eliannee

• Klemetsen, Terje; Endresen, Dag; Johnsen, Arild; Boer, Hugo de; Fossøy, Frode & Ekrem, Torbjørn [Show all 11 contributors for this article] (2026). Strengthening molecular biodiversity research and monitoring in Norway – connecting tools, data and people. F1000 Research. 15, p. (ELIXIR)–(ELIXIR). doi: 10.12688/f1000research.179210.1. Full text in Research Archive Show summary

  Background Norway’s diverse ecosystems and strong research community are well-positioned to leverage molecular approaches (DNA barcoding, eDNA, whole-genome sequencing) for biodiversity research and monitoring. However, progress is constrained by gaps in data accessibility, standardisation, and interoperability across molecular, ecological, and biobank datasets. Methods ELIXIR’s Norwegian Molecular Biodiversity Working Group mapped national actors and networks through a desk review (2024–2025) and conducted a national survey (58 questions; open from 18 February to 8 March 2024) targeting data management, standards, tooling, infrastructures, and training. The survey was implemented in Nettskjema and received 58 responses from biodiversity-related researchers. Results We identified 19 Norwegian institutes active in molecular biodiversity and 28 relevant networks, with 11 networks involving three or more institutes. The survey results highlight gaps between policy and practice: 60% of respondents were familiar with the FAIR principles, but only 29% consistently made data fully open or FAIR-compliant. Data linkage with physical specimens was often reported as missing (38% of respondents), and taxonomic assignment was frequently challenging (39.3%). Most researchers reuse published datasets (90%), but data discovery and reuse are hindered: only 41% find it easy to locate relevant data, 32% struggle to find appropriate sequence databases, 54% cite insufficient metadata, and 72% need to harmonise combined datasets. Tool discoverability and documentation were limited (32% knew bio.tools; 5% WorkflowHub; 32% agreed tools are well documented and user-friendly). Data publication is not straightforward (63.8% find it hard or answered neutral). Conclusions Norway can strengthen molecular biodiversity research by 1) connecting molecular and ecological data, collections, and biobanks using persistent identifiers; 2) adhering to international metadata standards (e.g., DwC, MIxS) and rewarding data stewardship; 3) consolidating national collaborative networks; and 4) building capacity through targeted training and dedicated data steward roles. Implementing these measures will enhance interoperability, FAIR data sharing, and Norway’s leadership in biodiversity research and conservation.

• Kavakiotis, Ioannis; Woollard, Peter; Babo, Camila; Egge, Elianne; Krawczyk, Dawid & Laamanen, Tiina [Show all 14 contributors for this article] (2026). Navigating the European aquatic eDNA landscape: Opportunities for metadata standardisation and data mobilisation. Metabarcoding and Metagenomics. 10. doi: 10.3897/mbmg.10.173612. Full text in Research Archive Show summary

  Environmental DNA (eDNA) has emerged as a transformative tool for monitoring aquatic biodiversity, offering a non-invasive and highly sensitive approach to detecting organisms across diverse ecosystems. However, its effective downstream application across Europe in environmental management is hindered by inconsistencies in data standardisation, metadata reporting, and accessibility. This perspective comprehensively evaluates current data repositories, data submission workflows, and standardisation efforts within the European aquatic eDNA landscape. By employing a multi-method approach, including an inventory of eDNA databases, a metadata assessment, a stakeholder questionnaire, and a generative Artificial Intelligence (AI)-driven analysis of scientific literature, our findings reveal substantial variability in metadata reporting practices, with several areas misaligned with Findable, Accessible, Interoperable, and Reusable (FAIR) principles. While some repositories demonstrate strong data curation and accessibility, others lack essential metadata descriptors, limiting interoperability. We identify critical gaps in metadata submission, particularly concerning sampling methods and wet lab workflows, which heavily impact data reusability. The use of generative AI in this study further enabled large-scale identification of recurring reporting weaknesses, highlighting structural challenges that extend beyond individual studies. Addressing these gaps and leveraging advanced computational approaches through international standards and harmonised guidelines represents a clear way forward, as articulated in the recent “Making eDNAFAIR” paper by Takahashi et al. (2025), which is based on the use of Darwin Core (DwC) and Genomics Standards Consortium (GSC) MIxS standards, as well as Global Biodiversity Information Facility (GBIF)’s “Publishing DNA-derived data through biodiversity data platforms” guidelines. Furthermore, additional complementary principles strengthen this framework. The Collective benefit, Authority to control, Responsibility, Ethics (CARE) principles emphasise Indigenous data governance and responsible sample stewardship, while the Transparency, Responsibility, User focus, Sustainability, Technology (TRUST) principles provide criteria for repository reliability and long-term digital preservation. Together, the combined application of FAIR, CARE, and TRUST principles provides a structured foundation for ensuring robust, interoperable, and ethically managed eDNA data that support aquatic biodiversity research, management, and conservation across Europe.

• Egge, Elianne Dunthorn; Vaulot, Daniel; Larsen, Aud & Edvardsen, Bente (2025). The community of marine alveolate parasites in the Atlantic inflow to the Arctic Ocean is structured by season, depth, and water mass. Arctic Science. ISSN 2368-7460. 11, p. 1–16. doi: 10.1139/as-2024-0016. Full text in Research Archive Show summary

  The marine alveolates (MALVs) are a highly diverse group of parasitic dinoflagellates, which may regulate populations of a wide range of hosts, including other dinoflagellates, copepods, and fish eggs. Knowledge on their distribution and ecological role is still limited, as they are difficult to study with morphological methods. In this work, we describe the taxonomic composition and seasonal and depth distribution of MALVs in the Arctic Ocean west and north of Svalbard, based on 18S V4 rRNA metabarcoding data from five cruises. We recovered amplicon sequence variants (ASVs) representing all major groups previously described from environmental sequencing studies (Dino-Groups I–V), with Dino-Groups I and II being the most diverse. The community was structured by season, depth, and water mass. In the epipelagic zone, the taxonomic composition varied strongly by season; however, there was also a difference between Arctic and Atlantic water masses in winter. The spring and summer epipelagic communities were characterized by a few dominating ASVs present in low proportions during winter and in mesopelagic summer samples, suggesting that they proliferate under certain conditions, e.g., when specific hosts are abundant. Mesopelagic samples were more similar across months, and may harbor parasites of deep-dwelling organisms, little affected by season.

• Egge, Elianne Dunthorn; Elferink, Stephanie; Vaulot, Daniel; John, Uwe; Bratbak, Gunnar & Larsen, Aud [Show all 7 contributors for this article] (2021). An 18S V4 rDNA metabarcoding dataset of protist diversity in the Atlantic inflow to the Arctic Ocean, through the year and down to 1000 m depth. Earth System Science Data. 13, p. 4913–4928. doi: 10.5194/essd-13-4913-2021. Full text in Research Archive Show summary

  Arctic marine protist communities have been understudied due to challenging sampling conditions, in particular during winter and in deep waters. The aim of this study was to improve our knowledge on Arctic protist diversity through the year, in both the epipelagic (< 200 m depth) and mesopelagic zones (200–1000 m depth). Sampling campaigns were performed in 2014, during five different months, to capture the various phases of the Arctic primary production: January (winter), March (pre-bloom), May (spring bloom), August (post-bloom), and November (early winter). The cruises were undertaken west and north of the Svalbard archipelago, where warmer Atlantic waters from the West Spitsbergen Current meet cold Arctic waters from the Arctic Ocean. From each cruise, station, and depth, 50 L of seawater was collected, and the plankton was size-fractionated by serial filtration into four size fractions between 0.45–200 µm, representing picoplankton (0.45–3 µm), small and large nanoplankton (3–10 and 10–50 µm, respectively), and microplankton (50–200 µm). In addition, vertical net hauls were taken from 50 m depth to the surface at selected stations. The net hauls were fractionated into the large nanoplankton (10–50 µm) and microplankton (50–200 µm) fractions. From the plankton samples DNA was extracted, the V4 region of the 18S rRNA-gene was amplified by polymerase chain reaction (PCR) with universal eukaryote primers, and the amplicons were sequenced by Illumina high-throughput sequencing. Sequences were clustered into amplicon sequence variants (ASVs), representing protist genotypes, with the dada2 pipeline. Taxonomic classification was made against the curated Protist Ribosomal Reference database (PR2). Altogether, 6536 protist ASVs were obtained (including 54 fungal ASVs). Both ASV richness and taxonomic composition varied between size fractions, seasons, and depths. ASV richness was generally higher in the smaller fractions and higher in winter and the mesopelagic samples than in samples from the well-lit epipelagic zone during summer. During spring and summer, the phytoplankton groups diatoms, chlorophytes, and haptophytes dominated in terms of relative read abundance in the epipelagic zone. Parasitic and heterotrophic groups such as Syndiniales and certain dinoflagellates dominated in the mesopelagic zone all year, as well as in the epipelagic zone during the winter. The dataset is available at https://doi.org/10.17882/79823 (Egge et al., 2014).

• Stadniczeñko, Sandra Gran; Krabberød, Anders Kristian; Sandaa, Ruth-Anne; Yau, Sheree; Egge, Elianne Dunthorn & Edvardsen, Bente (2019). Seasonal dynamics of algae-infecting viruses and their inferred interactions with protists. Viruses. 11(11), p. 1–16. doi: 10.3390/v11111043. Full text in Research Archive Show summary

  Viruses are a highly abundant, dynamic, and diverse component of planktonic communities that have key roles in marine ecosystems. We aimed to reveal the diversity and dynamics of marine large dsDNA viruses infecting algae in the Northern Skagerrak, South Norway through the year by metabarcoding, targeting the major capsid protein (MCP) and its correlation to protist diversity and dynamics. Metabarcoding results demonstrated a high diversity of algal viruses compared to previous metabarcoding surveys in Norwegian coastal waters. We obtained 313 putative algal virus operational taxonomic units (vOTUs), all classified by phylogenetic analyses to either the Phycodnaviridae or Mimiviridae families, most of them in clades without any cultured or environmental reference sequences. The viral community showed a clear temporal variation, with some vOTUs persisting for several months. The results indicate co-occurrences between abundant viruses and potential hosts during long periods. This study gives new insights into the virus-algal host dynamics and provides a baseline for future studies of algal virus diversity and temporal dynamics.

• Gran-Stadniczenko, Sandra; Egge, Elianne; Hostyeva, Vladyslava; Logares, Ramiro; Eikrem, Wenche & Edvardsen, Bente (2019). Protist Diversity and Seasonal Dynamics in Skagerrak Plankton Communities as Revealed by Metabarcoding and Microscopy. Journal of Eukaryotic Microbiology. ISSN 1066-5234. 66(3), p. 494–513. doi: 10.1111/jeu.12700. Full text in Research Archive Show summary

  Protist community composition and seasonal dynamics are of major importance for the production of higher trophic levels, such as zooplankton and fish. Our aim was to reveal how the protist community in the Skagerrak changes through the seasons by combining high‐throughput sequencing and microscopy of plankton collected monthly over two years. The V4 region of the 18S rRNA gene was amplified by eukaryote universal primers from the total RNA/cDNA. We found a strong seasonal variation in protist composition and proportional abundances, and a difference between two depths within the euphotic zone. Highest protist richness was found in late summer‐early autumn, and lowest in winter. Temperature was the abiotic factor explaining most of the variation in diversity. Dinoflagellates was the most abundant and diverse group followed by ciliates and diatoms. We found about 70 new taxa recorded for the first time in the Skagerrak. The seasonal pattern in relative read abundance of major phytoplankton groups was well in accordance with microscopical biovolumes. This is the first metabarcoding study of the protist plankton community of all taxonomic groups and through seasons in the Skagerrak, which may serve as a baseline for future surveys to reveal effects of climate and environmental changes.

• Mahé, Frédéric; Vargas, Colomban De; Bass, David; Czech, Lucas; Stamatakis, Alexandros & Lara, Enrique [Show all 22 contributors for this article] (2017). Parasites dominate hyperdiverse soil protist communities in Neotropical rainforests. Nature Ecology and Evolution. 1:0091(4), p. 1–8. doi: 10.1038/s41559-017-0091. Full text in Research Archive
• Stadniczenko, Sandra Gran; Supraha, Luka; Egge, Elianne Dunthorn & Edvardsen, Bente (2017). Haptophyte Diversity and Vertical Distribution Explored by 18S and 28S Ribosomal RNA Gene Metabarcoding and Scanning Electron Microscopy. Journal of Eukaryotic Microbiology. ISSN 1066-5234. 64(4), p. 514–532. doi: 10.1111/jeu.12388. Full text in Research Archive Show summary

  Haptophyta encompasses more than 300 species of mostly marine pico‐ and nanoplanktonic flagellates. Our aims were to investigate the Oslofjorden haptophyte diversity and vertical distribution by metabarcoding, and to improve the approach to study haptophyte community composition, richness and proportional abundance by comparing two rRNA markers and scanning electron microscopy (SEM). Samples were collected in August 2013 at the Outer Oslofjorden, Norway. Total RNA/cDNA was amplified by haptophyte‐specific primers targeting the V4 region of the 18S, and the D1‐D2 region of the 28S rRNA. Taxonomy was assigned using curated haptophyte reference databases and phylogenetic analyses. Both marker genes showed Chrysochromulinaceae and Prymnesiaceae to be the families with highest number of Operational Taxonomic Units (OTUs), as well as proportional abundance. The 18S rRNA data set also contained OTUs assigned to eight supported and defined clades consisting of environmental sequences only, possibly representing novel lineages from family to class. We also recorded new species for the area. Comparing coccolithophores by SEM with metabarcoding shows a good correspondence with the 18S rRNA gene proportional abundances. Our results contribute to link morphological and molecular data and 28S to 18S rRNA gene sequences of haptophytes without cultured representatives, and to improve metabarcoding methodology.

• Johannessen, Torill Vik; Larsen, Aud; Bratbak, Gunnar; Pagarete, António; Edvardsen, Bente & Egge, Elianne Dunthorn [Show all 7 contributors for this article] (2017). Seasonal dynamics of haptophytes and dsDNA algal viruses suggest complex virus-host relationship. Viruses. 9(4). doi: 10.3390/v9040084. Full text in Research Archive Show summary

  Viruses influence the ecology and diversity of phytoplankton in the ocean. Most studies of phytoplankton host–virus interactions have focused on bloom-forming species like Emiliania huxleyi or Phaeocystis spp. The role of viruses infecting phytoplankton that do not form conspicuous blooms have received less attention. Here we explore the dynamics of phytoplankton and algal viruses over several sequential seasons, with a focus on the ubiquitous and diverse phytoplankton division Haptophyta, and their double-stranded DNA viruses, potentially with the capacity to infect the haptophytes. Viral and phytoplankton abundance and diversity showed recurrent seasonal changes, mainly explained by hydrographic conditions. By 454 tag-sequencing we revealed 93 unique haptophyte operational taxonomic units (OTUs), with seasonal changes in abundance. Sixty-one unique viral OTUs, representing Megaviridae and Phycodnaviridae, showed only distant relationship with currently isolated algal viruses. Haptophyte and virus community composition and diversity varied substantially throughout the year, but in an uncoordinated manner. A minority of the viral OTUs were highly abundant at specific time-points, indicating a boom-bust relationship with their host. Most of the viral OTUs were very persistent, which may represent viruses that coexist with their hosts, or able to exploit several host species.

• Edvardsen, Bente; Egge, Elianne Dunthorn & Vaulot, Daniel (2016). Diversity and distribution of haptophytes revealed by environmental sequencing and metabarcoding – a review. Perspectives in Phycology. ISSN 2364-6993. 3(2), p. 77–91. doi: 10.1127/pip/2016/0052. Full text in Research Archive
• Forster, Dominik; Dunthorn, Micah; Mahé, Frédéric; Dolan, John R.; Audic, Stéphane & Bass, David [Show all 35 contributors for this article] (2016). Benthic protists: The under-charted majority. FEMS Microbiology Ecology. ISSN 0168-6496. 92(8), p. 1–11. doi: 10.1093/femsec/fiw120. Full text in Research Archive
• Egge, Elianne Sirnæs; Eikrem, Wenche & Edvardsen, Bente (2015). Deep-branching novel lineages and high diversity of haptophytes in the Skagerrak (Norway) uncovered by 454 pyrosequencing. Journal of Eukaryotic Microbiology. ISSN 1066-5234. 62(1), p. 121–140. doi: 10.1111/jeu.12157. Full text in Research Archive Show summary

  Microalgae in the division Haptophyta may be difficult to identify to species by microscopy because they are small and fragile. Here, we used high-throughput sequencing to explore the diversity of haptophytes in outer Oslofjorden, Skagerrak, and supplemented this with electron microscopy. Nano- and picoplanktonic subsurface samples were collected monthly for 2 yr, and the haptophytes were targeted by amplification of RNA/cDNA with Haptophyta-specific 18S ribosomal DNA V4 primers. Pyrosequencing revealed higher species richness of haptophytes than previously observed in the Skagerrak by microscopy. From ca. 400,000 reads we obtained 156 haptophyte operational taxonomic units (OTUs) after rigorous filtering and 99.5% clustering. The majority (84%) of the OTUs matched environmental sequences not linked to a morphological species, most of which were affiliated with the order Prymnesiales. Phylogenetic analyses including Oslofjorden OTUs and available cultured and environmental haptophyte sequences showed that several of the OTUs matched sequences forming deep-branching lineages, potentially representing novel haptophyte classes. Pyrosequencing also retrieved cultured species not previously reported by microscopy in the Skagerrak. Electron microscopy revealed species not yet genetically characterised and some potentially novel taxa. This study contributes to linking genotype to phenotype within this ubiquitous and ecologically important protist group, and reveals great, unknown diversity.

• Johannessen, Torill Vik; Bratbak, Gunnar; Larsen, Aud; Ogata, Hirotaka; Egge, Elianne Sirnæs & Edvardsen, Bente [Show all 8 contributors for this article] (2015). Characterisation of three novel giant viruses reveals huge diversity among viruses infecting Prymnesiales (Haptophyta). Virology. ISSN 0042-6822. 476, p. 180–188. doi: 10.1016/j.virol.2014.12.014. Full text in Research Archive
• Egge, Elianne Sirnæs; Johannessen, Torill Vik; Andersen, Tom; Eikrem, Wenche; Bittner, Lucie & Larsen, Aud [Show all 8 contributors for this article] (2015). Seasonal diversity and dynamics of haptophytes in the Skagerrak, Norway, explored by high-throughput sequencing. Molecular Ecology. ISSN 0962-1083. 24(12), p. 3026–3042. doi: 10.1111/mec.13160. Full text in Research Archive Show summary

  Microalgae in the division Haptophyta play key roles in the marine ecosystem and in global biogeochemical processes. Despite their ecological importance, knowledge on seasonal dynamics, community composition and abundance at the species level is limited due to their small cell size and few morphological features visible under the light microscope. Here, we present unique data on haptophyte seasonal diversity and dynamics from two annual cycles, with the taxonomic resolution and sampling depth obtained with high-throughput sequencing. From outer Oslofjorden, S Norway, nano- and picoplanktonic samples were collected monthly for 2 years, and the haptophytes targeted by amplification of RNA/cDNA with Haptophyta-specific 18S rDNA V4 primers. We obtained 156 operational taxonomic units (OTUs), from c. 400.000 454 pyrosequencing reads, after rigorous bioinformatic filtering and clustering at 99.5%. Most OTUs represented uncultured and/or not yet 18S rDNA-sequenced species. Haptophyte OTU richness and community composition exhibited high temporal variation and significant yearly periodicity. Richness was highest in September–October (autumn) and lowest in April–May (spring). Some taxa were detected all year, such as Chrysochromulina simplex, Emiliania huxleyi and Phaeocystis cordata, whereas most calcifying coccolithophores only appeared from summer to early winter. We also revealed the seasonal dynamics of OTUs representing putative novel classes (clades HAP-3–5) or orders (clades D, E, F). Season, light and temperature accounted for 29% of the variation in OTU composition. Residual variation may be related to biotic factors, such as competition and viral infection. This study provides new, in-depth knowledge on seasonal diversity and dynamics of haptophytes in North Atlantic coastal waters.

• Egge, Elianne Sirnæs; Bittner, Lucie; Andersen, Tom; Audic, Stéphane; Vargas, Colomban de & Edvardsen, Bente (2013). 454 Pyrosequencing to Describe Microbial Eukaryotic Community Composition, Diversity and Relative Abundance: A Test for Marine Haptophytes. PLOS ONE. 8(9). doi: 10.1371/journal.pone.0074371. Full text in Research Archive Show summary

  Next generation sequencing of ribosomal DNA is increasingly used to assess the diversity and structure of microbial communities. Here we test the ability of 454 pyrosequencing to detect the number of species present, and assess the relative abundance in terms of cell numbers and biomass of protists in the phylum Haptophyta. We used a mock community consisting of equal number of cells of 11 haptophyte species and compared targeting DNA and RNA/cDNA, and two different V4 SSU rDNA haptophyte-biased primer pairs. Further, we tested four different bioinformatic filtering methods to reduce errors in the resulting sequence dataset. With sequencing depth of 11000–20000 reads and targeting cDNA with Haptophyta specific primers Hap454 we detected all 11 species. A rarefaction analysis of expected number of species recovered as a function of sampling depth suggested that minimum 1400 reads were required here to recover all species in the mock community. Relative read abundance did not correlate to relative cell numbers. Although the species represented with the largest biomass was also proportionally most abundant among the reads, there was generally a weak correlation between proportional read abundance and proportional biomass of the different species, both with DNA and cDNA as template. The 454 sequencing generated considerable spurious diversity, and more with cDNA than DNA as template. With initial filtering based only on match with barcode and primer we observed 100-fold more operational taxonomic units (OTUs) at 99% similarity than the number of species present in the mock community. Filtering based on quality scores, or denoising with PyroNoise resulted in ten times more OTU99% than the number of species. Denoising with AmpliconNoise reduced the number of OTU99% to match the number of species present in the mock community. Based on our analyses, we propose a strategy to more accurately depict haptophyte diversity using 454 pyrosequencing. © 2013 Egge et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

• Dittami, Simon; Hostyeva, Vladyslava; Egge, Elianne Sirnæs; Kegel, Jessica U.; Eikrem, Wenche & Edvardsen, Bente (2013). Seasonal dynamics of harmful algae in outer Oslofjorden monitored by microarray, qPCR, and microscopy. Environmental Science and Pollution Research. ISSN 0944-1344. 20(10), p. 6719–6732. doi: 10.1007/s11356-012-1392-0. Full text in Research Archive
• Bittner, Lucie; Gobet, Angelique; Audic, Stéphane; Romac, Sarah; Egge, Elianne Sirnæs & Santini, Sebastien [Show all 10 contributors for this article] (2013). Diversity patterns of uncultured Haptophytes unravelled by pyrosequencing in Naples Bay. Molecular Ecology. ISSN 0962-1083. 22(1), p. 87–101. doi: 10.1111/mec.12108. Full text in Research Archive
• Sym, Stuart; Pienaar, Richard; Edvardsen, Bente & Egge, Elianne Sirnæs (2011). Fine structure and systematics of Prymnesium radiatum sp. nov. (Prymnesiophyceae) from False Bay and Franskraal, South Africa. European journal of phycology. ISSN 0967-0262. 46(3), p. 229–248. doi: 10.1080/09670262.2011.554886. Full text in Research Archive Show summary

  A novel colonial prymnesiophyte from the inshore waters of South Africa, which is reminiscent of the genus Corymbellus, is described at light and electron microscope levels. It differs from the only species of this genus, Corymbellus aureus, in scale structure, cell shape and colony morphology and has a complement of unusual morphological features that link it most with members of the Prymnesiales. Phylogenetic analyses of the nuclear-encoded SSU and LSU ribosomal DNA sequences indicate that this organism is closely related to members of the genus Prymnesium sensu lato and it is thus considered as a novel species, here named P. radiatum. The closest relative to P. radiatum in the SSU rDNA phylogenetic tree was Prymnesium neolepis (formerly Hyalolithus neolepis). The reconfiguration of the cytoskeleton during cell division in this organism is also novel, with a progressive elaboration of existing elements, rather than the massive reorganization expected in the prymnesiophytes.

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• Krzeminski, Pawel; Chand, Anita; Ribeiro, Anne Luise; Gjeitnes, Mari; Egge, Elianne & Umar, Muhammad [Show all 9 contributors for this article] (2026). Membrane filtration effectiveness for removal of antibiotic resistance genes from water and wastewater. Full text in Research Archive
• Krzeminski, Pawel; Chand, Anita; Egge, Elianne; Umar, Muhammad; Schwermer, Carsten Ulrich & Khezri, Abdolrahman [Show all 7 contributors for this article] (2025). Membrane filtration as a method of preventing the spread of AMR during water and sewage treatment. Full text in Research Archive
• 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.

• Krzeminski, Pawel; Egge, Elianne Dunthorn; Schwermer, Carsten Ulrich; Wennberg, Aina Charlotte; Umar, Muhammad & d'Auriac, Marc Anglès (2023). Effectiveness of membrane filtration for removal of cell free antibiotic resistance genes from water and wastewater. Full text in Research Archive
• Edvardsen, Bente; Supraha, Luka; Egge, Elianne Dunthorn & Saubrekka, Karoline (2023). Diversity and distribution of marine protists in the Arctic explored by a polyphasic approach. Full text in Research Archive
• Krzeminski, Pawel; Egge, Elianne Dunthorn; Umar, Muhammad; Schwermer, Carsten Ulrich; Wennberg, Aina Charlotte & d'Auriac, Marc Anglès (2022). Removal Of Cell Free Antibiotic Resistance Genes From Water By Membrane Filtration And From Membrane Concentrate By 265 Nm UV-LED. Full text in Research Archive Show summary

  Mitigation of antibiotic resistance genes (ARGs) emissions has become a high priority and technologies able to effectively decrease their release to the environment are needed. Membrane filtration, in particular nanofiltration (NF) or reverse osmosis (RO) may be an effective technology. The study focused on mitigation of antibiotic resistance genes (ARGs) emissions to aquatic environment and the aim was to understand whether and to what extent ARGs can be removed by different membrane filtration processes. The specific objective was to assess the removal rate of the ARGs from ultrapure water and wastewater treatment plant (WWTP) effluent during experiments with ultrafiltration (UF), nanofiltration (NF) and reverse osmosis (RO) membranes. In addition, the potential of UV-LED at 265 nm for the treatment of the ARG-rich membrane concentrate was assessed.

• Edvardsen, Bente; Supraha, Luka; Egge, Elianne Dunthorn & John, Uwe (2022). Harmful haptophyte blooms in Norway - bloom dynamics and ecology, with special focus on the Chrysochromulina leadbeateri blooms. Full text in Research Archive
• Edvardsen, Bente; Supraha, Luka & Egge, Elianne Dunthorn (2022). Diversity and distribution of marine protists in the Arctic explored by a polyphasic approach. Full text in Research Archive
• Edvardsen, Bente; Egge, Elianne Dunthorn; Vaulot, Daniel; Larsen, Aud; Bratbak, Gunnar & Moreau, Hervé [Show all 7 contributors for this article] (2017). Protist community structure in Atlantic Arctic through the year as revealed by high throughput sequencing. Full text in Research Archive
• Egge, Elianne Dunthorn (2017). Metabarcoding of haptophytes. Full text in Research Archive
• Egge, Elianne Dunthorn; Vaulot, Daniel; Larsen, Aud; Bratbak, Gunnar; Uwe, John & Edvardsen, Bente (2017). Protist community structure in Atlantic Arctic through the year as revealed by high throughput sequencing. Full text in Research Archive Show summary

  Unicellular protists, including microalgae are main suppliers of photosynthetic products that higher trophic levels depend upon. Yet, the Arctic protist community contains a vast unknown diversity and many of the described species are poorly known. Diversity and dynamics throughout the polar night and at great depths remains particularly understudied due to limited access. In the MicroPolar project we asked “Who are present and when during the year?”, “How is the community structured by depth and geography?” and “What are the environmental driving forces for the observed distribution?” Sampling cruises to North and West of Svalbard were carried out five times during 2014 (January, March, May, August and November). Samples were collected at 3-6 stations and four depths (1-1000m). Fifty litres were divided into four size fractions from micro- to picoplankton. The 18S V4 region of nuclear rDNA and the 16S V9 region of chloroplast rDNA and rRNA were high throughput sequenced with Illumina. We obtained c. 35 000 Operational Taxonomic Units (OTUs) clustered at 98% similarity. The protist community composition differed significantly between the dark and light seasons, and between surface water and beyond the photic zone. Also OTU richness varied significantly with depth and season. OTU richness was significantly higher in the deeper layers all months except March. The May samples had lowest richness, whereas August had highest. Both in terms of OTU richness and proportional read abundance Dinophyta was dominating in most samples, except in the May samples representing the spring bloom, where diatoms dominated. The 200 most frequent OTUs were detected all seasons and in both surface and deeper layers. The majority of these were assigned to defined clades consisting of environmental sequences only, such as MAST-clades and Dino-Group clades. This highlights the need for more reference DNA sequences from cultures. Several abundant and frequent OTUs matched well-known Arctic species, such as Chaetoceros gelidus (socialis), Phaeocystis pouchetii, Gyrodinium fusiforme and Micromonas pusilla. Interestingly, OTUs assigned to Picobiliphyta were also among the most ubiquitous OTUs. Picobiliphyta were first described in 2007 in particular from samples from the Arctic Ocean, and all are thought to be heterotrophic. As global climate change is expected to be most severe in the Arctic and may affect microbial communities and biogeochemical cycles more seriously in this region than anywhere else, this study is important to be able to assess the impact of climate change in the Arctic at the microbial level.

• Edvardsen, Bente; Vaulot, Daniel & Egge, Elianne Sirnæs (2016). A global haptophyte 18S rRNA gene phylogeny including potentially novel lineages, and a curated reference sequence database for taxonomic assignment of metabarcodes. Full text in Research Archive Show summary

  Microalgae of the division Haptophyta are a major component of the marine nanoplankton and present in all seas. They are important primary producers and grazers of picoplankton in the ocean, and their metabolic products can have an impact on global climate. Due to their small size, species are mostly difficult to distinguish by microscopy. Environmental sequencing studies have revealed a high marine haptophyte diversity. We have constructed a curated haptophyte 18S rRNA-gene reference database comprising c. 970 sequences, mostly >800 bp for taxonomic assignment of environmental sequences and metabarcoding reads. We have taxonomically assigned all sequences by phylogenetic analyses, removed chimeras, updated the taxonomy according to recent revisions, and defined clades without cultured and sequenced representatives. Haptophyta embrace numerous clades potentially representing novel lineages from genus to class level. Here we present current knowledge on their distribution based on available 18S rRNA gene sequences.

• Edvardsen, Bente; Egge, Elianne Dunthorn; John, Uwe & Vaulot, Daniel (2016). Protist diversity revealed by metabarcoding in Kongsfjorden, Svalbard mesocosm experiment. Full text in Research Archive Show summary

  As a part of the MicroPolar project a mesocosm experiment was conducted in Kongsfjorden, Svalbard in July 2015. The aim was to assess the effect of grazing pressure and levels of organic carbon on the microbial composition and relative abundance over time. In this part of the project we studied how the protist community composition and relative abundance were affected by these two factors. Water samples (2L) were harvested 5 times during a 10 days incubation, and DNA from the size fractions 0.2-3 and 3-50 µm were PCR amplified by eukaryote general V4 18 rRNA gene primers and tag sequenced by Illumina. Both composition and relative abundance differed significantly in response to the two factors.

• Edvardsen, Bente; Egge, Elianne Sirnæs; Stadniczenko, Sandra Gran; Johannessen, Torill Vik; Eikrem, Wenche & Sandaa, Ruth-Anne [Show all 10 contributors for this article] (2015). Diversity and seasonal dynamics of marine haptophytes and their viruses and the role of biotic interactions. Full text in Research Archive Show summary

  Members of the phytoplankton division Haptophyta are a major component in marine pico- and nanoplankton communities. They often occur in bloom concentrations that may have a major impact on the global carbon balance, on climate forcing and sometimes cause fish-kills. Because haptophytes are tiny and difficult to identify in the microscope little is known about their seasonal dynamics and ecological role at the species level. Virus may terminate haptophyte blooms and, according to the “killing the winner” concept, possibly prevent blooms by keeping them under constant control. The aim of this study within the HAPTODIV project was to reveal the diversity and dynamics of marine haptophytes to species level and how this relates to abiotic factors and viruses. We assessed the haptophyte and Phycodnaviridae/ Mimiviridae (algal viruses) taxonomic composition, OTU richness and relative abundance over time by high-throughput amplicon sequencing (metabarcoding) of monthly samples over 2 years from the outer Oslofjorden, Skagerrak, Southern Norway. Metabarcoding revealed higher haptophyte diversity (156 OTUs estimating species) than previously observed in the area with electron and light microscopy (85 spp), and most (84%) of this diversity remains to be cultured and sequenced. Many may represent novel lineages at the class to genus level, or species new for science. More than half of the OTUs (93) were affiliated with the order Prymnesiales such as members of e.g. Chrysochromulina and Prymnesium. Haptophyte richness and community composition showed high temporal variation and significant yearly periodicity correlating with light and temperature, with highest richness in autumn (Sep-Nov) and lowest in the spring (Apr-May). Our results indicated, however, that the abiotic factors only accounted for about 30% of the variation, and suggest that biotic factors explain some of the residual variation. Also algal virus diversity was high and showed temporal variations with highest richness in Sept-Oct. Biotic interactions between haptophytes and algal viruses were assessed by co-occurrence analyses. We detected 56 haptophyte-virus pairs with significant co-occurrence, of 49 000 possible pairs. The distribution patterns of these pairs may shed light on the role of virus infection on phytoplankton community composition and dynamics. We suggest that this approach may be a first step to test the “killing-the-winner” concept on haptophyte diversity and distribution.

• Edvardsen, Bente; Egge, Elianne Sirnæs; Stadniczenko, Sandra Gran; Johannessen, Torill Vik; Larsen, Aud & Sandaa, Ruth-Anne [Show all 7 contributors for this article] (2015). Diversity, seasonal dynamics and biotic interactions in marine phytoplankton and virus communities. Full text in Research Archive Show summary

  The taxonomic composition of phytoplankton communities and relative abundance of taxa in oceanic ecosystems undergo continuous change. This community reorganization is of major importance to higher trophic levels and biogeochemical cycles. This succession is partly accounted for by hydrographical and meteorological variations that select for different traits in time and space, but also by biological processes, such as pathogens. Virus may terminate haptophyte blooms and, according to the “killing the winner” concept, possibly prevent blooms by keeping them under constant control. We assessed the haptophyte (algal host) and Phycodnaviridae/Mimiviridae (virus) taxonomic composition and relative abundance by high-throughput amplicon sequencing of monthly samples over 2 years from the outer Oslofjorden. Haptophyte richness and community composition exhibited high temporal variation and significant yearly periodicity, with highest richness in autumn (Sept-Oct) and lowest in the spring (April-May). Also, algal virus diversity showed seasonal variations with highest richness in September-October and lowest in August. Biotic interactions between haptophytes and viruses and among haptophytes were evaluated to provide new insight in the role of biotic processes for phytoplankton community composition and dynamics.

• Edvardsen, Bente; Egge, Elianne Sirnæs; Johannessen, Torill Vik; Eikrem, Wenche; Sandaa, Ruth-Anne & Bittner, Lucie [Show all 10 contributors for this article] (2014). Diversity and seasonal dynamics of marine haptophytes and their viruses. Full text in Research Archive Show summary

  Members of the division Haptophyta are phytoplankton and a major component in marine pico- and nanoplankton communities. They often occur in bloom concentrations that may have a major impact on the global carbon balance, on climate forcing and sometimes cause fish-kills. Because haptophytes are small and difficult to identify in the microscope little is known about their seasonal dynamics and ecological role at the species level. We have studied the diversity and seasonal dynamics of marine haptophytes and their viruses, and how species composition and diversity are related to environmental factors using 454 pyrosequencing, complemented with electron microscopy and flow cytometry. This study revealed higher species richness of haptophytes than previously observed in the area with electron and light microscopy. The majority of the OTUs matched genetically uncharacterised taxa, most of which were affiliated with the order Prymnesiales. Several of the OTUs matched sequences forming deep-branching lineages, potentially representing novel classes of haptophytes. Haptophyte richness and community composition exhibited high temporal variation and significant yearly periodicity, with highest richness in autumn and lowest in the spring. Some taxa, such as some bloom forming species were present all year round, whereas most coccolithophores only appeared from summer to early winter. Also the algal virus (Phycodnaviridae) diversity was high and showed seasonal variations. Our results indicated that the abiotic factors only accounted for about 30% of the variation, and suggests that biotic factors may explain some of the residual variation.

• Edvardsen, Bente; Stadniczenko, Sandra Gran; Eikrem, Wenche; Hostyeva, Vladyslava; Logares, Ramiro & Egge, Elianne Sirnæs (2014). Diversity and seasonal dynamics of small dinoflagellates in the Skagerrak, Norway revealed by 454 pyrosequencing and microscopy. Full text in Research Archive Show summary

  Some dinoflagellates are small and difficult to identify under the light microscope and thus little is known about their seasonal dynamics at the species level. Here we combined high-throughput sequencing and microscopy to explore their diversity and seasonal dynamics, and relate this to environmental factors. We collected 21 monthly samples of nanoplankton (3-45 μm size fraction) from outer Oslofjorden, southern Norway over two years. The 18S V4 ribosomal DNA was amplified from RNA/cDNA and 454-pyrosequenced. The reads were cleaned, denoised and clustered to 99% in Qiime and assigned to taxon. From 46250 reads assigned to Dinoflagellata we detected 367 unique operational taxonomic units (OTUs) assessed to represent species or genera. The most OTU-rich orders were Gymnodiniales (32%), Syndiniales (22%), and Peridiniales (17%), followed by Dinophysiales (8%), Gonyaulacales (7%) and Suessiales (4%). Reads assigned to Gymnodiniales dominated in all samples except June and August 2010 when reads assigned to Suessiales dominated. We observed strong seasonal variation and significant yearly periodicity in dinoflagellate richness and species composition. OTU richness was highest in late autumn and lowest in winter-spring. Seasonal dynamics of potentially toxic taxa were examined. We also assess and discuss the ability to detect potentially toxic dinoflagellate species with 18S V4 high throughput sequencing and compare this with standard microscopical methods and electron microscopy. Potentially toxic species <45 μm observed under the microscope included e.g. Alexandrium pseudogonyaulax, A. ostenfeldii, Azadinium spinosum, Karenia mikimotoi, Karlodinium veneficum and Prorocentrum minimum.

• Edvardsen, Bente; Egge, Elianne Sirnæs & Eikrem, Wenche (2013). Morphology, phylogeny and diversity of haptophytes. Full text in Research Archive
• Edvardsen, Bente; Egge, Elianne Sirnæs; Vik, Johannessen Torill; Sandaa, Ruth-Anne; Eikrem, Wenche & Larsen, Aud [Show all 12 contributors for this article] (2013). Diversity and dynamics of marine haptophytes and their viruses. Full text in Research Archive Show summary

  Haptophytes are nano- and picoplanktonic microalgae and important primary producers in the sea. They often form blooms that may impact on global carbon balance and climate forcing, and at times cause fish kills. Viruses may terminate these blooms. Knowledge on haptophyte diversity, quantitative distribution and dynamics at species level is limited because they are small and fragile, and species identification usually requires electron microscopy or molecular methods. In the project HAPTODIV we have developed methods to explore the diversity and dynamics of haptophytes and their viruses, using 454-pyrosequencing, environmental clone libraries, DNA-sequencing of new isolates, pulsed field gel electrophoresis, quantitative PCR, flow cytometry and microscopy. Plankton samples and environmental data were collected monthly from the Oslofjorden and Raunefjorden for two years. A high diversity of haptophytes was revealed, and a majority of the sequences represent unknown or uncultured species. Several taxa are recorded for the first time in Norwegian and North European waters and some may represent new taxonomic lineages (orders and class). In Oslofjorden and Raunefjorden, some taxa are present at all times, such as bloom-formers in the genera Emiliania, Phaeocystis, Chrysochromulina and Prymnesium, whereas the calcifying coccolithophorids were found mainly in summer-autumn, the period with highest diversity and temperature. The diversity of virus infecting algae (Phycodnaviridae), including haptophyte specific viruses, differed over time and with locality and was highest in spring and lowest in winter. We have isolated and characterised four new haptophyte specific viruses that differ more in genome size, DNA sequence or infection cycle than previously shown. Genetic characterisation of viruses and their haptophyte hosts have revealed their diversity, and also improved our understanding of virus-host interactions and fundamental biological processes in the ocean.

• Edvardsen, Bente; Egge, Elianne Sirnæs; Bittner, Lucie; Eikrem, Wenche; Audic, Stéphane & Andersen, Tom [Show all 9 contributors for this article] (2012). Diversity and dynamics of marine haptophytes as revealed by 454 pyrosequencing. Full text in Research Archive Show summary

  Haptophytes are microalgae and a major component of marine plankton communities. Our aim is to provide new knowledge on the diversity and distribution of haptophytes below the genus-level, and how this is affected by environmental factors. We have developed and tested methods for analysing diversity using 454-pyrosequencing, We designed haptophyte-specific rDNA primers and constructed haptophyte databases and phylogenies for taxonomic assignation. We sequenced an artificial haptophyte community and compared the diversity and relative abundances from DNA and RNA/cDNA using various rDNA primers, and different programs to 18 remove errors from sequence data. We applied 454-pyrosequencing to samples from six European coastal sites and seasonal samples from Oslofjorden, and combined this with electron microscopy. We propose a strategy to more accurately depict the haptophyte diversity using 454-pyrosequencing and present results using this strategy.

• Edvardsen, Bente; Egge, Elianne Sirnæs; Bittner, Lucie; Audic, Stéphane & Vargas, Colomban de (2012). A strategy for 454-pyrosequencing of ribosomal SSU DNA and RNA to more accurately assess protist diversity and relative abundance. Full text in Research Archive Show summary

  Next generation sequencing of ribosomal DNA is increasingly used to assess the biodiversity and structure in microbial communities. Our aim was to develop a method to depict the diversity and community structure of marine planktonic haptophytes to species level. We used a mock community consisting of equal number of cells of 11 species representing all known haptophyte orders to investigate the ability to detect and assess the number of species present, and assess the relative abundance in terms of cell numbers and biomass by 454-pyrosequencing. We compared DNA to RNA/cDNA, 454-pyrosequencing to Sanger sequencing of clone libraries, and two different V4-SSU rDNA haptophyte biased primer pairs. Further, we tested 5 different strategies to clean the sequence data from errors. Up to 6000 unique tags per sample (with avg. 16500 reads) were obtained before sequence cleaning and clustering, and higher diversity was obtained from cDNA than DNA. The distribution of reads assigned to a species was significantly different from the initial proportions of cells or biomass in the culture mix, but cell numbers were better reflected by proportion of cDNA than DNA reads. Here we propose a strategy to more accurately depict the haptophyte diversity and assess relative abundance using 454-pyrosequencing.

• Egge, Elianne Sirnæs; Eikrem, Wenche; Hostyeva, Vladyslava; Andersen, Tom; Bittner, Lucie & Johannessen, Torill Vik [Show all 8 contributors for this article] (2012). Diversity and seasonal dynamics of haptophytes in outer Oslofjorden revealed by 454 pyrosequencing. Full text in Research Archive
• Egge, Elianne Sirnæs; Eikrem, Wenche; Hostyeva, Vladyslava; Andersen, Tom; Bittner, Lucie & Johannesen, Torill [Show all 9 contributors for this article] (2012). Diversity and seasonal dynamics of haptophytes in outer Oslofjorden revealed by 454 pyrosequencing. Full text in Research Archive
• Egge, Elianne Sirnæs; Eikrem, Wenche; Hostyeva, Vladyslava; Andersen, Tom; Bittner, Lucie & Johannesen, Torill [Show all 9 contributors for this article] (2012). Diversity and seasonal dynamics of haptophytes in outer Oslofjorden revealed by 454 pyrosequencing. Full text in Research Archive
• Egge, Elianne Sirnæs; Eikrem, Wenche; Andersen, Tom & Edvardsen, Bente (2012). HAPTODIV-Diversity and dynamics of marine haptophytes. Full text in Research Archive
• Egge, Elianne Sirnæs & Edvardsen, Bente (2011). QUANTIFICATION OF HAPTOPHYTE SPECIES BY PYROSEQUENCING: IS READ ABUNDANCE PROPORTIONAL TO CELL NUMBERS? Journal of Phycology. ISSN 0022-3646. 47, p. S63–S63. Full text in Research Archive
• Egge, Elianne Sirnæs & Edvardsen, Bente (2011). HAPTODIV - Diversity and dynamics of marine haptophytes. Full text in Research Archive
• Edvardsen, Bente & Egge, Elianne Sirnæs (2011). QUANTIFICATION OF HAPTOPHYTE SPECIES BY PYROSEQUENCING: IS READ ABUNDANCE PROPORTIONAL TO SPECIES BIOVOLUME? Full text in Research Archive Show summary

  Amplicon-sequencing of ribosomal RNA genes has become a standard for assessing microbial diversity in environmental samples. Abundance is of interest in addition to presence/absence of species to assess their ecological importance. The proportion of DNA sequences/reads from a particular species may, however, not reflect the proportion of the species in a sample in terms of cell number. We investigated the relationship between cell number and biovolume in an artificial community of haptophyte species, and the number of DNA sequences/reads appearing in libraries produced by cloning and 454-pyrosequencing nucleic acids extracted from this community. One million cells from each of 11 haptophyte species were pooled, and DNA and RNA extracted, and the V4 region of the small subunit ribosomal gene was amplified using haptophyte specific primers. The amplicons were sequenced by 454-pyrosequencing or Sanger sequencing. Pyrosequencing with 17000 reads per sample recovered all species in the culture mix, whereas clone libraries with 50-80 sequences per sample only recovered <50% of the species. Our results show that the proportion of reads from the different species in the 454-libraries were significantly different from the proportion of cells in the pool. There was a positive correlation between cell volume and read abundance, and thus cell size should be taken into account when interpreting 454-sequence data quantitatively.

• Bittner, Lucie; Gobet, Angelique; Egge, Elianne Sirnæs; Audic, Stéphane; Santini, Sebastien & Ogata, Hiroyuki [Show all 10 contributors for this article] (2011). Diversity of Haptophyta in the Bay of Naples as revealed by next generation sequencing (NGS): "anything new under the sea"? Full text in Research Archive
• Egge, Elianne Sirnæs & Edvardsen, Bente (2011). QUANTIFICATION OF HAPTOPHYTE SPECIES BY PYROSEQUENCING: IS READ ABUNDANCE PROPORTIONAL TO SPECIES BIOVOLUME? Full text in Research Archive
• Edvardsen, Bente; Nersveen, Lars; Torgrimsby, Tonie Leonora; Engesmo, Anette; Egge, Elianne Sirnæs & Eikrem, Wenche (2011). Diversity and distribution of nano- and picoeukaryotes in the Southern Ocean as revealed by 454-pyrosequencing, clone libraries and microscopy. Full text in Research Archive Show summary

  In this study we explored the diversity and distribution of planktonic nano- and picoeukaryotes in Antarctic waters by combining 454-pyrosequencing, clone libraries and electron microscopy. Water samples were collected and physico-chemical parameters measured during summer 2008 with the Norwegian R/V G.O. Sars in the Atlantic sector of the Southern Ocean, at stations along a transect (15°E) between 45-67o S. Ribosomal DNA of plankton in the size range 0.8-35µm was amplified with universal eukaryotic and haptophyte specific primers followed by pyro- and Sanger sequencing. Most rDNA sequences could not be assigned to a cultured and sequenced species (at ≥99,3% identity level) indicating that a large fraction of the plankton community remains to be genetically characterized. Electron microscopy revealed some of this diversity, but more cultured strains are needed as reference for a precise identification. The taxonomic groups represented with highest number of clones/reads were dinoflagellates, stramenopiles and haptophytes. The species composition was significantly different at the northernmost station compared to further south, suggesting that nano- and picoeukaryote species composition and distribution may serve as indicators of climate change in polar waters.

• Egge, Elianne Sirnæs; Moe, S. Jannicke; Ropstad, Erik; Andersen, Tom & Stenseth, Nils Christian (2010). Combined effects of POPs and density dependence: A size-structured population model for laboratory zebrafish. Full text in Research Archive
• Egge, Elianne Sirnæs; Moe, S. Jannicke; Andersen, Tom; Stenseth, Nils Christian & Ropstad, Erik (2008). POPs exposure and population density stress in a 3-generations experiment: Zebrafish populations as a model system. Full text in Research Archive
• Engesmo, Anette; Egge, Elianne; Saesin, Pipatthra; Norli, Marit; Harvey, E. Therese & Gitmark, Janne Kim [Show all 11 contributors for this article] (2026). Miljøovervåkning i Ytre Oslofjord - Årsrapport 2025. Norsk institutt for vannforskning (NIVA). ISSN 9788257779443. Full text in Research Archive Show summary

  Rapporten oppsummerer miljøovervåkningen gjort i 2025 i Ytre Oslofjord på vegne av fagrådet for Ytre Oslofjord. Det er gjennomført vannmasseundersøkelser ved 15 stasjoner; hvorav en stasjon fikk dårlig, sju moderat og sju stasjoner god tilstandsklasse. Ålegras en inkludert i programmet for første gang, fem enger ble undersøkt hvorav to fikk moderat og tre fikk god tilstandsklasse. Ingen av stasjonene fikk svært god. Videre er det gjennomført tilførselsberegninger for 2024: Jordbruket var den største enkeltkilden til både fosfor- og nitrogentilførsel, med hhv. 50 og 41%. Naturlig avrenning fra utmarksområder var den nest største kilden (hhv. 17 og 34%), mens kommunalt avløp var den tredje største kilden med hhv. 14 og 19 % av fosfor- og nitrogentilførselene dette året.

• Engesmo, Anette; Lerch, Sara Joanne; Gran-Stadniczeñko, Sandra; Kistenich, Sonja; Egge, Elianne Dunthorn & Naustvoll, Lars Johan [Show all 7 contributors for this article] (2026). Assessment of the national Norwegian classification of nutrients and chlorophyll in coastal waters. Norsk institutt for vannforskning (NIVA). ISSN 9788257779009. Full text in Research Archive Show summary

  All available environmental monitoring data from water masses along the Norwegian coast were compiled to a comprehensive dataset. This was used to recommend new reference values and class limits for chlorophyll-a, and new class limits for nutrients for classification of ecological status according to the Water Framework Directive.

• Sildever, Sirje; Edvardsen, Bente; Egge, Elianne Dunthorn; Engesmo, Anette; Harðardóttir, Sara & Jacobsen, Ása [Show all 25 contributors for this article] (2025). Reliable environmental DNA detection of planktonic biodiversity: Minimum sample volume for DNA metabarcoding. Nordic Council of Ministers. ISSN 9789289381468. doi: 10.6027/temanord2025-509. Full text in Research Archive Show summary

  Environmental DNA (eDNA)-based detection has become an attractive method for determining biodiversity as it can provide more detailed information compared to traditional morphology-based approaches. This is especially relevant for targeting overall biodiversity or screening for the presence of harmful algal bloom (HAB) species. However, despite the availability of several general guidelines, the workflow for marine environments has yet to be standardised. This lack of standardisation complicates the comparison between samples across different monitoring programmes and projects. This project focused on the first step of the workflow – determining and standardising the minimum reliable sample volume needed to detect phytoplankton diversity under various environmental and biological conditions. A study and a workshop were conducted to test different sample volumes (1000 mL, 500 mL, 200 mL, and 20 mL), using samples collected from the Baltic and North Seas and northwestern Atlantic Ocean under various environmental conditions. Across the studied samples, 200 mL was identified as a sufficient sample volume to detect various species across the different volumes tested. This result represents an important first step towards standardising the eDNA-based approach and incorporating it into routine monitoring. Furthermore, the results of this project are expected to contribute to reducing the time and resources required for monitoring.

• Ekrem, Torbjørn; Majaneva, Markus; Stur, Elisabeth; Falahati-Anbaran, Mohsen; Christensen, Guttorm & Schartau, Ann Kristin [Show all 9 contributors for this article] (2025). Overvåkning av fjærmygg i innsjøer med bruk av miljø-DNA. NTNU Vitenskapsmuseet. ISSN 9788283224238. doi: https:/www.ntnu.no/documents/10476/1365939152/Notat+2025-6+Sluttrapport+bruk+av+eDNA+.pdf/032a6c84-0354-0ef6-4dbd-cbdff7c8c391?t=1750254772629. Full text in Research Archive Show summary

  DNA-metastrekkoding av filtrerte vannprøver gjør det mulig å påvise arter i et miljø uten å samle inn selve organismene. Metoden har vist seg lovende for identifisering av bunndyr i rennende vann, men det finnes få studier som vurderer hvor godt den egner seg til å påvise denne artsgruppen i lotiske miljøer. Fjærmygg (Diptera: Chironomidae) er blant de mest artsrike insektgruppene i ferskvann, men har vært lite brukt i norsk miljøovervåkning. Dette skyldes i stor grad at morfologisk artsidentifisering er tidkrevende og krevende. Med et godt utbygd referansebibliotek for norske fjærmyggarter basert på DNA-strekkoder, åpner metastrekkoding for effektiv og nøyaktig identifisering, noe som kan gjøre fjærmygg til en realistisk indikatorgruppe i fremtidig overvåkning – særlig i innsjøer med lav bunndyrdiversitet. I dette studiet undersøkte vi om metastrekkoding av filtrerte vannprøver kunne påvise fjærmyggarter i Selbusjøen (Trøndelag) samt i Diesetvassdraget og Linnévassdraget på Spitsbergen, og hvor robust denne påvisningen er mellom biologiske replikater. I Selbusjøen ble det påvist DNA fra over 200 arter, men mange arter ble kun registrert i én av tre replikater, noe som indikerer lav robusthet. Det var også liten overlapp mellom artssammensetning i vannprøver og det som ble registrert med tradisjonelle metoder som sparkeprøver og sedimentprøver. Som forventet ble det påvist mange terrestriske og lotiske arter nær bekke- og elveutløp. Resultatene viser at metastrekkoding har potensial for bruk av fjærmygg i biomonitorering, men at det er behov for videre undersøkelser for å avklare om filtrert vann eller sedimentprøver best egner seg til å påvise stedegne arter, og hvor mange replikater som kreves for en pålitelig deteksjon. I tillegg bør eksperimentell prøvetaking gjennomføres for å forstå hvordan miljø-DNA fra fjærmygg distribueres både horisontalt og vertikalt i innsjøsystemer.

• Egge, Elianne Dunthorn; Bekkby, Trine; Borgersen, Gunhild; Brkljacic, Marijana Stenrud; Eikrem, Wenche & Fagerli, Camilla With [Show all 11 contributors for this article] (2025). ØKOKYST – DP Norskehavet Sør, Årsrapport 2024. Norsk institutt for vannforskning (NIVA). ISSN 9788257778569. Full text in Research Archive Show summary

  Overvåkingsprogrammet "Økosystemovervåking i Kystvann – Økokyst" overvåker miljøtilstanden langs norskekysten i henhold til vannforskriften. Økokyst delprogram Norskehavet Sør dekker kyststrekningen fra Ulsteinvik i sør til Helgeland i nord. I 2024 ble det gjort undersøkelser av de biologiske kvalitetselementene hardbunn, ålegress, bløtbunn og planteplankton. I alt ble 12 vannforekomster undersøkt. Makroalger, bløtbunnsfauna og planteplankton hadde “god” eller “svært god” tilstand, mens ålegress hadde «moderat» ved begge stasjonene i 2024, noe som er en nedgang fra «god» i 2023. Fysisk-kjemiske støtteparametere hadde “god” eller “svært god” tilstand, med unntak av oksygen i bunnvannet ved Skinnbrokleia, og TOC i sediment ved Skinnbrokleia og Korsen, som alle fikk «moderat» tilstand. The monitoring program "Ecosystem Monitoring in Coastal Water - Økokyst" monitors the environmental status along the Norwegian coast according to the Water Framework Directive. The subprogram Norskehavet Sør covers the coastal area along the Norwegian Sea, from Ulsteinvik in the South to Helgeland in the North. In 2024, the biological quality elements macroalgae, eel grass, soft bottom and phytoplankton were examined. In all, 12 water bodies were examined. The biological quality elements obtained “good” or “very good” status, except eelgrass which obtained “moderate”. The physico-chemical parameters were classified as “good” or “very good”, except for the oxygen conditions in the deep water at Skinnbrokleia, and TOC contents in the sediments at Skinnbrokleia and Korsen, which all obtained “moderate” status.

• Borgersen, Gunhild; Bekkby, Trine; Brkljacic, Marijana Stenrud; Egge, Elianne Dunthorn; Eikrem, Wenche & Fagerli, Camilla With [Show all 12 contributors for this article] (2025). Økokyst - DP Nordsjøen, Årsrapport 2024. Norsk institutt for vannforskning (NIVA). ISSN 9788257778484. Full text in Research Archive Show summary

  Overvåkingsprogrammet "Økosystemovervåking i Kystvann – Økokyst" har til hensikt å overvåke miljøtilstanden langs norskekysten i henhold til vannforskriften. Økokyst Nordsjøen dekker kyststrekningen fra Lista til Sognefjorden. Alle biologiske kvalitetselementer fikk «god» eller «svært god» økologisk tilstand på alle stasjoner i 2024 med unntak av én ålegresstasjon i Gulafjorden. I Hardangerfjorden og i Rogalandsfjordene var det lavt innhold av oksygen i bunnvannet, tilsvarende «moderat» eller dårligere tilstand. The monitoring program "Ecosystem Monitoring in Coastal Water - Økokyst" aims to monitor the environmental status along the Norwegian coast according to the Water Framework Directive. Økokyst Nordsjøen includes the coastline from Lista to Sognefjorden. All biological quality elements were in "good" or "very good" ecological status at all stations in 2024, except for one eelgrass-station in Gulafjorden. In Hardangerfjorden and the Rogaland fjords, there was low oxygen content in the bottom waters, corresponding to "moderate" or poorer status.

• Engesmo, Anette; Egge, Elianne Dunthorn; Norli, Marit; Borgersen, Gunhild; Beylich, Bjørnar & Gitmark, Janne Kim [Show all 9 contributors for this article] (2025). Eutrofiovervåkning i Ytre Oslofjord – Samlerapport 2019-2024. Norsk institutt for vannforskning (NIVA). ISSN 9788257778507. Full text in Research Archive Show summary

  Samlerapport som oppsummerer resultater fra overvåkningsprogrammet i Ytre Oslofjord i 2024, samt sammenstiller disse med tidligere resultater fra programmet, og andre relevante undersøkelser i Oslofjorden. Det gjøres årlige tilførselsberegninger og vannmasseundersøkelser, samt jevnlige undersøkelser av hard- og bløtbunn. Modellerte tilførsler av fosfor og nitrogen fra ulike kilder viser at jordbruket var den største enkeltkilden for både fosfor (55 %) - og nitrogenforbindelser (41 %). Kommunalt avløp bidro med hhv. 14 % av fosfat og 18 % av nitrogentilførslene. Vannmasseundersøkelsene ved 18 stasjoner gir åtte stasjoner god og ti moderat tilstand for den siste tre-årsperioden (2022-2024). Det rettes særlig bekymring rundt utviklingen i Mossesundet, Bolærne og Sandefjordsfjorden. Hardbunnsundersøkelsene av nedre voksegrense plasserer de fleste stasjoner i god eller moderat tilstand, og viser ingen tydelige trender. Men en sammenstilling av hardbunn- og vannmasseresultater viser at nedre voksegrense er negativt korrelert med siktdyp og konsentrasjonen nitrat+nitritt i overflatelaget om sommeren. Bløtbunnsundersøkelsene viser at de fleste stasjoner havner i god tilstand, unntakene er Drammensfjorden og Tønsbergfjorden, hvor det observeres en generell reduksjon i artsdiversitet og økologisk tilstand med økende innhold av organisk karbon i sedimentet, og med økende grad av oksygensvinn i bunnvannet.

• Egge, Elianne Dunthorn; Bekkby, Trine; Borgersen, Gunhild; Eikrem, Wenche; Fagerli, Camilla With & Gitmark, Janne Kim [Show all 11 contributors for this article] (2024). ØKOKYST – DP Norskehavet Sør, Årsrapport 2023. Norsk institutt for vannforskning (NIVA). ISSN 9788257777258. Full text in Research Archive Show summary

  Overvåkingsprogrammet "Økosystemovervåking i Kystvann – Økokyst" har til hensikt å overvåke miljøtilstanden langs norskekysten i henhold til vannforskriften. Økokyst delprogram Norskehavet Sør dekker kyststrekningen fra Ulsteinvik i sør til Helgeland i nord. I 2023 ble det gjort undersøkelser av de biologiske kvalitetselementene hardbunn, ålegress, bløtbunn og planteplankton. Av de 16 vannforekomstene som kunne klassifiseres fikk fem “svært god” og 11 “god” samlet tilstand. De biologiske kvalitetselementene hadde alle “god” eller “svært god” tilstand. Fysisk-kjemiske parameter hadde også “god” eller “svært god” tilstand, med unntak av oksygen i bunnvannet ved Skinnbrokleia utenfor Ulsteinvik. The monitoring program "Ecosystem Monitoring in Coastal Water - Økokyst" monitors the environmental status along the Norwegian coast according to the Water Framework Directive. The subprogram Norskehavet Sør covers the coastal area along the Norwegian Sea, from Ulsteinvik in the South to Helgeland in the North. In 2023, the biological quality elements macroalgae, eel grass, soft bottom and phytoplankton were examined. Out of the 16 water bodies which could be classified, five obtained “very good” and 11 “good” status. The biological quality elements all had “good” or “very good” status. The physico-chemical parameters also classified as “good” or “very good”, except for the oxygen conditions in the deep water at Skinnbrokleia outside Ulsteinvik.

• Egge, Elianne; Deininger, Anne; Bekkby, Trine; Eikrem, Wenche; Mengeot, Caroline & Frigstad, Helene [Show all 12 contributors for this article] (2023). ØKOKYST – DP Norskehavet Sør, Årsrapport 2022. Norsk institutt for vannforskning (NIVA). ISSN 9788257776343. Full text in Research Archive Show summary

  Overvåkingsprogrammet "Økosystemovervåking i Kystvann – Økokyst" har til hensikt å overvåke miljøtilstanden langs norskekysten i henhold til vannforskriften. Økokyst delprogram Norskehavet Sør dekker kyststrekningen fra Ulsteinvik i sør til Helgeland i nord. Av de ni vannforekomstene som kunne klassifiseres i 2022 fikk én samlet «svært god» tilstand, sju «god» tilstand, mens én fikk «moderat» tilstand, der oksygenverdier i bunnvann trakk ned. De to ålegress-stasjonene var lokalisert i samme vannforekomst og fikk begge “god” tilstand. I tillegg til parameterne brukt til klassifisering ble klimaparameterne dyreplankton, lys og organisk materiale overvåket ved én stasjon i vannforekomst Steinsfjorden nær Ulsteinvik.

• Ekrem, Torbjørn; Baussant, Thierry; Dunshea, Glenn John; Dunthorn, Micah; Egge, Elianne Dunthorn & Engesmo, Anette [Show all 15 contributors for this article] (2023). The use of eDNA and DNA based methods to assess and monitor alien and doorknocker species. Norwegian Environment Agency. Full text in Research Archive Show summary

  All organisms leave traces of their DNA in the environment they live in. This environmental DNA (eDNA) can be used to detect and monitor single species as well as communities, and potentially be utilized in early warning systems to detect alien species. In this report, we give an overview of eDNA-based methods used to detect and monitor alien species, and give examples of speciesspecific assays designed to identify species that are alien to Norwegian nature or have the potential to establish viable populations in Norway (doorknockers). We emphasize the need for several stages of testing before species-specific assays can be operational, and discuss the importance of including models to assess detection probabilities. Going through standards for sampling and analyses, we suggest a number of minimum requirements for eDNA sampling, laboratory practice, bioinformatics and the use of reference libraries, as well as for reporting results from eDNA studies. The origin and fate of eDNA in different environments can influence its usefulness in detecting and monitoring alien species. We outline factors for terrestrial, freshwater and marine ecosystems and provide examples from six case studies where eDNA has been used to detect and/or monitor alien invasive species: invertebrates and vascular plants in soil of imported ornamental plants, freshwater crayfish and crayfish plague, Gyrodactylus salaris, pink salmon, Canadian pondweed, and American lobster. We provide a decision diagram for detection and monitoring of invasive species starting with early considerations for implementation of a monitoring program, and ending with management decision points depending on detection outcomes at different stages. Finally, we provide some key recommendations for the use of eDNA in assessments of alien and doorknocker species.

• Engesmo, Anette; Egge, Elianne Dunthorn; Knudsen, Steen Wilhelm; Christensen, Guttorm; Hesselsøe, Martin & d'Auriac, Marc Anglès (2022). Overvåking og kartlegging av fremmed ferskvannsfisk ved bruk av miljø-DNA 2021. Norsk institutt for vannforskning (NIVA). ISSN 9788257774684. Full text in Research Archive Show summary

  Det ble samlet miljø-DNA prøver fra Akersvannet og Virikbekken som ble analysert for gjedde og ørret. Resultatene viste et forutsigbart mønster i Virikbekken, med størst konsentrasjon av gjedde DNA øverst og størst konsentrasjon av ørret DNA nederst mot fjorden. Grense Jakobselv, samt tre lokasjoner på Svalbard ble prøvetatt for å analysere for pukkellaks og sameksisterende anadrome laksefisk (ørret, atlantisk laks og røye). Analysene ble utført med tre prøvetakningsreplikater og seks tekniske replikater for å gi statistisk relevans for å analysere resultatene kvantitativt. Videre ble det utviklet nye deteksjonssystemer for ørekyt (tentativt validert til nivå 4) og sørv (validert til nivå 3).

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