Gust Bilcke

Diatom genomics


  1. Bilcke, G., & Kamakura, S. (2023). Scaling the invisible wall: Molecular acclimation of a salinity‐tolerant diatom to freshwater. Molecular Ecology, 32(11), 2692–2694.
    In aquatic ecosystems, marine and freshwater environments are separated by steep salinity gradients. The osmotic stress induced by this 'invisible wall' forms an insurmountable barrier for many aquatic lifeforms, including bacteria, algae and animals. Because the osmotic differences when transiting a salinity divide are so hard to overcome, most species have adapted exclusively to a marine or a freshwater lifestyle. A major consequence of this physiological specialization into marine and freshwater organisms is that transitions are relatively rare, impeding regular contact and colonization. While some animals use specialized organs or behaviour to cope with unfavourable salinity levels, unicellular algae such as diatoms are completely dependent on cellular mechanisms to mitigate salinity stress. In this issue of Molecular Ecology, Downey and colleagues investigate the transcriptomic response of a salinity-tolerant diatom to a shock treatment with freshwater (Molecular Ecology, 2023). Through frequent sampling and integration of existing RNA sequencing data, a fine-grained model of the acclimation to hypo-osmotic stress emerges. Deciphering the pathways that drive the acute and long-term acclimation to freshwater has major implications for diatom ecology, diversification and resilience to global change.
  2. Bilcke, G., Immacolata Ferrante, M., Montresor, M., De Decker, S., De Veylder, L., & Vyverman, W. (2022). Life cycle regulation. In A. Falciatore & T. Mock (Eds.), The molecular life of diatoms (pp. 205–228).
    Diatom life cycles are unusual among microalgae by being diplontic with a long diploid vegetative phase and a short-lived haploid phase (gametes). Life cycle progression in diatoms is controlled by the cell size reduction-restitution cycle and is intimately linked to their peculiar mode of cell division and siliceous cell wall. Sexual reproduction is primarily cell-size dependent although environmental cues may be needed to trigger gametogenesis in centric diatoms. Although population genetic data suggest sexual reproduction to occur in most species and meiotic genes are widely conserved among diatoms, sexual events are seldom observed in nature. Recent laboratory studies have started to unveil complex pheromone signaling cascades during sexual reproduction in pennate diatoms. Likewise, significant progress has been made in the identification of mating type determination mechanisms in heterothallic species, where several conserved, but as yet functionally uncharacterized, genes involved in sexual reproduction have been identified. While many aspects of diatom life cycle regulation remain to be discovered, the recent development of new model species allowing genetic modification and the rapidly increasing genomic and transcriptomic resources hold much promise for advanced understanding of this key process.
  3. Bulánková, P., Bilcke, G., Vyverman, W., & De Veylder, L. (2022). Cellular hallmarks and regulation of the diatom cell cycle. In A. Falciatore, & T. Mock (Eds.), The molecular life of diatoms (pp. 229–263).
    Diatoms are one of the oldest experimental models for studying the mitotic cell cycle, with microscopic descriptions of cell division dating back to the nineteenth century. In recent years, the advent of genetic and genomic tools has improved our understanding of the mechanisms driving cell cycle progression in diatoms. Diatom species thrive in almost all aquatic habitats and several of them form blooms under specific environmental conditions. In order to optimize their growth rate to the prevailing conditions, species-specific cell cycle checkpoints have evolved that integrate cues such as light, nutrients, and sex pheromones. This chapter reviews the structural events occurring during each cell cycle stage, focusing on organelle division, the unique mitotic spindle of diatoms, and the different steps of mitosis. The conservation of the core cell cycle components in diatom genomes is briefly explored. External conditions that activate the G1/S and G2/M checkpoints of the interphase are discussed, with special attention to the light-dependent G1 phase checkpoint in P. tricornutum, which is currently the best characterized regulatory cell cycle pathway in diatoms. The chapter concludes with an outlook on how novel technologies can contribute to solving the specificities of the diatom cell cycle at a molecular level.
  4. Bilcke, G., Osuna, C., Santana Silva, M., Poulsen, N., D’hondt, S., Bulánková, P., … Vandepoele, K. (2021). Diurnal transcript profiling of the diatom Seminavis robusta reveals adaptations to a benthic lifestyle. PLANT JOURNAL, 107(1), 315–336.
    Coastal regions contribute an estimated 20% of annual gross primary production in the oceans, despite occupying only 0.03% of their surface area. Diatoms frequently dominate coastal sediments, where they experience large variations in light regime resulting from the interplay of diurnal and tidal cycles. Here, we report on an extensive diurnal transcript profiling experiment of the motile benthic diatom Seminavis robusta. Nearly 90% (23 328) of expressed protein-coding genes and 66.9% (1124) of expressed long intergenic non-coding RNAs showed significant expression oscillations and are predominantly phasing at night with a periodicity of 24 h. Phylostratigraphic analysis found that rhythmic genes are enriched in highly conserved genes, while diatom-specific genes are predominantly associated with midnight expression. Integration of genetic and physiological cell cycle markers with silica depletion data revealed potential new silica cell wall-associated gene families specific to diatoms. Additionally, we observed 1752 genes with a remarkable semidiurnal (12-h) periodicity, while the expansion of putative circadian transcription factors may reflect adaptations to cope with highly unpredictable external conditions. Taken together, our results provide new insights into the adaptations of diatoms to the benthic environment and serve as a valuable resource for the study of diurnal regulation in photosynthetic eukaryotes.
  5. Bilcke, G., Van den Berge, K., De Decker, S., Bonneure, E., Poulsen, N., Bulánková, P., … Vyverman, W. (2021). Mating type specific transcriptomic response to sex inducing pheromone in the pennate diatom Seminavis robusta. ISME JOURNAL, 15, 562–576.
    Sexual reproduction is a fundamental phase in the life cycle of most diatoms. Despite its role as a source of genetic variation, it is rarely reported in natural circumstances and its molecular foundations remain largely unknown. Here, we integrate independent transcriptomic datasets to prioritize genes responding to sex inducing pheromones (SIPs) in the pennate diatomSeminavis robusta. We observe marked gene expression changes associated with SIP treatment in both mating types, including an inhibition of S phase progression, chloroplast division, mitosis, and cell wall formation. Meanwhile, meiotic genes are upregulated in response to SIP, including a sexually induced diatom specific cyclin. Our data further suggest an important role for reactive oxygen species, energy metabolism, and cGMP signaling during the early stages of sexual reproduction. In addition, we identify several genes with a mating type specific response to SIP, and link their expression pattern with physiological specialization, such as the production of the attraction pheromone diproline in mating type - (MT-) and mate-searching behavior in mating type + (MT+). Combined, our results provide a model for early sexual reproduction in pennate diatoms and significantly expand the suite of target genes to detect sexual reproduction events in natural diatom populations.
  6. Bilcke, G. (2021). Life history regulation of the benthic pennate diatom Seminavis robusta : a transcriptomic, comparative genomic and physiological study. Ghent University. Faculty of Sciences, Ghent, Belgium.
  7. Bilcke, G., Van Craenenbroeck, L., Castagna Mourão e Lima, A., Osuna, C., Vandepoele, K., Sabbe, K., … Vyverman, W. (2021). Light intensity and spectral composition drive reproductive success in the marine benthic diatom Seminavis robusta. SCIENTIFIC REPORTS, 11(1).
    The properties of incident light play a crucial role in the mating process of diatoms, a group of ecologically important microalgae. While species-specific requirements for light intensity and photoperiod have been observed in several diatom species, little is known about the light spectrum that allows sexual reproduction. Here, we study the effects of spectral properties and light intensity on the initiation and progression of sexual reproduction in the model benthic diatom Seminavis robusta. We found that distinct stages of the mating process have different requirements for light. Vigorous mating pair formation occurred under a broad range of light intensities, ranging from 10 to 81 mu E m(-2) s(-1), while gametogenesis and subsequent stages were strongly affected by moderate light intensities of 27 mu E m(-2) s(-1) and up. In addition, light of blue or blue-green wavelengths was required for the formation of mating pairs. Combining flow cytometric analysis with expression profiling of the diatom-specific cyclin dsCyc2 suggests that progression through a blue light-dependent checkpoint in the G1 cell cycle phase is essential for induction of sexual reproduction. Taken together, we expand the current model of mating in benthic pennate diatoms, which relies on the interplay between light, cell cycle and sex pheromone signaling.
  8. Osuna Cruz, C. M., Bilcke, G., Vancaester, E., De Decker, S., Bones, A. M., Winge, P., … Vandepoele, K. (2020). The Seminavis robusta genome provides insights into the evolutionary adaptations of benthic diatoms (vol 11, 3320, 2020).
  9. Stock genannt Schroer, F., Bilcke, G., De Decker, S., Osuna, C., Van den Berge, K., Vancaester, E., … Vyverman, W. (2020). Distinctive growth and transcriptional changes of the diatom Seminavis robusta in response to quorum sensing related compounds. FRONTIERS IN MICROBIOLOGY, 11.
    In aquatic habitats, diatoms are frequently found in association with Proteobacteria, many members of which employ cell-to-cell communication via N-acyl homoserine lactones (AHLs). It has been suggested that diatoms could distinguish between beneficial and algicidal bacteria in their surroundings by sensing AHLs. Although some microalgae can interfere with AHL signaling, e.g., by releasing AHL mimics or degrading them, molecular responses to AHLs in microalgae are still unclear. Therefore, we tested the effects of short-chained AHLs, i.e., N-hexanoyl homoserine lactone (C6-HSL), N-3-hydroxyhexanoyl homoserine lactone (OH-C6-HSL), and N-3-oxohexanoyl homoserine lactone (oxo-C6-HSL) and long-chained AHLs, i.e., N-tetradecanoyl homoserine lactone (C14-HSL), N-3-hydroxytetradecanoyl homoserine lactone (OH-C14-HSL), and N-3-oxotetradecanoyl homoserine lactone (oxo-C14-HSL), on growth of the benthic diatom Seminavis robusta. All tested short-chained AHLs did not affect diatom growth, while long-chained AHLs promoted (C14-HSL) or inhibited (OH-C14-HSL and oxo-C14-HSL) growth. To investigate the physiological effects of these long-chained AHLs in more detail, an RNA-seq experiment was performed during which S. robusta was treated with the growth-promoting C14-HSL and the growth-inhibiting oxo-C14-HSL. One tetramic acid was also tested (TA14), a structural rearrangement product of oxo-C14-HSL, which also induced growth inhibition in S. robusta. After 3 days of treatment, analysis revealed that 3,410 genes were differentially expressed in response to at least one of the compounds. In the treatment with the growth-promoting C14-HSL many genes involved in intracellular signaling were upregulated. On the other hand, exposure to growth-inhibiting oxo-C14-HSL and TA14 triggered a switch in lipid metabolism towards increased fatty acid degradation. In addition, oxo-C14-HSL led to downregulation of cell cycle genes, which is in agreement with the stagnation of cell growth in this treatment. Combined, our results indicate that bacterial signaling molecules with high structural similarity induce contrasting physiological responses in S. robusta.
  10. Osuna, C., Bilcke, G., Vancaester, E., De Decker, S., Bones, A. M., Winge, P., … Vandepoele, K. (2020). The Seminavis robusta genome provides insights into the evolutionary adaptations of benthic diatoms. NATURE COMMUNICATIONS, 11(1).
    Benthic diatoms are the main primary producers in shallow freshwater and coastal environments, fulfilling important ecological functions such as nutrient cycling and sediment stabilization. However, little is known about their evolutionary adaptations to these highly structured but heterogeneous environments. Here, we report a reference genome for the marine biofilm-forming diatom Seminavis robusta, showing that gene family expansions are responsible for a quarter of all 36,254 protein-coding genes. Tandem duplications play a key role in extending the repertoire of specific gene functions, including light and oxygen sensing, which are probably central for its adaptation to benthic habitats. Genes differentially expressed during interactions with bacteria are strongly conserved in other benthic diatoms while many species-specific genes are strongly upregulated during sexual reproduction. Combined with re-sequencing data from 48 strains, our results offer insights into the genetic diversity and gene functions in benthic diatoms. Available genomics studies have mostly focused on planktonic centric diatom. Here, the authors report the genome assembly of the marine biofilm-forming diatom Seminavis robusta and the resequencing data of a panel of accessions to reveal their evolutionary adaptations.
  11. Cirri, E., De Decker, S., Bilcke, G., Werner, M., Osuna, C., De Veylder, L., … Pohnert, G. (2019). Associated bacteria affect sexual reproduction by altering gene expression and metabolic processes in a biofilm inhabiting diatom. FRONTIERS IN MICROBIOLOGY, 10.
    Diatoms are unicellular algae with a fundamental role in global biogeochemical cycles as major primary producers at the base of aquatic food webs. In recent years, chemical communication between diatoms and associated bacteria has emerged as a key factor in diatom ecology, spurred by conceptual and technological advancements to study the mechanisms underlying these interactions. Here, we use a combination of physiological, transcriptomic, and metabolomic approaches to study the influence of naturally coexisting bacteria, Maribacter sp. and Roseovarius sp., on the sexual reproduction of the biofilm inhabiting marine pennate diatom Seminavis robusta. While Maribacter sp. severely reduces the reproductive success of S. robusta cultures, Roseovarius sp. slightly enhances it. Contrary to our expectation, we demonstrate that the effect of the bacterial exudates is not caused by altered cell-cycle regulation prior to the switch to meiosis. Instead, Maribacter sp. exudates cause a reduced production of diproline, the sexual attraction pheromone of S. robusta. Transcriptomic analyses show that this is likely an indirect consequence of altered intracellular metabolic fluxes in the diatom, especially those related to amino acid biosynthesis, oxidative stress response, and biosynthesis of defense molecules. This study provides the first insights into the influence of bacteria on diatom sexual reproduction and adds a new dimension to the complexity of a still understudied phenomenon in natural diatom populations.