Candidate phyla (or candidate divisions) are deeply rooted groups of Bacteria or Archaea that currently lack cultivated representatives. By combining traditional enrichment and cultivation practices with modern metagenomic based techniques, this work describes two candidate phyla more thoroughly than could have been produced by focusing on one aspect alone.
Members of the candidate phylum OP11 were enriched from two geographically distinct geothermal springs: one from Ngatamariki, Waikato, New Zealand and the other from Lakelse, B.C., Canada. The organisms were grown under thermophilic and anaerobic conditions, using cellulose as the sole substrate. Stable isotope probing was also used to confirm carbon flow from cellulose to OP11 in both sites. Continued studies on the Canadian spring demonstrated that the OP11 organism was possibly utilizing H2 and a degradation byproduct of cellulose under fermentative conditions as its energy source. Additionally, this work provides evidence for symbiosis between the OP11 and a member of the Chloroflexi phylum; a result that has not been demonstrated previously. Metagenomic analysis of the two organisms further described the relationship, where the Chloroflexi was likely acting as the primary cellulolytic organism, and OP11 was consuming degradation byproducts.
Additionally, a natural FeSO4 spring site, located in Kootenay National Park, B.C., Canada was also studied for the prevalence of the WPS-2 candidate phylum. The work includes an environmental survey using 16S rRNA gene based community analysis to demonstrate the candidate phylum’s distribution throughout the site. High-throughput metagenomic sequencing and microfluidic cell sorting coupled with whole genome sequencing were used to create a genomic reconstruction of a member of the WPS-2 candidate phylum. This represents the first genomic reconstruction from this group of organisms.
Through this work, substantial progress was made in further describing several deeply rooted, uncultured groups of bacteria. It presents a thorough exploration of these largely unstudied organisms, and presents a discussion on combining modern metagenomics based techniques with more traditional tools of environmental microbiology in order to describe currently uncultivated organisms.