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An abstract of the article "Comparative Functional Genomics of Virus-Susceptible and Virus-Resistant Strains of Emiliania huxleyi," by J. U. Kegel, U. John, S. Frickenhaus, K. Metfies and K. Valentin, is presented.

The haptophyte Phaeocystis antarctica is endemic to the Southern Ocean, where iron supply is sporadic and its availability limits primary production. In iron fertilization experiments, P. antarctica showed a prompt and steady increase in cell abundance compared to heavily silicified diatoms along with enhanced colony formation. Here we utilized a transcriptomic approach to investigate molecular responses to alleviation of iron limitation in P. antarctica. We analyzed the transcriptomic response before and after (14 h, 24 h and 72 h) iron addition to a low-iron acclimated culture. After iron addition, we observed indicators of a quick reorganization of cellular energetics, from carbohydrate catabolism and mitochondrial energy production to anabolism. In addition to typical substitution responses from an iron-economic toward an iron-sufficient state for flavodoxin (ferredoxin) and plastocyanin (cytochrome c 6 ), we found other genes utilizing the same strategy involved in nitrogen assimilation and fatty acid desaturation. Our results shed light on a number of adaptive mechanisms that P. antarctica uses under low iron, including the utilization of a Cu-dependent ferric reductase system and indication of mixotrophic growth. The gene expression patterns underpin P. antarctica as a quick responder to iron addition., (© 2020 The Authors. Journal of Phycology published by Wiley Periodicals, Inc. on behalf of Phycological Society of America.)

Enrichment of the oceans with CO 2 may be beneficial for some marine phytoplankton, including harmful algae. Numerous laboratory experiments provided valuable insights into the effects of elevated pCO 2 on the growth and physiology of harmful algal species, including the production of phycotoxins. Experiments close to natural conditions are the next step to improve predictions, as they consider the complex interplay between biotic and abiotic factors that can confound the direct effects of ocean acidification. We therefore investigated the effect of ocean acidification on the occurrence and abundance of phycotoxins in bulk plankton samples during a long-term mesocosm experiment in the Gullmar Fjord, Sweden, an area frequently experiencing harmful algal blooms. During the experimental period, a total of seven phycotoxin-producing harmful algal genera were identified in the fjord, and in accordance, six toxin classes were detected. However, within the mesocosms, only domoic acid and the corresponding producer Pseudo-nitzschia spp. was observed. Despite high variation within treatments, significantly higher particulate domoic acid contents were measured in the mesocosms with elevated pCO 2 . Higher particulate domoic acid contents were additionally associated with macronutrient limitation. The risks associated with potentially higher phycotoxin levels in the future ocean warrants attention and should be considered in prospective monitoring strategies for coastal marine waters., (Copyright © 2019 Elsevier B.V. All rights reserved.)

Dinoflagellates are microbial eukaryotes that have exceptionally large nuclear genomes; however, their organelle genomes are small and fragmented and contain fewer genes than those of other eukaryotes. The genus Amoebophrya (Syndiniales) comprises endoparasites with high genetic diversity that can infect other dinoflagellates, such as those forming harmful algal blooms (e.g., Alexandrium ). We sequenced the genome (~100 Mb) of Amoebophrya ceratii to investigate the early evolution of genomic characters in dinoflagellates. The A. ceratii genome encodes almost all essential biosynthetic pathways for self-sustaining cellular metabolism, suggesting a limited dependency on its host. Although dinoflagellates are thought to have descended from a photosynthetic ancestor, A. ceratii appears to have completely lost its plastid and nearly all genes of plastid origin. Functional mitochondria persist in all life stages of A. ceratii , but we found no evidence for the presence of a mitochondrial genome. Instead, all mitochondrial proteins appear to be lost or encoded in the A. ceratii nucleus.

Rationale: High-resolution mass spectrometry (HRMS) with high sample throughput has become an important analytical tool for the analysis of highly complex samples and data processing has become a major challenge for the user community. Evaluating direct-infusion HRMS data without automated tools for batch processing can be a time-consuming step in the analytical pipeline. Therefore, we developed a new browser-based software tool for processing HRMS data., Methods: The software, named UltraMassExplorer (UME), was written in the R programming language using the shiny library to build the graphical user interface. The performance of the integrated formula library search algorithm was tested using HRMS data derived from analyses of up to 50 extracts of marine dissolved organic matter., Results: The software supports the processing of lists of calibrated masses of neutral, protonated or deprotonated molecules, with masses of up to 700 Da and a mass accuracy <3 ppm. In the performance test, the number of assigned peaks per second increased with the number of submitted peaks and reached a maximum rate of 4745 assigned peaks per second., Conclusions: UME offers a complete data evaluation pipeline comprising a fast molecular formula assignment algorithm allowing for the swift reanalysis of complete datasets, advanced filter functions and the export of data, metadata and publication-quality graphics. Unique to UME is a fast and interactive connection between data and their visual representation. UME provides a new platform enabling an increased transparency, customization, documentation and comparability of datasets., (© 2018 John Wiley & Sons, Ltd.)

Next-generation sequencing is a common method for analysing microbial community diversity and composition. Configuring an appropriate sequence processing strategy within the variety of tools and methods is a nontrivial task and can considerably influence the resulting community characteristics. We analysed the V4 region of 18S rRNA gene sequences of marine samples by 454-pyrosequencing. Along this process, we generated several data sets with QIIME, mothur, and a custom-made pipeline based on DNAStar and the phylogenetic tree-based PhyloAssigner. For all processing strategies, default parameter settings and punctual variations were used. Our results revealed strong differences in total number of operational taxonomic units (OTUs), indicating that sequence preprocessing and clustering had a major impact on protist diversity estimates. However, diversity estimates of the abundant biosphere (abundance of ≥1%) were reproducible for all conducted processing pipeline versions. A qualitative comparison of diatom genera emphasized strong differences between the pipelines in which phylogenetic placement of sequences came closest to light microscopy-based diatom identification. We conclude that diversity studies using different sequence processing strategies are comparable if the focus is on higher taxonomic levels, and if abundance thresholds are used to filter out OTUs of the rare biosphere., (© 2017 John Wiley & Sons Ltd.)

A diesel spill occurring at Carlini Station (King George Island (Isla 25 de Mayo), South Shetland Islands) in 2009 started the study of the fate of the hydrocarbons and their effect on the bacterial communities of the Potter Cove ecosystem. Soils and sediments were sampled across the 200-meter long diesel plume towards Potter Cove four and 15months after the spill. The sampling revealed a second fuel leakage from an underground pipeline at the spill site. The hydrocarbon fraction spilt over frozen and snow-covered ground reached the sea and dispersed with the currents. Contrary, diesel that infiltrated unfrozen soil remained detectable for years, and was seeping with ground water towards coastal marine sediments. Structural changes of the bacterial communities as well as hydrocarbon, carbon and nitrogen contents were investigated in sediments in front of the station, two affected terrestrial sites, and a terrestrial non-contaminated reference site. Bacterial communities (16S rRNA gene clone libraries) changed over time in contaminated soils and sediments. At the underground seepage site of highest contamination (5812 to 366μgg -1 dw hydrocarbons from surface to 90-cm depth), communities were dominated by Actinobacteria (18%) and a betaproteobacterium closely related to Polaromonas naphthalenivorans (40%). At one of the spill sites, affected exclusively at the surface, contamination disappeared within one year. The same bacterial groups were enriched at both contaminated sites. This response at community level suggests that the cold-adapted indigenous microbiota in soils of the West Antarctic Peninsula have a high potential for bioremediation and can support soil cleaning actions in the ecosystem. Intensive monitoring of pollution and site assessment after episodic fuel spills is required for decision-making towards remediation strategies., (Copyright © 2017 Elsevier B.V. All rights reserved.)

Thermal tolerance windows serve as a powerful tool for estimating the vulnerability of marine species and their life stages to increasing temperature means and extremes. However, it remains uncertain to which extent additional drivers, such as ocean acidification, modify organismal responses to temperature. This study investigated the effects of CO 2 -driven ocean acidification on embryonic thermal sensitivity and performance in Atlantic cod, Gadus morhua, from the Kattegat. Fertilized eggs were exposed to factorial combinations of two PCO 2 conditions (400 μatm vs. 1100 μatm) and five temperature treatments (0, 3, 6, 9 and 12 °C), which allow identifying both lower and upper thermal tolerance thresholds. We quantified hatching success, oxygen consumption (MO 2 ) and mitochondrial functioning of embryos as well as larval morphometrics at hatch and the abundance of acid-base-relevant ionocytes on the yolk sac epithelium of newly hatched larvae. Hatching success was high under ambient spawning conditions (3-6 °C), but decreased towards both cold and warm temperature extremes. Elevated PCO 2 caused a significant decrease in hatching success, particularly at cold (3 and 0 °C) and warm (12 °C) temperatures. Warming imposed limitations to MO 2 and mitochondrial capacities. Elevated PCO 2 stimulated MO 2 at cold and intermediate temperatures, but exacerbated warming-induced constraints on MO 2 , indicating a synergistic interaction with temperature. Mitochondrial functioning was not affected by PCO 2 . Increased MO 2 in response to elevated PCO 2 was paralleled by reduced larval size at hatch. Finally, ionocyte abundance decreased with increasing temperature, but did not differ between PCO 2 treatments. Our results demonstrate increased thermal sensitivity of cod embryos under future PCO 2 conditions and suggest that acclimation to elevated PCO 2 requires reallocation of limited resources at the expense of embryonic growth. We conclude that ocean acidification constrains the thermal performance window of embryos, which has important implication for the susceptibility of cod to projected climate change., (© 2016 John Wiley & Sons Ltd.)

The Southern Ocean houses a diverse and productive community of organisms. Unicellular eukaryotic diatoms are the main primary producers in this environment, where photosynthesis is limited by low concentrations of dissolved iron and large seasonal fluctuations in light, temperature and the extent of sea ice. How diatoms have adapted to this extreme environment is largely unknown. Here we present insights into the genome evolution of a cold-adapted diatom from the Southern Ocean, Fragilariopsis cylindrus, based on a comparison with temperate diatoms. We find that approximately 24.7 per cent of the diploid F. cylindrus genome consists of genetic loci with alleles that are highly divergent (15.1 megabases of the total genome size of 61.1 megabases). These divergent alleles were differentially expressed across environmental conditions, including darkness, low iron, freezing, elevated temperature and increased CO 2 . Alleles with the largest ratio of non-synonymous to synonymous nucleotide substitutions also show the most pronounced condition-dependent expression, suggesting a correlation between diversifying selection and allelic differentiation. Divergent alleles may be involved in adaptation to environmental fluctuations in the Southern Ocean.

Cross-system studies on the response of different ecosystems to global change will support our understanding of ecological changes. Synoptic views on the planet's two main realms, the marine and terrestrial, however, are rare, owing to the development of rather disparate research communities. We combined questionnaires and a literature review to investigate how the importance of anthropogenic drivers of biodiversity change differs among marine and terrestrial systems and whether differences perceived by marine vs. terrestrial researchers are reflected by the scientific literature. This included asking marine and terrestrial researchers to rate the relevance of different drivers of global change for either marine or terrestrial biodiversity. Land use and the associated loss of natural habitats were rated as most important in the terrestrial realm, while the exploitation of the sea by fishing was rated as most important in the marine realm. The relevance of chemicals, climate change and the increasing atmospheric concentration of CO 2 were rated differently for marine and terrestrial biodiversity respectively. Yet, our literature review provided less evidence for such differences leading to the conclusion that while the history of the use of land and sea differs, impacts of global change are likely to become increasingly similar., (Copyright © 2016 Office national des forêts. Published by Elsevier B.V. All rights reserved.)