Beneficial plant-bacterial interactions

390 Pages·2020·10.251 MB·English

by  BR Glick

Bernard R. Glick
Beneficial
Plant-Bacterial
Interactions
Second Edition
Beneficial Plant-Bacterial Interactions
Bernard R. Glick
Beneficial Plant-Bacterial
Interactions
Second Edition
BernardR.Glick
DepartmentofBiology
UniversityofWaterloo
Waterloo,ON,Canada
ISBN978-3-030-44367-2 ISBN978-3-030-44368-9 (eBook)
https://doi.org/10.1007/978-3-030-44368-9
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To Rav Avram Hersh Glick,
Born circa 1850, died 1914 (Belz, Austria-
Hungary)
And, to his great-great-great-grandchildren
Benjamin, Aviva and Gabrielle Glick
Born 2009, 2011 and 2014, respectively
(Ottawa, Canada)
Preface
In the past 15–20 years, there has been increasing interest throughout the world in
studies involving plant growth-promoting bacteria (PGPB) and their positive
interactions with plants. This interest is a consequence of the fact that every year
more and more of these bacteria are being used as a component of sustainable
agricultural practice. The interest inusing PGPB isbased onanumber ofdifferent
factors. For example, the increasing world population necessitates that agricultural
output be significantly increased within a relatively short period of time without
depletingourlimitednatural resourcesincluding prime agricultural land. Thus,the
possibility exists that we can partially or even (eventually) completely replace the
excessive use of chemicals (fertilizers, herbicides and pesticides) that are currently
employedinagriculture.
Scientists worldwide have come to a juncture where there is an ever-increasing
understandingofmanyofthefundamentalbiochemicalandgeneticmechanismsthat
areoperativeinplant–bacterialinteractions.Sincepracticaladvancesintheemploy-
mentofthistechnologyaredependentuponthedevelopmentofasolidunderstand-
ing of the fundamental processes involving the interactions between PGPB and
plants, it is clear that we are on the verge of a paradigm shift in agriculture where
wewillsoonutilizethistechnologygloballyonapracticalandlargescale.However,
forPGPBtechnologytodeveloptorealizeitsfullpotential,itisimperativethatthe
fundamentalresearchinthisfieldcontinuesunabated.
Inthepastnumberofyears,there havebeenarelativelylargenumberofbooks
dealingwithvariousaspectsoftheinteractionsbetweenplantsandmicroorganisms
(both bacteria and fungi). Nearly all of these books are compilations of articles
written by various specialists in this field and are almost exclusively intended for
burgeoning practitioners. On the other hand, this book was written to serve as a
textbook(guidebook)foraone-semesterundergraduateorgraduatecourseinplant–
bacterialinteractions.ItisbasedonacoursethathasbeenofferedattheUniversityof
Waterloo for the past number of years and attempts to present a broad, although
admittedlybiased,perspectiveofthisareaofresearch.Thebookassumessomebasic
knowledge of microbiology, plant biology, molecular biology and biochemistry.
Thisnotwithstanding, noteveryonewhouses thisbookwill havehadanextensive
vii
viii Preface
backgroundinallofthesedisciplines.Therefore,thisbookisintentionallywrittenin
a simple, coherent, easy to comprehend jargon-free style in which as much of the
background material as is necessary to understand the major concepts is provided.
Thebookshouldthereforebeusefultoanyone,includingthenon-specialist,whois
interestedindevelopingarelativelybroadfundamentalperspectiveonplant–bacte-
rialinteractions.
Waterloo,ON,Canada BernardR.Glick
Acknowledgements
Individual chapters of this book were reviewed by the following scientists
(in alphabetical order): Drs. Olubakola Babalola (South Africa), Zhenyu Cheng
(Canada), Cinzia Forni (Italy), Eloise Foo (Australia), Elisa Gamalero (Italy),
Jennifer Mesa (Spain), Francisco Nascimento (Portugal) and Gustavo Santoyo
(Mexico). Their comments and criticisms were extremely useful in making the
manuscript as error free as possible. While their input is highly appreciated, any
remainingerrorsormisunderstandingsareentirelymyfaultandresponsibility.
ix
Contents
1 IntroductiontoPlantGrowth-PromotingBacteria. . . . . . . . . . . . . 1
1.1 TheProblem. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1
1.2 PossibleSolutions. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4
1.3 PlantGrowth-PromotingBacteria. . . . . . . . . . . . . . . . . . . . . . . 5
1.3.1 OrganismsinSoil. . . . . .. . . . . . . . . .. . . . . . . . . .. . 7
1.3.2 RootExudation. . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8
1.3.3 EffectofPGPBonPlants. . . . . . . . . . . . . . . . . . . . . . 10
1.4 PGPBMechanisms. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16
1.5 ScreeningforNewPGPB. . . . . . . . . . . . . . . . . . . . . . . . . . . . 18
1.6 CommercialInoculants. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 22
1.6.1 CommercialConsiderations. . . . . . . . . . . . . . . . . . . . 23
1.6.2 InoculationMethods. . . . . . . . . . . . . . . . . . . . . . . . . . 24
1.6.3 Large-ScaleGrowthofPGPB. . . . . . . . . . . . . . . . . . . 28
1.6.4 CommercializedInoculantExamples. . . . . . . . . . . . . . 31
Bibliography. .. . . . .. . . . .. . . . .. . . . .. . . . .. . . . .. . . . .. . . . .. 34
2 MicrobiomesandEndophytes. . . . . . . . . . . . . . . . . . . . . . . . . . . . . 39
2.1 Microbiomes. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 39
2.1.1 RootMicrobiome. . . . . . . . . . . . . . . . . . . . . . . . . . . . 42
2.1.2 SeedMicrobiome. . . . . . . . . . . . . . . . . . . . . . . . . . . . 48
2.1.3 SyntheticMicrobiomes. . . . . . . . . . . . . . . . . . . . . . . . 51
2.2 Endophytes. . .. . . .. . . .. . . .. . . .. . . .. . . .. . .. . . .. . . .. 52
2.2.1 EndophyticGenes. . . . . . . . . . . . . . . . . . . . . . . . . . . 52
2.2.2 IsolatingEndophytes. . . . . . . . . . . . . . . . . . . . . . . . . 54
2.2.3 EndophytesandFlowers. . . . . . . . . . . . . . . . . . . . . . . 57
2.2.4 EndophyticFungi. . . . . . . . . . . . . . . . . . . . . . . . . . . . 58
Bibliography. .. . . . .. . . . .. . . . .. . . . .. . . . .. . . . .. . . . .. . . . .. 59
3 SomeTechniquesUsedtoElaboratePlant–Microbe
Interactions. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 63
3.1 Next-GenerationDNASequencing. . . . . . . . . . . . . . . . . . . . . . 64
3.1.1 DNASequencesofCompleteBacterialGenomes. . . . . 64
3.2 ThePolymeraseChainReaction. . . . . . . . . . . . . . . . . . . . . . . . 66
3.2.1 Real-TimePCR. . . . . . . . . . . . . . . . . . . . . . . . . . . . . 68
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xii Contents
3.3 Transcriptomics. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 69
3.3.1 DNAMicroarrayTechnology. . . . . . . . . . . . . . . . . . . 70
3.4 Proteomics. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 73
3.5 Metabolomics. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 76
3.6 CRISPR. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 78
3.7 Imaging. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 79
3.7.1 High-ResolutionScanning. . . . . . . . . . . . . . . . . . . . . 80
3.7.2 LabelingPGPB. . . . . . . . . . . . . . . . . . . . . . . . . . . . . 81
3.8 Microencapsulation. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 85
Bibliography. .. . . . .. . . . .. . . . .. . . . .. . . . .. . . . .. . . . .. . . . .. 88
4 ResourceAcquisition. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 91
4.1 NitrogenFixation. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 91
4.1.1 Cyanobacteria. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 92
4.1.2 Rhizobia. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 95
4.1.3 Free-LivingBacteria. . . . . . . . . . . . . . . . . . . . . . . . . . 100
4.1.4 Nitrogenase. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 101
4.1.5 Nodulation.. . . . . . .. . . . . . . .. . . . . . . .. . . . . . . .. 111
4.1.6 Hydrogenase. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 118
4.2 SequesteringIron. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 122
4.2.1 SiderophoreStructure. . . . . . . . . . . . . . . . . . . . . . . . . 125
4.2.2 SiderophoreBiosynthesisGenes. . . . . . . . . . . . . . . . . 126
4.2.3 RegulationofIronUptake. . .. . . . . .. . . . . .. . . . . .. 128
4.2.4 SiderophoresintheRhizosphere. . . . . . . . . . . . . . . . . 128
4.3 SolubilizingPhosphorus. . . . . . . . . . . . . . . . . . . . . . . . . . . . . 130
Bibliography. .. . . . .. . . . .. . . . .. . . . .. . . . .. . . . .. . . . .. . . . .. 135
5 ModulatingPhytohormoneLevels. . . . . . . . . . . . . . . . . . . . . . . . . . 139
5.1 Auxin. . . .. . . . .. . . . .. . . .. . . . .. . . . .. . . .. . . . .. . . . .. 140
5.1.1 BiosyntheticPathways. . . . . . . . . . . . . . . . . . . . . . . . 143
5.1.2 Regulation. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 148
5.1.3 EffectsonPGPBSurvival. . . . . . . . . . . . . . . . . . . . . . 152
5.2 Cytokinin. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 154
5.3 Gibberellin. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 156
5.4 Ethylene. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 159
5.4.1 EthyleneBiosynthesisandModeofAction. . . . . . . . . 159
5.4.2 ACCDeaminase. . . . . . . . . . . . . . . . . . . . . . . . . . . . 161
5.4.3 EthyleneandNodulation. .. . . .. . . .. . . .. . . .. . . .. 167
5.4.4 EthyleneandPlantTransformation. . . . . . . . . . . . . . . 172
5.5 VolatileOrganicCompounds. . . . . . . . . . . . . . . . . . . . . . . . . . 173
Bibliography. .. . . . .. . . . .. . . . .. . . . .. . . . .. . . . .. . . . .. . . . .. 177
6 BiocontrolofBacteriaandFungi. . . . . . . . . . . . . . . . . . . . . . . . . . 181
6.1 Phytopathogens. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 181
6.2 AllelochemicalsIncludingAntibioticsandHCN. . . . . . . . . . . . 184