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Introduction

Diatoms (Bacillariophyta) are one of the most distinctive and successful groups of unicellular algae, occurring throughout the world in marine, brackish and fresh waters, as well as in damp subaerial habitats. They are usually estimated to contribute about 25-35 % of the world’s productivity (in terms of carbon fixation) and to be represented by 50 – 200 thousand species depending upon one’s species concept. Their most distinctive characteristic is the possession of elaborate, siliceous cell walls, features of which are used to define and classify species. Because silica resists degradation, diatoms are regularly preserved in both freshwater and marine sediments, and in conjunction with knowledge of their ecological specificity, such records have been used to infer lake or ocean histories. In particular, diatoms in lake sediments have been used to deduce changes in pH and nutrient status, as well as climate change. They are also used extensively to infer water quality in contemporary aquatic systems.

Morphology

Fig. 1 Diagram of frustule, labelling valves and bands.

Diatom cell walls (frustules) are essentially bipartite structures, with an older and a younger half (valve), each with a series of linking bands (girdle bands or cingula), often likened to a petri dish or pill-box (Fig. 1). Once formed, the siliceous components are rigid and cell expansion is only possible by the addition of extra girdle bands associated with the younger valve. Valves vary in shape and symmetry, as well as in the type and arrangement of pores, slits and other processes of the silica wall, and these features have formed the basis of their identification and classification.

Diatom cells are often approximated to geometric shapes and described in relation to their major axes and planes, radial, apical, transapical and valvar (Fig. 2). Because they are three-dimensional structures, shape will differ depending on the aspect presented to the viewer, either valve or girdle view. Occasionally cells are seen end-on, but this is unlikely in fixed or cleaned material, since cells tend to lie with their largest face on the slide.

Fig. 2A Axes of a centric diatom. a-a radial, b-b valvar

B Axes of a pennate diatom. a-a apical, b-b valvar, c-c transapical.

Diatoms may be divided into two major groups based on valve symmetry (Fig. 3), those that are circular with essentially radial symmetry, the centric diatoms, and those that are more elongate, with primarily bilateral symmetry, the pennate diatoms. The latter group is further sub-divided on the presence or absence of a paired slit system (the raphe) in the valve, associated with motility, into the araphid and raphid diatoms. Raphid diatoms are subdivided into biraphid and monoraphid taxa. Monoraphid diatoms have a functional raphe system on one valve only, the R valve. The other valve (P valve) has a solid raphe sternum since the raphe slit has been filled in with silica during morphogenesis. From the point of view of identification, these are useful groupings, however, they do not necessarily reflect the phylogenetic relationships of the diatoms; neither the centric, araphid nor monoraphid diatoms are now considered monophyletic.

Fig. 3A A centric diatom showing radial symmetry.

B A pennate diatom showing bilateral symmetry.

The position and path of the raphe slits, and the presence or absence of associated ribs or struts  are important features by which taxa can be identified and classified. In some groups of diatoms, e.g. Nitzschia, Hantzschia, the raphe slits are positioned along one edge of the valve face, often raised along a ridge (keel) and spanned internally by struts (fibulae), which may appear as refractive lines or dots. In another group of diatoms, Surirellales, the fibulate raphe slits are positioned such that one runs along each long margin of the valve face, interrupted at both poles by “nodules” (e.g. Surirella brebisonii). Ontogenetically, one corresponds to the central nodule (the origin of the raphe system), the other to two fused polar nodules.

In addition to being perforated by pores and / or slits, some diatoms are ornamented with spines, often around the margin of the valve at the junction of the valve face and the valve mantle, or they may possess hollow processes (strutted or labiate processes) associated with the production of chitin fibres or mucilage fultoportula. These features may facilitate the formation of colonies. Specialised areas of simple pores (apical pore fields) often allow the secretion of mucilage pads or stalks  for attachment to a substratum or to other cells in a colony. Some species have the ability to live as motile individuals or to attach to a substratum, depending on the circumstances.

Aspects of diatom life history

Fig. 4 Diatom cell division. Diagram shows divided cell, sectioned in girdle view. The parent valves and girdle bands lie outside the forming daughter valves. Each is enclosed in a silicalemma, inside its respective protoplast, but lies close to its sibling and the surface topography of one valve may be modified by that of its sibling.

Vegetative cell division in diatoms requires the formation of one new valve for each daughter cell, the new valve being deposited in a membrane-bound vesicle within the daughter protoplast, released to the exterior on completion (Fig. 4). New sibling valves are usually formed in close juxtaposition to each other, so that their surface topographies may interact, e.g. where there is a depression on one sibling valve a raised area is formed on the other (e.g. Cyclotella meneghiniana). Other species may link sibling valves by the formation of interlocking spines, as in Fragilaria and related genera.

Because of the rigidity of the cell walls, new valves may be slightly smaller than the parent valves and, over time, the average size of a diatom population will decrease. This has a number of consequences. One of these is that diatoms must be able to escape the inevitable size diminution if they are to survive. This is usually achieved via sexual reproduction in which gametes are formed and fuse outside the confines of the parent frustules, forming a zygote that expands to the species maximum, then laying down new silica valves to form new vegetative cells. Another consequence of size reduction, particularly for pennate diatoms, is that smaller cells may be mistaken for other taxa because valve outline and proportions may differ from that of larger cells (Fig. 5). This is due to a greater reduction in valve length than width, sometimes accompanied by a change in apical shape. Sometimes apices in smaller individuals are simpler, but not for all species.

	Fig. 5 Size reduction Examples of changes in valve outline and perceived shape with size reduction. a. Navicula reinhardtii; b. Gomphonema gracile / Gomphonema parvulum (photographs courtesy of Dawn Rose); c. Dickiea subinflatoides / Dickiea ulvacea; d. Navicula capitata.

Live features

The protoplast is enclosed within the frustule, the interphase configuration of nucleus, chloroplast (s) and other cytoplasmic components being characteristic for species and genera (see live features). Diatom chloroplasts are usually golden-brown in colour, however, they can vary from very pale to dark chestnut brown, and a few appear greenish, even when healthy. Centric diatoms usually have several to many, simple, rounded chloroplasts arranged around their cell periphery (e.g. Melosira varians). Raphid pennate diatoms on the other hand, have one, two or four (rarely more) chloroplasts per cell, varying in shape and configuration within the cell according to genus and family, usually with a conspicuous central cytoplasmic bridge in which the nucleus is located (e.g. Navicula lanceolata). Araphid pennate diatoms may have one or two large chloroplasts per cell, like raphid diatoms, or many small chloroplasts, like centric diatoms. Chloroplast number and arrangement can be particularly informative for many naviculoid genera. Most diatom chloroplasts contain pyrenoids, more refractive proteinaceous bodies, which may be rounded or angular, one to many per chloroplasts. Their visibility depends upon their size, shape and position. The rounded pyrenoids of Gomphonema and Cymbella are often easily seen in valve view at the centre of the chloroplast, the rod-shaped pyrenoids of Navicula are rarely seen because they are only visible in girdle view. Colony formation and mode of attachment are sometimes indicative of the presence of particular structures, e.g. linking spines, if cells are linked valve face to valve face, or pore fields if cells are linked by pads of mucilage or attached to substrata by pads or stalks.

Identifying diatoms

Identification seeks to put the correct name to a specimen. It does not depend upon any knowledge of the evolutionary or systematic relationships of the species, and can use any feature that is helpful in discriminating between specimens, regardless of its distribution across the group. Therefore the taxa selected by choosing a particular character state are not necessarily closely related. Correct identification in this CD-ROM rests on the unique combination of character states of the species in question.

Conventionally diatoms are identified based on the morphology of the siliceous wall (frustule) although protoplast features can also be used. For both, however, it is first essential to establish which view of the diatom is visible. Cells will normally lie in either valve or girdle view, depending upon which has the larger and/or flatter surface. Girdle views can usually be recognised by being more or less rectangular, with the girdle bands being thinner in cross-section than the valves. Some girdle views are curved, biconvex or occasionally undulate, but all are usually “squared-off” in some way. There are very few diatoms whose valve view has right angles (or is approximately right-angled).

Although the SEM has revealed much about diatom ultrastructure, we have tried to describe characters as they are seen in LM, to make the key accessible to those who lack knowledge of diatom ultrastructure. There has therefore been no attempt to describe all the structural details of different taxa; more information on this can be obtained from conventional publications (e.g., Round et al. 1990), which also provide details of diatom life histories, etc.

For the purposes of this CD-ROM, elongate valve shapes are first considered without reference to the apices, i.e. any protracted apices are ignored. Apex shape is considered independently. Similarly, shapes of axial and central areas are considered independently, the former extending as far as the central raphe endings in raphid diatoms, the latter being opposite the gap between the central raphe endings. In diatoms without a raphe system, the axial area is along the apical axis and the central area is in the middle of the valve.

The presence, absence and position of features such as raphe slits are important. It should be noted that some diatoms have a raphe system on one valve only (monoraphid diatoms), so the valves of a cell differ. We have designed this key so that the raphid and araphid valves can be identified independently. In other words it is not necessary to know that they represent different parts of the same species to reach a correct identification.