Station for Experimental Ecology in Moulis
Environmental Management Infrastructures
Genomic, Transcriptomic, Proteomics and Metabolomics Facilities
Environmental Health Research Facilities
Biomedical Imaging Facilities
Extreme Conditions Facilities
Collections of Biological Resources (e.g. Microorganisms, Biobanks and Seed Banks)
Atmospheric Measurement Facilities
In situ Marine/Freshwater Observatories
Agronomy, Forestry, Plant Breeding Centres
Earth and Environmental Sciences
Capsis is a simulation platform for forestry growth / dynamics models (INRA). It is a tool for forest scientists, forest managers and education. It makes it possible to implement models of various types (stand models, distance-independent or distance-dependent tree models, mixed models…), to run simulations and then compare different scenarios in a single software. Thanks to its flexible architecture, it is possible to integrate heterogeneous models (uneven-aged, several species) with various processes (growth, competition, mortality, regeneration, dispersion…) and to run simulations in interactive or script modes. Some models can have very particular properties, e.g. radiative balance, genetics information at the individual level, internal biomechanics or wood quality. Forestry modellers can join the Capsis project and learn how to integrate their models within Capsis.
Modelling and simulation of biodiversity show a need for complex models taking into account numerous parameters and assuming the comparison of diverse models as much for modelers as for model users and decision-makers. Moreover, interactions between existing models will be prevalent in a near future. To meet these challenges, a biodiversity modelling platform was developed in three mains steps. The current version of the platform allows an easy-to-use web-server with keyword search for modelling tools that perform in the domain. To achieve the final aim of the platform, the next version will propose a graphical framework which will allow a friendly use of the tools with progressive implementation of the interactions and the links with the databases of the ANAEE-France infrastructure. Finally, the platform will allow a human interface to create new models de novo or by integrating shared modules; the focus will be put on the coupling of the existing models.
The EcoInformatic Group developp Information System in order to manage data collected from the long-term experimental and observatory sites (SOEREs).
The Ecotron allows a precise conditioning of the environment and on line measurements of states and activities (fluxes) of organisms and ecosystems at various scales. It confines ecosystem’s samples in an experimental chamber in order to control in an easier and better way (compared to in natura) the environmental conditions and at the same time it takes advantage of this confinement to measure precisely the exchange of molecules between the ecosystem compartments, including the above atmosphere. This facility bridges the gap between the complexity of in natura studies and the simplicity of laboratory experiments.
The Observatory alpine lakes (SOERE OLA) aims to provide scientific data to understand and ultimately model the evolution of the ecological state and functioning of lake systems simultaneously subjected to changes in local pressure (anthropisation) and climate. The three natural lakes peri-Alpine (Lake Annecy, Bourget and Geneva) are the focus of this observatory, thanks to the ecological monitoring program initiated on these systems for decades. Other lake sites have joined more recently SOERE including altitude lakes and a meromictic lake, Lake Pavin.
The facility comprises 48 units, each stretches 100-m², 2-m height, bordered by a thin mesh net. 20m long -corridors between patches can be flexibly open or closed. Temperature, humidity and illuminance can be independently controlled within each patch. Climatic conditions are recorded.
RECORD ("REnovation and COorDination of agroecosystems") is a modeling platform developed and maintened at INRA in Toulouse (France). It is dedicated to the study of agrosystems (also agroecosystems). It provides a set of tools and services to cover the different steps of modeling work, experimental design, and simulation. It includes: i) “VLE” the core software of the platform. Its graphical interface helps modellers build new models by a “wire and box” approach where boxes represent the different modules and wires correspond to the connexions between modules for informations exchanges during simulation. Different modeling formalisms are available (e.g. difference equations, differential equations, state charts, Forrester, decision …). VLE provides a robust response to the challenge of coupling models, and in particular heterogeneous models. ii) a library of models and modules that can be reused by modelers to build new models. iii) various companion tools: to link to external data, to bind dynamically to other softwares such as R (for statistical work, pre and post treatment of data and simulation results) or Python language. Experimental plans can be designed and simulated iv) services to develop web application around models. The platform has a e-learning site where tutorials and examples are provided. Training sessions are organized twice a year by the team that is in charge of the platform. C++ is the native language of the platform. It is distributed under GPL license. There is a users charter.
The Soere PRO is a network of experimental sites to study the effects of organic waste products agricultural recycling. Those sites, on the plot scale, enable to measure, from more than 10 years for some of them, the long term evolution of the different agroecosystem's compartments (soil, plants, water, atmosphere, organic waste products) when they are submitted to spreading.
BBEES provides AnaEE France short-term experimentation services with technical and scientific supports to build, structure, perpetuate and pool their databases.
The SOERE ACBB is comprised of 3 agro-ecosystems, over 4 experimental sites : • Lusignan site to study crop-grassland rotation systems dynamics, • Theix and Laqueille sites to study natural grasslands dynamics, • Mons en Chaussée site to study the evolution of arable crop systems and their introduction to provide energetic biomass.
The objectives of the platform Biochem-Env are to provide skills and innovative tools for biochemical characterizations of soils, sediments, and living micro-macroorganisms. These approaches are related to the assessment of ecosystems functioning. The scope of the platform Biochem-Env includes: 1) the technology intelligence and the development of tools used for the biochemical characterization of solid environmental matrices and macrofauna, 2) the development of an Environmental Information System (referential for functional biodiversity) for managing the traceability of samples and data, and improve our ability to characterize the biological status of environmental matrices. Available as a scientific partner in the frame of collaborative research projects, the platform’s abilities ranges from advice providing (sampling, protocols and data analysis), to technical training, including analysis and experimentation in regional, national and international research programs. The tools of the platform have been deployed in programs targeted at assessing the sensitivity and restrictions of biological indicators of soil quality, subjected to various constraints (waste landfilling, farming practices, contaminated sites and soils…). For example, long-term experimental sites provide opportunities to assess the effects of pressures and threats on soils and their functioning. In a context of soil contamination, we can conclude using global soil enzymatic activities that soil functioning is enhanced in biological farming comparatively to conventional practices.
GenoSol is designed to provide a logistic and technical structure for the acquisition, conservation, characterization and provision of soil microbial genetic resources (DNA) derived from wide-scale soil sampling (several hundred to several thousand samples corresponding to large spatial and/or time scales).
The research infrastructure provides the scientific community with access to a set of experimental equipment with a high level of instrumentation: (1) Sixteen artificial lakes with a volume of several hundreds of cubic metres, connected to each other and equipped with a extensive instrumentation. These systems are innovative in that they integrate littoral, benthic and pelagic zones and that they are large. They should facilitate studies of the functioning of complex communities with particular spatial distributions. (2) Mesocosms with a volume of several cubic metres to several tens of cubic metres, with a high degree of control over thermal gradients and water mixing; mesocosms equipped with beaters to generate waves, making it possible to generate the physical structure of a column of water linked to the mixing of the medium. These facilities, adapted from systems used in fluid mechanics, are the only such facilities anywhere in the world; (3) Instrumentation including sensors to do measurement of the physical and biological properties of water bodies, probes to conduct non-automated, spot measurements of environmental data, and analytical techniques implemented in the laboratory.
F-ORE-T brings together 15 sites highly instrumented (ten in metropolitan France and five in the humid intertropical zone) and two networks: Renecofor in metropolitan france and Guyafor in French Guiana coastal belt. It is the reference french network in the field of carbon cycles, water and mineral elements analysis in forests. More precisely, the observatory aims at understanding ecosystems functioning thanks to carbon stocks and fluxes, water and mineral elements analysis. It also evaluates ecosystems responses whatever they are quick or slow, natural or anthropogenic (climate, sylviculture, land-use change).
The Station Alpine Joseph Fourier (SAJF) research platform includes all infrastructures for carrying out experimental research in high mountain ecosystems under controlled conditions or in the field. - 3 buildings for accommodation (hosting capacity of 25 persons), laboratories (100 m2), conference/workshop room (hosting capacity of 80 persons). - experimental gardens (300m2) contain plots to grow plants and simplified communities under semi-controlled conditions. - subalpine grasslands (1.9 ha) are available for experimentations, including electrified plots, equipped with instrumentation to control the pluviometry and monitor temperature, radiation, water, snow, nutrient fluxes, ecosystem phenology, exchanges of carbon, water vapour and energy in the soil/snowpack/vegetation/atmosphere continuum. Various land uses are mimicked, notably mowing and fertilization. - plots of land are also leased to local farmers and/or provided for free by the local authorities (partnerships developped since the early 2000) to set-up instruments and to implement monitoring programs The SAJF also offers manpower to support technical field work, plant nursery and expertise in botany (4 full-time equivalent technicians and engineers). It also provides facilities for public education through the alpine botanical garden associated to the research platform (guides, exhibition room).
The VSoil platform has the following objectives : i) to make models use and development user-friendly and accessible to all scientists involved in studying processes occurring in the soil or at its interfaces with atmosphere, plants and groundwaters, ii) to ease the collaboration between scientists operating in various thematic fields e.g. physics, chemistry, biology, etc.., iii) to favour the reuse of existing models and pieces of code, iv) to make most recent approaches readily available to all researchers using the platform, v) to serve as a hub for exchanging knowledge and modeling tools. The platform is based on the idea that processes can be defined and associated with the variables they need as inputs and outputs. We suppose that several numerical expressions and computer codes (modules) can be derived to represent a process. We intentionally make a clear distinction between a process and its modules. Last, the elementary processes, and, for each, one of their associated modules, can be linked to create an integrated numerical tool that is called a model. The platform is designed as a suite of four softwares that can be used independently. One is dedicated to processes and variables definitions. A second provides assistance to the development and test of modules. The third software helps in assembling modules to create and test a model. The fourth software is dedicated to run available models.
French Guiana is a privileged territory for developing research projects in ecology and environment. The Nouragues European Tropical Research Station (NETRS) was established in an undisturbed forest of central French Guiana to study the dynamics of plant and animal populations. It is located within a Natural Reserve in a pristine lowland tropical moist forest with no recent history of human disturbance. The Nouragues station has two living camps, distant 8 kilometers. Both sites are equipped for science for a few days to several months. - Inselberg camp, especially suitable for studies of the various types of tropical forest vegetation. It is a reference point for the study of wildlife in an area free from hunting pressure. - Saut Parare camp, it serves more studies of riparian forests and river communities. Traditional sleeping houses (carbets) are available on both sites, as well as electricity, refrigerators and drinking water. Communication with the outside is made by satellite phone and satellite Internet. 20 persons can be accomodated on each site. Climate data are available upon demand (Temperature, humidity, precipitation, solar irradiation) The COPAS instrument (Canopy Operational Permanent Access System) allows a new dimension to the research, opening more than 1,5 ha of canopy to experimentation, set up of long term instruments, collection of samples.
PEARL is dedicated to the implementation of experiments on (semi)-artificial aquatic ecosystems. PEARL facilities may be used to perform experimental test of theoretical assumptions and to provide data in support to modelling activities. The effects of physical and biological characteristics of the ecosystems, and those of various stressors (e.g., toxicants) or forcing factors (e.g., nutrients, temperature) may be assessed on structural and functional endpoints. These endpoints may be measured at several levels of organization (e.g., individuals, population, community, ecosystem). Indoor facilities (total surface: 800 m²) include a set of 15 rooms. Some rooms are dedicated to the production of model organisms (algae, aquatic invertebrates, fish). Other may be customised according to the requirements of the experiments. Among them, some are dedicated to experiments including xenobiotics or invasive species. In addition, a lab is available for preliminary treatment of samples or other purposes. The outdoor mesocosm facility hosts a hundred of experimental ponds (volume ranging from 0.5 to 30 m3). These systems may be customised (e.g., sediment, macrophytes, sampling devices, …) according to the requirements of users to study their functioning and responses to stressors or forcing factors. In addition, thirty large ponds (surface ranging from 100 to 1,000 m2) are available. They may be used for rearing model organisms or for functional studies (e.g., pond aquaculture).
The Ecotron IIeDefrance is located in Saint-Pierre-lès-Nemours at the CEntre Experimental Research in Ecology and Predictive (CEREEP) and coordinated in partnership with Ecole normale supérieure. It is in construction and will consist of a research building of 800 m2, a platform of 18 climate chambers (called Ecolab plaform) and a platform of aquatic microcosms. Equipments allow the detailed simulation of climatic environments in artificial conditions for ecological and evolutionary studies on small terrestrial and aquatic ecosystems.
The M-POETE aims at offering the capability of characterizing most relevant components of different ecosystem compartments (soil, vegetation, water) by providing capacity to collect and adequately prepare samples. It will also offer the capacity of characterizing in situ gaz isotopic signatures, an explicit description of vegetation structure, half-hourly VOC fluxes splitted between the ground and the canopy, and the determination of immediate fingerprint of microbiological activity from VOC (Volatile Organic Compounds). This latter is a promising way to characterize microbial community that is complementary to DNA or biochemical fingerprints described further. The MobileLab (M-POETE) will be implemented during short field surveys on the different sites of the infrastructure including Ecotrons and will offer the following facilities: Sampling facilities for soil and water sampling (corer, sieving, pump, filters), sample preparation (extraction, homogenization, centrifugation, weighting, drying), plant tissue and DNA extraction (using storage in liquid N2), chemical and biochemical identification and characterization of plants. Characterization of soil, sediment and water processes through new approaches using gas analysers which can provide information on processes intensity (e.g. CO2 fluxes), characteristics of processes (isotopes such as13-C and 18-O), VOC fluxes and the type and diversity of the biotic communities involved in these processes thanks to their VOC signature measured by Proton Transfer Reaction-Mass spectroscopy (PTR-MS) method. Characterization of the terrestrial vegetation: structure will be analyzed with the LiDAR (Light Detection and Ranging) laser technology to provide 3D representations of vegetation. Properties of canopy components composition will be analyzed using the developing technologies of proxy detection (spectral and hyperspectral reflectance...).
The RMI facility includes an in vivo Animal Imager quad-detector System (magnet 3 Tesla) with accessories adapted to small animals (invertebrates to passerine birds), an ingeneer dedicated to technical manipulations and a data base. The facility is under construction and may be operational in 2016.