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dc.contributor.authorVuorio, Kristiina
dc.contributor.authorMäki, Anita
dc.contributor.authorSalmi, Pauliina
dc.contributor.authorAalto, Sanni L.
dc.contributor.authorTiirola, Marja
dc.date.accessioned2020-03-11T09:20:39Z
dc.date.available2020-03-11T09:20:39Z
dc.date.issued2020
dc.identifier.citationVuorio, K., Mäki, A., Salmi, P., Aalto, S. L., & Tiirola, M. (2020). Consistency of Targeted Metatranscriptomics and Morphological Characterization of Phytoplankton Communities. <i>Frontiers in Microbiology</i>, <i>11</i>, Article 96. <a href="https://doi.org/10.3389/fmicb.2020.00096" target="_blank">https://doi.org/10.3389/fmicb.2020.00096</a>
dc.identifier.otherCONVID_34940552
dc.identifier.urihttps://jyx.jyu.fi/handle/123456789/68134
dc.description.abstractThe composition of phytoplankton community is the basis for environmental monitoring and assessment of the ecological status of aquatic ecosystems. Community composition studies of phytoplankton have been based on time-consuming and expertise-demanding light microscopy analyses. Molecular methods have the potential to replace microscopy, but the high copy number variation of ribosomal genes and the lack of universal primers for simultaneous amplification of prokaryotic and eukaryotic genes complicate data interpretation. In this study, we used our previously developed directional primer-independent high-throughput sequencing (HTS) approach to analyze 16S and 18S rRNA community structures. Comparison of 83 boreal lake samples showed that the relative abundances of eukaryotic phytoplankton at class level and prokaryotic cyanobacteria at order level were consistent between HTS and microscopy results. At the genus level, the results had low correspondence, mainly due to lack of sequences in the reference library. HTS was superior to identify genera that are extensively represented in the reference databases but lack specific morphological characteristics. Targeted metatranscriptomics proved to be a feasible method to complement the microscopy analysis. The metatranscriptomics can also be applied without linking the sequences to taxonomy. However, direct indexing of the sequences to their environmental indicator values needs collections of more comprehensive sample sets, as long as the coverage of molecular barcodes of eukaryotic species remains insufficient.en
dc.format.mimetypeapplication/pdf
dc.languageeng
dc.language.isoeng
dc.publisherFrontiers Media
dc.relation.ispartofseriesFrontiers in Microbiology
dc.rightsCC BY 4.0
dc.subject.otherfreshwater
dc.subject.otherhigh-throughput sequencing
dc.subject.othermicroscopy
dc.subject.otherphytoplankton
dc.subject.otherribosomal RNA
dc.titleConsistency of Targeted Metatranscriptomics and Morphological Characterization of Phytoplankton Communities
dc.typearticle
dc.identifier.urnURN:NBN:fi:jyu-202003112370
dc.contributor.laitosBio- ja ympäristötieteiden laitosfi
dc.contributor.laitosDepartment of Biological and Environmental Scienceen
dc.contributor.oppiaineYmpäristötiedefi
dc.contributor.oppiaineAkvaattiset tieteetfi
dc.contributor.oppiaineEnvironmental Scienceen
dc.contributor.oppiaineAquatic Sciencesen
dc.type.urihttp://purl.org/eprint/type/JournalArticle
dc.description.reviewstatuspeerReviewed
dc.relation.issn1664-302X
dc.relation.volume11
dc.type.versionpublishedVersion
dc.rights.copyright© 2020 the Authors
dc.rights.accesslevelopenAccessfi
dc.relation.grantnumber615146
dc.relation.grantnumber615146
dc.relation.projectidinfo:eu-repo/grantAgreement/EC/FP7/615146/EU//
dc.subject.ysomorfologia
dc.subject.ysomikroskopia
dc.subject.ysosyanobakteerit
dc.subject.ysosekvensointi
dc.subject.ysoRNA
dc.subject.ysomikrolevät
dc.subject.ysoplankton
dc.format.contentfulltext
jyx.subject.urihttp://www.yso.fi/onto/yso/p1524
jyx.subject.urihttp://www.yso.fi/onto/yso/p16290
jyx.subject.urihttp://www.yso.fi/onto/yso/p3324
jyx.subject.urihttp://www.yso.fi/onto/yso/p25917
jyx.subject.urihttp://www.yso.fi/onto/yso/p7689
jyx.subject.urihttp://www.yso.fi/onto/yso/p26977
jyx.subject.urihttp://www.yso.fi/onto/yso/p3053
dc.rights.urlhttps://creativecommons.org/licenses/by/4.0/
dc.relation.doi10.3389/fmicb.2020.00096
dc.relation.funderEuroopan komissiofi
dc.relation.funderEuropean Commissionen
jyx.fundingprogramEU:n 7. puiteohjelma (FP7)fi
jyx.fundingprogramFP7 (EU's 7th Framework Programme)en
jyx.fundinginformationThe study was funded by the Academy of Finland, projects 260797 (RNA-unit) awarded to MT and 311229 (MiDAS) awarded to KV and by the European Research Council (ERC) grant awarded to MT under the European Union’s Seventh Framework Programme (FP/2007-2013, grant agreement No. 615146).


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