Cost-effective DNA extraction method optimized for high yield and long fragments from coastal sediments.

Area of Science:

• Environmental microbiology
• Molecular biology
• Genomics

Background:

• Efficient DNA extraction is crucial for microbial community analysis, particularly for long-read sequencing requiring high-molecular-weight DNA.
• Coastal sediments present challenges for DNA extraction due to their composition and low biomass.

Purpose of the Study:

• To compare a cost-effective laboratory-made (LM) DNA extraction method with two commercial kits (Qiagen DNEasy™ PowerSoil™ Pro and PowerMax™ Soil).
• To evaluate DNA yield, fragment length, amplification success, microbial diversity metrics, and cost-effectiveness for different sediment types.

Main Methods:

• Comparison of DNA extraction efficiency using a laboratory-made method versus two commercial kits.
• Analysis of DNA yield, fragment length, and 18S rRNA gene amplification.
• Assessment of prokaryotic and eukaryotic microbial diversity using sequencing data.
• Cost-benefit analysis of the different extraction methods.

Main Results:

• The LM method yielded up to 13 times more DNA and 4-fold longer fragments than commercial kits in sandy, low-organic-matter sediments.
• The LM method was superior for 18S rRNA gene amplification, enabling sequencing in challenging samples.
• While prokaryotic diversity was similar, eukaryotic richness varied with sample amount, highlighting its importance.
• The LM method proved reproducible and recovered taxa missed by commercial kits, at a significantly lower cost per sample.

Conclusions:

• The laboratory-made DNA extraction method is a robust, economical, and effective alternative to commercial kits for coastal sediments.
• This method is particularly advantageous for sandy or low-biomass sediments and studies requiring high-quality DNA for long-read sequencing.
• Validation of DNA extraction protocols based on sediment type and research objectives is essential for accurate microbial community studies.