and (c) show the centroids of diatoms #1, #2, and #3, respectively.Figure A5 Mean square displacement (MSD) data of diatom trajectories. Diatom motion recordings were divided into segments that are 500 frames long and MSD data of each segment was calculated. The black dashed line represents the mean MSD and red line represents the best fit to the MSD for all diatoms (diatom #1 – (a), diatom #2 – (b), diatom #3 – (c)). All MSD data falls into the range shown by gray shaded areas in the figures.Figure A6 Normalized velocity autocorrelation of all the diatoms (diatom #1 – (a), diatom #2 – (b), diatom #3 – (c)). The same trajectory segments as in calculation of diatom MSD data were used. All repetitions were used in calculating the autocorrelation.Figure A7 The publicly available video [2.87] was analyzed using the SURF feature detection algorithm (please see the main text for the details); (a) displacement calculated in pixels as a function of the frame number; (b) the overlay of the features detected at frame numbers 422 (crosses) and 423 (circles). pts = points. Scale bar was not present in the original video.3 Chapter 3Figure 3.1 Vesicles carrying mucilage (black arrows) on sections of cells of Pleurosigma sp. near the girdle bands (a) and Encyonema ventricosum (b) in the area of areolae (TEM). Around the cells Encyonema ventricosum are visible fibers between the plasmalemma and the frustule and a dense layer of mucilage fibers on the surface of the frustule, however, the connections between them are absent. Chl - chloroplasts; m - mitochondrion. Scale – 200 nm.Figure 3.2 The surface cells of Nitzschia sp. (a, b) and Pleurosigma sp. (c, d) after removal of frustules (SEM). At the tips of the precisely repeated contour of the frustules in the area of the raphe system of Nitzschia sp. in some cases separated fragments (arrows) are visible; it may be the place where the cell is firmly attached to the valve. The frustule of Pleurosigma does not have so extremely relief, but the contours of the cell here is very accurately repeated especially in the area of the raphe (arrows). It is possibly that most of the surface is not diatotepum, as this polysaccharide layer is very firmly attached to the leaf, which is very well illustrated by the E. ventricosum (Figure 3.1b). Scale: (a, d) – 10 μm; (b) – 5 μm; (c) – 1 μm.Figure 3.3 Secretion of mucilage (arrow) through the raphe of the E. ventricosum (a) and vesicle (arrow), containing mucus near the raphe of Pleurosigma sp. (b) on ultra-thin cross sections (TEM) Scale: (a) – 200 nm; (b) – 500 nm.Figure 3.4 Staining of actin microfilaments (phalloidin Alexa Fluor 488, green fluorescence) and nuclei (DAPI, blue fluorescence) in Pleurosigma sp. (a-b’) and Nitzschia sp. (c, d). Scale: (a, b) – 15 μm; (b’) – 5 μm; (c, d) – 10 μm.
4 Chapter 4Figure 4.1 Morphology of an araphid diatom (a), Staurosira construens var. venter (scale bar: 2 μm) and a raphid diatom (b), Navicula radiosa (scale bar: 10 μm), diatom on valve view. The raphe (indicated by a white arrow) runs through the whole valve and is a primary structure for adhesion to surfaces and moving. (c) A close-up of the raphe (indicated by a white arrow) is shown (scale bar: 1 μm). (SEM images downloaded from diatoms.org with permission [4.107] [4.120] [4.143].)Figure 4.2 Schematic of a benthic biofilm. Algae, predominantly pennate biofilms together with bacteria, protists, and fungi, are embedded within a protective matrix of extracellular polymeric substances (EPS). A benthic biofilm experiences high variability of spatial and temporal gradients of environmental factors such as inorganic nutrients, dissolved organic matter (DOM), and light. (Figure from Sabater et al. [4.129]. Reprinted under CC-BY license.)Figure 4.3 A summary of some factors and gradients affecting diatom adhesion and motility on intertidal sediment. While adhering to the surface, cells sense their wettability through the production of intracellular nitric oxide (NO), which in turn mediates EPS production. Pennates generally have a preference for hydrophobic surfaces for attachment. Shear force or water flow affects substrate attachment with weakly attached cells easily dislodged by stronger shear. Once attached, the gliding capability and reversal control are mediated by the availability of extracellular and intracellular Ca2+, respectively. As light only penetrates a few mm on the sediment, the substrate is divided into the photic and aphotic zone. Cells undergo diel vertical migration to the photic zone to photosynthesize on the surface with a taxa-specific temporal rhythm, thus leading to micro-niche segregation. Nutrient concentrations vary with depth, and motile raphids take up dissolved silicate (dSi) and phosphate (dP) on the aphotic zone as there are higher concentrations of these mineral nutrients with depth. The aphotic zone also provides a protected and stable environment for vegetative and sexual reproduction. (Figure modified and redrawn from Saburova et al. [4.132] and adapted from Fenchel [4.59]. Reprinted with permission.)Figure 4.4 (a) Scanning electron microscopy (SEM) images of EPS or mucilage trails and strands from the motile raphid diatom, Navicula sp. (scale bar: 5 μm). EPS trails were observed to be either straight or curved. (SEM images from Chen et al. [4.26]. (Reprinted under CC-BY license); (b) Adhesion of Nitzschia palea towards surfaces with different surface wettabilities (scale bar: 15 μm). Cells adhered more to hydrophobic surfaces after 4 hours. Insets are duplicate experiments. (Optical microscopy images from Laviale et al. Reprinted (adapted) with permission from Laviale et al. Copyright 2019 American Chemical Society [4.91]).Figure 4.5 (a) A representative cell trajectory of Seminavis robusta showing the run-reverse motility of cells from high cell density experiments. (Cell track replotted from data from Bondoc et al. [4.15]). (b) The circular run-reverse gliding technique observed in Nitzschia communis under isotropic environmental conditions. Cells form arc-like runs with constant speed, reverse, and continue the arc-like runs in the opposite clock direction. Filled squares signifies the starting point of the cells. (Figure from Gutiérrez-Medina et al. [4.68]. Reprinted with permission.)Figure 4.6 Motility of the model raphid pennate Seminavis robusta towards different stimuli across its life cycle. For every mitotic division, cells undergo size reduction until they reach a sexual size threshold (SST). Cells can either continue to undergo vegetative growth or sexual reproduction to reconstitute their size and escape death. Throughout vegetative growth, cells require nutrients. Gradients of dissolved silicate (dSi) and phosphate (dP) elicited starved cells to accumulate at point sources within 5 and 20 min, respectively. Dissolved germanium (dGe) did not elicit any attraction, pointing to substrate specificity response. Meanwhile, starved cells also did not respond to gradients of dissolved nitrate or ammonium (collectively called dN). Once cells reach SST, they release sex-inducing pheromones (SIPs) that control the production of diproline (DPR) on MT– cells. This pheromone is used by the MT+ cells as a chemical guide on locating MT– spatially and pair with it. Sexual reproduction requires trace amounts of dSi for the reconstitution of the silica frustule of the initial cells. Additionally, SIP priming is essential for cells that recently crossed SST. On the other hand, critically small-sized cells can bypass the priming process and be readily attracted to diproline. This self-priming could be a self-preserving strategy for the cells to avoid extinction. (Figure from Bondoc et al. [4.16]. Reprinted with CC-BY license.)
5 Chapter 5Figure 5.1 The effect of incubation time on Stauroneis response times in a mixed culture of Craticula cuspidata and Stauroneis phoenicenteron. This graph displays the average direction change response times for Stauroneis phoenicenteron cells in the presence of ca. 9:1 ratio of live C. cuspidata: S. phoenicenteron cells. S. phoenicenteron cells were isolated and washed from culture and incubated together with C. cuspidata cells (C/S) in a 9:1 C. cuspidata:S. phoenicenteron ratio. Cells were then irradiated at their leading end with high irradiance (ca. 104 μmol/m2s) 1s pulses of blue (470 nm) light, and observed to determine the time until they changed direction (response time). Response times significantly increased almost 2-fold from the initial incubation interval (0-10 min) within 20-30 min (30±2 μm/s and 57±7 μm/s respectively, P=0.003). Graphs represent the mean values of response times ± 1 SE. For comparison, unirradiated Stauroneis cell response times were 155±11 μm/s. Error bars represent ± 1 SE.Figure 5.2 The effect of Craticula cuspidata or Pinnularia viridis presence on Stauroneis phoenicenteron response times. This graph displays the average direction change response times for S. phoenicenteron cells alone on slide chamber (Control). On a mixed slide chamber in a group by themselves (Isolated) or in a slide chamber in the presence of a high ratio of live C. cuspidata or P. viridis cells to S. phoenicenteron cells. Cells were then irradiated at their leading end with high irradiance 1s pulses of blue light,
