Professional Documents
Culture Documents
ÇM Book 1
ÇM Book 1
Introduction to Environmental
Microbiology
Raina M. Maier, Ian L. Pepper and Charles P. Gerba
Hazardous Industrial
waste/ Microbiology
Bioremediation
Soil Food
Microbiology safety
Environmental Occupational
health/Infection
Aeromicrobiology
Microbiology control
Aquatic Diagnostic
Microbiology
microbiology
Water quality
Biotechnology
FIGURE 1.1 Environmental microbiology interfaces with many other fields of microbiology.
TABLE 1.1 Recently Discovered Microbes That Have Had a Significant Impact on
Human Health
Agent Type of Mode of Disease/symptoms
microorganism transmission
SARS (a coronavirus) Virus Fomites Respiratory
Escherichia coli O157:H7 Bacterium Foodborne, waterborne Enterohemorrhagic fever,
kidney failure
Hepatitis E virus Virus Waterborne, foodborne Hepatitis
Bird flu (avian Virus Aerosol, fomites, Respiratory
influenza A (H5N1)) foodborne
Norovirus Virus Waterborne, foodborne Diarrhea
Helicobacter pylori Bacterium Foodborne, waterborne Stomach ulcers
Cyclospora Protozoan Foodborne, waterborne Diarrhea
MRSA (antibiotic- Bacterium Fomites Severe skin infections
resistant Staphylococcus
aureus)
thought that threats from waterborne disease had been drinking water. Water quality continues to be a major focus
eliminated. However, case studies began to accumulate in environmental microbiology because new waterborne
suggesting that other agents, such as viruses and protozoa, pathogens continue to emerge. One of the best documented
were more resistant to disinfection than enteric bacteria. and largest outbreaks occurred in 1993 when more than
This concern became a reality with the discovery of water- 400,000 people became ill and over 100 died in Milwaukee,
borne outbreaks caused by the protozoan parasite Giardia Wisconsin, during a waterborne outbreak caused by the
and by Norovirus, both of which were found in disinfected protozoan parasite Cryptosporidium. Table 1.1 lists many
Chapter | 1 Introduction to Environmental Microbiology 5
Information Box 1.1 Large-Scale Food Recalls Due TABLE 1.2 Common Contaminants Found in the
to Foodborne Outbreaks Environment
of the important pathogens that have emerged in the past Polychlorinated Arochlor, Clophen, Phenoclor, Fenchlor,
biphenyls (PCB) Kanechlor, Tarnol
30 years. Even more worrisome, recent studies suggest that
10 to 50% of diarrhea-associated illness is caused by water- Pharmaceuticals, Endocrine disruptors (e.g., estradiol,
food additives, nonylphenol, polybrominated diphenyl
borne microbial agents we have yet to identify.
and cosmetics ethers (PBDEs)), antibiotics, surfactants, dyes
Pathogens in our food supply is a second area of
immense concern. One of the difficult questions facing the Fluorocarbons Chlorofluorocarbons (CFCs),
hydrochlorofluorocarbons (HCFCs),
food industry is that of importation of vegetables and fruits.
fluoropolymers (Teflon)
On the one hand, there is consumer demand for a wide vari-
ety of high quality imported produce; on the other hand, Fertilizers NH3 (gas), CO(NH2)2 (urea), (NH4)3PO4,
superphosphate
there is an increased danger of importing pathogens along
with the produce. One example is the protozoan pathogen Metals Lead, cadmium, mercury, arsenic,
Cyclospora. This organism gained notoriety as the causative chromium, nickel, zinc
agent of a disease outbreak affecting approximately 1000 Radioactive Uranium, strontium, cobalt, plutonium
people in the United States between early May and mid- contaminants
July 1996. The Cyclospora outbreak was due to consump-
tion of raspberries imported from Guatemala. Foodborne
outbreaks have resulted in major recalls of various foods
(see Information Box 1.1). These examples illustrate the
types of questions that are addressed by environmental cumulative, resulting in cancer many years following expo-
microbiologists. How do pathogens survive in the environ- sure or, more immediately, resulting in birth defects. Table
ment, and how can they be detected and eliminated rapidly 1.2 shows a partial list of the chemical contaminants that are
and economically to allow both protection of human health routinely found in soil and groundwater. The cost of cleanup
and rapid consumption of fresh produce? Determining the or remediation of the contaminated sites in the United States
presence and significance of pathogenic organisms in food, alone would require more than $1 trillion. Given this price
water, and air supplies is a challenge that will keep environ- tag, it is increasingly recognized that biological cleanup
mental microbiologists occupied in the coming decades. alternatives, known as bioremediation, may have profound
As concern about chemicals in the environment emerged economic advantages over traditional physical and chemical
in the 1960s, perhaps best highlighted by Rachel Carson’s remediation techniques.
landmark book Silent Spring, it became clear that this was Once thought unpredictable and ineffective, bioremedia-
a natural extension for the field of environmental microbi- tion is now a viable and preferred alternative for cleanup of
ology. We now know that chemical pollutants in soil and many sites. The efficacy of bioremediation was clearly illus-
groundwater have profound effects on human health and trated in 1989 when the Exxon Valdez spilled almost 11 million
welfare, in terms of both potential disease that the intake gallons of North Slope crude oil into Prince William
of these chemicals can cause, and the economic impact of Sound — the largest tanker spill in U.S. history. A com-
cleaning up contaminated environments. Health effects bination of physical removal of free product, physical
from chemical contaminants have been difficult to assess washing of the contaminated shoreline, and bioremedia-
because the impact is not acute as for pathogens but rather tion has been used to slowly restore Prince William Sound.
6 PART | I Review of Basic Microbiological Concepts
This was the first large-scale documentation of success- and surface waters that serve as our potable water resources.
ful use of bioremediation to clean up a contaminated site. In addition, our ability to detect chemicals has gotten bet-
Bioremediation is most successful when it takes advantage ter and more comprehensive. For these reasons we have
of naturally occurring microorganisms in the contaminated discovered contamination in previously “clean” sources of
area. This realization has engendered a modern apprecia- water. Further, as society grows, we put increasing stress
tion of the role of microorganisms in elemental cycling and on water resources. In many parts of the United States, for
environmental sustainability as well as the use of microor- example, groundwater is currently being used at a faster
ganisms for resource production and recovery. rate than it is being recharged. Add to this increasing waste
discharges containing biological and chemical contamina-
tion that enter our water resources, and it becomes clear
1.3 MODERN ENVIRONMENTAL that environmental microbiologists face large challenges
MICROBIOLOGY in this arena. These issues also arise in contaminated soil
environments. As the global population increases, land
In modern environmental microbiology, pathogens and resources are becoming more valuable and communities
bioremediation remain fundamental to the field, but in are encroaching on contaminated sites, including landfills,
both cases these subject areas have been greatly enhanced mine tailings sites, and agricultural fields with years of pes-
through the application of molecular genetics and biotech- ticide applications. New strategies are needed in this area to
nology tools. For example, development and assessment of treat sites that contain emerging contaminants, contaminant
new methods of detection and elimination of pathogens in mixtures, and low levels of contaminants. Applications
our water and food supply, as well as the indoor environ- of risk assessment to target the need for control where it
ment we live in today, have become critical to public health is most effective, and for community education to reduce
with the global growth in population. Arguably, human and risks associated with living next to contaminated sites, are
environmental hygiene efforts have had the greatest impact also becoming more important.
on reducing human suffering throughout the past century. A third important area of environmental microbiol-
This is also true today as we see the evolution of new ogy has emerged over the past decade, that of molecular
and more virulent forms of environmentally transmitted ecology. Molecular ecology as it relates to environmental
pathogens. This has been highlighted by concerns about microbiology can be defined as investigating diversity in
the spread of SARS and the potential for the rapid spread the environment, and mining and exploiting that diversity
of avian bird flu. Vaccine development is often not rapid for new natural products and activities. Molecular-based
enough to guarantee protection and so the environmental methodologies are now enabling us to detect, define, and
microbiologist must be prepared to develop better methods better understand the ecology not only of natural habitats
to reduce or stop the spread of these agents throughout the such as soil and water, but also of anthropologic environ-
environment. Continuing outbreaks of norovirus diarrhea ments such as households, fomites, or municipal wastes.
on cruise ships has demonstrated how difficult an environ- Powerful molecular-based tools are becoming available to
mentally spread agent can be to control. New strategies allow the examination of microbial communities through
are needed, such as the development of self-disinfecting analysis of microbial DNA and RNA (PCR, gene probes,
surfaces, environmentally friendly disinfectants, more DNA sequencing, metagenomics) as well as proteins
rapid methods of detecting indicators and pathogens in our (proteomics). Such techniques now allow us to search for
environment. In addition, application of risk assessment to new microbes in extreme environments such as hot springs,
target the need for control where it is most effective and caves, deep-sea thermal vents, and deep subsurface envi-
better products for the consumer are reducing the risk asso- ronments. Molecular sequence analysis of community DNA
ciated with environmentally transmitted infections. permits a new appreciation of microbial diversity, and also
The beginning of this century brought a new task for of how microbial communities function and communicate
environmental microbiologists in the area of pathogen via quorum sensing. This new evaluation of the microbial
detection. The impact of just a few letters contaminated environment is also affording innovative approaches to the
with anthrax spores demonstrated how rapidly a terror- discovery of high value “green” products that can be used
ist could disseminate a highly virulent pathogen across an in medicine, agriculture, and industry. Examples include
entire region of a nation. It also demonstrated how little we new antibiotics and other natural products, plant-growth-
know about the transport, survival, and methods of decon- promoting bacteria to enhance growth of crops, and new
tamination of lethal agents that could be used by bioterror- chemicals that can be used as detergents, solvents, surfac-
ists. National security now depends on the development of tants, pesticides, and in food processing.
methods for detection of select agents in the environment Holistically, these three fundamental areas of environ-
and models to assess their fate and control. mental microbiology enable us to pursue the goal of environ-
New challenges have similarly emerged in the area of mental sustainability, which we define as “the utilization of
bioremediation. New chemicals have been detected in ground environmental resources for the benefit of human health and
Chapter | 1 Introduction to Environmental Microbiology 7
welfare without deterioration of the physical environment or in which they are situated, the methodologies used to moni-
the biological communities contained therein.” Critical com- tor microorganisms and their activities, and finally the pos-
ponents of these biological communities are the microbial sible effects of microorganisms on human activities. We
communities housed within the environment. Clearly then, have more fully defined and increased the number of sec-
the challenge for modern environmental microbiologists is tions in the second edition to eight: (1) a review of basic
to enhance our understanding of these communities in order microbiological concepts; (2) a description of the various
to achieve environmental sustainability. microbial environments encountered in the field including
soil, water, and the atmosphere; (3) a discussion of method-
ologies available for detection, enumeration, and identifica-
1.4 PURPOSE AND ORGANIZATION tion of microbes and their activities; (4) an examination of
OF THIS TEXT microbial communication, activities, and interactions with
their environment and how these activities affect the cycling
Our purpose in writing this book is to provide a text that of nutrients; (5) a discussion of how microorganisms can
can be used in teaching environmental microbiology as well be exploited for remediation of both organic and metal
as a general reference book for practitioners in the field of contaminants; (6) a description of important waterborne
environmental microbiology. This textbook is designed for and foodborne pathogens as well as indicator organisms;
senior-level undergraduate and graduate classes in environ- (7) an examination of the wastewater treatment and
mental microbiology. It is expected that students using this disinfection processes used to treat our largest (in terms of
text have a background in general microbiology and organic volume) societal waste problem; and (8) a consideration of
chemistry. The overall objective of the text is to define the urban microbiology or the study of how microorganisms
important microorganisms involved in environmental micro- can impact an increasingly populated world.
biology, the nature of the different possible environments