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Encyclopedia of Microbiology Anne Maczulak, Ph.D Foreword By Robert H Ruskin, Ph.D ENCYCLOPEDIA OF MICROBIOLOGY Copyright © 2011 by Anne Maczulak, Ph.D All rights reserved No part of this book may be reproduced or utilized in any form or by any means, electronic or mechanical, including photocopying, recording, or by any information storage or retrieval systems, without permission in writing from the publisher For information contact: Facts On File, Inc An imprint of Infobase Learning 132 West 31st Street New York NY 10001 Library of Congress Cataloging-in-Publication Data Maczulak, Anne E (Anne Elizabeth), 1954–â•… Encyclopedia of microbiology / author, Anne Maczulak; foreword, Robert H Ruskin p cm Includes bibliographical references and index ISBN 978-0-8160-7364-1 (alk paper) ISBN 978-1-4381-3406-2 (e-book) Microbiology—Encyclopedias I Title [DNLM: Microbiology—Encyclopedias— English QW 13 M177e2011] QR9.M33 2011 579.03—dc22 2010004551 Facts On File books are available at special discount when purchased in bulk quantities for businesses, associations, institutions, or sales promotions Please call our Special Sales Department in New York at (212) 967-8800 or (800) 322-8755 You can find Facts On File on the World Wide Web at http://www.infobaselearning.com Excerpts included herewith have been reprinted by permission of the copyright holders; the author has made every effort to contact copyright holders The publishers will be glad to rectify, in future editions, any errors or omissions brought to their notice Text design by Cathy Rincon Composition by A Good Thing, Inc Photo research by Elizabeth H Oakes Cover printed by Sheridan Books, Inc., Ann Arbor, Mich Book printed and bound by Sheridan Books, Inc., Ann Arbor, Mich Date printed: April 2011 Printed in the United States of America 10 This book is printed on acid-free paper Contents Foreword vii Acknowledgments ix Introduction xi Entries A–Z Feature Essays: “Antibiotics and Meat” by Wanda C Manhanke 48 “Where Are Germs Found?” by Anne Maczulak, Ph.D 66 “Realities of Bioterrorism” by Richard E Danielson, Ph.D 131 “Does Immigration Lead to Increased Incidence of Disease?” by Anne Maczulak, Ph.D 273 “Sanitation in Restaurants” by Anne Maczulak, Ph.D 314 “Why AIDS Is Not Going Away” by Carlos Enriquez, Ph.D 398 “Will Global Warming Influence Emerging Infectious Diseases?” by Kelly A Reynolds, Ph.D 443 “Microbes Meeting the Need for New Energy Sources” by Anne Maczulak, Ph.D 522 “The Day Care Dilemma” by Anne Maczulak, Ph.D 608 “Bioengineered Microbes in the Environment” by Anne Maczulak, Ph.D 665 “Do Disinfectants Cause Antibiotic Resistance?” by Nokhbeh M Reza, Susan Springthorpe, and Syed A Sattar, Ph.D 676 “How Safe Is Air Travel?” by Philip M Tierno, Jr., Ph.D 766 “Does Vaccination Improve or Endanger Our Health?” by Anne Maczulak, Ph.D 773 Appendixes: I Chronology 804 II Glossary 806 III Further Resources 810 IV Proposed Hierarchy of Biota 812 V Classification of Bacteria and Archaea 813 VI Viruses of Animals and Plants 826 VII Major Human Diseases Caused by Microorganisms 830 Index 833 Foreword Recently, we have been besieged every day, via every available medium—television, newspapers, radio, the Internet, Twitter, and so on—with reports about the swine flu and H1N1 virus People are asking themselves questions such as What exactly is a global pandemic? Why are people dying? What can I to protect myself and my family from this virus? What is a vaccine? How are vaccines made? What is the difference between swine flu and annual flu? There is a lot of misinformation concerning the current pandemic What is the difference between a bacterial infection and a viral infection? Among young adults in both high school and junior college there seems to be genuine fascination about the general subject of microbiology and the concept of disease To be sure, much of this interest is due to the current outbreak of swine flu For some, fear is driving their interest; for others, they have been assigned a paper on some topic pertaining to microbiology; and for still others, they are asking themselves about what types of careers are available in microbiology Most people would be astounded to learn of the diverse fields in science supported by microbiology A partial list would include environmental science, marine science, food science, manufacturing, mining, and, of course, both medical and public health sciences, to name a few Microbiologists are hired both by public (state and federal institutions) and private companies The degree and type of education required to work in these fields vary from a high school diploma (with the supervision of a microbiologist) to a Ph.D In general, however, a four-year university degree in chemistry, biology, or the like, includes at least one full year of microbiology course work Encyclopedia of Microbiology is an excellent reference by Dr Anne Maczulak, whose doctorate is in microbiology and animal nutrition and who is the author of numerous books and professional papers on environmental microbiology and environmental science, including the enjoyable The Five Second Rule and Other Myths about Germs In Encyclopedia of Microbiology, Dr Maczulak addresses many of the questions students considering careers in this field might have The encyclopedia is also a wonderful resource for the general public who may simply be interested in the world of microorganisms Arranged as a collection of literate entries, the encyclopedia is enhanced by 13 essays on topics relevant to today’s microbiology—for example, global warming and emerging infectious diseases, antibiotics in our meat supply, the microbial hazards of air travel, and bioengineered microorganisms in the environment The more than 200 entries have also been selected to cover the most recent advances and focus areas in microbiology Some examples are those on gene therapy, nanobiology, and bioremediation The encyclopedia includes tables, charts, diagrams, and photos that both highlight and facilitate the understanding of the topics The author covers the expansive area of microbiological science well: She provides readers interested in microbiology with a single source that is easy to understand, accessible, and very well written The major topics in microbiology are organized in alphabetical order, and each entry includes crossreferences to related topics and essays, in addition to resources for further reading on the subject For those seriously considering microbiology as a career, opportunities exist in teaching, research, and industry, or in public service as a microbiologist at the U.S Centers for Disease Control or the U.S Public Health Service The American Society for Microbiology additionally describes the many subspecialty areas focused on bacteria, fungi, protozoa, algae, and viruses These are but a few of the professional organizations that deal with microbiology, a science that expands almost daily with our changing environment Encyclopedia of Microbiology is an excellent start to an exploration of this intriguing field of study —Robert H Ruskin, Ph.D Director of Laboratory Research, Retired Water Resources Research Institute University of the Virgin Islands, St Thomas vii Acknowledgments This encyclopedia could not have been written without the guidance I received from my colleagues in microbiology throughout my career Some of these scientists graciously contributed essays that discuss current issues and problems in microbiology My thanks go to the following essayists: •â•‡R ichard E Danielson, Ph.D., BioVir Laboratories, Benicia, California •â•‡Carlos Enriquez, Ph.D., Chabot College, Hayward, California •â•‡Wanda C Manhanke, M.S., St Louis Children’s Hospital, St Louis •â•‡Kelly A Reynolds, Ph.D., College of Public Health, University of Arizona, Tucson •â•‡Nokhbeh M Reza, Centre for Research on Environmental Microbiology, University of Ottawa •â•‡Syed A Sattar, Ph.D., Centre for Research on Environmental Microbiology, University of Ottawa •â•‡Susan Springthorpe, Centre for Research on Environmental Microbiology, University of Ottawa •â•‡Philip M Tierno, Jr., Ph.D., Clinical Microbiology and Immunology, New York University Special thanks are due to Philip M Tierno, who contributed to the discussions on hygiene and germ transmission I owe Robert H Ruskin, Ph.D., a great deal of gratitude for outlining numerous entry topics, proofreading, fact checking, and offering insight on marine microorganisms I could not have completed this project without his help I also thank Dana Gonzalez, Ph.D., for input on infectious agents and disinfection My gratitude also goes to the literary agent Jodie Rhodes, the photo researcher Elizabeth Oakes, and, especially, the executive editor Frank K Darmstadt, for his encouragement, timely news stories, and belief in this encyclopedia as a valuable resource for students of biology and microbiology ix Aspergillus    71 of a variety of enzymes that break down food constituents The main examples of Aspergillus enzymes that have commercial value are amylase, which digests starch, and lipase, which breaks down fats Both enzymes are ingredients in laundry detergents for dissolving stains; lipase also contributes in leather tanning Aspergillus serves as a source of additional and varied industrial enzymes Oxidase enzyme, for example, acts as a bleaching agent for making paper and producing fabrics Makers of fruit juices use A niger’s pectinase enzyme to break down a fibrous molecule called pectin, found in apples and pears Pectin affects the consistency of fruit products, so manufacturers use pectinase to make their products more palatable and easier to digest Finally, protease enzymes made by A oryzae work as meat tenderizers and leather softeners Proteases are chosen for these uses because they digest proteins Statins are drugs that lower cholesterol levels in the blood A terreus has become an important natural source of lovastatin, and in 1987 it became the first statin approved by the U.S Food and Drug Administration (FDA) for treating high cholesterol level The human body makes cholesterol naturally, but some people either make too much or cannot break down excess cholesterol Lovastatin works by inhibiting an enzyme the body needs to synthesize cholesterol Food Items Produced by Aspergillus Aspergillus is a key microorganism in the food industry, where it has long been used for carrying out fermentations in certain foods Soy sauce is a food made from steamed soybeans combined with roasted wheat In the initial step, soy sauce makers inoculate soybean-wheat mixtures with A oryzae, A soyae, or A japonicus The fungal enzymes soon begin degrading the soybean and wheat constituents The producer then adds salt and allows the partially degraded mixture to undergo fermentation with yeast The fermentation results in the dark brown liquid known as soy sauce In Asian diets, A oryzae has been used for making miso (a fermented paste used as a spread or ingredient in dishes) from soybeans In the Philippines, the same Aspergillus produces tao-si (a type of soy sauce), also from soybeans In Ghana, kenkey (also komi or dokonu) is ground corn fermented by Aspergillus The table below lists other diverse uses of Aspergillus in food production In addition to the major foods shown in the table, the food industry has found uses for Aspergillus as a source of food product ingredients The following Aspergillus-produced ingredients are common in packaged foods: citric acid (a preservative), riboflavin (a vitamin), and glucose oxidase (a preservative) Food Contamination Though Aspergillus has been used for centuries to make foods, in the wrong foods and under the wrong conditions, it is a harmful food-borne pathogen Aspergillus species grow well in any place that contains organic matter Fruits, vegetables, grains, and peanuts have been special trouble spots for Aspergillus contamination, so food producers must check these foods carefully for molds and dirt before and during Food Products from Aspergillus Raw Ingredient Food Product Role of Aspergillus raw fruit juices clarified fruit juices amylase digests starches beer fermentation mixture finished beer cellulase enzyme removes cloudiness essential oils, fruits, herbs flavorings cellulase helps extract flavor compounds raw milk concentrated milk products lactase enzyme removes lactose cornstarch corn syrup glucoamylase enzyme converts most of the starch to sugar dairy products cheeses lactase digests fats and adds flavor dough mixtures baked products protease helps dough consistency and mixing 72    Aspergillus processing In fatty foods, Aspergillus and other molds produce enzymes that convert fats into compounds called ketones that produce bad tastes and odors Such fatty foods as butter, margarine, and cream contain enough moisture to allow Aspergillus to grow, and spoilage soon follows This type of spoilage wherein fatty compounds degrade into undesirable compounds is called rancidity Food microbiologists control most mold contaminations in food processing plants by properly heating the foods, by lowering the moisture content of the foods, or by doing both Toxin poisoning from Aspergillus presents a more serious type of contamination than food spoilage Usually people identify spoiled foods by noticing altered colors or odors These signals offer a valuable safety warning But aflatoxins produced in food are invisible Only careful protection of foods from mold during storage and processing helps prevent aflatoxin contamination Aflatoxin poisoning is called aflatoxicosis Humans and other animals that contract aflatoxicosis from foods or feeds, respectively, suffer from damage to the liver and possible liver cancers This infection is rare in humans, partially because the poisoning often is misdiagnosed In animals, aflatoxicosis takes two different forms The first is acute (rapid, severe, and short duration) aflatoxicosis, which leads to death, mainly in livestock The second form is chronic (longlasting) aflatoxicosis, which does not kill but causes liver damage and poor growth Food and feed suppliers prevent contamination of products by keeping the moisture content low in peanuts, cottonseed, soybeans, corn, cereal grains, and the tree nuts (Brazil, pecans, pistachios, and walnuts) They also try to store these items well below 70°F (21°C) to slow mold growth Food analysis laboratories test these foods and feeds for aflatoxin by breaking the food into its components—proteins, fats, fibers, carbohydrates— and chemically analyzing them Some analyses provide very sensitive detection for the presence or absence of the toxin as well as its concentration Concentrations as low as micrograms per liter (µg/l), also called parts per billion, have been measured by chemical methods It should not be surprising that a microorganism as ubiquitous as Aspergillus has been studied in detail This mold has been used as far back in history as ancient civilizations for food production and other uses Aspergillus has also been a nuisance as a food contaminant or a more serious threat to health when it produces aflatoxin Aspergillus symbolizes the major characteristics of many molds: commonplace in the environment; either harmful of harmless, depending on circumstances; and a microorganism that is very hard to avoid or kill See also food-borne illness; food microbiology; fungus; industrial microbiology; opportunistic pathogen Further Reading Banwart, George J Basic Food Microbiology, 2nd ed New York: Chapman & Hall, 1989 Center for Food Safety and Nutrition, U.S Food and Drug Administration “Aflatoxins.” Available online URL: http://www.cfsan.fda.gov/~mow/chap41.html Accessed March 15, 2009 Larone, Davise H Medically Important Fungi: A Guide to Identification, 4th ed Washington, D.C.: American Society for Microbiology Press, 2002 Merck Veterinary Manual, 9th ed Whitehouse Station, N.J.: Merck, 2005 “Sick Building Syndrome: Healing Health Facilities.” BusinessWeek August 13, 2008 Available online URL: www.businessweek.com/innovate/content/aug2008/ id20080813_845797.htm Accessed March 15, 2009 B Bacillusâ•… Bacillus is a genus of gram-positive, developed a new method for differentiating microorganisms This method involved analyzing a cellular constituent called ribosomal ribonucleic acid (rRNA) This breakthrough changed many of the classifications that had been used in bacteriology for decades It also enabled microbiologists to make clear distinctions between Bacillus species that appeared identical Although bacillis all look alike, rRNA analysis began to reveal wide diversity in the genus For example, the following three species appear almost identical under a microscope, yet they perform very diverse functions in the environment: endospore-forming, and rod-shaped bacteria that normally inhabit soil and are also found in water The general term bacillus (plural: bacilli) describes any rod-shaped bacteria Bacillus belongs to family Bacillaceae, which is the largest family in the order Bacillales Bacillales makes up one of two orders in class Bacilli (The other order in the class is Lactobacillales.) Bacillus cells measure 0.5–2.0 micrometers (µm) in width and 1.5–6 µm in length, though a few species have been found to grow to larger sizes Cell shape consists of straight rods, rather than curved, and the cells possess flagella distributed evenly over their surface to provide motility This type of arrangement is referred to as peritrichous flagella Bacillus species exist as either aerobes or facultative anaerobes (Facultative species can live with or without oxygen.) They use chemoheterotrophic metabolism, meaning they grow on a variety of organic compounds for energy and carbon Bacillus deoxyribonucleic acid (DNA) contains two subunits (called bases), guanine (G) and cytosine (C), that make up 32–69 percent of the genus’s total DNA The remainder of the DNA contains the bases adenine and thymine For this reason, microbiologists group Bacillus with other genera of grampositive bacteria called low G + C bacteria (High G + C bacteria contain, by comparison, higher ratios of G and C to the other two bases.) The Bacillus species look and behave very similarly, and so, for many years, microbiologists struggled to find accurate ways to distinguish individual species from others In the late 1970s, the University of Illinois microbiologist Carl R Woese •â•‡ Bacillus thuringiensis produces a natural insecticide •â•‡ Bacillus cereus can contaminate foods •â•‡ Bacillus anthracis causes anthrax disease Common among all of the Bacillus is the ability to convert into an endospore form An endospore is a dormant, thick-walled form of a cell that enables the bacteria to withstand extremes in heating, drying, freezing, irradiation, and chemical exposure This spore-forming capability has made Bacillus a feared pathogen and a troublesome contaminant, but it also gives this microorganism qualities of commercial value Important Bacillus Species Activities carried out by various Bacillus species fall into the following four general categories: degradation of organic compounds in nature, commercial 73 74    Bacillus sources of antibiotics and bacteriocins, sources of industrial enzymes, and pathogens in humans and animals Within each of these categories, individual species often have additional distinctive capabilities Some of the important Bacillus species are summarized as follows Bacillus thuringiensis B thuringiensis (Bt) makes a solid crystal protein during its endospore formation This protein acts as a poison in more than 100 different species of caterpillars, moths, grubs, and beetles when ingested by the insect (Fortunately, the Bt crystal does not harm bees that are critical for the pollination of commercial and garden plants.) The protein destroys the insect’s digestive processes and so protects any plant upon which the insect preys Gardening supply stores sell liquid or freeze-dried mixtures of Bt endospores or the toxic protein alone Growers then spray the Bt product onto their plants to protect against insect infestation Colorado State University Extension Service has explained on its Web site the characteristics of the Bt toxin: “Unlike typical nerve-poison insecticides, Bt acts by producing proteins (delta-endotoxin, the ‘toxic crystal’) that react with the cells of the gut lining of susceptible insects These Bt proteins paralyze the digestive system, and the infected insect stops feeding within hours Bt-affected insects generally die from starvation, which can take several days.” Even dead Bacillus cells carry the toxic protein, and when the cells lyse (break apart) in the digestive tract, they still act as an effective insecticide Farmers have used Bt for many years as a natural method for protecting crops Although scientists had already learned that the Bt toxin works inside insect guts, Bt still held a few secrets on the details of life inside that tiny environment In 2006, the microbiologist Jo Handelsman and her graduate student Nichole Broderick of the University of Wisconsin set up an experiment to show the degree to which native bacteria inside insects might combat Bt; natural microbial populations are known to prevent outsiders from entering a habitat Could certain insects contain bacteria that combatted Bt? In other words, could a normally Bt-susceptible insect become resistant with the right bacteria in its gut? In an experiment using gypsy moths, Broderick found a relationship between Bt and other bacteria, but not the result she expected “Initially, I was testing the hypothesis that the gut bacteria were actually protecting the moth,” she said Broderick cleared the insects’ digestive tracts of their normal bacteria, fed the insects Bt toxin, and reported, “I found that once they [moths] did not have a gut community (of bacteria) I could no longer kill them with Bt.” This find- ing suggested that the Bt toxin works in an unusual partnership with the insect’s normal bacteria While microbiologists pursue studies on the Bt mechanism inside insects, molecular biologists have begun using the Bt gene in ingenious ways The gene for the Bt toxin resides on a plasmid in the Bacillus cell’s watery contents called cytoplasm A plasmid is a circular piece of DNA that many bacterial species possess and that lies separate from the main DNA Molecular biologists have isolated the Bt gene and put it into other types of bacteria and even into plant cells by a process called genetic engineering For instance, the Bt gene inserted into the DNA of potato plants enables each plant leaf to produce its own Bt insecticide This method saves income that potato growers would lose to crops destroyed by the Colorado potato beetle and other pests The insecticide-producing plants also reduce the need for chemical insecticide sprays Organic farmers and others who oppose genetic engineering either avoid the use of bioengineered bacteria or the spray a mixture of Bt cells directly onto their plants to kill insects Bacillus cereus B cereus acts similarly to B thuringiensis but does not produce an insecticide Instead, B cereus acts as a food-borne pathogen The species also causes rare cases of meningitis in humans and spontaneous abortions in herd animals The facultative anaerobic B cereus is a foodborne pathogen found in a variety of foods: meat, milk, fish, cheeses, vegetables, and rice products The pathogen causes symptoms by producing either of two proteins: a large-molecular-weight protein or a smaller, heat-stable protein Both types of protein induce characteristic abdominal cramps and nausea The large protein also causes diarrhea; the smaller protein causes vomiting (The small protein is sometimes referred to as a peptide, which contains fewer amino acids than a typical protein.) Because one form of the B cereus toxin resists heat, cooking contaminated foods may not destroy it completely Bacillus anthracis B anthracis causes the lethal anthrax disease in farm animals and humans B anthracis is unusual among Bacillus because its cells are nonmotile, meaning they cannot propel themselves under their own power The large cells (1.5 ì àm) possess square ends, making them look rectangular, and they usually form end-to-end chains This facultative anaerobe produces protein toxins, called exotoxins, that it releases into the cell’s surroundings The toxin causes three forms of anthrax disease: cutaneous, pulmonary, and gastrointestinal Cutaneous anthrax is associated with localized skin infections, Bacillus    75 pulmonary anthrax results from inhaling B anthracis endospores, and gastrointestinal anthrax arises from ingesting the endospores Each type of disease becomes a health threat only when cells grow out of the dormant endospore in a process called germination B anthracis, as can many Bacillus species, can remain in the endospore form in the soil for centuries When endospores germinate, they revert into a regular reproducing cell form, called vegetative cells Vegetative cells then produce the toxin that causes the disease’s symptoms Anthrax is most often contracted by people who are around farm animals or who frequently handle hides and pelts This is very rare in the United States; the Centers for Disease Control and Prevention (CDC) report on the Web site the incidence of anthrax since the year 1900 is less than two cases a year The U.S Food and Drug Administration (FDA) and the CDC have identified B anthracis as a possible biological weapon Although farm animals receive anthrax vaccine on a routine basis to protect livestock investments, only high-risk groups in the general U.S population have access to a vaccine The CDC considers the following four groups as high-risk groups in regard to anthrax disease: laboratory workers who handle B anthracis, people who frequently handle hides and furs, people working with farm animals in high-incidence areas, and military personnel Bacillus subtilis Aerobic B subtilis cells take a very slender (0.8 µm wide), elongated shape This species produces a variety of extracellular enzymes that are useful in commercial products B subtilis enzymes digest starches, proteins, and gelatins B subtilis provides an example of a species that conducts quorum sensing In this process, cells monitor their own population density using signal molecules they release into the environment When the signal molecules reach a certain concentration, they induce a response in the bacteria that produced them In the case of B subtilis, nutrient-poor conditions make the bacteria respond in one of two ways: endospore formation or cooperative growth Cooperative growth comprises activities within a colony that enable the cells to take in as much nutrient as possible for as many cells as possible This capability becomes critical in colonies grown on nutrient-poor agar in a laboratory Cooperative-growth colonies of B subtilis produce distinctive shapes, such as snowflakelike shapes, that have not been observed by microbiologists at any other time Bacillus stearothermophilus This species is a thermophile, a microorganism that grows in a temperature range of 130–150°F (55–65°C) Microbiologists take advantage of this capability of B stearothermophilus by using it to test for sterile conditions In this role, the microorganism is called a sterility indicator When sterilizing a large volume of liquid or a densely packed volume of dry materials in an autoclave, a microbiologist adds a vial or a paper strip containing B stearothermophilus endospores to an autoclave along with items to be sterilized An autoclave is a chamber that kills all microorganisms by applying steam heat under pressure After the sterilization cycle has completed, the microbiologist inoculates the vial’s contents or the strip to growth medium, and then incubates the inoculated medium After incubation, a lack of growth indicates that the heat-resistant B stearothermophilus has been killed in the sterilization process This result tells the microbiologist that the sterilization procedure also killed all other microorganisms, because normal contaminants cannot withstand the high temperatures that B stearothermophilus tolerates The ability to withstand extreme heat makes this species an extremophile Other Bacillus extremophiles are B psychrophilus (grows at low temperatures) and B alcalophilus (grows at high pH) Bacillus sphaericus Bacillus sphaericus provides an example of the hardiness of the bacterial endospore The very slender (0.5–1.0 µm wide) motile cells of this species form endospores, typical constituents of Bacillus: That is, they contain an inner membrane, a middle cortex layer, and a protective spore coat This species also served to demonstrate the incredible durability of Bacillus endospores In 1993, the American microbiologist Razl Cano reported a B sphaericus–like microorganism inside a primitive bee that had become trapped in amber 25–40 million years ago Discover magazine described Cano’s finding but also pointed out that he had faced some skepticism The B sphaericus endospores, wrote the reporter Lori Oliwenstein, go into “a state of suspended animation In times of stress a number of microbes knit themselves a strong, protective protein coat called a spore and slow all their cellular processes until they are effectively (but not actually) dead Once they sense the presence of sufficient nutrients—a sort of bacterial all’s-well signal—they resurrect themselves.” But the article also noted, “His [Cano’s] critics, however, are not quite ready to raise a glass to him They say it’s impossible for any living creature to have survived for so long Instead of an ancient microbe, they argue, Cano has simply found a modern contaminant.” But Bacillus endospores have been recovered from 2,000-yearold tombs, 10,000-year-old fossils, and objects dated much older than the remarkable amber specimen found by Cano Cano conducted DNA analysis on the 76    bacteria Major Enzymes Produced by Bacillus Enzyme Its Substrate End Product amylase starch sugars protease proteins amino acids, peptides lipase fats glycerol and fatty acids glucanase glucan polymers short-chain saccharides pullulanase maltodextrans sugars amber’s Bacillus and compared it to modern Bacillus DNA and concluded that the two varieties were not related enough to suggest they are contemporaries B sphaericus vegetative cells also produce a toxin that kills Culex mosquito larvae feeding in water Some state health departments spray B sphaericus mixtures on still waters, such as stagnant ponds and pooled rainwater, during the spring and summer to control mosquito populations Bacillus polymyxa This facultative anaerobic, motile species produces a number of enzymes with commercial uses Bacillus polymyxa breaks down starches, the protein casein, gelatin, and pectins In addition, this species produces polymyxin antibiotics, which are effective against many gram-negative pathogens These large compounds kill other bacteria by infiltrating the cell membrane and causing cell constituents to leak out A well-known polymyxin used in human and veterinary medicine is polymyxin B Bacillus megaterium B megaterium produces a very large cell, 1.5–3.0 µm wide Because of its size, B megaterium serves as a common teaching tool for studying endospore formation and the life cycle of Bacillus Biotechnology also favors B megaterium in cloning experiments and in plasmid production Commercial Uses of Bacillus Bacillus has two attributes that make it attractive in industrial microbiology: the rugged endospore and production of a wide variety of enzymes Because endospores resist damage by heat, cold, and chemicals, manufacturers can include them in product formulas with confidence that the bacteria will remain alive For example, Bacillus makes up the main ingredient in septic tank additives and drain openers as well as the insecticide products already mentioned The endospore gives these formulas a long shelf life, and Bacillus’s enzymes deliver the product’s desired effect Various Bacillus species produce the enzymes listed in the table Some species, such as B subtilis, excrete more than one Makers of cleaners, detergents, stain removers, and food additives also use Bacillus enzymes in their products Other industries take advantage of Bacillus activities for certain manufacturing steps Brewers use ß-glucanase produced by B subtilis to clarify beer, and the food industry uses Bacillus enzymes to make high-fructose corn syrup, a sweetener added to a multitude of processed foods See also anthrax; bacteria; spore Further Reading Biello, David “Bt Pesticide No Longer Kills on Its Own, Overturning Orthodoxy.” Scientific American, 25 September 2006 Available online URL: www.sciam com/article.cfm?id=bt-pesticide-no-killer-on Accessed March 15, 2009 Cano, Raúl, Heridrik N Poinar, Norman J Pieniazek, Aftim Acra, and George O Poinar “Amplification and Sequencing of DNA from a 125–130-Million-Year-Old Weevil.” Nature 363 (1993): 536–538 Available online URL: www.nature.com/nature/journal/v363/n6429/ abs/363536a0.html Accessed March 29, 2009 Centers for Disease Control and Prevention “Anthrax.” Available online URL: www.bt.cdc.gov/agent/anthrax Accessed March 15, 2009 Colorado State University Extension Service “Bacillus thuringiensis.” Available online URL: www.ext.colostate edu/pubs/Insect/05556.html Accessed March 15, 2009 Oliwenstein, Lori “They Came from the Oligocene, He Said.” Discover, January 1996 Available online URL: http://discovermagazine.com/1996/jan/theycamefromtheo651 Accessed March 12, 2009 Todar, Kenneth “The Genus Bacillus.” Todar’s Online Textbook of Bacteriology Available online URL: www textbookofbacteriology.net/Bacillus.html Accessed March 16, 2009 bacteria (singular: bacterium)â•… Bacteria are singlecelled organisms with a cell wall characterized by the large compound peptidoglycan They are in the kingdom of prokaryotes, so they lack a true nucleus and organelles surrounded by membrane Bacteriology encompasses all aspects of bacteria Specialties in bacteriology include, but are not limited to, the following: pathogens in humans, animals, and plants; clinical isolates; intestinal flora; rumen flora; genetic engineering; serotyping; morphology; environmental studies; food preservation; food production; industrial products; and enzymology bacteria    77 Bacteria comprise a diverse group of microorganisms that display a wide range of physiologies and live in a variety of habitats Their diversity allows them to participate in almost every biological activity on Earth Higher organisms could not exist for long without their native bacteria, that is, the bacteria that normally reside in or on the body The planet also relies almost entirely on bacteria to cycle nutrients from sediments through animal and plant life, then through the atmosphere and back to the earth Bacterial numbers reach enormous levels in many habitats on Earth More bacterial cells live on or in the human body than there are human cells The classification of bacteria within the world of living things has not come easily New classifications of species arose as new methods of identification developed in microbiology From the 1800s to the 1960s, advances in microscopy enabled microbiologists to see ever-finer structures in and on bacterial cells During this time, microscopic features (morphology) seemed the best way to group bacteria But as the science of biochemistry grew, biochemical reactions carried out by bacteria replaced or supplemented groupings based on morphology In the 1980s, molecular biologists discovered methods for determining the subunit, or base, sequences of deoxyribonucleic acid (DNA) This technique allowed biologists to study how the world’s organisms are related and the closeness of those relationships, called relatedness Microbiologists began rearranging bacteria classifications on the basis of common ancestries between species, as told by their DNA composition One technique, DNA hybridization, found genes common to different bacteria that had heretofore been thought of as unrelated In the process, bacteria that evolved along similar paths were soon distinguished from others that were not as closely related Throughout the 1980s and 1990s, laboratories sequenced hundreds of bacterial genes During that period, the bacteriologists Carl Woese at the University of Illinois and Mitch Sogin at the Marine Biological Laboratory in Wood’s Hole, Massachusetts, developed another sequencing method They determined the nucleic acid sequences of 16S subunits of ribosomal ribonucleic acid (rRNA), the cell structures involved in protein assembly Although Woese had been pursuing the genetic makeup of cells for much of his career, Sogin took a different route into a specialty that would have a tremendous impact on biology and the study of evolution Sogin told PBS in 2002, “During the third year of my undergraduate career I reached the realization that I didn’t want to be a physician Molecular biology was an emerging field and I had the opportunity to work with microbiologists and physicists who were joining forces to explore questions in evolutionary biology I was sim- ply in the right place at the right time.” Sogin may have described his contributions in modest terms, but the bacterial family trees established by him, Woese, and their colleagues remain in use today Bacteria on Earth Living things, called biota, on Earth can be divided into prokaryotes and eukaryotes The eukaryotes range from single cells to multicellular plants and animals All the eukaryotic cells possess membraneenclosed organelles Prokaryotes contain two domains: bacteria and the archaea The 16S rRNA sequencing studies, of the 1990s, have shown that domain Bacteria and domain Archaea evolved separately from each other, very early in the evolution of life For this reason, most texts divide the world of living things into three domains: Bacteria, Archaea, and Eukarya Older texts sometimes use the term eubacteria to describe the “true bacteria” and the term archaebacteria to signify the archaea In fact, archaea are not bacteria, and the term archaebacteria can be misleading The actual number of bacterial species on Earth is unknown and may never be known Determining the number would rely on sampling every type of environment and accounting for every mutation New species of bacteria are discovered almost daily, but only about 5,000 species have been completely characterized Microbiologists have discovered additional species that they cannot yet identify or have not devised a way to keep alive in a laboratory These bacteria are called VNC (or VBNC) for “viable but noncultivable.” A second way of thinking about the number of bacterial species on Earth proposes that the numbers of calculated species could be an overestimate Because bacteria freely exchange genetic material between cells, microbiologists could argue that trying to place each into a genus and species is meaningless; bacteria are all related to each other to some degree Many microbiologists estimate that less than percent of all bacteria on Earth have been cultured and characterized In 1998, the University of Georgia microbiologist William B Whitman led a team of scientists in estimating the number of bacteria by counting samples from a wide array of habitats as well as carbon content measurements in those places “By combining direct measurements of the number of prokaryotic cells in various habitats,” Whitman said, “we found the total number of cells was much larger than we expected.” They found the greatest number of bacteria located in the subsurface of the earth or deep soils and in the ocean Whitman’s estimate equaled five million trillion trillion (5 × 1030) bacteria! Whitman’s studies also produced a calculation for the mass of bacteria on Earth based on car- 78    bacteria bon content Whitman estimated that bacteria total 3.5–5.5 × 1017 grams of carbon, or about the same amount as all of Earth’s plant life Determining the number of bacteria on Earth has been understandably a difficult process By using the 16S rRNA classification scheme, microbiologists can divide bacteria into groups even if a new discovery has not been identified or named Microbiology often uses general groupings of bacteria based on a combination of physical and genetic features For instance, prevalent groups of bacteria often go by nicknames: spore formers, alphas, spirochetes, lactic acid bacteria, or nitrogen fixers Nicknames perhaps serve to highlight the extraordinary diversity of bacteria and their many roles For official scientific naming, microbiologists use Bergey’s Manual of Determinative Bacteriology to help them classify new bacteria These five volumes serve as the main reference in systematics of bacteria, which is the science of classifying and naming organisms History of Bacteriology Bacteria’s history with humans extends to the earliest documented civilization Species recovered from remnants of ancient civilizations include Bacillus endospores and the Mycobacterium that causes tuberculosis The actual study of these tiny creatures unfolded over centuries, beginning with the explorations of the stars and the seas Humanity’s place in the universe became a question for scholars in the 15th century, when a few explorers peered into the smallest universe rather than outward across the oceans or the stars The Italian Girolamo Fracastoro (1478–1553) was one such visionary, who proposed that infection transmitted as tiny particles on clothes, bodies, or commonly touched inanimate objects Fracastoro had essentially defined the core idea of disease transmission, but finding these microscopic specks proved difficult without the technologies that would only emerge in the next century In 1597, the glassmaker Zacharias Janssen (1585–1632) and his father, Hans, developed a useful instrument for looking at small things by arranging lenses in sequence By creating this method for magnification, the Janssens had invented the first compound microscope Antoni van Leeuwenhoek (1632–1723), a tradesman living in Holland, applied his own collection of lenses 75 years later to see tiny “animalcules” in a drop of water Van Leeuwenhoek’s observations of microscopic life, in 1677, have been credited as the first detailed studies of bacteria at the microscopic level Viewing a drop of water into which he had ground pepper granules, van Leeuwenhoek wrote, “I found a great plenty of them in one drop of water, which were no less than or 10,000, and they looked to my eye, through the Microscope, as common sand doth to the naked eye.” Van Leeuwenhoek made painstaking notes of his discoveries, which modern microbiologists now recognize as very sophisticated studies Simple microscopes encouraged scientists to debate, for the next 90 years, about the theory of spontaneous generation, in which living organisms were believed to arise from nonliving matter The so-called golden age of microbiology, from the mid1800s to about 1915, encompassed some of microbiology’s most important breakthroughs: the germ theory, the principles of infection and disease, and immunity Hans Christian Gram’s (1853–1938) contribution in finding a biological stain for making better observations of bacteria began the science of classifying bacteria according to cellular features When the structure and function of DNA became revealed in the 1940s and 1950s, microbiologists delved into the bacterial chromosome, the entire collection of a cell’s genetic matter A significant advance occurred in the 1980s, when university researchers transferred pieces of bacterial DNA, or genes, from one species to another, unrelated species Molecular biology was born From it, the field of biotechnology grew, as scientists manipulated an increasing variety of bacterial genes to make new products Certain aspects of genetic engineering and medical therapies would not be available today if not for bacteria The Bacterial Cell The diverse bacteria on Earth range in size from nanobacteria of less than 0.2 micrometer (µm) diameter to the immense marine Thiomargarita namibiensis, measuring 0.75 mm in diameter, about the size of the period at the end of this sentence Most bacteria fall in a range of 0.2–2 µm in width and 4–8 µm in length In the world of microscopic particles, bacteria are 10–100 times greater in size than viruses and about one tenth the size of a human red blood cell Bacterial cells reproduce by binary fission, in which a single parent cell splits asexually to form two identical daughter cells Each daughter cell assumes the size and shape characteristic of the genus Bacteria fall into five categories based on shape, as follows: •â•‡ cocci—round cells (singular: coccus) •â•‡ bacilli—rod-shaped cells (singular: bacillus) •â•‡ vibrios—curved rods bacteria    79 Bacterial species divide from one cell to many in  characteristic confi gurations. Different cell morphologies  and orientations of cells aid in genus identifi cation • spirochetes—helical or corkscrew shaped • pleomorphic—many different shapes within a species Bacteria that are always round, rod-shaped, curved, or helical are referred to as monomorphic, because they are genetically programmed to produce only one shape A few species produce unique shapes, such as the star-shaped bacteria of the genus Stella Bacteria that grow different shapes are called pleomorphic Cocci and bacilli consist of various arrangements as cells multiply and produce greater numbers of identical cells Dividing cocci, first, form a pair of joined cells, a diplococcus Further division leads to one of two arrangements Some cocci form elongated chains, like a string of pearls, called streptococci Others form a tetrad of four cells from the diplococcus by dividing in two planes A second division in three planes forms cubes of eight cells called sarcinae Continued division leads to large numbers of cells in grapelike clusters characteristic of staphylococci Bacilli create similar groups of cells as they divide, although chains are more common in bacilli than clusters Thus, a bacillus forms a diplobacillus, which with continued division forms a chain of streptobacilli Short, squat bacilli having a rounded appearance are called coccobacilli Bacteriologists further defi ne bacteria by structures on the outside of cells Cells with whiplike tails called fl agella are motile, meaning they have the ability to move on their own Motility is one characteristic used for identifying bacteria, as is cell morphology, the study of microbial structure Cell morphology has been helped by advances in microscopy, and it has developed into a separate specialty within bacteriology The cell interior contains structures that are common to most bacteria but different from eukaryotic cells Bacteria are like eukaryotes, in that cytoplasm fills most of the cell contents Cytoplasm is fairly homogeneous, watery—70–85 percent water by weight—and shapeless (The outer cell membrane holds cytoplasm together.) All of the cell’s reproductive activities take place within the cytoplasm Reproduction requires a chromosome, the bacteria’s main depository of DNA The chromosome contains each species’s entire genetic code, and without it, life could not continue Bacterial DNA exists in two places in the cell: the nucleoid, a region in the cytoplasm dense in DNA but not surrounded by a membrane, and, in some species, a separate piece of DNA called a plasmid, located in the cytoplasm separate from the nucleoid Bacteria employ plasmids for 80    bacteria transferring genes between cells and plasmids often contain genes for antibiotic resistance Bacterial cells also contain ribosomes, vacuoles, and inclusion bodies The ribosomes function in protein synthesis by reading DNA’s genetic code Vacuoles are open spaces in the cytoplasm and shaped by a protein lining Vacuoles contain gas and serve two main functions: storage of atmospheric gases and creation of cell buoyancy by expanding or collapsing The role and composition of inclusion bodies vary among species Some bacteria use inclusion bodies to store nutrients, while others use them for regulating osmotic pressure, which is the pressure of the cell interior relative to the exterior Vacuoles filled with air are called gas vacuoles and may behave similarly to inclusion bodies On the outer surface, in addition to flagella, gram-negative bacteria may contain short fimbrae These appendages measure 5–10 µm long and cover most of the cell They contribute to motility and allow cells to attach to surfaces Even smaller outshoots called pili, about 2–3 µm long, number no more than 10 per cell and are used for exchanging genetic material between cells The bacterial cell wall provides strength and protection from the outside environment and gives each species its characteristic shape Almost all bacteria are divided into one of two groups based on cell wall structure These groups are the gram-positive species and the gram-negative species The distinction between positive and negative results from the cell wall’s capacity to absorb the Gram stain Some species (gram-positive) turn purple when exposed to one of the chemicals used in the Gram stain method Other species (gram-negative) not hold this stain and cannot turn purple Though biologists have invented sophisticated ways to classify bacteria, such as DNA and rRNA sequencing, the Gram stain remains a fundamental technique in every microbiology laboratory Classifications of Bacteria Each domain within the prokaryotic kingdom is divided into phyla, each phylum into classes, each class into orders, and each order into families Families contain genera, and almost all bacterial genera have more than one species In bacteriology, bacteria are known by their genus and species name For example, Pseudomonas aeruginosa is a species of the genus Pseudomonas Domain Bacteria contains 23 phyla (see Appendix V) Over decades of study, bacteriologists have learned much more about some phyla than others Microbiology has made the biggest strides in characterizing species that have important associations with humans, domestic animals, and plants, or spe- cies that carry out key reactions in the environment The table on page 81 summarizes the main groups studied in bacteriology Proteobacteria Proteobacteria is the largest group of bacteria that have been characterized by bacteriologists The group is divided into five classes, all having similar base sequences in their RNA: alpha, beta, delta, epsilon, and gamma This group’s physiologies and morphologies are very varied; no single type of metabolism or cell feature represents all species of proteobacteria except that they are all gram-negative The alpha proteobacteria include members that perform nitrogen fixation in plants (Rhizobium), use methane as a carbon-energy source (Methylobacterium), or use chemolithotrophic metabolism (Nitrobacter),) which employs inorganic compounds for energy and carbon dioxide as a carbon source The alpha proteobacteria can live on very low levels of nutrients, and they contribute to Earth’s cycling of nitrogen from the atmosphere to the land and biota A general group called purple nonsulfur bacteria live in freshwater and marine waters, and their need for oxygen varies among species They gather energy from light and use organic compounds as both electron and carbon sources Many beta proteobacteria act as nitrifying bacteria: That is, they convert ammonia or nitrites to nitrates in a chemical step called oxidation Beta proteobacteria tend to use the end products made by anaerobic species, such as hydrogen gas, ammonia, or methane Many beta proteobacteria live in water environments and in sewage The delta proteobacteria contain predators that feast on other bacteria and members that contribute to Earth’s sulfur cycle Anaerobic sulfate- and sulfur-reducing delta proteobacteria live in watery habitats, especially mud, and often grow well in polluted streams and lakes Epsilon proteobacteria make up a small group containing human and animal pathogens as well as species that form large mats on water surfaces rich in hydrogen sulfide These mat communities have been discovered living in harsh oil- or sulfur-polluted places, so they are thought of as extremophiles Microbiologists who seek new bacteria for cleaning up pollution (a process called bioremediation) have looked to epsilon proteobacteria because of their ability to degrade pollutants The gamma proteobacteria are the largest and most diverse class in the phylum Bergey’s Manual divides them into 14 orders and 25 families Many gamma proteobacteria are facultative anaerobes, meaning they can live with or without oxygen; bacteria    81 Important Groups of Bacteria Group Common   Name Phylum Classes Important Genera Important Features bacteroids XX: Bacteroidetes Bacteroides Flavobacteria Sphingobacteria Bacteroides Prevotella Flavobacterium degrade complex polysaccharides, rumen inhabitant, sewage treatment chlamydia XVI: Chlamydiae Chlamydiae Chlamydia sexually transmitted disease in humans fusobacteria XXI: Fusobacteria Fusobacteria Fusobacterium Leptotrichia in habitant of human gastrointestinal (GI) tract high G + C gram-positives XIV: Actinobacteria Actinobacteria Actinomyces Corynebacterium Frankia Gardnerella Mycobacterium Nocardia Propionibacterium Streptomyces aerobic and anaerobic fermentations, soil inhabitants, antibiotic production low G + C gram-positives XIII: Firmicutes Clostridia Millicutes Bacilli Clostridium Sarcina Mycoplasma Bacillus Listeria Lactococcus Leuconostoc Staphylococcus Enterococcus Lactobacillus Streptococcus inhabit mammals, plants, and insects; endospore formation; acid fermentation photosynthetic bacteria (green bacteria and cyanobacteria) VI: Chloroflexi X: Cyanobacteria XI: Chlorobi Chloroflexi Cyanobacteria Chlorobia Anabaena Gloeocapsa Chlorobium Chloroflexus aerobic and anaerobic photosynthesis proteobacteria (purple bacteria) XII: Proteobacteria alpha, beta,gamma, delta, or epsilon proteobacteria Beggiatoa Campylobacter Escherichia Rhizobium Salmonella Shigella Vibrio human and plant pathogens, nitrogen fixation, nitrification, sulfur oxidation and reduction, sewage treatment, fermentations, photosynthesis spirochetes XVII: Spirochaetes Spirochaetes Borrelia Leptospira Treponema inhabitant of mammal GI tract, mollusk and insect digestive tract Note: See Appendix V for microbial classifications 82    bacteria others are aerobes Gamma proteobacteria also use varied means of generating energy Gamma proteobacteria contain photosynthetic microorganisms collectively nicknamed the purple sulfur bacteria The purple sulfur bacteria require strict anaerobic conditions and live in sulfide-rich zones in still lakes, swamps, bogs, and lagoons Photosynthetic Bacteria Photosynthetic bacteria belong to three different phyla: Chloroflexi, Chlorobi, and Cyanobacteria All are gram-negative and contain the pigment chlorophyll Most of these bacteria live in deep regions of lakes and ponds where much of the light penetration has been blocked by plants living in shallow layers This may explain why these bacteria use a region of the light spectrum not used by plants Some of the Chloroflexi even grow in complete dark The photosynthetic bacteria—some proteobacteria are also photosynthetic, but not included here—use water as an electron source in energy metabolism and generate oxygen Chloroflexi contains motile species that grow into orange-red mats in natural hot springs Nevertheless, many members of Chloroflexi are nicknamed the green nonsulfur bacteria They grow with or without oxygen and use a variety of carbon sources This phylum additionally contains nonphotosynthetic bacteria (Herpetosiphon) Chlorobi are known as the green sulfur bacteria They are strict anaerobes that use hydrogen sulfide, sulfur, or hydrogen as electron donors and carbon dioxide as a carbon source Chlorobi have unique vesicles called chlorosomes, which contain chlorophylls a, c, d, and e and serve as the location for photosynthesis The cyanobacteria make up another large and diverse group Cyanobacteria have a characteristic blue-green color caused by the relative levels of pigments in their cells, mainly phycocyanin These bacteria not grow well as pure cultures in laboratories, so bacteriologists have had a difficult time classifying them For many years, biologists classified cyanobacteria as blue-green algae Cyanobacteria photosynthesize and fix nitrogen, and, unlike Chlorobi and Chlorofexi, cyanobacteria perform oxygenic photosynthesis, meaning they produce oxygen Low G + C Gram-Positive Bacteria Gram-positive bacteria fall into two groups: low G + C and high G + C Low G + C bacteria generally have less than 50 percent of their DNA as guanine and cytosine High G + C DNA bacteria have more than 50 percent guanine and cytosine Three important types of bacteria belong to the low G + C gram-positives: the mycoplasmas, the gram-positive rods and cocci, and endosporeforming bacilli Members of the genus Mycoplasma are unique because they lack a cell wall because of their inability to make peptidoglycan Without a cell wall, Mycoplasma cells are fragile and readily lyse (break apart) in liquids containing a high concentration of dissolved molecules Mycoplasma species cause diseases in humans and livestock and are best known as the cause of respiratory diseases in humans, especially tuberculosis The most familiar genera in the low G + C group possess similar cell wall structures and are among the most studied bacteria in microbiology The low G + C bacteria contain the following genera: Staphylococcus, Streptococcus, Lactobacillus, Micrococcus, Lactococcus, Leuconostoc, and Streptomyces The genera Clostridium and Bacillus are alike because they form a strong, resistant, and protective structure called an endospore Both genera live primarily in soil and contain both rods and cocci They differ from each other, however, in their metabolism; Clostridium is an anaerobe, Bacillus is an aerobe High G + C Gram-Positive Bacteria The major gram-positive bacteria containing a high percentage of G + C in their chromosome are the actinomycetes This is a general group of aerobic species that form branching filaments as they grow Viewed in a microscope, actinomycetes can resemble filamentous fungi more than they resemble bacteria A familiar genus within the actinomycetes is Streptomyces This soil inhabitant includes about 500 species In the environment, Streptomyces contributes to nutrient cycling, decomposition of organic matter, and antibiotic production, and it causes some plant and animal diseases A few other bacteria in this group are so unrelated to actinomycetes, the classification seems to make little sense One important example is the Mycobacterium genus These bacteria grow very slowly—taking up to a month in laboratory cultures—and their cell walls contain an unusually high content of fatty substances called lipids M bovis plays an important role in this group because it causes tuberculosis in humans and most other warm-blooded vertebrates Examples of animals susceptible to M bovis infection are the following: cattle, sheep, goats, deer, elk, pigs, dogs, cats, monkeys, large apes, and exotic hoofed animals in zoos Bacteroids Bacteroids is a general term for gram-negative bacteria belonging to phylum Bacteroidetes They live as either strict anaerobes or anaerobes that tolerate only low oxygen levels (aerotolerant) They inhabit the human mouth and intestinal tract and the stomach of ruminant animals In the intestines, members of Bacteroides degrade complex carbohydrates such as starch, pectin, and cellulose Microbiology historians believe van Leeuwenhoek may have been bacteria    83 Borrelia burgdorferi is a spirochete, which is a corkscrew, or spiral-shaped, bacterium These cells of 10–25 µm in length cause Lyme disease.  (CDC, Public Health Image Library) the first person to observe bacteroides in a microscope because some of his studies focused on matter scraped from between his teeth A second notable group within Bacteroidetes belongs to the gliding bacteria Certain bacteria placed in this group are also part of other classifications For example, Myxococcus also belongs with the delta proteobacteria Gliding bacteria are motile yet not possess flagella They glide across solid surfaces using a mechanism not well understood but believed to include a screwlike twisting motion in some species and flexing or twitching in other species These bacteria travel at rates ranging from to 600 µm per minute, often in the direction of nutrients Gliders excrete enzymes particularly active in breaking down paper and other materials containing cellulose They have been used for many years for retting woody plants, meaning they digest the plants’ strong fibers to make them softer The textile industry also uses gliding bacteria for recovering natural fibers from tough plant matter As an example, fabric mills use the enzymes from these bacteria to recover textile fibers made from hemp plants Notable genera in this group are the following: Desulfonema, Flavobacterium, Flexibacter, Heliobacterium, Myxococcus, and Oscillatoria Spirochetes The spirochetes are so named because of their spiral or corkscrew shape These gram-negative bacteria grow in a range of oxygen environments and on diverse nutrients Their unique motility results from filaments that spiral around the outer cell surface; the movement of spirochetes through water is not unlike a screw’s being driven into a piece of wood Spirochetes live in the human mouth and in the intestinal tract of various animals The important spirochete genera appear in the following list: •â•‡ Treponema—includes T palladium, the cause of syphilis •â•‡ Leptospira—water and soil contaminant car ried by domestic dogs and cats; the cause of leptospirosis in animals •â•‡ Borrelia—cause of relapsing fever and Lyme disease, carried by insects Chlamydia Since Chlamydia cell walls (gram-negative) not contain peptidoglycan, their cells are weaker than those of most other bacteria For this reason, 84    bacteria Chlamydia must live inside other cells In humans, Chlamydia infection gives rise to the following two sexually transmitted diseases: nongonococcal urethritis and lymphogranuloma venereum Transmission of these bacteria also occurs through the air to cause respiratory infections Fusobacteria The fusobacteria are, like the bacteroids, common gram-negative anaerobes of the mouth and intestinal tract, where they help digest food Their cell shape is fusiform, meaning they are shaped like spindles, rods that are tapered at each end The Roles of Bacteria Bacteria play roles in nature, in human and animal health, in association with plants and insects, and as tiny factories for manufacturing industrial materials In general, their roles may be classified into three major areas: environmental, industrial, and medical Environmental microbiology covers bacterial metabolism in the earth, in natural waters, and in the air Bacteria and fungi in soil and water both degrade organic wastes and recycle the elements carbon, nitrogen, phosphorus, and sulfur, among others in the earth’s biogeochemical cycles In the process of degrading the earth’s organic matter, some bacteria produce the gases methane, carbon dioxide, hydrogen, oxygen, and nitrous oxide, which convert to nitrogen gas Bacteria, therefore, are major contributors to the composition of the atmosphere, and they carry out these reactions even when they are inside plants or animals Many live in commensal relationships with higher organisms and affect the health of their hosts In such a relationship, the bacteria help their hosts by digesting nutrients and secreting compounds made during their normal metabolism, which the host then absorbs and uses in its own metabolism The most important of these secretions are acids, alcohols, antibiotics, proteins and amino acids, enzymes, and vitamins Because some bacteria produce large amounts of secretions useful to humans, industrial microbiology developed to take advantage of this activity Industrial microbiologists harness bacteria in laboratories to produce compounds useful in commercial products In addition to antibiotics and the other secretions listed, bacteria produce biological polymer compounds, biopolymers, which are long polysaccharides These compounds act as stabilizers in liquid formulas such as paint, lubricants, absorbents, and additives to drugs and foods Food production also relies on specific bacteria For example, Lactobacillus species make a number of dairy products: buttermilk, yogurt, and cheeses Food microbiologists must also constantly seek the best ways to preserve foods against the many bacteria that cause spoilage or food-borne illnesses The field of biotechnology has taken advantage of bacteria’s ability to accept new genes into their chromosomes By inserting genes into bacteria, bioengineers create unique new products, especially for medicine Biotechnology is now a specialized branch of industrial microbiology that focuses on genetically modified bacteria and fungi Medical microbiology not only depends on bacterial products such as antibiotics, but it also involves ways to combat pathogens Pathogenic bacteria are the bacteria that cause disease Medical microbiology covers all aspects of pathogen virulence, transmittance, infection, and disease Clinical microbiology focuses on the bacteria and other microorganisms isolated from patients who are infected with one or more pathogens This field includes methods for identifying pathogens and selecting drugs to kill infectious bacteria in the body Almost every subject in microbiology is connected in some way to bacteria They have been called the “keepers of the biosphere” because of their vast contributions to the geology and biology on Earth Evolution of life itself on Earth would not have begun without the formation of prokaryotic cells It would be impossible to study biology or many of the Earth sciences without an understanding of the world’s bacteria See also binary fission; biogeochemical cycles; cell wall; culture; cyanobacteria; enteric flora; hybridization; identification; metabolism; morphology; motility; organelle; peptidoglycan; plasmid; proteobacteria; purple bacteria; spore; systematics; taxonomy Further Reading De la Maza, Luis M., Marie T Pezzlo, Janet T Shigei, and Ellena M Peterson Color Atlas of Medical Bacteriology Washington, D.C.: American Society for Microbiology Press, 2004 Dyer, Betsey D A Field Guide to Bacteria Ithaca, N.Y.: Cornell University Press, 2003 Garrity, George M., ed Bergey’s Manual of Systematic Bacteriology Vol 1, The Archaea and the Deeply Branching Phototrophic Bacteria, 2nd ed New York: SpringerVerlag, 2001 ——— Bergey’s Manual of Systematic Bacteriology Vol 2, The Proteobacteria (Part C) The Alpha-, Beta-, Delta-, and Epsilonproteobacteria, 2nd ed New York: Springer-Verlag, 2005 Gest, Howard Microbes: An Invisible Universe Washington, D.C.: American Society for Microbiology Press, 2003 Karlen, Arno Biography of a Germ New York: Anchor Books, 2000 bacteriocin    85 Needham, Cynthia, Mahlon Hoagland, Kenneth McPherson, and Bert Dodson Intimate Strangers: Unseen Life on Earth Washington, D.C.: American Society for Microbiology Press, 2000 Schaechter, Moselio, John L Ingraham, and Frederick C Neidhardt Microbe Washington, D.C.: American Society for Microbiology Press, 2006 Sea Studios Foundation “The Shape of Life.” PBS interview with Mitchell Sogin Available online URL: www pbs.org/kcet/shapeoflife/explorations/bio_sogin.html Accessed March 16, 2009 Sherman, Irwin W Twelve Diseases That Changed Our World Washington, D.C.: American Society for Microbiology Press, 2007 Todar, Kenneth Todar’s Online Textbook of Bacteriology Available online URL: www.textbookofbacteriology net Accessed March 16, 2009 University of Georgia “First-Ever Estimate of Total Bacteria on Earth.” San Diego Earth Times, September 1998 Available online URL: www.sdearthtimes.com/et0998/ et0998s8.html Accessed March 14, 2009 bacteriocinâ•… A bacteriocin is a protein or a smaller chain of amino acids called a peptide made by bacteria to inhibit the growth of other similar bacteria They differ from antibiotics in two ways: Most antibiotics are not proteins, and, in general, bacteriocins target cells of the same species while antibiotics target cells of different species Bacteriocins resemble antibiotics in at least one way, however, because they are substances made by one microorganism to kill other microorganisms The food industry has used bacteriocins as preservatives in food products such as fermented dairy products and packaged meats Biotechnology has also become interested in various bacteriocins as alternatives to antibiotics This new medical role of bacteriocins may become increasingly important in treating diseases caused by pathogens that have developed resistance to most of today’s antibiotics and in direct competition with each other for water, nitrogen, salts, and carbon Bacteria must develop ways to outcompete similar bacteria that occupy the same niche and fight for the same space Bacteriocins represent one way that bacteria gain advantage over their closely related competitors Bacteriocins not kill the cells that produce them To protect against self-destruction, producers make other proteins to counteract the effect of their own bacteriocins Genes that control the synthesis of bacteriocin are said to be synthetic genes, and genes that control a protective protein are called immunity genes If a bacteriocin producer were to lose its immunity genes, it would fall victim to the very bacteriocin it makes for killing other cells Bacteriocin Production and Activity Bacteriocins are either cidal or static; they kill or inhibit growth, respectively Six different modes of action have been uncovered for bacteriocins of either cidal or static effect These actions take place in the cell wall, cell membrane, or chromosome or on ribosomes, summarized as follows: 1.╇formation of pores in the cytoplasmic membrane, causing increased permeability and disrupted energy metabolism 2.╇inhibition of DNA gyrase, which controls the normal spiral twisting of DNA 3.╇destruction of DNA through deoxyribonuclease (DNase) enzyme activity 4.╇damage to cell walls by inhibition of peptidoglycan synthesis 5.╇breakdown of peptidoglycan 6.╇stopping replication by interfering with ribosomes The Role of Bacteriocins Bacteria communicate with each other in their environment through the substances they excrete Bacteriocins and antibiotics participate in this communication by giving bacteria the ability to control the types and amounts of other microorganisms in their vicinity Bacteriocins also offer an advantage to their producers in habitats where nutrients are scarce For example, the normal bacteria of the skin consist of a variety of species that have adapted to conditions that may be very dry, moist, oily, or poorly aerated The species that occupy a niche in the skin’s microbial community are often similar Bacteriocin genes can be located either on the main bacterial DNA or on plasmids Some bacteria may share the bacteriocin genes by transferring plasmids from cell to cell in a process called gene transfer The cell regulates bacteriocin synthesis the same way it regulates the production of other cell constituents, by controlling gene expression Gene expression is the conversion of information contained in specific genes into specific, functioning proteins After making a bacteriocin, the cell excretes it by either of two methods: increased membrane permeability (ability to let substances move in or out) to allow the bacteriocin to escape into the sur- ... angle when the agar solidifies allow the agar also to harden at an angle This type of agar surface is called a slant Slanted agars provide a larger surface area for bacteria or fungi that grow better... Spread plates differ from streak plates by holding an inoculum made as a wide swath across the agar surface After incubation, a spread plate contains a uniform layer of adjacent colonies called a. .. II Glossary 806 III Further Resources 810 IV Proposed Hierarchy of Biota 812 V Classification of Bacteria and Archaea 813 VI Viruses of Animals and Plants 826 VII Major Human Diseases Caused by

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