ROME is a basic research project that will focus on Rare and Overlooked Microbial Eukaryotes, an unexplored reservoir of novel 'species', genes, and metabolic pathways. We will focus on the ecological functions and roles of “rare” (i.e., below 0.01 to 1% of the total number of pyrosequence reads) and “neglected abundant” (primarily zoosporic organisms) species in two contrasting, well-circumscribed and well-studied systems, Lake Pavin and the Eastern English Channel. Deep environmental sequencing, coupled with experimental manipulations and microscopic observations, will unveil the ecological potentials of rare and neglected “ microbial eukaryotes in aquatic ecosystems. Our central hypothesis is that abrupt environmental changes result in novel communities. Among the neglected abundant eukaryotes, zoosporic chytrid pathogens of phytoplankton likely play a key and hitherto unrecognised role in food web dynamics. To explore this possibility, the genomes of one host-pathogen system will be sequenced, annotated and used as a reference to explore gene function in the environment. This information will be combined with functional ecological measurements performed on field communities and mesocosm experiments, in order to model fluxes in the ecosystems under study. We will combine analytical, biochemical, microbiological, and molecular biological techniques in an integrative study of organisms with neglected ecological functions. ROME is a unique collaboration between researchers with complementary expertise in microbial food web interactions and trophic relations, purification/culture and microscope identification of protists and zoosporic organisms, molecular ecology, functional genomics, analysis of community structure, and food web modelling.

MANA (Spirit in Polynesian) is dedicated to the development of tools for the management of exploited atoll lagoons facing a changing environment. Specifically, it addresses atoll lagoons dedicated to aquaculture in the Central Pacific Ocean, a Polynesian area vulnerable and exposed to global change, but with poor adaptation capabilities. The development of management tools requires inter-disciplinary collaborations to serve the applied objectives and socioeconomic priorities put forward by governmental management entities in two island countries (French Polynesia and Cook Islands). While adaptation, innovation, degradation, and transformation have been common in tropical islands since 50 years (e.g., by embracing aquaculture in the 1980s), islands, and particularly atolls, have also now to adapt to climate change within a global, market-driven, biosphere. Adaptation in front of such challenges is beyond the immediate reach of remote islanders. Long-term planning, taking into account local specificities (environmental and societal), is required and can be implemented only through a combination of top-down and bottom-up governance. The MANA project aims to contribute to this approach by bringing integrated tools to both managers and islanders in charge of tropical lagoons. MANA intends to contribute to better coastal tropical communities livelihoods in the next 20 years. Specifically, MANA targets the management of the aquaculture of the black lip oyster Pinctada margaritifera that produces the prized black pearls. This is the second source of income in French Polynesia, a major contributor for Cook Islands, and also for other Pacific Island countries. The culture of P. margaritifera requires several steps. The first is spat collecting, where oyster larvae are collected on artificial substrates. Then, as adults, they are grafted to produce pearls. Incomes thus depend on the success of spat collecting, but spatial and temporal variabilities are high even in favorable atolls due to environmental variations. Furthermore, the consequences of climate change on these processes remain poorly understood Several successful spat-collecting atolls have also steadily declined. Identified high priority management tools are «Spat collecting forecasting», «Management of oyster stocks», «Marine concession spatial planning and zoning tool» and «Climate change consequences». To help managing this activity, MANA will investigate and model the processes controlling spat collection: distribution of the reproductive stock, larvae survival during their dispersal phase, food available for larvae and adults, dispersal by lagoon currents, influence of weather on currents, and collectors location. The sensitivity to these processes will be studied, mapped, modeled, and integrated for a set of atolls with different geomorphological configurations. The MANA project is carried out as a PRC (Collaborative Research Project) involving 9 Partners, including two governmental management entities in French Polynesia and Cook Islands. These entities have already substantially invested in oceanographic instruments in 2016, defined the targeted sites, and will contribute to the project by provision of data and staff for field activities. Eventually, they will host and run the MANA decision support tools. The consortium is built on a solid foundation of past collaborations, with 10 years of intensive past research dedicated to atoll lagoon ecosystems and pearl oyster farming management. The 4-year project is articulated around 7 interconnected main tasks, which are T1: Project coordination; T2: Regional-scale atoll typology, T3: Lagoon 3D circulation modelling; T4: Lagoon coupled bio-physical modelling; T5: Lagoon field data collection; T6: Regional-scale environmental forcing and climate change; T7: Decision support tools. The scientific tasks (T2-T6) are coordinated (T1) to converge towards an applied T7 task that will implement these management tools.