Alexander Eiler

In lakes, fungi play pivotal roles in biogeochemical processes, particularly in the decomposition of organic matter. However, these organisms have been 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 data sets spanning a vast latitudinal gradient across Norway and Sweden, diverse climatic zones ranging from nemoral to arctic, and a wide spectrum of nutrient conditions. Utilizing eukaryotic 18S primers, we reveal that fungi contribute, on average, 2.07% in the Norwegian and 5.4% in the Swedish sequencing data set, with remarkable spikes of up to 55% in forested lakes. Fungus-specific 5.8S-ITS2 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. Null model analyses on the entire community, as well as subsets of transient and resident members, revealed that deterministic selection plays a secondary role. Instead, community assembly was overwhelmingly governed by stochastic ecological drift across all tested groups. These findings challenge conventional paradigms of eukaryotic communities being strongly guided by deterministic processes and underscore the complexity of community assembly processes across the fungal kingdom. The dominance of ecological drift and stochasticity in the assembly process emphasizes that conservation should target entire communities, processes, and areas instead of single species, as should be the case in deterministically assembled communities. IMPORTANCE: Fungi perform a range of key functions in freshwater environments. Here, we show that fungi, including members of the phyla Ascomycota , Rozellomycota , Basidiomycota , and Chytridiomycota , represent a diverse part of the epilimnetic planktonic community in Scandinavian lakes. Fungal community assembly across northern climate zones is shown to have a low signal for determinism, as environmental sorting was weak in overwriting dispersal-related processes and ecological drift. Furthermore, we expand knowledge of the ecological range of key freshwater fungi and link taxa to biogeographic patterns in lakes.

As ecologists increasingly use metagenomic time series to track evolution in the wild, there is a risk of misinterpreting ecological dynamics as rapid adaptation. This Perspective identifies methodological limitations that generate misleading signatures of microbial evolution. A primary issue is confusing evolutionary change (driven by de novo mutation or horizontal gene transfer) with ecological lineage turnover, such as seasonal oscillations or the reactivation of dormant lineages. Current metagenome-assembled genomes can collapse micro-diverse lineages and decouple adaptive mobile elements, creating inaccurate genomic signatures of sweeps or stasis. To address these issues, I propose a framework integrating long-read sequencing, pangenome graph theory, and forward-time simulations to model populations as temporal genetic networks and better resolve microbial evolutionary dynamics.

Permafrost landscapes act as reservoirs for per- and polyfluoroalkyl substances (PFASs) and represent crucial carbon pools in the global carbon cycle. With the intensification of climate warming, permafrost is undergoing rapid degradation, exposing previously trapped organic carbon to microbial decomposition and thereby leading to substantial greenhouse gas emissions. However, this thaw also liberates legacy chemical pollutants into active biological zones. The role of PFAS contaminants in modulating microbial community composition and metabolic activity during permafrost thawing remains poorly understood. A sampling campaign was conducted in a high-latitude permafrost region, and a dose-response exposure experiment was performed with concentrations ranging from ng to µg of Perfluorooctanoic acid (PFOA; C8HF15O2) per gram sediment with multiple cores from a thermokarst pond. Our findings demonstrate a high susceptibility of microbial communities to PFOA pollution in particular methane-cycling. PFOA led to distinct changes in microbial functional potential, including a dual effect on methane-cycling communities: surfactant-induced inhibitory effects on sensitive methanogenic taxa, and the inactive persistence and relative enrichment of methanotrophs. This pollutant-driven shift was paralleled by a significant, concentration-dependent suppression of net methane emissions. Path analysis revealed that this suppression was driven primarily by direct PFOA inhibition rather than community turnover, despite substantial PFOA-induced restructuring of the broader prokaryotic community. This study provides novel insights into the ecotoxicity of emerging contaminants on key biogeochemical cycles, underscoring the need to account for contaminant-induced shifts when projecting future Arctic climate feedbacks.

Permafrost landscapes act as reservoirs for per- and polyfluoroalkyl substances (PFASs) and represent crucial carbon pools in the global carbon cycle. With the intensification of climate warming, permafrost is undergoing rapid degradation, exposing previously trapped organic carbon to microbial decomposition and thereby leading to substantial greenhouse gas emissions. However, the role of PFAS contaminants in modulating microbial community composition and metabolic activity during permafrost thawing remains poorly understood. A sampling campaign was conducted in high-latitude permafrost region, and an exposure experiment was performed with concentrations ranging from ng to µg of Perfluorooctanoic acid (PFOA; C8HF15O2) per gram sediment with multiple cores from a thermokarst pond. Our findings demonstrate a high susceptibility of microbial communities to PFOA pollution in particular methane-cycling. PFOA led to distinct changes in microbial functional potential, including a dual effect on methane-cycling communities with stimulatory effects on methanotrophs and inhibitory effects on methanogenic taxa. This shift was paralleled by a significant, concentration-dependent suppression of net methane emissions. Path analysis revealed that this suppression was driven primarily by direct PFOA inhibition rather than community turnover, despite substantial PFOA-induced restructuring of the broader prokaryotic community. This study provides novel insights into the relationships between emerging contaminants, greenhouse gas emissions, and microbial communities in permafrost ecosystems, underscoring the need to account for contaminant-induced shifts in biogeochemical cycles when projecting future Arctic climate feedbacks.

Small ponds and lakes and their surrounding riparian zone are ecological hot spots in the Arctic landscape. They are important for biogeochemical cycling and habitats for terrestrial and aquatic organisms. Arctic birds may have strong impact on these small aquatic ecosystems. In particular, the increasing populations of Arctic geese are strongly associated with ponds and can significantly influence the physico-chemical properties and ecological communities of these waterbodies. Birds supply nutrients via feces, grubbing and physical disturbance leading to increased erosion and run-off. We examined how the pond ecosystems, including phytoplankton and zooplankton communities respond to increased bird impact. Six ponds on Svalbard differentially impacted by birds were sampled in summer 2022. Bird-impacted ponds were characterized by higher nutrient concentrations, especially of phosphorus. They also had significantly higher phytoplankton biomass with a different phytoplankton community. Although mixotrophic species constituted a substantial part of the community in all ponds, we observed increased dominance of both cryptophytes and cyanobacteria at high bird impact. High bird impact was also associated with low metazoan zooplankton abundance and high ciliate abundance. Phytoplankton and metazoan zooplankton taxa richness was much lower in the most impacted pond compared to the other waterbodies. Bird impact did not significantly relate to diffusive CO ₂ and methane fluxes from the ponds. Thus, high bird impact was associated with hypereutrophic pond conditions characterized by decreased diversity and a likely stimulation of the microbial loop. The results may hint at some of the future changes in Arctic ecosystems in ponds increasingly influenced by birds.

Macroecological approaches in ecology seek to understand global statistical relationships between species’ abundances, their spatial and temporal variability, and diversity. Although environmental filtering, microbial interactions, diversification, dispersal, and local extinction have been observed to drive patterns of diversity and species distribution, a comparison of macroecological dynamics among the three domains of life is currently missing. Here we used environmental DNA (eDNA) metabarcoding data from the Australian Microbiome Initiative to explore the biodiversity of Archaea, Bacteria and Eukaryotes (including metazoans and protists) in marine and terrestrial biomes at continental scales. Our results show remarkably different community assembly patterns across the three domains of life in both biomes while presenting a consistent effect of spatial adjacency on environmental filtering and dispersal.

Understanding bacterial dynamics in large river systems is crucial for predicting continental-scale ecological functioning under anthropogenic pressures. Here, two consecutive surveys 6-years apart along the 2600 km Danube River found that carbon incorporation per cell and hour decreased by 5000 atoms every kilometer and that cells multiplied five times during their travel down the entire river. Resolving these cell turnovers taxonomically revealed taxa with a hundredfold difference from these average numbers. Bacterial community turnover was due to replacement (phylotype turnover) and could be linked to species sorting. This was despite an overall decrease in diversity richness downstream. Using linear models, we were able to relate carbon, cell, phylotype and diversity turnover rates to water residence time and discharge with outliers associated with human impacts. As such the reproduceable macroecological models predict microbial changes from anthropogenic and climate alterations along a continental drainage system providing insights into their ecological consequences.

Modeling bacterial dynamics in large river systems is crucial for predicting continental-scale ecosystem functioning under anthropogenic pressures. Although the River Continuum and Metacommunity concepts have provided theoretical frameworks, quantitative parameters necessary for microbial macroecological models remain scarce. Here, we present results from two whole-river surveys, conducted six years apart along 2600 km of the Danube River. Using bacterial secondary production, cell counts, and 16S ribosomal RNA (rRNA) gene amplicon sequencing, we quantified carbon, cell, phylotype, and diversity turnover along the river. Carbon incorporation per cell declined with water travel time by 6000–21 000 atoms per hour. Bacterial cells multiplied every eight days, resulting in four to six doublings during downstream transport. Growth responses at the level of individual phylotypes differed up to a hundredfold from these bulk community estimates. Bacterial diversity dynamics were dominated by phylotype turnover rather than phylotype loss. Turnover ranged from 0.92 to 0.96 along the river, indicating an almost complete replacement of phylotypes with 2%–11% of headwater-associated amplicon sequence variants (ASVs) persisting under base-flow conditions. Richness declined gradually downstream at a rate of ~0.13 ASVs per hour. Variations in bacterial secondary production, cell abundance, and observed ASVs were best explained by models combining hydrological and water quality parameters, whereas beta diversity followed a gradual development primarily structured by water travel time. Together, these results identify water travel time as the key integrative parameter governing microbial macroecological dynamics along large rivers, with environmental conditions fine-tuning local responses. These models can help predict changes in microbial diversity and functioning under anthropogenic alterations.

In the face of climate change, the accelerating nature crisis, and other anthropogenic impacts, conserving biodiversity demands effective monitoring. While innovative approaches have emerged to enhance biodiversity assessment, significant data gaps persist, particularly within marine ecosystems. In this study, we assess the utility of combining citizen (community) science with environmental DNA (eDNA) metabarcoding for characterizing and quantifying marine fish biodiversity. Over the summer of 2022, 32 volunteers conducted extensive water sampling in a large Norwegian fjord, yielding 96 samples. Contrasting eDNA findings with conventional observational surveys (such as a national species registration database and beach seine surveys) unveiled a substantial overlap in recorded species inventories. The eDNA citizen science initiative identified previously undocumented species and rediscovered others emphasizing an increase in warm‐water species within the study area. Additionally, eDNA data unveiled reduced diversity within the inner fjord relative to the outer fjord. To conclude, our study demonstrates the successful integration of eDNA within a citizen science framework, facilitating comprehensive biodiversity tracking across coastal marine regions. These findings hold promise for advancing marine conservation efforts by providing valuable data to inform critical decision‐making processes.