Microbial Environmental Genomics (MEG)

370 Pages·2023·13.914 MB·English

by  Francis Martin, Stephane Uroz

Methods in
Molecular Biology 2605
Francis Martin
Stephane Uroz Editors
Microbial
Environmental
Genomics (MEG)
Second Edition
M M B
ETHODS IN OLECULAR IO LO GY
SeriesEditor
JohnM.Walker
School of Lifeand MedicalSciences
University ofHertfordshire
Hatfield, Hertfordshire, UK
Forfurther volumes:
http://www.springer.com/series/7651
For over 35 years, biological scientists have come to rely on the research protocols and
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Microbial Environmental
Genomics (MEG)
Second Edition
Edited by
Francis Martin
Tree-Microbe Interact (IAM); Biogeochem, UMR1136 INRA/University of Lorraine, Labex ARB,
Champenoux, France
Stephane Uroz
Université de Lorraine, INRAE, UMR1136 “Interactions Arbres-Microorganismes”,
F-54280 Champenoux, France; INRAE, UR1138 “Biogéochimie des écosystèmes forestiers”,
F-54280 Champenoux, France; INRAE, USC1371 “Labex ARBRE”, F-54280 Champenoux, France
Editors
FrancisMartin StephaneUroz
Tree-MicrobeInteract(IAM); Universite´deLorraine,INRAE,UMR1136
Biogeochem “InteractionsArbres-Microorganismes”
UMR1136INRA/University F-54280Champenoux,France
ofLorraine,LabexARB
INRAE,UR1138“Bioge´ochimiedes
Champenoux,France
e´cosyste`mesforestiers”
F-54280Champenoux,France
INRAE,USC1371“LabexARBRE”
F-54280Champenoux,France
ISSN1064-3745 ISSN1940-6029 (electronic)
MethodsinMolecularBiology
ISBN978-1-0716-2870-6 ISBN978-1-0716-2871-3 (eBook)
https://doi.org/10.1007/978-1-0716-2871-3
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Preface
While we raise the head to look at the sky to discover new planets and new stars, and
potential new forms of life, we are far to have characterized the full diversity of organisms
livingonEarth,theirfunctions,andtheirrelativerole.Eachyearnewspeciesarediscovered,
including macro-organisms, and many scientists wonder if we may lose species before we
even know that they existed. Determining the exact number of species is still a scientific
challengeandparticularlyforsmall-sizemicrobiotamembers.Betheyconsideredasextreme
ornot,nearlyalltheenvironmentsofourplanetareinhabitedbymicroorganisms,andmost
oftheseenvironmentsallowedfortheidentificationofnewspecieswithparticularfunctions.
Onemaywonderwhyitisimportanttoinventorythediversityofthebiosphere.Character-
izing this biodiversity is essential as all the organisms are part of our environment and
participate in ecosystem functioning, homeostasis, and in the services they provide. They
also represent for many of them a fundamental part, an extension, of the macro-organism
functioning.Indeed,itisnowclear thathuman,animal,orplantdevelopment;physiology;
and adaptation involve their associated microbiota. By adapting to their local environment
andchangingconditions,microorganismshavedevelopedparticular functionsandevolved
in different ways. Characterizing this evolution through the analysis of the genomic and
biochemical resources permits to investigate the continual evolution cycle, to understand
thekeysteps,andtopredictscenariosaccordingtoactualandfutureenvironmentalchanges.
Characterizing the functions of these microorganisms also permits to elaborate on the
phenomenaofconvergentanddivergentevolutionaswellasonthefunctionalredundancy,
but also on the relative role of these microorganisms and on their potential use. In the
presentenvironmentalandenergetictransitionsthatarefacingoursocieties,environmental
resources and microorganisms represent new options to develop environmental friendly
bioprocesses and biomolecules. At the same time, it is essential to understand how these
microorganismsadapttorapidlychangingconditions(i.e.,climatechange,fertilisation).It
is so essential to understand who they are (i.e., taxonomic identification)? Where they are
distributed(i.e.,fromsmalltolargescales)?Whattheyaredoing(i.e.,functionalcharacteri-
zation)?Withwhomtheyareinteracting(i.e.,complexityintegration)?Andhowtheyadapt
toglobalchanges?
This bookpresentsa seriesof 17chapters to guideresearch inenvironmental microbi-
ologyandgenomicstocharacterizeandimagerareorevenhithertounknowntaxaandtheir
interactions, to identify new functions and biomolecules, and to understand how environ-
mentalchanges(climate,nutrientavailability,drought,urbanization)conditiontheactivity
and the response of the organisms living with us or/and in our environment. Methods to
v
vi Preface
analyze the diversity of different organism types (i.e., archaea, bacteria, fungi, protest,
microfauna, and microeukaryotes) are presented in Chaps. 1, 2, 3, and 4. Notably,
Chap. 4 presents a combined set of methods to survey seed colonizing fungi using both
traditional culture-based methods and culture-free metabarcoding. Chapters 5, 6, and 7
describe methods to produce high-quality DNA adapted to the sequencing technologies
from particular fungi, complex systems, or ancient samples. Chapters 8 and 9 present
methodstoinvestigatethemicrobialcommunitiesdirectlyinvolvedincomplexinteractions
orprocessesthroughstableisotopeprobing(DNA-andRNA-SIP).Methodstoidentifyand
characterizenewfunctionalgenesortaxonomicmarkersarepresentedinChaps.10,11,and
12.Theseincludeprotocolsforgenecapture,fosmidlibraryconstruction,andscreeningas
well as the Tnseq approach. Databases and bioinformatics analysis tools are presented in
Chaps. 13 and 14 (i.e., MAGE and MycoCosm). Methods to investigate complex interac-
tions and image in situ interactions are presented in Chaps. 15, 16, and 17. In situ
hybridization(insituFISH)methodispresentedtoimagefungalendobacteriainChap.15.
By investigating the composition, function, complex interactions, and spatial distribu-
tion of microbiota members in their environment, this book represents a primary research
reference for scientists and lab managers in environmental microbiology working in the
expanding field of environmental microbiology and genomics. The level of presentation is
technicallyadvancedwithastrongemphasisondescribingcutting-edgeprotocolsinlightof
thepossiblefuturedirectionsforresearch.Weanticipateinafutureedition,thepresentation
of microfluidic-based protocols for high-throughput functional screening or to analyse
complexinteractionsaswellastheuseofimagingmassspectrometrytovisualizethespatial
distributionofmetabolitesonthesurfaceofthesamples(e.g.,bacterialor fungalcolony).
Champenoux,France FrancisMartin
StephaneUroz
Contents
Preface ..................................................................... v
Contributors................................................................. ix
1 MetabarcodingApproachesforSoilEukaryotes,Protists,
andMicrofauna..... ....... ........ ....... ....... ........ ....... ........ 1
GuillaumeLentendu,EnriqueLara,andStefanGeisen
2 MetabarcodingoftheThreeDomainsofLifeinAquatic
SalineEcosystems.......... ........ ....... ....... ........ ....... ........ 17
DelphineMelayah,Ze´liaBontemps,MaximeBruto,
Agne`sNguyen,PhilippeOger,andMyle`neHugoni
3 SamplePreparationforFungalCommunityAnalysisbyHigh-Throughput
SequencingofBarcodeAmplicons ..... ..... ...... ....... .. ....... ........ 37
KarinaE.Clemmensen,KatarinaIhrmark,
MikaelBrandstr¨omDurling,andBj¨ornD.Lindahl
4 CharacterizationofSeedMycobiotaUsingCulture-Dependent
andCulture-IndependentApproaches....... ....... ........ ....... ........ 65
GillianE.Bergmann,SabrinaJ.Heitmann,
PosyE.Busby,andJohanH.J.Leveau
5 TissueCultivation,Preparation,andExtractionofHighMolecular
WeightDNAforSingle-MoleculeGenomeSequencing
ofPlant-AssociatedFungi........... ....... ....... ........ ....... ........ 79
LaureFauchery,MaximKoriabine,LillianP.Moore,
YukoYoshinaga,KerrieBarry,AnnegretKohler,andJanaM.U’Ren
6 AnalysisofAncientMicrobialDNA ......... ....... ........ ....... ........ 103
OlivierGorge´,E.AndrewBennett,DiyendoMassilani,
JulienDaligault,Eva-MariaGeigl,andThierryGrange
7 Whole-GenomeSequencingofBacterialEndophytesFromFresh
andPreservedPlantSpecimens ...... ....... ....... ........ ....... ........ 133
BramDanneelsandAure´lienCarlier
8 InvestigatingtheBacterialandFungalCommunitiesInvolved
inDeadBiomassDegradationinForestSoils........ ........ ....... ........ 157
MartinaSˇtursova´,RubenL(cid:1)opez-Monde´jar,andPetrBaldrian
9 StableIsotopeProbing-RNAStrategytoStudyPlant/Fungus
Interactions .... .... ....... ........ ....... ....... ........ ....... ........ 169
AmandineLeˆ Van,MarieDuhamel,AchimQuaiser,
andPhilippeVandenkoornhuyse
10 Targeted16SrRNAGeneCapturebyHybridization
andBioinformaticAnalysis.......... ....... ....... ........ ....... ........ 187
SophieComtet-Marre,OshmaChakoory,andPierrePeyret
vii
viii Contents
11 ConstructionofaTransposonMutantLibraryinthePathogen
AgrobacteriumtumefaciensC58andIdentificationofGenes
InvolvedinGallNicheExploitationandColonization........ ....... ........ 209
MartaTorres,AlmudenaGonzalez-Mula,DelphineNaquin,
andDenisFaure
12 High-ThroughputScreeningofFosmidLibrariesforIncreasedIdentification
ofNovelN-AcylHomoserineLactoneDegradingEnzymes.......... ........ 227
StephaneUrozandPhilippeOger
13 AnalyzingProkaryoticTranscriptomicsintheLightofGenomeData
withtheMicroScopePlatform....... ....... ....... ........ ....... ........ 241
DavidRoche,AlexandraCalteau,andDavidVallenet
14 MycoCosm,theJGI’sFungalGenomePortalforComparative
GenomicandMultiomicsDataAnalyses..... ....... ........ ...... ....... .. 271
StevenR.Ahrendt,StephenJ.Mondo,SajeetHaridas,
andIgorV.Grigoriev
15 InvestigatingEndobacteriathatThriveWithinMucoromycota ....... ........ 293
AlessandroDesiro`,YusukeTakashima,GregoryBonito,Tomoyasu
Nishizawa,KazuhikoNarisawa,andPaolaBonfante
16 ConfocalLaserScanningMicroscopyApproachtoInvestigate
Plant–FungalInteractions........... ....... ....... ........ ....... ........ 325
F.Fracchia,V.Basso,F.Guinet,C.Veneault-Fourrey,andAure´lieDeveau
17 VisualizationofFungiDuringWoodColonizationandDecomposition
byMicroscopy:FromLighttoElectronMicroscopy ......... ....... ........ 337
ArnaudBesserer,ChristopheRose,andAure´lieDeveau
Index ...................................................................... 363
Contributors
STEVENR.AHRENDT • U.SDepartmentofEnergyJointGenomeInstitute,LawrenceBerkeley
NationalLaboratory,Berkeley,CA,USA
PETRBALDRIAN • LaboratoryofEnvironmentalMicrobiology,InstituteofMicrobiologyofthe
CzechAcademyofSciences,Praha,CzechRepublic
KERRIEBARRY • BIO5InstituteandDepartmentofBiosystemsEngineering,TheUniversityof
Arizona,Tucson,AZ,USA
V.BASSO • Universite´deLorraine,INRAE,IAM,Nancy,France
E.ANDREWBENNETT • Universite´ParisCite´,CNRS,InstitutJacquesMonod,UMR7592,
Paris,France
GILLIANE.BERGMANN • DepartmentofPlantPathology,UniversityofCalifornia-Davis,
Davis,CA,USA
ARNAUDBESSERER • Universite´deLorraine,4370EALERMAB,Epinal,France
PAOLA BONFANTE • DepartmentofLifeSciencesandSystemsBiology,UniversityofTorino,
Torino,Italy
GREGORYBONITO • DepartmentofPlantSoilandMicrobialSciences,MichiganState
University,EastLansing,MI,USA
ZE´LIABONTEMPS • Universite´deLyon,Universite´ClaudeBernardLyon1,CNRS,INRAE,
VetAgroSup,UMR5557EcologieMicrobienne,Villeurbanne,France
MAXIMEBRUTO • Universite´deLyon,VetAgroSup,Anses,UMRMycoplasmosesAnimales,
Marcyl’Etoile,France
POSYE.BUSBY • DepartmentofBotanyandPlantPathology,OregonStateUniversity,
Corvallis,OR,USA
ALEXANDRACALTEAU • LABGeM,Ge´nomiqueMe´tabolique,CEA,Genoscope,Institut
Franc¸oisJacob,CNRS,Universite´d’E´vry,Universite´Paris-Saclay,Evry,France
AURE´LIENCARLIER • LIPME,Universite´deToulouse,INRAE,CNRS,Castanet-Tolosan,
France;LaboratoryofMicrobiology,GhentUniversity,Ghent,Belgium
OSHMACHAKOORY • Universite´Clermont-Auvergne,INRAE,MEDiS,Clermont-Ferrand,
France
KARINAE.CLEMMENSEN • DepartmentofForestMycologyandPlantPathology,Swedish
UniversityofAgriculturalSciences,Uppsala,Sweden
SOPHIE COMTET-MARRE • Universite´Clermont-Auvergne,INRAE,MEDiS,Clermont-
Ferrand,France
JULIENDALIGAULT • Universite´ParisCite´,CNRS,InstitutJacquesMonod,UMR7592,
Paris,France
BRAMDANNEELS • LIPME,Universite´deToulouse,INRAE,CNRS,Castanet-Tolosan,
France;CBU,DepartmentofInformatics,UniversityofBergen,Bergen,Norway
ALESSANDRODESIRO` • DepartmentofPlantSoilandMicrobialSciences,MichiganState
University,EastLansing,MI,USA
AURE´LIE DEVEAU • UniversitydeLorraine,INRAE,UMR1136Interactionsarbre
microorganismes,CentreINRAEGrandEst-Nancy,Champenoux,France
MARIEDUHAMEL • Universite´deRennes1,CNRS,UMR6553Ecobio,Rennes,France;
WageningenPlantResearch,BiointeractionsandPlantHealth,Wageningen,The
Netherlands
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