Distinct nitrogen cycling and steep chemical gradients in Trichodesmium colonies.

Trichodesmium is an important dinitrogen (N2)-fixing cyanobacterium in marine ecosystems. Recent nucleic acid analyses indicate that Trichodesmium colonies with their diverse epibionts support various nitrogen (N) transformations beyond N2 fixation. However, rates of these transformations and concentration gradients of N compounds in Trichodesmium colonies remain largely unresolved. We combined isotope-tracer incubations, micro-profiling and numeric modelling to explore carbon fixation, N cycling processes as well as oxygen, ammonium and nitrate concentration gradients in individual field-sampled Trichodesmium colonies. Colonies were net-autotrophic, with carbon and N2 fixation occurring mostly during the day. Ten percent of the fixed N was released as ammonium after 12-h incubations. Nitrification was not detectable but nitrate consumption was high when nitrate was added. The consumed nitrate was partly reduced to ammonium, while denitrification was insignificant. Thus, the potential N transformation network was characterised by fixed N gain and recycling processes rather than denitrification. Oxygen concentrations within colonies were ~60-200% air-saturation. Moreover, our modelling predicted steep concentration gradients, with up to 6-fold higher ammonium concentrations, and nitrate depletion in the colony centre compared to the ambient seawater. These gradients created a chemically heterogeneous microenvironment, presumably facilitating diverse microbial metabolisms in millimetre-sized Trichodesmium colonies.

A new mathematical model to explore microbial processes and their constraints in phytoplankton colonies and sinking marine aggregates.

N2-fixing colonies of cyanobacteria and aggregates of phytoplankton and detritus sinking hundreds of meters per day are instrumental for the ocean's sequestration of CO2 from the atmosphere. Understanding of small-scale microbial processes associated with phytoplankton colonies and aggregates is therefore crucial for understanding large-scale biogeochemical processes in the ocean. Phytoplankton colonies and sinking aggregates are characterized by steep concentration gradients of gases and nutrients in their interior. Here, we present a mechanistic mathematical model designed to perform modeling of small-scale fluxes and evaluate the physical, chemical, and biological constraints of processes that co-occur in phytoplankton colonies and sinking porous aggregates. The model accurately reproduced empirical measurements of O2 concentrations and fluxes measured in sinking aggregates. Common theoretical assumptions of either constant concentration or constant flux over the entire surface did not apply to sinking aggregates. Consequently, previous theoretical models overestimate O2 flux in these aggregates by as high as 15-fold.

A new tool for long-term studies of POM-bacteria interactions: overcoming the century-old Bottle Effect.

Downward fluxes of particulate organic matter (POM) are the major process for sequestering atmospheric CO2 into aquatic sediments for thousands of years. Budget calculations of the biological carbon pump are heavily based on the ratio between carbon export (sedimentation) and remineralization (release to the atmosphere). Current methodologies determine microbial dynamics on POM using closed vessels, which are strongly biased towards heterotrophy due to rapidly changing water chemistry (Bottle Effect). We developed a flow-through rolling tank for long term studies that continuously maintains POM at near in-situ conditions. There, bacterial communities resembled in-situ communities and greatly differed from those in the closed systems. The active particle-associated community in the flow-through system was stable for days, contrary to hours previously reported for closed incubations. In contrast to enhanced respiration rates, the decrease in photosynthetic rates on particles throughout the incubation was much slower in our system than in traditional ones. These results call for reevaluating experimentally-derived carbon fluxes estimated using traditional methods.

Cyclic 100-ka (glacial-interglacial) migration of subseafloor redox zonation on the Peruvian shelf.

The coupling of subseafloor microbial life to oceanographic and atmospheric conditions is poorly understood. We examined diagenetic imprints and lipid biomarkers of past subseafloor microbial activity to evaluate its response to glacial-interglacial cycles in a sedimentary section drilled on the Peruvian shelf (Ocean Drilling Program Leg 201, Site 1229). Multiple and distinct layers of diagenetic barite and dolomite, i.e., minerals that typically form at the sulfate-methane transition (SMT), occur at much shallower burial depth than the present SMT around 30 meters below seafloor. These shallow layers co-occur with peaks of (13)C-depleted archaeol, a molecular fossil of anaerobic methane-oxidizing Archaea. Present-day, non-steady state distributions of dissolved sulfate also suggest that the SMT is highly sensitive to variations in organic carbon flux to the surface shelf sediments that may lead to shoaling of the SMT. Reaction-transport modeling substantiates our hypothesis that shallow SMTs occur in response to cyclic sediment deposition with a high organic carbon flux during interglacials and a low organic carbon flux during glacial stages. Long diffusion distances expectedly dampen the response of deeply buried microbial communities to changes in sediment deposition and other oceanographic drivers over relatively short geological time scales, e.g., glacial-interglacial periods. However, our study demonstrates how dynamically sediment biogeochemistry of the Peru Margin has responded to glacial-interglacial change and how these changes are now preserved in the geological record. Such changes in subsurface biogeochemical zonation need to be taken into account to assess the role of the subseafloor biosphere in global element and redox cycling.

Diffusion-limited retention of porous particles at density interfaces.

Downward carbon flux in the ocean is largely governed by particle settling. Most marine particles settle at low Reynolds numbers and are highly porous, yet the fluid dynamics of this regime have remained unexplored. We present results of an experimental investigation of porous particles settling through a density interface at Reynolds numbers between 0.1 and 1. We tracked 100 to 500 µm hydrogel spheres with 95.5% porosity and negligible permeability. We found that a small negative initial excess density relative to the lower (denser) fluid layer, a common scenario in the ocean, results in long retention times of particles at the interface. We hypothesized that the retention time was determined by the diffusive exchange of the stratifying agent between interstitial and ambient fluid, which increases excess density of particles that have stalled at the interface, enabling their settling to resume. This hypothesis was confirmed by observations, which revealed a quadratic dependence of retention time on particle size, consistent with diffusive exchange. These results demonstrate that porosity can control retention times and therefore accumulation of particles at density interfaces, a mechanism that could underpin the formation of particle layers frequently observed at pycnoclines in the ocean. We estimate retention times of 3 min to 3.3 d for the characteristic size range of marine particles. This enhancement in retention time can affect carbon transformation through increased microbial colonization and utilization of particles and release of dissolved organics. The observed size dependence of the retention time could further contribute to improve quantifications of vertical carbon flux.

Finite-size anisotropy in statistically uniform porous media.

Anisotropy of the permeability tensor in statistically uniform porous media of sizes used in typical computer simulations is studied. Although such systems are assumed to be isotropic by default, we show that de facto their anisotropic permeability can give rise to significant changes in transport parameters such as permeability and tortuosity. The main parameter controlling the anisotropy is a/L , being the ratio of the obstacle to system size. Distribution of the angle alpha between the external force and the volumetric fluid stream is found to be approximately normal, and the standard deviation of alpha is found to decay with the system size as (a/L);{d/2} , where d is the space dimensionality. These properties can be used to estimate both anisotropy-related statistical errors in large-scale simulations and the size of the representative elementary volume. For porous media types studied here, the anisotropy effect becomes negligible only if a/L < or = 0.01 . This constraint was apparently violated in many previous computer simulations that need now to be recalculated.

Lattice Boltzmann model for exterior flows with an annealing preconditioning method.

In this paper we propose a highly efficient and stable lattice Boltzmann method for solving low Reynolds number exterior flows using a preconditioning technique. The present method is based on replacing the constant preconditioning parameter (gamma) within uniform grids [Guo, Phys. Rev. E 70, 066706 (2004)] by a space- and time-dependent one in a nested mesh-refined domain. To do this, for the transition from a fine to the neighboring coarser grid, gamma has been divided by a factor K , which is large initially and anneals stepwise to a small value after some iterations. With this technique, more than one order of magnitude larger convergence rate can be achieved, and several orders of magnitude larger system size can be treated.

Acceleration of steady-state lattice Boltzmann simulations for exterior flows.

The simulation of a stationary fluid flow past an obstacle by the lattice Boltzmann method (LBM) in two dimensions is discussed. The combination of second-order expressions for far-field boundary conditions and a suitable treatment of the no-slip boundary condition at the obstacle surface with the nested grid-refinement technique can be applied to the LBM, resulting in a highly efficient method for the treatment of exterior flows. Furthermore, via replacing the nested time stepping by local time stepping, the resolution process can be substantially accelerated. A highly accurate drag coefficient was used to make an error assessment for various no-slip boundary conditions imposed on the obstacle surface. The analysis showed that the equilibrium method for treating the no-slip conditions is superior to halfway bounce-back and full-way bounce-back no-slip conditions when the relaxation time tau=1 . Also a tau -dependence test was made to evaluate the performance of different methods in the treatment of the no-slip boundary conditions.

Tortuosity-porosity relation in porous media flow.

We study numerically the tortuosity-porosity relation in a microscopic model of a porous medium arranged as a collection of freely overlapping squares. It is demonstrated that the finite-size, slow relaxation and discretization errors, which were ignored in previous studies, may cause significant underestimation of tortuosity. The simple tortuosity calculation method proposed here eliminates the need for using complicated, weighted averages. The numerical results presented here are in good agreement with an empirical relation between tortuosity (T) and porosity (varphi) given by T-1 proportional, variantlnvarphi , that was found by others experimentally in granule packings and sediments. This relation can be also written as T-1 proportional, variantRSvarphi with R and S denoting the hydraulic radius of granules and the specific surface area, respectively. Applicability of these relations appears to be restricted to porous systems of randomly distributed obstacles of equal shape and size.

Instabilities and patterns in horizontally oscillating particulate suspension.

The mean flow and the linear stability characteristics of a two-dimensional particulate suspension, driven horizontally via harmonic oscillation, are analyzed. A constitutive model based on the kinetic theory of granular materials, which takes into account the dissipative collisional interactions among particles as well as their interactions with the interstitial fluid, is used; the effects of the interstitial fluid are incorporated in the balance equations for the particle phase. Assuming that the suspension is thin along the vertical direction, the effects of driving are incorporated into the governing equations in a mean-field manner. Using Floquet theory, a linear stability analysis of the time-periodic mean flow indicates that the oscillatory suspension supports stationary- and traveling-wave instabilities which correspond to particle banding patterns that are aligned parallel or orthogonal or at an oblique angle to the driving direction. The effects of external driving parameters and various system control parameters on the phase diagram of instabilities are studied. The fluid-particle interaction is shown to be responsible for the emergence of traveling instabilities in this flow.