(BQ) Part 1 book Prescott''s microbiology presentation of content: The evolution of microorganisms and microbiology, microscopy, bacterial cell structure, eukaryotic cell structure, viruses and other acellular infectious agents, microbial growth, antimicrobial chemotherapy, antimicrobial chemotherapy,... and other contents.
Trang 3B , Succeed"
PRESCOTT'S MICROBIOLOGY, NINTH EDITION
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Trang 4Joanne M Willey has been a
professor at Hofstra University on Long
Island, New York, since 1993, where she
is Professor of Microbiology; she holds a
joint appointment with the Hofstra
University School of Medicine Dr Willey
received her B A in Biology from the
University of Pennsylvania, where her
interest in microbiology began with
work on cyanobacterial growth in
eutrophic streams She earned her Ph.D
in biological oceanography (specializing
in marine microbiology) from the
Massachusetts Institute of Technology
Woods Hole Oceanographic Institution
Joint Program in 1987 She then went to
Harvard University, where she spent her
postdoctoral fellowship study ing the
filamentous soil bacterium Streptomyces
coelicolor Dr Willey continues to
investigate this fascinating microbe
and has coauthored a number of
publications that focus on its complex
developmental cycle She is an active
member of the American Society for
Microbiology (ASM), and served on the
editorial board of the journal Applied
and Environmental Microbiology for nine
years and as Chair of the Division of
General Microbiology Dr Willey
regularly teaches microbiology to
biology majors as well as medical
students She also teaches courses in cell
biology, marine microbiology, and
laboratory techniques in molecular
genetics Dr Willey lives on the north
shore of Long Island with her husband
and two sons She is an avid runner and
enjoys skiing, hiking, sailing, and
reading She can be reached at
joanne.m.willey@hofstra.edu
About the Authors
Linda M Sherwood is a member
of the Department of Microbiology at Montana State University Her interest in microbiology was sparked by the last course she took to complete a B.S degree in Psychology at Western Illinois University
She went on to complete an M.S degree in Microbiology at the University of Alabama, where she studied histidine utilization
by Pseudomonas acidovorans She subsequently earned a Ph.D in Genetics at Michigan State University, where she studied sporulation in Saccharomyces cerevisiae She briefly left the microbial world to study the molecular biology of dunce fruit flies at Michigan State University before moving to Montana State University Dr Sherwood has always had a keen interest in teaching, and her psychology training has helped her to understand current models of cognition and learning and their implications for teaching Over the years, she has taught courses in general microbiology, genetics, biology, microbial genetics, and microbial physiology She has served as the editor for ASM's Focus on Microbiology Education and has participated in and contributed
to numerous ASM Conferences for Undergraduate Educators (ASMCUE)
She also has worked with K-12 teachers to develop a kit-based unit to introduce microbiology into the elementary school curriculum and has coauthored with Barbara Hudson a general microbiology laboratory manual, Explorations in Microbiology: A Discovery Approach, published by Prentice-Hall Her association with McGraw-Hill began when she prepared the study guides for the fifth and sixth editions of Microbiology Her non
academic interests focus primarily on her family She also enjoys reading, hiking, gardening, and traveling She can be reached at lsherwood@montana.edu
Christopher J Woolverton is founding professor of Environmental Health Science, College of Public Health at Kent State University (Kent, OH), and is the Director of the Kent State University (KSU) Center for Public Health Preparedness, overseeing its BSL-3 Training Facility
Dr Woolverton serves on the KSU graduate faculty of the College of Public Health, the School of Biomedical Sciences, and the Department of Biological Sciences He holds
a joint appointment at Akron Children's Hospital (Akron, OH) He earned his B.S in Biology from Wilkes College (PA), and his M.S and Ph.D in Medical Microbiology from West Virginia University, School of Medicine He spent two years as a postdoctoral fellow at UNC-Chapel-Hill
Dr Woolverton's current research is focused
on real-time detection and identification of pathogens using a liquid crystal (LC) biosensor that he patented in 2001 Dr Woolverton has published and lectured widely on the mechanisms by which LCs act
as biosensors and on the LC characteristics
of microbial proteins Professor Woolverton teaches microbiology, communicable diseases, immunology, prevention and control of disease, and microbial physiology He is on the faculty of the National Institutes of Health National Biosafety and Biocontainment Training Program, teaching laboratory safety, risk assessment, decontamination strategies, and bioterrorism readiness An active member
of the American Society for Microbiology, Woolverton serves on its Board of Education and as the editor-in-chief of its Journal of Microbiology and Biology Education
Woolverton and his wife, Nancy, have three daughters, a son-in-law, and a grandson He enjoys time with his family, ultra-light hiking and camping, and is an avid cyclist His e-mail address is cwoolver@kent.edu
iii
Trang 58
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Trang 6Digital Tools for Your Success
A diagnostic, adaptive learning
system to increase preparedness
Now Available for the Ninth Edition!
McGraw-Hill LearnSmartTM is an adaptive learning system de
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v
Trang 7Evolution as a Framework
Introduced immediately in chapter 1 and used as an overarching
theme throughout, evolution helps unite microbiological con
cepts and provides a framework upon which students can build
their knowledge
Separate Chapters on Bacteria and Archaea
In recognition of the importance and prevalence of archaea, the
structure, genetics, and taxonomic and physiologic diversity of
these microbes are now covered in chapters that are separate
from those about bacteria
An Introduction to the Entire
Microbial World
Now covered in chapters 3-6, the separate chapters on the
structure and function of bacteria and archaea are followed by
the discussion of eukaryotic cells preceding viruses
Secondary Lymphoid Organs and Tissues
The8plecn is the most highly organized secondary lymphoid
functions to filter the blood and trap blood-borne particles to
be ass�ssed for foreignness by phagocytes (figure 33.14) Mac
rophages and dendritic cells are present in abundance, and
pathogen is phagocytosed, killed, and digested 1he resulting
antigens are presented to lymphocytes, activating a specific im
mune response
Lymph nodes lk at the junctions oflymphaticvessds, where
macro phages md dendritic cells trap particles that enter the lym
phaticsyslem(figure33.14c).If a parlicle isfollndlobe foreign,il
arcprcscntcdto lymphocytcs
Lymphoid tissues are found througholll the body as highly
organi7.ed or loosely associated cellular complexes (figure 33.14)
such as skin (skin-associated lymphoid tissue, or SALT) and mu
cous membranes (mucosal-associated lymphoid tissue, or
lymphoid tissues that featuremacrophages surrounded by spe
cific areas of B and T lymphocytes and sometimes dendritic cells
Loosely associated lymphoid tissue is best represented by the
cellular partitioning The primary role of these lymphoid tissues
is to efficiently organi7.e leukocytes to increase intc:raction be
tween the innate and the adaptive arms of the immune response
'lhus, the lymphoid tissues serve as the interface between the in
nate resistance mechanisms and adaptive immunity of a host
We now discuss these tissues in more detail
Despite the skin's defenses, at times pathogenic microorgan
isms gain access to the tissue under the skin surface Here they
lymphoid ti!lsue (SALT) ( figure 33.15 ) The major function of
SALT is to confine microbial invaders to the area immediately
underlying the epidermis and to preventthemfrom gaining ac
hans cell, a dendritic ccll that phagocytoses microorganisms
that penetrate th� skin Once the Langerhans cell has int�mal
i7.ed a foreign particle or microorganism, it migrates from the
epidermis to nearby lymph nodes, where it presents antigen to
activate nearby lymphocytes, inducing a specific immnne re
tion illustrates another bridge between innate resistance and
adaptive immunity
The epidermis also contains another type of SALT cell
called the intraepidfrmal lymphocytf (figure 33.15), a spe
cialized T cellhavingpotentcytolyticand immunoregulatory
skin so that they can intercept any antigens that breach the first
line of defense Most of these specialized SALT cells have limiL.ed
rcceptordiversity andhavelikelyevolvedto recogni7.ecommon
skin pathogen patterns
The specialized lymphoid tissue in mllcous membranes is called mucosal-associated lymphoid tissue (MALT) There are sneral types of MALT The system mo$l studied is the gut
sils, adenoids, diffllse lymphoid areas along the gut, and well-organized MALT also occurs in the respiratory system and
Aboutthe Authors 111 Preface iv
Part One Introduction to Microbiology
' + -1 The Evolution ofMicroorganr.;m� and Microbiology 1
2 Micro5t:opy 22
3 BacteriaiCeiiStructure 42
4 ArchaeaiCeiiStructure 82
5 EukaryoticCeiiStructure 92
6 Viruses and Other Acellular lnfedklus Agents
Part Two Microbial Nutrition, Growth, and Control
Part Five The Diversity of the Microbial World
19 Microbial Taxonomy and the Evolution of Diversity
20 TheArchaea 469
21 TheDeinococci,Mollicutes,andNonproteobacterial Gram-Negative Bacteria 489
29 Methods In Microbial Ecology 15415
30 Microorgani5ms in Marine and Fre5hwater Ecosystems 660
Credits C-1
23 Firmicutes:ThelowG+CGram-PositiveBilcteria 542 Index 1-1
Molecular Microbiology and Immunology
The ninth edition includes updates on genetics, biotechnology, genomics, and immunology The discussion of eukaryotic and archaeal genetics has been expanded and makes up a separate chapter to reflect the relatedness of genetic information flow A streamlined discussion of immunity with enhanced detail between innate and adaptive linkages helps students grasp the complexity and specificity of immune responses
Trang 8A Modern Approach to Microbiology
tionoom'tttSihl$eKtra nitr.te toN,and
lhe rnctlft g:Jftnllotue nltro�no.Ddes
This cycle of nilrific.atioo/denitrification
respoosibleforthe highestN00levels in
650.000)'1lUS
What are the<:<�n�u nus of di•
rupting lhccarbon andnitrogencycles!
Globlllclimate change itthemost obvi
ous example k is important to keep in
mind that weaber is oot the same a11 cli
mate While North America has 1uffered
lomtoftheholl«l tll1llmtnon recordln
Julytlu.t is panio:ubrly hot!8not, by it·
Globf.l clim•te change is mmuredovtr
lucha.&urf�tempenolure on landand Flgure28.12 , tur•llndHum;m·MidtlnftutnotSonlht"llrO!I"ICJdt
on and In tb atmmpbere and trope· MICRO INQUIIIV "Mwnorga.rJlmibfntfir(romnirril\caticln1
optMre;rates of
precipitation;andfre-quency of extreme Wt'ather Based on
these analyr.e�o,the average global temperature has incrnK<I
0.74"C,a00this rise is directly corrdatedwithfouilfuel
com-bustion toCO,( fipre2S.l3 ).Dtpending on the r;rte ofconlln·
nedincrease in greenhouse gases.the average global surface
temperatureis predictedtorise betweenl.land6.4"Clr)'2100
Mo imporunt question is how will microbes re�poOO 10 a
changingworid.ll<>:;auoe for thevast majority ofl'.arilishistory,
m.iCI'O(lrganimu have bun the drtvm of elememzl C)'(llng
2.DiK11Mthe,_.;bleroleDffureot•in the controiDfCO,
l Howdo<�"9"'inthe nitrogencyd"caused bylertilization
lnflu ncetheurbon�?
4 GIVen !hit "idl mkroblal �roup ha• a n optimum temperalllre
r;m!JI11or !Jfll'l"th."- migl1t you predict cl1�nges to a soli mlcrolllal
comll'lllnity1Mng inyourgeog�pl1ica�7
Flgure28.13 GlobaiAnnuai-MeanSo.ufaceAirTm.per1ture Change Dani<defrvedfmmthPmrtromlogic.ll•laOOnnetwOO:,Goddard lnstituteforSpaceS<:iero: ,hnp:l/rlilta.!Ji".n""'.!JOVIilislem¢1rapW
Special Interest Essays
Organized into four themes-Microbial Diversity &
Ecology, Techniques & Applications, Historical High
lights, and Disease-these focused and interesting essays
provide additional insight to relevant topics
3.1 Gram Positive and Gram Negative or Monoderms and Diderms?
The importance of the Gram stain in the history of microbi
ology cannot be overstated The Gram stain reaction was for
bacterial taxonomists to construct taxa, and it is still useful
done to differentiate bacteria that stained Gram positive
organisms such as Bacillus subtilis (Gram positive) and Esch
erichia coli (Gram negative) At the time, it was thought that
all other bacteria would have similar cell wall structures
However, as the cell walls of more bacteria have been charac
refer to bacteria as Gram positive or Gram negative In other
words, the long-held models of Gram-positive and Gram
negative cell walls do not hold true for aU bacteria Recently
Iain Sutcliffe has proposed that microbiologists stop refer
ring to bacteria as either Gram positive or Gram negative He
suggests that instead we should more precisely describe bac
tion that some bacteria have envelopes with a single
membrane-the plasma membrane as seen in typical Gram
positive bacteria-while others have envelopes with two
as seen in typical Gram-negative bacteria He proposed call
ing the former monoderms and the latter diderms
But why make this change? Sutcliffe begins by pointing
out that some bacteria staining Gram positive are actually
moooderms By referring to Gram-positive-staining diderms
and many a budding microbiologist into thinkil bacterium has a typical Gram-positive envelope
gues that by relating cell envelope architecture tot evolution of these architectures He notes that th•
micutes and Actinobacterta are composed almost
of monoderm bacteria, whereas almost all othe phyla consist of diderms
There are interesting exceptions to the rela1 phylogeny and cell envelope structure For instanet
of the genus Mycobacterium (e.g., M tubercula
to the predominantly monoderm phylum Acti1 Mycobacteria have cell walls that consist of pep
of mycolic adds rather than the phospholipid�
cells' outer membrane tfi Suborder Corynet (section 24.1)
Members of the genus Deinococcus are anotb ing exception These bacteria stain Gram positive derms Their cell envelopes consist of the plasma · what appears to be a typical Gram-negative cdl � outer S-layer Their outer membrane is distinctivt
It is now known that there are several taxa with c branes that substitute other molecules for LPS
Soun;e:Sutcliffe,I.C.lfJIO.A phylum level perspectiveonbl�tetUicenMvelope
�tchirecwr• lrendsUieroblol fB{I0/ 64-70
21st-Century Microbiology Prescott's Microbiology leads the way with updated text devoted
to global climate change, biofuels, and microbial fuel cells For more, see chapters 28, 30, 42, and 43
Metagenomics and the Human Microbiome The updated genomics chapter covers the technical aspects of metagenomics, and the human microbiome is discussed in the context of microbial interactions in chapters 18 and 32
Laboratory Safety Reflecting forthcoming recommendations from the American Society for Microbiology, chapter 37 provides specific guidance for laboratory best practices to help instructors provide safe conditions during the teaching of laboratory exercises
ure ) This is the hallmark of white-nose syndrome (WNS), and if its rate of infection continues unchecked, it is projected
to eliminate the most common bat species In eastern North America (Myotis lucifugus) by 2026
WNS was first spotted in 2006 among bats hibernating in
a cave near Albany, NY Scientists qukkly became alarmed for least six bat species and is now found from the mid-Atlantic New Brunswick), and as far west as Oklahoma Second, it is deadly A population of bats declines from 30 to 99% in any given infected hibernacula (the place where bats hibernate, which unfortunatdy rhymes with Dracula)
WNS is caused by the ascomycete Geomyces destructans
It colonizes a bat's wings, muzzle, and ears where it first
Geomyces destructans causes WNS A little brown bat {Myotis lucifugus) with the white fungal hyphae(,mow) for which WNS is named
erodes the epidermis and then invades the underlying skin site of infection (and the anatomical site harmed most) is the wing Wings provide a large surface area for colonization, and once infected, the thin layer of skin is easily damaged, These in turn result in premature awakening, loss of essential fat reserves, and strange behavior
Where did this pathogen come from and why does it infect bats? The best hypothesis regarding Its origin Is that causes mild infection in at least one hibernating bat species pollution-the human introduction of invasive pathogens of wildlife and domestic animal populations that threaten bio diversity and ecosystem function
The capacity of G destructans to sweep through bat populations results from a "perfect storm" of host- and with a growth optimum around trC; it does not grow above 20°C All infected bat species hibernate in cold and humid environments such as caves and mines Because their meta bolic rate is drastically reduced during hibernation, their body temperature reaches that of their surroundings, be tween 2 and 7°C Thus WNS is only seen in hibernating bats metabolically active, the bat's body temperature is too Vl-atm
to support pathogen growth
While it is too late to save the estimated 6 million bats that have already succumbed to WNS, microbiologists, con servationists, and government agencies are trying to limit clo.�ed to human traffic, and protocols for decontamination spread from cave to cave Although we cannot cure sick this pathogen
Re•dmorti:Frict,W.F.era/.,2UIU.Anemerylngth$u$1JcausuregioMipop u l•tlon col/1ps• of• common NarthAm•ric•n Nt 1p1cilr S�itnca 319:679-682
Trang 9States.Hot dogsarJdluochmeats arepopularat outingssuch asbilsebi!ll
!Jilmesandin lunchescarried towarkor schooi.Yeteachyearintfle
Urlited Stat, ,apprmimately1,600peopleare sickenedby•bacterium
that can wntominate the meat and even worse survive arid grow when
the"""'atis properlyrefrigerated
Thediseasecul, itisLis teriamonocytogenes,aGram-positive rOO
fourtdinsoil aridmanyotherenvironrnental sites.lt isnot orllycoldtolerant
butsaltandaddtolerantas weii.AithoLJgh itisinthe minorleago.�eswhen
compared to someofthe big hitters offo OObome disease (e.g., So/monel/a
fflterico),it isofcoocernfortwo reasons:who itkillsanclhowrTIIlnyitk�ls
L./'OOil()[ytvgfflesUrgets theyOlllgand old,pregrlilntwomen,and
immunocompromised individuals; about 15%ofthose inf!'Cted die
ltseffectonpregnantwo"""'n is partkularlyheortbreaking.The
cantaloupe sedan outbreokof listeriosisin20statesin theUnited Stille ich infected over l:lO and k�led over 20 Viruses as agents of good will come as a surprise to many Typically we thinkofthemasmajorcausesofdisease.However,viruses are>ignilicamfor otherrea>ens.Theyarevitalmembersofaquatic ecosystems.Ttlerethe interact with cellulor mkrobesand contribute to the mo\lement ganic
Bialogica/wntrolafmkroorganisms tian8.7) Readiness Check:
flased onwhatyouhilvelearnedpreviousfy,youshoul dbe ableto
II Definetheterm acellular
II Compareand contrast ingeneralterms viruses,viroids,satelites,aOO prions(sectionU)
woman usually only suffers mild, flu like symptoms; however these 6.1 Viruses
innocuous symptomsbelie thefactthatthechildshe carries isin serious
danger Herpregnaocyoftenendsin miscarriageor stillbirth.Newborns After reading this section, you should be �ble to
infected with the bacterium are likely to develop meningitis Many will die • Define the terms virology, bacterioptloges, and ptloges
as a result.Thme whosurviveoftenhave neurologicaldisorders • Li>torganism> thatarehoststo viruses
Currently,pregnant wamenare coonseledagainst eatingrBldy-to-eat
food>unlesstheyhavebeencookedpriorto consumption.f-lowever,
L monacyrogene� is koown to contaminate many foods other than tlot dogs
andthesecan't alwaysbeheated.ln2006th�U.S.FoodandDrug
Administration(FDA)appro•ed a new approachto preventlisteriosis:
spraying •irusesthatattackanddestroythebacteriuman reody-to-eatcold
cutsalldlllncheonmeats.lnother words.the viruseo areafood additive!
The"""'thodissafet>ecausethe viruses onlyattackL.mooocyrogene<>.not
New! Newsworthy Stories-Each chapter begins with a real-life story illustrating the relevance of the content covered in the upcoming text
New! Readiness Check-The introduction to each chapter includes a skills checklist that defines the prior knowledge
a student needs to understand the material that follows
New! Learning Outcomes-Every section in each chapter begins with a list of content-based activities students should be able to perform after reading
Sinceapproval.the uoeof virusesto controlthetransmissionof
listeriosisbyotherfoodshasbeenstudied.Unfununately,thosestudiesdid, """'" '"'"""""-"""'-�"-"'-""-_ �"'"""""' -' -,
ootindudefoodssuchas freshfruit.ln2011Lfl"lOIJO!:}'W9enes-contaminated
Micro Inquiry-Select figures
throughout every chapter
contain probing questions,
adding another assessment
opportunity for the student
MICRO INQUIRY l'ihydotheemptyw,7'ii'f>rem1ioc;;fc;ch<rftothf cei/,;f�rtM·tiro.'i)i'rlOiMffitmrhel;c:otct//1
Animation Icon-This symbol indicates material presented in the text is also accompanied by an animation on the text website at www.mhhe.com/willey9
Cross-Referenced NotesIn-text references refer students to other parts of the book to review
Retrieve, Infer, ApplyQuestions within the narrative of each chapter assist students in mastering section concepts before moving on to other topics
Trang 10Student-Friendly Organization
Vivid Instructional Art Program-Three
dimensional renditions and bright, attractive
colors enhance learning r�>cuglliti<Ml 'H:c�· th.:.�\ �-ncaiie thc micmo•·glnN:l5 within a
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Recognition of Foreignness
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m�n;•'.itfrtflll :';�;hr)�r"1 art n:��ni1� fQa<:fi'�'lf l'h:or,rx-)1f•
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More Annotated Figures-All key metabolic
pathways and molecular processes are now anno
tated, so that each step is clearly illustrated and
explained
Key Concepts-At the end of each
chapter and organized by num
bered headings, this feature dis
tills the content to its essential
components with completely cross
referenced figures and tables
Compare, Hypothesize, Invent
Includes questions taken from cur
rent literature; designed to stimulate
analytical problem-solving skills
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ix
Trang 11Each chapter has been thoroughly reviewed and many have un
dergone significant revision All now feature pedagogical ele
ments, including a Readiness Check for the chapter and Learning
Outcomes for each section therein
Part I
Chapter 1- Evolution is the driving force of all biological sys
tems; this is made clear by introducing essential concepts of mi
crobial evolution first
Chapter 3-Coverage of bacterial cellular structure and function
The chapter now includes a discussion of nutrient uptake in the
section on bacterial plasma membranes
Chapter 4-G rowing understanding of the distinctive character
istics of archaea has warranted the creation of a new chapter that
focuses on their cell structure and function Comparisons to bac
teria are made throughout the chapter
Chapter 5- An introduction to eukaryotic cell structure and
function, with emphasis on eukaryotic microbes More de
tailed information on protist and fungal cells is presented in
chapters 25 (The Protists) and 26 (The Fungi), which also focus
on the diversity of these microbes Comparisons between bac
teria, archaea, and eukaryotes are included throughout the
chapter
Chapter 6- This chapter, entitled Viruses and Other Acellular In
fectious Agents, surveys the essential morphological, physiologi
cal, and genetic elements of viruses as well as viroids, satellites,
and prions This chapter completes our four-chapter introduction
of microbial life
Part II
Chapter 7-Reorganized to initially focus on the growth of mi
crobes outside the laboratory (including growth in oligotrophic
environments) and the environmental factors that influence
microbial reproduction Topics related to laboratory culture of
microbes follow
Chapter 8-Reorganized to reflect emphasis on interruption of nor
mal growth and reproduction functions to control microorganisms
Chapter 9-Content focuses on the mechanism of action of each
antimicrobial agent and stresses usage to limit drug resistance
Part III
Chapter 10- This introduction to metabolism includes a new
section that outlines the nature of biochemical pathways and
introduces the concept of metabolic flux through the interconnected biochemical pathways used by cells
Chapter 11- The chapter now begins with an introduction to metabolic diversity and nutritional types
Chapter 12-Updated coverage ofCOrfixation pathways
PartlY Chapter 13-Now focuses on bacterial genetic information flow with improved coverage of bacterial promoters, sigma factors, termination of DNA replication, transcription cycle, and protein folding and secretion
Chapter 14-Now focuses on the regulation of bacterial cellular processes The coverage of regulation of complex cellular behaviors has been significantly updated and expanded, including new material on cyclic dimeric GMP
Chapter 15-A new chapter that considers eukaryal and archaeal genome replication and expression together In both cases, the discussion has been updated and expanded, and reflects the similarity of information flow as carried out by members of Archaea and Eukarya
Chapter 16-Covers mutation, repair, and recombination in the context of processes that introduce genetic variation into populations This is now related to the evolution of antibiotic-resistant bacteria
Chapter 17- The use of recombinant DNA approaches to construct a synthetic genome is highlighted
Chapter 18-New principles and applications of genomic techniques, including massively parallel genome sequencing and single cell genome sequencing, are now reviewed The growing importance of metagenomics to environmental microbiology and its use in exploring the human microbiome are introduced here
PartY Chapter 19-Microbial evolution, introduced in chapter 1, is expanded with a complete discussion of the endosymbiotic theory, and the concept and definition of a microbial species
Chapter 20- Expanded coverage of archaeal physiology includes new figures presenting archaeal-specific anabolic and catabolic pathways The evolutionary advantage of each pathway is discussed in the context of archaeal ecology
Chapter 21-Now includes mycoplasmas, in keeping with Bergey's Manual; new figures illustrating the life cycle of Chlamydia are included
Trang 12List of Content Changes
Chapter 22-Expanded coverage of proteobacterial physiology
with content on Cl metabolism, including several figures
Chapter 24- Increased coverage of streptomycetes, with new
graphics illustrating their life cycle and their importance in anti
biotic production
Chapter 27-Updated discussion of virus taxonomy and phylog
eny, including increased coverage of archaeal viruses and the
CRISPR/CAS system
Part VI
Chapter 28-The description of each nutrient cycle is accom
panied by a new "student-friendly" figure that distinguishes
between reductive and oxidative reactions Expanded cover
age of the interaction between nutrient cycles is also newly
illustrated
Chapter 29-This chapter continues to emphasize culture-based
techniques as the "gold standard" and reviews some new, innova
tive approaches The chapter also discusses a variety of culture
independent techniques used to assess populations and
communities
Chapter 30-Updated and expanded discussion of freshwater
microbiology is complemented by discussion of carbon cycling in
the open ocean and its implications for global climate change
Chapter 31-New and updated coverage of mycorrhizae, with an
emphasis on host-microbe communication and evolutionary
similarities to rhizobia
Chapter 32-Microbial relationships are presented along with
human-microbe interactions, helping to convey the concept that
the human body is an ecosystem New and increased coverage of
the human microbiome
Part VII
Chapter 33-Reorganized and updated, this chapter on innate
host resistance provides in-depth coverage of physical and
chemical components of the nonspecific host response fol
lowed by an overview of cells, tissues, and organs of the im
mune system This includes a step-by-step discussion of how
microorganisms and damaged tissues are identified by the host
using pattern recognition to remove them Discussions of
phagocytosis and inflammation are updated and reflect mo
lecular mechanisms The groundwork is laid for a full apprecia
tion of the connections between the adaptive and innate arms
of the immune system
Chapter 34-Reorganized and updated to enhance linkages between innate and adaptive immune activities Discussions integrate cell biology, physiology, and genetics concepts to present the immune system as a unified response having various components Implications of dysfunctional immune actions are also discussed
Chapter 35-This chapter has been re-titled Pathogenicity and Infection, reflecting its emphasis on microbial strategies for survival that can lead to human disease The essential elements required for a pathogen to establish infection are introduced and virulence mechanisms highlighted It follows the immunology chapters to stress that the host-parasite relationship is dynamic, with adaptations and responses offered by both host and parasite
Part VIII Chapter 36-This chapter has been updated to reflect the workflow and practice of a modern clinical laboratory Emphasis is on modern diagnostic testing to identify infectious disease
Chapter 37-Expanded focus on the important role of laboratory safety, especially in the teaching laboratory Discussion emphasizes modern epidemiology as an investigative science and its role in preventative medicine Disease prevention strategies are highlighted
Chapter 38-Updated and expanded coverage includes viral pathogenesis and common viral infections
Chapter 39-Expanded coverage of bacterial organisms and their common methods leading to human disease
Chapter 40-Refocused to reflect disease transmission routes as well as expanded coverage of fungal and protozoal diseases
Part IX Chapter 41-Expanded discussion of probiotics in the context of the human microbiome
Chapter 42-This chapter has been reorganized to illustrate the importance of industrial microbiology by presenting common microbial products-including biofuels-first This is followed by
an updated discussion of strain development, including in vivo and in vitro directed evolution
Chapter 43-Updated discussion of water purification, wastewater treatment, and bioremediation This includes the development and use of microbial fuel cells
xi
Trang 13We would like to thank the Reviewers, who provided constructive reviews of every chapter Their specialized knowledge helped us assimilate more reliable sources of information and find more effective ways of expressing
an idea for the student reader
Reviewers
Tamarah Adair, Baylor University
Richard Adler, University of Michigan-Dearborn
Fernando Agudelo-Silva, College of Marin
Shivanthi Anandan, Drexel University
Penny Antley, University of Louisiana at Lafayette
Suzanne Barth, The University of Texas at Austin
Larry Barton, University of New Mexico
Nancy Boury, Iowa State University
Ginger Brininstool, Louisiana State University-Baton Rouge
Linda Bruslind, Oregon State University
Alison Buchan, University of Tennessee
Jim Buritt, University of Wisconsin-Stout
Martha Smith Caldas, Kansas State University
Joseph Caruso, Florida Atlantic University-Boca Raton
Andrei Chistoserdov, University of Louisiana at Lafayette
Carlton Cooper, University of Delaware
Susan Deines, Colorado State University
John Dennehy, Queens College
James Dickson, Iowa State University
Ronald Dubreuil, University of Illinois at Chicago
Paul Dunlap, University of Michigan-Ann Arbor
Mary Farone, Middle Tennessee State University
Babu Fathepure, Oklahoma State University-Stillwater
Kathy Feldman, University of Connecticut Storrs
Bernard Frye, University of Texas Arlington
Sandra Gibbons, University of Illinois at Chicago
Elizabeth Good, University of Illinois at Urbana-Champaign
Melanie Griffin, Kennesaw State University
Janet Haynes, Long Island University, Brooklyn
Michael Ibba, The Ohio State University
David Jenkins, Ihe University of Alabama Birmingham
Dennis Kitz, Southern Illinois University Edwardsville
James Koukl, Ihe University of Texas at Tyler
Shashi Kumar, Saint Mary Mercy Hospital
Jeffrey Leblond, Middle Tennessee State University
Richard Long, University of South Carolina
Jean Lu, Kennesaw State University
Mark McBride, University of Wisconsin-Milwaukee Vance McCracken, Southern Illinois University Edwardsville Donald Mcgarey, Kennesaw State University
Robert McLean, Texas State University Tamara Mcnealy, Clemson University Rita Moyes, Texas A&M University Karen Nakaoka, Weber State University Comer Patterson, Texas A&M University, College Station
Ed Perry, Faulkner State Community College Thomas Pistole, University of New Hampshire Ronald Porter, Penn State University-University Park Jackie Reynolds, Richland College
Margaret Richey, Centre College Veronica Riha, Madonna University Timberley Roane, University of Colorado Denver Jerry Sanders, University of Michigan-Flint Pratibha Saxena, The University of Texas at Austin Mark Schneegurt, Wichita State University Sasha A Showsh, University ofWisconsin-Eau Claire Khalifah Sidik, University of Illinois College of Medicine at Rockford Deborah Siegele, Texas A&M University
Jack Steiert, Missouri State University Raji Subramanian, NOVA Community College Annandale Karen Sullivan, Louisiana State University-Baton Rouge Cristina Takacs-Vesbach, University of New Mexico Monica Tischler, Benedictine University
Virginia Young, Mercer University Jianmin Zhong, Humboldt State University The authors wish to extend their gratitude to our editors, Kathy Lowenberg, Kathleen Timp, Angela FitzPatrick, Sandy Wille, and Lynn Breithaupt We would also like to thank our photo editor, Mary Reeg, and the tremendous talent and patience displayed by the artists We are also very grateful to the many reviewers who provided helpful criticism and analysis Finally,
we thank our spouses and children who provided support and tolerated our absences (mental, if not physical) while we completed this demanding project
Trang 14Contents
5.4 Organelles of the Secretory Preface iv
5.5 Organelles Involved in Genetic Control
0 The Evolution of Microorganisms 5.6 5.7 Organelles Involved in Energy Conservation External Structures 104 103
1.1 Members of the Microbial World 1 The r e Was an Old Woman Who Swa ll owed a F ly 1 06
1.2 Microbial Evolution 4 5.8 Comparison of Bacterial, Archaeal,
<!
G Microscopy 22 Viruses and Other Acellular Infectious Agents 6.1 Viruses 112 112
2.2 Light Microscopes 23 Microbial Diversity & Ecology 6.1
2.3 Preparation and Staining of Specimens 31 H os t -Independent G r ow t h of an Archaea l V ir us 114
0 Bacterial Cell Structure 42 6.5 6.6 Cultivation and Enumeration of Viruses Viroids and Satellites 127 129
3.2 A Typical Bacterial Cell 43
3.3 Bacterial Plasma Membranes 47
3.4 Bacterial Cell Walls 53 Part Two Microbial Nutrition, Growth, and Control
Microbial Diversity & Ecology 3.1
0 Microbial Growth
3.5 Cell Envelope Layers Outside the Cell Wall 61 7.2 Bacterial Cell Cycle 134 3.6 Bacterial Cytoplasm 62 Microbial Diversity & Ecology 7.1
3.8 Bacterial Motility and Chemotaxis 72 7.3 Influences of Environmental Factors
0 Archaeal Cell Structure 82 7.4 7.5 Microbial Growth in Natural Environments Laboratory Culture of Cellular Microbes 149 154
4.1 A Typical Archaeal Cell 82 7.6 Growth Curve: When One Becomes
4.3 Archaeal Cytoplasm 87 7.7 Measurement of Microbial Population Size 164 4.4 External Structures 88 7.8 Continuous Culture of Microorganisms 168 4.5 Comparison of Bacteria and Archaea 90
Trang 158.7 Biological Control of Microorganisms 186 11.10 Chemolithotrophy 253
10.2 ATP: The Major Energy Currency of Cells 213 Bacterial Genome Replication
Catabolism: Energy Release and Conservation 230 13.8 Protein Maturation and Secretion 319 11.1 Metabolic Diversity
~ 4
Trang 16Contents
~ 5 Eukaryotic and Archaeal Genome Replication 18.5 Proteomics 437
15 1 Why Cons i der Eukaryotic and Archaeal 18.7 Comparative Genomics 440
15.3 Transc ription 358 Part Five The Diversity of the Microbial World
15.4 Translation and Protein Maturation and
(, 9
~ 6 Mechanisms of Genetic Variation 372 19.1 19.2 Introduction to Microbial Taxonomy Taxonomic Ranks 449 448
16.4 Creating Additional Genetic Variability 383 of a Microbial Species 459
16.5 Transposable Elements 385 19.6 Bergey's Manual of Systematic Bacteriology 464
16.6 Bacterial Conjugation 387 Microbial Diversity & Ecology 19.1
16.7 Bacteria l Transformation 393 "Offic i al " Nomenclat u r e Lis ts - A Letter fro m Bergey's 465
17 1 Key Developments in Recombinant The Deinococci, Mollicutes, and
DNA Technology 405 Nonproteobacterial Gram-Negative Bacteria 489
17.2 Po lymer ase Chain Reaction 411 21.3 Class Mollicutes (Phylum Tenericutes) 491
17 6 Expressing Foreign Genes
18.1 Determining DNA Sequences 424 Microbial Diversity & Ecology 22.1
XV
Trang 170 Climate Change 632
~ 4 Actinobacteria: The High G + C 28.1 Biogeochemical Cycling 28.2 Global Climate Change 642 633
Gram-Positive Bacteria 555
6 5 The Protists 568 29.3 Assessing Microbial Community Activity 655
(i o
~ Microorganisms in Terrestrial Ecosystems 679
c; 6
0
Disease 26.1 Wolbachia pipienris: The Wor l d's Most
I nfect i ous M i crobe? 70 1
Wh it - Nose Synd r o m e I s Dec i mating
North Ameri c an Bat Popu l at i ons 599 32.2 Human - Microbe Interactions 713
D o Bacte ria Make Peop l e F at? 714
c; 7 Viruses
604
Microbial Diversity & Ecology 27.1
~ 3 Innate Host Resistance
27.9 Reverse Transcribing DNA Viruses
628
Trang 18Contents
37.4 Patterns of Infectious Disease
34.1 Overv ie w of Adapt i ve Immunity 753
34 6 B-Cell Biology 764 37.6 Health - Care-Associated Infections 841 34.7 Ant i bodies 767 37.7 Prevention and Control of Epidemics 843
34 9 Acquired Immune Tolerance 778 Historical Highlights 37.6
34 10 Immune Disorders 779 13 46 - T he F ir t R eco rd ed B io l o i ca l
~ 8
35.1 Pathogenicity and Infectious Disease 790 Human Diseases Caused by Viruses
35.3 Exposure a nd Transmission 802 38.1 Airborne Dise a ses 855
T he F ir s t I n i cations of P e r son - o - Pe r son 38.3 Direct Contact Diseases 865
Sp r e d o an I n f ec ti u s D is e as e 803
38.4 Food-Borne and Waterborne D i seases 878
Historical Highlights 38.1
A B r i ef H i s t o r y o f Po l o 88 1
Part Eight Microbial Diseases, Detection, 38.5 Zoonotic Diseases 881
~ 6 Clinical Microbiology and Immunology 808 Viral H i sto H r y Less e m o rr o h n g i c F eve r s A Mic r o i a 882
36.1 Overv i ew of the Clinical Microbiology 38.6 Prion Diseases 885
36.2 Biosafe t y 809 ~ 9 Human Diseases Caused by Bacteria 888
36.3 I dentification of Microorganisms
39 2 Ar t hropod - Borne Diseases 898 36.4 Clinical Immunology 820
39.3 Direct Contact Diseases 901
f 7 Epidemiology and Public Health Microbiology 830 Disease 39. 1
37.1 Epidemiology 830 A B r i e H i s t o r y o f S y h i s 909
Jo h n Snow, th e F i r st Epi d m io l o gi s 832 C l os t ri di a Tox i n s as T h r a eu t i c A ge nt s
37.2 Epidemiolog i cal Methods 832 B ene fi ts o f Na tur e's Mos t T ox i c Pr o t ei n s 9 9
SA R : E volu t i o n of a V iru s 833 39 6 Opportunistic Diseases 926
xvii
Trang 1940.3 Arthropod-Borne Diseases 937 42.3 Growing Microbes in Industrial Settings 983
A Br i e Histo r y of Ma l a a 938 Industrial Microbiology 985 40.4 Direct Contact D i seases 944 42.5 Agricultural Biotechnology 990
Waterborne Diseases 948
~ 3
40.6 Opportunistic Diseases 952 Applied Environmental Microbiology 996
43.1 Water Purification and Sanitary Analysis 996
Techniques & Applications 43.1 Part Nine Applied Microbiology Wa t e r borne Diseases, Water S u pp l es,
~ 1 Microbiology of Food 958 43.2 Wastewater and Slow Sand Treatment Fi l t at i on 1001 999
41.1 Microbial Growth and Food Spoilage 959 43.3 Microbial Fuel Cells 1008 41.2 Controlling Food Spoilage 961 43.4 Biodegradation and Bioremediation 1009 41.3 Food-Borne Disease Outbreaks 964
41.4 Detection of Food - Borne Pathogens 967 Appendi x 1 A Review of the Chemistry
41.5 Microbiology of Fermented Foods 969 of Biological Molecules A-1
Choco l a t e T he Sweet Si d e of F ermen t a t i on 970
Glossary G - 1
Credits C - 1 Index 1-1
Trang 20About the Authors iii
Preface iv
Part One Introduction to Microbiology
1 The Evolution of Microorganisms and Microbiology
2 Microscopy 22
3 Bacterial Cell Structure 42
4 Archaeal Cell Structure 82
5 Eukaryotic Cell Structure 92
6 Viruses and Other Acellular Infectious Agents 112
Part Two Microbial Nutrition, Growth, and Control
11 Catabolism: Energy Release and Conservation 230
12 Anabolism: The Use of Energy in Biosynthesis 266
Part Four Microbial Molecular Biology and Genetics
13 Bacterial Genome Replication and Expression 287
14 Regulation of Bacterial Cellular Processes 325
15 Eukaryotic and Archaeal Genome Replication
and Expression 353
16 Mechanisms of Genetic Variation 372
17 Recombinant DNA Technology 404
18 Microbial Genomics 424
Part Five The Diversity of the Microbial World
19 Microbial Taxonomy and the Evolution of Diversity 447
Part Six Ecology and Symbiosis
28 Biogeochemical Cycling and Global Climate Change 632
29 Methods in Microbial Ecology 646
Ecosystems 660
31 Microorganisms in Terrestrial Ecosystems 679
32 Microbiallnteractions 699
Part Seven Pathogenicity and Host Response
33 Innate Host Resistance 723
34 Adaptive Immunity 753
35 Pathogenicity and Infection 789
Control
36 Clinical Microbiology and Immunology 808
37 Epidemiology and Public Health Microbiology
38 Human Diseases Caused by Viruses and Prions
39 Human Diseases Caused by Bacteria 888
Part Nine Applied Microbiology
41 Microbiology of Food 958
830
854
932
42 Biotechnology and Industrial Microbiology 979
43 Applied Environmental Microbiology 996
of Biolog i cal Mo l ecules A - 1
Glossary G - 1
Credits C - 1 Index 1-1
Trang 221
The Evolution
of Microorganisms
and Microbiology
In February 2012, the National Aeronautics and Space Administration (NASA) reported that over 2,000 potential planets had been discovered
by the 2009 Kepler mission Using a telescope in space, the light
emanating from stars as far as 3,000 light-years away had been
monitored every half-hour The Kepler telescope identified planets as
they circulated their star and caused a brief decrease in emitted light; just
as an object is detected as a blip by radar, a blip of "darkness" indicates a
planet
Unless you are a science fiction fan, you might wonder why NASA is
interested in finding planets By finding other planets, scientists can
gather evidence to support or refute current models of planet formation
These models predict a process that is chaotic and violent Planets are
thought to begin as dust particles circling around newly formed stars As
these particles collide, they grow in size, forming larger chunks Eventually
a series of such collisions results in planet-sized bodies Astrobiologists are
interested in identifying characteristics of a planet that may allow it to
support life Using Earth as a model, they hypothesize that life-supporting
planets will share many features with Earth But how will life be recog
nized? Again, scientists look to life on Earth to answer this question, and
increasingly they are turning to microbiologists for help
Earth formed 4.5 billion years ago Within the next billion years, the
first cellular life forms-microbes-appeared Since that time, microorgan
isms have evolved and diversified to occupy virtually every habitat on Earth:
from oceanic geothermal vents to the coldest Arctic ice The diversity of
cellular microorganisms is best exemplified by their metabolic capabilities
Some carry out respiration, just as animals do Others perform photosynthe
sis, rivaling plants in the amount of carbon dioxide they capture, forming
organic matter and releasing oxygen into the atmosphere Indeed,
Prochlorococcus, a cyanobacterium (formerly called a blue-green alga), is
thought to be the most abundant photosynthetic organism on Earth and
Artist's rendition of the six planets orbiting a star called Kepler-11 The drawing is based on observations made of the system by the Kepler spacecraft on August 26,2010 Some are Earth-sized and
may be habitable by life
thus a major contributor to the functioning of the biosphere In addition to these familiar types of metabolism, other microbes are able to use inorganic molecules as sources of energy in both oxic (oxygen available) and anoxic (no oxygen) conditions It is these microbes that are of particular interest to NASA scientists, as it is thought that the organisms on other planets may have similar unusual metabolisms
Our goal in this chapter is to introduce you to this amazing group of organisms and to outline the history of their evolution and discovery Microbiology is a biological science, and as such, much of what you will learn
in this text is similar to what you have learned in high school and college biology classes that focus on large organisms But microbes have unique properties, so microbiology has unique approaches to understanding them These too will be introduced But before you delve into this chapter, check to see if you have the background needed to get the most from it
Readiness Check:
Based on what you have learned previously, you should be able to:
tl List the features of eukaryotic cells that distinguish them from other cell types
tl List the attributes that scientists use to determine if an object is alive
1.1 Members of the Microbial World
After reading this section, you should be able to:
• Differentiate the biological entities studied by microbiologists from those studied by other biologists
• Explain Carl Woese's contributions in establishing the three domain system for classifying cellular life
• Provide an example of the importance to humans of each of the major types of microbes
• Determine the type of microbe (e.g., bacterium, fungus, etc.) when given a description of a newly discovered microbe
Trang 23Organisms and biological entities studied by microbiologists
includes
Yeasts Algae Escherichia
Figure 1.1 Concept Map Showing the Types of Biological Entities Studied by Microbiologists
M 1 C RO IN Q u 1 RY How would you alter this concept map so that it also distinguishes the cellular organisms from each other?
Microorganisms are defined as those organisms and acellular
biological entities too small to be seen clearly by the unaided
eye ( figure 1.1 ) They are generally 1 millimeter or less in diam
eter Although small size is an important characteristic of mi
crobes, it alone is not sufficient to define them Some cellular
microbes, such as bread molds and filamentous photosynthetic
microbes, are actually visible without microscopes These mac
roscopic microbes are often colonial, consisting of small aggre
gations of cells Some macroscopic microorganisms are
multicellular They are distinguished from other multicellular
life forms such as plants and animals by their lack of highly dif
ferentiated tissues Most unicellular microbes are microscopic
However, there are interesting exceptions, as we describe in
chapter 3 In summary, cellular microbes are usually smaller
than 1 millimeter in diameter, often unicellular and, if multi
cellular, lack differentiated tissues
The diversity of microorganisms has always presented a
challenge to microbial taxonomists The early descriptions of
cellular microbes as either plants or animals were too simple
For instance, some microbes are motile like animals but also
have cell walls and are photosynthetic like plants Such mi
crobes cannot be placed easily into either kingdom An im
portant breakthrough in microbial taxonomy arose from
studies of their cellular architecture, when it was discovered
that cells exhibited one of two possible "floor plans." Cells that
came to be called prokaryotic cells (Greek pro, before, and
karyon, nut or kernel; organisms with a primordial nucleus)
have an open floor plan That is, their contents are not divided
into compartments ("rooms") by membranes ("walls") The most obvious characteristic of these cells is that they lack the membrane-delimited nucleus observed in eukaryotic cells
(Greek eu, true, and karyon, nut or kernel) Eukaryotic cells not only have a nucleus but also many other membrane-bound organelles that separate some cellular materials and processes from others
These observations eventually led to the development of a classification scheme that divided organisms into five kingdoms: Monera, Protista, Fungi, Animalia, and Plantae Microorganisms (except for viruses and other acellular infectious agents, which have their own classification system) were placed in the first three kingdoms In this scheme, all organisms with prokaryotic cell structure were placed in Monera The five-kingdom system was an important development in microbial taxonomy, but it is no longer accepted by microbiologists This is because not all "prokaryotes" are the same and therefore should not be grouped together in a single kingdom Furthermore, it is currently argued that the term prokaryote is not meaningful and should be abandoned As we describe next, this discovery required several advances in the tools used to study microbes �I The ''prokaryote" controversy (section 3.1)
Great progress has been made in three areas that profoundly affect microbial classification First, much has been learned about the detailed structure of microbial cells from the use of electron microscopy Second, microbiologists have determined the biochemical and physiological characteristics of many different microorganisms Third, the sequences of nucleic acids and
Trang 24proteins from a wide variety of organisms have been compared
The comparison of ribosomal RNA (rRNA), begun by Carl
Woese in the 1970s, was instrumental in demonstrating that
there are two very different groups of organisms with prokary
otic cell architecture: Bacteria and Archaea Later studies based
on rRNA comparisons showed that Protista is not a cohesive
taxonomic unit (i.e., taxon) and that it should be divided into
three or more kingdoms These studies and others have led many
taxonomists to reject the five-kingdom system in favor of one
that divides cellular organisms into three domains: Bacteria
(sometimes referred to as true bacteria or eubacteria), Archaea
(sometimes called archaeobacteria or archaebacteria), and
Eukarya (all eukaryotic organisms) ( figure 1.2 ) We use this
system throughout the text A brief description of the three
domains and of the microorganisms placed in them follows
�I Nucleic acids (appendix I); Proteins (appendix I)
Members of domain Bacteria are usually single-celled or
ganisms.1 Most have cell walls that contain the structural mol
ecule peptidoglycan Although most bacteria exhibit typical
prokaryotic cell structure (i.e., they lack a membrane-bound
nucleus), a few members of the unusual phylum Planctomycetes
have their genetic material surrounded by a membrane This
inconsistency is another argument made for abandoning the
term "prokaryote." Bacteria are abundant in soil, water, and
air, including sites that have extreme temperatures, pH, or sa
linity Bacteria are also major inhabitants of our skin, mouth,
and intestines Indeed, more microbial cells are found in and
on the human body than there are human cells These microbes
begin to colonize humans shortly after birth As the microbes
establish themselves, they contribute to the development of the
body's immune system Those microbes that inhabit the large
intestine help the body digest food and produce vitamins In
these and other ways, microbes help maintain the health and
well-being of their human hosts �I Phylum Planctomycetes
(section 21.5)
Unfortunately, some bacteria cause disease, and some of
these diseases have had a huge impact on human history In 1347
the plague (Black Death), an arthropod-borne disease, struck
Europe with brutal force, killing one-third of the population
(about 25 million people) within four years Over the next
80 years, the disease struck repeatedly, eventually wiping out
75% of the European population The plague's effect was so
great that some historians believe it changed European culture
and prepared the way for the Renaissance Because of such
plagues, it is easy for people to think that all bacteria are patho
gens, but in fact, relatively few are Most play beneficial roles,
from global impact to maintaining human health They break
down dead plant and animal material and, in doing so, cycle
elements in the biosphere Furthermore, they are used exten
sively in industry to make bread, cheese, antibiotics, vitamins,
enzymes, and other products
1.1 Members of the Microbial World 3
1 1 rRNA sequence change
� Unresolved branching order
Figure 1.2 Universal Phylogenetic Tree These evolutionary relationships are based on rRNA sequence comparisons To save space, many lineages have not been identified
MICRO 1 N Q u 1 RY How many of the taxa listed in the figure include microbes?
Members of domain Archaea are distinguished from bacteria by many features, most notably their distinctive rRNA sequences, lack of peptidoglycan in their cell walls, and unique membrane lipids Some have unusual metabolic characteristics, such as the methanogens, which generate methane (natural) gas Many archaea are found in extreme environments, including those with high temperatures (thermophiles) and high concentrations of salt (extreme halophiles) Although some archaea are members of a community of microbes involved in gum disease
in humans, their role in causing disease has not been clearly established
Domain Eukarya includes microorganisms classified as protists or fungi Animals and plants are also placed in this domain Protists are generally unicellular but larger than most bacteria and archaea They have traditionally been divided into protozoa and algae Despite their use, none of these terms has taxonomic value as protists, algae, and protozoa do
1 In this text, the term bacteria (s., bacterium) is used to refer to those microbes belonging to domain Bacteria, and the term archaea (s., archaean) is used to refer to those that belong to domain Archaea
In some publications, the term bacteria is used to refer to all cells having prokaryotic cell structure That is not the case in this text
Trang 25not form cohesive taxa However, for convenience, we use
them here
The major types of protists are algae, protozoa, slime molds,
and water molds Algae are photosynthetic They, together with
cyanobacteria, produce about 75% of the planet's oxygen and are
the foundation of aquatic food chains Protozoa are unicellular,
animal-like protists that are usually motile Many free-living
protozoa function as the principal hunters and grazers of the
microbial world They obtain nutrients by ingesting organic
matter and other microbes They can be found in many different
environments, and some are normal inhabitants of the intestinal
tracts of animals, where they aid in digestion of complex materi
als such as cellulose A few cause disease in humans and other
animals Slime molds are protists that behave like protozoa in
one stage of their life cycle but like fungi in another In the pro
tozoan phase, they hunt for and engulf food particles, consum
ing decaying vegetation and other microbes Water molds are
protists that grow on the surface of freshwater and moist soil
They feed on decaying vegetation such as logs and mulch Some
water molds have produced devastating plant infections, includ
ing the Great Potato Famine of 1846-1847 in Ireland I The
protists (chapter 25)
Fungi are a diverse group of microorganisms that range
from unicellular forms (yeasts) to molds and mushrooms Molds
and mushrooms are multicellular fungi that form thin, thread
like structures called hyphae They absorb nutrients from their
environment, including the organic molecules they use as
sources of carbon and energy Because of their metabolic capa
bilities, many fungi play beneficial roles, including making
bread rise, producing antibiotics, and decomposing dead organ
isms Some fungi associate with plant roots to form mycorrhi
zae Mycorrhizal fungi transfer nutrients to the roots, improving
growth of the plants, especially in poor soils Other fungi
cause plant diseases (e.g., rusts, powdery mildews, and smuts)
and diseases in humans and other animals I The Fungi
(chapter 26)
The microbial world also includes numerous acellular infec
tious agents Viruses are acellular entities that must invade a
host cell to multiply The simplest viruses are composed only of
proteins and a nucleic acid, and can be extremely small (the
smallest is 10,000 times smaller than a typical bacterium) How
ever, their small size belies their power: they cause many animal
and plant diseases and have caused epidemics that have shaped
human history Viral diseases include smallpox, rabies, influ
enza, AIDS, the common cold, and some cancers Viruses also
play important roles in aquatic environments, and their role in
shaping aquatic microbial communities is currently being ex
plored Viroids and satellites are infectious agents composed
only of ribonucleic acid (RNA) Viroids cause numerous plant
diseases, whereas satellites cause plant diseases and some im
portant animal diseases such as hepatitis Finally, prions, infec
tious agents composed only of protein, are responsible for
causing a variety of spongiform encephalopathies such as scra
pie and "mad cow disease." I Viruses and other acellular in
fectious agents (chapter 6)
Retrieve, Infer, Apply
1 How did the methods used to classify microbes change, particularly
in the last half of the twentieth century? What was the result of these technological advances?
2 Identify one characteristic for each of these types of microbes that distinguishes it from the other types: bacteria, archaea, protists, fungi, viruses, viroids, satellites, and prions
1.2 Microbial Evolution
After reading this section, you should be able to:
• Propose a time line of the origin and history of microbial life and integrate supporting evidence into it
• Design a set of experiments that could be used to place a newly discovered cellular microbe on a phylogenetic tree based on small subunit (SSU) rRNA sequences
• Compare and contrast the definitions of plant and animal species, microbial species, and microbial strains
A review of figure 1.2 reminds us that in terms of the number of taxa, microbes are the dominant organisms on Earth How has microbial life been able to radiate to such an astonishing level of diversity? To answer this question, we must consider microbial evolution The field of microbial evolution, like any other scientific endeavor, is based on the formulation of hypotheses, the gathering and analysis of data, and the reformation of hypotheses based on newly acquired evidence That is to say, the study of microbial evolution is based on the scientific method (see www
.mhhe.com/willey9) To be sure, it is sometimes more difficult to amass evidence when considering events that occurred millions, and often billions, of years ago, but the advent of molecular methods has offered scientists a living record of life's ancient history This section describes the outcome of this scientific research
Evidence for the Origin of Life Dating meteorites through the use of radioisotopes places our planet at an estimated 4.5 to 4.6 billion years old However, conditions on Earth for the first 100 million years or so were far too harsh to sustain any type of life Eventually bombardment by meteorites decreased, water appeared on the planet in liquid form, and gases were released by geological activity to form Earth's atmosphere These conditions were amenable to the origin of the first life forms But how did this occur, and what did these life forms look like?
Clearly, in order to find evidence of life and to develop hypotheses about its origin and subsequent evolution, scientists must be able to define life Although even very young children can examine an object and correctly determine whether it is living or not, defining life succinctly has proven elusive for scientists Thus most definitions of life consist of a set of attributes The attributes of particular importance to paleobiologists are an orderly structure, the ability to obtain
Trang 26and use energy (i.e., metabolism), and the ability to reproduce
Just as NASA scientists are using the characteristics of mi
crobes on Earth today to search for life elsewhere (p 1), so too
are scientists examining extant organisms, those organisms
present today, to explore the origin of life Some extant organ
isms have structures and molecules that represent "relics" of
ancient life forms Furthermore, they can provide scientists
with ideas about the type of evidence to seek when testing
hypotheses
The first direct evidence of primitive cellular life was the
1977 discovery of microbial fossils in the Swartkoppie chert
Chert is a type of granular sedimentary rock rich in silica The
Swartkoppie chert fossils as well as those from the Archaean
Apex chert of Australia have been dated at about 3.5 billion
years old (figures 1.3 and 1.4) Despite these findings, the mi
crobial fossil record is understandably sparse Thus to piece to
gether the very early events that led to the origin of life, biologists
must rely primarily on indirect evidence Each piece of evidence
must fit together as in a jigsaw puzzle for a coherent picture to
emerge
RNA World
The origin of life rests on a single question: How did early cells
arise? At a minimum, modern cells consist of a plasma membrane
enclosing water in which numer
ous chemicals are dissolved and subcellular structures float It seems likely that the first self-replicating entity was much sim
pler than even the most primitive modern living cells Before there was life, most evidence suggests that Earth was a very different place: hot and anoxic, with an atmosphere rich in water vapor, carbon di-oxide, and nitrogen In the oceans, hydrogen, methane, and carboxylic acids were formed by geological and chemical processes Areas near hydrothermal vents or
in shallow pools may have provided the conditions that allowed chemicals to react with one another, randomly
"testing" the usefulness of the reaction and the stability
of its products Some tions released energy and would eventually become the basis of modern cellular
reac-Figure 1.3 Microfossils of the Archaeon Apex Chert of Australia
These microfossils are similar to modern filamentous cyanobacteria
1.2 Microbial Evolution 5
metabolism Other reactions generated molecules that could function as catalysts, some aggregated with other molecules to form the predecessors of modern cell structures, and others were able to replicate and act as units of hereditary information
In modern cells, three different molecules fulfill the roles of catalysts, structural molecules, and hereditary molecules (figure 1.5 ) Proteins have two major roles in modern cells: structural and catalytic Catalytic proteins are called enzymes, and they speed up the myriad of chemical reactions that occur
in cells DNA stores hereditary information and can be replicated to pass the information on to the next generation RNA is involved in converting the information stored in DNA into protein Any hypothesis about the origin of life must account for the evolution of these molecules, but the very nature of their relationships to each other in modern cells complicates attempts to imagine how they evolved As demonstrated in figure 1.5, proteins can do cellular work, but their synthesis involves other proteins and RNA, and uses information stored in DNA DNA can't do cellular work It stores genetic information and serves as the template for its own replication, a process that requires proteins RNA is synthesized using DNA as the template and proteins as the catalysts for the reaction
Based on these considerations, it is hypothesized that at some time in the evolution of life, there must have been a single molecule that could do both cellular work and replicate itself
A possible molecule was suggested in 1981 when Thomas Cech discovered a catalytic RNA molecule in a protist (Tetrahymena sp.) that could cut out an internal section of itself and splice the remaining sections back together Since then, other catalytic RNA molecules have been discovered, including an RNA found in ribosomes that is responsible for forming peptide bondsthe bonds that hold together amino acids, the building blocks of proteins Catalytic RNA molecules are now called ribozymes The discovery of ribozymes suggested that RNA at some time had the ability to catalyze its own replication, using itself
as the template In 1986 Walter Gilbert coined the term RNA world to describe a precellular stage in the evolution of life in which RNA was capable of storing, copying, and expressing genetic information, as well as catalyzing other chemical reactions However, for this precellular stage to proceed to the evolution of cellular life forms, a lipid membrane must have formed around the RNA (figure 1.6) This important evolutionary step
is easier to imagine than other events in the origin of cellular life forms because lipids, major structural components of the membranes of modern organisms, spontaneously form liposomes-vesicles bounded by a lipid bilayer A fascinating experiment performed by Marin Hanczyc, Shelly Fujikawa, and Jack Szostak in 2003 showed that clay triggers the formation of liposomes that actually grow and divide Together with the data on ribozymes, these data suggest that early cells may have been liposomes containing RNA molecules (figure 1.6)
�I Lipids (appendix I) Apart from its ability to perform catalytic activities, the function of RNA suggests its ancient origin Consider that much of the cellular pool of RNA in modern cells exists in the
Trang 27= Cambrian
+ 7 mya-Hominids first appear
+225 mya-Dinosaurs and mammals first appear
+300 mya-Reptiles first appear
+450 mya-Large terrestrial colonization by plants and animals
�1520 mya-First vertebrates; first land plants
533-525 mya Cambrian explosion creates diverse animal life
+1.5 bya -Multicellular eukaryotic organisms first appear
I
+2.5-2.0 bya-Eukaryotic cells first appear
I
+ 3.5 bya-Fossils of primitive filamentous microbes
+ 3.8-3.5 bya-First cells appear
Trang 28Serves as template for synthesis of new
Encodes sequence of nucleotides in
DNA
RNA
Catalyzes synthesis of
Regulates
expression of
Functions in Catalyzes synthesis of synthesis of
Forms
Encodes sequence of amino acids in
Protein
Catalyzes
Relationships to Each Other in Modern Cells
Involved in synthesis
of more
ribosome, a structure that consists largely of rRNA and uses
messenger RNA (mRNA) and transfer RNA (tRNA) to construct
proteins Also recall that rRNA itself catalyzes peptide bond for
mation during protein synthesis Thus RNA seems to be well
poised for its importance in the development of proteins Be
cause RNA and DNA are structurally similar, RNA could have
given rise to double-stranded DNA It is suggested that once
DNA evolved, it became the storage facility for genetic informa
tion because it provided a more chemically stable structure Two
other pieces of evidence support the RNA world hypothesis: the
fact that the energy currency of the cell, ATP, is a ribonucleotide
and the more recent discovery that RNA can regulate gene ex
pression So it would seem that proteins, DNA, and cellular en
ergy can be traced back to RNA �I ATP (section 10.2);
Riboswitches (sections 14.3 and 14.4)
Despite the evidence supporting the hypothesis of an RNA
world, it is not without problems, and many argue against it
Another area of research is also fraught with considerable
Probiont: RNA only
Probiont: RNA and proteins
Cellular life: RNA, DNA, and proteins
Trang 29(a) (b)
Figure 1.7 Stromatolites (a) Section of a fossilized stromatolite Evolutionary biologists think the layers of material were formed when mats of cyanobacteria, layered one on top of each other, became mineralized (b) Modern stromatolites from Western Australia Each stromatolite is a rocklike structure, typically 1 m in diameter, containing layers of cyanobacteria
as does the discovery of ancient stromatolites ( figure 1.7a ) Stro
matolites are layered rocks, often domed, that are formed by the
incorporation of mineral sediments into layers of microorganisms
growing as thick mats on surfaces (figure 1.7b) The appearance of
cyanobacteria-like cells was an important step in the evolution of
life on Earth The oxygen they released is thought to have altered
Earth's atmosphere to its current oxygen-rich state, allowing the
evolution of additional energy-capturing strategies such as aerobic
respiration, the oxygen-consuming metabolic process that is used
by many microbes and animals
Evolution ofthe Three Domains of Life
As noted in section 1.1, rRNA comparisons were an important
breakthrough in the classification of microbes; this analysis also
provides insights into the evolutionary history of all life What
began with the examination of rRNA from relatively few organisms
has been expanded by the work of many others, including Nor
man Pace Dr Pace has developed a universal phylogenetic tree
(figure 1.2) based on comparisons of small subunit rRNA mole
cules (SSU rRNA), the rRNA found in the small subunit
of the ribosome Here we examine how these comparisons
are made and what the universal phylogenetic tree tells us
onomy and phylogeny (section 19.3)
Comparing SSU rRNA Molecules
The details of phylogenetic tree construction are discussed in
chapter 19 However, the general concept is not difficult to under
stand In one approach, the sequences of nucleotides in the genes
that encode SSU rRNAs from diverse organisms are aligned, and
pair-wise comparisons of the sequences are made For each pair
of SSU rRNA gene sequences, the number of differences in the
nucleotide sequences is counted ( figure 1.8 ) This value serves as
a measure of the evolutionary distance between the organisms;
the more differences counted, the greater the evolutionary
dis-tance The evolutionary distances from many comparisons are used by sophisticated computer programs to construct the tree Each branch in the tree represents one of the organisms used in the comparison The distance from the tip of one branch to the tip
of another is the evolutionary distance between the two organisms represented by the branches
Two things should be kept in mind when examining phylogenetic trees developed in this way The first is that they are molecular trees, not organismal trees In other words, they represent, as accurately as possible, the evolutionary history of a molecule and the gene that encodes it Second, the distance between branch tips is a measure of relatedness, not of time If the distance along the lines is very long, then the two organisms are more evolutionarily diverged (i.e., less related) However, we do not know when they diverged from each other This concept is analogous to a map that accurately shows the distance between two cities but because of many factors (traffic, road conditions, etc.) cannot show the time needed to travel that distance
LUCA
What does the universal phylogenetic tree tell us about the evolution of life? At the center of the tree is a line labeled "Origin" (figure 1.2) This is where the data indicate the last universal common ancestor (LUCA) to all three domains should be placed LUCA is on the bacterial branch, which means that Archaea and
Eukarya evolved independently, separate from Bacteria Thus the universal phylogenetic tree presents a picture in which all life, regardless of eventual domain, arose from a single common ancestor One can envision the universal tree of life as a real tree that grows from a single seed
The evolutionary relationship of Archaea and Eukarya is still the matter of considerable debate According to the universal phylogenetic tree we show here, Archae a and Eukarya shared common ancestry but diverged and became separate domains Other versions suggest that Eukarya evolved out of Archaea The
Trang 30Cells from organism 1
Lyse cells to release contents and isolate DNA
I Use polymerase chain reaction to amplify
• and purify SSU rRNA genes
� SSU rRNA genes
+ Sequence genes
ATGCTCAAGTCA
+ Repeat process for other organisms
+ Align sequences to be compared
Organism SSU rRNA sequence
ATGCTCAAGTCA TAGCTCG TGTAA AAGCTCTAGTTA AACCTCATGTTA
1
-3
4
! Count the number of nucleotide differences between
each pair of sequences and calculate evolutionary
distance (E0)
For organisms 1 and 2, 5 of the 12
�, ,;,.; �.;,;, � nucleotides are different:
0.33 0.44
0.25 0.30
E0 = 5/12 = 0.42 The initial ED calculated is corrected using a statistical method that considers for each site the probability
of a mutation back to the original nucleotide or of additional forward mutations
I Feed data into computer and use appropriate software
T to construct phylogenetic tree
3
Unrooted phylogenetic tree Note that distance f rom one tip to another is proportional to the E0
Figure 1.8 The Construction of Phylogenetic Trees
Using a Distance Method
MICRO INQuIRY Why does the branch length indicate amount of
evolutionary change but not the time it took for that change to occur?
1.2 Microbial Evolution 9
close evolutionary relationship of these two forms of life is still evident in the manner in which they process genetic information For instance, certain protein subunits of archaeal and eukaryotic RNA polymerases, the enzymes that catalyze RNA synthesis, resemble each other to the exclusion of those of bacteria However, archaea have other features that are most similar
to their counterparts in bacteria (e.g., mechanisms for conserving energy) This has further complicated and fueled the debate The evolution of the nucleus and endoplasmic reticulum is also
at the center of many controversies However, hypotheses regarding the evolution of other membrane-bound organelles are more widely accepted and are considered next
Endosymbiotic Origin of Mitochondria, Chloroplasts, and Hydrogenosomes
The endosymbiotic hypothesis is generally accepted as the origin of three eukaryotic organelles: mitochondria, chloroplasts, and hydrogenosomes Endosymbiosis is an interaction between two organisms in which one organism lives inside the other The initial statement of the endosymbiotic hypothesis proposed that over time a bacterial endosymbiont of an ancestral cell in the eukaryotic lineage lost its ability to live independently, becoming either a mitochondrion, if the intracellular bacterium used aerobic respiration, or a chloroplast, if the endosymbiont was a photosynthetic bacterium (see figure 19.11) Although the mechanism by which the endosymbiotic relationship was established is unknown, there is considerable evidence to support the hypothesis Mitochondria and chloroplasts contain DNA and ribosomes; both are similar to bacterial DNA and ribosomes Indeed, inspection of figure 1.2 shows that both organelles belong to the bacterial lineage based on SSU rRNA analysis Further evidence for the origin of mitochondria comes from the genome sequence of the
bacterium Rickettsia prowazekii, an obligate intracellular parasite and the cause of epidemic (lice-borne) typhus Its genome is more similar to that of modern mitochondrial genomes than to any other bacterium The chloro
plasts of plants and green algae are thought to have descended from an ancestor of the cyanobacterial genus Prochloron, which con
tains species that live within marine invertebrates
Recently the endosymbiotic hypothesis for mitochondria has been modified by the hydrogen hypothesis This asserts that the endosymbiont was an anaerobic bacterium that produced H2 and C02 as end products of its metabolism Over time, the host became dependent on the H2 produced by the endosymbiont Ultimately the endosymbiont evolved into one of two organelles
If the endosymbiont developed the capacity to perform aerobic respiration, it evolved into a mitochondrion However, if the endosymbiont did not develop this capacity, it evolved into a hydrogenosome-an organelle found in some extant protists that produce ATP by a process called fermentation (see figure 5.16)
Trang 31Evolution of Cellular Microbes
Although the history of early cellular life forms may never be
known, we know that once they arose, they were subjected to the
same evolutionary processes as modern organisms The ances
tral bacteria, archaea, and eukaryotes possessed genetic infor
mation that could be duplicated, lost, or mutated These
mutations could have many outcomes Some led to the death of
the mutant microbe, but others allowed new functions and char
acteristics to evolve Those mutations that allowed the organism
to increase its reproductive ability were selected for and passed
on to subsequent generations In addition to selective forces, iso
lation of populations allowed some groups to evolve separately
from others Thus selection and isolation led to the eventual de
velopment of new collections of genes (i.e., genotypes) and many
new species
In addition to mutation, other mechanisms exist for re
configuring the genotypes of a species and therefore creating
genetic diversity Most eukaryotic species increase their ge
netic diversity by reproducing sexually Thus each offspring
of the two parents has a mixture of parental genes and a
unique genotype Bacterial and archaeal species do not repro
duce sexually They increase their genetic diversity by hori
zontal (lateral) gene transfer (HGT) During HGT, genetic
information from a donor organism is transferred to a recipi
ent, creating a new genotype Thus genetic information can
be passed from one generation to the next as well as between
individuals of the same generation and even between differ
ent microbial species Genome sequencing has revealed that
HGT has played an important role in the evolution of bacte
rial and archaeal species Importantly, HGT still occurs and
continues to shape their genomes, leading to the evolution of
species with antibiotic resistance, new virulence properties,
and novel metabolic capabilities The outcome of HGT is
that many bacterial and archaeal species have mosaic ge
nomes composed of bits and pieces of the genomes of other
organisms ( figure 1.9 ) �I Microbial evolutionary processes
(section 19.5)
Microbial Species
All students of biology are introduced early in their careers to
the concept of a species But the term has different meanings,
depending on whether the organism is sexual or not Taxono
mists working with plants and animals define a species as a
group of interbreeding or potentially interbreeding natural
populations that is reproductively isolated from other groups
This definition also is appropriate for the many eukaryotic
microbes that reproduce sexually However, bacterial and
archaeal species cannot be defined by this criterion, since
they do not reproduce sexually An appropriate definition is
currently the topic of considerable discussion A common
definition is that bacterial and archaeal species are a collec
tion of strains that share many stable properties and differ
Y Horizontal gene transfer events
Figure 1.9 The Mosaic Nature of Bacterial and Archaeal Genomes Horizontal gene transfer (HGT) events move pieces of the genome of one organism to another Over time, HGT creates organisms having mosaic genomes composed of portions of the genomes of other microbes The length of segments drawn is arbitrary and is not meant to represent the actual size of the portion of genome transferred
significantly from other groups of strains A strain consists
of the descendants of a single, pure microbial culture Strains within a species may be described in a number of different ways Biovars are variant strains characterized by biochemical
or physiological differences, morphovars differ morphologically, serovars have distinctive properties that can be detected
by antibodies (p 17), and pathovars are pathogenic strains distinguished by the plants in which they cause disease �I Evolutionary processes and the concept of a microbial species (section 19.5)
Microbiologists name microbes using the binomial system
of the eighteenth-century biologist and physician Carl Linnaeus The Latinized, italicized name consists of two parts The first part, which is capitalized, is the generic name (i.e., the name of the genus to which the microbe belongs), and the second
is the uncapitalized species epithet For example, the bacterium that causes plague is called Yersinia pestis Often the name of an organism will be shortened by abbreviating the genus name with
a single capital letter (e.g., Y pestis)
Retrieve, Infer, Apply
1 Why is RNA thought to be the first self-replicating biomolecule?
2 Explain the endosymbiotic hypothesis of the origin of mitochondria, hydrogenosomes, and chloroplasts List two pieces of evidence that support this hypothesis
3 What is the difference between a microbial species and a strain?
4 What is the correct way to write this microbe's name: bacillus subtilis, Bacillus subtilis, Bacillus Subtilis, or Bacillus subtilis?
Identify the genus name and the species epithet
Trang 321.3 Microbiology and Its Origins
After reading this section, you should be able to:
• Evaluate the importance of the contributions to microbiology
made by Hooke, Leeuwenhoek, Pasteur, Koch, Cohn, Beijerinck,
von Behring, Kitasato, Metchnikoff, and Winogradsky
• Outline a set of experiments that might be used to decide if a
particular microbe is the causative agent of a disease
• Predict the difficulties that might arise when using Koch's
postulates to determine if a microbe causes a disease unique to
humans
Even before microorganisms were seen, some investigators sus
pected their existence and role in disease Among others, the
Roman philosopher Lucretius (about 98-55 BCE) and the physi
cian Girolamo Fracastoro (1478-1553) suggested that disease
was caused by invisible living creatures However, until microbes
could actually be seen or studied in some other way, their exis
tence remained a matter of conjecture Therefore microbiology
is defined not only by the organisms it studies but also by the
tools used to study them The development of microscopes was
the critical first step in the evolution of the discipline However,
microscopy alone is unable to answer the many questions micro
biologists ask about microbes A distinct feature of microbiology
is that microbiologists often remove microorganisms from their
normal habitats and culture them isolated from other microbes
This is called a pure or axenic culture The development of tech
niques for isolating microbes in pure culture was another criti
cal step in microbiology's history However, it is now recognized
as having limitations Microbes in pure culture are in some ways
like animals in a zoo; just as a zoologist cannot fully understand
the ecology of animals by studying them in zoos, microbiolo
gists cannot fully understand the ecology of microbes by study
ing them in pure culture Today molecular genetic techniques
and genomic analyses are providing new insights into the lives of
microbes .,.I Methods in microbial ecology (chapter 29);
Microbial genomics (chapter 18)
Here we describe how the tools used by microbiologists
have influenced the development of the field As microbiology
evolved as a science, it contributed greatly to the well-being of
humans This is exemplified by the number of microbiologists
who have won the Nobel Prize (see www.mhhe.com/willey9)
The historical context of some of the important discoveries in
microbiology is shown in figure 1.10
Microscopy and the Discovery
of Microorganisms
The earliest microscopic observations of organisms appear to
have been made between 1625 and 1630 on bees and weevils by
the Italian Francesco Stelluti (1577-1652), using a microscope
probably supplied by Galileo (1564-1642) Robert Hooke
(1635-1703) is credited with publishing the first drawings of
1.3 Microbiology and Its Origins 11
microorganisms in the scientific literature In 1665 he published
a highly detailed drawing of the fungus Mucor in his book Micrographia Micrographia is important not only for its exquisite drawings but also for the information it provided on building microscopes One design discussed in Micrographia was probably a prototype for the microscopes built and used by the amateur microscopist Antony van Leeuwenhoek (1632-1723)
of Delft, the Netherlands ( figure l.lla) Leeuwenhoek earned his living as a draper and haberdasher (a dealer in men's clothing and accessories) but spent much of his spare time constructing simple microscopes composed of double convex glass lenses held between two silver plates (figure 1.11b) His microscopes could magnify about 50 to 300 times, and he may have illuminated his liquid specimens by placing them between two pieces
of glass and shining light on them at a 45° angle to the specimen plane This would have provided a form of dark-field illumination whereby organisms appeared as bright objects against a dark background (figure 1.11c) Beginning in 1673, Leeuwenhoek sent detailed letters describing his discoveries to the Royal Society of London It is clear from his descriptions that he saw both bacteria and protists
Culture-Based Methods for Studying Microorganisms
As important as Leeuwenhoek's observations were, the development of microbiology essentially languished for the next 200 years until techniques for isolating and culturing microbes in the laboratory were formulated Many of these techniques began to be developed as scientists grappled with the conflict over the theory of spontaneous generation This conflict and the subsequent studies
on the role played by microorganisms in causing disease ultimately led to what is now called the golden age of microbiology
Spontaneous Generation
From earliest times, people had believed in spontaneous generation-that living organisms could develop from nonliving matter This view finally was challenged by the Italian physician Francesco Redi (1626-1697), who carried out a series of experiments on decaying meat and its ability to produce maggots spontaneously Redi placed meat in three containers One was uncovered, a second was covered with paper, and the third was covered with fine gauze that would exclude flies Flies laid their eggs on the uncovered meat and maggots developed The other two pieces of meat did not produce maggots spontaneously However, flies were attracted to the gauze-covered container and laid their eggs on the gauze; these eggs produced maggots Thus the generation of maggots by decaying meat resulted from the presence of fly eggs, and meat did not spontaneously generate maggots, as previously believed Similar experiments by others helped discredit the theory for larger organisms
Leeuwenhoek's communications on microorganisms renewed the controversy Some proposed that microbes arose by spontaneous generation even though larger organisms did not
Trang 33�:r :;:;:; , � �� � � ��discovers "animacules." � ���:;:; � � :: ::
1798 Jenner introduces
on heliocentric
solar system
1620 Francis Bacon argues for importance
that Bacillus anthracis
causes anthrax
1887-1890
Winogradsky studies sulfur and nitrifying bacteria
1885 Pasteur develops rabies vaccine
published; Metchnikoff describes phagocytosis;
autoclave developed;
Gram stain developed
virus can cause cancer
1900 Planck �� virus causes tobacco mosaic disease
develops quantum theory
1918 Influenza pandemic -' kills over 50 million people 1927 Lindberg's
1937 Krebs discovers citric acid cycle
transAtlantic flight
1933 Hitler
1929 Stock
1928 Griffith discovers bacterial transformation
Crick propose DNA double helix
microscope
1990 First human gene therapy testing begun
isolated and identified by Gallo and Montagnier;
Mullis develops PCR technique
2001 Anthrax bioterrorism attacks in New York, Washington, D.C., and Florida
of antisense therapy
f_i_ 2005 1918 Genome of influenza
walks on the moon
1973 Vietnam War ends
1980 First home computers
2003 Second war with Iraq
2001 World Trade 2010 H1 N1 Center attack influenza outbreak
in black
Trang 34Leeuwenhoek (b) A brass replica of the Leeuwenhoek microscope Inset photo
shows how it is held (c) Leeuwenhoek's drawings of bacteria from the human mouth
1.3 Microbiology and Its Origins 13
They pointed out that boiled extracts of hay or meat gave rise to microorganisms after sitting for a while Indeed, such extracts were the forerunners of the culture media still used today in many microbiology laboratories
In 1748 the English priest John Needham (1713-1781)
reported the results of his experiments on spontaneous generation Needham boiled mutton broth in flasks that he then tightly stoppered Eventually many of the flasks became cloudy and contained microorganisms He thought organic matter contained a vital force that could confer the properties
of life on nonliving matter
A few years later, the Italian priest and naturalist Lazzaro Spallanzani (1729-1799) improved on Needham's experimental design by first sealing glass flasks that contained water and seeds
If the sealed flasks were placed in boiling water for about 45 minutes, no growth took place as long as the flasks remained sealed
He proposed that air carried germs to the culture medium but also commented that the external air might be required for growth of animals already in the medium The supporters of spontaneous generation maintained that heating the air in sealed flasks destroyed its ability to support life
Several investigators attempted to counter such arguments Theodore Schwann (1810-1882) allowed air to enter a flask containing a sterile nutrient solution after the air had passed through a red-hot tube The flask remained sterile Subsequently Georg Friedrich Schroder (1810-1885) and Theodor von Dusch
(1824-1890) allowed air to enter a flask of heat-sterilized medium after it had passed through sterile cotton wool No growth occurred in the medium even though the air had not been heated Despite these experiments, the French naturalist Felix Pouchet (1800-1872) claimed in 1859 to have carried out experiments conclusively proving that microbial growth could occur without air contamination
Pouchet's claim provoked Louis Pasteur (1822-1895) to settle the matter of spontaneous generation Pasteur ( figure 1.12 )
first filtered air through cotton and found that objects resembling plant spores had been trapped If a piece of the cotton was placed
in sterile medium after air had been filtered through it, microbial growth occurred Next he
placed nutrient solutions in flasks, heated their necks in a flame, and drew them out into a variety of curves The swan-neck flasks that he pro
duced in this way had necks open to the atmosphere Pas
teur then boiled the solutions for a few minutes and allowed them to cool No growth took place even though the con
tents of the flasks were ex
posed to the air ( figure 1.13 )
Pasteur pointed out that growth did not occur because dust and germs had been Figure 1.12 Louis Pasteur
Trang 35Neck on second sterile flask
is broken;
growth occurs
Neck intact; airborne microbes are trapped at base, and broth is sterile
Figure 1.13 Pasteur's Experiments with Swan-Neck Flasks
trapped on the walls of the curved necks If the necks were bro
ken, growth commenced immediately Pasteur had not only re
solved the controversy by 1861 but also had shown how to keep
solutions sterile
The English physicist John Tyndall (1820-1893) and the Ger
man botanist Ferdinand Cohn (1828-1898) dealt a final blow to
spontaneous generation In 1877 Tyndall demonstrated that dust
did indeed carry germs and that if dust was absent, broth remained
sterile even if directly exposed to air During the course of his
studies, Tyndall provided evidence for the existence of exception
ally heat-resistant forms of bacteria Working independently,
Cohn discovered that the heat-resistant bacteria recognized by
Tyndall were species capable of producing bacterial endospores
Cohn later played an instrumental role in establishing a classifica
tion system for bacteria based on their morphology and physiology
�I Bacterial endospores (section 3.9)
Clearly, these early microbiologists not only disproved
spontaneous generation but also contributed to the rebirth of
microbiology They developed liquid media for culturing mi
crobes They also developed methods for sterilizing media and
maintaining their sterility These techniques were next applied
to understanding the role of microorganisms in disease
Retrieve, Infer, Apply
1 What does the theory of spontaneous generation propose? How did
Pasteur, Tyndall, and Cohn finally settle the spontaneous generation
controversy?
2 What did Pasteur prove when he showed that a cotton plug that
had filtered air would trigger microbial growth when transferred
to the medium? What argument made previously was he
addressing?
Microorganisms and Disease Although Fracastoro and a few others had suggested that invisible organisms produced disease, most people believed that disease was caused by supernatural forces, poisonous vapors called miasmas, and imbalances among the four humors thought to be present in the body The role of the four humors (blood, phlegm, yellow bile [choler], and black bile [melancholy]) in disease had been widely accepted since the time of the Greek physician Galen (129-199) Support for the idea that microorganisms cause disease-that is, the germ theory of disease-began to accumulate in the early nineteenth century from diverse fields Agostino Bassi (1773-1856) demonstrated in 1835 that a silkworm disease was due to a fungal infection He also suggested that many diseases were due to microbial infections In 1845
M J Berkeley (1803-1889) proved that the great potato blight
of Ireland was caused by a water mold (then thought to be a fungus), and in 1853 Heinrich deBary (1831-1888) showed that smut and rust fungi caused cereal crop diseases
Pasteur also contributed to this area of research in several ways His contributions began in what may seem an unlikely way Pasteur was trained as a chemist and spent many years studying the alcoholic fermentations that yield ethanol and are used in the production of wine and other alcoholic beverages When he began his work, the leading chemists were convinced that fermentation was due to a chemical instability that degraded the sugars in grape juice and other substances to alcohol Pasteur did not agree; he believed that fermentations were carried out by living organisms
In 1856 M Bigo, an industrialist in Lille, France, where Pasteur worked, requested Pasteur's assistance His business produced ethanol from the fermentation of beet sugars, and the alcohol yields had recently declined and the product had become sour Pasteur discovered that the fermentation was failing because the yeast normally responsible for alcohol formation had been replaced by bacteria that produced acid rather than ethanol In solving this practical problem, Pasteur demonstrated that all fermentations were due to the activities of specific yeasts and bacteria, and he published several papers on fermentation between 1857 and 1860
Pasteur was also called upon by the wine industry in France for help For several years, poor-quality wines had been produced Pasteur referred to the wines as diseased and demonstrated that particular wine diseases were linked to particular microbes contaminating the wine He eventually suggested a method for heating the wines to destroy the undesirable microbes The process is now called pasteurization
Indirect evidence for the germ theory of disease came from the work of the English surgeon Joseph Lister (1827-1912) on the prevention of wound infections Lister, impressed with Pasteur's studies on fermentation and putrefaction, developed a system of antiseptic surgery designed to prevent microorganisms from entering wounds Instruments were heat sterilized, and phenol was used on surgical dressings and at times sprayed over the surgical area The approach was remarkably successful and transformed surgery It also provided strong indirect evidence for the role of
Trang 36Figure 1.14 Robert Koch Koch examining a specimen in his laboratory
microorganisms in disease because phenol, which kills bacteria,
also prevented wound infections
Koch's Postulates
The first direct demonstration that bacteria cause disease came
from the study of anthrax by the German physician Robert Koch
(1843-1910) Koch (figure 1.14 ) used the criteria proposed by his
former teacher Jacob Henle (1809-1885) and others to establish
the relationship between Bacillus anthracis and anthrax; he pub
lished his findings in 1876 Koch injected healthy mice with ma
terial from diseased animals, and the mice became ill After
transferring anthrax by inoculation through a series of 20 mice,
he incubated a piece of spleen containing the anthrax bacillus in
beef serum The bacteria grew, reproduced, and produced endo
spores When isolated bacteria or their spores were injected into
healthy mice, anthrax developed His criteria for proving the
causal relationship between a microorganism and a specific dis
ease are known as Koch's postulates Koch's proof that B anthracis
caused anthrax was independently confirmed by Pasteur and his
coworkers They discovered that after burial of dead animals, an
thrax spores survived and were brought to the surface by earth
worms Healthy animals then ingested the spores and became ill
After completing his anthrax studies, Koch fully outlined his
postulates in his work on the cause of tuberculosis (figure 1.15 ) In
1884 he reported that this disease was caused by the rod-shaped
bacterium Mycobacterium tuberculosis, and in 1905 he was
awarded the Nobel Prize in Physiology or Medicine Koch's pos
tulates were quickly adopted by others and used to connect many
diseases to their causative agent
While Koch's postulates are still widely used, their applica
tion is at times not feasible For instance, organisms such as
1.3 Microbiology and Its Origins 15
Mycobacterium leprae, the causative agent of leprosy, cannot be isolated in pure culture Some human diseases are so deadly (e.g., Ebola hemorrhagic fever) that it would be unethical to use humans as the experimental organism; if an appropriate animal model does not exist, the postulates cannot be fully met To avoid some of these difficulties, microbiologists sometimes use molecular and genetic evidence For instance, molecular methods might be used to detect the nucleic acid of a virus in body tissues, rather than isolating the virus, or the genes thought to be associated with the virulence of a pathogen might be mutated In this case, the mutant organism should have decreased ability to cause disease Introduction of the normal gene back into the mutant should restore the pathogen's virulence
Pure Culture Methods During Koch's studies on bacterial diseases, it became necessary
to isolate suspected bacterial pathogens in pure culture (p 11)
At first Koch cultured bacteria on the sterile surfaces of cut, boiled potatoes, but the bacteria did not always grow well Eventually he developed culture media using meat extracts and protein digests, reasoning these were similar to body fluids Initially
he tried to solidify the media by adding gelatin Separate bacterial colonies developed after the surface of the solidified medium had been streaked with a bacterial sample The sample could also
be mixed with liquefied gelatin medium When the medium hardened, individual bacteria produced separate colonies Despite its advantages, gelatin was not an ideal solidifying agent because it can be digested by many microbes and melts at temperatures above 28°C A better alternative was provided by Fanny Eilshemius Hesse (1850-1934), the wife of Walther Hesse (1846-1911), one of Koch's assistants She suggested the use of agar, which she used to make jellies, as a solidifying agent Agar was not attacked by most bacteria Furthermore, it did not melt until reaching a temperature of 100°C and, once melted, did not solidify until reaching a temperature of 50°C; this eliminated the need to handle boiling liquid Some of the media developed
by Koch and his associates, such as nutrient broth and nutrient agar, are still widely used Another important tool developed in Koch's laboratory was a container for holding solidified mediathe Petri dish (plate), named after Richard Petri (1852-1921), who devised it These developments directly stimulated progress
in all areas of microbiology 11+-1 Culture media (section 7.5); Enrichment and isolation of pure cultures (section 7.5)
Our focus thus far has been on the development of methods for culturing bacteria But viral pathogens were also being studied during this time, and methods for culturing them were also being developed The discovery of viruses and their role in disease was made possible when Charles Chamberland (1851-1908), one of Pasteur's associates, constructed a porcelain bacterial filter in
1884 Dimitri Ivanowski (1864-1920) and Martinus Beijerinck (pronounced "by-a-rink''; 1851-1931) used the filter to study tobacco mosaic disease They found that plant extracts and sap from diseased plants were infectious, even after being filtered with Chamberland's filter Because the infectious agent passed through
Trang 37Postulate Experimentation
1 The microorganism must be
present in every case of the
disease but absent from
healthy organisms
Koch developed a staining technique to examine human tissue Mycobacterium tuberculosis could be identified in diseased tissue
2 The suspected microorganisms
must be isolated and grown in a
3 The same disease must result
when the isolated microorganism
is inoculated into a healthy host
Koch injected cells from the pure culture of M tuberculosis into guinea pigs The guinea pigs subsequently died of tuberculosis
4 The same microorganisms must
be isolated again from the
diseased host
Koch isolated M tuberculosis in pure culture on coagulated blood serum from the dead guinea pigs
M tuberculosis
colonies
a filter that was designed to trap bacterial cells, they reasoned that
the agent must be something smaller than a bacterium Beijerinck
proposed that the agent was a "filterable virus:' Eventually viruses
were shown to be tiny, acellular infectious agents
Retrieve, Infer, Apply
1 Discuss the contributions of Lister, Pasteur, and Koch to the germ
theory of disease and the treatment or prevention of diseases What
other contributions did Koch make to microbiology?
2 Describe Koch's postulates What is a pure culture? Why are pure
cultures important to Koch's postulates?
Immunology
The ability to culture microbes also played an important role in
early immunological studies During studies on the bacterium
that causes chicken cholera, Pasteur and Pierre Roux (1853-1933)
discovered that incubating the cultures for long intervals between
transfers resulted in cultures that had lost their ability to cause the
disease These cultures were said to be attenuated When the chickens were injected with attenuated cultures, they not only remained healthy but also were able to resist the disease when exposed to virulent cultures Pasteur called the attenuated culture a vaccine (Latin vacca, cow) in honor of Edward Jenner (1749-1823) because, many years earlier, Jenner had used material from cowpox lesions to protect people against smallpox (see Historical Highlights 37.5) Shortly after this, Pasteur and Chamberland developed an attenuated anthrax vaccine I Vaccines and immunizations (section 37.7)
Pasteur also prepared a rabies vaccine using an attenuated strain of rabies virus During the course of these studies, Joseph Meister, a nine-year-old boy who had been bitten by a rabid dog, was brought to Pasteur Since the boy's death was certain in the absence of treatment, Pasteur agreed to try vaccination Joseph was injected 13 times over the next 10 days with increasingly virulent preparations of the attenuated virus He survived In gratitude for Pasteur's development of vaccines, people from around the world contributed to the construction of the Pasteur
Trang 38Institute in Paris, France One of the initial tasks of the institute
was vaccine production
These early advances in immunology were made without
any concrete knowledge about how the immune system works
Immunologists now know that the immune system uses chemi
cals produced by several types of blood cells to provide protec
tion Among the chemicals are soluble proteins called antibodies,
which can be found in blood, lymph, and other body fluids The
role of soluble substances in preventing disease was recognized
by Emil von Behring (1854-1917) and Shibasaburo Kitasato
(1852-1931) After the discovery that diphtheria was caused by
a bacterial toxin, they injected inactivated diphtheria toxin into
rabbits The inactivated toxin induced rabbits to produce an
antitoxin, which protected against the disease Antitoxins are now
known to be antibodies that specifically bind toxins, neutraliz
ing them The first immune system cells were discovered when
Elie Metchnikoff (1845-1916) found that some white blood
cells could engulf disease-causing bacteria He called these
cells phagocytes and the process phagocytosis (Greek phagein,
eating)
Microbial Ecology
Culture-based techniques were also applied to the study of mi
crobes in soil and aquatic habitats Early microbial ecologists
studied microbial involvement in the carbon, nitrogen, and sul
fur cycles The Russian microbiologist Sergei Winogradsky
(1856-1953) made many contributions to soil microbiology He
discovered that soil bacteria could oxidize iron, sulfur, and am
monia to obtain energy and that many of these bacteria could
incorporate C02 into organic matter much as photosynthetic
organisms do Winogradsky also isolated anaerobic nitrogen
fixing soil bacteria and studied the decomposition of cellulose
Martinus Beijerinck was one of the great general microbiolo
gists who made fundamental contributions not only to virology
but to microbial ecology as well He isolated aerobic nitrogen
fixing bacteria (Azotobacter spp.), a root nodule bacterium also
capable of fixing nitrogen (genus Rhizobium), and sulfate
reducing bacteria Beijerinck and Winogradsky also developed
the enrichment culture techniques and the use of selective
media, which have been of great importance in microbiology
�I Biogeochemical cycling (section 28.1); Culture media
(section 7.5)
Retrieve, Infer, Apply
1 How did Jenner, Pasteur, von Behring, Kitasato, and Metchnikoff
contribute to the development of immunology? How was the ability
to culture microbes important to their studies?
2 How did Winogradsky and Beijerinck contribute to the study of
microbial ecology? What new culturing techniques did they develop
in their studies?
3 How might the work ofWinogradsky and Beijerinck have
contributed to research on bacterial pathogens? Conversely, how
might Koch and Pasteur have influenced Winogradsky's and
Beijerinck's study of microbial ecology?
1.4 Microbiology Today 17
After reading this section, you should be able to:
• Construct a concept map, table, or drawing that illustrates the diverse nature of microbiology and how it has improved human conditions
• Support the belief held by many microbiologists that microbiology is experiencing its second golden age
Microbiology today is as diverse as the organisms it studies It has both basic and applied aspects The basic aspects are concerned with the biology of microorganisms themselves The applied aspects are concerned with practical problems such as disease, water and wastewater treatment, food spoilage and food production, and industrial uses of microbes The basic and applied aspects of microbiology are intertwined Basic research
is often conducted in applied fields, and applications often arise out of basic research
An important recent development in microbiology is the increasing use of molecular and genomic methods to study microbes and their interactions with other organisms These methods have led to a time of rapid advancement that rivals the golden age of microbiology Indeed, many feel that microbiology is in its second golden age Here we describe some of the important advances that have enabled microbiologists to use molecular and genomic techniques We then discuss some of the important research being done in the numerous subdisciplines of microbiology
Molecular and Genomic Methods for Studying Microbes
Molecular and genomic methods for studying microbes rely on the ability of scientists to manipulate the genes and genomes of the organisms being studied An organism's genome is all the genetic information that organism contains To study single genes or the entire genome, microbiologists must be able to isolate DNA and RNA, cut DNA into smaller pieces, insert one piece of DNA into another, and determine the sequence of nucleotides in DNA
Cutting double-stranded DNA into smaller pieces was accomplished using bacterial enzymes now known as restriction endonucleases, or simply, restriction enzymes These enzymes were discovered by Werner Arber and Hamilton Smith in the 1960s Their discovery was followed by the report in 1972 that David Jackson, Robert Symons, and Paul Berg had successfully generated recombinant DNA molecules-molecules made by combining two or more different DNA molecules together They did this by cutting DNA from two different organisms with the same restriction enzyme, mixing the two DNA molecules together, and linking them together with an enzyme called DNA ligase �I Key developments in recombinant DNA technology (section 17.1)
The next major breakthrough was the development of methods to determine the sequence of nucleotides in DNA In the late
Trang 391970s, Frederick Sanger introduced a method that has since been
modified and adapted for use in automated systems Today en
tire genomes of organisms can be sequenced in a matter of days
In addition, newer, even more rapid sequencing methods have
been devised "'"I Genome sequencing (section 18.2)
Genome sequencing is the first step in genomic analysis
Once the genome sequence is in hand, microbiologists must
decipher the information found in the genome This involves
identifying potential protein-coding genes, determining what
they code for, and identifying other regions of the genome that
may have other important functions (e.g., genes encoding
tRNA and rRNA or sequences playing a role in regulating the
function of genes) This work requires the use of computers,
which has given rise to the scientific discipline bioinformatics
Bioinformaticists manage the ever-increasing amount of ge
netic information available for analysis They also determine
the function of genes and generate hypotheses that can be
tested either in silica (i.e., in the computer) or in the laboratory
Major Fields in Microbiology
As noted in section 1.1, pathogenic microbes, though relatively
few in number, have had and continue to have considerable im
pact on humans Thus one of the most active and important fields
in microbiology is medical microbiology, which deals with dis
eases of humans and animals Medical microbiologists identify
the agents causing infectious diseases and help plan measures for
their control and elimination Frequently they are involved in
tracking down new, unidentified pathogens such as those causing
variant Creutzfeldt-Jakob disease (the human version of "mad
cow disease''), hantavirus pulmonary syndrome, and West Nile
encephalitis These microbiologists also study the ways microor
ganisms cause disease As described in section 1.3, our under
standing of the role of microbes in disease began to crystallize
when we were able to isolate them in pure culture Today, clinical
laboratory scientists, the microbiologists who work in hospital
and other clinical laboratories, use a variety of techniques to pro
vide information needed by physicians to diagnose infectious dis
ease Increasingly, molecular genetic techniques are also being
used
Major epidemics have regularly affected human history The
1918 influenza pandemic is of particular note; it killed more than
50 million people in about a year Public health microbiology is
concerned with the control and spread of such communicable
diseases Public health microbiologists and epidemiologists mon
itor the amount of disease in populations Based on their observa
tions, they can detect outbreaks and developing epidemics, and
implement appropriate control measures They also conduct sur
veillance for new diseases as well as bioterrorism events Public
health microbiologists working for local governments monitor
community food establishments and water supplies to ensure
they are safe and free from pathogens
To understand, treat, and control infectious disease, it is
important to understand how the immune system protects the
body from pathogens; this question is the concern of immunology Immunology is one of the fastest growing areas in science Much of the growth began with the discovery of the human immunodeficiency virus (HIV), which specifically targets cells
of the immune system Immunology also deals with the nature and treatment of allergies and autoimmune diseases such as rheumatoid arthritis "'"' Innate host resistance (chapter 33); Adaptive immunity (chapter 34)
Microbial ecology is another important field in microbiology Microbial ecology developed when early microbiologists such as Winogradsky and Beijerinck chose to investigate the ecological role of microorganisms rather than their role in disease Today, a variety of approaches, including non-culture-based techniques, are used to describe the vast diversity of microbes in terms of their morphology, physiology, and relationships with organisms and the components of their habitats The importance
of microbes in global and local cycling of carbon, nitrogen, and sulfur is well documented; however, many questions are still unanswered Of particular interest is the role of microbes in both the production and removal of greenhouse gases such as carbon dioxide and methane Microbial ecologists also are employing microorganisms in bioremediation to reduce pollution A new frontier in microbial ecology is the study of the microbes normally associated with the human body-so-called human microbiota Scientists are currently trying to identify all members of the human microbiota using molecular techniques that grew out of Woese's pioneering work to establish the phylogeny of microbes
bioremediation (section 43.4) Agricultural microbiology is a field related to both medical microbiology and microbial ecology Agricultural microbiology
is concerned with the impact of microorganisms on agriculture Microbes such as nitrogen-fixing bacteria play critical roles in the nitrogen cycle and affect soil fertility Other microbes live in the digestive tracts of ruminants such as cattle and break down the plant materials these animals ingest There are also plant and animal pathogens that have significant economic impact if not controlled Furthermore, some pathogens of domestic animals also can cause human disease Agricultural microbiologists work on methods to increase soil fertility and crop yields, study rumen microorganisms in order to increase meat and milk production, and try to combat plant and animal diseases Currently many agricultural microbiologists are studying the use of bacterial and viral insect pathogens as substitutes for chemical pesticides
Agricultural microbiology has contributed to the ready supply of high-quality foods, as has the discipline of food and dairy microbiology Numerous foods are made using microorganisms On the other hand, some microbes cause food spoilage or are pathogens that are spread through food Excellent examples of the latter are the rare Escherichia coli 0104:H4, which in 2011 caused a widespread outbreak of disease in Europe thought to have been spread by bean sprouts, and also in 2011, contaminated ground turkey was implicated
in a Salmonella outbreak in the United States Food and dairy
Trang 40microbiologists explore the use of microbes in food produc
tion They also work to prevent microbial spoilage of food
and the transmission of food-borne diseases This involves
monitoring the food industry for the presence of pathogens
Increasingly, molecular methods are being used to detect
pathogens in meat and other foods Food and dairy microbi
ologists also conduct research on the use of microorganisms
as nutrient sources for livestock and humans _.,.1 Microbi
ology of food (chapter 41)
Humans unknowingly exploited microbes for thousands of
years However, the systematic and conscious use of microbes in
industrial microbiology did not begin until the 1800s Industrial
microbiology developed in large part from Pasteur's work on alco
holic fermentations, as described in section 1.3 His success led to
the development of pasteurization to preserve wine during storage
Pasteur's studies on fermentation continued for almost 20 years
One of his most important discoveries was that some fermentative
microorganisms were anaerobic and could live only in the absence
of oxygen, whereas others were able to live either aerobically or
anaerobically _.,.1 Controlling food spoilage (section 41.2)
Another important advance in industrial microbiology
occurred in 1929 when Alexander Fleming discovered that the
fungus Penicillium sp produced what he called penicillin, the
first antibiotic that could successfully control bacterial infec
tions Although it took World War II for scientists to learn how
to mass-produce penicillin, scientists soon found other micro
organisms capable of producing additional antibiotics Today
industrial microbiologists also use microorganisms to make
products such as vaccines, steroids, alcohols and other sol
vents, vitamins, amino acids, and enzymes Microbes are also
being used to produce biofuels such as ethanol These alterna
tive fuels are renewable and may help decrease pollution associ
ated with burning fossil fuels _.,.1 Major products of industrial
microbiology (section 42.1); Biofuel production (section 42.2)
Industrial microbiologists identify or genetically engineer
microbes of use to industrial processes, medicine, agriculture,
and other commercial enterprises They also utilize techniques to
improve production by microbes and devise systems for cultur
ing them and isolating the products they make
Members ofthe Microbial World
• Microbiology studies microscopic cellular organisms that
are often unicellular or, if multicellular, do not have highly
differentiated tissues Microbiology also focuses on
biological entities that are acellular (figure 1.1)
• Microbiologists divide cellular organisms into three
domains: Bacteria, Archaea, and Eukarya (figure 1.2)
• Domains Bacteria and Archaea consist of prokaryotic
microorganisms The eukaryotic microbes (protists and
Key Concepts 19
The advances in medical microbiology, agricultural microbiology, food and dairy microbiology, and industrial microbiology are in many ways outgrowths of the labor of many microbiologists doing basic research in areas such as microbial physiology, microbial genetics, molecular biology, and bioinformatics Microbes are metabolically diverse and can employ a wide variety of energy sources, including organic matter, inorganic molecules (e.g., H2 and NH3), and sunlight Microbial physiologists study many aspects of the biology of microorganisms, including their metabolic capabilities They also study the synthesis
of antibiotics and toxins, the ways in which microorganisms survive harsh environmental conditions, and the effects of chemical and physical agents on microbial growth and survival Microbial geneticists, molecular biologists, and bioinformaticists study the nature of genetic information and how it regulates the development and function of cells and organisms The bacteria E coli
and Bacillus subtilis, the yeast Saccharomyces cerevisiae (baker's yeast), and bacterial viruses such as T4 and lambda continue to
be important model organisms used to understand biological phenomena
Clearly, the future of microbiology is bright Genomics in particular is revolutionizing microbiology, as scientists are now beginning to understand organisms in toto, rather than in a reductionist, piecemeal manner How the genomes of microbes evolve, the nature of host-pathogen interactions, the minimum set of genes required for an organism to survive, and many more topics are aggressively being examined by molecular and genomic analyses This is an exciting time to be a microbiologist Enjoy the journey
Retrieve, Infer, Apply
1 Since the 1970s, microbiologists have been able to study individual genes and whole genomes at the molecular level What advances made this possible?
2 Briefly describe the major subdisciplines in microbiology Which do you consider to be applied fields? Which are basic?
3 Log all the microbial products you use in a week Be sure to consider all foods and medications (including vitamins)
4 List all the activities or businesses you can think of in your community that directly depend on microbiology
fungi) are placed in Eukarya Viruses, viroids, satellites, and prions are acellular entities that are not placed in any of the domains but are classified by a separate system
1.2 Microbial Evolution
• Evolutionary biologists and others interested in the origin
of life must rely on many types of evidence
• Earth is approximately 4.5 billion years old Within the first
1 billion years of its existence, life arose (figure 1.4)