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RNA extraction from decaying wood for (meta)transcriptomic analyses.

Martino Adamo1,2, Samuele Voyron1, Mariangela Girlanda1

  • 1a Università degli Studi di Torino, Dipartimento di Scienze della Vita e Biologia dei Sistemi, Viale Mattioli 25, 10125 Torino, Italy.

Canadian Journal of Microbiology
|August 10, 2017
PubMed
Summary

Researchers developed a new RNA extraction method for studying wood-decaying microbes. This protocol enables analysis of genes involved in the carbon cycle and lignocellulose breakdown in diverse wood types.

Keywords:
RNA extractiondégradation du boisextraction d’ARNmetatranscriptomicsmétatranscriptomiquewood degradation

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Area of Science:

  • Microbiology
  • Forest Ecology
  • Biochemistry

Background:

  • Wood decomposition is crucial for the terrestrial carbon cycle and involves fungi and bacteria.
  • Understanding microbial gene expression during wood decay is essential for ecological and economic insights.
  • Recalcitrant wood, rich in polysaccharides and phenolics, poses challenges for molecular analysis.

Purpose of the Study:

  • To develop an effective RNA extraction protocol for diverse, recalcitrant wood samples.
  • To enable the study of gene expression in microbial communities involved in wood decay.
  • To lay the groundwork for metatranscriptomic analyses of natural wood degradation.

Main Methods:

  • Developed and optimized an RNA extraction protocol from various wood species.
  • Applied the protocol to 22 wood samples from Angiosperms and Gymnosperms.
  • Converted extracted RNA to cDNA and amplified fungal and bacterial protein-coding genes.

Main Results:

  • Successfully extracted RNA from all tested wood samples.
  • Amplified protein-coding genes, including those for lignocellulose hydrolysis, from fungal and bacterial communities.
  • Demonstrated the protocol's applicability across diverse tree species and wood types.

Conclusions:

  • The new RNA extraction protocol is effective for analyzing microbial gene expression in decomposing wood.
  • This method facilitates the study of microbial roles in the carbon cycle and wood degradation.
  • The protocol is a significant step towards metatranscriptomic studies of wood decay under natural conditions.