Vicente Fernández

Lagrangian transport through an ocean front in the North-Western Mediterranean Sea

Abstract With the tools of lobe dynamics, the authors analyze the structures present in the velocity field obtained from a numerical simulation of the surface circulation in the northwestern Mediterranean Sea. In particular, focus is placed on the North Balearic Front, the westernmost part of the transition zone between saltier and fresher waters in the western Mediterranean, which is here interpreted in terms of the presence of a semipermanent “Lagrangian barrier,” across which little transport occurs. Identified are relevant hyperbolic trajectories and their manifolds, and it is shown that the transport mechanism known as the turnstile, previously identified in abstract dynamical systems and simplified model flows, is also at work in this complex and realistic ocean flow. In addition, nonlinear dynamics techniques are shown to be powerful enough to identify the key geometric structures in this part of the Mediterranean. The construction also reveals the spatiotemporal routes along which this transport h...

Vortical ciliary flows actively enhance mass transport in reef corals

Significance The fitness of corals and their ability to form large reefs hinge on their capacity to exchange oxygen and nutrients with their environment. Lacking gills or other ventilating organs, corals have been commonly assumed to depend entirely on ambient flow to overcome the mass transport limitations associated with molecular diffusion. Here, we show that corals are not enslaved to ambient flow but instead, can actively enhance mass transport by producing intense vortical flows with their epidermal cilia. By vigorously stirring the water immediately adjacent to their surface, this active process allows corals to increase mass transport and thus, can be a fundamental survival mechanism in regions or at times of weak ambient flow. The exchange of nutrients and dissolved gasses between corals and their environment is a critical determinant of the growth of coral colonies and the productivity of coral reefs. To date, this exchange has been assumed to be limited by molecular diffusion through an unstirred boundary layer extending 1–2 mm from the coral surface, with corals relying solely on external flow to overcome this limitation. Here, we present direct microscopic evidence that, instead, corals can actively enhance mass transport through strong vortical flows driven by motile epidermal cilia covering their entire surface. Ciliary beating produces quasi-steady arrays of counterrotating vortices that vigorously stir a layer of water extending up to 2 mm from the coral surface. We show that, under low ambient flow velocities, these vortices, rather than molecular diffusion, control the exchange of nutrients and oxygen between the coral and its environment, enhancing mass transfer rates by up to 400%. This ability of corals to stir their boundary layer changes the way that we perceive the microenvironment of coral surfaces, revealing an active mechanism complementing the passive enhancement of transport by ambient flow. These findings extend our understanding of mass transport processes in reef corals and may shed new light on the evolutionary success of corals and coral reefs.

Lateral-line inspired sensor arrays for navigation and object identification

Found to affect numerous aspects of behavior, including maneuvering in complex fluid environments with poor visibility, the lateral line is a critical component of fish sensory systems. This sensory organ could fill the gap left by sonar and vision systems in turbid, cluttered environments; it has no analog in modern ocean vehicles, despite its utility and ubiquity in nature. A linear array of pressure sensors is used along with analytic models of the fluid in order to emulate the lateral line and characterize its object-tracking and shape recognition capabilities. Position, shape, and size of various objects in both passive and active sensing schemes are thus determined. The authors find that tracking a moving cylinder can be effectively achieved via a particle filter, based on pressure information. The authors are also able to reliably distinguish between cylinders of different cross section, using principal component analysis, as well as identify the critical flow signature information that leads to the shape identification. The authors employ pressure measurements on an artificial fish and an unscented Kalman filter in a second application in order to successfully identify the shape of an arbitrary static cylinder. The authors conclude that, based on the experiments, a linear pressure sensor array for identifying small objects should have a sensor-to-sensor spacing of less than 0.03 (relative to the length of the sensing body) and resolve pressure differences of at least 10 Pa. These criteria employ conductive polymer technologies to form a flexible array of small pressure sensors in order to be used in the development of an artificial lateral line adaptable to the curved hull of an underwater vehicle.

Chemotaxis toward phytoplankton drives organic matter partitioning among marine bacteria

Significance Microscale interactions between bacteria and phytoplankton underpin ocean biogeochemistry and frequently involve bacterial chemotaxis to phytoplankton dissolved organic matter (DOM). Yet, it remains unclear how the effects of this interaction propagate to ecosystem scales. We address this gap through a hybrid approach where high-resolution observations of chemotaxis toward a diatom are directly used in a resource utilization model. We find that chemotactic bacteria consume most diatom DOM under resource-rich or bacteria-rich conditions, that DOM is partitioned among distinct populations based on diffusivity, and that consumption is skewed toward very few cells. Nonmotile oligotrophic bacteria dominate when productivity is low. Motile copiotrophs dominate during blooms. Ocean chemotaxis thus partitions resources spatially, by molecular size, and temporally through seasonal and episodic blooms. The microenvironment surrounding individual phytoplankton cells is often rich in dissolved organic matter (DOM), which can attract bacteria by chemotaxis. These “phycospheres” may be prominent sources of resource heterogeneity in the ocean, affecting the growth of bacterial populations and the fate of DOM. However, these effects remain poorly quantified due to a lack of quantitative ecological frameworks. Here, we used video microscopy to dissect with unprecedented resolution the chemotactic accumulation of marine bacteria around individual Chaetoceros affinis diatoms undergoing lysis. The observed spatiotemporal distribution of bacteria was used in a resource utilization model to map the conditions under which competition between different bacterial groups favors chemotaxis. The model predicts that chemotactic, copiotrophic populations outcompete nonmotile, oligotrophic populations during diatom blooms and bloom collapse conditions, resulting in an increase in the ratio of motile to nonmotile cells and in the succession of populations. Partitioning of DOM between the two populations is strongly dependent on the overall concentration of bacteria and the diffusivity of different DOM substances, and within each population, the growth benefit from phycospheres is experienced by only a small fraction of cells. By informing a DOM utilization model with highly resolved behavioral data, the hybrid approach used here represents a new path toward the elusive goal of predicting the consequences of microscale interactions in the ocean.

Leaking method approach to surface transport in the Mediterranean Sea from a numerical ocean model

Abstract We use Lagrangian diagnostics (the leaking and the exchange methods) to characterize surface transport out of and between selected regions in the Western Mediterranean. Velocity fields are obtained from a numerical model. Residence times of water of Atlantic origin in the Algerian subbasin, with a strong seasonal dependence, are calculated. Exchange rates between these waters and the ones occupying the northern basin are also evaluated. At surface, northward transport is dominant, and involves filamental features and eddy structures that can be identified with the Algerian eddies. The impact on these results of the presence of small scale turbulent motions is evaluated by adding Lagrangian diffusion.

A microfluidics-based in situ chemotaxis assay to study the behaviour of aquatic microbial communities

Microbial interactions influence the productivity and biogeochemistry of the ocean, yet they occur in miniscule volumes that cannot be sampled by traditional oceanographic techniques. To investigate the behaviours of marine microorganisms at spatially relevant scales, we engineered an in situ chemotaxis assay (ISCA) based on microfluidic technology. Here, we describe the fabrication, testing and first field results of the ISCA, demonstrating its value in accessing the microbial behaviours that shape marine ecosystems.A microfluidics-based assay for in situ chemotaxis experiments.

Microbial Morphology and Motility as Biosignatures for Outer Planet Missions.

Abstract Meaningful motion is an unambiguous biosignature, but because life in the Solar System is most likely to be microbial, the question is whether such motion may be detected effectively on the micrometer scale. Recent results on microbial motility in various Earth environments have provided insight into the physics and biology that determine whether and how microorganisms as small as bacteria and archaea swim, under which conditions, and at which speeds. These discoveries have not yet been reviewed in an astrobiological context. This paper discusses these findings in the context of Earth analog environments and environments expected to be encountered in the outer Solar System, particularly the jovian and saturnian moons. We also review the imaging technologies capable of recording motility of submicrometer-sized organisms and discuss how an instrument would interface with several types of sample-collection strategies. Key Words: In situ measurement—Biosignatures—Microbiology—Europa—Ice. Astrobiology 16, 755–774.

Wind influence on surface current variability in the Ibiza Channel from HF Radar

Surface current variability is investigated using 2.5 years of continuous velocity measurements from an high frequency radar (HFR) located in the Ibiza Channel (Western Mediterranean Sea). The Ibiza Channel is identified as a key geographical feature for the exchange of water masses but still poorly documented. Operational, quality controlled, HFR derived velocities are provided by the Balearic Islands Coastal Observing and Forecasting System (SOCIB). They are assessed by performing statistical comparisons with current-meter, ADCP, and surface lagrangian drifters. HFR system does not show significant bias, and its accuracy is in accordance with previous studies performed in other areas. The main surface circulation patterns are deduced from an EOF analysis. The first three modes represent almost 70 % of the total variability. A cross-correlation analysis between zonal and meridional wind components and the temporal amplitudes of the first three modes reveal that the first two modes are mainly driven by local winds, with immediate effects of wind forcing and veering following Ekman effect. The first mode (37 % of total variability) is the response of meridional wind while the second mode (24 % of total variability) is linked primarily with zonal winds. The third and higher order modes are related to mesoscale circulation features. HFR derived surface transport presents a markedly seasonal variability being mostly southwards. Its comparison with Ekman-induced transport shows that wind contribution to the total surface transport is on average around 65 %.

Extended Kalman filter estimates the contour length of a protein in single molecule atomic force microscopy experiments

Atomic force microscopy force spectroscopy has become a powerful biophysical technique for probing the dynamics of proteins at the single molecule level. Extending a polyprotein at constant velocity produces the now familiar sawtooth pattern force-length relationship. Customarily, manual fits of the wormlike chain (WLC) model of polymer elasticity to sawtooth pattern data have been used to measure the contour length L(c) of the protein as it unfolds one module at a time. The change in the value of L(c) measures the number of amino acids released by an unfolding protein and can be used as a precise locator of the unfolding transition state. However, manual WLC fits are slow and introduce inevitable operator-driven errors which reduce the accuracy of the L(c) estimates. Here we demonstrate an extended Kalman filter that provides operator-free real time estimates of L(c) from sawtooth pattern data. The filter design is based on a cantilever-protein arrangement modeled by a simple linear time-invariant cantilever model and by a nonlinear force-length relationship function for the protein. The resulting Kalman filter applied to sawtooth pattern data demonstrates its real time, operator-free ability to accurately measure L(c). These results are a marked improvement over the earlier techniques and the procedure is easily extended or modified to accommodate further quantities of interest in force spectroscopy.

Logarithmic sensing in Bacillus subtilis aerotaxis

Aerotaxis, the directed migration along oxygen gradients, allows many microorganisms to locate favorable oxygen concentrations. Despite oxygen’s fundamental role for life, even key aspects of aerotaxis remain poorly understood. In Bacillus subtilis, for example, there is conflicting evidence of whether migration occurs to the maximal oxygen concentration available or to an optimal intermediate one, and how aerotaxis can be maintained over a broad range of conditions. Using precisely controlled oxygen gradients in a microfluidic device, spanning the full spectrum of conditions from quasi-anoxic to oxic (60 n mol/l–1 m mol/l), we resolved B. subtilis’ ‘oxygen preference conundrum’ by demonstrating consistent migration towards maximum oxygen concentrations (‘monotonic aerotaxis’). Surprisingly, the strength of aerotaxis was largely unchanged over three decades in oxygen concentration (131 n mol/l–196 μ mol/l). We discovered that in this range B. subtilis responds to the logarithm of the oxygen concentration gradient, a rescaling strategy called ‘log-sensing’ that affords organisms high sensitivity over a wide range of conditions. In these experiments, high-throughput single-cell imaging yielded the best signal-to-noise ratio of any microbial taxis study to date, enabling the robust identification of the first mathematical model for aerotaxis among a broad class of alternative models. The model passed the stringent test of predicting the transient aerotactic response despite being developed on steady-state data, and quantitatively captures both monotonic aerotaxis and log-sensing. Taken together, these results shed new light on the oxygen-seeking capabilities of B. subtilis and provide a blueprint for the quantitative investigation of the many other forms of microbial taxis.