Polarization vision and its role in biological signaling

Visual pigments, the molecules in photoreceptors that initiate the process of vision, are inherently dichroic, differentially absorbing light according to its axis of polarization. Many animals have taken advantage of this property to build receptor systems capable of analyzing the polarization of incoming light, as polarized light is abundant in natural scenes (commonly being produced by scattering or reflection). Such polarization sensitivity has long been associated with behavioral tasks like orientation or navigation. However, only recently have we become aware that it can be incorporated into a high-level visual perception akin to color vision, permitting segmentation of a viewed scene into regions that differ in their polarization. By analogy to color vision, we call this capacity polarization vision. It is apparently used for tasks like those that color vision specializes in: contrast enhancement, camouflage breaking, object recognition, and signal detection and discrimination. While color is very useful in terrestrial or shallow-water environments, it is an unreliable cue deeper in water due to the spectral modification of light as it travels through water of various depths or of varying optical quality. Here, polarization vision has special utility and consequently has evolved in numerous marine species, as well as at least one terrestrial animal. In this review, we consider recent findings concerning polarization vision and its significance in biological signaling.

An evaluation of the evidence for linkages between mangroves and fisheries: A synthesis of the literature and identification of research directions

There is a widely held paradigm that mangroves are critical for sustaining production in coastal fisheries through their role as important nursery areas for fisheries species. This paradigm frequently forms the basis for important management decisions on habitat conservation and restoration of mangroves and other coastal wetlands. This paper reviews the current status of the paradigm and synthesises the information on the processes underlying these potential links. In the past, the paradigm has been supported by studies identifying correlations between the areal and linear extent of mangroves and fisheries catch. This paper goes beyond the correlative approach to develop a new framework on which future evaluations can be based. First, the review identifies what type of marine animals are using mangroves and at what life stages. These species can be categorised as estuarine residents, marine-estuarine species and marine stragglers. The marine-estuarine category includes many commercial species that use mangrove habitats as nurseries. The second stage is to determine why these species are using mangroves as nurseries. The three main proposals are that mangroves provide a refuge from predators, high levels of nutrients and shelter from physical disturbances. The recognition of the important attributes of mangrove nurseries then allows an evaluation of how changes in mangroves will affect the associated fauna. Surprisingly few studies have addressed this question. Consequently, it is difficult to predict how changes in any of these mangrove attributes would affect the faunal communities within them and, ultimately, influence the fisheries associated with them. From the information available, it seems likely that reductions in mangrove habitat complexity would reduce the biodiversity and abundance of the associated fauna, and these changes have the potential to cause cascading effects at higher trophic levels with possible consequences for fisheries. Finally, there is a discussion of the data that are currently available on mangrove distribution and fisheries catch, the limitations of these data and how best to use the data to understand mangrove-fisheries links and, ultimately, to optimise habitat and fisheries management. Examples are drawn from two relatively data-rich regions, Moreton Bay (Australia) and Western Peninsular Malaysia, to illustrate the data needs and research requirements for investigating the mangrove-fisheries paradigm. Having reliable and accurate data at appropriate spatial and temporal scales is crucial for mangrove-fisheries investigations. Recommendations are made for improvements to data collection methods that would meet these important criteria. This review provides a framework on which to base future investigations of mangrove-fisheries links, based on an understanding of the underlying processes and the need for rigorous data collection. Without this information, the understanding of the relationship between mangroves and fisheries will remain limited. Future investigations of mangrove-fisheries links must take this into account in order to have a good ecological basis and to provide better information and understanding to both fisheries and conservation managers.

Can the nitrogenous composition of xylem sap be used to assess salinity stress in Casuarina glauca?

It is predicted that dryland salinity will affect up to 17 Mha of the Australian landscape by 2050, and therefore, monitoring the health of tree plantings and remnant native vegetation in saline areas is increasingly important. Casuarina glauca Sieber ex Spreng. has considerable salinity tolerance and is commonly planted in areas with a shallow, saline water table. To evaluate the potential of using the nitrogenous composition of xylem sap to assess salinity stress in C. glauca, the responses of trees grown with various soil salinities in a greenhouse were compared with those of trees growing in field plots with different water table depths and groundwater salinities. In the greenhouse, increasing soil salinity led to increased allocation of nitrogen (N) to proline and arginine in both stem and root xylem sap, with coincident decreases in citrulline and asparagine. Although the field plots were ranked as increasingly saline-based on ground water salinity and depth-only the allocation of N to citrulline differed significantly between the field plots. Within each plot, temporal variation in the composition of the xylem sap was related to rainfall, rainfall infiltration and soil salinity. Periods of low rainfall and infiltration and higher soil salinity corresponded with increased allocation of N to proline and arginine in the xylem sap. The allocation of N to citrulline and asparagine increased following rainfall events where rain was calculated to have infiltrated sufficiently to decrease soil salinity. The relationship between nitrogenous composition of the xylem sap of C. glauca and soil salinity indicates that the analysis of xylem sap is an effective method for assessing changes in salinity stress in trees at a particular site over time. However, the composition of the xylem sap proved less useful as a comparative index of salinity stress in trees growing at different sites.

A Devonian (Givetian) fore-reef slope sequence at Liangshuijing and implication for Devonian platform-to-depression development in Guilin, South China

Three Bahama-like carbonate plaforms-the Guilin, Yangshuo and Yanshan-occurred in Guilin and the surrounding regions during Middle and Late Devonian, which, at a broad scale, are part of an extensive carbonate platform (Xiangzhou carbonate platform) facies in South China. The intraplatform depression facies, a unique characteristic of the Chinese Devonian depositional sequence, separates Bahama-like (platform-to-depression) carbonate subplatfonns. Intraplatform depressions resulted from syndepositional faulting that cut the basement of carbonate subplatforms and affected further platform development. The Liangshuijing section, located between the Guilin platform in the north and the Yangshuo platform in the south, is representative of the fore-reef slope facies neighboring an intraplatform. depression. The South edge of the fore-reef slope lies adjacent to the Yangshuo reef carbonate platform, and the north edge graded into the Yangdi pelagic depression facies. A detailed sedimentary and microfacies analysis work done in this study at the Liangshuijing section shows a distinct vertical facies change from back-reef, restricted platform, hemipelagic, to fore-reefslope facies, differing from either shallow-water benthic facies or typical pelagic facies. Various benthic and pelagic lithofacies and their associations have been recognized in the Liangshuijing section, including dolomitic rudstone, gastropod wackestone, Amphipora floatstone, tentaculitoid wackestone, stromatolite and oncoid limestone, Amphipora grainstone, grain flows, laminated limestone, flat-pebble and brachiopod floatstone, and carbonate turbidites. Eight types of sedimentary cycles composed of two or three lithofacies have been distinguished, which are able to indicate environment changes. Stromatolites, oncoids, grain flows, carbonate turbidites, and tentaculitoid limestones characterize the slope and intraplatform depression lithofacies. Analysis of the vertical sedimentary cycles in the Liangshuijinag section and the lateral stratigraphic equivalents suggest the differing facies patterns occurred at the middle Varcus Zone (Givetian) of Middle Devonian, coeval with the development of fore-reef slope facies in the Guilin area in response to syndeposifional faulting.

Parameters affecting the performance of wetting and drying in a two-dimensional finite element long wave hydrodynamic model

The marsh porosity method, a type of thin slot wetting and drying algorithm in a two-dimensional finite element long wave hydrodynamic model, is discussed and analyzed to assess model performance. Tests, including comparisons to simple examples and theoretical calculations, examine the effects of varying the marsh porosity parameters. The findings demonstrate that the wetting and drying concept of marsh porosity, often used in finite element hydrodynamic modeling, can behave in a more complex manner than initially expected.

Benthic microalgae in coral reef sediments of the southern Great Barrier Reef, Australia

The abundance and productivity of benthic microalgae in coral reef sediments are poorly known compared with other, more conspicuous (e.g. coral zooxanthellae, macroalgae) primary producers of coral reef habitats. A survey of the distribution, biomass, and productivity of benthic microalgae on a platform reef flat and in a cross-shelf transect in the southern Great Barrier Reef indicated that benthic microalgae are ubiquitous, abundant (up to 995.0 mg chlorophyll (chl) a m(-2)), and productive (up to 110 mg O-2 m(-2) h(-1)) components of the reef ecosystem. Concentrations of benthic microalgae, expressed as chlorophyll a per surface area, were approximately 100-fold greater than the integrated water column concentrations of microalgae throughout the region. Benthic microalgal biomass was greater on the shallow water platform reef than in the deeper waters of the cross-shelf transect. In both areas the benthic microalgal communities had a similar composition, dominated by pennate diatoms, dinoflagellates, and cyanobacteria. Benthic microalgal populations were potentially nutrient-limited, based on responses to nitrogen and phosphorus enrichments in short-term (7-day) microcosm experiments. Benthic microalgal productivity, measured by O-2 evolution, indicated productive communities responsive to light and nutrient availability. The benthic microalgal concentrations observed (92-995 mg chl a m(-2)) were high relative to other reports, particularly compared with temperate regions. This abundance of productive plants in both reef and shelf sediments in the southern Great Barrier Reef suggests that benthic microalgae are key components of coral reef ecosystems.

Metamorphosis of a scleractinian coral in response to microbial biofilms

Microorganisms have been reported to induce settlement and metamorphosis in a wide range of marine invertebrate species. However, the primary cue reported for metamorphosis of coral larvae is calcareous coralline algae (CCA). Herein we report the community structure of developing coral reef biofilms and the potential role they play in triggering the metamorphosis of a scleractinian coral. Two-week-old biofilms induced metamorphosis in less than 10% of larvae, whereas metamorphosis increased significantly on older biofilms, with a maximum of 41% occurring on 8-week-old microbial films. There was a significant influence of depth in 4- and 8-week biofilms, with greater levels of metamorphosis occurring in response to shallow-water communities. Importantly, larvae were found to settle and metamorphose in response to microbial biofilms lacking CCA from both shallow and deep treatments, indicating that microorganisms not associated with CCA may play a significant role in coral metamorphosis. A polyphasic approach consisting of scanning electron microscopy, fluorescence in situ hybridization (FISH), and denaturing gradient gel electrophoresis (DGGE) revealed that coral reef biofilms were comprised of complex bacterial and microalgal communities which were distinct at each depth and time. Principal-component analysis of FISH data showed that the Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria, and Cytophaga-Flavobacterium of Bacteroidetes had the largest influence on overall community composition. A low abundance of Archaea was detected in almost all biofilms, providing the first report of Archaea associated with coral reef biofilms. No differences in the relative densities of each subdivision of Proteobacteria were observed between slides that induced larval metamorphosis and those that did not. Comparative cluster analysis of bacterial DGGE patterns also revealed that there were clear age and depth distinctions in biofilm community structure; however, no difference was detected in banding profiles between biofilms which induced larval metamorphosis and those where no metamorphosis occurred. This investigation demonstrates that complex microbial communities can induce coral metamorphosis in the absence of CCA.

The functional roles of passive electroreception in non-electric fishes

Passive electroreception is a complex and specialised sense found in a large range of aquatic vertebrates primarily designed for the detection of weak bioelectric fields. Particular attention has traditionally focused on cartilaginous fishes, but a range of teleost and non-teleost fishes from a diversity of habitats have also been examined. As more species are investigated, it has become apparent that the role of electroreception in fishes is not restricted to locating prey, but is utilised in other complex behaviours. This paper presents the various functional roles of passive electroreception in non-electric fishes, by reviewing much of the recent research on the detection of prey in the context of differences in species' habitat (shallow water, deep-sea, freshwater and saltwater). A special case study on the distribution and neural groupings of ampullary organs in the omnihaline bull shark, Carcharhinus leucas, is also presented and reveals that prey-capture, rather than navigation, may be an important determinant of pore distribution. The discrimination between potential predators and conspecifics and the role of bioelectric stimuli in social behaviour is discussed, as is the ability to migrate over short or long distances in order to locate environmentally favourable conditions. The various theories proposed regarding the importance and mediation of geomagnetic orientation by either an electroreceptive and/or a magnetite-based sensory system receives particular attention. The importance of electroreception to many species is emphasised by highlighting what still remains to be investigated, especially with respect to the physical, biochemical and neural properties of the ampullary organs and the signals that give rise to the large range of observed behaviours.

Two-dimensional approximation for tide-induced watertable fluctuations in a sloping sandy beach

The prediction of watertable fluctuations in a coastal aquifer is important for coastal management. However, most previous approaches have based on the one-dimensional Boussinesq equation, neglecting variations in the coastline and beach slope. In this paper, a closed-form analytical solution for a two-dimensional unconfined coastal aquifer bounded by a rhythmic coastline is derived. In the new model, the effect of beach slope is also included, a feature that has not been considered in previous two-dimensional approximations. Three small parameters, the shallow water parameter (epsilon), the amplitude parameter (a) and coastline parameter (beta) are used in the perturbation approximation. The numerical results demonstrate the significant influence of both the coastline shape and beach slopes on tide-driven coastal groundwater fluctuations. (c) 2004 Elsevier Ltd. All rights reserved.

Steepness expansion for free surface flows in coastal aquifers

Free surface flow of groundwater in aquifers has been studied since the early 1960s. Previous investigations have been based on the Boussinesq equation, derived from the non-linear kinematic boundary condition. In fact, the Boussinesq equation is the zeroth-order equation in the shallow-water expansion. A key assumption in this expansion is that the mean thickness of the aquifer is small compared with a reference length, normally taken to be the linear decay length. In this study, we re-examine the expansion scheme for free surface groundwater flows, and propose a new expansion wherein the shallow-water assumption is replaced by a steepness assumption. A comparison with experimental data shows that the new model provides a better prediction of water table levels than the conventional shallow-water expansion. The applicable ranges of the two expansions are exhibited. (c) 2004 Elsevier B.V. All rights reserved.

Changes in morphology and physiology of an East Mediterranean sponge in different habitats

The sponge Tetilla sp. (Tetractinomorpha: Tetillidae) is a common species in the eastern Mediterranean. This sponge inhabits four different habitat types differing in wave impact and irradiance levels. Two of these habitats (a shallow cave and deep water) are characterized by relatively calm water, whereas the other two (shallow exposed site and tide pools) are in turbulent water with high energy flow. The present study examined the influence of physical (depth, illumination and water motion) and biotic factors on morphology, skeletal plasticity and reproductive traits among the four spatially separated populations. Sponges from tidal pools had significantly larger body volume than sponges from deep water and from shallow caves (ANOVA: tidal-deep P< 0.0001; tidal-shallow caves P< 0.05). Sponges from exposed habitats were significantly larger than deep-water sponges (ANOVA: P=0.01). In addition, individuals from tide pools and from the exposed habitat had a significantly higher proportion of structural silica than sponges from the calmer deep water and from the cave sites. Oxea spicules in sponges from the calm habitats were significantly shorter than in those from the tidal pools and the exposed habitats. The percentage of spicules out of a sponge's dry weight in individuals transplanted from deep (calm) to shallow (turbulent) water significantly increased by 21.9&PLUSMN; 12.9%. The new spicule percentage did not differ significantly from that of sponges originally from shallow water. Oocyte diameter differed significantly between habitats. The maximal size of mature eggs was found in deep-water sponges in June (97&PLUSMN; 5 μ m). In the shallow habitats, a smaller maximal oocyte diameter was found in the cave, in May (56.5&PLUSMN; 3 μ m). Furthermore, oocyte density in shallow-water sponges was highest in May and decreased in June (with 88.2&PLUSMN; 9 and 19.3&PLUSMN; 9 oocytes mm(-2), respectively). At the same time (June), oocyte density of deep-water sponges had just reached its maximum (155&PLUSMN; 33.7 oocytes mm(-2)). The difference in oocyte size and density between deep- and shallow-water individuals indicates an earlier gamete release in the shallow sponge population. The results suggest that plasticity in skeletal design of this sponge indicates a trade off between spicule production and investment in reproduction.

The interaction of nitrogen application and temperature during reproductive stage on spikelet sterility in field-grown rice

Increased grain yield in response to high rates of application of nitrogen (N) fertiliser is often limited by increased spikelet sterility, particularly under low temperature conditions in the New South Wales ( NSW) rice industry. In 3 field experiments, different N rates were applied for different sowing dates to investigate the interaction between N rate and temperature during microspore development on spikelet sterility and grain yield. In one experiment the effect of water depth on spikelet sterility was also investigated. Engorged pollen production, spikelet sterility, and yield and its components were recorded. Application of N affected a few different processes that lead into spikelet sterility. Application of N at both pre-flood (PF) and panicle initiation ( PI) significantly reduced the number of engorged pollen grains per anther, which was negatively correlated with spikelet sterility. Application of N and low temperature during microspore development with the absence of deep water also decreased pollen engorgement efficiency ( the percentage of pollen grains that were engorged). Application of N further increased spikelet density, which, in turn, increased both spikelet sterility and grain yield. The combined effect of spikelet density and low temperature during microspore development explained the 44% of variation in the number of engorged pollen grains per anther. Grain yield was decreased by low temperature during microspore development in the shallow water when N was applied. Spikelet sterility as a result of late sowing was strongly correlated with minimum temperature during flowering. It is concluded that N application reduced pollen number per anther as a result of increased spikelet density, and this made the spikelets more susceptible to low temperature, causing increased spikelet sterility.

Long wave generation by the shoaling and breaking of transient wave groups on a beach

This paper presents new laboratory data on the generation of long waves by the shoaling and breaking of transient-focused short-wave groups. Direct offshore radiation of long waves from the breakpoint is shown experimentally for the first time. High spatial resolution enables identification of the relationship between the spatial gradients of the short-wave envelope and the long-wave surface. This relationship is consistent with radiation stress theory even well inside the surf zone and appears as a result of the strong nonlinear forcing associated with the transient group. In shallow water, the change in depth across the group leads to asymmetry in the forcing which generates significant dynamic setup in front of the group during shoaling. Strong amplification of the incident dynamic setup occurs after short-wave breaking. The data show the radiation of a transient long wave dominated by a pulse of positive elevation, preceded and followed by weaker trailing waves with negative elevation. The instantaneous cross-shore structure of the long wave shows the mechanics of the reflection process and the formation of a transient node in the inner surf zone. The wave run-up and relative amplitude of the radiated and incident long waves suggests significant modification of the incident bound wave in the inner surf zone and, the dominance of long waves generated by the breaking process. It is proposed that these conditions occur when the primary short waves and bound wave are not shallow water waves at the breakpoint. A simple criterion is given to determine these conditions, which generally occur for the important case of storm waves.

The impact of spectral composition and light periodicity on the activity of two antioxidant enzymes (SOD and CAT) in the coral Favia favus

In oligotrophic waters the light spectrum is mostly blue, and therefore the physiological and biochemical responses to blue light occurring in the coral tissue and in the symbiotic algae are important. Examination of the wavelength dependence of two free radical scavenger enzyme activity revealed an increase in activity in the blue light range (440-480 nm) compared to the red (640680 nm) in the full visible light (400-700 nm) range. These data show for the first time the relationship between the action spectra of photosynthesis and the activity of two main antioxidant enzymes in the symbiotic coral Favia favus. It was found that in the animal (host) the enzyme response to the spectral distribution of light was higher than that of the zooxanthellae, probably due to accumulation of free radicals within the host tissue. Furthermore, we found that the activity of these enzymes is affected in nature by the length of the day and night, and in the laboratory, by the duration of the illumination. Changes in the pigment concentrations were also observed in response to growth under the blue region and the whole PAR spectrum, while fluorescence measurements with the fast repetition rate fluorometer (FRRF) showed a decrease in the sigma cross section and a decrease in the quantum yield also in the blue part of the spectrum. These changes of scavenger enzymes activity, pigment concentration and fluorescence yield at different light spectra are vital in acclimatization and survival of corals in shallow water environments with high light radiation. (c) 2005 Elsevier B.V. All rights reserved.