Chapter 10 Classification of Microorganisms

Microbiology is the study of microorganisms /

microbes which is visible only with a microscope.

The diverse group of organisms includes algae, archae, bacteria,

cyanobacteria, fungi, protozoa, viruses.

Most of the microorganisms are harmless.

99% are good. Eg: Cynobacteria (blue green algae)

1% are bad. Eg: Pathogens

MICROBIOLOGY

Discovery Era Transition Era Golden Era Modern Era

ANTONY VON LEEUWENHOEK

(1632-1723)

First person - Invented microscope and discovered the microbial world.

Draper (cloth merchant), Holland.

Hobby - grind lenses and make microscopes.

Leeuwenhoek microscopes could magnify objects about 200-300 times

Leeuwenhoek observed a variety of things including rain water, pond water, blood and scrapings from his own teeth using his own microscope

He saw minute moving objects which he called ―little animalcules‖.

He made accurate sketches and communicated his findings to ―Royal society of London‖.

Origin of Life Controversy

• Where did microbes come from? Many believed they arose from simple materials by process of spontaneous generation. This notion had been posited by Aristotle (382-322 B.C.) and other Greek philosophers to explain decay and appearance of animals such as flies and frogs, and was widely held as common sense even in 1700's and 1800's.

Spontaneous Generation theory From earliest times, people had believed in spontaneous generation—that living organisms could develop from nonliving matter. Even the great Aristotle (384–322 B.C.) thought some of the simpler invertebrates could arise by spontaneous generation. This view finally was challenged by the Italian physician Francesco Redi (1626–1697),

• Francisco Redi (1626-1697) demonstrated that flies did not arise spontaneously from rotting meat by simple experiment. If jar of meat was covered by fine muslin, maggots did not arise.

However, the simpler life forms discovered by Leeuwenhoek lacked visible complexity, and most people still believed these could arise spontaneously.

Francesco Redi

John Needham (1731-1781),

a Scottish clergyman and naturalist, showed that microbes

grew in soups exposed to air. Claimed existence of a "life

force" present in inorganic matter that could cause

spontaneous generation. One of his more convincing

demonstrations was to boil some soup (briefly), pour into

clean flasks with cork lids, and show that microbes would

soon arise.

Lazzaro Spallanzani (1729-1799) - Italian priest claimed Needham's organisms came from heat-resistant microbes. If flasks were boiled long enough (1-2 h), nothing grew. But Needham countered that prolonged heating destroyed the "life force". Spallanzani said that every form of life takes its origin from their parents, germ cells or seeds. This theory of biogenesis was later proved and supported by Louis Pasteur.

Theodore Schwann (1810–1882) allowed air to enter a flask containing a sterile nutrient solution after the air had passed through a red-hot tube. The flask remained sterile.

Subsequently Georg Friedrich Schroder and Theodor von

Dusch allowed air to enter a flask of heat-sterilized medium after it

had passed through sterile cotton wool.

No growth occurred in the medium even though the air had not

been heated.

Despite these experiments the French naturalist Felix Pouchet

claimed in 1859 to have carried out experiments conclusively

proving that microbial growth could occur without air

contamination.

Louis Pasteur (1822-1895) He developed several experiments that finally deflated claims for spontaneous generation. Pasteur filtered air through cotton to trap airborne materials, then dissolved the cotton and examined the particulate matter under a microscope; many bacteria and spores of other life forms such as molds were present. Since most skeptics kept arguing that overheating killed the life force present in air, Pasteur developed and ingenious experiment using a swan neck flask that allowed fresh air to remain in contact with boiled materials. The long passageway prevented airborne microbes from reaching the nutrient liquid, without impeding access to air. One of Pasteur's flasks is still sterile after 100+ years of being exposed to the air (Pasteur Institute, Paris).

Contributions of Louis Pasteur • Disproved the SG theory • Discovered that fermenting fruit to alcohol by microbes • He selected a particular strain (Yeast) for high quality wine. • He developed a method to remove the undesired microbes from juice without affecting its quality. Heating the juice at 62.8°C for half-an hour did the job. This technique is called as Pasteurization, which is commonly used in the field of milk industry. • He discovered that parasites (protozoa) causing pebrine disease of silk worm. • He isolated the anthrax causing bacilli from the bloods of cattle, sheep and human being. • He also demonstrated the virulence (ability of microbe to cause disease) of bacteria • He developed vaccine (a killed or attenuated microbe to induce the immunity) against rabbis from the brains and spinal cord of rabbit

The English physicist John Tyndall (1820–1893) dealt a final blow to spontaneous generation in 1877 by demonstrating that dust did indeed carry germs and that if dust was absent, broth remained sterile even if directly exposed to air. During the course of his studies, Tyndall provided evidence for the existence of exceptionally heat-resistant forms of bacteria. He also developed a sterilization method ―Tyndallization‖, referred as intermittent or fractional sterilization. The subsequent cooling and heating by steam for 3 days will remove the germs and their spores. Working independently, the German botanist Ferdinand Cohn (1828–1898) discovered the existence of heat-resistant bacterial endospores .

Robert Koch (1893-1910)

He demonstrated the role of bacteria in causing disease.

He perfected the technique of isolating

bacteria in pure culture.

Robert Koch used gelatin to prepare

solid media but it was not an ideal because

(i) Since gelatin is a protein, it is digested by many bacteria capable of producing a proteolytic exoenzyme gelatinase that hydrolyses the protein to amino acids.

(ii) It melts when the temperature rises above 25°C.

Koch’s Postulates

1. A specific organism should be found constantly in association with the disease.

2. The organism should be isolated and grown in a pure culture in the laboratory.

3. The pure culture when inoculated into a healthy susceptible animal should produce symptoms/lesions of the same disease.

4. From the inoculated animal, the microorganisms should be isolated in pure culture.

5. An additional criterion introduced is that specific antibodies to the causative organism should be demonstrable in patient’s serum.

Joseph Lister (1878) He is the father of antiseptic surgery. Lister concluded that wound infections were due to microorganisms.

Developed Pure culture technique. Pure culture referred as the growth of mass of cells of same species in a vessel. He developed the pure cultures of bacteria using serial dilution technique. He also discovered that carbolic acid (phenol) to disinfect the surgical equipments and dressings leads the reduction of post-operational deaths/infections

Alexander Fleming (1928)

• identified Penicillium notatum inhibiting Staphylococcus aureus and identified the antibiotic Penicillin • Discovered antibiotic penicillin –important milestone in medical microbiology • Found that natural substances having antimicrobial activity- Saliva,Nasal mucous • Worked on Staphylococcus aureus,-inhibition of growth due to Penicillin

Fanne Eilshemius Hesse (1850 - 1934)

One of Koch's assistant first proposed

the use of agar in culture media.

It was not attacked by most bacteria.

Agar is better than gelatin because of its

higher melting pointing (96°c) and solidifying

(40 – 45°c)points.

Richard Petri (1887)

He developed the Petri dish (plate), a container used for solid culture

media.

Edward Jenner (1749-1823)

First to prevent small pox.

He discovered the technique of vaccination.

Paul Erlich (1920)

He discovered the treatment of syphilis by using arsenic

He Studied toxins and antitoxins in quantitative terms & laid foundation of biological standardization.

Bacterial Classification

Early Systems of Classification

Taxonomy branch of biology that names and groups organisms according to their characteristics and evolutionary history

First classified 2,000 years ago by Greek philosopher Aristotle

Aristotle’s Classification

First classified either plant or animal

Then classified animals as: Land dwellers

Water dwellers

Air dwellers

Classified plants into 3 groups according to stem structure

15th and 16th Centuries

• More and more species discovered

• Artistotle’s sytem not sufficient

Also common names provided a problem

• Language differences

– Fish/pla, etc

• Didn’t describe accurately

– Jellyfish = fish

Linnaeus’s System

Swedish naturalist Carolus Linnaeus (1707-1778) made system of grouping organisms into hierarchical categories

Used mostly morphology (form and structure)

Levels of Classification • Linnaeus made heirarchy of 7 levels

• Largest category kingdom – Two kingdoms, plant and animal

• Each subset in kingdom phylum/division; animal/plant

• class

• Order

• Family

• Genus

• Species

Want to remember the levels? Remember ―Kings Play Chess On Funny Green Squares‖

Kingdom, Phylum, Class, Order, Family, Genus, Species

The Taxonomic Hierarchy

Binomial Nomenclature

• In Linnaeus’s system, the species name (also called the scientific name) of an organism has 2 parts

• First part = name of the genus

• Second part = species identifier – Usually a descriptive word

– Homo sapiens sapiens = ―wise‖

• This system of 2-part names is binomial nomenclature

In binomial nomenclature, genus name is capitalized

Both names either underlined or italic

Homo sapiens Homo sapiens

Because names are in Latin, they are the same throughout the world

Modern Systems of Classification

Aristotle classified organisms as either plants or animals, but today we recognize that many forms of life are neither. In this section you will learn about two alternative classification system that are in current use. But remember, organizational systems are imposed by humans and therefore may be flawed. As is true of everything in science, they are subject to change as new information arises.

Taxonomy

The science of classifying organisms

Provides universal names for organisms

Provides a reference for identifying organisms

3 Domain System

• Compares sequences of rRNA in different organisms

• Because all organisms have ribosomes

• Domain Archaea archaebacteria

• Domain Bacteria eubacteria

• Domain Eukarya protists, fungi, plant, animal – Have true nuclei with linear chromosomes and

membrane-bound organelles

The Three-Domain System

Kingdom Archaebacteria

Archae- is Greek for ―ancient‖

Unicellular prokaryotes

Some species autotrophic, making food by chemosynthesis

Many live in harsh environments Hot springs

Underwater volcano

Kingdom Eubacteria

Eu- is Greek for ―true‖

Unicellular prokaryotes

Most bacteria that affects your life (tooth decay, food poisoning, etc)

Together with Archaebacteria these are the greatest number of living things on Earth

Kingdom Protista

Variety of eukaryotes, mostly single-celled

Some multicellular (giant kelp)

Of 50,000 species, none are plant, none are animals

Contains diverse collection of eukaryotic organisms

Protozoa – algae – slime molds – water molds

Kingdom Fungi

• Heterotrophic unicellular and multicellular eukaryotes

• Absorb nutrients instead of ingesting them

• 100,000 species

• 2 basic types

1. Molds tangled masses of filaments of cells

2. Yeasts unicellular organisms whose colonies resemble those of bacteria

Kingdom Animalia

• Eukaryotic, multicellular heterotrophs

• Almost all have standard sexual cycle that uses meiosis

Systematics, or Phylogeny

The study of the evolutionary history of organisms

All Species Inventory (2001–2025) To identify all species of life on Earth

A Model of the Origin of Eukaryotes

Figure 10.2

Phylogenetics

Each species retains some characteristics of its ancestor

Grouping organisms according to common properties implies that a group of organisms evolved from a common ancestor

Anatomy

Fossils

rRNA

Classification of Prokaryotes

Prokaryotic species: A population of cells with similar characteristics

Culture: Grown in laboratory media

Clone: Population of cells derived from a single cell

Strain: Genetically different cells within a clone

Figure 10.6

Phylogenetic Relationships of Prokaryotes

Classification of Eukaryotes

Eukaryotic species: A group of closely related organisms that breed among themselves

Classification of Eukaryotes

Animalia: Multicellular; no cell walls; chemoheterotrophic

Plantae: Multicellular; cellulose cell walls; usually photoautotrophic

Fungi: Chemoheterotrophic; unicellular or multicellular; cell walls of chitin; develop from spores or hyphal fragments

Protista: A catchall kingdom for eukaryotic organisms that do not fit other kingdoms

Grouped into clades based on rRNA

Classification of Viruses

Viral species: Population of viruses with similar characteristics that occupies a particular ecological niche

Classification and Identification

Classification: Placing organisms in groups of related species. Lists of characteristics of known organisms.

Identification: Matching characteristics of an ―unknown‖ organism to lists of known organisms.

Clinical lab identification

Identification Methods

Morphological characteristics: Useful for identifying eukaryotes

Differential staining: Gram staining, acid-fast staining

Biochemical tests: Determines presence of bacterial enzymes

Identifying Bacteria

Figure 10.9

Numerical Identification

Serology

Combine known antiserum plus unknown bacterium

Slide agglutination test

Figure 18.14

ELISA

Enzyme-linked immunosorbent assay

Known antibodies

Unknown type of bacterium

Antibodies linked to enzyme

Enzyme substrate

Phage Typing of Salmonella enterica

Figure 10.14

Genetics DNA base composition

Guanine + cytosine moles% (GC)

DNA fingerprinting Electrophoresis of restriction enzyme digests

rRNA sequencing

Polymerase chain reaction (PCR)