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dc.contributor.authorEiler, Alexander
dc.contributor.authorDrakare, Stina
dc.contributor.authorBertilsson, Stefan
dc.contributor.authorPernthaler, Jakob
dc.contributor.authorPeura, Sari
dc.contributor.authorRofner, Carina
dc.contributor.authorSimek, Karel
dc.contributor.authorYang, Yang
dc.contributor.authorZnachor, Petr
dc.contributor.authorLindström, Eva S
dc.date.accessioned2014-01-09T09:22:02Z
dc.date.available2014-01-09T09:22:02Z
dc.date.issued2013
dc.identifier.citationEiler, A., Drakare, S., Bertilsson, S., Pernthaler, J., Peura, S., Rofner, C., Simek, K., Yang, Y., Znachor, P., & Lindström, E. S. (2013). Unveiling distribution patterns of freshwater phytoplankton by a next generation sequencing based approach. <i>PLOS ONE</i>, <i>8</i>(1). <a href="https://doi.org/10.1371/journal.pone.0053516" target="_blank">https://doi.org/10.1371/journal.pone.0053516</a>
dc.identifier.otherCONVID_22819330
dc.identifier.otherTUTKAID_57804
dc.identifier.urihttps://jyx.jyu.fi/handle/123456789/42771
dc.description.abstractThe recognition and discrimination of phytoplankton species is one of the foundations of freshwater biodiversity research and environmental monitoring. This step is frequently a bottleneck in the analytical chain from sampling to data analysis and subsequent environmental status evaluation. Here we present phytoplankton diversity data from 49 lakes including three seasonal surveys assessed by next generation sequencing (NGS) of 16S ribosomal RNA chloroplast and cyanobacterial gene amplicons and also compare part of these datasets with identification based on morphology. Direct comparison of NGS to microscopic data from three time-series showed that NGS was able to capture the seasonality in phytoplankton succession as observed by microscopy. Still, the PCR-based approach was only semi-quantitative, and detailed NGS and microscopy taxa lists had only low taxonomic correspondence. This is probably due to, both, methodological constraints and current discrepancies in taxonomic frameworks. Discrepancies included Euglenophyta and Heterokonta that were scarce in the NGS but frequently detected by microscopy and Cyanobacteria that were in general more abundant and classified with high resolution by NGS. A deep-branching taxonomically unclassified cluster was frequently detected by NGS but could not be linked to any group identified by microscopy. NGS derived phytoplankton composition differed significantly among lakes with different trophic status, showing that our approach can resolve phytoplankton communities at a level relevant for ecosystem management. The high reproducibility and potential for standardization and parallelization makes our NGS approach an excellent candidate for simultaneous monitoring of prokaryotic and eukaryotic phytoplankton in inland waters.fi
dc.language.isoeng
dc.publisherPublic Library of Science
dc.relation.ispartofseriesPLOS ONE
dc.relation.urihttp://www.plosone.org/article/authors/info%3Adoi%2F10.1371%2Fjournal.pone.0053516
dc.subject.otherkasviplankton
dc.subject.othersekvenssitietokanta
dc.subject.otherkloroplasti
dc.subject.othersinibakteerit
dc.subject.otherjärvi
dc.subject.otherribosomaalinen RNA
dc.subject.otherphytoplankton
dc.subject.othersequence databases
dc.subject.otherribosomal RNA
dc.titleUnveiling distribution patterns of freshwater phytoplankton by a next generation sequencing based approach
dc.typearticle
dc.identifier.urnURN:NBN:fi:jyu-201401081034
dc.contributor.laitosBio- ja ympäristötieteiden laitosfi
dc.contributor.laitosDepartment of Biological and Environmental Scienceen
dc.contributor.oppiaineAkvaattiset tieteetfi
dc.contributor.oppiaineAquatic Sciencesen
dc.type.urihttp://purl.org/eprint/type/JournalArticle
dc.date.updated2014-01-08T13:17:50Z
dc.type.coarjournal article
dc.description.reviewstatuspeerReviewed
dc.relation.issn1932-6203
dc.relation.numberinseries1
dc.relation.volume8
dc.type.versionpublishedVersion
dc.rights.copyright© 2013 Eiler et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
dc.rights.accesslevelopenAccessfi
dc.subject.ysoviherhiukkaset
dc.subject.ysosyanobakteerit
dc.subject.ysojärvet
jyx.subject.urihttp://www.yso.fi/onto/yso/p21157
jyx.subject.urihttp://www.yso.fi/onto/yso/p3324
jyx.subject.urihttp://www.yso.fi/onto/yso/p9374
dc.rights.urlhttp://creativecommons.org/licenses/by/3.0/
dc.relation.doi10.1371/journal.pone.0053516


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© 2013 Eiler et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
Except where otherwise noted, this item's license is described as © 2013 Eiler et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.