Numerical modelling of the shelf break ecosystem: reproducing benthic and pelagic measurements
Identifieur interne : 002D28 ( Istex/Corpus ); précédent : 002D27; suivant : 002D29Numerical modelling of the shelf break ecosystem: reproducing benthic and pelagic measurements
Auteurs : Karline Soetaert ; Peter M. J Herman ; Jack J. Middelburg ; Carlo Heip ; Claire L. Smith ; Paul Tett ; Karen Wild-AllenSource :
- Deep-Sea Research Part II [ 0967-0645 ] ; 2001.
Abstract
A coupled pelagic-benthic biogeochemical model, embedded in a turbulence-closure formulation is employed for the Goban Spur shelf-break area (northeast Atlantic). Our main objectives are to examine the impact of in situ atmospheric conditions on ecosystem dynamics, to reproduce biogeochemical distributions in the water column and the sediments, and to derive a nitrogen budget for the area. Given a data set of atmospheric forcing conditions at 3-h intervals, the model successfully explains the time evolution of the temperature field. Most biochemical water column properties are reasonably well simulated, both in timing and in magnitude. Some of the short-term variability, apparent in the data, can be reproduced, suggesting that this may result from variability in the in situ atmospheric forcing. In summer, intermittent mixing events generate increased ammonium and nitrate concentrations in the upper water column, consistent with observations. These short-term nutrient injections substantially increase euphotic zone production, mainly by stimulating new production. The model also reproduces a set of benthic nutrient profiles, measured on two occasions, both qualitatively and quantitatively. The results suggest that there is a significant variability in benthic properties. A tentative nitrogen budget for the Goban Spur shelf break area is proposed. The sediments account for about 7% of organic nitrogen respiration; about 42% occurs in the euphotic zone, and the remaining 50% takes place in the water column below the euphotic zone. About 3% of the annual primary production of organic nitrogen is denitrified in the sediments and is replenished from lateral sources in the model. Nitrification mainly takes place in the water column below the euphotic zone (66%); sedimentary nitrification and ammonium oxidation in the euphotic zone both account for 17%. Over the year, only 55% of euphotic zone nitrogen assimilation is based on the in situ regenerated inorganic nitrogen, the remainder is mainly supplied by mixing from below the euphotic zone, either in the form of nitrate (72%) or ammonium (28%). The implications of these nitrogen pathways in the euphotic zone on the measured f-ratio are discussed.
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DOI: 10.1016/S0967-0645(01)00035-2
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<record><TEI wicri:istexFullTextTei="biblStruct"><teiHeader><fileDesc><titleStmt><title>Numerical modelling of the shelf break ecosystem: reproducing benthic and pelagic measurements</title><author><name sortKey="Soetaert, Karline" sort="Soetaert, Karline" uniqKey="Soetaert K" first="Karline" last="Soetaert">Karline Soetaert</name><affiliation><mods:affiliation>E-mail: soetaert@cemo.nioo.knaw.nl</mods:affiliation></affiliation><affiliation><mods:affiliation>Netherlands Institute of Ecology, Centre for Estuarine and Coastal Ecology, P.O. Box 140, 4400-AC Yerseke, The Netherlands</mods:affiliation></affiliation></author><author><name sortKey="Herman, Peter M J" sort="Herman, Peter M J" uniqKey="Herman P" first="Peter M. J" last="Herman">Peter M. J Herman</name><affiliation><mods:affiliation>Netherlands Institute of Ecology, Centre for Estuarine and Coastal Ecology, P.O. Box 140, 4400-AC Yerseke, The Netherlands</mods:affiliation></affiliation></author><author><name sortKey="Middelburg, Jack J" sort="Middelburg, Jack J" uniqKey="Middelburg J" first="Jack J" last="Middelburg">Jack J. Middelburg</name><affiliation><mods:affiliation>Netherlands Institute of Ecology, Centre for Estuarine and Coastal Ecology, P.O. Box 140, 4400-AC Yerseke, The Netherlands</mods:affiliation></affiliation></author><author><name sortKey="Heip, Carlo" sort="Heip, Carlo" uniqKey="Heip C" first="Carlo" last="Heip">Carlo Heip</name><affiliation><mods:affiliation>Netherlands Institute of Ecology, Centre for Estuarine and Coastal Ecology, P.O. Box 140, 4400-AC Yerseke, The Netherlands</mods:affiliation></affiliation></author><author><name sortKey="Smith, Claire L" sort="Smith, Claire L" uniqKey="Smith C" first="Claire L" last="Smith">Claire L. Smith</name><affiliation><mods:affiliation>Department of Biology, Napier University, Edinburgh EH10 5DT, UK</mods:affiliation></affiliation></author><author><name sortKey="Tett, Paul" sort="Tett, Paul" uniqKey="Tett P" first="Paul" last="Tett">Paul Tett</name><affiliation><mods:affiliation>Department of Biology, Napier University, Edinburgh EH10 5DT, UK</mods:affiliation></affiliation></author><author><name sortKey="Wild Allen, Karen" sort="Wild Allen, Karen" uniqKey="Wild Allen K" first="Karen" last="Wild-Allen">Karen Wild-Allen</name><affiliation><mods:affiliation>Department of Biology, Napier University, Edinburgh EH10 5DT, UK</mods:affiliation></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">ISTEX</idno><idno type="RBID">ISTEX:9C96C3BC936B62579563D725010C07A78A025D41</idno><date when="2001" year="2001">2001</date><idno type="doi">10.1016/S0967-0645(01)00035-2</idno><idno type="url">https://api.istex.fr/document/9C96C3BC936B62579563D725010C07A78A025D41/fulltext/pdf</idno><idno type="wicri:Area/Istex/Corpus">002D28</idno></publicationStmt><sourceDesc><biblStruct><analytic><title level="a">Numerical modelling of the shelf break ecosystem: reproducing benthic and pelagic measurements</title><author><name sortKey="Soetaert, Karline" sort="Soetaert, Karline" uniqKey="Soetaert K" first="Karline" last="Soetaert">Karline Soetaert</name><affiliation><mods:affiliation>E-mail: soetaert@cemo.nioo.knaw.nl</mods:affiliation></affiliation><affiliation><mods:affiliation>Netherlands Institute of Ecology, Centre for Estuarine and Coastal Ecology, P.O. Box 140, 4400-AC Yerseke, The Netherlands</mods:affiliation></affiliation></author><author><name sortKey="Herman, Peter M J" sort="Herman, Peter M J" uniqKey="Herman P" first="Peter M. J" last="Herman">Peter M. J Herman</name><affiliation><mods:affiliation>Netherlands Institute of Ecology, Centre for Estuarine and Coastal Ecology, P.O. Box 140, 4400-AC Yerseke, The Netherlands</mods:affiliation></affiliation></author><author><name sortKey="Middelburg, Jack J" sort="Middelburg, Jack J" uniqKey="Middelburg J" first="Jack J" last="Middelburg">Jack J. Middelburg</name><affiliation><mods:affiliation>Netherlands Institute of Ecology, Centre for Estuarine and Coastal Ecology, P.O. Box 140, 4400-AC Yerseke, The Netherlands</mods:affiliation></affiliation></author><author><name sortKey="Heip, Carlo" sort="Heip, Carlo" uniqKey="Heip C" first="Carlo" last="Heip">Carlo Heip</name><affiliation><mods:affiliation>Netherlands Institute of Ecology, Centre for Estuarine and Coastal Ecology, P.O. Box 140, 4400-AC Yerseke, The Netherlands</mods:affiliation></affiliation></author><author><name sortKey="Smith, Claire L" sort="Smith, Claire L" uniqKey="Smith C" first="Claire L" last="Smith">Claire L. Smith</name><affiliation><mods:affiliation>Department of Biology, Napier University, Edinburgh EH10 5DT, UK</mods:affiliation></affiliation></author><author><name sortKey="Tett, Paul" sort="Tett, Paul" uniqKey="Tett P" first="Paul" last="Tett">Paul Tett</name><affiliation><mods:affiliation>Department of Biology, Napier University, Edinburgh EH10 5DT, UK</mods:affiliation></affiliation></author><author><name sortKey="Wild Allen, Karen" sort="Wild Allen, Karen" uniqKey="Wild Allen K" first="Karen" last="Wild-Allen">Karen Wild-Allen</name><affiliation><mods:affiliation>Department of Biology, Napier University, Edinburgh EH10 5DT, UK</mods:affiliation></affiliation></author></analytic><monogr></monogr><series><title level="j">Deep-Sea Research Part II</title><title level="j" type="abbrev">DSRII</title><idno type="ISSN">0967-0645</idno><imprint><publisher>ELSEVIER</publisher><date type="published" when="2001">2001</date><biblScope unit="volume">48</biblScope><biblScope unit="issue">14–15</biblScope><biblScope unit="page" from="3141">3141</biblScope><biblScope unit="page" to="3177">3177</biblScope></imprint><idno type="ISSN">0967-0645</idno></series><idno type="istex">9C96C3BC936B62579563D725010C07A78A025D41</idno><idno type="DOI">10.1016/S0967-0645(01)00035-2</idno><idno type="PII">S0967-0645(01)00035-2</idno></biblStruct></sourceDesc><seriesStmt><idno type="ISSN">0967-0645</idno></seriesStmt></fileDesc><profileDesc><textClass></textClass><langUsage><language ident="en">en</language></langUsage></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">A coupled pelagic-benthic biogeochemical model, embedded in a turbulence-closure formulation is employed for the Goban Spur shelf-break area (northeast Atlantic). Our main objectives are to examine the impact of in situ atmospheric conditions on ecosystem dynamics, to reproduce biogeochemical distributions in the water column and the sediments, and to derive a nitrogen budget for the area. Given a data set of atmospheric forcing conditions at 3-h intervals, the model successfully explains the time evolution of the temperature field. Most biochemical water column properties are reasonably well simulated, both in timing and in magnitude. Some of the short-term variability, apparent in the data, can be reproduced, suggesting that this may result from variability in the in situ atmospheric forcing. In summer, intermittent mixing events generate increased ammonium and nitrate concentrations in the upper water column, consistent with observations. These short-term nutrient injections substantially increase euphotic zone production, mainly by stimulating new production. The model also reproduces a set of benthic nutrient profiles, measured on two occasions, both qualitatively and quantitatively. The results suggest that there is a significant variability in benthic properties. A tentative nitrogen budget for the Goban Spur shelf break area is proposed. The sediments account for about 7% of organic nitrogen respiration; about 42% occurs in the euphotic zone, and the remaining 50% takes place in the water column below the euphotic zone. About 3% of the annual primary production of organic nitrogen is denitrified in the sediments and is replenished from lateral sources in the model. Nitrification mainly takes place in the water column below the euphotic zone (66%); sedimentary nitrification and ammonium oxidation in the euphotic zone both account for 17%. Over the year, only 55% of euphotic zone nitrogen assimilation is based on the in situ regenerated inorganic nitrogen, the remainder is mainly supplied by mixing from below the euphotic zone, either in the form of nitrate (72%) or ammonium (28%). The implications of these nitrogen pathways in the euphotic zone on the measured f-ratio are discussed.</div></front></TEI><istex><corpusName>elsevier</corpusName><author><json:item><name>Karline Soetaert</name><affiliations><json:string>E-mail: soetaert@cemo.nioo.knaw.nl</json:string><json:string>Netherlands Institute of Ecology, Centre for Estuarine and Coastal Ecology, P.O. Box 140, 4400-AC Yerseke, The Netherlands</json:string></affiliations></json:item><json:item><name>Peter M.J Herman</name><affiliations><json:string>Netherlands Institute of Ecology, Centre for Estuarine and Coastal Ecology, P.O. Box 140, 4400-AC Yerseke, The Netherlands</json:string></affiliations></json:item><json:item><name>Jack J Middelburg</name><affiliations><json:string>Netherlands Institute of Ecology, Centre for Estuarine and Coastal Ecology, P.O. Box 140, 4400-AC Yerseke, The Netherlands</json:string></affiliations></json:item><json:item><name>Carlo Heip</name><affiliations><json:string>Netherlands Institute of Ecology, Centre for Estuarine and Coastal Ecology, P.O. Box 140, 4400-AC Yerseke, The Netherlands</json:string></affiliations></json:item><json:item><name>Claire L Smith</name><affiliations><json:string>Department of Biology, Napier University, Edinburgh EH10 5DT, UK</json:string></affiliations></json:item><json:item><name>Paul Tett</name><affiliations><json:string>Department of Biology, Napier University, Edinburgh EH10 5DT, UK</json:string></affiliations></json:item><json:item><name>Karen Wild-Allen</name><affiliations><json:string>Department of Biology, Napier University, Edinburgh EH10 5DT, UK</json:string></affiliations></json:item></author><language><json:string>eng</json:string></language><abstract>A coupled pelagic-benthic biogeochemical model, embedded in a turbulence-closure formulation is employed for the Goban Spur shelf-break area (northeast Atlantic). Our main objectives are to examine the impact of in situ atmospheric conditions on ecosystem dynamics, to reproduce biogeochemical distributions in the water column and the sediments, and to derive a nitrogen budget for the area. Given a data set of atmospheric forcing conditions at 3-h intervals, the model successfully explains the time evolution of the temperature field. Most biochemical water column properties are reasonably well simulated, both in timing and in magnitude. Some of the short-term variability, apparent in the data, can be reproduced, suggesting that this may result from variability in the in situ atmospheric forcing. In summer, intermittent mixing events generate increased ammonium and nitrate concentrations in the upper water column, consistent with observations. These short-term nutrient injections substantially increase euphotic zone production, mainly by stimulating new production. The model also reproduces a set of benthic nutrient profiles, measured on two occasions, both qualitatively and quantitatively. The results suggest that there is a significant variability in benthic properties. A tentative nitrogen budget for the Goban Spur shelf break area is proposed. The sediments account for about 7% of organic nitrogen respiration; about 42% occurs in the euphotic zone, and the remaining 50% takes place in the water column below the euphotic zone. About 3% of the annual primary production of organic nitrogen is denitrified in the sediments and is replenished from lateral sources in the model. Nitrification mainly takes place in the water column below the euphotic zone (66%); sedimentary nitrification and ammonium oxidation in the euphotic zone both account for 17%. Over the year, only 55% of euphotic zone nitrogen assimilation is based on the in situ regenerated inorganic nitrogen, the remainder is mainly supplied by mixing from below the euphotic zone, either in the form of nitrate (72%) or ammonium (28%). The implications of these nitrogen pathways in the euphotic zone on the measured f-ratio are discussed.</abstract><qualityIndicators><score>8</score><pdfVersion>1.2</pdfVersion><pdfPageSize>544 x 743 pts</pdfPageSize><refBibsNative>true</refBibsNative><keywordCount>0</keywordCount><abstractCharCount>2228</abstractCharCount><pdfWordCount>10808</pdfWordCount><pdfCharCount>65160</pdfCharCount><pdfPageCount>37</pdfPageCount><abstractWordCount>332</abstractWordCount></qualityIndicators><title>Numerical modelling of the shelf break ecosystem: reproducing benthic and pelagic measurements</title><pii><json:string>S0967-0645(01)00035-2</json:string></pii><genre><json:string>research-article</json:string></genre><host><volume>48</volume><pii><json:string>S0967-0645(00)X0046-X</json:string></pii><pages><last>3177</last><first>3141</first></pages><issn><json:string>0967-0645</json:string></issn><issue>14–15</issue><genre><json:string>Journal</json:string></genre><language><json:string>unknown</json:string></language><title>Deep-Sea Research Part II</title><publicationDate>2001</publicationDate></host><categories><wos><json:string>OCEANOGRAPHY</json:string></wos></categories><publicationDate>2001</publicationDate><copyrightDate>2001</copyrightDate><doi><json:string>10.1016/S0967-0645(01)00035-2</json:string></doi><id>9C96C3BC936B62579563D725010C07A78A025D41</id><fulltext><json:item><original>true</original><mimetype>application/pdf</mimetype><extension>pdf</extension><uri>https://api.istex.fr/document/9C96C3BC936B62579563D725010C07A78A025D41/fulltext/pdf</uri></json:item><json:item><original>true</original><mimetype>text/plain</mimetype><extension>txt</extension><uri>https://api.istex.fr/document/9C96C3BC936B62579563D725010C07A78A025D41/fulltext/txt</uri></json:item><json:item><original>false</original><mimetype>application/zip</mimetype><extension>zip</extension><uri>https://api.istex.fr/document/9C96C3BC936B62579563D725010C07A78A025D41/fulltext/zip</uri></json:item><istex:fulltextTEI uri="https://api.istex.fr/document/9C96C3BC936B62579563D725010C07A78A025D41/fulltext/tei"><teiHeader><fileDesc><titleStmt><title level="a">Numerical modelling of the shelf break ecosystem: reproducing benthic and pelagic measurements</title></titleStmt><publicationStmt><authority>ISTEX</authority><publisher>ELSEVIER</publisher><availability><p>ELSEVIER</p></availability><date>2001</date></publicationStmt><notesStmt><note type="content">Fig. 1: Model structure, encompassing the physical submodel, the biogeochemical pelagic and diagenetic model. Circles denote state variables, related quantities are in rectangles. (□=not modelled).</note><note type="content">Fig. 2: An example of non-linear fits used to estimate mixed layer depth, MLD (a); depth of the nitracline, (zn) and mean nitrate concentration (b) and the position of the ammonium maximum, (zm) and mean ammonium concentration (c).</note><note type="content">Fig. 3: Fit of modelled and observed temperature (a, 0–5; b, 50; c, 100; and d, 150m) and fit of modelled and observed mixed layer depth (e).</note><note type="content">Fig. 4: a. Wind speed used as a forcing function (ms−1). b. Spatio-temporal evolution of the vertical diffusivity coefficient (Kz, m2s−1). Emphasised here are two wind-driven mixing events. c. Relationship between wind speed and the modelled diffusivity coefficient at 5m below the surface.</note><note type="content">Fig. 5: a. Fit of modelled and observed nitrate concentrations (μmoll−1, mean, surficial and deep concentration) and nitracline depth (m). Circles are data for which the two-layer model used to fit the data was not significantly better than the constant nitrate concentration model. (see material and methods). b. Fit of modelled and observed ammonium concentrations (μmoll−1, mean, surficial and deep concentration) and depth of ammonium maximum (m). Solid squares are data for which the non-linear fitting of profiles by means of a shifted Gaussian was significantly the best; circles are data for which a constant concentration model was significantly best. c. Fit of modelled and observed oxygen concentrations (μmoll−1, surficial and deep concentration).</note><note type="content">Fig. 6: a. Fit of modelled and observed chlorophyll concentrations (μgl−1, mean, surficial) and the position of the chlorophyll maximum (m). b. Fit of modelled and measured euphotic zone primary production (left, mmol-Cm−2d−1) and the euphotic-zone nitrate uptake rate as a fraction of total (nitrate+ammonium) N-uptake (right, f-ratio) based on satellite observations and 15N techniques. c. Fit of modelled and observed microzooplankton concentration in the upper 10m of the water column (μmol-Cl−1).</note><note type="content">Fig. 7: a. Fit of modelled and observed sediment community oxygen consumption rates (mmolm−2d−1). b. Fit of modelled and observed sedimentary oxygen, nitrate and ammonium profiles obtained at day 291 (26/10/93) and at day 508 (23/05/94).</note><note type="content">Fig. 8: a. Spatio-temporal plot of the modelled fields of temperature, chlorophyll, nitrate and ammonium in the water column for the year 1994. b. Spatio-temporal plot of the oxygen, ammonium and nitrate concentrations in the sediment for the year 1994.</note><note type="content">Fig. 9: Yearly-averaged nitrogen budget (1994) of the euphotic zone (defined as the depth where 1% of surficial PAR is retained), the water column below the euphotic zone (aphotic), and the sediment. All fluxes are in mmol-Nm−2a−1. For comparison, the average total load of pelagic nitrogen was 1840mmolm−2, benthic nitrogen (upper m) amounts on average to 265mmolm−2. (a) the N-fluxes to the phytoplankton (left), the pelagic detritus+microzooplankton (right) and the sediment compartment; (b) the relative contribution of the main processes in the three zones.</note><note type="content">Fig. 10: Comparison of euphotic zone production based on a model run with weather forcing (3-hourly resolution, dashed line) and atmospheric forcing (smooth sinus function or constant forcing, solid line).</note><note type="content">Table 1: The conservation equations for the physical submodela</note><note type="content">Table 2: Parameter values used in the physical submodel</note><note type="content">Table 3: The conservation equations used in the biogeochemical pelagic modela</note><note type="content">Table 4: Parameter values used in the biochemical part of the model</note><note type="content">Table 5: Forcing functionsa</note></notesStmt><sourceDesc><biblStruct type="inbook"><analytic><title level="a">Numerical modelling of the shelf break ecosystem: reproducing benthic and pelagic measurements</title><author><persName><forename type="first">Karline</forename><surname>Soetaert</surname></persName><email>soetaert@cemo.nioo.knaw.nl</email><note type="correspondence"><p>Corresponding author. Tel.: +31-113-577487; fax: +31-113-573616</p></note><affiliation>Netherlands Institute of Ecology, Centre for Estuarine and Coastal Ecology, P.O. Box 140, 4400-AC Yerseke, The Netherlands</affiliation></author><author><persName><forename type="first">Peter M.J</forename><surname>Herman</surname></persName><affiliation>Netherlands Institute of Ecology, Centre for Estuarine and Coastal Ecology, P.O. Box 140, 4400-AC Yerseke, The Netherlands</affiliation></author><author><persName><forename type="first">Jack J</forename><surname>Middelburg</surname></persName><affiliation>Netherlands Institute of Ecology, Centre for Estuarine and Coastal Ecology, P.O. Box 140, 4400-AC Yerseke, The Netherlands</affiliation></author><author><persName><forename type="first">Carlo</forename><surname>Heip</surname></persName><affiliation>Netherlands Institute of Ecology, Centre for Estuarine and Coastal Ecology, P.O. Box 140, 4400-AC Yerseke, The Netherlands</affiliation></author><author><persName><forename type="first">Claire L</forename><surname>Smith</surname></persName><affiliation>Department of Biology, Napier University, Edinburgh EH10 5DT, UK</affiliation></author><author><persName><forename type="first">Paul</forename><surname>Tett</surname></persName><affiliation>Department of Biology, Napier University, Edinburgh EH10 5DT, UK</affiliation></author><author><persName><forename type="first">Karen</forename><surname>Wild-Allen</surname></persName><affiliation>Department of Biology, Napier University, Edinburgh EH10 5DT, UK</affiliation></author></analytic><monogr><title level="j">Deep-Sea Research Part II</title><title level="j" type="abbrev">DSRII</title><idno type="pISSN">0967-0645</idno><idno type="PII">S0967-0645(00)X0046-X</idno><imprint><publisher>ELSEVIER</publisher><date type="published" when="2001"></date><biblScope unit="volume">48</biblScope><biblScope unit="issue">14–15</biblScope><biblScope unit="page" from="3141">3141</biblScope><biblScope unit="page" to="3177">3177</biblScope></imprint></monogr><idno type="istex">9C96C3BC936B62579563D725010C07A78A025D41</idno><idno type="DOI">10.1016/S0967-0645(01)00035-2</idno><idno type="PII">S0967-0645(01)00035-2</idno></biblStruct></sourceDesc></fileDesc><profileDesc><creation><date>2001</date></creation><langUsage><language ident="en">en</language></langUsage><abstract xml:lang="en"><p>A coupled pelagic-benthic biogeochemical model, embedded in a turbulence-closure formulation is employed for the Goban Spur shelf-break area (northeast Atlantic). Our main objectives are to examine the impact of in situ atmospheric conditions on ecosystem dynamics, to reproduce biogeochemical distributions in the water column and the sediments, and to derive a nitrogen budget for the area. Given a data set of atmospheric forcing conditions at 3-h intervals, the model successfully explains the time evolution of the temperature field. Most biochemical water column properties are reasonably well simulated, both in timing and in magnitude. Some of the short-term variability, apparent in the data, can be reproduced, suggesting that this may result from variability in the in situ atmospheric forcing. In summer, intermittent mixing events generate increased ammonium and nitrate concentrations in the upper water column, consistent with observations. These short-term nutrient injections substantially increase euphotic zone production, mainly by stimulating new production. The model also reproduces a set of benthic nutrient profiles, measured on two occasions, both qualitatively and quantitatively. The results suggest that there is a significant variability in benthic properties. A tentative nitrogen budget for the Goban Spur shelf break area is proposed. The sediments account for about 7% of organic nitrogen respiration; about 42% occurs in the euphotic zone, and the remaining 50% takes place in the water column below the euphotic zone. About 3% of the annual primary production of organic nitrogen is denitrified in the sediments and is replenished from lateral sources in the model. Nitrification mainly takes place in the water column below the euphotic zone (66%); sedimentary nitrification and ammonium oxidation in the euphotic zone both account for 17%. Over the year, only 55% of euphotic zone nitrogen assimilation is based on the in situ regenerated inorganic nitrogen, the remainder is mainly supplied by mixing from below the euphotic zone, either in the form of nitrate (72%) or ammonium (28%). The implications of these nitrogen pathways in the euphotic zone on the measured f-ratio are discussed.</p></abstract></profileDesc><revisionDesc><change when="2001">Published</change></revisionDesc></teiHeader></istex:fulltextTEI></fulltext><metadata><istex:metadataXml wicri:clean="Elsevier, elements deleted: ce:floats; body; tail"><istex:xmlDeclaration>version="1.0" encoding="utf-8"</istex:xmlDeclaration><istex:docType PUBLIC="-//ES//DTD journal article DTD version 4.5.2//EN//XML" URI="art452.dtd" name="istex:docType"><istex:entity SYSTEM="gr1" NDATA="IMAGE" name="gr1"></istex:entity><istex:entity SYSTEM="gr2" NDATA="IMAGE" name="gr2"></istex:entity><istex:entity SYSTEM="gr3" NDATA="IMAGE" name="gr3"></istex:entity><istex:entity SYSTEM="gr4" NDATA="IMAGE" name="gr4"></istex:entity><istex:entity SYSTEM="gr5a" NDATA="IMAGE" name="gr5a"></istex:entity><istex:entity SYSTEM="gr5bc" NDATA="IMAGE" name="gr5bc"></istex:entity><istex:entity SYSTEM="gr6a" NDATA="IMAGE" name="gr6a"></istex:entity><istex:entity SYSTEM="gr6bc" NDATA="IMAGE" name="gr6bc"></istex:entity><istex:entity SYSTEM="gr7" NDATA="IMAGE" name="gr7"></istex:entity><istex:entity SYSTEM="gr8" NDATA="IMAGE" name="gr8"></istex:entity><istex:entity SYSTEM="gr9" NDATA="IMAGE" name="gr9"></istex:entity><istex:entity SYSTEM="gr10" NDATA="IMAGE" name="gr10"></istex:entity><istex:entity SYSTEM="fx1" NDATA="IMAGE" name="fx1"></istex:entity><istex:entity SYSTEM="fx2" NDATA="IMAGE" name="fx2"></istex:entity><istex:entity SYSTEM="fx3" NDATA="IMAGE" name="fx3"></istex:entity><istex:entity SYSTEM="fx4" NDATA="IMAGE" name="fx4"></istex:entity><istex:entity SYSTEM="fx5" NDATA="IMAGE" name="fx5"></istex:entity><istex:entity SYSTEM="fx6" NDATA="IMAGE" name="fx6"></istex:entity></istex:docType><istex:document><converted-article version="4.5.2" docsubtype="fla"><item-info><jid>DSRII</jid><aid>873</aid><ce:pii>S0967-0645(01)00035-2</ce:pii><ce:doi>10.1016/S0967-0645(01)00035-2</ce:doi><ce:copyright type="full-transfer" year="2001">Elsevier Science Ltd</ce:copyright></item-info><head><ce:title>Numerical modelling of the shelf break ecosystem: reproducing benthic and pelagic measurements</ce:title><ce:author-group><ce:author><ce:given-name>Karline</ce:given-name><ce:surname>Soetaert</ce:surname><ce:cross-ref refid="AFFA"><ce:sup>a</ce:sup></ce:cross-ref><ce:cross-ref refid="CORR1">*</ce:cross-ref><ce:e-address>soetaert@cemo.nioo.knaw.nl</ce:e-address></ce:author><ce:author><ce:given-name>Peter M.J</ce:given-name><ce:surname>Herman</ce:surname><ce:cross-ref refid="AFFA"><ce:sup>a</ce:sup></ce:cross-ref></ce:author><ce:author><ce:given-name>Jack J</ce:given-name><ce:surname>Middelburg</ce:surname><ce:cross-ref refid="AFFA"><ce:sup>a</ce:sup></ce:cross-ref></ce:author><ce:author><ce:given-name>Carlo</ce:given-name><ce:surname>Heip</ce:surname><ce:cross-ref refid="AFFA"><ce:sup>a</ce:sup></ce:cross-ref></ce:author><ce:author><ce:given-name>Claire L</ce:given-name><ce:surname>Smith</ce:surname><ce:cross-ref refid="AFFB"><ce:sup>b</ce:sup></ce:cross-ref></ce:author><ce:author><ce:given-name>Paul</ce:given-name><ce:surname>Tett</ce:surname><ce:cross-ref refid="AFFB"><ce:sup>b</ce:sup></ce:cross-ref></ce:author><ce:author><ce:given-name>Karen</ce:given-name><ce:surname>Wild-Allen</ce:surname><ce:cross-ref refid="AFFB"><ce:sup>b</ce:sup></ce:cross-ref></ce:author><ce:affiliation id="AFFA"><ce:label>a</ce:label><ce:textfn>Netherlands Institute of Ecology, Centre for Estuarine and Coastal Ecology, P.O. Box 140, 4400-AC Yerseke, The Netherlands</ce:textfn></ce:affiliation><ce:affiliation id="AFFB"><ce:label>b</ce:label><ce:textfn>Department of Biology, Napier University, Edinburgh EH10 5DT, UK</ce:textfn></ce:affiliation><ce:correspondence id="CORR1"><ce:label>*</ce:label><ce:text>Corresponding author. Tel.: +31-113-577487; fax: +31-113-573616</ce:text></ce:correspondence></ce:author-group><ce:abstract><ce:section-title>Abstract</ce:section-title><ce:abstract-sec><ce:simple-para>A coupled pelagic-benthic biogeochemical model, embedded in a turbulence-closure formulation is employed for the Goban Spur shelf-break area (northeast Atlantic). Our main objectives are to examine the impact of in situ atmospheric conditions on ecosystem dynamics, to reproduce biogeochemical distributions in the water column and the sediments, and to derive a nitrogen budget for the area. Given a data set of atmospheric forcing conditions at 3-h intervals, the model successfully explains the time evolution of the temperature field. Most biochemical water column properties are reasonably well simulated, both in timing and in magnitude. Some of the short-term variability, apparent in the data, can be reproduced, suggesting that this may result from variability in the in situ atmospheric forcing. In summer, intermittent mixing events generate increased ammonium and nitrate concentrations in the upper water column, consistent with observations. These short-term nutrient injections substantially increase euphotic zone production, mainly by stimulating new production. The model also reproduces a set of benthic nutrient profiles, measured on two occasions, both qualitatively and quantitatively. The results suggest that there is a significant variability in benthic properties.</ce:simple-para><ce:simple-para>A tentative nitrogen budget for the Goban Spur shelf break area is proposed. The sediments account for about 7% of organic nitrogen respiration; about 42% occurs in the euphotic zone, and the remaining 50% takes place in the water column below the euphotic zone. About 3% of the annual primary production of organic nitrogen is denitrified in the sediments and is replenished from lateral sources in the model. Nitrification mainly takes place in the water column below the euphotic zone (66%); sedimentary nitrification and ammonium oxidation in the euphotic zone both account for 17%. Over the year, only 55% of euphotic zone nitrogen assimilation is based on the in situ regenerated inorganic nitrogen, the remainder is mainly supplied by mixing from below the euphotic zone, either in the form of nitrate (72%) or ammonium (28%). The implications of these nitrogen pathways in the euphotic zone on the measured <ce:italic>f</ce:italic>-ratio are discussed.</ce:simple-para></ce:abstract-sec></ce:abstract></head></converted-article></istex:document></istex:metadataXml><mods version="3.6"><titleInfo><title>Numerical modelling of the shelf break ecosystem: reproducing benthic and pelagic measurements</title></titleInfo><titleInfo type="alternative" contentType="CDATA"><title>Numerical modelling of the shelf break ecosystem: reproducing benthic and pelagic measurements</title></titleInfo><name type="personal"><namePart type="given">Karline</namePart><namePart type="family">Soetaert</namePart><affiliation>E-mail: soetaert@cemo.nioo.knaw.nl</affiliation><affiliation>Netherlands Institute of Ecology, Centre for Estuarine and Coastal Ecology, P.O. Box 140, 4400-AC Yerseke, The Netherlands</affiliation><description>Corresponding author. Tel.: +31-113-577487; fax: +31-113-573616</description><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">Peter M.J</namePart><namePart type="family">Herman</namePart><affiliation>Netherlands Institute of Ecology, Centre for Estuarine and Coastal Ecology, P.O. Box 140, 4400-AC Yerseke, The Netherlands</affiliation><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">Jack J</namePart><namePart type="family">Middelburg</namePart><affiliation>Netherlands Institute of Ecology, Centre for Estuarine and Coastal Ecology, P.O. Box 140, 4400-AC Yerseke, The Netherlands</affiliation><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">Carlo</namePart><namePart type="family">Heip</namePart><affiliation>Netherlands Institute of Ecology, Centre for Estuarine and Coastal Ecology, P.O. Box 140, 4400-AC Yerseke, The Netherlands</affiliation><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">Claire L</namePart><namePart type="family">Smith</namePart><affiliation>Department of Biology, Napier University, Edinburgh EH10 5DT, UK</affiliation><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">Paul</namePart><namePart type="family">Tett</namePart><affiliation>Department of Biology, Napier University, Edinburgh EH10 5DT, UK</affiliation><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">Karen</namePart><namePart type="family">Wild-Allen</namePart><affiliation>Department of Biology, Napier University, Edinburgh EH10 5DT, UK</affiliation><role><roleTerm type="text">author</roleTerm></role></name><typeOfResource>text</typeOfResource><genre type="research-article" displayLabel="Full-length article"></genre><originInfo><publisher>ELSEVIER</publisher><dateIssued encoding="w3cdtf">2001</dateIssued><copyrightDate encoding="w3cdtf">2001</copyrightDate></originInfo><language><languageTerm type="code" authority="iso639-2b">eng</languageTerm><languageTerm type="code" authority="rfc3066">en</languageTerm></language><physicalDescription><internetMediaType>text/html</internetMediaType></physicalDescription><abstract lang="en">A coupled pelagic-benthic biogeochemical model, embedded in a turbulence-closure formulation is employed for the Goban Spur shelf-break area (northeast Atlantic). Our main objectives are to examine the impact of in situ atmospheric conditions on ecosystem dynamics, to reproduce biogeochemical distributions in the water column and the sediments, and to derive a nitrogen budget for the area. Given a data set of atmospheric forcing conditions at 3-h intervals, the model successfully explains the time evolution of the temperature field. Most biochemical water column properties are reasonably well simulated, both in timing and in magnitude. Some of the short-term variability, apparent in the data, can be reproduced, suggesting that this may result from variability in the in situ atmospheric forcing. In summer, intermittent mixing events generate increased ammonium and nitrate concentrations in the upper water column, consistent with observations. These short-term nutrient injections substantially increase euphotic zone production, mainly by stimulating new production. The model also reproduces a set of benthic nutrient profiles, measured on two occasions, both qualitatively and quantitatively. The results suggest that there is a significant variability in benthic properties. A tentative nitrogen budget for the Goban Spur shelf break area is proposed. The sediments account for about 7% of organic nitrogen respiration; about 42% occurs in the euphotic zone, and the remaining 50% takes place in the water column below the euphotic zone. About 3% of the annual primary production of organic nitrogen is denitrified in the sediments and is replenished from lateral sources in the model. Nitrification mainly takes place in the water column below the euphotic zone (66%); sedimentary nitrification and ammonium oxidation in the euphotic zone both account for 17%. Over the year, only 55% of euphotic zone nitrogen assimilation is based on the in situ regenerated inorganic nitrogen, the remainder is mainly supplied by mixing from below the euphotic zone, either in the form of nitrate (72%) or ammonium (28%). The implications of these nitrogen pathways in the euphotic zone on the measured f-ratio are discussed.</abstract><note type="content">Fig. 1: Model structure, encompassing the physical submodel, the biogeochemical pelagic and diagenetic model. Circles denote state variables, related quantities are in rectangles. (□=not modelled).</note><note type="content">Fig. 2: An example of non-linear fits used to estimate mixed layer depth, MLD (a); depth of the nitracline, (zn) and mean nitrate concentration (b) and the position of the ammonium maximum, (zm) and mean ammonium concentration (c).</note><note type="content">Fig. 3: Fit of modelled and observed temperature (a, 0–5; b, 50; c, 100; and d, 150m) and fit of modelled and observed mixed layer depth (e).</note><note type="content">Fig. 4: a. Wind speed used as a forcing function (ms−1). b. Spatio-temporal evolution of the vertical diffusivity coefficient (Kz, m2s−1). Emphasised here are two wind-driven mixing events. c. Relationship between wind speed and the modelled diffusivity coefficient at 5m below the surface.</note><note type="content">Fig. 5: a. Fit of modelled and observed nitrate concentrations (μmoll−1, mean, surficial and deep concentration) and nitracline depth (m). Circles are data for which the two-layer model used to fit the data was not significantly better than the constant nitrate concentration model. (see material and methods). b. Fit of modelled and observed ammonium concentrations (μmoll−1, mean, surficial and deep concentration) and depth of ammonium maximum (m). Solid squares are data for which the non-linear fitting of profiles by means of a shifted Gaussian was significantly the best; circles are data for which a constant concentration model was significantly best. c. Fit of modelled and observed oxygen concentrations (μmoll−1, surficial and deep concentration).</note><note type="content">Fig. 6: a. Fit of modelled and observed chlorophyll concentrations (μgl−1, mean, surficial) and the position of the chlorophyll maximum (m). b. Fit of modelled and measured euphotic zone primary production (left, mmol-Cm−2d−1) and the euphotic-zone nitrate uptake rate as a fraction of total (nitrate+ammonium) N-uptake (right, f-ratio) based on satellite observations and 15N techniques. c. Fit of modelled and observed microzooplankton concentration in the upper 10m of the water column (μmol-Cl−1).</note><note type="content">Fig. 7: a. Fit of modelled and observed sediment community oxygen consumption rates (mmolm−2d−1). b. Fit of modelled and observed sedimentary oxygen, nitrate and ammonium profiles obtained at day 291 (26/10/93) and at day 508 (23/05/94).</note><note type="content">Fig. 8: a. Spatio-temporal plot of the modelled fields of temperature, chlorophyll, nitrate and ammonium in the water column for the year 1994. b. Spatio-temporal plot of the oxygen, ammonium and nitrate concentrations in the sediment for the year 1994.</note><note type="content">Fig. 9: Yearly-averaged nitrogen budget (1994) of the euphotic zone (defined as the depth where 1% of surficial PAR is retained), the water column below the euphotic zone (aphotic), and the sediment. All fluxes are in mmol-Nm−2a−1. For comparison, the average total load of pelagic nitrogen was 1840mmolm−2, benthic nitrogen (upper m) amounts on average to 265mmolm−2. (a) the N-fluxes to the phytoplankton (left), the pelagic detritus+microzooplankton (right) and the sediment compartment; (b) the relative contribution of the main processes in the three zones.</note><note type="content">Fig. 10: Comparison of euphotic zone production based on a model run with weather forcing (3-hourly resolution, dashed line) and atmospheric forcing (smooth sinus function or constant forcing, solid line).</note><note type="content">Table 1: The conservation equations for the physical submodela</note><note type="content">Table 2: Parameter values used in the physical submodel</note><note type="content">Table 3: The conservation equations used in the biogeochemical pelagic modela</note><note type="content">Table 4: Parameter values used in the biochemical part of the model</note><note type="content">Table 5: Forcing functionsa</note><relatedItem type="host"><titleInfo><title>Deep-Sea Research Part II</title></titleInfo><titleInfo type="abbreviated"><title>DSRII</title></titleInfo><genre type="Journal">journal</genre><originInfo><dateIssued encoding="w3cdtf">2001</dateIssued></originInfo><identifier type="ISSN">0967-0645</identifier><identifier type="PII">S0967-0645(00)X0046-X</identifier><part><date>2001</date><detail type="volume"><number>48</number><caption>vol.</caption></detail><detail type="issue"><number>14–15</number><caption>no.</caption></detail><extent unit="issue pages"><start>2971</start><end>3294</end></extent><extent unit="pages"><start>3141</start><end>3177</end></extent></part></relatedItem><identifier type="istex">9C96C3BC936B62579563D725010C07A78A025D41</identifier><identifier type="DOI">10.1016/S0967-0645(01)00035-2</identifier><identifier type="PII">S0967-0645(01)00035-2</identifier><accessCondition type="use and reproduction" contentType="">© 2001Elsevier Science Ltd</accessCondition><recordInfo><recordContentSource>ELSEVIER</recordContentSource><recordOrigin>Elsevier Science Ltd, ©2001</recordOrigin></recordInfo></mods></metadata><enrichments><istex:catWosTEI uri="https://api.istex.fr/document/9C96C3BC936B62579563D725010C07A78A025D41/enrichments/catWos"><teiHeader><profileDesc><textClass><classCode scheme="WOS">OCEANOGRAPHY</classCode></textClass></profileDesc></teiHeader></istex:catWosTEI></enrichments><serie></serie></istex></record>Pour manipuler ce document sous Unix (Dilib)
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