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Background Lake littoral sediments are dynamic environments supporting diverse ecological functions, yet the temporal dynamics of their microbial communities remain understudied. This study investigated the temporal changes in microbial communities within the surficial sediments of Lake Bourget, with a high temporal resolution (2.3 ± 2 days over five months). We hypothesized that microbial temporal dynamics are shaped by different ecological processes (deterministic vs. stochastic), depending on the organizational scales considered. To test this, we examined patterns at both the whole-community and sub-community (module) scales, combining β-diversity metrics with co-occurrence network analysis. Results At the community scale, temporal changes in microbial composition were relatively constrained. Null model analysis indicated that stochastic processes, such as ecological drift and homogenizing dispersal, predominated, while deterministic processes from environmental variables played a minimal role. This was supported by variance partitioning, which showed that environmental parameters explained only 17% of the temporal variation in community structure. By reducing the community into smaller co-varying groups of taxa (modules) using network-based clustering, we identified six microbial modules, each with distinct temporal patterns. The two largest modules showed contrasting responses to environmental variables, highlighting distinct ecological niches succeeding over time. At the module scale, environmental variables explained a larger fraction of temporal variation (up to 51% for Module M3), indicating that deterministic processes, particularly environmental filtering, played a more dominant role than at the whole-community scale. Conclusion Our study demonstrates that considering multiple organizational scales within microbial communities provides deeper insights into the ecological processes driving microbial temporal dynamics. Finer-scale resolution via network modules reveals patterns and drivers that may be masked at the broader community level, allowing for a better understanding of the balance between stochastic and deterministic forces in sediment microbiomes.

The “bloody-red shrimp” species Hemimysis anomala , native to the Ponto-Caspian Region, has spread rapidly and adapted over recent decades to new aquatic ecosystems worldwide, causing many ecological alterations. The reported impacts associated with this invasion are numerous, including overall food web structure modifications. This review focuses on H. anomala , examining its biology, ecology, distribution and ecological impacts. The species’ rapid success is attributed to its high fecundity, fast growth rates and broad adaptability to various habitats. Recent observations suggest that its distribution may expand further, especially in Western European lakes, reservoirs and the Laurentian Great Lakes. We present insights into its habitat, seasonal dynamics and influence on trophic interactions within native zooplankton communities. Additionally, we discuss methods used to study H. anomala , including citizen-science initiatives that enhance data collection and community engagement. The objective of this research is to provide up-to-date pieces of information on H. anomala ’s ecology, including new data on its habitat preferences collected through scientific diving and participatory research. By characterising the spatial and temporal variation in its occurrence and abundance, we identify key environmental and biotic factors that may limit or support its further spread. We also highlight knowledge gaps and research priorities for future studies to better assess its impacts on the food webs of invaded ecosystems.

Lakes are essential ecosystems that provide a large number of ecosystem services whose quality is strongly impacted by human pressures. Optimal uses of lakes require adapted magement practices which in turn rely on physico-chemical and biological monitoring. Long-term ecological monitoring provides large sets of environmental data. When such data are available, they have to be associated to metadata and to be stored properly to be accessible and useable by the scientific community. We present a data informatics system accessible to anyone who requests it. Maintained online since 2014 (https://si-ola.inrae.fr), it is origited from the Observatory on LAkes (OLA). It contains long-term data from 4 peri-alpine lakes (Lakes Aiguebelette, Annecy, Bourget, Geneva/Léman) and 24 high-altitude lakes of the northern French Alps. We describe the generated long-term data series, the data type, the methodologies and quality control procedures, and the information system where data are made accessible. Data use is allowed under the condition of providing reference to the origil source. We show here how such a platform clearly enhances data sharing and scientific collaboration. Various studies referring to these data are regularly published in peer-reviewed jourls; providing in fine a better understanding of lakes’ ecosystems functioning under local and global pressures.

Chironomidae are a major group of littoral secondary producers whose spatial changes in assemblage structures are shaped by diverse variables. Using their subfossil remains, we aimed at disentangling the relative impact of environmental, topographic, littoral occupation and hydrodynamic variables on the littoral assemblages as well as identifying taxa and sites of primary importance for the β-diversity in a large lake (Lake Bourget). A redundancy analysis coupled with a variance partitioning indicated that 22 % of the assemblage variability was explained by slope, carbonate concentration and littoral occupation. A non-negligible fraction of non-separable variance among these variables likely highlights the topographic constraint on anthropogenic development and environmental conditions. Taxonomic turnover overwhelmingly (93.2 %) dominated the assemblage changes indicating site-specific taxonomic composition. The taxa contribution to β-diversity was positively correlated with their mean abundances. The local abundances were either positively or negatively correlated with local contribution of sites to β-diversity (LCBD) providing evidence for different contributions of taxa to β-diversity. A couple of taxa ( i.e. Cricotopus spp., Microtendipes sp. and Cladotanytarsus sp.) and sites ( i.e. LB57, LB31, LB2) clearly supported the major variations of β-diversity and are therefore identified as being of primary importance regarding conservation programs. Both LCBD variations and taxa spatial autocorrelations suggest that chironomid assemblages were the most variable at a spatial-scale ranging from 500 m to 1 km, characterizing the spatial successions of littoral contexts. These results illustrate the need for considering short spatial scales to reveal the extent of the benthic diversity in the littoral areas of large lakes. Les Chironomidae constituent un groupe important de producteurs secondaires littoraux dont les changements spatiaux dans les structures d'assemblage sont façonnés par diverses variables. À partir de leurs restes subfossiles, le rôle relatif des variables environnementales, topographiques, de l'occupation du littoral et de l'hydrodynamisme sur les assemblages littoraux a été recherché avant d'identifier les taxons et les sites de première importance pour la diversité β dans un grand lac alpin (le lac du Bourget). Une analyse de redondance couplée à un partitionnement de la variance a indiqué que 22 % de la variabilité des assemblages était expliquée par la pente, la concentration de carbonate et l'occupation du littoral. Une fraction non négligeable de la variance non séparable parmi ces variables met probablement en évidence l'effet de la contrainte topographique sur le développement anthropique et les conditions environnementales. Le renouvellement taxonomique a dominé les changements d'assemblage (93,2 %) mettant en évidence des compositions taxonomiques spécifiques pour les différents sites. La contribution des taxons à la diversité β était positivement corrélée à leur abondance moyenne, tandis que les abondances locales étaient corrélées positivement ou négativement à la contribution locale des sites à la diversité β (LCBD), suggérant différentes contributions des taxons à la diversité β. Un ensemble de taxons ( Cricotopus spp., Microtendipes sp. et Cladotanytarsus sp.) et des sites (LB57, LB31, LB2) supportaient clairement les variations majeures de la diversité β et sont donc identifiés comme étant d'intérêt prioritaire pour des actions de conservation. Les variations de LCBD et les autocorrélations spatiales des taxons suggèrent que les assemblages de chironomes étaient les plus variables à une échelle spatiale allant de 500 m à 1 km, caractérisant les successions spatiales des contextes littoraux. Ces résultats illustrent la nécessité d'envisager de courtes échelles spatiales pour appréhender la diversité benthique dans les zones littorales des grands lacs alpins.

Recent decades have witnessed widespread deoxygenation of temperate lakes. The intricate interplay between climate change and nutrient loading and its impact on oxygen dynamics still lacks clear understanding. We develop a paleo-data-model coupling approach to investigate long-term variations of dissolved oxygen conditions in Lake Geneva over the period 1850-2100. Our approach provides first estimates of oxygen baseline conditions and quantifies duration of hypoxia since pre-disturbance. Over the 19 th and 20 th centuries, an increase in DO consumption rates (from 0.3 to 2.5 g O 2 m À2 d À1 ) following nutrient over-enrichment caused the onset of hypoxia, and its intensity and duration were governed by the combined influence of climatic forcing and high phosphorus concentration. In the future, hypoxia will be primarily disrupted by reduced frequency of full mixing events.

Trophic interactions are central in understanding ecosystem processes and the management of natural ecosystems but are frequently complex to estimate. To address this issue, body size has been shown to be a useful trait to reconstruct species interactions, particularly in aquatic ecosystems. An allometric niche model (aNM) considering body size as a niche trait is proposed to predict trophic interactions in temperate freshwater ecosystems. The aNM calibration was based on 26 ubiquitous freshwater species with known minimal and maximum prey body sizes that permitted the establishment of prey body size ranges for vertebrate and invertebrate consumers. The aNM inferences were validated for 13 empirical freshwater food webs, and the model was applied to an extensive inventory of 474 species (spanning six orders of body size magnitude) from the largest natural French lake (Lake Bourget). This application permitted to strengthen the aNM validation with predator‐prey mass ratio comparisons, predicted diet analyses, and allowed the exploration of the lake food web structure. The aNM provided appreciable intrinsic validity (specificity = 87 ± 12%, sensitivity = 59 ± 29%, accuracy = 81 ± 10%), and departures among inferred and empirical trophic interactions were explained by foraging specificities or limited sampling of stomach contents. In Lake Bourget, 26,037 trophic links were inferred. Predator–prey mass ratios for vertebrates and invertebrates were consistent with those empirically established and were occasionally higher for invertebrates as the aNM considers small prey (e.g., bacteria) as possible resources for invertebrates. The inferred diets for three species selected for their well‐known foraging ecology also revealed plausible outcomes of the aNM. The nested structure of the lake food web was determined by highlighting different topologies among the benthic and the pelagic food sub‐webs and the role of top predator fish in the coupling of both food sub‐webs. Due to the large number of species inventories available worldwide for freshwater ecosystems anchored in the ecological monitoring, the aNM may represent a valuable tool for both ecologists and managers to address complementary facets of applied biodiversity studies (e.g., reconstruct highly resolved food webs, predict pressures on important species or new interactions with invasive species).

Non-native species are a major threat to aquatic ecosystems and the assessment of their invasiveness may be limited by the diverse ecological features needed to be accounted for. In this study, we combined complementary features of the autoecology and trophic ecology of Hemimysis anomala in a large deep lake (Lake Bourget) to assess its invasiveness. It was present in more than 80% of the 23 sites explored, indicating an extensive colonization of the lake. The mysid exhibited at least two generations per year, and the median individual growth rate was ~ 0.04 mg dry mass day−1 and ~ 0.09 mg dry mass day−1 for juveniles and adults, respectively. Consequently, the daily production for a typical reproductive swarm could reach more than 250 mg dry mass day−1 m−2 representing an important hotspot of secondary production. Individual measurements of stable carbon (δ13C) and nitrogen (δ15N) isotopes highlighted a trophic ontogenetic shift and indicated that subpopulations of H. anomala could mainly rely either on benthic or pelagic resources depending on the slope of the site. Because of its extensive colonization, its high growth rate, and trophic plasticity, H. anomala exhibits a high invasiveness and may strongly alter the food web of Lake Bourget.

A study of trace metal (TM) contamination was conducted at Lake Tonga (Algeria), a site surrounded by several indirect contamination point sources such as an abandoned mine and steelworks. Studying two sampling sites over four seasons, we were able to depict the spatial and temporal variability of TM contamination in the lake. Among the seven TM examined (Pb, Cd, Fe, Zn, Ni, Cu, and Cr), only Fe, Pb, and Cd showed concentrations significantly higher than the site’s geological background. The contamination index (sediment concentration/background concentration) calculated for these three TM (Cd = 1.9 ± 1.6, Fe = 6.8 ± 1.8, and Pb = 3.3 ± 2.6) clearly indicated anthropogenic contamination. Sediment TM contamination differed both between sampling sites and seasons despite environmental variables (e.g., oxygen and pH) being similar, thus suggesting different TM contamination sources. Fe contamination was high at the two sampling sites and over all studied seasons, possibly indicating general lake-scale Fe contamination, probably related to atmospheric deposition of steelworks emissions both on the lake and within the watershed. Lake tributaries were further suspected of channeling Fe contamination from the watershed into the lake. On the other hand, the sampling site close to the outlet was especially rich in Cd and Pb typically reflecting contamination by mine wastes. The indirect connection between the abandoned mine and the lake indicates that runoff of mine leachates through groundwater was likely a candidate in explaining the specificity of the TM contamination in this part of the lake. This study provides insights for management of TM contamination by addressing both spatial and temporal variability within the lake as well as differences in contamination sources.

The trophic niche of invasive species can vary overtime because of different processes related to ecological opportunity and invader activity that condition biological interactions with the native biodiversity. We conducted an annual-based survey of the trophic niche of the mysid Hemimysis anomala in the largest European peri-alpine lake by combining molecular and isotope analyses. We hypothesized that the population trophic niche width would vary seasonally, expanding in warm periods due to greater ecological opportunities and higher mysid metabolic activity. Molecular analyses identified a diversified set of prey throughout the year ranging from autotrophic protists to zooplankton and converged with isotope analyses to support the diet seasonality hypothesis of H. anomala with wider trophic niches and, in a lower extent, richer diets in spring and summer when compared to autumn and winter. Isotope analyses also highlighted a seasonal pattern in resources used with a dominance of pelagic reliance in summer and autumn. These results underlined the significant seasonal variability in the trophic niche of this invasive mysid suggesting that future assessments of its ecological impacts should account for the temporal variations of its trophic interactions with the native biodiversity.

To attempt to determine the effects of temperature and salinity on the dynamics of the dinoflagellate community, a monthly sampling was carried out from October 2008 to March 2009 at eight sampling stations in Ghar El Melh Lagoon (GML; Mediterranean Sea, Northern Tunisia). Dinoflagellates were dominant among plankton, accounting for 73.9 % of the lagoon’s overall plankton community, and were comprised of 25 different species among which 17 were reported in the literature as harmful. While no significant difference was found in the distribution of dinoflagellates among the stations, a strong monthly difference was observed. This temporal variability was due to an increase in the abundance of Prorocentrum micans from December to February, leading to a strong decrease in the Shannon diversity index from station to station. At the onset of P. micans development, dinoflagellate abundances reached 1.26.10 5 cells l −1 . A redundance analysis indicates that both temperature and salinity have a significant effect on the dynamics of the dinoflagellate community. Using a generalized additive model, both temperature and salinity appear to have significant nonlinear relationships with P. micans abundances. Model predictions indicate that outbreaks of P. micans may occur at a temperature below 22.5 °C and with salinity above 32.5. We discuss our results against a backdrop of climate change which, by affecting temperature and salinity, is likely to have an antagonistic impact on P. micans development and subsequently on the dinoflagellate dynamics in GML.