Small Genomes and Sparse Metabolisms of Sediment-Associated Bacteria from Four Candidate Phyla

ABSTRACT Cultivation-independent surveys of microbial diversity have revealed many bacterial phyla that lack cultured repre-sentatives. These lineages, referred to as candidate phyla, have been detected across many environments. Here, we deeply se-quencedmicrobial communities from acetate-stimulated aquifer sediment to recover the complete and essentially complete ge-nomes of single representatives of the candidate phyla SR1,WWE3, TM7, and OD1. All four of these genomes are very small, 0.7 to 1.2 Mbp, and have large inventories of novel proteins. Additionally, all lack identifiable biosynthetic pathways for several key metabolites. The SR1 genome uses the UGA codon to encode glycine, and the same codon is very rare in the OD1 genome, sug-gesting that the OD1 organism could also transition to alternate coding. Interestingly, the relative abundance of the members of SR1 increased with the appearance of sulfide in groundwater, a pattern mirrored by a member of the phylum Tenericutes. All four genomes encode type IV pili, which may be involved in interorganism interaction. On the basis of these results and other recently published research, metabolic dependence on other organismsmay be widely distributed across multiple bacterial can-didate phyla. IMPORTANCE Few or no genomic sequences exist for members of the numerous bacterial phyla lacking cultivated representatives, making it difficult to assess their roles in the environment. This paper presents three complete and one essentially complete ge-nomes of members of four candidate phyla, documents consistently small genome size, and predicts metabolic capabilities o