http://lod.bco-dmo.org/id/dataset/663689
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
2016-11-01
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Q incubation data from the R/V Melville (MV1405) cruise along the California coast during July 2014
2016-10-28
publication
2016-10-28
revision
BCO-DMO Linked Data URI
2016-10-28
creation
http://lod.bco-dmo.org/id/dataset/663689
Adrian Marchetti
University of North Carolina at Chapel Hill
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: Marchetti, A. (2016) Q incubation data from the R/V Melville (MV1405) cruise along the California coast during July 2014. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2016-10-28 [if applicable, indicate subset used]. http://lod.bco-dmo.org/id/dataset/663689 [access date]
Q incubation data from MV1405 Dataset Description: <p>Water was collected from 4 different locations and incubation experiments were performed, with 22 incubations total per site. The data&nbsp;details physiological parameters associated with each incubation sample (Q ID).</p> Methods and Sampling: <p><strong>Methodology from the IRNBRU cruise report</strong></p>
<p>During the IRNBRU (MV1405) cruise, multiple incubation experiments were performed at different locations in relation to varying iron environments, including regions of high iron, upwelled waters as well as relatively low iron waters. Incubated phytoplankton community response was assessed using physiological and molecular methods in order to examine the effects of varying biogeochemical environments on metabolism and gene expression. Each experiment contained several treatments and time points consisting of the following: a 5 nmol L-1&nbsp;FeCl3&nbsp;addition, a 200 nmol L-1&nbsp;desferroxamine&nbsp;B (DFB) addition, an initial 5 nmol L-1&nbsp;FeCl3&nbsp;addition followed by a 200 nmol L-1&nbsp;DFB addition during the midpoint of the experiment, and an unamended control.&nbsp; For three of the experiments (sites 1, 2, and 4), seawater was collected from the near surface (2-5m) using a&nbsp;trace-metal&nbsp;clean sampling system which consisted of a towed GeoFish sampler attached to KevlarTM&nbsp;line, PFA Teflon tubing and a Teflon dual-diaphragm pump that pumped seawater directly into a positive pressure trace-metal clean bubble constructed in the main laboratory of the ship. The seawater was placed into a large 55 gallon acid-cleaned HDPE drum for homogenization before being distributed into10L flexible acid-cleaned polyethylene&nbsp;cubitainers&nbsp;and placed in on-deck plexiglass incubators with flow-through seawater to maintain near-ambient surface temperatures. For the experiment at site 3, seawater was obtained from the depth corresponding to the 10 deg C isotherm (91 m) in order to simulate an upwelling event. Cleaning protocols for all&nbsp;cubitainers&nbsp;included soaking the inside walls in 1.2 mol L-1&nbsp;hydrochloric acid (reagent grade) for 3 d followed by three rinses with Milli-Q H20, soaking in 1.2 mol L-1&nbsp;hydrochloric acid (trace metal grade) for 1 week followed by three rinses with Milli-Q H20, and soaking in 0.1 mol L-1&nbsp;acetic acid (trace-metal&nbsp;grade). Prior to filling the&nbsp;cubitainers&nbsp;with seawater, the dilute acetic acid was removed and the&nbsp;cubitainers&nbsp;were rinsed thoroughly three times with ambient, low-iron seawater. Incubators were covered with neutral density screening to reduce irradiance to&nbsp;ca. 30% of the incident. For sample collection from initial conditions, triplicate&nbsp;cubitainers&nbsp;were immediately filtered. All incubations were initiated and terminated just prior to dawn. Following 96 hours of incubation, the seawater was removed from the incubators and stored in a dark, cool room until filtration. Subsamples for dissolved nutrients, size-fractionated chlorophyll&nbsp;a&nbsp;,Fv/Fm, particulate nutrients, nutrient uptake, biogenic silica, domoic acid, dissolved iron, and RNA were collected from each&nbsp;cubitainer. Methods performed on the ship for each measurement are briefly explained below.</p>
<p>Dissolved nitrate + nitrite (NO3-&nbsp;+ NO2-), phosphate (PO43-), and silicic acid (H4SiO4) concentrations were measured shipboard using a Lachat Quick Chem 8000 Flow Injection Analysis system. Particles were removed by filtering the sample through a GF/F filter using a syringe prior to analysis. Reference materials for nutrients in seawater (Lots BY and CA, KANSO Technos, Osaka, Japan) were run alongside samples for quality control.</p>
<p>For biomass determination, 400 mL of seawater was&nbsp;gravity-filtered&nbsp;through a 5 um polycarbonate filter (47 mm) followed by a GF/F filter (25 mm) under gentle vacuum pressure (&lt;100 mm Hg)&nbsp; using a series filter cascade for size fractionation. Filters were rinsed with 0.45 um filtered seawater and immediately frozen at -80 deg C until analysis. Chlorophyll&nbsp;a&nbsp;extraction&nbsp;was performed on the ship using 90% acetone at -20 deg C for 24 hours and measured via&nbsp;in vitro&nbsp;fluorometry using a Turner Designs 10-AU fluorometer.</p>
<p>In order to assess changes in photophysiology among treatments, the maximum photochemical yield of Photosystem II (Fv:Fm) was measured shipboard using a Satlantic FIRe. Before each measurement, a subsample (5 mL) of each culture was placed in the dark for 20 minutes. The resulting Fv:Fm&nbsp;was derived from the induction profile using a saturating pulse (20,000&nbsp;umol&nbsp;photons m2&nbsp;s-1) for a duration of 100-200 us.</p>
<p>Particulate nitrate (PN), carbon (PC) and nitrate (NO3-) uptake was obtained by spiking 500 mL of seawater with&nbsp;15N-NH4Cl at no more than 10% of ambient nitrate concentration and incubated for 8 hours in the flow-through plexiglass incubator. Following incubation, seawater filtration commenced immediately and was performed by gravity through a 5 um polycarbonate filter (47 mm), and with an in-line vacuum (&lt;100 mm Hg) onto a precombusted (450 deg C for 5 hours) GF/F filter (25 mm). Cells on the 5 um polycarbonate filter were then rinsed onto an additional precombusted GF/F filter (25 mm) using an artificial saline solution. Filters were then stored at -20 deg C. In the laboratory, filters were heated at 50 deg C for 24 hours, wrapped in tin capsules, and pelletized in preparation for analysis of the atom %&nbsp;15N, PN, and PC using an elemental analyzer paired with an isotope ratio mass spectrometer (EA-IRMS).</p>
<p>For inorganic carbon uptake, or measurements of primary productivity, 60mL samples from each&nbsp;cubitainer&nbsp;were distributed into a light and dark bottles cleaned with 10% HCl. For each bottle, 1.2 uCi of NaH14CO3&nbsp;was added. A 1 mL subsample was taken and added to vials containing NaOH. The light and dark bottles were incubated on-deck for 6.5-8 hours and stacked polycarbonate filters (5 um and 1 um) with a mesh spacer between them. The blanks were filtered onto a GF/F filter after 5 minutes. Filters were vacuumed dried, placed in scintillation vials with 0.5 mL of 6M HCl, permitted to degas for 24h, and counted using a Beckman Coulter LS 6500 scintillation counter.</p>
<p>Biogenic silica was determined shipboard via filtration of 335 mL onto 1.2 um polycarbonate filters (45 mm). Concentrations were measuring using a NaOH digestion in&nbsp;teflon&nbsp;tubes3&nbsp;and a colorimetric ammonium molybdate method.</p>
<p>Samples for iron (Fe) analysis were acidified at sea with the equivalent of 4 mL 6N quartz-distilled HCl per liter of seawater (to pH 1.7-1.8) and stored in LDPE bottles that had been cleaned as per the&nbsp;<a href="http://www.geotraces.org/images/stories/documents/intercalibration/Cookbook.pdf" target="_blank">GEOTRACES cookbook</a>&nbsp;(<a href="http://www.geotraces.org/science/">http://www.geotraces.org/science/</a>intercalibration/222-sampling-and-sample-handling-protocols-for-geotraces-cruises). Samples were analyzed by preconcentrating the Fe on 2 cm columns of&nbsp;Nobias&nbsp;chelate PA1&nbsp;resin,&nbsp;and analyzing the eluent on the Thermo-Element&nbsp;high-resolution&nbsp;XR ICP-MS&nbsp;at UC Santa Cruz. The resin columns are&nbsp;rinsed and conditioned with 0.05 M NH4Ac buffer at pH 6.0, and the samples are buffered to pH 6.0 with NH4Ac immediately before loading. The samples are eluted from the columns with ~1 mL of 1N quartz distilled HNO3. One to three days before preconcentration, samples were irradiated with UV light for 2 hours to ensure full recovery of other metals of interest.</p>
<p>Seawater for RNA analysis was filtered directly onto 0.8 um Pall Supor filters (142 mm) using a peristaltic pump. Filters were placed in&nbsp;cyrovials&nbsp;and immediately flash frozen in liquid nitrogen. Samples were later transferred to storage in -80 deg C freezers until RNA extractions were performed. Filters were briefly thawed on ice before being extracted individually using the ToTALLY RNA Total RNA Isolation Kit (Ambion). RNA-Seq library prep was conducted with the Illumina TruSeq Stranded mRNA Library Preparation Kit and HiSeq v4 reagents. Bioinformatic pipeline consisted of the following: trimming of reads for quality and removal of adapters, contig assemblies, read mapping for quantitative analysis, taxonomic and functional assignment, and differential gene expression determination.</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1334935 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1334935
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1334632 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1334632
completed
Adrian Marchetti
University of North Carolina at Chapel Hill
919-843-3473
123 South Rd.
Chapel Hill
NC
27514
USA
amarchet@email.unc.edu
pointOfContact
asNeeded
Dataset Version: 1
Unknown
site
lat
lon
Q_ID
timepoint
treatment
replicate
NO3
PO4
SiO4
Chl_greaterThan5um
Chl_GFF
FvFm
relative_sigma
biogenic_silica
bSi_new
rho
Vb
primaryProductivity_02um
primaryProductivity_1um
primaryProductivity_5um
LDPE bottles
Lachat Quick Chem 8000 Flow Injection Analysis system
Turner Designs 10-AU fluorometer
GeoFish Sampler
EA-IRMS
Beckman Coulter LS 6500 scintillation counter
Teflon dual-diaphragm pump
Flow-through plexiglass incubator
theme
None, User defined
site
latitude
longitude
sample identification
sample time
treatment
replicate
Nitrate
reactive phosphorus (PO4)
Silicate (reactive silica)
chloride
Fv to Fm ratio
sigma-t
Silicon
primary production
featureType
BCO-DMO Standard Parameters
Bottle
Flow Injection Analyzer
Fluorometer
GeoFish Towed near-Surface Sampler
Isotope-ratio Mass Spectrometer
Liquid Scintillation Counter
Pump
Shipboard Incubator
instrument
BCO-DMO Standard Instruments
MV1405
service
Deployment Activity
California Coastline
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.
Collaborative Research: Investigating the Ecological Importance of Iron Storage in Diatoms
https://osprey.bco-dmo.org/project/527114
Collaborative Research: Investigating the Ecological Importance of Iron Storage in Diatoms
<p><em>NSF Award Abstract:</em><br />
Diatoms are responsible for a significant fraction of primary production in the ocean. They are associated with enhanced carbon export and usually dominate the response of phytoplankton to additions of the micronutrient iron in high-nutrient, low-chlorophyll (HNLC) regions. Diatoms, particularly those isolated from the open ocean, appear to have a significant capacity to store iron for later use, and in some groups of diatoms this ability is enabled by the iron storage protein ferritin. Such luxury uptake of iron has long been observed in laboratory cultures and hypothesized to provide diatoms with an ecological benefit in the low-iron waters that cover 40% of the global ocean. However iron storage has been difficult to observe in natural systems due to the methodological challenges of working with mixed plankton assemblages, and a physiological understanding of the impacts of iron on ocean diatoms is lacking. This project combines state-of-the-art high-throughput transcriptomic sequencing and single-cell element analysis with novel laboratory and field incubation experiments to quantify iron storage abilities of cultured and natural diatoms that either contain or lack ferritin and determine the ecological impacts of this process. The overall objective of this project is to examine the ecological importance of iron storage as a selective mechanism controlling the distributions of diatoms along iron gradients in marine ecosystems. The proposed research includes three specific objectives:</p>
<p>A. Determine if there is a consistent physiological difference in the ability of pennate versus centric diatoms to store iron.</p>
<p>B. Examine whether iron storage capacities across diverse diatom taxa consistently provide a mechanistic explanation for continued growth in the absence of iron.</p>
<p>C. Determine whether enhanced iron storage provides diatoms with a competitive within natural phytoplankton assemblages in both coastal and oceanic regions.</p>
<p>Transcriptomic sequencing on a variety of ecologically important pennate and centric diatoms will be used to survey for the presence of ferritin-like genes in order to establish biogeographical and/or phylogenetic patterns of occurrence of diatom ferritin. Laboratory culture experiments will be used to quantify the iron storage abilities of these diatoms, as well as the number of cell divisions that can be supported by the stored iron, providing valuable physiological data to inform the understanding of plankton ecology in iron-limited coastal and HNLC systems. The laboratory experiments will be complemented by measurements of ferritin expression and iron storage in coastal and ocean diatoms sampled across gradients of iron availability on two cruises-of-opportunity to the northeast Pacific Ocean.</p>
<p>The NCBI bioproject page can be found <a href="https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJNA320398" target="_blank">here</a>.</p>
Diatom Iron Storage
largerWorkCitation
project
eng; USA
oceans
California Coastline
-125
-121.44
35.56
42.4
2014-01-01
2014-12-31
North Pacific, California coast and subarctic gyre
0
BCO-DMO catalogue of parameters from Q incubation data from the R/V Melville (MV1405) cruise along the California coast during July 2014
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/663743.rdf
Name: site
Units: unitless
Description: <p>Numbered experiment site ID</p>
http://lod.bco-dmo.org/id/dataset-parameter/663744.rdf
Name: lat
Units: decimal degrees
Description: <p>Latitude; N is positive</p>
http://lod.bco-dmo.org/id/dataset-parameter/663745.rdf
Name: lon
Units: decimal degrees
Description: <p>Longitude; E is positive</p>
http://lod.bco-dmo.org/id/dataset-parameter/663746.rdf
Name: Q_ID
Units: unitless
Description: <p>Incubation sample ID</p>
http://lod.bco-dmo.org/id/dataset-parameter/663747.rdf
Name: timepoint
Units: hours
Description: <p>Sampling timepoint in hours</p>
http://lod.bco-dmo.org/id/dataset-parameter/663748.rdf
Name: treatment
Units: unitless
Description: <p>Incubation treatment; C Fe DFB or FeDFB</p>
http://lod.bco-dmo.org/id/dataset-parameter/663749.rdf
Name: replicate
Units: unitless
Description: <p>Replicate code; A B or C</p>
http://lod.bco-dmo.org/id/dataset-parameter/663750.rdf
Name: NO3
Units: uM
Description: <p>Nitrate concentration</p>
http://lod.bco-dmo.org/id/dataset-parameter/663751.rdf
Name: PO4
Units: uM
Description: <p>Phosphate concentration</p>
http://lod.bco-dmo.org/id/dataset-parameter/663752.rdf
Name: SiO4
Units: uM
Description: <p>Silicate concentration</p>
http://lod.bco-dmo.org/id/dataset-parameter/663753.rdf
Name: Chl_greaterThan5um
Units: micrograms per liter (ug/L)
Description: <p>Concentration of chloride over 5 um</p>
http://lod.bco-dmo.org/id/dataset-parameter/663754.rdf
Name: Chl_GFF
Units: micrograms per liter (ug/L)
Description: <p>Concentration of chloride over 0.7 um</p>
http://lod.bco-dmo.org/id/dataset-parameter/663755.rdf
Name: FvFm
Units: dimensionless
Description: <p>Maximum quantum yield</p>
http://lod.bco-dmo.org/id/dataset-parameter/663756.rdf
Name: relative_sigma
Units: (kilograms/meters cubed) - 1000
Description: <p>Sigma t density</p>
http://lod.bco-dmo.org/id/dataset-parameter/663757.rdf
Name: biogenic_silica
Units: uM
Description: <p>Concentration of biogenic silica</p>
http://lod.bco-dmo.org/id/dataset-parameter/663758.rdf
Name: bSi_new
Units: micromoles of silica per liter (umol Si/L)
Description: <p>32Si silica production rate; bSi new</p>
http://lod.bco-dmo.org/id/dataset-parameter/663759.rdf
Name: rho
Units: micromoles of silica per liter (umol Si/L)
Description: <p>32Si silica production rate; rho</p>
http://lod.bco-dmo.org/id/dataset-parameter/663760.rdf
Name: Vb
Units: d -1
Description: <p>32Si silica production rate; Vb</p>
http://lod.bco-dmo.org/id/dataset-parameter/663761.rdf
Name: primaryProductivity_02um
Units: moles of carbon per liter per hour (mol C/L/h)
Description: <p>Primary productivity greater than 0.2 um</p>
http://lod.bco-dmo.org/id/dataset-parameter/663762.rdf
Name: primaryProductivity_1um
Units: moles of carbon per liter per hour (mol C/L/h)
Description: <p>Primary productivity greater than 1 um</p>
http://lod.bco-dmo.org/id/dataset-parameter/663763.rdf
Name: primaryProductivity_5um
Units: moles of carbon per liter per hour (mol C/L/h)
Description: <p>Primary productivity greater than 5 um</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
9726
https://datadocs.bco-dmo.org/file/A88rzqyHZ7BzNy/Q_incubations.csv
Q_incubations.csv
Primary data file for dataset ID 663689
download
https://osprey.bco-dmo.org/dataset/663689/data/download
download
onLine
dataset
<p><strong>Methodology from the IRNBRU cruise report</strong></p>
<p>During the IRNBRU (MV1405) cruise, multiple incubation experiments were performed at different locations in relation to varying iron environments, including regions of high iron, upwelled waters as well as relatively low iron waters. Incubated phytoplankton community response was assessed using physiological and molecular methods in order to examine the effects of varying biogeochemical environments on metabolism and gene expression. Each experiment contained several treatments and time points consisting of the following: a 5 nmol L-1&nbsp;FeCl3&nbsp;addition, a 200 nmol L-1&nbsp;desferroxamine&nbsp;B (DFB) addition, an initial 5 nmol L-1&nbsp;FeCl3&nbsp;addition followed by a 200 nmol L-1&nbsp;DFB addition during the midpoint of the experiment, and an unamended control.&nbsp; For three of the experiments (sites 1, 2, and 4), seawater was collected from the near surface (2-5m) using a&nbsp;trace-metal&nbsp;clean sampling system which consisted of a towed GeoFish sampler attached to KevlarTM&nbsp;line, PFA Teflon tubing and a Teflon dual-diaphragm pump that pumped seawater directly into a positive pressure trace-metal clean bubble constructed in the main laboratory of the ship. The seawater was placed into a large 55 gallon acid-cleaned HDPE drum for homogenization before being distributed into10L flexible acid-cleaned polyethylene&nbsp;cubitainers&nbsp;and placed in on-deck plexiglass incubators with flow-through seawater to maintain near-ambient surface temperatures. For the experiment at site 3, seawater was obtained from the depth corresponding to the 10 deg C isotherm (91 m) in order to simulate an upwelling event. Cleaning protocols for all&nbsp;cubitainers&nbsp;included soaking the inside walls in 1.2 mol L-1&nbsp;hydrochloric acid (reagent grade) for 3 d followed by three rinses with Milli-Q H20, soaking in 1.2 mol L-1&nbsp;hydrochloric acid (trace metal grade) for 1 week followed by three rinses with Milli-Q H20, and soaking in 0.1 mol L-1&nbsp;acetic acid (trace-metal&nbsp;grade). Prior to filling the&nbsp;cubitainers&nbsp;with seawater, the dilute acetic acid was removed and the&nbsp;cubitainers&nbsp;were rinsed thoroughly three times with ambient, low-iron seawater. Incubators were covered with neutral density screening to reduce irradiance to&nbsp;ca. 30% of the incident. For sample collection from initial conditions, triplicate&nbsp;cubitainers&nbsp;were immediately filtered. All incubations were initiated and terminated just prior to dawn. Following 96 hours of incubation, the seawater was removed from the incubators and stored in a dark, cool room until filtration. Subsamples for dissolved nutrients, size-fractionated chlorophyll&nbsp;a&nbsp;,Fv/Fm, particulate nutrients, nutrient uptake, biogenic silica, domoic acid, dissolved iron, and RNA were collected from each&nbsp;cubitainer. Methods performed on the ship for each measurement are briefly explained below.</p>
<p>Dissolved nitrate + nitrite (NO3-&nbsp;+ NO2-), phosphate (PO43-), and silicic acid (H4SiO4) concentrations were measured shipboard using a Lachat Quick Chem 8000 Flow Injection Analysis system. Particles were removed by filtering the sample through a GF/F filter using a syringe prior to analysis. Reference materials for nutrients in seawater (Lots BY and CA, KANSO Technos, Osaka, Japan) were run alongside samples for quality control.</p>
<p>For biomass determination, 400 mL of seawater was&nbsp;gravity-filtered&nbsp;through a 5 um polycarbonate filter (47 mm) followed by a GF/F filter (25 mm) under gentle vacuum pressure (&lt;100 mm Hg)&nbsp; using a series filter cascade for size fractionation. Filters were rinsed with 0.45 um filtered seawater and immediately frozen at -80 deg C until analysis. Chlorophyll&nbsp;a&nbsp;extraction&nbsp;was performed on the ship using 90% acetone at -20 deg C for 24 hours and measured via&nbsp;in vitro&nbsp;fluorometry using a Turner Designs 10-AU fluorometer.</p>
<p>In order to assess changes in photophysiology among treatments, the maximum photochemical yield of Photosystem II (Fv:Fm) was measured shipboard using a Satlantic FIRe. Before each measurement, a subsample (5 mL) of each culture was placed in the dark for 20 minutes. The resulting Fv:Fm&nbsp;was derived from the induction profile using a saturating pulse (20,000&nbsp;umol&nbsp;photons m2&nbsp;s-1) for a duration of 100-200 us.</p>
<p>Particulate nitrate (PN), carbon (PC) and nitrate (NO3-) uptake was obtained by spiking 500 mL of seawater with&nbsp;15N-NH4Cl at no more than 10% of ambient nitrate concentration and incubated for 8 hours in the flow-through plexiglass incubator. Following incubation, seawater filtration commenced immediately and was performed by gravity through a 5 um polycarbonate filter (47 mm), and with an in-line vacuum (&lt;100 mm Hg) onto a precombusted (450 deg C for 5 hours) GF/F filter (25 mm). Cells on the 5 um polycarbonate filter were then rinsed onto an additional precombusted GF/F filter (25 mm) using an artificial saline solution. Filters were then stored at -20 deg C. In the laboratory, filters were heated at 50 deg C for 24 hours, wrapped in tin capsules, and pelletized in preparation for analysis of the atom %&nbsp;15N, PN, and PC using an elemental analyzer paired with an isotope ratio mass spectrometer (EA-IRMS).</p>
<p>For inorganic carbon uptake, or measurements of primary productivity, 60mL samples from each&nbsp;cubitainer&nbsp;were distributed into a light and dark bottles cleaned with 10% HCl. For each bottle, 1.2 uCi of NaH14CO3&nbsp;was added. A 1 mL subsample was taken and added to vials containing NaOH. The light and dark bottles were incubated on-deck for 6.5-8 hours and stacked polycarbonate filters (5 um and 1 um) with a mesh spacer between them. The blanks were filtered onto a GF/F filter after 5 minutes. Filters were vacuumed dried, placed in scintillation vials with 0.5 mL of 6M HCl, permitted to degas for 24h, and counted using a Beckman Coulter LS 6500 scintillation counter.</p>
<p>Biogenic silica was determined shipboard via filtration of 335 mL onto 1.2 um polycarbonate filters (45 mm). Concentrations were measuring using a NaOH digestion in&nbsp;teflon&nbsp;tubes3&nbsp;and a colorimetric ammonium molybdate method.</p>
<p>Samples for iron (Fe) analysis were acidified at sea with the equivalent of 4 mL 6N quartz-distilled HCl per liter of seawater (to pH 1.7-1.8) and stored in LDPE bottles that had been cleaned as per the&nbsp;<a href="http://www.geotraces.org/images/stories/documents/intercalibration/Cookbook.pdf" target="_blank">GEOTRACES cookbook</a>&nbsp;(<a href="http://www.geotraces.org/science/">http://www.geotraces.org/science/</a>intercalibration/222-sampling-and-sample-handling-protocols-for-geotraces-cruises). Samples were analyzed by preconcentrating the Fe on 2 cm columns of&nbsp;Nobias&nbsp;chelate PA1&nbsp;resin,&nbsp;and analyzing the eluent on the Thermo-Element&nbsp;high-resolution&nbsp;XR ICP-MS&nbsp;at UC Santa Cruz. The resin columns are&nbsp;rinsed and conditioned with 0.05 M NH4Ac buffer at pH 6.0, and the samples are buffered to pH 6.0 with NH4Ac immediately before loading. The samples are eluted from the columns with ~1 mL of 1N quartz distilled HNO3. One to three days before preconcentration, samples were irradiated with UV light for 2 hours to ensure full recovery of other metals of interest.</p>
<p>Seawater for RNA analysis was filtered directly onto 0.8 um Pall Supor filters (142 mm) using a peristaltic pump. Filters were placed in&nbsp;cyrovials&nbsp;and immediately flash frozen in liquid nitrogen. Samples were later transferred to storage in -80 deg C freezers until RNA extractions were performed. Filters were briefly thawed on ice before being extracted individually using the ToTALLY RNA Total RNA Isolation Kit (Ambion). RNA-Seq library prep was conducted with the Illumina TruSeq Stranded mRNA Library Preparation Kit and HiSeq v4 reagents. Bioinformatic pipeline consisted of the following: trimming of reads for quality and removal of adapters, contig assemblies, read mapping for quantitative analysis, taxonomic and functional assignment, and differential gene expression determination.</p>
Specified by the Principal Investigator(s)
<p><strong>BCO-DMO Data Processing Notes:</strong></p>
<p>-reformatted column names to comply with BCO-DMO standards<br />
-filled in blank cells 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
LDPE bottles
LDPE bottles
PI Supplied Instrument Name: LDPE bottles PI Supplied Instrument Description:Contained seawater samples 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.
Lachat Quick Chem 8000 Flow Injection Analysis system
Lachat Quick Chem 8000 Flow Injection Analysis system
PI Supplied Instrument Name: Lachat Quick Chem 8000 Flow Injection Analysis system PI Supplied Instrument Description:Dissolved nitrate + nitrite (NO3- + NO2-), phosphate (PO43-), and silicic acid (H4SiO4) concentrations were measured shipboard. Instrument Name: Flow Injection Analyzer Instrument Short Name:FIA Instrument Description: An instrument that performs flow injection analysis. Flow injection analysis (FIA) is an approach to chemical analysis that is accomplished by injecting a plug of sample into a flowing carrier stream. FIA is an automated method in which a sample is injected into a continuous flow of a carrier solution that mixes with other continuously flowing solutions before reaching a detector. Precision is dramatically increased when FIA is used instead of manual injections and as a result very specific FIA systems have been developed for a wide array of analytical techniques. Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/LAB36/
Turner Designs 10-AU fluorometer
Turner Designs 10-AU fluorometer
PI Supplied Instrument Name: Turner Designs 10-AU fluorometer PI Supplied Instrument Description:Chlorophyll a extraction was performed on the ship using 90% acetone at -20 deg C for 24 hours and measured via in vitro fluorometry. 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/
GeoFish Sampler
GeoFish Sampler
PI Supplied Instrument Name: GeoFish Sampler PI Supplied Instrument Description:Used to collect seawater Instrument Name: GeoFish Towed near-Surface Sampler Instrument Short Name:GeoFish Instrument Description: The GeoFish towed sampler is a custom designed near surface (2 meters or less) sampling system for the collection of trace metal clean seawater. It consists of a PVC encapsulated lead weighted torpedo and separate PVC depressor vane supporting the intake utilizing all PFA Teflon tubing connected to a deck mounted, air-driven, PFA Teflon dual-diaphragm pump which provides trace-metal clean seawater at up to 3.7L/min. The GeoFish is towed at up to 13kts off to the side of the vessel outside of the ship's wake to avoid possible contamination from the ship's hull. It was developed by Geoffrey Smith and Ken Bruland (University of California, Santa Cruz). Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/31/
EA-IRMS
EA-IRMS
PI Supplied Instrument Name: EA-IRMS PI Supplied Instrument Description:Analysis of the atom % 15N, PN, and PC using an elemental analyzer paired with an isotope ratio mass spectrometer. Instrument Name: Isotope-ratio Mass Spectrometer Instrument Short Name:IR Mass Spec; IRMS Instrument Description: The Isotope-ratio Mass Spectrometer is a particular type of mass spectrometer used to measure the relative abundance of isotopes in a given sample (e.g. VG Prism II Isotope Ratio Mass-Spectrometer). Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/LAB16/
Beckman Coulter LS 6500 scintillation counter
Beckman Coulter LS 6500 scintillation counter
PI Supplied Instrument Name: Beckman Coulter LS 6500 scintillation counter PI Supplied Instrument Description:Scintillation vials with 0.5 mL of 6M HCl, permitted to degas for 24h were counted. 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/
Teflon dual-diaphragm pump
Teflon dual-diaphragm pump
PI Supplied Instrument Name: Teflon dual-diaphragm pump PI Supplied Instrument Description:Pumped seawater directly into a positive pressure trace-metal clean bubble constructed in the main laboratory of the ship. Instrument Name: Pump Instrument Short Name: Instrument Description: A pump is a device that moves fluids (liquids or gases), or sometimes slurries, by mechanical action. Pumps can be classified into three major groups according to the method they use to move the fluid: direct lift, displacement, and gravity pumps
Flow-through plexiglass incubator
Flow-through plexiglass incubator
PI Supplied Instrument Name: Flow-through plexiglass incubator PI Supplied Instrument Description:Particulate nitrate (PN), carbon (PC) and nitrate (NO3-) uptake was obtained by spiking 500 mL of seawater with 15N-NH4Cl at no more than 10% of ambient nitrate concentration and incubated for 8 hours. Instrument Name: Shipboard Incubator Instrument Short Name: Instrument Description: A device mounted on a ship that holds water samples under conditions of controlled temperature or controlled temperature and illumination.
Cruise: MV1405
MV1405
R/V Melville
Community Standard Description
International Council for the Exploration of the Sea
R/V Melville
vessel
MV1405
Kenneth W. Bruland
University of California-Santa Cruz
R/V Melville
Community Standard Description
International Council for the Exploration of the Sea
R/V Melville
vessel