Bio-acidification.

As water matures in the aquarium environment, its pH tends to drop slowly. A fancy term for this phenomenon is "bio-acidification." Where is this biologically-generated acid coming from? You could ask it another way: where are all these extra H+ ions coming from, to drive down your pH like that?

The main end products of aerobic metabolisms, when all is said and done, are water and CO₂. Now, you're already aware that when carbon dioxide dissolves in water it forms some carbonic acid, which immediately breaks down and contributes an acidifying H+ ion to the water. So the combined respiration of all the aerobic organisms in the aquarium, breathing out carbon dioxide, has the effect of continually pumping carbonic acid into the water, and that acidifies it. The pH will resist change, as long as there is some carbonate buffer. But if the buffer eventually becomes exhausted, the pH may begin to fall. This drop in pH that results from metabolisms is what people are referring to when they talk about "bio-acidification."

When you're considering the CO₂ production from respiration in your aquarium, including the vast population of microscopic organisms that are free-floating in water as plankton and also covering every surface as biofilm, once again it's easy to ignore the cellular respiration of algae and plants, even in their root cells, which aren't photosynthesizing. In dimly-lit tanks, where plants aren't doing well, they may contribute to lowered pH, through their respiration--— and also through the decay of their softening leaves. On the other hand, in a densely-planted and well-lighted aquarium with soft, scarcely buffered water, the pH will test lower first thing in the morning and higher towards the end of the light period, when CO₂ has been scavenged. This daily rhythm is natural. It's the slow, steady "breathing" of the entire system, which the fish take in stride like changes of atmospheric pressure. It's not part of the constant erosion of buffering that results in "bio-acidification."

Respired CO₂ isn't the only biological source of acids. Another source of biogenic acid in the aquarium is the basic osmoregulation by which fish maintain the balance of sodium in their system. Osmoregulation involves ion-exchange at the gill surfaces, where a H+ ion is released in exchange for an ion of sodium from the water. That has a constant acidifying effect.

"Bio-acidification" is also in play in the aerobic decomposition of organic matter by bacteria and some fungi. These processes both consume oxygen and also produce ammonia.

Nitric acid. Though carbon dioxide is a major source of bio-acidification, there are further biologically generated sources of acids.

The nitrification "arc" of the nitrogen cycle produces acids. The process in which bacteria transform ammonia/ammonium into nitrite ("nitritation"), produces unstable nitrous acid (HNO₂). (Its corresponding salt, if you dehydrate it, is nitrite, NO₂.) "Nitration," in which nitrite is then oxidized into nitrate, partly chemically, by dissolved oxygen in the water, but mostly by bacterial metabolisms, produces a more stable product, nitric acid (HNO₃). (Its salt is nitrate.) Released nitric and nitrous acids react with the carbonate buffering, eroding it to release CO₂.

Although industrial emissions of nitrogen oxides reacting with water vapor or droplets are a major component of acid rain, you see that some nitric acid is a natural component of freshwater. Like all acids, it is neutralized by the aquarium's buffers.

Nitrous acid has a pH-dependent equilibrium with nitrite Together, nitrous acid and nitrite act as an acid/base buffer, not unlike the more familiar acid/base buffer of carbonic acid and carbonate. Andrew Inniss posted in a discussion of biogenic decalcification that is archived at www.thekrib.com : "During nitritation, the higher the pH, the more nitrous acid is produced and the less nitrite; the lower the pH, just the reverse."

The nitrification cycle, in which ammonia is eventually metabolized to nitrate, has an additional side effect that generates more acid: the bacterially-oxidized molecule of ammonium finally produces--— in addition to nitrate--— a molecule of water and two protons (H+). Those dissociated H+ ions released into the water additionally lower the pH. Since the nitrifying communities also contribute CO₂, they are an essential part of bio-acidification. Diana Walstad says, "Tanks with water that becomes acidic over time are unbalanced, usually due to excessive nitrification in the filter" (in Ecology of the Planted Aquarium, pp 4-5).

Nitrous and nitric acids are also produced when cellulose is decomposed by a consortium of fungi and bacteria in the biofilm. As soon as the nitro groups are detached from the cellulose polymer during decomposition, they combine with water to form nitrous acid (HNO₂), which is rapidly metabolized by nitrifying bacteria to nitric acid.

Sulfuric acid. Minor amounts of sulfuric acid are also generated in the aquarium. They are produced by anaerobic bacteria, mostly in the lower levels of the substrate, but also in well-established biofilms.

Once again, whether these mild acids depress your pH or not depends on the alkalinity of your system.

"Bio-alkalinification?" If aerobic respiration plus aerobic decomposition plus processes of nitrification all contribute to the lowering of pH, then any process that consumes CO₂ would help raise the pH, wouldn't it? You could think of it as "bio-alkalinification." Photosynthesis is the major counterbalance to bio-acidification. But the anaerobic bacterial processes of de-nitrification, constantly at work in the lower levels of the substrate where oxygen becomes scarce, also consume carbon dioxide, as the nitrates they metabolize are turned by several steps into nitrogen gas.

There's also a non-biological process that helps balance CO₂ and thus helps counter "bio-acidification:" the diffusion of any extra CO₂ into the air, constantly occuring at the water's surface. In a softwater system, where the buffering is very light and so pH values fluctuate sensitively, you may even find that increased aeration, such as splash at the filter outflow, will actually help raise the pH.

"Old Tank Syndrome" and "pH Shock." Sometimes there are mass fish mortalities after a long-established tank has received a past-overdue cleaning and a good refreshing water change, say 50%. The fish show immediate distress, gasp and flare their gills, lose balance, lie on their sides and die. This is called "old tank syndrome" and it used to be mysterious. What has happened is this: "bio-acidification" has slowly consumed the carbonate buffer, and the pH has eventually begun to drop, unnoticed. The process has been gradual, and the fish have adjusted. They have been helped by the fact that at lower pH, most of the toxic ammonia is in its non-toxic ionized form, ammonium (NH₄). But if the pH sinks, the nitrifying bacteria begin to be repressed. Non-toxic ammonium may build up harmlessly enough in such acidic water, especially where there aren't plants to scavenge it. Then, with a water change (perhaps using tapwater that already has a pH above neutral), the buffer is suddenly restored. Ammonium reconverts to its toxic form, NH₃, and fishes die of ammonia poisoning, though perhaps the diagnosis is rendered as "pH shock."