http://lod.bco-dmo.org/id/dataset/996646
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
2026-04-10
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Time series of phytoplankton cells released from carbonate sands column experiment in Marathon, FL Keys in Jul and Aug 2025
2026-04-23
publication
2026-04-23
revision
BCO-DMO Linked Data URI
2026-04-23
creation
http://lod.bco-dmo.org/id/dataset/996646
Markus Huettel
Florida State 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: Huettel, M. (2026) Time series of phytoplankton cells released from carbonate sands column experiment in Marathon, FL Keys in Jul and Aug 2025. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2026-04-23 [if applicable, indicate subset used]. http://lod.bco-dmo.org/id/dataset/996646 [access date]
Phytoplankton in carbonate sands column experiment Dataset Description: Methods and Sampling: <p>The columns used for this experiment had a length of 10 cm and a diameter of 1 cm. The sands used were carbonate sands with the grain size diameter ranges 1) 125 to 250 um and 2) 250-500 um. Prior to the experiments, the sands were cleaned through repeated washing in NaCl solution (salinity 35). For testing particle separation within these sands, seawater with a natural phytoplankton&nbsp;community dominated by green algae (5-10 um cell diameter) and cyanobacteria (1-5 nm cell diameter) were pumped through the sand. Computer-controlled syringe pumps pushed the seawater with the algae through the columns at a pore front velocity of 20 cm per hour. The eluent of the 2 columns were collected in a rotating sampler at 15 minute intervals. A total of 36 fractions was collected for each of the sand column for a flushing period of 9 h. The resulting samples were analyzed in a Cytoflex flow cytometer with gating adjusted to capture the green algae and cyanobacteria. Data collected include the area under the forward scatter peak, which provides information on cell size side scatter data, which are related to cell granularity. Calibration of the instrument used calibration beads with particle size ranging from 0.29 to 16.8 um. Explanations regarding flow cytometer analysis of phytoplankton samples as performed here are presented in Trask et al. (1982), best practices in Gallot et al. (2025), and details on the more recent instrumentation in Ugawa et. al (2024).</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-2148635 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=2148635
onGoing
Markus Huettel
Florida State University
850-645-1394
Department of Earth, Ocean and Atmospheric Science
Tallahassee
FL
32306-4520
USA
mhuettel@fsu.edu
pointOfContact
asNeeded
Dataset Version: 1
Unknown
grain_size_lower_bound
fraction_number
Event
Time
FSC_H
FSC_A
SSC_H
SSC_A
FITC_H
FITC_A
PE_H
PE_A
APC_H
APC_A
APC_A750_H
APC_A750_A
FSC_Width
Beckman CytoFlex flow cytometer
theme
None, User defined
treatment
sample identification
event
time_elapsed
height
area
featureType
BCO-DMO Standard Parameters
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.
Chromatographic separation and degradation of dissolved and particulate organic matter in permeable shelf sediment
https://osprey.bco-dmo.org/project/895930
Chromatographic separation and degradation of dissolved and particulate organic matter in permeable shelf sediment
<p><strong>NSF Award Abstract:</strong><br />
This project will study the role of sandy sediments in the carbon cycle. Sandy sediments cover about one-third of the continental shelf but are not well studied. Like a sand filter, marine sands separate and trap dissolved and particulate materials as seawater moves through. These processes influence organic matter cycling in sediments. Because smaller particles travel more easily through the pore space than larger ones, they move deeper into the seabed. This causes a separation of particulate matter by size. Likewise, changes in oxygen and dissolved chemicals with depth alter the surface properties of the sediment grains. Molecules with different properties are separated based on these surface characteristics. The fates of organic carbon, dissolved nutrients and pollutants in the coastal ocean are linked to uptake by sediments, physical and microbial processes within sediments, and release. Thus, it is important to understand the processes that control the transport and accumulation of materials in the seabed. This project will study the separation of particulate and dissolved organic matter transported through marine sands. It will provide information critical for understanding the cycling of carbon and nutrients at the seafloor. Graduate and undergraduate students working on this project will receive training in marine sediment functions and state-of-the-art methods that can help solve pressing environmental issues.</p>
<p>The main objectives of this research are to: 1) demonstrate and quantify the chromatographic separation of organic matter in shelf sediments through the analysis of sediment cores from silicate and carbonate sand beds, 2) characterize and quantify the separation process of dissolved and particulate organic matter and identify key factors controlling this separation in the sands, and 3) quantify the influence of organic matter chromatographic separation on sedimentary oxygen consumption and dissolved inorganic carbon production in these sands. The researchers will test the hypothesis that chromatographic separation of particles and solutes takes place in both sand types but differs with respect to the substances affected and the effectiveness of the separation. Intra-grain permeability of biogenic sands can enhance separation in carbonate sands through exclusion chromatography effects. The separation process is expected to enhance decomposition activities through the concentration of degradable materials in specific sediment layers. The research objectives will be addressed with a combination of field and laboratory studies that include tracer experiments and the analysis of dissolved and particulate organic matter distribution in sand sediment cores sampled in the field. Oxygen consumption and dissolved inorganic carbon production will be measured to reveal the relevance of this process for the sedimentary degradation process. The demonstration of chromatographic separation of particles and solutes in marine sands will close a gap in our understanding of the chemical processes that govern the fate of organic matter, nutrients, and pollutants. This project will provide research training opportunities for graduate and undergraduate students. Results from this study will help improve models of the global cycles of elements that can be used for predicting global environmental change.</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>
Sand Chromatography
largerWorkCitation
project
eng; USA
biota
oceans
-81.0019
-81.0019
24.821
24.821
2025-07-01
2025-08-01
Gulf of Mexico
0
BCO-DMO catalogue of parameters from Time series of phytoplankton cells released from carbonate sands column experiment in Marathon, FL Keys in Jul and Aug 2025
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/998463.rdf
Name: grain_size_lower_bound
Units: unitless
Description: <p>Lower bound of the sand grain size range for the column from which the sample was collected; values of 125 and 250 correspond to grain size ranges of 125–250 µm and 250–500 µm</p>
http://lod.bco-dmo.org/id/dataset-parameter/998464.rdf
Name: fraction_number
Units: unitless
Description: <p>Sequential number of the eluent fraction collected from the sand column; fractions were collected at 15-minute intervals over a 9-hour flushing period, yielding 36 fractions per column (1–36).</p>
http://lod.bco-dmo.org/id/dataset-parameter/998465.rdf
Name: Event
Units: unitless
Description: <p>The sequential number of the analyzed particle (or cell)</p>
http://lod.bco-dmo.org/id/dataset-parameter/998466.rdf
Name: Time
Units: unitless
Description: <p>The timestamp for the event or the elapsed time since the start of acquisition</p>
http://lod.bco-dmo.org/id/dataset-parameter/998467.rdf
Name: FSC_H
Units: cell size
Description: <p>Forward Scatter Height; related to cell size</p>
http://lod.bco-dmo.org/id/dataset-parameter/998468.rdf
Name: FSC_A
Units: cell size
Description: <p>Forward Scatter Area; a measure of total scatter intensity</p>
http://lod.bco-dmo.org/id/dataset-parameter/998469.rdf
Name: SSC_H
Units: cell size
Description: <p>Side Scatter Height; indicates granularity or complexity</p>
http://lod.bco-dmo.org/id/dataset-parameter/998470.rdf
Name: SSC_A
Units: cell size
Description: <p>Side Scatter Area; measures overall side scatter intensity</p>
http://lod.bco-dmo.org/id/dataset-parameter/998471.rdf
Name: FITC_H
Units: cell size
Description: <p>Height of the fluorescence signal for FITC in channel 1</p>
http://lod.bco-dmo.org/id/dataset-parameter/998472.rdf
Name: FITC_A
Units: cell size
Description: <p>Area of the fluorescence signal for FITC in channel 1</p>
http://lod.bco-dmo.org/id/dataset-parameter/998473.rdf
Name: PE_H
Units: cell size
Description: <p>Height of the fluorescence signal for PE (Phycoerythrin) in channel 2</p>
http://lod.bco-dmo.org/id/dataset-parameter/998474.rdf
Name: PE_A
Units: cell size
Description: <p>Area of the fluorescence signal for PE in channel 2</p>
http://lod.bco-dmo.org/id/dataset-parameter/998475.rdf
Name: APC_H
Units: cell size
Description: <p>Height of the fluorescence signal for APC (Allophycocyanin) in channel 3</p>
http://lod.bco-dmo.org/id/dataset-parameter/998476.rdf
Name: APC_A
Units: cell size
Description: <p>Area of the fluorescence signal for APC in channel 3</p>
http://lod.bco-dmo.org/id/dataset-parameter/998477.rdf
Name: APC_A750_H
Units: cell size
Description: <p>Height of the fluorescence signal for APC 750 in channel 4</p>
http://lod.bco-dmo.org/id/dataset-parameter/998478.rdf
Name: APC_A750_A
Units: cell size
Description: <p>Area of the fluorescence signal for APC 750 in channel 4</p>
http://lod.bco-dmo.org/id/dataset-parameter/998479.rdf
Name: FSC_Width
Units: cell size
Description: <p>Width of the forward scatter pulse; reflects the cell's shape or structure</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://osprey.bco-dmo.org/dataset/996646/data/download
download
onLine
dataset
<p>The columns used for this experiment had a length of 10 cm and a diameter of 1 cm. The sands used were carbonate sands with the grain size diameter ranges 1) 125 to 250 um and 2) 250-500 um. Prior to the experiments, the sands were cleaned through repeated washing in NaCl solution (salinity 35). For testing particle separation within these sands, seawater with a natural phytoplankton&nbsp;community dominated by green algae (5-10 um cell diameter) and cyanobacteria (1-5 nm cell diameter) were pumped through the sand. Computer-controlled syringe pumps pushed the seawater with the algae through the columns at a pore front velocity of 20 cm per hour. The eluent of the 2 columns were collected in a rotating sampler at 15 minute intervals. A total of 36 fractions was collected for each of the sand column for a flushing period of 9 h. The resulting samples were analyzed in a Cytoflex flow cytometer with gating adjusted to capture the green algae and cyanobacteria. Data collected include the area under the forward scatter peak, which provides information on cell size side scatter data, which are related to cell granularity. Calibration of the instrument used calibration beads with particle size ranging from 0.29 to 16.8 um. Explanations regarding flow cytometer analysis of phytoplankton samples as performed here are presented in Trask et al. (1982), best practices in Gallot et al. (2025), and details on the more recent instrumentation in Ugawa et. al (2024).</p>
Specified by the Principal Investigator(s)
<p>Cells penetrating through the sand columns were identified by analyzing forward (FSC) and sideward scatter (SSC) signals. The signals are used to gate and identify different cell populations. By combining information from the two scatter signals, particles can be distinguished based on their size and granularity.&nbsp;</p>
Specified by the Principal Investigator(s)
- Loaded sheets 1-3 from 250402_Carb125_Cyto10cm_algae.xlsx and sheets 5-36 from the same file, using filename as resource name, with "" and "nd" treated as missing values
- Loaded sheets 1-36 from 250402_Carb250_Cyto10cm_algae.xlsx using filename as resource name, with "" and "nd" treated as missing values
- Concatenated 71 resources (35 from Carb125, 36 from Carb250) into a single resource; added a resource_name column to track the source sheet/file
- Renamed fields to replace hyphens and double-colon notation with underscores: FSC-H to FSC_H, FSC-A to FSC_A, SSC-H to SSC_H, SSC-A to SSC_A, FITC-H::FL1-H to FITC_H, FITC-A::FL1-A to FITC_A, PE-H::FL2-H to PE_H, PE-A::FL2-A to PE_A, APC-H::FL3-H to APC_H, APC-A::FL3-A to APC_A, APC-A750-A::FL4-A to APC_A750_A, FSC-Width to FSC_Width, APC-A750-H::FL4-H to APC_A750_H
- Split resource_name field using pattern 250402_carb(.*)_cyto10cm_algae-(.*) into two new fields: grain_size_lower_bound (lower bound of sand grain size range; 125 = 125–250 µm, 250 = 250–500 µm) and fraction_number (sequential eluent fraction number 1–36, collected at 15-minute intervals over a 9-hour flushing period); original resource_name field preserved
- Deleted resource_name field
- Reordered fields to: grain_size_lower_bound, fraction_number, Event, Time, FSC_H, FSC_A, SSC_H, SSC_A, FITC_H, FITC_A, PE_H, PE_A, APC_H, APC_A, APC_A750_H, APC_A750_A, FSC_Width
- Output written to 996646_v1_carb125_carb250_cyto10cm_algae
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
Beckman CytoFlex flow cytometer
Beckman CytoFlex flow cytometer
PI Supplied Instrument Name: Beckman CytoFlex flow cytometer PI Supplied Instrument Description:The resulting samples were analyzed in a Cytoflex flow cytometer with gating adjusted to capture the green algae and cyanobacteria. 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/