Biological diversity within species is an overlooked but fundamental level of biodiversity which contributes to the stability of ecosystems, as well as to adaptation to heterogeneous and changing environments. The coexistence of specialised ecotypes and morphotypes within a species, as well as adaptation to local environments is promoted by peculiar genomic structural variants called chromosomal inversions. Inversion-associated diversity nevertheless shows contrasting patterns, from widespread polymorphism to fixation between habitats or lineages, and it is still unclear what causes and consequences of such different evolutionary dynamics are. In particular, an inversion behaves and evolves like a large-effect single locus (“supergene”) under selective and demographic processes that shape its evolutionary trajectory. Then, inside the inversion, there is a second level of diversity, the DNA content, that varies and evolves, but the feedback loops between the two levels are poorly understood empirically. In this project, I propose contrasting two adaptive inversions in the seaweed fly Coleopa frigida that follow different evolutionary dynamics: one is widely polymorphic and the other is strongly structured along latitudinal clines. By combining experimental and genomic approaches on four parallel replicates across continents, my team and I will assess the relative role of selection and historical processes in determining inversions' distributions. Then, we will test the prediction that the evolutionary trajectories of inversions condition the evolution of its content. Altogether, those results will shed light on the evolution of genetic and phenotypic diversity within species, and push forward our knowledge about inversions which are widespread structural variants relevant for fitness and adaptation but also human health.

Climate change is the biggest challenge that we are facing for food production. Increase in atmospheric carbon dioxide, in temperature and in variability of precipitation, directly affect the abiotic environment of crops, their geographical distribution and their biotic interactions, leading to increased crop vulnerability. Rethinking new strategies that will mitigate these impacts is a priority for agriculture. Compared with domesticated forms monitored by humans, crop wild relatives are facing continuous challenges in their natural environments and encompass more genetic diversity. Therefore, they constitute an untapped reservoir of alleles, which could be used to increase adaptive capacity of cultivated species in the face of global changes. Genetic exploitation of wild relatives in crop improvement is a key alternative strategy to the massive use of inputs, and promotes the sustainability of agroecosystems. It is however conditioned by cross compatibilities between wild and domesticated forms, and fertility of the resulting progenies. The DOMISOL project aims at characterizing the extent and molecular nature of reproductive barriers between wild and domesticated forms, and at investigating the underlying evolutionary processes. Owing to their recent divergence, barriers between wild and domesticates are incomplete and can therefore be ‘caught in the act’ in their set-up. We propose here to focus on 14 wild/domesticates systems representing a low to high continuum of divergence, in order to undertake a comparative approach. We are pursuing two major objectives. The first one is to take advantage of this broad diversity of systems to perform a quantitative assessment of reproductive barriers in F1 hybrids obtained from wild x domesticates crosses; and to investigate the links between these barriers, the evolutionary history these forms, their phenotypic and genomic divergence, in order to infer the evolutionary parameters that determine the strength of reproductive isolation. The second one is to focus on three of the 14 systems to refine our understanding of the molecular mechanisms underlying reproductive isolation. This includes the description of transcriptional changes in healthy versus unhealthy F1 hybrids, as well as the detection of segregation distortions in F1 and F2 progenies that will be used subsequently for mapping loci involved in hybrid fitness defects. DOMISOL brings together complementary expertise of four partners in the production and valorization of genetic resources, agronomy, evolutionary genomics, plant genetics and modeling. This ambitious project is an exceptional opportunity to produce unique genetic material on several systems and datasets that will serve as bases for collaborations among actors of the plant genetics and genomics community in France. The outcomes will provide a better understanding of the processes at work in the early stages of reproductive isolation, and their consequences on fitness-related traits; but will also help to characterize the extent and genetic nature of barriers to reproduction between wild and cultivated forms. This is an essential step to overcome them and exploit the full reservoir of adaptive alleles to improve crop sustainability in agro-ecosystems. We will take advantage of the data produced for teaching activities to illustrate the application of high-throughput sequencing in plant breeding, and to raise general public awareness of the importance of preserving wild populations.

Species diversification results from biogeographic processes and selective pressures which promote genetic and ecological divergence among populations. Understanding how species functional traits relate to genetic and environmental variability is necessary to infer mechanisms that generate diversity, as well as to anticipate species’ response to anthropogenic change. Adaptions to climatic conditions usually evolve over a long timeframe and multiple generations. However, rapid ongoing climate change is now strongly affecting biodiversity and notably ectotherms, leading to contrasted ecological responses even among closely related species. A major challenge for living organisms is that climate change combines both (1) gradual increase in temperature (seasons, years) and (2) acute weather events (days, weeks) such as heatwaves. The fast pace of current change exacerbates the risks of crossing physiological limits and lethal thresholds and the benefits of plastic responses (physiological and behavioral) at the individual level. In this context, an integrated understanding of the thermal niche is essential to clarify the proximate basis of past climatic adaptation and current species vulnerability. Using the monophyletic group of the snakes of the genus Vipera (15 species) as case study, DIVCLIM deals with this challenge, addressing the diversification of their thermal niche (WP2) and response to climatic stressors (WP3), also focusing at the population level in one species along a climatic gradient in Western Europe (WP4), to provide a novel mechanistic insight on drivers of species vulnerability to climate change (WP5).

The deep subsurface is conventionally thought as a carbon and energy-poor environment, with limited microbial growth and biogeochemical process rates. In recent years, there has been increasing evidence of the existence of deep microbial communities, able to actively respond to changes in hydrological and geochemical changes. These subsurface communities are thought to catalyse a large array of redox reactions but their impact on geochemical processes, rates and fluxes have remained largely elusive so far. IRONSTONE assembles an interdisciplinary team of scientists with complementary expertise in Earth sciences, microbial ecology and fluid mechanics to explore the interplay between hydrological, geochemical and microbial processes in the critical zone. The central hypothesis that will be tested is that flow and chemical gradients enhance microbial activity at depth by promoting the formation of redox driven habitats and triggering biogeochemical processes that would not occur in homogeneous environments. By investigating the mechanisms and scales that control these microbial hot spots and hot moments, IRONSTONE will provide a new understanding of how microbially enhanced reactivity influence landscape-scale biogeochemical fluxes. For this purpose, IRONSTONE will focus on iron oxidation and iron oxidizing bacteria (FeOB). Iron redox transformations play a central role in global biogeochemical cycles and FeOB are primary producer of organic carbon that potentially strongly influence deep microbial communities. We recently demonstrated that mixing between superficial oxygenated water and deep iron-rich groundwater drives the formation of microoxic environments, where FeOB can thrive in deep fractured rocks. This mechanism is likely representative of the dynamics of other microorganisms that depend on electron donors and acceptors that are spatially segregated, leading to strongly enhanced microbial activity in mixing zones. As such, it may profoundly change representations and models of deep subsurface environments. IRONSTONE will rely on an original methodology coupling microfluidics, genomics, geochemistry and hydrology to understand and quantify the dynamics of FeOB hot spots and their impact on critical zone cycles and fluxes. This methodology may be extended to a range of microorganisms and reactions. IRONSTONE will make the most of the rapid developments in microfluidics and microimaging to interrogate the concept of geochemical gradients at microscale. Innovative microfluidic devices and experiments will allow observing growth, distribution and morphology of mineralized FeOB colonies subjected to precise concentrations or gradients of O2 and Fe(II) (WP1). These microscale observation will be combined with the characterization of reactive pathways and geochemical fluxes associated to FeOB hot spots formation and degradation (WP2). For this, IRONSTONE will couple metagenomics and metatranscriptomics, isotopic labelling, and microimaging, molecular and thermodynamics approaches. Upscaling to field scale will be investigated using novel tracer tests based on continuous dissolved gas and isotopic measurements, including isotopic fractionation of O2, to quantify microbiological controls on reactions and elemental fluxes (WP3). The highly interdisciplinary approach developed in IRONSTONE will thus provide new opportunities to understand how spatial heterogeneity and temporal variation of environmental conditions affect the dynamics of microbial growth and the kinetics of microbially catalyzed reactions in the subsurface, leading to a new framework to integrate deep microbial dynamics in critical zone cycles and fluxes.

The ECOBIO laboratory and the company Cellenion propose to create the Joint MICROSCALE-lab Laboratory, in the fields of microbiology and molecular biology, for the analysis of single prokaryotic cells. MICROSCALE-lab is divided into three R&D axes: (i) IsoCell which targets the isolation of single microbial cells from a complex community using the cellenONE systems, (ii) IsoGenes and (iii) IsoTrans, focusing on the analysis of genomes and transcriptomes, respectively, of single microbial cells. The overall objective of these three axes is to offer a complete system (isolation, preparation of sequencing libraries and bioinformatic analysis) for the analysis of single microbial cells, creating a conceptual and technological breakthrough for the study of microbial communities. Indeed, while leading to significant advances in the field of microbiology during the last decades, the widely used 'meta-omics' approaches are currently showing their limits. A need for new tools to better understand microbial communities (i.e. microbiota), and especially to link microbial diversity and functions, is emerging. MICROSCALE-lab intends to fulfil this need by transferring single-cell sorting systems previously used on eukaryotic cells to prokaryotes, and by combining them with molecular analysis and bioinformatics tools. This will bring new insights in various fields of research, both fundamental and applied, targeting the microbiota. MICROSCALE-lab will benefit from the partnership between the ECOBIO laboratory, expert in microbial ecology and environmental genomics, and the company Cellenion, specialized in the design of tools for the isolation and study of single cells, and in molecular biology. The two LabCom’s partners will move forward in close collaboration on the three R&D axes, making the best use of their respective infrastructures, skills and expertise. For 20 years, the ECOBIO laboratory has been developing research activities in the fields of microbial ecology and environmental microbiology that are internationally recognized and associated with the publication of numerous international peer-reviewed articles in high impact factor journals. The research team mobilized for MICROSCALE-lab is thus made up of microbiologists with complementary specialties, crossing different scientific disciplines centred on microbial ecology. In addition, MICROSCALE-lab will rely on the technical and human resources of the Environmental and Human Genomics (GEH) platform hosted by the ECOBIO laboratory. For its part, Cellenion, a fast-growing SASU, develops products and solutions for the isolation of single cells, including the cellenONE technology, which is internationally marketed. Cellenion's multidisciplinary research team combines robust expertise in molecular and cellular biology and microbiology, with strong skills in (bio)informatics and automation and optics engineering. Based on the strength of this partnership between ECOBIO and Cellenion, MICROSCALE-lab will target the industrial market devoted to the analysis of single cells which is currently in full expansion. It will position itself in microbiota study in the field of health, environment, bioproduction, agrifood, cosmetics, etc, and will open up new possibilities for generating new data on microbiota and their functioning, increasing major fundamental knowledge in microbiology and microbial ecology.