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

BD1-5, OP11, and OD1 bacteria have been widely detected in anaerobic environments, but their metabolisms remain unclear owing to lack of cultivated representatives and minimal genomic sampling. We uncovered metabolic characteristics for members of these phyla, and a new lineage, PER, via cultivation-independent recovery of 49 partial to near-complete genomes from an acetate-amended aquifer. All organisms were nonrespiring anaerobes predicted to ferment. Three augment fermentation with archaeal-like hybrid type II/III ribulose-1,5-bisphosphate carboxylase-oxygenase (RuBisCO) that couples adenosine monophosphate salvage with CO(2) fixation, a pathway not previously described in Bacteria. Members of OD1 reduce sulfur and may pump protons using archaeal-type hydrogenases. For six organisms, the UGA stop codon is translated as tryptophan. All bacteria studied here may play previously unrecognized roles in hydrogen production, sulfur cycling, and fermentation of refractory sedimentary carbon.

Climate change threatens to release abundant carbon that is sequestered at high latitudes, but the constraints on microbial metabolisms that mediate the release of methane and carbon dioxide are poorly understood. The role of viruses, which are known to affect microbial dynamics, metabolism and biogeochemistry in the oceans, remains largely unexplored in soil. Here, we aimed to investigate how viruses influence microbial ecology and carbon metabolism in peatland soils along a permafrost thaw gradient in Sweden. We recovered 1,907 viral populations (genomes and large genome fragments) from 197 bulk soil and size-fractionated metagenomes, 58% of which were detected in metatranscriptomes and presumed to be active. In silico predictions linked 35% of the viruses to microbial host populations, highlighting likely viral predators of key carbon-cycling microorganisms, including methanogens and methanotrophs. Lineage-specific virus/host ratios varied, suggesting that viral infection dynamics may differentially impact microbial responses to a changing climate. Virus-encoded glycoside hydrolases, including an endomannanase with confirmed functional activity, indicated that viruses influence complex carbon degradation and that viral abundances were significant predictors of methane dynamics. These findings suggest that viruses may impact ecosystem function in climate-critical, terrestrial habitats and identify multiple potential viral contributions to soil carbon cycling.

The results dramatically expand genomic sampling of the domain Archaea and clarify taxonomic designations within a major superphylum. This study, in combination with recently published work on bacterial phyla lacking cultivated representatives, reveals a fascinating phenomenon of major radiations of organisms with small genomes, novel proteome composition, and strong interdependence in both domains.