MANUAL of Environmental Microbiology THIRD EDITION

Total Page:16

File Type:pdf, Size:1020Kb

MANUAL of Environmental Microbiology THIRD EDITION MANUAL OF Environmental Microbiology THIRD EDITION EDITOR IN CHIEF Christon J. Hurst Department of Biology, Xavier University, Cincinnati, Ohio and Facultad de Ingenierfa, Universidad del Valle, Ciudad Universitaria Melendez, Santiago de Cali, Colombia EDITORS Ronald L. Crawford Aaron L. Mills Environmental Biotechnology Institute Department of Environmental Sciences University of Idaho University of Virginia Moscow, Idaho Charlottesville, Virginia Jay L. Garland Linda D. Stetzenbach Dynamac Corporation Department of Environmental and Kennedy Space Center, Florida Occupational Health School of Public Health University of Nevada, Las Vegas David A. Lipson Las Vegas, Nevada Department of Biology San Diego State University San Diego, California ASM -PRESS Washington, D.C. Address editorial correspondence to ASM Press, 1752 N St. NW, Washington, DC 20036-2904, USA Send orders to ASM Press, P.O. Box 605, Herndon, VA 20172, USA Phone: (800) 546-2416 or (703) 661-1593 Fax: (703) 661-1501 E-mail: [email protected] Online: estore.asm.org Copyright 0 1997, 2002, 2007 ASM Press American Society for Microbiology 1752 N St. NW Washington, DC 20036-2904 Library of Congress Cataloging-in-Publication Data Manual of environmental microbiology / editor in chief, Christon J. Hurst ; editors, Ronald L. Crawford .. [et al.].-3rd ed. p. ; cm. Includes bibliographical references and index. ISBN-13: 978- 1-55581-379-6 (hardcover) ISBN- 10: 1-55581-3 79-8 (hardcover) 1. Microbial ecology-Laboratory manuals. 2. Sanitary microbiology-Laboratory manuals. I. Hurst, Christon J. 11. Crawford, Ronald L., 1947- [DNLM: 1. Environmental Microbiology. QW 55 M294 20071 QR100.M36 2007 579l.174~22 2006034637 10 9 8 7 6 5 4 3 2 1 All Rights Reserved Printed in the United States of America Preface Environmental microbiology is a fascinating field of science readers. Two hundred seven scientists have contributed to this which captured my imagination when I first got out my third edition of the Manual, including more than 100 new trowel 32 years ago to collect soil from beneath a suburban authors, and I welcome each of them. I offer special apprecia- tree. While following the trail which ensued, I have sam- tion for the fact that nearly all of the former editors have pled the drainage from coal mines, dug infiltration basins in remained among our group as authors. the desert, dredged sediments from bays and rivers, and The most difficult part of compiling such a volume is chopped holes through surface ice. I even have learned that deciding which topics will receive center stage and which sometimes the sample bottle gets filled in unusual ways, must be given a reduced representation. It also is important such as when the surf washed over my head or when I to recognize that the research of any given field flows and slipped sideways into a river. The latter event was observed sometimes changes its path over time. The authors and edi- by three of my students, who were courteous enough not to tors of this manual are dedicated to helping you, our read- laugh too loudly. The Manual of Environmental Microbiology ers, keep a balanced perspective. We always will be certain is an effort to combine the results and my excitement from that the basic foundations of environmental microbial my own discoveries with those of many colleagues. I feel methodology are thoroughly covered and also try to keep honored to be a part of this collaborative effort. It is an idea you up to date with the front of that flow. To keep that which began handwritten on the back of an envelope in objective and meet our responsibility to our readers, we January 1991, and I still cherish that envelope. have updated all of those chapters that were carried over The process of organizing, writing, and finally publishing from the second edition, and many of them have been com- this manual has been a joint volunteer effort by many hun- pletely rewritten. You also will find that this edition con- dreds of people, each of whom has contributed generously of tains numerous chapters on new topics. their own experiences and expertise. Together, as a group of In addition to thanking the authors and editors, without 136 scientists, we saw our efforts come to initial fruition with whose selfless volunteer efforts the American Society for publication of the first edition of the Manual in the fall of 1996. Microbiology could not bring forth this manual, I offer par- By bringing to you this third edition, we now present a com- ticular thanks to several specific individuals. Jeff Holtmeier, plete update of our field. Jay Garland, David Lipson, and the director of ASM Press, has lent us his utmost support. Aaron Mills have been added as new volume editors for this Ken April of ASM Press served as our production editor. Ken, edition, replacing Michael McInerney and Guy Knudsen, who most of all, has coordinated the entire process and kept us on now have become emeritus editors. Four of the section editors course. Although his job is not easy, Ken somehow manages from the second edition, Robert Christian, Steven Newell, to seem calm and cheerful while surviving it all. The editors David Stahl, and Linda Thomashow, likewise have become also thank the following individuals who assisted us by serv- emeritus editors. It is with pride that I welcome in their stead ing as ad hoc reviewers for this edition of the Manual: Anne Meredith Hullar, Jonathan Lloyd, Se6n OConnell, and Ming Bernhard, Haluk Beyenal, Rima Franklin, Jim Fredrickson, Tien, who have joined the editorial board as new section edi- Robert Genter, Tim Griffin, Jo Handelsman, Heribert Insam, tors for this edition. Many of the contributing authors from the Scott Kelley, George Kling, Mike Lehman, John Lindquist, first two editions have been called in other directions, and Henry Mainwaring, Andrew Martin, Andrzej Paszczynski, those departing contributors now are our alumni, each of Gary Sayler, Kathleen T. Scott, Claus Sternberg, Ben Van whom knows that his or her efforts were appreciated by our Mooy, and Darla Wise. CHRISTON J . HURST xxi Contents Editorial Board / xi 7 Cultivation of Algae and Protozoa / 79 Contributors / xiii JOHN G. DAY, UNDINE ACHILLES-DAY, Preface / xxi SUSAN BROWN, AND ALAN WARREN 8 Cultivation and Assay of Animal Viruses / 93 SECTION I PIERRE PAYMENT INTRODUCTION TO ENVIRONMENTAL MICROBIOLOGY / 1 9 Cultivation of Microbial Consortia VOLUME EDITOR JAY L. GARLAND and Communities / 101 GIDEON M. WOLFAARDT, DARREN R. KORBER, 1 Introduction to Environmental AND JOHN R. LAWRENCE Microbiology / 3 CHRISTON J. HURST 10 Lipid Analyses for Viable Microbial Biomass, Community Composition, Metabolic 2 Neighborhoods and Community Status, and In Situ Metabolism / 112 Involvement: No Microbe Is an Island / 6 DAVID B. HEDRICK, AARON D. PEACOCK, CHRISTON J. HURST AND DAVID C. WHITE 3 Prokaryotic Diversity: Form, Ecophysiology, 11 Physiological Profiling of Microbial and Habitat / 20 Communities / 126 FREDERICK S. COLWELL JAY L. GARLAND, COLIN D. CAMPBELL, AND EDWARD R. LEADBETTER AND AARON L. MILLS 12 Molecular Approaches for the SECTION II Measurement of Density, Diversity, GENERAL METHODOLOGY / 35 and Phylogeny / 139 WEN-TSO LIU AND DAVID A. STAHL VOLUME EDITOR JAY L. GARLAND SECTION EDITOR SEAN P. O'CONNELL 13 Phylogenetic and Genomic Analysis / 157 DIRK GEVERS AND TOM COENYE 4 Overview: General Microbiology / 37 JAY L. GARLAND AND SEAN P. O'CONNELL 14 Bioreporters, Biosensors, and Microprobes / 169 5 Analytical Imaging and Microscopy ROBERT S. BURLAGE Techniques / 40 J. R. LAWRENCE, D. R. KORBER, AND T. R. NEU 15 Ecology at Long-Term Research Sites: Integrating Microbes and Ecosystems / 182 6 Cultivation of Bacteria and Fungi / 69 JOHN E. HOBBIE, MICHELE BAHR, RALPH S. TANNER AND ANNA-LOUISE REYSENBACH V vi H CONTENTS 16 Quality Assurance / 190 28 Modeling the Fate of Microorganisms in A. J. CROSS-SMIECINSKI Water, Wastewater, and Soil / 355 CHRISTON J. HURST 17 Issues of Study Design and Statistical Analysis for Environmental Microbiology / 199 29 Estimating the Risk of Infectious Disease KENNETH M. PORTIER AND RONALD CORSTANJE Associated with Pathogens in Drinking Water 1365 CHRISTON J. HURST SECTION Ill WATER MICROBIOLOGY IN PUBLIC 30 Toxic Photosynthetic Microbes / 378 HEALTH / 217 WESLEY CLINTON JACKSON, JR. VOLUME EDITOR CHRISTON J. HURST SECTION EDITOR GARY A. TORANZOS SECTION IV AQUATIC ENVIRONMENTS / 391 18 Overview of Water Microbiology as It VOLUME EDITOR CHRISTON J. HURST Relates to Public Health / 219 SECTION EDITOR MEREDITH A. J. HULLAR CHRISTON J. HURST 19 Waterborne Transmission of Infectious 31 An Overview of Methodologies in Aquatic Agents / 222 Microbial Ecology / 393 CHRISTINE L. MOE MEREDITH A. J. HULLAR 20 Detection of Microorganisms in 32 Cultivating Microorganisms from Dilute Environmental Freshwaters and Drinking Aquatic Environments: Melding Traditional Waters / 249 Methodology with New Cultivation Techniques GARY A. TORANZOS, GORDON A. McFETERS, and Molecular Methods / 399 JUAN JOSE BORREGO, AND MARION SAVILL JAMIE W. BECKER, MARINA L. BRANDON, AND MICHAEL S. RAPPE 21 Detection of Protozoan Parasites in Primary Productivity and Producers / Source and Finished Drinking Water / 265 33 407 HANS W. PAERL FRANK W. SCHAEFER I11 34 Bacterial Secondary Productivity / 421 22 Microbial Indicators of Marine GERARD0 CHIN-LEO AND COLLEEN T. EVANS Recreational Water Quality / 280 STEPHEN B. WEISBERG, RACHEL T. NOBLE, 35 Community Structure: Bacteria AND JOHN F. GRIFFITH and Archaea / 434 JED A. FUHRMAN 23 Detection of Viruses in Environmental Waters, Sewage, and Sewage Sludges I 290 36 Viral Community Structure / 445 CHRISTON J. HURST AND KELLY A. REYNOLDS ALEXANDER I. CULLEY AND CURTIS A. SUTTLE 24 Detection of Bacterial Pathogens in 37 Protistan Community Structure / 454 Wastewater and Sludge / 300 DAVID A. CARON AND ASTRID SCHNETZER RICHARD E. DANIELSON AND ROBERT C. COOPER 38 Decomposition and Fungal Community 25 Detection of Pathogenic Bacteria, Viruses, Structure in Aquatic Environments / 469 and Parasitic Protozoa in Shellfish / 31 1 FELIX BARLOCHER LEE-ANN JAYKUS 39 Bacterial Organic Carbon Cycling 26 Control of Microorganisms in Source in Aquatic Environments / 479 Water and Drinking Water / 325 MATTHEW T.
Recommended publications
  • Localizing Transcripts to Single Cells Suggests an Important Role of Uncultured Deltaproteobacteria in the Termite Gut Hydrogen Economy
    Localizing transcripts to single cells suggests an important role of uncultured deltaproteobacteria in the termite gut hydrogen economy Adam Z. Rosenthala,1, Xinning Zhanga,1, Kaitlyn S. Luceya, Elizabeth A. Ottesena, Vikas Trivedib, Harry M. T. Choib, Niles A. Pierceb,c, and Jared R. Leadbettera,2 aRonald and Maxine Linde Center for Global Environmental Science, bDepartment of Bioengineering, and cDepartment of Computing and Mathematical Sciences, California Institute of Technology, Pasadena, CA 91125 Edited by James M. Tiedje, Michigan State University, East Lansing, MI, and approved August 13, 2013 (received for review April 29, 2013) Identifying microbes responsible for particular environmental and in situ assays to address such matters directly. We interro- functions is challenging, given that most environments contain gated a tiny, yet complex environment that accommodates robust, an uncultivated microbial diversity. Here we combined approaches stable, and species-rich microbial communities—the hindgut of a to identify bacteria expressing genes relevant to catabolite flow wood-feeding lower termite, Zootermopsis nevadensis (1). and to locate these genes within their environment, in this case Termites and their gut microbiota digest lignocellulose, the the gut of a “lower,” wood-feeding termite. First, environmental most abundant natural composite material on Earth. For some time now, it has been known that a key activity in this nutritional transcriptomics revealed that 2 of the 23 formate dehydrogenase + (FDH) genes known in the system accounted for slightly more than mutualism involves the bacterial conversion of H2 CO2, gen- one-half of environmental transcripts. FDH is an essential enzyme erated during wood polysaccharide fermentation, into acetate in a process called CO -reductive acetogenesis (2, 3).
    [Show full text]
  • Sporulation Evolution and Specialization in Bacillus
    bioRxiv preprint doi: https://doi.org/10.1101/473793; this version posted March 11, 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. Research article From root to tips: sporulation evolution and specialization in Bacillus subtilis and the intestinal pathogen Clostridioides difficile Paula Ramos-Silva1*, Mónica Serrano2, Adriano O. Henriques2 1Instituto Gulbenkian de Ciência, Oeiras, Portugal 2Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Oeiras, Portugal *Corresponding author: Present address: Naturalis Biodiversity Center, Marine Biodiversity, Leiden, The Netherlands Phone: 0031 717519283 Email: [email protected] (Paula Ramos-Silva) Running title: Sporulation from root to tips Keywords: sporulation, bacterial genome evolution, horizontal gene transfer, taxon- specific genes, Bacillus subtilis, Clostridioides difficile 1 bioRxiv preprint doi: https://doi.org/10.1101/473793; this version posted March 11, 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. Abstract Bacteria of the Firmicutes phylum are able to enter a developmental pathway that culminates with the formation of a highly resistant, dormant spore. Spores allow environmental persistence, dissemination and for pathogens, are infection vehicles. In both the model Bacillus subtilis, an aerobic species, and in the intestinal pathogen Clostridioides difficile, an obligate anaerobe, sporulation mobilizes hundreds of genes.
    [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]
  • Supplementary Figure Legends for Rands Et Al. 2019
    Supplementary Figure legends for Rands et al. 2019 Figure S1: Display of all 485 prophage genome maps predicted from Gram-Negative Firmicutes. Each horizontal line corresponds to an individual prophage shown to scale and color-coded for annotated phage genes according to the key displayed in the right- side Box. The left vertical Bar indicates the Bacterial host in a colour code. Figure S2: Projection of virome sequences from 183 human stool samples on A. Acidaminococcus intestini RYC-MR95, and B. Veillonella parvula UTDB1-3. The first panel shows the read coverage (Y-axis) across the complete Bacterial genome sequence (X-axis; with bp coordinates). Predicted prophage regions are marked with red triangles and magnified in the suBsequent panels. Virome reads projected outside of prophage prediction are listed in Table S4. Figure S3: The same display of virome sequences projected onto Bacterial genomes as in Figure S2, But for two different Negativicute species: A. Dialister Marseille, and B. Negativicoccus massiliensis. For non-phage peak annotations, see Table S4. Figure S4: Gene flanking analysis for the lysis module from all prophages predicted in all the different Bacterial clades (Table S2), a total of 3,462 prophages. The lysis module is generally located next to the tail module in Firmicute prophages, But adjacent to the packaging (terminase) module in Escherichia phages. 1 Figure S5: Candidate Mu-like prophage in the Negativicute Propionispora vibrioides. Phage-related genes (arrows indicate transcription direction) are coloured and show characteristics of Mu-like genome organization. Figure S6: The genome maps of Negativicute prophages harbouring candidate antiBiotic resistance genes MBL (top three Veillonella prophages) and tet(32) (bottom Selenomonas prophage remnant); excludes the ACI-1 prophage harbouring example characterised previously (Rands et al., 2018).
    [Show full text]
  • Gene Conservation Among Endospore-Forming Bacteria Reveals Additional Sporulation Genes in Bacillus Subtilis
    Gene Conservation among Endospore-Forming Bacteria Reveals Additional Sporulation Genes in Bacillus subtilis Bjorn A. Traag,a Antonia Pugliese,a Jonathan A. Eisen,b Richard Losicka Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts, USAa; Department of Evolution and Ecology, University of California Davis Genome Center, Davis, California, USAb The capacity to form endospores is unique to certain members of the low-G؉C group of Gram-positive bacteria (Firmicutes) and requires signature sporulation genes that are highly conserved across members of distantly related genera, such as Clostridium and Bacillus. Using gene conservation among endospore-forming bacteria, we identified eight previously uncharacterized genes that are enriched among endospore-forming species. The expression of five of these genes was dependent on sporulation-specific transcription factors. Mutants of none of the genes exhibited a conspicuous defect in sporulation, but mutants of two, ylxY and ylyA, were outcompeted by a wild-type strain under sporulation-inducing conditions, but not during growth. In contrast, a ylmC mutant displayed a slight competitive advantage over the wild type specific to sporulation-inducing conditions. The phenotype of a ylyA mutant was ascribed to a defect in spore germination efficiency. This work demonstrates the power of combining phy- logenetic profiling with reverse genetics and gene-regulatory studies to identify unrecognized genes that contribute to a con- served developmental process. he formation of endospores is a distinctive developmental the successive actions of four compartment-specific sigma factors Tprocess wherein a dormant cell type (the endospore) is formed (appearing in the order ␴F, ␴E, ␴G, and ␴K), whose activities are inside another cell (the mother cell) and ultimately released into confined to the forespore (␴F and ␴G) or the mother cell (␴E and the environment by lysis of the mother cell (1, 2).
    [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]
  • Diderm Firmicutes Challenge the Gram-Positive/Gram-Negative Divide Daniela Megrian, Najwa Taib, Jerzy Witwinowski, Christophe Beloin, Simonetta Gribaldo
    One or two membranes? Diderm Firmicutes challenge the Gram-positive/Gram-negative divide Daniela Megrian, Najwa Taib, Jerzy Witwinowski, Christophe Beloin, Simonetta Gribaldo To cite this version: Daniela Megrian, Najwa Taib, Jerzy Witwinowski, Christophe Beloin, Simonetta Gribaldo. One or two membranes? Diderm Firmicutes challenge the Gram-positive/Gram-negative divide. Molecular Microbiology, Wiley, 2020, 10.1111/MMI.14469. pasteur-02505848 HAL Id: pasteur-02505848 https://hal-pasteur.archives-ouvertes.fr/pasteur-02505848 Submitted on 11 Mar 2020 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 - NonCommercial| 4.0 International License DR. SIMONETTA GRIBALDO (Orcid ID : 0000-0002-7662-021X) Article type : MicroReview One or two membranes? Diderm Firmicutes challenge the Gram-positive/Gram-negative divide Daniela Megrian1,2, Najwa Taib1,3, Jerzy Witwinowski1, Christophe Beloin4, and Simonetta Gribaldo1* 1 Institut Pasteur, Department of Microbiology, Unit Evolutionary Biology of the Microbial Cell,
    [Show full text]
  • Taxonomic and Functional Characterization of Human Gut Microbes Involved in Dietary Plant Lignan Metabolism
    Taxonomic and Functional Characterization of Human Gut Microbes Involved in Dietary Plant Lignan Metabolism Isaac M. Elkon A thesis submitted in partial fulfillment of the requirements for the degree of Master of Science University of Washington 2015 Committee: Johanna W. Lampe Meredith A.J. Hullar Program Authorized to Offer Degree: School of Public Health © Copyright 2015 Isaac M. Elkon University of Washington Abstract Taxonomic and Functional Characterization of Human Gut Microbes Involved in Dietary Plant Lignan Metabolism Isaac M. Elkon Chair of the Supervisory Committee: Research Professor Johanna W. Lampe Department of Epidemiology Background: Dietary plant lignans, such as secoisolariciresinol diglucoside (SDG), are metabolized to the enterolignans, enterodiol (END) and enterolactone (ENL), by gut microbes. Evidence suggests that enterolignans may reduce risk of cardiovascular disease and several forms of cancer. Our aim was to characterize the microbial community involved in enterolignan production by using an in vitro batch culture system to enrich for lignan-metabolizing organisms. Methods: Stool samples from eight participants were incubated separately for ~1 week with a mineral salts media containing formate, acetate, glucose, and 6.55 µM SDG. Daily secoisolariciresinol (SECO), END, and ENL concentrations were measured using gas chromatography–mass spectrometry (GCMS). Microbial community in initial stool (Day 1) and in vitro-incubated fecal suspensions (final-day) was assessed via Illumina paired-end 16S rRNA gene amplicon and whole-metagenome shotgun sequencing. 16S rRNA gene sequences were taxonomically annotated using an in-house QIIME pipeline. Metagenomic shotgun sequences were taxonomically annotated using MetaPhlAn and functionally annotated using DIAMOND and HUMAnN. Annotation-based alpha diversity, organism abundance, and functional gene abundance were used to assess differences between Day 1 and final-day microbial community composition.
    [Show full text]
  • Localizing Transcripts to Single Cells Suggests an Important Role of Uncultured Deltaproteobacteria in the Termite Gut Hydrogen Economy
    Localizing transcripts to single cells suggests an important role of uncultured deltaproteobacteria in the termite gut hydrogen economy Adam Z. Rosenthala,1, Xinning Zhanga,1, Kaitlyn S. Luceya, Elizabeth A. Ottesena, Vikas Trivedib, Harry M. T. Choib, Niles A. Pierceb,c, and Jared R. Leadbettera,2 aRonald and Maxine Linde Center for Global Environmental Science, bDepartment of Bioengineering, and cDepartment of Computing and Mathematical Sciences, California Institute of Technology, Pasadena, CA 91125 Edited by James M. Tiedje, Michigan State University, East Lansing, MI, and approved August 13, 2013 (received for review April 29, 2013) Identifying microbes responsible for particular environmental and in situ assays to address such matters directly. We interro- functions is challenging, given that most environments contain gated a tiny, yet complex environment that accommodates robust, an uncultivated microbial diversity. Here we combined approaches stable, and species-rich microbial communities—the hindgut of a to identify bacteria expressing genes relevant to catabolite flow wood-feeding lower termite, Zootermopsis nevadensis (1). and to locate these genes within their environment, in this case Termites and their gut microbiota digest lignocellulose, the the gut of a “lower,” wood-feeding termite. First, environmental most abundant natural composite material on Earth. For some time now, it has been known that a key activity in this nutritional transcriptomics revealed that 2 of the 23 formate dehydrogenase + (FDH) genes known in the system accounted for slightly more than mutualism involves the bacterial conversion of H2 CO2, gen- one-half of environmental transcripts. FDH is an essential enzyme erated during wood polysaccharide fermentation, into acetate in a process called CO -reductive acetogenesis (2, 3).
    [Show full text]
  • Candidatus Adiutrix Intracellularis
    Lawrence Berkeley National Laboratory Recent Work Title 'Candidatus Adiutrix intracellularis', an endosymbiont of termite gut flagellates, is the first representative of a deep-branching clade of Deltaproteobacteria and a putative homoacetogen. Permalink https://escholarship.org/uc/item/08v1q91p Journal Environmental microbiology, 18(8) ISSN 1462-2912 Authors Ikeda-Ohtsubo, Wakako Strassert, Jürgen FH Köhler, Tim et al. Publication Date 2016-09-01 DOI 10.1111/1462-2920.13234 Peer reviewed eScholarship.org Powered by the California Digital Library University of California ‘Candidatus Adiutrix intracellularis’, a homoacetogenic deltaproteobacteriumFor Peer colonizingReview the cytoplasm Only of termite gut flagellates (Trichonympha collaris) Journal: Environmental Microbiology and Environmental Microbiology Reports Manuscript ID: EMI-2015-1306 Manuscript Type: EMI - Research article Journal: Environmental Microbiology Date Submitted by the Author: 09-Sep-2015 Complete List of Authors: Brune, Andreas; Max Planck Institute for Terrestrial Microbiology, Dept. of Biogeochemistry Ikeda-Ohtsubo, Wakako; Tohoku University, Graduate School of Agricultural Science Strassert, Jürgen; Max Planck Institute for Terrestrial Microbiology, Dept. of Biogeochemistry Mikaelyan, Aram; Max Planck Institute for Terrestrial Microbiology, Dept. of Biogeochemistry Tringe, Susannah; DOE Joint Genome Institute, termite gut flagellates, intracellular symbionts, reductive acetogenesis, Keywords: hydrogen, Deltaproteobacteria Wiley-Blackwell and Society for Applied Microbiology
    [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]