Poster Presentation Australian Microbial Ecology 2019

Phylogenomic analysis of two recently recognised Firmicutes classes, TC1 and Dehalobacteriia (#119)

Young C Song 1 , David W Waite 1 2 , Ulrike Kappler 3 , Philip Hugenholtz 1
  1. Australian Centre of Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, St.Lucia, Queensland, Australia
  2. School of Biological Sciences, The University of Auckland, Auckland, New Zealand
  3. School of Chemistry and Molecular Biosciences, The University of Queensland, St.Lucia, Queensland, Australia

The Firmicutes is one of the most widely recognised and best studied bacterial lineages, yet substantial uncultured diversity is still being revealed within the phylum courtesy of metagenome-assembled genomes (MAGs).  Prominent examples include the two sister lineages TC1 and Dehalobacteriia, which were recently elevated to the rank of class under the rank normalised GTDB (Genome Taxonomy Database 1) taxonomy.  The GTDB has been recently created as part of an initiative to standardise microbial taxonomy based on genomic phylogeny. TC1 currently comprises only two MAGs, one of which is an endosymbiont of a fresh-water ciliate, Trimyema compressum 2, and the other from an n-alkene degrading enrichment culture. Dehalobacteriia comprises six MAGs and the genome of the first recognised cultured representative, Dehalobacterium formicoaceticum, after which the class is named. D. formicoaceticum utilises dichloromethane as its sole source of energy and carbon 3-4, while other members of this class were obtained from n-alkene- or naphthalene-degrading cultures. Metabolic reconstruction of the genomes belonging to these two classes has revealed an incomplete central carbohydrate pathway, including the tricarboxylic acid (TCA) cycle, indicative of a fermentative lifestyle in both groups. Pathways and key genes that are central to ecosystem function of the isolation source, such as methanogenesis and n-alkene and naphthalene degradation are also absent, suggesting that they scavenge organic compounds, including C1 compounds, from primary producers. All nine genomes possess complete or near-complete pathways for synthesising and degrading a number of amino acids, including arginine, serine and threonine.  Some members of the two classes also contain syntrophic propionate pathway to oxidize propionate to acetate. Such pathway has previously been described in organisms such as syntrophic sulfate-reducer, Syntrophobacter fumaroxidans 5.  These findings therefore open new possibilities toward examining the metabolic potentials of uncultured bacterial diversities obtained from syntrophic communities.

  1. Parks, D et al. Nat. Biotech. 36, 996-1004 (2018).
  2. Shinzato, N et al. Micro. Ecol. 54, 627-636 (2007).
  3. Magli, A et al. Appl. Environ. Microbiol. 64, 646-650 (1998).
  4. Magli, A et al. Arch. Microbiol. 166, 101-108 (1996).
  5. Sieber, J et al. Annu. Rev. Microbiol. 66, 429-452 (2012).