Mesoscale activity drives the habitat suitability of yellowfin tuna in the Gulf of Mexico.

Yellowfin tuna, Thunnus albacares, represents an important component of commercial and recreational fisheries in the Gulf of Mexico (GoM). We investigated the influence of environmental conditions on the spatiotemporal distribution of yellowfin tuna using fisheries' catch data spanning 2012-2019 within Mexican waters. We implemented hierarchical Bayesian regression models with spatial and temporal random effects and fixed effects of several environmental covariates to predict habitat suitability (HS) for the species. The best model included spatial and interannual anomalies of the absolute dynamic topography of the ocean surface (ADTSA and ADTIA, respectively), bottom depth, and a seasonal cyclical random effect. High catches occurred mainly towards anticyclonic features at bottom depths > 1000 m. The spatial extent of HS was higher in years with positive ADTIA, which implies more anticyclonic activity. The highest values of HS (> 0.7) generally occurred at positive ADTSA in oceanic waters of the central and northern GoM. However, high HS values (> 0.6) were observed in the southern GoM, in waters with cyclonic activity during summer. Our results highlight the importance of mesoscale features for the spatiotemporal distribution of yellowfin tunas and could help to develop dynamic fisheries management strategies in Mexico and the U.S. for this valuable resource.

Extraction of persistent lagrangian coherent structures for the pollutant transport prediction in the Bay of Bengal.

Lagrangian Coherent Structures (LCS) are the hidden fluid flow skeletons that provide meaningful information about the Lagrangian circulation. In this study, we computed the monthly climatological LCSs (cLCS) maps utilizing 24 years (1994-2017) of HYbrid Coordinate Ocean Model (HYCOM) currents and ECMWF re-analysis winds in the Bay of Bengal (BoB). The seasonal reversal of winds and associated reversal of currents makes the BoB dynamic. Therefore, we primarily aim to reveal the cLCSs associated with seasonal monsoon currents and mesoscale (eddies) processes over BoB. The simulated cLCS were augmented with the complex empirical orthogonal functions to confirm the dominant lagrangian transport pattern features better. The constructed cLCS patterns show a seasonal accumulation zone and the transport pattern of freshwater plumes along the coastal region of the BoB. We further validated with the satellite imagery of real-time oil spill dispersion and modelled oil spill trajectories that match well with the LCS patterns. In addition, the application of cLCSs to study the transport of hypothetical oil spills occurring at one of the active oil exploration sites (Krishna-Godavari basin) was described. Thus, demonstrated the accumulation zones in the BoB and confirmed that the persistent monthly cLCS maps are reasonably performing well for the trajectory prediction of pollutants such as oil spills. These maps will help to initiate mitigation measures in case of any occurrence of oil spills in the future.

Estimating daily semantic segmentation maps of classified ocean eddies using sea level anomaly data from along-track altimetry.

Mesoscale eddies, which are fast-moving rotating water bodies in the ocean with horizontal scales ranging from 10 km to 100 km and above, are considered to be the weather of the oceans. They are of interest to marine biologists, oceanographers, and geodesists for their impact on water mass, heat, and nutrient transport. Typically, gridded sea level anomaly maps processed from multiple radar altimetry missions are used to detect eddies. However, multi-mission sea level anomaly maps obtained by the operational processors have a lower effective spatiotemporal resolution than their grid spacing and temporal resolution, leading to inaccurate eddy detection. In this study, we investigate the use of higher-resolution along-track sea level anomaly data to infer daily two-dimensional segmentation maps of cyclonic, anticyclonic, or non-eddy areas with greater accuracy than using processed sea level anomaly grid map products. To tackle this challenge, we propose a deep neural network that uses spatiotemporal contextual information within the modality of along-track data. This network is capable of producing a two-dimensional segmentation map from data with varying sparsity. We have developed an architecture called Teddy, which uses a Transformer module to encode and process spatiotemporal information, and a sparsity invariant CNN to infer a two-dimensional segmentation map of classified eddies from the ground tracks of varying sparsity on the considered region. Our results show that Teddy creates two-dimensional maps of classified eddies from along-track data with higher accuracy and timeliness when compared to commonly used methods that work with less accurate preprocessed sea level anomaly grid maps. We train and test our method with a carefully curated and independent dataset, which can be made available upon request.

Influence of oceanic mesoscale eddies on the deep chlorophyll maxima.

The deployment of the biogeochemical Argo network significantly enhances our understanding of the ecological effects of mesoscale eddies at different ocean depths. In this study, satellite data and more than one hundred thousand biogeochemical Argo float profiles were used to analyze the responses of the deep chlorophyll maximum (DCM) to mesoscale eddies. The DCM profiles were categorized into two types: DAM (adaptation maximum) and DBM (biomass maximum), based on their adaptation to light and maximum biomass characteristics. The variabilities in the DCM profiles in terms of latitude, seasonality, and their response to mesoscale eddies were subsequently investigated on a global scale. Our analysis demonstrates that light and nutrient availability explain a significant portion of the variability in the phytoplankton distribution across different regions and seasons. Statistical analysis reveals that cyclonic (anticyclonic) eddies enhance (weaken) the intensity of the DCM. The magnitude of this enhancement or weakening exhibits regional differences. Specifically, high-latitude regions are more influenced by eddies in terms of light-adapted DCM intensity, while in mid-latitude regions, eddies exhibit a stronger effect on the maximum biomass-driven DCM intensity. Moreover, our findings suggest that eddies in the North Atlantic Subtropical Gyre contribute to a downward shift in the euphotic zone depth, leading to an increased DCM depth and strengthened DCM intensity. However, in the equatorial region, eddies impact the DCM depth by influencing the nitracline (a layer in a body of water in which the nitrate concentration changes rapidly with depth). Similar patterns are frequently observed in different regions at the same latitude, providing a foundation for further detailed investigations of the DCM in specific areas.

Scaling strategy for cell and gene therapy bioreactors based on turbulent parameters.

So far, power input has been used as the main parameter for bioreactor scale-up/-down in upstream process development and manufacturing. The rationale is that maintaining a consistent power input per unit volume should result in comparable mixing times at different scales. However, shear generated from turbulent flow may compromise the integrity of non-robust cells such as those used during the production of cell and gene therapies, which may lead to low product quality and yield. Of particular interest is the Kolmogorov length parameter that characterizes the smallest turbulent eddies in a mixture. To understand its impact on scale-up/-down decisions, the distribution of Kolmogorov length along the trajectory flow of individual particles in bioreactors was estimated in silico with the help of computational fluid dynamics simulations. Specifically, in this study the scalability of iPSC-derived lymphocyte production and the impact of shear stress across various differentiation stages were investigated. The study used bioreactors of volumes from 0.1 to 10 L, which correspond to the scales most used for parameter optimization. Our findings, which align with in vitro runs, help determine optimal agitation speed and shear stress adjustments for process transfer between scales and bioreactor types, using vertically-oriented wheel and pitched-blade impellers. In addition, empirical models specific to the bioreactors used in this study were developed. The provided computational analysis in combination with experimental data supports selection of appropriate bioreactors and operating conditions for various cell and gene therapy process steps.

The Impact of Fine-Scale Currents on Biogeochemical Cycles in a Changing Ocean.

Fine-scale currents, O(1-100 km, days-months), are actively involved in the transport and transformation of biogeochemical tracers in the ocean. However, their overall impact on large-scale biogeochemical cycling on the timescale of years remains poorly understood due to the multiscale nature of the problem. Here, we summarize these impacts and critically review current estimates. We examine how eddy fluxes and upscale connections enter into the large-scale balance of biogeochemical tracers. We show that the overall contribution of eddy fluxes to primary production and carbon export may not be as large as it is for oxygen ventilation. We highlight the importance of fine scales to low-frequency natural variability through upscale connections and show that they may also buffer the negative effects of climate change on the functioning of biogeochemical cycles. Significant interdisciplinary efforts are needed to properly account for the cross-scale effects of fine scales on biogeochemical cycles in climate projections.

Enhancing impacts of mesoscale eddies on Southern Ocean temperature variability and extremes.

As a major sink of anthropogenic heat and carbon, the Southern Ocean experienced pronounced warming with increasing extreme temperature events over the past decades. Mesoscale eddies that strongly influence the uptake, redistribution, and storage of heat in the ocean are expected to play important roles in these changes, yet observational evidence remains limited. Here, we employ a comprehensive analysis of over 500,000 historical hydrographic profile measurements combined with satellite-based eddy observations to show enhanced thermal eddy imprints in the Southern Ocean. Our observations reveal that anticyclonic (cyclonic) eddies are responsible for nearly half of the subsurface high (low)-temperature extremes detected, although only 10% of the profiles are located in eddy interiors. Over the past decade (2006 to 2019), both mean and extreme temperature anomalies within eddies in the Antarctic Circumpolar Current increased significantly, promoting the rise in subsurface ocean temperature variability. This enhanced role of eddies is likely a result of enhanced eddy pumping due to the increase in eddy intensity and ocean stratification caused by ocean warming. Our analysis underscores the crucial role of eddies in amplifying ocean temperature variability and extremes, with their effects expected to be even more pronounced as global warming persists.

Assemblages of pelagic thaliaceans in oceanographic features at the tropical-temperate transition zone of a western boundary current.

Mesoscale oceanographic features influence the composition of zooplankton. Cyclonic eddies can promote upwelling and production of gelatinous zooplankton, which play critical roles in ocean biogeochemical cycling. We examined variation in assemblages of thaliaceans (salps, doliolids and pyrosomes) among mesoscale oceanographic features at the tropical-temperate boundary of the East Australian Current (EAC) in Spring 2019 and Autumn 2021. The influence of cyclonic eddies was examined in a large offshore cyclonic eddy in 2019 and a newly formed frontal eddy in 2021. Pyrosomes were most abundant in the offshore EAC jet, and salps and doliolids were most abundant in coastal features, including within eddies that were transported offshore. In 2019, Salpa fusiformis increased 4-fold over 8 days in the large cyclonic eddy, and in 2021, doliolids increased > 50-fold over 2 weeks in a chlorophyll-rich coastal eddy while abundances of other thaliaceans remained unchanged or decreased. Correlations between abundances of thaliaceans and chlorophyll-a concentrations across the 102 samples collected during both voyages revealed that doliolids occupy a wider range of chlorophyll-a concentrations than salps. Our observations indicate that doliolids thrive in productive shelf environments, salps occur in less productive shelf waters and pyrosomes are most abundant in oligotrophic waters of the south Coral Sea.

Empirical mode decomposition of the atmospheric flows and pollutant transport over real urban morphology.

The momentum transport and pollutant dispersion in the atmospheric surface layer (ASL) are governed by a broad spectrum of turbulence structures. Whereas, their contributions have not been explicitly investigated in the context of real urban morphology. This paper aims to elucidate the contributions from different types of eddies in the ASL over a dense city to provide the reference of urban planning, realizing more favorable ventilation and pollutant dispersion. The building-resolved large-eddy simulation dataset of winds and pollutants over the Kowloon downtown, Hong Kong, is decomposed into a few intrinsic mode functions (IMFs) via empirical mode decomposition (EMD). EMD is a data-driven algorithm that has been successfully implemented in many research fields. The results show that four IMFs are generally enough to capture most of the turbulence structures in real urban ASL. In particular, the first two IMFs, which are initiated by individual buildings, capture the small-scale vortex packets that populate within the irregular building clusters. On the other hand, the third and fourth IMFs capture the large-scale motions (LSMs) detached to the ground surface that are highly efficient in transport. They collectively contribute to nearly 40% of vertical momentum transport even with relatively low vertical turbulence kinetic energy (TKE). LSMs are long, streaky structures that mainly consist of streamwise TKE components. It is found that the open areas and regular streets promote the portion of streamwise TKE in LSMs, improving the vertical momentum transport and pollutant dispersion. In addition, these streaky LSMs are found to play a crucial role in pollutant dilution in the near field after the pollutant source, while the small-scale vortex packets are more efficient in transport in the mid-field and far-field.

Bioluminescent eddies of the World Ocean.

Mesoscale eddies of the ocean (with a characteristic diameter of about 100 km and a life time-span of about several weeks) are habitats of plankton organisms, many of which are bioluminescent. The spatial heterogeneity of bioluminescence of the upper mixed layer associated with the impact of mesoscale eddies is poorly studied. The 45-year historical data set was retrieved, in order to select the bathy-photometric surveys carried out in the form of station grids and transects across eddies. Data from 71 expeditions deployed in 1966-2022 to the Atlantic Ocean, Indian Ocean and Mediterranean Sea basin were analyzed, in order for the spatial heterogeneity of bioluminescent fields to be elucidated across eddy fields. The stimulated bioluminescence intensity was characterized by the bioluminescent potential, which represented the maximal amount of radiant energy emitted in a given volume of water by bioluminescent organisms. The normalized bioluminescent potential over oceanographic station grids exhibited correlation with the eddy kinetic energy and zooplankton biomass (r = 0.8, at P = 0.001 and r = 0.7, at P = 0.05, respectively), in a broad range of energy and bioluminescence units (0.02-0.2 m2  s-2 ; 0.4-92.0 × 10-8  W cm-2  L-1 , respectively). Overall, estimates of bioluminescent potential variability on the mesoscale contribute to the assessment of the multiple-scale variation of the bioluminescent field of the World Ocean.

Phytoplankton Responses to Bacterially Regenerated Iron in a Southern Ocean Eddy.

In the Subantarctic sector of the Southern Ocean, vertical entrainment of iron (Fe) triggers the seasonal productivity cycle but diminishing physical supply during the spring to summer transition forces microbial assemblages to rapidly acclimate. Here, we tested how phytoplankton and bacteria within an isolated eddy respond to different dissolved Fe (DFe)/ligand inputs. We used three treatments: one that mimicked the entrainment of new DFe (Fe-NEW), another in which DFe was supplied from bacterial regeneration of particles (Fe-REG), and a control with no addition of DFe (Fe-NO). After 6 days, 3.5 (Fe-NO, Fe-NEW) to 5-fold (Fe-REG) increases in Chlorophyll a were observed. These responses of the phytoplankton community were best explained by the differences between the treatments in the amount of DFe recycled during the incubation (Fe-REG, 15% recycled c.f. 40% Fe-NEW, 60% Fe-NO). This additional recycling was more likely mediated by bacteria. By day 6, bacterial production was comparable between Fe-NO and Fe-NEW but was approximately two-fold higher in Fe-REG. A preferential response of phytoplankton (haptophyte-dominated) relative to high nucleic acid (HNA) bacteria was also found in the Fe-REG treatment while the relative proportion of diatoms increased faster in the Fe-NEW and Fe-NO treatments. Comparisons between light and dark incubations further confirmed the competition between picophytoplankton and HNA for DFe. Overall, our results demonstrate great versatility by microorganisms to use different Fe sources that results in highly efficient Fe recycling within surface waters. This study also encourages future research to further investigate the interactions between functional groups of microbes (e.g. HNA and cyanobacteria) to better constraint modeling in Fe and carbon biogeochemical cycles.

Bioluminescence of the tropical Indian Ocean: a multiple-scale variation.

Large-scale surveys represented by 5800 bathymetric casts in the western Indian Ocean (0-22o N, 54-58o E), elucidated the 10-fold variation of the bioluminescent potential (BP) in the upper mixed layer, during the winter (north-east) monsoon season. The mesoscale survey in February 2017 consisted of 26 drift stations (4o N-3o S, 65-68o E) on which 5-10 bathymetric casts were deployed down to 60 m. The maximal BP was associated with the periphery of a cyclonic eddy. The two-fold to three-fold variation of BP characterized the spatial heterogeneity modulated by a detected eddy. High-frequency casts on drift stations resembled the fine-scale heterogeneity in which the three-fold variation was observed within the BP maximum at a 37 ± 13 m depth. The latter one was located above the deep chlorophyll maximum at a 80 m depth. A general decline of the BP variance from the large scale through mesoscale to fine scale, fits that of the zooplankton biomass.

High-resolution hydrodynamics and TS structure database of the Brazilian continental shelf and adjacent waters.

This data set was obtained from two ROMS model simulations in the region of Brazil located at 60°W-15°W / 25°S - 15°N. One of the simulations takes into account the tide (obtained from the TPXO7 product) and the other one does not. The rest of the configuration was similar for both simulations, taking bathymetry from ETOPO2 and surface forcings from COADS climatology. Moreover, all boundaries were considered open and lateral conditions were taken from SODA, while initial conditions are derived from WOA09 and the river discharge climatology was obtained from Dai and Trenberth. In both experiments the KPP parameterization was used as vertical mixing scheme. The output files are in NetCDF format and are separated by months with a frequency of daily averages, containing 12 files for the simulation with tide and 12 for the simulation without tide, which are organized in two directories: Tide and noTide. This dataset is hosted at https://www.scidb.cn/en/detail?dataSetId=e1f188c4684048459823aaec4f168cc3.

Genomic and transcriptomic evidence for the diverse adaptations of Synechococcus subclusters 5.2 and 5.3 to mesoscale eddies.

Mesoscale eddies are ubiquitous oceanographic features that influence the metabolism and community structure of Synechococcus. However, the metabolic adaptations of this genus to eddy-associated environmental changes have rarely been studied. We recovered two high-quality Synechococcus metagenome-assembled genomes (MAGs) from eddies in the South China Sea and compared their metabolic variations using metatranscriptomic samples obtained at the same time. The two MAGs (syn-bin1 and syn-bin2) are affiliated with marine Synechococcus subclusters 5.2 (S5.2) and 5.3 (S5.3), respectively. The former exhibited a higher abundance at the surface layer, whereas the latter was more abundant in the deep euphotic layer. Further analysis indicated that syn-bin1 had a strong ability to utilize organic nutrients, which could help it to thrive in the nutrient-deprived surface water. By contrast, syn-bin2 had the genetic potential to perform chromatic acclimation, which could allow it to capture green or blue light at different depths. Additionally, transcriptomic analysis showed that syn-bin2 upregulated genes involved in the synthesis of C4 acids, photosystem II proteins, and HCO3- transporters in the deep euphotic layer, which might contribute to its predominance in low-light environments. Overall, this study expands our understanding of oceanic S5.2 and S5.3 Synechococcus by revealing their metabolic adaptations to mesoscale eddies.

Impact of Mesoscale Eddies on Deep Chlorophyll Maxima.

Deep Chlorophyll Maxima (DCM) are ubiquitous features in stratified oceanic systems. Their establishment and maintenance result from hydrographical stability favoring specific environmental conditions with respect to light and nutrient availability required for phytoplankton growth. This stability can potentially be challenged by mesoscale eddies impacting the water column's vertical structure and thus the environmental parameters that condition the subsistence of DCMs. Here, data from the global BGC-Argo float network are collocated with mesoscale eddies to explore their impact on DCMs. We show that cyclonic eddies, by providing optimal light and nutrient conditions, increase the occurrence of DCMs characterized by Deep Biomass Maxima for phytoplankton. In contrast, DCMs in anticyclonic eddies seem to be driven by photoacclimation as they coincide with Deep Acclimation Maxima without biomass accumulation. These findings suggest that the two types of eddies potentially have different impacts on the role of DCMs in global primary production.

Long term simulations of potential oil spills around Cuba.

Simulations over eight years of continuous surface oil spills around Cuba are carried out to identify the most likely stranding (beaching) locations. The open source Lagrangian oil drift model OpenOil is applied with high resolution hydrodynamic forcing. The actual fraction of the released oil mass reaching different regions is calculated, revealing small differences between a light and a heavy crude oil type. Similar stranding rates for the two oil types are found. Another important conclusion is that, due to the high temporal variability in stranding rates, short term simulations of a few weeks are not suitable to assess environmental risk. The highest stranding rates are simulated in winter in Northern Cuba. It is also found that oil could reach Northern Cuba, Yucatan or Florida in about 3-5 days after a spill.

Rapid assessment tool for oil spill planning and contingencies.

The Rapid Oil Spill Hazard Assessment is presented as a demonstration of concept for a tool providing a framework for managers and planners to assess potential impact areas of oil spills. The tool consists of precomputed oil spill scenarios derived from the analysis of twenty years of modeled current data using Self-Organizing Maps to identify 16 representative patterns. These patterns were used to provide boundary conditions for hydrodynamic and wave models to generate higher resolution current fields, used to drive a Lagrangian oil particle transport model creating the most probable oil spill dispersion patterns. To demonstrate the concept, the tool is applied to the Perdido region in the western Gulf of Mexico. A total of 896 oil spill simulations were performed, considering surface and bottom spills, and were stored in a database for easy access to map arrival probabilities and times to be used in risk and vulnerability analysis.

Coupling of the Surface and Near-Bottom Currents in the Gulf of Mexico.

Coupling between the surface and near-bottom currents in the Gulf of Mexico (GoM) has been reported in many case studies. However, geographical variations of this coupling need more examination. In this study, surface geostrophic currents derived from satellite-observed sea surface height and subsurface currents from a collection of deep ocean moorings are used to examine the surface and bottom coupling in different parts of the GoM. The short-period (30-90 days) fluctuations generated by the Loop Current (LC) and the LC eddies (LCEs) have a more vertically coherent structure and stronger deep ocean expressions than the long-period fluctuations (>90 days). In addition, the strength of the coupling is modulated by the long-period variations of the LC and LCE sheddings. Moreover, the surface and bottom coupling varies geographically. In the LC region, the surface fluctuations along the eastern side of the LC are important in causing the bottom current fluctuations through baroclinic instability under the LC and through traveling topographic Rossby waves (TRWs) north of the LC. In the central deep GoM, the bottom currents are affected by the upper fluctuations of the northern LC through both local baroclinic instability and remote TRW propagation. In the northwestern GoM, the bottom current fluctuations are largely related to the remote surface variability from the west side of the LC by TRWs propagating northwestward. This study will help us better understand mechanisms of the bottom current fluctuations that are important for the dispersal of deep ocean materials and properties.

Simulation of Enhanced Growth of Marine Group II Euryarchaeota From the Deep Chlorophyll Maximum of the Western Pacific Ocean: Implication for Upwelling Impact on Microbial Functions in the Photic Zone.

Mesoscale eddies can have a strong impact on regional biogeochemistry and primary productivity. To investigate the effect of the upwelling of seawater by western Pacific eddies on the composition of the active planktonic marine archaeal community composition of the deep chlorophyll maximum (DCM) layer, mesoscale cold-core eddies were simulated in situ by mixing western Pacific DCM layer water with mesopelagic layer (400 m) water. Illumina sequencing of the 16S rRNA gene and 16S rRNA transcripts indicated that the specific heterotrophic Marine Group IIb (MGIIb) taxonomic group of the DCM layer was rapidly stimulated after receiving fresh substrate from 400 m water, which was dominated by uncultured autotrophic Marine Group I (MGI) archaea. Furthermore, niche differentiation of autotrophic ammonia-oxidizing archaea (MGI) was demonstrated by deep sequencing of 16S rRNA, amoA, and accA genes, respectively. Similar distribution patterns of active Marine Group III (MGIII) were observed in the DCM layer with or without vertical mixing, indicating that they are inclined to utilize the substrates already present in the DCM layer. These findings underscore the importance of mesoscale cyclonic eddies in stimulating microbial processes involved in the regional carbon cycle.

Increased dispersion of oil from a deep water seabed release by energetic mesoscale eddies.

Hydrodynamics play a critical role in determining the trajectory of an oil spill. Currents, stratification and mesoscale processes all contribute to how a spill behaves. Using an industry­leading oil spill model, we compare forecasts of oil dispersion when forced with two different hydrodynamic models of the North-West European Shelf (7 km and 1.5 km horizontal resolution). This demonstrates how the trajectory of a deep water (>1000 m) release in the central Faroe-Shetland Channel is influenced by explicitly resolving mesoscale processes. The finer resolution hydrodynamic model dramatically enhances the horizontal dispersion of oil and transports pollutant further afield. This is a consequence of higher mesoscale variability. Stratification influences the depth of subsurface plume trapping and subsequently the far-field transport of oil. These results demonstrate that the choice of hydrodynamic model resolution is crucial when designing particle tracking or tracer release experiments.