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Exploring the Root Microbiome: Extracting Bacterial Community Data from the Soil, Rhizosphere, and Root Endosphere
Published on: May 2, 2018
Soil eukaryotic functional diversity, a metatranscriptomic approach
Julie Bailly1, Laurence Fraissinet-Tachet, Marie-Christine Verner
1Ecologie Microbienne, UMR CNRS, USC INRA, Université de Lyon, Université Lyon 1, Villeurbanne, France.
The ISME Journal
|November 29, 2007
Summary
Investigating forest soil microbial communities using a metatranscriptome approach revealed high species richness and novel genes. This method uncovers adaptations and biotechnological resources from soil eukaryotes.
Area of Science:
- Microbiology
- Ecology
- Molecular Biology
Background:
- Soil harbors diverse eukaryotic microbial communities crucial for ecosystem function.
- Understanding the functional diversity of these communities is essential for ecological studies.
- Metatranscriptomics offers a powerful tool to explore gene expression within complex microbial ecosystems.
Purpose of the Study:
- To evaluate an experimental approach for assessing functional diversity in soil eukaryotic microbial communities.
- To construct and screen a forest soil cDNA library representing the community's metatranscriptome.
- To analyze the taxonomic composition and identify novel genes within the soil microbial community.
Main Methods:
- Extraction of polyadenylated mRNA from forest soil to create a cDNA library.
- Sequencing of 18S rDNA genes from soil DNA and reverse-transcribed RNA for taxonomic diversity assessment.
- Sequencing of cDNA clones to identify expressed genes and their functions.
- Functional complementation of a histidine auxotrophic yeast mutant to validate gene isolation.
Main Results:
- The soil community comprised predominantly fungi, protists, and metazoa, with richness estimators suggesting over 180 species.
- Sequencing of 119 cDNA clones revealed 32% of genes with no database homologues, indicating novel functions.
- A discrepancy was observed between the taxonomic distribution of 18S rDNA and cDNA, with under-representation of protists in the cDNA library.
- Successful isolation and functional complementation of yeast mutants by specific fungal cDNAs were demonstrated.
Conclusions:
- Metatranscriptomic analysis of soil eukaryotic communities provides insights into functional diversity and ecological adaptations.
- The study highlights the potential of environmental cDNA libraries as a source of novel genes for biotechnological applications.
- Functional complementation in heterologous hosts like Saccharomyces cerevisiae is a viable strategy for isolating and characterizing genes from uncultured soil microorganisms.
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