http://lod.bco-dmo.org/id/dataset/994900
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
2026-03-17
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Cell abundance in HMW-DOM amended mesocosm incubations from water collected in the Western North Atlantic during the research cruise EN638 in May 2019 aboard R/V Endeavor
2026-03-17
publication
2026-03-17
revision
BCO-DMO Linked Data URI
2026-03-17
creation
http://lod.bco-dmo.org/id/dataset/994900
Carol Arnosti
University of North Carolina at Chapel Hill
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: Lloyd, C., Brown, S. A., Arnosti, C., Ghobrial, S. (2026) Cell abundance in HMW-DOM amended mesocosm incubations from water collected in the Western North Atlantic during the research cruise EN638 in May 2019 aboard R/V Endeavor. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2026-03-17 [if applicable, indicate subset used]. http://lod.bco-dmo.org/id/dataset/994900 [access date]
EN638 LV Cell Counts Dataset Description: Methods and Sampling: <p>Water was collected via Niskin bottles mounted on a rosette, equipped with a CTD.</p>
<p>For mesocosm (large volume) incubation experiments (referred to as “LV” incubations), seawater was transferred to 20 L carboys that were rinsed three times with water from the sampling depth and then filled with seawater from a single Niskin bottle, using silicone tubing that had been acid washed then rinsed with distilled water prior to use. Four carboys were filled at each depth from bottom water, water from the depth at which oxygen showed a minimum, and deep chlorophyll maximum (DCM) water, according to the CTD. Triplicate 20L carboys were amended with ca. 500 mg (exact mass was recorded for each addition) of HMW <em>Thalassiosira</em>; unamended single carboys were used for controls.&nbsp;All mesocosms were incubated in the dark at near in-situ temperatures. Mesocosms were sub-sampled at the start of incubation (0 days), and then after at approximately 2 days, 6 or 7 days, 11 days, and 16 days for multiple assays including total cell abundance.</p>
<p>Total cell abundance was quantified following Giljan et al. (2023). In brief, 25-50 mL of water was fixed with a final concentration of 1% formaldehyde and subsequently filtered onto 0.2 µm polycarbonate filters (Millipore). The DNA of filtered cells were simultaneously counterstained and mounted using a 1 ng/µL working solution of 4’,6-diamidin-2-phenylindol (DAPI) mixed with Citifluor/VectaShield (4:1) solution. A minimum of 45 microscopic images were acquired per sample using an automated imaging system (Zeiss AxioImager.Z2 microscope stand; 63x magnification oil immersion plan apochromatic objective with 1.4 NA, Carl Zeiss). Final cell abundance was determined using ACMETOOL 3 (http://www.tchnobiology.ch and Max Planck Institute of Marine Microbiology, Bremen). Quantification of DAPI-stained cells (signal:background &gt; 1.5) is reported as total cell abundance. Note that for the amended mesocosms, in many cases the cells were too dense to count automatically. For these samples, 15 microscopic images were manually counted using the ACMETOOL 3 software; a minimum of 12 of 4510 images are needed to accurately capture the total cell abundance per filter. In some cases, moreover, there were not enough cells to calculate total cell abundance or the filters needed to determine cell abundance were not available (i.e., samples were lost during transit; some filters were dropped during experimental subsampling), so the data presented for each timepoint in several cases originates from different replicate mesocosms during the time course of incubation.</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1736772 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1736772
onGoing
Carol Arnosti
University of North Carolina at Chapel Hill
919-962-5754
Dept. of Marine Sciences 3117A Venable/Murray Hall
Chapel Hill
NC
27599-3300
USA
arnosti@email.unc.edu
pointOfContact
asNeeded
Dataset Version: 1
Unknown
Deployment
Station
latitude
longitude
time_sampled
cast_number
depth_sequence
depth_m
in_situ_temp
incub_temp
sample_type
unamended_amended
timepoint_number
time_elapsed_days
cell_abundance
cell_abundance_flag
CTD
Zeiss AxioImager.Z2
Niskin bottles
theme
None, User defined
Cruise identfier
station
latitude
longitude
sample time
cast
site description
depth
water temperature at measurement depth
incubation or cultivation temperature (not ambient water temp)
sample type
treatment
time_point
time_elapsed
abundance
quality flag
featureType
BCO-DMO Standard Parameters
CTD Sea-Bird SBE 911plus
Fluorescence Microscope
Niskin bottle
instrument
BCO-DMO Standard Instruments
EN638
service
Deployment Activity
Northern Atlantic
place
Locations
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.
A mechanistic microbial underpinning for the size-reactivity continuum of dissolved organic carbon degradation
https://osprey.bco-dmo.org/project/809975
A mechanistic microbial underpinning for the size-reactivity continuum of dissolved organic carbon degradation
<p><em>NSF Award Abstract:</em><br />
Marine dissolved organic matter (DOM) is one of the largest actively-cycling reservoirs of organic carbon on the planet, and thus a major component of the global carbon cycle. The high molecular weight (HMW) fraction of DOM is younger in age and more readily consumed by microbes than lower molecular weight (LMW) fractions of DOM, but the reasons for this difference in reactivity between HMW DOM and LMW DOM are unknown. Two factors may account for the greater reactivity of HMW DOM: (i) targeted uptake of HMW DOM by specific bacteria, a process the PI and her collaborators at the Max Planck Institute for Marine Microbiology (MPI) recently identified in surface ocean waters; and (ii) a greater tendency of HMW DOM to aggregate and form gels and particles, which can be colonized by bacteria that are well-equipped to breakdown organic matter. Scientists and students from the University of North Carolina (UNC) - Chapel Hill will collaborate with researchers at the MPI for Marine Microbiology (Bremen, Germany) to investigate this breakdown of HMW DOM by marine microbial communities. These investigations will include a field expedition in the North Atlantic, during which HMW DOM degradation rates and patterns will be compared in different water masses and under differing conditions of organic matter availability. DOM aggregation potential, and degradation rates of these aggregates, will also be assessed. Specialized microscopy will be used in order to pinpoint HMW DOM uptake mechanisms and rates. The work will be complemented by ongoing studies of specific bacteria that breakdown HMW DOM, their genes, and their proteins. Graduate as well as undergraduate students will participate as integral members of the research team in all aspects of the laboratory and field work; aspects of the project will also be integrated into classes the scientist teaches at UNC.</p>
<p>The existence of a size-reactivity continuum of DOM - observations and measurements showing that HMW DOM tends to be younger and more reactive than lower MW DOM - has been demonstrated in laboratory and field investigations in different parts of the ocean. A mechanistic explanation for the greater reactivity of HMW DOM has been lacking, however. This project will investigate the mechanisms and measure rates of HMW DOM degradation, focusing on identifying the actors and determining the factors that contribute to rapid cycling of HMW DOM. Collaborative work at UNC and MPI-Bremen recently identified a new mechanism of HMW substrate uptake common among pelagic marine bacteria: these bacteria rapidly bind, partially hydrolyze, and transport directly across the outer membrane large fragments of HMW substrates that can then be degraded within the periplasmic space, avoiding production of LMW DOM in the external environment. This mode of substrate processing has been termed selfish, since targeted HMW substrate uptake sequesters resources away from other members of microbial communities. Measurements and models thus must account for three modes of substrate utilization in the ocean: selfish, sharing (external hydrolysis, leading to low molecular weight products), and scavenging (uptake of low molecular weight hydrolysis products without production of extracellular enzymes). Using field studies as well as mesocosm experiments, the research team will investigate the circumstances and locations at which different modes of substrate uptake predominate. A second focal point of the project is to determine the aggregation potential and microbial degradation of aggregated HMW DOM. Preliminary studies have demonstrated that particle-associated microbial communities utilize a broader range of enzymatic capabilities than their free-living counterparts. These capabilities equip particle-associated communities to effectively target a broad range of complex substrates. The project will thus focus on two key aspects of HMW DOM - the abilities of specialized bacteria to selectively sequester HMW substrates, as well as the greater potential of HMW substrates to aggregate ? and will quantify these factors at different locations and depths in the ocean. The project will thereby provide a mechanistic underpinning for observations of the DOC size-reactivity continuum, an essential part of developing an overall mechanistic understanding of organic matter degradation in the ocean.</p>
Microbial DOC Degradation
largerWorkCitation
project
eng; USA
biota
oceans
Northern Atlantic
-72.0021
-53.3949
34.6369
42.83954
2019-05-15
2019-05-30
Northern Atlantic, Southern Indian Ocean, Svalbard
0
BCO-DMO catalogue of parameters from Cell abundance in HMW-DOM amended mesocosm incubations from water collected in the Western North Atlantic during the research cruise EN638 in May 2019 aboard R/V Endeavor
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/994936.rdf
Name: Deployment
Units: unitless
Description: <p>Cruise ID</p>
http://lod.bco-dmo.org/id/dataset-parameter/994937.rdf
Name: Station
Units: unitless
Description: <p>Station number for cruise: 18, 19, or 20</p>
http://lod.bco-dmo.org/id/dataset-parameter/994938.rdf
Name: latitude
Units: decimal degrees
Description: <p>Latitude, south is negative</p>
http://lod.bco-dmo.org/id/dataset-parameter/994940.rdf
Name: longitude
Units: decimal degrees
Description: <p>Longitude, west is negative</p>
http://lod.bco-dmo.org/id/dataset-parameter/994942.rdf
Name: time_sampled
Units: unitless
Description: <p>Date and time of sample collection</p>
http://lod.bco-dmo.org/id/dataset-parameter/994943.rdf
Name: cast_number
Units: unitless
Description: <p>Cast number (refers to cast of CTD/Niskin bottles on cruise)</p>
http://lod.bco-dmo.org/id/dataset-parameter/994944.rdf
Name: depth_sequence
Units: unitless
Description: <p>Sequence of depths sampled (1 is surface; higher numbers at greater depths)</p>
http://lod.bco-dmo.org/id/dataset-parameter/994945.rdf
Name: depth_m
Units: meters
Description: <p>Actual depth at which water was collected</p>
http://lod.bco-dmo.org/id/dataset-parameter/994947.rdf
Name: in_situ_temp
Units: degrees Celsius
Description: <p>Temperature of bulk water at depth at time of collection</p>
http://lod.bco-dmo.org/id/dataset-parameter/994948.rdf
Name: incub_temp
Units: degrees Celsius
Description: <p>Temperature of mesocosm incubation</p>
http://lod.bco-dmo.org/id/dataset-parameter/994949.rdf
Name: sample_type
Units: unitless
Description: <p>Sample from bulk water (Bulk) or Large Volume (LV) incubation</p>
http://lod.bco-dmo.org/id/dataset-parameter/994950.rdf
Name: unamended_amended
Units: unitless
Description: <p>Refers to whether high molecular weight <em>Thalassiosira Weissflogii</em> extract was added to the incubation or was left unamended</p>
http://lod.bco-dmo.org/id/dataset-parameter/994951.rdf
Name: timepoint_number
Units: unitless
Description: <p>Timepoint number of sample collection (t0, t1, t2, t3, or t4)</p>
http://lod.bco-dmo.org/id/dataset-parameter/994952.rdf
Name: time_elapsed_days
Units: days
Description: <p>Incubation time elapsed at sample collection in days</p>
http://lod.bco-dmo.org/id/dataset-parameter/994953.rdf
Name: cell_abundance
Units: cells/mL
Description: <p>Total cell abundance from mesocosm experiments subsampled at each timepoint</p>
http://lod.bco-dmo.org/id/dataset-parameter/994954.rdf
Name: cell_abundance_flag
Units: unitless
Description: <p>Flags for cell_abundance: - indicates where no data are available because samples were lost or images were not acquired due to technical difficulties; * indicates that there were too few cells to accurately quantify</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/994900/data/download
download
onLine
dataset
<p>Water was collected via Niskin bottles mounted on a rosette, equipped with a CTD.</p>
<p>For mesocosm (large volume) incubation experiments (referred to as “LV” incubations), seawater was transferred to 20 L carboys that were rinsed three times with water from the sampling depth and then filled with seawater from a single Niskin bottle, using silicone tubing that had been acid washed then rinsed with distilled water prior to use. Four carboys were filled at each depth from bottom water, water from the depth at which oxygen showed a minimum, and deep chlorophyll maximum (DCM) water, according to the CTD. Triplicate 20L carboys were amended with ca. 500 mg (exact mass was recorded for each addition) of HMW <em>Thalassiosira</em>; unamended single carboys were used for controls.&nbsp;All mesocosms were incubated in the dark at near in-situ temperatures. Mesocosms were sub-sampled at the start of incubation (0 days), and then after at approximately 2 days, 6 or 7 days, 11 days, and 16 days for multiple assays including total cell abundance.</p>
<p>Total cell abundance was quantified following Giljan et al. (2023). In brief, 25-50 mL of water was fixed with a final concentration of 1% formaldehyde and subsequently filtered onto 0.2 µm polycarbonate filters (Millipore). The DNA of filtered cells were simultaneously counterstained and mounted using a 1 ng/µL working solution of 4’,6-diamidin-2-phenylindol (DAPI) mixed with Citifluor/VectaShield (4:1) solution. A minimum of 45 microscopic images were acquired per sample using an automated imaging system (Zeiss AxioImager.Z2 microscope stand; 63x magnification oil immersion plan apochromatic objective with 1.4 NA, Carl Zeiss). Final cell abundance was determined using ACMETOOL 3 (http://www.tchnobiology.ch and Max Planck Institute of Marine Microbiology, Bremen). Quantification of DAPI-stained cells (signal:background &gt; 1.5) is reported as total cell abundance. Note that for the amended mesocosms, in many cases the cells were too dense to count automatically. For these samples, 15 microscopic images were manually counted using the ACMETOOL 3 software; a minimum of 12 of 4510 images are needed to accurately capture the total cell abundance per filter. In some cases, moreover, there were not enough cells to calculate total cell abundance or the filters needed to determine cell abundance were not available (i.e., samples were lost during transit; some filters were dropped during experimental subsampling), so the data presented for each timepoint in several cases originates from different replicate mesocosms during the time course of incubation.</p>
Specified by the Principal Investigator(s)
<p>Image analysis was performed with ACMETOOL (Zeder, M. 2005-2021, Software for Biology, http://www.technobiology.ch and Max Planck Institute for marine microbiology, Bremen, version 3) and Zen software package (Carl Zeiss).</p>
Specified by the Principal Investigator(s)
- Loaded CSV file "20251114_EN638_CellCounts_Processed_BCODMO.csv" with header row 1; treated empty strings and "nd" as missing values
- Extracted non-numeric values from cell_abundance into a new flag field cell_abundance_flag, to capture symbols that were present in the "cell_abundance" values ("-" indicating lost samples or missing images, "*" indicating too few cells to quantify) without corrupting the numeric column
- Applied find/replace to time_sampled to normalize timestamps lacking seconds by appending ":00" to values matching the pattern m/d/yyyy h:mm
- Converted time_sampled from format "%m/%d/%Y %H:%M:%S" to ISO 8601 format "%Y-%m-%dT%H:%M" as a string field
- Renamed field "in-situ_temp" to "in_situ_temp" to remove the hyphen
- Exported file as "994900_v1_en638_lv_cell_counts.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
CTD
CTD
PI Supplied Instrument Name: CTD PI Supplied Instrument Description:Water was collected via Niskin bottles mounted on a rosette, equipped with a CTD. Instrument Name: CTD Sea-Bird SBE 911plus Instrument Short Name:CTD SBE 911plus Instrument Description: The Sea-Bird SBE 911 plus is a type of CTD instrument package for continuous measurement of conductivity, temperature and pressure. The SBE 911 plus includes the SBE 9plus Underwater Unit and the SBE 11plus Deck Unit (for real-time readout using conductive wire) for deployment from a vessel. The combination of the SBE 9 plus and SBE 11 plus is called a SBE 911 plus. The SBE 9 plus uses Sea-Bird's standard modular temperature and conductivity sensors (SBE 3 plus and SBE 4). The SBE 9 plus CTD can be configured with up to eight auxiliary sensors to measure other parameters including dissolved oxygen, pH, turbidity, fluorescence, light (PAR), light transmission, etc.). more information from Sea-Bird Electronics Community Standard Description: http://vocab.nerc.ac.uk/collection/L22/current/TOOL0058/
Zeiss AxioImager.Z2
Zeiss AxioImager.Z2
PI Supplied Instrument Name: Zeiss AxioImager.Z2 PI Supplied Instrument Description:A minimum of 45 microscopic images were acquired per sample using an automated imaging system (Zeiss AxioImager.Z2 microscope stand; 63x magnification oil immersion plan apochromatic objective with 1.4 NA, Carl Zeiss). Instrument Name: Fluorescence Microscope Instrument Short Name: Instrument Description: Instruments that generate enlarged images of samples using the phenomena of fluorescence and phosphorescence instead of, or in addition to, reflection and absorption of visible light. Includes conventional and inverted instruments. Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/LAB06/
Niskin bottles
Niskin bottles
PI Supplied Instrument Name: Niskin bottles PI Supplied Instrument Description:Water was collected via Niskin bottles mounted on a rosette, equipped with a CTD. Instrument Name: Niskin bottle Instrument Short Name:Niskin bottle Instrument Description: A Niskin bottle (a next generation water sampler based on the Nansen bottle) is a cylindrical, non-metallic water collection device with stoppers at both ends. The bottles can be attached individually on a hydrowire or deployed in 12, 24, or 36 bottle Rosette systems mounted on a frame and combined with a CTD. Niskin bottles are used to collect discrete water samples for a range of measurements including pigments, nutrients, plankton, etc. Community Standard Description: http://vocab.nerc.ac.uk/collection/L22/current/TOOL0412/
Cruise: EN638
EN638
R/V Endeavor
Community Standard Description
International Council for the Exploration of the Sea
R/V Endeavor
vessel
EN638
Carol Arnosti
University of North Carolina at Chapel Hill
R/V Endeavor
Community Standard Description
International Council for the Exploration of the Sea
R/V Endeavor
vessel