Microorganisms in Soils: Roles in Genesis and Functions

425 Pages·2005·5.78 MB·English

by  François Buscot (auth.)

Soil Biology
3
Series Editor: Ajit Varma
Franc¸ois Buscot • Ajit Varma (Eds.)
Microorganisms
in Soils:
Roles in Genesis
and Functions
With71Figures
123
ProfessorDr.AjitVarma ProfessorDr.Franc¸oisBuscot
JawaharlalNehruUniversity UniversitätLeipzig
SchoolLifeScience InstitutfürBotanik
Mol.GeneticsLab. Abt.TerrestrischeÖkologie
NewMehrauliRoad Johannisallee21
110067NewDelhi 04103Leipzig
India Germany
e-mail:[email protected]
and
AmityInstitute
ofHerbalandMicrobialStudies
Sector125
NewSuperExpressHighway
Noida
India
e-mail:[email protected]
LibraryofCongressControlNumber:2004111759
ISSN1613-3382
ISBN3-540-22220-0SpringerBerlinHeidelbergNewYork
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Preface
The inspiration and concept for preparing this volume were conceived
while both of us were sipping a cup of Columbian coffee in the Goethe
Gallery, Jena (Germany). The idea developed that soils are dynamic bio-
logicalsystemsandcertainlynotastaticsubstratethatsupportsthelifeof
microbes,plantsandanimals.Microorganismsplayavitalroleincreating
thisuniverseandmaintaininglifeinit.Dealingwiththeinterrelationships
oforganismsandtherelationshipsbetweenorganismsandtheirenviron-
ment was formerly more or less confined to a small group of specialists
within the scientific community. This has changed in the current sce-
nario. Growing environmental problems have created a public awareness
of the ecological disturbances and dangers related to excessive industrial
expansionand theway of life in“disposablesocieties”. As a consequence
of the perceived importance of ecology, research in this field has devel-
opedrapidly.Asoneofthethreeenvironmentalmediabesideswaterand
air, soils have now become a central concern for a broad range of scien-
tists.
In the golden era of microbiology, the study of soil organisms soon
becameanareaofinteresttoalargenumberofearlybacteriologists,andthe
pioneeringinvestigationsofWinogradsky,Omeliansky,andBeijerinckstill
standasmajorcontributionstoourknowledgeofthebacterialpopulation.
At the same time, it became apparent to soil scientists that the surface
crustoftheearthisnotmerelyastaticphysiochemicalmatrixuponwhich
green plants grow, but also a biological system in a continuous dynamic
equilibrium. In the realm of pure science, information on the ecology,
function, and biochemistry of microflora has grown considerably so that
aclearpictureofsoilbiologyisbeginningtoemerge.
Theinnumerabledevelopmentsinrecentyearsmakeacompletereview
impossiblewithinthescopeofasinglevolume.Someofthemoredetailed
points have been omitted for brevity, yet, where conflicts still exist, con-
trastingviewpointsarepresented. Timemaychangetheseviews,butitis
in the very nature of science to be in a continual state of flux and for the
errors of one generation to be amended by the next. Soil microbiologyis
not a pure discipline. Its parentage may be traced through bacteriology,
mycology, and soil science; biochemistry and plant pathology have also
madetheirmark,especiallyinrecentyears.
VI Preface
Intheframeworkofagriculture,themicrofloraisofsignificanceforman’s
ability to feed himself. For the microbial inhabitant, the soil functions as
auniqueecosystemtowhichtheorganismmustadaptandfromwhichit
mustobtainsustenance.However,inthefinalanalysis,microbiologistscan
find definitive answers as to how these processes are brought about only
throughbiochemicalinquiries.
We have attempted to bring together the major aspects of rhizosphere
researchandprinciplesofrhizosphereecologyforthebenefitofdeveloping
youngscientistsandtechnologies,aswellasfortheestablishedprofessional
researcherandteacher.Aprimeobjectiveandhopeisthatthisvolumemight
generateideasthatwillbringforthnewapproachesandmethodologylead-
ing to further advances in our understanding of rhizosphere interactions
and their implications for agriculture and forestry. Nevertheless, even if
therhizosphereisthecompartmentfromwhichplantsacquiretheirwater
and nutrients and a hot spot of microbial and animal activity, this com-
partmentcanonlybeunderstoodinthecontextofwholesoilfunctioning,
fromsoilgenesistothenutrientcycling,andincludingtheexchangeswith
waterandatmosphere.Theseaspectsthereforeoccupyalargepartofthe
volume.
Referencesareofgreatvaluenotonlytotheresearchworker,buttothe
advancedstudentaswell.Theblindacceptanceofsecondarysourceswhen
primary material is readily accessible is not the hallmark of the serious
student.Whereavailable,reviewsareincludedinthereferencelistsofeach
chaptersothatthefinerpointsofeachtopicmaybesoughtout.Pertinent
originalcitationsarelikewiseincludedsincethesepermitthestudentand
researcheraliketoexaminetheoriginalsource,observethetechniquesuti-
lized,anddrawtheirownconclusions.However,amereliteraturereviewis
notintended,sincemuchgoodworkhasnotbeencited.Wehavedeliber-
atelydrawnuponsomeoldresearchinformation,largelyforthebenefitof
advancedstudentsandyoungscientists,toshowwhereresearchhascome
fromandwhereitmaybegoing.Indoingthis,webelievewehaverevealed
manygapsinourknowledgewhichareyettobefilled.Emphasisisgiven
to the more recent papers, but certain classical works are also included,
particularly where the studies have been of such a nature as to define
a unique approach. It may also be of value to students majoring in other
fields,suchassoilscience,geology,hydrology,plantecology,zooecology,
phytopathology,agronomy,forestry, or the environmental, cropsciences,
naturalsciencemanagement,agriculturalengineering,biologicalsciences,
animalsciences,andlifesciences.
For meaningful contributions to be made in the future, the need for
refinedtechnologyandamultidisciplinarypoolingofexpertisebysoilmi-
crobiologists,phytopathologists,soilphysicistsandchemists,plantphysi-
ologists,andzoologistsshouldbeclearlyevident.
Preface VII
Thepresentationisessentiallyarrangedintosixmainparts.TheIntro-
duction or Part I outlines the definition of soils and dynamics to the mi-
crobialdiversity.PartIIdealswithvariedfunctionsofthemicroorganisms
andsoilgenesis.InPartIII,wehighlightthebiogeochemicalprocesses.The
bioticinteractionsintermsofplant/microorganismsinvolvingsymbiosis
aregiveninPartIV.Functionsofmicrobesinspecificsoilcompartments
are discussed in Part V. Modern tools and techniques to understand soil
biologyareelucidatedinPartVI.
Itishopedthatthegroundworkwillbelaidhereinforafullerenquiry
onthepartofthereaders.Ifthisgoalisachievedeveninpart,thevolume
willhaveserveditspurpose.
Molecularmicrobiologicalstudieshavefocusedourattentioninrecent
times on the characterization of known as well as unknown microbial
speciesimplicatedinsoiltransformationandplantgrowth.
While assuming sole responsibility for any omissions or errors in the
book,wearegratefultoallthoseunselfishindividualswhohavecontributed
tothechapters.Finally,wewouldliketoaskthereadertomakeallowances
for our lack of linguistic proficiency considering that English is not our
mothertongue.
Wearegratefultothemanypeoplewhohelpedbringthisvolumetolight.
WewishtothankDr.DieterCzeschlikandDr.JuttaLindenborn,Springer-
Verlag, Heidelberg for generous assistance and patience in finalizing the
volume.Finally,specificthanksgotoourfamily,immediate,andextended,
notforgettingthememoryofthosewhopassedaway,fortheirsupportor
theirincentive in putting everything together. Ajit Varmain particularis
very thankful to Dr. Ashok K. Chanhan, founder president, An Institute
ofRitnandBalvedEducationFondation(Amity),NewDelhi,forthekind
support and constant encouragement received. Special thanks are due to
myPh.D.studentsMs.RinaKamariandMr.RamPrasadforcompilingthe
subjectindex.
Leipzig,Germany Fran¸coisBuscot
NewDelhi,India AjitVarma
June2004
Contents
Part I Introduction
1 WhatAreSoils? 3
Fran¸coisBuscot
1 Introduction.................................................................. 3
2 SoilGenesis ................................................................... 4
2.1 RockWeatheringorDecay...................................... 4
2.2 ImportanceofSoilTexture...................................... 5
2.3 InputofOrganicMatterintoSoilsandAggregation.... 7
2.4 MigrationProcesses............................................... 8
3 BiogeochemicalProcessesinSoils..................................... 8
3.1 EnergyandCarbon................................................ 8
3.2 NitrogenandPhosphorus....................................... 10
4 BioticInteractionsInvolvingSoilMicroorganisms............... 11
4.1 CompetitionVersusFacilitation............................... 11
4.2 TheExampleofMycorrhizas................................... 12
5 IntegrativeConsiderationsonFunctionsofMicroorganisms
inSpecificSoilCompartments.......................................... 13
5.1 ReleaseofTransgenicOrganismsasaTool
toTraceEffectsofEcologicalDisruptions
onSoilMicroorganisms.......................................... 13
5.2 SoilPollutionbyHeavyMetals
asaMoreComplexDisruption................................ 14
5.3 UnderstandingComplexFunctionalDomains
inSoilHabitats...................................................... 15
6 ConclusionorBacktoBiodiversityofSoilMicrobes............. 15
References............................................................................. 16
2 MicrobialDiversityinSoils 19
Bhoopander Giri, Pham Huong Giang, Rina Kumari, Ram Prasad,
AjitVarma
1 Introduction.................................................................. 19
2 OriginofMicrobialDiversity............................................ 20
X Contents
2.1 OxygenRevolution ................................................ 21
2.2 OriginoftheFirstEukaryotes.................................. 22
3 TypesofSoilMicroorganisms........................................... 22
3.1 Eubacteria............................................................ 24
3.2 Archaebacteria...................................................... 29
3.3 Fungi................................................................... 31
3.4 Algae................................................................... 33
4 MicrobialDiversityandBiologicalSpheres......................... 33
4.1 TheDetritusphere ................................................. 34
4.2 TheDrilosphere.................................................... 34
4.3 ThePorosphere..................................................... 35
4.4 TheAggregatusphere............................................. 35
4.5 TheRhizosphere ................................................... 36
5 MicrobialDiversityandChemicalTransformation............... 37
5.1 NitrogenTransformation........................................ 38
5.2 PhosphorusTransformation.................................... 39
5.3 SulfurTransformation............................................ 41
5.4 IronTransformation.............................................. 42
6 MicrobialDiversityandBioticInteractions......................... 42
7 Conclusion .................................................................... 47
References............................................................................. 49
Part II Microorganisms and Soil Genesis
3 RoleofMicroorganismsinWearDownofRocksandMinerals 59
AnnaA.Gorbushina,W.E.Krumbein
1 RockWeatheringorRockWearDown? .............................. 59
2 CarbonDioxideandRockWearDown............................... 63
3 BalanceofCarbonDioxideSourcesandSinks..................... 68
4 RockWearDownasaPotentialCarbonDioxideSink........... 70
5 TheFractalDimensionofBiologicalRockWearDown......... 71
6 CalciumCarbonateandSilicateWearDown,
DissolutionandPrecipitation
WithSpecialReferencetoBiologicalRockDegradation........ 74
7 Conclusions................................................................... 79
References............................................................................. 80
4 HumificationandMineralizationinSoils 85
GeorgGuggenberger
1 DefinitionsandIntroduction............................................ 85
2 SoilOrganicMatterResources.......................................... 86
Contents XI
2.1 PlantCompounds.................................................. 87
2.2 MicrobialCompounds............................................ 89
2.3 BlackCarbon........................................................ 90
3 MineralizationandHumificationPathways......................... 91
3.1 FactorsAffectingDecompositionandMineralization.. 92
3.2 HumificationProcesses .......................................... 95
4 Conclusions................................................................... 102
References............................................................................. 104
5 ImportanceofMicroorganismsforSoilAggregation 107
Jean-LucChotte
1 Introduction.................................................................. 107
2 EvidenceoftheRoleofSoilMicroorganisms....................... 108
3 MicrobialMetabolitesResponsibleforSoilAggregation ....... 110
3.1 Polysaccharides..................................................... 110
3.2 Glomalin.............................................................. 111
3.3 Lipids .................................................................. 112
4 ManipulationofMicrobiallyMediatedProcesses
toImproveSoilAggregation............................................. 113
4.1 TheRhizosphereMicrobialCommunity.................... 113
4.2 OrganicResidues................................................... 113
4.3 InoculationwithMicroorganisms............................ 114
5 Conclusion .................................................................... 115
References............................................................................. 115
Part III Microorganisms and Biogeochemical Processes in Soils
6 MicrobialEnergeticsinSoils 123
OliverDilly
1 Introduction.................................................................. 123
2 Soil,EnergyandMicroorganisms...................................... 124
3 MicrobialCommunities................................................... 127
4 MicrobialMetabolisminSoil............................................ 129
4.1 Catabolism........................................................... 129
4.2 Anabolism............................................................ 131
4.3 Soil OrganicC, MicrobialC and BiologicalActive C
andInteractionswithN.......................................... 133
5 HolisticApproachestoEvaluateEnergeticStrategies
ofSoilMicrobialCommunities ......................................... 133
6 Conclusions................................................................... 136
References............................................................................. 136
XII Contents
7 RoleofMicroorganismsinCarbonCyclinginSoils 139
EllenKandeler,MichaelStemmer,MartinH.Gerzabek
1 Introduction.................................................................. 139
2 CarbonSources.............................................................. 140
3 SpatialDistributionandProtectionofCarbonSources......... 142
4 SpatialDistributionofSoilMicroorganisms
andTheirActivities......................................................... 143
5 MicroorganismsandEnzymesInvolvedinCCycling ........... 147
6 DynamicsofOrganicMatterDecomposition
inAgroecosystems.......................................................... 148
7 SoilOrganicMatter,Below-GroundProcesses
andClimateChange........................................................ 151
References............................................................................. 153
8 ContributionofBacteriatoInitialInputandCyclingofNitrogen
inSoils 159
LaurentPhilippot,J.C.Germon
1 Introduction.................................................................. 159
2 NitrogenTransformationsintheSoil................................. 160
3 BacteriaInvolvedintheNitrogenCycle.............................. 162
3.1 Nitrogen-FixingBacteria........................................ 162
3.2 Nitrifiers.............................................................. 164
3.3 NitrateReducers,Denitrifiers
andNitriteAmmonifiers......................................... 165
4 NitrogenFluxes.............................................................. 167
4.1 BiologicalNitrogenFixation.................................... 168
4.2 NitrogenMineralization......................................... 169
4.3 Nitrification.......................................................... 169
4.4 DissimilatoryNitrateReductiontoAmmonium......... 170
4.5 Denitrification...................................................... 171
References............................................................................. 172
9 InfluenceofMicroorganismsonPhosphorusBioavailability
inSoils 177
AnnetteDeubel,WolfgangMerbach
1 Introduction.................................................................. 177
2 MicrobialEffectsonRhizodeposition................................ 177
3 MechanismsofMicrobialInfluence
onPhosphorusAvailability............................................... 179
3.1 SolubilizationofCalciumPhosphates....................... 179
3.2 MobilizationofIron-andAluminum-Bound
Phosphorus.......................................................... 181