Introduction

What is microbiology?
Study of diverse group of organisms that exist as either single cells or clusters of cells. Also include viruses, which are microscopic but not cellular - they do not carry out energy transformations for example.

What is microbiology all about?
Living cells and how they work.
Free-living microorganisms including bacteria
Microbial diversity and evolution
What microorganisms do in the world at large including our bodies and animals and plants. Central to basic biological sciences - helps in understanding the biology of higher organisms.

Why study microbiology?
Basic science
Simple model systems to study general processes common to all living organisms.
Two advantages of microorganisms:
1. They are small. As small organisms, large volumes of high densities of microbes can be obtained for studying.
2. They have short generation time compares to most higher organisms. E. coli can double every 20 minutes under specific conditions.
Examples include the discovery that DNA is the genetic material of organisms. Fred Griffith and subsequent studies of Avery, MacLeod and McCarty.
One gene - one polypeptide concept of Beadle and Tatum.
In the Department of Microbiology and Molecular Genetics there are several Pis using microorganisms to study properties of higher organisms.
Dr. R. Burnap uses a bluegreen bacteria to study photosystems analogous to higher plant photosystems.
Dr. J. Hadwiger uses slime mold to study signal transduction and gene regulation analogous to higher organisms signal transduction pathways.

Applied science
Microbes are important in the areas of:
medicine - Important diseases are caused by microbes.
agriculture - Microbes play a very important role in soil fertility and animal production.
industry - Microbes carry out many important industrial processes such as wine, beer, yogurt, cheese, sauerkraut production. They make enzymes and hormones. They produce solvents (e.g., butanol and acetone) from organic wastes.
Industry has taken advantage of a number of features of microbes and capitalized on them in the area of biotechnology.

Historical aspects
It had long been suspected that there were organisms too small to see with the eye. Their discovery and subsequent advances in the field of microbiology has been linked to the invention and development of the microscope.
In 1676, Antoni van Leeuwenhoek was the first person to see microbes in detail using primitive microscopes he built. Published his observations in the Royal Society of London proceedings.
For almost 200 years nothing much happened in the field of microbiology per se. There were numerous significant findings about microbial mediated processes in natural environments. Advances in microbiology were slow because there were few changes in the microscope.

In the latter part of the 19th century there were two pressing questions that were foremost in microbiology.
1. Does spontaneous generation occur?
2. What is the nature of contagious disease?

Pasteur and spontaneous generation
Observations: meat left out putrefied. Bacteria could be seen on the putrefied meat. Where did they come from? Some believed that they arose spontaneously from the meat. Others believed that they were deposited from the air - airborne bacteria.
Pasteur was able to show that there were infact microorganisms in the air. Using the scientific method of observations, hypothesis, experiments, and conclusions, Pasteur was able to put the question about spontaneous generation to rest. How?
Observations - Pasteur showed that there were microorganisms in the air that were indistinguishable from those on the putrefied meat.
Hypothesis - Pasteur hypothesized that cells were constantly being deposited on the meat.
Experiments - cooked meat and found it did not putrefy. Cooking was known to kill microorganisms.
Conclusion - Pasteur's hypothesis was shown to be valid.

In another experiment to test his hypothesis and disprove the theory of spontaneous generation, Pasteur set up experiments using Swan-necked flasks.
Pasteur heated a non-sterile solution of nutrient broth in a flask with a swan neck.
Tip the flask and there would be growth in the medium.
All of this led to the areas of sterilization and pasteurization procedures that are very important in food processing. What about spores produced by some bacteria? These are extremely heat resistant. John Tyndall and Ferdinand Cohn found that some samples could not be sterilized by simply boiling for 5 minutes. Cohn discovered the endospores of bacilli by microscopic observations.

Germ theory of disease and Robert Koch.
By the mid 1800's the concept of contagion - a transferable agent that caused disease - was well accepted. The contagion could spread throughout a population in a contagious fashion.
Many assumed that microorganisms were the contagion responsible for many contagious diseases. Early work of Joseph Lister supported this idea, but there was no solid proof.
Robert Koch was studying anthrax - a disease of cattle and sometimes humans. Diseased animals had blood teaming with bacilli. Did the bacilli cause anthrax or where the bacilli the result of anthrax?
Koch begin using mice to study anthrax.
Diseased mice always had blood teaming with bacilli.
Blood from diseased mice injected into healthy mice caused disease.
Cultured organisms from the blood of diseased mice could cause disease in healthy mice.

Koch's postulates
1. Microbe should be present in diseased animal only, not in healthy animals.
2. Microbe must be cultured away from the animal.
3. Pure culture inoculated into an animal model should cause disease in otherwise healthy animals.
4. Microbe should be reisolated from diseased animal and should be the same microbe as inoculated into the animal.
These postulates are still used today in animal and plant disease studies.

Koch and pure culture studies
Koch was the first to grow bacteria on a solid surface. First employed potato slices, then gelatin. Gelatin's main fault was that it was not solid at 35 oC. Walter Hesse's wife suggested agar and Hesse wrote Koch to suggest agar. Today we still use agar to solidify medium.
Richard Petri suggested a double dish system to contain the agar and allow the bacteria to be exposed to the air. Today we still use the Petri dish.

Pure cultures of bacteria
We will practice this in the laboratory as well since it is a very important skill of microbiologists.
Pure cultures are cultures of only one kind of microbe.
Requires proper medium to grow on.
Free of other contaminating bacteria.
Requires aseptic techniques to maintain purity.

The Cell
1664 Robert Hooke observed small, well organized units in cork material. These became known as cells which are the fundamental unit of life - analogous to the atom in chemistry.

What are the hallmarks of a cell?
Self feeding or nutrition
Take up nutrients from the environment, transform them in the cell to extract energy and intermediate molecules of biosynthesis, and eliminate waste products.
Self replicating or growth
Cells direct their own synthesis. As a result the cell divides and produces two nearly identical cells.
Differentiation
Cells can undergo changes in form and function as part of the cell life cycle. Specialized structures involved with sexual reproduction, dispersal or survival when confronted with unfavorable conditions.
Examples: Vegetative bacillus form spores during times of unfavorable conditions.
Non-spore formers go into a starvation mode of survival when carbon becomes limiting. A whole array of genes specific to this mode of cell physiology is induced in response to carbon starvation.
Chemical signaling
Microbes respond to chemical and physical environmental stimuli.
Examples - chemotaxis is a response by the cell to a chemical. Chemical may either be an attractant in which case the cell if motile may move towards the chemical or a repellent in which case the cell moves away.
Quorum sensing - signal molecules that are indicators of cell density, e.g., N-acyl-homoserine lactone, are used to measure cell density before carrying out some function.
Conjugation in Enterococcus faecalis
Light production in Vibrio fisheri
Clumping of Rhodobacter sphaeroides
Evolution
Change and adapt genetically to their environment in an inheritable fashion. Mutations ad natural selection operate to select microbes most suited for life in a particular environment.
Cells and thermodynamics. Cells work against the laws of thermodynamics which states that the universe is becoming more random = increase in entropy (S). Cells are fro from random but are highly ordered. How? Cells are open systems that take energy in and use this to reduce entropy or maintain order in the cell. Analysis of the chemical make up of a cell is highly indicative of the nonrandom nature of cells. The macronutrients C, H, O, N, S, and P are at concentrations greater than what is found in the environment. Cells have to accumulate them against a concentration gradient of sorts.
Cells carry out two main functions
Machine-like function
carry out chemical transformation where molecules are degraded (= catabolism) and new molecules are synthesized (= anabolism) in what is called metabolism. Enzymes, composed of amino acids, carry out these reactions.
Coding function
DNA, composed of nucleotides, stores genetic information for the cell. Each enzyme is coded for by a gene in the DNA. DNA is replicated before cell division. DNA is also transcribed into RNA (mRNA, rRNA, and tRNA) and mRNA is translated into a polypeptide.
General structure of prokaryotic cells vs. eukaryotic cells
All cells have a cytoplasmic membrane - a barrier between the inside and outside of the cell. Plants and bacteria have a cell wall but animal cells do not. All cells have cytoplasm - a mixture of substances ad structures bathed in the cytosol.
Differences between prokaryotic and eukaryotic cell:
Eukaryotic cells have a membrane bound nucleus, organelles, and are larger. Includes plants, animals, algae, fungi, ad protozoa which are microscopic.
Prokaryotic (before nucleus) cells have a nucleoid, a region where the DNA is found in the cell, few to no organelles and are small.
Evolutionary relationships among microbes
Three separate lineages gave rise to the domains - eukarya, prokarya and archaea. All three evolved from a universal ancestor. Bacteria and Archaea never evolved past the microbial state whereas eukarya evolved into multicellular organisms. Within each domain there is enormous diversity.
Among Bacteria there are heterotrophs and phototrophs. Some grow in oxic and other in anoxic environments.
Most Archaea are anaerobes and many thrive in very unusual growth conditions - extreme environments. These organisms stretch the limits of inhabitable environments. Environments including boiling water, salty water, highly acidic or alkaline soils. Many Archaea have unusual metabolic properties like methane production in energy metabolism.
Eukarya include fungi, protozoa and microscopic algae as well as higher plants and animals.