Thermococcus stetteri sp. nov., a New Extremely Thermophilic Marine Sulfur-Metabolizing Archaebacterium

Screening for Hyperthermophilic Electrotrophs for the Microbial Electrosynthesis of Organic Compounds

Microbial electrosynthesis has recently emerged as a promising technology for the sustainable production of organic acids, bioplastics, or biofuels from electricity and CO2. However, the diversity of catalysts and metabolic pathways is limited to mainly mesophilic acetogens or methanogens. Here, eleven hyperthermophilic strains related to Archaeoglobales, Thermococcales, Aquificales, and methanogens were screened for microbial electrosynthesis. The strains were previously isolated from deep-sea hydrothermal vents, where a naturally occurring, spontaneous electrical current can serve as a source of energy for microbial metabolism. After 6 days of incubation in an electrochemical system, all strains showed current consumption, biofilm formation, and small organic molecule production relative to the control. Six selected strains were then incubated over a longer period of time. In the course of one month, a variety of metabolic intermediates of biotechnological relevance such as succinic acid and glycerol accumulated. The production rates and the promotion of specific metabolic pathways seemed to be influenced by the experimental conditions, such as the concentration of CO2 in the gas phase and electron acceptor limitation. Further work is necessary to clearly identify these effects to potentially be able to tune the microbial electrosynthesis of compounds of interest.

A review on anaerobic microorganisms isolated from oil reservoirs

The Role of microorganisms in the petroleum industry is wide-ranging. To understand the role of microorganisms in hydrocarbon transformation, identification of such microorganisms is vital, especially the ones capable of in situ degradation. Microorganisms play a pivotal role in the degradation of hydrocarbons and remediation of heavy metals. Anaerobic microorganisms such as Sulphate Reducing Bacteria (SRB), responsible for the production of hydrogen sulphide (H₂S) within the reservoir, reduces the oil quality by causing reservoir souring and reduction in oil viscosity. This paper reviews the diversity of SRB, methanogens, Nitrogen Reducing Bacteria (NRB), and fermentative bacteria present in oil reservoirs. It also reviews the extensive diversity of these microorganisms, their applications in petroleum industries, characteristics and adaptability to survive in different conditions, the potential to alter the petroleum hydrocarbons properties, the propensity to petroleum hydrocarbon degradation, and remediation of metals.

Microbial Diversity in Extreme Marine Habitats and Their Biomolecules

Extreme marine environments have been the subject of many studies and scientific publications. For many years, these environmental niches, which are characterized by high or low temperatures, high-pressure, low pH, high salt concentrations and also two or more extreme parameters in combination, have been thought to be incompatible to any life forms. Thanks to new technologies such as metagenomics, it is now possible to detect life in most extreme environments. Starting from the discovery of deep sea hydrothermal vents up to the study of marine biodiversity, new microorganisms have been identified, and their potential uses in several applied fields have been outlined. Thermophile, halophile, alkalophile, psychrophile, piezophile and polyextremophile microorganisms have been isolated from these marine environments; they proliferate thanks to adaptation strategies involving diverse cellular metabolic mechanisms. Therefore, a vast number of new biomolecules such as enzymes, polymers and osmolytes from the inhabitant microbial community of the sea have been studied, and there is a growing interest in the potential returns of several industrial production processes concerning the pharmaceutical, medical, environmental and food fields.

The temperature gradient-forming device, an accessory unit for normal light microscopes to study the biology of hyperthermophilic microorganisms

To date, the behavior of hyperthermophilic microorganisms in their biotope has been studied only to a limited degree; this is especially true for motility. One reason for this lack of knowledge is the requirement for high-temperature microscopy-combined, in most cases, with the need for observations under strictly anaerobic conditions-for such studies. We have developed a custom-made, low-budget device that, for the first time, allows analyses in temperature gradients up to 40°C over a distance of just 2 cm (a biotope-relevant distance) with heating rates up to ∼5°C/s. Our temperature gradient-forming device can convert any upright light microscope into one that works at temperatures as high as 110°C. Data obtained by use of this apparatus show how very well hyperthermophiles are adapted to their biotope: they can react within seconds to elevated temperatures by starting motility-even after 9 months of storage in the cold. Using the temperature gradient-forming device, we determined the temperature ranges for swimming, and the swimming speeds, of 15 selected species of the genus Thermococcus within a few months, related these findings to the presence of cell surface appendages, and obtained the first evidence for thermotaxis in Archaea.

Thermococcus nautili sp. nov., a hyperthermophilic archaeon isolated from a hydrothermal deep-sea vent

Thermococcus nautili, strain 30-1T (formerly reported as Thermococcus nautilus), was isolated from a hydrothermal chimney sample collected from the East Pacific Rise at a depth of 2633 m on the ‘La chainette PP57’ area. Cells were motile, irregular cocci with a polar tuft of flagella (0.8–1.5 µm) and divided by constriction. The micro-organism grew optimally at 87.5 °C (range 55–95 °C), at pH 7 (range pH 4–9) and with 2 % NaCl (range 1–4 %). Doubling time was 64 min in Zillig’s broth medium under optimal conditions. Growth was strictly anaerobic. It grew preferentially in the presence of elemental sulfur or cystine, which are reduced to H2S, on complex organic substrates such as yeast extract, tryptone, peptone, Casamino acids and casein. Slow growth was observed on starch and pyruvate. Strain 30-1T was resistant to chloramphenicol and tetracyclin (at 100 µg ml−1) but sensitive to kanamycin and rifampicin. The G+C content of the genomic DNA was 54 mol%. Strain 30-1T harboured three plasmids named pTN1, pTN2 and pTN3 and produced membrane vesicles that incorporate pTN1 and pTN3. As determined by 16S rRNA gene sequence analysis, strain 30-1T is related most closely to Thermococcus sp. AM4 (99.3 % similarity) and Thermococcus gammatolerans DSM 15229T (99.2 %). DNA–DNA hybridization values (in silico) with these two closest relatives were below the threshold value of 70 % (33 % with Thermococcus sp. AM4 and 32 % with T. gammatolerans DSM 15229T) and confirmed that strain 30-1 represents a novel species. On the basis of the data presented, strain 30-1T is considered to represent a novel species of the genus Thermococcus , for which the name Thermococcus nautili sp. nov. is proposed. The type strain is 30-1T ( = CNCM 4275 = JCM 19601).

Diversity of thermophilic anaerobes

Thermophilic anaerobes are Archaea and Bacteria that grow optimally at temperatures of 50 degrees C or higher and do not require the use of O(2) as a terminal electron acceptor for growth. The prokaryotes with this type of physiology are studied for a variety of reasons, including (a) to understand how life can thrive under extreme conditions, (b) for their biotechnological potential, and (c) because anaerobic thermophiles are thought to share characteristics with the early evolutionary life forms on Earth. Over 300 species of thermophilic anaerobes have been described; most have been isolated from thermal environments, but some are from mesobiotic environments, and others are from environments with temperatures below 0 degrees C. In this overview, the authors outline the phylogenetic and physiological diversity of thermophilic anaerobes as currently known. The purpose of this overview is to convey the incredible diversity and breadth of metabolism within this subset of anaerobic microorganisms.

Thermococcus celericrescens sp. nov., a fast-growing and cell-fusing hyperthermophilic archaeon from a deep-sea hydrothermal vent

A fast-growing and cell-fusing hyperthermophilic archaeon was isolated from a hydrothermal vent at Suiyo Seamount, Izu-Bonin Arc, Western Pacific Ocean. Strain TS2T is an irregular, motile coccus that is generally 0.7–1.5 μm in diameter and possesses a polar tuft of flagella. In the mid-exponential phase of growth, cells that appeared black under phase-contrast microscopy fused at room temperature in the presence of a DNA-intercalating dye, as previously observed in Thermococcus coalescens. Cell fusion was not observed in later growth phases. Transmission electron microscopy revealed that the cells in the mid-exponential phase had a 5 nm-thick, electron-dense cell envelope that appeared to associate loosely with the cytoplasmic membrane. As the growth stage progressed, a surface layer developed on the membrane under the envelope and the envelope eventually peeled off. These observations suggest that the surface layer prevents the fusion of cells. Cells of strain TS2T grew at 50–85 °C, pH 5.6–8.3 and at NaCl concentrations of 1.0 to 4.5 %, with optimal growth occurring at 80 °C, pH 7.0 and 3.0 % NaCl. Under optimal growth conditions, strain TS2T grew very fast with an apparent doubling time of 20 min. It is suggested that the biosynthesis of the surface layer cannot catch up with cell multiplication in the mid-exponential phase and thus cells without the surface layer are generated. Strain TS2T was an anaerobic chemo-organotroph that grew on either yeast extract or tryptone as the sole growth substrate. The genomic DNA G+C content was 54.6 mol%. Phylogenetic analysis based on 16S rRNA gene sequencing indicated that the isolate belongs to the genus Thermococcus. However, no significant DNA–DNA hybridization was observed between the genomic DNA of strain TS2T and phylogenetically related Thermococcus species. On the basis of this evidence, strain TS2T is proposed to represent a novel species, Thermococcus celericrescens sp. nov., a name chosen to reflect the fast growth of the strain. The type strain is TS2T (=NBRC 101555T=JCM 13640T=DSM 17994T).

Thermococcus coalescens sp. nov., a cell-fusing hyperthermophilic archaeon from Suiyo Seamount

A cell-fusing hyperthermophilic archaeon was isolated from hydrothermal fluid obtained from Suiyo Seamount of the Izu-Bonin Arc. The isolate, TS1(T), is an irregular coccus, usually 0.5-2 microm in diameter and motile with a polar tuft of flagella. Cells in the exponential phase of growth fused at room temperature in the presence of DNA-intercalating dye to become as large as 5 microm in diameter. Fused cells showed dark spots that moved along in the cytoplasm. Large cells with a similar appearance were also observed upon culture at 87 degrees C, suggesting the occurrence of similar cell fusions during growth. Transmission electron microscopy revealed that cells in the exponential phase possessed a thin and electron-lucent cell envelope that could be lost subsequently during culture. The fragile cell envelope must be related to cell fusion. The cells grew at 57-90 degrees C, pH 5.2-8.7 and at NaCl concentrations of 1.5-4.5 %, with the optima being 87 degrees C, pH 6.5 and 2.5 % NaCl. The isolate was an anaerobic chemo-organotroph that grew on either yeast extract or tryptone as the sole growth substrate. The genomic DNA G+C content was 53.9 mol%. Phylogenetic analysis based on 16S rRNA gene sequencing indicated that the isolate was closely related to Thermococcus species. However, no significant DNA-DNA hybridization was observed between genomic DNA of strain TS1(T) and phylogenetically related Thermococcus species. We propose that isolate TS1(T) represents a novel species, Thermococcus coalescens sp. nov., with the name reflecting the cell fusion activity observed in the strain. The type strain is TS1(T) (=JCM 12540T=DSM 16538T).

Effects of shallow-water hydrothermal venting on biological communities of coastal marine ecosystems of the western Pacific

This review is based on integrated studies of the composition, structure and function of shallow-water ecosystems in the western Pacific that are influenced by underwater gas-hydrothermal activity. Most of the data were collected from 1985 to 1997 by the Institute of Marine Biology of the Far East Branch of the Russian Academy of Science during expeditions to zones of modern volcanism. Gas-hydrothermal activity of volcanoes has a great influence on the physicochemical characteristics of the water column and plankton, and of bottom sediment and benthic communities. The abundance of nutrients (SiO(3)(2-), PO(4)(3-), NO(3)(-)), gases (CO(2), CH(4), H(2), H(2)S) and other reduced compounds (C(n)H(n), S(0), S(2)O(3)(2-), NH(4)(+)) in zones of shallow-water hydrothermal vents provides conditions for the use of two energy sources for primary production: sunlight (photosynthesis) and the oxidation of reduced compounds (bacterial chemosynthesis). In areas of shallow-water volcanic activity, chemosynthesis occurs not only in the immediate vicinity of venting fluid release but also in the surface layer of the water column, where it occurs together with intense photosynthesis. This surface photosynthesis is found below the layer of chemosynthesis, which is related to the distribution of hydrothermal fluids at the water surface. The contribution of each of these processes to total primary production depends on the physical and chemical conditions created by the vents and on the range and adaptation potential of the organisms. On the seabed in zones of shallow-water venting, microorganisms form mats that consist of bacteria of various physiological groups, microalgae, the products of their metabolism and sedimentary particles. Oxygenic photosynthesis of benthic diatoms, bacterial photosynthesis (anoxygenic photosynthesis) and autotrophic chemosynthesis in algobacterial and bacterial mats generate organic matter additional to that produced in the water column. The high rates of primary production, abundance of organic matter in the water column and intense development of benthic microflora ensure the formation of an abundant benthic fauna. In Kraternaya Bight, Matupi Harbour and Bay of Plenty, the macrozoobenthos has low species diversity. The taxonomic composition of the populations is determined by geographical region (temperate or tropical), by the character of the seabed (hard or soft bottoms, rigid lava flows or hydrothermal structures), by the temperature of bottom sediments and of volcanic fluids and lastly by the chemical composition of the vent fluid (sulfide or nonsulfide). In most of the surveyed areas the fauna is derived from locally common species or from opportunistic species that can form high-density populations in eutrophic waters. The benthic communities of shallow-water venting areas have many characteristics in common with communities subject to anthropogenic impact (thermal, residential or industrial) or to changes resulting from a sharp deterioration of the marine environment. In contrast to the fauna of deeper water hydrothermal communities (i.e., those that exist below 200 m), shallow-water venting communities lack obligate hydrothermal species. The structure and function of the pelagic and benthic communities in areas of shallow-water venting can be regarded as transitional between those of deep-water vent communities and the normal communities of the coast.

Life in hot carbon monoxide: the complete genome sequence of Carboxydothermus hydrogenoformans Z-2901

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.

Carboxydothermus hydrogenoformans, a bacterium isolated from a Russian hotspring, is studied for three major reasons: it grows at very high temperature, it lives almost entirely on a diet of carbon monoxide (CO), and it converts water to hydrogen gas as part of its metabolism. Understanding this organism's unique biology gets a boost from the decoding of its genome, reported in this issue of PLoS Genetics. For example, genome analysis reveals that it encodes five different forms of the protein machine carbon monoxide dehydrogenase (CODH). Most species have no CODH and even species that utilize CO usually have only one or two. The five CODH in C. hydrogenoformans likely allow it to both use CO for diverse cellular processes and out-compete for it when it is limiting. The genome sequence also led the researchers to experimentally document new aspects of this species' biology including the ability to form spores. The researchers then used comparative genomic analysis to identify conserved genes found in all spore-forming species, including Bacillus anthracis, and not in any other species. Finally, the genome sequence and analysis reported here will aid in those trying to develop this and other species into systems to biologically produce hydrogen gas from water.

Desulfurococcus fermentans sp. nov., a novel hyperthermophilic archaeon from a Kamchatka hot spring, and emended description of the genus Desulfurococcus

An obligately anaerobic, hyperthermophilic, organoheterotrophic archaeon, strain Z-1312T, was isolated from a freshwater hot spring of the Uzon caldera (Kamchatka Peninsula, Russia). The cells were regular cocci, 1–4 μm in diameter, with one long flagellum. The cell envelope was composed of a globular layer attached to the cytoplasmic membrane. The temperature range for growth was 63–89 °C, with an optimum between 80 and 82 °C. The pH range for growth at 80 °C was 4·8–6·8, with an optimum at pH 6·0. Strain Z-1312Tgrew by hydrolysis and/or fermentation of a wide range of polymeric and monomeric substrates, including agarose, amygdalin, arabinose, arbutin, casein hydrolysate, cellulose (filter paper, microcrystalline cellulose, carboxymethyl cellulose), dextran, dulcitol, fructose, lactose, laminarin, lichenan, maltose, pectin, peptone, ribose, starch and sucrose. No growth was detected on glucose, xylose, mannitol or sorbitol. Growth products when sucrose or starch were used as the substrate were acetate, H2and CO2. Elemental sulfur, thiosulfate and nitrate added as potential electron acceptors for anaerobic respiration did not stimulate growth when tested with starch as the substrate. H2at 100 % in the gas phase did not inhibit growth on starch or peptone. The G+C content of the DNA was 42·5 mol%. 16S rRNA gene sequence analysis placed the isolated strain Z-1312Tas a member of the genusDesulfurococcus, where it represented a novel species, for which the nameDesulfurococcus fermentanssp. nov. (type strain Z-1312T=DSM 16532T=VKM V-2316T) is proposed.

Thermococcus marinus sp. nov. and Thermococcus radiotolerans sp. nov., two hyperthermophilic archaea from deep-sea hydrothermal vents that resist ionizing radiation

Enrichments for anaerobic, organotrophic hyperthermophiles were performed with hydrothermal chimney samples collected from the Mid-Atlantic Ridge at a depth of 3,550 m (23 degrees 22'N, 44 degrees 57'W) and the Guaymas Basin (27 degrees 01'N, 111 degrees 24'W) at a depth of 2,616 m. Positive enrichments were submitted to gamma-irradiation at doses of 20 and 30 kGy. Two hyperthermophilic, anaerobic, sulfur-metabolizing archaea were isolated. Strain EJ1T was isolated from chimney samples collected from the Mid-Atlantic Ridge after gamma-irradiation at 20 kGy, and strain EJ2T was isolated from the Guaymas Basin after gamma-irradiation at 30 kGy. Only strain EJ2T was motile, and both formed regular cocci. These new strains grew between 55 and 95 degrees C with the optimal temperature being 88 degrees C. The optimal pH for growth was 6.0, and the optimal NaCl concentration for growth was around 20 g l(-1). These strains were obligate anaerobic heterotrophs that utilized yeast extract, tryptone, and peptone as a carbon source for growth. Ten amino acids were essential for the growth of strain EJ1), such as arginine, aspartic acid, isoleucine, leucine, methionine, phenylalanine, proline, threonine, tyrosine, and valine, while strain EJ2T was unable to grow on a mixture of amino acids. Elemental sulfur or cystine was required for EJ2T growth and was reduced to hydrogen sulfide. Rifampicin inhibited growth for both strains EJ1T and EJ2T. The G + C contents of the genomic DNA were 52.3 and 54.5 mol% for EJ1T and EJ2T, respectively. As determined by 16S rRNA gene sequence analysis, these strains were more closely related to Thermococcus gorgonarius, T. celer, T. guaymasensis, T. profundus, and T. hydrothermalis. However, no significant homology was observed between them with DNA-DNA hybridization. These novel organisms also possess phenotypic traits that differ from those of its closest phylogenetic relatives. Therefore, it is proposed that these isolates, which are amongst the most radioresistant hyperthermophilic archaea known to date with T. gammatolerans (Jolivet et al. 2003a), should be described as novel species T. marinus sp. nov. and T. radiotolerans sp. nov. The type strain of T. marinus is strain EJ1T (= DSM 15227T = JCM 11825T) and the type strain of T. radiotolerans is strain EJ2T (= DSM 15228T = JCM 11826T).

Two kinds of archaeal group II chaperonin subunits with different thermostability in Thermococcus strain KS-1

The thermostability of the recombinant alpha- and beta-subunit homo-oligomers (alpha16mer and beta16mer) and of natural chaperonins purified from cultured Thermococcus strain KS-1 cells was measured to understand the mechanism for the thermal acclimatization of T. KS-1. The beta-subunit content of the natural chaperonin from cells grown at 90 degrees C was higher than that at 80 degrees C. The optimum temperature for ATPase activity of the natural chaperonins was 80-90 degrees C, whereas that for alpha16mer and beta16mer was 60 degrees C and over 90 degrees C respectively. Judging from the ATPase activity, beta16mer was more thermostable than alpha16mer. The thermostabilities of the natural chaperonins were intermediate between alpha16mer and beta16mer, whereas the natural chaperonin with a higher beta-subunit content was more stable than that with a lower beta-subunit content. Native polyacrylamide gel electrophoresis (PAGE) revealed that the chaperonin oligomers thermally dissociated to their ATPase-inactive monomers. The thermal denaturation process monitored by circular dichroism showed that the free beta-subunit was more stable than the free alpha-subunit, and that the secondary structure of the chaperonin monomer in the oligomer was more stable than that in the free monomer. These results suggest that the structure of these subunits was stabilized in the oligomer, and that an increase in the beta-subunit content conferred higher thermostability to the natural hetero-oligomeric chaperonin.

Energetics of overall metabolic reactions of thermophilic and hyperthermophilic Archaea and bacteria

Thermophilic and hyperthermophilic Archaea and Bacteria have been isolated from marine hydrothermal systems, heated sediments, continental solfataras, hot springs, water heaters, and industrial waste. They catalyze a tremendous array of widely varying metabolic processes. As determined in the laboratory, electron donors in thermophilic and hyperthermophilic microbial redox reactions include H2, Fe(2+), H2S, S, S2O3(2-), S4O6(2-), sulfide minerals, CH4, various mono-, di-, and hydroxy-carboxylic acids, alcohols, amino acids, and complex organic substrates; electron acceptors include O2, Fe(3+), CO2, CO, NO3(-), NO2(-), NO, N2O, SO4(2-), SO3(2-), S2O3(2-), and S. Although many assimilatory and dissimilatory metabolic reactions have been identified for these groups of microorganisms, little attention has been paid to the energetics of these reactions. In this review, standard molal Gibbs free energies (DeltaGr(0)) as a function of temperature to 200 degrees C are tabulated for 370 organic and inorganic redox, disproportionation, dissociation, hydrolysis, and solubility reactions directly or indirectly involved in microbial metabolism. To calculate values of DeltaGr(0) for these and countless other reactions, the apparent standard molal Gibbs free energies of formation (DeltaG(0)) at temperatures to 200 degrees C are given for 307 solids, liquids, gases, and aqueous solutes. It is shown that values of DeltaGr(0) for many microbially mediated reactions are highly temperature dependent, and that adopting values determined at 25 degrees C for systems at elevated temperatures introduces significant and unnecessary errors. The metabolic processes considered here involve compounds that belong to the following chemical systems: H-O, H-O-N, H-O-S, H-O-N-S, H-O-C(inorganic), H-O-C, H-O-N-C, H-O-S-C, H-O-N-S-C(amino acids), H-O-S-C-metals/minerals, and H-O-P. For four metabolic reactions of particular interest in thermophily and hyperthermophily (knallgas reaction, anaerobic sulfur and nitrate reduction, and autotrophic methanogenesis), values of the overall Gibbs free energy (DeltaGr) as a function of temperature are calculated for a wide range of chemical compositions likely to be present in near-surface and deep hydrothermal and geothermal systems.

Hyperthermophilic enzymes: sources, uses, and molecular mechanisms for thermostability

Enzymes synthesized by hyperthermophiles (bacteria and archaea with optimal growth temperatures of > 80 degrees C), also called hyperthermophilic enzymes, are typically thermostable (i.e., resistant to irreversible inactivation at high temperatures) and are optimally active at high temperatures. These enzymes share the same catalytic mechanisms with their mesophilic counterparts. When cloned and expressed in mesophilic hosts, hyperthermophilic enzymes usually retain their thermal properties, indicating that these properties are genetically encoded. Sequence alignments, amino acid content comparisons, crystal structure comparisons, and mutagenesis experiments indicate that hyperthermophilic enzymes are, indeed, very similar to their mesophilic homologues. No single mechanism is responsible for the remarkable stability of hyperthermophilic enzymes. Increased thermostability must be found, instead, in a small number of highly specific alterations that often do not obey any obvious traffic rules. After briefly discussing the diversity of hyperthermophilic organisms, this review concentrates on the remarkable thermostability of their enzymes. The biochemical and molecular properties of hyperthermophilic enzymes are described. Mechanisms responsible for protein inactivation are reviewed. The molecular mechanisms involved in protein thermostabilization are discussed, including ion pairs, hydrogen bonds, hydrophobic interactions, disulfide bridges, packing, decrease of the entropy of unfolding, and intersubunit interactions. Finally, current uses and potential applications of thermophilic and hyperthermophilic enzymes as research reagents and as catalysts for industrial processes are described.

Distribution and physiological characteristics of hyperthermophiles in the Kubiki oil reservoir in Niigata, Japan

The distribution of culturable hyperthermophiles was studied in relation to environmental conditions in the Kubiki oil reservoir in Japan, where the temperature was between 50 and 58 degrees C. Dominant hyperthermophilic cocci and rods were isolated and shown to belong to the genera Thermococcus and Thermotoga, respectively, by 16S rDNA analyses. Using the most-probable-number method, we found that hyperthermophilic cocci were widely distributed in several unconnected fault blocks in the Kubiki oil reservoir. In 1996 to 1997, their populations in the production waters from oil wells were 9.2 x 10(3) to 4.6 x 10(4) cells/ml, or 10 to 42% of total cocci. On the other hand, hyperthermophilic rods were found in only one fault block of the reservoir with populations less than 10 cells/ml. Dominant Thermococcus and Thermotoga spp. grew at reservoir temperatures and utilized amino acids and sugars, respectively, as sole carbon sources. While organic carbon was plentiful in the environment, these hyperthermophiles were unable to grow in the formation water due to lack of essential nutrients. Concentrations of some organic and inorganic substances differed among fault blocks, indicating that the movement of formation water between fault blocks was restricted. This finding suggests that the supply of nutrients via fluid current is limited in this subterranean environment and that the organisms are starved in the oil reservoir. Under starved conditions at 50 degrees C, culturable cells of Thermococcus sp. remained around the initial cell density for about 200 days, while those of Thermotoga sp. decreased exponentially to 0. 01% of the initial cell density after incubation for the same period. The difference in survivability between these two hyperthermophiles seems to reflect their populations in the fault blocks. These results indicate that hyperthermophilic cocci and rods adapt to the subterranean environment of the Kubiki oil reservoir by developing an ability to survive under starved conditions.

Purification and characterization of an extremely thermostable cyclomaltodextrin glucanotransferase from a newly isolated hyperthermophilic archaeon, a Thermococcus sp

The extremely thermophilic anaerobic archaeon strain B1001 was isolated from a hot-spring environment in Japan. The cells were irregular cocci, 0.5 to 1.0 micrometers in diameter. The new isolate grew at temperatures between 60 and 95 degrees C (optimum, 85 degrees C), from pH 5.0 to 9.0 (optimum, pH 7.0), and from 1.0 to 6.0% NaCl (optimum, 2.0%). The G+C content of the genomic DNA was 43.0 mol%. The 16S rRNA gene sequencing of strain B1001 indicated that it belongs to the genus Thermococcus. During growth on starch, the strain produced a thermostable cyclomaltodextrin glucanotransferase (CGTase). The enzyme was purified 1,750-fold, and the molecular mass was determined to be 83 kDa by sodium dodecyl sulfate (SDS)-polyacrylamide gel electrophoresis. Incubation at 120 degrees C with SDS and 2-mercaptoethanol was required for complete unfolding. The optimum temperatures for starch-degrading activity and cyclodextrin synthesis activity were 110 and 90 to 100 degrees C, respectively. The optimum pH for enzyme activity was pH 5.0 to 5.5. At pH 5.0, the half-life of the enzyme was 40 min at 110 degrees C. The enzyme formed mainly alpha-cyclodextrin with small amounts of beta- and gamma-cyclodextrins from starch. This is the first report on the presence of the extremely thermostable CGTase from hyperthermophilic archaea.

Effects of temperature, salinity, and medium composition on compatible solute accumulation by thermococcus spp

The effects of salinity and growth temperature on the accumulation of intracellular organic solutes were examined by nuclear magnetic resonance spectroscopy (NMR) in Thermococcus litoralis, Thermococcus celer, Thermococcus stetteri, and Thermococcus zilligii (strain AN1). In addition, the effects of growth stage and composition of the medium were studied in T. litoralis. A novel compound identified as beta-galactopyranosyl-5-hydroxylysine was detected in T. litoralis grown on peptone-containing medium. Besides this newly discovered compound, T. litoralis accumulated mannosylglycerate, aspartate, alpha-glutamate, di-myo-inositol-1,1'(3,3')-phosphate, hydroxyproline, and trehalose. The hydroxyproline and beta-galactopyranosyl-5-hydroxylysine were probably derived from peptone, while the trehalose was derived from yeast extract; none of these three compounds was detected in the other Thermococcus strains examined. Di-myo-inositol-1,1'(3,3')-phosphate, aspartate, and mannosylglycerate were detected in T. celer and T. stetteri, and the latter organism also accumulated alpha-glutamate. The only nonmarine species studied, T. zilligii, accumulated very low levels of alpha-glutamate and aspartate. The levels of mannosylglycerate and aspartate increased in T. litoralis, T. celer, and T. stetteri in response to salt stress, while di-myo-inositol-1,1'(3,3')-phosphate was the major intracellular solute at supraoptimal growth temperatures. The phase of growth had a strong influence on the types and levels of compatible solutes in T. litoralis; mannosylglycerate and aspartate were the major solutes during exponential growth, while di-myo-inositol-1,1'(3,3')-phosphate was the predominant organic solute during the stationary phase of growth. This work revealed an unexpected ability of T. litoralis to scavenge suitable components from the medium and to use them as compatible solutes.

Lipids of Thermococcus hydrothermalis, an archaea isolated from a deep-sea hydrothermal vent

The membrane lipids of a deep-sea hydrothermal vent archaea, Thermococcus hydrothermalis, were isolated, purified, and structurally characterized. On the basis of acid methanolysis and spectroscopic studies, the polar lipids, amounting to 4.5% (w/w) of the dry cells, comprised diphytanyl glycerol diethers and dibiphytanyldiglycerol tetraethers, in a 45:55 ratio. No cyclopentane ring was present in the tetraethers. From the neutral lipids, accounting for 0.4% (w/w) of the dry cells, besides low amounts of di- and tetraethers occurring in a free form, four acyclic tetraterpenoid hydrocarbons, di- and tri-unsaturated were identified. All were structurally related to lycopane. The presence of these hydrocarbons provides some evidence that lycopane, widely distributed in oceans, could be derived, at least partially, from the hydrocarbons synthesized by some thermophilic Archaea. Finally, analysis of the uninoculated culture medium indicates that fatty acid derivatives and some steroid and triterpenoid compounds identified in the lipidic extract of the archaea originated from the culture medium.

Isolation and characterization of Thermococcus barossii, sp. nov., a hyperthermophilic archaeon isolated from a hydrothermal vent flange formation

A new hyperthermophilic microorganism, Thermococcus barossii, was isolated from rock fragments of a hydrothermal vent flange formation, located along the East Pacific Rise of the Juan de Fuca Ridge. This organism is obligately anaerobic and grows over a temperature range of at least 60-92 degrees C in artificial seawater-based media, containing elemental sulfur, tryptone and yeast extract. The addition of a maltooligosaccharide mixture and tungsten to this medium improved growth to some extent. At the Topt for growth (82.5 degrees C), cell densities as high as 4 x 10(8) cells/ml could be obtained in 18-liter batch fermentations, with a doubling time of approximately 40 minutes, if culture access to elemental sulfur was sufficient. In continuous culture at the same temperature, comparable cell densities could be obtained but only at slower growth rates. Morphologically, T. barossii is coccoid-shaped, forming irregularly-shaped spheres; under optimal conditions, these coccoids become more regular and smaller, a characteristic of other hyperthermophilic archaea. Negatively-stained preparations showed no pili or flagella associated with the cell surface. 16S rRNA sequencing reveals that T. barossii is most similar to Thermococcus celer (99.7%). Yet, further comparisons with T. celer showed that T. barossii is a new Thermococcus species: different growth temperature optimum (82.5 degrees C vs. 88 degrees C), obligate requirement for sulfur, higher G + C content (60% vs. 56.7%) and 47.7% DNA-DNA hybridization. The nucleotide and translated amino acid sequence for the gene encoding a DNA polymerase from T. barossii was compared to sequences of related genes from other Thermacoccales. The polymerase phylogenies were congruent with those obtained from the 16S rRNA phylogenetic analyses. Based on the high degree of similarity among members of the genus Termococcus for the criteria used thus far, aspects of enzymology may be an important mechanism of differenting one species from another.

Utilization of Serine, Leucine, Isoleucine, and Valine byThermoanaerobacter brockiiin the Presence of Thiosulfate orMethanobacteriumsp. as Electron Acceptors

Thermoanaerobacter brockii fermented serine to acetate and ethanol. It oxidized leucine to isovalerate, isoleucine to 2-methylbutyrate, and valine to isobutyrate only in the presence of thiosulfate, or when co-cultured with Methanobacterium sp. This oxidative deamination was rendered thermodynamically possible by the ability ofT. brockii to reduce thiosulfate to sulfide or the transfer of reducing equivalents to the hydrogenotrophic methanogen. The results suggest that T. brockii may be of ecological significance in thermal environments in the turnover of amino acids, especially with thiosulfate or H(2)-utilizing methanogens are present.

Growth Physiology of the Hyperthermophilic Archaeon Thermococcus litoralis: Development of a Sulfur-Free Defined Medium, Characterization of an Exopolysaccharide, and Evidence of Biofilm Formation

Nutritional characteristics of the hyperthermophilic archaeon Thermococcus litoralis have been investigated with emphasis on the development of a sulfur-free, defined growth medium, analysis of an exocellular polysaccharide, and formation of a biofilm. An artificial-seawater-based medium, containing 16 amino acids, adenine, uracil, vitamins, and trace elements, allowed T. litoralis to attain growth rates and cell densities similar to those found with complex media. Four amino acids (alanine, asparagine, glutamine, and glutamate) were not included due to their lack of effect on growth rates and cell yields. In this medium, cultures reached densities of 10(sup8) cells per ml, with doubling times of 55 min (without maltose) or 43 min (with maltose). Neither the addition of elemental sulfur nor the presence of H(inf2) significantly affected cell growth. A sparingly soluble exopolysaccharide was produced by T. litoralis grown in either defined or complex media. Analysis of the acid-hydrolyzed exopolysaccharide yielded mannose as the only monosaccharidic constituent. This exopolysaccharide is apparently involved in the formation of a biofilm on polycarbonate filters and glass slides, which is inhabited by high levels of T. litoralis. Biofilm formation by hyperthermophilic microorganisms in geothermal environments has not been examined to any extent, but further work in this area may provide information related to the interactions among high-temperature organisms.

A gene, han1A, encoding an archaeal histone-like protein from the Thermococcus species AN1: homology with eukaryal histone consensus sequences and the implications for delineation of the histone fold

The han1A gene, encoding a subunit of the histone-like protein HAN1 from the Thermococcus species AN1, has been cloned and sequenced. Sequence analysis of the translation product of the gene demonstrates homology with other archaeal histone-like proteins of the 'HMf family' and eukaryal consensus sequences, particularly H4. The region of highest homology between the AN1 histone subunit, termed the HAN1A1 subunit, and the H4 consensus is suggested, by the 3-dimensional structure of the histone octamer, to interact with the minor groove of DNA. The results presented add further weight to the notion that the 'archaeal histones' and the eukaryal histones are indeed related and that the approximate 65 amino acid residue length of the archaeal histones represents the archaeal equivalent of the histone fold structural building block common to all eukaryal histones.

Metabolism in hyperthermophilic microorganisms

Hyperthermophilic microorganisms grow at temperatures of 90 degrees C and above and are a recent discovery in the microbial world. They are considered to be the most ancient of all extant life forms, and have been isolated mainly from near shallow and deep sea hydrothermal vents. All but two of the nearly twenty known genera are classified as Archaea (formerly archaebacteria). Virtually all of them are strict anaerobes. The majority are obligate heterotrophs that utilize proteinaceous materials as carbon and energy sources, although a few species are also saccharolytic. Most also depend on the reduction of elemental sulfur to hydrogen sulfide (H2S) for significant growth. Peptide fermentation involves transaminases and glutamate dehydrogenase, together with several unusual ferredoxin-linked oxidoreductases not found in mesophilic organisms. Similarly, a novel pathway based on a partially non-phosphorylated Entner-Doudoroff scheme has been postulated to convert carbohydrates to acetate, H2 and CO2, although a more conventional Embden-Meyerhof pathway has also been identified in one saccharolytic species. The few hypethermophiles known that can assimilate CO2 do so via a reductive citric acid cycle. Two S(o)-reducing enzymes termed sulfhydrogenase and sulfide dehydrogenase have been purified from the cytoplasm of a hyperthermophile that is able to grow either with or without S(o). A scheme for electron flow during the oxidation of carbohydrates and peptides and the reduction of S(o) has been proposed. However, the mechanisms by which S(o) reduction is coupled to energy conservation in this organism and in obligate S(o)-reducing hyperthermophiles is not known.

Life in hot springs and hydrothermal vents

Hot springs and hydrothermal systems occurring within volcanic areas are inhabited by hyperthermophilic microorganisms, some of which grow at temperatures up to 110 degrees C. Hyperthermophiles grow anaerobically or aerobically by diverse metabolic types. Within the high temperature ecosystems, primary production is independent from solar energy.

Preliminary description and nutritional characterization of a chemoorganotrophic archaeobacterium growing at temperatures of up to 110 ° isolated from a submarine hydrothermal vent environment

Summary: An extremely thermophilic coccoid bacterium, designated strain ES4, was isolated from a flange (a newly described geological structure associated with massive sulphide mounds) at the Juan de Fuca Ridge hydrothermal vent system. The organism is a salt-requiring obligately anaerobic chemoorganotroph which reduces elemental sulphur but can grow very poorly in the absence of sulphur. Organic substrates utilized include yeast extract, peptone and amino acid hydrolysate as well as individual amino acids, the peptide Leu-Ser and starch. When growing on a defined medium, ES4 requires a supplement of vitamins and 20 amino acids at trace concentrations. Growth is most rapid in the temperature range 90-99 °C, with a maximum growth temperature of about 110 °C. In the optimal temperature range for growth, ES4 has a doubling time of about 1 h and can reach densities of 109 cells ml-1. Insensitivity to the antibiotics vancomycin, streptomycin and chloramphenicol, and the presence of di- and tetra-ether phytanyl lipids, indicate that ES4 is an archaeobacterium.