[Directory] [Data...]

Biology 

Data Object Biology
contact PIs:
name        title
Dr David M. Nelson         Co-Principal Investigator
Dr Nick Bates         Co-Principal Investigator
Dr Anthony Knap         Co-Principal Investigator
Dr Michael W. Lomas         Principal Investigator
Dr Michael W. Lomas         Contact
Dr Fredric Lipschultz         Co-Principal Investigator

Dataset description

New Production - Biology Data

Acquisition description

Detailed methods for all data collected as part of this study can be found in one of the three
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. Next, data were plotted as depth profiles and compared to a quality control window
for the February/March period at BATS. The QC window consisted of the upper and lower 95% confidence
limits based upon all data collected at BATS during February/March from 1989-2005. If our data
fell well within these bounds it was considered ‘acceptable’. For those data that fell near or
outside the QC window, we went back to the original data run to ensure there was no miscalculation
or other error. 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 extremes 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, dissolved inorganic
and organic carbon). 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 <10-15% 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.

References:
Detailed information on phytoplankton analysis.
Lomas, M.W., Roberts, N., Lipschultz, F., Krause, J.W., Nelson, D.M., and Bates, N.R. 2009.
Biogeochemical responses to late-winter storms in the Sargasso Sea. IV. Rapid succession of
major phytoplankton groups.
Deep Sea Research I, 56: 892-909.
doi:10.1016/j.dsr.2009.03.004

Detailed information on all silica cycle measurements.
Krause, J.W., Nelson, D.M., and Lomas, M.W. 2009. Biogeochemical responses to late-winter
storms in the Sargasso Sea. 2009. II. Increased rates of biogenic silica production and export.
Deep Sea Research I, 56: 861-875.
doi:10.1016/j.dsr.2009.01.002

Maiti, K., Benitez-Nelson, C.R., Lomas, M.W., and Krause, J. W. 2009. Biogeochemical responses
to late-winter storms in the Sargasso Sea. IV. Comparison of Export Production by 234Th and
Sediment Traps.
Deep Sea Research I, 56: 875-892.
doi:10.1016/j.dsr.2009.01.008

Detailed information on general biogeochemical measurements.
Lomas, M.W., Lipschultz, F., Nelson, D.M., and Bates, N.R. 2009. Biogeochemical responses
to late-winter storms in the Sargasso Sea. I. Pulses of new and primary production.
Deep Sea Research I, 56: 843-861.
doi:10.1016/j.dsr.2008.09.002

Processing description

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 shortly before each cruise,
however, most sensor data were ‘calibrated’ using data collected in this project. 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 save 1,
regression statistics were very strong and linear, and represent an offset (y-intercept) and drop in
sensitivity (slope of the regression). 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. OCE399-3 had a problem
with the dissolved oxygen sensor that could not be resolved so only manual oxygen data are reported for
that cruise.

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 1.5nM for nitrate and nitrite
using a standard autoanalyzer with a 1m fiber optic flow cell, ~20nM for phosphate on a standard autoanalyzer,
and <100nM for Si(OH)4 by manual analysis and a 10cm cuvette. Samples below the MDL are reported as calculated
for the reason that they somewhere between the MDL and a true zero; we consider listing them as either to be
incorrect. Carbon productivity rate measurements, particularly at the base of the euphotic or below, on
occasion are negative due to subtraction of the dark incubated sample from the light incubated sample.
This was not considered below the MDL because there is a reasonable explanation for negative values.
These measurements were ~14h deployments and it is possible that at very low light there can be less 14C
in the light bottles due to grazing, than in the dark bottles that are subtracted from the light bottles.
Moreover, light and dark respiration rates are not the same and therefore this correction is not a perfect
correction for inherent respiration by the autotrophs.

BCO-DMO Edits
- Parameter names modified to conform to BCO-DMO convention
- CruiseId, date, time, lat, lon added from event log
- NOTE: OC408-2 Station 62 is CTD Out date, time, lat, lon (no posit for CTD In)
- OC408-2, Station 67 latitude corrected from 13 to 31 degs

Field Names List

ParameterDescriptionUnits
CruiseIdCruise Idtext
stationCTD drop numberinteger
datedate operation occurred (GMT)YYYYMMDD
timetime operation occurred (GMT)HHMM
lonLongitude position (West is negative)decimal degrees
latLatitude position (South is negative)decimal degrees
NiskinNiskin bottle numberinteger
depthdepth where Niskin was firedmeters
Fluor_ChlCTD Chlorophyll ananograms/liter
FCM_SynechoFlowcytometer Synechococcus countscells/milliliter
FCM_ProchloroFlowcytometer Prochlorococcus countscells/milliliter
FCM_PicoeuksFlowcytometer Picoeukaryote countscells/milliliter
FCM_gt_3umEuksFlowcytometer >3um Eukaryote countscells/milliliter
Chl_c3HPLC Chlorophyll c3nanograms/liter
Chl_c2HPLC Chlorophyll c2nanograms/liter
Chl_c1HPLC Chlorophyll c1nanograms/liter
Chlide_aHPLC Chlorophyllide ananograms/liter
Phide_aHPLC Phaeophorbidenanograms/liter
PeridHPLC Peridininnanograms/liter
Butan_fucoxHPLC 19-Butanoyloxyfucoxanthinnanograms/liter
FucoHPLC Fucoxanthinnanograms/liter
NeoHPLC Neoxanthinnanograms/liter
PrasHPLC Prasinoxanthinnanograms/liter
ViolaHPLC Violaxanthinnanograms/liter
Hex_fucoHPLC 19-Hexanoyloxyfucoxanthinnanograms/liter
DiadinoHPLC Diadinoxanthinnanograms/liter
AlloHPLC Alloxanthinnanograms/liter
DiatoHPLC Diatoxanthinnanograms/liter
ZeaHPLC Zeaxanthinnanograms/liter
LutHPLC Luteinnanograms/liter
Gyr_diesterHPLC Gyrodinium diesternanograms/liter
Chl_bHPLC Chlorophyll bnanograms/liter
DV_chl_aHPLC Divinyl Chlorophyll ananograms/liter
Chl_aHPLC Chlorophyll ananograms/liter
Phytin_aHPLC Phaeophytinnanograms/liter
CaroHPLC a+b Carotenenanograms/liter
TChl_aHPLC Chlorophyll a + Divinyl Chlorophyll ananograms/liter

Platforms List

R/V Oceanus OC399-3 R/V Oceanus OC408-1 R/V Oceanus OC408-2

Instruments List

  1. CTD Seabird 911:

    SBE 911+ Deck Unit and CTD Rosette

This document is created from the content of the BCO-DMO metadata database.    2010-02-09  15:34:27

info app: /home/bco/dbase-v2 v.100108 CLC
Data URL: http://data.bco-dmo.org/jg/serv/BCO/NewProduction/Biology.