http://lod.bco-dmo.org/id/dataset/969846
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
2025-07-24
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Flow cytometry data from Incurrent and Excurrent flow samples collected from shallow artificial reef sponges and seawater in the Florida Keys, USA from Apr 2021 to Aug 2021
2025-08-29
publication
2025-08-29
revision
Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)
2025-11-12
publication
https://doi.org/10.26008/1912/bco-dmo.969846.1
Cole G. Easson
Middle Tennessee State University
principalInvestigator
Cara L. Fiore
Appalachian State University
principalInvestigator
Christopher J. Freeman
College of Charleston
principalInvestigator
Robert W. Thacker
Stony Brook University
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: Easson, C. G., Freeman, C. J., Fiore, C. L., Thacker, R. W. (2025) Flow cytometry data from Incurrent and Excurrent flow samples collected from shallow artificial reef sponges and seawater in the Florida Keys, USA from Apr 2021 to Aug 2021. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2025-08-29 [if applicable, indicate subset used]. doi:10.26008/1912/bco-dmo.969846.1 [access date]
Flow cytometry data from Incurrent and Excurrent flow Dataset Description: Methods and Sampling: <p><strong>Location</strong><br />
Samples were collected on shallow reefs (&lt;10m) in the Florida Keys, USA. The temporary artificial reef was constructed adjacent to patch reefs within the Looe Key special preservation area. At the conclusion of the experiment, the reef was completely dismantled.&nbsp;The environment was well mixed by wave action within minimal tidal influence.</p>
<p><strong>Collection and Analysis</strong></p>
<p>One-milliliter of seawater samples were collected via VacuSIP and preserved in&nbsp;paraformaldehyde (0.5% final concentration),&nbsp;flash frozen in liquid nitrogen, and then shipped to Bigelow Laboratory for Ocean Sciences.&nbsp;At this laboratory, the following methodology was used:</p>
<div>
<p>A ZE5 Cell Analyzer flow cytometer (Bio-Rad, Hercules, CA, USA) was used to measure optical properties of single cells from each sample and quantify requested populations. To ensure accurate calibration of the flow cytometer, ZE5 QC beads (Bio-Rad, Hercules, CA, USA) were run daily.</p>
<p>Picophytoplankton (less than 3 µm) and nanophytoplankton (3-20 µm) were analyzed using a slight modification of the method described in Lomas et al., 2010. Immediately after thawing at room temperature, 300-400 µl of sample was prescreened through 70 µm mesh and run at a flow rate of 1 µl sec-1. Particles were excited with a 488 nm blue laser and data acquisition was triggered on red fluorescence. Signals were recorded from detectors with bandpass filters for forward scatter (FSC), right angle light scatter (SSC) and fluorescence emission in red (692/80 nm) indicative of chlorophyll a, and orange (593/52 nm) for phycoerythrin. Data files were analyzed from logarithmic dot plots based on fluorescence and characteristic light scattering properties (DuRand &amp; Olson, 1996) using FlowJo 10.6 software&nbsp;(FlowJo, 2023)&nbsp;(Becton Dickinson &amp; Company, San Jose, CA, USA). Total pico and nano phytoplankton populations were identified based upon cell size and red fluorescence. Phycoerythrin containing cell populations were determined by orange fluorescence. Based upon these gating criteria, the number of cells in each identified population was enumerated and converted to cell abundances using the processed sample volume and adjusted for dilution by preservative.</p>
<p>For total bacteria analysis, samples were thawed, diluted 1:10 with Tris EDTA (TE) Buffer pH 8.0 and stained using a 10x working stock of SYBR Green I Nucleic Acid Stain (Thermofisher Scientific, USA) at room temperature in the dark for 15 min using the protocol of Marie et al. (2005). At a flow rate of 0.5 µl sec-1, 180 µl of the diluted sample was run. Particles were excited with a 488 nm blue laser and data acquisition was triggered on green fluorescence. Signals were recorded from detectors with bandpass filters for forward scatter (FSC), right angle light scatter (SSC) and fluorescence emission in green (525/35nm). Data files were analyzed from two logarithmic scatter plots based on fluorescence and characteristic light scattering properties. Total bacteria counts were identified based on size and presence of green fluorescence and counts were converted to cell abundances using the volume of sample processed including adjustments for preservation, dilution and staining.</p>
</div>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1915949 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1915949
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1756799 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1756799
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1929293 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1929293
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1756114 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1756114
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1756249 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1756249
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1756171 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1756171
completed
Cole G. Easson
Middle Tennessee State University
615-898-5822
1672 Greenland Drive SCI 2044
Murfreesboro
TN
37132
USA
Cole.Easson@mtsu.edu
pointOfContact
Cara L. Fiore
Appalachian State University
828-262-7548
572 Rivers St
Boone
NC
28607
USA
fiorec@appstate.edu
pointOfContact
Christopher J. Freeman
College of Charleston
817-707-5840
66 George Street Department of Biology
Charleston
SC
29424
USA
freemancj@cofc.edu
pointOfContact
Robert W. Thacker
Stony Brook University
631-632-9949
West 5510 FRK MEL LIB
Stony Brook
NY
11794
USA
robert.thacker@stonybrook.edu
pointOfContact
asNeeded
Dataset Version: 1
Unknown
Collection_Date
Latitude
Longitude
Sample_ID
Species
Species_Abbreviation
In_or_Ex
Replicate
Collection_day
TotPhyto_Conc
Syn_Conc
Pro_Conc
Photosynthetic_Eukaryotes
TotBact_Conc
HNA_Conc
LNA_Conc
LSID
AphiaID
VacuSIP
ZE5 Cell Analyzer flow cytometer (Bio-Rad, Hercules, CA, USA)
theme
None, User defined
date
latitude
longitude
sample identification
species scientific name (binomial)
No BCO-DMO term
sample description
replicate
days
abundance
synechococcus abundance from flow cytometry
prochlorococcus abundance
heterotrophic bacteria abundance from flow cytometry
heterotrophic bacteria abundance
Life Science Identifier (LSID)
taxon_code
featureType
BCO-DMO Standard Parameters
Discrete water sampler
Flow Cytometer
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.
Collaborative Research: Investigations into microbially mediated ecological diversification in sponges
https://osprey.bco-dmo.org/project/772220
Collaborative Research: Investigations into microbially mediated ecological diversification in sponges
<p><em>NSF Award Abstract:</em><br />
Coral reefs represent a paradox because, despite their immense productivity and biodiversity, they are found in nutrient-poor habitats that are equivalent to "marine deserts." High biodiversity is often associated with a division of resources that allows many types of organisms to coexist with minimal competition. Indeed, unlike many other organisms on coral reefs, sponges are adapted to efficiently remove bacteria, phytoplankton, and dissolved organic matter from seawater by filter-feeding. Sponges are a dominant component of coral reefs worldwide and in the Caribbean, where their biomass exceeds that of reef-building corals. For almost a quarter century, the success of sponges in the Caribbean has been linked to their filter-feeding ability. However, recent work demonstrated that coexisting sponges on Caribbean reefs host unique communities of bacteria that might allow sponges to access multiple pools of nutrients that are not available to other organisms. In this project, the investigators will test the hypothesis that ecologically dominant sponge species in the Caribbean have unique metabolic strategies that are mediated by their associations with microbes that live within the sponge body. This research will combine manipulative field experiments with a novel combination of modern analytical tools to investigate both filter-feeding by sponge hosts and the metabolic pathways of their microbes. This work will advance our understanding of the ecological and evolutionary forces that have helped shape the species present on Caribbean coral reefs. Additionally, this project will support three early-career investigators and provide training opportunities for graduate and undergraduate students at Nova Southeastern University, Appalachian State University, Stony Brook University, and Smithsonian Marine Station. The investigators will also develop innovative outreach programs that expand existing platforms at their institutions to increase public engagement and scientific literacy.</p>
<p>Marine sponges have been widely successful in their expansion across ecological niches in the Caribbean, with biomass often exceeding that of reef-building corals and high species diversity. However, whether this success is linked to efficient heterotrophic filter-feeding on organic carbon in the water column or to their evolutionary investment in microbial symbionts is yet to be fully elucidated. Microbial symbionts expand the metabolic capabilities of host sponges, supplementing heterotrophic feeding with inorganic carbon and nitrogen, mediating the assimilation of dissolved organic matter, and facilitating recycling of host-derived nitrogen. Despite these benefits, microbial symbiont communities are widely divergent across coexisting sponge species and there is substantial variation in host reliance on symbiont-derived carbon and nitrogen among host sponges; therefore, these associations likely mediate the ecological diversification of coexisting sponge species. The goal of this project is to test this transformative hypothesis by adopting an integrative approach to assess the individual components of holobiont metabolism (i.e., microbial symbionts and sponge host) in ten of the most common sponge species in the Caribbean. The investigators will isolate autotrophic and heterotrophic metabolic pathways and explore potential links between microbial symbiont community composition and the assimilation of particulate and dissolved organic matter (POM and DOM) from seawater. This project will elucidate whether Caribbean sponge species are on similar or divergent evolutionary trajectories, and will provide information that is critical for our understanding of how conditions in the Caribbean basin have shaped the evolution of benthic organisms.</p>
Ecological Diversification in Sponges
largerWorkCitation
project
eng; USA
biota
oceans
-81.408711
-81.408711
24.562003
24.562003
2021-04-01
2021-08-31
Caribbean coast of Panama
0
BCO-DMO catalogue of parameters from Flow cytometry data from Incurrent and Excurrent flow samples collected from shallow artificial reef sponges and seawater in the Florida Keys, USA from Apr 2021 to Aug 2021
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/983616.rdf
Name: Collection_Date
Units: unitless
Description: <p>Date of sample collection</p>
http://lod.bco-dmo.org/id/dataset-parameter/983617.rdf
Name: Latitude
Units: decimal degrees
Description: <p>Latitude of sample collection; North is positive</p>
http://lod.bco-dmo.org/id/dataset-parameter/983618.rdf
Name: Longitude
Units: decimal degrees
Description: <p>Longitude of sample collection; West is negative</p>
http://lod.bco-dmo.org/id/dataset-parameter/983619.rdf
Name: Sample_ID
Units: unitless
Description: <p>Sample identifier</p>
http://lod.bco-dmo.org/id/dataset-parameter/983620.rdf
Name: Species
Units: unitless
Description: <p>Sponge species sampled</p>
http://lod.bco-dmo.org/id/dataset-parameter/983621.rdf
Name: Species_Abbreviation
Units: unitless
Description: <p>Abbreviation of sponge species</p>
http://lod.bco-dmo.org/id/dataset-parameter/983622.rdf
Name: In_or_Ex
Units: unitless
Description: <p>Incurrent or Excurrent water sampled</p>
http://lod.bco-dmo.org/id/dataset-parameter/983623.rdf
Name: Replicate
Units: unitless
Description: <p>Replicate number</p>
http://lod.bco-dmo.org/id/dataset-parameter/983624.rdf
Name: Collection_day
Units: unitless
Description: <p>Day of collection</p>
http://lod.bco-dmo.org/id/dataset-parameter/983625.rdf
Name: TotPhyto_Conc
Units: mL-1
Description: <p>Total Phytoplankton (Syn + Pro+ Photosynthetic Eukaryotes)</p>
http://lod.bco-dmo.org/id/dataset-parameter/983626.rdf
Name: Syn_Conc
Units: mL-1
Description: <p>Synechococcus concentration</p>
http://lod.bco-dmo.org/id/dataset-parameter/983627.rdf
Name: Pro_Conc
Units: mL-1
Description: <p>Prochlorococcus concentration</p>
http://lod.bco-dmo.org/id/dataset-parameter/983628.rdf
Name: Photosynthetic_Eukaryotes
Units: mL-1
Description: <p>Photosynthetic Eukaryote concentration</p>
http://lod.bco-dmo.org/id/dataset-parameter/983629.rdf
Name: TotBact_Conc
Units: mL-1
Description: <p>Total Heterotrophic bacteria (HNA + LNA)</p>
http://lod.bco-dmo.org/id/dataset-parameter/983630.rdf
Name: HNA_Conc
Units: mL-1
Description: <p>High nucleic acid bacteria</p>
http://lod.bco-dmo.org/id/dataset-parameter/983631.rdf
Name: LNA_Conc
Units: mL-1
Description: <p>Low Nucleic acid bacteria</p>
http://lod.bco-dmo.org/id/dataset-parameter/983632.rdf
Name: LSID
Units: unitless
Description: <p>Life Science Identifier (LSID) for the sponge species</p>
http://lod.bco-dmo.org/id/dataset-parameter/983633.rdf
Name: AphiaID
Units: unitless
Description: <p>Unique identifier for the sponge species in the Aphia database</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
17902
https://darchive.mblwhoilibrary.org/server/api/core/bitstreams/f9816a9b-a77b-447e-ab06-2283755fbf4f/content
download
https://doi.org/10.26008/1912/bco-dmo.969846.1
download
onLine
dataset
<p><strong>Location</strong><br />
Samples were collected on shallow reefs (&lt;10m) in the Florida Keys, USA. The temporary artificial reef was constructed adjacent to patch reefs within the Looe Key special preservation area. At the conclusion of the experiment, the reef was completely dismantled.&nbsp;The environment was well mixed by wave action within minimal tidal influence.</p>
<p><strong>Collection and Analysis</strong></p>
<p>One-milliliter of seawater samples were collected via VacuSIP and preserved in&nbsp;paraformaldehyde (0.5% final concentration),&nbsp;flash frozen in liquid nitrogen, and then shipped to Bigelow Laboratory for Ocean Sciences.&nbsp;At this laboratory, the following methodology was used:</p>
<div>
<p>A ZE5 Cell Analyzer flow cytometer (Bio-Rad, Hercules, CA, USA) was used to measure optical properties of single cells from each sample and quantify requested populations. To ensure accurate calibration of the flow cytometer, ZE5 QC beads (Bio-Rad, Hercules, CA, USA) were run daily.</p>
<p>Picophytoplankton (less than 3 µm) and nanophytoplankton (3-20 µm) were analyzed using a slight modification of the method described in Lomas et al., 2010. Immediately after thawing at room temperature, 300-400 µl of sample was prescreened through 70 µm mesh and run at a flow rate of 1 µl sec-1. Particles were excited with a 488 nm blue laser and data acquisition was triggered on red fluorescence. Signals were recorded from detectors with bandpass filters for forward scatter (FSC), right angle light scatter (SSC) and fluorescence emission in red (692/80 nm) indicative of chlorophyll a, and orange (593/52 nm) for phycoerythrin. Data files were analyzed from logarithmic dot plots based on fluorescence and characteristic light scattering properties (DuRand &amp; Olson, 1996) using FlowJo 10.6 software&nbsp;(FlowJo, 2023)&nbsp;(Becton Dickinson &amp; Company, San Jose, CA, USA). Total pico and nano phytoplankton populations were identified based upon cell size and red fluorescence. Phycoerythrin containing cell populations were determined by orange fluorescence. Based upon these gating criteria, the number of cells in each identified population was enumerated and converted to cell abundances using the processed sample volume and adjusted for dilution by preservative.</p>
<p>For total bacteria analysis, samples were thawed, diluted 1:10 with Tris EDTA (TE) Buffer pH 8.0 and stained using a 10x working stock of SYBR Green I Nucleic Acid Stain (Thermofisher Scientific, USA) at room temperature in the dark for 15 min using the protocol of Marie et al. (2005). At a flow rate of 0.5 µl sec-1, 180 µl of the diluted sample was run. Particles were excited with a 488 nm blue laser and data acquisition was triggered on green fluorescence. Signals were recorded from detectors with bandpass filters for forward scatter (FSC), right angle light scatter (SSC) and fluorescence emission in green (525/35nm). Data files were analyzed from two logarithmic scatter plots based on fluorescence and characteristic light scattering properties. Total bacteria counts were identified based on size and presence of green fluorescence and counts were converted to cell abundances using the volume of sample processed including adjustments for preservation, dilution and staining.</p>
</div>
Specified by the Principal Investigator(s)
<p>Raw data is presented here.&nbsp;Data analysis includes univariate and multivariate statistics.</p>
Specified by the Principal Investigator(s)
- Imported "Flow_cytometry_BCO-DMO.csv" into BCO-DMO system
- Converted "Lat" and "Lon" to decimal degrees to conform with BCO-DMO guidance
- Converted "Datetime" (only included date) to YYYY-MM-DD ISO 8601 date format to conform with BCO-DMO guidance
- Removed "Day " part of string of values representing day of collection to convert value to an integer
- Renamed fields to comply with BCO-DMO naming conventions, removing units, special characters, and spaces
- Exported file as "969846_v1_flow_cytometry_incurrent_excurrent_flow.csv"
Taxonomic names were checked using the World Register of Marine Species Taxa Match tool (WoRMS). All names matched a known name exactly, except Amphimedon compressa (https://www.marinespecies.org/aphia.php?p=taxdetails&id=166666), which was recently superseded by Amphimedon nodosa (https://www.marinespecies.org/aphia.php?p=taxdetails&id=1814728) earlier in 2025 after work for this dataset was completed. Submitter requested Amphimedon compressa be used in the dataset. The URI locator provides access to the latest taxonomic information.
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
VacuSIP
VacuSIP
PI Supplied Instrument Name: VacuSIP PI Supplied Instrument Description:One milliliter of seawater samples were collected via VacuSIP and preserved in paraformaldehyde (0.5% final concentration), flash frozen in liquid nitrogen, and then shipped to Bigelow Laboratory for Ocean Sciences. Instrument Name: Discrete water sampler Instrument Short Name: Instrument Description: A device that collects an in-situ discrete water sample from any depth and returns it to the surface without contamination by the waters through which it passes, such as a water bottle.
ZE5 Cell Analyzer flow cytometer (Bio-Rad, Hercules, CA, USA)
ZE5 Cell Analyzer flow cytometer (Bio-Rad, Hercules, CA, USA)
PI Supplied Instrument Name: ZE5 Cell Analyzer flow cytometer (Bio-Rad, Hercules, CA, USA) PI Supplied Instrument Description:A ZE5 Cell Analyzer flow cytometer (Bio-Rad, Hercules, CA, USA) was used to measure optical properties of single cells from each sample and quantify requested populations. To ensure accurate calibration of the flow cytometer, ZE5 QC beads (Bio-Rad, Hercules, CA, USA) were run daily. Instrument Name: Flow Cytometer Instrument Short Name:Flow Cytometer Instrument Description: Flow cytometers (FC or FCM) are automated instruments that quantitate properties of single cells, one cell at a time. They can measure cell size, cell granularity, the amounts of cell components such as total DNA, newly synthesized DNA, gene expression as the amount messenger RNA for a particular gene, amounts of specific surface receptors, amounts of intracellular proteins, or transient signalling events in living cells.
(from: http://www.bio.umass.edu/micro/immunology/facs542/facswhat.htm) Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/LAB37/