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Using quantitative PCR to determine the distribution Of a semicryptic benthic diatom, Navicula phyllepta (Bacillariophyceae)
Creach, V.; Ernst, A.; Sabbe, K.; Vanelslander, B.; Vyverman, W.; Stal, L.J. (2006). Using quantitative PCR to determine the distribution Of a semicryptic benthic diatom, Navicula phyllepta (Bacillariophyceae). J. Phycol. 42(5): 1142-1154. dx.doi.org/10.1111/j.1529-8817.2006.00268.x
In: Journal of Phycology. Blackwell Science: New York. ISSN 0022-3646; e-ISSN 1529-8817
Peer reviewed article  
Available in  Authors 
    Vlaams Instituut voor de Zee: Open Marine Archive 225690 [ download pdf ]
Keywords
    Acids > Organic compounds > Organic acids > Nucleic acids > DNA
    Algae > Diatoms
    Clones
    Physics > Mechanics > Dynamics > Sediment dynamics
    Sediments
    Spatial distribution
    Taxa > Species > Cosmopolite species
    Temporal variations > Periodic variations > Seasonal variations
    Water bodies > Coastal waters > Coastal landforms > Coastal inlets > Estuaries
    Bacillariophyceae [WoRMS]; Navicula phyllepta Kützing, 1844 [WoRMS]
    ANE, Netherlands, Westerschelde [Marine Regions]
    Brackish water
Author keywords
    diatoms; estuary; Navicula phyllepta; niche differentiation; real-time qPCR; semi-cryptic species
Authors  Top 
  • Creach, V.
  • Ernst, A.
  • Sabbe, K., editor
  • Vanelslander, B.
  • Vyverman, W.
  • Stal, L.J.
Abstract
    Evidence has accumulated during the last decade showing that many established diatom morpho-species actually consist of several semicryptic or truly cryptic species. As these species are difficult or even impossible to differentiate by microscopic analysis, there is virtually no information on how they behave in natural environments. In this study, we developed a quantitative real-time PCR (qPCR) assay using TaqMan probes® targeted to the internal transcribed spacer 1 (ITS1) to assess the spatial distribution and seasonal dynamics of an important component of the microphytobenthos of intertidal sediments. Navicula phyllepta Kützing is a brackish-marine morpho-species with a cosmopolitan distribution. Axenic clones of this species were isolated from natural assemblages of benthic diatoms at different intertidal stations in the Westerschelde estuary (The Netherlands). At least two distinct semicryptic species of N. phyllepta were present, as shown by differences in the quantity of DNA per cell, the ITS1 sequences and the copy number of ITS per cell. DNA and chl a concentrations extracted from sediment surface samples were closely correlated, showing that the DNA used for subsequent analysis mostly belonged to the microalgal community. The results of real-time qPCR from sites throughout the estuary and over several seasons agreed well with microscopic counts. Additionally, the seasonal pattern of the two forms of N. phyllepta showed an overlapping, but unique distribution along the estuary.
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