Microbes in Human Welfare

Microbes are far too small to see without a microscope, yet a good part of an ordinary Indian kitchen runs on them. The moment you set milk for curd, you are running a controlled microbial culture on your kitchen shelf.

Curd is made by a group of bacteria called lactic acid bacteria, usually shortened to LAB, of which Lactobacillus is the best known member. The small amount of old curd you add to warm milk is the starter, or inoculum: it is not a chemical but a living population of LAB cells. These bacteria multiply in the fresh milk and convert the milk sugar lactose into lactic acid. The acid lowers the pH of the milk, and at that lower pH the milk protein casein can no longer stay dissolved and coagulates, so liquid milk sets into a semi-solid mass. That is why curd tastes slightly sour, and why it sets faster in summer than in winter - the bacteria multiply faster when it is warm. LAB do more than change the texture. They improve the nutritional quality of the milk by increasing its content of vitamin B₁₂. In our stomach and intestine, LAB also do useful work by checking the growth of disease-causing microbes.

Dough is the second everyday example. The dough used for making bread is fermented using baker's yeast, Saccharomyces cerevisiae. Working without oxygen, the yeast breaks sugar down and releases carbon dioxide gas. The gas cannot escape from the sticky dough, so it collects as bubbles and the dough rises. Idli and dosa batter puffs up in exactly the same physical way, because carbon dioxide is trapped in it, but that batter is fermented by bacteria rather than by baker's yeast. This is a small difference that is very easy to get wrong: bread dough with yeast, idli and dosa batter with bacteria, both rising because of trapped carbon dioxide.

Toddy is a traditional drink of some parts of southern India. It is made by fermenting the sap that is tapped from palm trees; microbes present in and around the sap ferment its sugars and produce alcohol.

Microbes are also used in processing cheese, one of the oldest foods in which microbes were deliberately employed. Different cheeses get their character from different microbes, and the two named examples are worth learning as a pair. The large holes in Swiss cheese are made by a bacterium, Propionibacterium sharmanii, which produces a large amount of carbon dioxide as the cheese ripens; the gas is trapped inside the solid curd and leaves behind round cavities. Roquefort cheese is ripened by growing a specific fungus of the genus Penicillium on it, which gives that cheese its blue-green veins and its particular flavour and smell. Notice that the same fungal genus turns up again later in this chapter as the source of the first antibiotic, so do not let the two uses blur into one.

When microbes are grown deliberately in very large vessels to make a useful product on a commercial scale, the vessel is called a fermentor and the work is industrial microbiology. Two families of products dominate this section: alcoholic beverages and antibiotics.

The yeast Saccharomyces cerevisiae is used for fermenting malted cereals such as barley, and for fermenting fruit juices such as grape juice. In the absence of oxygen the yeast breaks sugar down into ethanol and carbon dioxide. Because the very same organism is used both for raising dough and for brewing, it carries two common names - baker's yeast and brewer's yeast - and both names refer to one species.

The distinction to hold on to here is between beverages that are distilled and beverages that are not. Wine and beer are produced without distillation. The fermented broth itself, after it is cleared, is the drink, so the alcohol content stays low. Whisky, brandy and rum are produced by distillation of the fermented broth. Distillation separates and concentrates the alcohol, which is why these are much stronger drinks. Along with that, remember the raw material: wine is made from fruit juice, beer from malted cereals.

Antibiotics are chemical substances produced by some microbes that can kill or retard the growth of other, disease-causing microbes. The word itself is put together from anti and bio, meaning against life, and it is used for substances that act against the life of harmful microbes while being safe enough at low concentration for a patient to take.

Penicillin, the first antibiotic to be discovered, was found by accident. Alexander Fleming was working with cultures of Staphylococci bacteria. He came back to an unwashed culture plate and found that a mould had grown on it, and that immediately around the mould there was a clear ring in which the Staphylococci had not grown at all. Something diffusing out of the mould was stopping the bacteria from growing. He identified the mould as Penicillium notatum and named the active chemical penicillin after it. Fleming, however, could neither obtain the substance in useful quantity nor demonstrate what it could do in patients.

That second half of the work was done by Ernest Chain and Howard Florey, who established the full potential of penicillin as an effective antibiotic. Its value became obvious during the Second World War, when it was used to treat wounded soldiers whose injuries had become infected. Fleming, Chain and Florey shared the Nobel Prize in 1945 for this work. Many more antibiotics have been obtained from other microbes since then, and they have been decisive in bringing once-deadly bacterial diseases such as plague, whooping cough, diphtheria and leprosy under control. Keep the two halves of the story separate: who observed and named, and who proved and produced.

One more idea belongs beside the production of antibiotics, and that is their judicious use. An antibiotic acts on bacteria and on certain other microbes; it has no effect at all on viruses, so it does nothing for a viral illness such as a common cold. When antibiotics are taken where they are not called for, or when a prescribed course is left unfinished, the least susceptible bacteria in the population survive and go on multiplying. Over time such populations become resistant, and an antibiotic that once cleared an infection stops working against it. Careful and prescribed use is therefore part of keeping the antibiotics we already have effective.

Beyond food and antibiotics, microbes are the commercial source of a long list of organic acids, alcohols, enzymes and specialised medicines. In each case the microbe is grown in a fermentor under controlled conditions and the product is then harvested from the broth. The work in this section is matching the organism to the product correctly, so learn the pairs rather than only the general idea.

Among organic acids, the fungus Aspergillus niger is the producer of citric acid. The bacterium Acetobacter aceti produces acetic acid, the acid of vinegar. The bacterium Clostridium butylicum produces butyric acid, and Lactobacillus, which you already met in curd, produces lactic acid. For alcohol the producer is again the yeast Saccharomyces cerevisiae, which is why yeast appears both in the beverage list and in the chemical list. There is a useful pattern here: of these acid producers, only citric acid comes from a fungus and the rest come from bacteria.

Microbes are also harvested for their enzymes. Lipases are enzymes that break down fats, and they are added to detergent formulations so that oily stains on clothes are digested and washed off. Pectinases and proteases are used to clarify bottled fruit juices. Freshly squeezed juice is cloudy because it carries suspended pectin and protein particles; these enzymes break those particles down and the juice turns clear.

Then there are bioactive molecules - microbial products used directly as medicine.

Streptokinase is produced by the bacterium Streptococcus and is modified by genetic engineering before it is used. It acts as a clot buster: it is used to remove clots from the blood vessels of patients who have had a heart attack, that is, a myocardial infarction. Be careful with the producer here. It is Streptococcus, a bacterium, and not Streptomyces, which is a different genus altogether and is well known as a source of antibiotics. The names differ by only a few letters, so read them carefully.

Cyclosporin A is produced by the fungus Trichoderma polysporum and is used as an immunosuppressive agent in organ transplant patients. A patient's immune system would ordinarily treat a transplanted organ as foreign material and attack it; cyclosporin A damps that response down so that the graft is not rejected. Note that other species of Trichoderma are free-living soil fungi used as biocontrol agents, which is an entirely different role - the genus does two unrelated jobs in this chapter.

Statins are produced by the fungus Monascus purpureus and are used as blood-cholesterol lowering agents. Their mechanism is worth stating precisely, because it is easy to state loosely: statins act by competitively inhibiting the enzyme responsible for the synthesis of cholesterol. The statin molecule resembles the normal substrate closely enough to occupy the active site of that enzyme, so the enzyme is blocked and less cholesterol is made in the body.

Sewage is the municipal waste water carried away by the drains of a town or city. It contains a large amount of organic matter and enormous numbers of microbes, many of them pathogenic. If sewage is let straight into a river, the organic matter feeds bacteria which then use up the dissolved oxygen of the water, fish and other aquatic life die for want of oxygen, and the pathogens spread waterborne disease. So sewage is treated in sewage treatment plants (STPs) before the water is released. The striking point about an STP is that the actual cleaning is not done by any added chemical. It is done by the heterotrophic microbes naturally present in the sewage itself. The plant simply supplies the conditions in which those microbes can work fast.

Treatment is carried out in two stages.

Primary treatment is physical. Nothing is being digested at this stage; particles are only being taken out. Floating debris is removed by sequential filtration, and grit - soil and small pebbles - is removed by sedimentation, that is, by letting it settle. All the solids that settle in the primary settling tank form the primary sludge, and the liquid standing above the sludge is the primary effluent. This effluent is what is carried forward to the next stage.

Secondary treatment is biological, and is also called biological treatment for that reason. The primary effluent is passed into large aeration tanks, where it is constantly agitated mechanically and air is pumped into it. Both the stirring and the pumped air serve one purpose: to keep the water rich in oxygen, because the microbes that do the work in this tank are aerobic. Under these conditions useful aerobic microbes grow vigorously and form flocs. A floc is a mass of bacteria held together with fungal filaments, or mycelia, into a mesh-like structure. Picture a loose woolly clump drifting in the water rather than free-swimming single cells; that clump shape is what lets the microbes later settle out together. These flocs consume the major part of the organic matter in the effluent.

As the organic matter is consumed, the BOD of the effluent falls. BOD stands for biochemical oxygen demand, and it is defined as the amount of oxygen that would be consumed if all the organic matter in one litre of water were oxidised by bacteria. In practice the BOD test measures the rate at which microorganisms take up oxygen from a sample of water. Since that oxygen is being used to break down organic matter, BOD is an indirect measure of how much organic matter the water contains. The greater the BOD of waste water, the greater is its polluting potential. So a falling BOD is the signal that treatment is succeeding: it tells you the organic load has been eaten up and the water is getting cleaner. Read the logic in whichever direction the question asks - high BOD means dirty water, low BOD means clean water.

Once the BOD has been reduced significantly, the effluent is passed into a settling tank where the bacterial flocs are allowed to sediment. This sediment is called the activated sludge. A small part of the activated sludge is pumped back into the aeration tank, where it serves as the inoculum that starts off the next lot of effluent. The remaining major part is pumped into large tanks called anaerobic sludge digesters. Here, as the name says, there is no oxygen, and anaerobic bacteria digest the bacteria and fungi of the sludge itself. In doing so they release a mixture of gases - methane, hydrogen sulphide and carbon dioxide - which is biogas and can be burnt as fuel. The treated water that remains at the end is generally released into natural water bodies such as rivers and streams. Under the Ganga Action Plan and the Yamuna Action Plan, large numbers of such plants have been taken up to save major rivers from pollution.

Biogas is a mixture of gases produced by microbial activity and used as a fuel. Its main component, and the one that burns, is methane; carbon dioxide and hydrogen are also present in the mixture. Different groups of microbes produce different gases during fermentation, so the exact composition of the mixture depends on which microbes are at work and on what material they are fed.

The bacteria that matter here grow anaerobically - that is, without oxygen - on cellulose-rich material, and they produce large amounts of methane along with carbon dioxide and hydrogen. Because of the methane they produce, they are called methanogens, and the common example you should be able to name is Methanobacterium. Two habitats matter for these bacteria: the anaerobic sludge during sewage treatment, which links this section straight back to the sludge digester, and the rumen of cattle.

The rumen is the first and largest chamber of the stomach of cattle, and it holds a huge microbial population. The food of cattle is grass and fodder, which contains a great deal of cellulose. Cattle have no enzyme of their own that can break cellulose down. The microbes of the rumen, methanogens among them, do that job for the animal, so these bacteria play an important part in the nutrition of cattle. This is exactly why cattle dung, commonly called gobar, is so rich in methanogens - the bacteria leave the animal along with the dung, still alive and still able to work. It is also why biogas generated from dung is popularly called gobar gas. If a question asks why cattle dung is preferred as raw material, the answer is not that dung is cheap or plentiful but that it already carries the methanogens.

A biogas plant is a concrete tank, about ten to fifteen feet deep, into which bio-wastes and a slurry of dung are fed. A floating cover is placed over the slurry. As gas is produced under it, this cover is pushed upward, so the height of the cover is a rough indicator of how much gas has collected inside. The plant has an outlet connected to a pipe which delivers the biogas to nearby houses, where it is used for cooking and for lighting. Spent slurry is removed through a second outlet and is used as fertiliser, so almost nothing is wasted - the same batch of material gives fuel first and manure afterwards. In India this technology was developed largely through the efforts of the Indian Agricultural Research Institute and the Khadi and Village Industries Commission.

Biological control, or biocontrol, means using living organisms to control pests and plant diseases instead of relying on chemical insecticides and fungicides. The argument for it is straightforward. Chemical pesticides are toxic and harmful not only to the target pest but to human beings, to farm animals, and to the many harmless and useful insects living in a field; they also leave residues in the crop and in the soil. A well-chosen biocontrol agent hits a narrow range of targets and leaves the rest of the system alone. The organic farmer's outlook is that a field is a whole interacting web of organisms, and that the aim should be to hold pests down to a manageable level rather than to wipe out every insect in sight.

Two familiar predatory examples are worth remembering as a pair: the ladybird beetle, which is used against aphids, and the dragonfly, which is used against mosquitoes.

Bacillus thuringiensis, usually shortened to Bt, is the standard microbial insecticide. It is sold as dried spores in sachets. The spores are mixed with water and sprayed on vulnerable plants such as brassicas and fruit trees. The spray does not poison the plant, and it does no harm merely by touching an insect - it works only when it is eaten. Insect larvae, that is, caterpillars, feeding on the sprayed leaves swallow the spores along with the leaf. Inside the gut of the larva, which is alkaline, the toxin is released in its active form, and the larva is killed. That dependence on an alkaline gut is the whole reason for the safety of Bt: our own stomach is strongly acidic, so the toxin is never activated in us, and insects without an alkaline gut are unaffected too. The same principle has been carried further using genetic engineering. The Bt gene has been introduced into plants themselves, giving crops such as Bt cotton, which manufacture the toxin in their own tissues so that no spraying is needed.

Trichoderma is a genus of free-living fungi that is very common in root ecosystems, that is, in the soil around plant roots. Several species are effective biocontrol agents of plant pathogens. Note carefully what this means: Trichoderma is used against disease-causing organisms of plants, not against insects. It is easy to slip and write that Trichoderma kills insect larvae, but it does not.

Baculoviruses are viruses that attack insects and other arthropods. The majority of baculoviruses used as biological control agents belong to the genus Nucleopolyhedrovirus. Their great advantage is that they are excellent candidates for species-specific, narrow-spectrum insecticidal applications: they have no negative impact on plants, on mammals, on birds, on fish, or even on non-target insects. That makes them especially valuable when the aim is to conserve the beneficial insects of a field, and in an integrated pest management programme where chemical use is being kept to a minimum.

A biofertiliser is an organism that enriches the nutrient quality of the soil. The reason for using them is much the same as the reason for biocontrol. Heavy use of chemical fertilisers does raise yields, but the excess washes into ponds, lakes and rivers and pollutes them, and the soil itself deteriorates over years of such use. A living source of nutrients avoids much of that damage. The main sources of biofertilisers are bacteria, fungi and cyanobacteria.

Rhizobium is the classic example. It lives in a symbiotic association inside the root nodules of leguminous plants - the pulses such as gram and pea, and crops such as groundnut and beans. Inside the nodule it fixes atmospheric nitrogen, which means it converts the nitrogen gas of the air, a form that plants cannot use at all, into a combined form the plant can absorb and build into proteins. The relationship is genuinely two-way: the plant supplies the bacterium with food and a protected place to live, and the bacterium supplies the plant with usable nitrogen. There are also free-living nitrogen-fixing bacteria in the soil - Azospirillum and Azotobacter - which need no host plant and enrich the nitrogen content of the soil directly.

Many fungi form symbiotic associations with the roots of higher plants, and such an association is called a mycorrhiza. Many members of the genus Glomus form mycorrhiza. Here the nutrient exchanged is a different one, and this is the point most easily confused: the fungal partner absorbs phosphorus from the soil and passes it on to the plant. So keep the pair straight - Rhizobium for nitrogen, mycorrhiza for phosphorus. Plants that carry mycorrhizal associations also show a set of further advantages: resistance to root-borne pathogens, tolerance of salinity and of drought, and an overall increase in growth and development.

Cyanobacteria are autotrophic microbes, widely distributed in both aquatic and terrestrial environments, and many of them fix atmospheric nitrogen. The examples to know are Anabaena, Nostoc and Oscillatoria. In paddy fields cyanobacteria serve as an important biofertiliser: a flooded paddy field is exactly the wet, sunlit habitat these organisms like, and while growing there they add fixed nitrogen to the field at no cost to the farmer. Blue-green algae also add organic matter to the soil as they die and decay, and in that way further increase its fertility. So their contribution is of two kinds, nitrogen while alive and organic matter afterwards.