Alexander Eiler

• Kline, Simon Hasselø; Hyvärinen, Olli Petteri; Valestrand, Louise; Andersen, Tom; Eikrem, Wenche & Titelman, Josefin [Show all 8 contributors for this article] (2026). 15-year shift in protist communities and a decline of heterotrophic dinoflagellates in the Oslofjord and Skagerrak. Frontiers in Marine Science. 13. doi: 10.3389/fmars.2026.1876109. Full text in Research Archive
• Eiler, Alexander (2026). Rethinking evolutionary inference in metagenomic time series. mSystems. 11(9). doi: 10.1128/msystems.00693-26. Full text in Research Archive Show summary

  ABSTRACT 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.

• Sanchez, Pedro Maria Martin; Wurzbacher, Christian; Fontaine, Laurent; Lara, Maria Jimenez; Juottonen, Heli & Valiente, Nicolas [Show all 9 contributors for this article] (2026). Low determinism in community assembly of transient and resident pelagic fungi across climate zones in Scandinavian lakes. mSystems. 11(9). doi: 10.1128/msystems.00691-26. Full text in Research Archive Show summary

  ABSTRACT 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.

• Demeter, Katalin; Savio, Domenico; Kirschner, Alexander K T; Reischer, Georg H; Kolarevic, Stoimir & Parajka, Juraj [Show all 14 contributors for this article] (2026). Hydrological regime of a continental river system predicts bacterial macroecological patterns. The ISME Journal. ISSN 1751-7362. 19(1). doi: 10.1093/ismejo/wrag013. Full text in Research Archive Show summary

  Abstract 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.

• Szabó, Attila; Székely, Anna J.; Boros, Emil; Márton, Zsuzsanna; Csitári, Bianka & Barteneva, Natalie [Show all 11 contributors for this article] (2025). A matter of salt: Global assessment of the effect of salt ionic composition as a driver of aquatic bacterial diversity. Limnology and Oceanography Letters. 11(1). doi: 10.1002/lol2.70088. Full text in Research Archive Show summary

  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.

• Jensen, Thomas Correll; Schartau, Ann Kristin; Skjelbred, Birger; Eiler, Alexander; Loonen, Maarten J. J. E. & Veraart, Annelies J. (2025). Bird impacts on ecological structure, composition and function in Arctic ponds. Polar Biology. ISSN 0722-4060. 48. doi: 10.1007/s00300-025-03426-1. Full text in Research Archive Show summary

  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.

• Eriksen, Elke; Graff, Pål; Eiler, Alexander; Straumfors, Anne & Afanou, Komlavi Anani (2025). DNA metabarcoding and its potential in microbial risk assessment in waste sorting plants. Scientific Reports. 15(1). doi: 10.1038/s41598-025-93697-9. Full text in Research Archive Show summary

  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.

• Barrantes-Jiménez, Kenia; Lejzerowicz, Franck; Tran, Tam; Calderón-Osorno, Melany; Rivera-Montero, Luis & Rodríguez-Sánchez, César [Show all 11 contributors for this article] (2025). Anthropogenic imprint on riverine plasmidome diversity and proliferation of antibiotic resistance genes following pollution and urbanization. Water Research. ISSN 0043-1354. 281. doi: 10.1016/j.watres.2025.123553. Full text in Research Archive Show summary

  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.

• Carlsen, Eira Catharine Lødrup; Wei, Jing; Lejzerowicz, Franck; Kjær, Sigrid Trier; Westermann, Sebastian & Hessen, Dag Olav [Show all 8 contributors for this article] (2025). Redox determines greenhouse gas production kinetics and metabolic traits in water-saturated thawing permafrost peat. ISME Communications. 5(1). doi: 10.1093/ismeco/ycaf009. Full text in Research Archive Show summary

  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.

• Carlsen, Eira Catharine Lødrup; Hjelset, Sverre; Gomes, Tania; Igartua, Amaia; Sørensen, Lisbet & Booth, Andy [Show all 8 contributors for this article] (2024). Synthetic and natural rubber associated chemicals drive functional and structural changes as well as adaptations to antibiotics in in vitro marine microbiomes. Ecotoxicology and Environmental Safety. ISSN 0147-6513. 273. doi: 10.1016/j.ecoenv.2024.116134. Full text in Research Archive Show summary

  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.

• Kvalheim, Lone; Stensrud, Eivind; Knutsen, Halvor; Hyvärinen, Olli Petteri & Eiler, Alexander (2024). Integration of citizen science and eDNA reveals novel ecological insights for marine fish conservation. Environmental DNA. 6(4). doi: 10.1002/edn3.584. Full text in Research Archive Show summary

  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.

• Wei, Jing; Fontaine, Laurent; Parra, Nicolas Valiente; Dörsch, Peter; Hessen, Dag Olav & Eiler, Alexander (2023). Trajectories of freshwater microbial genomics and greenhouse gas saturation upon glacial retreat. Nature Communications. 14. doi: 10.1038/s41467-023-38806-w. Full text in Research Archive Show summary

  Abstract Due to climate warming, ice sheets around the world are losing mass, contributing to changes across terrestrial landscapes on decadal time spans. However, landscape repercussions on climate are poorly constrained mostly due to limited knowledge on microbial responses to deglaciation. Here, we reveal the genomic succession from chemolithotrophy to photo- and heterotrophy and increases in methane supersaturation in freshwater lakes upon glacial retreat. Arctic lakes at Svalbard also revealed strong microbial signatures form nutrient fertilization by birds. Although methanotrophs were present and increased along lake chronosequences, methane consumption rates were low even in supersaturated systems. Nitrous oxide oversaturation and genomic information suggest active nitrogen cycling across the entire deglaciated landscape, and in the high Arctic, increasing bird populations serve as major modulators at many sites. Our findings show diverse microbial succession patterns, and trajectories in carbon and nitrogen cycle processes representing a positive feedback loop of deglaciation on climate warming.

• Eriksen, Elke; Madsen, Anne Mette; Afanou, Komlavi Anani; Straumfors, Anne; Eiler, Alexander & Graff, Pål (2023). Occupational exposure to inhalable pathogenic microorganisms in waste sorting. International Journal of Hygiene and Environmental Health. ISSN 1438-4639. 253. doi: 10.1016/j.ijheh.2023.114240. Full text in Research Archive Show summary

  This study assessed microorganisms in personal inhalable work air samples aiming to identify potential human pathogens, and correlate exposure to adverse health outcomes in waste workers. Full-shift personal exposure was measured in six different waste sorting plants. Microbial concentrations in inhalable air samples were analysed using MALDI-TOF MS for cultivable, and next generation sequencing (NGS) for non-cultivable microorganisms. Concentrations of bacterial and fungal CFUs varied substantially within and between waste sorting plants, ranging from no identifiable organisms to a maximum concentration in the order of 105 CFU/m3. Bacillus and Staphylococcus were among the most abundant bacterial genera, whilst fungal genera were dominated by Aspergillus and Penicillium. Approximately 15% of all identified species were human pathogens classified in risk group 2, whereas 7% belonged to risk group 1. Furthermore, significant correlations between concentrations of fungi in risk group 1 and self-reported adverse symptoms, such as wheezing were identified in exposed workers. The combination of culture-based methods and NGS facilitated the investigation of infectious microbial species with potential pathophysiological properties as well as non-infectious biological agents in inhalable work air samples and thereby contributed to the risk assessment of occupational exposure in waste sorting.

• 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. 6. doi: 10.1038/s42003-023-05237-8. Full text in Research Archive Show summary

  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.

• Parra, Nicolas Valiente; 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. 10. doi: 10.3389/fenvs.2022.880619. Full text in Research Archive Show summary

  Boreal lakes are the most abundant lakes on Earth. Changes in acid rain deposition, climate, and catchment land use have increased lateral fluxes of terrestrial dissolved organic matter (DOM), resulting in a widespread browning of boreal freshwaters. This browning affects the aqueous communities and ecosystem processes, and boost emissions of the greenhouse gases (GHG) CH 4 , CO 2 , and N 2 O. In this study, we predicted biotic saturation of GHGs in boreal lakes by using a set of chemical, hydrological, climate, and land use parameters. For this purpose, concentrations of GHGs and nutrients (organic C, -P, and -N) were determined in surface water samples from 73 lakes in south-eastern Norway covering wide ranges in DOM and nutrient concentrations, as well as catchment properties and land use. The spatial variation in saturation of each GHG is related to explanatory variables. Catchment characteristics (hydrological and climate parameters) such as lake size and summer precipitation, as well as NDVI, were key determinants when fitting GAM models for CH 4 and CO 2 saturation (explaining 71 and 54%, respectively), while summer precipitation and land use data were the best predictors for the N 2 O saturation, explaining almost 50% of deviance. Our results suggest that lake size, precipitation, and terrestrial primary production in the watershed control the saturation of GHG in boreal lakes. These predictions based on the 73-lake dataset was validated against an independent dataset from 46 lakes in the same region. Together, this provides an improved understanding of drivers and spatial variation in GHG saturation in boreal lakes across wide gradients of lake and catchment properties. The assessment highlights the need to incorporate multiple explanatory parameters in prediction models of GHGs for extrapolation across the boreal biome.

• Suarez, Carolina; Sedlacek, Christopher J.; Gustavsson, David J. I.; Eiler, Alexander; Modin, Oskar & Hermansson, Malte [Show all 7 contributors for this article] (2022). Disturbance-based management of ecosystem services and disservices in partial nitritation-anammox biofilms. npj Biofilms and Microbiomes. 8(1). doi: 10.1038/s41522-022-00308-w. Full text in Research Archive Show summary

  Abstract The resistance and resilience provided by functional redundancy, a common feature of microbial communities, is not always advantageous. An example is nitrite oxidation in partial nitritation-anammox (PNA) reactors designed for nitrogen removal in wastewater treatment, where suppression of nitrite oxidizers like Nitrospira is sought. In these ecosystems, biofilms provide microhabitats with oxygen gradients, allowing the coexistence of aerobic and anaerobic bacteria. We designed a disturbance experiment where PNA biofilms, treating water from a high-rate activated sludge process, were constantly or intermittently exposed to anaerobic sidestream wastewater, which has been proposed to inhibit nitrite oxidizers. With increasing sidestream exposure we observed decreased abundance, alpha-diversity, functional versatility, and hence functional redundancy, among Nitrospira in the PNA biofilms, while the opposite patterns were observed for anammox bacteria within Brocadia . At the same time, species turnover was observed for aerobic ammonia-oxidizing Nitrosomonas populations. The different exposure regimens were associated with metagenomic assembled genomes of Nitrosomonas , Nitrospira , and Brocadia , encoding genes related to N-cycling, substrate usage, and osmotic stress response, possibly explaining the three different patterns by niche differentiation. These findings imply that disturbances can be used to manage the functional redundancy of biofilm microbiomes in a desirable direction, which should be considered when designing operational strategies for wastewater treatment.

• Osman, Omneya Ahmed; Andersson, Johan; Sanchez, Pedro Maria Martin & Eiler, Alexander (2022). National eDNA-based monitoring of Batrachochytrium dendrobatidis and amphibian species in Norway. Metabarcoding and Metagenomics. 6, p. 305–317. doi: 10.3897/mbmg.6.85199. Full text in Research Archive Show summary

  Freshwaters represent the most threatened environments with regard to biodiversity loss and, therefore, there is a need for national monitoring programs to effectively document species distribution and evaluate potential risks for vulnerable species. The monitoring of species for effective management practices is, however, challenged by insufficient data acquisition when using traditional methods. Here we present the application of environmental DNA (eDNA) metabarcoding of amphibians in combination with quantitative PCR (qPCR) assays for an invasive pathogenic chytrid species ( Batrachochytrium dendrobatidis - Bd ), a potential threat to endemic and endangered amphibian species. Statistical comparison of amphibian species detection using either traditional or eDNA-based approaches showed weak correspondence. By tracking the distribution of Bd over three years, we concluded that the risk for amphibian extinction is low since Bd was only detected at five sites where multiple amphibians were present over the sampled years. Our results show that eDNA-based detection can be used for simultaneous monitoring of amphibian diversity and the presence of amphibian pathogens at the national level in order to assess potential species extinction risks and establish effective management practices. As such our study represents suggestions for a national monitoring program based on eDNA.

• Rieder, Jessica; Sanchez, Pedro Maria Martin; Osman, Omneya A.; Adrian-Kalchhauser, Irene & Eiler, Alexander (2022). Detecting aquatic pathogens with field-compatible dried qPCR assays. Journal of Microbiological Methods. ISSN 0167-7012. 202. doi: 10.1016/j.mimet.2022.106594. Full text in Research Archive Show summary

  Field-ready qPCR assays with extended shelf-life support monitoring programs for emerging aquatic pathogens and enable quick conservation and management decisions. Here, we developed, validated, and tested the shelf-life of qPCR assays targeting Gyrodactylus salaris and Aphanomyces astaci with lyophilization and air-drying.

• Allesson, Lina; Parra, Nicolas Valiente; Dörsch, Peter; Andersen, Tom; Eiler, Alexander & Hessen, Dag Olav (2022). Drivers and variability of CO2:O2 saturation along a gradient from boreal to Arctic lakes. Scientific Reports. 12. doi: 10.1038/s41598-022-23705-9. Full text in Research Archive Show summary

  Abstract Lakes are significant players for the global climate since they sequester terrestrially derived dissolved organic carbon (DOC), and emit greenhouse gases like CO 2 to the atmosphere. However, the differences in environmental drivers of CO 2 concentrations are not well constrained along latitudinal and thus climate gradients. Our aim here is to provide a better understanding of net heterotrophy and gas balance at the catchment scale in a set of boreal, sub-Arctic and high-Arctic lakes. We assessed water chemistry and concentrations of dissolved O 2 and CO 2 , as well as the CO 2 :O 2 ratio in three groups of lakes separated by steps of approximately 10 degrees latitude in South-Eastern Norway (near 60° N), sub-Arctic lakes in the northernmost part of the Norwegian mainland (near 70° N) and high-Arctic lakes on Svalbard (near 80° N). Across all regions, CO 2 saturation levels varied more (6–1374%) than O 2 saturation levels (85–148%) and hence CO 2 saturation governed the CO 2 :O 2 ratio. The boreal lakes were generally undersaturated with O 2 , while the sub-Arctic and high-Arctic lakes ranged from O 2 saturated to oversaturated. Regardless of location, the majority of the lakes were CO 2 supersaturated. In the boreal lakes the CO 2 :O 2 ratio was mainly related to DOC concentration, in contrast to the sub-Arctic and high-Arctic localities, where conductivity was the major statistical determinant. While the southern part is dominated by granitic and metamorphic bedrock, the sub-Arctic sites are scattered across a range of granitic to sedimentary bed rocks, and the majority of the high-Arctic lakes are situated on limestone, resulting in contrasting lake alkalinities between the regions. DOC dependency of the CO 2 :O 2 ratio in the boreal region together with low alkalinity suggests that in-lake heterotrophic respiration was a major source of lake CO 2 . Contrastingly, the conductivity dependency indicates that CO 2 saturation in the sub-Arctic and high-Arctic lakes was to a large part explained by DIC input from catchment respiration and carbonate weathering.

• 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. 1. doi: 10.1038/s43705-021-00038-8. Full text in Research Archive 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.

• Pin, Lorenzo; Eiler, Alexander; Fazi, Stefano & Friberg, Nikolai (2021). Two different approaches of microbial community structure characterization in riverine epilithic biofilms under multiple stressors conditions: Developing molecular indicators. Molecular Ecology Resources. ISSN 1755-098X. 21(4), p. 1200–1215. doi: 10.1111/1755-0998.13341. Full text in Research Archive Show summary

  Microbial communities are major players in the biogeochemical processes and ecosystem functioning of river networks. Despite their importance in the ecosystem, biomonitoring tools relying on prokaryotes are still lacking. Only a few studies have employed both metabarcoding and quantitative techniques such as catalysed reported deposition fluorescence in situ hybridization (CARD‐FISH) to analyse prokaryotic communities of epilithic biofilms in river ecosystems. We intended to investigate the efficacy of both techniques in detecting changes in microbial community structure associated with environmental drivers. We report a significant correlation between the prokaryotic community composition and pH in rivers from two different geographical areas in Norway. Both CARD‐FISH and metabarcoding data were following the pattern of the environmental variables, but the main feature distinguishing the community composition was the regional difference itself. Beta‐dispersion analyses on both CARD‐FISH abundance and metabarcoding data revealed higher accuracy of metabarcoding to differentiate regions and river systems. The CARD‐FISH results showed high variability, even for samples within the same river, probably due to some unmeasured microscale ecological variability which we could not resolve. We also present a statistical method, which uses variation coefficient and overall prevalence of taxonomic groups, to detect possible biological indicators among prokaryotes using metabarcoding data. The development of new prokaryotic bioindicators would benefit from both techniques used in this study, but metabarcoding seems to be faster and more reliable than CARD‐FISH for large scale bio‐assessment.

• Peura, Sari; Wauthy, Maxime; Simone, Domenico; Eiler, Alexander; Einarsdottir, Karolina & Rautio, Milla [Show all 7 contributors for this article] (2020). Ontogenic succession of thermokarst thaw ponds is linked to dissolved organic matter quality and microbial degradation potential. Limnology and Oceanography. ISSN 0024-3590. 65(1), p. S248–S263. doi: 10.1002/lno.11349. Full text in Research Archive Show summary

  Warming climate is thawing the permafrost in arctic and subarctic regions, leading to formation of thermokarst ponds. During the formation and geomorphological succession of these ponds, carbon that has been trapped in frozen soils for thousands of years is hydrologically mobilized and returned to the active carbon cycle. We sam- pled 12 thermokarst ponds representing three different stages of pond succession to study the potential of micro- bial communities to metabolize the organic carbon in the water. We investigated the quality of the dissolved organic carbon (DOC) in the water column based on the spectrophotometric and fluorometric properties of the chromophoric dissolved organic matter combined with parallel factor analysis and the potential of the microbial community for degrading these carbon compounds based on genetic markers related to carbon degradation. Our analysis showed a clear difference in the DOC quality across the different developmental stages. In the younger ponds, organic matter quality suggested that it was originating from the degrading permafrost and in the metagenomes collected from these ponds, the normalized abundance of genes related to degradation of carbon compounds was higher. There was also a shift in the degradation potential in the water column of the ponds, with higher potential for organic matter degradation in deeper, anoxic layers. In conclusion, our results show that the DOC quality and the genetic potential of the microbial community for carbon cycling change across the pond ontogeny, suggesting a capacity of the microbial communities to adapt to changing environmental conditions.

• Allesson, Lina; Andersen, Tom; Dörsch, Peter; Eiler, Alexander; Wei, Jing & Hessen, Dag Olav (2020). Phosphorus availability promotes bacterial DOC-mineralization, but not cumulative CO2-production. Frontiers in Microbiology. 11. doi: 10.3389/fmicb.2020.569879. Full text in Research Archive Show summary

  The current trend of increasing input of terrestrially derived dissolved organic carbon (DOC) to boreal freshwater systems is causing increased levels of carbon dioxide (CO 2 ) supersaturation and degassing. Phosphorus (P) is often the most limiting nutrient for bacterial growth and would thus be expected to increase overall mineralization rates and CO 2 production. However, high carbon (C) to P ratios of terrestrially derived DOC could also cause elevated cell-specific respiration of the excess C in heterotrophic bacteria. Using data from a survey of 75 Scandinavian lakes along an ecosystem gradient of DOC, we estimated in situ CO 2 production rates. These rates showed a unimodal response with DOC-specific CO 2 production negatively related to DOC:total phosphorus (TP) ratio, and a turning point at 5 mg C L −1 , indicating higher DOC turnover rates in productive than in unproductive lakes. To further assess the dependency of bacterial respiration (BR) on DOC and P, we monitored CO 2 production in incubations of water with a gradient of DOC crossed with two levels of inorganic P. Finally, we crossed DOC and P with a temperature gradient to test the temperature dependency of respiration rates [as oxygen (O 2 ) consumption]. While total CO 2 production seemed to be unaffected by P additions, respiration rates, and growth yields, as estimated by ribosomal gene copy numbers, suggest increased bacterial growth and decreased cell-specific respiration under non-limited P conditions. Respiration rates showed a sigmoid response to increasing DOC availability reaching a plateau at about 20 mg C L −1 of initial DOC concentrations. In addition to these P and DOC level effects, respiration rates responded in a non-monotonic fashion to temperature with an increase in respiration rates by a factor of 2.6 (±0.2) from 15 to 25°C and a decrease above 30°C. The combined results from the survey and experiments highlight DOC as the major determinant of CO 2 production in boreal lakes, with P and temperature as significant modulators of respiration kinetics.

• Fernandez, Leyden; Peura, Sari; Eiler, Alexander; Linz, Alexandra M; McMahon, Kathrine D & Bertilsson, Stefan (2020). Diazotroph Genomes and Their Seasonal Dynamics in a Stratified Humic Bog Lake. Frontiers in Microbiology. 11, p. 1–16. doi: 10.3389/fmicb.2020.01500. Full text in Research Archive Show summary

  Aquatic N-fixation is generally associated with the growth and mass development of Cyanobacteria in nitrogen-deprived photic zones. However, sequenced genomes and environmental surveys suggest active aquatic N-fixation also by many non-cyanobacterial groups. Here, we revealed the seasonal variation and genomic diversity of potential N-fixers in a humic bog lake using metagenomic data and nif gene clusters analysis. Groups with diazotrophic operons were functionally divergent and included Cholorobi, Geobacter, Desulfobacterales, Methylococcales, and Acidobacteria. In addition to nifH (a gene that encodes the dinitrogenase reductase component of the molybdenum nitrogenase), we also identified sequences corresponding to vanadium and iron-only nitrogenase genes. Within the Chlorobi population, the nitrogenase (nifH) cluster was included in a well-structured retrotransposon. Furthermore, the presence of light-harvesting photosynthesis genes implies that anoxygenic photosynthesis may fuel nitrogen fixation under the prevailing low-irradiance conditions. The presence of rnf genes (related to the expression of H+/Na+-translocating ferredoxin: NAD+ oxidoreductase) in Methylococcales and Desulfobacterales suggests that other energy-generating processes may drive the costly N-fixation in the absence of photosynthesis. The highly reducing environment of the anoxic bottom layer of Trout Bog Lake may thus also provide a suitable niche for active N-fixers and primary producers. While future studies on the activity of these potential N-fixers are needed to clarify their role in freshwater nitrogen cycling, the metagenomic data presented here enabled an initial characterization of previously overlooked diazotrophs in freshwater biomes.

• Zha, Yinghua; Lindström, Eva S.; Eiler, Alexander & Svanback, Richard (2020). Different roles of environmental selection, dispersal, and drift in the assembly of intestinal microbial communities of freshwater fish with and without a stomach. Frontiers in Ecology and Evolution. 8, p. 1–15. doi: 10.3389/fevo.2020.00152. Full text in Research Archive Show summary

  The composition of intestinal microbiota commonly varies among animal hosts and may affect host health. However, we have limited knowledge about the different relative roles of assembly processes, such as drift, dispersal and environmental selection, for the composition of gut microbiota. Here, we conducted a field study analyzing intestinal microbial communities of two fish species that either have (perch) or lack (roach) a stomach. We used a suite of statistical tools to evaluate the role of different assembly processes for intestine microbiota, including null model analysis (Chase et al., 2011; Fine and Kembel, 2011; Stegen et al., 2013), SourceTracker analysis (Knights et al., 2011) and several multivariate analyses, such as pRDA and PLS analysis. Drift, dispersal (i.e., microbes associated with food sources) and environmental factors (i.e., diet, host habitats), appeared to be of equal importance for the assembly of intestinal microbial communities in roach, while drift appeared most important in perch, followed by dispersal and environmental selection. Furthermore, we found that microbes associated with macroinvertebrates had a positive association to fish body condition (weight/length3) whereas microbes associated with zooplankton had a negative association to fish body condition. These results emphasize the important combined roles of drift, dispersal and environmental selection in shaping the host-associated microbial communities. We conclude that general conclusions about fish as a whole are not justified since different species differ in the relative roles of these important drivers of community assembly.

• 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.

• Eriksson, KM; Sanli, Kemal; Nilsson, RH; Eiler, Alexander; Corcoll, N & Johansson, CH [Show all 9 contributors for this article] (2020). Triclosan changes community composition and selects for specific bacterial taxa in marine periphyton biofilms in low nanomolar concentrations. Ecotoxicology. ISSN 0963-9292. 29, p. 1083–1094. doi: 10.1007/s10646-020-02246-9. Full text in Research Archive
• Peura, Sari; Buck, Moritz; Aalto, SL; Morales, Sergio E; Nykänen, Hannu & Eiler, Alexander (2018). Novel Autotrophic Organisms Contribute Significantly to the Internal Carbon Cycling Potential of a Boreal Lake. mBio. ISSN 2161-2129. 9. doi: 10.1128/mBio.00916-18. Full text in Research Archive
• Garcia, Sarahi L.; Buck, Moritz; Hamilton, Joshua J.; Wurzbache, Christian; Grossart, Hans-Peter & McMahon, Katherine D. [Show all 7 contributors for this article] (2018). Model Communities Hint at Promiscuous Metabolic Linkages between Ubiquitous Free-Living Freshwater Bacteria. mSphere. 3(3). doi: 10.1128/mSphere.00202-18. Full text in Research Archive
• Bagatini, Inessa Lacativa; Eiler, Alexander; Bertilsson, Stefan; Klaveness, Dag; Tessarolli, Leticia Piton & Vieira, Armando Augusto Henriques (2014). Host-Specificity and Dynamics in Bacterial Communities Associated with Bloom-Forming Freshwater Phytoplankton. PLOS ONE. 9(1). doi: 10.1371/journal.pone.0085950. Full text in Research Archive

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• Stensrud, Eivind; Hyvärinen, Olli Petteri; Rostum, Tarjei; Angell, Thorvald; Knutsen, Halvor & Lundström, Karl [Show all 8 contributors for this article] (2026). PREDATORS AS SENTINELS: UNRAVELING TROPHIC SHIFTS IN A DARKENING FJORD USING dDNA AND STABLE ISOTOPES OVER THE LAST 20 YEARS. Full text in Research Archive Show summary

  The Greater Oslofjord, like many other coastal systems, is undergoing rapid ecological shifts driven by climate change, coastal freshening and darkening. To understand how these bottom-up stressors restructure food webs, we utilized a multi-trophic approach analyzing three sympatric predators (approx. 500 individuals): Harbour seals (Phoca vitulina), Great Cormorants (Phalacrocorax carbo), and Atlantic Cod (Gadus morhua). We combined dietary DNA (dDNA) metabarcoding with stable isotope analysis (δ13C, δ15N) to trace temporal and spatial dietary changes over 20 years. Traditional morphological methods often fail to capture soft-bodied prey and secondary consumption; thus, we used dDNA combined with novel reference databases to maximize taxonomic resolution. Our dDNA results revealed high-resolution predation data, including the detection of secondary consumption (zoo- and phytoplankton) alongside primary prey, effectively mapping the food web from top predators down to primary producers. Isotope data complemented this by delineating trophic niche widths and source of primary production (land vs. sea). We observed distinct dietary variations linking predator foraging behavior to environmental gradients. This included observable changes over the last 20 years, such as an increase in invasive species in their diet and a shift in zoo- and phytoplankton composition. These findings demonstrate that combining molecular and isotopic analysis of top predators provides a powerful tool for monitoring the cascading effects of anthropogenic changes on marine food webs.

• Carlsen, Eira Catharine Lødrup; Pismeniuk, Anfisa; Wei, Jing; Ippach, Mats Rouven; Dörsch, Peter & Westermann, Sebastian [Show all 9 contributors for this article] (2026). FROM PEAT TO PONDS: LANDSCAPE HETEROGENEITY DRIVES METABOLIC NETWORKS AND GREENHOUSE GAS RELEASE FROM THAWING PERMAFROST. Full text in Research Archive Show summary

  As permafrost landscapes degrade, they transform into a hydrological mosaic of dry palsas, collapsing thermokarst slumps, and water-saturated ponds. This physical reorganization creates steep gradients in redox potential and organic matter quality, fundamentally altering the thermodynamic constraints on microbial metabolism. We investigated greenhouse gas (CO2, CH4, N2O) production potentials across several permafrost thaw gradients in sub-Arctic peatlands of Northern Norway, linking landscape-scale changes to genome-resolved metabolic networks. By integrating high-resolution metagenomics with organic matter and greenhouse gas production characterization, we found that thaw features act as distinct thermodynamic bioreactors. In water-saturated, anoxic peat layers, oxygen limitation selects for "slow" metabolic guilds specialized in fermentation and methanogenesis while other oxygenated features are constrained by the quality of organic matter—specifically the accumulation of polyphenols and aromatic compounds acts as a metabolic "latch". We show that the shift from oxic to anoxic conditions triggers a non-linear restructuring of the microbial network, where less efficient central metabolism drives high N2O and CH4 yields but suppressed CO2 production. These findings demonstrate that predicting the permafrost-carbon feedback requires mapping the "metabolic landscape"—where organic matter quality and redox thresholds ultimately tune the greenhouse gas release from thawing landscapes to the atmosphere.

• Riis-Pedersen, Christine; Carlsen, Eira Catharine Lødrup; Lejzerowicz, Franck Laurent Patrick; Hessen, Dag Olav & Eiler, Alexander (2026). HOW OPTICS AND THERMODYNAMICS SHAPE METHANE EMISSIONS FROM LAKES. Full text in Research Archive Show summary

  The interactions of light regime and physical stratification can be argued to dictate greenhouse gas flux through determining the thermodynamics in lake systems. Using geochemical profiling and metagenomics, we reconstructed metabolic networks in a wide range of lakes including ferruginous (iron-rich) and euxinic (sulfide-rich) systems. We observed significant methane accumulation in the anoxic monimolimnion—up to 420 µM in ferruginous lakes—yet surface levels remained low, indicating a highly efficient biofilter at the chemoclines. We identified a tight thermodynamic coupling between phototrophs and methanotrophs driven by oxidant regeneration. In ferruginous lakes, anoxygenic phototrophs likely use reduced iron (Fe2+) as an electron donor. This process regenerates oxidized iron (Fe3+), while in euxinic light energy is utilized to recycle essential electron acceptors such as SO42- (e.g., Chlorobium), required for anaerobic methane oxidation. Oxygenic phototrophs (e.g., Cyanobium) detected at and above the chemocline likely provide oxygen. This supply sustains aerobic methanotrophs like Crenothrix and Methylobacter even in suboxic waters. Hence methanotrophic capacity is ultimately constrained by optical properties selecting for low-intensity light anoxygenic or high-intensity oxygenic phototrophs. Consequently, levels of chromophoric dissolved organic matter determine methane oxidation rates. We conclude that chemoclines function as dynamic, light-powered engines for methane removal, sensitive to brownification and climate-induced shifts in stratification.

• Riis-Pedersen, Christine; Carlsen, Eira Catharine Lødrup; Hessen, Dag Olav; Lejzerowicz, Franck Laurent Patrick; Andersen, Tom & Dörsch, Peter [Show all 8 contributors for this article] (2025). Microbial drivers of methane cycling in meromictic as compared to holomictic lakes. Full text in Research Archive
• Carlsen, Eira Catharine Lødrup; Wei, Jing; Lejzerowicz, Franck Laurent Patrick; Ippach, Mats Rouven; Pismeniuk, Anfisa & Kjær, Sigrid Trier [Show all 10 contributors for this article] (2025). Greenhouse gas production kinetics and metabolic traits in thawing permafrost peat. Full text in Research Archive Show summary

  While numerous drivers of greenhouse gas emission (GGE) have been suggested to drive variabilities across thawing landscapes, experimental validations are still widely lacking . Here, I will present results from several experimental studies capturing drivers of GGE across thawing permafrost landscapes like redox, organic matter and microbial source community. Our findings reveal clear responses of the greenhouse gases to redox conditions across the landscape. CO2 production showed a drastic decline when O2 dropped below 100 μM; specifically, under anoxic conditions, CO2 yield and maximum net production rates decreased by around 90 % compared to oxic conditions. CH4 levels remained consistent across O2 gradients, until at least 6 months upon thawing. Functional groups like N2O reducers, fermenters, denitrifiers, and sulfur reducers increased under anoxic conditions, and the reduced CO2 production rates and yields under anoxic conditions were reflected by genomic changes towards reduced central metabolic efficiency. Our data thus points towards critical GGE thresholds under suboxic conditions across thawing landscapes. Moreoever, gas dynamics seem to be primarily influenced by permafrost conditions rather than source community colonization. Our experiments provide increased knowledge on the variable GGE across thawing permaforst landscapes influenced by variable redox conditions and permafrost´s organic matter legacy.

• Wennberg, Aina Charlotte; Gundersen, Cathrine Brecke; Eiler, Alexander; Grung, Merete & Reid, Malcolm James (2025). Will carbon capture plants contaminate drinking water? Biodegradation potential of nitramines in lake water. Full text in Research Archive Show summary

  There is a potential risk associated with (potentially) carcinogenic nitrosamines (NSAs) and nitramines (NAs) that can form in the air from amines escaping amine-based carbon capture plants (CCP). These are very soluble molecules that can end up in drinking water sources such as lakes and groundwater basins. In Norway, a drinking water threshold of 4 ng/L has been set for the sum of NSAs and NAs. A dynamic modelling tool is under development to guide the industry and regulators to ensure that the safety limit will not be exceeded. In the model, the major removal mechanism for NSAs is photodegradation, while biodegradation is the dominant removal mechanisms for NAs. Thus, reliable biodegradation rates for NAs are needed to realistically simulate future levels in the water compartment. A modified OECD 309 simulation test for biodegradation in surface water was used to assess biodegradation rates of three representative nitramines. Caffein was used as positive reference control. The study site was a drinking water lake located in the vicinity of a planned CO2 capture plant. Water and sediment were collected at different seasons, and the tests were performed with and without added sediment. The three nitramines were added either separately or together to the test bottles, and primary degradation was measured by LC-MS/MS compared to the abiotic control. The biodegradation rates varied between experiments. However, the difference in degradation rates was consistent with (monoethanol)-nitramine (MEA) being the most rapidly degradable, 2-methyl-2-(nitramine)-1-propanol (AMP) being moderately degradable and N-nitropiperazine (NIPZ) having limited degradation after 60 days. Adding sediment to the surface water increased biodegradation rates. The effect of different modifications of the test set up (with/without sediment and single vs mixture of test substance) will be presented and discussed.

• Kline, Simon Hasselø; Saubrekka, Karoline; Eikrem, Wenche; Valestrand, Louise; Egge, Elianne Dunthorn & Eiler, Alexander [Show all 8 contributors for this article] (2024). Seasonal dynamics of the protist community in the Oslofjord and Skagerrak in a changing ocean. Full text in Research Archive Show summary

  Protists and prokaryotes compose approximately 90% of the biomass in the oceans, and any changes within this microbial community are likely to have reverberating effects throughout the ecosystem. Due to climate coastal marine systems are experiencing increased freshwater discharge from land and a darkening of the water column along with changes in nutrient concentrations. The phenology is also changing and in the inner Oslofjord the spring blooms starts on average 2 weeks later that 15 years ago. The causes for this delay in unclear. In this study we examine the diversity and seasonal dynamics of the protist community by metabarcoding in the inner and outer Oslofjord, and possible changes during 14 years. Monthly plankton samples were collected at two localities and two depths during 2023 and similar samples were collected in 2009-2011, to be sequenced by current high throughput technology (Illumina). Various environmental parameters have been measured including CDOM (colored dissolved organic matter). We ask whether browning or other physico-chemical conditions can explain the delayed spring bloom and other observed changes in the protist community in the Oslofjord and Skagerrak.

• Jensen, Thomas Correll; Schartau, Ann Kristin; Majaneva, Markus; Veraart, A.J.; Hessen, Dag Olav & Eiler, Alexander [Show all 8 contributors for this article] (2023). Bird impacts on biological communities in Arctic ponds. Full text in Research Archive
• Jensen, Thomas Correll; Schartau, Ann Kristin; Majaneva, Markus; Hessen, Dag Olav; Eiler, Alexander & Loonen, Maarten J.J.E. [Show all 7 contributors for this article] (2023). Bird impacts on biological communities in Arctic ponds – preliminary results. Full text in Research Archive
• Carlsen, Eira Catharine Lødrup; Hylland, Ketil; Gomes, Tania; Sørensen, Lisbet; Booth, Andrew & Eiler, Alexander (2022). Plastic leachates as drivers for bacterial community structure and functioning, including antibiotic resistance. Full text in Research Archive
• Allesson, Lina; Andersen, Tom; Dörsch, Peter; Eiler, Alexander; Wei, Jing & Hessen, Dag Olav (2020). Corrigendum: Phosphorus Availability Promotes Bacterial DOC-Mineralization, but Not Cumulative CO2-Production (Front.Microbiol, (2020), 11, (569879), 10.3389/fmicb.2020.569879). Frontiers in Microbiology. 11. doi: 10.3389/fmicb.2020.614974. Full text in Research Archive
• Angell, Thorvald; Eiler, Alexander & Stensrud, Eivind (2026). Changes at the Base of the Food Web in the Oslofjord and Skagerrak. Top predators as food web sentinels using DNA metabarcoding and stable isotope analysis. Universitetet i Oslo. Full text in Research Archive Show summary

  The coastal food webs of the Oslofjord and Skagerrak are undergoing alterations in structure, energy transfer, and basal organic matter (OM) sources due to multiple anthropogenic drivers, including eutrophication, increased terrestrial runoff, and climate change. These interacting pressures elevate the influx of terrestrial OM (tOM) and are associated with an increase in chromophoric dissolved OM (cDOM) to the coastal areas. As these allochthonous inputs increasingly exceed the autochthonous OM production, the resulting brownification alters the light attenuation regimes and thus drives the base of coastal ecosystems towards heterotrophic processes. Despite these documented biogeochemical shifts, the extent to which they disrupt the base of the food web and propagate upward through trophic interactions to the top predators remains poorly understood. Resolving how anthropogenic stressors restructure trophic pathways is also essential for predicting ecosystem responses to conservation and restoration strategies. To investigate how anthropogenic pressures have altered the coastal food web over the last two decades, dietary DNA metabarcoding was conducted on gut content from harbour seal (Phoca vitulina) and great cormorant (Phalacrocorax carbo), targeting secondary consumption with emphasis on the base of the food web. Two complementary gene markers were used: 18s rRNA V4 (Pirreda) to characterize the eukaryotic protist communities and COI (Leray-XT) to identify metazoan prey, including fish and invertebrates. To assess temporal shift in basal energy and organic matter sources, stable isotope analysis of top predator tissue was complemented with longterm monitoring data of Atlantic cod (Gadus morhua) and blue mussel (Mytilus edulis). These multiple approaches successfully characterized the food web from top predators down to the base of the food web. Although the findings revealed diet partitioning in the top predators primary consumption, reflecting different foraging strategies, they exhibit a strong overlap in the lower trophic levels and at the base of the food web. This suggests that the top predators are affected by the same bottom-up regime, rendering them mutually susceptible to the cascading effects of anthropogenic pressures, particularly increased terrestrial organic matter inputs. Finally, complementary isotopic data revealed a significant decrease in d 13C over the past 20 years, signaling a systemic shift in the coastal food web’s primary energy base toward allochthonous carbon sources.

• Eiler, Alexander; Riis-Pedersen, Christine; Hessen, Dag Olav & Minde, August Woldseth (2026). Under ice: The methane cycle in meromictic lakes during winter. Universitetet i Oslo. Full text in Research Archive Show summary

  Anthropogenic pressures and climate warming are increasingly driving freshwater ecosystems toward permanent stratification, yet the implications for the global carbon cycle remain poorly constrained. Meromictic lakes act as substantial reservoirs for dissolved greenhouse gases in their anoxic monimolimnia, but the efficiency of the chemocline in attenuating upward-diffusing methane (CH4) during winter ice- cover requires quantification. This study investigates depth-resolved CH4 and carbon dioxide (CO2) concentrations, alongside stable carbon isotope (δ13C) profiles, in two contrasting boreal meromictic lakes (euxinic Pollevannet and ferruginous Oppsjø) under winter conditions. High-resolution profiling revealed massive deep-water gas accumulation, with monimolimnetic CH4 concentrations exceeding 106 nM in both systems. In Pollevannet, δ13C − CH4 profiles exhibited a sharp 20‰ depletion across a 2-meter interval at the chemocline, providing isotopic evidence of a highly efficient microbial methane oxidation barrier. Furthermore, biogeochemical profiles suggest this barrier is reinforced by cryptic metabolic coupling; anoxygenic phototrophy at the low-light euxinic boundary likely regenerates sulfate (SO2−4 ), potentially subsidizing anaerobic methane oxidation in the underlying water. Oppsjø displayed a broader transition zone with more gradual isotopic shifts, reflecting its distinct ferruginous redox architecture. These findings demonstrate that stable winter stratification sustains a rigid, interdependent microbial bio-filter that effectively sequesters carbon in deep waters and decouples benthic methanogenesis from surface emissions.

• Mørch, Mikkel Martinussen; Hyvärinen, Olli Petteri; Eiler, Alexander; Werner, Even; Gagnon, Karine & Thormar, Jonas (2026). Biodiversity patterns and blue carbon characteristics of Zostera marina meadows in the Oslofjord. Universitet i Oslo. Full text in Research Archive Show summary

  Seagrass meadows are coastal foundation habitats that support biodiversity and store organic carbon in sediments, a process often referred to as blue carbon storage. However, both biodiversity and sediment carbon storage can vary strongly among meadows, and it remains unclear how local meadow structure, hydrodynamic exposure, organic-matter sources, and associated fauna interact in temperate eelgrass systems. This thesis investigated biodiversity and blue carbon characteristics of Zostera marina meadows in the Oslofjord, Norway. The study combined two complementary approaches: citizen-science-based environmental DNA (eDNA) water sampling across eelgrass meadows and seasons, and researcher-led field sampling at three meadows along an inner-outer Oslofjord gradient. The field-sampled meadows represented contrasting coastal settings: an inner-fjord meadow at Fornebu, a sheltered meadow near Sætre/Sandspollen, and a more wave- exposed outer-fjord meadow at Holmestrand. The water eDNA dataset provided broad spatial and seasonal coverage, but ecological interpretation was limited by uneven sampling and read-depth loss after filtering. After taxonomic partitioning of the cytochrome c oxidase I (COI) metabarcoding dataset, only 20.5% of reads were retained as faunal reads, while 79.5% were classified as non-faunal reads. The retained faunal water eDNA dataset did not show clear winter-spring or Oslofjord-section structure. Instead, it contained a mixed coastal signal, including pelagic planktonic taxa and benthic or soft-sediment-associated taxa. In contrast, the non-faunal fraction showed clearer winter-spring structuring, largely associated with microalgal and protist groups. This indicates that broad COI water eDNA can capture useful biodiversity signals, but also that faunal and non-faunal datasets should be separated before ecological interpretation. The strongest ecological patterns were found in the field-measured meadows. The sheltered Sætre/Sandspollen meadow had continuous eelgrass cover, low sediment bulk density, high and consistent organic carbon stocks, and the highest apparent seagrass-like carbon contribution. The more wave- exposed Holmestrand meadow was patchier and had higher bulk density, lower organic carbon stocks, and the lowest apparent seagrass-like carbon contribution. The inner-fjord Fornebu meadow had intermediate sediment carbon stock, bulk density, and apparent seagrass-like carbon contribution, but showed greater within-meadow variability. Stable isotope composition supported these meadow-level differences and indicated variation in both carbon-source characteristics and assimilated nitrogen among meadows. Benthic eDNA showed clear separation between seagrass-blade epifaunal communities and sediment-core infaunal communities. Infaunal communities were most strongly associated with sedimentary gradients and were dominated by sediment-associated annelids, including lugworms and other ii taxa linked to deposit feeding, burrowing, sediment reworking, and bioirrigation. In contrast, the epifaunal signal was dominated more strongly by sessile or surface-associated taxa, including barnacles, bryozoans, and hydrozoans, rather than by mobile mesograzers. Overall, this thesis shows that eelgrass meadows in the Oslofjord can differ substantially in meadow structure, sediment carbon characteristics, stable isotope composition, and associated benthic fauna. The results support a descriptive interpretation in which blue-carbon characteristics and benthic biodiversity vary together at local meadow scale, particularly through the association between sediment conditions and infaunal community structure. Broader inference about Oslofjord-wide seasonal biodiversity patterns will require more balanced repeated sampling but the study demonstrates the value of combining citizen-science water eDNA with targeted field measurements when assessing biodiversity and blue carbon in eelgrass meadows.

• Negård, Jesper Nilsen; Hyvärinen, Olli Petteri & Eiler, Alexander (2025). Characterization of the Carbon Export Potential of Commercially Important Fish Species in the Oslofjord. Universitetet i Oslo. Full text in Research Archive
• Røsbak, Silje K.; Edvardsen, Bente; Eiler, Alexander; Saubrekka, Karoline & Fon, Mathias (2023). Mikrobielt samfunn i kulturer av Chrysochromulina leadbeateri og relaterte svepeflagellater, undersøkt med metastrekkoding. Universitetet i Oslo. Full text in Research Archive Show summary

  Skadelige marine algeoppblomstringer er et tilbakevendende problem over hele verden, der skadene har en påvirkning på økosystemer og lokal økonomi. Chrysochromulina leadbeateri var årsak til en massiv fiskedød i 2019, men mekanismene bak denne oppblomstringen er fortsatt ukjent. Målet med oppgaven var å undersøke bakteriediversiteten i kulturer av den fiske-giftige Chrysochromulina leadbeateri, og sammenligne denne mot andre beslektede svepeflagellater, både hos potensielt giftige og ikke-giftige arter. I tillegg til dette ble bakteriediversiteten av mikrobiomet mellom fastsittende bakterier på algecellene og frittlevende bakterier i kultur undersøkt. I denne oppgaven ble det prokaryote mikrobiomet i kulturer av tre stammer av Chryochromulina leadbeateri og 6 stammer av beslektede svepeflagellatarter analysert. Dette ble gjort ved metastrekkoding av det ribosomale 16S rRNA-genet. Det ble påvist et mangfoldig mikrobiom der hele bakteriedatasettet inneholdt 3 rekker, 14 ordener og 53 slekter. Bakteriesamfunnets sammensetning bestod hovedsakelig av medlemmer i rekken Proteobacteria etterfulgt av medlemmer av rekken Bacteroidota, og kun noen få ASVer i rekken Actinobacteria. Av de 14 ordenene var Rhodobacterales, Flavobacteriales, Caulobacterales, Rhiszobiales og Cytophagales de mest vanlige. Av de 53 slektene var Marivita (Rhodobacterales) den mest abundante, etterfulgt av Roseovarius (Rhodobacterales), Jannaschia (Rhodobacterales), Hoefla (Rhizobiales), Seohaeicola (Rhodobacterales), Hyphomonas (Rhodobacterales) og Sulfitobacter (Rhodobacterales). Taksonomisk fordeling av bakterieslekter mellom de potensielt giftige og ikke-giftige svepeflagellatene viste forskjeller, der de potensielt giftige hadde flest unike identifiserte bakterieslekter. Når det gjelder alfadiversitet (forskjeller innad i et samfunn) viser de to gruppene derimot ingen store forskjeller i mikrobiomet. Det ble funnet en svak signifikant sammenheng i mikrobiomets betadiversitet (forskjeller mellom samfunn) mellom kulturer av potensielt giftige og ikke-giftige svepeflagellater, der svepeflagellatens giftighet innen slekt hadde en svak effekt i denne studien. I tillegg viste slekten til svepeflagellaten til å ha en signifikant betydning for hvilke bakteriearter som ble funnet i algekulturer. Ved en sammenligning av fordelingen av bakterieslekter som er fastsittende til algecellen og frittlevende i algekultur, deler de to gruppene 80 % av bakterieslektene, og har dermed høy likhet. De frittlevende bakteriene har høyest antall ASVer, noe som indikerer at de fleste bakterie-typene lever fritt i kultur. Dette vises også ved de statistiske analysene, der alfadiversiteten for de frittlevende bakteriene i kultur har et signifikant rikere mikrobiom i forhold til fastsittende bakterier til algecellen. Betadiversiteten mellom fastsittende og frittlevende bakterier viser derimot ingen signifikante forskjeller, som vil si at mikrobiom-sammensetningen ikke kan forklares ut ifra om det er fastsittende på algecellene eller frittlevende i kultur.

• Carlsen, Eira Catharine Lødrup; Eiler, Alexander; Hylland, Ketil & Gomes, Tania (2022). Double trouble: plastic leachates as drivers for increased adaptations to antibiotics? The effects of plastic leachates and ciprofloxacin on the sea urchin microbiome. Universitetet i Oslo. Full text in Research Archive
• Hjelset, Sverre; Eiler, Alexander; Hylland, Ketil & Gomes, Tania (2021). Weak toxicity of chemical additives extracted from car tire rubber on the microbiome of Atlantic cod and Norway pout. Universitetet i Oslo. Full text in Research Archive Show summary

  We exposed the microbiome derived from two species of cod, from the outer and inner Oslo fjord to extracts derived from car tire rubber. To determine toxicity we look at growth rate and bacterial diversity as endpoints. We observed low effects overall, except for some significant changes to microbial diversity at some concentrations.

• Finstad, Anders Gravbrøt; Boer, Hugo de; Brurberg, May Bente; Dahle, Geir; Edgar, Kristin Skarsfjord & Eiler, Alexander [Show all 25 contributors for this article] (2020). Kriterier for lagring av miljø-DNA prøver og data, herunder henvisning til referansemateriale. Criteria for depositing eDNA samples and data, including vouchered specimens. Miljødirektoratet. Full text in Research Archive

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