Realistic modelling of shelf-estuary regions

A very high-resolution modelling configuration was created for the estuary of Baía de Todos os Santos – BTS, Brazil (300 to 400 m), and adjacent coastal waters (600 to 1200 m). The adoption of a multi-corner domain approach allowed the variable spatial resolution required to resolve the shelf, the bay and their interactions. Seven years were simulated using realistic oceanic, atmospheric and riverine forcing. Model validation was done against observations showing the model skill to reproduce the thermohaline field, the tidal currents, as well as the variability of the free surface at tidal and sub-tidal time scales. The results provide the first representation of the tidal wave propagation along the bay, in terms of maps of amplitudes, phases and ellipses of the barotropic currents for the main tidal constituents. By analysing the residual currents at different depths, in terms of averages over the simulation period, several prominent structures were identified and named: (i) Salvador eddy (up to 0.2 m s⁻¹); (ii) St Antonio current (up to 0.45 m s⁻¹); (iii) Salvador current (up to 0.5 m s⁻¹); (iv) Itaparica eddy (up to 0.2 m s⁻¹); (v) Ilha dos Frades southern eddy (up to 0.1 m s⁻¹); and (vi) Ilha dos Frades northern eddy (up to 0.2 m s⁻¹). The model set-up proved to be highly efficient and robust simulating the BTS shelf-estuary region and such an approach may be suitable to other estuarine systems.

     

Why do certain species dominate? What we can learn from a rare case of Microdictyon dominance on a Caribbean reef

Many Caribbean reefs have shifted from coral dominance to macroalgal dominance, often by brown algae such as Dictyota and Lobophora. However, the north side of Cayman Brac in the Cayman Islands is dominated seasonally by the green macroalga Microdictyon (percent cover of Microdictyon is 4% in the winter and ~40% of the reef in the summer), although it is absent from the south side of the island and the remainder of the country. Indeed, Microdictyon is rare in much of the Caribbean, so this situation on Cayman Brac provides an opportunity to investigate the conditions that facilitate its distribution and dominance. The impact of herbivory, competition, nutrient input and other abiotic conditions were examined as factors that could influence the distribution and dominance of Microdictyon. While herbivory or nutrient input are frequently found to be key drivers of benthic community composition on coral reefs, here consumption of Microdictyon by herbivores was low, and thus, the alga was not subject to strong top-down control by herbivory. So, in this case, neither herbivore abundance nor feeding preference appeared to influence the distribution of Microdictyon. Nutrient input was also similar to both sides of the island suggesting nutrients played little role in differential distribution. But, in a controlled transplant experiment where Microdictyon was protected from herbivory and competition, it experienced almost complete mortality (93.3%) when transplanted to the south side, compared to only 11.8% mortality on the north. The south side was exposed to the strongest wave action 92% of the days in our study and was on average a slight, but significant 0.2°C warmer. Thus, these data suggest physical forcing (i.e. wave exposure) is the most likely factor dictating Microdictyon distribution. Conversely, a combination of reduced herbivory and increased competitive strength may explain the seasonal dominance of Microdictyon on the north side of Cayman Brac. Microdictyon was a competitive inferior to the other common algae in winter but increased in competitive strength to equal other species in summer. These results add to the literature on Microdictyon and on the forces impacting benthic community structure of coral reefs.     

A Variable Mesh Spacing for Large-Eddy Simulation Models in the Convective Boundary Layer

A variable vertical mesh spacing for large-eddy simulation (LES) models in a convective boundary layer (CBL) is proposed. The argument is based on the fact that in the vertical direction the turbulence near the surface in a CBL is inhomogeneous and therefore the subfilter-scale effects depend on the relative location between the spectral peak of the vertical velocity and the filter cut-off wavelength. From the physical point of view, this lack of homogeneity makes the vertical mesh spacing the principal length scale and, as a consequence, the LES filter cut-off wavenumber is expressed in terms of this characteristic length scale. Assuming that the inertial subrange initial frequency is equal to the LES filter cut-off frequency and employing fitting expressions that describe the observed convective turbulent energy one-dimensional spectra, it is feasible to derive a relation to calculate the variable vertical mesh spacing. The incorporation of this variable vertical grid within a LES model shows that both the mean quantities (and their gradients) and the turbulent statistics quantities are well described near to the ground level, where the LES predictions are known to be a challenging task.     

The Serra da Graciosa A-type Granites and Syenites, southern Brazil. Part 3: Magmatic evolution and post-magmatic breakdown of amphiboles of the alkaline association

Amphiboles are the main mafic minerals in most metaluminous to peralkaline alkali-feldspar granites and syenites, and they usually preserve an important record of the compositional evolution of the melts from which they crystallize. In the alkaline association of the Serra da Graciosa A-type Granites and Syenites (southern Brazil), amphibole compositions span a large range, including calcic, sodic–calcic, and sodic amphiboles. Calcic amphiboles are typically observed in the metaluminous rocks, while sodic amphiboles are characteristic of the more strongly peralkaline rocks; sodic–calcic amphiboles are found in intermediate varieties. Compositional variations record the differentiation trends within two petrographic series of the alkaline association. The overall evolution of amphibole compositions is similar in both: they reveal a progressive increase in Na and Fe³⁺ with differentiation (increase in alkalinity of the magmas), a characteristic shared by undersaturated peralkaline (or agpaitic) differentiation trends. In detail, however, the evolutions of the amphibole compositions in the two series are distinct. In Alkaline series 1, the cores of the crystals form a continuum from calcic to sodic compositions, with the exception of a small compositional gap within the sodic–calcic amphiboles. The rims, however, show compositions that diverge from this main trend; this divergence results from increasing amounts of the oxy-amphibole component, and reflects more oxidizing conditions at the final stages of magmatic crystallization. In Alkaline series 2, these oxidation trends are much more subtle and a reverse trend is observed in the sodic amphiboles. Sodic–calcic amphiboles are in several cases replaced by intergrowths of post-magmatic sodic amphibole and Al-poor (“tetrasilicic”) biotite.     

Continuous Monitoring Reveals Drivers of Dissolved Oxygen Variability in a Small California Estuary

Estuarine ecosystem diversity and function can be degraded by low oxygen concentrations. Understanding the spatial and temporal patterns of dissolved oxygen (DO) variation and the factors that predict decreases in DO is thus essential to inform estuarine management. We investigated DO variability and its drivers in Elkhorn Slough, a shallow, well-mixed estuary affected by high nutrient loading and with serious eutrophication problems. Long-term (2001–2012), high-resolution (15 min) time series of DO, water level, winds, and solar radiation from two fully tidal sites in the estuary showed that hypoxia events close to the bottom are common in the summer at the more upstream estuarine station. These events can occur in any lunar phase (spring to neap), at any time of the day, and both on sunny or cloudy days. They are, however, short-lived (lasting in average 40 min) and mainly driven by momentary low turbulent diffusion around slack tides (both at high and low water). Tidal advective transport explains up to 52.1% of the daily DO variability, and the water volume (or DO reservoir) contained in the estuary was not sufficient to avoid hypoxia in the estuary. Solar radiation was responsible for a positively correlated DO daily cycle but caused a decreased in the averaged DO in the summer at the inner station. Wind-driven upwelling reduced the average DO at the more oceanic station during spring. The approach we employed, using robust techniques to remove suspect data due to sensor drift combined with an array of statistical techniques, including spectral, harmonic, and coherence spectrum analysis, can serve as a model for analyses of long-term water quality datasets in other systems. Investigations such as ours can inform coastal management by identifying key drivers of hypoxia in estuaries.     

The Bishop Tuff giant magma body: an alternative to the Standard Model

The Bishop Tuff, one of the most extensively studied high-silica rhyolite bodies in the world, is usually considered as the archetypical example of a deposit formed from a magma body characterized by thermal and compositional vertical stratification—what we call the Standard Model for the Bishop magma body. We present here new geothermometry and geobarometry results derived using a large database of previously published quartz-hosted glass inclusion compositions. Assuming equilibrium between melt and an assemblage composed of quartz, ±plagioclase, ±sanidine, +zircon, ±fluid, we use Zr contents in glass inclusions to derive quartz crystallization temperatures, and we use (1) silica contents in glass, (2) projection of glass compositions onto the haplogranitic (quartz-albite-orthoclase) ternary, and (3) phase equilibria calculations using rhyolite-MELTS, to constrain crystallization pressures. We find crystallization temperatures of ~740–750 °C for all inclusions from both early- and late-erupted pumice. Crystallization pressures for both early- and late-erupted inclusions are also very similar to each other, with averages of ~175–200 MPa. We find no evidence of late-erupted inclusions having been entrapped at higher temperatures or pressures than early-erupted inclusions, as would be expected by the Standard Model. We argue that the thermal gradient inferred from Fe–Ti oxides—the backbone of the Standard Model—does not reflect equilibrium pre-eruptive conditions; we also note that H₂O–CO₂ systematics of glass inclusions yields overlapping pressure ranges for early- and late-erupted inclusions, similar to the results presented here; and we show that glass inclusion and phenocryst compositions show bimodal distributions, suggestive of compositional separation between early- and late-erupted populations. These findings are inconsistent with the Standard Model. The similarity in crystallization conditions and the compositional separation between early- and late-erupted magmas suggest that two laterally juxtaposed independent magma reservoirs existed in the same region at the same time and co-erupted to form the Long Valley Caldera and the Bishop Tuff. This hypothesis would explain the lack of mixing between early- and late-erupted crystal populations in pumice clasts; it could also explain the inferred eruption pattern—which resulted in early-erupted magmas being deposited only to the south of the caldera—if the early-erupted magma body resided to the south and the late-erupted magma body was located to the north. Our alternative model is consistent with the patchy distribution of thermal anomalies and the inference of co-eruption of distinct magma types in active volcanic areas such as the central Taupo Volcanic Zone.     

Cloning a new cytochrome P450 isoform (CYP356A1) from oyster Crassostrea gigas

We have cloned the full-length cDNA of the first member of a new cytochrome P450 (CYP) family from the Pacific oyster Crassostrea gigas. This new CYP gene was obtained based on an initial 331bp fragment previously identified among the list of the differentially expressed genes in oysters exposed to untreated domestic sewage. The full-length CYP has an open reading frame of 1500bp and based on its deduced amino acid sequence was classified as a member of a new subfamily, CYP356A1. A phylogenetic analysis showed that CYP356A1 is closely related to members of the CYP17 and CYP1 subfamilies. Semi-quantitative RT-PCR was performed to analyze the CYP356A1 expression in different tissues of the oyster (digestive gland, gill, mantle and adductor muscle). Results showed slightly higher CYP356A1 expression in digestive gland and mantle, than the other tissues, indicating a possible role of the CYP356A1 in xenobiotic biotransformation and/or steroid metabolism.     

Toarcian–Aalenian (Early–Middle Jurassic) radiolarian fauna from the Los Molles Formation,Neuquén Basin,Argentina: Taxonomy and paleobiogeographic affinities

This paper reports the occurrence of a Toarcian–Aalenian (Early–Middle Jurassic) radiolarian fauna in the Los Molles Formation, Neuquén Basin, Argentina, as well as comments on its paleobiogeographic affinities. The micropaleontologic analysis was carried out in fine-grained rocks from a turbiditic section of the Los Molles Formation. These samples were first chemically processed using only hydrogen peroxide (H₂O₂), and afterward treated with acetic (CH₃COOH) and hydrofluoric (HF) acids. The first chemical procedure permitted the recovery of only few spongy spumellarians, while the second one enabled to recover more diversified radiolarian assemblages. In general, the studied fauna presents low diversity and abundance, with a strong dominance of spumellarians over nassellarians. The fauna is composed by the genera Paronaella, Homoeoparonaella, Praeconocaryomma, Archaeocenosphaera, Orbiculiformella, Praeparvicingula, and some unidentified spumellarians and nassellarians. According to paleobiogeographic models, the studied Toarcian–Aalenian fauna presents a mid to high latitude affinity. It is possible to infer from those data a bipolar distribution of some taxa, such as Praeparvicingula and probably Praeconocaryomma, between the Northern and Southern hemispheres since the Early Jurassic (Toarcian).     

Phase-equilibrium geobarometers for silicic rocks based on rhyolite-MELTS. Part 2: application to Taupo Volcanic Zone rhyolites

Constraining the pressure of crystallisation of large silicic magma bodies gives important insight into the depth and vertical extent of magmatic plumbing systems; however, it is notably difficult to constrain pressure at the level of detail necessary to understand shallow magmatic systems. In this study, we use the recently developed rhyolite-MELTS geobarometer to constrain the crystallisation pressures of rhyolites from the Taupo Volcanic Zone (TVZ). As sanidine is absent from the studied deposits, we calculate the pressures at which quartz and feldspar are found to be in equilibrium with melt now preserved as glass (the quartz +1 feldspar constraint of Gualda and Ghiorso, Contrib Mineral Petrol 168:1033. doi: 10.1007/s00410-014-1033-3. 2014). We use glass compositions (matrix glass and melt inclusions) from seven eruptive deposits dated between ~320 and 0.7 ka from four distinct calderas in the central TVZ, and we discuss advantages and limitations of the rhyolite-MELTS geobarometer in comparison with other geobarometers applied to the same eruptive deposits. Overall, there is good agreement with other pressure estimates from the literature (amphibole geobarometry and H₂O–CO₂ solubility models). One of the main advantages of this new geobarometer is that it can be applied to both matrix glass and melt inclusions—regardless of volatile saturation. The examples presented also emphasise the utility of this method to filter out spurious glass compositions. Pressure estimates obtained with the new rhyolite-MELTS geobarometer range between ~250 to ~50 MPa, with a large majority at ~100 MPa. These results confirm that the TVZ hosts some of the shallowest rhyolitic magma bodies on the planet, resulting from the extensional tectonic regime and thinning of the crust. Distinct populations with different equilibration pressures are also recognised, which is consistent with the idea that multiple batches of eruptible magma can be present in the crust at the same time and can be tapped simultaneously by large eruptive events.