Microbial Communities Inhabiting a Rare Earth Element Enriched Birnessite-Type Manganese Deposit in the Ytterby Mine, Sweden

Abstract

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.

Microbiomes in a manganese oxide producing ecosystem in the Ytterby mine, Sweden: impact on metal mobility

“…Part of the Bacteroidetes cluster identified in our previous study (Sjöberg et al . 2018 ) was detected in the Chitinophagaceae family (Ytterby clone 1 A02, MG657061). Within the Saprospiraceae family, the genus Haliscomenobacter was represented together with groups of undetermined Saprospiraceae most similar to clones from lithifying microbialites (KP589290 and KP514320, Corman et al .…”

“…and one fungus ( Cladosporium sp.) were also previously isolated from the Ytterby system, grown in the dark at a low temperature of 8°C (Sjöberg 2019 ). The two bacterial species accounted for a maximum of 0.09% and 0.03% respectively in the YBS biofilm sequence data, while the fungus was not detected at all.…”

“…Yet another bacterial species ( Rhizobium sp.) was observed to be involved in Mn-oxidation but results implied a synergistic relationship with other species (Sjöberg 2019 ).…”

“… Plot showing whether an element is enriched or depleted from the fracture water after it has percolated through the Mn precipitation zone: from the top of the rock wall as the water emerges from the fracture (FW YBS T), to the bottom of the deposit after it has passed through the Mn precipitates down the 2 m tall rock wall (FW YBS B) (modified from Sjöberg 2019 ). Enrichment or depletion of an element is expressed as concentration ratios, FW YBS B/FW YBS T and are plotted vs atomic mass.…”

“…A porous dark substance, here denoted Ytterby Black Substance (YBS), was observed in 2012 exuding from fractures in an underground tunnel leading to the main shaft of the Ytterby mine, Sweden. It was established that the main component was a microbially mediated birnessite-type Mn-oxide with the assessed composition M 0.4–0.6 [Mn(III, IV)] 2 O 4 ∙(H 2 O) n , where M was predominantly Ca, Mg and rare earth elements (REE) (Sjöberg et al 2017 , 2018 ). The REE fraction constituted as much as 10 000 ppm of the dry mass, but there were also a number of other elements associated with the birnessite phase.…”