We are ready for faunistic surveys of bdelloid rotifers through DNA barcoding: the example of Sphagnum bogs of the Swiss Jura Mountains

Fontaneto, Diego; Eckert, Ester M.; Anicic, Nikoleta; Lara, Enrique; Mitchell, Edward A. D.

doi:10.23818/limn.38.02

Cited by 8 publications

(2 citation statements)

References 24 publications

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“…Another promising gene for metabarcoding is the COI. This gene is conserved across most animals (Hebert et al, 2003) and is used for rotifers, where it largely outperforms the 18S rRNA gene in terms of taxonomic resolution (Fontaneto et al, 2019). COI is also a reference for soil microarthropods (Porter et al, 2019).…”

Section: Potential For Species-level Resolution In Eukaryotic Metabar...mentioning

confidence: 99%

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

Lara,

Geisen

2024

Preprint

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A major fraction of biodiversity on Earth resides in soils. This diversity consists of prokaryotes (bacteria and archaea) and eukaryotes (fungi, protists and metazoa). Especially the prokaryotic diversity is almost entirely studies using molecular tools, with a recent transfer also to eukaryotes.. Eukaryotes differ from prokaryotes in many additional characteristics such as genomic organization and mode of evolution, which together determine the methods to study their diversity. As such, approaches that have been designed for prokaryotes like environmental sequencing cannot simply be transferred to eukaryotes. Indeed, methodological and analytical differences between domains range from how the basic diversity units are measured to interpretation of community taxonomic composition and quantitative data. Jurburg et al. (“All together now: Limitations and recommendations for the simultaneous analysis of all eukaryotic soil sequences” Molecular Ecology Methods, 2021 https://doi.org/10.1111/1755-0998.13401) have highlighted some important eukaryote-specific technical issues that need consideration into account in DNA-based studies. We here highlight additional domain-specific considerations that should be taken into account in eukaryote-focused studies. Only that will allow to reliably and comprehensively unravel the entire eukaryotic biodiversity in soils.

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Section: Potential For Species-level Resolution In Eukaryotic Metabar...mentioning

confidence: 99%

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

Lara,

Geisen

2024

Preprint

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“…Another promising gene for metabarcoding is the COI. This gene is conserved across most animals (Hebert et al ., 2003 ) and is used for rotifers, where it largely outperforms the 18S rRNA gene in terms of taxonomic resolution (Fontaneto et al ., 2019 ). COI is also a reference for soil microarthropods (Porter et al ., 2019 ).…”

Section: Future Perspectives On Eukaryotic Metabarcoding In Soilsmentioning

confidence: 99%

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

Lara

Geisen

2022

Environmental Microbiology

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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.

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Metabarcoding Approaches for Soil Eukaryotes, Protists, and Microfauna

Lentendu

Lara

Geisen

2022

Microbial Environmental Genomics (MEG)

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We are ready for faunistic surveys of bdelloid rotifers through DNA barcoding: the example of Sphagnum bogs of the Swiss Jura Mountains

Cited by 8 publications

References 24 publications

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

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

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

Metabarcoding Approaches for Soil Eukaryotes, Protists, and Microfauna

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