The tree of life is one of the most important organizing principles in biology1. Gene surveys suggest the existence of an enormous number of branches2, but even an approximation of the full scale of the tree has remained elusive. Recent depictions of the tree of life have focused either on the nature of deep evolutionary relationships3–5 or on the known, well-classified diversity of life with an emphasis on eukaryotes6. These approaches overlook the dramatic change in our understanding of life's diversity resulting from genomic sampling of previously unexamined environments. New methods to generate genome sequences illuminate the identity of organisms and their metabolic capacities, placing them in community and ecosystem contexts7,8. Here, we use new genomic data from over 1,000 uncultivated and little known organisms, together with published sequences, to infer a dramatically expanded version of the tree of life, with Bacteria, Archaea and Eukarya included. The depiction is both a global overview and a snapshot of the diversity within each major lineage. The results reveal the dominance of bacterial diversification and underline the importance of organisms lacking isolated representatives, with substantial evolution concentrated in a major radiation of such organisms. This tree highlights major lineages currently underrepresented in biogeochemical models and identifies radiations that are probably important for future evolutionary analyses.

TitleUnusual biology across a group comprising more than 15% of domain Bacteria . Here we reconstructed 8 complete and 789 draft genomes from bacteria representing >35 phyla and documented features that consistently distinguish these organisms from other bacteria. We infer that this group, which may comprise >15% of the bacterial domain, has shared evolutionary history, and describe it as the candidate phyla radiation (CPR). All CPR genomes are small and most lack numerous biosynthetic pathways. Owing to divergent 16S ribosomal RNA (rRNA) gene sequences, 50-100% of organisms sampled from specific phyla would evade detection in typical cultivation independent surveys. CPR organisms often have selfsplicing introns and proteins encoded within their rRNA genes, a feature rarely reported in bacteria. Furthermore, they have unusual ribosome compositions. All are missing a ribosomal protein often absent in symbionts, and specific lineages are missing ribosomal proteins and biogenesis factors considered universal in bacteria. This implies different ribosome structures and biogenesis mechanisms, and underlines unusual biology across a large part of the bacterial domain. MainWe sampled microbial communities from an aquifer adjacent to the Colorado River near the town of Rifle, Colorado, USA in 2011. Groundwater was filtered through a 1.2 µm prefilter and cells were collected on serial 0.2 and 0.1 μm filters (Extended Data Fig. 1 ). Post0.2 µm filtrates were targeted because CPR bacteria were predicted to have ultrasmall cells on the basis of their small genomes2 . Groundwater was sampled before and during an acetate amendment experiment that reproduced conditions that generated the first genomes from CPR bacteria2 Table 1 ). Total DNA and RNA were extracted from filters and sequenced. We obtained 224 gigabase pairs (Gb) of pairedend metagenomic sequence from 12 samples (150 bp reads, 6 time points, 0.2 and 0.1 μm filters; Supplementary Table 2 ). Sequence assembly generated 3.9 Gb of contiguous sequences ≥5 kb. We also obtained 181 Gb of metatranscriptomic sequence from six samples (50 bp reads, 0.2 μm filters).Assembled scaffolds were binned into genomes on the basis of their GC content, DNA sequence coverage, abundance pattern across samples, and taxonomic affiliation (binning was validated with a tetranucleotide sequence signature method; Extended Data Fig. 2 ). Overall, we reconstructed >1,750

The subterranean world hosts up to one-fifth of all biomass, including microbial communities that drive transformations central to Earth's biogeochemical cycles. However, little is known about how complex microbial communities in such environments are structured, and how inter-organism interactions shape ecosystem function. Here we apply terabase-scale cultivation-independent metagenomics to aquifer sediments and groundwater, and reconstruct 2,540 draft-quality, near-complete and complete strain-resolved genomes that represent the majority of known bacterial phyla as well as 47 newly discovered phylum-level lineages. Metabolic analyses spanning this vast phylogenetic diversity and representing up to 36% of organisms detected in the system are used to document the distribution of pathways in coexisting organisms. Consistent with prior findings indicating metabolic handoffs in simple consortia, we find that few organisms within the community can conduct multiple sequential redox transformations. As environmental conditions change, different assemblages of organisms are selected for, altering linkages among the major biogeochemical cycles.