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A robust, cost-effective method for DNA, RNA and protein co-extraction from soil, other complex microbiomes and pure cultures.
Thorn, Camilla E; Bergesch, Christian; Joyce, Aoife; Sambrano, Gustavo; McDonnell, Kevin; Brennan, Fiona; Heyer, Robert; Benndorf, Dirk; Abram, Florence.
Afiliación
  • Thorn CE; Functional Environmental Microbiology, School of Natural Sciences, National University of Ireland Galway, Galway, Ireland.
  • Bergesch C; Functional Environmental Microbiology, School of Natural Sciences, National University of Ireland Galway, Galway, Ireland.
  • Joyce A; Functional Environmental Microbiology, School of Natural Sciences, National University of Ireland Galway, Galway, Ireland.
  • Sambrano G; Functional Environmental Microbiology, School of Natural Sciences, National University of Ireland Galway, Galway, Ireland.
  • McDonnell K; Functional Environmental Microbiology, School of Natural Sciences, National University of Ireland Galway, Galway, Ireland.
  • Brennan F; Department of Environment, Soils and Land-use, Teagasc, Wexford, Ireland.
  • Heyer R; Bioprocess Engineering, Max Planck Institute for Dynamics of Complex Technical Systems, Otto von Guericke University, Magdeburg, Germany.
  • Benndorf D; Bioprocess Engineering, Max Planck Institute for Dynamics of Complex Technical Systems, Otto von Guericke University, Magdeburg, Germany.
  • Abram F; Functional Environmental Microbiology, School of Natural Sciences, National University of Ireland Galway, Galway, Ireland.
Mol Ecol Resour ; 19(2): 439-455, 2019 Mar.
Article en En | MEDLINE | ID: mdl-30565880
The soil microbiome is inherently complex with high biological diversity, and spatial heterogeneity typically occurring on the submillimetre scale. To study the microbial ecology of soils, and other microbiomes, biomolecules, that is, nucleic acids and proteins, must be efficiently and reliably co-recovered from the same biological samples. Commercial kits are currently available for the co-extraction of DNA, RNA and proteins but none has been developed for soil samples. We present a new protocol drawing on existing phenol-chloroform-based methods for nucleic acids co-extraction but incorporating targeted precipitation of proteins from the phenol phase. The protocol is cost-effective and robust, and easily implemented using reagents commonly available in laboratories. The method is estimated to be eight times cheaper than using disparate commercial kits for the isolation of DNA and/or RNA, and proteins, from soil. The method is effective, providing good quality biomolecules from a diverse range of soil types, with clay contents varying from 9.5% to 35.1%, which we successfully used for downstream, high-throughput gene sequencing and metaproteomics. Additionally, we demonstrate that the protocol can also be easily implemented for biomolecule co-extraction from other complex microbiome samples, including cattle slurry and microbial communities recovered from anaerobic bioreactors, as well as from Gram-positive and Gram-negative pure cultures.
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Texto completo: 1 Colección: 01-internacional Base de datos: MEDLINE Asunto principal: Microbiología del Suelo / ADN / ARN / Proteínas / Proteómica / Metagenómica / Microbiota Tipo de estudio: Health_economic_evaluation Idioma: En Revista: Mol Ecol Resour Año: 2019 Tipo del documento: Article País de afiliación: Irlanda Pais de publicación: Reino Unido
Texto completo
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Texto completo: 1 Colección: 01-internacional Base de datos: MEDLINE Asunto principal: Microbiología del Suelo / ADN / ARN / Proteínas / Proteómica / Metagenómica / Microbiota Tipo de estudio: Health_economic_evaluation Idioma: En Revista: Mol Ecol Resour Año: 2019 Tipo del documento: Article País de afiliación: Irlanda Pais de publicación: Reino Unido