week 4 - what microbes need to live

Question 1

what microbes?

Answer 1

energy

nutrients

Question 2

what microbes
- energy

Answer 2

o Energy sources (catabolism)
 Light: phototrophs
 Chemical reactions: chemotrophs

Question 3

what microbes
- nutrients

Answer 3

o Precursors for the synthesis of biomass (anabolism)
o Which elements do microbes need to grow?
o Some bacteria may need organic growth factors

Question 4

what nutrients do microbes need to grow
elements

Answer 4

o C, O, H, N, S
o Composition of proteins and DNA/RNA
o Ass metal ions: K, Mg
 Not required by all but a large no.: Na, Ca, Fe
o Macronutrients: the above elements
o Micronutriens: Fe and many others

Question 5

what nutreints do microbes need to grow
growth factors (organic compounds)

Answer 5

o Requiremenys vary from non to many (some bacteria have more essential amino acids than us)
o Vitamins (coenzymes), amino acids, purines, pyrimidines, etc.

Question 6

macronutrients (overview)

Answer 6

• Biomass composition
  o Approx.. like a carbohydrate (e.g. glucose): <Ch2O>n
  o Plus nitrogen
   Example biomass composition: yeast ash free dry mass:</Ch2O>
• C1H1.83o0.56N0.17
• In mas C48%, H7%, O36%, n9%
  o Rule of thumb need to remember
   C 50 %
   N 10%
  Simplified
• Petroleum (oil spill), loads of carbon but little nitrogen, microorganism needs nitrogen –> so microorganisms cannot grow in petroleum… so if want to clean up oil spill addition of nitrogen aids this (fertilizer)

Question 7

Macronutrients: Carbon (C)

Answer 7

• Carbon sources:
  o CO2 as carbon source: autotrophic microbes (autotrophs)
   Phototrophic or chemotrophic
• Photo trophy and autotrophy are not coupled
  o Organic compounds as carbon source (heterotrophs)
   Phototrophic or chemotrophic
• Organic carbon also used a energy source (as electron donor that is oxidised with oxygen, nitrate, sulphate etc. as electron acceptor)

Question 8

Macronutrients: Oxygen (O)

Answer 8

• Oxygen in catabolism:
  o Electron acceptor in aerobic respiration (must be O2)
  o Not forming part of biomolecules
• Ocygen sources for anabolism
  o Oxygen eneters synthesi of biomolecules in the form o H2O, O2 (required to make cholesterol), other organic compounds)
• Oxygen relationships (Brock p. 196-200)
  o Oxygen in air saturated water only ~250uM
  o Quicly gone, especially when a lot of organic matter is decomposed
  o Gut, sewage treatment, lake/ocean sediments, rice paddies, subsurface

Question 9

aerobe

Answer 9

o Only grows in the presence of oxygen and respires oxygen (Homo, Bacillus, Psedomonas)

Question 10

• Facultative anerobe

Answer 10

Aerobe that can grow without oxygen, using anaerobic respiration or fermentation (E. coli)

Question 11

• Anaerobe

Answer 11

o Does not grow in the presence of oxygen and does not use oxygen (Clostridium. Methanobacterium (methanogenic archaeon), some fungi and protozoa

Question 12

Macronutrients: other
hydrogen

Answer 12

o H20, H2, organic compounds

Question 13

Macronutrients: other
nitrogen

Answer 13

o NH3 (ammonia, can be used by all bacteria and is the reduced form of N incorporated into amino groups)
o NO3- (nitrate needs to be reduced to NH3 before it can be incorporated, not all bacteria can do that)
o N2 (dinitrogen needs to be reduced to NH3 too, only some nitrogen foxing prokaryotes can do that)
o Organic nitrogen compounds

Question 14

macronutrients
sulphur

Answer 14

o SO4^2- (sulphate, most bacteria can reduce sulphate to sulphide)
o H2S (sulphide, reduced form that can be directly incorporated into cysteine, toxic, reacts with oxygen

Question 15

macronutrients
phosphorous

Answer 15

• PO4^3- (phosphate, full oxidised, no need to reduce before incorporation into biomass unlike nitrate and sulphate

Question 16

macronutrients: metal and anions
potassium

Answer 16

 K required for the activity of many enzymes
 K is compatible at high concs. In the cell, Na+ not, so cells pump Na+ out and K+ in

Question 17

macronutrients: metal and anions
sodium

Answer 17

o Na: sodium, Na+ (not needed by all)
 Many contain some Na but do not use it, it is less compatible than K
 Some use a sodium motive force instead of a proton motive force

Question 18

macronutrients: metal and anions
calcium

Answer 18

o Ca: Calcium, Ca+ (not needed by all)
 Stabilizes cell walls, large amount in endospores

Question 19

macronutrients: metal and anions
magnesium

Answer 19

o Mg: Magnesium, Mg+
 ATP really is MgATP
 Mg required for stability of nucleic acids/ribosomes, membranes

Question 20

macronutrients: metal and anions
anions

Answer 20

• Anions to balance charge
  o E.g. Cl- or organic acids (electroneutrality)

Question 21

micronutrients
iron

Answer 21

e (iron)
- Most microbes need Fe to make cytochromes and FeS protein for electron transport chains
- By taking iron away can strop microorganisms from growing
- But not all:
o E.g. lactic acid bacteria (fermentation of sugar does not need a respiratory chain), Lactobacillus acidophilus.

Question 22

micronutrients
iron solubility

Answer 22

• Solubility of Fe low therefore difficult to take up:
  o Fe2+ is relatively soluble, but oxidises (rusts) in presence of oxygen
  o Fe3+ (rust) very low solubility at neutral pH
   Solubility product of Fe(OH)3 = 10^-38
  o Between pH 0-3, Fe3+ is soluble
  o Many bacteria produce sidephores to scavenge Fe from the environment
  o These have very high affinity for Fe
   Usually chelated by catechol or hydroxamate groups

Question 23

micronutrients
iron defence against pathogens

Answer 23

• Defence against pathogens:
  o Keep free Fe concentration in body very low by binding loctoferrin and transferrin (nutritional immunity)
  o Making it difficult for bacteria to grow in the body
   The affinity of transferrin for Fe(III) is extremely high (10^23M-1 at pH 7.4)
   Lactoferrin affinity for irn is 300 x higher (protection, keeps milk from spoiling)
  o Demonstrates the importance of nutrition for immunity
   Bacteria fight for iron

Question 24

micronutrients
other transition metals

Answer 24

o Mn, Co, Ni, Cu, Zn, Mo, W
 Like vitamins in active sites of enzymes
 Only traces required
 Often enough in ‘distilled’ water and as impurities in other media components

Question 25

micronutrients
other trace elements

Answer 25

Se
- ‘rare’ ‘earth’ elements (lanthanides)
o Used as fertilizer and recently shown to ve required for some bacterial methanol dehydrogenases (pol et al., 2014)

Question 26

media for growth
- defined media

Answer 26

o You know exactly what molecules are in the medium and how much
o Essential for physiological studies
o An contain a long list of components
o Can contain more than necessary

Question 27

media for growth
- minimal media

Answer 27

o A defined medium that only conatins whats essential
o Lactic acid bacteria need ~40 growth factors so a minimal media may contain many different components

Question 28

media for growth
complex media

Answer 28

o Usually digested animal or plant matter
o Beef extract = boiled cow
o Contain lots of goodies but who knows what

Question 29

media for growth
LB: lysogeny Brothe

Answer 29

(a.k.a Luria-Bertani medium) contains per L
- 10g typronw
- 5g yeast extract
- 10g NaCl
- Tryptone: casein (predominant milk protein) digested by the protease trypsin
- Yeast extract: autolysed (self-digest) yeast cells
o Contains everything yeast and other organisms need
- This is a DEFINED MEDIUM

Question 30

minimal media for E. coli

Answer 30

• Amounts per L distilled water, pH 7
  o K2HPO4 7g
  o KH2PO4 2g
  o (NH4)2SO4 1g
  o CaCl2 0.02g
  o Glucose 5g
• Assume all required trace elements including Fe are contained in the water at sufficient concentration so they are not listed here