Laurent Fontaine

• Fontaine, Laurent; Pin, Lorenzo; Savio, Domenico; Friberg, Nikolai; Kirschner, Alexander K. T. & Farnleitner, Andreas H. [Show all 7 contributors for this article] (2023). Bacterial bioindicators enable biological status classification along the continental Danube river. Communications Biology. ISSN 2399-3642. 6. doi: 10.1038/s42003-023-05237-8. Full text in Research Archive
• Wei, Jing; Fontaine, Laurent; Valiente Parra, Nicolas; Dörsch, Peter; Hessen, Dag Olav & Eiler, Alexander (2023). Trajectories of freshwater microbial genomics and greenhouse gas saturation upon glacial retreat. Nature Communications. ISSN 2041-1723. 14. doi: 10.1038/s41467-023-38806-w. Full text in Research Archive
• Valiente Parra, Nicolas; Eiler, Alexander; Allesson, Lina; Andersen, Tom; Clayer, Francois & Crapart, Camille Marie [Show all 13 contributors for this article] (2022). Catchment properties as predictors of greenhouse gas concentrations across a gradient of boreal lakes. Frontiers in Environmental Science. ISSN 2296-665X. 10. doi: 10.3389/fenvs.2022.880619. Full text in Research Archive
• Fontaine, Laurent; Khomich, Maryia; Andersen, Tom; Hessen, Dag Olav; Rasconi, Serena & Davey, Marie Louise [Show all 7 contributors for this article] (2021). Multiple thresholds and trajectories of microbial biodiversity predicted across browning gradients by neural networks and decision tree learning. ISME Communications. ISSN 2730-6151. 1. doi: 10.1038/s43705-021-00038-8. Show summary

  Ecological association studies often assume monotonicity such as between biodiversity and environmental properties although there is growing evidence that nonmonotonic relations dominate in nature. Here, we apply machine-learning algorithms to reveal the nonmonotonic 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 nonmonotonic 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 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 nonmonotonic responses of individual bacterial sequence variants to browning. Furthermore, the nonmonotonic 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.

• Juottonen, Heli; Fontaine, Laurent; Wurzbacher, Christian; Drakare, Stina; Peura, Sari & Eiler, Alexander (2020). Archaea in boreal Swedish lakes are diverse, dominated by Woesearchaeota and follow deterministic community assembly. Environmental Microbiology. ISSN 1462-2912. 22(8), p. 3158–3171. doi: 10.1111/1462-2920.15058. Full text in Research Archive Show summary

  Despite their key role in biogeochemical processes, particularly the methane cycle, archaea are widely underrepresented in molecular surveys because of their lower abundance compared with bacteria and eukaryotes. Here, we use parallel high-resolution small subunit rRNA gene sequencing to explore archaeal diversity in 109 Swedish lakes and correlate archaeal community assembly mechanisms to large- scale latitudinal, climatic (nemoral to arctic) and nutrient (oligotrophic to eutrophic) gradients. Sequencing with universal primers showed the con- tribution of archaea was on average 0.8% but increased up to 1.5% of the three domains in forest lakes. Archaea-specific sequencing revealed that freshwater archaeal diversity could be partly explained by lake variables associated with nutrient status. Combined with deterministic co-occurrence patterns this finding suggests that ecological drift is overridden by environmental sorting, as well as other deterministic processes such as biogeographic and evolutionary history, leading to lake-specific archaeal biodiversity. Acetoclastic, hydrogenotrophic and methylotrophic methanogens as well as ammonia- oxidizing archaea were frequently detected across the lakes. Archaea-specific sequencing also revealed representatives of Woesearchaeota and other phyla of the DPANN superphylum. This study adds to our understanding of the ecological range of key archaea in freshwaters and links these taxa to hypotheses about processes governing biogeochemical cycles in lakes.

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