lecture 1 Flashcards
microbiology kevin purdy
what is microbiology?
Study of organisms too small to see with the naked eye •Bacteria •Archaea •Fungi •Protozoa
what are the 3 main domains?
archaea, bacteria, protista/eukarya
what are 4 types of microbes?
•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
what is the estimate of total microbial cells on Earth?
4-6 x 10^30 cells
significance in global biomass
Bacteria and archaea:
• are the major portion of biomass on Earth
• key reservoirs of nutrients for ALL life
why are there so many microorganisms?
• 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)
nutritional categories (6)
- 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)
what are prototrophs?
what are fastidious bacteria?
prototrophs synthesise all their own cellular components (including ALL
amino acids, nucleotides, vitamins)
fastidious bacteria need some of these in the media
what medium does e coli need?
pH at 7 no complex compounds, e coli can make them defined medium phosphate sources sulfate sources glucose trace elements
medium for e coli and neiserria spp
glucose peptone yeast extract kh2po4 ph 7
peptone and yeast extract are undefined chemicals containing cellular material
what is the most complex media?
Some microbes have to be grown inside eukaryotic cells or
in an animal
how do bacteria grow and reproduce?
• 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
why is bacterial growth limited?
all environments are limited, organisms can only
grow so much
• carrying capacity of the medium
•Growth is limited by space and availability of nutrients
explain the steps of a bacterial growth curve
• 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
different measurements of growth (3) and what they measure (5)
- haemocytometry
- dilution plating
- turbidmetry
measure cell number, optical density, fresh/dry weight, protein, dna
what is the total viable count?
• 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)
what is the problem with identification of microorganisms?
Problem: limited morphological diversity, most
microbes look similar down a microscope
ways to identify microorganisms
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
what is selective media?
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)
what is differential media?
•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
testing of enzyme activities: explain the process of the ApiZym test system
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
Microorganisms need primary nutrients to grow in the lab.
what are the macronutrients and micronutrients we could use?
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)
what does gonorrhoeae need in the media to grow?
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)
what is the advantage of growing on a complex medium?
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.
explain the assumption used to count the colonies using CFU
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).
why is ApiZym useless for looking at environmental organisms?
because they are growing in a different system from the one this presumes it grows in.
define lateral gene transfer
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
difference between defined and complex media
defined medium - with known substances
complex medium - we don’t know what is in the media
