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
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| 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., more
- Ernst, A.
- Sabbe, K., editor, more
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| 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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