A global atlas of subsurface microbiomes reveals phylogenetic novelty, large scale biodiversity gradients, and a marine-terrestrial divide.

Marine and terrestrial subsurface environments represent one of the largest habitats for microbial life on Earth. Despite the global importance of microbial communities for biogeochemical cycling and biodiversity, the differences in diversity and composition between marine and terrestrial as well as between surface and subsurface microbiomes remain unclear. We analyzed 523 archaeal and 1211 bacterial 16S rRNA gene amplicon datasets and 136 metagenomes from globally distributed environments, including lakes, estuaries, caves, hot springs, aquifers, coasts, hydrothermal vents, cold seeps, and the subseafloor. All samples were sequenced on the same sequencer using the same chemistry and workflows to minimize bias and ensure comparability. Archaeal and bacterial richness, evenness and composition fundamentally differed between marine and terrestrial microbiomes, revealing a marine-terrestrial divide that mirrors patterns in plant and animal diversity. We further show that marine microbiomes are more phylogenetically diverse than terrestrial microbiomes. Within marine and terrestrial biomes, we find substantial community overlap between surface and subsurface environments suggesting a global diversity continuum rather than a discrete subsurface biosphere. Subsurface archaeal diversity far exceeded that of surface ecosystems suggesting that the subsurface holds a remarkable and largely underestimated fraction of Earth"s archaeal diversity. We identify specific archaeal and bacterial clades predominantly found in marine (e.g., Lokiarchaeia, Caldatribacteria) and terrestrial (e.g., Hadarchaeia, Firmicutes) subsurface ecosystems. Our analyses of metagenome-derived 16S rRNA genes and ribosomal protein S3 genes support the observed trends and findings. None of the included subsurface ecosystems appeared to be exhaustively sampled, indicating that considerable microbial biodiversity and metabolic capabilities remain to be discovered. This work improves our understanding of global-scale microbial ecology and biogeography.