Four-Hundred-and-Ninety-Million-Year Record of Bacteriogenic Iron Oxide Precipitation at Sea-Floor Hydrothermal Vents

Fe oxide deposits are commonly found at hydrothermal vent sites at mid-ocean ridge and back-arc sea floor spreading centers, seamounts associated with these spreading centers, and intra-plate seamounts, and can cover extensive areas of the seafloor. These deposits can be attributed to several abiogenic processes and commonly contain micron-scale filamentous textures. Some filaments are cylindrical casts of Fe oxyhydroxides formed around bacterial cells and are thus unquestionably biogenic. The filaments have distinctive morphologies very like structures formed by neutrophilic Fe oxidizing bacteria. It is becoming increasingly apparent that Fe oxidizing bacteria have a significant role in the formation of Fe oxide deposits at marine hydrothermal vents. The presence of Fe oxide filaments in Fe oxides is thus of great potential as a biomarker for Fe oxidizing bacteria in modern and ancient marine hydrothermal vent deposits. The ancient analogues of modern deep-sea hydrothermal Fe oxide deposits are jaspers. A number of jaspers, ranging in age from the early Ordovician to late Eocene, contain abundant Fe oxide filamentous textures with a wide variety of morphologies. Some of these filaments are like structures formed by modern Fe oxidizing bacteria. Together with new data from the modern TAG site, we show that there is direct evidence for bacteriogenic Fe oxide precipitation at marine hydrothermal vent sites for at least the last 490 Ma of the Phanerozoic

Challenges and Prospects in Ocean Circulation Models

We revisit the challenges and prospects for ocean circulation models following Griffies et al. (2010). Over the past decade, ocean circulation models evolved through improved understanding, numerics, spatial discretization, grid configurations, parameterizations, data assimilation, environmental monitoring, and process-level observations and modeling. Important large scale applications over the last decade are simulations of the Southern Ocean, the Meridional Overturning Circulation and its variability, and regional sea level change. Submesoscale variability is now routinely resolved in process models and permitted in a few global models, and submesoscale effects are parameterized in most global models. The scales where nonhydrostatic effects become important are beginning to be resolved in regional and process models. Coupling to sea ice, ice shelves, and high-resolution atmospheric models has stimulated new ideas and driven improvements in numerics. Observations have provided insight into turbulence and mixing around the globe and its consequences are assessed through perturbed physics models. Relatedly, parameterizations of the mixing and overturning processes in boundary layers and the ocean interior have improved. New diagnostics being used for evaluating models alongside present and novel observations are briefly referenced. The overall goal is summarizing new developments in ocean modeling, including: how new and existing observations can be used, what modeling challenges remain, and how simulations can be used to support observations.Peer reviewe

Challenges and Prospects in Ocean Circulation Models

We revisit the challenges and prospects for ocean circulation models following Griffies et al. (2010). Over the past decade, ocean circulation models evolved through improved understanding, numerics, spatial discretization, grid configurations, parameterizations, data assimilation, environmental monitoring, and process-level observations and modeling. Important large scale applications over the last decade are simulations of the Southern Ocean, the Meridional Overturning Circulation and its variability, and regional sea level change. Submesoscale variability is now routinely resolved in process models and permitted in a few global models, and submesoscale effects are parameterized in most global models. The scales where nonhydrostatic effects become important are beginning to be resolved in regional and process models. Coupling to sea ice, ice shelves, and high-resolution atmospheric models has stimulated new ideas and driven improvements in numerics. Observations have provided insight into turbulence and mixing around the globe and its consequences are assessed through perturbed physics models. Relatedly, parameterizations of the mixing and overturning processes in boundary layers and the ocean interior have improved. New diagnostics being used for evaluating models alongside present and novel observations are briefly referenced. The overall goal is summarizing new developments in ocean modeling, including: how new and existing observations can be used, what modeling challenges remain, and how simulations can be used to support observations

The sediment trapping efficiency of the macro-tidal Daly Estuary, tropical Australia

Field studies were carried out on the water and sediment dynamics in the tropical, macro-tidal, Daly Estuary. The estuary is shallow, very-turbid, about 100 km long, and the entrance is funnel-shape. In the wet, high flow season, normal tidal ranges can be suppressed in the estuary, depending on inflow rates, and freshwater becomes dominant up to the mouth. At that time a fraction of the fine sediment load is exported offshore as a bottom-tagging nepheloid layer after the sediment falls out of suspension of the thin, near-surface, river plume. The remaining fraction and the riverine coarse sediment form a large sediment bar 10 km long, up to 6 m in height and extending across the whole width of the channel near the mouth. This bar, as well as shoals in the estuary, partially pond the mid- to upper-estuary. This bar builds up from the deposition of riverine sediment during a wet season with high runoff and can raise mean water level by up to 2 m in the upper estuary in the low flow season. This ponding effect takes about three successive dry years to disappear by the sediment forming the bar being redistributed all over the estuary by tidal pumping of fine and coarse sediment in the dry season, which is the low flow season. The swift reversal of the tidal currents from ebb to flood results in macro-turbulence that lasts about 20 min. Bed load transport is preferentially landward and occurs only for water currents greater than 0.6 m s(-1). This high value of the threshold velocity suggests that the sand may be cemented by the mud. The Daly Estuary thus is a leaky sediment trap with an efficiency varying both seasonally and inter-annually. (c) 2006 Elsevier Ltd. All rights reserved

On some spurious mode issues in shallow-water models using a linear algebra approach

Numerical methods that are usually employed in ocean modelling are typically finite-difference, finite and spectral-element techniques. For most of these methods the coupling between the momentum and continuity equations is a delicate problem and it usually leads to spurious solutions in the representation of inertia-gravity waves. The spurious modes have a wide range of characteristics and may take the form of pressure (surface-elevation), velocity and/or Coriolis modes. The modes usually cause aliasing and an accumulation of energy in the smallest-resolvable scale, leading to noisy solutions. The Fourier analysis has proven practical and beneficial to describe the spurious solutions of several classical schemes. However it is restricted to uniform meshes on which the variables are regularly distributed. In this paper, a linear algebra approach is proposed to study the existence and the behaviour of stationary spurious modes associated with zero frequency, for some popular finite-difference and finite-element grids. The present approach is performed on uniform meshes but it applies equally well to regular as well as unstructured meshes with irregular geometry for the finite-element schemes. © 2004 Elsevier Ltd. All rights reserved

Comparison of unstructured, staggered grid methods for the shallow water equations

Unstructured grid models are receiving increased attention mainly because of their ability to provide a flexible spatial discretization. Hence, some areas can be resolved in great detail while not over-resolving other areas. Development of these models is an ongoing process with significant longstanding issues with spurious computational modes, efficiency, advection and Coriolis approximations, and so forth. However, many of these problems have been solved with the current generation of models which have much promise for coastal to global scale ocean modelling. Our purpose is to intercompare a class of unstructured grid models where the continuity equation reduces to a finite volume approximation. The momentum equations can be approximated with finite difference, finite element, or finite volume methods. Each of these methods can have advantages and disadvantages in different classes of problems that range from hydraulics to coastal and global ocean flows. Some of the more important differences are restrictions on grid irregularity and stability of the Coriolis term. The finite element version of the model has important advantages in the discretization of the Coriolis term and does not require a reconstruction of a tangential velocity component. The comparison is illustrated with a simple test case. (C) 2008 Elsevier Ltd. All rights reserved

A tale of two elements: P1ncP1 and RTO

The and RT0 finite element schemes are among the most promising low order elements for use in unstructured mesh marine and lake models. They are both free of spurious elevation modes, have good dispersive properties and have a relatively low computational cost. In this paper, we derive both finite element schemes in the same unified framework and discuss their respective qualities in terms of conservation, consistency, propagation factor and convergence rate. We also highlight the impact that the local variables placement can have on the model solution. The main conclusion that we can draw is that the choice between elements is highly application dependent. We suggest that the element is better suited to purely hydrodynamical applications while the RT0 element might perform better for hydrological applications that require scalar transport calculations