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ZPS7 InfoHub

Links to data, tools, and other useful resources
for plankton and ecosystem research.

This page was created to support workshop W02 "Today I Learned: Useful tools and data resources that every researcher should know" being held at the 7th Zooplankton Production Symposium (Tasmania, March 17-23, 2024).

As work continues on this page, we will improve the aesthetics and features of this webpage.

"Today I Learned" Submitted Content:
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    MetaZooGene Atlas & Database

    The MZGdb summarizes the presence and barcoding status of major marine fauna and flora groups and species, reported-by geographic regions, oceans, and seas (e.g., "North Atlantic pteropods", "Arctic pinnipeds", "Mediterranean Sea decapods"). The MZGdb also lets the user download data from any of these taxonomic/geographic subsets, which can help reduce sequence matching and processing times.

    The Biological Ocean Observer

    An online portal for visualization of IMOS data.

    Plankton Lifeform Extraction Tool

    A tool for exploring northeast North Atlantic plankton data and time series.


    KRILLBASE is a data rescue and compilation project which aims to improve the availability of information on two of the Southern Ocean's most important zooplankton taxa: Antarctic krill (Euphausia superba) and salps (Family Salpidae).

    COPEPOD: A global plankton database

      [ DATA | TOOL | INFO ]     2024-03-14-002

      Contact:   Todd O'Brien

    COPEPOD's global plankton database component provides plankton and ecosystem researchers with an integrated data set of quality-reviewed, globally distributed plankton abundance, biomass and composition data. Its visual, interactive interface is designed to help the user see exactly what data are currently available and then download them in a variety of usable formats and compilations. In addition to data distribution maps, COPEPOD offers a variety of text and graphical content summaries and searching options.

    COPEPODITE: The Interactive Time Series Explorer

    COPEPOD's Interactive Time-series Explorer (COPEPODITE) was born from a compilation of time series analysis tools and graphical visualizations developed in support of ICES and SCOR plankton time series working groups (e.g. ICES WGZE and WGPME, SCOR WG125 and WG137). These tools were used to pursue the working groups' research as well as to produce the ICES Plankton Status Report series for the North Atlantic. As work progressed, more and more tools were added to the toolkit, and more and more outside parties requested access to making similar figures for their own work. An online processing and plotting interface was developed, and COPEPODITE was born.

    Miller 2023: Oar Feet and Opal Teeth: About Copepods and Copepodologists

      [ PUBLICATION | INFO ]     2024-01-10-003

      URL/DOI/Ref:   Google "Oar Feet and Opal Teeth" for book sellers.

    Oar Feet and Opal Teeth is about free-living copepods and the copepodologists who study them. Copepods are a subclass of the arthropod class Crustacea. They act as dominant herbivores and small predators in the planktonic ecosystems of oceans, estuaries, and lakes. Copepods are likely the largest assemblage of complex animals on earth. These strikingly beautiful small crustaceans are of wide ecological significance and as complex and precisely adapted as insects. Yet few biologists and others interested in animals are familiar with them. In Oar Feet and Opal Teeth, Charles B. Miller introduces these small crustaceans and the scientists devoting their careers to revealing their biology. In twenty-one chapters, Miller details the defining features and general biology of copepods. They typically have four or five pairs of oar-like feet to drive escape jumps. Teeth on mandible extensions are formed with siliceous minerals akin to opal. The first two chapters of the book closely examine the oar feet and mouth parts. Subsequent chapters describe internal anatomy, taxonomy, and many aspects of copepod natural history. Recent evolutionary insights about them are reviewed; those are based on molecular genetics and reach back to the Cambrian explosion.

    Atkinson et al 2023: Steeper size spectra with decreasingphytoplankton biomass indicate strongtrophic amplification and future fish declines

      [ PUBLICATION | INFO ]     2024-01-10-002

      Contact:   Angus Atkinson

    Steeper size spectra with decreasingphytoplankton biomass indicate strongtrophic amplification and future fish declines. Atkinson et al. 2023 Under climate change, model ensembles suggest that declines in phyto-plankton biomass amplify into greater reductions at higher trophic levels, withserious implications for fisheries and carbon storage. However, the extent andmechanisms of this trophic amplification vary greatly among models, andvalidation is problematic. In situ size spectra offer a novel alternative, com-paring biomass of small and larger organisms to quantify the net efficiency ofenergy transfer through natural food webs that are already challenged withmultiple climate change stressors. Our global compilation of pelagic sizespectrum slopes supports trophic amplification empirically, independentlyfrom model simulations. Thus, even a modest (16%) decline in phytoplanktonthis century would magnify into a 38% decline in supportable biomass of fishwithin the intensively-fished mid-latitude ocean. We also show that thisamplification stems not from thermal controls on consumers, but mainly fromtemperature or nutrient controls that structure the phytoplankton baseline ofthe food web. The lack of evidence for direct thermal effects on size structurecontrasts with most current thinking, based often on more acute stressexperiments or shorter-timescale responses. Our synthesis of size spectraintegrates these short-term dynamics, revealing the net efficiency of foodwebs acclimating and adapting to climatic stressors.

    McEvoy et al 2023: The Western Channel Observatory: a century of physical, chemical and biological data compiled from pelagic and benthic habitats in the western English Channel

    The Western Channel Observatory: a century of physical, chemical and biological data compiled from pelagic and benthic habitats in the western English Channel. McEvoy et al 2023. The Western Channel Observatory (WCO) comprises a series of pelagic, benthic and atmospheric sampling sites within 40 km of Plymouth, UK, that have been sampled by the Plymouth institutes on a regular basis since 1903. This longevity of recording and the high frequency of observations provide a unique combination of data; for example temperature data were first collected in 1903, and the reference station L4, where nearly 400 planktonic taxa have been enumerated, has been sampled on a weekly basis since 1988. While the component datasets have been archived, here we provide the first summary database bringing together a wide suite of the observations. This provides monthly average values of some of the key pelagic and benthic measurements for the inshore site L4, the offshore site E1 and the intermediate L5 site. In brief, these data include the following: water temperature (from 1903); macronutrients (from 1934); dissolved inorganic carbon and total alkalinity (from 2008); methane and nitrous oxide (from 2011); chlorophyll a (from 1992); high-performance liquid chromatography (HPLC)-derived pigments (from 1999); <20 um plankton by flow cytometry, including bacteria (8 functional groups from 2007); phytoplankton by microscopy (6 functional groups from 1992); microplankton and mesozooplankton from FlowCam (6 groups from 2012); Noctiluca sp. dinoflagellate (from 1997); mesozooplankton by microscopy (8 groups from 1988); Calanus helgolandicus egg production rates (from 1992); fish larvae from the Young Fish Trawl survey (4 groups from 1924); benthic macrofauna (4 groups from 2008); demersal fish (19 families from 2008); blue shark, Prionace glauca (from 1958); and 16S alpha diversity for sediment and water column (from 2012). These data have varying coverage with respect to time and depth resolution. The metadata tables describe each dataset and provide pointers to the source data and other related Western Channel Observatory datasets and outputs not compiled here. We provide summaries of the main trends in seasonality and some major climate-related shifts that have been revealed over the last century. The data are available from the Data Archive for Seabed Species and Habitats (DASSH): (McEvoy and Atkinson, 2023). Making these data fully accessible and including units of both abundance and biomass will stimulate a variety of uptakes. These may include uses as an educational resource for projects, for models and budgets, for the analysis of seasonality and long-term change in a coupled benthicpelagic system, or for supporting UK and north-eastern Atlantic policy and management.