Sulfide Oxidation, Nitrate Respiration, Carbon Acquisition, and Electron Transport Pathways Suggested by the Draft Genome of a Single Orange Guaymas Basin Beggiatoa (Cand. Maribeggiatoa) Sp. Filament

Mar Genomics. 2013 Sep;11:53-65. doi: 10.1016/j.margen.2013.08.001. Epub 2013 Sep 3.


A near-complete draft genome has been obtained for a single vacuolated orange Beggiatoa (Cand. Maribeggiatoa) filament from a Guaymas Basin seafloor microbial mat, the third relatively complete sequence for the Beggiatoaceae. Possible pathways for sulfide oxidation; nitrate respiration; inorganic carbon fixation by both Type II RuBisCO and the reductive tricarboxylic acid cycle; acetate and possibly formate uptake; and energy-generating electron transport via both oxidative phosphorylation and the Rnf complex are discussed here. A role in nitrite reduction is suggested for an abundant orange cytochrome produced by the Guaymas strain; this has a possible homolog in Beggiatoa (Cand. Isobeggiatoa) sp. PS, isolated from marine harbor sediment, but not Beggiatoa alba B18LD, isolated from a freshwater rice field ditch. Inferred phylogenies for the Calvin-Benson-Bassham (CBB) cycle and the reductive (rTCA) and oxidative (TCA) tricarboxylic acid cycles suggest that genes encoding succinate dehydrogenase and enzymes for carboxylation and/or decarboxylation steps (including RuBisCO) may have been introduced to (or exported from) one or more of the three genomes by horizontal transfer, sometimes by different routes. Sequences from the two marine strains are generally more similar to each other than to sequences from the freshwater strain, except in the case of RuBisCO: only the Guaymas strain encodes a Type II enzyme, which (where studied) discriminates less against oxygen than do Type I RuBisCOs. Genes subject to horizontal transfer may represent key steps for adaptation to factors such as oxygen and carbon dioxide concentration, organic carbon availability, and environmental variability.

Keywords: Hybrid cluster protein; ONR; Octaheme cytochrome; RuBisCO; TCA; rTCA.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Amino Acid Sequence
  • Bayes Theorem
  • Beggiatoa / genetics*
  • Carbon / metabolism
  • DNA, Bacterial / genetics
  • Electron Transport / genetics
  • Genome, Bacterial*
  • Geologic Sediments / microbiology
  • Likelihood Functions
  • Models, Genetic
  • Molecular Sequence Data
  • Nitrates / metabolism
  • Oxidative Phosphorylation
  • Phylogeny*
  • Pigmentation
  • Sequence Analysis, DNA
  • Sulfides / metabolism


  • DNA, Bacterial
  • Nitrates
  • Sulfides
  • Carbon