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.

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.

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.

Climate change induced warming of temperate coastal waters is expected to affect the biodiversity, community structure, seasonality and production in planktonic protist communities, and benefit heterotrophic taxa. We investigated long-term changes in the plankton protist community of the Outer Oslofjord by comparing two distinct periods across 15 years (2009–2011 vs. 2023–2024). Monthly 18S rRNA gene metabarcoding (V4 region) revealed dinoflagellates and diatoms as the dominating major taxonomic groups, with a 5.6-fold decrease in the dinoflagellate:diatom ratio and a 3.1-fold decrease in the heterotrophic dinoflagellate:phototrophic dinoflagellate ratio. These changes were primarily driven by a decrease in relative read abundance of the heterotrophic dinoflagellate genus Gyrodinium, and a widespread increase in the relative read abundances of diatoms (24 out of 27 ASVs with significant increase) between the time periods. Our results indicate that projected trends of heterotrophic protists profiting from changing oceanic conditions due to climate change, e.g. in temperate coastal waters, may not be the case for all coastal ecosystems.

Redox conditions, influenced by the availability of oxygen, are expected to dictate the rate of CO2 and CH4 production and to shape the composition and metabolism of microbial communities. Here, we use thawing permafrost peat in thermokarst water under a gradient of initial O2 concentrations to experimentally cover the variability in redox conditions potentially found across thawing landscapes. The three main greenhouse gases, CO2, CH4 and N2O, responded differently to O2 absence. CO2 production along the O2 gradient could be modeled by the Michaelis Menten equation revealing a sharp decrease when oxygen dropped under 100 μM. Under anoxic conditions CO2 yield decreased by 98% and maximum net production rate by 85% when compared to oxic conditions during the 11 days after thaw. N2O production was observed under anoxic conditions, while CH4 yield and CH4 accumulation rates did not differ across the redox gradient. The latter is due to the release of stored CH4 due to thawing. Differences between oxic and anoxic conditions were reflected in the microbial genomic composition, with changes in taxonomic and functional groups, such as N2O reducers, fermenters, denitrifiers and sulfur reducers increasing under anoxic conditions. Genomic changes towards less efficient central metabolism further explained the CO2 production yields and rates limited by O2 availability as predicted by thermodynamics. Together with the Michaelis Menten models the metabolic reconstruction pinpoint to critical thresholds of CO2 release at suboxic conditions and thus need to be considered when explaining and modeling highly variable CO2 emissions across thawing landscapes.

Exposure to hazardous microorganisms during waste handling is a potential health concern. Molecular biological techniques provide means of profiling the microbial community at high taxonomic resolution, allow the identification of critical human pathogens on the species level and thereby aid the risk assessment of work tasks. The present study used high-throughput sequencing to characterise the microbiome in personal full-shift air samples collected at contemporary waste sorting plants (WSPs) and identified large variations in community composition within (alpha diversity) and between (beta diversity) WSPs. Seasonality did not contribute to differences in the community composition. Cladosporium sp. was dominant among fungi, whereas Aerococcus sp. was dominant among bacteria. The personal air-samples contained potential human pathogens, such as Aspergillus sp., Fusarium sp. and Enterobacteriaceae, that encompass strains with the potential to develop drug-resistance. This study provided characterization of the microbial community composition of personal bioaerosol samples and provided evidence for the occurrence of potential human pathogens in contemporary waste sorting plants. Furthermore, this study highlighted the potential of microbial metabarcoding to detect critical human pathogens that may be encountered in working environments.

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. ### Competing Interest Statement The authors have declared no competing interest. FWF Austrian Science Fund, , W1219-N22, P25817-B22, P32464-B City of Vienna, , Groundwater Resource Systems Vienna Swedish Foundation for Strategic Research, , ICA10-0015 Swedish Research Council, , VR2012-4592 Uninett Sigma2 AS, , nn9744k

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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 Arctic, climate change leads to increased nutrient levels and organic carbon in freshwaters, caused by factors like permafrost thaw and growing populations of geese. Such alterations significantly impact freshwater ecosystems, potentially influencing community composition and diversity across various levels, including general microbial metabolism. We tested the hypothesis that a transition from autotrophy to heterotrophy occurs across a chronosequence of lakes in the high Arctic as a result of glacier retreat, influenced by distinct nutrient supplies and varying ecological succession statuses. To do so, we studied 5 lakes in the vicinity of Ny-Ålesund (Svalbard) following a chronosequence. The older lakes, closer to the fjord, were strongly impacted by birds, notably geese. For each lake, we tested the response to nutrients by adding an artificial nutrient solution with N and P, and the response to light or dark conditions. We incubated unfiltered water samples (80 mL) at 4 ºC in 120 mL flasks with atmospheric air as headspace. After 24h, samples for gases (O2, CO2, CH4 and N2O), nutrients (organic C, P and N) and eDNA (16S metabarcoding) were collected. Ar-corrected gas saturation of each GHG was used as a proxy of net metabolic changes. Regardless of the treatment applied, our results showed an increase in N2O saturation coupled with a decrease in O2 saturation after 24h in bird-impacted lakes, likely related to heterotrophic microbial activity. In such lakes, dark conditions promoted P accumulation, while N accumulated equally in light and dark incubations. In younger lakes (i.e., not impacted by birds), increased O2 saturation after 24h of incubation suggested that phototrophic metabolism was dominant. For nutrients, no significant pattern was observed for both light and dark incubations in younger lakes. Bacterial community composition differed between locations after 24h of incubation with a greater uniformity of species in younger lakes. This research advances our understanding of how nutrient enrichment affects biodiversity in the Arctic and metabolism in freshwater ecosystems.

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 CO2 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.

While the influence of salinity on microbial diversity is well documented in marine and brackish ecosystems, the impact of different dissolved inorganic ion types remains largely unexplored. In this study, we assessed how ionic composition shapes planktonic bacterial community structure in inland saline aquatic habitats, compared to the effects of salinity alone, spatial factors, and other environmental variables. We collected and analyzed 16S rRNA gene amplicon datasets from freshwater to hypersaline aquatic environments worldwide (375 samples from 130 lakes). The composition of major ions explained more variability in bacterioplankton structure than bulk salinity. Taxa contributing the most to the observed dissimilarity between communities included lineages characteristic of specific habitat types, such as Actinobacteria acI in freshwater, Halomonadaceae in saline waters, or Nitriliruptorales in soda- and soda-saline systems. Many of these indicator lineages for specific habitat types were monophyletic, further underpinning ionic composition as a crucial eco-evolutionary driver of aquatic microbial diversity.

Plasmids are key determinants in microbial ecology and evolution, facilitating the dissemination of adaptive traits and antibiotic resistance genes (ARGs). Although the molecular mechanisms governing plasmid replication, maintenance, and transfer have been extensively studied, the specific impacts of urbanization-induced pollution on plasmid ecology, diversity, and associated ARGs in tropical regions remain underexplored. This study investigates these dynamics in a tropical aquatic ecosystem, providing novel insights into how pollution shapes plasmid composition and function. In contrast to the observed decrease in chromosomal diversity, we demonstrate that pollution associated with urbanization increases the diversity and taxonomic composition of plasmids within a bacterial community (plasmidome). We analyzed eighteen water and sediment metagenomes, capturing a gradient of pollution and ARG contamination along a tropical urban river. Plasmid and chromosomal diversity profiles were found to be anti-correlated. Plasmid species enrichment along the pollution gradient led to significant compositional differences in water samples, where differentially abundant species suggest plasmid maintenance within specific taxonomic classes. Additionally, the diversity and abundance of ARGs related to the plasmidome increased concomitantly with the intensity of fecal and chemical pollution. These findings highlight the critical need for targeted plasmidome studies to better understand plasmids' environmental spread, as their dynamics are independent of chromosomal patterns. This research is crucial for understanding the consequences of bacterial evolution, particularly in the context of environmental and public health.

Occupational exposure during handling and sorting of waste has previously been identified as causative agent for occupational disease. New work operations and technological progress facilitate the waste sorting industry with means to reach global sustainability goals, however, generate unknown work-exposure scenarios. Full-shift personal work air samples were collected to investigate levels of infectious and non-infectious microbial components in bioaerosols and to study the potential of organic dust to elicit an immune response in vitro (TLR activation cell model) and in vivo (plasma biomarkers). Large variation in assessed exposure measurements between and within WSP, as well as between seasons was identified. Dust levels were generally below the current Norwegian OEL (5mg/m3), however contained substantial levels of endotoxins, fungal particles, and microbial agents with immunostimulatory potential. Viable microorganisms in the inhalable fraction were dominated by fungi in the genus Aspergillus and bacteria in the genus Bacillus and Staphylococcus. The samples contained a substantial fraction of risk group 2 human pathogens. Thirty per cent of the organic dust samples elicited TLR activation in vitro. Monocyte levels, plasma levels of IL-1RA, IL-18 and TNFα as well as symptom prevalence of respiratory and general symptoms were higher among exposed waste workers compared to an unexposed control group. The present study indicates that Norwegian waste workers are potentially exposed to relatively high levels of microbial agents that may cause adverse health effects in susceptible individuals.

The leaching of additives from plastics and elastomers (rubbers) has raised concerns due to their potential negative impacts on the environment and the development of antibiotic resistance. In this study, we investigated the effects of chemicals extracted from two types of rubber on microbiomes derived from a benthic sea urchin and two pelagic fish species. Additionally, we examined whether bacterial communities preconditioned with rubber-associated chemicals displayed adaptations to antibiotics. At the highest tested concentrations of chemicals, we observed reduced maximum growth rates and yields, prolonged lag phases, and increased alpha diversity. While the effects on alpha and beta diversity were not always conclusive, several bacterial genera were significantly influenced by chemicals from the two rubber sources. Subsequent exposure of sea urchin microbiomes preconditioned with rubber chemicals to the antibiotic ciprofloxacin resulted in decreased maximum growth rates. This indicates a more sensitive microbiome to ciprofloxacin when preconditioned with rubber chemicals. Although no significant interaction effects between rubber chemicals and ciprofloxacin exposure were observed in bacterial alpha and beta diversity, we observed log-fold changes in two bacterial genera in response to ciprofloxacin exposure. These findings highlight the structural and functional alterations in microbiomes originating from various marine species when exposed to rubber-associated chemicals and underscore the potential risks posed to marine life.

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.

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.

While the strong general effects of salinity on microbial diversity are well-known and described for marine and freshwater habitats, the impact of the specific composition of major inorganic ions remains largely unexplored. In this study, we assess how microbial community structure in inland saline aquatic habitats is influenced by ionic composition as compared to salinity, spatial factors, and other environmental parameters. We collected and analysed 16S rRNA gene V4 and V3-V4 amplicon datasets from freshwater to hypersaline aquatic environments worldwide (in total 375 samples from 130 lakes). With an emphasis on saline inland waters characterised by highly variable ionic composition, we demonstrated that the ionic composition of the major ions explained more variability in community composition than bulk salinity and that the geographic location of the sampling sites had only an ambiguous effect. We also identified the taxa contributing the most to the observed dissimilarity between communities from sites with different ionic composition and found mostly lineages known to be characteristic for a given habitat type, such as Actinobacteria acI in freshwater, Halomonadaceae in saline, or Nitriliruptorales in soda and soda-saline habitats. Many of these habitat type-specific indicator lineages were monophyletic, underpinning ionic composition as a crucial eco-evolutionary driver of aquatic microbial diversity.### Competing Interest StatementThe authors have declared no competing interest.

Despite the importance of bacteria in aquatic ecosystems and their predictable diversity patterns across space and time, biomonitoring tools for status assessment relying on these organisms are widely lacking. This is partly due to insufficient data and models to identify reliable microbial predictors. Here, we show metabarcoding in combination with multivariate statistics and machine learning allows to identify bacterial bioindicators for existing biological status classification systems. Bacterial beta-diversity dynamics follow environmental gradients and the observed associations highlight potential bioindicators for ecological outcomes. Spatio-temporal links spanning the microbial communities along the river allow accurate prediction of downstream biological status from upstream information. Network analysis on amplicon sequence veariants identify as good indicators genera Fluviicola, Acinetobacter, Flavobacterium , and Rhodoluna , and reveal informational redundancy among taxa, which coincides with taxonomic relatedness. The redundancy among bacterial bioindicators reveals mutually exclusive taxa, which allow accurate biological status modeling using as few as 2–3 amplicon sequence variants. As such our models show that using a few bacterial amplicon sequence variants from globally distributed genera allows for biological status assessment along river systems.