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Biogenic Decalcification


  1. CO2 uptake mechanisms
    by Paul Krombholz <> (Mon, 03 Jul 95)
  2. Aquatic Plants Digest V1 #72
    by krombhol-at-felix.TECLink.Net (Paul Krombholz) (Wed, 15 Nov 1995)
  3. chicken and Egg?-biogenic decalcification
    by krombhol/ (Paul Krombholz) (Sat, 25 Apr 1998)
  4. biogenic decalcification
    by "Roger S. Miller" <rgrmill/> (Sat, 25 Apr 1998)
  5. How does light intensity effect CO2?
    by "A. Inniss" <andrewi/> (Thu, 9 Apr 1998)

CO2 uptake mechanisms

by Paul Krombholz <>
Date: Mon, 03 Jul 95

>      I'm confused by your explanation of 3 modes of uptake.  Plants don't
>      actively "take up" CO2---it passively diffuses through the stomata in the
>      leaves, so it would seem that the uptake in water or in air would be via
>      the same mechanism.  Have aquatic plants evolved more efficient strategies
>      for living in CO2 impoverished environments?  Receptors for CO2 perhaps?
>      If so I'd love to hear more.  I'm skeptical.

>      Bob Hoesch
>      National Fish & Wildlife Forensics Laboratory
>      Ashland, OR

A number of species of aquatic plants can absorb the bicarbonate ion, keep the CO2, and 
excrete hydroxide.  They tend to live in crowded conditions where there is not much 
flow-through of water, and, in good light, they can raise the pH to 10.  They often 
precipitate calcium carbonate on their leaves.  Elodea, Najas, and Ceratophyllum are 
examples.  Another group can't do this, and apparently are able to only absorb free CO2.  
This information should be in any textbook of limnology. 
Paul Krombholz

Aquatic Plants Digest V1 #72

by krombhol-at-felix.TECLink.Net (Paul Krombholz)
Date: Wed, 15 Nov 1995

>On another matter, I decided I've had enough with weekly pruning of my
>plants (enough credit at the fish store to last a while), so I disconnected
>my CO2 injection last week, hoping to slow down the growth.  The plants are
>still okay, but I have noticed that the Anacharis have formed a sandy layer
>on the leaves.  Is this the decalcification effect?  And will it be bad? I
>have been monitoring the pH, and it's about stable at 7.6 (tap water here i=
>8.1 pH, 18dGH, 8.4 dKH).  pH was around 7.2 with CO2 injection.  What else
>should I do to balance things out if I don't want the plants to grow so
>fast?  Reduce lighting duration?  Right now it's about 10 hours of 120W (80
>bright Watts of Ultra TriLux, plus 40 dimmer Watts of Vita-Lite, on 75
>gallon aquarium) plus 3/4 hour of sunrise/sunset periods on each end (40W).
The sandy layer on the leaves is calcium carbonate.  Anacharis ( called
Egeria densa in M=FChlberg.s book) is capable of utilizing the bicarbonate
ion.  It takes in bicarbonate, HCO3-, keeps the CO2, and leaves behind OH-.
In strong light, this process can create enough alkalinity at the leaf
surface to precipitate calcium carbonate, CaCO3.  As long as your pH is OK,
I wouldn't worry, but you should keep close watch on the pH.  I once saw
that my zebra fish in a tank with 3 T12 fluorescents and a lot of Anacharis
looked a little sick.  I took the pH and found it to be 9.6.  I added some
CO2 and the zebras looked a lot happier.  Plants like Elodea, Najas,
Vallisneria, and ceratophyllum that can utilize the bicarbonate ion can
raise the pH in well-lit aquaria to almost lethal levels for fish.

>BTW, what is the scientific name for Anacharis sold in the Western United
>States?  I can't decide if it's Egeria densa or Elodea canadensis.
It is probably the latter.  Elodea canadensis is a much smaller plant with
leaves usually less than 1 cm. long.

Paul Krombholz                  Tougaloo College, Tougaloo, MS  39174

chicken and Egg?-biogenic decalcification

by krombhol/ (Paul Krombholz)
Date: Sat, 25 Apr 1998

>Larry Frank wrote, Friday, Apr. 24:

>....So this is sort of a chicken and egg question. Does the rise in PH due to
>CO2 being pulled from solution cause biogenic decalsification. Or does
>biogenic decalsification cause a rise in PH?
Plants like Elodea, Najas, Eigeria, Ceratophyllum, and Vallisneria are able
to utilize the bicarbonate ion, HCO3-,   They remove CO2, leaving behind
OH-.  The high pH created causes precipitation of calcium carbonate on the
leaf.  The increased OH- drives the equation, HCO3- -------> H+ + CO3--  to
the right.  The H+ combines with the OH- to form H2O, and the CO3--
combines with Ca++ to precipitate out as CaCO3.

Paul Krombholz, in cool central Mississippi, where it is going to get

biogenic decalcification

by "Roger S. Miller" <rgrmill/>
Date: Sat, 25 Apr 1998

Well, Larry asked for it...

> Here's a question for a chemist or bio-chemist:
> I am a little confused about the mechanism of biogenic decalsification.

In short, plants force the pH up when they take CO2 or bicarbonate out of 
the water.  Decalcification happens as an incidental side effect of the 
increased pH.

> I
> have read that CO2 causes calcium hardness in water by forming Carbonic
> acid which dissolves Calcium carbonate. The Carbonic acid is also
> responsible for the lowering of Ph with CO2 injection.( Equations I and
> II).

[cut and paste]

> I   CO2 + H2O <--> H2CO3
>               (Carbonic acid)
> II  H2CO3      +       CaCO3       <-->     Ca(HCO3)2
>    (C. Acid)      (Calcium carbonate)   (Calcium bicarbonate)

> Now biogenic decalsification occurs when the calcium bicarbonate comes out
> of solution and forms calcium carbonate. My confusion is over the
> mechanism. Does this occur by plants pulling CO2 out of solution causing
> Equation I to reverse, and in turn causing equation II to reverse. ( The
> rise in PH from reversing equation I would cause a reverse in equation II?)

For starters, "H2CO3" (at least in geochemical literature) is regarded as
just H20 + CO2.  H2CO3 has never been isolated as a pure component.  It
might be conceptually helpful, but it complicates the formulas.  I've 
seen other data that seems to dispute this, but the common thermochemical 
tables are pretty clear.

Second, the species "Ca(HCO3)2" exists as an ion association in sea water 
and other concentrated solutions, but isn't significant in freshwater.  
Ca(HCO3)2 should be replaced with Ca+2 + 2(HCO3-).

So, replace equation I with

I'	CO2 + H2O <--> H+ + HCO3-

The reaction is forced to the right when CO2 concentrations increase and
pH drops.  The reaction can be forced to the left by plants consuming CO2
and in that case the pH increases.  I think plants will force this
reaction only while CO2 is available at "practical" levels - at levels
where the plant can actually use it.  So plant uptake of CO2 can increase 
pH, but only to moderately high levels, not to the 9+ levels that 
sometimes occur.

If calcium carbonate is present, then equation II might go on as:

II'	H+ + CaCO3 <--> Ca+2 + HCO3-

When when we force reaction I' to the right by adding CO2 the increased H+
from the reaction also forces reaction II' to the right.  That tends to
use up the increased H+ and cancel the pH drop created by adding CO2.  It
also increases general hardness and alkalinity.  But it only works if
CaCO3 is present.  If CaCO3 isn't present then the reaction can't go to
the right.  It can be forced to the left (precipitating calcium carbonate)
if something causes an increase in pH. 

We can also force this reaction to the right with ion-exchange softening,
which removes Ca+2 and replaces it with 2Na+.  Calcium carbonate 
dissolves and cancels out the work done to soften the water.

Snails force the reaction to the left when they build their shells.  That
is a form of biogenic decalcification and I don't know how they do it. 
Because of snails, this system seems to procede to the left in my tanks,
even with added CO2. 

These reactions could also be written with magnesium in the place of calcium.

Equations I' and II' probably do not operate on the same time scales.  
I' occurs entirely in solution and is a relatively fast reaction.  II' 
occurs only at the surface of solid CaCO3 and is a relatively slow reaction.
You will see changes caused by I' over the scale of minutes, but changes 
caused by II' over the course of hours or days.

> Or as suggested in some literature the plants force equation III ( or in
> extreme cases Equation IV--Which must require more energy because it is
> claimed that plants which use IV raise the PH higher than from using III)
> In this case equation III would force a reverse in equation II which in
> turn would reverse equation I , thus lowering the PH.

[cut and paste]

> III CA(HCO3)2   ---> CaCO3    + H2O   + CO2
>                                        (Taken directly from Calcium bicarbonates
>                                         by plants)
> IV H2CO3 ---> CO2 + H20                 (Taken directly from the carbonate
> ion
>                                         by plants)

These are really just the first 2 equations, combined and written 
in reverse order.

As I understand the process, some aquatic plants are capable of breaking 
down bicarbonate ion to obtain CO2.  The reaction might happen on the 
surface of the plant and might be written as:

2(HCO3-) --> CO3-2 + CO2 + H2O.

CO2 is imported by the plant, and the CO3-2 remains in the water.  (This
same reaction occurs when bicarbonates are heated.  Throw sodium bicarb
on a grease fire and it breaks down to sodium carbonate and the released
CO2 smothers the fire.)

You could also look at this as two reactions:

HCO3- --> OH- + CO2
OH- + HCO3- --> CO3-2 + H2O

The reaction might also be done inside the plant, which would import 
HCO3- in one area of the plant surface and export CO3-2 at another area.  
This is mechanistically a little more difficult.

Either way, the result is uptake of CO2 and production of carbonate 
ion at the plant's surface.  The carbonate ion reacts with any available 
H+ to form bicarbonate ion and that increases the pH:

III'	CO3-2 + H+ <--> HCO3-

Plant production of CO3-2 can force pH over 9.

The carbonate can also react with calcium ion to precipitate calcium 

IV'	CO3-2 + Ca+2 <--> CaCO3
Reaction IV' goes to the right (thus precipitating calcium carbonate) at
very high pH levels that are created at the plant's surface.  If the pH
gets high enough farther away from the leaf then reaction II' will also 
precipitate calcium carbonate.

Equation IV' reacting to the right is probably what is usually called
biogenic decalcification when we're talking about plants.

> So this is sort of a chicken and egg question. Does the rise in PH due to
> CO2 being pulled from solution cause biogenic decalsification. Or does
> biogenic decalsification cause a rise in PH?

Equations I' and III' express equilibrium conditions between dissolved 
inorganic carbon species.  It's this equilibrium that normally 
determines the pH of water.  When plants remove CO2 they increase the 
pH.  At higher pH they remove HCO3- and that forces the pH even higher.

Equations II' and IV' are the decalcification reactions.  In both
reactions, precipitation of calcium carbonate (decalcification) can be
induced by the increase in pH caused by plant consumption of dissolved
inorganic carbon.

Enough already!

Roger Miller

How does light intensity effect CO2?

by "A. Inniss" <andrewi/>
Date: Thu, 9 Apr 1998
Newsgroup: rec.aquaria.freshwater.plants

On Thu, 9 Apr 1998 wrote:

> YIKES, I think I got it now. Without enough CO2, the plants resort to
> biogenic decalcification to obtain CO2 resulting in a sharp climb in PH.
> Humic acid release will buffer this rise depending on the amount of acid. I
> presume if I was to remove all my plants my PH would drop back to the
> original level of the water.
There are two ways in which a planted tank with "insufficient" CO2 could
see a pH rise: the first is biogenic decalcification, in which you see
steady rise in pH; the other possibility is a daily pH swing,with the pH
rising during the day, and falling back somewhat at night.  In the latter
case, the pH rise is caused by the plants' consuming CO2 more rapidly than
can be compensated for by diffusion.  
	In the first case (biogenic decalcification), I suppose the pH
would eventually, and steadily go back down.  In the second case, it
shouldn't take long at all for the pH to go back down...assuming no other
significant pH affecting factors ;-)
> The biogenic decalcification process is when plants use carbonates to form
> CO2. Since I used soft water, 30ppm, will that effect this process any?

	Interesting question: I suppose the extent to which biogenic
decalcification can go would be somewhat limited, but perhaps only
negligibly?  Hmmm...

> have a 30 gallon tank, 3 years planted, no CO2, low light, (55 watts total)
> with aponogetons, anubias and java ferns. Has a steady PH of 6.8 and has
> never risen. My Apon. ulv. grow quickly and are blooming and others doing
> very well. The substrate has a lot of mulm and some clay litter. There is a
> fairly high fish load.	I guess I had a low tech tank and didnt know it! If I
> was to bring the light in this tank up to 80 watts, would this wreck the
> balance I have attained, and send my PH up?

	A pH rise is certainly a good possibility, but it depends on other
factors that could affect pH (such as the amount of acidity being produced
through nitrification, and various other organic acids).  Still, I would
be prepared to inject CO2 if you see a pH rise of either sort described
> I was taught that surface agitation depletes CO2, but I gather this is only a
> concern when adding additional CO2. I thought I was conserving CO2 by not
> having any surface agitation. Until I get an injector, would adding an
> airstone help my situation any? My cannister filter empties below the water
> surface.
	Surface agitation may raise _or_ lower pH, depending on the
relative CO2 concentrations in you tank to that in the atmosphere.  For
instance, if you have, say, 80 small tetras in a 40 gal with very little
surface agitation, your tank's relative CO2 concentration will probably 
be higher than the atmosphere's, because CO2 accumulation from all that
fish respiration will be more rapid than diffusion from the atmosphere
can compensate.  Should you suddenly decide to run in this tank a large
bubble wand with a Tetra Luft pump, you will most likely see a
dramatic rise in pH. The amount of surface agitation here would cause the
rapid equilibration of the tank's CO2 concentration to that of the
atmosphere's concentration.  Conversely, the same 40 gal. tank with 2
small tetras and very little surface agitation will probably have a 
CO2 concentration less than the atmosphere's, so the introduction of a
bubble wan would most likely increase the amount of CO2 in the tank,
thereby causing a potential pH drop.  

> Sidebar: As a tank and substrate matures, the PH lowers. How does this relate
> to if at all to what we have been talking about?
	For one, nitration (the process by which nitrite is transformed
into nitrate) produces nitric acid.  Also, nitritation (ammonia/ammonium
into nitrite) produces nitrous acid.  I'm not sure just how much nitrous
acid production is relevant here, since it has a pH dependent equilibrium
with nitrite: During nitritation, the higher the pH, the more nitrous acid
is produced and the less nitrite; the lower the pH, just the reverse.  At
any rate, the upshot of this is that the reduction of nitrogen produces
acids.  Also, more mature tanks tend to accumulate a whole wealth of
dissolved organic acids.

> I guess I am going to have to add CO2 to this 100 gallon tank. DIY seems too
> messy, systems in the store are way to expensive.  Some investigating is
> going to have to be done.

	DIY sugar/yeast/sodium bicarb. isn't too bad, other than having to
remix your batch every 2-8 weeks.

	Hope I've helped, and not made too many simplifications or plain
errors.  Someone will no doubt correct me where I've gone astray ;-).


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