The curse of physiology—challenges and opportunities in the interpretation of geochemical data from mollusk shells

Physiology corrupts geochemical records of mollusk shells in many ways, e.g., by actively controlling the incorporation of trace elements in the skeleton. However, the effects of variable biomineralization rates and growth cessation have largely remained unconsidered. Mediated by endogenous timekeeping mechanisms, mollusks stop growing skeletal material on a regular basis ranging from ultradian to annual timescales. During growth cessation, the shells do not record environmental conditions. Shell growth also stops when environmental conditions are beyond the physiological tolerance of the organism, e.g., above and below genetically determined, species-specific thermal extremes where shell growth slows and eventually ceases. Such growth disruptions can occur at non-periodic time intervals. Due to growth retardations and halts, proxy records of mollusk shells are thus incomplete, and reconstructed environmental amplitudes prone to truncation. Furthermore, environmental records are biased toward the physiological optimum of the animal. Favorable environmental conditions increase shell growth, whereas adverse environmental conditions result in reduced shell production and lowered overall metabolism. Not least, the duration of the growing season and overall growth rate decrease as the mollusk grows older. Mathematical modeling approaches can significantly improve proxy records obtained from mollusk shells. For example, if the duration of growth cessation is known, it may be possible to model the missing environmental record. It is also fairly easy to account for age-related growth trends, or variable time-averaging in different portions of the shell. However, a major premise for a reliable interpretation of proxy records from a mollusk shell or other organisms secreting biogenic hard parts is a proper understanding of the physiology, and of course, a high-resolution record of the many different environmental factors that may influence physiology and shell growth. The present paper reviews examples from the literature, and unpublished data on how physiology influences geochemical proxy records from mollusk shells, and presents methods how to eliminate such adverse effects.     

Nitrification in Kochi backwaters

Nitrification rates, as oxidation of ¹⁵N-labelled ammonium and loss of nitrite from N-Serve treated samples, were measured in Kochi backwaters during three seasons. Nitrification rates ranged from undetectable to 166 nmol N L⁻¹ h⁻¹ in the water column and up to 17 nmol N (g wet wt)⁻¹ h⁻¹ in sediments. Nitrification rates were higher in intermediate salinities than in either freshwater or seawater end. Within this salinity range, nitrification rates could be related to ammonium concentrations. As shown by the relation between ammonification and nitrification rates, it is also likely that nitrification is more regulated by renewal rates, rather than by in situ concentrations, of substrate. Among other environmental parameters, temperature and pH may have an influence on nitrification. Potential nitrification rates calculated from loss of nitrite from N-Serve treated, nitrite-enriched samples were about 800 nmol N L⁻¹ h⁻¹ in the water column and 40 nmol N (g wet wt)⁻¹ h⁻¹ in sediments. While these rates are in balance with those of biological ammonium production they may be inadequate to mitigate ammonium pollution in this estuary.     

Developing a building policy for the erosion zone: Solutions to some key (Dutch) questions

In those coastal communities where the most seaward strip of mainland consists of dunes, these dunes often serve as a flexible sea defence. In addition, this strip offers large potential for housing and commercial enterprises. Unfortunately, due to severe storm surges part of this strip (the erosion zone) is subject to erosion, and as a result of which any buildings or infrastructure located here, are destroyed. Therefore, as we will illustrate in this paper, a building policy for this zone should reflect a compromise between two opposite interests: exploitation of the existing potential and, prevention of an unacceptable high risk due to erosion. Accordingly, the authors have developed a framework for such a building policy on the basis of which the desirability of various different types of investments and the location within the erosion zone of such investments can be determined. The examples that are used to illustrate this framework in this paper are limited to experiences in The Netherlands as relevant data and experiences are available and relatively easy accessible here. Nevertheless, the approach as is described is generic and applicable worldwide suggesting that the discovered unused potential for exploitation is not just limited to The Netherlands.     

The effect of a topographic high on the morphological stability of a two-inlet bay system

The cross-sectional stability of two tidal inlets connecting the same back-barrier lagoon to the ocean is investigated. The condition for equilibrium is the cross-sectional area tidal prism relationship. In an earlier study [Van de Kreeke, J., 1990. Can multiple inlets be stable? Estuarine, Coastal and Shelf Science 30: 261–273.], using the same equilibrium condition, it was concluded that where two inlets connect the same basin to the ocean ultimately one inlet will close. One of the major assumptions in that study was that the water level in the basin fluctuated uniformly. In hindsight this assumption might be too restrictive. For example, in the Wadden Sea the back barrier lagoon consists of a series of basins, rather than one single basin, separated by topographic highs. These topographic highs limit but do not exclude the exchange of water between the sub-basins. For this reason in the present study, a topographic high in the form of a weir was added, separating the back-barrier lagoon in two sub-basins. The water level in the sub-basins, rather than in the back-barrier as a whole, is assumed to fluctuate uniformly. For this schematization the hydrodynamic equations are solved using a finite difference method. The results, together with the equilibrium condition, yield the equilibrium flow curve for each of the inlets. The intersections of the two equilibrium flow curves represent combinations of cross-sectional areas for which both inlets are in equilibrium. The stability of the equilibriums was investigated using a non-linear stability analysis resulting in a flow diagram. Calculations were carried out for different inlet and weir characteristics. Sinussoidal tides were the same for both inlets. The results show that for relatively large wetted cross-sectional areas over the topographic high, approaching the situation of a single basin, there are no combinations of inlet cross-sectional areas for which both inlets are in a stable equilibrium. This supports the conclusion in the earlier study. For relatively small wetted cross-sectional areas over the topographic high there is one set of stable equilibriums. In that case the two-inlet bay system approaches that of two single-inlet bay systems.     

Interactions between submarine channel systems and deformation in deepwater fold belts: Examples from the Levant Basin, Eastern Mediterranean sea

Submarine channel levee systems form important hydrocarbon reservoirs in many deep marine settings and are often deposited within a structurally active setting. This study focuses on recent submarine channels that developed within a deepwater fold and thrust belt setting from the Levant Basin, eastern Mediterranean Sea. Compressional deformation within the study area is driven by the up-dip collapse of the Nile cone above the ductile Messinian Evaporites. Structures such as folds and strike slip faults exert a strong control on channel location and development over time. From this study four end-member submarine channel–structure interactions can be defined: Confinement, diversion, deflection and blocking. Each of these channel–structure interactions results in a distinct submarine channel morphology and pattern of development compared to unconfined channel levee systems. Each interaction can also be used to assess timing relationships between submarine channel development and deformation.     

Fundamental study for morphodynamic modelling: Sand mounds in oscillatory flows

Experiments on sand mounds in oscillatory flow, undertaken in controlled, large-scale laboratory conditions, have produced well-defined data sets for model comparison. Three bathymetries with different levels of submergence, including a surface-piercing case, were tested. The maximum slope was about 1:5.5. Sediment transport is due to bed load with ripple formation. The principal time-dependent bulk parameters are the vertical distance of the centre of gravity above the base and the volume of the mound. A semi-implicit finite-volume depth-averaged hydrodynamic model is used to drive morphodynamics, using van Rijn's sediment flux model generalized to take account of bed slope, and some justification is given for depth-averaged modeling in these conditions. Starting the model runs with the conditions at the end of the first cycle avoided initial atypical physical behaviour. In general good predictions were obtained with an angle of repose reduced from the standard value of about 30° for stationary beds to 15°. For these situations, morphodynamics was largely unaffected by a hydrodynamic roughness height in the range 2.5D₅₀ to 51D₅₀, with larger values accounting for ripple roughness. The reduced angle of repose may be physically expected with mobile beds but this specific value is only expected to be suited to this form of bed motion. In one case an exaggerated ripple formed near the top of the mound reducing agreement with experiment. For the submerged case with normal ripple structure excellent predictions were obtained. For the initially surface-piercing mound, the time of submergence was better predicted with a 30° angle of repose, presumably due to the prominent influence of the near stationary bed near the wet/dry interface, although long term predictions were better predicted with 15°. The occurrence of vortex shedding in the first cycle modeled was in agreement with experimental observation.     

Geoacoustic Inversions of Horizontal and Vertical Line Array Acoustic Data From a Surface Ship Source of Opportunity

The application of an inversion methodology produces the first demonstration of a simultaneous solution for geoacoustic and source track parameters from acoustic data collected in a shallow-water, sandy sediment environment. Inversion solutions from data collected in the 2006 Shallow Water Experiment (SW06) are extracted from noise measurements of a surface ship source on an L-array. The methodology includes a screening algorithm to determine a set of frequencies for the inversion data. In addition, the methodology assesses the accuracy of the inversion solution and incorporates an estimation of parameter value uncertainties. The solution from the inversion of the horizontal component of the L-array data from the surface ship source before its closest point of approach (CPA) is used to construct modeled propagation loss for comparison with observed received level (RL) structure as the source departs from CPA. Inversion of the data from a single element in the vertical component of the L-array produces a solution that agrees with the solution obtained from the inversion of horizontal subaperture data. Also, modeled transmission loss (TL) structure obtained from the single-element inversion solution reproduces the depth dependence of the RL structure observed at other elements of the vertical component of the L-array.      

Large bio-geographical shifts in the north-eastern Atlantic Ocean: From the subpolar gyre, via plankton, to blue whiting and pilot whales

Pronounced changes in fauna, extending from the English Channel in the south to the Barents Sea in the north-east and off Greenland in the north-west, have occurred in the late 1920s, the late 1960s and again in the late 1990s. We attribute these events to exchanges of subarctic and subtropical water masses in the north-eastern North Atlantic Ocean, associated with changes in the strength and extent of the subpolar gyre. These exchanges lead to variations in the influence exerted by the subarctic or Lusitanian biomes on the intermediate faunistic zone in the north-eastern Atlantic. This strong and persistent bottom-up bio-physical link is demonstrated using a numerical ocean general circulation model and data on four trophically connected levels in the food chain – phytoplankton, zooplankton, blue whiting, and pilot whales. The plankton data give a unique basin-scale depiction of these changes, and a long pilot whale record from the Faroe Islands offers an exceptional temporal perspective over three centuries. Recent advances in simulating the dynamics of the subpolar gyre suggests a potential for predicting the distribution of the main faunistic zones in the north-eastern Atlantic a few years into the future, which might facilitate a more rational management of the commercially important fisheries in this region.     

Distribution patterns of interstitial polychaetes in sandy beaches of southern Brazil

This study describes the distribution patterns of interstitial polychaetes along morphodynamic gradients on six exposed sandy beaches in Santa Catarina and Paraná (South Brazil). Three random transects were sampled at two points on each beach, one at the swash and another at the surf zone, in winter and summer conditions. Six sediment replicates were collected at each sampling point using a corer of 4.6 cm internal diameter that removed 10 cm into the sediment. Abundance and composition of interstitial polychaete were correlated to wave height, slope, grain size, CaCO₃, chlorophyll a , omega indexes, temperature and relative tide range using a canonical correspondence analysis (CCA). A factorial ANOVA showed that taxa richness, mean density and Shannon's diversity were significantly higher at the reflective beaches, but average values differ significantly between transects and these differences change according to the beach zones on both sampling dates. PERMANOVA showed that polychaete associations differ among transects according to the beach zones. The composition of interstitial polychaete associations was significantly correlated to beach morphodynamics and features (P < 0.01). Polychaete associations of reflective beaches were more diverse than in other morphodynamic states. Intermediate beaches may also sustain diverse associations due to temporal variability of the morphodynamic patterns. Beaches presenting extreme dissipative morphodynamics and compacted sediments appear to be unfavourable for the occurrence of interstitial polychaetes.     

Identifying anthropogenic sources of nitrogen oxide emissions from calculations of Lagrangian trajectories and the observational data from a tall tower in Siberia during the spring-summer period of 2007

The task of identifying climatically significant regional anthropogenic emissions and estimating their contribution to the variability of nitrogen oxides observed at a monitoring station is considered on the basis of NO and NO₂ surface concentrations measured at the Zotino background observation station (60°26′ N, 89°24′ E, Krasnoyarsk Territory). The approach used is based on an estimation of the conditional probability of polluted air arriving from individual regions by using the results of calculating backward Lagrangian trajectories in the lower troposphere. It is established that the contribution of air masses supplied from industrial regions in the south of the Krasnoyarsk Territory to episodes of high concentrations of nitrogen oxides (>0.7 ppb) is larger than the contribution from cities and towns located in the south of Western Siberia. The results indicate that anthropogenic sources of pollution substantially affect the balance of minor gases in the lower troposphere on a regional scale and that this factor must be taken into account when observational data from the Zotino background station are analyzed and interpreted.