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Assessment of methods to recover DNA from bacteria, fungi and archaea in complex environmental samples

Guillén Navarro, Griselda Karina [autora] | Herrera López, David [autor] | López Chávez, Mariana Yadira [autora] | Cancino Gómez, Máximo [autor] | Reyes Reyes, Ana Laura [autora].
Tipo de material: Artículo en línea Artículo en línea Tema(s): Ácido desoxirribonucléico | Pulpa de café | Sedimentos fluviales | Comunidades microbianasTema(s) en inglés: Deoxyribonucleic acid | Coffee pulp | River sediments | Microbial communitiesDescriptor(es) geográficos: Finca Argovia, Tapachula (Chiapas, México) | Sistema Lagunar Pampa Murillo, Tapachula (Chiapas, México) | Finca La Concepción, Tapachula (Chiapas, México) Nota de acceso: Disponible para usuarios de ECOSUR con su clave de acceso En: Folia Microbiologica. volumen 60, número 6 (November 2015), páginas 551-558. --ISSN: 1874-9356Número de sistema: 54708Resumen:
Inglés

DNA extraction from environmental samples is a critical step for metagenomic analysis to study microbial communities, including those considered uncultivable. Nevertheless, obtaining good quality DNA in sufficient quantities for downstream methodologies is not always possible, and it depends on the complexity and stability of each ecosystem, which could be more problematic for samples from tropical regions because those ecosystems are less stable and more complex. Three laboratory methods for the extraction of nucleic acids from samples representing unstable (decaying coffee pulp and mangrove sediments) and relatively stable (compost and soil) environments were tested. The results were compared with those obtained using two commercial DNA extraction kits. The quality of the extracted DNA was evaluated by PCR amplification to verify the recovery of bacterial, archaeal, and fungal genetic material. The laboratory method that gave the best results used a lysis procedure combining physical, chemical, and enzymatic steps.

Recurso en línea: http://link.springer.com/article/10.1007%2Fs12223-015-0403-1
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Disponible para usuarios de ECOSUR con su clave de acceso

DNA extraction from environmental samples is a critical step for metagenomic analysis to study microbial communities, including those considered uncultivable. Nevertheless, obtaining good quality DNA in sufficient quantities for downstream methodologies is not always possible, and it depends on the complexity and stability of each ecosystem, which could be more problematic for samples from tropical regions because those ecosystems are less stable and more complex. Three laboratory methods for the extraction of nucleic acids from samples representing unstable (decaying coffee pulp and mangrove sediments) and relatively stable (compost and soil) environments were tested. The results were compared with those obtained using two commercial DNA extraction kits. The quality of the extracted DNA was evaluated by PCR amplification to verify the recovery of bacterial, archaeal, and fungal genetic material. The laboratory method that gave the best results used a lysis procedure combining physical, chemical, and enzymatic steps. eng

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