Fungal filaments are the most abundant organic features in weathered profiles developed on chalky limestone ("platy calcrete"). Their activity affects the mineral dynamics of the pore/carbonate microsystem. A theoretical biogeochemical model is proposed to describe the Ca-oxalate-carbonate cycle related to fungal activity in dry environments.
The system studied is the pore itself (defined as the reactor) delimited by its wall and its content: solutions, gases (air and CO2), microorganic material, their transformation products and the minerals present (calcite and calcium oxalate). The system exchanges gas and solution with the outside environment, which includes micritic calcite, solutions, a gaseous phase (air and CO2), and the nanoporosity of the pore wall constituted by the micritic matrix. A diagram of pH = f(log |Ca2+|) is constructed to simulate the behaviour of various fungal excretions, whether the system is open or semi-closed. Two steps are studied. In the first step, the fungi is in full metabolic activity, and assumed to secrete i) an organic diacid (BH2) of soluble calcium salt, or ii) oxalic acid, or iii) soluble sodium oxalate, or iv) CO2. In the second step, bacteria transform the oxalates into carbonates. In the first step, the model concurs with petrographic observations, on the condition that the system is semi-closed and the aggressive agent produced by the hypha is mostly oxalic acid (COOH)2. In the second step, the pore solution becomes saturated in calcite, whether the system is open or semi-closed. This explains the calcium carbonate precipitation inside the pore as needles or microsparite and impregnation of the micritic matrix around the pores. In conclusion, the presence of fungi allows a redistribution of calcium carbonate. This secondary cementation is strong in the case of recrystallization of pore walls and weaker when infilling voids with needles.