http://lod.bco-dmo.org/id/dataset/906562
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
2023-08-21
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Water characteristics measured in Narragansett Bay over two years, from March 2021 to September 2023
2025-04-03
publication
2025-04-03
revision
Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)
2024-02-06
publication
https://doi.org/10.26008/1912/bco-dmo.906562.1
Nathan A. Ahlgren
Clark University
principalInvestigator
Marcia Marston
Roger Williams 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: Ahlgren, N. A., Marston, M. (2025) Water characteristics measured in Narragansett Bay over two years, from March 2021 to September 2023. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 2) Version Date 2025-04-03 [if applicable, indicate subset used]. doi:10.26008/1912/bco-dmo.906562.2 [access date]
Narragansett Bay RWU Time-series Dataset Description: Methods and Sampling: <p>Water was collected at the reported time, and water collection was in nearly all cases taken on the incoming tide. Water was collected from a dock in a 1 liter (L) bottle, from which water temperature, salinity, and chlorophyll a were measured. Water samples for macronutrients were also taken from the 1 L sample bottle and filtered through a 0.45-micrometer (µm) filter and collected in duplicate and stored in 60-milliliter (mL) HDPE bottles at -20 degrees Celsius before being sent for analysis. Macronutrients (silicate, orthophosphate, ammonium, nitrite, and nitrate + nitrite) were measured from duplicate samples by the Center for Coastal Studies using a nutrient autosampler system. Duplicate 1 mL water samples were preserved with 0.125% EM grade glutaldehyde and frozen and stored at -80 degrees Celsius for flow cyometry analysis at a later time. Water temperature and salinity were measured with certified instruments. In situ chlorophyll a was measured by reading fluorescence of a whole water sample on a calibrated instrument.</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-2023175 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=2023175
completed
Nathan A. Ahlgren
Clark University
508-793-7107
950 Main St
Worcester
MA
01610
USA
nahlgren@clarku.edu
pointOfContact
Marcia Marston
Roger Williams University
401-254-3673
Department of Biology 1 Old Ferry Road
Bristol
RI
02809
USA
mmarston@rwu.edu
pointOfContact
asNeeded
Dataset Version: 2
Unknown
ISO_DateTime_Local
ISO_DateTime_UTC
WaterTemp
AirTemp
Salinity
ChlA
NO2NO3
PO4
SiO4
NH4
NO2
NH4_flag
NO3NO2_flag
Latitude
Longitude
bottle
Turner Designs C-FLUOR Probe (Model: 2120-000)
nutrient autosampler
Portable Refractometer
VEEGEE Scientific encapsulated thermometer model #80704E
theme
None, User defined
ISO_DateTime_Local
ISO_DateTime_UTC
water temperature at measurement depth
air temperature
salinity
chlorophyll a
nitrate plus nitrite
reactive phosphorus (PO4)
Silicate (reactive silica)
Ammonium
Nitrite
flag
latitude
longitude
featureType
BCO-DMO Standard Parameters
Bottle
Fluorometer
Nutrient Autoanalyzer
Refractometer
Water Temperature Sensor
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: Characterization of Synechococcus-cyanophage interactions across phylogenetic and temporal scales
https://osprey.bco-dmo.org/project/815414
Collaborative research: Characterization of Synechococcus-cyanophage interactions across phylogenetic and temporal scales
<p><em>NSF Award Abstract:</em><br />
Viral infection influences the flow of nutrients in the oceans and the diversity and structure of ecologically important microbial communities. Understanding which viruses infect which hosts is critical to understanding the exact impact of viruses, but there are still critical gaps in knowledge about how widely viruses can infect specific bacteria types and how this can change over time. This project includes the isolation and characterization of hundreds of co-occurring photosynthetic bacteria (cyanobacteria from the genus Synechococcus) and viruses that infect them (cyanophage) from Narragansett Bay, Rhode Island to assess the degree to which they can infect each other and identify specific genes that control cross-infection. DNA collected for over 10 years from Narragansett Bay is used to track Synechococcus and cyanophage communities to determine how virus-host interactions play out in shaping the diversity of natural Synechococcus and cyanophage communities over seasonal cycles and from year to year. This work provides knowledge of how individual viral-host interactions in a natural community can lead to the stable co-existence of particular species of viruses and bacteria in a coastal ecosystem over time. This project supports 15 undergraduate student researchers, a graduate student and a postdoctoral fellow who also receives training in effective practices in science teaching. Integration of the study's results into undergraduate courses and outreach activities facilitates authentic opportunities for students to contribute to research and engagement of local junior and senior high school students.</p>
<p>The team of scientists and students are conducting a phylogenetically-informed study of natural communities of co-occurring Synechococcus and cyanophage, a model tractable system in Narragansett Bay, to characterize phage-host interactions across different scales of diversity and time. The team's goal is to isolate a large collection of ~100 Synechococcus and ~200 cyanophage from Narragansett Bay and to conduct infection assays and comparative genomics on these isolates. They employ amplicon sequencing of highly variable loci for both Synechococcus and cyanophage to characterize community dynamics across broad to fine genetic scales - ecotypes to within-species variants - for 10 years of archived monthly samples and a new weekly time-series over two years. These studies address the following three key questions: 1) Are there inherent boundaries of genetic relatedness (i.e. ecotype, species, or finer levels) at which the patterns of infection networks fundamentally shift from being mostly nested to mostly modular? (2) What are the underlying mechanisms and genetic loci that determine the boundaries of infection, i.e., host range and phage susceptibility? and, (3) How do host-phage interactions at different phylogenetic levels influence community structure over short (weeks to months) and long (year-to-year) time scales? Results from this project help to better understand how phytoplankton and bacterioplankton communities are shaped by viral predation and how host and phage diversity is created, maintained, and structured in the oceans.</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>
NB_Syn_cyanophage
largerWorkCitation
project
eng; USA
oceans
-71.256378
-71.256378
41.649737
41.649737
2021-03-10
2023-09-27
Narragansett Bay (dock at Roger Williams University): 41°38’59”N, 71°15’24”W
0
BCO-DMO catalogue of parameters from Water characteristics measured in Narragansett Bay over two years, from March 2021 to September 2023
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/957858.rdf
Name: ISO_DateTime_Local
Units: unitless
Description: <p>Date and approximate time of water sampling in the local time zone (EST/EDT) in ISO 8601 format</p>
http://lod.bco-dmo.org/id/dataset-parameter/957859.rdf
Name: ISO_DateTime_UTC
Units: unitless
Description: <p>Date and approximate time of water sampling in UTC in ISO 8601 format</p>
http://lod.bco-dmo.org/id/dataset-parameter/957860.rdf
Name: WaterTemp
Units: degrees Celsius
Description: <p>Water temperature</p>
http://lod.bco-dmo.org/id/dataset-parameter/957861.rdf
Name: AirTemp
Units: degrees Fahrenheit
Description: <p>Air temperature in Fahrenheit</p>
http://lod.bco-dmo.org/id/dataset-parameter/957862.rdf
Name: Salinity
Units: Practical salinity units (PSU)
Description: <p>Water salinity</p>
http://lod.bco-dmo.org/id/dataset-parameter/957863.rdf
Name: ChlA
Units: micrograms per liter (ug/L)
Description: <p>Chlorophyll a</p>
http://lod.bco-dmo.org/id/dataset-parameter/957864.rdf
Name: NO2NO3
Units: micromolar (uM)
Description: <p>Water nitrate plus nitrite; BDL = below detection limit</p>
http://lod.bco-dmo.org/id/dataset-parameter/957865.rdf
Name: PO4
Units: micromolar (uM)
Description: <p>Water orthophosphate; BDL = below detection limit</p>
http://lod.bco-dmo.org/id/dataset-parameter/957866.rdf
Name: SiO4
Units: micromolar (uM)
Description: <p>Water silicate; BDL = below detection limit</p>
http://lod.bco-dmo.org/id/dataset-parameter/957867.rdf
Name: NH4
Units: micromolar (uM)
Description: <p>Water ammonium; BDL = below detection limit</p>
http://lod.bco-dmo.org/id/dataset-parameter/957868.rdf
Name: NO2
Units: micromolar (uM)
Description: <p>Water nitrite; BDL = below detection limit</p>
http://lod.bco-dmo.org/id/dataset-parameter/957869.rdf
Name: NH4_flag
Units: unitless
Description: <p>Flag for ammonium data. 0 = mean of duplicate measurements; 1 = value of one of the duplicates, the other duplicate was BDL.</p>
http://lod.bco-dmo.org/id/dataset-parameter/957870.rdf
Name: NO3NO2_flag
Units: unitless
Description: <p>Flag for nitrate plus nitrite data. 0= mean of duplicate measurements; 1= value of one of the duplicates, the other duplicate was BDL.</p>
http://lod.bco-dmo.org/id/dataset-parameter/957871.rdf
Name: Latitude
Units: decimal degrees
Description: <p>Approximate latitude where sample was collected</p>
http://lod.bco-dmo.org/id/dataset-parameter/957872.rdf
Name: Longitude
Units: decimal degrees
Description: <p>Approximate longitude where sample was collected</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
13389
https://darchive.mblwhoilibrary.org/server/api/core/bitstreams/b226a90a-e5a0-4e81-a7cc-528cf576882b/content
download
10064
https://darchive.mblwhoilibrary.org/server/api/core/bitstreams/6b110151-1f1f-4bd8-b9dd-42f10dfdf9fa/content
download
https://doi.org/10.26008/1912/bco-dmo.906562.1
download
onLine
dataset
<p>Water was collected at the reported time, and water collection was in nearly all cases taken on the incoming tide. Water was collected from a dock in a 1 liter (L) bottle, from which water temperature, salinity, and chlorophyll a were measured. Water samples for macronutrients were also taken from the 1 L sample bottle and filtered through a 0.45-micrometer (µm) filter and collected in duplicate and stored in 60-milliliter (mL) HDPE bottles at -20 degrees Celsius before being sent for analysis. Macronutrients (silicate, orthophosphate, ammonium, nitrite, and nitrate + nitrite) were measured from duplicate samples by the Center for Coastal Studies using a nutrient autosampler system. Duplicate 1 mL water samples were preserved with 0.125% EM grade glutaldehyde and frozen and stored at -80 degrees Celsius for flow cyometry analysis at a later time. Water temperature and salinity were measured with certified instruments. In situ chlorophyll a was measured by reading fluorescence of a whole water sample on a calibrated instrument.</p>
Specified by the Principal Investigator(s)
<p>Duplicate samples for macronutrient measurements were made. This dataset reports the mean value of duplicate measurements when both measurements were above the detection limit (flag=0). In rare cases where one duplicate was measured as below detection limit and the other duplicate value was above the detection limit, the latter was reported and a flag value for that measurement is provided (flag=1).</p>
Specified by the Principal Investigator(s)
Version History:
Version 1:
Version date: 2023-08-21
Description: This version contained data from 2021-03-10 to 2023-03-29. Additional data have been added in version 2 and important corrections were made to existing data. Notably, in version 1 the units for AirTemp were incorrectly reported as degrees Celsius and the data were offset by 2 weeks.
BCO-DMO Processing for v1:
- Imported original file named "RWU_cyanophage_timeseries_env_data.csv" into the BCO-DMO system.
- Renamed fields to comply with BCO-DMO naming conventions (replaced "." with underscore).
- Converted the original date/time field to ISO 8601 format (local time zone of EST/EDT).
- Created a date/time field in ISO 8601 format in UTC time zone.
- Removed the original date/time field.
- Added columns for the sampling site latitude and longitude.
- Saved the final file as "906562_v1_narragansett_bay_time-series.csv".
Version 2:
version date: 2025-04-03
Description: This version extends the dataset to include sampling dates of 2021-03-10 to 2023-09-27. Important corrections have also been made to existing data. Notably, in version 1 the units for AirTemp were incorrectly reported, and the data were offset by 2 weeks. Version 2 corrects these issues.
BCO-DMO Processing for v2:
- Imported original file "RWU_cyanophage_timeseries_env_data_v2_w_localtime.csv" to the BCO-DMO system.
- Removed "NA" (missing data are empty/blank in the final csv file).
- Saved the final file as "906562_v2_narragansett_bay_time-series.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
bottle
bottle
PI Supplied Instrument Name: bottle PI Supplied Instrument Description:Water was collected from a dock in a 1 L bottle. Instrument Name: Bottle Instrument Short Name:Bottle Instrument Description: A container, typically made of glass or plastic and with a narrow neck, used for storing drinks or other liquids.
Turner Designs C-FLUOR Probe (Model: 2120-000)
Turner Designs C-FLUOR Probe (Model: 2120-000)
PI Supplied Instrument Name: Turner Designs C-FLUOR Probe (Model: 2120-000) PI Supplied Instrument Description:Used to measure in situ chlorophyll a; Fluorometer model: Turner Designs C-FLUOR Probe (Model: 2120-000) coupled with a Turner Designs DataBank Datalogger. Instrument Name: Fluorometer Instrument Short Name:Fluorometer Instrument Description: A fluorometer or fluorimeter is a device used to measure parameters of fluorescence: its intensity and wavelength distribution of emission spectrum after excitation by a certain spectrum of light. The instrument is designed to measure the amount of stimulated electromagnetic radiation produced by pulses of electromagnetic radiation emitted into a water sample or in situ. Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/113/
nutrient autosampler
nutrient autosampler
PI Supplied Instrument Name: nutrient autosampler PI Supplied Instrument Description:Macronutrients (silicate, orthophosphate, ammonium, nitrite, and nitrate + nitrite) were measured from duplicate samples by the Center for Coastal Studies using a nutrient autosampler system. Instrument Name: Nutrient Autoanalyzer Instrument Short Name:Nutrient Autoanalyzer Instrument Description: Nutrient Autoanalyzer is a generic term used when specific type, make and model were not specified. In general, a Nutrient Autoanalyzer is an automated flow-thru system for doing nutrient analysis (nitrate, ammonium, orthophosphate, and silicate) on seawater samples. Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/LAB04/
Portable Refractometer
Portable Refractometer
PI Supplied Instrument Name: Portable Refractometer PI Supplied Instrument Description:Used to measure salinity; Portable Refractometer: Model RHS-10ATC. Instrument Name: Refractometer Instrument Short Name:Refractometer Instrument Description: A refractometer is a laboratory or field device for the measurement of an index of refraction (refractometry). The index of refraction is calculated from Snell's law and can be calculated from the composition of the material using the Gladstone-Dale relation.
In optics the refractive index (or index of refraction) n of a substance (optical medium) is a dimensionless number that describes how light, or any other radiation, propagates through that medium.
VEEGEE Scientific encapsulated thermometer model #80704E
VEEGEE Scientific encapsulated thermometer model #80704E
PI Supplied Instrument Name: VEEGEE Scientific encapsulated thermometer model #80704E PI Supplied Instrument Description:Used to measure water temperature; Thermometer model: VEEGEE Scientific encapsulated thermometer model #80704E. Instrument Name: Water Temperature Sensor Instrument Short Name:Water Temp Sensor Instrument Description: General term for an instrument that measures the temperature of the water with which it is in contact (thermometer). Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/134/