Lacustrine Deep Biosphere and Sediment Substrates along a Million-Year Ferruginous Archive

Lake Towuti, Indonesia exhibits anoxic bottom waters with ferruginous (iron-rich, sulfate-poor) conditions underlain by a long depositional record tinged with redox changes. As a modern analogue of Earth's early ferruginous oceans, it enables the study of an active microbial subsurface biosphere and its role in organic matter and iron mineralization. Combining 16S rRNA genes, cell counts, pore water geochemistry and bulk sediment profiles from a 100-m-long core, we present the first comprehensive characterization of the deep biosphere along a million-year lacustrine archive. Due to ferruginous conditions, pore water electron acceptors became depleted in shallow sediments, resulting in a drastic decrease in cell densities into the fermentative zone, with Bathyarchaeia predominating in the microbial composition. Although microbial alpha and beta diversity reflected initial depletion of substrates during burial, they also varied across the successive lithologies composing the stratigraphy, indicating some entanglement with Lake Towuti's depositional history. The upper unit (0-20 mblf) sheltered a dense and diverse microbial community involved in organic matter remineralization, actively producing and converting volatile fatty acids into carbon dioxide and methane. The second unit (20-70 mblf) harboured poorly diverse microbial communities pre-adapted to nutrient limitation. In contrast, the lowermost unit (70-100 mblf) revealed an increased microbial diversity reflecting terrigenous sources. Despite Bathyarchaeia persisting as prime constituents of the deep biosphere, increased variability in 16S rRNA gene composition was observed in discrete sediment layers (tephra, diatom oozes, turbidites, peat). This demonstrated that dynamic depositional conditions are still traceable in selective assemblages, whereas stratified microbial communities drive reductive diagenesis.