Seasonal dynamics of algae-infecting viruses and their inferred interactions with protists

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.publishedVersio

ØKOKYST – DP Norskehavet Sør, Årsrapport 2022

Prosjektleder: Elianne EggeOvervåkingsprogrammet "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.MiljødirektoratetpublishedVersio

Parasites dominate hyperdiverse soil protist communities in Neotropical rainforests

High animal and plant richness in tropical rainforest communities has long intrigued naturalists. It is unknown if similar hyperdiversity patterns are reflected at the microbial scale with unicellular eukaryotes (protists). Here we show, using environmental metabarcoding of soil samples and a phylogeny-aware cleaning step, that protist communities in Neotropical rainforests are hyperdiverse and dominated by the parasitic Apicomplexa, which infect arthropods and other animals. These host-specific parasites potentially contribute to the high animal diversity in the forests by reducing population growth in a density-dependent manner. By contrast, too few operational taxonomic units (OTUs) of Oomycota were found to broadly drive high tropical tree diversity in a host-specific manner under the Janzen-Connell model. Extremely high OTU diversity and high heterogeneity between samples within the same forests suggest that protists, not arthropods, are the most diverse eukaryotes in tropical rainforests. Our data show that protists play a large role in tropical terrestrial ecosystems long viewed as being dominated by macroorganisms

Population-level ecotoxicology : combined effects of POPs exposure and density stress on zebrafish populations

A challenge in ecotoxicology is the translation of individual-level effects of exposure, as measured in for instance laboratory tests, into population-level effects that have more ecological relevance. It is not necessarily possible to predict effects of toxicant exposure on the population level directly from observations on individual-level endpoints. Density-dependent processes within natural populations is a major complicating factor. In this study, laboratory populations of zebrafish (Danio rerio) were exposed to a naturally occurring mixture of persistent organic pollutants (POPs) at three levels of population density. It was found that toxicant exposure decreased somatic growth in juveniles and adults, and increased time to sexual maturation. Increasing population density had the same effects. For fish populations, individual growth can be an important regulatory mechanism. Size-structured matrix population models were therefore developed in order to synthesise the toxicant effects on vital rates into population-level endpoints. Subsequently, two sets of simulations were run, one with a density-independent model and one with a model where larval survival, juvenile and adult growth and fecundity were modeled as functions of population density. The outcome of the simulations with the density-independent model indicated that exposure to POPs may result in reduced population growth rate and reduced population abundance. When density dependence was taken into account in the model, the simulation results indicated that under certain regimes of density dependence, toxicant exposure has the potential to relieve effects of density stress on individual-level vital rates. Measures of population growth rate and/or abundance may be difficult to obtain in an experimental setting, and thus population models are important tools in ecological risk assessment of toxicants. Further analysis of the models developed in this thesis should include sensitivity and elasticity analysis. These types of analyses may provide valuable information about the magnitudes of the population-level impacts of given toxicant-induced reductions in the different vital rates

454 Pyrosequencing to Describe Microbial Eukaryotic Community Composition, Diversity and Relative Abundance: A Test for Marine Haptophytes

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

Table_S2_Egge_et_al_2015_jeukmic

Table containing information about the haptophyte V4 SSU rRNA OTUs recorded in Skagerrak in the period September 2009 – June 2011. First published in Egge ES, Eikrem W, Edvardsen B (2015) “Deep-branching Novel Lineages and High Diversity of Haptophytes in the Skagerrak (Norway) Uncovered by 454 Pyrosequencing”, Journal of Eukaryotic Microbiology 62, 121-140. DOI: 10.1111/jeu.1215

Haptophyte diversity and vertical distribution explored by 18S and 28S ribosomal RNA gene metabarcoding and scanning electron microscopy

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 setalso 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.De två första författarna delar förstaförfattarskapet.</p

Diversity and distribution of haptophytes reavealed by environmental sequencing - a review. Perspectives in Phycology. Supplementary material.

<p><b></b> </p><p><b>7. Fig. S1. </b>Maximum-likelihood tree<b> </b>(RAxML v. 8.026, GTRCAT) based on 971 haptophyte 18S rRNA gene sequences from Table S1, 451 are from cultured strains and 520 from environmental clone libraries. Bootstrap values are marked at the nodes. The colours indicate taxonomic groups.</p> <p><b>8. Table S1. </b>Haptophyte 18S rRNA gene sequence reference database including 971 sequences, 451 from cultures and 520 from environmental clone libraries. See File S1 for description of its construction. Chimeras (32) identified by uchime in mothur and by manual blast are listed on sheet 2.</p> <p><b>9. Table S2</b>. Information on selected, commonly used PCR primers for environmental sequencing and metabarcoding of haptophytes.</p> <p><b>10. File S1.</b> Description of the construction of the Haptophyte 18S rRNA gene reference sequence database, alignment and final RAxML phylogenetic tree.</p> <p><b>11. File S2. </b>Fasta file with accession numbers and 18S rRNA gene sequence of 971 reference sequences for taxonomic assignment in mothur or Qiime. </p> <p><b>12. File S3. </b>Taxonomy file with systematic placement of 971 haptophyte reference sequences for taxonomic assignment in mothur or Qiime. </p> <p><b>13. File S4. </b>Curated haptophyte 18S rRNA gene alignment for Figs 2 and S1.</p

Protist Diversity and Seasonal Dynamics in Skagerrak Plankton Communities as Revealed by Metabarcoding and Microscopy

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

An 18S V4 rRNA metabarcoding dataset of protist diversity in the Atlantic inflow to the Arctic Ocean, through the year and down to 1000 m depth

International audienceArctic 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 (&lt; 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)