ALBERT

Description: Climate change is significantly impacting the structure and function of marine ecosystems world wide with implications for species distribution ranges. In coastal systems, climate change may also alter other abiotic factors such as salinity, which may decrease due increased glacial melting in the Arctic or precipitation in temperate regions. Despite the prime ecological importance of kelps (order Laminariales) which dominate rocky benthic ecosystems in temperate to polar regions, the acclimation mechanisms and transcriptomic responses remain understudied. Here, we investigate the physiological and transcriptomic responses in sporophytes of the sugar kelp, Saccharina latissima to salinity stress after acclimation to temperature and their nterrelationships. Juvenile sporophytes of a strain from Roscoff, France were pre-cultivated at 8°C and 30 PSU for three months. After seven days of acclimation to 0°C and 15°C, sporophytes were exposed to a low salinity treatment (20 PSU) for 24 h. We established a reference transcriptome from all reads obtained through Illumina HiSeq. A total of 205 363 transcripts were assembled containing 135 959 “Trinity’s genes”. Gene expression is mostly driven by salinity stress than by temperature. The highest number of regulated genes, in comparison to the control, was found in response to the treatment 0°C low salinity (3003), followed by 8°C low salinity (1491) and 15°C low salinity (1158). Moreover, only few genes (168) were found to be differentially expressed in all low salinity treatments, showing that the response to low salinity is modulated by temperature. Growth, photosynthetic efficiency and pigment content were also impacted by stress.

Description: 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.

Description: The Southern Ocean is characterized by longitudinal water circulations crossed by strong latitudinal gradients. How this oceanographic background shapes planktonic populations is largely unknown, despite the significance of this region for global biogeochemical cycles. Here, we show, based on genomic, morphometric, ecophysiological and mating compatibility data, an example of ecotypic differentiation and speciation within an endemic pelagic inhabitant, the diatom Fragilariopsis kerguelensis. We discovered three genotypic variants, one present throughout the latitudinal transect sampled, the others restricted to the north and south, respectively. The latter two showed reciprocal monophyly across all three genomes and significant ecophysiological differences consistent with local adaptation, but produced viable offspring in laboratory crosses. The third group was also reproductively isolated from the latter two. We hypothesize that this pattern originated by an adaptive expansion accompanied by ecotypic divergence, followed by sympatric speciation.

Description: Kelp species (Laminariales, Phaeophyceae) are globally widespread along temperate to Polar rocky coastal lines. Here we analyse the mitochondrial and chloroplast genomes of Laminaria rodriguezii, in comparison to the organellar genomes of other kelp species. We also provide the complete mitochondrial genome sequence of another endemic kelp species from a Polar habitat, the Arctic Laminaria solidungula. We compare phylogenetic trees derived from twenty complete mitochondrial and seven complete chloroplast kelp genomes. Interestingly, we found a stretch of more than 700 bp in the mitochondrial genome of L.rodriguezii, which is not present in any other yet sequenced member of the Phaeophyceae. This stretch matches a protein coding region in the mitochondrial genome from Desmarestia viridis, another brown seaweed. Their high similarity suggests that these sequences originated through independent introduction into the two species. Their origin could have been by infection by yet unknown similar mitoviruses, currently only known from fungi and plants.

Description: Kelps are important providers and constituents of marine ecological niches, the coastal kelp forests. Kelp species have differing distribution ranges, but mainly thrive in temperate and arctic regions. Although the principal factors determining biogeographic distribution ranges are known, genomics could provide additional answers to this question. We sequenced DNA from two Laminaria species with contrasting distribution ranges, Laminaria digitata and Laminaria solidungula. Laminaria digitata is found in the Northern Atlantic with a southern boundary in Brittany (France) or Massachusetts (USA) and a northern boundary in the Arctic, whereas L. solidungula is endemic to the Arctic only. From the raw reads of DNA, we reconstructed both chloroplast genomes and annotated them. A concatenated data set of all available brown algae chloroplast sequences was used for the calculation of a robust phylogeny, and sequence variations were analyzed. The two Laminaria chloroplast genomes are collinear to previously analyzed kelp chloroplast genomes with important exceptions. Rearrangements at the inverted repeat regions led to the pseudogenization of ycf37 in L. solidungula, a gene possibly required under high light conditions. This defunct gene might be one of the reasons why the habitat range of L. solidungula is restricted to lowlight sublittoral sites in the Arctic. The inheritance pattern of single nucleotide polymorphisms suggests incomplete lineage sorting of chloroplast genomes in kelp species. Our analysis of kelp chloroplast genomes shows that not only evolutionary information could be gleaned from sequence data. Concomitantly, those sequences can also tell us something about the ecological conditions which are required for species well‐being.

Description: Background: Kelps (Laminariales, Phaeophyceae) are brown macroalgae of utmost ecological, and increasingly economic, importance on temperate to polar rocky shores. Omics approaches in brown algae are still scarce and knowledge of their acclimation mechanisms to the changing conditions experienced in coastal environments can benefit from the application of RNA-sequencing. Despite evidence of ecotypic differentiation, transcriptomic responses from distinct geographical locations have, to our knowledge, never been studied in the sugar kelp Saccharina latissima so far. Results: In this study we investigated gene expression responses using RNA-sequencing of S. latissima from environments with contrasting temperature and salinity conditions – Roscoff, in temperate eastern Atlantic, and Spitsbergen in the Arctic. Juvenile sporophytes derived from uniparental stock cultures from both locations were pre-cultivated at 8 °C and SA 30. Sporophytes acclimated to 0 °C, 8 °C and 15 °C were exposed to a low salinity treatment (SA 20) for 24 h. Hyposalinity had a greater impact at the transcriptomic level than the temperature alone, and its effects were modulated by temperature. Namely, photosynthesis and pigment synthesis were extensively repressed by low salinity at low temperatures. Although some responses were shared among sporophytes from the different sites, marked differences were revealed by principal component analysis, differential expression and GO enrichment. The interaction between low temperature and low salinity drove the largest changes in gene expression in sporophytes from Roscoff while specimens from Spitsbergen required more metabolic adjustment at higher temperatures. Moreover, genes related to cell wall adjustment were differentially expressed between Spitsbergen and Roscoff control samples. Conclusions: Our study reveals interactive effects of temperature and salinity on transcriptomic profiles in S. latissima. Moreover, our data suggest that under identical culture conditions sporophytes from different locations diverge in their transcriptomic responses. This is probably connected to variations in temperature and salinity in their respective environment of origin. The current transcriptomic results support the plastic response pattern in sugar kelp which is a species with several reported ecotypes. Our data provide the baseline for a better understanding of the underlying processes of physiological plasticity and may help in the future to identify strains adapted to specific environments and its genetic control.

Description: Sea ice is a large environment controlled by a number of abiotic factors (i.e. low temperatures and high salinities). Despite these harsh conditions, it is inhabited by a diverse community and significantly contributing to primary production in ice-covered regions. While this biodiversity has been investigated in the past by classical methods, little is known about its functional biodiversity, i.e. which species are actively contributing with which functions to the community. By sequencing 18S rRNA and rDNA amplicons, we were able to compare the “total” biodiversity (rDNA-based) with the “active” biodiversity (rRNA-based) and found an over-representation of certain groups (i.e. Bacillariophyceae and Ciliophora) in the active part of the community. Furthermore, we were able to isolate an abundant naviculoid sea ice diatom member (CCMP2297) of the Arctic sea ice community and conducted temperature stress experiments (10 °C, 5 °C, -2 °C, -5 °C) and analyzed not only physiological responses to high and cold temperature stress, but also the molecular responses to thermal stress by sequencing the transcriptome. We found that based on physiological parameters this diatom has a broad thermal range (5 °C to -5 °C) but significantly changes its gene expression pattern at higher temperatures.

Description: Macroalgae of the order Laminariales (kelp) are important components of cold-temperate coastal ecosystems. Major factors influencing their distribution are light including UV radiation and temperature. Therefore, future global environmental changes potentially will impact their zonation, distribution patterns, and primary productivity.Many physiological studies were performed on UV radiation and temperature stress in kelp but combinatory effects have not been analyzed and so far no study is available on the molecular processes involved in acclimation to these stresses. Therefore, sporophytes of Saccharina latissima were exposed for two weeks to 12 combinations of photosynthetically active radiation, UV radiation and temperature. Subsequently, microarray hybridizations were performed to determine changes in gene expression patterns. Several effects on the transcriptome were observed after exposure experiments. Strongest effect of temperature on gene expression was observed at 2°C. Furthermore, UV radiation had stronger effects on gene expression than high PAR, and caused stronger induction genes correlated to categories such as photosynthetic components and vitamin B6 biosynthesis. Higher temperatures ameliorated the negative effects of UV radiation in S. latissima. Regulation of ROS scavenging seems to work in a compartment specific way. Gene expression profiles of ROS scavengers indicate a high amount of oxidative stress in response to the 2°C condition as well as to excessive light at 12°C. Interestingly stress levels that did not lead to physiological alterations already caused a transcriptomic response.

Description: The Arctic region is currently facing substantial environmental changes. Melting of glaciers as a consequence of increasing temperature subsequently creates stressful environmental conditions, such as reduced salinity in coastal habitats of kelp beds. We investigated the physiological and transcriptomic performance of the sugar kelp Saccharina latissima from Kongsfjorden (Svalbard, Norway) over a 24-hour exposure at two salinities (20 and 30 psu) after a 7- day pre-acclimation at three temperatures (0, 8 and 15°C). The results demonstrate that the maximum quantum yield of PS II (Fv/Fm) at 15° C was significantly higher than at 0° C, but showed no difference at the two salinities. Pigment content exhibited similar response patterns. Salinity, however, affected gene expression much stronger than temperature. The highest number of differentially expressed genes (DEGs;-DESeq2 with log2Ratio≥2), compared to the control at 8°C and normal salinity, was found in the specimens at 8°C and low salinity (1,374), followed by samples at 0°C and low salinity (1,193). The lowest number of DEGs appeared in the individuals at 0°C and normal salinity (274). Expression profile changes mainly focused on regulations of photosynthetic components and transport processes, as well as induction of ROS scavengers. On the physiological level, our findings indicate a high plastic performance of S. latissima at higher temperatures and lower salinities accompanied by significant gene expression modulation