Molecular identification of diatoms (Bacillariophyta): development of markers and their application to marine benthic and planktonic diatoms in Canada

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University of New Brunswick


Diatoms are the largest, most successful group of microalgae whose diversity is not well described (only ⁓ 25,000 of 200,000 potential species have been described). Morphological identification of diatoms is difficult, relying primarily on features whose genetic basis is not well known, but a molecular technique, DNA barcoding, may assist diatom identification. The goals of this dissertation were: to test the 5' end of the cytochrome c oxidase I gene (COI-5P) as a barcode marker for diatoms and develop alternative marker(s) if necessary; to use these markers to explore the diversity of marine tube-forming diatoms in Canada; and to estimate the species richness of two widespread, species-rich genera (Chaetoceros and Thalassiosira) in the Bay of Fundy. The COI-5P could distinguish diatom species, but did not display universality (i.e., successful PCR amplification). Four alternative markers were tested including: ⁓ 1400 bp of the RUBISCO large subunit (rbcL); 748 bp at the 3' end of the rbcL (rbcL-3P); the variable D2/D3 region of the large ribosomal subunit DNA (LSU D2/D3); and the universal plastid amplicon (UPA). The rbcL-3P and LSU D2/D3 were chosen as the best primary and secondary barcode markers, respectively. These markers, in addition to a third marker (the internal transcribed spacer 2; ITS2), were used to examine the diversity of marine tube-forming diatoms in Canadian waters. By comparing data from these three markers, unexpected diversity (14 genetic species based on rbcL-3P data) and extensive cohabitation among multiple genetic lines of the Berkeleya rutilans species complex was uncovered. In addition, rbcL-3P and LSU D2/D3 regions were utilized for a molecular-based survey to estimate the species richness of Chaetoceros and Thalassiosira in the Bay of Fundy. Molecular methods uncovered nine cryptic species pairs and four overlooked species that were missed during a routine morphology-based survey. The relative merits of morphology versus molecular-based monitoring methodologies for planktonic diatoms are discussed.