Illuminating Biological Dark Matter: Novel Biology in the Deep Sea

The deep biosphere, defined as the life residing in soils and sediments extending from the Earth surface down to the several kilometers, is one of the last frontiers on Earth. Microbes residing in these nutrient- and oxygen-poor deep niches are at the proverbial ‘biotic edge’. 

We hypothesize that the biomolecule makeup, and small molecule chemistry, of the unexplored deep biosphere ecosystem is fundamentally different from the contemporary human and animal microbiomes that are being investigated elsewhere. Genes from the deep marine sediment biosphere encode enzymes that appear to be capable of producing yet-uncharacterized variations of small molecules. 

Our preliminary analyses reveal that all basic life processes – from translation machinery, to chemical defense, to organismal interaction – are different in the deep biosphere. 

More broadly, so-called biological dark matter, ‘hypothetical’ gene products without homology to proteins of known function found in publicly available DNA sequence databases, contains blueprints for new biomolecules with potential uses in biotechnology, medicine, energy, and agriculture. 

The mission of this research program is to overcome key technical, organizational, and logistical challenges that currently hinder interdisciplinary study of biological dark matter in the deep biosphere, with longer term impacts on decoding biological dark matter more generally. Mining biological dark matter has vast potential for breakthrough bio-inspired products.

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