Universität zu Köln

Geisen, S., Laros, I., Vizcaino, A., Bonkowski, M. and De Groot, G. A. (2015). Not all are free-living: high-throughput DNA metabarcoding reveals a diverse community of protists parasitizing soil metazoa. Mol. Ecol., 24 (17). S. 4556 - 4570. HOBOKEN: WILEY. ISSN 1365-294X

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Abstract

Protists, the most diverse eukaryotes, are largely considered to be free-living bacterivores, but vast numbers of taxa are known to parasitize plants or animals. High-throughput sequencing (HTS) approaches now commonly replace cultivation-based approaches in studying soil protists, but insights into common biases associated with this method are limited to aquatic taxa and samples. We created a mock community of common free-living soil protists (amoebae, flagellates, ciliates), extracted DNA and amplified it in the presence of metazoan DNA using 454 HTS. We aimed at evaluating whether HTS quantitatively reveals true relative abundances of soil protists and at investigating whether the expected protist community structure is altered by the co-amplification of metazoan-associated protist taxa. Indeed, HTS revealed fundamentally different protist communities from those expected. Ciliate sequences were highly over-represented, while those of most amoebae and flagellates were under-represented or totally absent. These results underpin the biases introduced by HTS that prevent reliable quantitative estimations of free-living protist communities. Furthermore, we detected a wide range of nonadded protist taxa probably introduced along with metazoan DNA, which altered the protist community structure. Among those, 20 taxa most closely resembled parasitic, often pathogenic taxa. Therewith, we provide the first HTS data in support of classical observational studies that showed that potential protist parasites are hosted by soil metazoa. Taken together, profound differences in amplification success between protist taxa and an inevitable co-extraction of protist taxa parasitizing soil metazoa obscure the true diversity of free-living soil protist communities. See also the Perspective by Wegener Parfrey

Item Type:	Journal Article
Creators:	Creators Email ORCID ORCID Put Code Geisen, S. UNSPECIFIED UNSPECIFIED UNSPECIFIED Laros, I. UNSPECIFIED UNSPECIFIED UNSPECIFIED Vizcaino, A. UNSPECIFIED UNSPECIFIED UNSPECIFIED Bonkowski, M. UNSPECIFIED UNSPECIFIED UNSPECIFIED De Groot, G. A. UNSPECIFIED UNSPECIFIED UNSPECIFIED
URN:	urn:nbn:de:hbz:38-395744
DOI:	10.1111/mec.13238
Journal or Publication Title:	Mol. Ecol.
Volume:	24
Number:	17
Page Range:	S. 4556 - 4570
Date:	2015
Publisher:	WILEY
Place of Publication:	HOBOKEN
ISSN:	1365-294X
Language:	English
Faculty:	Unspecified
Divisions:	Unspecified
Subjects:	no entry
Uncontrolled Keywords:	Keywords Language GREGARINES APICOMPLEXA; LEVEL CLASSIFICATION; IDENTIFICATION; ACANTHAMOEBA; PROTOZOA; AMEBAS; SPP.; RDNA; BIODIVERSITY; POPULATIONS Multiple languages Biochemistry & Molecular Biology; Ecology; Evolutionary Biology Multiple languages
URI:	http://kups.ub.uni-koeln.de/id/eprint/39574