Cyanobacteria, Phytoplankton
& Microalgae
Topic 21 gave you the machinery of photosynthesis. This topic introduces the organisms that actually run it — and they are almost all invisible. Four groups of single-celled drifters produce between 50% and 80% of the world's oxygen, feed nearly every marine food web, built the atmosphere you are breathing, and laid down the chalk and the glass-mud on the seabed. They can also poison an entire bay in a week.
Some nights the surf along the Cape coast glows. Every breaking wave lights up electric blue, and footprints in the wet sand flash for a second and fade. A few weeks later, the same stretch of coast can turn rust-red by day, shellfish harvesting gets shut down, and dead fish wash up. Different events, same cause. What is it?
Dinoflagellates — single-celled algae, each smaller than a grain of talcum powder, present in their billions. Some species are bioluminescent: when the water around them is physically agitated by a breaking wave, a paddle or a propeller, they emit a flash of blue-green light. That glow is called phosphorescence, and it is the same organism doing the same chemistry whether it lights up a wave at Muizenberg or the wake of a boat.
Give those same cells a sudden flood of nutrients and they multiply until the water is a reddish cloud — a red tide. Depending on the species, dense colonies can release toxins that poison marine consumers directly, or accumulate in filter feeders like mussels and reach people who eat them. That is why these population explosions are called harmful algal blooms (HABs).
Beautiful and dangerous, from the same microscopic organism. That double edge runs through this entire topic.
The Invisible Majority
"Phytoplankton" is a job description, not a family. It means any drifting organism that photosynthesises — and the four groups that do most of it come from three different kingdoms.
They are microscopic, but their sheer numbers and high turnover rate make them the vital primary producers of the planet. They drive almost all marine food chains, and conservative estimates put their oxygen production at 50–80% of the world's total. Here is the fact that surprises everyone: the seaweeds and kelps you can actually see — the ones in the next three topics — account for only about 5% of ocean productivity. The other ~95% is done by organisms you need a microscope to find.
The four groups CAPS asks you to know are cyanobacteria (photosynthetic bacteria — prokaryotes, Topic 16), diatoms and coccolithophores (both Kingdom Chromista, alongside the brown algae of Topic 24), and dinoflagellates (Kingdom Protista, Topic 18). Different ancestors, same job — exactly the point Topic 17 made about plankton being a lifestyle rather than a group.
And they are not only feeding the present ocean. Cyanobacteria built the oxygen atmosphere, diatoms lay down siliceous ooze, coccolithophores build chalk and limestone, and dinoflagellates power coral reefs. The monumental architecture of this planet was authored almost entirely by the invisible.
Under the Microscope — the Big Four
A single drop of Benguela seawater, seen at about ×400. Four organisms, three kingdoms, one job. Tap each one to see what it is, what it is made of, and what it leaves behind.
Cyanobacteria — the Oldest Engine
Photosynthetic bacteria, only 0.2 to 2 micrometres across. Because of that size they are classed as picoplankton, they were only documented properly very recently — and they are among the oldest organisms in the entire fossil record.
~ CAPS asks you to be able to explain the structure of a cyanobacterium with a labelled diagram like this one
They gave us the air
Cyanobacteria are believed to be responsible for adding the oxygen to the early Earth's atmosphere — the change that made every other form of life possible. For roughly the first half of Earth's history there was effectively no free oxygen; then these organisms, photosynthesising in shallow seas, slowly filled the air with it. Every animal that has ever breathed owes its existence to a bacterium 2 micrometres wide. And they have not stopped: they are still responsible for significant levels of photosynthesis today, taking in CO₂ and releasing O₂ across almost all aquatic microbial systems.
Too small to be eaten — so where does their food go?
Here is the CAPS point learners miss. Despite all that photosynthesis, cyanobacteria are not regarded as producers in conventional food chains, because at 0.2–2 µm they are too small to be collected by consumers — no copepod can filter them out. Instead their energy enters the microbial nutrient loop you met in Topic 16: they are consumed by other microbes, which are consumed by slightly larger ones, and only several steps later does that energy reach a size any conventional consumer can eat. A parallel food web, running alongside the visible one.
Diatoms — Life in a Glass Box
Microscopic members of the Kingdom Chromista — the same kingdom as the kelps in Topic 24. Each diatom is a single cell living inside a frustule: a clear silica (glass) wall made of two closely fitting halves, called valves, that sit together like the lid and base of a pillbox.
Frustule & perforations
Small holes perforate the frustule, letting substances move into and out of the cell. The pattern of those holes is specific to each species — which is how scientists identify diatoms under a microscope, and why a diatom slide looks like engraved glass.
Pigments & buoyancy
Chlorophyll and accessory pigments give diatoms a distinctive yellow-green colour. Much of the food they make is stored as fatty acids and oils — which are less dense than water, so they keep a heavy glass box floating at the depth where light is still available.
The shrinking problem — run it yourself
Diatoms reproduce by binary fission (mitotic division). But they divide inside a rigid glass box, and each daughter cell inherits one valve and builds a new, slightly smaller one inside it. Press the button and watch what that does over a few generations.
The two reproductive strategies — an exam favourite
Favourable conditions → asexual. Binary fission, over and over. Many of the new cells do not separate, so they form long chains, with each new individual smaller and smaller. Eventually the mass of all that additional silica weighs them down and they sink to the ocean floor, forming thick layers of silica-rich mud: siliceous ooze.
Unfavourable conditions → sexual. When nutrients run short or temperatures turn unsuitable, a sexual reproductive process produces large auxospores, which can stay dormant until conditions improve. The auxospore then forms a new full-sized frustule and the asexual cycle starts again. Sexual reproduction is the diatom's size reset button.
You have met their graveyard before
Those sinking glass boxes are the siliceous ooze of Topic 19 — a biogenous sediment by origin, pelagic by situation — and the diatom-and-radiolarian rain of Topic 18. Diatom frustules also give us diatomaceous earth, mined and used in pool filters, toothpaste and insect powders. Everything in this course connects: the producer at the surface becomes the sediment on the seabed becomes the rock in the quarry.
Coccolithophores — Armour of Chalk
Also single-celled, also Kingdom Chromista — but where a diatom builds with silica, a coccolithophore secretes shields of calcium carbonate from its cell walls, overlapping like the plates of a microscopic football.
| Diatoms | Coccolithophores | |
|---|---|---|
| Kingdom | Chromista | Chromista — the same |
| Cell covering | Frustule of silica (glass), two valves | Shields of calcium carbonate (CaCO₃) |
| Where in the water | Mid-water, held up by oils and fatty acids | Closer to the surface, in the brightest light |
| Reproduction | Binary fission, plus auxospores when conditions are poor | Binary fission, regularly, in good conditions |
| What they leave behind | Siliceous ooze — silica-rich mud | Chalk and limestone |
Niche partitioning — why wear armour in bright light?
Coccolithophores are found closer to the surface, where the light is strongest. It is possible that the calcium-carbonate shields reduce the amount of incoming light so that it is not too bright — effectively a pair of sunglasses. That would be an adaptation for niche partitioning: it lets coccolithophores occupy an exclusive zone right at the top, out of competition, while other phytoplankton migrate further down during the day. Different species, different depths, less competition — a theme you will meet again in every ecology topic.
From plankton to landscape
As older coccolithophores die they sink, shedding those heavy calcium shields. Millions of years of that microscopic rain has produced some of Earth's thickest sediment layers, which become chalk and limestone — the White Cliffs of Dover are one enormous coccolithophore graveyard. The chalk a teacher writes with is the discarded armour of organisms that drifted in a sea long before there were teachers.
📌 Not every limestone is a coccolithophore graveyard, though — and the nearest one to us is not. The limestone quarried on the Western Cape coast for cement comes from the Malmesbury Group, laid down roughly 1 000–550 million years ago and later cooked and squeezed by mountain-building. That is Precambrian — older than coccolithophores themselves. Same rock type, completely different story. Worth remembering whenever you meet the phrase "limestone is made of tiny shells": sometimes it is, and sometimes it is not.
Dinoflagellates — the Ones That Swim
Single-celled protists (Topic 18) with two flagella — whip-like threads that let them move up and down the water column instead of simply drifting. Many, but not all, species are autotrophic, which is why they count as phytoplankton; some of those also prey on other plankton to supplement their food reserves.
Zooxanthellae ⚠ see note
Some dinoflagellates live inside the ectodermal cells of coral polyps as mutualistic partners — these are the zooxanthellae. They photosynthesise using nutrients extracted from the polyp's excretory products, and produce enough food for themselves and the polyp, which otherwise gets very little food from the water around it. Coral reefs exist because of this deal. (Topic 30, Cnidaria.)
Red tides & HABs
In favourable high-nutrient environments some species reproduce so fast that the population resembles reddish clouds under the surface — a red tide. Depending on the species, those dense colonies can form toxins directly harmful to marine consumers, or to secondary consumers — including humans — who eat affected filter feeders. Hence harmful algal bloom (HAB).
Phosphorescence
Some HAB and other dinoflagellate species are bioluminescent — able to emit light from their bodies. They glow blue or green at night when the water is agitated: a propeller, a paddle, a hull, a breaking wave. The phenomenon is known as phosphorescence, and it is what lights up the surf in the hook at the top of this page.
Where zooxanthellae actually live — your sources and current science disagree
Write "ectoderm" if a paper asks. CAPS says "Some inhabit ectoderm of coral polyps" and your Two Oceans booklet says "Some live within the ectodermal cells of coral polyps", so that is the answer a memo will be marked against, and it is what this page says above.
But the current science places them in the gastrodermis. A coral polyp is built from two cell layers: an outer ectoderm facing the sea, and an inner gastrodermis lining the gut cavity, which develops from the embryonic endoderm. Zooxanthellae live inside membrane-bound vacuoles in the gastrodermal cells — the inner layer, not the outer one.
📌 And it makes sense that way round. The alga is being fed the polyp's waste nitrogen and CO₂ and is handing back sugars, so it sits where that exchange happens — against the gut, not on the outside surface where it would be exposed and easily lost. You will meet the two germ layers properly in Topic 30 (Cnidaria), where that topic's own booklet and examinable definition say endodermal — so your sources disagree with each other. In a Cnidaria question, use the endodermal definition; Topic 30 explains.
The Double Edge
CAPS and the Two Oceans booklet both ask the same question directly: how can phytoplankton be both beneficial and harmful? Learn it as two lists.
✔ Beneficial — the producers
- They are the vital primary producers that drive almost all marine food chains — a massive biomass at the base of nearly every ocean food web.
- They produce between 50% and 80% of the world's oxygen, taking in CO₂ and releasing O₂ as they go.
- They pull carbon dioxide out of the water and atmosphere, and build the organic compounds everything else eats.
- Their remains build the seabed itself — siliceous ooze, chalk and limestone.
⚠ Harmful — the suffocators
- After an exceptional upwelling event, a bloom can introduce more food than the ecosystem can possibly consume.
- The uneaten cells die and sink, driving a bacterial bloom whose respiration uses up almost all the available oxygen — anoxic conditions.
- Animals that cannot move out of the area die en masse; rock lobsters walk out of the sea onto the beach to escape.
- Some dense dinoflagellate colonies form toxins that poison marine consumers — and people who eat affected filter feeders.
How a bloom becomes a catastrophe
Exceptional upwelling
A huge pulse of nutrients arrives in the coastal water — far more food than usual.
Unchecked bloom
Phytoplankton multiply explosively. Consumers cannot eat them fast enough.
Die-off & bacterial feast
Uneaten cells die and sink. Decomposing bacteria bloom on the falling organic matter.
Oxygen stripped
Bacterial respiration (Topic 21) consumes almost all the dissolved O₂ — the water turns anoxic.
Collapse
Immobile animals suffocate. Rock lobsters crawl out onto the beach — the famous "walkouts".
Why do red tides seem to happen more often now?
The booklet asks you to think of three possible causes. Reasonable, defensible answers: (1) more nutrients reaching the sea — fertiliser run-off from farms, sewage and industrial discharge all act like the upwelling in step 1, feeding blooms that would not otherwise happen; (2) warmer, more stratified surface water under climate change, which suits many bloom-forming species and changes when and where upwelling occurs; (3) species being moved around the world in ships' ballast water, introducing bloom-formers to coasts that never had them. A fourth, honest answer: we are simply watching much harder — with satellites, monitoring programmes and shellfish-toxin testing, blooms that would once have gone unrecorded are now counted.
Our Own Microscopic Coast
Local connection — the West Coast is a phytoplankton coast
The Benguela upwelling makes the South African West Coast one of the most phytoplankton-rich stretches of ocean on Earth, and it is diatoms that dominate those blooms — which is why the water so often looks green-brown rather than blue, and why the anchovy, sardine and rock-lobster fisheries exist at all.
The same productivity produces the dark side of this topic. Harmful algal blooms and low-oxygen events are a recurring feature of St Helena Bay and Elands Bay, where Jasus lalandii rock lobsters have repeatedly walked out onto the beaches in their thousands during anoxic events — the exact five-step cascade above. South Africa's shellfish-farming areas on the West Coast are monitored for algal toxins, and mussel and oyster harvesting is suspended when toxin levels rise — a public-health system built entirely around single-celled algae.
And on the gentler side: phosphorescent surf is regularly reported around the Cape Peninsula and False Bay, where a night-time dinoflagellate bloom turns every breaking wave electric blue. Same organisms. Same coast. Completely different night out.
In the Lab — the CAPS Investigations
CAPS sets a "photo identification exercise (or with a microscope if suitable samples can be obtained)" and asks you to "include drawing exercise in the practical" — diagrams of diatoms, coccolithophores and dinoflagellates. The practical sheet does both, with described specimens so no mark depends on owning a microscope.
Four investigations · a plankton net, a pencil, paper and four jars
- 🟠 microscope Identify a plankton sample — twelve specimens and a key. Four of them are not phytoplankton at all: can you catch the radiolarian, the foraminiferan, the copepod and the dinoflagellate that eats?
- 🟢 desk The drawing exercise — labelled scientific drawings of a diatom, a dinoflagellate, a coccolithophore and a cyanobacterium, with a magnification.
- 🟢 desk The shrinking diatom — follow a diatom family tree as its glass boxes shrink, and work out when it must make an auxospore.
- 🟢 kitchen Grow a bloom — pond water and plant fertiliser in four jars, measured with a phone light meter. Watch the bloom grow, level off and crash.
→ Open the Topic 22 practical sheet — printable, with supplied data for every task.
Key Vocabulary
Tap each card to flip it. These eight terms come straight from the topic's examinable definition list.
Those plankton that measure between 0.2 and 2 micrometres. Cyanobacteria fall in this class — and because of that size they cannot be collected by conventional consumers, so their energy enters the microbial nutrient loop instead.
The protective, silica-rich walls secreted by diatoms. It consists of two closely fitting halves (valves), perforated with small holes that let substances pass into and out of the cell — and whose pattern identifies the species.
A special structure formed by diatoms — through a sexual reproductive process — enabling them to remain in a dormant state until favourable conditions allow their life cycle to continue. The auxospore then forms a new full-sized frustule and the asexual cycle restarts.
Thick layers of ocean sediment formed by an accumulation of dead diatoms. Their silica frustules sink once the cells become too small and heavy, blanketing the deep seabed in silica-rich mud. (Biogenous sediment — Topic 19.)
The ability of certain organisms to emit light from their bodies. Some HAB and other dinoflagellate species glow blue or green at night when the water they are in is agitated.
A glow in the dark — the name given to the light produced when bioluminescent dinoflagellates in the water are disturbed by a propeller, a paddle or a breaking wave.
Dense colonies of dinoflagellates, forming in high-nutrient environments, that may give rise to toxins and harmful algal blooms. Named for the reddish colour the dense population gives the water.
Having no oxygen. Anoxic conditions develop when a massive bloom dies and the bacteria decomposing it consume almost all the dissolved oxygen in the water — the state that causes mass die-offs and rock-lobster walkouts.
Also worth being able to define
Photosynthetic: able to take in CO₂ and release O₂, using light energy to make food (Topic 21). · Niche partitioning: an adaptation that lets an organism occupy an exclusive zone and so avoid competition — e.g. coccolithophores using their shields to tolerate the bright surface. · Protists: single-celled eukaryotes, often with flagella for movement, which may be autotrophic or prey on other plankton. · Zooxanthellae: dinoflagellates living mutualistically inside coral polyps. · HAB: harmful algal bloom.
Quick Check
Question 1
Well done!
Next: Seaweeds (Macroalgae) — Green and Red. From the invisible 95% to the 5% you can actually pick up off a rock.