| 1. |
- Bachimanchi, Harshith, et al.
(författare)
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Deep-learning-powered data analysis in plankton ecology
- 2024
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Ingår i: Limnology And Oceanography Letters. - 2378-2242.
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Forskningsöversikt (refereegranskat)abstract
- The implementation of deep learning algorithms has brought new perspectives to plankton ecology. Emerging as an alternative approach to established methods, deep learning offers objective schemes to investigate plankton organisms in diverse environments. We provide an overview of deep-learning-based methods including detection and classification of phytoplankton and zooplankton images, foraging and swimming behavior analysis, and finally ecological modeling. Deep learning has the potential to speed up the analysis and reduce the human experimental bias, thus enabling data acquisition at relevant temporal and spatial scales with improved reproducibility. We also discuss shortcomings and show how deep learning architectures have evolved to mitigate imprecise readouts. Finally, we suggest opportunities where deep learning is particularly likely to catalyze plankton research. The examples are accompanied by detailed tutorials and code samples that allow readers to apply the methods described in this review to their own data.
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| 2. |
- Pereyra, Ricardo T., 1974, et al.
(författare)
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Clones on the run: The genomics of a recently expanded partially clonal species
- 2023
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Ingår i: Molecular Ecology. - 0962-1083. ; 32:15, s. 4209-23
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Tidskriftsartikel (refereegranskat)abstract
- Why species that in their core areas mainly reproduce sexually become enriched with clones in marginal populations ("geographic parthenogenesis") remains unclear. Earlier hypotheses have emphasized that selection might promote clonality because it protects locally adapted genotypes. On the other hand, it also hampers recombination and adaptation to changing conditions. The aim of the present study was to investigate the early stages of range expansion in a partially clonal species and what drives an increase in cloning during such expansion. We used genome-wide sequencing to investigate the origin and evolution of large clones formed in a macroalgal species (Fucus vesiculosus) during a recent expansion into the postglacial Baltic Sea. We found low but persistent clonality in core populations, while at range margins, large dominant clonal lineages had evolved repeatedly from different sexual populations. A range expansion model showed that even when asexual recruitment is less favourable than sexual recruitment in core populations, repeated bottlenecks at the expansion front can establish a genetically eroded clonal wave that spreads ahead of a sexual wave into the new area. Genetic variation decreases by drift following repeated bottlenecks at the expansion front. This results in the emerging clones having low expected heterozygosity, which corroborated our empirical observations. We conclude that Baker's Law (clones being favoured by uniparental reproductive assurance in new areas) can play an important role during range expansion in partially clonal species, resulting in a complex spatiotemporal mosaic of clonal and sexual lineages that might persist during thousands of generations.
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| 3. |
- Andersson, Björn, et al.
(författare)
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Strain-specific metabarcoding reveals rapid evolution of copper tolerance in populations of the coastal diatom Skeletonema marinoi
- 2023
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Ingår i: Molecular Ecology. - 0962-1083 .- 1365-294X.
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Tidskriftsartikel (refereegranskat)abstract
- Phytoplankton have short generation times, flexible reproduction strategies, large population sizes and high standing genetic diversity, traits that should facilitate rapid evolution under directional selection. We quantified local adaptation of copper tolerance in a population of the diatom Skeletonema marinoi from a mining-exposed inlet in the Baltic Sea and in a non-exposed population 100 km away. We hypothesized that mining pollution has driven evolution of elevated copper tolerance in the impacted population of S. marinoi. Assays of 58 strains originating from sediment resting stages revealed no difference in the average tolerance to copper between the two populations. However, variation within populations was greater at the mining site, with three strains displaying hyper-tolerant phenotypes. In an artificial evolution experiment, we used a novel intraspecific metabarcoding locus to track selection and quantify fitness of all 58 strains during co-cultivation in one control and one toxic copper treatment. As expected, the hyper-tolerant strains enabled rapid evolution of copper tolerance in the mining-exposed population through selection on available strain diversity. Within 42 days, in each experimental replicate a single strain dominated (30%–99% abundance) but different strains dominated the different treatments. The reference population developed tolerance beyond expectations primarily due to slowly developing plastic response in one strain, suggesting that different modes of copper tolerance are present in the two populations. Our findings provide novel empirical evidence that standing genetic diversity of phytoplankton resting stage allows populations to evolve rapidly (20–50 generations) and flexibly on timescales relevant for seasonal bloom progressions.
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| 4. |
- 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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| 5. |
- Johansson, Oskar N., 1984, et al.
(författare)
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Friends With Benefits: Exploring the Phycosphere of the Marine Diatom Skeletonema marinoi
- 2019
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Ingår i: Frontiers in Microbiology. - : Frontiers Media SA. - 1664-302X. ; 10
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Tidskriftsartikel (refereegranskat)abstract
- Marine diatoms are the dominant phytoplankton in the temperate oceans and coastal regions, contributing to global photosynthesis, biogeochemical cycling of key nutrients and minerals and aquatic food chains. Integral to the success of marine diatoms is a diverse array of bacterial species that closely interact within the diffusive boundary layer, or phycosphere, surrounding the diatom partner. Recently, we isolated seven distinct bacterial species from cultures of Skeletonema marinoi, a chain-forming, centric diatom that dominates the coastal regions of the temperate oceans. Genomes of all seven bacteria were sequenced revealing many unusual characteristics such as the existence of numerous plasmids of widely varying sizes. Here we have investigated the characteristics of the bacterial interactions with S. marinoi, demonstrating that several strains (Arenibacter algicola strain SMS7, Marinobacter salarius strain SMRS, Sphingorhabdus flavimaris strain SMR4y, Sulfitobacter pseudonitzschiae strain SMR1, Yoonia vestfoldensis strain SMR4r and Roseovarius mucosus strain SMR3) stimulate growth of the diatom partner. Testing of many different environmental factors including low iron concentration, high and low temperatures, and chemical signals showed variable effects on this growth enhancement by each bacterial species, with the most significant being light quality in which green and blue but not red light enhanced the stimulatory effect on S. marinoi growth by all bacteria. Several of the bacteria also inhibited growth of one or more of the other bacterial strains to different extents when mixed together. This study highlights the complex interactions between diatoms and their associated bacteria within the phycosphere, and that further studies are needed to resolve the underlying mechanisms for these relationships and how they might influence the global success of marine diatoms.
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| 6. |
- Johansson, Oskar N., 1984, et al.
(författare)
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Phenomics reveals a novel putative chloroplast fatty acid transporter in the marine diatom Skeletonema marinoi involved in temperature acclimation
- 2019
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Ingår i: Scientific Reports. - : Springer Science and Business Media LLC. - 2045-2322. ; 9
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Tidskriftsartikel (refereegranskat)abstract
- Diatoms are the dominant phytoplankton in temperate oceans and coastal regions and yet little is known about the genetic basis underpinning their global success. Here, we address this challenge by developing the first phenomic approach for a diatom, screening a collection of randomly mutagenized but identifiably tagged transformants. Based upon their tolerance to temperature extremes, several compromised mutants were identified revealing genes either stress related or encoding hypothetical proteins of unknown function. We reveal one of these hypothetical proteins is a novel putative chloroplast fatty acid transporter whose loss affects several fatty acids including the two omega-3, long-chain polyunsaturated fatty acids - eicosapentaenoic and docosahexaenoic acid, both of which have medical importance as dietary supplements and industrial significance in aquaculture and biofuels. This mutant phenotype not only provides new insights into the fatty acid biosynthetic pathways in diatoms but also highlights the future value of phenomics for revealing specific gene functions in these ecologically important phytoplankton.
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| 7. |
- Johansson, Oskar N., 1984, et al.
(författare)
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Skeletonema marinoi as a new genetic model for marine chain-forming diatoms
- 2019
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Ingår i: Scientific Reports. - : Springer Science and Business Media LLC. - 2045-2322. ; 9
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Tidskriftsartikel (refereegranskat)abstract
- Diatoms are ubiquitous primary producers in marine ecosystems and freshwater habitats. Due to their complex evolutionary history, much remains unknown about the specific gene functions in diatoms that underlie their broad ecological success. In this study, we have genetically transformed the centric diatom Skeletonema marinoi, a dominant phytoplankton species in temperate coastal regions. Transformation of S. marinoi is the first for a true chain-forming diatom, with the random genomic integration via non homologous recombination of a linear DNA construct expressing the resistance gene to the antibiotic zeocin. A set of molecular tools were developed for reliably identifying the genomic insertion site within each transformant, many of which disrupt recognizable genes and constitute null or knock-down mutations. We now propose S. marinoi as a new genetic model for marine diatoms, representing true chain-forming species that play a central role in global photosynthetic carbon sequestration and the biogeochemical cycling of silicates and various nutrients, as well as having potential biotechnological applications.
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| 8. |
- Pinder, Matthew I. M., 1990, et al.
(författare)
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Genome Sequence of Kordia sp. Strain SMS9 Identified in a Non-Axenic Culture of the Diatom Skeletonema marinoi.
- 2019
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Ingår i: Journal of genomics. - : Ivyspring International Publisher. - 1839-9940. ; 7, s. 46-49
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Tidskriftsartikel (refereegranskat)abstract
- Initial efforts to sequence the genome of the marine diatom Skeletonema marinoi were hampered by the presence of genetic material from bacteria, and there was sufficient material from some of these bacteria to enable the assembly of full chromosomes. Here, we report the genome of strain SMS9, one such bacterial species identified in a non-axenic culture of S. marinoi strain ST54. Its 5,482,391 bp circular chromosome contains 4,641 CDSs, and has a G+C content of 35.6%. Based on 16S rRNA comparison, phylotaxonomic analysis, and the genome similarity metrics dDDH and OrthoANI, we place this strain in the genus Kordia, and to the best of our knowledge, this is the first Kordia species to be initially described from European waters. As attempts to culture this strain have failed, however, the specifics of its relationship with S. marinoi are still uncertain.
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| 9. |
- Pinder, Matthew I. M., 1990
(författare)
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Survivors of the Sea: Investigating the genomics and survival strategies of the diatom Skeletonema marinoi
- 2023
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Diatoms are an ecologically important group of phytoplankton, responsible for around 20% of global primary production. One of the features contributing to their success is their ability to form resting stages, a response to adverse conditions in which they enter a dormant state and sink to the sediment. While some resting stages may germinate upon the return of favourable conditions and become resuspended, others can become buried in the dark, anoxic sediment for long periods, retaining their viability. Resting stages of some species have been revived in the lab after over a century, yet the precise mechanisms behind this ability to survive so long in this state is not well understood. One such species capable of forming long-lived resting stages is Skeletonema marinoi. The draft reference genome of this marine diatom was recently assembled and annotated, and thus my thesis has involved using this genome as a tool to explore the species and investigate its resting stage survival. In paper I, the use of ancient diatom DNA (i.e. DNA obtained from revived diatom resting stages) in research was reviewed, with particular attention to S. marinoi. While much insight has already been gained using this resource, developments in several fields have led to exciting prospects for future research. In papers II and III, I compared gene expression between vegetative cells of S. marinoi, and resting stages induced by exposure to darkness, anoxia, and nitrogen starvation. After re-exposure to nitrate, the resting stages’ gene expression was measured using RNA sequencing over the course of six months. In paper II, I performed a differential expression analysis to determine which processes were active in this ‘dormant’ life stage. Much of the resting stages’ central metabolism has undergone shifts in expression, and genes involved in protein synthesis were upregulated throughout the resting stage. In paper III, I examined the RNA sequencing results from the perspective of allelic expression bias, and identified a handful of genes showing significant shifts in expression bias between alleles between vegetative and resting cells. Of these, I noted several that formed complete pathways related to the formation of diatoms’ silica cell walls. Lastly, in paper IV, I developed a bioinformatic tool – Bamboozle – to identify novel, intraspecific genomic barcoding loci, capable of tracking the relative abundance of multiple strains of S. marinoi in co-culture over time. This tool was initially applied to 54 strains of S. marinoi, revealing loci that enabled subsequent tracking of strains during an artificial evolution experiment. Bamboozle has been further developed to accommodate haploid organisms, and was used to identify intraspecific barcoding loci in the model green alga Chlamydomonas reinhardtii. The results of this thesis provide insights and highlight further questions regarding diatom resting stages, as well as providing a novel tool for studying these fascinating phytoplankton. Application of additional omics methods to diatom resting stages in future, and testing of Bamboozle on natural diatom populations, should both lead to further understanding of this taxon.
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| 10. |
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| 11. |
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| 12. |
- Töpel, Mats H., 1973, et al.
(författare)
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Complete Genome Sequence of Novel Sulfitobacter pseudonitzschiae Strain SMR1, Isolated from a Culture of the Marine Diatom Skeletonema marinoi.
- 2019
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Ingår i: Journal of Genomics. - : Ivyspring International Publisher. - 1839-9940. ; 7, s. 7-10
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Tidskriftsartikel (refereegranskat)abstract
- When studying diatoms, an important consideration is the role of associated bacteria in the diatom-microbiome holobiont. To that end, bacteria isolated from a culture of Skeletonema marinoi strain R05AC were sequenced, one of which being bacterial strain SMR1, presented here. The genome consists of a circular chromosome and seven circular plasmids, totalling 5,121,602 bp. After phylotaxonomic analysis and 16S rRNA sequence comparison, we place this strain in the taxon Sulfitobacter pseudonitzschiae on account of similarity to the type strain. The annotated genome suggests similar interactions between strain SMR1 and its host diatom as have been shown previously in diatom-associated Sulfitobacter, for example bacterial production of growth hormone for its host, and breakdown of diatom-derived DMSP by Sulfitobacter for use as a sulfur source.
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| 13. |
- Töpel, Mats H., 1973, et al.
(författare)
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Complete Genome Sequence of the Diatom-Associated Bacterium Sphingorhabdus sp. Strain SMR4y
- 2019
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Ingår i: Microbiology Resource Announcements. - : American Society for Microbiology. - 2576-098X. ; 8:29
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Tidskriftsartikel (refereegranskat)abstract
- The bacterial strain SMR4y belongs to the diverse microbiome of the marine diatom Skeletonema marinoi strain R05AC. After assembly of its genome, presented here, and subsequent analyses, we placed it in the genus Sphingorhabdus. This strain has a 3,479,724-bp circular chromosome (with 3,340 coding sequences) and no known plasmids.
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| 14. |
- Töpel, Mats H., 1973, et al.
(författare)
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Genome sequence of arenibacter algicola strain SMS7, found in association with the marine diatom skeletonema marinoi
- 2019
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Ingår i: Microbiology Resource Announcements. - 2576-098X. ; 8
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Tidskriftsartikel (refereegranskat)abstract
- Copyright © 2019 Töpel et al. Arenibacter algicola strain SMS7 was isolated from a culture of the marine diatom Skeletonema marinoi strain ST54, sampled from top-layer sediments in Kosterfjord, Sweden. Here, we present its 5,857,781-bp genome, consisting of a circular chromosome and one circular plasmid, in all containing 4,932 coding sequences.
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| 15. |
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| 16. |
- Töpel, Mats H., 1973, et al.
(författare)
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Whole Genome Sequence of Marinobacter salarius Strain SMR5, Shown to Promote Growth in its Diatom Host.
- 2019
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Ingår i: Journal of Genomics. - : Ivyspring International Publisher. - 1839-9940. ; 7, s. 60-63
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Tidskriftsartikel (refereegranskat)abstract
- Attempts to obtain axenic cultures of the marine diatom Skeletonema marinoi often result in poor growth, indicating the importance of the microbiome to the growth of its host. In order to identify the precise roles played by these associated bacteria, individual strains were isolated, cultured and sequenced. We report the genome of one such strain - SMR5, isolated from a culture of S. marinoi strain R05AC sampled from top layer sediments of the Swedish west coast. Its genome of 4,630,160 bp consists of a circular chromosome and one circular plasmid, and 4,263 CDSs were inferred in the annotation. Comparison of 16S rRNA sequences and other markers, along with phylotaxonomic analysis, leads us to place strain SMR5 in the taxon Marinobacter salarius. Pathway analysis and previous experimental work suggest that this strain may produce a growth factor, as well as improve iron availability for its host via siderophores.
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| 17. |
- Töpel, Mats H., 1973, et al.
(författare)
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Whole-Genome Sequence of the Novel Antarctobacter heliothermus Strain SMS3, Found in Association with the Marine Diatom Skeletonema marinoi.
- 2018
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Ingår i: Journal of Genomics. - : Ivyspring International Publisher. - 1839-9940. ; 6, s. 113-116
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Tidskriftsartikel (refereegranskat)abstract
- As part of an ongoing investigation into the microbiome of the marine diatom Skeletonema marinoi, the bacterial strain SMS3 was isolated from a culture of S. marinoi strain ST54, which had been propagated from a sample of top layer marine sediments taken from the Swedish west coast. We present here the sequenced genome of this bacterium, which we place in the taxon Antarctobacter heliothermus, based on a phylotaxonomic analysis and its high 16S rRNA sequence similarity to the A. heliothermus type strain DSM 11445T. Its 5,331,190 bp genome consists of a circular chromosome and three circular plasmids, and contains 5,019 CDSs. Strain SMS3 contains a phosphatidylcholine synthase gene, as well as genes involved in DMSP degradation, both of which imply a potential symbiotic relationship with its host.
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