DOCSLIB.ORG

Sporomusa Malonica Sp. Nov., a Homoacetogenic Bacterium Growing by Decarboxylation of Malonate Or Succinate

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Sporomusa Malonica Sp. Nov., a Homoacetogenic Bacterium Growing by Decarboxylation of Malonate Or Succinate Sporomusa malonica sp. nov., a homoacetogenic bacterium growing by decarboxylation of malonate or succinate Irmtraut Dehning 1 Marion Stieb 2, and Bernhard Schink a 1 Lehrstuhl Mikrobiologie I, Eberhard-Karls-Universit/it, Morgenstelle 28, D-7400 T/ibingen, Federal Republic of Germany z Dornier System GmbH, Space Development Division, D-7900 Friedrichshafen 1, Federal Republic of Germany Abstract. A new strictly anaerobic bacterium was isolated acetogens were described which were assigned to the new from an enrichment culture with glutarate as sole substrate genus Sporomusa (M611er et al. 1984). and freshwater sediment as inoculum, however, glutarate We report here on the isolation and characterization of was not metabolized by the pure culture. The isolate was a a new Gram-negative spore-forming homoacetogen which mesophilic, spore-forming, Gram-negative, motile curved oxidizes a broad variety of organic substrates and can also rod. It fermented various organic acids, alcohols, fructose, grow by decarboxylation of malonate or succinate as sole acetoin, and H2/CO2 to acetate, usually as the only product. energy and carbon sources. Other acids were fermented to acetate and propionate or acetate and butyrate. Succinate and malonate were de- carboxylated to propionate or acetate, respectively, and served as sole sources of carbon and energy for growth. No Materials and methods inorganic electron acceptors except CO2 were reduced. Yeast extract (0.05 % w/v) was required for growth. Small amounts Sources of microorganisms of cytochrome b were detected in membrane fractions. The guanine-plus-cytosine content of the DNA was Strain WoG12 was isolated from enrichment cultures inocu- 44.1 + 2 tool%. The isolate is described as a new species of lated with anoxic mud of a polluted freshwater creek near the genus Sporomusa, S. malonica. Konstanz, FRG. Sporomusa acidovorans DSM 3132 was obtained from the German collection of Microorganisms Key words: Sporomusa malonica sp. nov. - Gram-negative (DSM), Braunschweig, FRG. sporeformer - Homoacetogenesis - Malonic acid de- carboxylation - Bioenergetics Media and growth conditions All procedures for isolation and cultivation were the same as described in earlier papers (Pfennig and Triiper 1981; Widdel and Pfennig 1981). The freshwater mineral medium (Schink and Pfennig 1982) which was carbonate-buffered (30 mM) and sulfide-reduced (1 mM) contained 7-vitamin Several species of acetogenic bacteria have been described solution (Widdel and Pfennig 1981), selenite-tungstate solu- which gain their growth energy by the reduction of carbon tion, and the trace element solution SL10 (Widdel et al. dioxide to acetic acid. Clostridium aceticum was the first 1983). The pH was 7.2-7.4 and the growth temperature homoacetogenic bacterium isolated from mud by Wieringa 28- 30~ Growth was determined by measuring turbidity (1940). Other spore-forming Gram-positive acetogens were in a Spectronic 70 spectrophotometer (Bausch and Lomb, discovered: C. thermoaceticum (Fontaine et al. 1942), C. Rochester, NY, USA) in 20 ml screw-cap tubes. Substrates formicoaceticum (Andreesen et al. 1970), C. thermoautotro- were added from sterile, neutralized stock solutions. phicum (Wiegel et al. 1981), and C. magnum (Schink 1984). For further characterization, also a commercial media Also non spore-forming Gram-positive acetogenic bac- system (API 20A, BioM6rieux, Nfirtingen, FRG) was ap- teria were isolated: Acetobacterium woodii (Balch et al. plied. 1977), A. wieringae (Braun and Gottschalk 1982), A. earbinolicum (Eichler and Schink 1984), and the thermo- philic Acetogenium kivui (Leigh et al. 1981). Other strains Cytological characterization such as Eubacterium limosum (Sharak Genthner et al. 1981) or Butyribacterium methylotrophicum (Zeikus et al. 1980) Gram-staining was carried out according to Magee etal. produce acetate and butyrate during growth with H2/CO 2 (1975) with Acetobacterium woodii and Klebsiella sp. as refer- or methanol. Recently, Gram-negative spore-forming ence organisms. Cytochromes were assayed in French press cell extracts Offprint requests to: I. Dehning as well as in membrane preparations (150000 x g, 1 h) by 422 redox difference spectroscopy (dithionite-reduced minus air- oxidized) in an Uvikon 860 photometer (Kontron, Ziirich, Switzerland). The DNA base composition was determined by thermal denaturation according to De Ley (1970) after extraction as described by Marmur (1961). Escherichia coli strain K12, DSM 498, was used as reference strain. Chemical analyses Sulfide formation from sulfate or sulfur was analyzed by the methylene blue method (Cline 1969), nitrite formation from nitrate with sulfanilic acid and c~-naphthylamine (Pro- ch~zkov~t 1959). Fatty acids were assayed with a Carlo Erba Vega 6000 gas chromatograph (Milano, Italy) with flame ionization Fig. l. Phase contrast photomicrograph of the isolate WoG12 show- detector and a glass column (2 m x 2 mm) packed with 60/80 ing vegetative cells, free spores and subterminal spore-formation. Carbopak C/0.3% Carbowax 20 M/0.1% H3PO4 (Supelco, Bar equals 10 ~tm Inc., USA). Injector and detector temperatures were 180 ~C, column temperature 120 ~C, carrier gas nitrogen, 45 ml/min, injection volume 2 ~tl. Samples and standards were acidified prior to injection with formic acid to 0.5 M final concen- tration. Chromatograms were recorded with a Merck- Hitachi D-2000 integrator (Tokyo, Japan). Malonate was quantified as dimethyl ester by capillary gas chromatography as described earlier (Dehning and Schink 1989). All chemicals (analytical grade) were obtained from Fluka, Neu-Ulm, or Merck, Darmstadt, FRG. Results Isolation Enrichment cultures in freshwater medium with 10 mM glutarate as sole energy and carbon source were inoculated Fig. 2. Electron micrograph of an ultrathin section of strain WoG12 with freshwater sediment samples. Gas production started showing a multilayered cell wall. Bar = 0.2 p.m after 3 - 4 weeks, and the glutarate-degrading bacterial com- munity could be transferred at 1:10 ratio into subcultures which grew up again within 1-2 weeks. After the fifth transfer, the culture was diluted in agar shake series with mostly single and sometimes in pairs (Fig. 1). Growing cells various substrates. exhibited tumbling movement. Flagella staining revealed In the dilution series with glutarate as sole substrate, 2- 5 flagella per cell which were inserted on the concave cell growing colonies were observed only in the first two tubes side. Oval spores (1.2 x 1.5 btm) were sporadically formed indicating that the glutarate-degrading bacteria depended subterminally and were released into the medium (Fig. 1). on a cooperation with other bacteria. The glutarate- Spores survived pasteurization at 80~ for 15 min. fermenting bacteria could not be isolated, no matter whether The Gram staining reaction was negative. Electron yeast extract or hydrogen-scavenging methanogens or micrographs of ultrathin sections showed a typical Gram- sulfate reducers were added to the medium. negative, multilayered cell wall, consisting of a convoluted In agar medium with 10 mM crotonate, brown, lens- outer membrane, a thin peptidoglycan layer, and an inner shaped colonies developed within 2 weeks up to the sixth cytoplasmic membrane (Fig. 2). dilution tube. Colonies were picked with sterile Pasteur pi- Redox difference spectra of cell-free extracts and mem- pettes, resuspended in small amounts of anoxic medium, brane preparations showed weak absorption bands at about and again diluted in shake series with the same substrate. 559, 529, and 428 nm indicating the presence of a cyto- The resulting isolates were checked for purity by microscopic chrome b at very low concentration (i -2 mg/g protein in control and by inoculation into complex AC-medium the cell-free extract). The spectra did not vary qualitatively (Difco, Detroit, MI, USA) with and without added croto- or quantitatively, no matter whether malonate or fumarate nate. The isolated strain WoG12 required yeast extract (at was used as substrate. No cytoehrome was detected in the least 0.01%) for growth with crotonate in pure culture, and cytoplasmic fraction. did not utilize glutarate. The guanine-plus-cytosine content of the DNA was de- termined to be 44.1 4- 2 tool%. Analysis by high-performance liquid chromatography of Morphology and cytological characterization the corrinoid preparation extracted from this acetogenic Cells of strain WoG12 were slightly curved, spore-forming bacterium revealed with a high probability a p-cresolyl- rods with rounded ends, 0.7 x 2.6-4.8 btm in size, occurring cobamide. 423 I 021 - -40 0.3 lff 0.2 E )-- o o i01 0.1 tad O- I-- O CO CO 0 t/) 0.1 0.3 0.5 YEAST EXTRACT (%1 Fig. 3. Dependence of growth of strain WoG12 on the amount of yeast extract (w/v) added to mineral medium containing malonate 0t 12 28 0 at various concentrations. Symbols: * no malonate, -k no malonate, TINE (h) 10mM acetate, t0mM malonate, O 20mM malonate, 30 mM malonate. OD58o: optical density at580 nm Fig. 4. Fermentation time course of strain WoG12 in mineral me- dium containing 40 mM malonate and 0.05% (w/v) yeast extract. Experiments were performed at 30~ in 130ml serum bottles. Samples were removed with a syringe and the headspace was flushed Physiology and fermentation stoichiometry with N2/CO2. Symbols: (3 cell density, ~ malonate, acetate Growth of strain WoG12 was possiNe only under strictly formed anaerobic conditions. The isolate grew in freshwater as well as in brackish water medium Containing 10 g NaC1 and 1.5 g MgCle x 6 HzO per liter, but not in saltwatermedium. Phosphate up to 50 mM concentration did not inhibit acetate and propionate. The fermentation of citrate, growth. pyruvate, lactate, acetoin, formate, fructose, glutamate, Growth occurred only in the presence of at least 0.01% methanol, ethanol, H2/CO2, and the methoxyl groups of (w/v) yeast extract. Higher concentrations stimulated trimethoxycinnamic acid led to acetate as sole fermentation growth (Fig. 3); a concentration of 0.2% was optimal. How- product. ever, yeast extract did not serve as energy source.
Load more

Recommended publications
  • Robust Taxonomic Classification of Uncharted Microbial Sequences and Bins with CAT and BAT
    bioRxiv preprint doi: https://doi.org/10.1101/530188; this version posted January 24, 2019. 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 4.0 International license. Robust taxonomic classification of uncharted microbial sequences and bins with CAT and BAT F.A. Bastiaan von Meijenfeldt1,†, Ksenia Arkhipova1,†, Diego D. Cambuy1, Felipe H. Coutinho2,3, Bas E. Dutilh1,2,* 1 Theoretical Biology and Bioinformatics, Science for Life, Utrecht University, The Netherlands. 2 Centre for Molecular and Biomolecular Informatics, Radboud University Medical Centre, Nijmegen, The Netherlands. 3 Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil. * To whom correspondence should be addressed. Tel: +31 30 253 4212; Email: [email protected]. † These authors contributed equally to this work. Present Address: [Felipe H. Couthinho], Evolutionary Genomics Group, Departamento de Produccíon y Microbiología, Universidad Miguel Hernández, Campus San Juan, San Juan, Alicante 03550, Spain. ABSTRACT Current-day metagenomics increasingly requires taxonomic classification of long DNA sequences and metagenome-assembled genomes (MAGs) of unknown microorganisms. We show that the standard best-hit approach often leads to classifications that are too specific. We present tools to classify high- quality metagenomic contigs (Contig Annotation Tool, CAT) and MAGs (Bin Annotation Tool, BAT) and thoroughly benchmark them with simulated metagenomic sequences that are classified against a reference database where related sequences are increasingly removed, thereby simulating increasingly unknown queries. We find that the query sequences are correctly classified at low taxonomic ranks if closely related organisms are present in the reference database, while classifications are made higher in the taxonomy when closely related organisms are absent, thus avoiding spurious classification specificity.
    [Show full text]
  • Chlorate Reduction by an Acetogenic Bacterium, Sporomusa Sp., Isolated from an Underground Gas Storage
    Appl Microbiol Biotechnol (2010) 88:595–603 DOI 10.1007/s00253-010-2788-8 ENVIRONMENTAL BIOTECHNOLOGY (Per)chlorate reduction by an acetogenic bacterium, Sporomusa sp., isolated from an underground gas storage Melike Balk & Farrakh Mehboob & Antonie H. van Gelder & W. Irene C. Rijpstra & Jaap S. Sinninghe Damsté & Alfons J. M. Stams Received: 12 March 2010 /Revised: 16 July 2010 /Accepted: 16 July 2010 /Published online: 3 August 2010 # The Author(s) 2010. This article is published with open access at Springerlink.com Abstract A mesophilic bacterium, strain An4, was isolated Keywords Sporomusa sp. Perchlorate . from an underground gas storage reservoir with methanol Underground gas storage as substrate and perchlorate as electron acceptor. Cells were Gram-negative, spore-forming, straight to curved rods, 0.5– 0.8 μm in diameter, and 2–8 μm in length, growing as Introduction single cells or in pairs. The cells grew optimally at 37°C, and the pH optimum was around 7. Strain An4 converted Perchlorate and chlorate are used in a wide range of various alcohols, organic acids, fructose, acetoin, and applications. Chlorate is used as an herbicide or defoliant. H2/CO2 to acetate, usually as the only product. Succinate Perchlorate salts have been manufactured in large quantities was decarboxylated to propionate. The isolate was able to and used as ingredients in solid rocket fuels, highway safety respire with (per)chlorate, nitrate, and CO2. The G+C flares, air bag inflators, fireworks, and matches (Renner content of the DNA was 42.6 mol%. Based on the 16S 1998; Logan 2001; Motzer 2001). Perchlorate is chemically rRNA gene sequence analysis, strain An4 was most closely very stable and has low reactivity even in highly reducing related to Sporomusa ovata (98% similarity).
    [Show full text]
  • EXPERIMENTAL STUDIES on FERMENTATIVE FIRMICUTES from ANOXIC ENVIRONMENTS: ISOLATION, EVOLUTION, and THEIR GEOCHEMICAL IMPACTS By
    EXPERIMENTAL STUDIES ON FERMENTATIVE FIRMICUTES FROM ANOXIC ENVIRONMENTS: ISOLATION, EVOLUTION, AND THEIR GEOCHEMICAL IMPACTS By JESSICA KEE EUN CHOI A dissertation submitted to the School of Graduate Studies Rutgers, The State University of New Jersey In partial fulfillment of the requirements For the degree of Doctor of Philosophy Graduate Program in Microbial Biology Written under the direction of Nathan Yee And approved by _______________________________________________________ _______________________________________________________ _______________________________________________________ _______________________________________________________ New Brunswick, New Jersey October 2017 ABSTRACT OF THE DISSERTATION Experimental studies on fermentative Firmicutes from anoxic environments: isolation, evolution and their geochemical impacts by JESSICA KEE EUN CHOI Dissertation director: Nathan Yee Fermentative microorganisms from the bacterial phylum Firmicutes are quite ubiquitous in subsurface environments and play an important biogeochemical role. For instance, fermenters have the ability to take complex molecules and break them into simpler compounds that serve as growth substrates for other organisms. The research presented here focuses on two groups of fermentative Firmicutes, one from the genus Clostridium and the other from the class Negativicutes. Clostridium species are well-known fermenters. Laboratory studies done so far have also displayed the capability to reduce Fe(III), yet the mechanism of this activity has not been investigated
    [Show full text]
  • Phylogenomic Analysis Supports the Ancestral Presence of LPS-Outer Membranes in the Firmicutes
    Phylogenomic analysis supports the ancestral presence of LPS-outer membranes in the Firmicutes. Luisa Cs Antunes, Daniel Poppleton, Andreas Klingl, Alexis Criscuolo, Bruno Dupuy, Céline Brochier-Armanet, Christophe Beloin, Simonetta Gribaldo To cite this version: Luisa Cs Antunes, Daniel Poppleton, Andreas Klingl, Alexis Criscuolo, Bruno Dupuy, et al.. Phy- logenomic analysis supports the ancestral presence of LPS-outer membranes in the Firmicutes.. eLife, eLife Sciences Publication, 2016, 5, pp.e14589. 10.7554/eLife.14589.020. pasteur-01362343 HAL Id: pasteur-01362343 https://hal-pasteur.archives-ouvertes.fr/pasteur-01362343 Submitted on 8 Sep 2016 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. Distributed under a Creative Commons Attribution| 4.0 International License RESEARCH ARTICLE Phylogenomic analysis supports the ancestral presence of LPS-outer membranes in the Firmicutes Luisa CS Antunes1†, Daniel Poppleton1†, Andreas Klingl2, Alexis Criscuolo3, Bruno Dupuy4, Ce´ line Brochier-Armanet5, Christophe Beloin6, Simonetta Gribaldo1* 1Unite´ de
    [Show full text]
  • Genome Diversity of Spore-Forming Firmicutes MICHAEL Y
    Genome Diversity of Spore-Forming Firmicutes MICHAEL Y. GALPERIN National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894 ABSTRACT Formation of heat-resistant endospores is a specific Vibrio subtilis (and also Vibrio bacillus), Ferdinand Cohn property of the members of the phylum Firmicutes (low-G+C assigned it to the genus Bacillus and family Bacillaceae, Gram-positive bacteria). It is found in representatives of four specifically noting the existence of heat-sensitive vegeta- different classes of Firmicutes, Bacilli, Clostridia, Erysipelotrichia, tive cells and heat-resistant endospores (see reference 1). and Negativicutes, which all encode similar sets of core sporulation fi proteins. Each of these classes also includes non-spore-forming Soon after that, Robert Koch identi ed Bacillus anthracis organisms that sometimes belong to the same genus or even as the causative agent of anthrax in cattle and the species as their spore-forming relatives. This chapter reviews the endospores as a means of the propagation of this orga- diversity of the members of phylum Firmicutes, its current taxon- nism among its hosts. In subsequent studies, the ability to omy, and the status of genome-sequencing projects for various form endospores, the specific purple staining by crystal subgroups within the phylum. It also discusses the evolution of the violet-iodine (Gram-positive staining, reflecting the pres- Firmicutes from their apparently spore-forming common ancestor ence of a thick peptidoglycan layer and the absence of and the independent loss of sporulation genes in several different lineages (staphylococci, streptococci, listeria, lactobacilli, an outer membrane), and the relatively low (typically ruminococci) in the course of their adaptation to the saprophytic less than 50%) molar fraction of guanine and cytosine lifestyle in a nutrient-rich environment.
    [Show full text]
  • Sporomusa Intestinalis Sp. Nov., a Homoacetogenic Bacterium Isolated from the Gut of a Higher Termite, Termes Comis (Termitinae)
    J. Gen. Appl. Microbiol., 59, 321‒324 (2013) Short Communication Sporomusa intestinalis sp. nov., a homoacetogenic bacterium isolated from the gut of a higher termite, Termes comis (Termitinae) Satoshi Hattori,1,* Yuichi Hongoh,2,3 Takashi Itoh,3 Pinsurang Deevong,4 Savitr Trakulnaleamsai,4 Napavarn Noparatnaraporn,4 Toshiaki Kudo,5 and Moriya Ohkuma3 1 Department of Food, Life, and Environmental Sciences, Faculty of Agriculture, Yamagata University, Tsuruoka, Yamagata 997‒8555, Japan 2 Department of Biological Sciences, Tokyo Institute of Technology, Meguro-ku, Tokyo 152‒8550, Japan 3 Japan Collection of Microorganisms, RIKEN, BioResource Center, Koyadai, Tsukuba, Ibaraki 305‒0074, Japan 4 Department of Microbiology, Kasetsart University, Bangkok 10900, Thailand 5 Graduate School of Fisheries Science and Environmental Studies, Nagasaki University, Nagasaki 852‒8521, Japan (Received April 5, 2013; Accepted April 30, 2013) Key Words—Firmicutes; higher termite; homoacetogens; 16S rRNA gene; Sporomusa intestinalis sp. nov. The genus Sporomusa belongs phylogenetically to and characterization of a novel Sporomusa species, the family Vellionellaceae of the phylum Firmicutes. designated strain Tc2AT (JCM13218T=DSM17189T) The members of this genus are known to be anaerobic from the gut content of wood/soil interface-feeding or aerotolerant, homoacetogenic bacteria which grow higher termite, and propose a new species to accom- autotrophically on H2/CO2 or heterotrophically on vari- modate it. ous substrates such as sugars, alcohols, amino acids, Strain Tc2AT was obtained from the gut of the inter- and organic acids. To date, the genus Sporomusa com- face-feeding higher termite Termes comis (Termitinae), prises nine species: Sporomusa ovata, Sporomusa which was collected in Pathum Thani, Thailand.
    [Show full text]
  • The Biology and Community Structure of CO2-Reducing
    The Biology and Community Structure of CO2-Reducing Acetogens in the Termite Hindgut Thesis by Elizabeth Ann Ottesen In Partial Fulfillment of the Requirements for the Degree of Doctor of Philosophy California Institute of Technology Pasadena, California 2009 (Defended September 25, 2008) i i © 2009 Elizabeth Ottesen All Rights Reserved ii i Acknowledgements Much of the scientist I have become, I owe to the fantastic biology program at Grinnell College, and my mentor Leslie Gregg-Jolly. It was in her molecular biology class that I was introduced to microbiology, and made my first attempt at designing degenerate PCR primers. The year I spent working in her laboratory taught me a lot about science, and about persistence in the face of experimental challenges. At Caltech, I have been surrounded by wonderful mentors and colleagues. The greatest debt of gratitude, of course, goes to my advisor Jared Leadbetter. His guidance has shaped much of how I think about microbes and how they affect the world around us. And through all the ups and downs of these past six years, Jared’s enthusiasm for microbiology—up to and including the occasional microscope session spent exploring a particularly interesting puddle—has always reminded me why I became a scientist in the first place. The Leadbetter Lab has been a fantastic group of people. In the early days, Amy Wu taught me how much about anaerobic culture work and working with termites. These last few years, Eric Matson has been a wonderful mentor, endlessly patient about reading drafts and discussing experiments. Xinning Zhang also read and helped edit much of this work.
    [Show full text]
  • New Insights Into the Ecology and Physiology of Methanomassiliicoccales from Terrestrial and Aquatic Environments
    Supplementary Material New insights into the ecology and physiology of Methanomassiliicoccales from terrestrial and aquatic environments. Marc Cozannet1, Guillaume Borrel2, Erwan Roussel1, Yann Moalic1, Maxime Allioux1, Amandine Sanvoisin1, Laurent Toffin1 & Karine Alain1,* 1 Univ Brest, CNRS, IFREMER, IRP 1211 MicrobSea, Laboratoire de Microbiologie des Environnements Extrêmes LM2E, UMR 6197, IUEM, Rue Dumont d’Urville, F-29280 Plouzané, France; [email protected] (M.C.); [email protected] (E.R.); [email protected] (Y.M.); [email protected] (M.A.); [email protected] (L.T.); [email protected] (K.A.) 2 Department of Microbiology, Unit Evolutionary Biology of the Microbial Cell, Institut Pasteur, Paris, France; [email protected] (G.B.) * Correspondence: [email protected]; Tel.: +33-0298-4988-53 Received: date; Accepted: date; Published: date Supplementary Text Text S1. Pre-metabarcoding screening Section 1.1. Total DNA extraction In order to search for natural samples containing Methanomassiliicoccales, an initial large-scale molecular screening was carried out on a wide range of anoxic samples (86 in total). DNA extractions were carried out in triplicate with a protocol adapted to each type of matrix. Two types of DNA extraction procedures have been implemented depending on the nature of the matrices: (i) Nucleic acids were extracted from sediments, mud and peatland soils by combining a mechanical lysis step to a commercial DNA extraction kit for soil type matrices. The first extraction step consisted of mechanical cell lysis of 0.5 g of sample by bead-beating (5500 rpm, 30 s), using the Precellys 24® tissue homogenizer (Bertin instruments, France).
    [Show full text]
  • Veillonella Parvula Type Strain (Te3)
    View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by eScholarship - University of California Lawrence Berkeley National Laboratory Recent Work Title Complete genome sequence of Veillonella parvula type strain (Te3). Permalink https://escholarship.org/uc/item/6nm4q0jz Journal Standards in genomic sciences, 2(1) ISSN 1944-3277 Authors Gronow, Sabine Welnitz, Sabine Lapidus, Alla et al. Publication Date 2010-01-28 DOI 10.4056/sigs.521107 Peer reviewed eScholarship.org Powered by the California Digital Library University of California Standards in Genomic Sciences (2009) 1:57-65 DOI:10.4056/sigs.521107 Complete genome sequence of Veillonella parvula type strain (Te3T) Sabine Gronow1, Sabine Welnitz1, Alla Lapidus2, Matt Nolan2, Natalia Ivanova2, Tijana Glavina Del Rio2, Alex Copeland2, Feng Chen2, Hope Tice2, Sam Pitluck2, Jan-Fang Cheng2, Elizabeth Saunders2,3, Thomas Brettin2,3, Cliff Han2,3, John C. Detter2,3, David Bruce2,3, Lynne Goodwin2,3, Miriam Land2,4, Loren Hauser2,4, Yun-Juan Chang2,4, Cynthia D. Jeffries2,4, Amrita Pati2, Konstantinos Mavromatis2, Natalia Mikhailova2, Amy Chen5, Krishna Palaniappan5, Patrick Chain2,3, Manfred Rohde6, Markus Göker1, Jim Bristow2, Jonathan A. Eisen2,7, Victor Markowitz5, Philip Hugenholtz2, Nikos C. Kyrpides2*, Hans-Peter Klenk1, and Susan Lucas2 1 DSMZ – German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany 2 DOE Joint Genome Institute, Walnut Creek, California, USA 3 Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA 4 Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA 5 Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, Berkeley, California, USA 6 HZI – Helmholtz Centre for Infection Research, Braunschweig, Germany 7 University of California Davis Genome Center, Davis, California, USA *Corresponding author: Nikos C.
    [Show full text]
  • S41598-021-92658-2.Pdf
    www.nature.com/scientificreports OPEN Profling temporal dynamics of acetogenic communities in anaerobic digesters using next‑generation sequencing and T‑RFLP Abhijeet Singh*, Bettina Müller & Anna Schnürer* Acetogens play a key role in anaerobic degradation of organic material and in maintaining biogas process efciency. Profling this community and its temporal changes can help evaluate process stability and function, especially under disturbance/stress conditions, and avoid complete process failure. The formyltetrahydrofolate synthetase (FTHFS) gene can be used as a marker for acetogenic community profling in diverse environments. In this study, we developed a new high‑throughput FTHFS gene sequencing method for acetogenic community profling and compared it with conventional terminal restriction fragment length polymorphism of the FTHFS gene, 16S rRNA gene‑ based profling of the whole bacterial community, and indirect analysis via 16S rRNA profling of the FTHFS gene‑harbouring community. Analyses and method comparisons were made using samples from two laboratory‑scale biogas processes, one operated under stable control and one exposed to controlled overloading disturbance. Comparative analysis revealed satisfactory detection of the bacterial community and its changes for all methods, but with some diferences in resolution and taxonomic identifcation. FTHFS gene sequencing was found to be the most suitable and reliable method to study acetogenic communities. These results pave the way for community profling in various biogas processes and in other environments where the dynamics of acetogenic bacteria have not been well studied. Anaerobic digestion (AD) is a microbiological process through which almost any biodegradable material can be transformed into renewable biofertiliser and biogas, which is mainly a mixture of methane (60–70%) and carbon dioxide (30–40%)1–4.
    [Show full text]
  • Old Acetogens, New Light Steven L
    Eastern Illinois University The Keep Faculty Research & Creative Activity Biological Sciences January 2008 Old Acetogens, New Light Steven L. Daniel Eastern Illinois University, [email protected] Harold L. Drake University of Bayreuth Anita S. Gößner University of Bayreuth Follow this and additional works at: http://thekeep.eiu.edu/bio_fac Part of the Bacteriology Commons, Environmental Microbiology and Microbial Ecology Commons, and the Microbial Physiology Commons Recommended Citation Daniel, Steven L.; Drake, Harold L.; and Gößner, Anita S., "Old Acetogens, New Light" (2008). Faculty Research & Creative Activity. 114. http://thekeep.eiu.edu/bio_fac/114 This Article is brought to you for free and open access by the Biological Sciences at The Keep. It has been accepted for inclusion in Faculty Research & Creative Activity by an authorized administrator of The Keep. For more information, please contact [email protected]. Old Acetogens, New Light Harold L. Drake, Anita S. Gößner, & Steven L. Daniel Keywords: acetogenesis; acetogenic bacteria; acetyl-CoA pathway; autotrophy; bioenergetics; Clostridium aceticum; electron transport; intercycle coupling; Moorella thermoacetica; nitrate dissimilation Abstract: Acetogens utilize the acetyl-CoA Wood-Ljungdahl pathway as a terminal electron-accepting, energy-conserving, CO2-fixing process. The decades of research to resolve the enzymology of this pathway (1) preceded studies demonstrating that acetogens not only harbor a novel CO2-fixing pathway, but are also ecologically important, and (2) overshadowed the novel microbiological discoveries of acetogens and acetogenesis. The first acetogen to be isolated, Clostridium aceticum, was reported by Klaas Tammo Wieringa in 1936, but was subsequently lost. The second acetogen to be isolated, Clostridium thermoaceticum, was isolated by Francis Ephraim Fontaine and co-workers in 1942.
    [Show full text]
  • A Variety of Hydrogenotrophic Enrichment Cultures Catalyse
    www.nature.com/scientificreports OPEN A variety of hydrogenotrophic enrichment cultures catalyse cathodic reactions Received: 20 August 2018 Soroush Saheb-Alam 1, Frank Persson1, Britt-Marie Wilén1, Malte Hermansson2 & Accepted: 18 December 2018 Oskar Modin 1 Published: xx xx xxxx Biocathodes where living microorganisms catalyse reduction of CO2 can potentially be used to produce valuable chemicals. Microorganisms harbouring hydrogenases may play a key role for biocathode performance since H2 generated on the electrode surface can act as an electron donor for CO2 reduction. In this study, the possibility of catalysing cathodic reactions by hydrogenotrophic methanogens, acetogens, sulfate-reducers, denitrifers, and acetotrophic methanogens was investigated. The cultures were enriched from an activated sludge inoculum and performed the expected metabolic functions. All enrichments formed distinct microbial communities depending on their electron donor and electron acceptor. When the cultures were added to an electrochemical cell, linear sweep voltammograms showed a shift in current generation close to the hydrogen evolution potential (−1 V versus SHE) with higher cathodic current produced at a more positive potential. All enrichment cultures except the denitrifers were also used to inoculate biocathodes of microbial electrolysis cells operated with H+ and bicarbonate as electron acceptors and this resulted in current densities between 0.1–1 A/m2. The microbial community composition of biocathodes inoculated with diferent enrichment cultures were as diferent from each other as they were diferent from their suspended culture inoculum. It was noteworthy that Methanobacterium sp. appeared on all the biocathodes suggesting that it is a key microorganism catalysing biocathode reactions. Limitation of conventional energy sources and their impact on our climate, ecosystems and health has motivated a development of technologies that harvest renewable energy and allow environmentally friendly production of chemicals.
    [Show full text]