Drying as an effective method to store soil samples for DNA-based microbial community analyses: a comparative study

Area of Science:

• Environmental science
• Microbiology
• Molecular ecology

Background:

• Soil environmental DNA (eDNA) studies are crucial for understanding microbial communities.
• Logistical challenges, particularly lack of freezers, limit eDNA sampling in remote areas.
• Alternative preservation methods are needed for room temperature storage of soil samples.

Purpose of the Study:

• To evaluate the efficacy of five room-temperature preservation methods (CD1 solution, 95% Ethanol, Dry & Dry silica gel, RNAlater, LifeGuard) against freezing (-20°C) for soil eDNA.
• To assess the impact of preservation methods on DNA concentration, quality, and microbial community structure (bacterial and fungal) over three weeks.
• To identify a suitable, accessible preservation method for field-based eDNA sampling.

Main Methods:

• Soil samples (organic and mineral) were preserved using five methods and freezing (-20°C) or immediately extracted.
• DNA concentration and quality were measured.
• DNA metabarcoding was employed to analyze bacterial and fungal community composition and diversity.
• Preservation effects were assessed over a three-week period.

Main Results:

• Drying with Dry & Dry silica gel packs showed no significant differences in DNA yield or community structure compared to immediate extraction.
• RNAlater resulted in lower DNA concentrations but comparable community structures to freezing.
• CD1 solution, 95% Ethanol, and LifeGuard caused significant shifts in community structure, DNA degradation, or altered diversity metrics.

Conclusions:

• Silica gel desiccation is a reliable, cost-effective, and easily applicable method for short-term, room-temperature storage of soil samples for microbial eDNA analysis.
• This method overcomes logistical limitations associated with cold storage in field settings.
• Other tested preservatives (CD1, Ethanol, LifeGuard) are not recommended for preserving microbial community integrity in soil eDNA.