CLASSIFICATION OF

MICROORGANISM
LEARNING OUTCOMES

At the end of this topic, students should be able to:

▪ Understand the concept of living things.

▪ Differentiate prokaryotes and eukaryotes.
▪ Understand classification of microorganisms.
▪ Explain the structure of bacteria.
 LIVING THINGS

▪ Living things consist of atom of different

elements.
▪ ELEMENTS: There are 92 naturally
occurring elements. 14 more are created
in the laboratory.
▪ The most abundant elements in major
life forms are:
✔ Hydrogen, Carbon, Nitrogen, Oxygen,
Sodium, Magnesium, Phosphorus, Sulfur,
Chlorine, Potassium, Calcium, Iron.
▪ FUNCTIONAL MOLECULES: Two or more atoms joined
together are called a molecule.
▪ Molecules can be simple (water) or complex (DNA)
mixture of atoms. These atoms are joined together by
bonds:
▪ Covalent bond: Formed when atoms share electron.
Covalent bond is extremely stable. Need high energy to
break. Ex. carbon dioxide.
▪ Ionic bond: Formed by the attraction between oppositely
charged molecules. The bond is not as strong as covalent.
They are easily dissociated. Ex: NaCl, NaOH, HCl.
▪ Hydrogen bond: Formed when hydrogen atoms are shared
between two molecules. Hydrogen bonds are weak. Ex:
Glucose, carbohydrates.
▪ BUILDING BLOCKS:
▪ Are functional groups of molecules bonded
together to form compounds of special functions:
Proteins, carbohydrates, nucleic acids,
polysaccharides.

▪ FUNCTIONAL STRUCTURES AND APPENDAGES:

▪ The assembly of building blocks is a process of
growth and consists of numerous reactions
catalyze by enzymes.
 WATER

▪ Importance of water to life:

▪ Act as an agent for hydrogen
bonding. Supplies H+ and OH- for
completion of respiration.

▪ Water’s polarity makes it an

excellent solute for chemical
reaction.
▪ Hydrophilic / Hydrophobic.
▪ All living cells can be classified as
either eukaryotic (having a true
nucleus) or prokaryotic (lacking
true nucleus and other
membrane enclosed structures).
 MAJOR DIFFERENCES
BETWEEN PROKARYOTES AND EUKARYOTES
PROKARYOTES EUKARYOTES
Single celled organisms. All bacteria. Single (amoeba, etc) and multicell (plant, animals)

DNA not enclosed: Lack nuclear membrane DNA enclosed in nuclear membrane
Lack histones Presence of histones

No mitochondria (enzymes in cell membrane) Energy synthesizing enzymes in mitochondria

Lack Golgi apparatus Has Golgi apparatus
Ribosomes 70S 80S in cytoplasm 70S in organelles
Cytoskeleton absent Cytoskeleton present
Cell wall of peptidoglycan Cellulose or chitin on plant and fungal
Absence of cilia/presence of flagella Present on some (paramecium)

Presence of pilli on some Absence

Division by binary fission, asexual Mitotic or meiotic, sexual or asexual

▪ General
characteristics for
identification
purposes of the
microorganisms:
▪ The Bergey’s
Manual is the
preferred
reference.
 Classifications and nomenclature

▪ The first letter in the genus is

Capitalized. The species is written in
small letters. Subtype can be
numbers.
▪ When printed it is in italic, when
written it is underlined.
▪ Escherichia coli type II E. coli.
 Genus and species

▪ This name can represent certain historical origin of the bacteria. Eg:
✔ Pasteurella pestis: Based on the person who first discovers and registered the
organism.
Bacillus subtilis
Staphylococcus aureus Based on basic shapes and physical morphology.
Streptococcus faecalis

✔ Enterobacter aerogenes: Based on where it was isolated from (natural habitat).

Vibrio cholera: Based on disease it caused.
✔ Thiobacillus ferrooxidans Based on specific biochemical functions.
✔ Saccharomyces cerevisiae
▪ Subtype; is used to differentiated species that are different but closely related,
having similar characteristics. E. coli O157.H7.
WHAT IS MICROBIOLOGY?

▪Microbiology can be broken-down to several

sub-disciplines including:
Virology – study of viruses
Parasitology – study of parasites: protozoa & helminths
Mycology – study of yeast and fungi
Bacteriology – study of bacteria
Phycology – study of algae (or more specific micro-algae)
BACTERIAL CELL SIZE

https://goo.gl/images/kS7Zuy
 BACTERIA AND ARCHAEA (ancient bacteria)

▪ Microscopic, single celled (unicellular), prokaryotic.

▪ Cell wall of peptidoglycan.
▪ About 3000 species. Only close to 10% are pathogens.
▪ Modern bacteria (= Eubacteria): common.
▪ Archaea (ancient bacteria capable of utilizing unusual source for growth,
found in unusual habitats (extreme):
✔ Deinococcus sp. found in radioactive waste water.
✔ Methanegens found in petrols and organic solvents.
✔ Stearothermophilus sp. found in hot boiling water.
 FUNGI

▪ Eukaryotic. Habitat: water, soil, decaying matter.

▪ Facultative or obligate anaerobes.
▪ Mostly chemotrophic saprophyte (live on dead organic matters) capable
of producing extracellular enzymes.
▪ Pathogenic to animals and plants.
▪ Have rigid cell wall.
▪ Lack photosynthesis.
▪ Some produce antibiotics.
▪ Growth forms: Yeast and Molds.
Yeast

▪ Unicellular growth of fungi.

▪ Spherical to ellipsoidal 3-5 um. May
produce capsule (slime layer).
▪ Reproduce by budding. When growing
as yeast, no spores will be formed.
▪ Produce colony 0.5-3 mm, pasty,
opaque, cream colored or pigmented.
Cannot be ascertain based on
morphology.
 Molds

▪ Mold form of growth refers to the production

of wooly mycelium filamentous colonies (aerial
growth), and hyphae (subterranean growth).
▪ Characteristic branching, cylindrical tubules.
Can be septated or aseptated (coenocytic).
▪ Mycelial growth can produce fruiting bodies
(conidiophores/sporangiophores) This is
asexual reproduction. Some fungi are capable
of sexual reproduction (Karyogamy).
 Molds

▪ Identification can be based on microscopic

morphology of fruiting bodies,
mycelium/hyphae type.
▪ Mushrooms are fruiting bodies of the Family
Basidiomycetes.
▪ Dimorphism: The ability of some species of
fungi to grow in more than one form under
different environment.
▪ Ex: Some pathogenic fungi grow as yeasts at
37 ᵒC and as mold at 25 ᵒC.
 Importance of fungi in food industries

▪ Persistent contaminant for soil related

product.
▪ Production of amatoxins and
phallotoxins (potent: by poisonous
mushrooms).
▪ Aflatoxin/mycotoxin from fungi
contaminated agricultural and poultry
products.
▪ Food spoilage associated with moisture
content.
▪ Ex Rhizopus nigricans :Black bread mold
Importance of fungi in food industries
 VIRUSES

▪ Particles of proteins (capsid ) and nucleic acid

(DNA or RNA )
▪ Inactive or inert virion (non living outside of
living host) active in living host cells. Can
remain inactive for a long time.
▪ Obligatory parasites: requires to be in a living
host cells to survive.
 Host infection process:

▪ Need to have specific receptors to attach to a permissible host cell. Availability of

receptors is determine by nature. And evolution.
▪ Upon successful infection DNA or RNA is injected into host cell cytoplasm. Capsid ghost
remains outside.
▪ Viral DNA inserts into host DNA. Host cell machinery is taken over.
▪ Direct the synthesis of viral particles using the cellular machinery of the host.
▪ Assembly of particles.
▪ Initiate cell lysis or buds out infecting neighboring cells. Normally undetected by the
body defense system once the virus penetrates a cell.
Host infection process:
 Bacteriophage

▪ A virus small enough to infect

bacteria.
▪ Bacteriophage T-4 infects E. coli.
Schematic lifecycle of a bacteriophage
PROTOZOA
HELMINTHS
HELMINTHS

▪ Helminths are divided into:

1. Round Worms 2. Flat Worms

(Nemathelminths) (Platyhelminths)

(Flukes) (Tape worms)

Class Nematoda Class Trematoda Class Cestoda

Classification of algae
CLASSIFICATION SYSTEM FOR
BACTERIA & ARCHAE
MAJOR GROUPS OF BACTERIA
Group Characteristics Examples

Proteobacteria gram-negative, diverse soil bacterium capable of

group capable  converting
of numerous biochemical ammonium to nitrate
pathways

Chlamydias parasites on animal cells,  bacterium causing

gram-negative blindness and 
urethritis

Spirochetes helical heterotrophs syphilis-causing

bacterium

Cyanobacteria photoautotrophs important planktonic

organism in
oceans

Gram-positive bacteria gram-positive, diverse soil bacteria used to

group important  produce
both ecologically and in the antibiotic
human disease streptomycin
 The Major Groups of Bacteria

1. Proteobacteria (Purple Bacteria).

▪ Largest, most physiologically diverse group of bacteria. At least five subdivisions.
Three subdivisions have phototrophic members; many are heterotrophs or
chemolithotrophs, such as Sulfur oxidizers, sulfur reducers, nitrate/nitrite oxidizers;
etc. Very diverse, and most highly evolved group.

2. Cyanobacteria:
▪ Heterogeneous group. Characterized by oxygen-evolving photosynthesis, the
presence of chlorophylls and phycobiliproteins.

3. Gram-positive bacteria.
▪ Divided into Low G+C and High G+C groups. Contains one photosynthetic group
(Helicobacteria), a relative of Clostridium. Low G+C group includes Bacillus,
Clostridium, Helicobacteria, and lactic acid bacteria. High G+C group includes
Corynebacterium, propionic acid bacteria, mycobacteria, Nocardia, Streptomyces,
Micromonospora.
4. Chlamydia.
▪ Obligate intracellular parasites; lack peptidoglycan, but have
outer membrane; agent of some sexually transmitted
infections.

5. Planctomyces-Pirella. Planctomyces-Pirella
▪ Budding organisms that lack peptidoglycan, have a
proteinaceous cell wall. Obligate aerobes, prefer dilute
nutrients.

6. Bacteriodes-Flavobacteria.
▪ Major line of Gram-negative bacteria. Cytophaga/Flavobacteria
is one lineage; Bacteroides a 2nd. Mixture of properties,
including obligate fermentative anaerobes (Bacteroides), Cytophaga/Flavobacteria
obligate aerobes (Sporocytophaga).
7. Green sulfur bacteria.
▪ All are strictly anaerobic phototrophs; contain
chlorosomes, bacteriochlorophylls, and fix carbon
by reverse TCA cycle.

8. Spirochetes. (Spirochaeta, Borrelia, Treponema).

▪ Free-living or parasitic; many are pathogens.
Unique morphology is a valid taxonomix criterion.

9. Deinococcus-Thermus.
▪ Only two well-known genera, one Gram-positive
and one Gram-negative. Deinococcus is highly
Deinococcus
radiation resistant; Thermus is a
chemoorganotrophic thermophile.
10. Green nonsulfur bacteria.
▪ Confusing properties. Affinities to both cyanobacteria, Chloroflexus
purple bacteria and green bacteria. Appear to have
evolved and diverged very early. Ex. Chloroflexus.

11. Thermotoga-Thermosipho.
▪ Only 2 genera. Anaerobic, fermentative, marine
hyperthermophiles (55-90°C).
Thermotoga
12. Aquifex-Hydrogenobacter.
▪ Extreme thermophiles (85-90°C). Aquifex is an aerobic
chemolithotroph that oxidizes H2 or reduced sulfur
compounds. Hydrogenobacter oxidizes only H2.

Aquifex
 The Major Groups of Archaea (formerly Archaebacteria)

1. Extremely halophilic Archaea.

▪ Halobacterium sp. Unique phototrophy based on bacteriorhodopsin.

2. Thermoplasma acidophilum.
▪ Acidophilic thermophile (55°C). Aerobic chemoheterotroph.

3. Hyperthermophiles. Halobacterium
▪ Some grow above 100°C; most are strictly anaerobic and require
elemental sulfur as an electron acceptor. Can oxidize H2 or organic
compounds. Sulfolobus oxidizes sulfur aerobically. Archaeoglobus reduces
sulfate and can produce methane as well.

4. Methanogens.
▪ Strictly anaerobic organisms that produce CH4. CO2 can be reduced with
electrons from various sources (often H2) or CH4 can be produced from
methyl substrates such as CH3OH (methanol). Archaeoglobus