Microbiology Flashcards
(159 cards)
1
Q
What did Robert Hooke do?
A
- Robert Hooke wrote the first book devote to microscopic observations
2
Q
What did Antoni Van Leeuwenhoek do?
A
- Antoni Van Leeuwenhoek first described bacteria, referred to them as animalcules
3
Q
What did Lois Pasteur do?
A
- Louis Pasteur – spontaneous generation vs seeds/germs from the air
o Showed heat could be used to sterilise
4
Q
What did Robert Koch do?
A
- Robert Koch – showed microorganisms are often the cause of disease
o Careful examination of blood from diseases animals showed presence of bacteria – cause or effect?
o Used mice and anthrax (disease caused by a bacterium called bacillus anthacis) to develop Koch postulates
5
Q
What were Kochs postulates?
A
1) The suspected pathogen must be present in all cases of the disease and absent from healthy animals (microscopy staining)
2) The suspected pathogen must be grown in pure culture (laboratory cultures)
3) Cells from a pure culture of the suspected pathogen must cause disease in healthy animal (experimental techniques)
4) The suspected pathogen must be reisolated and shown to be the same as the original
6
Q
How are organisms grown?
A
- Only a tiny fraction of the microorganisms we have discovered can be cultivated in the lab
- Need to grow microorganisms in nutrient solution
o Also known as culture media - Requires careful preparation
o Choose the right recipe for your microbe
o Keep sterile - Can be solidified with agar of left as a liquid
7
Q
What are plates?
A
- Picking individual colonies
- Identifying population diversity
- Isolation of species from a mixture
8
Q
What are slopes?
A
- Tubes containing solid agar set in a slope
- Used for pure growth of an organism
9
Q
What is liquid culture?
A
- Blood culture
- Sterility tests
- Continuous cultures
10
Q
What are the 4 different types of light microscopy?
A
- Bright field: staining can improve contrast, but kill specimen
- Phase contrast
- Dark-field (both can improve contrast without killing cells)
- Fluorescence: to visualise cells that fluoresce, eg chlorophyll, DAPI stain
11
Q
What are the features of a light microscope?
A
- Ocular lens
- Objective lens
- Stage
- Condenser
- Focusing knobs
- Light source
12
Q
What are the 3 lenses in microscopes?
A
- Ocular lens (eye piece)
- Objective lens
- Condenser lens
13
Q
What is Differential Interface Contrast Microsopy?
A
- Form of light microscopy
- Uses polarised light (light in a single plane)
- Cellular structures appear more 3 dimensional
14
Q
What is atomic force microscopy?
A
- Measure forces between a probe and the atoms on the surface of the specimen
- Measure deviations from flat surface
15
Q
What is confocal scanning laser microscopy?
A
- Couples a laser source to a fluorescent microscope
- Focuses through the specimen in layers – reconstruct layers into a 3D image
- Cells typically stained with fluorescent dyes to make them more distinct
16
Q
What is electron microscopy?
A
- Uses electrons instead of visible light
- Electromagnets function as lenses
- Whole system operates in a vacuum
17
Q
What is transmission electron microscopy?
A
- High magnification and high resolution (0.2nm)
- Can see structures at the molecular level
- Have to make thin sections of specimen – electrons don’t penetrate into tissue well
18
Q
What is scanning electron microscopy?
A
- Shows external surfaces of cells
- Intact specimen coated in a thin film of heavy metal like gold
- Electrons scatter from metal coating and are collected and processed to form an image
19
Q
Why study microbes?
A
- All cells have much in common, so discoveries made in microbial cells can be applied to multicellular organisms
- Don’t take up much space
- Grows rapidly
- Easily manipulated
- They are both useful and interesting
20
Q
Understanding microbes - disease
A
It is importantly to understand microorganisms
Disease:
- Humans
- Plants
- Animals
o Bacillus anthacis causes anthrax
21
Q
Understanding microbes- food preservation
A
Food preservation
- How to stop microbes ruining food
22
Q
Understanding microbes - agriculture
A
Agriculture
- Nitrogen fixing bacteria
- Mychorizae
23
Q
Understanding microbes - animal husbandry
A
Animal husbandry
- Ruminants require bacteria to digest cellulose
24
Q
Understanding microbes - fermentation and biofuels
A
Fermentation
- Yeast
Biofuels
- Biofuels production from plants require microbes for fermentation step
- Some microorganisms produce biofilms
25
Why are microbes useful tools?
- Genetically modified organisms (GMOs)
- Pharmtech
- Gene therapy
26
How to generate a phylogenetic tree?
- Isolate DNA from each organism
- Make copies of rRNA gene by PCR
- Sequence DNA
- Analyse sequence
- Generate phylogenetic tree
27
What are the different types of microorganisms?
- Bacteria
- Archaea
- Protozoa
- Algae
- Prions
- Viruses
- Fungi
28
What are bacteria?
- Proteobacteria – the largest phylum of bacteria, includes e.coli
- Gram positive/negative bacteria
- Cyanobacteria – photosynthetic, first oxygen in phototropism to inhabit the earth
- Many more phyla
29
What are archaea?
- Unique properties, separating them from bacteria
- Only 2 phyla – the eukarchaeota and the Crenarchaeota
- Classification is difficult as the majority have not been isolated in the laboratory
- Usually look similar to bacteria but often have genes and metabolic pathways more similar to eukaryotes
30
What are Protozoa?
- Unicellular eukaryotes
- Live in soil, wet sand, fresh and salt waters
- Great diversity in shape, mobility and metabolism
31
What is algae?
- Eukaryotes
- Contain chloroplasts
- Have cell walls
- Both terrestrial and aquatic
32
What are the cell sizes for prokaryotes and eukaryotes?
- Size range for prokaryotes: 0.2um to >700um in diameter
o Epulopiscium fishelsoni – unusually large prokaryote
- Size range for eukaryotic cells: 10um to >200um
33
How is a higher surface area to volume ratio an advantage to smaller cells?
- Small cells have a higher surface area to volume ratio than large cells
o Faster nutrient exchange per unit cell volume
o Therefore grow faster
o Support a larger population
34
How is faster evolution an advantage to cells?
- Faster evolution
o DNA is replicated as cells divide
o During replication, mutations occur
o Higher rate of cell division -> higher rate of mutation within population
o Mutations are ‘raw material’ for evolution
o Allows rapid adaptation to changing environments
35
What is the lower limit to cell size?
- You’ve still got to fit everything in
- A cell 0.15um diameter would only just fit in all the essential components
- Anything you see down a microscope less than 0.1um is unlikely to be a cell
36
What are endospores?
- Highly differentiated cells
- Produced by certain species of bacteria
- Highly resistant to heat, harsh chemicals and radiation
- Survival structures – like a nuclear bunker
37
What is sporulation?
- An essential nutrient is exhausted eg carbon or nitrogen
- Vegetative cell stops growing
- Endospores develops within vegetative cell and is released
- Spore can remind dormant for years
- Germinates into a vegetative cell when conditions are good
38
What is Endospore structure?
- Strongly refractive and impermeable to most dyes
- Usually seen as unstained regions within cells
39
What are the 3 Endospore morphologies?
- Terminal endospores
- Sub terminal endospores
- Central endospores
40
What are Fimbriae and pili?
- Filamentous structures composed of protein extending from surface of a cell
41
What are Fimbriae?
- Enables cells to stick to surfaces and each other
- Instances where Fimbriae assist the disease process:
o Salmonella species (Salmonellosis)
o Neisseria gonorrhoeae (gonorrhoeae)
o Bordetella pertussis (whooping cough)
42
What are pili?
- Similar to Fimbriae but typically longer and only one or two present
- Best seen under electron microscope when coated with virus particles
- sex pili and type IV pili
43
2 major functions of pili?
1) Conjugation – genetic exchange between cells
2) Adhesion of pathogens to specific host tissues and subsequent invasion
o Can also be involved in mobility
44
What is microbial locomotion? Taxis?
- Most microbial cells can move under their own power
- Enables cells to reach different parts of their environment
- Taxis- movement towards something that will aid growth towards or away from toxins
45
What are the 2 microbial taxes?
- Chemotaxis – response to chemicals
- Phototaxis – response to light
Evolutionary advantage to moving to a better growth environment
46
What are flagellum?
- The flagellum (plural, flagella) rotate to push or pull cell through a liquid
- Gram positive and gram negative bacteria
- Can only be seen with light microscopy after being stained
47
What are the 3 different attachment points of the flagella?
- Polar flagellation: Flagella are attached at one or both ends
- A tuft: a group of flagella attached to one end of the cell
- Peritrichous flagellation: flagella inserted at many locations
48
What is the structure of flagella? Motor structure?
- Flagella are helical
- The wavelength (distance between curves) is characteristic for given species
- Filament is composed of many copies of a protein is called flagellin
- Molecular motor that drives rotation of flagellin filament is embedded in cell membrane
- Motor:
o Central rod
o Passes through a series of rings
o MOT proteins – act as stators
- The rod and the ring will rotate while MOT proteins stay still
49
What is the proton turbine model?
- Energy for rotation:
o Proton movement across membrane through MOT complex
o Protons flow through channel
o Exert electrostatic forces on helically arranged charges on rings
o Attraction and repulsion between charges causes rotation
- Mechanism is very similar to the ATP synthase
50
What is petrichous change in direction?
- Bundled flagella (CCW rotation)
- Tumble – flagella pushed apart (CW rotation)
- Flagella bundled (CCW rotation)
51
What is polar change of direction? 2 types?
- Reversible flagella – CCW rotation and CW rotation
- Unidirectional flagella – CW rotation, cell stops, reorients, CW rotation
52
How to control direction of movement?
- Toward attractant – longer runs fewer tumbles
53
What is gliding?
- Considerably slower than swimming with flagella
- Cells must be in contact with a solid surface to glide
- Colonies of gliding bacteria have distinct morphologies
54
What is a gliding mechanism?
- Not thoroughly understood
- More than one mechanism is responsible
- Polysaccharide slime:
o Connects cells surface with solid surface
o As slime adheres to surface, the cell is pulled along
- Twitching motility
o Repeated extension and retraction of type IV pili
55
What are multicellular structures?
- The myxobacteria
- Form multicellular structures – fruiting bodies
- Life cycles indicate intercellular communication
56
What is the life cycle of myxobacteria?
1) Myxospores – myxospores are resistant resting cells released from sporangioles upon favourable conditions
2) Germination – myxospores germinate and form gram-negative cells, which divide to reproduce
3) Vegetative growth cycle – vegetative myxobacteria are motile by gliding, forming visible slime traits
4) Aggregation – under favorable conditions, the vegetative cells swarm to central locations, forming an aggregation
5) Mounding – aggregations of cells heap up into a mound, an early fruiting body
6) Mounds of myxobacteria differentiate into a mature fruiting body which produces myxospores packed within sporangioles
57
What are fruiting bodies?
- Often strikingly coloured and morphologically elaborate
58
What is the myxobacteria glide?
- Vegetative cells excrete slime to move across surfaces
- Leaves behind a slime trail
59
What is the myxobacteria swarm?
- Slime trail picked up by other bacteria
- Radiating pattern of established slime trails
60
What are the 2 options for carbon sources?
- Fix your own carbon from Co2
- Eat something that’s got carbon in it
61
What is an autotroph?
- Use CO2 as their carbon source
- Primary producers
- Synthesise new organic matter
62
What is a heterotroph?
- Use organic compounds as their carbon source
- Either feed directly on other cells
- Or live off products other organisms excrete
63
What is symbiotic or mutualistic?
o Cooperative relationship with the host
64
What is parasitic?
o Antagonistic relationship with the host
65
What is saprotophic?
o The host is dead
66
How do microbes get the energy they need to grow?
Energy sources = chemicals, light
- Chemotrophy and phototrophy
- Chemoorganotrophs, chemolithotrophs, phototrophs
- All producing ATP
67
What is photosynthesis?
- The conversion of light to chemical energy
- Organisms that perform photosynthesis are phototrophs
- Most are also autotrophs (use CO2 to make organic compounds)
68
What are the 2 types of phototrophs?
- Algae and green plants – oxygenic photosynthesis
- Anoxygenic photosynthesis
69
What are Chemoorganotrophs?
Chemoorganotrophs (chemical organic feeders)
- Thousands of different organic chemicals (carbon containing) available
- Oxidation of organic compounds releases energy, stored as ATP
- Can be aerobic (only grows in presence of oxygen) or anaerobic (only grows in the absence of oxygen) or both
70
What are chemolithotrophs?
Chemolithotrophs (rock chemical feeders)
- Oxidation of inorganic compounds releases energy stored as ATP
- Only occurs in prokaryotes
- Several inorganic compounds can be oxidised
o Eg H2, H2S (hydrogen sulphide), NH3 (ammonia)
- A related group of chemolithotrophs specialises in oxidation of a related group of inorganic compounds
- Sulphur bacteria
- Iron bacteria
71
What is the metabolic strategy of chemolithotrophs?
Chemolithotrophs – a good metabolic strategy
- Competition from Chemoorganotrophs is not an issue
- Many of the inorganic compounds used by chemolithotrophs are waste products of Chemoorganotrophs
- It’s common for species from these 2 groups to live in close association
72
What is nitrogen fixation?
- Some bacteria can ‘fix nitrogen’ – convert atmospheric nitrogen gas into a form that can be used by cells
- N2 + 8H+ + 8e- — 2NH3 + H2
- No known eukaryotes can fix nitrogen
73
What are the 2 types of nitrogen fixing bacteria?
- Not all bacteria can fix nitrogen
- 2 types
o Free living, requires no host, they live free
o Symbiotic, can only exist in association with certain plants, live in root nodules
74
What is nitrogenase? What are the 2 distinct proteins that make up its complex?
- Nitrogenase cataylses the following reaction –
o N2 + 8H+ +8e- — 2NH3 +H2
- A complex of 2 distinct proteins
o Dinitrogenase – contains iron and molybdenum
o Dinitrogenase reductase – contains iron
75
What is nitrifying bacteria? What are the 2 groups and what oxidation reaction do they perform?
- Nitrification – oxidation of inorganic nitrogen compounds (ammonium, nitrate, nitrite)
- Performed by nitrifying bacteria
- Nitrifying bacteria are widely distributed in soils and water
- 2 groups of organisms, each performing a different oxidation reaction
o Nitrosomas 2NH4+ +3O2 – 2NO2- +4H+ + 2H2O + energy
o Nitrobacter 2NO2- + O2 — 2NO3- + energy
76
Why is nitrogen fixation and nitrification important?
Nitrogen fixation and nitrification is of enormous importance to plant productivity and for sewerage and wastewater treatment, removing toxic amines and ammonia
77
What are nutrient cycles?
Both microorganisms and microorganisms contribute to nutrient cycling but microbial activities dominate
78
What is the carbon cycle?
- A large amount of carbon is in plants (forests, grasslands, agriculture – major site of CO2 fixation through photosynthesis)
79
What is humus?
- More carbon is bound in humus than in living organisms
o Complex mixture of organic materials that have resisted rapid decomposition, derived primarily from plants and microorganisms
80
What are microorganisms in the carbon cycle?
- The most important contributor of CO2 to the atmosphere
o Microbial decomposition of dead organic material and humus
81
What is the definition of growth in multicellular organisms vs unicellular organisms?
Multicellular organisms:
- Growth involves the whole organism getting bigger
Single celled organisms:
- Growth is defined as an increased number of cells in a population
82
What is binary fission?
- One cell divides into 2
- Prokaryotes and some eukaryotes
- All bacteria
83
What is the process of binary fission?
1) Cell replicates its DNA
2) The cytoplasmic membrane elongates, separating its DNA molecules
3) Cross wall forms membrane invaginates – septum
4) Cross wall forms completely
5) Daughter cells
84
What is generation time?
The time required for one generation to occur
- Highly variable between species
- Also variable within species
o Depends on nutritional and environmental factors such as temperature
- E.coli in a laboratory culture is about 20 minutes
85
Reality check outside of laboratory conditions?
- Cells grow much slower in nature where conditions are not optimised
- Generation times of hours or day are much more common
- Microbial communities in nature also face competition with other species for resources and space
86
What is meant by population growth?
- Bacterial growth is an increase in the number of cells in a population
- So the dynamics of population is what’s measured in a laboratory experiment – not growth of individuals
87
What is exponential growth?
The y axis can be one of 2 scales:
- Arithmetic scale: increase in units of 1
- Logarithmic sclae: increase to the power of 10
o Referred to as semi logarithmic graphs (x axis is still linear)
- Semi logarithmic graphs can be used to estimate generation time
o G = generation time
o T = time
o N = number of generations in time t
o G = t /n
88
What is the lag phase?
- Time between when culture is inoculated into fresh media and significant growth
- Length varies – depends on the history of the inoculum, nature of the medium and growth conditions
o Longer lag: cells are depleted of essential constituents, time is required for their biosynthesis. Cells must start synthesising essential metabolites. Time taken to do this results in a delay before growth
89
What is the exponential phase?
- Cell population doubles at regular intervals
- Depends on availability of environmental conditions (temperature, nutrients etc) and genetic characteristic of the organism
- The healthiest cell state
90
What is indefinite growth?
- Organisms growing in an enclosed vessels cannot grow exponentially indefinitely
91
What is the stationary phase?
- Essential nutrient in the culture medium runs out
- Organisms waste products build up to toxic levels
- No net increase or decrease in cell numbers
- Growth rate = 0
- Cell growth = cell death
92
What is the death phase?
- Exponential decline of viable cells
- Rate of cell death typically faster than the rate of growth
- Viable cells may remain in culture for months or even years
93
3 ways to measure growth?
1. Microscopic counts
2. Viable counts
3. Spectrophotometry
94
What are microscopic counts?
- Count the number of cells present
- Samples dried onto slides or liquid samples
o Can be stained to increase contrast between cells and their background
o Use a counting chamber or a flow cytometer
95
What are viable counts?
- Viable cell = able to divide and produce offspring
- These are usually the cells we’re most interested in
- AKA a plate count
- Main assumption – each viable cell will divide to form one colony
96
What is the spread plate method? What is further required?
Spread plate method
- Sample is pipetted onto surface of agar plate
- Sample is spread evenly over surface of agar using sterile glass spreader
- Typical spread-plate results
Must do a serial dilution to get an appropriate number of colonies
- 1 colony = 1 original cell from sample
97
Sources of error in growth?
- Culture medium, incubation conditions and incubation have a big effect
- In mixed cultures
o Not all cells grow at the same rate (different generation times)
o Colony sizes vary – may miss small ones
- Inaccurate pipetting, non-uniform sample (cell clumps), insufficient mixing, heat intolerance (if poured plates are used)
98
What is Spectrophotometry?
- Cells scatter light
- Turbidity can be used to estimate cell mass in a sample
- More light scattering = more cell mass = more cells
99
What are the issues with Spectrophotometry?
- It is quick and easy but –
- Turbidity does not equal number of cells (but the 2 can be assumed to be related)
o Cell size matters
o Debris causes false positives
o Cell clumping messes with reading
- Different light measurements also give different density measurements
- Can only be used with clear broths
100
What is microbial ecology?
- Like macroorganisms (animals and plants), microbes have an ecology
- A certain species lives in certain places but not others
- Environments differ in their ability to support diverse microbial populations
101
What is an ecosystem?
- A dynamic complex of plant and microbial communities and their non-living surroundings which interact as a functional unit
102
Microbes in ecosystems?
- Great metabolic diversity
- Primary catalysts of nutrient cycles
- Very important members of the ecosystem
103
What are microenvironments?
- Microorganisms are very small so only directly experience a tiny local environment
- For a typical 3um bacterium, a distance of 3mm is like 2km for a human
- Metabolic activities from microorganisms can alter the conditions
- Numerous micro environments can exist within a given habitat
104
Why is diffusion important for microbes?
- If you are small, diffusion often determines the availability of resources
- Use microelectrodes to measure the oxygen concentration in a soil particle
- Many microenvironments within a very short distance
- Microorganisms near outer edges consume all oxygen before it can diffuse to the centre
- Anaerobic organisms thrive near the centre
- Aerobic organisms live in the outer layers
105
What are habitats? Different types?
- Pathogenic/symbiotic associations with plants/animals/humans/eachother
- Terrestrial
o Soils
o Subsurface
- Aquatic
o Freshwater
o Coastal/ocean
o Deep sea
106
Describe microbial growth in soils.
- Most extensive microbial growth takes place on surfaces of soil particles
- Highly promoted in the rhizosphere – roots exclude nutrients which microbes can absorb
107
How does water availability affect microbes?
- Water content of soil highly variable
- Depends on soil composition, rainfall, drainage and plant cover
- Water has minerals dissolved in it = soil solution
- Water content also affects oxygen levels, water logged = low oxygen
108
How does nutrient availability affect microbes?
- Greatest microbial activity in organic rich soil surface layers
- Especially around rhizosphere
- Numbers and activities of microbes greatly depends on type and amount of nutrient present
109
What is the subsurface?
- Groundwater – water in soils and rocks deep underground
- A little explored microbial habitat
- Microbial life extends down at least 3km into the earth
- May account for as much as 40% of global biomass
110
Are microbes just surface level?
- Chemolithotrophic and autotrophic bacteria and archaea found at 3km deep in South Africa
- Must survive on a very nutrient poor diet
- Probably use H2 as the electron donor for respiration
- Nitrogen fixing capacity
111
What is meant by highly variable conditions?
- Cell numbers in ground water vary by several orders of magnitude (10^2-10^8 per ml)
- Due to nutrient availability – especially dissolved organic carbon
- Generation time vary from days to centuries
- Data is scarce
112
What are aquatic habitats?
- Freshwater vs marine differ in many ways
o Salinity
o Average temperature
o Depth
o Nutrient content
113
What are freshwater habitats?
- Highly variable in resources and conditions
- Both oxygen consuming and oxygen production organisms present
- The balance controls the cycle of nutrients
114
What are oxygenic phototrophs? What are the 2 types?
- Include algae and Cyanobacteria
- Primary producers
o Energy comes form light
- Plankotonic
o Floating
- Benthic
o Attached to bottom off sides of lake/stream
115
How can habitat change with depth?
- Water column in lakes becomes stratified
- Transition zone
- During winter the surface waters cool and sink to the bottom
- Layers get mixed
- Seasonal changes to bottom layer
116
What is organic rich wastewater?
- Decrease in O2 caused by spike in bacterial respiration
117
Describe microbes in coastal and ocean waters.
- Very low nutrient levels, especially nitrogen, phosphorus and iron
- Water temperatures are cooler and are more constant with seasons than freshwater
- Overall microbial numbers are lower in marine compared to freshwater habitats 10^6/ml vs 20^7 / ml
118
Describe microbes in the ocean.
- Very small cells
o Typical characteristic of living in nutrient poor environment
o Requires less energy for cell maintenance
- Require greater number of transport enzymes relative to cell volume to acquire nutrients from very dilute environment
119
Why are oceanic microbes important?
- Oxygenic photosynthesis in the oceans is a major factor in controlling the earths carbon balance
- Because oceans are so large
- Coastal areas of more productive (distribution of chlorophyll)
120
How does growth change with depth?
- Bacteria predominate in waters above 1000m
- Photic zone = where light can penetrate to
- Oceans contain the largest microbial biomass on the surface of the earth
121
What are hydrothermal vents?
- Underwater hot volcanic springs
- Found 1000m to greater than 4000m deep
122
What are abiotic growth factors?
Organisms must be finely tuned to their conditions
1) Nutrient availability
2) Temperature
3) PH
4) Moisture
5) Oxygen
6) Pressure
7) Light
123
What are the 3 cardinal temperatures?
- Arguably the most important factor effecting growth
- All specie have:
o Minimum temperature – growth isn’t possible below (membrane gelling, transport processes so slow that growth cannot occur)
o Optimum temperature – growth is most rapid (enzymatic reactions occurring at maximal possible rate)
o Maximum temperature – growth isn’t possible above (protein denaturation; collapse of the cytoplasmic membrane; thermal lysis)
- These are called the cardinal temperatures
o Different for every species
124
What does variation in cardinal temperatures between species result in?
Cardinal temperatures vary between species
- 4 broad classes of microbes according to their temperature optima
o Psychrophile (4*)
o Mesophile (39*)
o Thermophile (60*)
o Hyperthermophile (88*)(106*)
125
How does pH vary between habitats?
- Alkaliphiles
- Audiophiles
126
What are the pH effects on microbial growth?
- Most microbes show a growth range of 2-3 pH units
- Most natural environments have a pH between 4 and 9
- Organisms optimised to this range are most common
127
What is internal cell pH?
- Optimal pH – measure of the extracellular environment
- The intracellular pH must remain relatively close to neutrality
128
Describe oxygen in microbes.
- Microbes have different oxygen requirements
- Oxygen is poorly soluble in water
- Oxygen can quickly become exhausted so anoxic (o2 free) habitats are common
o Muds, bogs, marshes, waterlogged soils, intestinal tracts, sewage sludge, deep subsurface
- Can be aerobic, anaerobic, facultive, microaerophilic, aerotolerant
129
What is meant by aerobic?
- Grow at full oxygen tensions
- Respire oxygen
- Eg staphhyloccocus aureus (common cause of skin infections)
130
What is meant by anaerobic?
- Cannot respire
- Obligate anaerobes are inhibited or even killed by oxygen
- There are no anaerobic algae
- Eg clostridium botulinum, causes botulism
131
What is meant by facultative?
- Under appropriate conditions will either grow inner oxic or anoxic conditions
132
What is meant by microaerophiles?
- Aerobes that can use o2 when its present at levels lower than air
- Eg campylocbacter jejuni, causes food poisoning
133
What is meant by aerotolerant?
- Anaerobic but can tolerate oxygen
- However they do not use oxygen in their metabolism
- Eg cutibacterium acnes, causes acne
134
What is an extremophile?
- An organism whose growth is dependent on extremes of temperature, salinity, pH, pressure or radiation, which are greatly inhospitable to most forms of life
135
What are the coldest environments for microbes naturally?
- Oceans
o Over half the worlds surface
o Average 5*
o 1-3* in depths
- The poles
o Vast areas permanently frozen
- Glaciers
o Network of liquid water channels that are teeming with microorganisms
136
What are 2 important distinctions between seasonality in environments?
- Environments that are constantly cold
o Antarctic lakes have permanent ice several meters thick
- Environments that are seasonally cold
o Could have summer temperatures as high as 40*c
137
What is a pscyhrophile?
- Optimal growth temperature 15*c or lower
- Max growth temperature 20*c
- Killed by warming, found in constantly cold environments
- Psychromonas – sea ice bacterium – grows at -12*c – longest known
- But probably can go lower
- Some enzymes found to function at -20*c
138
What is psychrotolerant?
- Can grow at 0*c
- Optima is 20-40*c
- More widely distributed
- Found in temperature climates, meat, dairy products, cider, vegetables and fruit as standard refrigeration temperatures
139
What are the 2 main molecular adaptations to the cold?
- Enzymes have optimal activities at low temperatures
o Molecular basis not fully understood
o Primary structure: more polar amino acids, fewer weak bonds
o Secondary structure: greater a-helix, less b-sheet, gives protein greater flexibility (b-pleated sheets are quite rigid)
- Cytoplasmic membranes must remain functional
o High content of unsaturated and shorter chain fatty acids
o Helps membrane remain in semifluid state at low temperatures
140
What are cold shock proteins?
- Maintain other proteins activity and bind specific mRNAs to facilitate their translation
- Not limited to psychrophiles – eg found in e.coli
141
What are cyroprotectants?
- Solutes (eg glycerol or sugars) that help prevent the formation of ice crystals in the cell
142
Name some environments that have hotter temperatures.
- Surface soils
o In full sunlight can heat above 50*c at midday
- Compost heaps/silage
o Fermenting materials can reach 70*c
- Host springs
o Most extreme high-temperature environment
- Terrestrial
o Temperature around boiling point
- Hydrothermal vents
o Can be 350*c or greater
143
What is a Thermophile?
- Growth temperature optimum greater than 45*C
- Less extreme than the hyperthermophiles
- Found in a wide range of habitats
o Edges of hot springs
o Soil surfaces
o Fermenting environments
o Artificial environments eg hot water heaters
o This list is no where near exhausted
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What is a Hyperthermophile?
- Growth temperature optimum greater than 80*c
- Found in hot springs
- Only prokaryotes
- Growth rates often quite high – generation times as short as 1hr have been recorded
- The most heat-tolerant example is Methanopyrus – can grow at 122*c
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What are species gradients?
- As boiling water leaves hot springs it cools, creating a thermal gradient
- Different species grow at the different temperatures along the gradient
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What are the 3 things learned from studying temperature gradients?
1. Prokaryotes can grow at much higher temperatures than eukaryotes
2. Archaea are the most Thermophilic of all prokaryotes
3. Non-phototrophic organisms can tolerate higher temperatures than phototrophic organisms
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What are the key molecular adaptations to high temperatures?
- Heat stable enzymes and proteins
o Amino acid sequence often differs very little from heat sensitive forms
o Critical amino acid substitutions at a few locations allow the protein to fold in a heat-stable way
- More ionic bonds between basic/acidic amino acids
- Often highly hydrophobic interiors
- All make protein more resistant to unfolding
- Increased DNA stability
o Increase cellular compatible solute levels – prevents chemical damage to DNA
o Reverse DNA gyrase – a special DNA topoisomerase only found in hyperthermophiles, introduces positive super coils into DNA (rather than negative, as in other prokaryotes), more heat stable
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What does heat usually do to lipid bilayers?
Heat usually peels apart lipid bilayers
- Heat stable membranes
- More saturated fatty acids
o Form a stronger hydrophobic environment
- More long chain fatty acids
o Have a higher melting point
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What are Hyperthermophile membranes?
- Do not contain fatty acids
- Have C40 hydrocarbons (repeating units of isoprene) bonded to glycerol phosphate by ether (rather than ester) link
- Forms a monolayer
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What are acidophiles?
- Grow best at pH 5.5 or below
- Different classes optimised to different pHs
- Those with a pH optima of below 1 are very rare
- Most cannot grow above 7
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What are alkaliphiles?
- Grow best at pH 8 or above
- A few extremophiles have a very high pH optima – as high as pH 11
- Found in environments such as soda lakes and high carbonate soils
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What are alkaphile bioenergetics?
- In an alkaline environment, external H+ will be very low
- How to generate a proton motive force for transport?
o Use sodium instead
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What is cytoplasmic pH?
- Must remain near neutrality
- Optimal pH for growth refers to extracellular environment only
- Intracellular pH must stay near pH 7 to prevent destruction of macromolecules
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Why does salt cause problems?
- High salt – makes solute potential of environment more negative
- Osmotic gradient out of the cell
- Makes extracting water from the surrounding very difficult
- Physiological drought
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High salt environments?
- Sea water 3% NaCl
- Salt lake (eg Utah) 42% NaCl
- The Dead Sea 34% NaCl
- Also salt foods
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What are halophiles and halotolerant?
- Halophiles require NaCl for growth
- Halotolerant – can tolerate NaCl but grow best in absence of solute
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How to prevent water leaving the cell into hypertonic environment?
- Increase the internal solute concentration
- But can’t just let NaCl into the cell – its toxic
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What are compatible solutes? Charged ions? Neutrally charged?
- Organic compounds which are highly soluble and don’t interphere with cellular metabolism
o Charged ions – penetrate hydration shells of proteins and interfere with non covalent bonding
o Neutrally charged – do not penetrate hydration shell of protein
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Examples of compatible solutes
- Glycine betaine
- Sucrose
- Trehalose
- Glycerol
