River loads of suspended solids, nitrogen, phosphorus and herbicides delivered to the Great Barrier Reef lagoon

Degradation of coastal ecosystems in the Great Barrier Reef (GBR) lagoon, Australia, has been linked with increased land-based runoff of suspended solids, nutrients and pesticides since European settlement. This study estimated the increase in river loads for all 35 GBR basins, using the best available estimates of pre-European and current loads derived from catchment modelling and monitoring. The mean-annual load to the GBR lagoon for (i) total suspended solids has increased by 5.5 times to 17,000ktonnes/year, (ii) total nitrogen by 5.7 times to 80,000tonnes/year, (iii) total phosphorus by 8.9 times to 16,000tonnes/year, and (iv) PSII herbicides is 30,000kg/year. The increases in river loads differ across the 10 pollutants and 35 basins examined, reflecting differences in surface runoff, urbanisation, deforestation, agricultural practices, mining and retention by reservoirs. These estimates will facilitate target setting for water quality and desired ecosystem states, and enable prioritisation of critical sources for management.     

Semiautomatic and Automatic Cooperative Inversion of Seismic and Magnetotelluric Data

Natural source electromagnetic methods have the potential to recover rock property distributions from the surface to great depths. Unfortunately, results in complex 3D geo-electrical settings can be disappointing, especially where significant near-surface conductivity variations exist. In such settings, unconstrained inversion of magnetotelluric data is inexorably non-unique. We believe that: (1) correctly introduced information from seismic reflection can substantially improve MT inversion, (2) a cooperative inversion approach can be automated, and (3) massively parallel computing can make such a process viable. Nine inversion strategies including baseline unconstrained inversion and new automated/semiautomated cooperative inversion approaches are applied to industry-scale co-located 3D seismic and magnetotelluric data sets. These data sets were acquired in one of the Carlin gold deposit districts in north-central Nevada, USA. In our approach, seismic information feeds directly into the creation of sets of prior conductivity model and covariance coefficient distributions. We demonstrate how statistical analysis of the distribution of selected seismic attributes can be used to automatically extract subvolumes that form the framework for prior model 3D conductivity distribution. Our cooperative inversion strategies result in detailed subsurface conductivity distributions that are consistent with seismic, electrical logs and geochemical analysis of cores. Such 3D conductivity distributions would be expected to provide clues to 3D velocity structures that could feed back into full seismic inversion for an iterative practical and truly cooperative inversion process. We anticipate that, with the aid of parallel computing, cooperative inversion of seismic and magnetotelluric data can be fully automated, and we hold confidence that significant and practical advances in this direction have been accomplished.     

ParBreZo: A parallel,unstructured grid,Godunov-type,shallow-water code for high-resolution flood inundation modeling at the regional scale

Topographic data are increasingly available at high resolutions (<10 m) over large spatial extents to support detailed flood inundation modeling and loss estimation analyses required for flood risk management. This paper describes ParBreZo, the parallel implementation of a two-dimensional, Godunov-type, shallow-water code, to address the computational demand of high-resolution flood modeling at the regional scale (10²–10⁴ km²). A systematic approach to unstructured grid partitioning (domain decomposition) is presented, and the Single Process Multiple Data (SPMD) paradigm of distributed-memory parallelism is implemented so the code can be executed on computer clusters with distributed memory, shared memory, or some combination of the two (now common with multi-core architectures). In a fully-wetted, load-balanced test problem, the code scales very well with a parallel efficiency of close to 100% on up to 512 processes (maximum tested). A weighted grid partitioning is used to partially address the load balancing challenge posed by partially wetted domains germane to flooding applications, where the flood extent varies over time, while the partitioning remains static. An urban dam-break flood test problem shows that weighted partitions achieve a parallel efficiency exceeding 70% using up to 48 processes. This corresponds to a 97% reduction in execution time so results are obtained in a matter of minutes, which is attractive for routine engineering analyses. A hurricane storm surge test problem shows that a 10 m resolution, 12 h inundation forecast for a 40 km length of coastline can be completed in under 2 h using 512 processors. Hence, if coupled to a hurricane forecast system capable of resolving storm surge, inundation forecasts could be made at 10 m resolution with at least a 10 h lead time.     

Bioenergetics modeling to investigate habitat use by the nonindigenous crab,Carcinus maenas, in Willapa Bay, Washington

A bioenergetics model was developed and applied to questions of habitat use and migration behavior of nonindigenous European green crab (Carcinus maenas) in Willapa Bay, Washington, USA. The model was parameterized using existing data from published studies on the ecology and physiology ofC. maenas and allied brachyuran crabs., Simulations of the model were run describing four scenarios of habitat use and behavior during a 214-d simulation period (April–October) including crabs occupying mid littoral habitat, high littoral habitat, sublittoral habitat, and sublittoral habitat but undertaking intertidal migrations. Monthly trapping was done along an intertidal gradient in Willapa Bay to determine the actual distribution of crabs for the same time interval as the simulation period, and model results were compared to the observed pattern. Model estimates suggest no intrinsic energetic incentive for crabs to occupy littoral habitats since metabolic costs were c. 6% higher for these individuals than their sublittoral counterparts. Crabs in the littoral simulations were also less efficient than sublittoral crabs at converting consumed energy into growth. Monthly trapping revealed thatC. maenas are found predominantly in mid littoral habitats of Willapa Bay and there is no evidence of resident sublittoral populations. The discrepancy intimates the significance of other factors, including interspecific interactions, that are not incorporated into the model but nonetheless increase metabolic demand. Agonistic encounters with native Dungeness crabs (Cancer magister) may be chief among these additional costs, andC. maenas may largely avoid interactions by remaining in littoral habitats neglected by native crabs, such as meadows of nonindigenous smooth cordgrass (Spartina alterniflora). AdultC. maenas in Willapa Bay may occupy tidal elevations that minimize such encounters, and metabolic costs, while simultaneously maximizing submersion time and foraging opportunities.     

Identification of Burrowing Shrimp Food Sources Along an Estuarine Gradient Using Fatty Acid Analysis and Stable Isotope Ratios

Two species of burrowing shrimp occur in high densities in US West Coast estuaries, the ghost shrimp, Neotrypaea californiensis, and the blue mud shrimp, Upogebia pugettensis. Both species of shrimp are considered ecosystem engineers as they bioturbate and irrigate extensive galleries within the sediment. While their burrows comprise a dominant habitat type in west coast estuaries, little is known about these shrimps’ diet and their role in estuarine food webs. The primary goals of this study were to identify major components of burrowing shrimp diets and detect variation in these diets along an estuarine gradient using combined fatty acid (FA) and stable isotope (SI) analyses. Shrimp and potential food sources including eelgrass blades, epiphytes, Ulva, sedimentary particulate organic matter (SPOM), burrow walls, and particulate organic material (POM) were sampled at different locations within Yaquina Bay, Oregon in August 2012. Both SI and FA analyses indicated differences in food resources assimilated by shrimp along the estuarine gradient. SI values showed that diets for U. pugettensis consisted of carbon sources derived primarily from POM and SPOM, while POM and epiphytes were primary carbon sources for N. californiensis. Shrimp from lower estuarine sites had high levels of 16:1ω7 and 20:5ω3 FAs suggesting their diet is enriched with marine diatoms. Shrimp from upriver showed greater proportion of FA associated with dinoflagellates and terrestrial sources as indicated by a high percentage of C₁₈ polyunsaturated FAs (PUFAs). This is the first study to evaluate diets of these two shrimp species using complimentary FA and SI approaches.     

Measurement of Particle-Bound Reactive Oxygen Species in Rubidoux Aerosols

The diurnal variations in the concentrations of reactive oxygen species (ROS) in various size fractions were determined for ambient particles in Rubidoux, CA. Sampling of particles was conducted at 3 h intervals using a cascade impactor. The collected particles were reacted with dichlorofluorescin (DCFH), a non-fluorescent probe that fluoresces when oxidized. The factors affecting the diurnal variation in ROS concentration were also investigated with special emphasis on the relation between ROS concentration and the intensity of photochemical reactions where the ozone concentration was taken as an index. The intensity of photochemical reactions was found to be a moderate factor affecting the daytime ROS concentration. The concentration of ROS was found to be higher on the smaller particles of the ambient aerosol. An erratum to this article is available .