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Agulhas rings provide the principal route for ocean waters to circulate from the Indo-Pacific to the Atlantic basin. Their influence on global ocean circulation is well known, but their role in plankton transport is largely unexplored. We show that, although the coarse taxonomic structure of plankton communities is continuous across the Agulhas choke point, South Atlantic plankton diversity is altered compared with Indian Ocean source populations. Modeling and in situ sampling of a young Agulhas ring indicate that strong vertical mixing drives complex nitrogen cycling, shaping community metabolism and biogeochemical signatures as the ring and associated plankton transit westward. The peculiar local environment inside Agulhas rings may provide a selective mechanism contributing to the limited dispersal of Indian Ocean plankton populations into the Atlantic.

Accompanying material, text, data and figures for the article de Vargas et al., 'Eukaryotic plankton diversity in the sunlit ocean', Science 348, 1261605 (2015), doi: 10.1126/science.1261605

Les dinoflagellés forment un groupe complexe de protistes avec une grande diversité de morphologies, physiologies, et cycles de vies qui leur confèrent une forte capacité d'adaptation à l'ensemble des milieux (marins et dulçaquicoles) et habitats (pélagiques et benthiques) aquatiques rendant difficile l¿étude de leur diversité et de leur écologie. L'objectif de cette thèse a été la recherche de patrons globaux de biodiversité et de structuration des communautés de dinoflagellés pélagiques marins à l'échelle planétaire. Un protocole d'échantillonnage morphogénétique, couvrant la totalité de leur spectre de taille et une partie importante de leurs variabilités spatio-temporelles, a été développé (Tara-Oceans). Divers outils d'acquisition automatique à haut débit des données ont été testés. La diversité, l'abondance relative et la distribution géographique des espèces du genre Neoceratium ont été évaluées en mer Méditerranée par FlowCAM. Une étude de la structuration de la biodiversité a été réalisée par metabarcoding de l¿ADNr 18S (fragment V9). La construction d'une base de séquences ADNr de référence (DinR2) a permis l¿assignation taxonomique des metabarcodes environnementaux. L¿approche par metabarcode révèle une diversité remarquable et insoupçonnée des pico-dinoflagellés (<5µm) et que, indépendamment de l'écosystème étudié et de la période d'échantillonnage, l¿abondance des différents ordres dépend essentiellement de la taille (pico-, nano-, micro-, et meso-plancton). La structuration des communautés de dinoflagellés de différentes fractions de tailles de la zone photique a été confrontée à certains facteurs environnementaux ouvrant des pistes de recherche prometteuses Dinoflagellates form a complex group of protists with a variety of morphologies, physiologies, and life cycles that give them a strong adaptation to all aquatic environments (marine and freshwater) and habitats (pelagic and benthic) making difficult to study their diversity and ecology. The objective of this thesis was the search for global biodiversity patterns and community structure of marine pelagic dinoflagellates across the world?s oceans. A morphogenetic sampling protocol, covering the entire spectrum of their size and an important part of their spatio-temporal variability, was developed (Tara-Oceans). Various tools for an automatic acquisition broadband data were tested. Diversity, relative abundance and geographical distribution of the genus Neoceratium were evaluated by FlowCAM in Mediterranean Sea. A study of the structure of biodiversity was conducted by metabarcoding with 18S rDNA (V9 fragment). Building a base of rDNA reference sequences (DinR2) allowed the taxonomic assignment of environmental metabarcodes. The metabarcode approach reveals a remarkable and unexpected diversity of pico-dinoflagellates (<5?m) and, regardless of the studied ecosystem and the sampling period, that abundance of different levels mainly depends to the size fractions (pico-, nano-, micro- and meso- plankton). Structuring of dinoflagellates communities in different size fractions of the photic zone was facing to some environmental factors and opens promising avenues for research

Farmland biodiversity is an important component of Europe’s biodiversity. More than half the continent is occupied by agricultural lands. They host specific habitats and species, which – in addition to their conservation values they provide – perform vital ecological functions. Indicators are needed to enable the monitoring of biodiversity at the farm level for the purpose of assessing the impacts of farming practices and of agricultural policies. Our research aims at identifying farmland biodiversity indicators which are scientifically sound, operational and relevant for stakeholders. We screened the literature for farmland biodiversity indicators and, in an iterative process with stakeholders, we identified 28 candidate indicators for genetic, species and habitat diversity. Those selected biodiversity indicators, as well as 14 management indicators that are known to relate to biodiversity, were assessed in 12 case study regions across Europe. Each case study region represents a typical production system (i.e. specialist field crops, horticulture and permanent crops; specialist grazing with cattle and other livestock types; mixed crop and livestock farming). In each region, 8 – 20 farms were randomly selected, mostly within the two groups of organic and non-organic farms, to obtain a gradient of farming intensity. Indicators were measured applying standardized sampling procedures and farm interviews. Sampling effort was recorded in order to assess the cost of indicator measurement. For each case study region, biodiversity indicators are presently being evaluated in conjunction with management indicators. Surrogate indicators will be proposed when possible and indicators will be prioritized taking into account their validity, practicality, cost and priority for stakeholders. Based on preliminary results, the presentation will focus on the specific challenges of farm level monitoring, addressing issues of sampling design within the farms and up-scaling from plot to farm to region.

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