Dataset: bottle_samples_PS

 dates:           14 February 2002 to 21 February 2002  (20020214-20020221)
 location:        N: -65.23  S: -66.59  W: -173.00  E: -170.53 
 project/cruise:  SOFeX/USCGC Polar Star (WAGB-10) cruise: PS02
 platform:        USCGC Polar Star


Methodology

SOFeX 2002 Polar Star cruise
PI notes for all water sample bottle data

13 February 2007: Prepared for OCB data system by Cyndy Chandler, OCB DMO (WHOI).
Contact: Ken Buesseler (WHOI) with any questions pertaining to this dataset.

Bottle sample data included in Master Water File:
SF6/DOC/DIC/pCO2/23Th/HPLC/bSi/salinity/nutrients/Chl/phyto/bacteria

Original Excel file downloaded from MBARI:
copy of original Excel file

All Polar Star data are preliminary & comparisons to other cruises should be made
with caution until final QC and intercalibration work are completed.
For further inquiries contact Ken Buesseler (kbuesseler@whoi.edu)

The original Excel file contained multiple spreadsheets:
The Master Water File includes sample information for all water samples
collected underway and from casts as well as associated nutrient, SF6, FRRf,
chlorophyll, TCO2, TA and CTD data. This data set was updated 12/3/02 with nutrient
values rerun at MBARI. All original nutrient values were deleted (KJ).

Sampling and analysis methods for many of the data types are described in a SOFeX
'cruise report' contributed in April 2002 by Bob Bidigare and converted to a href="http://ocb.whoi.edu/SOFeX/PI-NOTES/SOFeX_Cruise_Report_UH_MIT.pdf">PDF file. Sampling methods described in
the cruise report are listed in the table below.

Publications associated with this dataset

Buesseler, K.O., J.E. Andrews, S. Pike, M.A. Charette, L.E. Goldson, M.A. Brzezinski
and V.P. Lance (2005). Particle export during the Southern Ocean Iron Experiment (SOFeX).
Limnology and Oceanography, 50: 311-327. [ PDF ]

Notes regarding this dataset:

chlorophyll

One complexity with the Polar Star chlorophyll data is that chlorophyll was measured on board (Turner fluorometer);
Dick Barber's group measured chlorophyll in the lab (reported in the larger bottle file, with size fractionated data too)
and there are some HPLC pigment data, which also result in a measure of HPLC derived total Chl-a. Users of
this dataset are encouraged to read the documentation carefully to ascertain which analysis technique was used to estimate
chlorophyll values.

notes pertaining to chlorophyll (A. Hilting)
1. Peter Croot calibrated the fluorometer on the Polar Star with a one-point calibration using a chla standard made on board ship from a powder. The concentration of the standard can not be verified. The calibration assumes constant extraction volumes (8 ml) and filtration volumes (500 ml). Contact R. Barber or P. Croot for calibration equations.

2. Unless the volumes vary, Fo and Fa can be read directly from the fluorometer.

3. The edited spreadsheets correct for variation in filtration volumes (extraction volume does not appear to vary).

4. Chl-a is calculated as (Fo-Fa)1.909. 1.909 is = (r/r-1) where r is the before to after acidification ratio specific to Duke's Turner 10-AU fluorometer (The fluorometer used on the Melville during SOFeX) and r = 2.1. Polar Star used a Turner 10-AU fluorometer. The equation is from EPA Method 445.0 (Revision 1.2), In Vitro Determination of Chlorophyll a and Pheophytin a in Marine and Freshwater Algae by Fluorescence. (Arar and Collins, September 1997). The equations [chl a] = [r/(r-1)(Fo-Fa)]v/V and [phaeophytin a] = [(r/(r-1)(rFa-Fo)]v/V.

5. Phaeophytin is calculated as (2.1Fa-Fo)1.909

6. Unspecified (not logged) filter sizes are assumed to be GF/F and unspecified filtration volumes
are assumed to be 500 ml.

7. CH Stations and Underway grid samples 28 A-I are settling column experiments samples. See Ed Abraham for methods.

8. Bottle Cast two values are not included in the merged file. We are not sure which bottles the samples came from.

9. The size fractionation used a stacked set of funnels, with the water draining through the set by gravity, except for the lowermost 0.2 um filter,which was attached to a vacuum pump. (Size (Size Fractions: 0.22 mm, 2 mm, 5 mm, 20 mm). Note that this method differs from the methods used on the Melville and the Revelle.

10. GF/Fs were filtered separately on a 25 mm rig.

11. Per K. Buesseler, the sea surface water intake was 6 meters or less. We have assumed a actual depth of 6 meters for all underway samples.

12. A more detailed version is available. Contact K. Buesseler or R. Barber for more information.

FRRF estimation of chlorophyll

The shipboard surface/underway sampling system used a Fast Repetition Rate Fluorometer (FRRF) as another way
to determine chlorophyll concentration in the surface waters. The change in the quantum yield of chlorophyll
fluorescence induced by actinic light is used to derive photosynthetic parameters related to
Photosystem II (PS II). The functional (i.e., the photochemically effective) absorption cross-section of
PS II (Sigma PS II) describes the maximal efficiency of light utilization for photochemistry in PS II in units
of angstrom^2/quanta. The FRRF measures fluorescence transients induced by a series of brief subsaturating excitation
pulses, or `flashlets,' where the intensity, duration, and interval between them is independently controlled (Kolber et al., 1998).

For an in depth explanation of techniques used for determining FRRF results (including equations), please see the
complete reference:
Kolber, Z.S., O. Prasil, and P.G. Falkowski. 1998. Measurements of variable chlorophyll
fluorescence using fast repetition rate techniques: defining methodology and
experimental protocols. Biochimica et Biophysica Acta (BBA) - Bioenergetics, 1367(1-3), pgs. 88-106. [ ScienceDirect href="http://www.sciencedirect.com/science/article/B6T1S-3V3M4TP-3/2/672f628df257260fe72a2fef612d26d8">PDF
or DOI: doi:10.1016/S0005-2728(98)00135-2 ]

SF6 data

Surface & Transect data: see worksheet "underwaySF6" for complete SF6 dataset
SF6 still considered preliminary as of Feb 2007 version of .xls merged file

Notes extracted from Excel comments

this information was extracted from comments embedded within the Excel worksheet data cells
(organized here by data parameter name)

station
T1: 5 stations with subsurface sampling using 10L Niskin on Kevlarsurface SF6 
    per usual "W to E" Transect
T2: is A. Hilting satellite image transect

cast or sample comments:
T2: Th I and J do not correspond to chl I and J
uw grid 3: ahilting: Station number of the 5 um SF changed from uwg 5 to uwg 3. Date & time matched other uwg 3 stations.
uw grid 4: ahilting: no station number logged. Uw station 4 assumed from date & time logged.
uw grid 7: ahilting:  station for 20 SF changed from uwg 2 to uwg 7. Date & time matched other uwg7 stations.
SC28 *: ahilting: Ed Abraham's settling column experiment. Size Fraction, volume extracted from E. Abraham.


depth: 
BC: see comments in BC methods .html
T1: 25 m sample depth is an estimate from 'wire out' 

SiO4
Johnson: MBARI VALUES
Selected Polar Star nutrients were reanalyzed at MBARI.  
All of the original values are deleted and only the rerun values are listed here.

fluor_chl
R200: ahilting: u/w fluor logged under 20 SF

GFF CHl Rep1
R259: ahilting: not in SI transect 2 worksheet. Found in Uw_all worksheet
R279: ahilting:0.27 was reported as 5 um. GF/F was not reported. There were two 5 um values. Assumed error.

several Total HPLC Chls (mg/l) observations are mean values:
station	depth
BC6	38.5
CTD5	19.6
CTD6	10.2
CTD6	35.4
CTD6	80.2 

PI notes (embedded comments from the Excel column named: orign sample # or comments)

comments:  
B1	68.0	4 10L bottles on Kevlar w/WHOI pressure & T logger on deepest bottleshallow bottle did not 
		tripSample for SF6, DOC, DIC, salts, nuts, chl, FRRF, 234Th
B2	125.0	6 10L bottles on Kevlar w/WHOI pressure & T logger on deepest bottleSample for 
		SF6, DIC, salts, nuts, chl, FRRF, settle, 234Th, bacteria
CTD2	5.2	ahilting:IN PATCH "shoulder?"24 x 10 L bottlesTransmission, Flu, & CTD1st In patch station w/Melville
		Sample for SF6, DOC, DIC, salts, nuts, chla, HPLC, 234Th, POC, 15N, 13C, 3H, DNA, bSi (0.6 um), 
		phyto (lugols)CTD to 250m, 1st bottle at 150m
B3	119.0	6 10L bottles on Kevlar w/Polar Star CTD logger on end of line (20m below last bottle)
		Sample for SF6, DOC, DIC, salts, nuts, chl, FRRF, bSi, HPLC, 234Th
B4	132.4	OUT STATION "low chl". 6 10L bottles on Kevlar w/Polar Star CTD logger & Flu senso on end of line 
		(20m below last bottle) Sample for SF6, DOC, DIC, salts, nuts, 234Th, Chl, HPLC, bSi, phyto (lugols)
B5	106.6	OUT STATION "high chl"6 10L bottles on Kevlar w/Polar Star CTD logger & Flu senso on end of line 
		(20m below last bottle) Sample for SF6, DOC, DIC, sals, nuts, 23Th, Chl, HPLC, bSi, phyto (lugols), bacteria
B6	118.5	OUT STATION "NW station"6 10L bottles on Kevlar w/Polar Star CTD logger & Flu senso on end of line 
		(20m below last bottle) Sample for SF6, DOC, DIC, salts, nuts, 234Th, Chl, HPLC, bSi, phyto (lugols), 
		15N, 13C, bacteria
CTD4	9.7	ahilting:IN PATCH "deep cast"24 x 10 L bottlesTransmission, Flu, & CTD
		Sample for SF6, DOC, DIC, salts, nuts, chla, AP, bSi (0.6 um) , phyto (lugols), settling, 
		234Th, 15N, 13C, bacteria, DNA, CTD to 500m, 1st bottle at 500m
CTD4	30.2	bottle 19 and 15: nutrients from Nis 19 & 15 both labeled 15; so could be switched
CTD5	9.3	OUT STN "east"24 x 10 L btlsTrans., Flu, & CTD Sample for SF6, DIC, salts, nuts, chla-SF, AP, bSi (1um), 
		phyto (lugols), settling, HPLC, 234Th, 15N, 13C, bacteria, DNA, CTD to 250m, 1st btl at 150m subsurface 
		chl max @ 50-60mswitch to 1.0 nucleopores for this cast & all later bSi on cruise
CTD6	4.9	ahilting:IN PATCH "last call station"24 x 10 L bottlesTransmission, Flu, & CTD
		Sample for SF6, DOC, DIC, salts, nuts, chla, AP, bSi (1um), phyto (lugols), CTD to 250m, 
		1st bottle at 150muse 1.0um for bSi    

In addition, this information from email exchanges (August 2002) between Ann Hilting (Duke University
NSEES Marine Laboratory) and Edward Abraham (National Institute of Water and Atmospheric Research, New Zealand) may be useful.

Underway grid, Samples 28, A-I had no filter size associated with them originally.
Per Chrissy's instructions, they should be GF/F samples but I think it is likely that
they are from different sized filters.

I gathered as much information as I could for each sample. For underway stations,
I used time and date to get location and other information from the underway files.
For the bottle and CTD stations, I gathered data from bottle and CTD summary files.
The spreadsheet "merged all chl values" contains all of the gathered information.
We will select parameters from this spreadsheet for the file that will be distributed.

Because I am not sure of the time and date of the CH stations (and thus the location),
I have not yet included them in the merged spreadsheet ("merged all chl values"). Because
I am not sure of the filter size for Samples 28, A-I, I have not entered the calculated (GF/F)
chlorophyll values in the merged spreadsheet. I am also not including chlorophyll data for
bottle cast two because we are not sure which bottles or depths the samples came from.

Remaining issues to be resolved:

Need correct time and date for the CH stations?
Need filter sizes for underway grid sample 28 A-I?
Need confirmation that these are the only Settling Column samples included in the spreadsheets?
Which rig was used for the GF/Fs and were the GF/F filters 47 mm?

Edward Abraham noted that the fluorometric chl's were on the low side compared
with those observed on the Revelle.

The settling column sample numbers were all samples that began with the prefix SC. They were experimental
treatments put into a darkened, still, column to let the phytoplankton settle before sampling
out of the top and the bottom after 2 hours. The concentrations will therefore vary relative to what
was in the original sample, and this reflects phytoplankton sinking (and floating).
Although they won't be of use to other people, they may as well be left on the master sheet so that the
same calibration can be applied to all the data.