An improved method for extraction of microbial DNA from alkaline-saline soil

Authors

DOI:

https://doi.org/10.28940/terra.v39i0.887

Keywords:

DNA extraction, DNA sequencing, PCR amplification, saline-alkaline soil

Abstract

A modified method for the direct extraction of DNA from alkaline-saline soils with minimum DNA fragmentation and a possible reduction in chimera formation during polymerase chain reaction (PCR) was developed. The commercial extraction kit Power Soil DNA (Mo Bio™ Laboratories, Inc.) was used as a reference technique. The method reported here was based on cell lysis employing ethylenediaminetetraacetic acid (EDTA), sodium dodecyl sulfate (SDS), and cell disruption with mechanical force with FastPrep-24™ equip followed by one cycle of freezing at -40 °C for 60 min and thawing at 65 °C for 20 min. The extraction method was tested for allophonic soils with large concentrations of organic matter, fulvic and humic acids, electrolytic conductivity (EC) ranging between 2.6 dS m-1 and 39.9 dS m-1, and pH between 8.8 and 10.9. The yield of DNA extracted depended on soil type, i.e., DNA extracted from soil varied between 2.35 (Texcoco-2) to 3.66 (Texcoco-1) μg DNA g-1 soil. The proposed method in this study produced enough DNA with yield and quality for PCR amplification of 16S rDNA when bovine serum albumin (BSA) was added to the reaction buffer. The DNA obtained had sufficient quality and yield for later use for 16S sequencing or possible use in other sequencing technologies, e.g. whole metagenome shotgun sequencing.

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Author Biographies

Valentín Pérez-Hernández, Instituto Tecnológico de Tuxtla-Gutiérrez, Tecnológico Nacional de México

Laboratory of Soil Ecology, Department of Chemistry and Biochemistry, Instituto Tecnológico de Tuxtla-Gutiérrez, Tecnológico Nacional de México, Tuxtla-Gutiérrez, México.

Mario Hernández-Guzmán, CINVESTAV-IPN

Laboratory of Soil Ecology, Department of Biotechnology and Bioengineering, CINVESTAV-IPN, Mexico D.F., Mexico.

César Valenzuela-Encinas, CINVESTAV-IPN

Laboratory of Soil Ecology, Department of Biotechnology and Bioengineering, CINVESTAV-IPN, Mexico D.F., Mexico.

Rocío Alcántara-Hernández, CINVESTAV-IPN

Laboratory of Soil Ecology, Department of Biotechnology and Bioengineering, CINVESTAV-IPN, Mexico D.F., Mexico.

Isabel Estrada-Alvarado, CINVESTAV-IPN

Laboratory of Soil Ecology, Department of Biotechnology and Bioengineering, CINVESTAV-IPN, Mexico D.F., Mexico.

Luc Dendooven, Cinvestav, GIB

Laboratory of Soil Ecology, Department of Biotechnology and Bioengineering, CINVESTAV-IPN, Mexico D.F., Mexico.

Rodolfo Marsch, Cinvestav, GIB

Laboratory of Soil Ecology, Department of Biotechnology and Bioengineering, CINVESTAV-IPN, Mexico D.F., Mexico.

Federico Gutiérrez-Miceli, Instituto Tecnológico de Tuxtla-Gutiérrez, Tecnológico Nacional de México

Laboratory of Soil Ecology, Department of Chemistry and Biochemistry, Instituto Tecnológico de Tuxtla-Gutiérrez, Tecnológico Nacional de México, Tuxtla-Gutiérrez, México.

Víctor M. Ruíz-Valdiviezo, Instituto Tecnológico de Tuxtla-Gutiérrez, Tecnológico Nacional de México

Laboratory of Soil Ecology, Department of Chemistry and Biochemistry, Instituto Tecnológico de Tuxtla-Gutiérrez, Tecnológico Nacional de México, Tuxtla-Gutiérrez, México.

Joaquín A. Montes-Molina, Instituto Tecnológico de Tuxtla-Gutiérrez, Tecnológico Nacional de México

Laboratory of Soil Ecology, Department of Chemistry and Biochemistry, Instituto Tecnológico de Tuxtla-Gutiérrez, Tecnológico Nacional de México, Tuxtla-Gutiérrez, México.

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Published

2021-06-29

How to Cite

Pérez-Hernández, V., Hernández-Guzmán, M., Valenzuela-Encinas, C., Alcántara-Hernández, R., Estrada-Alvarado, I., Dendooven, L., … Montes-Molina, J. A. (2021). An improved method for extraction of microbial DNA from alkaline-saline soil. REVISTA TERRA LATINOAMERICANA, 39. https://doi.org/10.28940/terra.v39i0.887

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Scientific Papers

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