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Desulfotomaculum Halophilum Sp. Now, a Halophi I Ic Sulfate-Reducing

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Desulfotomaculum Halophilum Sp. Now, a Halophi I Ic Sulfate-Reducing International Journal of Systematic Bacteriology (1 998), 48, 333-338 Printed in Great Britain Desulfotomaculum halophilum sp. now, a halophiI ic sulfate-reducing bacterium isolated from oil production facilities C. Tardy-Jacquenod,' M. Magot,' B. K. C. Patel,3 R. Matheron4 and P. Caumette' Author for correspondence: P. Caumette. Tel: + 33 5 56 22 39 01. Fax: + 33 5 56 83 51 04. 1 La boratoire A halophilic endospore-forming,sulfate-reducing bacterium was isolated from d'OcCa nograp h ie an oilfield brine in France. The strain, designated SEBR 3139, was composed of Biologique, UniversitC Bordeaux 1, 2 rue du long, straight to curved rods. It grew in 1-14% NaCl with an optimum at 6%. Professeur Jolyet, F-33120 On the basis of morphological, physiologicaland phylogenetical Arcachon, France characteristics, strain SEBR 3139 should be classified in the genus 2 Sanofi Recherche, Centre Desulfotomaculum. However, it is sufficiently different from the hitherto de Lab&ge, F-31676 described Desulfotomaculum species to be considered as a new species. Strain Labege, France SEBR 3139' (= DSM 115593 represents the first moderate halophilic species of 3 Faculty of Science and the genus Desulfofomaculum. The name Desulfotomaculum halophilum Technology, Griff ith University, Nathan, sp. nov. is proposed. Brisbane, Australia 41 11 4 Laboratoire de Microbiologie, UniversitC Keywords: Desulfotomaculum halophilum, halophile, sulfate-reducing bacterium, oil des Sciences et Techniques production de Saint-JCrdme, F-13397 Marseille cedex 20, France INTRODUCTION NaCl. Strain SEBR 3 139 represents the first halophilic spore-forming, sulfate-reducing bacterium described Sulfate-reducing bacteria that form heat-resistant so far. Based on 16s rDNA sequence comparisons, endospores are classified in the genus Desulfoto- strain SEBR 3139 was found to be phylogenetically rnaculum (3). The genus currently includes thermo- related to Desulfotornaculurn, but is sufficiently dif- philic and mesophilic species, all of which are capable ferent from the recognized Desulfutornaculum species of using a large number of substrates (26). Most to be classified as a new species of the genus. We Desulfotomaculum species grow best in freshwater propose the name Desulfotomaculum halophilum sp. media and tolerate low salt concentrations. Desulfotu- nov. rnaculurn geothermicum (7), isolated from saline geo- thermal ground water, was described as a halotolerant species of this genus. In addition, two other unnamed METHODS types, probably adapted to a saline environment, were Source of the isolate. Strain SEBR 3139T (T = type strain) isolated from an oilfield (6) and from marine sediments was isolated from a French oil-producing well in the Paris (13). In 1979, Nazina & Rozanova (20) described a Basin. Anoxic samples of a mixture of formation saline subspecies of a thermophilic and slightly halophilic ground water and oil were aseptically collected at the Desulfotornaculum from oil deposits. The strain named wellhead. Sampling and primary cultures of SRB were done Desulfotomaculum nigrijicayts subsp. salinus was able as previously described (1, 17). The in situ temperature of the fluid at the depth of 1820 m was 85 "C, and the pressure was to tolerate up to 4% NaCl. 19.4 MPa. The fluid temperature at the wellhead was 60 "C. In the course of a survey of different oilfields, we The total salinity of this formation water was 70 g 1-1 (55 g isolated several strains of sulfate-reducing bacteria (1, 1-1 NaC1). The salinity of the culture medium was adjusted 18, 24, 25), including the mesophilic spore-forming according to the in situ conditions, but the incubation strain designated SEBR 3 139, an isolate from a French temperature was 35 "C. oilfield brine able to grow at salinities of about 14% Media and culture conditions. The strain was isolated using the streak plate method as described elsewhere (17). The strain was grown and maintained in anoxic medium con- The GenBanUEMBL accession number for thel6S rDNA sequence of strain taining (1-1 distilled water) : 3.0 g Na,SO,, 6.0 g CaCl, .2H,O, SEBR 313gT is U88891. 40 g NaCl, 2.0 g KC1, 0.3 g NH,Cl, 0.2 g KH,PO,, 8.0 g 00602 0 1998 IUMS 333 C. Tardy-Jacquenod and others boiling, the medium was cooled under an N,/CO, (90: 10) gas mixture and the pH was adjusted to 7.2-7-3. The medium was dispensed into tubes for anaerobic cultures (Bellco) and plasma bottles (60 ml) containing 1-2 g iron powder (Pro- labo) per 10 ml medium. Tubes and plasma bottles were then sealed with black butyl rubber stoppers, gassed with N,/CO, (90: lo), and autoclaved for 30 min at 105 "C. Only tubes with anoxic culture medium (as indicated by resazurine colour reduction from pink to colourless) were used. The purity of the strain was checked by using both phase- contrast microscopy and growth tests (both aerobically and anaerobically) in sulfate-free TYG medium (2). Morphology. The cell morphology was observed with a phase-contrast microscope (Olympus BH-2). Photomicro- graphs were obtained using the agar slide method (22). Negative staining of cells was achieved with 1 YOphospho- tungstic acid and viewed with a transmission electron microscope. The fine structure of the cells was studied by transmission electron microscopy after fixation of a cell pellet with osmic acid and ultrathin sectioning of the cells according to Glazer et al. (12). Photomicrographs of the sections were obtained with a JEOL 1200 EX electron microscope. Fig. 7. Phase-contrast photomicrograph of D. halophilum strain SEBR 313gT, grown with lactate as carbon and energy source. Metabolism and physiology. The physiological and meta- Bar, 10pm. The various parts show different stages of cell bolic tests used to characterize the strains included the sporulation. ability to use different carbon substrates and energy sources, a variety of electron acceptors, fermentative growth (Table l), and growth tests at different temperature, pH and MgC1,. 6H,O, 0.1 g SrCl,, 1 ml trace element solution SL 12 salinity; they have been described in a previous paper (17). (9), 0-1 ml 1 YOresazurine solution, 3-0 g MOPS buffer, 6 ml Bacterial growth was estimated after two consecutive trans- 60 YOsodium lactate solution, and 1.0 g yeast extract. After fers in the same test culture medium, by (i) observing the Fig. 2. Electron micrographs of D. halophilum strain SEBR 313gT. (a) Negative staining showing polar flagellum; bar, 500nm; (b) thin section of a cell showing the Gram-positive cell wall; bar, 200 nm. 334 International Journal of Systematic Bacteriology 48 Desulfotomaculum halophilum sp. nov. formation of black deposits in the tubes revealing sulfide Table 7. Electron donors and acceptors tested for the production ; (ii) observing bacterial division microscopi- growth of D. halophilum strain SEBR 313gT cally; and (iii) measuring end products from substrate .. .. .. .. .. .. , .. , . , , .. , . , .. , .. , .. .. .. utilization by HPLC as described by Cayol et al. (5). Growth was checked after 7 d incubation. - No growth; + G + C content of the DNA. The G + C content of strain SEBR good growth; (+) slight growth. The following substrates 3 139T DNA was determined by HPLC at the Identification were tested in the presence of sulfate, but were not utilized Service of the DSMZ - Deutsche Sammlung von Mikro- (mM): fumarate (lo), succinate (lo), propionate (lo), glycerol organismen und Zellkulturen (Braunschweig, Germany). (lo), n-butyrate (lo), isobutyrate (9,valerate (3,crotonate (2), octanoate (2), nonanoate (2), palmitate (9,tartrate (2), 165 rRNA sequence studies. Purification of genomic DNA, benzoate (5), 3,4,5-trimethoxybenzoate(25), citrate (9,2- amplification and purification of the 16s rRNA gene (16s oxoglutarate (9,gluconate (lo), glutarate (9,gallate (5), rDNA) from strain SEBR 3139T were by previously de- glycollate (2), thioglycollate (2), thioacetamide (2), methanol scribed techniques (16, 23). The purified PCR product was (lo), 2-propanol (lo), acetone(5), glucose (9,fructose (9, sequenced directly on an ABI automated DNA sequencer by catechol (05), alanine (9,lysine (lo), methionine (lo), using a Prism Dideoxy Terminator Cycle Sequencing Kit cysteine (9,glutamate (9,aspartate (3,glycine betaine (9, and protocols recommended by the manufacturer (Applied glycine (5), indole (0.25), phenol (0.5), nicotinate (2). Biosystems). Using the sequence editor, ae2, the 16s rDNA sequence of the strain SEBR 3139T was aligned with Characteristic Result sequences obtained from the Ribosomal RNA Database Project, version 5.0 (19), and from GenBank. Positions of sequence and alignment uncertainty were omitted from the Growth (with 20 mM sulfate) on: analysis, and pairwise evolutionary distances of 820 un- H,+CO, (0.1 MPa )* ambiguous nucleotides from a total of 1526 nucleotides H,+acetate (0.1 MPa, 10 mM) sequenced were computed. Phylogenetic analysis was per- Lactate (10 mM) formed using programs which form part of the PHYLIP Pyruvate (10 mM) package and include DNADIST (Jukes & Cantor option), Malate (10 mM) NEIGHBOR-JOINING,transversion analysis and DNAPARS (1 1). Formate + acetate (1 0 mM) Tree topology was re-examined using 100 bootstrapped data Acetate (10 mM) sets for which a script file with the following PHYLIP programs was used : SEQBOOT,DNADIST, FITCH and CONSENSE. Ethanol( 10 mM) Programs in the phylogenetic package MEGA (15) were also Butanol(l0 mM) used. PHYLIP programs were run on a Sun SPARC work Crude oil? station and MEGA was run on a Compaq notebook (Contura Growth (without sulfate) on : model 41 OCX). Pyruvate (10 mM) Lactate (10 mM) RESULTS Electron acceptors (with lactate) : Cell morphology Sulfate (20 mM) Sulfite (1 0 mM) The cells of strain SEBR 3 39T are straight to curved Thiosulfate (10 mM) rods, 0.5 pm wide and 3-6 Im long (Fig. 1). They are Sulfur motile by a single polar flagellum (Fig. 2a). The Fumarate (10 mM) formation of oval and terminal spores was observed. Nitrate (10 mM) Gas vesicles were never observed.
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