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Vocabulary

SeaDataCloud Flow Cytometry Standardised Cluster Names

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URI http://vocab.nerc.ac.uk/collection/F02/current/
DescriptionTerms recommended by the SeaDataCloud working group on flow cytometry data to standardise the naming and definition of clusters.
CreatorSeaDataNet
Modified2018-06-02
Version Info3
Identifier F02
Register Manager British Oceanographic Data Centre
Register Owner SeaDataNet
Members
Identifier PrefLabel Definition Date
F0200007 Coccolithophores Coccolithophores are nanoplanktonic cells that build calcium carbonate coccoliths. When the cells have coccolith shells,due to their CaCO3 platelet covering, they are characterized by a high depolarization ratios (Horizontally polarized Forward Light Scatter over Vertically polarized Forward Light Scatter (HFLS/VFLS)) and a high sideward scatter. Their forward scatter and red fluorescence signals are similar to those of the eukaryote nanophytoplankton group. No staining is required to distinguish them by flow cytometry. 2017-11-20
F0200006 Cryptophytes Cryptophytes have higher forward scatter and orange fluorescence intensities than Synechococcus and a higher orange to red fluorescence ratio compared to other eukaryotic phytoplankton. Cryptophytes form their own cluster separated from the eukaryote nanophytoplankton cluster due to the presence of phycoerythrin and phycocyanin fluorescence signals. No staining is required to detect and discriminate them by flow cytometry. Their forward scatter signal can reach values close to that of microphytoplankton. They contain high amounts of phycoerythrin and may contain phycocyanin that can be excited by a red laser. If cryptophyte cells contain both phycoerythrin and phycocyanin, then they will emit a higher red fluorescence signal than cells containing only chlorophyll-a (energy transfer to red fluorescence). 2017-11-20
F0200005 Eukaryote nanophytoplankton The eukaryote nanophytoplankton group is defined by cells with a size range between 2 and 20 microns. No staining is required to distinguish them by flow cytometry. They differ from eukaryotic picophytoplankton by their larger red fluorescence, sideward scatter and forward scatter signals. Eukaryote nanophytoplankton cells can be separated from the cryptophyte cells due to their lack of orange fluorescence. 2017-11-20
F0200004 Eukaryote picophytoplankton The eukaryote picophytoplankton group is defined by cells with a size range between 2 and 3 microns. No staining is required to distinguish them by flow cytometry. The smallest known eukaryotic picophytoplankton is Ostreococcus. Eukaryotic picophytoplankton exhibit a well-defined flow cytometry signature, with forward scatter and red fluorescence signals larger than that of Prochlorococcus and Synechococcus, and smaller than that of nanophytoplankton cells, though some overlap may happen. The forward scatter signal of 2 micron beads is widely used as an optical standard to localize this group. It is important to keep in mind that cell cycle within this group may generate cells with size greater than 2 microns (2-4 um in theory). They do not have an orange fluorescence signal. 2017-11-20
F0200009 Heterotrophic prokaryotes Heterotrophic prokaryotes include both bacteria and Archea. They do not contain any photosynthetic pigments and thus do not have any autofluorescence properties exploitable by flow cytometry. Thus, they require a staining with some fluorescent dye to be resolved by flow cytometry. In most studies a nucleic acid dye is used. Staining of nucleic acids by a dye emitting in the green when excited by a blue laser enables heterotrophic prokaryotes to be distinguished in various groups thanks to sideward scatter (or FWS) and FLG signatures : Cells with a lower FLG correspond to heterotrophic prokaryotes with a Lower Nucleic Acid content (LNA) and cells with a higher FLG correspond to a Higher Nucleic Acid content (HNA). Their scatter signals (FWS, SWS) are lower than those of Synechoccocus and eukaryotic picophytoplankton, and may overlap those of Prochlorococcus. 2017-11-20
F0200010 Heterotrophic prokaryotes - HNA Heterotrophic prokaryote cells with a Higher Nucleic Acid (HNA) content as defined by flow cytometry, based on the intensity of their fluorescence signal induced by a nucleic acid dye. 2018-02-02
F0200011 Heterotrophic prokaryotes - LNA Heterotrophic prokaryote cells with a Lower Nucleic Acid (HNA) content as defined by flow cytometry, based on the intensity of their fluorescence signal induced by a nucleic acid dye. 2018-02-02
F0200012 Heterotrophic prokaryotes - MNA Heterotrophic prokaryote cells with a Medium Nucleic Acid (MNA) content as defined by flow cytometry, based on the intensity of their fluorescence signal induced by a nucleic acid dye. 2018-06-01
F0200008 Microphytoplankton The microphytoplankton group is defined by cells with a size range between 20 and 200 microns. No staining is required to distinguish microphytoplankton by flow cytometry. This group is discriminated thanks to its forward scatter and red fluorescence signals larger than those of the other groups. Due to the low volumes analyzed by flow cytometry, this group is not always accurately quantified when cells are not abundant. It is possible to distinguish this group from nanophytoplankton (2-20 microns in diameter) when the forward scatter signal is calibrated to detect the forward scatter channel corresponding to the 20 micron limit in size. On cytometers equipped with an image in flow device, pictures are also used to measure cell size. Chains or colonies may outpass flow cytometry analysis depending on instrument performance (tubing size, pulse shape analysis or not). If large cryptophytes or coccolithophores are observed, they will be considered in a separate group thanks to their distinguishable optical properties. 2017-11-20
F0200002 Prochlorococcus Prochlorococcus cells are defined as the smallest cyanobacteria found in the marine environment. No staining is required to distinguish them by flow cytometry. Compared to any other group, their forward scatter and red fluorescence signatures are the smallest recorded up to now and require sensitive Photo Multiplier Tube (PMT) or high powered lasers. The cluster, when well defined (often deep water communities) is below or may overlap that of the Synechococcus group, and is often partially masked by the instrument background noise. In samples stained for heterotrophic prokaryote detection, Prochlorococcus can be distinguished using the sideward scatter vs red fluorescence cytogram. They do not emit orange fluorescence because they lack phycoerythrin. 2017-11-20
F0200001 Standard beads A standard is a reference defined by a user, a laboratory, or any acknowledged authority. Properties of standard beads are accurately known by the manufacturers (i.e. size, material, fluorescence properties). These fluorescent microbeads (or microsphere) are used as an absolute reference for quantitative and qualitative comparisons. Standard beads are analyzed routinely in every flow cytometry analyses in order to have confidence in the instrument performance (alignment and fluidics) and as well as in the results. 2017-11-20
F0200003 Synechococcus Synechococcus are unicellular photosynthetic cyanobacteria with flow cytometry forward scatter and sideward scatter signatures larger than those of most of marine heterotrophic bacteria. No staining is required to distinguish them by flow cytometry. The Synechococcus cluster has higher forward scatter and red fluorescence signatures than Prochlorococcus and a distinct orange fluorescence signature from their phycoerythrin accessory pigment when excited by lasers whose wavelength is below 533 nanometres. Cyanobacteria may contain phycocyanin, excited by a red laser and emitting above the chlorophyll-a emission wavelength. The Synechococcus cluster is well resolved in red vs green and in red vs orange fluorescence cytograms. Due to their small size (0.8 to 1.2 microns as reported in the literature), Synechococcus cells exhibit low intensity of forward and sideward scatters and red fluorescence signals. 2017-11-20