The draft genome of the hyperthermophilic archaeon Pyrodictium delaneyi strain hulk, an iron and nitrate reducer, reveals the capacity for sulfate reduction

Abstract

Pyrodictium delaneyi strain Hulk is a newly sequenced strain isolated from chimney samples collected from the Hulk sulfide mound on the main Endeavour Segment of the Juan de Fuca Ridge (47.9501 latitude, -129.0970 longitude, depth 2200 m) in the Northeast Pacific Ocean. The draft genome of strain Hulk shared 99.77% similarity with the complete genome of the type strain Su06^T, which shares with strain Hulk the ability to reduce iron and nitrate for respiration. The annotation of the genome of strain Hulk identified genes for the reduction of several sulfur-containing electron acceptors, an unsuspected respiratory capability in this species that was experimentally confirmed for strain Hulk. This makes P. delaneyi strain Hulk the first hyperthermophilic archaeon known to gain energy for growth by reduction of iron, nitrate, and sulfur-containing electron acceptors. Here we present the most notable features of the genome of P. delaneyi strain Hulk and identify genes encoding proteins critical to its respiratory versatility at high temperatures. The description presented here corresponds to a draft genome sequence containing 2,042,801 bp in 9 contigs, 2019 protein-coding genes, 53 RNA genes, and 1365 hypothetical genes.

Keywords: Hyperthermophile; Juan de Fuca ridge; Pyrodictiaceae; Pyrodictium delaneyi strain Hulk; Sulfate reducer.

Fig. 1

Phylogenetic tree constructed with the maximum likelihood algorithm comparing the 16S rRNA gene sequence from P. delaneyi, strain Hulk to the species type strain Su06^T and other hyperthermophilic archaea. GenBank accession numbers are listed in parentheses. Bootstrap values displayed at branch points were determined from 100 replicates [72, 73]

Fig. 2

Morphological features. Transmission (a) and scanning (b) electron micrographs of a cell of strain Hulk grown with formate as the electron donor and Fe(III) citrate and sulfate as the electron acceptors, respectively. Arrow in (a) points at the lophotrichous flagella and in (b) at membrane vesicles. Scale bars, 200 nm

Fig. 3

Sulfur metabolism. a Predicted pathway for sulfate (SO₄ ²⁻) and thiosulfate (S₂O₃ ²⁻) membrane transport and cytoplasmic assimilation (black arrows) or dissimilation (gray arrows) by strain Hulk. Dashed arrows with question marks indicate reaction enzymes lacking obvious matches in the draft genome. The sulfate, thiosulfate, and sulfite (SO₃ ²⁻) anions and the sulfide (H₂S) product are boxed. Annotated ORF and Enzyme Commission (EC) numbers are shown in gray for each reaction enzyme. b-c Growth with formate and AQDS (b) or DMSO (c) as electron acceptors. The reduction of AQDS by strain Hulk turns the cultures first brown, then orange (b). The reduction of DMSO supports increases in cell numbers compared to controls without the electron donor (c). All cultures were prepared at the optimum pH and salt concentration (7 and 2%, respectively) and incubated at the optimum temperature (90 °C)

Fig. 4

Central metabolism. EMP pathway (a), TCA cycle (b), and ribulose monophosphate (RuMP) pathway (c) predicted from the draft genome of strain Hulk. Abbreviations: P, phosphate; DHAP, dihydroxyacetone phosphate. The annotated ORF number (top) and corresponding EC number (bottom, italicized) are shown in gray. Dashed gray arrows indicate reactions catalyzed by enzymes not annotated in the draft genome

Fig. 5

Iron metabolism and motility. a-b Growth (cell numbers, black) and Fe(II) accumulation (maroon) of P. delaneyi strain Hulk in cultures with H₂ and poorly crystalline Fe(III) oxides (a) or with formate and Fe(III) citrate (b). No donor controls (open symbols) are also shown. Each data point shows the average of two biological replicates. c Archaellum gene cluster in the draft genome of strain Hulk. (DD, Death Domain superfamily protein)

Fig. 6

Nitrogen metabolism. a Genomic predictions for ammonium (NH₄) assimilation and Nap pathway for the reduction of nitrate (NO₃ ⁻) to nitrite (NO₂ ⁻) in strain Hulk. (CM, cytoplasmic membrane). b Growth (cell numbers per ml) of strain Hulk with formate and nitrate at optimum conditions of temperature (90 °C), pH (7), and osmolarity (2% NaCl) in reference to controls without the electron donor (formate)