Universität zu Köln

Fiore-Donno, Anna Maria ORCID: 0000-0001-6265-1907, Rixen, Christian, Rippin, Martin, Glaser, Karin, Samolov, Elena, Karsten, Ulf, Becker, Burkhard ORCID: 0000-0002-7965-1396 and Bonkowski, Michael (2018). New barcoded primers for efficient retrieval of cercozoan sequences in high-throughput environmental diversity surveys, with emphasis on worldwide biological soil crusts. Mol. Ecol. Resour., 18 (2). S. 229 - 240. HOBOKEN: WILEY. ISSN 1755-0998

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Abstract

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 hypervariable 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 (c. 350bp) 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 grassland 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 operational taxonomic units (OTUs) at 97% similarity threshold from 26 samples, with c. 50,000 sequences per site, and only 8% of noncercozoan sequences. We could report a further increase in the diversity of Cercozoa, as 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.

Item Type:	Journal Article
Creators:	Creators Email ORCID ORCID Put Code Fiore-Donno, Anna Maria UNSPECIFIED orcid.org/0000-0001-6265-1907 UNSPECIFIED Rixen, Christian UNSPECIFIED UNSPECIFIED UNSPECIFIED Rippin, Martin UNSPECIFIED UNSPECIFIED UNSPECIFIED Glaser, Karin UNSPECIFIED UNSPECIFIED UNSPECIFIED Samolov, Elena UNSPECIFIED UNSPECIFIED UNSPECIFIED Karsten, Ulf UNSPECIFIED UNSPECIFIED UNSPECIFIED Becker, Burkhard UNSPECIFIED orcid.org/0000-0002-7965-1396 UNSPECIFIED Bonkowski, Michael UNSPECIFIED UNSPECIFIED UNSPECIFIED
URN:	urn:nbn:de:hbz:38-193549
DOI:	10.1111/1755-0998.12729
Journal or Publication Title:	Mol. Ecol. Resour.
Volume:	18
Number:	2
Page Range:	S. 229 - 240
Date:	2018
Publisher:	WILEY
Place of Publication:	HOBOKEN
ISSN:	1755-0998
Language:	English
Faculty:	Faculty of Mathematics and Natural Sciences
Divisions:	Faculty of Mathematics and Natural Sciences > Department of Biology > Botanical Institute
Subjects:	no entry
Uncontrolled Keywords:	Keywords Language TESTATE AMEBAS; REVEALS; PHYLOGENY; COMMUNITY; RHIZARIA; PROTOZOA; PARASITES; PROTISTS; AMPLIFICATION; BIODIVERSITY Multiple languages Biochemistry & Molecular Biology; Ecology; Evolutionary Biology Multiple languages
Refereed:	Yes
URI:	http://kups.ub.uni-koeln.de/id/eprint/19354