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Collection and Extraction of Occupational Air Samples for Analysis of Fungal DNA
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Published on: May 2, 2018

Total fungal RNA extraction from complex solid- state fermentation products.

Mikael Terp1, Christian Enrico Rusbjerg-Weberskov1, Teis E Sondergaard1

  • 1Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark.

Applied Microbiology and Biotechnology
|July 6, 2026
PubMed
Summary
This summary is machine-generated.

A new RNA extraction method effectively isolates fungal genetic material from complex agricultural waste, enabling gene expression studies in solid-state fermentation (SSF). This method reveals temporal regulation of hydrophobin NC2 in Neurospora intermedia.

Keywords:
Neurospora intermediaBrewer’s spent grainFilamentous fungiRNA extractionSolid-state fermentation

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Area of Science:

  • Biotechnology
  • Molecular Biology
  • Mycology

Background:

  • Investigating fungal gene expression in solid-state fermentation (SSF) is crucial for optimizing industrial processes.
  • Traditional RNA extraction methods often fail with complex substrates like agricultural biomass, hindering gene expression analysis.
  • Challenges exist in obtaining high-quality RNA from filamentous fungi grown on diverse plant-based materials.

Purpose of the Study:

  • To develop and validate a robust RNA extraction protocol for filamentous fungi in complex SSF systems.
  • To apply the optimized method for analyzing the temporal gene expression of hydrophobin NC2 in Neurospora intermedia.
  • To demonstrate the method's versatility across different fungal species and challenging substrates.

Main Methods:

  • Optimization of an RNA extraction protocol specifically for fungal samples rich in plant biomass from SSF.
  • Application of the protocol to Neurospora intermedia grown on various brewer's spent grain (BSG) sources.
  • RT-qPCR analysis to quantify the relative expression of the class II hydrophobin NC2 gene.

Main Results:

  • The developed method successfully yielded high-purity RNA from complex SSF substrates, outperforming commercial kits.
  • Temporal expression analysis revealed a peak in NC2 gene expression in Neurospora intermedia around day 6.
  • The microbrewery BSG batch showed the highest peak NC2 expression, indicating substrate-specific regulation.
  • The protocol was validated on other fungi (Aspergillus oryzae, Trichoderma asperellum) and substrates (rapeseed press cake, oat hulls).

Conclusions:

  • A reliable and efficient RNA extraction protocol for complex fungal SSF products has been established.
  • The study demonstrates the temporal regulation of hydrophobin NC2 expression in Neurospora intermedia on BSG.
  • This method facilitates accurate gene expression analysis in challenging SSF applications, aiding process optimization.