the Creative Commons Attribution 4.0 License.
the Creative Commons Attribution 4.0 License.
| 15 Jul 2024
A compilation of surface inherent optical properties and phytoplankton pigment concentrations from the Atlantic Meridional Transect
Abstract. In situ measurements of particulate inherent optical properties (IOPs) – absorption (ap(λ)), scattering (bp(λ)), and beam attenuation (cp(λ)) – are crucial for development of optical algorithms that retrieve biogeochemical quantities such as Chlorophyll a, particulate organic carbon (POC) and total suspended matter (TSM). Here we present a compilation of particulate absorption-attenuation spectrophotometric data measured underway on nine Atlantic Meridional Transect (AMT) cruises between 50° north to 50° south from 2009–2019. The compilation includes co-incident high performance liquid chromatography (HPLC) phytoplankton pigment concentrations, which are used to calibrate transects of Total Chlorophyll a (Tot_Chl_a) concentrations derived from the ap(λ) line-height method. The IOP data are processed using a consistent methodology, and include propagated uncertainties for each IOP variable, uncertainty quantification for the Tot_Chl_a concentrations based on HPLC match-ups, application of consistent set of quality-control filters, and standardisation of output data fields and formats. The total IOP dataset consists of ~310,000 measurements at a 1 minute binning (~270,000 hyper-spectral) and > 700 co-incident HPLC pigment surface samples (~600 of which are coincident with hyper-spectral IOPs). We present geographic variation in the IOPs, HPLC phytoplankton pigments, and the ap-derived Tot_Chl_a concentrations, which are shown to have uncertainties between 8–20 %. Additionally, to stimulate further investigation of accessory pigment extraction from ap(λ), we quantify pigment correlation matrices and identify spectral characteristics of end-member ap(λ) spectra where accessory pigment groupings are present in higher concentrations relative to Tot_Chl_a. All data are made publicly available in SeaBASS and NetCDF formats via the following links: https://seabass.gsfc.nasa.gov/archive/PML/AMT, and https://doi.org/10.5281/zenodo.12527954.
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Status: closed
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RC1: 'Comment on essd-2024-267', Emmanuel Boss, 24 Jul 2024
Publisher’s note: a supplement was added to this comment on 30 July 2024.
Evaluation of the manuscript: A compilation of surface inherent optical properties and
phytoplankton pigment concentrations from the Atlantic Meridional Transect, by Jordan et al.
Reviewer: Emmanuel Boss, UMaine.
This data set is unique, comprehensive and I have little doubt it will be used in numerous future studies of upper ocean optics, links to satellite, phytoplankton and their pigments.
Are the data and methods presented new?
Yes, though some have been used in previous papers.
Is there any potential of the data being useful in the future?
Yes, the more data of this kind that is being collected and shared the more we can study ocean processes.
Are methods and materials described in sufficient detail?
Yes.
Are any references/citations to other data sets or articles missing or inappropriate?
Only a few, and I reference them in my comments returned in the annotated PDF document.
Is the article itself appropriate to support the publication of a data set?
It is.
Check the data quality: is the data set accessible via the given identifier?
Yes
Is the data set complete? Are error estimates and sources of errors given (and discussed in the article)? Are the accuracy, calibration, processing, etc. state of the art?
Yes, mostly. A missing part is a discussion wrt the scattering correction of the AC-S and its impact on uncertainties (currently not included).
Are common standards used for comparison?
Yes.
Is the data set significant – unique, useful, and complete?
Yes. Such data is needed and has only been collected by a handful of groups.
Consider article and data set: are there any inconsistencies within these, implausible assertions or data, or noticeable problems which would suggest the data are erroneous (or worse). If possible, apply tests (e.g. statistics). Unusual formats or other circumstances which impede such tests in your discipline may raise suspicion.
As I added in the text, application of the Gaussian decomposition to a_p and comparison to the pigment groups would be nice, though not necessary.
Is the data set itself of high quality?
Yes. The various sources of HPLC have raised an interesting problem for the first time and can/should be used to provide additional uncertainties on pigments available in data bases that merge all HPLC pigments (e.g. Meike Vogt work).
Check the presentation quality: is the data set usable in its current format and size?
Yes.
Are the formal metadata appropriate?
Yes.
Check the publication: is the length of the article appropriate?
Yes.
Is the overall structure of the article well structured and clear?
Yes.
Is the language consistent and precise?
Yes. It is a well written paper.
Are mathematical formulae, symbols, abbreviations, and units correctly defined and used?
Yes.
Are figures and tables correct and of high quality?
Yes.
Is the data set publication, as submitted, of high quality?
Yes.
Finally: By reading the article and downloading the data set, would you be able to understand and (re-)use the data set in the future?
Yes.
Rating
Uniqueness: 2
Significance: 1
Data quality: 1
Presentation quality: 1
- AC1: 'Reply on RC1', Thomas Jordan, 11 Nov 2024
-
RC2: 'Comment on essd-2024-267', Piotr Kowalczuk, 25 Oct 2024
Dr Annick Bricaud
Earth System Science Data
Editorial Support Team
Attn: Review of the manuscript by Thomas M. Jordan, Giorgio Dall'Olmo, Gavin Tilstone, Robert J. W. Brewin, Francesco Nencioli, Ruth Airs, Crystal S. Thomas, and Louise Schlüter entitled “A compilation of surface inherent optical properties and phytoplankton pigment concentrations from the Atlantic Meridional Transect” submitted to Earth System Science Data and coded essd-2024-267.
Dear Dr Bricaud,
After reading the manuscript by Jordan et al., submitted to Earth System Science Data and coded essd-2024-267 I recommend to consider this paper for publication in this journal almost as is.
General opinion
Authors have presented and described in thorough details an impressive data set consisting with more than 300 000 measurements points of spectral values of particulate absorption ap(l), scattering bp(λ) and beam attenuation cp(λ) coefficient, measured along track of nine Atlantic Meridional Transect cruises between 2009-2019. Measurements were conducted with use spectral absorption and attenuation meter ac-9 at nine spectral channels (SeaBird Inc. USA) or its hyperspectral version asc, in the spectral range ∼ 400–750 nm at ∼ 4 nm spectral resolution. Presented data set includes ca. 700 coincident measurements of phytoplankton pigments concentrations with use of the high performance liquid chromatography methods (HPLC). Phytoplankton pigments concentrations measured in collected water sample were used to derive continues transect of the total chlorophyll-a concentration in the surface water based on regression between HPLC total chlorophyll-a concentration and absorption line height at 676 nm parameter calculated from red part of particulate absorption spectrum. This study covered very detailed spectral uncertainty budget of optical measurements and thorough discussion of uncertainty associated with inter laboratory results of the HPLC analysis. Author also included the correlation matrix between total chlorophyll-a concentration and identified accessory pigments and identified spectral characteristics of end-member ap(λ) spectra where accessory pigment groupings were present in higher concentrations relative to Tot_Chl_a. Authors have also presented distribution of selected values of bio-optical parameters in sampled biogeographic provinces of the Atlantic Ocean which make this study not only presentation of data collection but additionally very detailed research paper presenting very valuable bio-optical characterization of the Atlantic Ocean between 50 deg. N and 50 deg. S.
I am impressed by the quality of the data set, and how authors have presented it. I am truly confident that this study shall be published as is. There are very few minor mistakes that I have spotted, by those can be corrected during proof edition. Manuscript does not need any further review.
Congratulations to Authors. Very well done.
Detailed comments
I have spotted just two minor mistake:
Page 4, line 114
Is: “ACS systems (spectral range ∼ 400–750 nm at ∼ 15 nm spectral resolution)…”
Actually the spectral resolution of the acs instrument is ca. 4.3 nm. According to technical specification provided by manufacturer acs measures absorption and attenuation in the spectral range 400–750 nm at 80 spectral channels which makes 4.3 nm spectral spacing between channels. Please correct.
Page 7, Equation 4
Is: b′p(λ) = ap,m(λ)−cp,m(λ),
Shall be
b’p(l) = cp,m(l) – ap,m(l)
Use of Equation 4 as written in the original manuscript would results in negative values of spectral scattering coefficient, as spectral attenuation coefficient values are greater than spectral absorption coefficient values. Please correct.
Best regards
Piotr Kowalczuk
- AC1: 'Reply on RC1', Thomas Jordan, 11 Nov 2024
Status: closed
-
RC1: 'Comment on essd-2024-267', Emmanuel Boss, 24 Jul 2024
Publisher’s note: a supplement was added to this comment on 30 July 2024.
Evaluation of the manuscript: A compilation of surface inherent optical properties and
phytoplankton pigment concentrations from the Atlantic Meridional Transect, by Jordan et al.
Reviewer: Emmanuel Boss, UMaine.
This data set is unique, comprehensive and I have little doubt it will be used in numerous future studies of upper ocean optics, links to satellite, phytoplankton and their pigments.
Are the data and methods presented new?
Yes, though some have been used in previous papers.
Is there any potential of the data being useful in the future?
Yes, the more data of this kind that is being collected and shared the more we can study ocean processes.
Are methods and materials described in sufficient detail?
Yes.
Are any references/citations to other data sets or articles missing or inappropriate?
Only a few, and I reference them in my comments returned in the annotated PDF document.
Is the article itself appropriate to support the publication of a data set?
It is.
Check the data quality: is the data set accessible via the given identifier?
Yes
Is the data set complete? Are error estimates and sources of errors given (and discussed in the article)? Are the accuracy, calibration, processing, etc. state of the art?
Yes, mostly. A missing part is a discussion wrt the scattering correction of the AC-S and its impact on uncertainties (currently not included).
Are common standards used for comparison?
Yes.
Is the data set significant – unique, useful, and complete?
Yes. Such data is needed and has only been collected by a handful of groups.
Consider article and data set: are there any inconsistencies within these, implausible assertions or data, or noticeable problems which would suggest the data are erroneous (or worse). If possible, apply tests (e.g. statistics). Unusual formats or other circumstances which impede such tests in your discipline may raise suspicion.
As I added in the text, application of the Gaussian decomposition to a_p and comparison to the pigment groups would be nice, though not necessary.
Is the data set itself of high quality?
Yes. The various sources of HPLC have raised an interesting problem for the first time and can/should be used to provide additional uncertainties on pigments available in data bases that merge all HPLC pigments (e.g. Meike Vogt work).
Check the presentation quality: is the data set usable in its current format and size?
Yes.
Are the formal metadata appropriate?
Yes.
Check the publication: is the length of the article appropriate?
Yes.
Is the overall structure of the article well structured and clear?
Yes.
Is the language consistent and precise?
Yes. It is a well written paper.
Are mathematical formulae, symbols, abbreviations, and units correctly defined and used?
Yes.
Are figures and tables correct and of high quality?
Yes.
Is the data set publication, as submitted, of high quality?
Yes.
Finally: By reading the article and downloading the data set, would you be able to understand and (re-)use the data set in the future?
Yes.
Rating
Uniqueness: 2
Significance: 1
Data quality: 1
Presentation quality: 1
- AC1: 'Reply on RC1', Thomas Jordan, 11 Nov 2024
-
RC2: 'Comment on essd-2024-267', Piotr Kowalczuk, 25 Oct 2024
Dr Annick Bricaud
Earth System Science Data
Editorial Support Team
Attn: Review of the manuscript by Thomas M. Jordan, Giorgio Dall'Olmo, Gavin Tilstone, Robert J. W. Brewin, Francesco Nencioli, Ruth Airs, Crystal S. Thomas, and Louise Schlüter entitled “A compilation of surface inherent optical properties and phytoplankton pigment concentrations from the Atlantic Meridional Transect” submitted to Earth System Science Data and coded essd-2024-267.
Dear Dr Bricaud,
After reading the manuscript by Jordan et al., submitted to Earth System Science Data and coded essd-2024-267 I recommend to consider this paper for publication in this journal almost as is.
General opinion
Authors have presented and described in thorough details an impressive data set consisting with more than 300 000 measurements points of spectral values of particulate absorption ap(l), scattering bp(λ) and beam attenuation cp(λ) coefficient, measured along track of nine Atlantic Meridional Transect cruises between 2009-2019. Measurements were conducted with use spectral absorption and attenuation meter ac-9 at nine spectral channels (SeaBird Inc. USA) or its hyperspectral version asc, in the spectral range ∼ 400–750 nm at ∼ 4 nm spectral resolution. Presented data set includes ca. 700 coincident measurements of phytoplankton pigments concentrations with use of the high performance liquid chromatography methods (HPLC). Phytoplankton pigments concentrations measured in collected water sample were used to derive continues transect of the total chlorophyll-a concentration in the surface water based on regression between HPLC total chlorophyll-a concentration and absorption line height at 676 nm parameter calculated from red part of particulate absorption spectrum. This study covered very detailed spectral uncertainty budget of optical measurements and thorough discussion of uncertainty associated with inter laboratory results of the HPLC analysis. Author also included the correlation matrix between total chlorophyll-a concentration and identified accessory pigments and identified spectral characteristics of end-member ap(λ) spectra where accessory pigment groupings were present in higher concentrations relative to Tot_Chl_a. Authors have also presented distribution of selected values of bio-optical parameters in sampled biogeographic provinces of the Atlantic Ocean which make this study not only presentation of data collection but additionally very detailed research paper presenting very valuable bio-optical characterization of the Atlantic Ocean between 50 deg. N and 50 deg. S.
I am impressed by the quality of the data set, and how authors have presented it. I am truly confident that this study shall be published as is. There are very few minor mistakes that I have spotted, by those can be corrected during proof edition. Manuscript does not need any further review.
Congratulations to Authors. Very well done.
Detailed comments
I have spotted just two minor mistake:
Page 4, line 114
Is: “ACS systems (spectral range ∼ 400–750 nm at ∼ 15 nm spectral resolution)…”
Actually the spectral resolution of the acs instrument is ca. 4.3 nm. According to technical specification provided by manufacturer acs measures absorption and attenuation in the spectral range 400–750 nm at 80 spectral channels which makes 4.3 nm spectral spacing between channels. Please correct.
Page 7, Equation 4
Is: b′p(λ) = ap,m(λ)−cp,m(λ),
Shall be
b’p(l) = cp,m(l) – ap,m(l)
Use of Equation 4 as written in the original manuscript would results in negative values of spectral scattering coefficient, as spectral attenuation coefficient values are greater than spectral absorption coefficient values. Please correct.
Best regards
Piotr Kowalczuk
- AC1: 'Reply on RC1', Thomas Jordan, 11 Nov 2024
Data sets
SeaBASS archive for: `Surface inherent optical properties and phytoplankton pigment concentrations from the Atlantic Meridional Transect (2009 - 2019)' Thomas M. Jordan, Giorgio Dall’Olmo, Gavin Tilstone, Robert J. W. Brewin, Francesco Nencioli, Ruth Airs, Crystal S. Thomas, and Louise Schlüter https://seabass.gsfc.nasa.gov/archive/PML/AMT
Surface inherent optical properties and phytoplankton pigment concentrations from the Atlantic Meridional Transect (2009 - 2019): NetCDF format Thomas M. Jordan, Giorgio Dall’Olmo, Gavin Tilstone, Robert J. W. Brewin, Francesco Nencioli, Ruth Airs, Crystal S. Thomas, and Louise Schlüter https://zenodo.org/records/12527954
Model code and software
AMT IOP processing code Giorgio Dall’Olmo, Thomas M. Jordan, and Francesco Nencioli https://github.com/tjor/AMT19_underway
AMT IOP processing code Giorgio Dall’Olmo, Thomas M. Jordan, and Francesco Nencioli https://github.com/tjor/AMT22_underway
AMT IOP processing code Giorgio Dall’Olmo, Thomas M. Jordan, and Francesco Nencioli https://github.com/tjor/AMT23_underway
AMT IOP processing code Giorgio Dall’Olmo, Thomas M. Jordan, and Francesco Nencioli https://github.com/tjor/AMT24_underway
AMT IOP processing code Giorgio Dall’Olmo, Thomas M. Jordan, and Francesco Nencioli https://github.com/tjor/AMT25_underway
AMT IOP processing code Giorgio Dall’Olmo, Thomas M. Jordan, and Francesco Nencioli https://github.com/tjor/AMT26_underway
AMT IOP processing code Giorgio Dall’Olmo, Thomas M. Jordan, and Francesco Nencioli https://github.com/tjor/AMT27_underway
AMT IOP processing code Giorgio Dall’Olmo, Thomas M. Jordan, and Francesco Nencioli https://github.com/tjor/AMT28_underway
AMT IOP processing code Giorgio Dall’Olmo, Thomas M. Jordan, and Francesco Nencioli https://github.com/tjor/AMT29_underway
Interactive computing environment
Data access script and plot functions for ESSD paper Thomas M. Jordan https://github.com/tjor/AMT_ACSpaperplots
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