Novel Protocol for Acute In Situ Ecotoxicity Test Using Native Crustaceans Applied to Groundwater Ecosystems

Current standardized laboratory test protocols use model species that have limitations to accurately assess native species responses to stressors. We developed and tested a novel acute in situ protocol for testing field-collected organisms. We used Asellus aquaticus and NaCl as a reference toxicant to test for the effects of location (laboratory vs. in situ), medium (synthetic vs. field water), substrate (presence vs. absence), and protocol replicability. We further tested the protocol using groundwater-adapted isopods: Proasellus assaforensis for the effect of location, P. cavaticus of medium and P. lusitanicus of substrate. Our results showed that A. aquaticus’ lethality obtained with the novel acute in situ protocol did not significantly differ from those from laboratory testing. However, laboratory tested P. assaforensis showed a higher sensitivity, suggesting that its acclimation to laboratory conditions might have pernicious effects. A. aquaticus and P. cavaticus showed a higher mortality using synthetic medium in situ and under laboratory conditions, which overestimated the stressor’s effect. Besides, substrate use had no significant effect. The novel acute in situ protocol allows the use of native species under realistic scenarios. It is particularly well adapted for assessing the risk of groundwater ecosystems but it can be applied to a wide range of ecosystems.info:eu-repo/semantics/publishedVersio

Less effective selection leads to larger genomes

International audienceThe evolutionary origin of the striking genome size variations found in eukaryotes remains enigmatic. The effective size of populations, by controlling selection efficacy, is expected to be a key parameter underlying genome size evolution. However, this hypothesis has proved difficult to investigate using empirical datasets. Here, we tested this hypothesis using twenty-two de novo transcriptomes and low-coverage genomes of asellid isopods, which represent eleven independent habitat shifts from surface water to resource-poor groundwater. We show that these habitat shifts are associated with higher transcriptome-wide dN/dS. After ruling out the role of positive selection and pseudogenization, we show that these transcriptome-wide dN/dS increases are the consequence of a reduction in selection efficacy imposed by the smaller effective population size of subterranean species. This reduction is paralleled by an important increase in genome size (25% increase on average), an increase also confirmed in subterranean decapods and mollusks. We also control for an adaptive impact of genome size on life history traits but find no correlation between body size, or growth rate, and genome size. We show instead that the independent increases in genome size measured in subterranean isopods are the direct consequence of increasing invasion rates by repeated elements, which are less efficiently purged out by purifying selection. Contrary to selection efficacy, polymorphism is not correlated to genome size. We propose that recent demographic fluctuations and the difficulty to observe polymorphism variations in polymorphism-poor species can obfuscate the link between effective population size and genome size when polymorphism data is used alone

Groundwater is a hidden global keystone ecosystem

Groundwater is a vital ecosystem of the global water cycle, hosting unique biodiversity and providing essential services to societies. Despite being the largest unfrozen freshwater resource, in a period of depletion by extraction and pollution, groundwater environments have been repeatedly overlooked in global biodiversity conservation agendas. Disregarding the importance of groundwater as an ecosystem ignores its critical role in preserving surface biomes. To foster timely global conservation of groundwater, we propose elevating the concept of keystone species into the realm of ecosystems, claiming groundwater as a keystone ecosystem that influences the integrity of many dependent ecosystems. Our global analysis shows that over half of land surface areas (52.6%) has a medium‐to‐high interaction with groundwater, reaching up to 74.9% when deserts and high mountains are excluded. We postulate that the intrinsic transboundary features of groundwater are critical for shifting perspectives towards more holistic approaches in aquatic ecology and beyond. Furthermore, we propose eight key themes to develop a science‐policy integrated groundwater conservation agenda. Given ecosystems above and below the ground intersect at many levels, considering groundwater as an essential component of planetary health is pivotal to reduce biodiversity loss and buffer against climate change

Fundamental research questions in subterranean biology

Five decades ago, a landmark paper inSciencetitledThe Cave Environmentheralded caves as ideal natural experimental laboratories in which to develop and address general questions in geology, ecology, biogeography, and evolutionary biology. Although the 'caves as laboratory' paradigm has since been advocated by subterranean biologists, there are few examples of studies that successfully translated their results into general principles. The contemporary era of big data, modelling tools, and revolutionary advances in genetics and (meta)genomics provides an opportunity to revisit unresolved questions and challenges, as well as examine promising new avenues of research in subterranean biology. Accordingly, we have developed a roadmap to guide future research endeavours in subterranean biology by adapting a well-established methodology of 'horizon scanning' to identify the highest priority research questions across six subject areas. Based on the expert opinion of 30 scientists from around the globe with complementary expertise and of different academic ages, we assembled an initial list of 258 fundamental questions concentrating on macroecology and microbial ecology, adaptation, evolution, and conservation. Subsequently, through online surveys, 130 subterranean biologists with various backgrounds assisted us in reducing our list to 50 top-priority questions. These research questions are broad in scope and ready to be addressed in the next decade. We believe this exercise will stimulate research towards a deeper understanding of subterranean biology and foster hypothesis-driven studies likely to resonate broadly from the traditional boundaries of this field.Peer reviewe

Etude structurale et dynamique de la protéine TCTP : vers la caractérisation d’un réseau d’interaction complexe dans la réversion tumorale

TCTP is a small (20~kDa) globular protein that interacts with many partners with consequences in various cellular and physiological functions, with well-documented roles in tumoral reversion program. Cells that undergo such program spontaneously loose their malignant phenotype and recover characteristics associated with benign cells, such as apoptosis. In cancer cells, TCTP inhibits MDM2 degradation, thus decreasing p53 levels and favoring tumor maintenance and progression. TCTP also contains a BH3-like motif known to regulate Bcl-2 family members and TCTP directly interacts with Bcl-xL and Mcl-1 to reinforce their pro-survival properties. In TCTP structure, the BH3-like motif is not readily accessible for interaction. Consistently with its importance in tumor maintenance, TCTP is a validated pharmacological target in cancer treatment with ongoing clinical trials using the TCTP-targeting antidepressant drug sertraline. However, little is known about TCTP structure in complex with partners, thus impeding the development of drugs and the understanding of how TCTP could adapt to its myriad of partners. Thus, we investigated the molecular mechanism by which TCTP associates with proteins and ligands using various biophysical methods (NMR, SAXS, CD, SEC, DSF...). We have demonstrated that full length TCTP binds to Bcl-xL and Mcl-1 in their BH3-binding groove. In the complexes, the TCTP BH3-like region is engaged in the intermolecular interface and the core TCTP structure is destabilized into a molten-globule (MG) state. We further showed that only a minor pre-existing form of TCTP, namely TCTP*, is competent for interactions with the Bcl-2 protein partners. In TCTP*, the BH3-like region is unpinned and accessible to Bcl-xL/Mcl-1 proteins and the core structure is also in MG state. We also collected preliminary interaction data between TCTP and sertraline, RNA, the RNA binding YB-1 protein and the MDM2 N-terminal domain. Finally, we characterized the Plk-1-mediated S46 phosphorylated TCTP (pTCTP), a marker of tumor aggressivity and its interaction properties. Overall, this work established the structural versatility of TCTP that is mandatory to exert its cellular functions and this versatility should be taken into account in drug-design strategies targeting TCTP.TCTP est une petite protéine globulaire (20~kDa) qui interagit avec de nombreux partenaires et qui est impliquée dans diverses fonctions cellulaires et physiologiques, avec un rôle bien documenté dans la réversion tumorale qui est un phénomène rare et spontané où une cellule cancereuse perd tout ou partie de son phénotype malin et retrouve des caractéristiques associées aux cellules bénignes telles que la sensibilité à l'apoptose. Dans les cellules cancéreuses, TCTP inhibe la dégradation de MDM2, diminuant ainsi les niveaux de p53 et favorisant le maintien et la progression du cancer. TCTP contient également un motif BH3-like connu pour réguler les membres de la famille Bcl-2 et elle interagit directement avec Bcl-xL et Mcl-1 pour renforcer leurs propriétés anti-apoptotiques. Dans la structure TCTP, le motif BH3-like n'est pas facilement accessible pour une interaction avec un partenaire. Conformément à son importance dans le maintien de la tumeur, TCTP est une cible pharmacologique validée dans le traitement du cancer et fait l’objet d’essais cliniques en cours avec une molécule d'abord connue comme anti-depresseur, la sertraline. Cependant, on en sait peu sur la structure de TCTP en complexe avec ses partenaires, ce qui entrave le développement de médicaments et ne permet pas de comprendre comment TCTP peut s'adapter à une telle variété de partenaires. Ainsi, nous avons étudié le mécanisme moléculaire par lequel TCTP s'associe à des protéines et à des ligands en utilisant diverses méthodes biophysiques (RMN, SAXS, CD, SEC, DSF...). Nous avons démontré que la protéine TCTP se lie à Bcl-xL et à Mcl-1 dans le sillon de liaison des motifs BH3. Dans les complexes, la région BH3-like est engagée dans l'interface intermoléculaire et la structure centrale de TCTP est déstabilisée dans un état de globule fondu (molten-globule). Nous avons en outre montré que seule une forme mineure pré-existante de TCTP, à savoir TCTP*, est compétente pour les interactions avec les partenaires Bcl-xL et Mcl-1. Dans TCTP*, la région BH3-like est détachée du domaine structuré et elle est accessible aux protéines Bcl-xL/Mcl-1 tandis qu'on retrouve un état globule fondu dans la partie globulaire de TCTP*. Nous avons également collecté des données d'interaction préliminaires entre TCTP et la sertraline, des ARN, la protéine YB-1 se liant à l'ARN et le domaine N-terminal de MDM2. Enfin, nous avons caractérisé TCTP phosphorylé (pTCTP) au résidu S46 en utilisant la Plk-1 car cette modification a un impact sur les interactions et est un marqueur de l'aggressivité tumorale. En résumé, ces travaux ont établi la versatilité de TCTP en terme de structure et ont montré que cette versatilité est indispensable pour exercer ses fonctions cellulaires. En conséquence, ceci devrait être pris en compte dans les stratégies de développement de nouvelles molécules thérapeutiques ciblant TCTP

Structural Insights into TCTP and Its Interactions with Ligands and Proteins

International audienc

Cryptic species as a window into the paradigm shift of the species concept

International audienceThe species concept is the cornerstone of biodiversity science, and any paradigm shift in the delimitation of species affects many research fields. Many biologists now are embracing a new “species” paradigm as separately evolving populations using different delimitation criteria. Individual criteria can emerge during different periods of speciation; some may never evolve. As such, a paradigm shift in the species concept relates to this inherent heterogeneity in the speciation process and species category which is fundamentally overlooked in biodiversity research. Cryptic species fall within this paradigm shift: they are continuously being reported from diverse animal phyla but are poorly considered in current tests of ecological and evolutionary theory. The aim of this review is to integrate cryptic species in biodiversity science. In the first section, we address that the absence of morpho- logical diversification is an evolutionary phenomenon, a “process” counterpart to the long studied mechanisms of morphological diversification. In the next section regarding taxonomy, we show that molecular delimitation of cryptic species is heavily biased towards dis- tance-based methods. We also stress the importance of formally naming of cryptic species for better integration into research fields that use species as units of analysis. Finally, we show that incorporating cryptic species leads to novel insights regarding biodiversity pat- terns and processes, including large-scale biodiversity assessments, geographic variation in species distribution and species coexistence. It is time for incorporating multicriteria spe- cies approaches aiming to understand speciation across space and taxa, thus allowing inte- gration into biodiversity conservation while accommodating for species uncertainty

Faune stygobie : émergence d'un monde inconnu

Cave faunas : the emergence of an unknown world Often out of reach and invisible, the life in subterranean waters remained for a long time secret or anecdotal. The stygobie fauna characterized by an exclusive life in subterranean waters is however well developed. Rhone-Alpes has around 130 species, mostly molluscs and crustaceans. Approximately 78 % of the current regional knowledge is post-1960 and recent researches show that the regional biodiversity is widely under-estimated. The knowledge in terms of occurrence and abundance of the species remain very partial because of an under exploration of certain types of aquifers (porous and fissured) and of many geographical areas. The stygobie fauna was only taken into account in the inventories of patrimonial species to protect it in a very marginal way, although numerous forms are rare, endemic, or vulnerable.Souvent hors de portée et invisible, la vie dans les eaux souterraines est restée très longtemps secrète ou anecdotique. La faune stygobie, caractérisée par une vie exclusive dans les eaux souterraines, est cependant bien développée. En région Rhône-Alpes elle est représentée par plus de 130 espèces appartenant en majorité au groupe des Mollusques et surtout des Crustacés. Environ 78 % de la connaissance régionale actuelle est postérieure à 1960 et des recherches récentes montrent que la biodiversité régionale est largement sous estimée. Les connaissances en termes d'occurrence et d'abondance des espèces restent très partielles en raison d'une sous exploration de certains types d'aquifères (poreux et fissurés) et de certaines aires géographiques. La faune stygobie n'a été prise en compte dans les inventaires d'espèces patrimoniales ou à protéger que de manière très marginale, bien que de nombreuses formes soient rares, endémiques, ou vulnérables.Dole Olivier Marie-José, Malard Florian. Faune stygobie : émergence d'un monde inconnu. In: Bulletin mensuel de la Société linnéenne de Lyon, hors-série numéro 2, 2010. Évaluation de la biodiversité rhônalpine. pp. 145-152

L'aquifère de la source du Lez : un réservoir d'eau... et de biodiversité

The Lez spring aquifer : a reservoir of water... and biodiversity (Hérault, France). The Lez spring is the main source of drinking water for the inhabitants of the city of Montpellier. This spring has been exploited since the eighteenth century but the amount of groundwater pumped has markedly increased over the last 30 years. This karst harbours an extremely diversified community of groundwater species (at least 37 species) that is a several Million-year-old heritage. Overpumping induces a loss of habitats by lowering the water table during periods of low groundwater recharge. It also results in an artificial fragmentation of mesohabitats by increasing the hydraulic disconnection of different regions in the saturated zone. Thus, overpumping may strongly affect the groundwater fauna but few data are available yet to evaluate the potential loss of biodiversity. There is clearly a need to integrate studies of groundwater fauna within the framework of interdisciplinary groundwater monitoring, management and/or protection programmes.La source du Lez est la principale source en eau potable pour la ville de Montpellier. Elle est exploitée depuis le 18e siècle, mais la quantité d'eau pompée a augmenté considérablement pendant les 30 dernières années. Cette source n'est pas seulement une ressource en eau potable mais un véritable réservoir de biodiversité. En effet, l'aquifère abrite une riche communauté d'organismes aquatiques souterrains (au moins 37 espèces) qui constitue un patrimoine vieux de plusieurs millions d'années. Les pompages effectués sur la source du Lez modifient l'importance et la nature des liaisons hydrauliques entre les différents systèmes annexes de l'aquifère. Ces conséquences peuvent fortement affecter la faune souterraine. Des études écologiques sont nécessaires afin de déterminer les effets de tels pompages sur la perte, la fragmentation et la connectivité des habitats de ce vaste écosystème karstique. Il est donc nécessaire de prendre en compte la faune souterraine dans les programmes de gestion des eaux souterraines.Malard Florian, Gibert Janine, Laurent Roger. L'aquifère de la source du Lez : un réservoir d'eau... et de biodiversité. In: Karstologia : revue de karstologie et de spéléologie physique, n°30, 2e semestre 1997. Interprétation morphométrique et spéléogenèse (Basse-Provence) pp. 49-54