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

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Abstract

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.

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Acknowledgements

This work was funded by the National Council of Science and Technology project CB-2008-01-101389. MYL-C thanks scholarship number 14877 from the National Council of Science and Technology. We thank Guillermo Vázquez-Martínez for technical assistance with PCR reactions. We thank Michael F. Dunn for reviewing the manuscript.

Conflicts of interest

The authors declare that they have no conflicts of interest.

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Authors and Affiliations

  1. Laboratorio de Biotecnología Ambiental y Agroecológica, El Colegio de la Frontera Sur, CONACYT, Carretera Antiguo Aeropuerto Km 2.5, C.P. 30700, Tapachula, Chiapas, Mexico

    Karina Guillén-Navarro, David Herrera-López, Mariana Y. López-Chávez & Máximo Cancino-Gómez

  2. Programa de Bioenergía, Instituto Nacional de Investigaciones Forestales Agrícolas y Pecuarias, Campo Experimental Rosario Izapa, Km 18 Carretera Tapachula-Cacahoatán, Tuxtla Chico, Chiapas, Mexico

    Ana L. Reyes-Reyes

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  1. Karina Guillén-Navarro
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  2. David Herrera-López
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  3. Mariana Y. López-Chávez
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  4. Máximo Cancino-Gómez
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  5. Ana L. Reyes-Reyes
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Correspondence to Karina Guillén-Navarro.

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Guillén-Navarro, K., Herrera-López, D., López-Chávez, M.Y. et al. Assessment of methods to recover DNA from bacteria, fungi and archaea in complex environmental samples. Folia Microbiol 60, 551–558 (2015). https://doi.org/10.1007/s12223-015-0403-1

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  • DOI: https://doi.org/10.1007/s12223-015-0403-1

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