DOCSLIB.ORG

ABC. See ATP-Binding Cassette Acetate Production Cellulomonas

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
ABC. See ATP-Binding Cassette Acetate Production Cellulomonas 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,
Load more

Recommended publications
  • Genome-Resolved Meta-Analysis of the Microbiome in Oil Reservoirs Worldwide
    microorganisms Article Genome-Resolved Meta-Analysis of the Microbiome in Oil Reservoirs Worldwide Kelly J. Hidalgo 1,2,* , Isabel N. Sierra-Garcia 3 , German Zafra 4 and Valéria M. de Oliveira 1 1 Microbial Resources Division, Research Center for Chemistry, Biology and Agriculture (CPQBA), University of Campinas–UNICAMP, Av. Alexandre Cazellato 999, 13148-218 Paulínia, Brazil; [email protected] 2 Graduate Program in Genetics and Molecular Biology, Institute of Biology, University of Campinas (UNICAMP), Rua Monteiro Lobato 255, Cidade Universitária, 13083-862 Campinas, Brazil 3 Biology Department & CESAM, University of Aveiro, Aveiro, Portugal, Campus de Santiago, Avenida João Jacinto de Magalhães, 3810-193 Aveiro, Portugal; [email protected] 4 Grupo de Investigación en Bioquímica y Microbiología (GIBIM), Escuela de Microbiología, Universidad Industrial de Santander, Cra 27 calle 9, 680002 Bucaramanga, Colombia; [email protected] * Correspondence: [email protected]; Tel.: +55-19981721510 Abstract: Microorganisms inhabiting subsurface petroleum reservoirs are key players in biochemical transformations. The interactions of microbial communities in these environments are highly complex and still poorly understood. This work aimed to assess publicly available metagenomes from oil reservoirs and implement a robust pipeline of genome-resolved metagenomics to decipher metabolic and taxonomic profiles of petroleum reservoirs worldwide. Analysis of 301.2 Gb of metagenomic information derived from heavily flooded petroleum reservoirs in China and Alaska to non-flooded petroleum reservoirs in Brazil enabled us to reconstruct 148 metagenome-assembled genomes (MAGs) of high and medium quality. At the phylum level, 74% of MAGs belonged to bacteria and 26% to archaea. The profiles of these MAGs were related to the physicochemical parameters and recovery management applied.
    [Show full text]
  • Marsarchaeota Are an Aerobic Archaeal Lineage Abundant in Geothermal Iron Oxide Microbial Mats
    Marsarchaeota are an aerobic archaeal lineage abundant in geothermal iron oxide microbial mats Authors: Zackary J. Jay, Jacob P. Beam, Mansur Dlakic, Douglas B. Rusch, Mark A. Kozubal, and William P. Inskeep This is a postprint of an article that originally appeared in Nature Microbiology on May 14, 2018. The final version can be found at https://dx.doi.org/10.1038/s41564-018-0163-1. Jay, Zackary J. , Jacob P. Beam, Mensur Dlakic, Douglas B. Rusch, Mark A. Kozubal, and William P. Inskeep. "Marsarchaeota are an aerobic archaeal lineage abundant in geothermal iron oxide microbial mats." Nature Microbiology 3, no. 6 (May 2018): 732-740. DOI: 10.1038/ s41564-018-0163-1. Made available through Montana State University’s ScholarWorks scholarworks.montana.edu Marsarchaeota are an aerobic archaeal lineage abundant in geothermal iron oxide microbial mats Zackary J. Jay1,4,7, Jacob P. Beam1,5,7, Mensur Dlakić2, Douglas B. Rusch3, Mark A. Kozubal1,6 and William P. Inskeep 1* The discovery of archaeal lineages is critical to our understanding of the universal tree of life and evolutionary history of the Earth. Geochemically diverse thermal environments in Yellowstone National Park provide unprecedented opportunities for studying archaea in habitats that may represent analogues of early Earth. Here, we report the discovery and character- ization of a phylum-level archaeal lineage proposed and herein referred to as the ‘Marsarchaeota’, after the red planet. The Marsarchaeota contains at least two major subgroups prevalent in acidic, microaerobic geothermal Fe(III) oxide microbial mats across a temperature range from ~50–80 °C. Metagenomics, single-cell sequencing, enrichment culturing and in situ transcrip- tional analyses reveal their biogeochemical role as facultative aerobic chemoorganotrophs that may also mediate the reduction of Fe(III).
    [Show full text]
  • Archaeology of Eukaryotic DNA Replication
    Downloaded from http://cshperspectives.cshlp.org/ on September 25, 2021 - Published by Cold Spring Harbor Laboratory Press Archaeology of Eukaryotic DNA Replication Kira S. Makarova and Eugene V. Koonin National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894 Correspondence: [email protected] Recent advances in the characterization of the archaeal DNA replication system together with comparative genomic analysis have led to the identification of several previously un- characterized archaeal proteins involved in replication and currently reveal a nearly com- plete correspondence between the components of the archaeal and eukaryotic replication machineries. It can be inferred that the archaeal ancestor of eukaryotes and even the last common ancestor of all extant archaea possessed replication machineries that were compa- rable in complexity to the eukaryotic replication system. The eukaryotic replication system encompasses multiple paralogs of ancestral components such that heteromeric complexes in eukaryotes replace archaeal homomeric complexes, apparently along with subfunctionali- zation of the eukaryotic complex subunits. In the archaea, parallel, lineage-specific dupli- cations of many genes encoding replication machinery components are detectable as well; most of these archaeal paralogs remain to be functionally characterized. The archaeal rep- lication system shows remarkable plasticity whereby even some essential components such as DNA polymerase and single-stranded DNA-binding protein are displaced by unrelated proteins with analogous activities in some lineages. ouble-stranded DNA is the molecule that Okazaki fragments (Kornberg and Baker 2005; Dcarries genetic information in all cellular Barry and Bell 2006; Hamdan and Richardson life-forms; thus, replication of this genetic ma- 2009; Hamdan and van Oijen 2010).
    [Show full text]
  • The Role of Polyphosphate in Motility, Adhesion, and Biofilm Formation in Sulfolobales. Microorganisms 2021, 9
    microorganisms Article The Role of Polyphosphate in Motility, Adhesion, and Biofilm Formation in Sulfolobales Alejandra Recalde 1,2 , Marleen van Wolferen 2 , Shamphavi Sivabalasarma 2 , Sonja-Verena Albers 2, Claudio A. Navarro 1 and Carlos A. Jerez 1,* 1 Laboratory of Molecular Microbiology and Biotechnology, Department of Biology, Faculty of Sciences, University of Chile, Santiago 8320000, Chile; [email protected] (A.R.); [email protected] (C.A.N.) 2 Laboratory of Molecular Biology of Archaea, Institute of Biology II-Microbiology, University of Freiburg, 79085 Freiburg, Germany; [email protected] (M.v.W.); [email protected] (S.S.); [email protected] (S.-V.A.) * Correspondence: [email protected] Abstract: Polyphosphates (polyP) are polymers of orthophosphate residues linked by high-energy phosphoanhydride bonds that are important in all domains of life and function in many different processes, including biofilm development. To study the effect of polyP in archaeal biofilm formation, our previously described Sa. solfataricus polyP (−) strain and a new polyP (−) S. acidocaldarius strain generated in this report were used. These two strains lack the polymer due to the overexpression of their respective exopolyphosphatase gene (ppx). Both strains showed a reduction in biofilm formation, decreased motility on semi-solid plates and a diminished adherence to glass surfaces as seen by DAPI (40,6-diamidino-2-phenylindole) staining using fluorescence microscopy. Even though arlB (encoding the archaellum subunit) was highly upregulated in S. acidocardarius polyP (−), no archaellated cells were observed. These results suggest that polyP might be involved in the regulation of the expression of archaellum components and their assembly, possibly by affecting energy availability, phosphorylation or other phenomena.
    [Show full text]
  • Insights Into Archaeal Evolution and Symbiosis from the Genomes of a Nanoarchaeon and Its Inferred Crenarchaeal Host from Obsidian Pool, Yellowstone National Park
    University of Tennessee, Knoxville TRACE: Tennessee Research and Creative Exchange Microbiology Publications and Other Works Microbiology 4-22-2013 Insights into archaeal evolution and symbiosis from the genomes of a nanoarchaeon and its inferred crenarchaeal host from Obsidian Pool, Yellowstone National Park Mircea Podar University of Tennessee - Knoxville, [email protected] Kira S. Makarova National Institutes of Health David E. Graham University of Tennessee - Knoxville, [email protected] Yuri I. Wolf National Institutes of Health Eugene V. Koonin National Institutes of Health See next page for additional authors Follow this and additional works at: https://trace.tennessee.edu/utk_micrpubs Part of the Microbiology Commons Recommended Citation Biology Direct 2013, 8:9 doi:10.1186/1745-6150-8-9 This Article is brought to you for free and open access by the Microbiology at TRACE: Tennessee Research and Creative Exchange. It has been accepted for inclusion in Microbiology Publications and Other Works by an authorized administrator of TRACE: Tennessee Research and Creative Exchange. For more information, please contact [email protected]. Authors Mircea Podar, Kira S. Makarova, David E. Graham, Yuri I. Wolf, Eugene V. Koonin, and Anna-Louise Reysenbach This article is available at TRACE: Tennessee Research and Creative Exchange: https://trace.tennessee.edu/ utk_micrpubs/44 Podar et al. Biology Direct 2013, 8:9 http://www.biology-direct.com/content/8/1/9 RESEARCH Open Access Insights into archaeal evolution and symbiosis from the genomes of a nanoarchaeon and its inferred crenarchaeal host from Obsidian Pool, Yellowstone National Park Mircea Podar1,2*, Kira S Makarova3, David E Graham1,2, Yuri I Wolf3, Eugene V Koonin3 and Anna-Louise Reysenbach4 Abstract Background: A single cultured marine organism, Nanoarchaeum equitans, represents the Nanoarchaeota branch of symbiotic Archaea, with a highly reduced genome and unusual features such as multiple split genes.
    [Show full text]
  • A Survey of Carbon Fixation Pathways Through a Quantitative Lens
    Journal of Experimental Botany, Vol. 63, No. 6, pp. 2325–2342, 2012 doi:10.1093/jxb/err417 Advance Access publication 26 December, 2011 REVIEW PAPER A survey of carbon fixation pathways through a quantitative lens Arren Bar-Even, Elad Noor and Ron Milo* Department of Plant Sciences, The Weizmann Institute of Science, Rehovot 76100, Israel * To whom correspondence should be addressed. E-mail: [email protected] Received 15 August 2011; Revised 4 November 2011; Accepted 8 November 2011 Downloaded from Abstract While the reductive pentose phosphate cycle is responsible for the fixation of most of the carbon in the biosphere, it http://jxb.oxfordjournals.org/ has several natural substitutes. In fact, due to the characterization of three new carbon fixation pathways in the last decade, the diversity of known metabolic solutions for autotrophic growth has doubled. In this review, the different pathways are analysed and compared according to various criteria, trying to connect each of the different metabolic alternatives to suitable environments or metabolic goals. The different roles of carbon fixation are discussed; in addition to sustaining autotrophic growth it can also be used for energy conservation and as an electron sink for the recycling of reduced electron carriers. Our main focus in this review is on thermodynamic and kinetic aspects, including thermodynamically challenging reactions, the ATP requirement of each pathway, energetic constraints on carbon fixation, and factors that are expected to limit the rate of the pathways. Finally, possible metabolic structures at Weizmann Institute of Science on July 3, 2016 of yet unknown carbon fixation pathways are suggested and discussed.
    [Show full text]
  • The Archaeal Ced System Imports DNA
    The archaeal Ced system imports DNA Marleen van Wolferena,1, Alexander Wagnera,1, Chris van der Doesa, and Sonja-Verena Albersa,2 aMolecular Biology of Archaea, Institute of Biology II – Microbiology, University of Freiburg, 79104 Freiburg, Germany Edited by Norman R. Pace, University of Colorado at Boulder, Boulder, CO, and approved January 12, 2016 (received for review July 13, 2015) The intercellular transfer of DNA is a phenomenon that occurs species exchange chromosomal DNA between cells connected by in all domains of life and is a major driving force of evolution. bridges (11). This transfer is thought to occur in a bidirectional Upon UV-light treatment, cells of the crenarchaeal genus Sulfo- manner via cell fusion leading to the formation of diploid cells with lobus express Ups pili, which initiate cell aggregate formation. mixed chromosomes (12). Interestingly, this type of DNA transfer Within these aggregates, chromosomal DNA, which is used for was shown to occur between different Haloferax species and in- the repair of DNA double-strand breaks, is exchanged. Because volved DNA fragments of up to 500 kbp DNA (13). Nevertheless, so far no clear homologs of bacterial DNA transporters have the mechanism of DNA transfer is so far not understood. Other been identified among the genomes of Archaea, the mechanisms described archaeal conjugative systems include self-transmissible of archaeal DNA transport have remained a puzzling and under- plasmids, which have so far only been studied for Sulfolobus spe- saci_0568 saci_0748, investigated topic. Here we identify and cies. These plasmids are grouped into the so-called pKEF and Sulfolobus acidocaldarius two genes from that are highly in- pARN plasmids (14, 15) and only a few of their genes encode duced upon UV treatment, encoding a transmembrane protein homologs of bacterial conjugation proteins, including the so-far- and a membrane-bound VirB4/HerA homolog, respectively.
    [Show full text]
  • Actinomycetes from the Coffee Plantation Soils of Western Ghats: Diversity and Enzymatic Potentials
    Int.J.Curr.Microbiol.App.Sci (2018) 7(8): 3599-3611 International Journal of Current Microbiology and Applied Sciences ISSN: 2319-7706 Volume 7 Number 08 (2018) Journal homepage: http://www.ijcmas.com Original Research Article https://doi.org/10.20546/ijcmas.2018.708.364 Actinomycetes from the Coffee Plantation Soils of Western Ghats: Diversity and Enzymatic Potentials Banu Sameera1, Harishchandra Sripathy Prakash2 and Monnanda Somaiah Nalini1* 1Department of Studies in Botany, 2Department of Studies in Biotechnology, University of Mysore, Manasagangotri, Mysore–570 006, Karnataka, India *Corresponding author ABSTRACT 230 soil actinomycetes were isolated from the coffee plantation of Western Ghats, Karnataka, India along the altitudinal gradients and depths. 24 morphologically distinct species were obtained based on the aerial spore chains and by the sequencing of the 16S K e yw or ds rRNA gene. The strains were assigned to the order Micrococcales, and novel orders Plantation soils, Pseudonocardiales ord. nov., Streptomycetales ord. nov., and Streptosporangiales ord. nov. Coffea arabica, The frequently isolated genus was Streptomyces, along with rare actinomycetes Streptomycetes, Actinomadura, Spirillospora, Actinocorallia, Arthrobacter, Saccharopolyspora and Rare actinomycetes, Nonomuraea. This study is the first report on Nonomuraea antimicrobica as a soil Soil properties, actinomycete. Diversity studies on the distribution of soil actinomycetes indicated enzymes significant differences (P< 0.05) among Shannon diversity indices of sample group depths Article Info along the slope. An attempt was made to correlate the total actinomycete count with soil parameters, by PCA based multiple linear regression (MLR) which significantly correlated Accepted: (P<0.0001) with pH, moisture, available nitrogen and phosphorous. About 91.6% of the 20 July 2018 isolates screened were found to be potentials for enzymatic activity.
    [Show full text]
  • (Gid ) Genes Coding for Putative Trna:M5u-54 Methyltransferases in 355 Bacterial and Archaeal Complete Genomes
    Table S1. Taxonomic distribution of the trmA and trmFO (gid ) genes coding for putative tRNA:m5U-54 methyltransferases in 355 bacterial and archaeal complete genomes. Asterisks indicate the presence and the number of putative genes found. Genomes Taxonomic position TrmA Gid Archaea Crenarchaea Aeropyrum pernix_K1 Crenarchaeota; Thermoprotei; Desulfurococcales; Desulfurococcaceae Cenarchaeum symbiosum Crenarchaeota; Thermoprotei; Cenarchaeales; Cenarchaeaceae Pyrobaculum aerophilum_str_IM2 Crenarchaeota; Thermoprotei; Thermoproteales; Thermoproteaceae Sulfolobus acidocaldarius_DSM_639 Crenarchaeota; Thermoprotei; Sulfolobales; Sulfolobaceae Sulfolobus solfataricus Crenarchaeota; Thermoprotei; Sulfolobales; Sulfolobaceae Sulfolobus tokodaii Crenarchaeota; Thermoprotei; Sulfolobales; Sulfolobaceae Euryarchaea Archaeoglobus fulgidus Euryarchaeota; Archaeoglobi; Archaeoglobales; Archaeoglobaceae Haloarcula marismortui_ATCC_43049 Euryarchaeota; Halobacteria; Halobacteriales; Halobacteriaceae; Haloarcula Halobacterium sp Euryarchaeota; Halobacteria; Halobacteriales; Halobacteriaceae; Haloarcula Haloquadratum walsbyi Euryarchaeota; Halobacteria; Halobacteriales; Halobacteriaceae; Haloquadra Methanobacterium thermoautotrophicum Euryarchaeota; Methanobacteria; Methanobacteriales; Methanobacteriaceae Methanococcoides burtonii_DSM_6242 Euryarchaeota; Methanomicrobia; Methanosarcinales; Methanosarcinaceae Methanococcus jannaschii Euryarchaeota; Methanococci; Methanococcales; Methanococcaceae Methanococcus maripaludis_S2 Euryarchaeota; Methanococci;
    [Show full text]
  • Post-Genomic Characterization of Metabolic Pathways in Sulfolobus Solfataricus
    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
    [Show full text]
  • 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.
    [Show full text]
  • 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.
    [Show full text]