Microbial Lifestyles and Metabolism (Dr. Kreft) : Nutrients and Media Flashcards
What is the volume of a single cell of E. coli?
1um^3= (10^-6um)^3= 10^-18= 10^-15L = 1fL (femto)
What is the weight of E. coli?
- 80% is water
- density of the cell is only slightly higher than water (5-10%)
-water= 1000g/L
-mass= density * volume
= 10^3g/L * 10^-15L= 10^-12g =1pg (pico)
Consequences of being small?
- experience the world differently (wind can transport them around the world. Their speed of sinking is too slow ..it takes years to travel the world).
- water: coasting when stopping to swim, stopping dead immediately, flagellum more like a cork screw
- Eating: sit there and food comes to them via diffusion …diffusion very fast on um(ms) but very slow on cm scale (dye)
Because microorganisms are tiny, they?
- are very dependent on the enviornment, cannot adjust temp, pH etc. They take on the conditions of the enviornment.
- reproduce fast –> very large numbers
- evolve fast -> also high rate of dispersal
- small and simple cell –> they master metabolism
- large surface area to volume ratio.
What are their two growth requirements?
- Energy
2. Nutrients
Growth Requirements:
- Energy?
- source = catabolism
L> Light: phototrophs
L> Chemical reactions: Chemotrophs
Growth Requirements:
- Nutrients?
- precursors for the synthesis of biomass (anabolism)
- may need organic growth factors
What elements do microbes need to grow?
- N, C, O, H, S, P (similar to composition of RNA/DNA and proteins)
- metal ions: K, (Na), (Ca), Mg and (Fe)
- Macronutrients : the above elements
- Micronutrients: (Fe), others as well
What growth factors do microbes need to grow?
- vitamins (coenzymes)
- Amino acids
- purines, pyrimidines, etc
- *they range from needing none to needing more than us
Macronutrients:
-what is the biomass composition of a microbe?
- approximately 50% carbon and 10% nitrogen
Macronutrients:
- example biomass comp of yeast ash?
- C48%, H 7%, O 36%, N 9%
Macronutrients:
- why do they need N?
- Nitrogen content on wood is low …growth would stop because of this so microbes need a high concentration of nitrogen.
Carbon sources?
- CO2 –> atmospheric microbes (autotrophs)..phototrophic or chemotrophic (light or chemical energy)
- Organic compounds as carbon source = heterotroph
L> phototrophic or chemotrophic
L>organic carbon also used as energy source ( as electron donor, oxidized with oxygen etc as electron acceptor)
Oxygen in catabolism acts as what?
- an electron acceptor in aerobic respiration (also reacts with enzymes)
What are oxygen sources for anabolism?
H2O, O2, organic compounds
Oxygen relationship with microbes - three types!
- oxygen in air saturated water only ~250uM
- quickly gone, especially when a lot of organic matter is decomposed
- gut, sewage treatment, lake/ocean sediments, rice paddles, subsurface
1. Aerobe, 2. Facultative aerobe and 3. Anaerobe
Aerobe?
- only grows in the presence of oxygen and requires oxygen
ex: homo, Bacillus, Pseudomonas
Facultative aerobe?
- aerobe that can grow without oxygen, using anaerobic respiration or fermentation (E. coli)
Anaerobe?
-does not grow in the presence of oxygen and does not use oxygen ( Clostridium, Methanobacterium(methanogenic archaeon), some fungi and protozoa)
Nitrogen:
- biomass %?
10% of biomass: amino acids, bases in DNA/RNA etc
Sources of Nitrogen?
- NH3(ammonia): all bacteria can use this as N-source and that is the form of N incorporated into amino acids
- Organic compounds like amino acids
- NO3 (nitrate): needs to be reduced to NH3 before it can be incorporated not biomass, not all bacteria can do (need enzymes to do this! Aerobic environments = already in reduced form therefore bacteria can’t do nitrogen fixing)
- N2 (di)nitrogen: needs to be reduced to NH3 too, some bacteria and archaea (but never eukaryotes) can do that (Azotobacter and other nitrogen-fixing prokaryotes)
Macronutrients continued:
- H sources?
- H2O, H2, organic compounds
Macronutrients continued:
- P source?
- PO4 3-
- P mostly oxidized in biomass, e.g. ATP, nucleic acid backbone, phospholipids, sometimes reduced like N or S
- *faster growing cells need/ have more P (needs lots of RNA to grow)
Macronutrients continued:
- S sources?
- sulphur (sulfur) (thio-> i aa it is in the reduced form)
- SO4 2- (sulphide can be used directly)
L> most bacteria can reduce sulphate to H2S - H2S
L> can be directly incorporated into amino acids etc
L> not present in aerobic habitats as it chemically reacts with oxygen
L> anaerobic bacteria may use it as it’s easier to incorporate into biomass
Macronutrients continued:
- cation metals?
K, Na, Ca and Mg
**positively charged –> cations
Macronutrients continued:
- Potassium (K)?
-required for the activity of many enzymes. K is compatible at high concentrations in the cell, Na not, so cells pump Na out and K in
Macronutrients continued:
- Sodium (Na)?
- not all organisms need it
- many contain some Na but do not use it, less compatible than K
- some use it instead of H+ (sodium motive force
Macronutrients continued:
- Calcium (Ca)?
-stabilizes cell walls, large amount in endospores
Macronutrients continued:
-Magnesium (Mg)?
- ATP really is Mg/ATP
- Mg required for stability of nucleic acids/ ribosomes, membranes
Macronutrients continued:
-Anions?
- to balance charge, eg Cl- or organic acids (electroneutrality –> cells need to be this)
Micronutrients:
- Most need Fe why?
- to make cytochromes and FeS proteins for electron transport chains
Micronutrients:
- example of one that does not need Fe?
- Lactic acid bacteria (fermentation of sugar does not need respiratory chain) Lactobacillus acidophilus
- *aka organisms that do not respire
Micronutrients:
- Fe, solubility issues?
- solubility low therefore difficult to get
L> Fe 2+ is relatively soluble, but oxidizes (rusts) in presence of oxygen
L> Fe 3+ (rust) very low solubility at neutral pH..solubility product of Fe(OH)3 (i.e. fresh rust) = 10^-38
L> between pH 0-3, Fe 3+ is soluble (its hard to extract Fe from the environment with oxygen present)
L> many bacteria produce siderophores to scavenge Fe from the environment (iron carrier –>excrete compounds that capture Fe)
L> These have very high affinity for Fe
L> usually chelated by catechol or hydroxamate groups
Micronutrients:
- Fe aids with defence against?
- pathogens: keep Fe concentration in body very low (Lactoferrin, transferrin) -> nutritional immunity
- the affinity of transferrin for Fe(III) is extremely high (10^23 M-1 at pH 7.4)
- Lactoferrin affinity for iron is 300 times higher
Micronutrients:
- other transition metals that are important with enzyme reactions?
- Mn, Co, Ni, Cu, Zn, Mo, W
L> like vitamins in active sites of enzymes
L> only traces required
L> often enough in distilled water and other media components –> this is why we do not add them
Micronutrients: Other trace elements?
- Se
Micronutrients:
- how do we apply knowledge on requirements of trace metals in the rearward?
- waste water treatment plants have an anaerobic digester stage where aerobic sludge is digested to produce methane
- biotechnology
Micronutrients:
- How can methane production be improved?
- adding trace elements to the digester improved productivity by about 40%
What is never required by microbes? (nutrients wise)
- Arsenic
What nutrients are not always used by all microbes?
- Na, Fe, Ca
Is it possible to grow in medium with not highly pure water and air alone?
- Tap water and air would be enough for phototrophic organisms using light energy. Also methane in the air (at 2ppm) is sufficient as carbon and energy source for some bacteria (methanotrophs)
What are the four types of media commonly used when growing microbes?
- Defined media
- Minimal media
- Complex media
- Solid or liquid media
Describe a defined media
- you know exactly what molecules are in the medium and how much
- essential for physiological studies
- can be a long list of components
- can contain more than necessary
Describe a minimal media
- a defined medium that only contains what is essential
- ex: lactic acid bacteria need ~40 growth factors
Describe a complex media
- usually digested animal or plant matter
- beef extract = boiled cow
- contains lots of goodies but who knows what
solid vs liquid media??
- solid medium same as liquid medium but agar brother solidifying agents are added
- solid medium to check for purity or isolate cultures
Luria-Bertani medium contains??
- 10 g tryptone
- 5 g yeast extract
- 10g NaCl
- Tryptone: casein (predominant milk protein) digested by the protease trypsin
- Yeast extract: autolysed (self digested) yeast cells - contains everything yeast and other organisms need
Is Luria-Bertani medium a defined medium?
- no ! Tryptone and yeast extract are undefined containing 1000+ molecules in unknown/ varying proportions
Minimal Medium for E. coli:
- Amounts per L distilled water, pH 7 :
- K2HPO4 7g
- KH2PO4 2g
- (NH4)2SO4 1g
- CaCl2 0.02g
- Glucose 5g
- Is there anything missing?
- Magnesium (Mg)
* *all required trace elements including Fe are provided but not listed
