Skip to content



Aerotopes (arrows) are gas vesicles, often seen at the poles of cells in cyanobacteria such as Pseudanabaena. Under lower magnification they are often recognisable because the cells appear not to quite connect.


Akinetes (arrows) are specialised, thick-walled, resistant cells produced to survive periods of adverse conditions, under which vegetative cells would not be able to grow. They are often produced towards the end of a growth cycle and are common in some cyanobacteria.

Antheridia (Charophyte)

Oogonia (indicated by "O") and antheridia (indicated by "A") are female and male reproductive cells, respectively. The oogonium contains the oospore, and the antheridium the motile sperm cells. In Charales these structures are born on secondary branches; some species produce both on one filament, whereas others produce one or other on different filaments. Note the characteristic spiralled cells on the oogonium. Mature oospores are ornamented, and the walls persist in sediment cores, allowing information to be deduced about ancient lake environments.

Antheridia (Oedogoniales)

In Oedogoniales (in this guide, Oedogonium and Bulbochaete) the oogonia - female reproductive cells (indicated by "O") - are large and obvious, taking the form of swollen beads spaced at intervals along a filament. The oospore inside is often deeply pigmented when mature. By contrast, the antheridia (indicated by "A") are more difficult to observe, being short colourless cells, each containing one or two motile sperm cells. There is considerable variation in life cycles in these genera. On the left, an example is shown with oogonia and antheridia on the same filament. The species on the right bears antheridia on specialised dwarf male filaments ("DM") that attach to the female, ensuring sperm are produced in close proximity.


A cell that produces male gametes

Apical cell

Cell at the end of a filament


Some diatoms lack raphes (slit-like structures that extrude jelly, conferring motility to the cells), or only possess a raphe on one of the two valves. In Ulnaria shown here, neither valve possesses a raphe. The material is shown living (top), cleaned under the light microscope (middle), and cleaned under the scanning electron microscope (bottom).


Tiny pores/holes in the valves of diatoms


An axial structure occupies a central position in the cell (vs the edge, for instance; see "parietal"). In this cell of Zygnema, the chloroplasts (arrow) are in an axial position.




Some diatoms possess raphes (slit-like structures that extrude jelly, conferring motility to the cells). Biraphid diatoms have raphes on each of the two valves. The top image shows a diatom frustule that has been damaged in such a way that the faces of both valves (V1 and V2) are visible by scanning electron microscopy, and the raphes on both are indicated. The lower image indicates the raphes on one valve face in live material; through-focussing will reveal the raphes on the second valve.


Significant population growth, may be to nuisance levels.



A calyptra (plural: calyptrae) is a thickened cap (arrow) on the terminal cell of a cyanobacterial filament. The terminal region of the filament can also be tapered, as shown here in Phormidium.

Cell wall

"Cell wall" is a general term for the outer rigid or semi-rigid covering around a cell, outside the cell membrane (the lipid bilayer surrounding the cell's contents). Note, however, that not all cells possess cell walls, including some algae and the animal kingdom. Top row: two chlorophytes having rigid cell walls (arrows), Desmodesmus (left) and Bracteacoccus (right). Middle row: in euglenoids, the cell wall is known as a pellicle and takes the form of proteinaceous strips. These are usually flexible enough to allow the cell to change shape (a process known as "metaboly"). Although the strips can only be seen in close examination, metaboly is very evident in this Euglena - the two images are the same cell photographed a few seconds apart. Bottom row: the cell walls (frustules) of diatoms are made of silica. This can be difficult to discern in living material (left) but is obvious in the dead cell to the right, where the ornamentations can be seen. These cell walls persist after cell death, and are well known in the fossil record.

Central area

Diatoms have silicified cell walls that are ornamented in a variety of ways. Often an area clear of ornamentations extends between the poles of pennate diatoms such as Gomphonema (shown here). In the centre of the cell, the clear area becomes wider, and this is referred to as the "central area". It can be difficult to discern in living material (left) but easier in dead, cleaned material (centre, arrow). It is obvious in the scanning electron micrograph to the right; the lower area indicates the clear strip between the poles, and the upper arrow the central area.


Membrane-bound structure (=plastid) in a cell containing photosynthetic pigment.

Chloroplast (golden brown)

Chloroplasts are membrane-bound organelles found in the cells of photosynthetic eukaryotes (in this guide, this can be taken to mean "microbial plants with nuclei"). The conversion of CO2 and water to food and oxygen, using sunlight energy, takes place in the chloroplast. In this guide, both chrysophyceans and diatoms will be found to contain brown or golden-brown chloroplasts (arrows). In Chrysocapsa (top left) the chloroplasts are cup shaped. In Diatoma (top right), the chloroplasts are small and discoid. In Navicula (bottom left), the chloroplasts are shaped as two bands on each side of the cell, closely appressed to the wall. In Melosira (bottom right), the chloroplasts are delicately lobed.

Chloroplast (green)

Chloroplasts are membrane-bound organelles found in the cells of photosynthetic eukaryotes (in this guide, this can be taken to mean "microbial plants with nuclei"). The conversion of CO2 and water to food and oxygen, using sunlight energy, takes place in the chloroplast. Green algae have a great variety of chloroplast shapes. Here they are shown with drawings to assist interpretation. Top row left, the chloroplast is cup-shaped in a Chlorella-like cell. Top row middle, the chloroplast is star-shaped and axial in Zygnema. Top row right, the chloroplast is a band encircling the cell in Ulothrix. Bottom row left, the chloroplast of Spirogyra is spiral-shaped with lobed edges. Bottom row middle, the chloroplast of Microspora is shaped like a net (shown at two planes of focus). Bottom row right, the chloroplasts of Stichococcus are small and disc-like.

Chloroplast (none)

Cyanobacteria do not have chloroplasts. Chloroplasts are membrane-bound organelles found in the cells of photosynthetic eukaryotes (in this guide, this can be taken to mean "microbial plants with nuclei"). The conversion of CO2 and water to food and oxygen, using sunlight energy, takes place in the chloroplast. In cyanobacteria, this occurs on thylakoid membranes free in the cytoplasm of the cell, which are not enclosed in a membrane. Pigments are thus more diffuse in the cells (top row) compared to a eukaryote (the red alga Audouinella, below). In fact, cyanobacteria and chloroplasts share a common ancestor, the latter being derived by the engulfment of a cyanobacterium by a non-photosynthetic eukaryote in the very ancient past.

Chloroplast (red)

Chloroplasts are membrane-bound organelles found in the cells of photosynthetic eukaryotes (in this guide, this can be taken to mean "microbial plants with nuclei"). The conversion of CO2 and water to food and oxygen, using sunlight energy, takes place in the chloroplast. The chloroplasts of red algae (arrows) may appear red, but often also grey-green or blue-green. Both the examples shown are from the same collection of Audouinella.

Chloroplast (yellow green)

Chloroplasts are membrane-bound organelles found in the cells of photosynthetic eukaryotes (in this guide, this can be taken to mean "microbial plants with nuclei"). The conversion of CO2 and water to food and oxygen, using sunlight energy, takes place in the chloroplast. The chloroplasts of yellow-green algae (xanthophyceans) resemble those of green algae, but are typically a slightly lighter shade than "grass green". Top row, left and middle: chloroplasts in Botrydiopsis are indicated at two planes of focus, showing their discoidal shape. Top row right, chloroplasts in Tribonema are indicated. Bottom: the large siphonous tubes of Vaucheria contain thousands of small discoidal chloroplasts, which are often released in a cloud when the tube walls break on a microscope slide.


Groove around dinoflagellate cells containing a flagellum.


Zygnemataleans are also known as the "conjugating green algae". Conjugation is a type of sexual reproduction peculiar to this group, and involves the connection of two cells of complementary mating type and the fusion of gametes, without the presence of any swimming cells (which are totally absent from Zygnematales). The process is perhaps best-known in filamentous forms, but it also takes place in unicellular forms (desmids). As shown above, amoeboid gametes move from one filament to another (or sometimes meeting in the middle) via conjugation tubes. The resulting zygospores are tough-walled resistant stages, and are usually pigmented when mature.

Connections between cells

Large, complex cyanobacteria such as Stigonema may show connections between cells (arrow, with drawing to aid interpretation).

Corticated stems

The cells of charophytes are coenocytic (long siphonous tubes containing numerous chloroplasts and nuclei). In most species of Chara the stems may nonetheless be subdivided by a layer of thinner cells growing around the main axis, giving a "brick wall like" appearance on close examination. Observation of this corticating layer definitively identifies Chara. The examples shown contrast a corticated stem of Chara with a stem of Nitella.


Costae are thickened silica ribs (arrows) that cross the valve face of some diatoms. Unlike some diatom ornamentation, costae are usually easy to see in live material. Large image on the left: Meridion. The remaining images are species of Diatoma in valve and girdle views. Note that the thickenings appear as lines in valve view, and as dots in girdle view.


Cross walls are walls that subdivide a filament into smaller compartments. In many filaments these compartments are individual cells, each with a single nucleus (this is not the case in charophytes, for instance, the cells of which are coenocytic). The upper image shows Ulothrix, which has cross walls (arrows), whereas the lower specimen (Vaucheria) lacks them, except during reproduction.


Cytoplasm is the matrix within a cell. While tempting to view this as "jelly", it is actually much more complex, to enable transport of substances and facilitate cell division. It is, however, often difficult to visualise, except in special circumstances such as in Spirogyra, where most of the cell volume is vacuolar space, and the nucleus is suspended in the centre in strands of cytoplasm (arrow, left image), or in Haematococcus, in which the cell wall is connected to the cell membrane with similar strands (arrow, image on right).




Dinoflagellates are complex cells, with some of the components shown on this cell of Gymnodinium. There are two flagella, one of which encircles the cell and is housed in an equatorial groove called a cingulum, and the other emerges from the sulcus, a groove running perpendicular to the cingulum. The cell is enclosed in thecal plates; where these are well developed, the species is said to be "armoured" (Ceratium is an example).



In Chamaesiphon, a cyanobacterium, exospores (arrow) are produced by budding from the end of a short filament which is attached to a substrate (often another larger alga) at the other end.


An eyespot is a red-coloured spot (arrows), pigmented by carotenoids, that is thought to be involved in light perception. (It is also known as a stigma, but this should not be confused with an unrelated structure of the same name on some diatom frustules.) In Chlamydomonas (left), the eyespot occurs in the chloroplast. In Euglena (middle), the eyespot is large and well clear of the chloroplast. In Botrydiopsis (right, upper) each small chloroplast contains a tiny eyespot. In Tetraspora (right, upper) the eyespot occupies a similar position as in Chlamydomonas.


False branching

Different types of branching occur in filamentous cyanobacteria. In false branching, there is an appearance of a branch, but the cells in one branch are not actually continuous with those of the other. This occurs in two main ways: double false branching (as in Scytonema, upper left) and single false branching (as in Tolypothrix, upper right and lower left); this kind of false branching often begins at a heterocyte. Both of these types of false branching can be readily distinguished from true branching, as show by Stigonema (lower right).


Fibulae are arch-shaped silica structures that support a canal, in which the raphe is housed in some pennate diatoms. They are clearly visible at the cell margin in Nitzschia, as shown here (arrows). Left, living material. Middle, a dead cleaned cell in which the fibulae are more obvious. Right, a transmission electron micrograph, in which the circled area is enlarged, and the nature of the fibulae clearly seen.


Flagella are whip-like organelles that enable cells to swim. They are variable in number and in the way they propel a cell. Two is a common number in green algae such as Chlamydomonas (top left), in which cells swim using their flagella in a "rowing" motion. Cf. Trachelomonas, top right, has a single flagellum. Gymnodinium (bottom row) is shown in two focal planes to illustrate the two flagella: one encircling the cell (left) and one emerging perpendicular to the first (right).


The cell wall of a diatom is composed of silica, and structured in two halves (valves) joined by a girdle. Collectively, these are known as a frustule. The top drawing illustrates a stylised frustule, compared with a frustule of Planothidium photographed using a scanning electron microscope.



The silicon rings/bands circling the valves of diatoms.


Granules and vesciles are structures commonly seen inside the cells of cyanobacteria (arrows). It is important not to confuse these with the organelles of eukaryotic algae, such as chloroplasts and nuclei.


In cryptomonads, the gullet is a pouch-like structure (arrow) at the anterior end of the cell, from which flagella emerge.


H-shaped wall pieces

H-shaped wall material appears in a number of filamentous genera, especially in older material. However, two genera in this guide (Microspora and Tribonema) possess these structures around all their cells. Top row, these damaged cells of Microspora allow the H-shaped wall pieces to be seen. They are also obvious in the older specimen below (black arrowhead indicates the nucleus).

Hair cell

Hair cells are very long, thin, colourless, attenuated cells that may form extensions to filaments (in Draparnaldia, left), or be produced as specialised cells in their own right (Bulbochaete, right).


Large, often rounded nitrogen-fixing cells in some filamentous cyanobacteria


A heterocyte (or heterocyst, in older terminology) is a specialised thick-walled cell that is dedicated to fixing atmospheric nitrogen in nostocalean cyanobacteria. These cells do not photosynthesise, since the enzyme that carries out nitrogen fixation is inhibited by oxygen. Some cyanobacteria that lack heterocytes can fix nitrogen, but they must down-regulated their photosynthesis in order to do so. Heterocytes can be distinguished by their thicker walls, internal bumps ("pores") at the ends connected to other cells, often by size, and by their lack of pigmentation. Top left, heterocytes in the middle of a filament (termed "intercalary"). Top right, a heterocyte in a germling ("hormogone") of Stigonema. Bottom left, heterocytes can occur in clusters in some genera. Bottom right, heterocytes in Nostoc are often larger than the vegetative cells.


The terms isopolar and heteropolar are commonly used to describe both cyanobacterial filaments and diatom valves. An isopolar shape has two ends the same (in the top images, the two ends of the filament and the frustule taper symmetrically with respect to each other). A heteropolar shape has differing ends (on the left, the filament begins with a basal heterocyte and develops in one direction, leading to the long tapered tail; on the right, Didymosphenia and Gomphonema display ends of distinctly different shape.


A holdfast is a structure used to attach a cell to another object. The image shows an example in Oedogonium, after dissociating the filament from the wall of a culture vessel.

Horse shoe

In the diatom genus Planothidium, the "horseshoe" is a U-shaped silica structure inside one of the two valves, visible in live and cleaned material (arrows). Electron microscopy shows that it is the attachment point for a flap of silica (also known as a "hood").



Intercalary heterocyte

Intercalary and basal are terms usually applied to heterocytes in cyanobacteria. A basal heterocyte occurs at one end of the filament, usually the end associated with attachment to a surface or the start of a false branch. An intercalary heterocyte occurs midway along a filament rather than at the end.


An isthmus, or constriction, is a distinctive narrowing in the centre of the cell in some types of desmids.



A lorica is a protective covering (arrows) produced by some cells, often mineralised and some distance from the cell wall or membrane. The images show examples in Dinobryon (left), and Trachelomonas (the upper image of which is deeply pigmented, obscuring the cell).



Some diatoms possess raphes (slit-like structures that extrude jelly, conferring motility to the cells). Monoraphid diatoms have raphes on only one of the two valves. The example shown is Planothidium. The left image shows a group of cells with the raphid valve in the focal plane (arrows indicate the raphes). The middle image shows the same cells, with the araphid valve in the focal plane (the "horseshoe" can also be seen). The image on the right, taken using a scanning electron microscope, shows two valve faces, one with a raphe (arrows).

Mother cell wall

A remnant mother cell wall is a structure derived from the cell that gave rise to daughter cells prior to a previous cell division. In some algae this wall persists for some time, joining cells of Dictyosphaerium together (left, with arrows showing the wall) and remaining among the colony after release of the daughter cells in Coelastrella (right).


Algae are able to move (be motile) in various ways. Cyanobacterial filaments are often able to glide; images at top left show two filaments photographed over a 30 second interval as they travel towards each other. Top right, Chlamydomonas moves using whip-like organelles called flagella (arrows), which it can flex in a "rowing" motion. Bottom, some pennate diatoms can extrude jelly through a slit-like structure called a raphe (indicated by the single-headed arrow), moving the cell in the direction shown (it is also able to pivot on its axis).


Mucilage is a general term for jelly-like material produced by cells, composed of polysaccharide. Top left, the orderly appearance of these cells shows that the colony is embedded in mucilage. Top right, the edges of mucilage produced by these Chrysocapsa cells can be seen by the location of bateria (arrow) that have been unable to penetrate the mucilage. Middle row: the mucilage produced by a colony of Nostoc can become firm and pigmented. The right image shows an old filament, with layers of mucilage produced over time. Bottom: zygnematalean filaments have a thin layer of mucilage covering them, giving the material a "soapy" or slimey feel to the touch.



In Euastrum, the notch is a cleft (arrows) at each end of the cell, usually easy to see on close inspection.


The nucleus (arrows) is the organelle in eukaryotes that contains the genetic material. The nucleolus (arrowheads), which has a specific genetic function, is often also visible in the centre of the nucleus as a darker sphere. The nucleus is colourless, not pigmented, but is commonly confused with the green pyrenoid. Top left, the nucleus in Chlamydomonas is often difficult to see. In Spirogyra (top middle) it is classically easy, being suspended by cytoplasmic threads in the centre of the cell. In Microspora (top right) and Klebsormidium (bottom) it is to one side of the cell.


Oblique division plane

Some species of Coccomyxa distinctively divide by forming a new wall in an orientation not parallel with either axis of the cell. The arrows show the direction of this plane.


Female egg-producing structure


The most common organelles visualised using a light microscope - by far - are chloroplasts and nuclei (C and N respectively in the images). The top image shows these in the eukaryote Klebsormidium. By contrast, the cyanobacterial cells shown below, which are prokaryotic, lack these structures.



Paramylon (arrows) is the cellular storage material in euglenoids, and is often visible in the form of rods or discs. Under high magnification it can almost have a metallic sheen. It is laid down outside the chloroplasts. These distinguish euglenoids from the green algae, in which the storage material is starch, which is always found inside the chloroplasts.


Parietal is a term used to describe the position of chloroplasts - lying against the edge of the cell, rather than in the middle (axial).


There are two types of diatoms: pennate and centric. Pennate diatoms (e.g. Gomphonema, shown here, cleaned and living material) are usually narrow ("boat-shaped") in valve view. Centric diatoms are circular, or at least radially symmetric, in valve view (e.g. Cyclotella, shown here, cleaned and living material). Both types are typically sqaure or rectangular in girdle view (although there are many exceptions to this).

Primary axis

The primary axis is the main stem of a filament, and is often wider than the side branches. In charophytes, reproductive stages are not found on the primary axis.


Processes: a term used to describe outgrowths from a cell wall, such as the spines occuring on Xanthidium (arrows).


In Stigeoclonium, development begins with a creeping (prostrate) system of filaments on a surface, from which upright filaments ultimately arise. The images show the progression of this development, followed clockwise. The dense green region in the middle will produce the upright structures.


In Tetraspora, pseudoflagella (arrows) resemble flagella (the whip-like organelles used by swimming cells), but in this case they are composed of mucilage and do not confer motility. They may require high magnification to observe.

Pulsing vacuole

By careful observation, many single cells or cells in colonies can be seen to possess vacuoles - appearing as small bubbles - that slowly inflate, and suddenly discharge their contents. They expel water from the cell and maintain an osmotic balance. In the images to the left, a Chrysocapsa cell is shown with an inflated and deflated vacuole (arrow). On the right, a view of a Chlamydomonas cell from the anterior reveals the two pulsing vacuoles.


Pyrenoids (arrows) are spherical inclusions inside chloroplasts that contain high concentrations of enzymes involved in starch production. The deposition of storage material around them makes them very visible in the green algae, and the shape of the starch shell varies. They are sometimes mistaken for nuclei. Top left: this Chlamydomonas contains a large pyrenoid with a complex starch shell. Top middle: Klebsormidium has a pyrenoid with a very complex shell composed of small starch grains. This is also found in Interfilum (top right), to which it is closely related. Middle row: Desmodesmus and Coelastrella have pyrenoids with simple starch shells. Bottom: pyrenoids in Mougeotia; note the paler nucleus in the centre of the cell.



The raphe (arrows) is a slit-like structure that extrudes jelly and confers motility to many pennate diatoms. It is easiest to see when it is positioned away from the edge of the cell, as shown here in Cymbella (left, both living and cleaned material). In Epithemia sorex (two images top right) the raphe curves from the edge onto the valve face, and is visible in both girdle and valve views (left and right respectively). In Nitzschia (bottom), the raphe is confined to the edge of the valve, and is difficult to see, but its position can be seen by the dark fibuale on the lower edge.


The reservoir (arrows) is a sac-like structure at the anterior end of a euglenoid cell, adjacent to the eyespot. The flagellum emerges from this and passes through a canal to the cell exterior.

Rings of scar tissue

In Oedogoniales (in this guide, Oedogonium and Bulbochaete), cell division leaves a thin ring of wall material at the end of one of the parent cells. After many divisions, these rings appear as a stack (arrows), and are distinctive to the group.



The single cells of some desmids are divided into two halves (shown by the red bars), known as semi-cells. These continue to share a single nucleus located in the narrow constriction (isthmus) separating the semi-cells. Examples shown are (clockwise from top left) Staurastrum, Xanthidium, Cosmarium, and Euastrum.


In cyanobacteria, the sheath is a film of jelly (mucilage) coating the cells. In some forms it can be thick and pigmented (such as Ammatoidea, top, in which the filament emerges from the sheath at the end). In others it can be very thin, and barely visible unless the cells are absent over a section (Wilmottia, middle). In Microcoleus (bottom), many filaments share a common sheath.


In Audouinella, sporangia (cells containing numerous small reproductive cells) are born on side branches. The lower arrow indicates a sporangium that is still intact; the upper arrow shows a sporangium that has released its contents.


Some diatoms attach to objects by producing stalks of gelatinous material (arrows). This most famously occurs in Didymosphenia (top), in which the stalks can be extremely abundant. Indigenous diatoms of various kinds also produce stalks, however, such as Gomphoneis (lower), a close relative of Didymosphenia.


In pennate diatoms, which have a silica-based cell wall, a thick line of silica runs between the poles of each valve face (this is the first part of a new valve to be created at cell division). In some diatoms, such as Stauroneis (left, living and cleaned material), the sternum contains the raphe. In others, such as Ulnaria (right, living and cleaned material), the sternum lacks a raphe.


Stipulodes and bract cells, as indicated, are small spiky cells on charophyte filaments. The former are unique to Chara.


Diatoms have silicified cell walls that are ornamented in a variety of ways. One of these is by lines of tiny pores called areolae; a line of these (red bar) is a stria (arrows; plural: striae). Although the individual areolae are difficult to discern with a light microscope, the striae are often easy to see, as shown here in Cymbella aspera. Left, live material; middle, dead cleaned material; right, an enlargement taken using scanning electron microscopy under which the areolae can be seen.


Thylakoid membrane

Photosynthesis in cyanobacteria takes place on thylakoid membranes that are free in the cell matrix, rather than being bound in an organelle (as in other groups of algae). In some cyanobacteria, the thylakoids are often arranged towards the cell periphery, and this is visible under the light microscope by a deeper blue-green colour at the edge of the cell (arrows), as in this filament of Pseudanabaena.



"Uniseriate" and "multiseriate" refer to the width of a filament (in terms of the number of cells). Uniseriate filaments (such as Chroodactylon, left) are only one cell wide. Multiseriate filaments (such as Compsopogon, right) are more than one cell wide. Some taxa, such as Stigonema, may have uniseriate and multiseriate parts.



The two main components of the silicon cases of diatoms

Valve view

Diatoms have a silica-based cell wall, structured roughly in the form of a box (called a "frustule"). The frustule is composed of two valves, connected by a girdle, as shown stylised in the "oblique view". The appearance of the cell varies according to which direction it is viewed. If viewed from the side (girdle view) it appears as a square or rectangle, and if viewed from above or below it appears as an oval with ornamentations on the valve face (valve view). Two examples are shown: light micrographs of Pinnularia and electron micrographs of Gomphonema (which departs from the stylised square/oval shape).