Plant Microbiome Paradigm

312 Pages·2020·5.591 MB·English

by  Ajit Varma, Swati Tripathi, Ram Prasad

Ajit Varma
Swati Tripathi
Ram Prasad  Editors
Plant
Microbiome
Paradigm
Plant Microbiome Paradigm
(cid:129) (cid:129)
Ajit Varma Swati Tripathi Ram Prasad
Editors
Plant Microbiome Paradigm
Editors
AjitVarma SwatiTripathi
AmityInstituteofMicrobialTechnology AmityInstituteofMicrobialTechnology
AmityUniversity AmityUniversity
Noida,UttarPradesh,India Noida,UttarPradesh,India
RamPrasad
DepartmentofBotany
MahatmaGandhiCentralUniversity
Motihari,Bihar,India
ISBN978-3-030-50394-9 ISBN978-3-030-50395-6 (eBook)
https://doi.org/10.1007/978-3-030-50395-6
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Contents
1 InteractionofEpiphyllicBacteriawithPlantCuticles. . . . . . . . . . . 1
FilipFuchs,CharlottePetruschke,andLukasSchreiber
2 PlantMicrobiomeandItsImportantinStressfulAgriculture. . . . . 13
BahmanKhoshru,SajjadMoharramnejad,
NahidHosseinzadehGharajeh,BehnamAsgariLajayer,
andMansourGhorbanpour
3 Plant-MicrobeInteractions:ApplicationsforPlant-Growth
PromotionandInSituAgri-wasteManagement. . . . . . . . . . . . . . . 49
AnuKaliaandJayeshSingh
4 Plant-Microbe-MetalInteractions:ABiochemicalandMolecular
AnalysisforPhytoremediation. . . . . . . . . . . . . . . . . . . . . . . . . . . . 71
NamrataBudhiraja,PriyanshiSrivastava,SakshiAgrahari,
DivyanshuShukla,BhawnaMudgil,ShikhaSaxena,RajeshDahiya,
andSiddharthVats
5 EcosystemDiversityasaFunctionofPlantandSoil-Microbe
Interactions. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 93
SanjuktaDey,SoumaryyaBhattacharyya,
andRabindranathBhattacharyya
6 PlantGrowth-PromotingPotentialsofEndophyticFungi
fortheManagementofAgriculturalCropsandGrasses. . . . . . . . . 105
SivaSundaraKumarDurairajan,SuchitraRakesh,
BarkaviDurairajan,KaushikRajaram,NagarathinamArunkumar,
andRajeshJeewon
7 BiologicalControlofPlantDiseases:Opportunities
andLimitations. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 121
AkankshaSingh,VipinKumarSingh,AbhishekKumarDwivedy,
Deepika,ShikhaTiwari,AwanindraDwivedi,
andNawalKishoreDubey
v
vi Contents
8 CircadianRedoxRhythmsPlayanImportantRole
inPlant-PathogenInteraction. . . . . . . . . . . . . . . . . . . . . . . . . . . . . 147
SnigdhaTiwari,SiddarthN.Rahul,AlkaSehrawat,andBeenaRawat
9 RhizosphericMicroorganismsfortheRemediation
ofContaminantsforEcologicalRestoration. . . . . . . . . . . . . . . . . . 163
AshitaRai,JyotiFulekar,andM.H.Fulekar
10 TheRhizosphereMicrobiome:MicrobialCommunitiesandPlant
Health. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 175
SandeepJain,JyotiJain,andJayeshSingh
11 OnthePossibilityofAcceleratingSuccessionbyManipulating
SoilMicroorganisms. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 191
VirgilIordache
12 CompositionandDynamicsofMicrobialCommunitiesinFly
Ash-AmendedSoil. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 231
AyushiVarshney,SumedhaMohan,andPraveenDahiya
13 MolecularInsightintoPlant-FungalPathogenInteraction:
EmergingTrendsandImplicationinDesigningClimate-Smart
FieldCrops. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 247
RichaKamboj,ManojNath,BhavnaThakur,TapanKumarMondal,
DeepeshBhatt,andDeepakSinghBisht
14 BiochemicalDynamicsofPlant-MicrobeInteractions. . . . . . . . . . . 267
PriyankaLonakadi,RenittaJobby,NitinDesai,andPamelaJha
15 EndophyticSecondaryMetabolitesforBiologicalControl:
ALatestPerspective. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 293
G.V.S.BhanuPrakashandT.Srinivasan
Chapter 1
Interaction of Epiphyllic Bacteria with Plant
Cuticles
FilipFuchs,CharlottePetruschke,andLukasSchreiber
Abstract Thephyllosphereisoneofthelargestecologicalnichesonourplanet.Itis
formedbytheplantcuticle,whichisahighlyimpermeable,hydrophobicbiopolymer
coveringallprimaryabovegroundplantorgansprotectingthemagainstdesiccation.
Althoughlivingconditionsinthephyllosphereareconsideredharsh,agreatvariety
of microorganisms can live within this habitat. Commensals as well as pathogenic
canbefoundontheplantsurfacecompetingfornichesandrarenutrientsources.It
wasfoundthatthephysicochemicalpropertiesofthecuticlearemodifiedactivelyby
epiphyllic microorganisms. This modification by microorganisms can lead to
enhanced wetting of the leaf surface. This is promoted by the secretion of
biosurfactants by epiphyllic bacteria promoting and as a consequence leaching of
solutesfromtheapoplasttotheplantsurfacecanbeenhanced.
1.1 Introduction
Withtheriseofthelandplantsapproximately500millionyearsago,anewcomplex
and versatile ecological niche appeared, the phyllosphere, consisting of all green
abovegroundpartsofplants.Itisestimatedthatthephyllosphereisapproximatelyas
big as the surface of the whole planet which displays it as the greatest biological
surfaceonearth(KenrickandCrane1997;LindowandBrandl2003).Mostofthis
areaiscolonizedbyadifferentmixtureofmicrobialspecies,predominantlybacteria,
yeast,andfilamentousfungiandtosomeextendprotozoaandevenalgaeandmosses
(Morrisetal.2002;Singhetal.2019).Thedegreeofcolonizationstronglydepends
onvariousfactorsstartingwiththeplantspecies,thehabitatofthehostplant(e.g.,
tropical rain forest, coniferous woodland, or grassland), and the age of the leaf
(Kinkel 1997). Additionally to these rather constant factors, the phyllosphere and
itsinhabitantsareaffectedbyrapidlychangingclimaticconditionssuchastemper-
ature, humidity, and irradiation. Over the course of a day or with fast changes of
F.Fuchs·C.Petruschke·L.Schreiber(*)
InstituteofCellularandMolecularBotany(IZMB),UniversityofBonn,Bonn,Germany
e-mail:s6fi[email protected];[email protected];[email protected]
©SpringerNatureSwitzerlandAG2020 1
A.Varmaetal.(eds.),PlantMicrobiomeParadigm,
https://doi.org/10.1007/978-3-030-50395-6_1
2 F.Fuchsetal.
Fig.1.1 Schematicviewonleafcrosssectionandsurface:bacterialconglomeratespreferentially
settling above cell-cell junctions and at the base of trichomes. Stomata may serve as possible
infiltration sites for pathogenic microorganisms. Arrows (blue and red) indicate the potential
exchangeofmolecules(water,irons,sugars,hormones)betweenbacteriaandleavestakingplace
acrosstheplantcuticle.Intheupperrightpartofthescheme,amagnifiedbacterialcellproduces
extrapolymericsubstanceswhichtogetherwithmotilityarecrucialforsurvivalinthephyllosphere
weatherconditions,thosefluctuationsarerapidlyfollowedbychangesinthedensity
and number of microorganisms colonizing the leaf surface (Leben 1965). Bacteria
aredominatingthephyllospherebyfarinbothnumberanddiversitywithupto106–
107 bacteria per cm2. It is assumed that 96% of those bacteria live as commensals
withnoeffectontheirhostplants’healthorfitness,whereas2%arebelievedtobe
pathogens, and another 2% can be referred to as plant growth-promoting bacteria
(PGPB) (Lindow and Leveau 2002). These PGPBs could contribute to the overall
fitnessoftheirhostplantsbyinducingsystemicresistance,activelyproducingplant
growthhormonessuchasauxin,orsuppressingpathogensbyproducingantimicro-
bial compounds (Brandl et al. 1996; Vorholt 2012; Prasad et al. 2015). The most
abundant forms of colonization in the phyllosphere are biofilms or aggregates on
hydrophobicleafsurfaces(LindowandLeveau2002).Thevastmajorityofbacterial
cells on leaves are clustered and embedded in extra polymeric substances (EPS),
covering as a thin layer the outer surface of the plant cuticle, preferentially above
cell-celljunctionsoratthebaseoftrichomes(Fig.1.1)(MonierandLindow2004).
The cuticular membrane (CM) is a lipophilic, extracellular biopolymer covering
outerepidermalcellwallsofleavesandfruitswhichareexposedtotheatmosphere
(Schönherr 1982). The cuticle was the evolutionary answer to the biggest problem
plants hadtofacewhen theyconqueredlandhabitats:desiccation.Ononesidethe
greatly enlarged surface area of plants results in a more efficient absorption of
photosyntheticactiveradiation(PAR)andpromotesarapidgasexchangeofcarbon
dioxide and oxygen; on the other side, due to an ubiquitous gradient in water
potential between atmosphere (low) and leaf (high), a bigger surface is coercively
connectedwith anincreaseinwaterloss(SchreiberandSchönherr2009).TheCM
1 InteractionofEpiphyllicBacteriawithPlantCuticles 3
serves as an efficient transport barrier for the passive diffusion of water and ulti-
matelyprotectstheplantfromrapiddesiccation(Schönherr1982).
In the past the main focus of research in plant microbe interaction was dealing
withthehiddenhalfofplants,theso-calledrhizospherewhereuptakeandallocation
ofwateraswellasmineralsbytheplantrootsystemtakeplace(Varmaetal.2019,
2020). A tremendous amount of plant/microbe interactions is taking place in the
rhizosphere (Hiltner 1904; Whipps 2001; Prasad et al. 2020). In recent years
microbiologyofthephyllospheregainedincreasingsignificance,anditisnolonger
neglected. To describe and understand the underlying mechanisms in water and
solutetransportwithinthephyllosphereandtheentanglementofplantandmicrobe
physiology, combining classical plant ecophysiology with microbiological
approachesrepresentthemainresearchquestionsinthisfield.
1.2 The Hydrophobic Plant Cuticle as Interface Between
Epiphyllic Bacteria and Plants
The bulk of terrestrial biomass is produced by plants via photosynthesis
(GroombridgeandJenkins2002).Toimproveefficiencyacommontrendinevolu-
tionistheenlargementofsurface area, whichultimately leadstotheriseofspatial
twodimensionalleafsstructuresasweknowthemtoday.Thesuccessoflandplants
goesalongwiththeirabilitytoprotectthemselvesfromdesiccation.Thisisensured
bytheplantcuticlewhichcoversallprimaryabovegroundplantorgans(Schönherr
1982).Thecuticleisanextracellularlipidpolymerofhydroxyfattyacids,whichare
esterified and in addition often linked by ether bonds and direct carbon–carbon
bondsbetweenthemonomers(Pollardetal.2008;Villenaetal.1999).Additionally
polysaccharideslikecelluloseandpectinscouldbedetectedwithintheCM,mainly
at the inner side of the CM facing the primary epidermal cell wall. There they are
emanatingfromtheepidermalcellwallintothecutinpolymerandthuscontributeto
thestructureoftheCMoritsattachmenttothecellwall(Guzmanetal.2014;Segado
etal.2016).Ithasbeensuggestedthatthesepolarpolymersformaqueouspathsof
transport within the lipophilic cutin polymer thus promoting the diffusion of polar
and charged solutes and ions across the CM (Schreiber and Schönherr 2009).
Togetherwithintracuticularandepicuticularwax,thecutinpolymerformsahydro-
phobichighlyimpermeablebarrier(Tukey1970;Schönherr1982).Cuticularwaxes
are diverse in their chemical composition (Buschhaus and Jetter 2011) consisting
mainly of two fractions namely monomeric linear long-chain aliphatic compounds
andpentacyclictriterpenoids.Thosewaxesaresolidandpartiallycrystallineatroom
temperature(ReynhardtandRiederer1994).Duetothishighlyorderedstructureof
cuticular waxes on the molecular level, they seal the plant cuticle and make it not
only the main barrier for passive diffusion of water into the atmosphere but also
hinder dissolved organic and inorganic solutes to pass (Schreiber and Schönherr
2009).Whereaswaxesareresponsibleforestablishingthediffusionbarrier,thecutin
polymer serves as a stable matrix for wax deposition (Kolattukudy 1984; Nawrath
4 F.Fuchsetal.
2006). Epicuticular waxes on the surface can form different kinds of three-
dimensional structures such as scales, platelets, and spikes depending on their
diversechemicalcompositions(Barthlottetal.1998).Thesemicroscopicstructures
inthenanometerrangesignificantlyincreasetheleafsurfaceroughnessandconse-
quently impede the attachment of bacteria, fungal spores, and other microscopic
invaders. The increased roughness also promotes the self-cleaning “lotus effect,”
whenwaterdropletscannotattachtoaleafsurfaceandrollofftheleaftakingdust
particles with them (Barthlott and Neinhuis 1997). However, with increasing leaf
age,thesurfaceroughnessdecreasesduetoerosionoftheepicuticularwaxcrystals,
and roughness becomes less decisive for the attachment of epiphyllic microorgan-
isms(NeinhuisandBarthlot1998).Theprevalentconditionsontheleafsurfaceare
aridity, lack of nutrients, and rapidly changing temperatures. Due to these circum-
stances,thephyllosphereisconsideredanuninvitingandharshhabitatformicroor-
ganisms. To cope with these various stresses, bacteria evolved different strategies
suchasgrowingasabiofilmorproducingbiosurfactants.Biofilmsarethepredom-
inant form of bacterial living on the planet (Flemming and Wingender 2010). A
biofilmisaconglomerateofbacterialcellssurroundedbyEPSwhichisattachedto
anyinertorlivingsurface.Therearebiofilmsattheinterfaceofasolidphaseandthe
atmosphere or at the interface of a solid and a liquid phase or even between two
liquid phases (Jenkinson and Lappin-Scott 2001). In most cases biofilms harbor
multiple species, in different niches within the biofilm (Xavier and Foster 2007).
There are physiological dependencies between different bacteria but also competi-
tionamongthemmakingabiofilmaverycomplexanddiversehabitatformicroor-
ganisms.Thebulkmassofabiofilmconsistsofextracellularmatrix(ECM),actively
segregated by their inhabitants. The majority of the ECM consists of EPS. Poly-
saccharides as well as extracellular DNA (eDNA) form the largest proportion of
EPS, followed by proteins and various lipid compounds, mostly phospholipids or
lipopolysaccharides (Branda et al. 2005). This highly hydrated periphery forms a
slimymatrixinwhichthebacterialcellsareembedded.Thebiofilmlifestyleonaleaf
surfacehasmanyadvantagesfortheirinhabitants.ThehydratedECMpreventsthe
bacteria from desiccation and can serve as a sink for toxic metabolites. In case of
starvation, some components can be used as carbon or energy source (Sutherland
2001). Pigments can accumulate in the ECM protecting the bacteria from strong
irradiation,andadditionallythebiofilmdisplaysacertainprotectionagainstgrazing
protozoa (Flemming and Wingender 2010). Biofilm formation often starts with
singlemotilebacteriapropagatedbywindandrainsplash(Lindow1996).Theinitial
interaction between a bacterial cell and a surface is defined by the cell surface
hydrophobicity, nonspecific van der Waals, and electrostatic forces. This loose
contact is reinforced by surface/host-specific adhesins, located on the cell surface
or on bacterial appendages such as pili and fimbriae (Romantschuk 1992; Vorholt
2012).Thisresultsintheirreversibleattachmentofthebacterialcelltothesurface.
Onceabacterialcellhassuccessfullyattachedtotheleafsurface,itstartsmultiplying
and forms small aggregates or microcolonies embedded in EPS. Those aggregates
growandeventuallyfusewithothercellaggregatestoformamaturebiofilm(Ramey
etal.2004).Thefinal,yetimportantstageofbiofilmdevelopmentisthedispersalof
pioneercells.Single“swarming”cellsdetachfromthebiofilmandactivelymoveto