A remarkable feature of acid-tolerant microbes is that the insides of their cells are not particularly acidic – about pH6. Acidity is a measure of hydrogen ion concentration. It is a logarithmic scale so that pH zero has one million times the concentration of hydrogen ions as pH6. Somehow the bacteria are able to maintain a million-fold concentration difference of protons (remember that a hydrogen ion, H+, is just a proton) across their cell membranes. It is not entirely clear how the bacteria achieve this feat; presumably either by excluding protons from their cells or by possessing a very efficient proton pump to pump them out.
The extreme alkaline end of the pH scale (10–14) is also harmful to most animals and plants. Strong alkaline solutions such as caustic soda dissolve cell membranes and destroy cells. Many plants and microbes are however fairly tolerant of soils that may have pH values up to about 10. Environments more alkaline than pH10 are rare on this planet. The only stable systems are soda lakes fed by bicarbonate-rich natural springs. The pH of these lakes may be as high as 11.5, yet they are often rich in microbial life.
High concentrations of salt are toxic to most living organisms; as attested by salt-curing to prevent microbial growth and preserve meat and fish. When cells are suspended in salt, their internal water is sucked out of their cells by osmosis, which dehydrates and eventually kills cells. There are however many natural saline environments on Earth. The sea, with a salt concentration of about three per cent, is toxic to most land animals and plants but is of course haven to marine creatures. The Dead Sea is a twenty-eight per cent solution of salts, nearly ten times the salinity of sea water. Yet the Dead Sea is far from dead. Although no fish swim in its waters, it contains algae and a rich microbial flora. One of these microbes, called Halobacterium, produces a purple pigment, bacteriorhodopsin that is able to harvest light energy and is the only non-chlorophyll based natural light-harvesting system that we know of. Halobacteria are so salt tolerant that they can survive intact inside salt crystals. Salt-loving bacteria employ two principal mechanisms to survive the osmotic pressures of their saline habitats. The first is simply to accumulate lots of salt (usually potassium chloride) within their own cells. The second strategy is to synthesize large quantities of small organic molecules (like glycerol) inside their cells, which counteract the pull of the external salt.
The Gulf War left devastation in the Persian Gulf. Burning oil wells belched noxious black smoke and leaked millions of tons of crude oil into the surrounding land. It was an environmental disaster that many predicted would take centuries to mend. Yet only a few years later, wild flowers returned to the oil well sites. The key to the rapid recovery was the presence of oil-eating microbes in the soil. Many microbes can tolerate or even feed on chemicals poisonous to plants and animals. The soils surrounding the oil wells were probably already rich in these microbes before but thrived in the oil-polluted soil left by the war. The microbes fed on the crude oil, degrading it into less non-toxic chemicals. Microbes are able to feed on a wide range of chemicals poisonous to many other creatures, such as benzene, toluene, cyclohexane and kerosene.
LIFE WITHOUT AIR
Living and breathing are, for humans, inextricably linked. We talk of ‘the breath of life’. Animals need oxygen to live. Yet there are many living organisms for which the breath of life is poisonous. Microbes, known as anaerobes, do not breathe air: indeed many are instantly killed on exposure to oxygen. This sensitivity makes anaerobes difficult to study and so their prevalence has not been appreciated until fairly recently. It may come as a surprise to you to know that more than eighty per cent of your faeces is made up of anaerobic bacteria. Very little air penetrates our lower bowels, making it an ideal environment for the proliferation of these microbes. The vast majority of these gut bacteria are entirely harmless colonizers of our intestinal tract or even beneficial; but they may occasionally cause problems (mostly abscesses and ulcers) particularly if introduced into the rest of the body by wounds or surgery. Anaerobic microbes are also widespread in the environment. They are found in the soil and in fresh and seawater, particularly in the air-depleted sediments at the bottom of lakes, rivers, seas and oceans.
So how do anaerobes live without oxygen? It’s easy – it’s living with oxygen that is the difficult feat. Toxic to all living organisms, oxygen is highly reactive – reacting with tissue to generate even more unpleasant chemicals such as hydrogen peroxide (used to bleach hair) and molecules known as free radicals. Air-breathing organisms have an armoury of protective enzymes to remove and destroy these toxic chemicals. Strict anaerobes lack these protective enzymes and are killed by oxygen.
So why do we go to so much trouble to breathe air when one of its chief components, oxygen, is so toxic? We use it to burn our food in the process known as respiration. Chapter 5 will examine respiration more closely, but briefly: electrons are harvested from our food and rolled down a kind of energy cascade to oxygen. The difference in energy (high-energy electrons from food to low-energy electrons in oxygen) is captured, providing energy for the cell. Oxygen-based respiration is a very efficient means of extracting maximum energy from food and has thus superseded the anaerobic metabolism in most higher organisms.
Some anaerobes burn their food in respiration, but not with oxygen. Many minerals (such as sulfate or nitrate) serve as low-energy electron dumps for their respiratory cascade. You may well have noticed that the sand alongside estuary waters is often black and smelly. The bad smell is hydrogen sulfide and the blackness is due to the presence of iron sulfide, both products of anaerobic bacteria’s respiration in these estuarine waters. In fact, a wide range of minerals can be utilized by bacteria for respiration; some bacteria can even breathe iron.
Still other anaerobes do not actually respire at all but derive their energy from chopping up their food molecules into small pieces, usually into simple acids or alcohol, in a process known as fermentation. Fermented foods and beverages like wine, beer, sauerkraut, cheese and even coffee, depend upon the actions of these busy microbes. Anaerobes are of enormous ecological importance since they are often responsible for the final decay of organic matter. A giant compost heap would have long since enveloped the whole planet were it not for these bacteria. Cows and other ruminants have learned to harness the powers of these microbes. Their stomachs house an internal compost heap of plant material decomposing through the activity of billions of fermentative bacteria. One of the by-products of their fermentation is the greenhouse gas, methane. The huge quantities of the gas flatulently emitted by (the bacteria inside) domesticated ruminants is thought to contribute signifycantly to the greenhouse effect.
Far from being the breath of life, life carries on very well in oxygen’s complete absence. This must of course be so, since (as covered further in Chapter 4) life emerged on this planet in an atmosphere completely devoid of oxygen. It was only after photosynthetic plants and microbes began to pour oxygen into the earth’s atmosphere that aerobic life became possible on Earth.
JOURNEY TO THE CENTRE OF THE EARTH
Descend into the crater of Yocul of Sneffels, which the shade of Scartaris caresses, before the kalends of July, audacious traveller, and you will reach the centre of the earth. I did it.
ARNE SAKNUSSEMM
These were the instructions that, in Jules Verne’s famous tale, led Professor Hardwigg and his companions to descend into ‘the great volcano of Sneffels’, following in the footsteps of the intrepid Icelander. Miles below the surface, they crossed a subterranean sea to discover a fabulous world of gigantic mushrooms,