Léo Berline

Determinants of community structure in the global plankton interactome

Species interaction networks are shaped by abiotic and biotic factors. Here, as part of the Tara Oceans project, we studied the photic zone interactome using environmental factors and organismal abundance profiles and found that environmental factors are incomplete predictors of community structure. We found associations across plankton functional types and phylogenetic groups to be nonrandomly distributed on the network and driven by both local and global patterns. We identified interactions among grazers, primary producers, viruses, and (mainly parasitic) symbionts and validated network-generated hypotheses using microscopy to confirm symbiotic relationships. We have thus provided a resource to support further research on ocean food webs and integrating biological components into ocean models.

Plankton networks driving carbon export in the oligotrophic ocean.

The biological carbon pump is the process by which CO2 is transformed to organic carbon via photosynthesis, exported through sinking particles, and finally sequestered in the deep ocean. While the intensity of the pump correlates with plankton community composition, the underlying ecosystem structure driving the process remains largely uncharacterized. Here we use environmental and metagenomic data gathered during the Tara Oceans expedition to improve our understanding of carbon export in the oligotrophic ocean. We show that specific plankton communities, from the surface and deep chlorophyll maximum, correlate with carbon export at 150 m and highlight unexpected taxa such as Radiolaria and alveolate parasites, as well as Synechococcus and their phages, as lineages most strongly associated with carbon export in the subtropical, nutrient-depleted, oligotrophic ocean. Additionally, we show that the relative abundance of a few bacterial and viral genes can predict a significant fraction of the variability in carbon export in these regions.

Incremental Analysis Update Implementation into a Sequential Ocean Data Assimilation System

This study deals with the enhancement of a sequential assimilation method applied to an ocean general circulation model (OGCM). A major drawback of sequential assimilation methods is the time discontinuity of the solution resulting from intermittent corrections of the model state. The data analysis step can induce shocks in the model restart phase, causing spurious high-frequency oscillations and data rejection. A method called Incremental Analysis Update (IAU) is now recognized to efficiently tackle these problems. In the present work, an IAU-type method is implemented into an intermittent data assimilation system using a low-rank Kalman filter [Singular Evolutive Extended Kalman (SEEK)] in the case of an OGCM with a 1/3° North Atlantic grid. A 1-yr (1993) experiment has been conducted for different setups in order to evaluate the impact of the IAU scheme. Results from all of the different tests are compared with a specific interest in high-frequency output behaviors and solution consistency. The improvements brought up by the IAU implementation, such as the disappearance of spurious high-frequency oscillations and the time continuity of the solution, are shown. An overall assessment of the impact of this new approach on the assimilated runs is discussed. Advantages and drawbacks of the IAU method are pointed out.

Modeling jellyfish Pelagia noctiluca transport and stranding in the Ligurian Sea.

Jellyfish blooms are generally attributed to a biological response to the environment, neglecting the role of transport patterns in redistributing existing populations. Here, we use high-resolution (1.25km) ocean modeling to examine the role of transport in the onshore arrival and abundance of the pelagic stinging jellyfish Pelagia noctiluca on the Ligurian Sea coast. Jellyfish are modeled as Lagrangian particles with a 0-300-m diel vertical migration typical of P. noctiluca. Over the course of a year, onshore arrivals are not restricted to the summer. Arrivals are concentrated at capes, but abundance can reach maxima in bays and in the lee of capes. Two factors impact jellyfish arrivals at the coast: the position of the Northern Current and the wind. A comparison of summer 2006 and available onshore jellyfish observations suggests a correct capture of the main stranding events by the model. These results have implications for understanding long-term fluctuations.

A Connectivity-Based Eco-Regionalization Method of the Mediterranean Sea

Ecoregionalization of the ocean is a necessary step for spatial management of marine resources. Previous ecoregionalization efforts were based either on the distribution of species or on the distribution of physical and biogeochemical properties. These approaches ignore the dispersal of species by oceanic circulation that can connect regions and isolates others. This dispersal effect can be quantified through connectivity that is the probability, or time of transport between distinct regions. Here a new regionalization method based on a connectivity approach is described and applied to the Mediterranean Sea. This method is based on an ensemble of Lagrangian particle numerical simulations using ocean model outputs at 1/12° resolution. The domain is divided into square subregions of 50 km size. Then particle trajectories are used to quantify the oceanographic distance between each subregions, here defined as the mean connection time. Finally the oceanographic distance matrix is used as a basis for a hierarchical clustering. 22 regions are retained and discussed together with a quantification of the stability of boundaries between regions. Identified regions are generally consistent with the general circulation with boundaries located along current jets or surrounding gyres patterns. Regions are discussed in the light of existing ecoregionalizations and available knowledge on plankton distributions. This objective method complements static regionalization approaches based on the environmental niche concept and can be applied to any oceanic region at any scale.

Deep sediment resuspension and thick nepheloid layer generation by open-ocean convection

The Gulf of Lions in the northwestern Mediterranean is one of the few sites around the world ocean exhibiting deep open-ocean convection. Based on 6-year long (2009-2015) time series from a mooring in the convection region, shipborne measurements from repeated cruises, from 2012 to 2015, and glider measurements, we report evidence of bottom thick nepheloid layer formation, which is coincident with deep sediment resuspension induced by bottom-reaching convection events. This bottom nepheloid layer, which presents a maximum thickness of around 2000 m in the center of the convection region, probably results from the action of cyclonic eddies that are formed during the convection period and can persist within their core while they travel through the basin. The residence time of this bottom nepheloid layer appears to be less than a year. In-situ measurements of suspended particle size further indicate that the bottom nepheloid layer is primarily composed of aggregates between 100 and 1000 µm in diameter, probably constituted of fine silts. Bottom-reaching open ocean convection, as well as deep dense shelf water cascading that occurred concurrently some years, lead to recurring deep sediments resuspension episodes. They are key mechanisms that control the concentration and characteristics of the suspended particulate matter in the basin, and in turn affect the bathypelagic biological activity

New insights into global biogeography, population structure and natural selection from the genome of the epipelagic copepod Oithona

In the epipelagic ocean, the genus Oithona is considered as one of the most abundant and widespread copepods and plays an important role in the trophic food web. Despite its ecological importance, little is known about Oithona and cyclopoid copepods genomics. Therefore, we sequenced, assembled and annotated the genome of Oithona nana. The comparative genomic analysis integrating available copepod genomes highlighted the expansions of genes related to stress response, cell differentiation and development, including genes coding Lin12‐Notch‐repeat (LNR) domain proteins. The Oithona biogeography based on 28S sequences and metagenomic reads from the Tara Oceans expedition showed the presence of O. nana mostly in the Mediterranean Sea (MS) and confirmed the amphitropical distribution of Oithona similis. The population genomics analyses of O. nana in the Northern MS, integrating the Tara Oceans metagenomic data and the O. nana genome, led to the identification of genetic structure between populations from the MS basins. Furthermore, 20 loci were found to be under positive selection including four missense and eight synonymous variants, harbouring soft or hard selective sweep patterns. One of the missense variants was localized in the LNR domain of the coding region of a male‐specific gene. The variation in the B‐allele frequency with respect to the MS circulation pattern showed the presence of genomic clines between O. nana and another undefined Oithona species possibly imported through Atlantic waters. This study provides new approaches and results in zooplankton population genomics through the integration of metagenomic and oceanographic data.

Variability of the Gulf Stream position and transport between 1992 and 1999: a re‐analysis based on a data assimilation experiment

A multivariate dataset resulting from the assimilation of sea surface height and sea surface temperature data in an ocean circulation model of the North Atlantic, is used to study the Gulf Stream position variability from October 1992 to October 1999. The analysis takes place between 75° W and 50° W and focuses on two regions, west and east of 65° W. By calculating zonal averages of the latitudinal position, a regular annual cycle of north–south oscillations of the Gulf Stream axis is identified in the eastern region, whereas inter‐annual variations dominate in the western region. An empirical orthogonal function (EOF) analysis of space–time position anomalies reveals that, even though the annual cycle dominates over the whole domain, the variability has a spatial consistency within each individual region. The assimilation dataset is further used to analyse the variability of the Gulf Stream transport towards the east. Compared to the latitudinal position analysis, the characterization of the transport variability is more complex. Semi‐annual fluctuations can be evidenced in both the regions; however, no significant correlation was found between the fluctuations of position and transport.