http://lod.bco-dmo.org/id/dataset/826878
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
2020-10-16
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Hydrocarbon concentrations, DIC isotopes, nutrients, and cyanobacteria counts from samples collected on R/V Neil Armstrong cruise AR16 in the western north Atlantic during May 2017
2020-10-16
publication
2020-10-16
revision
Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)
2020-12-03
publication
https://doi.org/10.26008/1912/bco-dmo.826878.1
David L. Valentine
University of California-Santa Barbara
principalInvestigator
Christopher Reddy
Woods Hole Oceanographic Institution
principalInvestigator
Robert Swarthout
Appalachian 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: Valentine, D. L., Reddy, C., Swarthout, R. (2020) Hydrocarbon concentrations, DIC isotopes, nutrients, and cyanobacteria counts from samples collected on R/V Neil Armstrong cruise AR16 in the western north Atlantic during May 2017. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2020-10-16 [if applicable, indicate subset used]. doi:10.26008/1912/bco-dmo.826878.1 [access date]
Methods and Sampling: <p><strong><em>in situ</em> Sampling and Quantification of Hydrocarbon Production</strong><br />
Water was collected with a rosette equipped with 12 L Niskin bottles just after sunrise (~ 8 AM) for all sampling except for the diel experiment. Salinity, density, temperature, fluorescence and percent photosynthetically active radiation (% PAR) were measured semi-continuously for each hydrocast. For diel sampling, a Lagrangian framework was used by following deployed particle traps set just below the DCM (150 m) and sampled at six-hour intervals through a full 24-hour cycle. Sampling targeted six light-penetration levels with depths held constant following initial collection, plus the DCM, which is a depth-variable feature. Water was collected from the Niskin into 2 L polycarbonate bottles via a polyvinyl chloride tube equipped with a 200 m mesh to filter out large zooplankton.</p>
<p>For <em>in situ</em> hydrocarbon concentration measurements, water in the 2 L polycarbonate bottles was immediately filtered through a 0.22 m Teflon filter under gentle vacuum with an oil-less vacuum pump. For the hydrocarbon production experiment ¹³C-bicarbonate tracer solution (with 45 g/L NaCl to sink the tracer to the bottom of the bottle) made from ¹³C-sodium bicarbonate (Cambridge Isotope Laboratories Inc., ¹³C 99%) was added to the 2L polycarbonate bottles to achieve a 480 ‰ enrichment in seawater DIC. Dark control bottles were covered completely beforehand with aluminum foil before tracer addition and kill control bottles were treated with Zinc Chloride to 2% ZnCl₂ (m/v) before tracer addition. 2 L bottles were then immediately placed into black mesh bags to attenuate light to the value from which it was collected (either 30%, 10% or 1% PAR) and placed into on-board seawater incubators with a continuous flow of surface water; this was marked as the start of incubation. Bottles were harvested at 0 hour (initial), 5, 10, 20 and 30 hour (final) time points for the 30% PAR light bags and at t = 0 hour and t = 30 hour final for the 10% and 1% light levels, care was taken to reduce light exposure in the ship-board laboratory when preparing for incubation by placing bottles into covered tubs. A 2 mL aliquot was taken for ¹³C-DIC prior to filtration. Filters were placed into pre-combusted aluminum foil packets and immediately frozen at -20 C for later analysis.</p>
<p><strong>Hydrocarbon Extraction and Analysis</strong><br />
A modified Bligh-Dyer method was used to extract hydrocarbons from membranes of frozen cells collected on Teflon filters. Dodecahydrotriphenylene (internal standard) and C23 ethyl ester (chromatographically remote secondary internal standard) were added to the dry filter before extraction. Once extracted into dichloromethane, sodium sulfate was added for drying, ~40 L of toluene was added to prevent complete dryness of the extracts and then the solution was rotary evaporated to ~30 L and placed into a 2 mL GC-vial with a combusted glass insert. Before analysis, a small volume of C23 methyl ester (external standard) was added. All glassware and solid chemicals were pre-combusted before use. Concentration analysis was done on a gas chromatograph flame ionization detector (GC-FID). GC-FID was performed with a 30 m x 0.25 mm ID, 0.25 m pore size, fused silica Restek 13323 Rxi-1 MS Capillary Column with a splitless 2 L injection. Initial oven temperature was at 70 °C held for 2 minutes, a 3 °C min⁻¹ ramp to 120 °C, then a 6 °C min⁻¹ ramp to the final temperature of 320 °C. A standard mix of pentadecane, heptadecane, internal standard, external standard and transesterification standard was run to calibrate response factors for every batch of samples (~20 per batch). Blanks were run every ~ six samples and peaks were manually integrated, there were no co-eluting peaks for pentadecane or heptadecane. Comprehensive two-dimensional chromatography was used on select samples to check for other hydrocarbons, contaminants, and quality of blank filters run through the extractive process.</p>
<p><strong>Compound-specific and Dissolved Inorganic Carbon Isotope Measurements</strong><br />
Compound-specific isotope analysis was performed after concentration analysis on a gas chromatograph combustion isotope ratio mass spectrometer (GC/C-IRMS) with a Trace GC (Thermo Finnigan) set up to a GC-C/TC III (FinniganTM) interface and a Deltaplus XP isotope ratio mass spectrometer (Thermo Finnigan). A J &amp; W Scientific DB-5 Capillary column (30 m, 0.25 mm, 0.25 m) was used with 2 L manual injections. Temperature ramp was conducted starting at 70 °C and held for 2 minutes, then a 3 °C min-1 ramp to 120 °C, hold for 0 minutes, then a 6 °C min-1 ramp to 185 °C, hold for 0 minutes then a 120 °C min⁻¹ ramp to 290 °C, hold for 3 minutes. Inlet temperature was 260 °C, flow rate was held at 2.2 mL He min-1 with a splitless injection held for 0.5 minutes after injection. Isotope ratio accuracy was calibrated with a C14 fatty acid methyl ester Schimmelmann reference material to Vienna PeeDee Belemnite. Precision was accounted for with a standard mix of nC15, nC16 and nC17 at ~1.2 ng L-1 and was run between every batch of ~20 samples. Peaks were manually integrated after establishing the baseline, analytical precision was ~0.9 ‰ δ13C for pentadecane. Dissolved inorganic carbon 13C isotope ratio measurements were made on a Gas Bench II (Thermo Finnigan) interfaced to the same Deltaplus XP isotope ratio mass spectrometer (Thermo Finnigan) used for the compound-specific analysis. Sample preparation and analysis were followed closely to the protocol outlines by the University of California, Davis, Stable Isotope Facility (<a href="https://stableisotopefacility.ucdavis.edu/dictracegas.html" target="_blank">https://stableisotopefacility.ucdavis.edu/dictracegas.html</a>).</p>
<p><strong>Cell Counts and Dissolved Nutrient Analysis</strong><br />
Sampling for nutrients and cell counts was conducted on the CTD cast immediately before the casts for hydrocarbon sampling (~ 1-hour difference), these casts were all at ~sunrise. Parallel sampling was conducted with the same cast water for the diel sampling. Flow cytometry analysis was performed by the Bigelow Laboratory for Ocean Sciences using a slightly modified protocol from Lomas et al., 2010. Samples were fixed with paraformaldehyde (0.5% final concentration) and stored at ~4 °C for 1-2 hours before long term storage in liquid nitrogen. An Influx cytometer was used with a 488 nm blue excitation laser, appropriate Chl-a (692 ± 20 nm) and phycoerythrin (585 ± 15 nm) bandpass filters, and was calibrated daily with 3.46 µm Rainbow Beads (Spherotech Inc. Lake Forest, Illinois, USA). Each sample was run for 4–6 min (∼0.2–0.3 ml total volume analyzed), with log-amplified Chl-a and phycoerythrin fluorescence, and forward and right-angle scatter signals recorded. Data files were analyzed from two-dimensional scatter plots based on red or orange fluorescence and characteristic light scattering properties using FlowJo 9.8 Software (Becton Dickinson, San Jose, CA). Pico-autotrophs were identified as either <em>Synechococcus</em> or <em>Prochlorococcus</em>, pico-eukaryotes based upon cell size and the presence or absence of phycoerythrin, respectively. Nutrients were analyzed by the University of Washington Marine Chemistry Laboratory.</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1756667 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1756667
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1635562 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1635562
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1634478
completed
David L. Valentine
University of California-Santa Barbara
805-893-2973
Department of Earth Science 1006 Webb Hall
Santa Barbara
CA
93106
USA
valentine@ucsb.edu
pointOfContact
Christopher Reddy
Woods Hole Oceanographic Institution
508-289-2316
183 Oyster Pond Road
Woods Hole
MA
02543
USA
creddy@whoi.edu
pointOfContact
Robert Swarthout
Appalachian State University
828-262-4083
525 Rivers St
Boone
NC
28609
USA
swarthoutrf@appstate.edu
pointOfContact
asNeeded
Dataset Version: 1
Unknown
sample
station
depth
PAR
id
replicate
time
time_inc
time_harvest
act_inc_time
cast_number
date_collected
time_collected
lat
long
temp
density
fluor
fluor_avgd_1m
fluor_avgd_2m
nC15
C17
C13_12C_nC15
C13_12C_DIC
sd_13C_DIC
Total_phyto
Syn_count
Pro_count
pEu_count
nEu_count
Hetero_count
depth_flowcyt
pro_notes
phosphate
silicone
nitrate
nitrite
ammonium
TPP
TPP_stdev
N_P
recovery_IS
notes
Sea-Bird SBE-911+
gas chromatograph flame ionization detector (GC-FID)
Influx cytometer
gas chromatograph flame ionization detector (GC-FID)
Deltaplus XP isotope ratio mass spectrometer (Thermo Finnigan)
gas chromatograph combustion isotope ratio mass spectrometer (GC/C-IRMS)
12 L Niskin bottles
Gas Bench II
theme
None, User defined
sample identification
station
depth
PAR
sample description
replicate
incubation time or duration
time of day
cast
date
latitude
longitude
water temperature at measurement depth
density
fluorescence
pentadecane
heptadecane
13C to 12C ratio in DIC
number
comments
phosphate
Silicon
Nitrate
Nitrite
Ammonium
Total Particulate Phosphorus
No BCO-DMO term
featureType
BCO-DMO Standard Parameters
CTD Sea-Bird SBE 911plus
Flame Ionization Detector
Flow Cytometer
Gas Chromatograph
Isotope-ratio Mass Spectrometer
Isotope-ratio Mass Spectrometer
Niskin bottle
Thermo-Fisher Scientific Gas Bench II
instrument
BCO-DMO Standard Instruments
AR16
service
Deployment Activity
Western North Atlantic
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: Do Cyanobacteria Drive Marine Hydrocarbon Biogeochemistry?
https://osprey.bco-dmo.org/project/819037
Collaborative Research: Do Cyanobacteria Drive Marine Hydrocarbon Biogeochemistry?
<p><em>NSF Award Abstract:</em><br />
While the release of petroleum hydrocarbons into the ocean is recognized as an environmental and human hazard, a recent study has estimated that on an annual basis, the release of natural hydrocarbons by a single phytoplankton group (cyanobacteria) contributes at least ten times more total hydrocarbon to the surface ocean. This project will be the first in-depth study of the latent biogeochemical cycling of this huge pool of biogenic hydrocarbons. Using field studies, laboratory incubations of cyanobacteria, and state-of-the art chemical analysis, the researchers will examine the molecular structures, rates and mechanisms of production and removal, and the environmental conditions that control the cycling of this major pool of oceanic hydrocarbons. The results of this study will reveal significant new knowledge for improved understanding of a major carbon cycle in the ocean. Additionally, data could indicate a role for cyanobacterial hydrocarbons in preparing natural marine bacteria to respond to, and degrade petroleum spills, as well as a possible atmospheric impact (e.g. cloud formation) resulting from air-sea exchange of certain components of the hydrocarbon pool.</p>
<p>This project will support undergraduate and graduate students, a postdoctoral investigator, and a new faculty member, and will engage participants from minority-serving institutions in California and North Carolina. Plans are also included to establish links with oil spill and biofuel researchers in order to evaluate additional practical applications for the data resulting from this study.</p>
<p>The annual production of 308,000,000 - 771,000,000 tons of hydrocarbons by cyanobacteria has recently been reported and is a factor of 10 larger than marine petroleum hydrocarbon input from spills and natural seeps. Consequently, these biogenic hydrocarbons almost certainly have significant implications for the carbon cycle and the bacterial community composition in the ocean but have never been the subject of rigorous study. This project will investigate the distribution, partitioning, and cycling of biogenic hydrocarbons in the ocean, focusing on the abundance and molecular diversity of biogenic hydrocarbons in relation to cyanobacterial populations; the extent to which volatilization to the atmosphere acts as a sink for biogenic hydrocarbons; and the rate at which hydrocarbons are produced by cyanobacteria and consumed by hydrocarbon-degrading bacteria. Field studies across natural gradients in phytoplankton community structure and abundance will employ state of the art chemical analysis to evaluate the distribution of biogenic hydrocarbons, and together with incubation experiments will determine quantitative rates for biogenic hydrocarbons cycling in the surface ocean. Laboratory studies will augment field studies by assessing hydrocarbon production and loss mechanisms under carefully controlled laboratory conditions. Together, the project will obtain a quantitative understanding of this important component of the oceanic carbon cycle.</p>
Cyanobacteria Hydrocarbons
largerWorkCitation
project
eng; USA
oceans
Western North Atlantic
-71.399
-64.1637167
29.0470333
40.4212167
2017-05-04
2017-05-20
North Atlantic Sub-tropical Gyre
0
BCO-DMO catalogue of parameters from Hydrocarbon concentrations, DIC isotopes, nutrients, and cyanobacteria counts from samples collected on R/V Neil Armstrong cruise AR16 in the western north Atlantic during May 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/826914.rdf
Name: sample
Units: unitless
Description: <p>sample identification</p>
http://lod.bco-dmo.org/id/dataset-parameter/826915.rdf
Name: station
Units: unitless
Description: <p>station number</p>
http://lod.bco-dmo.org/id/dataset-parameter/826916.rdf
Name: depth
Units: meters
Description: <p>depth</p>
http://lod.bco-dmo.org/id/dataset-parameter/826917.rdf
Name: PAR
Units: unitless
Description: <p>% photosynthetically active radiation</p>
http://lod.bco-dmo.org/id/dataset-parameter/826918.rdf
Name: id
Units: unitless
Description: <p>description: iso = isotope added; env, = no isotope added; dark = dark control; kill = killed with ZnCl; trap = sediment trap particle sample</p>
http://lod.bco-dmo.org/id/dataset-parameter/826919.rdf
Name: replicate
Units: unitless
Description: <p>replicate; A, B, or C</p>
http://lod.bco-dmo.org/id/dataset-parameter/826920.rdf
Name: time
Units: hours
Description: <p>duration of incubation</p>
http://lod.bco-dmo.org/id/dataset-parameter/826921.rdf
Name: time_inc
Units: unitless
Description: <p>time incubation started; format: HH:MM</p>
http://lod.bco-dmo.org/id/dataset-parameter/826922.rdf
Name: time_harvest
Units: unitless
Description: <p>time water was filtered; format: HH:MM</p>
http://lod.bco-dmo.org/id/dataset-parameter/826923.rdf
Name: act_inc_time
Units: hours
Description: <p>duration of incubation</p>
http://lod.bco-dmo.org/id/dataset-parameter/826924.rdf
Name: cast_number
Units: unitless
Description: <p>cast number of cruise</p>
http://lod.bco-dmo.org/id/dataset-parameter/826925.rdf
Name: date_collected
Units: unitless
Description: <p>date of collection; format: YYYY-MM-DD</p>
http://lod.bco-dmo.org/id/dataset-parameter/826926.rdf
Name: time_collected
Units: unitless
Description: <p>time of collection; format: HH:MM</p>
http://lod.bco-dmo.org/id/dataset-parameter/826927.rdf
Name: lat
Units: degrees North
Description: <p>Latitude</p>
http://lod.bco-dmo.org/id/dataset-parameter/826928.rdf
Name: long
Units: degrees East
Description: <p>Longitude</p>
http://lod.bco-dmo.org/id/dataset-parameter/826929.rdf
Name: temp
Units: degrees Celsius
Description: <p>water temperature</p>
http://lod.bco-dmo.org/id/dataset-parameter/826930.rdf
Name: density
Units: kilograms per cubic meter +1000 (kg/m^3 + 1000)
Description: <p>potential seawater density</p>
http://lod.bco-dmo.org/id/dataset-parameter/826931.rdf
Name: fluor
Units: milligrams chl per cubic meter (mg/m^3 Chl)
Description: <p>fluorescence</p>
http://lod.bco-dmo.org/id/dataset-parameter/826932.rdf
Name: fluor_avgd_1m
Units: milligrams chl per cubic meter (mg/m^3 Chl)
Description: <p>fluorescence averaged at that depth with fluorescence found one meter above and below</p>
http://lod.bco-dmo.org/id/dataset-parameter/826933.rdf
Name: fluor_avgd_2m
Units: milligrams chl per cubic meter (mg/m^3 Chl)
Description: <p>fluorescence averaged at that depth with fluorescence found two meters above and below</p>
http://lod.bco-dmo.org/id/dataset-parameter/826934.rdf
Name: nC15
Units: nanograms per liter (ng/L)
Description: <p>pentadecane concentration</p>
http://lod.bco-dmo.org/id/dataset-parameter/826935.rdf
Name: C17
Units: nanograms per liter (ng/L)
Description: <p>heptadecane concentration</p>
http://lod.bco-dmo.org/id/dataset-parameter/826936.rdf
Name: C13_12C_nC15
Units: permill to VPDB
Description: <p>13C isotope value pentadecane</p>
http://lod.bco-dmo.org/id/dataset-parameter/826937.rdf
Name: C13_12C_DIC
Units: permill to VPDB
Description: <p>13C isotope value dissolved inorganic carbon</p>
http://lod.bco-dmo.org/id/dataset-parameter/826938.rdf
Name: sd_13C_DIC
Units: permill to VPDB
Description: <p>standard deviation of 13C/12C_DIC measurements done in triplicate</p>
http://lod.bco-dmo.org/id/dataset-parameter/826939.rdf
Name: Total_phyto
Units: number per milliliter (#/mL)
Description: <p>number of all counted phytoplankton</p>
http://lod.bco-dmo.org/id/dataset-parameter/826940.rdf
Name: Syn_count
Units: number per milliliter (#/mL)
Description: <p>number of Synechococcus cells per mL</p>
http://lod.bco-dmo.org/id/dataset-parameter/826941.rdf
Name: Pro_count
Units: number per milliliter (#/mL)
Description: <p>number of Prochlorococcus cells per mL</p>
http://lod.bco-dmo.org/id/dataset-parameter/826942.rdf
Name: pEu_count
Units: number per milliliter (#/mL)
Description: <p>number of picoeukaryote phytoplankton per mL</p>
http://lod.bco-dmo.org/id/dataset-parameter/826943.rdf
Name: nEu_count
Units: number per milliliter (#/mL)
Description: <p>number of nanoeukaryote phytoplankton per mL</p>
http://lod.bco-dmo.org/id/dataset-parameter/826944.rdf
Name: Hetero_count
Units: number per milliliter (#/mL)
Description: <p>number of heterotrophic bacteria per mL</p>
http://lod.bco-dmo.org/id/dataset-parameter/826945.rdf
Name: depth_flowcyt
Units: meters
Description: <p>depth of flow cytometry sample</p>
http://lod.bco-dmo.org/id/dataset-parameter/826946.rdf
Name: pro_notes
Units: unitless
Description: <p>notes of flow cytometry measurement</p>
http://lod.bco-dmo.org/id/dataset-parameter/826947.rdf
Name: phosphate
Units: micrograms per liter (ug/L)
Description: <p>concentration of phosphate</p>
http://lod.bco-dmo.org/id/dataset-parameter/826948.rdf
Name: silicone
Units: micrograms per liter (ug/L)
Description: <p>concentration of silicone</p>
http://lod.bco-dmo.org/id/dataset-parameter/826949.rdf
Name: nitrate
Units: micrograms per liter (ug/L)
Description: <p>concentration of nitrate</p>
http://lod.bco-dmo.org/id/dataset-parameter/826950.rdf
Name: nitrite
Units: micrograms per liter (ug/L)
Description: <p>concentration of nitrite</p>
http://lod.bco-dmo.org/id/dataset-parameter/826951.rdf
Name: ammonium
Units: micrograms per liter (ug/L)
Description: <p>concentration of ammonium</p>
http://lod.bco-dmo.org/id/dataset-parameter/826952.rdf
Name: TPP
Units: nanomolar (nM)
Description: <p>total particulate phosphorus</p>
http://lod.bco-dmo.org/id/dataset-parameter/826953.rdf
Name: TPP_stdev
Units: nanomolar (nM)
Description: <p>standard deviation of TPP measurements</p>
http://lod.bco-dmo.org/id/dataset-parameter/826954.rdf
Name: N_P
Units: unitless
Description: <p>ratio of N to P</p>
http://lod.bco-dmo.org/id/dataset-parameter/826955.rdf
Name: recovery_IS
Units: unitless (percent)
Description: <p>percent (%) recovery of internal standard for nC15 extractions</p>
http://lod.bco-dmo.org/id/dataset-parameter/826956.rdf
Name: notes
Units: unitless
Description: <p>notes</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
133787
https://darchive.mblwhoilibrary.org/bitstream/1912/26435/1/dataset-826878_sargasso-sea-hydrocarbons__v1.tsv
download
https://doi.org/10.26008/1912/bco-dmo.826878.1
download
onLine
dataset
<p><strong><em>in situ</em> Sampling and Quantification of Hydrocarbon Production</strong><br />
Water was collected with a rosette equipped with 12 L Niskin bottles just after sunrise (~ 8 AM) for all sampling except for the diel experiment. Salinity, density, temperature, fluorescence and percent photosynthetically active radiation (% PAR) were measured semi-continuously for each hydrocast. For diel sampling, a Lagrangian framework was used by following deployed particle traps set just below the DCM (150 m) and sampled at six-hour intervals through a full 24-hour cycle. Sampling targeted six light-penetration levels with depths held constant following initial collection, plus the DCM, which is a depth-variable feature. Water was collected from the Niskin into 2 L polycarbonate bottles via a polyvinyl chloride tube equipped with a 200 m mesh to filter out large zooplankton.</p>
<p>For <em>in situ</em> hydrocarbon concentration measurements, water in the 2 L polycarbonate bottles was immediately filtered through a 0.22 m Teflon filter under gentle vacuum with an oil-less vacuum pump. For the hydrocarbon production experiment ¹³C-bicarbonate tracer solution (with 45 g/L NaCl to sink the tracer to the bottom of the bottle) made from ¹³C-sodium bicarbonate (Cambridge Isotope Laboratories Inc., ¹³C 99%) was added to the 2L polycarbonate bottles to achieve a 480 ‰ enrichment in seawater DIC. Dark control bottles were covered completely beforehand with aluminum foil before tracer addition and kill control bottles were treated with Zinc Chloride to 2% ZnCl₂ (m/v) before tracer addition. 2 L bottles were then immediately placed into black mesh bags to attenuate light to the value from which it was collected (either 30%, 10% or 1% PAR) and placed into on-board seawater incubators with a continuous flow of surface water; this was marked as the start of incubation. Bottles were harvested at 0 hour (initial), 5, 10, 20 and 30 hour (final) time points for the 30% PAR light bags and at t = 0 hour and t = 30 hour final for the 10% and 1% light levels, care was taken to reduce light exposure in the ship-board laboratory when preparing for incubation by placing bottles into covered tubs. A 2 mL aliquot was taken for ¹³C-DIC prior to filtration. Filters were placed into pre-combusted aluminum foil packets and immediately frozen at -20 C for later analysis.</p>
<p><strong>Hydrocarbon Extraction and Analysis</strong><br />
A modified Bligh-Dyer method was used to extract hydrocarbons from membranes of frozen cells collected on Teflon filters. Dodecahydrotriphenylene (internal standard) and C23 ethyl ester (chromatographically remote secondary internal standard) were added to the dry filter before extraction. Once extracted into dichloromethane, sodium sulfate was added for drying, ~40 L of toluene was added to prevent complete dryness of the extracts and then the solution was rotary evaporated to ~30 L and placed into a 2 mL GC-vial with a combusted glass insert. Before analysis, a small volume of C23 methyl ester (external standard) was added. All glassware and solid chemicals were pre-combusted before use. Concentration analysis was done on a gas chromatograph flame ionization detector (GC-FID). GC-FID was performed with a 30 m x 0.25 mm ID, 0.25 m pore size, fused silica Restek 13323 Rxi-1 MS Capillary Column with a splitless 2 L injection. Initial oven temperature was at 70 °C held for 2 minutes, a 3 °C min⁻¹ ramp to 120 °C, then a 6 °C min⁻¹ ramp to the final temperature of 320 °C. A standard mix of pentadecane, heptadecane, internal standard, external standard and transesterification standard was run to calibrate response factors for every batch of samples (~20 per batch). Blanks were run every ~ six samples and peaks were manually integrated, there were no co-eluting peaks for pentadecane or heptadecane. Comprehensive two-dimensional chromatography was used on select samples to check for other hydrocarbons, contaminants, and quality of blank filters run through the extractive process.</p>
<p><strong>Compound-specific and Dissolved Inorganic Carbon Isotope Measurements</strong><br />
Compound-specific isotope analysis was performed after concentration analysis on a gas chromatograph combustion isotope ratio mass spectrometer (GC/C-IRMS) with a Trace GC (Thermo Finnigan) set up to a GC-C/TC III (FinniganTM) interface and a Deltaplus XP isotope ratio mass spectrometer (Thermo Finnigan). A J &amp; W Scientific DB-5 Capillary column (30 m, 0.25 mm, 0.25 m) was used with 2 L manual injections. Temperature ramp was conducted starting at 70 °C and held for 2 minutes, then a 3 °C min-1 ramp to 120 °C, hold for 0 minutes, then a 6 °C min-1 ramp to 185 °C, hold for 0 minutes then a 120 °C min⁻¹ ramp to 290 °C, hold for 3 minutes. Inlet temperature was 260 °C, flow rate was held at 2.2 mL He min-1 with a splitless injection held for 0.5 minutes after injection. Isotope ratio accuracy was calibrated with a C14 fatty acid methyl ester Schimmelmann reference material to Vienna PeeDee Belemnite. Precision was accounted for with a standard mix of nC15, nC16 and nC17 at ~1.2 ng L-1 and was run between every batch of ~20 samples. Peaks were manually integrated after establishing the baseline, analytical precision was ~0.9 ‰ δ13C for pentadecane. Dissolved inorganic carbon 13C isotope ratio measurements were made on a Gas Bench II (Thermo Finnigan) interfaced to the same Deltaplus XP isotope ratio mass spectrometer (Thermo Finnigan) used for the compound-specific analysis. Sample preparation and analysis were followed closely to the protocol outlines by the University of California, Davis, Stable Isotope Facility (<a href="https://stableisotopefacility.ucdavis.edu/dictracegas.html" target="_blank">https://stableisotopefacility.ucdavis.edu/dictracegas.html</a>).</p>
<p><strong>Cell Counts and Dissolved Nutrient Analysis</strong><br />
Sampling for nutrients and cell counts was conducted on the CTD cast immediately before the casts for hydrocarbon sampling (~ 1-hour difference), these casts were all at ~sunrise. Parallel sampling was conducted with the same cast water for the diel sampling. Flow cytometry analysis was performed by the Bigelow Laboratory for Ocean Sciences using a slightly modified protocol from Lomas et al., 2010. Samples were fixed with paraformaldehyde (0.5% final concentration) and stored at ~4 °C for 1-2 hours before long term storage in liquid nitrogen. An Influx cytometer was used with a 488 nm blue excitation laser, appropriate Chl-a (692 ± 20 nm) and phycoerythrin (585 ± 15 nm) bandpass filters, and was calibrated daily with 3.46 µm Rainbow Beads (Spherotech Inc. Lake Forest, Illinois, USA). Each sample was run for 4–6 min (∼0.2–0.3 ml total volume analyzed), with log-amplified Chl-a and phycoerythrin fluorescence, and forward and right-angle scatter signals recorded. Data files were analyzed from two-dimensional scatter plots based on red or orange fluorescence and characteristic light scattering properties using FlowJo 9.8 Software (Becton Dickinson, San Jose, CA). Pico-autotrophs were identified as either <em>Synechococcus</em> or <em>Prochlorococcus</em>, pico-eukaryotes based upon cell size and the presence or absence of phycoerythrin, respectively. Nutrients were analyzed by the University of Washington Marine Chemistry Laboratory.</p>
Specified by the Principal Investigator(s)
<p><strong>BCO-DMO Processing:</strong><br />
- replaced "NA" with "nd" as missing data identifier;<br />
- renamed fields to conform with BCO-DMO naming conventions (e.g. no special characters; names must begin with letters)<br />
- converted date format to YYYY-MM-DD;<br />
- replaced commas with semi-colons in the sample column;<br />
- made longitude values to negative to indicate degrees 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
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For questions regarding this resource, please contact BCO-DMO via the email address provided.
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Sea-Bird SBE-911+
Sea-Bird SBE-911+
PI Supplied Instrument Name: Sea-Bird SBE-911+ Instrument Name: CTD Sea-Bird SBE 911plus Instrument Short Name:CTD SBE 911plus Instrument Description: The Sea-Bird SBE 911 plus is a type of CTD instrument package for continuous measurement of conductivity, temperature and pressure. The SBE 911 plus includes the SBE 9plus Underwater Unit and the SBE 11plus Deck Unit (for real-time readout using conductive wire) for deployment from a vessel. The combination of the SBE 9 plus and SBE 11 plus is called a SBE 911 plus. The SBE 9 plus uses Sea-Bird's standard modular temperature and conductivity sensors (SBE 3 plus and SBE 4). The SBE 9 plus CTD can be configured with up to eight auxiliary sensors to measure other parameters including dissolved oxygen, pH, turbidity, fluorescence, light (PAR), light transmission, etc.). more information from Sea-Bird Electronics Community Standard Description: http://vocab.nerc.ac.uk/collection/L22/current/TOOL0058/
gas chromatograph flame ionization detector (GC-FID)
gas chromatograph flame ionization detector (GC-FID)
PI Supplied Instrument Name: gas chromatograph flame ionization detector (GC-FID) Instrument Name: Flame Ionization Detector Instrument Short Name:FID Instrument Description: A flame ionization detector (FID) is a scientific instrument that measures the concentration of organic species in a gas stream. It is frequently used as a detector in gas chromatography. Standalone FIDs can also be used in applications such as landfill gas monitoring, fugitive emissions monitoring and internal combustion engine emissions measurement in stationary or portable instruments.
Influx cytometer
Influx cytometer
PI Supplied Instrument Name: Influx cytometer 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/
gas chromatograph flame ionization detector (GC-FID)
gas chromatograph flame ionization detector (GC-FID)
PI Supplied Instrument Name: gas chromatograph flame ionization detector (GC-FID) Instrument Name: Gas Chromatograph Instrument Short Name:Gas Chromatograph Instrument Description: Instrument separating gases, volatile substances, or substances dissolved in a volatile solvent by transporting an inert gas through a column packed with a sorbent to a detector for assay. (from SeaDataNet, BODC) Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/LAB02/
Deltaplus XP isotope ratio mass spectrometer (Thermo Finnigan)
Deltaplus XP isotope ratio mass spectrometer (Thermo Finnigan)
PI Supplied Instrument Name: Deltaplus XP isotope ratio mass spectrometer (Thermo Finnigan) 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/
gas chromatograph combustion isotope ratio mass spectrometer (GC/C-IRMS)
gas chromatograph combustion isotope ratio mass spectrometer (GC/C-IRMS)
PI Supplied Instrument Name: gas chromatograph combustion isotope ratio mass spectrometer (GC/C-IRMS) 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/
12 L Niskin bottles
12 L Niskin bottles
PI Supplied Instrument Name: 12 L Niskin bottles PI Supplied Instrument Description:Water was collected with a rosette equipped with 12 L Niskin bottles. 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/
Gas Bench II
Gas Bench II
PI Supplied Instrument Name: Gas Bench II Instrument Name: Thermo-Fisher Scientific Gas Bench II Instrument Short Name:GasBench II Instrument Description: An on-line gas preparation and introduction system for isotope ratio mass spectrometry that is designed for high precision isotope and molecular ratio determination of headspace samples, including water equilibration, carbonates and atmospheric gases. The instrument allows for the use of a dual viscous flow inlet system of repetitive measurements of sample and standard gas on a continuous flow isotope ratio mass spectrometer (CF-IRMS) system. The sample volume is the sample vial (instead of a metal bellows), and the reference gas volume is a pressurized gas tank. The instrument consists of a user programmable autosampler, a gas sampling system, a maintenance-free water removal system, a loop injection system, an isothermal gas chromatograph (GC), an active open split interface, a reference gas injection system with three reference ports, and one or two optional LN2 traps for cryofocusing. The gas sampling system includes a two port needle which adds a gentle flow of He into the sample vial, diluting and displacing sample gas. Water is removed from the sample gas through diffusion traps. The loop injector aliquots the sample gas onto the GC column, which separates the molecular species. The reference gas injection system allows accurate referencing of each sample aliquot to isotopic standards. The system can be used with several options including a carbonate reaction kit that allows injection of anhydrous phospohric acid into sample vials.
Note "Finnigan GasBench-II" is the previous brand name of this instrument.
Cruise: AR16
AR16
International Council for the Exploration of the Sea
R/V Neil Armstrong
vessel
AR16
Benjamin A.S. Van Mooy
Woods Hole Oceanographic Institution
International Council for the Exploration of the Sea
R/V Neil Armstrong
vessel