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2,345 results for “shark”
Count data of air-breathing fauna from visual transect surveys including water temperature, time, sea and weather conditions in Shark Bay Marine Park, Western Australia from February 2008 to July 2014
This dataset provides information on the relative abundances of air breathing fauna (dugongs, dolphins, sea snakes, marine birds, and sea turtles) in the study area of the Eastern Gulf of Shark Bay, Western Australia. The dataset comprises transects that quantify animal abundances in three microhabitats (shallow seagrass banks, seagrass bank edges, and deep sandy channels). These microhabitats vary in their food supply as well as their potential to facilitate or inhibit detection and escape from predators, mainly the tiger shark (Galeocerdo cuvier). As a result these data have been used to examine risk-specific habitat use behaviors of these fauna, in addition to general abundance estimates.
Marine turtles captured during haphazard at-sea surveys in Shark Bay, Australia from February 2008 to December 2013
This dataset provides information on marine turtles captured during long-term, haphazard surveys of our study site in Shark Bay, Western Australia. Taxon found in the study area include Chelonia mydas, Caretta caretta and Eretmochelys imbricata.
Stationary camera observations, set, and environmental data from Shark Bay Marine Park, Western Australia from July 2011 to June 2012
This dataset provides information on stationary video cameras set within the study area from 2011 to 2012, including animals viewed along with relevent environmental and camera data. These data provide insight into teleost communities that utilize various habitats within Shark Bay.
Fish trap catch, set, and environmental data from Shark Bay Marine Park, Western Australia from May 2010 to July 2012
This dataset provides information on fish traps set within the study area from 2010 to 2012, including animals caught, relevent environmental and trap data, animal specific measurements and logging of samples retained. Additionally the dataset contains stable isotope values for individuals that were retained for Stable Isotope Analysis in addition to stomach content data. These data provide insight into teleost communities that utilize various habitats within Shark Bay with further insights into their trophic relationships.
Biogeochemical data collected from Northeast Shark River Slough, Everglades National Park, Florida, USA, September 2006 - April 2025
This project was established in 2006 to document the pattern of abundance of key ecological indicators (e.g., surface water, soil, floc, periphyton and sawgrass) across the NESRS landscape. A total of 30 sites were established and monitored in 2006, 2007 and 2008. After the completion of 1-mile bridge in 2012, additional 10 new sites were established to observe the ecological impact of 1-mile bridge (known as Bridge & Census sites). In 2015, additional 40 sites were established along eight transects (T1-T8, known as near canal sites) in ENP marshes starting at, and roughly perpendicular to the L-29 canal. The purpose of these sites was to monitor the potential effects of Modified Water Deliveries (MWD) operations on changing nutrient concentrations and ratios in key ecological compartments due to increased downstream discharges from the L-29 canal beneath the 1-mile and 2.6-mile bridges and culverts along Tamiami Trail. Data collection is complete.
Monthly monitoring fluorescence data for Shark River Slough and Taylor Slough, Everglades National Park, Florida, USA (FCE LTER) for 2012 - 2020
Dissolved organic matter plays an important role in biogeochemical processes in aquatic environments such as elemental cycling, microbial loop energetics, and the transport of materials across landscapes. Since most of N (> 90%) and P (around 90%) is in the organic form in the oligotrophic subtropical Florida Coastal Everglades (FCE), study of the source and dynamics of dissolved organic matter (DOM) in the ecosystem is crucial for the better understanding of the biogeochemical cycling of nutrients. FCE are composed of estuaries with distinct regions with different biogeochemical processes. Freshwater marsh primarily receives terrestrial input and local autochthonous vegetation production. Mangrove ecotone, nevertheless, is affected by the tidal contributions from Florida Bay and local mangrove production. Florida Bay (FB) is a wedge-shaped shallow oligotrophic estuary which lays south of the Everglades, the bottom of which is covered with a dense biomass of seagrass. The sources of both freshwater and nutrients in FCE are difficult to quantify, owing to the non-point source nature of runoff from the Everglades and the dendritic cross channels in the mangroves. Furthermore, the combination of multiple DOM sources (freshwater marsh vegetation, mangroves, phytoplankton, seagrass, etc.), and the potential seasonal variability of their relative contribution, along with the history of (photo)chemical and microbial diagenetic processing, and complex advective circulation, makes the study of DOM dynamics in FCE particularly difficult using standard schemes of estuarine ecology. Quantitative information of DOM is very useful to investigate the biogeochemical cycling of DOM to a certain degree, however, qualitative information is necessary to better understand the source and dynamics of DOM. Since fluorescence spectroscopic techniques are very sensitive, quick and simple, they have been applied to investigate the fate of DOM in estuaries.Monthly fluorescence monitoring data
Inventory of High-resolution phylogenetic profiles of the planktonic microbial communities (via 16S and 18S rRNA gene amplicons) from Shark River Slough and Taylor Slough, Everglades National Park (FCE LTER), Florida, USA, 2017 - ongoing
Planktonic microbial communities mediate many vital biogeochemical processes in wetland ecosystems, yet compared to other aquatic ecosystems, like oceans, lakes, rivers, or estuaries, they remain relatively underexplored. Our study site, the Florida Everglades (USA)—a vast iconic wetland consisting of a slow-moving system of shallow rivers connecting freshwater marshes with coastal mangrove forests and seagrass meadows—is a highly threatened model ecosystem for studying salinity and nutrient gradients, as well as the effects of sea level rise and saltwater intrusion. This dataset provides the first high-resolution phylogenetic profiles of planktonic bacterial and eukaryotic microbial communities (using 16S and 18S rRNA gene amplicons) from these environments. The dataset contains 16S and 18S rRNA data from 2017, and contains 16S rRNA data for monthly (2019) and quarterly water samples (2020-ongoing). The 2017 data are published in Laas et al. 2022. A detailed list of sequence data and their accession numbers in GenBank is provided and will be updated as more data are published. This data package is an inventory of sequence read archive (SRA) entries available through GenBank BioProject PRJNA525456 (at https://www.ncbi.nlm.nih.gov/bioproject/PRJNA525456) and BioProject PRJNA1018945 (at https://www.ncbi.nlm.nih.gov/bioproject/PRJNA1018945). This data package is associated with the following publication: Laas, P., Ugarelli, K., Travieso, R., Stumpf, S., Gaiser, E. E., Kominoski, J. S., & Stingl, U. (2022). Water column microbial communities vary along salinity gradients in the Florida Coastal Everglades wetlands. Microorganisms, 10(2), 215. https://doi.org/10.3390/microorganisms10020215 Instead of citing this package, which is an inventory, please cite the original GenBank data or journal article, as appropriate. Citation guidance for the journal article is available on the respective publisher's website.
Alligator pond food-web sampling in Shark River Slough and Taylor Slough, Everglades National Park, Florida, USA, 2018–2019
These datasets were used to investigate if American Alligators engineer differences in nutrient availability and changes to community structure by their creation of “alligator ponds” compared to the surrounding phosphorus (P)-limited oligotrophic marsh in the Everglades. We used a halo sampling design of three distinct habitats extending outward from ten active alligator ponds across a hydrological gradient. We performed nutrient analysis on basal food-web resources and quantitative community analyses, and stoichiometric analyses on plants and animals. These data underly the work in Strickland et al. (2023). An apex predator engineers wetland food-web heterogeneity through nutrient enrichment and habitat modification. Journal of Animal Ecology.
Long-Term Aquatic Faunal Sampling via Throw Trap in Shark River Slough, Everglades, Florida, USA, 1978 – 2021
Long-term monitoring of fish communities in the Everglades using 1-m2 throw traps started in 1978 and is ongoing. Data represent the number of individuals per species collected per throw trap (i.e., individuals per square meter). From 1978-1995 sampling occurred five times per year, referred to as periods, at one plot per site and the number of throws was determined by estimates of inter-sample variance. In 1996, the spatial extent of monitoring was expanded to include additional sites and multiple plots per site. At each plot 5-7 throw trap samples were collected with sampling location within a plot being drawn from a random number table. Days since dry (DSD) are calculated as the number of days since depth was last < 5 cm using the Everglades Depth Estimation Network and in situ depth measurements. Statistical comparisons of community composition can be found in FCE1258_community_change.Rmd
Mangrove Leaf Litter Carbon and Nutrients from the Shark River Slough, Everglades National Park (FCE), South Florida, USA, January 2019 - ongoing
Mangrove litterfall dynamics have been monitored in all Shark River sites (SRS-4, SRS-5, SRS-6) since January 2001 using the same collection method stated in Castañeda-Moya et al. 2013 (metadata: knb-lter-fce.1195) and Danielson et al. 2017. Briefly, litterfall was collected monthly at all sites (10 baskets per site) using permanent 0.25 m2 wooden baskets supported approximately 1.3 m above the soil surface and lined with 1 mm mesh screening. Litterfall from each basket was sorted, dried, and weighed by leaf species, reproductive parts by species, and woody material. Leaf litter data from different years (2019, 2020, 2021, 2023) were selected for each site to identify species-specific foliar carbon and nutrient (N and P) content. Monthly leaf litter samples were analyzed separately by species for all years after grinding with a Wiley Mill to pass through a 40-µm mesh screen. Total leaf litter C and N contents were determined with a Carlo-Erba NA-1500 elemental analyzer (Fisons Instruments Inc., Danvers, MA, USA). Total leaf litter P was extracted using an acid-digest (HCl) extraction, and concentrations of SRP were determined by spectrophotometric analysis (Methods 365.4 and 365.2, USA EPA 1983). Litterfall data collection is ongoing every year since 2001, while C and nutrients analyses are performed every other year after 2021. See also Shark River mangrove litterfall data (knb-lter-fce.1195) on the FCE LTER website's data catalog or in the EDI repository (https://portal.edirepository.org/nis/mapbrowse?scope=knb-lter-fce&identifier=1195). References: Castañeda-Moya, E., Twilley, R. R., & Rivera-Monroy, V. H. (2013). Allocation of biomass and net primary productivity of mangrove forests along environmental gradients in the Florida Coastal Everglades, USA. Forest Ecology and Management, 307, 226-241. Danielson, T.M., V.H. Rivera-Monroy, E. Castaneda-Moya, H. Briceno, R. Travieso, B.D. Marx, E. Gaiser, and L.M. Farfan. 2017. Assessment of Everglades mangrove forest re
Root productivity of riverine and scrub mangroves from the Shark River Slough and Taylor Slough, Everglades National Park (FCE LTER), Florida, USA, March 2024 - April 2024
Root productivity of riverine and scrub mangroves in the Florida Everglades: Mangrove root productivity in the shallow root zone (0-45 cm depth) was estimated at all Shark River (SRS-4, SRS-5, SRS-6, SRS-7) and Taylor River (TS/Ph-6, TS/Ph-7) sites in March-April 2024. Root productivity was estimated with the ingrowth core technique using the same sampling protocol previously published for the study area (Castañeda-Moya et al. 2011). Ingrowth cores (10.2 cm diameter x 45 cm length) were made of synthetic material (3 mm mesh) and filled with root-free commercial sphagnum peat moss. This material has similar soil properties (i.e., bulk density, organic matter content, total C and N) as mangrove peat in our study sites as previously reported by Castañeda-Moya et al. (2011). Ingrowth cores were installed in holes made out with a PVC coring device (10.2 cm diameter x 45 cm length). At each site, 8 ingrowth cores were deployed vertically into the soil to a depth of 45 cm and retrieved one year later (March-April 2024). After collection, ingrowth cores were processed individually and initially rinsed with water through a 1-mm screen mesh to remove soil particles and peat moss material. Live roots were separated manually based on their buoyancy, turgor, and color (Castañeda-Moya et al. 2011; Cormier et al. 2015; Medina-Calderon et al. 2021). Live roots were further sorted into three size diameter classes including fine (<2 mm), small (2-5 mm), and coarse (5-20 mm). Roots greater than 20 mm in diameter were not included in this study due to sampling limitations (i.e., core area). All root samples were oven-dried at 60°C to a constant mass and weighed. Root growth within each ingrowth core following one year of incubation was used to estimate annual root productivity (g m⁻² yr⁻¹) in the shallow root zone across all mangrove sites. All data collection and processing were funded by FCE-LTER. Data collection is complete. References: Castañeda-Moya, E., R.R. Twilley, V.H. Rivera-
Metagenomics of a pustular microbial mat from Shark Bay, Australia: Raw sequences and assembled MAGs
<p>This data accompanies the paper, "<a href="https://www.nature.com/articles/s43705-022-00128-1">Metagenomic, (bio)chemical, and microscopic analyses reveal the potential for the cycling of sulfated EPS in Shark Bay pustular mats</a>" which looks at the cycling of sulfated polysaccharides in peritidal pustular mats from Shark Bay, Australia. The microbial community was sequenced, assembled, and binned. The raw sequencing reads used in this analysis are the following:</p> <ul> <li>SB_forward_paired_copy.fastq.gz </li> <li>SB_reverse_paired_copy.fastq.gz </li> </ul> <p>The resulting metagenome-assembled genomes (MAGs) are presented in the following folder:</p> <ul> <li>MAGs.zip</li> </ul> <p> </p> <ul> </ul> <p> </p>
Satellite tracking data of white sharks in the southwest Indian Ocean (2012-2014)
<p>These data comprise locations and individual metadata from 34 white sharks (<em>Carcharodon carcharias</em>) instrumented March-May 2012 with telemetry devices along the coast of South Africa. These devices were SPOT5 transmitters (SPOT-257, SPOT-258; Wildlife Computers) which transmit locations via ARGOS CLS. All research methods were approved and conducted under the South African Department of Environmental Affairs: Oceans and Coasts permitting authority.</p> <p>This dataset is linked to the manuscript Kock et al. 2021 "Sex and size influence the spatiotemporal distribution of white sharks, with implications for interactions with fisheries and spatial management in the southwest Indian Ocean".</p> <p>The data are structured in long format, so that each row in the dataset represents an observation. The columns in the data are as follows.</p> <p>DeployID: This a factor variable identifying each individual shark. It has 34 levels.</p> <p>SPOT: This is a numeric variable identifying the tag number unique to each shark.</p> <p>Date: This is a date variable (POSIXct) that gives the date and time of a geographic location record in UTC time.</p> <p>Type: This is a character variable identifying the type of location record.</p> <p>Quality: This is a character variable made up of numbers and letters giving the location error associated with each location as provided by ARGOS.</p> <p>Latitude: This is a numeric variable and gives the latitude of the shark at the time of each record.</p> <p>Longitude: This is a numeric variable and gives the longitude of the shark at the time of each record.</p> <p>Area_tagged: This is a character variable that gives the area where the shark was tagged.</p> <p>Sex: This is a character variable identifying the sex of the shark, either "F" or "M" for female and male.</p> <p>TL: This is a numeric variable giving the total length of the shark in centimetres.</p> <p>Maturity: This is a character variable giving the maturity of the shark based on its total length following Malcolm et al. 2001: juveniles (male and female: 175-300 cm TL), sub-adults (male: >300-360 cm TL; females: >300-480 cm TL) and adults (male: >360 cm TL; female: >480 cm TL).</p> <p> </p>
Sharkipedia: A Curated Open Access Database of Shark and Ray Life History Traits and Abundance Time-series
<p>This dataset represent the intial launch of Sharkipedia: a curated open access database of shark and ray life history traits and abundance time-series. A curated database of shark and ray biological data is increasingly necessary both to support fisheries management and conservation efforts, and to test the generality of hypotheses of vertebrate macroecology and macroevolution. Sharks and rays are one of the most charismatic, evolutionary distinct, and threatened lineages of vertebrates, comprising around 1,250 species. To accelerate shark and ray conservation and science, we developed Sharkipedia as a curated open-source database and research initiative to make all published biological traits and population trends accessible to everyone. Sharkipedia hosts information on 58 life history traits from 264 sources, for 170 species, from 39 families, and 12 orders related to length (n=9 traits), age (8), growth (12), reproduction (19), demography (5), and allometric relationships (5), as well as 871 population time-series from 202 species. Sharkipedia relies on the backbone taxonomy of the IUCN Red List and the bibliography of Shark-References. Sharkipedia has profound potential to support the rapidly growing data demands of fisheries management, international trade regulation as well as anchoring vertebrate macroecology and macroevolution.</p>
Water Temperature measured at Shark River, Everglades National Park (FCE) from October 2007 to August 2008
American alligators (Alligator mississippiensis) are top predators in the Florida Coastal Everglades (FCE), but their movement patterns and role in the ecosystem are largely unknown. Proposed restoration and management efforts in the Everglades are likely to influence both alligator movements and the spatiotemporal patterns of their effects on ecosystem and community dynamics, making studies of the factors influencing alligator movements important at this time. In October 2007, we initiated a study of alligators in the Shark River Slough of Everglades National Park using two tracking techniques that have yet to be used on crocodilians: GPS tracking and passive acoustic telemetry. GPS units attached to two alligators have provided 120 positions over a two month period while acoustic transmitters attached to 12 alligators have been detected 34,000 times on an array of 8 monitoring stations within the river system. GPS positions are more accurate than acoustic monitoring and can provide data over the entire range an alligator might move, but acoustic transmitters provide more temporally detailed information on movements within a monitoring array and over a longer duration (potentially years rather than months). Our preliminary results show that alligators may remain in localized areas for weeks at a time, but make long-distance moves from the mouth of the river system to the marsh-mangrove ecotone and likely into the marsh. In general, most alligators moved upstream as freshwater inputs decreased, but some individuals remained near the river mouth even when salinities were high. Ultimately, by characterizing alligator movements in relation to spatiotemporal variation in environmental factors we will be able to predict how alligator distributions and populations will respond to planned increases in freshwater flow. Furthermore, movement data combined with dietary and stable isotopic studies may shed light on the possible role of alligators in the redistribution of nutri
Water Temperature, Salinity and other physical measurements taken at Shark River, Everglades National Park (FCE LTER) from February 2010 to March 2014
In early 2010 we established three new permanent water quality monitoring stations in the Shark River Estuary. These stations expanded FCE's spatial coverage in terms of salinity and also established the first continuous dissolved oxygen monitoring in the estuary.
Water Temperature measured at Shark River, Everglades National Park (FCE) from July 2007 to June 2011
Between 2007 and 2011 we placed HOBO continuous water temperature loggers at 17 locations in the Shark River Estuary for various lengths of times. These stations expanded FCE's spatial coverage in terms of temperature monitoring in the estuary.
Community structure of aquatic vertebrates and macroinvertebrates in relation to hydrologic variables in the Shark River Slough, Everglades National Park, Florida USA: Ongoing since 2012
The purpose of this project is to characterize the community structure of aquatic fauna (macroinvertebrates and fishes) and floating mats (including periphyton) across the heterogenous landscape of the NE Shark River Slough in Everglades NP. The community structure (abundance, biomass, and species composition) of floating mat, emergent vascular plants, fishes, and macroinvertebrates, and the spatial distribution of the latter in relation to hydrology, are among the key performance measures targeted for monitoring. The aim of our study is to provide a baseline characterization of these parameters so that the impact of future management activities (e.g., Modified Water Deliveries and Comprehensive Everglades Restoration Plan) can be assessed. The study area is sampled during the late wet season (September through November) to capture data when all sites are innundated with water and aquatic animal standing stocks are typically at their maximum. We document landscape-scale patterns in the NE Shark River Slough from this comprehensive sampling.
Inventory of soil prokaryotic microbiome (via 16S based on rRNA gene amplicons) in freshwater and brackish water marshes following saltwater intrusion along Shark River Slough boundary, Everglades National Park (FCE LTER), Florida, USA, September 2018
Global sea-level rise is transforming coastal ecosystems, especially freshwater wetlands, in part due to increased episodic or chronic saltwater exposure, leading to shifts in microbial communities and related ecological services. Soil prokaryotes play a fundamental role in regulating important biogeochemical processes in coastal wetland ecosystem. Yet, it is still difficult to predict how soil prokaryotic communities respond to the saltwater exposure because of poorly understood prokaryotic sensitivity within complex wetland soil microbial communities, as well as the high heterogeneity of wetland soils and saltwater exposure. To address this, a four-year experimental simulation of saltwater intrusion in a pristine freshwater site and a previously saltwater-impacted site was conducted. The saltwater addition started in October 2014 on a monthly basis and continued through October 2018. The dataset contains amplicon sequencing date of 16S rRNA gene obtained from saltwater-exposed soils and unmanipulated native soils in both sites (collected in September 2018). The 2018 data are published in Zhao et al. 2023. A detailed list of sequence data and their accession numbers in GenBank is provided, and data collection is complete. This data package is an inventory of sequence read archive (SRA) entries available through GenBank BioProject PRJNA804545 (https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJNA804545). This data package is associated with the following publication: Zhao, J., Chakrabarti, S., Chambers, R., Weisenhorn, P., Travieso, R., Stumpf, S., Standen, E., Briceno, H., Troxler, T., Gaiser, E., Kominoski, J., Dhillon, B., & Martens-Habbena, W. (2023). Year-around survey and manipulation experiments reveal differential sensitivities of soil prokaryotic and fungal communities to saltwater intrusion in Florida Everglades wetlands. Science of The Total Environment, 858, 159865. https://doi.org/10.1016/j.scitotenv.2022.159865 Instead of citing this package, which is an
Inventory of soil prokaryotic and fungal microbiome (via 16S rRNA gene amplicons and ITS sequencing) from Shark River Slough and Taylor Slough, Everglades National Park (FCE LTER), Florida, USA, February 2019 - October 2020
Global sea-level rise is transforming coastal ecosystems, especially freshwater wetlands, in part due to increased saltwater exposure, leading to change in soil microbial communities and many important biogeochemical processes. Given the high spatial and temporal heterogeneity in coastal wetlands, especially in tropical or subtropical climates characterized by seasonal temperature, precipitation, and tidal fluctuations, it remains unclear which environmental factors influence the compositions of soil microbial communities in wetlands affected by varying degrees of sea-water intrusion. To address this, a two-year survey was conducted on microbial community structure in submerged surface soils from 14 wetland sites across the Florida Everglades, representing three major ecosystem types, i.e. freshwater marshes, mangrove forests, and seagrass meadows. Bulk surface soil samples of each site were collected from February 2019 to October 2020 to cover dry and wet seasons. In addition to bulk soil samples, soil cores were collected from each site in August 2020 to assess vertical gradients of microbial communities. The dataset contains amplicon sequencing data of 16S rRNA gene (both bulk soil and soil cores) and ITS gene (only the bulk soil). The 2019 to 2020 data are published in Zhao et al. 2023. A detailed list of sequence data and their accession numbers in GenBank is provided, and data collection is complete. This data package is an inventory of sequence read archive (SRA) entries available through GenBank BioProject PRJNA804243 (https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJNA804243), PRJNA804246 (https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJNA804246), and PRJNA804228 (https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJNA804228). This data package is associated with the following publication: Zhao, J., Chakrabarti, S., Chambers, R., Weisenhorn, P., Travieso, R., Stumpf, S., Standen, E., Briceno, H., Troxler, T., Gaiser, E., Kominoski, J., Dhillon, B., & Martens-H
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Allen Brain Atlas
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