http://lod.bco-dmo.org/id/dataset/736702
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
2018-05-16
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Counts of picocyanobacteria from SMILE cruise (SKQ201703S) at the North Pacific Subtropical Front in March 2017
2018-05-16
publication
2018-05-16
revision
Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)
2022-03-18
publication
https://doi.org/10.26008/1912/bco-dmo.736702.1
Anne W. Thompson
Portland State 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: Thompson, A. (2022) Counts of picocyanobacteria from SMILE cruise (SKQ201703S) at the North Pacific Subtropical Front in March 2017. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2018-05-16 [if applicable, indicate subset used]. doi:10.26008/1912/bco-dmo.736702.1 [access date]
SMILE counts Dataset Description: <p>Counts of prochlorococcus, synechococcus, and picoeukaryotes from SMILE cruise (SKQ201703S) at the North Pacific Subtropical Front in March 2017.&nbsp;</p> Methods and Sampling: <p>Water was sampled from the CTD into 15mL sterile polypropylene tubes. 2mL samples were fixed with 0.125% glutaraldehyde then flash frozen in liquid nitrogen and stored until analysis.&nbsp;</p>
<p>Cell counts were determined by flow cytometry using a BD Biosciences Influx high speed cell sorter. A 488nm laser was used in addition to chlorophyll and phycoerythrin filters, forward scatter relative to 1um beads, and side scattered light.</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1646709 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1646709
completed
Anne W. Thompson
Portland State University
503-725-8052
PO Box 751
Portland
OR
97201
USA
awt@pdx.edu
pointOfContact
asNeeded
Dataset Version: 1
Unknown
castNum
date
day_of_March
depth
latitude
longitude
temperature
salinity
oxygen
PAR
prochlorococcus_per_mL
synechococcus_per_mL
picoeukaryotes_per_mL
BD Biosciences Influx high speed cell sorter
theme
None, User defined
cast
date
day of month
depth
latitude
longitude
water temperature at measurement depth
salinity
dissolved Oxygen
PAR
prochlorococcus abundance
synechococcus abundance
pico_euks
featureType
BCO-DMO Standard Parameters
CTD - profiler
Flow Cytometer
instrument
BCO-DMO Standard Instruments
SKQ201703S
service
Deployment Activity
Honolulu, HI to Newport, OR
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.
Ocean Time-series Sites
https://osprey.bco-dmo.org/program/562656
Ocean Time-series Sites
Program description text taken from Chapter 1: Introduction from the Global Intercomparability in a Changing Ocean: An International Time-Series Methods Workshop report published following the workshop held November 28-30, 2012 at the Bermuda Institute of Ocean Sciences. The full report is available from the workshop Web site hosted by US OCB: http://www.whoi.edu/website/TS-workshop/home
Decades of research have demonstrated that the ocean varies across a range of time scales, with anthropogenic forcing contributing an added layer of complexity. In a growing effort to distinguish between natural and human-induced earth system variability, sustained ocean time-series measurements have taken on a renewed importance. Shipboard biogeochemical time-series represent one of the most valuable tools scientists have to characterize and quantify ocean carbon fluxes and biogeochemical processes and their links to changing climate (Karl, 2010; Chavez et al., 2011; Church et al., 2013). They provide the oceanographic community with the long, temporally resolved datasets needed to characterize ocean climate, biogeochemistry, and ecosystem change.
The temporal scale of shifts in marine ecosystem variations in response to climate change are on the order of several decades. The long-term, consistent and comprehensive monitoring programs conducted by time-series sites are essential to understand large-scale atmosphere-ocean interactions that occur on interannual to decadal time scales. Ocean time-series represent one of the most valuable tools scientists have to characterize and quantify ocean carbon fluxes and biogeochemical processes and their links to changing climate.
Launched in the late 1980s, the US JGOFS (Joint Global Ocean Flux Study; http://usjgofs.whoi.edu) research program initiated two time-series measurement programs at Hawaii and Bermuda (HOT and BATS, respectively) to measure key oceanographic measurements in oligotrophic waters. Begun in 1995 as part of the US JGOFS Synthesis and Modeling Project, the CARIACO Ocean Time-Series (formerly known as the CArbon Retention In A Colored Ocean) Program has studied the relationship between surface primary production, physical forcing variables like the wind, and the settling flux of particulate carbon in the Cariaco Basin.
The objective of these time-series effort is to provide well-sampled seasonal resolution of biogeochemical variability at a limited number of ocean observatories, provide support and background measurements for process-oriented research, as well as test and validate observations for biogeochemical models. Since their creation, the BATS, CARIACO and HOT time-series site data have been available for use by a large community of researchers.
Data from those three US funded, ship-based, time-series sites can be accessed at each site directly or by selecting the site name from the Projects section below.
Ocean Time-series
largerWorkCitation
program
Microbial ecology of coexisting ecotypes: Are all Prochlorococcus equal?
https://osprey.bco-dmo.org/project/632763
Microbial ecology of coexisting ecotypes: Are all Prochlorococcus equal?
<p><em>Description from the NSF award abstract:</em><br />
Prochlorococcus is a photosynthetic organism that is tremendously abundant in the ocean and influences biogeochemical cycles on global scales. This project aims to link Prochlorococcus community structure to primary productivity in situ. The twelve known Prochlorococcus ecotypes exhibit extensive diversity. It is thought that this diversity allows the Prochlorococcus "collective" to maintain numerical dominance across gradients in light, nutrients, and temperature that accompany changes in depth, season, and latitude. A large gap in our understanding lies in whether we should assess the ecosystem value of Prochlorococcus by its abundance or by its community structure or both. Ecosystem models assign all ecotypes the same role. However, genomic and physiological evidence from cultivated isolates and wild populations suggests tentatively that distinct genotypes may contribute differently to the ecosystem through variation in light and nutrient physiologies and interactions with other microorganisms. The consequences of these molecular-level differences to primary productivity in situ are unknown. This project tests whether absolute abundance, or community structure, determines the contributions of Prochlorococcus to biogeochemical dynamics by measuring the contributions of different ecotypes to primary productivity. The results of this project will inform ecosystem models towards better representation of how shifts in climate and Prochlorococcus diversity will affect global nutrient cycles, trophic cascades, and interactions with other bacteria, viruses, and grazers. The insights and approaches delineated by this work will be generally applicable to the ecology of abundant microbial populations in the open ocean such as pigmented and non-pigmented eukaryotes, heterotrophic bacteria, and other cyanobacterial lineages. A basic understanding of differences between coexisting ecotypes will provide inroads into understanding mechanisms of cooperation, competition, and collaboration among ecotypes in all microbial ecosystems. The investigators will build a teaching module to expose high school students to microbial oceanography, big data, and systems biology through virtual ocean exploration. The primary objective will be to impress upon students the importance of an "invisible forest" of microorganisms in the ocean. Students will examine the distribution patterns of abundant microbial groups in the context of oceanographic data from large publically available databases. High school teachers and student interns, a graduate student, the investigators, and an educational specialist will design, implement, and test the module for classrooms nationwide. This effort will follow a successful education model (Systems Education Experience - SEE) developed previously.</p>
<p>The investigators will address an overarching hypothesis that Prochlorococcus ecotypes vary in their contribution to the ecosystem as primary producers. More specifically, the investigators hypothesize that patterns of cell division and carbon fixation vary between coexisting ecotypes, and these differences are a function of genome content, gene expression, environmental conditions, and community composition. The technical approach will involve two field-based experiments will be applied to three different depths, at the oceanographic Station ALOHA, that differ in Prochlorococcus community composition. Experiment 1 will examine whether coexisting ecotypes vary in cell division, using 16S rRNA sequencing to quantify ecotype abundance in G1, S, and G2 cells. Experiment 2 will examine how carbon fixation varies between coexisting ecotypes using RNA-stable isotope probing and 16S rRNA sequencing of RNA enriched in 13C after incubation with 13C-bicarbonate. These experiments will be performed with Prochlorococcus communities under native in situ conditions and shifts in conditions to mimic light and temperature of other depths. In both experiments, the temporal gene expression of a selected set of carbon fixation and cell division genes will be examined to link gene expression patterns to primary productivity. All data will be related to the oceanographic environment including its physical, chemical, and biological features.</p>
ProEco
largerWorkCitation
project
eng; USA
biota
oceans
Honolulu, HI to Newport, OR
-147.0968
-139.241
25.98495
35.18034
2017-03-06
2017-03-27
North Pacific Ocean, Station ALOHA
0
BCO-DMO catalogue of parameters from Counts of picocyanobacteria from SMILE cruise (SKQ201703S) at the North Pacific Subtropical Front in March 2017
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/736711.rdf
Name: castNum
Units: unitless
Description: <p>Cast number</p>
http://lod.bco-dmo.org/id/dataset-parameter/736712.rdf
Name: date
Units: unitless
Description: <p>Year, month, and day of sampling (formatted as yyyy-mm-dd)</p>
http://lod.bco-dmo.org/id/dataset-parameter/736713.rdf
Name: day_of_March
Units: unitless
Description: <p>Day of the month</p>
http://lod.bco-dmo.org/id/dataset-parameter/736714.rdf
Name: depth
Units: meters
Description: <p>Sample depth</p>
http://lod.bco-dmo.org/id/dataset-parameter/736715.rdf
Name: latitude
Units: decimal degress
Description: <p>Latitude; positive values = North</p>
http://lod.bco-dmo.org/id/dataset-parameter/736716.rdf
Name: longitude
Units: decimal degress
Description: <p>Longitude; negative values = West</p>
http://lod.bco-dmo.org/id/dataset-parameter/736717.rdf
Name: temperature
Units: degrees Celsius
Description: <p>Temperature</p>
http://lod.bco-dmo.org/id/dataset-parameter/736718.rdf
Name: salinity
Units: psu
Description: <p>Salinity</p>
http://lod.bco-dmo.org/id/dataset-parameter/736719.rdf
Name: oxygen
Units: micromoles per kilogram (umol/kg)
Description: <p>Oxygen</p>
http://lod.bco-dmo.org/id/dataset-parameter/736720.rdf
Name: PAR
Units: unknown
Description: <p>PAR</p>
http://lod.bco-dmo.org/id/dataset-parameter/736721.rdf
Name: prochlorococcus_per_mL
Units: cells per milliliter
Description: <p>Prochlorococcus counts per mL</p>
http://lod.bco-dmo.org/id/dataset-parameter/736722.rdf
Name: synechococcus_per_mL
Units: cells per milliliter
Description: <p>Synechococcus counts per mL</p>
http://lod.bco-dmo.org/id/dataset-parameter/736723.rdf
Name: picoeukaryotes_per_mL
Units: cells per milliliter
Description: <p>Picoeukaryote counts per mL</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
43779
https://darchive.mblwhoilibrary.org/bitstream/1912/28214/1/dataset-736702_smile-counts__v1.tsv
download
https://doi.org/10.26008/1912/bco-dmo.736702.1
download
onLine
dataset
<p>Water was sampled from the CTD into 15mL sterile polypropylene tubes. 2mL samples were fixed with 0.125% glutaraldehyde then flash frozen in liquid nitrogen and stored until analysis.&nbsp;</p>
<p>Cell counts were determined by flow cytometry using a BD Biosciences Influx high speed cell sorter. A 488nm laser was used in addition to chlorophyll and phycoerythrin filters, forward scatter relative to 1um beads, and side scattered light.</p>
Specified by the Principal Investigator(s)
<p>The program BD Software was using to collect flow cytometry data and generate distinct files for analysis. The program Flow Jo (version 7.6.5) was used to process flow cytometry files.</p>
<p>BCO-DMO Processing:<br />
- modified parameter names to conform with BCO-DMO naming conventions;<br />
- created date field with month and year (original dataset only had column for day of march);<br />
- changed lon values from positive degrees west to negative degrees east.</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
PI Supplied Instrument Name: Instrument Name: CTD - profiler Instrument Short Name: Instrument Description: The Conductivity, Temperature, Depth (CTD) unit is an integrated instrument package designed to measure the conductivity, temperature, and pressure (depth) of the water column. The instrument is lowered via cable through the water column. It permits scientists to observe the physical properties in real-time via a conducting cable, which is typically connected to a CTD to a deck unit and computer on a ship. The CTD is often configured with additional optional sensors including fluorometers, transmissometers and/or radiometers. It is often combined with a Rosette of water sampling bottles (e.g. Niskin, GO-FLO) for collecting discrete water samples during the cast.
This term applies to profiling CTDs. For fixed CTDs, see https://www.bco-dmo.org/instrument/869934. Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/130/
BD Biosciences Influx high speed cell sorter
BD Biosciences Influx high speed cell sorter
PI Supplied Instrument Name: BD Biosciences Influx high speed cell sorter Instrument Name: Flow Cytometer Instrument Short Name:Flow Cytometer Instrument Description: Flow cytometers (FC or FCM) are automated instruments that quantitate properties of single cells, one cell at a time. They can measure cell size, cell granularity, the amounts of cell components such as total DNA, newly synthesized DNA, gene expression as the amount messenger RNA for a particular gene, amounts of specific surface receptors, amounts of intracellular proteins, or transient signalling events in living cells.
(from: http://www.bio.umass.edu/micro/immunology/facs542/facswhat.htm) Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/LAB37/
Cruise: SKQ201703S
SKQ201703S
R/V Sikuliaq
Community Standard Description
International Council for the Exploration of the Sea
R/V Sikuliaq
vessel
SKQ201703S
James Girton
University of Washington
R/V Sikuliaq
Community Standard Description
International Council for the Exploration of the Sea
R/V Sikuliaq
vessel