lecture 1

Question 1

what is microbiology?

Answer 1

Study of organisms too small to see with the naked
eye
•Bacteria
•Archaea
•Fungi
•Protozoa

Question 2

what are the 3 main domains?

Answer 2

archaea, bacteria, protista/eukarya

Question 3

what are 4 types of microbes?

Answer 3

•Bacteria
mostly very small 1-6 μm in size
largest bacteria are visible to the eye!
•Archaea
once thought to be extremophiles only
also an extreme anaerobe because it produces methane as a waste product
no known pathogenic archaea
•Fungi
size varies enormously
largest fungal colony ~10,000 Kg!
•Protists
very diverse, most eukaryotes are protists
size range from 1-150 μm

Question 4

what is the estimate of total microbial cells on Earth?

Answer 4

4-6 x 10^30 cells

Question 5

significance in global biomass

Answer 5

Bacteria and archaea:
• are the major portion of biomass on Earth
• key reservoirs of nutrients for ALL life

Question 6

why are there so many microorganisms?

Answer 6

• Rapid growth rate even in the environment
• Many chances of speciation through random mutations
• Exchange of genetic material (lateral gene transfer)
• Every available niche is occupied by specifically adapted
microbes
• A very long evolutionary history (~3.8 billion years)

Question 7

nutritional categories (6)

Answer 7

• phototrophs: use light to create nutrients
• chemotrophs: use chemical bonds
• organotrophs: organic compounds as electron donors
• lithotrophs: inorganic compounds as electron donors
• autotrophs: fixing CO2 as carbon source
• heterotrophs: organic carbon as carbon source

(combinations:
Photo-litho-autotroph - light, water as e- donor, fix co20
Chemo-organo-heterotroph - chem bond energy, organic compounds for e-, carbon source
Chemo-litho-autotroph - chem bond energy, inorganic compound for e-, fix co2)

Question 8

what are prototrophs?

what are fastidious bacteria?

Answer 8

prototrophs synthesise all their own cellular components (including ALL
amino acids, nucleotides, vitamins)

fastidious bacteria need some of these in the media

Question 9

what medium does e coli need?

Answer 9

pH at 7
no complex compounds, e coli can  make them
defined medium
phosphate sources
sulfate sources
glucose
trace elements

Question 10

medium for e coli and neiserria spp

Answer 10

glucose
peptone
yeast extract
kh2po4
ph 7

peptone and yeast extract are undefined chemicals containing cellular material

Question 11

what is the most complex media?

Answer 11

Some microbes have to be grown inside eukaryotic cells or

in an animal

Question 12

how do bacteria grow and reproduce?

Answer 12

• Asexual reproduction by binary fission or budding (cells double in size then split into two)
• Exponential growth because one cell becomes two
becomes four etc.
• Incomplete separation produces pairs or larger
assemblies of bacteria

Question 13

why is bacterial growth limited?

Answer 13

all environments are limited, organisms can only
grow so much
• carrying capacity of the medium

•Growth is limited by space and availability of nutrients

Question 14

explain the steps of a bacterial growth curve

Answer 14

• Lag phase: adaptation to (new)
conditions
• Log/exponential phase:
exponential growth
• Stationary phase: limitation by
nutrients, buildup of waste
products that inhibit growth
• Death: organisms start dying off
and may lyse

Question 15

different measurements of growth (3) and what they measure (5)

Answer 15

• haemocytometry
• dilution plating
• turbidmetry

measure cell number, optical density, fresh/dry weight, protein, dna

Question 16

what is the total viable count?

Answer 16

• Count cfu (colony forming units)
• Plate serial dilutions onto solidified
media
• Based on how dilute the sample is
calculate total viable count (e.g.
106 cfu g-1 soil)

Question 17

what is the problem with identification of microorganisms?

Answer 17

Problem: limited morphological diversity, most

microbes look similar down a microscope

Question 18

ways to identify microorganisms

Answer 18

Traditionally, identify using a range of methods:
• Microscopy and staining
• Growth on selective/differential media
• Testing substrate spectrum supporting growth
• Testing of enzyme activities
• Characterisation of cell chemical constituents (lipids, cell
wall components, DNA base ratio, quinones etc.)

Modern identification is mainly based on sequencing of
specific conserved genes (next lecture)
•Additional testing as above is still required

Question 19

what is selective media?

Answer 19

Selective media allow the growth of only some types of
organisms
–> In diagnostic clinical microbiology selective media is used
to culture/identify presumed pathogens from clinical
specimens (blood, sputum, faeces, urine, biopsies, tissue
swabs)

Question 20

what is differential media?

Answer 20

•Differential media allows the identification of organisms
based on growth and appearance on that medium
(often based on colour differences)
• Use to determine whether a culture is potentially
pathogenic

Question 21

testing of enzyme activities: explain the process of the ApiZym test system

Answer 21

ApiZym, a common test system, is mainly optimised
towards pathogens

• A culture of the organism is grown
• Cells resuspended in a buffer
• Test wells are inoculated
• Resulting colour in test strip is compared against a
database
• Can help to distinguish between pathogenic and benign
strains

Question 22

Microorganisms need primary nutrients to grow in the lab.

what are the macronutrients and micronutrients we could use?

Answer 22

Macronutrients (c, h, o, n, s, p, k, mg, na, ca, fe)

Micronutrients as trace metals (b, cr, co, cu, fe, mn, mo, ni, se, w, v, zn)

Question 23

what does gonorrhoeae need in the media to grow?

Answer 23

Gonorrhoeae grows inside human cells to find amino acids, vitamins and nucleotides so that it doesn’t need to make any of them.

so to grow on a plate, it just needs some glucose, lactose, acetate and CO2 (because it’s used to growing in an environment with high amounts of co2 in a human cell)

Question 24

what is the advantage of growing on a complex medium?

Answer 24

Complex media allows us to grow things easily because the bacteria then don’t need to spend energy and time into making these substances.

Some microbes can’t be grown in a media we create ourselves because they only grow inside eukaryotic cells or in an animal. These are the most complex media.

Question 25

explain the assumption used to count the colonies using CFU

Answer 25

Count the colonies that are growing from the culture. Assumption is that the colony is growing from a single cell so tend to call the count CFU (colony forming units).

Question 26

why is ApiZym useless for looking at environmental organisms?

Answer 26

because they are growing in a different system from the one this presumes it grows in.

Question 27

define lateral gene transfer

Answer 27

movement of genetic material between unicellular / multicellular organisms other than by the transmission of DNA from parent to offspring. LGT is an important factor in the evolution of many organisms

Question 28

difference between defined and complex media

Answer 28

defined medium - with known substances

complex medium - we don’t know what is in the media