Life Sciences Commons^™

Shoreline Characterization In The Northern Indian River Lagoon, Melinda Donnelly, Michelle Shaffer, Suzanne Connor, Linda Walters

CEELAB Research Data

The purpose of this project was to evaluate current conditions of estuarine shorelines in the northern section of the Indian River Lagoon system, including Mosquito Lagoon, north Indian River, and Banana River. From January 2016 through June 2018, we evaluated structural and functional characteristics of 374 miles of shoreline, from Ponce Inlet in Volusia County to Sebastian Inlet in Brevard County (11,000+ data points). Hard-armoring accounted for approximately 50% of total shoreline, evenly divided between shoreline with bulkheads (25%) and hardened slopes (25%). Forty-five percent of shoreline without hard-armoring had anthropogenic alterations (i.e. mosquito impoundments, railroads and roadways, residential and …

Mitochondrial Dna Sequence Alignments For Phylogenetic Analysis Of The Shrimp Genus Farfantepenaeus, Laura Timm, S. Simon, Heather Bracken-Grissom Dr.

DEEPEND Datasets

This dataset includes 12S, 16S, and COI sequence data. Sequences were obtained from the eight recognized species of Farfantepenaeus: F. aztecus, F. brasiliensis, F. brevirostris, F. californiensis, F. duorarum, F. isabelae, F. notialis, and F. subtilis. Also included are several sequences from species of Litopenaeus, which serve as outgroup(s).

Gulf-Wide Seafloor Surface Benthic Foraminifera Stable Isotopes From Sediment Cores Collected On Multiple Cruises From 2010-06-13 To 2017-07-19, Patrick Schwing, David J. Hollander

C-IMAGE data

This dataset includes baseline stable carbon and oxygen isotope measurements from benthic foraminifera throughout the Gulf of Mexico. Stable isotope measurements were performed on Cibicidoides spp. The dataset contains the sediment core information such as location, date, and depth; and benthic foraminiferal stable carbon and oxygen isotopes. Sediment cores were collected on multiple cruises from 2010-06-13 to 2017-07-19.

Benthic Foraminiferal Assemblages From Sediment Cores Collected On Multiple Cruises In The Gulf Of Mexico From 2010-11-18 To 2017-05-22, Patrick Schwing, David J. Hollander

C-IMAGE data

This dataset includes baseline assemblage measurements from benthic foraminifera throughout the Gulf of Mexico. The dataset is a compilation of seafloor surface benthic foraminifera assemblages from sediment cores collected on multiple cruises and field sampling in the Gulf of Mexico from 2010-11-18 to 2017-05-22. The dataset contains the Gulf-wide diversity indices and the full benthic taxonomic counts for two regions: Cuba and the southern Gulf of Mexico. The Gulf-wide file contains the total density and diversity calculations using Fisher’s Alpha and Shannon indices from the surface-most sub-sample from each core (typically 0-2 mm). The Gulf-wide spreadsheet is comprised of data …

A Climatological Dataset Of Nutrient, Chlorophyll, And Particulate Matter Distributions On The Ross Sea Continental Shelf Derived From Cruise-Based Measurements Spanning 1967 To 2016, Walker O. Smith Jr., Daniel E. Kaufman

Data

This dataset includes data used in the publication Smith and Kaufman (2018), Progress in Oceanography, which examines the temporal and spatial distributions of nutrients and particulate matter in the Ross Sea continental Shelf using cruise-based observations, and compares the resulting annual productivity estimates with previously reported satellite-based estimates. Specifically, these data represent distributions of nutrients, chlorophyll, particulate organic carbon, particulate organic nitrogen, and biogenic silica that were compiled from 42 cruises (from 1967 - 2016) to the Ross Sea continental shelf to generate a comprehensive climatological dataset for November, December, January, and February. This climatology provides a novel look at …

Presence/Absence And Density Data For Epipelagic Tows Collected During R/V Blazing Seven Cruises Lf2016a And Lf2016b, Northern Gulf Of Mexico From 2016-06-09 To 2016-07-28, Jay R. Rooker, David Wells

DEEPEND Datasets

This dataset reports presence/absence and density data for epipelagic tows collected in the northern Gulf of Mexico during R/V Blazing Seven cruises LF2016A and LF2016B (2016-06-09 to 2016-07-28). Larval fishes were sampled from 48 stations and cruise data were collected at each site including latitude/longitude, date, time, environmental data (temperature, salinity, dissolved oxygen) and Sargassum dry weight. Larval catch data before and after the oil spill will be compared to improve our understanding of the causes of temporal variability as it relates to the Deep-Water Horizon oil spill (DWHOS). Habitat associations of selected taxa (billfishes, tunas, dolphinfishes, flyingfishes) will be …

Catch Data From Fish Collected Throughout The Gulf Of Mexico From 2011 Until 2017, Steven A. Murawski

C-IMAGE data

This dataset represents collections taken by demersal longline fishing gears throughout the Gulf of Mexico from 2011 until 2017. They include station location information and standardized fish catch data (numbers, weights, sex, length). Catch data were classified into five sub-regions: West Florida Shelf (WFS), North Central (NC), North West (NW), South West (SW), Yucatan Peninsula (YP) and Cuba (CUB). Catch data were also classified into four species groups: Elasmobranch (EL), Other demersal (OD), Pelagic (LP) and Snapper/Grouper (SG). Data from 2011 until 2014 are also reported in C-IMAGE I dataset R1.x135.120:0002, Lesion data from fish collected off Terrebonne Bay, LA …

Inventory Of Oceanic Fauna Data Including Species, Weight, And Measurements From R/V Point Sur (Cruise Dp05) In The Gulf Of Mexico From 2017-05-01 To 2017-05-11, April Cook, Tracey Sutton

DEEPEND Datasets

This dataset includes an inventory of Gulf of Mexico oceanic fauna data including species, weight, and measurements collected from R/V Point Sur (Cruise DP05) from 2017-05-01 to 2017-05-11. The main gear type used was a 10-m2 Multiple Opening Closing Net and Environmental Sensing System (MOCNESS). The MOCNESS was fitted with 6 nets which were opened according to the following depth scheme: net 0 from the surface to 1500m, net 1 from 1500-1200m, net 2 from 200-1000m, net 3 from 1000-600m, net 4 from 600-200m, and net 5 from 200m to the surface. Two trawls were conducted at each station sampled …

Input, Output And Complete Run Files For The Atlantis Ecosystem Model Deepwater Horizon Oil Spill Simulations, Cameron Ainsworth

C-IMAGE data

Data are complete input, output, and executable model run files for Atlantis simulations of the Deepwater Horizon oil spill. The model outputs in these folders describe simulations from 2010 to 2035; the spatial domain is the entire Gulf of Mexico. Simulations are published as Ainsworth, C.H., Paris, C.B., Perlin, N., Dornberger, L.N., Patterson, W., Chancellor, E., Murawski, S., Hollander, D., Daly, K., Romero, I.C., Coleman, F. and Perryman, H. 2018. Impacts of the Deepwater Horizon oil spill evaluated using an end-to-end ecosystem model. PLoS One, 13(1): e0190840 doi: 10.1371/journal.pone.0190840

Ichthyology Field Notebooks Spreadsheet, Karisa Boyer

Ichthyology Collection

No abstract provided.

Dataset For: Tracking An Oil Tanker Collision And Spilled Oils In The East China Sea Using Multisensor Day And Night Satellite Imagery, Shaojie Sun

C-IMAGE data

In this dataset, we used a multi-sensor day and night satellite approach to track the SANCHI oil tanker collision and oil spill event in January 2018 in the East China Sea. The drifted on fire oil tanker was tracked by Visible Infrared Imaging Radiometer Suite (VIIRS) Nightfire product and Day/Night Band (DNB) imagery. Such pathway and locations were also reproduced with a numerical model, with RMS error of < 15 km. MultiSpectral Instrument (MSI) optical imagery during daytime shows smokes on 13 January 2018, further confirms the drifted tanker location. MSI imagery after 4 days of the tanker’s sinking (18 January 2018) reveals oil on the ocean surface to the east and northeast of the tanker sinking location. This combination of all available remote sensing and modeling techniques can provide effective means to monitor marine accidents and oil spills to assist event response.

Dispersant Enhances Hydrocarbon Degradation And Alters The Structure Of Metabolically Active Microbial Communities In Shallow Seawater From The Northeastern Gulf Of Mexico, Lena Chu, Elisa Mercando, Roger C. Prince, Isabel C. Romero, David Hollander

C-IMAGE data

The seawater samples were collected from Pensacola Beach, FL in June and August, 2016. The seawater was incubated with low concentration of oil (2ppm) with or without dispersant. Oil analysis and sequencing data were generated.

Microbiome And Bacterioplankton Rrna Gene Sequence Data Collected From Gulf Of Mexico Seawater Samples, Cruises Dp03 And Dp04 From April - August 2016, Cole Easson, Lindsey Freed

DEEPEND Datasets

Seawater was collected and filtered for microbiome and bacterioplankton sequencing and analyses at various depths during planned DEEPEND cruise expeditions to the GOM in 2016. Filters were stored and then processed for total environmental genomic DNA according to standard methods (see earthmicrobiome.org). 16S rRNA amplicon libraries covering the V4 hypervariable regions were generated with universal PCR primers and then sequenced on an Illumina MiSeq DNA sequencing platform. Raw paired-end sequences were joined and quality filtered in the bioinformatics program, QIIME. Vertical baseline characterizations will track alpha and beta diversity at different depths ranging from 0 – 1500 m, assess seasonal …

Evaluation Of Diet Matrix Uncertainty For The Atlantis Model, Cameron Ainsworth

C-IMAGE data

We conducted 1000 Atlantis simulations, using permutated diet matrices created by drawing from a beta distribution that represented uncertainty in predator diet. We also employed a statistical emulator which simulates the production of many more Atlantis runs than could be achieved through numerical simulation. This dataset includes 3 products: statistical emulator output, diet matrices, and Atlantis simulations. These are each contained in their own zip file.

Mitochondrial Dna Sequence Alignments And Raw Fastq Files For The Population Genetic Analysis Of The Deep Sea Isopod, Bathynomus Giganteus, Laura Timm, Barbara Moahamed

DEEPEND Datasets

This data set includes three alignments (12S, 16S, COI) of mitochondrial DNA sequences, as well as two raw fastq files generated through the next-generation sequencing (NGS) method ddRADseq. This data was collected from Bathynomus giganteus specimens collected from throughout the northeastern Gulf of Mexico.

Chlorophyll Concentration And Optical Absorption Spectra Of Particulate And Dissolved Material, Collected At Several Depths On Deepend Cruises Dp05 From January-December 2017, Chuanmin Hu

DEEPEND Datasets

The optical absorption spectra from seawater’s particulate and dissolved components can be used to compute the penetration of light to various depths, estimate the proportion of living to non-living particulate matter, assess photosynthetic light availability and the type of phytoplankton present, and to validate satellite or airborne ocean color measurements. Chlorophyll and phaeopigment concentrations are often used to estimate the amount of phytoplankton present, and to allow extrapolation of in situ fluorometric measurements. Water was collected using a CTD rosette near the surface and from several depths at each sampling station occupied by the DEEPEND cruise DP05 (see GRIIDC dataset …

Stable Isotope (13c/15n) Data Of Meso- And Bathypelagic Nekton, Northern Gulf Of Mexico, March - September 2011, T. M. Richards, E. E. Gipson

DEEPEND Datasets

These data represent stable isotope values (13C/15N) of eight species of meso- and bathypelagic nekton collected in the northern Gulf of Mexico during spring (22-March to 11-April), summer (23-June to 13-July), and fall (8-September to 27-September) of 2011. The species examined in this study include: Anoplogaster cornuta, Chauliodus sloani, Coccorella atlantica, Gigantura chuni, Gigantura indica, Omosudis lowii, Photostomias guernei, and Stomias affinis. Isotope values are derived from white muscle tissue dissected from 212 individual fish that were collected using large mid-water trawls towed from the surface to depths of either 700 or 1400 m. The samples were collected as part …

16s And Coi Barcoding Sequences For Crustaceans Collected From The Northern Gulf Of Mexico For Cruises Dp02, Dp03, And Dp04 From August 2015 - August 2016, Heather Bracken-Grissom Dr.

DEEPEND Datasets

These are the 16S and COI barcoding sequences for crustaceans collected on cruises DP02, DP03, and DP04. These barcodes, obtained from the species we collected, will be used to aid in species identification efforts, evolutionary relationships analyses, adult-larval linkages, and new species discoveries. Samples were taken from animals collected during cruises that took place in the northern Gulf of Mexico from August 2015 - August 2016.

Habitat Classification Of The Gulf Of Mexico (Gom) Using The Hybrid Coordinate Ocean Model (Hycom) And Salinity/Temperature Profiles, Cruises Dp01-Dp04, May 2015 To August 2016, Matt Johnston, Rosanna Milligan, Cole Easson, Sergio Derada, Brad Penta, Tracey Sutton

DEEPEND Datasets

Deep pelagic habitat from the entire Gulf of Mexico (GOM) was classified using the deviation of sea surface height (SSH) from mean SSH for the entire GOM and water temperature at 300 m water depth, founded on ocean condition data from the 1/25° GOM HYbrid Coordinate Ocean Model (HYCOM). Pelagic habitats were segregated into anticyclonic, mixed boundaries, and common water units – all of which likely produce varying levels of forage for deep-sea fauna and may be trophic drivers. Model classifications were compared to classifications based on water column temperature and salinity at depth, as measured by CTD casts during …

Managing Seagrass Resilience Under Cumulative Dredging Affecting Light: Predicting Risk Using Dynamic Bayesian Networks [Dataset], Paul Pao-Yen Wu, Kathryn Mcmahon, Michael A. Rasheed, Gary A. Kendrick, Paul H. York, Kathryn Chartrand, M. Julian Carey, Kerrie Mengerson

Research Datasets

Coastal development is contributing to ongoing declines of ecosystems globally. Consequently, understanding the risks posed to these systems, and how they respond to successive disturbances, is paramount for their improved management. We study the cumulative impacts of maintenance dredging on seagrass ecosystems as a canonical example. Maintenance dredging causes disturbances lasting weeks to months, often repeated at yearly intervals. We present a risk-based modelling framework for time varying complex systems centred around a dynamic Bayesian network (DBN). Our approach estimates the impact of a hazard on a system's response in terms of resistance, recovery and persistence, commonly used to characterise …

Effects Of Small-Scale, Shading-Induced Seagrass Loss On Blue Carbon Storage: Implications For Management Of Degraded Seagrass Ecosystems [Dataset], Stacey M. Trevathan-Tackett, Caitlin Wessel, Just Cebrian, Peter J. Ralph, Pere Masque´, Peter I. Macreadie

Research Datasets

1. Seagrass meadows are important global ‘blue carbon’ sinks. Despite a 30% loss of seagrasses globally during the last century, there is limited empirical research investigating the effects of disturbance and loss of seagrass on blue carbon stocks.

2. In this study, we hypothesised that seagrass loss would reduce blue carbon stocks. Using shading cloth, we simulated small-scale die-offs of two subtropical seagrass species, Halodule wrightii and Thalassia testudinum, in a dynamic northern Gulf of Mexico lagoon. The change in quantity and quality of sediment organic matter and organic carbon were compared among kill, control and bare plots before the …

Latitudinal Variation In Seagrass Herbivory: Global Patterns And Explanatory Mechanisms [Dataset], Adriana Vergés, Christopher Doropoulos, Robert Czarnik, Kathryn Mcmahon, Nil Llonch, Alistair G. B. Poore

Research Datasets

Aim: The aim was to quantify latitudinal patterns in seagrass–herbivore interactions in the context of a warming climate. Location: We carried out a global meta‐analysis combined with a field experiment across 1,700 km and 12° of latitude in Western Australia. Time period: 1984–2014. Major taxa studied: Seagrasses. Methods: We first synthesized the global literature on herbivore exclusion experiments in seagrasses to test whether differences in herbivore impacts are related to latitude and sea surface temperature. We then quantified leaf production and consumption rates in the field at nine meadows of the seagrass Amphibolis antarctica across 1,700 km, from tropical to …