Search for: All records

The recent development of biological sensors has extended marine plankton studies from conducting laboratory bench work to in vivo and real-time observations. Flow cytometry (FCM) has shed new light on marine microorganisms since the 1980s through its single-cell approach and robust detection of the smallest cells. FCM records valuable optical properties of light scattering and fluorescence from cells passing in a single file in front of a narrow-collimated light source, recording tens of thousands of cells within a few minutes. Depending on the instrument settings, the sampling strategy, and the automation level, it resolves the spatial and temporal distribution of microbial marine prokaryotes and eukaryotes. Cells are usually classified and grouped on cytograms by experts and are still lacking standards, reducing data sharing capacities. Therefore, the need to make FCM data sets FAIR (Findability, Accessibility, Interoperability, and Reusability of digital assets) is becoming critical. In this paper, we present a consensus vocabulary for the 13 most common marine microbial groups observed with FCM using blue and red-light excitation. The authors designed a common layout on two-dimensional log-transformed cytograms reinforced by a decision tree that facilitates the characterization of groups. The proposed vocabulary aims at standardising data analysis and definitions, to promote harmonisation and comparison of data between users and instruments. This represents a much-needed step towards FAIRification of flow cytometric data collected in various marine environments. 

Abstract. Plankton form the base of the marine food web and are sensitive indicatorsof environmental change. Plankton time series are therefore an essentialpart of monitoring progress towards global biodiversity goals, such as theConvention on Biological Diversity Aichi Targets, and for informingecosystem-based policy, such as the EU Marine Strategy Framework Directive.Multiple plankton monitoring programmes exist in Europe, but differences insampling and analysis methods prevent the integration of their data,constraining their utility over large spatio-temporal scales. The PlanktonLifeform Extraction Tool brings together disparate European planktondatasets into a central database from which it extracts abundancetime series of plankton functional groups, called “lifeforms”, according toshared biological traits. This tool has been designed to make complexplankton datasets accessible and meaningful for policy, public interest, andscientific discovery. It allows examination of large-scale shifts inlifeform abundance or distribution (for example, holoplankton beingpartially replaced by meroplankton), providing clues to how the marineenvironment is changing. The lifeform method enables datasets with differentplankton sampling and taxonomic analysis methodologies to be used togetherto provide insights into the response to multiple stressors and robustpolicy evidence for decision making. Lifeform time series generated with thePlankton Lifeform Extraction Tool currently inform plankton and food webindicators for the UK's Marine Strategy, the EU's Marine Strategy FrameworkDirective, and for the Convention for the Protection of the MarineEnvironment of the North-East Atlantic (OSPAR) biodiversity assessments.The Plankton Lifeform Extraction Tool currently integrates 155 000 samples,containing over 44 million plankton records, from nine different planktondatasets within UK and European seas, collected between 1924 and 2017.Additional datasets can be added, and time series can be updated. The PlanktonLifeform Extraction Tool is hosted by The Archive for Marine Species andHabitats Data (DASSH) at https://www.dassh.ac.uk/lifeforms/ (last access: 22 November 2021, Ostle et al., 2021). The lifeform outputs are linked to specific, DOI-ed, versions of thePlankton Lifeform Traits Master List and each underlying dataset.