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Euringer, K. ; Lüders, T.

An optimised PCR/T-RFLP fingerprinting approach for the investigation of protistan communities in groundwater environments.

J. Microbiol. Methods 75, 262-268 (2008)
DOI
Open Access Green as soon as Postprint is submitted to ZB.
Due to the scarcity or complete absence of higher organisms, protists may represent an important higher trophic level (above Prokaryotes) in the food webs of groundwater habitats. Nevertheless, the importance of aquifer protists, especially in contaminated groundwater environments, is poorly understood. Partly, this may be due to a lack of adequate PCR and fingerprinting approaches for protists in aquifers, which can be considered low in protistan or high in non-target rRNA gene copy numbers. Therefore, we have validated the suitability of distinct eukaryote-targeted primer pairs and restriction endonucleases for T-RFLP fingerprinting of protistan communities. By in silico predictions, and by fingerprinting, cloning and sequencing of microeukaryote amplicons from hydrocarbon-contaminated aquifer sediment DNA, we show that the Euk20f/Euk516r primer set in combination with Bsh1236I digestion is best suited for the recovery of diverse protistan 18S rRNA lineages. In contrast to other tested primer sets, a preferred recovery of fungal and archaeal non-target amplicons was not observed. In summary, we present an optimised microeukaryote-targeted PCR/T-RFLP fingerprinting approach which may be of value for the characterisation of protistan communities in groundwater and other habitats.
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Publication type Article: Journal article
Document type Scientific Article
Keywords Aquifer microbes; Groundwater protests; T-RFLP fingerprinting; 18S rRNA genes; PCR selection
ISSN (print) / ISBN 0167-7012
e-ISSN 1872-8359
Journal Journal of Microbiological Methods
Quellenangaben Volume: 75, Issue: 2, Pages: 262-268 Article Number: , Supplement: ,
Publisher Elsevier
Publishing Place Amsterdam
Reviewing status Peer reviewed
Institute(s) Institute of Groundwater Ecology (IGOE)