Many true aquatic plants do not have stomata and use ectohydric (surface capillary structures) to obtain carbon dioxide through a process called laminar boundary layer conductance, which is a measure of diffusion. Some floating aquatic plants evolved non-functional permanently open stomata, and some simply exhibit a "
loss of function" that could still allow them to adapt and close during periods of environmental stress. Pteridophytes which include ferns like
Bolbitis, mosses, and certain liverworts, evolved a kidney-shaped (reniform) graminoid stomata, many of which stay open and retain the ability to close in dryer conditions. Marchantialean liverworts like
Riccardia evolved without them, using special pores for photosynthetic gas exchange on the under sides of their leaves, and with humid air chambers beneath the cuticle. The role of air chambers is to enable endohydrotic conductance and this is thought to enhanced gaseous exchange and strike a balance between hydroscopic (wet) and hygrophytic (damp) environmental conditions (
Vascular Transport in Plants, pages 69-89); there are also
suggestions that some plants form similar air spaces (aerenchyma) as an adaptation to when they have been flooded. Generally speaking, plants that did evolve stomata, did so on the under side of leaves (hypostomatous), on both sides (amphistomatous), or on the top (epistomatous) to favour their own ecological niche.
However, plants that evolved "true" stomata, probably did so in more hydrodynamic conditions, and they make up the bulk of "immersed" aquarium stem plants that people are usually interested in enriching. When we see "pearling" we are probably observing very fast degassing, and it is likely that plants have opened their stomata to facilitate a rapid gaseous exchange. Flooding-induced stomatal closure is common in many terrestrial plants but
nobody really knows how this happens. If certain immersed aquarium plants respond in the same way, then the question is, do they open back up again. And another question on my mind is, when they are closed, how big is the actual gap, and does this facilitate access of carbon dioxide bubbles into the intercellular spaces behind the guard cells; nano-bubbles are < 200 nm, so they only need a small gap to enter. For each plant species it is going to be slightly different and will depend upon varying environmental factors, but there have been suggestions that stomata in most species will open back up again when the osmotic conditions are suitable. It would be great if we knew the mechanism or if immersed aquarium species were studied independently, but for the time being this is simply a guess.
It is probably untrue to assume that stomata reduce in prevalence on immersed aquarium plants as an adaptation. They may close and be less recurrent in new growth, but there is not conclusive evidence that they disappear. Arabidopsis (stomatal initiation) is the process that governs whether the leaf meristemoid mother cell differentiates into either a pavement cell (standard epidermal) or a stomatal guard cell. It governs the stomatal abundance of a leaf (e.g. the stomatal index), and this is confined by the
“one cell spacing” rule, and many other factors such as light intensity, gaseous exchange and temperature play an important role in stomatal abundance. We know that many
C3 plants will often increase stomatal abundance when there are lower carbon dioxide levels and this seems to be a long-term evolutionary trait, but there is also species specific variation. Whether this process is affected by immersed growing conditions is also likely to be species specific.
If stomata are open, then both hypostomatous and amphistomatous leaves will have a potential for capturing carbon dioxide bubbles of all sizes as well as dissolved carbon dioxide. That would imply that pH measurement and ppm approximations might not really be the target of investigation. Instead, "pearling" may be a far more accurate way to measure photosynthesis, not least because it is a measure of the effect of enrichment, as others have pointed out above. Plants that do this are good indicators that conditions are right. Plus it is best not to eliminate the role of aqueous pores and other
gateways that probably provide a route for carbon dioxide bubbles to enter directly. After all, carbon dioxide
diffusivity is about 10,000 times higher in air than in water, so if it is present in bubbles inside plant tissue (intercellular gaps) or sitting as a bubble in the stomatal opening, then the rate of diffusion into chloroplasts will be far faster. The rate of diffusion of an ionic solute or carbon dioxide molecules is inverse to the distance. It is a bit like standing next to the speaker in a punk rock concert, compared to hearing the faint rumble of a rave going on several miles away!