http://lod.bco-dmo.org/id/dataset/984885
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
2025-09-22
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Phytoplankton abundance in seawater samples collected from Project "DaVINCi" incubations in the Gulf of Naples, Italy from April to May 2022
2025-09-22
publication
2025-09-22
revision
Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)
2025-10-02
publication
https://doi.org/10.26008/1912/bco-dmo.984885.1
Kimberlee Thamatrakoln
Rutgers 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: Thamatrakoln, K. (2025) Phytoplankton abundance in seawater samples collected from Project "DaVINCi" incubations in the Gulf of Naples, Italy from April to May 2022. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2025-09-22 [if applicable, indicate subset used]. doi:10.26008/1912/bco-dmo.984885.1 [access date]
Phytoplankton Cell Abundance Dataset Description: Methods and Sampling: <p>Samples were fixed with 1% Lugol's. The quantitative analysis is carried out using an inverted microscope after the settling of a variable volume of sample (Utermhöl, 1958). The settled volumes vary in relation to the number of cells present in the sample, which is estimated on the basis of the chlorophyll a concentration or of the depth of the Secchi Disk. The counting is carried out on various proportions of the sedimentation chamber (transects, random fields or the entire chamber), depending on the characteristics of the sample.</p>
<p>The abundance of phytoplankton cells present in the sample is calculated by applying the following general formula:</p>
<p>C = N × factor × 1000/v</p>
<p>where C = concentration of phytoplankton expressed as cells per liter (cells L-1);<br />
N = number of cells counted;<br />
v = volume of settled sample (milliliters (mL));<br />
factor = ratio between the total area of the chamber and the explored area.</p>
<p>Instruments: Samples from incubation bottle treatments were collected after gently mixing bottles and dispensing 250 mLs into a dark glass bottle containing 1% Lugol's solution and stored in the dark at 4 degrees Celsius.</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-2049386 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=2049386
completed
Kimberlee Thamatrakoln
Rutgers University
848-932-3464
Department of Marine and Coastal Sciences 71 Dudley Road
New Brunswick
NJ
08901
USA
thamat@marine.rutgers.edu
pointOfContact
asNeeded
Dataset Version: 1
Unknown
Date
Incubation
Bag
Incubation_Timepoint_d
Treatment
Replicate
Diatoms
Dinoflagellates
Coccolithophores
Other_flagellates
inverted microscope
Secchi Disk
theme
None, User defined
date
sample identification
time_point
treatment
abundance
featureType
BCO-DMO Standard Parameters
Inverted Microscope
Secchi Disc
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.
Shunt or shuttle? Nutrient-driven biogeochemical consequences of diatom host-virus interactions
https://osprey.bco-dmo.org/project/875296
Shunt or shuttle? Nutrient-driven biogeochemical consequences of diatom host-virus interactions
<p>NSF abstract:</p>
<p>Diatoms are a type of microscopic marine algae that form the base of the ocean food web and generate about 20% of the oxygen on the planet. Admired since the Victorian age, these organisms are often referred to as the ‘glass houses of the sea’ because of the intricate architecture of their cell walls made of silicon dioxide, or glass. When these organisms die, the cellular-associated carbon and other elements can be either recycled and reused by other phytoplankton or, because glass is heavier than seawater, lost by sinking out of the surface ocean. Thus, the contribution diatoms make to carbon cycling is dictated by the balance between the factors that facilitate recycling and those that stimulate export. As the most abundant entity in the ocean, viruses have, for decades, been characterized as efficient recyclers, acting as ‘shunts’ by preventing the transfer of energy up the food chain through host mortality and lysis. However, it has been suggested that viruses may also act as ‘shuttles’ to the deep ocean, stimulating cellular processes that facilitate sinking. This project is testing this emerging hypothesis and determining how different nutrient regimes influence the fate of diatoms through impacts on viral infection dynamics and death. This is particularly timely given major national and international initiatives currently seeking to quantify how ecosystem interactions regulate carbon export in the ocean. Results of this project have the potential to challenge the canonical role of diatom viruses in carbon cycling and transform the understanding of host-virus interactions in the ocean. This project provides critical funding support for a soft-money, underrepresented, female oceanographer, as well a graduate student and undergraduates. Proposed fieldwork leverages a Rutgers and European Union-funded project, fostering ongoing collaborations with researchers at the Stazione Zoologica Anton Dohrn in Naples, Italy. To facilitate ocean literacy, the PIs are working with the Rutgers’ Education and Outreach team to conduct a series of Teen Cafes focused on carbon cycling, phytoplankton, and viruses utilizing the ‘Tools of Science’ (ToS), a series of educational videos and lesson plans designed to introduce middle, high school, and undergraduate students in underrepresented and underserved communities to core scientific practices.</p>
<p>Diatoms contribute almost 40% of marine primary productivity, dominating the biological pump and disproportionately contributing to carbon export due to the ballasted nature of a silica-based cell wall. The contribution of diatoms to carbon sequestration is dictated by the balance between upper ocean remineralization and sinking, yet we still cannot explain widespread spatio-temporal variability in diatom-mediated export. As the most abundant predatory entities in the ocean, viruses play a critical role in shaping microbial ecosystems and driving global biogeochemical cycles. The premise of this proposal is that nutrient regimes drive the biogeochemical consequences of diatom host-virus interactions. For decades, the role of viruses as ‘shunts’, redirecting particulate matter away from higher trophic levels and into the dissolved fraction through host lysis, has dominated microbial ecology and marine virology. However, the idea that viruses may also act as ‘shuttles’, facilitating carbon export by stimulating aggregation and/or ballast production, is now emerging as a potential mechanism for carbon flux. This project is conducting laboratory-based studies on diverse diatom host-virus systems and manipulative studies on natural diatom communities to compare the impact of viral infection on processes that facilitate sinking – mineral ballast production and particle aggregation – to those that stimulate remineralization – bacterial-mediated hydrolysis and subsequent remineralization of diatom particulate organic matter and silica. Taken together, this work is characterizing the relative balance between these diametrically opposing outcomes within the ecophysiological context of nutrient regime (specifically, silicon and iron limitation), ultimately elucidating the impact of viral infection on the fate of diatom organic matter in the ocean.</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>
Shunt or Shuttle
largerWorkCitation
project
eng; USA
oceans
14.25
14.25
40.81667
40.81667
2022-04-27
2022-05-19
Gulf of Naples, Italy approx. 40 degrees N, 14 degrees E
0
BCO-DMO catalogue of parameters from Phytoplankton abundance in seawater samples collected from Project "DaVINCi" incubations in the Gulf of Naples, Italy from April to May 2022
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/984916.rdf
Name: Date
Units: unitless
Description: <p>Date sample was collected</p>
http://lod.bco-dmo.org/id/dataset-parameter/984917.rdf
Name: Incubation
Units: unitless
Description: <p>Incubation number identifier</p>
http://lod.bco-dmo.org/id/dataset-parameter/984918.rdf
Name: Bag
Units: unitless
Description: <p>Bag number</p>
http://lod.bco-dmo.org/id/dataset-parameter/984919.rdf
Name: Incubation_Timepoint_d
Units: day
Description: <p>Timepoint during the incubation the sample was collected</p>
http://lod.bco-dmo.org/id/dataset-parameter/984920.rdf
Name: Treatment
Units: unitless
Description: <p>Nutrient status consisting of either ambient (unamended), replete (amended with 30 uM N, 1.87 uM P, and 30 uM Si), or Si-limited (amended with 30 uM N, 1.87 uM P, 10 uM Si)</p>
http://lod.bco-dmo.org/id/dataset-parameter/984921.rdf
Name: Replicate
Units: unitless
Description: <p>Replicate bag number</p>
http://lod.bco-dmo.org/id/dataset-parameter/984922.rdf
Name: Diatoms
Units: cells per liter (cells/L)
Description: <p>Diatom cell abundance</p>
http://lod.bco-dmo.org/id/dataset-parameter/984923.rdf
Name: Dinoflagellates
Units: cells per liter (cells/L)
Description: <p>Dinoflagellate cell abundance</p>
http://lod.bco-dmo.org/id/dataset-parameter/984924.rdf
Name: Coccolithophores
Units: cells per liter (cells/L)
Description: <p>Coccolithophore cell abundance</p>
http://lod.bco-dmo.org/id/dataset-parameter/984925.rdf
Name: Other_flagellates
Units: cells per liter (cells/L)
Description: <p>Other flagellates cell abundance</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
1639
https://darchive.mblwhoilibrary.org/server/api/core/bitstreams/984fdbaa-3e7e-4dbe-81c9-3d8db07df352/content
download
https://doi.org/10.26008/1912/bco-dmo.984885.1
download
onLine
dataset
<p>Samples were fixed with 1% Lugol's. The quantitative analysis is carried out using an inverted microscope after the settling of a variable volume of sample (Utermhöl, 1958). The settled volumes vary in relation to the number of cells present in the sample, which is estimated on the basis of the chlorophyll a concentration or of the depth of the Secchi Disk. The counting is carried out on various proportions of the sedimentation chamber (transects, random fields or the entire chamber), depending on the characteristics of the sample.</p>
<p>The abundance of phytoplankton cells present in the sample is calculated by applying the following general formula:</p>
<p>C = N × factor × 1000/v</p>
<p>where C = concentration of phytoplankton expressed as cells per liter (cells L-1);<br />
N = number of cells counted;<br />
v = volume of settled sample (milliliters (mL));<br />
factor = ratio between the total area of the chamber and the explored area.</p>
<p>Instruments: Samples from incubation bottle treatments were collected after gently mixing bottles and dispensing 250 mLs into a dark glass bottle containing 1% Lugol's solution and stored in the dark at 4 degrees Celsius.</p>
Specified by the Principal Investigator(s)
- Imported original file "Incubation_PhytoCellCounts.csv" into the BCO-DMO system.
- Flagged "NA" as a missing data value (missing data are empty/blank in the final CSV file).
- Renamed fields to comply with BCO-DMO naming conventions.
- Converted Date column to YYYY-MM-DD format.
- Saved the final file as "984885_v1_phytoplankton_cell_abundance.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
inverted microscope
inverted microscope
PI Supplied Instrument Name: inverted microscope Instrument Name: Inverted Microscope Instrument Short Name: Instrument Description: An inverted microscope is a microscope with its light source and condenser on the top, above the stage pointing down, while the objectives and turret are below the stage pointing up. It was invented in 1850 by J. Lawrence Smith, a faculty member of Tulane University (then named the Medical College of Louisiana).
Inverted microscopes are useful for observing living cells or organisms at the bottom of a large container (e.g. a tissue culture flask) under more natural conditions than on a glass slide, as is the case with a conventional microscope. Inverted microscopes are also used in micromanipulation applications where space above the specimen is required for manipulator mechanisms and the microtools they hold, and in metallurgical applications where polished samples can be placed on top of the stage and viewed from underneath using reflecting objectives.
The stage on an inverted microscope is usually fixed, and focus is adjusted by moving the objective lens along a vertical axis to bring it closer to or further from the specimen. The focus mechanism typically has a dual concentric knob for coarse and fine adjustment. Depending on the size of the microscope, four to six objective lenses of different magnifications may be fitted to a rotating turret known as a nosepiece. These microscopes may also be fitted with accessories for fitting still and video cameras, fluorescence illumination, confocal scanning and many other applications. Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/LAB05/
Secchi Disk
Secchi Disk
PI Supplied Instrument Name: Secchi Disk Instrument Name: Secchi Disc Instrument Short Name:Secchi Disc Instrument Description: Typically, a 16 inch diameter white/black quadrant disc used to measure water optical clarity Community Standard Description: http://vocab.nerc.ac.uk/collection/L22/current/TOOL0430/