Anders Kristian Krabberød

• Hornslien, Karina Stensland; Myking, Ida Velle; Bjerkan, Katrine Nergård; Krabberød, Anders Kristian; Miller, Jason Rafe & Grini, Paul (2026). Parent-of-origin specific allelic expression in outbreeding Arabidopsis arenosa identifies antagonistic parental enrichment in protein degradation pathways. New Phytologist. ISSN 0028-646X. doi: 10.1111/nph.71551. Full text in Research Archive
• Baalsrud, Helle Tessand; Garmann-Aarhus, Benedicte; Enevoldsen, Emily Louise Gilbert; Krabberød, Anders Kristian; Dominik, Fischer, & Tooming-Klunderud, Ave [Show all 13 contributors for this article] (2026). Centromeric satellite expansion drives genome evolution in the snowy owl. Genome Biology. ISSN 1474-7596. doi: 10.1186/s13059-026-04175-y. Full text in Research Archive Show summary

  Comparative genomic studies in birds have revealed that bird genomes are relatively repeat-poor and stable in terms of karyotype, size, and gene synteny/collinearity compared to other vertebrates. One notable exception is the owls, with cytogenetic studies demonstrating large variations in karyotypes and the evolution of unusual centromeric satellite repeats in some species. However, there has so far not been an investigation into genome architecture and repeat landscape of owls. Here, we present a chromosome-level genome assembly for the snowy owl (Bubo scandiacus). We find that the repeat DNA content in the relatively large snowy owl genome (1.6 Gb) is among the highest reported for any bird genome to date (28.34% compared to an average of ~ 10% in other birds). The bulk of the snowy owl genomic repeat landscape consists of extensive centromeric satellite arrays that form large contiguous blocks across multiple chromosomes. These arrays represent one of the largest centromeric satellite expansions reported in birds and are consistent with rapid turnover and amplification of centromeric repeats. Using gene collinearity analyses we show that the position of the centromeres are not homologous with chicken centromeres, and are located in regions with collinearity breaks to other bird genomes due to chromosomal rearrangements. Our results support rapid satellite turnover at lineage-specific centromeres, which could have played a role in centromeric drive, reproductive isolation and speciation of the snowy owl. The extensive centromeric satellite arrays uncovered in this genome highlight centromere evolution as a potentially important driver of genome evolution in owls.

• Guslund, Naomi Croft; Jonsson, Alexandra; Krabberød, Anders Kristian; Porras, Adrian Lopez; Nørstebø, Simen Foyn & Sørum, Henning [Show all 9 contributors for this article] (2026). IgM-mediated protection drives early B-cell activation and mucosal containment of Vibrio anguillarum in Atlantic cod (Gadus morhua). Frontiers in Immunology. 17. doi: 10.3389/fimmu.2026.1771403. Full text in Research Archive Show summary

  Background: Atlantic cod lack functional MHC class II and CD4, raising fundamental questions about how vaccination generates protection in this species. Methods: We combined single-cell transcriptomic profiling of splenic cells with qRT-PCR across complementary active vaccination and passive serum-transfer experiments to define cellular and transcriptional correlates of immunity to Vibrio anguillarum. Results: Bath-vaccinated fish and recipients of immune serum showed effective containment of infection, with bacterial signals largely restricted to gills and minimal detection in spleen or head kidney, whereas naïve fish frequently developed high systemic bacterial loads by day 3 post-infection. All groups exhibited increased splenic macrophage abundance following challenge, but only naïve fish showed strong and sustained inflammatory activation, consistent with their higher pathogen burden. Vaccinated fish and immune-serum recipients displayed only transient or weak myeloid responses despite similar early neutrophil activation. Across both experimental models, a transcriptionally distinct B-cell subset expanded at the peak of infection. This population showed increased immunoglobulin and MHC class I expression together with innate sensing features, consistent with an activated B-cell state. Although this B-cell subset increased in all groups, the largest expansions were observed in vaccinated fish and immune-serum recipients. Overall, these findings are consistent with antigen-specific IgM enhancing early B-cell activation and contributing to protection against V. anguillarum through coordinated humoral and innate-like B-cell responses. Discussion: These findings identify an antibody-driven mode of immune coordination that operates independently of classical CD4+ T-cell help and provide insight into how effective vaccination can be achieved in vertebrates with divergent adaptive immune architectures.

• Fonseca, Jose Mauricio Salamanca; Sanchez, Adriana; Corrales, Adriana; Kauserud, Håvard; Thoen, Ella & Krabberød, Anders K. [Show all 7 contributors for this article] (2025). Beyond seasonal and host factors: ecosystem dynamics drive palm-associated root fungal communities at a local scale. Plant and Soil. ISSN 0032-079X. 514, p. 1027–1041. doi: 10.1007/s11104-025-07438-y. Full text in Research Archive Show summary

  Background and Aims The increase of extreme weather events due to climate change may alter ecosystem dynamics. In the tropics, little is known about how ecosystems and species will respond to droughts or floods. Identifying the most important biotic and abiotic factors in ecosystems at the local level is key to developing better forest management practices and understanding the effects of climate change on the fungal community. Methods We conducted a random sampling of adult individuals from several palm species across three adjacent ecosystems with different hydrological conditions, during rainy and dry seasons. Using next-generation sequencing, we identified fungal communities and determined the influence of soil physicochemical properties, as well as host and seasonal variables, on the relative abundance of the root- and rhizosphere-associated fungal communities. Results The composition of the fungal communities was similar between the seasonally flooded forest and the terra-firme forest, while the palm swamp diverged due to differences in soil physicochemical properties. Seasonal analyses revealed significant differences in the relative abundance of several taxa, mainly associated with the seasonally flooded forest. However, no influence of palm species on fungal abundance was detected at any taxonomic level. Conclusion This study highlights the importance of studying ecosystems at the local scale and considering ecosystem dynamics into the study of fungal communities and other microorganisms. Such an approach is crucial for improving predictions under climate change scenarios and understanding the consequences of altering these dynamics in vulnerable, often understudied ecosystems.

• Thoen, Ella; Krabberød, Anders K.; Nogerius, Veera Tuovinen; Skrede, Inger; Rosling, Anna & Kauserud, Håvard (2025). Short‐ and long‐read metabarcoding of Archaeorhizomycetes reveals high phylogenetic diversity structured by vegetation and climate. New Phytologist. ISSN 0028-646X. 249 (2026)(1), p. 418–432. doi: 10.1111/nph.70682. Full text in Research Archive Show summary

  Summary Archaeorhizomycetes is a class of globally widespread soil‐dwelling fungi, originally proposed to be associated with plant roots, but their ecology and nutritional mode are not clearly defined. To increase the knowledge about Archaeorhizomycetes' ecology and biogeography, we investigate how they are distributed along major environmental gradients, as well as different soil compartments. To assess their abundance and diversity, we use both short‐ and long‐read metabarcoding with class‐specific primers for the long reads. The short‐read sequences revealed that Archaeorhizomycetes is proportionally abundant and a dominant fungal class in alpine vegetation types, as well as boreal spruce and pine forests. The long‐read sequences revealed high phylogenetic diversity of Archaeorhizomycetes, with 120 OTUs grouping into 13 clades with potentially differing ecologies and biogeographic distributions. Vegetation types and climate primarily structure the Archaeorhizomycetes community, while community composition was similar in litter, soil, and roots. However, Archaeorhizomycetes were significantly more abundant in soil and plant roots than litter, supporting the idea that Archaeorhizomycetes depend on the presence of plant roots. Our study illustrates that targeted group‐specific amplification coupled with long‐read sequencing is a powerful approach for exploring the diversity and ecology of specific fungal groups.

• Tørresen, Ole Kristian; Garmann-Aarhus, Benedicte; Hoff, Siv Nam Khang; Jentoft, Sissel; Svensson, Mikael & Schartum, Eivind Sandvik [Show all 11 contributors for this article] (2025). Comparison of whole-genome assemblies of European river lamprey (Lampetra fluviatilis) and brook lamprey (Lampetra planeri). Journal of Heredity. ISSN 0022-1503. 117, p. 96–106. doi: 10.1093/jhered/esaf036. Full text in Research Archive
• Landor, Lotta Anni Ingeborg; Tjendra, Jesslyn; Erstad, Karen; Krabberød, Anders Kristian; Töpper, Joachim Paul & Våge, Selina (2024). At what cost? The impact of bacteriophage resistance on the growth kinetics and protein synthesis of Escherichia coli. Environmental Microbiology Reports. 16(6). doi: 10.1111/1758-2229.70046. Full text in Research Archive Show summary

  Cost of bacteriophage resistance (COR) is important in explaining processes of diversification and coexistence in microbial communities. COR can be expressed in different traits, and the lack of universally applicable methods to measure fitness trade-offs makes COR challenging to study. Due to its fundamental role in growth, we explored protein synthesis as a target for quantifying COR. In this study, the growth kinetics of three genome-sequenced strains of phage-resistant Escherichia coli, along with the phage-susceptible wild-type, were characterized over a range of glucose concentrations. Bioorthogonal non-canonical amino acid tagging (BONCAT) was used to track differences in protein synthetic activity between the wild-type and phage-resistant E. coli. Two of the resistant strains, with different levels of phage susceptibility, showed mucoid phenotypes corresponding with mutations in genes associated with the Rcs phosphorelay. These mucoid isolates, however, had reduced growth rates and potentially lower protein synthetic activity. Another resistant isolate with a different mutational profile maintained the same growth rate as the wild-type and showed increased BONCAT fluorescence, but its yield was lower. Together, these findings present different patterns of trade-offs resulting from the phage-induced mutations and demonstrate the potential applicability of BONCAT as a tool for measuring COR.

• Baalsrud, Helle Tessand; Garmann-Aarhus, Benedicte; Enevoldsen, Emily Louise Gilbert; Krabberød, Anders Kristian; Fischer, Dominik & Tooming-Klunderud, Ave [Show all 13 contributors for this article] (2024). Evolutionary new centromeres in the snowy owl genome putatively seeded from a transposable element. BioRxiv. ISSN 0362-4331. doi: 10.1101/2024.07.05.602039. Full text in Research Archive
• Reinar, William Brynildsen; Krabberød, Anders Kristian; Lalun, Vilde Olsson; Butenko, Melinka Alonso & Jakobsen, Kjetill Sigurd (2024). Short tandem repeats delineate gene bodies across eukaryotes. Nature Communications. 15(1), p. 1–13. doi: 10.1038/s41467-024-55276-w. Full text in Research Archive Show summary

  Short tandem repeats (STRs) have emerged as important and hypermutable sites where genetic variation correlates with gene expression in plant and animal systems. Recently, it has been shown that a broad range of transcription factors (TFs) are affected by STRs near or in the DNA target binding site. Despite this, the distribution of STR motif repetitiveness in eukaryote genomes is still largely unknown. Here, we identify monomer and dimer STR motif repetitiveness in 5.1 billion 10-bp windows upstream of translation starts and downstream of translation stops in 25 million genes spanning 1270 species across the eukaryotic Tree of Life. We report that all surveyed genomes have gene-proximal shifts in motif repetitiveness. Within genomes, variation in gene-proximal repetitiveness landscapes correlated to the function of genes; genes with housekeeping functions were depleted in upstream and downstream repetitiveness. Furthermore, the repetitiveness landscapes correlated with TF binding sites, indicating that gene function has evolved in conjunction with cis-regulatory STRs and TFs that recognize repetitive sites. These results suggest that the hypermutability inherent to STRs is canalized along the genome sequence and contributes to regulatory and eco-evolutionary dynamics in all eukaryotes.

• Krabberød, Anders Kristian; Stokke, Embla Elen; Thoen, Ella; Skrede, Inger & Kauserud, Håvard (2024). The Ribosomal Operon Database: A Full-Length rDNA Operon Database Derived From Genome Assemblies. Molecular Ecology Resources. ISSN 1755-098X. doi: 10.1111/1755-0998.14031. Full text in Research Archive Show summary

  Current rDNA reference sequence databases are tailored towards shorter DNA markers, such as parts of the 16/18S marker or the internally transcribed spacer (ITS) region. However, due to advances in long-read DNA sequencing technologies, longer stretches of the rDNA operon are increasingly used in environmental sequencing studies to increase the phylogenetic resolution. There is, therefore, a growing need for longer rDNA reference sequences. Here, we present the ribosomal operon database (ROD), which includes eukaryotic full-length rDNA operons fished from publicly available genome assemblies. Full-length operons were detected in 34.1% of the 34,701 examined eukaryotic genome assemblies from NCBI. In most cases (53.1%), more than one operon variant was detected, which can be due to intragenomic operon copy variability, allelic variation in non-haploid genomes, or technical errors from the sequencing and assembly process. The highest copy number found was 5947 in Zea mays. In total, 453,697 unique operons were detected, with 69,480 operon variant clusters remaining after intragenomic clustering at 99% sequence identity. The operon length varied extensively across eukaryotes, ranging from 4136 to 16,463 bp, which will lead to considerable polymerase chain reaction (PCR) bias during amplification of the entire operon. Clustering the full-length operons revealed that the different parts (i.e., 18S, 28S, and the hypervariable regions V4 and V9 of 18S) provide divergent taxonomic resolution, with 18S, the V4 and V9 regions being the most conserved. The ROD will be updated regularly to provide an increasing number of full-length rDNA operons to the scientific community.

• Ikenoue, Takahito; Bjørklund, Kjell Rasmus; Krabberød, Anders Kristian; Nishino, Shigeto & Wassmann, Paul (2023). Radiolaria and Phaeodaria (siliceous Rhizaria) in south-western and northern Norwegian fjords during late summer 2016: dominant species and biomass in shallow-water assemblages. Polar Research. ISSN 0800-0395. 42. doi: 10.33265/polar.v42.9584. Full text in Research Archive Show summary

  To determine the present-day community composition of siliceous Rhizaria (Radiolaria and Phaeodaria) in Norwegian fjords, plankton tows were conducted in south-western and northern Norwegian fjords in September 2016. The mean total abundance of radiolarians was 306 m^–3 in the Sognefjord complex, which was the southern research site, and, in the north, 945 m^–3 in Malangen and 89 m^–3 in Balsfjord, both above the Arctic Circle. Sticholonche zanclea was the most abundant radiolarian in the Sognefjord complex and Malangen, accounting for 78–100% (mean 89%) of radiolarian abundance. The mean total abundance of phaeodarians was 1554 m^–3 in the Sognefjord complex, 51 m^–3 in Malangen and 11 m^–3 in Balsfjord. Medusetta arcifera was the most abundant phaeodaria in the Sognefjord complex, accounting for >99% of phaeodarian abundance, but was absent in Malangen and Balsfjord, where Protocystis tridens accounted for >96% of phaeodarian abundance. The carbon biomass of S. zanclea and M. arcifera was 188 and 438 µg C m^–3, respectively, which is similar to and 8.6 times higher than, respectively, that of phaeodarians >1 mm in the western North Pacific, suggesting that M. arcifera contributes to organic carbon transport in the Sognefjord complex. Amphimelissa setosa (Nassellaria, Radiolaria), which was a dominant species in the study area in 1982–83, was absent in the present study in all sampled fjords. This could have been caused by the approximately 2 °C increase in water temperature that has occurred since 1990 and can be taken as evidence of a climate-change-associated local temperature rise linked to the warming of advected Atlantic Water.

• Bramsiepe, Jonathan; Krabberød, Anders Kristian; Bjerkan, Katrine Nergård; Alling, Renate; Nielsen, Ida & Hornslien, Karina Stensland [Show all 9 contributors for this article] (2023). Structural evidence for MADS-box type I family expansion seen in new assemblies of Arabidopsis arenosa and A. lyrata. The Plant Journal. ISSN 0960-7412. 116(3), p. 942–961. doi: 10.1111/tpj.16401. Full text in Research Archive Show summary

  SUMMARY Arabidopsis thaliana diverged from A. arenosa and A. lyrata at least 6 million years ago. The three species differ by genome‐wide polymorphisms and morphological traits. The species are to a high degree reproductively isolated, but hybridization barriers are incomplete. A special type of hybridization barrier is based on the triploid endosperm of the seed, where embryo lethality is caused by endosperm failure to support the developing embryo. The MADS‐box type I family of transcription factors is specifically expressed in the endosperm and has been proposed to play a role in endosperm‐based hybridization barriers. The gene family is well known for its high evolutionary duplication rate, as well as being regulated by genomic imprinting. Here we address MADS‐box type I gene family evolution and the role of type I genes in the context of hybridization. Using two de‐novo assembled and annotated chromosome‐level genomes of A. arenosa and A. lyrata ssp. petraea we analyzed the MADS‐box type I gene family in Arabidopsis to predict orthologs, copy number, and structural genomic variation related to the type I loci. Our findings were compared to gene expression profiles sampled before and after the transition to endosperm cellularization in order to investigate the involvement of MADS‐box type I loci in endosperm‐based hybridization barriers. We observed substantial differences in type‐I expression in the endosperm of A. arenosa and A. lyrata ssp. petraea , suggesting a genetic cause for the endosperm‐based hybridization barrier between A. arenosa and A. lyrata ssp. petraea .

• Bjorbækmo, Marit Frederikke Markussen; Brodie, Juliet; Krabberød, Anders Kristian; Logares, Ramiro; Fuss, Janina & Fredriksen, Stein [Show all 9 contributors for this article] (2023). 18S rDNA gene metabarcoding of microeukaryotes and epi-endophytes in the holobiome of seven species of large brown algae. Journal of Phycology. ISSN 0022-3646. 59(5), p. 859–878. doi: 10.1111/jpy.13377. Full text in Research Archive Show summary

  Brown algae (Phaeophyceae) are habitat-forming species in coastal ecosystems and include kelp forests and seaweed beds that support a wide diversity of marine life. Host-associated microbial communities are an integral part of phaeophyte biology, and whereas the bacterial microbial partners have received considerable attention, the microbial eukaryotes associated with brown algae have hardly been studied. Here, we used broadly targeted “pan-eukaryotic” primers (metabarcoding) to investigate brown algal-associated eukaryotes (the eukaryome). Using this approach, we aimed to investigate the eukaryome of seven large brown algae that are important and common species in coastal ecosystems. We also aimed to assess whether these macroalgae harbor novel eukaryotic diversity and to ascribe putative functional roles to the host-associated eukaryome based on taxonomic affiliation and phylogenetic placement. We detected a significant diversity of microeukaryotic and algal lineages associated with the brown algal species investigated. The operational taxonomic units (OTUs) were taxonomically assigned to 10 of the eukaryotic major supergroups, including taxonomic groups known to be associated with seaweeds as epibionts, endobionts, parasites, and commensals. Additionally, we revealed previously unrecorded sequence types, including novel phaeophyte OTUs, particularly in the Fucus spp. samples, that may represent fucoid genomic variants, sequencing artifacts, or undescribed epi-/endophytes. Our results provide baseline data and technical insights that will be useful for more comprehensive seaweed eukaryome studies investigating the evidently lineage-rich and functionally diverse symbionts of brown algae.

• Kersten, Oliver Sven; Star, Bastiaan; Krabberød, Anders Kristian; Atmore, Lane; Tørresen, Ole K. & Anker-Nilssen, Tycho [Show all 12 contributors for this article] (2023). Hybridization of Atlantic puffins in the Arctic coincides with 20th-century climate change. Science Advances. 9(40). doi: 10.1126/sciadv.adh1407. Full text in Research Archive Show summary

  The Arctic is experiencing the fastest rates of global warming,leading to shifts in the distribution of its biota and increasing the potential for hybridization. However, genomic evidenc eof recent hybridization events in the Arctic remains unexpectedly rare. Here, we use whole-genome sequencing of contemporary and 122-year-old historical specimens to investigate the origin of an Arctic hybrid population of Atlantic puffins(Fratercula arctica) on Bjørnøya, Norway. We show that the hybridization between the High Arctic, large-bodied subspecies F.a. naumanni and the temperate, smaller-sized subspecies F.a. arctica began as recently as six generations ago due to an unexpected southward range expansion of F.a. naumanni. Moreover, we find a significant temporal loss of genetic diversity across Arctic and temperate puffin populations.Our observations provide compelling genomic evidence of the impacts of recent distributional shifts and loss of diversity in Arctic communities during the 20th century.

• Deutschmann, Ina Maria; Krabberød, Anders Kristian; Latorre, Francisco; Delage, Erwan; Marrasé, Cèlia & Balagué, Vanessa [Show all 11 contributors for this article] (2023). Disentangling temporal associations in marine microbial networks. Microbiome. 11, p. 1–16. doi: 10.1186/s40168-023-01523-z. Full text in Research Archive Show summary

  Background Microbial interactions are fundamental for Earth’s ecosystem functioning and biogeochemical cycling. Nevertheless, they are challenging to identify and remain barely known. Omics-based censuses are helpful in predicting microbial interactions through the statistical inference of single (static) association networks. Yet, microbial interactions are dynamic and we have limited knowledge of how they change over time. Here, we investigate the dynamics of microbial associations in a 10-year marine time series in the Mediterranean Sea using an approach inferring a time-resolved (temporal) network from a single static network. Results A single static network including microbial eukaryotes and bacteria was built using metabarcoding data derived from 120 monthly samples. For the decade, we aimed to identify persistent, seasonal, and temporary microbial associations by determining a temporal network that captures the interactome of each individual sample. We found that the temporal network appears to follow an annual cycle, collapsing, and reassembling when transiting between colder and warmer waters. We observed higher association repeatability in colder than in warmer months. Only 16 associations could be validated using observations reported in literature, underlining our knowledge gap in marine microbial ecological interactions. Conclusions Our results indicate that marine microbial associations follow recurrent temporal dynamics in temperate zones, which need to be accounted for to better understand the functioning of the ocean microbiome. The constructed marine temporal network may serve as a resource for testing season-specific microbial interaction hypotheses. The applied approach can be transferred to microbiome studies in other ecosystems. Video Abstract

• Guslund, Naomi Croft; Krabberød, Anders Kristian; Nørstebø, Simen Foyn; Solbakken, Monica Hongrø; Jakobsen, Kjetill Sigurd & Johansen, Finn-Eirik [Show all 7 contributors for this article] (2022). Lymphocyte subsets in Atlantic cod (Gadus morhua) interrogated by single-cell sequencing. Communications Biology. 5:689(1), p. 1–9. doi: 10.1038/s42003-022-03645-w. Full text in Research Archive Show summary

  Abstract Atlantic Cod ( Gadus morhua ) has lost the major histocompatibility complex class II presentation pathway. We recently identified CD8-positive T cells, B cells, and plasma cells in cod, but further characterisation of lymphocyte subsets is needed to elucidate immune adaptations triggered by the absence of CD4-positive T lymphocytes. Here, we use single-cell RNA sequencing to examine the lymphocyte heterogeneity in Atlantic cod spleen. We describe five T cell subsets and eight B cell subsets and propose a B cell trajectory of differentiation. Notably, we identify a subpopulation of T cells that are CD8-negative. Most of the CD8-negative T lymphocytes highly express the homologue of monocyte chemotactic protein 1b , and another subset of CD8-negative T lymphocytes express the homologue of the scavenger receptor m130 . Uncovering the multiple lymphocyte cell sub-clusters reveals the different immune states present within the B and T cell populations, building a foundation for further work.

• Krabberød, Anders Kristian; Deutschmann, Ina Maria; Bjorbækmo, Marit Frederikke Markussen; Balagué, Vanessa; Giner, Caterina R. & Ferrera, Isabel [Show all 10 contributors for this article] (2022). Long-term patterns of an interconnected core marine microbiota. Environmental Microbiome. 17(1). doi: 10.1186/s40793-022-00417-1. Full text in Research Archive Show summary

  Background Ocean microbes constitute ~ 70% of the marine biomass, are responsible for ~ 50% of the Earth’s primary production and are crucial for global biogeochemical cycles. Marine microbiotas include core taxa that are usually key for ecosystem function. Despite their importance, core marine microbes are relatively unknown, which reflects the lack of consensus on how to identify them. So far, most core microbiotas have been defined based on species occurrence and abundance. Yet, species interactions are also important to identify core microbes, as communities include interacting species. Here, we investigate interconnected bacteria and small protists of the core pelagic microbiota populating a long-term marine-coastal observatory in the Mediterranean Sea over a decade. Results Core microbes were defined as those present in > 30% of the monthly samples over 10 years, with the strongest associations. The core microbiota included 259 Operational Taxonomic Units (OTUs) including 182 bacteria, 77 protists, and 1411 strong and mostly positive (~ 95%) associations. Core bacteria tended to be associated with other bacteria, while core protists tended to be associated with bacteria. The richness and abundance of core OTUs varied annually, decreasing in stratified warmers waters and increasing in colder mixed waters. Most core OTUs had a preference for one season, mostly winter, which featured subnetworks with the highest connectivity. Groups of highly associated taxa tended to include protists and bacteria with predominance in the same season, particularly winter. A group of 13 highly-connected hub-OTUs, with potentially important ecological roles dominated in winter and spring. Similarly, 18 connector OTUs with a low degree but high centrality were mostly associated with summer or autumn and may represent transitions between seasonal communities. Conclusions We found a relatively small and dynamic interconnected core microbiota in a model temperate marine-coastal site, with potential interactions being more deterministic in winter than in other seasons. These core microbes would be essential for the functioning of this ecosystem over the year. Other non-core taxa may also carry out important functions but would be redundant and non-essential. Our work contributes to the understanding of the dynamics and potential interactions of core microbes possibly sustaining ocean ecosystem function.

• Arandia-Gorostidi, Nestor; Krabberød, Anders Kristian; Logares, Ramiro; Deutschmann, Ina Maria; Scharek, Renate & Morán, Xosé Anxelu G. [Show all 8 contributors for this article] (2022). Novel Interactions Between Phytoplankton and Bacteria Shape Microbial Seasonal Dynamics in Coastal Ocean Waters. Frontiers in Marine Science. 9. doi: 10.3389/fmars.2022.901201. Full text in Research Archive Show summary

  Trophic interactions between marine phytoplankton and heterotrophic bacteria are at the base of the biogeochemical carbon cycling in the ocean. However, the specific interactions taking place between phytoplankton and bacterial taxa remain largely unexplored, particularly out of phytoplankton blooming events. Here, we applied network analysis to a 3.5-year time-series dataset to assess the specific associations between different phytoplankton and bacterial taxa along the seasonal scale, distinguishing between free-living and particle-attached bacteria. Using a newly developed network post-analysis technique we removed bacteria-phytoplankton correlations that were primarily driven by environmental parameters, to detect potential biotic interactions. Our results indicate that phytoplankton dynamics may be a strong driver of the inter-annual variability in bacterial community composition. We found the highest abundance of specific bacteria-phytoplankton associations in the particle-attached fraction, indicating a tighter bacteria-phytoplankton association than in the free-living fraction. In the particle-associated fraction we unveiled novel potential associations such as the one between Planctomycetes taxa and the diatom Leptocylindrus spp. Consistent correlations were also found between free-living bacterial taxa and different diatoms, including novel associations such as those between SAR11 with Naviculales diatom order, and between Actinobacteria and Cylindrotheca spp. We also confirmed previously known associations between Rhodobacteraceae and Thalassiosira spp. Our results expand our view on bacteria-phytoplankton associations, suggesting that taxa-specific interactions may largely impact the seasonal dynamics of heterotrophic bacterial communities.

• Gulbrandsen, Øyvind Sætren; Andresen, Ina Jungersen; Krabberød, Anders Kristian; Bråte, Jon & Shalchian-Tabrizi, Kamran (2021). Phylogenomic analysis restructures the Ulvophyceae. Journal of Phycology. ISSN 0022-3646. 57(4), p. 1223–1233. doi: 10.1111/jpy.13168. Full text in Research Archive Show summary

  Here, we present new transcriptome sequencing data from seven species of Dasycladales (Ulvophyceae) and a phylogenomic analysis of the Chlorophyta with a particular focus on Ulvophyceae. We have focused on a broad selection of green algal groups and carefully selected genes suitable for reconstructing deep eukaryote evolutionary histories. Increasing the taxon sampling of Dasycladales restructures the Ulvophyceae by identifying Dasycladales as closely related to Scotinosphaerales and Oltmannsiellopsidales. Contrary to previous studies, we do not find support for a close relationship between Dasycladales and a group with Cladophorales and Trentepohliales. Instead, the latter group is sister to the remainder of the Ulvophyceae. Furthermore, our analyses show high and consistent statistical support for a sister relationship between Bryopsidales and Chlorophyceae in trees generated with both homogeneous and heterogeneous (heterotachy) evolutionary models. Our study provides a new framework for interpreting the evolutionary history of Ulvophyceae and the evolution of cellular morphologies.

• Deutschmann, Ina Maria; Lima-Mendez, Gipsi; Krabberød, Anders Kristian; Raes, Jeroen; Vallina, Sergio M. & Faust, Karoline [Show all 7 contributors for this article] (2021). Disentangling environmental effects in microbial association networks. Microbiome. 9(232), p. 1–18. doi: 10.1186/s40168-021-01141-7. Full text in Research Archive Show summary

  Background Ecological interactions among microorganisms are fundamental for ecosystem function, yet they are mostly unknown or poorly understood. High-throughput-omics can indicate microbial interactions through associations across time and space, which can be represented as association networks. Associations could result from either ecological interactions between microorganisms, or from environmental selection, where the association is environmentally driven. Therefore, before downstream analysis and interpretation, we need to distinguish the nature of the association, particularly if it is due to environmental selection or not. Results We present EnDED (environmentally driven edge detection), an implementation of four approaches as well as their combination to predict which links between microorganisms in an association network are environmentally driven. The four approaches are sign pattern, overlap, interaction information, and data processing inequality. We tested EnDED on networks from simulated data of 50 microorganisms. The networks contained on average 50 nodes and 1087 edges, of which 60 were true interactions but 1026 false associations (i.e., environmentally driven or due to chance). Applying each method individually, we detected a moderate to high number of environmentally driven edges—87% sign pattern and overlap, 67% interaction information, and 44% data processing inequality. Combining these methods in an intersection approach resulted in retaining more interactions, both true and false (32% of environmentally driven associations). After validation with the simulated datasets, we applied EnDED on a marine microbial network inferred from 10 years of monthly observations of microbial-plankton abundance. The intersection combination predicted that 8.3% of the associations were environmentally driven, while individual methods predicted 24.8% (data processing inequality), 25.7% (interaction information), and up to 84.6% (sign pattern as well as overlap). The fraction of environmentally driven edges among negative microbial associations in the real network increased rapidly with the number of environmental factors. Conclusions To reach accurate hypotheses about ecological interactions, it is important to determine, quantify, and remove environmentally driven associations in marine microbial association networks. For that, EnDED offers up to four individual methods as well as their combination. However, especially for the intersection combination, we suggest using EnDED with other strategies to reduce the number of false associations and consequently the number of potential interaction hypotheses. Video abstract

• Latorre, Francisco de; Deutschmann, Ina M.; Labarre, Aurélie; Obiol, Aleix; Krabberød, Anders Kristian & Pelletier, Eric [Show all 11 contributors for this article] (2021). Niche adaptation promoted the evolutionary diversification of tiny ocean predators. Proceedings of the National Academy of Sciences of the United States of America (PNAS). ISSN 0027-8424. 118(25). doi: 10.1073/pnas.2020955118. Full text in Research Archive Show summary

  Significance The oceans are populated by an astronomical number of predominantly uncultured microbes, which altogether guarantee ecosystem function. Unicellular eukaryotic predators represent basal links in marine food webs and have so far been predominantly characterized as a functional group, despite having different ecologies and evolutionary histories. In order to better understand the ecoevolution of the ocean’s smallest predators, we have investigated four species belonging to an uncultured cosmopolitan family: marine stramenopiles (MAST)-4. Using state-of-the-art single-cell genomics and metaomics approaches, we found that members of this predatory family have different distributions in the surface ocean and different genes to degrade food, which likely represent niche adaptations. Our work highlights the importance of understanding the species-level ecology and genomics of tiny ocean predators.

• Furumizu, Chihiro; Krabberød, Anders Kristian; Hammerstad, Marta; Alling, Renate; Wildhagen, Mari & Sawa, Shinichiro [Show all 7 contributors for this article] (2021). The sequenced genomes of non-flowering land plants reveal the innovative evolutionary history of peptide signaling. The Plant Cell. ISSN 1040-4651. 33(9), p. 2915–2934. doi: 10.1093/plcell/koab173. Full text in Research Archive Show summary

  Abstract An understanding of land plant evolution is a prerequisite for in-depth knowledge of plant biology. Here we extract and explore information hidden in the increasing number of sequenced plant genomes, from bryophytes to angiosperms, to elucidate a specific biological question—how peptide signaling evolved. To conquer land and cope with changing environmental conditions, plants have gone through transformations that must have required innovations in cell-to-cell communication. We discuss peptides mediating endogenous and exogenous changes by interaction with receptors activating intracellular molecular signaling. Signaling peptides were discovered in angiosperms and operate in tissues and organs such as flowers, seeds, vasculature, and 3D meristems that are not universally conserved across land plants. Nevertheless, orthologs of angiosperm peptides and receptors have been identified in nonangiosperms. These discoveries provoke questions regarding coevolution of ligands and their receptors, and whether de novo interactions in peptide signaling pathways may have contributed to generate novel traits in land plants. The answers to such questions will have profound implications for the understanding of the evolution of cell-to-cell communication and the wealth of diversified terrestrial plants. Under this perspective, we have generated, analyzed, and reviewed phylogenetic, genomic, structural, and functional data to elucidate the evolution of peptide signaling.

• Andresen, Ina Jungersen; Orr, Russell John Scott; Krabberød, Anders Kristian; Shalchian-Tabrizi, Kamran & Bråte, Jon (2021). Genome sequencing and de novo assembly of the giant unicellular alga Acetabularia acetabulum using droplet MDA. Scientific Reports. 11. doi: 10.1038/s41598-021-92092-4. Full text in Research Archive
• Mundra, Sunil; Kjønaas, O. Janne; Morgado, Luis; Krabberød, Anders Kristian; Ransedokken, Yngvild & Kauserud, Håvard (2021). Soil depth matters: shift in composition and inter-kingdom co-occurrence patterns of microorganisms in forest soils. FEMS Microbiology Ecology. ISSN 0168-6496. 97(3). doi: 10.1093/femsec/fiab022. Full text in Research Archive Show summary

  Soil depth represents a strong physiochemical gradient that greatly affects soil-dwelling microorganisms. Fungal communities are typically structured by soil depth, but how other microorganisms are structured is less known. Here, we tested whether depth-dependent variation in soil chemistry affects the distribution and co-occurrence patterns of soil microbial communities. This was investigated by DNA metabarcoding in conjunction with network analyses of bacteria, fungi, as well as other micro-eukaryotes, sampled in four different soil depths in Norwegian birch forests. Strong compositional turnover in microbial assemblages with soil depth was detected for all organismal groups. Significantly greater microbial diversity and fungal biomass appeared in the nutrient-rich organic layer, with sharp decrease towards the less nutrient-rich mineral zones. The proportions of copiotrophic bacteria, Arthropoda and Apicomplexa were markedly higher in the organic layer, while patterns were opposite for oligotrophic bacteria, Cercozoa, Ascomycota and ectomycorrhizal fungi. Network analyses indicated more intensive inter-kingdom co-occurrence patterns in the upper mineral layer (0–5 cm) compared to the above organic and the lower mineral soil, signifying substantial influence of soil depth on biotic interactions. This study supports the view that different microbial groups are adapted to different forest soil strata, with varying level of interactions along the depth gradient.

• Botnen, Synnøve Smebye; Thoen, Ella; Eidesen, Pernille Bronken; Krabberød, Anders Kristian & Kauserud, Håvard (2020). Community composition of arctic root-associated fungi mirrors host plant phylogeny. FEMS Microbiology Ecology. ISSN 0168-6496. 96. doi: 10.1093/femsec/fiaa185. Full text in Research Archive Show summary

  The number of plant species regarded as non-mycorrhizal increases at higher latitudes, and several plant species in the High-Arctic Archipelago Svalbard have been reported as non-mycorrhizal. We used the rRNA ITS2 and 18S gene markers to survey which fungi, as well as other micro-eukaryotes, were associated with roots of 31 arctic plant species not usually regarded as mycorrhizal in Svalbard. We assessed to what degree the root-associated fungi showed any host preference and whether the phylogeny of the plant hosts may mirror the composition of root-associated fungi. Fungal communities were largely structured according to host plant identity and to a less extent by environmental factors. We observed a positive relationship between the phylogenetic distance of host plants and the distance of fungal community composition between samples, indicating that the evolutionary history of the host plants plays a major role for which fungi colonize the plant roots. In contrast to the ITS2 marker, the 18S rRNA gene marker showed that chytrid fungi were prevalently associated with plant roots, together with a wide spectrum of amoeba-like protists and nematodes. Our study confirms that arbuscular mycorrhizal (AM) fungi are present also in arctic environments in low abundance.

• Logares, Ramiro; Deutschmann, Ina M.; Junger, Pedro; Giner, Caterina R.; Krabberød, Anders Kristian & Schmidt, Thomas S. B. [Show all 15 contributors for this article] (2020). Disentangling the mechanisms shaping the surface ocean microbiota. Microbiome. 8(55), p. 1–17. doi: 10.1186/s40168-020-00827-8. Full text in Research Archive Show summary

  Background The ocean microbiota modulates global biogeochemical cycles and changes in its configuration may have large-scale consequences. Yet, the underlying ecological mechanisms structuring it are unclear. Here, we investigate how fundamental ecological mechanisms (selection, dispersal and ecological drift) shape the smallest members of the tropical and subtropical surface-ocean microbiota: prokaryotes and minute eukaryotes (picoeukaryotes). Furthermore, we investigate the agents exerting abiotic selection on this assemblage as well as the spatial patterns emerging from the action of ecological mechanisms. To explore this, we analysed the composition of surface-ocean prokaryotic and picoeukaryotic communities using DNA-sequence data (16S- and 18S-rRNA genes) collected during the circumglobal expeditions Malaspina-2010 and TARA-Oceans. Results We found that the two main components of the tropical and subtropical surface-ocean microbiota, prokaryotes and picoeukaryotes, appear to be structured by different ecological mechanisms. Picoeukaryotic communities were predominantly structured by dispersal-limitation, while prokaryotic counterparts appeared to be shaped by the combined action of dispersal-limitation, selection and drift. Temperature-driven selection appeared as a major factor, out of a few selected factors, influencing species co-occurrence networks in prokaryotes but not in picoeukaryotes, indicating that association patterns may contribute to understand ocean microbiota structure and response to selection. Other measured abiotic variables seemed to have limited selective effects on community structure in the tropical and subtropical ocean. Picoeukaryotes displayed a higher spatial differentiation between communities and a higher distance decay when compared to prokaryotes, consistent with a scenario of higher dispersal limitation in the former after considering environmental heterogeneity. Lastly, random dynamics or drift seemed to have a more important role in structuring prokaryotic communities than picoeukaryotic counterparts. Conclusions The differential action of ecological mechanisms seems to cause contrasting biogeography, in the tropical and subtropical ocean, among the smallest surface plankton, prokaryotes and picoeukaryotes. This suggests that the idiosyncrasy of the main constituents of the ocean microbiota should be considered in order to understand its current and future configuration, which is especially relevant in a context of global change, where the reaction of surface ocean plankton to temperature increase is still unclear. Video Abstract

• 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.

• Langlete, Petter; Krabberød, Anders Kristian & Winther-Larsen, Hanne Cecilie (2019). Vesicles from vibrio cholerae contain AT-rich DNA and shorter mRNAs that do not correlate with their protein products. Frontiers in Microbiology. 10, p. 1–16. doi: 10.3389/fmicb.2019.02708. Full text in Research Archive Show summary

  Extracellular vesicles secreted by Gram-negative bacteria have proven to be important in bacterial defense, communication and host-pathogen relationships. They resemble smaller versions of the bacterial mother cell, with similar contents of proteins, LPS, DNA, and RNA. Vesicles can elicit a protective immune response in a range of hosts, and as vaccine candidates, it is of interest to properly characterize their cargo. Genetic sequencing data is already available for vesicles from several bacterial strains, but it is not yet clear how the genetic makeup of vesicles differ from that of their parent cells, and which properties may characterize enriched genetic material. The present study provides evidence for DNA inside vesicles from Vibrio cholerae O395, and key characteristics of their genetic and proteomic content are compared to that of whole cells. DNA analysis reveals enrichment of fragments containing ToxR binding sites, as well as a positive correlation between AT-content and enrichment. Some mRNAs were highly enriched in the vesicle fraction, such as membrane protein genes ompV, ompK, and ompU, DNA-binding protein genes hupA, hupB, ihfB, fis, and ssb, and a negative correlation was found between mRNA enrichment and transcript length, suggesting mRNA inclusion in vesicles may be a size-dependent process. Certain non-coding and functional RNAs were found to be enriched, such as VrrA, GcvB, tmRNA, RNase P, CsrB2, and CsrB3. Mass spectrometry revealed enrichment of outer membrane proteins, known virulence factors, phage components, flagella and extracellular proteins in the vesicle fraction, and a low, negative correlation was found between transcript-, and protein enrichment. This result opposes the hypothesis that a significant degree of protein translation occurs in vesicles after budding. The abundance of viral-, and flagellar proteins in the vesicle fraction underlines the importance of purification during vesicle isolation.

• Giner, Caterina R.; Balagué, Vanessa; Krabberød, Anders Kristian; Ferrera, Isabel; Reñé, Albert & Garcés, Esther [Show all 9 contributors for this article] (2019). Quantifying long-term recurrence in planktonic microbial eukaryotes. Molecular Ecology. ISSN 0962-1083. 28(5), p. 923–935. doi: 10.1111/mec.14929. Full text in Research Archive
• Bjorbækmo, Marit Frederikke Markussen; Evenstad, Andreas; Røsæg, Line Lieblein; Krabberød, Anders Kristian & Logares, Ramiro (2019). The planktonic protist interactome: where do we stand after a century of research? The ISME Journal. ISSN 1751-7362. 14, p. 544–559. doi: 10.1038/s41396-019-0542-5. Full text in Research Archive Show summary

  Microbial interactions are crucial for Earth ecosystem function, but our knowledge about them is limited and has so far mainly existed as scattered records. Here, we have surveyed the literature involving planktonic protist interactions and gathered the information in a manually curated Protist Interaction DAtabase (PIDA). In total, we have registered ~2500 ecological interactions from ~500 publications, spanning the last 150 years. All major protistan lineages were involved in interactions as hosts, symbionts (mutualists and commensalists), parasites, predators, and/or prey. Predation was the most common interaction (39% of all records), followed by symbiosis (29%), parasitism (18%), and ‘unresolved interactions’ (14%, where it is uncertain whether the interaction is beneficial or antagonistic). Using bipartite networks, we found that protist predators seem to be ‘multivorous’ while parasite–host and symbiont–host interactions appear to have moderate degrees of specialization. The SAR supergroup (i.e., Stramenopiles, Alveolata, and Rhizaria) heavily dominated PIDA, and comparisons against a global-ocean molecular survey (TARA Oceans) indicated that several SAR lineages, which are abundant and diverse in the marine realm, were underrepresented among the recorded interactions. Despite historical biases, our work not only unveils large-scale eco-evolutionary trends in the protist interactome, but it also constitutes an expandable resource to investigate protist interactions and to test hypotheses deriving from omics tools.

• Bjerkan, Katrine; Hornslien, Karina Stensland; Johannessen, Ida Marie; Krabberød, Anders Kristian; Ekelenburg, Yuri Stephan van & Kalantarian, Maryam [Show all 11 contributors for this article] (2019). Genetic variation and temperature affects hybrid barriers during interspecific hybridization. The Plant Journal. ISSN 0960-7412. 101, p. 122–140. doi: 10.1111/tpj.14523. Full text in Research Archive Show summary

  Genomic imprinting regulates parent‐specific transcript dosage during seed development and is mainly confined to the endosperm. Elucidation of the function of many imprinted genes has been hampered by the lack of corresponding mutant phenotypes, and the role of imprinting is mainly associated with genome dosage regulation or allocation of resources. Disruption of imprinted genes has also been suggested to mediate endosperm‐based post‐zygotic hybrid barriers depending on genetic variation and gene dosage. Here, we have analyzed the conservation of a clade from the MADS‐box type I class transcription factors in the closely related species Arabidopsis arenosa, A. lyrata, and A. thaliana, and show that AGL36‐like genes are imprinted and maternally expressed in seeds of Arabidopsis species and in hybrid seeds between outbreeding species. In hybridizations between outbreeding and inbreeding species the paternally silenced allele of the AGL36‐like gene is reactivated in the hybrid, demonstrating that also maternally expressed imprinted genes are perturbed during hybridization and that such effects on imprinted genes are specific to the species combination. Furthermore, we also demonstrate a quantitative effect of genetic diversity and temperature on the strength of the post‐zygotic hybridization barrier. Markedly, a small decrease in temperature during seed development increases the survival of hybrid F1 seeds, suggesting that abiotic and genetic parameters play important roles in post‐zygotic species barriers, pointing at evolutionary scenarios favoring such effects.

• Swalethorp, Rasmus; Dinasquet, Julie; Logares, Ramiro; Bertilsson, Stefan; Kjellerup, Sanne & Krabberød, Anders Kristian [Show all 9 contributors for this article] (2019). Microzooplankton distribution in the Amundsen Sea Polynya (Antarctica) during an extensive Phaeocystis antarctica bloom. Progress in Oceanography. ISSN 0079-6611. 170, p. 1–10. doi: 10.1016/j.pocean.2018.10.008. Full text in Research Archive
• Krabberød, Anders Kristian; Orr, Russell; Bråte, Jon; Kristensen, Tom; Bjørklund, Kjell Rasmus & Shalchian-Tabrizi, Kamran (2017). Single cell transcriptomics, mega-phylogeny and the genetic basis of morphological innovations in Rhizaria. Molecular Biology and Evolution (MBE). ISSN 0737-4038. doi: 10.1093/molbev/msx075. Full text in Research Archive Show summary

  The innovation of the eukaryote cytoskeleton enabled phagocytosis, intracellular transport and cytokinesis, and is responsible for the diversity of eukaryotic morphologies. Still, the relationship between phenotypic innovations in the cytoskeleton and their underlying genotype is poorly understood. To explore the genetic mechanism of morphological evolution of the eukaryotic cytoskeleton we provide the first single cell transcriptomes from uncultured, free-living unicellular eukaryotes: the polycystine radiolarian Lithomelissa setosa (Nassellaria) and Sticholonche zanclea (Taxopodida). A phylogenomic approach using 255 genes finds Radiolaria and Foraminifera as separate monophyletic groups (together as Retaria), while Cercozoa is shown to be paraphyletic. Analysis of the genetic components of the cytoskeleton and mapping of the evolution of these to the revised phylogeny of Rhizaria reveal lineage-specific gene duplications and neofunctionalization of α and β tubulin in Retaria, actin in Retaria and Endomyxa, and Arp2/3 complex genes in Chlorarachniophyta. We show how genetic innovations have shaped cytoskeletal structures in Rhizaria, and how single cell transcriptomics can be applied for resolving deep phylogenies and studying gene evolution in uncultured protist species.

• Krabberød, Anders Kristian; Bjorbækmo, Marit Markussen; Shalchian-Tabrizi, Kamran & Logares, Ramiro (2017). Exploring the oceanic microeukaryotic interactome with metaomics approaches. Aquatic Microbial Ecology. ISSN 0948-3055. 79(1), p. 1–12. doi: 10.3354/ame01811. Full text in Research Archive
• Ikenoue, Takahito; Bjørklund, Kjell Rasmus; Dumitrica, Paulian; Krabberød, Anders Kristian; Kimoto, Katsunori & Matsuno, Kohei [Show all 7 contributors for this article] (2016). Two new living Entactinaria (Radiolaria) species from the Arctic province: Joergensenium arcticum n. sp. and Joergensenium clevei n. sp. Marine Micropaleontology. ISSN 0377-8398. 124, p. 75–94. doi: 10.1016/j.marmicro.2016.02.003. Full text in Research Archive
• Kumar, Surendra; Krabberød, Anders Kristian; Neumann, Ralf Stefan; Michalickova, Katerina; Zhao, Sen & Zhang, Xiaoli [Show all 7 contributors for this article] (2015). BIR pipeline for preparation of phylogenomic data. Evolutionary Bioinformatics. 11, p. 79–83. doi: 10.4137/EBO.S10189. Full text in Research Archive
• Bråte, Jon; Krabberød, Anders Kristian; Dolven, Jane Karine Lønne; Ose, Randi Frida; Kristensen, Tom & Bjørklund, Kjell Rasmus [Show all 7 contributors for this article] (2012). Radiolaria Associated with Large Diversity of Marine Alveolates. Protist. ISSN 1434-4610. 163(5), p. 767–777. doi: 10.1016/j.protis.2012.04.004. Full text in Research Archive Show summary

  We have isolated cells of unculturable radiolarians from marine coastal waters. Individual cells were subjected to single cell whole genome amplification (SCWGA) and gene-targeted PCR. Using this approach we recover a surprisingly large diversity of sequences related to the enigmatic marine alveolate groups 1 and 2 (MALV I and MALV II) that most likely represent intracellular symbionts or parasites of the radiolarian cells. 18S rDNA phylogeny of the MALV sequences reveals 4 distinct clades of radiolarian associates here named Radiolarian Associated Sequences (RAS) 1-4. One clade of both phaeodarian and radiolarian associates and one clade of only phaeodarian associates are also identified. The MALV sequences cluster according to host type, i.e. sequences from associates identified in radiolarians, fish, copepods, ciliates or dinoflagellates are not intermixed but separated into distinct clades. This implies several independent colonizations of host lineages and links a large diversity of MALV to radiolarian-associated species. This demonstrates that radiolarians may be an important reservoir for MALV, making them a key group for understanding the impact of intracellular symbionts on the marine ecosystem. This study shows that applying SCWGA on unculturable cells is a promising approach to study the vast diversity and interactions of intracellular eukaryote organisms.

• Krabberød, Anders Kristian; Bråte, Jon; Dolven, Jane Karine Lønne; Ose, Randi Frida; Klaveness, Dag & Kristensen, Tom [Show all 8 contributors for this article] (2011). Radiolaria Divided into Polycystina and Spasmaria in Combined 18S and 28S rDNA Phylogeny. PLOS ONE. 6(8). doi: 10.1371/journal.pone.0023526. Full text in Research Archive Show summary

  Radiolarians are marine planktonic protists that belong to the eukaryote supergroup Rhizaria together with Foraminifera and Cercozoa. Radiolaria has traditionally been divided into four main groups based on morphological characters; i.e. Polycystina, Acantharia, Nassellaria and Phaeodaria. But recent 18S rDNA phylogenies have shown that Phaeodaria belongs within Cerocozoa, and that the previously heliozoan group Taxopodida should be included in Radiolaria. 18S rDNA phylogenies have not yet resolved the sister relationship between the main Radiolaria groups, but nevertheless suggests that Spumellaria, and thereby also Polycystina, are polyphyletic. Very few sequences other than 18S rDNA have so far been generated from radiolarian cells, mostly due to the fact that Radiolaria has been impossible to cultivate and single cell PCR has been hampered by low success rate. Here we have therefore investigated the mutual evolutionary relationship of the main radiolarian groups by using the novel approach of combining single cell whole genome amplification with targeted PCR amplification of the 18S and 28S rDNA genes. Combined 18S and 28S phylogeny of sequences obtained from single cells shows that Radiolaria is divided into two main lineages: Polycystina (Spumellaria+Nassellaria) and Spasmaria (Acantharia+Taxopodida). Further we show with high support that Foraminifera groups within Radiolaria supporting the Retaria hypothesis.

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• Naranjo-Ortiz, Miguel Angel; Skrede, Inger; Peris, David; Krabberød, Anders Kristian; Lü, Dabao Sun & Bendiksby, Mika (2025). Expansive pangenome sin the Agaricomycetes. Full text in Research Archive Show summary

  Trichaptum abietinum (Dicks.) Ryvarden (Hymenochaetales) is a pioneer wood rot mushroom common across the Northern Hemisphere, usually growing on conifer wood. The species has emerged in recent years as a model for mushroom genomics, and extensive genomic resources are available. Here, we have analyzed patterns of gene presence-absence variation across a dataset covering T. abietinum known intraspecific geographical and genetic diversity. Our results suggest that Trichaptum abietinum has a large proportion of its genome under Presence-Absence variation, over 40% of all genes for any particular strain. This pattern seem to be common across Agaricomycetes, but not across other groups of Fungi. Core and accessory genes have distinct properties. Core genes also tend to cluster towards chromosome centers, while accessory genes are more abundant at the extremes. Core genes tend to be longer, have more introns and appear closer to other genes. Distribution of Accessory genes across the species depends on genetic distance, but this variable alone can only explain a fraction of the observed pattern. Unlike most other groups of fungi that tend to be haploid, Agaricomycetes spend most of their life cycle as a dikaryotic mycelium. Cell division in this mycelium is typically tightly regulated, which would be unnecessary were this a simple diploid. We hypothesize that extensive PAV has the potential of causing interference during mitotic recombination events, thus promoting genomic unstability. This is then prevented by keeping the two nuclei separated until meiosis. This life cycle would allow these fungi to access a much larger gene pool than it would be possible for any single haploid genet.

• Reinar, William Brynildsen; Krabberød, Anders Kristian; Lalun, Vilde Olsson; Butenko, Melinka Alonso & Jakobsen, Kjetill Sigurd (2025). Author Correction: Short tandem repeats delineate gene bodies across eukaryotes. Nature Communications. 16(1), p. 1350–1350. doi: 10.1038/s41467-025-56684-2. Full text in Research Archive
• Ortiz, Miguel Angel Naranjo; Skrede, Inger; Bendiksby, Mika; Lü, Dabao Sun; Navarro, David Peris & Krabberød, Anders Kristian (2024). Pangenome analyses of the mushroom Trichaptum abietinum (Hymenochaetales) reveals extensive presence-absence variation. Full text in Research Archive
• Ronold, Eivind Kverme; Maurice, Sundy; Torp, Vilde Åvesland; Kostich-Nilsen, Celina Alexandria; Methlie, Ine-Susanne Hopland & Schmidt, Frida [Show all 17 contributors for this article] (2024). USING eDNA TO ASSESS THE EFFECTS OF CLEAR-CUTTING FORESTRY ON FUNGAL DIVERSITY IN BOREAL SPRUCE FORESTS. Full text in Research Archive
• Kvernvik, Ane Cecilie; Gabrielsen, Tove M.; Krabberød, Anders Kristian & Vader, Anna (2023). Insights from Metatranscriptomics: Activity of Protist Communities between Seasons and along a North-South Transect in the Barents Sea. Full text in Research Archive
• Winther-Larsen, Hanne Cecilie; Langlete, Petter & Krabberød, Anders Kristian (2023). Loading cargo and messenging by bacterial extracellular vesicles. Full text in Research Archive
• Deutschmann, Ina M.; Lima-Mendez, Gipsi; Krabberød, Anders Kristian; Raes, Jeroen; Vallina, Sergio M. & Faust, Karoline [Show all 7 contributors for this article] (2021). Correction to: Disentangling environmental effects in microbial association networks (Microbiome, (2021), 9, 1, (232), 10.1186/s40168-021-01141-7). Microbiome. 9(1). doi: 10.1186/s40168-021-01209-4. Full text in Research Archive
• Johannessen, Ida Marie; Hornslien, Karina Stensland; Krabberød, Anders Kristian; Bramsiepe, Jonathan; Brysting, Anne Krag & Grini, Paul Eivind (2018). The Genetic Basis of Post-Zygotic Hybridization Barriers Between Arabidopsis lyrata and A. arenosa. Full text in Research Archive
• Krabberød, Anders Kristian; Deutschmann, Ina M.; Lima-Mendez, G.; Giner, Caterina R.; Balagué, Vanessa & Reñé, Albert [Show all 11 contributors for this article] (2017). Exploring the marine microbial interactome over 10 years. Full text in Research Archive Show summary

  There is a multitude of microbes that populate the oceans, but we still have a limited knowledge about their ecological interactions. Here we have constructed microbial association networks using monthly samples from a 10-year time-series in the North-Western Mediterranean (Blanes Bay Microbial Observatory). Community 18S and 16S rDNA amplicons from two size fractions (pico-plankton [0.2-3μm] and nano-plankton [3-20μm]) were sequenced with Illumina MiSeq. Positive or negative correlations between Operational Taxonomic Units (OTUs) were determined using extended Local Similarity Analyses (eLSA), including 18 environmental parameters. A co-occurrence network for the pico-eukaryotic OTUs present in >20% of the samples comprised 40,004 significant edges and 401 OTUs. Most edges (99.1%) were positive (co-occurrences), while 0.9% were negative (co-exclusions), suggesting cooperative associations or similar habitat preferences. The network was highly connected, featuring a mean number of node neighbours of 198.0 and a clustering coefficient (C) of 0.8, which was considerable larger than what is obtained from a random network of the same size (C=0.4). The network also had a small characteristic path length (L=1.56), pointing to small-world characteristics. So far, our results suggest that multiple ecological interactions are taking place among pico-eukaryotes over a time period of 10 years. Ongoing work including other community components as well as network deconvolution will allow us to predict diverse ecological interactions increasing our knowledge of the marine microbial interactome.

• Krabberød, Anders Kristian; Deutschmann, Ina M.; Lima-Mendez, G.; Giner, Caterina R.; Balagué, Vanessa & Reñé, Albert [Show all 11 contributors for this article] (2017). Exploring 10 years of marine microbial interactions. Full text in Research Archive
• Johannessen, Ida Marie; Hornslien, Karina Stensland; Krabberød, Anders Kristian; Bramsiepe, Jonathan; Brysting, Anne Krag & Grini, Paul Eivind (2017). The genetic basis of post-zygotic hybridization barriers between Arabidopsis lyrata and A. arenosa. Full text in Research Archive
• Enevoldsen, Emily; Liow, Lee Hsiang; Voje, Kjetil L.; Orr, Russell; Shalchian-Tabrizi, Kamran & Krabberød, Anders Kristian (2014). Macroevolution through molecular and morphological lenses: a history of microporellids. Full text in Research Archive
• Bråte, Jon; Krabberød, Anders Kristian; Dolven, Jane Karine Lønne; Ose, Randi Frida; Kristensen, Tom & Bjørklund, Kjell Rasmus [Show all 7 contributors for this article] (2010). Diversity of unculturable Radiolaria and their symbionts revealed by 18S rDNA phylogeny. Full text in Research Archive

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