A large number of microorganisms are responsible for the oxidation of Mn-(aq)(2+) to insoluble Mn3+/4+ oxides (MnOx) in natural aquatic systems. This paper reports the structure of the biogenic MnOx, including a quantitative analysis of cation vacancies, formed by the freshwater bacterium Leptothrix discophora SP6 (SP6-MnOx). The structure and the morphology of SP6-MnOx were characterized by transmission electron microscopy (TEM), X-ray absorption spectroscopy (XAS), including full multiple-scattering analysis, and powder X-ray diffraction (XRD). The biogenic precipitate consists of nanoparticles that are approximately 10 nm by 100 nm in dimension with a fibrillar morphology that resembles twisted sheets. The results demonstrate that this biogenic MnOx is composed of sheets of edge-sharing of Mn4+O6 octahedra that form layers. The detailed analysis of the EXAFS spectra indicate that 12 +/- 4% of the Mn4+ layer cation sites in SP6-MnOx are vacant, whereas the analysis of the XANES suggests that the average oxidation state of Mn is 3.8 +/- 0.3. Therefore, the average chemical formula of SP6-MnOx is Myn+Mn0.123+[rectangle Mn-0.12(0.88)4+]O-2. zH(2)O, where M-y(n+) represents hydrated interlayer cations, rectangle(0.12) represents Mn4+ cation vacancies within the layer, and Mn-0.12(3+) represents hydrated cations that occupy sites above/below these cation vacancies.