Exploring Genomics and Microbial Ecology: Analysis of <i>Bidens pilosa</i> L. Genetic Structure and Soil Microbiome Diversity by RAD-Seq and Metabarcoding
<i>Bidens pilosa</i> L., native to South America and commonly used for medicinal purposes, has been understudied at molecular and genomic levels and in its relationship with soil microorganisms. In this study, restriction site-associated DNA markers (RADseq) techniques were implemented t...
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| Format: | Article |
| Language: | English |
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MDPI AG
2024-01-01
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| Series: | Plants |
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| Online Access: | https://www.mdpi.com/2223-7747/13/2/221 |
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| author | Wendy Lorena Reyes-Ardila Paula Andrea Rugeles-Silva Juan Diego Duque-Zapata Glever Alexander Vélez-Martínez Lina Tarazona Pulido Karen Melissa Cardona Tobar Sergio Alberto Díaz Gallo Jaime Eduardo Muñoz Flórez Lucia Ana Díaz-Ariza Diana López-Alvarez |
| author_facet | Wendy Lorena Reyes-Ardila Paula Andrea Rugeles-Silva Juan Diego Duque-Zapata Glever Alexander Vélez-Martínez Lina Tarazona Pulido Karen Melissa Cardona Tobar Sergio Alberto Díaz Gallo Jaime Eduardo Muñoz Flórez Lucia Ana Díaz-Ariza Diana López-Alvarez |
| author_sort | Wendy Lorena Reyes-Ardila |
| collection | DOAJ |
| description | <i>Bidens pilosa</i> L., native to South America and commonly used for medicinal purposes, has been understudied at molecular and genomic levels and in its relationship with soil microorganisms. In this study, restriction site-associated DNA markers (RADseq) techniques were implemented to analyze genetic diversity and population structure, and metabarcoding to examine microbial composition in soils from Palmira, Sibundoy, and Bogotá, Colombia. A total of 2,984,123 loci and 3485 single nucleotide polymorphisms (SNPs) were identified, revealing a genetic variation of 12% between populations and 88% within individuals, and distributing the population into three main genetic groups, F<sub>ST</sub> = 0.115 (<i>p</i> < 0.001) and F<sub>IT</sub> = 0.013 (<i>p</i> > 0.05). In the soil analysis, significant correlations were found between effective cation exchange capacity (ECEC) and apparent density, soil texture, and levels of Mg and Fe, as well as negative correlations between ECEC and Mg, and Mg, Fe, and Ca. Proteobacteria and Ascomycota emerged as the predominant bacterial and fungal phyla, respectively. Analyses of alpha, beta, and multifactorial diversity highlight the influence of ecological and environmental factors on these microbial communities, revealing specific patterns of clustering and association between bacteria and fungi in the studied locations. |
| first_indexed | 2024-03-08T09:47:27Z |
| format | Article |
| id | doaj.art-0096f9ca1d4a45e3a06b650ba8c7d68d |
| institution | Directory Open Access Journal |
| issn | 2223-7747 |
| language | English |
| last_indexed | 2024-03-08T09:47:27Z |
| publishDate | 2024-01-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Plants |
| spelling | doaj.art-0096f9ca1d4a45e3a06b650ba8c7d68d2024-01-29T14:11:05ZengMDPI AGPlants2223-77472024-01-0113222110.3390/plants13020221Exploring Genomics and Microbial Ecology: Analysis of <i>Bidens pilosa</i> L. Genetic Structure and Soil Microbiome Diversity by RAD-Seq and MetabarcodingWendy Lorena Reyes-Ardila0Paula Andrea Rugeles-Silva1Juan Diego Duque-Zapata2Glever Alexander Vélez-Martínez3Lina Tarazona Pulido4Karen Melissa Cardona Tobar5Sergio Alberto Díaz Gallo6Jaime Eduardo Muñoz Flórez7Lucia Ana Díaz-Ariza8Diana López-Alvarez9Grupo de Investigación en Diversidad Biológica, Departamento de Ciencias Biológicas, Facultad de Ciencias Agropecuarias, Universidad Nacional de Colombia, Sede Palmira, Palmira 763533, ColombiaGrupo de Investigación en Diversidad Biológica, Departamento de Ciencias Biológicas, Facultad de Ciencias Agropecuarias, Universidad Nacional de Colombia, Sede Palmira, Palmira 763533, ColombiaGrupo de Investigación en Diversidad Biológica, Departamento de Ciencias Biológicas, Facultad de Ciencias Agropecuarias, Universidad Nacional de Colombia, Sede Palmira, Palmira 763533, ColombiaGrupo de Investigación en Diversidad Biológica, Departamento de Ciencias Biológicas, Facultad de Ciencias Agropecuarias, Universidad Nacional de Colombia, Sede Palmira, Palmira 763533, ColombiaGrupo de Investigación en Diversidad Biológica, Departamento de Ciencias Biológicas, Facultad de Ciencias Agropecuarias, Universidad Nacional de Colombia, Sede Palmira, Palmira 763533, ColombiaGrupo de Investigación en Diversidad Biológica, Departamento de Ciencias Biológicas, Facultad de Ciencias Agropecuarias, Universidad Nacional de Colombia, Sede Palmira, Palmira 763533, ColombiaGrupo de Investigación en Agricultura Biológica, Departamento de Biología, Pontificia Universidad Javeriana, Sede Bogotá, Bogotá D.C. 110231, ColombiaGrupo de Investigación en Diversidad Biológica, Departamento de Ciencias Biológicas, Facultad de Ciencias Agropecuarias, Universidad Nacional de Colombia, Sede Palmira, Palmira 763533, ColombiaGrupo de Investigación en Agricultura Biológica, Departamento de Biología, Pontificia Universidad Javeriana, Sede Bogotá, Bogotá D.C. 110231, ColombiaGrupo de Investigación en Diversidad Biológica, Departamento de Ciencias Biológicas, Facultad de Ciencias Agropecuarias, Universidad Nacional de Colombia, Sede Palmira, Palmira 763533, Colombia<i>Bidens pilosa</i> L., native to South America and commonly used for medicinal purposes, has been understudied at molecular and genomic levels and in its relationship with soil microorganisms. In this study, restriction site-associated DNA markers (RADseq) techniques were implemented to analyze genetic diversity and population structure, and metabarcoding to examine microbial composition in soils from Palmira, Sibundoy, and Bogotá, Colombia. A total of 2,984,123 loci and 3485 single nucleotide polymorphisms (SNPs) were identified, revealing a genetic variation of 12% between populations and 88% within individuals, and distributing the population into three main genetic groups, F<sub>ST</sub> = 0.115 (<i>p</i> < 0.001) and F<sub>IT</sub> = 0.013 (<i>p</i> > 0.05). In the soil analysis, significant correlations were found between effective cation exchange capacity (ECEC) and apparent density, soil texture, and levels of Mg and Fe, as well as negative correlations between ECEC and Mg, and Mg, Fe, and Ca. Proteobacteria and Ascomycota emerged as the predominant bacterial and fungal phyla, respectively. Analyses of alpha, beta, and multifactorial diversity highlight the influence of ecological and environmental factors on these microbial communities, revealing specific patterns of clustering and association between bacteria and fungi in the studied locations.https://www.mdpi.com/2223-7747/13/2/221medicinal plantsgenetic diversitypopulation structuremicrobial communities |
| spellingShingle | Wendy Lorena Reyes-Ardila Paula Andrea Rugeles-Silva Juan Diego Duque-Zapata Glever Alexander Vélez-Martínez Lina Tarazona Pulido Karen Melissa Cardona Tobar Sergio Alberto Díaz Gallo Jaime Eduardo Muñoz Flórez Lucia Ana Díaz-Ariza Diana López-Alvarez Exploring Genomics and Microbial Ecology: Analysis of <i>Bidens pilosa</i> L. Genetic Structure and Soil Microbiome Diversity by RAD-Seq and Metabarcoding Plants medicinal plants genetic diversity population structure microbial communities |
| title | Exploring Genomics and Microbial Ecology: Analysis of <i>Bidens pilosa</i> L. Genetic Structure and Soil Microbiome Diversity by RAD-Seq and Metabarcoding |
| title_full | Exploring Genomics and Microbial Ecology: Analysis of <i>Bidens pilosa</i> L. Genetic Structure and Soil Microbiome Diversity by RAD-Seq and Metabarcoding |
| title_fullStr | Exploring Genomics and Microbial Ecology: Analysis of <i>Bidens pilosa</i> L. Genetic Structure and Soil Microbiome Diversity by RAD-Seq and Metabarcoding |
| title_full_unstemmed | Exploring Genomics and Microbial Ecology: Analysis of <i>Bidens pilosa</i> L. Genetic Structure and Soil Microbiome Diversity by RAD-Seq and Metabarcoding |
| title_short | Exploring Genomics and Microbial Ecology: Analysis of <i>Bidens pilosa</i> L. Genetic Structure and Soil Microbiome Diversity by RAD-Seq and Metabarcoding |
| title_sort | exploring genomics and microbial ecology analysis of i bidens pilosa i l genetic structure and soil microbiome diversity by rad seq and metabarcoding |
| topic | medicinal plants genetic diversity population structure microbial communities |
| url | https://www.mdpi.com/2223-7747/13/2/221 |
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