A DNA metabarcoding approach for recovering plankton communities from archived samples fixed in formalin

Area of Science:

• Marine Biology
• Molecular Ecology
• Genetics

Background:

• Plankton samples are routinely preserved in formalin for over a century.
• DNA analysis of these archived samples offers insights into historical plankton diversity.
• The impact of formalin fixation on plankton community DNA has not been previously assessed.

Purpose of the Study:

• To develop and validate a DNA extraction method for formalin-fixed plankton samples.
• To assess the reliability of DNA metabarcoding for analyzing historical plankton communities.
• To evaluate the impact of formalin fixation on DNA integrity and community structure.

Main Methods:

• Developed a novel DNA extraction protocol using a borate-NaOH buffer, SDS, and proteinase K.
• Applied DNA metabarcoding targeting the 18S rRNA gene.
• Compared DNA metabarcoding results with traditional microscopy analysis.
• Assessed DNA integrity by storing samples post-fixation.

Main Results:

• The developed lysis solution effectively cleaved formalin cross-links, enabling DNA extraction from decades-old samples.
• DNA metabarcoding results for diatoms showed good agreement with microscopy.
• 18S rRNA gene community structures remained stable in formalin-fixed samples after 1.5 years compared to fresh samples.
• The method accurately reflects the original plankton community structure.

Conclusions:

• The new method reliably extracts DNA from formalin-preserved plankton, allowing for accurate historical community structure analysis.
• This approach validates the use of long-term formalin-archived plankton collections for molecular ecological studies.
• The findings support the examination of long-term plankton diversity changes using DNA metabarcoding.