INTRODUCTION TO

MICROBIAL STRUCTURE,
DIVERSITY AND TAXONOMY

Dr Godwin Chakolwa
 Student Learning Objectives
• Define and differentiate prokaryotes and eukaryotes
• List and define the different groups of microbes
• Describe the structure of microbes
• Define bacteriology, mycology, parasitology, immunology &
virology.
• Describe the spontaneous generation theory , cell theory,
Germ theory
• State the applications modern day application of
microbiology
 Student Learning Objectives
• Define taxonomy, taxon, systematics, and phylogeny.

• List the different levels of classification

• State the classification criteria of cellular and acellular

organisms .

• Describe the different identification criteria used to group

and identify microbes

• Explain why taxonomy of organisms is important to

microbiologists

• State the rules of nomenclature

 Microbiology
• Microbiology is the study of microorganisms
usually less than 1mm in diameter which requires
some form of magnification( Microscope) to be
seen clearly.

• These microorganisms live around us and inside

our body.

• Includes bacteria, viruses, prions, fungi, algae,

protozoa and helminthes.
 Why Study Microbiology?
• Microorganisms are part of the human
environment and are therefore important to
human health and activities.

• The study of microorganisms provides insight into

life processes in all forms of life

• A microorganism can be unicellular, multicellular

or acellular , visible only under a microscope.
 Types of Microorganisms
• Acellular entities
– Viruses

– Prions

• Prokaryotic
– Bacteria

– Archaea

• Eukaryotes
– Fungi

– Algae

– Multicellular animal parasites

– Protozoa
 A. Acellular Entities
• A virus is a submicroscopic, parasitic, acellular
entity composed of a nucleic acid (RNA/DNA) core
surrounded by a protein coat(capsid).

• Have either DNA or RNA in core

• Core is surrounded by a protein coat.

• Coat may be enclosed in a lipid envelope.

 Viruses
• Viruses: Nucleic acid covered in protein.

• Exist at the borderline of life and death.

• They are obligate intracellular parasites

• They lack an independent biochemical machinery

for biosynthesis of their molecules

Basic Structure of Animal Viruses

Lipid Envelope Nucleic Acid

Protein
Capsid

Virion
Associated
Spike
Polymerase
Projections
 Viruses

• Viroids

– These are viruses that lack protein but have

nucleic acid

– Usually infect plants

 Prions
• Prions: Aberrant forms of normal prion proteins
that infectious.

•Normal prion protein has amino acids in alpha helix

with less than 5% of beta sheets.

•Abnormal prion protein is a misfolded protein, where

majority of alpha helices are converted into beta
sheets resulting in more than 50% of beta sheets
 Prions
• they are essentially proteins without any nucleic acids

• Cause degenerative nervous system diseases in animal

and man

• Causes Bovine Spongiform Encephalopathy (BSE)

• Also causes Creutzfeldt-Jacob Disease (CJD)

Prions
 Key Points
• Cellular organisms

– Type of cell

• Prokaryotic

• Eukaryotic

– Number of cells

• Unicellular

• Multicellular
 Key Points

• Acellular

• Protein only

• Nucleoproteins
 B. Prokaryotes

• Two groups

– Eubacteria: Cell wall made of peptidoglycan

– Archaea: cell wall not of peptidoglycan

 Bacteria
• A bacterium is a unicellular prokaryotic microorganism

• Characteristics

– No true nucleus and membrane bound organelles

– Many posses peptidoglycan cell wall

– Only a small population cause diseases

– Reproduction by binary fission

• Gain energy from use of

• organic chemicals, inorganic chemicals

 Archaea
• Live in extreme environments
• Many are extremophiles loving extreme temp,pH,
salinities, hydrostatic and osmotic pressures
• Include
– Methanogens
– Extreme halophiles
– Extreme thermophiles
 C. Eukaryotes

• Fungi

• Algae

• Protozoa

• Helminthes
Eukaryotic Unicellular Organisms
 Fungi
•Fungi are non-photosynthetic eukaryotic

organisms that Can be unicellullar (yeasts) or

multicellular (molds)

• are often microscopic and absorb nutrients from

the environment.

•Survives in nature as parasites or saprobes

•May have cell wall made of chitin

 Algae
• A heterogeneous group of plant-like unicellular and

multicellular eukaryotic photosynthetic organisms

• They are a source of food for other organisms

• Posses cellulose cell walls

• Only Prototheca species cause disease in humans

 Protozoa
• Protozoa are eukaryotic animal-like single-cell
microorganisms that can be found in aquatic
environments.

• A diverse group of eukaryotic, typically unicellular

microorganisms

• Cause diseases like malaria and sleeping sickness

 Protozoa
•Mostly saprobes and commensals obtainnig food by
ingesting or engulfing smaller microorganims.

•May be motile by means of pseudopod, cilia or

flagella

•Responsible for diseases such as malaria & sleeping

sickness
 Helminthes

• The are eukaryotic multicellular animal parasites

• The study of worms is called helminthology

• Includes tapeworms, flatworms and roundworms

Worms
 Importance & Application of
Microbiology
•Pharmaceuticals- produce complex drug molecules.

(ex. insulin )

•Bioremediation - using microbes to clean pollution

•Fundamental Biology most biochemical pathways

worked out with microbes

•Recycling of chemicals such as carbon, nitrogen,

 Application of Microbiology
• Biological roles- decomposers, recyclers,
symbionts

• Animal digestion - ruminants, methane

• Food Microbiology - yogurt, sauerkraut, Kim

cheese, beer, bread etc.

• Food safety - prevent putrefaction, disease etc.

Summary
CLASSIFICATION OF
MICROORGANISMS
 Systematics

• Systematics is the study of the diversity and

relationships among organisms. All embracing term,

includes Taxonomy

• Taxonomy is the branch of systematics concerned with

classification, nomenclature and identification of

organisms.
 Taxonomy
• Classification - arrangement of organisms into groups based
on common properties, i.e., mutual similarity or evolutionary
relatedness.
• Nomenclature - assignment of names to taxonomic groups
according to the published rules, i.e. process of allocating
names to taxa.
• Identification – Provides the criteria for determining that
a particular microorganism belongs to a recognized taxon
(group), i.e, means by which unknown organisms are
allocated to previously described taxa.
 Why Classify Organisms

• To establish the uniform criteria for identifying

organisms.

• To arrange related organism into groups

• To provide important information on how organisms

evolved.

• To ensure uniformity in the naming of microorganisms

 Backgroud
• Evolution usually progresses toward greater complexity

• All new species originate from preexisting species

• Changes favoring survival are retained and less

beneficial changes are lost

• Closely related organisms have similar features

because they evolved from common ancestral forms

• Classification seeks to put related and similar organisms

in groups for easier uniform identification
 History of Classification

• Aristotle Classification System

• Linnaeus Classification System

 History of Classification
• Classified organisms as land dwellers, water dwellers,
and air dwellers. Plants-three categories based on the
differences in their stems.
• Shortfalls
– Categories were not specific enough.
– Common names did not describe a species
accurately.
– Names were long and hard to remember.
 History of Classification
• Placed organisms in same groups based on similarities in
morphology into kingdoms Amimalia and plantae.

• Note: Phyla and family were not in Linnaeus’s

classification system but were added by modern
scientists.

• Basis for the modern classification of microbes

• Modern classification places organisms into seven levels

of organization.
History of Classification
 Criteria of Taxonomy
•Phylogenetic Classification System: Groups reflect

genetic similarity and evolutionary relatedness

•Phenetic Classification System: Groups do not necessarily

reflect genetic similarity or evolutionary relatedness.

Instead, groups are based on convenient or observable

characteristics.
 1. Classification of
Microorganisms
• All cellular organisms have similar classification

and naming system

• These include fungi, bacteria, algae and archaea

• Acellular microorganisms like viruses have a

different classification and naming system

Classification Cellular Microbes
• NB: Excluding domain, King Philip Came Over For Grandma’s
Soup.

Domain-3

Kingdom-6

Phylum

Class

Order

Family

Genus

Species
 Classification Taxa
• A genus consists of species that differ from each other in
certain ways but are related by descent

• Number of similar species make up a genus

• Family: a group of related genera

• Order :a group of similar families

• Class: a group of similar orders

• Phylum: a group of related classes

• Kingdom is group of related phyla

• A group of similar kingdoms is called a domain

Classification Example
Classification of Microorganisms
• Three domains

– Bacteria (Eubacteria)

– Archaea

– Eukarya

• Protists

• Fungi

• Plants

• Animals
THREE DOMAINS
 The Six Kingdoms of Life
• Most biologists use a six-kingdom system.
– Animalia
– Plantae
– Fungi
– Protista
– Archaebacteria
– Bacteria
• Domains - taxonomic level above kingdoms
Classification of Prokaryotes
 Kingdom Archaeabacteria
• Unicellular prokaryotes with distinctive cell

membranes, biochemical and genetic properties

• Some are autotrophic, producing food by

chemosynthesis. Most are heterotrophic.

• Many archaebacteria live in harsh environments

such as sulfurous hot springs, very salty lakes.

 Kingdom Eubacteria
• They are unicellular prokaryotes.

• Eubacteria are both autotrophic and

heterotrophic.

• Includes the disease-causing bacteria

• Reproduce by binary fission, but they do have

some ways to recombine genes, allowing evolution
to occur.
Classification of Eukaryotes
 Domain Eukarya
• 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
 2. Nomenclature
• Binomial (scientific) nomenclature gives each cellular
microbe two names:
– Genus – noun & species - adjective

• genus name is capitalized and may be abbreviated

• species name is never abbreviated. eg: Bacillus subtilis as B.

subtilis

• Both the genus and species name are italicized or underlined

– Escherichia coli (E. coli)
– Entamoeba coli (E. coli)
Rules of Binomial
Nomenclature
 Binomial Nomenclature
• The Genus name refers to the relatively small group
of organisms to which a particular type of organism
belongs.

• The Species name is usually a Latin description of

some important characteristic of the organism.

• The assigned names either describe the organism or

honor the scientist who discovered the organism
 Sources of Names
Scientific Binomial Source of Genus Source of
Name Specific Epithet

Klebsiella pneumoniae Honors Edwin Klebs The disease

Pfiesteria piscicida Honors Lois Pfiester Disease in fish

Salmonella Honors Daniel Salmon Stupor (typh-) in

typhimurium mice (muri-)
Streptococcus Chains of cells Forms pus (pyo-)
pyogenes (strepto-)
Penicillium Tuftlike (penicill-) Produces a yellow
chrysogenum (chryso-) pigment
Corkscrew-like Honors Oswaldo
Trypanosoma cruzi (trypano-, borer; Cruz
soma-, body)
 3. Identification
• Identification: Matching characteristics of
an “unknown” to lists of known organisms.

• Microbiologists use a taxonomical key to

identify organisms.

• The most common taxonomical key is called

the dichotomous key
 Classification of Viruses
Historically based on:

•Host preference:

–Plant viruses

– animal viruses

–Bacteria viruses (bacteriophages)

•Target organ: dermotropic, neurotropic,

viscerotropic, or pneumotropic
 History of Viral Classification
 Mode of transmission

– Vector: arboviruses

 Overlapping, inconsistent
 Virus Classification
• Currently based on molecular biology of genome and

biophysical structure

• Viruses with similar structural, genomic & replication

properties are grouped into families (suffix: viridae)

e.g. Herpesviridae

• Families subdivided into genera (suffix: virus)

Levels of Taxonomy-Viruses
 Viruses are never put in kingdoms, Why?

• Viruses have no nucleus, cytoplasm, organelles, or cell

membrane, so can not carry out cellular functions.

• Only able to replicate by infecting cells and using the

organelles and enzymes within

• Consists of two parts: a nucleic acid and a protein coat

called a capsid

• Some viruses have a membrane-like structure outside

the capsid called an envelope.