Introduction and historical perspective of

environmental microbiology
 INTRODUCTION
• Microbiology often has been defined as the study of
organisms and agents too small to be seen clearly by the
unaided eye—that is, the study of microorganisms.
• Because objects less than about one millimeter in diameter
cannot be seen clearly and must be examined with a
microscope, microbiology is concerned primarily with
organisms and agents that are small and smaller.
• However, some microorganisms, particularly some eukaryotic
microbes, are visible without microscopes. For example,
– bread molds
– Thiomargarita namibiensis (bacterium)
– filamentous algae are studied by microbiologists, yet are visible to
the naked eye
• The difficulty in setting the boundaries of microbiology has
led to the suggestion of other criteria for defining the field.
– For instance, an important characteristic of microorganisms,
even those that are large and multicellular, is that they are
relatively simple in their construction,
– lacking highly differentiated cells and distinct tissues.
• Another suggestion, made by Roger Stanier, is that the
field also be defined in terms of its techniques.
– Microbiologists usually first isolate a specific microorganism
from a population and then culture it.
• Thus microbiology employs techniques—such as
– sterilization and
– the use of culture media—that are necessary for successful
isolation and growth of microorganisms.
 A BRIEF HISTORY OF MICROBIOLOGY

• Microbiology has a long, rich history, initially

centered in knowing the cause of infectious
diseases but now including practical
applications of the science.
• Many individuals have made significant
contributions to the development of
microbiology
 Early history of microbiology
• Historians are unsure who made the first
observations of microorganisms, but the
microscope was available during the mid‐
1600s, and an English scientist named Robert
Hooke made key observations.
• He is reputed to have observed strands of
fungi among the specimens of cells he viewed.
• In the 1670s and the decades thereafter, a Dutch
merchant named Anton van Leeuwenhoek made
careful observations of microscopic organisms,
which he called animalcules (Latin = tiny animal). 
• Until his death in 1723, van Leeuwenhoek
revealed the microscopic world to scientists of
the day and is regarded as one of the first to
provide accurate descriptions of protozoa, fungi,
and bacteria.
Drawing of animalcules
• After van Leeuwenhoek died, the study of microbiology
did not develop rapidly because microscopes were rare
and the interest in microorganisms was not high.
• In those years, scientists debated the theory
of spontaneous generation, which stated that
microorganisms arise from lifeless matter such as beef
broth.
• An English cleric named John Needham advanced
spontaneous generation, but Lazzaro Spallanzani disputed
the theory by showing that boiled broth would not give
rise to microscopic forms of life.
Louis Pasteur and the germ theory
• Louis Pasteur worked in the middle and late 1800s. He
performed numerous experiments to discover why
wine and dairy products became sour, and he found
that bacteria were to blame.
• He is known for developing the technique of
Pasteurization
• Pasteur called attention to the importance of
microorganisms in everyday life and stirred scientists
to think that if bacteria could make the wine “sick,”
then perhaps they could cause human illness.
• Pasteur had to disprove theory of spontaneous generation
to sustain his theory, and he therefore devised a series
of swan‐necked flasks filled with broth.
• He left the flasks of broth open to the air, but the flasks had
a curve in the neck so that microorganisms would fall into
the neck, not the broth.
• The flasks did not become contaminated (as he predicted
they would not), and Pasteur's experiments put to rest the
notion of spontaneous generation. His work also
encouraged the belief that microorganisms were in the air
and could cause disease.
• Pasteur postulated the germ theory of disease, which states
that microorganisms are the cause of infectious diseases.
• Pasteur's attempts to prove the germ theory were
unsuccessful.
• However, the German scientist Robert Koch provided the
proof by cultivating anthrax bacteria apart from any other
type of organism.
• He then injected pure cultures of the bacilli into mice and
showed that the bacilli invariably caused anthrax. The
procedures used by Koch came to be known as Koch's
postulates.
• They provided a set of principles whereby other
microorganisms could be related to other diseases.
SOME OF THE
MAJOR AND MINOR
CONTRIBUTIONS IN
THE FIELD OF
MICROBIOLOGY
 The development of microbiology
• In the late 1800s and for the first decade of the
1900s, scientists seized the opportunity to further
develop the germ theory of disease as enunciated by
Pasteur and proved by Koch.
• There emerged a Golden Age of Microbiology during
which many agents of different infectious diseases
were identified.
• Many of the infectious agents of microbial disease
were discovered during that period, leading to the
ability to halt epidemics by interrupting the spread of
microorganisms
• Despite the advances in microbiology, it was
rarely possible to provide life‐saving therapy
to an infected patient.
• Then, after World War II, the antibiotics were
introduced to medicine.
• The incidence of pneumonia, tuberculosis,
meningitis, syphilis, and many other diseases
declined with the use of antibiotics.
• Work with viruses could not be effectively performed until
instruments were developed to help scientists see these
disease agents.
• In the 1940s, the electron microscope was developed and
perfected.
• In that decade, cultivation methods for viruses were also
introduced, and the knowledge of viruses developed
rapidly.
• With the development of vaccines in the 1950s and 1960s,
such viral diseases as polio, measles, mumps, and rubella
came under control.
 Modern microbiology
• Modern microbiology reaches into many fields of human
endeavor, including the development of pharmaceutical
products, the use of quality‐control methods in food and
dairy product production, the control of disease‐causing
microorganisms in consumable waters, and the industrial
applications of microorganisms.
• Microorganisms are used to produce vitamins, amino
acids, enzymes, and growth supplements.
• They manufacture many foods, including fermented dairy
products (sour cream, yogurt, and buttermilk), as well as
other fermented foods such as pickles, breads, and
alcoholic beverages.
• One of the major areas of applied microbiology
is biotechnology. 
• In this discipline, microorganisms are used as living
factories to produce pharmaceuticals that otherwise
could not be manufactured.
• These substances include the human hormone insulin,
the antiviral substance interferon, numerous blood‐
clotting factors and clot dissolving enzymes, and a
number of vaccines.
• Bacteria can be reengineered to increase plant resistance
to insects and frost, and biotechnology will represent a
major application of microorganisms in the next century
Brief overview of environmental
microbiology
HISTORY OF ENVIRONMENTAL MICROBIOLOGY
• The initial scientific focus of the field of environmental
microbiology was on water quality and the fate of
pathogens in the environment in the context of
protection of public health.
• The roots for water quality go back to the turn of the
twentieth century, when the treatment of water supplies
by filtration and disinfection resulted in a dramatic
decrease in the incidence of typhoid fever and cholera.
• Application of these processes throughout the developed
world has essentially eliminated waterborne bacterial
diseases except when treatment failures occur.
 Contaminants of water

• Until the 1960s, it was thought that threats from waterborne diseases
had been eliminated.
• However, case studies began to accumulate suggesting that other
agents, such as viruses and protozoa, were more resistant to
disinfection than enteric bacteria.
• This concern became a reality with the discovery of waterborne
outbreaks caused by the protozoan parasite Giardia and by Norovirus ,
both of which were found in disinfected drinking water.
• Water quality continues to be a major focus in environmental
microbiology because new waterborne pathogens continue to emerge
• One of the best documented and largest outbreaks occurred in 1993
when more than 400,000 people became ill and over 100 died in
Milwaukee, Wisconsin, during a waterborne outbreak caused by the
protozoan parasite Cryptosporidium .
 Food contaminants
• Pathogens in our food supply is a second area of immense
concern. One of the difficult questions facing the food industry is
that of importation of vegetables and fruits.
• On the one hand, there is consumer demand for a wide variety of
high quality imported produce; on the other hand, there is an
increased danger of importing pathogens along with the produce.
• One example is the protozoan pathogen Cyclospora. This organism
gained notoriety as the causative agent of a disease outbreak
affecting approximately 1000 people in the United States between
early May and mid- July 1996.
• The Cyclospora outbreak was due to consumption of raspberries
imported from Guatemala.
 Chemical contaminants
• As concern about chemicals in the environment
emerged in the 1960s, perhaps best highlighted by
Rachel Carson’s landmark book Silent Spring , it became
clear that this was a natural extension for the field of
environmental microbiology.
• We now know that chemical pollutants in soil and
groundwater have profound effects on human health
and welfare, in terms of both potential disease that the
intake of these chemicals can cause, and the economic
impact of cleaning up contaminated environments.
• Health effects from chemical contaminants have been
difficult to assess because the impact is not acute as for
pathogens but rather cumulative, resulting in cancer
many years following exposure or, more immediately,
resulting in birth defects
• The cost of cleanup or remediation of the contaminated
sites in the United States alone would require more than
$1 trillion.
• Given this price tag, it is increasingly recognized that
biological cleanup alternatives, known as
bioremediation, may have profound economic
advantages over traditional physical and chemical
remediation techniques.
 Bioremediation as an option
• Once thought unpredictable and ineffective, bioremediation is now a
viable and preferred alternative for cleanup of many sites.
• The efficacy of bioremediation was clearly illustrated in 1989 when the
Exxon Valdez spilled almost 11 million gallons of North Slope crude oil
into Prince William Sound — the largest tanker spill in U.S. history.
• A combination of physical removal of free product, physical washing of
the contaminated shoreline, and bioremediation has been used to slowly
restore Prince William Sound.
• This was the first large-scale documentation of successful use of
bioremediation to clean up a contaminated site.
• Bioremediation is most successful when it takes advantage of naturally
occurring microorganisms in the contaminated area.
• This realization has engendered a modern appreciation of the role of
microorganisms in elemental cycling and environmental sustainability as
well as the use of microorganisms for resource production and recovery
MODERN ENVIRONMENTAL MICROBIOLOGY
• In modern environmental microbiology, pathogens and bioremediation
remain fundamental to the field, but in both cases these subject areas have
been greatly enhanced through the application of molecular genetics and
biotechnology tools.
• For example, development and assessment of new methods of detection
and elimination of pathogens in our water and food supply, as well as the
indoor environment we live in today, have become critical to public health
with the global growth in population.
• Arguably, human and environmental hygiene efforts have had the greatest
impact on reducing human suffering throughout the past century.
• This is also true today as we see the evolution of new and more virulent
forms of environmentally transmitted pathogens.
• This has been highlighted by concerns about the spread of SARS and the
potential for the rapid spread of avian bird flu.
• Vaccine development is often not rapid enough to guarantee protection
and so the environmental microbiologist must be prepared to develop
better methods to reduce or stop the spread of these agents
throughout the environment (recent example of COVID-19 outbreak).
• Continuing outbreaks of norovirus diarrhea on cruise ships has
demonstrated how difficult an environmentally spread agent can be to
control.
• New strategies are needed, such as the development of self-disinfecting
surfaces, environmentally friendly disinfectants, more rapid methods of
detecting indicators and pathogens in our environment.
• In addition, application of risk assessment to target the need for control
where it is most effective and better products for the consumer are
reducing the risk associated with environmentally transmitted
infections
• The beginning of this century brought a new task for
environmental microbiologists in the area of pathogen detection.
• The impact of just a few letters contaminated with anthrax spores
demonstrated how rapidly a terrorist could disseminate a highly
virulent pathogen across an entire region of a nation.
• It also demonstrated how little we know about the transport,
survival, and methods of decontamination of lethal agents that
could be used by bioterrorists.
• National security now depends on the development of methods
for detection of select agents in the environment and models to
assess their fate and control.
• New challenges have similarly emerged in the area of
bioremediation.
• New chemicals have been detected in ground and
surface waters that serve as our potable water
resources.
• In addition, our ability to detect chemicals has gotten
better and more comprehensive.
• For these reasons we have discovered contamination in
previously “ clean ” sources of water. Further, as society
grows, we put increasing stress on water resources.
• As the global population increases, land resources are
becoming more valuable and communities are encroaching
on contaminated sites, including landfills, mine tailings sites,
and agricultural fields with years of pesticide applications.
• New strategies are needed in this area to treat sites that
contain emerging contaminants, contaminant mixtures, and
low levels of contaminants.
• Applications of risk assessment to target the need for
control where it is most effective, and for community
education to reduce risks associated with living next to
contaminated sites, are also becoming more important.