Soil is a dynamic habitat for an enormous variety of life-forms. It gives a mechanical support to plants from which they extract nutrients. It shelters many animal types, from invertebrates such as worms and insects up to mammals like rabbits, moles, foxes and badgers. It also provides habitats colonised by a staggering variety of microorganisms. All these forms of life interact with one another and with the soil to create continually changing conditions. This allows an on-going evolution of soil habitats.

The activity of living organisms in soil helps to control its quality, depth, structure and properties. The climate, slope, locale and bedrock also contribute to the nature of soil in different locations. The interactions between these multiple factors are responsible for the variation of soil types. Consequently, the same fundamental soil structure in different locations may be found to support very different biological communities. These complex communities contribute significantly to the continuous cycling of nutrients across the globe.

What habitats are provided by soil?

Soil forms by the breakdown of bedrock material. Erosion of rocks may be the result of chemical, physical or biological activity, or combinations of the three factors. Dissolved carbon dioxide and other gases cause rain water to become slightly to moderately acid. This pH effect may cause the breakdown of rocks such as limestone. Physical or mechanical erosion can result from the action of wind or water, including ice erosion.

How do microbes cause disease and how do we defend ourselves from infection

The vast majority of microbes that humans encounter on a daily basis do no harm. Indeed, the microbes that constitute our commensal flora are, on balance, beneficial under most circumstances. Only a minority of microbes can interact with humans to cause disease. These are known as pathogens from the Greek word pathos, meaning ‘suffering’. Some pathogens cause mild illnesses: others are responsible for life-threatening infections. Some infections are chronic, developing slowly over many months or years: others may be rapidly fatal. Virulence is the term used to describe the degree to which an organism can cause disease. This term is derived from the Latin word virus, meaning a poison. Some authors do use the terms ‘pathogenicity’ and ‘virulence’ interchangeably. Other authors prefer to reserve the term ‘virulence’ for a quantitative description of the degree to which a microbe can damage its host.

Infections spread from a source known as the reservoir of infection. These may be human beings, as with Salmonella typhi, animals, as with Salmonella typhimurium, or the environment. Soil is the reservoir of infection for tetanus, caused by Clostridium tetani, and water for Legionnaire's disease, caused by Legionella pneumophila. The source of infection is the individual or location from which an infection is acquired.

How do microbes affect food?

An inevitable consequence of the start of agricultural practices that heralded the dawn of civilisation was the need to store crops from one season to the next. This brought with it the risk of microbial contamination and spoilage. The problems of food spoilage are, therefore, as old as civilisation. Not all spoilage, however, is detrimental. Fermentation, for example, can vastly improve the flavours of foods and can also turn an inedible food into a delicacy. The food processing industry has thus been exploiting microbes for centuries. Even so, it is only in the last 150 years or so that we have realised the contribution that microbes make to food production.

How are fungi used as food?

Probably the most familiar edible fungus is the mushroom. We have been eating mushrooms for centuries. The Romans valued mushrooms but were also very familiar with their potentially fatal effects. Sometimes they used this knowledge to great effect when someone important obstructed their ambitions. Agrippina murdered the emperor Claudius by feeding him mushrooms so her son Nero could succeed him as emperor. Nero then declared mushrooms the food of the gods, since it was mushrooms that had made Claudius a god. There is even a mushroom known as Caesar's mushroom (Amanita caesarea). This is a rather rare and highly prized specimen: a close relative of the death cap mushroom (Amanita phalloides).

What are mycorrhizas?

The name mycorrhiza is derived from two Greek words, mukes meaning a mushroom and rhiza, a root, illustrating a very important mutualistic interrelationship between plants and fungi. These partnerships have a long history. The fossil record shows that fungi and higher plants have lived in the close association of mycorrhizal relationships for at least 400 million years. The first recorded observations of mycorrhizal associations were made in the mid-nineteenth century. The numbers of plants that form mutualistic associations with fungi perhaps best illustrates the importance of mycorrhizal relationships. Over 80% of higher plants and ferns grow in association with a fungal partner. The range of higher plants affected include hard- and softwood trees, shrubs and other flowering plants as well as grasses.

The fungi that form mycorrhizal partnerships greatly extend the active surface area of the root system of plants. Fungi replace and extend the root system of the plant. The roots of trees that carry mycorrhizas are typically short and dichotomously branched. Unaffected roots are much longer. Orchids have evolved to such a degree that their mycorrhizal fungi have even replaced the plant root hairs. Plants that support mycorrhizas have much greater access to inorganic nutrients, particularly nitrates, phosphates and water. In return, the plant partner supplies its fungus with a source of organic nutrients and, in many cases, vitamins.

What constitutes the resident and transient flora of humans?

It has been estimated that the human body contains cells. Of these, 90% are not of human origin. They represent the microbes of our commensal flora. The term commensal is partly derived from the Latin word mensa, meaning table. Commensal organisms are considered to share their food from a common table; one that we provide as human hosts. Different anatomical sites are associated with a flora peculiar to each location.

During our time in the womb we live in a sterile environment, protected on one side by the placenta and on the other by the amniotic sac. From the moment of birth, however, we are subjected to a huge array of microbes. The first organisms that we as babies come across are those present in the birth canal. During birth we inhale, swallow and acquire on our surface a vast diversity of microbes as a result of contact with the new environment. This process will continue throughout our lifetime. If the organisms with which we come into contact find themselves in a suitable ecological niche, whether on an internal or an external surface, they will multiply and form complex communities. They will interact with each other and with their human host. This process requires the microbes to adhere to the host as an initial step in the colonisation process and then the microbes must multiply.

Water is essential for the maintenance of all life on Earth. It also acts as the vector for many diseases caused by bacteria, viruses, protozoa and worms. For water to be regarded as potable, i.e. of a quality fit and safe for drinking, it must be free from such pathogens. Furthermore, it must not contain any other noxious substances such as chemical hazards including pesticides, insecticides or herbicides, artificial fertilisers or heavy metal ions. Potable water should not have an unpleasant odour or taste.

What are water-borne diseases?

Among the bacterial infections that are spread by water are cholera, the enteric fevers and dysentery. Hepatitis A and poliovirus cause infections after drinking contaminated water. Amoebic dysentery is caused by the protozoan Entamoeba histolytica and is spread either by drinking contaminated water or by eating food such as fresh fruit, salad or raw vegetables that have been washed in contaminated water. Other protozoal diseases such as those caused by Giardia intestinalis (Giardia lamblia), Balantidium coli and Cryptosporidium species are spread in a similar fashion. Schistosomiasis, also known as bilharzia, is a water-borne infestation caused by worms of the genus Schistosoma.

Cholera

Cholera is a disease that has been known since ancient times. It was confined to the Indian sub-continent but between 1817 and 1923 there were six pandemics in which cholera spread from its original home across the world. It is now also endemic in South America as well as in Asia.

Breast cancer This is the second most common cancer of women in the world, causing some 500,000 deaths each year. In North America, it carries a 12.5% ‘risk rate’, which means that about one in eight women will develop breast cancer, and each year some 46,000 will die from it. For the United Kingdom the rate is 1 in 12, or an 8% risk, with a similar proportion of women who die. Although detection rates have improved, and therefore the incidence appears to be rising, the death rates have remained stable. There are many factors that increase the risk of getting breast cancer, ranging from a woman's age, where she was born, her standard of socio-economic grouping, whether she is overweight, to family histories of breast and ovarian cancers. The fact that it often occurs around the age of 50, and is less common in younger women, may be related to the levels of the female sex hormones, particularly oestrogen, as they are growth stimulators. As breast cancer progresses so the cancer cells stop responding to oestrogens and become ‘fixed’ in a proliferating mode. The levels of these hormones wax and wane throughout life, especially through the menstrual cycle, pregnancy and the menopause, as well as with the degree of obesity. Women who have had their ovaries removed before the age of 35 years rarely get breast cancer.

Alopecia areata It is said that the hair of Marie Antoinette turned white over-night before her execution in the French Revolution. How could this happen? Similar, but usually slower, changes occur in people who suffer alopecia areata or hair loss diseases. These are different from the hair loss described as male pattern baldness which is a normal part of ageing in men. In many cases of alopecia areata, the onset of disease follows illness or extreme stress. The exact cause of hair loss is not known, although recently it has been demonstrated that autoantibodies are present in disease sufferers, suggesting that the body is for some reason reacting against its own hair follicles and causing them to thin at the roots to form what are called ‘exclamation mark’ hairs. These weakened hairs fall out, or can be brushed out easily. Since it is always the pigmented hairs that are attacked, the white hairs of the head are left. The patient appears to turn grey rapidly, but actually the greying hairs were there all the time, but masked by the coloured hairs. In addition any hairs that regrow may now be white instead of the original colour.

Alopecia can appear in both men and women, at any age and over any hair-bearing site. There are several forms of the condition. The most common and mild is patchy alopecia. The hair may fall out or be brushed out in small patches on the scalp, and regrow again later.

Meningitis There are several forms of meningitis, caused by viruses and bacteria, all of which result in acute or chronic inflammation of the membranes over the brain. This covering is called the meninges, hence meningitis means inflammation of this region. Many viruses causing common diseases such as mumps and polio, and the enteroviruses can, after infecting the rest of the body, enter the meninges of the brain. Viral meningitis is often slower to develop than bacterial meningitis and is generally milder. Bacterial meningitis is not so common, but is often a much more serious disease which can kill in a short period of time. It may start as an upper respiratory tract infection, fever and a rash, and can be passed on by coughing and sneezing. Once in the body the causative agents pass to the brain via the blood. If the meningitis is caused by Neisseria meningitidis (meningococcus) the rash that may occur on the limbs is purplish. This used to be known as spotted fever. Streptococcus pneumoniae (pneumococcus) is another infective agent, and in babies it is often Escherichia coli or Listeria monocytogenes that causes meningitis. In the west of America, in California, Arizona, Texas and Mexico, meningitis can be caused by a fungus, Coccidioides immitis. This fungus is very common in the soil and as many as 90% of the population may show evidence of having been infected previously. In severe infections, this form of meningitis may become a killer.

Psoriasis This skin condition, which affects about 2% of the population, often develops in people between the ages of 20 and 30 years who have a certain genetic disposition to develop the disease. This is because of their major histocompatibility complex (MHC) genes in the Cw6 region of chromosome 6 – see Chapter 1. Large scaly lesions form, particularly on the skin of the elbows, knuckles and knees. In severe cases much more of the body becomes affected, so the patient finds it cosmetically embarrassing. About 10% of patients suffer a form of arthritis which flares up as the psoriasis is controlled. At each affected site, the skin cells proliferate rather faster than elsewhere and develop in a slightly different manner, and there are changes underneath that include alterations to the fine blood vessels under the skin, allowing the lesions to bleed easily. Thus the normal skin barrier to the body is weakened at these sites, and bacteria often live in the lesions. One bacterium called Staphylococcus aureus is quite harmful if it gets inside the body. Surgeons are careful to avoid cutting into such psoriatic lesions to prevent the spread of the associated bacteria. The treatment of the disease is difficult but ultraviolet light lessens the severity of the lesions. In some cases, the anti-cancer drugs can be used since they generally reduce cell proliferation and the lesions shrink.

Major Defences

The first and most important protection against invaders is a good barrier to their entry.

Allergies It has been estimated that, in developed societies, about one in four people are allergic to something. Most of these suffer hayfever, which is a form of allergic rhinitis, or asthma. Many allergens (i.e. antigens that cause allergies in hypersensitive people) have been isolated and described in detail. These allergens are generally antigens derived from plant or fungal proteins. However, allergy to cats is the most common allergic condition world-wide, followed by allergy to house mite dust. All babies are capable of being allergic to foods and inhaled allergens, since their immune system is just developing the ability to react in an adult manner. Generally they only receive breast milk or formula feed for several months so the reactions are not common but, if foods are not introduced slowly enough, babies up to about nine months to one year of age can show allergic responses. Then the body learns to tolerate, or not react to, the potentially allergenic substances and the baby can eat a mixed diet without reactions. About 2–5% of adults remain allergic to foods such as cow's milk, peanuts or seafoods, and about 5–10% of children may suffer asthma, with the numbers rising each year. One-third of these may grow out of asthma, but another 10% of adults are newly added to the list of sufferers. The cost of asthma to the American economy in 1990 alone was around $3.6 billion.