The microsporidium Nosema ceranae (a fungi) and the ectoparasite Varroa destructor (a mite) are common biotic stressors of honeybees that produce serious damages to the colonies. The parasitic cycle of V. destructor is composed of a phoretic and reproductive phase. During the latter, the parasite enters brood cells, reproduces and feeds on the hemolymph and fat bodies of bee pupae impinging on their immune system resulting in more frequent physical deformities in newborn bees. In addition, N. ceranae, a gut intracellular parasite, causes nosemosis, the most widespread disease of adult bees. As the main source of lipids and proteins in honey bees, pollen is a major nutrient involved in development and health since many studies have shown its role in shaping honeybee traits, especially immune competence and tolerance against pathogens and parasites. The aim of this project is to investigate the impact of pollen supplementation in adult honeybees exposed to Nosema and previously to Varroa at the larval stage. Impacts of Varroa parasitism in laboratory conditions will be investigated on bee larval growth and on the microbiome in emerging bees. Long term effects on these experimental bees will examine their tolerance and resistance against Nosema exposure both in lab and semi-field conditions. We will focus on the relationships existing between gene expressions, peptidome/proteome modulation and phenotypic traits. We will describe how biotic stressors effects are coupled to interactions between feeding behavior and the microbiota composition. Given our joint expertise, we propose a unique experimental design. This includes impact of nutrition at adult stage and its interaction with most common pathogens, Varroa and Nosema, in both laboratory and semi-field experiments in a simple 4-Tunnels disposition. This interdisciplinary project allows us to examine the effects of those stressors observed all along the beekeeping season.

Anthropogenic climate change has already started to affect the distribution of species. Species are not only valuable in their own right, but also because they are responsible for the capture, conversion and flow of energy and nutrients through ecosystems. It has proven challenging to study the impacts of climate change on ecosystem processes, first because effects on single species cannot be extrapolated to the complex network of species interactions, second because it is difficult to manipulate entire ecosystems, and third because it is not clear how results from one location can be used to predict responses across entire regions when species show biogeographic turnover in composition and traits. Our approach to these issues is two-fold. First, we will manipulate a small, spatially discrete food web (the microbial-faunal food web inhabiting water-filled bromeliads) to determine the role of species interactions in determining ecosystem responses. Second, we take advantage of the fact that our focal food web occurs over a broad biogeographic gradient to examine the generality of food web responses. We concentrate on precipitation because it is understudied (compared to temperature) and has potentially profound impact for ecosystems, and specifically on Neotropical ecosystems, which are expected to lose more species than their temperate counterparts. The general aims of this project are: (1) to understand the interaction between biogeographic changes and climate change, and (2) to disseminate a robust, multi-regional theory of how climate affects ecosystems. Our project comprises three hierarchical tasks: (i) To determine if the responses of populations and multipartite interactions (from bacteria to metazoa) and ecosystem function (carbon and nitrogen dynamics, decomposition, carbon dioxide and methane emission) to altered precipitations differ between countries; (ii) To use a biogeographic analogue experiment inspired from geneticists’ twin studies to determine whether this variance between countries is driven by biogeographic changes in species composition or differences in local conditions; (iii) To disentangle the direct effects of precipitation change mediated by organism physiology from the indirect effects mediated by interactions between species. To answer these questions, we will experimentally change precipitation entering bromeliad ecosystems from baseline levels in 3 field sites covering the range of faunal diversity in general in the Americas: French Guiana, the centre of bromeliad radiation and a hotspot for bromeliad faunal diversity, Costa Rica which has a moderate species pool, and Puerto Rico, a Caribbean site with a depauperate species pool. If we understand the mechanisms underlying biogeographic effects, we can consider how our results can be extrapolated to unstudied portions of the biogeographic gradient. We will experimentally increase or decrease precipitation entering bromeliads to study effects on the bromeliad ecosystem. Manipulations will involve either a 40% decrease in rainfall by deflecting rain with cone-shaped shelters, a 40% increase by concentrating rain with inverted (funnel-shaped) shelters, or no change (shelter sides vertical). Our major findings will be disseminated to scientists, students, stakeholders, and public schools. Ecologists have a limited timeframe in which studies on consequences of climate change will be useful to society, so need to seek shortcuts by which results from particular fieldsites can be extrapolated to other regions with differing species pool. This project will provide a fresh approach on how to predict the ecosystem consequences of climate change.

Most agricultural production relies on the use of chemicals to maintain high crop yields. The use of these chemicals in farming practices is viewed as an integral part of the success of the intensive farming. However, most of the pesticides applied to agricultural lands may affect non-target organisms and contaminate soil and water media. Increasing public concern about the impact of pesticides on the environment, and European legislation has led to develop some strategies to evaluate and to prevent the potential impacts of different land management practices. In this context, new generations of less environmentally dangerous molecules, such as lower impact pesticides, biopesticides and natural product-based pesticides have been introduced. Despite this, a lot of work has to be carried out concerning several aspects of the development of these news substances and particularly to evaluate the possible risks and adverse effects of such compounds on environment and humans. The TRICETOX project focuses on studying the ß-triketone herbicide family, a post-emergence maize selective herbicides belonging to this new generation of molecules which have been introduced on the market, in replacement of atrazine, banned in several European countries in 2003. Inside this family, four compounds will be studied in detail, two synthetic ones, i.e. sulcotrione and mesotrione and two natural ones i.e. leptospermome and myrigalone. The TRICETOX project aims precisely to answer the following questions: (1) How to develop analytical tools suitable for a high capacity monitoring of the ß-triketone herbicides in the framework of environmental risk assessment? (2) What are the microbial genes coding for the catabolic enzymes involved in the bacterial biodegradation of ß-triketone herbicides? Are these genes regulated and how? (3) Is ß-triketone biodegradation enough for their dissipation in the environment? Are those microorganisms and/or enzymes suitable for a potential bioremediation solution? (4) Are the natural ß-triketone herbicides a safe alternative to synthetic ones? The objectives of this project are: (i) to develop bioassays and biosensors as innovative and low cost analytical tools for the detection of the ß-triketone herbicides. (ii) to characterize the genetic system involved in the synthetic ß-triketone herbicide degradation pathways of the sulcotrione degrading strain Pseudomonas putida 1OP, and the mesotrione degrading strain Bacillus sp. 3B6. (iii) to focus on the natural ?-triketone herbicides by addressing their soil behaviour, by studying their impact on soil microbial communities with microcosm studies, by studying their biodegradation pathways and by testing the toxicity of these compounds and their degradation products. (iv) to communicate to scientific and general public, to contribute to higher education program, and to promote results towards industrial partners. This innovating project will search for gaining new insights about the global environmental impact of the triketone herbicides, towards multidisciplinary scientific approaches, bringing together specialists from complementary disciplinary areas (microbial ecologists, biochemists, analytical chemists, and molecular biologists). From an academic point of view, the expected results of this study will help in a better understanding of the fate and behaviour of those pesticides, and on the relevance of the natural triketone herbicides compared to their synthetic counterparts. The obtained results will undoubtedly lead to improving current knowledge and state-of-the-art in genetic characterisation of bacterial adaptation mechanisms, and to develop analytical innovative and competitive tools, suitable for environmental risk assessment.

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.

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.