Many infections are life-threatening, and when epidemics result in large numbers of people dying, it significantly reduces the diversity of our collective gene pool. This was particularly true during the early days of our evolution, yet even more recent episodic diseases have significantly changed the course of our history. For instance, during the Middle Ages in Europe, nearly 1/3 of its entire population died from several waves of bubonic plague that arrived in that region as the result of the Crusades. In the early 1500's in the New World, the population of Mesoamerica fell from a robust population of some 50 million before the Spanish conquistadors arrived, to just under 4 million a short 150 years later. The precipitous drop was not due to Spanish bullets and swords, but rather to the introduction of European microbes such as measles, small pox, and influenza. In 1917-1919, two percent of the world's population succumbed to a particularly virulent form of influenza. Today, it is the HIV-AIDS epidemic that is decimating our ranks, particularly for those living on the African continent.

Most of the time, however, infections present as chronic illness. They disable us with fever, diarrhea, headache, weight loss, and malaise, symptoms that prevent us from carrying out our day-to-day lives unencumbered. For hundreds of millions of children, this means not attending school on a regular basis. Unrealized genetic potential for those unfortunate enough to be affected by them is the result; a far more subtle outcome than death of the host, but just as crucial in terms of our ultimate destiny. Regardless of the severity of infection, one thing is certain. The local environment in each ecosystem in which we live helps to maintain them, periodically allowing for the recurrence of outbreaks.

In addition to those agents restricted to infecting the human host, relatively un-disturbed ecosystems (i.e., those natural regions that have experienced little in the way of human activity) harbor numerous zoonotic infections (i.e., animal-specific parasites) that occasionally infect humans. Good examples include leishmaniasis, Lyme disease, rabies, and African sleeping sickness.  Millions suffer, and many die from these entities each year. However, it is the disturbed environment that affects even larger populations, resulting in epidemics caused by the microbes that routinely infect us. Cholera, polio, malaria, and tuberculosis are already endemic in many regions of the world. Agriculture, encroachment due to expanding human populations, civil unrest and war serve only to exacerbate them, not infrequently eliciting epidemics. For example, war forces already highly stressed peoples into unoccupied landscapes, de-stabilizing ecological balances and disconnecting ecosystem functions from many of the indigenous plants and animals. Recycling of nutrients and energy flow are two functions highly sensitive to encroachment, an activity that almost invariably re-arranges associations between assemblages of plants and animals, causing fundamental changes in the ways they interact with each other, as well as with us.

Frequently, the shuffling of established associations leads to increased transmission, particularly for those agents that are acquired through drinking contaminated water, or ones that are vector borne. Lyme disease is an excellent example of this later type of microbe. In certain parts of the northeastern United States, upwards of 50% of the Lyme disease-carrying ticks are infected. This is unprecedented among vector borne diseases, in which an infection rate of 1-2% is the norm. This situation resulted solely from human activity, in which heavily forested areas were “manicured,” reducing the density of trees to savanna-like ecological setting. Savannas favor the survival of white-tailed deer populations. Restrictions on hunting and the loss of natural predator species further encourage the spread and maintenance of Lyme disease.

Regardless of where it is practiced, farming creates ecotones that attract animals and plants unique to that narrow zone. Rare infectious disease agents seem to be particularly attracted to these small, altered zones, and often become commonplace. Infectious disease transmission is frequently enhanced within this zone, and in particular when human settlement created it. Obtaining water for irrigation is another example of an agricultural practice that leads to increased disease transmission. Organisms that are water borne or that depend upon transmission from arthropods that breed in freshwater, are the beneficiaries of this human behavior. Water borne and food borne pathogens associated with dam building have become wide-spread in tropical settings.

Fertilizer composed largely of human solid wastes is a popular resource used to supplement nutrient-poor soils where naturally occurring elements have been repeatedly removed by centuries of traditional farming. This potentially beneficial product must be treated to kill any pathogenic microbes that might be present. However, this is not usually done in most under-developed countries that rely heavily on this easily obtained material. Its use in an untreated form actually encourages transmission cycles of some organisms dependent upon gaining entrance into the human host via the fecal oral route. This activity, alone, accounts almost entirely for the extremely high rate of enteric infections, especially in children, in most rural communities throughout the tropical and sub-tropical world.

There are now some 6.3 billion humans on earth. We have been spared the ravages of most opportunistic microbes by the concomitant development of a robust immune system that has co-evolved with them. Because of this, in the great majority of instances, microbes fail to establish themselves. The mechanism by which this has come about is largely by the process of random mutation of our immune response genes and selection on the part of potentially lethal microbes. Infectious agents of all kinds have attempted to colonize us. Those individuals fortunate enough to carry mutated genes whose products adversely affected the survival of new invaders went on to pass them to their offspring. In this way, most of the world's population has become acclimatized to their presence. Geographic isolation narrows the selective pressure, and thus occasionally, a disease entity unknown to that population is introduced that can result in large numbers of deaths.

When water, food, or air borne microbes do succeed in colonizing, we refer to them as non-vector borne infections. Some have even evolved to a position of being indispensable to our lives. Witness the E. coli bacteria living in our intestinal tract which produce vitamin K. Without this essential substance, we would be unable to clot our blood. Others, however, have yet to come into balance, like the rabies and Ebola viruses. The mortality rate for these agents is high.

Other disease-causing agents invade us with the help of a wide range of invertebrate vectors, such asmosquitoes, black flies, tsetse flies, kissing bugs, and ticks. African sleeping sickness, Chagas' Disease, malaria, river blindness, elephantiasis, a wide variety of viral encephailitis viruses, and many others are introduced into us by the blood sucking activities of these temporarily parasitic arthropods. Most of the microbes that they transmit are capable of causing serious, life-threatening illnesses if left untreated.

We will consider many of these two kinds of infectious agents in this section. All of the ones listed have an environmental component to them with respect to how they come into contact with us. To help explain the complexity of interplay between the environment, vectors, animal reservoirs, and human disease requires integration of an extensive set of ecological data with those obtained from the molecular biological laboratory. What follows is a summary of those findings together with a comprehensive list of references and internet websites designed to lead the user into as great a depth of knowledge as they so desire.

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