Genome sequencing of a single cell of the widely distributed marine subsurface Dehalococcoidia, phylum Chloroflexi

Kenneth Wasmund*, Lars Schreiber, Karen G. Lloyd, Dorthe G. Petersen, Andreas Schramm, Ramunas Stepanauskas, Bo Barker Jørgensen, Lorenz Adrian

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

Abstract

Bacteria of the class Dehalococcoidia (DEH), phylum Chloroflexi, are widely distributed in the marine subsurface, yet metabolic properties of the many uncultivated lineages are completely unknown. This study therefore analysed genomic content from a single DEH cell designated 'DEH-J10' obtained from the sediments of Aarhus Bay, Denmark. Real-time PCR showed the DEH-J10 phylotype was abundant in upper sediments but was absent below 160 cm below sea floor. A 1.44 Mbp assembly was obtained and was estimated to represent up to 60.8% of the full genome. The predicted genome is much larger than genomes of cultivated DEH and appears to confer metabolic versatility. Numerous genes encoding enzymes of core and auxiliary beta-oxidation pathways were identified, suggesting that this organism is capable of oxidising various fatty acids and/or structurally related substrates. Additional substrate versatility was indicated by genes, which may enable the bacterium to oxidise aromatic compounds. Genes encoding enzymes of the reductive acetyl-CoA pathway were identified, which may also enable the fixation of CO 2 or oxidation of organics completely to CO 2. Genes encoding a putative dimethylsulphoxide reductase were the only evidence for a respiratory terminal reductase. No evidence for reductive dehalogenase genes was found. Genetic evidence also suggests that the organism could synthesise ATP by converting acetyl-CoA to acetate by substrate-level phosphorylation. Other encoded enzymes putatively conferring marine adaptations such as salt tolerance and organo-sulphate sulfohydrolysis were identified. Together, these analyses provide the first insights into the potential metabolic traits that may enable members of the DEH to occupy an ecological niche in marine sediments.

Original languageEnglish
Pages (from-to)383-397
Number of pages15
JournalISME Journal
Volume8
Issue number2
Early online date22 Aug 2013
DOIs
Publication statusPublished - 26 Feb 2014

Keywords

  • marine
  • sediment
  • Dehalococcoidia
  • Chloroflex
  • single-cell
  • genome

Fingerprint

Dive into the research topics of 'Genome sequencing of a single cell of the widely distributed marine subsurface Dehalococcoidia, phylum Chloroflexi'. Together they form a unique fingerprint.

Cite this