DOI: 10.5281/zenodo.10478781
title: Dataset originating from various imaging devices used during the Tara Ocean Cruise and associated with the manuscript "Ubiquity of inverted 'gelatinous' ecosystem pyramids in the global ocean"

description: Datasets are provided in 3 different layers.

 1) Raw datasets as obtained from Ecotaxa exports (imaging devices) and as either fcs files for Accuri flowcytometry or concentration, size and biovolumes for Facscalibur flowcytometry.

They are provided as separate .zip files for

-Fascalibur flowcytometry

-Accuri flowcytometry

-eHFCM (H5) from the 5µm nets

-eHFCM (H20) from the 20µm nets

-Flowcam (both from Niskin bottles and bongo 20µm net (b20)

-Imaging flowcytobot (IFCB); one file every 5 minutes

-Zooscan from the WP2 (200µm) net

-Zooscan from the bongo (300µm) net

-Zooscan from the Regent (680µm) net

-UVP data

 

2)    Mergedbase.mat : one line per station

Pre-processed (https://github.com/ecotaxa/ecotaxatoolbox ) and merged datasets where quality checked for potential errors in volume sampled against initial log sheets and corrected if needed, all concentrations have been calculated, biovolume calculated for every individual image obtained and normalized biovolume size spectra calculated assuming 3 different calculations (plain area biovolume, extruded area biovolume and ellipsoidal equivalent biovolume assuming prolate ellipsoids).

Data are organized within a structured matlab file with a common architecture for every stations.

The architecture of this file is similar for every station and instrument and includes in addition to every relevant metadata (position, date, volumes etc) the features described below for the different fractions of a sample (d1, d2... dx fractions; when scanned in several scans) in tot (sum of dx fractions); or in regrouped (further grouped in living/non-living// functional groups// trophic groups). Each levels contains the following derived datasets:

-       Ab: abundance per groups (ind.m-3)

-       Bv: biovolume per groups (mm3.m-3) Calculated from ellipsoidal estimate

-       Ybv_Plain_Area_BV_spectra: NBSSbiovolume per groups per size class (mm3.mm-3.m-3) from Area estimated ESD

-       Ybv_Riddled_Area_BV_spectra: NBSSbiovolume per groups per size class (mm3.mm-3.m-3) from Area_extruded estimated ESD

-       Ybv_Ellipsoid_BV_spectra: NBSSbiovolume per groups per size class (mm3.mm-3.m-3) from ellipsoidal estimate

-       X is the Middle of each biovolume size class (caution: it is log transformed here) (log(mm3))

-       X1 is the amplitude of each biovolume size class - used for de-normalizing NBSS (mm3)

-       ESD vector is the conversion of X in ESD (µm this time)

-       ESDquartilesmoyenne are the 5 25 50 75 95 % quartiles of ESD (+ mean and std) of each groups

This file is enriched with various environmental measures and with proportions of the used functional types and trophic levels from metabarcoding

 3)    MergedbaseC.mat A similar file but where all three NBSS have been converted to carbon units to obtain a normalized biomass size spectra (mgC.mm-3.m-3)

 4)    “metaplankton(…).mat” one line per station. For every station, all different observations have been selected depending on several data availability to provides a coherent measurement across stations.  The different files diverge in the data collected (day or night), the fact that they are un biovolume or carbon units, or the addition of Facsalibur flowcytometry measurements (not size resolved):

metaplankton.mat contains only Day data in biovolume (all data in mm3/m3 or mm3/mm3/m3 for NBSS)

metaplanktonC.mat contains only Day data in Carbon content (all data in mgC/m3 or mgC/mm3/m3 for NBSS)

metaplanktonnight.mat contains only night data in biovolume (all data in mm3/m3 or mm3/mm3/m3 for NBSS)

metaplanktonfacs.mat contains only day data in biovolume (all data in mm3/m3 or mm3/mm3/m3 for NBSS) + addition of Facscalibur flowcytometer data (not finely size resolved)

metaplanktonCfacs.mat contains only day data in Carbon content (all data in mgC/m3 or mgC/mm3/m3 for NBSS)+ addition of Facscalibur flowcytometer data (not finely size resolved)

 

each of those files contains always the same type of data structure and content:

If several observations have been made (often the case for UVP or IFCB) a mean observation is provided for one station (either day or night).

For each instrument several NBSS (ellipsoid estimate only) are present either with the different tested corrections across instruments:

-“raw” are uncorrected data

-“trunked” are NBSS spectra where extreme data have been removed to ignore regions of incorrect efficiency (too small organisms or too large, rare ones) and calculate a slope (b) and the intercept (a) of the NBSS

-“interceptadjusted” are correction of the intercept on the basis of WP2 measurments

-“adjusted_site” are corrections of the intercept based on concurrent measurments of similar size class by several instruments (when possible)

-“adjusted” are corrected by the median of correction between instruments (median of every “adjusted_site” corrections.

-“final” are the final correction after manual QC of the different possibility of corrections above

Those data are present either as total living organisms, and regrouped within their original taxonomic identification (“original”), in different functional groups (“pft”) or trophic (“trophic”) groups. For each of them the name of the groups is provided (nameoriginal, namepft). Trophic groups are organized such at position 1 is primary producers (trophic position in matrix: 1); 1.5 is mixotrophs (trophic position in matrix: 2) ; 2 is herbivorous (trophic position in matrix: 3); 2.5 is omnivorous (trophic position in matrix: 4) ; 3 is carnivorous (trophic position in matrix: 5) ; 3.5 is undefined trophic mode (trophic position in matrix: 6)

For quality control purpose a figure is generated for each station and for each of the above coherent compilation of datasets allowing to control the different corrections and the different final products obtained. Those are saved under the name metaplankton.pdf,  metaplanktonC.pdf, metaplanktonnight.pdf, metaplanktonfacs.pdf and metaplanktonCfacs.pdf

Those single instruments measurements have afterward been merged in several subproducts:

-merged (not recommended because of the heterogeneity of number of instruments merged ): all possible instruments have been combined for every stations (mostly used for diagnostics plots and systematic inspection of data. Called "Meta-Plk heterogeneous” in the manuscript.

-merged4devicesmin: spans organisms ranging from 0.8 µm to several cm (including flow-cytometry, IFCB, Flowcam, Zooscan from several nets and UVP and with a complete coverage in between), it is only available from the Arctic ecosystem and covers 20 sites. Called " Meta-Plk >0.8 µm” in the manuscript.

-mergedpft4devicesincomplete: is similar from the above but adds few stations which miss some observation for particular organism sizes, notably due to the absence of Flowcam analyses from the 20 µm net fractions. Called " Meta-Plk >0.8 µm incomplete” in the manuscript.

-merged2netsUVPH20: spans organisms ranging from 20 µm to several cm (using e-HFCM with 20 µm net, Zooscan from WP2 and Regent nets and UVP). It covers both TO and TOPC parts of the expedition and includes 63 stations. Called " Meta-Plk >20 µm” in the manuscript.

 Some other trials (using only two nets : WP2 and Regent; merged2nets; or also including the UVP; merged2netsUVP) but not used in the manuscript are also included.

 

Each of those “merged” products contains the full NBSS spectra for each functional groups (“datapft”) and in BSS spectra (ie. biovolume per size class; “datapft_denorm”), the total biovolume of each functional groups (“donut”) the same done for trophic levels (“datatrophic”; “datatrophic_denorm”) and the cumulated abundance and biovolume of the different trophic levels (“trophicpyramidnb”; “trophicpyramidbv”)

The same grouping into functional groups and trophic groups was done from metabarcoding (18S, V9) genomic data for the size fraction 180-2000µm (pft180 and trophic180) or from the 20-200µm fraction (pft20 and trophic20)

slopes and intercepts of the NBSS size spectra (slopesbss, ie. non normalized size spectra are also provided) relationship for every instrument and every merged datasets in the order:

(1)    Accuri flowcytometry

(2)    IFCB

(3)    Flowcam-Niskin

(4)    Flowcam b20

(5)    Zooscan-WP2 net

(6)    Zooscan-bongo net

(7)    Zooscan-Regent net

(8)    UVP-in situ

(9)    E-HFCM-5µm net

(10) E-HFCM-20µm net

(11) Meta-Plk >200µm (ie. “merged2nets” product)

(12) Meta-Plk >200µm-UVP (ie. “merged2netsUVP” product)

(13) Meta-Plk >0.8µm (ie. “merged4devicesmin” product)

(14) Meta-Plk >0.8µm- incomplete (ie. “merged4devicesminincomplete” product)

(15) Meta-Plk heterogeneous (ie. “merged” product)

(16) Meta-Plk >20µm (ie. “merged2netsUVPH20” product)