In-situ Measurement Protocols. - Acrimermaid.acri.fr/dataproto/CO-SCI-ARG-TN-0008_In... · Date:...

In-situ

Measurement

Protocols: IOPs

& Constituents

Ref: CO-SCI-ARG-TN-008

Title: In-situ measurement Protocols:

IOPs and Constituents

Issue: 1.0

Date: March 2013

PAGE: i

All rights reserved, ARGANS Ltd 2013

Doc. no: CO-SCI-ARG-TN-0008

Issue: 1.0

Date: March 2013

In-situ Measurement Protocols.

Part B:

Inherent Optical Properties and in-water constituents

In-situ

Measurement

Protocols: IOPs

& Constituents




Issue: 1.0

Date: March 2013

PAGE: ii


Document Signatures

Name Function Company Signature Date

Editor Kathryn

Barker Project Manager ARGANS

March 2013

Verification Jean-Paul

Huot MVT Coordinator ESA

March 2013

Approval Philippe

Goryl

Contract Manager,

ESA ESA

Updates

Issue Date Description

1.0 March 2013 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.

http://hermes.acri.fr/mermaid/dataproto

In-situ

Measurement

Protocols: IOPs

& 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

In-situ

Measurement

Protocols: IOPs

& Constituents




Issue: 1.0

Date: March 2013

PAGE: iv


Table of Content 1. 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

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

In-situ

Measurement

Protocols: IOPs

& Constituents




Issue: 1.0

Date: March 2013

PAGE: v


2.7 AERONET-OC: Computed Chla .................................................................................................... 13

3. 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

4. IOPs ......................................................................................................................................................... 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 CASES (Arctic Waters) ................................................................................................................... 19

4.3.1 Plumes and Blooms ................................................................................................................. 20

4.3.2 NOMAD .................................................................................................................................. 21

4.3.3 PMLNorthSeaWEC ................................................................................................................. 24

5. AOPs ....................................................................................................................................................... 25


5.2 BOUSSOLE .................................................................................................................................... 25

5.3 CaliCurrent ...................................................................................................................................... 25

5.4 CASES ............................................................................................................................................. 26

5.5 NOMAD .......................................................................................................................................... 26

6. 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

CO-SCI-ARG-TN-000X_MERIS_Bio-Optical_Measurement_Protocols_Issue1_Jan2013_v1.0.doc#_Toc349647823



In-situ

Measurement

Protocols: IOPs

& 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

In-situ

Measurement

Protocols: IOPs

& Constituents




Issue: 1.0

Date: March 2013

PAGE: i


List of Symbols

Symbol Definition Dimension / units

Geometry (see fig. 2.1)

Wavelength nm

s Solar zenith angle (s = cos(s)) degrees

v, Satellite or view zenith angle (v = cos(v)) degrees

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

Radiometric quantities

L(,s,v,) Spectral radiance W m-2

sr-1

nm-1

Inherent Optical Properties (IOPs)

),( Volume scattering function (VSF) sr-1

)(~ Normalised volume scattering function sr

-1 m

-1

a() Total absorption coefficient for wavelength m-1

apig(442) Pigment absorption coefficient at 442 nm m-1

b() Total scattering coefficient for wavelength m-1

c() Attenuation coefficient for wavelength m-1

bb() Backscattering coefficient m-1

Apparent Optical Properties (AOPs) and derived quantities

w(,s,v,) Water reflectance dimensionless

wn() Fully normalised water reflectance (i.e. the reflectance

if there were no atmosphere, and for s = v = 0) dimensionless

Eu() Upwelling irradiance W m-2

nm-1

Ed() Downwelling irradiance, above the surface W m-2

nm-1

Es (λ) Total downwelling irradiance just above the sea surface, W m-2

nm-1

denoted also as Ed (λ, 0+).

Lw (λ) 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

R(, 0-) Diffuse reflectance at null depth, or irradiance reflectance dimensionless

(Eu / Ed)

F0() Mean extraterrestrial spectral irradiance W m-2

nm-1

f Ratio of R(0-) to (bb/a); subscript 0 when s = 0 dimensionless

In-situ

Measurement

Protocols: IOPs

& Constituents




Issue: 1.0

Date: March 2013

PAGE: ii


f’ Ratio of R(0-) to (bb/(a + bb)); subscript 0 when s = 0 dimensionless

Q(,s,v,) 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

τa() Aerosol optical thickness dimensionless

τray() Rayleigh (or molecular) optical thickness dimensionless

O3

() Ozone optical thickness dimensionless

Tray (λ) Rayleigh transmittance dimensionless

Ta (λ) Aerosol transmittance dimensionless

TO3 (λ) Ozone transmittance dimensionless

Td (λ) Total downwelling transmittance (diffuse + direct) dimensionless

Tu (λ) Total upwelling transmittance (diffuse + direct) dimensionless

Ps Surface pressure hPa

uO3 Ozone concentration cm-atm

RH Relative humidity percent

),( sdT Downwelling total transmittance at sea surface level dimensionless

Air-water interface

)'( Geometrical factor, accounting for multiple reflections and dimensionless

refractions at the air-sea interface (Morel and Gentilli, 1996).

n refractive index of sea water dimensionless

f() Fresnel reflectance at the air-sea interface for the scattering angle dimensionless

mean reflection coefficient for the downwelling irradiance at the

sea surface dimensionless

r 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 dimensionless

and viewing configurations (s, v, )

Miscellaneous

ws Wind-speed just above sea level m s-1

ln Natural (or Neperian) logarithm

log10 Decimal logarithm

In-situ

Measurement

Protocols: IOPs

& Constituents




Issue: 1.0

Date: March 2013

PAGE: iii


Abbreviations and Definitions

AERONET Aerosol Robotic Network

AOP Apparent Optical Property

ARGANS Applied Research in Geomatics, Atmosphere, Nature and Space

BBOP Bermuda Bio-Optics Project

BOUSSOLE BOUée pour l'acquiSition d'une Série Optique à Long termE

(Buoy for the acquisition of long-term optical time series)

CalCOFI California Cooperative Oceanic Fisheries Investigations

CDOM Coloured Dissolved Organic Matter

Chl Chlorophyll-a concentration mg m-3

CTD Conductivity Temperature Depth

EO Earth Observation

ESA European Space Agency

GPS Global Positioning System

HPLC High Performance Liquid Chromatography

IOP Inherent Optical Property

LOA Laboratoire d'Optique Atmosphérique

LISE Laboratoire Interdisciplinaire des Sciences de l'Environnement

LOV Laboratoire Océanographique in Villefranche sur mer

MERIS Medium Resolution Imaging Spectrometer

MERMAID MERis MAtch-up In-situ Database

MODIS Moderate Resolution Imaging Spectrometer

MQC Measurement Quality Control

MUMM Management Unit of the North Sea Mathematical Models

MVT MERIS Validation Team

NASA National Aeronautics and Space Administration

NIR Near Infrared

NOMAD NASA bio-Optical Marine Algorithm Dataset

OC Ocean Color

ODESA Optical Data Processor of the European Space Agency

OBPG Ocean Biology Processing Group

PAR Photosynthetically Available Radiation

PI Principle Investigator

PQC Processing Quality Control

QWG Quality Working Group

RMD Reference Model Document

SeaBASS SeaWiFS Bio-Optical Archive and Storage System

SeaWiFS Sea-viewing Wide Field-of-view Sensor

SPM Suspended Particulate Matter

SPMR SeaWiFS Profiling Multichannel Radiometer

TACCS Tethered Attenuation Coefficient Chain Sensor

TSM Total Suspended Matter (g m-3

)

UK United Kingdom

YS Yellow Substance absorption coefficient (m-1

)

In-situ

Measurement

Protocols: IOPs

& Constituents




Issue: 1.0

Date: March 2013

PAGE: iv


YSBPA 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)

In-situ

Measurement

Protocols: IOPs

& Constituents




Issue: 1.0

Date: March 2013

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_Third-

Reprocessing_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:

04.1)]442([0.21][ pigaChl (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:

)442(73.1)( 3

pbmgTSM (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.

https://earth.esa.int/instruments/meris/rfm/MERIS_RMD_Third-Reprocessing_OCEAN_Aug2012.pdf


In-situ

Measurement

Protocols: IOPs

& Constituents




Issue: 1.0

Date: March 2013

PAGE: 2


1.3 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.

1.3.1 Data submission and feedback

PI’s should write to [email protected] 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 [email protected] to express interest and

provide a description of your project.

Figure 1-1: MERMAID project website:

http://hermes.acri.fr/mermaid.

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

http://hermes.acri.fr/mermaid

mailto:[email protected]

http://hermes.acri.fr/mermaid/policy/policy.php

mailto:[email protected]

http://hermes.acri.fr/mermaid/proto

In-situ

Measurement

Protocols: IOPs

& Constituents




Issue: 1.0

Date: March 2013

PAGE: 3


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

HPLC_chla_ONLY

_IS

SPECT_chla

_IS

Fluor_chla_IS AERONET_Chla

_IS

UNIT mg m-3 mg m-3 mg m-3 mg m-3 mg m-3

Description Total Chla derived

from HPLC pigment

analysis.

Sum of HPLC chla,

div. chla, chlide-a +

phaeopigments

Chla only

derived from

HPLC pigment

analysis

Spectrophoto

-metric Chla

Calibrated

fluorometric chla

(check protocols

for calibration)

Chlorophyll-a

computed in

the

AERONET-

OC processor

from

SeaPRISM

radiances.

Equivalent

MERIS L2

product:

API1 API2 PI to state

whether they

consider

their Chla

equivalent to

API1 or

API2.

(See

respective

protocols)

API1

Available

MERMAID

sites

Algarve

BOUSSOLE

CASES

PortCoast

NOMAD

Plumes and

Blooms

PMLNorthSeaWEC

BSH-

SummerSurvey

Algarve

MUMM

REPHY

Wadden Sea

Algarve

NW Baltic

Bristol

Channel and

Irish Sea

MAREL

NOMAD

Plumes and

Blooms

BSH-

SummerSurvey

AAOT

Abu Al-

Bukhoosh

COVE

SeaPRISM

Gloria

Gustav-Dahlen

Tower

Helsinki

Lighthouse

LISCO

LJCO

MVCO

Palgrunden

WAVE_CIS

In-situ

Measurement

Protocols: IOPs

& Constituents




Issue: 1.0

Date: March 2013

PAGE: 4


2.2 Site overview

Table 2-2: Summary of site providing Chla , MERIS product it is comparable to and the PI definitions

SITE PI Chla type

Compares

to

AP1 or

AP2?

PI definition (where relevant)

Algarve

J. Icely

HPLC_chla_TOTAL_IS API1

Combination of methods. Not clear which

values correspond to which method. Next

dataset to split by method.

HPLC_chla_ONLY_IS API2 HPLC only

SPECT_chla_IS

BioOptEuro-

fleets E. Canuti HPLC_chla_TOTAL_IS API1

BOUSSOLE D. Antoine /

J. Ras HPLC_chla_TOTAL_IS

API1 and

API2

TChla = sum(Chlorophyll a + Divinyl

Chlorophyll a + Chlorophyllide a).

Another 'Chla' is available:

sum(Chlorophyll a + allomers + epimers)

Bristol

Channel

& IrishSea D. Mckee

SPECT_chla_IS API1 A1: Trichromatic equations give chla

(and b, c, caretonoids)

SPECT_chla_IS API2 A2: Acidification produces chla and

phaeopigments

BSH

SummerSurvey H. Klein HPLC_chla_ ONLY _IS API2

CASES

(Arctic) S. Belanger HPLC_chla_TOTAL_IS API1

Chlorophyll a + Divinyl Chlorophyll a +

Chlorophyllide a

English

Channel H. Loisel SPECT_chla_IS API1

French

Guiana

Helgoland R. Doerffer HPLC_chla_TOTAL_IS API1 Chla + degradation products

IFREMER

MAREL C. Belin

Fluor_chla_IS API2

IFREMER

REPHY HPLC_chla_ONLY_IS API2

Chla only derived from HPLC pigment

analysis

NOMAD

(World) J. Werdell


Chla = Chla + DV_Chl_a + Chlide_a

WHERE: HPLC Chla = MV_chl_a +

allomers + epimers.

Fluor_chla_IS

Fluorometrically/spectrophotometrically-

derived chlorophyll a

NW Baltic S. Kratzer SPECT_chla_IS API2

PMLNorthSea

WEC G. Tilstone HPLC_chla_TOTAL_IS API1

PnB

(California) D. Siegel


Total chlorophyll a (HPLC method) = the

sum of Chla (including allomers and

epimers) + mono vinyl Chla + Divinyl

Chla + Chlorophyllide-a

Fluor_chla_IS API2 Comparable to Total chlorophyll a

measured by HPLC

PortCoast V. Brotas HPLC_chla_TOTAL_IS API1

Wadden Sea A.

Hommersom HPLC_chla_ONLY_IS API2

In-situ

Measurement

Protocols: IOPs

& Constituents




Issue: 1.0

Date: March 2013

PAGE: 5


2.3 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 Conditions

0 1 100 0 0 Injection

4 1 0 100 0 Linear gradient




29 1 100 0 0 Equilibration

Measurements of absorption coefficients of aquatic particles were made using the T-R (Transmission-

Reflectance) 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.

In-situ

Measurement

Protocols: IOPs

& Constituents




Issue: 1.0

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

In-situ

Measurement

Protocols: IOPs

& Constituents




Issue: 1.0

Date: March 2013

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.

In-situ

Measurement

Protocols: IOPs

& Constituents




Issue: 1.0

Date: March 2013

PAGE: 8


2.3.7 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).

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

Figure 2-2: Map of 2005-2008 sampling

locations for PortCoast dataset

In-situ

Measurement

Protocols: IOPs

& Constituents




Issue: 1.0

Date: March 2013

PAGE: 9


Quantified pigment: Chl a (Chla

+epimers+allomers+DvChla) [μg.L‐1]

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).

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).

Figure 2-3: Map of 2009-2012 sampling

locations for PortCoast dataset

In-situ

Measurement

Protocols: IOPs

& Constituents




Issue: 1.0

Date: March 2013

PAGE: 10


2.3.9 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 HPLC Chlorophyll a only

2.4.1 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.

In-situ

Measurement

Protocols: IOPs

& Constituents




Issue: 1.0

Date: March 2013

PAGE: 11


2.4.2 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 Spectrophotometry

2.5.1 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).

lxV

vxaommgaChl

.)665665(7.26)( 3

(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

In-situ

Measurement

Protocols: IOPs

& Constituents




Issue: 1.0

Date: March 2013

PAGE: 12


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).

lxV

vxoammgntsphaeopigme

.)665]665[7.1(7.26)( 3

(4)

2.5.2 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).

In-situ

Measurement

Protocols: IOPs

& Constituents




Issue: 1.0

Date: March 2013

PAGE: 13


y = 1.03 x + 0.18

R² = 0.99 n =32

0.00

5.00

10.00

15.00

20.00

25.00

0.00 5.00 10.00 15.00 20.00 25.00

Ch

l sp

ec µ

g l

-1

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 Fluorometry

2.6.1 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.


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.

In-situ

Measurement

Protocols: IOPs

& Constituents




Issue: 1.0

Date: March 2013

PAGE: 14


3. Suspended Sediments


Table 3-1: Suspended sediment definitions in MERMAID, and available sites providing matchups.

FIELD TSM_IS OSM_IS MSM_IS POC_IS

Unit g m-3

g m-3

g m-3

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

CASES

NOMAD

3.2 Bristol Channel and Irish Sea

TSM is measured by filtering a volume of seawater (usually 5L) through a pre-combusted and pre-

weighed 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.

In-situ

Measurement

Protocols: IOPs

& Constituents




Issue: 1.0

Date: March 2013

PAGE: 15


3.5 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.

In-situ

Measurement

Protocols: IOPs

& Constituents




Issue: 1.0

Date: March 2013

PAGE: 16


4. IOPs


Table 4-1: IOP definitions in MERMAID and available sites providing matchups.

* denotes availability at several wavelengths

Absorptions

FIELD a_IS_* ap_IS_* adet_IS_* aph_IS_* ag_IS_*

Unit m-1

m-1

m-1

m-1

m-1

Description Absorption

coefficient at

lambda (*)

(incl. aw, NASA

protocols)

a = aw+ag+ap

Particulate

absorption at

lambda (*)

ap = aph+adet

ap = a- aw - ag

Detrital

absorption at

lambda (*)

Algal pigment

absorption at

lambda (*)

aph = ap - adet

In-situ measured

Coloured

Dissolved

Organic Matter

(Yellow

substance), at

lambda (*)

ag = a- aw - ap

Available

sites

NOMAD NOMAD

PnB

NOMAD

PnB

PnB

CASES

CASES

PnB (ag)

WaddenSea

NOMAD

Scattering

FIELD b_IS_* bs_IS bp_IS_* bb_IS_* bbs_IS

Unit m-1

Dimensionless m-1

m-1

Dimensionless

Descrip-tion Scattering at

lambda (*)

b = bw +bp

Scatter-ing

spectral slope

Particulate

scattering

(phytoplan-kton

+ detritus) at

lambda (*)

Backscattering

at lambda (*)

bb = bbw+bbp

Backscattering

spectral slope

Available

sites

NOMAD

PnB

PMLNorthSea

WEC

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.


In-situ

Measurement

Protocols: IOPs

& Constituents




Issue: 1.0

Date: March 2013

PAGE: 17


4.2.1 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).

f

s

pT

pTpT (5)

4.2.2 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).

f

s

pR

pRpR (6)

4.2.3 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

In-situ

Measurement

Protocols: IOPs

& Constituents




Issue: 1.0

Date: March 2013

PAGE: 18


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).

pT

f

pRpT

f

sR

RpTa

1

1)(

(7)

))750(5.0)((17.015.1)( TrTr ODOD (8)

where ODTr is the optical density measured in the transmission mode.

The sample absorption, as, was converted then to sample absorbance in (9).

)1(

1log10

s

sa

A

(9)

and then to the equivalent particle suspension absorbance Asus by means of the empirical correlation

[Asus(), As)] shown in (10).

λA+λA=λAsssus 20.4790.423 (10)

4.2.4 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

In-situ

Measurement

Protocols: IOPs

& Constituents




Issue: 1.0

Date: March 2013

PAGE: 19


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).

l

A=λa

g

g

2.303 (11)

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

In-situ

Measurement

Protocols: IOPs

& Constituents




Issue: 1.0

Date: March 2013

PAGE: 20


and 500 nm using a non-linear regression method (Levenberg-Marquardt).

)0()0()( S

gg eaa (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:

)()()( mmwt baa (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).


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.

In-situ

Measurement

Protocols: IOPs

& Constituents




Issue: 1.0

Date: March 2013

PAGE: 21


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):

)]([exp)()( 00 xxx Saa (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:

2)(

)(5.0

x

x

a

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.

In-situ

Measurement

Protocols: IOPs

& Constituents




Issue: 1.0

Date: March 2013

PAGE: 22


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 fixed-

depth 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 1-

meter 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

In-situ

Measurement

Protocols: IOPs

& Constituents




Issue: 1.0

Date: March 2013

PAGE: 23


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:

).)(()()(0

0

v

bpbwb bbb

(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).

In-situ

Measurement

Protocols: IOPs

& Constituents




Issue: 1.0

Date: March 2013

PAGE: 24


4.3.3 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.

In-situ

Measurement

Protocols: IOPs

& Constituents




Issue: 1.0

Date: March 2013

PAGE: 25


5. AOPs


Table 5-1: AOP definitions in MERMAID, and available sites providing matchups.

FIELD PAR_IS_* PARz1%_IS KPAR_IS Kd_IS_* Kd490_IS

Unit W m-2

m m-1

m-1

m-1

Description Photo-

synthetically

Available

Radiation

Euphotic

depth: depth

of 1% light

level of Photo-

synthetically

Available

Radiation

(PAR, Wm-2

)

Diffuse

downwelling

attenuation

coefficient for

Photo-

synthetically

Available

Radiation (PAR,

Wm-2

), KPAR

Diffuse

attenuation

coefficient for

downwelling

irradiance at

lambda (*)

Diffuse attenuation

coefficient for

downwelling

irradiance, Kd at

490 nm.

(for sites where

other bands do not

exist).

Available

sites

CaliCurrent NOMAD CaliCurrent

NOMAD

BOUSSOLE

CaliCurrent

CASES

NOMAD

BOUSSOLE

CaliCurrent

CASES

5.2 BOUSSOLE

A diffuse attenuation coefficient for the downward irradiance in the upper layers is computed as:

z

EzEK dd

d

))0((/))(log((

(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

In-situ

Measurement

Protocols: IOPs

& Constituents




Issue: 1.0

Date: March 2013

PAGE: 26


(1998) transformed the remote sensing reflectance to the normalized water-leaving radiance as:

)(),0()( 0 FRL RSwm

(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:

1

90 )0,(),( ekEzkE dd (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.

In-situ

Measurement

Protocols: IOPs

& Constituents




Issue: 1.0

Date: March 2013

PAGE: 27


6. References

Austin, R. W. (1974).The remote sensing of spectral radiance from below the ocean surface. In

Optical Aspects of Oceanography, 317-344 (Eds N. G. Jerlov and E. Steemann-Nielsen). New

York: Academic Press, London.

Babin, M., Morel, A., Fournier-Sicre, V., Fell, F. &Stramski, D. (2003a). Light scattering properties

of marine particles in coastal and open ocean waters as related to the particle mass

concentration. Limnology and Oceanography 48(2): 843-859.

Babin, M., Stramski, D., Ferrari, G. M., Claustre, H., Bricaud, A., Obolensky, G. &al., e. (2003b).

Variations in the light absorption coefficients of phytoplankton, non algal particles, and

dissolved organic matter in coastal waters around europe. Journal of Geophysical Research

108: 3211 (doi: 3210.1029/2001JC000882).

Balch, W. M. &Drapeau, D. T. (2003).Backscattering by coccolithophorids and coccoliths: sample

preparation, measurement, and analysis protocols. In Ocean Optics Protocols for Satellite

Ocean Color Sensor Validation, Revision 5, Volume V: Biogeochemical and Bio-optical

Measurements and Data Analysis Protocols, Vol. NASA Tech. Memo. 2003-211621, Rev. 5,

Vol. V, 27-36 (Eds J. L. Mueller, G. Fargion and C. McClain). Greenbelt, Maryland:

NASA/GSFC.

Belanger, S., Xie, H., Krotkov, N., Larouche, P., Vincent, W. F. &Babin, M. (2006).

Photomineralization of terrigenous dissolved organic matter in Arctic coastal waters from

1979 to 2003: Interannual variability and implications of climate change. Global

Biogeochemical Cycles 20(GB4005, doi:10.1029/2006GB002708.).

Boss, E. &Pegau, W. S. (2001). The relationship of light scattering at an angle in the backward

direction to the backscattering coefficient. Applied Optics 40: 5503-5507.

Brotas, V. &Plante-Cuny, M. R. (1996). Identification et quantification des pigments chlorophylliens

et caroténoïdes des sédiments marins: un protocole d’analyse par HPLC. Oceanologica Acta

19: 623-634.

Ferrari, G. M., Dowell, M., Grossi, S. &Targa, C. (1996). Relationship between the optical properties

of chromophoric dissolved organic matter and total concentration of dissolved organic carbon

in the southern Baltic Sea region. Marine Chemistry 55: 299–316.

Gallegos, C. L. &Neale, P. J. (2002). Partitioning spectral absorption in case 2 waters: discrimination

of dissolved and particulates components. Applied Optics 41(21): 4220-4233.

Gordon, H. R. (1992). Diffuse reflectance of the ocean: influence of nonuniform phytoplankton

pigment profile. Applied Optics 31(12): 2116-2129.

Gordon, H. R. &Clark, D. K. (1980). Remote sensing optical properties of a stratified ocean: an

improved interpretation. Applied Optics 19: 3428-3430.

Gordon, H. R. &McCluney, W. R. (1975). Estimation of depth of sunlight penetration in sea for

remote-sensing. Applied Optics 14: 413-416.

Hooker, S. B., Thomas, C., Van Heukelem, L., Schlüter, L., Russ, M., Ras, J., Claustre, H.,

Clementson, L., Canuti, E., Berthon, J.-F., Perl, J., Normandeau, C., Cullen, J., Kienast, M.

&Pinckney, J. (2010).The Fourth SeaWiFS HPLC Analysis Round-Robin Experiment

(SeaHARRE-4). Vol. NASA/TM–2010–215857Greenbelt, Maryland.: NASA/GSFC.

Jeffrey, S. W., Mantoura, R. F. C. &Write, S. W. (1997). Phytoplankton pigments in oceanography:

guidelines to modern methods. UNESCO Publishing.

Kahru, M. &Mitchell, B. G. (1999). Empirical chlorophyll algorithm and preliminary SeaWiFS

validation for the California Current. International Journal of Remote Sensing 20: 3423-3429.

Kishino, M., Takahashi, M., Okami, N. &Ichimura, S. (1985a). Estimation of the spectral absorption-

coefficients of phytoplankton in the sea. Bulletin of Marine Science 37: 634–642.

Kishino, M., Takahashi, M., Okami, N. &Ichimura, S. (1985b). Estimation of the spectral absorption

coefficients of phytoplankton in the sea. Bulletin of Marine Science 37(2): 634-642.

Kopelevich, O. (1983).Small-parameter model of optical properties of sea water. In Ocean Optics, I:

In-situ

Measurement

Protocols: IOPs

& Constituents




Issue: 1.0

Date: March 2013

PAGE: 28


Physical Ocean Optics, 208-234 (Ed A. S. Monin). Moscow: Nauka Publishing.

Kraay, G. W., Zapata, M. &Veldhuis, M. J. (1992). Separation of chlorophylla c1, c2 and c, of marine

phytoplankton by reversed phase C18 high performance liquid chromatography. Journal of

Phycology 28: 708-712.

Laurion, I., Blouin, F. &Roy, S. (2003). The quantitative filter technique for measuring phytoplankton

absorption : Interference by MAAs in the UV waveband. Limnology and Oceanography-

Methods 1(1): 1-9.

Lorenzen, C. (1967a).Determination of chlorophyll and pheopigments: spectrophotometric equations.

Vol. 12, 343-346 San Diego: Scripps Institution of Oceanography, University of California.

Lorenzen, C. (1967b). Determination of chlorophyll and pheopigments:spectrophotometric equations

Limnology and Oceanography 12(2): 343-346.

Maffione, R. A. &Dana, D. R. (1997). Instruments and methods for measuring the backward-

scattering coefficient of ocean waters. Applied Optics 36(24): 6057-6067.

Mitchell, B. G., Bricaud, A., Carder, K. L., Cleveland, J. S., Ferrari, G. M. &Gould, R.

(2000).Determination of spectral absorption coefficients of particles, dissolved material, and

phytoplankton for discrete water samples in ocean optics protocols for satellite ocean color

sensor validation. In NASA Technical Series, 125–153 (Eds G. Fargion and J. L. Mueller).

Greenbelt, Maryland.

Mitchell, B. G. &Kahru, M. (1998).Algorithms for SeaWIFS standard products developed with the

CALCOFI bio-optical data set. In CALCOFI Report, Vol. 39, 15pp.

Moore, C., Zaneveld, J. R. V. &Kitchen, J. C. (1992).Preliminary results from an in-situ spectral

absorption meter. In SPIE Society of Optical Engineering, Vol. 1750, 330-337.

Morel, A. (1973).Diffusion de la lumière par les eaux de mer: Résultats experimentaux et approach

théoretique. Vol. 61, 3.1.1-3.1.76: NATO AGARD Lecture Series.

Morel, A. (1974).Optical properties of pure seawater. In Optical Aspects of Oceanography., 1-24 (Eds

N. G. Jerlov and E. Steeman-Nielsen).

Morel, A. &Antoine, D. (1999).Pigment index retrieval in Case1 waters. In ENVISAT-MERIS

Algorithm Theoretical Basis Document 2.9, 25: European Space Agency.

Mueller, J. L. (2000).SeaWiFS algorithm for the diffuse attenuation coefficient, K(490), using water-

leaving radiances at 490 and 555 nm In SeaWiFS postlaunch calibration and validation

analyses: Part 3. NASA Technical Memorandum, Vol. 11, 24-27 (Eds S. B. Hooker and E. R.

Firestone). Greenbelt, Maryland, USA.: NASA Goddard Space Flight Center.

Mueller, J. L. &Austin, R. W. (1995).Ocean optics protocols for SeaWiFS validation, Revision 1. In

NASA Tech. Memo., Vol. 25(Eds S. B. Hooker, E. R. Firestone and J. Acker). Greenbelt,

Maryland: NASA Goddard Space Flight Center.

Mueller, J. L., Bidigare, R. R., Trees, C., Balch, W. M., Dore, J. &Drapeau, D. T. (2003a).Ocean

optics protocols for satellite ocean colour sensor validation, Revision 5, Volume V:

Biogeochemical and bio-opitcal measurements and data analysis protocols., 36 Greenbelt,

MD: NASA/GSFC.

Mueller, J. L., Fargion, G. &McClain, C. (2003b).Ocean optics protocols for satellite ocean color

sensor validation, Revision 4. Vol. I - VII, 141 Greenbelt, Maryland: NASA.

Park, Y., Van Mol, B. &Ruddick, K. (2006).Validation of MERIS water products for Belgian coastal

waters: 2002- 2005. In MERIS Validation Team Meeting.

Press, W. H., Flannery, B. P., Teukolsky, S. A. &Vetterlin, W. T. (1992). Numerical Recipes in C:

The Art of Scientific Computing. London: Cambridge University Press.

Ras, J., Uitz, J. &Claustre, H. (2008). Spatial variability of phytoplankton pigment distributions in the

Subtropical South Pacific Ocean: comparison between in situ and modelled data.

Biogeosciences 5: 353-369.

Roesler, C. A., Perry, M. J. &Carder, K. L. (1989). In-situ phytoplankton absorption, fluorescence

emission, and particulate backscattering spectra determined from reflectance. Journal of

Geophysical Research 100: 13279-13294.

In-situ

Measurement

Protocols: IOPs

& Constituents




Issue: 1.0

Date: March 2013

PAGE: 29


Sørensen, K., Aas, E. &Hokedal, J. (2007). Validation of MERIS water products and biooptical

relationships in the Skagerrak. International Journal of Remote Sensing 28: 555–568.

Sosik, H. (1999). Storage of marine particulate samples for light-absorption measurements. Limnology

and Oceanography 44(4): 1139-1141.

Stramska, M., Stramski, D., Hapter, R., Kaczmarek, S. &Stoń, J. (2003). Bio-optical relationships and

ocean color algorithms for the north polar region of the Atlantic. Journal of Geophysical

Research 108(NO. C5, 3143, doi:10.1029/2001JC001195).

Strickland, J. D. H. &Parsons, T. R. (1972). A practical handbook of the sea water analysis. Fisheries

Research Board Canada Bulletin: 167-311.

Tassan, S. &Ferrari, G. M. (1995). Proposal for the measurement of backward and total scattering by

mineral particles suspended in water. Applied Optics 34: 8345–8353.

Tassan, S. &Ferrari, G. M. (1998). Measurement of light absorption by aquatic particles retained on

filters: Determination of the optical pathlength amplification by the ‘transmittance-

reflectance’ method. Journal of Plankton Research 20: 1699–1709.

Tassan, S. &Ferrari, G. M. (2002). A sensitivity analysis of the Transmittance-Reflectance methods

for measuring light absorption by aquatic particles. Journal of Plankton Analysis 24: 757-774.

Tilstone, G. H., Moore, G. F., Sørensen, K., Doerffer, R., Røttgers, R., Ruddick, K., Pasterkamp, R.

&Jørgensen, P. V. (2002).REVAMP Regional Validation of MERIS Chlorophyll products in

North Sea coastal waters., 78 Plymouth: Plymouth Marine Laboratory.

Tilstone, G. H., Peters, S., van der Woerd, H. J., Eleveld, M., Ruddick, K., Schönfeld, W.,

Krasemann, H., Martinez-Vicente, V., Blondeau-Pattissier, D., Röttgers, R., Sørensen, K.,

Jørgensen, P. V. &Shutler, J. (2012). Variability in specific-absorption properties and their

use in a semi-analytical ocean colour algorithm for MERIS in North Sea and Western English

Channel Coastal Waters. Remote Sensing of the Environment 118: 320–338.

Vaillancourt, R. D., Brown, C., Guillard, R. R. &Balch, W. M. (2004). Light backscattering properties

of marine phytoplankton: relationship to cell size, chemical composition and taxonomy.

Journal of Plankton Research 26: 191-212.

Van Heukelem, L. &Thomas, C. (2001). Computer-assisted high-performance liquid chromatography

method development with applications to the isolation and analysis of phytoplankton

pigments. Journal of Chromatography A 910: 31-49.

Van Heukelem, L. &Thomas, C. (2009).The HPL Method. In The Third SeaWiFS HPLC Analysis

Round-Robin Experiment (SeaHARRE-3), Vol. NASA TM 2009-215849, 97 pp. (Eds S. B.

Hooker, L. Van Heukelem, C. Thomas, H. Claustre, J. Ras, L. Schlüter, L. Clementson, D.

Van der Linde, E. Develi-Eker, J.-F. Berthon, R. G. Barlow, H. Sessions, H. Ismail and J.

Perl). Greenbelt, Maryland.: NASA/GSFC.

Vidussi, F., Claustre, H., Manca, B., Luchetta, A. &Marty, J. (2001). Phytoplankton pigment

distribution in relation to upper thermocline circulation in the eastern Mediterranean Sea

during winter. Journal of Geophysical Research 106: 19,939-919,956.

Werdell, P. J. (2005).An evaluation of Inherent Optical Property data for inclusion in the NASA bio-

Optical Marine Algorithm Data set. 6pp.: NASA Ocean Biology Processing Group.

Werdell, P. J. &Bailey, S. W. (2005). An improved in situ bio-optical data set for ocean colour

algorithm development and satellite data product validation. Remote Sensing of Environment

98: 122-140.

Zaneveld, J. R. V., Kitchen, J. C. &Moore, C. (1994).The scattering Error Correction of Reflecting-

Tube Absorption Meters. In Ocean Optics XII, Vol. 2258, 44-55 (Ed J. S. Jaffe). Bergen:

SPIE.

Zapata, M., Rodriguez, F. &Garrido, J. L. (2000). Separation of chlorophylls and carotenoids from

marine phytoplankton: a new HPLC method using a reversed phase C column and pyridine-

containing mobile phases Marine Ecology Progress Series 195: 29-45.

In-situ Measurement Protocols. - Acrimermaid.acri.fr/dataproto/CO-SCI-ARG-TN-0008_In... · Date:...

Documents

Transcript of In-situ Measurement Protocols. - Acrimermaid.acri.fr/dataproto/CO-SCI-ARG-TN-0008_In... · Date:...