New groups of highly divergent proteins in families as old as cellular life with important biological functions in the ocean

Abstract

Metagenomics has considerably broadened our knowledge of microbial diversity, unravelling fascinating microbial adaptations and characterising multiple novel major taxonomic groups, e.g. CPR bacteria, DPANN and Asgard archaea, and novel viruses. Such findings profoundly reshaped the structure of the tree of life and emphasised the central role of investigating uncultured organisms. However, despite significant progresses, a large portion of proteins predicted from metagenomes remain today unannotated, both taxonomically and functionally, across many biomes and in particular in oceanic waters, including at relatively lenient clustering thresholds. Here, we used an iterative network-based approach to probe a dataset of 40 million ORFs, predicted in marine environments. We assessed the environmental diversity of a selection of 53 gene families as old as cellular life, broadly distributed across the Tree of Life. About half of them harboured clusters of environmental homologs that diverged significantly from the known diversity of published complete genomes, with representatives distributed across all the ocean. Network analyses also enabled the detection of environmental clades with new structural variants of essential genes (SMC), divergent polymerase subunits forming deep branching clades in the polymerase tree, and potentially deep taxonomic groups at the basis of Archaea or Bacteria, from ultra-small microorganisms distinct from CPR and DPANN. These diverse results provide a strong proof of concept for the capabilities of sequence network approaches to make better sense of microbial dark matter across taxonomical scales. Still, further methodological developments appear warranted in order to better comprehend the most divergent members of the oceanic microbial dark matter.