Manual of environmental microbiology

1089 Pages·2007·36.609 MB·English

by  Crawford, Ronald L., Garland, Jay L., Hurst, Christon J

MANUAL OF Yates MANUAL OF
Nakatsu
ENVIRONMENTAL MICROBIOLOGY
Miller
FOURTH EDITION
Pillai
ENVIRONMENTAL
The single most comprehensive resource for environmental microbiology
Environmental microbiology, the study of the roles that microbes play in all planetary environments, is one of
the most important areas of scientific research. The Manual of Environmental Microbiology, Fourth Edition, provides
comprehensive coverage of this critical and growing field. FOURTH EDITION MICROBIOLOGY
MEM
Thoroughly updated and revised, this manual is the definitive reference for information on microbes in air, water,
and soil and their impact on human health and welfare. Written in accessible, clear prose, this manual covers four N
broad areas: general methodologies, environmental public health microbiology, microbial ecology, and biodegradation I A
C
and biotransformation. This wealth of information is divided into 17 sections each containing chapters written by V
N F O U R T H E D I T I O N
acknowledged topical experts from the international community.
R
I
Specifically, the new edition of this manual ORU
O Editor in Chief Marylynn V. Yates
• Contains completely new sections covering microbial risk assessment, quality control, A
B
and microbial source tracking
INL Editors
• Incorporates a summary of the latest methodologies used to study microorganisms in various environments O

MO Cindy H. Nakatsu | Robert V. Miller | Suresh D. Pillai
• Synthesizes the latest information on the assessment of microbial presence and microbial
L
activity in natural and artificial environments
E
O F
The Manual of Environmental Microbiology is an essential reference for environmental microbiologists, microbial
N

ecologists, and environmental engineers, as well as those interested in human diseases, water and wastewater
G
treatment, and biotechnology.
T
Y
A

L
Marylynn V. Yates, Ph.D., is Editor in Chief of this manual and professor of Environmental

Microbiology and Distinguished Teaching Professor at the University of California, Riverside.
Her research interests include characterizing and predicting the fate and transport of human
enteric pathogenic microorganisms in soils, water, and wastewater; development of methods
for rapid, sensitive detection of infective enteric viruses in water samples; human pathogen
considerations associated with wastewater reuse and biosolids application to land; and the use
of indicators for predicting pathogen occurrence and behavior in the environment. She is a
fellow of the American Association for the Advancement of Sciences, the American Academy
of Microbiology, and a National Associate of the National Academies of Science.
ISBN 9781555816025
90000 >

9 781555 816025
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LibraryofCongressCataloging-in-PublicationData
Names:Yates,M.V.(MarylynnV.),editor.|Nakatsu,CindyH.,editor.| Miller,RobertV.(RobertVerne),
1945-editor.|Pillai,SureshD.,1962-editor.
Title:Manualofenvironmentalmicrobiology/editorinchief,MarylynnV.Yates;editors,
CindyH.Nakatsu,RobertV.Miller,SureshD.Pillai.
Description:Fourthedition.|Washington,DC:ASMPress,[2016]|
Includesbibliographicalreferencesandindex.
Identifiers:LCCN2016014816(print)|LCCN2016016986(ebook)|
ISBN9781555816025(hardcover)|ISBN9781555818821()
Subjects:LCSH:Microbialecology–Laboratorymanuals.|Sanitarymicrobiology–Laboratorymanuals.
Classification:LCCQR100.M362016(print)|LCCQR100(ebook)|DDC577.8–dc23
LCrecordavailableathttps://lccn.loc.gov/2016014816
AllRightsReserved
PrintedinCanada
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Online:http://www.asmscience.org
Contents
EditorialBoard ix 2.3.2 PCR,Real-TimePCR,DigitalPCR,and
IsothermalAmplification/2.3.2-1
Contributors xi RACHELA.BARTHOLOMEW,JANINE
R.HUTCHISON,TIMOTHYM.STRAUB,
ANDDOUGLASR.CALL
1.1.1 Introduction/1.1.1-1
2.3.3 Microarray-BasedEnvironmental
MARYLYNNV.YATES
Diagnostics/2.3.3-1
DARRELLP.CHANDLER
2.3.4 FieldApplicationofPathogenDetection
GENERAL METHODOLOGY Technologies/2.3.4-1
TIMOTHYM.STRAUB,DOUGLAS
VOLUMEEDITOR:SURESHD.PILLAI R.CALL,CINDYBRUCKNER-LEA,
HEATHERCOLBURN,CHERYLL.BAIRD,
SECTIONEDITORS:YOICHIKAMAGATA,
RACHELA.BARTHOLOMEW,
CLEBERC.OUVERNEY,DOUGLASR.CALL,
RICHARDOZANICH,AND
STEFANJ.GREEN,YILDIZT.CHAMBERS,AND
KRISTINJARMAN
JOHNSCOTTMESCHKE
2.1 CULTURE-BASEDANDPHYSIOLOGICAL 2.4 MICROBIALCOMMUNITYANALYSISOF
DETECTION ENVIRONMENTALSAMPLESWITH
N -G S
2.1.1 DetectionofSpecificTaxaUsing EXT ENERATION EQUENCING
ChromogenicandFluorogenic
2.4.1 IntroductiontoMicrobial
Media/2.1.1-1
CommunityAnalysisofEnvironmental
MOHAMMADMANAFI
SampleswithNext-Generation
2.1.2 AnaerobicCultivation/2.1.2-1 Sequencing/2.4.1-1
TAKASHINARIHIROANDYOICHI STEFANJ.GREENANDJOSHD.NEUFELD
KAMAGATA
2.4.2 MicrobialCommunityAnalysisUsing
2.1.3 NewDevicesforCultivation/2.1.3-1 High-ThroughputAmplicon
YOSHITERUAOIANDSLAVAEPSTEIN Sequencing/2.4.2-1
2.2 MICROSCOPICMETHODS DANNYIONESCU,WILLA.OVERHOLT,
MICHAELD.J.LYNCH,JOSHD.NEUFELD,
2.2.1 Gold-BasedInSituHybridizationfor
ANKURNAQIB,ANDSTEFANJ.GREEN
PhylogeneticSingle-CellDetectionof
2.4.3 FunctionalMetagenomics:Proceduresand
ProkaryotesinEnvironmental
Progress/2.4.3-1
Samples/2.2.1-1
LAURAS.MORRISANDJULIAN
THILOEICKHORSTANDHANNESSCHMIDT
R.MARCHESI
2.2.2 AssessmentofProkaryoticBiologicalActivity
2.4.4 Metagenomics:AssigningFunctional
attheSingle-CellLevelbyCombining
StatustoCommunityGene
MicroautoradiographyandFluorescence
Content/2.4.4-1
insituHybridization/2.2.2-1
NASEERSANGWANANDRUPLAL
CLEBERC.OUVERNEY
2.3 T -S D 2.4.5 GenerationandAnalysisofMicrobial
ARGET PECIFIC ETECTION
Metatranscriptomes/2.4.5-1
2.3.1 Antibody-BasedTechnologiesfor NEHASARODE,DARRENJ.PARRIS,SANGITA
EnvironmentalBiodetection/2.3.1-1 GANESH,SHERRYL.SESTON,ANDFRANK
CHERYLL.BAIRDANDSUSANM.VARNUM J.STEWART
v
vi ▪ CONTENTS
2.5 QA/QC E
IN NVIRONMENTAL 3.1.2 BestPracticesforCyanobacterialHarmful
MICROBIOLOGY AlgalBloomMonitoring/3.1.2-1
TIMOTHYG.OTTENANDHANSW.PAERL
2.5.1 IntroductiontoPrinciplesofQuality
3.1.3 AssessingtheEfficiencyofWastewater
Assurance/2.5.1-1
Treatment/3.1.3-1
KEVINK.CONNELL
GRACIELARAMÍREZTOROANDHARVEY
2.5.2 GeneralQualityControl/2.5.2-1
MINNIGH
ROBINK.OSHIRO
3.1.4 EpidemiologicAspectsofWaterborne
2.5.3 QualityControlforBacteriological
InfectiousDisease/3.1.4-1
Analyses/2.5.3-1
SAMUELDOREVITCH
ELLENBRAUN-HOWLAND
3.1.5 WaterborneEntericViruses:Diversity,
2.5.4 QualityControlforVirological
Distribution,andDetection/3.1.5-1
Analyses/2.5.4-1
MORTEZAABBASZADEGANANDABSAR
RICHARDE.DANIELSON
ALUM
2.5.5 QualityControlforUSEPAMethod1623
3.1.6 DetectionofProtozoainSurfaceandFinished
ProtozoanAnalysisandPCR
Waters/3.1.6-1
Analyses/2.5.5-1 ABSARALUM,ERICN.VILLEGAS,SCOTT
GEORGED.DIGIOVANNIANDGREGORY P.KEELY,KELLYR.BRIGHT,LAURA
D.STURBAUM Y.SIFUENTES,ANDMORTEZA
2.5.6 TheRoleofStatisticalThinkingin ABBASZADEGAN
EnvironmentalMicrobiology/2.5.6-1 3.1.7 DrinkingWaterMicrobiology/3.1.7-1
J.VAUNMCARTHURANDR.CARY MARYLYNNV.YATES
TUCKFIELD
3.2 A
IR
2.5.7 StudyDesign/2.5.7-1
YILDIZT.CHAMBERSANDROBINK.OSHIRO 3.2.1 IntroductiontoAerobiology/3.2.1-1
PAULAKRAUTERANDLINDA
2.6 S M
AMPLING ETHODS
D.STETZENBACH
2.6.1 WaterSamplingandProcessing 3.2.2 SamplingforAirborne
TechniquesforPublicHealth-Related Microorganisms/3.2.2-1
Microbes/2.6.1-1 SERGEYA.GRINSHPUN,MARKP.BUTTNER,
VINCENTHILL GEDIMINASMAINELIS,ANDKLAUS
2.6.2 SurfaceSampling/2.6.2-1 WILLEKE
LAURAJ.ROSE,JUDITHNOBLE-WANG,AND 3.2.3 AnalysisofBioaerosolSamples/3.2.3-1
MATTHEWJ.ARDUINO PATRICIACRUZANDMARKP.BUTTNER
2.6.3 SoilSamplingforMicrobialAnalyses/2.6.3-1 3.2.4 FateandTransportofMicroorganismsin
JOHNBROOKS Air/3.2.4-1
2.6.4 MicrobiologicalSamplingofWastewaterand GARYS.BROWNANDALANJEFFMOHR
Biosolids/2.6.4-1 3.2.5 AirborneFungiandMycotoxins/3.2.5-1
NICOLETTEA.ZHOU,ERICC.THOMPSON, DE-WEILI,ECKARDTJOHANNING,ANDCHIN
ANDJOHNSCOTTMESCHKE S.YANG
3.2.6 AirborneBacteria,Archaea,and
Endotoxin/3.2.6-1
PETERS.THORNE,CAROLINEDUCHAINE,
E P H
NVIRONMENTAL UBLIC EALTH ANDPASCALEBLAISLECOURS
M 3.2.7 AirborneViruses/3.2.7-1
ICROBIOLOGY
SYEDA.SATTAR,NITINBHARDWAJ,AND
VOLUMEEDITOR:MARYLYNNV.YATES M.KHALIDIJAZ
SECTIONEDITORS:GARYA.TORANZOS,MARK 3.2.8 AerobiologyofAgricultural
P.BUTTNER,EDTOPP,VALERIEJ.HARWOOD, Pathogens/3.2.8-1
ANDMARYLYNNV.YATES ESTELLELEVETIN
3.1 W 3.2.9 LegionellaeandLegionnaires’
ATER
Disease/3.2.9-1
3.1.1 CurrentandDevelopingMethodsforthe CLARESSAE.LUCASANDBARRYS.FIELDS
DetectionofMicrobialIndicatorsin
3.3 S
OIL
EnvironmentalFreshwatersandDrinking
Waters/3.1.1-1 3.3.1 PathogenicVirusesandProtozoaTransmitted
TASHAM.SANTIAGO-RODRIGUEZ, bySoil/3.3.1-1
JULIEKINZELMAN,ANDGARYA. PASCALDELAQUIS,JULIEBRASSARD,AND
TORANZOS ALVINGAJADHAR
CONTENTS ▪ vii
3.3.2 NaturalSoilReservoirsforHumanPathogenic 4.1.1 PhylogenomicNetworksofMicrobial
andFecalIndicatorBacteria/3.3.2-1 GenomeEvolution/4.1.1-1
MARIALAURABOSCHIROLI,JOSEPH TALDAGAN,OVIDIUPOPA,THORSTEN
FALKINHAM,SABINEFAVRE-BONTÉ,SYLVIE KLÖSGES,ANDGIDDYLANDAN
NAZARET,PASCALPIVETEAU,MICHAEL
4.1.2 EvolutionaryEcologyofMicroorganisms:
SADOWSKY,MURULEEBYAPPANAHALLI,
FromtheTamedtotheWild/4.1.2-1
PASCALDELAQUIS,ANDALAIN
JAYT.LENNONANDVINCENTJ.DENEF
HARTMANN
4.2 A E
QUATIC NVIRONMENTS
3.4 M S T
ICROBIAL OURCE RACKING
4.2.1 TheMicrobialEcologyofBenthic
3.4.1 TheEvolvingScienceofMicrobialSource
Environments/4.2.1-1
Tracking/3.4.1-1
ROBERTH.FINDLAYANDTOMJ.BATTIN
VALERIEJ.HARWOOD,CHARLESHAGEDORN,
ANDMICHAELSADOWSKY 4.2.2 HeterotrophicPlanktonicMicrobes:Viruses,
Bacteria,Archaea,andProtozoa/4.2.2-1
3.4.2 ValidationofMicrobialSourceTracking
JEDA.FUHRMANANDDAVIDA.CARON
MarkersandDetectionProtocols:
4.2.3 AquaticBiofilms:Development,Cultivation,
ConsiderationsforEffective
Analyses,andApplications/4.2.3-1
Interpretation/3.4.2-1
JOHNR.LAWRENCE,THOMASR.NEU,
ASJAKORAJKIC,DONSTOECKEL,ANDJOHN
ARMELLEPAULE,DARRENR.KORBER,AND
F.GRIFFITH
GIDEONM.WOLFAARDT
3.4.3 OverviewofMicrobialSourceTracking
4.3 E E
MethodsTargetingHumanFecalPollution XTREME NVIRONMENTS
Sources/3.4.3-1 4.3.1 TheMicrobiologyofExtremelyAcidic
ORINC.SHANKS,HYATTGREEN,ASJA Environments/4.3.1-1
KORAJKIC,ANDKATHARINEG.FIELD D.BARRIEJOHNSONANDANGELES
3.4.4 MethodsofTargetingAnimalSourcesofFecal AGUILERA
PollutioninWater/3.4.4-1 4.3.2 LifeinHighSalinityEnvironments/4.3.2-1
ANICETR.BLANCH,ELISENDABALLESTÉ, AHARONOREN
JENNIFERWEIDHAAS,JORGESANTO
4.3.3 MicrobialLifeinExtremeLow-Biomass
DOMINGO,ANDHODONRYU
Environments:AMolecularApproach/4.3.3-1
3.4.5 MicrobialSourceTracking:FieldStudy KASTHURIVENKATESWARAN,MYRONT.LA
PlanningandImplementation/3.4.5-1 DUC,PARAGVAISHAMPAYAN,ANDJAMES
JULIEKINZELMANANDWARISHAHMED A.SPRY
3.4.6 FecalIndicatorOrganismModelingand 4.3.4 LifeinHigh-Temperature
MicrobialSourceTrackinginEnvironmental Environments/4.3.4-1
Waters/3.4.6-1 BRIANP.HEDLUND,SCOTTC.THOMAS,
MEREDITHB.NEVERS,MURULEEDHARA JEREMYA.DODSWORTH,ANDCHUANLUN
N.BYAPPANAHALLI,MANTHA L.ZHANG
S.PHANIKUMAR,ANDRICHARDL.WHITMAN
4.4 A -G M
NIMAL UT ICROBIOMES
3.5 M R A
ICROBIAL ISK SSESSMENT
4.4.1 InvertebrateGutAssociations/4.4.1-1
3.5.1 RiskAssessmentFramework/3.5.1-1 DANIELEDAFFONCHIO,ALBERTOALMA,
MARYLYNNV.YATES GUIDOFAVIA,LUCIANOSACCHI,AND
3.5.2 ExposureAssessment/3.5.2-1 CLAUDIOBANDI
SUSANR.PETTERSONANDNICHOLAS 4.4.2 StudyingtheMammalianIntestinal
J.ASHBOLT MicrobiomeUsingAnimalModels/4.4.2-1
3.5.3 Dose-ResponseModelingandUse:Challenges FLOORHUGENHOLTZ,JINGZHANG,PAUL
andUncertaintiesinEnvironmental W.O’TOOLE,ANDHAUKESMIDT
Exposure/3.5.3-1 4.4.3 AnimalGutMicrobiomes/4.4.3-1
MARKH.WEIR RICHARDJ.ELLISANDCHRISTOPHERS.
MCSWEENEY
M E
ICROBIAL COLOGY
B
IODEGRADATIONAND
VOLUMEEDITOR:ROBERTV.MILLER B
IOTRANSFORMATION
SECTIONEDITORS:LARRYJ.FORNEY,ROBERT
H.FINDLAY,BRIANP.HEDLUND,ANDJULIAN
VOLUMEEDITOR:CINDYH.NAKATSU
R.MARCHESI
SECTIONEDITORS:CINDYH.NAKATSUAND
4.1 THEORY CHRISTOPHERRENSING
viii ▪ CONTENTS
5.1 B
IODEGRADATION 5.1.5 ABasicIntroductiontoAerobic
BiodegradationofPetroleumAromatic
5.1.1 GenomicFeaturesandGenome-Wide Compounds/5.1.5-1
AnalysisofDioxin-LikeCompound KENGOINOUE,ONRUTHAIPINYAKONG,
Degraders/5.1.1-1 KANOKASUGA,ANDHIDEAKINOJIRI
MASAKISHINTANIANDKAZUHIDE
5.1.6 EnvironmentalSystemsMicrobiologyof
KIMBARA
ContaminatedEnvironments/5.1.6-1
5.1.2 BiodegradationofOrganochlorine TERRYC.HAZENANDGARYS.SAYLER
Pesticides/5.1.2-1 5.2 B
IOTRANSFORMATION
YUJINAGATA,MICHIROTABATA,
YOSHIYUKIOHTSUBO,AND 5.2.1 BreathingIron:MolecularMechanismof
MASATAKATSUDA MicrobialIronReductionbyShewanella
oneidensis/5.2.1-1
5.1.3 AnaerobicDegradationofAromatic
REBECCAE.COOPER,JENNIFERL.GOFF,BEN
Compounds/5.1.3-1
C.REED,RAMANANSEKAR,ANDTHOMAS
WEIMINSUN,VALDISKRUMINS,DONNA
J.DICHRISTINA
E.FENNELL,LEEJ.KERKHOF,ANDMAX
M.HÄGGBLOM 5.2.2 ExperimentalGeomicrobiology:FromFieldto
Laboratory/5.2.2-1
5.1.4 MicrobialElectrochemicalTechnologies
TIMOTHYS.MAGNUSONANDRHESA
ProducingElectricityandValuableChemicals
N.LEDBETTER
fromBiodegradationofWasteOrganic
5.2.3 MicrobialUsesintheRemediationof
Matters/5.1.4-1
TAEHOLEE,AKIHIROOKAMOTO,SOKHEE Metal-ImpactedSoils/5.2.3-1
JUNG,RYUHEINAKAMURA,JUNGRAEKIM, TIMBERLEYROANEANDMUNIRALANTZ
KAZUYAWATANABE,ANDKAZUHITO
HASHIMOTO Index I-1