| 1. |
- Kaur-Kahlon, G., et al.
(författare)
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Response of a coastal tropical pelagic microbial community to changed salinity and temperature
- 2016
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Ingår i: Aquatic Microbial Ecology. - 0948-3055 .- 1616-1564. ; 77:1, s. 37-50
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Tidskriftsartikel (refereegranskat)abstract
- Studies on the responses of tropical microbial communities to changing hydrographic conditions are presently poorly represented. We present here the results from a mesocosm experiment conducted in southwest (SW) coastal India to investigate how changes in temperature and salinity may affect a coastal tropic microbial community. The onset of algal and bacterial blooms, the maximum production and biomass, and the interrelation between phytoplankton and bacteria were studied in replicated mesocosms. The treatments were set up featuring ambient conditions (28 °C, 35 PSU), hyposalinity (31 PSU), warming (31 °C) and a double manipulated treatment with warming and hyposalinity (31 °C, 31 PSU). The hyposaline treatment had the most considerable influence manifested as significantly lower primary production, and the most dissimilar microphytoplankton species community. The increased temperature acted as a catalyst in the double manipulated treatment and higher primary production was maintained. We investigated the dynamics of the microbial community with a structural equation model approach, and found a significant interrelation between phytoplankton biomass and bacterial abundance. Using this methodology, it became evident that temperature and salinity changes, individually and together, mediate direct and indirect effects that influence different compartments of the microbial loop. In the face of climate change, we suggest that in relatively nutrient replete tropical coastal zones, salinity and temperature changes will affect nutrient assimilation with subsequent significant effects on the quantity of microbial biomass and production.
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| 2. |
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| 3. |
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| 4. |
- Amato, Alberto, et al.
(författare)
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Grazer-induced transcriptomic and metabolomic response of the chain-forming diatom Skeletonema marinoi
- 2018
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Ingår i: ISME Journal. - : Springer Science and Business Media LLC. - 1751-7362 .- 1751-7370. ; 12, s. 1594-1604
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Tidskriftsartikel (refereegranskat)abstract
- Diatoms and copepods are main actors in marine food webs. The prey-predator interactions between them affect bloom dynamics, shape marine ecosystems and impact the energy transfer to higher trophic levels. Recently it has been demonstrated that the presence of grazers may affect the diatom prey beyond the direct effect of grazing. Here, we investigated the response of the chain-forming centric diatom Skeletonema marinoi to grazer cues, including changes in morphology, gene expression and metabolic profile. S. marinoi cells were incubated with Calanus finmarchicus or with Centropages typicus and in both cases responded by reducing the chain length, whereas changes in gene expression indicated an activation of stress response, changes in the lipid and nitrogen metabolism, in cell cycle regulation and in frustule formation. Transcripts linked to G protein-coupled receptors and to nitric oxide synthesis were differentially expressed suggesting involvement of these signalling transduction pathways in the response. Downregulation of a lipoxygenase in the transcriptomic data and of its products in the metabolomic data also indicate an involvement of oxylipins. Our data contribute to a better understanding of the gene function in diatoms, providing information on the nature of genes implicated in the interaction with grazers, a crucial process in marine ecosystems.
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| 5. |
- Andersson, Björn, 1985, et al.
(författare)
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Differences in metal tolerance among strains, populations, and species of marine diatoms – Importance of exponential growth for quantification
- 2020
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Ingår i: Aquatic Toxicology. - : Elsevier BV. - 0166-445X .- 1879-1514. ; 226
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Tidskriftsartikel (refereegranskat)abstract
- © 2020 The Author(s) Strains of microalgae vary in traits between species and populations due to adaptation or stochastic processes. Traits of individual strains may also vary depending on the acclimatization state and external forces, such as abiotic stress. In this study we tested how metal tolerance differs among marine diatoms at three organizational levels: species, populations, and strains. At the species level we compared two pelagic Baltic Sea diatoms (Skeletonema marinoi and Thalassiosira baltica). We found that the between-species differences in tolerance (EC50) to the biologically active metals (Cu, Co, Ni, and Zn) was similar to that within-species. In contrast, the two species differed significantly in tolerance towards the non-essential metals, Ag (three-fold higher in T. baltica), Pb and Cd (two and three-fold higher in S. marinoi). At the population level, we found evidence that increased tolerance against Cu and Co (17 and 41 % higher EC50 on average, respectively) had evolved in a S. marinoi population subjected to historical mining activity. On a strain level we demonstrate how the growth phase of cultures (i.e., cellular densities above exponential growth) modulated dose-response relationships to Ag, Cd, Co, Cu, and Zn. Specifically, the EC50's were reduced by 10–60 % in non-exponentially growing S. marinoi (strain RO5AC), depending on metal. For the essential metals these differences were often larger than the average differences between the two species and populations. Consequently, without careful experimental design, interactions between nutrient limitation and metal stress may interfere with detection of small, but evolutionary and ecologically important, differences in tolerance between microalgae. To avoid such artifacts, we outline a semi-continuous cultivation approach that maintains, and empirically tests, that exponential growth is achieved. We argue that such an approach is essential to enable comparison of population or strain differences in tolerance using dose-response tests on cultures of microalgae.
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| 6. |
- Apine, E., et al.
(författare)
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Comparative analysis of the intestinal bacterial communities in mud crab Scylla serrata in South India
- 2021
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Ingår i: Microbiologyopen. - : Wiley. - 2045-8827. ; 10:2
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Tidskriftsartikel (refereegranskat)abstract
- Little is known about the functions of the crustacean gut microbiome, but environmental parameters and habitat are known to affect the composition of the intestinal microbiome, which may in turn affect the physiological status of the host. The mud crab Scylla serrata is an economically important species, and is wild-caught, and farmed across the Indo-Pacific region. In this study, we compared the composition of the gut microbiome (in terms of gut microbial species richness and abundance) of S. serrata collected from wild sites, and farms, from the east and west coast of India, and also tested the effects of the environment on the composition. The water temperature had a statistically significant effect on gut microbiome composition, with microbial biodiversity decreasing with increasing water temperature. This could have negative effects on both wild and farmed mud crabs under future climate change conditions, although further research into the effects of temperature on gut microbiomes is required. By comparison, salinity, crab mass and carapace width, geographical location as well as whether they were farmed or wild-caught crabs did not have a significant impact on gut microbiome composition. The results indicate that farming does not significantly alter the composition of the gut microbiome when compared to wild-caught crabs.
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| 7. |
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| 8. |
- Bengtsson-Palme, Johan, 1985, et al.
(författare)
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Improved software detection and extraction of ITS1 and ITS2 from ribosomal ITS sequences of fungi and other eukaryotes for analysis of environmental sequencing data
- 2013
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Ingår i: Methods in Ecology and Evolution. - 2041-210X. ; 4:10, s. 914-919
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Tidskriftsartikel (refereegranskat)abstract
- The nuclear ribosomal internal transcribed spacer (ITS) region is the primary choice for molecular identification of fungi. Its two highly variable spacers (ITS1 and ITS2) are usually species specific, whereas the intercalary 5.8S gene is highly conserved. For sequence clustering and blast searches, it is often advantageous to rely on either one of the variable spacers but not the conserved 5.8S gene. To identify and extract ITS1 and ITS2 from large taxonomic and environmental data sets is, however, often difficult, and many ITS sequences are incorrectly delimited in the public sequence databases. We introduce ITSx, a Perl-based software tool to extract ITS1, 5.8S and ITS2 – as well as full-length ITS sequences – from both Sanger and high-throughput sequencing data sets. ITSx uses hidden Markov models computed from large alignments of a total of 20 groups of eukaryotes, including fungi, metazoans and plants, and the sequence extraction is based on the predicted positions of the ribosomal genes in the sequences. ITSx has a very high proportion of true-positive extractions and a low proportion of false-positive extractions. Additionally, process parallelization permits expedient analyses of very large data sets, such as a one million sequence amplicon pyrosequencing data set. ITSx is rich in features and written to be easily incorporated into automated sequence analysis pipelines. ITSx paves the way for more sensitive blast searches and sequence clustering operations for the ITS region in eukaryotes. The software also permits elimination of non-ITS sequences from any data set. This is particularly useful for amplicon-based next-generation sequencing data sets, where insidious non-target sequences are often found among the target sequences. Such non-target sequences are difficult to find by other means and would contribute noise to diversity estimates if left in the data set.
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| 9. |
- Cheregi, Otilia, et al.
(författare)
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Marine microalgae for outdoor biomass production - a laboratory study simulating seasonal light and temperature for the west coast of Sweden
- 2021
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Ingår i: Physiologia plantarum. - : Wiley. - 1399-3054 .- 0031-9317. ; 173:2, s. 543-554
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Tidskriftsartikel (refereegranskat)abstract
- At Nordic latitudes, year-round outdoor cultivation of microalgae is debatable due to seasonal variations in productivity. Shall the same species/strains be used throughout the year, or shall seasonal-adapted ones be used? To elucidate this, a laboratory study was performed where two out of 167 marine microalgal strains were selected for intended cultivation at the west coast of Sweden. The two local strains belong to Nannochloropsis granulata (Ng) and Skeletonema marinoi (Sm142). They were cultivated in photobioreactors and compared in conditions simulating variations in light and temperature of a year divided into three growth seasons (spring, summer and winter). The strains grew similarly well in summer (and also in spring), but Ng produced more biomass (0.225 versus 0.066 g DW L-1 d-1 ) which was more energy rich (25.0 versus 16.6 MJ kg-1 DW). In winter, Sm142 grew faster and produced more biomass (0.017 versus 0.007 g DW L-1 d-1 ), having similar energy to the other seasons. The higher energy of the Ng biomass is attributed to a higher lipid content (40 versus 16% in summer). The biomass of both strains was richest in proteins (65%) in spring. In all seasons, Sm142 was more effective in removing phosphorus from the cultivation medium (6.58 versus 4.14 mg L-1 d-1 in summer), whereas Ng was more effective in removing nitrogen only in summer (55.0 versus 30.8 mg L-1 d-1 ). Our results suggesting that, depending on the purpose, either the same or different local species can be cultivated are relevant when designing outdoor pilot studies. This article is protected by copyright. All rights reserved.
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| 10. |
- Cheregi, Otilia, et al.
(författare)
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Microalgae biotechnology in Nordic countries - the potential of local strains.
- 2019
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Ingår i: Physiologia plantarum. - : Wiley. - 1399-3054 .- 0031-9317. ; 166:1, s. 438-450
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Forskningsöversikt (refereegranskat)abstract
- Climate change, energy use and food security are the main challenges that our society is facing nowadays. Biofuels and feedstock from microalgae can be part of the solution if high and continuous production is to be ensured. This could be attained in year-round, low cost, outdoor cultivation systems using strains that are not only champion producers of desired compounds but also have robust growth in a dynamic climate. Using microalgae strains adapted to the local conditions may be advantageous particularly in Nordic countries. Here, we review the current status of laboratory and outdoor-scale cultivation in Nordic conditions of local strains for biofuel, high-value compounds and water remediation. Strains suitable for biotechnological purposes were identified from the large and diverse pool represented by saline (NE Atlantic Ocean), brackish (Baltic Sea) and fresh water (lakes and rivers) sources. Energy-efficient annual rotation for cultivation of strains well adapted to Nordic climate has the potential to provide high biomass yields for biotechnological purposes.
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| 11. |
- Cheregi, Otilia, et al.
(författare)
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Transcriptome analysis reveals insights into adaptive responses of two marine microalgae species to Nordic seasons
- 2023
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Ingår i: Algal Research. - 2211-9264. ; 74
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Tidskriftsartikel (refereegranskat)abstract
- There is an increasing interest in algae-based biomass produced outdoors in natural and industrial settings for biotechnological applications. To predict the yield and biochemical composition of the biomass, it is important to understand how the transcriptome of species and strains of interest is affected by seasonal changes. Here we studied the effects of Nordic winter and summer on the transcriptome of two phytoplankton species, namely the diatom Skeletonema marinoi (Sm) and the eustigmatophyte Nannochloropsis granulata (Ng), recently identified as potentially important for biomass production on the west coast of Sweden. Cultures were grown in photobioreactors in simulated Nordic summer and winter, and the gene expression in two phases was quantified by Illumina RNA-sequencing. Five paired comparisons were made among the four conditions. Sm was overall more responsive to seasons since 70 % of the total transcriptome (14,783 genes) showed differential expression in at least one comparison as compared to 1.6 % (1403 genes) for Ng. For both species, we observed larger differences between the seasons than between the phases of the same season. In summer phase 1, Sm cells focused on photosynthesis and polysaccharide biosynthesis. Nitrate assimilation and recycling of intracellular nitrogen for protein biosynthesis were more active in summer phase 2 and throughout winter. Lipid catabolism was upregulated in winter relative to summer to supply carbon for respiration. Ng favored lipid accumulation in summer, while in winter activated different lipid remodeling pathways as compared to Sm. To cope with winter, Ng upregulated breakdown and transport of carbohydrates for energy production. Taken together, our transcriptome data reveal insights into adaptive seasonal responses of Sm and Ng important for biotechnological applications on the west coast of Sweden, but more work is required to decipher the molecular mechanisms behind these responses.
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| 12. |
- Day, J. G., et al.
(författare)
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Challenges for the Maintenance and Cryopreservation of Multiple Isolates of Model Microorganisms: An Example Using the Marine Diatom Skeletonema marinoi
- 2017
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Ingår i: Biopreservation and Biobanking. - : Mary Ann Liebert Inc. - 1947-5535 .- 1947-5543. ; 15:3, s. 191-202
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Tidskriftsartikel (refereegranskat)abstract
- Modern genomic and metabolomic tools have provided the possibility of generating and interrogating large datasets that can provide answers to previously imponderable taxonomic, evolutionary, ecological, and physiological questions. However, the curatorial tools needed to provide and maintain the relevant biological resources on which new knowledge can be built have not kept pace with this meteoric rise in scientific capacity, its associated activity, or the huge increase in published science. The availability of biological material of guaranteed identity and quality in Biological Resource Centers is fundamental for scientific research, but it crucially depends on there being adequate preservation/maintenance methods that are capable of ensuring phenotypic, genotypic, and functional security of the biological material(s). This article highlights the challenges to the long-term maintenance of genetic resources in general, focusing specifically on the issues associated with the maintenance of a large collection of strains of the ecologically significant diatom Skeletonema marinoi. This research collection, held at the Department of Marine Sciences, University of Gothenburg, has been systematically tested for its capacity to survive cryopreservation. A method, involving incubation in the dark for 20-24 hours before cryopreservation, followed by cryoprotection employing 10% dimethysulphoxide (DMSO) and conventional cooling in a passive cooler, before plunging into liquid nitrogen was successfully applied to similar to 80% of the strains tested. In addition, the growth characteristics of exemplar strains were confirmed after storage.
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| 13. |
- Ellegaard, M., et al.
(författare)
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Dead or alive: sediment DNA archives as tools for tracking aquatic evolution and adaptation
- 2020
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Ingår i: Communications Biology. - : Springer Science and Business Media LLC. - 2399-3642. ; 3:1
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Tidskriftsartikel (refereegranskat)abstract
- DNA can be preserved in marine and freshwater sediments both in bulk sediment and in intact, viable resting stages. Here, we assess the potential for combined use of ancient, environmental, DNA and timeseries of resurrected long-term dormant organisms, to reconstruct trophic interactions and evolutionary adaptation to changing environments. These new methods, coupled with independent evidence of biotic and abiotic forcing factors, can provide a holistic view of past ecosystems beyond that offered by standard palaeoecology, help us assess implications of ecological and molecular change for contemporary ecosystem functioning and services, and improve our ability to predict adaptation to environmental stress. Ellegaard et al. discuss the potential for using ancient environmental DNA (eDNA), combined with resurrection ecology, to analyse trophic interactions and evolutionary adaptation to changing environments. Their Review suggests that these techniques will improve our ability to predict genetic and phenotypic adaptation to environmental stress.
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| 14. |
- Ellegaard, M., et al.
(författare)
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The species concept in a marine diatom: LSU rDNA-based phylogenetic differentiation in Skeletonema marinoi/dohrnii (Bacillariophyceae) is not reflected in morphology
- 2008
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Ingår i: Phycologia. - : Informa UK Limited. - 0031-8884. ; 47:2, s. 156-167
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Tidskriftsartikel (refereegranskat)abstract
- The ubiquitous marine diatom genus Skeletonema includes several newly described species. This paper presents a study of morphology and LSU sequence diversity of one of these new species, Skeletonema marinoi. The 15 monoclonal strains (from the Swedish west coast, the Swedish east coast, Portugal and Canada) included in the study showed differences in LSU rDNA sequence within the morphospecies, with differences seen even among clones established from a single plankton net sample. Morphologically, all clones were indistinguishable from each other and from the closely related species Skeletonema dohrnii. In the original description of these two species, they were differentiated by the structure of the girdle bands. However, the girdle band types of both species were found within single samples of almost all clones of S. marinoi in this study. The LSU-based phylogeny is consistent with the split into two species, and there may be a difference in their bioaeoszraphical distribution. We therefore do not at present suggest that the two species be merged. Questions regarding species delimitation and cryptic species within protists often arise from such studies that include data from both morphological and DNA sequence analysis, and such questions are addressed here.
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| 15. |
- Ellegaard, Marianne, et al.
(författare)
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Time capsules in natural sediment archives-Tracking phytoplankton population genetic diversity and adaptation over multidecadal timescales in the face of environmental change
- 2018
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Ingår i: Evolutionary Applications. - : Wiley. - 1752-4563 .- 1752-4571. ; 11:1, s. 11-16
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Tidskriftsartikel (refereegranskat)abstract
- © 2017 John Wiley & Sons Ltd. Undisturbed records of resting stages produced in the past and stored in coastal sediments are very valuable to science, because they may provide unique insights into past evolutionary and ecological trajectories. Within marine phytoplankton, multidecadal time series of monoclonal strains germinated from resting stages have been established for diatoms (Skeletonema marinoi) and dinoflagellates (Pentapharsodinium dalei), spanning ca. a century. Phenotypic and genotypic analyses of these time series have revealed effects of past environmental changes on population genetic structure. Future perspectives include direct comparisons of phenotypes and genotypic data of populations, for example, by genomewide assays that can correlate phenotypic trends with genotypes and allele frequencies in temporally separated strains. Besides their usefulness as historical records, "seed" banks of phytoplankton resting stages also have the potential to provide an inoculum that influences present populations through "dispersal from the past" (the storage effect) and are important for adaptation to future environments through their standing genetic diversity.
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| 16. |
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| 17. |
- Ferrante, M. I., et al.
(författare)
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Exploring Molecular Signs of Sex in the Marine Diatom Skeletonema marinoi
- 2019
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Ingår i: Genes. - : MDPI AG. - 2073-4425. ; 10:7
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Tidskriftsartikel (refereegranskat)abstract
- Sexual reproduction plays a fundamental role in diatom life cycles. It contributes to increasing genetic diversity through meiotic recombination and also represents the phase where large-sized cells are produced to counteract the cell size reduction process that characterizes these microalgae. With the aim to identify genes linked to the sexual phase of the centric planktonic diatom Skeletonema marinoi, we carried out an RNA-seq experiment comparing the expression level of transcripts in sexualized cells with that of large cells not competent for sex. A set of genes involved in meiosis were found upregulated. Despite the fact that flagellate gametes were observed in the sample, we did not detect the expression of genes involved in the synthesis of flagella that were upregulated during sexual reproduction in another centric diatom. A comparison with the set of genes changing during the first phases of sexual reproduction of the pennate diatom Pseudo-nitzschia multistriata revealed the existence of commonalities, including the strong upregulation of genes with an unknown function that we named Sex Induced Genes (SIG). Our results further broadened the panel of genes that can be used as a marker for sexual reproduction of diatoms, crucial for the interpretation of metatranscriptomic datasets.
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| 18. |
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| 19. |
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| 20. |
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| 21. |
- Godhe, Anna, 1967, et al.
(författare)
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Comparison of three common molecular tools for distinguishing among geographically separated clones of the diatom Skeletonema marinoi Sarno et Zingone (bacillariophyceae)
- 2006
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Ingår i: Journal of Phycology. - : Wiley. - 0022-3646 .- 1529-8817. ; 42:2, s. 280-291
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Tidskriftsartikel (refereegranskat)abstract
- Skeletonema marinoi Sarno et Zingone is a planktonic marine diatom with a widespread geographic distribution. Different populations of this species may show distinct genetic signatures. We have evaluated the utility of three common molecular methods for distinguishing clones of S. marinoi from different geographic regions. Clonal cultures were isolated from the Canadian west coast, south west Portugal, and the east and west coasts of Sweden. All strains originated from resting stages in sediment. More than 90% of the individually isolated chains grew to densities suitable for DNA extraction. Genetic signatures of clones from each sample location were assessed by sequencing variable domains (D1-D3) of the nuclear large subunit (LSU) rRNA gene and internal transcriber spacer (ITS) (ITS-1, 5.8S and ITS-2) regions, and also by analysis of randomly amplified polymorphic DNA patterns. Analysis of molecular variance showed that strains from the four geographic areas were significantly separated by all three methods but that differences among European samples were best resolved by ITS 2 sequences.
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| 22. |
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| 23. |
- Godhe, Anna, 1967, et al.
(författare)
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Genetic and Microscopic Evidence for Sexual Reproduction in the Centric Diatom Skeletonema marinoi
- 2014
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Ingår i: Protist. - : Elsevier BV. - 1434-4610 .- 1618-0941. ; 165:4, s. 401-416
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Tidskriftsartikel (refereegranskat)abstract
- This study provides microscopic and molecular evidence for sexual reproduction in the homothallic centric diatom Skeletonema marinoi isolated from the Baltic Sea. The species is capable of restoring cell size asexually through an auxospore-like stage. However, cells were sexualized after shifting strains from low (6 PSU) to high (16 PSU) salinity. We observed flagellate male gametes and oogonia, with diameters of 3-4 and 3.2-6.3 m, respectively. Fertilization took place followed by the formation of round auxospores surrounded by thin siliceous incunabular scales. Auxosporulation was synchronized, and a maximum of auxospores was detected on day three following the salinity shift. The proportion of auxospores to vegetative cells ranged from 0.02 to 0.18. There was a significant correlation between auxosporulation success and inoculum cell density. At lower cell concentration (5,000 cells ml-1), pro- portionally fewer auxospores were formed. Auxospores were formed in single strains and in crosses of strains. The proportion of auxospores differed significantly among strains and crosses of strains. Additionally, we isolated single auxospores, obtained F1 strains and performed microsatellite based pedigree analysis of parental generations and their offspring. We proved that the auxospores were formed sexually, either by inter- or by intra-strain fertilization.
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| 24. |
- Godhe, Anna, 1967, et al.
(författare)
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Influence of benthic and pelagic environmental factors on the distribution of dinoflagellate cysts in surface sediments along the Swedish west coast
- 2003
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Ingår i: Aquatic Microbial Ecology. - 0948-3055. ; 32:2, s. 185-201
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Tidskriftsartikel (refereegranskat)abstract
- Abundance and frequency of dinoflagellate cysts in 19 surface sediment samples from the northern part of the Swedish west coast has been related to physical and chemical characters of the sediment, hydrography of the overlying water column, and plankton species data from the area. Density of cysts varied between 5000 and 10 1000 cysts g(-1) dw, and the most commonly encountered species were Lingulodinium polyedrum and Protoceratium reticulatum. In all, 46 environmental variables were tested for their relation to dinoflagellate cyst densities, proportion of autotrophic and heterotrophic taxa, and individual species distribution and frequency. The outcomes of multivariate analyses, projection to latent structures (PLS) and canonical correspondence analysis (CCA) were consistent with each other and the actual cyst count. The density of the total cyst assemblage (>90% autotrophic taxa) was primarily related to surface temperature, macronutrients, and inversely to phytoplankton competitors, such as diatoms. The abundance of heterotrophic taxa was governed by the preferences of their prey, i.e. diatom-favourable conditions, and, in most cases, higher proportions of heterotrophic taxa were found at well-mixed sites. Some possible effects of anthropogenic contaminants were also noted. Several taxa showed distinct distribution patterns with respect to the environmental variables. A discrepancy between the species constituting the planktonic and the benthic community was revealed when data from 6 yr of plankton monitoring was compared to the data on distribution of dinoflagellate cysts. In particular, cyst-forming species were only a minor part of the plankton, suggesting that these dinoflagelldtes spend much of their life in the sediments.
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| 25. |
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