A simple and cost-effective extraction for piscine environmental DNA metabarcoding using guanidine hydrochloride...

Area of Science:

• Aquatic ecology
• Molecular biology
• Conservation science

Background:

• Environmental DNA (eDNA) metabarcoding is crucial for biodiversity monitoring.
• High costs and complexity of DNA extraction limit its widespread use, particularly in developing nations.
• Developing affordable and efficient eDNA extraction protocols is essential for broader adoption.

Purpose of the Study:

• To develop and evaluate a cost-effective eDNA extraction method using guanidine hydrochloride (GuHCl).
• To compare the performance of the GuHCl protocol against a commercial kit for fish community detection.
• To assess the method's suitability for large-scale ecological studies and conservation.

Main Methods:

• Utilized a guanidine hydrochloride (GuHCl) buffer, proteinase-K digestion, and isopropanol precipitation for DNA extraction.
• Employed MiFish universal primers for eDNA metabarcoding.
• Compared the GuHCl protocol with the Qiagen DNeasy Blood & Tissue Kit using freshwater and brackish water samples.

Main Results:

• The GuHCl protocol identified more fish species in freshwater samples compared to the Qiagen kit.
• Both methods showed comparable performance in relative read abundance metrics.
• The GuHCl method experienced higher PCR inhibition in brackish water samples, likely due to salinity and natural inhibitors.

Conclusions:

• The GuHCl-based eDNA extraction method is a cost-effective and viable alternative for assessing aquatic biodiversity.
• This protocol offers enhanced sensitivity for detecting low-abundance species in freshwater environments.
• The method supports large-scale eDNA metabarcoding for ecological research and conservation management.