Dynamic model of integrated processes in the ecosystem of the northwest shelf of the Black Sea

For the ecosystem of the northwest shelf of the Black Sea studied as an example, we construct a dynamic model of the integrated processes of development of phyto-and zooplankton, larvae, and fish and the variations of the concentrations of biogenic elements and detritus. The data of many-year observations over these processes are generalized and the scheme of genetic relations between these processes is proposed. By the method of adaptive balance of causes, we establish the dynamic model equations of the ecosystem. It is proposed to use the method of analytic hierarchy process for the estimation of the coefficients of the model with regard for the degree of influence of external and internal factors on the dynamics of the ecosystem. Some examples of analysis of various scenarios of the development of integrated processes running in the ecosystem are presented and their comparison with the data of many-year observations in this region is performed. __________ Translated from Morskoi Gidrofizicheskii Zhurnal, No. 4, pp. 48–69, July–August, 2007.     

The applicability of the shallow water equations for modelling violent wave overtopping

The shallow water equations (SWE) have been used to model a series of experiments examining violent wave overtopping of a near-vertical sloping structure with impacting wave conditions. A finite volume scheme was used to solve the shallow water equations. A monotonic reconstruction method was applied to eliminate spurious oscillations and ensure proper treatment of bed slope terms. Both the numerical results and physical observations of the water surface closely followed the relevant Rayleigh probability distributions. However, the numerical model overestimated the wave heights and suffered from the lack of dispersion within the shallow water equations. Comparisons made on dimensionless parameters for the overtopping discharge and percentage of waves overtopping between the numerical model and the experimental observations indicated that for the lesser impacting waves, the shallow water equations perform satisfactorily and provide a good alternative to computationally more expensive methods.     

Dynamic-Stochastic Modeling of Natural Processes

We propose a method for the construction of dynamic-stochastic models of natural systems based on the assimilation of the data of observations in the prognostic equations of coupled processes. In these models, the method of adaptive balance of causes is used to deduce evolutionary equations of the analyzed processes and assimilate the data of observations in these equations. The deduced general equations are considered for an example of a marine ecosystem characterized by the development of four coupled processes. It is shown that the optimal prediction of these processes requires the solution of 11 systems of equations with simultaneous adaptation of prognostic estimates and the coefficients of the models to the data of observations. A numerical simulation experiment explaining the algorithm of the proposed method of modeling is considered. A conclusion is made that the application of this method in the geoinformation systems of monitoring of the environment is quite promising.__________Translated from Morskoi Gidrofizicheskii Zhurnal, No. 6, pp. 31–42, November–December, 2004.     

Mathematical model for the ecosystem of the Black Sea hydrogen sulphide zone

A model for the ecosystem of the Black Sea hydrogen sulphide zone is suggested which incorporates seven components, namely, the concentrations of hydrogen sulphide, oxygen, dead organic matter, thiosulphates, molecular sulphur, and the biomass of sulphate-reducing and thiobacteria. With the minor terms neglected in the equations governing the system under consideration, the latter was divided into subsystems which allow an approximate calculation of the model components' vertical stationary profiles. The derived components' profiles agree qualitatively with available observations.Translated by V. Puchkin.     

Modelling phytoplankton succession on the Bering Sea shelf: role of climate influences and trophic interactions in generating Emiliania huxleyi blooms 1997–2000

Several years of continuous physical and biological anomalies have been affecting the Bering Sea shelf ecosystem starting from 1997. Such anomalies reached their peak in a striking visual phenomenon: the first appearance in the area of bright waters caused by massive blooms of the coccolithophore Emiliania huxleyi (E. huxleyi). This study is intended to provide an insight into the mechanisms of phytoplankton succession in the south-eastern part of the shelf during such years and addresses the causes of E. huxleyi success by means of a 2-layer ecosystem model, field data and satellite-derived information. A number of potential hypotheses are delineated based on observations conducted in the area and on previous knowledge of E. huxleyi general ecology. Some of these hypotheses are then considered as causative factors and explored with the model. The unusual climatic conditions of 1997 resulted most notably in a particularly shallow mixed layer depth and high sea surface temperature (about 4 °C above climatological mean). Despite the fact that the model could not reproduce for E. huxleyi a clear non-bloom to bloom transition (pre- vs. post-1997), several tests suggest that this species was favoured by the shallow mixed layer depth in conjunction with a lack of photoinhibition. A top-down control by microzooplankton selectively grazing phytoplankton other than E. huxleyi appears to be responsible for the long persistence of the blooms. Interestingly, observations reveal that the high N:P ratio hypothesis, regarded as crucial in the formation of blooms of this species in previous studies, does not hold on the Bering Sea shelf.     

Reevaluation of historical ocean heat content variations with time-varying XBT and MBT depth bias corrections

As reported in former studies, temperature observations obtained by expendable bathythermographs (XBTs) and mechanical bathythermographs (MBTs) appear to have positive biases as much as they affect major climate signals. These biases have not been fully taken into account in previous ocean temperature analyses, which have been widely used to detect global warming signals in the oceans. This report proposes a methodology for directly eliminating the biases from the XBT and MBT observations. In the case of XBT observation, assuming that the positive temperature biases mainly originate from greater depths given by conventional XBT fall-rate equations than the truth, a depth bias equation is constructed by fitting depth differences between XBT data and more accurate oceanographic observations to a linear equation of elapsed time. Such depth bias equations are introduced separately for each year and for each probe type. Uncertainty in the gradient of the linear equation is evaluated using a non-parametric test. The typical depth bias is +10 m at 700 m depth on average, which is probably caused by various indeterminable sources of error in the XBT observations as well as a lack of representativeness in the fall-rate equations adopted so far. Depth biases in MBT are fitted to quadratic equations of depth in a similar manner to the XBT method. Correcting the historical XBT and MBT depth biases by these equations allows a historical ocean temperature analysis to be conducted. In comparison with the previous temperature analysis, large differences are found in the present analysis as follows: the duration of large ocean heat content in the 1970s shortens dramatically, and recent ocean cooling becomes insignificant. The result is also in better agreement with tide gauge observations. On leave from the Meteorological Research Institute of the Japan Meteorological Agency.     

Three-dimensional refined modeling of water quality in Victoria Harbour

Ｔｈｒｅｅ－ｄｉｍｅｎｓｉｏｎａｌｒｅｆｉｎｅｄｍｏｄｅｌｉｎｇｏｆｗａｔｅｒｑｕａｌｉｔｙｉｎＶｉｃｔｏｒｉａＨａｒｂｏｕｒＳｈｅｎＹｏｎｇｍｉｎｇ,ＱｉｕＤａｈｏｎｇ,Ａ．Ｔ．Ｃｈｗａｎｇ（ＲｅｃｅｉｖｅｄＳｅｐｔｅｍｂｅｒ１２,１９９６;ａｃｃ...     

Modeling iron limitation of primary production in the coastal Gulf of Alaska

A lower trophic level NPZD ecosystem model with explicit iron limitation on nutrient uptake is coupled to a three-dimensional coastal ocean circulation model to investigate the regional ecosystem dynamics of the northwestern coastal Gulf of Alaska (CGOA). Iron limitation is included in the NPZD model by adding governing equations for two micro-nutrient compartments: dissolved iron and phytoplankton-associated iron. The model has separate budgets for nitrate (the limiting macro-nutrient in the standard NPZD model) and for iron, with iron limitation on nitrate uptake being imposed as a function of the local phytoplankton realized Fe:C ratio. While the ecosystem model represents a simple approximation of the complex lower trophic level ecosystem of the northwestern CGOA, simulated chlorophyll concentrations reproduce the main characteristics of the spring bloom, high shelf primary production, and “high-nutrient, low-chlorophyll” (HNLC) environment offshore. Over the 1998–2004 period, model-data correlations based on spatially averaged, monthly mean chlorophyll concentrations are on average 0.7, with values as high as 0.9 and as low as 0.5 for individual years. The model also provides insight on the importance of micro- and macro-nutrient limitation on the shelf and offshore, with the shelfbreak region acting as a transition zone where both nitrate and iron availability significantly impact phytoplankton growth. Overall, the relative simplicity of the ecosystem model provides a useful platform to perform long-term simulations to investigate the seasonal and interannual CGOA ecosystem variability, as well as to conduct sensitivity studies to evaluate the robustness of simulated fields to ecosystem model parameterization and forcing. The ability of the model to differentiate between nitrate-limited, and iron-limited growth conditions, and to identify their spatial and temporal occurrences, is also a first step towards understanding the role of environmental gradients in shaping the complex CGOA phytoplankton community structure.     

海洋赤潮生态模型参数优化研究

根据中日合作海洋生态围隔试验观测资料,对乔方利等１９９８年提出的赤潮过程生态模型（乔方利等,２０００）进行参数优化研究,得到赤潮过程营养２盐半饱和常数：硅藻,ＫＮ＝１．４ｕｍｏｌ／Ｌ、ＫＰ＝０．１２９ｕｍｏｌ／Ｌ、ＫＳｉ＝１．１６ｕｍｏｌ／Ｌ;鞭毛藻,ＫＮ＝０．３４５ｕｍｏｌ／Ｌ、ＫＰ＝０．１１３ｕｍｏｌ／Ｌ以及其它等共１８个参数的最优取值,并详细讨论了目标泛函的构造和多目标函数参数优化的方法。     

The near-bottom boundary layer in the black sea: Hydrological structure and modelling

The paper discusses the parameters derived through deep-sea precision CTD-probings, characteristic of the structure of the near-bottom boundaries layer, specifically, the depth of the layer's upper boundary and the mean vertical potential temperature/salinity gradients, as well as the density ratio over the layer of the near-bottom convection. The peculiarities of the parameters' spatial distribution have been identified. The conclusion derived from the analysis of the model implies that the near-bottom boundary layer occurs, aside from the presence of the bottom geothermal heat flux, due to the strong dependence of the Bosphorus salt flux on stratification. The dependence of the Black Sea buoyancy flux and vertical diffusion coefficient on depth has been estimated. Translated by Vladimir A. Puchkin     

Multilevel hydrothermodynamic model of a deep basin

A hydrothermodynamic model based on the traditional system of differential equations is discussed. The model uses conservative finite-difference schemes based on the methods of identifying the barotropic and baroclinic velocity components and on the complete inversion of the dynamic operator. Test computations for the Black Sea basin have been conducted.Translated by Vladimir A. Puchkin.     

Detecting regime shifts in the ocean: Data considerations

We review observational data sets that have been used to detect regime shifts in the ocean. Through exploration of data time series we develop a definition of a regime shift from a pragmatic perspective, in which a shift is considered as an abrupt change from a quantifiable ecosystem state. We conclude that such changes represent a restructuring of the ecosystem state in some substantial sense that persists for long enough that a new quasi-equilibrium state can be observed. The abruptness of the shift is relative to the life-scale or the reproductive time-scale of the higher predators that are influenced by the shift. In general, the event-forcing is external to the biological ecosystem, usually the physical climate system, but we also identify shifts that can be ascribed to anthropogenic forcing, in our examples fishing. This pragmatic definition allows for several different types of regime shift ranging from simple biogeographic shifts to non-linear state changes. In practice it is quite difficult to determine whether observed changes in an oceanic ecosystem are primarily spatial or temporally regulated. The determination of ecosystem state remains an unresolved, and imprecise, oceanographic problem.We review observations and interpretation from several different oceanic regions as examples to illustrate this pragmatic definition of a regime shift: the Northeast Pacific, the Northwest and Northeast Atlantic, and Eastern Boundary Currents. For each region, different types of data (biological and physical) are available for differing periods of time, and we conclude, with varying degrees of certainty, whether a regime shift is in fact detectable in the data.     

Numerical simulation of solitary and randomwave propagation through vegetation based on VOFmethod

A vertical two-dimensional numerical model has been applied to solving the Reynolds Averaged Navier- Stokes （RANS} equations in the simulation of current and wave propagation through vegetated and non- vegetated waters. The k-e model is used for turbulence closure of RANS equations. The effect of vegeta- tion is simulated by adding the drag force of vegetation in the flow momentum equations and turbulence model. To solve the modified N-S equations, the finite difference method is used with the staggered grid system to solver equations. The Youngs＇ fractional volume of fluid （VOF） is applied tracking the free sur- face with second-order accuracy. The model has been tested by simulating dam break wave, pure current with vegetation, solitary wave runup on vegetated and non-vegetated channel, regular and random waves over a vegetated field. The model reasonably well reproduces these experimental observations, the model- ing approach presented herein should be useful in simulating nearshore processes in coastal domains with vegetation effects.     

Eddy-resolving simulation of plankton ecosystem dynamics in the California Current System

We study the dynamics of the planktonic ecosystem in the coastal upwelling zone within the California Current System using a three-dimensional (3-D), eddy-resolving circulation model coupled to an ecosystem/biogeochemistry model. The physical model is based on the Regional Oceanic Modeling System (ROMS), configured at a resolution of 15 km for a domain covering the entire US West Coast, with an embedded child grid covering the central California upwelling region at a resolution of 5 km. The model is forced with monthly mean boundary conditions at the open lateral boundaries as well as at the surface. The ecological/biogeochemical model is nitrogen based, includes single classes for phytoplankton and zooplankton, and considers two detrital pools with different sinking speeds. The model also explicitly simulates a variable chlorophyll-to-carbon ratio. Comparisons of model results with either remote sensing observations (AVHRR, SeaWiFS) or in-situ measurements from the CalCOFI program indicate that our model is capable of replicating many of the large-scale, time-averaged features of the coastal upwelling system. An exception is the underestimation of the chlorophyll levels in the northern part of the domain, perhaps because of the lack of short-term variations in the atmospheric forcing. Another shortcoming is that the modeled thermocline is too diffuse, and that the upward slope of the isolines toward the coast is too small. Detailed time-series comparisons with observations from Monterey Bay reveal similar agreements and discrepancies. We attribute the good agreement between the modeled and observed ecological properties in large part to the accuracy of the physical fields. In turn, many of the discrepancies can be traced back to our use of monthly mean forcing. Analysis of the ecosystem structure and dynamics reveal that the magnitude and pattern of phytoplankton biomass in the nearshore region are determined largely by the balance of growth and zooplankton grazing, while in the offshore region, growth is balanced by mortality. The latter appears to be inconsistent with in situ observations and is a result of our consideration of only one zooplankton size class (mesozooplankton), neglecting the importance of microzooplankton grazing in the offshore region. A comparison of the allocation of nitrogen into the different pools of the ecosystem in the 3-D results with those obtained from a box model configuration of the same ecosystem model reveals that only a few components of the ecosystem reach a local steady-state, i.e. where biological sources and sinks balance each other. The balances for the majority of the components are achieved by local biological source and sink terms balancing the net physical divergence, confirming the importance of the 3-D nature of circulation and mixing in a coastal upwelling system.     

A three-dimensional numerical model of hydrodynamics and water quality in Hakata Bay

The hydrodynamics and water quality in Hakata Bay, Japan, are strongly affected by the seasonal variations in both the gravitational circulation and the stratification in the bay. The three-dimensional hydrodynamics and water quality model has been developed to simulate the long-term transport and fate of pollutants in the system. The model is unique in that it completely integrates the refined modelling of the hydrodynamics, biochemical reactions and the ecosystem in the coastal areas. It is a 3-dimensional segmented model which is capable of resolving mean daily variations in all the parameters relevant to pollution control. It predicts daily fluctuations in the oxygen content at different depths in water throughout the year. It takes into account transport and settling of pollutant particles. It predicts light penetration from computed turbidity variations. It includes interactions between the ecosystem and water quality, through nutrient cycling and photosynthesis. The model has been calibrated well against the data set of historical water quality observations in Hakata Bay.     

A general ecosystem model for applications to primary productivity and carbon cycle studies in the global oceans

We have developed a general 1-D multi-component ecosystem model that incorporates a skillful upper ocean mixed layer model based on second moment closure of turbulence. The model is intended for eventual incorporation into coupled 3-D physical–biogeochemical ocean models with potential applications to modeling and studying primary productivity and carbon cycling in the global oceans as well as to promote the use of chlorophyll concentrations, in concert with satellite-sensed ocean color, as a diagnostic tool to delineate circulation features in numerical circulation models. The model is nitrogen-based and the design is deliberately general enough and modular to enable many of the existing ecosystem model formulations to be simulated and hence model-to-model comparisons rendered feasible. In its more general form (GEM10), the model solves for nitrate, ammonium, dissolved nitrogen, bacteria and two size categories of phytoplankton, zooplankton and detritus, in addition to solving for dissolved inorganic carbon and total alkalinity to enable estimation of the carbon dioxide flux at the air–sea interface. Dissolved oxygen is another prognostic variable enabling air–sea exchange of oxygen to be calculated. For potential applications to HNLC regions where productivity is constrained by the availability of a trace constituent such as iron, the model carries the trace constituent as an additional prognostic variable. Here we present 1-D model simulations for the Black Sea, Station PAPA and the BATS site. The Black Sea simulations assimilate seasonal monthly SST, SSS and surface chlorophyll, and the seasonal modulations compare favorably with earlier work. Station PAPA simulations for 1975–1977 with GEM5 assimilating observed SST and a plausible seasonal modulation of surface chlorophyll concentration also compare favorably with earlier work and with the limited observations on nitrate and pCO₂ available. Finally, GEM5 simulations at BATS for 1985–1997 are consistent with the available time series. The simulations suggest that while it is generally desirable to employ a comprehensive ecosystem model with a large number of components when accurate depiction of the entire ecosystem is desirable, as is the prevailing practice, a simpler formulation such as GEM5 (N²PZD model) combined with assimilation of remotely sensed SST and chlorophyll concentrations may suffice for incorporation into 3-D prediction models of primary productivity, upper ocean optical clarity and carbon cycling.     

胶州湾北部水层-底栖耦合生态系统的动力数值模拟分析

基于胶州湾1995年5航次的生态动力学综合实验观测，建立了一个水层－底栖生态系耦合的动力学箱式模型，其中水层亚模型包括浮游植物、浮游动物、无机氮、无机磷以及DOC、POC和溶解氧7变量，底栖部分包括大型、小型底栖生物、细胞、碎屑及无机氮和磷6变量。模型考虑了海面太阳辐照度变化、海水及底泥温度变化，以及营养盐与DOC陆源流入的影响，利用该模型成功地模拟了胶州湾北部各生态变量的季节变化特征。同吴增茂等（1999）水层模型模拟结果相比可以看出，耦合模型的结果更加合理。     

基于生态通道模型的长江口及邻近海域生态系统能流动态分析

本文根据2004年长江口及其邻近海域生态调查数据,运用生态通道模型(Ecopath模型)构建生态系统能流网络,分析本区域生态系统营养结构及功能,并与1985—1986年研究数据进行对比,解析两个时期生态系统营养结构与功能的差异。研究结果显示,2004年长江口及其邻近海域生态系统营养级范围为1～4.34,相较于1985—1986年研究结果,底层无脊椎动物食性鱼类和头足类的营养级变动较大。牧食食物链占据主导地位,浮游植物在浮游动物和水母的能量来源中所占比例均在60%以上;碎屑食物链所占能流比为44%。系统总能流为6342.081 t·km–2·a–1。渔获物平均营养级下降,生态营养效率平均值较高,但是碎屑和浮游植物的生态营养效率却明显下降,碎屑趋于累积。生态系统统计量整体显示,长江口及邻近海域生态系统成熟度降低。     

Wave characteristics and extreme parameters in the Bohai Sea

This paper is aimed at the whole Bohai Sea,as the complement and improvement of wave characteristics and extreme parameters.Wave fields were simulated in the Bohai Sea by using wave model SWAN from 1985 to 2004.The input data based on the hindcast of high-resolution wind fields from RAMS and water level fields from POM,which have been tested and verified well.Comparisons of significant wave heights between simulation and station observations show a good agreement in general.By statistical analysis,the wave characteristics such as significant wave heights, dominant wave directions and their seasonal variations are discussed.In addition,main wave extreme parameters and directional extreme values particularly for 100-year return period are investigated.     

Impacts of a bivalve mass mortality event on an estuarine food web and bivalve grazing pressure

Declines in bivalve populations have been quite common worldwide, often associated with coastal development, pollution and climate change. In addition to the impacts of these chronic stressors, occasional mass mortality events may have severe consequences on ecosystem services and biodiversity. In this study, we examined the impact of a mass mortality event of the clam (Austrovenus stutchburyi) on an estuarine food web and the grazing pressure exerted by the bivalve population. In February 2009, c. 60% of the clam population died in Whangateau Harbour, New Zealand. Population clearance rate calculations suggest that the clam population do not exert significant top-down control on phytoplankton biomass in the estuary, and thus the impact of the mortality event on bivalve grazing pressure was less severe than the reduction in abundance would suggest. A trophic model shows that phytoplankton play a limited role in the estuary food web, which is instead dominated by microphytobenthos and clams. This study highlights the importance of microphytobenthos in shallow estuaries, and the application of the trophic model is a useful tool that can identify key components of the ecosystem and could help inform monitoring programmes.