School of Agriculture, Dev Bhoomi Uttarakhand University, Dehradun – 248007, IndiaIndia
Department of Floriculture & Landscaping, College of Horticulture, Sardarkrushinagar Dantiwada Agricultural University, Sardarkrushinagar – 385506, Gujarat, IndiaIndia
Department of Agriculture, SAM Global University, Raisen, Madhya Pradesh – 462026, IndiaIndia
Agronomy Department, School of Agriculture, Lovely Professional University, Phagwara – 144411, Punjab, IndiaIndia
Department of Sunrise University, IndiaIndia
Department of Shri Khushal Das University, IndiaIndia
Department of Environmental Sciences, Tamil Nadu Agricultural University, Coimbatore – 641003, Tamil Nadu, IndiaIndia
Department of Plant Physiology, Institute of Agricultural Sciences, Banaras Hindu University, Varanasi – 221005, Uttar Pradesh, IndiaIndia
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The hidden diversity of viruses (the “virome”) in plant and soil ecosystems is being uncovered by metagenomic sequencing, revealing many novel viruses in crops, wild plants and microbial hosts. Plant viromes often dominated by RNA viruses can influence disease emergence, host resistance and stress tolerance. At the same time, synthetic microbiomes (laboratory-designed consortia of beneficial bacteria, fungi and other microbes) are being developed to bolster plant defenses and resilience. This review synthesizes current knowledge on plant-associated viromes and engineered microbiomes, focusing on how they reshape plant disease and pest dynamics in the Anthropocene. We first define key concepts: the plant virome, microbiome and synthetic community and outline the scope of their relevance. We describe methodologies for virome detection (including untargeted sequencing and computational virus discovery) and for designing synthetic communities (from isolation to in planta assembly). We examine ecological and evolutionary consequences: for example, how virus reservoirs in wild flora can spill over into crops, how coevolution under stress may convert viruses into mutualists and how tailored microbial consortia can suppress pathogens or affect insect pests. We then discuss potential risks of horizontal gene transfer, ecological imbalance, public acceptance and the evolving regulatory landscape for engineered microorganisms. Finally, we identify knowledge gaps (uncharacterized viral taxa, multi-kingdom community dynamics, long-term field outcomes) and propose research priorities for integrating virome science and microbiome engineering into sustainable agriculture.
Keywords: Viruses; viromes; detection; evolution; pathogens; pests
Theidentificationofvirusesinfectingplantsgoesback tothelate19thcentury.In1886,AdolfMayerdescribed adiseaseoftobaccoandlaterDmitriIwanowski(1892) Viromearethecombinedviralgeneticmaterialinside andMartinusBeijerinck(1898)showedthattobacco anenvironment(here,coupledwithplants). Itcommosaicvirus(TMV)wasanon-bacterial,“contagium prisesvirusesthatinfecttheplantitself(pathogens, vivumfluidum”.ThecrystallizationofTMVbyW.M.Stan- persistentviruses),virusesofplant-associatedmicroorleyin1935confirmedthevirusconceptandgaveriseto ganisms (bacteriophages, mycoviruses) and viruses plantvirology[1,2].The20thcenturysawthediscovery ininvertebratevectors. Mostplantviromesaredomofdozensofplantvirusesandtheemergenceofideas inatedbyRNAviruses(single-anddouble-stranded) likecross-protection(usingmildvirusestosafeguard [14].Manyvirusesare‘cryptic’–theyinfectplantsor crops)[3].Atthesametime,therelevanceofsoiland microorganisms,butwithoutanyevidentsymptoms. rootmicroorganismsbecameclearintheearly20th Viralgroupsthathavebeenrecentlyfound(e.g. new century.However,theconcentrationofmicrobiology phylaofRNAviruses)increasetheknownvirosphere onbacteriaandfungimeantthatplant-associatedmi- enormously. crobiomeswereconceptuallyseparated[4].Theterm “microbiome”(laterappliedtothehumangutflora)and theconceptofaplant“holobiont”(plantwithitsmicroorganisms)weremorewidelyusedinthe21stcentury. Microbialcommunitieswerediversifiedinroot zones(rhizospheres)andleafsurfaces(phyllospheres) impactingplanthealth[5,6].
ThenotionoftheAnthropoceneisthathumanactivity (industrialagriculture,globalcommerceandclimate change)hasprofoundlychangedEarth’secosystems: emergedabout2000[7].DuringtheageoftheGreen Revolutioninagriculture,therewereextensivemonocultures, widespread use of agrochemicals and fast worldwidemovementofcropsandpests. Theseapproacheshaveenhancedagriculturalyields,butalso resultedinsoildegradation,insectinfestationsandclimaticstressonplants[8].Atthesametime,advances insequencingandbiotechnology(around2010s)allowedanunprecedentedexaminationofmicrobialand viraldiversityincropsandwildplants. Inthe2010s, TheAnthropocene(theageofmajorhumaninfluence) researchersstartedtointentionallyassemblesynthetic ischaracterizedbycausessuchasclimatewarming, microbialcommunities(SynComs)toenhanceagricul- habitatfragmentation,monoculturefarming,pesticide turalattributesanddeepsequencingrevealedenor- usageandglobalcommercethathavechangeddisease mousundiscoveredviromesinfarmandnaturalsys- andpestdynamics[20,21].Warmertemperaturesare tems. So,intheAnthropocene,plantpathologyand seeingthespreadofpests.Intensiveagriculturemayreentomologyareinseparablefrommicrobialecology ducethediversityofmicrobiomes.Pestsandillnesses andsyntheticbiology,transformingthewaywethink traveltheworld.Thesechangesinteractwithviromes about andcontrolplant disease andpestdynamics andmicrobiomes,sometimesupsettingecosystems, [9,10]. sometimesprovidingnewoptions(e.g. syntheticso-
Plantmicrobiomeistheaggregateofallmicroorgan- approaches)isaunifyingthemethroughout[22]. ismsassociatedwithplants(bacteria,fungus,archaea, protistsandviruses)thatcolonizeroots,leaves,flowers and seeds. Conceptually it extends to the phytobiome(planthost,relatedorganismsandenvironment).Plantsactivelyaltertheirmicrobiomesviaroot The revolution in plant virome identification via adexudatesandothersignalsandmicrobiomesinturn vancesingenomicsandanalyticshasalsodrivenSynregulateplantnutrition,growthandimmunity.Acore Comdesign.Importantmethodologicalpointsare: areconsistentlypresentinahostplantthroughoutsettings[11,12,13].
Syntheticmicrobiomes(SynComs)arespecificallydesignedcommunitiesofbacteriathatmimicorimprove desiredfunctionalitiesofnaturalmicrobiomes[15,16]. Thesemaybebacteria,fungi,orevenvirusesthathave beenchosenforfeaturessuchastheabilitytosuppress pathogensortoleratestress.SynComdesignmayrely oncoremicrobiomemembersofhealthyplants, on microbialconsortiafoundinsuppressivesoils,oron createdstrains[17].Itistypicallycomparedtostrain bioinoculants(whichmaybeinconsistent);SynComs seeksynergisticstability.Thereviewdealswithplant diseases(causedbypathogenicmicrobes:fungus,bacteria,oomycetes,nematodes,viruses)andpests(herbivoressuchasinsectsandworms).Bothareaffected bymicrobialcommunities[18].Forexample,certain rhizospherebacteriamaygeneratesystemicresistance toinsectherbivoresandvirusescanbespreadbyinsectvectors. Itcoverspestsingeneral,althoughthe mainemphasisisondiseases[19].
lutions). Sustainableagriculture(biologicallybased
ples of plant tissue (leaves, roots, seeds), soil orrhizosphereandinsectvectorsarecollected.
WeextracttotalRNAorDNA.Inviromestudies, enrichmentproceduresareoftenusedforviral particles(e.g. filtration,nucleasetreatmentor 3. dsRNAcapturekits)toincreasethevirussignal [23,24].
• High-throughputsequencing(HTS): Unbiased sequencing is important to virome discovery.
Short-readplatforms(Illumina)areusedtopro- 4. duce large amounts of sequences from whole ordouble-strandedRNAdepletedofrRNA.Completeviralgenomescanbeassembledonlongread technologies (PacBio, Oxford Nanopore).
Librarypreparationbiases: poly(A)-tailenrich- 5. ment procedures will prefer polyadenylated RNA(e.g.many+ssRNAviruses),whereasrRNA depletion or whole RNA kits will catch nonpolyadenylatedviruses(e.g.dsRNAviruses,DNA viruses)[25,26].
Contigsareconstructedfromthesequencereads.
Viral sequences are searched for via similarity todatabases(BLASTversusviralgenomes)and by signature techniques. Tools like VirSorter, VirFinder and deep-learning algorithms (e.g., VirHunter)maypredictinfectiouscontentwithoutclosehomology.Thesetechnologiescanfind wholenewviruses. Also,shortRNA(siRNA)sequencingfromplantsmaybeindicativeofviral infection[27,28].
• Validation by targeted assays: Candidate viruses found by HTS are often confirmed by PCR or ELISA (if antibodies exist), especially Thistableindicatesthatamixofbiologicalandcompufor known viruses. Novel virus genomes may tationalapproachesisnecessarytouncoverthehidden be verified by RT-PCR and Sanger sequencing virome.Ontheotherhand,thebuildingofsyntheticmi- [29,30,31]. crobiomesintegratesbothclassicalmicrobiologyand • Forsyn- modernsystemstechnology. Forexample, deepse-
theticmicrobiomes,traditionalmicrobiologyis quencingmightidentifyvirusesthatarealreadyknown stillused:culturingbacteriaandfungifromplant andnetworkanalysiscouldidentifypossiblemicrobial tissuesorsoilandcharacterizingthem.Isolation partnersforSynComs[58]. isinherentlybiased(manymicrobesareuncultivable),butitallowsfunctionaltesting[32,33]. EcologicalandEvolutionaryImpactsonPlant
Comstypicallyfollowsthesesteps: Plantviromesandmicrobiomeshaveprofoundeffects 1. Sequencing(16S/ITSamplicons,metagenomes) to detect bacteria consistently linked with healthy plants or soils that suppress disease. Thisisthefirststageinthecorememberidentifi- • cationprocess. Thesearethecoreorkeystone speciesandtheyaretheprospectivecontenders tobecomeamemberofSynCom[34].
Choose isolates with beneficial traits (antagonism to pathogens, PGP traits) for the in vitro communitybuildingprocedure.Theyshouldbe cultivatedtogethertoseewhethertheyarecompatibleornot[35].
Greenhousevalidation:Inoculateaxenicordisinfectedplantswiththesyntheticconsortiumto assessthegrowthoftheplants,thesuppression ofillnessesortheirresiliencetostresscompared tothecontrols[36].
Iteration:Changecompositionaccordingtoperformance,addorremovestrains,introducegenetically engineered microorganisms with improved features (e.g. nitrogen-fixing bacteria modifiedbyCRISPR)[37].
Formulationdevelopment(liquid,powder,seed coating) for field application. This is the fifth phaseinscale-uppreparation[38].
• Bioinformatic and modelling tools: DesigningSynComsisaidedbynetworkanalysis(cooccurrencenetworkstofindinteractingpairs), genomemining(topredictmetabolicfunctions) andmachinelearning(topredictstablecombinations). Computationalmodelscansimulate communitystabilityunderdifferentconditions [39].
engineeredmicrobesareused,biocontainment strategies (auxotrophic strains, kill-switch circuits)andecologicalassaysareappliedtominimizerisk[40,41].
Thefollowingtablessummarizerepresentativemethodsandvirustaxa:
EngineeringSyn- DiseaseandPestDynamics
on the ecology and evolution of plant disease and pestsystems[59].Theinteractionscanbebroadlydescribedasfollows: Reservoirsandspillover: Wildplants,weeds and non-crop hosts commonly carry viruses and bacteria that may flow over into agriculturalsystems.Wildfloraarereservoirsforplant
High-throughput Virome Detec- Deep sequencing(Illumina) tion extracts; detects known and novel
Long-readsequencing Virome Detec- Generates long contigs (often full vi- (PacBio/ONT) tion ralgenomes)directly;usefulforcom-
rRNA-depleted total LibraryPrep RemovesribosomalRNAtoenrichvi- RNAseq ral and microbial RNA; broad detec-
Poly(A)-capture RNA LibraryPrep Enriches polyadenylated transcripts; seq catches +ssRNA viruses with poly(A)
dsRNA capture/enzy- Virome Enrich- Enrichesdouble-strandedorviralRNA; maticenrichment ment improvessignalfordsRNAviruses. VANA (Virion- Virome Enrich- Isolates virus particles from extracts Associated Nucleic ment beforesequencing;recoversbothRNA Acids) andDNAviruses.
Virus-specific Validation/DiagnoTsatrigcsetsknownviruseswithprimersor PCR/ELISA antibodies;confirmspresenceinsam-
VirFinder,VirSorter Computational Detectsviralsequencesbysequence
Shotgun metage- Microbialprofil- Whole-communityDNAsequencingto nomics(microbes) ing discoverpotentialbeneficialmicrobes
Biofertilizer formula- Delivery PackagingSynCominoculantsforaption (seed coat, gran- method plication (coating seeds, mixing into ules) soil)tointroducebeneficialconsortia
viruses;forexample,severalsymptomlessinfectionswithvirusessuchasTurnipmosaicvirus (TuMV) or Cucumber mosaic virus (CMV) have beenfoundinweedspeciesborderingagricultural areas. These hidden reservoirs may reinfect crops and influence disease outbreaks. • Pathogensandbeneficialmicroorganismsmay alsotransferacrosswildandcontrolledecosystemswithimplicationsforregionaldiseasepatterns[60,61,62].
• Disease-suppressive microbiomes: Certain soilsorrootmicrobiomesnaturallysuppressparticulardiseases(e.g.take-alldecreaseinwheat, Fusariumwiltsuppression).Thesearesuppres- • sivesoilswithmicrobialcommunitiesthatsupsequencing of total RNA/DNA
viruses; high coverage of small genomes.Shortreadsrequireassemblytorecoverviralgenomes.
plexorrepetitiveviralgenomes;lower throughput.
tion of RNA viruses, especially nonpolyadenylatedtypes.
tails(e.g.Potyvirus),butmissesmany others.
ples;requirespriorknowledge.
Tool signatures(k-mers,genecontent)withoutknownhomology.Usefulfornovel viruses.
(genesforPGPtraits,antimicrobials).
atplanting.
pressdiseasesviacompetition,antibiosisorinducedplantresistance. Syntheticmicrobiome techniques aim at recreating or transplanting suchsuppressivenessbyassemblingimportant microbialtaxa[63,64].
Pathogen helpers and dysbiosis: Not all microorganismsaregoodforplants.Somemaypromoteillness(“pathogenhelpers”),forexample byregulatinghostimmunity,ordeliveringnutrientstoapathogen.Stressorgeneticsmayalter normalmicrobialcontrol,resultinginthedominanceofopportunisticpathogensandadysbiotic(imbalanced)microbiome[65,66,67].
denviromesprovideareservoirofgeneticvari-
Apple (orchard 5rootbacteria+3beneficial SuppressApplereplantdissoil) fungi (e.g. Bacillus, Tricho- ease(ARD)
Maize (drought- 8drought-adaptedbacteria Enhancedroughttolerance, pronefield) (from sugarcane rhizo- yield
Tomato (green- 4 phyllosphere bacteria Suppressbacterialwilt(Ralhouse) (fromhealthytomatoleaves) stonia) Soybean(field) 6 nitrogen-fixers + PGP rhi- Increaseyield,soilNfertility
Cucumber(field) 3antagonistic Pseudomonas ControlFusariumwilt
Rice(seedling) 2 endophytic bacteria with Saltstresstolerance
Wheat(field) Streptomyces + Trichoderma Suppresscommonrootrot
Soybean (green- Mock community of 3 soil Primeimmunesystem(ISR) house) fungi Lettuce (hydro- Yeast+ Bacillus inoculum ponic) Pepper(field) Phage cocktail + beneficial Controlbacterialspot(Xan-
Cotton (saline Salt-tolerantrhizobacteria+ Improvesalttolerance,yield field) mycorrhizalfungi
ety;newviralstrainsorspeciesmayarisewith changedhostrangesorvirulence. RNAviruses havehighmutationratesandrecombination,allowing them to evolve rapidly. In the Anthro- • pocene,hostsareunderheavyselection,with concentratedagricultureandmonoculturesfavoringvirulentstrainssuitedtohomogeneous crops[68,69].
• Mutualistic viruses: Viruses may be advantageous to hosts under certain circumstances. Someplantviruseshavebeenshowntoincrease resistancetodroughtorcold.Ithasbeendemonstratedthatplantssufferingfromdroughtmay generatemutualisticplantvirusesthatimprove hostsurvival.Similarly,mycoviruses(virusesof fungi) may reduce the virulence of fungal diseasesandtherebyprovideefficientprotection • totheplanthost[70,71].
plant microbiome also impacts insect pests.
Volatilesorpoisonsthatrepelherbivoresmay beproducedbyrhizosphereorphyllospheremicrobes.Certainendophyticfungiorbacteria,for example,producesystemicresistancethatlowersinsectfeeding[72].Bycontrast,insectvectors transmitbothplantvirusesandtheirownsym- •
derma)
sphere)
zobacteria
spp.
ACC-deaminaseactivity
consortium
Biofilm formation, nutrient uptake
rhizobacteria thomonas)
bioticbacteria/viruses,thusadesignedmicrobiomeinthevectororplantmight,inprinciple, interferewithtransmission[73,74].
change intensifies these connections. Higher temperatures may boost replication rates of viruses or extend ranges of vectors. Elevated CO2 anddroughtchangerootexudatesandmicrobiota composition [75]. Land-use change (deforestation, intensive tillage) homogenizes soil ecosystems, sometimes resulting in the loss of beneficial bacteria. Global commerce maybringnon-nativeinfectionsintonaïvemicrobiomes, frequently with disastrous consequences(e.g. chestnutblight, citrusgreening, ortomatobrownrugosefruitvirus)[76].
fense: Plantsco-evolvewiththeirmicrobiomes.
Domesticationandbreedinghaveoftentargeted plantimmunitygenes,howeverthereisincreasingevidencethatplantschoosehelpfulbacteria via exudates and immune regulation. Futureplantgenotypesmightbeselectedtoattract more protective microbiomes or to withstand transgenicstrains[77,78].
Inthismodel,plants,pathogens,pestsandmi-
Tobamovirus +ssRNA (non- Tobacco, tomato, Mechanical (sap),
Potyvirus +ssRNA Many crops (e.g. Aphid (non-
Geminivirus(Bego- ssDNA(circular) Tomato, cotton, Whiteflies(Bemisia movirus) legumes, vegeta- tabaci)
Bromoviridae +ssRNA (multi- Cucurbits, stone Aphidsorpollen
Tombusviridae +ssRNA Variouswildplants Mechanical (sap); (Carmovirus/N- (monopar- andcrops(e.g. let- someviabeetles odamovirus) titeorbipartite) tuce,spinach) Tospovirus(Ortho- -ssRNA (en- Vegetables Thrips (Franklintospovirus) veloped) (tomato, pep- iella, Thrips)
Rhabdovirus -ssRNA (en- Several
Caulimovirus dsDNA (with Banana, citrus, Aphids or white- (Pararetrovirus) RNA intermedi- strawberry, brassi- flies
Nanovirus ssDNA (multi- Legumes(e.g.faba Aphids
Endornavirus dsRNA Many
Luteovirus +ssRNA Cereals, legumes, Aphids(persistent)
Benyvirus +ssRNA (multi- Sugar beet, hops, Polymyxa protists
Sobemovirus +ssRNA Cerealcrops,some Insects, possibly
Partitivirus dsRNA (seg- Fungi and plants Seed,pollen(verti-
crobiotaformanetworkofinteractions.Thenativemicrobiomecaninhibitdiseaseandpests, but it can also harbor latent pathogens and viruses. Introducing a synthetic community aimstostrengthenbeneficialinteractions(e.g.
pathogensuppression)anddisruptharmfulones.
Anthropocenefactors(warming,habitatchange) affectallcompartments[79].
Several recent studies illustrate how understanding viromesandusingsyntheticmicrobiomescanreshape planthealthinpractice:
ARDoftenarisesfromtheaccumulationofsoil pathogens in perennial orchards. A synthetic enveloped) cucumber,others seeds
potato virus Y; persistent) cereals;legumes)
bles
partite) fruits,ornamentals
per,beans) crops Aphids veloped) (e.g. maize, rice, lettuce)
ate) cas
component) bean);coconut plants Vertical (grasses,legumes) (seed/pollen)
potato
partite) cereals (soilbornevector)
dicots seeds
mented) (some spores, cal) seeds)
consortiumofbeneficialbacteriaandfungiderivedfromhealthyrhizospheressalvagedplant growth.ApplicationofaSynComof Bacillus, Trichoderma andotherrootcolonizerstoreplanted appleorrosesoilsledtoasignificantdecrease intheseverityofreplantdiseasesymptoms,possiblyasaconsequenceofantagonismof Fusarium and Pythium pathogens.Onestudyshowed thattheincidenceofFusariumwiltwasreduced in greenhouse tests by combining 5–10 rootassociatedbacteriaintoasyntheticmicrobiota (SynMs),providingaproofofconceptofhowconsortiamightbeusedasareplacementforchemicalfumigation[80,81].
cereals: InoculationofmaizefieldswithaSyn- Comisolatedfromsugarcaneenhancedbiomass underwaterstressandstabilizedoutput. Similarly,desiccation-resistantbacterialconsortia enhancedcropgrowthparameters(height,root weight)indroughttests.Insoybeanfieldtests, multi-straininoculantsboostedyieldbyupto 30–40%overcontrolsdemonstratingthatwelldesignedconsortiamaytranslatetoreal-world benefits[82].
• Control of vegetable pathogens: SynComs have been used in plants for defense against soilbornewiltandblight. Forexample, aconsortiumofrhizobacteria(including Bacillus and • Pseudomonas spp.) treated tomato plants reducedthewiltcausedby Ralstoniasolanacearum by generating resistance. In cucumber, foliar sprayapplicationofasyntheticleafmicrobiome mix(fromdiseasesuppressivefields)decreased powderymildewseveritybyboostingtheabundance of beneficial yeast and bacteria on the leaves[83].
Metagenomic monitoring has revealed unexpectedvirusesinweedsclosetocropsleading tonovelmanagementstrategies. Forinstance, • high-throughputsequencingrevealedtwonovel potexvirusesinweedsclosetobeanfields,resultinginimprovedsanitationtechniquestoeliminate weed reservoirs. In another case a new ilarviruswasidentifiedinnightshadeandthis ledtofarmerschangingtheircroprotationand thuspreventingapossibleepidemicintomatoes [84,85].
Theviromemethodisnowbeingusedtopests aswell:bacteriophagesspecificto Xanthomonas or Erwinia (bacterialplantdiseases)havebeen • createdtotreatfireblightinorchards.Incertain vineyards,rootstocksoilsprayedwithvirus-like particles(bacteriophages)killed Agrobacterium, reducingcrowngalldisease. Similarly,thediscoveryandenhancementofnaturallyexisting predatorybacteria(Bdellovibrio-likespecies)in therhizospherehaspromiseasasyntheticbiocontrol[86].
Whilesyntheticmicrobiomesofferbenefits,theyraise importantrisksandgovernanceissues.Keyconsiderationsinclude:
andinvasiveness): Engineeredorimportedbacteriamayswapgeneswithnaturalpopulations.
Antibioticresistance,orsyntheticfeatures(e.g. newmetabolicenzymes)mightbetransferred intopathogensorsoilmicroorganisms,thereby changingtheecologicaldynamics.Atransgenic designedstrain(e.g. withenhancedpesticidal potential)maydistributeitsgenesbyplasmidsor phages.Introducedmicroorganismsmaypotentiallybecomeinvasivebyoutcompetingnative speciesparticularlyiftheyhavegrowthbenefits.
Thismayleadtoalossofbiodiversityordisruptionofestablishedplant-microbeassociations [91,92].
Containment and biosafety: To reduce dangers,syntheticmicroorganismsaresometimes engineeredwithbuilt-incontrols(e.g.auxotrophyneedingnutrientsprovidedbythelab,“kill switches”thataretriggeredoutsidelabsettings). Increasinglyregulatorsdemandextensiveecological risk studies before field release. Controlledfieldexperiments(withmonitoring)are neededtoassessunexpectedimpactsonnontargetspecies(e.g.beneficialinsects,soilfauna). QuestionsalsoarisefromtheuseofCRISPR/Cas toaltermicrobialgenomes[93,94].
Regulatorylandscape: Thelawsgoverninggeneticallymodifiedmicroorganismsdifferworldwide. Under current frameworks, authorities likeUSDA-APHISorEPAmayassessmodifiedmicroorganismsforagricultureintheUnitedStates.
TheEuropeanUnion’suseoftheprecautionary principlemeansGMOsaremoretightlyregulated.
Moreover,internationalagreements(e.g.CartagenaProtocolonBiosafety)regulatetransboundarymovementofGMOs.Evennon-GMSynComs maybesubjecttoscrutinyas“biofertilizers”or “biopesticides”underregulations[95,96].
ersandconsumersmaybeskepticalaboutthe useofmodifiedmicrobiomes.Equityconcerns come up: Who owns the strains of microbes?
Patentingasyntheticcommunityorawildmicroorganismmightposeissuesofbenefitsharing,particularlyifisolatesareobtainedfromindigenousterritories.Smallholderfarmerscould worryaboutdependenceonproprietaryinoculants.Ethicsframeworksmustincludeautonomy (farmerchoice),fairness(fairsharingofbenefits/risks)andopenness(publiccommunication) [97,98].
quencingofwildplantviromesraisesethicalissuesof“bioprospecting”.Thediscoveryofanew viruswithadvantageousfeatures(e.g.induction ofdroughttolerance)maybeasusefulasamicrobialgene.Butthepurposefulreleaseormodificationofvirusesforcropdevelopmentcouldhave unforeseenimpactsonwildflora.Hence,virome researchneedsacompromisebetweenopenscienceandbiosafetyandbiosecurity[99,100].
• Integratedpestanddiseasemanagement:synthetic microorganisms or manipulation of viromesmustbeanadditiontoecologicalstrategies,notareplacement.Ethicalpestcontrolin theAnthropoceneisbasedontheconservation ofnaturalenemies,cropvarietyandreduction ofchemicalinputs[101].
• Sustainable crop protection: Helpful bacteria and viruses might mean farmers can use less hazardous pesticides and fertilizers. Syn- Coms that increase nutrient uptake or induce immunitymightpartlyreplacefertilizersandfoliarsprays,therebyimprovingsustainability.Vi- • romemonitoringisanearlywarningsystemfor novelvirusesandallowsforpreventativesteps [102,103].
• Resiliencetoclimatechange: Engineeredmicrobialconsortiaprovideameanstobuffercrops againsttemperatureextremes,saltanddrought– allanticipatedtoincreaseunderclimatechange. • Combining microbiome solutions with plant breeding(microbiomeresponsivevarieties)may leadtotheestablishmentofresilientagroecosystems. Furthermore, microbiomes contribute inmaintainingorimprovingsoilhealth,which helpsincarbonsequestrationandecosystemservices[104].
managementofplanthealthviatheuseofmicrobiomesiscompatiblewiththeprotectionof biodiversity.Bothmorediversifiedagricultural techniquesandecologicalintensificationareadvantageoustoplantandsoilecosystems[105].
• One-Health perspective: The plant microbiomeispartoftheenvironmentalmicrobiome.
Synthetictechniquesmaybecoupledwithpest control(e.g.phagesagainstzoonoticinfections • oncrops).Insightsfromplant-microbeinteractionsmighttranslatetomicrobialtherapeutics inhumanhealthandviceversa[106].
• Policyandglobalequity: Onthepolicyside, incorporatingmicrobiomeresearchintothefabricoflifeinvolvesrevisingrulesfor“biologicals” and investing in microbial infrastructure (e.g., microbialgenomebiobanks). Tohaveaworldwideeffect,microbiome-basedsolutionsmust beavailabletosmallholdersinunderdeveloped countrieswhowouldlikelygainthemost[107].
Despite progress, many questions remain. Notable gapsinclude: • Uncovered viral diversity: The bulk of plant viruses remain unknown from metagenomic studies.Therolesofthemajorityoftheviralsequencesidentifiedinplantorsoilareuncharacterized.Thereisneedforsystematicviromemapping across a range of environments (tropical woods,dryregions,cropsunderstress).Also,the functionsofnon-plantviruses(bacteriophages, mycoviruses)inplanthealtharenotwellrecognized. New computational techniques will be required to forecast virus-host interactions at scale.
tions: Amechanisticunderstandingofhowviral andmicrobialpopulationsinteracttojointlyaffectplantimmunologyandmetabolismislacking. Advancedsystemsbiologymethods(transcriptomics,metabolomicsoftheholobiont)will assisttoclarifytheprocesses.
Most SynCom research is focused on bacteria (somefungus),howeverplantsnaturallyinteract withbacteria,fungi,archaeaandprotists. Synthetic communities with many kingdoms (e.g.
bacteria + beneficial fungus + mycoviruses or phages)areunexplored.Multi-kingdomsynergy isafrontiertounderstand.
Efficacyandstabilityinthefield: Successin controlled environments sometimes does not transfertothefield.Long-termfieldexperiments under realistic agricultural circumstances are needed. Modelsarerequiredforthedynamics of inoculants in open systems. Systematic examinationofquestionsaboutdose,timingand administration(seedcoatingsversussoildrench) isrequired.
Syntheticcommunitieswillemerge.Strainsmay shedcharacteristicsiftheyarenotrequiredor mutateinsitu. Horizontalgenetransferinthe SynComorwithsoilbacteriamightleadtonew strains. Adaptive evolution procedures (trainingSynComsunderselectivesettings)maypreadaptcommunitiesbutalsocomplicateriskassessment.
SynComdesignismostlyempiricalatthemoment. We need concepts or algorithms that willforecastwhatcombinationswouldworkin 4.
a particular environment. Standardized inoculation techniques, trait databases for plantassociated microorganisms and phenotyping processescouldspeedrationaldesign.
• Socio-economicresearch: Howwillfarmersuse 5. microbiometools?Technicalworkhastobecomplementedbystudiesoffarmerattitudes,costbenefit analysis of SynCom inputs and socioethicalstudyonbioprospectingrights. 6.
Thispaperhasprovidedanoverviewoftheinterface ofthetwinfrontiersofplantviromicsandsynthetic microbiomeengineeringwithplantdiseaseandpest dynamics.Thevirusesarehiddeninplanttissuesand soilsandaregenerallyunrecognized,yettheyimpact planthealthandecosystemfunction.Atthesametime, scientistsarelearninghowtoengineermicrobialpopulationstoprovideplantswithimprovedresistance andresilience.Together,thesestudiesredefinedplant pathology and entomology in ecological and evolutionaryterms: planthealthisaresultofawebofinteractionsamonghost,pathogens,symbiontsandthe environment.
In the Anthropocene, with its accelerating climate changeandhabitatmodification,theuseofmicrobial andviralpartnersisasustainablewayahead.Butfulfillingthispromiseinvolvesthoroughriskassessment, 10. ethicalforesight,andintegratedresearchthatbridges thegapbetweenlabandfield.Theecologicalcomplexityofmulti-speciesgroupsdefiesourpredictioncapac- 11. ityandmanybasicproblemshavetobeanswered.But asourcapacitytoreadandwritemicrobialgenomesdevelops,sotoodoesthepotentialfordesigningagricul- 12. turalsystemsthatfunctioninpartnershipwithnature’s microbiome.Inconclusion,wecanseethatconcealed viromesandsyntheticmicrobiomeswillbeimportant toplantprotectioninthefuturebutsuccesswillde- 13. pendonprofoundscientificknowledge,cautiousmanagement,andworldwidecooperation.