F3 Microbial diversity Flashcards
Factors that influence growth
- temperature
- pH (acidic, alkaline conditions)
- salts
- pressure (osmotic or physical)
- light
- oxygen
- radiation
?: greek for loving, an organism that thrives in a certain condition
?: an organism that can endure a certain condition
?: organism growing under ’normal’ conditions
-phile
-tolerant
mesophile
extremophiles are often archaea, but bacteria and fungi can be extremophiles as well
examples of extremophiles:
- thermophile (hot springs, over 100 °C possible)
- psychrophile (ice caps, up to -20 °C)
- acidophile (acid mine drainage)
- alkaliphile (soda lakes, often also halophile)
- halophile (salt lakes)
- piezophile (deep sea, often also psychrophile)
temperature affects the membrane …
fluidity
Adaptation to extreme temperatures, Psychrophiles:
proteins
• more alpha helices, less beta sheets
• more polar, less hydrophobic amino acids
• fewer protein-protein interactions
membranes
• short fatty acids
• unsaturated fatty acids
• branched fatty acids
stress repsonses
• cold shock proteins (stabilize RNA)
• cryoprotectants (e.g. glycerol)
Adaptation to extreme temperatures, Thermophiles:
proteins • more beta sheets, less alpha helices • more hydrophylic amino acids on the surface (increased interactions) • many hydrophobic amino acids in the core (protection against unfolding in aqueous environments) • many protein-protein interactions
membranes
• long, unbranched fatty acids
• fully saturated lipids
• isoprene lipids (similar to cholesterol)
stress responses
• heat shock proteins
why is thermophiles and their enzymes interesting for biotechnology?
+ give examples of use
- higher temperture -> higher reaction speed -> more efficient production
- less risk of contamination
- thermostable enzymes are often generally more stable
examples of use:
• PCR polymerases (thermostability)
• biofuel production (butanol resistance)
Acidophiles
• viable at acidic conditions (pH 1-5)
• extreme: Picrophilus oshimae optimum pH 0.7, 60 °C
• many yeasts (e.g. baker’s yeast) can survive at pH 2.5 to over 7
• many bacteria (lactic acid bacteria, acetobacteraceae)
• most pathogens do not like low pH
-> conservation method (sauerkraut)
-> skin pH 5.5
-> exception: Helicobacter pylori (stomach ulcers)
Alkaliphiles
• viable at high pH (8-11)
• produce many alkaline-stable enzymes, e.g. lipases, proteases
-> laundry detergent
- acidic conditions can damage … , proteins, and membranes
- alkalic conditions can damage … , proteins, and membranes
RNA
DNA
both acidophiles and alkaliphiles regulate their intracellular pH by …
transport of H+
- obligate aerobe: …
- obligate anaerobe: …
- facultative anaerobes: …
- aerotolerant anaerobes: …
- microaerophiles: …
- obligate aerobe: needs O2
- obligate anaerobe: O2 is toxic
- facultative anaerobes: grow better with O2 but can also live under anaerobic conditions
- aerotolerant anaerobes: do not need O2 to grow, but are not sensitive to it
- microaerophiles: need a specific level of low O2 concentrations
Growing aerobic bacteria
- never fill up a flask completely (10% of the volume)
- always shake
- oxygen depletion -> stress
- once cells shift to anaerobic metabolism, it takes time to adapt to aerobic metabolism again (long lag phase)
Growing anaerobic bacteria
- N2 to deplete O2
- Anaerob jar with Petri plates
- Openings of an anaerobic box sealed by glove-like sleeves for handling of cultures inside the box
examples of anaerobic microbes (fermentation: no O2)
lactic acid bacteria, yeast
examples of reactive oxygen species (ROS, reaktiva syreföreningar):
singlet oxygen
superoxid anjon
väteperoxid
hydroxyl radikal
oxidative stress causes …
cellular damages
- oxidation of enzyme metal centers
- oxidative lesions (skada) in protein, DNA and lipids
oxidative stress response
- activation of regulators
- up-regulation of scavenging (renhållnings-) enzymes
- repair of cellular damages
exempel på enzymer som bryter ner toxiska syreformer:
katalas
peroxidas
superoxid dismutas
osmotic stress
hypertonic pressure: …
isotonic pressure: …
hypotonic pressure: …
hypertonic pressure: more solutes, less solvents
isotonic pressure: same concentration of solutes and solvents
hypotonic pressure: less solutes, more solvents
Mechanosensitive channels
Mechanosensitive channels respond to membrane tension by altering their conformation between an open state and a closed state.
Spores
A spore is a cell that certain fungi, plants (moss, ferns), and bacteria produce. Certain bacteria make spores as a way to defend themselves. Spores have thick walls. They can resist high temperatures, humidity, and other environmental conditions.
macronutrients / micronutrients / growth factors
macronutrients • necessary for growth • large amounts • basis forcellular macromolecules • ion homeostasis
micronutrients • necessary for growth • small amounts • trace metals • co-factors in enzymes • varies greatly between organisms
growth factors
• organic molecules
• can normally be synthesized by the cells
• improve growth when added to medium
Chemical composition of a cell
carbon source: ..
nitrogen source: …
phosphorus source: ..
sulfur source: …
carbon source: organic molecules, often sugars but also glycerol possible for example
nitrogen source: amino acids, ammonium
(some bacteria can use nitrate or nitrite, some bacteria can use N2 -> nitrogen fixation)
phosphorus source: phosphates
sulfur source: sulfate
growth media
complex full media: …
defined (minimal) media: …
selective media: …
differentiation media: …
complex full media: contains everything the microbe needs, derived from microbial or animal sources, exact composition often
unknown, eg. LB
defined (minimal) media: all nutrient the microbe needs are mixed together, composition is known,
selective media: media that allow growth of some bacteria, but not others, eg. glycerol as carbon source
differentiation media: media that allow growth of several species, but allow distinction between them, eg. pH-indicators
MacConcey agar plates is an example of a … medium.
It uses the pH indicator …, which turns pink at … pH
differentiation
neutral red
low
phototroph: …
chemotroph: …
heterotroph: …
autotroph: …
phototroph: energy source is light
chemotroph: energy source is chemical (e.g. sugars)
heterotroph: carbon source is an organic chemical
autotroph: carbon source is CO2
Phototrophic bacteria
- bacteria that can use sunlight as primary energy source
- generate ATP through photosynthesis
- use Calvin cycle to fix carbon from CO2 (make CO2 into glucose)
Chemoautotrophs and chemolithotrophs use … carbon and energy sources
inorganic
- often live in difficult habitats where no other organisms can survive
- often do not tolerate oxygen (obligate anaerobe)
- often also tolerate high temperatures
- often archaea, but also bacteria
Methanogens
Microorganisms producing methane in the absence of oxygen (or with very little oxygen)
Chemoheterotrophs use … carbon and energy sources
organic
all organisms need nitrogen, but why?
- nitrogen is essential for proteins (amino acids)
* nitrogen is also essential for DNA and RNA (nucleobases)
all organisms need sulfur, but why?
- sulfur is important for protein synthesis (methionine)
* sulfur compounds help detoxifying ROS
bacteria help converting … and … between its different forms and make it accessible for different organisms
nitrogen
sulfur
