Environmental microbiology PDF
Preview Environmental microbiology
Environmental Microbiology Third edition Environmental Microbiology Third edition Ian L. Pepper Charles P. Gerba Terry J. Gentry AMSTERDAM(cid:129)BOSTON(cid:129)HEIDELBERG(cid:129)LONDON(cid:129)NEWYORK(cid:129)OXFORD PARIS(cid:129)SANDIEGO(cid:129)SANFRANCISCO(cid:129)SINGAPORE(cid:129)SYDNEY(cid:129)TOKYO AcademicPressisanimprintofElsevier AcademicPressisanimprintofElsevier 525BStreet,Suite1800,SanDiego,CA92101-4495,USA 32JamestownRoad,LondonNW17BY,UK 225WymanStreet,Waltham,MA02451,USA Copyrightr2015,2009,2000ElsevierInc.Allrightsreserved. Nopartofthispublicationmaybereproduced,storedinaretrievalsystem,ortransmittedinanyform orbyanymeanselectronic,mechanical,photocopying,recordingorotherwisewithoutthepriorwritten permissionofthepublisher. 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BritishLibraryCataloguing-in-PublicationData AcataloguerecordforthisbookisavailablefromtheBritishLibrary LibraryofCongressCataloging-in-PublicationData AcatalogrecordforthisbookisavailablefromtheLibraryofCongress ISBN:978-0-12-394626-3 ForinformationonallAcademicPresspublications visitourwebsiteatelsevierdirect.com PrintedandboundintheUnitedStatesofAmerica 15 16 17 18 19 10 9 8 7 6 5 4 3 2 1 Thisbookisdedicatedtomyfriend,whowasalwaysa“Blaze”ofglory! IanPepper ThisbookisdedicatedtomywifeandsonsPeterandPhillipforalltheirsupport CharlesGerber This book is dedicated to my grandparents, Coy and Sybal, who gave me the opportunity and encouragement to pursue mydreams TerryGentry Preface Everywhere on Earth, microorganisms are abundant, even technologies utilized to study microbes and their activities; within our own human bodies. Astonishingly, an adult (iv)chaptersonbiochemicalandindustrialtransformations, human contains ten times as many microbial cells as including microbial transport; (v) chapters on bacterial mammalian cells, carrying around approximately 1.25kg diversity and communication; (vi) chapters on pathogens of microbes. Bacteria are found all over our skin, in our found within water and food and their potential risks; mouths, up our noses, and within every part of our inte- (vii) chapters on waste- and potable-water treatment and rior bodies, particularly within the gastrointestinal tract. distribution; and finally (viii) chapters on urban microbiol- Outside of ourselves, microorganisms including viruses, ogyandglobalemergingissues. bacteria, fungi, and protozoa proliferate in every known Thistextbookisdesignedforasenior-levelundergradu- environment, from the frozen arctic regions to the warm ate class,or a graduate level class in environmental micro- tropics. We define “Environmental Microbiology” as the biology.Becauseenvironmentalmicrobiologyisconstantly study of microbes within all earthly habitats, and evolving, new beneficial and pathogenic microbes have their beneficial and detrimental effects on human health emerged since the second edition was published in 2009 andwelfare.Assuch,environmentalmicrobiologyinvolves (Table 1.2, Chapter 1). Likewise, new technologies have theeffectorimpactofmicrobesonhumanactivities,either been developed that aid our understanding of microbes. directly or indirectly. Examples of the role of microbes in These recent discoveries are documented in Information our daily lives are shown in Table 1.1 (Chapter 1), which Box1.2(Chapter1). illustrates that life without environmental microbes is Also, there are a number of changes in the third impossible. edition. The authors are Professors Pepper, Gerba, and Environmental microbiology is not only a dynamic Gentry, who collectively have expertise over a broad field of science; it is transformative, constantly changing spectrum of environmental microbiology. Key contribu- asnew microbesare discoveredand new aspects ofmicro- tions to the text were also made by nine colleagues who bial activities are understood. Ultimately microbes impact have collaborated with the authors at The University the quality of our environment, which subsequently of Arizona and Texas A & M University. Overall, there impacts human health. In this textbook we invite you to are five new chapters in the third edition, and seven join us on a journey into the extraordinary world of how chapters that have undergone significant change or mod- microbes impact our environment and how we put them to ification. All of the remaining chapters were updated usetoenhancetheworldwelivein. with respect to references, and many new graphics have Thisthirdeditionhaseightsubjectareas:(i)foundation been added. chapters that provide adequate background for subsequent IanPepper advanced chapters; (ii) chapters on microbial environ- CharlesGerba ments; (iii) chapters on the microbial methods and TerryGentry Instructors:Forlectureslidesandanswerstotheendofchaptertests,pleasevisittheinstructorwebsiteathttp://textbooks. elsevier.com/web/product_details.aspx?isbn59780123946263 xvii The Authors Ian L. Pepper Ph.D., The Ohio State Terry J. Gentry Ph.D., The University, 1975. Currently Professor UniversityofArizona,2003.Currently of Environmental Microbiology. Associate Professor and Director of Dr.Pepper’sdiverseresearchinterests the Soil and Aquatic Microbiology are reflected in the fact that he is LaboratoryatTexasA&MUniversity. Fellow of The American Association Dr. Gentry is an environmental for the Advancement of Science, The microbiologist specializing in the American Academy of Microbiology, development and use of molecular the Soil Science Society of America, technologies to enhance the detection and the American Society of and remediation of environmental contamination. This Agronomy. He is also Director of the National Science includes the use of genotypic methods to detect and Foundation Water and Environmental Technology Center identify microbial contaminants from animal, human, and attheUniversityofArizona.Dr. Pepperhas beenactivein natural sources and also the characterization of microbial the area of soil molecular ecology as well as waste utiliza- populations and communities contributing to applied tion including biosolids and effluent reuse. More recently processes such as the bioremediation of organic and he has been pursuing research on real-time monitoring of metal contaminants and ecosystem restoration and sus- microbial contaminants in potable water, and “smart water tainability. Dr. Gentry teaches an undergraduate course distributionsystems.” in soil and water microbiology and a graduate course in environmental microbiology. Charles P. Gerba Ph.D., University of Miami, 1973. Currently, Professor of Microbiology. Dr. Gerba is a Fellow of the American Academy of Microbiology. He is recipient of the A.P. Black Award from the American Water Works Association foroutstandingcontributionstoWater Science, and the McKee Award from the Water Environment Federation for outstanding contributions to groundwater protection. He has an international reputation for his methodologies for pathogen detection in water and food, pathogen occur- renceinhouseholds,andriskassessment. xix Contributing Authors John P. Brooks USDA ARS Mississippi JuliaW.Neilson TheUniversityofArizona, State,MS Tucson,AZ Marilyn J. Halonen The University of DeborahT.Newby IdahoNationalLaboratory, Arizona,Tucson,AZ IdahoFalls,ID Emily B. Hollister Baylor College of Leland S. Pierson III Texas A & M Medicine,Houston,TX University,CollegeStation,TX RainaM.Maier TheUniversityofArizona, TimberleyM.Roane UniversityofColorado, Tucson,AZ Denver,CO xxi xxii ContributingAuthors Channah Rock The University of Arizona, Berenise Rivera The University of Arizona, Maricopa,AZ Tucson,AZ Virginia I. Rich The University of Arizona, Hye-Weon Yu The University of Arizona, Tucson,AZ Tucson,AZ Chapter 1 Introduction to Environmental Microbiology Ian L. Pepper, Charles P. Gerba and Terry J. Gentry 1.1 EnvironmentalMicrobiology 1.2.2 WhatInfectsUs 1.3 EnvironmentalMicrobiology asaDiscipline 1.2.3 WhatHealsUs in2014 1.2 MicrobialInfluencesonourDaily 1.2.4 WhatWeDrink QuestionsandProblems Lives 1.2.5 WhatWeEat ReferencesandRecommendedReading 1.2.1 OverallHealthofthePlanet 1.2.6 WhatWeBreathe 1.1 ENVIRONMENTAL MICROBIOLOGY water and wastewater treatment dramatically reduced AS A DISCIPLINE bacterial waterborne disease. However, other microbial agents such as viruses and protozoa, which are more resistant to disinfection than enteric bacteria, still cause We define “environmental microbiology” as the study of microbes within all habitats, and their beneficial and detri- problems, resulting in water quality continuing to be a mental impacts on human health and welfare. major focus in environmental microbiology. There is an estimated 20,000,000 cases of illness per year due to Environmentalmicrobiologyisrelatedto,butalsodifferent drinking contaminated water (Reynolds et al., 2008). The from, “microbial ecology,” which focuses on the interac- largest waterborne outbreak of disease in the United tionsofmicroorganismswithinanenvironmentsuchasair, States occurred in 1993, when over 400,000 people waterorsoil.Theprimarydifferencebetweenthetwodisci- became ill and around 100 died in Milwaukee, plinesisthatenvironmentalmicrobiologyisanappliedfield Wisconsin,duetotheprotozoanparasiteCryptosporidium inwhichweattempttoimprovetheenvironmentandbene- fit society. Environmental microbiology is also related to (Eisenberg et al., 2005). In developing countries, poor manyotherdisciplines(Figure1.1). sanitation resulting from a lack of water and wastewater treatmentstillresultsinmillionsofdeathsannually. Microorganisms occur everywhere on Earth. An adult Controlling the contamination of our food supply also human body contains 10 times as many microbial cells as continues to be a concern; and the Centers for Disease mammalian cells, consisting of approximately 1.25kg of Control estimates that in the United States each year there microbial biomass (Wilson, 2005). Although the study of are 48 million cases with 128,000 people hospitalized and microbial inhabitants of humans resides within clinical 3000 deaths. The third most deadly outbreak of foodborne microbiology, itwasthediscoveryofenvironmentalpath- ogenic microorganisms that invaded the human body that infectionintheUnitedStatesoccurredin2011,when29per- resulted in the beginning of environmental microbiology. sons died from Listeria contamination of cantaloupe. Information Box 1.1 documents some of these foodborne These roots were enabled by the work of Louis Pasteur outbreaks. and Robert Koch, who developed the Germ Theory of Untilthemiddleofthe20thcentury,industrialchemicals Disease in the 1870s, following which, the presence of in the United States were routinely disposed of by dumping waterborne human pathogens then became the initial them into sewers, soils, rivers or oceans, without regard to focus of environmental microbiology. In developed coun- the pollution that this caused, or the subsequent adverse tries, applied environmental studies related to drinking I.L.Pepper,C.P.Gerba,T.J.Gentry:EnvironmentalMicrobiology,Thirdedition.DOI:http://dx.doi.org/10.1016/B978-0-12-394626-3.00001-6 ©2015ElsevierInc.Allrightsreserved. 3 4 PART | I ReviewofBasicMicrobiologicalConcepts Hazardous Industrial Waste/ Microbiology Bioremediation Food Soil Microbiology Safety Environmental Occupational Aeromicrobiology Microbiology Health/Infection Control Aquatic Diagnostic Microbiology Microbiology Water Quality Biotechnology FIGURE1.1 Environmentalmicrobiologyinterfaceswithmanyotherdisciplines. potentially be degraded by heterotrophic microorganisms InformationBox1.1 Large-scaleFoodRecallsDueto including bacteria and fungi. The field of bioremediation FoodborneOutbreaks within environmental microbiology involves enhancing and optimizing microbial degradation of organic pollutants, FoodRecall Year Organism #People resulting in environmental cleanup and reduced adverse Involved human health effects. The efficacy of bioremediation was Turkeyandchicken 2002 Listeria 120 products demonstrated in 1989, when the Exxon Valdez oil tanker Greenonions 2003 HepatitisA 600 spilled approximately 11 million gallons of crude oil into Spinach 2006 E.coliO157:H7 200 Prince William Sound. Optimization of bioremediation was Cannedmeat 2007 Clostridium 4 a major factor in cleaning up and restoring Prince William products botulinum Sound. Bioremediation has also been shown to be critically Cannedbeef 2007 E.coliO157:H7 14 Freshsalsa 2008 Salmonellaenterica 1442 important in cleaning up the more recent 2010 Gulf of Peanutbutter 2009 Salmonella 22,500 Mexicooilspill(seeChapter31). Eggs 2010 Salmonella 2000 Also in the 20th century, soil microbiology, a compo- Cantaloupe 2011 Listeria 29 nent of environmental microbiology, became important as Strawberries 2012 Norovirus 11,200 a means to enhance agricultural production. Studies on the rhizosphere (the soil surrounding plant roots), and specific studies on root-microbial interactions involving ecologicalandhumanhealtheffects.Thisallchangedinthe nitrogen fixing rhizobia, and mycorrhizal fungi that 1960s when concern over a toxic dump was highlighted by enhanced phosphorus uptake, were all utilized to improve Rachel Carson’s landmark book Silent Spring. In essence, plant growth. Other studies of plant growth-promoting this resulted in the birth of the environmental movement in bacteria that reduced the incidence of plant pathogens theUnitedStates,andanewfieldofstudyforenvironmental were also effective in aiding the “Green Revolution,” microbiology known as “bioremediation.” Many chemicals which resulted in stunning increases in crop yields dischargedintotheenvironmentwithoutregardtotheconse- throughout the United States and in many parts of the quenceshave been shown to resultin adverse human health world. Overall, these fundamental study areas have impacts. However, since hydrocarbons, chlorinated solvents helped shape the current discipline of environmental and most pesticides are organic in nature, they can microbiology,andallaffectoureverydaylife.
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