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Index A identification of, 740–46 habitat of, 656 isolation and cultivation of, 735 identification of, 659–60 ABC. See ATP-binding cassette phylogeny of, 729 morphology of, 768–69 Acetate production species characteristics of, 747 phylogenetic tree of, 663 Cellulomonas, 988 Acrocarpospora corrugata, 729, Actinokineospora diospyrosa, 654 Propionibacterium, 408–9 734–35 Actinokineospora globicatena, 654 Acetate utilization Acrocarpospora macrocephala, 729, Actinokineospora inagensis, 654 Corynebacterium, 804–5 734 Actinokineospora riparia, 654, 660 Methanocalculus, 223 Acrocarpospora pleiomorpha, 729, Actinokineospora terrae, 654 Methanocorpusculum, 220–22 734 Actinomadura, 682–714, 725 Methanoculleus, 217–18 Actinoalloteichus, 654 habitats of, 688 Methanofollis, 219–20 morphology of, 768–69 identification of, 694–708 Methanogenium, 215–16 Actinobacteria isolation and cultivation of, Methanoplanus, 218 Actinobacteridae, 797, 819 690–91 Methanosaeta, 253–54 Actinomycetales, 430, 983, 1020 morphological characteristics of, Methanosarcina, 248 families and genera of, 298 701–2, 756, 768–69, 778 Methanosarcinales, 244–45 phylogenetic tree of, 302 phylogenetic tree of, 689 Micrococcus, 966 Propionibacterinaea, 383 physiological characteristics of, Streptomyces, 612 Pseudonocardiniae, 654 703 Acetyl-CoA synthase, species and genera of, 302–4 taxonomic history of, 695–97, Thermococcales,75 taxonomy of, 297–316 755–57 Acetyl-CoA synthetase Actinobacteridae, Actinomycetales, Actinomadura carminata, 713 Archaeoglobus,89 797, 819 Actinomadura citrea, 688, 713 Desulfurococcales,65 Actinobaculum, 430–39, 470–71, Actinomadura cremea, 688 Acidianus, 25, 28–31, 33, 38 493–98 Actinomadura dassonvillei, 755, 757. Acidianus ambivalens, 24–25, 31, characteristics of, 493–97 See also Nocardiopsis 33–35, 40 epidemiology of, 497–98 dassonvillei Acidianus ambivalens Lei1T,25 habitat and ecology of, 497 Actinomadura echinospora, 688 Acidianus brierleyi, 24–25, 29–31, 33 taxonomy of, 493–97 Actinomadura flava. See Acidianus brierleyi DSM 1651T,25 Actinobaculum massiliae, 432, Lechevalieria flava Acidianus infernus, 24–25, 28–29, 31, 493–94, 497 Actinomadura formosensis, 691, 699 34 Actinobaculum schaalii, 432, 439, Actinomadura kijaniata, 691, 713 Acidianus infernus So-4aT,25 447, 493–94, 497 Actinomadura latina, 688, 708–9 Acidilobus, 56–57, 61 Actinobaculum suis, 430, 432, 436, Actinomadura macra, 691, 713 Acidilobus aceticus, 52, 56 439, 447, 493–94, 497 Actinomadura madurae, 688, 690, Acidimicrobium, 305–6 Actinobaculum urinale, 432, 493–94, 698–700, 708–9, 755 Acidimicrobium ferrooxidans, 305–6 497 Actinomadura oligospora, 713 Acidophiles Actinocorallia, 682–714 Actinomadura pelletieri, 688, 690, Sulfolobales, 26–27, 29–30 enzymatic activities of, 704 698, 708–9, 755 Thermoplasma, 108 habitats of, 688 Actinomadura rubrobrunea, 684, Acidothermaceae, 669–78 identification of, 694–708 688, 691 phylogenetic tree of, 670–71 morphological characteristics of, Actinomadura rugatobispora, 729 taxonomy of, 672 701–2, 768–69 Actinomadura spadix, 688, 691 Acidothermus, 669–70 phylogenetic tree of, 689 Actinomadura umbrina, 688 isolation of, 674 species characteristics of, 705 Actinomadura verrucosospora, 688 physiology of, 674–75 taxonomic history of, 695–97 Actinomadura vinacea, 691 preservation and cultivation of, Actinocorallia aurantiaca, 705 Actinomadura viridilutea, 684, 688, 674 Actinocorallia glomerata, 705 691, 713 Acidothermus cellulolyticus, 669, 674 Actinocorallia herbida, 691, 705 Actinomadura viridis, 729, 731 Acrocarpospora, 726 Actinocorallia libanotica, 705 Actinomadura yumaensis, 713 chemotaxonomic and Actinocorallia longicatena, 705 Actinomyces, 430–93 morphological features of, Actinokineospora, 654–61, 666 chemotaxonomic properties, 727 characteristics of, 661 446–48, 468–69, 494 1116 Index cultivation of, 464 Actinomyces oricola, 431, 441, 445, identification of, 635–39 disease from, 482–83 456 isolation of, 630–35, 642–45 in animals, 490–93 Actinomyces radicidentis, 431–32, Actinopolymorpha, characteristics in humans, 483–90 435, 441, 445, 456 of, 1105, 1108 treatment for, 489–90 Actinomyces radingae, 431–32, 435, Actinopolyspora, morphological ecology of, 479–82 438, 440, 447, 456, 487 characteristics of, 756, habitats of, 455–57 Actinomyces slackii, 431–32, 435, 768–69, 778 identification of, 464–79 440, 457 Actinosynnema, 654–62, 666 isolation of, 457–63 Actinomyces suimastiditis, 431–32, characteristics of, 662 morphology of, 442–46, 465–67, 435, 457 habitat of, 656 469 Actinomyces turicensis, 431–32, 435, identification of, 660–61 cellular, 442–43 440, 447, 456, 487 morphology of, 768–69 colony, 442–46, 466–67 Actinomyces urogenitalis, 431–32, phylogenetic tree of, 663 physiological properties of, 435, 441, 445, 456 Actinosynnema mirum, 655, 661 448–55, 469, 474–75 Actinomyces vaccimaxillae, 432, 441, Actinosynnema pretiosum, 655 species of, 431–33 457, 492 Actinosynnema pretiosum subsp. taxonomy of, 439–55 Actinomyces viscosus, 431–32, auranticum, 655, 660 Actinomyces bovis, 430–32, 435–36, 435–36, 439–40, 443, 445, Actinosynnema pretiosum subsp. 439–40, 444–45, 447–48, 455, 447–49, 454–57, 476, 480–83, pretiosum, 660 457, 467, 491–92 486–87, 489, 491–92 Actinosynnemataceae Actinomyces bowdenii, 431–32, 435, Actinomycetaceae, 430–516 Actinokineospora, 654–61, 666 441, 457, 492 Actinobaculum, 430–39, 470–71, Actinosynnema, 654–62, 666 Actinomyces canis, 430–32, 438, 457 493–98 chemotaxonomic properties of, Actinomyces cardiffensis, 431–32, Actinomyces, 430–93 658–59 435, 441, 445, 456 Arcanobacterium, 430–39, 470–71, identification of, 658–65 Actinomyces catuli, 431, 445, 457, 498–505 isolation and cultivation of, 492 clusters of, 433–39 656–58 Actinomyces coleocanis, 431–32, 435, introduction to, 430 Lechevalieria, 654–59, 665–66 438, 441, 457, 492 Mobiluncus, 430–39, 506–16 Lentzea, 654–59, 663–66 Actinomyces denticolens, 431–32, phylogenetic tree of, 434 phylogenetic tree of, 655, 663 435, 440, 445, 457 phylogeny of, 430–39 Saccharothrix, 654–59, 661–64, 666 Actinomyces europaeus, 431–32, 435, Varibaculum, 430–39, 470, 505–6 Aerobes 438, 441, 447, 456 Actinomycetales Agreia, 1021 Actinomyces funkei, 431, 456 Actinomycineae, 430, 433 Arthrobacter, 945 Actinomyces georgiae, 431–32, 435, Corynebacterineae, 797, 819 Brevibacterium, 1013 440, 447, 455, 480 Microbacteriaceae, 1020 Curtobacterium, 1043 Actinomyces gerencseriae, 431–32, Micrococcineae, 307, 983, 1002 Desulfurococcales,52 435, 440–41, 443–45, 447, 454, Streptomycetaceae, 605 Friedmanniella, 391 456, 479–80, 483, 486–87 Streptosporangineae, 682 Glycomyces, 306 Actinomyces graevenitzii, 431–32, Actinomycetes. See Actinobacteria Gordonia, 846 435, 441, 445, 455 Actinomycin production, Halobacteriales, 143 Actinomyces hongkongensis, 431–32, Streptomyces, 566 Herbidospora, 729 435, 438, 449, 456 Actinomycineae, Actinomycetaceae, Microbacteriaceae, 1020 Actinomyces hordeovulneris, 431–32, 430, 433 Microbispora, 730 435, 438, 440–41, 445, 449, Actinoplanaceae, 725 Microtetraspora, 731 457, 491–92 Actinoplanes, 623–49, 725 Mycobacterium, 889 Actinomyces howellii, 431, 457 characteristics of, 639–42 Nocardia, 848 Actinomyces hyovaginalis, 431–32, chemotaxonomic properties of, Nonomuraea, 731 435, 441, 447, 491 636–39 Okibacterium, 1068 Actinomyces israelii, 431–32, 435–36, ecophysiology of, 623–30 Picrophilus, 109 439–45, 447–49, 454–56, identification of, 635–39 Planobispora, 732 459–61, 467, 478–80, 483, isolation of, 630–35, 642–45 Planomonospora, 733 486–87, 489, 491 morphology of, 636 Planotetraspora, 734 Actinomyces marimammalium, Actinoplanes azureus, 648 Skermania, 847 431–32, 435, 438, 441, 457, 492 Actinoplanes brasiliensis, 624–25 Sulfolobales, 26–27, 33 Actinomyces meyeri, 431–32, 435–36, Actinoplanes caeruleus, 639, 648 Tsukamurella, 850–51 440, 445, 449, 456, 465, 467, Actinoplanes cyaneus, 639 Williamsia, 847–48 479, 487 Actinoplanes ferrugineus, 639, 646 Aeromicrobium, characteristics of, Actinomyces naeslundii, 431–32, 435, Actinoplanes garbadinensis, 639 1105, 1108 439–40, 442–45, 448–49, Actinoplanes ianthinogenes, 639 Aeropyrum, 53, 56–58 454–57, 476, 479–83, 486–87, Actinoplanes italicus, 639 Aeropyrum pernix, 53, 57–58, 64–65 489, 492 Actinoplanes minutisporangius, 639 Agreia, 1020–26 Actinomyces nasicola, 431–32, 435, Actinoplanes missouriensis, 624 characteristics of, 1023–24, 1057, 438, 441, 456 Actinoplanes philipinensies, 607 1078 Actinomyces neuii, 431–32, 435, 438, Actinoplanes rectilineatus, 639 habitats of, 1025 447, 456, 488 Actinoplanes teichomyceticus, 639, phylogenetic tree of, 1022 Actinomyces odontolyticus, 431–32, 648 Agreia bicolorata, 1021, 1025–26 435, 440, 445, 455–56, 479–80, Actinoplanetes, 623–49 Agreia pratensis, 1021, 1025–26 486–87, 489 ecophysiology of, 623–30 Agrococcus, 1020, 1026–27 Index 1117 characteristics of, 1023–24, 1027, Desulfurococcales, 30, 52, 56, 64 Clavibacter, 1040 1057 Gardnerella, 365 Corynebacterium, 805–10 habitats of, 1026 Methanobacteriaceae, 236 Curtobacterium, 1046–48 phylogenetic tree of, 1022 Methanobacteriales, 231 Desulfurococcales, 65–66 Agrococcus baldri, 1026–27 Methanobacterium, 236 Frankineae, 677–78 Agrococcus citrea, 1026–27 Methanococcales, 259–61 Gordonia, 871–72 Agrococcus jenensis, 1026–27 methanogens, 165 Halobacteriales, 150–51 Agromyces, 1020, 1027–31, 1081 Methanomicrobiales, 208 Leifsonia, 1055 characteristics of, 1023–24, 1030, Methanosarcinales, 244 methanogens, 198–99 1057 Methanothermus, 241–42 Microbacterium, 1066 habitats of, 1028–29 Pyrobaculum,11 Micrococcus, 968 phylogenetic tree of,
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    Post-Genomic Characterization of Metabolic Pathways in Sulfolobus solfataricus Jasper Walther Thesis committee Thesis supervisors Prof. dr. J. van der Oost Personal chair at the laboratory of Microbiology Wageningen University Prof. dr. W. M. de Vos Professor of Microbiology Wageningen University Other members Prof. dr. W.J.H. van Berkel Wageningen University Prof. dr. V.A.F. Martins dos Santos Wageningen University Dr. T.J.G. Ettema Uppsala University, Sweden Dr. S.V. Albers Max Planck Institute for Terrestrial Microbiology, Marburg, Germany This research was conducted under the auspices of the Graduate School VLAG Post-Genomic Characterization of Metabolic Pathways in Sulfolobus solfataricus Jasper Walther Thesis Submitted in fulfilment of the requirements for the degree of doctor at Wageningen University by the authority of the Rector Magnificus Prof. dr. M.J. Kropff, in the presence of the Thesis Committee appointed by the Academic Board to be defended in public on Monday 23 January 2012 at 11 a.m. in the Aula. Jasper Walther Post-Genomic Characterization of Metabolic Pathways in Sulfolobus solfataricus, 164 pages. Thesis, Wageningen University, Wageningen, NL (2012) With references, with summaries in Dutch and English ISBN 978-94-6173-203-3 Table of contents Chapter 1 Introduction 1 Chapter 2 Hot Transcriptomics 17 Chapter 3 Reconstruction of central carbon metabolism in Sulfolobus solfataricus using a two-dimensional gel electrophoresis map, stable isotope labelling and DNA microarray analysis 45 Chapter 4 Identification of the Missing
  • Lipids of Sulfolobus Spp. | Encyclopedia

    Lipids of Sulfolobus Spp. | Encyclopedia

    Lipids of Sulfolobus spp. Subjects: Biophysics | Biotechnology Contributors: Kerstin Rastaedter , David J. Wurm Submitted by: Kerstin Rastaedter Definition Archaea, and thereby, Sulfolobus spp. exhibit a unique lipid composition of ether lipids, which are altered in regard to the ratio of diether to tetraether lipids, number of cyclopentane rings and type of head groups, as a coping mechanism against environmental changes. Sulfolobales mainly consist of C40-40 tetraether lipids (caldarchaeol) and partly of C20-20 diether lipids (archaeol). A variant of caldarchaeol called glycerol dialkylnonitol tetraether (GDNT) has only been found in Sulfolobus and other members of the Creanarchaeota phylum so far. Altering the numbers of incorporated cyclopentane rings or the the diether to tetraether ratio results in more tightly packed membranes or vice versa. 1. The Cell Membrane and Lipids of Sulfolobus spp. The thermoacidophilic genus Sulfolobus belongs to the phylum Crenarchaeota and is a promising player for biotechnology [1], since it harbors a couple of valuable products, such as extremozymes[ 2], trehalose [3], archaeocins [4] and lipids for producing archaeosomes [5]. Genetic tools for this genus have rapidly advanced in recent years[ 6], generating new possibilities in basic science and for biotechnological applications alike. The cultivation conditions are preferably at around 80 °C and pH 3 [7]. Sulfolobus species are able to grow aerobically and can be readily cultivated on a laboratory scale. These organisms became a model organism for Crenarchaeota and for adaption processes to extreme environments [8][9][10][11][12][13]. Sulfolobus species were found in solfataric fields all over the world[ 14]. A major drawback of cultivating this organism was the lack of a defined cultivation medium.
  • Inter-Domain Horizontal Gene Transfer of Nickel-Binding Superoxide Dismutase 2 Kevin M

    Inter-Domain Horizontal Gene Transfer of Nickel-Binding Superoxide Dismutase 2 Kevin M

    bioRxiv preprint doi: https://doi.org/10.1101/2021.01.12.426412; this version posted January 13, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. 1 Inter-domain Horizontal Gene Transfer of Nickel-binding Superoxide Dismutase 2 Kevin M. Sutherland1,*, Lewis M. Ward1, Chloé-Rose Colombero1, David T. Johnston1 3 4 1Department of Earth and Planetary Science, Harvard University, Cambridge, MA 02138 5 *Correspondence to KMS: [email protected] 6 7 Abstract 8 The ability of aerobic microorganisms to regulate internal and external concentrations of the 9 reactive oxygen species (ROS) superoxide directly influences the health and viability of cells. 10 Superoxide dismutases (SODs) are the primary regulatory enzymes that are used by 11 microorganisms to degrade superoxide. SOD is not one, but three separate, non-homologous 12 enzymes that perform the same function. Thus, the evolutionary history of genes encoding for 13 different SOD enzymes is one of convergent evolution, which reflects environmental selection 14 brought about by an oxygenated atmosphere, changes in metal availability, and opportunistic 15 horizontal gene transfer (HGT). In this study we examine the phylogenetic history of the protein 16 sequence encoding for the nickel-binding metalloform of the SOD enzyme (SodN). A comparison 17 of organismal and SodN protein phylogenetic trees reveals several instances of HGT, including 18 multiple inter-domain transfers of the sodN gene from the bacterial domain to the archaeal domain.