Peri-urban lakes are of major significance to urban ecology and to the public. Apart from the phytoplankton, investigated because of their importance, our knowledge of the microbial communities they host and their functions is still limited. Understanding the effect of eutrophication, an indicator of anthropization, on freshwater bodies is an archetypal “One Health” problem. Indeed, the interdependencies between ecosystem, animal and human health are so strong, particularly in peri-urban areas, that holistic approaches must be adopted to adequately and simultaneously address the issues of environmental health and human well-being. However, larger-scale evaluation of eutrophication effect on lakes microbiome is currently mostly lacking. In COM2LIFE, we propose to evaluate the effect of eutrophication on the biodiversity of microbial communities occurring in peri-urban lakes in the very densely populated Île-de-France region. Specifically, it will investigate the taxonomic and functional diversity of Archaea, Bacteria, Eukarya, and viruses in the water, sediment and fishes microbial communities along a eutrophication gradient. COM2LIFE will test two hypotheses. First, we expect that the spatial and temporal heterogeneity of environmental factors related to anthropic pressure at the regional scale will result in differences in the taxonomic and functional diversity of lakes microbial communities. Second, we expect that the microbial communities observed in the water column, sediment, and fish compartments may vary in space and time, but that the functions they provide will be conserved due to functional redundancy among organisms and compartments. To test these hypotheses, we will perform time-series monitoring of microbial communities composition, structure, and metabolic potential by applying state-of-the-art next generation sequencing technologies, coupled with physico-chemical characterization of the compartments. The spatio-temporal heterogeneity of environmental factors related to anthropic pressure and their influence on the taxonomic composition and functional potential of microbial communities, as well as their interactions, will be deciphered using the most recent data analyses tools and modeling approaches. This will allow us to identify the key factors governing microbial community dynamics at the regional scale. The project will thus identify the biotic and abiotic parameters that constrain community compositions and functions at the lake and regional scales and the influence of eutrophication levels. This approach has the potential to provide new candidate bioindicators for evaluating anthropic pressures and water/ecosystem quality.

In the context of climate change, forests will face more frequent and intense periods of water deficit. How forests react to this climatic stress will depend, to a large extent, on their access to the soil water resource. For a long time, the so-called “available water content” (AWC, in millimeters of water) has been identified as a key ecosystem parameter, modulating the forest response to water shortage. Yet, AWC is typically determined over shallow depths (e.g. 1-m), and does not consider that in many cases, trees can access deep water resources, the depth and quantity of which is currently not known. Recent works developed by our consortium have introduced the concept of Total Available Water (TAW) to trees, a concept that adds “deep water” to the AWC estimate. Deployed at scales from the forest site to Metropolitan France and supported by an interdisciplinary consortium, the TAW-tree project aims (1) to quantify the TAW reserve in forests through a combination of geophysical (WP1) and ecophysiological (WP2) approaches, (2) to upscale TAW at regional scale using remote sensing (WP3) in order to (3) quantify the influence of TAW on the functioning, growth and vulnerability of temperate and Mediterranean forests facing climate change (WP4). Our working hypotheses are (hypothesis 1) that AWC generally underestimates TAW, often in a considerable way in forests, (hypothesis 2) that the variations of TAW in a particular forest drive a large part of the inter-tree differences in their response to water shortage, (hypothesis 3) that TAW, and particularly its deep component, has a critical role in the functioning and vulnerability of forests exposed to heat and drought stresses and that it changes the forests’ contribution to groundwater discharge.

More than 300 million ha in Latin America are devoted to agroforestry (mixtures of productive and shade trees) where the impacts of cyclical events of El Niño droughts, background climate change, institutional turmoil and stochastic price variation of agroforestry goods is very strong. For more than 30 years, agroforestry areas in Latin America have been abandoned for other uses like cattle ranching or simply left alone because of rural exodus to cities. In this regard, agroforestry abandonment can be considered a critical transition of a social-ecological system. We chose here to examine the said combined effects in two pilot zones: the Central Andes of Colombia where institutional presence is strong but incomplete and the highland Amazonia in Ecuador populated mostly indigenous people where risk management is highly conditioned by cultural aspects and where women play the leading role in the management of the agricultural systems. The work is divided in 5 complementary work-packages that will collect time series of land productivity of the target areas from both remote sensing and local data, that in turn will be correlated to variation in the El Niño indices and used to fit predictive models. In parallel, an institutional analysis will be conducted to understand how knowledge about climatic and economical risk is acquired and used (or not) by the selected actors in Colombia and Ecuador. A special focus will be given to the dynamics of a pioneer program by FAO that channels meteorological information to growers, including El Niño conditions, that has been deployed in various parts of Colombia. Through workshops, the project will co-construct scenarios of the potential different combined effects of climatic, economic and institutional risks to lay the bases of an early warning system of unfavorable conditions that may lead to land abandonment in the target countries.

Recent advances in environmental microbiology, metagenomics and phylogenomics strongly suggest that the eukaryotic cell evolved from symbiotic consortia involving one member of the Asgard archaea and, at least, the alphaproteobacterial ancestor of the mitochondrion. However, many genes of prokaryotic origin in the last common eukaryotic ancestor were neither archaeal nor alphaproteobacterial. To ascertain their origin, it is essential to better understand the microbial ecology of symbiotic consortia involving Asgard archaea to know with whom they interact in natural ecosystems. In this project, we will combine metagenomic, single-cell, microscopy and cultivation approaches to identify members of Asgard syntrophic consortia in redox transition environments and characterize their metabolic interactions. Through the study of favored partner lineages in these consortia and the bacterial lineages co-existing with Asgard archaea in the same environment, we hope to identify putative bacterial gene donors to Asgard ancestors of eukaryotes. All this information might help us refining current models on eukaryogenesis.

The FLORAS project puts forward a system of identifying and knowing about plants their environment, with close ties between academic pluridisciplinary partners, naturalist associations, local authorities as well as other communites involved in favor of biodiversity. The system is that of floras (digitial or paper books) suited to a particular ecosystem or environment (from the agroecology garden to a region), built with relevant local actors. These floras will comprise, on the first hand, in a morphological description that is accurate and uniform of species present in the considered environment, to permit getting to know them, and on the other, identification keys, produced automatically from the descriptions to permit recognizing them. Evolutive and based on a participative information input, these tools will represent diveristy of form at all level of organisation (plant, population, species), and will be resilient to mistakes and uncertainties thanks to a probabilistic model of morphological characters and a bayesian method. Simple, understandable and easily deployed by small communities, they will be conceived to guarantee the autonomy of actors from technology and social group that owns it. We plan thus to accompany the change of how humans and plant relate, based on care and recognition rather than domination and distance, which have their part of responsability in the crossing of several planetary limits.