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A comparative genome analysis of the Bacillota (Firmicutes) class Dehalobacteriia.

Young C Song1, Sophie I Holland2,3, Matthew Lee2

  • 1The University of Queensland, School of Chemistry and Molecular Biosciences, Australian Centre for Ecogenomics, St Lucia, Queensland, 4072, Australia.

Microbial Genomics
|June 9, 2023
PubMed
Summary

Dehalobacteriia members are primarily fermentative scavengers, utilizing amino acids for growth. Anaerobic dichloromethane degradation is a recently acquired trait found only in some Dehalobacteriales.

Keywords:
Dehalobacteriiacomparative genomicsdichloromethane degradationmetabolic reconstructionproteome

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Area of Science:

  • Microbiology
  • Environmental Science
  • Genomics

Background:

  • Dehalobacterium formicoaceticum anaerobically ferments dichloromethane (DCM).
  • D. formicoaceticum is the sole axenic representative of the Dehalobacteriia class.
  • Culture-independent studies reveal significant Dehalobacteriia diversity in anoxic environments.

Purpose of the Study:

  • To conduct a comparative analysis of 10 Dehalobacteriia members.
  • To infer the evolutionary history of anaerobic DCM degradation within the Dehalobacteriia.
  • To identify conserved and variable traits across the class.

Main Methods:

  • Comparative genomic analysis of 10 Dehalobacteriia species.
  • Inference of metabolic pathways and functional traits.
  • Experimental confirmation of growth substrates for D. formicoaceticum.

Main Results:

  • Anaerobic DCM degradation appears to be a recently acquired trait, limited to certain Dehalobacteriales.
  • Common class-wide traits include amino acid utilization, diverse electron-bifurcating complexes, and S-layers.
  • D. formicoaceticum can grow on serine without DCM; DCM growth shows high abundance of electron-bifurcating and S-layer proteins.

Conclusions:

  • Dehalobacteriia are likely low-abundance fermentative scavengers in anoxic habitats.
  • The class exhibits metabolic versatility, with DCM degradation being a specialized adaptation.
  • Electron-bifurcating complexes and S-layers are key features of this bacterial lineage.