 Taxonomy is the study of the classification of

organisms.

 There is a five-kingdom system of

classification used to classify all living things.

 The five kingdoms are:

◦ Monera (Prokaryotae)
◦ Protista (Protocista)
◦ Fungi
◦ Plantae (plants)
◦ Animalia (animals)
 Each of the five kingdoms is subdivided into
smaller categories.

 Each successive category contains organisms

that are more and more similar.

 The final category is the species.

 Microorganisms (microbes) are organisms
that can only be seen individually using a
microscope.
◦ They include bacteria, some fungi and some
protista e.g. certain algae.

 They occupy a wide range of habitats in both

terrestrial (land) and aquatic (water)
environments.
 Fungi are mainly found in terrestrial habitats.

 Bacteria are found in salt water, fresh water,

soil, dust, air, plants and animals.

 Bacteria can be
found in extreme
environments from
inside hot springs
to inside the
human stomach at
a pH of 2.
e.g. Bacteria
 Bacteria are very small, unicellular (single-
celled) organisms.

 The cytoplasm of the bacteria contains

storage granules and ribosomes but no
membrane bound organelles.

 The cell membrane surrounds the cytoplasm

and can have infoldings called mesosomes
that carry out respiration.
 The cell wall gives the bacteria shape and
structural support.
 A capsule or slime layer may also surround
the cell wall for further protection.
 They have one bacterial chromosome
consisting of a circular strand of DNA without
any surrounding membrane.
◦ They may also have one or more small loops of
DNA called plasmids that contain genes responsible
for antibiotic resistance.
 Many bacteria contain flagella which allows
them to move by themselves.
 The basic structure of different bacteria is the
same but their shapes vary.

 Bacteria are classified into three groups

depending on their shape:
◦ Spherical (coccus – plural cocci)
◦ Rod (bacillus – plural bacilli)
◦ Spiral (spirillum – plural spirilla)
Spherical
 Spherical or round
bacteria are found
in pairs, chains or
clusters.
Rod

Spiral
 Bacteria reproduce asexually by a method
called binary fission.
◦ The DNA strand replicates itself forming two
identical strands of DNA.
◦ The cell elongates pushing the DNA strands apart.
◦ The cell splits into two identical daughter cells or
organisms.

 Bacteria can divide every twenty minutes if

conditions are right.
Mutations
 As bacteria reproduce asexually their
offspring are genetically identical.
◦ This means that they don’t show genetic variation
and are slow to evolve.

 However, bacteria can evolve very fast due to

the speed at which mutations spread within
rapidly growing bacteria.
◦ Mutations are how bacteria evolve a resistance to
new antibiotics.
 Some bacteria can withstand harsh and
unfavourable conditions by producing
endospores.
◦ The DNA strand replicates and one of the new
strands becomes enclosed by a tough-walled
endospore.
◦ The parent cell breaks down and the endospore
remains dormant.
◦ When conditions become favourable again the
endospore takes in water and its tough wall breaks
down.
 Endospores are very difficult to kill as they
can withstand:
◦ Lack of food and water
◦ High temperatures
◦ Most poisons

 Some endospores can survive for hundreds of

years.
 Nutrition is the way in which an organism
gets its food.

 Bacteria can get their food in four ways:

◦ Autotrophic
 Photosynthetic Bacteria
 Chemosynthetic Bacteria
◦ Heterotrophic
 Saprophytes
 Parasites
Autotrophic
 Autotrophic means an organism makes its
own food.
◦ Photosynthetic bacteria often have chlorophyll on
membranes within the cell (not in chloroplasts) and
use light energy to make food e.g. purple sulphur
bacteria.
◦ Chemosynthetic bacteria use energy from chemical
reactions to make food e.g. nitrifying bacteria.
Heterotrophic
 Heterotrophic means an organism takes in
food made by other organisms.
◦ Saprophytes are organisms that take in food from
dead organic matter and are often called
decomposers e.g. bacteria of decay.
◦ Parasites are organisms that take in food from a live
host and usually cause them harm e.g. disease-
causing bacteria.
 The growth of bacteria is affected by five
factors:
◦ Temperature
◦ pH
◦ Oxygen concentration
◦ External solute concentration
◦ Pressure

 Too much or too little of any one of these

factors will slow down, or stop, the growth of
the bacteria.
Temperature
 Most bacteria grow well at temperatures
between 20°C and 30°C.
◦ Some can tolerate much higher temperatures
without their enzymes being denatured.
◦ Low temperatures slow down their rate of growth.

pH
 Bacterial enzymes work at specific pH values
and will become denatured at unsuitable pH
values.
◦ Most bacteria grow at or near pH 7 (neutral).
◦ Some can tolerate very acidic or alkaline pH values.
Oxygen Concentration
 Aerobic bacteria require oxygen for
respiration.
◦ This is why oxygen is sometimes bubbled through
bioreactors.

 Anaerobic bacteria do not require oxygen for

respiration.
◦ Facultative anaerobes can respire with or without
oxygen present.
◦ Obligate anaerobes can only respire in the absence
of oxygen.
External Solute Concentration
 The growth of bacteria is affected by the
external solute concentration because
bacteria gain or lose water by osmosis.
◦ If the external solution has a higher solute (e.g.
salt) concentration than the bacterial cytoplasm the
bacteria will lose water stopping its enzymes from
working.
◦ If the external solution has a lower solute
concentration than the bacterial cytoplasm then
water will move into the bacteria but the cell wall
will prevent it from bursting.
Pressure
 The growth of most bacteria is inhibited by
high pressures as their cell walls are not
strong enough to withstand the pressure.
◦ Some bacteria can withstand high pressures e.g.
those found in deep-sea vents.
◦ Pressure-tolerant bacteria are formed by genetic
engineering techniques for use in bioreactors.
Benefits
 Bacteria such as Lactobacillus are used to
convert milk to products such as yoghurt and
cheese.

 Genetically modified bacteria such as E. coli

are used to make products such as insulin,
drugs, enzymes and vitamins.
Disadvantages
 Pathogens are microorganisms that cause
disease.

 Bacteria can cause plant and animal diseases

such as some strains of E. coli which cause
food poisoning.

 Bacteria can cause food spoilage e.g.

Lactobacillus causes milk to go sour.
 Antibiotics are chemicals produced by
microorganisms that stop the growth of, or
kill, other microorganisms without damaging
human tissue.
 Antibiotics are normally used to control
bacterial infection but they can treat some
fungal diseases.
◦ Antibiotics do not affect viruses.

 Originally antibiotics were isolated from fungi

e.g. penicillin.
◦ New antibiotics are mostly produced by genetically
engineered bacteria.
 When antibiotics are used to treat a bacterial
infection most of the bacteria are killed.

 Antibiotic-resistant bacteria have developed

by mutations.
◦ These bacteria are not affected by the antibiotic and
they have no competition as the other bacteria are
killed by the antibiotic.
◦ This means that new antibiotics must be produced
continually to treat newly resistant bacteria.
 Bacterial strains have emerged that are
resistant to almost all known antibiotics.

 These bacteria are said to be multi-resistant.

◦ One example of these ‘superbugs’ is MRSA.
◦ These bacteria are becoming widespread, especially
in hospitals.
 The overuse of antibiotics results in the
increased growth of antibiotic-resistant
bacteria.
◦ This is because they have no competition from
other bacteria.

 The failure of some patients to complete their

treatment of antibiotics allows the bacteria to
survive and grow.
◦ This increases the risk of the growth of antibiotic-
resistant bacteria.
 Bacteria are prokaryotes as they have no
membrane-bound nucleus or cell organelles.
◦ Apart from the kingdom Monera, all other
kingdoms contain eukaryotes.
 Binary fission results in a very fast increase in
bacterial numbers.
 The growth curve for a typical population of
bacteria growing on nutrient agar is shown
below.
 The graph can be divided into five phases
which are explained as follows:

A – Lag Phase
 During this phase bacteria are adapting to
their new environment.
◦ They may be producing new enzymes needed for
digestion.
 There is little increase in bacterial numbers
during the lag phase.
B – Log Phase
 The bacteria are reproducing at their
maximum rate and their numbers are
doubling in every new generation.
◦ This is due to ideal conditions e.g. food, moisture,
space and oxygen.
C – Stationary Phase
 There is no increase in bacterial numbers.
◦ The growth rate of new bacteria is equal to the
death rate of other bacteria.
 The rate of growth slows down due to factors
such as:
◦ Lack of food
◦ Lack of space
◦ Lack of moisture
◦ Lack of oxygen
◦ Build-up of toxic waste products.
D – Decline Phase
 Bacteria numbers fall when the death rate is
greater than the rate of reproduction.
◦ The slow rate of reproduction is caused by the
same factors as in the stationary phase.

E – Survival Phase
 A small number of bacteria may survive as
endospores which remain dormant until
conditions are suitable again.
 Bioprocessing is the use of miroorganisms to
produce a product.
◦ Bioprocessing can be used to produce a vast range
of products such as cheeses, beer, antibiotics,
vaccines, methane gas, food flavours, vitamins and
perfumes.

 There are two main methods of production:

◦ Batch Culture (fermentation)
◦ Continuous Flow Culture (fermentation)

 A bioreactor is a container in which living

cells are used to make a product.
Batch Culture
 A fixed amount of sterile nutrient is added to
the microorganisms in the bioreactor.
 The microorganisms go through the lag, log
and stationary stages of a growth curve.
◦ It is often stopped before the decline phase as very
little product is made at this stage.
 The nutrients are used up and the product is
formed.
◦ At the end of production the bioreactor is emptied,
the product is purified, the bioreactor is cleaned
and the process repeated.
Continuous Flow Culture
 Nutrients are continually added to the
bioreactor.
◦ At the same time, some culture medium, bacteria
and product are continually removed.
 Microorganisms are maintained at the log
phase of growth.
 The conditions are kept constant in order to
maintain the log phase and maximum
production.
◦ This is difficult and for this reason continuous flow
culture is less used than batch culture.
 Batch Culture vs. Continuous Flow Culture
Batch Continuous Flow
Fixed amount of nutrient Nutrients added all the time.
added at the start.

Microorganisms go through Microorganisms maintained

the lag, log, stationary in the log phase at all times.
phases.

Product formed for a short Product formed all the time

time and the process may for a long period of time.
start again.
e.g. Rhizopus and Yeast
 Fungi have the following main characteristics:
◦ They are heterotrophic – they secrete enzymes onto
their food and absorb the digested molecules.
◦ They reproduce by means of spores.
◦ They have cell walls made of a carbohydrate called
chitin.
◦ The body structure consists of tubes called hyphae.
◦ A visible mass of these hyphae is called a mycelium.
 As fungi are heterotrophs they are either:
◦ Parasites – absorb food from hosts.
 Obligate Parasites
 Facultative Parasites
◦ Saprophytes – absorb food from dead organic
matter.
Parasites
 Parasitic fungi mostly take their food from
plants.
◦ The fungus penetrates between the cells of the
plant, secretes enzymes and absorbs food.
 Some fungal parasites live on animals e.g.
athlete’s foot.
 Obligate parasites live on live hosts and do
not normally kill them.
 Facultative parasites may kill their hosts and
feed on the dead remains.
Saprophytes
 Most fungi are saprophytes e.g. mushrooms
and moulds.
 They are found in the soil, on rotting leaves,
trees and dead animals.
 As they digest the dead organic matter
minerals are released and recycled.
◦ For this reason saprophytic fungi are vital in the
environment.
 Some fungi are edible but many are highly
poisonous.
 Edible fungi include field mushrooms, morels
and truffles.
 Poisonous fungi are numerous and some can
cause death by eating only one cap.
◦ The most common poisonous mushrooms are the
death cap and destroying angel.
 Rhizopus appears as
black circular patches.
 It consists of thread-like structures called
hyphae.
◦ These have no cross walls i.e. they form a tube.
◦ They are multinucleate (have many nuclei), each
nucleus is haploid.
 A stolon is an aerial hypha which allows the
fungus to spread.
 Rhizoids are hyphae that provide extra
surface area for absorption.
 Rhizopus is a saprophyte of starchy food e.g.
bread, vegetables and stored fruits.

 The hyphae are used for digestion.

◦ They secrete enzymes onto the substrate (food).
◦ These enzymes digest the substrate outside the
fungus.
◦ The digested nutrients are then absorbed.
Asexual Reproduction (Sporulation)
 After a few days sporangiophores grow up
from the surface of the substrate.
 Their tips swell to form sporangia.
◦ The cells within each sporangium divides by mitosis
to form spores.
◦ The columella provides food for spore production.
 In dry conditions the sporangium dries out
and opens to release the spores.
◦ Each spore blows away and grows into a new hypha
and mycelium if it lands on a suitable substrate.
Sexual Reproduction
 Sexual reproduction in Rhizopus is triggered
by adverse conditions such as dehydration.

 Rhizopus exists as two separate strains:

◦ Plus strain
◦ Minus strain

 These strains look identical but sexual

reproduction can only occur between
opposite strains.
Steps of Sexual Reproduction
1. Hyphae from opposite strains grow close
together and swellings form opposite each
other.
2. The swellings touch and nuclei (the gametes)
move into each swelling forming
progametangia.
3. Cross walls form to produce gametangia.
4. The walls between the gametangia dissolve
allowing many fertilisations to take place and
forming many diploid zygote nuclei.
5. A tough-walled zygospore forms around
these nuclei.
6. The zygospore can remain dormant for
months.
◦ This allows the zygospore to survive adverse
conditions such as dehydration.
◦ It also gives time for dispersal.
7. When conditions are suitable it germinates
by meiosis.
8. A haploid hypha grows out of the zygospore
and produces a sporangium at the tip, this
releases spores as in asexual reproduction.
 Yeast are unicellular (single-celled) fungi.
◦ They are tiny oval cells and are only clearly seen
using an electron microscope.
 Yeast cells have a thin cell wall made of the
carbohydrate chitin.
 They have a dense cytoplasm that contains
food storage vacuoles.
◦ Usually one large vacuole is present.
 Yeasts respire anaerobically, breaking down
sugars into ethanol and carbon dioxide.
 Asexual reproduction in yeast occurs by
budding.
 The nucleus of the parent cell divides by
mitosis.
 One daughter nucleus and some cytoplasm
enters a small developing bud on the outside
of the parent cell.
 This bud may separate or remain attached.
 If it remains attached the new bud can divide
again and eventually a colony is formed.
Beneficial Fungi
 Yeasts are used to produce breads and
alcohols such as wine and beer.
 Fungi can be used as a source of food e.g.
field mushrooms.
Harmful Fungi
 Fungi can cause food spoilage e.g. rhizopus
growing on bread.
 Fungi such as athlete’s foot and ringworm
can infect animals resulting in financial loses.
 Fungi are eukaryotes as they have a nucleus
and membrane-enclosed cell organelles.
◦ All kingdoms, other than the kingdom Monera,
contain eukaryotes.
Laboratory Procedures
 Always assume that all microorganisms are
potentially harmful, unless it is stated or
proven otherwise.

 We use aseptic techniques and sterilise

equipment to prevent contamination from
microorganisms.
 Asepsis (or aseptic) means that measures are
taken to exclude unwanted microorganisms
e.g. pathogenic microorganisms.

 Aseptic methods include the following:

1. Wash your hands before and after each experiment.
2. Wash the bench with disinfectant before and after
each experiment.
3. Don’t put fingers, food, drink or equipment in or
near your mouth.
4. Keep all containers closed where possible.
5. When microorganisms are in a petri dish seal the
dish with adhesive tape.
 Sterile means that all microorganisms are
destroyed i.e. there is nothing living.

 Sterile techniques include the following:

1. Sterilise all equipment before and after use.
◦ This can be done by placing the equipment in a pressure
cooker (or autoclave) at 120°C for 15 minutes or immersing
in Dettol for 24 hours.
2. Flame all needles or loops by heating them in the
flame of a Bunsen burner before and after use.
3. Pass the neck of test tubes through a flame.
4. At the end of the experiment immerse all equipment
and cultures in sterilising fluid and dispose of in a
bin.
e.g. Amoeba
 Amoeba is a microscopic organism that lives
at the bottom of shallow freshwater ponds
and streams.
◦ Other species are found in seawater.

 It is unicellular and eukaryotic.

 Amoeba is a heterotroph and is omnivorous.

◦ It eats other single-celled protists.
 The protoplasm (living material) in the cell is
surrounded by a flexible membrane.
◦ The shape of the cell is constantly changing to
allow it to move from place to place.

 The cytoplasm consists of the:

◦ Ectoplasm – this is the outer cytoplasm, it is clear
and stiff.
◦ Endoplasm – this is the inner cytoplasm, it is more
fluid and has a grainy appearance due to the
presence of food vacuoles, fat droplets and wastes.
 The food vacuoles secrete acids to kill prey
and then produce enzymes to digest them.

 The contractile vacuole collects water that

enters Amoeba and expels it again.

 The pseudopodia extends in the direction the

Amoeba wishes to move and the cytoplasm
moves into the pseudopodia causing the cell
to move.
◦ Pseudopodia are also used to engulf prey.
e.g. The Flowering Plant
 The plant kingdom will be outline by
reference to the flowering plant under the
headings of:
◦ Plant Structure
◦ Plant Transport
◦ Photosynthesis
◦ Reproduction in Plants
◦ Plant Response to Stimuli
e.g. The Human
 The animal kingdom will be outline by
reference to the human in the majority of the
topics in the leaving certificate biology
course.