Thermococcus paralvinellae sp. nov. and Thermococcus cleftensis sp. nov. of hyperthermophilic heterotrophs from deep-sea hydrothermal vents

Abstract

Two heterotrophic hyperthermophilic strains, ES1 T and CL1 T , were isolated from Paralvinella sp. polychaete worms collected from active hydrothermal vent chimneys in the north-eastern Pacific Ocean. Both were obligately anaerobic and produced H 2 S in the presence of elemental sulfur and H 2 . Complete genome sequences are available for both strains. Phylogenetic analyses based on 16S rRNA gene sequences showed that the strains are more than 97 % similar to most other species of the genus Thermococcus. Therefore, overall genome relatedness index analyses were performed to establish that these strains are novel species. For each analysis, strain ES1 T was determined to be most similar to Thermococcus barophilus MP T , while strain CL1 T was determined to be most similar to Thermococcus sp. 4557. The average nucleotide identity scores for these strains were 84 % for strain ES1 T and 81 % for strain CL1 T , genome-to-genome direct comparison scores were 23 % for strain ES1 T and 47 % for strain CL1 T , and the species identification scores were 89 % for strain ES1 T and 88 % for strain CL1 T . For each analysis, strains ES1 T and CL1 T were below the species delineation cut-off. Therefore, based on their whole genome sequences, strains ES1 T and CL1 T are suggested to represent novel species of the genus Thermococcus for which the names Thermococcus paralvinellae sp. nov. and Thermococcus cleftensis sp. nov. are proposed, respectively. The type strains are ES1 T (5DSM 27261 T 5KACC 17923 T ) and CL1 T (5DSM 27260 T 5KACC 17922 T ).The genus Thermococcus is composed of hyperthermophilic obligate anaerobes that couple the oxidation of peptides and polysaccharides to the reduction of elemental sulfur (S u ) and protons (Bertoldo & Antranikian, 2006). In this study, the complete genome sequences of two strains of the genus Thermococcus, strain ES1 T and strain CL1 T (Jung et al., 2012, were used to establish the novelty of these strains. Both strains were isolated from Paralvinella sp. polychaete worms collected from active hydrothermal vent chimneys on the Juan de Fuca Ridge in the northeastern Pacific Ocean (Pledger & Baross, 1989;Holden et al., 2001). Notably, in a survey of 20 species of the genera Thermococcus and Pyrococcus, both strains produced noticeable amounts of H 2 even when grown on S u (Oslowski et al., 2011). In this study, strains ES1 T and CL1 T were adapted for growth without S u at 82 u C through serial transfers on 0.5 % (w/v) maltose and tryptone medium as previously described (Adams et al., 2001). The concentrations of cells and H 2 were monitored in duplicate at certain time intervals by phase-contrast microscopy (Nikon 55i) and GC (Shimadzu GC-8A). The growth rate of strain ES1 T was the same despite the presence or absence of S u (doubling times of 65 and 72 min, respectively) (Fig. 1a) while strain CL1 T grew much slower without S u (doubling time of 190 min) relative to cultures with S u (doubling time of 52 min) (Fig. 1b). Both strains grew and produced 3.25-5.05 millimoles of H 2 per Abb...

Formate hydrogenlyase and formate secretion ameliorate H2 inhibition in the hyperthermophilic archaeon Thermococcus paralvinellae

“…The question remains as to whether fhl was lost in many Thermococcus species through genetic drift or obtained by a few species through horizontal gene transfer. The fhl operon is found in distantly related Thermococcus such as T. paralvinellae and T. onnurineus (Hensley et al ., ), which may be indicative of horizontal gene transfer. However, there is no evidence of insertion elements near the operon nor G + C mol% differences that support this notion.…”

“…T. paralvinellae DSM 27261 (Hensley et al ., ) was provided by Deutsche Sammlung von Mikroorganismen und Zellkulturen (DSM). The growth media are based DSM medium 282 (Jones et al ., ) and is composed of the following per litre: 30 g of NaCl, 3.40 g of MgSO 4 ·7H 2 O, 4.1 g of MgCl 2 ·6H 2 O, 0.33 g of KCl, 0.25 g of NH 4 Cl, 0.14 g of K 2 HPO 4 , 0.14 g of CaCl 2 ·2H 2 O, 0.5 mg of NiCl 2 ·6H 2 O, 0.5 mg of Na 2 SeO 3 ·5H 2 O, 1 g of NaHCO 3 , 0.63 g of Na 2 S 2 O 3 , 0.1 g of yeast extract (vitamin B 12 ‐fortified; Difco), 10 ml of DSM medium 141 trace elements solution, 10 ml of DSM medium 141 vitamins solution, 1 ml of 0.01% (wt vol −1 ) each of (NH 4 ) 2 Fe (SO 4 ) 2 ·6H 2 O and (NH 4 ) 2 Ni(SO 4 ) 2 , 1 µM of Na 2 WO 4 ·2H 2 O and 50 µl of 0.5% (wt vol −1 ) resazurin.…”

Restoration of the di-myo-inositol-phosphate pathway in the piezo-hyperthermophilic archaeon Thermococcus barophilus

“…In this study we show that the lack of DIP accumulation of DIP in T. barophilus is linked to the presence of the putative sugar transporter locus between the IPS and IPCT/PIPS genes. A survey of the proteins involved in the synthesis of DIP performed on the sequences of the two genes (IPCT/PIPS and IPS) as well as on the putative sugar transporter genes present upstream of IPS in 6 Thermococcus species clearly shows a congruence between the phylogeny of this locus (Figure S1) and the core genome (Figure 4) and 16Sphylogenies[51] with one exception. All topologies demonstrate a well supported group containing 5 of the 6 species harboring the PST locus, comprising T. barophilus, T. litoralis, T. sibiricus, T. sp.…”

Hydrogen Production and Enzyme Activities in the Hyperthermophile Thermococcus paralvinellae Grown on Maltose, Tryptone, and Agricultural Waste

“…T. paralvinellae ES1 was isolated from a polychaete worm collected from a deep-sea hydrothermal vent in the northeastern Pacific Ocean and is commonly associated with growth on peptides and sulfur to produce H 2 S (Pledger and Baross, 1989 ). However, T. paralvinellae possesses seven hydrogenase gene clusters (Jung et al, 2014 ) and produces H 2 in lieu of H 2 S when sulfur is omitted from the medium (Hensley et al, 2014 ). In this study, T. paralvinellae produced H 2 when grown without sulfur on either a carbohydrate (maltose) or on peptides and under potentially inhibiting conditions such as high acetate concentrations and at pH 5.…”

“…Thermococcus onnurineus also produces H 2 using a formate-dependent membrane hydrogenase (Kim et al, 2010 ; Bae et al, 2012 ) and a CO-dependent membrane hydrogenase (Kim et al, 2013 ). Thermococcus paralvinellae produced H 2 when grown on both maltose and tryptone (0.5% wt vol −1 of each) without sulfur (Hensley et al, 2014 ). Its complete genome sequence contains seven hydrogenase gene clusters (Jung et al, 2014 ).…”