Discrepancies between prokaryotes and eukaryotes need to be considered in soil DNA-based studies

Area of Science:

• Environmental microbiology
• Eukaryotic ecology
• Molecular ecology

Background:

• Metabarcoding significantly advances soil biodiversity research, primarily focusing on bacterial communities.
• Soil eukaryotes (fungi, algae, protists, Metazoa) are increasingly studied using similar methods as prokaryotes.
• Fundamental biological differences necessitate tailored approaches for eukaryotic metabarcoding.

Purpose of the Study:

• To review the differences between prokaryotic and eukaryotic metabarcoding.
• To identify challenges in current soil eukaryotic metabarcoding methods.
• To propose future optimization strategies for eukaryotic metabarcoding.

Main Methods:

• Historical overview of environmental metabarcoding development.
• Compilation and discussion of domain-specific differences impacting metabarcoding.
• Focus on short-read sequencing limitations for eukaryotes.

Main Results:

• Direct transfer of prokaryotic metabarcoding methods to eukaryotes is hindered by divergent diversity concepts and morphological variations affecting sampling and DNA extraction.
• Variable evolutionary rates in eukaryotes complicate capturing full diversity with single short-read sequencing protocols.
• Eukaryotic metabarcoding offers superior potential for functional characterization and quantitative analysis.

Conclusions:

• Current metabarcoding approaches need significant adaptation for soil eukaryotes.
• Future research should focus on optimizing eukaryotic-specific protocols.
• Enhanced eukaryotic metabarcoding will improve soil biodiversity assessment and functional understanding.