Chapter 1. The main themes of Microbiology1.1 The scope of Microbiology1.Definemicrobiologyandmicroorganisms,and identify the major organisms included inthe science of microbiology.Microbiology is a specialized area ofbiology thatdeals with tiny lifeformsthatare notreadilyobservedwithoutmagnificationSuchmicroscopic organismsarecollectivelyreferredtoasmicroorganisms,microbes.There are severalmajor groups of microorganisms that we will be studying.They arebacteria,viruses,fungi,protozoa,algae,andhelminths(parasiticworms).2.Name and define the primary areas included in microbiology studies.TABLE1.ASamplingofFlelds andOccupations In MicroblologyAImmunologyC.BiotechnologyThis branch studies the complex web of protective substances andThisheaechisdefinedhthereactions caused byinvadingmicrobesand otherharmful entities.living things to arrive at aderanging frombeertostenincludes suchdiverseareasasblood testing,vaccination,and aleycellsItincmicrobiology.which uses microbes t(soechaptens15.16.and 17)produceand harvest largequantities of suchsubsaccFigureAAspecilist in the CDC special pathogensnitreadsamicroscopictesttoscreenforinfectionthatisbasedon animmunereacticnFigure CAbiotechnology techniciortorva8.Public Health Microbiology and EpidemiologyThesebranches mooitor and control the spreadof diseasesinD,GeneticEngineeringandRecombinantDNATechncommuniticSomeofthe institutions chucsodwiththisteskarethTbeseinterreluted feldsivolvedeliberate alleclas ofthegenetiU.S.Public Health Senvice (USPHS) andtheCenters forDiseasemakeupofonganismstocreatenovelmicrbes.plants,andanimsContret andPrevention (CDC).TheCDCcollects infocmutioa andwithuniquebhavorand phyiologyhisisarapidlyexpandingstatistics on diseases from aroundthe United States andpublishes itinathat ofles complkemeots biotechnology (see chapter icnewsleter,TheMorbidiryandMortaliyWetlyReport (saechapter13)FigureD Ageneticistat theUsFigure BPublic health microbiologistsDepartment ot Agriculture examines a wheatexamine mice and takesamples to determine ifthey catry the hantavirus,one of the emergingplant that has been genetically engineered topathogensthat concernsthe CDCtesist a fungal pathogen
1 Chapter 1. The main themes of Microbiology 1.1 The scope of Microbiology 1. Define microbiology and microorganisms, and identify the major organisms included in the science of microbiology. Microbiology is a specialized area of biology that deals with tiny life forms that are not readily observed without magnifi cation. Such microscopic organisms are collectively referred to as microorganisms, microbes. There are several major groups of microorganisms that we will be studying. They are bacteria, viruses, fungi, protozoa, algae, and helminths (parasitic worms). 2. Name and define the primary areas included in microbiology studies
TABLE1.(continued)FoodMicrobilogy,DaryMicrblogy,and AquatF.Agricultural MicrobiologyMicroblologyThishranch is concerned with therelntionshiptweenmicrobesandThesehranchesexaminhecoloicaladpacticalrolesofmicodomesticated plaats and animitks.in fod and wateaisFoodmicobologistsareconredwithteftsofmicrobnferactionsincluding such areas asfood spoilage,foodbone diseases,andAnimat specialists work with infectious diseuses and othesproductionsociationsanimalshhavewithmicroocganisms?Aqustic microbiologists exploee the ecology of natural watersaswellas the impact of microbes on waler purity and treatmentG. Branches of MicrobiologyBranchChapterInvolvedin the Study of:Bacterlology4Thehacteriasmall inglcelledprokyticoganis5.22MycologyThefunggropofeukaytethaincludesbhmicoscoicukaryotes(moldsandyeasts)andlargerorgansint(mushrooms, puftballs)5.23ProtozologyThpotoznmkndmoslysinglceedryVirology6. 24,25VisesminuteoncelurparicksthparasitizecellsParasitlogy5.23Parasitism and perasitic organisms-traditionnly iecludingpathogenic protozoa,helminth worms, and certain insectnPhycology orSimple photosynthetic eukaryotes, the algae, ranging fromNigalogysingle-cellodforms to lange seawaeds4.5.6MorphologyThe detaled structureof micorganism7.8Microbial function (metabolism)at the celluliar andPhyslologymolecular levels14.5TaxonomyCasificaionmng,adintifcfmcogsMicroblal Geneties,9:10Thefunction of genectic materiat and biochemicat neactions thaMolecular Biologynake upa cell'smetabolismMicroblal Ecology7,26Intemeltioatipsbetwenmicrobesadteeironmentheroles of microernganisms in the mutrient cycles and natural1.2 General characteristics of Microorganisms and their role in the Earth's environment.1.Describe the basic characteristics of prokaryotic cells and eukaryotic cells and theirevolutionaryorigins.The term that is used to defi ne these types of cells is prokaryotic, referring to the lack ofa nucleus (karyon).The fossil recorddatingfromancient rocks and sediments points tobacterialike cells that existed at least 3.5 billion years ago. These simple cells were thedominant cells on earth for about 2 billion years.About 1.8 billion years ago, there appeared in the fossil record a more complex cell,which contained a nucleus and other complex internal structures.Thesetypes of cells andorganisms are defined as eukaryotic in reference to their “true” nucleus. The earlyeukaryotes,probably similar to algae and protozoa, started lines of evolution thateventually gave rise to fungi,plants,and multicellular animals such as worms and insects.The bacteria preceded even the earliest animals by about 3billion years.2.State several ways that microbes are involved in the earth's ecosystem.The microbes in all naturalenvironments have lived and evolved there for billions of years.We do not yet know everything they do, but it is likely they are vital components of thestructure and function ofthese ecosystemsand criticalto the operationsofthe earth.Microbes are deeply involved in the flow of energy andfood through the earth's ecosystems.Most people are aware that plants carry out photosynthesis,which is the light-fueledconversion of carbondioxideto organic material, accompanied by theformation of oxygenBut microorganisms werephotosynthesizing long before the first plants appeared.In fact, theywere responsible for changing the atmosphere of the earth from one without oxygen to onewith oxygen,Today photosynthetic microorganisms (including algae)account for more than50%oftheearth'sphotosynthesis,contributing themajorityoftheoxygen to theatmosphere.Another process that helps keep the earth in balance is the process of biological2
2 1.2 General characteristics of Microorganisms and their role in the Earth’s environment. 1. Describe the basic characteristics of prokaryotic cells and eukaryotic cells and their evolutionary origins. The term that is used to defi ne these types of cells is prokaryotic, referring to the lack of a nucleus (karyon). The fossil record dating from ancient rocks and sediments points to bacterialike cells that existed at least 3.5 billion years ago. These simple cells were the dominant cells on earth for about 2 billion years. About 1.8 billion years ago, there appeared in the fossil record a more complex cell, which contained a nucleus and other complex internal structures. These types of cells and organisms are defined as eukaryotic in reference to their “true” nucleus. The early eukaryotes, probably similar to algae and protozoa, started lines of evolution that eventually gave rise to fungi, plants, and multicellular animals such as worms and insects. The bacteria preceded even the earliest animals by about 3 billion years. 2. State several ways that microbes are involved in the earth’s ecosystem. The microbes in all natural environments have lived and evolved there for billions of years. We do not yet know everything they do, but it is likely they are vital components of the structure and function of these ecosystems and critical to the operations of the earth. Microbes are deeply involved in the flow of energy and food through the earth’s ecosystems. Most people are aware that plants carry out photosynthesis, which is the light-fueled conversion of carbon dioxide to organic material, accompanied by the formation of oxygen. But microorganisms were photosynthesizing long before the first plants appeared. In fact, they were responsible for changing the atmosphere of the earth from one without oxygen to one with oxygen. Today photosynthetic microorganisms (including algae) account for more than 50% of the earth’s photosynthesis, contributing the majority of the oxygen to the atmosphere. Another process that helps keep the earth in balance is the process of biological
decomposition and nutrient recycling.Decomposition involves thebreakdown of deadmatterand wastes into simple compounds that can bedirected back into the natural cycles of livingthings.If it were not for multitudes of bacteria and fungi, many chemical elements wouldbecome locked up and unavailable to organisms. In the long-term scheme of things,microorganisms are the main forces that drive the structure and content of the soil, water, andatmosphere.3.Describe the cellular makeup of microorganisms and their size range, and indicate howvirusesdifferfromcellularmicrobes.As a general rule, prokaryotic cells are smaller than eukaryotic cells, and in addition tolacking a nucleus, theylack other complex internal compartments called organelles.Organellesarestructures incellsthat areboundbyoneormoremembranesThe dimensions of macroscopic organisms are usually given in centimeters (cm) andmeters(m),whereasthoseofmostmicroorganismsfall withintherangeofmicrometers(μum)and,sometimes,nanometers (nm)andmillimeters(mm).The sizerangeofmostmicrobes extends from the smallest viruses, measuring around 10 nm and actuallynotmuchbiggerthan alargemolecule, toprotozoansmeasuring3to4mmandvisiblewiththe naked eye.Virusesarenon-cellularmicroorganisms.1.3Humanuseofmicroorganisms.1,Discussthewaysmicroorganismsmaybeappliedtosolvehumanproblems.Humans have been usingmicroorganisms for thousands of years to improve life and even tofurther human progress. Food industry, antibiotics, bioenergy products have been producedwith microorganisms. Genetic engineering is a newer area of biotechnology that manipulatesthe genetics of microbes, plants, and animals for the purpose of creating new products andgenetically modified organisms. Another way of tapping into the unlimited potential ofmicroorganisms is the relatively new science of bioremediation.This process introducesmicrobes into the environment to restore stability or to clean up toxic pollutants.Bioremediation is required to control themassive levels of pollution that result from humanactivities.1.4Humanuseofmicroorganisms.1.Review the roles of microorganisms as parasites and pathogens that cause infection anddisease.Some microbes have adapted to a non-free-living lifestyle called parasitism.Aparasitelives in or on the body of a larger organism called the host and derives most of itsrequirements from that host.Aparasite's actions can damagethehost through infectionand disease. Another term that can be used to specify this type of microbe is pathogen.1.5Thehistorical fundationsofmicrobiology.1. Outline the major events in the history of microbiology, including the major contributors tothe earlydevelopment ofmicroscopy,medical advances, aseptictechniques, and thegerm theoryof disease.The early development of microscopy.True awareness of the widespread distribution of3
3 decomposition and nutrient recycling. Decomposition involves the breakdown of dead matter and wastes into simple compounds that can be directed back into the natural cycles of living things. If it were not for multitudes of bacteria and fungi, many chemical elements would become locked up and unavailable to organisms. In the long-term scheme of things, microorganisms are the main forces that drive the structure and content of the soil, water, and atmosphere. 3. Describe the cellular makeup of microorganisms and their size range, and indicate how viruses differ from cellular microbes. As a general rule, prokaryotic cells are smaller than eukaryotic cells, and in addition to lacking a nucleus, they lack other complex internal compartments called organelles. Organelles are structures in cells that are bound by one or more membranes. The dimensions of macroscopic organisms are usually given in centimeters (cm) and meters (m), whereas those of most microorganisms fall within the range of micrometers (μm) and, sometimes, nanometers (nm) and millimeters (mm). The size range of most microbes extends from the smallest viruses, measuring around 10 nm and actually not much bigger than a large molecule, to protozoans measuring 3 to 4 mm and visible with the naked eye. Viruses are non-cellular microorganisms. 1.3 Human use of microorganisms. 1. Discuss the ways microorganisms may be applied to solve human problems. Humans have been using microorganisms for thousands of years to improve life and even to further human progress. Food industry, antibiotics, bioenergy products have been produced with microorganisms. Genetic engineering is a newer area of biotechnology that manipulates the genetics of microbes, plants, and animals for the purpose of creating new products and genetically modified organisms. Another way of tapping into the unlimited potential of microorganisms is the relatively new science of bioremediation. This process introduces microbes into the environment to restore stability or to clean up toxic pollutants. Bioremediation is required to control the massive levels of pollution that result from human activities. 1.4 Human use of microorganisms. 1. Review the roles of microorganisms as parasites and pathogens that cause infection and disease. Some microbes have adapted to a non-free-living lifestyle called parasitism. A parasite lives in or on the body of a larger organism called the host and derives most of its requirements from that host. A parasite’s actions can damage the host through infection and disease. Another term that can be used to specify this type of microbe is pathogen. 1.5 The historical fundations of microbiology. 1. Outline the major events in the history of microbiology, including the major contributors to the early development of microscopy, medical advances, aseptic techniques, and the germ theory of disease. The early development of microscopy. True awareness of the widespread distribution of
microorganisms and some of their characteristics was finally made possible by thedevelopment of the first microscopes. The most careful and exacting observations awaitedthe simple single-lens microscope hand-fashioned by Antonie van Leeuwenhoek, aDutch linen merchant and self-made microbiologist Because of Leeuwenhoek'sextraordinary contributions to microbiology,he is sometimes considered the father ofbacteriology and protozoology.The development of medical microbiology. Early experiments on the sources ofmicroorganisms led to the profound realization that microbes are everywhere: Not onlyare air and dust full of them, but the entire surface of the earth, its waters, and all objectsare inhabited by them. This discovery led to immediate applications in medicine. Thus theseeds of medical microbiology were sown in the middle to latter half of the nineteenthcentury with the introduction ofthegerm theory ofdisease and the resulting use of sterile.aseptic, andpure culture techniques.About 125 years ago, the first studies by Robert Koch clearly linked a microscopicorganism with a specific disease.The English surgeon Joseph Lister took notice of theseobservations and was the first to introduce aseptie techniques aimed at reducingmicrobes in a medical setting and preventing wound infections. Lister's concept ofasepsiswas much more limited than our modern precautions. It mainly involved disinfecting thehands and the air with strong antiseptic chemicals, such as phenol, prior to surgery.The Discovery of Pathogens and the Germ Theory of Disease.Two ingenious foundersof microbiology,Louis Pasteur of France and Robert Koch of Germany introducedtechniques that are still used today.Pasteur invented pasteurization and completed someof the first studies showing that human diseases could arise from infection.2. Explain the main features of the scientifi c method, and differentiate between inductive anddeductivereasoningand betweenhypothesis andtheory.The general approach taken by scientists to explain a certain natural phenomenon is calledthe scientific method. A primary aim of this method is to formulate a hypothesis, atentative explanationtoaccountfor what has been observed ormeasured.Alengthyprocessof experimentation, analysis, and testing eventually leads to conclusions that either supportorrefutethehypothesis.Atheoryis a collection of statements,propositions,or conceptsthat explains or accounts for a natural event A theory is not the result of a singleexperiment repeated over and over again but is an entire body of ideas that expresses orexplainsmany aspects ofaphenomenon.HypothePredlcclpothesisis trueBacterial endosporefA00d00celsFigure1.10.Thepatternofdeductivereasprocessstartswithagensh:ay'ofmorinciplethathasboeenthoroughlytestedoverthepasta
4 microorganisms and some of their characteristics was finally made possible by the development of the first microscopes. The most careful and exacting observations awaited the simple single-lens microscope hand-fashioned by Antonie van Leeuwenhoek, a Dutch linen merchant and self-made microbiologist. Because of Leeuwenhoek’s extraordinary contributions to microbiology, he is sometimes considered the father of bacteriology and protozoology. The development of medical microbiology. Early experiments on the sources of microorganisms led to the profound realization that microbes are everywhere: Not only are air and dust full of them, but the entire surface of the earth, its waters, and all objects are inhabited by them. This discovery led to immediate applications in medicine. Thus the seeds of medical microbiology were sown in the middle to latter half of the nineteenth century with the introduction of the germ theory of disease and the resulting use of sterile, aseptic, and pure culture techniques. About 125 years ago, the first studies by Robert Koch clearly linked a microscopic organism with a specific disease. The English surgeon Joseph Lister took notice of these observations and was the first to introduce aseptic techniques aimed at reducing microbes in a medical setting and preventing wound infections. Lister’s concept of asepsis was much more limited than our modern precautions. It mainly involved disinfecting the hands and the air with strong antiseptic chemicals, such as phenol, prior to surgery. The Discovery of Pathogens and the Germ Theory of Disease. Two ingenious founders of microbiology, Louis Pasteur of France and Robert Koch of Germany introduced techniques that are still used today. Pasteur invented pasteurization and completed some of the first studies showing that human diseases could arise from infection. 2. Explain the main features of the scientifi c method, and differentiate between inductive and deductive reasoning and between hypothesis and theory. The general approach taken by scientists to explain a certain natural phenomenon is called the scientific method. A primary aim of this method is to formulate a hypothesis, a tentative explanation to account for what has been observed or measured. A lengthy process of experimentation, analysis, and testing eventually leads to conclusions that either support or refute the hypothesis. A theory is a collection of statements, propositions, or concepts that explains or accounts for a natural event. A theory is not the result of a single experiment repeated over and over again but is an entire body of ideas that expresses or explains many aspects of a phenomenon
1.6Taxonomy:Organizing,Classifying,and Naming Microorganisms1. Define taxonomy and its supporting terms classification, nomenclature, and identification.The formal system for organizing classifying, and naming living things is taxonomy.Theprimary concernsof taxonomy areclassification,nomenclature,and identificationThese three areas are interrelated and play a vital role in keeping a dynamic inventory of theextensivearrayof living things.Classification is anorderlyarrangement of organisms intogroups that indicate evolutionary relationships and history.Nomenclature is the process ofassigning names tothevarious taxonomic rankings of each microbial species.Identificationis the process of determining and recording the traits of organisms to enable their placementinan overall taxonomic scheme.2. Explain how the levels of a taxonomic scheme relate to each other Give the names of thelevels, and place them in a hierarchy.The order of taxa between thetop and bottom levels is, in descending order:domain,kingdom,phylum * or division, class, order, family,genus, * and species.3.Describethegoalsof nomenclatureandhowthebinomial system isstructured.Knowhowto correctly write a scientific name.The method of assigning the scientific or specific name is called the binomial (two-name)system of nomenclature.The scientific name is always a combination ofthegeneric(genus)namefollowed by the species name.The generic part of the scientific name is capitalized,and the species part begins with a lowercase letter.1.61.7TheOriginandEvolutionof Microorganisms1.Discuss the fundamentals ofevolution and how they are used in studying organisms.The natural relatedness between groups of living things is called theirphylogeny Sobiologists use phylogenetic relationships to create a system of taxonomy.Evolution is animportanttheme that underlies all of biology,includingmicrobiologyPut simply,evolutionstates that living things change gradually through hundreds of millions of years and that theseevolvements result in various types of structural and functional changes through manygenerations. The process of evolution is selective: Those changes that most favor the survivalof aparticular organismorgroupof organisms tend toberetained, and thosethatarelessbenefi cial to survival tend to be lost. Space does not permit a detailed analysis ofevolutionary theories, but the occurrence of evolution is supported by a tremendous amountof evidencefrom the fossil record and from the study of morphology (structure),physiology(function), and genetics (inheritance)Evolution isfounded on two preconceptions:(1)that all new species originate frompreexisting species and (2)that closely related organisms have similar features because theyevolvedfromcommonancestralforms.2. Outline some of the primary evidence used to verify evolutionary trends3. Explain how trees of life are constructed, and tell what characteristics are used in organizingtheorganismsonthesetrees.Thephylogeny,or evolutionaryrelatedness, oforganisms isoften represented bya diagramwitha branching,treelike format.Thetrunk ofthe treerepresents the main ancestral lines, and
5 1.6 Taxonomy: Organizing, Classifying, and Naming Microorganisms 1. Define taxonomy and its supporting terms classification, nomenclature, and identification. The formal system for organizing, classifying, and naming living things is taxonomy. The primary concerns of taxonomy are classifi cation, nomenclature, and identification. These three areas are interrelated and play a vital role in keeping a dynamic inventory of the extensive array of living things. Classification is an orderly arrangement of organisms into groups that indicate evolutionary relationships and history. Nomenclature is the process of assigning names to the various taxonomic rankings of each microbial species. Identification is the process of determining and recording the traits of organisms to enable their placement in an overall taxonomic scheme. 2. Explain how the levels of a taxonomic scheme relate to each other. Give the names of the levels, and place them in a hierarchy. The order of taxa between the top and bottom levels is, in descending order: domain, kingdom, phylum * or division, class, order, family, genus, * and species. 3. Describe the goals of nomenclature and how the binomial system is structured. Know how to correctly write a scientific name. The method of assigning the scientific or specific name is called the binomial (two-name) system of nomenclature. The scientific name is always a combination of the generic (genus) name followed by the species name. The generic part of the scientific name is capitalized, and the species part begins with a lowercase letter. 1.6 1.7 The Origin and Evolutionof Microorganisms 1. Discuss the fundamentals of evolution and how they are used in studying organisms. The natural relatedness between groups of living things is called their phylogeny. So biologists use phylogenetic relationships to create a system of taxonomy. Evolution is an importanttheme that underlies all of biology, including microbiology. Put simply, evolution states that living things change gradually through hundreds of millions of years and that these evolvements result in various types of structural and functional changes through many generations. The process of evolution is selective: Those changes that most favor the survival of a particular organism or group of organisms tend to be retained, and those that are less benefi cial to survival tend to be lost. Space does not permit a detailed analysis of evolutionary theories, but the occurrence of evolution is supported by a tremendous amount of evidence from the fossil record and from the study of morphology (structure), physiology (function), and genetics (inheritance). Evolution is founded on two preconceptions: (1) that all new species originate from preexisting species and (2) that closely related organisms have similar features because they evolved from common ancestral forms. 2. Outline some of the primary evidence used to verify evolutionary trends. 3. Explain how trees of life are constructed, and tell what characteristics are used in organizing the organisms on these trees. The phylogeny, or evolutionary relatedness, of organisms isoften represented by a diagram with a branching, treelike format.The trunk of the tree represents the main ancestral lines, and