estuarine, coastal and shelf science · estuarine, coastal and shelf science 86 (2010) 450–466....

lable at ScienceDirect

Estuarine, Coastal and Shelf Science 86 (2010) 450–466

Contents lists avai

Estuarine, Coastal and Shelf Science

journal homepage: www.elsevier .com/locate/ecss

Modeling phytoplankton production in Ise Bay, Japan: Use of nitrogen isotopesto identify dissolved inorganic nitrogen sources

Ryo Sugimoto a,b,*, Akihide Kasai a, Toshihiro Miyajima c, Kouichi Fujita d

a Graduate School of Agriculture, Kyoto University, Oiwake, Kitashirakawa, Sakyo, Kyoto 606-8502, Japanb Field Science Education and Research Center, Kyoto University, Oiwake, Kitashirakawa, Sakyo, Kyoto 606-8502, Japanc Ocean Research Institute, University of Tokyo, Minimidai 1-15-1, Nakano, Tokyo 164-8639, Japand Mie Prefecture Fisheries Research Institute, Shiroko 1-6277-4, Suzuka, Mie 510-0243, Japan

a r t i c l e i n f o

Article history:Received 29 January 2009Accepted 13 October 2009Available online 30 October 2009

Keywords:ecosystem modelestuarine circulationIse baynitrogen isotopesphytoplankton productionseasonal variation

* Corresponding author. Present address: Research CFukui Prefectural University, 49-8-2 Katsumi, Obama-c

E-mail address: [email protected] (R. Sugimoto).

0272-7714/$ – see front matter � 2009 Elsevier Ltd.doi:10.1016/j.ecss.2009.10.011

a b s t r a c t

An important aspect of the nitrogen cycle in coastal environments concerns the source of the nitrogenused in primary production. Phytoplankton production in Ise Bay, one of the most eutrophic embaymentsin Japan, is supported by external nitrogen derived from rivers and the ocean, and regenerated nitrogenformed in hypoxic water within the bay. We evaluated the contribution of each source of dissolvedinorganic nitrogen (DIN) to phytoplankton production in Ise Bay. A unique three-dimensional ecosystemmodel including nitrogen isotopes (d15N) was developed based on precise observations. Model resultsrevealed that DIN (¼ammoniumþ nitrate) consumption by phytoplankton exceeds the DIN supply fromthe rivers and ocean, indicating that a large amount of phytoplankton production in Ise Bay depends onregenerated DIN within the bay rather than on newly supplied DIN. However, the ratio of consumption toexternal supply differs seasonally. Distributions of simulated d15N clearly showed the source of nitrogenincorporated by phytoplankton in each source. The intrusion depth of oceanic water changes from thebottom to the middle layer in spring. Oceanic nitrate is transported into the euphotic layer by the middlelayer intrusion and stimulates phytoplankton production at the bay mouth. The subsurface chlorophyllmaximum layer then develops. In autumn, however, the intrusion depth of oceanic water changes fromthe middle layer to the bottom layer. Regenerated NO3

�, which is accumulated in the hypoxic water mass,is uplifted and continuously supplied to the euphotic layer. These results imply that phytoplanktonproduction in Ise Bay is mainly dominated by the internal cycle rather than the external supply.

� 2009 Elsevier Ltd. All rights reserved.

1. Introduction

Nitrogen is a key element in phytoplankton production andsubsequent ecosystem processes in the sea because it often limitsprimary production. The form of nitrogen incorporated by phyto-plankton determines the partitioning between new and regen-erated production. Various nitrogen sources, including riverine,oceanic, atmospheric, and regenerated nitrogen, maintain thephytoplankton production in coastal ecosystems. Of these majornitrogen sources, riverine input affected by anthropogenicallyperturbed nitrogen flux from land areas to the coast has beenconsidered primarily responsible for eutrophication in coastalzones (Vitousek et al., 1997). However, research has revealed thata large amount of nitrogen, comparable to terrestrial input, is

enter for Marine Bioresources,ity, Fukui 917-0003, Japan

All rights reserved.

supplied from the adjacent marginal sea to the coastal region (e.g.,Fujiwara et al., 1997c). Intrusion of nutrient-rich shelf water stim-ulates phytoplankton production in coastal ecosystems (e.g.,Sugimoto et al., 2009b). Moreover, seasonal variation in watertemperature affects the vertical structure of the water column. Inresponse to water-column stratification during the warm season,oxygen concentrations in the lower water change seasonally, withbottom waters often isolated and becoming hypoxic in summer(e.g., Takahashi et al., 2000). As another source in a seasonal scale,rich organic matter in the sediments and the water column ineutrophic coastal ecosystems supply a large amount of regeneratednitrogen, which accumulates in this oxygen-depleted watermass. However, the quantitative contribution of each nitrogensource to phytoplankton production in coastal environments is stillunclear.

In recent years, variations in the natural abundance of stableisotopes of nitrogen (d15N) in marine ecosystems have attractedconsiderable research attention. The ability to detect small differ-ences in the 15N:14N ratio of various pools of nitrogen, combined

mailto:[email protected]

www.sciencedirect.com/science/journal/02727714

http://www.elsevier.com/locate/ecss

Fig. 1. Study area. Circles indicate the sampling locations in the Kiso Rivers (Kiso,Nagara and Ibi Rivers), the central part of the bay, and the bay mouth (Irago Strait).

R. Sugimoto et al. / Estuarine, Coastal and Shelf Science 86 (2010) 450–466 451

with knowledge of kinetic isotope discrimination during chemicaland biological reactions, potentially provides novel ways tomonitor nitrogen fluxes in marine ecosystems on various temporaland spatial scales. Utilization of d15N to study marine environmentsrequires biological and/or chemical knowledge of sources and sinksand an understanding of isotope discrimination during sink andsource processes.

Knowledge of isotope discrimination would enable researchersto use the 15N:14N signal of phytoplankton to estimate the extentand/or source of nitrogen used by phytoplankton. The d15N value ofphytoplankton is principally determined by the substrate d15N andisotope discrimination as demonstrated by several ocean studies(e.g., Brandes et al., 1998; Sigman et al., 1999). However, the exactrelationship in coastal ecosystems is difficult to interpret becausethe isotopic composition of the source nitrogen is variable and cancause uncertainty when interpreting isotope discrimination,especially if more than one form of nitrogen is present (e.g., NO3

�

and NH4þ), or if more than one source of nitrogen is available (e.g.,

riverine, oceanic, and regenerated nitrogen). Moreover, thetemporal and spatial variabilities of substrate nitrogen sources incoastal environments are controlled by complex physical–biolog-ical–chemical interaction processes associated with externalloading, advection/diffusion, and tidal mixing, as well as oceanicwater inputs.

Since these complicated processes are strongly non-linearlycoupled, studies on the relationships between nutrient behaviorand phytoplankton production have usually relied on physical-ecosystem models that include inorganic and organic mattertransformation and utilization (e.g., Zheng et al., 2004; Kobayashiand Fujiwara, 2008). However, ecosystem models have been criti-cized in regard to reproducibility since they have a large number ofunknown parameters. Generally, these parameters are adjusted toreproduce observed data. Moreover, incubation experiments do notnecessarily provide actual fluxes and rates. These experiments areusually restricted to small spaces and short times, and conductingincubation experiments under actual conditions is difficult.

Phytoplankton production in Ise Bay is supported by nutrientsderived from the river, ocean, and regeneration inside the bay. Atthe head of the bay, the surface chlorophyll maximum is observednear the river mouth. Phytoplankton blooms consume manyterrestrial nutrients from rivers (Sugimoto et al., 2004). In contrast,the subsurface chlorophyll maximum (SCM) develops from thecenter to the mouth of the bay (Fujiwara et al., 1997a; Kasai et al.,2007). The concentration of phytoplankton in the subsurface layerincreases from spring to summer (Kasai et al., 2007). Fujiwara et al.(1997a) suggested that the amount of phytoplankton in the SCMlayer may be larger than that in the river mouth. Possible NO3

�

sources for the SCM are the nutrients supplied from the adjacentcontinental shelf (Kasai et al., 2007). Moreover, nutrients thataccumulate in the hypoxic water mass in the lower layer might beanother source for the SCM (e.g., Fujiwara et al., 1997a; Kakehi et al.,2004). DIN to DIP ratio in the lower layer was high in winter (w20)and low in summer (w5), because of the nitrogen loss by denitri-fication and phosphorous addition by release from the sediments(Kakehi and Fujiwara, 2007). This indicates the nitrogen limits theprimary production in Ise Bay in summer seasons. The form of DINalso changes seasonally with the development of hypoxia. NH4

þ

dominates in spring, and is transformed to NO3� to summer (Sugi-

moto et al., 2008). In autumn, phytoplankton blooms in the surfacelayer (e.g., Kakehi et al., 2005; Kasai et al., 2007). Water mixingreleases nutrients, which is accumulated in the lower layer insummer, to the euphotic layer, and induces the autumn blooms ofphytoplankton. However, the quantitative contribution of differentnutrient sources (river, ocean and regeneration) to primaryproduction in Ise Bay is still unknown. Of these three major

nitrogen sources, the river input has been held primarily respon-sible for the observed long-term eutrophication in Ise Bay. Thequantitative characterization of DIN sources to phytoplanktonproduction is needed for the management of DIN input from therivers.

To address these issues, we developed a unique three-dimen-sional physical-ecosystem model coupled with d15N to evaluate thecontribution of the three major nitrogen sources to phytoplanktonproduction. In particular, we focused on reproducing accumulationof DIN in the lower layer and phytoplankton production in thesubsurface layer. Although regenerated DIN generally means NH4

þ

rather than NO3� in the ocean, here we refer the regenerated

nitrogen to the recycled nitrogen within the bay, which includesNH4þ and NO3

�. In other words, the external DIN sources of river andocean are only the new nitrogen. The d15N values of major nitrogensources (riverine, oceanic, and regenerated) in Ise Bay, Japan, wereidentified by field observations. Such precise observations of d15Nclarify the behavior of DIN and phytoplankton production. More-over, in our previous study, we reported on isotopic discriminationfor nitrification and denitrification in Ise Bay (Sugimoto et al.,2008). Consequently, combining the ecosystem model with d15Nobservations allows us to reveal the comprehensive flow ofnitrogen in the coastal ecosystem.

2. Study area

Ise Bay is one of the largest inner bays in Japan. It has a surfacearea of 1738 km2, volume of 33.9 km3, and mean depth of 19.5 m,with the deepest longitudinal depression extending over 35 mdeep in the middle of the bay (Fig. 1). At its mouth, Ise Bay opens to

R. Sugimoto et al. / Estuarine, Coastal and Shelf Science 86 (2010) 450–466452

the Pacific Ocean via the narrow Irago Strait (w10 km wide). Waterexchange between Ise Bay and the Pacific Ocean takes placethrough Irago Strait. Three major rivers (the Kiso, Nagara, and IbiRivers), known collectively as the Kiso Rivers, flow into the head ofthe bay in the north and contribute w85% of the total freshwaterdischarge into the bay. The discharge of the Kiso Rivers showsseasonal variation, with large discharge in summer and smalldischarge in winter, and an annual mean of w400 m3 s�1. Semi-diurnal constituents dominate the tide in Ise Bay. The typicalamplitude of tidal currents is 0.1 m s�1 in the bay. At Irago Strait,tidal flow converges, and its speed exceeds 0.8 m s�1 during springtides (Fujiwara et al., 2002).

The estuarine gravitational circulation is often dominant in theregions of freshwater influence; lighter water flows seaward in theupper layer, while heavier water flows landward in the lower layer(e.g., Fujiwara et al., 1997b; Kasai et al., 2000). However, recentsurveys in Ise Bay have shown that the longitudinal circulation doesnot always follow the classical estuarine circulation pattern;instead, the flow pattern has a bimodal character. The tidally mixedstrait water flows into the bay through the bottom layer in thecooling season, while it flows through the middle layer in theheating season (e.g., Takahashi et al., 2000). In winter, weak strat-ification is maintained only by freshwater buoyancy near the bayhead. Sea surface cooling causes the freshwater to mix with thedeeper water, so that the water in the bay is lighter than that at thestrait. This density difference leads to bottom inflow in the coolingseason, following the conventional estuarine circulation pattern.During summer, however, the effect of surface heating is restrictedto the upper layer by the strong thermocline and halocline in thestratified area (inside the bay), while it extends to the bottom dueto the strong tidal currents in the well-mixed area around the baymouth (Irago Strait). The water temperature increases faster in thestrait than in the bottom water inside the bay, causing the bottombay water to become denser than the strait water. The well-mixedstrait water thus has a density equivalent to the middle layer insidethe bay and tends to flow through the middle layer when it intrudesinto the bay in the heating season (Takahashi et al., 2000). Asa consequence, relict water in the lower layer within the bay isexcluded from the exchange circulation and forms a cold watermass (Takahashi et al., 2000; Fujiwara et al., 2002; Kasai et al.,2002). The residence time of the isolated water mass was estimatedto be w50 days (Fujiwara et al., 2002). A pycnocline in the verticaland strong fronts in the horizontal prevent oxygen supply from thesurrounding waters to the isolated water mass (Fujiwara et al.,2002; Kasai et al., 2002). Consequently, the isolated water massbecomes hypoxic with time as the oxygen consumption exceedsthe oxygen supply.

3. Field observations

3.1. Observations

Observations to obtain endmember values for each nitrogensource and confirm the reproducibility of data were conductedfrom May 2005 to July 2006. First, seasonal observations to identifyendmenber values of riverine nitrogen were conducted in the lowerparts of the Kiso, Nagara, and Ibi Rivers (Stn. R in Fig. 1). Formeasurements of nutrient concentrations and nitrogen isotoperatios of NH4

þ, NO3�, and particulate nitrogen (PN), surface water

samples were collected at the center part of the streams frombridges using a clean plastic bucket. Water temperature and salinitywere measured using a temperature-salinity meter (Alec Elec-tronics, ACT20-D). Second, the oceanic nitrogen endmembers weredetermined by seasonal observations at the bay mouth (Stn. I). Fornutrient and isotopic analysis of mixed water at 30 m depth at Irago

Strait, samples were taken using 2.6-L Niskin bottles attached toa rosette with a conductivity-temperature-depth (CTD) sensor (SeaBird, SBE-911 plus). Finally, water samples for reproducible dataand isotope discrimination were collected at 5-m intervals from thesurface to 1 m above the bottom (34 m) at the center of Ise Bay (Stn.C). All water samples were filtered immediately through pre-combusted (450 �C, 4 h) glass fiber filters (Whatman GF/F). Filtersand filtrate samples were stored at �30 �C until analyses.

3.2. Analyses

Nutrient concentrations (NH4þ, NO2

�, NO3�, and PO4

3�) weremeasured using an AutoAnalyzer (TRACSS 2000, Bran-Luebbe).Measurement of d15NNH4

was based on that of Holmes et al. (1998).Filtrate samples were transferred to incubation bottles to whichNaCl, MgO, and NH4

þ traps were added. The NH4þ trap consisted of

an acidified 1-cm diameter GF/D filter sandwiched between twoTeflon membrane filters (2.5-cm diameter, 10-mm pore size). Thetraps floated on the saline samples. Samples and references wereincubated for 10–14 days so that all NH4

þ could diffuse out of thesolution and be trapped. During incubation, samples were shakengently and maintained at 40 �C. After incubation, filter packageswere removed from the incubation bottles, dried, and stored ina desiccator containing concentrated sulfuric acid for isotopeanalysis. The procedure for d15NNO3

followed the methods of Sig-man et al. (1997). Filtrate samples were transferred to incubationbottles with MgO and pre-incubated at 65 �C for 5 days. After pre-incubation, samples were boiled to concentrate NO3

� and to removeNH4þ by volatilization. Devarda’s alloy was then added to the

samples and references to reduce NO3� to NH4

þ. The subsequentprocedures were conducted in the same manner as for d15NNH4

.Values of d15N were determined using an elemental analyzer con-nected online to an isotope-ratio mass spectrometer (FLASH EA-Conflo III-DELTAPLUS XP, Thermo-electron). Reproducibility wasbetter than �0.2&. These analyses were executed only for thesamples containing >1.0 mM of NH4

þ and NO3�.

The GF/F filters for elemental and isotopic analyses were treatedas follows. Each sample was dried and wrapped with a tin capsule.PN concentration and its d15N were measured using a mass spec-trometer (Delta S, Finnigan MAT) coupled with an elementalanalyzer (EA1108, Carlo Erba). The d15N values are expressed by theusual d notation (&) relative to atmospheric N2. Reproducibility ofd15NPN was better than �0.3&.

3.3. Observed riverine and oceanic d15N

Fig. 2a shows the relationships between the d15N values in the KisoRivers and the total river discharge of the Kiso Rivers. The riverined15N values are weighted average values of each nitrogen flux for thethree rivers. The d15NNO3

of the Kiso Rivers decreases logarithmicallyfrom 8 to 1& with the increase in river discharge (RD). Thus d15NNO3

obeys a simple logarithmic decreasing relationship with the riverdischarge (r2¼ 0.76, solid line in Fig. 2a) as follows:

d15NNO3 ¼ �2:52� lnðRDÞ þ 18:88: (1)

Although d15NPN rapidly decreases from 6 to 1& untilw400 m3 s�1 of river discharge, d15NPN converges to w2& withhigher river discharge (>w400 m3 s�1). An exponential equation ofthe form y¼ ae�bxþ c was fitted to the observed data, where y is thed15NPN, x is the RD, a and b are constants, and c is an asymptoticvalue of d15NPN. The best-fit curve (r2¼ 0.59, dashed line in Fig. 2a)was calculated by the least-squares method as

d15NPN ¼ 17:20e�0:01RD þ 2:09: (2)

Fig. 2. (a) River discharge vs. d15N values of NO3� (squares), NH4

þ (triangles), and particulate organic nitrogen (circles) at the Kiso Rivers (Stn. R). Solid and dashed lines are the best-fitted curves for d15NNO3

and d15NPN, respectively. (b) Concentrations vs. d15N values of NO3� (squares) and particulate organic nitrogen (circles) at Irago Strait (Stn. I). The solid line is

the linear regression line for d15NNO3.

Fig. 3. Topography of the model basin. The bold line indicates the open boundary.Fresh water flows into the shaded grid.


These relationships indicate that compositions of NO3� and PN

are largely dependent on the discharge. However, no clear rela-tionship was found between d15NNH4

and the river discharge(triangles in Fig. 2a), suggesting that characteristics of NH4

þ aremore complex than those of NO3

� and PN.Fig. 2b shows the relationship between concentrations and d15N

values of NO3� and PN of the mixing water at the strait from May

2005 to July 2006. The d15NNO3value at the strait would be influ-

enced by the mixing between the two different sources at the shelfregion off Ise Bay; lower d15NNO3

in the subsurface layer (w50 m)and higher d15NNO3

in the lower layer (>100 m) (Sugimoto et al.,2009a,b). A strong correlation was thus found between d15NNO3

andthe NO3

� concentrations (r2¼ 0.71, solid line in Fig. 2b), given as

d15NNO3¼ 1:19�

hNO�3

i� 2:25; (3)

where [NO3�] is the concentration of NO3

�. This relationship can beadapted as the variable endmenber for the ecosystem model. Therewas no clear relationship between d15NPN and PN concentrations(circles in Fig. 2b).

In our previous study (Sugimoto et al., 2008), we reported datafor isotope discrimination values by nitrification and denitrificationat the center of the bay (Stn. C). d15NNO3

dramatically shifted from�8.5� 2.0& in May to 8.4� 0.7& in July, in response to thedevelopment of a hypoxic water mass and oxidation from NH4

þ toNO3�. In particular, newly generated NO3

� by nitrification involveda large degree of isotope discrimination (¼24.5&), displayingsignificantly 15N-depleted values during periods with an oxic watercolumn. Although prominent deficits of NO3

� in hypoxic bottomwaters due to denitrification were revealed in July, there was littleisotope discrimination of denitrification in the sediments (¼w1&).

4. Model description

4.1. Model domain

Fig. 3 presents an overall view of the computational grid used inthis study. The horizontal grid coordinates have 18 (x-axis)� 21 (y-axis) points, and the gird size is 20 � 20 (3052.16 m� 3697.87 m).Vertical layers are uniformly distributed every 4 m in depth witha maximum 15 layers (60 m). The open boundary is set outside ofthe bay mouth (bold line in Fig. 3), w70 km from the river mouth.Freshwater from the Kiso Rivers empties into the surface box at thehead of the bay (shaded area in Fig. 3).

4.2. Ecosystem model

The ecosystem model has five compartments, the prognosticvariables being concentrations of nitrogen (mmol L�1). Fig. 4 illus-trates the nitrogen cycle with the compartments, namely NH4

þ,NO3�, phytoplankton (PHY), zooplankton (ZOO) and detritus (DET).

Two other parameters, dissolved inorganic phosphorus (PO43�) and

dissolved oxygen (DO), are also included. The Appendix describesthe formulation of PO4

3� and DO, following the method of Kakehiet al. (2005). The evolutions of these compartments are describedwith differential equations composed of biological source and sinkterms, external loading terms, diffusion terms, and advectionterms. The mass conservation can be mathematically written as

vCvtþ u

vCvxþ v

vCvyþw

vCvz¼ v

vx

�Kh

vCvx

�þ v

vy

�Kh

vCvy

�þ v

vz

�Kz

vCvz

�þ Aþ B; ð4Þ

NO3- NH4

+

Nitrification Remineralization

noit

alimi

ssA

Assimilation

noit

ercx

E

ytila

tro

M

noit

segE

Grazing

noit

atne

mide

S

Sediment

esae

leR

Mortality

Riverine Loading

Detritus

ZooplanktonPhytoplankton

Boundary Flux

noit

acifi

rtine

D

NO3- NH4

+

Nitrification Remineralization

noit

alimi

ssA

Assimilation

noit

ercx

E

ytila

tro

M

noit

segE

Grazing

noit

atne

mide

S

Sediment

esae

leR

Mortality

Riverine Loading

Detritus

ZooplanktonPhytoplankton

Boundary Flux

noit

acifi

rtine

D

Fig. 4. Schematic view of the ecosystem model. Boxes represent nitrogen-based standing stocks. Dashed and solid arrows indicate nitrogen flows with and without isotopefractionation, respectively.


where C represents the specific compartments in the model, A isthe function that represents the internal source or sink, B is theexternal loading, u and v are the horizontal velocity components inthe x and y directions, respectively, and w indicates the verticalvelocity components in the z direction. Kh and Kz are the horizontaland vertical eddy diffusivity, respectively.

The mathematical expressions for the internal sources or sinksof each compartment are given as follows:

vhNO�3

ivt

¼ �ðPhotosynthesisÞ � Fnew þ ðNitrificationÞ

� ðDenitrificationÞ; (5)

vhNHþ4

ivt

¼ �ðPhotosynthesisÞ � ð1� FnewÞ þ ðExcretionÞ

þ ðRemineralizationÞ � ðNitrificationÞ þ ðReleaseÞ;(6)

v½PHY�vt

¼ ðPhotosynthesisÞ � ðGrazingÞ � ðMortalityPHYÞ

þ ðSinkingPHYÞ; (7)

v½ZOO�vt

¼ ðGrazingÞ � ðMortalityZOOÞ � ðEgestionÞ

� ðExcretionÞ; (8)

v½DET�vt

¼ ðMortalityPHYÞ þ ðMortalityZOOÞ þ ðEgestionÞ

� ðRemineralizationÞ þ ðSinkingDETÞþ ðSedimentationÞ; (9)

Square brackets indicate the concentration of each compart-ment, and Fnew (f-ratio) is the uptake ratio of NO3

� to total DIN byphytoplankton. To calculate the time evolution of the

compartments, all processes described in Fig. 4 must be formulated.The equations and parameters (Table 1) for the nitrogen cycle areessentially based on the ecosystem model developed by Kawamiyaet al. (1995).

Photosynthesis is determined by temperature (T, �C), [NH4þ],

[NO3�], [PO4

3�], and light intensity (I, W m�2), and is expressed as

ðPhotosynthesisÞ ¼ VmaxFTFNFI½PHY�; (10)

where Vmax is the maximum photosynthetic rate of phytoplankton,and FN is the nutrient limitation factor that is assumed to follow theMichaelis–Menten function, given as

FN ¼ min

( hNO�3

ihNO�3

iþ kNO3

exp��J

hNHþ4

i�

þ

hNHþ4

ihNHþ4

iþ kNH4

;

hPO3�

4

ihPO3�

4

iþ kPO4

); (11)

where kNO3; kNH4

and kPO4represent half-saturation constants for

NO3�, NH4

þ, and PO43�, respectively, and J is the NH4

þ inhibitioncoefficient. To express the dependence on temperature (FT) andlight intensity (FI), the following formulae are used (Steel, 1962):

FT ¼T

Toptexp

�1� T

Topt

�; (12)

FI ¼I

exp�

1� I�; (13)

Iopt Iopt

I ¼ I0expð�LzÞ; (14)

L ¼ 1:45Ds

; (15)

where Topt and Iopt are optimum temperature and light for phyto-plankton growth, respectively, and I0 (W m�2) is light intensity at

Table 1Biological parameters.

Parameters Symbols Values Unit Remarks

Maximum photosynthetic rate Vmax 2.4 /dayOptimum temperature Topt 25 �COptimum light intensity Iopt 104.7 W/m2

Half-saturation coefficient for NH4þ kNH4

0.2 mmol/LHalf-saturation coefficient for NO3

� kNO32.0 mmol/L

Half-saturation coefficient for PO43� kPO4

0.17 mmol/LAmmonium inhibition coefficient j 1.5 L/mmolPhytoplankton mortality rate at 0 �C VMP 0.002 L/mg dayTemperature coefficient for phytoplankton mortality kMP 0.0693 /�CZooplankton mortality rate at 0 �C VMZ 0.0064 L/mg dayTemperature coefficient for zooplankton mortality kMZ 0.069 /�CMaximum grazing rate at 0 �C Gmax 0.15 /day TuningTemperature coefficient for grazing kG 0.0693 /�CIvlev constant l 0.1 L/mg dayThreshold value for grazing Chl* 0.602 mgN/LAssimilation efficiency of zooplankton a 0.4Growth efficiency of zooplankton b 0.3Remineralization rate at 0 �C VRem 0.03 /dayTemperature coefficient for remineralization kRem 0.0693 /�CNitrification rate at 0 �C VNit 0.0012 /day TuningTemperature coefficient for nitrification kNit 0.32 /�C TuningDenitrification rate at 0 �C VDenit 0.01 /day TuningTemperature coefficient for denitrification kDenit 0.14 /�C TuningNH4þ release rate at 0 �C VRel 0.3 /day Tuning

Temperature coefficient for NH4þ release kRel 0.0693 /�C Tuning

Sinking velocity of phytoplankton VSP 0.17 m/daySinking velocity of detritus VSD 1.73 m/daySedimentation rate of detritus VSED 0.3 /day Tuning

The above parameters were obtained from the studies of Kawamiya et al. (1995), Hayashi and Yanagi (2002), Yoshikawa et al. (2005), and Kakehi (2006).


the sea surface. The light dissipation coefficient (L) is calculatedusing the transparency (Ds), given by Secchi disk measurements,following Walker (1980). Boundary conditions of I0 at the surfacewater are described by

I0 ¼ ImaxðidayÞ$cos�

pday timeðidayÞ$ðihour � 12Þ

�; (16)

ImaxðidayÞ ¼ 500þ 300sin�

2pTy

$ðiday� 20Þ�; (17)

day timeðidayÞ ¼ 12þ 1:5sin�

2pTy

$ðiday� 20Þ�; (18)

where Imax(iday), day_time(iday) and ihour are the maximum lightintensity per iday, the insolation hour per day, and the calculationhour in the day cycle, respectively. Ty and iday are the year cycle(¼360 days) and the calculation day from the initial day(1 March¼ 0), respectively.

The f-ratio is calculated as

f � ratio ¼

hNO�3

ihNO�3

iþ kNO3

exp��J

hNHþ4

i�hNO�3

ihNO�3

iþ kNO3

exp��J

hNHþ4

i�þ

hNHþ4

ihNHþ4

iþ kNH4

:

(19)

Mortality of phytoplankton and zooplankton, grazing, excretion,egestion, and remineralization are represented as:

ðMortalityPHYÞ ¼ VMPexpðkMPTÞ½PHY�2; (20)

ðMortalityZOOÞ ¼ VMZexpðkMZTÞ½ZOO�2; (21)

ðGrazingÞ ¼ Max 0;GmaxexpðkGTÞn h � �io o
n
1� exp l Chl* � Chl ½ZOO� ; ð22Þ

ðExcretionÞ ¼ ða� bÞðGrazingÞ; (23)

ðEgestionÞ ¼ ð1� aÞðGrazingÞ; (24)

ðRemineralizationÞ ¼ VRemexpðkRemTÞ½DET�; (25)

where VMP and kMP are the phytoplankton mortality rate at 0 �C andtemperature coefficient of phytoplankton mortality, respectively;VMZ and kMZ are the zooplankton mortality rate at 0 �C andtemperature coefficient of zooplankton mortality, respectively;Gmax, kG, l, and Chl* are the maximum grazing rate of zooplankton,temperature coefficient of zooplankton grazing, Ivlev constant, andthreshold value for grazing, respectively; a and b are the assimi-lation efficiency and growth efficiency of zooplankton, respectively;and VRem and kRem are the remineralization rate of detritus to NH4

þ

at 0 �C and temperature coefficient for detritus remineralization,respectively.

Nitrification may be influenced by many factors, including thesubstrate concentration, oxygen, light, suspended particulatematter, pH, and salinity (Herbert, 1999). However, Berounsky andNixon (1990) reported that seasonal rates of nitrification are morestrongly correlated with temperature than with other factors. Theyfound that the temperature coefficient of nitrification (kNit) ina water column was considerably higher than that in the sediments.In Ise Bay, nitrification in the water column is more importantprocess in the nitrogen cycle, than that in the sediments (Sugimotoet al., 2008). Nitrification in the water column would be governedby temperature and light intensity rather than DO concentration(Sugimoto et al., 2009c). The nitrification rate in the aphotic watercolumn is thus assumed to be simply dependent on T and [NH4

þ] inthe aphotic water column.

Tabel 2Nitrogen isotope discrimination (3) in biogeochemical processes.

Process Notation 3 (&) Remarks

NO3� assimilationby phytoplankton

31 3 Field estimates8–9 (Altabet et al., 1991)4–6 (Sigman et al., 1999)5 (Altabet et al., 1999)Culture estimates1–23 (Wada and Hattori, 1978)0–15 (Montoya and McCarthy, 1995)9 (Pennock et al., 1996)4–5 (Waser et al., 1998a, 1998b)2–6 (Needoba et al., 2003)

NH4þ assimilation

by phytoplankton32 8 Field estimates

9 (Cifuentes et al., 1989)7–8 (Montoya et al., 1991)Culture estimates5–29 (Pennock et al., 1996)15–25(Waser et al., 1998a,b)

Excretion byzooplankton

33 5 Field estimate2–8 (Checkley and Miller, 1989)

Egestion byzooplankton

34 �2 No data

Nitrification 35 25 Field estimates (in waters)12–17 (Horrigan et al., 1990)20 (Sebilo et al., 2006)25 (Sugimoto et al., 2008)Field estimate (in sediments)7 (Brandes and Devol, 1997)Culture estimates35 (Mariotti et al., 1981)14–38 (Casciotti et al., 2003)

Denitrification 36 1 Field estimates (in waters)30–40 (Cline and Kaplan, 1975)22–30 (Brandes et al., 1998)30–35 (Sutka et al., 2004)Field Estimates (in sediments)0–3 (Brandes and Devol, 2002)w5 (Sigman et al., 2003)w1 (Sugimoto et al., 2008)Culture Estimates25–30 (Mariotti et al., 1981)29 (Barford et al., 1999)

This table was complied largely from the report of Yoshikawa et al. (2005). 35 and 36

are values in Ise Bay observed by Sugimoto et al. (2008). 31, 32, 33, and 34 are theadjusted values. 3 values express substrate minus product.


ðNitrificationÞ ¼ VNitexpðkNitTÞ½NH4�; (26)

where VNit is the nitrification rate at 0 �C. In photic layers, wenegrected nitrification term.

Denitrification in Ise Bay occurs in the sediments (Sugimoto et al.,2008). The NO3

� in water overlying the sediments is used as thesubstrate for sedimentary denitrification (Herbert,1999). Kakehi et al.(2005) suggested that denitrification occurs throughout the year.Potential of denitrification is high in summer, but in low in winter(Kakehi and Fujiwara, 2007). The denitrification rate in the anoxicsediment is thus assumed to be simply dependent on the tempera-ture and NO3

� concentration of the water overlying the sediments.

ðDenitrificationÞ ¼ VDenitexpðkDenitTÞ½NO3�; (27)

where VDenit and kDenit are the denitrification rate at 0 �C andtemperature coefficient for the denitrification rate, respectively.

Release of NH4þ from the organic-rich sediment into the over-

lying water can be assumed to depend on the DO concentrationsand temperature in the overlying water. In general, NH4

þ release isdominated by the strength of coupling process between the supply(regeneration) and consumption (sedimentary nitrification) of NH4

þ

within the sediments. In Ise Bay, temperature and DO concentra-tions in bottom waters change seasonally. Seasonal changes ofwater temperature directly affect activities of heterotrophicbacteria, which decompose organic nitrogen to NH4

þ, and nitrifyingbacteria. Bacterial activity generally increases with increasingtemperature, while those in DO concentration affect directlyoxygen conditions in the sediments. This means that bottomhypoxic waters in the stratified periods would inhibit sedimentarynitrification, because there is no oxygen supply from the water tothe sediment. In such a case, NH4

þ is released from the sedimentinto the overlying water according to increasing water tempera-ture. Our model therefore assumes that NH4

þ is released when DOconcentrations decrease to below 6.5 mg L�1 in the bottom waters:

ðReleaseÞ ¼ VRelexpðkRelTÞ � Sedfactor; (28)

where VRel and kRel are the release rate at 0 �C and temperaturecoefficient for NH4

þ release, respectively; and Sedfactor is the sedi-ment factor (¼ 20), which is adjusted to reproduce the observed[NH4

þ] and [NO3�] concentrations at the bottom water.

Sinking and sedimentation processes are written as

ðSinking PHYÞ ¼ �v

vzVSP½PHY�; (29)

ðSinking DETÞ ¼ �v

vzVSD½DET�; (30)

ðSedimentationÞ ¼ �VSED$½DET�; (31)

where VSP, VSD, and VSED are the sinking velocity of phytoplankton,sinking velocity of detritus, and sedimentation rate, respectively.Sinking is set to zero in the bottom layers, while sedimentationoccurs only in the bottom layers.

The external loading terms are as follows. [NO3�], [NH4

þ], [PO43�],

and Chl-a concentrations and the temperature and salinity observedat Irago Strait are used as the open boundary conditions. The Chl-a concentration is converted into [PHY] using the carbon to Chl-a weight ratio (C/Chl-a¼ 40) and Redfield mol ratio (C:N¼ 106:16).The concentrations of zooplankton are assumed to be 10% of [PHY].[DET], assumed to be a constant (¼0.5 mM), was observed off Ise Bayas the PN concentration (Sugimoto et al., 2009a). Although nitrogenconcentrations in the Kiso Rivers showed wide ranges when riverdischarge was low, there were no clear relationships with between

the nitrogen concentration and the river discharge (Sugimoto,unpublished data). Therefore, the [NO3

�], [NH4þ], [PO4

3�], and [DET](zPN) of the Kiso Rivers are assumed to be constant values at 50 mM,8 mM, 0.1 mM, and 5 mM, respectively.

4.3. Computation of d15N

The fractionation of nitrogen isotopes in the model occurs in theprocesses of assimilation (photosynthesis) of NO3

� and NH4þ by

phytoplankton, excretion and egestion by zooplankton, and nitrifi-cation and denitrification (dashed arrows in Fig. 4; their 3 values arelisted in Table 2). During photosynthesis, the lighter isotope (14N) ismore readily incorporated into the tissue of phytoplankton. Thus,the d15N values of NO3

� and NH4þ increase as phytoplankton take up

these nutrients (e.g., Waser et al.,1998a,b). The 3 value during uptakeof NO3

� by phytoplankton is estimated to range from 4 to 9& in thefield and from 0 to 23& in cultures. For NH4

þ, the 3 value is estimatedto range from 7 to 9& in the field and from 5 to 29& in cultures. Inthe laboratory, 3 values arising from nitrification are generally large(14–38&), although 3 can vary substantially depending on thespecific nitrification enzymes involved (Mariotti et al., 1981; Cas-ciotti et al., 2003). However, in the field, 3 values by nitrificationdiffer between in water and sediment. Apparent 3 values are esti-mated to be 12–25& in water and 7& in the sediment.


Denitrification within the ocean water column can result in 3 valuesof 22–45&, which are similar to laboratory-based estimates of 25–30&. However, denitrification in various sedimentary environmentshas little effect on the net isotope enrichment (3¼ 0–5&). The NH4

þ

excreted by zooplankton is lighter (2–8&) in d15N than the bulknitrogen of their bodies (Checkley and Miller, 1989). However, thed15N of zooplankton fecal pellets is slightly heavier than that of thediet (Altabet and Small,1990; Montoya et al.,1990). The net result ofthese two processes is an increase in d15N of roughly 3& per trophiclevel (Minagawa and Wada, 1984; Wu et al., 1997).

For the present model, 3 values of nitrification in the watercolumn and denitrification in the sediments were estimated byfield observations (Sugimoto et al., 2008). Excretion and egestion byzooplankton were cited from Yoshikawa et al. (2005). The otherassimilation processes were adjusted to reproduce the observedd15N values based on the reference 3 values in Table 2. The modelexpresses each process from substrate to product, and thus theisotopic fractionation coefficient al (l¼ 1, 2, ., 6) is assumed to be

al ¼ exp��3l

1000

�; (32)

where 3l is the isotope discrimination listed in Table 2.All equations for the 15N cycle are based on the above equations

for the nitrogen cycle. The prognostic variables for the 15N cycle arecalculated as a function of t using the following five governingequations:

v½15NNO3�

vt¼ �ðPhotosynthesisÞ � Fnew � RNO3

� a1

þ ðNitrificationÞ � RNH4� a5 � ðDenitrificationÞ

� RNO3� a6;

(33)

v½15NNH4�

vt¼ �ðPhotosynthesisÞ � ð1� FnewÞ � RNH4

� a2

þ ðExcretionÞ � RZOO � a3 þ ðDecompositionÞ� RDET � ðNitrificationÞ � RNH4

� a5 þ ðReleaseÞ� Rsediment;

(34)

v½15NPHY�vt

¼ ðPhotosynthesisÞ � Fnew � RNO3� a1

þ ðPhotosynthesisÞ � ð1� FnewÞ � RNH4� a2

� ðMortalityZOOÞ � RPHY � ðGrazingÞ � RPHY

þ SinkingPHY � RPHY;

(35)

v½15NZOO�vt

¼ ðGrazingÞ�RPHY�ðMortalityZOOÞ�RZOO

�ðEgestionÞ�RZOO�a4�ðExcretionÞ�RZOO�a3;

ð36Þ

v½15NDET�vt

¼ ðMortalityPHYÞ � RPHY þ ðMortalityZOOÞ � RZOO

þ ðEgestionÞ � RZOO � a4 � ðDecompositionÞ� RDET þ SinkingDET � RDET þ Sedimentation

� RDET; ð37Þ

where RC is the ratio of 15N/14N for a specific compartment C. Thed15N values for a specific compartment C are calculated by:

d15N ¼

8><>:

½15N�

½N� � ½15N�

!C

½15N�½N� � ½15N�

!Atmospheric N2

� 1

9>=>;� 1000; (38)

where Atmospheric N2 is defined as the standard sample including[15N] and equals 0.365%.

The d15N values of external loading nitrogen are as follows: d15Nof NO3

� and detritus (zPN) in the Kiso Rivers are described usingEqs. (1) and (2), depending on the river discharge. The averagevalue (14&) is used as the d15N of NH4

þ in the Kiso Rivers. At theopen boundary, d15N of NO3

� is described by Eq. (3) with [NO3�]. The

other d15N values are assumed to be 5&, which is the oceanicaverage (e.g., Altabet et al., 1999; Sigman et al., 1999).

5. Model results

5.1. Reproducibility of seasonal variations of phytoplanktonand DIN

Initial temperature, salinity, and velocity fields were given asthose in March calculated by the physical model (detailed in theAppendix). Initial concentrations and isotope ratios of all nitrogenwere set to zero. The equations were integrated for 48 months, andthe results in the last 12 months were used to analyze the prop-erties of seasonal variations.

Fig. 5 shows the seasonal variations in observed and calcu-lated concentrations of Chl-a, NH4

þ, and NO3� in the subsurface

(10 m) and bottom (34 m) layer at the central part of Ise Bay(Stn. C in Fig. 1). Calculated concentrations of each compartmentshow seasonal patterns similar to observed pattern. The calcu-lated concentrations of Chl-a in the subsurface layer are high inspring (w4.5 mg L�1) and autumn (w3.5 mg L�1) and low in winter(w1 mg L�1). Chl-a maximum in spring well reproduces the SCMin Ise Bay. The concentrations of NH4

þ and NO3� and their

seasonal variation in the subsurface layer are smaller and lowerthan those in the bottom layer. The NO3

� concentration in thesubsurface layer decreases to w1 mM during the spring bloom. Inthe bottom layer, the NH4

þ concentration peaks in spring(w7 mM), while NO3

� concentration peaks in summer (w12 mM).This temporal shift from NH4

þ to NO3� in the lower layer

clearly displays the effect of nitrification, indicating the accu-mulation of regenerated NO3

� in the lower layer during thestratified periods.

Fig. 6 shows the seasonal variations in observed and calculatedd15N values of PN, NH4

þ, and NO3� in the subsurface and bottom

layers at the central part of Ise Bay (Stn. C in Fig. 1). In this study,d15N of phytoplankton was not observed in the field since it wasdifficult to separate phytoplankton from organic detritus. Thus,observed d15NPN was assumed to be the same as calculated d15NPN,which is the weighted average value of phytoplankton,zooplankton, and detritus. The calculated d15NPN value of PN in thesubsurface layer decreases from winter (w10&) to spring (w6&),but increases from spring (w6&) to summer. This seasonal vari-ation in calculated d15NPN is consistent with observations,although the calculated d15NPN was slightly lower than theobserved d15NPN from summer to autumn. In the bottom layer,seasonal variation in the calculated d15NPN successfully reproducesthat in the observed d15NPN throughout the year. In the bottomlayer, d15NPN shows a minimum in spring (w5&) and maximum in

Fig. 5. Seasonal variation in observed and calculated concentrations of Chl-a, NH4þ, and NO3

� in the subsurface (10 m depth) and bottom waters (34 m depth) at the central part of IseBay (Stn. C). Symbols and lines present observed and calculated values, respectively.


summer (w10&). Calculated d15NNO3in the bottom layer has

a prominent minimum in spring (w�6&) when the NH4þ

concentration reaches its maximum (Fig. 5), indicating the isotopeeffect of nitrification in the water column. From spring to summer,d15NNO3

increases to w8&. Seasonal variation in the calculated

Fig. 6. Seasonal variation in observed and calculated nitrogen isotope ratios (d15N) of partic(34 m depth) at the central part of Ise Bay (Stn. C). Symbols and lines are the observed and

d15NNO3in the bottom layer well reproduces the observed

seasonal variation. Calculated d15NNH4values in the bottom layer

are low from winter to spring (<15&) and high from summer toautumn (>20&). Calculated and observed d15NNH4

in spring alsohave similar values. The developed d15N coupled ecosystem model

ulate nitrogen (PN), NH4þ, and NO3

� in the subsurface (10 m depth) and bottom waterscalculated values, respectively.

Month

)yad/Nt( xulf

NID

-240

-160

-80

0

80

Month

ylppuS/noitp

musnoC

0.5

1.0

1.5

2.0

2.5

3.0

1 3 5 7 9 112 4 6 8 1210 1 3 5 7 9 112 4 6 8 1210

a b

Fig. 7. (a) Seasonal variation in the nitrogen budgets. Positive budgets indicate supply of DIN (¼NH4þ þNO3

�) from the rivers (thin dashed line) and ocean (solid bold line), whilenegative budgets mean consumption of DIN by phytoplankton in Ise Bay (thin solid line). (b) Seasonal variation in the ratio of DIN consumption by phytoplankton to DIN supplyfrom the outer regions (rivers and ocean). A linear line of 1.0 indicates equilibrium between external DIN supply and internal DIN consumption.


represents the seasonal variation in the concentrations and d15Nvalues of observed nitrogen.

5.2. Relationships between phytoplankton production and DINsources in each season

Fig. 7a shows the seasonal variation in DIN (¼NH4þþNO3

�) fluxesof the new supply from the river and ocean, and the consumptionrates of DIN by phytoplankton within the bay. The riverine flux wascalculated as a product of the DIN concentration and the riverdischarge. The flux of DIN from the outer ocean to the inner sea wasestimated through the transverse section at the open boundary(Fig. 3). The oceanic flux was computed by integration of northwardvelocities multiplied by the concentration in each grid. Consump-tion rates rapidly increase from w70 to w200 tN d�1 with thephytoplankton bloom in spring (Fig. 5). In this period, the supply ofDIN from the shelf increases from w30 to w60 tN d�1 because ofthe strengthened estuarine circulation. High assimilation continuesduring summer (w200 tN d�1), peaking in autumn (w220 tN d�1).However, the DIN supply from the river and shelf shows decreasingtrends in autumn. In winter, consumption rates rapidly decreases to<80 tN d�1. Fig. 7b presents the ratio of DIN consumption byphytoplankton to the supply from the river and shelf (consump-tion/supply ratio). The ratio is higher than 1.0 throughout the year,indicating that the external supply of DIN is insufficient and thatthe phytoplankton production largely depends on the regeneratedDIN within the bay. The consumption/supply ratio considerablydiffers in spring and autumn. The lower ratio in spring (<1.5)suggests a larger contribution of the external DIN supply from theriver and ocean, while the higher ratio in autumn (w3) suggests thedominant contribution of regenerated DIN. In Ise Bay, physicalproperties change seasonally (e.g., Takahashi et al., 2000). Thisseasonal difference in the relationships between phytoplanktonand DIN sources is discussed later.

In spring, seasonal thermo and haloclines largely divide thewater properties into two layers: upper and lower layers (Fig. 8a). Inthe upper layer, there are two prominent Chl-a maxima: a surfacemaximum at the bay head and a subsurface maximum at the baymouth. The lower f-ratio at the bay head indicates that phyto-plankton mainly takes up NH4

þ within 10 km from the river mouth.However, phytoplankton change their utilization rates of nitrogenforms from NH4

þ to NO3� moving from the bay head to the bay

center, as evidenced by the f-ratio increase from 0.2 to 0.7. Thed15NPHY in the surface Chl-a maximum also shows the horizontal

gradient associated with the f-ratio. On the other hand, a high f-ratio (>0.7) indicates that phytoplankton take up NO3

� as the mainnitrogen source in the subsurface Chl-a maximum at the baymouth. However, riverine NO3

� has already been depleted (<1 mM)by surface production at the bay head. Under such conditions,d15NPHY expresses d15NNO3

values similar to the source NO3� because

there is little isotope effect. Possible NO3� sources for the subsurface

Chl-a maximum must be regenerated NO3� and/or oceanic NO3

�. Inthe lower layer, NO3

� with a significantly low d15N (<�4&) accu-mulates, resulting from the isotope effect of nitrification. If phyto-plankton uses such negative d15NNO3

as their main nitrogen source,the d15NPHY value should be negative. On the contrary, the d15NNO3

(>2&) of oceanic NO3� at the bay mouth was clearly higher than

that of regenerated NO3� (<2&), and thus the most plausible source

for the subsurface Chl-a maximum would be external nitrogenfrom the outer ocean. The intrusion depth of oceanic water byestuarine circulation changes from bottom to middle in spring(Takahashi et al., 2000). The d15NNO3

distribution clearly displaysthe middle layer intrusion of oceanic NO3

�. Thus, increased DIN fluxfrom the outer ocean (Fig. 7a) and the shift of the intrusion depthwould induce the spring phytoplankton production at the bay head.However, the lower f-ratio (w0.5) in the upper layer also indicatesthat the regenerated NH4

þ with lower d15N by remineralizationwithin the upper layer is utilized and largely affects the primaryproduction in the bay.

Water stratification is strengthened by surface heating and highfreshwater discharge in summer (Fig. 8b). In the bottom layer, thecold water mass (<18 �C) is isolated from the surrounding watersby the horizontal thermo and haloclines and the vertical bottomfront. This cold water mass becomes hypoxic (DO< 3 mg L�1). TheChl-a concentrations show two prominent maxima as in spring. Asboth NH4

þ and NO3� are depleted in the upper layer, the d15NPHY of

the two Chl-a maxima expresses the d15N values of assimilatednitrogen because there is little isotope fractionation. Near the rivermouth, the slightly high d15NPHY (w7&) and low f-ratio (<0.6)indicate uptakes of riverine NH4

þ, which has low d15N values(<20&) compared to those of regenerated NH4

þ (>40&) in thelower layer. Moving from the bay head to the center of the bay,phytoplankton tends to use the NO3

� instead of NH4þ. On the other

hand, at the bay mouth, the phytoplankton forming the subsurfaceChl-a maximum takes up NO3

� as the major nitrogen source.However, the NO3

� source (oceanic and/or regenerated) cannot bedetermined because both types of NO3

� have similar isotope valuesin summer. The consumption/supply ratio (w2, Fig. 7b) suggests

Fig. 8. Vertical distributions of simulated temperature, salinity, f-ratio, [Chl], [NH4þ], [NO3

�], d15NPN, d15NNH4, and d15NNO3

along the longitudinal section in (a) spring (1 May),(b) summer (1 August), (c) autumn (1 November), and (d) winter (1 February), respectively.


that the contribution of regenerated NO3� is comparable to that of

external DIN supplied from the rivers and shelf. On the other hand,the high (>0.6) f-ratio indicates the weak contribution of NH4

þ tophytoplankton production in the upper layer. The d15NNH4

in theupper layer is considerably lower than that in the lower layer. Thisindicates that residual NH4

þ is left by nitrification processes in thelower layer, while the new NH4

þ is produced by remineralization inthe upper layer. Mino et al. (2002) found that d15N values of sus-pended matters decrease with the uptake of regenerated NH4

þ

rather than the uptake of new NO3� supplied from the deep layer in

the Atlantic Ocean. The relatively low d15NPHY values (<10&)associated with lower f-ratios (<0.6) indicate that phytoplanktondo not take up the residual NH4

þ by nitrification; rather, they takeup the newly generated NH4

þ by remineralization in the upper layer.Fluxes of newly regenerated NH4

þ by remineralization (33.5 tN d�1)and excretion (19.8 tN d�1) in the upper layer (>12 m) was found tobe considerably larger than fluxes of NH4

þ supplied from the lowerlayer (<12 m) to the upper layer by advection (3.9 tN d�1) anddiffusion (12.3 tN d�1).

In autumn, thermal stratification is weakened, and saline water(>33) intrudes into the bay through the bottom layer (Fig. 8c). Incontrast to spring, in autumn the intrusion depth of the oceanicwater changes from the middle to the bottom layer (Takahashiet al., 2000). Thus, oceanic NO3

� with low d15N (<5&) is suppliedinto the lower layer by the bottom intrusion. Two maxima in Chl-a concentration occur at the bay head and the bay mouth. Thehigher f-ratio indicates that phytoplankton extensively take up NO3

�

as substrate nitrogen except for near the river mouth, where higherd15NPHY (>7&) and lower f-ratio (<0.5) indicate the utilization ofriverine NH4

þ. Riverine NO3� is also consumed at the river mouth,

and thus NO3� is exhausted in the upper layer from the center to the

bay mouth. Moreover, the high consumption/supply ratio (w3,Fig. 7b) means that the regenerated DIN is the dominant source forphytoplankton production. The homogeneous vertical profile of thed15NNO3

in the center of Ise Bay clearly displays the supply ofregenerated NO3

� into the euphotic layer by vertical mixing.Although NO3

� is depleted (w1 mM) in the upper layer, d15NNO3is

comparable to that in the bottom layer. The finding of little verticaldifference of d15NNO3

indicates that the regenerated NO3� is

continuously supplied from the bottom layer into the euphoticlayer.

Water convection in winter creates vertically homogeneoustemperature and salinity (Fig. 8d). The consumption/supply ratio(w1.5, Fig. 7b) suggests that two-thirds of phytoplankton produc-tion depends on the external DIN supply rather than the regen-erated DIN. Within the bay, Chl-a concentrations are considerablylow (<1 mg L�1) because of low temperature and low DIN concen-trations. d15NPHY at the bay head is higher than that at the baymouth. The concentrations and d15N values of NO3

- are homoge-neous within the bay, indicating that the spatial difference ofd15NPHY is caused by the NH4

þ assimilation by phytoplankton. Thelow f-ratio also indicates that phytoplankton preferentially take upNH4þ. However, the f-ratio shows slightly horizontal gradients from

lower values (<0.3) at the bay head to higher values (>0.3) at the

Fig. 8. (continued).


bay mouth. In addition, d15NNH4at the bay mouth is higher than

that at the bay head. Therefore, d15NPHY at the head of the bay hashigher d15NPHY values.

5.3. Annual nitrogen budgets in Ise Bay

Fig. 9 shows the annual average nitrogen flux (tN d�1) of eachprocess and of standing stocks (tN) in Ise Bay. The nitrogen supplyof 32 tN d�1 from the river is composed of 24 tN d�1 as NO3

�,5 tN d�1 of NH4

þ, and 3 tN d�1 as detritus. The net nitrogen flux fromthe ocean reaches 29 tN d�1, which is comparable to the riverinenitrogen flux. Dissolved forms, NO3

� (37 tN d�1) and NH4þ

(11 tN d�1), are supplied from the ocean to the bay, while particu-late forms composed of phytoplankton (12 tN d�1), zooplankton(2 tN d�1), and detritus (7 tN d�1) flow out from the bay to theocean. A total of 77 tN d�1 of DIN is supplied to the inner bay as newnitrogen.

In contrast, the nitrogen flux for each process within the bay isconsiderably larger than the new nitrogen flux from the outerregions. Phytoplankton takes up 93 tN d�1 of NO3

� and 67 tN d�1 ofNH4þ. The total flux of phytoplankton assimilation (160 tN d�1) is

more than twice the total flux from the river and ocean. This resultmeans that more than half the amount of annual phytoplanktonproduction is supported by the regenerated DIN. However, highconsumption/supply ratios (>2.0) occur only in only periods fromSeptember to November (Fig. 7b), suggesting that regenerated DIN,which is accumulated in the hypoxic water mass during the strat-ified season, contributes significantly to annual phytoplankton

production. Because a large amount of phytoplanktonic nitrogen istransferred to detritus (94 tN d�1) rather than zooplankton(54 tN d�1), phytoplankton mortality accounts for more than 70% ofthe total detritus supply, which is one of the largest processes in IseBay. Sedimentation of detritus is larger than the NH4

þ release fromthe sediments. Regenerated nitrogen from remineralization(54 tN d�1) and release from sediments (55 tN d�1) also showslarge flux. These two fluxes account for w70% of the total NH4

þ

supply, suggesting that they are the most important sources forphytoplankton production. Moreover, zooplankton excretionaccounts for 16% of the total NH4

þ supply. A large supply of NO3� is

nitrification (80 tN d�1), which accounts for w60% of the total NO3�

supply. The denitrification loss of 48 tN d�1 is twice as large as theNO3� supply from the river (24 tN d�1). The calculated denitrifica-

tion rate is comparable to that estimated from the Redfield stoi-chiometry (42 tN d�1; Kakehi et al., 2005) and larger than thepotential denitrification rate (19–28 tN d�1; Sugawara, 2003).These results indicate that phytoplankton production in Ise Bay ismainly dominated by the internal cycle (DIN assimilation byphytoplankton, mortality of phytoplankton, remineralization ofdetritus, release from the sediments, nitrification, and denitrifica-tion) rather than the external supply (fluxes from rivers and theocean).

6. Summary and discussion

We developed an ecosystem model coupled with d15N to eval-uate the seasonal variation in nitrogen dynamics, with particular



focus on the relationship between phytoplankton production andDIN behavior. DIN (¼NH4

þþNO3�) consumption by phytoplankton

exceeds DIN supply from the river and ocean (Figs. 7 and 9), indi-cating that phytoplankton production in Ise Bay largely depends onregenerated DIN within the bay rather than on newly supplied DIN.Similar results were reported from several other coastal environ-ments. In Escambia Bay, Florida, the nutrient demand for phyto-plankton production exceeds the terrestrial nutrient supply fromthe rivers, implying that phytoplankton rely on recycled nutrientsto support growth, requiring that available nutrient pools be usedseveral times (Murrell et al., 2007). In Monterey Bay, California,NO3� regenerated by nitrification in the euphotic zone plays

a substantial role in gross productivity, ultimately supporting w30%of the total NO3

�-based primary production (Wankel et al., 2007).Modeling studies of eutrophic coastal environments in Japan havealso reported the significance of regenerated nitrogen (e.g., Hayashiand Yanagi, 2002; Kittiwanich et al., 2006.

In Ise Bay, the formation of a cold water mass isolated fromsurrounding waters during the stratified periods is key to the largecontributions of regenerated nitrogen to phytoplankton produc-tion, because the cold water mass covers a large volume in thelower layer (e.g., Fujiwara et al., 2002). The oxygen within theisolated water mass is mainly consumed by remineralization oforganic matter in the waters and sediments, and thus a largeamount of DIN accumulates in the hypoxic water mass during thestratified periods (Kakehi et al., 2005; Sugimoto et al., 2008).Consequently, the standing stock of DIN in the lower layer is high(w2500 tN) in summer, but low in winter (w1400 tN; Kakehi et al.,

2005). The consumption/supply ratio differs considerably byseason (Fig. 7b). The lower ratio in spring (<1.5) means that thedirect DIN supply from the rivers and ocean is more important thanthat from regeneration, while the higher ratio in autumn (w3)means that regenerated DIN is the major source for phytoplanktonproduction (Fig. 7b).

Although the riverine DIN stimulates phytoplankton productionat the bay head and forms a Chl-a maximum in the surface layer,phytoplankton production at the bay mouth is largely controlled bythe estuarine circulation. In spring, the intrusion depth of oceanicwater changes from the bottom to the middle layer. d15NNO3

distributions clearly show that oceanic NO3� is transported into the

euphotic layer by the middle intrusion and stimulates phyto-plankton production at the bay mouth. Kasai et al. (2007) alsopointed out the importance of the middle intrusion of oceanicwater for the SCM layer. In autumn, the intrusion depth of oceanicwater changes from the middle layer to the bottom layer. Regen-erated NO3

�, which is accumulated in the hypoxic water mass, isvertically supplied into the euphotic layer. This vertical supply ofregenerated nitrogen induces the maximum DIN consumption rate(w220 tN d�1, Fig. 7a). These results show that seasonal shifts of theintrusion depth of estuarine circulation induce spatial andtemporal differences in DIN behavior and subsequent phyto-plankton production.

In recent years, ecosystem models incorporating d15N haveproven to be powerful tools for elucidating nitrogen dynamics inboth the past and modern ocean. Giraud et al. (2000, 2003)developed a simple ecosystem model for simulation of d15N of



sediments in the Mauritanian upwelling region. Their model,consisting of four compartments (phytoplankton, zooplankton,detritus, and nutrient), was the first generalized ecosystem modelto include nitrogen isotopes. However, their model did not distin-guish between NH4

þ and NO3�, although isotopic discrimination by

assimilation and nitrification of NH4þ is large (see Table 2). Yoshi-

kawa et al. (2005) developed a six-compartment (phytoplankton,zooplankton, PON, DON, NH4

þ, and NO3�) ecosystem model

including d15N and examined the seasonal variation in d15N ofsinking PN in the Sea of Okhotsk. From sensitivity analyses ofchange in the isotope discrimination factor, they found that theisotope effect of NO3

� and NH4þ assimilation by phytoplankton and

nitrification is important for d15N variation in sinking PN. Yoshi-kawa et al. (2006) adapted their model to the western and centralequatorial Pacific surface waters. However, the d15N-ecosystemmodels developed by Giraud et al. (2000, 2003) and Yoshikawaet al. (2005, 2006) were coupled with two dimensional physicalmodels (two and/or multi-layers models), because the physicalproperties in their study regions are relatively simple. Moreover,their studies focused on the modeling, and thus used relatively fewfield-observed isotope data and 3 values.

On the other hand, the d15N coupling ecosystem model wedeveloped is fully three-dimensional and includes a multi-levelphysical model, since the temporal and spatial distributions ofnutrients in Ise Bay are controlled by complex physical–biological–chemical interaction processes associated with external loading,advection/diffusion, oceanic water inputs, and sedimentary release.Precise and seasonal observations of d15N of NO3

�, PN, and part of

NH4þ in the boundary conditions (river and ocean) and within the

bay and adoption of observed 3 values enhance the accuracy of theecosystem model. Therefore, our d15N coupling model providescrucial information to distinguish DIN sources within the bay and toevaluate the contribution of each source to primary production. Inparticular, simulated d15NNO3

distributions show the intrusionpathway of oceanic NO3

�. These results strongly supported theimportance of oceanic NO3

� for phytoplankton production duringthe stratified periods as reported by previous field studies (Kasaiet al., 2007; Sugimoto et al., 2009b). This work is the first attempt atsuch an inclusive and integrative study is not only in coastal butalso in oceanic systems.

During the past three decades, researches have actively inves-tigated the rate processes of biological nitrogen transformation inthe sea using the 15N tracer technique alone or in combinationwith other chemical techniques. The information collected bythese investigations, together with data on nutrients, PON, DON,and biomass, have improved our present understanding ofnitrogen dynamics in marine ecosystems. Many models have alsobeen presented to describe the kinetics of nitrogen trans-formations and to identify factors that regulate the processes.However, validation of transformation processes by only concen-tration data is difficult. Furthermore, incorporation of rate dataestimated by incubation experiments does not necessarily provideactual fluxes and concentrations. Since each approach hastemporal and/or spatial problems, combination studies providea more comprehensive understanding of nitrogen dynamics inmarine ecosystems. Our model successfully reproduced the

NH +

80 54

93

67

22 18 12

54

48 66

Sediment

55

94

Riverine Loading

37

11

7

12

2

5

24

3

Boundary Flux

NO3-=3313 4

+=416

Sediment

Riverine Loading

Detritus=452

Zooplankton=159Phytoplankton=606

Boundary Flux

Fig. 9. Annual averages of nitrogen fluxes (tN d�1) and standing stocks (tN) in Ise Bay. The magnitude of flux is visually shown by the thickness of lines. Each arrow corresponds tothose in Fig. 4.


observed concentrations and d15N values of NO3�, NH4

þ, and PNthroughout the year. Because changes in each d15N value occurduring nitrogen transformation processes, validation of d15Nvalues and adoption of observed 3 values allow us to estimatemore comprehensive reaction rates for each nitrogen trans-formation process than those estimated by traditional ecosystemmodels. For example, isotopic discrimination of nitrification in thewater column is the largest process in Ise Bay (Table 2). Our modelwell reproduces the decrease of d15NNO3

by the isotope effect ofnitrification in spring. The temperature coefficient of nitrificationadjusted in this model (¼0.32 �C) is larger than that in Yoshikawa’set al. (2005) model (¼0.0693 �C), while similar to the observedvalue (¼0.29 �C) at the Providence River estuary (Berounsky andNixon, 1990). However, further observation of d15N values of NH4

þ

and sensitivity studies are needed to estimate more comprehen-sive values.

Our model shows that phytoplankton production in Ise Bay ismainly dominated by the internal cycle rather than by the externalsupply. However, the river discharge of the Kiso Rivers can changewithin short time periods, and floods frequently occur over dailytime scales (e.g., Sugimoto et al., 2006). Therefore, our study mighthave underestimated the effect of riverine loadings. The abruptincrease in riverine nitrogen input may change nitrogen dynamicsin the bay. Unfortunately, the field observations made in this studydid not show the physical and biogeochemical characteristics ofhigh-discharge conditions. Further observations including floodperiods are needed to more precisely elucidate the effects ofriverine loadings on the coastal environment.

Acknowledgments

We thank Dr. T. Fujiwara of the Graduate School of Agriculture,Kyoto University and Dr. S. Kakehi of the Tohoku National FisheriesResearch Institute, Fisheries Research Agency, for helpful discus-sions and suggestions. We are grateful to the captain and crew ofthe R/V Asama of the Mie Prefecture Fisheries Research Institute for

help with observations, We also extend our thanks to the staff ofthe Center for Ecological Research, Kyoto University, and of theOcean Research Institute, University of Tokyo, where we conductedthe isotope analysis.

Appendix

The physical model in this study was a fully three-dimensional(3-D) coastal ocean model. The objective of this model is toreproduce the seasonal variation in temperature, salinity, andvelocities. The model is based on hydrostatic primitive equations.Briefly, the equations for the 3D flow are as follows:

vuvtþ u

vuvxþ v

vuvyþw

vuvz� f v ¼ � 1

r0

vPvxþ v

vx

�Nh

vuvx

�þ v

vy

�Nh

vuvy

�

þ v

vz

�Nz

vuvz

�þ TSx; ðA1Þ

vv

vtþ u

vv

vxþ v

vv

vyþw

vv

vzþ fu ¼ � 1

r0

vPvyþ v

vx

�Nh

vv

vx

�þ v

vy

�Nh

vv

vy

�

þ v

vz

�Nz

vv

vz

�þ TSy;

(A2)

Z0r0 � r

P ¼ r0gxþ r0

zr0

gdz; (A3)

vuvxþ vv

vyþ vw

vz¼ 0; (A4)

vx v Zx !

v Zx !

vt¼ �

vx�H

udz �vy

�H

v dz ; (A5)


vTvtþ u

vTvxþ v

vTvyþw

vTvz¼ v

vx

�Kh

vTvx

�þ v

vy

�Kh

vTvy

�þ v

vz

�Kz

vTvz

�;

(A6)

vSvtþu

vSvxþv

vSvyþw

vSvz¼ v

vx

�Kh

vSvx

�þ v

vy

�Kh

vSvy

�þ v

vz

�Kz

vSvz

�; (A7)

where u and v are the horizontal velocity components in the x and ydirections, respectively, and w is the vertical velocity component inthe z direction; t is time, P is pressure, f is the Coriolis parameter(¼0.8� 10�4 s�1), r0 is the mean density (¼1020 kg m�3), r isdensity, x is the height from the piezometric surface, g is the gravityconstant (¼9.8 m2 s�1), H is the water depth, T is temperature, S issalinity, Nh is horizontal eddy viscosity (¼2.5 m2 s�1), and Kh ishorizontal eddy diffusivity (¼2.5 m2 s�1). The vertical eddyviscosity (Nz) and vertical eddy diffusivity (Kz) are calculated as

Nz ¼ Kz ¼ 10�4$ffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiuT þ vTp

$H; (A8)

where uT and vT are the tidal amplitude in x and y directions,respectively, and Nz and Kz are 60�10�4 m2 s�1 at the bay mouthand 2�10�4 m2 s�1 at the bay center. Tidal stresses of the x and ycomponents are calculated using the tidal model (Kakehi, 2006):

TSx ¼ ��

u0vu0

vxþ v0

vu0

vyþw0

vu0

vz

�; (A9)

TSy ¼ ��

u0vv0

vxþ v0

vv0

vyþw0

vv0

vz

�; (A10)

where overbars indicate the average per tidal cycle. u0, v0, and w0 arethe velocity, calculated by the tidal model, in the x, y, and z direc-tions, respectively.

Boundary conditions are briefly determined as follows. Monthlyobserved temperature and salinity at the open boundary at theIrago Strait were obtained by from the Mie Prefecture FisheriesResearch Institute. Seasonal variation in river discharge (Qf) andsurface heat flux (Qs) are expressed as:

Qf ¼ 250sin�

2pTy

$ðiday� 30Þ�þ 400; (A11)

Qs ¼ 11:4sin�

2pTy

$iday�; (A12)

where Ty and iday are the year cycle (¼360 days) and the calculationday from the initial day (1 March), respectively. Bottom frictions arecalculated as follows:

sbx ¼

83p

r$g2b$uT$u; (A13)

sby ¼ �

83p

r$g2b$vT$v; (A14)

where gb2 is the coefficient of bottom friction (¼2.6�10�3).

The two compartments, DO and PO43�, are calculated using

stoichiometry methods as follows. The Redfield relationship is

ðCH2OÞ106ðNH3ÞH3PO4 þ 138O2

¼ 106CO2 þ 16HNO3 þ H3PO4 þ 122H2O: (A15)

Thus, the mathematical expression for the internal sources or sinksof DO concentrations (mg L�1) is given as follows (Kakehi, 2006):

v½DO�vt

¼ RFDO=Chl$ðPhotosynthesisÞ � DOdrð�DOdbÞ (A16)

where RFDO/PHY (¼0.139 mg mg�1) is the ratio of oxygen and Chl-a ofEq. (A1), and thus the first term on the right side indicates theoxygen supply by photosynthesis. The second and third terms givethe oxygen consumption by remineralization in the water columnand in the sediments. DOdr (g m�3 d�1) and DOdb (g m�2 d�1) areexpressed as follows:

DOdr ¼ 0:062þ 0:05sin�

2pTy

$ðiday� 30Þ�; (A17)

DOdb ¼ hDO$DOdr; (A18)

where hDO (¼7 m) is the factor for the unit changes, which isadjusted to reproduce the observed DO concentrations (Kakehi,2006).

The mathematical expression for the internal sources or sinks ofPO4

3� concentrations (mmol L�1) is given as follows (Kakehi, 2006):

vhPO3�

4

ivt

¼ RFPO4=PHY$v½DO�

vt

þPO4 RF dev

; (A19)

where RFPO4=PHY (¼ 0.225 mmol mg�1) is the ratio of PO43� to Chl-a of

Eq. (A1). PO4RF_dev (mM mo�1) is the deviation from the Redfieldrelationship such as by release and adsorption. PO4RF_dev is deter-mined by the temperature and DO concentration in the bottomwaters and is expressed as

PO4RF dev ¼ hPO4$ð � 20:697þ 0:0288$T � 0:00321$DOÞ;

(A20)

where hPO4(¼10 m) is the factor for the unit changes, which is

adjusted to reproduce the observed DO concentrations (Kakehi,2006).

References

Altabet, M.A., Deuser, W.G., Honjo, S., Stienen, C., 1991. Seasonal and depth-relatedchanges in the source of sinking particles in the North Atlantic. Nature 354,136–139.

Altabet, M.A., Pilskaln, C., Thunell, R., Pride, C., Sigman, D., Chavez, F., Francois, R.,1999. The nitrogen isotope biogeochemistry of sinking particles from themargin of the eastern north pacific. Deep-Sea Research I 46, 655–679.

Altabet, M.A., Small, L.F., 1990. Nitrogen isotope ratios in fecal pellets produced bymarine zooplankton. Geochimica et Cosmochimica Acta 54, 155–163.

Barford, C.C., Montoya, J.P., Altabet, M.A., Mitchell, R., 1999. Steady-state nitrogenisotope effects of N2 and N2O production in Paracoccus denitrificans. Appliedand Environmental Microbiology 65, 989–994.

Berounsky, V.M., Nixon, S.W., 1990. Temperature and the annual cycle of nitrifi-cation in waters of Narragansett Bay. Limnology and Oceanography 35,1610–1617.

Brandes, J.A., Devol, A.H., 1997. Isotopic fractionation of oxygen and nitrogen incoastal marine sediments. Geochimica et Cosmochimica Acta 61, 1793–1801.

Brandes, J.A., Devol, A.H., 2002. A global marine-fixed nitrogen isotopic budget:implications for Holocene nitrogen cycling. Global Biogeochemical Cycles 16(4), 1120. doi:10.1029/2001GB001856.

Brandes, J.A., Devol, A.H., Yoshinari, T., Jayakumar, D.A., Naqvi, S.W.A., 1998. Isotopiccomposition of nitrate in the central Arabian Sea and eastern tropical NorthPacific: a tracer for mixing and nitrogen cycles. Limnology and Oceanography43, 1680–1689.

Casciotti, K.L., Sigman, D.M., Ward, B.B., 2003. Linking diversity and stable isotopefractionation in ammonia-oxidizing bacteria. Geomicrobiology Journal 20,335–353.

Checkley, D.M., Miller, C.A., 1989. Nitrogen isotope fractionation by oceaniczooplankton. Deep-Sea Research 36, 1449–1456.

Cifuentes, L., Fogel, M.L., Pennock, J.R., Sharp, J.H., 1989. Biogeochemical factors thatinfluence the stable nitrogen isotope ratio of dissolved ammonium in theDelaware estuary. Geochimica et Cosmochimica Acta 53, 2713–2721.

Cline, J.D., Kaplan, I.R., 1975. Isotope fractionation of dissolved nitrate during the deni-trification in the eastern tropical north pacific ocean. Marine Chemistry 3, 271–299.


Fujiwara, T., Fukui, S., Kasai, A., Sakamoto, W., Sugiyama, Y., 1997a. Nutrientstransport and subsurface chlorophyll maximum in Ise Bay. Umi-to-Sora 73, 55–61 (in Japanese with English abstract).

Fujiwara, T., Sanford, L.P., Nakatsuji, K., Sugiyama, Y., 1997b. Anti-cyclonic circulationdriven by the estuarine circulation in a gulf type ROFI. Journal of MarineSystems 12, 83–99.

Fujiwara, T., Takahashi, T., Kasai, A., Sugiyama, Y., Kuno, M., 2002. The role ofcirculation in the development of hypoxia in Ise Bay, Japan. Estuarine, Coastaland Shelf Science 54, 19–31.

Fujiwara, T., Uno, N., Tada, M., Nakatsuji, K., Kasai, A., Sakamoto, W., 1997c. Nutrientflux and residual current in Kii Channel. Umi-to-Sora 73, 63–72 (in Japanesewith English abstract).

Giraud, X., Bertrand, P., Carcon, V., Dadou, I., 2000. Modeling d15N evolution: firstpaleoceanographic applications in a coastal upwelling system. Journal ofMarine Systems 58, 609–630.

Giraud, X., Bertrand, P., Carcon, V., Dadou, I., 2003. Interpretation of the nitrogenisotopic signal variations in the Mauritainian upwelling with a 2D physical-biological model. Global Biogeochemical Cycles 17, 1059. doi:10.1029/2002GB001951.

Hayashi, M., Yanagi, T., 2002. Comparison of the lower trophic level ecosystem withSuo-Nada and the inner part of Osaka Bay. Oceanography in Japan 11, 591–611(in Japanese with English abstract).

Herbert, R.A., 1999. Nitrogen cycling in coastal marine ecosystems. FEMS Micobi-ology Reviews 23, 563–590.

Holmes, R.M., McClelland, J.W., Sigman, D.M., Fry, B., Peterson, B.J., 1998. Measuring15N-NH4

þ in marine, estuarine and fresh waters: an adaptation of the ammoniadiffusion method for samples with low ammonium concentrations. MarineChemistry 60, 235–243.

Horrigan, S.G., Montoya, J.P., Nevins, J.L., McCarthy, J.J., 1990. Natural isotopiccomposition of dissolved inorganic nitrogen in the Chesapeake Bay. Estuarine,Coastal and Shelf Science 30, 393–410.

Kakehi, S., 2006. Seasonal variation in flow structure and nutrient dynamics in theeutrophic coastal basin. Ph.D thesis, Kyoto University, pp. 138 (in Japanese).

Kakehi, S., Fujiwara, T., 2007. Dynamics of nutrients in Ise Bay: seasonal variations ofnon-conservative change of nutrients. Oceanography in Japan 16, 437–453 (inJapanese).

Kakehi, S., Fujiwara, T., Sugiyama, Y., 2004. Upwelling induced by intermittentbottom intrusion of oceanic water into Ise Bay. Oceanography in Japan 13, 537–551 (in Japanese with English abstract).

Kakehi, S., Fujiwara, T., Yamada, H., 2005. Seasonal variations in the nutrientsstanding mass and nutrient budget of Ise Bay. Oceanography in Japan 14, 527–540 (in Japanese with English abstract).

Kasai, A., Fujiwara, T., Simpson, J.H., Kakehi, S., 2002. Circulation and cold dome ina gulf-type ROFI. Continental Shelf Research 22, 1579–1590.

Kasai, A., Hill, A.E., Fujiwara, T., Simpson, J.H., 2000. Effect of the Earth’s rotation onthe circulation in regions freshwater influence. Journal of Geophysical Research105, 16961–16969.

Kasai, A., Sugimoto, R., Akamine, S., 2007. Formation mechanism of subsurfacechlorophyll maximum in a coastal embayment. Umi-to-Sora 82, 53–60 (inJapanese with English abstract).

Kawamiya, M., Kishi, M.J., Yamanaka, Y., Suginohara, N., 1995. An ecological-physicalcoupled model applied to station Papa. Journal of Oceanography 51, 635–664.

Kittiwanich, J., Yamamoto, T., Hashimoto, T., Tsuji, K., Kawaguchi, O., 2006. Phos-phorus and nitrogen cyclings in the pelagic system of Hiroshima Bay: results ofnumerical model simulation. Journal of Oceanography 62, 493–509.

Kobayashi, S., Fujiwara, T., 2008. Long-term variability of shelf water intrusion andits influence on hydrographic and biogeochemical properties of the Seto InlandSea, Japan. Journal of Oceanography 64, 595–603.

Mariotti, A., Germon, J.G., Hubert, P., Kaiser, P., Letolle, R., Tardieux, A., Tardieux, P.,1981. Experimental determination of nitrogen kinetic isotope fractionation:some principles; illustration for the denitrification and nitrification processes.Plant and Soil 62, 413–430.

Minagawa, M., Wada, E., 1984. Stepwise enrichment of 15N along food chains:further evidence and the relation between d15N and animal age. Geochimica etCosmochimica Acta 48, 1135–1140.

Mino, Y., Saino, T., Suzuki, K., Maranon, E., 2002. Isotopic composition of suspendedparticulate nitrogen (d15Nsus) in surface waters of the Atlantic Ocean from 50�Nto 50�S. Global Biogeochemical Cycles 16, 1059. doi:10.1029/2001/GB001635.

Montoya, J.P., Horrigan, S.G., McCarthy, J.J., 1990. Natural abundance of 15N inparticulate nitrogen and zooplankton in the Chesapeake Bay. Marine EcologyProgress Series 65, 35–61.

Montoya, J.P., Horrigan, S.G., McCarthy, J.J., 1991. Rapid, storm-induced changes inthe natural abundance of 15N in a planktonic ecosystem, Chesapeake Bay, USA.Geochimica et Cosmochimica Acta 55, 3627–3638.

Montoya, J.P., McCarthy, J.J., 1995. Isotopic fractionation during nitrate uptake by phyto-plankton grown in continuous culture. Journal of Plankton Research 17, 439–464.

Murrell, M.C., Hagy III, J.D., Lores, E.M., Greene, R.M., 2007. Phytoplanktonproduction and nutrient distributions in a subtropical estuary: importance offreshwater flow. Estuaries and Coasts 30, 390–402.

Needoba, J.A., Waser, N.A., Harrison, P.J., Calvert, S.E., 2003. Nitrogen isotope frac-tionation in 12 species of marine phytoplankton during growth on nitrate.Marine Ecology Progress Series 255, 81–91.

Pennock, J.R., Velinsky, D.J., Ludlam, J.M., Sharp, J.H., Fogel, M.L., 1996. Isotopicfractionation of ammonium and nitrate during uptake by Skeletonema costatum:implications for d15N dynamics under bloom conditions. Limnology andOceanography 41, 451–459.

Sebilo, M., Billen, G., Mayer, B., Billou, D., Grably, M., Garnier, J., Mariotti, A., 2006.Assessing nitrification and denitrification in the Seine River and estuary usingchemical and isotopic techniques. Ecosystems 9, 564–577.

Sigman, D.M., Altabet, M.A., McCorkle, D.C., Francois, R., Fischer, G., 1999. The d15N ofnitrate in the southern ocean: consumption of nitrate in surface waters. GlobalBiogeochemical Cycles 13, 1149–1166.

Sigman, D.M., Altabet, M.A., Michener, R., McCorkle, D.C., Fry, B., Holmes, R.M., 1997.Natural abundance-level measurement of the nitrogen isotopic composition ofoceanic nitrate: an adaptation of the ammonia diffusion method. MarineChemistry 57, 227–242.

Sigman, D.M., Robinson, R., Knapp, A.N., van Geen, A., McCorkle, D.C.,Brandes, J.A., Thunell, R.C., 2003. Distinguishing between water column andsedimentary denitrification in the Santa Barbara Basin using the stableisotopes of nitrate. Geochemistry, Geophysics, Geosystems 4, 1040.doi:10.1029/2002GC000384.

Steel, J.H., 1962. Environmental control of photosynthesis in the sea. Limnology andOceanography 7, 137–150.

Sugawara, Y., 2003. Denitrification rate in the sediments. Report by. In: Studies ofEcosystem Recovery for Ise Bay. Mie Pref. Science & Technology PromotionCenter, pp. 18–22 (in Japanese).

Sugimoto, R., Kasai, A., Yamao, S., Fujiwara, T., Kimura, T., 2004. Variation inparticulate organic matter accompanying changes of river discharge in Ise Bay.Bulletin of the Japanese Society of Fisheries Oceanography 68, 142–150 (inJapanese with English abstract).

Sugimoto, R., Kasai, A., Yamao, S., Fujiwara, T., Kimura, T., 2006. Short-term variationin behavior of allochthonous particulate organic matter accompanying changesof river discharge in Ise Bay, Japan. Estuarine, Coastal and Shelf Science 66,267–279.

Sugimoto, R., Kasai, A., Miyajima, T., Fujita, K., 2008. Nitrogen isotopic discrimina-tion by water column nitrification in a shallow coastal environment. Journal ofOceanography 64, 39–48.

Sugimoto, R., Kasai, A., Miyajima, T., Fujita, K., 2009a. Nitrogen isotope ratios ofnitrate as a clue to the origin of nitrogen on the pacific coast of Japan. Conti-nental Shelf Research 29, 1303–1309.

Sugimoto, R., Kasai, A., Miyajima, T., Fujita, K., 2009b. Transport of oceanic nitratefrom the continental shelf to the coastal basin in relation to the path of theKuroshio. Continental Shelf Research 29, 1678–1688.

Sugimoto, R., Kasai, A., Miyajima, T., Fujita, K., 2009c. Controlling factors of seasonalvariation in the nitrogen isotope ratio of nitrate in a eutrophic coastal envi-ronment. Estuarine, Coastal and Shelf Science 85, 231–240.

Sutka, R.L., Ostrom, N.E., Ostrom, P.H., Phanikumar, M.S., 2004. Stable nitrogenisotope dynamics of dissolved nitrate in a transect from the north pacificsubtropical Gyre to the eastern tropical north pacific. Geochimica et Cosmo-chimica Acta 68, 517–527.

Takahashi, T., Fujiwara, T., Kuno, M., Sugiyama, Y., 2000. Seasonal variation inintrusion depth of oceanic water and the hypoxia in Ise Bay. Oceanography inJapan 9, 265–271 (in Japanese with English abstract).

Vitousek, P.M., Aber, J.D., Howarth, R.W., Likens, G.E., Matson, P.A., Schindler, D.W.,Schlesinger, W.H., Tilman, D.G., 1997. Human alteration of the global nitrogencycle: sources and consequences. Ecological Applications 7, 737–750.

Wada, E., Hattori, A., 1978. Nitrogen isotope effects in the assimilation of inorganicnitrogenous compounds by marine diatoms. Geomicrobiology Journal 1,85–101.

Walker, T.A., 1980. A correction to the Poole and Atkins Secchi disk/light attenuationformula. The Marine Biological Association of the UK 60, 769–771.

Wankel, S.D., Kendall, C., Pennington, J.T., Chavez, F.P., Paytan, A., 2007. Nitrificationin the euphotic zone as evidenced by nitrate dual isotopic composition:observations from Monterey Bay, California. Global Biogeochemical Cycles 21,GB2009. doi:10.1029/2006GB002723.

Waser, N.A., Harrison, P.J., Nielsen, B., Calvert, S.E., Turpin, D.H., 1998a. Nitrogenisotope fractionation during the uptake and assimilation of nitrate, nitrite,ammonium and urea by a marine diatom. Limnology and Oceanography 43,215–224.

Waser, N.A., Yin, K., Yu, Z., Tada, K., Harrison, P.J., Turpin, D.H., Calvert, S.E., 1998b.Nitrogen isotope fractionation during nitrate, ammonium and urea uptake bymarine diatoms and coccolithophores under various conditions of N availability.Marine Ecology Progress Series 169, 29–41.

Wu, J., Calvert, S.E., Wong, C.S., 1997. Nitrogen isotope variations in the subarcticnortheast Pacific: relationships to nitrate utilization and trophic structure.Deep-Sea Research I 44, 287–314.

Yoshikawa, C., Yamanaka, Y., Nakatsuka, T., 2005. An ecosystem model includingnitrogen isotopes: perspectives on a study of the marginal nitrogen cycle.Journal of Oceanography 61, 921–942.

Yoshikawa, C., Yamanaka, Y., Nakatsuka, T., 2006. Nitrate-nitrogen isotopic patternsin surface waters of the western and central equatorial pacific. Journal ofOceanography 62, 511–525.

Zheng, L., Chen, C., Zhang, F.Y., 2004. Development of water quality model in theSatilla River estuary, Georgia. Ecological Modeling 178, 457–482.

estuarine, coastal and shelf science · estuarine, coastal and shelf science 86 (2010) 450–466....

Documents