http://lod.bco-dmo.org/id/dataset/991168
eng; USA
utf8
dataset
Highest level of data collection, from a common set of sensors or instrumentation, usually within the same research project
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
2026-01-08
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Drop Sampling Data from Port Fourchon, Louisiana collected in 2006, 2016, 2022 and 2023
2026-01-08
publication
2026-01-08
revision
Woods Hole Oceanographic Institution (WHOI BCO-DMO)
2026-04-14
publication
https://doi.org/10.26008/1912/bco-dmo.991168.1
James Nelson
University of Georgia
principalInvestigator
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
publisher
Cite this dataset as: Nelson, J. (2026) Drop Sampling Data from Port Fourchon, Louisiana collected in 2006, 2016, 2022 and 2023. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2026-01-08 [if applicable, indicate subset used]. doi:10.26008/1912/bco-dmo.991168.1 [access date]
Dataset Description: <p>This is one of four datasets that were produced with the "Fourchon Nekton Turnover Workflow"&nbsp; (v1.0.0, doi: https://doi.org/10.5281/ZENODO.18165331). The datasets and supplemental data produced by this workflow have had minor modifications to enhance the interoperability of the data (See more in section "BCO-DMO Processing"). The workflow contains the exact formats of the data files produced and used by the workflow scripts. It also contains scripts, configurations, readme files, and input/output files for four stages listed below. Each workflow stage corresponds to a dataset in the "Related Datasets" section.<br />
<br />
"Fourchon Nekton Turnover Workflow" steps with corresponding dataset IDs:</p>
<ul>
<li>"1_raw_data" = includes raw drop-sampling data corresponding to BCO-DMO dataset 991168&nbsp;(doi: 10.26008/1912/bco-dmo.991168.1)</li>
<li>"2_gbif_workflow" = includes&nbsp;GBIF species observation data&nbsp;corresponding to metadata in BCO-DMO dataset 991175&nbsp;(doi:&nbsp;10.26008/1912/bco-dmo.991175.1)</li>
<li>"3_CTI_calculations" = includes community temperature index (CTI) data corresponding to BCO-DMO dataset 941250&nbsp;(doi: 10.26008/1912/bco-dmo.941250.1)</li>
<li>"4_species_of_interest" = includes&nbsp;the results of a species pool analysis identifying species of interest&nbsp;corresponding to BCO-DMO dataset 991182 (doi:&nbsp;10.26008/1912/bco-dmo.991182.1)</li>
</ul>
<p>The workflow release (v1.0.0) contains data and scripts used to run analyses and produce figures for publication Leavitt, H; Thomas, A; Doerr, J; Johnson, D; Nelson, J. (In press) Resilient Nekton Composition in the Face of Climate-Driven Foundation Species Shifts. Ecology. Accepted 2025-11-14</p> Methods and Sampling: <p>Species Collections</p>
<p>All species in this study were collected using a drop sampler method specifically designed for flooded marsh habitats, providing a standardized approach across sampling years. The design of the drop samplers used in 2006, 2015, and 2022 varied slightly in terms of construction materials and deployment mechanisms to adapt to equipment improvements over time, but the essential structure remained the same. Each sampler employed a 1-m² cylinder, suspended from a boom arm, to minimize disturbance prior to deployment. The cylinder was rapidly lowered to enclose a section of flooded marsh habitat, ensuring precise capture of benthic and water-column organisms (Nelson et al., 2019; Zimmerman et al., 1984).</p>
<p>Once the sampler was in position, a 1" pump &nbsp;was used to evacuate the water inside the cylinder to concentrate captured organisms. Special care was taken to prevent loss of organisms during pumping by filtering the outflow through a 1mm plastic mesh screen mesh screen. After the water was removed, captured animals were collected manually or with fine nets and frozen until long-term identification and analysis.&nbsp;</p>
<p>All samples were transported to the laboratory for taxonomic identification. Species were identified to the lowest taxonomic level possible using a dissecting, typically genus or species.&nbsp;</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-2418012 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=2418012
completed
James Nelson
University of Georgia
jimmy.nelson@uga.edu
pointOfContact
asNeeded
Dataset Version: 1
Unknown
SampleID
Year
date
bay
taxon
abundance
AphiaID
drop sampler
theme
None, User defined
sample identification
year
date
site description
taxon
abundance
taxon_code
featureType
BCO-DMO Standard Parameters
Microscope - Optical
no_bcodmo_term
instrument
BCO-DMO Standard Instruments
otherRestrictions
otherRestrictions
Access Constraints: none. Use Constraints: Please follow guidelines at: http://www.bco-dmo.org/terms-use Distribution liability: Under no circumstances shall BCO-DMO be liable for any direct, incidental, special, consequential, indirect, or punitive damages that result from the use of, or the inability to use, the materials in this data submission. If you are dissatisfied with any materials in this data submission your sole and exclusive remedy is to discontinue use.
CAREER: Integrating Seascapes and Energy Flow: learning and teaching about energy, biodiversity, and ecosystem function on the frontlines of climate change
http://www.nelsonecolab.net/career
CAREER: Integrating Seascapes and Energy Flow: learning and teaching about energy, biodiversity, and ecosystem function on the frontlines of climate change
<p><em>NSF Award Abstract:</em><br />
Coastal marshes provide a suite of vital functions that support natural and human communities. Humans frequently take for granted and exploit these ecosystem services without fully understanding the ecological feedbacks, linkages, and interdependencies of these processes to the wider ecosystem. As demands on coastal ecosystem services have risen, marshes have experienced substantial loss due to direct and indirect impacts from human activity. The rapidly changing coastal ecosystems of Louisiana provide a natural experiment for understanding how coastal change alters ecosystem function. This project is developing new metrics and tools to assess food web variability and test hypotheses on biodiversity and ecosystem function in coastal Louisiana. The research is determining how changing habitat configuration alters the distribution of energy across the seascape in a multitrophic system. This work is engaging students from the University of Louisiana Lafayette and Dillard University in placed-based learning by immersing them in the research and local restoration efforts to address land loss and preserve critical ecosystem services. Students are developing a deeper understanding of the complex issues facing coastal regions through formal course work, directed field work, and outreach. Students are interacting with stakeholders and managers who are currently battling coastal change. Their directed research projects are documenting changes in coastal habitat and coupling this knowledge with the consequences to ecosystems and the people who depend on them. By participating in the project students are emerging with knowledge and training that is making them into informed citizens and capable stewards of the future of our coastal ecosystems, while also preparing them for careers in STEM. The project is supporting two graduate students and a post-doc.</p>
<p>The transformation and movement of energy through a food web are key links between biodiversity and ecosystem function. A major hurdle to testing biodiversity ecosystem function theory is a limited ability to assess food web variability in space and time. This research is quantifying changing seascape structure, species diversity, and food web structure to better understand the relationship between biodiversity and energy flow through ecosystems. The project uses cutting edge tools and metrics to test hypotheses on how the distribution, abundance, and diversity of key species are altered by ecosystem change and how this affects function. The hypotheses driving the research are: 1) habitat is a more important indirect driver of trophic structure than a direct change to primary trophic pathways; and 2) horizontal and vertical diversity increases with habitat resource index. Stable isotope analysis is characterizing energy flow through the food web. Changes in horizontal and vertical diversity in a multitrophic system are being quantified using aerial surveys and field sampling. To assess the spatial and temporal change in food web resources, the project is combining results from stable isotope analysis and drone-based remote sensing technology to generate consumer specific energetic seascape maps (E-scapes) and trophic niche metrics. In combination these new metrics are providing insight into species’ responses to changing food web function across the seascape and through time.</p>
<p>This project is jointly funded by Biological Oceanography and the Established Program to Stimulate Competitive Research (EPSCoR).</p>
<p>This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.</p>
Louisiana E-scapes
largerWorkCitation
project
eng; USA
oceans
-90.244
-90.16
29.095
29.168
2006-01-01
2023-01-08
Saltmarsh ecosystem near Port Fourchon, LA
0
BCO-DMO catalogue of parameters from Drop Sampling Data from Port Fourchon, Louisiana collected in 2006, 2016, 2022 and 2023
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
http://lod.bco-dmo.org/id/dataset-parameter/991551.rdf
Name: SampleID
Units: unitless
Description: <p>SampleID for site and sampling identifier</p>
http://lod.bco-dmo.org/id/dataset-parameter/991552.rdf
Name: Year
Units: unitless
Description: <p>Year of sampling</p>
http://lod.bco-dmo.org/id/dataset-parameter/991553.rdf
Name: date
Units: unitless
Description: <p>Date of sampling (not available for all years).</p>
http://lod.bco-dmo.org/id/dataset-parameter/991554.rdf
Name: bay
Units: unitless
Description: <p>Name of the bay sampling occurred (not available for all years).</p>
http://lod.bco-dmo.org/id/dataset-parameter/991555.rdf
Name: taxon
Units: unitless
Description: <p>Taxonomic name. Supplemental file aphia_codex.csv includes this as "name_in_primary_table" which can be consulted for more information.</p>
http://lod.bco-dmo.org/id/dataset-parameter/991556.rdf
Name: abundance
Units: count
Description: <p>Abundance of the identified taxon</p>
http://lod.bco-dmo.org/id/dataset-parameter/991557.rdf
Name: AphiaID
Units: unitless
Description: <p>AphiaID for "taxon" column in this table. AphiaID is the World Register of Marine Species (WoRMS) taxonomic name identifier. Supplemental file aphia_codex.csv includes this as "name_in_primary_table_AphiaID""</p>
GB/NERC/BODC > British Oceanographic Data Centre, Natural Environment Research Council, United Kingdom
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
https://doi.org/10.26008/1912/bco-dmo.991168.1
download
onLine
dataset
<p>Species Collections</p>
<p>All species in this study were collected using a drop sampler method specifically designed for flooded marsh habitats, providing a standardized approach across sampling years. The design of the drop samplers used in 2006, 2015, and 2022 varied slightly in terms of construction materials and deployment mechanisms to adapt to equipment improvements over time, but the essential structure remained the same. Each sampler employed a 1-m² cylinder, suspended from a boom arm, to minimize disturbance prior to deployment. The cylinder was rapidly lowered to enclose a section of flooded marsh habitat, ensuring precise capture of benthic and water-column organisms (Nelson et al., 2019; Zimmerman et al., 1984).</p>
<p>Once the sampler was in position, a 1" pump &nbsp;was used to evacuate the water inside the cylinder to concentrate captured organisms. Special care was taken to prevent loss of organisms during pumping by filtering the outflow through a 1mm plastic mesh screen mesh screen. After the water was removed, captured animals were collected manually or with fine nets and frozen until long-term identification and analysis.&nbsp;</p>
<p>All samples were transported to the laboratory for taxonomic identification. Species were identified to the lowest taxonomic level possible using a dissecting, typically genus or species.&nbsp;</p>
Specified by the Principal Investigator(s)
<p>Script compiles each dataset&nbsp;into a standardized format for analysis. Also compiles some species into genera or families based on the lowest common resolution of all datasets or changes to taxonomic&nbsp;classifications over time.&nbsp;<br />
&nbsp;</p>
<hr />
<p><br />
This dataset corresponds to Step <span style="font-size:13px">"1_raw_data"</span> of the study's processing workflow&nbsp;'Fourchon Nekton Turnover Workflow',(doi: 10.5281/zenodo.18165331).&nbsp; See "Description" and "BCO-DMO Processing" sections for context about the relationship between the workflow files and the data as published at BCO-DMO.</p>
<p>Workflow README for&nbsp;Step&nbsp;"1_raw_data"&nbsp;:<br />
&nbsp;</p>
<h1 dir="auto">Step 1: Raw Data Merge and Presence Tables</h1>
<p dir="auto">Purpose: consolidate drop sample datasets (2006, 2016, 2022, 2023) and produce community matrices and presence summaries for downstream CTI analyses.</p>
<p dir="auto">Primary script/notebook</p>
<ul dir="auto">
<li dir="auto">dataset_merge_and_process_BCODMO.ipynb: annotated Jupyter notebook that loads raw CSVs, standardizes taxonomic names, and outputs presence/community products.</li>
</ul>
<p dir="auto">Inputs (inputs/)</p>
<ul dir="auto">
<li dir="auto">raw_2006_fish.csv,&nbsp;raw_2006_invert.csv,&nbsp;raw_2006_peneid.csv,&nbsp;2006_site_data.csv&nbsp;(+ parameter descriptions).</li>
<li dir="auto">raw_2016.csv&nbsp;(+ parameter description).</li>
<li dir="auto">raw_2022.csv,&nbsp;raw_2023.csv&nbsp;(+ parameter descriptions).</li>
<li dir="auto">final_aphia_codex_edited.csv&nbsp;(taxonomic lookup across survey years).&nbsp; Additional columns added to "aphia_codex.csv" in the BCO-DMO dataset.</li>
<li dir="auto">species_presence_2006_2016_2022.csv&nbsp;(coarse presence metadata).</li>
</ul>
<p dir="auto">Outputs (outputs/)</p>
<ul dir="auto">
<li dir="auto">pivot_all.csv: community matrix (SampleID x Taxon) with Year column. [BCO-DMO note:&nbsp;this data is listed as&nbsp;<span style="font-size:13px">991168_v1_port-fourchon_drop-sampling.csv on the BCO-DMO page, See BCO-DMO Processing section for minor differences between the workflow file and the BCO-DMO hosted file]</span></li>
<li dir="auto">presence_summary.csv,&nbsp;presence_pivot.csv: per-taxon site-level presence proportions.</li>
<li dir="auto">presence_summary2.csv,&nbsp;presence_pivot_merged_sp.csv: presence after taxonomic harmonization for CTI use.</li>
</ul>
<p dir="auto">Software</p>
<p dir="auto">Run order</p>
<ol dir="auto">
<li dir="auto">Open and run&nbsp;dataset_merge_and_process_BCODMO.ipynb.</li>
<li dir="auto">Confirm outputs in&nbsp;outputs/&nbsp;before proceeding to GBIF downloads (Step 2).</li>
</ol>
Specified by the Principal Investigator(s)
Version 1 (2026-01-08):
Data from the processing workflow were prepared and published at BCO-DMO after reorganization into datasets with minor changes performed to meet the required conventions implemented by BCO-DMO designed for interoperability, standardization, and a variety of data access methods.
Submitted data files for this dataset correspond to the study's outputs in workflow (doi: 10.5281/zenodo.18165331) step 1:
The primary data table for this dataset corresponds to the Workflow data file 1_raw_data/outputs/pivot_all.csv
* Data within pivot_all.csv imported into the BCO-DMO data system. Two duplicate column names "Unknown Fish" were renamed "Unknown_Fish_1" and "Unknown_Fish_2."
* The table contained abundances presented in a column per taxon identification. This was unpivoted to be presented in columns SampleID,Year,taxon,abundance (instead of an abundance column per species). This allowed characters within the taxon names (corresponding to final_aphia_codex_edited.csv) to be preserved. BCO-DMO column naming conventions are more restrictive than data values in order to support broad interoperability between data systems (column names can only contain letters, numbers and underscores).
* The bay and collection date were joined into the primary data table from data within raw_2016.csv based on joining on the SampleID. This was done because BCO-DMO includes collection information where possible for field data including date, time(if applicable), lat, lon, depth and any other relevant context identifiers for site,station, cast as applicable. The main data table includes a year and SampleID which corresponds to a sampling instance (site and date/year) but due to the nature of the data source from literature and study objectives, the typical set of collection information BCO-DMO datasets typically include are not included for this dataset.
---
Supplemental files:
All supplemental files correspond to files within the Workflow stage 1_raw_data/inputs and 1_raw_data/outputs. The only differences being:
* Any un-named leading columns were not included as presented at BCO-DMO. The data submitter indicated this was a legacy column not needed.
* date formats changed to ISO 8601 format yyyy-mm-dd (affects raw_2016.csv)
* Additions made to final_aphia_codex_edited.csv using the World Register of Marine Species on 2026-01-16. The AphiaID in this table was not identifying the true_name or valid_name columns in some cases but was identifying a different unaccepted synonym in some cases. The true_name did match the currently accepted names as of 2026-01-16 so additional columns true_name_AphiaID and true_name_LSID were added. Table added to this dataset as aphia_codex.csv. Values "API request failed" for no-matches were replaced with missing data values (blank by default in csv files).
* Precise column descriptions were supplied by the submitter as excel files. These were exported to csv and added to this dataset within supplemental file "supplemental_file_column_info.zip"
Note: All supplemental files meet BCO-DMO naming conventions designed for interoperability purposes except for raw_2016.csv as changing the identification column names would affect the ability to pair the taxon information for the name using information in aphia_codex.csv
Specified by BCO-DMO Data Managers
asNeeded
7.x-1.1
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
PI Supplied Instrument Name: Instrument Name: Microscope - Optical Instrument Short Name: Instrument Description: Instruments that generate enlarged images of samples using the phenomena of reflection and absorption of visible light. Includes conventional and inverted instruments. Also called a "light microscope". Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/LAB05/
drop sampler
drop sampler
PI Supplied Instrument Name: drop sampler PI Supplied Instrument Description:All species in this study were collected using a drop sampler method specifically designed for flooded marsh habitats, providing a standardized approach across sampling years. The design of the drop samplers used in 2005, 2015, and 2022 varied slightly in terms of construction materials and deployment mechanisms to adapt to equipment improvements over time, but the essential structure remained the same. Each sampler employed a 1-m² cylinder, suspended from a boom arm, to minimize disturbance prior to deployment. The cylinder was rapidly lowered to enclose a section of flooded marsh habitat, ensuring precise capture of benthic and water-column organisms (Nelson et al., 2019; Zimmerman et al., 1984). Instrument Name: no_bcodmo_term Instrument Short Name: Instrument Description: No relevant match in BCO-DMO instrument vocabulary. Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/999/