An amorphous or nanocrystalline calcium carbonate (ACC) phase with aragonite-like short-range order was found to be a transient precursor phase of calcite precipitation mediated by cyanobacteria of the strain Synechococcus leopoliensis PCC 7942. Using scanning transmission X-ray microscopy (STXM), different Ca-species such as calcite, aragonite-like CaCO3, and Ca adsorbed on extracellular polymers were discriminated and mapped, together with various organic compounds, at the 30 nm-scale. The nucleation of the amorphous aragonite-like CaCO3 was found to take place within the tightly bound extracellular polymeric substances (EPS) produced by the cyanobacteria very close to the cell wall. The aragonite-like CaCO3 is a type of ACC since it did not show either X-ray or electron diffraction peaks. The amount of aragonite-like CaCO3 precipitated in the EPS was dependent on the nutrient supply during bacterial growth. Higher nutrient concentrations (both N and P) during the cultivation of the cyanobacteria resulted in higher amounts of precipitation of the aragonite-like CaCO3, whereas the amount of Ca2+ adsorbed per volume of EPS was almost independent of the nutrient level. After the onset of the precipitation of the thermodynamically stable calcite and loss of supersaturation the aragonite-like CaCO3 dissolved whereas Ca2+ remained sorbed to the EPS albeit at lower concentrations. Based on these observations a model describing the temporal and spatial evolution of calcite nucleation on the surface of S. leopoliensis was developed. In another set of STXM experiments the amount of aragonite-like CaCO3 precipitated on the cell surface was found to depend on the culture growth phase: cells in the exponential growth phase adsorbed large amounts of Ca within the EPS and mediated nucleation of ACC, while cells at the stationary/death phase neither adsorbed large amounts of Ca2+ nor mediated the formation of aragonite-like CaCO3. It is suggested that precipitation of an X-ray amorphous CaCO3 layer by cyanobacteria could serve as a protection mechanism against uncontrolled precipitation of a thermodynamically stable phase calcite on their surface. (c) 2009 Elsevier Ltd. All rights reserved.