vacuoles on each side of the nucleus visible behind the glass cell wall and chloroplasts; axial area outlines by lineate striae.
3 Terminal bent striae (terminal striae convergent at the margins and bent back toward the central area). Striae are radiate next to the axial area.
4 Voigt discontinuity identifies the secondary side of the valve morphogenesis. Ontogeny in diatoms varies with morphology; in Naviculoid diatoms, the secondary side shows the completion of silica deposition around the raphe.
5 Distal raphe positioned on the broad, rounded apices and curved toward the primary side of the valve in the opposite direction when compared to the proximal raphe ends. Scale bars, 10 μm.
Frustule morphogenesis, deposits SDVs and needs more research with new tools. However, it has been established that the silica morphogenesis of centric species will begin at the center of the valve, and it begins by creating a primary rib in pennate species [1.21]. Completion of the sternum around the raphe slit morphologically can be identified with the Voight discontinuity (Figure 1.3b). From that onset within the mother frustule, the silica will continue to form outward to complete the shape as well as inward to create more layers, with the oldest silica being on the most outside layer [1.46]. The silicic acid (or its anions) is taken from the environment, condensed, associated with proteins synthesized by the endoplasmic reticulum and packaged in a globular vesicle in the Golgi apparatus. Then finally, these vesicles (silica deposition vesicles) are transported by microtubules, likely in a genetically predetermined pattern, and delivered to the new valve interface. These are not the only groups that pull silicic acid (an inorganic compound contains silicon) out of the water and use it to make a frustule, but diatoms do it uniquely.
Diatom frustules are porous with multilayer, multiscalar porosity, a property that is unique for each species, giving frustules their beautiful ornamentation [1.17]. The major bigger pores within the valves are called “areolae” and usually arranged in rows known as “striae”, which could be either branched or not. In the most general way, diatoms can be divided into centric and pennate diatoms, which are classified based on the valve symmetry. Centric diatoms are radially symmetric and lack raphes. Pennate diatoms usually have bilateral symmetry and there can be no, one, or two raphes. Pennate diatoms can further be classified based on variations in the position of the raphe on valve. The raphe is used for motility [1.4] and attachment [1.12]. Sometimes, the frustules are also covered in spines, which can allow some species to hook together and form chains (Figure 1.1e).
The frustule’s morphological features of diatoms are required for identification. Specialized terminology has been collected in [1.5–1.7, 1.15, 1.16], and a general guide to the literature is in [1.10]. Characters continue to be discovered and new descriptive terminologies are proposed [1.23].
1.2 Tools to Explore Diatom Frustule Morphology
The beauty of diatoms was missed until the early, curious microscopists started observing ambiguous glassy microorganisms under their optical microscopes in the 18th century [1.22, 1.38]. Although the light microscope (LM) helped us to reveal the diatoms’ world, diatom frustules also helped the microscopists in developing and testing the quality and resolution of their optical microscopes [1.24, 1.25]. Since the nineteenth century, several works have been published on diatoms, its morphology, and taxonomy by remarkable workers including Kützing, Schmidt, Ehrenberg, Grunow, Hustedt, Krammer, Lange-Bertalot, and more (see references in Round et al. [1.38]). They described both living cells and clean frustules extensively using LM. The unique structure of diatom frustules under LM, with a variety of shapes and symmetries, has captured a wide interest; however, most of the diatom’s real art, at the nanoscale, was kept hidden. The limitations for observing frustule ultrastructure, especially details below 200 nm, were solved after the invention of the electron microscope [1.26]. In 1936, the transmission electron microscope (TEM) was used to capture the first micrograph of a diatom frustule [1.26, 1.27], using it as a test object for the quality and resolution of TEM. After that TEM was used to explore diatom ultrastructure. Following, the scanning electron microscope (SEM) was invented and used extensively as a more effective tool for exploring frustules morphology and ultrastructure [1.24, 1.28, 1.36, 1.38].
The details observed using the SEM and TEM reflected the beauty of diatoms when many hidden details became observable. For instance, some bright striae under an optical microscope appear as arrays of fine pores under the electron microscope (Figure 1.5a). It was, to some extent, a kind of revolution for diatom classification and taxonomy with the morphological details that became available down to 15 nm with SEM and below 10 nm with TEM (Figure 1.5b). Nowadays, the observation of diatom frustule morphology and ultrastructure using LM, SEM, and TEM became routine work for people working on ecology, environment, forensic, nanotechnological, and other applications that concern frustule ultrastructure, monitoring diatom species, and taxonomy.
Although 2D information can be collected from LM and TEM and the 3D-shape appeared under SEM, the information about the surface topology, internal ultrastructure, and siliceous element relationships within diatom frustules was missing. Therefore, more tools were evolved and involved in the exploration and understanding of the 3D complex ultrastructure of the frustule, which could be the reason for their various natural features, including unique photonic, mechanical, and hydrokinetic properties [1.9, 1.45]. The new tools include the atomic force microscope (AFM) and the focused ion beam SEM (FIBSEM) [1.32, 1.34, 1.35, 1.41].
Figure 1.4 Cleaned diatoms in valve (g, h–j, m–r, u, v) and girdle views (a–f, k, l, s, t, w, x). (a–e, g) Rhoicosphenia spp., frustules are clavate and strongly flexed, one valve is concave with long raphe branches and the other valve convex with shortened raphe, different depth pseudosepta visible; (f, k, l) Gomphonema spp. showing valve heterogeneity; (h) Gomphonella olivacea (Hornemann) Raben. (i) Planothidium lanceolatum (Bréb. Ex Kütz.) Lange-Bert, rapheless valve shown with asymmetrical central area containing depression; (j) Geissleria cascadensis (Sovereign) Stancheva and S. A. Spaulding, valves elliptic, with cuneate apices, coarse areolae, three pairs of annulae are present at each apex; (m) Planothidium delicatulum (Kütz.) Round and Bukht. Rapheless valve shown, lacking a central area and two middle striae spaced distantly. Cleaned diatoms in valve (g, h–j, m–r, u, v) and girdle views (a–f, k, l, s, t, w, x). (n) Gomphonema sp. valve heteropolar wider in the middle, axial area narrow, central area irregular outlined by two shortened striae and opposite to a single striae finishing with an isolated pore, striae parallel toward the headpole, radiate toward the foot pole; (o) Amphora ovalis, dorsal fascia visible and dorsal striae interrupted transapically by intercostal ribs; (p) Gomphonema micropus Reichardt lanceolate valve with headpole widely drawn out and wider than foot pole, striae radiate, central area unilaterally rectangular with shortened central stria, on the opposite side longer striae finishing with a stigmoid; (q) Navicula genovefae Fusey valve linear-lanceolate with rostrate broadly rounded apices, punctate striae radiate and curved, becoming nearly parallel at the apices, less dense around the well-defined central area; (r) Cocconeis placentula Ehrenb. Valves elliptic, striae radiate and interrupted by a hyaline ring positioned close to the valve margin, siliceous bridges (imbriae extending from valvocopula) visible; (s) Amphora pediculus (Kütz.) Grunow focus from dorsal site of two frustules; (t, u) Caloneis sp. on girdle view striae continue on valve mantle, on the linear valve view with rounded apices, axial area is narrow, broadening to a transverse fascia; (v) Navicula cryptocephala Kütz. Valve lanceolate with protracted apices and visible large, circular central area; (w) Mastogloia pseudosmithii Sylvia S. Lee, E. E. Gaiser, Van de Vijver, Edlund, and S. A. Spaulding, evenly sized partecta (chambers on the valvocopula) on both valves; (x) Navicula cf. tripunctata (O.F. Müll.) Bory. Scale bar, 10 μm. These micrographs were obtained and identified by KMM.
In 1992, the first observation of diatoms using an AFM has been done [1.33]. In general, AFM is used as an advanced tool to explore