Fluid dynamical niches of phytoplankton types

Nitrogen uptake rates and phytoplankton composition across contrasting North Atlantic Ocean coastal regimes north and south of Cape Hatteras

Understanding nitrogen (N) uptake rates respect to nutrient availability and the biogeography of phytoplankton communities is crucial for untangling the complexities of marine ecosystems and the physical, biological, and chemical forces shaping them. In the summer of 2016, we conducted measurements of bulk microbial uptake rates for six 15N-labeled substrates: nitrate, nitrite, ammonium, urea, cyanate, and dissolve free amino acids across distinct marine provinces, including the continental shelf of the Mid-and South Atlantic Bights (MAB and SAB), the Slope Sea, and the Gulf Stream, marking the first instance of simultaneously measuring six different N uptake rates in this dynamic region. Total measured N uptake rates were lowest in the Gulf Stream followed by the SAB. Notably, the MAB exhibited significantly higher N uptake rates compared to the SAB, likely due to the excess levels of pre-existing phosphorus present in the MAB. Together, urea and nitrate uptake contributed approximately 50% of the total N uptake across the study region. Although cyanate uptake rates were consistently low, they accounted for up to 11% of the total measured N uptake at some Gulf Stream stations. Phytoplankton groups were identified based on specific pigment markers, revealing a dominance of diatoms in the shelf community, while Synechococcus, Prochlorococcus, and pico-eukaryotes dominated in oligotrophic Gulf Stream waters. The reported uptake rates in this study were mostly in agreement with previous studies conducted in coastal waters of the North Atlantic Ocean. This study suggests there are distinct regional patterns of N uptake in this physically dynamic region, correlating with nutrient availability and phytoplankton community composition. These findings contribute valuable insights into the intricate interplay of biological and chemical factors shaping N dynamics in disparate marine ecosystems.

Chaotic turnover of rare and abundant species in a strongly interacting model community

The composition of ecological communities varies not only between different locations but also in time. Understanding the fundamental processes that drive species toward rarity or abundance is crucial to assessing ecosystem resilience and adaptation to changing environmental conditions. In plankton communities in particular, large temporal fluctuations in species abundances have been associated with chaotic dynamics. On the other hand, microbial diversity is overwhelmingly sustained by a "rare biosphere" of species with very low abundances. We consider here the possibility that interactions within a species-rich community can relate both phenomena. We use a Lotka-Volterra model with weak immigration and strong, disordered, and mostly competitive interactions between hundreds of species to bridge single-species temporal fluctuations and abundance distribution patterns. We highlight a generic chaotic regime where a few species at a time achieve dominance but are continuously overturned by the invasion of formerly rare species. We derive a focal-species model that captures the intermittent boom-and-bust dynamics that every species undergoes. Although species cannot be treated as effectively uncorrelated in their abundances, the community's effect on a focal species can nonetheless be described by a time-correlated noise characterized by a few effective parameters that can be estimated from time series. The model predicts a nonunitary exponent of the power-law abundance decay, which varies weakly with ecological parameters, consistent with observation in marine protist communities. The chaotic turnover regime is thus poised to capture relevant ecological features of species-rich microbial communities.

Submesoscale coupling of krill and whales revealed by aggregative Lagrangian coherent structures

In the marine environment, dynamic physical processes shape biological productivity and predator-prey interactions across multiple scales. Identifying pathways of physical-biological coupling is fundamental to understand the functioning of marine ecosystems yet it is challenging because the interactions are difficult to measure. We examined submesoscale (less than 100 km) surface current features using remote sensing techniques alongside ship-based surveys of krill and baleen whale distributions in the California Current System. We found that aggregative surface current features, represented by Lagrangian coherent structures (LCS) integrated over temporal scales between 2 and 10 days, were associated with increased (a) krill density (up to 2.6 times more dense), (b) baleen whale presence (up to 8.3 times more likely) and (c) subsurface seawater density (at depths up to 10 m). The link between physical oceanography, krill density and krill-predator distributions suggests that LCS are important features that drive the flux of energy and nutrients across trophic levels. Our results may help inform dynamic management strategies aimed at reducing large whales ship strikes and help assess the potential impacts of environmental change on this critical ecosystem.

Exploring the mesoscale connectivity of phytoplankton periodic assemblages' succession in northern Adriatic pelagic habitats

An appropriate model for phytoplankton distribution patterns is critical for understanding biogeochemical cycles and trophic interactions in the oceans and seas. Because phytoplankton dynamics in coastal waters are more complex due to shallow depth and proximity to land, more accurate models applied to the correct spatial and temporal scales are needed. Our study investigates the role of the atmosphere and hydrosphere in pelagic habitat by modelling phytoplankton assemblages at two Long Term Ecological Research sites in the northern Adriatic Sea using niche-forming environmental variables (wind, temperature, salinity, river discharge, rain, and water column stratification). To study the synchronization between the phytoplankton community and these environmental variables at the two LTER sites, we applied current linear and nonlinear numerical methods for ecological modelling. The aim was to use periodic and/or non-periodic properties of the environmental variables to classify the phytoplankton assemblages at one LTER site (Gulf of Trieste - Slovenia) and then predict them at another LTER site 100 km away (Gulf of Venice - Italy). We found that periodicity played a role in the explanatory and predictive power of the environmental variables and that it was more important than non-periodic events in defining the common structure of the two pelagic habitats. The non-linear classification functions of the neural networks further increased the predictive power of these variables. We observed partial synchronization of communities at the mesoscale and differences between the original and predicted assemblages under similar environmental conditions. We conclude that mesoscale connectivity plays an important role in phytoplankton communities in the northern Adriatic. However, the loss of periodicity of niche-forming variables due to more frequent extreme meteorological and hydrological events could loosen these connections and affect the temporal succession of phytoplankton assemblages.

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.

Eukaryotic genomes from a global metagenomic data set illuminate trophic modes and biogeography of ocean plankton

Metagenomics is a powerful method for interpreting the ecological roles and physiological capabilities of mixed microbial communities. Yet, many tools for processing metagenomic data are neither designed to consider eukaryotes nor are they built for an increasing amount of sequence data. EukHeist is an automated pipeline to retrieve eukaryotic and prokaryotic metagenome-assembled genomes (MAGs) from large-scale metagenomic sequence data sets. We developed the EukHeist workflow to specifically process large amounts of both metagenomic and/or metatranscriptomic sequence data in an automated and reproducible fashion. Here, we applied EukHeist to the large-size fraction data (0.8-2,000 µm) from Tara Oceans to recover both eukaryotic and prokaryotic MAGs, which we refer to as TOPAZ (Tara Oceans Particle-Associated MAGs). The TOPAZ MAGs consisted of >900 environmentally relevant eukaryotic MAGs and >4,000 bacterial and archaeal MAGs. The bacterial and archaeal TOPAZ MAGs expand upon the phylogenetic diversity of likely particle- and host-associated taxa. We use these MAGs to demonstrate an approach to infer the putative trophic mode of the recovered eukaryotic MAGs. We also identify ecological cohorts of co-occurring MAGs, which are driven by specific environmental factors and putative host-microbe associations. These data together add to a number of growing resources of environmentally relevant eukaryotic genomic information. Complementary and expanded databases of MAGs, such as those provided through scalable pipelines like EukHeist, stand to advance our understanding of eukaryotic diversity through increased coverage of genomic representatives across the tree of life.IMPORTANCESingle-celled eukaryotes play ecologically significant roles in the marine environment, yet fundamental questions about their biodiversity, ecological function, and interactions remain. Environmental sequencing enables researchers to document naturally occurring protistan communities, without culturing bias, yet metagenomic and metatranscriptomic sequencing approaches cannot separate individual species from communities. To more completely capture the genomic content of mixed protistan populations, we can create bins of sequences that represent the same organism (metagenome-assembled genomes [MAGs]). We developed the EukHeist pipeline, which automates the binning of population-level eukaryotic and prokaryotic genomes from metagenomic reads. We show exciting insight into what protistan communities are present and their trophic roles in the ocean. Scalable computational tools, like EukHeist, may accelerate the identification of meaningful genetic signatures from large data sets and complement researchers' efforts to leverage MAG databases for addressing ecological questions, resolving evolutionary relationships, and discovering potentially novel biodiversity.

Surface and subsurface oceanographic features drive forage fish distributions and aggregations: Implications for prey availability to top predators in the US Northeast Shelf ecosystem

Forage fishes are a critical food web link in marine ecosystems, aggregating in a hierarchical patch structure over multiple spatial and temporal scales. Surface-level forage fish aggregations (FFAs) represent a concentrated source of prey available to surface- and shallow-foraging marine predators. Existing survey and analysis methods are often imperfect for studying forage fishes at scales appropriate to foraging predators, making it difficult to quantify predator-prey interactions. In many cases, general distributions of forage fish species are known; however, these may not represent surface-level prey availability to predators. Likewise, we lack an understanding of the oceanographic drivers of spatial patterns of prey aggregation and availability or forage fish community patterns. Specifically, we applied Bayesian joint species distribution models to bottom trawl survey data to assess species- and community-level forage fish distribution patterns across the US Northeast Continental Shelf (NES) ecosystem. Aerial digital surveys gathered data on surface FFAs at two project sites within the NES, which we used in a spatially explicit hierarchical Bayesian model to estimate the abundance and size of surface FFAs. We used these models to examine the oceanographic drivers of forage fish distributions and aggregations. Our results suggest that, in the NES, regions of high community species richness are spatially consistent with regions of high surface FFA abundance. Bathymetric depth drove both patterns, while subsurface features, such as mixed layer depth, primarily influenced aggregation behavior and surface features, such as sea surface temperature, sub-mesoscale eddies, and fronts influenced forage fish diversity. In combination, these models help quantify the availability of forage fishes to marine predators and represent a novel application of spatial models to aerial digital survey data.

Proliferating active matter

The fascinating patterns of collective motion created by autonomously driven particles have fuelled active-matter research for over two decades. So far, theoretical active-matter research has often focused on systems with a fixed number of particles. This constraint imposes strict limitations on what behaviours can and cannot emerge. However, a hallmark of life is the breaking of local cell number conservation by replication and death. Birth and death processes must be taken into account, for example, to predict the growth and evolution of a microbial biofilm, the expansion of a tumour, or the development from a fertilized egg into an embryo and beyond. In this Perspective, we argue that unique features emerge in these systems because proliferation represents a distinct form of activity: not only do the proliferating entities consume and dissipate energy, they also inject biomass and degrees of freedom capable of further self-proliferation, leading to myriad dynamic scenarios. Despite this complexity, a growing number of studies document common collective phenomena in various proliferating soft-matter systems. This generality leads us to propose proliferation as another direction of active-matter physics, worthy of a dedicated search for new dynamical universality classes. Conceptual challenges abound, from identifying control parameters and understanding large fluctuations and nonlinear feedback mechanisms to exploring the dynamics and limits of information flow in self-replicating systems. We believe that, by extending the rich conceptual framework developed for conventional active matter to proliferating active matter, researchers can have a profound impact on quantitative biology and reveal fascinating emergent physics along the way.

The distribution and diversity of eukaryotic phytoplankton in the Icelandic marine environment

Phytoplankton play a crucial role in the marine food web and are sensitive indicators of environmental change. Iceland is at the center of a contrasting hydrography, with cold Arctic water coming in from the north and warmer Atlantic water from the south, making this geographical location very sensitive to climate change. We used DNA metabarcoding to determine the biogeography of phytoplankton in this area of accelerating change. Seawater samples were collected in spring (2012-2018), summer (2017) and winter (2018) together with corresponding physico-chemical metadata around Iceland. Amplicon sequencing of the V4 region of the 18S rRNA gene indicates that eukaryotic phytoplankton community composition is different between the northern and southern water masses, with some genera completely absent from Polar Water masses. Emiliania was more dominant in the Atlantic-influenced waters and in summer, and Phaeocystis was more dominant in the colder, northern waters and in winter. The Chlorophyta picophytoplankton genus, Micromonas, was similarly dominant to the dominant diatom genus, Chaetoceros. This study presents an extensive dataset which can be linked with other 18s rRNA datasets for further investigation into the diversity and biogeography of marine protists in the North Atlantic.

Mistaking plastic for zooplankton: Risk assessment of plastic ingestion in the Mediterranean sea

Floating plastic debris is a pervasive pollutant in seas and oceans, affecting a wide range of animals. In particular, microplastics (<5 mm in size) increase the possibility that marine species consume plastic and enter the food chain. The present study investigates this potential mistake between plastic debris and zooplankton by calculating the plastic debris to zooplankton ratio over the whole Mediterranean Sea. To this aim, in situ data from the Tara Mediterranean Expedition are combined with environmental and Lagrangian diagnostics in a machine learning approach to produce spatially-explicit maps of plastic debris and zooplankton abundance. We then analyse the plastic to zooplankton ratio in regions with high abundances of pelagic fish. Two of the major hotspots of pelagic fish, located in the Gulf of Gabès and Cilician basin, were associated with high ratio values. Finally, we compare the plastic to zooplankton ratio values in the Pelagos Sanctuary, an important hotspot for marine mammals, with other Geographical Sub-Areas, and find that they were among the larger of the Western Mediterranean Sea. Our results indicate a high potential risk of contamination of marine fauna by plastic and advocate for novel integrated modelling approaches which account for potential trophic transfer within the food chain.

Spatial population genetics with fluid flow

The growth and evolution of microbial populations is often subjected to advection by fluid flows in spatially extended environments, with immediate consequences for questions of spatial population genetics in marine ecology, planktonic diversity and origin of life scenarios. Here, we review recent progress made in understanding this rich problem in the simplified setting of two competing genetic microbial strains subjected to fluid flows. As a pedagogical example we focus on antagonsim, i.e., two killer microorganism strains, each secreting toxins that impede the growth of their competitors (competitive exclusion), in the presence of stationary fluid flows. By solving two coupled reaction-diffusion equations that include advection by simple steady cellular flows composed of characteristic flow motifs in two dimensions (2D), we show how local flow shear and compressibility effects can interact with selective advantage to have a dramatic influence on genetic competition and fixation in spatially distributed populations. We analyze several 1D and 2D flow geometries including sources, sinks, vortices and saddles, and show how simple analytical models of the dynamics of the genetic interface can be used to shed light on the nucleation, coexistence and flow-driven instabilities of genetic drops. By exploiting an analogy with phase separation with nonconserved order parameters, we uncover how thesegeneticdrops harness fluid flows for novel evolutionary strategies, even in the presence of number fluctuations, as confirmed by agent-based simulations as well.

Rapid evolution allows coexistence of highly divergent lineages within the same niche

Marine microbial communities are extremely complex and diverse. The number of locally coexisting species often vastly exceeds the number of identifiable niches, and taxonomic composition often appears decoupled from local environmental conditions. This is contrary to the view that environmental conditions should select for a few locally well-adapted species. Here we use an individual-based eco-evolutionary model to show that virtually unlimited taxonomic diversity can be supported in highly evolving assemblages, even in the absence of niche separation. With a steady stream of heritable changes to phenotype, competitive exclusion may be weakened, allowing sustained coexistence of nearly neutral phenotypes with highly divergent lineages. This behaviour is robust even to abrupt environmental perturbations that might be expected to cause strong selection pressure and an associated loss of diversity. We, therefore, suggest that rapid evolution and individual-level variability are key drivers of species coexistence and maintenance of microbial biodiversity.

Influence of nutrient supply on plankton microbiome biodiversity and distribution in a coastal upwelling region

The ecological and oceanographic processes that drive the response of pelagic ocean microbiomes to environmental changes remain poorly understood, particularly in coastal upwelling ecosystems. Here we show that seasonal and interannual variability in coastal upwelling predicts pelagic ocean microbiome diversity and community structure in the Southern California Current region. Ribosomal RNA gene sequencing, targeting prokaryotic and eukaryotic microbes, from samples collected seasonally during 2014-2020 indicate that nitracline depth is the most robust predictor of spatial microbial community structure and biodiversity in this region. Striking ecological changes occurred due to the transition from a warm anomaly during 2014-2016, characterized by intense stratification, to cooler conditions in 2017-2018, representative of more typical upwelling conditions, with photosynthetic eukaryotes, especially diatoms, changing most strongly. The regional slope of nitracline depth exerts strong control on the relative proportion of highly diverse offshore communities and low biodiversity, but highly productive nearshore communities.

Coastal upwelling sustains some of the most productive ocean regions. Here, the authors find that spatial patterns and temporal changes in nutrient supply explain marine microbial community structure and diversity in the Southern California Current region.

Variability in spring phytoplankton blooms associated with ice retreat timing in the Pacific Arctic from 2003-2019

The Arctic is experiencing rapid changes in sea-ice seasonality and extent, with significant consequences for primary production. With the importance of accurate monitoring of spring phytoplankton dynamics in a changing Arctic, this study further examines the previously established critical relationship between spring phytoplankton bloom types and timing of the sea-ice retreat for broader temporal and spatial coverages, with a particular focus on the Pacific Arctic for 2003–2019. To this end, time-series of satellite-retrieved phytoplankton biomass were modeled using a parametric Gaussian function, as an effective approach to capture the development and decay of phytoplankton blooms. Our sensitivity analysis demonstrated accurate estimates of timing and presence/absence of peaks in phytoplankton biomass even with some missing values, suggesting the parametric Gaussian function is a powerful tool for capturing the development and decay of phytoplankton blooms. Based on the timing and presence/absence of a peak in phytoplankton biomass and following the classification developed by the previous exploratory work, spring bloom types are classified into three groups (under-ice blooms, probable under-ice blooms, and marginal ice zone blooms). Our results showed that the proportion of under-ice blooms was higher in the Chukchi Sea than in the Bering Sea. The probable under-ice blooms registered as the dominant bloom types in a wide area of the Pacific Arctic, whereas the marginal ice zone bloom was a relatively minor bloom type across the Pacific Arctic. Associated with a shift of sea-ice retreat timing toward earlier dates, we confirmed previous findings from the Chukchi Sea of recent shifts in phytoplankton bloom types from under-ice blooms to marginal ice zone blooms and demonstrated that this pattern holds for the broader Pacific Arctic sector for the time period 2003–2019. Overall, the present study provided additional evidence of the changing sea-ice retreat timing that can drive variations in phytoplankton bloom dynamics, which contributes to addressing the detection and consistent monitoring of the biophysical responses to the changing environments in the Pacific Arctic.

Fine-scale structures as spots of increased fish concentration in the open ocean

Oceanic frontal zones have been shown to deeply influence the distribution of primary producers and, at the other extreme of the trophic web, top predators. However, the relationship between these structures and intermediate trophic levels is much more obscure. In this paper we address this knowledge gap by comparing acoustic measurements of mesopelagic fish concentrations to satellite-derived fine-scale Lagrangian Coherent Structures in the Indian sector of the Southern Ocean. First, we demonstrate that higher fish concentrations occur more frequently in correspondence with strong Lagrangian Coherent Structures. Secondly, we illustrate that, while increased fish densities are more likely to be observed over these structures, the presence of a fine-scale feature does not imply a concomitant fish accumulation, as other factors affect fish distribution. Thirdly, we show that, when only chlorophyll-rich waters are considered, front intensity modulates significantly more the local fish concentration. Finally, we discuss a model representing fish movement along Lagrangian features, specifically built for mid-trophic levels. Its results, obtained with realistic parameters, are qualitatively consistent with the observations and the spatio-temporal scales analysed. Overall, these findings may help to integrate intermediate trophic levels in trophic models, which can ultimately support management and conservation policies.

Fine-scale sampling unveils diazotroph patchiness in the South Pacific Ocean

Diazotrophs are important contributors to nitrogen availability in the ocean. Oceanographic cruise data accumulated over the past three decades has revealed a heterogeneous distribution of diazotroph species at regional to global scales. However, dynamic fine-scale physical structures likely affect the distribution of diazotrophs at smaller spatiotemporal scales. The interaction between fine-scale ocean dynamics and diazotrophs remains poorly understood due to typically insufficient spatiotemporal sampling resolution and the lack of parallel detailed physical studies. Here we show the distribution of five groups of diazotrophs in the South Pacific at an unprecedented resolution of 7-16 km. We find a patchy distribution of diazotrophs, with each group being differentially affected by parameters describing fine-scale physical structures. The observed variability in species abundance and distribution would be masked by a coarser sampling resolution, highlighting the need to consider fine-scale physics to resolve the distribution of diazotrophs in the ocean.

Bistability in oxidative stress response determines the migration behavior of phytoplankton in turbulence

Turbulence has long been known to drive phytoplankton fitness and species succession: motile species dominate in calmer environments and non-motile species in turbulent conditions. Yet a mechanistic understanding of the effect of turbulence on phytoplankton migratory behavior and physiology is lacking. By combining a method to generate turbulent cues, quantification of stress accumulation and physiology, and a mathematical model of stress dynamics, we show that motile phytoplankton use their mechanical stability to sense the intensity of turbulent cues and integrate these cues in time via stress signaling to trigger switches in migratory behavior. The stress-mediated warning strategy we discovered provides a paradigm for how phytoplankton cope with turbulence, thereby potentially governing which species will be successful in a changing ocean.

Turbulence is an important determinant of phytoplankton physiology, often leading to cell stress and damage. Turbulence affects phytoplankton migration both by transporting cells and by triggering switches in migratory behavior, whereby vertically migrating cells can actively invert their direction of migration upon exposure to turbulent cues. However, a mechanistic link between single-cell physiology and vertical migration of phytoplankton in turbulence is currently missing. Here, by combining physiological and behavioral experiments with a mathematical model of stress accumulation and dissipation, we show that the mechanism responsible for the switch in the direction of migration in the marine raphidophyte Heterosigma akashiwo is the integration of reactive oxygen species (ROS) signaling generated by turbulent cues. Within timescales as short as tens of seconds, the emergent downward-migrating subpopulation exhibited a twofold increase in ROS, an indicator of stress, 15% lower photosynthetic efficiency, and 35% lower growth rate over multiple generations compared to the upward-migrating subpopulation. The origin of the behavioral split as a result of a bistable oxidative stress response is corroborated by the observation that exposure of cells to exogenous stressors (H₂O₂, UV-A radiation, or high irradiance), in lieu of turbulence, caused comparable ROS accumulation and an equivalent split into the two subpopulations. By providing a mechanistic link between the single-cell mechanics of swimming and physiology on the one side and the emergent population-scale migratory response and impact on fitness on the other, the ROS-mediated early warning response we discovered contributes to our understanding of phytoplankton community composition in future ocean conditions.

Phytoplankton taxonomic and functional diversity patterns across a coastal tidal front

Oceanic physics at fine scale; e.g. eddies, fronts, filaments; are notoriously difficult to sample. However, an increasing number of theoretical approaches hypothesize that these processes affect phytoplankton diversity which have cascading effects on regional ecosystems. In 2015, we targeted the Iroise Sea (France) and evidenced the setting up of the Ushant tidal front from the beginning of spring to late summer. Seawater samples were taken during three sampling cruises and DNA-barcoding allowed us to investigate patterns of eukaryotic phytoplankton diversity across this front. First focusing on patterns of taxonomic richness, we evidenced that the front harbored a hotspot of eukaryotic phytoplankton diversity sustained throughout summer. We then detail the ecological processes leading to the formation of this hotspot by studying shifts in community composition across the Iroise Sea. Physical mixing mingled the communities surrounding the front, allowing the formation of a local ecotone, but it was cycles of disturbances and nutrient inputs over the front that allowed a decrease in competitive exclusion, which maintained a higher diversity of rare phytoplankton taxa. These processes did not select a specific ecological strategy as inferred by a trait approach coupled to our taxonomic approach. Instead the front favored higher richness within widespread strategies, resulting in functional redundancy. We detail how fine-scale ocean physics affect phytoplankton diversity and suppose that this interplay is a major control on regional ecosystems.

On star-convex volumes in 2-D hydrodynamical flows and their relevance for coherent transport

Oceanic surface flows are dominated by finite-time mesoscale structures that separate two-dimensional flows into volumes of qualitatively different dynamical behavior. Among these, the transport boundaries around eddies are of particular interest since the enclosed volumes show a notable stability with respect to filamentation while being transported over significant distances with consequences for a multitude of different oceanic phenomena. In this paper, we present a novel method to analyze coherent transport in oceanic flows. The presented approach is purely based on convexity and aims to uncover maximal persistently star-convex (MPSC) volumes, volumes that remain star-convex with respect to a chosen reference point during a predefined time window. Since these volumes do not generate filaments, they constitute a sub-class of finite-time coherent volumes. The new perspective yields definitions for filaments, which enables the study of MPSC volume formation and dissipation. We discuss the underlying theory and present an algorithm, the material star-convex structure search, that yields comprehensible and intuitive results. In addition, we apply our method to different velocity fields and illustrate the usefulness of the method for interdisciplinary research by studying the generation of filaments in a real-world example.

A matter of time and proportion: the availability of phosphorus-rich phytoplankton influences growth and behavior of copepod nauplii

Although consumers may use selective feeding to cope with suboptimal resource quality, little work has examined the mechanisms that underlie selective feeding, the efficiency of this behavior or its influence on consumer growth rate. Furthermore, a consumer's exposure to suboptimal resources may also influence the consumer's behavior and life history, including growth rate. Here, we studied how the availability of P-rich and P-poor phytoplankton influences the growth and behavior of copepod nauplii. We observed that copepod nauplii preferentially feed on P-rich prey. We also found that even relatively short exposure to P-rich phytoplankton yielded higher nauplii growth rates, whereas the presence of P-poor phytoplankton in a mixture impaired growth. Overall, we observed that swimming speed decreased with increasing phytoplankton P-content, which is a behavioral adjustment that may improve utilization of heterogeneously distributed high-quality food in the field. Based on our results, we propose that the optimal prey C: P ratio for copepod nauplii is very narrow, and that deviations from this optimum have severe negative consequences for growth.

Monitoring the Influence of the Mesoscale Ocean Dynamics on Phytoplanktonic Plumes around the Marquesas Islands Using Multi-Satellite Missions

The Marquesas islands are a place of strong phytoplanktonic enhancement, whose original mechanisms have not been explained yet. Several mechanisms such as current−bathymetry interactions or island run-off can fertilize waters in the immediate vicinity or downstream of the islands, allowing phytoplankton enhancement. Here, we took the opportunity of an oceanographic cruise carried out at the end of 2018, to combine in situ and satellite observations to investigate two phytoplanktonic blooms occurring north and south of the archipelago. First, Lagrangian diagnostics show that both chlorophyll-a concentrations (Chl) plumes are advected from the islands. Second, the use of Finite-size Lyaponov Exponent and frontogenesis diagnostics reveal how the Chl plumes are shaped by the passage of a mesoscale cyclonic eddy in the south and by a converging front and finer-scale dynamic activity in the north. Our results based on these observations provide clues to the hypothesis of a fertilization from the islands themselves allowing phytoplankton to thrive. They also highlight the role of advection to disperse and shape the Chl plumes in two regions with contrasting dynamical regimes.

Ocean currents promote rare species diversity in protists

Oceans host communities of plankton composed of relatively few abundant species and many rare species. The number of rare protist species in these communities, as estimated in metagenomic studies, decays as a steep power law of their abundance. The ecological factors at the origin of this pattern remain elusive. We propose that chaotic advection by oceanic currents affects biodiversity patterns of rare species. To test this hypothesis, we introduce a spatially explicit coalescence model that reconstructs the species diversity of a sample of water. Our model predicts, in the presence of chaotic advection, a steeper power law decay of the species abundance distribution and a steeper increase of the number of observed species with sample size. A comparison of metagenomic studies of planktonic protist communities in oceans and in lakes quantitatively confirms our prediction. Our results support that oceanic currents positively affect the diversity of rare aquatic microbes.

Complementarity in spatial subsidies of carbon associated with resource partitioning along multiple niche axes

The co-occurrence of several species, all of which share similar resource requirements, remains a paradox in ecology. Here, I evaluated resource use along multiple environmental axes to understand the potential for niche partitioning and complementarity in a guild of suspension-feeding rocky shore invertebrates. I focused on the mussels Perna canaliculus, Mytilus galloprovincialis, Aulacomya maoriana, and Xenostrobus pulex, all of which coexist along the coastline of the South Island of New Zealand. I quantified the mussels' distributions, both vertically on the shore and within the three-dimensional mussel bed matrix, and used carbon (δ¹³C) and nitrogen (δ¹⁵N) stable isotope ratios to compare species' diets. Mussels exhibited niche partitioning along all resource axes. Given the mussels' use of different spatial and food resources, I evaluated the potential for complementarity with respect to mussels' roles as mediators of an important spatial subsidy, carbon inputs from the nearshore ocean into rocky-shore ecosystems. In these systems, mussels are basal species, capturing and consuming particulate organic matter in the ocean and making it available for local consumption within the benthic community. I found that mussel diversity matters; even the most productive species-Perna canaliculus-only contributed about half of the mussel-mediated carbon that accumulated over a year. Multiple co-occurring species are, therefore, likely to provide more carbon at the base of the intertidal food web than any one species living independently, and complementarity in resource use along multiple environmental axes is likely an important mechanism underlying this relationship.

Stabilization of extensive fine-scale diversity by ecologically driven spatiotemporal chaos

It has recently become apparent that the diversity of microbial life extends far below the species level to the finest scales of genetic differences. Remarkably, extensive fine-scale diversity can coexist spatially. How is this diversity stable on long timescales, despite selective or ecological differences and other evolutionary processes? Most work has focused on stable coexistence or assumed ecological neutrality. We present an alternative: extensive diversity maintained by ecologically driven spatiotemporal chaos, with no assumptions about niches or other specialist differences between strains. We study generalized Lotka-Volterra models with antisymmetric correlations in the interactions inspired by multiple pathogen strains infecting multiple host strains. Generally, these exhibit chaos with increasingly wild population fluctuations driving extinctions. But the simplest spatial structure, many identical islands with migration between them, stabilizes a diverse chaotic state. Some strains (subspecies) go globally extinct, but many persist for times exponentially long in the number of islands. All persistent strains have episodic local blooms to high abundance, crucial for their persistence as, for many, their average population growth rate is negative. Snapshots of the abundance distribution show a power law at intermediate abundances that is essentially indistinguishable from the neutral theory of ecology. But the dynamics of the large populations are much faster than birth-death fluctuations. We argue that this spatiotemporally chaotic "phase" should exist in a wide range of models, and that even in rapidly mixed systems, longer-lived spores could similarly stabilize a diverse chaotic phase.

Microbial plankton configuration in the epipelagic realm from the Beagle Channel to the Burdwood Bank, a Marine Protected Area in Sub-Antarctic waters

Marine microbial plankton hold high structural and functional diversity, however, high-resolution data are lacking in a large part of the Global Ocean, such as in subpolar areas of the SW Atlantic. The Burdwood Bank (BB) is a submerged plateau (average depth 100 m) that constitutes the westernmost segment of the North Scotia Ridge (54°-55°S; 56°-62°W). The BB hosts rich benthic biodiversity in low chlorophyll waters of the southern Patagonian Shelf, Argentina, declared Namuncurá Marine Protected Area (NMPA) in 2013. So far, the pelagic microorganisms above the bank have not been described. During austral summer 2016, we assessed the microbial plankton (0.2-200 μm cell size) biomass and their taxonomical and functional diversity along a longitudinal transect (54.2-55.3°S, 58-68°W) from the Beagle Channel (BC) to the BB, characterized by contrasting hydrography. Results displayed a marked zonation in the composition and structure of the microbial communities. The biomass of phytoplankton >5 μm was 28 times higher in the BC, attributed mainly to large diatom blooms, than in oceanic waters above the BB, where the small coccolithophore Emiliania huxleyi and flagellates <10 μm dominated. In turn, the biomass of microheterotrophs above the BB doubled the biomass in the BC due to large ciliates. Notably, toxic phytoplankton species and their phycotoxins were detected, in particular high abundance of Dinophysis acuminata and pectenotoxins above the bank, highlighting their presence in open subpolar regions. Picophytoplankton (<2 μm), including Synechococcus and picoeukaryotes, were remarkably important above the BB, both at surface and deep waters (up to 150 m). Their biomass surpassed by 5 times that of phytoplankton > 5 μm, emphasizing the importance of small-sized phytoplankton in low chlorophyll waters. The homogeneous water column and high retention above the bank seem to favor the development of abundant picophytoplankton and microzooplankton communities. Overall, our findings unfold the plankton configuration in the Southern Patagonian Shelf, ascribed as a sink for anthropogenic CO2, and highlight the diverse ecological traits that microorganisms develop to adjust their yield to changing conditions.

Numerical modelling of the effect of intermittent upwelling events on plankton blooms

In the marine environment, biological processes are strongly affected by oceanic currents, particularly by eddies (vortices) formed by the hydrodynamic flow field. Employing a kinematic flow field coupled to a population dynamical model for plankton growth, we study the impact of an intermittent upwelling of nutrients on triggering harmful algal blooms (HABs). Though it is widely believed that additional nutrients boost the formation of HABs or algal blooms in general, we show that the response of the plankton to nutrient plumes depends crucially on the mesoscale hydrodynamic flow structure. In general, nutrients can either be quickly washed out from the observation area, or can be captured by the vortices in the flow. The occurrence of either scenario depends on the relation between the time scales of the vortex formation and nutrient upwelling as well as the time instants at which upwelling pulses occur and how long they last. We show that these two scenarios result in very different responses in plankton dynamics which makes it very difficult to predict whether nutrient upwelling will lead to a HAB or not. This may in part explain why observational data are sometimes inconclusive in establishing a connection between upwelling events and plankton blooms.

Discrete Eulerian model for population genetics and dynamics under flow

Marine species reproduce and compete while being advected by turbulent flows. It is largely unknown, both theoretically and experimentally, how population dynamics and genetics are changed by the presence of fluid flows. Discrete agent-based simulations in continuous space allow for accurate treatment of advection and number fluctuations, but can be computationally expensive for even modest organism densities. In this report, we propose an algorithm to overcome some of these challenges. We first provide a thorough validation of the algorithm in one and two dimensions without flow. Next, we focus on the case of weakly compressible flows in two dimensions. This models organisms such as phytoplankton living at a specific depth in the three-dimensional, incompressible ocean experiencing upwelling and/or downwelling events. We show that organisms born at sources in a two-dimensional time-independent flow experience an increase in fixation probability.

Surface mixing and biological activity in the North-West African upwelling

Near-shore water along the North-West African margin is one of the world's major upwelling regions. It is associated with physical structures of oceanic fronts which influence the biological productivity. The study of these coherent structures in connection with chlorophyll concentration data is of fundamental importance for understanding the spatial distributions of the plankton. In this work, we study the horizontal stirring and mixing in different upwelling areas using Lagrangian coherent structures (LCSs). These LCSs are calculated using the recent geodesic theory of LCSs. We use these LCSs to study the link between the chlorophyll fronts concentrations and surface mixing, based on 10 years of satellite data. These LCSs move with the flow as material lines, thus the horizontal mixing is calculated from the intersection of these LCSs with the finite time Lyapunov exponent maps. We compare our results with those of a recent study conducted over the same area, but based on finite size Lyapunov exponents (FSLEs), whose output is a plot of scalar distributions. We discuss the differences between FSLE and geodesic theory of LCS. The latter yields analytical solutions of LCSs, while FSLEs can only provide LCSs for sharp enough ridges of nearly constant height.

Fixation probabilities in weakly compressible fluid flows

Competition between biological species in marine environments is affected by the motion of the surrounding fluid. An effective 2D compressibility can arise, for example, from the convergence and divergence of water masses at the depth at which passively traveling photosynthetic organisms are restricted to live. In this report, we seek to quantitatively study genetics under flow. To this end, we couple an off-lattice agent-based simulation of two populations in 1D to a weakly compressible velocity field-first a sine wave and then a shell model of turbulence. We find for both cases that even in a regime where the overall population structure is approximately unaltered, the flow can significantly diminish the effect of a selective advantage on fixation probabilities. We understand this effect in terms of the enhanced survival of organisms born at sources in the flow and the influence of Fisher genetic waves.

The role of submesoscale currents in structuring marine ecosystems

From microbes to large predators, there is increasing evidence that marine life is shaped by short-lived submesoscales currents that are difficult to observe, model, and explain theoretically. Whether and how these intense three-dimensional currents structure the productivity and diversity of marine ecosystems is a subject of active debate. Our synthesis of observations and models suggests that the shallow penetration of submesoscale vertical currents might limit their impact on productivity, though ecological interactions at the submesoscale may be important in structuring oceanic biodiversity.

Short-lived three-dimensional submesoscale currents, responsible for swirling ocean color chlorophyll filaments, have long been thought to affect productivity. Current research suggests they may not be effective in enhancing phytoplankton growth, but may have important contributions to biodiversity.

Mesoscale activity facilitates energy gain in a top predator

How animal movement decisions interact with the distribution of resources to shape individual performance is a key question in ecology. However, links between spatial and behavioural ecology and fitness consequences are poorly understood because the outcomes of individual resource selection decisions, such as energy intake, are rarely measured. In the open ocean, mesoscale features (approx. 10-100 km) such as fronts and eddies can aggregate prey and thereby drive the distribution of foraging vertebrates through bottom-up biophysical coupling. These productive features are known to attract predators, yet their role in facilitating energy transfer to top-level consumers is opaque. We investigated the use of mesoscale features by migrating northern elephant seals and quantified the corresponding energetic gains from the seals' foraging patterns at a daily resolution. Migrating elephant seals modified their diving behaviour and selected for mesoscale features when foraging. Daily energy gain increased significantly with increasing mesoscale activity, indicating that the physical environment can influence predator fitness at fine temporal scales. Results show that areas of high mesoscale activity not only attract top predators as foraging hotspots, but also lead to increased energy transfer across trophic levels. Our study provides evidence that the physical environment is an important factor in controlling energy flow to top predators by setting the stage for variation in resource availability. Such understanding is critical for assessing how changes in the environment and resource distribution will affect individual fitness and food web dynamics.

Estimating stable and unstable sets and their role as transport barriers in stochastic flows

We consider the situation of a large-scale stationary flow subjected to small-scale fluctuations. Assuming that the stable and unstable manifolds of the large-scale flow are known, we quantify the mean behavior and stochastic fluctuations of particles close to the unperturbed stable and unstable manifolds and their evolution in time. The mean defines a smooth curve in physical space, while the variance provides a time- and space-dependent quantitative estimate where particles are likely to be found. This allows us to quantify transport properties such as the expected volume of mixing as the result of the stochastic fluctuations of the transport barriers. We corroborate our analytical findings with numerical simulations in both compressible and incompressible flow situations. We moreover demonstrate the intimate connection of our results with finite-time Lyapunov exponent fields, and with spatial mixing regions.

Front tracking velocimetry in advection-reaction-diffusion systems

In advection-reaction-diffusion systems, the spreading of a reactive scalar can be significantly influenced by the flow field in which it grows. In systems with sharp boundaries between reacted and unreacted regions, motion of the reaction fronts that lie at those boundaries can quantify spreading. Here, we present an algorithm for measuring the velocity of reaction fronts in the presence of flow, expanding previous work on tracking reaction fronts without flow. The algorithm provides localized measurements of front speed and can distinguish its two components: one from chemical dynamics and another from the underlying flow. We validate that the algorithm returns the expected front velocity components in two simulations and then show that in complex experimental flows, the measured front velocity maps fronts from one time step to the next self-consistently. Finally, we observe a variation of the chemical speed with flow speed in a variety of experiments with different time scales and length scales.

A Satellite-Based Lagrangian View on Phytoplankton Dynamics

The well-lit upper layer of the open ocean is a dynamical environment that hosts approximately half of global primary production. In the remote parts of this environment, distant from the coast and from the seabed, there is no obvious spatially fixed reference frame for describing the dynamics of the microscopic drifting organisms responsible for this immense production of organic matter-the phytoplankton. Thus, a natural perspective for studying phytoplankton dynamics is to follow the trajectories of water parcels in which the organisms are embedded. With the advent of satellite oceanography, this Lagrangian perspective has provided valuable information on different aspects of phytoplankton dynamics, including bloom initiation and termination, spatial distribution patterns, biodiversity, export of carbon to the deep ocean, and, more recently, bottom-up mechanisms that affect the distribution and behavior of higher-trophic-level organisms. Upcoming submesoscale-resolving satellite observations and swarms of autonomous platforms open the way to the integration of vertical dynamics into the Lagrangian view of phytoplankton dynamics.

Optimal stretching in the reacting wake of a bluff body

We experimentally study spreading of the Belousov-Zhabotinsky reaction behind a bluff body in a laminar flow. Locations of reacted regions (i.e., regions with high product concentration) correlate with a moderate range of Lagrangian stretching and that range is close to the range of optimal stretching previously observed in topologically different flows [T. D. Nevins and D. H. Kelley, Phys. Rev. Lett. 117, 164502 (2016)]. The previous work found optimal stretching in a closed, vortex dominated flow, but this article uses an open flow and only a small area of appreciable vorticity. We hypothesize that optimal stretching is common in advection-reaction-diffusion systems with an excitation threshold, including excitable and bistable systems, and that the optimal range depends on reaction chemistry and not on flow shape or characteristic speed. Our results may also give insight into plankton blooms behind islands in ocean currents.

The Implications of Eco-Evolutionary Processes for the Emergence of Marine Plankton Community Biogeography

Models of community assembly have been used to illustrate how the many functionally diverse species that compose plankton food webs can coexist. However, the evolutionary processes leading to the emergence of plankton food webs and their interplay with migratory processes and spatial heterogeneity are yet to be explored. We study the eco-evolutionary dynamics of a modeled plankton community structured in both size and space and physiologically constrained by empirical data. We demonstrate that a complex yet ecologically and evolutionarily stable size-structured food web can emerge from an initial set of two monomorphic phytoplankton and zooplankton populations. We also show that the coupling of spatial heterogeneity and migration results in the emergence of specific biogeographic patterns: (i) the emergence of a source-sink structure of the plankton metacommunities, (ii) changes in size diversity dependent on migratory intensity and on the scale at which diversity is considered (local vs. global), and (iii) the emergence of eco-evolutionary provinces (i.e., a spatial unit characterized by some level of abiotic heterogeneity but of homogenous size composition due to horizontal movements) at spatial scales that increase with the strength of the migratory processes.

Recent progress in diatom genomics and epigenomics

Diatoms are one of the most diverse and successful groups of phytoplankton at the base of the food chain, sustaining life in the ocean and performing vital biogeochemical functions. The last fifteen years have witnessed the comprehensive analysis of several diatom genomes, revealing that they bear traces of their endosymbiotic origins from algal and heterotrophic ancestors, as well as significant gene transfer from bacteria. Their chimeric genomes are further regulated by a range of chromatin-based processes that are characteristic of both plant and animal genomes. We discuss the conservation of gene regulatory mechanisms in diatoms and propose that epigenetic processes may have a significant role in mediating responses to a highly dynamic and unpredictable environment in these organisms.

Dispersion/dilution enhances phytoplankton blooms in low-nutrient waters

Spatial characteristics of phytoplankton blooms often reflect the horizontal transport properties of the oceanic turbulent flow in which they are embedded. Classically, bloom response to horizontal stirring is regarded in terms of generation of patchiness following large-scale bloom initiation. Here, using satellite observations from the North Pacific Subtropical Gyre and a simple ecosystem model, we show that the opposite scenario of turbulence dispersing and diluting fine-scale (∼1–100 km) nutrient-enriched water patches has the critical effect of regulating the dynamics of nutrients–phytoplankton–zooplankton ecosystems and enhancing accumulation of photosynthetic biomass in low-nutrient oceanic environments. A key factor in determining ecological and biogeochemical consequences of turbulent stirring is the horizontal dilution rate, which depends on the effective eddy diffusivity and surface area of the enriched patches. Implementation of the notion of horizontal dilution rate explains quantitatively plankton response to turbulence and improves our ability to represent ecological and biogeochemical processes in oligotrophic oceans.

The degree to which horizontal transport affects phytoplankton ecosystems remains understudied. Here, the authors combine satellite observations, ARGO float data and a simple ecosystem model to explore the impact of horizontal stirring on naturally-stimulated fine-scale phytoplankton blooms.

Optimal Stretching in Advection-Reaction-Diffusion Systems

We investigate growth of the excitable Belousov-Zhabotinsky reaction in chaotic, time-varying flows. In slow flows, reacted regions tend to lie near vortex edges, whereas fast flows restrict reacted regions to vortex cores. We show that reacted regions travel toward vortex centers faster as flow speed increases, but nonreactive scalars do not. For either slow or fast flows, reaction is promoted by the same optimal range of the local advective stretching, but stronger stretching causes reaction blowout and can hinder reaction from spreading. We hypothesize that optimal stretching and blowout occur in many advection-diffusion-reaction systems, perhaps creating ecological niches for phytoplankton in the ocean.

Dimensionality matters in the collective behaviour of active emulsions

The behaviour of artificial microswimmers consisting of droplets of a mesogenic oil immersed in an aqueous surfactant solution depends qualitatively on the conditions of dimensional confinement; ranging from only transient aggregates in Hele-Shaw geometries to hexagonally packed, convection-driven clusters when sedimenting in an unconfined reservoir. We study the effects of varying the swimmer velocity, the height of the reservoir, and the buoyancy of the droplet swimmers. Two simple adjustments of the experimental setting lead to a suppression of clustering: either a decrease of the reservoir height below a certain value, or a match of the densities of droplets and surrounding phase, showing that the convection is the key mechanism for the clustering behaviour.

Estimating planktonic diversity through spatial dominance patterns in a model ocean

In the open ocean, the observation and quantification of biodiversity patterns is challenging. Marine ecosystems are indeed largely composed by microbial planktonic communities whose niches are affected by highly dynamical physico-chemical conditions, and whose observation requires advanced methods for morphological and molecular classification. Optical remote sensing offers an appealing complement to these in-situ techniques. Global-scale coverage at high spatiotemporal resolution is however achieved at the cost of restrained information on the local assemblage. Here, we use a coupled physical and ecological model ocean simulation to explore one possible metrics for comparing measures performed on such different scales. We show that a large part of the local diversity of the virtual plankton ecosystem - corresponding to what accessible by genomic methods - can be inferred from crude, but spatially extended, information - as conveyed by remote sensing. Shannon diversity of the local community is indeed highly correlated to a 'seascape' index, which quantifies the surrounding spatial heterogeneity of the most abundant functional group. The error implied in drastically reducing the resolution of the plankton community is shown to be smaller in frontal regions as well as in regions of intermediate turbulent energy. On the spatial scale of hundreds of kms, patterns of virtual plankton diversity are thus largely sustained by mixing communities that occupy adjacent niches. We provide a proof of principle that in the open ocean information on spatial variability of communities can compensate for limited local knowledge, suggesting the possibility of integrating in-situ and satellite observations to monitor biodiversity distribution at the global scale.

Plankton dynamics and biogeochemical fluxes in the Costa Rica Dome: introduction to the CRD Flux and Zinc Experiments

The Costa Rica Dome (CRD) is an open-ocean upwelling system in the Eastern Tropical Pacific that overlies the ocean's largest oxygen minimum zone (OMZ). The region has unique characteristics, biomass dominance by picophytoplankton, suppressed diatoms, high biomass of higher consumers and presumptive trace metal limitation, but is poorly understood in terms of pelagic stock and process relationships, including productivity and production controls. Here, we describe the goals, project design, physical context and major findings of the Flux and Zinc Experiments cruise conducted in June-July 2010 to assess trophic flux relationships and elemental controls on phytoplankton in the CRD. Despite sampling during a year of suppressed summertime surface chlorophyll, cruise results show high productivity (∼1 g C m^-2 day^-1), high new production relative to export, balanced production and grazing, disproportionate biomass-specific productivity of large phytoplankton and high zooplankton stocks. Zinc concentrations are low in surface waters relative to phosphorous and silicate in other regions, providing conditions conducive to picophytoplankton, like Synechococcus, with low Zn requirements. Experiments nonetheless highlight phytoplankton limitation or co-limitation by silicic acid, driven by a strong silica pump that is linked to low dissolution of biogenic silica in the cold shallow thermocline of the lower euphotic zone.