Related Experiment Video
Updated: Oct 6, 2025
10:24
Next-generation Sequencing of 16S Ribosomal RNA Gene Amplicons
Published on: August 29, 2014
83.8K
Sediment-associated microbial community profiling: sample pre-processing through sequential membrane filtration for
Joeselle M Serrana1, Kozo Watanabe2
1Center for Marine Environmental Studies (CMES), Ehime University, Bunkyo-cho 3, Matsuyama, Ehime, 790-8577, Japan.
BMC Microbiology
|January 21, 2022
Summary
Sequential membrane filtration effectively pre-processes sediment samples for microbial DNA analysis without significantly altering microbial diversity or community composition. This method ensures reliable DNA quality for profiling sediment-associated microorganisms.
Area of Science:
- Microbiology
- Environmental Science
- Molecular Biology
Background:
- Sequential membrane filtration is a potential pre-processing method for sediment microbial DNA analysis.
- Its impact on DNA quality, sequencing, and microbial profiling is not well understood.
- Further evaluation is needed on pre-processing effects on DNA quantity, sequencing reads, and detected taxa.
Purpose of the Study:
- To assess the impact of sequential membrane filtration pre-processing on freshwater sediment samples.
- To compare DNA quality, quantity, sequencing reads, and microbial community profiling between non- and pre-processed samples.
- To evaluate method-driven differences in microbial diversity and composition.
Main Methods:
- Sequential membrane filtration (10, 5, and 0.22 μm pore sizes) was used for pre-processing.
- 16S rRNA gene sequencing was employed for microbial community profiling.
- Extracted DNA, PCR amplicons, sequencing reads, diversity, and composition were analyzed.
Main Results:
- No significant differences were found in DNA/PCR amplicon quality and quantity between methods.
- Shared amplicon sequence variants (ASVs) accounted for 74% of the total read abundance.
- Both methods revealed comparable microbial diversity and community composition, with minor differences in unique/shared taxa.
Conclusions:
- Sequential membrane filtration is a feasible pre-processing method for sediment microbial community analysis.
- Further research on sampling strategies is recommended for optimal study designs.
- This method supports ambient temperature preservation of DNA for profiling.
