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Capturing marine microbiomes and environmental DNA: A field sampling guide.

Nastassia Virginia Patin^1,2,3, Kelly D Goodwin^1,3

¹Atlantic Oceanographic and Meteorological Laboratory, Ocean Chemistry and Ecosystems Division, National Oceanic and Atmospheric Administration, Miami, FL, United States.

Frontiers in Microbiology

|January 30, 2023

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Standardizing marine microbiome and environmental DNA (eDNA) sample collection and preservation is crucial for comparative studies. This work provides guidelines for fit-for-purpose protocols, emphasizing freezing over buffer preservation for better results.

Area of Science:

Marine biology
Environmental science
Molecular ecology

Background:

Growing interest in marine microbiome and environmental DNA (eDNA) necessitates standardized sampling and preservation methods.
Current practices vary widely, hindering cross-study comparisons and meta-analyses.
Lack of standardized protocols limits the reliability and comparability of marine microbiome and eDNA data.

Purpose of the Study:

To provide guidelines for marine microbiome and eDNA sample collection and preservation.
To enable the design of fit-for-purpose protocols tailored to specific research goals.
To support comparative assessments and meta-analyses of marine microbiome and eDNA data.

Main Methods:

Review of published methods and field sampling experiences.

Keywords:

eDNA field methods microbiome molecular ecological methods sampling

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Consideration of environmental factors, resource availability, and experimental objectives.

Focus on sample processing, storage, and eDNA extraction protocols for prokaryotic and microeukaryotic eDNA.

Main Results:

Development of guidelines for designing fit-for-purpose sampling protocols.
Recommendations include rigorous decontamination, pilot studies for filtration volume, and prioritizing sample freezing.
An annotated list of relevant studies and a sample protocol for oceanographic vessels are provided.

Conclusions:

Standardized, fit-for-purpose protocols are essential for robust marine microbiome and eDNA research.
Prioritizing sample freezing and conducting pilot studies are key recommendations.
These guidelines will aid scientists in making informed decisions for marine eDNA and microbiome sampling.