http://lod.bco-dmo.org/id/dataset/970493 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 2025-07-31 ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data ISO 19115-2:2009(E) Bacterial abundance collected from project "DaVINCi" incubations in the Gulf of Naples, Italy from April to May 2022 2025-07-31 publication 2025-07-31 revision BCO-DMO Linked Data URI 2025-07-31 creation http://lod.bco-dmo.org/id/dataset/970493 Kimberlee Thamatrakoln Rutgers University principalInvestigator Kay D. Bidle Rutgers University principalInvestigator Chana F. Kranzler Bar-Ilan 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., Bidle, K. D., Kranzler, C. F. (2025) Bacterial abundance 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 2025-07-31 [if applicable, indicate subset used]. http://lod.bco-dmo.org/id/dataset/970493 [access date] Bacterial Abundance Dataset Description: Methods and Sampling: &lt;p&gt;Samples were collected at Station MareChiara (40°49'N, 14°15'E), Gulf of Naples, Italy. Whole seawater (whole) or seawater filtered through a 3-micrometer (um) polycarbonate filter (&amp;lt;3 um) is transferred to a cryovial containing a final concentration of glutarldehyde of 0.5%. The sample is stored at 4 degrees Celsius (C) for 30 minutes, then flash frozen in liquid nitrogen and stored at -80 degrees C. Upon analysis, samples were thawed, and a final concentration of 10 micrograms per milliliter (ug/ml) of Tween-80 was added. Samples were sonicated at 50 watts (W) in a water bath for 1 minute. Samples were added to 1X TE buffer (0.01 molar (M) Tris, pH 8.0, 5 micromolar (uM) EDTA) with Sybr Gold (1:20,000 dilution) and heated at 80 degrees C for 10 minutes in the dark. Samples were cooled to room temperature for ~5 minutes before analyzing on an Accuri C6 Plus flow cytometer. Bacteria were gated based on SybrGold fluorescence and side scatter.&lt;/p&gt; 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 onGoing 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 Kay D. Bidle Rutgers University 848-932-3467 Department of Marine and Coastal Sciences 71 Dudley Road New Brunswick NJ 08901 USA bidle@marine.rutgers.edu pointOfContact Chana F. Kranzler Bar-Ilan University chana.kranzler@biu.ac.il pointOfContact asNeeded Dataset Version: 1 Unknown Date Incubation Incubationn_Timepoint Bag Treatment Replicate_Bag Size_fraction Bacterial_abundance Accuri C6+ (BD Biosciences) theme None, User defined date experiment id time_point sample description treatment sample fraction (includes size fractions) abundance featureType BCO-DMO Standard Parameters BD Biosciences Accuri C6 Plus 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. 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 2022-04-30 2022-05-19 Gulf of Naples, Italy approx. 40 degrees N, 14 degrees E 0 BCO-DMO catalogue of parameters from Bacterial abundance 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/970522.rdf Name: Date Units: unitless Description: <p>Date the sample was collected</p> http://lod.bco-dmo.org/id/dataset-parameter/970523.rdf Name: Incubation Units: unitless Description: <p>Incubation number identifier</p> http://lod.bco-dmo.org/id/dataset-parameter/970524.rdf Name: Incubationn_Timepoint Units: day Description: <p>Timepoint during the incubation the sample was collected</p> http://lod.bco-dmo.org/id/dataset-parameter/970525.rdf Name: Bag Units: unitless Description: <p>Bag number</p> http://lod.bco-dmo.org/id/dataset-parameter/970526.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/970527.rdf Name: Replicate_Bag Units: unitless Description: <p>Replicate bag number</p> http://lod.bco-dmo.org/id/dataset-parameter/970528.rdf Name: Size_fraction Units: unitless Description: <p>Whole (unfiltered) or &lt;3 um (3 um filtered) seawater</p> http://lod.bco-dmo.org/id/dataset-parameter/970529.rdf Name: Bacterial_abundance Units: cells per milliliter (cells/ml) Description: <p>Bacteria 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 https://osprey.bco-dmo.org/dataset/970493/data/download download onLine dataset &lt;p&gt;Samples were collected at Station MareChiara (40°49'N, 14°15'E), Gulf of Naples, Italy. Whole seawater (whole) or seawater filtered through a 3-micrometer (um) polycarbonate filter (&amp;lt;3 um) is transferred to a cryovial containing a final concentration of glutarldehyde of 0.5%. The sample is stored at 4 degrees Celsius (C) for 30 minutes, then flash frozen in liquid nitrogen and stored at -80 degrees C. Upon analysis, samples were thawed, and a final concentration of 10 micrograms per milliliter (ug/ml) of Tween-80 was added. Samples were sonicated at 50 watts (W) in a water bath for 1 minute. Samples were added to 1X TE buffer (0.01 molar (M) Tris, pH 8.0, 5 micromolar (uM) EDTA) with Sybr Gold (1:20,000 dilution) and heated at 80 degrees C for 10 minutes in the dark. Samples were cooled to room temperature for ~5 minutes before analyzing on an Accuri C6 Plus flow cytometer. Bacteria were gated based on SybrGold fluorescence and side scatter.&lt;/p&gt; Specified by the Principal Investigator(s) &lt;p&gt;Events in gate were corrected for the sample volume and dilutions to obtain bacteria abundance in cells per milliliter (cells/mL).&lt;/p&gt; Specified by the Principal Investigator(s) - Imported original file &quot;Incubations_BacteriaAbundance.csv&quot; into the BCO-DMO system. - Converted Date column to YYYY-MM-DD format. - Renamed fields to comply with BCO-DMO naming conventions. - Saved the final file as &quot;970493_v1_bacterial_abundance.csv&quot;. 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 Accuri C6+ (BD Biosciences) Accuri C6+ (BD Biosciences) PI Supplied Instrument Name: Accuri C6+ (BD Biosciences) Instrument Name: BD Biosciences Accuri C6 Plus flow cytometer Instrument Short Name:Accuri C6 Plus Instrument Description: A flow cytometer designed to detect fluorochromes (including FITC, PE, APC), polymer dyes, and fluorescent proteins (including GFP, YFP, mCherry). The instrument is equipped with a blue and red laser, two light scatter detectors, and four fluorescence detectors with user-interchangeable filters. A non-pressurised peristaltic pump system drives the fluidics. The system monitors the sample volume pulled per run and can calculate absolute counts or sample concentration per microliter (uL). In the standard configuration (3-blue/1-red), three detectors read fluorescence emissions from fluorochromes excited by the blue laser, while a fourth detector reads emissions from fluorochromes excited by the red laser. The optional Selectable Laser Module allows the system to operate in 2-blue/2-red and 4-blue configurations. The minimum detectable particle size and sample volume are 0.5 micrometers (um) and 0.5 uL respectively. The maximum number of events is 1 million with an acquisition rate of up to 10,000 events/second.