http://lod.bco-dmo.org/id/dataset/726253
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
2018-02-05
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Bacteria, picoeukaryote, and Synecoccus cell counts, nutrients (POC, PON, POP) and chlorophyll from nitrate and vitamin-B enriched treatments, from up-welled coastal waters off Southern California, March 2015 (B-vitamin plankton succession project)
2018-02-02
publication
2018-02-02
revision
BCO-DMO Linked Data URI
2018-02-02
creation
http://lod.bco-dmo.org/id/dataset/726253
Sergio A. Sanudo-Wilhelmy
University of Southern California
principalInvestigator
Feixue Fu
University of Southern California
principalInvestigator
David A. Hutchins
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: Sanudo-Wilhelmy, S. A., Hutchins, D. A., Fu, F. (2018) Bacteria, picoeukaryote, and Synecoccus cell counts, nutrients (POC, PON, POP) and chlorophyll from nitrate and vitamin-B enriched treatments, from up-welled coastal waters off Southern California, March 2015 (B-vitamin plankton succession project). Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2018-02-02 [if applicable, indicate subset used]. http://lod.bco-dmo.org/id/dataset/726253 [access date]
Nutrients and picoplankton cell counts with nitrate and B vitamins from San Pedro Ocean Timeseries (SPOT), 2015 Dataset Description: <p>This dataset includes nutrients (POC, PON, POP) and chlorophyll&nbsp;concentrations, and cell counts for picoplankton (picoeukaryotes, Synechococcus, bacteria) collected in water samples&nbsp;from the San Pedro Ocean Time-series (SPOT), 2015. They were incubated with six treatments of nitrate and vitamin B.</p> Methods and Sampling: <p>Water samples were collected from 3 meters depth at the San Pedro Ocean Time-series (SPOT) station (33°33'N, 118°24'W) off the coast of Southern California in March 2015. Six treatments were used: control, nitrate, nitrate+B1, nitrate+B7, nitrate+B12, and nitrate+B1+B7+B12 with triplicate 10L incubations.&nbsp;Growth was tracked daily. Samples were collected initially, and at two points during the experiment: exponential growth and stationary phase. Exponential growth occurred at day 7 and stationary growth varied between treatment ranging from 10-12 days. The incubations were co-limited by nitrate and B12. Samples were flash frozen and stored at -80C until analysis. For further details on the methodology, see Suffridge et al (2017).</p>
<p>Cell counts were made with using flow cytometry. Samples for flow cytometry were collected, fixed with 2% formalin, and frozen at -80C. Analysis for the cellular abundance of heterotrophic bacteria, Synechococcus, and pircoeukaryotes was conducted using a BD Accuri C6 flow cytometer (Becton Dickerson and Company).</p>
<p>Elemental ratios were obtained by measuring particulate organic nutrients: carbon and nitrogen (POC and PON), and particulate organic phosphorus (POP). For particulate organic carbon and nitrogen (POC and PON), 100 ml was filtered onto pre-combusted POC and PON were analyzed on a Costech Elemental Analyzer using methionine and acetanilide as references to calibrate the system at the beginning of the measurements (Fu et al. 2007).</p>
<p>For particulate organic phosphorus (POP) samples, 40 mls were filtered onto precombusted (500°C, 2 h) GF/F filters and rinsed twice with 2 ml 0.17 mol L-1 Na2SO4 solution. The filters were placed in 20 ml borosilicate scintillation vials (pre-combusted at 500°C, overnight) to which was added 2ml 0.017 mol L-1 MgSO4 solution. The vials were then covered with aluminum foil and dried at 95 °C, followed by combustion at 450-500 °C for 2 h. After cooling to room temperature, 5 ml of 0.2 mol L-1 HCl solution was added to each vial, which were then tightly capped and heated at 80°C for thirty minutes to digest POP into inorganic phosphate. The standard molybdate colorimetric method was used to analyze the samples (Solorzano and Sharp 1980). Three GF/F filters were treated in the same way as the samples for blank determinations. POP quantification was done using a Shimadzu UV-1800 UV/Visible Scanning Spectrophotometer.</p>
<p>Chl-a concentrations were measured using the protocol described by Welschmeyer (1994). 40 ml of water samples from each replicate were filtered through GF/F glass fiber filters, 3.0-μm and 8.0-μm polycarbonate membrane for size fractionated Chl-a analyses. After adding 6 ml of 90% acetone, Chl-a was extracted in the freezer at -20°C and measured using the non-acidification method with a Turner Designs 10-AUTM fluorometer after 24 hours.</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1435666 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1435666
completed
Sergio A. Sanudo-Wilhelmy
University of Southern California
213-821-1302
3616 Trousdale Pkwy Dept. of Biological Sciences, AHF 206, Mail Code: 0371
Los Angeles
CA
90089
USA
sanudo@usc.edu
pointOfContact
Feixue Fu
University of Southern California
2137403188
Department of Biology, MC 0371, University of Southern California 3616 Trousdale Pkwy
Los Angeles
CA
90089
USA
ffu@usc.edu
pointOfContact
David A. Hutchins
University of Southern California
213-740-5616
Department of Biological Sciences 3616 Trousdale Parkway, AHF 20
Los Angeles
CA
90089
USA
dahutch@usc.edu
pointOfContact
asNeeded
Dataset Version: 1
Unknown
sampleid
treatment
timepoint
date
sizefrac
biorep
POC
PON
POP
chla_gff
Chla_3um
Chla_7_3um
picoeukaryotes
Synechococcus
bacteria
BD Accuri C6 flow cytometer (Becton Dickerson and Company)
Costech Elemental Analyzer
Shimadzu UV-1800 UV/Visible Scanning Spectrophotometer
theme
None, User defined
sample identification
treatment
time_point
date
filter_size
replicate
particulate organic Carbon (POC)
particulate organic nitrogen
particulate organic phosphorus
chlorophyll a
cell_concentration
featureType
BCO-DMO Standard Parameters
CTD - profiler
Flow Cytometer
Niskin bottle
Nutrient Autoanalyzer
Spectrophotometer
instrument
BCO-DMO Standard Instruments
lab_Sanudo_2015
service
Deployment Activity
near Los Angeles, California
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.
Can the availability of B-vitamins control phyto-and-bacterioplankton successions in a coastal upwelling region?
https://osprey.bco-dmo.org/project/516960
Can the availability of B-vitamins control phyto-and-bacterioplankton successions in a coastal upwelling region?
<p><em>Description from NSF award abstract:</em><br />
B-vitamins (thiamin (B1), biotin (B7), and cobalamin (B12)) are organic molecules used by all organisms for many biochemical reactions ranging from DNA and amino acid synthesis to carbon dioxide assimilation. Despite their metabolic importance, many marine organisms cannot make them and need to obtain them from the environment. Because the requirement for a specific vitamin is different for different organisms, changes in the species composition of algae could be explained by their different B-vitamin requirements. For example, changes in the biological properties of waters during an algal bloom (removal of needed vitamins and release of other vitamins) may favor algae that require the vitamin released by the previous bloom (setting up a floral succession). This selective preconditioning of the waters may be one factor in the seasonal succession of algal species. However, evaluating the role of vitamins in marine ecology has been difficult. No study to date has been comprehensive enough to estimate the importance of vitamins in primary productivity and species succession. This is especially true in coastal upwelling regions that although relatively small in area, are orders of magnitude more productive than their open-ocean counterparts. In fact, those regions contribute a significant portion of the world fisheries. Therefore, in order to try to predict future changes in the world ocean due to human activity, the variables that influence or control the algal communities that dominate the very productive food chains of upwelling regions need to be identified.</p>
<p>This study will investigate how the availability of B-vitamins affects the dynamics of algal- and bacterioplankton population growth in coastal waters of an upwelling region off Southern California. This comprehensive field investigation will determine in situ temporal concentrations of several dissolved and particulate B-vitamins, inorganic micro- and macronutrients, concurrently with seasonal changes in phytoplankton and bacterial abundances and species composition at a long-term time series station within the San Pedro Basin near Los Angeles. Those measurements will be complemented with field incubation experiments with natural plankton assemblages to study the effect of organic and inorganic nutrient amendments on phytoplankton and bacterial community structure. This study will establish for the first time that the availability of ambient B-vitamins influence algal and bacterial species succession in a highly productive coastal upwelling region and that multiple and differing B-vitamin requirements limit growth of some phytoplankton species in those areas. Furthermore, this study will try to show that coastal upwelling transports some B-vitamins to the phytoplankton community in the photic zone from bacterially-influenced source waters within the upper mesopelagic zone.</p>
B-vitamin plankton succession
largerWorkCitation
project
eng; USA
biota
oceans
near Los Angeles, California
-118.3983
-118.3983
33.5478
33.5478
2015-03-11
2015-03-23
Southern California Bight
0
BCO-DMO catalogue of parameters from Bacteria, picoeukaryote, and Synecoccus cell counts, nutrients (POC, PON, POP) and chlorophyll from nitrate and vitamin-B enriched treatments, from up-welled coastal waters off Southern California, March 2015 (B-vitamin plankton succession 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
http://lod.bco-dmo.org/id/dataset-parameter/726267.rdf
Name: sampleid
Units: unitless
Description: <p>sample identifier</p>
http://lod.bco-dmo.org/id/dataset-parameter/726268.rdf
Name: treatment
Units: unitless
Description: <p>treatments: control; nitrate (N); nitrate+B1 (N+B1); nitrate+B7 (N+B7); nitrate+B12 (N+B12); and nitrate+B1+B7+B12 (All)</p>
http://lod.bco-dmo.org/id/dataset-parameter/726269.rdf
Name: timepoint
Units: unitless
Description: <p>code for sampling period during one of three growth phases of the population: 0=initial sampling; 1=exponential phase; 2=stationary phase. Dates: 2015-03-12 (time 0); 2015-03-20 (time 1); 2015-03-25 (time 2)</p>
http://lod.bco-dmo.org/id/dataset-parameter/726270.rdf
Name: date
Units: unitless
Description: <p>date of experiment formatted as yyyy-mm-dd</p>
http://lod.bco-dmo.org/id/dataset-parameter/726271.rdf
Name: sizefrac
Units: microns
Description: <p>size fraction of filtered sample; either 0.2 microns (picoplankton) or 3 microns (nanoplankton and microplankton)</p>
http://lod.bco-dmo.org/id/dataset-parameter/726272.rdf
Name: biorep
Units: unitless
Description: <p>sample replicate identifier</p>
http://lod.bco-dmo.org/id/dataset-parameter/726273.rdf
Name: POC
Units: micromoles/Liter
Description: <p>Particulate Organic Carbon concentration</p>
http://lod.bco-dmo.org/id/dataset-parameter/726274.rdf
Name: PON
Units: micrograms/L
Description: <p>Particulate Organic Nitrogen concentration</p>
http://lod.bco-dmo.org/id/dataset-parameter/726275.rdf
Name: POP
Units: micrograms/L
Description: <p>Particulate Organic Phosphorous concentration</p>
http://lod.bco-dmo.org/id/dataset-parameter/726276.rdf
Name: chla_gff
Units: unitless
Description: <p>Chlorophyll-a Rf as collected with GFF filter</p>
http://lod.bco-dmo.org/id/dataset-parameter/726277.rdf
Name: Chla_3um
Units: unitless
Description: <p>Chlorophyll-a Rf as collected with a 3 micron filter</p>
http://lod.bco-dmo.org/id/dataset-parameter/726278.rdf
Name: Chla_7_3um
Units: unitless
Description: <p>Chlorophyll-a Rf of fraction between 0.7 and 3 microns</p>
http://lod.bco-dmo.org/id/dataset-parameter/726279.rdf
Name: picoeukaryotes
Units: cells/milliliter
Description: <p>cell count of picoeukaryotes</p>
http://lod.bco-dmo.org/id/dataset-parameter/726280.rdf
Name: Synechococcus
Units: cells/milliliter
Description: <p>cell count of Synechococcus</p>
http://lod.bco-dmo.org/id/dataset-parameter/726281.rdf
Name: bacteria
Units: cells/milliliter
Description: <p>cell count of bacteria</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
4465
https://datadocs.bco-dmo.org/file/p99npZDT95n6AB/Vitacopss_biomass.csv
Vitacopss_biomass.csv
Primary data file for dataset ID 726253
download
https://osprey.bco-dmo.org/dataset/726253/data/download
download
onLine
dataset
<p>Water samples were collected from 3 meters depth at the San Pedro Ocean Time-series (SPOT) station (33°33'N, 118°24'W) off the coast of Southern California in March 2015. Six treatments were used: control, nitrate, nitrate+B1, nitrate+B7, nitrate+B12, and nitrate+B1+B7+B12 with triplicate 10L incubations.&nbsp;Growth was tracked daily. Samples were collected initially, and at two points during the experiment: exponential growth and stationary phase. Exponential growth occurred at day 7 and stationary growth varied between treatment ranging from 10-12 days. The incubations were co-limited by nitrate and B12. Samples were flash frozen and stored at -80C until analysis. For further details on the methodology, see Suffridge et al (2017).</p>
<p>Cell counts were made with using flow cytometry. Samples for flow cytometry were collected, fixed with 2% formalin, and frozen at -80C. Analysis for the cellular abundance of heterotrophic bacteria, Synechococcus, and pircoeukaryotes was conducted using a BD Accuri C6 flow cytometer (Becton Dickerson and Company).</p>
<p>Elemental ratios were obtained by measuring particulate organic nutrients: carbon and nitrogen (POC and PON), and particulate organic phosphorus (POP). For particulate organic carbon and nitrogen (POC and PON), 100 ml was filtered onto pre-combusted POC and PON were analyzed on a Costech Elemental Analyzer using methionine and acetanilide as references to calibrate the system at the beginning of the measurements (Fu et al. 2007).</p>
<p>For particulate organic phosphorus (POP) samples, 40 mls were filtered onto precombusted (500°C, 2 h) GF/F filters and rinsed twice with 2 ml 0.17 mol L-1 Na2SO4 solution. The filters were placed in 20 ml borosilicate scintillation vials (pre-combusted at 500°C, overnight) to which was added 2ml 0.017 mol L-1 MgSO4 solution. The vials were then covered with aluminum foil and dried at 95 °C, followed by combustion at 450-500 °C for 2 h. After cooling to room temperature, 5 ml of 0.2 mol L-1 HCl solution was added to each vial, which were then tightly capped and heated at 80°C for thirty minutes to digest POP into inorganic phosphate. The standard molybdate colorimetric method was used to analyze the samples (Solorzano and Sharp 1980). Three GF/F filters were treated in the same way as the samples for blank determinations. POP quantification was done using a Shimadzu UV-1800 UV/Visible Scanning Spectrophotometer.</p>
<p>Chl-a concentrations were measured using the protocol described by Welschmeyer (1994). 40 ml of water samples from each replicate were filtered through GF/F glass fiber filters, 3.0-μm and 8.0-μm polycarbonate membrane for size fractionated Chl-a analyses. After adding 6 ml of 90% acetone, Chl-a was extracted in the freezer at -20°C and measured using the non-acidification method with a Turner Designs 10-AUTM fluorometer after 24 hours.</p>
Specified by the Principal Investigator(s)
<p><strong>BCO-DMO Processing:</strong></p>
<p>- added conventional header with dataset name, PI name, version date<br />
- renamed parameters to BCO-DMO standard<br />
- reformatted columns by replacing 'analyte' and 'organism' columns with&nbsp;new columns POC, PON, POP, chla_gff, chla_3um, chla_7_3um, picoeukaryotes, Synechococcus, and bacteria -replacing type, units, and value in order to keep one type of data in each column.<br />
-&nbsp;changed 'syn' to 'Synechococcus', 'PEUK' to 'picoeukaryotes', 'bac' to 'bacteria', CHlA and CHLA to Chla<br />
- changed B1, B7, B12 to N+B1, N+B7, N+B12<br />
- reduced decimal precision<br />
- changed dates from 2011 to 2015</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 Accuri C6 flow cytometer (Becton Dickerson and Company)
BD Accuri C6 flow cytometer (Becton Dickerson and Company)
PI Supplied Instrument Name: BD Accuri C6 flow cytometer (Becton Dickerson and Company) PI Supplied Instrument Description:Used for cell counts. Samples for flow cytometry were collected, fixed with 2% formalin, and frozen at -80C. Analysis for the cellular abundance of heterotrophic bacteria, Synechococcus, and pircoeukaryotes was conducted using a BD Accuri C6 flow cytometer (Becton Dickerson and Company). 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/
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/
Costech Elemental Analyzer
Costech Elemental Analyzer
PI Supplied Instrument Name: Costech Elemental Analyzer PI Supplied Instrument Description:Used to measure particulate organic nutrients: carbon and nitrogen (POC and PON). 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/
Shimadzu UV-1800 UV/Visible Scanning Spectrophotometer
Shimadzu UV-1800 UV/Visible Scanning Spectrophotometer
PI Supplied Instrument Name: Shimadzu UV-1800 UV/Visible Scanning Spectrophotometer PI Supplied Instrument Description:Used to measure particulate organic phosphorus (POP). Instrument Name: Spectrophotometer Instrument Short Name:Spectrophotometer Instrument Description: An instrument used to measure the relative absorption of electromagnetic radiation of different wavelengths in the near infra-red, visible and ultraviolet wavebands by samples. Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/LAB20/
Cruise: lab_Sanudo_2015
lab_Sanudo_2015
R/V Yellowfin
R/V Yellowfin
vessel
lab_Sanudo_2015
Sergio A. Sanudo-Wilhelmy
University of Southern California
R/V Yellowfin
R/V Yellowfin
vessel