show Abstracthide AbstractMicrobial Dark Matter project: Applying single-cell genomics, we targeted and sequenced uncultivated archaeal and bacterial cells from nine diverse habitats belonging to 28 major uncharted branches of the tree of life. With this genomic information, we could resolve numerous intra- and inter-phylum level relationships and discovered unexpected metabolic features that extend our understanding of biology and challenge established boundaries between the three domains of life.