Chapter 11 — Bio Geo Chemical Cycles

Every ecosystem runs on two currencies, and they behave very differently. Energy enters as sunlight, is captured by green plants in photosynthesis, passes to herbivores, carnivores and decomposers along food chains, and at every step most of it is lost as heat that radiates away into space. Energy therefore flows through an ecosystem in one direction and must be replaced continuously by the sun; there is no energy cycle. Matter, on the other hand, the carbon, hydrogen, oxygen, nitrogen, phosphorus, sulphur and the thirty or so other elements that make up living bodies, is not lost. The Earth receives almost no new matter from space and loses almost none. The same atoms are taken up by organisms, built into their bodies, passed along food chains, returned to the soil, water and air by excretion, death and decomposition, and taken up again. Matter cycles.

A biogeochemical cycle is the pathway by which a chemical element or compound moves through the biotic (living) and abiotic (geological: land, water, air) parts of the Earth. The word combines bio (living organisms), geo (the Earth's rocks, soil, water and atmosphere) and chemical (the changes of chemical form along the way). Each cycle has reservoirs (pools), places where the element is stored, such as the atmosphere for nitrogen, the oceans for water, limestone rock for carbon, and living biomass for all of them; and fluxes, the processes that move the element from one reservoir to another, such as photosynthesis, respiration, evaporation, weathering and decomposition. Some reservoirs are large and slow, such as rock, from which an element may take millions of years to escape; others are small and fast, such as the bodies of bacteria, through which an element may pass in hours.

Biogeochemical cycles are of two types. Gaseous cycles have their main reservoir in the atmosphere or the oceans and move quickly: the water, carbon, nitrogen and oxygen cycles. Sedimentary cycles have their main reservoir in the Earth's crust, in rocks and sediments, and move slowly: the phosphorus, sulphur, calcium, potassium and iron cycles. Sedimentary cycles are more easily disrupted, because once an element is washed to the sea bottom it may not return to land for millions of years.

The cycles are not separate. Water carries dissolved nitrogen and phosphorus; carbon and oxygen are exchanged in the same reactions of photosynthesis and respiration; sulphur and nitrogen both cause acid rain. Living organisms, particularly plants, bacteria and fungi, are the engines that drive every cycle, and this is why the cycles are studied in biology. And the cycles are the reason that life has continued for more than three thousand million years on a planet with a fixed stock of matter: without recycling, all the carbon would long ago have been locked in dead bodies and all the nitrogen washed to the sea.

The rest of the chapter takes each cycle in turn, showing its reservoirs, its fluxes, the organisms that drive it and the ways in which human beings have altered it.

Water is the medium of all life and the carrier of every other cycle, and the water (hydrological) cycle is the continuous movement of water between the oceans, the atmosphere, the land and living organisms, powered by the sun and by gravity. About 97 per cent of the Earth's water is in the oceans, 2 per cent is frozen in ice caps and glaciers, less than 1 per cent is fresh water in the ground, lakes and rivers, and a tiny fraction, about 0.001 per cent, is in the atmosphere at any moment; yet it is this tiny fraction, turned over every nine days or so, that delivers all the rain.

The cycle has these steps. Evaporation: the sun's heat turns liquid water on the surface of oceans, lakes, rivers, wet soil and leaves into water vapour, which rises into the air; about 85 per cent of the vapour in the atmosphere comes from the oceans. Transpiration: plants draw water from the soil through their roots and release it as vapour through the stomata of their leaves; a large tree may transpire hundreds of litres a day, and a forest returns more water to the air than an equal area of open water; evaporation and transpiration together are evapotranspiration. Sublimation, the direct change of snow and ice to vapour, adds a little. Condensation: as moist air rises it cools, and the vapour condenses on dust particles into the droplets and ice crystals of clouds, fog and dew. Precipitation: when the droplets grow heavy enough they fall as rain, snow, sleet or hail; the south-west monsoon that reaches Andhra Pradesh in June is water evaporated from the Arabian Sea and the Bay of Bengal, condensed as the moist winds rise over the Western Ghats and the Eastern Ghats. Interception: part of the rain is caught on leaves and evaporates back at once. Infiltration and percolation: rain that reaches the ground soaks into the soil and percolates down to become groundwater, which fills the pores of soil and rock as an aquifer and feeds wells, springs and the base flow of rivers. Runoff: water that cannot soak in flows over the surface into streams, rivers, tanks and lakes and back to the sea, carrying soil and dissolved minerals with it. Storage: water rests for a time in glaciers, lakes, aquifers, soil and living bodies before moving on.

Living organisms are part of the cycle. Plants take up water for photosynthesis and transpiration; animals drink it and return it by breathing, sweating and excretion; every organism is mostly water; and, importantly, forests and vegetation control the cycle on land, breaking the force of rain, holding the soil, letting water infiltrate rather than run off, feeding groundwater, and transpiring moisture that seeds further rain. Cutting a forest makes the same rainfall run off faster in floods and leave the ground drier afterwards.

The water cycle purifies water, since evaporation leaves salts and pollutants behind, and it distributes fresh water over the land; without it the continents would be desert. Human beings have changed it by damming and diverting rivers, by pumping groundwater faster than it is recharged (as in Rayalaseema, where the water table has dropped hundreds of metres), by paving cities so that rain runs off instead of soaking in, by clearing forests, and by warming the climate, which increases evaporation and makes rainfall more intense and irregular. Rainwater harvesting, watershed management, afforestation and efficient irrigation are the ways of keeping the local water cycle in balance.

Carbon is the element of life: every protein, carbohydrate, fat and nucleic acid is built on chains of carbon atoms, and living matter is about 18 per cent carbon by weight (about 50 per cent of dry weight). The carbon cycle is the movement of carbon between the atmosphere, where it exists as carbon dioxide (CO₂, about 0.04 per cent of the air, or 420 parts per million); the oceans, where it is dissolved as CO₂, bicarbonate and carbonate ions and holds about fifty times as much carbon as the air; living organisms and their dead remains in soil; and the rocks, chiefly limestone (calcium carbonate) and the fossil fuels coal, petroleum and natural gas, which hold by far the largest store.

The heart of the cycle is a pair of opposite reactions. In photosynthesis, green plants, algae and cyanobacteria take carbon dioxide from the air (or from water) and, using the energy of sunlight captured by chlorophyll, combine it with water to make glucose and release oxygen: 6CO₂ + 6H₂O → C₆H₁₂O₆ + 6O₂. This is the only large-scale process by which inorganic carbon enters the living world, and it fixes about 120 thousand million tonnes of carbon a year on land and about the same in the sea. The glucose is built into the starch, cellulose, proteins and fats of the plant, and passes to herbivores that eat plants, to carnivores that eat herbivores, and to decomposers that consume the dead remains of all of them. In respiration, every living cell, plant, animal, fungus or bacterium, oxidises food to release the energy it needs and returns the carbon to the air as carbon dioxide: C₆H₁₂O₆ + 6O₂ → 6CO₂ + 6H₂O + energy. Plants themselves respire day and night, using about half of what they fix. Decomposition is the respiration of bacteria and fungi feeding on dead matter; it returns the carbon of leaf litter, corpses and dung to the air, and the small part that resists decay stays in the soil as humus, which holds more carbon than all the vegetation on Earth.

Other fluxes join in. Combustion, the burning of wood, dung, crop residues and forests, returns carbon to the air quickly, as fires have always done. The oceans exchange carbon dioxide with the air across their surface; cold water dissolves it and warm water releases it; marine algae fix it, and marine animals such as corals, molluscs and foraminifera use it to build shells of calcium carbonate that settle to the sea floor as limestone. Volcanoes and the weathering of limestone by acidic rain slowly return rock carbon to the air. And over millions of years, plant remains buried in swamps without oxygen became coal, and marine plankton buried in sediments became petroleum and natural gas: the fossil fuels, a store of carbon removed from the cycle for hundreds of millions of years.

In a natural ecosystem the cycle is balanced: the carbon fixed by photosynthesis each year roughly equals that returned by respiration, decomposition and fire, so the carbon dioxide in the air stayed at about 280 parts per million for thousands of years before industry. Carbon has a short residence in the air (a few years), a longer one in biomass (years to centuries), longer in soil and ocean (centuries to millennia), and immense in rock (millions of years).

For all of human history until about 1800 the carbon cycle was in balance. Since then we have been digging up and burning the carbon that the cycle had buried over 300 million years, and returning it to the air in two centuries. This is the largest human disturbance of any biogeochemical cycle, and its consequence is global warming.

The mechanism is the greenhouse effect, which in itself is natural and necessary. The sun's short-wave radiation passes through the atmosphere and warms the Earth's surface; the warm surface radiates long-wave infrared (heat) back towards space; certain gases in the atmosphere, chiefly water vapour, carbon dioxide, methane, nitrous oxide and ozone, absorb this outgoing heat and radiate part of it back down, like the glass of a greenhouse that lets sunlight in but keeps heat from escaping. Without these greenhouse gases the Earth's average temperature would be about minus 18 °C instead of plus 15 °C, and there would be no liquid water and no life as we know it. The problem is not the effect but its enhancement by the extra gases we add.

The sources are these. Burning fossil fuels, coal in power stations and steel plants, petrol and diesel in vehicles, gas in kitchens and factories, releases about 37 thousand million tonnes of carbon dioxide a year worldwide. Deforestation and burning of forests releases the carbon stored in trees and soil and removes the trees that would have absorbed carbon dioxide; it adds a further 10 per cent. Cement making decomposes limestone and releases its carbon. Methane, 28 times as powerful as carbon dioxide over a century, comes from flooded paddy fields (where bacteria in the airless mud produce it), from the rumen of cattle and buffaloes, from rotting garbage in dumps, from coal mines and gas leaks. Nitrous oxide, 265 times as powerful, comes from nitrogen fertiliser and manure. Chlorofluorocarbons and their replacements, from refrigerators and air conditioners, are thousands of times as powerful and also destroy ozone. As a result carbon dioxide has risen from 280 parts per million before industry to about 420 today, higher than at any time in at least three million years, and half of what we emit stays in the air; the rest is taken up by the oceans, which are becoming more acidic as a result, and by forests.

The Earth's average surface temperature has risen about 1.2 °C since 1850, and the last decade was the warmest on record. The consequences are already seen: melting of glaciers in the Himalaya that feed India's rivers, and of polar ice; rise in sea level, about 20 cm so far and accelerating, that threatens the deltas of the Godavari and Krishna, the Sundarbans and every coastal city; more frequent and intense cyclones on the Andhra coast, heat waves that kill hundreds in Andhra Pradesh and Telangana in May, droughts in Rayalaseema and floods elsewhere as the monsoon becomes erratic; falling yields of wheat and rice as nights warm; the spread of malaria and dengue mosquitoes into new areas; the bleaching of corals and the shifting of fish; and the extinction of species that cannot move or adapt fast enough. The poor, who depend on rain-fed farming and live in flood-prone and cyclone-prone areas, suffer first and most.

The remedy is to restore the balance of the carbon cycle: to reduce emissions by moving from coal and oil to solar, wind, hydro and nuclear energy (Andhra Pradesh has among India's largest solar parks), by using energy efficiently, by public transport and electric vehicles, by reducing methane from paddies through alternate wetting and drying and from waste through composting and biogas; and to increase absorption by protecting and planting forests and mangroves, by farming that builds soil carbon, and by restoring wetlands. The Paris Agreement of 2015 commits every country, India included, to limit warming to well below 2 °C, and India has pledged net-zero emissions by 2070. Every student's habits, the lights switched off, the cycle ridden instead of the scooter, the tree planted, are part of the same cycle.

Nitrogen is needed by every organism to make proteins, nucleic acids (DNA and RNA), chlorophyll, vitamins and many other molecules, and shortage of nitrogen is the commonest limit on plant growth. The paradox of nitrogen is that it is everywhere and yet scarce. The atmosphere is 78 per cent nitrogen gas (N₂), the largest reservoir, but the two atoms of N₂ are held together by a triple bond so strong that neither plants nor animals can break it. Nitrogen gas is inert to almost all life. Plants can use nitrogen only as ammonium ions (NH₄⁺) or nitrate ions (NO₃⁻) dissolved in soil water, and animals can use it only as the amino acids of proteins made by plants. The nitrogen cycle is the set of processes, almost all of them carried out by bacteria, that convert the useless gas into usable forms, pass it through living things, and return it to the air.

The cycle has five main steps, which the next topics examine in detail. Nitrogen fixation converts N₂ into ammonia (NH₃) or ammonium; it is done by certain free-living and symbiotic bacteria and cyanobacteria, by lightning, and by fertiliser factories. Assimilation is the uptake of ammonium and nitrate by plants and their conversion into amino acids and proteins, which pass to animals along food chains. Ammonification is the release of ammonia from the proteins, urea and uric acid of dead organisms and excreta by decomposing bacteria and fungi. Nitrification is the conversion of ammonium to nitrite (NO₂⁻) and then to nitrate by nitrifying bacteria in aerated soil. Denitrification is the conversion of nitrate back into nitrogen gas by denitrifying bacteria in waterlogged, airless soil, which completes the cycle and returns nitrogen to the atmosphere.

Nitrogen thus passes from the air into the soil, from the soil into plants, from plants into animals, from plants and animals back into the soil, around and around within the soil between ammonium and nitrate, and finally back into the air. In a natural ecosystem such as a forest, very little nitrogen is lost; it is recycled tightly, and the small losses by denitrification and leaching are balanced by fixation. Nitrogen does not accumulate in the atmosphere from human activity in the way carbon dioxide does, because the N₂ reservoir is already so huge; the problem with the nitrogen cycle is the opposite: we have learnt to fix nitrogen artificially on such a scale that we have doubled the amount entering the living world, with consequences described later.

The organisms of the nitrogen cycle are worth learning by name, because the board examination asks for them: Rhizobium, Azotobacter, Clostridium, Anabaena and Nostoc for fixation; Nitrosomonas and Nitrobacter for nitrification; Pseudomonas and Thiobacillus denitrificans for denitrification; and the general decomposing bacteria and fungi for ammonification. These microscopic organisms, unseen in every handful of soil, keep the world's protein supply running.

Nitrogen fixation is the conversion of the inert nitrogen gas of the air into ammonia or other compounds that living things can use. It is the gateway of the whole cycle, and it happens in three ways.

Biological nitrogen fixation is by far the most important in nature, accounting for about 90 per cent of natural fixation. Only certain prokaryotes, bacteria and cyanobacteria, possess the enzyme nitrogenase, which breaks the triple bond of N₂ and reduces it to ammonia at ordinary temperature, using a great deal of energy and working only in the absence of oxygen. Symbiotic fixers live inside plants and exchange fixed nitrogen for sugars. The best known is Rhizobium, which infects the root hairs of legumes (groundnut, red gram, black gram, green gram, chickpea, soybean, beans, peas, clover, and trees such as Acacia and Sesbania) and multiplies inside swellings called root nodules; the nodules are pink inside from leghaemoglobin, a protein that keeps oxygen away from nitrogenase while supplying the bacteria's own respiration. A good crop of groundnut fixes 50 to 100 kg of nitrogen per hectare, and this is why legumes are grown in rotation and as green manure. Other symbiotic fixers are Frankia in the nodules of Casuarina and alder, and the cyanobacterium Anabaena in the leaves of the water fern Azolla that floats on paddy fields, and in the coralloid roots of Cycas. Free-living fixers live independently in soil and water: Azotobacter (aerobic, in soil), Clostridium (anaerobic), Rhodospirillum (photosynthetic), and the cyanobacteria (blue-green algae) Anabaena, Nostoc and Aulosira in flooded rice fields and on wet rocks, which fix 20 to 30 kg per hectare a season and are used as biofertiliser. Azospirillum lives loosely associated with the roots of grasses, sorghum and maize.

Atmospheric (physical) fixation is by lightning. The enormous energy of a lightning flash makes the nitrogen and oxygen of the air combine into nitric oxide (NO), which is oxidised to nitrogen dioxide (NO₂) and dissolves in rain as nitric acid, reaching the soil as nitrate. This contributes about 5 to 10 per cent of natural fixation, a few kilograms per hectare a year; the first rains of the monsoon, after a thunderstorm, bring a little free fertiliser. Volcanic activity and forest fires add a little more.

Industrial fixation is by the Haber-Bosch process, invented in Germany in 1909, in which nitrogen from the air and hydrogen from natural gas are combined into ammonia at about 450 °C and 200 atmospheres pressure over an iron catalyst: N₂ + 3H₂ → 2NH₃. The ammonia is converted into urea, ammonium sulphate, ammonium nitrate and other fertilisers. India makes and uses about 20 million tonnes of nitrogen fertiliser a year, and the world about 120 million tonnes of nitrogen, which is now more than all natural fixation on land combined. Industrial fixation has fed the growing human population, half of whose protein now comes ultimately from Haber-Bosch nitrogen, but it uses about 1 to 2 per cent of the world's energy, and its products leak into water and air, as the topic on human disturbance describes.

Nitrogen fixation, whether by a bacterium in a groundnut nodule or by a fertiliser plant at Visakhapatnam, is the source of every atom of nitrogen in every protein on Earth. A shortage of it limits life; an excess of it pollutes.

Once nitrogen has been fixed, it circulates within the soil and the living world through three processes that, together, convert dead matter back into plant food.

Assimilation is the uptake of inorganic nitrogen by plants and its building into organic molecules. Roots absorb nitrate (NO₃⁻) and ammonium (NH₄⁺) ions from the soil solution through their root hairs. Nitrate is first reduced inside the plant to ammonium, which is then combined with carbon compounds from photosynthesis to make amino acids, and from these proteins, nucleic acids, chlorophyll and the rest. Animals cannot make most amino acids from inorganic nitrogen; they obtain their nitrogen ready-made by eating plants or other animals, digesting the proteins into amino acids and rebuilding them into their own proteins. Nitrogen thus climbs the food chain as protein. Rice, which grows in flooded soil where nitrate is quickly lost, prefers ammonium; most dry-land crops prefer nitrate.

Ammonification (mineralisation) is the return of nitrogen from organic matter to the inorganic form. When plants and animals die, and when animals excrete urea (mammals), uric acid (birds, reptiles, insects) or ammonia (fish), decomposing bacteria and fungi in the soil, such as Bacillus, Clostridium, Proteus and many moulds, break down the proteins and nucleic acids into amino acids and then split off the nitrogen as ammonia (NH₃), which dissolves in soil water as ammonium. The enzyme urease converts urea to ammonia and carbon dioxide within a day or two, which is why a cattle shed smells of ammonia and why urea fertiliser must be covered with soil quickly or its nitrogen escapes into the air. Ammonification releases nitrogen from dung, compost, green manure, crop residues and leaf litter, and it is the process by which manures feed crops.

Nitrification is the oxidation of ammonium to nitrate, in two steps, each by a specialised group of aerobic soil bacteria that gain their energy from the reaction (they are chemoautotrophs, making their own food from carbon dioxide with this energy instead of sunlight). In the first step Nitrosomonas (and Nitrosococcus) oxidise ammonium to nitrite (NO₂⁻): 2NH₄⁺ + 3O₂ → 2NO₂⁻ + 4H⁺ + 2H₂O. In the second step Nitrobacter oxidises nitrite to nitrate (NO₃⁻): 2NO₂⁻ + O₂ → 2NO₃⁻. Nitrite is poisonous to plants, but it is normally converted so fast that it does not accumulate. Nitrification needs oxygen, moisture, warmth (fastest at 25 to 35 °C) and a pH near neutral; it stops in waterlogged, cold or very acid soils. It has two consequences for farmers. Nitrate, unlike ammonium, carries a negative charge and is not held by the negatively charged clay particles, so it is easily leached away by rain and irrigation into groundwater; and the hydrogen ions released make the soil acidic. Nitrification inhibitors and neem-coated urea slow the process so that the crop can take up the nitrogen before it is lost.

Between them, ammonification and nitrification turn the protein of a dead leaf or a cow's dung into the nitrate that a rice plant absorbs, closing the loop within the soil. They are the reason that a forest floor, receiving nothing but its own leaf fall, stays fertile for ever, and they are the reason that manure works.

Denitrification closes the nitrogen cycle. It is the reduction of nitrate (NO₃⁻) back to nitrogen gas (N₂), with nitrite and the gases nitric oxide (NO) and nitrous oxide (N₂O) as intermediates, and its products escape from the soil into the atmosphere, returning nitrogen to the great reservoir from which fixation drew it. It is carried out by denitrifying bacteria, chiefly Pseudomonas denitrificans, Thiobacillus denitrificans, Micrococcus, Bacillus and Paracoccus. These are facultative anaerobes: when oxygen is available they respire normally, but when the soil is waterlogged and oxygen is used up they switch to using the oxygen of nitrate to oxidise their food, releasing the nitrogen as gas. Denitrification therefore happens in flooded paddy fields, in marshes and swamps, in compacted or waterlogged soils, in the bottom mud of tanks and lakes, in sewage works and in the oxygen-poor layers of the ocean, and it is fastest when there is plenty of organic matter for the bacteria to feed on, warmth, and a good supply of nitrate.

From the farmer's point of view denitrification is a loss: nitrate fertiliser applied to a paddy field just before flooding may lose half its nitrogen to the air within days, which is why ammonium and urea, rather than nitrate, are used for rice and why they are placed deep in the reduced mud where nitrification cannot turn them into nitrate. From the point of view of the ecosystem denitrification is essential: without it, nitrate would accumulate in soils and water and the atmospheric reservoir would slowly empty. It is also used deliberately in sewage treatment to remove nitrogen from waste water before it is discharged, preventing eutrophication. Its drawback is that the intermediate nitrous oxide is a greenhouse gas 265 times as powerful as carbon dioxide and also destroys ozone, and the heavy use of nitrogen fertiliser has increased its release.

Other losses from the soil are leaching of nitrate into groundwater and rivers, volatilisation of ammonia from urea and manure into the air, erosion of nitrogen-rich topsoil, and harvest, which removes the nitrogen in grain and straw from the field. Other gains besides fixation are the nitrogen in rain and dust, in irrigation water, in manures brought from elsewhere and, mostly, in fertiliser.

In a natural ecosystem gains and losses balance. A tropical forest holds most of its nitrogen in living biomass and recycles it tightly through litter fall and decomposition, losing very little; a grassland stores much in soil humus; a lake receives nitrogen from its catchment and loses it to denitrification in its mud. In an agricultural ecosystem the balance is broken twice a year by harvest, and must be restored by fertiliser, manure, legumes and fallow; a field that receives less than it loses becomes exhausted, and one that receives far more than the crop can use leaks the surplus into water and air.

A simple nitrogen budget makes the point. A hectare of rice yielding 5 tonnes removes about 100 kg of nitrogen in grain and straw. If the farmer applies 120 kg of urea nitrogen, about 40 to 50 kg are taken up by the crop, 20 to 30 kg leach as nitrate, 10 to 20 kg escape as ammonia and nitrous oxide, and the rest is held in soil organic matter or lost by denitrification. The recovery of applied nitrogen by the crop in India averages only 30 to 40 per cent. Raising this recovery, through timing, placement, split doses, slow-release forms and organic sources, is the single most effective way to protect the nitrogen cycle while feeding the country.

Oxygen is the most abundant element in the Earth's crust and the second most abundant gas in the atmosphere, about 21 per cent by volume. It is essential for the aerobic respiration of almost all organisms, for combustion, for the decay of organic matter, and for the weathering of rocks, and it forms the ozone layer that shields life from ultraviolet radiation. The oxygen cycle is the movement of oxygen between the atmosphere, the biosphere (living organisms), the hydrosphere (water) and the lithosphere (rocks and minerals).

The oxygen cycle is bound to the carbon cycle, because the same two reactions drive both. Photosynthesis is the only significant source of free oxygen: green plants, algae and cyanobacteria split water molecules using light energy and release the oxygen as gas, 6CO₂ + 6H₂O → C₆H₁₂O₆ + 6O₂. About half the world's photosynthetic oxygen is produced by the microscopic phytoplankton of the oceans and half by land plants, with tropical forests contributing most on land; the Amazon has been called the lungs of the Earth, though in fact it consumes almost as much as it produces. Before photosynthesis evolved, some 2,400 million years ago, the atmosphere had no free oxygen at all; every molecule of oxygen we breathe was released by a living cell.

Respiration is the main consumer: every aerobic organism, plant, animal, fungus and bacterium, takes in oxygen and combines it with food to release energy, returning the oxygen bound in carbon dioxide and water. Decomposition of dead matter by aerobic microbes uses oxygen in the same way, which is why a polluted river full of sewage runs out of dissolved oxygen and its fish die. Combustion of wood, coal, oil and gas consumes oxygen in large amounts: burning a litre of petrol uses about 2.5 kg of oxygen. Weathering and oxidation of rocks and minerals, the rusting of iron, the oxidation of sulphides and the formation of oxides, remove oxygen into the lithosphere, where in fact the largest reservoir of oxygen lies, locked in silicates, oxides and carbonates. The oxygen dissolved in water is taken up by fish and other aquatic animals through their gills, released by aquatic plants and algae, and exchanged with the air at the surface.

A third part of the cycle involves ozone (O₃). In the stratosphere, 15 to 35 kilometres up, ultraviolet radiation splits oxygen molecules into atoms, which combine with other oxygen molecules to form ozone; ozone absorbs ultraviolet radiation and breaks back into oxygen; the balance of these reactions maintains the ozone layer that filters out the ultraviolet-B rays which cause skin cancer, cataracts and damage to plankton and crops. Chlorofluorocarbons released by refrigerators, air conditioners and spray cans rise to the stratosphere, where their chlorine atoms destroy ozone molecules by the thousand, and by the 1980s a hole in the ozone layer had opened over Antarctica each spring; the Montreal Protocol of 1987 phased out CFCs, and the layer is now slowly recovering, the best example so far of a broken cycle repaired by international action. Ozone at ground level, by contrast, formed from vehicle exhaust in sunlight, is a pollutant that damages lungs and crops.

Oxygen also cycles through water (H₂O), carbon dioxide (CO₂), nitrate, phosphate and sulphate, so that it takes part in every other cycle. Because the atmospheric reservoir is so large, about 1.2 million million tonnes, human activity has not measurably reduced it, though we consume it in fuel and reduce its production by clearing forests; the oxygen cycle is disturbed locally, in polluted water and in the stratosphere, rather than globally.

Phosphorus is a small but vital part of every organism: it is in the ATP that carries energy in every cell, in the backbone of DNA and RNA, in the phospholipids of cell membranes, in the bones and teeth of vertebrates (as calcium phosphate), and in the shells of many animals. Plants need it for root growth, flowering, seed formation and energy transfer, and after nitrogen it is the nutrient most often short in Indian soils.

The phosphorus cycle differs from the water, carbon, nitrogen and oxygen cycles in one important way: phosphorus has no gaseous phase. There is no phosphorus gas in the atmosphere, and the cycle does not pass through the air (except as dust and sea spray). Its reservoir is the Earth's crust, in rocks such as apatite (calcium phosphate) and in the phosphate rock deposits laid down as marine sediments; it is therefore a sedimentary cycle, and it is slow.

The cycle runs as follows. Weathering of phosphate rocks by rain, especially acidic rain, slowly dissolves phosphate ions (PO₄³⁻, HPO₄²⁻) into soil water. Plants absorb the dissolved phosphate through their roots, greatly helped by mycorrhizal fungi, whose threads spread through the soil and gather phosphate for the plant in exchange for sugar, and by phosphate-solubilising bacteria that release phosphate bound to calcium, iron and aluminium. The plant builds it into ATP, nucleic acids and phospholipids. Animals obtain phosphorus by eating plants or other animals and use it for bones, teeth and cells. Decomposers break down dead plants and animals and their excreta and return phosphate to the soil, where it is taken up again; the guano (droppings) of sea birds on islands is so rich in phosphate that it was mined as fertiliser. Much soil phosphate is fixed by reacting with calcium in alkaline soils (as in the black cotton soils) or with iron and aluminium in acid soils (as in red and laterite soils), forming insoluble compounds that plants cannot use; as a result, most of the phosphorus in a soil is unavailable at any time, and phosphate fertiliser applied this year may become available only years later. Runoff and erosion carry phosphate, mostly attached to soil particles, into streams, tanks, lakes and eventually the sea, where marine organisms use it, and when they die their remains sink and are buried as marine sediments. Over millions of years these sediments harden into phosphate rock, and only geological uplift brings them back to land where weathering can begin the cycle again. Fish and sea birds return a little phosphorus from the sea to the land each year, but for the most part phosphorus that reaches the sea is lost to the land for geological ages.

Human beings have changed the phosphorus cycle by mining phosphate rock (mostly in Morocco, China, the United States and Russia; India imports nearly all its needs) at a rate of about 250 million tonnes a year to make superphosphate and diammonium phosphate fertilisers, and by using it in detergents. Much of this phosphorus ends up in rivers and lakes through runoff from fields, sewage and detergent-laden waste water, where, because phosphorus is normally the limiting nutrient in fresh water, even small amounts cause eutrophication: explosive growth of algae and water hyacinth, followed by decay, loss of oxygen and death of fish, as in Hussain Sagar in Hyderabad and Kolleru lake. Meanwhile the world's phosphate rock reserves are finite and may be largely exhausted within one to three centuries, and unlike nitrogen there is no way to make more from the air. The phosphorus cycle is therefore a warning: we are moving a scarce element from rock to sea in a single direction. The remedies are to recover phosphorus from sewage sludge, manure and food waste, to apply fertiliser only where a soil test shows need, to control erosion, to use mycorrhiza and phosphate-solubilising biofertilisers, and to ban phosphate detergents.

Sulphur is a constituent of two amino acids (cysteine and methionine) and hence of every protein, of some vitamins and enzymes, and of the compounds that give onion, garlic, mustard and cabbage their pungency; oilseeds such as groundnut, sunflower and mustard need large amounts of it, and sulphur deficiency is now widespread in Indian oilseed fields. The sulphur cycle is partly sedimentary, with its main reservoir in rocks (as sulphides such as pyrite, and sulphates such as gypsum) and in ocean sediments, and partly gaseous, since sulphur compounds pass through the atmosphere as sulphur dioxide (SO₂), hydrogen sulphide (H₂S) and dimethyl sulphide.

In the soil, plants absorb sulphur as sulphate ions (SO₄²⁻), which come from the weathering of rocks, from rain, from the decay of organic matter, and from fertilisers such as ammonium sulphate, single superphosphate and gypsum. The plant reduces sulphate and builds it into amino acids and proteins; animals obtain it by eating plants. When plants and animals die, decomposer bacteria and fungi release the sulphur of proteins as hydrogen sulphide (H₂S), the gas that smells of rotten eggs, especially in airless conditions such as waterlogged soils, marshes, the mud of tanks and mangrove swamps, and sewers; in oxygen-free mud, sulphate-reducing bacteria such as Desulfovibrio also convert sulphate directly to hydrogen sulphide, which blackens the mud by forming iron sulphide. In aerated soil and water, sulphur-oxidising bacteria such as Thiobacillus and Beggiatoa oxidise hydrogen sulphide and elemental sulphur back to sulphate, gaining energy from the reaction and forming sulphuric acid in the process, which is why Thiobacillus is used to acidify alkaline soils and why pyrite mine wastes produce acid drainage; the photosynthetic purple and green sulphur bacteria of shallow ponds use hydrogen sulphide instead of water in their photosynthesis and deposit sulphur.

Sulphur enters the atmosphere from volcanoes, which emit sulphur dioxide and hydrogen sulphide, from the decay of organic matter in swamps and tidal flats, from sea spray, and from marine phytoplankton, which release dimethyl sulphide that helps clouds to form over the ocean. In the air these are oxidised to sulphur dioxide and then to sulphate and sulphuric acid, which return to land and sea in rain as a natural weak acid, supplying a few kilograms of sulphur per hectare a year. Sulphate washed into the sea accumulates in sea water (it is the third most abundant ion) and in sediments, as gypsum in evaporating lagoons and as pyrite in oxygen-poor muds, and returns to land by uplift over geological time.

Human beings have more than doubled the flow of sulphur to the atmosphere. Burning coal and oil, which contain 1 to 4 per cent sulphur, in power stations, industries and vehicles, and smelting sulphide ores of copper, zinc and lead, release about 70 million tonnes of sulphur dioxide a year. In the air it forms acid rain, which damages forests, lakes, soils, crops and buildings, and sulphate aerosols that cause haze and lung disease; sulphur dioxide itself injures leaves, causing bleached spots between the veins, and the lichens that are sensitive to it disappear from polluted cities. Acid rain from the power stations of Singrauli, Korba and Vijayawada falls on the fields and forests around them. The remedies are low-sulphur fuels, flue-gas desulphurisation (scrubbers that trap sulphur dioxide as gypsum, itself a useful fertiliser), cleaner smelting and the shift to renewable energy. Ironically, the reduction of sulphur emissions from Indian power plants has revealed sulphur deficiency in crops that had been receiving free sulphur from polluted rain, so that sulphur fertiliser is now recommended for oilseeds and pulses.

In every cycle described so far the same step recurs: dead matter is broken down and its elements returned to the soil, water and air. This is the work of the decomposers, chiefly bacteria and fungi, helped by a host of small animals, and without them every cycle would stop. If decomposition ceased, dead leaves, wood, corpses and dung would pile up, the carbon, nitrogen, phosphorus and sulphur in them would stay locked away, the soil would be starved, plants would fail, and life would end within a few years for want of raw material. Decomposers are the most important organisms on Earth that most people never think about.

Decomposition proceeds in stages. Detritivores, animals that feed on dead matter, begin it: earthworms, termites, ants, beetles, millipedes, woodlice, springtails, mites, snails, dung beetles, and in water the snails, worms and larvae of the bottom mud. They chew, shred and swallow litter, wood and dung, breaking it into small pieces with a huge surface area, mixing it with soil and inoculating it with microbes in their guts; a termite colony can consume a fallen tree within a season, and earthworms pass tonnes of soil and litter through their bodies each year. Then the fungi take over the tough materials: their thread-like hyphae penetrate wood, leaves and straw and secrete enzymes that break down cellulose and, uniquely among decomposers, lignin, the hard substance of wood; the bracket fungi and mushrooms on a rotting log are the fruiting bodies of a fungus that has been digesting the log for years. Meanwhile the bacteria, present in thousands of millions per gram of soil, attack the softer materials, proteins, sugars, starch and fats, and finish what the fungi begin, each species specialised on certain compounds; some work with oxygen and some without. Between them, fungi and bacteria carry out mineralisation: the conversion of organic compounds into the inorganic forms, carbon dioxide, water, ammonium, nitrate, phosphate and sulphate, that plants can absorb. What resists decay, mainly the remains of lignin and microbial cells, becomes humus, which decomposes very slowly over decades and centuries, holding nutrients and water in the soil meanwhile.

The rate of decomposition depends on the conditions. Temperature: it doubles for every 10 °C rise up to about 35 °C, so tropical litter disappears in months while Himalayan litter lasts years. Moisture: decomposers need water, so decomposition is slow in deserts and stops in dry seasons; but in waterlogged soil, without oxygen, it is slow too and produces methane, hydrogen sulphide and acids, which is how peat and coal formed. Oxygen: aerobic decomposition is fast and complete; anaerobic is slow and partial. The nature of the material: sugars and proteins decay in days, cellulose in months, lignin and wood in years; materials with a high ratio of carbon to nitrogen (straw, sawdust) decay slowly because the microbes are starved of nitrogen, which is why compost heaps need dung or green matter mixed with straw. Soil pH: bacteria prefer neutral soils, fungi tolerate acid ones. And pollution: pesticides, heavy metals and acid slow or stop decomposition by killing the decomposers.

Human beings use decomposers deliberately in composting, in vermicomposting, in biogas plants (anaerobic bacteria turning dung into methane and slurry), in sewage treatment (the activated sludge of a treatment plant is a mass of decomposer bacteria), in the retting of jute and coir, in the making of curd, cheese and soy sauce, and in bioremediation of oil and pesticide pollution. The decomposers in a compost pit are the same cycle, sped up and put to work in a corner of the farm.

Every biogeochemical cycle on land passes through the soil. Water infiltrates it and is stored in it; carbon is held in its humus and released from it by decomposition; nitrogen is fixed, nitrified and denitrified in it; phosphorus and sulphur are weathered from its minerals and cycled through its organisms. The soil is not a passive container but a living reactor in which the cycles meet, and its health decides whether the cycles run smoothly or break down.

Consider what a single gram of fertile topsoil contains: several thousand million bacteria of thousands of species, hundreds of metres of fungal hyphae, tens of thousands of protozoa, hundreds of nematodes, and numerous mites and springtails, together with roots and root hairs, clay and humus particles with enormous surface area, and water films holding dissolved nutrients. In this crowded space the reactions of the cycles run side by side: a Rhizobium fixes nitrogen in a nodule a millimetre from a Nitrosomonas oxidising ammonium, while a mycorrhizal fungus gathers phosphate from a mineral grain, an earthworm mixes the litter, and, in an airless crumb nearby, a Pseudomonas denitrifies. Soil animals and roots keep the soil porous so that water and oxygen enter; clay and humus hold nutrient ions on their surfaces (cation exchange) so that they are not washed away but remain available to roots; and humus buffers the pH and stores carbon.

The soil links the cycles to one another. Adding organic matter (carbon) feeds the decomposers that release nitrogen, phosphorus and sulphur; the balance between carbon and nitrogen in the material decides whether nitrogen is released or locked up. Water controls oxygen, and oxygen controls whether nitrogen is nitrified or denitrified, whether sulphur becomes sulphate or sulphide, whether carbon becomes carbon dioxide or methane. Acidity, itself affected by the nitrogen and sulphur cycles through nitric and sulphuric acid, controls the availability of phosphorus and the activity of bacteria. A change in any one cycle changes the others.

This is why the degradation of soil, described in the previous chapter, is also the breaking of the cycles. Erosion removes the humus and the organisms with it. Salinisation and waterlogging halt decomposition and nitrification. Pesticides and heavy metals kill the fixers, nitrifiers and decomposers. Continuous chemical fertilising without organic matter exhausts the humus that holds the nutrients, so that the cycles leak: nitrate to the groundwater, phosphate to the tank, carbon to the air. And the loss of forest and grassland cover exposes the soil to sun and rain that speed the burning of its carbon and the washing away of its nutrients.

Conversely, the practices of soil health repair the cycles: returning crop residues and manure to feed the carbon cycle; growing legumes and using biofertilisers to strengthen nitrogen fixation; keeping the soil covered and porous so that water infiltrates and oxygen enters; using mycorrhiza and phosphate-solubilising bacteria to unlock phosphorus; liming acid soils and draining waterlogged ones; and avoiding the pesticides and excess salts that kill the soil's workers. A farmer who builds humus is building the capacity of the soil to run all the cycles at once, and a soil rich in humus and life is the most reliable guarantee of the cycles' balance.

The ocean plays the same role at sea: its surface waters are where carbon is fixed and oxygen released by phytoplankton, its depths where nutrients are regenerated by decomposition and returned by upwelling, and its sediments the long-term store of carbon, phosphorus and sulphur. The east coast upwelling off Andhra Pradesh in the monsoon, which brings nutrients up and feeds the sardine and mackerel fishery, is the ocean's version of a healthy soil.

The carbon cycle's disturbance, global warming, is the most famous, but human beings have altered the nitrogen and phosphorus cycles even more in proportion, and the effects are felt in every tank, river and coastal sea of Andhra Pradesh.

Doubling the nitrogen cycle. Before industry, about 100 million tonnes of nitrogen a year were fixed on land by bacteria and lightning. Today humans fix about the same amount again: about 120 million tonnes a year in fertiliser factories by the Haber-Bosch process, about 40 million tonnes by the legume crops we plant, and about 30 million tonnes as nitrogen oxides from burning fossil fuels at high temperature in engines and furnaces, which combine the nitrogen and oxygen of the air. We have thus doubled the flow of reactive nitrogen into the living world, and because crops recover only 30 to 40 per cent of the fertiliser applied, most of the rest cascades through the environment, doing harm at every stage.

The consequences follow the nitrogen. Nitrate in groundwater from leaching exceeds the safe limit of 45 mg per litre in wells across the intensively farmed districts, causing methaemoglobinaemia in infants and possibly cancers. Eutrophication of fresh and coastal waters from nitrogen and phosphorus runoff and sewage: the nutrients feed explosive growth of algae and floating weeds; the mass of plants shades out submerged plants; when it dies, decomposers use up the dissolved oxygen, fish and other animals suffocate, and the water body turns into a stinking, weed-choked swamp. Kolleru lake, Hussain Sagar, the tanks of every town, and the coastal waters at the mouths of the Godavari and Krishna show it; in the world's seas over 400 dead zones of oxygen-starved water, the largest at the mouth of the Mississippi, have formed from farm runoff. Ammonia volatilised from urea and manure, and nitrogen oxides from vehicles and power stations, pollute the air, form fine particles that damage lungs, and fall as acid rain and as nitrogen deposition that fertilises forests and grasslands so that a few nitrogen-loving species crowd out the many that were adapted to poor soil, reducing biodiversity. Nitrous oxide from fertilised soil is the third most important greenhouse gas and now the largest destroyer of stratospheric ozone. And in the soil itself, excess nitrogen acidifies, exhausts humus and unbalances nutrients.

Short-circuiting the phosphorus cycle. Phosphorus, which nature moves from rock to sea only over millions of years, is now mined at 250 million tonnes of rock a year and moved to fields, and from fields, sewers and detergents into water within a single season. Because phosphorus is the limiting nutrient in most fresh water, its arrival triggers eutrophication even where nitrogen is scarce, and the blue-green algae that bloom in such water release toxins that kill cattle and make water unfit to drink. At the same time the world's phosphate rock, a non-renewable resource, is being used up, and India, which imports 90 per cent of its phosphate, is exposed.

The remedies are known. On the farm: soil testing and balanced fertilising, split and placed doses, neem-coated and slow-release urea, nitrification inhibitors, legumes, green manures and biofertilisers, organic matter to hold nutrients, buffer strips of grass and trees along streams to catch runoff, and the natural farming that reduces purchased nitrogen altogether. In the city: sewage treatment plants that remove nitrogen and phosphorus, a ban on phosphate detergents, and the recovery of phosphorus from sludge and food waste as fertiliser. In energy and transport: catalytic converters and cleaner fuels to cut nitrogen oxides. And in the diet: since animal products need several times as much fertiliser nitrogen per unit of protein as pulses, eating more pulses and less meat lightens the load on the cycle. Restoring the cycles' balance means closing the loops that we have opened.

Three further disturbances show how the cycles are linked, so that a change in one appears as damage in another.

Ozone depletion is a disturbance of the oxygen cycle in the stratosphere. The ozone layer, formed and destroyed continuously by ultraviolet light acting on oxygen, absorbs the ultraviolet-B radiation that would otherwise damage the DNA of every organism on the surface. Chlorofluorocarbons (CFCs), invented as safe, non-toxic gases for refrigerators, air conditioners, spray cans and foam, are so stable that they survive for decades, drift up to the stratosphere, and there are broken by ultraviolet light to release chlorine atoms; each chlorine atom catalyses the destruction of thousands of ozone molecules before it is removed. Halons from fire extinguishers (bromine), methyl bromide (a soil fumigant) and nitrous oxide from fertiliser add to it. The result was discovered in 1985: a hole in the ozone layer over Antarctica each spring, with ozone reduced by more than half, and a thinning of a few per cent worldwide. More ultraviolet-B reaching the ground increases skin cancer, cataracts and suppression of the immune system in people, damages the phytoplankton at the base of ocean food chains and so the carbon and oxygen cycles, reduces crop yields, and degrades plastics and paints. The Montreal Protocol of 1987, signed by every country in the world, phased out CFCs, and India stopped their production by 2010; the ozone layer is now recovering and should be back to its 1980 state by about 2060. It is the clearest proof that a global cycle, once understood, can be protected by agreement.

Acid rain links the sulphur and nitrogen cycles to the water cycle and the soil. Sulphur dioxide from coal and smelters and nitrogen oxides from vehicles and furnaces are oxidised in the air and dissolved in cloud water as sulphuric and nitric acids, which fall as rain with a pH as low as 4, and as dry acid dust; natural rain, in equilibrium with carbon dioxide, has a pH of about 5.6. Acid rain acidifies soils, leaching calcium, magnesium and potassium and releasing toxic aluminium, so that trees lose their fine roots and mycorrhizae, weaken and die; whole forests in Germany, Scandinavia and eastern North America were damaged in the 1970s and 1980s. It acidifies lakes, killing fish, frogs and insects; thousands of Scandinavian and Canadian lakes became lifeless. It damages crops, corrodes buildings, bridges and monuments, the marble of the Taj Mahal among them, and harms lungs. Its control, by desulphurisation, low-sulphur fuels, catalytic converters and cleaner energy, has greatly reduced acid rain in Europe and North America, while it continues around India's and China's coal belts.

The linkages are the lesson. Nitrous oxide from fertiliser (nitrogen cycle) warms the climate (carbon cycle) and destroys ozone (oxygen cycle). Warming (carbon cycle) increases evaporation and extreme rainfall (water cycle), speeds decomposition and denitrification (nitrogen cycle), and acidifies the ocean as it absorbs carbon dioxide, which dissolves the shells of the organisms that build limestone (carbon and calcium cycles). Deforestation releases carbon, breaks the local water cycle and lets the nitrogen and phosphorus of the soil wash away. Eutrophication (nitrogen and phosphorus cycles) removes oxygen from water (oxygen cycle) and releases methane and nitrous oxide (carbon and nitrogen cycles). The cycles are one system, and so are the remedies: a forest planted for carbon also holds water, fixes nitrogen and retains phosphorus; a field that receives organic matter instead of excess urea stores carbon, leaks less nitrate and needs less pesticide; a city that treats its sewage protects its lake's oxygen, its river's fish and its own drinking water. To protect one cycle wisely is to protect them all.

The balance of nature is the state in which the biogeochemical cycles run steadily, the inputs to each reservoir roughly equalling the outputs, so that the composition of the air, the fertility of the soil, the chemistry of the sea and the numbers of organisms stay within limits from year to year and century to century. It is not a fixed, motionless balance, for the Earth has always changed: ice ages have come and gone, carbon dioxide has been higher and lower, and the oxygen in the air was built up by photosynthesis over thousands of millions of years. But those changes were slow enough for life to adapt and for the cycles to adjust. What is new is the speed and scale of human change: carbon dioxide raised by half in two centuries, the nitrogen cycle doubled in one, phosphorus moved from rock to sea in a season, forests cleared in decades, the ozone layer holed in fifty years. The cycles are being pushed faster than their self-correcting mechanisms can respond.

The cycles do have self-correcting mechanisms. More carbon dioxide stimulates plant growth that absorbs some of it; the oceans take up half of what we emit; weathering of rocks removes carbon dioxide over thousands of years; denitrification removes excess nitrate; ozone re-forms once chlorine is gone. But these feedbacks are slow or limited, and some feedbacks go the other way: warming melts permafrost that releases methane and carbon dioxide, causing more warming; warming reduces the ocean's ability to dissolve carbon dioxide; drought kills forests that then release their carbon; and eutrophication releases greenhouse gases. There are tipping points beyond which a change cannot be reversed on any human time scale, the collapse of ice sheets or of the Amazon forest, and the aim of the world's climate agreements is to stay below them.

Restoring the balance is a matter of closing the loops that we have opened, and the measures gather up everything in this chapter. For the carbon cycle: renewable energy, efficiency, public and electric transport, protection and planting of forests and mangroves, carbon-storing farming, and less waste. For the nitrogen and phosphorus cycles: fertiliser used by soil test and in balance, legumes, biofertilisers, organic matter, buffer strips, sewage treatment with nutrient recovery, phosphate-free detergents, cleaner engines and a diet richer in pulses. For the water cycle: rainwater harvesting, watershed management, afforestation, efficient irrigation, wetland protection and the end of groundwater over-pumping. For the oxygen cycle: the completion of the CFC phase-out and the prevention of organic pollution that starves water of oxygen. For the sulphur cycle: low-sulphur fuels and scrubbers. And for all of them: the protection of the forests, grasslands, wetlands, soils and oceans in which the cycles run, since an ecosystem is the machinery of the cycles and cannot be replaced once destroyed.

These are not only tasks for governments. The habits of a Class 9 student in Andhra Pradesh are part of the carbon cycle (the lights left on, the scooter ride, the tree planted, the plastic refused), the nitrogen and phosphorus cycles (the food wasted, the detergent chosen, the compost made), the water cycle (the tap left running, the rainwater harvested at school) and the oxygen cycle (the old refrigerator properly disposed of). Every atom of carbon, nitrogen, phosphorus and sulphur in our bodies has been round the cycles countless times and will go round again after us; we are borrowers, not owners. Understanding the cycles is the beginning of using the Earth in a way that its cycles can sustain, and that is the purpose of this chapter and of biology itself.