Introduction to Microbiology: Then and Now

NOT FORSALEORDISTRIBUTION © Jones&BartlettLearning,LLC NOT FORSALEORDISTRIBUTION © Jones&BartlettLearning,LLC NOT FORSALEORDISTRIBUTION © Jones&BartlettLearning, LLC NOT FORSALEORDISTRIBUTION © Jones&BartlettLearning,LLC 9781284240535_CH01_001_024.indd 1

(right) Courtesy of Jed Alan Fuhrman, University of Southern California. (left) Courtesy of JPL-Caltech/NASA. 1-4 1-3 1-2 (smaller dots),andadiatom(center). Photographic imageofnearbygalaxies andstarsinspace(left)alight microscope image(right)ofbacterial cells(larger dots),viruses 1-5 1-1 CHAPTER KEYCONCEPTS Microbiology: Then andNow Introduction to NOT FORSALEORDISTRIBUTION © Jones&BartlettLearning,LLC NOT FORSALEORDISTRIBUTION © Jones&BartlettLearning,LLC NOT FORSALEORDISTRIBUTION © Jones&BartlettLearning,LLC invisible frontier here onEarth.Thisisthemicrobial universe, whichconsists ofmore than10 an estimated 350billionlarge galaxies and more than10 Space and the universe often appear to be an unlimited frontier. Thechapter opener image on the left shows one of Earth’s Microbiomes around theglobe. (the “then”) thatfirst putmicrobes onthemap, andfinally recognize somechallenges facing microbiology now. and then examine the community of microbes that inhabit the human body. We will, learn of the historical events organisms ontheplanet. phere. Beingthatthey are soprolific globally, thesemicrobes must play important roles inthevery survival ofother is to characterize Earth’s microbial diversity inallits environments, includingtheoceans, landmasses, andatmos- Earth where living organisms are found. This effort is called the scientists from manyscientificfields are cataloging themicrobial diversity ofthebiosphere,regions ofthe but, aswe willsee,they are magnificent intheirevolutionary diversity andastounding intheirsheernumbers. (or

CHAPTER 1 microbes for short).Asthechapter openerimageontherightshows, microbes might bemicroscopic insize, Microbiology Now The Microbial World IsCat Microbiology Then:ThePioneers The HumanBodyHasIts OwnMicrobiome Microbial CommunitiesSupportandAffect AllLife onEarth So, first, let’s discover whataday islike for someofEarth’s microbes inshapingthefundamental life processes A majorfocus ofthis chapter isto give you a“first look” at microbes. We willexamine Earth’s microbiomes This global community ofmicrobes andtheirgenesforms Earth’s microbiome.Today, microbiologists and © Jones&Bartlett Learning LLC,anAscendCompany. NOTFORSALEORDISTRIBUTION. NOT FORSALEORDISTRIBUTION © Jones&BartlettLearning,LLC NOT FORSALEORDISTRIBUTION © Jones&BartlettLearning,LLC NOT FORSALEORDISTRIBUTION © Jones&BartlettLearning,LLC : Challenges Remain aloged into UniqueGroups NOT FORSALEORDISTRIBUTION © Jones&BartlettLearning,LLC NOT FORSALEORDISTRIBUTION © Jones&BartlettLearning,LLC NOT FORSALEORDISTRIBUTION © Jones&BartlettLearning, LLC NOT FORSALEORDISTRIBUTION © Jones&BartlettLearning,LLC 24 stars intheknown universe. However, there isanother Earth MicrobiomeProject, and its challenge NOT FORSALEORDISTRIBUTION © Jones&BartlettLearning,LLC NOT FORSALEORDISTRIBUTION © Jones&BartlettLearning,LLC NOT FORSALEORDISTRIBUTION © Jones&BartlettLearning,LLC NOT FORSALEORDISTRIBUTION © Jones&BartlettLearning,LLC NOT FORSALEORDISTRIBUTION © Jones&BartlettLearning,LLC NOT FORSALEORDISTRIBUTION © Jones&BartlettLearning,LLC 30

microorganisms 30/12/20 1:18 PM 1 2 Chapter 1 Introduction to Microbiology: Then and Now

© Jones Figure& Bartlett 1-1 SEEING Learning, THE CONCEPT LLC © Jones & Bartlett Learning, LLC NOT FOREarth’s SALE microbiomes OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION The microorganisms that comprise Earth’s microbiomes represent an untapped source of genetic diversity and chemical transformations of matter and material. © Vadik4444/Shutterstock. © Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION

The Atmospheric Microbiome © Jones & BartlettEach Learning,cubic meter of air LLC contains 9,000 to 300,000 microbes© Jonesand more than& Bartlett Learning, LLC NOT FOR SALE315 OR diff erentDISTRIBUTION types of bacteria have been identified in air massesNOT FOR10 SALE OR DISTRIBUTION kilometers (more than 6 miles) above the Earth’s surface. While each air mass has its own unique community of biological particles, microbes along with fungal spores account for 20% of these particles. Every day the atmospheric microbiome: • Plays an integral role with marine microbes in the formation of © Jones & Bartlett Learning, LLC water vapor (clouds). © Jones & Bartlett Learning, LLC • Helps support the formation of raindrops and snowflakes. NOT FOR SALE OR DISTRIBUTION • Affects the chemical compositionNOT FOR of the SALEatmospher ORe. DISTRIBUTION • Influences weather cycles, altering the composition of rain and snow, and shaping daily weather patterns.

© Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION The Marine Microbiome The oceans and seas cover more than 70% of the Earth’s surface and represent the foundation that maintains our planet in a habitable condition. A critical factor in this maintenance is the 3 × 1029 microbes that represent 90% of the ocean’s biomass. High densities of single-celled © Jones & Bartlett Learning,microbes and LLCviruses can be found anywhere from© theJones frozen polar& Bartlett regions Learning, LLC NOT FOR SALE OR DISTRIBUTIONto the hot, volcanic thermal vents and the cold seepsNOT on theFOR dark SALEseafloor. OR DISTRIBUTION Every day the marine microbiome: • Creates the foundation for all marine food webs on which all fish and ocean mammals directly or indirectly depend. • Provides through photosynthesis up to 50% of the oxygen gas that we breathe, and many other organisms use to stay alive. © • JonesControls atmospheric& Bartlett aerosols Learning, and cloud LLCformation through © Jones & Bartlett Learning, LLC the sea spray ejected into the atmosphere. NOT • Co nsumesFOR SALE50% of the OR dead DISTRIBUTION plant and animal matter NOT FOR SALE OR DISTRIBUTION generated on Earth each day. • Operates exclusively as the engines that drive and control nutrient and mineral cycling and regulates energy flow, both of which can affect long-term climate change. © Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION

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The Soil Microbiome Microbial activity in soil is as impressive as that of its marine partners. In fact, microbes are found in every type of soil environment, from the tops © Jones & Bartlett Learning, LLC of the highest mountains© Jones to the & deepest Bartlett cave s.Learning, A kilogram of moistLLC garden soil can have up to 1013 microbes living in the water-filled pore spaces of NOT FOR SALE OR DISTRIBUTION the soil. Every dayNOT the soilFOR microbiome: SALE OR DISTRIBUTION • Influences soil fertility by carrying out 90% of all biochemical reactions occurring in the soil. • Recycles dead plant and animal material and returning carbon dioxide to the atmosphere. • Represents a source for many of today’s antibiotics. © Jones & Bartlett Learning, • Degrades LLC pesticides and other synthetic pollutants© Jones that & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION contaminate the soil. NOT FOR SALE OR DISTRIBUTION • Provides plants with access to important nutrients, such as carbon, nitrogen, sulfur, and phosphorus.

The Deep Earth Microbiome Scientists have drilled kilometers into the Earth’s subsurface on land or below the seafloor. In this solid rock, microbiologists have discovered communities of © Jones & Bartlett Learning, LLC microbes© Jones that are& sealedBartlett off from Learning, the rest of the LLCworld. NOT FOR SALE OR DISTRIBUTION AlthoughNOT FOR less well SALE studied, ORscientists DISTRIBUTION believe that every day the deep earth microbiome: • Alters the chemical makeup of minerals. • Degrades pollutants. • Changes the mineral content of ground water. © Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION

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Almost 4 billion years ago, Earth was a microbial no less impressive in its daily activities than that of its planet. The diverse and© Jonesnumerous & Bartlettmicroorganisms Learning, marine LLC counterparts. In fact, ©every Jones time you& Bartlett walk on Learning, LLC populating the planet NOTwere beginningFOR SALE the processesOR DISTRIBUTION the soil, you step on billions ofNOT microbes FOR ( FigureSALE 1-3 OR). DISTRIBUTION that would create the environment that sustains and Moreover, like their cousins in the oceans, they are shapes our planet and that has made Earth habitable found in every imaginable environment, from the tops for larger organisms like plants and animals. Scien- of the highest mountains to the deepest caves. The tists today continue to uncover more key roles being World Bank reports that almost 40% of the terrestrial carried ©out Jones within & Earth’s Bartlett microbiome. Learning, So, LLCwith the © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION aid of SEEING THE CONCEPT (Figure 1-1 previous page), let’s travel around the world and discover some Figure 1-2 The marine microbiome of Earth’s microbiomes that constitute the life support In this light microscopy image, each large dot is one bacterial cell, and each small dot is a virus normally system of the biosphere. found in one drop of seawater. (Bar = 10 μm) © Jones & Bartlett Learning, LLC © JonesCourtesy of Rachel Parsons,& Bartlett Bermuda Institute of Ocean Learning, Science. LLC NOT FORThe SALE Marine OR DISTRIBUTION Microbiome Is One NOT FOR SALE OR DISTRIBUTION of the Largest Microbiomes on the Planet The oceans and seas cover© Jones more than & Bartlett 70% of planetLearning, LLC © Jones & Bartlett Learning, LLC Earth and represent the foundation that maintains NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION our planet in a habitable condition. This foundation is controlled by the marine microbiome, which represents the microorganisms found everywhere from the frozen polar regions to the hot, volcanic thermal vents and© Jones the cold & seepsBartlett on the Learning, dark seafloor. LLC This © Jones & Bartlett Learning, LLC amountsNOT to someFOR 3 SALE × 1029 ORmicrobes DISTRIBUTION and represents NOT FOR SALE OR DISTRIBUTION 90% of the marine biomass (total mass of all organisms in an area). Look back at Seeing the Concept (Figure 1-1), which lists several of the daily roles of the marine microbiome in regulating life on Earth. © Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC Viruses are the most abundant infectious agents NOT FORon Earth.SALE In OR the DISTRIBUTIONoceans, they outnumber the bacteria NOT FOR SALE OR DISTRIBUTION 10 to 1 (Figure 1-2). Although most of these viruses remain uncharacterized, they can infect marine microbes Figure 1-3 The soil microbiome If a few grains of soil are placed in a culture dish, and affect marine life in many ways. For example, ma- aggregations of bacteria and fungi (brownish clusters) rine viruses kill 20% to ©40% Jones of all marine& Bartlett bacteria Learning, ev- grow. LLC © Jones & Bartlett Learning, LLC 29 ery day and are responsibleNOT for FOR swapping SALE 10 OR genes DISTRIBUTION © Alexander Gold/Shutterstock. NOT FOR SALE OR DISTRIBUTION between bacteria each day. These effects alone suggest that viruses control the course of bacterial evolution and the daily activities in these marine microbiomes. As such,© manyJones scientists & Bartlett believe Learning, viruses represent LLC the © Jones & Bartlett Learning, LLC most dominant agents affecting life on Earth. NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION

The Soil Microbiome Shapes the World Around Us © JonesThe & Bartlettsoil microbiome Learning, represents LLC a dynamic group of © Jones & Bartlett Learning, LLC NOT FORdistinct SALE microbial OR DISTRIBUTION communities associated with plants, NOT FOR SALE OR DISTRIBUTION soil animals, and the soil itself. Soil microbial diversity is on a par with that in the marine environments and is

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environment is used for agriculture. Coupled with the The atmospheric microbiome © JonesFigure & Bartlett 1-4 Learning, LLC © Jones & Bartlettfact that aLearning, kilogram of LLCmoist farming soil can have up If an air sample from as high up as 10 kilometers NOT FOR SALEto 10 13OR microbes DISTRIBUTION living in the soil’s water-filled NOTpore FOR(6.2 miles) SALE is OR exposed DISTRIBUTION to nutrients in a culture dish, spaces, it becomes clear that the daily activities of many different species of bacteria (small dots) and fungi (larger fuzzy circles) soon appear. these microbes are essential to life. Seeing the Concept © Khamkhlai Thanet/Shutterstock. (Figure 1-1) lists some of the daily activities carried out by soil microbes.© Jones As the &drivers Bartlett of soil Learning, chemistry, LLC © Jones & Bartlett Learning, LLC soil microbes are NOTprotectors FOR of SALEthe soil’s OR health, DISTRIBUTION and in NOT FOR SALE OR DISTRIBUTION so doing are helping to feed the world.

The© Jones Atmospheric & Bartlett Learning, Microbiome LLC © Jones & Bartlett Learning, LLC CarriesNOT FOR a SALE Diverse OR DISTRIBUTION Community NOT FOR SALE OR DISTRIBUTION of Bacteria and Fungi When seen from space, planet Earth has been referred to as a “pale blue dot” washed in white clouds. In this atmosphere though, events like soil erosion hurl soil © Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC microbes, ocean evaporation lifts marine microbes, NOT FOR SALE OR DISTRIBUTION NOT FORFigure SALE 1-5 The OR deep DISTRIBUTION Earth microbiome and coughing and sneezing launch microbes and vi- Dr. Beth Orcutt (left front row) from the Bigelow ruses into the air. In fact, more than 315 different types Laboratory for Ocean Sciences in Maine and other of bacteria have been identified in air masses 10 kilo- researchers are trying to understand how life meters (more than 6 miles) above the Earth’s surface. below the seafloor can survive and thrive. These microbes, along© Jones with fungal& Bartlett spores, Learning, account for LLCCourtesy of Jennifer Magnusson/IODP. © Jones & Bartlett Learning, LLC 20% of all particles—biologicalNOT FOR SALE and nonbiological—in OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION the atmosphere (Figure 1-4). Although less studied than the ocean and soil microbiomes, scientists believe that these atmospheric communities also perform essential daily© Jones roles (see & BartlettSeeing the Learning, Concept in Figure LLC 1-1). © Jones & Bartlett Learning, LLC Today, microbiologists believe they have dis- NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION covered only about 2% of all microbes. Besides the oceans, soil, and atmosphere, where else are microbes found?

© Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC NOT FOR SALEThe OR Deep DISTRIBUTION Earth Microbiome NOT FOR SALE OR DISTRIBUTION Is Home to Vast and Unusual Communities of Microbial Life Today, scientists are beginning a real-life journey to- century. Yet, as listed in Figure 1-1, they might have ward the center ©of Jonesthe Earth. & BartlettThese scientists Learning, have LLC © Jones & Bartlett Learning, LLC roles in the daily functions of the planet equal to those drilled up to 5 kilometersNOT FOR (3 SALEmiles) intoOR theDISTRIBUTION Earth’s NOT FOR SALE OR DISTRIBUTION living underworld (subsurface) on land or below the of the other microbiomes of the biosphere. Today, the workforce comprising the global mi- seafloor (Figure 1-5). In the water-filled pore spaces of solid rock, they have discovered another frontier crobiome is still being cataloged, and their numbers composed of microbes (primarily bacteria and fungi) and daily activities keep growing. As Louis Pasteur, © Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC that are sealed off from the rest of the world and live in one of the fathers of microbiology, once stated, “Life perpetualNOT FOR darkness. SALE These OR DISTRIBUTION so-called “deep microbes” [plant andNOT animal] FOR wouldSALE not OR long DISTRIBUTION remain possible in that survive in these inhospitable conditions (e.g., ex- the absence of microbes.” treme heat, no light, sparse nutrients) might make up 70% of the microbes on Earth and more than 50% of © Jones & Bartlettthe biomass Learning, of the planet. LLC These relatively slow-grow© Jones- Concept& Bartlett Check Learning, 1-1 LLC NOT FOR SALEing microbes OR DISTRIBUTION often are called “zombie” bacteria NOTbe- FOR SALE OR DISTRIBUTION 1. What are microbiomes, and what are some of the cause they seem to be barely alive. Some might be roles they play globally? up to 100 million years old, reproducing only once a

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The presence and need for microbes can be found come from mother’s birth canal during delivery. Soon, much closer to home. Microbiomes© Jones & cohabit Bartlett the bodiesLearning, this LLC human microbiome is strengthened© Jones through& Bartlett con- Learning, LLC of all plants and animals. In the case of animals, every tact with microbes coming from caregivers, family NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION animal from termites to bees, cows, and humans has members, family pets, foods, and other environmen- an intimate set of microbial communities associated tal sources. The result is the development of unique and coevolving with it. The human microbiome microbial communities of microbes on the skin, in the (formerly and sometimes still called the “microflora”) mouth and respiratory tract, and especially in the gut. consists© of Jones some 38 & trillion Bartlett microbes Learning, composing LLC more Although© some Jones microbes & Bartlett in the body Learning, are tempo LLC- than 4,000NOT different FOR SALEtypes of OR bacteria DISTRIBUTION and fungi found rary, most membersNOT FOR of the SALEhuman ORmicrobiome DISTRIBUTION spend on and in the human body. This is greater than the each day carrying out an amazing array of metabolic number of cells (30 trillion) forming the human body reactions. The microbes of the gastrointestinal tract (Figure 1-6A). All human microbiomes do not share help prevent infectious disease, aid in the breakdown © Jonesthe & same Bartlett set of Learning, microbes. Rather, LLC each individual has © Jonesfood, provide & Bartlett essential Learning, nutrients LLCand vitamins that NOT FORa unique SALE microbiome OR DISTRIBUTION specific to the skin, the mouth, NOTthe FORbody cannotSALE make,OR DISTRIBUTION and chemically communicate and the gut that results from physiological differences, with the brain and immune system. These microbes age, diet, and geographic location (Figure 1-6B). In might even influence the risk of developing obesity, fact, the belly button alone has a unique combination asthma, and allergies. To be human and healthy, we of more than 50 types of bacteria! Where did these must share our daily lives with homegrown commu- microbial companions come© Jones from, &and Bartlett what good Learning, are nities LLC of microbes. © Jones & Bartlett Learning, LLC they? NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION The communities of microbes living on and in the body did not appear by accident. A healthy human Concept Check 1-2 fetus is free of most microbes until birth. Then, during and immediately after birth, body surfaces (e.g., skin, 2. Where on and in the body of a healthy human are © Jones & Bartlett Learning, LLC microbes© normally Jones f ound?& Bartlett Learning, LLC mouth, eyes, nose, gut) on and in the newborn that NOT FOR SALE OR DISTRIBUTION 3. Identify someNOT of FOR the roles SALE the human OR DISTRIBUTION microbiome have contact with the environment become populated plays in daily life. with a large variety of these microbes. Initially, most

One aspect of a microbe’s daily life that we have over- inquiry stimulated the quest to understand the cor- looked until now is its role in infectious disease. Only relation between microbes and infectious disease. To an exceedingly small minority© Jones of microbes & Bartlett are respon Learning,- begin LLC our story, we reach back© to Jonesthe 1600s, & Bartlettwhere we Learning, LLC sible for infections andNOT disease. FOR Although SALE suchOR DISTRIBUTIONdis- encounter some very inquisitiveNOT individuals. FOR SALE OR DISTRIBUTION ease-causing agents, called pathogens, are rare, some, such as those causing diseases like plague, malaria, and smallpox, throughout history have swept through Hooke and Leeuwenhoek cities and© Jones villages, & devastated Bartlett populations, Learning, andLLC killed Discover© theJones Microbial & Bartlett Learning,World LLC great leadersNOT FOR and SALEcommoners OR DISTRIBUTIONalike. Coronavirus Robert Hooke,NOT an English FOR natural SALE philosopher OR DISTRIBUTION (the term disease 2019 (COVID-19) is the most recent to join “scientist” was not coined until 1833), was one of the this pandemic group. As a result, microbes have been most inventive and ingenious minds in the history of instrumental in transforming politics, economies, and science. As the Curator of Experiments for the Royal public health on a global scale. However, only a small Society of London, Hooke published a book in 1665 © Jonesminority & Bartlett of microbes Learning, are dedicated LLC pathogens. © Jonescalled Micrographia & Bartlett, in Learning, which he took LLC advantage of the NOT FOR SALEIn this ORsection, DISTRIBUTION we will see how microbes were NOTmagnification FOR SALE abilities OR DISTRIBUTIONof the early microscopes. In this first discovered and how curiosity and scientific book, he made detailed drawings of many diverse living

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Figure 1-6 The human microbiome © Jones & Bartlett Learning, LLC © Jones & BartlettThe human Learning, microbiome LLC comprises all the individual microbial communities that live on or within human tissues (A) NOT FOR SALEand corresponding OR DISTRIBUTION anatomical sites (B). What is commonNOT to allFOR the humanSALE body OR sites DISTRIBUTION having a microbiome? B: Courtesy of NIH Medical Arts and Printing.

A B The cells of the human microbiome (bacte- Each human possesses several anatomcal areas that rial and fungal) outnumber the human each contain a unique microbiome. cells© Jonesin the body. & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION

Fungal (8%)

Bacterial (49%) © Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION

objects, including fleas, lice, and peacock feathers. Per- Aware of Hooke’s Micrographia, Leeuwenhoek haps his most famous description was for the structure turned his microscope to the invisible world. Begin- © Jones & Bartlettof cork, theLearning, buoyant, LLClight brown substance obtained© Jones ning & Bartlettin 1673 and Learning, until his deathLLC in 1723, Leeuwen- from the outer layer of the bark of the cork oak. Seeing hoek communicated his microscope observations NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION “a great many little boxes,” he called these boxes cella (= through some 300 letters sent to England’s Royal So- “rooms”), and from that observation, today we have the ciety of London, one of the most respected scientific word “cell” to describe the basic unit of life (Figure 1-7). societies of the time. In 1674, one of his first letters Micrographia represents one of the most import- described a sample of lake water. Placing the sam- ant books in science© Jones history. &It Bartlettawakened Learning,the learned LLCple before his lens, he described© Jones hundreds & Bartlett of moving Learning, LLC and general populationNOT FORof Europe SALE to the OR world DISTRIBUTION of the particles. He thought theyNOT must FOR be SALE tiny living OR DISTRIBUTIONani- very small, revolutionized the art of scientific investi- mals, so he called them animalcules (cul = “little”). gation, and showed that the microscope was an im- This discovery represents one of the most important portant tool for unlocking the secrets of an unseen observations in history because Leeuwenhoek had world:© Jones the world & Bartlett of the cell. Learning, LLC described© Jones and illustrated & Bartlett for the Learning, first time theLLC micro- NOTAt FORthis same SALE time, OR across DISTRIBUTION the North Sea in Delft, bial world.NOT FOR SALE OR DISTRIBUTION Holland, Antoni van Leeuwenhoek was grinding sin- Equally significant was a 1676 letter in which he gle pieces of glass into fine magnifying lenses. As a suc- describes and draws the first unmistakable observa- cessful tradesman and dry goods dealer, he used these tions of bacteria (Figure 1-8C). Among the other letters hand lenses to inspect the quality of his cloth. Placing sent to the Royal Society, he described all the different © Jones & Bartlettsuch a lens Learning, between two LLC metal plates riveted together,© Jones types & Bartlett of microbes Learning, (except viruses)LLC that we know of NOT FOR SALELeeuwenhoek’s OR DISTRIBUTION “simple microscope” could greatly NOTout FORtoday. SALE This ORincluded DISTRIBUTION details of yeast cells, threadlike magnify Hooke’s microscope (Figure 1-8A, B). fungi, and microscopic algae and protozoa.

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Figure 1-7 Hooke’s Micrographia Figure 1-8 Viewing animalcules © JonesMicrographia & Bartlett was Learning, the first important LLC work involving © JonesTo view his & animalcules,Bartlett Learning, Leeuwenhoek LLC used a simple NOT FORmicroscopy. SALE Hooke’sOR DISTRIBUTION drawing and description of NOTmicroscope FOR SALE with one OR lens DISTRIBUTION (A). When held up to the cork was the first use of the word “cell” to describe light (B), Leeuwenhoek could see his animalcules (C). biological objects. Why would Leeuwenhoek believe his living (and moving) Robert Hooke. Micrographia: or, Some physiological descriptions of minute bodies made by magnifying glasses. London: J. Martyn creatures were tiny animals? and J. Allestry, 1665. (first edition). B: Collection of the University of Michigan Health System, Gift of Pfizer, Inc. (UMHS.15); C: © Royal Society, London. © Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC A NOT FOR SALE OR DISTRIBUTION A drawing of Leeuwenhoek'sNOT FOR SALE OR DISTRIBUTION microscope.

Lens

Specimen © Jones & Bartlett Learning, LLC © Jonesmount & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION NOTSc rewFOR SALE OR DISTRIBUTION plate

Elevating screw © Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTIONB NOT FOR SALE OR DISTRIBUTION Leeuwenhoek observed a specimen by looking through the lens of his microscope.

The process of observation is an important skill © Jonesfor & all Bartlett scientists Learning, and remains LLC the cornerstone of all © Jones & Bartlett Learning, LLC NOT FORscientific SALE inquiry. OR DISTRIBUTION Hooke and Leeuwenhoek are excel- NOT FOR SALE OR DISTRIBUTION lent examples of individuals with sound observational skills. Unfortunately, Leeuwenhoek invited no one to work with him, nor did he show anyone how he made his lenses. Thus, naturalists at the time found it diffi- © Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC cult to repeat and verify his observations, which also C NOT FOR SALE OR DISTRIBUTIONFrom the microscope observations,NOT FOR Leeuwen- SALE OR DISTRIBUTION are key components of scientific inquiry. Still, Leeu- hoek drew the animalcules he saw. wenhoek’s observations of animalcules opened yet a second door to another entirely new microscopic world: the world of the microbe. © Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION

Concept Check 1-3A

4. How were the first microbes discovered? © Jones 5.& BartlettIf you were Learning, alive in Leeuwenhoek’s LLC time, how © Jones & Bartlett Learning, LLC NOT FOR SALEwould youOR explain DISTRIBUTION the origin for the animalcules NOT FOR SALE OR DISTRIBUTION he saw with his simple microscope?

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For many years, natural philosophers debated Louis Pasteur and fermentation bacteria © JonesFigure & Bartlett 1-9 Learning, LLC © Jones & Bartlettthe origins Learning, of Leeuwenhoek’s LLC animalcules. Some Louis Pasteur (A) believed bacteria spoiled wine, as he NOT FOR SALEsaid they OR aroseDISTRIBUTION from a “vital force” that reorganizedNOT FORcould SALE see these OR cells DISTRIBUTION through his microscope (B). dead and decaying matter into organized life. Others A: Courtesy of National Library of Medicine. countered that the animalcules only arose from other A Louis Pasteur as a 46-year-old professor of chemistry at living animalcules, often found in the air. Then, in the University of Paris. 1861, the French© chemist Jones and & Bartlettscientist Louis Learning, Pasteur LLC © Jones & Bartlett Learning, LLC (Figure 1-9A) settledNOT the FOR debate. SALE Through OR DISTRIBUTIONan elegant NOT FOR SALE OR DISTRIBUTION series of experiments, he showed that animalcules (microbes) do come from others present in the air. Investigating the Microbial World 1 outlines the process© Jones of scientific & Bartlett inquiry Learning,and Pasteur’s LLCexperiments. © Jones & Bartlett Learning, LLC So, Pasteur was able to prove that microbes only NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION come from the reproduction of other microbes. How- ever, no one before Pasteur had considered whether these microbes found in the air could be agents of infectious disease. Then, in the early 1850s, research © Jones & Bartlettinto the associationLearning, between LLC microbes and the disease© Jones & Bartlett Learning, LLC NOT FOR SALEprocess OR blossomed. DISTRIBUTION Over the next 60 years, the founNOT- FOR SALE OR DISTRIBUTION dations would be laid for the maturing process that has led to the modern science of microbiology. This period is referred to as the classical or first Golden Age B of microbiology. Pasteur believed that bacterial cells, similar © Jones & Bartlett Learning, LLC to these that he saw© byJones with the µscope, Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION could cause the souringNOT of FOR wine. (Bar SALE = 5 μm) OR DISTRIBUTION Pasteur Proposes That Germs Cause Infectious Disease Trained as a chemist, Louis Pasteur believed that problems© Jones in &science Bartlett could Learning, be solved in LLC the laboratory © Jones & Bartlett Learning, LLC withNOT the FOR results SALE having OR practical DISTRIBUTION applications. NOT FOR SALE OR DISTRIBUTION

Fermentation Always one to tackle big problems, Pasteur set out © Jones & Bartlettto understand Learning, the chemical LLC process of fermentation.© Jones & Bartlett Learning, LLC The prevailing theory in the early 1850s held that fer- NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION mentation was strictly a chemical process, and that the yeasts needed for fermentation were simply inert chemical “globules” that stimulated the process. Pas- teur was unconvinced. His microscope observations consistently revealed© Jones large &numbers Bartlett of Learning,tiny yeast LLC © Jones & Bartlett Learning, LLC cells in fermentedNOT juice. FOR When SALE he mixed OR DISTRIBUTIONyeast in a have contaminated a batchNOT of yeastFOR and, SALE as another OR DISTRIBUTION ex- sugar–water solution in the absence of air, the yeast ample of a biological process, produced the acids that multiplied and converted the sugar to alcohol. Fer- caused the souring. Pasteur recommended a practi- mentation, then, was a biological process, and yeasts cal solution for the “wine disease” problem: heat the were© Jones living &agents Bartlett responsible Learning, for the LLC fermentation wine gently© Jones to kill & the Bartlett harmful Learning,bacterial cells LLC but not process.NOT FOR SALE OR DISTRIBUTION so stronglyNOT as FORto affect SALE the quality OR DISTRIBUTIONof the wine. His con- On the applied side, Pasteur demonstrated that trolled heating technique solved the wine problem and, wines, beers, and vinegar each contained different what would become known as pasteurization, soon and specific types of microorganisms that had spe- was applied to other products. Today, pasteurization is cific properties. For example, in studying a local a universal method used to kill pathogens and retard © Jones & Bartlettproblem Learning,of wine souring, LLC he observed that only ©the Jones spoilage & Bartlett in milk Learning, and many other LLC foods and beverages. NOT FOR SALEsoured OR wines DISTRIBUTION contained populations of bacterial cellsNOT FOR SALEIf “wine OR disease” DISTRIBUTION could be caused by tiny, living (Figure 1-9B). Pasteur concluded that these cells must bacteria, Pasteur reasoned that infections and disease

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Science certainly is a body of knowledge, but science also is a process—a way of learning. Often, we accept and integrate into our understanding new information because it appears consistent with what we believe is true. But, are we confident our beliefs© Jones are always & Bartlett in line with Learning, what is accurate? LLC To test or challenge current© Jones beliefs, & scientists Bartlett Learning, LLC must present logical argumentsNOT FOR supported SALE by OR well-designed DISTRIBUTION and carefully performed experimentsNOT FOR. SALE OR DISTRIBUTION The Components of Scientific Inquiry There are many ways of finding out the answer to a problem. In science, scientific inquiry—or what commonly has been called the “scientific method”—is a variety of procedures used to investigate a problem. Let’s understand how scientific© Jones inquiry & Bartlett works by followingLearning, the logicLLC of the experiments Louis© Pasteur Jones published & Bartlett to show Learning, that LLC microbes are present in the air. Pasteur set up the following experiment to test the hypothesis. NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION Results Pasteur and the microbes in air ■ No growth (microbes) was First, broth in a swan-necked flask (flask with a long, tapered neck) is boiled. If seen in the intact flasks. allowed to cool and remain undisturbed, air can enter the flask, but the curvature ■ Microbes (cloudy liquid) of the neck traps dust particles and microorganisms, preventing them from © Jones & Bartlettwere found Learning, in the flasks LLCreaching the broth. If a similar© Jones flask &of sterilizedBartlett broth Learning, has the neck LLC snapped off NOT FOR SALEafter the OR neck DISTRIBUTION was (A), or the flask is tippedNOT so broth FOR enters SALE the neck OR(B) DISTRIBUTION, organisms will contact the snapped off or the flask broth and grow. tipped so the broth General When studying a problem, the inquiry process usually begins with observations. Pasteur’s earlier observations entered the neck. observations suggested that germs might be in the air. Next comes the question, which can be asked in many ways but usually as a “what,” “why,” or “how” question. Conclusions © Jones &Question BartlettFor exLearning,ample, Pasteur asked, LLC “How can I show that microbes are in the air?”© Jones & Bartlett Learning, LLC Let’s analyze the results.NOT FOR SALE ORA hypothesis DISTRIBUTION is a provisional but testable explanation for the question or obserNOTvation. PaFORsteur’s hy pothesisSALE OR DISTRIBUTION was that “Microbes appearing in the sterile flask come from other germs in the air.” If so, then air allowed to Hypothesis Pasteur had a preconceived enter the sterile flask will contain germs that will grow in such profusion that they will be seen as a cloudy notion of what should happen liquid. if his hypothesis was correct. Swan-necked flask Experiments In his experiments, only one Dust and microorganisms “variable”© Jones (an adjustable & Bartlett Learning, LLC © Jones & BartlettAir are Learning, trapped LLC Flask Time enters condition)NOT changed. FOR SALE In the OR DISTRIBUTION cooled NOT passesFOR SALE OR DISTRIBUTION experiment, the flasks were left intact or they were exposed to the air by breaking Sterile brothNo organisms The experiment appear the neck or tipping the flask. begins with a boiled AB Pasteur kept all other factors broth solution. Flask neck Flask tilted so © Jones & Bartlett Learning, LLC © snappedJones off & Bartlettbroth en tersLearning, neck Time LLC the same; that is, the broth passes NOT FORwas SALE the same OR in DISTRIBUTION each flask, NOT FOR SALE OR DISTRIBUTION it was heated the same Results length of time, and similar Organisms appear Organisms appear flasks were used in each experiment. © Jones Conclusions& Bartlett Learning, LLC © Jones & Bartlett Learning, LLC Thus, the experiment had rigorous “controls” (theNOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION comparative condition), which were the intact swan-necked flasks. Pasteur’s finding that no microbes appeared in these flasks is interesting but tells us little by itself. Its significance comes© byJones comparing & Bartlett this to the Learning, broken-neck LLC (or tipped) flasks where microbes© Jones quickly & appeared. Bartlett These Learning, LLC experiments validated his hypothesis. NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION Hypothesis and Theory A “theory” is defined as a hypothesis that has been tested and shown to be correct every time by many separate investigators. So, at some point, if validated by others, enough evidence exists to say a hypothesis is now a theory. However, theories are not written in stone. They are open to further experimentation, and so can be proven false. © Jones As& Bartletta side note, Learning, today a theory LLC often is used incorrectly in everyday© Jones conversation & Bartlett and Learning, in the news media. LLC In these NOT FORcases, SALE a theory OR DISTRIBUTIONis equated incorrectly with a hunch or belief—whetherNOT FOR thereSALE is evidence OR DISTRIBUTION to support it or not.

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also might be caused by other microorganisms in the sheep suffering from anthrax. He noticed the mice © Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC environment—what he called germs. soon developed the same disease symptoms seen NOT FOR SALE OR DISTRIBUTION NOT FORin theSALE sheep. OR Next, DISTRIBUTION he isolated a few rod-shaped bacterial cells from the blood and, with his micro- Silkworm Disease scope, watched for hours as the bacterial cells mul- Pasteur sought more evidence for his germ theory idea. tiplied, formed tangled threads, and finally reverted In 1865, he had the opportunity to study pébrine, an © Jones & Bartlett Learning, LLCto spores. He then took© Jonesseveral spores& Bartlett on a Learning,sliver LLC infectious disease of silkworms. After several setbacks NOT FOR SALE OR DISTRIBUTIONof wood and injected NOTthem intoFOR healthy SALE mice. OR DISTRIBUTIONThe and 5 years of work, he finally identified a new type signs of anthrax soon appeared, and when Koch au- of germ, unlike the bacterial cells and yeast he had ob- topsied the animals, he found their blood swarming served with his microscope. These tiny germs, which with the same type of bacterial cells. Here was the he called “corpuscular parasites,” were the infectious first evidence that a specific germ was the infectious agent© Jones in silkworms & Bartlett and on Learning, the mulberry LLC leaves fed to © Jones & Bartlett Learning, LLC agent of a specific disease. theNOT worms. FOR By SALE separating OR the DISTRIBUTION healthy silkworms from NOT FOR SALE OR DISTRIBUTION When Koch presented his final version of the the diseased silkworms and their contaminated food, guidelines at a scientific meeting, fellow scientists he managed to quell the spread of the silkworm dis- were astonished. Here was the verification of the germ ease. Today, we know the “corpuscular parasites” were theory that had eluded Pasteur. Koch’s guidelines be- a type of protozoan. © Jones & Bartlett Learning, LLC © Jonescame & Bartlett known as Learning, LLC and were quickly From these scientific investigations, Pasteur for- Koch’s postulates NOT FOR SALE OR DISTRIBUTION NOT FORadopted SALE as ORthe DISTRIBUTIONformalized standards for implicat- mulated the , which held germ theory of disease ing a specific germ with a specific disease. SEEING that some microorganisms are responsible for infec- THE CONCEPT ( ) outlines the four-step tious disease. However, to validate the germ theory, Figure 1-10 process. what Pasteur was missing was the ability to isolate a In doing his studies, Koch found that grow- specific germ from© Jonesa diseased & animalBartlett and Learning,demonstrate LLC © Jones & Bartlett Learning, LLC ing pure cultures of bacterial cells was cumber- that the isolated germNOT caused FOR thatSALE same OR disease DISTRIBUTION in an- NOT FOR SALE OR DISTRIBUTION some. Then, in 1880, he observed a slice of potato other healthy animal. on which small masses of bacterial cells, which he termed colonies, were multiplying in number. Koch tried adding gelatin to his broth to prepare a similar © Jones & Bartlett Learning, LLC solid culture© Jones surface. & Bartlett He then Learning, inoculated LLCbacterial NOTConcept FOR CheckSALE 1-3BOR DISTRIBUTION cells onNOT the surfaceFOR SALE and set OR the DISTRIBUTION dish aside to incu- bate. Within 24 hours, visible colonies were grow- 6. How did Pasteur’s studies of wine fermentation and souring suggest to him that germs might ing on the surface, each colony representing a pure cause human infectious disease? culture containing only one bacterial type. By 1882, © Jones & Bartlett7. How Learning, did Pasteur’s LLC studies of pébrine influence © Jonesa polysaccharide& Bartlett Learning, called agar LLC that was derived from his idea for the germ theory of disease? marine algae replaced gelatin as Koch’s preferred so- NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION lidifying agent, as MicroFocus 1-1 recounts. Today, the agar plate containing nutrients remains the standard way to culture microorganisms. Germ identification using Koch’s postulates soon Koch Formalizes© Jones Standards& Bartlett Learning, to LLCbecame the normal method© Jones of work. & Bartlett Koch’s lab Learning, fo- LLC Equate GermsNOT FORwith SALE Infectious OR DISTRIBUTION cused on disease causationNOT (FORetiology SALE). He OR identi DISTRIBUTION- Disease fied the bacterial agents responsible for tuberculosis Pasteur’s idea that germs caused disease stimulated (1882) and cholera (1883). Pasteur’s lab, on the other others to investigate the association of microbes with hand, was more concerned with preventing disease infectious© Jones disease. & Bartlett Among Learning, these so-called LLC “microbe through© vaccination. Jones & BartlettThis culminated Learning, in 1885, LLC when hunters”NOT FOR was SALERobert Koch,OR DISTRIBUTION a German country doctor. Pasteur’sNOT rabies FOR vaccine SALE saved OR the DISTRIBUTION life of a young boy In the 1870s, Koch’s primary interest was anthrax, a who had been bitten by a rabid dog. deadly blood disease in cattle and sheep. He wanted By the turn of the century, the germ theory of to know if there was a specific germ that caused disease had set a new course for studying and treat- anthrax. ing infectious disease. The detailed studies carried © Jones & BartlettKoch Learning, tried to define LLC a set of rules to establish© Jones out & byBartlett Pasteur Learning, and Koch LLCmade the discipline of NOT FOR SALEa link OR between DISTRIBUTION a specific microbe and anthrax.NOT FORbacteriology SALE OR, theDISTRIBUTION study of bacterial organisms, a In 1875, Koch injected mice with the blood from well-respected field of study Figure( 1-11).

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© Jones Figure& Bartlett 1-10 SEEING Learning, THE CONCEPT LLC © Jones & Bartlett Learning, LLC NOT FORKoch’s SALE postulates OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION Robert Koch (inset) developed a set of guidelines to relate a specific microorganism to a specific disease. What is the relationship between postulates 2 and 4? Inset: Courtesy of National Library of Medicine.

© JonesPostulate & Bartlett 1 Learning, LLC © Jones & Bartlett Learning, LLC NOT FORThe suspec SALEted mic roORbe must DISTRIBUTION NOT FOR SALE OR DISTRIBUTION be associated with the disease and be present in every case of the disease. Diseased animal Healthy animal © Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC

NOT FOR SALE ORPostulate DISTRIBUTION 2 NOT FOR SALE OR DISTRIBUTION The suspected microbes are isolated from diseased animals and grown in pure culture.

© Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION Postulate 3 A sample of pure cultured microbes are inoculated into healthy, susceptible animals.

Postulate 4 The test animals exhibit the same disease and the same suspected microbe is isolated from the animals. © Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION

© Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION Pasteur and Koch inspired more scientists to be microbe hunters. Many of these individuals discov- Concept Check 1-3C ered other germs (bacterial, fungal, protozoal, viral) 8. Explain why Koch’s postulates were critical to causing other human diseases© Jones (Table & Bartlett 1-1). Such Learning, dis- LLCvalidating the germ theory© of Jonesdisease. & Bartlett Learning, LLC coveries established other disciplines within the field NOT FOR SALE OR DISTRIBUTION9. How did the development ofNOT pure FORcultures SALE OR DISTRIBUTION of microbiology (see Figure 1-11). advance the germ theory of disease?

As time went on, more and more microorganisms understand what an organism is. Simply defined, an © Jonesand & Bartlettviruses were Learning, identified LLC and studied. Before we © Jonesorganism & Bartlettis any living Learning, system consisting LLC of one or NOT FORbriefly SALE survey OR DISTRIBUTIONwhat is known today about the basic NOTmore FOR cells. SALE Thus, aOR “microorganism” DISTRIBUTION is a living system characteristics of these microbial groups, we need to consisting of an extremely small (microscopic) cell.

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One of the major developments in microbiology was Robert Koch’s Fanny Hesse use of a solid culture surface on which bacterial colonies would Courtesy of National Library of Medicine. grow. He accomplished© Jones this &by Bartlettsolidifying beefLearning, broth with LLC gelatin. © Jones & Bartlett Learning, LLC When inoculatedNOT onto theFOR surface SALE of the OR nutritious DISTRIBUTION medium, NOT FOR SALE OR DISTRIBUTION bacterial cells grew vigorously at room temperature and produced discrete, visible colonies. On occasion, however, Koch was dismayed to find that the gelatin turned to liquid because some bacterial species produced ©a Joneschemical & substance Bartlett that Learning, digested the LLC gelatin. Moreover, gelatin © Jones & Bartlett Learning, LLC NOTliquefied FOR at the SALE warm OR incubator DISTRIBUTION temperatures commonly used to NOT FOR SALE OR DISTRIBUTION cultivate many bacterial species. An associate of Koch’s, Walther Hesse, mentioned the problem to his wife and laboratory technician, Fanny Hesse. She had a possible solution. For years, she had been using a seaweed- © Jones & Bartlettderived Learning, powder called LLC agar (pronounced ah’gar) to ©solidify Jones her & Bartlett Learning, LLC jams and jellies. Agar was valuable because it mixed easily with NOT FOR SALEmost OR liquids, DISTRIBUTION and once gelled, it did not liquefy at warmNOT incubator FOR SALE OR DISTRIBUTION temperatures. In 1881, Walther Hesse recommend agar to Koch. Soon Koch was using it routinely to grow bacterial species, and, in 1884, he first mentioned agar in his paper on the isolation of the bacterial organism responsible© Jones for tuberculosis. & Bartlett It isLearning, noteworthy thatLLC Fanny © Jones & Bartlett Learning, LLC Hesse is one of theNOT first FOR Americans SALE (she OR was DISTRIBUTION originally from New NOT FOR SALE OR DISTRIBUTION York City) to make a significant contribution to microbiology. Another key development, the common petri dish (culture plate), also was invented about this time (1887) by a German microbiologist Julius Petri, who also was one of Koch’s assistants. © Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION

Figure 1-11 Microbiology disciplines © Jones & BartlettThis simple Learning, concept map LLC shows the relationship between© Jones microbiology & Bartlett and its variousLearning, disciplines. LLC NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION Microbiology

studies

in the including disciplines of © Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION Bacteriology Parasitology Mycology Virology Other infectious (Bacteria and (Multicellular (Fungi) (Viruses) agents Archaea) animals)

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© JonesTable & Bartlett 1-1 Other Learning, International LLC Scientists Who Identified© SpecificJones Human& Bartlett Pathogens Learning, During LLCthe Golden Age NOT FORof Microbiology SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION Investigator (Year) Country Disease (Infectious Agent) Otto Obermeier (1868) Germany Relapsing fever (bacterium) Gerhard Hansen (1873) © Jones & Bartlett Learning,Norway LLC Leprosy (bacterium) © Jones & Bartlett Learning, LLC Albert Neisser (1879) NOT FOR SALE OR GermanyDISTRIBUTION Gonorrhea (bacterium)NOT FOR SALE OR DISTRIBUTION Charles Laveran (1880) France Malaria (protozoan) Karl Eberth (1880) Germany Typhoid fever (bacterium) Edwin Klebs (1883) Germany Diphtheria (bacterium) © Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC Arthur Nicolaier (1884) Germany Tetanus (bacterium) NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION Theodore Escherich (1885) Germany Infant diarrhea (bacterium) Albert Fraenkel (1886) Germany Pneumonia (bacterium) David Bruce (1887) Australia Undulant fever (bacterium) © JonesAnton & Bartlett Weichselbaum Learning, (1887) LLC Austria © Jones &Cerebrospinal Bartlett Learning, meningitis LLC(bacterium) NOT FORA. A.SALE Gärtner OR (1888) DISTRIBUTION GermanyNOT FOR SALEFood poisoning/salmonellosis OR DISTRIBUTION (bacterium) William Welch and George Nuttall (1892) United States Gas gangrene (bacterium) S. Kitasato and A. Yersin (1894) Japan and France (Independently) Bubonic plague (bacterium) Emile van Ermengem (1896)© Jones & Bartlett Learning,Belgium LLC Botulism (bacterium)© Jones & Bartlett Learning, LLC Kiyoshi Shiga (1898) NOT FOR SALE OR JapanDISTRIBUTION Bacterial dysentery (bacterium)NOT FOR SALE OR DISTRIBUTION Walter Reed (1900) United States Yellow fever (virus) Robert Forde and Joseph Everett Dutton (1902) Great Britain African sleeping sickness (protozoan) Fritz Schaudinn and Erich Hoffman (1903) Germany Syphilis (bacterium) © Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC Jules BordetNOT FORand Octave SALE Gengou OR (1906)DISTRIBUTION France WhoopingNOT FORcough/pertussis SALE OR (bacterium) DISTRIBUTION George McCoy and Charles Chapin (1911) United States Tularemia (bacterium)

Despite their microscopic size, microorganisms Beside the remarkable unity of characteristics, © Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC share a common set of characteristics, or emerging the cells of all organisms are of two differing types: NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION properties, with all living organisms. These include: prokaryotic and eukaryotic. Prokaryotic cells • Hereditary Material. Information in the form of (pro = “before”; karyo = “nucleus”) have their genetic DNA is used by all organisms for cell function and information in the form of DNA, but it is not local- reproduction. ized within a structure called the cell nucleus. They • Complex Biochemical© Jones Patterns & Bartlett (Metabolism Learning,). also LLC lack most of the specialize© internal Jones cell & structuresBartlett Learning, LLC The information inNOT an organism’s FOR SALE DNA OR controls DISTRIBUTION typical of other microbes and multicellularNOT FOR organisms.SALE OR DISTRIBUTION metabolism, which also requires the uptake of en- Such single-celled organisms are called prokaryotes. ergy to power these reactions. Eukaryotic cells (eu = “true”) have a distinct cell • Reproduction. During cell division, the complete nucleus and numerous specialized internal struc- set© of Jonesgenetic information& Bartlett is Learning, replicated and LLC passed tures called ©organelles Jones &. SuchBartlett organisms Learning, are called LLC . to NOTdescendant FOR cells. SALE OR DISTRIBUTION eukaryotes NOT FOR SALE OR DISTRIBUTION • Response to Stimuli. Cells and organisms sel- dom live in isolation but rather interact in many The Prokaryotes: Bacteria different ways by responding to stimuli. and Archaea Evolutionary Adaptation. Cell and organism More than 200,000 different types of prokaryotes © Jones• & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC changes (adaptations) over time provide those have been described, and scientists estimate there NOT FOR SALEbest suited OR to DISTRIBUTION the environment the best chance of NOTmight FOR be SALEmany millions OR DISTRIBUTION of different types in nature. survival. The prevalence of bacteria has made them the most

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intensively studied group of microorganisms since the wall, and many common ones are spherical, spiral, or © Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC time of Pasteur and Koch. rod shaped (Figure 1-12A). Many get their food (nu- NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION Most bacteria are small, single-celled (unicellu- trients) from the environment, although some make lar) organisms, although some form filaments, and the their own food through photosynthesis. majority associate into “multicellular” communities In addition to the disease-causing members, some called biofilms that often compose a microbiome. bacteria are responsible for food spoilage, whereas These organisms ©include Jones all & bacteria Bartlett of medicalLearning, im- LLCothers are useful in the ©food Jones industry. & Bartlett Many bacterial Learning, LLC portance. AlmostNOT all bacterial FOR SALE cells have OR aDISTRIBUTION rigid cell members, along with severalNOT fungi, FOR are SALE decomposers OR DISTRIBUTION,

Figure 1-12 The microbial menagerie Microscopy images (A-D) of prokaryotic and eukaryotic cells, and viruses. A ©& D: CourtesyJones of CDC; B: © & Lebendkulturen.de/Shutterstock; Bartlett Learning, C: © Heribert Cypionka. LLC © Jones & Bartlett Learning, LLC

NOTA FOR SALE OR DISTRIBUTION B NOT FOR SALE OR DISTRIBUTION Light microscopy of red-stained bacterial cells, which lack Light microscopy of several eukaryotic (algal) cells, each the organelles typically found in a eukaryotic cell. The containing a cell nucleus and organelles. (Bar = 10 μm) green ovals are bacterial spores. (Bar = 2 μm)

NOT FOR SALE OR DISTRIBUTION NOTCell nucleusFOR SALE OR DISTRIBUTION (DNA)

C D Phase-contrast microscopy of oval yeast cells. (Bar = 10 μm) False-color transmission electron microscopy of a cluster of © Jones & Bartlett Learning, LLC © Jones &flu Bartlett viruses. (Bar Learning, = 60 nm) LLC NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION

9781284240535_CH01_001_024.indd 15 30/12/20 1:20 PM 16 Chapter 1 Introduction to Microbiology: Then and Now

organisms that bring about the release and reuse of cell wall. Fungi, therefore, live in their own food sup- © Jones & Bartlett Learning, LLC © Jonesnutrients & Bartlett from Learning,dead organisms. LLC They are essential to ply. If that source of food is a human, diseases such NOT FOREarth’s SALE microbiomes OR DISTRIBUTION mentioned at the beginning of NOTas ringworm FOR SALE or vaginal OR DISTRIBUTION yeast infections might result. this chapter. Fungi have an immense impact on environmental Based on recent biochemical, molecular, and health, biodiversity, ecology, agriculture, and industry. gene-sequencing studies, many bacterial organisms For example, together with many bacterial species, have been reassigned into© anotherJones unique & Bartlett evolutionary Learning, numerous LLC molds play a major© role Jones as decomposers. & Bartlett In Learning, LLC group of prokaryotes calledNOT theFOR Archaea SALE. AlthoughOR DISTRIBUTION the pharmaceutical industry, NOTsome FORfungi areSALE sources OR DISTRIBUTION archaeal cells resemble bacterial cells when observed for useful products, such as antibiotics. Other molds with the microscope, many were originally identified are used in the food industry to impart distinctive fla- in environments that are extremely hot (such as the vors in foods such as cheeses. Yellowstone© Jones hot springs), & Bartlett extremely Learning, salty (such LLC as the © Jones & Bartlett Learning, LLC Dead Sea), or of extremely low pH (such as acid mine NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION drainage). Since then, many other archaeal organisms Other Infectious Agents: have been found in temperate soils and water. Oth- The Viruses ers, along with bacteria, are an integral part of the Viruses are “infectious agents,” some version of which microbiome in the digestive tracts of animals. No ar- potentially can infect organisms at every scale, from © Joneschaeal & Bartlett members Learning, are known LLCto be pathogens, but like © Jonesbacteria &to Bartletttulips to Learning,blue whales. LLC Scientists suggest NOT FORthe SALEbacterial OR microbes, DISTRIBUTION they are an important part of NOTthere FOR might SALE be more OR thanDISTRIBUTION 100 million different vi- Earth’s microbial workforce. ruses. To put this in perspective, Carl Zimmer, the popular science writer, said that “If you were to stack one virus on top of another, you’d create a tower that The Microbial Eukaryotes: would stretch beyond the moon, beyond the sun, be- © Jones & Bartlett Learning,yond LLC Alpha Centauri, out past© theJones edge &of Bartlettthe Milky Learning, LLC Protists and FungiNOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION The protists consist mostly of the so-called protozoa Way, past neighboring galaxies, to reach a height of and the single-celled algae. They are about 10 to 200 million light years.” 50 times larger than prokaryotic cells. Protists are the Because they lack cellular structure, viruses are most diverse of all of the eukaryotic groups, including not organisms. They have genetic material in the form plants ©and Jones animals. & BartlettScientists Learning,have identified LLC more of DNA or RNA© Jones (but not & both).Bartlett The Learning,material is sur LLC- than 200,000NOT FOR different SALE protists, OR DISTRIBUTIONwith many more yet rounded by aNOT protein FOR coat. SALE Viruses OR infect DISTRIBUTION organisms to be discovered. for one reason only: to replicate; that is, to make more Some protists are free living, whereas others live of themselves. However, although viruses have the ge- in association with plants or animals. Protists obtain netic information needed to direct their own replica- nutrients in different ways. The protozoa lack a cell tion, they need the metabolic machinery and chemical © Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC wall and absorb nutrients from the surrounding envi- building blocks found inside living cells to carry out NOT FORronment SALE or ORingest DISTRIBUTION smaller microorganisms, including NOTthe FORreplication SALE process. OR DISTRIBUTION By affecting living organisms, bacteria. The unicellular, colonial, and filamentous viruses have played a crucial role in the evolution and algae have a rigid cell wall and can carry out pho- adaptability of life. Most viruses do not cause disease tosynthesis (Figure 1-12B). Although most protists are and death, with only a small percentage affecting hu- harmless, some protozoa© Jonesare among & Bartlettthe most Learning,clini- mans. LLC The viruses that cause© Ebola, Jones measles, & Bartlett AIDS, Learning, LLC cally important pathogensNOT of FOR humans, SALE capable OR DISTRIBUTION of the flu, and COVID-19 are NOTa few FORnotable SALE examples OR DISTRIBUTION causing malaria, several types of diarrhea, and sleep- (Figure 1-12D). ing sickness. Table 1-2 summarizes the general characteristics of The fungi are all nonphotosynthetic eukaryotes. the different groups of microorganisms and viruses. About ©125,000 Jones species & Bartlett of fungi Learning, have been described; LLC © Jones & Bartlett Learning, LLC however,NOT scientists FOR SALEestimate OR there DISTRIBUTION might more than NOT FOR SALE OR DISTRIBUTION 6 million different species in nature. Concept Check 1-4 Some fungi grow as unicellular yeasts, which are 10. Explain the difference between prokaryotes and slightly larger than many bacteria (Figure 1-12C). Other eukaryotes. Identify the differences between the groups of fungi grow as filamentous networks calledmolds , 11. © Joneswhich & Bartlett usually areLearning, found in warm, LLC moist places. Fungi © Joneseukaryotic & Bartlett microbes. Learning, LLC NOT FOR SALE OR DISTRIBUTION NOT12. FOR Describe SALE why OR viruses DISTRIBUTION are called infectious secrete digestive enzymes that break down nutrients agents rather than organisms. into smaller bits that can be absorbed easily across the

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© Jones & BartlettTable 1-2 Learning, Distinguishing LLC Characteristics of the© Major Jones Groups & Bartlett of Microorganisms Learning, and LLC Viruses NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTIONPresence of Prokaryote or Group Cellular Structure Eukaryote Genetic Material Potential Pathogens Bacteria Yes Prokaryote DNA, but not in a cell nucleus Some; most are harmless Archaea Yes© Jones & BartlettProkaryote Learning, LLC DNA, but not in a cell nucleus© Jones No known & pathogens Bartlett Learning, LLC Fungi YesNOT FOR SALEEukaryote OR DISTRIBUTION DNA in a cell nucleusNOT Some; FOR most SALE are harmless OR DISTRIBUTION Protists Yes Eukaryote DNA in a cell nucleus Some; most are harmless Viruses No Neither DNA or RNA Many © Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION KEY CONCEPT 1-5 Microbiology Now: Challenges Remain © Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC NOT FOR SALEMicrobiology OR DISTRIBUTION is one of the most intensively studiedNOT FORserious SALE public OR health DISTRIBUTION events that endanger interna- fields in the biological sciences, in part due to the ba- tional public health and global populations. Two of sic science and applied science topics described thus them were the Ebola virus epidemic in West Africa far in this chapter. However, microbiology also faces in 2014 to 2016 and the Zika virus disease epidemic several challenges, many of which concern infectious that spread through the Americas in 2015 to 2016. diseases that are ©responsible Jones & for Bartlett millions Learning, of illnesses LLCThen, in 2020, there was© the Jones COVID-19 & Bartlett pandemic. Learning, In LLC each year and responsibleNOT FOR for SALE16% of allOR deaths DISTRIBUTION glob- fact, according to the WHO,NOT over FOR the SALE past 30 OR year, DISTRIBUTION the ally (Figure 1-13). Until 2020, the World Health Or- number of disease outbreaks globally has increased ganization (WHO) over the last decade had declared threefold, from 1,000 per year to more than 3,000 per four global health emergencies, which represent year. © Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC FigureNOT 1-13FOR Global SALE mortality OR DISTRIBUTION from infectious diseases NOT FOR SALE OR DISTRIBUTION On a global scale, some 15 million people die each year from infectious diseases. Estimated deaths from COVID-19 for 2020 have been included. Can you identify what some of the “other infectious diseases” might be? Data from World Health Organization. World Health Statistics 2011. Retrieved from: https://www.who.int/whosis/whostat/2011/en/. Accessed February 7, 2019. COVID-19: Johns Hopkins Coronavirus Research Center.

HIV/AIDS

Tuberculosis © Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC NOT FOR SALECOVID-19 OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION Malaria

Meningitis © Jones & Bartlett Learning,Pertussis LLC © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTIONMeasles NOT FOR SALE OR DISTRIBUTION

Hepatitis B

Other infectious diseases © Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC 0 0.5 11.5 2 2.5 3 3.5 4 4.5 NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION Number of Deaths (millions)

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Here are a few of the major challenges facing mi- Drug-resistant pathogens © JonesFigure 1-14 & Bartlett Learning, LLC © Jonescrobiology & Bartlett today. Learning, LLC Many bacterial pathogens around the world are NOT FOR SALE OR DISTRIBUTION NOTbecoming FOR resistantSALE OR to antibiotics. DISTRIBUTION Courtesy of CDC. Drug-Resistant Pathogens Today, many people around the world often are given or ask for antibiotics or© other Jones antimicrobial & Bartlett drugs Learning, to LLC © Jones & Bartlett Learning, LLC help fight a bacterial infectionNOT FOR they SALE have contracted. OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION Unfortunately, the effectiveness of these drugs to treat such infections is weakening. The reason is that many pathogens have become resistant to one or more of these drugs.© Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC The vast majority of antibiotics were discovered NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION in the 1950s and 1960s. It was believed by many in the medical community at the time that bacterial infections in humans finally would be vanquished and no longer pose a threat due to the effectiveness of © Jonesthese & Bartlett drugs. Unfortunately, Learning, LLCmany health experts did © Jones & Bartlett Learning, LLC NOT FORnot SALErecognize OR that DISTRIBUTION bacteria have a natural ability to de- NOT FOR SALE OR DISTRIBUTION velop resistance to antibiotics. Pathogens can undergo beneficial mutations or acquire new genes from other bacteria for antibiotic resistance. Warnings from scientists that bacteria were becoming© Jones resistant & Bartlett to antibiot Learning,- LLC © Jones & Bartlett Learning, LLC ics largely went unnoticed.NOT Today, FOR antibiotic SALE resistanceOR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION has resulted in many previously effective therapies becoming obsolete, leaving fewer treatment options for many infections (Figure 1-14). Although antibiotics have saved the lives of millions of individuals, since 1980 deaths© Jones from & most Bartlett major Learning,infectious diseases LLC in © Jones & Bartlett Learning, LLC the UnitedNOT States FOR have SALE declined OR byDISTRIBUTION only 20%. NOT FOR SALE OR DISTRIBUTION Perhaps the most pressing issue facing microbi- Emerging and Reemerging ology today is the increased number of bacteria and Infectious Diseases other microbes that have become resistant to multi- Infectious diseases today have the potential to spread © Jonesple & antibiotics. Bartlett Learning,Such superbugs LLC are becoming harder © Jonesfaster and & farther. Bartlett Experts Learning, estimate LLCthat more than five and harder to treat effectively largely due to human billion people traveled by air in 2018. With so many NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION activities and behavior. The abuse and misuse of an- people traveling globally, a human disease outbreak tibiotics by the medical profession and the public has or epidemic in one part of the world is only a few air- created an environment that encourages the devel- line hours away from becoming a potentially danger- opment of antibiotic resistance by once-susceptible ous threat in another region of the globe. This is only pathogens. Consequently,© Jonesa global & crusade Bartlett has Learning,been too LLC clear with the COVID-19© pandemic Jones &that Bartlett quickly Learning, LLC waged to restrain the inappropriateNOT FOR use SALE of these OR drugs DISTRIBUTION spread worldwide to EuropeNOT and FORNorth SALE America. OR DISTRIBUTION by doctors and to educate patients not to demand an- Moreover, trade in commodities and animals is hap- tibiotics in situations that do not call for them. pening at a faster pace. If these goods or animals carry The challenge facing microbiologists and the med- disease, the pathogens also are transported. Health ex- ical community© Jones now & Bartlettis to find Learning,new and effective LLC anti- perts report that© Jones almost 75%& Bartlett of newly Learning, emerging infec LLC- biotics NOTto which FOR pathogens SALE willOR not DISTRIBUTION develop resistance tious diseasesNOT are spread FOR to SALE humans OR by DISTRIBUTIONanimals, Ebola quickly before the current arsenal is useless. Unfortu- and COVID-19 being two examples. But, no matter nately, the growing threat of antibiotic resistance has how a disease is spread, when introduced to a new been accompanied by a decline in new drug discovery location, most humans will be susceptible to infec- and an increase in the time to develop a drug from tion because they lack immunity to the new pathogen. © Jonesdiscovery & Bartlett to market.Learning, Consequently, LLC drug-resistant © JonesTherefore, & Bartlettthe threat Learning,of epidemics LLC and pandemics is NOT FORpathogens SALE haveOR becomeDISTRIBUTION a major health threat. NOTever-present. FOR SALE OR DISTRIBUTION

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Figure 1-15 Emerging and reemerging diseases © Jones & BartlettMap showing Learning, global emerging LLC and reemerging infectious© Jones diseases & recordedBartlett over Learning, the last 30 years.LLC COVID-19 that NOT FOR SALEoriginated OR inDISTRIBUTION China is but the latest. NOT FOR SALE OR DISTRIBUTION NIAID.

© JonesOver the & pastBartlett few decades,Learning, new LLC diseases have gonorrhea.© Jones Cholera, & Bartlettdengue fever, Learning, and, for LLCthe first beenNOT identified FOR SALE at the OR unprecedented DISTRIBUTION rate of one or time inNOT the Western FOR SALEHemisphere, OR DISTRIBUTION West Nile virus dis- more per year, such that today there are nearly 40 in- ease also represent reemerging diseases. fectious diseases present that were unknown a gener- The challenge of emerging and reemerging dis- ation ago. These diseases fall into one of two groups eases can be addressed by developing better surveil- © Jones & Bartlett(Figure 1-15 Learning,). LLC © Joneslance & Bartlett of disease Learning, outbreaks LLCand mandating stricter An is one that has compliance with hygiene and sanitation practices. NOT FOR SALE ORemerging DISTRIBUTION infectious disease NOT FOR SALE OR DISTRIBUTION apparently surfaced in the human population for the Developing new vaccines and antimicrobial drugs also first time. The microbes causing first-time diseases are critical to the challenge. are really just existing microbes that have changed their genetic makeup so they can infect humans or have evolved as more© Jones dangerous & Bartlett pathogens. Learning, Among LLCBioterrorism © Jones & Bartlett Learning, LLC the more newsworthyNOT have FOR been SALE AIDS, OR Lyme DISTRIBUTION disease, Bioterrorism representsNOT the FOR intentional SALE or OR threat DISTRIBUTION- Ebola virus disease in West Africa, Zika virus infection ened use of biological agents to cause fear in or in the Western Hemisphere, and, on a truly global actually inflict death or disease upon a large pop- scale COVID-19. To date, there is no cure for any of ulation. The 2001 anthrax attack carried out using these© Jones diseases, & Bartlett and, given Learning, the opportunity, LLC there un- the U.S.© PostalJones Service & Bartlett is one Learning,example. The LLC conse- doubtedlyNOT FOR are SALE more pathogens, OR DISTRIBUTION like COVID-19, ready quencesNOT of this FOR event SALE made OR millions DISTRIBUTION of Americans to emerge. anxious, and simply opening mail became a danger- A reemerging infectious disease is one that ous undertaking. had been controlled in the past but is now showing Most of the recognized bioterror agents are micro- resurgence in drug-resistant forms or expansion in organisms, viruses, or microbial toxins. What makes © Jones & Bartlettgeographic Learning, range. Among LLC the more prominent ©re Jones- them & Bartlett dangerous Learning, is that many LLC could be disseminated NOT FOR SALEemerging, OR DISTRIBUTIONdrug-resistant diseases are tuberculosis NOTand FORthrough SALE water OR or DISTRIBUTION the air (Figure 1-16).

9781284240535_CH01_001_024.indd 19 30/12/20 1:20 PM 20 Chapter 1 Introduction to Microbiology: Then and Now

Figure 1-16 Bioterrorism © JonesCombatting & Bartlett the threatLearning, of bioterrorism LLC often requires © JonesThe Climate & Bartlett Crisis Learning, LLC NOT FORspecial SALE equipment OR DISTRIBUTION and protection because many NOTGeologists FOR SALE have proposed OR DISTRIBUTION that our current geological bioterror agents can be spread through the air. era, where human activity has had a dominant influ- © Photodisc. ence on the oceans, soils, and atmosphere, be called the Anthropocene. One very controversial issue © Jones & Bartlett Learning,of LLC human influence in this era© Jones concerns & theBartlett current Learning, LLC NOT FOR SALE OR DISTRIBUTIONclimate crisis (including warmingNOT temperaturesFOR SALE and OR DISTRIBUTION changing rainfall patterns). Specifically, could such changes in the coming decades affect the frequency and distribution of infectious diseases around the world? © Jones & Bartlett Learning, LLC Today, disease-carrying© Jones & Bartlett mosquitoes Learning, kill about LLC NOT FOR SALE OR DISTRIBUTION 1 million peopleNOT globally FOR everySALE year. OR As DISTRIBUTION temperatures rise in various parts of the world, mosquitoes might broaden their range. This could spread diseases like malaria and dengue fever to more temperate climates, © Jones & Bartlett Learning, LLC © Jonesincluding & NorthBartlett America Learning, and Europe LLC (Figure 1-17). NOT FOR SALE OR DISTRIBUTION NOTWarming FOR SALEocean waters OR DISTRIBUTION also could provide ideal environments for the spread of waterborne diseases like cholera. Microbiologists, epidemiologists, climate scientists, and many other scientists are studying new © Jones & Bartlett Learning,strategies LLC that can better predict© Jones what &populations Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTIONmight be subjected to potentialNOT disease FOR spread. SALE The OR DISTRIBUTION challenge is to expand the understanding of the dy- namics of the climate crisis and to recognize how such changes might affect the behaviors of potentially © Jones & Bartlett Learning, LLC emerging and© reemergingJones & Bartlettdiseases that Learning, could affect LLC NOT FOR SALE OR DISTRIBUTION the health of NOTplants, FOR wildlife, SALE livestock, OR DISTRIBUTIONand humans. Lessening the chances that someone would use these agents represents another challenge. Solutions to the challenge include improving the ways that bio- Concept Check 1-5 terror agents are detected quickly, discovering effec- © Jones & Bartlett Learning, LLC © Jones13. List & and Bartlett briefly discussLearning, the four LLC described tive measures to protect the public, and developing challenges facing microbiology today. NOT FORnew SALE and effective OR DISTRIBUTION treatments against these pathogens. NOT FOR SALE OR DISTRIBUTION

As a Final Point© Jones . . &. Bartlett Learning, LLC © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION Microbiology (from then until now) has gone from such distinct fields as genetics, ecology, medicine, observing the first microbes as curiosities (Leeuwen- and, yes, microbiology. hoek) to identifying and studying individual micro- Much of the material in this chapter is based on organisms© Jones as pathogens & Bartlett (Pasteur, Learning, Koch, and LLC others) the fact that ©microorganisms—and Jones & Bartlett all Learning, life—evolves. LLC to appreciatingNOT FOR microbiomes SALE OR as theDISTRIBUTION engines that sup- In fact, microbialNOT evolutionFOR SALE was occurringOR DISTRIBUTION for some port all life on Earth (today). It was Charles Darwin— 2 billion years before the first truly eukaryotic cells another of the scientists who combined observation appeared on the planet. Although challenging to with a “prepared mind”—who in 1859 first outlined study, it is possible today to use prokaryotic cells to the principles of evolution. Today, evolutionary theory “replay history” by following the accumulation of © Jonesis &the Bartlett unifying forceLearning, in modern LLC biology, tying together © Jonesunpredictable, & Bartlett chance Learning, events (mutations) LLC that lead NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION

9781284240535_CH01_001_024.indd 20 30/12/20 1:20 PM As a Final Point . . . 21

to evolutionary novelty characteristic of the mi- drug-resistant pathogens, to treat infectious diseases, © Jones & Bartlett Learning, LLC © Jones & Bartlettcrobes. In Learning, addition, today LLC microbial evolution stud- and to better understand the role of microbes in hu- NOT FOR SALEies are OR putting DISTRIBUTION together new approaches to improveNOT FORman SALE health. OR One DISTRIBUTION has to wonder what Darwin would agricultural productivity, to monitor and assess the make of the microbial world if he were alive today. climate crisis, and even to produce clean fuels and Microbiology from then until now has come a long energy. The new field ofevolutionary medicine way but has a much longer way yet to go and many is providing new© strategies Jones &to Bartlettslow the evolutionLearning, of LLCchallenges to face. © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION

Figure 1-17 Microbes and the climate crisis As temperatures rise over the next 60 years, scientists project that unless the climate crisis is slowed or solved the range© Jones of mosquitoes & Bartlett will expand Learning, farther intoLLC more northern temperate© climates Jones that & wereBartlett once inhospitableLearning, areas LLC for mosquito reproduction. How might the spread of mosquitoes affect your area of the world? NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION Koko Nakajima/NPR

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Summary of Key© Jones Concepts & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC 1-1 Microbial CommunitiesNOT FOR SALE Support OR DISTRIBUTION changes. He proposed theNOT germ FOR theory SALE of OR DISTRIBUTION disease, which stated that some microbes, the and Affect All Life on Earth germs, could cause infectious disease in animals 1. Earth’s microbiomes are communities of and humans. microorganisms in the oceans, soils, air, and 6. Koch’s work with anthrax and development © Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC deep underground that shape and sustain the of pure cultures led to a method (Koch’s planetNOT for FOR all organisms. SALE OR (Figure DISTRIBUTION 1-1) postulatesNOT) to FORrelate aSALE specific OR microorganism DISTRIBUTION to a specific disease. (Figure 1-10) 1-2 The Human Body Has Its Own 1-4 The Microbial World Is Cataloged © Jones & BartlettMicrobiome Learning, LLC © Jones & Bartlett Learning, LLC into Unique Groups NOT FOR2. SALECommunities OR DISTRIBUTION of microorganisms (primarily NOT FOR SALE OR DISTRIBUTION bacteria) form the human microbiome, 7. Microbiology is split into several subdisciplines inhabiting many parts on and in the human based on the type of microscopic agent. body (skin, mouth, intestinal tract, respiratory (Figure 1-11) tract, and urogenital tract). (Figure 1-6) 8. Microbes can be structurally separated into those 3. The human microbiome© Jones has many & Bartlett essential Learning, LLCpossessing prokaryotic cells© Jones (Bacteria & andBartlett Learning, LLC functions to maintainNOT a healthy FOR body,SALE OR DISTRIBUTIONArchaea) and those with eukaryoticNOT FOR cells SALE (fungi OR DISTRIBUTION including helping with digestion, supporting and protists). Viruses represent noncellular the development of the immune system, and agents. preventing infections. 9. Each group of microbes has unique features that © Jones & Bartlett Learning, LLC separate it© fr Jonesom the other& Bartlett groups. Learning, (Figure 1-12) LLC 1-3 Microbiology NOT FOR SALE Then: OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION The Pioneers 1-5 Microbiology Now: Challenges 4. The observations with the microscope made Remain by Hooke and especially Leeuwenhoek, 10. In the 21st century, fighting drug-resistant © Jones & whoBartlett reported Learning, the existence LLC of animalcules © Jonespathogens & Bartlett, identifying Learning, emerging LLC and NOT FOR SALE(microorganisms), OR DISTRIBUTION sparked interest in an NOT FORreemerging SALE infectiousOR DISTRIBUTION diseases, countering unknown world of microscopic life. the bioterrorism threat, and addressing the (Figure 1-8) potential spread of infectious diseases due to the 5. Pasteur’s fermentation studies suggested that climate crisis are some of the challenges facing microorganisms could produce chemical microbiology, healthcare systems, and society. © Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION Chapter Self-Test For more practice quizzes, assessments, anima- For Steps A–C, you can find answers to ques- tions, videos, and other study aids, go online to tions and problems in Appendix F. NAVIGATE 2© Jones. & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION STEP A: Recall Read each question or statement carefully before se- 3. Who was the first person to see bacterial cells lecting an answer. with a microscope? © Jones1. & DefineBartlett microbiome. Learning, LLC © JonesA. Pasteur & Bartlett Learning, LLC B. Koch NOT FOR2. SALEWhich partOR ofDISTRIBUTION the human body is home to the NOT FOR SALE OR DISTRIBUTION greatest number of bacteria? C. Leeuwenhoek D. Hooke

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4. What two scientific investigations led Pasteur to A. Bacteria © Jones & Bartlett Learning, LLC © Jones & Bartlettformulate Learning, his germ LLC theory of disease? B. Viruses NOT FOR SALE5. Which OR DISTRIBUTION of the following statements is NOT partNOT FOR SALEC. Archaea OR DISTRIBUTION of Koch’s postulates? D. Fungi A. The microorganism must be isolated from a 7. Which of the following would NOT be dead animal and pure cultured. considered an emerging infectious disease? B. The microorganism© Jones and & Bartlettdisease can Learning, be LLC A. Polio © Jones & Bartlett Learning, LLC identifiedNOT from FORa mixed SALE cultur e.OR DISTRIBUTION B. Zika virus infectionNOT FOR SALE OR DISTRIBUTION C. The pure cultured organism is inoculated into C. COVID-19 a healthy, susceptible animal. D. AIDS D. The same microorganism must be present in 8. What two groups of organisms comprise the © Jonesevery & case Bartlett of the disease. Learning, LLC protists?© Jones & Bartlett Learning, LLC 6. Which group of microorganisms has a variety of NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION internal organelles?

STEP B: Application and Analysis © Jones & Bartlett9–12. Which Learning, of the following LLC statements are true ©(T Jones) 14. & You Bartlett discover Learning, a new species LLC of microbe growing NOT FOR SALEand which OR DISTRIBUTION are false (F)? If the statement is false, subNOT- FOR SALEin the soil. OR How DISTRIBUTION would you determine if the stitute a word or phrase for the underlined word or microbe is a prokaryotic or eukaryotic cell? phrase to make the statement true. Suppose that it is a eukaryote. What information 9. Leeuwenhoek believed that animalcules would be needed to determine if it is a member caused anthrax. of the protists or a member of the fungi? 10. Pasteur© proposed Jones &the Bartlett germ theory. Learning, LLC15. As microbiologists continue© Jones to &explore Bartlett the Learning, LLC 11. VirusesNOT must FOR infect SALEother cells OR to DISTRIBUTION replicate. microbial universe, NOTit is becoming FOR SALE more apparentOR DISTRIBUTION 12. When talking about antibiotic resistance, that microbes are “invisible emperors” that rule “resistance” refers to the human body not the world. Now that you have completed this responding to the antibiotic. chapter, provide three examples to support the 13.© JonesComplete & theBartlett concept Learning, map for Microbial LLC statement:© Jones Microbes & Bartlett rule! Learning, LLC NOTAgents FOR on SALE the right OR by DISTRIBUTION using the following NOT FOR SALE OR DISTRIBUTION terms to fill in the empty boxes. Each term should be used only once. Microbial Agents • Algae Archaeal cells that are represented by the © Jones & Bartlett• Learning, LLC © Jones & Bartlett Learning, LLC Bacterial cells NOT FOR SALE• OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION • Cellular agents • Eukaryotes • Fungi composing the such as the • Molds • Noncellular© Jonesagents & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC NucleatedNOT cells FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION • which include the which have • Prokaryotes • Protists • Protozoa © Jones• Viruses & Bartlett Learning, LLC © Jones & Bartlettthat are found Learning, in the LLC Yeasts NOT• FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION

composing the composing the

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© JonesSTEP & Bartlett C: Evaluation Learning, LLC and Discussion© Jones & Bartlett Learning, LLC NOT FOR16. SALECan you OR think DISTRIBUTION of an environment on Earth NOT FORmicrobiomes, SALE ORwhy DISTRIBUTIONmight plant and animal life where microbes would not be found naturally? suffer without microbes? 17. Judge the importance of (a) the germ theory 19. When you tell a friend that you are taking of disease and (b) Koch’s postulates to the microbiology this semester, she asks, “Exactly identification of microbes© Jones as agents& Bartlett of infectious Learning, LLCwhat is microbiology?” How© Jones do you answer& Bartlett her? Learning, LLC disease. NOT FOR SALE OR DISTRIBUTION20. Who would you select as NOTthe “first FOR SALE OR DISTRIBUTION 18. Louis Pasteur once stated, “Life [plant and microbiologist”? (a) Leeuwenhoek? (b) Hooke? animal] would not long remain possible in the (c) Pasteur and Koch? Support your decision. absence of microbes.” From your reading about © Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION

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