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Chiswell S.M.,NIWA - National Institute of Water and Atmospheric Research
Journal of Physical Oceanography | Year: 2013

Argo floats cannot be regarded as true Lagrangian drifters because they periodically rise to the surface. Hence, previous estimates of eddy diffusivity at depth using single-particle statistics have been limited to one submerged cycle. However, unless the Lagrangian time scale is significantly shorter than the Argo cycle time, this single-particle calculation can have a large bias. Here, eddy diffusivity computed from single-particle statistics using Argo data is compared to that computed by assuming that Eulerian scales at depth are the same as at the surface, and that the relationship between Lagrangian and Eulerian time scales derived by Middleton is valid. If the methods provide the same answer, one can have confidence in both methods. Eddy diffusivity calculated from the single-particle statistics shows the same spatial structure as that computed from inferred time scale, but is smaller by a factor of about 2. It is suggested that this is because the deep Lagrangian time scale over much of the region is comparable to, or longer than, the 10-day Argo submergence cycle. ©2013 American Meteorological Society.

Larned S.T.,NIWA - National Institute of Water and Atmospheric Research
Freshwater Biology | Year: 2012

1. Phreatic ecosystems (saturated groundwater ecosystems in porous and fractured-rock aquifers) are research frontiers for freshwater ecology. Many ecological issues that have been explored at length in surface-water and hyporheic systems are unexplored in phreatic systems. Phreatic ecology is currently dominated by observational studies rather than experiments and focuses on pattern-detection and description, rather than hypothesis-testing and mechanistic explanations. These are characteristics of science disciplines in early developmental stages. 2. Progress in phreatic ecology has been impeded by logistical problems including poor access, limited information about ecosystem boundaries and spatial heterogeneity, a lack of detailed habitat templates, limited taxonomic and biogeographic knowledge and the difficulties of field experiments. Each of these problems is assessed in this review, along with analytical techniques, instruments and concepts that may help researchers overcome them. 3. Access to undisturbed phreatic systems is generally limited to narrow zones around wells. Limited access and sparse well arrays make detecting ecological patterns and relationships and delineating ecosystem boundaries difficult. Spatial resolution can be increased by installing wells in configurations suited to specific research topics; geostatistical methods are available for positioning new wells and optimising interpolation between them. 4. Phreatic systems are characterised by multi-scaled spatial and temporal heterogeneity. Lithofacies aggregations, buried fluvial bedforms, rock fractures and other geomorphic elements create structural and hydraulic heterogeneity, which lead in turn to spatial variation in solutes, biota and biogeochemical processes. The structural and hydraulic heterogeneity of study areas can be characterised and mapped with geophysical surveys and groundwater flow models. These models can help to identify flowpaths, recharge zones and aquifer boundaries and provide ecologically relevant hydrological variables. 5. Physical habitat templates and classifications are needed to explain variation in phreatic populations and communities. A candidate classification system is proposed, based on environmental factors that govern the distribution and quality of groundwater habitats: climate, lithology, aquifer, confinement, recharge, hydrofacies and flowpath. 6. Many phreatic species and higher-level taxa remain undescribed, and the taxonomic resolution used in phreatic ecology studies is generally coarse. These problems impede progress in community ecology, biogeography and conservation biology. DNA barcoding and other molecular taxonomy methods are now being applied to groundwater fauna. Combining molecular taxonomy and traditional morphological methods could increase the accuracy and efficiency of species identification and help to define taxonomic boundaries. 7. Field experiments and mensurative studies are rarely used in phreatic ecology, but they are needed to detect spatial and temporal patterns, quantify ecological relationships and test hypotheses and classification systems. Techniques from groundwater remediation and recharge studies can be adapted to ecological field experiments that utilise natural aquifer structures and groundwater flow dynamics. © 2012 Blackwell Publishing Ltd.

Lassey K.R.,NIWA - National Institute of Water and Atmospheric Research
Animal Feed Science and Technology | Year: 2013

Implementations of the sulphur hexafluoride (SF6) tracer technique to determine methane (CH4) emission rates from individual ruminant animals involve measuring levels of both CH4 and SF6 in background air. In well-ventilated settings, including grazing, background sampling is straightforward and the algebraic correction for background levels is then usually minor. In a recent paper in this journal (Vol. 170, p. 265-276), Williams et al. drew attention to the much more careful consideration that is needed for background sampling in experiments that use the SF6 tracer technique with housed animals when both CH4 and SF6 levels can build up unevenly within the housing. This note builds on that study to show specifically and rigorously: (a) what is meant by background air, and that background corrections to CH4 emission estimates are unaffected by the recycling of CH4 and SF6 through inhalation of self-exhaled gases; (b) that in studies of the role of various treatments on CH4 emission rates, the siting of background samplers can crucially impact on findings; and, in particular, (c) that reports of a possible dependence of estimated CH4 emission rates upon the rate of SF6 release in the rumen are called into question due to the sensitivity of those findings to the siting of background samplers. © 2012 Elsevier B.V..

Chiswell S.M.,NIWA - National Institute of Water and Atmospheric Research
Marine Ecology Progress Series | Year: 2011

The critical-depth model for the onset of the spring phytoplankton bloom in the North Atlantic has recently been called into question by several researchers. The critical-depth model considers that the spring bloom starts when the mixed layer shoals to become shallower than a critical depth. Satellite and in situ measurements of chlorophyll are used here to show that the critical-depth model is indeed flawed. It is shown that the critical-depth model does not apply in the spring because the basic assumption of an upper layer that is well-mixed in plankton is not met. Instead, the spring bloom forms in shallow near-surface layers that deepen with the onset of thermal stratification. A stratification-onset model for the annual cycle in plankton is proposed that adheres to the conventional idea that the spring bloom represents a change from a deepmixed regime to a shallow light-driven regime, but where the upper layers are not well mixed in plankton in spring and so the critical-depth model does not apply. Ironically, perhaps, the criticaldepth model applies in the autumn and winter when plankton are well-mixed to the seasonal thermocline, so that the critical-depth model can be used to determine whether net winter production is positive or negative. model © 2011 Inter-Research.

Francis R.I.C.C.,NIWA - National Institute of Water and Atmospheric Research
Canadian Journal of Fisheries and Aquatic Sciences | Year: 2011

The conclusions drawn from fisheries stock assessment models can depend strongly on the relative weights assigned to different data sets. However, there is no consensus amongst practitioners as to the best approach to data weighting. From a discussion of some key questions concerning data weighting in stock assessment models, I draw three guiding principles: (i) do not let other data stop the model from fitting abundance data well; (ii) when weighting age or length composition data, allow for correlations; and (iii) do not down-weight abundance data because they may be unrepresentative. I propose an approach to data weighting based on these principles. Two factors that complicate this approach are that some decisions are inevitably subjective (which underlines the need for expert knowledge in stock assessment), and some technical problems are unresolved.

In this study the aggregate effects of lipophilic toxins extracted from cultures of three closely-related dinoflagellates, Karenia concordia, Karenia brevisulcata and Karenia mikimotoi, on 18 species of microalgae from five algal classes, have been evaluated. In terms of toxicity, cells of all 5 algal classes tested are found to be more vulnerable to those produced by K. brevisulcata and K. concordia than that of K. mikimotoi. Toxin extracts of both K. brevisulcata and K. concordia destroyed cells in a matter of few minutes to tens of minutes ('fast-acting') and that of K. mikimotoi in tens of minutes to hours ('slow-acting'). Overall, cells of both the flagellates (Class Cryptophyceae, Class Raphidophyceae and Class Prasinophyceae) and diatoms (Class Bacillariophyceae) were more sensitive to toxin extracts of all the three Karenia spp. than those of dinoflagellates (both armoured and unarmoured) (Class Dinophyceae). Cells of both Chattonella marina and Alexandrium catenella, sensitive to toxin extracts of all three Karenia spp., were found to exhibit distinct responses before cell destruction. In the case of A. catenella, cells exposed to toxin extract of K. concordia showed partial disintegration of both the theca wall and the cytoplasmic membrane. These effects were not observed in cells exposed to those of K. brevisulcata and K. mikimotoi. The unique response of A. catenella cells to toxin extract of K. concordia is discussed. © 2010 Elsevier B.V.

McDowall R.M.,NIWA - National Institute of Water and Atmospheric Research
Reviews in Fish Biology and Fisheries | Year: 2010

Amphidromous fishes are found predominantly on the tropical and subtropical islands of the globe and there are few amphidromous species on continents. I suggest that this idiosyncratic distribution relates in part to problems in self-recruitment on islands that are often young or volcanic, and which may have streams with ephemeral flows across relatively short times scales. Amphidromy provides the ability to invade new habitats as these become available either on newly emergent (often volcanic) islands, or following perturbation after stream dewatering or the impacts of volcanism on older islands as a consequence of expatrial dispersal. Source/sink population dynamics may also be involved with islands 'downstream' in oceanic current systems behaving as sinks, with little or no self-recruitment. Streams in steep topography seem to be favoured by amphidromous species, perhaps because they provide more rapid transport to sea of the tiny, newly hatched larvae. © Springer Science+Business Media B.V. 2009.

Popinet S.,NIWA - National Institute of Water and Atmospheric Research
Ocean Dynamics | Year: 2011

The well-balanced, positivity-preserving scheme of Audusse et al. (SIAM J Sci Comput 25(6):2050-2065, 2004), for the solution of the Saint-Venant equations with wetting and drying, is generalised to an adaptive quadtree spatial discretisation. The scheme is validated using an analytical solution for the oscillation of a fluid in a parabolic container, as well as the classic Monai tsunami laboratory benchmark. An efficient database system able to dynamically reconstruct a multiscale bathymetry based on extremely large datasets is also described. This combination of methods is successfully applied to the adaptive modelling of the 2004 Indian ocean tsunami. Adaptivity is shown to significantly decrease the exponent of the power law describing computational cost as a function of spatial resolution. The new exponent is directly related to the fractal dimension of the geometrical structures characterising tsunami propagation. The implementation of the method as well as the data and scripts necessary to reproduce the results presented are freely available as part of the open-source Gerris Flow Solver framework. © 2011 Springer-Verlag.

Popinet S.,NIWA - National Institute of Water and Atmospheric Research
Natural Hazards and Earth System Science | Year: 2012

The 11 March 2011 Tohoku tsunami is simulated using the quadtree-adaptive Saint-Venant solver implemented within the Gerris Flow Solver. The spatial resolution is adapted dynamically from 250 m in flooded areas up to 250 km for the areas at rest. Wave fronts are tracked at a resolution of 1.8 km in deep water. The simulation domain extends over 73°of both latitude and longitude and covers a significant part of the north-west Pacific. The initial wave elevation is obtained from a source model derived using seismic data only. Accurate long-distance wave prediction is demonstrated through comparison with DART buoys timeseries and GLOSS tide gauges records. The model also accurately predicts fine-scale flooding compared to both satellite and survey data. Adaptive mesh refinement leads to orders-of-magnitude gains in computational efficiency compared to non-adaptive methods. The study confirms that consistent source models for tsunami initiation can be obtained from seismic data only. However, while the observed extreme wave elevations are reproduced by the model, they are located further south than in the surveyed data. Comparisons with inshore wave buoys data indicate that this may be due to an incomplete understanding of the local wave generation mechanisms. © 2012 Author(s).

Green M.O.,NIWA - National Institute of Water and Atmospheric Research | Coco G.,University of Cantabria
Reviews of Geophysics | Year: 2014

Waves are fundamentally important to the physical and biological functioning of estuaries. Understanding and predicting contaminant transport, development of sedimentary structures, geomorphological response to changes in external forcings such as rising sea level, and response of estuarine ecosystems to contaminant stressors require understanding of the relative roles of wave- and current-driven sediment transport. We review wave-driven sediment resuspension and transport in estuaries, including generation of bed shear stress by waves, initiation of sediment motion by waves, and the ways waves modulate, add to, and interact with sediment transport driven by currents. A key characteristic of the wave-induced force on the seabed is extreme spatial and temporal variations; simple analytical models are revealing of the way such patterns develop. Statistical methods have been widely applied to predict wave resuspension of intertidal-flat bed sediments, and physically based predictors of resuspension developed from open-coast studies appear to also apply to short-period estuarine waves. There is ample experimental evidence to conclude that over the long term, waves erode and tidal currents accrete intertidal flats. Waves indirectly add to the formation of fluid mud by adding to the estuarine pool of fine sediment, and waves may fluidize subtidal seabeds, changing bed erodibility. Models have been used to explore the dynamic balance between sediment transport by waves and by currents and have revealed the key control of waves on estuarine morphology. Estuarine intertidal flats are excellent natural laboratories that offer opportunities for working on a number of fundamental problems in sediment transport. © 2013. American Geophysical Union. All Rights Reserved.

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