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

Enrique Lara*, David Singer, Stefan Geisen

*Corresponding author for this work

Research output: Contribution to journalArticleAcademicpeer-review


Metabarcoding approaches are exponentially increasing our understanding of soil biodiversity, with a major focus on the bacterial part of the microbiome. Part of the soil diversity are also eukaryotes that include fungi, algae, protists and Metazoa. Nowadays, soil eukaryotes are targeted with the same approaches developed for bacteria and archaea (prokaryotes). However, fundamental differences exist between domains. After providing a short historical overview of the developments of metabarcoding applied to environmental microbiology, we compile the most important differences between domains that prevent direct method transfers between prokaryotic and eukaryotic soil metabarcoding approaches, currently dominated by short-read sequencing. These include the existence of divergent diversity concepts and the variations in eukaryotic morphology that affect sampling and DNA extraction. Furthermore, eukaryotes experienced much more variable evolutionary rates than prokaryotes, which prevent capturing the entire eukaryotic diversity in a soil with a single amplification protocol fit for short-read sequencing. In the final part we focus on future potentials for optimization of eukaryotic metabarcoding that include superior possibility of functionally characterizing eukaryotes and to extend the current information obtained, such as by adding a real quantitative component. This review should optimize future metabarcoding approaches targeting soil eukaryotes and kickstart this promising research direction.

Original languageEnglish
Pages (from-to)3829-3839
JournalEnvironmental Microbiology
Issue number9
Early online date2022
Publication statusPublished - Sep 2022


Dive into the research topics of 'Discrepancies between prokaryotes and eukaryotes need to be considered in soil DNA-based studies'. Together they form a unique fingerprint.

Cite this