Insights into the phylogeny and coding potential of microbial dark matter

TLDR

Genome sequencing expands our understanding of biological diversity, yet the microbial genomes available today are phylogenetically limited because most microorganisms cannot be cultivated in the laboratory. The study aims to sequence 201 uncultivated archaeal and bacterial cells from nine diverse habitats to investigate microbial dark matter. Using single‑cell genomics, the authors targeted and sequenced cells from 29 largely uncharted branches of the tree of life. The resulting genomes clarified intra‑ and inter‑phylum relationships, proposed two new superphyla, revealed novel metabolic traits such as opal‑codon amino acid usage, archaeal‑type purine synthesis in bacteria, and shared sigma factors, anchored up to 20 % of metagenomic reads, and substantially expanded the tree of life’s genomic representation.

Abstract

Genome sequencing enhances our understanding of the biological world by providing blueprints for the evolutionary and functional diversity that shapes the biosphere. However, microbial genomes that are currently available are of limited phylogenetic breadth, owing to our historical inability to cultivate most microorganisms in the laboratory. We apply single-cell genomics to target and sequence 201 uncultivated archaeal and bacterial cells from nine diverse habitats belonging to 29 major mostly uncharted branches of the tree of life, so-called 'microbial dark matter'. With this additional genomic information, we are able to resolve many intra- and inter-phylum-level relationships and to propose two new superphyla. We uncover unexpected metabolic features that extend our understanding of biology and challenge established boundaries between the three domains of life. These include a novel amino acid use for the opal stop codon, an archaeal-type purine synthesis in Bacteria and complete sigma factors in Archaea similar to those in Bacteria. The single-cell genomes also served to phylogenetically anchor up to 20% of metagenomic reads in some habitats, facilitating organism-level interpretation of ecosystem function. This study greatly expands the genomic representation of the tree of life and provides a systematic step towards a better understanding of biological evolution on our planet.