It seems to be related to inorganic carbon uptake by the alga: 2HCO3- -> CO32- + {CO2}.

I think the precipitation can can be minimized by maintaining CO2(aq)/H2CO3 in the water at the equilibrium concentration with the atmosphere or - if the experiment allows it - even higher. Provide strong aeration or continued dosing of CO2 gas.

In my office I keep a planted aquarium with a CO2 supply from a yeast reactor that has higher alkalinity and Ca2+-concentration and I never see precipitation. 

http://www.qsl.net/w2wdx/aquaria/diyco2.html

the presence of biofilms containing large amount os solid caco3 is often observed on structures submerged in hard fresh waters.the information of such calcified biofilms may involve two processes.firstly ,calcium salts produced within the main body of water by either chemical or biological means become trapped and bound within mucilage rich films,and secondly ,organisms of biofilms may mediate the percipitation of caco3.

Nine green algae, a diatom and three cyanobacteria are known to precipitate CaCO3 in batch culture, when grown in the light in a hard water medium containing 68 mg L−1 soluble calcium. Deposition occurred as a direct result of photosynthesis which caused an increase in the pH of the medium. Once a critical pH has been reached, typically approximately pH 9.0, precipitation begin evidence by a fall in the concentration of soluble calcium in the medium. Certain characteristics of the precipitation process displayed by the diatom Navicula sp. were different to those of the other algae. All algae produced extracellular crystals of irregular morphology.

Using a standardized protocol employing the green algae Chlorococcum sp. and Stigeoclonium variabile, the effects of various inhibitors of CaCO3 nucleation or growth of crystals can be used. Most materials effectively delayed deposition of CaCO3, many decreased precipitation rates and all have a marked effect on crystal morphology. The most effective compound is HEDP (1-hydroxyethylene 1,1 diphosphonic acid), which inhibite precipitation completely at a concentration of 2.5 mg L−1 The use of such compounds to reduce the precipitation of calcium salts within algal biofilms in natural hard waters.

The formation of calcium carbonate and its precipitation depends on the oxidation of bicarbonate to the carbonate species and precipitation. The oxidation always took place in presence of oxygen which is released in enormous amount from the algae during photosynthesis. This release of oxygen guring photosynthesis and oxidation of calcium bicarbonate to carbonate is the major reason for calcium precipitation.

If I have any advice, I propose to use isotopic analysis of the deposits of limestone formations and CO2-dic dissolves in water to know the origin of CO2. I also propose a monitoring stable isotope 13C and 15N bio-Films and algae to confirm the hypothesis that the algae is directly behind huge deposits of calcium and limestone formations.