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Caracterización de la Diversidad Microbiana de Suelos Destinados a Cultivos de Ananas comosus (piña), Tratados con Distintos Plaguicidas en el Municipio de Lebrija, Santander

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dc.contributor.advisorRueda Forero, Nohora Juliana
dc.contributor.advisorSuárez Barrera, Miguel Orlando
dc.contributor.authorBravo Granados, Natalia Andrea
dc.date.accessioned2021-08-21T01:16:20Z
dc.date.available2021-08-21T01:16:20Z
dc.date.issued2021-05-06
dc.descriptionDigitalspa
dc.description.abstractEl suelo es un hábitat diverso, su composición varía dependiendo del uso, condiciones climáticas y actividades antropogénicas; y conocer los microorganismos presentes requiere la implementación de herramientas de secuenciación de nueva generación. Ananás comosus es un cultivo de gran importancia para Santander, sin embargo, los estudios referentes a la caracterización biológica del suelo asociado, son escasas en la región y en el país. En ese sentido, este trabajo se centró en la caracterización microbiana del suelo destinado a un cultivo de piña. Para lograrlo, las muestras se tomaron aleatoriamente de cuatro lotes a 20 cm de profundidad, obteniendo un total de 14 muestras. Se estandarizó el protocolo de extracción de ADN genómico total de suelo y la cantidad de ADN de cada muestra fue >60 ng/μl. Posteriormente se enviaron a secuenciar a MacroGen mediante la plataforma Illumina MiSeq (2x300 pb), obteniéndose un total de 1’518.101 secuencias de las muestras analizadas. El empleo de herramientas metagenómicas como el FASTQC y el MG-RAST, permitieron establecer la calidad de las secuencias obtenidas y la clasificación desde dominio hasta género de los microorganismos presentes en los suelos estudiados. Filo como Actinobacteria (>50%), Acidobacteria (>18%), Firmicutes (>16%) y Verrumicrobia (>10%), se encontraron con mayor predominancia entre las 14 muestras estudiadas. A nivel de género se encontraron en abundancia Candidatus Koribacter, Streptomyces, Isosphaera, Bacillus, Candidatus Solibacter y Actinomadura. Con respecto a la diversidad α, esta varía por las condiciones nutricionales del suelo, es por esto que en la muestra del suelo Blanco los valores de esta diversidad son los más bajos. Finalmente, se evidenció elevada similitud entre la composición de las comunidades microbianas de los cuatro suelos en estudio, indicando que el plaguicida y el bioplaguicida, no tienen un efecto significativo en la composición de la población microbiana presentes en la rizosfera del cultivo de piña.spa
dc.description.abstractThe soil is a diverse habitat, its composition varies depending on the use, climatic conditions and anthropogenic activities; and knowing the groups of microorganisms present requires the implementation of next-generation sequencing tools. Ananas comosus is a crop of great importance for Santander, however, studies referring to the biological characterization of the associated soil are scarce in the region and the country. In this sense, this work focused on the microbial characterization of the soil destined for a pineapple crop. The samples were randomly taken from four batches at a depth of 20 cm, obtaining a total of 14 samples. The total genomic soil DNA extraction protocol was standardized and the amount of DNA in each sample was> 60 ng / μl. Subsequently, they were sent to be sequenced to MacroGen using the Illumina MiSeq platform, obtaining a total of 1,518,101 sequences of the analyzed samples. The use of metagenomic tools such as FASTQC and MG-RAST made it possible to establish the quality of the sequences obtained and the classification from domain to the gender of the microorganisms present in the soils studied. Phylum such as Actinobacteria (> 50%), Acidobacteria (> 18%), Firmicutes (> 16%) and Verrumicrobia (> 10%), were found to be more prevalent among the 14 samples studied. At the genus level, Candidatus Koribacter, Streptomyces, Isosphaera, Bacillus, Candidatus Solibacter and Actinomadura were found in abundance. Concerning the diversiteng
dc.description.degreelevelPregradospa
dc.description.degreenameMicrobiólogo Industrialspa
dc.description.edition1 ed.spa
dc.description.tableofcontentsIntroducción ..............................................................................................................................15 Marco Teórico ...........................................................................................................................18 El Suelo .................................................................................................................................18 Aspectos Físicos del Suelo ................................................................................................19 Aspectos Químicos del Suelo ............................................................................................21 Materia Orgánica ...............................................................................................................23 La Agricultura .....................................................................................................................24 Microbiota del Suelo ..............................................................................................................25 Microorganismos de la Rizosfera .......................................................................................25 Funciones de los Microorganismos ....................................................................................26 Secuenciación de Nueva Generación ....................................................................................28 NGS en la Agricultura ........................................................................................................32 Illumina ..............................................................................................................................33 Análisis Bioinformático de Secuencias ..................................................................................39 MG-RAST como Herramienta Bioinformática .....................................................................41 Análisis Estadístico................................................................................................................43 Past Software ....................................................................................................................44 Estado del Arte .........................................................................................................................46 Marco Legal ..............................................................................................................................50 Planteamiento y Justificación del Problema ..............................................................................51 Pregunta de investigación .........................................................................................................52 Hipótesis ...................................................................................................................................53 Objetivos ...................................................................................................................................54 Objetivo General ...................................................................................................................54 Objetivos Específicos ............................................................................................................54 Metodología ..............................................................................................................................55 Especificaciones del Cultivo de Piña .....................................................................................55 Muestreo ...............................................................................................................................56 Extracción de ADN Genómico ...............................................................................................57 Amplificación y Secuenciación del Gen Ribosomal 16S. .......................................................58 Análisis Bioinformáticos .........................................................................................................58 Análisis Estadísticos ..............................................................................................................59 Análisis Físico-Químicos (realizados por los estudiantes de la UPB, sede Bucaramanga) ....59 Resultados y Análisis de Resultados ........................................................................................60 Extracción y Cuantificación de ADN Metagenómico ..............................................................60 Análisis Bioinformático de Secuencias ..................................................................................61 Clasificación por Dominios .................................................................................................61 Clasificación por filo ...........................................................................................................63 Clasificación por Género ....................................................................................................65 Diversidad α .......................................................................................................................67 Abundancia Relativa de Géneros Dominantes ...................................................................68 Géneros Únicos y Comunes en los Tratamientos ..............................................................69 Géneros predominantes .....................................................................................................71 Análisis Estadísticos ..............................................................................................................73 Análisis de Componentes Principales (ACP) ......................................................................73 Diversidad β .......................................................................................................................77 Discusión ..................................................................................................................................78 Análisis Fisicoquímicos .........................................................................................................78 Propiedades Físicas del Suelo ...........................................................................................78 Propiedades Químicas del Suelo .......................................................................................78 Extracción de ADN ................................................................................................................81 Análisis Bioinformático de Secuencias ..................................................................................83 Clasificación por Dominio ...................................................................................................84 Clasificación por filo ...........................................................................................................85 Clasificación por Género ....................................................................................................91 Diversidad α ..................................................................................................................... 101 Abundancia Relativa y Efecto del Plaguicida (Lorsban) y Bioplaguicida (Nicotina y Capsaicina). ..................................................................................................................... 102 Géneros Únicos y Comunes en los Tratamientos ................................................................ 104 Análisis de Componentes Principales (ACP) ....................................................................... 106 Diversidad β ........................................................................................................................ 107 Conclusiones .......................................................................................................................... 109 Recomendaciones .................................................................................................................. 111 Referencias Bibliográficas ....................................................................................................... 112 Apéndices ............................................................................................................................... 149 Apendice A. Protocolo de Extracción de ADN Estandarizado: Kit E.Z.N.A.® Soil DNA Kit (OMEGA) ............................................................................................................................ 149 Apéndice B. Concentración de ADN Genómico Total de Suelos ......................................... 151 Apéndice C. Calidad del ADN Extraído ................................................................................ 152 Apéndice D. Secuencias Obtenidas por Muestra ................................................................. 153 Apéndice E. Curva de Rarefacción de los Suelos Analizados ............................................. 154 Apéndice F. Prueba de Kruskal Wallis – Composición microbiana sin diferencia significativa ............................................................................................................................................ 156 Apéndice G. Propiedades físicoquímicas de los suelos estudiados, realizados por los estudiantes de la Universidad Pontificia Bolivariana sede Bucaramanga ............................ 157 Cálculo de Nitrógeno de mg NTK/Kg a %. ........................................................................... 159spa
dc.format.extent159 pspa
dc.format.mimetypeapplication/pdfspa
dc.identifier.localT 33.21 B719c
dc.identifier.urihttps://repositorio.udes.edu.co/handle/001/5530
dc.language.isospaspa
dc.publisherBucaramanga : Universidad de Santander, 2021spa
dc.publisher.facultyFacultad de Ciencias Exactas, Naturales y Agropecuariasspa
dc.publisher.placeBucaramanga, Colombiaspa
dc.publisher.programMicrobiología Industrialspa
dc.rightsDerechos Reservados - Universidad de Santander, 2021spa
dc.rights.accessrightsinfo:eu-repo/semantics/openAccessspa
dc.rights.creativecommonsAtribución-NoComercial-SinDerivadas 4.0 Internacional (CC BY-NC-ND 4.0)spa
dc.rights.urihttps://creativecommons.org/licenses/by-nc-nd/4.0/spa
dc.subject.proposalMetagenómicaspa
dc.subject.proposalPiñaspa
dc.subject.proposalADNspa
dc.subject.proposalSecuenciaciónspa
dc.subject.proposalIlluminaMiSeqeng
dc.subject.proposalMetagenomicsspa
dc.subject.proposalPineapplespa
dc.subject.proposalDNAspa
dc.titleCaracterización de la Diversidad Microbiana de Suelos Destinados a Cultivos de Ananas comosus (piña), Tratados con Distintos Plaguicidas en el Municipio de Lebrija, Santanderspa
dc.typeTrabajo de grado - Pregradospa
dc.type.coarhttp://purl.org/coar/resource_type/c_7a1fspa
dc.type.contentTextspa
dc.type.driverinfo:eu-repo/semantics/bachelorThesisspa
dc.type.redcolhttps://purl.org/redcol/resource_type/TPspa
dc.type.versioninfo:eu-repo/semantics/acceptedVersionspa
dcterms.audienceTodas las Audienciasspa
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