Chapter 2 Introduction to Microbiology

Microbes are the most populous groups of organisms on the planet. Not only have they evolved to occupy almost every habitat on Earth, but they appeared about 3.5 billion years ago.

Nevertheless, microorganisms are important because they play a major role to proper functioning of the biosphere - microorganisms are responsible for recycling essential elements. Furthermore, microorganisms are the basis of the food web - some microorganisms are photosynthetic and are a source of nutrients. Microbes also contain 50% of all biological carbon and 90% of all biological nitrogen on Earth.

While it is important to realize that microbes have a huge benefit to society (e.g., food production, antibiotics and vitamins, wastewater cleaning, cleaning oil spills), they can also cause disease in insects, plants, and animals (e.g., Botulism)!

2.1 The Three Domains of Life

There are currently three domains of life based on rRNA (i.e., ribosomal RNA) sequences.

1. Bacteria
2. Archaea
3. Eukarya

2.1.1 Bacteria

These are unicellular organisms that have peptidoglycan in their cell walls.

These organisms also lack membrane-bound organelles; some bacterial species also live in extreme environments, and some even produce oxygen through photosynthesis.

2.1.2 Archaea

These species have unique rRNA sequences that differ from bacteria.

However, peptidoglycan is missing from the cell wall of these organisms - some archaeans have unusual metabolic characteristics (e.g., methanogens), and some archaeans also live in extreme environments.

2.1.3 More Infectious Agents

Viruses are the smallest of all microbes and requires a host cell to replicate. Viruses also cause a range of disease and even cancers!

Viroids are infectious, encapsualted RNA that only infect plants.

Prions, on the other hand, are misfolded, infectious proteins that cause disease (e.g., Kuru, variant CJD, etc).

2.2 Traits of Living Organisms

All living organisms have the following traits:

1. Cell membrane and organization
2. Metabolism
3. Reproduction
4. Sensing the outside environment
5. Homeostasis
6. Excretion and evolution
7. Nutrition
8. Growth

Mnemonic: C MR. SHENG

2.3 Key Discoveries in Microbiology

Some discoveries include the discovery of micro-organisms, the discovery of disease-causing microbes, and the discovery of chemoautotrophy and elemental cycling by microorganisms.

2.3.1 Spontaneous Generation

Lucretius (384 - 355 BC) first claimed that diseases were caused by “invisible living creatures.”

Aristotle then coined the idea of “spontaneous generation” (i.e., life comes from non-living matter): an idea that prevailed for 2000 years before finally being debunked.

In the 17^th century, Francesco Redi discredited spontaneous generation: he showed that maggots on decaying meat came from fly eggs in this simple experiment setup:

Figure 2.1: Francesco Redi’s Meat Jar Experiment

As seen above, meat that has cheesecloths placed over them did not develop maggots.

Several experiments also discredited the idea of “spontaneous generation.” John Needham showed that boiled borth placed and sealed still became turbid; Lazzaro Spallanzani, on the contrary, boiled broths that had already been previously sealed - the broths did not become turbid. Hence, this suggested that air was required for microbes to grow.

2.3.1.1 Louis Pasteur

Pasteur was the first scientist to connect cause (i.e., microorganisms) to effect (i.e., disease, growth, and metabolic products).

He was responsible for the following advancements:

1. Discovering fermentation by microorganisms, thereby helping the French wine industry.
2. Developing psateurization to avoid wine / milk spoilage by microbes.
3. Determining that a silkworm disease was caused by a protozoan.
4. Disproving spontaneous generation.

In his famous Swan-neck flask experiment, he:

1. Placed nutrient solutions in flasks.
2. Boiled the solution.
3. Left both flasks exposed to air.

Figure 2.2: Louis Pasteur’s Swan-Neck Experiment

No microbial growth was observed in the broth - this suggested that microbes comes from the outside (i.e., they weren’t “created”).

2.4 John Tyndall

He is a scientist who proposed that “dust carries ‘germs’.” Hence, if dust was absent, then the nutrient broth would remain clear even if exposed to air.

Tyndallization is the process of successive heating and cooling to kill heat-resistant spores.

For this reason, Tyndall was also credited with proving the existence of heat-resistant microorganisms.

2.5 Microorganisms and Disease

Needless to say, the role of microorganisms were not immediately obvious. Rather, infectious diseases were believe to be caused by the imbalance of the body’s four humors.

Unsurprisingly, the tools needed to link bacteria, viruses, or fungi to disease were absent.

2.5.1 Evidence for relationship between microbes and disease

Agostini Bassi proved that a silkworm disease was caused by a fungus.

Miles J. Berkeley showed that the great potato blight of Ireland was caused by a water mold.

Heinrich de Bary suggested that cereal crop diseases are caused by smut and rust fungi.

2.5.2 Joseph Lister

He had indirect evident that microorganisms cause disease.

He also suggested treating instruments and surgical dresses with carbolic acid (a phenol), hence reducing the amount of post-operative infections.

However, the link between phenolic-treatment and the killing of microorganisms was not understood.

2.5.3 Robert Koch and his postulates

This last scientist established a relationship between Bacillus anthracis and anthrax using criteria that had been developed by his teacher.

This “criteria” became known as Koch’s postulates. His postulates demonstrate that a bacteria is pathogenic via the following criteria:

1. The disease-causing organism must always be present in animals with the illness, but not in healthy animals.
2. The organism must be cultivated in a pure culture away from the animal’s body.
3. The isolated organism must then cause disease when innoculated into a healthy animal.
4. Another culture must then be obtained from the newly-infected animal; the culture should also be the same as the original culture.

Yet, it is important to note that there are limitations to Koch’s postulates. Not only must a pure culture be used, but pathogens that required complex nutrients from their host cell will not grow. Furthermore, the postulates do not account for slow-growing organisms and assume that the microorganism will grow on the provided media.

2.6 Bacteria in Earth Systems

As mentioned at the beginning of the chapter, bacteria were the first life forms and consequently, the foundation of Biology.

It is also important to be aware that the vast majority of microorganisms do not cause disease; for the first two billion years of Earth’s history, only anaerobic metabolism was present.

Earth’s current atmosphere (aerobic) was made possible due to microbes.

2.6.1 Sergei Winogradsky

Winogradsky was a microbiologist, ecologist, and soil scientist who discovered carbon fixation in bacteria; he found that bacteria played a major role in large biogeochemical cycles (using the nitrogen cycle as an example):

Figure 2.3: The Nitrogen Cycle

2.7 Recent Developments in Microbiology: Molecular and Genomic Methods

Some major, recent discoveries include:

1. Restriction endonucleases
2. Synthesis of recombinant molecules
3. DNA sequencing methods
4. Bioinformatics and large-scale genomic sequencing