Shape matters: The relationship between cell geometry and diversity in phytoplankton
Ryabov, Alexey et al. (2021), Shape matters: The relationship between cell geometry and diversity in phytoplankton, Dryad, Dataset, https://doi.org/10.5061/dryad.r7sqv9sb6
We compiled the most comprehensive data set of phytoplankton and other marine protists in terms of sizes, shapes, genus, and species names. Samples were obtained from seven globally distributed marine areas: Baltic Sea, North Atlantic (Scotland), Mediterranean Sea (Greece and Turkey), Indo-Pacific (the Maldives), South-western Pacific (Australia), Southern Atlantic (Brazil).
See details in Ryabov et al Ecology Letters 'Shape matters: the relationship between cell geometry and diversity in phytoplankton', https://doi.org/10.1111/ele.13680
6Regions_Original.xlsx and BalticSea_Original.xlsx include genus and species names, linear dimenstions and identified shapes of phytoplankton cells
Baltic+6Regions_genera_sizes.xlsx calculated surface, volume and other geometric characteristis for both original datasets
the data is aggregated by Genus, Site and Shape.
See details in: Ryabov et al Ecology Letters 'Shape matters: the relationship between cell geometry and diversity in phytoplankton'
The data sources include two datasets. The first dataset represents the results of monitoring in several stations in Baltic Sea over the past 25 years (with interval 1-2 months from May to November) and contains information on phytoplankton species and heterotrophic dinoflagellates covering a total of 308 genera. The second dataset includes a biogeographical snapshot survey of phytoplankton assemblages obtained by Ecology Unit of Salento University performed during summer in 2011 and 2012 in six coastal areas with different biogeographical conditions (ecoregions) around the globe (Roselli et al. 2017). This survey included 3 concurrent data replicas from each of 116 local sites. This data covers a total of 193 genera sampled from 23 ecosystems of different typology (coastal lagoons, estuaries, coral reefs, mangroves and inlets or silled basins). The data used in this study are available online (ICES CEIM; LifeWatch ERIC), see also Data availability for the data included in manuscript submission.
Sampling methods and dataset description
The measurements for the Baltic dataset were done by the HELCOM Phytoplankton Expert Group (PEG), and described in more detail by Olenina et al. (2006). The phytoplankton samples were taken in accordance with the guidelines of HELCOM (1988) as integrated samples from surface 0-10, or 0-20 m water layers, using either a rosette sampler (pooling equal water volumes from discrete depths: 1; 2,5; 5; 7,5 and 10 m) or a sampling hose. The samples were preserved with acid Lugol’s solution (Willén 1962). The inverted microscope technique (Utermöhl 1958) was used for identification of the phytoplankton species. After concentration in a sedimentation 10-, 25-, or 50-ml chamber, phytoplankton cells were measured for the further determination of species-specific shape and linear dimensions. All measurements were performed under high microscope magnification (400–945 times) using an ocular scale.
The second dataset includes the results of sampling of three to nine ecosystems per ecoregion and three locations for each system, yielding a total of 116 local sites replicated three times. Phytoplankton were collected with a 6 μm mesh plankton net equipped with a flow meter for determining filtered volume. Water samples for phytoplankton quantitative analysis were preserved with Lugol (15 mL/L of sample). Phytoplankton were examined following Utermöhl (1958). Phytoplankton were analysed by inverted microscope (Nikon T300E, Nikon Eclipse Ti) connected to a video-interactive image analysis system (L.U.C.I.A Version 4.8, Laboratory Imaging). Taxonomic identification and linear dimension measurements were performed at individual level on 400 phytoplankton cells for each sample. Overall, the data on 142 800 cells are included. The data on the dimensions of the same species were averaged for each replicate.
If you use this data please cite some of the following papers
- Ryabov et al Ecology Letters 'Shape matters: the relationship between cell geometry and diversity in phytoplankton'
- Olenina, I., Hajdu, S., Edler, L., Andersson, A., Wasmund, N., Busch, S., et al. (2006). Biovolumes and size-classes of phytoplankton in the Baltic Sea. HELCOM Balt.Sea Environ. Proc., 106.
- Roselli, L., Litchman, E., Elena, S., Cozzoli, F. & Basset, A. (2017). Individual trait variation in phytoplankton communities across multiple spatial scales. J. Plankton Res., 39, 577–588.
If you need to calculate surface area and volume, you can use MATLAB and Phyton scripts from: https://github.com/AlexRyabov/Cell-shape
Ask email@example.com, if you need a Julia or R script for that.
Regione Puglia, Award: PS126 'PhytoBioImaging'
Deutsche Forschungsgemeinschaft, Award: KE 1970/1‐1
Deutsche Forschungsgemeinschaft, Award: KE 1970/2‐1
Deutsche Forschungsgemeinschaft, Award: BL 772/6‐1
Niedersächsisches Ministerium für Wissenschaft und Kultur, Award: POSER