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.

Soil organisms are neglected by conservation policies compared to the biodiversity contained in most other habitats (e.g. EU water framework directive). Indeed, below-ground biodiversity is hard to monitor at scale due to its cryptic living and low recognition in public and science. Yet, stakeholders (e.g. farmers, gardeners, local authorities, urban planners and natural area managers) show a growing interest in obtaining simple and reliable indicators to assess soil biodiversity, quality and functioning. Among soil organisms, earthworms are widely recognised as relevant bioindicators of soil quality. They are also considered as soil ecosystem engineers. In the context of decreasing biodiversity, conserving high abundance and diversity of earthworms is of major interest, since they represent an important below-ground node maintaining above-ground trophic networks. SoilRise takes earthworms to exemplify an approach of combining cross-European sampling of earthworms through Citizen Science (CS) with barcode analyses (sequence of the COI gene) to ensure high data quality to model earthworm distribution and communities at European scale. Barcoding will help to harmonize taxonomic dissent and to improve and validate morphological identification keys. SoilRise will contribute to the specifications of Essential Biodiversity Variables (EBVs) and Essential Ecosystem Services Variables (EESVs) within EuropaBON efforts for below-ground biodiversity in terrestrial systems. SoilRise will develop an interactive network between academia and the public to enable extensive and accurate soil biodiversity monitoring. In the current context of biodiversity depletion and climate change, there is a serious need for models and scenarios to predict and anticipate the combined effects of environmental factors on earthworm taxonomic and functional diversity that determine the ecosystem functioning. Within its innovative stakeholder-research network, SoilRise will use co-produced CS data to model species distribution from European to local scales, considering pedoclimatic conditions, land use types in rural versus urban environments, and management practices, respectively. SoilRise data will enable us to identify environmental factors affecting the composition and abundance of earthworm communities. The cross-European sampling in various habitats allows SoilRise to explore genetic diversity and to clarify taxonomic issues. Scientific environmental research carried out in large part by non-professionals can be an effective way to generate large quantities of data that can be used for policy making. SoilRise will use available data and complete them with new CS data that may have a better territorial coverage and spatial precision, and also benefit from local knowledge through the dialogue between scientists and citizens. The public that is involved in environmental research gains more intimate knowledge and may ultimately use that knowledge to direct political decisions in democratic processes. By involving decision-makers in the scientific process, such research is also more likely to improve the management of habitats for biodiversity and ecosystem functioning conservation. As a novel improvement based on approved national CS approaches, SoilRise will conceive and implement a network of CS mentors, i.e. students trained in formal education settings in each partner country. Becoming a mentor involves learning how to train and guide stakeholders (urban gardeners and managers) participating in CS in close and interactive exchanges. These students as mentors may multiply CS monitoring of soil biodiversity across the region. The real-life application of the SoilRise improved mentor-based CS approach will allow us to evaluate its contribution to ecological research and its societal impact with the aim to extend such student-stakeholder networks to other universities thereby increasing local to regional impacts across Europe to a transnational scale.

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.

Quaternary ammonium compounds (QACs) are widely used non-therapeutic biocides that can have a range of unintended environmental consequences, including harmful effects on natural microbial communities and biogeochemical cycles. BITTER-PROPHECY will investigate sources, fate and transport of QACs in mixed land use catchments, quantify their natural attenuation and evaluate their impacts on the activity of denitrifying microbes. A field survey will be complemented with laboratory experiments to establish the role organic matter and environmental minerals in modulating the mobility of QACs, and the effects of exposure to QACs on denitrification capacity. The effects of QACs will be determined on strains of nitrate reducing bacteria, as well as on natural denitrifying communities inhabiting natural sediments. Ultimately, the results will help characterize, sources, transport and risks related to QACs in the environment and their impact on ecosystem functioning

Gene regulation plays an essential role in shaping species differences and modulating phenotypes across development and environmental conditions. It essentially works through the recruitment of trans-acting intermediates to cis-acting DNA sequences affecting the expression of the nearby gene. While gene expression regulation is central in molecular, cellular, developmental, and system biology, its detailed mechanisms have relatively little been incorporated into modern evolutionary theory. We previously discovered two processes specific to gene expression evolution in diploids, cis-regulator runaway and divergence. They arise because of (i) transient dominance modifications that automatically occur following the evolution of cis-acting regulatory elements and (ii) coevolution of these cis-acting elements with trans-acting regulators. We have shown that accounting for these processes calls into question a half-century of theory on sex chromosome evolution and may completely rejuvenate empirical and theoretical work in this field. Here, we will develop the evolutionary theory of cis- and trans-regulators at full scale and empirically test its core features and predictions. Specifically, there are sound reasons to believe that this new theory also has the potential to revolutionize our understanding of other fundamental and enigmatic features of eukaryotic life. It may be a crucial missing element for illuminating the deep evolutionary mysteries of (i) the origin of eukaryotic genome complexity and (ii) the structure of eukaryotic gene regulatory networks. It also may explain (iii) how and why sex – asex transitions fail or succeed and, therefore, why eukaryotic sex is maintained. CisTransEvol offers a radically new groundbreaking approach to important problems in evolutionary biology. If successful, it will be a tremendous advance in our understanding of eukaryotic life-forms and provides a general framework for gene expression evolution in eukaryotes.