Dataset: Bottle Data
Deployment: SJ0609

CTD Bottle Data

Principal Investigator:

Jonathan P. Zehr (University of California-Santa Cruz, UCSC)

Co-Principal Investigator:

Matthew J. Church (University of Hawaii at Manoa, SOEST)

Joseph Montoya (Georgia Institute of Technology, GA Tech)

BCO-DMO Data Manager:

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

Project:

Biology and Ecology of Newly Discovered Diazotrophs in the Open Ocean (DIAZOTROPHS)

Current State:

Final no updates expected

Version:

12Nov2009

Version Date:

2009-11-12

Data URL:

https://www.bco-dmo.org/dataset-deployment/452926/data

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Description

DIAZOTROPHS - CTD bottle data
These data were collected as part of a study of the diversity and
activity of nitrogen-fixing organisms in oligotrophic waters.

Methods & Sampling

Dataset acquisition description

See Platform deployments for cruise specific documentation

Deployment-specific acquisition description

* Sea-Bird SBE 9 Data File:
* FileName = C:CTD_2006MontoyaSJ0609_003-01.dat
* Software Version Seasave Win32 V 5.30b
* Temperature SN = 2462
* Conductivity SN = 1851
* Number of Bytes Per Scan = 44
* Number of Voltage Words = 5
* Number of Scans Averaged by the Deck Unit = 1
* Append System Time to Every Scan
* System UpLoad Time = Jun 27 2006 17:46:38
* NMEA Latitude = 12 15.42 N
* NMEA Longitude = 056 08.75 W
* NMEA UTC (Time) = Jun 27 2006 17:46:31
* Store Lat/Lon Data = Append to Every Scan
** Ship: RVSJ
** Cruise: RV0609
** Station: 003.01
** Latitude:
** Longitude:
# nquan = 18
# nvalues = 2001
# units = specified
# name 0 = prDM: Pressure, Digiquartz [db]
# name 1 = t090C: Temperature [ITS-90, deg C]
# name 2 = t190C: Temperature, 2 [ITS-90, deg C]
# name 3 = c0S/m: Conductivity [S/m]
# name 4 = c1S/m: Conductivity, 2 [S/m]
# name 5 = sbeox0V: Oxygen Voltage, SBE 43
# name 6 = par: PAR/Irradiance, Biospherical/Licor
# name 7 = flSP: Fluorescence, Seapoint
# name 8 = spar: SPAR/Surface Irradiance
# name 9 = xmiss: Beam Transmission, Chelsea/Seatech/Wetlab CStar [%]
# name 10 = depSM: Depth [salt water, m], lat = 12.257
# name 11 = sal00: Salinity [PSU]
# name 12 = sal11: Salinity, 2 [PSU]
# name 13 = density00: Density [density, Kg/m^3]
# name 14 = sigma-t00: Density [sigma-t, Kg/m^3 ]
# name 15 = sbeox0Mm/Kg: Oxygen, SBE 43 [umol/Kg], WS = 2
# name 16 = sbeox0PS: Oxygen, SBE 43 [% saturation], WS = 2
# name 17 = flag: flag
# span 0 = 4.023, 2025.307
# span 1 = 3.4898, 28.4555
# span 2 = 3.4888, 28.4552
# span 3 = 3.294679, 5.739951
# span 4 = 3.416995, 5.953153
# span 5 = 1.3257, 2.7303
# span 6 = 4.5700e-01, 4.5700e-01
# span 7 = 5.0092e-02, 4.0023e-01
# span 8 = 6.2045e+01, 3.3034e+02
# span 9 = 123.5789, 126.3601
# span 10 = 4.000, 2004.000
# span 11 = 31.7058, 36.8765
# span 12 = 33.0329, 38.4291
# span 13 = 1019.7891, 1037.0679
# span 14 = 19.7719, 27.8131
# span 15 = 115.612, 245.998
# span 16 = 39.85958, 95.55322
# span 17 = 0.0000e+00, 0.0000e+00
# interval = meters: 1
# start_time = Jun 27 2006 17:46:38
# bad_flag = -9.990e-29
# sensor 0 = Frequency 0 temperature, primary, 2462, 05 April 06
# sensor 1 = Frequency 1 conductivity, primary, 1851, 12 April 06, cpcor = -9.5700e-08
# sensor 2 = Frequency 2 pressure, 0468, 21 Dec 04
# sensor 3 = Frequency 3 temperature, secondary, 2146, 5 April 06
# sensor 4 = Frequency 4 conductivity, secondary, 2171, 12 April 06, cpcor = -9.5700e-08
# sensor 5 = Extrnl Volt 2 Oxygen, SBE, primary, 0556, 12 April 06
# sensor 6 = Extrnl Volt 4 altimeter
# sensor 7 = Extrnl Volt 5 irradiance (PAR), primary, 4661, 19 April 06
# sensor 8 = Extrnl Volt 6 Fluorometer, Seapoint, primary
# sensor 9 = Extrnl Volt 7 transmissometer, primary, CST-487DR, 27 April 06
# sensor 10 = Extrnl Volt 9 surface irradiance (SPAR), degrees = 0.0
# datcnv_date = Jun 28 2006 06:21:59, 5.37e
# datcnv_in = C:CTDCTDRawsj0609_003-01.dat C:CTDCTDRawsj0609_003-01.CON
# datcnv_skipover = 0
# filter_date = Jun 28 2006 06:22:48, 5.37e
# filter_in = C:CTDCTDRawsj0609_003-01.cnv
# filter_low_pass_tc_A = 0.030
# filter_low_pass_tc_B = 0.150
# filter_low_pass_A_vars = xmiss
# filter_low_pass_B_vars = prDM
# alignctd_date = Jun 28 2006 06:24:07, 5.37e
# alignctd_in = C:CTDCTDRawsj0609_003-01.cnv
# alignctd_adv = c0S/m -0.010, sbeox0V 5.000
# celltm_date = Jun 28 2006 06:25:11, 5.37e
# celltm_in = C:CTDCTDRawsj0609_003-01.cnv
# celltm_alpha = 0.0300, 0.0300
# celltm_tau = 7.0000, 7.0000
# celltm_temp_sensor_use_for_cond = primary, secondary
# loopedit_date = Jun 28 2006 06:25:51, 5.37e
# loopedit_in = C:CTDCTDRawsj0609_003-01.cnv
# loopedit_minVelocity = 0.250
# loopedit_surfaceSoak: do not remove
# loopedit_excl_bad_scans = yes
# Derive_date = Jun 28 2006 06:26:44, 5.37e
# Derive_in = C:CTDCTDRawsj0609_003-01.cnv C:CTDCTDRawsj0609_003-01.CON
# derive_time_window_docdt = seconds: 2
# binavg_date = Jun 28 2006 06:28:00, 5.37e
# binavg_in = C:CTDCTDRawsj0609_003-01.cnv
# binavg_bintype = meters
# binavg_binsize = 1
# binavg_excl_bad_scans = yes
# binavg_skipover = 0
# binavg_surface_bin = yes, min = 0.000, max = 1.000, value = 0.000
# file_type = ascii
*END*

Data Processing Description

Dataset Processing Description

BCO-DMO Processing Notes
Generated from original files contributed to BCO-DMO as zipped data/docs files by Joseph Montoya

BCO-DMO Edits
- Date formatted to YYYYMMDD
- Time formatted to HHMM
- Parameter names modified to conform to BCO-DMO convention
- Duplicate date column deleted
- empty cells filled with 'nd' (no data)
- 'trans' parameter added to KM0703 data set with 'nd' for data values
- Data values padded to consistent decimal places

Deployment-specific processing description

Data Processsing Notes 
Seabird Data Processing v 5.37e was used to post-process the raw data files from KM0703. 
File names have the basic format, km0703_xxx-yy.*, which reflects the station number (xxx) and 
event number (yy) of the cast, and the file type. For example, km0703_011-01.hex is the raw 
data file for hydrocast 011.01 (the first event at station 011). 
This directory contains binned ascii files (*.asc), bottle files (*.btl), binned binary files 
(*.cnv), and header files (*.hdr) for each cast. The data processing routines and parameters used 
are listed below in order of application. 
datcnv 
Produce *.ros bottle summary files. Derive depth, salinity, density & O2 for the rosette summary. 
rossum 
Produce bottle files (*.btl). 
datcnv 
Produce *.cnv cast files for further processing. 
filter 
Filter pressure with a time constant of 0.15 seconds. 
align 
Optimal alignments found iteratively by inspection of S&permil; spikes at sharp T°C gradients. 
Advanced primary conductivity by +0.020 seconds 
Advanced secondary conductivity by 0.00 seconds. 
Optimal O2 advance found iteratively by inspection of O2 vs T°C plot of up/down casts. 
Advanced O2 voltage by 5 seconds. 
celltm 
Processed using default values of alpha = 0.03 and 1/beta = 7 to correct both primary and 
secondary conductivity values using corresponding temperature sensors. 
loopedit 
Filter data using fixed minimum velocity of 0.25 m/s. Remove initial surface soak (10 m) 
derive 
Calculate depth, salinity, density, [O2], potential T. 
binavg 
Average downcast into 1 m bins. Append "_bin" to raw file name. 
asciiout 
Translate to ascii data file (*.asc) , strip the header info and save it as a separate file (*.hdr).

More information about this dataset deployment

Funding

Award Number	Funding Source
OCE-0425363	NSF Division of Ocean Sciences
OCE-0425583	NSF Division of Ocean Sciences
unknown DIAZOTROPHS Moore	Gordon and Betty Moore Foundation

Instruments

CTD Sea-Bird 911

Supplied Name: CTD Seabird 911

Supplied Description:

CTD-rosette

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.

Fluorometer

Supplied Description:

Seapoint

Instrument Type

Generic Name: Fluorometer

Community Identifier: http://vocab.nerc.ac.uk/collection/L05/current/113/

Generic 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.

Niskin bottle

Supplied Name: Niskin Bottle

Supplied Description:

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.

Nutrient Autoanalyzer

Supplied Name: Nutrient Analyzer

Supplied Description:

Lachat Quikchem 8000 FIA system (nutrients)

Instrument Type

Generic Name: Nutrient Autoanalyzer

Community Identifier: http://vocab.nerc.ac.uk/collection/L05/current/LAB04/

Generic Description:

Nutrient Autoanalyzer is a generic term used when specific type, make and model were not specified. In general, a Nutrient Autoanalyzer is an automated flow-thru system for doing nutrient analysis (nitrate, ammonium, orthophosphate, and silicate) on seawater samples.

Sea-Bird SBE 43 Dissolved Oxygen Sensor

Supplied Name: CTD Seabird SBE 43

Supplied Description:

Instrument Type

Generic Name: Sea-Bird SBE 43 Dissolved Oxygen Sensor

Acronym: SBE-43 DO

Community Identifier: http://vocab.nerc.ac.uk/collection/L22/current/TOOL0036/

Generic Description:

The Sea-Bird SBE 43 dissolved oxygen sensor is a redesign of the Clark polarographic membrane type of dissolved oxygen sensors. more information from Sea-Bird Electronics

Parameters

Supplied Name	Supplied description	Supplied Units	Standard Name
Cruise	Cruise Id	text	cruiseid
Station	Station Id (Station number.Cast number at station)	nn.xx	station
depth	depth	meters	depth
bot	bottle number	integer	bot
date	date sampling began	YYYYMMDD	date
time	time sampling began	hhmm	time
lon	longitude; negative denotes West	decimal degrees	lon
lat	latitude; negative denotes South	decimal degrees	lat
press	pressure; from CTD	decibars	press
temp	temperature; from CTD; ITS-90	degrees Celsius	temp
sal	salinity; from CTD; PSS-78 (PSU)	dimensionless	sal
trans	transmissivity	voltage	trans
Density	Density	kg/m3	density
SigmaT	SigmaT	unitless	sigma_t
fluor	fluorescence; uncalibrated	voltage	fluor
O2	oxygen; dissolved from SBE 43	umol/kg	O2
O2_satP	oxygen saturation (percentage)	percent	O2sat
Nutrient_Sample_ID	Nutrient Sample ID	text	sample
PO4	phosphate	umol/L	PO4
SiO2	silicate	umol/L	no_bcodmo_term
NO3_NO2	nitrate + nitrite	umol/L	NO3_NO2
NO2	nitrite	umol/L	NO2

Database

Contribute Data

Dataset: Bottle Data
Deployment: SJ0609

Dataset acquisition description

Deployment-specific acquisition description

Dataset Processing Description

Deployment-specific processing description

Database

Contribute Data

Dataset: Bottle DataDeployment: SJ0609

Dataset acquisition description

Deployment-specific acquisition description

Dataset Processing Description

Deployment-specific processing description

Dataset: Bottle Data
Deployment: SJ0609