Chapter 3: Heat-Loving Archaea
Archaea (Archaebacteria), adapted to warm, hot, and boiling water. Archaea living on inorganic food, on organic food, or on both. Why is there life on earth? How complex have the first living cells been? What was needed, to think them out and to make them?
Thermoplasma acidophilum is a heat loving archaea. Where does it live now? What does it eat? How long is its genome (DNA-chain). And since when has it lived on this earth? What have scientists found out about this?
Cells irregular varying from spherical (about 0.1-5 µm in diameter) to filamentous structures. Cells mostly motile and flagellated. Gram-negative. Cells lack a rigid cell wall and are surrounded only by a cytoplasmatic membrane. Obligately thermoacidophilic. Growth between pH 0.5-4 at 33-67°C. They grow in the presence of up to at least 2% salt. Obligately heterotrophic. Growth on extracts of yeast, meat, and eu- and archaea. Facultatively aerobic. Anaerobic growth is strongly enhanced by elemental sulfur, which is reduced to H2S by means of sulfur respiration. Members of the genus Thermoplasma were isolated from self-heated coal refuse piles and acidic solfatara fields.
Usually, monopolar, montrichous flagellation is found, but sometimes multiflagellated cells were also observed. On solid media, colonies of Thermoplasma are usually small (about 0.5 mm in diameter) and are either colorless or brownish. Thermoplasma spp. Are heterotrophic, facultatively anaerobic thermophiles that require the presence of yeast extract or similar extracts for growth. They can also grow in the presence of meat extract or bacterial extracts. Therefore, the nutrition of Thermoplasma in its natural habitat is most likely based on the products of decomposing cells of organisms sharing the biotope. Thermoplasma spp. Grow as facultative anaerobes on molecular sulfur by sulfur respiration, forming large amounts of H2S.
The growth temperatures range from about 45 to 63°C for T. acidophilum, and from about 33°C to 67°C for T. volcanium. The optimum growth temperature is around 59°C. Both species grow within a pH range of 0.4 to 4 with an optimum around pH2. - Segerer, A. H. and K. O. Stetter (1992:714-716).
How long is the genome of the archae Thermoplasma acidophilum?
T. D. Brock and M. T. Madigan report: The genome of Thermoplasma is extremely small, perhaps the smallest of all free-living bacteria. The DNA of Thermoplasma has a molecular weight of 8·108. Christiansen et al. (1975) found the genome size of Thermoplasma to be about 109 Daltons. Whereas Searcy and Doyle (1975) found an even smaller genome size, 8.4·109. According to these latter workers, the genome size of Thermoplasma DNA is the smallest yet reported for any non-parasitic organism. Brock, T. D. (1987:97); Brock and Madigan (1991:812, 813).
Claus Christiansen and co-workers report about Thermoplasma acidophilum: the calculated genome size varied within the narrow range of 9.4·108 and 1.0·109 daltons. Genome size of three different strains of Thermoplasma acidophilum: 9.4·108 daltons, 9.7·108 daltons, and 1.0·109 daltons. (1975:100, Table 1).
How many base pairs of DNA do these genomes have? How long are they? - One average base pair has a molecular weight of 660. And 3000 base pairs (bp) are 1 mm long (Kronberg, A. and T. B. Baker, 1992:20).
8.0·108 Da = 1 212 121 bp = 404 mm long
8.4·108 Da = 1 272 727 bp 424 mm long
9.4·108 Da = 1 424 242 bp = 478 mm long
9.7·108 Da =1 469 697 bp = 490 mm long
1.0·109 Da = 1 515 151 bp = 505 mm long
What are the volume and surface of Thermoplasma acidophilum, and their ratio? Colonies of small Thermoplasma have a diameter of 0.5 µm. 0.065 449 846 94 µm³ volume. 0.785 398 163 3 µm² surface. Ratio of volume to surface: 1:12.
Genome. The genome length of 5 different strains of the archaea Thermoplasma acidophilum has been published: 1 212 121 bp, 1 272 727 bp, 1 424 242 bp, 1 496 697 bp, and 1 515 151 bp, as calculated from their molecular weight. The average length of these five strains is 1 378 787 bp. - What are the sequence alternatives of this genome? How many yes/no decisions were needed, to put its nucleotide pairs into the right place?
1 387 787 bp log 4 = 10830 112 bit.
Ribosomal RNA and Protein. The Thermoplasmales have a ribosomal 30S mass of 1 100 000, and protein mass of 605 000; and 50S mass 1 810 000, protein mass 780 000, as reported by Marco Acca et al. (1994:634).
Its total rRNA mass of its 30S and 50S subunits is 1 525 000 : 330 = 4 621 nucleotides log 4 = 102 782 bit.
Total protein mass of its 30S and 50S = 1 385 000 : 110 = 12 590 amino acids log 20 = 1016 379 bit.
The 23S RNA of Thermoplasma acidophilum has 2908 bases, as stated by H. K. Ree et al. (1993:333-341). It has an information content of at least 101 750 bit.
Total information content of the genome and ribosome nucleotides of Thermoplasma acidophilum is 10848.232 bit.
Thermoplasma volcanium isolated from hot springs. Cells are 1-2 µm in diameter. Notice abundant flagella. From A. Segerer and K. O. Stetter. In M. T. Madigan et al. (1997:765) Fg. 17.24.
Where has one found the archae Sulfolobus acidocaldarius? How large is it? How long is its genome? What was needed, to think it out and to make it?
Cells coccoid, highly irregular, about 0.8-2 µm in diameter, usually occurring singly. Neither motility nor flagella were detected. Cell envelope composed of protein subunits in hexagonal array. Aerobic lithotrophic growth via oxidation of sulfur, sulfide, or tetrathionate. Organitrophic growth by oxidizing complex organic material (e.g. yeast extract), sugars or amino acids. Thermoacidophilic. Growth temperature 55-85°C (87°C) opt. 70-75°C. pH optimum 2-3. All Sulfolobales are extremely acidophilic thermophilic sulfur metabolizers. Bergey's Manual (1989:2250), The Prokaryotes (1992:692).
Sulfolobus was isolated from acidic continental solfatara fields including Yellowstone National Park (Wyoming), New Mexico, Solfatara Crater and Pisciarelle Solfatare (Naples, Italy), Dominica, El Salvador, New Zealand, Iceland, Japan, The Azores, and Sumatra. This indicates a worldwide distribution. Sulfolobus is Gram-negative.
Most Sulfolobus isolates are able to gain their energy lithotrophically by oxidation of sulfur with the formation of sulfuric acid. They can also obtain their energy by oxidizing sulfide to molecular sulfur. Many Sulfulobus strains are able to oxidize ferrous iron, which therefore acts anaerobically as an electron acceptor. A few isolates are able to grow on sulfidic ores. Under these strains are moderate thermophiles with growth maxima around 70 to 75°C. However, Sulfolobus-like organisms, growing on ores at temperatures up to at least 95°C, have been isolated recently.
Many Sulfolobus isolates can grow autotrophically. In the case of Sulfolobus brierleyi, CO2 fixation most likely occurs via a reductive carboxylic acid pathway. Alternately, most Sulfolobus isolates, including Sulfulobus brierleyi, are able to grow heterotrophically by aerobic respiration of organic material, including yeast extract, peptone, amino acids and sugars. Some isolates, like B 6/2 from Japan and NA 4 and Kra 23 from Italy and Iceland, respectively, are obligate chemolithoautotrophs. Sulfolobus brierlyi (DSM 1651) can grow also strictly anaerobically by the formation of H2S from H2 and S°. - Stetter, K. O. in Brock, T.D. (1986:47, 48).
The archae Sulfolobus lives in acidic solfatara fields, in acidic environments. Since when? Has it been one of the first kinds of one-celled organisms on earth?
Prof. T. D. Brock (1978:174, 175) replies: "There is good reason, to believe that the acidic environments did not arise on earth until the atmosphere became oxidizing. Sulfuric acid can only form under oxidizing conditions, since the only significant source of oxidizing power is O2. It is true that sulfuric acid can be formed anaerobically by the oxidation of sulfide with iron. But ferric iron itself can only be formed, if O2 is present, because of the high oxidation-reduction potential of the Fe³+/Fe²+ pair. Thus, it seems unlikely that Sulfolobus was an early form of life.
"The existence of Sulfobus reveals the remarkable adaptability of living protoplasma. The ability to grow in hot environments is impressive enough. But the ability to grow in hot and acidic environments is truly amazing. ... And the fact that similar or identical organisms can be found as far apart as Yellowstone and New Zealand suggests that the available hot, acidic habitats on earth have been colonized by a single organism."
Volume and surface of spherical cell of Sulfolobus acidocaldarius. The smallest diameter of this versatile archae is 0.8 µm. Its volume is then 0.268 082 573 µm. And its surface is 2.010 619 299 µm. Ratio of volume to surface: 1 : 7.5.
Genome. The heat-loving archae Sulfolobus acidocaldarius has a chromosome size of 2,760,000 base pairs, as determined by Kondo et al. (1993) and quoted by Rowan A. Grayling et al. (1994:596). 2,760,000 bp are 101 661 685 bit (sequence alternatives).
Sulfolobus solfataricus Ron 12/III has a genome size of 2,705,000 base pairs. C. Bauman et al. in Extremophiles (1998) 2:104 Table 2.
Ribosomal RNA and Protein. The Sulfolobales have a ribosomal 30S mass of 1 140 000, and a protein mass of 665 000. Their 50S has a mass of 1 800 000, and a protein mass of 7 700 000, as reported by Marco Acca (1994:634).
Total protein mass of 30S and 50S = 1 415 000 MW : 110 = 12 863 amino acids log 20 = 1016 735. Total information content of its genome and its ribosomal RNA and protein is 101 678 420 bit.
Thin sections of Sulfolobus acidocaldariusstrain B6 normal. From K. O. Stetter and W. Zillig in Carl R. Woese, The Bacteria, Volume VIII (1985:94) Fig. 1.
Hans-Peter Klenk and co-workers have studied the whole genome of the hyperthermophillic, sulphate-reducing archaeon Archaeoglobus fulgidus. They report about their findings in Nature, vol. 390, 27 November 1997 p. 364-369. It has 2,178,400 base pairs. Cells are irregular spheres with a glycoprotein envelope and monopolar flagellar. It grows between 60 and 95°C, best at 83°C. It needs at least 4 hours, to double itself. The organism grows organoheterotrophically. It uses a variety of carbon and energy sources. But it can also grow lithoautotrophicially on hydrogen, thiosulphate and carbon dioxide. The genome of A. fulgidus consists of a single, circular chromosome of 1,178,400 base pairs (bp). Like most autotrophic microorganisms, A. fulgidus is able to synthesize many essential compounds, including amino acids, cofactors, carriers, purines and pyriminines.
Figure 3, on page 367 shows an integrated view of metabolism and soluble transport of A. fulgidus. Biochemical pathways for energy production, biosynthesis of organic compounds, and degradation of amino acids, aldehydes and acids are shown with the central components of A. fulgidus metabolism, sulphate, lactate and acetyl-CoA highlighted. This is very complicated. Much of this, the scientists have found out only a few years ago. And the scientists who drew this, must have intensely studied microbiology and biochemisty for many years. But the tiny archaebacterium Archaeoglobus fulgidus has known this already several billion years ago. This tiny creature, only a fraction of a millimeter across, knows all this about biochemistry. It is also able to work with it very efficiently. Certainly better, than any human scientist. Why does this bacterium know all this, what the human scientist first had to learn? This question should be answered.
M. L. Miroshnichenko and co-workers (1989:257-262) report about an extremely thermophilic marine sulfur-metabolizing archaea:
Four strains of a new extremely thermophilic anaerobic archaebacteria were isolated from marine solfataric fields of Kraternaya cove (Ushishir archipelago, Northern Kurils). The cells are irregular cocci 1 to 2 µm in diameter. Two strains are motile due to a tuft of flagella. Two strains are non-motile. The cell envelope consists of two layers of subunits. Two strains (non-motile) grow at temperatures from 55 to 95°C (opt. 75°C) and two (motile) from 75 to 98°C. The pH range for growth of all strains is 5.7 to 7.2 (opt. around 6.5). Salt (opt. 2.5% NaCl) and elemental sulfur are obligately required for growth. Peptides and polysacharides are utilized. The generation time for strain K-3 under optimal cultivation conditions (= 76°C, pH 6.4, 2.5° sea salt, 0.3% peptone, 0.05% yeast extract, 1% sulfur) was 72 min. They multiply by restriction. It inhabits marine hydrothermal vents in Kraternaya cove (Northern Kurils).
Annemarie Neuner and co-workers (1990:205-207) have studied Thermococcus litoralis. This species is an extremely thermophile marine archaea.
They are spherical, irregular to regular cocci, with a varying width of 0.5-3.0 µm. In the electron microscope a protein envelope covering the membrane was found. No flagellation was found. The Strain NS-C grew between 55°C and 98C, with optimum at 88°C. We found a slight difference to isolate A3, which had the growth range between 50°C and 96°C and the optimum at 85°C. They grew between pH 4.0 and pH 8.5, with an optimum at pH 6.0.
They are able to grow on complex substrates, like yeast extract, peptone, tryptone, meat extract, and casein. In the presence of elemental sulfur, higher growth yields were observed. They are able to reduce sulfur. Isolated from shallow submarine solfataras at Lucrino/Naples and Porto di Levante/Vulcano.
What are their volume, surface, and volume/surface ratio? - Thermococcus litoralis has the shape of a ball, and a diameter of 0.5-3.0 µm. We shall use here its smallest diameter of 0.5 µm:
Volume: 0.065 449 µm³. Surface: 0.785 398 µm². Ratio: 1:12.
Wolfram Zillig writes in The Prokaryotes (1992:702): All known species of the Thermococcales are ... anaerobes thriving in marine or terrestrial solfatara situations. They utilize peptides, yeast extracts, in some cases proteins or amino acids, and, rarely, carbohydrates as carbon sources. Elemental sulfur has also been found to stimulate growth considerably (tenfold for the growth of T. celer on yeast extract) together with the formation of H2S.
Thermococcus celer has an optimal growth temperature of 88°C, and a maximal growth temperature of >93°C. Optimal pH 7. Carbon source: peptides, proteins. Generation time < 50 minutes.
T. D. Brock and M. T. Madigan state: "Like those of eubacteria, the genomes of archaebacteria consist of a single covalently closed circular DNA molecule. The genome of the extremely thermophile Thermococcus celer, for which a restriction enzyme map has been constructed, contains about 1900 kilobase pairs of DNA, less than half that of Escherichia coli (4700 kilobase pairs)." (1991:794, 795).
Kenneth M. Noll, Center for Prokaryotic Genome Analysis, Department of Microbiology, University of Illinois, Urbana, U.S.A. reports: The chromosome of the thermophilic archae Thermococcus celer VU 13 has 1,890 kilobase pairs. The genome of T. celer is composed of a single, circular DNA molecule approximately 1,890 kilobases (kb) in size. The totals of six measurements of the chromosome of T. celer:
1,858 1,907 1,856.5 1,893 1,9085 1,918.5 kb
The average of these six measurements is 1,890 kb. The chromosome appears to be composed of a single DNA molecule. There are no other large chromosomal elements. Finally, the genome is relatively small. It is similar in size to the smallest methanogen chromosomes, the Thermoplasma acidophilum chromosome. - Noll, K. M. (1989:6720-6724).
Members of the order Thermococcales include Thermococcus and Pyrococcus. W. Zillig (1992:703).
The heat loving archae Thermococcus celer lives at a temperature of up to 93°C. It has a circular genome of DNA with 1,890 kilobase pairs. These 1 890 000 base pairs are 630 µm long. Hence, it is 630 longer, than the cell's diameter of 1 µm. It has 1 247 400 000 daltons. Its cell volume is 0.523 598 µm. Its surface is 3.141 593 µm. Ratio of volume to surface: 1:6.
Genome. The genome size of six strains of the heat loving archae Thermococcus celer has been determined. They have the following number of base pairs: 1 850 000, 1 907 000, 1 856 500, 1 893 000, 1 908 500, and 1 918 500. The average genome size of Thermococcus celer is 1 890 250 base pairs. It has 101 138 043 bit of information (sequence alternatives).
Ribosonal RNA and Protein. The 16S rRNA of Thermococcus has 1486 nucleotides. The ribosomal 30S mass of the Thermococcales is 1 140 000. Its protein mass is 646 000. Its 50S has a total mass of 1 900 000, and a protein mass of 870 000, according to Marco Acca et al. (1994:634).
The 16S rRNA chain of Thermococcus, with its 1486 nucleotides, has 10894 bit of information. The total protein mass of 30S and 50S in Thermococcus celer is 1 385 000 : 110 = 12 590 amino acids log 20 = 1016 379 bit. The total rRNA mass of 30S and 50S in Thermococcus celer is 1 525 000 : 330 = 4 621 nucleotides log 4 = 102782 bit. Total information content of its genome and its ribosomal rRNA and protein is 101 158 098 bit.
Thin section of Thermococcus celer. From K. O. Stetter and W. Zillig. In Carl R. Woese, The Bacteria (1985:124) Fig. 13, Vol. VIII.
Wolfram Zillig and co-workers have studied Pyrococcus woesei. It is an ultra-thermophilic marine archae. They write (1987:62-70):
Pyrococcus woesei was isolated from samples taken from marine solfataras at the northern beach of Porto Levante, Vulcano, Eolian Islands, Italy. The temperature was maximally 102 to 103°C. The anaerobic sulfur-reducing archaebacterium Pyrococcus woesei is an 'ultra-thermophile' growing optimally between 100 and 103°C at pH 6 and 6.5 and 30 g/NcCl. Growth proceeds by sulfur respiration of yeast extract or peptides, on yeast extract also without S° in the presence of H2, or on polysaccharides in the presence of H2 and S°. The generation time was as low as 35 minutes.
No purely chemolithoautotrophic growth, with CO2 as sole carbon source and H2 + S° as energy source, was observed. The maximal growth temperature was 104.8°C. Most rapid growth was observed over a temperature range between 100 and 103°C. At 100°C the organism multiplied 5 times faster than at 95°C. The optimal NaCl concentration was 3%. In nature, it occurs in the same environmental niche as Pyrodictium.
Roughly spherical to elongated, often constricted, cells of 0.5 to 2 µm, frequently linked to doublets by short thin threads, Gram-negative with large bundles of smoothly bent filaments (flagellae?) attached to one pole, when cells grow on solid supports.
Pyrococcus woesei is roughly spherical, with a cell diameter of 0.5 to 2 µm. What are its volume, surface, and volume/surface ratio, when using its smallest diameter of 0.5µm?
Volume: 0.065 450 µm³. Surface: 0.785 398 µm². Ratio: 1:12.
A marine archae, growing optimally at 100°C: Pyrococcus furiosus. Gerhard Fiala and co-workers have studied it (1986:56-61):
Ten strains representing a novel genus of marine thermophilic archaebacteria growing between 70 and 103°C with an optimal temperature of 100°C. Its doubling time is only 37 min. They were isolated from geothermally heated marine sediments at the beach of Porto di Levante, Vulcano, Italy. The organisms are spherically-shaped, 0.8 to 2.5 µm in width. They have monopolar polytrichous flagellation. They are strictly anaerobic heterotrophs. They grow on starch, maltose, peptone, and complex organic substrates.
In the light microscope the new organisms appear as motile, regular to slightly irregular cocci of 0.8 to 2.5 µm in width, often occurring in pairs. They stain Gram-negative. Each cell has about 50 monopolar polytrichous flagella. Each one measures about 7 nm in width and 7 µm in length.
The new organisms grew within a temperature range of 70 to 103°C, and multiplied best at 100°C. Their shortest doubling time was then 37 min. It did not grow at 65 or 105°C. It grows on yeast extract, peptone, meat extract, extracts of eu- (Lactobacillus bavaricus DSM 2088), Methanosarcina strain G 1, DSM 3338), casein, starch and maltose as carbon- and energy sources. Pyrococcus is a very efficient consumer of the organic material found on the geothermally heated sea floor of Vulcano. It belongs to the archaebacterial kingdom.
Pyrococcus furiosus is a sphere, with a diameter of 0.8 to 2.5 µm. What are its volume, surface, and volume/surface ratio, when using its smallest diameter of 0.8 µm?
Volume: 0.268 082 µm³. Surface: 2.01 691 µm². Ratio: 1:7.5
Ribosomal RNA and Protein. The 16S rRNA of the Pyrococcus species has 1486 nucleotides, as reported by Marco Acca (1994:634). 1486 log 4 = 10895 bit. The 30S of Pyrococcus woesei has a total mass of 1 140 000, and a protein mass of 645 000. Its 50S has a total mass of 1 840 000, and a protein mass of 810 000.
The total rRNA mass of its 30S and 50S is 1 525 000 : 330 = 4 621 nucleotides log 4 = 102782 bit. The total protein mass of its 30S and 50 S is 1 455 000 : 110 = 13 227 amino acids log 20 = 1017 208 bit.
102782 and 1017 208 and 10895 = 1020 885 bit. This means, so much information is needed, just to put the rRNA nucleotides and the amino acids of its protein into the right place. Mathematics and information is non-material, spiritual. It always has its source in a non-material, spiritual world: in the mind of an intelligent person, of the Creator.
Pyrococcus horikoshii
Juan M. Gonzáles, University of Maryland, USA, and co-workers report: A hyperthermophilic, anaerobic archaeon was isolated from hydrothermal fluid samples obtained at the Okinawa Trough vents in the NE Pacific Ocean, (27°33´ N, 126°56 E) at a depth of 1395 m. The strain is obligately heterotrophic, and utilizes complex proteinacous media (peptone, tryptone, or yeast extract), or a 21-amino-acid mixture supplemented with vitamins, as growth substrates. Sulphur greatly enhances growth. The cells are irregular cocci with a tuft of flagella, growing optimally at 98°C (maximum growth temperature 102°C), but capable of prolonged survival at 105°C. Optimum growth was at pH 7 (range 5-8) and NCl concentration 2.4% (range 1%-5%."
A total of 1463 nucleotides of the 16S rRNA sequence from the isolate were determined. Cells are slightly irregular cocci between 0.8 and 2 µm in diameter, showing a polar tuft of flagella. Obligate anaerobe. Growth occurs at temperatures between 80°C and 102°C, with an optimum at 90°C. Optimum pH for growth is 7.0, and growth occurs from pH 5-8, with no growth observed at pH 8.5. NaCl concentration allowing growth ranges from 1% to 5%: optimum 2.44%. The shortest doubling time is 32 min. Gonzales, J. M. (1998:123-129).