http://lod.bco-dmo.org/id/dataset/885939
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
2022-12-28
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Environmental data, nutrients, and leucine and thymidine bacterial production from samples collected by CTD during cruises in the San Pedro Channel on R/V Yellowfin from 2005 to 2018
2022-12-29
publication
2022-12-29
revision
Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)
2023-01-30
publication
https://doi.org/10.26008/1912/bco-dmo.885939.1
Jed A. Fuhrman
University of Southern California
principalInvestigator
Yi-Chun Yeh
University of Southern California
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: Yeh, Y., Fuhrman, J. A. (2023) Environmental data, nutrients, and leucine and thymidine bacterial production from samples collected by CTD during cruises in the San Pedro Channel on R/V Yellowfin from 2005 to 2018. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2022-12-29 [if applicable, indicate subset used]. doi:10.26008/1912/bco-dmo.885939.1 [access date]
SPOT Environmental Data 2005-2018 Dataset Description: Methods and Sampling: <p>Monthly San Pedro Ocean Time-series (SPOT) cruises on R/V Yellowfin were conducted in the San Pedro Channel, off the coast of Los Angeles, California, USA (33 N, 118 W). Variables including temperature, oxygen, and fluorescence were recorded by a Seabird Scientific SBE25plus Sealogger CTD at the time of sample collection. Nutrient variables including nitrite, nitrate, and phosphate were analyzed by MSI Analytical Lab at the University of California Santa Barbara. Satellite sea surface temperature, chlorophyll-a concentration, and surface productivity estimates were downloaded from the NOAA Coastwatch browser website. Leucine and thymidine bacterial production assays were performed by incubating seawater with H3-tagged leucine or thymidine for one hour, killing with trichloroacetic acid, filtered onto a 0.45 µm MCE filter (EMD Millipore HAWP02500). Activity on the filters is measured using a liquid scintillation counter (Beckman Coulter LS6500), and then the rate of uptake is used to calculate bacterial cells per milliliter of each sample.</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1737409 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1737409
Funding provided by Gordon and Betty Moore Foundation: Marine Microbiology Initiative (MMI) Award Number: GBMF3779
Funding provided by Simons Foundation (Simons) Award Number: CBIOMES 549943
completed
Jed A. Fuhrman
University of Southern California
213-740-5757
Dept. Biological Sciences, Dornsife College of Letters, Arts, and Sciences 3616 Trousdale Parkway
Los Angeles
CA
90089-0371
USA
fuhrman@usc.edu
pointOfContact
Yi-Chun Yeh
University of Southern California
yichuny@usc.edu
pointOfContact
asNeeded
Dataset Version: 1
Unknown
Date
DepthBin
depth
CTDTemp
CTDSal
CTDOxy
CTDFlu
NO2NO3
PO4
ChlMo
Chl8day
MEI
SST
PP
mean_Leu
sd_Leu
mean_Thy
sd_Thy
Beckman Coulter LS6500
Seabird Scientific SBE25plus Sealogger CTD
theme
None, User defined
date
depth
water temperature at measurement depth
salinity
dissolved Oxygen
chlorophyll a
nitrate plus nitrite
reactive phosphorus (PO4)
No BCO-DMO term
sea surface temperature
primary production
leucine incorporation rate
thymidine incorporation rate
featureType
BCO-DMO Standard Parameters
Liquid Scintillation Counter
Sea-Bird SBE 25 Sealogger CTD
instrument
BCO-DMO Standard Instruments
SPOT_Yellowfin_Cruises
service
Deployment Activity
San Pedro Ocean Time Series
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.
Protistan, prokaryotic, and viral processes at the San Pedro Ocean Time-series
https://osprey.bco-dmo.org/project/743049
Protistan, prokaryotic, and viral processes at the San Pedro Ocean Time-series
<p>Planktonic marine microbial communities consist of a diverse collection of bacteria, archaea, viruses, protists (phytoplankton and protozoa) and small animals (metazoan). Collectively, these species are responsible for virtually all marine pelagic primary production where they form the basis of food webs and carry out a large fraction of respiratory processes. Microbial interactions include the traditional role of predation, but recent research recognizes the importance of parasitism, symbiosis and viral infection. Characterizing the response of pelagic microbial communities and processes to environmental influences is fundamental to understanding and modeling carbon flow and energy utilization in the ocean, but very few studies have attempted to study all of these assemblages in the same study. This project is comprised of long-term (monthly) and short-term (daily) sampling at the San Pedro Ocean Time-series (SPOT) site. Analysis of the resulting datasets investigates co-occurrence patterns of microbial taxa (e.g. protist-virus and protist-prokaryote interactions, both positive and negative) indicating which species consistently co-occur and potentially interact, followed by examination gene expression to help define the underlying mechanisms. This study augments 20 years of baseline studies of microbial abundance, diversity, rates at the site, and will enable detection of low-frequency changes in composition and potential ecological interactions among microbes, and their responses to changing environmental forcing factors. These responses have important consequences for higher trophic levels and ocean-atmosphere feedbacks. The broader impacts of this project include training graduate and undergraduate students, providing local high school student with summer lab experiences, and PI presentations at local K-12 schools, museums, aquaria and informal learning centers in the region. Additionally, the PIs advise at the local, county and state level regarding coastal marine water quality.</p>
<p>This research project is unique in that it is a holistic study (including all microbes from viruses to small metazoa) of microbial species diversity and ecological activities, carried out at the SPOT site off the coast of southern California. In studying all microbes simultaneously, this work aims to identify important ecological interactions among microbial species, and identify the basis(es) for those interactions. This research involves (1) extensive analyses of prokaryote (archaean and bacterial) and eukaryote (protistan and micro-metazoan) diversity via the sequencing of marker genes, (2) studies of whole-community gene expression by eukaryotes and prokaryotes in order to identify key functional characteristics of microorganismal groups and the detection of active viral infections, and (3) metagenomic analysis of viruses and bacteria to aid interpretation of transcriptomic analyses using genome-encoded information. The project includes exploratory metatranscriptomic analysis of poorly-understood aphotic and hypoxic-zone protists, to examine their stratification, functions and hypothesized prokaryotic symbioses.</p>
SPOT
largerWorkCitation
project
eng; USA
oceans
San Pedro Ocean Time Series
-118.24
-118.24
33.33
33.33
2005-01-19
2018-07-18
San Pedro Channel off the coast of Los Angeles
0
BCO-DMO catalogue of parameters from Environmental data, nutrients, and leucine and thymidine bacterial production from samples collected by CTD during cruises in the San Pedro Channel on R/V Yellowfin from 2005 to 2018
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/885960.rdf
Name: Date
Units: unitless
Description: <p>Day of collection</p>
http://lod.bco-dmo.org/id/dataset-parameter/885961.rdf
Name: DepthBin
Units: unitless
Description: <p>Bin category corresponding to targeted sampling depths. DCM is Deep Chlorophyll Maximum, which varies depending on environmental conditions.</p>
http://lod.bco-dmo.org/id/dataset-parameter/885962.rdf
Name: depth
Units: meters (m)
Description: <p>Actual depth sampled for given DepthBin</p>
http://lod.bco-dmo.org/id/dataset-parameter/885963.rdf
Name: CTDTemp
Units: degrees Celsius
Description: <p>Temperature as recorded by onboard CTD</p>
http://lod.bco-dmo.org/id/dataset-parameter/885964.rdf
Name: CTDSal
Units: PSU
Description: <p>Salinity as recorded by onboard CTD</p>
http://lod.bco-dmo.org/id/dataset-parameter/885965.rdf
Name: CTDOxy
Units: milliliters per liter (ml/L)
Description: <p>Oxygen concentration as recorded by onboard CTD</p>
http://lod.bco-dmo.org/id/dataset-parameter/885966.rdf
Name: CTDFlu
Units: milligrams per cubic meter (mg/m^3)
Description: <p>Chlorophyll fluorescence as recorded by onboard CTD</p>
http://lod.bco-dmo.org/id/dataset-parameter/885967.rdf
Name: NO2NO3
Units: micromolar (uM)
Description: <p>Total nitrate and nitrite</p>
http://lod.bco-dmo.org/id/dataset-parameter/885968.rdf
Name: PO4
Units: micromolar (uM)
Description: <p>Phosphate</p>
http://lod.bco-dmo.org/id/dataset-parameter/885969.rdf
Name: ChlMo
Units: milligrams per cubic meter (mg/m^3)
Description: <p>Satellite-observed monthly average chlorophyll-a concentration</p>
http://lod.bco-dmo.org/id/dataset-parameter/885970.rdf
Name: Chl8day
Units: milligrams per cubic meter (mg/m^3)
Description: <p>Satellite-observed 8-day average chlorophyll-a concentration</p>
http://lod.bco-dmo.org/id/dataset-parameter/885971.rdf
Name: MEI
Units: unitless
Description: <p>Multivariate ENSO index</p>
http://lod.bco-dmo.org/id/dataset-parameter/885972.rdf
Name: SST
Units: degrees Celsius
Description: <p>Satellite-observed monthly average sea surface temperature</p>
http://lod.bco-dmo.org/id/dataset-parameter/885973.rdf
Name: PP
Units: milligrams carbon per square meter per day (mg C/m^2/day)
Description: <p>Satellite-observed monthly average primary productivity</p>
http://lod.bco-dmo.org/id/dataset-parameter/885974.rdf
Name: mean_Leu
Units: cells per milliliter per day (cell/ml/day)
Description: <p>Mean cell/mL/day based on leucine uptake</p>
http://lod.bco-dmo.org/id/dataset-parameter/885975.rdf
Name: sd_Leu
Units: cells per milliliter per day (cell/ml/day)
Description: <p>Standard deviation for leucine uptake assay in cells/mL/day</p>
http://lod.bco-dmo.org/id/dataset-parameter/885976.rdf
Name: mean_Thy
Units: cells per milliliter per day (cell/ml/day)
Description: <p>Mean cell/mL/day based on thymidine uptake</p>
http://lod.bco-dmo.org/id/dataset-parameter/885977.rdf
Name: sd_Thy
Units: cells per milliliter per day (cell/ml/day)
Description: <p>Standard deviation for thymidine uptake assay in cells/mL/day</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
102059
https://darchive.mblwhoilibrary.org/server/api/core/bitstreams/59406416-99fc-508d-92b1-631d4755e7fc/content
download
https://doi.org/10.26008/1912/bco-dmo.885939.1
download
onLine
dataset
<p>Monthly San Pedro Ocean Time-series (SPOT) cruises on R/V Yellowfin were conducted in the San Pedro Channel, off the coast of Los Angeles, California, USA (33 N, 118 W). Variables including temperature, oxygen, and fluorescence were recorded by a Seabird Scientific SBE25plus Sealogger CTD at the time of sample collection. Nutrient variables including nitrite, nitrate, and phosphate were analyzed by MSI Analytical Lab at the University of California Santa Barbara. Satellite sea surface temperature, chlorophyll-a concentration, and surface productivity estimates were downloaded from the NOAA Coastwatch browser website. Leucine and thymidine bacterial production assays were performed by incubating seawater with H3-tagged leucine or thymidine for one hour, killing with trichloroacetic acid, filtered onto a 0.45 µm MCE filter (EMD Millipore HAWP02500). Activity on the filters is measured using a liquid scintillation counter (Beckman Coulter LS6500), and then the rate of uptake is used to calculate bacterial cells per milliliter of each sample.</p>
Specified by the Principal Investigator(s)
<p><strong>BCO-DMO Processing:</strong><br />
- converted dates to YYYY-MM-DD format;<br />
- replaced "No data" with "nd".</p>
Specified by the Principal Investigator(s)
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 Coulter LS6500
Beckman Coulter LS6500
PI Supplied Instrument Name: Beckman Coulter LS6500 Instrument Name: Liquid Scintillation Counter Instrument Short Name:LSC Instrument Description: Liquid scintillation counting is an analytical technique which is defined by the incorporation of the radiolabeled analyte into uniform distribution with a liquid chemical medium capable of converting the kinetic energy of nuclear emissions into light energy. Although the liquid scintillation counter is a sophisticated laboratory counting system used the quantify the activity of particulate emitting (ß and a) radioactive samples, it can also detect the auger electrons emitted from 51Cr and 125I samples.
Liquid scintillation counters are instruments assaying alpha and beta radiation by quantitative detection of visible light produced by the passage of rays or particles through a suitable scintillant incorporated into the sample. Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/LAB21/
Seabird Scientific SBE25plus Sealogger CTD
Seabird Scientific SBE25plus Sealogger CTD
PI Supplied Instrument Name: Seabird Scientific SBE25plus Sealogger CTD PI Supplied Instrument Description:Serial Number 0251231 Instrument Name: Sea-Bird SBE 25 Sealogger CTD Instrument Short Name:CTD SBE 25 Instrument Description: The Sea-Bird SBE 25 SEALOGGER CTD is battery powered and is typically used to record data in memory, eliminating the need for a large vessel, electrical sea cable, and on-board computer. All SBE 25s can also operate in real-time, transmitting data via an opto-isolated RS-232 serial port. Temperature and conductivity are measured by the SBE 3F Temperature sensor and SBE 4 Conductivity sensor (same as those used on the premium SBE 9plus CTD). The SBE 25 also includes the SBE 5P (plastic) or 5T (titanium) Submersible Pump and TC Duct. The pump-controlled, TC-ducted flow configuration significantly reduces salinity spiking caused by ship heave, and in calm waters allows slower descent rates for improved resolution of water column features. Pressure is measured by the modular SBE 29 Temperature Compensated Strain-Gauge Pressure sensor (available in eight depth ranges to suit the operating depth requirement). The SBE 25's modular design makes it easy to configure in the field for a wide range of auxiliary sensors, including optional dissolved oxygen (SBE 43), pH (SBE 18 or SBE 27), fluorescence, transmissivity, PAR, and optical backscatter sensors. More information from Sea-Bird Electronics: http:www.seabird.com. Community Standard Description: http://vocab.nerc.ac.uk/collection/L22/current/TOOL0040/
Cruise: SPOT_Yellowfin_Cruises
SPOT_Yellowfin_Cruises
R/V Yellowfin
R/V Yellowfin
vessel
R/V Yellowfin
R/V Yellowfin
vessel