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Applied and Environmental Microbiology, September 2008, p. 5305-5316, Vol. 74, No. 17
0099-2240/08/$08.00+0     doi:10.1128/AEM.01271-08
Copyright © 2008, American Society for Microbiology. All Rights Reserved.

Feasibility of Assessing the Community Composition of Prasinophytes at the Helgoland Roads Sampling Site with a DNA Microarray{triangledown}

Christine Gescher,1,{dagger}* Katja Metfies,3,{dagger} Stephan Frickenhaus,1 Britta Knefelkamp,2 Karen H. Wiltshire,2 and Linda K. Medlin4

Alfred Wegener Institute for Polar and Marine Research, Am Handelshafen 12, 27570 Bremerhaven, Germany,1 Alfred Wegener Institute for Polar and Marine Research (BAH), Kurpromenade, 27498 Helgoland, Germany,2 GKSS Research Centre, Max Planck Strasse 1, 21502 Geesthacht, Germany,3 Marine Biological Association of the United Kingdom, The Laboratory Citadel Hill, Plymouth PL1 2PB, United Kingdom4

Received 8 June 2008/ Accepted 4 July 2008

The microalgal class Prasinophyceae (Chlorophyta) contains several picoeukaryotic species, which are known to be common in temperate and cold waters and have been observed to constitute major fractions of marine picoplankton. However, reliable detection and classification of prasinophytes are mainly hampered by their small size and few morphological markers. Consequently, very little is known about the abundance and ecology of the members of this class. In order to facilitate the assessment of the abundance of the Prasinophyceae, we have designed and evaluated an 18S rRNA gene-targeted oligonucleotide microarray consisting of 21 probes targeting different taxonomic levels of prasinophytes. The microarray contains both previously published probes from other hybridization methods and new probes, which were designed for novel prasinophyte groups. The evaluation of the probe set was done under stringent conditions with 18S PCR fragments from 20 unialgal reference cultures used as positive targets. This microarray has been applied to assess the community composition of prasinophytes at Helgoland, an island in the North Sea where time series data are collected and analyzed daily but only for the nano- and microplankton-size fractions. There is no identification of prasinophytes other than to record them numerically in the flagellate fraction. The samples were collected every 2 weeks between February 2004 and December 2006. The study here demonstrates the potential of DNA microarrays to be applied as a tool for quick general monitoring of this important picoplanktonic algal group.

* Corresponding author. Mailing address: Nettelbeckstr. 4, 26131 Oldenburg, Germany. Phone: 49 441 3091430. E-mail: Christine.Gescher{at}web.de

{triangledown} Published ahead of print on 11 July 2008.

{dagger} These authors contributed equally to this publication.

Applied and Environmental Microbiology, September 2008, p. 5305-5316, Vol. 74, No. 17
0099-2240/08/$08.00+0     doi:10.1128/AEM.01271-08
Copyright © 2008, American Society for Microbiology. All Rights Reserved.





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