Lozupone CA, Knight R. Global patterns in bacterial diversity. Proc Natl Acad Sci USA. 2007;104:11436–40.
Google Scholar
Logares R, Bråte J, Bertilsson S, Clasen JL, Shalchian-Tabrizi K, Rengefors K. Infrequent marine-freshwater transitions in the microbial world. Trends Microbiol. 2009;17:414–22.
Google Scholar
Cavalier-Smith T. Megaphylogeny, cell body plans, adaptive zones: causes and timing of eukaryote basal radiations. J Eukaryot Microbiol. 2009;56:26–33.
Google Scholar
Nakov T, Beaulieu JM, Alverson AJ. Diatoms diversify and turn over faster in freshwater than marine environments. Evolution. 2019;73:2497–511.
Google Scholar
Dittami SM, Heesch S, Olsen JL, Collén J. Transitions between marine and freshwater environments provide new clues about the origins of multicellular plants and algae. J Phycol. 2017;53:731–45.
Google Scholar
Dickson B, Yashayaev I, Meincke J, Turrell B, Dye S, Holfort J. Rapid freshening of the deep North Atlantic Ocean over the past four decades. Nature. 2002;416:832–7.
Google Scholar
Aretxabaleta AL, Smith KW, Kalra TS. Regime changes in global sea surface salinity trend. J Mar Sci Eng. 2017;5:57.
López-Maury L, Marguerat S, Bähler J. Tuning gene expression to changing environments: from rapid responses to evolutionary adaptation. Nat Rev Genet. 2008;9:583–93.
Google Scholar
Björck S. A review of the history of the Baltic Sea, 13.0-8.0 ka BP. Quat Int. 1995;27:19–40.
Krauss W. Baltic sea circulation. In: Steele JH, editor. Encyclopedia of ocean sciences. Oxford: Academic Press; 2001. p. 236–44.
Telesh I, Schubert H, Skarlato S. Life in the salinity gradient: discovering mechanisms behind a new biodiversity pattern. Estuar Coast Shelf Sci. 2013;135:317–27.
Johannesson K, Le Moan A, Perini S, André C. A Darwinian laboratory of multiple contact zones. Trends Ecol Evol. 2020;35:1021–36.
Google Scholar
Olofsson M, Hagan JG, Karlson B, Gamfeldt L. Large seasonal and spatial variation in nano- and microphytoplankton diversity along a Baltic Sea-North Sea salinity gradient. Sci Rep. 2020;10:17666.
Google Scholar
Sjöqvist C, Godhe A, Jonsson PR, Sundqvist L, Kremp A. Local adaptation and oceanographic connectivity patterns explain genetic differentiation of a marine diatom across the North Sea-Baltic Sea salinity gradient. Mol Ecol. 2015;24:2871–85.
Google Scholar
Jochem F. Distribution and importance of autotrophic ultraplankton in a boreal inshore area (Kiel Bight, Western Baltic). Mar Ecol Prog Ser. 1989;53:153–68.
Wasmund N, Nausch G, Gerth M, Busch S, Burmeister C, Hansen R, et al. Extension of the growing season of phytoplankton in the western Baltic Sea in response to climate change. Mar Ecol Prog Ser. 2019;622:1–16.
Google Scholar
van Wirdum F, Andrén E, Wienholz D, Kotthoff U, Moros M, Fanget A-S, et al. Middle to Late Holocene variations in salinity and primary productivity in the Central Baltic Sea: a multiproxy study from the Landsort Deep. Front Mar Sci. 2019;6:51.
Alverson AJ. Timing marine–freshwater transitions in the diatom order Thalassiosirales. Paleobiology. 2014;40:91–101.
Nakov T, Beaulieu JM, Alverson AJ. Insights into global planktonic diatom diversity: the importance of comparisons between phylogenetically equivalent units that account for time. ISME J. 2018;12:2807–10.
Google Scholar
Kremp A, Godhe A, Egardt J, Dupont S, Suikkanen S, Casabianca S, et al. Intraspecific variability in the response of bloom-forming marine microalgae to changed climate conditions. Ecol Evol. 2012;2:1195–207.
Google Scholar
Olofsson M, Kourtchenko O, Zetsche E-M, Marchant HK, Whitehouse MJ, Godhe A, et al. High single-cell diversity in carbon and nitrogen assimilations by a chain-forming diatom across a century. Environ Microbiol. 2019;21:142–51.
Google Scholar
Olofsson M, Almén A-K, Jaatinen K, Scheinin M. Temporal escape – adaptation to eutrophication by Skeletonema marinoi. FEMS Microbiol Lett. 2022;fnac011. https://pubmed.ncbi.nlm.nih.gov/35137038/.
Godhe A, Härnström K. Linking the planktonic and benthic habitat: genetic structure of the marine diatom Skeletonema marinoi. Mol Ecol. 2010;19:4478–90.
Google Scholar
Dobin A, Gingeras TR. Mapping RNA-seq reads with STAR. Curr Protoc Bioinform. 2015;51:11.14.1–11.14.19.
Anders S, Pyl PT, Huber W. HTSeq-a Python framework to work with high-throughput sequencing data. Bioinformatics. 2015;31:166–9.
Google Scholar
Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol. 1990;215:403–10.
Google Scholar
Jones P, Binns D, Chang H-Y, Fraser M, Li W, McAnulla C, et al. InterProScan 5: genome-scale protein function classification. Bioinformatics. 2014;30:1236–40.
Google Scholar
Aramaki T, Blanc-Mathieu R, Endo H, Ohkubo K, Kanehisa M, Goto S, et al. KofamKOALA: KEGG Ortholog assignment based on profile HMM and adaptive score threshold. Bioinformatics. 2020;36:2251–2.
Google Scholar
Emms DM, Kelly S. OrthoFinder: phylogenetic orthology inference for comparative genomics. Genome Biol. 2019;20:238.
Google Scholar
Almagro Armenteros JJ, Salvatore M, Emanuelsson O, Winther O, von Heijne G, Elofsson A, et al. Detecting sequence signals in targeting peptides using deep learning. Life Sci Alliance. 2019;2:e201900429.
Google Scholar
Gruber A, Rocap G, Kroth PG, Armbrust EV, Mock T. Plastid proteome prediction for diatoms and other algae with secondary plastids of the red lineage. Plant J. 2015;81:519–28.
Google Scholar
Bendtsen JD, Nielsen H, von Heijne G, Brunak S. Improved prediction of signal peptides: SignalP 3.0. J Mol Biol. 2004;340:783–95.
Google Scholar
Gschloessl B, Guermeur Y, Cock JM. HECTAR: a method to predict subcellular targeting in heterokonts. BMC Bioinforma. 2008;9:393.
Claros MG. MitoProt, a Macintosh application for studying mitochondrial proteins. Comput Appl Biosci. 1995;11:441–7.
Google Scholar
Robinson MD, McCarthy DJ, Smyth GK. edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics. 2010;26:139–40.
Google Scholar
Van den Berge K, Soneson C, Robinson MD, Clement L. stageR: a general stage-wise method for controlling the gene-level false discovery rate in differential expression and differential transcript usage. Genome Biol. 2017;18:151.
Google Scholar
Heller R, Manduchi E, Grant GR, Ewens WJ. A flexible two-stage procedure for identifying gene sets that are differentially expressed. Bioinformatics. 2009;25:1019–25.
Google Scholar
Alexa A, and Rahnenfuhrer J. topGO: Enrichment Analysis for GeneOntology. R package version 2.44.0. 2021. https://bioconductor.org/packages/release/bioc/html/topGO.html.
Wu D, Smyth GK. Camera: a competitive gene set test accounting for inter-gene correlation. Nucleic Acids Res. 2012;40:e133.
Google Scholar
Supek F, Bošnjak M, Škunca N, Šmuc T. REVIGO summarizes and visualizes long lists of gene ontology terms. PLoS ONE. 2011;6:e21800.
Google Scholar
Bussard A, Corre E, Hubas C, Duvernois-Berthet E, Le Corguillé G, Jourdren L, et al. Physiological adjustments and transcriptome reprogramming are involved in the acclimation to salinity gradients in diatoms. Environ Microbiol. 2017;19:909–25.
Google Scholar
Matthijs M, Fabris M, Obata T, Foubert I, Franco-Zorrilla JM, Solano R, et al. The transcription factor bZIP14 regulates the TCA cycle in the diatom Phaeodactylum tricornutum. EMBO J. 2017;36:1559–76.
Google Scholar
Kong L, Price NM. Transcriptomes of an oceanic diatom reveal the initial and final stages of acclimation to copper deficiency. Environ Microbiol. 2021;24:951–66.
Amato A, Sabatino V, Nylund GM, Bergkvist J, Basu S, Andersson MX, et al. Grazer-induced transcriptomic and metabolomic response of the chain-forming diatom Skeletonema marinoi. ISME J. 2018;12:1594–604.
Google Scholar
Maumus F, Allen AE, Mhiri C, Hu H, Jabbari K, Vardi A, et al. Potential impact of stress activated retrotransposons on genome evolution in a marine diatom. BMC Genomics. 2009;10:624.
Google Scholar
Pargana A, Musacchia F, Sanges R, Russo MT, Ferrante MI, Bowler C, et al. Intraspecific diversity in the cold stress response of transposable elements in the diatom Leptocylindrus aporus. Genes. 2019;11:9.
Google Scholar
Smith SR, Dupont CL, McCarthy JK, Broddrick JT, Oborník M, Horák A, et al. Evolution and regulation of nitrogen flux through compartmentalized metabolic networks in a marine diatom. Nat Commun. 2019;10:4552.
Google Scholar
Kageyama H, Tanaka Y, Shibata A, Waditee-Sirisattha R, Takabe T. Dimethylsulfoniopropionate biosynthesis in a diatom Thalassiosira pseudonana: Identification of a gene encoding MTHB-methyltransferase. Arch Biochem Biophys. 2018;645:100–6.
Google Scholar
Nakov T, Judy KJ, Downey KM, Ruck EC, Alverson AJ. Transcriptional response of osmolyte synthetic pathways and membrane transporters in a euryhaline diatom during long-term acclimation to a salinity gradient. J Phycol. 2020;56:1712–28.
Google Scholar
Kageyama H, Tanaka Y, Takabe T. Biosynthetic pathways of glycinebetaine in Thalassiosira pseudonana; functional characterization of enzyme catalyzing three-step methylation of glycine. Plant Physiol Biochem. 2018;127:248–55.
Google Scholar
Krell A, Funck D, Plettner I, John U, Dieckmann G. Regulation of proline metabolism under salt stress in the psychrophilic diatom Fragilariopsis cylindrus (Bacillariophyceae). J Phycol. 2007;43:753–62.
Google Scholar
Latta LC, Weider LJ, Colbourne JK, Pfrender ME. The evolution of salinity tolerance in Daphnia: a functional genomics approach. Ecol Lett. 2012;15:794–802.
Google Scholar
Ferrante MI, Entrambasaguas L, Johansson M, Töpel M, Kremp A, Montresor M, et al. Exploring molecular signs of sex in the marine diatom Skeletonema marinoi. Genes. 2019;10:494.
Kroth PG. The biodiversity of carbon assimilation. J Plant Physiol. 2015;172:76–81.
Google Scholar
Obata T, Fernie AR, Nunes-Nesi A. The central carbon and energy metabolism of marine diatoms. Metabolites. 2013;3:325–46.
Google Scholar
Smith SR, Abbriano RM, Hildebrand M. Comparative analysis of diatom genomes reveals substantial differences in the organization of carbon partitioning pathways. Algal Res. 2012;1:2–16.
Google Scholar
Kroth PG, Chiovitti A, Gruber A, Martin-Jezequel V, Mock T, Parker MS, et al. A model for carbohydrate metabolism in the diatom Phaeodactylum tricornutum deduced from comparative whole genome analysis. PLoS ONE. 2008;3:e1426.
Google Scholar
Furumoto T, Yamaguchi T, Ohshima-Ichie Y, Nakamura M, Tsuchida-Iwata Y, Shimamura M, et al. A plastidial sodium-dependent pyruvate transporter. Nature. 2011;476:472–5.
Google Scholar
Chen G-Q, Jiang Y, Chen F. Salt-induced alterations in lipid composition of diatom Nitzschia laevis (Bacillariophyceae) under heterotrophic culture condition. J Phycol. 2008;44:1309–14.
Google Scholar
Sayanova O, Mimouni V, Ulmann L, Morant-Manceau A, Pasquet V, Schoefs B, et al. Modulation of lipid biosynthesis by stress in diatoms. Philos Trans R Soc Lond B Biol Sci. 2017;372:20160407.
Google Scholar
Vårum KM, Myklestad S. Effects of light, salinity and nutrient limitation on the production of β-1,3-d-glucan and exo-d-glucanase activity in Skeletonema costatum (Grev.) Cleve. J Exp Mar Bio Ecol. 1984;83:13–25.
Radchenko IG, Il’yash LV. Growth and photosynthetic activity of diatom Thalassiosira weissflogii at decreasing salinity. Biol Bull. 2006;33:242–7.
Google Scholar
Adams C, Bugbee B. Enhancing lipid production of the marine diatom Chaetoceros gracilis: synergistic interactions of sodium chloride and silicon. J Appl Phycol. 2014;26:1351–7.
Google Scholar
Shetty P, Gitau MM, Maróti G. Salinity stress responses and adaptation mechanisms in eukaryotic green microalgae. Cells. 2019;8:1657.
Jacob A, Kirst GO, Wiencke C, Lehmann H. Physiological responses of the Antarctic green alga Prasiola crispa ssp. antarctica to salinity stress. J Plant Physiol. 1991;139:57–62.
Google Scholar
Bazzani E, Lauritano C, Mangoni O, Bolinesi F, Saggiomo M. Chlamydomonas responses to salinity stress and possible biotechnological exploitation. J Mar Sci Eng. 2021;9:1242.
Cheng R-L, Feng J, Zhang B-X, Huang Y, Cheng J, Zhang C-X. Transcriptome and gene expression analysis of an oleaginous diatom under different salinity conditions. Bioenergy Res. 2014;7:192–205.
Google Scholar
Stock W, Blommaert L, Daveloose I, Vyverman W, Sabbe K. Assessing the suitability of imaging-PAM fluorometry for monitoring growth of benthic diatoms. J Exp Mar Bio Ecol. 2019;513:35–41.
Reichmann D, Voth W, Jakob U. Maintaining a healthy proteome during oxidative stress. Mol Cell. 2018;69:203–13.
Google Scholar
Latowski D, Kuczyńska P, Strzałka K. Xanthophyll cycle-a mechanism protecting plants against oxidative stress. Redox Rep. 2011;16:78–90.
Google Scholar
Chen D, Shao Q, Yin L, Younis A, Zheng B. Polyamine function in plants: metabolism, regulation on development, and roles in abiotic stress responses. Front Plant Sci. 2018;9:1945.
Google Scholar
Liu Q, Nishibori N, Imai I, Hollibaugh JT. Response of polyamine pools in marine phytoplankton to nutrient limitation and variation in temperature and salinity. Mar Ecol Prog Ser. 2016;544:93–105.
Google Scholar
Scoccianti V, Penna A, Penna N, Magnani M. Effect of heat stress on polyamine content and protein pattern in Skeletonema costatum. Mar Biol. 1995;121:549–54.
Google Scholar
Alscher RG, Erturk N, Heath LS. Role of superoxide dismutases (SODs) in controlling oxidative stress in plants. J Exp Bot. 2002;53:1331–41.
Google Scholar
Kumar M, Kumari P, Gupta V, Reddy CRK, Jha B. Biochemical responses of red alga Gracilaria corticata (Gracilariales, Rhodophyta) to salinity induced oxidative stress. J Exp Mar Bio Ecol. 2010;391:27–34.
Google Scholar
von Alvensleben N, Magnusson M, Heimann K. Salinity tolerance of four freshwater microalgal species and the effects of salinity and nutrient limitation on biochemical profiles. J Appl Phycol. 2016;28:861–76.
Rijstenbil JW, Wijnholds JA, Sinke JJ. Implications of salinity fluctuation for growth and nitrogen metabolism of the marine diatom Ditylum brightwellii in comparison with Skeletonema costatum. Mar Biol. 1989;101:131–41.
Google Scholar
Mansour MMF. Nitrogen containing compounds and adaptation of plants to salinity stress. Biol Plant. 2000;43:491–500.
Google Scholar
Garcia N, Lopez Elias JA, Miranda A, Martinez Porchas M, Huerta N, Garcia A. Effect of salinity on growth and chemical composition of the diatom Thalassiosira weissflogii at three culture phases. Lat Am J Aquat Res. 2012;40:435–40.
Van den Berge K, Hembach KM, Soneson C, Tiberi S, Clement L, Love MI, et al. RNA sequencing data: Hitchhiker’s guide to expression analysis. Annu Rev Biomed Data Sci. 2019;2:139–73.
Kremp A. Effects of cyst resuspension on germination and seeding of two bloom-forming dinoflagellates in the Baltic Sea. Mar Ecol Prog Ser. 2001;216:57–66.
Juneau P, Barnett A, Méléder V, Dupuy C, Lavaud J. Combined effect of high light and high salinity on the regulation of photosynthesis in three diatom species belonging to the main growth forms of intertidal flat inhabiting microphytobenthos. J Exp Mar Bio Ecol. 2015;463:95–104.
Google Scholar
Vargas C, Argandoña M, Reina-Bueno M, Rodríguez-Moya J, Fernández-Aunión C, Nieto JJ. Unravelling the adaptation responses to osmotic and temperature stress in Chromohalobacter salexigens, a bacterium with broad salinity tolerance. Saline Syst. 2008;4:14.
Google Scholar
Khmelenina VN, Sakharovskii VG, Reshetnikov AS, Trotsenko YA. Synthesis of osmoprotectants by halophilic and alkaliphilic methanotrophs. Microbiology. 2000;69:381–6.
Google Scholar
Fenizia S, Thume K, Wirgenings M, Pohnert G. Ectoine from bacterial and algal origin is a compatible solute in microalgae. Mar Drugs. 2020;18:42.
Google Scholar
Amin SA, Hmelo LR, van Tol HM, Durham BP, Carlson LT, Heal KR, et al. Interaction and signalling between a cosmopolitan phytoplankton and associated bacteria. Nature. 2015;522:98–101.
Google Scholar
Krell A, Beszteri B, Dieckmann G, Glöckner G, Valentin K, Mock T. A new class of ice-binding proteins discovered in a salt-stress-induced cDNA library of the psychrophilic diatom Fragilariopsis cylindrus (Bacillariophyceae). Eur J Phycol. 2008;43:423–33.
Google Scholar
Helliwell KE, Kleiner FH, Hardstaff H, Chrachri A, Gaikwad T, Salmon D, et al. Spatiotemporal patterns of intracellular Ca2+ signalling govern hypo-osmotic stress resilience in marine diatoms. N Phytol. 2021;230:155–70.
Google Scholar
Kaczmarska I, Poulíčková A, Sato S, Edlund MB, Idei M, Watanabe T, et al. Proposals for a terminology for diatom sexual reproduction, auxospores and resting stages. Diatom Res. 2013;28:263–94.
Godhe A, Kremp A, Montresor M. Genetic and microscopic evidence for sexual reproduction in the centric diatom Skeletonema marinoi. Protist. 2014;165:401–16.
Google Scholar
Annunziata R, Mele BH, Marotta P, Volpe M, Entrambasaguas L, Mager S, et al. Trade-off between sex and growth in diatoms: Molecular mechanisms and demographic implications. Sci Adv. 2022;8:eabj9466.
Google Scholar
Ajani PA, Petrou K, Larsson ME, Nielsen DA, Burke J, Murray SA. Phenotypic trait variability as an indication of adaptive capacity in a cosmopolitan marine diatom. Environ Microbiol. 2021;23:207–23.
Google Scholar
Sjöqvist CO, Kremp A. Genetic diversity affects ecological performance and stress response of marine diatom populations. ISME J. 2016;10:2755–66.
Google Scholar
Godhe A, Rynearson T. The role of intraspecific variation in the ecological and evolutionary success of diatoms in changing environments. Philos Trans R Soc Lond B Biol Sci. 2017;372:20160399.
Google Scholar
Bulankova P, Sekulić M, Jallet D, Nef C, van Oosterhout C, Delmont TO, et al. Mitotic recombination between homologous chromosomes drives genomic diversity in diatoms. Curr Biol. 2021;31:3221–32. e9
Google Scholar
Pinseel E, Janssens SB, Verleyen E, Vanormelingen P, Kohler TJ, Biersma EM, et al. Global radiation in a rare biosphere soil diatom. Nat Commun. 2020;11:2382.
Google Scholar
Savchuk OP. Large-scale nutrient dynamics in the Baltic sea, 1970–2016. Front Mar Sci. 2018;5:95.
Gomez-Mestre I, Jovani R. A heuristic model on the role of plasticity in adaptive evolution: plasticity increases adaptation, population viability and genetic variation. Proc Biol Sci. 2013;280:20131869.
Google Scholar
Lambert BS, Groussman RD, Schatz MJ, Coesel SN, Durham BP, Alverson AJ, et al. The dynamic trophic architecture of open-ocean protist communities revealed through machine-guided metatranscriptomics. Proc Natl Acad Sci USA. 2022;119:e2100916119.
Harrison PF, Pattison AD, Powell DR, Beilharz TH. Topconfects: a package for confident effect sizes in differential expression analysis provides a more biologically useful ranked gene list. Genome Biol. 2019;20:67.
Google Scholar
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