Caracterización del metagenoma de la comunidad microbiana edáfica asociada a un cultivo de arroz (oryza sativa) bajo un esquema agronómico de manejo de agricultura por ambientes
ilustraciones, diagramas, fotografías a color
- Autores:
-
Saavedra Correa, Juan David
- Tipo de recurso:
- Fecha de publicación:
- 2023
- Institución:
- Universidad Nacional de Colombia
- Repositorio:
- Universidad Nacional de Colombia
- Idioma:
- eng
- OAI Identifier:
- oai:repositorio.unal.edu.co:unal/84610
- Palabra clave:
- 570 - Biología::577 - Ecología
Microbiología agrícola
Ecología Microbiana
Arroz
Agricultura sostenible
Rice
Sustainable agriculture
Rice soil metagenomics
Bulk soil Microbiomes
Rhizosphere microbiomes
Amplicon sequencing
Shotgun sequencing
Metagenómica del suelo de arroz
Microbiomas de suelo de soporte
Microbiomas de rizosfera
Secuenciacion shotgun
- Rights
- openAccess
- License
- Atribución-SinDerivadas 4.0 Internacional
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UNACIONAL2_7d449dfe86843923c453674f0c1462e9 |
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oai:repositorio.unal.edu.co:unal/84610 |
| network_acronym_str |
UNACIONAL2 |
| network_name_str |
Universidad Nacional de Colombia |
| repository_id_str |
|
| dc.title.spa.fl_str_mv |
Caracterización del metagenoma de la comunidad microbiana edáfica asociada a un cultivo de arroz (oryza sativa) bajo un esquema agronómico de manejo de agricultura por ambientes |
| dc.title.translated.eng.fl_str_mv |
Metagenomic characterization of the edaphic microbial community associated with a rice crop (Oryza sativa) under an agronomic scheme of agriculture management by management zones |
| title |
Caracterización del metagenoma de la comunidad microbiana edáfica asociada a un cultivo de arroz (oryza sativa) bajo un esquema agronómico de manejo de agricultura por ambientes |
| spellingShingle |
Caracterización del metagenoma de la comunidad microbiana edáfica asociada a un cultivo de arroz (oryza sativa) bajo un esquema agronómico de manejo de agricultura por ambientes 570 - Biología::577 - Ecología Microbiología agrícola Ecología Microbiana Arroz Agricultura sostenible Rice Sustainable agriculture Rice soil metagenomics Bulk soil Microbiomes Rhizosphere microbiomes Amplicon sequencing Shotgun sequencing Metagenómica del suelo de arroz Microbiomas de suelo de soporte Microbiomas de rizosfera Secuenciacion shotgun |
| title_short |
Caracterización del metagenoma de la comunidad microbiana edáfica asociada a un cultivo de arroz (oryza sativa) bajo un esquema agronómico de manejo de agricultura por ambientes |
| title_full |
Caracterización del metagenoma de la comunidad microbiana edáfica asociada a un cultivo de arroz (oryza sativa) bajo un esquema agronómico de manejo de agricultura por ambientes |
| title_fullStr |
Caracterización del metagenoma de la comunidad microbiana edáfica asociada a un cultivo de arroz (oryza sativa) bajo un esquema agronómico de manejo de agricultura por ambientes |
| title_full_unstemmed |
Caracterización del metagenoma de la comunidad microbiana edáfica asociada a un cultivo de arroz (oryza sativa) bajo un esquema agronómico de manejo de agricultura por ambientes |
| title_sort |
Caracterización del metagenoma de la comunidad microbiana edáfica asociada a un cultivo de arroz (oryza sativa) bajo un esquema agronómico de manejo de agricultura por ambientes |
| dc.creator.fl_str_mv |
Saavedra Correa, Juan David |
| dc.contributor.advisor.none.fl_str_mv |
Gonzalez Sayer, Sandra Milena Aristizabal Gutierrez, Fabio Ancizar |
| dc.contributor.author.none.fl_str_mv |
Saavedra Correa, Juan David |
| dc.contributor.researchgroup.spa.fl_str_mv |
Bioprocesos y Bioprospección |
| dc.contributor.orcid.spa.fl_str_mv |
Saavedra, Juan David [0000-0003-1527-0428] |
| dc.contributor.cvlac.spa.fl_str_mv |
https://scienti.minciencias.gov.co/cvlac/visualizador/generarCurriculoCv.do?cod_rh=0000074382 |
| dc.subject.ddc.spa.fl_str_mv |
570 - Biología::577 - Ecología Microbiología agrícola Ecología Microbiana |
| topic |
570 - Biología::577 - Ecología Microbiología agrícola Ecología Microbiana Arroz Agricultura sostenible Rice Sustainable agriculture Rice soil metagenomics Bulk soil Microbiomes Rhizosphere microbiomes Amplicon sequencing Shotgun sequencing Metagenómica del suelo de arroz Microbiomas de suelo de soporte Microbiomas de rizosfera Secuenciacion shotgun |
| dc.subject.lemb.spa.fl_str_mv |
Arroz Agricultura sostenible |
| dc.subject.lemb.eng.fl_str_mv |
Rice Sustainable agriculture |
| dc.subject.proposal.eng.fl_str_mv |
Rice soil metagenomics Bulk soil Microbiomes Rhizosphere microbiomes Amplicon sequencing Shotgun sequencing |
| dc.subject.proposal.spa.fl_str_mv |
Metagenómica del suelo de arroz Microbiomas de suelo de soporte Microbiomas de rizosfera Secuenciacion shotgun |
| description |
ilustraciones, diagramas, fotografías a color |
| publishDate |
2023 |
| dc.date.accessioned.none.fl_str_mv |
2023-08-29T14:56:13Z |
| dc.date.available.none.fl_str_mv |
2023-08-29T14:56:13Z |
| dc.date.issued.none.fl_str_mv |
2023-06-05 |
| dc.type.spa.fl_str_mv |
Trabajo de grado - Maestría |
| dc.type.driver.spa.fl_str_mv |
info:eu-repo/semantics/masterThesis |
| dc.type.version.spa.fl_str_mv |
info:eu-repo/semantics/acceptedVersion |
| dc.type.content.spa.fl_str_mv |
Text |
| dc.type.redcol.spa.fl_str_mv |
http://purl.org/redcol/resource_type/TM |
| status_str |
acceptedVersion |
| dc.identifier.uri.none.fl_str_mv |
https://repositorio.unal.edu.co/handle/unal/84610 |
| dc.identifier.instname.spa.fl_str_mv |
Universidad Nacional de Colombia |
| dc.identifier.reponame.spa.fl_str_mv |
Repositorio Institucional Universidad Nacional de Colombia |
| dc.identifier.repourl.spa.fl_str_mv |
https://repositorio.unal.edu.co/ |
| url |
https://repositorio.unal.edu.co/handle/unal/84610 https://repositorio.unal.edu.co/ |
| identifier_str_mv |
Universidad Nacional de Colombia Repositorio Institucional Universidad Nacional de Colombia |
| dc.language.iso.spa.fl_str_mv |
eng |
| language |
eng |
| dc.relation.references.spa.fl_str_mv |
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Molecular Ecology Resources, 20(1), 170–184. https://doi.org/10.1111/1755-0998.13097 Liu, M., Clarke, L. J., Baker, S. C., Jordan, G. J., & Burridge, C. P. (2020). A practical guide to DNA metabarcoding for entomological ecologists. Ecological Entomology, 45(3), 373–385. https://doi.org/10.1111/een.12831 Liu, Qin, Y., Chen, T., Lu, M., Qian, X., Guo, X., & Bai, Y. (2021). A practical guide to amplicon and metagenomic analysis of microbiome data. Protein & Cell, 12(5), 315–330. https://doi.org/10.1007/s13238-020-00724-8 Mayday, M., Khan, L., Chow, E. D., Zinter, M. S., & DeRisi, J. L. (2019). High- Throughput Library Pooling for NGS. https://www.protocols.io/view/high- throughput-library-pooling-for-ngs-tcdeis6 Nilsson, R. H., Anslan, S., Bahram, M., Wurzbacher, C., Baldrian, P., & Tedersoo, L. (2019). Mycobiome diversity: High-throughput sequencing and identification of fungi. Nature Reviews Microbiology, 17(2), Article 2. https://doi.org/10.1038/s41579-018-0116-y Pecundo, M. H., Chang, A. C. G., Chen, T., dela Cruz, T. E. E., Ren, H., & Li, N. (2021). Full-Length 16S rRNA and ITS Gene Sequencing Revealed Rich Microbial Flora in Roots of Cycas spp. In China. Evolutionary Bioinformatics, 17, 1176934321989713. https://doi.org/10.1177/1176934321989713 Pollock, J., Glendinning, L., Wisedchanwet, T., & Watson, M. (2018). The Madness of Microbiome: Attempting To Find Consensus “Best Practice” for 16S Microbiome Studies. Applied and Environmental Microbiology, 84(7), e02627-17. https://doi.org/10.1128/AEM.02627-17 Prasad, S., Malav, L. C., Choudhary, J., Kannojiya, S., Kundu, M., Kumar, S., & Yadav, A. N. (2021). Soil Microbiomes for Healthy Nutrient Recycling. In A. N. Yadav, J. Singh, C. Singh, & N. Yadav (Eds.), Current Trends in Microbial Biotechnology for Sustainable Agriculture (pp. 1–21). Springer. https://doi.org/10.1007/978-981-15- 6949-4_1 Prodan, A., Tremaroli, V., Brolin, H., Zwinderman, A. H., Nieuwdorp, M., & Levin, E. (2020). 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Atribución-SinDerivadas 4.0 Internacionalhttp://creativecommons.org/licenses/by-nd/4.0/info:eu-repo/semantics/openAccesshttp://purl.org/coar/access_right/c_abf2Gonzalez Sayer, Sandra Milena3593b682e7c51b52ccc3853f2df6738fAristizabal Gutierrez, Fabio Ancizar50cb08feda89e1535b0cf798399c1a3cSaavedra Correa, Juan David6fb7c9a118b93d93d383ea8d1e04238eBioprocesos y BioprospecciónSaavedra, Juan David [0000-0003-1527-0428]https://scienti.minciencias.gov.co/cvlac/visualizador/generarCurriculoCv.do?cod_rh=00000743822023-08-29T14:56:13Z2023-08-29T14:56:13Z2023-06-05https://repositorio.unal.edu.co/handle/unal/84610Universidad Nacional de ColombiaRepositorio Institucional Universidad Nacional de Colombiahttps://repositorio.unal.edu.co/ilustraciones, diagramas, fotografías a colorDada la importancia del cultivo del arroz en Colombia, se han utilizado muchas estrategias para incrementar el rendimiento por hectárea, las cuales buscan incentivar directa e indirectamente la promoción de servicios ecosistémicos como el ciclaje de nutrientes, siendo el microbioma del suelo un factor clave en la modulación de muchos nutrientes presentes en el suelo, con un efecto en la productividad de las plantas. Se propuso como objetivo de este trabajo de investigación, estudiar los microbiomas edáficos de un campo comercial de arroz y su relación con las propiedades físico-químicas del suelo. Para ello, se tomaron muestras de suelo de soporte y rizosférico en un lote de arroz de 33 hectáreas, previamente caracterizadas según el historial de datos de rendimiento, en tres zonas de manejo (rendimiento alto, rendimiento medio y rendimiento bajo). Las muestras de suelo se tomaron antes de la siembra del cultivo y después de la última fertilización química; Además, se realizaron análisis fisicoquímicos del suelo y extracción de ADN. Inicialmente se planteó una estrategia para el estudio de microbiomas a través de 16s rRNA y amplicones ITS, sin embargo, los resultados obtenidos con esta metodología no fueron lo suficientemente confiables, por lo que se tomó la decisión de realizar el análisis desde la perspectiva de la metagenómica, para su posterior secuenciación por “shotgun” y análisis de metagenoma. Las comunidades microbianas del campo de arroz reportaron una baja diversidad en general, se encontró que las muestras estaban dominadas por los filos Proteobacteria, Acidobacteria y Actinobacteria. Aunque hubo variaciones en la composición y estructura de los microbiomas del suelo de soportea lo largo del tiempo y entre los microbiomas asociados con las tres zonas de manejo, no se encontraron diferencias significativas. Se encontró que la diversidad, la composición y la función predicha de los microbiomas de la rizosfera eran significativamente diferentes de los microbiomas del suelo de soporte. Además, se identificó que estos suelos tenían un pH particularmente ácido, y también se pudo detectar que la materia orgánica incidía en la diversidad de los microbiomas, asi como las prácticas de manejo. (Texto tomado de la fuente)Given the importance of rice cultivation in Colombia, many strategies have been used to increase yield per hectare, which seek to directly and indirectly encourage the promotion of ecosystem services such as nutrient cycling, with the soil microbiome being a key factor in the modulation of many nutrients present in the soil and having an effect on plant productivity, it was proposed as the objective of this research, to study the edaphic microbiomes of a commercial field of rice and its relationship with the physico-chemical properties of the soil. For this, bulk and rhizosphere soil samples were taken in a 33-hectare rice plot, previously characterized according to the yield data history, in three management zones (high, medium, and low yield). The soil samples were taken before planting the crop and seventy days after plants germination; moreover, physicochemical analyzes of the soil and DNA extraction were performed. Initially, a strategy for the study of microbiomes through 16s rRNA and ITS amplicons was proposed, however, the results obtained with this methodology were not reliable enough, for which the decision was made to carry out the analysis from the perspective of metagenomics, for subsequent shotgun sequencing and metagenome analysis. The microbial communities from the rice field reported a low diversity in general, the samples were found to be dominated by the phyla Proteobacteria, Acidobacteria, and Actinobacteria. Even though, there were variations in the composition and structure of the bulk soil microbiomes across time and between the microbiomes associated with the three management zones, no significant differences were discovered. The diversity, composition, and predicted function of rhizosphere microbiomes were found to be significantly different from the bulk soil microbiomes. Moreover, it was identified that these soils had a particularly acid pH, and it was also possible to detect that organic matter, as well as management practices had an impact on the diversity of the microbiomes.FEDEARROZ - FNAMaestríaMagíster en Ciencias - Microbiología130 páginasapplication/pdfengUniversidad Nacional de ColombiaBogotá - Ciencias - Maestría en Ciencias - MicrobiologíaFacultad de CienciasBogotá, ColombiaUniversidad Nacional de Colombia - Sede Bogotá570 - Biología::577 - EcologíaMicrobiología agrícolaEcología MicrobianaArrozAgricultura sostenibleRiceSustainable agricultureRice soil metagenomicsBulk soil MicrobiomesRhizosphere microbiomesAmplicon sequencingShotgun sequencingMetagenómica del suelo de arrozMicrobiomas de suelo de soporteMicrobiomas de rizosferaSecuenciacion shotgunCaracterización del metagenoma de la comunidad microbiana edáfica asociada a un cultivo de arroz (oryza sativa) bajo un esquema agronómico de manejo de agricultura por ambientesMetagenomic characterization of the edaphic microbial community associated with a rice crop (Oryza sativa) under an agronomic scheme of agriculture management by management zonesTrabajo de grado - Maestríainfo:eu-repo/semantics/masterThesisinfo:eu-repo/semantics/acceptedVersionTexthttp://purl.org/redcol/resource_type/TMAndrew, J., & Edwards, A. 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Soil Biology and Biochemistry, 143, 107741. https://doi.org/10.1016/j.soilbio.2020.107741EXPLORACIÓN DE LA INTERACCIÓN DE LO FÍSICO, COMPONENTES QUÍMICOS Y BIOLÓGICOS DEL SUELO EN LA PRODUCTIVIDAD DEL CULTIVO DE ARROZ EN AGRICULTURA POR AMBIENTESUniversidad Nacional de ColombiaEstudiantesLICENSElicense.txtlicense.txttext/plain; charset=utf-85879https://repositorio.unal.edu.co/bitstream/unal/84610/1/license.txteb34b1cf90b7e1103fc9dfd26be24b4aMD51ORIGINALJuan_Saavedra_Rice_Microbiomes_THESIS_MSc.pdfJuan_Saavedra_Rice_Microbiomes_THESIS_MSc.pdfTesis de Maestría en Ciencias - Microbiologíaapplication/pdf3543431https://repositorio.unal.edu.co/bitstream/unal/84610/2/Juan_Saavedra_Rice_Microbiomes_THESIS_MSc.pdf52b81b252f299e8af41026407a5cf683MD52THUMBNAILJuan_Saavedra_Rice_Microbiomes_THESIS_MSc.pdf.jpgJuan_Saavedra_Rice_Microbiomes_THESIS_MSc.pdf.jpgGenerated 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