This chapter provides an introduction to environmental microbiology as a discipline. It also illustrates the significance of environmental microbes to our daily lives in terms of not only the overall health of the planet, but also: what infects us; what heals us; what we drink; what we eat; and what we breathe. Following this, a discussion of emerging microbial issues is presented, including detrimental microbial pathogenic outbreaks as well as beneficial microbial bioremediation success stories. Finally are presented some of the latest and most advanced techniques and methodologies that are revolutionizing modern environmental microbiology through state-of-the-art science.

Keywords

environmental microbiology; microbial bioremediation; microbial natural products; microbial pathogens; mycotoxins; next generation sequencing; rhizosphere microorganisms

1.1 Environmental Microbiology as a Discipline

1.2 Microbial Influences on our Daily Lives

1.2.1 Overall Health of the Planet

1.2.2 What Infects Us

1.2.3 What Heals Us

1.2.4 What We Drink

1.2.5 What We Eat

1.2.6 What We Breathe

1.3 Environmental Microbiology in 2014

Questions and Problems

References and Recommended Reading

1.1 Environmental Microbiology as a Discipline

We define “environmental microbiology” as the study of microbes within all habitats, and their beneficial and detrimental impacts on human health and welfare. Environmental microbiology is related to, but also different from, “microbial ecology,” which focuses on the interactions of microorganisms within an environment such as air, water or soil. The primary difference between the two disciplines is that environmental microbiology is an applied field in which we attempt to improve the environment and benefit society. Environmental microbiology is also related to many other disciplines (Figure 1.1).

Microorganisms occur everywhere on Earth. An adult human body contains 10 times as many microbial cells as mammalian cells, consisting of approximately 1.25 kg of microbial biomass (Wilson, 2005). Although the study of microbial inhabitants of humans resides within clinical microbiology, it was the discovery of environmental pathogenic microorganisms that invaded the human body that resulted in the beginning of environmental microbiology. These roots were enabled by the work of Louis Pasteur and Robert Koch, who developed the Germ Theory of Disease in the 1870s, following which, the presence of waterborne human pathogens then became the initial focus of environmental microbiology. In developed countries, applied environmental studies related to drinking water and wastewater treatment dramatically reduced bacterial waterborne disease. However, other microbial agents such as viruses and protozoa, which are more resistant to disinfection than enteric bacteria, still cause problems, resulting in water quality continuing to be a major focus in environmental microbiology. There is an estimated 20,000,000 cases of illness per year due to drinking contaminated water (Reynolds et al., 2008). The largest waterborne outbreak of disease in the United States occurred in 1993, when over 400,000 people became ill and around 100 died in Milwaukee, Wisconsin, due to the protozoan parasite Cryptosporidium (Eisenberg et al., 2005). In developing countries, poor sanitation resulting from a lack of water and wastewater treatment still results in millions of deaths annually.

Controlling the contamination of our food supply also continues to be a concern; and the Centers for Disease Control estimates that in the United States each year there are 48 million cases with 128,000 people hospitalized and 3000 deaths. The third most deadly outbreak of foodborne infection in the United States occurred in 2011, when 29 persons died from Listeria contamination of cantaloupe. Information Box 1.1 documents some of these foodborne outbreaks.

Until the middle of the 20th century, industrial chemicals in the United States were routinely disposed of by dumping them into sewers, soils, rivers or oceans, without regard to the pollution that this caused, or the subsequent adverse ecological and human health effects. This all changed in the 1960s when concern over a toxic dump was highlighted by Rachel Carson’s landmark book Silent Spring. In essence, this resulted in the birth of the environmental movement in the United States, and a new field of study for environmental microbiology known as “bioremediation.” Many chemicals discharged into the environment without regard to the consequences have been shown to result in adverse human health impacts. However, since hydrocarbons, chlorinated solvents and most pesticides are organic in nature, they can potentially be degraded by heterotrophic microorganisms including bacteria and fungi. The field of bioremediation within environmental microbiology involves enhancing and optimizing microbial degradation of organic pollutants, resulting in environmental cleanup and reduced adverse human health effects. The efficacy of bioremediation was demonstrated in 1989, when the Exxon Valdez oil tanker spilled approximately 11 million gallons of crude oil into Prince William Sound. Optimization of bioremediation was a major factor in cleaning up and restoring Prince William Sound. Bioremediation has also been shown to be critically important in cleaning up the more recent 2010 Gulf of Mexico oil spill (see Chapter 31).

Also in the 20th century, soil microbiology, a component of environmental microbiology, became important as a means to enhance agricultural production. Studies on the rhizosphere (the soil surrounding plant roots), and specific studies on root-microbial interactions involving nitrogen fixing rhizobia, and mycorrhizal fungi that enhanced phosphorus uptake, were all utilized to improve plant growth. Other studies of plant growth-promoting bacteria that reduced the incidence of plant pathogens were also effective in aiding the “Green Revolution,” which resulted in stunning increases in crop yields throughout the United States and in many parts of the world. Overall, these fundamental study areas have helped shape the current discipline of environmental microbiology, and all affect our everyday life.

1.2 Microbial Influences on our Daily Lives

Some of the influences that microorganisms have on our daily lives are shown in Table 1.1. These influences can be summarized in terms of: