Abstract:

As part of an interdisciplinary manuscript, we have compiled data on zooplankton, marine snow distribution (for particles > 1 mm in size), particulate organic carbon, particulate organic nitrogen, biogenic silica, primary productivity, ocean currents, CTD on the middle corridor during Fall (October 30, 2015), Spring (April 4, 2016), and Summer (July 25, 2016) seasons. We also performed a literature review to compile information about oil extraction activities near river-dominated ecosystems found throughout the world. This dataset supports the publication: Greer, A.T., A.M. Shiller, E.E. Hofmann, J.D. Wiggert, S.J. Warner, S.M. Parra, C. Pan, J.W. Book, D. Joung, S. Dykstra, J.W. Krause, B. Dzwonkowski, I.M. Soto, M.K. Cambazoglu, A.L. Deary, C. Briseño-Avena, A.D. Boyette, J.A. Kastler, V. Sanial, L. Hode, U. Nwankwo, L.M. Chiaverano, S.J. O’Brien, P.J. Fitzpatrick, Y.H. Lau, M.S. Dinniman, K.M. Martin, P. Ho, A.K. Mojzis, S.D. Howden, F.J. Hernandez, I. Church, T.N. Miles, S. Sponaugle, J.N. Moum, R.A. Arnone, R.K. Cowen, G.A. Jacobs, O. Schofield, and W.M. Graham. 2018. Functioning of coastal river-​dominated ecosystems and implications for oil spill response: From observations to mechanisms and models. Oceanography 31(3):90–103. doi:10.5670/oceanog.2018.302

Suggested Citation:

Adam T. Greer, Sabrina M. Parra, Laura Hode, Uchenna Nwankwo, Jeff Krause, Christian Briseno-Avena, Robert K. Cowen, William M. Graham. 2019. Dataset for: Functioning of coastal river-​dominated ecosystems and implications for oil spill response: From observations to mechanisms and models. Distributed by: GRIIDC, Harte Research Institute, Texas A&M University–Corpus Christi. doi:10.7266/N7697236

Publications:

Greer, A., Shiller, A., Hofmann, E., Wiggert, J., Warner, S., … Graham, W. (2018). Functioning of Coastal River-Dominated Ecosystems and Implications for Oil Spill Response: From Observations to Mechanisms and Models. Oceanography, 31(3). doi:10.5670/oceanog.2018.302

Purpose:

This dataset is supposed to be a repository for data used in the "synthesis paper" of consortium for oil spill exposure pathways in coastal river-​dominated ecosystems (CONCORDE) activities.

Data Parameters and Units:

The file PhytoDataSummary.csv: Cruise; Local time (hhhh); Station name; Latitude (decimal degrees); Longitude (decimal degrees); Consecutive sample #; Bottom depth (m); Target depth (m); Total particulate organic carbon (POC, ug/L); >5 um Particulate organic carbon (ug/L); <5 um Particulate organic carbon (ug/L); Total Particulate organic nitrogen (PON, ug/L); >5 um Particulate organic nitrogen (ug/L); <5 um Particulate organic nitrogen (ug/L); Chlorophyll a (CHL, ug/L); Chlorophyll a (percentage in >5 um cells, largechl, ug/L); Chlorophyll a (percentage in <5 um cells, smallchl, ug/L); Biogenic silica (bSi, umol Si/L); Gross rate of biogenic silica production (32Si rho, umol Si/L/d); Biomass-normalized silica production rates (32Si Vb, per day); Primary production (14CProd, mg C/m^3/d); Size-fractionated primary production <5 microns (Small14CProd ,mg C/m^3/d); Size-fractioned primary production >5 microns (Large14cprod, mg C/m^3/d); Total carbon production (PB, g C/g Chl/d); carbon production per unit biomass, > 5 microns (LargePB, g C/g Chl/d); Carbon production per unit biomass < 5 microns (SmallPB, g C/g Chl/d); Distance along the transect (dist, m), NA=data not collected. The folder “PhysicalData” contains the In Situ Ichthyoplankton Imaging System (ISIIS) along track information for October 30, 2015 (20151030physical.csv), April 4, 2016 (040416-physical.csv and 040416-physical2.csv), and July 25, 2016 (072516physical.csv). Hour (central, CTZ); Julian time; Hour (UTC); Unix timestamp; Altitude (m); CTD temperature (degrees C); fluorescence (voltage units); forward velocity (m/s); Heading (degrees); Dissolved oxygen (mg/L); Dissolved oxygen (VDC); Photosynthetically available radiation (PAR, μE m−2 s−1); PAR (VDC); Pitch (degrees); Roll (degrees); Salinity (ppt); Latitude (decimal degrees); Longitude (decimal degrees), Vertical velocity (m/s2); altitude (good=1, 0=not good). The file OilandRivers.csv: Locations of coastal river-dominated ecosystems around the world with nearby oil extraction activities that are similar to the CONCORDE domain. River name; Latitude (decimal degrees); Longitude (decimal degrees); Basin name; Average freshwater river discharge (m3/s), Future recoverable oil (billions of barrels). The files 103015-sal-interp.csv, 0404SalinityInterp.csv, and 072516-sal-interp.csv contain interpolated salinity data from October 30, 2015, April 4, 2016, and July 25, 2016, respectively from the ISIIS tow-yo transect. Distance along transect (m); Depth (m); Interpolated salinity (ppt). The file 404currents.csv contains the moored ADCP data from the southernmost CONCORDE mooring (M6, 30.05125 deg. N, 88.12261 deg. W). Depth (m); North/south speed of current (m/s, negative is south); Distance (m) along the CONCORDE middle sampling corridor (MCORR) transect. The folders GOMCounts1030, GOMCounts404, and GOMCounts725 contain .txt files with the number of particles less than 1 mm equivalent spherical diameter in each image for the samples dates of October 30, 2015, April 4, 2016, and July 25, 2016, respectively. The images are organized in "stacks" with between 1020 and 1717 images per stack. Each image within the stack is referred to as a "slice." Each filename represents the date (YYYYMMDDHHMMSS.SSS). Each file contains the slice (image number within the stack), count (number of particles), total area (sum of the pixel area covered by particles), average size (total area/count), percent area covered by particles, and the total perimeter distance (in pixels) of the particles. The image field of view is 4.3 cm by 4.3 cm, so pixels can be converted to distance (or size, ~238 pixels = 1 cm). The folders GOMHistograms1030, GOMHistograms404, and GOMHistograms725 contain .txt files with a mean and standard deviation of the pixel gray level (from 0 (black) to 255 (white)) for each image in the stack. The first column is the mean pixel gray level value, and the second column is the standard deviation of pixel gray level values. The histograms and the counts were both extracted from the images using an ImageJ macro program. An example of the program that was used to extract the histogram and particle count data can be found in the file "ParticleCounterGOM-histandcount-summary.txt". This macro can be run inside ImageJ by selecting from the dropdown menu Plugins -> Macros -> Run. The folder “DrifterandDyeSimulations” contains the tracks simulated drifter releases on September 4, 2015 (folder final_drifter_plot) and the simulated neutrally buoyant tracer release at the southern edge of the CONCORDE model domain in the Mississippi Bight. Tracer distribution (integrated 1 m surface concentration in arbitrary units ranging from 0 to 100—concentration is 100 at the site of the release) after 21 days of continuous release and passive advection during fall (October 1–21) and spring (March 18–April 7) seasons (folder final_dye_plot). Matlab codes to recreate the figures 4 and 5 in the manuscript were provided. The folder “ImagesFromFigure” contain the ISSIS and Flowcam images from Figure 6 in the associated manuscript Greer et al.,2018. This dataset includes the R-code used to generate the plots in the associated manuscript Greer et al.,2018.

Methods:

Image analysis (image thresholding and particle counting for anything above 1 mm in size), the literature review for oil reserves and average annual river discharge. We also ran image analysis of the image histogram (gray levels) for each image, which was used to correct the particle counts by removing images that were likely to produce errors in the particle counts (i.e., images with Schlieren distortion or sediment obscuring the image). If the image histogram mean was below 217, it was determined that it was likely to produce erroneous counts. All of the code used to process and plot these data are included in the "SynthesisPlots.R" file.

Instruments:

In Situ Ichthyoplankton Imaging System, Bottom moored acoustic doppler current profiler (ADCP), CTD, chlorophyll and nutrient measurements.

Individual Files: