The complete sequence of the genome of a hyper-thermophilic archaebacterium, Pyrococcus horikoshii OT3, has been determined by assembling the sequences of the physical map-based contigs of fosmid clones and of long polymerase chain reaction (PCR) products which were used for gap-filling. The entire length of the genome was 1,738,505 bp. The authenticity of the entire genome sequence was supported by restriction analysis of long PCR products, which were directly amplified from the genomic DNA. As the potential protein-coding regions, a total of 2061 open reading frames (ORFs) were assigned, and by similarity search against public databases, 406 (19.7%) were related to genes with putative function and 453 (22.0%) to the sequences registered but with unknown function. The remaining 1202 ORFs (58.3%) did not show any significant similarity to the sequences in the databases. Sequence comparison among the assigned ORFs in the genome provided evidence that a considerable number of ORFs were generated by sequence duplication. By similarity search, 11 ORFs were assumed to contain the intein elements. The RNA genes identified were a single 16S-23S rRNA operon, two 5S rRNA genes and 46 tRNA genes including two with the intron structure. All the assigned ORFs and RNA coding regions occupied 91.25% of the whole genome. The data presented in this paper are available on the internet at http:@www.nite.go.jp.

We report here the sequencing and analysis of the genome of the thermophilic bacterium Carboxydothermus hydrogenoformans Z-2901. This species is a model for studies of hydrogenogens, which are diverse bacteria and archaea that grow anaerobically utilizing carbon monoxide (CO) as their sole carbon source and water as an electron acceptor, producing carbon dioxide and hydrogen as waste products. Organisms that make use of CO do so through carbon monoxide dehydrogenase complexes. Remarkably, analysis of the genome of C. hydrogenoformans reveals the presence of at least five highly differentiated anaerobic carbon monoxide dehydrogenase complexes, which may in part explain how this species is able to grow so much more rapidly on CO than many other species. Analysis of the genome also has provided many general insights into the metabolism of this organism which should make it easier to use it as a source of biologically produced hydrogen gas. One surprising finding is the presence of many genes previously found only in sporulating species in the Firmicutes Phylum. Although this species is also a Firmicutes, it was not known to sporulate previously. Here we show that it does sporulate and because it is missing many of the genes involved in sporulation in other species, this organism may serve as a ''minimal'' model for sporulation studies. In addition, using phylogenetic profile analysis, we have identified many uncharacterized gene families found in all known sporulating Firmicutes, but not in any non-sporulating bacteria, including a sigma factor not known to be involved in sporulation previously.

A new anaerobic, thermophilic, CO-utilizing marine bacterium, strain JM T , was isolated from a submarine hot vent in Okinawa Trough. Cells of strain JM T were non-motile thin straight rods, sometimes branching, with a cell wall of the Gram-positive type, surrounded with an S-layer. Chains of three to five cells were often observed. The isolate grew chemolithotrophically on CO, producing equimolar quantities of H 2 and CO 2 (according to the equation COMH 2 O 4 CO 2 MH 2 ) and organotrophically on peptone, yeast extract, starch, cellobiose, glucose, galactose, fructose and pyruvate, producing H 2 , acetate and CO 2 . Growth was observed from 50 to 80 SC with an optimum at 70 SC. The optimum pH was 68-71. The optimum concentration of sea salts in the medium was 205-255 g l V1 . The generation time under optimal conditions was 71 h. The DNA GMC content was 33 mol %. Growth of isolate JM T was not inhibited by penicillin, but ampicillin, streptomycin, kanamycin and neomycin completely inhibited growth. The results of 16S rDNA sequence analysis revealed that strain JM T belongs to the Thermoanaerobacter phylogenetic group within the Bacillus-Clostridium subphylum of Gram-positive bacteria but represents a separate branch of this group. On the basis of morphological and physiological features and phylogenetic data, this isolate should be assigned to a new genus, for which the name Carboxydobrachium is proposed. The type species is Carboxydobrachium pacificum ; the type strain is JM T (l DSM 12653 T ).Keywords : submarine hot vents, carbon monoxide utilization, thermophilic anaerobe, Carboxydobrachium pacificum INTRODUCTIONDeep-sea hydrothermal fields are inhabited by unique microbial communities that rely on the energy of reduced inorganic compounds of volcanic origin (Jannasch, 1995). Many thermophilic prokaryotes have been isolated from such habitats over the past decade . However, most of these organisms were hyperthermophilic archaea of the Euryarchaeota and Crenarchaeota kingdoms. Among them were methanogens of genera Methanopyrus (Kurr et al., 1991) and Methanococcus (Jones et al., 1983 ;Jeanthon et al., 1998) reducers of the genus Archaeoglobus (Burggraf et al., 1990 ; Huber et al., 1997) ; Pyrolobus fumarii, oxidizing molecular hydrogen either aerobically or via nitrate reduction (Blo$ chl et al., 1997) ; and numerous anaerobic organotrophs belonging to the genera Staphylothermus (Fiala et al., 1986), Thermococcus (Kobayshi et al., 1994 ; Gonza! lez et al., 1995, etc.), Pyrococcus (Erauso et al., 1993 ; Gonza! lez et al., 1998) and Pyrodictium (Pley et al., 1991). The information on the presence of thermophilic bacteria in the microbial communities of deep-sea hot vents is up to now much more sparse. The presence of organotrophic anaerobes and aerobes belonging to the genera Thermotoga, Thermus and Bacillus in deep-sea hydrothermal habitats has been reported (Marteinsson et al., 1995(Marteinsson et al., , 1996a T. G. Sokolova and others esiensis has been isolated in pure culture (Antoine et al., 1997). ...