Chapter 1 - Basic of Microbiology PDF

Linear vs Circular Economy
Resources (raw Wastes (solid, gas,

materials, human, water, heat etc)
energy, water etc)
Production and
consumption
Production and
consumption
Dept of Chem Eng, UM Dr. Adeline Chua S.M. 2

Fossil-based vs Bio(based) Economy
Resources (raw Wastes (solid, gas,

materials, human, Fossil-based economy water, heat etc)
energy, water etc)
Production and
consumption
Biobased products
Bioeconomy Bioprocess/Biotechnology
Production and
consumption Resources optimization
Biological resources
Recycle and reuse
Sustainable
Waste minimization
Chapter 1: Basics of Microbiology
1. Cell and types of cell
2. Classification of organisms
3. Cell structures and functions
4. Microbial eukaryotes and prokaryotes
5. Microbial diversity
6. Habitats and environments
7. Naming of organisms
>> CO 1: Distinguish different types of microorganisms and

biomolecules.
Overview: Microbiology – study of microorganisms
All living organisms made Microorganisms

up of cells
Types of microbes
Types of cell
Basic characteristics
Classification of organisms Further classification

based on energy/carbon
source, living conditions
Industrial applications

Cells
 Basic units or fundamental building block of life.
 Cells can be distinguished from non-living matters in four critical

ways:
1. Capable of growth and reproduction;
2. Are highly organised and selectively restrict what crosses

their boundaries;
3. Composed of major elements (C, H, O, N, P and S).
4. Are self-feeding, take up necessary elements, electrons, and

energy from external environment.

Two types of cell
 Eukaryotic cells  Prokaryotic cells

 Eukaryotic cells have a  Prokaryotic cells have
distinct membrane- neither of these.
enclosed nucleus, and
well-defined internal
compartmentation.

Classification of organisms according to cell type
 Group of organisms with  Group of organisms with

eukaryotic cells is called prokaryotic cells is called
Eukaryotes which include: Prokaryotes which include:
 Plants  Bacteria
 Animals
 Archaea
 Algae
 Fungi
 Protozoa  All are unicellular.
 They maybe unicellular

or multicellular.

3 major domains comprise all organisms
Source: Pratt (Figure 1.15 Evolutionary tree based on genetic analysis of ribosomal RNA).

Prokaryotic cells
Prokaryotic Cells
 Class of prokaryotes includes bacteria, and archaea.
 Least developed but most abundant and widespread

organisms.
 Size may range from 1 to 10 m.

 1012 bacteria in a gram of dry solid weight.
 Surface area represented is about 12 m2/g – what does this
imply???
 A wide variety shapes, and cellular aggregation patterns.
 Much simpler than eukaryotic cell structure.
 Unique structures not observed in eukaryotes.

Structure of a typical prokaryotic cell
 Cellular components are encapsulated within a cell membrane

and rigid cell wall.
 Outside surface is often covered by flagella (for locomotion).
 Pili are responsible for DNA transfer during sexual conjugation

and for attachment to surfaces.
 Cell interior, cytoplasm is a gel-like, heterogenous suspension

of biomolecules including small molecules (inclusion bodies),
soluble enzymes, ribosomes and coiled DNA in nucleoid
region.
 Each cell has one chromosome, a single copy of DNA.



Eukaryotic cells
Eukaryotic Cells
 Class of eukaryotes includes plants, animals, fungi, yeasts, protozoa
and algae.
 Much larger than prokaryotic cells. Size ranging from 10 – 100 um.
 Cells surrounded by a cell/plasma membrane made up of protein and

lipid.
 Possess a membrane-enclosed nucleus.
 Contain more than one chromosome.
 Internal structures are more complex than that of prokaryotic cells.
 A unique feature is compartmentation of cellular components called

organelles, which are actually membrane-enclosed packages of
organised macromolecules. E.g. nucleus, endoplasmic reticulum,
mitochondria, chloroplasts.

Structure of a typical eukaryotic cell – animal cell

Structure of a typical eukaryotic cell – plant cell

Eukaryotic microorganisms
- Fungi
- Algae
- Protozoa
Many of them are of major economic importance (in both

negative and positive way).
Fungi
 Two major groups of fungi: molds and yeasts.
 Can be unicell (yeast) or multicells (some molds).
 What are the macroscopic fungi you are familiar with?
 Not photosynthetic.
 Derived energy from either living material (parasitic) or dead

organic material (saprophytic).
 Ability to decompose complex materials such as cellulose and

lignin, thus play important role in nature: decomposing dead
material such as leaves, wood.

Typical structure of a fungus growing on and in a
solidified substrate

Fungi
 Industrial applications:
 Molds are used to produce many antibiotics such as
penicillins (Penicillium chrysogenum) and cephalosporins.
 Molds are used for the production of citric acid (Aspergillus
niger).
 Used in food and drink industry in brewing, baking (yeast),
mushroom farming etc.
 Production of enzymes e.g. cellulase, lignase etc.
 Decompose complex polymers of cellulose and lignin (in
nature)
 Causing diseases:
 Responsible for many plant diseases including rusts, blights,
and mildew.
 Skin diseases.
Fungi: Molds
Mildew
Cheese with edible mold
Penicillium chrysogenum
Moldy bread Rusts

Fungi: Yeast
 Humans have used it since

ancient time for production of
food and alcoholic beverage.
 A single cell microorganism.
 It ferments carbohydrates
(sugars) to produce carbon
dioxide and alcohol.
 Widely used nowadays in genetic

engineering and biotechnology:
 Genetically modified yeast is now
used to produce insulin Yeast budding
Source:
http://io.uwinnipeg.ca/~simmons/16cm05/1116/16fungi.htm

Algae
 They are photosynthetic eukaryotes.
 Can be unicell or multicells.
 Generally found free-living in fresh and salt water.
 Mostly exist as unicellular unattached algae floating free in water.
 Seaweed: macroscopic algae that inhabit the seashore.

Algae
 Divided into different groups based mainly on the colored
secondary pigments other than the chlorophylls that give the
algae their characteristics color (red, blue, green etc).
 Very versatile in their metabolism.
 Generally have a rigid cell wall.
 Variety in morphology: unicellular, to colonial, filamentous etc.
 Industrial applications:
 Food supplement e.g. chlorella (single cell algae), spirulina
(microalgae)
 Biomass feedstock for third generation biofuel

Eutrophication
 Algal bloom in water bodies

– eutrophication.
 Caused by enrichment of
an ecosystem with chemical
nutrients, typically
compounds containing
nitrogen (N) and/or
phosphorus (P).
 A serious water environment

problem worldwide.

Red tide

Protozoa
 Unicellular, motile, relatively large ( 1-50 um), non-
photosynthetic, and lacking cell walls.
 Usually obtain food by ingesting other small organisms, such as

bacteria, or other food particles (phagotrophic).
 Play an important role in biological wastewater treatment

processes:
 Their functions there?
 Cause human diseases like malaria and African sleeping

disease.
 Can serve as indicators of the presence of toxic materials, to

which many protozoa are quite sensitive.

Protozoa
Amoeba Ciliate Flagellate

Prokaryotic microorganisms
- Bacteria
- Archaea
- Morphologies
- Importance of prokaryotes in various fields.
Bacteria and Archaea in tree of life

Bacteria
 Many bacteria are of industrial interest:

 Antibiotics
 Lactic acid
 Fermented milk products e.g. yogurt, yogurt drinks.
 Amino acids e.g. MSG, lysine, aspartic acid & phenylalanine
(artificial sweetener)
 Enzymes
 Biopolymers such as polyhydroxyalkanoates
 Biological wastewater treatment process e.g. activated sludge
process: bacteria such as nitrifiers, polyphosphate accumulating
organisms, filamentous bacteria play important roles in the
treatment performance.
 Biofuel (bioethanol, biogas/methane)
 Cosmetic products

Archaea
 Look identical to many bacteria under the microscope.
 But are different structurally and genetically from bacteria.
 Many archaea are extremophiles such as hyperthermophiles,

halophiles, acidophile. They can live in extreme environments such as
high acidity, high alkalinity, high salt, high temperature, high pressure,
high radioactivity.
 They can be found in hot springs or in volcanic areas, ocean

hydrothermal vents.
 Production of high-temperature tolerant enzymes, activated sludge

process.

Morphologies of Prokaryotes
 Morphology refers to shape, size, structure, and spatial

relationship to one another.
 A way to classify bacteria, but not a good way. Why???
 Morphology does not tell the physiology of a bacteria/archaea.

Morphology of Prokaryotes
 cocci (s., coccus) – spheres
 diplococci (s., diplococcus) – pairs
 streptococci – chains
 staphylococci – grape-like clusters
 tetrads – 4 cocci in a square
 sarcinae – cubic configuration of 8 cocci
 bacilli (s., bacillus) – rods

 coccobacilli – very short rods
 vibrios – curved rods
 mycelium – network of long, multinucleate filaments
 spirilla (s., spirillum) – rigid helices
 spirochetes – flexible helices
 pleomorphic – organisms that are variable in shape

Morphologies of Prokaryotes

Viruses
Viruses
 Where do they fit into?
 Generally not considered to be ‘living” entities. Why???
 Can be replicated only when in associated with a living cell.
 Viruses are submicroscopic genetic elements consisting of

nucleic acid (DNA or RNA) surrounded by protein.
 Size: 15-300 nm.

HIV
H1N1
SARS
coronavirus
Source: Wikipedia

Microbial Diversity
The diversity of microorganisms we see today is the result of nearly
4 billion years of evolution.
Microbial diversity can be seen in many ways besides phylogeny,

including cell size and morphology (shape), physiology, motility,
mechanism of cell division, pathogenicity, developmental biology,
adaptation to environmental extremes, etc.
We will briefly discuss the microbial diversity in the context of

metabolic diversity, habitats, and environments.
Metabolic diversity
 All cells require an energy source and a metabolic strategy for

living.
 Energy can be tapped from three sources in nature: organic

chemicals, inorganic chemicals, and light.

Chemoorganotrophs
 Organisms that conserve energy from chemicals are called

chemotrophs.
 Those that use organic chemicals are called

chemoorganotrophs.
 Thousands of different organic chemicals can be used. For

example?
 Energy is conserved from the oxidation of the compounds and is

stored in the cell in energy-rich bonds of adenosine triphosphate
(ATP).

Chemolithotrophs
 Many prokaryotes can tap energy available from the oxidation of
inorganic compounds – this form of metabolism is called
chemolithotrophy.
 Organisms that carry out this metabolism are called chemolithotrophs

(only prokaryotes).
 Inorganic compounds that can be oxidized; e.g. H2, H2S, NH4+, and Fe2+
(sulfur bacteria, iron bacteria).
 A good metabolic strategy:

 Avoid energy competition from chemoorganotrophs.
 Can utilize waste products of chemoorganotrophs such as H2, H2S.
 Live in close association with chemoorganotrophs.

Phototrophs
 Unlike chemotrophs, phototrophs do not require chemicals as a

source of energy.
 Phototrophic microorganisms contain pigments that allow them to

convert light energy into chemical energy.
 An important metabolic advantage because?
 Two major forms of phototrophy are known in prokaryotes:

 Oxygenic photosynthesis, O2 is produced (e.g. cyanobacteria and
algae).
 Anoxygenic photosynthesis, no O2 is produced (e.g. purple and
green bacteria, heliobacteria).

Heterotrophs and Autotrophs
 Besides energy source, all cells require carbon in large

amounts.
 Heterotrophs – those require organic compounds as their C

source.
 Autotrophs – those use inorganic carbon such as CO2 as their

carbon source (sometimes called primary producers)
 By definition, chemoorganotrophs are heterotrophs.
 Oppositely, most (but not all) chemolithotrophs and phototrophs

are autotrophs.

Habitats and Environments
Habitats and Environments
 Microorganisms are present everywhere on Earth that will

support life – soil, water, animals, plants, etc.
 Some microbial habitats are ones in which humans could not

survive, too hot or too cold, too acidic or too caustic, or too salty.
Organisms inhabiting such extreme environments are called
extremophiles.
 They do not just tolerate but actually require it in order to grow.

Extrememophiles

Temperature
 Those microbes who can grow

best at: thermophiles
 < 20C: psychrophiles. mesophiles Hyper
Growth rate
thermophiles
psychrophiles
 20-50C: mesophiles.
 > 50C: thermophiles,

hyperthermophiles.
 Knowledge of temperature
classes of bacteria useful in
design and operation of many
biotechnological applications.

Habitats of thermophiles
Geothermal area in Chile
Hot spring in Yellowstone National Park,

US
Source:
http://serc.carleton.edu/microbelife/extreme/extrem
eheat/index.html

pH and Water
 pH:  Water:
 Most microbes have a  Most organisms can grow
narrow pH range for only where water activity is
growth. high.
 Optimum pH for most  Some can grow on barely

microbes: pH 6-8. moist solid surface.
 Acidophiles: those only  Some can grow in solutions

grow at low pH 1-4. with high salt concentration
– halophiles.
 Alkaliphiles :those can
grow above pH 9.

Oxygen
 Oxygen:
 Aerobes: require oxygen for growth.
 Anaerobes: can only grow in the absence of oxygen.

 Obligate anaerobes are killed by presence of O2.
 Microaerophiles: only grow at reduced O2 concentration.
 Facultative bacteria: can grow in the presence or absence of

O2 .

Nutrients
 Microorganisms need to obtain C, H, O, N, P, S, and a variety of

trace elements from their environment or medium.
 Lack of one will restrict growth.
 Microorganisms exhibit considerable diversity in the compounds

they use for growth.

Significance of microbial diversity
 The great diversity of microorganisms provides the engineer

with an immense variety of potential tools.
 For example, two thermophilic species Thermus aquaticus and

Thermococcus litoralis are used as sources of the enzyme DNA
polymerase, for the polymerase chain reaction (PCR) in DNA
fingerprinting >>> contribute to a Noble Prize in Chemistry
(1993)!
 Many potential tools of the microbes are yet to be exploited.

Exercise 3: Relate microbiology to bioprocess
1. Expand Exercise 1 to include the following:

 group of microorganisms involved
 names of the microbes
 what is their energy and carbon sources? name them
accordingly to their metabolic requirements
 the optimum pH and temperature for growth. Do they need
oxygen? Name them according to the growth requirements
2. Give at least 3 examples of industrial applications of each group

of microbes discussed in Chapter 1.
3. Explain how protozoa “polish up” the effluent of an activated

sludge process.

Exercise 1: Products from bioprocesses
 Treated sewage
 Penicillin
 Insulin
 Citric acid
 Lactic acid
 Bread
 Yoghurt
 Cheese
 Beer
 Wine
 Bioethanol
 Vinegar
 Hyaluronic acid in Hada Labo facial products
 SKII miracle water
Dept of Chem Eng, UM Dr. Adeline Chua S. M. 64

Naming of organisms
A brief description of how organisms are classified

and named; the science of taxonomy.
Taxonomy
 Is the science of identification, classification, and
nomenclature.
 Organize organisms into progressively more inclusive

groups on the basis of either phenotypic similarity or
evolutionary relationship (phylogeny).
 The hierarchical nature of classification is such as:

 A species is made up of several strains, similar
species are grouped into genera. Similar genera are
grouped into families, families into orders, orders into
classes, up to the domain, the highest-level taxon.
 Table 16.4 (Brock)

Nomenclature
 Nomenclature is the actual naming of organisms and follows the

binomial system of nomenclature devised by the Swedish
medical doctor and botanist, Carl Linneaus, and used throughout
biology.
 The genus and species levels are used to provide names for
organisms.
 The names are Latin or Latinized Greek derivations, often

descriptive of some key property of the organisms, and are
printed in italics. First letter of Genus name in capital.

Example: Escherichia coli
 Escherichia is the genus.
 coli is the species.
 When writing a report or paper, give full name when organism is

first mentioned, but in subsequent discussion abbreviate the
genus to the first letter (E. coli).
 Although organisms that belong to the same species all share

the same major characteristics, there are subtle and often
technologically important variations within species. E.g. E.coli
used in one laboratory may differ from that used in another.
Thus, various strains and substrains are designated by the
addition of letters and numbers, e.g. E.coli B/r A, E.coli K12.

Importance of Taxonomy and Nomenclature
 By classifying organisms into groups and naming then, we order

the microbial world and make it possible to communicate
effectively about all aspects of particular organisms, including
their behaviour, ecology, physiology, pathogenesis, and
evolutionary relationships.
 The creation of new names must follow the rules described in

The International Code of Nomenclature of Bacteria.
 provides the formal framework by which Bacteria and
Archaea are to be officially named and the procedures by
which existing names can be changed.

Bergey’s Manual and The Prokaryotes
 Two major taxonomic compilations of Bacteria and Archaea.
 Bergey’s Manual of Systematic Bacteriology – most widely

accepted classification system by microbiologists since 1923.
 A compendium of information on all recognized prokaryotes.
 The Prokaryotes – a reference that provides deatiled information

on the enrichment, isolation, and culture of Bacteria and
Archaea.

Culture Collections
 National microbial culture collections (Table 16.5) are an important
foundation of microbial systematics.
 Catalog and store microorganisms
 Store microbes as vialable cultures, typically frozen or in a freeze-
dried state (maintain the cells indefinitely in a living state).
 Provide them upon request, usually for a fee, to researchers and
industry
 Play an important role in protecting microbial diversity
 Table 16.5 (Brock) – their websites contain searchable databases of

strain holdings, together with information on the environmental sources
of strains and publications on them.

Terminology
 Domain in a taxonomic sense, the highest level of biological

classification
 Phylogeny the evolutionary history of an organisms based on
16S RNA analysis.
 Phenotype is the observable characteristics of an organisms,
such as its morphology, motility, metabolism, cell checmistry etc.
 Phylum is a major lineage of cells in one of the three domain of
life
 Taxonomy - the science of identification, classification, and
nomenclature.
 Systematics – the study of the diversity of organisms and their
relationship, include taxonomy and phylogeny.

 The End.

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Linear vs Circular Economy

Resources (raw Wastes (solid, gas,

Dept of Chem Eng, UM Dr. Adeline Chua S.M. 2

Resources (raw Wastes (solid, gas,

>> CO 1: Distinguish different types of microorganisms and

All living organisms made Microorganisms

Classification of organisms Further classification

Dept of Chem Eng, UM Dr. Adeline Chua S.M. 6

 Cells can be distinguished from non-living matters in four critical

2. Are highly organised and selectively restrict what crosses

3. Composed of major elements (C, H, O, N, P and S).

4. Are self-feeding, take up necessary elements, electrons, and

Dept of Chem Eng, UM Dr. Adeline Chua S.M. 7

 Eukaryotic cells  Prokaryotic cells

Dept of Chem Eng, UM Dr. Adeline Chua S.M. 8

 Group of organisms with  Group of organisms with

 They maybe unicellular

Dept of Chem Eng, UM Dr. Adeline Chua S.M. 9

Dept of Chem Eng, UM Dr. Adeline Chua S.M. 10

 Class of prokaryotes includes bacteria, and archaea.

 Least developed but most abundant and widespread

 Size may range from 1 to 10 m.

 A wide variety shapes, and cellular aggregation patterns.

 Much simpler than eukaryotic cell structure.

 Unique structures not observed in eukaryotes.

Dept of Chem Eng, UM Dr. Adeline Chua S.M. 12

 Cellular components are encapsulated within a cell membrane

 Outside surface is often covered by flagella (for locomotion).

 Pili are responsible for DNA transfer during sexual conjugation

 Cell interior, cytoplasm is a gel-like, heterogenous suspension

 Each cell has one chromosome, a single copy of DNA.

Dept of Chem Eng, UM Dr. Adeline Chua S.M. 14

Dept of Chem Eng, UM Dr. Adeline Chua S.M. 16

 Cells surrounded by a cell/plasma membrane made up of protein and

 Possess a membrane-enclosed nucleus.

 Contain more than one chromosome.

 Internal structures are more complex than that of prokaryotic cells.

 A unique feature is compartmentation of cellular components called

Dept of Chem Eng, UM Dr. Adeline Chua S.M. 19

Dept of Chem Eng, UM Dr. Adeline Chua S.M. 20

Dept of Chem Eng, UM Dr. Adeline Chua S.M. 21

Many of them are of major economic importance (in both

 Can be unicell (yeast) or multicells (some molds).

 What are the macroscopic fungi you are familiar with?

 Derived energy from either living material (parasitic) or dead

 Ability to decompose complex materials such as cellulose and

Dept of Chem Eng, UM Dr. Adeline Chua S.M. 24

Dept of Chem Eng, UM Dr. Adeline Chua S.M. 25

Moldy bread Rusts

Dept of Chem Eng, UM Dr. Adeline Chua S.M. 27

 Humans have used it since

 A single cell microorganism.

 Widely used nowadays in genetic

Dept of Chem Eng, UM Dr. Adeline Chua S.M. 28

 Can be unicell or multicells.

 Generally found free-living in fresh and salt water.

 Mostly exist as unicellular unattached algae floating free in water.

 Seaweed: macroscopic algae that inhabit the seashore.

Dept of Chem Eng, UM Dr. Adeline Chua S.M. 29

 Very versatile in their metabolism.

 Generally have a rigid cell wall.

 Variety in morphology: unicellular, to colonial, filamentous etc.