Dataset: Biogeochemical survey 2015-2018

Name: Survey biogeochemical data from R/V Atlantis AT32, AT34, AT38, and AT39-06 in the western North Atlantic Ocean (35°N to 57°N; 45°W) in Nov. 2015, May 2016, Sep 2017, Mar/Apr 2018
Published: 2020-09-14
Keywords: biota, oceans

Cite This Dataset

DOI:10.26008/1912/bco-dmo.659131.2

Spatial Extent: N:56.341 E:-37.514 S:39.187 W:-46.148

Temporal Extent: 2015-11-12 - 2018-04-05

Project:

Tracking the temporal and spatial variability of dissolved organic matter, its diagenetic state and bioavailability during various bloom states in the North Atlantic (DOM_SeasonalDynamics)

Program:

North Atlantic Aerosols and Marine Ecosystems Study (NAAMES)

Principal Investigator:

Craig A. Carlson (University of California-Santa Barbara, UCSB-MSI)

BCO-DMO Data Manager:

Nancy Copley (Woods Hole Oceanographic Institution, WHOI BCO-DMO)

Version:

Version Date:

2020-09-14

Restricted:

Validated:

Yes

Current State:

Final no updates expected

Survey biogeochemical data from R/V Atlantis AT32, AT34, AT38, and AT39-06 in the western North Atlantic Ocean (35°N to 57°N; 45°W) in Nov. 2015, May 2016, Sep 2017, Mar/Apr 2018

Abstract:

This dataset includes analyses from Niskin bottle samples collected on R/V Atlantis cruises AT32, AT34, AT38 and AT39-6 as part of the NASA NAAMES campaign (2015-2018). Reported are survey biogeochemical including dissolved organic carbon, dissolved organic nitrogen, total dissolved amino acids.

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Archival Copy

Version Date	Archive	Persistent Identifier	Date Assigned
2020-09-14	Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)	10.26008/1912/bco-dmo.659131.2	2020-09-21

Description

Methods & Sampling

Samples were collected on RV/Atlantis cruises in the North Atlantic between November 2015 and April 2018. Bacterial abundance was determined by flow cytometry on AT32 and by direct microscope counts for the rest of the cruises (AT34, AT38, AT39-6). Amino acid analysis was conducted for cruises AT34, AT38, and AT39-06.

Dissolved organic carbon DOC) and total dissolved nitrogen (TDN): See Supplemental Files.
Carlson C, Hansell D, Nelson N, Siegel D, Smethie W, Khatiwala S et al. (2010). Dissolved organic carbon export and subsequent remineralization in the mesopelagic and bathypelagic realms of the North Atlantic basin. Deep Sea Res Part II: Topical Stud Oceanogr 57: 1433–1445.

Bacterial production by Leucine Incorporation: See Supplemental Files.
Smith, D.C. and F. Azam (1992). A simple, economical method for measuring bacterial protein synthesis rates in seawater using 3H-leucine. Marine Microbial Food Webs 6:107-114.

Bacterioplankton abundance by flow cytometry: See Supplemental Files.
Nelson, C.E., A.L. Alldredge, E.A. McCliment, L.A. Amaral-Zettler, and C.A. Carlson. 2011. Depleted dissolved organic carbon and distinct Bacterial communities in the water column of a rapid-flushing coral reef ecosystem. The ISME Journal 5: 1374–1387. doi:10.1038/ismej.2011.12

Bacterioplankton abundance by DAPI DNA binding stain and epifluorescence microscopy: See Supplemental Files.
BATS Methods Manual. Chapter 17. Determination of Bacterial Abundance.Updated by K.Orcutt 4/1997, pp. 111-114.version 4.

Amino acid concentration using HPLC: See Supplemental Files (includes reference list.)

Data Processing Description

BCO-DMO Processing:
- added conventional header with dataset name, PI name, version date
- replaced blank cells and those with -999 with 'nd' (no data)

Data Files

File
biogeochem_all.csv (Comma Separated Values (.csv), 977.59 KB) MD5:4444e94b5e8f660a491ee44f6ad0b2d4 Primary data file for dataset ID 659131

Supplemental Files

File
Bacterial abundance using DAPI DNA binding stain and Epifluorescence microscopy filename: Bacterial_Abundance_using_DAPI_DNA_binding_stain_and_EFM.pdf (Portable Document Format (.pdf), 367.91 KB) MD5:bcc7f60bea95a080fe056e1bb095536e C. Carlson [version date: 2017-08-29]
Determination of Amino Acid Concentrations using HPLC filename: Method-total_dissolved_amino_acids_Carlson_2020-08-19.pdf (Portable Document Format (.pdf), 435.78 KB) MD5:fd43f2485298a9bde730c64b516f56cc This procedure describes the measurement of total dissolved amino acids (TDAA) and its 18 constituents using high performance liquid chromatography (HPLC). Craig Carlson [2018-10-30]
Flow Cytometry Protocol for Determination of Bacterial Abundance filename: Flow_Cytometry_Protocol_for_Determination_of_Bacterial_Abundance.pdf (Portable Document Format (.pdf), 369.15 KB) MD5:d44db238e643d3f4828a732ee3447215 Flow Cytometry Protocol for Determination of Bacterial Abundance Craig Carlson [version date: 2017-08-29]
Protocol: Bacterial Production Rates via 3H-Leucine incorporation filename: Microcentrifuge_Method_for_Bacterial_Production_Rates_via_3H-Leucine_incorp.pdf (Portable Document Format (.pdf), 445.74 KB) MD5:08a05d9a15af3ba56cabb7836296f99f Microcentrifuge Method Protocol for Determination of Bacterial Production Rates via 3H-Leucine incorporation. Craig Carlson [version date: 2017-08-29]
Protocols for Dissolved Organic Carbon and Total Dissolved Nitrogen Analysis filename: DOC_TDN_method_Carlson.pdf (Portable Document Format (.pdf), 258.09 KB) MD5:46973edce747f7f77099db51ac36acfa Version date: 2017-10-10. UCSB - CRAIG CARLSON. v

More Information about this dataset

Funding Sources

Funding Source	Award Number
NSF Division of Ocean Sciences	OCE-1537943

Deployments

Deployment	Synonyms	Start Date	Platform	Investigator
AT32	NAAMES_1	2015-11-06	R/V Atlantis	Dr Michael J. Behrenfeld (Chief Scientist)	data info
AT34	NAAMES_2	2016-05-11	R/V Atlantis	Dr Michael J. Behrenfeld (Chief Scientist)	data info
AT38	NAAMES_3	2017-08-30	R/V Atlantis	Dr Michael J. Behrenfeld (Chief Scientist)	data info
AT39-06	NAAMES_4	2018-03-20	R/V Atlantis	Dr Michael J. Behrenfeld (Chief Scientist)	data info

Instruments

Centrifuge

Supplied Name:

Supplied Description:

For measurement of bacterial production.

Instrument Type

Generic Name: Centrifuge

Generic Description:

A machine with a rapidly rotating container that applies centrifugal force to its contents, typically to separate fluids of different densities (e.g., cream from milk) or liquids from solids.

Flow Cytometer

Supplied Name: BD LSR II equipped with a BD High Throughput Sampler (HTS) - Biosciences, San Jose, CA, USA

Supplied Description:

Used to measure bacterial abundance.
Flow cytometer equipped with a high throughput sampler, coherent sapphire 488nm laser and a default suite of six detectors (side-scatter and forward-scatter photodiodes and green, orange, red and far-red photomultipliers).

Instrument Type

Generic Name: Flow Cytometer

Community Identifier: http://vocab.nerc.ac.uk/collection/L05/current/LAB37/

Generic 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)

Fluorescence Microscope

Supplied Name: Olympus BX51 Epiflourescence Microscope

Supplied Description:

For bacterial abundance estimates

Instrument Type

Generic Name: Fluorescence Microscope

Community Identifier: http://vocab.nerc.ac.uk/collection/L05/current/LAB06/

Generic Description:

Instruments that generate enlarged images of samples using the phenomena of fluorescence and phosphorescence instead of, or in addition to, reflection and absorption of visible light. Includes conventional and inverted instruments.

GO-FLO Bottle

Supplied Name:

Supplied Description:

For water sample collection

Instrument Type

Generic Name: GO-FLO Bottle

Acronym: GO-FLO

Community Identifier: http://vocab.nerc.ac.uk/collection/L05/current/30/

Generic Description:

GO-FLO bottle cast used to collect water samples for pigment, nutrient, plankton, etc. The GO-FLO sampling bottle is specially designed to avoid sample contamination at the surface, internal spring contamination, loss of sample on deck (internal seals), and exchange of water from different depths.

High-Performance Liquid Chromatograph

Supplied Name: Dionex ICS 5000+

Supplied Description:

Used for amino acid concentration measurements.

Instrument Type

Generic Name: High-Performance Liquid Chromatograph

Acronym: HPLC

Community Identifier: http://vocab.nerc.ac.uk/collection/L05/current/LAB11/

Generic Description:

A High-performance liquid chromatograph (HPLC) is a type of liquid chromatography used to separate compounds that are dissolved in solution. HPLC instruments consist of a reservoir of the mobile phase, a pump, an injector, a separation column, and a detector. Compounds are separated by high pressure pumping of the sample mixture onto a column packed with microspheres coated with the stationary phase. The different components in the mixture pass through the column at different rates due to differences in their partitioning behavior between the mobile liquid phase and the stationary phase.

Liquid Scintillation Counter

Supplied Name: Hidex 300 Liquid Scintillation Analyzer

Supplied Description:

For microcentrifuge method protocol for determination of bacterial production rates via 3H-Leucine incorporationEnergy window settings:
Channel A: 0-19 KeV
Channel B: 2-19 KeV

Instrument Type

Generic Name: Liquid Scintillation Counter

Acronym: LSC

Community Identifier: http://vocab.nerc.ac.uk/collection/L05/current/LAB21/

Generic 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.

Niskin bottle

Supplied Name:

Supplied Description:

For water sample collection

Instrument Type

Generic Name: Niskin bottle

Community Identifier: http://vocab.nerc.ac.uk/collection/L22/current/TOOL0412/

Generic 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.

Shimadzu TOC-V Analyzer

Supplied Name:

Supplied Description:

Used to measure dissolved organic carbon (DOC) and total dissolved nitrogen (TDN).
Shimadzu TOC-V analyzers (Shimadzu Scientific Instruments, Columbia, MD, USA) were slightly modified from the manufacturer’s model system. The condensation coil was removed and the head space of an internal water trap was reduced to minimize system dead space. The combustion tube contained 0.5 cm Pt pillows placed on top of Pt alumina beads to improve peak shape and to reduce alteration of the combustion matrix throughout the analytical run. CO2-free carrier gas was delivered to the TOC-V systems via commercial ultra high purity gas cylinders or a Whatmans gas generator. A magnesium perchlorate trap was added to the existing water and halide traps to ensure removal of water vapor from the gas line prior to entering a nondispersive infrared detector. The resulting peak area was integrated with Shimadzu chromatographic software.

Instrument Type

Generic Name: Shimadzu TOC-V Analyzer

Acronym: Shimadzu TOC-V

Community Identifier: http://onto.nerc.ac.uk/CAST/124

Generic Description:

A Shimadzu TOC-V Analyzer measures DOC by high temperature combustion method.

Parameters

Date and time formats are described in python strftime() syntax.

Supplied Name	Supplied description	Supplied Units	Standard Name
Cruise	Cruise	unitless	cruise_id
Station	Station	unitless	station
Type	Sample Type (ODV format)	unitless	sample_type
Time_Stamp	Date/Time (ODV format); formatted as ISO_DateTime yyyy-mm-ddThh:mm or yyyy-mm-ddT	unitless	ISO_DateTime_UTC
Latitude	Latitude; north is positive	decimal degrees	lat
Longitude	Longitude; east is positive	decimal degrees	lon
Bottom_Z	Bottom Depth	meters	depth_w
CruiseCN	Cast number according to CTD/Bottle log sheets (cruise sequential cast number)	unitless	cast
SCN	Cast numbers restart at each station i.e. for Station x; Biology Cast 1 = SxC1; Biology Cast 2 = SxC2; Deep Cast 1 =SxC3; Deep Cast 2 = SxC4 (station sequential cast number)	unitless	cast
CampCN	Cast numbers carried through the entire NAAMES campaign; never resetting for an individual cruise nor station (campaign sequential cast number)	unitless	cast
Niskin	Niskin Number	unitless	bottle
Cast_Type	Biology; Deep; Shallow (does not fit Biology or Deep cast scheme); Microlayer	unitless	cast_type
Target_Z	Target Depth according to CTD/Bottle log sheets	meters	depth_n
Pressure	Pressure from Digiquartz sensor	decibars (db)	press
Density00	Density; 1st sensor	kilograms/meter^3 (kg/m3)	density
Density11	Density; 2nd sensor	kilograms/meter^3 (kg/m3)	density
Sal11	Salinity; 2nd Sensor	Practical Salinity Units (psu)	sal
SoundVel	Sound velocity; 1st sensor	meters/second (m/s)	sound_vel
SoundVel1	Sound velocity; 2nd sensor	meters/second (m/s)	sound_vel
Oxygen_uM	Oxygen; 1st sensor	micromol/liter (umol/l)	O2
Oxygen_V	Oxygen; 1st sensor; voltage	volts (V)	O2_v
Temperature	Temperature; 1st sensor	degrees C	temp
Temperature1	Temperature; 2nd sensor	degrees C	temp
Conductivity	Conductivity; 1st sensor	Siemans/meter (S/m)	cond
Conductivity1	Conductivity; 2nd sensor	Siemans/meter (S/m)	cond
BeamT	Beam Transmission; 1st Sensor	percent	trans
BeamAt	Bean Attenuation; 1st sensor	per meter	beam_cp
Fluorescence	Fluorescence; 1st sensor	milligrams/meter^3 (mg/m3)	fluor
Turbidity	Turbidity; 1st sensor	Nephelometric Turbidity Units (NTU)	turbidity
TOC	Total Organic Carbon; Method: High temperature combustion/oxidation (HTCO) (Carlson et al; 2010)	micromol carbon/liter (umol C/L)	TOC
TOC_QF	Total Organic Carbon Quality Flag: 1 sample taken; 2 acceptable measurement; 3 Questionable measurement; 4 Bad measurement; 5 not reported; 9 no sample drawn	unitless	flag
TOC_sd	Total Organic Carbon Standard Deviation	micromol carbon/liter (umol C/L)	TOC
DOC	Dissolved Organic Carbon; Method: High temperature combustion/oxidation (HTCO). Glass fiber filtrate type GF/F (Whatman) (Carlson et al; 2010)	micromol carbon/liter (umol C/L)	DOC
DOC_QF	Dissolved Organic Carbon Quality Flag: WOCE Quality Flags (QF): 1 sample taken; 2 acceptable measurement; 3 Questionable measurement; 4 Bad measurement; 5 not reported; 9 no sample drawn	unitless	flag
DOC_sd	Dissolved Organic Carbon Standard Deviation	micromol carbon/liter (umol C/L)	DOC
TDN	Total Dissolved Nitrogen	micromol nitrogen/liter (umol N/L)	TDN
TDN_QF	Total Dissolved Nitrogen Quality Flag: WOCE Quality Flags (QF): 1 sample taken; 2 acceptable measurement; 3 Questionable measurement; 4 Bad measurement; 5 not reported; 9 no sample drawn	unitless	flag
TDN_sd	Total Dissolved Nitrogen Standard Deviation	micromol nitrogen/liter (umol N/L)	TDN
BactProd	Bacterial Production by 3H Leu uptake (Smith & Azam; 1992)	picomol Leucine/liter/hour (pmol Leu /L/h)	leuc_incorp
BactProd_QF	Bacterial Production Quality Flag:WOCE Quality Flags (QF): 1 sample taken; 2 acceptable measurement; 3 Questionable measurement; 4 Bad measurement; 5 not reported; 9 no sample drawn	unitless	flag
BactProd_sd	Bacterial Production Standard Deviation	picomol Leucine/liter/hour (pmol Leu /L/h)	leuc_incorp
BactAbund	Bacterial abundance by epifluorescent microscopy and flow cytometry (Porter & Feig,1980; Halewood et al, 1980)	10^8 cells/liter (E8 cells/L)	bact_abund
BactAbund_QF	Bacterial Abundance; Quality Flag: 1 sample taken; 2 acceptable measurement; 3 Questionable measurement; 4 Bad measurement; 5 not reported; 9 no sample drawn	unitless	flag
BactAbund_sd	Bacterial Standard Deviation	10^8 cells/liter (E8 cells/L)	bact_abund
TDAA	Total Dissolved Amino Acids by High performance liquid chromatography (HPLC) (Liu et al; 2020)	nanomolar (nM)	amino_conc
TDAA_QF	Total Dissolved Amino Acids Quality Flag: 1 sample taken; 2 acceptable measurement; 3 Questionable measurement; 4 Bad measurement; 5 not reported; 9 no sample drawn	unitless	flag
TDAA_sd	Total Dissolved Amino Acids Standard Deviation	nanomolar (nM)	amino_conc
Asp	Aspartic Acid concentration by High performance liquid chromatography (HPLC) (Liu et al; 2020)	nanomolar (nM)	amino_conc
Glu	Glutamic Acid concentration by High performance liquid chromatography (HPLC) (Liu et al; 2020)	nanomolar (nM)	amino_conc
His	Histadine concentration by High performance liquid chromatography (HPLC) (Liu et al; 2020)	nanomolar (nM)	amino_conc
Ser	Serine concentration by High performance liquid chromatography (HPLC) (Liu et al; 2020)	nanomolar (nM)	amino_conc
Arg	Arginine concentration by High performance liquid chromatography (HPLC) (Liu et al; 2020)	nanomolar (nM)	amino_conc
Thr	Threonine concentration by High performance liquid chromatography (HPLC) (Liu et al; 2020)	nanomolar (nM)	amino_conc
Gly	Glycine concentration by High performance liquid chromatography (HPLC) (Liu et al; 2020)	nanomolar (nM)	amino_conc
Tau	Taurine concentration by High performance liquid chromatography (HPLC) (Liu et al; 2020)	nanomolar (nM)	amino_conc
Bala	Beta-alanine concentration by High performance liquid chromatography (HPLC) (Liu et al; 2020)	nanomolar (nM)	amino_conc
Tyr	Tyrosine concentration by High performance liquid chromatography (HPLC) (Liu et al; 2020)	nanomolar (nM)	amino_conc
Ala	Alanine concentration by High performance liquid chromatography (HPLC) (Liu et al; 2020)	nanomolar (nM)	amino_conc
GABA	Gamma-aminobutyric acid concentration by High performance liquid chromatography (HPLC) (Liu et al; 2020)	nanomolar (nM)	amino_conc
Met	Methionine concentration by High performance liquid chromatography (HPLC) (Liu et al; 2020)	nanomolar (nM)	amino_conc
Val	Valine concentration by High performance liquid chromatography (HPLC) (Liu et al; 2020)	nanomolar (nM)	amino_conc
Phe	Phyenylalanine concentration by High performance liquid chromatography (HPLC) (Liu et al; 2020)	nanomolar (nM)	amino_conc
Ile	Isoleucine concentration by High performance liquid chromatography (HPLC) (Liu et al; 2020)	nanomolar (nM)	amino_conc
Leu	Leucine concentration by High performance liquid chromatography (HPLC) (Liu et al; 2020)	nanomolar (nM)	amino_conc
Lys	Lysine by concentration High performance liquid chromatography (HPLC) (Liu et al; 2020)	nanomolar (nM)	amino_conc
file_name	All cruise data tables were combined into one table. This is the original file name.	unitless	file_name

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Dataset: Biogeochemical survey 2015-2018