Environmental Microbiology: Fundamentals and Applications: Microbial Ecology

933 Pages·2015·31.702 MB·English

by  Jean-Claude Bertrand, Pierre Caumette, Philippe Lebaron, Robert Matheron, Philippe Normand, Télesphore Sime-Ngando (eds.)

Jean-Claude Bertrand · Pierre Caumette
Philippe Lebaron · Robert Matheron
Editors
Philippe Normand · Télesphore Sime-Ngando
Environmental
Microbiology:
Fundamentals
and Applications
Microbial Ecology
Environmental Microbiology: Fundamentals
and Applications

Jean-Claude Bertrand • Pierre Caumette
Philippe Lebaron • Robert Matheron
Philippe Normand • Te´lesphore Sime-Ngando
Editors
Environmental Microbiology:
Fundamentals
and Applications
Microbial Ecology
Editors
Jean-ClaudeBertrand PierreCaumette
InstitutMe´diterrane´en InstitutdesSciencesAnalytiquesetdePhysico-chimiepour
d’Oce´anologie(MIO) l’EnvironnementetlesMate´riaux(IPREM)
UM110,CNRS7294IRD235, UMRCNRS5254,Universite´dePauetdesPaysdel’Adour
Universite´deToulon,Aix-Marseille PauCedex,France
Universite´
MarseilleCedex9,France RobertMatheron
InstitutMe´diterrane´endeBiodiversite´et
PhilippeLebaron d’Ecologiemarineetcontinentale(IMBE)
ObservatoireOce´anologiquedeBanyuls, UMR-CNRS-IRD7263,Aix-MarseilleUniversite´
LaboratoiredeBiodiversite´et MarseilleCedex20,France
BiotechnologieMicrobiennes(LBBM)
SorbonneUniversite´s,UPMCUniv Te´lesphoreSime-Ngando
Paris06,USRCNRS3579 LaboratoireMicroorganismes:Ge´nome
Banyuls-sur-Mer,France etEnvironnement(LMGE)
UMRCNRS6023,Universite´BlaisePascal,
PhilippeNormand ClermontUniversite´
MicrobialEcologyCenter Aube`reCedex,France
UMRCNRS5557/USCINRA1364
Villeurbanne,France
Editors
Jean-ClaudeBertrand
PierreCaumette
PhilippeLebaron
RobertMatheron
PhilippeNormand
Title
E´cologiemicrobienne
Microbiologiedesmilieuxnaturelsetanthropise´s
Publisher/Location
PressesUniversitairesdePauetdesPaysdel’Adour
www.presses-univ-pau.fr
Copyrightyear:2011
Translation
ThecontributingauthorsintheirroleastranslatorsofthechaptersfromFrenchtoEnglish.
Content
Updated(previouslypublishedcontent—intheFrenchtitle—butnowincludes
updatedmaterialand/orsectionsthathavebeenadded)
ISBN978-94-017-9117-5 ISBN978-94-017-9118-2(eBook)
DOI10.1007/978-94-017-9118-2
SpringerDordrechtHeidelbergNewYorkLondon
LibraryofCongressControlNumber:2014956023
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Preface
The average citizen thinks of microbes as dangerous or at least as nasty enemies to her/his
healththatshe/hecannotsee.Theinvisibilitytothenakedeyeisthereasonwhymicrobesare
sopoorlyknown,theirwideactionandimportanceinnaturealmostfullyneglected.Andthis
also has the consequence that they play no or only a subordinate role in the international
conventions for the protection of species. The French born English writer Hilaire Belloc
(1870–1953)putthisdilemmaintoasimplepoemthatstarts:“Themicrobeissoverysmall,
you cannot make him out at all, but many sanguine people hope to see him through
the microscope ...”. There is no doubt, that only a minority of people have the opportunity
todosoandthusthemajoritystaysignorantandcontinuestoharboronlythenegativeimage
ofmicrobes.
Thisbookaboutmicrobialecologywillopentheignoranteyestounderstandandappreciate
theroleandimportanceoftheubiquitous“invisiblemicrobes”innatureaswellasindailylife.
Inthetwenty-firstcentury,withmankindfacingnewthreatslikecontaminationofsoils,rivers,
the oceans, air pollution, global warming, climate change, desertification, newly evolving
diseases,etc.,itisnecessary–morethaneverbefore–toassesstheimportanceofmicrobes,
of their ecological behavior and implication in these processes. A prerequisite for that is a
multi-facetted knowledge of microbes, their diversity, their metabolism, their interactions,
the ecological rules controlling them and the biotopes they inhabit. Tools and methods for
the study of ecological interactions are as necessary as the physicochemical axioms and
mathematics behind them. Ecology is predominantly seen as an outdoor science, but has by
principle two quite different localities of research: Laboratory work is as important as the
study of the sometimes rather inaccessible natural habitats. It is essential for the modern
ecologisttobeascompetentandexperiencedinthefieldasatthelabbench.
The six editors of this book, Jean Claude Bertrand, Pierre Caumette, Philippe Lebaron,
RobertMatheron,PhilippeNormandandTe´lesphoreSime-Ngandoaretobecongratulatedfor
findingsuchaperfectlistofauthorialteams,allverywellknownexpertsinthefield.Thebook
is divided in five parts: “general chapters”, “taxonomy and evolution”, “microbial habitats”,
“roleandfunctioningofmicrobialecosystems”,and“toolsandmicrobialgeneticsappliedto
the environment”, each containing 3–5 chapters, altogether written by 59 authors, of whom
many were involved in more than one chapter. Thirteen chapters are co-authored by one or
moreoftheeditors!Thusandbymeansofmultipleauthorshiptheeditorsmadesurethatthe
book comes out as a single consistent effort, not a collection of more or less divergent
chapters.Asacomprehensivetreatiseitdefinitelyhasachancetobecomeatleastanimportant
referenceandtextbookforgraduateandpostgraduatestudentsinmicrobialecology,butmost
probablyingeneralmicrobiology,too.Textbooksingeneralmicrobiology(withexceptions)
usually put emphasis on metabolism, systematics, structure etc., not on ecology. This book,
however,positionsecologyatthecenterandtheotherfieldsaroundit.Quiteoftenonemisses
themicrobialeukaryotesorvirusesinmicrobialecologybooks.Notinthisone.Thisisanall
microbes embracing effort and therefore constitutes a complete treatise of the field. What is
welcomed andemphasizesthecompletenessofthebookisthatitdevotesonechaptertothe
history of microbial ecology, depicting the development of theories, increase of knowledge,
changes in thinking over the centuries towards more modern and global views. In other
v
vi Preface
chapters, historical aspects are also mentioned where necessary. Divergent ideas and
conceptionsarenotsuppressed,butopenlydiscussed,asscientificdisputedemands.
Therefore it will gain the full attention of not only microbial ecologists, but of all
microbiologists who need to modernize their views of ecology. Also plant and animal
ecologists in general should brush up their knowledge on the often neglected part that
microbes play in the global environment. For all who are involved in contamination and
remediationofsoilsandwaters,inwastetreatment,inlandscaping,inmaintenanceofnatural
resorts, food microbiology, biotechnology, phytopathology, medical and veterinarian micro-
biology,thisbookcontainsvaluableinformation.Thistreatiseisrelevantforeveryaspectof
modernmicrobiologyandbelongsintothehandofeverymicrobiologist.
Personswhohavestudiedthisbookthoroughlywillbeabletoappreciatetheprofoundtruth
of Louis Pasteur’s sentence: “Ce sont les microbes qui auront le dernier mot” (“It is the
microbesthatwillhavethelastsay”).
Bonn,Germany HansG.Tru¨per
Acknowledgements
Wearegratefultoallthosewhohelpedustoachievethisbookwhosepublicationhasrequired
theassistanceandcommentsofmanycontributors.
MostoftheillustrationsareduetothetalentofMarie-Jose´eBodiouandVale´rieDomien,
graphicdesignersatAragoLaboratoryinBanyuls-sur-mer,whosecontributionwasindispens-
able to the realization of the work; we wish to thank both very much for all the work
accomplishedwithskillandgoodhumor.
Ourthanksalsogotothefollowingpersonswhowereresponsibleforproofreadingpartsof
thebook,whoexpressedconstructivecriticism,orhelpeduswiththeirskills:MichelGuiliano,
Fortunat Joos, Dominique Lefevre, Louis Legendre, Roland Marmeisse, Danielle Marty,
Gilbert Mille, Fereidoun Rassoulzadegan, Marc Troussellier, Francesca Vidussi, and all
membersoftheGDR“FoodWebs.”
vii

Contents
PartI GeneralChapters
1 TheThematicFieldsofMicrobialEcology. . . . . . . . . . . . . . . . . . . . . . . . . 3
Jean-ClaudeBertrand,PierreCaumette,PhilippeLebaron,
andPhilippeNormand
2 SomeHistoricalElementsofMicrobialEcology. . . . . . . . . . . . . . . . . . . . . 9
PierreCaumette,Jean-ClaudeBertrand,andPhilippeNormand
3 StructureandFunctionsofMicroorganisms:Production
andUseofMaterialandEnergy. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25
RobertMatheronandPierreCaumette
PartII TaxonomyandEvolution
4 ForThreeBillionYears,MicroorganismsWeretheOnly
InhabitantsoftheEarth. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 75
Jean-ClaudeBertrand,Ce´lineBrochier-Armanet,
ManoloGouy,andFrancesWestall
5 SystematicandEvolutionofMicroorganisms:GeneralConcepts. . . . . . . . 107
Charles-Franc¸oisBoudouresque,PierreCaumette,Jean-ClaudeBertrand,
PhilippeNormand,andTe´lesphoreSime-Ngando
6 TaxonomyandPhylogenyofProkaryotes. . . . . . . . . . . . . . . . . . . . . . . . . . 145
PierreCaumette,Ce´lineBrochier-Armanet,andPhilippeNormand
7 TaxonomyandPhylogenyofUnicellularEukaryotes. . . . . . . . . . . . . . . . . 191
Charles-Franc¸oisBoudouresque
PartIII MicrobialHabitats:Diversity,AdaptationandInteractions
8 BiodiversityandMicrobialEcosystemsFunctioning. . . . . . . . . . . . . . . . . . 261
PhilippeNormand,RobertDuran,XavierLeRoux,CindyMorris,
andJean-ChristophePoggiale
9 AdaptationsofProkaryotestoTheirBiotopesandtoPhysicochemical
ConditionsinNaturalorAnthropizedEnvironments. . . . . . . . . . . . . . . . . 293
PhilippeNormand,PierreCaumette,PhilippeGoulas,
PetarPujic,andFlorenceWisniewski-Dye´
10 TheExtremeConditionsofLifeonthePlanetandExobiology. . . . . . . . . . 353
Jean-LucCayol,BernardOllivier,DidierAlazard,RicardoAmils,
AnneGodfroy,FlorencePiette,andDanielPrieur
ix