Dataset: Biogeochemistry
Deployment: X0606

Biogeochemistry Data

Principal Investigator:

Michael W. Lomas (Bermuda Institute of Ocean Sciences, BIOS)

Co-Principal Investigator:

James Ammerman (Sea Grant, SGNY)

Sonya T. Dyhrman (Woods Hole Oceanographic Institution, WHOI)

Contact:

Michael W. Lomas (Bermuda Institute of Ocean Sciences, BIOS)

BCO-DMO Data Manager:

Stephen R. Gegg (Woods Hole Oceanographic Institution, WHOI BCO-DMO)

Project:

DOP Utilization in the Sargasso Sea: Quantifying Taxon-specific Rates of Hydrolysis and Uptake (ATP3)

Current State:

Final no updates expected

Version:

06 December 2011

Deployment Synonyms:

ATP3, DOP, AE0606

Version Date:

2011-12-06

Data URL:

https://www.bco-dmo.org/dataset-deployment/453083/data

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Description

DOP Utilization (ATP3, DOP) Biogeochemistry Data
Biogeochemical data collected on transect cruises studying
Dissolved Organic Phosphorus throughout the western Sargasso Sea.
Data are from several cruises over the span 2006 to 2008.

Note the cruise identifiers for the Atlantic Explorer were originally formatted as XYY## (e.g. X0806 was the 6th cruise in 2008). The data files include cruise IDs of this type. The vessel operator changed the cruise ID syntax several years after the cruise and the official cruise ID syntax was changed to AEYY##. For example, AE0810 should be the same cruise as X0810. One exception for this dataset is that X0804 is cruise ID AE0810.

Related files and references:
Detailed information on analyses:
Lomas, M.W., Burke, A., Lomas, D.A., Bell, D.W., Shen, C., Ammerman, J.W., Dyhrman, S.T. 2010.
Sargasso Sea phosphorus biogeochemistry: An important role for dissolved organic phosphorus (DOP).
Biogeosciences 7: 695-710.

Other published work:
Michelou, V.K., Lomas, M.W., Kirchman, D.L. Phosphate and ATP uptake by cyanobacteria and heterotrophic
bacteria in the Sargasso Sea. Limnology and Oceanography, in press.

McLaughlin, K., Sohm, J.A., Cutter, G.A., Lomas, M.W., Paytan, A. 2010. Phosphate cycling in the Sargasso Sea:
Investigation using the oxygen isotopic composition of phosphate, enzyme labeled fluorescence, and turnover times.
Journal of Geophysical Research - Biogeosciences, in press.

Longnecker, K., Lomas, M.W., and Van Mooy, B.A.S. 2010. Characterizing the abundance and diversity of
heterotrophic bacterial cells assimilating phosphate in the sub-tropical North Atlantic Ocean.
Environmental Microbiology, in press.

Orchard, E.D., Ammerman, J.W., Lomas, M.W., Dyhrman, S.T. 2010. Dissolved inorganic and organic phosphorus
uptake in Trichodesmium and the microbial community: The importance of phosphorus ester in the Sargasso Sea.
Limnology and Oceanography, 55:1390-1399.

Casey, J., Lomas, M.W., Michelou, V., Orchard, E.D., Dyhrman, S.T., Ammerman, J.W., and Sylvan, J. 2009.
Phytoplankton taxon-specific orthophosphate (Pi) and ATP uptake in the northwestern Atlantic subtropical gyre.
Aquatic Microbial Ecology, 58:31-44.

Van Mooy, B.A.S., Fredricks, H.F., Pedler, B.F., Dyhrman, S.T., Karl, D.M., Koblizek, M., Lomas, M.W., Moore,
L.R., Moutin, T., Rappé, M.S., and Webb, E.A. 2009. Phytoplankton in the oligotrophic ocean use non-phosphorus lipids in response to phosphorus scarcity. Nature Geosciences, doi:10.1038/nature07659.

Methods & Sampling

Dataset acquisition description

Sampling and Analytical Methodology:
Detailed methods for all data collected as part of this study can be found in the publications
arising from this study (references given below). This contains information on analytical
machines and certified standards where applicable.

Sample QA/QC procedures followed those of the Bermuda Atlantic Time-series Study (BATS).
At the point of collection, any leaking niskin bottles were noted on the master cast sheets
and samples were taken from a different niskin fired at the same depth as the leaking bottle.
No data are reported for leaking Niskin bottles. During sample analysis standard curves
and/or certified standards were carefully examined to ensure that they were consistent with
expectations and accurate. If nothing was found, then we examined other data from that
niskin to see if other samples are in question. If no obvious error or problem was found,
the data were considered OK and in the range of environmental data that this study hoped
to observe.

Sample accuracy and precision:
Sample accuracy was assessed by using certified standards, for those measurements where
standards are available (dissolved oxygen, nutrients, salinity). Certified standards were
run with each analytical run and compared to long term control charts for respective analyses.
Samples were not run until certified standards were shown to be accurate for that analytical
run. Sample precision was determined by analyzing replicate samples (not replicate analyses
on the same sample) and therefore is higher than analytical precision due to the inclusion
of sampling error. At the concentrations observed during this study, sample precision was
<5% for stock measurements and <10% for rate measurements. Some analyses, namely dissolved

oxygen and salinity, were much better and often had a sample precisions <1%. These precision

estimates are consistent with the long term QA/QC seen with the BATS program.

The provided data files are complete matrices and therefore not every sample (columns) will be
taken from every Niskin fired (rows). Data that were either not collected, or were associated
with leaking Niskins, or were found to be in error for other reasons are denoted by "nd" in the
spreadsheets.

Data Processing Description

Dataset Processing Description

Data Processing:
Most of the data given in this dataset are not derived variables and are calculated using
reasonably standard equations as given in the appropriate reference above. The one exception
is CTD data. Raw CTD data were processed using SBE-Data Processing software using configuration
and calibration files provided by the Shipboard Science technician. Sensors were calibrated
every 6 months. Manual determinations of dissolved oxygen, salinity and HPLC Chlorophyll a,
once passing the above QA/QC steps, were taken as correct. CTD sensor data was regressed against
the appropriate manual variable. In all cases, regression statistics were very strong and linear.
CTD data were corrected to manual measurements using the regression data and it is this corrected
data that is given in the associated data files.

Only nutrient analyses were close to analytical method detection limits (MDL). MDLs were estimated
as 3x the standard deviation of the lowest standard used for the analysis and are ~30nM for nitrate
and phosphate using a standard autoanalyzer. We used the MAGIC co-precipitation method for phosphate
which lowered our MDL to ~1.5nM. Samples below the MDL are reported as calculated for the reason
that they are somewhere between the MDL and a true zero; we consider listing them as either to be
incorrect.

BCO-DMO Edits
- Parameter names modified to conform to BCO-DMO convention
- Note: Parameter names starting with 33P_xxx changed to P33_xxx for use within system
- date reformatted to YYYYMMDD
- time reformatted to HHMM
- lat/lon padded to 7 decimal places
- added CruiseId column and combined all BGC data into one dataset
- X0606 station 7 year corrected from 2007 to 2006

- "-9.99" changed to "nd" (no data) for X0804

More information about this dataset deployment

Funding

Award Number	Funding Source
OCE-0453023	NSF Division of Ocean Sciences

Instruments

CTD Sea-Bird 911

Supplied Description:

1.0 CTD

1.1 Seabird Electronics SBE 9/11+ Max Depth is 6800m for all CTD sensors except

Chelsea Fluorometer, Wetlabs Transmissometer and Altimeter which are all

6000m. Aluminum frame holds 24 12 liter water samplers.

1.2 Sensors include Seabird SBE 9/11+, Dual pumped Temperature, conductivity

and Dissolved Oxygen. Chelsea Aquatracka III Flourometer, Wetlabs SeaStar

25cm/660nm Transmissometer, Benthos PSA9000 Altimeter. All data logged with

Seabird Software.

1.3 Water Samplers - 24x12 liter Ocean Test Equipment (OTE) Niskin Water

samplers and 4x10 liter OTE Go-Flo's.

Instrument Type

Generic Name: CTD Sea-Bird 911

Acronym: CTD SBE 911

Community Identifier: http://vocab.nerc.ac.uk/collection/L22/current/TOOL0035/

Generic Description:

The Sea-Bird SBE 911 is a type of CTD instrument package. The SBE 911 includes the SBE 9 Underwater Unit and the SBE 11 Deck Unit (for real-time readout using conductive wire) for deployment from a vessel. The combination of the SBE 9 and SBE 11 is called a SBE 911. The SBE 9 uses Sea-Bird's standard modular temperature and conductivity sensors (SBE 3 and SBE 4). The SBE 9 CTD can be configured with auxiliary sensors to measure other parameters including dissolved oxygen, pH, turbidity, fluorescence, light (PAR), light transmission, etc.). More information from Sea-Bird Electronics.

Niskin bottle

Supplied Name: Niskin Bottle

Supplied Description:

3.0 Water Samplers

3.1 36x12 liter Ocean Test Equipment Niskin sampling bottles; 8x12 liter Go Flo

bottles with 1000 meters Spectra Line

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.

Parameters

Supplied Name	Supplied description	Supplied Units	Standard Name
CruiseId	Cruise Id	text	cruiseid
Station	Station Id	integer	station
Cast	CTD drop number	integer	cast
date	date of operation (GMT)	YYYYMMDD	date
time	time of operation (GMT)	HHMM	time
lon	Longitude position West is negative	decimal degrees	lon
lat	Latitude position South is negative	decimal degrees	lat
Niskin	Niskin bottle number	integer	bottle
Depth	target bottle fire depth	meters	depth
CTD_bottlefire_depth	CTD sensor value when bottle fired; depth	meters	depth
CTD_bottlefire_Temp	CTD sensor value when bottle fired; Temp	oC	temp
CTD_bottlefire_Salinity	CTD sensor value when bottle fired; Salinity	dimensionless	sal
CTD_bottlefire_density	CTD sensor value when bottle fired; density	kg/m3	density
CTD_bottlefire_Fluorometer	CTD sensor value when bottle fired; Fluorometer	rfu	fluor
CTD_bottlefire_DO	CTD sensor value when bottle fired; Dissolved Oxygen	umol/kg	O2
NO3	autoanalyzer nitrate concentration	microM	NO3
NO2	autoanalyzer nitrite concentration	microM	NO2
PO4	autoanalyzer phosphate concentration	microM	PO4
SiOH4	autoanalyzer silicate concentration	microM	Silicate
TDP	manual total dissolved phosphorus concentration	nM	no_bcodmo_term
SRP	manual phosphate (MAGIC method) concentration	nM	no_bcodmo_term
DOP	manual dissolved organic phosphorus concentration by subtraction	nM	DOP
POP	manual particulate organic phosphorus concentration	nmolP/L	no_bcodmo_term
POC	elemental analyzer particulate organic carbon concentration	micromol C/L	POC
PON	elemental analyzer particulate organic nitrogen concentration	micromol N/L	PON
F_Chla	extracted chlorophyll concentration	ng/L	no_bcodmo_term
F_Phaeoph	extracted phaeopigment concentration	ng/L	no_bcodmo_term
Prochloro	Prochlorococcus abundance	cells/ml	coccus_p
Synecho	Synechococcus abundance	cells/ml	coccus_s
P_euks	Pico-eukaryote abundance	cells/ml	no_bcodmo_term
N_euks	Nano-eukaryote abundance	cells/ml	no_bcodmo_term
APA_whole	manual alkaline phosphatase activity	nmol/L/h	APA
P33_PO4_uptake	radiotracer phosphate uptake Note: Original parameter names was 33P_PO4_uptake. Changed to P33 for use within BCO-DMO system.	nmol/L/h	P33_PO4_uptake
P33_PO4_turnover_time	radiotracer phosphate turnover time Note: Original parameter names was 33P_PO4_turnover_time. Changed to P33 for use within BCO-DMO system.	/hr	P33_PO4_turnover_time
P33_PO4_turnover_rate	radiotracer phosphate turnover rate Note: Original parameter names was 33P_PO4_turnover_rate. Changed to P33 for use within BCO-DMO system.	percent/h	P33_PO4_turnover_rate
P33_ATP_uptake	radiotracer Adenosinetriphosphate (ATP) uptake Note: Original parameter names was 33P_ATP_uptake. Changed to P33 for use within BCO-DMO system.	nmol/L/h	P33_ATP_uptake
P33_ATP_turnover_time	radiotracer Adenosinetriphosphate (ATP) turnover time Note: Original parameter names was 33P_ATP_turnover_time. Changed to P33 for use within BCO-DMO system.	/hr	P33_ATP_turnover_time
P33_ATP_turnover_rate	radiotracer Adenosinetriphosphate (ATP) turnover rate Note: Original parameter names was 33P_ATP_turnover_rate. Changed to P33 for use within BCO-DMO system.	percent/h	P33_ATP_turnover_rate

Database

Contribute Data

Dataset: Biogeochemistry
Deployment: X0606

Dataset acquisition description

Dataset Processing Description

Database

Contribute Data

Dataset: BiogeochemistryDeployment: X0606

Dataset acquisition description

Dataset Processing Description

Dataset: Biogeochemistry
Deployment: X0606