In-situ
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& Constituents
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Title: In-situ measurement Protocols:
IOPs and Constituents
Issue: 1.0
Date: March 2013
PAGE: i
In-situ Measurement Protocols.
Part B:
Inherent Optical Properties and in-water constituents
Doc. no:
CO-SCI-ARG-TN-0008
Issue:
Date:
1.0
March 2013
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2013
Ref: CO-SCI-ARG-TN-008
Title: In-situ measurement Protocols:
In-situ
Measurement
Protocols: IOPs
& Constituents
IOPs and Constituents
Issue: 1.0
Date: March 2013
PAGE: ii
Document Signatures
Editor
Verification
Approval
Name
Function
Company
Signature
Date
Kathryn
Barker
Project Manager
ARGANS
March 2013
Jean-Paul
Huot
MVT Coordinator
ESA
March 2013
Philippe
Goryl
Contract Manager,
ESA
ESA
Updates
Issue
Date
1.0
March 2013
Description
Version 1.0 released on MERMAID website
This is a public document, available for download on the MERMAID website:
http://hermes.acri.fr/mermaid/dataproto
Acknowledgement
ESA Contract numbers: 21091/07/I-OL and 21652/08/I-OL respectively.
To all MERIS Validation Team members for their interest in MERMAID and their feedback on the database
and the Protocols document, and to the MERIS QWG who have contributed to the MERIS Third
Reprocessing and provided inputs to this document where appropriate.
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In-situ
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Title: In-situ measurement Protocols:
IOPs and Constituents
Issue: 1.0
Date: March 2013
PAGE: iii
Protocol contributors
NAME
AFFILIATION
S. AHMED
City College of New York, USA
D. ANTOINE
LOV, France
S. Belanger
Univeristé du Québec, Canada
V. BRANDO
CSIRO, Australia
P-Y. DESCHAMPS
LOA, France
R. DOERFFER
HZG, Germany
B. GIBSON
Coastal Studies Institute, LSU, USA
B. HOLBEN
NASA GSFC
A. HOMMERSOM
Water Insight, Netherlands.
J. ICELY
University of Algarve
M. KAHRU
University of California, USA
S. KRATZER
University of Stockholm, Sweden
H. LOISEL; C. JAMET
Universite du Littoral Cote d'Opale, France
D. MCKEE
University of Strathclyde, UK
K. VOSS; M. ONDRUSEK
NOAA
K. RUDDICK
MUMM, Belgium
D. SIEGEL; S. MARITORENA
University of California, Santa Barbara, USA
K. SORENSEN
NIVA
J. WERDELL (on behalf of NOMAD contributors)
NASA/GSFC
G. ZIBORDI
JRC, Italy
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In-situ
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& Constituents
Ref: CO-SCI-ARG-TN-008
Title: In-situ measurement Protocols:
IOPs and Constituents
Issue: 1.0
Date: March 2013
PAGE: iv
Table of Content
1.
2.
Introduction ............................................................................................................................................... 1
1.1
Document purpose and scope ............................................................................................................ 1
1.2
Overview of MERIS Bio-optical products ........................................................................................ 1
1.3
MERMAID ........................................................................................................................................ 2
1.3.1
Data submission and feedback................................................................................................... 2
1.3.2
User login and Password ........................................................................................................... 2
Chlorophyll-a ............................................................................................................................................. 3
2.1
MERMAID and MVT definitions ..................................................................................................... 3
2.2
Site overview ..................................................................................................................................... 4
2.3
HPLC Total Chlorophyll-a ................................................................................................................ 5
2.3.1
Algarve: ..................................................................................................................................... 5
2.3.2
BioOptEurofleets ....................................................................................................................... 6
2.3.3
BOUSSOLE .............................................................................................................................. 6
2.3.4
CASES (Arctic Waters) ............................................................................................................. 7
2.3.5
Helgoland .................................................................................................................................. 7
2.3.6
Plumes and Blooms ................................................................................................................... 7
2.3.7
PortCoast (Portuguese Coast) .................................................................................................... 8
2.3.8
NOMAD .................................................................................................................................... 9
2.3.9
PMLNorthSeaWEC ................................................................................................................. 10
2.4
HPLC Chlorophyll a only ................................................................................................................ 10
2.4.1
Algarve .................................................................................................................................... 10
2.4.2
BSHSummerSurvey................................................................................................................. 11
2.4.3
IFREMER REPHY .................................................................................................................. 11
2.4.4
MUMM.................................................................................................................................... 11
2.4.5
Wadden Sea ............................................................................................................................. 11
2.5
Spectrophotometry .......................................................................................................................... 11
2.5.1
Algarve .................................................................................................................................... 11
2.5.2
Bristol Channel and Irish Sea .................................................................................................. 12
2.5.3
BSHSummerSurvey................................................................................................................. 12
2.5.4
French Guiana and English Channel ....................................................................................... 12
2.5.5
NWBaltic Sea .......................................................................................................................... 12
2.6
Fluorometry ..................................................................................................................................... 13
2.6.1
IFREMER MAREL ................................................................................................................. 13
2.6.2
NOMAD .................................................................................................................................. 13
2.6.3
Plumes and Blooms ................................................................................................................. 13
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In-situ
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2.7
3.
4.
Ref: CO-SCI-ARG-TN-008
Title: In-situ measurement Protocols:
IOPs and Constituents
Issue: 1.0
Date: March 2013
PAGE: v
AERONET-OC: Computed Chla .................................................................................................... 13
Suspended Sediments .............................................................................................................................. 14
3.1
MERMAID and MVT definitions ................................................................................................... 14
3.2
Bristol Channel and Irish Sea .......................................................................................................... 14
3.3
CASES (Arctic Waters) ................................................................................................................... 14
3.4
Helgoland ........................................................................................................................................ 14
3.5
PMLNorthSeaWEC ......................................................................................................................... 15
IOPs ......................................................................................................................................................... 16
4.1
MERMAID and MVT definitions ................................................................................................... 16
4.2
Algarve: Estimates of absorption coefficient for aquatic particles .................................................. 16
4.2.1
Transmission-Reflectance (T-R) measurements of sample particles: measurement in
transmission mode ................................................................................................................................... 17
4.2.2
T-R measurements of sample particles: measurement in reflection mode .............................. 17
4.2.3
T-R measurements of sample particles after chemical oxidation of pigments ........................ 17
4.2.4
Absorption by gelbstoff, ag ...................................................................................................... 18
4.2.5
Spectrophotometric determination of ag .................................................................................. 18
4.3
5.
6.
CASES (Arctic Waters) ................................................................................................................... 19
4.3.1
Plumes and Blooms ................................................................................................................. 20
4.3.2
NOMAD .................................................................................................................................. 21
4.3.3
PMLNorthSeaWEC ................................................................................................................. 24
AOPs ....................................................................................................................................................... 25
5.1
MERMAID and MVT definitions ................................................................................................... 25
5.2
BOUSSOLE .................................................................................................................................... 25
5.3
CaliCurrent ...................................................................................................................................... 25
5.4
CASES ............................................................................................................................................. 26
5.5
NOMAD .......................................................................................................................................... 26
References ............................................................................................................................................... 27
List of Figures
Figure 1-1: MERMAID project website:........................................................................................................... 2
Figure 2-1: Schematic view of the integrating sphere used for the CINTRA dual beam spectrophotometer
used in this study (from Tassan & Ferrari, 2002). ................................................................................ 6
Figure 2-2: Map of 2005-2008 sampling locations for PortCoast dataset ......................................................... 8
Figure 2-3: Map of 2009-2012 sampling locations for PortCoast dataset ......................................................... 9
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In-situ
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& Constituents
Ref: CO-SCI-ARG-TN-008
Title: In-situ measurement Protocols:
IOPs and Constituents
Issue: 1.0
Date: March 2013
PAGE: vi
Figure 2-4: (A) Location of 468 stations sampled from 1998-2003 for the determination of biogeochemical
concentrations and absorption properties. The stations are partitioned into 10 geographic regions;
inverted triangle, Skagerrak; diamond, West Jutland; sideways triangle, NW North Sea; plus, SE
North Sea; cross, German Bight; star, East Anglia UK coast; circles, Dutch coast; dot, Belgium
coast; triangle, Celtic Sea; square, Western English Channel. (B) Location of 61 stations sampled
from 2003-2006 for satellite accuracy assessment. (Tilstone et al., 2012) ....................................... 10
Figure 2-5: Intercomparison of two methods to measure chl a: trichromatic (spectrophotometric) method
from Stockholm University (using GF/F filters, 30 sec sonication and 30 min extraction in 90%
acetone) compared to NIVA’s HPLC method. Data 32 stations in total: 10 samples from MAVT
intercalibration 2 (natural water samples from Norwegian coastal areas in 2002), 4 stations from
Askö 2002, 18 stations from Askö 2008. ........................................................................................... 13
Figure 4-1: Map of spectrophotometric absorption data in NOMAD (Werdell, 2005). .................................. 22
Figure 4-2: Map of backscattering data in NOMAD (Werdell, 2005). ........................................................... 23
List of Tables
Table 2-1: Chla definitions in MERMAID, and available sites providing matchups. ..................................... 3
Table 2-2: Summary of site providing Chla , MERIS product it is comparable to and the PI definitions ........ 4
Table 2-3. Chromatographic parameters used for the identification and quantification of phytoplanktonic
pigments. .............................................................................................................................................. 5
Table 3-1: Suspended sediment definitions in MERMAID, and available sites providing matchups. ........... 14
Table
4-1: IOP definitions in MERMAID, and available sites providing matchups.
* denotes availability at several wavelengths ..................................................................................... 16
Table 5-1: AOP definitions in MERMAID, and available sites providing matchups. .................................... 25
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Ref: CO-SCI-ARG-TN-008
Title: In-situ measurement Protocols:
IOPs and Constituents
Issue: 1.0
Date: March 2013
PAGE: i
List of Symbols
Symbol
Definition
Dimension / units
Wavelength
nm
Solar zenith angle (s = cos(s))
degrees
Satellite or view zenith angle (v = cos(v))
degrees
Geometry (see fig. 2.1)


s

v, 


Refracted view zenith angle ( ’ = sin-1(n.sin(v)))
degrees

π-θ
degrees

Relative azimuth angle between the sun-pixel and

pixel-sensor directions
degrees
Spectral radiance
W m-2 sr-1 nm-1
Radiometric quantities
L(,s,v,)
Inherent Optical Properties (IOPs)
 ( ,  )
~
 ( )
Volume scattering function (VSF)
sr-1
Normalised volume scattering function
sr-1 m-1
Total absorption coefficient for wavelength 
m-1
Pigment absorption coefficient at 442 nm
m-1
b()
Total scattering coefficient for wavelength 
m-1
c()
Attenuation coefficient for wavelength 
m-1
m-1
a()
apig(442)
b b ()
Backscattering coefficient
Apparent Optical Properties (AOPs) and derived quantities
 w(,s,v,)
Water reflectance

Fully normalised water reflectance (i.e. the reflectance
wn()
Eu ( )
Ed()
Es (λ)
dimensionless
if there were no atmosphere, and for s = v = 0)
dimensionless
Upwelling irradiance
W m-2 nm-1
Downwelling irradiance, above the surface
W m-2 nm-1
Total downwelling irradiance just above the sea surface,
W m-2 nm-1
denoted also as Ed (λ, 0+).
Water-leaving radiance
sr-1
Lwn (λ)
Fully normalised water-leaving reflectance
sr-1
Lwn_f/Q
Normalised Water Leaving Radiance - f/Q corrected
sr-1
Diffuse reflectance at null depth, or irradiance reflectance
dimensionless
Lw (λ)
R(, 0-)
(Eu / Ed)
F0 ( )
f
Mean extraterrestrial spectral irradiance
W m-2 nm-1
Ratio of R(0-) to (bb/a); subscript 0 when s = 0
dimensionless
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f’
Q(,s,v,)
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Title: In-situ measurement Protocols:
IOPs and Constituents
Issue: 1.0
Date: March 2013
PAGE: ii
Ratio of R(0-) to (bb/(a + bb)); subscript 0 when s = 0
dimensionless
Factor describing the bidirectionality character of
sr-1
R(, 0-) Subscript 0 when s = v = 0; Q = Eu/Lu
Other atmosphere and aerosol properties
α
Angström exponent (α < 0).
dimensionless
ε
Eccentricity of the Earth’s elliptic orbit
dimensionless
Aerosol optical thickness
dimensionless
τray()
O3()
Rayleigh (or molecular) optical thickness
dimensionless
Ozone optical thickness
dimensionless
Tray (λ)
Rayleigh transmittance
dimensionless
Ta (λ)
Aerosol transmittance
dimensionless
Ozone transmittance
dimensionless
Td (λ)
Total downwelling transmittance (diffuse + direct)
dimensionless
Tu (λ)
Total upwelling transmittance (diffuse + direct)
dimensionless
Surface pressure
hPa
Ozone concentration
cm-atm 
RH Relative humidity
Downwelling total transmittance at sea surface level
percent
dimensionless
Geometrical factor, accounting for multiple reflections and
dimensionless
τa()


TO3 (λ)
Ps
uO3
Td ( ,  s )
Air-water interface
( ' )
refractions at the air-sea interface (Morel and Gentilli, 1996).
n
f()

dimensionless
Fresnel reflectance at the air-sea interface for the scattering angle 
dimensionless
mean reflection coefficient for the downwelling irradiance at the
sea surface
dimensionless
average reflection for upwelling irradiance at the air-water interface
dimensionless

Root-mean square of wave facet slopes
dimensionless

Angle between the local normal and the normal to a wave facet
p
probability density function of facet slopes for the illumination
r

refractive index of sea water
dimensionless
and viewing configurations (s, v, )
Miscellaneous
ws
Wind-speed just above sea level
ln
Natural (or Neperian) logarithm
log10
m s-1
Decimal logarithm
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IOPs and Constituents
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Date: March 2013
PAGE: iii
Abbreviations and Definitions
AERONET
AOP
ARGANS
BBOP
BOUSSOLE
CalCOFI
CDOM
Chl
CTD
EO
ESA
GPS
HPLC
IOP
LOA
LISE
LOV
MERIS
MERMAID
MODIS
MQC
MUMM
MVT
NASA
NIR
NOMAD
OC
ODESA
OBPG
PAR
PI
PQC
QWG
RMD
SeaBASS
SeaWiFS
SPM
SPMR
TACCS
TSM
UK
YS
Aerosol Robotic Network
Apparent Optical Property
Applied Research in Geomatics, Atmosphere, Nature and Space
Bermuda Bio-Optics Project
BOUée pour l'acquiSition d'une Série Optique à Long termE
(Buoy for the acquisition of long-term optical time series)
California Cooperative Oceanic Fisheries Investigations
Coloured Dissolved Organic Matter
Chlorophyll-a concentration mg m-3
Conductivity Temperature Depth
Earth Observation
European Space Agency
Global Positioning System
High Performance Liquid Chromatography
Inherent Optical Property
Laboratoire d'Optique Atmosphérique
Laboratoire Interdisciplinaire des Sciences de l'Environnement
Laboratoire Océanographique in Villefranche sur mer
Medium Resolution Imaging Spectrometer
MERis MAtch-up In-situ Database
Moderate Resolution Imaging Spectrometer
Measurement Quality Control
Management Unit of the North Sea Mathematical Models
MERIS Validation Team
National Aeronautics and Space Administration
Near Infrared
NASA bio-Optical Marine Algorithm Dataset
Ocean Color
Optical Data Processor of the European Space Agency
Ocean Biology Processing Group
Photosynthetically Available Radiation
Principle Investigator
Processing Quality Control
Quality Working Group
Reference Model Document
SeaWiFS Bio-Optical Archive and Storage System
Sea-viewing Wide Field-of-view Sensor
Suspended Particulate Matter
SeaWiFS Profiling Multichannel Radiometer
Tethered Attenuation Coefficient Chain Sensor
Total Suspended Matter (g m-3)
United Kingdom
Yellow Substance absorption coefficient (m-1)
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In-situ
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YSBPA
Ref: CO-SCI-ARG-TN-008
Title: In-situ measurement Protocols:
IOPs and Constituents
Issue: 1.0
Date: March 2013
PAGE: iv
Absorptions of dissolved and bleached particulate matter (m-1)
Case 2(S) water:
Case 2 water dominated by TSM (see ATBD: PO-TN-MEL-GS-0005)
Case 2(Y) water:
Case 2 water dominated by yellow substances (see ATBD: PO-TN-MEL-GS-0005)
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IOPs and Constituents
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PAGE: 1
1. Introduction
1.1
Document purpose and scope
This document provides a summary of the MERIS bio-optical products and a definition of the
variables (as agreed and used by the MERIS Validation Team, MVT) required to validate them using
the ESA MERMAID (MERis Matchup In-situ Database) facility. The bio-optical and non-optical
parameters accepted in MERMAID are listed and defined for MERMAID in Section 2, and associated
protocols provide for sites providing these parameters. Although phaeopigments are derived via
HPLC, other than chlorophyll-a they are not included in MERMAID but are described in overall
procedure descriptions.
This document is organised by parameter, and measurement procedure and then by site.
For detail of the MERIS product definitions see the MERIS Ocean Reference Model Document at:
https://earth.esa.int/instruments/meris/rfm/MERIS_RMD_ThirdReprocessing_OCEAN_Aug2012.pdf
1.2
Overview of MERIS Bio-optical products

API1: the algal pigment index 1 (Morel and Antoine, 1999), expressed as a chlorophyll
concentration in mg.m-3, given in Case 1 waters.

API2: the algal pigment index 2, expressed as a Chl concentration in mg.m-3. Chl2 is related in
the neural network algorithm via a scaling equation to pigment absorption at 442nm, apig(442),
given in all waters. As applied in the MERIS product, and defined in the MERIS RMD (AD [3]),
we have:
[Chl ]  21.0 [a pig (442)] 1.04

(1)
TSM, total suspended matter concentration, expressed as concentration in g.m-3, given in all
waters. TSM is related in the neural network algorithm via a scaling factor to a particle scattering
at 442 nm, bp(442), given in all waters. As applied in the MERIS product, and defined in the
MERIS RMD (AD [3]), we have:
TSM ( g m 3 )  1.73 b p (442)
(2)

YSBPA: proxy for the sum of absorptions of dissolved and bleached particulate matter at
442.5nm in m-1. “YS” will be used for MERIS yellow substance (CDOM; ag being the in-situ
term) absorption, and BPA will be used for bleached particle absorption. YSBPA = YS+BPA.

Case 2_S: a flag indicating the presence of TSM in significant concentration.

Case 2_Anom: a flag indicating abnormally high scattering in Case 1 water.

Case 2_Y: a flag indicating YS loaded water. This flag is at the moment inactivated in the ground
segment processing pending validation.

Inherent Optical Properties (IOPs): Aside from YSBPA, IOPs are not Level 2 MERIS
products. However, they are still invaluable for validating algorithms.
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1.3
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Title: In-situ measurement Protocols:
IOPs and Constituents
Issue: 1.0
Date: March 2013
PAGE: 2
MERMAID
The MERis Matchup In-situ Database (MERMAID) is the
ESA facility for MERIS Ocean Colour validation.
MERMAID incorporates in-situ data from over 30 sites,
and the concurrent sensor matchups and extraction
products.
More information about the project can be found at
http://hermes.acri.fr/mermaid.
MERMAID in-situ parameters include:

Optical: Radiometry (water and sky), IOPs, AOPs;

Bio-optical: Chla , sediment and yellow substance
concentrations; pigments;

Atmospheric.
The Optical Measurement Protocols describing the
measurement and processing protocols for all sites
providing optical in-situ data are also available at
http://hermes.acri.fr/mermaid/proto
1.3.1
Figure 1-1: MERMAID project website:
http://hermes.acri.fr/mermaid.
Data submission and feedback
PI’s should write to mermaid@esa.int to enquire about data submission. ARGANS is the next point of
contact for the PI, who is requested to submit data in any format (e.g. ASCII, HDF), as long as it is
adequately labelled and accompanied by a protocol describing measurement and processing methods.
1.3.2
User login and Password
MERMAID is subject to a strict data access policy viewable at
http://hermes.acri.fr/mermaid/policy/policy.php.
The database is made available to the MERIS QWG, the MVT and the contributing PIs through an
access-restricted data extraction page, for which a unique password is provided. PIs are given access
if they have submitted in-situ data and matchups are confirmed. Restricted access such as this allows
for better security and for site-use monitoring.
The password and login details must not be passed on to others; the MERMAID team must be
contacted and the colleague in question will be considered but not guaranteed access.
We welcome use of MERMAID outside the scope of the MERIS maintenance and evolution project.
Interested users who are not part of the MQWG, MVT or are not PIs, can request access with a unique
password through a Service Level Agreement. Please email mermaid@acri.fr to express interest and
provide a description of your project.
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2. Chlorophyll-a
2.1
MERMAID and MVT definitions
Table 2-1: Chla definitions in MERMAID, and available sites providing matchups.
FIELD
HPLC_chla_TOTAL
_IS
UNIT
mg m-3
Description
Total Chla derived
from HPLC pigment
analysis.
Sum of HPLC chla,
div. chla, chlide-a +
phaeopigments
Equivalent
MERIS L2
product:
Available
MERMAID
sites
HPLC_chla_ONLY
_IS
mg m-3
SPECT_chla
_IS
Fluor_chla_IS
AERONET_Chla
_IS
mg m-3
mg m-3
mg m-3
Chla only
derived from
HPLC pigment
analysis
Spectrophoto
-metric Chla
Calibrated
fluorometric chla
(check protocols
for calibration)
Chlorophyll-a
computed in
the
AERONETOC processor
from
SeaPRISM
radiances.
API1
API2
API1
Algarve
BOUSSOLE
CASES
PortCoast
NOMAD
Plumes and
Blooms
PMLNorthSeaWEC
BSHSummerSurvey
Algarve
MUMM
REPHY
Wadden Sea
PI to state
whether they
consider
their Chla
equivalent to
API1 or
API2.
(See
respective
protocols)
Algarve
NW Baltic
Bristol
Channel and
Irish Sea
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MAREL
NOMAD
Plumes and
Blooms
BSHSummerSurvey
AAOT
Abu AlBukhoosh
COVE
SeaPRISM
Gloria
Gustav-Dahlen
Tower
Helsinki
Lighthouse
LISCO
LJCO
MVCO
Palgrunden
WAVE_CIS
In-situ
Measurement
Protocols: IOPs
& Constituents
2.2
Ref: CO-SCI-ARG-TN-008
Title: In-situ measurement Protocols:
IOPs and Constituents
Issue: 1.0
Date: March 2013
PAGE: 4
Site overview
Table 2-2: Summary of site providing Chla , MERIS product it is comparable to and the PI definitions
SITE
PI
Algarve
J. Icely
Chla type
Compares
to
AP1 or
AP2?
HPLC_chla_TOTAL_IS
API1
HPLC_chla_ONLY_IS
API2
PI definition (where relevant)
Combination of methods. Not clear which
values correspond to which method. Next
dataset to split by method.
HPLC only
SPECT_chla_IS
BioOptEurofleets
E. Canuti
BOUSSOLE
D. Antoine /
J. Ras
Bristol
Channel
& IrishSea
BSH
SummerSurvey
CASES
(Arctic)
English
Channel
French
Guiana
Helgoland
IFREMER
MAREL
IFREMER
REPHY
NOMAD
(World)
HPLC_chla_TOTAL_IS
API1
HPLC_chla_TOTAL_IS
API1 and
API2
SPECT_chla_IS
API1
SPECT_chla_IS
API2
H. Klein
HPLC_chla_ ONLY _IS
API2
S. Belanger
HPLC_chla_TOTAL_IS
API1
H. Loisel
SPECT_chla_IS
API1
R. Doerffer
HPLC_chla_TOTAL_IS
API1
Fluor_chla_IS
API2
HPLC_chla_ONLY_IS
API2
HPLC_chla_TOTAL_IS
API1
D. Mckee
Chlorophyll a + Divinyl Chlorophyll a +
Chlorophyllide a
Chla + degradation products
C. Belin
Chla only derived from HPLC pigment
analysis
Chla = Chla + DV_Chl_a + Chlide_a
WHERE: HPLC Chla = MV_chl_a +
allomers + epimers.
Fluorometrically/spectrophotometricallyderived chlorophyll a
J. Werdell
Fluor_chla_IS
NW Baltic
PMLNorthSea
WEC
PnB
(California)
PortCoast
Wadden Sea
S. Kratzer
SPECT_chla_IS
API2
G. Tilstone
HPLC_chla_TOTAL_IS
API1
HPLC_chla_TOTAL_IS
API1
Fluor_chla_IS
API2
HPLC_chla_TOTAL_IS
API1
HPLC_chla_ONLY_IS
API2
Total chlorophyll a (HPLC method) = the
sum of Chla (including allomers and
epimers) + mono vinyl Chla + Divinyl
Chla + Chlorophyllide-a
Comparable to Total chlorophyll a
measured by HPLC
D. Siegel
V. Brotas
A.
Hommersom
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TChla = sum(Chlorophyll a + Divinyl
Chlorophyll a + Chlorophyllide a).
Another 'Chla' is available:
sum(Chlorophyll a + allomers + epimers)
A1: Trichromatic equations give chla
(and b, c, caretonoids)
A2: Acidification produces chla and
phaeopigments
2013
Ref: CO-SCI-ARG-TN-008
Title: In-situ measurement Protocols:
In-situ
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& Constituents
2.3
IOPs and Constituents
Issue: 1.0
Date: March 2013
PAGE: 5
HPLC Total Chlorophyll-a
2.3.1
Algarve:
Two sets of water samples, one of 1 litre and the other of 3-4 litres, were filtered through 47 mm
Whatman GF/F glass fibre filters with pore size of 0.7 µm using a filtration ramp and pump, a
filtration tower comprising a scintered glass base to support the filter, and a 350 ml glass column that
was fixed to the base with a metal clamp. After filtration, the filters were stored in a field dewar, filled
with liquid nitrogen for transport to Faro. A much larger laboratory dewar was used for longer term
storage before further processing of the filters.
HPLC enabled the quantification of Chl a together with a range of other chlorophylls and associated
phytoplanktonic pigments. The analysis of the samples by HPLC followed the Scientific Committee
Oceanic Research’s (SCOR) procedures described in Jeffrey et al. (1997).
GF/F 47 mm Whatman® filters containing the filtered residues of seawater for each sampling station,
were allowed to warm up at room temperature and then placed in glass tubes; 5 ml of HPLC grade
90% acetone were added to each tube, sonicated for 20s and the pigments were left to extract for 4
hours. After the extraction period, samples were sonicated again for about 15 s and then centrifuged
for 10 minutes. Extracts were then analyzed in the HPLC system (Waters 600E Pump), using a C18
Thermo-Hypersil Keystone part nº 28105-020 (ODS-2) column with 25 cm length, 4 mm diameter,
and 5 m particle size. The elution system was tertiary, using the following solvents:

Solvent A – 80:20 Methanol: 0,5M Ammonium Acetate (v/v, HPLC grade)

Solvent B – 90:10 Acetonitrile (UV cut-off grade)

Solvent C – Ethyl Acetate (HPLC grade)
The solvent system program, as well as other chromatographic parameters, is described in Table 2-3.
The detection was carried out through a Waters 2996 diode array detector, selecting the detection
wavelengths of 436 and 450nm for chlorophylls and carotenoids, respectively.
Table 2-3. Chromatographic parameters used for the identification and quantification of phytoplanktonic pigments.
Time
(min)
Flow rate
(ml min -1)
%A
%B
%C
0
1
4
1
18
Conditions
100
0
0
Injection
0
100
0
Linear gradient
1
0
20
80
Linear gradient
21
1
0
100
0
Linear gradient
24
1
100
0
0
Linear gradient
29
1
100
0
0
Equilibration
Measurements of absorption coefficients of aquatic particles were made using the T-R (TransmissionReflectance) bleach method with a dual beam spectrophotometer with an integrating sphere.
Coefficients for the absorption of aquatic particles by dual beam spectrophotmetery were obtained by
the method developed by Tassan & Ferrari (2002). Figure 2-1 illustrates the scheme for this method.
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Date: March 2013
PAGE: 6
Figure 2-1: Schematic view of the integrating sphere used for the CINTRA dual beam spectrophotometer used in this
study (from Tassan & Ferrari, 2002).
2.3.2
BioOptEurofleets
The BioOptEurofleets Chla dataset follows the SEAHARRE-4 description given in Hooker et al.
(2010):
The HPLC method adopted by the JRC is the Van Heukelem and Thomas (2001) method, as modified
for SeaHARRE-3 (Van Heukelem and Thomas, 2009). This method has been successfully applied to a
wide range of pigment concentrations from oligotrophic to eutrophic coastal waters. Here, it allowed
for the separation and the quantification of 22 different pigments including the monovinyl and divinyl
forms of chlorophyll-a. The samples are extracted in a 100% acetone solution including an internal
standard (vitamin E acetate) and analyzed by HPLC using a C8 column with a binary solvent gradient.
The different pigments are identified using a diode array detector on the basis of the absorption
spectra at two different wavelengths (450 and 665 nm). The quality control of the data is assured by
injecting a chlorophyll a standard at the beginning of each sequence, in order to check the calibration,
as well as a mixture of pigments in order to check the retention times, and the system accuracy and
precision.
2.3.3
BOUSSOLE
Quantity in MERMAID: Total Chla defined as: Chlorophyll a + Divinyl Chlorophyll a +
Chlorophyllide a (mg m-3), following the following methods:
1. Filters extracted in 100% methanol, disrupted by sonication and clarified by filtration (GF/F
Whatman)
2. Analysis by HPLC was carried out the same day (except in cases of technical problems).
3. Method A: undetected pigments are represented by a "zero" value. For this method (applied
until May 2004), the analytical procedure is derived from Vidussi et al. (2001).
4. Method B: undetected pigments are represented by "LOD" (Limit of detection, see Note 8).
This method (applied from June 2004 to present) follows the analytical procedure described
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PAGE: 7
in Ras et al (2008).
a. For the method flagged C , the analysis (method B) was carried out with a new HPLC
system (Agilent Technologies 1200 series)
b. Detection of carotenoids and chlorophylls c and b: 450 nm; chlorophyll a and
derivatives: 676 nm; bchla : 770 nm.
c. Performance metrics for method B:

Total chla precision between replicate samples: 2.3%

Calibration precision: 0.5%

Injection precision: 0.4%
d. Total chla accuracy: 7% Calibration accuracy: 0.5%
e. Limits of detection for method B: calculated as the concentrations corresponding to a
signal:noise ratio of 3 and for a filtered volume of 2.8 L.
2.3.4
CASES (Arctic Waters)
Particulate matter for pigments analysis was collected by filtration of seawater through 25-mm GF/F
filters (pore size of 0.7 μm) under low vacuum. Samples were flash-frozen in liquid nitrogen after the
filtration and kept at -80°C until analyses. After the cruise, the filters were sent to the Laboratoire
Océanographique de Villefranche (LOV) for pigment analysis by High-Performance Liquid
Chromatography (HPLC). The pigment concentrations were determined following the method
described by Van Heukelem and Thomas (2001), as modified by Ras et al. (2008). For this study total
chlorophyll a concentration is calculated as the sum of Chlorophyll-a, Divinyl Chlorophyll-a and
Chlorophillide-a, as recommended by the National Aeronautics and Space Administration (NASA)
protocol for ocean colour algorithms development and validation (Hooker et al., 2005).
2.3.5
Helgoland
Total Chla was determined from HPLC, and is the concentration sum of chlorophyll-a and its
degradation products (like iso, allomer, phaeophytine). The method applied followed Zapata et al.
(2000), based on a reversed-phase C8 column and pyridine-containing mobile phases was developed
for the simultaneous separation of chlorophylls and carotenoids.
2.3.6
Plumes and Blooms
Chla was measured by HPLC, and includes chlorophyll-a plus its allomers and epimers. Total
chlorophyll-a (HPLC method) is the sum of Chla (including allomers and epimers) + mono vinyl
Chla + Divinyl Chla + Chlorophyllide-a.
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Issue: 1.0
Date: March 2013
PAGE: 8
PortCoast (Portuguese Coast)
Dataset time range in MERMAID: 2005-2012
2005-2008 Protocols
Cruises: PG05, NR05, PG06, NR06, DC06, DC07,
DC08
Quantified pigment: Chloropyll a (plus epimers and
allomers) [μg.L-1]
Sample collection: water collected with a rosette
equipped with Niskin bottles for all cruises, except for
PG05 where an “Aquaflow” pumping system was used.
Volume filtered: 5L
Filters: Whatman GF/F (47mm ∅, 0.7μm nominal pore
size)
Extraction: 5-6 ml 95% cold-buffered methanol (2%
ammonium acetate) for 30 min at –20°C
Method: HPLC C18 column, solvent gradient
followed Kraay et al. (1992) adapted by Brotas and
Plante-Cuny (1996).
Figure 2-2: Map of 2005-2008 sampling
locations for PortCoast dataset
Water samples (5 L) were filtered onto Whatman GF/F filters (nominal pore size 0.7 μm and 47 mm
diameter). The filters were deep-frozen immediately and stored at –80°C. Phytoplanktonic pigments
were extracted with 5-6 mL of 95% cold-buffered methanol (2% ammonium acetate) for 30 min at –
20°C, in the dark. Samples were sonicated (Bransonic, model 1210, w: 80, Hz: 47) for 1 min at the
beginning of the extraction period. The samples were then centrifuged at 1100 g for 15 min, at 4°C.
Extracts were filtered (Fluoropore PTFE filter membranes, 0.2 μm pore size) and immediately
injected in the HPLC. Pigment extracts were analyzed using a Shimadzu HPLC comprised of a
solvent delivery module (LC-10ADVP) with system controller (SCL-10AVP), a photodiode array
(SPD-M10ADVP), and a fluorescence detector (RF-10AXL). Chromatographic separation was
carried out using a C18 column for reverse phase chromatography (Supelcosil; 25 cm long; 4.6 mm in
diameter; 5 mm particles) and a 35 min elution program. The solvent gradient followed Kraay et al.
(1992) adapted by Brotas and Plante-Cuny (1996) with a flow rate of 0.6 mL min-1 and an injection
volume of 100 μL. Pigments were identified from both absorbance spectra and retention times and
concentrations calculated from the signals in the photodiode array detector. The HPLC system was
previously calibrated with pigment standards from Sigma (chlorophyll a, b and β-carotene) and DHI
(for other pigments). Chlorophyll a was calculated as the sum of Chl a, epimers and allomers.
2009-2012 Protocols
Cruises: GC09, GC09_M, GC10, HS10, GC11, HS11
Monitoring programs: Cs, CSA
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In-situ
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Quantified
pigment:
Chl
+epimers+allomers+DvChla) [μg.L‐1]
a
Ref: CO-SCI-ARG-TN-008
Title: In-situ measurement Protocols:
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Issue: 1.0
Date: March 2013
PAGE: 9
(Chla
Sample collection: Water collected with a rosette equipped
with Niskin bottles.
Volume filtered: 0.5‐2L
Filters: Whatman GF/F (25mm, 0.7μm nominal pore size)
Extraction: 2‐3 ml 95% cold‐buffered methanol (2%
ammonium acetate) for 1h at ‐20ºC (with internal standard)
for all samples except for GC09 which were extracted for
30 min at –20°C (with no internal standard)
Method: HPLC C8 column, following Zapata et al. (2000).
Figure 2-3: Map of 2009-2012 sampling
locations for PortCoast dataset
Water samples (0.5‐2 L) were filtered onto Whatman GF/F filters (nominal pore size 0.7 μm and 25
mm diameter). The filters were deep‐frozen immediately and stored at –80°C. Phytoplanktonic
pigments from GC09 samples were extracted with 2‐3 ml of 95% cold‐buffered methanol (2%
ammonium acetate) for 30min at –20°C, in the dark. Previously sonicated (Bransonic, model 1210, w:
80, Hz: 47) for 1 min and, after extraction period, centrifuged at 1100 g for 15 min, at 4°C. The other
samples were extracted with 2‐3 ml of 95% cold‐buffered methanol (2% ammonium acetate) enriched
with a known concentration of trans‐beta‐apo‐8’‐carotenal (used as internal standard) for 1h at ‐20ºC,
in the dark. At half‐time period of extraction, samples were sonicated for 5 min and after extraction
period centrifuged for 5 min. All extracts were filtered (Fluoropore PTFE filter membranes, 0.2 μm
pore size) and immediately injected in the HPLC. Pigment extracts were analyzed using a Shimadzu
HPLC comprised of a solvent delivery module (LC‐10ADVP) with system controller (SCL‐10AVP),
a photodiode array (SPD‐M10ADVP), and a fluorescence detector (RF‐10AXL). Chromatographic
separation was carried out using a C8 column for reverse phase chromatography (Symmetry C8, 15
cm long, 4.6 mm in diameter, and 3.5 μm particle size) and a 40 min elution program. The solvent
gradient followed Zapata et al. (2000) with a flow rate of 1 mL min‐1 and an injection volume of 100
μL. Pigments were identified from both absorbance spectra and retention times and concentrations
calculated from the signals in the photodiode array detector. The HPLC system was previously
calibrated with pigment standards from DHI. Chlorophyll a was calculated as the sum of Chla ,
epimers and allomers and Divinyl Chl a.
2.3.8
NOMAD
The following description of the total HPLC Chla in NOMAD is an extract from Werdell and Bailey
(2005).
Following SSPO protocols, only total chlorophyll a was considered, and calculated as the sum of
chlorophyllide a, chlorophyll a epimer, chlorophyll a allomer, monovinyl chlorophyll a, and divinyl
chlorophyll a, where the latter two were physically separated (Mueller et al., 2003a).
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Title: In-situ measurement Protocols:
IOPs and Constituents
Issue: 1.0
Date: March 2013
PAGE: 10
PMLNorthSeaWEC
The following description is extracted and adapted from Tilstone et al. (2012).
Measurements of bio-optical properties and associated biogeochemical concentrations, including
Chlorophyll-a, were made by seven research institutes over a number of cruises between 1998 and
2006 in the North Sea, Western English Channel and Celtic Sea (Figure 2-4).
Danish Meteorological Institute (DMI), Institute for Coastal Research (HZG), Management Unit of
the North Sea Mathematical Models (MUMM), Norwegian Institute for Water Research (NIVA) and
Plymouth Marine Laboratory (PML) measured Chla by High Pressure Liquid Chromatography
(HPLC). Between 0.25 and 2 L of seawater were filtered onto 25 mm, 0.7 μm GF/F filters and
phytoplankton pigments were extracted in methanol containing an internal standard apocarotenoate
(Sigma-Aldrich Company Ltd.). Chla extraction was either by freezing at −30 °C or using an
ultrasonic probe following the methods outlined in Sørensen et al. (2007) . Pigments were identified
using retention time and spectral match using Photo Diode Array (Jeffrey et al., 1997) and Chla
concentration was calculated using response factors generated from calibration using a Chla standard
(DHI Water and Environment, Denmark). The Institute for Environmental Studies (IVM) extracted
Chla using 80% ethanol at 75 °C and concentrations were determined spectrophotometrically, by
measuring the extinction coefficients at 665 and 750 nm before and after acidification with 0.20 mL
HCl (0.4 mol L−1) per 20 mL of filtrate.
Figure 2-4: (A) Location of 468 stations sampled from 1998-2003 for the determination of biogeochemical
concentrations and absorption properties. The stations are partitioned into 10 geographic regions; inverted triangle,
Skagerrak; diamond, West Jutland; sideways triangle, NW North Sea; plus, SE North Sea; cross, German Bight;
star, East Anglia UK coast; circles, Dutch coast; dot, Belgium coast; triangle, Celtic Sea; square, Western English
Channel. (B) Location of 61 stations sampled from 2003-2006 for satellite accuracy assessment. (Tilstone et al., 2012)
2.4
2.4.1
HPLC Chlorophyll a only
Algarve
HPLC enabled the quantification of Chla together with a range of other chlorophylls and associated
phytoplanktonic pigments, as described in section 2.3.1.
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PAGE: 11
BSHSummerSurvey
The full dataset spans 08/2005 – 08/2011. From 08/2007, HPLC was used to estimate Chla only.
2.4.3
IFREMER REPHY
HPLC Chla (only) measurements.
2.4.4
MUMM
Water samples taken in surface water (0.5m depth) are filtered on-board with GF/F filters, which are
then frozen in liquid nitrogen and stored long term at –80°C. Pigments are extracted in 90% acetone
with the use of a cell-homogenizer, followed by centrifugation. The chlorophyll pigments are
separated with reversed phase HPLC (Park et al., 2006).
2.4.5
Wadden Sea
All samples were taken with a bucket. For Chl concentration measurements GF/F filters were used.
After filtration the filters were frozen at -20 °C and transferred to -80 °C in the lab within two weeks
of taking the first sample. Chl samples were analysed on HPLC, mainly according to the Ocean
Optics protocol (Mueller et al., 2003b), except for the solvent gradient program, which was modified
to improve separation. Peak areas were measured relative to the peak areas of a Chl standard in fresh
water. Concentrations of the standard were determined in acetone with a spectrophotometer. A
correction is applied for the amount of water that remains in a filter following Mueller et al. (2003b).
In an experiment the amount of water retained in a 47 mm GF/F filter was found to be 0.58 ml.
2.5
2.5.1
Spectrophotometry
Algarve
Two sets of water samples, one of 1 liter and the other of 3-4 liters, were filtered through 47 mm
Whatman GF/F glass fiber filters with pore size of 0.7 µm using a filtration ramp and pump, a
filtration tower comprising a scintered glass base to support the filter, and a 350 ml glass column that
was fixed to the base with a metal clamp. After filtration, the filters were stored in a field dewar, filled
with liquid nitrogen for transport to Faro. A much larger laboratory dewar was used for longer term
storage before further processing of the filters.
The standardised procedure developed by the Joint Global Ocean Flux Study group (Lorenzen,
1967b) was used for this analysis. Each filter was placed in a 15 ml centrifuge tube to which was
added 10 ml of 90% acetone. Each tube was wrapped in aluminium foil to reduce the degradation of
pigments by ambient light. Pigments were extracted for 12 hours in the fridge before the tubes were
centrifuged and the supernatant decanted into cuvettes. The extinction at the wavelengths 750, 664,
647 and 630 nm were estimated with a UV-Vis Thermo-Unicam spectrophotometer. Concentrations
were calculated from (3).
Chl  a(mg m 3 )  26.7 (665o  665a)
x.v
V xl
(3)
where v is the extraction volume, V is the volume of filtered sample and l is the pathlength.
Estimation of total phaeopigments used the same procedure for Chla up to measurement of the
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extinction of the extract at 665 and 750 nm, after which two drops of dilute hydrochloric acid were
added to the cuvette and the extinction at the two wavelengths were remeasured. Each reading at
750nm was subtracted from the corresponding 665 nm extinction and the concentrations were
calculated from (4).
phaeopigments (mg m 3 )  26.7 (1.7 [665a]  665o)
2.5.2
x.v
V xl
(4)
Bristol Channel and Irish Sea
The Chl samples were analysed using spectrophotometry. However the two values correspond to two
different techniques. The first uses trichromatic equations to estimate Chl_a (as well as Chl_b, Chl_c
and carotenoids) and the second estimates Chl_a and Phaeopigment. In effect both are estimates of
Chl_a only, therefore comparable only to MERIS Algal pigment 2.
2.5.3
BSHSummerSurvey
The full dataset spans 08/2005 – 08/2011. From 08/2003, the methodology to determine chla follows
Lorenzen (1967a).
2.5.4
French Guiana and English Channel
Spectrophotometric chla was determined following the methods of Stramska et al. (2003) and
Lorenzen (1967a).
2.5.5
NWBaltic Sea
For the estimation of photosynthetic pigments the 1-2 l of water samples were filtered through 47 mm
GF/F filters and stored in liquid nitrogen for maximum 1 month. For analysis, the filters were put in
10 ml 90% acetone, sonicated for 30 sec, centrifuged for 10 min at 3000 RPM. After 30 min
extraction the sample was decanted into a 1 cm quartz cuvettes and scanned against 90% acetone in a
Shimadzu UVPC 2401 dual beam spectrophotometer. Chlorophyll a was calculated according to the
trichromatic method (Jeffrey and Humphrey 1975; Parsons et al. 1984; Jeffrey et al. 1997).
This spectrophotometric method was evaluated to derive chlorophyll using the trichromatic method.
Additional replicates of our field samples were sampled and sent to NIVA (Norway) packed in dry
ice, to be processed using HPLC. The results in Figure 2-5 below show that our method compares
very well to chl a measured by NIVA (which includes only chlorophyll-a, not its by-products, i.e.
algal_2).
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25.00
y = 1.03 x + 0.18
R² = 0.99 n =32
Chl spec µg l-1
20.00
15.00
10.00
5.00
0.00
0.00
5.00
10.00
15.00
20.00
25.00
Chl HPLC µg l-1
Figure 2-5: Intercomparison of two methods to measure chl a: trichromatic (spectrophotometric) method from
Stockholm University (using GF/F filters, 30 sec sonication and 30 min extraction in 90% acetone) compared to
NIVA’s HPLC method. Data 32 stations in total: 10 samples from MAVT intercalibration 2 (natural water samples
from Norwegian coastal areas in 2002), 4 stations from Askö 2002, 18 stations from Askö 2008.
2.6
2.6.1
Fluorometry
IFREMER MAREL
Fluorometric measurements (converted to Chla after). The linear conversion used is 1.8*
(fluorometric measurement) to get the Chla (Units mg.m-3).
2.6.2
NOMAD
The following description of the fluorometric Chla in NOMAD is an extract from Werdell and Bailey
(2005).
Continuous depth profiles and underway observations were collected via calibrated in-situ
fluorometers, either mounted to CTD packages or coupled to shipboard sea chests. For both, only
calibrated data (concentrations, not voltages) were considered to ensure first-order quality assurance
by the data contributor and to eliminate the need for additional OBPG data preparation. Discrete
pigment measurements made only at the sea surface were also acquired, and replicate measurements
were averaged.
2.6.3
Plumes and Blooms
Since in fluorometry, one can only measure chlorophyll a in bulk, PnB fluorometric Chla includes all
forms of chlorophyll a and is comparable to Total chlorophyll a measured by HPLC.
Surface chlorophyll a concentrations were obtained by fluorometry from Niskin bottle samples
following the study by Strickland and Parsons (1972) and using a Turner Designs 10AU fluorometer.
2.7
AERONET-OC: Computed Chla
All AERONET-OC sites are provided with a chlorophyll-a parameter which has been algorithmically
derived as Total Chla minus pheaophytin_a.
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3. Suspended Sediments
3.1
MERMAID and MVT definitions
Table 3-1: Suspended sediment definitions in MERMAID, and available sites providing matchups.
FIELD
-3
OSM_IS
MSM_IS
-3
-3
POC_IS
gm
gm
gm
gC m-3
Description
Total Suspended Matter =
Mineral Suspended Matter +
Organic Suspended Matter
Organic
Suspended Matter
Mineral
Suspended
Matter
Particulate
Organic Carbon
Available
MERMAID
sites
CASES
WaddenSea
PMLNorthSeaWEC
Helgoland
BristolChannel
and IrishSea
Helgoland
BristolChannel
and IrishSea
Helgoland
Unit
3.2
TSM_IS
CASES
NOMAD
Bristol Channel and Irish Sea
TSM is measured by filtering a volume of seawater (usually 5L) through a pre-combusted and preweighed 90mm GF/F filter which is subsequently rinsed with ~150ml MilliQ. The filter is then stored
frozen for analysis back at the lab. The filter is dried in a drying oven at ~80oC for several hours until
completely dry. The filter is then re-weighed at least three times to establish a stable value, being
returned to the dying oven between measurements. After TSM values have been established, the
filters are placed in a furnace at 500oC for several hours until there are no signs of soot on the filter.
Filters are re-weighed at least three times to establish a stable value of MSM, being returned to the
drying oven between measurements. The weight of combustible (organic) material is obtained by
subtracting MSM from TSM.
3.3
CASES (Arctic Waters)
Total suspended matter (TSM) was concentrated (in triplicates) by filtering up to 2-L of seawater
through pre-weighted 0.2 μm 47 mm Anodiscs® filters. After filtration, the filters were dried for ~4h
at 60°C and stored at –80 ˚C until analysis. In the laboratory, the filters were thawed, dried again in
desiccators and weighted using a Mettler MT5 electrobalance. TSM (in μg L -1) was calculated as the
difference between the filter weight with and without particle and normalized by the volume of
filtered seawater. The triplicate measurements were checked to eliminate abnormal values (coefficient
of variation > 10%) and the mean of the remaining samples was calculated at each station.
3.4
Helgoland
The suspended sediment in the Helgoland dataset was derived as:
1. dry weight of total suspended matter;
2. dry weight of the inorganic (mineral) and organic fraction of TSM.
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PMLNorthSeaWEC
The following description is extracted and adapted from Tilstone et al. (2012).
Measurements of bio-optical properties and associated biogeochemical concentrations, including
TSM, were made by seven research institutes over a number of cruises between 1998 and 2006 in the
North Sea, Western English Channel and Celtic Sea (Figure 2-4).
Between 0.5 and 3 L of seawater was filtered onto 47 mm, 0.7 μm GF/F filters in triplicate, which
were ashed at 450 °C and then washed for 5 min in 0.5 L of MilliQ to remove friable fractions that
can be dislodged during filtration. The filters were then dried in a hot air oven at 75 °C for 1 hour,
pre-weighed and stored in desiccators. Seawater samples were filtered in triplicate and the filters and
filter rim were washed three times with 0.05 L MilliQ to remove residual salt.
Blank filters were also washed with MilliQ to quantify any potential error due to incomplete drying.
The filters were then dried at 75 °C for 24 h and weighed on microbalances (detection limit 10 μg).
TSM concentrations were determined from the difference between blank and sample filters and the
volume of seawater filtered. Samples analysed by DMI were measured in the same way but were
dried at 65 °C for 1 hour. The IVM samples were pre-ashed at 550 °C and then dried at 105 °C.
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4. IOPs
4.1
MERMAID and MVT definitions
Table 4-1: IOP definitions in MERMAID and available sites providing matchups.
* denotes availability at several wavelengths
Absorptions
FIELD
Unit
Description
Available
sites
a_IS_*
ap_IS_*
adet_IS_*
aph_IS_*
ag_IS_*
m-1
m-1
m-1
m-1
m-1
Algal pigment
absorption at
lambda (*)
In-situ measured
Coloured
Dissolved
Organic Matter
(Yellow
substance), at
lambda (*)
aph = ap - adet
ag = a- aw - ap
PnB
CASES
CASES
PnB (ag)
WaddenSea
NOMAD
Absorption
coefficient at
lambda (*)
(incl. aw, NASA
protocols)
Particulate
absorption at
lambda (*)
a = aw+ag+ap
ap = aph+adet
ap = a- aw - ag
NOMAD
NOMAD
PnB
Detrital
absorption at
lambda (*)
NOMAD
PnB
Scattering
FIELD
Unit
Descrip-tion
b_IS_*
bs_IS
bp_IS_*
bb_IS_*
bbs_IS
m-1
Dimensionless
m-1
m-1
Dimensionless
Particulate
scattering
(phytoplan-kton
+ detritus) at
lambda (*)
Backscattering
at lambda (*)
Scattering at
lambda (*)
Scatter-ing
spectral slope
b = bw +bp
Backscattering
spectral slope
bb = bbw+bbp
NOMAD
PnB
PMLNorthSea
WEC
Available
sites
PMLNorthSea
WEC
Subscript definitions: w: water; g: gelbstoff; p: particulate; ph: phytoplankton; det: detritus
The MERIS Ocean Reference Model Document provides more detail:
https://earth.esa.int/instruments/meris/rfm/MERIS_RMD_Third-Reprocessing_OCEAN_Aug2012.pdf.
4.2
Algarve: Estimates of absorption coefficient for aquatic particles
Two replicate samples of 500 ml were filtered through 25mm Whatman GF/F glass fiber filter with a
pore size of 0.7mm supported on a smaller glass base and 150 ml filtration tower glass. The filters
were stored under liquid nitrogen in the field dewar.
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Transmission-Reflectance (T-R) measurements of sample particles: measurement in
transmission mode
Transmission mode is the normal measurement that is made on spectrophotometer and it is used both
in Tassan and Ferrari’s (Tassan and Ferrari, 2002) method as in the previous methods to determine
aquatic particles absorption. The difference and advantage of Tassan and Ferrari’s method is that,
using an integrating sphere on the spectrophotometer, we can measure what is transmitted and also
what is reflected from the filter, eliminating errors from backscattering of light by the particles. In this
way, this is not a calibration, but all the filters are measured both in transmission and in reflection
modes, and both measurements are used to determine the final optical density of the sample, as seen
in Equation (5).
A sample filtered through a GF/F filter in Sagres was thawed to room temperature in the laboratory in
Faro and dampened with drops of ultrafiltered seawater (0.7µm) to maintain the osmotic pressure. For
measurements in transmission mode, the filter was placed onto a “transmittance” support, with the
fibers orientated vertically and the filtered material facing the sample beam in port A1 (Tassan and
Ferrari, 2002). Each filter was oriented in the same way to reduce the variability in the measurements.
Port B1 was left open and ports A2 and B2 were closed with Spectralon plates (see Figure 2-1). In
contrast to Tassan and Ferrari (2002), port B1 was not covered with a GF/F filter but was exposed to
the air for the reference beam. The measurements for beam transmittance from the sample filter were
carried out after accurate centering of this filter relative to the axis of the sample beam.
Measurement of a blank filter for transmittance involved immersing a 25mm GF/F filter for 1 hour in
Milli Q water and then carrying out a blank measurement (pTf) using the same support and geometry
of the integrating sphere that was used for the transmittance measurement of the sample filter (pTs ). A
correction for pT was calculated from (5).
pT 
4.2.2
pT s
pT f
(5)
T-R measurements of sample particles: measurement in reflection mode
For measurements in reflection mode, the same filter measured for transmission was now placed
against port A2 with a black trap holder with ports B1 and A1 left open and port B2 closed with a
Spectralon plate. This gave a reading for pRs.
Again a GF/F filter that had been immersed in Milli Q water was used with the same geometry of the
integrating sphere to provide a blank measurement, pRf. A correction for pR was calculated from (6).
pR 
4.2.3
pR s
pR f
(6)
T-R measurements of sample particles after chemical oxidation of pigments
The sample on the holder was transferred back to a Petri dish where it was exposed to a few drops of
NaClO (bleach) until the oxidation was complete. The time for this could vary from a few minutes up
to an hour depending on the nature of the phytoplankton. The sample filter was transferred back to a
filtration apparatus where 25 ml of Milli Q water was added and the filtrate was extracted under a
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gentle vacuum. Finally, the sample was transferred back to the dual beam spectrophotometer and the
transmission and reflectance measurements described above were repeated. If there were still signals
in the 670-680nm range for chlorophyll absorption, it indicated that the oxidation procedure was
incomplete and it should be repeated.
Using the parameters estimated in (5) and (6), it was possible to calculate as from (7) which was the
absorption by the particles due to a normally incident parallel light beam on a single throughway.
However τ, which was the factor accounting for diffuse radiation backscattered from particles on the
filter, was calculated from (8).
as 
1  pT  R f
1 Rf
( pT  pR)
(7)
pT
 ( )  1.15  0.17(OD Tr ( )  0.5 ODTr (750))
(8)
where ODTr is the optical density measured in the transmission mode.
The sample absorption, as, was converted then to sample absorbance in (9).
As  log 10
1
(1  a s )
(9)
and then to the equivalent particle suspension absorbance Asus by means of the empirical correlation
[Asus(), As)] shown in (10).
Asus λ  = 0.423 As λ + 0.479 A 2 λ 
s
4.2.4
(10)
Absorption by gelbstoff, ag
ag: For each campaign, approximately 75 ml of MilliQ water was filtered through a 47 mm Whatman
Nucleopore polycarbonate filter, with a pore size of 0.2 µm using an all glass filtration apparatus. The
filtrate was discarded and a further 250-300 ml of MilliQ was filtered to provide a blank. The initial
75ml of filtrate from each sample was discarded and a further 250-300 ml stored in amber glass
bottles at 4ºC in a refrigerator, before further treatment within 24 hrs at Faro.
YSBPA: YSBPA is the sum of the absorption by ag and the absorption by the bleached filter pad
(BPA), i.e. of any material which remains on a filter of type Whatman GF/F after bleaching with
sodium hypochlorite (NaClO); both absorptions should be measured at 443 nm.
4.2.5
Spectrophotometric determination of ag
The measurement of yellow substances (i.e. ag) in the samples and blanks followed the Ocean Optics
Protocols for Satellite Ocean Colour Sensor Validation (Revision 2), from NASA / REVAMP
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Protocols (Tilstone et al., 2002).
The CINTRA dual beam spectrophotometer was also used to record spectra for YS. Before
measurements were taken, both field samples and the MiliQ water were taken out of the fridge were
allowed to adjust to room temperature. The 10 cm quartz path length cuvette was inspected for
cleanliness before any measurements, and, if needed, soaked in 10% HCl and rinsed thoroughly with
MiliQ water. The cuvettes, as well as the optical windows of the spectrophotometer, were cleaned
with MiliQ water and dried thoroughly with lint free laboratory tissues. The instrument scan speed
was programmed to 120 and to slit width 2, and a baseline was recorded between 350-800 nm. The
blank spectrum was observed by filling the cuvette carefully with filtered MiliQ water to avoid
bubbles and comparing the scan with that of air in the reference cell. After recording the spectrum, the
MiliQ was discarded and the cuvette was rinsed three times with 5 to 10 ml of a field sample. The
spectrum was recorded for this field sample under the same conditions used for the blank. To check
the stability of the instrument, a MiliQ scan was run after completing the scans for the field samples
from each station. The data processing consisted firstly in subtracting the MiliQ spectrum from the
sample spectrum. The absorption coefficient, ag, of dissolved organic matter was calculated from the
measured absorbance, Ag, using (11).
a g λ  =
2.303 Ag
(11)
l
where l is the cuvette path length.
4.3
CASES (Arctic Waters)
Details on the IOP measurements for COASTlOOC can be found in Babin et al. (2003a; 2003b).
Similar protocols were adopted during the Canadian Arctic Shelf Exchange Study (CASES) with few
modifications as described below. At each station, a sample of ~20 L of surface water was collected
with a clean bucket for spectrophotometric analyses. Subsamples for the determination of ag were
filtered through 0.2-m Anotop® syringe filters (Whatman) and kept into 100-mL acid-cleaned
amber glass bottles. For the determination of the absorption coefficient of particles, ap, suspended
particles were retained onto 25-mm GF/F glass fiber filters (Whatman) by filtering 0.1 to 3.5 L of
seawater. The glass bottles and GF/F filters were stored frozen (seawater: -20 °C; particle: -80 °C) in
the dark until being analyzed two to four months later in the land based laboratory. Samples treatment
and methods applied to determine the ap and ag spectra are detailed in Bélanger et al. (2006).
Briefly, ap() was determined at 1-nm resolution between 350 and 750 nm according to the
transmittance-reflectance protocol developed by Tassan and Ferrari (2002). The measurements were
stopped at 350 nm due to the sharp decrease in the signal-to-noise ratio resulting from the high
absorption by the GF/F filters below that wavelength, and the possible artifact in ap() introduced by
the possible presence of mycosporine-like amino acids (Laurion et al., 2003; Sosik, 1999). The ap()
values for < 350 were obtained by extrapolation using an exponential function fitted to the data
between 350 and 360 nm (same as eq. 1). After ap measurements, the filters were soaked during ~30
minutes in 90% methanol to extract phytoplankton pigments (Kishino et al., 1985b), and the
transmittance-reflectance measurements were repeated for the determination of non-algal absorption
(adet). The absorption coefficient of phytoplankton (aph) was assumed equal to ap() – adet(). The
ag() was measured in 10-cm quartz cuvettes between 250 and 800 nm with 1-nm increments using a
dual beam spectrophotometer (Perkin-Elmer Lambda 35). A background correction was applied by
subtracting the absorbance value averaged over an interval of 5 nm around 685 nm from all the
spectral values (Babin et al., 2003b). Then, the following model was fitted to the data between 300
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and 500 nm using a non-linear regression method (Levenberg-Marquardt).
a g ( )  a g ( 0)e S ( 0 )
(12)
where 0 is a reference wavelength (here 443 nm) and S is the spectral slope of the ag() spectrum.
The spectral absorption and beam attenuation coefficients of seawater constituents (i.e. excluding pure
seawater itself), at-w and ct-w, were determined at nine wavelengths (412, 440, 488, 510, 532, 555, 650,
676 and 715 nm) using a submersible spectrophotometer (ac-9, WET Labs Inc.). The ac-9 was either
operated in the shipborne laboratory where ~20 L of surface water were passed through the instrument
by gravity, or deployed from the deck or from a zodiac to obtain vertical profiles from surface down
to ~40 m. The manufacturer calibration was checked daily using ~10 L of water purified onboard
(Milli-Q Gradient A10, filtered with a Millipore RiOs 8). Temperature and salinity corrections were
applied using the latest coefficients determined by the manufacturer. The ac-9 overestimates
absorption coefficients due to the loss of scattered photons within the reflecting tube before they reach
the detector (Zaneveld et al., 1994). To correct for that error, the following expression was applied:
a t  w ( )  a m ( )  bm ( )
(13)
where am() is the measured absorption coefficient, bm() is the measured scattering coefficient
calculated as the difference ct-w() - am()), and  is the fraction of the scattering coefficient that
corresponds to photons not detected by the sensor. We used the matrix inversion procedure proposed
by Gallegos and Neale (2002) to estimate . The spectral shapes for ag(), adet() and aph(), and the
relationship between adet(440) and bm(440), which are necessary in the inversion, were determined
using measurements on discrete water samples (described above) following the statistically
augmented method described by Gallegos and Neale (2002). When available, the vertical at-w()
profiles were optically averaged from surface down to the first attenuation length using the weighting
function approach proposed by Gordon (1992).
4.3.1
Plumes and Blooms
A Shimadzu UV2401-PC (a Perkin-Elmer Lambda 2 before mid-2003) spectrophotometer was used
to obtain the spectra of the phytoplankton absorption coefficient aph (λ), the CDOM absorption
coefficient ag (λ), and the detrital absorption coefficient ad (λ) at each station from the surface bottle
samples.
A HobiLabs Hydroscat-6 was used to obtain profiles of the backscattering coefficient bb (λ) at each
station for λ = 442, 470, 510, 589, 671, and 870 nm. Pure water calibrations (done at the factory and
UCSB semiannually) were applied. The HS-6 measures the total volume scattering function β at 140o.
β is then converted to the total backscattering coefficient using bb (λ) = 2πχp(β - βw) + bb w (λ) where
bw and bb w (λ) come from the study by Morel (1974) and χp = 1.18 (Boss and Pegau, 2001). The upper
15 m of data from the downcasts were filtered and averaged to obtain a surface backscattering value.
The σ (λ) correction was then applied to correct for light attenuated in the measurement path of the
instrument (Maffione and Dana, 1997) using concurrent AC-9 surface data. Spectra which were not
monotonically decreasing were rejected as unreliable.
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A WetLabs AC-9 absorption and attenuation meter (Moore et al., 1992) was used to obtain profiles of
in-situ absorption at each station [a (λ) at 412, 440, 488, 510, 555, 630, 650, 676, and 715 nm].
4.3.2
NOMAD
The following descriptions are extracted from Werdell (2005) who provides further detail.
Absorption
For storage efficiency, and as aph is a derived product, NASA retained only ap, ad, and ag for
NOMAD. Occasionally, aph, was recorded in lieu of ap. Each time this occurred, ap was reconstructed
via aph + ad. All spectra above 30-meters were retained and were visually inspected, and geophysically
unreasonable data (e.g., those with excessive noise or monotonically increasing magnitudes for ad and
ag) were removed. To remove moderate noise, often resulting from instrument artefacts or poor
sample baselines, smooth fits were derived for ad and ag following the form of Roesler et al. (1989):
a x ( )  a x (0 ) exp [S x (  0 )]
(14)
where x indicates either d or g, S defines the spectral shape of the curves, and λ0 is a reference
wavelength, often 400-nm. For each sample, average values for S via linear least-squares regression
over the ranges 380 – 530-nm and 380 – 600-nm were computed. The fit with the higher correlation
coefficient was retained. All original spectra and fits were simultaneously visually inspected and data
with fitting errors were reanalyzed or discarded.
For both ad and ag, data at specific wavebands were discarded unless the following condition was
satisfied:
 a ( ) 
0.5   xx
2
 a ( ) 
(15)
where a^x indicates fit data.
For ad, these outliers were typically located near the near-infrared Ca absorption peak, likely resulting
from an incomplete methanol extraction. For ag, such outliers showed no spectral dependence and
were often suspected to result from cell lyses during filtering.
For stations with observations at multiple depths, data were optically weighted following Section
2.3.2 of Werdell and Bailey (2005) which involves, briefly, using the method of Gordon and Clark
(1980) and relevant Kd (490) measurements to derive a single remote-sensing relevant absorption
spectrum for each station.
Both aph and a^ph (= ap – a^d) were visually and statistically evaluated Spectra with negative values or
questionable shapes were reanalyzed or discarded. As a final quality control measure, time series of
derived Sx and ax(443) were inspected on a cruise-by-cruise basis to identify local outliers.
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Figure 4-1: Map of spectrophotometric absorption data in NOMAD (Werdell, 2005).
Backscattering
Measurements of the spectral backscattering coefficient, bb, in NOMAD are obtained from HOBI
Labs HydroScat, a-βeta, and c-βeta sensors (http://www.hobilabs.com), WET Labs ECO-BB and
ECO-VSF sensors (http://www.wetlabs.com), and Wyatt Technology Corporation DAWN
photometers(http://www.wyatt.com). All data were collected as vertical depth profiles with the
exception of those from the Scotia Prince Ferry program, which were collected underway via a fixeddepth shipboard flowthrough system (Balch and Drapeau, 2003). In processing the data, all
contributors applied a sigma-correction to correct for light attenuation in the path of the instrument,
and most used the dimensionless coefficient, χp, derived by Maffione and Dana (1997) to relate the
volume scattering function to bb. For the latter, data from the Plumes and Blooms program were
processed using the χp from Boss and Pegau (2001), and Scotia Prince Ferry data collected in 2003
and later were processed using χp from Vaillancourt et al. (2004). Since the seawater contribution, bbw,
is well known and readily available to an end user (Morel 1974; Lee et al. 1996), bbw is not subtracted
from bb to derive a bbp product (bbp = bb – bbw).
All depth profiles were visually inspected and those with significant noise or without measurements
collected more shallow than 5-meters removed. Nearly 80% of the profiled data were binned to 1meter depth resolution prior to submission to SeaBASS; therefore, the remaining profiles are binned
via:
(i) designation of a site-specific bin size (e.g., 1 meter);
(ii) application of a statistical filter to data within each bin to exclude observations outside Mz
±1.5 sz, where Mz and sz are the population median and standard deviation of the bin; and
(iii) calculation of the arithmetic mean of all remaining data points.
As for absorption, profiled data were optically weighted following Section 2.3.2 of Werdell and
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Bailey (2005).
We processed the remaining Scotia Prince Ferry flow-through data following Section 2.3.3 of Werdell
and Bailey (2005). These data required an additional magnitude adjustment as described in Balch et
al. (2003). All spectra were visually inspected and geophysically unreasonable data (e.g., those with
monotonically increasing magnitudes or negative values) were removed.
To remove moderate noise, often resulting from instrument artefacts or calibration, we derived
smooth fits for bb presupposing the form:
v
 
bb ( )  bbw ( )  (bbp (0 ) .  )
 0 
(16)
where v is a unitless parameter that defines spectral slope of particulate backscattering (Morel, 1973),
for example, –1.7 and –0.3 for small and large particles, respectively (Kopelevich, 1983), and λ0 is a
reference wavelength, often 550-nm. For reference, the spectral slope is approximately –4.3 for
molecular backscattering (Morel, 1974). For each sample, average values for the spectral slope, v -,
were calculated over the range 380 – 700-nm via nonlinear multidimensional minimization of the
bracketed part of (16) onto the measured bbp (Press et al., 1992). Values ranged from –2.46 to 0.0,
with a mean of –1.02. bb was reconstructed using (2) at twenty wavebands listed in Table 6 of Werdell
and Bailey (2005) using v and the calculated regression intercept. All original spectra and fits (for
both bb and bbp) were simultaneously visually inspected and data with fitting errors were reanalyzed or
discarded.
Werdell (2005) recommends that end users adopt cautious approaches to using these data. First,
measuring backscattering is complicated and multiple approaches and instruments have been used to
estimate bb.
Figure 4-2: Map of backscattering data in NOMAD (Werdell, 2005).
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PMLNorthSeaWEC
The following descriptions are from Tilstone et al. (2012).
Measurements of bio-optical properties and associated biogeochemical concentrations, including aph
and ag, were made by seven research institutes over a number of cruises between 1998 and 2006 in the
North Sea, Western English Channel and Celtic Sea (Figure 2-4).
aph
HZG, NIVA and PML filtered between 0.25 and 2 L of seawater onto 25 mm, 0.7 μm GF/F filters.
The absorbance of the material captured on the filter was then measured from 350 to 750 nm at a 1 nm
bandwidth using dual beam spectrophotometers retro-fitted with spectralon coated integrating spheres,
following the transmission reflectance method of (Tassan and Ferrari, 1995). Measurements were
made of total particulate absorption (apart (λ)) and aNAP (λ), the absorption coefficient of non-algal
particles) retained on GF/F filters before and after pigment extraction with NaClO 1% active chloride.
The path length amplification correction of (Tassan and Ferrari, 1998) was used and aph(λ) was
derived from the difference between apart (λ) and aNAP (λ). IVM and DMI measured apart(λ) in
transmission mode only with an Ocean Optics FC UV200-2 and a Shimadzu UV-2401
spectrophotometer, respectively. The aNAP (λ) was also measured in transmission mode after pigment
extraction in 80% ethanol at 75 °C following the methods of (Kishino et al., 1985a). Chlorophyll
specific absorption coefficients (aph*(λ)) and suspended particulate matter specific absorption
coefficients (aNAP*(λ)) were calculated by dividing aph(λ) and aNAP(λ) by their respective Chla and TSM
concentrations.
ag
All laboratories filtered replicate seawater samples through 0.2 μm Whatman Nuclepore membrane
filters into acid cleaned glassware. The first two 0.25 L of the filtered seawater were discarded and
aCDOM(λ), i.e. ag (λ), of the third sample was determined in a 10 cm quartz cuvette from 350 to 750 nm
relative to a bi-distilled MilliQ reference blank. The samples were analysed immediately on board
using the spectrophotometers except for samples collected off East Anglia, UK, which were spiked
with 0.5 mL solution of 10 gL−1 of NaN3 per 100 mL of seawater (Ferrari et al., 1996) and stored in a
refrigerator for less than 10 days until analysis to prevent sample degradation (Mitchell et al., 2000).
The ag (λ) was calculated from the optical density of the sample and the cuvette path length.
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5. AOPs
5.1
MERMAID and MVT definitions
Table 5-1: AOP definitions in MERMAID, and available sites providing matchups.
FIELD
PAR_IS_*
-2
PARz1%_IS
KPAR_IS
Kd_IS_*
Wm
m
m
m
m-1
Description
Photosynthetically
Available
Radiation
Euphotic
depth: depth
of 1% light
level of Photosynthetically
Available
Radiation
(PAR, Wm-2)
Diffuse
downwelling
attenuation
coefficient
for
Photosynthetically
Available
Radiation (PAR,
Wm-2), KPAR
Diffuse
attenuation
coefficient for
downwelling
irradiance at
lambda (*)
Diffuse attenuation
coefficient
for
downwelling
irradiance, Kd at
490 nm.
NOMAD
CaliCurrent
NOMAD
BOUSSOLE
CaliCurrent
CASES
NOMAD
5.2
CaliCurrent
-1
Kd490_IS
Unit
Available
sites
-1
(for sites where
other bands do not
exist).
BOUSSOLE
CaliCurrent
CASES
BOUSSOLE
A diffuse attenuation coefficient for the downward irradiance in the upper layers is computed as:
Kd  
log(( E d ( z )) / ( E d (0  ))
z
(17)
where: z is the deepest of two depths on the BOUSSOLE buoy (nominally the 9 m ‘arm’), and Ed (0-)
is simply Es reduced by transmission across the air-water interface, i.e., Es * 0.97 (Austin, 1974).
5.3
CaliCurrent
Vertical profiles of downwelling spectral irradiance and upwelling radiance were measured with
underwater radiometers (Biospherical Instruments MER-2040 and MER-2048) as part of the
California Cooperative Oceanic Fisheries Investigations (CalCOFI) bio-optical program (Kahru and
Mitchell, 1999; Mitchell and Kahru, 1998), and following SeaWiFS bio-optical protocols (Mueller
and Austin, 1995). Downwelling spectral irradiance (Ed) and upwelling radiance (Lu) at the following
nominal wavelengths were measured by the MER-2040: 340, 380, 395, 412, 443, 455, 490, 510, 532,
555, 570, and 665 nm. A MER-2041 deck-mounted reference radiometer also measured downwelling
irradiance at the following nominal wavelengths: 340, 380, 395, 412, 443, 490, 510, 555, 570, 665, 780,
and 875 nm, PAR.
Mitchell and Kahru (1998) estimated the surface-layer diffuse attenuation coefficients Kd(λ) from the
depth range that was used to derive the Lu,(O-,λ) and Ed(O-,λ) surface extrapolations. For comparison
to previous Kd(490) algorithms and the relationship between Kd(A) and Kd(490), Mitchell and Kahru
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(1998) transformed the remote sensing reflectance to the normalized water-leaving radiance as:
Lwm ( )  RRS (0  ,  ) F0 ( )
(18)
where F0(λ) is the mean extraterrestrial irradiance.
5.4
CASES
Kd(λ, 1%) = diffuse attenuation coefficient average for the euphotic zone as defined as Ed (z, λ) / Ed
(0-, λ).
5.5
NOMAD
Gordon and McCluney (1975) demonstrated that 90% of remotely sensed radiance originates in the
upper layer, defined by depth z90, corresponding to the first optical attenuation length as defined by
Beer’s Law. Measurements of Ed (k, z) were smoothed using a weighted least-square polynomial fit.
Using the smoothed data and the previously calculated subsurface irradiance, values for z90(k) were
identified as the depth which satisfied the condition:
Ed (k , z90 )  Ed (k ,0  ) e 1
(19)
Remote sensing diffuse attenuation coefficients, Krs(k), were calculated from the original irradiance
profiles by applying a linear exponential fit over the depth range from z = 0 - to z90(k). Radiometric
profiles with retrieved Krs(k) values less than the value for pure water (Kw (490) = 0.016 m-1; Mueller,
2000) were considered questionable and discarded. Otherwise, both Krs(k) and z90(k) were recorded.
SeaBASS data contributors occasionally provided water-leaving radiances and diffuse attenuation
coefficients derived from in-water measurements without providing the radiance and irradiance
profiles. In such cases, the contributor commonly estimated diffuse attenuation coefficients over the
irradiance extrapolation interval, Kd (k, z1 to z2), where z1 and z2 indicate the minimum and maximum
depths in the interval. Such values differ from the remote sensing diffuse attenuation coefficient, Krs
(k,0_ to z90), in the presence of a stratified water column where the water mass is heterogeneous at
depths less than z90.
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