http://lod.bco-dmo.org/id/dataset/753624
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
2019-01-23
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Nutrient concentrations and microbial counts from Niskin bottle collections on R/V Atlantic Explorer A1620 in the Bermuda Atlantic Time-series Study site from Sept 2016
2019-01-23
publication
2019-01-23
revision
Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)
2019-09-30
publication
https://doi.org/10.1575/1912/bco-dmo.753624.1
Stephen Giovannoni
Oregon State University
principalInvestigator
Craig A. Carlson
University of California-Santa Barbara
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: Giovannoni, S., Carlson, C. (2019) Nutrient concentrations and microbial counts from Niskin bottle collections on R/V Atlantic Explorer A1620 in the Bermuda Atlantic Time-series Study site from Sept 2016. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2019-01-23 [if applicable, indicate subset used]. doi:10.1575/1912/bco-dmo.753624.1 [access date]
bottle data AE1620 Dataset Description: <p>Nutrient concentrations and microbial counts from Niskin bottle collections on R/V Atlantic Explorer A1620 in the Bermuda Atlantic Time-series Study site from Sept 2016.</p> Methods and Sampling: <p>See Supplemental Documents below.</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1436865 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1436865
completed
Stephen Giovannoni
Oregon State University
541-737-1835
OSU/Department of Microbiology Nash Hall Rm 248
Corvallis
OR
97331
United States
stephen.giovannoni@oregonstate.edu
pointOfContact
Craig A. Carlson
University of California-Santa Barbara
(805) 893-2541
University of California Department of Ecology, Evolution and Marine Biology
Santa Barbara
CA
93106-6150
USA
craig_carlson@ucsb.edu
pointOfContact
asNeeded
Dataset Version: 1
Unknown
sample_id
Cruise
Cast
Niskin
date
date_decyr
time_UTC
lat
lon
Depth
Temp
CTD_S
Pressure
Sigma_theta
Conductivity
Fluor
Par
O2
beam_trans_CStarTr0
NO3_NO2
NO3_NO2_QF
PO4
PO4_QF
POC_mg_L
POC_mmol_L
POC_QF
PON_mg_L
PON_mmol_L
PON_QF
DOC
DOC_QF
TDN
TDN_QF
Bact
Bact_QF
Bact_Prod
Bact_Prod_QF
Epifluorescence microscope
Shimadzu High Temperature Combustion system
theme
None, User defined
sample identification
Cruise identfier
cast
bottle
date
time of day
latitude
longitude
depth
water temperature at measurement depth
salinity
water pressure
sigma-t
conductivity
fluorescence
PAR
dissolved Oxygen
transmission
nitrate plus nitrite
quality flag
reactive phosphorus (PO4)
particulate organic Carbon (POC)
particulate organic nitrogen
dissolved organic Carbon
Total Dissolved Nitrogen
cell_concentration
leucine incorporation rate
featureType
BCO-DMO Standard Parameters
CTD - profiler
Fluorescence Microscope
Liquid Scintillation Counter
Niskin bottle
Shimadzu TOC-V Analyzer
instrument
BCO-DMO Standard Instruments
AE1620
service
Deployment Activity
Western Sargasso Sea, Bermuda Atlantic Time Series Site: Hydrostation S
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.
Dissolved Organic Carbon Cycling by SAR11 Marine Bacteria
https://osprey.bco-dmo.org/project/615543
Dissolved Organic Carbon Cycling by SAR11 Marine Bacteria
<p>SAR11 (Pelagibacterales) are the most abundant group of bacterioplankton in the oceans. Globally, they are estimated to oxidize to carbon dioxide (CO2) between 5 and 22% of all the organic carbon produced by photosynthesis each day. The activities of bacterioplankton such as SAR11 determine the residence times of different forms of organic carbon, and ultimately shape the composition of dissolved organic pools in the oceans, which rival atmospheric CO2 in mass. Accurate and detailed information about the oceanic carbon cycle is used in models that are valued for their potential to predict and understand future changes in ocean ecosystems. This grant supports analyses of genomic data that predict the carbon oxidation functions of SAR11 cells, and supports experiments with cells in culture, where high-resolution mass spectrometry technology is applied to discover new organic carbon oxidation biochemistry. To assess the importance of SAR11 carbon oxidation functions in ocean ecosystems, this project includes four short oceanographic cruises to the Bermuda Atlantic Time-series Study (BATS) site, in the western Sargasso Sea. On these cruises the concentrations and oxidation rates of organic compounds will be measured, and linked to variation in planktonic SAR11 populations. </p>
<p>
It is a paradox that SAR11 cells are the most abundant in the oceans, but also have among the smallest genomes known. The central goal of this proposal is to understand what types of dissolved organic matter (DOM) are oxidized to CO2 by SAR11. Implicit to this approach is the perspective that some abundant chemoheterotrophic bacterioplankton taxa, particularly those with small genomes, have evolved specialist strategies for oxidizing organic matter. Understanding these strategies can lead to a more detailed and accurate understanding of the biological processes that recycle biological production to CO2. Major project aims are: 1) investigate SAR11 genomes and assay cells in culture with high-resolution mass spectrometry approaches and isotopic labeling to identify the range of compounds these cells can oxidize to CO2; 2) at BATS, measure biological oxidation rates of DOM compounds used by SAR11; 3) link spatiotemporal SAR11 genome variation to patterns of DOM oxidation in the ocean surface layer (0-300 m). This projects includes four short cruises to BATS that target the four microbial plankton community types at this site: upper euphotic zone, deep chlorophyll maximum, spring bloom and upper mesopelagic. Products of this activity will include new information about variation in labile DOM oxidation across the surface layer, and specific links to genome features that will improve the accuracy of interpretation of global ocean metagenomic data.</p>
Bacterial DOC cycling
largerWorkCitation
project
eng; USA
oceans
Western Sargasso Sea, Bermuda Atlantic Time Series Site: Hydrostation S
-64.665
-64.496
32.164
32.172
2016-09-07
2016-09-09
Western Sargasso Sea, Bermuda Atlantic Time Series Site: Hydrostation S
0
BCO-DMO catalogue of parameters from Nutrient concentrations and microbial counts from Niskin bottle collections on R/V Atlantic Explorer A1620 in the Bermuda Atlantic Time-series Study site from Sept 2016
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/753642.rdf
Name: sample_id
Units: unitless
Description: <p>Unique Identified Code for each sample collected</p>
http://lod.bco-dmo.org/id/dataset-parameter/753643.rdf
Name: Cruise
Units: unitless
Description: <p>cruise name</p>
http://lod.bco-dmo.org/id/dataset-parameter/753644.rdf
Name: Cast
Units: unitless
Description: <p>cast number</p>
http://lod.bco-dmo.org/id/dataset-parameter/753645.rdf
Name: Niskin
Units: unitless
Description: <p>Niskin bottle number</p>
http://lod.bco-dmo.org/id/dataset-parameter/753646.rdf
Name: date
Units: unitless
Description: <p>Date (yyyymmdd)</p>
http://lod.bco-dmo.org/id/dataset-parameter/753647.rdf
Name: date_decyr
Units: unitless
Description: <p>Date (decimal year)</p>
http://lod.bco-dmo.org/id/dataset-parameter/753648.rdf
Name: time_UTC
Units: unitless
Description: <p>Timestamp (UTC) hh:mm</p>
http://lod.bco-dmo.org/id/dataset-parameter/753649.rdf
Name: lat
Units: decimal degrees
Description: <p>Latitude; north is positive</p>
http://lod.bco-dmo.org/id/dataset-parameter/753650.rdf
Name: lon
Units: decimal degrees
Description: <p>Longitude; east is positive</p>
http://lod.bco-dmo.org/id/dataset-parameter/753651.rdf
Name: Depth
Units: meters
Description: <p>Sampling depth in meters</p>
http://lod.bco-dmo.org/id/dataset-parameter/753652.rdf
Name: Temp
Units: degrees celsius
Description: <p>CTD temperature</p>
http://lod.bco-dmo.org/id/dataset-parameter/753653.rdf
Name: CTD_S
Units: pratical salinity units (PSU)
Description: <p>CTD salinity</p>
http://lod.bco-dmo.org/id/dataset-parameter/753654.rdf
Name: Pressure
Units: decibars
Description: <p>CTD Pressure</p>
http://lod.bco-dmo.org/id/dataset-parameter/753655.rdf
Name: Sigma_theta
Units: kilogram/meter^3
Description: <p>CTD sigma theta (potental density)</p>
http://lod.bco-dmo.org/id/dataset-parameter/753656.rdf
Name: Conductivity
Units: Siemens per meter
Description: <p>CTD Conductivity</p>
http://lod.bco-dmo.org/id/dataset-parameter/753657.rdf
Name: Fluor
Units: milligram per Liter
Description: <p>CTD Fluorescence</p>
http://lod.bco-dmo.org/id/dataset-parameter/753658.rdf
Name: Par
Units: micro-Einsteins/meter^2/second (uE/m^2/sec)
Description: <p>CTD photosynthetically available radiation</p>
http://lod.bco-dmo.org/id/dataset-parameter/753659.rdf
Name: O2
Units: millimole per kilogram
Description: <p>CTD Oxygen</p>
http://lod.bco-dmo.org/id/dataset-parameter/753660.rdf
Name: beam_trans_CStarTr0
Units: unitless
Description: <p>CTD beam transmission as percent</p>
http://lod.bco-dmo.org/id/dataset-parameter/753661.rdf
Name: NO3_NO2
Units: millimole per Liter
Description: <p>Nitrate+Nitrite concentration by flow injection autoanalyzer (Lachat QuikChem 8000)</p>
http://lod.bco-dmo.org/id/dataset-parameter/753662.rdf
Name: NO3_NO2_QF
Units: unitless
Description: <p>Quality Flags (QF): 0 good; 1 unknown; 4 questionable measurement; 8 bad measurement</p>
http://lod.bco-dmo.org/id/dataset-parameter/753663.rdf
Name: PO4
Units: millimole per Liter
Description: <p>ortho-Phosphate concentration by flow injection autoanalyzer (Lachat QuikChem 8000)</p>
http://lod.bco-dmo.org/id/dataset-parameter/753664.rdf
Name: PO4_QF
Units: unitless
Description: <p>Quality Flags (QF): 0 good; 1 unknown; 4 questionable measurement; 8 bad measurement</p>
http://lod.bco-dmo.org/id/dataset-parameter/753665.rdf
Name: POC_mg_L
Units: milligram per Liter
Description: <p>Particulate organic carbon measured by combustion analysis (CEC 440HA). Collected on Glass fiber filter type GF/F (Whatman)</p>
http://lod.bco-dmo.org/id/dataset-parameter/753666.rdf
Name: POC_mmol_L
Units: millimole per Liter
Description: <p>Particulate organic carbon</p>
http://lod.bco-dmo.org/id/dataset-parameter/753667.rdf
Name: POC_QF
Units: unitless
Description: <p>Quality Flags (QF): 0 good; 1 unknown; 4 questionable measurement; 8 bad measurement</p>
http://lod.bco-dmo.org/id/dataset-parameter/753668.rdf
Name: PON_mg_L
Units: milligram per Liter
Description: <p>Particulate organic nitrogen measured by combustion analysis (CEC 440HA). Collected on Glass fiber filter type GF/F (Whatman)</p>
http://lod.bco-dmo.org/id/dataset-parameter/753669.rdf
Name: PON_mmol_L
Units: millimole per Liter
Description: <p>Particulate organic nitrogen</p>
http://lod.bco-dmo.org/id/dataset-parameter/753670.rdf
Name: PON_QF
Units: unitless
Description: <p>Quality Flags (QF): 0 good; 1 unknown; 4 questionable measurement; 8 bad measurement</p>
http://lod.bco-dmo.org/id/dataset-parameter/753671.rdf
Name: DOC
Units: micromolar
Description: <p>Dissolved organic carbon concentration by HTCO. Glass fiber filtrate type GF/F (Whatman). Methodological reference is Carlson et al. 2010 DSRII</p>
http://lod.bco-dmo.org/id/dataset-parameter/753672.rdf
Name: DOC_QF
Units: unitless
Description: <p>Quality Flags (QF): 0 good; 1 unknown; 4 questionable measurement; 8 bad measurement</p>
http://lod.bco-dmo.org/id/dataset-parameter/753673.rdf
Name: TDN
Units: micromolar
Description: <p>Total dissolved nitrogen concentration by HTCO. Glass fiber filtrate type GF/F (Whatman).</p>
http://lod.bco-dmo.org/id/dataset-parameter/753674.rdf
Name: TDN_QF
Units: unitless
Description: <p>Quality Flags (QF): 0 good; 1 unknown; 4 questionable measurement; 8 bad measurement</p>
http://lod.bco-dmo.org/id/dataset-parameter/753675.rdf
Name: Bact
Units: cells per milliliter
Description: <p>Bacterioplankton abundance by microscopy. Methodological reference: K.G. Porter and Y.S. Feig (1980). The use of DAPI for identifying and counting aquatic microflora. Limnol. Oceanogr 25(5): 943-948.</p>
http://lod.bco-dmo.org/id/dataset-parameter/753676.rdf
Name: Bact_QF
Units: unitless
Description: <p>Quality Flags (QF): 0 good; 1 unknown; 4 questionable measurement; 8 bad measurement</p>
http://lod.bco-dmo.org/id/dataset-parameter/753677.rdf
Name: Bact_Prod
Units: picomoles per liter per hour
Description: <p>Heterotrophic bacterial production by 3H Leu uptake. Methodological reference: Smith DC & Azam F (1992) A simple economical method for measuring bacterial protein synthesis rates in seawater using 3H-leucine. Mar Microb Food Webs 6: 107_114.</p>
http://lod.bco-dmo.org/id/dataset-parameter/753678.rdf
Name: Bact_Prod_QF
Units: unitless
Description: <p>Quality Flags (QF): 0 good; 1 unknown; 4 questionable measurement; 8 bad measurement</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
67684
https://darchive.mblwhoilibrary.org/bitstream/1912/24631/1/dataset-753624_ae1620-bottles-biogeochemical-and-microbial-data__v1.tsv
download
https://doi.org/10.1575/1912/bco-dmo.753624.1
download
onLine
dataset
<p>See Supplemental Documents below.</p>
Specified by the Principal Investigator(s)
<p><strong>BCO-DMO Processing Notes:</strong><br />
- added conventional header with dataset name, PI name, version date<br />
- modified parameter names to conform with BCO-DMO naming conventions<br />
- replaced blank cells with ‘nd’ (no data)<br />
- changed sign of longitude (lon) so negative values represent west</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/
Epifluorescence microscope
Epifluorescence microscope
PI Supplied Instrument Name: Epifluorescence microscope PI Supplied Instrument Description:Used to enumerate bacterial abundance Instrument Name: Fluorescence Microscope Instrument Short Name: Instrument Description: Instruments that generate enlarged images of samples using the phenomena of fluorescence and phosphorescence instead of, or in addition to, reflection and absorption of visible light. Includes conventional and inverted instruments. Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/LAB06/
PI Supplied Instrument Name: PI Supplied Instrument Description:Used to count microbial cells 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 to 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/
PI Supplied Instrument Name: Instrument Name: Niskin bottle Instrument Short Name:Niskin bottle Instrument Description: A Niskin bottle (a next generation water sampler based on the Nansen bottle) is a cylindrical, non-metallic water collection device with stoppers at both ends. The bottles can be attached individually on a hydrowire or deployed in 12, 24, or 36 bottle Rosette systems mounted on a frame and combined with a CTD. Niskin bottles are used to collect discrete water samples for a range of measurements including pigments, nutrients, plankton, etc. Community Standard Description: http://vocab.nerc.ac.uk/collection/L22/current/TOOL0412/
Shimadzu High Temperature Combustion system
Shimadzu High Temperature Combustion system
PI Supplied Instrument Name: Shimadzu High Temperature Combustion system PI Supplied Instrument Description:Used to measure non-purgeable Organic Carbon (NPOC) and Total Dissolved Nitrogen (TDN) Instrument Name: Shimadzu TOC-V Analyzer Instrument Short Name:Shimadzu TOC-V Instrument Description: A Shimadzu TOC-V Analyzer measures DOC by high temperature combustion method. Community Standard Description: http://onto.nerc.ac.uk/CAST/124
Cruise: AE1620
AE1620
R/V Atlantic Explorer
Community Standard Description
International Council for the Exploration of the Sea
R/V Atlantic Explorer
vessel
AE1620
Stephen Giovannoni
Oregon State University
https://datadocs.bco-dmo.org/docs/Bacterial_DOC_cycling/data_docs/Cruise_Report_Giov_1620.pdf
Report describing AE1620
R/V Atlantic Explorer
Community Standard Description
International Council for the Exploration of the Sea
R/V Atlantic Explorer
vessel