The Invisible Living World

Start with a simple list. Write down every living thing you can see from where you are sitting right now — classmates, a teacher, a crow on the window ledge, a line of ants near the door, a neem tree in the ground outside, maybe a stray dog. It feels like a full list. It is not even close. For every living thing on that list there are uncountable others in the same room, on the same desk, on your own hands, that you will never see with your eyes alone.

The reason is simple. Your eye is a good instrument, but it has a limit. Two things that are closer together than roughly one-tenth of a millimetre blur into a single blob, and below about that size you cannot make out the shape of an object at all. A full stop printed in a book is only a few times bigger than that limit. Now imagine a living creature hundreds of times smaller across than that full stop, complete with everything it needs to feed, grow and make copies of itself. That is an ordinary bacterium. We call all such living things microorganisms, or microbes: living things too small to be seen without a microscope.

How small is small? Scientists measure them in micrometres. One micrometre is a thousandth of a millimetre, which is a millionth of a metre. Most bacteria are only about one or two micrometres across. Viruses are far smaller still — so small that an ordinary light microscope cannot show them at all.

Now the more surprising part: where they live. The honest answer is almost everywhere. A pinch of garden soil holds an enormous number of them. So does a drop of pond water, a spoon of curd, the air in this room, the surface of an unwashed fruit, the inside of your mouth and the whole length of your food pipe and intestine. They are on doorknobs, currency notes, mobile screens and the tap handle you touched this morning. They also live in places where nothing else survives — the near-boiling water of a hot spring, thick ice, water so salty that fish cannot live in it, and the dark cold floor of the deep sea. When conditions turn bad, many bacteria and fungi form tough resting stages called spores, sit still for months or years, and start growing again the moment warmth and moisture return. This is exactly why a dry packet of flour is safe for months but turns mouldy within days once it gets damp.

One more idea, and it clears up a lot of confusion. You often do see microorganisms — you just do not see them one at a time. The greenish fuzzy patch on stale bread, the slimy green film on a wet bathroom wall, the pond scum on still water, the cloudy swirl in spoiled milk: in each case you are looking at millions of individuals crowded together. The crowd is visible; the member is not.

Finally, the most important correction most students need. Microorganisms are not the enemy. The great majority are harmless to us, and a large number are useful — some are the reason you have curd with your lunch, some keep farm soil fertile, some break down the dead leaves that would otherwise pile up forever, and some live inside you and help you stay well. Only a small fraction cause disease. Those few get all the attention, but judging the whole invisible world by them is like judging a city by its pickpockets.

For most of human history nobody knew any of this. People saw milk turn sour, wounds turn septic and whole villages fall ill, and had no way to see the cause. The invisible world stayed invisible not because people were not curious, but because they had no tool. The tool, when it arrived, was the microscope.

Begin with the simplest version, which you have probably used. A hand lens or magnifying glass is a single convex lens. Hold it a few centimetres from a leaf or an insect and you see an enlarged, upright image — useful for counting the legs of an ant or seeing the veins in a petal, but it magnifies only a few times. That is nowhere near enough for a bacterium. This is called a simple microscope, because it uses one lens.

A compound microscope is the real instrument. It uses two lens systems in a tube. The lens near the object is the objective; the lens you look through is the eyepiece. The objective makes an enlarged image, and the eyepiece then enlarges that image again. Because the two act one after the other, their magnifying powers multiply instead of adding. An eyepiece marked 10× used with an objective marked 40× gives 10 × 40 = 400 times magnification. Swap in a 100× objective and the same eyepiece gives 1000 times.

The parts are worth knowing by name, and they are easy to recognise once you have handled the instrument yourself. A heavy base and a curved arm hold everything steady. The flat stage carries the glass slide, held by two clips, with a hole in the middle so light can pass through. Below the stage a mirror or a small lamp throws light upward through the specimen. Several objectives are screwed into a rotating nosepiece, so you can turn a different power into place. Two knobs move the tube: the coarse adjustment for large movements and the fine adjustment for the last delicate bit of focusing.

Using it well is mostly about patience. The specimen must be thin and flat enough for light to get through it, which is why you use a thin peel, a smear or a single drop, spread on a slide and covered with a coverslip so that it does not dry up. Lower the coverslip slowly from one edge, or air bubbles get trapped underneath and are easily mistaken for cells. Always start with the lowest-power objective, find the object, and only then move to a higher power. Two things surprise students the first time: the image is upside down and left-right reversed, so moving the slide to the right moves the image to the left; and at high power the tiniest touch throws everything out of focus.

The history is short and remarkable. In 1665 Robert Hooke published a book of drawings made through an early compound microscope. Looking at a thin slice of cork, he saw tiny empty boxes like the rooms of a monastery and gave them the name cell — a word biology has used ever since. A few years later, in the 1670s, a Dutch cloth merchant named Antonie van Leeuwenhoek ground tiny glass beads into astonishingly good single lenses and turned them on pond water, rain water, scrapings from his own teeth and much else. He saw things moving. He described tiny living creatures, which came to be known in English as animalcules, and reported them in letters to the Royal Society in London. He was the first human being to see bacteria.

Even the best light microscope has a ceiling, because light itself sets a limit to how fine a detail can be separated. Viruses lie below that ceiling. They stayed unseen until the electron microscope was developed in the 1930s. Instead of light it uses a beam of electrons, and it can magnify hundreds of thousands of times — enough to photograph a single virus particle.

Once the microscope existed, the same discovery kept repeating itself. A shaving of cork, a peel lifted off an onion, a scraping from the inside of a cheek, a thin slice of a leaf, a drop of blood — every one of them turned out to be built out of small compartments packed together. That is the biggest idea in this chapter, and it is worth saying plainly: every living thing, from a single bacterium to a banyan tree to you, is made of cells. A cell is the smallest unit that can carry out the activities we call life — taking in food, using energy, growing, getting rid of waste and producing more of its own kind.

Cells differ enormously in shape and size, but the same few structures turn up again and again. The cell membrane is a thin covering that holds the cell together and controls what goes in and what comes out; nothing enters or leaves without crossing it. Inside is the cytoplasm, a jelly-like material that fills the cell. Most of the cell’s chemical work goes on there, and the other structures are held in it. Most cells also have a nucleus, a rounded, denser body that carries the instructions for running the cell and passes them on when the cell divides. Because it directs what the cell does, the nucleus is often called the control centre of the cell.

A plant cell has some structures an animal cell does not. Outside its membrane lies a stiff cell wall that gives the cell a definite shape and holds it firm — one reason a leaf keeps its shape while a drop of blood does not. Many plant cells contain plastids; the green ones hold chlorophyll and are where food is made in sunlight, and they are the green specks you actually see when you look at a leaf under a microscope. A mature plant cell also usually has one large vacuole, a bag of watery fluid that stores dissolved substances and, when it is full, presses outwards and keeps the plant firm; animal cells have only small vacuoles. This is why a plant that has not been watered goes limp and picks up again within hours of being watered. A bacterial cell is simpler than either: it has a membrane and cytoplasm, but no nucleus with a covering of its own. Its genetic material lies in one region of the cytoplasm, called the nucleoid.

Nearly all cells are far too small to see, which is why nobody suspected they existed before the microscope. Not all, though. The yolk of a hen’s egg is a single cell, big enough to hold in a spoon, and some nerve cells in your own body are thin but long enough to run from the lower back down to the toe. Size is not what makes something a cell; being a complete working unit is.

Some living things finish the whole job with one cell. A bacterium, an Amoeba, a Paramecium and a yeast cell are unicellular: that single cell feeds, grows, throws out waste and divides, all by itself. Others are multicellular, built from very large numbers of cells that have divided the work between them. In a multicellular body no single cell has to do everything, so cells become specialists — a muscle cell shortens and pulls, a nerve cell carries messages, a root hair cell soaks up water from the soil.

That specialisation leads to a neat ladder, and it is worth learning in order. Similar cells doing the same job form a tissue. Different tissues working together as one structure form an organ, such as the heart, the stomach or a leaf. Organs that co-operate on one large task form an organ system, such as the digestive system in you or the shoot system of a plant. All the systems together make the whole organism. Cell, then tissue, then organ, then organ system, then organism: each step is built out of the one before it. Muscle cell, muscle tissue, heart, circulatory system, human being — run that example through in your head and the ladder stops being a list to memorise.

Put the pieces together and you can see why biologists call the cell the basic unit of life. Every living thing is made of one cell or of many. The smallest living things are single cells, and nothing smaller than a cell is alive on its own — a virus, as you will see in a moment, is not even a cell, which is exactly why it can do nothing at all until it gets inside one. And every new cell comes from a cell that already existed, whether that is a bacterium splitting in two or the millions of divisions that build a whole baby from one fertilised cell. Cells are where life is carried on, and cells are where new life comes from.

The invisible world is not one kind of thing. It is at least five very different kinds, and the whole chapter becomes easier once you can tell them apart. Take them one at a time.

Bacteria. Each bacterium is a single cell, and a simple one: it has no nucleus with a covering of its own, so its genetic material lies in a region of the cytoplasm called the nucleoid. They come in a few recognisable shapes — round, rod-shaped, comma-shaped and spiral. They multiply by simply splitting in two: one becomes two, two become four, four become eight. When food, warmth and moisture are all available this splitting happens fast, and a handful of bacteria on a plate of leftover rice can become an enormous population in a few hours. That single fact explains most of what you will read later about food spoiling and about why cooked food should not be left standing in the heat. Examples worth remembering: Lactobacillus, which sets your curd, and Rhizobium, which enriches farm soil.

Viruses. Viruses break the pattern. A virus is not a cell at all. It is a small package of genetic material wrapped in a protein coat, and nothing more. It cannot eat, cannot grow, and cannot make copies of itself on its own. It multiplies only after it gets inside a living cell — of a plant, an animal, a human being, or even a bacterium — where it forces that cell to build new virus particles. Outside a living cell a virus is as inactive as a grain of dust. Because of this, biologists describe viruses as sitting on the border between the living and the non-living. The common cold, influenza, chickenpox, measles, polio and dengue are all caused by viruses.

Fungi. Fungi are not plants, and this trips students up because they often look plant-like. They have no chlorophyll, so they cannot make their own food. Instead they grow into or over something and absorb ready-made food from it. That is why they turn up on damp bread, on leather shoes and cloth left in a humid cupboard, on rotting fruit and on wet walls. Yeast is a single-celled fungus that multiplies by budding — a small bulge grows on the parent cell and breaks away. Bread mould, Rhizopus, spreads as cottony white threads dotted with black pinheads. Mushrooms are fungi too, and a useful reminder that not every fungus is microscopic.

Protozoa. Protozoa are single-celled but animal-like: they move about and take in food rather than making it. Amoeba has no fixed shape and creeps along by pushing out finger-like extensions of itself. Paramecium is slipper-shaped and swims using rows of tiny hair-like structures. Not all are harmless — Plasmodium causes malaria, and another protozoan causes amoebic dysentery. A drop of pond water under a microscope is the classic place to meet them.

Algae. Algae are the green ones. They contain chlorophyll, make their own food by photosynthesis and release oxygen, exactly as land plants do. Chlamydomonas is a single swimming cell; Spirogyra forms the slippery green threads you can lift out of a village pond on a stick; diatoms drift in their millions in seawater inside beautiful glassy cases. The green film on a wet wall after the rains and the green water in a neglected tank are algae. Like fungi, not all of them are tiny — seaweeds are algae as well. A large part of the oxygen produced on Earth comes from algae and other tiny drifting life in the oceans, which makes this the most underrated group on the list.

Now for the useful side, which is the larger side. Human beings have been putting microorganisms to work for thousands of years, mostly without knowing they existed.

Curd. Warm a little milk, stir in a spoonful of yesterday’s curd, cover it and leave it. The spoonful is a starter: it carries Lactobacillus bacteria, which multiply in the warm milk and convert milk sugar into lactic acid. The acid does two things — it gives curd its pleasant sourness, and it makes the proteins of milk clump together so that the liquid sets into a soft solid. You can watch the temperature matter with your own eyes. In summer the curd sets in a few hours; in winter the same milk may sit all night and stay runny, which is why people wrap the pot in a cloth or keep it near the stove.

Fermented batters and bread. The same idea, slightly different microbes. Idli and dosa batter is left overnight and rises, froths and turns pleasantly sour because bacteria and yeasts already present in the rice, the dal and the air get to work. The gas they release is carbon dioxide, and the bubbles it forms are what make a steamed idli soft and full of holes instead of dense. Bakers do the same job with a chosen fungus: baker’s yeast is mixed into dough with a little sugar, it releases carbon dioxide, the trapped gas pushes the dough up, and the holes stay behind in the baked loaf. The general name for this whole business is fermentation — microorganisms breaking down sugars without oxygen and giving out acids, gases or alcohol. In the nineteenth century Louis Pasteur showed that fermentation is not a chemical accident but the work of living microorganisms, which changed both science and industry. Cheese, vinegar, soy sauce and traditional pickles all depend on the same principle.

Feeding the soil. About seventy-eight per cent of the air is nitrogen, and plants need nitrogen to build proteins — yet they cannot take it straight from the air. Certain bacteria can. Rhizobium lives inside swellings called root nodules on the roots of leguminous plants — gram, moong, arhar, pea, bean and groundnut. It converts nitrogen from the air into a form the plant can absorb, and in return the plant feeds and shelters it — both sides gain. Other nitrogen-fixing bacteria live free in the soil, and blue-green algae do the same job in flooded paddy fields. This is the science behind an old farming habit: growing pulses in rotation with cereals, or ploughing the crop back in, leaves the field richer in nitrogen and cuts the amount of fertiliser the next crop needs. Cultures of such helpful microorganisms are sold to farmers as biofertilisers.

Clearing up. Bacteria and fungi are the decomposers. They break down fallen leaves, crop stubble, cattle dung, kitchen waste and the bodies of dead animals into simple substances that go back into the soil for the next generation of plants. Without them, dead matter would pile up and the nutrients locked inside it would never return. We use this deliberately: a compost pit turns household and farm waste into manure, and a biogas plant lets microorganisms digest cattle dung in a sealed tank, giving a burnable gas for the kitchen and a good manure as what is left. Sewage treatment plants clean waste water the same way, using microorganisms to eat the organic dirt in it.

Medicine. In 1928 Alexander Fleming noticed that a mould had drifted onto a dish where he was growing bacteria, and that the bacteria near the mould had been wiped out. The mould was Penicillium, and the substance it made became penicillin, the first widely used antibiotic. Antibiotics are medicines, obtained from moulds and from certain bacteria, that kill bacteria or stop them multiplying. Note the word bacteria carefully: antibiotics do nothing at all to viruses, so taking one for an ordinary cold is useless, and they should only ever be taken when a doctor prescribes them. Microorganisms living in your own intestine are useful too: they help with digestion, crowd out harmful microbes and help produce certain vitamins, including vitamin K.

Now the small minority that cause trouble. A microorganism that causes disease is called a pathogen, and a disease that can pass from an infected person to a healthy person is called a communicable disease. Microbes travel by ordinary routes: in the tiny droplets thrown out when an infected person coughs or sneezes, in drinking water or food that has been contaminated, by direct contact and shared towels or combs, and on small animals such as mosquitoes and houseflies that pick up a germ in one place and leave it in another. Each route has an obvious block — covering a cough, boiling or filtering drinking water, washing hands with soap, covering food, and not letting water stand around the house.

It helps to keep the causes sorted by group. Bacteria cause tuberculosis, cholera and typhoid. Viruses cause the common cold, influenza, chickenpox, measles, polio, dengue and hepatitis. Protozoa cause malaria and amoebic dysentery. Fungi cause ringworm and similar skin infections. Sorting a disease correctly is not just tidiness — it tells you whether an antibiotic can help at all, since an antibiotic acts on bacteria and on nothing else in that list.

Plants and farm animals suffer too. Citrus canker, a bacterial disease, damages orange and lemon trees. Rust of wheat is caused by a fungus and can ruin a standing crop. Yellow vein mosaic of bhindi is caused by a virus and is carried from plant to plant by an insect. In cattle, anthrax is caused by a bacterium and foot and mouth disease by a virus. For a farming family these are not textbook entries; a diseased crop or a sick animal is lost income.

Food spoilage. Microorganisms land on food from the air, from hands, from utensils and from insects. They then use the food as their own meal, and in doing so change its smell, taste, colour and texture — milk turns sour, cooked rice smells off, bread grows a fuzzy patch, cut fruit goes slimy. Some of them also produce poisonous substances called toxins, and eating such food causes food poisoning, with vomiting, stomach pain and diarrhoea that can be serious. Two practical rules follow. First, do not simply scrape the mould off a piece of bread or a fruit and eat the rest — the fungal threads and any toxins reach deeper than the visible patch. Second, a bulging packet, an off smell or a slimy surface means the food should go, whatever it cost.

Behind all of this sits one short list. Microorganisms multiply fast when they get food, moisture and a comfortable warmth, and many of them need air as well. You can watch each condition working. Cooked food left standing spoils within hours on a summer afternoon but keeps far longer on a cold night. A sealed packet of flour sits unchanged for months and grows mould within days of getting damp. A compost pit that is kept moist and turned over breaks down waste quickly, while the same waste left dry and packed tight sits there almost unchanged. Learn that list properly, because every method of keeping food safe in the next section is simply one of those four conditions being taken away.

You already have the list of what microorganisms need in order to grow: water, a comfortable temperature, food, and in many cases air. Take away any one of them and growth stops. That single idea makes every method of food preservation obvious rather than a list to be memorised. Every technique below is just one of those four ideas in a different costume.

Taking away water — drying. The oldest method and still one of the best. Grain is dried before it is stored; papad, vadi, badi, dried chillies, dried methi leaves, dried fish and mango slices are all preserved simply by putting them in the sun until almost no moisture is left. Microorganisms cannot grow without water, so they sit there, dormant and harmless — which is also why a stored packet must be kept sealed and dry, since letting moisture back in wakes everything up.

Taking away water — salt and sugar. Salt and sugar work by the same underlying trick, without any drying in the sun. When food is packed in a strong solution of salt or sugar, water is pulled out of the microbial cells, and a shrivelled cell cannot multiply. Salt preserves raw mango and lemon pickle, amla, fish and meat. Sugar preserves jam, jelly, murabba and squash. This is why a jam that looks sweet and harmless is in fact a hostile place for a microbe.

Changing the surroundings — oil and vinegar. The layer of oil floating on top of a pickle jar is not decoration. It seals the surface, keeping out air and moisture, so microbes below cannot get established. Vinegar does it differently, by making the food too acidic for most microorganisms to survive. Together they are the reason an Indian pickle can sit on a shelf through a whole year.

Using heat. High temperature kills most microorganisms, although the tough spores of some can survive a short boiling. Boiling milk before storing it, cooking food thoroughly, and reheating leftovers until they are steaming hot all work on this principle. The industrial version is pasteurisation, named after Louis Pasteur: milk is heated to around 70 °C for roughly fifteen to thirty seconds and then chilled quickly. That is hot enough to kill harmful microbes but short enough to leave the taste and food value of the milk largely intact, and the sudden chilling stops any survivors from multiplying.

Using cold. This one is regularly misunderstood, so read it slowly. Cold does not kill microorganisms; it only slows them down. A refrigerator makes them sluggish, and a freezer makes them almost inactive, but they are still there and they resume the moment the food warms up. That is why cooked food keeps for a day or two in the fridge but not for a week, why food should be cooled and put away rather than left standing on the counter, and why thawed food should not be refrozen casually.

Keeping new microbes out. Airtight jars, sealed tins, canned food, tetra packs and vacuum-sealed packets all keep out both air and fresh microorganisms. Once the seal is broken the clock starts, which is exactly why packets carry an instruction to refrigerate after opening and to use within a few days.

Chemical preservatives. Small, legally permitted amounts of chemicals such as sodium benzoate and sodium metabisulphite are added to jams, squashes, sauces and packed foods to hold microbial growth back. They are listed on the label, and the permitted quantities are fixed by food safety rules.

Finally, everyday habits matter as much as any technique. Use a clean, dry spoon in the pickle jar — a wet spoon introduces both water and microbes in one go. Keep cooked and raw food separate. Cover everything. Wash fruit and vegetables. Check the date on packed food, and treat a swollen or leaking packet as spoiled without opening it.