http://dx.doi.org/10.56369/tsaes.5196 |
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| author | Gómez-Godínez, Lorena Jacqueline Ochoa, Víctor Faggioli, Valeria Soledad Cristancho, Marco |
| author_browse | Cristancho, Marco Faggioli, Valeria Soledad Gómez-Godínez, Lorena Jacqueline Ochoa, Víctor |
| author_facet | Gómez-Godínez, Lorena Jacqueline Ochoa, Víctor Faggioli, Valeria Soledad Cristancho, Marco |
| author_sort | Gómez-Godínez, Lorena Jacqueline |
| collection | INTA Digital |
| description | Introduction: Coffee is one of the leading tropical crops produced worldwide. Colombia ranks third in coffee production in the world. Microorganisms associated with coffee plants can have many biotechnological applications, such as plant growth promotion and biological control. Objective: To describe the bacteria present in the soil associated with coffee cultivation. This was done using a bulk sequencing or 16S rRNA metabarcoding approach. Methodology: Soil samples were collected to analyze their microbiome from three different departments of Colombia (Cauca, Risaralda and Magdalena). The plants were of different ages, and the crop management was different (conventional and organic). Subsequently, an analysis was carried out using Qiime2 to describe the communities associated with coffee cultivation and soil chemical properties. Results: Some important genera were identified, such as Janthinobacterium, Bacillus, Actinomadura and Actinoallomurus. These genera can be used as plant growth promoters, organic matter transformers, producers of antibiotics and metabolites with potential biotechnological applications. Implications: The study presented in this manuscript describes the communities associated with the soil in coffee cultivation. However, a much more complex approach could be through metagenomics, where the bacterial communities and the functions of; however, this vision is up to ten times higher in cost. Conclusion: Through the results obtained, it is concluded that the studies carried out through metabarcoding help to understand the composition of the microorganisms associated with coffee and, with this, try to elucidate the functions of the associated microorganisms. |
| format | info:ar-repo/semantics/artículo |
| id | INTA21385 |
| institution | Instituto Nacional de Tecnología Agropecuaria (INTA -Argentina) |
| language | Inglés |
| publishDate | 2025 |
| publishDateRange | 2025 |
| publishDateSort | 2025 |
| publisher | Universidad Autónoma de Yucatán |
| publisherStr | Universidad Autónoma de Yucatán |
| record_format | dspace |
| spelling | INTA213852025-02-21T12:09:54Z Exploring the soil-associated bacterial microbiome of coffee plantations in different regions of Colombia: a metabarcoding approach = Exploración del microbioma bacteriano asociado al suelo de plantaciones de café en diferentes regiones de Colombia: un enfoque de metabarcoding Gómez-Godínez, Lorena Jacqueline Ochoa, Víctor Faggioli, Valeria Soledad Cristancho, Marco Coffea Metabarcoding Microbiomes Bacteria Metabarcodificación Microbiomas Colombia Cafeto Introduction: Coffee is one of the leading tropical crops produced worldwide. Colombia ranks third in coffee production in the world. Microorganisms associated with coffee plants can have many biotechnological applications, such as plant growth promotion and biological control. Objective: To describe the bacteria present in the soil associated with coffee cultivation. This was done using a bulk sequencing or 16S rRNA metabarcoding approach. Methodology: Soil samples were collected to analyze their microbiome from three different departments of Colombia (Cauca, Risaralda and Magdalena). The plants were of different ages, and the crop management was different (conventional and organic). Subsequently, an analysis was carried out using Qiime2 to describe the communities associated with coffee cultivation and soil chemical properties. Results: Some important genera were identified, such as Janthinobacterium, Bacillus, Actinomadura and Actinoallomurus. These genera can be used as plant growth promoters, organic matter transformers, producers of antibiotics and metabolites with potential biotechnological applications. Implications: The study presented in this manuscript describes the communities associated with the soil in coffee cultivation. However, a much more complex approach could be through metagenomics, where the bacterial communities and the functions of; however, this vision is up to ten times higher in cost. Conclusion: Through the results obtained, it is concluded that the studies carried out through metabarcoding help to understand the composition of the microorganisms associated with coffee and, with this, try to elucidate the functions of the associated microorganisms. El café es uno de los principales cultivos tropicales producidos a nivel mundial. Colombia ocupa el tercer lugar en producción de café en el mundo. Los microorganismos asociados a las plantas de café pueden tener una gran cantidad de aplicaciones biotecnológicas, como la promoción de crecimiento vegetal y el control biológico. Objetivo: Describir las bacterias presentes en el suelo asociadas al cultivo del café. Esto se hizo mediante un enfoque de secuenciación masiva o metabarcoding del gen ARNr 16s. Metodología: Se recolectaron muestras de microbioma del suelo de tres departamentos diferentes de Colombia (Cauca, Risaralda y Magdalena). Las plantas tuvieron diferentes edades y el manejo del cultivo fue diferente (convencional y orgánico). Posteriormente se realizó un análisis mediante Qiime2 para describir las comunidades asociadas al cultivo de café. Resultados: Se identificaron algunos Phylum importantes como, por ejemplo, Acidobacterias, Actinobacterias, Firmicutes y Verrucomicrobia. Dentro de los géneros importantes, se lograron identificar a Janthinobacterium, Bacillus, Actinomadura y Actinoallomurus. Estos géneros pueden ser utilizados como promotores del crecimiento vegetal, transformadores de materia orgánica, productores de antibióticos y metabolitos con potenciales aplicaciones biotecnológicas. Implicaciones: El estudio presentado en este manuscrito es descriptivo, de las comunidades asociadas al suelo en el cultivo de café, sin embargo, un enfoque mucho más complejo podría ser a través de metagenómica donde se puede describir a las comunidades de bacterias y las funciones de estas, sin embargo, esta visión es hasta diez veces más elevada en cuestiones de costo. Conclusión: A través de los resultados se concluye que los estudios realizados a través de metabarcoding ayudan a entender la composición de los microorganismos asociados al café y con esto tratar de dilucidar las funciones de los microorganismos asociados. EEA Marcos Juárez Fil: Gómez-Godínez, Lorena Jacqueline. Instituto Nacional de Investigación Forestales, Agrícolas y Pecuarios. Centro Nacional de Recursos Genéticos. Laboratorio de Recursos Genéticos Microbianos; México Fil: Ochoa, Víctor. National Center for Coffee Research- CENICAFE. Plant Pathology Department; Colombia Fil: Faggioli, Valeria Soledad. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria Marcos Juárez; Argentina Fil: Cristancho, Marco. National Center for Coffee Research- CENICAFE. Plant Pathology Department; Colombia 2025-02-21T12:06:26Z 2025-02-21T12:06:26Z 2024-08 info:ar-repo/semantics/artículo info:eu-repo/semantics/article info:eu-repo/semantics/publishedVersion http://hdl.handle.net/20.500.12123/21385 https://www.revista.ccba.uady.mx/ojs/index.php/TSA/article/view/5196 1870-0462 http://dx.doi.org/10.56369/tsaes.5196 eng info:eu-repo/semantics/openAccess http://creativecommons.org/licenses/by-nc-sa/4.0/ Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0) application/pdf Universidad Autónoma de Yucatán Tropical and Subtropical Agroecosystems 27 (2) : 047 (May - August 2024) |
| spellingShingle | Coffea Metabarcoding Microbiomes Bacteria Metabarcodificación Microbiomas Colombia Cafeto Gómez-Godínez, Lorena Jacqueline Ochoa, Víctor Faggioli, Valeria Soledad Cristancho, Marco Exploring the soil-associated bacterial microbiome of coffee plantations in different regions of Colombia: a metabarcoding approach = Exploración del microbioma bacteriano asociado al suelo de plantaciones de café en diferentes regiones de Colombia: un enfoque de metabarcoding |
| title | Exploring the soil-associated bacterial microbiome of coffee plantations in different regions of Colombia: a metabarcoding approach = Exploración del microbioma bacteriano asociado al suelo de plantaciones de café en diferentes regiones de Colombia: un enfoque de metabarcoding |
| title_full | Exploring the soil-associated bacterial microbiome of coffee plantations in different regions of Colombia: a metabarcoding approach = Exploración del microbioma bacteriano asociado al suelo de plantaciones de café en diferentes regiones de Colombia: un enfoque de metabarcoding |
| title_fullStr | Exploring the soil-associated bacterial microbiome of coffee plantations in different regions of Colombia: a metabarcoding approach = Exploración del microbioma bacteriano asociado al suelo de plantaciones de café en diferentes regiones de Colombia: un enfoque de metabarcoding |
| title_full_unstemmed | Exploring the soil-associated bacterial microbiome of coffee plantations in different regions of Colombia: a metabarcoding approach = Exploración del microbioma bacteriano asociado al suelo de plantaciones de café en diferentes regiones de Colombia: un enfoque de metabarcoding |
| title_short | Exploring the soil-associated bacterial microbiome of coffee plantations in different regions of Colombia: a metabarcoding approach = Exploración del microbioma bacteriano asociado al suelo de plantaciones de café en diferentes regiones de Colombia: un enfoque de metabarcoding |
| title_sort | exploring the soil associated bacterial microbiome of coffee plantations in different regions of colombia a metabarcoding approach exploracion del microbioma bacteriano asociado al suelo de plantaciones de cafe en diferentes regiones de colombia un enfoque de metabarcoding |
| topic | Coffea Metabarcoding Microbiomes Bacteria Metabarcodificación Microbiomas Colombia Cafeto |
| url | http://hdl.handle.net/20.500.12123/21385 https://www.revista.ccba.uady.mx/ojs/index.php/TSA/article/view/5196 http://dx.doi.org/10.56369/tsaes.5196 |
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