Characterization of a black substance exuding from fractured bedrock in a subterranean tunnel revealed a secondary manganese oxide mineralisation exceptionally enriched in rare earth elements (REE). Concentrations are among the highest observed in secondary ferromanganese precipitates in nature. The tunnel is located in the unsaturated zone at shallow depth in the former Ytterby mine, known for the discovery of yttrium, scandium, tantalum and five rare earth elements.

Elemental analysis and X-ray diffraction of the black substance establish that the main component is a manganese oxide of the birnessite type. Minor fractions of calcite, other manganese oxides, feldspars, quartz and about 1% organic matter were also found, but no iron oxides were identified. The Ytterby birnessite contains REE, as well as calcium, magnesium and traces of other metals. The REE, which constitute 1% of the dry mass and 2% of the metal content, are firmly included in the mineral structure and are not released by leaching at pH 1.5 or higher. A strong preference for the trivalent REE over divalent and monovalent metals is indicated by concentration ratios of the substance to fracture water. The REE-enriched birnessite has the general formula Mx(Mn3+,Mn4+)(2)O-4 center dot(H2O)(n) with M = (0.37-0.41) Ca + 0.02 (REE + Y), 0.04 Mg and (0.02-0.03) other metals, and with [Mn3+]/[Mn4+] = 0.86-1.00.

The influence of microorganisms on the accumulation of this REE enriched substance is demonstrated by electron paramagnetic resonance spectroscopy. Results show that it is composed of two or more manganese phases, one of which has a biogenic signature. In addition, the occurrence of C-31 to C-35 extended side chain hopanoids among the identified lipid biomarkers combined with the absence of ergosterol, a fungal lipid biomarker, indicate that the in-situ microbial community is bacterial rather than fungal.

The dominant initial phase formed during microbially mediated manganese oxidation is a poorly crystalline birnessite-type phyllomanganate. The occurrence of manganese deposits containing this mineral is of interest for increased understanding of microbial involvement in the manganese cycle. A culture independent molecular approach is used as a first step to investigate the role of microorganisms in forming rare earth element enriched birnessite-type manganese oxides, associated with water bearing rock fractures in a tunnel of the Ytterby mine, Sweden. 16S rRNA gene results show that the chemotrophic bacterial communities are diverse and include a high percentage of uncultured unclassified bacteria while archaeal diversity is low with Thaumarchaeota almost exclusively dominating the population. Ytterby clones are frequently most similar to clones isolated from subsurface environments, low temperature milieus and/or settings rich in metals. Overall, bacteria are dominant compared to archaea. Both bacterial and archaeal abundances are up to four orders of magnitude higher in manganese samples than in fracture water. Potential players in the manganese cycling are mainly found within the ferromanganese genera Hyphomicrobium and Pedomicrobium, and a group of Bacteroidetes sequences that cluster within an uncultured novel genus most closely related to the Terrimonas. This study strongly suggest that the production of the YBS deposit is microbially mediated.

Biofilms scavenge and bind reduced Mn(II) as well as stabilize highly reactive Mn(III), favouring formation of Mn oxides. Mn oxidation and precipitation involve closely connected and concomitant abiotic and biotic biogeochemical mechanisms, often making the biogenicity of the mineral product difficult to determine. In order to use these precipitates as potential biosignatures, profound knowledge of the formation pathways is required. Here we have access to an underground Mn oxide producing ecosystem in which epilithic biofilms precipitate yttrium and rare earth element enriched birnessite-type Mn oxides. Microbial community composition combined with elemental data is investigated to provide insight into how different subsystems of this ecosystem (fracture water, Mn oxide producing biofilm, and bubble biofilm) interact with each other to form the birnessite. We find that the microbial assembly of the feeding water has little impact on the derived biofilms, in which the signature microbial groups rather results from water chemistry and environmental conditions. In the Mn oxide producing biofilm, bacteria  are adapted to the emerging extreme environment (low temperature, no light, high metal concentration) which is generated by the biofilm itself. Microstructural characterizations show that the birnessite has a dendritic/shrublike or spherulitic/botryoidal growth pattern. Nucleation occurs in close association to the biofilm and Mn encrustations of cells and other organic structures serve as stable nuclei for further growth. The influence of organics decrease in importance as precipitates grow. In more evolved crystals, a repetitive pattern, Liesegang-type of rings, implies that abiotic factors dominate. Grown on a solid substrate, four bacterial (Hydrogenophaga sp., Pedobacter sp., Rhizobium sp. and Nevskia sp.) and one fungal species (Cladosporium sp.) are involved in Mn oxide production. Hydrogenophaga and Pedobacter oxidize Mn independently while Rhizobium needs a synergistic relationship with selected species (e.g., Nevskia). Members of the Pedobacter and Nevskia genera are previously not known Mn oxidizers. The onset of Mn precipitaiton takes place at different locations with respect to the cells for the different species. Precipitates are located intracellularly (possibly post mortem), on the bacterial cell walls, at the outer edges of more well developed crystals, within the extracellular organic matter (EOM) and on hyphal surfaces.

A porous black substance exuding from fractures in an underground tunnel leading to the shaft of the Ytterby mine, Sweden, was observed in 2012 and characterized as a secondary manganese (Mn) oxide in 2015. The oxide was identified in 2017 as a birnessite variety, M_x[Mn(III,IV)]₂O₄∙(H₂O)_n  where M usually is Ca, Na and x is around 0.5, but the Ytterby birnessite appears to be unique with M being Ca, Mg but also yttrium and rare earth elements (YREE), constituting up to 2% of the metal content. The biogenic origin of the Ytterby birnessite was established in 2018. Studies of the formation of this unique birnessite phase has progressed during 2018-19 with detailed studies of the hydrochemistry of the fracture water as well of the exchangeability of the metals M in the structure: Na, Ca, Fe and La representing the YREE. Exposure to solutions of  Na, Ca, Fe, and La, respectively (1 M) led to exchanges and altered distribution of the metals constituting M, with a preference of YREE (trivalent) over Ca (divalent) over Na (monovalent), all of similar ionic radii, as well as higher affinity for YREE over Fe(III), being smaller. Fe(III) did not replace Mn(III) in the structure, despite the fact that their radii are almost identical. No discrete new Fe phase was indicated, and the structure of the birnessite phase was almost identical after exchanges of M, as indicated from XRD. The formation of birnessite in the fracture opening on the tunnel wall appears to be a fast and dynamic process, as indicated by a significant depletion of Mn as well as of YREE in the fracture water during the passage over the precipitation zone, from top to bottom.