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54
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Introduction
Sakina-Dorothée Ayata is Associate Professor at Sorbonne Université in France. She currently works at the Laboratoire d'Océanographie de Villefranche-sur-mer, where she does research in marine ecology and ecosystem modelling of plankton communities.
Additional affiliations
September 2012 - present
Publications
Publications (54)
AbstractThe aim of this study is to evaluate the consequences of accounting for variable Chl:C (chlorophyll:carbon) and C:N (carbon:nitrogen) ratios in the formulation of phytoplankton growth in biogeochemical models. We compare the qualitative behaviour of a suite of phytoplankton growth formulations with increasing complexity: 1) a Redfield formu...
For many marine species, larval dispersal plays a crucial role in population persistence, re-colonization of disturbed areas, and distribution of species range limits through the control of population connectivity. Along the French Atlantic coast (NE Atlantic), a biogeographical transition zone has been reported between temperate and cold-temperate...
The honeycomb worm Sabellaria alveolata forms biogenic reefs which constitute diversity hotspots on tidal flats. The largest known reefs in Europe, located in the Bay of Mont-Saint-Michel (English Channel), are suffering increasing anthropogenic disturbances which raise the question of their sustainability. As the ability to recover depends partly...
Carbon fixation is a key metabolic function shaping marine life, but the underlying taxonomic and functional diversity involved is only partially understood. Using metagenomic resources targeted at marine piconanoplankton, we provide a reproducible machine learning framework to derive the potential biogeography of genomic functions through the mult...
Imaging is increasingly used to capture information on the marine environment thanks to the improvements in imaging equipment, devices for carrying cameras and data storage in recent years. In that context, biologists, geologists, computer specialists and end-users must gather to discuss the methods and procedures for optimising the quality and qua...
Mesozooplankton is a very diverse group of small animals ranging in size from 0.2 to 20 mm not able to swim against ocean currents. It is a key component of pelagic ecosystems through its roles in the trophic networks and the biological carbon pump. Traditionally studied through microscopes, recent methods have been however developed to rapidly acq...
Biodiversity is studied notably because of its reciprocal relationship with ecosystem functions such as production. Diversity is traditionally described from a taxonomic, genetic or functional point of view but the diversity in organism morphology is seldom explicitly considered, except for body size. We describe morphological diversity of marine z...
In Arctic marine ecosystems, large planktonic copepods form a crucial hub of matter and energy. Their energy-rich lipid stores play a central role in marine trophic networks and the biological carbon pump. Since the past ~15 years, in situ imaging devices provide images whose resolution allows us to estimate an individual copepod’s lipid sac volume...
Primary production, performed by RUBISCO, and often associated with carbon concentration mechanisms, is of major importance in the oceans. Thanks to growing metagenomic resources (e.g., eukaryotic Metagenome-Assembled-Genomes; MAGs), we provide the first reproducible machine-learning-based framework to derive the potential biogeography of a given f...
Abstract Pigmentation is often overlooked in zooplankton, since these organisms are mostly colorless to fit the translucid water medium. However, one of the dominant zooplankton taxa in aquatic ecosystems—copepods—often show a bright red‐orange or blue coloration owing to the accumulation of carotenoid pigments in some parts of their bodies. Even t...
Marine protists are major components of the oceanic microbiome that remain largely unrepresented in culture collections and genomic reference databases. The exploration of this uncharted protist diversity in oceanic communities relies essentially on studying genetic markers from the environment as taxonomic barcodes. Here we report that across 6 la...
For more than a decade, high‐throughput sequencing has transformed the study of marine planktonic communities and has highlighted the extent of protist diversity in these ecosystems. Nevertheless, little is known relative to their genomic diversity at the species‐scale as well as their major speciation mechanisms. An increasing number of data obtai...
Functional traits are increasingly used to assess changes in phytoplankton community structure and to link individual characteristics to ecosystem functioning. However, they are usually inferred from taxonomic identification or manually measured for each organism, both time consuming approaches. Instead, we focus on high throughput imaging to descr...
Plankton imaging systems supported by automated classification and analysis have improved ecologists' ability to observe aquatic ecosystems. Today, we are on the cusp of reliably tracking plankton populations with a suite of lab‐based and in situ tools, collecting imaging data at unprecedentedly fine spatial and temporal scales. But these data have...
Quantitative imaging instruments produce a large number of images of plankton and marine snow, acquired in a controlled manner, from which the visual characteristics of individual objects and their in situ concentrations can be computed. To exploit this wealth of information, machine learning is necessary to automate tasks such as taxonomic classif...
Vertical variations in physical and chemical conditions drive changes in marine zooplankton community composition. In turn, zooplankton communities play a critical role in regulating the transfer of organic matter produced in the surface ocean to deeper layers. Yet, the links between zooplankton community composition and the strength of vertical fl...
Marine microbes play a crucial role in climate regulation, biogeochemical cycles, and trophic networks. Unprecedented amounts of data on planktonic communities were recently collected, sparking a need for innovative data-driven methodologies to quantify and predict their ecosystemic functions. We reanalyze 885 marine metagenome-assembled genomes th...
Imaging techniques are increasingly used in ecology studies, producing vast quantities of data. Inferring functional
traits from individual images can provide original insights on ecosystem processes. Morphological traits are,
as other functional traits, individual characteristics influencing an organism’s fitness. We measured them from in
situ ima...
Aquatic ecologists face challenges in identifying the general rules of the functioning of ecosystems. A common framework, including freshwater, marine, benthic, and pelagic ecologists, is needed to bridge communication gaps and foster knowledge sharing. This framework should transcend local specificities and taxonomy in order to provide a common gr...
In this paper we review the technologies available to make globally quantitative observations of particles in general—and plankton in particular—in the world oceans, and for sizes varying from sub-microns to centimeters. Some of these technologies have been available for years while others have only recently emerged. Use of these technologies is cr...
Mixotrophy, or the ability to acquire carbon from both auto- and heterotrophy, is a widespread ecological trait in marine protists. Using a metabarcoding dataset of marine plankton from the global ocean, 318,054 mixotrophic metabarcodes represented by 89,951,866 sequences and belonging to 133 taxonomic lineages were identified and classified into f...
Aquatic ecologists face a common challenge: identifying the general rules of the functioning of aquatic ecosystems and developing a more predictive ecological understanding. However, freshwater and marine ecologists traditionally form two distinct scientific communities that barely communicate with each other. A common language is needed to foster...
Aim
To assess the impact of climate change on the functional diversity of marine zooplankton communities.
Location
The Mediterranean Sea.
Methods
We used the functional traits and geographic distributions of 106 copepod species to estimate the zooplankton functional diversity of Mediterranean surface assemblages for the 1965–1994 and 2069–2098 pe...
Aim
To assess the degree of overlap between the environmental niches of marine planktonic copepods and test if the distribution of copepod functional groups differs across environmental gradients.
Location
The Mediterranean Sea.
Methods
Functional groups were defined based on clustering of functional traits in 106 marine copepod species using a m...
Regionalisation aims at delimiting provinces within which physical conditions, chemical properties, and biological communities are reasonably homogeneous. This article proposes a synthesis of the many recent regionalisations of the open-sea regions of the Mediterranean Sea. The nine studies considered here defined regions based on different, and so...
With global climate change altering marine ecosystems, research on plankton ecology is likely to navigate uncharted seas. Yet, a staggering wealth of new plankton observations, integrated with recent advances in marine ecosystem modeling, may shed light on marine ecosystem structure and functioning. A EuroMarine foresight workshop on the “Impact of...
Distribution of each BGCR on a 0.2° grid
Depth of the Epi/meso, meso/bathy, and bottom on 0.2° grid
Ensemble niche modelling has become a common framework to predict changes in assemblages composition under climate change scenarios. The amount of uncertainty generated by the different components of this framework has rarely been assessed. In the marine realm forecasts have usually focused on taxa representing the top of the marine food-web, thus...
Information on the functional traits was gathered for the most commonly-sampled copepod species of the Mediterranean Sea. Our database includes 191 species described by 7 traits encompassing diverse ecological functions: minimal and maximal body length (mm), trophic group (Omnivore/Carnivore/Herbivore/Detritivore), feeding type (Cruise-feeding/Filt...
We gathered information on the functional traits of the most representative copepod species in the Mediterranean Sea. Our
database includes 191 species described by 7 traits encompassing diverse ecological functions: minimal and maximal body length,
trophic group, feeding type, spawning strategy, diel vertical migration and vertical habitat. Cluste...
PERSEUS project aims to identify the most relevant pressures exerted on the ecosystems of the Southern European Seas (SES), highlighting knowledge and data gaps that endanger the achievement of SES Good Environmental Status (GES) as mandated by the Marine Strategy Framework Directive (MSFD). A complementary approach has been adopted, by a meta-anal...
Phytoplankton are ectotherms and are thus directly influenced by temperature. They experience temporal variation in temperature which results in a selection pressure. Using the Adaptive Dynamics theory and an optimization method, we study phytoplankton thermal adaptation (more particulary the evolution of the optimal growth temperature) to temperat...
In recent decades, it has been found useful to partition the ocean using the concept of
ecoregionalisation where within each region it is assumed that environmental conditions and
species associations are distinguishable and unique. Indeed, all partitions of the ocean that has
been proposed aimed to delineate the main oceanographical, ecological pa...
Phytoplankton C:N stoichiometry is highly flexible due to physiological plasticity, which could lead to high variations in carbon fixation efficiency (carbon consumption relatively to nitrogen). However, the magnitude, as well as the spatial and temporal scales of variability, remain poorly constrained. We used a high resolution biogeochemical mode...
In recent decades, it has been found useful to ecoregionalise the pelagic environment assuming that within each partition environmental conditions are distinguishable and unique. Indeed, each partition of the ocean that is proposed aimed to delineate the main oceanographical and ecological patterns to provide a geographical framework of marine ecos...
The relationship between meroplankton distribution and spatio-temporal variability of coastal mesoscale hydrological structure
was investigated in the northern Bay of Biscay, North-East Atlantic. For the three coastal polychaetes studied, i.e. Pectinaria koreni, Owenia fusiformis and Sabellaria alveolata, the highest larval abundances were sampled...
Climate may act on the dispersal and connectivity of marine populations through changes in the oceanic circulation and temperature, and by modifying species’ prey and predator distributions. As dispersal and connectivity remain difficult to assess in situ, a first step in studying the effects of climate change can be achieved using biophysical mode...
Human-mediated transport and aquaculture have promoted the establishment of non-indigenous species in many estuaries around
the world over the last century. This phenomenon has been demonstrated as a major cause of biodiversity alterations, which
has prompted scientists to provide explanations for the success or failure of biological invasions. Cre...
By ensuring the dispersal, the larval phase plays a fundamental role in the population dynamics of benthic invertebrates with a complex life cycle and determines the connectivity within marine metapopulations. Hence, the connectivity influences directly the dynamics of metapopulations and the persistence of local populations, the expansion abilitie...
En assurant la dispersion, la phase larvaire joue un role fondamental dans la dynamique des populations d'invertébrés marins à cycle de vie bentho-pélagique et détermine la connectivité au sein des métapopulations marines. La connectivité en milieu marin influence ainsi directement la dynamique des métapopulations et la persistance des populations...
