Proposed minimal standards for description of methanogenic archaea

Methanogenic archaea are a diverse, polyphyletic group of strictly anaerobic prokaryotes capable of producing methane as their primary metabolic product. It has been over three decades since minimal standards for their taxonomic description have been proposed. In light of advancements in technology and amendments in systematic microbiology, revision of the older criteria for taxonomic description is essential. Most of the previously recommended minimum standards regarding phenotypic characterization of pure cultures are maintained. Electron microscopy and chemotaxonomic methods like whole-cell protein and lipid analysis are desirable but not required. Because of advancements in DNA sequencing technologies, obtaining a complete or draft whole genome sequence for type strains and its deposition in a public database are now mandatory. Genomic data should be used for rigorous comparison to close relatives using overall genome related indices such as average nucleotide identity and digital DNA-DNA hybridization. Phylogenetic analysis of the 16S rRNA gene is also required and can be supplemented by phylogenies of the mcrA gene and phylogenomic analysis using multiple conserved, single-copy marker genes. Additionally, it is now established that culture purity is not essential for studying prokaryotes, and description of Candidatus methanogenic taxa using single-cell or metagenomics along with other appropriate criteria is a viable alternative. The revisions to the minimal criteria proposed here by the members of the Subcommittee on the Taxonomy of Methanogenic Archaea of the International Committee on Systematics of Prokaryotes should allow for rigorous yet practical taxonomic description of these important and diverse microbes.

The ocean sampling day consortium

Ocean Sampling Day was initiated by the EU-funded Micro B3 (Marine Microbial Biodiversity, Bioinformatics, Biotechnology) project to obtain a snapshot of the marine microbial biodiversity and function of the world’s oceans. It is a simultaneous global mega-sequencing campaign aiming to generate the largest standardized microbial data set in a single day. This will be achievable only through the coordinated efforts of an Ocean Sampling Day Consortium, supportive partnerships and networks between sites. This commentary outlines the establishment, function and aims of the Consortium and describes our vision for a sustainable study of marine microbial communities and their embedded functional traits.

Desulfurobacterium atlanticum sp. nov., Desulfurobacterium pacificum sp. nov. and Thermovibrio guaymasensis sp. nov., three thermophilic members of the Desulfurobacteriaceae fam. nov., a deep branching lineage within the Bacteria

Three thermophilic, anaerobic, strictly chemolithoautotrophic, sulphur- and/or thiosulphate-reducing bacteria, designated SL17T, SL19T and SL22T, were isolated from deep-sea hydrothermal samples collected at 13 °N (East Pacific Rise), Guaymas Basin (Gulf of California) and 23 °N (Mid-Atlantic Ridge), respectively. These strains differed in their morphology, temperature range and optimum for growth, energy substrates and 16S rRNA gene sequences. The G+C content of the genomic DNA was 41 mol% (SL22T), 42 mol% (SL17T) and 46 mol% (SL19T). Comparative analysis of phenotypic and phylogenetic traits indicated that strains SL17T and SL22T represented two novel species of the genus Desulfurobacterium and that strain SL19T should be considered as a novel species of the genus Thermovibrio. The names Desulfurobacterium pacificum sp. nov. (type strain SL17T=DSM 15522T=JCM 12127T), Desulfurobacterium atlanticum sp. nov. (type strain SL22T=DSM 15668T=JCM 12129T) and Thermovibrio guaymasensis sp. nov. (type strain SL19T=DSM 15521T=JCM 12128T) are proposed for these organisms. Furthermore, phylogenetic data based on 16S rRNA gene sequence analyses correlated with the significant phenotypic differences between members of the lineage encompassing the genera Desulfurobacterium, Thermovibrio and Balnearium and that of the families Aquificaceae and Hydrogenothermaceae. It is therefore proposed that this lineage represents a new family, Desulfurobacteriaceae fam. nov., within the order Aquificales.

Vulcanibacillus modesticaldus gen. nov., sp. nov., a strictly anaerobic, nitrate-reducing bacterium from deep-sea hydrothermal vents

A novel anaerobic, moderately thermophilic, spore-forming bacterium, designated strain BRT, was isolated from deep-sea hydrothermal core samples collected at the Rainbow vent field on the Mid-Atlantic Ridge (36 degrees 14' N 33 degrees 54' W). The cells were found to be rod-shaped, non-motile, Gram-positive and spore-forming. The organism grew in the temperature range 37-60 degrees C, with an optimum at 55 degrees C, and at pH values in the range 6-8.5, with an optimum around pH 7. NaCl concentrations for growth were in the range 10-40 g l(-1), with an optimum at 20-30 g l(-1). Strain BRT grew chemo-organoheterotrophically with carbohydrates, proteinaceous substrates and organic acids with nitrate as electron acceptor. The novel isolate was not able to ferment. The G+C content of the genomic DNA was 34.5 mol%. Phylogenetic analysis of the 16S rRNA gene sequence placed strain BRT in the Bacillaceae within the class 'Bacilli'. On the basis of the phenotypic and phylogenetic data, this isolate should be described as a member of a novel genus, for which the name Vulcanibacillus gen. nov. is proposed. The type species is Vulcanibacillus modesticaldus sp. nov., with the type strain BRT (=DSM 14931T=JCM 12998T).

Thermodesulfatator indicus gen. nov., sp. nov., a novel thermophilic chemolithoautotrophic sulfate-reducing bacterium isolated from the Central Indian Ridge

A thermophilic, marine, anaerobic, chemolithoautotrophic, sulfate-reducing bacterium, strain CIR29812T, was isolated from a deep-sea hydrothermal vent site at the Kairei vent field on the Central Indian Ridge. Cells were Gram-negative motile rods that did not form spores. The temperature range for growth was 55-80 degrees C, with an optimum at 70 degrees C. The NaCl concentration range for growth was 10-35 g l(-1), with an optimum at 25 g l(-1). The pH range for growth was 6-6.7, with an optimum at approximately pH 6.25. H2 and CO2 were the only electron donor and carbon source found to support growth of the strain. However, several organic compounds were stimulatory for growth. Sulfate was used as electron acceptor, whereas elemental sulfur, thiosulfate, sulfite, cystine, nitrate and fumarate were not. No fermentative growth was observed with malate, pyruvate or lactate. The phenotypic characteristics of strain CIR29812T were similar to those of Thermodesulfobacterium hydrogeniphilum, a recently described thermophilic, chemolithoautotrophic sulfate-reducer. However, phylogenetic analyses of the 16S rRNA gene sequences showed that the new isolate was distantly related to members of the family Thermodesulfobacteriaceae (similarity values of less than 90%). The chemotaxonomic data (fatty acids and polar lipids composition) also indicated that strain CIR29812T could be distinguished from Thermodesulfobacterium commune, the type species of the type genus of the family Thermodesulfobacteriaceae. Finally, the G+C content of the genomic DNA of strain CIR29812T (46.0 mol%) was not in the range of values obtained for members of this family. On the basis of phenotypic, chemotaxonomic and genomic features, it is proposed that strain CIR29812T represents a novel species of a new genus, Thermodesulfatator, of which Thermodesulfatator indicus is the type species. The type strain is CIR29812T (=DSM 15286T=JCM 11887T).

Methanocaldococcus indicus sp. nov., a novel hyperthermophilic methanogen isolated from the Central Indian Ridge

An autotrophic, hyperthermophilic methanogen, strain SL43(T), was isolated from a deep-sea hydrothermal chimney sample collected on the Central Indian Ridge at a depth of 2420 m. The coccoid, surface-layer-carrying, Gram-negative-staining cells were heavily flagellated and exhibited a slight tumbling motility. The temperature range for growth at pH 6.5 was 50-86 degrees C, with optimum growth at 85 degrees C. The optimum pH for growth was 6.6 and the optimum NaCl concentration for growth was 30 g l(-1). The novel isolate used H(2) and CO(2) as the only substrates for growth and produced methane. Selenium and yeast extract stimulated growth significantly. In the presence of CO(2) and H(2), the organism reduced elemental sulfur to hydrogen sulfide. Growth was inhibited by chloramphenicol and rifampicin, but not by ampicillin, kanamycin, penicillin or streptomycin. The G+C content of the genomic DNA was 30.7 mol%. On the basis of 16S rRNA gene sequence analysis, this organism was most closely related to Methanocaldococcus infernus ME(T) (3.2 % distance). Its phylogenetic distinctiveness was confirmed by RFLP analysis of the 16S rDNA, a reliable tool for differentiating hyperthermophilic methanococci. On the basis of phylogenetic and physiological characteristics, it is proposed that strain SL43(T) (=DSM 15027(T)=JCM 11886(T)) be designated as the type strain of a novel species, Methanocaldococcus indicus sp. nov.

Caminibacter profundus sp. nov., a novel thermophile of Nautiliales ord. nov. within the class ‘Epsilonproteobacteria’, isolated from a deep-sea hydrothermal vent

A novel moderately thermophilic, microaerobic to anaerobic, chemolithoautotrophic bacterium, designated strain CRT, was isolated from a deep-sea hydrothermal vent site at 36°N on the Mid-Atlantic Ridge. Cells were Gram-negative, non-motile rods. The organism grew at 45–65 °C and pH 6·5–7·4, with optimum growth at 55 °C and pH 6·9–7·1. The NaCl range for growth was 5–50 g l−1(optimum 30 g l−1). Strain CRTwas an obligate chemolithoautotroph, growing with H2as energy source, sulfur, nitrate or oxygen as electron acceptors and CO2as carbon source. Hydrogen sulfide and ammonium were the respective products of sulfur and nitrate reduction. The G+C content of the genomic DNA was 32·1 mol%. Based on 16S rRNA gene sequence analysis, this organism was most closely related toCaminibacter hydrogeniphilus(94·9 % similarity). On the basis of phenotypic and phylogenetic data, it is proposed that the isolate represents a novel species,Caminibacter profundussp. nov. The type strain is CRT(=DSM 15016T=JCM 11957T). The phylogenetic data also correlate well with the significant phenotypic differences between the lineage encompassing the generaNautiliaandCaminibacterand other members of the class ‘Epsilonproteobacteria’. The lineage encompassing the generaNautiliaandCaminibacteris therefore proposed as a new order,Nautilialesord. nov., represented by a single family,Nautiliaceaefam. nov.

Deferribacter abyssi sp. nov., an anaerobic thermophile from deep-sea hydrothermal vents of the Mid-Atlantic Ridge

Two strains of thermophilic, anaerobic, chemolithoautotrophic bacteria, designated JR(T) and DR, were isolated from hydrothermal samples collected on the Mid-Atlantic Ridge from the Rainbow (36 degrees 16' N, 33 degrees 54' W) and Menez Gwen (37 degrees 50' N, 31 degrees 50' W) vent fields, respectively. Cells of both isolates were short, straight- to vibrio-shaped, motile rods with one polar flagellum, and were Gram-negative and non-sporulating. Strain JR(T) was characterized in detail. It was found to grow optimally at pH 6.5-6.7, at 60 degrees C and in the presence of 30 g NaCl l(-1). Strain JR(T) could use molecular hydrogen, acetate, succinate, pyruvate and proteinaceous compounds as electron donors, and elemental sulfur, nitrate or Fe(III) as electron acceptors. No fermentation of organic substrates occurred. The G+C content of the DNA of strain JR(T) was 30.8 mol%. Strain DR (=DSM 14927) possessed the same morphology and pH, temperature and salinity optima and ranges, and used the same electron acceptors as strain JR(T). On the basis of their 16S rDNA sequences (1517 nucleotides), strains JR(T) and DR were identical and distantly related to Deferribacter thermophilus and Deferribacter desulfuricans (95.3 and 95.2 % sequence similarity, respectively). Based on their phenotypic and phylogenetic characteristics, it is proposed that both strains are members of a new species of the genus Deferribacter, for which the name Deferribacter abyssi (type strain JR(T)=DSM 14873(T)=JCM 11955(T)) is proposed.

Vulcanithermus mediatlanticus gen. nov., sp. nov., a novel member of the family Thermaceae from a deep-sea hot vent

A novel thermophilic, microaerophilic, facultatively chemolithoheterotrophic bacterium designated strain TR(T) was isolated from a sample of a deep-sea hydrothermal chimney collected at the Rainbow vent field on the Mid-Atlantic Ridge (36 degrees 14'N). Gram-negative, non-spore-forming, non-motile rods occurred singly or in pairs. The organism grew in the temperature range 37-80 degrees C with an optimum at 70 degrees C and at pH 5.5-8.4 with an optimum around 6.7. The NaCl range for growth was 10-50 g l(-1) with an optimum of 30 g l(-1). Strain TR(T) grew chemoorganoheterotrophically with carbohydrates, proteinaceous substrates, organic acids and alcohols using oxygen or nitrate as electron acceptors. The isolate was able to grow at oxygen concentrations from 0.5 to 21%. Oxygen concentrations that promoted fastest growth ranged from 4 to 8% under agitation. The novel isolate was able to grow lithoheterotrophically with molecular hydrogen as the energy source. The G + C content of the genomic DNA was 68.4 mol%. Phylogenetic analysis of the 16S rDNA sequence placed strain TR(T) within the phylum Deinococcus-Thermus of the Bacteria. On the basis of phenotypic and phylogenetic data, it is proposed that this isolate should be described as a member of a novel species of a new genus as Vulcanithermus mediatlanticus gen. nov., sp. nov. The type strain is TR(T) (= DSM 14978T = VKM B-2292T = JCM 11956T).

Oceanithermus profundus gen. nov., sp. nov., a thermophilic, microaerophilic, facultatively chemolithoheterotrophic bacterium from a deep-sea hydrothermal vent

A novel moderately thermophilic, organotrophic, microaerophilic, facultatively chemolithotrophic bacterium, designated strain 506(T), was isolated from a deep-sea hydrothermal vent site at 13 degrees N in the East Pacific Rise. Cells were Gram-negative, non-motile rods. The organism grew in the temperature range 40-68 degrees C, with an optimum at 60 degrees C, and in the pH range 5.5-8.4, with an optimum around pH 7.5. The NaCl concentration for growth was in the range 10-50 g l(-1), with an optimum at 30 g l(-1). Strain 506(T) grew chemoorganoheterotrophically with carbohydrates, proteinaceous substrates, organic acids and alcohols using oxygen or nitrate as electron acceptor. Alternatively, strain 506(T) was able to grow lithoheterotrophically with molecular hydrogen as the energy source. The G +C content of the genomic DNA was 62.9 mol%. Phylogenetic analysis of the 16S rDNA sequence placed strain 506(T) in the family Thermaceae. On the basis of phenotypic and phylogenetic data, strain 506(T) (= DSM 14977(T) = VKM B-2274(T)) is proposed as the type strain of a novel species in a new genus, Oceanithermus profundus gen. nov., sp. nov.

Petrotoga olearia sp. nov. and Petrotoga sibirica sp. nov., two thermophilic bacteria isolated from a continental petroleum reservoir in Western Siberia

Strictly anaerobic, thermophilic bacteria (strains SL24T, SL25T, SL27, SL29 and SL32) were isolated from a deep, continental oil reservoir in Western Siberia (Russia). These motile, rod-shaped organisms were surrounded by a sheath-like structure, a feature characteristic of the Thermotogales. On the basis of partial 16S rDNA sequences (500 nucleotides), strains SL25T, SL27, SL29 and SL32 were identical. Therefore, only strains SL24T and SL25T were studied in detail. The optimum temperature for growth of both strains was 55 degrees C. Their optimum pH for growth was 7.5 and their optimum NaCl concentration was between 20 and 30 g l(-1). The novel isolates reduced elemental sulfur and cystine, but not thiosulfate or sulfate, to hydrogen sulfide. The G+C contents of the genomic DNA of strains SL24T and SL25T were respectively 35 and 33 mol%. Phylogenetically, both strains are most closely related to Petrotoga miotherma, there being 98.9-99.4% similarity between their 16S rDNA sequences. Phenotypic properties and DNA-DNA hybridization experiments indicate that the strains belong to two novel species, for which the names Petrotoga olearia (type strain SL24T = DSM 13574T = JCM 11234T) and Petrotoga sibirica (type strain SL25T= DSM 13575T = JCM 11235T) are proposed.

Nautilia lithotrophica gen. nov., sp. nov., a thermophilic sulfur-reducing epsilon-proteobacterium isolated from a deep-sea hydrothermal vent

A novel, strictly anaerobic, thermophilic sulfur-reducing bacterium, strain 525T, was isolated from tubes of the deep-sea hydrothermal vent polychaete Alvinella pompejana, collected on the East Pacific Rise (13 degrees N). This organism grew in the temperature range 37-68 degrees C, the optimum being 53 degrees C, and in the pH range 6.4-7.4, the optimum being 6.8-7.0. The NaCl range for growth was 0.8-5.0%, the optimum being 3.0%. Strain 525T grew lithoautotrophically with H2 as energy source, S0 as electron acceptor and CO2 as carbon source. Alternatively, strain 525T was able to use formate as an energy source. The G+C content of the genomic DNA was 34.7 mol%. Phylogenetic analysis of the 16S rDNA gene sequence placed strain 525T in the epsilon-subclass of the Proteobacteria, where it forms a deep cluster with recently isolated relatives. On the basis of phenotypic and phylogenetic differences between strain 525T and its closest phylogenetic relatives, it is proposed that the new isolate should be described as a member of a new genus, Nautilia, for which the name Nautilia lithotrophica gen. nov., sp. nov. is proposed. The type strain is strain 525T (= DSM 13520T).

Bacterial origin for the isoprenoid biosynthesis enzyme HMG-CoA reductase of the archaeal orders Thermoplasmatales and Archaeoglobales

The enzyme 3-hydroxy-3-methylglutaryl coenzyme A reductase (HMG-CoA reductase or HMGR) fulfills an essential role in archaea, as it is required for the synthesis of isoprenoid ethers, the main component of archaeal cell membranes. There are two clearly homologous but structurally different classes of the enzyme, one found mainly in eukaryotes and archaea (class 1), and the other found in bacteria (class 2). This feature facilitated the identification of several cases of interdomain lateral gene transfer (LGT), in particular, the bacterial origin for the HMGR gene from the archaeon Archaeoglobus fulgidus. In order to investigate if this LGT event was recent and limited in its scope or had a broad and long-term impact on the recipient and its related lineages, the HMGR gene was amplified and sequenced from a variety of archaea. The survey covered close relatives of A. fulgidus, the only archaeon known prior to this study to possess a bacterial-like HMGR; representatives of each main euryarchaeal group were also inspected. All culturable members of the archaeal group Archaeoglobales were found to display an HMGR very similar to the enzyme of the bacterium Pseudomonas mevalonii. Surprisingly, two species of the genus Thermoplasma also harbor an HMGR of bacterial origin highly similar to the enzymes found in the Archaeoglobales. Phylogenetic analyses of the HMGR gene and comparisons to reference phylogenies from other genes confirm a common bacterial origin for the HMGRs of Thermoplasmatales and Archaeoglobales. The most likely explanation of these results includes an initial bacteria-to-archaea transfer, followed by a another event between archaea. Their presence in two divergent archaeal lineages suggests an important adaptive role for these laterally transferred genes.

Zobellia galactanovorans gen. nov., sp. nov., a marine species of Flavobacteriaceae isolated from a red alga, and classification of [Cytophaga] uliginosa (ZoBell and Upham 1944) Reichenbach 1989 as Zobellia uliginosa gen. nov., comb. nov

A mesophilic, aerobic, non-flagellated, gliding bacterium, forming yellow colonies and designated DsijT, was isolated from a red alga on the sea-shore of Roscoff, Brittany, France. DsijT was selected for its ability to actively degrade both agars and carrageenans. The Gram-negative cells occurred singly or in pairs as long rods. The temperature range for growth was 13-45 degrees C, with an optimum at 35 degrees C. The pH range for growth at 35 degrees C was from 6.0 to 8.5, with an optimum around pH 7.0. The NaCl concentrations required for growth at 35 degrees C and pH 7.0 ranged from 5 to 60 g l(-1), with an optimum around 25 g l(-1). The G+C content of the genomic DNA was 42-43 mol%. Phylogenetic analysis of 16S rRNA gene sequences indicated that strain DsijT is closely related to [Cytophaga] uliginosa DSM 2061T. Phenotypic features, however, allowed DsijT and [Cytophaga] uliginosa strains to be distinguished on the basis of ten traits (spreading behaviour, assimilation of eight compounds and amylase production). Their total protein profiles were also different and DNA-DNA hybridization experiments confirmed that DsijT constitutes a new species, distinct from [Cytophaga] uliginosa. Based on the phenotypic features and the phylogenetic relationships of the Flavobacteriaceae, a new genus designated Zobellia gen. nov. is proposed to include Zobellia galactanovorans gen. nov., sp. nov., while [Cytophaga] uliginosa becomes Zobellia uliginosa comb. nov. The type strain of Zobellia galactanovorans is DsijT (= DSM 12802T = CIP 106680T).

Phylogenetic analyses of two "archaeal" genes in thermotoga maritima reveal multiple transfers between archaea and bacteria

The genome sequence of Thermotoga maritima revealed that 24% of its open reading frames (ORFs) showed the highest similarity scores to archaeal genes in BLAST analyses. Here we screened 16 strains from the genus Thermotoga and other related Thermotogales for the occurrence of two of these "archaeal" genes: the gene encoding the large subunit of glutamate synthase (gltB) and the myo-inositol 1P synthase gene (ino1). Both genes were restricted to the Thermotoga species within the Thermotogales. The distribution of the two genes, along with results from phylogenetic analyses, showed that they were acquired from Archaea during the divergence of the Thermotogales. Database searches revealed that three other bacteria-Dehalococcoides ethenogenes, Sinorhizobium meliloti, and Clostridium difficile-possess archaeal-type gltBs, and the phylogenetic analyses confirmed at least two lateral gene transfer (LGT) events between Bacteria and Archaea. These LGT events were also strongly supported by gene structure data, as the three domains in bacterial-type gltB are homologous to three independent ORFs in Archaea and Bacteria with archaeal-type gltBs. The ino1 gene has a scattered distribution among Bacteria, and apart from the Thermotoga strains it is found only in Aquifex aeolicus, D. ethenogenes, and some high-G+C Gram-positive bacteria. Phylogenetic analysis of the ino1 sequences revealed three highly supported prokaryotic clades, all containing a mixture of archaeal and bacterial sequences, and suggested that all bacterial ino1 genes had been recruited from archaeal donors. The Thermotoga strains and A. aeolicus acquired this gene independently from different archaeal species. Although transfer of genes from hyperthermophilic Archaea may have facilitated the evolution of bacterial hyperthermophily, between-domain transfers also affect mesophilic species. For hyperthermophiles, we hypothesize that LGT may be as much a consequence as the cause of adaptation to hyperthermophily.

Investigation of structure and antigenic capacities of Thermococcales cell envelopes and reclassification of "Caldococcus litoralis" Z-1301 as Thermococcus litoralis Z-1301

Fourteen strains of hyperthermophilic organotrophic anaerobic marine Archaea were isolated from shallow water and deep-sea hot vents, and four of them were characterized. These isolates, eight previously published strains, and six type strains of species of the order Thermococcales were selected for the study of cell wall components by means of thin sectioning or freeze-etching electron microscopy. The cell envelopes of most isolates were shown to consist of regularly arrayed surface protein layers, either single or double, with hexagonal lattice (p6) symmetry, as the exclusive constituents outside the cytoplasmic membrane. The S-layers studied differed in center-to-center spacing and molecular mass of the constituent protein subunits. Polyclonal antisera raised against the cells of 10 species were found to be species-specific and allowed 12 new isolates from shallow water hot vents to be identified as representatives of the species Thermococcus litoralis, Thermococcus stetteri, Thermococcus chitonophagus, and Thermococcus pacificus. Of the 7 deep-sea isolates, only 1 was identified as a T. litoralis strain. Thus, hyperthermophilic marine organotrophic isolates obtained from deep-sea hot vents showed greater diversity with regard to their S-layer proteins than shallow water isolates.

Rapid identification of hyperthermophilic methanococci isolated from deep-sea hydrothermal vents

16S rDNAs amplified by PCR from 22 hyperthermophilic methanococci isolated from deep-sea hydrothermal vents were compared with those of the six type strains of the genus Methanococcus by RFLP analysis. Restriction fragments obtained with Haelli enabied four of the type species to be distinguished. Restrictions with HhaI, BstUI and MspI were necessary to differentiate Methanococcus jannaschii and Methanococcus fervens. The results indicate that the 16S rDNA PCR-RFLP method provides a rapid and reliable tool for the identification of newly isolated hyperthermophilic Methanococcus spp.

Methanococcus vulcanius sp. nov., a novel hyperthermophilic methanogen isolated from East Pacific Rise, and identification of Methanococcus sp. DSM 4213T as Methanococcus fervens sp. nov

An autotrophic, hyperthermophilic methanogen (M7T) was isolated from a deep-sea hydrothermal chimney sample collected on the East Pacific Rise at a depth of 2600 m. The coccoid-shaped cells are flagellated and exhibit a slight tumbling motility. The temperature range for growth at pH 6.5 was 49-89 degrees C, with optimum growth at 80 degrees C. The optimum pH for growth was 6.5, and the optimum NaCl concentration for growth was around 25 g l-1. The new isolate used H2 and CO2 as the only substrates for growth and methane production. Tungsten, selenium and yeast extract stimulated growth significantly. In the presence of CO2 and H2, the organism reduced elemental sulphur to hydrogen sulphide. Growth was inhibited by chloramphenicol and rifampicin, but not by ampicillin, kanamycin, penicillin and streptomycin. The G + C content of the genomic DNA was 31 mol%. As determined by 16S rDNA gene sequence analysis, this organism was closely related to Methanococcus jannaschii strain JAL-1T. However, despite the high percentage of similarity between their 16S rDNA sequences (97.1%), the DNA-DNA hybridization levels between these strains were less than 5%. On the basis of these observations and physiological traits, it is proposed that this organism should be placed in a new species, Methanococcus vulcanius. The type strain is M7T (= DSM 12094T). During the course of this study, the 16S rDNA sequence analysis placed Methanococcus sp. strain AG86T (= DSM 4213T) as a close relative of M. jannaschii strain JAL-1T. However, the weak level of DNA-DNA hybridization with this strain (< 10%) allowed the proposal that strain AG86T also constitutes a new species, Methanococcus fervens.

Desulfurobacterium thermolithotrophum gen. nov., sp. nov., a novel autotrophic, sulphur-reducing bacterium isolated from a deep-sea hydrothermal vent

A thermophilic, anaerobic, strictly autotrophic, sulphur-reducing bacterium, designated BSAT (T = type strain), was isolated from a deep-sea hydrothermal chimney sample collected at the mid-Atlantic ridge. Gram-negative cells occurred singly or in pairs as small highly motile rods. Spores were not observed. The temperature range for growth was 40 to 75 degrees C, with an optimum at 70 degrees C. The pH range for growth at 70 degrees C was from 4.4 to 7.5, with an optimum around 6.0. The sea salt concentration range for growth was 15-70 gI(-1) with an optimum at 35 gI(-1). Elemental sulphur, thiosulphate and sulphite were reduced to hydrogen sulphide. Sulphate and cystine were not reduced. The G+C content of the genomic DNA was 35 mol%. Phylogenetic analyses of the 16S rRNA gene indicated that the strain was a member of the domain Bacteria and formed a branch that was almost equidistant from members of the orders Aquificales and Thermotogales. The new organism possesses phenotypic and phylogenetic traits that do not allow its classification as a member of any previously described genus; therefore, it is proposed that this isolate should be described as a member of a novel species of a new genus, Desulfurobacterium gen. nov., of which Desulfurobacterium thermolithotrophum sp. nov. is the type species. The type strain is BSAT (= DMS 11699T).

Methanococcus infernus sp. nov., a novel hyperthermophilic lithotrophic methanogen isolated from a deep-sea hydrothermal vent

An autotrophic, extremely thermophilic methanogen (ME(T)) was isolated from a deep-sea hydrothermal chimney sample collected on the Mid-Atlantic Ridge at a depth of 3000 m. The heavily flagellated cells are motile and coccoid shaped. The new strain growths between 55 and 91 degrees C, with an optimum growth temperature at 85 degree C. The optimum pH for growth is 6.5, and the optimum sea salt concentration for growth is around 25 g l-1. The organism uses H2 and CO2 as the only substrate for growth and methane production. Tungsten, selenium and yeast extract stimulate growth significantly. In the presence of CO2 and H2, the organism reduces elemental sulphur to hydrogen sulphide. The G+C content of the genomic DNA is 33 mol%. As determined by 16S gene sequence analysis, this organism is closely related to Methanococcus jannaschii strain JAL-1T. However, no significant homology was observed between them with DNA-DNA hybridization. It is proposed that this organism should be placed in a new species, Methanococcus infernus. The type strain is ME(T) (= DSM 11812T).

Thermotoga subterranea sp. nov., a new thermophilic bacterium isolated from a continental oil reservoir

A thermophilic, strictly anaerobic bacterium, designated strain SL1, was isolated from a deep, continental oil reservoir in the East Paris Basin (France). This organism grew between 50 and 75 degrees C, with an optimum at 70 degrees C. It was inhibited by elemental sulfur and was able to reduce cystine and thiosulfate to hydrogen sulfide. The G+C content (40 mol%), the presence of a lipid structure unique to the genus Thermotoga, and the 16S rRNA sequence of strain SL1 indicated that the isolate belongs to the genus Thermotoga. Based on DNA-DNA hybridization, isolate SL1 does not show species-level similarity with the recognized species T. maritima, T. neapolitana, and T. thermarum. Based on this description of strain SL1, we propose the recognition of a new species: Thermotoga subterranea.