NPZ Models of Plankton Dynamics: Their Construction, Coupling to Physics, and Application

Nutrient-phytoplankton-zooplankton (NPZ) models have been in use in oceanography for at least three decades, and are still a common research tool. Given the discoveries of the last two decades, particularly concerning the role of bacteria in the plankton, there are questions as to whether NPZ models can still be supported as a useful tool in planktonic research. Here I review the construction of NPZ models, and some of the physical platforms they have been coupled to. I then discuss the applications of NPZ-physical models, and conclude that they still constitute an important and viable research tool, provided that the questions being explored are clearly stated. This revised version was published online in August 2006 with corrections to the Cover Date.     

Changes in the hydrography of Central California waters associated with the 1997–98 El Niño

Oceanographic conditions off Central California were monitored by means of a series of 13 hydrographic cruises between February 1997 and January 1999, which measured water properties along an oceanographic section perpendicular to the California Coast. The 1997–98 El Niño event was defined by higher than normal sea levels at Monterey, which began in June 1997, peaked in November 1997, and returned to normal in March 1998. The warming took place in two distinct periods. During June and July 1997, the sea level increased as a result of stronger than normal coastal warming below 200 dbars and within 100 km of the coast, which was associated with poleward flow of saltier waters. During this period, deeper (400–1000 dbar) waters between 150–200 km from shore were also warmed and became more saline. Subsequently, sea level continued to rise through January 1998, mostly as a result of the warming above 200 dbars although, after a brief period of cooling in September 1997, waters below 200 dbar were also warmer than normal during this period. This winter warm anomaly was also coastally trapped, extending 200 km from shore and was accompanied by cooler and fresher water in the offshore California current. In March and April 1998, sea level dropped quickly to normal levels and inshore waters were fresher and warmer than the previous spring and flowed southward.The warming was consistent with equatorial forcing of Central California waters via propagation of Kelvin or coastally-trapped waves. The observed change in heat content associated with the 1997–98 El Niño was the same as that observed during the previous seasonal cycle. The warming and freshening events were similar to events observed during the 1957–58 and 1982–83 El Niños.     

Imbalance in the carbonate budget of surficial sediments in the North Atlantic Ocean: variations over the last millenium?

Fluxes contributing to the particulate carbonate system in deep-sea sediments were investigated at the BENGAL site in the Porcupine Abyssal Plain (Northeast Atlantic). Deposition fluxes were estimated using sediment traps at a nominal depth of 3000 m and amounted to 0.37±0.1 mmol C m⁻² d⁻¹. Dissolution of carbonate was determined using flux of total alkalinity from in situ benthic chambers, is 0.4±0.1 mmol C m⁻² d⁻¹. Burial of carbonate was calculated from data on the carbonate content of the sediment and sedimentation rates from a model age based on ¹⁴C dating on foraminifera (0.66±0.1 mmol C m⁻² d⁻¹). Burial plus dissolution was three times larger than particle deposition flux which indicates that steady-state is not achieved in these sediments. Mass balances for other components (BSi, ²¹⁰Pb), and calculations of the focusing factor using ²³⁰Th, show that lateral inputs play only a minor role in this imbalance. Decadal variations of annual particle fluxes are also within the uncertainty of our average. Long-term change in dissolution may contribute to the imbalance, but can not be the main reason because burial alone is greater than the input flux. The observed imbalance is thus the consequence of a large change of carbonate input flux which has occured in the recent past. A box model is used to check the response time of the solid carbonate system in these sediments and the time to reach a new steady-state is in the order of 3 kyr. Thus it is likely that the system has been perturbed recently and that large dissolution and burial rates reflect the previously larger particulate carbonate deposition rates. We estimate that particulate carbonate fluxes have certainly decreased by a factor of at least 3 and that this change has occurred during the last few centuries.     

Volcanogenic complexes of the Sea of Okhotsk and the Sea of Japan (Comparative analysis)

Several coeval volcanogenic complexes indicating synchronous volcanic events in the Sea of Japan and the Sea of Okhotsk are defined. Volcanics from different-age complexes of the Sea of Okhotsk show many features in common and are attributed to the Pacific type of calc-alkaline series. They were formed in geodynamic settings of the active continental margin and point to its origination on the continental crust of the fragmented Asian continent margin. The volcanic rocks developed in the Sea of Japan reflect different rifting stages. The initial stage was marked by an eruption of calc-alkaline lavas (Paleocene-Eocene complex). At the stage of the marginal-sea spreading, erupted volcanics of the middle Miocene-Pliocene complex were melted from the depleted mantle and magmatism terminated by an eruption of postspreading Pliocene-Holocene volcanics melted from the enriched mantle EM I. Along with the differences, the magmatism in the Sea of Japan and Sea of Okhotsk has some features in common. In both cases, the sialic component of the lithosphere substantially influenced the magma generation.     

Transformation of black-sea waters in the Sea of Marmara

The analysis is performed on the basis of comparison of the hydrological characteristics of prestrait regions of the Sea of Marmara. It is shown that, in summer, the Black-Sea waters are weakly mixed with the Mediterranean waters and the levels of salinity in the prestrait regions differ by 0.6–0.9‰. In winter, the indicated difference increases and the level of salinity near the entrance of Dardanelles reaches 29‰ and exceeds the level observed near the entrance of Bosporus by 5.5‰. In the analyzed regions, we observe local temperature maxima and minima near the interface of two water masses. This is explained by the presence of strong seasonal variations of temperature for the Black-Sea waters and their absence for the Mediterranean waters. The physical mechanisms responsible for the seasonal variations of the intensity of transformations of the Black-Sea waters are discussed. __________ Translated from Morskoi Gidrofizicheskii Zhurnal, No. 2, pp. 49–55, March–April, 2007.     

Experimental studies on the slowly varying drift motion of a berthed container ship model

The effects of free-surface waves on the floating structures are of great importance in the offshore industry. Among the six degrees of motions of a surface ship the absence of restoring forces in surge, sway and yaw led to critical situations for moored ships in the recent times. The order of forces in horizontal plane and their exciting frequencies are matters of interest. The resonance with the presence of moored chains led to many accidents in the recent past. The lines in dry conditions may not give good damping and in wet condition they may trigger the system to chaotic motions and jumps. Two different loading conditions of a container ship model are tested with waves in laboratory conditions in two different drafts. The mooring lines are chosen as per scale law and the energy under the response spectrum is determined from the plots. The results give new insights into the movement of a berthed ships subjected to waves. Response of the moored ship to different loading conditions in different water depths are discussed in this paper. The paper gives the order of energy due to first-order and slowly varying movement of a berthed container model in a towing tank.     

The dimensions of sand ripples in full-scale oscillatory flows

New large-scale experiments have been carried out in two oscillatory flow tunnels to study ripple regime sand suspension and net sand transport processes in full-scale oscillatory flows. The paper focuses on ripple dimensions and the new data are combined with existing data to make a large dataset of ripple heights and lengths for flows with field-scale amplitudes and periods. A feature of the new experiments is a focus on the effect of flow irregularity. The combined dataset is analysed to examine the range of hydraulic conditions under which oscillatory flow ripples occur, to examine the effects of flow irregularity and ripple three-dimensionality on ripple dimensions and to test and improve existing methods for predicting ripple dimensions.The following are the main conclusions. (1) The highest velocities in a flow time-series play an important role in determining the type of bedform occurring in oscillatory flow. Bedform regime is well characterised by mobility number based on maximum velocity in the case of regular flow and based on the mean of the highest one tenth peak velocities in the case of irregular flow. (2) For field-scale flows, sand size is the primary factor determining whether equilibrium ripples will be 2D or 3D. 2D ripples occur when the sand D₅₀ ≥ 0.30 mm and 3D ripples occur when D₅₀ ≤ 0.22 mm (except when the flow orbital diameter is low). (3) Ripple type (2D or 3D) is the same for regular and irregular flows and ripple dimensions produced by equivalent regular and irregular flows follow a similar functional dependence on mobility number, with mobility number based on maximum velocity in the case of regular flow and based on the mean of the highest one tenth velocities in the case of irregular flow. For much of the ripple regime, ripple dimensions have weak dependency on mobility number and ripple dimensions are similar for regular and irregular flows with the same flow orbital amplitude. However, differences in ripples produced by equivalent regular and irregular flows become significant at the high mobility end of the ripple regime. (4) Ripple dimensions predicted using the Wiberg and Harris formulae are in poor agreement with measured ripple dimensions from the large-scale experiments. Predictions based on the Mogridge et al. and the Nielsen formulae show better overall agreement with the data but also show systematic differences in cases of 3D ripples and ripples generated by irregular flows. (5) Based on the combined large-scale data, modifications to the Nielsen ripple dimension equations are proposed for the heights and lengths of 2D ripples. The same equations apply to regular and irregular flows, but with mobility number appropriately defined. 3D ripples are generally smaller than 2D ripples and estimates of 3D ripple height and length may be obtained by applying multipliers of 0.55 and 0.73 respectively to the 2D formulae. The proposed modified Nielsen formulae provide an improved fit to the large-scale data, accounting for flow irregularity and ripple three-dimensionality.     

Parameter sensitivity of three Kalman filter schemes for assimilation of water levels in shelf sea models

In applications of data assimilation algorithms, a number of poorly known assimilation parameters usually need to be specified. Hence, the documented success of data assimilation methodologies must rely on a moderate sensitivity to these parameters. This contribution presents a parameter sensitivity study of three well known Kalman filter approaches for the assimilation of water levels in a three dimensional hydrodynamic modelling system. The filters considered are the ensemble Kalman filter (EnKF), the reduced rank square root Kalman filter (RRSQRT) and the steady Kalman filter. A sensitivity analysis of key parameters in the schemes is undertaken for a setup in an idealised bay. The sensitivity of the resulting root mean square error (RMSE) is shown to be low to moderate. Hence the schemes are robust within an acceptable range and their application even with misspecified parameters is to be encouraged in this perspective. However, the predicted uncertainty of the assimilation results are sensitive to the parameters and hence must be applied with care. The sensitivity study further demonstrates the effectiveness of the steady Kalman filter in the given system as well as the great impact of assimilating even very few measurements.