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

• Published in: Marine genomics Vol. 11; pp. 53 - 65
• Main Authors: MacGregor, Barbara J., Biddle, Jennifer F., Harbort, Christopher, Matthysse, Ann G., Teske, Andreas
• Format: Journal Article
• Language: English
• Published: Netherlands Elsevier B.V 01.09.2013
• Subjects: acetates; Amino Acid Sequence; Bayes Theorem; Beggiatoa; Beggiatoa - genetics; Beggiatoa alba; Beggiatoaceae; carbon; Carbon - metabolism; carbon dioxide; carboxylation; decarboxylation; DNA, Bacterial; DNA, Bacterial - genetics; electron transfer; Electron Transport; Electron Transport - genetics; freshwater; genes; genetics; Genome, Bacterial; Geologic Sediments; Geologic Sediments - microbiology; Hybrid cluster protein; Likelihood Functions; Marine; metabolism; microbiology; Models, Genetic; Molecular Sequence Data; nitrates; Nitrates - metabolism; Octaheme cytochrome; ONR; Oryza sativa; oxidation; Oxidative Phosphorylation; oxygen; paddies; Phylogeny; Pigmentation; ribulose-bisphosphate carboxylase; rTCA; RuBisCO; sediments; Sequence Analysis, DNA; succinate dehydrogenase; succinate dehydrogenase (quinone); Sulfides; Sulfides - metabolism; TCA; tricarboxylic acid cycle; ISE, Mexico, California Gulf, Guaymas Basin; Hybrid cluster protein; ONR; TCA; RuBisCO; Octaheme cytochrome; rTCA
• DOI: 10.1016/j.margen.2013.08.001
• ISSN: 1874-7787; 1876-7478

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.