A metagenomic view of novel microbial and metabolic diversity found within the deep terrestrial biosphere

ABSTRACT

The deep terrestrial subsurface is a large and diverse microbial habitat and a vast repository of biomass. However, in relation to its size and physical heterogeneity we have limited understanding of taxonomic and metabolic diversity in this realm. Here we present a detailed metagenomic analysis of samples from the Deep Mine Microbial Observatory (DeMMO) spanning depths from the surface to 1.5 km deep in the crust. From these eight geochemically and spatially distinct fluid samples we reconstructed ∼600 metagenome assembled genomes (MAGs), representing 50 distinct phyla and including 18 candidate phyla. These novel clades include many members of the Patescibacteria superphylum and two new MAGs from candidate phylum OLB16, a phylum originally identified in DeMMO fluids and for which only one other MAG is currently available. We find that microbes spanning this expansive phylogenetic diversity and physical space are often capable of numerous dissimilatory energy metabolisms and are poised to take advantage of nutrients as they become available in relatively isolated fracture fluids. This metagenomic dataset is contextualized within a four-year geochemical and 16S rRNA time series, adding another invaluable piece to our knowledge of deep subsurface microbial ecology.