As organisms that can cause death and disease in their hosts, parasites are forms of life that can have important ecological effects on the host populations that they exploit. Switches in host can occur as parasites jump to new host species in new environments and in the process will adapt their biology. As every different animal is a new potential host, parasites can diversify greatly and huge numbers of uncharacterized parasite species may exist. Each of these parasites could potentially represent a future danger both to human health and ecosystems. This great diversity of parasites is not immediately obvious because of their mainly microscopic and hidden nature, which means that they cannot be easily seen or described without sampling and dissecting hosts. Therefore how many different species of parasites exist and how successfully they transfer to new hosts and habitats are still unknown factors. DNA-based methods represent a rapid and inexpensive way to sample a wide range of biological diversity present in environmental samples, and importantly provide a means to survey previously unsampled microscopic lifeforms. It is now possible to collect a wide diversity of invertebrates and other small animals present in soil, ponds and marine environments and then extract the DNA from all these organisms along with that of their associated parasites and use state of the art gene sequencing technology to sequence the same gene for each parasite in the sample. By studying the diversity of this DNA we can identify the number and diversity of microscopic parasites present in the original sample. Here we will use this strategy to begin to enumerate the number of particular parasite groups in diverse environments, varying in geographic location, season, and including marine, terrestrial and freshwater environments. The group of parasites that we will survey are the microsporidia. These are highly unusual relatives of fungi that are adapted to live inside the cells of a variety of different animals. In humans, microsporidia can cause serious infections in those with seriously impaired immune systems, for example in people in the late stages of AIDS, or recipients of organ transplants. They also infect economically important animals such as farmed fish and honeybees. Microsporidia have been found in all major animal lineages and in all environment types worldwide. Currently over 1200 species of microsporidia are known to exist, though research suggests that large amounts of uncovered species are present in the environment. We intend to sample freshwater, estuarine, marine and soil environments across different seasons and geographic locations and use DNA methodologies to enumerate the distinct molecular types of microsporidia in each sample as a measure of species number. We can then use this data to try to understand: 1) How our current estimates of parasite species numbers compares to actual environmental numbers 2) Whether numbers of microsporidian species vary with geographic location 3) Which environmental factors, for example season, latitude, or environment type are associated with high levels of diversity of microsporidian parasites This type of quantification of different species will enable us to tell how successfully microsporidia have diversified in different environments. It will indicate whether there are particular environments that have allowed these parasites to thrive over evolutionary timescales. By characterising the differences in types of parasites found in different environments we can understand whether climate change or human movement by trade or travel has the potential to introduce new parasites into new areas. This can indicate how much potential there is for microsporidia to cause new infections in humans and wildlife.

The main objective of this project is to uncover the role and the global ecological importance of members of the Euryarchaeota phylum in aquatic ecosystems. Euryarchaeota, together with Thaumarchaeota, are the two main phyla belonging to the Archaea. Archaea were seen as specialist microorganisms that thrive in habitats of elevated temperature, low pH, high salinity, or strict anoxia. However, their importance in the functioning of oxic aquatic ecosystem has appeared clearly in recent years. Thaumarchaeota (previously known as Crenarchaeota) in particular are now recognized as key players in oxidizing ammonia and can outcompete the bacteria in the nitrogen cycle. In contrast to the effort put into understanding the relevance of Thaumarchaeota in aquatic habitats, basically nothing is known about the metabolisms and the ecology of uncultivated Euryarchaeota. This lack of information is critical as the high number of Euryarchaeota, that are often more abundant than Thaumarchaeota in aquatic ecosystems, suggests a pivotal ecological role for these microorganisms. The recent years have, however, seen advances regarding the biodiversity, and the spatial and temporal dynamics of their communities, but the role of these enigmatic microbes remains unknown. The objective of this project is thus to uncover the metabolisms, the distribution and the activity of the most common uncultured aquatic Euryarchaeota groups. We will target the Group II (subgroups a and b) that is particularly abundant in marine systems, and the LDS and RC-V groups that are often found in freshwater ecosystems. The technological aim of this unique project is to combine an array of state of the art methods with an approach going from the molecular to the community level, and from in silico data to environmental samples. We will use the complementary approaches of data mining, single cell genomic and environmental metagenomics to build a broad and solid base to bring new knowledge on the ecology of Euryarchaeota. This knowledge will be then channeled back to the field for an in situ assessment of the ecological importance of Euryarchaeota.

Nitrogen-containing compounds, including glycine betaine (GBT), choline and trimethylamine N-oxide (TMAO) are ubiquitous in marine organisms. They are used by marine organisms as compatible solutes in response to changes in environmental conditions, such as increasing salinity, because they do not interfere with cell metabolism. They also have beneficial effects in protecting proteins against denaturation due to chemical or physical damage. In the marine environment, these compounds are frequently released from these organisms directly into seawater due to changing environmental conditions, such as by viral lysis or grazing. The released nitrogenous osmolytes serve as important nutrients for marine microorganisms, which can use them as carbon, nitrogen and energy sources. It is well known that the degradation of these nitrogenous osmolytes contribute to the release of climate-active gases, including volatile methylamines. Methylamines are important sources of aerosols in the marine atmosphere, which help to reflect sunlight and cause a cooling effect on the climate. Our NERC-funded research is starting to understand the microbial metabolism of these compounds and their seasonal cycles in the coastal surface seawater, but our understanding across the world's oceans is limited. Of particular importance to the Earth's climate is the Southern Ocean. The Southern Ocean is an important player in the Earth climate system, and is an ideal region to study ocean-atmosphere connections because of its isolation from continental emissions and the strong circumpolar atmospheric circulation, rendering its air pristine. Opportunities to study the Southern Ocean are rare however, and it remains under sampled even for the most routine measurements compared to the rest of the World's oceans. We have a unique opportunity within the Antarctic Circumnavigation Expedition (ACE) to make measurements and collect samples around the entire Southern Ocean, and near Antarctica. Twenty one other international projects will also be conducting research from the same expedition, and six of these projects have excellent links to our research. Unfortunately, there are no plans for after the expedition for the projects to collaborate and integrate data, which is a real missed opportunity. This proposal aims to develop a new international network with six ACE projects and use post-cruise activities to exploit data and knowledge generated to capitalise on our NERC-funded research on nitrogenous osmolytes and to increase its international breadth.

The dynamics of sediment fluxes in the fluvial and marine environments are still poorly known, particularly at a regional scale. Measurement techniques as well as numerical models still require research in order to assess these fluxes from their continental source to the shelf edge; this reseach would also benefit from improved and shared monitoring networks. SunRISE gathers a large community of French and European research laboratories, consulting companies and governing agencies in order to address i) climate change related issues, particularly in the current context of coastal vulnerability, ii) European Directives issues, for which pertinent state indicators and monitoring strategies have to be developed. SunRISE is organized around 5 worpackages (WP) aiming at identifying which are the priority research topics to address in order to tackle the following issues : “sediment fluxes at a regional scale in a changing climate”, and “definition of state indicators for the physical parameters describing the marine environment”. WP1 will define the priority processes to account for, WP2 will define the necessary innovations in terms of observation, WP3 will investigate the various modelling approaches, WP4 will work on the research needed in order to come up with state indicators. The last WP is transversal and will help define the main orientations of projects to be designed to answer 2016 ANR and/or H2020 calls for proposals. The financial support sought from the ANR will contribute to fund workshops aiming at writing these projects. The originality of this network lies in the fact that it will bring together Frecnh and European teams working at defining integrative descriptors of the physical regional and coastal environment. Such a structure is essential in order to lead coordinated action at the European level, in particular in the framework of the Marine Strategy Framework Directive (MSFD). The strong participation of European partners (who accepted to lead three of the five WPs on their own budgets) illustrates this initiative relevance.

The ANR MEDSALT project aims to consolidate and expand a scientific network recently formed with the purpose to use scientific drilling to address the causes, timing, emplacement mechanisms and consequences of the largest and most recent 'salt giant' on Earth: the late Miocene (Messinian) salt deposit in the Mediterranean basin. After obtaining the endorsement of the International Ocean Discovery Program (IODP) on a Multiplatform Drilling Proposal (umbrella proposal) in early 2015, the network is planning to submit a site-specific drilling proposal to drill a transect of holes with the R/V Joides Resolution in the evaporite-bearing southern margin of the Balearic promontory in the Western Mediterranean - the aim is to submit the full proposal before the IODP dealine of April 1st 2017, following the submission of a pre-proposal on October 1st 2015. Four key issues will be addressed: 1) What are the causes, timing and emplacement mechanisms of the Mediterranean salt giant ? 2) What are the factors responsible for early salt deformation and fluid flow across and out of the halite layer ? 3) Do salt giants promote the development of a phylogenetically diverse and exceptionally active deep biosphere ? 4) What are the mechanisms underlying the spectacular vertical motions inside basins and their margins ? Our nascent scientific network will consit of a core group of 22 scientists from 10 countries (7 European + USA + Japan + Israel) of which three french scientists (G. Aloisi, J. Lofi and M. Rabineau) play a leading role as PIs of Mediterranean drilling proposals developed within our initiative. Support to this core group will be provided by a supplementary group of 21 scientists that will provide critical knowledge in key areas of our project. The ANR MEDSALT network will finance key actions that include: organising a 43 participants workshops to strengthen and consolidate the Mediterranean drilling community, supporting the participation of network scientists to seismic well site-survey cruises, organising meetings in smaller groups to work on site survey data and finance trips to the US to defend our drilling proposal in front of the IODP Environmental Protection and Safety Panel (EPSP). The MEDSALT drilling initiative will impact the understanding of issues as diverse as submarine geohazards, sub-salt hydrocarbon reservoirs and life in the deep subsurface. This is a unique opportunity for the French scientific community to play a leading role, next to our international partners, in tackling one of the most intellectually challenging open problems in the history of our planet.