Viruses &
Bacteria
A single teaspoon of seawater holds somewhere between 50 and 500 million virus particles. Scale that up to the whole ocean and you get roughly 1030 of them — more viruses in the sea than there are stars in the observable universe. Almost none of them want to hurt you. Most are hunting bacteria. And the bacteria, in turn, are running every nutrient cycle in the sea. The kingdom-by-kingdom tour begins where life itself begins: with the invisible engine of the ocean.
You hear "virus" and you think disease. Flu. Covid. Something to avoid. But the ocean is swarming with viruses — 10 to 100 million per millilitre of seawater. If they were all attacking us, every swimmer on Earth would be dead within minutes. So what are they actually doing out there?
Almost all of them are eating bacteria. Marine viruses are extremely specific — each kind targets one specific type of host cell, and the vast majority of marine viruses are bacteriophages ("bacteria-eaters"). They drift inertly through the sea, bump into a bacterium, hijack its machinery, build hundreds of copies of themselves, then burst the bacterium open and drift off looking for the next host. Every day this kills somewhere between 20% and 40% of all bacteria in the ocean.
That doesn't sound great — until you realise what happens to all those nutrients trapped inside the dead bacteria. They spill into the seawater and immediately feed the next generation of microbes. This recycling system is called the microbial nutrient loop, and it sits underneath every marine food web on Earth. Cyanobacteria photosynthesise and produce roughly half the oxygen you breathe. Decomposer bacteria break down everything that dies. Deep-sea chemosynthetic bacteria feed entire ecosystems with no sunlight at all. Viruses, bacteria and a small role for fungi — the things you can't see — are the things that keep the ocean alive.
Particles, Cells, and the Invisible Engine
Viruses are inert particles that hijack other cells to reproduce. Bacteria are real prokaryotic cells that decompose, photosynthesise, chemosynthesise — and form the base of every marine food chain.
Technically, viruses are not alive. Outside a host cell, a virus exhibits zero life processes — no movement, no respiration, no reproduction. That's why they're classified as particles, not organisms. The only way they reproduce is to attach to a specific host cell, inject their nucleic acids, and force the host's machinery to manufacture new viruses until the cell bursts. Because they always damage or kill their host to reproduce, every virus is a pathogen — a disease-causer. Scientists call them obligate parasites (or holoparasites) because the parasitism is total: no host = no virus.
Bacteria, by contrast, are genuine living cells — small, prokaryotic (no nucleus, see Topic 14), capable of moving with flagellae, eating a huge variety of substances, and reproducing on their own by splitting in two roughly every 30 minutes. A few bacteria cause disease (just like a few of any organism do), but the overwhelming majority are vital. They decompose dead matter, they recycle nitrogen and carbon, they live where nothing else can — in the freezing dark abyss, in boiling hydrothermal vents, under kilometres of seabed sediment — and they generate huge amounts of food and oxygen at the base of every marine food web.
How We Know: The Discovery Gap
Everything above raises an obvious question. If the ocean has been full of viruses for billions of years, and they are running the place, why did nobody know until recently? CAPS makes this the first thing it says about marine viruses, and the answer is not about biology at all — it is about equipment.
Marine viruses are 0.02 to 0.2 micrometres across. That is small enough to be invisible to a light microscope, and small enough to slip through anything you might reasonably call a filter. So for most of the history of marine science there was no way to separate them from everything else in a bucket of seawater, and no way to see them once separated. Both problems had to be solved before anyone could say what viruses were doing out there.
Two inventions had to arrive before marine virology could exist
1 — A way to separate them. Unglazed porcelain is naturally porous, and its pore size happens to fall between a bacterium and a virus. Push seawater through it and the bacteria are trapped on top while the viruses pass through with the water. What drips out the bottom is a virus-only sample — which is the only way to study something you cannot pick out individually. The filter must be unglazed: glaze is a glassy coating that seals the surface, and a sealed filter is just a cup.
2 — A way to see them. Even a pure sample is useless if every particle in it is invisible. At 0.02–0.2 µm, viruses are below the resolving limit of any light microscope, so counting them needed modern scanning and electron-microscope technology. Filtering gave scientists the sample; scanning let them look at it. Only with both did the 10–100 million per millilitre figure become measurable — and that number is the whole reason this topic exists.
The thing worth taking from this
The viruses were always there. What changed was not the ocean but what we could measure — and the moment the measurement became possible, the most abundant biological entity on the planet appeared in it. That is a general lesson about science and a specific one about the sea: "we have never found any" and "there are none" are different statements, and the gap between them is usually a piece of equipment. You met the same idea in Topic 8, where "absent from the fossil record" turned out not to mean "extinct".
Two Tiny Architectures
The two main microscopic players in the ocean look completely different under an electron microscope. Both are CAPS-examinable as labelled drawings.
A bacteriophage
~ a virus that targets bacteria
A bacterium
~ a prokaryotic single cell
The Viral Life Cycle
Tap each numbered stage to see what's happening at that point in the cycle. The whole sequence — from contact to release — takes about 30 minutes, and produces hundreds of new viruses from each successful attack.
The Microbial Nutrient Loop
Viruses destroy huge quantities of bacteria, phytoplankton and zooplankton — removing them from the normal food chain. But the destroyed cells spill their contents into the seawater, releasing dissolved nutrients that immediately feed the next generation of microbes. This sub-cycle, mostly invisible to us, is called the microbial nutrient loop.
~ the invisible recycling system underneath every marine food web
Why this matters
Without the microbial nutrient loop, the dissolved nutrients in the upper ocean would be sucked up by phytoplankton, eaten by zooplankton, and exported to deep water as the bigger fish ate the smaller ones — never to return to the surface. Viruses keep nutrients circulating in the sunlit zone by lysing (bursting) bacteria and phytoplankton fast enough to keep their chemical contents in the upper water column. Roughly 20%–40% of marine bacteria are killed by viruses every day. The "loss" feeds the engine.
Bacteria — The Indispensables
Bacteria reproduce by binary fission — a parent cell grows, copies its single circular chromosome, and pinches in half. In ideal conditions, a single bacterium can divide every 20 to 30 minutes. In just 8 hours, one cell becomes over 16 million. To keep up with rapid environmental changes, bacteria can also join with another bacterium of the same species but a different genetic strain and exchange pieces of DNA, creating genetic variation without sexual reproduction. This is why bacteria adapt so fast — and why antibiotic resistance evolves the way it does.
Your Topic 16 booklet says bacteria reproduce "by growing and then splitting in two through mitosis", and the Invisible Ocean slide deck repeats it word for word. This is incorrect, and you can prove it from what you already know.
Mitosis requires a nucleus. It is a process in which chromosomes condense, line up on a spindle, and are pulled apart into two daughter nuclei. A bacterium is prokaryotic — this page says so two paragraphs up, and Topic 14 says so at length. It has no nucleus, no chromosomes in that sense, and no spindle fibres. There is nothing for mitosis to happen to.
What actually happens in binary fission is simpler: the single circular chromosome is copied, the two copies move to opposite ends of the cell, the cell grows, and then it pinches in half. No spindle, no nuclear envelope to dissolve and rebuild, which is part of why it can be done in twenty minutes.
What to do in an exam: the same rule as every flag in this course — use the term the question uses, and never lose a mark arguing with a paper. But if you are asked to describe binary fission, describe it correctly and do not mention a spindle. Being able to say why a prokaryote cannot do mitosis is worth considerably more than the word itself.
🦠 Viruses
| Classification | Inert particle / obligate parasite. Not technically alive. |
|---|---|
| Reproduction | Must hijack a host cell — no host, no reproduction. |
| Size | 0.02 to 0.2 μm (need an electron microscope to see). |
| Ecological role | Pathogens; destroyer-recyclers. Their kills feed the microbial nutrient loop. |
🧫 Bacteria
| Classification | Genuine prokaryotic organism (Kingdom Bacteria). |
|---|---|
| Reproduction | Independent binary fission, doubling every 20–30 minutes; plus DNA exchange. |
| Size | 1 to 5 μm (visible with a good light microscope). |
| Ecological role | Primary decomposers · chemosynthesisers at vents · cyanobacteria produce huge oxygen + biomass · base of food webs. |
Four things bacteria do that nothing else can
CAPS lists these as four separate key concepts, and they are worth learning as four separate answers rather than one blur about "bacteria being useful".
🍂 Decomposers
~ CAPS concept 2
The ocean's primary decomposers, and therefore vital in all nutrient cycles. Everything that dies at sea is broken back down into usable chemicals by bacteria.
Found everywhere in the oceans — surface to trench, open water to sediment.
💨 Anaerobes
~ CAPS concept 3
Anaerobic bacteria can function in the complete absence of oxygen. This is a general bacterial ability, not an exotic speciality — and it is why decomposition does not simply stop where the oxygen runs out.
It is what lets bacteria dominate the deep sea and the sediments below it, where oxygen is scarce or absent.
🌋 Chemosynthesisers
~ CAPS concept 4
Around hydrothermal vents, chemosynthetic bacteria use the chemical energy in hydrogen sulphide instead of sunlight to make their own food.
They drive unique deep-water food webs — giant tube worms, vent crabs and white shrimp live off them, with no sunlight involved at any step. (More in Topic 21.)
🧊 Extremophiles
~ CAPS concept 5
Bacteria that survive great temperature and pressure — boiling vent water on the Mid-Atlantic Ridge (Topic 11), freezing brines under Antarctic ice.
They live even deep in ocean floor sediments, below the seabed, still driving nutrient cycles down there.
Watch the overlap — these four are not the same list
It is easy to blur anaerobic, chemosynthetic and extremophile into one deep-sea category, and a question that asks for one will not accept another. Anaerobic describes what a bacterium does without — oxygen. Chemosynthetic describes how it feeds — chemical energy rather than light. Extremophile describes where it lives — conditions that would kill anything else. A vent bacterium may well be all three at once, but plenty of anaerobes live nowhere extreme at all, including in the mud of Algoa Bay and inside your own gut.
A Word on Marine Fungi
Marine fungi are far less well studied than bacteria, but they play a real (if minor) role:
- Decomposers — break down driftwood, dead seaweed, fallen mangrove leaves. Especially active in rocky shores, estuaries and mangrove swamps where the habitat is frequently exposed to air.
- Parasites — some target animals with weakened immune systems, which makes them opportunists rather than aggressive killers. CAPS names the two sectors where that matters most: the mariculture and aquarium industries. In SA that means high-density farms of abalone (perlemoen), oysters, mussels and trout — and equally the tanks at a public aquarium or a home marine tank. Two reasons in both cases: animals are crowded together so infection spreads fast, and the stress of captivity weakens their immune defences. 📌 Note what that implies — a fungus that is harmless in the open sea can become a serious problem the moment you put the same animals in a tank.
- Symbionts — some marine fungi live as partners inside seagrass roots and in lichens on intertidal rocks (the orange-and-grey crusts you can see at Cape Recife at low tide are fungus-and-algae partnerships).
Local connection — the SA mariculture industry
South Africa has a significant abalone-farming sector — particularly along the Western Cape coast at Hermanus and Gansbaai. Haliotis midae ("perlemoen") is farmed for export, and disease management is critical to the industry. Tank conditions are kept clean, water filtered, animals separated by size class, and antibiotics used sparingly — all to keep bacterial and fungal pathogens at bay. Similar disease pressures affect Saldanha Bay mussel farms (Mytilus galloprovincialis) and the growing trout-farming industry in the Western Cape mountains. The link to this topic: every kilogram of farmed seafood you buy in Cape Town depends on someone managing the unseen microbial life around it.
In the Lab — the CAPS Investigations
CAPS sets one real investigation for this block and it is a proper microbiology practical: grow bacteria on agar plates, then look at them under a strong microscope using Gram-positive and Gram-negative stains. The Resources column backs it with agar mix, Petri dishes and a microscope.
What CAPS asks for, word for word
Investigations column, block 44: "Show micrographs" · "Grow bacteria on agar plates and investigate under a strong microscope, using gram + and – stains". Resources: "Slides · Photographs · Diagrams · Charts · Video clips · Agar mix · Petri dishes · Microscope".
Your booklet then adds three drawing outcomes in its core-concepts list: explain the bacteriophage life cycle "by means of an annotated drawing", show the microbial nutrient loop "in an annotated flow diagram", and give the general structure of a bacterium "using a labelled drawing". Those are three things you must be able to produce, not just recognise — so all three are on the practical sheet as blank-page tasks.
Why the Gram stain is on the syllabus at all — it is about the cell wall
A Gram stain looks like a party trick: add dye, some bacteria go purple, others go pink. But the split is not cosmetic. It is a direct read-out of cell-wall chemistry — the one structural feature that separates the two great groups of bacteria.
Gram-positive bacteria have a thick outer layer of peptidoglycan. It traps the first dye (crystal violet) and holds onto it through the wash, so the cell stays purple. Gram-negative bacteria have only a thin peptidoglycan layer with an extra outer membrane over it. The wash strips the violet straight out, so they take up the second, pink counterstain instead and finish pink or red.
📌 Look back at the bacterium diagram in section three. Its cell wall is labelled "rigid, plant-like" — and this is what that wall is actually made of, and why it is worth labelling. The Gram stain is the reason the cell wall is a definitive feature rather than just another ring on the drawing. It also has a very practical consequence: because the two groups have different walls, they respond differently to antibiotics, so a doctor treating an infection wants the Gram result before choosing a drug.
Four investigations · one needs a lab, and it ships as data
- 🟡 kitchen agar Grow bacteria on plates — CAPS's own investigation, run with home-made gelatine-or-agar plates in clean jars. Swab a few surfaces, seal, incubate, count and describe the colonies. Supplied plate photographs and counts if you would rather not culture anything.
- 🔴 lab only Gram staining — the stains and a strong microscope are genuinely school-lab items, so this arrives as described micrographs, the same pattern Topic 14 uses. You still classify every sample and explain every result.
- 🟢 desk The three examinable drawings — the bacteriophage annotated, the bacterium labelled, and the microbial nutrient loop drawn as a flow diagram from a blank page.
- 🟢 desk Disease in a tank — the booklet's own question on why infections spread in mariculture and aquarium facilities, built out with SA abalone-farm context.
→ Open the Topic 16 practical sheet — printable, with supplied data for every task.
A word about growing bacteria at home
You can culture bacteria in a kitchen and the practical shows you how, but there are two rules the sheet takes seriously. Seal the plates once they are growing and never open them again — you do not know what you have cultured, and a sealed plate is safe while an open one is a bad idea. And dispose of them unopened, in the bin, inside a second bag. Nothing you grow off a doorhandle is likely to be dangerous, but "likely" is not a word to build a safety rule on.
Key Vocabulary
Tap each card to flip it. Five of these are on your booklet's examinable definitions list — bacteriophage · cyanobacteria · holoparasites · obligate parasites · microbial nutrient loop — and pathogen is on its general-terminology list. The rest are CAPS key concepts or practical terms in their own right: you cannot answer this block without binary fission, anaerobic, chemosynthesis, extremophile, prokaryotic, decomposer, lysis and Gram staining, whether or not they appear in a glossary.
⚠️ Watch holoparasite and obligate parasite — your booklet lists them as two examinable definitions and then gives them the same wording. They are two names for one idea, and a question may use either.
A virus that specifically targets a bacterium. Has a distinctive lunar-lander shape: an icosahedral protein head containing DNA, plus a tail with attachment fibres that grip the bacterium. The most abundant biological entity in the ocean.
A parasitic organism (or particle) that takes over the functions of the host cell's nucleus to carry out all its own life functions, including reproduction. Same idea as an obligate parasite: cannot survive or reproduce without the host. Every virus is one.
A harmful parasite that must infect a host organism to survive and reproduce — and causes disease in the process. All viruses are pathogens; only a small fraction of bacteria and fungi are.
A nutrient-cycling sub-system in marine ecosystems that passes nutrients only between microorganisms (bacteria, phytoplankton, zooplankton, viruses), recycling them within the upper water column. Viruses kill microbes; the dead cells spill their nutrients; new microbes use them. The "loop" keeps the surface ocean from going barren.
A phylum of bacteria that can photosynthesise. The first organisms ever to release oxygen on Earth (~2.4 billion years ago, see Topic 9). Modern marine cyanobacteria like Prochlorococcus are the most abundant photosynthesisers on the planet and produce a huge share of Earth's oxygen.
Bacterial asexual reproduction by splitting in two. Under ideal conditions, a single bacterium can grow and split every 20–30 minutes, producing an exponential population doubling. It is not mitosis — mitosis needs a nucleus and spindle fibres, and a bacterium has neither. The single circular chromosome simply copies itself, the two copies move to opposite ends, and the cell pinches in half.
Production of energy-rich organic compounds using chemical energy from inorganic substances (typically hydrogen sulphide), instead of sunlight. Performed by specialised bacteria at hydrothermal vents, where it drives entire ecosystems with no light at all.
An organism — usually a bacterium or archaeon — that thrives in extreme conditions: extreme heat, cold, pressure, salinity, acidity or alkalinity. Found at hydrothermal vents, under ice sheets, in deep seabed sediments, and in hypersaline lakes.
A parasite that cannot survive or reproduce without its host — the dependence is total, not optional. Your booklet gives this and holoparasite as two separate examinable definitions and then defines them identically: "parasitic organisms which take over the functions of host cell nuclei to carry out all of their own life functions, including reproduction." Treat them as two names for one idea, and use whichever the question uses.
A cell with no true nucleus and no membrane-bound organelles. Its DNA sits free in the cytoplasm as a closed loop called the nucleoid. All bacteria are prokaryotic — and this single fact is why binary fission cannot be mitosis: there is no nucleus and no spindle for mitosis to use. Compare eukaryotic in Topic 14.
Able to function in the complete absence of oxygen. A general and widespread bacterial ability — not a rare deep-sea speciality. It is what allows bacteria to keep decomposing material in the oxygen-starved deep sea and in seabed sediments, where nothing that needs oxygen could work at all. Opposite: aerobic.
The rupturing of a cell so that its contents spill out. It is stage 6 of the viral life cycle: the new viruses burst the host bacterium open and escape. Lysis is the exact moment the microbial nutrient loop turns — the host dies, and everything that was inside it becomes dissolved food for the next generation of microbes.
An organism that breaks dead material down into simpler chemical substances, returning them to the environment for reuse. Bacteria are the ocean's primary decomposers and are therefore vital in all nutrient cycles; marine fungi play a smaller version of the same role, mostly where the habitat is regularly exposed to air.
A staining technique that sorts bacteria into two groups by cell-wall chemistry. Gram-positive cells have a thick peptidoglycan wall that holds the violet dye → they finish purple. Gram-negative cells have a thin wall plus an outer membrane, so the violet washes out and they take the counterstain → pink. The difference also changes which antibiotics work.
Quick Check
Question 1
Well done!
Next: Plankton — the drifting community that turns sunlight into the base of every marine food web.