Chapter 3:Taxonomy of microbes(major

groups of microorganisms)
Phylogenetic Vs Phenetic classification
•Phylogenetic classification :groups reflect genetic
similarity and evolutional relatedness
•Phylogeny: The Study of Evolutionary Relationships
of Living Organisms
•Phenetic classification : groups do not necessarily reflect
genetic similarity or evolutionary relatedness. Instead,
groups are based on convenient or observable
characteristics.
 Over 1.5 million different organisms have been

identified to date.
 Many similarities among living organisms:

 Made up of cells surrounded by a plasma

membrane.
 Use ATP as energy source.

 Store genetic information as DNA.

 Ribosomes are the site of protein synthesis.

 Both differences and similarities among organisms are caused
by natural selection (Darwin, 1858).
 Organisms can be classified into taxonomic categories (taxa),

based on the differences and similarities among them.

Ancient Greeks classified all living organisms into two groups

 Kingdom Plantae

 Kingdom Animalia
 In 1850s bacteria and fungi were incorrectly placed in

the Plant Kingdom.

 In 1860s Kingdom Protista was proposed to include

bacteria, fungi, algae, and protozoa, but many

scientists still classified bacteria and fungi as plants.

Intense disagreement over classification of bacteria

and fungi persisted over 100 years.
In 1930s electron microscopy made it clear that bacterial cells
lacked a nucleus. The term prokaryote was introduced in
1937.
 In 1959 Kingdom Fungi was established.

 In 1961 the current definition of the term prokaryote was

established.
 In 1968 the Kingdom Prokaryotae was accepted by

biologists.
 In 1969 Robert Whitaker proposed a five-kingdom system of

biological classification for all living organisms.

Five-Kingdom System of Biological
Classification
Proposed in 1969 by Robert Whitaker :
1. Kingdom Prokaryotae (Monera): Oldest known cells.
Lived over 3.5 billion years ago. Lack a nucleus and
membrane bound organelles.

The other four kingdoms are eukaryotes. Have a true

nucleus and membrane bound organelles.
2. Kingdom Protista: Mostly unicellular, lack tissue
organization. Most have flagella during life.

3. Kingdom Fungi: May be unicellular (yeasts) or

multicellular (molds). Many are saprotrophs.

4. Kingdom Plantae: Multicellular, photosynthetic.

5. Kingdom Animalia: Multicellular, heterotrophs that

ingest food through a mouth or oral cavity.
Five-Kingdom Classification System
 Differences Between Eukaryotic and
Prokaryotic Cells
Prokaryotes Eukaryotes
Cell size 0.2-2 um in diameter 10-100 um in diameter
Nucleus Absent Present
Membranous
Organelles Absent Present
Cell Wall Chemically complex When present, simple
Ribosomes Smaller (70S) Larger (80S) in cell
70S in organelles
DNA Single circular Multiple linear
chromosome chromosomes (histones)
Cell Division Binary fission Mitosis
Procaryotes: Lack Nucleus and Membrane-
Bound Organelles
Phylogeny
The Three Domain System
Domain: In 1978 Carl Woese proposed this level of
classification above kingdom.
There are three domains based on the following
distinguishing criteria:
 Cell wall composition
 Membrane lipids
 RNA sequence
 Protein synthesis
 Antibiotic sensitivity
I. Domain Eubacteria: “True bacteria”.
II. Domain Archaeabacteria: “Ancient bacteria”
III. Domain Eukarya: All eukaryotes: Protista,
Fungi, Plantae, and Animalia.
Phylogeny:
The Three Domain System
Recent developments in molecular biology and
biochemistry have revealed that there are two
types of procaryotic cells, based on differences in
their ribosomes, cell walls, and metabolism.
1. Eubacteria: “True bacteria”.
 Cell wall contains peptidoglycan.
 Sensitive to antibiotics.
2. Archaeabacteria: “Ancient bacteria”
 Cell walls lack peptidoglycan, resistant to antibiotics.
 Live in extreme environments
 Three kingdoms:
1. Methanogens: Strict anaerobes that produce methane.
2. Extreme Halophiles: Require high salt concentrations.
3. Thermoacidophiles: Live in hot, acidic environments.
Phylogenetic Relationships of Prokaryotes
Classification of Organisms
Scientific Nomenclature
 Scientific nomenclature: Universal system for naming and
classifying living organisms. Initially developed in the 18th
century by Carl Linnaeus.
 Binomial nomenclature: Each organism (species) has a two part
name. Names are either italicized or underlined.
 Genus name: Always capitalized, always a noun. May use initial.
 species name: Always lower case, usually an adjective.
 Names are usually derived from Latin (or Greek) or may have
latinized endings. Examples:
 Homo sapiens (H. sapiens): Human
 Penicillium notatum (P. notatum): Mold that produces penicillin
 Canis familiaris (C. familiaris): Domestic dog
Classification of Organisms
Hierarchy of Taxonomic Categories
DOMAIN
Kingdom
 Phylum or Division (Bacteria)
 Class
 Order
 Family
 Genus
species
 Taxonomic Categories

Division
(Bacteria)
Eukaryotic microbes
 Algae
A) Plant like organism that possess photosynthetic pigments
and a cell wall
B) These are further divided into groups on the basis of which
pigment are present
1)Only two are threat to human health
a)Gymnodinium and gonyaulax which causes paralytic
shellfish poisoning
Diverse group of eukaryotic organisms
use light to convert carbon dioxide and water in to
carbohydrates
Includes both microscopic unicellular and macroscopic
multicellular organisms.
 Classification of algae
Algae not a distinct classification term grouped for identification
based on numerous properties
 Photosynthetic pigment
 Cell wall structure
 Type of storage products
 Mechanism of motility
 Mode of reproduction
 names are derived from major color displayed by group
Algae habitats
– Found in both fresh and slat water and soil
– Aquatic algae major producers of oxygen
• Also important users of carbon dioxide
– Algae often grow where other life forms cannot
• Often first to become established in barren environment
Algae reproduction

 Most algae cells are reproduce by binary fission

– Chromosome goes through mitosis

 Some algae reproduce through fragmentation

– Portion of parent organism breaks off to form new

organism
 Sexual reproduction through meiosis also occurs
 Algae do not cause disease directly
– Numerous algae produce toxins
• Toxins are poisonous to human
– Some species such as dinoflagellates produce
neurotoxins
– dinoflagellates eaten by shellfish and produce
toxin
– Toxin accumulates in shellfish tissues
– Human eat shellfish and suffer paralytic
shellfish poisoning
 Fungi
 Mycology is the study of fungi

 Fungi are mostly saprophytes, all are heterotrophs

– Saprophytes decay non living organic matter
• Fungi are the kind of decomposer

– Heterotroph use pre-formed organic matter

• Non autotrophies; not photosynthetic

 Fungi grow into through their food

– Release extracellular enzymes break down polymers into LMW
compounds for transport
Heterotrophic by absorption
• Fungi get carbon from organic sources

• Hyphal tips release enzymes

• Enzymatic breakdown of substrates

• Products diffuse back into hypha

Fungi terminology and structure
 Hypha (singular) hyphae (plural) threat
– Hypha may be partially separated into cells or not
at all (coenocytes)
• Cytoplasm is continuous through out hypha
• Mycelium (plural mycelia) a mass of hyphae
– Like a bacteria colony except really all one organism
Some fungi are molds some are yeasts
yeasts are oval, unicellular
Dimorphic: able to grow as either form
typically of some disease causing fungi
Fungal Classification
 Sexual reproduction
 Spores are formed following fusion of male and female
strains and formation of sexual structure
 Sexual spores and spore-forming structures are one
basis for classification
 Zygospores
 Ascospores
 Basidiospores
Fungal Classification
 Subkingdom Amastigomycota
 Terrestrial inhabitants including those of
medical importance:

1. Zygomycota – zygospores; sporangiospores and

some conidia
2. Ascomycota – ascospores; conidia
3. Basidiomycota – basidiospores; conidia
4. Deuteromycota – majority are yeasts and molds;
no sexual spores known; conidia
Reproduction by spore
 Spore are reproductive cells
– Sexual (meiotic in origin)
– Asexual (mitotic in origin)
Formed
directly on hyphae
inside sporangia
fruiting bodies
Impacts of fungi
 Disease: mycosis
– Most are saprobes, but some cause disease
 Antibiotic production
– Penicillium, Cephalosporium
 Food industry
– soy sauce, cheeses
 Decomposition
– Cellulose and other plant polymers wood
– Stone, paintings, paint, plastic
 Plant pathogens
– Rice, fruit ,etc…
mycorrhizae
 Fungus roots

 Mutualism between : fungi and plants

– Fungus (nutrient and water uptake for the plant)

– Plants (carbohydrate for fungus)

 Several kinds

– Zygomycota hyphae invade root cells

– Ascomycota and basidiomycota hyphae invade root but do not penetrate cells

 Extremely important ecological role

Protozoans
 Animal like organism because the lake a cell wall and are heterotrophic

 These are further divided on the basis of their locomotion

1. Mastigophora - motile by flagella

a.Trypanosoma cause African sleeping sickness

b. Trichomonas vaginalis a sexual transmitted protozoan that cause

vaginitis

c. Giardia lamblia intestinal parasitic ; cause giardiasis (diarrheal illness)

2. Sarcodia - motile by psedopodia

a. Entamoeba histoleyica – cause amoebic dysentery

3. Ciliophora – motile by cilli

a. Balantidium coli – causes dysentery

4. Microspora - motile via polar filament

a. Microsporidium – causes diarrhea; commonly infects persons with AIDS

5. Apicomplexa – non motile

a. Plasmodium – causes malaria

b. Cryptosporidium – causes food borne diarrheal illness

Classification of Bacteria
Scientific Nomenclature
 Bacterial species: Population of cells with similar characteristics.
 Bacterial strain: A subgroup of a bacterial species that has
distinguishing characteristics. Identified by numbers, letters, or
names that follow the scientific name.
 Escherichia coli O157:H7: Strain that causes bloody diarrhea.
 Bergey’s Manual: Provides a reference for identifying and
classifying bacteria.
 Classification initially based on cell morphology, staining, metabolism,
biochemistry, serology, etc.
 More recently, DNA, RNA, and protein sequence analysis are being used
to study evolutionary relationships.
 Classification Systems in the
Procaryotae
1. Microscopic morphology
2. Macroscopic morphology – colony appearance
3. Physiological / biochemical characteristics
4. Chemical analysis
5. Serological analysis
6. Genetic and molecular analysis
• G + C base composition
• DNA analysis using genetic probes
• Nucleic acid sequencing and rRNA analysis
 Bacterial Taxonomy Based on
Bergey’s Manual
 Bergey’s Manual of Determinative
Bacteriology – five volume resource
covering all known prokaryotes
 classification based on genetic information –
phylogenetic
 two domains: Archaea and Bacteria
 five major subgroups with 25 different phyla
Major Taxonomic Groups of Bacteria

 Vol 1A: Domain Archaea

 primitive, adapted to extreme habitats and modes of
nutrition
 Vol 1B: Domain Bacteria
 Vol 2-5:
 Phylum Proteobacteria – Gram-negative cell walls
 Phylum Firmicutes – mainly Gram-positive with low G
+ C content
 Phylum Actinobacteria – Gram-positive with high G +
C content
Diagnostic Scheme for Medical
Use

 Uses phenotypic qualities in identification

 restricted to bacterial disease agents
 divides based on cell wall structure, shape,
arrangement, and physiological traits
 Species and Subspecies
 Species
 collection of bacterial cells which share an overall similar pattern
of traits in contrast to other bacteria whose pattern differs
significantly
 Strain or variety
 culture derived from a single parent that differs in structure or
metabolism from other cultures of that species (biovars,
morphovars)
 Type
 subspecies that can show differences in antigenic makeup
(serotype or serovar), susceptibility to bacterial viruses (phage
type) and in pathogenicity (pathotype)
Classification of Viruses
 Viruses are not considered living organisms by most
biologists, because they lack cells and their own anabolic
machinery.
 Obligate intracellular parasites. Must have evolved after
their host cell evolved.
 Viral species: Population of viruses with similar
characteristics that occupies a particular ecological niche.
 Morphology
 Genes
 Enzymes