An anaerobic microbial enrichment culture was used to study members of candidate phyla that are difficult to grow in the lab. We were able to visualize tiny “
Nealsonbacteria” cells attached to a large
cell, revealing a novel episymbiosis.
AbstractThe Candidate Phyla Radiation (CPR, or superphylum Patescibacteria) is a very large group of bacteria with few cultivated representatives first discovered by culture-independent metagenomic analyses. Within the CPR, the candidate phylum Parcubacteria (previously OD1) is prevalent in anoxic lake sediments and groundwater. We identified a bacterium belonging to the Parcubacteria in a methanogenic benzene-degrading enrichment culture originally derived from oil-contaminated sediments. Candidatus Nealsonbacteria DGGOD1a is the only bacterium other than a previously identified benzene-degrading fermenter (Deltaproteobacteria Candidate Sva0485 clade ORM2) consistently and abundantly detected in all active benzene-degrading transfers of this culture. Therefore, we hypothesized that DGGOD1a must serve an important role in sustaining anaerobic benzene metabolism in the consortium. Growth experiments using a variety of possible substrates suggested that it is involved in biomass recycling. Microscopic observations supported by molecular analyses and a closed genome revealed an epibiont lifestyle with very small Ca. Nealsonbacteria DGGOD1a closely associated with much larger Methanosaeta. The images reveal a first example of cross-domain episymbiosis that may apply to other Ca. Nealsonbacteria found in diverse environments.
AbstractThe 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.