Biology subjects

Fontaine, L.

Publications and source records attributed to Fontaine, L..

4 recordsLinked to original sources

bioRxiv2024

Low determinism in pelagic fungal community assembly across climate zones in Scandinavian lakes

In lakes, fungi play pivotal roles in biogeochemical processes, particularly in the decomposition of organic matter. However, these organisms have been historically underrepresented and taxonomically unresolved in previous research. In this study, we employ high-resolution sequencing to delve into the fungal diversity within two distinct Scandinavian lake datasets spanning a vast latitudinal gradient, diverse climatic zones ranging from nemoral to arctic, and a wide spectrum of nutrient conditions. Utilizing eukaryotic primers, we reveal that fungi contribute, on average, 2.07% in the Norwegian and 5.4% in the Swedish sequencing dataset, with remarkable spikes of up to 55% in forested lakes. Fungal-specific sequencing identified the prevalence of several fungal phyla, including Ascomycota, Rozellomycota, Basidiomycota, Chytridiomycota, Aphelidiomycota, and Mortierellomycota. Notably, our research uncovers a striking degree of variability in fungal communities across the studied lakes, defying correlations with measured environmental factors or geographic distance. Null model analyses suggest that deterministic processes do not consistently override the influence of ecological drift in shaping these biogeographic patterns. However, signals for dispersal limitations and mass effects could be detected. These findings challenge conventional paradigms of eukaryotic communities being strongly guided by deterministic processes and underscore the complexity of fungal community assembly processes across climate zones.

microbiology↗

bioRxiv2024

Providing insight into the mechanism of action of Cationic Lipidated Oligomers (CLOs) using metabolomics

The increasing resistance of clinically relevant microbes against current commercially available antimicrobials underpins the urgent need for alternative and novel treatment strategies. Cationic lipidated oligomers (CLOs) are innovative alternatives to antimicrobial peptides, and have reported antimicrobial potential. An understanding of their antimicrobial mechanism of action is required to rationally design future treatment strategies for CLOs, either in monotherapy or synergistic combinations. In the present study, metabolomics was used to investigate the potential metabolic pathways involved in the mechanisms of antibacterial activity of one CLO, C12-o-(BG-D)-10, which we have previously shown to be effective against methicillin-resistant Staphylococcus aureus (MRSA) ATCC 43300. The metabolomes of MRSA ATCC 43300 at 1, 3 and 6 h following treatment with C12-o-(BG-D)-10 (48 {micro}g/mL i.e., 3x MIC) were compared to those of the untreated controls. Our findings reveal that the studied CLO, C12-o-(BG-D)-10, disorganized the bacterial membrane as the first step towards its antimicrobial effect, as evidenced by marked perturbations in the bacterial membrane lipids and peptidoglycan biosynthesis observed at early time points i.e., 1, and 3 h. Central carbon metabolism, and biosynthesis of DNA, RNA, and arginine were also vigorously perturbed, mainly at early time points. Moreover, bacterial cells were under osmotic and oxidative stress across all time points, evident by perturbations of trehalose biosynthesis and pentose phosphate shunt. Overall, this metabolomics study has, for the first time, revealed that the antimicrobial action of C12-o-(BG-D)-10 may potentially stem from the dysregulation of multiple metabolic pathways. ImportanceAntimicrobial resistance poses a significant challenge to healthcare systems worldwide. Novel anti-infective therapeutics are urgently needed to combat drug-resistant microorganisms. Cationic lipidated oligomers (CLOs) show promise as new antibacterial agents against Gram-positive pathogens like Staphylococcus aureus (MRSA). Understanding their molecular mechanism(s) of antimicrobial action may help design synergistic CLO treatments along with monotherapy. Here, we describe the first metabolomics study to investigate the killing mechanism(s) of CLOs against MRSA. The results of our study indicate that the CLO, C12-o-(BG-D)-10, had a notable impact on the biosynthesis and organization of the bacterial cell envelope. C12-o-(BG-D)-10 also inhibits arginine, histidine, central carbon metabolism, and trehalose production, adding to its antibacterial characteristics. This work illuminates the unique mechanism of action of C12-o-(BG-D)-10 and opens an avenue to design innovative antibacterial oligomers/polymers for future clinical applications.

microbiology↗

bioRxiv2021

Neural networks and extreme gradient boosting predict multiple thresholds and trajectories of microbial biodiversity responses due to browning

Ecological association studies often assume monotonicity such as between biodiversity and environmental properties although there is growing evidence that non-monotonic relations dominate in nature. Here we apply machine learning algorithms to reveal the non-monotonic association between microbial diversity and an anthropogenic induced large scale change, the browning of freshwaters, along a longitudinal gradient covering 70 boreal lakes in Scandinavia. Measures of bacterial richness and evenness (alpha diversity) showed non-monotonic trends in relation to environmental gradients, peaking at intermediate levels of browning. Depending on the statistical methods, variables indicative for browning could explain 5% of the variance in bacterial community composition (beta diversity) when applying standard methods assuming monotonic relations and up to 45 % with machine learning methods (i.e. extreme gradient boosting and feed-forward neural networks) taking non-monotonicity into account. This non-monotonicity observed at the community level was explained by the complex interchangeable nature of individual taxa responses as shown by a high degree of non-monotonic responses of individual bacterial sequence variants to browning. Furthermore, the non-monotonic models provide the position of thresholds and predict alternative bacterial diversity trajectories in boreal freshwater as a result of ongoing climate and land use changes, which in turn will affect entire ecosystem metabolism and likely greenhouse gas production.

microbiology↗

bioRxiv2020

Genetics of nodulation in Aeschynomene evenia uncovers new mechanisms of the rhizobium-legume symbiosis

Among legumes (Fabaceae) capable of nitrogen-fixing nodulation, several Aeschynomene spp. use a unique symbiotic process that is independent of Nod factors and infection threads. They are also distinctive in developing root and stem nodules with photosynthetic bradyrhizobia. Despite the significance of these symbiotic features, their understanding remains limited. To overcome such limitations, we conducted genetic studies of nodulation in Aeschynomene evenia, supported by the development of a genome sequence for A. evenia and transcriptomic resources for 10 additional Aeschynomene spp. Comparative analysis of symbiotic genes substantiated singular mechanisms in the early and late nodulation steps. A forward genetic screen also showed that AeCRK, coding a novel receptor-like kinase, and the symbiotic signaling genes AePOLLUX, AeCCamK, AeCYCLOPS, AeNSP2 and AeNIN, are required to trigger both root and stem nodulation. This work demonstrates the utility of the A. evenia model and provides a cornerstone to unravel new mechanisms underlying the rhizobium-legume symbiosis.

plant biology↗