New barcoded primers for efficient retrieval of cercozoan sequences in high-throughput environmental diversity surveys, with emphasis on worldwide biological soil crusts Article Swipe
Anna Maria Fiore‐Donno
,
Christian Rixen
,
Martin Rippin
,
Karin Glaser
,
Elena Samolov
,
Ulf Karsten
,
Burkhard Becker
,
Michael Bonkowski
·
YOU?
·
· 2017
· Open Access
·
· DOI: https://doi.org/10.1101/171611
YOU?
·
· 2017
· Open Access
·
· DOI: https://doi.org/10.1101/171611
We describe the performance of a new metabarcoding approach to investigate the environmental diversity of a prominent group of widespread unicellular organisms, the Cercozoa. Cercozoa is an immensely large group of protists and although it may dominate in soil and aquatic ecosystems, its environmental diversity remains undersampled. We designed PCR primers targeting the hyper-variable region V4 of the small subunit ribosomal RNA (SSU or 18S) gene, which is the recommended barcode marker for Cercozoa. The length of the amplified fragment (ca. 350 bp) is suitable for Illumina MiSeq, the most cost-effective platform for molecular environmental surveys. We provide barcoded primers, an economical alternative to multiple libraries for multiplex sequencing of over a hundred samples. In silico , our primers matched 68% of the cercozoan sequences of the reference database and performed better than previously proposed new generation sequencing primers. In mountain grasslands soils and in biological soil crusts from a variety of climatic regions, we were able to detect cercozoan sequences encompassing nearly the whole range of the phylum. We obtained 901 OTUs at 97% similarity threshold from 26 samples, with ca. 50,000 sequences per site, and only 8% of non-cercozoan sequences. We could contribute to a further increase of the diversity of Cercozoa, since only 43% of the OTUs were 97-100% similar to any known sequence. Our study thus provides an advanced tool for cercozoan metabarcoding and to investigate their diversity and distribution in the environment.
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Metadata
- Type
- preprint
- Language
- en
- Landing Page
- https://doi.org/10.1101/171611
- https://www.biorxiv.org/content/biorxiv/early/2017/08/02/171611.full.pdf
- OA Status
- green
- Cited By
- 9
- References
- 60
- Related Works
- 10
- OpenAlex ID
- https://openalex.org/W2742059377
All OpenAlex metadata
Raw OpenAlex JSON
- OpenAlex ID
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https://openalex.org/W2742059377Canonical identifier for this work in OpenAlex
- DOI
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https://doi.org/10.1101/171611Digital Object Identifier
- Title
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New barcoded primers for efficient retrieval of cercozoan sequences in high-throughput environmental diversity surveys, with emphasis on worldwide biological soil crustsWork title
- Type
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preprintOpenAlex work type
- Language
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enPrimary language
- Publication year
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2017Year of publication
- Publication date
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2017-08-02Full publication date if available
- Authors
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Anna Maria Fiore‐Donno, Christian Rixen, Martin Rippin, Karin Glaser, Elena Samolov, Ulf Karsten, Burkhard Becker, Michael BonkowskiList of authors in order
- Landing page
-
https://doi.org/10.1101/171611Publisher landing page
- PDF URL
-
https://www.biorxiv.org/content/biorxiv/early/2017/08/02/171611.full.pdfDirect link to full text PDF
- Open access
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YesWhether a free full text is available
- OA status
-
greenOpen access status per OpenAlex
- OA URL
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https://www.biorxiv.org/content/biorxiv/early/2017/08/02/171611.full.pdfDirect OA link when available
- Concepts
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Environmental DNA, Biology, In silico, Barcode, Computational biology, Phylum, Multiplex, DNA sequencing, Ribosomal RNA, Evolutionary biology, Ecology, Biodiversity, Gene, Genetics, Computer science, Operating systemTop concepts (fields/topics) attached by OpenAlex
- Cited by
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9Total citation count in OpenAlex
- Citations by year (recent)
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2024: 1, 2023: 1, 2021: 2, 2020: 2, 2019: 2Per-year citation counts (last 5 years)
- References (count)
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60Number of works referenced by this work
- Related works (count)
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10Other works algorithmically related by OpenAlex
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