Imagine a typical dreary day at the Scheldt estuary in The Netherlands. The weak springtime sun paints the exposed tidal plains in a dull brownish hue. However, unbeknownst to the casual observer, the sediment surface of the mudflat is teeming with microscopic life. This so-called “secret garden” [1] typically takes the form of complex multi-layered biofilms, where microalgae coexist with heterotrophic bacteria [2]. Such phototrophic biofilms are very efficient in their use of solar energy and provide important ecosystem services such as erosion resistance and nutrient cycling [3]. Marine biofilms are in many cases dominated by benthic diatoms [4], which are far more species-rich compared to planktonic diatoms [5]. Nevertheless, laboratory studies of diatoms have mostly focussed on planktonic diatoms. To counter this, my favorite benthic diatom Seminavis robusta was introduced as a new experimental model organism to help us understand diatom life cycles and adaptation to a benthic habitat [6]

S. robusta first came on the scene 20 years ago, when it received its current name and the first investigation of its sexual reproduction stages took place [7,8] (Fig. 1). The species inhabits soft sediments and rock surfaces of coastal lagoons in the Northern hemisphere [6,7,9,10]. The experimental toolkit of S. robusta is extensive, comprising cryopreservation [11], experimental assays to test the effects of sex pheromones [12,13], chemical synthesis of the attraction pheromone diproline [12,14], a culture collection hosting >100 strains [6], procedures to sexually cross compatible cultures [8,9] and movement-tracking methods to study chemotaxis [15,16]. To complement this, we recently constructed a reference genome for S. robusta containing more than 36,000 protein-coding genes, the largest number found in any diatom so far [17]! Altogether, these tools spurred research into diverse facets of S. robusta’s benthic lifestyle, such as mate finding, cell migration and interactions with associated bacteria (Fig. 1).

 

Figure 1: timeline of research on the benthic diatom S. robusta. Live cells are pictured. S. robusta’s valve length ranges from ~70µm (initial cells) to ~15µm (smallest viable cell). 

A key feature of diatoms is their size-dependent sexual life cycle. During consecutive mitotic (asexual) divisions, the average cell size of populations diminishes below a sexual size threshold, only to be restored by the formation of an auxospore during sexual reproduction (Fig. 2). Several sexual species are being used to study the life cycle in the laboratory: Pseudo-nitzschia multistriata [18–20], Skeletonema marinoi [21], Pseudostaurosira trainorii [22] and, of course, S. robusta.  

At the onset of the new year, I want to take a moment to reflect on what we learned about S. robusta’s life cycle in 2021 (Fig. 2): (1) In a series of elegant experiments, Bulankova and colleagues showed that recombination during mitosis is remarkably common [23]. This finding may have important implications for researchers that use established strains, because their genomes gradually diverge from the original isolates. (2) A day/night RNA sequencing experiment revealed that almost all S. robusta genes display rhythmic expression and that the cell cycle was strongly synchronized to the photoperiod [24]. Several peculiar characteristics of the day/night transcriptome were discovered that may prove to be adaptations to the challenges of the benthic environment, such as fluctuations in light and temperature, tidal cycles and rhythmic migration [17,24]. (3) We showed that light conditions have a profound impact on sexual reproduction of S. robusta. Indeed, exposing cultures to low intensity light in the blue spectrum massively boosted the formation of auxospores [25]. (4) Assessing cells’ sensitivity to analogs of the attraction pheromone diproline, Bonneure and colleagues built a proof of concept for diazirine and azide labeling of diproline, opening corridors to identify the diproline receptor [14]. (5) Finally, we compared gene expression between the two mating types (sexes) of S. robusta after treatment with sex inducing pheromones [26]. These pheromones typically result in a cell cycle arrest and cause the start of diproline production, which was reflected in specific gene expression patterns (Fig. 2).

 

Figure 2New clues about S. robusta’s life history in the year 2021. Sources: [14,23–26]

On the whole, it is clear that S. robusta played an important role in our current understanding of the lifestyle of benthic diatoms. Nevertheless, the diatom life cycle remains poorly understood from a molecular point of view. One of the greatest remaining mysteries is certainly the mechanism used by cells to measure their own size, which allows them to become sexual only when they become small enough. Furthermore, there are remarkably few microscopic observations of sexual reproduction in the wild. Hence, the timing and geography of diatom sexual reproduction in nature is an area where a lot of progress can be made. To this end, experimental data on the factors that determine the balance between growth and sex is needed to fully understand natural diatom life cycles. Given these fundamental questions, I am very excited to see what S. robusta will teach us in the next 20 years!

 

Gust Bilcke is a postdoctoral researcher at Ghent University (Belgium). He is fascinated by the genetic and genomic programs behind the diversity in life cycle strategies of diatoms, in particular sexual reproduction and diurnal/circadian rhythms. You can email Gust at Gust.Bilcke[at]psb.vib-ugent.be or leave a message in the comments section if you have any question about the blog post.

 

References

[1] Macintyre HL, Geider RJ, Miller DC. Microphytobenthos: The ecological role of the “secret garden” of unvegetated, shallow-water marine habitats. I. Distribution, abundance and primary production. Estuaries 1996;19:186–201. https://doi.org/10.2307/1352224.

[2] Congestri R, Albertano P. Benthic diatoms in biofilm culture. The Diatom World, 2011, p. 227–243. https://doi.org/10.1007/978-94-007-1327-7_10.

[3] Hope JA, Paterson DM, Thrush SF. The role of microphytobenthos in soft-sediment ecological networks and their contribution to the delivery of multiple ecosystem services. Journal of Ecology 2020;108:815–830. https://doi.org/10.1111/1365-2745.13322.

[4] de Carvalho CCCR. Marine biofilms: A successful microbial strategy with economic implications. Frontiers in Marine Science 2018;5:126. https://doi.org/10.3389/fmars.2018.00126.

[5] Nakov T, Beaulieu JM, Alverson AJ. Accelerated diversification is related to life history and locomotion in a hyperdiverse lineage of microbial eukaryotes (Diatoms, Bacillariophyta). New Phytologist 2018;219:462–473. https://doi.org/10.1111/nph.15137.

[6] Chepurnov VA, Mann DG, Von Dassow P, Vanormelingen P, Gillard J, Inzé D, et al. In search of new tractable diatoms for experimental biology. BioEssays 2008;30:692–702. https://doi.org/10.1002/bies.20773.

[7] Danielidis DB, Mann DG. The systematics of Seminavis (Bacillariophyta): The lost identities of Amphora angusta, A. ventricosa and A. macilenta. European Journal of Phycology 2002;37:429–448. https://doi.org/10.1017/S0967026202003724.

[8] Chepurnov VA, Mann DG, Vyverman W, Sabbe K, Danielidis DB. Sexual reproduction, mating system, and protoplast dynamics of Seminavis (Bacillariophyceae). Journal of Phycology 2002;38:1004–1019. https://doi.org/10.1046/j.1529-8817.2002.t01-1-01233.x.

[9] De Decker S, Vanormelingen P, Pinseel E, Sefbom J, Audoor S, Sabbe K, et al. Incomplete reproductive isolation between genetically distinct sympatric clades of the pennate model diatom Seminavis robusta. Protist 2018;169:569–583. https://doi.org/10.1016/j.protis.2018.05.003.

[10] Umemura K, Sadoya Y, Nagao K, Oikawa R, Hanada Y, Sugioka K, et al. Single cell analysis using a glass microchamber for studying movement fluctuations of Navicula pavillardii and Seminavis robusta diatom cells. Micron 2015;77:41–43. https://doi.org/10.1016/j.micron.2015.05.005.

[11] Stock W, Pinseel E, De Decker S, Sefbom J, Blommaert L, Chepurnova O, et al. Expanding the toolbox for cryopreservation of marine and freshwater diatoms. Scientific Reports 2018;8:4279. https://doi.org/10.1038/s41598-018-22460-0.

[12] Gillard J, Frenkel J, Devos V, Sabbe K, Paul C, Rempt M, et al. Metabolomics enables the structure elucidation of a diatom sex pheromone. Angewandte Chemie – International Edition 2013;52:854–857. https://doi.org/10.1002/anie.201208175.

[13] Moeys S, Frenkel J, Lembke C, Gillard JTF, Devos V, Van Den Berge K, et al. A sex-inducing pheromone triggers cell cycle arrest and mate attraction in the diatom Seminavis robusta. Scientific Reports 2016;6:19252. https://doi.org/10.1038/srep19252.

[14] Bonneure E, De Baets A, De Decker S, Van den Berge K, Clement L, Vyverman W, et al. Altering the sex pheromone cyclo(L-pro-l-pro) of the diatom Seminavis robusta towards a chemical probe. International Journal of Molecular Sciences 2021;22:1–14. https://doi.org/10.3390/ijms22031037.

[15] Bondoc KGV, Heuschele J, Gillard J, Vyverman W, Pohnert G. Selective silicate-directed motility in diatoms. Nature Communications 2016;7:10540. https://doi.org/10.1038/ncomms10540.

[16] Bondoc KGV, Lembke C, Vyverman W, Pohnert G. Searching for a mate: pheromone-directed movement of the benthic diatom Seminavis robusta. Microbial Ecology 2016;72:287–294. https://doi.org/10.1007/s00248-016-0796-7.

[17] Osuna-Cruz CM, Bilcke G, Vancaester E, De Decker S, Bones AM, Winge P, et al. The Seminavis robusta genome provides insights into the evolutionary adaptations of benthic diatoms. Nature Communications 2020;11:3320. https://doi.org/10.1038/s41467-020-17191-8.

[18] Basu S, Patil S, Mapleson D, Russo MT, Vitale L, Fevola C, et al. Finding a partner in the ocean: molecular and evolutionary bases of the response to sexual cues in a planktonic diatom. New Phytologist 2017;215:140–156. https://doi.org/10.1111/nph.14557.

[19] Fiorini F, Borgonuovo C, Ferrante MI, Brönstrup M. A metabolomics exploration of the sexual phase in the marine diatom Pseudo-nitzschia multistriata. Marine Drugs 2020;18:313. https://doi.org/10.3390/md18060313.

[20] Russo MT, Vitale L, Entrambasaguas L, Anestis K, Fattorini N, Romano F, et al. MRP3 is a sex determining gene in the diatom Pseudo-nitzschia multistriata. Nature Communications 2018;9:5050. https://doi.org/10.1038/s41467-018-07496-0.

[21] 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. https://doi.org/10.3390/genes10070494.

[22] Sato S, Beakes G, Idei M, Nagumo T, Mann DG. Novel sex cells and evidence for sex pheromones in diatoms. PLoS ONE 2011;6:e26923. https://doi.org/10.1371/journal.pone.0026923.

[23] 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. Current Biology 2021:1–12. https://doi.org/10.1016/j.cub.2021.05.013.

[24] Bilcke G, Osuna-Cruz CM, Silva MS, Poulsen N, D’hondt S, Bulankova P, et al. Diurnal transcript profiling of the diatom Seminavis robusta reveals adaptations to a benthic lifestyle. The Plant Journal 2021:tpj.15291.

[25] Bilcke G, Van Craenenbroeck L, Castagna A, Osuna‑Cruz CM, Vandepoele K, Sabbe K, et al. Light intensity and spectral composition drive reproductive success in the marine benthic diatom Seminavis robusta. Scientific Reports 2021:1–15. https://doi.org/10.1038/s41598-021-92838-0.

[26] Bilcke G, Van den Berge K, De Decker S, Bonneure E, Poulsen N, Bulankova P, et al. Mating type specific transcriptomic response to sex inducing pheromone in the pennate diatom Seminavis robusta. ISME Journal 2021;15:562–576. https://doi.org/10.1038/s41396-020-00797-7.