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All sourcesNASA NTRSDOE OSTI
NASA NTRS2022

ThermoBase: A Database of the Phylogeny and Physiology of Thermophilic and Hyperthermophilic Organisms

Thermophiles and hyperthermophiles are those organisms which grow at high temperature (> 40°C). The unusual properties of these organisms have received interest in multiple fields of biological research, and have found applications in biotechnology, especially in industrial processes. However, there are few listings of thermophilic and hyperthermophilic organisms and their relevant environmental and physiological data. Such repositories can be used to standardize definitions of thermophile and hyperthermophile limits and tolerances and would mitigate the need for extracting organism data from diverse literature sources across multiple, sometimes loosely related, research fields. Therefore, we have developed ThermoBase, a web-based and freely available database which currently houses comprehensive descriptions for 1238 thermophilic or hyperthermophilic organisms. ThermoBase reports taxonomic, metabolic, environmental, experimental, and physiological information in addition to literature resources. This includes parameters such as coupling ions for chemiosmosis, optimal pH and range, optimal temperature and range, optimal pressure, and optimal salinity. The database interface allows for search features and sorting of parameters. As such, it is the goal of ThermoBase to facilitate and expedite hypothesis generation, literature research, and understanding relating to thermophiles and hyperthermophiles within the scientific community in an accessible and centralized repository. ThermoBase is freely available online at the Astrobiology Habitable Environments Database (AHED; https://ahed.nasa.gov), at the Database Center for Life Science (TogoDB; http://togodb.org/db/thermobase), and in the S1 File.

Thermophiles↗
NASA NTRS2003

Alpha-amylase from the Hyperthermophilic Archaeon Thermococcus thioreducens

Extremophiles are microorganisms that thrive in, from an anthropocentric view, extreme environments such as hot springs. The ability of survival at extreme conditions has rendered enzymes from extremophiles to be of interest in industrial applications. One approach to producing these extremozymes entails the expression of the enzyme-encoding gene in a mesophilic host such as E.coli. This method has been employed in the effort to produce an alpha-amylase from a hyperthermophile (an organism that displays optimal growth above 80 C) isolated from a hydrothermal vent at the Rainbow vent site in the Atlantic Ocean. alpha-amylases catalyze the hydrolysis of starch to produce smaller sugars and constitute a class of industrial enzymes having approximately 25% of the enzyme market. One application for thermostable alpha-amylases is the starch liquefaction process in which starch is converted into fructose and glucose syrups. The a-amylase encoding gene from the hyperthermophile Thermococcus thioreducens was cloned and sequenced, revealing high similarity with other archaeal hyperthermophilic a-amylases. The gene encoding the mature protein was expressed in E.coli. Initial characterization of this enzyme has revealed an optimal amylolytic activity between 85-90 C and around pH 5.3-6.0.

Bernhardsdotter, E. C. M. J.↗
NASA NTRS2002

Thermococcus sulfurophilus sp. nov., a New Hyperthermophilic, Sulfur-Reducing Archaeon Isolated from Deep-Sea Hydrothermal Vent

A new hyperthermophilic, anaerobic, sulfur-reducing, organo-heterotrophic archaeon, strain OGL-20P, was isolated from "black smoker" chimney material at the Rainbow hydrothermal vent site in the Atlantic Ocean (36.2 N; 33.9 W). The cells of strain OGL-20P have irregular coccoid shape and are motile with a single flagellum. Growth occurs within pH range of 5.5-8.2 (optimal at pH 7.0-7.2), salinity range of 1-5% NaCl (optimal concentration 3% NaCl wt/vol), and temperature range of +55 C to +94 C (optimal growth at +83 C to +85 C). Strain OGL-20P is resistant to freezing (at -20 C). New isolate is strictly anaerobic with sulfur-type of respiration. A limited number of compounds are utilized as electron donors, including peptone, becto-tryptone, casamino-acids, and yeast extract but does not grow with separate amino acids. Sulfur and Iron can be used as electron acceptors; but not sulfate, sulfite, thiosulfate or nitrate. Strain OGL-20P is resistant to chloramphenicol, kanamycin, and gentamycin. Growth of str. OGL20P is inhibited by tetracyclin but not by Na2MoO4. The G+C content of DNA is 57.2 mol%. The 16S ribosomal RNA sequence analysis allows one to classify strain OGL-20P as a representative of a now species of Thermococcus genus. The name Thermococcus sulfurophilus op. nov., was suggested for the new isolate, type strain OGL-20P (sup T) (= ATCC BAA_394 (sup T) = DSM...(supT)).

Pikuta, Elena V.↗
NASA NTRS2003

Thermococcus Thioreducens sp. nov., A Novel Hyperthermophilic, Obligately Sulfur-Reducing Archaeon from a Deep-Sea Hydrothermal Vent

A novel hyperthermophilic organo-heterotrophic archaeon, strain OGL-20P(sup T), was isolated from 'black smoker' chimney material from the Rainbow hydrothermal vent site on the Mid-Atlantic Ridge (36.2 N; 33.9 W). The cells of strain OGL-20P(sup T) have an irregular coccoid shape and are motile with a single flagellum. Growth was observed to occur within the pH range 5.0-8.5 (optimum pH 7.0), NaCl concentration range 1-5 % (w/v) (optimum 3 %), and temperature range 55-94 C (optimum 83-85 C). Novel isolate is strictly anaerobic and obligately dependent from elemental sulfur as electron acceptor, but it cannot reduce sulfate, sulfite, thiosulfate, iron (III) or nitrate. Proteolysis products that can be utilized as substrates during sulfur-reduction are: peptone, bactotryptone, casamino-acids, and yeast extract. Strain OGL-20P(sup T) is resistant to ampicillin, chloramphenicol, kanamycin, and gentamycin, but sensitive to tetracycline and rifampicin. The G+C content of DNA is 57.1 mol% . Comparative 16S rRNA gene sequence analysis revealed that strain OGL-20P(sup T) is most closely related to Thermococcus celer and 'T. barossii', but no significant homology by DNA-DNA hybridization was observed between those species and the new isolate. On the basis of physiological and molecular properties of the new isolate, the name Thermococcus thioreducens sp. nov., is proposed. The type strain is OGL-20P(sup T) (= ATCC BAA-394(sup T) = DSM 1498(sup T)).

Pikuta, Elena V.↗
NASA NTRS2004

Cloning and Characterization of an alpha-amylase Gene from the Hyperthermophilic Archaeon Thermococcus Thioreducens

The gene encoding an extracellular alpha-amylase, TTA, from the hyperthermophilic archaeon Thermococcus thioreducens was cloned and expressed in Escherichia coli. Primary structural analysis revealed high similarity with other a-amylases from the Thermococcus and Pyrococcus genera, as well as the four highly conserved regions typical for a-amylases. The 1374 bp gene encodes a protein of 457 amino acids, of which 435 constitute the mature protein preceded by a 22 amino acid signal peptide. The molecular weight of the purified recombinant enzyme was estimated to be 43 kDa by denaturing gel electrophoresis. Maximal enzymatic activity of recombinant TTA was observed at 90 C and pH 5.5 in the absence of exogenous Ca(2+), and the enzyme was considerably stable even after incubation at 90 C for 2 hours. The thermostability at 90 and 102 C was enhanced in the presence of 5 mM Ca(2+). The extraordinarily high specific activity (about 7.4 x 10(exp 3) U/mg protein at 90 C, pH 5.5 with soluble starch as substrate) together with its low pH optimum makes this enzyme an interesting candidate for starch processing applications.

Bernhardsdotter, Eva C. M. J.↗
NASA NTRS2004

Cloning and Characterization of an Alpha-amylase Gene from the Hyperthermophilic Archaeon Thermococcus Thioreducens

The gene encoding an extracellular a-amylase, TTA, from the hyperthermophilic archaeon Thermococcus thioreducens was cloned and expressed in Escherichia coli. Primary structural analysis revealed high similarity with other a-amylases from the Thermococcus and Pyrococcus genera, as well as the four highly conserved regions typical for a-amylases. The 1374 bp gene encodes a protein of 457 amino acids, of which 435 constitute the mature protein preceded by a 22 amino acid signal peptide. The molecular weight of the purified recombinant enzyme was estimated to be 43 kDa by denaturing gel electrophoresis. Maximal enzymatic activity of recombinant TTA was observed at 90 C and pH 5.5 in the absence of exogenous Ca(2+), and the enzyme was considerably stable even after incubation at 90 C for 2 hours. The thermostability at 90 and 102 C was enhanced in the presence of 5 mM Ca(2+). The extraordinarily high specific activity (about 7.4 x 10(exp 3) U/mg protein at 90 C, pH 5.5 with soluble starch as substrate) together with its low pH optimum makes this enzyme an interesting candidate for starch processing applications.

Bernhardsdotter, Eva C. M. J.↗
NASA NTRS2001

Signature lipids and stable carbon isotope analyses of Octopus Spring hyperthermophilic communities compared with those of Aquificales representatives

The molecular and isotopic compositions of lipid biomarkers of cultured Aquificales genera have been used to study the community and trophic structure of the hyperthermophilic pink streamers and vent biofilm from Octopus Spring. Thermocrinis ruber, Thermocrinis sp. strain HI 11/12, Hydrogenobacter thermophilus TK-6, Aquifex pyrophilus, and Aquifex aeolicus all contained glycerol-ether phospholipids as well as acyl glycerides. The n-C(20:1) and cy-C(21) fatty acids dominated all of the Aquificales, while the alkyl glycerol ethers were mainly C(18:0). These Aquificales biomarkers were major constituents of the lipid extracts of two Octopus Spring samples, a biofilm associated with the siliceous vent walls, and the well-known pink streamer community (PSC). Both the biofilm and the PSC contained mono- and dialkyl glycerol ethers in which C(18) and C(20) alkyl groups were prevalent. Phospholipid fatty acids included both the Aquificales n-C(20:1) and cy-C(21), plus a series of iso-branched fatty acids (i-C(15:0) to i-C(21:0)), indicating an additional bacterial component. Biomass and lipids from the PSC were depleted in (13)C relative to source water CO(2) by 10.9 and 17.2 per thousand, respectively. The C(20-21) fatty acids of the PSC were less depleted than the iso-branched fatty acids, 18.4 and 22.6 per thousand, respectively. The biomass of T. ruber grown on CO(2) was depleted in (13)C by only 3.3 per thousand relative to C source. In contrast, biomass was depleted by 19.7 per thousand when formate was the C source. Independent of carbon source, T. ruber lipids were heavier than biomass (+1.3 per thousand). The depletion in the C(20-21) fatty acids from the PSC indicates that Thermocrinis biomass must be similarly depleted and too light to be explained by growth on CO(2). Accordingly, Thermocrinis in the PSC is likely to have utilized formate, presumably generated in the spring source region.

Carbon Isotopes/analysis↗
NASA NTRS1990

Methanococcus igneus sp. nov., a novel hyperthermophilic methanogen from a shallow submarine hydrothermal system

A novel hyperthermophilic strictly chemolithoautotrophic member of the genus Methanococcus was isolated from a shallow (depth: 106 m) submarine vent system at the Kolbeinsey ridge, Iceland. The isolate grew between 45 and 91 degrees C with an optimum around 88 degrees C (doubling time: 25 min). It differs from Methanococcus jannaschii in its 16S rRNA sequence, its non-hybridizing DNA, and its selenium-independent growth. Therefore, the isolate represents a new species which we name Methanococcus igneus. Type strain is isolate "Kol 5" (DSM 5666).

NASA Program Exobiology↗
NASA NTRS2007

Thermococcus Thioreducens sp. Nov., a Novel Hyperthermophilic, Obligately Sulfur-reducing Archaeon from a Deep-sea Hydrothermal Vent

A hyperthermophilic, sulfur-reducing, organo-heterotrophic archaeon, strain OGL-20P was isolated from black smoker chimney material from the Rainbow hydrothermal vent site on the Mid-Atlantic Ridge (36.2 N, 33.9 W). The cells of strain OGL-20P(sup T) have an irregular coccoid shape and are motile with a single flagellum. Growth was observed within the pH range 5.0-8.5 (optimum pH 7.0), NaCl concentration range 1-5 % (w/v) (optimum 3%), and temperature range 55-94 C (optimum 83-85 C). The novel isolate is strictly anaerobic and obligately dependent upon elemental sulfur as an electron acceptor, but it does not reduce sulfate, sulfite, thiosulfate, iron (III) or nitrate. Proteolysis products (peptone, bacto-tryptone, casamino-acids, and yeast extract) are utilized as substrates during sulfur-reduction. Strain OGL-20P(sup T) is resistant to ampicillin, chloramphenicol, kanamycin, and gentamycin, but sensitive to tetracycline and rifampicin. The G+C content of DNA is 52.9 mol%. The 16S rRNA gene sequence analysis revealed that strain OGL-20P(sup T) is closely related to Thermococcus coalescens and related species, but no significant homology by DNA-DNA hybridization was observed between those species and the new isolate. On the basis of physiological and molecular properties of the new isolate, we conclude that strain OGL-20P(sup T) represents a new separate species within the genus Thermococcus, and propose the name Thermococcus thioreducens sp. nov. The type strain is OGL-20P(sup T) (= ATCC BAA-394(sup T) = JCM 12859(sup T) = DSM 14981(sup T)).

Pikuta, Elena V.↗
NASA NTRS2007

Thermococcus thioreducens sp. nov., a Novel Hyperthermophilic, Obligately Sulfur-Reducing Archaeon from a Deep-Sea Hydrothermal Vent

A hyperthermophilic, sulfur-reducing, organo-heterotrophic archaeon, strain OGL-20P(sup T), was isolated from 'black smoker' chimney material from the Rainbow hydrothermal vent site on the Mid-Atlantic Ridge (36.2degN, 33.9degW). The cells of strain OGL-20P(T) have an irregular coccoid shape and are motile with a single flagellum. Growth was observed within a pH range of 5.0-8.5 (optimum pH 7.0), an NaCl concentration range of 1-5%(w/v) (optimum 3%)and a temperature range of 55-94 C (optimum 83-85 C). The novel isolate is strictly anaerobic and obligately dependent upon elemental sulfur as an electron acceptor, but it does not reduce sulfate, sulfite, thiosulfate, Fe(III) or nitrate. Proteolysis products (peptone, bacto-tryptone, Casamino acids and yeast extract) are utilized as substrates during sulfur reduction. Strain OGL-20P(sup T) is resistant to ampicillin, chloram phenicol, kanamycin and gentamicin, but sensitive to tetracycline and rifampicin. The G + C content of the DNA is 52.9 mol% The 16S rRNA gene sequence analysis revealed that strain OGL-20P(sup T) is closely related to Thermococcus coalescens and related species, but no significant homology by DNA-DNA hybridization was observed between those species and the new isolate. On the basis of physiological and molecular properties of the new isolate, we conclude that strain OGL-20P(sup T) represents a new separate species within the genus Thermococcus, for which we propose the name Thermococcus thioreducens sp. nov. The type strain is OGL-20P(sup T) (=JCM 12859(exp T) = DSM 14981(exp T)=ATCC BAA-394(exp T)).

Pikuta, Elena V.↗
NASA NTRS1996

Hydrolysis of Dihydrouridine and Related Compounds

Dihydrouridine is absent from the tRNA of almost all hyperthermophiles and most Archaea but is ubiquitous in the tRNA of Eubacteria and Eukaryotes. In order to investigate whether this could be due to instability, the rate of ring opening of dihydrouridine was measured between 25 and 120 C. The dihydrouridine ring is stable at 25 C, but the half-life at 100 C and pH 7 is 9.1 h, which is comparable to the doubling time of hyperthermophiles. This suggests an explanation for the absence of dihydrouridine from the tRNA of hyperthermophiles. The rates of ring opening of dihydrouracil, dihydrothymine, and 1-N-methyldihydrouracil were measured at 100 C and pH 6-9, as were the equilibrium constants for ring closure of the ureido acids to the dihydrouracils. The pH rate profiles for ring opening and ring closing were calculated from the data. Possible roles for dihydrouracils in the pre-RNA world are discussed.

House, Christopher H.↗
NASA NTRS1995

The Origin of Life--Did It Occur at High Temperatures

A high-temperature origin of life has been proposed, largely for the reason that the hyperthermophiles are claimed to be the last common ancestor of modern organisms. Even if they are the oldest extant organisms, which is in dispute, their existence can say nothing about the temperatures of the origin of life, the RNA world, and organisms preceding the hyperthermophiles. There is no geological evidence for the physical setting of the origin of life because there are no unmetamorphosed rocks from that period. Prebiotic chemistry points to a low-temperature origin because most biochemicals decompose rather rapidly at temperatures of 100 C (e.g., half-lives are 73 min for ribose, 21 days for cytosine, and 204 days for adenine). Hyperthermophiles may appear at the base of some phylogenetic trees because they outcompeted the mesophiles when they adapted to lower temperatures, possibly due to enhanced production of heat-shock proteins.

Miller, Stanley L.↗
NASA NTRS1994

Hydrothermal systems and the emergence of life

The author reviews current thought about life originating in hyperthermophilic microorganisms. Hyperthermophiles obtain food from chemosynthesis of sulfur and have an RNA nucleotide sequence different from bacteria and eucarya. It is postulated that a hyperthermophile may be the common ancestor of all life. Current research efforts focus on the synthesis of organic compounds in hydrothermal systems.

Non-NASA Center↗
NASA NTRS2003

Determining the Biogenicity of Microfossils in the Apex Chert, Western Australia, Using Transmission Electron Microscopy

For over a decade, the oldest evidence for life on this planet has been microfossils in the 3.5 Ga Apex Chert in Western Australia. Recently, the biogenicity of these carbon-rich structures has been called into question through reanalysis of the local geology and reinterpretation of the original thin sections. Although initially described as a stratiform, bedded chert of siliceous clasts, the unit is now thought to be a brecciated hydrothermal vein chert. The high temperatures of a hydrothermal environment would probably have detrimental effects to early non-hyperthermophilic life, compared to that of a shallow sea. Conversely, a hydrothermal origin would suggest that if the microfossils were valid, they might have been hyperthermophilic. Apex Chert controversy. The Apex Chert microfossils were originally described as septate filaments composed of kerogen similar in morphology to Proterozoic and modern cyanobacteria. However new thin section analysis shows that these carbonaceous structures are not simple filaments. Many of the original microfossils are branched and have variable thickness when the plane of focus is changed. Hydrothermal alteration of organic remains has also been suggested for the creation of these strange morphologies. Another point of contention lies with the nature of the carbon material in these proposed microfossils. Kerogen is structurally amorphous, but transforms into well-ordered graphite under high pressures and temperatures. Raman spectrometry of the carbonaceous material in the proposed microfossils has been interpreted both as partially graphitized kerogen and amorphous graphite. However, these results are inconclusive, since Raman spectrometry cannot adequately discriminate between kerogen and disordered graphite. There are also opposing views for the origin of the carbon in the Apex Chert. The carbon would be biogenic if the proposed microfossils are indeed the remains of former living organisms. However, an inorganic Fischer- Tropsch-type synthesis is also a possible explanation for the formation of large-aggregate carbonaceous particles and could also account for the depletion of (13)C observed.

DeGregorio, B. T.↗
NASA NTRS1998

Energetics of amino acid synthesis in hydrothermal ecosystems

Thermodynamic calculations showed that the autotrophic synthesis of all 20 protein-forming amino acids was energetically favored in hot (100 degrees C), moderately reduced, submarine hydrothermal solutions relative to the synthesis in cold (18 degrees C), oxidized, surface seawater. The net synthesis reactions of 11 amino acids were exergonic in the hydrothermal solution, but all were endergonic in surface seawater. The synthesis of the requisite amino acids of nine thermophilic and hyperthermophilic proteins in a 100 degreesC hydrothermal solution yielded between 600 and 8000 kilojoules per mole of protein, which is energy that is available to drive the intracellular synthesis of enzymes and other biopolymers in hyperthermophiles thriving in these ecosystems.

NASA Discipline Exobiology↗
NASA NTRS1996

Hydrothermal systems as environments for the emergence of life

Analysis of the chemical disequilibrium provided by the mixing of hydrothermal fluids and seawater in present-day systems indicates that organic synthesis from CO2 or carbonic acid is thermodynamically favoured in the conditions in which hyperthermophilic microorganisms are known to live. These organisms lower the Gibbs free energy of the chemical mixture by synthesizing many of the components of their cells. Primary productivity is enormous in hydrothermal systems because it depends only on catalysis of thermodynamically favourable, exergonic reactions. It follows that hydrothermal systems may be the most favourable environments for life on Earth. This fact makes hydrothermal systems logical candidates for the location of the emergence of life, a speculation that is supported by genetic evidence that modern hyperthermophilic organisms are closer to a common ancestor than any other forms of life. The presence of hydrothermal systems on the early Earth would correspond to the presence of liquid water. Evidence that hydrothermal systems existed early in the history of Mars raises the possibility that life may have emerged on Mars as well. Redox reactions between water and rock establish the potential for organic synthesis in and around hydrothermal systems. Therefore, the single most important parameter for modelling the geochemical emergence of life on the early Earth or Mars is the composition of the rock which hosts the hydrothermal system.

Non-NASA Center↗
NASA NTRS2013

Does Aspartic Acid Racemization Constrain the Depth Limit of the Subsurface Biosphere?

Previous studies of the subsurface biosphere have deduced average cellular doubling times of hundreds to thousands of years based upon geochemical models. We have directly constrained the in situ average cellular protein turnover or doubling times for metabolically active micro-organisms based on cellular amino acid abundances, D/L values of cellular aspartic acid, and the in vivo aspartic acid racemization rate. Application of this method to planktonic microbial communities collected from deep fractures in South Africa yielded maximum cellular amino acid turnover times of approximately 89 years for 1 km depth and 27 C and 1-2 years for 3 km depth and 54 C. The latter turnover times are much shorter than previously estimated cellular turnover times based upon geochemical arguments. The aspartic acid racemization rate at higher temperatures yields cellular protein doubling times that are consistent with the survival times of hyperthermophilic strains and predicts that at temperatures of 85 C, cells must replace proteins every couple of days to maintain enzymatic activity. Such a high maintenance requirement may be the principal limit on the abundance of living micro-organisms in the deep, hot subsurface biosphere, as well as a potential limit on their activity. The measurement of the D/L of aspartic acid in biological samples is a potentially powerful tool for deep, fractured continental and oceanic crustal settings where geochemical models of carbon turnover times are poorly constrained. Experimental observations on the racemization rates of aspartic acid in living thermophiles and hyperthermophiles could test this hypothesis. The development of corrections for cell wall peptides and spores will be required, however, to improve the accuracy of these estimates for environmental samples.

cellular↗
NASA NTRS2000

Methanogenesis, Mesospheric Clouds, and Global Habitability

Hyperthermophilic methanogens can exist in a deep hot biosphere up to 110 C, or 10 km deep. Methane (CH4) itself is thermodynamically stable to depths of 300 km. Geologic (microbial plus abiogenic thermal) methane is transported upward, attested to by its association with helium, to form petroleum pools. Near or at the surface, geologic CH4 mixes with other natural and with anthropogenic CH4 yielding annual emissions into the atmosphere of 500 Tg, of which 200 Tg are natural and 300 Tg are man-made. The atmospheric lifetime of CH4, a greenhouse gas 20 times more effective than CO2 in raising global temperatures, is approximately 10 years. It is removed from the atmosphere mainly by reactions with hydroxyl radical (OH) to form CO2, but also by dry soil and by conversion to H2O in the stratosphere and middle atmosphere. A sudden rise in atmospheric temperatures by 9-12 C some 55 million years ago has been explained by the release in a few thousand years of three trillion tons of CH4 out of 15 trillion tons that had formed beneath the sea floor. What prevented this CH4-induced greenhouse effect from running away? An analog to the CH4-burp of 55 million years ago is the CH4-doubling over the past century which resulted in a increase in upper level H2O from 4.3 ppmv to 6 ppmv. This 30% increase in H2O vapor yielded a tenfold increase in brightness of polar mesospheric clouds because of a strong dependence of the ice particle nucleation rate on the water saturation ratios. Models show that at a given temperature the optical depth of mesospheric clouds scales as [H2O]beta with beta varying between 4 and 8. Radiative transfer tools applied to mesospheric particles suggest that an optical depth of approximately one, or 1000 times the current mesospheric cloud optical depth, would result in tropospheric cooling of about 10 K. Assuming beta=6, a thousandfold increase in optical thickness would require a three-fold increase of H2O, or a 20-fold increase of CH4. At the current rate of anthropogenic emissions this is expected to occur within the next 1000 years. This timescale is also commensurate with what has been assumed for the CH4- burp 55 million years ago.

Pueschel, Rudolf F.↗