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FACS-iChip: a high-efficiency iChip system for microbial 'dark matter' mining
Haoze Liu1,2, Ran Xue1,2, Yiling Wang1,2
1Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, 310058 China.
Marine Life Science & Technology
|April 19, 2023
Summary
The new FACS-iChip method efficiently cultures previously uncultivable microorganisms from soil. This technique significantly enhances the recovery of microbial
Area of Science:
- Microbiology
- Environmental Science
Background:
- The isolation chip (iChip) method enables culturing of previously uncultivable microorganisms.
- A key limitation of the iChip is the inability to guarantee single-cell loading in wells.
Purpose of the Study:
- To enhance the iChip method for culturing uncultivable soil microorganisms.
- To integrate flow cytometry-based fluorescence-activated cell sorting (FACS) with the iChip (FACS-iChip).
- To mine microbial 'dark matter' in paddy soils and compare cultured microbes with bulk soil via 16S rRNA gene sequencing.
Main Methods:
- Integration of fluorescence-activated cell sorting with a modified isolation chip (FACS-iChip).
- Application of the FACS-iChip system to paddy soil samples.
- 16S rRNA gene sequencing for microbial community analysis.
Main Results:
- The FACS-iChip achieved a culture recovery rate of nearly 40% and a retrieval rate of 25%.
- Nearly 500 strains from 19 genera were cultured, but only six were identified by standard 16S rRNA gene sequencing.
- The method detected microbial strains missed by PCR-based sequencing.
Conclusions:
- The FACS-iChip system is highly efficient for culturing uncultivable microorganisms.
- This approach effectively mines microbial 'dark matter' and reveals limitations in current sequencing technologies.
- The FACS-iChip offers a readily available tool for exploring microbial diversity.
