Olivier Dézerald

All terrestrial and aquatic ecosystems are connected in some way. This implies that anthropogenic drivers and environmental change affect biodiversity across ecosystem borders. Therefore, we propose studying aquatic ecosystems as part of the land-freshwater-sea (LFS) continuum. Adopting an LFS continuum perspective, and integrating land, freshwater, and marine compartments, would improve our understanding of how aquatic ecosystems function and how they respond to environmental change and human disturbance. Furthermore, we argue that meta-ecosystem theory is a relevant conceptual framework, because it provides a means to understand how the exchange of matter and organisms between ecosystems drives changes in biodiversity and ecosystem services along the LFS continuum. We also highlight research gaps and societal challenges that could be addressed by improving our understanding of the linkages between ecosystems along the LFS continuum. Moreover, we advocate breaking down disciplinary boundaries and fostering institutional change to improve the research and management of aquatic ecosystems.

Abrupt regime shifts of complex ecosystems between alternative stable states are widespread in nature. Yet, our mechanistic understanding of disturbance-shift-ecosystem functioning relationships remains poor, and it is further unclear whether biotic disturbances can drive such shifts. Using a 5-year pond experiment, we demonstrate that invasion by the red swamp crayfish ( Procambarus clarkii ) drove a regime shift from a clear-water, macrophyte-dominated, to a turbid, phytoplankton-dominated state. The regime shift was associated with increased water temperature due to increased water turbidity enhanced light absorption, and with a seasonal switch of ecosystem metabolism from hetero-to autotrophy due to decreased respiration in summer, despite constant gross primary production. Reducing crayfish population densities by 44 % failed to move ecosystems back towards their initial state and functioning. Our results stress that biotic disturbances may have hardly-reversible consequences on the biophysical and biogeochemical processes that support ecosystem functioning.

Les forêts néotropicales accueillent une importante biodiversité encore méconnue. L’intégrité des écosystèmes naturels est menacée par les changements environnementaux (e.g., réchauffement climatique, destruction des habitats), par conséquent, identifier les facteurs structurants, naturels et anthropiques, du fonctionnement des écosystèmes, représente un défi scientifique crucial. L’inhérente complexité de ces milieux diversifiés pose de nombreux problèmes conceptuels et logistiques comme un échantillonnage exhaustif et/ou l’identification des espèces. Les broméliacées à réservoirs sont des écosystèmes miniatures adéquats pour pallier ces difficultés, car elles retiennent de l’eau de pluie et accumulent de la matière organique au creux de leurs feuilles, permettant ainsi de supporter des réseaux trophiques simples d’invertébrés aquatiques. Elles peuvent être échantillonnées exhaustivement, ont une forte abondance locale, et une large aire de répartition. De l’échelle locale à biogéographique, les travaux de cette thèse visent d’abord à comprendre comment ces communautés se structurent en réponse à l’hétérogénéité naturelle des forêts amazoniennes (e.g., ouverture de la canopée, fluctuations climatiques saisonnières), puis tente de prédire, par le biais d’expérimentations in situ et au laboratoire les réponses structurelles et fonctionnelles de ces communautés à divers scénarios de changement climatique. Une attention particulière a été portée sur l’impact de la température et des précipitations sur la physiologie et le comportement d’espèces clefs, et sur les interactions trophiques au sein des communautés.

1. Environmental DNA (eDNA) metabarcoding of water samples is increasingly used to detect fish species in streams. Several studies have concluded that it can outperform traditional inventory methods and recommend using it at large scales for fish-based ecological assessments. However, there is no standard protocol that can guarantee sufficient detection rates and repeatability, despite companies offering an extensive range of analyses. 2. We compared eDNA metabarcoding performed by four companies. Following their guidelines, samples were collected in a small tropical stream in the Maroni River (French Guiana) that hosts a species-rich fish community. We compared their inventories to each other and to a list of species captured during an extensive fish inventory performed immediately after sampling eDNA, as well as to current data on the species’ distributions. 3. The number of species detected by eDNA metabarcoding ranged from 5 to 48 among the companies, but these inventories contained many inaccuracies. All companies combined, 63 species were detected, of which 10 (16%) had never been reported in the Maroni River. The extensive inventory identified 50 species in the local fish community, of which 16-46 were not detected by eDNA metabarcoding (i.e. false negative detection rate of 32%-92% among the companies). 4. Reanalysis of raw sequencing data decreased differences among companies greatly, highlighting the importance of using a comprehensive and accurate DNA barcode database to assign species. Dissimilarity indices, calculated to compare the local fish community (based on presence/absence or fish catches) to eDNA detection, revealed large differences regardless of the company. 5. Summary and applications. The large percentage of species not detected by eDNA metabarcoding of water samples could strongly bias fish-diversity inventories in streams that host species-rich communities. This issue is not well documented in the literature, and we recommend that similar studies in the future focus on other stream contexts. The large differences between commercial eDNA inventories and the local fish community challenge the use of eDNA metabarcoding for fish-based ecological assessments of streams. The variable performance of eDNA companies indicates the need for a standard protocol and access to a comprehensive DNA database before beginning large-scale eDNA programmes. Highlights: - eDNA metabarcoding of water samples is widely used to detect species in streams - Detection performances of 4 private companies were compared to an exhaustive fish inventory - The number of undetected species varies from 32 to 92% depending on the company - Such discrepancies challenge the use of eDNA for fish-based ecological assessments

The elemental content of organisms links cellular biochemistry to ecological processes, from physiology to nutrient dynamics. While plant stoichiometry is thought to vary with climate and nutrient availability across latitudes, the consistency of these patterns across trophic groups and realms remains unclear. Using the StoichLife database, which includes nitrogen and phosphorus content data for 5443 species across 1390 sites, we examine how solar energy (temperature, radiation) and nutrients (nitrogen and phosphorus) influence stoichiometric variation. We find that plant stoichiometry in terrestrial and freshwater ecosystems is more strongly associated with environmental gradients, particularly nitrogen deposition, than animal stoichiometry. Contrary to expectations, temperature, radiation, and labile P show limited global effects. Latitudinal patterns in stoichiometry are more closely associated with species turnover rather than intraspecific variation. Given the strong links between stoichiometry and organismal performance, these findings underscore the need to predict the ecological consequences of anthropogenic disruption to global biogeochemical cycles.

Habitat modification in freshwaters is a dominant cause of lamprey population decline. While adult lampreys are well studied in the literature, we lack information on the ecology of larval stages. Larva, or ammocetes, require specific habitats for their development, but the key characteristics of microhabitats (substrate features, biological interactions) that influence lamprey larva remain poorly understood. The main objective of this study is to evaluate whether structure from motion photogrammetry can be used as a non‐destructive tool to predict the presence of larval lampreys in stream microhabitats, and how its predictive performance compares to models that include additional biological data. To complement the photogrammetric approach, we conducted surveys of macroinvertebrate communities to explore potential biological interactions influencing lamprey larvae. Despite challenging environmental conditions (e.g., high turbidity, low depth), we achieved a 63% success rate in generating 3D point clouds of habitat patches. The results obtained from photogrammetry suggest that the average thickness of surface features above the streambed (e.g., leaves, branches, pebbles) were positively correlated with the presence of lamprey larva. Our analyses of macroinvertebrate communities show that the presence of Ephemera is negatively correlated with the presence of lampreys. Additional analyses show that models with both biological and photogrammetric descriptors are more accurate at predicting ammocoetes presence in patches compared to those with photogrammetric descriptors alone. Although slightly less accurate (by 7.5%), the model based on photogrammetry alone offers the key advantage of being entirely non‐destructive and relying on standardized method, facilitating its consistent application for high resolution monitoring. With a few improvements, subaquatic photogrammetry can thus be used as a non‐destructive and high‐frequency approach to assess the habitat suitability for larva lamprey in streams.

The elemental content of life is a key trait shaping ecology and evolution, yet organismal stoichiometry has largely been studied on a case-by-case basis. This limitation has hindered our ability to identify broad patterns and mechanisms across taxa and ecosystems. To address this, we present StoichLife, a global dataset of 28,049 records from 5,876 species spanning terrestrial, freshwater, and marine realms. Compiled from published and unpublished sources, StoichLife documents elemental content and stoichiometric ratios (%C, %N, %P, C:N, C:P, and N:P) for individual plants and animals. The dataset is standardized and, where available, includes information on taxonomy, habitat, body mass (for animals), geography, and environmental conditions such as temperature, solar radiation, and nutrient availability. By providing an unprecedented breadth of organismal stoichiometry, StoichLife enables the exploration of global patterns, ecological and evolutionary drivers, and context-dependent variations. This resource advances our understanding of the chemical makeup of life and its responses to environmental change, supporting progress in ecological stoichiometry and related fields.

Aim: Arthropods are under‐represented in paleoecological studies but are critical agents in ecological processes. Despite rigorous documentation of diverse arthropod assemblages from ancient rodent (or paleo) middens worldwide, their use for studying ancient arthropod diversity has stalled in recent decades. Here, we review published studies to identify how paleomidden arthropods can be leveraged to address significant questions in ecology and synthesise spatiotemporal trends in ancient arthropod diversity.Location: Global with a focus on the Americas.Time Period: From ~40,000 to 100 years before present.Major Taxa Studied: Fossil arthropods preserved in rodent paleomiddens.Methods: We identified four primary objectives in ecology that can be advanced using paleomidden arthropod fossils: the reconstruction of ancient biodiversity, the elucidation of mechanisms and processes driving arthropod range shifts, the incorporation of arthropods into ancient trophic webs, and the assessment of adaptive responses to changing environments.Results: We identified 20 papers reporting arthropod remains, of which 14 provided data suitable for quantitative analyses. Although no significant differences in arthropod community diversity were found across broad geographic regions, substantial differences in community structure were observed. In North America, we also detected a decline in arthropod diversity from 10 to 5 ka BP, driven primarily by the absence of high‐diversity assemblages during this period.Main Conclusions: Paleomidden arthropods remain an underutilised ecological resource that can be leveraged to improve the inferential scope of arthropod research across spatiotemporal gradients. Collaboration between paleo‐ and neoecologists could help expand the sampling of ancient and modern arthropod communities, particularly those associated with paleomiddens, to create high‐resolution datasets spanning important periods in biogeographical history. Paleomidden arthropods will remain a fundamental component for understanding arthropod biodiversity changes in the past, present, and future.

Intraspecific variability is fundamental to ecology, yet we still know remarkably little about what governs the strength of the associations between traits expressed by individuals and ecological dynamics. To explore this overlooked aspect of diversity, we asked whether the strength of correlations between traits and a wide spectrum of ecological responses could differ ( i ) between intraspecific levels (among vs . within populations), ( ii ) among ecological responses across levels of biological organization (from ecological performance to ecosystem functioning), and ( iii ) among trait types (morphology, physiology, and behavior). We performed a meta-analysis synthesizing over a thousand effect sizes from nearly two hundred studies spanning approximately a hundred animal species across a broad range of traits and ecological responses. The average effect size was | r | = 0.26 (95% confidence interval: 0.21 – 0.30). At the individual level, effect sizes were larger for ecological performance (foraging, diet) than for fitness (reproduction), and tended to be larger for community responses (e.g., community composition of surrounding organisms). Physiology and behavior showed larger effect sizes than morphology. Our meta-analysis not only confirms that intraspecific trait variability is central to ecological dynamics, but also highlights physiology and behavior as key traits for unraveling the ecological consequences of individual variability.