Molecular Identification, Systematics, and Population Structure of Prokaryotes

327 Pages·2006·5.316 MB·English

by  Erko Stackebrandt (auth.), Professor Dr. Erko Stackebrandt (eds.)

Molecular Identification, Systematics,
and Population StructureofProkaryotes
Erko Stackebrandt (Ed.)
Erko Stackebrandt (Ed.)
Molecular Identification,
Systematics, and Population
Strudure of Prokaryotes
With 56 Figures and 11Tables
~
Springer
PROFESSORDR.ERKOSTACKEBRANDT
DSMZGmbH
MascheroderWeg1b
38124Braunschweig
Germany
E-mail: [email protected]
LibraryofCongress ControlNumber:2005932380
ISBN-IO3-540-23155-2Springer-VerlagBerlinHeidelbergNewYork
ISBN-13978-3-540-23155-4Springer-VerlagBerlinHeidelbergNewYork
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Preface
Oneofthe mostexciting developmentsinbiologyisthe change withinbac-
terialsystematicsthathas transformedadisciplineofdoubtfulimportance
to most scientists into arespecteddiscipline that nowprovides a phyloge-
netic frameworkforotherareas inmicrobiology. Sincethe firstdescription
ofabacterial species 130years ago,it has been the goal ofsystematists to
workwith auniformclassificationsysteminwhichthe genealogyoforgan-
isms provides the underlying basis of classification. Today,the 16SrRNA
genesequencesoftype strainsofthevastmajorityofdescribedspecieshave
beendetermined and have laid the foundations ofa single hierarchic sys-
tem. However,systematicbiologyhas afar wider application than merely
the provision of a reliable classification scheme for new strains. Within
the framework ofthe stabilizinghierarchic system, genomes, non-coding
regions, genes andtheirproductscan nowbe evaluatedin an evolutionary
context.Modificationsinthetempoandmodeoftheevolutionofindividual
markersmayinturnmodifythehierarchicsystem. Systematics,havingleft
its ivory tower,is a dynamic process which isconstantlyprogressing. The
timehas passedin which taxonomic schemeswere outlinedbyafewindi-
vidualsin afewcountries: systematicstodayisaglobal, multi-disciplinary
researchfieldwhichhascaughttheattentionofscientistswhohadneverbe-
lievedthattheywouldfollowwithinterestthe developmentofsystematics.
Microbial ecologists, searching the vast and largely undetected microbial
diversity by using the same molecular methods also in use by systema-
tists) developed an interest in identification and classification. Population
geneticists) searchingfor the spread ofthe causative agents ofdiseases by
molecularmethodscan reflecton the delineationofthe taxon(species)and
willunavoidablyinfluencethe thoughtson conceptsanddefinitions. Clini-
calandenvironmentalmicrobiologistsdevelop anduse DNAmicro-arrays
for rapidbacterialidentification,biosafetyandbiosecurityissues andalso
for diversity assessment. Their technologies will soon be applied by and
further enhancethe power ofsystematics.
Thisbookwillsummarizesomeoftherecentdevelopmentsinthemolec-
ular characterization of cultured and as yet uncultured Archaea and Bac-
teria, emphasisingthe strengthsandweaknessesofindividualapproaches.
Allthese techniques provide masses of molecular data which are retriev-
VI Preface
able from public databases. In contrast, the vast majority of phenotypic
informationonmicroorganismsisnot electronicallyaccessible.Thesedata
areneededfororganismsalreadydescribedandforspeciestobedescribed.
Systematics has not yet reached a state in which prokaryotes are defined
solely on a molecular basis. The Code ofNomenclature requires the de-
position of the type strain of each new species in public collections or
resource centers, making it impossible to describe a handful of genes or
gene products as a new species. Without any doubt, this information is
extremelyusefulasitpoints towards the existenceofnewspecies,possibly
providinginformation about their isolation. Mostimportantly, individual
disciplines havelearned to communicate on a common platform, leading
to anewlyemergingintegrateddiscipline named'systemsbiology'. In this
environment,organismswillbeembeddedinalandscape! ofinformation,
inwhichorganismsemerge aspeaksonatopographicmap.Thedenserthe
informationnetofgenetic and epigenetic information,theclearertheview
onthe pathofevolution ofindividualproperties.Whetherthese peakswill
receivetaxon status willbeopen tothoroughscrutiny.
Thenumberofphyladefined byasyetunculturedstrainsexceedsthose
containingtype strainsofculturedspeciestwo-fold/. Theneglibleincrease
of novel species can be explained by the demanding mode with which
species need to be circumscribed, the high costs involvedin a proper de-
scription, the lack of trained taxonomists, and the directives of funding
bodies not to collect and store diversity on a large scale.The chapters of
this book are compiled to stimulate students to enter the field of bacte-
rial diversity, to spread before them the patchwork carpet of fascinating
multi-faceted disciplines which open the field to ecosystem functioning,
communication within communities, symbiosis, lifein extreme environ-
ments, astrobiology, and more.
Braunschweig,October2005 Erko Stackebrandt
1 The term (landscape' in this context was first introduced to me by Jean Swings
(Gent,Belgium).
2FoxJL(2005)Ribosomalgenemilestonesmet, alreadyleftindust. ASMNews71:6-7
Contents
1 ExcitingTimes:The Challengetobe aBacterialSystematist 1
Erko Stackebrandt
1.1 Introduction 1
1.2 The EarlyHeroes (1860-1900) 3
1.3 TheDawnofMicrobialEcologyandtheContinuingStruggle
with ClassificationSystems(1900-1930)............................. 5
1.4 EncouragementandFrustration (The Era 1930-1950) 7
1.5 Expandingthe Range ofProperties:
The Genetic andEpigenetic Levels(1950-1980)................... 10
1.6 YetAnotherExciting Time:Unravelling the Genealogy(ies)
ofCulturedandAs-YetUnculturedProkaryotes................... 13
References 16
2 DNA-DNAReassociationMethods
Appliedto MicrobialTaxonomyandTheirCriticalEvaluation 23
RamonRossello-Mora
2.1 Introduction 23
2.2 SemanticConsiderations 26
2.3 DNA-DNAReassociationMeasurement,
Parameters andMethods 29
2.4 InterpretationofResultsandthe Boundaries
for SpeciesCircumscription............................................. 39
2.5 TheImpactofDNA-DNAHybridizationsontheConception
ofaSpeciesandChanges inthe Conceptand/orthe Definition 42
2.6 Epilogue........................................................................ 44
References 46
3 DNAFingerprintingTechniquesAppliedto theIdentification,
TaxonomyandCommunityAnalysis ofProkaryotes 51
RudigerPukall
3.1 Introduction 51
3.2 DNATypingMethods...................................................... 53
VIII Contents
3.2.1 DNATypingMethods Targetingthe WholeGenome
ofaBacterialStrain 53
3.2.2 DNATypingMethods TargetingGeneClusters
(Operons) . ... . 60
3.2.3 DNATypingMethods Targetingthe 16SrRNAGene... 64
References 71
4 Multiple LocusVNTR(VariableNumberofTandem Repeat)
Analysis 83
Gilles Vergnaud, ChristinePourcel
4.1 Introduction 83
4.2 MLVAOrigins................................................................. 83
4.3 MLVASet-up and Enrichment........................................... 84
4.3.1 Evaluationofthe Potential InterestofMLVA
foraGivenSpecies................................................. 85
4.3.2 MLVAValidation................................................... 86
4.3.3 DataManagement 87
4.4 ExistingFirst-generationMLVAAssays.............................. 88
4.4.1 Mycobacterium tuberculosis 91
4.4.2 Bacillusanthracis 93
4.4.3 Yersiniapestis....................................................... 94
4.4.4 Brucellasp. 95
4.4.5 Legionellapneumophila.......................................... 97
4.4.6 OtherBacteria....................................................... 97
4.5 Validatingand AnalysingMLVAData................................. 97
4.6 MLVAComparedto OtherMethods 100
References 101
5 BacterialPhylogenyReconstructionfrom MolecularSequences 105
ShigeakiHarayama, Hiroaki Kasai
5.1 Introduction 105
5.2 SpeciesDefinition 106
5.3 Bacterial Diversity 108
5.4 Phylogenetic AnalysisBasedon 16SrDNASequences 110
5.5 Phylogenetic AnalysisBasedon ProteinSequences 115
5.5.1 SelectionofTargetProteins 115
5.5.2 DesignofPCRPrimersforthe Amplification
ofProtein-encodingGenes:ACaseStudywithgyrB 121
5.6 Limitations in ReconstructingPhylogenetic Trees 126
5.7 Conclusion and Future Perspective 129
References 131
Contents IX
6 IntegratedDatabasing and Analysis 141
LueVauterin, Paul Vauterin
6.1 Introduction 141
6.2 Classes ofData 142
6.3 CharacterType Data 143
6.3.1 Definition 143
6.3.2 DataTransformation 145
6.3.3 ClusterAnalysis ofCharacterType Data 149
6.4 FingerprintType Data 149
6.4.1 Definition 149
6.4.2 PreprocessingofFingerprintData 150
6.4.3 ComparisonofFingerprintData 161
6.4.4 FingerprintTechniques
ThatRequire Special AnalysisMethods 172
6.5 SequenceType Data 174
6.5.1 Definition 174
6.5.2 AssemblingSequencerTrace Files
into Consensus Sequences 174
6.5.3 AlignmentofSequences 175
6.5.4 MultipleAlignment 179
6.5.5 PhylogeneticClustering 180
6.5.6 Multi-locusSequenceTyping 180
6.6 MatrixType Data 183
6.7 TrendType Data 184
6.8 Two-dimensionalGelType Data 186
6.8.1 Analyzing2DGels 188
6.9 The IntegratedDatabase 189
6.9.1 DistributedDatabases andPortabilityofData 189
6.10 HierarchicalClusterAnalysis 192
6.10.1 Similarity- or Distance-basedClusteringTechniques .. 192
6.10.2 PhylogeneticClusteringMethods 198
6.10.3 MinimumSpanningTrees 198
6.11 Consensus GroupingandClassification 203
6.11.1 ConcatenationofDataSets 205
6.11.2 AveragingResemblance Matrices 205
6.11.3 Consensus Trees 208
6.12 Erroron Dendrograms 208
6.12.1 DegeneracyofDendrograms 210
6.12.2 Dealingwith DendrogramDegeneracies 212
References 214
x
Contents
7 AssessmentofMicrobialPhylogeneticDiversity
Basedon EnvironmentalNucleicAcids 219
Josh D. Neufeld, William ~ Mohn
7.1 Introduction 219
7.2 MicrobialPhylogeneticsandthe 16SrRNAGene 220
7.3 16SrRNAandthe Environment 222
7.4 MolecularMethodologyin MicrobialEcology 224
7.5 GeneralConsiderationsofBias 228
7.6 PhylogeneticAssessmentofEnvironmentalNucleicAcids 232
7.7 Fingerprinting 233
7.7.1 DenaturingGradientGelElectrophoresis 234
7.7.2 TemperatureGradientGelElectrophoresis 235
7.7.3 Single-strandedConformationalPolymorphism 236
7.7.4 TerminalRestriction FragmentLength Polymorphism 236
7.7.5 RibosomalIntergenicSpacer Analysis 237
7.7.6 AdditionalConsiderations 238
7.8 Sequencing 239
7.8.1 16SrRNAGene Libraries 239
7.8.2 Serial Analysis ofRibosomalSequenceTags 241
7.9 Metagenomics 242
7.10 ArrayTechnology 243
7.11 CompositeMethodologies 245
7.12 Conclusion 246
References 247
8 MetagenomeAnalyses 261
Frank OliverGlockner, AnkeMeyerdierks
8.1 Introduction 261
8.2 ConstructionandScreeningofMetagenome Libraries 264
8.2.1 SmallandLargeInsertLibraries 265
8.2.2 High-capacityVectors:Cosmids, Fosmidsor BACs? 265
8.2.3 LibrarySize 267
8.2.4 IsolationandPurificationofHMWDNA 268
8.2.5 ConstructionofLarge InsertMetagenomic Libraries .. 269
8.2.6 Storage ofMetagenomicLibraries 270
8.2.7 ScreeningofMetagenomicLibraries 271
8.2.8 SequencingofLargeInsertConstructs 272
8.3 SequenceAnalysis 273
8.3.1 MarkerGenes 273
8.3.2 End-Sequences 275
8.3.3 Cosmids, Fosmidsor BACs 276
8.4 Summary,PitfallsandOutlook 280
References 281
Contents XI
9 DNAMicroarraysfor BacterialGenotyping 287
Ulrich Nubel, Markus Antwerpen, BirgitStrommenger,
Wolfgang Witte
9.1 Introduction 287
9.2 TechnicalPrinciples 288
9.3 Applications 290
9.3.1 ComparativeGenome Hybridization 290
9.3.2 DiagnosticDetectionofVirulence Genes 295
9.3.3 DiagnosticDetectionofResistance Determinants 296
9.3.4 Multi-locus Sequence TypingbyHybridization 298
9.3.5 CompositeGeneDetection
for EpidemiologicalTyping 299
9.3.6 DetectionofGenesAssociated
with Metabolic Functions 301
9.3.7 PhylogeneticIdentification 303
9.3.8 Random HybridizationFingerprinting 304
9.4 PresentLimitationsandFuture Prospects 305
References 306
SubjectIndex 315