Extreme Environments I: acidophiles and alkaliphiles Do more for high pH Flashcards
nomenclature
- acidophiles – require low pH to grow.
- alkaliphiles* – require high pH to grow.
- acidotolerant organisms can cope with low pH
- alkalitolerant organisms can cope with high pH
- extreme acidophiles are the organisms that low at the lowest pH, then acidophiles and moderate acidophiles, then neutralophiles
moderate alkaliphiles, alkaliphiles and extreme alkaliphiles.
pH and proton concentration
- three parameters to remember, here for a substance “x”:
- ax = activity of x (various units but usually mol/L) also written as {x} in shorthand
- bx = molality (molal concentration) of x (mol/kg = molal) also written as <x> in shorthand</x>
- cx = molarity (molar concentration) of x (mol/L = molar = M) also written as [x] as shorthand
- you will have been told:
pH = -log10 [H+]
it’s a lie – the truth is:
pH = -log10 [H3O+]
where:
H2O + H+ → H3O+ (hydronium ion) at circumneutral pH in very dilute solutions, [H+] ≈ [H3O+] but as pH lowers, they diverge.
below pH 2.0, we see these dominate:
the magic complex (H3O+(H2O)20)
the Eigen cation (H9O4+)
the Zundel cation (H5O2+)
the Stoyanov cation (H13O6+)
don’t need to learn structures
also note that even [H3O+] is wrong in equation – should be {H3O+} but again, at circumneutral pH,
concentration and activity match up at 1 atm and around 20-30 °C: not true for most ecosystems!
also note most pH electrodes (glass electrodes) don’t work below pH 2 or above pH 12, especially if there is
a lot of Na+ present.
activity=how much its bound up or is free to participate in reactions.
glass pH dont work below 2 (as no longer just [H3O+)or above 12(sodium ions bind to glass so they interfere)
fundamentals (neutrophiles)
- neutralophiles grow at about pH +/- 2 from their intracellular pH which is usually about pH 7.2, so pH 6.2 to pH 9.2 is fairly typical – some have wider and narrower ranges.
- even in extreme acido/alkaliphiles, intracellular
pH is still circumneutral except in Acetobacter spp. in which it is about pH 4.0. (only organism we know that has alow intracellular pH) - the most extreme organisms (as always) are the Archaea.
low pH ecosystems
- stomach of Homo sapiens L. (pH 1.0-1.5)
- vaginal cavity of Homo sapiens L. (pH 3.8-4.5)
- vinegar (pH 2.5)
- acid mine drainage (AMD) (pH -3.5 to +4.0)
- car battery acid (pH 0.5-1.0)
- juice of Citrus spp. L. (pH 3.3-4.3)
- fresh milk from Bos taurus subsp. taurus L. (pH
6.5) - yoghurt (pH 4.3-4.4)
- peat bogs (pH 3.5-6.5)
- soft cheese (pH 5.8-6.0)
- volcanic lakes (pH -2.0 to + 1.0)
AND MANY OTHERS!
what does low pH do to Life?
PROTEINS:
* unfold, losing secondary to quaternary structure, denaturing; at very low pH, primary structure is lost through acid hydrolysis of peptide bonds; loss of enzyme function and structural integrity.
LIPIDS:
* bilayers lose integrity.
* hydrolysis into fatty acids and e.g. phosphoglycerate.
heads and tail ester linkages will break down normally below pH2
NUCLEIC ACIDS:
* at pH > 4, dominant issue is loss of base-base hydrogen bonds in rRNA and DNA, both of which ‘melt’, AT-rich regions first. Why is ssDNA the problem? because you cant translate or do much with them Most enzymes that deal with DNA kike transcription they need both strands What can’t a cell do with ssDNA but can with dsDNA?
* DNA and RNA hydrolyse into oligonucleotides and individual bases at very low pH.
Think about metabolic cost associated with repair? What do you expect would happen to mS. A lot of energy needed to build up bases and then nucleotides so living at this pH is so expensive.
for E. coli at pH 7 versus pH 5?
what does low pH do to Life?
ENVIRONMENT:
- metals generally become more soluble: toxic metals are now mobilised and thus more of an issue.
- in laboratory we can buffer media to maintain a given pH – this also happens in the environment esp. in formation of karsts (cave in limestone) by sulfuric acid from sulfur-oxidisers – also links to how Achromatium maintain internal pH too:
H2SO4 + CaCO3 (limestone) → CaSO4 + H2CO3
H2CO3 → H2O + CO2
water in contact with limestone stays acts as a sort of buffer (acromascian) ??? - carboxylic acids become toxic from their acting as
pseudouncoupling agents – applies to all organisms below pKa of the acid.
fatty acids can cross the membrane but not their salts??? they become toxic and lower pH of cytoplasm and interfere with proton motive forces as it drops a proton and sends itin a different way. Acetate e.g can’t get back out the cell even though it got inside without a transporter.
what does low pH do to Life?
METABOLISM:
- the Δp will break down if cytosol pH drops ([H+] goes up) as you end up no longer building a gradient during respiration.
EXAMPLE BUGS:
Acidithiobacillus ferrooxidans (mines 35% of copper) a CBB chemolithoautotroph that can use Fe(II) or S-compounds. Found in AMD. Used in biotechnology extensively. Grows at pH 2.0.
Acetobacter aceti – a homoacetogen used to make vinegar – intracellular pH is lower and has different adaptations but see Menzer and Gottschalk
Picrophilus torridus resistant to dehydration) from the Archaea, grows around pH 0.
most extremophiles are polyphile e.g hot, acidic (same adaptations work for both stresses)
- Acetobacter-type adaptations
“what to do if protons get in?”
protein sequences are more like those found in thermophiles
* amino acids in proteins generally the negatively charged ones.
* chaperone proteins e.g. DnaK/Hsp70 and chaperonins (GroEL/GroES complex barrel with one lid) can help repair and refold damaged proteins.
* in some Archaea, proteins have Fe(III) ions as ‘rivets’ to hold protein structure more strongly.
pH specific adaptations as neutralophiles don’t have ions.
* deeper ‘burying’ of metal ions in proteins to prevent them
solubilising out as pH lowers.
N.B. as well as being the ‘last resort’ for other bugs, these adaptations are also common in membrane proteins in the other groups.
“keep the badness out”
- acidophile membranes are very impermeable to protons. The most extreme acidophile Archaea have tetraether lipids that span whole membrane
(one layer, each lipid has 2 heads) as leave no gaps in between. - isoprenoid lipids in Archaea
Extremophiles 2: - in Bacteria, ω-cyclohexyl groups on fatty acids make lipids pack more tightly.Large groups on ends of fatty acids that interact with each other to make lipids pack more compactly and rigid so protons and ions cant get through???
- these are not prone to acid hydrolysis like fatty acyl ester lipids are.
- channel proteins in membranes have lower calibre pores to prevent proton leakage into the cell (example in Amaro (1991) J Bacteriol 173: 910-915 in Acidithiobacillus ferrooxidans).
- Donnan potentials (a thing in physics!) can reverse membrane potentials making interior of membrane +ve charged so it repels protons
levels of disorder get in a line fire alarm???????
“if they get in, get them out!”
- H+ ATPases all over surface of cells of these organisms that translocate protons out of the cell (up a conc. gradient) at the expense of ATP. If electron donor/acceptor runs out, this of course there is a build up and the cells rapidly burst. big lump of pyrite so it wont run out of resources??
- in some acidophiles, mS is very high as a result of this, however, in others like Atb. ferrooxidans that hardly grows and uses most of the electron donor to pay for the above, it looks low but that’s kind of an artefact.
- enzymes to lyse carboxylic acids so that if any get in, they are destroyed before they can drop protons
Achromatium oxaliferum adaptations
(Used to be “Hillhousia mirabilis”)
- in the Thiotrichales of the Gammaproteobacteria along with Thiothrix, Thiolinea, Thiofilum, Thiomicrospira, Thiomicrorhabdus etc.
- sulfur oxidiser so lowers it’s own environmental pH!
- complex intracellular network of CaCO3 and not much cytoplasm (relatively).
- uses this to buffer pH like in limestone karsts.
never been grown in pure culture but easy to enrich by ‘panning’.
solid network of calcium carbonate (Cytoplam in channels). Cant grow or cultivate it. So dense. ??? add limestone to constantly balance the pH. It produces oxalic acid (found in leaves of rhubarb and sorrel).
crystals last a long time
high pH ecosystems
- caustic soda/lye (NaOH) (pH 13.6)
- seawater (pH 7.5-8.5)
- household bleach (pH 12.5)
- soda lakes and playas (pH 8.5-pH 12.5):
-Mono Lake, California, USA (dissolves arsenic) - Lake Natron, Tanzania
- Lake Magadi, Kenya
- Laka Bogoria, Kenya
- Soap Lake, Washington State, USA
- Lake O’Grady, Western Australia, Australia (good example of playa where it reforms and disappears over the year)
- Lonar Lake, India (pH14 Soda lake)
- AND MANY OTHERS
what does high pH do to Life?
PROTEINS:
* unfold, losing secondary to quaternary structure, denaturing; at very high pH, primary structure is lost through alkaline hydrolysis of peptide bonds; loss of enzyme function and structural integrity.
LIPIDS:
alkaline hydrolysis
* bilayers lose integrity.
* hydrolysis into fatty acids and e.g. phosphoglycerate.
NUCLEIC ACIDS:
* precipitation out of solution as a solid.
high-pH adaptations
- acidify the cytoplasm – intracellular polymers of glutamic acid which can deprotonate to glutamate, lowering the pH.
- modified peptidoglycans that can donate protons in same way.
- Na+/H+ antiporters that can push protons in at the expense of pushing Na+ out. If in high salinity system, ATP is needed to push Na+ out. so against conc gradient
KEY EXAMPLE BUG:
Natroniella acetigena grows at pH 10 by producing acetic acid with the Wood-Ljungdahl pathway to lower intracellular pH.
washing powder company want high pH organisms that can live in low temperatures.
