Zooplankton data: taxon-specific, fine-scale day and night distribution of mesozooplankton, with emphasis on gelatinous zooplankton taxa, in the Mississippi Bight collected aboard the R/V Point Sur, PTS03, from 2016-07-27 to 2016-07-28
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csv, R, tif
Gulf of Mexico Research Initiative (GoMRI)
Consortium for Oil Spill Exposure Pathways in Coastal River-Dominated Ecosystems (CONCORDE)
University of Southern Mississippi / Department of Coastal Sciences
2016-07-27 to 2016-07-28
jellyfish, zooplankton, hypoxia, diel vertical migration, In-situ Ichthyoplankton Imaging System, ISIIS, mesozooplankton, gelatinous zooplankton
This dataset contains Taxon-specific, fine-scale day and night distribution of mesozooplankton, with emphasis on gelatinous zooplankton taxa, in the Mississippi Bight collected aboard the R/V Point Sur, PTS03, from 2016-07-27 to 2016-07-28. As part of the CONCORDE field sampling campaign, an in-situ imaging system (ISIIS) was used to sample along one meridional transects spanning approximately 10 km. This dataset examines the western-most corridor for abundances of different mesozooplankton taxa, with emphasis on gelatinous zooplankton, during day and night in summer 2016. Three passes were conducted during the day and at night on the transect. Particles above a 2000-pixel size threshold (~3.3 mm equivalent spherical diameter) were automatically extracted and manually identified with the highest taxonomic resolution possible (in many cases, to genus). The ISIIS collected images of plankton along with high-resolution physical oceanographic data, which were merged using the nearest time stamp. The goal of the study was to describe the distribution of different plankton groups during the day and at night, with the goal of understanding vertical diel movements and potential oil exposure rates for different groups inhabiting the shelf ecosystem. The dataset contains the date, latitudes and longitudes of the sampling locations.
Chiaverano, Luciano, Adam Greer, Frank Hernandez, and Monty Graham. 2021. Zooplankton data: taxon-specific, fine-scale day and night distribution of mesozooplankton, with emphasis on gelatinous zooplankton taxa, in the Mississippi Bight collected aboard the R/V Point Sur, PTS03, from 2016-07-27 to 2016-07-28. Distributed by: Gulf of Mexico Research Initiative Information and Data Cooperative (GRIIDC), Harte Research Institute, Texas A&M University–Corpus Christi. doi:10.7266/AGA5PGF8
This dataset examines the fine-scale patterns of distribution, abundance, and environmental affinities of different zooplankton taxa in summer 2016, along an approximate 10 km transect in the Mississippi Bight. The goal of the study was to describe patterns of spatial distribution and abundance, as well as to establish taxon-specific, diel vertical migrations of the zooplankton community to understand potential oil exposure rates for different groups inhabiting this ecosystem.
Data Parameters and Units:
The cruise documentation was provided for the R/V Point Sur, PTS03. The cruise was led by chief scientist Dr. Christian Briseño-Avena. All the data collected at night located in the folder named "2-27-2016 NIGHT", while all the data collected during the day is in the folder called "2-28-2016 DAY". In each main folder, zooplankton is divided into two sub-folders, one for gelatinous zooplankton (hydromedusae, siphonophores, ctenophores and pelagic tunicates) and another one with the rest of zooplankton taxa. In each sub-folder, data is divided in "Images" and "CSV files and R-script files". The folders named "CSV files and R-script files" contain all the physical data (files with "physall" in their name, CSV), as well as taxon-specific gelatinous zooplankton count data (files with “BioPhys” in their name, CSV) and taxon-specific gelatinous zooplankton abundance data (files with “abundance” in their names, CSV) paired with physical data, and as R-script files with the codes used to process the raw data. There is one R-script file per main taxonomic group (ctenophora, siphonophora, hydromedusae, and tunicates), per transect (one transect in the Fall, two transects in Spring, and one transect in Summer). The folders named “Images” contain classified images by the ISIIS. The images represent segments extracted from raw images, and each segment represents, in most cases, one zooplankton individual. Description of columns in “biophys” csv files: Nearjul: nearest Julian time in the physical dataset used to merge with biological data Julian: julian time of the biological data(CDT) ID: final taxonomic identification Other: broader taxonomic classification Junk: N/A, Label: image file name Slice: image number within an image stack of 430 images Xloc = x pixel location within the larger frame Yloc = y pixel location within the larger frame Width = width of bounding box (pixels) Height = height of bounding box (pixels) UTC: time, timestamp: same as “label” Alt: distance from benthos (m) Temp: temperature (Celsius degrees) Depth (m) Flour: chlorophyll-a fluorescence (raw voltage) Fvel: forward velocity (m/sec), 0 indicates unreliable reading from Doppler Velocity Log (DVL) Heading: heading of the ISIIS vehicle (degrees) O2: oxygen concentration (invalid conversion to mg L - this conversion is made correctly in the R script) O2 volts: (volts) PAR: photosynthetic active radiation (micro Einsteins/cm^2) Parvolts: (volts) Pitch: pitch of ISIIS vehicle (degrees) Roll: roll of the ISIIS vehicle (degrees) Salinity (ppt), Lat = latitude (decimal degrees) Lon = longitude (decimal degrees) vertvel: vertical velocity (cm/sec) altok: binary variable that indicates if altitude data are valid (1-valid, 0-error) O2delay: oxygen in volts from the physical dataset oxygen: oxygen concentration (mg / L) Note: we used the formula supplied by the oxygen sensor (Seabird electronics) to convert the oxygen voltage, temperature, salinity, and depth to dissolved oxygen concentration, year, month, and day. Units were converted to mg/L by dividing the oxygen the mL/L concentration values by 0.75189 (see ICES unit conversion). The values for “O2” are incorrect due to an error in the software that converts the voltage. The appropriate conversions were made in the R scripts. Description of columns in “concentration” .csv files: Rdist: distance travelled by the ISIIS (m) from an initial reference point (distance zero). Each row on this column represents a different “transect bin”, each one of 19.25 m in length. This length is roughly equivalent to a sampled volume of 1 m^3 by the ISIIS. ID: taxonomic identification, mjul: mean julian time, pco: number of individuals per m3 (abundance), mdepth: mean depth (m), msal: mean salinity, mtemp: mean temperature (degrees Celsius), mlat: mean latitude, mfluor: mean chlorophyll-a fluorescence (raw voltage), moxyg: mean oxygen concentration (mg / L). ID codes (csv files): Hydromedusae: Clytia: Clytia spp, Corymorpha: Corymorpha nutans, Eutima: Eutima variabilis, Halicreas: Halicreas sp (?), Liriope: Liriope tetraphylla, Nenopsis: Nemopsis bachei(?), Pegantha: Cunina sp (?), Solmaris: Solmaris sp, Solmundella: Solmundella bitentaculata. Ctenophores: Lobate: Mnemiopsis leidyi, Nuda: Beroe sp. Siphonophores: SiphoA: Bassia basensis, SiphoB: Muggiaea (?) eudoxid stade, SiphoC: Nanomia bijuga, Sipho D: Lensia sp (?) (poligastric stage), SiphoE: Spheronectes gracilis, SiphoF: Muggiaea kochi. Tunicates: Doliolid: Doliolum intermedium, Salp: all salps (all species included). Each image name follows the same format. For example: “dolio_Plankton_20160726112037.919.tif_323_396_64_101_88”. This translates into: “ID_Plankton_YYYYMMDDHHMMSS.SSS. tif_Slice_xpos_ypos_xlength_ylength” - where the YYYY = year, MM = month, DD = day, HH = hour, MM = minute, SS.SSS = seconds to nearest thousandths of a second of the time of the first image in the image stack. ID (in images): Anem: pelagic anthozoan larvae, App: appendicularian, Aurelia: moon jellyfish, Chaeto: chaetognaths, crab: decapod (crab) larvae, Cteno: ctenophores, Diatom: diatom chain, Exo: crustacean exoskeleton, Fish: fish larva, Hydro: hydromedusa, marinesnow: marine snow, Poly: polychaeta, Phyllo: phyllosoma (lobster) larva, Schlie: schlieren effect, Other: other zooplankton, Sipho: siphonophora, schlie: Schlieren effect in images, Shrimp: decapod shrimp, Salp: pelagic tunicate (salps and doliolids), Stoma: Stomatopoda larva, Unk: unknown, unidentifiable object. Slice is the frame number within the image stack. Xpos and ypos are the x and y position of the segment within the image. Xlength and ylength are the lengths (in pixels) of the box bounding the segment in the image.
Data collection: The ISIIS was towed behind the ship at a speed of ∼5 knots (matching the scan rate of the line scan camera) in a tow-yo fashion. Using motor-actuated wings, the vehicle moved between different depths or at one constant depth, as controlled by a shipboard operator.
All images and physical data were collected by the In-situ Ichthyoplankton Imaging System (ISIIS).The ISIIS vehicle contains a suite of instruments that collect salinity, temperature, depth (Sea-Bird Electronics 49 Fastcat CTD), dissolved oxygen (SBE 43), chlorophyll-a fluorescence (Wetlabs Eco FL-RT), PAR (QCP2300), and speed through the water via a Doppler velocity log (DVL, Navquest 600). All of these sensors acquired data at a rate of at least 4 Hz.