The Geoglobus acetivorans genome: Fe(III) reduction, acetate utilization, autotrophic growth, and degradation of aromatic compounds in a hyperthermophilic archaeon

Abstract

Geoglobus acetivorans is a hyperthermophilic anaerobic euryarchaeon of the order Archaeoglobales isolated from deep-sea hydrothermal vents. A unique physiological feature of the members of the genus Geoglobus is their obligate dependence on Fe(III) reduction, which plays an important role in the geochemistry of hydrothermal systems. The features of this organism and its complete 1,860,815-bp genome sequence are described in this report. Genome analysis revealed pathways enabling oxidation of molecular hydrogen, proteinaceous substrates, fatty acids, aromatic compounds, n-alkanes, and organic acids, including acetate, through anaerobic respiration linked to Fe(III) reduction. Consistent with the inability of G. acetivorans to grow on carbohydrates, the modified Embden-Meyerhof pathway encoded by the genome is incomplete. Autotrophic CO2 fixation is enabled by the Wood-Ljungdahl pathway. Reduction of insoluble poorly crystalline Fe(III) oxide depends on the transfer of electrons from the quinone pool to multiheme c-type cytochromes exposed on the cell surface. Direct contact of the cells and Fe(III) oxide particles could be facilitated by pilus-like appendages. Genome analysis indicated the presence of metabolic pathways for anaerobic degradation of aromatic compounds and n-alkanes, although an ability of G. acetivorans to grow on these substrates was not observed in laboratory experiments. Overall, our results suggest that Geoglobus species could play an important role in microbial communities of deep-sea hydrothermal vents as lithoautotrophic producers. An additional role as decomposers would close the biogeochemical cycle of carbon through complete mineralization of various organic compounds via Fe(III) respiration.

FIG 1

Electron micrographs of G. acetivorans cells. (A) Flagellum-like structures. (B) Pilus-like structures connecting two cells with an Fe(III) mineral particle. Average dimensions of pili: diameter, 7 nm; length, 300 nm. Note the different sizes of the scale bars in panels A and B and the different thicknesses of the filaments. The fine structure was studied using a JEN-100 electron microscope. Negative staining of whole cells was done with 2% phosphotungstic acid.

FIG 2

Spectrophotometric characterization of Fe(III)-reducing c-type cytochromes in the membrane fraction of G. acetivorans. Redox spectra of c-type cytochromes interacting with soluble Fe(III)-EDTA (A) or insoluble ferrihydrite (B) are presented. On both spectrograms, curve 1 represents spectra of air-oxidized c-type cytochromes contained in the membrane fraction of G. acetivorans cells, curve 2 represents difference (reduced versus oxidized) spectra of the same cytochromes after their reduction with sodium dithionite, and curve 3 represents difference spectra of the cytochromes after their reoxidation from the reduced state with 1 mM Fe(III)-EDTA (A) or with ferrihydrite (B), containing 3 mM Fe(III). Characteristic absorbance peaks of oxidized (at 407 nm) and reduced (at 424, 522, or 553 nm) c-type cytochromes are marked. Arrows indicate red shift of γ bands of reduced (peak at 429 nm) and oxidized (reversed peak at 411 nm) cytochrome c forms after incomplete reoxidation of the reduced cytochromes with ferrihydrite. All the spectra are background corrected and presented at the same scale; a separate baseline was utilized to correct difference spectra 2 and 3.

FIG 3

Clusters of genes involved in the catabolism of aromatic compounds in G. acetivorans. The genes are represented by arrows, with their numbers shown below the arrows. Coordinates are shown in kilobases (kb) according to the G. acetivorans genome sequence. The dotted lines above the arrows show the affiliation of the orthologous genes of F. placidus to gene clusters (C1 and C2), responsible for the catabolism of aromatic compounds, defined in reference . Enzyme abbreviations: Bzd, benzoyl-CoA reductase (subunits Q, P, O, and N); BCL, benzoate-CoA ligase; Dph, didehydro-pimeloyl-CoA hydratase; Hgd, 2-hydroxyglutaryl-CoA dehydratase (subunits B, A, and C); Bad, cyclohex-1-ene-1-carboxyl-CoA hydratase (BadK), 2-hydroxycyclohexane-1-carboxyl-CoA dehydrogenase (BadH), and 2-ketocyclohexane-carboxyl-CoA hydrolase (BadI).