BioMetArchive: Deciphering the genetic content of metagenome-assembled genomes along the 1 Ma sedimentary sequence of ferruginous Lake Towuti, Indonesia

Ferruginous (iron-rich, sulfate-poor) conditions prevailed in the oceans through much of Earth's history. Yet ancient biogeochemical cycles inferred from the rock record remain elusive in terms of microbial enzymatic processes, as modern analogues in which to study an active subsurface biosphere are scarce. Lake Towuti, Indonesia, features ferruginous bottom waters and sediments that offer conditions similar to those of Earth's early oceans. In spring 2015, the International Continental scientific Drilling Program recovered a 100-m-long sediment core in 156 m water depth just below the oxycline, documenting 1 million years of redox changes at the sediment-water interface (SWI). The project BioMetArchive aims to characterize the presence of a subsurface biosphere in terms of microbial density, taxonomic and functional diversity, and comprehensively integrate metagenomic with geochemistry data.

Discrete water column samples resulted in 408 metagenome-assembled genomes (MAGs) that reflected a series of endogenic processes driven by planktonic populations, namely primary and secondary organic matter production alongside iron and ammonia oxidation with subsequent iron and sulfate reduction across water layers. Down to 1 m below lake floor (mblf), terminal electron acceptors became depleted, resulting in a drastic decrease in cell densities and microbial diversity. In the fermentative zone, sedimentary geochemical conditions selected for specific microorganisms, mainly Chloroflexota and Bathyarchaeia. Metagenomic sequencing from minute DNA amounts down to 68 mblf (~750 ka) resulted in 190 MAGs. Their genetic content revealed that Anaerolineae have metabolic potential to cope with oxygen fluctuations, inhabiting ferruginous bottom waters and the SWI. In sediments, Dehalococcoidia perform organic acid secondary fermentations combined with an acetogenic Wood-Ljungdahl pathway. Below the sulfate reduction zone, Bathyarchaeia prevailed as they harbour specific enzymes to harness reactive sulfur species from hydrogen sulfide. They exhibit metabolic potential for complex carbohydrate fermentation combined with a complete (homo)acetogenic Wood-Ljungdahl pathway. This shows that Bathyarchaeia rule carbon mineralization alongside methylotrophy in deep ferruginous sediments. Our findings suggest that the deep lacustrine biosphere persisting under ferruginous conditions requires energy conservation processes that show clear analogies to those of primeval microbial life.