BioMetArchive – Subsurface biosphere metagenomics along the 1 Ma sedimentary archive of ferruginous Lake Towuti, Indonesia

Lake Towuti, Indonesia is a stratified ferruginous (iron-rich, sulfate-poor) system whose deep basin experienced dynamic changes in trophic and redox conditions since the Middle Pleistocene. As wet and dry periods alternated and sediment accumulated, microbial life sustained by metals and organic substrates became entombed in the subsurface. A 1 Ma stratigraphic archive retrieved by the International Continental scientific Drilling Program (ICDP) was sampled aseptically on site for microbiology analysis. Through taxonomic and functional analyses (16S rRNA amplicons, metagenomics), the BioMetArchive project aims at the first comprehensive characterization of the lacustrine subsurface biosphere in terms of diversity, abundance and metabolic functions.

Metagenomic data combined with high resolution cell counts and pore water geochemistry allowed to characterize the distribution of microorganisms throughout the core and to identify which microbial taxa and metabolic features are involved in the major biogeochemical cycles and organic matter remineralization during sediment burial. Results show a drastic decrease in the cell counts (from 10⁹ to 10⁴) as electron acceptors in the pore water chemistry become depleted within the upper 5 m of the sediment. Results of taxonomic and metagenomic analyses indicate that the sediment ferruginous conditions predominantly select for fermentative Bathyarchaeia. Metabolic features attributed to this entirely uncultivated phylum explaining their selective growth were indicative of sulfur transformations, organic matter fermentation and homoacetogenic dark carbon fixation. Thus, Lake Towuti shelters a deep biosphere displaying similarities to early life’s processes in ferruginous systems, which provides a direct link between cryptic sulfur cycling and redox conservative fermentations.