Microbiology laboratory theory and application 3editon

i-xii Front Matter 8/31/11 3:27 PM Page vi i-xii Front Matter 8/31/11 3:27 PM Page i MICROBIOLOGY Laboratory Theory & Application THIRD EDITION Michael J Leboffe San Diego City College Burton E Pierce 925 W Kenyon Ave., Unit 12 Englewood, Colorado 80110 www.morton-pub.com i-xii Front Matter 8/31/11 3:27 PM Page ii Book Team Publisher: Biology Editor: Production Manager: Production Assistant: Typography: Copyediting: Illustrations: Cover Design: Douglas N Morton David Ferguson Joanne Saliger Desiree Coscia Patricia Billiot Ash Street Typecrafters, Inc Carolyn Acheson Imagineering Media Services, Inc Bookends Design Copyright © 2010 by Morton Publishing Company ISBN 10: 0-89582-830-8 ISBN 13: 978-0-89582-830-9 Library of Congress Control Number 2009944089 10 All rights reserved No part of this publication may be reproduced, stored in a retrieval system, or transmitted, in any form or by any means, electronic, mechanical, photocopying, recording, or otherwise, without the prior written permission of the copyright owners Printed in the United States of America i-xii Front Matter 8/31/11 3:27 PM Page iii Preface his third edition in many ways is like another first edition We have added 20 new exercises, incorporated four more exercises from MLTA Brief Edition, and have substantially rewritten several others Every exercise has been screened and updated for better clarity, comprehensiveness, and appropriate placement in the manual We have added three more of the boxed “A Word About ” features to offer expanded introductory material in Sections 4, 5, and Finally, we replaced many older photographs, and perhaps most important, employed a new artist to update the illustrations and enhance the overall beauty of the book Following are major features of each section T ✦ Introduction As in previous editions, the Introduction emphasizes safety Refinements include chemical safety awareness and examples of organisms to be handled at each BSL level ✦ Section Fundamental Skills Exercise 1-1 (The Glo-Germ™ Hand Wash Education System) was brought over from the Brief Edition This is a fun, eye-opening lab exercise, raising consciousness about how easily the “unseen” can be overlooked In Exercise 1-4 (Streak Plate Method of Isolation) we introduce alternative methods for streaking ✦ Section Microbial Growth Exercises 2-5 (Evaluation of Media) and 2-12 (Steam Sterilization) have been added from the Brief Edition Exercise 2-11 (The Effect of Osmotic Pressure on Microbial Growth) has been rewritten to include Halobacterium Exercise 2-13 (The Lethal Effect of Ultraviolet Radiation on Microbial Growth) has been renamed, and the procedure simplified ✦ Section Microscopy and Staining Exercise 3-1 (Introduction to the Light Microscope) has been rewritten to include an activity using the “Letter e” slide and the “Colored Thread” slide, both of which provide opportunities for novice microscopists to learn more about how to operate the light microscope Two new labs, Exercise 3-4 (Microscopic Examination of Pond Water) and Exercise 3-11 (Parasporal Crystal Stain), round out the changes for this section ✦ Section Selective Media This section has been updated for greater clarity and to address reviewers’ concerns The boxed item “A Word About Selective Media” has been added as an adjunct to the Section introduction, and Bile Esculin Test (Exercise 4-3) has been moved from Section to Selective Media for the Isolation of Gram-Positive Cocci ✦ Section Differential Tests This section has seen some reorganization and the addition of new material The boxed item “A Word About Biochemical Tests and Acid-Base Reactions,” has been added to supplement the introduction and help students better understand the recurring theme of fermentation seen in differential media Following the introductory material, the section begins with an exercise demonstrating Reduction Potential It is designed to be an easy and fun introduction to the concept of energy transformations in redox reactions, the understanding of which can be applied to many exercises that follow Novobiocin and Optochin susceptibility tests have been moved from Gram-positive coccus identification and combined with Bacitracin (Exercise 5-24) in the Antibacterial Susceptibility Testing subsection Because of popular demand to include both Kligler Iron Agar and Triple Sugar Iron Agar in the Combination iii i-xii Front Matter 8/31/11 3:27 PM Page iv IV MICROBIOLOGY: LABORATORY THEORY AND APPLICATION Differential Media subsection, we have written an exercise (5-21) that can be used with either or both media ✦ Section Quantitative Techniques In an ongoing effort to help students understand the dilutions and calculations necessary in quantitative techniques (and to simplify the terminology), we have rewritten the introduction to this section and the theory portion of Exercise 6-1 (Standard Plate Count) The terms “dilution factor” and “final dilution factor” associated with dilutions and platings have been replaced with “dilution” and “sample volume,” respectively We hope this helps ✦ Section Medical Microbiology In this section we have added one new lab demonstrating clinical biofilms (Exercise 7-4) Exercise 7-3 (Antimicrobial Susceptibility Testing) has been rewritten with new antibiotics and an optional exercise to demonstrate the difference between bacteriostatic and bacteriocidal agents Last, Exercise 7-9 (Identification of Gram-Positive Rods) rounds out the series of three unknown identifications ✦ Section Environmental Microbiology This is the section that has seen the most growth Of the 13 exercises, are new Exercise 8-1 (Winogradsky Column) should be done near the beginning of the semester so it can be used as a source of microorganisms in other labs (Exercises 8-6 through 8-8) The next seven exercises provide activities related to the Nitrogen Cycle (Exercises 8-2 through 8-5) and the Sulfur Cycle (Exercises 8-6 through 8-8) The other new lab is Exercise 8-10 (Soil Slide Culture), in which soil microorganisms are grown and then can be viewed in their proper spatial orientation Also included in this section is a brief explanation of trophic group terminology (“A Word About Trophic Groups”) ✦ Section Food Microbiology One exercise (that was problematic) has been removed from this section Otherwise, the content here is unchanged You can expect a lot of growth in the food microbiology section in subsequent editions of this manual ✦ Section 10 Microbial Genetics This section has been reorganized and three new exercises added to reflect the change in microbiology from traditional methods of identification to more sensitive techniques involving molecular biology Exercises 10-2 and 10-4 address two important methods of molecular biology: performing a restriction digest and polymerase chain reaction, respectively Exercise 10-7 (Phage Typing of E coli Strains) introduces the student to using viral susceptibility as a tool in microbial identification ✦ Section 11 Hematology and Serology Two of the seven exercises in this section are new Exercise 11-6 is a hemagglutination test used in the diagnosis of infectious mononucleosis Exercise 11-7 is a quantitative ELISA that models the identification and quantification of HIV antibodies ✦ Section 12 Eukaryotic Microbes This section continues to be a survey of the microscopic eukaryotes encountered in a medical microbiology laboratory One new exercise, Exercise 12-2 (Fungal Slide Culture) provides an opportunity to cultivate fungi in a way that their true structure can be observed microscopically ✦ Appendices Appendix G (Agarose Gel Electrophoresis) contains instructions for preparing and (multiple techniques for) staining agarose gels used in the electrophoresis portion of Exercises 10-2 and 10-5 Many additions have been made to Appendix H (Medium, Reagent, and Stain Recipes) to accompany all the new exercises The Glossary also has been updated and expanded Our book is maturing, becoming more complete and polished And as we use it, new ideas for presentation or content will occur to us for future changes That’s why new editions are numbered! i-xii Front Matter 8/31/11 3:27 PM Page v PREFACE Last, though we get compensated for our work, we are primarily educators We take great satisfaction that our efforts may in some small way contribute to your successful academic and professional careers All our best, Mike and Burt _ Acknowledgments Thanks so much to all of you who had a part in making this project a success We have thanked all of you personally; this is our opportunity to let our readers know who you are and why you are so appreciated Listed below, in no particular order, are the people who went out of their way to give time, advice, space, and patience to support us during this project We sincerely hope that, with the pages that follow, we have earned that support First of all, thanks to Debra Reed, Biology Laboratory Technician at San Diego City College, for her longstanding support of our projects Deb’s assistance spans more than a decade and includes help with test media and cultures, hand modeling for photos, and gentle directions when we occasionally forget where we are We thank Muu Vu for her assistance modeling for photos, and helping to make valuable contacts Thanks very much to Brett Ruston for the free lunch and the “loan” of several chemicals used in the Nitrogen and Sulfur cycle exercises Thanks to lab technician Laura Steininger for running interference by listening to Burt’s sustained belly-aching about living in an RV for a month without his dogs, Yancy, Megan, and Beau to keep him company Thanks also to Ed Sebring of the Chemistry Department who provided a pinch of this or that chemical when we were desperate Additionally, thank you to Dr Carla Sweet for helping with some new photographs as a hand model, Gary Wisehart for assisting with the Winogradsky column, Alicia Leboffe for editorial work, Nathan Leboffe for help in photography, and Dr Steven J Byers for piloting Mike around San Diego County so he could get aerial photographs Thanks to Dr Donna DiPaolo, Dr Anita Hettena, Dr Roya Lahijani, Erin Rempala, Dr David Singer, and Gary Wisehart of the San Diego City College Biology Department for patience and understanding about losing territory in the Biology Resource Center due to our set-up and for putting up with some of the foul odors produced by the cultures Thanks to Sonia Bertschi co-owner and manager of the Jacumba Hotsprings Spa and Lodge in Jacumba, California for a tour of her lovely resort and donation of natural mineral hot springs water Thanks to Jerry Davis, San Diego City College Vice President of Administrative Services and Joyce Thurman, San Diego City College Business Services Administrative Secretary, for expediting use of college facilities Thanks also to Dr Steve Barlow, Associate Director of the San Diego State University Electron Microscope Facility for his patience and humor as one of us learned how to use the transmission electron microscope A very special thank you goes to Dr Radu Popa, Portland State University Microbiology Professor for taking time on numerous occasions to give expert advice on many issues, but most specifically, sulfur biogeochemical transformations Also thank you to Jane Boone, Portland State University Biology Laboratory Coordinator, for giving Burt a workspace of his own and occasional needed advice Both Dr Popa and Ms Boone, who were working on their own advanced microbiology laboratory manual during this time, generously provided a collegial and sharing environment Thanks to Imagineering Media Services Inc from Toronto, Ontario, Canada for the new artwork included in this edition Thanks also to Bob Schram of Bookends Design for the cover design And, as always, thanks so much to Joanne Saliger at Ash Street V i-xii Front Matter 8/31/11 3:27 PM Page vi VI MICROBIOLOGY: LABORATORY THEORY AND APPLICATION Typecrafters, Inc., who capably (and cool-handedly) managed to produce a beautiful book out of moderately well organized scraps Thanks to Carolyn Acheson, who copyedited (and removed most of the split infinitives from) the manuscript We also are indebted to reviewers and students who provided valuable suggestions for improving our book Special recognition and thanks go to Dr Amy Warenda Czura of Suffolk County Community College and Dr Lisa Lyford of University of the Cumberlands for their thorough input A special thanks to Dr Jack G Chirikjian, Chairman of Edvotek, Inc for agreeing to the use of his company’s kits in Exercises 10-2, 10-4, 11-7, and Appendix G We, of course, remain grateful to the Morton Publishing team for their support and patience Specifically, thanks to Doug Morton, President, Chrissy Morton DeMier, Business Manager, David Ferguson, Acquisitions Editor, Carter Fenton, Sales and Marketing Manager, and Desiree Coscia, Publisher’s Assistant And as always, thanks to our wives Karen Leboffe and Michele Pierce for their continued support and understanding If writing a book is difficult, being married to an author is worse i-xii Front Matter 8/31/11 3:27 PM Page vii Contents Introduction Safety and Laboratory Guidelines A Word About Experimental Design Data Presentation: Tables and Graphs Data Presentation: Be Creative, But Complete! SECTION Fundamental Skills for the Microbiology Laboratory 11 1-1 Glo-Germ™ Hand Wash Education System 12 Basic Growth Media 14 EXERCISE 1-2 Nutrient Broth and Nutrient Agar Preparation 14 Aseptic Transfers and Inoculation Methods 17 EXERCISE 1-3 Common Aseptic Transfers and Inoculation Methods 18 EXERCISE 1-4 Streak Plate Methods of Isolation 25 EXERCISE 1-5 Spread Plate Method of Isolation 29 EXERCISE SECTION Microbial Growth 33 Diversity and Ubiquity of Microorganisms 34 EXERCISE 2-1 Ubiquity of Microorganims 34 EXERCISE 2-2 Colony Morphology 36 EXERCISE 2-3 Growth Patterns on Slants 44 EXERCISE 2-4 Growth Patterns in Broth 45 Environmental Factors Affecting Microbial Growth 46 EXERCISE 2-5 Evaluation of Media 46 Aerotolerance 48 EXERCISE 2-6 Agar Deep Stabs 48 EXERCISE 2-7 Fluid Thioglycollate Medium 50 EXERCISE 2-8 Anaerobic Jar 52 EXERCISE 2-9 The Effect of Temperature on Microbial Growth 54 EXERCISE 2-10 The Effect of pH on Microbial Growth 56 EXERCISE 2-11 The Effect of Osmotic Pressure on Microbial Growth 58 Control of Pathogens: Physical and Chemical Methods 60 2-12 Steam Sterilization 61 EXERCISE 2-13 The Lethal Effect of Ultraviolet Radiation EXERCISE on Microbial Growth 64 EXERCISE 2-14 Chemical Germicides: Disinfectants and Antiseptics 66 vii i-xii Front Matter 8/31/11 3:27 PM Page viii VIII MICROBIOLOGY: LABORATORY THEORY SECTION AND APPLICATION Microscopy and Staining 69 Microscopy 70 EXERCISE 3-1 Introduction to the Light Microscope 70 EXERCISE 3-2 Calibration of the Ocular Micrometer 76 EXERCISE 3-3 Microscopic Examination of Eukaryotic Microbes 79 EXERCISE 3-4 Microscopic Examination of Pond Water 84 Bacterial Structure and Simple Stains 95 EXERCISE 3-5 Simple Stains 100 EXERCISE 3-6 Negative Stains 103 Differential and Structural Stains 105 EXERCISE 3-7 Gram Stain 105 EXERCISE 3-8 Acid-Fast Stains 110 EXERCISE 3-9 Capsule Stain 115 EXERCISE 3-10 Endospore Stain 117 EXERCISE 3-11 Parasporal Crystal Stain 121 EXERCISE 3-12 Wet Mount and Hanging Drop Preparations 122 EXERCISE 3-13 Flagella Stain 124 EXERCISE SECTION 3-14 Morphological Unknown 126 Selective Media 129 A Word About Selective Media 130 Selective Media for Isolation of Gram-Positive Cocci 131 EXERCISE 4-1 Phenylethyl Alcohol Agar 131 EXERCISE 4-2 Columbia CNA With 5% Sheep Blood Agar 133 EXERCISE 4-3 Bile Esculin Test 135 EXERCISE 4-4 Mannitol Salts Agar 137 Selective Media for Isolation of Gram-Negative Rods 139 EXERCISE 4-5 MacConkey Agar 139 EXERCISE 4-6 Eosin Methylene Blue Agar 142 EXERCISE 4-7 Hektoen Enteric Agar 145 EXERCISE 4-8 Xylose Lysine Desoxycholate Agar 147 SECTION Differential Tests 149 A Word About Biochemical Tests and Acid-Base Reactions 150 Introduction to Energy Metabolism Tests 151 EXERCISE 5-1 Reduction Potential 152 EXERCISE 5-2 Oxidation–Fermentation Test 155 Fermentation Tests 158 EXERCISE 5-3 Phenol Red Broth 158 EXERCISE 5-4 Methyl Red and Voges-Proskauer Tests 161 Tests Identifying Microbial Ability to Respire 165 5-5 EXERCISE 5-6 EXERCISE 5-7 EXERCISE Catalase Test 165 Oxidase Test 168 Nitrate Reduction Test 171 707-772 Data Sheets 9-12,Gloss,Index 8/31/11 4:12 PM Page 758 758 MICROBIOLOGY: LABORATORY THEORY B bacillus Rod-shaped cell back mutation Mutation in a gene that reverses the effect of an original mutation bacteriophage Virus that attacks bacteria; usually host-specific basic stain Staining solution with a positively charged chromophore Basidiomycetes Division of fungi characterized by club-like appendages (basidia) that produce haploid spores; include common mushrooms and rusts basophil Category of white blood cells; one of three types of granulocyte (along with eosinophils and neutrophils) characterized by a cytoplasm with dark-staining granules and a lobed nucleus (often difficult to see because of the dark cytoplasmic granules) ␤-hemolysis The clearing around a colony on blood agar resulting from complete destruction of red blood cells; typical of certain members of Streptococcus ␤-lactamase Enzyme found in some bacteria that breaks a bond in the ␤-lactam ring of ␤-lactam antibiotics, rendering the antibiotic ineffective; the source of resistance against these antibiotics ␤-lactam antibiotic A group of structurally related antimicrobial chemicals that interfere with cross-linking of peptidoglycan subunits, which results in a defective wall structure and cell lysis; examples are penicillins and cephalosporins biofilm A layer of bacterial cells adhering to and reproducing on a surface; used commercially for acetic acid production and water purification bioluminescence Process by which a living organism emits light biosafety level (BSL) One of four sets of minimum standards for laboratory practices, facilities, and equipment to be used when handling organisms at each level; BSL-1 requires the least care, BSL-4 the most bound coagulase An enzyme (also called clumping factor) bound to the bacterial cell wall, responsible for causing the precipitation of fibrinogen and coagulation of bacterial cells C capnophile Microaerophile that requires elevated CO2 levels capsule Insoluble, mucoid, extracellular material surrounding some bacteria carbohydrate One of four families of biochemicals; characterized by containing carbon, hydrogen, and oxygen in the ratio 1:2:1 AND APPLICATION chemolithotroph Any organism that gets its energy from chemicals and its electrons from an inorganic source No eukaryotes are chemolithotrophic, only some prokaryotes such as sulfur and ammonia oxidizing bacteria chromogenic reducing agent A substance that produces color when it gives up electrons (becomes oxidized) chromophore The charged region of a dye molecule that gives it its color coagulase See bound coagulase; free coagulase coagulase-reacting factor Plasma component that reacts with free coagulase to trigger the clotting mechanism coccus Spherical cell coenzyme Nonprotein portion of an enzyme that aids the catalytic reaction (usually by accepting or donating electrons) coliform Member of Enterobacteriaceae that ferments lactose with production of gas within 48 hours at 37°C colony Visible mass of cells produced on culture media from a single cell or single CFU (cell forming unit); a pure culture colony forming unit Term used to define the cell or group of cells (e.g., staphylococci, streptococci) that produces a colony when transferred to plated media commensal Describes a synergistic relationship between two organisms in which one benefits from the relationship and the other is affected neither negatively nor positively common source epidemic An epidemic in which the disease is transmitted from a single source (such as water supply) and is not transmitted person-to-person compatible solutes Compounds such as amino acids that function both as metabolic constituents and solutes necessary to maintain osmotic balance between the internal and external environments competent cell Cell capable of picking up DNA from the environment; some cells are naturally competent, in other cases the cells are made to be competent artificially competitive inhibition Process whereby a substance attaches to an enzyme’s active site, thereby preventing attachment of the normal substrate complete medium A medium used in genetic experiments that supplies all nutrients for growth required by prototrophs and auxotrophs complex medium A medium in which at least one nutritional ingredient is of unknown composition or amount Media with any plant or animal extract are always complex carcinogen Any substance that causes cancer confirmatory test One last test after identification of an unknown, to further support the identification cardinal temperatures Minimum, optimum, and maximum temperatures for an organism conjugate acid A compound (one of a conjugate pair) that donates a proton in solution casease A family of hydrolytic enzymes that break down casein, often extracellularly conjugate base A compound (one of a conjugate pair) that accepts a proton in solution casein Milk protein that gives milk its white color conjugate pair A compound that alternates between acid and base forms by losing or gaining one proton Example: HCl/Cl– catalase Enzyme produced by some bacteria that catalyzes the breakdown of metabolic H2O2 cestode The class of parasitic worms commonly called tapeworms; characterized by having a head (scolex) with suckers and hooks and numerous segments (proglottids) that are little more than sex organs chemoheterotroph Any organism that uses chemicals for energy and organic compounds as a carbon source Usually the same organic compounds serve both purposes constitutive Term used to describe an enzyme that is produced continuously, as opposed to an enzyme produced only when its substrate is present See also induction cos site (cohesive end sites) In Lambda phage (linear) DNA, the single stranded tails at the 5' ends of both strands are complimentary to each other and can form a circular molecule These “sticky” ends can be a source of error in DNA fragment size determinations if not properly heated before running gel electrophoresis 707-772 Data Sheets 9-12,Gloss,Index 8/31/11 4:12 PM Page 759 GLOSSARY counter-stain Stain applied after decolorization to provide contrast between cells that were decolorized and those that weren’t culture A liquid or solid medium with microorganisms growing in or on it cyst “Resting stage” in life cycle of certain protozoans See also trophozoite cytochrome A class of iron-containing enzyme in electron transport chains Characterized by a porphyrin ring structure 759 disaccharide A sugar made of two monosaccharide subunits; e.g., the monosaccharides glucose and galactose can combine to make the disaccharide lactose disk diffusion test (Kirby-Bauer Test) This is one way to check susceptibility and resistance of a microbe to an antibiotic A paper disk containing an antibiotic is placed on a plate inoculated to produce confluent growth of a bacterium Susceptibility is determined by the size of the zone of inhibition of growth around the disk cytochrome oxidase An electron carrier in the electron transport chain of aerobes, facultative anaerobes, and microaerophiles that makes the final transfer of electrons to oxygen disproportionation reaction A redox reaction of some sulfur reducers whereby a substrate is split into two molecules, one that is more reduced and one that is more oxidized than the original compound Example: S2O32– Ǟ SO42– ‫ ם‬H2S cytoplasm The semifluid component of cells inside the cellular membrane in which many chemical reactions take place dissimilatory sulfate reduction A respiratory reaction in which sulfate is reduced exclusively for the purpose of gaining energy D DNA polymerase A group of enzymes that catalyze the addition of deoxyribonucleotides to the 3' end of an existing polynucleotide chain deaminase Enzyme that catalyzes the removal of the amine group (NH2) from an amino acid DNase See deoxyribonuclease death phase Closed system microbial growth phase immediately following stationary phase; characterized by population decline usually resulting from nutrient deficiencies or accumulated toxins Durham tube A small, inverted test tube used in some liquid media to trap gas bubbles and indicate gas production E decarboxylase Enzyme that catalyzes the removal of the carboxyl group (COOH) from an amino acid electromagnetic energy The energy that exists in the form of waves (including x-rays, ultraviolet, visible light, and radio waves) decimal reduction value Amount of time at a specific temperature to reduce a microbial population by 90% (one log cycle) electron donor A compound that can be oxidized to transfer electrons to another compound, which in turn becomes reduced defined medium A growth medium in which the exact amount and chemical formula (and thus identity) of each ingredient are known denaturation The first of three phases in a PCR cycle, followed by annealing and extension The separation of the strands in double stranded DNA electron transport chain A series of membrane-bound electron carriers that participate in oxidation-reduction reactions whereby electrons are transferred from one carrier to another until given to the final electron acceptor (oxygen in aerobes, other inorganic substances in anaerobes) in respiration denitrification The bacterial process in which nitrate is reduced to various forms of nitrogen in its role as final electron acceptor of anaerobic respiration endergonic Any metabolic reaction in which the products have more potential energy than the reactants These are usually associated with anabolic (synthesis) reactions deoxyribonuclease A family of hydrolytic enzymes that depolymerize DNA into polynucleotides The precise location of hydrolysis within the sugar-phosphate backbone depends on which DNase is acting These are usually secreted enzyme Deuteromycetes An unnatural grouping of fungi in which the sexual stages are either unknown or are not used in classification differential medium Growth medium that contains an indicator (usually color) to detect the presence or absence of a specific metabolic activity differential stain Staining procedure that allows distinction between cell types or parts of cells; often involves more than one stain, but not necessarily dilution blank A test tube containing a measured volume of sterile diluent (water, saline or buffer) used to serially dilute a concentrated solution or broth dilution factor Proportion of original sample present in a new mixture after it has been diluted; calculated by dividing the volume of the original sample by the total volume of the new mixture (Subsequent dilutions in a serial dilution must be multiplied by the dilution factor of the previous dilution.) diploid Defines a cell that has two complete sets of genetic information; one stage in the life cycle of all eukaryotic microorganisms (which also have a haploid [one set] stage) direct agglutination Serological test in which the combination of antibodies and naturally particulate antigens, if positive, form a visible aggregate See also indirect agglutination endospore Dormant, highly resistant form of bacterium; produced only by species of Bacillus, Clostridium, and a few others enteric bacteria Informal name given to bacteria that occupy the intestinal tract Enterobacteriaceae A group of Gram-negative rods that also are oxidase-negative, ferment glucose to acid, have polar flagella if motile, and usually are catalase-positive and reduce nitrate to nitrite enzyme A protein that catalyzes a metabolic reaction by interacting with the reactant(s) specifically; each metabolic reaction has its own enzyme eosinophil A category of white blood cells; one of three types of granulocyte (along with basophils and neutrophils) characterized by a cytoplasm with red (in typical stains) granules and lobed nucleus epitope That portion of an antigen that stimulates the immune system and reacts with antibodies eukaryote Type of cell with membranous organelles, including a nucleus, and having 80S ribosomes and many linear molecules of DNA exergonic Any metabolic reaction in which the reactants have more potential energy than the products These are usually associated with catabolic (degradative) reactions exoenzyme Enzyme that operates in the external environment after being secreted from the cells exponential phase Closed-system microbial growth phase immediately following the lag phase; characterized by constant maximal growth during which population size increases logarithmically 707-772 Data Sheets 9-12,Gloss,Index 8/31/11 4:12 PM Page 760 760 MICROBIOLOGY: LABORATORY THEORY AND APPLICATION extension The third of three phases in PCR, following denaturation and annealing, whereby a polymerase (usually TaqI) catalyzes the replication of a DNA template germ theory Theory holding that diseases and infections are caused by microorganisms; first hypothesized in the 16th century by Girolamo Fracastoro of Verona extracellular Pertains to the region outside a cell glycolysis Metabolic process by which a glucose molecule is split into two 3-carbon pyruvic acid molecules, producing two ATP (net) and two NADH2 molecules extreme halophile Organism that grows best at 15% or higher salinity extreme thermophile Organism that grows best at temperatures above 80°C F facultative anaerobe Microorganism capable of both fermentation and respiration; grows in the presence or absence of oxygen facultative thermophile Microorganism that prefers temperatures above 40°C but will grow in lower temperatures false negative Test result that is negative when the sample is actually positive; usually a result of lack of sensitivity in the test system false positive Test result that is positive when the sample is actually negative; usually a result of lack of specificity of the test system fastidious (microorganism) Describes a microorganism with strict physiological requirements; difficult or impossible to grow unless specific conditions are provided fatty acid A long chain, organic molecule with a carboxylic acid at one end with the rest of the carbons being bonded to hydrogens fermentation Metabolic process in which an organic molecule acts as an electron donor and one or more of its organic products act as the final electron acceptor, marking the end of the metabolic sequence (differs from respiration in that an inorganic substance is not needed to act as final electron acceptor) final electron acceptor (FEA) The molecule receiving electrons (it becomes reduced) at the end of a metabolic sequence of oxidation/ reduction reactions flavin adenine dinucleotide (FAD) Coenzyme used in oxidation/ reduction reactions that acts as an electron acceptor or donor, respectively gradient bacteria Microaerophiles with very narrow nutritional requirements living in habitats characterized by nutrients diffusing upward from sediments below and oxygen diffusing downward from air above granulocyte A category of white blood cells characterized by prominent cytoplasmic granules; includes neutrophils, eosinophils, and basophils group A streptococci ␣-hemolytic members of the genus Streptococcus, characterized by possessing the Lancefield group A antigen; belong to the species S pyogenes, an important human pathogen group B streptococci ␤-hemolytic members of the genus Streptococcus, characterized by possessing the Lancefield group B antigen; belong to the species S agalactiae group D streptococci Streptococci possessing the Lancefield group D antigen; include S bovis and species of the genus Enterococcus H halophile Microorganism that grows best at 3% or higher salinity haploid Describes a cell that has one complete set of genetic information; all eukaryotic microorganisms have a haploid stage and a diploid (two sets) stage in their life cycle; all prokaryotes are haploid hemagglutination General term applied to any agglutination test in which clumping of red blood cells indicates a positive reaction hemoglobin Iron-containing protein of red blood cells that is responsible for binding oxygen hemolysin A class of chemicals produced by some bacteria that break down hemoglobin and produce hemolysis heterocyst This is a hollow-appearing cell found in some cyanobacteria specialized to perform nitrogen fixation flavoprotein A flavin-containing protein in the electron transport chain, capable of receiving and transferring electrons as well as entire hydrogen atoms; sometimes bypasses normal route of transfer and reduces oxygen directly, forming hydrogen peroxide and superoxide radicals heterotroph An organism that requires carbon in the form of organic molecules See also autotroph free coagulase An enzyme produced and secreted by some microorganisms that initiates the clotting mechanism in plasma; seen as a solid mass in the coagulase tube test or clumps in the slide test hydrolysis The metabolic process of splitting a molecule into two parts, adding a hydrogen ion to one part and a hydroxyl ion to the other (One water molecule is used in the process.) free energy (of formation) The energy released by a molecule in a chemical reaction that is able to work (e.g., produce ATP) It is equivalent to the energy required to form the molecule from its individual elements free living A term used to describe nonparasitic organisms G gametangium A structure that produces gametes; used in describing fungi gamete Reproductive cell that must undergo fusion with another gamete to continue the life cycle; usually are haploid See also spore gelatinase Enzyme secreted by microorganisms, which catalyzes the hydrolysis of gelatin generation time The time required for a population to produce offspring (i.e., in bacteria that reproduce by binary fission, the time needed for the population to double); inverse of mean growth rate host An organism that serves as a habitat for another organism such as a parasite or a commensal hyperosmotic (solution) A term used to describe extracellular solute concentration relative to the cell; a solution that contains a higher concentration of solutes than the cell, such that water tends to move down its concentration gradient and diffuse out of the cell hypha A filament of fungal cells hyposmotic A term used to describe extracellular solute concentration relative to the cell; a solution that contains a lower concentration of solutes than the cell, such that water tends to move down its concentration gradient and diffuse into the cell I IMViC Acronym representing the four tests used in identification of Enterobacteriaceae: Indole, Methyl Red, Voges-Proskauer, and Citrate incomplete medium See minimal medium incubation The process of growing a culture by supplying it with the necessary environmental conditions 707-772 Data Sheets 9-12,Gloss,Index 8/31/11 4:12 PM Page 761 GLOSSARY 761 index case First occurrence of an infection or disease that results in an epidemic mesophile A microorganism that grows best at temperatures between 15°C and 45°C indirect agglutination Serological test in which artificially produced particulate antigens or antibodies are used to form a visible aggregate if positive See also direct agglutination methylation A protective enzymatic mechanism in many organisms whereby methyl groups (–CH3) attach to DNA, thus blocking attachment and destruction by restriction endonucleases induction Process by which a substrate (inducer) causes the transcription of the genes used in its digestion microaerophile A microorganism that requires oxygen, but can’t tolerate atmospheric levels of it infectious disease A transmissible illness or infection microbial growth curve Graphic representation of microbial growth in a closed system, consisting of lag phase, exponential (log) phase, stationary phase, and death phase inoculum The organisms used to start a new culture or transferred to a new place inorganic molecule A molecule that does not contain carbon and hydrogen intracellular Within the cell; as an intracellular enzyme catalyzing reactions inside the cell minimal medium A medium used in genetic experiments, supplying all nutrients for growth except the one required by auxotrophs, and thus supporting growth of only prototrophs iron-sulfur protein Iron-containing electron carrier in electron transport chains Differentiated from cytochromes by the lack of porphyrin ring structure minimum inhibitory concentration The lowest concentration of an antimicrobial substance required to inhibit growth of all microbial cells it contacts; on an agar plate, typically the outer edge of the zone of inhibition where the substance has diffused to the degree that it no longer inhibits growth isolate (v.) The process of separating individual cell types from a mixed culture; (n.) the group of cells resulting from isolation mitosis The process in which a nucleus divides to produce two identical nuclei isosmotic Describe extracellular solute concentration relative to the cell; a solution that contains the same concentration of solutes as the cell, such that water tends to move equally into and out of the cell mixed acid fermentation Vigorous fermentation producing many acid products including lactic acid, acetic acid, succinic acid, and formic acid, and subsequently lowering the pH of the medium to pH 4.4 or below K karyogamy The process of nuclear fusion that occurs after fertilization (plasmogamy) in sexual life cycles Krebs cycle A cyclic metabolic pathway found in organisms that respire aerobically or anaerobically L lag phase Closed-system microbial growth phase immediately preceding the exponential phase; characterized by a period of adjustment in which no growth takes place limit of resolution The closest two points can be together for the microscope lens to make them appear separate; two points closer than the limit of resolution will blur together lipase A family of hydrolytic enzymes that break down fats into their component parts: glycerol and up to three fatty acids lipid A fat lophotrichous Describes a flagellar arrangement with a group of flagella at one end of an elongated cell lymphocyte A category of white blood cells; one of two types of agranulocyte (along with monocytes); characterized by a large nucleus and little visible cytoplasm; involved in specific acquired immunity as T-cells and B-cells lysozyme A naturally occurring bactericidal enzyme in saliva, tears, urine, and other body fluids; functions by breaking peptidoglycan bonds lytic cycle The viral life cycle from attachment to lysis of the host cell M mean growth rate constant The number of generations produced per unit time; the inverse of generation time medium A substance used for growing microbes; may be liquid (usually a broth) or solid (usually agar) meiosis The process in which the nucleus of a diploid eukaryotic cell nucleus divides to make four haploid nuclei mold Informal grouping of filamentous fungi See also yeast monocyte A category of white blood cells; one of two types of agranulocyte (along with lymphocytes); characterized by large size and lack of cytoplasmic granules; the blood form of macrophages monotrichous Describes a flagellar arrangement consisting of a single flagellum morbidity Epidemiological measurement of incidence of a disease; typically accompanied by “incidence rate,” referring to the incidence of a disease over time morphology The shape of an organism mortality Epidemiological measurement of death caused by a disease; typically accompanied by “incidence rate,” referring to the incidence of death from a disease over time mutagen A substance that causes mutation in DNA; most mutagens are carcinogens mutation Alteration in a cell’s DNA mutualistic Describes a synergistic relationship between two organisms in which both benefit from the interaction mycelium A mass of fungal filaments (hyphae) N nematode A class of roundworms; environmentally abundant in some parasitic species neutrophil Category of white blood cells; one of three types of granulocyte (along with eosinophils and basophils) characterized by a granular cytoplasm and lobed nucleus; also known as “polymorphonuclear granulocytes” or “PMNs.” neutrophile Microorganism adapted to a habitat between pH 5.5 and 8.5 nicotinamide adenine dinucleotide (NAD) A coenzyme used in oxidation/reduction reactions that acts as an electron acceptor or donor, respectively nisin Antibiotic produced by Lactococcus lactis nitrate A highly oxidized form of nitrogen; NO3 707-772 Data Sheets 9-12,Gloss,Index 8/31/11 4:12 PM Page 762 762 MICROBIOLOGY: LABORATORY THEORY nitrate reductase An enzyme produced by all members of Enterobacteriaceae (and others) that catalyzes the reduction of nitrate (NO3) to nitrite (NO2) nitrification The chemical process in which nitrogen compounds, such as ammonia and nitrite are oxidized to form nitrate Typically, different bacteria perform these two steps in which ammonia is first oxidized to nitrite, which is subsequently oxidized to nitrate nitrite NO2, an oxidized form of nitrogen nitrogen fixation The bacterial process in which gaseous nitrogen (N2) becomes reduced to NH4 This is ecologically important because N2, while abundant in the atmosphere, is not in a form usable by most organisms, whereas NH4 is usable by plants and can thus enter food chains nitrogenase The enzyme involved in nitrogen fixation, that is, converting gaseous N2 to NH4 This is performed by free-living bacteria (e.g., Azotobacter), symbiotic bacteria (e.g., Rhizobium), and many cyanobacteria noninfectious diseases Conditions not caused by microorganisms; examples are stroke, heart disease, and emphysema O objective lens The microscope lens that first produces magnification of the specimen in a compound microscope obligate (strict) aerobe Microorganism that requires oxygen to survive and grow obligate (strict) anaerobe Microorganism for which oxygen is lethal; requires the complete absence of oxygen obligate thermophile Microorganism that grows only at temperatures above 40°C ocular lens The lens the microscopist looks through; produces the virtual image by magnifying the real image AND APPLICATION parthenogenesis A process in which females produce offspring from an unfertilized egg peptidoglycan The insoluble, porous, cross-linked polymer comprising bacterial cell walls; generally thick in Gram-positive organisms and thin in Gram-negative organisms peptone A digest of protein used in formulating some bacteriological media peritrichous Describes a flagellar arrangement in which flagella arise from the entire surface of the cell pH The measure of a solution’s alkalinity or acidity; the negative logarithm of the hydrogen ion concentration phage See bacteriophage phage host Bacteria attacked by a virus phototaxis Phototaxis is a response to light stimuli Positive phototaxis is movement toward a light stimulus, whereas negative phototaxis is movement away from light plaque The clearing produced in a bacterial lawn as a result of cell lysis by a bacteriophage; used to calculate phage titer (PFU/mL) when accompanied by a serial dilution plaque forming unit (PFU) Term that replaces “viral particle” or “single virus” when referring to phage titer; accounts for multiple particle arrangements in which more than one virus is responsible for initiating a plaque plasma The noncellular (fluid) portion of blood; consists of serum (including serum proteins) and clotting proteins plasmid Small, circular, extrachromosomal piece of DNA found in prokaryotic cells; often carries genes for antibiotic resistance plasmogamy The cytoplasmic fusion of gametes at the time of fertilization See also karyogamy ocular micrometer A uniformly graduated linear scale placed in the microscope ocular used for measuring microscopic specimens plasmolysis Shrinking of cell membrane (pulling away from the rigid cell wall) because of loss of water to the environment and reduced turgor pressure oligonucleotide A short nucleic acid molecule polar flagellum A single flagellum at one end of an elongated cell operon A prokaryotic structural and functional genetic unit consisting of two or more structural genes that code for enzymes in the same pathway and that are regulated together pour plate technique Method of plating bacteria in which the inoculum is added to the molten agar prior to pouring the plate opportunistic pathogen A microorganism not ordinarily thought of as pathogenic (i.e., most enterics) that will cause infection when out of its normal habitat organic molecule A molecule made of reduced carbon—that is, containing at least carbon and hydrogen osmosis Diffusion of water across a semipermeable membrane osmotolerant Microorganism that will grow outside of its preferred salinity range oxidation/reduction Chemical reaction in which electrons are transferred (The molecule losing the electrons becomes oxidized; the molecule gaining the electrons becomes reduced.) preadsorption period When performing a plaque assay, the time given to allow a bacteriophage to attach to the host before adding the mixture to the molten agar being plated precipitate An insoluble material that comes out of a solution during a precipitation reaction presumptive identification Tentative identification of an isolate based on one or more key test results primary stain The first stain applied in many differential staining techniques; usually subjected to a decolorization step that forms the basis for the differential stain oxidative deamination The metabolic process in which an amino acid has its amine removed, producing ammonia and an organic acid primer A short nucleotide sequence (typically 10–20 nucleotides) used in PCR to attach to DNA for the purpose of replicating a desired sequence of nucleotides Typically, two primers attach to sites on opposite strands, flanking the area (template) to be replicated oxidative phosphorylation The process by which an electron transport chain is used to add a phosphate to ADP to make ATP proglottid Tapeworm segments posterior to the scolex, used for absorption of nutrients and containing reproductive organs oxidizing agent A substance that removes electrons from (oxidizes) another See also reducing agent prokaryote Type of cell lacking internal compartmentalization (membranous organelles, including a nucleus) and having 70S ribosomes and a circular molecule of DNA; more primitive than eukaryotes P promoter site The patch of DNA upstream from the structural gene(s), which binds RNA polymerase to begin transcription parasite An organism that lives symbiotically with another, but to the detriment of the other organism (called a host) propagated transmission Conveying a disease person-to-person 707-772 Data Sheets 9-12,Gloss,Index 8/31/11 4:12 PM Page 763 GLOSSARY proteolytic Refers to catabolism of protein; e.g., a proteolytic enzyme prototroph A strain that is capable of synthesizing the nutrient that is acting as the marker in a particular genetic experiment; prototrophs will grow on complete and minimal medium See also auxotroph 763 respiration Metabolic process by which an organic molecule acts as an electron donor and an inorganic substance—such as oxygen, sulfur, or nitrate—acts as the final electron acceptor in an electron transport chain, marking the end of the metabolic sequence (differs from fermentation, which uses one of its own organic products as the final electron acceptor) pseudohypha A chain of fungal cells produced by budding (rather than by cytokinesis that produces two equally sized cells) and which is characterized by constrictions at cell junctions restriction enzyme Enzymes involved in cutting DNA at specific recognition sites, unique to the enzyme Involved in removing damaged DNA and destroying foreign (e.g., phage) DNA psychrophile A microorganism that grows only at temperatures below 20°C, with an optimum around 15°C reticuloendothelial system Combination of macrophages and associated cells located in the liver, spleen, bone marrow, and lymph nodes psychrotroph A microorganism that grows optimally at temperatures between 20 and 30°C but will grow at temperatures as low as 0°C and as high as 35°C pure culture Microbial culture containing only a single species purine nucleotide Purines are made of a sugar (ribose or deoxyribose), phosphate, and a nitrogen-containing base composed of two joined rings Examples are adenine (A) and guanine (G) These are found in DNA and RNA putrefaction The process of digesting dead organic material; decay pyrimidine nucleotide Pyrimidines are made of a sugar (ribose or deoxyribose), phosphate, and a nitrogen-containing base composed of a single ring Examples are cytosine (C) in DNA and RNA, thymine (T) in DNA, and uracil (U) in RNA pyruvic acid (pyruvate) A three-carbon compound produced at the end of glycolysis that may enter a respiration or a fermentation pathway; also serves as a starting point for synthesis of certain amino acids and an entry point for their digestion reverse citric acid cycle An energy consuming process used by green sulfur bacteria whereby molecules ordinarily associated with the oxidative respiratory reactions of the Krebs cycle perform reactions in the opposite direction to reduce carbon dioxide and form pyruvate reverse electron flow An energy consuming process used by purple sulfur bacteria whereby electrons transferred down the ETC of the photosystem are boosted upward against their thermodynamic gradient to reduce NADP+ needed by the Calvin cycle reversion In carbohydrate fermentation tests, the phenomenon of a microorganism fermentively depleting the carbohydrate and reverting to amino acid metabolism, thereby neutralizing acid products with alkaline products; produces a false negative rhizoid A root-like structure used for attachment of some fungi to the substrate RNA polymerase A group of enzymes that catalyze the addition of ribonucleotides to the 3' end of an existing polynucleotide chain S Q quinoidal (compound) A color-producing compound containing quinone as its central structure quorum sensing The phenomenon in bioluminescing bacteria whereby the light-emitting reaction of all cells takes place simultaneously when a threshold concentration of secreted autoinducer is reached R real image Magnified image of a specimen produced by the objective lens of a microscope; the real image is magnified again by the ocular lens to produce the virtual image recognition site A short DNA sequence where a restriction enzyme attaches Each enzyme recognizes and attaches to its own specific sequence reducing agent A substance that donates electrons to (reduces) another See also oxidizing agent reductase An enzyme that catalyzes the transfer of electrons from donor molecule to acceptor molecule, thereby reducing the acceptor reduction See oxidation/reduction refraction The bending of light as it passes from a medium with one refractive index into another medium with a different refractive index reservoir A nonhuman host or other site in nature serving as a perpetual source of pathogenic organisms resolution The clarity of an image produced by a lens; the ability of a lens to distinguish between two points in a specimen; high resolution in a microscope is desirable resolving power See limit of resolution saltern Salterns are low pools of saltwater Evaporation of the water leaves salt, which can then be harvested saprophyte A heterotroph that digests dead organic matter; a decomposer scolex The “head” of a tapeworm, often with suckers and hooks for attachment selective medium Growth medium that favors growth of one group of microorganisms and inhibits or prevents growth of others sensitivity This is a measure of a test’s ability to detect small amounts of the item being tested for The better the sensitivity, the fewer the false negatives (due to smaller amounts triggering a positive reaction), and the more useful the test is serial dilution Series of dilutions used to reduce the concentration of a culture and thereby produce between 30 and 300 colonies when plated, providing a means of calculating the original concentration serology A discipline that utilizes a serum containing antibodies (antiserum) to detect the presence of antigens in a sample; also refers to identification of antibodies in a patient’s serum serum Fluid portion of blood minus the clotting factors soft agar A semisolid growth medium containing a reduced concentration of agar; used in plaque assay to allow diffusion of bacteriophage while arresting movement of the bacteriophage host solute The dissolved substance in a solution solution The mixture of dissolved substance (solute) and solvent (liquid) solvent The liquid portion of a solution in which solute is dissolved specificity This is a measure of a test’s ability to produce a positive response only when reacting with the particular item being tested for The better the test’s specificity, the fewer the false positives (due to better discrimination), and the more useful it is 707-772 Data Sheets 9-12,Gloss,Index 8/31/11 4:12 PM Page 764 764 MICROBIOLOGY: LABORATORY THEORY AND APPLICATION spirillum Spiral-shaped cell tryptophan An amino acid sporangium Structure that produces spores tryptophanase Enzyme that catalyzes the hydrolysis of tryptophan into indole and pyruvic acid; detected in the indole test spore In bacteria, a dormant form of a microbe protected by specialized coatings produced under conditions of, and resistant to, adverse conditions; also known as an endospore; in fungi and plants, spores are specialized reproductive cells; frequently a means of dissemination spread plate technique Method of plating bacteria in which the inoculum is transferred to an agar plate and spread with a sterile bentglass rod or other spreading device stage micrometer A microscope ruler used to calibrate an ocular micrometer standard curve A graph constructed from data obtained using samples of known value for the independent variable; once made, can be used to experimentally determine the value of the independent variable when the dependent variable is measured on an unknown stationary phase Closed system microbial growth phase immediately following exponential phase; characterized by steady, level growth during which death rate equals reproductive rate stolons Surface hyphae of some molds (e.g., Rhizopus) that attach to the substrate with rhizoids turgor pressure The pressure inside a cell that is required to maintain its shape, tonicity, and necessary biochemical functions 2,3-butanediol fermentation The end-product of a metabolic pathway leading from pyruvate through acetoin with the associated oxidation of NADH; detected in the Voges-Proskauer test U undefined medium See complex medium urease Enzyme that catalyzes the hydrolysis of urea into two ammonias and one carbon dioxide utilization medium A differential medium that detects the ability or inability of an organism to metabolize a specific ingredient V variable A factor in a scientific experiment that is changed; the control and experimental groups in a good experiment differ in only one variable, the one being tested stormy fermentation Vigorous fermentation produced in litmus milk by some species that produce an acid clot but subsequently break it up because of heavy gas production (members of Clostridium) vector In genetic engineering, a means, often a plasmid or a virus, of introducing DNA into a new host streptolysin Hemolysin (blood hemolyzing exotoxin) produced and secreted by members of Streptococcus virtual image The image produced when the ocular lens of a microscope magnifies the real image; appears within or below the microscope superoxide dismutase Enzyme produced by some bacteria that catalyzes the conversion of superoxide radicals to hydrogen peroxide syntrophy A situation where two or more organisms, having differing metabolic capabilities, derive mutual benefit by providing and/or receiving essential nutrients otherwise not available to them 764 vegetative cell An actively metabolizing cell Voges-Proskauer test A differential test used to identify organisms that are capable of performing a 2,3-butanediol fermentation W T wavelength Measurement of a wave from crest to crest, usually in nanometers—as in electromagnetic energy thermal death time The amount of time required to kill a population of a specific size at a specific temperature whey Watery portion of milk as seen upon coagulation of casein in the production of a curd thermophile A microorganism that grows best at temperatures above 40°C X titer A measurement of concentration of a substance or particle in a solution; used in measurements of phage concentration X-Y scatter plot Graph presenting the relationship between two variables transformant cells Cells that have undergone transformation by picking up foreign DNA in a genetic engineering experiment Y transformation A form of genetic recombination performed by some bacteria in which DNA is picked up from the environment and incorporated into its genome yeast An informal grouping of unicellular fungi See also mold trematode A class of parasitic flatworms; also known as “flukes.” zone of inhibition On an agar plate, the area of nongrowth surrounding a paper disc containing an antimicrobial substance (The zone typically ends at the point where the diffusing antimicrobial substance has reached its minimum inhibitory concentration, beyond which it is ineffective.) trend line A line drawn on a graph to show the general relationship between X and Y variables; also known as a regression line triacylglycerol See triglyceride tricarboxylic acid cycle See Krebs cycle trichome A filament of cyanobacterial cells It does not include the sheath, if present triglyceride A molecule composed of glycerol and three long chain fatty acids trophozoite “Feeding” stage in the life cycle of certain protozoans See also cyst Z zygospore The product of fertilization and the site of meiosis in some molds zygote The product of gamete fusion (plasmogamy) and nuclear fusion (karyogamy); a fertilized egg 707-772 Data Sheets 9-12,Gloss,Index 4/10/12 7:53 AM Page 765 Index Note: Pages with photos and figures are indicated in boldface type ABO blood type, 384, 385 ABTS (azino-diethylbenz-thiazoline sulfonate), 389 acetaldehyde / acetate, 344 acetoin, 158, 161, 162, 164 acetyl-CoA, 151, 168, 196, 428, 431 acid(s) clot, 211, 212 weak, 150 acid-fast bacilli (AFB), 111 acid-fast stains, 105, 110-114 (exercise), 290, 472 acidophiles, 56, 318 Actinobacteria / actinomycetes, 329 Aequorea victoria, 354 aerobic bacteria / organisms, 296, 314, 318 respiration, 151, 165 aerobic electron transport chains (ETCs), 169, 342 See also electron transport chain Aerococcus, 218 Aeromonas hydrophilia, 238 Aeromonas sobria, 96, 115, 122, 126, 127 aerotolerance, 48, 50 African sleeping sickness, 412 agar See also Nutrient Agar plates and tubes in Ames Test, 367, 368 deep stabs, 48-49 (exercise), 434 (appendix) agarose electrophoresis, 351, 360, 455–458 (appendix) agar plates, 22, 25 bioluminescence on, 324 counting colonies on, 243 labeling, 372 placing filter on, 335 quadrant streak method, 25-26 agar slants, 21, 22, 44 agglutination / agglutinates, 373, 377, 382, 384, 385-386, 387, 388 agranulocytes, 374, 375, 376 AIDS-related infection, 414 akinetes, 84 albumin, equine, 377 Alcaligenes faecalis, 38, 39, 44, 49, 50, 52, 57, 155, 157, 213, 238 algae, 80, 81 See also green algae alkaliphiles, 56 American Public Health Association (APHA), 60 Ames Test, 345, 367-370, 459 amino acids, 192, 202, 206, 299, 300, 321, 428 See also proteins decarboxylation, 179, 180 ammonia, test for, 303, 304, 306, 307, 309 ammonia / ammonium phosphate / ammonium hydroxide, 175, 180, 182, 202, 322 ammonification, 308-309 (exercise) Ammonium Broth, 305-306, 460 amoebas, 80, 82, 92, 409 amoebic dysentery, 409 ampicillin, 355 amylase, 185 amylopectin, 184 Anabaena, 84, 302 anaerobes bacterial, 296 Gram-positive, 131 obligate and facultative, 48, 49, 50, 51, 52–53, 165, 168, 289, 322 respiration in, 165 anaerobic jar, 52-53 (exercise), 291, 293 anaerobic respiration / environment / organisms, 151, 152, 155, 165, 171, 298, 299, 300, 310, 318, 321, 322, 342 anaphylactic shock, 418 Ancylostoma duodenale, 422-423, 424 Animalia kingdom, 79 annelid worm, 93 Anopheles mosquito, 412 anthrax, 115, 117 antibacterial susceptibility test, 214, 268-271 (exercise) antibiotic resistance gene bla, 355 antibiotics, 214, 263, 268, 269, 270, 329, 345 antibiotic selective medium, 354 antibodies, 373, 377, 378, 379 heterophile, 387 HIV, 389 antigen(s), 373, 378, 380, 412 A and B, detecting, 384 adding to slide, 383 binding sites, 377 layering, 379 parasite’s, 418 soluble, 377 antigen-antibody specificity and reactions, 373, 377, 380, 382, 387, 389 antimicrobial susceptibility zones, 269 antiseptics, 60, 66 antiserum, 377, 378, 380, 384, 385, 386 Apicomplexa, 409 API 20 E identification system, 226-232 aquatic organisms / habitats, 297, 313, 318, 319 See also pond water arabinose and aribinose promoter, 354-355 araC, 355 Archaea, 79, 80, 313 arginine decarboxylation, 180 arthropods, 93 arthrospores, 398 Ascaris lumbricoides, 421, 424 Ascomycota / Ascomycetes, 398 ascospores, 400, 403 aseptic transfers, 11, 17, 18-24 (exercise) asexual reproduction, 86, 87, 400, 402 aspergillosis, 403 Aspergillus, 399, 402-403, 404-405, 406 Aspergillus fumigatus, 403 Aspergillus niger, 402, 403 Aspergillus oryzae, 403 Aspergillus soyae, 403 assimilatory sulfate reduction, 321 Association of Official Analytical Chemists (AOAC), 60 asymptomatic carrier, 410 ATP (adenosine triphosphate), 151, 152, 165, 299, 313, 321, 324, 425-428, 431 ATPases, 168, 214 autoclaves / autoclaving, 4-5, 6, 16, 17, 48, 61-62 autoradiograph, 455 autotrophs, 46, 86, 296, 305 auxochrome, 100 auxotrophs, 367, 367 axopodia, 92 azolitmin, 211 Azotobacter 299, 300, 301, 302, 327 Azotobacter cyst stain, 473 Bacillaria, 89 bacillariophytes, 88 bacilli arrangements, 95 Bacillus, 61, 100, 107, 117, 118, 121, 184, 329 Bacillus anthracis, 38, 115, 192, 289 Bacillus cereus, 38, 101, 103, 118, 185, 191, 192, 237, 289 Bacillus coagulans, 118, 237 Bacillus globigii and Bg/I, 350 Bacillus licheniformis, 214 Bacillus megaterium, 103, 118 Bacillus stearothermophilus, 55 Bacillus subtilis, 39, 44, 45, 64, 65, 96, 100, 118, 121, 126, 127, 193 Bacillus thuringiensis, 121 Bacitracin test, 214-216 (exercise) bacteria, 34, 46, 58, 84 aerobic and anaerobic, 296 bioluminescent, 324 catalase-producing, 166 chemolithotrophic, 300, 305 denitrifying, 300 enteric, 142, 150, 187, 232 gradient, 318 growth on agar plates, 36 heterotrophic, 151 lipolytic, 197 microaerophilic, 296 nitrifying, 305 nitrogen-fixing, 299, 302 oral, 150, 264 osmotolerant, 58 prokaryotic, 79 in saline habitats, 58 in soil microbial count, 329 sulfur, 296, 313, 314, 315-317 (exercise) sulfur-oxidizing, 318-320 (exercise) sulfur-reducing, 321-323 (exercise) thermal classifications of, 54 Bacteria domain, 79, 80, 84 bacterial growth patterns, 50, 51 host, 255 smear, 95, 101 bacterial transformation, 345, 354-358 (exercise) 765 707-772 Data Sheets 9-12,Gloss,Index 4/10/12 7:53 AM Page 766 766 MICROBIOLOGY: LABORATORY THEORY bacterial unknowns project, 237-241 (exercise) Bacteroides/ bacteroids, 18, 301, 302 bacteriochorophyll, 313 bacteriophages, 255, 257, 371 See also phage Lamda DNA, 350 balantidiasis, 410 Balantidium coli, 410-411, 415 Basidiomycota / Basidiomycetes, 398 basophils, 374, 376 BBLTM DrySlideTM, 168 BBL® EnterotubeTM II, 234 B-cells, 375, 376 Beggiatoa, 296, 318, 319 Bergey’s Manual of Systematic Bacteriology, 238, 281, 288, 293 BGLB Broth and test results, 336, 338, 339-340 Bile Esculin Agar, 131, 135, 460 bile esculin test, 135-136 (exercise) bile salts, 139, 140, 145, 147, 420 biochemical families, 46 biochemical pathways, 425-432 (appendix) biochemical tests / testing, 150, 293 See also differential tests biofilms, clinical, 272-273 (exercise) biological indicators, 61, 63 biological safety cabinet (BSC), 1, 2, bioluminescence, 295, 324-325 (exercise), 354 BioRad Laboratories, 354, 356 Biosafety in Microbiological and Biomedical Laboratories, biosafety levels (BSLs), 1, 2, biosynthetic processes / biosynthesis, 313, 321 biotechnology, 345 blastoconidia, 400 blastospores, 398 blood cell count See differential blood cell count smears, 375 Blood Agar, 217-219 (exercise), 220, 460 See also Sheep Blood Agar blood types / blood typing, 377, 384-386 (exercise) B-lymphocytes, 387 Bordetella, 155 botulism, 118, 289 Brain-Heart Infusion Broth / Agar, 47, 253, 285, 286, 460 Brewer’s yeast, 81, 82, 398 See also yeast Brilliant Green Lactose Bile (BGLB), 336, 338, 339, 460 bromcresol green, 264 bromcresol purple, 179, 209 Bromthymol blue dye, 145, 155, 175, 177 Brønsted/Lowry theory of acids and bases, 150 broth See also culture(s) fermentation, 61 flocculence in, 45 growth patterns in, 45 (exercise) LTB, BGLB, and EC, 338 obtaining a sample, 19, 20-23 tubes, inoculating, 22-23 broth culture, transfer from, 437-440 (appendix) BTSure Biological Indicators, 62 Bt toxin, 121 buffers, 57, 177, 187, 360, 471 Bunsen burner, 18, 29, 315, 334, 370, 406 calibration of ocular micrometer, 76-68 (exercise) Calvin Cycle, 315, 317 CAMP test, 220-221 (exercise) cancer See carcinogens Candida albicans, 399-400, 404 candidiasis, 400 capnophiles, 48 capsule stain, 115-116 (exercise) AND APPLICATION carbohydrate(s) fermentation, 158, 206, 264 See also fermentation metabolism, 155, 425 carbolfuchsin, 110, 111, 128, 472 carbon dioxide (CO2), 48, 150, 151, 155, 168, 180 carboxylic acids, 150 carcinogens, 345, 368 casease, 190, 212 casein / caseinogen, 131, 202, 211, 212 casein hydrolysis test, 190-191 (exercise) catabolic systems / catabolism, 151, 425 catalase, 165, 285 flowchart, 286 test, 165-166 (exercise), 286 cell(s) bacterial shape and arrangement, 95 walls, 106 density, 243 diploid and haploid, 400 epithelial, 79, 107 eukaryotic, 95 lysis, 266 morphology, 95 natural killer, 375 plasma, 375 stem, 374 vegetative, 400 Centers for Disease Control and Prevention (CDC), 60, 263, 274, 275, 341 Cephalosporium, 329 Ceratium, 91 cestodes, 416, 417-418 CFU See colony forming unit Charophyceans / charophyte, 88 chemical germicides, 66-68 (exercise) chemical safety and hazards, 1, 3, chemoheterotrophs, 297, 312 chemolithotrophic autotrophy / chemolithotrophs, 296, 297, 299, 300, 305, 312, 313, 314 chemolithotrophic sulfur-oxidizing bacteria, 318-320 (exercise) chitin, 81, 398 Chlamydomonas, 86 chlamydospores, 398, 400 chloramphenicol, 270, 271 Chlorobaculum, 315 Chlorobium, 322 chlorophytes, 87, 88 chloroplasts, 81, 86, 87, 88, 89, 90, 91 Christensen’s urea agar, 188 Chromatium, 315 Chromobacterium violaceum, 37, 42, 43, 44, 238 chromogen / chromophore, 100, 103 chromogenic cosubstrate, 389 ELISA, 394 reducing agents, 168, 169 chromoplasts, 88 Chroococcus, 86 chymotrypsin, 212 cilia / ciliates, 81, 90, 91, 93, 409, 410-411 Ciliophora, 409 ciprofloxacin, 270, 271 citrate-permease enzyme, 175 Citrate Agar, 461 citrate test, 175-176 (exercise) Citrobacter amalonaticus, 238 Citrobacter diversus, 45 Cladophora, 87 cleavage patterns, 350 clinical biofilms, 272-273 (exercise) clonorchiasis, 416 Clonorchis (Opisthorchis) sinensis, 416, 424 closed-system growth, 252-254 (exercise) Closterium, 88 Clostridium, 61, 117, 184, 197, 212, 289 Clostridium botulinum, 289 Clostridium perfringens, 192, 289 Clostridium sporogenes, 38, 49, 50, 52 Clostridium tetani, 192, 289 clover root nodules, 301 clumping factor, 222, 223 coagulase-reacting factor (CRF), 222 coagulase tests, 222-223 (exercise) cocci, 95, 98 See also gram-negative organisms; gram-positive cocci coccidian parasites, 111 Cocconeis, 89 coenzymes, 151, 168, 169, 177, 179, 315, 428 See also NAD and NADH coliform(s), 129, 139, 143, 295 colonies, calculating, 332, 333, 336 multiple tube fermentation method to determine, 336-339 (exercise) sample volumes, 335 coliphage, T4, 255 colistin, 133 134 colitis, 118, 289 collagen, 192 colony counter, 36, 247, 369 colony-forming unit (CFU), 25, 29, 243, 245246 in coliform colonies, 334 in urine culture, 248 colony morphology, 36-43 (exercise), 129, 279, 286 Columbia CNA Agar, 131 Columbia CNA with 5% Sheep Blood Agar, 133-134 (exercise), 461 combination differential media, 202 commensals, 278 competitive inhibition, 177 Computer Coding and Identification System (CCIS), 233-234 Congo red, 115, 473 conidia, 398, 402 conidiophore, 403, 404, 406 conjugate pairs, 150 conjugation, 88 contamination, reducing / preventing, 5-6, 17 See also fecal contamination Coomassie blue, 455 Coplin jars, 327 Corynebacterium, 184 Corynebacterium diphtheria, 289, 290 Corynebacterium xerosis, 40, 44, 45, 95, 97, 108, 126, 127, 237 Cosmarium, 88 cotton applicators / swabs, 17 in inoculation of agar plates, 27, 28, 35 transfers, 433-435 (appendix) countable plate, 245, 257, 332 counterstains, 110, 117 counting chamber, 250, 251 crateriform liquefaction, 192 crustaceans, 93 Cryptosporidium, 111 crystal violet stain, 100, 107, 108, 128, 139, 141, 272, 273 culture(s) See also media bacterial, nutrient broth and agar for, 14 bacterial and fungal, 11 broth, 20, 22, 437-440 (appendix) fungal slide, 406 mixed and pure, 25, 27, 29, 129 tubes and loops, 18, 22-23 curd formation, 212 cyanobacteria, 84, 301, 302 Cyclotella, 89 707-772 Data Sheets 9-12,Gloss,Index 4/10/12 7:53 AM Page 767 INDEX Cymbella, 89 cysteine, 206, 321, 322 putrefaction, 202 cysticercosis, 420 cysts / cyst stain, 300, 301, 409, 410, 411, 419 hydatid, 418 cytochromes, 168, 316, 342 cytochrome c oxidase, 165, 168, 169 cytoplasm, 87, 92, 95, 100, 255 D’Antoni’s iodine stain, 416, 417, 421 data presentation (tables and graphs), 7-9 Data Sheets, 7, 475 (appendix) daughter colonies / cells, 86, 95 deamination, 209, 308 oxidative, 300 tests, 179, 182-183 (exercise), 209 decarboxylase medium, 461 decarboxylases, 139, 179 decarboxylation, 147, 179-181 (exercise), 209 decimal reduction value (D value), 259 decolorization, 105, 106-107, 109, 110 decontamination, 60 denitrification, 171, 172, 310-311 (exercise) dental decay / caries, test for, 263, 264-265 deoxyribonuclease See DNase deoxyribonucleotides, free, 360 desmids, 88 desoxycholate, 139, 148 desoxycholate agar (modified Leifson), 461 Desulfovibrio Medium / tube, 322, 323, 461 desulfuration, 314 Desulfuromonas acetoxidans, 321-322 diacetyl, 161, 162, 344 diatoms, 80, 82, 88, 90 differential blood cell count, 373, 374-376 (exercise) differential tests / media, 129, 130, 133, 145, 147, 149, 150-151, 217 See also biochemical tests; combination differential media on agar plate, 435 (appendix) digital micropipettes, 243, 258 dilution blanks See serial dilution Dimethiyl Sulfoxide, DMSO, 367 dinoflagellates, 91 diphtheria, 280 diplococcus / diplobacilli, 95, 98, 106 Dipylidium caninum, 417-418, 424 direct count, 250-251 (exercise), 473 disaccharides, hydrolysis / fermentation, 158, 159, 198, 211, 344 disc-diffusion method, 214, 268 diseases / illnesses food-borne, 341 infectious, 274, 276, 403 notifiable (MMWR), 274, 275 disinfection / disinfectants, 60, 66 disk dispenser, 269 dissimilatory sulfate reduction, 321 DMABA, 202 DMSO, 367 DNA amplification / replication in PCR, 359 binding protein in bacterial transformation, 354, 355 E coli, 345 photolyase, 364 polymerase, 364 precipitated, 346 and restriction digest, 350 synthesis / replication, 131, 133, 270 thymine dimer in, 364 viral, 255 DNA extraction from bacterial cells, 346-349 (exercise) DNA hydrolysis test, 194-195 (exercise) DNase, 194, 346 DNase Agar, 184, 195, 462 drugs, bactericidal and bacteriostatic, 268 Durham tube, 171, 172, 311 See also tubes dyes acid tocsin, 145 indicator, 150, 161 pH of, 130-131, 332 EC Broth, 336, 338, 339-340, 462 Echinococcus granulosus, 418, 424 E coli, 23-24, 30, 169 See also Escheria coli culture in bacterial transformation, 355, 356 extraction of DNA from, 345, 346 mixed acid fermentation of, 161 phage typing of, 371-372 (exercise) repair process, 364 EcoRI methylase, 350 ectoplasm, 92 Ectothiorhodospira, 315 Edvotek®, 359 ELISA Kit, 389 Instastain®, 360, 457-458 electromagnetic energy / electromagnetic spectrum, 64, 364 electron acceptor, 153 See also final electron acceptor tower, 152 electron transport chain (ETC), 151, 155, 165, 168, 169, 315, 316, 425 electrophoresis, agarose / gel, 351, 352, 360, 361-362 elephantiasis, 423 ELISA test, 373, 377, 389-395, 412 Emden-Meyerhof-Parnas pathway, 344, 425-426 emulsions, 106 Endo Agar, 332, 333, 334, 462 endocarditis, 400 endonuclease, 364 endospore stain, 117-120 (exercise) energy of formation, 152 metabolism tests, 151 Entamoeba coli, 410, 415 Entamoeba histolytica, 409-410, 415 enterics, 278 See also bacteria and specific species pathogenic, 278, 341 Enterobacteriaceae, 45, 341 API 20 E system for, 226, 227 in combination differential media, 202-204, 212 in differential tests, 155, 158, 162, 168, 169, 171, 173, 176, 179, 180, 192, 194, 197, 217 facultative anaerobes in, 322 flowcharts to identify, 279, 280, 281, 282 identification of, 278-283 (exercise) in IMViC results, 278 motility in, 224 in selective media, 129, 139, 142, 147 in urine culture, 248 Enterobacter aerogenes, 45, 142, 162, 176, 177, 180, 224, 234, 238, 332 Enterobius vermicularis, 422, 424 Enterococcus, 131, 133, 139, 184, 200, 218 Enterococcus faecalis, 57, 131, 136, 140, 142, 146, 147, 159, 166, 173, 200, 238 Enterococcus faecium, 37, 45, 99, 213 Enterotube® II, 232-237 (exercise) Entner-Doudoroff pathway, 425, 427, 428 entropy, 152 environmental factors affecting microbial growth, 33, 46 influencing pigment production, 43 hazards, microbiology, 295 767 phases, 299 sample with cotton swab, 434 Environmental Protection Agency (EPA), 60 enzymes, 179 See also specific enzymes in bacterial transformation, 354, 355 coagulase, 222 denaturing of cellular, 56 extracellular, 192, 222 hydrolytic, tests detecting, 184, 185 in oxidase test, 168 proteolytic, 212 repair, 364 restriction, 350-351 Eosin Methylene Blue (EMB), 139, 142-144 (exercise), 462 epidemic, common source, 276 epidemic simulation, 276-277 (exercise) epidemiology / epidemiologists, 274, 276 epitopes, 377 Epstein-Barr virus (EBV), 387 equine albumin, 377 Erwinia amylovora, 40, 173, 238 erythrocytes, 99, 374, 414 See also red blood cells Escherichia coli, 47, 55, 59, 64, 65, 66, 67, 108, 238 See also E coli antibiotics, susceptibility to, 269 in bacterial transformation, 354 in combination differential media, 207, 210 in DNA extraction, 347 D values of, 260 in differential tests, 157, 159, 162, 168, 170, 173, 176, 177, 182, 185, 191, 193, 199 Gram-stain of, 332 multiple tube method to calculate density, 336 in population density, 246 and restriction digest, 350, 351 in selective media tests, 131, 133, 137, 140, 142, 146, 147 esculin, 135 See also bile esculin test esinophils, 374, 376 ETCs See electron transport chain ethidium bromide, 455 Euglena / Euglenids, 91 Eukarya kingdom, 80 eukaryotes, 46, 58, 79, 81, 88, 168, 169 photosynthetic, 313 (formula) protozoans as, 409 eukaryotic microbes, 79-83 (exercise), 397 excystation, 409 exoenzymes, 81, 184, 398 exotoxins, 217 experimental design / science / controls, 6-7 eyespot, 91 Fabaceae family, 300 facultative anaerobes, 296, 322 FAD / FADH2, 168, 169, 177, 196 fatty acids, 196 fecal contamination / coliforms, 139, 332, 333 fermentation / fermenters, 48, 150, 151, 155, 171, 172, 179, 428 See also lactose substrate broth, 61 carbohydrate, 158, 207 cheese, 403 glucose, 179, 206, 209, 264 KIA tests for, 202, 206 mannitol, 137, 138 of milk sugar lactose, 344 mixed acid, 158, 168, 162 pathways, 428, 431 stormy, 211 sucrose, 142, 145, 206 TSIA test for, 202, 206 2,3-butanediol, 162 707-772 Data Sheets 9-12,Gloss,Index 4/10/12 7:53 AM Page 768 768 MICROBIOLOGY: LABORATORY THEORY ferredoxin , 316 ferric ammonium citrate, 145, 147, 209 ferric choride, 182, 183 ferric citrate, 135 ferrous ammonium sulfate solution for sulfur reducing bacteria, 461 ferrous sulfide (FeS) / ferrous sulfate, 145, 147, 202, 203, 206, 322 fibrinogen, 222 filamentous growth, 39 filter housing, 334, 335 final (terminal) electron acceptor (FEA), 151, 158, 165, 300, 310 flagella, 81, 91, 91, 124 flagella stain, 124-125 (exercise), 473 flagellate(s), 409 protozoans, 411-312 flaming loops, tubes, rods / forceps, 18, 19, 21, 22, 29, 334, 370, 407 flavoprotein(s), 165, 168, 169 flies, as disease agents, 412 flocculence in broth, 45 flowchart(s) converting morphological unknown, 126-128 for identification of enterobacteriaceae, 278, 279, 280, 281, 282 for identification of gram-positive cocci, 286, 287 for identification of gram-positive rods, 292, 293 in medical microbiology, 263 sample, 240 Fluid Thioglycollate Medium, 50-51 (exercise) Food and Drug Administration (FDA), 60, 341 food microbiology, 341 food poisoning, 289 formate, 344 Fragillaria, 90 Francisella, 204 free energy, 152, 168 frustules, 88, 89 fucoxanthin, 88 fucsin and fucsin stain, 121, 473 fumarate, 177 fume hood, 327, 406 fungal slide culture, 406-408 (exercise) fungi, 81, 329, 397, 398-405 (exercise) See also molds; yeasts hypha, 327 Fungi kingdom, 79, 80 Fusobacterium, 184 galactose, 158, 211, 212, 344 gametangia, 398, 402 gametocytes, 414 gangrene, 118, 289 Gardnerella vaginalis, 184 GasPak® Anaerobic System, 52, 293 gelatin, 192 gelatinase(s), 184, 192, 193 gelatin hydrolysis test, 192-193 (exercise) gel electrophoresis, 352, 361-362, 455-457 (appendix) gel immunodiffusion (and saline agar), 380, 467 genes, structural, 354 genetic regulation / engineering, 345, 354, 355 genome, 255 Geobacillus, 61 Geobacillus stearothermophilus, 61 germicides, chemical, 60, 66-68 (exercise) Giardia lamblia, 411, 415 giardiasis, 411 glass pipette See pipette Glomeromycota, 398 glucose, 150, 156, 157, 158, 168, 184, 187, 206, 209, 211, 264, 344 See also fermentation; Krebs cycle AND APPLICATION Glucose Broth, 462 Glucose Salts Medium, 47, 462 glycerol, 196 Glycerol Yeast Extract Agar, 329, 330, 462 glycine, 344 glycocalyx, 272 glycolysis, 151, 159, 161, 162, 165, 168, 196, 344, 425, 426-431 glycoside, 135 Gomphonema, 90 gonorrhea, 98 gradient bacteria, 318 Gram-negative organisms, 129, 131, 133, 134, 135, 139, 141, 143, 145, 146, 148, 171, 202, 237, 238, 278 gram-negative rods, 129, 131, 132, 143, 158, 162, 171, 179, 132, 139, 147, 217, 226, 278, 300 Gram-positive cocci / organisms, 45, 129, 131, 132, 133, 139, 141, 142, 143, 145, 146, 148, 217, 222, 237-238, 263, 264 flowcharts, 286, 287 identification of, 284-288 (exercise) gram-positive rods, identification of, 289-294 (exercise) Gram stain, 95, 100, 105-109 (exercise), 128, 280, 300, 301, 318, 332, 473 granulocytes, 374, 376 graphs, in data presentation, 7-9 green algae, 81, 86, 87 Green Fluorescent Protein (GFP), 354, 355, 356 green sulfur bacteria, 315, 316, 322 Griffith, Fred, 354 growth anaerobic, 52 bacterial, 50, 51 filamentous, 39 filiform, 44 flocculent, 45 media, 14 patterns / characteristics, 33 swarming pattern, 40 growth patterns in broth, 45 (exercise) growth patterns on slants, 44 (exercise) growth patterns in Thioglycollate medium, 51 guanidine, 161, 162 Gyrosigma, 89 Hafnia alvei, 238 Halobacterium broth, 59 hand washing, 12-13 hanging drop preparations, 122, 123 (exercise) HCG (in pregnancy tests), 389 health hazards, heat-fixing, 100, 101, 115 Hektoen Enteric (HE) Agar, 139, 145-146 (exercise), 463 Heliozoans, 92 helminths, parasitic, 416-424 (exercise) hemacytometer, 76 hemagglutination, 377, 384, 387-388 (exercise) hematology, 373 hemoglobin, 217 hemolysis of RBCs, 41, 217, 218 heterocysts, 84, 85, 302 heterotroph / heterotrophy, 46, 81, 86, 91, 296, 398 heterotrophic catabolism, 300 histidine, 367 homeostasis, 130 hookworms, 422, 423, 424 See also worms horseradish peroxidase, 389 hosts, bacterial, 255, 418 See also parasites Hugh and Leifson’s O-F medium, 155, 157 human infections See infections Hydrodictyon, 87 hydrogen peroxide, 165, 166 hydrogen phosphate, 57 hydrogen sulfide (H2S), 145, 146, 165, 202-203, 206, 209, 296, 318 hydrolysis See also DNA hydrolysis test; lipid hydrolysis test; starch hydrolysis of antibiotics, 355 casein, 211 of disaccharides, 158 enzymes for, 184 of esculin, 135 of gelatin, 192 of lactose, 198 urea, 187 Hymenolepis (Vampirolepsis) nana, 418, 419420, 424 hyphae, 398, 399, 401, 402, 403 IgM immunoglobins, 387 illnesses See diseases immune system and response, 373, 376, 389, 412 immunodiffusion tests, 380 See also radial immunodiffusion immunoglobin antibody, 389 IMViC test battery, 162, 176, 203, 278, 280281 incidence rate, 274, 276 incineration, 17 incubation, 62 See also autoclaves in DNA hydrolysis test, 194 in gelatin hydrolysis, 192 in LIA tests, 209 in TSIA test, 206 in urea hydrolysis, 187 indicator(s), 130-131, 147 See also pH indicators bile esculin test, 135 coliforms as, 332 dyes, 150, 161 reaction, 373 sulfur reduction, 209 indole production tests, 202-204 infection(s) See also diseases; parasites; pathogens; worms; specific infectious diseases amoebic, 409 Aspergillus, 403 bacteriophage, 345 candida, 400 diagnosing, 377 hookworm, 422 mononucleosis hemagglutination test, 387-388 parasitic, 374, 416, 417, 422 plasmodium, 413 toxoplasma, 414 inhibitors, 130 inoculation methods See also cotton applicators; pipettes; spot inoculation; spread plate method; stab inoculation; streak plate methods for broth tubes, 22, 439 and instruments, 17 loops / needles, 18, 20-21, 22, 408 tube, 229 using quadrant streak, 25-26, 27, 28 with a turntable, 30 zigzag, 27, 55 insecticides, 121 InstaStain®, 457-458 (appendix) invertebrates, 93 iodine, 184, 184 iron, 206 isolation, streak plate methods, 25-28 (exercise), 129, 139, 142, 143, 145 Isopora, 111 707-772 Data Sheets 9-12,Gloss,Index 4/10/12 7:53 AM Page 769 INDEX jellyfish, 354 karyosome, 410 keratin, 117 Key Scientific Projects, 199 Kinyoun (K) method, 110, 111, 113, 114 Kirby-Bauer method, 268-271 (exercise) Klebsiella, 133, 142 Klebsiella pneumoniae, 37, 115, 126,127, 204, 213, 224, 278, 332 Kligler Iron Agar (KIA), 198-199, 202, 206-208 (exercise), 463 Kocuria, 285 Kocuria rosea, 42, 44, 238 KOH reagent, 235 Kovacs’ reagent, 202-205, 229, 235 Krebs cycle, 151, 155, 165, 175, 177, 196, 428, 430, 431 lab, microbiology equipment, safety, 3-5, 61 sterilizing temperatures in, 61 lactate, 322, 344 Lactobacilli, 264, 290 Lactobacillus delbrueckii subsp bulgaricus, 344 Lactobacillus plantarum, 44, 45, 57, 238 Lactococcus lactis, 47, 57, 96, 126, 127, 136, 213, 238 lactose substrate / fermenter, 129, 139, 150, 159, 202, 332, 344 See also fermentation hydrolysis, 212 tests for, 139-141, 142-144, 145-147, 158160, 198-199, 202-205, 206-207, 211 lactose hydrolysis, 212 lake water See pond water; water Lambda DNA, 350 Lauryl Tryptose Broth (LTB), 336, 338, 463 leghemoglobin, 301 legumes, 299, 300, 301, 302 Leishmania donovani, 81 leukocytes, 374, 375 LH (in ovulation tests), 389 light microscope, 95, 70-75 (exercise) lipases / lipase test, 196, 197 See also lipid hydrolysis test lipid / lipid catabolism, 196, 428 lipid hydrolysis test, 196-197 (exercise) liquefaction, 192 lithotrophs, 296 Litmus Milk Medium, 211-213 (exercise), 463 Lophotrichous flagella, 124 Löwenstein-Jensen media, 290 L-pyrrolidonyl arylamidase, 200 luciferase, 324 lung fluke, 416 Luria-Bertani Broth / Agar, 347, 463 lymphatic filariasis, 423 lymphocytes, 374, 375, 376 Lyngbya, 84 lysine deaminase, 209 lysine decarboxylation, 139, 147, 180, 209 Lysin Iron Agar (LIA), 209-210 (exercise), 464 lysozyme assay, 266-267 (exercise) Lysozyme buffer and substrate, 471 lytic cycle, 255 MacConkey Agar, 139-141 (exercise), 202, 226, 279, 464 macrofungi, 398, 399 macronucleus, 91 macrophages, 375 malachite green, 117, 118, 120, 474 malaria, 414 Malonate Broth, 175, 177, 178, 464 Maneval’s Stain, 473 malonate test, 177-178 (exercise) Mannitol Salt Agar, 131, 137-138 (exercise), 464 Mastigophora, 409 McFarland turbidity standard, 268, 270, 472 media, 11, 130 See also culture(s); differential tests / media; selective media complex, 12 EMB, 142 evaluation of, 46-47 (exercise) tubed, 16, 48 undefined, 130 meiosis, 88, 398, 400, 401, 402 m Endo Agar LES, 333 membrane filter technique, 295, 332-335 (exercise), 332, 333, 335 membrane permeability / integrity, 131, 133 Merismopedia, 85 merozoites, 414 mesophiles, 54 metabolic pathway, 354 metabolism / metabolic reaction, 48, 150, 151, 152, 192, 344 of carbohydrates, 155 energy, 425, 426 in nitrogen cycle, 299 pyruvate in, 428 methionine, 321 methylation, 350 methylene blue reductase reagent, 472 methylene blue reductase test, 342-343 (exercise) methylene blue stain and counterstain, 52, 100, 110, 111, 143, 144, 342, 398, 473 methyl green dye, 194 methyl red test, 158, 161, 162, 163, 164 (exercise) Micobacteriuom phlei, 44, 126, 127 microaerophiles, 48, 50, 51, 168, 296 microbes environmental, 295 eukaryotic, 79-83 (exercise), 397 in experiment, 6, 11, 14, 84 safe handling and disposal, soil, 326 microbial death, 259 microbial growth direct counts of, 250-251 environmental factors affecting, 33, 46 germicides and, 66 osmotic pressure effects on, 58-59 (exercise) phases, 252 pH effect on, 56-57 (exercise) temperature effect on, 54-55 (exercise) ultraviolet radiation effect on, 64-65 (exercise) microbiologists, clinical, environmental, industrial, medical, 129, 263, 296, 312 Micrococcacae, 166, 214 Micrococcus luteus, 23-24, 42, 44, 45, 101, 126, 127, 215, 238 Micrococcus lysodeikticus, 266 Micrococcus roseus, 42, 98, 107 Microcystis, 85 microgradient tubes, 318, 319, 464 micrograph, 71, 400 micrometers, 76, 77 See also ocular micrometer; stage micrometer microorganisms, 33 eukaryotic, 82, 397, 409 food, 341 halophilic, 59 salinities of, 58 ubiquity of, 34-35 (exercise) in water, 84, 297 micropipettes, digital, 243, 258 microscopy, 69, 71 See also light microscope fluorescence, 71, 73 769 Milk Agar, 184, 465, 468 milk test, 342-343 mineral oil, adding, 154, 155, 179, 180 minimum inhibitory concentration (MIC), 214, 268 mitochondria, 86 mitochondrial ETC, 169 mitosis, 409 mixed acid fermentation, 158, 161, 162 mixotrophs, 86 Mohr pipette, 437 molds, 81, 268, 398-405 (exercise) bread, 399, 401 Møller’s Decarboxylase Base Medium, 179, 180, 181, 461 monocytes, 374, 375, 376 mononucleosis, infectious, 377, 387 mononucleosis hemagglutination test, 387-388 (exercise) monosaccharides, 158, 159, 211 Moraxella, 155 Moraxella catarrhalis, 47, 101, 108, 126, 127, 170, 194, 238 Morbidity and Mortality Weekly Report (MMWR), 263, 274-275 (exercise) morbidity rate, 274 mordant, 124 Morganella, 182, 187 Morganella morganii, 204, 207, 238 morphological unknown, 126-128 (exercise) morphology, cell, 95 mortality rate, 274 mosquito infections, 414, 423 most probable number (MPN), 336 motility, 122, 125 agar, 217 bacterial, 224 in SIM, 202, 203, 204 motility test, 224-225 (exercise) Motility Test Medium, 465 MPN calculations, 336 MRSA, 268 MR-VP broth, 158, 164, 465 MR-VP Test Reagents, 471 mud culture, 297, 319 See also aquatic Mueller-Hinton agar, 268, 269, 270, 465 Mullis, Kary, 359 multiple test systems, 226 multiple tube fermentation method, 295, 336-340 (exercise) mushrooms, 398, 399 mutation / mutagens, 345, 367 mycelium 398, 400, 406, 408 Mycobacterium, 166 Mycobacterium kansasii, 71 Mycobacterium phlei, 110, 111 Mycobacterium smegmatis, 39, 44, 45, 111, 238 Mycobacterium tuberculosis, 45, 290 mycolic acids, 110 NAD and NADH, 168, 169, 196, 425-432 (appendix) nalidixic acid, 133, 134 nasal swab, cocci from, 96 National Committee for Clinical Laboratory Standards (NCCLS), 214 natural killer (NK) cells, 375 Navicula, 90 Necator americanus, 422, 423, 424 negative stains, 103-104 (exercise) Neisseria, 168, 184, 194, 197 Neisseria sicca, 238 nematode worm, 93, 416, 421 neutrophils / neutrophiles, 56, 374, 376 nigrosin stain, 103, 115 nitrate, 165, 172, 305, 306, 310, 311 707-772 Data Sheets 9-12,Gloss,Index 4/10/12 7:53 AM Page 770 770 MICROBIOLOGY: LABORATORY THEORY Nitrate Broth, 171, 172, 173, 310, 311, 465 nitrate reductase / reduction, 171, 300, 310 nitrate reduction test, 165, 171-174 (exercise) nitrate test reagents, 472 nitrification, 300, 305-307 (exercise) nitrite, 165, 171, 172, 305 test for, 306, 307 nitrogenase enzyme, 299 nitrogen cycle, 296, 299 nitrogen fixation (N-fixation), 300-304 (exercise) Nitrogen Free Broth, 302, 302, 465 nitrogen gas, 165 Nitrosomonas, 305 nitrous acid, 171, 172 Nitzschia, 89 Nocardia, 110 Nostoc, 85, 299 Novobiocin test, 214-216 (exercise) nucleotides, 364 nutrient(s) essential, 187 utilization tests, 175 Nutrient Agar plates and tubes, 15, 16, 53, 131-132, 133-134, 140, 143, 256, 329, 330, 465-466 Nutrient Broth, 466 nutrient broth and nutrient agar preparation, 14-16 (exercise) Nutrient Gelatin, 184, 192, 193, 466 nutritional components of media, 130 obligate aerobes and anaerobes, 206, 289, 296, 313, 318 OCD, 248, 250-251 ocular micrometer, calibration of, 76-78 (exercise) Oedogonium, 86 O-F Basal Medium, 466 O-F Carbohydrate Solution, 466 oil immersion lens, 77 ONPG test, 198-199 (exercise) oocysts, 111, 414 oogonia, 86 operons, 354, 355 opportunists, 278 Optochin test, 214-216 (exercise) organotrophs, 296 Oriental liver fluke, 416 original cell density (OCD), 248, 250, 331 ornithine decarboxylation, 180 Oscillatoria, 84, 85 osmotic pressure / balance effect on microbial growth, 58-59 equilibrium, 130 in PCR, 359 oxaloacetate, 175 oxidase test, 165, 168-170 (exercise) oxidase test reagent, 472 oxidation of acetoin, 162 ammonia, 305, 306, 307 glucose, 425 sulfur, 313 Oxidation-Fermentation (O-F) Test, 155-157 (exercise) oxidation of pyruvate, 428 oxidation-reduction reactions, 151, 152 oxidative deamination , 300 phosphorylation, 151, 165 oxygen See aerotolerance oxygen gradient, 296 palindromes, 350 palisades cell arrangement, 99 palladium, 52 AND APPLICATION paragonimiasis, 416 Paragonimus westermani, 416-417, 424 Paramecium, 91 Paramecium bursaria, 81 parasites, 81 animal, 417 cestode, 417-418 coccidian, 111 fungi as, 398 helminths, 397, 416-424 (exercise) nematode, 421 and parasitic infections, 374, 417, 422 plasmodia as, 412 trematode, 416-417 worms as, 416, 422 parasporal crystal stain, 121 (exercise) Pasteur pipettes, 17 pathogens, 34, 139, 409 bacterial, 110, 117-118 control of, 60 enteric, 278 opportunistic, 38, 97, 99, 222, 403 pathways, biochemical, 425-432 (appendix) PBS solutions, 472 wash, 392-393 PCR See polymerase chain reaction Pea family, 300 Pediastrum, 87 pellicle, 45, 302 penicillin, 270, 271, 355 Penicillium, 329, 403, 405, 404-405, 406 Penicillum camembertii, 403 Penicillium marneffei, 403 Penicillium notatum, 268, 404 Penicillium roquefortii, 403 pentose-phosphate pathway / cycle, 425, 428, 429 pepsin, 212 peptides, 190, 194, 270 peptidoglycan, 266, 270 peptone, 142, 158, 161, 179, 206, 209 Peptone Broth / Peptone Water, 308, 466 Peritrichous flagella, 124 peroxidase, 389 Petri dishes, 5, 26 Petroff-Hausser, 250-251 (exercise) PFU (plaque forming unit), 257 pGLOTM system, 354-358 (exercise) pH See also pH indicators affecting microbial growth, 33, 56-57 (exercise) calculation of, 56 meter, 11 scale, 56 phage lytic cycle, 255 typing of E-coli strains, 371-372 (exercise) phagocytosis, 222, 374, 376 phase contrast photomicrograph, 322 Phenol red, 137, 147, 187, 206 Phenol Red Broth, 158-160 (exercise), 466 phenylalanine / phenylalanine agar, 179, 182, 183, 466 phenylalanine deaminase test, 182-183 (exercise), 472 phenylenediamine reagent, 169 Phenylethyl Alcohol Agar (PEA), 131-132 (exercise), 467 phenylpyruvic acid, 182 phialides, 402, 403 pH indicators, 62, 130-131, 137, 139, 145, 147, 150, 151, 155, 184, 187, 206, 211, 264 phosphate buffered saline See PBS wash phosphorylation, 165 Photobacterium, 324 Photobacterium Broth, 467 photolysis, 302 photoreactivation, 364 photosynthesis, 313, 314 photosystems, 315, 316 photosynthetic sulfur bacteria, 315-317 (exercise) phototaxis, 86 phototrophs / photoautrotrophs / photoheterotrophs, 296, 297, 312, 313, 314, 367 phylogenetic tree, 79, 80 pigment production, 43 pinworm, 422 See also worm pipette / pipetting, 5, 17 digital, transfer using, 441-444 (appendix) glass, transfer using, 437-440 (appendix) planktonic microorganisms, 272 Plantae kingdom, 79 plaque assay of virus titre, 255-258 (exercise) alternative procedure, 450, 452 (appendix) plasma cell, 375 plasmid for GFP, 355, 356 Plasmodium, 412-414, 415 Plasmodium falciparum, 412-414 plasmolysis, 58 plate counts, 243, 244-247 (exercise) pleomorphism, 95, 97 pneumococcus, 354 pneumonia, Ascaris, 421 pollutants See fecal contamination polymerase chain reaction (PCR), 359-362 (exercise) polymorphonuclear neutrophils (PMNs), 374 polypeptides, 115 polysaccharides, 115, 184, 272 pond water, microscopic examination of, 84-94, 313, 322 See also aquatic population density (microbial), 243, 246 Potato Dextrose Agar, 404, 467 pour-plate technique, 256 precipitate / precipitation reactions / patterns, 373, 377, 378, 380 precipitin ring test, 377-379 (exercise) prevalence rate, 276 PR glucose broth, 160 See also Phenol Red Broth progametangia, 401, 402 prokaryotes, 58, 79, 82, 354, 425 Prosthecochloris, 315 protease, 346 proteins bacteria requiring, 190 breaking down, 150 hemolytic, 220 iron-sulfur, 168 Proteus, 106, 131, 133, 142, 182, 187, 188, 192, 204 Proteus mirabilis, 44, 45, 153, 210, 238, 278 Proteus vulgaris, 40, 124, 125, 159, 180, 182, 199 prothrombin, 222 Protista kingdom, 79, 80, 84 protists, 84, 86, 91, 92 protoscolex, 419 prototrophs, 367 protozoans, 79, 81, 397, 409-415 (exercise) amoeboid, 409-410 ciliate, 410-411 flagellate, 411-412 sporozoan, 412-415 Providencia, 139, 147, 148, 182, 187 Providencia rettgeri, 204 Providencia stuartii, 37, 147 pseudohyphae, 400 Pseudomonadaceae, 168 Pseudomonas, 133 707-772 Data Sheets 9-12,Gloss,Index 4/10/12 7:53 AM Page 771 INDEX Pseudomonas aeruginosa, 40, 43, 44, 66, 155, 157, 159, 173, 207, 213, 238 pseudopods / pseudopodia, 80, 92 psychrophiles and psychrotrophs, 54 puffballs, 398 purine, 299 Purple Broth, 467 purple sulfur bacteria, 315, 317 putrefaction of cysteine, 202 putrescine, 180 pyrenoids, 87 pyrimidine dimers, 364 nucleotides, 299 PYR test, 200-201 (exercise) pyruvate, 151, 155, 158, 161, 168, 175, 202, 204, 316, 344 oxidation of, 425, 428 (appendix) quadrant streak method, 25-26, 27, 28 qualitative procedure, 326 quantitative indirect ELISA, 389-395 (exercise) quantitative techniques / analysis, 243, 330, 377, 445-447 quorum sensing, 324 radial immunodiffusion, 377, 380-381 (exercise) radiation See ultraviolet radiation raphe, 88, 89 rapid disc test, 200 reactions, positive and negative, 131 reagents, 471 recognition sites (DNA), 350 red blood cells (RBCs), 217-218, 374, 377 clumping, 387 merozoites in, 414 redox reaction / pair, 152-153 reduced sulfur compounds, 317, 318 reduction potential, 152-154 (exercise) rennin, 212 reproduction See asexual reproduction; sexual reproduction reservoir, definition, 34 resistance mechanisms, 270 respiration aerobic and anaerobic, 48, 151, 153, 154, 171, 299, 310, 321, 322 tests identifying microbial ability, 165 restriction digest, 350-353 (exercise) reverse citric acid cycle, 315, 316 reverse electron flow, 315, 317 reversion, 206 Rh factor, 384, 385, 386 Rhizobium, 299, 300, 300, 301, 302 rhizoids, 400, 401 Rhizopus, 399, 400-402, 404 Rhizopus arrhizus, 401 Rhizopus oryzae, 401 Rhizopus stolonifer, 401 Rhodospirillum rubrum, 101, 103, 126, 127 Rivularia, 85 RNA polymerase, 354, 355 Rose Bengal Stain, 326, 327, 473 Rotifer, 93 roundworms See nematode worm rubella virus, 389 Rustigian and Stuart’s Broth, 188 Ryu stain, 125 Sabouraud Dextrose Agar, 329, 403, 404, 406, 407, 467 Saccharomyces cerevisiae, 82, 398, 400, 404 safety chemical, lab equipment, 1, rules, 3-5 of sterilizers, 61 safranin dye, 100, 117 salicin, 145 Saline Agar and saline agar plate, 381, 467 salinities, 58 Salmonella, 139, 142, 145, 161, 204, 209, 367, 368, 377 Salmonella enterica, 66 Salmonella H and O antigens, 382-383 Salmonella typhimurium, 140, 142, 146, 147, 180, 204, 207, 210, 278, 367, 368 Salt Agar, 468 salterns, 59 saprophytes, 81, 117, 289, 290, 329, 398 sarcina / sarcinae, 95, 98 Sarcodina, 409 Sarcomastigophora Phylum, 79, 409 Scenedesmus, 87 Schaeffer-Fulton method, 117, 119 Schistosoma mansoni, 417, 424 Seawater Agar, 468 Seawater Complete Medium (SWC), 324 sediment, 45 selective media, 129, 130-131 antibiotic, 345, 354 combination media to promote isolation, 202 for isolation of gram-negative rods, 139 for isolation of gram-positive cocci, 131 Sheep Blood Agar as, 133 SLD as, 147 semipermeable membrane, 58 septicemia, 423 Seradyn Color Slide II Mononucleosis Test, 387 serial dilution, 243, 244-245, 330, 450 (appendix) in ELISA test, 391 serology / serological reactions / tests, 373, 377, 384 Serratia, 192, 194 Serratia marcescens, 25, 30-31, 42, 43, 44, 55, 276, 277 sexual reproduction, 88, 401 sharps container, 4, 5-6 sheep blood / Sheep Blood Agar, 133, 215, 217, 218, 248 Shigella, 139, 145, 147, 148, 161, 209 Shigella dysenteriae, 278 Shigella flexneri, 126, 127, 146 SIM medium, 202, 468 Simmons Citrate Medium / Agar / slants, 175, 176 See also Citrate Agar simple stains, 100-102 (exercise), 474 skim milk agar, 191, 465 slants agar, 44 growth patterns on, 44 (exercise) inoculation of, 22 LIA, 210 pigment production on, 44 sleeping sickness, 412 slide agglutination, 377, 382-383 (exercise) smears, direct, 106 Snyder Test, 264-265 (exercise), 468 (medium) sodium chloride (NaCl), 131, 137, 138 sodium citrate, 175 Sodium Dodecyl Sulfate (SDS), 347 sodium ion concentration, 58 sodium thiosulfate, 145, 153, 202, 206, 209 soil microbial count, 295, 329-331 (exercise) soil samples, morphological diversity in, 41 soil slide culture, 326-328 (exercise) solute concentration, 58 Sørensen, Søren Peter Lauritz, 56 spectrophotometer, 253, 254, 266, 267, 346, 349, 445-447 (appendix) spirilla, 95, 97 Spirochete, 97 771 Spirogyra, 81, 88 Spirulina, 85 Spirilum volutans, 124 sporangia / sporangiospores / sporozoites, 398, 400-401, 402, 403, 404, 406, 414 spores bacillus, 289 bacterial, 61, 62, 117 See also endospore stain fungal, 398, 401 microbial, temperatures affecting, 259 stain, 293, 474 sporozoan protozoans, 412-415 sporulation and sporulation agar, 117, 291, 468 spot inoculation, 53, 129, 131, 132, 133, 139, 142, 143, 147, 195 of agar plate, 435 (appendix) spread plate method of isolation, 29-31 (exercise), 246, 260, 453-454 (appendix) See also inoculation stab inoculation, 155, 157, 192, 203, 204, 206, 209, 224-225, 318, 319 using inoculating needle, 434 (appendix) stage micrometer, 76, 77 staining / stains, 69, 95, 100 See also acid-fast stains; Gram stain; simple stains; structural stains acidic, 103 basic, 100 differential and structural, 105 precipitate, 107 simple, 474 standard plate count, 244-247 (exercise), 330 alternative, 449 450 (exercise) Staphylococcus, 98, 106, 107, 131, 138, 139, 194, 197, 214 Staphyhloccus aureus, 41, 45, 49, 50, 52, 59, 66, 67, 99 antibiotics, susceptibility to, 269, 270 biofilms, 272, 273 in differential tests, 192, 194, 195, 215, 220, 222, 223 quantitative techniques using, 238, 260 in MRSA, 268 in selective media, 131, 137, 138 Staphylococcus epidermidis, 37, 44, 47, 101, 108, 110, 111, 122, 125, 126, 127 in forming biofilms, 272 in selective media, 137 in differential tests, 166, 192, 195, 200, 215, 217, 223, 238 Staphyloccus saprophyticus, 214, 215 Starch Agar and starch agar plate, 184, 185, 186,468 starch hydrolysis, 184-186 (exercise) steam sterilization, 61-63 (exercise) Stentor, 91 sterilization, 18, 60 steam, 61-63 (exercise) Stomatococcus, 214 streak pattern on nutrient agar, 35 streak plate methods of isolation, 25-28 (exercise), 129, 138, 248 streak-stab technique, 218 streptobacillus arrangement, 95 Streptococcus / Streptococcacae, 45, 98, 99, 131, 133, 136, 166, 200, 217, 218, 248, 284 gram-positive, 284 oral, 264 Streptococcus agalactiae, 216, 220, 221, 284 Streptococcus bovis, 135 Streptococcus pneumoniae, 115, 215, 216, 217 Streptococcus pyogenes, 214, 285 Streptococcus thermophilus, 344 Streptomyces, 329 Streptomyces niveus, 214 707-772 Data Sheets 9-12,Gloss,Index 4/10/12 7:53 AM Page 772 772 MICROBIOLOGY: LABORATORY THEORY Strongyloides stercoralis, 423, 424 structural stains, 105 substrate(s), 130 substrate level phosphorylation, 151, 425 succinate / succinate dehydrogenase, 177 sucrose fermentation, 142, 145, 147, 159, 206 sugar arabinose, 354 sulfate, 165, 322 sulfide, 314, 321 sulfur bacteria reactions, 314 cycle, 313-314 oxidizer, 318, 320 photosynthetic, 315-317 (exercise) reduction / reducers, 202-203, 206, 207, 209, 317, 322 transformations, 314 sulfur microorganisms/ organisms / compounds, 296, 313 sulfur-oxidizing bacteria, 318-320 (exercise) sulfur-reducing bacteria (SRB), 321-323 (exercise) superoxide dismutase, 165 surface-to-volume ratio (cell), 95 symbionts, 300 Synedra, 90 syntrophic, communities, 313 syphilis, 97 Tabellaria, 89 tables, in data presentation, Taenia, 420, 424 Taenia saginata, 420 Taenia solium, 420, 421, 424 TaqDNA polymerase, 360 tapeworms, 416, 418, 420 See also worms T-cells, 375, 376 TDT curves, 260 temperatures cardinal, 54 sterilizing, 61 temperature effect on microbial growth, 54-55 (exercise) See also thermal death time terminal electron acceptor, 168 See also final electron acceptor tetanus, 118, 289 tetrads, 95 thermal death time (TDT), 259-262 (exercise) alternative procedure, 452-454 (appendix) Thermodynamics, Law of, 152 thermophiles, 54, 360 Thermus aquaticus, 360 Thiobacillus, 318, 319 Thioglycollate medium / broth, 50, 51, 291, 469 Thiopedia, 315 Thioplaca, 318 Thiospirillum, 315 thiosulfate / thiosiulfate reductase, 153, 202, 203, 206, 209, 318 Thiothrix, 318, 319 threadworm, 423 threonine, 344 throat cultures, 41 thymine dimers, 364 Thiobacillus Medium (modified), 469 Todd-Hewitt Broth, 45, 285, 288 AND APPLICATION tooth decay See dental decay Toxoplasma gondii, 414, 415 Trachelocerca, 91 transfer techniques / methods, 17, 20-23, 433435 (appendix) See also aseptic transfers transformation See bacterial transformation transketolase and transaldolase, 428 trematode parasites, 416-417 Treponema, 103 Treponema pallidum, 97 triacylglycerol, 196 tributyrin / Tributyrin Agar, 184, 196, 197, 469 tricarboxylic acid cycle, 151 trichomes, 84, 85 Trichomonas hominis, 412 Trichomonas tenax, 412 Trichomonas vaginalis, 411-412, 415 trichomoniasis, 411 triglycerides / triacylglycerols, 196 trimethoprim, 270, 271 Triple Sugar Iron Agar (TSIA), 206-108 (exercise), 209, 470 Tris-Acetate-EDTA buffer, 472 trophic groups, 312 levels, 326 trophozoites, 79, 409, 409, 410, 411, 414 trypanosomes, 412 Trypanosoma spp / Trypanosoma brucei, 412, 415 Tryptic Nitrate Medium, 470 Trypticase Soy Agar (TSA), 27-28, 48, 118, 126, 217, 291, 470 Tryptic Soy Broth / Agar, 272, 470 tryptophan / tryptophanase, 202, 203, 204 tsetse fly, 412 TTC (tetrazolium salt), 224 tuberculosis, 111 tubes Desulfovibrio, 323 inoculating, 22-23 LTB, BGLB and EC, 338 microgradient, 318, 319-320 turbidity, 45, 47, 59, 66, 266, 268, 322, 445 turgor / turgor pressure, 58 ubiquity of microorganisms, 34-35 (exercise) Ulothrix, 87 ultrasound for diagnosis, 418 ultraviolet (UV) radiation of bands formed by DNA fragments, 360 damage and repair, 364-366 (exercise) effect on bacteria, 345 effect on microbial growth, 64-65 (exercise) spectrophotometer, 346, 349 undecaprenyl phosphate, 214 undefined media, 130, 133 urea / Urea broth, 180, 187, 188 Urea Agar and Urease Agar test, 184, 187, 188 urea hydrolysis, 187-189 (exercise) Urease Agar, 470 Urease Broth, 471 urine culture, 248-249 (exercise) Use-Dilution Test, 66 utilization media, 175 UV See ultraviolet vacuoles, 88, 90, 92 vector, definition, 355 ventilation systems, viable count, 244-247 (exercise), 449-450 (appendix) Vibrio fischeri, 324 Vibrio harveyi, 101 Vibrio natriegens, 97, 253, 254 viral DNA, 255 viruses bacteria-infecting, 371 rubella, 389 virus titre, plaque assay of, 155-258 (exercise), 450-452 (appendix) Vogel-Bonner Salts, 474 Voges-Proskauer (VP), 158, 161, 162, 163, 164 (exercise) Volvox, 81, 86 vortex mixer, 20, 320, 322, 323 Vorticella, 90 VP broth, 162 waste management, control and disposal, 3, 61 water, 58 See also aquatic organisms; pond water contaminated, 276 fresh, 313 pH of, 56 wavelengths, 64, 72, 349, 364, 445 wet mounts, 82, 83, 122-123 (exercise) white blood cells (WBCs), 374, 375, 387 Winogradsky, Sergei, 296 Winogradsky column, 295, 296-298 (exercise), 315, 316 Wolfe’s Mineral Solution and Wolfe’s Vitamin Solution, 469 World Health Organization (WHO), 60 worms, 397 See also helminths parasitic, 416, 418, 421 Wright’s stain, 374, 375 Wuchereria, bancrofti, 423-424 X-ray for diagnosis, 418 Xylose Lysine Desoxycholate (XLD) Agar, 139, 147-148, 471 yeasts, 79, 81, 82, 398-405 (exercise) yeast extract, 48, 130, 133, 145, 177, 190, 209, 322, 347, 470 Yeast Extract Broth, 471 Yersinia pestis, 278 yogurt, making, 344 (exercise) Ziehl-Neelsen (ZN) method / stain, 110, 111-112, 113, 472 zigzag inoculation / pattern, 27, 55, 248 zinc, 172, 173 zone of clearing and no clearing, 371 zone of inhibition, 214, 268, 367, 368 Zygomycetes, 398 zygosporangia, 404 zygospores, 398, 401, 402 zygote(s), 81, 88, 398, 401, 414 ... cosmetics or handle contact lenses in the laboratory ✦ Wash your hands thoroughly with soap and water after handling living microbes and before leaving the laboratory each day Also, wash your hands after... 8/31/11 3:29 PM Page 12 12 MICROBIOLOGY: LABORATORY THEORY EXERCISE 1-1 AND APPLICATION Glo Germ™ Hand Wash Education System ✦ Theory ✦ In This Exercise The concept of good hand hygiene has evolved... Germicides: Disinfectants and Antiseptics 66 vii i-xii Front Matter 8/31/11 3:27 PM Page viii VIII MICROBIOLOGY: LABORATORY THEORY SECTION AND APPLICATION Microscopy and Staining