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 representatives. These lineages, referred to as candidate phyla, have been detected across many environments. Here, we deeply sequenced microbial communities from acetate-stimulated aquifer sediment to recover the complete and essentially complete genomes 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, suggesting 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 organisms may be widely distributed across multiple bacterial candidate phyla.

Recovery of nearly 8,000 metagenome-assembled genomes substantially expands the tree of life

“…Several tools have been developed that exploit these sources of information to produce genomes from metagenomic data [18][19][20][21] and there are ongoing efforts to evaluate the effectiveness of different approaches 22 . Although closed genomes have been obtained using metagenomic binning methods 10,23 , MAGs are typically incomplete and may contain contigs from multiple strains or species due to challenges in distinguishing between related community members both in the assembly and binning processes 19,24 . This has spurred the development of methods for assessing the quality of recovered MAGs in order to allow biological inferences to be made with regards to their estimated completeness and contamination 25,26 .…”

Metabolic interdependencies between phylogenetically novel fermenters and respiratory organisms in an unconfined aquifer

“…The results uncovered an obligatory fermentation-based lifestyle in CP organisms including members of SR1 (previously referred to as ACD80), OP11, OD1, PER, BD1-5 and WWE3 (three genomes previously assigned to OD1; Wrighton et al, 2012). This finding was later supported by complete genomes for members of SR1, OD1 and WWE3 recovered from acetate-stimulated sediments from this same site (Kantor et al, 2013). These phyla have been identified from non-carbon amended sediments from the same metal-contaminated aquifer and pristine environments (Briée et al, 2007;Peura et al, 2012).…”

“…In light of the importance of fermentation previously identified in CP genomes Kantor et al, 2013), we screened the entire community for genes encoding the hydrolysis of plant-derived materials and chitin, the two most abundant biopolymers (Berlemont and Martiny, 2013). We identified members of the OP11 (ACD38), OD1 (ACD8) and a genomic fragment with unknown affiliation (ACD79, 16x coverage) that could encode the capacity for the complete degradation of cellulose to monomeric carbon, which can be oxidized via glycolysis.…”

Genome reduction in an abundant and ubiquitous soil bacterium ‘Candidatus Udaeobacter copiosus’

“…U. copiosus genome (such as large numbers of pseudogenes or unusually large intergenic spaces). Although most contemporary free-living organisms with streamlined genomes inhabit aquatic environments 27,41 , compared to these aquatic environments, soil is more heterogeneous 42 , has greater overall microbial diversity 43 and slower carbon turnover 44 . Therefore, the functional complexity required by soil microbes to succeed within a given niche is probably large relative to that required by aquatic microbes.…”