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Peer-reviewedCC BYMethodsX

A culturomics-inspired multi-medium workflow for soil fungal isolation and ITS metabarcoding comparison.

  • Charbel Elias1,2
  • Aïcha Hamieh3
  • Stéphane Ranque4,1
  • Laure Malleret2
4 affiliations
  1. 1Aix Marseille University, SSA, AP-HM, UMR D, Risques Infectieux, Microorganismes Emergents (RITMES), Marseille, France.
  2. 2Aix Marseille University - CNRS, Laboratoire Chimie Environnement (LCE) , UMR 7376, Marseille, France.
  3. 3Aix Marseille University - APHM, MEPHI, Marseille, France.
  4. 4Institut Hospitalo-Universitaire Méditerranée Infection (IHU), Aix Marseille Université, Marseille, France.
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Abstract

This method article describes a reproducible workflow for recovering, identifying, and comparing soil-associated fungi using complementary culture-dependent and sequence-based approaches. The workflow was designed for environmental mycology studies in which fungal DNA detection needs to be complemented by the recovery of living isolates. It combines standardized soil suspension processing, parallel plating on five culture media, daily morphotype selection and purification, MALDI-TOF MS screening, targeted multilocus sequencing when required, and comparison with ITS1/ITS2 metabarcoding profiles. In its application to soil samples, the workflow recovered a diverse viable isolate collection, supporting its usefulness for expanding fungal recovery, improving lower-level taxonomic anchoring, enriching identification resources, and distinguishing culture-recovered from sequence-detected fungal fractions.•Five culture media are used in parallel to broaden the spectrum of viable soil fungi recovered under standardized incubation conditions.•Recovered isolates are identified using MALDI-TOF MS and targeted multilocus sequencing when necessary.•Culture-recovered taxa are compared with ITS1/ITS2 metabarcoding profiles to distinguish shared and method-specific fungal fractions.

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Cite

BibTeXRIS
BibTeX
@article{elias2026culturomicsinspired,
  title = {{A culturomics-inspired multi-medium workflow for soil fungal isolation and ITS metabarcoding comparison.}},
  author = {Charbel Elias and Aïcha Hamieh and Stéphane Ranque and Laure Malleret},
  journal = {MethodsX},
  year = {2026},
  month = sep,
  doi = {10.1016/j.mex.2026.104179},
  url = {https://europepmc.org/article/MED/42898600},
  note = {CC BY},
}
RIS
TY  - JOUR
TI  - A culturomics-inspired multi-medium workflow for soil fungal isolation and ITS metabarcoding comparison.
AU  - Charbel Elias
AU  - Aïcha Hamieh
AU  - Stéphane Ranque
AU  - Laure Malleret
PY  - 2026
DA  - 2026/09/27
JO  - MethodsX
DO  - 10.1016/j.mex.2026.104179
UR  - https://europepmc.org/article/MED/42898600
AB  - This method article describes a reproducible workflow for recovering, identifying, and comparing soil-associated fungi using complementary culture-dependent and sequence-based approaches. The workflow was designed for environmental mycology studies in which fungal DNA detection needs to be complemented by the recovery of living isolates. It combines standardized soil suspension processing, parallel plating on five culture media, daily morphotype selection and purification, MALDI-TOF MS screening, targeted multilocus sequencing when required, and comparison with ITS1/ITS2 metabarcoding profiles. In its application to soil samples, the workflow recovered a diverse viable isolate collection, supporting its usefulness for expanding fungal recovery, improving lower-level taxonomic anchoring, enriching identification resources, and distinguishing culture-recovered from sequence-detected fungal fractions.•Five culture media are used in parallel to broaden the spectrum of viable soil fungi recovered under standardized incubation conditions.•Recovered isolates are identified using MALDI-TOF MS and targeted multilocus sequencing when necessary.•Culture-recovered taxa are compared with ITS1/ITS2 metabarcoding profiles to distinguish shared and method-specific fungal fractions.
SN  - 2215-0161
ER  -