Microbiology is the study of microorganisms that are too small to be seen without magnification. There are several major groups of microorganisms including bacteria, algae, protozoa, fungi, and viruses. Microbiology has many branches and applications such as biotechnology, public health, food science, and more. Microorganisms were some of the earliest life on Earth and have profoundly shaped the planet through processes like photosynthesis and nutrient recycling. Humans have utilized microbes for thousands of years in applications like brewing and bread making, and more recently in biotechnology and bioremediation. Infectious microbes are also the cause of many human diseases. Taxonomy involves naming, classifying, and identifying

1. Microbiology: AMicrobiology: A
Systems ApproachSystems Approach
Hafiz Muzzammel RehmanHafiz Muzzammel Rehman

2. 1.1 The Scope of Microbiology1.1 The Scope of Microbiology
 MicrobiologyMicrobiology: The study of living things: The study of living things
too small to be seen without magnificationtoo small to be seen without magnification

MicroorganismsMicroorganisms oror microbesmicrobes- these- these
microscopic organismsmicroscopic organisms

Commonly calledCommonly called “germs, viruses, agents…”“germs, viruses, agents…”
but not all cause disease and many more arebut not all cause disease and many more are
useful or essential for human lifeuseful or essential for human life

3. Major Groups ofMajor Groups of
MicroorganismsMicroorganisms
 BacteriaBacteria,, algaealgae,, protozoaprotozoa,, helmintheshelminthes,,
andand fungifungi
 VirusesViruses- noncellular, parasitic, protein-- noncellular, parasitic, protein-
coated genetic elements that can infect allcoated genetic elements that can infect all
living things, including otherliving things, including other
microorganismsmicroorganisms

4. Branches of MicrobiologyBranches of Microbiology
 Agricultural microbiologyAgricultural microbiology
 BiotechnologyBiotechnology
 Food, dairy, and aquatic microbiologyFood, dairy, and aquatic microbiology
 Genetic engineering and recombinantGenetic engineering and recombinant
DNA technologyDNA technology
 Public health microbiology andPublic health microbiology and
epidemiologyepidemiology
 ImmunologyImmunology
 Many, many moreMany, many more

5. Emerging Areas of MicrobiologyEmerging Areas of Microbiology
 GeomicrobiologyGeomicrobiology
 Marine microbiologyMarine microbiology
 AstromicrobiologyAstromicrobiology

6. 1.2 The Impact of Microbes on Earth:1.2 The Impact of Microbes on Earth:
Small Organisms with a Giant EffectSmall Organisms with a Giant Effect
 Microorganisms have a profound influenceMicroorganisms have a profound influence
on all aspects of the earth and itson all aspects of the earth and its
residentsresidents
 Bacterial-like organisms in the fossilBacterial-like organisms in the fossil
record as far back as 3.5 billion years agorecord as far back as 3.5 billion years ago
((prokaryotesprokaryotes- organisms without a true- organisms without a true
nucleus)nucleus)
 2 billion years later,2 billion years later, eukaryoteseukaryotes
(organisms with a true nucleus) emerged(organisms with a true nucleus) emerged

7. Figure 1.1

8. Ubiquity of MicroorganismsUbiquity of Microorganisms
 Found nearly everywhereFound nearly everywhere
 Occur in large numbersOccur in large numbers
 Live in places many other organismsLive in places many other organisms
cannotcannot
Figure 1.2

9. Microbial Involvement in Energy andMicrobial Involvement in Energy and
Nutrient FlowNutrient Flow
 Bacteria conductedBacteria conducted photosynthesisphotosynthesis
before plants appearedbefore plants appeared

Anoxygenic photosynthesisAnoxygenic photosynthesis

Oxygenic photosynthesisOxygenic photosynthesis
 BiologicalBiological decompositiondecomposition and nutrientand nutrient
recyclingrecycling

10. 1.3 Human Use of1.3 Human Use of
MicroorganismsMicroorganisms
 Humans have beenHumans have been
using microorganismsusing microorganisms
for thousands of yearsfor thousands of years

BakerBaker’s and brewer’s’s and brewer’s
yeastyeast

CheesesCheeses

Moldy bread on woundsMoldy bread on wounds
Figure 1.3

11. Biotechnology andBiotechnology and
BioremediationBioremediation
 BiotechnologyBiotechnology- when humans manipulate- when humans manipulate
microorganisms to make products in an industrialmicroorganisms to make products in an industrial
settingsetting

Genetic engineeringGenetic engineering- create new products and- create new products and
genetically modified organisms (GMOs)genetically modified organisms (GMOs)

Recombinant DNA technologyRecombinant DNA technology- allows microbes to be- allows microbes to be
engineered to synthesize desirable proteins (i.e. drugs,engineered to synthesize desirable proteins (i.e. drugs,
hormones, and enzymes)hormones, and enzymes)
 BioremediationBioremediation- introducing microbes in to the- introducing microbes in to the
environment to restore stability or clean up toxicenvironment to restore stability or clean up toxic
pollutantspollutants

Oil spillsOil spills

Chemical spillsChemical spills

Water and sewage treatmentWater and sewage treatment

12. 1.4 Infectious Diseases and the1.4 Infectious Diseases and the
Human ConditionHuman Condition
 PathogensPathogens- disease-causing organisms- disease-causing organisms

13. Figure 1.4

14. Worldwide Infectious DiseasesWorldwide Infectious Diseases
 Increasing number of emerging diseasesIncreasing number of emerging diseases
(SARS, AIDS, hepatitis C, viral(SARS, AIDS, hepatitis C, viral
encephalitis)encephalitis)
 Other diseases previously not linked toOther diseases previously not linked to
microorganisms now are (gastric ulcers,microorganisms now are (gastric ulcers,
certain cancers, schizophrenia, multiplecertain cancers, schizophrenia, multiple
sclerosis, obsessive compulsive disorder,sclerosis, obsessive compulsive disorder,
coronary artery disease)coronary artery disease)
 Increasing number of drug resistantIncreasing number of drug resistant
strainsstrains

15. 1.5 The General Characteristics of1.5 The General Characteristics of
MicroorganismsMicroorganisms
 Cellular OrganizationCellular Organization

Prokaryotic vs. eukaryotic cellsProkaryotic vs. eukaryotic cells
• Prokaryotic cells are about 10 times smaller thanProkaryotic cells are about 10 times smaller than
eukaryotic cellseukaryotic cells
• Prokaryotic cells lack many cell structures such asProkaryotic cells lack many cell structures such as
organellesorganelles
• All prokaryotes are microorganisms, but only someAll prokaryotes are microorganisms, but only some
eukaryotes areeukaryotes are

16. Figure 1.5

17. VirusesViruses
 Not independently livingNot independently living
cellular organismscellular organisms
 Much simpler than cells-Much simpler than cells-
basically a small amount ofbasically a small amount of
DNA or RNA wrapped inDNA or RNA wrapped in
protein and sometimes by aprotein and sometimes by a
lipid membranelipid membrane
 Individuals are called aIndividuals are called a virusvirus
particleparticle oror virionvirion
 Depend on the infected cellDepend on the infected cell’s’s
machinery to multiply andmachinery to multiply and
dispersedisperse

18. Microbial DimensionsMicrobial Dimensions
Figure 1.7

19. Lifestyles of MicroorganismsLifestyles of Microorganisms
 Most live a free existence (in soil or water, for example)Most live a free existence (in soil or water, for example)
 Some areSome are parasitesparasites
Figure 1.6

20. 1.6 The Historical Foundations of1.6 The Historical Foundations of
MicrobiologyMicrobiology
 Key to the study of microorganisms wasKey to the study of microorganisms was
the development of thethe development of the microscopemicroscope
 Earliest record of microbes was from theEarliest record of microbes was from the
work ofwork of Robert HookeRobert Hooke in the 1660sin the 1660s
 The most careful observations of microbesThe most careful observations of microbes
was possible afterwas possible after Antonie vanAntonie van
LeeuwenhoekLeeuwenhoek created the single-lenscreated the single-lens
microscopemicroscope

Known as the father of bacteriology andKnown as the father of bacteriology and
protozoologyprotozoology

21. Figure 1.9

22. Establishment of theEstablishment of the ScientificScientific
MethodMethod
 Early scientists tended to explain natural phenomenaEarly scientists tended to explain natural phenomena
by a mixture of belief, superstition, and argumentby a mixture of belief, superstition, and argument
 During the 1600s, true scientific thinking developedDuring the 1600s, true scientific thinking developed
 From that, the development of the scientific methodFrom that, the development of the scientific method

Formulate aFormulate a hypothesishypothesis

Most use theMost use the deductive approachdeductive approach to apply the scientificto apply the scientific
methodmethod

Experimentation, analysis, and testing leads toExperimentation, analysis, and testing leads to
conclusionsconclusions

Either support or refute the hypothesisEither support or refute the hypothesis
 Hypotheses can eventually become theoriesHypotheses can eventually become theories
 Theories can eventually become laws or principlesTheories can eventually become laws or principles

23. Figure 1.10

24. The Development of MedicalThe Development of Medical
MicrobiologyMicrobiology
 The Discovery of Spores and SterilizationThe Discovery of Spores and Sterilization

Louis PasteurLouis Pasteur- worked with infusions in the mid-- worked with infusions in the mid-
1800s1800s

John TyndallJohn Tyndall- showed evidence that some- showed evidence that some
microbes have very high heat resistance and aremicrobes have very high heat resistance and are
difficult to destroydifficult to destroy

Ferdinand CohnFerdinand Cohn- spores and sterilization- spores and sterilization
 The Development of Aseptic TechniquesThe Development of Aseptic Techniques

Physicians and scientist began to suspect thatPhysicians and scientist began to suspect that
microorganisms could cause diseasemicroorganisms could cause disease

Joseph ListerJoseph Lister- introduced- introduced aseptic techniqueaseptic technique

25.  The Discovery ofThe Discovery of
Pathogens and thePathogens and the
Germ Theory ofGerm Theory of
DiseaseDisease

Louis PasteurLouis Pasteur
• PasteurizationPasteurization
• The Germ Theory ofThe Germ Theory of
DiseaseDisease

Robert KochRobert Koch
• KochKoch’s postulates’s postulates--
verified the germ theoryverified the germ theory
Figure 1.11

26. 1.7 Taxonomy: Naming, Classifying,1.7 Taxonomy: Naming, Classifying,
and Identifying Microorganismsand Identifying Microorganisms
 MicrobialMicrobial nomenclaturenomenclature- naming- naming
microorganismsmicroorganisms
 TaxonomyTaxonomy- classifying living things- classifying living things

Originated over 250 years ago with the workOriginated over 250 years ago with the work
of Carl von Linnéof Carl von Linné
 IdentificationIdentification- discovering and recording- discovering and recording
the traits of organisms so they can bethe traits of organisms so they can be
named and classifiednamed and classified
 Levels of ClassificationLevels of Classification

27. Figure 1.12

28. Assigning Specific NamesAssigning Specific Names
 A standardized nomenclature allowsA standardized nomenclature allows
scientists from all over the world to exchangescientists from all over the world to exchange
informationinformation
 TheThe binomial system of nomenclaturebinomial system of nomenclature

The generic (genus) name followed by theThe generic (genus) name followed by the
species namespecies name

Generic part is capitalized, species is lowercaseGeneric part is capitalized, species is lowercase

Both are italicized or underlined if italics arenBoth are italicized or underlined if italics aren’t’t
availableavailable

Staphylococcus aureusStaphylococcus aureus

29. The Origin and Evolution ofThe Origin and Evolution of
MicroorganismsMicroorganisms
 PhylogenyPhylogeny- the degree of relatedness between- the degree of relatedness between
groups of living thingsgroups of living things
 Based on the process ofBased on the process of evolutionevolution- hereditary- hereditary
information in living things changes graduallyinformation in living things changes gradually
through time; these changes result in structuralthrough time; these changes result in structural
and functional changes through many generationsand functional changes through many generations

Two preconceptions:Two preconceptions:
• All new species originate from preexisting speciesAll new species originate from preexisting species
• Closely related organisms have similar features becauseClosely related organisms have similar features because
they evolved from a common ancestorthey evolved from a common ancestor
 Phylogeny usually represented by a tree- showingPhylogeny usually represented by a tree- showing
the divergent nature of evolutionthe divergent nature of evolution

30. Figure 1.13

31. Figure 1.14