Posted on Authorea 24 Jun 2020 | The copyright holder is the author/funder. All rights reserved. No reuse without permission. | https://doi.org/10.22541/au.159302219.97279363 | This a preprint and has not been peer reviewed. Data may be preliminary. vltoayadeooia tde r fmjriprac o nesadn h atrsadcue of causes and patterns species. the native understanding replace for can importance species major invasive of as are biodiversity studies to ecological threats and Evolutionary major represent invasions Biological Introduction 1 exclusion competitive bacteria; transcriptomics; ; competition; pathogen D.dianthicola of why determinants reasons ecological KEYWORDS the the competitors. and endemic understanding of agrosystems, our maintenance production to the for contributes potato conditions into study the understanding invasion this of better D.solani broadly, and a invasion allowing the More insights and novel of brings VfmBPro persisted. causes thus while outcompeted study nevertheless and This population tubers, pattern VfmBPro tubers. on the the in aggressive co-infections, co-existed virulence of stem more been they In vfmB while having was the stems. population, which population on VfmBSer at of aggressiveness the VfmBSer VfmBSer, (56 similar the and a genomes exhibited that VfmBPro D.solani populations showed alleles, 76 VfmBSer uncharacterized inoculations of aerial two comparison Experimental in of A D.solani frequencies gene. on outcompeted tubers. balanced D.dianthicola D.solani in revealed assays, than co-infection co-existed here) aggressive In fields D.dianthicola sequenced more potato and tubers. was in D.solani on D.dianthicola D.dianthicola aggressive while resident more that parts, the was showed of D.solani we maintenance while experimentations, the parts, its and aerial Using and D.solani dynamics establishment invasion symptoms. of establishment the its over blackleg records the of assessing exhibiting Epidemiological revealed causes by France and species. Europe in D.dianthicola patterns in resident decade the agrosystems closely-related one studied the potato We against invaded disadvantages recently establishment. resident or displacing advantages that their by competitive solani of services, Dickeya cause ecosystem pathogen or the the production understand food of to health, need human we affect they and when species, threat a be can pathogens Invasive Abstract 2020 24, June 6 5 4 3 2 1 Faure Am´elie Beury Dewaegeneire Blin Pauline pathogen bacterial resident invasive the of pathogen establishment potato the of causes and Pattern Universit´e Paris-Sud Lyon Growers INSA Potato Seed of Federation French University Growers Jiangsu Potato Seed of Federation French CNRS 1 Dickeya; 1 K´evin Robic , 2 4 Ang´elique Laurent , yveReverchon-Pescheux sylvie , nain ln ahgn;pplto eois quorum-sensing; genomics; population pathogens; plant invasion; iky solani Dickeya .dianthicola D. 2 lmn Khayi Slimane , 2 a Jaszczyszyn Yan , 5 ain Giraud Tatiana , 1 J´er´emy, Cigna 1 n ftemitnneo the of maintenance the of and 1 a-a Hong Kar-Wai , 2 6 uhai Munier Euphrasie , Val´erie H´elias, 3 o-a Chan Kok-Gan , oau tuberosum Solanum 4 n Denis and , 2 Pauline , 3 , Posted on Authorea 24 Jun 2020 | The copyright holder is the author/funder. All rights reserved. No reuse without permission. | https://doi.org/10.22541/au.159302219.97279363 | This a preprint and has not been peer reviewed. Data may be preliminary. Blin-aeoe l,21;RoldsEsrse l,21) u tesdffrne ihnhs lnsremain plants host within differences fitness identified but 2019), been al., have et capacities (Laurila Essarts des metabolic magnitude Raoul as of 2019; such orders al., several differences et Functional by (Bellieny-Rabelo number 2016). in al., increase et between they Potrykus where 2008; host, al., plant where et waters, a from surface on transition the and lifestyle in soils copiotroph participate 2018). in signals quorum-sensing lifestyle Lojkowska, the oligotroph & factors, Golanowska,an virulence Hugouvieux-Cotte-Pattat, Potrykus, of 2013; synthesis , size the al., Potrykus, et modulating the By Nasser 2014; 2012; on the Lojkowska, (Cr´epinal., perception (reflecting reached et & and signals is the environment) of Hugouvieux-Cotte-Pattat, Vfm 2017). concentration sugars) the and by threshold in Reverchon, lactones plant a cells induced & N-acylhomoserine when of (mainly number expression the Nasser, being gene signals, physiology virulence quorum-sensing Hommais, regulated, activate of which host (Leonard, types tightly compounds, two plant signals) sense is on and (quorum-sensing that synthetize population pathogen pathogens process own the costly its inform a of that is chemicals factors of virulence these release loop enzymes feedback of these the positive substrate, Noticeably, in a a 2016). non-functional, in a as enzymes Reverchon, hence pectin the play macerating & Using wall L´eonard, PelE, producing Brochier-Armanet, plant-cell maceration. Nasser, by especially wall other (Duprey, of cell iron and plant expression including PelD elicit the remains, PelA, that of oligosaccharides initiation cell i.e., the tubers plant lyases, in of Pectate the role disease key siderophores. assimilating (including enzymes soft-rot achromobactin by macerating and proliferate and cell-wall plant stems chrysobactin and secrete on lyases) bacteria these disease pectate All blackleg the 2011). al., in et Toth resulting 2018; symptoms, (Charkowski similar causing pathogens from events The transfer gene two Horizontal the 2015). of al., each et 20 solani (Khayi in of motility analysis (SNP) revealed bacterial An polymorphism genomics in 2015). involved Population nucleotide al., 2014). et single al., Khayi non-synonymous et 2018; a Wolf al., der et van (Golanowska invasion 2009; during al., in et variation Slawiak genetic 2015; little Chen, & Zhang, potatoes, (Chen, from Aside as 2014). al., such Wyenandt, et Wolf plants & disease der van Kobayashi, with 2011; Patel, al., associated et Baldwin, (Toth was Patel, 2017; it al solani al., et where Dickeya Toth et North-America, 2018; (Oulghazi including al., 2015 et continents, in Sarfraz all 2019; farms in potato present in Nowadays, is outbreaks 2009). It al., et Europe. Parkinson in 2011; al., et (Toth of 70’s Isolation 1950s. the as early as such plants ornamental (P´erombelon, 2002), Europe in some of While causes proteobacteria). and patterns Europe, the in understanding competitor for related pathogen approaches resident, bacterial ecological the the 2011). and of Nowak, evolutionary Kinnunen establishment & used 2015; the Leger, we al., Perkins, work, et 2015; this (Gladieux Salles, animals In & and societies, Elsas, plants human invasive Mallon, et and than 2010; Gladieux ecosystems Litchman, studied 2006; to less 2016; al., threats well much et important as (Facon represent been invasions species have can of resident invasions & they outcompete dynamics microbial Gilbert, to Although the 19 them MacDougall, elucidating 2015). allow the 2018; at that al., Mandrak, invaders since aim of & approaches advantages studied Sodhi, the ecological extensively as Li, and been Evolutionary Campbell, have Cadotte, 2009). invasions 2018; Levine, Zheng, animal & and Murphy, plant (Burns, and invasions biological .solani D. aebe ouetd digo elcn eoi rget Kaie l,2015). al., et (Khayi fragments genomic replacing or adding documented, been have .solani D. Pectobacterium Hyacinthus a mre nptt rdcinssesi uoemc oercnl,i h al 2000s early the in recently, more much Europe in systems production potato in emerged has nae,a ela the as well as invader, and .dianthicola D. .dianthicola D. .solani D. and , inhs Dahlia Dianthus, Pectobacterium Iris .dianthicola D. Dickeya, Dickeya .dianthicola D. and nareetwt eetsra fti pce olwn bottleneck a following species this of spread recent a with agreement in , . Muscari ycmaaiegnmc,tasrpoisadbohmclapproaches biochemical and transcriptomics genomics, comparative by 01 rgte l,2018). al., et Wright 2011; , .dianthicola D. Dpe ta. 06 au e sat ta. 09.Tesecretion The 2019). al., et Essarts des Raoul 2016; al., et (Duprey pce nae ae,i w ucsiewvs is sltdfrom isolated First waves. successive two in later, invaded species w itrgnr mn h re fEtrbceae (Gamma- Enterobacterales of order the among genera sister two pce a ete ic eoete17si oaoagrosystems potato in 1970s the before since settled had species iky solani Dickeya and rmptt lns( plants potato from u h rmr ots fta pce eans uncertain remain(s) species that of host(s) primary the but , hr r w ao ldso oaobceilpathogens bacterial potato of clades major two are There . Begonia 2 and Dickeya .dianthicola D. , Pectobacterium .dianthicola D. nptt goytm n h aneac of maintenance the and agrosystems potato in .solani D. and oau tuberosum Solanum Pectobacterium scniee nedmcpathogen endemic an considered is a enioae rmornamental from isolated been has p.rsdns r necrotrophic are residents, spp. a enrpre nErp as Europe in reported been has fliC .solani D. and pelA atraaerr,t a to rare, are bacteria L .dianthicola D. . fliN ae akt the to back dates ) eoe identified genomes eei truncated, is gene ee htare that genes th Dickeya century tal et to D. ., Posted on Authorea 24 Jun 2020 | The copyright holder is the author/funder. All rights reserved. No reuse without permission. | https://doi.org/10.22541/au.159302219.97279363 | This a preprint and has not been peer reviewed. Data may be preliminary. nhriutrlcmoti niiulpt 2L nagenos taon 23 around at greenhouse a in L) (2 inoculation. pots plant individual before 28 in just assembled compost were horticultural either strains in different inoculations, of tuber suspensions ( and plants cell Potato plant species, of two for populations the used experimental of constitute being mixtures To populations. before in individually assembled or cultivated separately was strain bacterial Each by inoculations Plant 2.3 neutral with -80 g.L at 5 placement stored (tryptone phylogeny were strains regarding Bacterial different 2016). plant be produce to to ornamentals, chosen used were were ( PPO9019) strains markers Ds0432.1, The RNS05-1-2A, assays. IPO2222, inoculation RNS08-23-3-1A, were = isolates (3337 548 strains resulting The plants. Five 548 the of each transect from 2.2 a retained along was collected symptomatic isolate were blackleg single symptoms of taxonomically. blackleg taxonomically a 1% characterized with than and and isolates plants more field, collected 30 fields which hosting each Around were fields 2006), from in sampled. potato isolates year deeply 19 plants 1600 more 2016, the were diseased around to of plants 2013 fields, collecting exception from 541 parallel, by the From In (with sampled characterized. characterized. year and randomly Each recovered were the areas. were symptoms at producing characterized blackleg potato and French exhibiting plates in agar conducted on was purified in were listed (H´elias,primers Isolates medium 2012). pectate violet ( Andrivon, crystal genus & symptoms on Wolf, tissues disease plant Huchet, blackleg symptomatic with Hamon, from fields isolated were potato bacteria in Pectinolytic identification and sampling Pathogen in 2.1 traits invasion Methods to and associated Material in be variations 2 could novel far, revealing gene so 2015), quorum-sensing studied al., the been et not on (Khayi focused published We previously population. genomes 20 with together two the constrain the on or of focused facilitate abundances then of we relative determinants greenhouse, the ecological in compare assays and to allowed patterns France the geno- in lani decade population of one and understanding over inoculations our records experimental Epidemiological to fields, contribute potato to in records mics for exploited epidemiological importance differentially combined their we be despite Here, questions, could unsolved host remain host potato this the the exploiting Whether understanding when directly 2019). compete al., Raoul or 2010; et niches Wolf, der Shyntum van 2019; & Velvis, al., by Boer, de et Czajkowski, Essarts 2013; al., des et (Czajkowski investigated partially only ek otbl lnain eeiouae ywtrn h usrt ihaptoe elsseso at suspension cell pathogen a with substrate the watering by inoculated 10 were plantation) post-bulb weeks trl nf eoeifcin h ypo oioigwsaatdfo au e sat ta.(2015). recorded al. was et disease) Essarts (soft-rot hyacinths des and Raoul disease) from (blackleg adapted plants was potato monitoring symptomatic symptom of The number The infection. before knife sterile ° 9 .dianthicola D. )wt 2hu htpro.Ptt lns(he ek ottbrpatto)adhaits(four hyacinths and plantation) post-tuber weeks (three plants Potato photoperiod. 12-hour a with C) iky solani Dickeya ooyfriguis(F)prpt nawuddcniin h oaoroswr one iha with wounded were roots potato the condition, wounded a In pot. per (CFU) units colony-forming nae,the invader, .dianthicola D. Dickeya Dickeya iueS1 Figure al S2 Table .tuberosum S. -1 .dianthicola D. and es xrc g.L 3 extract yeast ; al S1 Table and pce.Fnly eotie rf eoeo 56 of genome draft a obtained we Finally, species. .solani D. tan RS14--A FP88 FP92 FP05 I3)adfive and MIE34) CFBP2015, CFBP2982, CFBP1888, (RNS11-47-1-1A, strains Pectobacterium .solani D. n egahcllctos slto er rhs fcleto ptt lnsvs plants (potato collection of host or years isolation locations, geographical and ) and .solani D. .Pyoeyaaye eecnutduigMG7(ua,Sehr Tamura, & Stecher, (Kumar, MEGA7 using conducted were analyses Phylogeny ). .dianthicola D. a.Bnj)adhaits( hyacinths and Bintje) var. w apigsrtge eeue.Fo 04t 05 ainlinventory national a 2015, to 2004 From used. were strategies sampling Two . invasion. .solani D. eietand resident salsmn,icuigcmeiino clgclncedffrne between differences niche ecological or competition including establishment, n hte h w ahgn tbyceitb sn ieetecological different using by coexist stably pathogens two the whether and -1 n pce ( species and ) iho ihu gr(5g.L (15 agar without or with ) .solani D. and ° ngyeo 2%vlvl.Te eecliae nT medium TY in cultivated were They vol/vol). (25% glycerol in C etbceimspp Pectobacterium tan sdi ln assays plant in used strains .dianthicola D. and .solani D. 3 vfmB ycnhsorientalis Hyacinthus .dianthicola D. oivsiaewehrisvrain hc has which variation, its whether investigate to and tan n xeietlpopulations experimental and strains sn xeietlppltosadplant and populations experimental Using . .solani D. .dianthicola D. -1 odtrieteeooia risthat traits ecological the determine to t28 at ) .solani D. . a.Dltbu)wr cultivated were blue) Delft var. ° ° C. mnmm20 (minimum C .sln,.dianthicola, solani,D. D. sltsta eanalyzed we that isolates eesuigtePCR the using levels ) .solani D. ° maximum C .solani D. .solani D. invasion. .so- D. or Posted on Authorea 24 Jun 2020 — The copyright holder is the author/funder. All rights reserved. No reuse without permission. — https://doi.org/10.22541/au.159302219.97279363 — This a preprint and has not been peer reviewed. Data may be preliminary. uesrisadmxue sioua ntefiue,agesvns aawr rsne spretg of percentage assays). as infection tuber presented potato were (in data values using aggressiveness DSI above figures, and described assay) the as infections In protocols stem same potato inocula. the (in as following plants mixtures performed symptomatic were and stems) strains in and characteristics pure tubers (their potato genomes in (on positions assays VfmB other carrying at isolates differing VfmB four group portals carrying chose isolates web we four data, and EzMol VfmB 3337) genomic and role (allele Using known Phyr2 serine protein. the a the VfmB Given either using 2018). exhibiting Sternberg, represented Islam, strains and Reynolds, the of 2015; modeled virulence Sternberg, was in & Wass, proteins Yates, VfmB Mezulis, (Kelley, the between of Structure differences The retained. fitness were the step mapping VfmB of the in Characterization reads) the 2.5 of % 99 InDels ([?] and in 2012). occurrence CLC SNPs variants Only high using allelic 10.1.3. a length) version of workbench with read representation genomic nucleotides) 50% CLC 9 from on to tool identity calling (1 37 variant (80% the from threshold using the ranging InDels stringency (Khayi against and coverage mild 10.1.3 mapped average at version and Workbench an strain, 0.05) Genomics 3337 to threshold the corresponding score from (quality obtained, genome, trimmed were kit were Sequencing reads reads Output million Paired-end High quality 18 using and sequenced to (w/v), then quantity 2.4 % and 1.0 After at strain electrophoresis each Illumina). 75 gel for agarose with (Epicentre, and constructed device were kit 1000) (ND libraries NanoDrop purification paired-end a using 56 RNA DNA extracted of and of controls each DNA from complete purified MasterPure was DNA Total 2.4 to advantage presented fitness formula a the to indicated following advantage values one (CI) than quantify index greater to competitive used of calculation also in were the hyacinths, permitted hyacinths) from and as well as see (SM2) tubers, tubers, and 10 solani stems to D. potato increase assigned from unit), classes (arbitrary tissues aggressiveness 100 Symptomatic five to presented the 0 are using from results calculated ranging figures, in values, was asymptomatic the formula which an DSI in in of as severity. data gravity used (DSI) aggressiveness symptom was index symptom the with tubers severity of the non-inoculated disease presentation to of the normalized set according facilitate as A to classes inoculated. order symptoms; aggressiveness were In severe five tubers control. most 10 in the least scored to at symptom and population, no half (from in tuber cut each were tubers the percentage 10 a at In as populations presented control. experimental are asymptomatic they ( an figures, tubers as the Potato plants used in potato was data 25 two plants to aggressiveness plants. (up non-inoculated the (hence symptomatic plants of of plants of potato visualization set 15 asymptomatic facilitate A using to hyacinths. (dpi) and order infection 8 symptomatic post and days of indicated) 60 when number at counted the was classes) conditions, symptom wounded in and symptoms unwounded of examples (see biweekly SM1 iky solani Dickeya Ser × Assessing . Ivleeult n niae neulfins between fitness equal an indicated one to equal value CI A . and ylso n luiaNxSq0 eune CR,GfsrYet,Fac) o ahstrain, each For France). Gif-sur-Yvette, (CNRS, sequencer NextSeq500 Illumina and on cycles 2 n VfmB and upeetr ehd (SM1). 1 Methods Supplementary .dianthicola D. .dianthicola D. .tuberosum S. vfm .dianthicola D. ouaingenomics population Pro eecutr(asre l,21) easse iuec ieecsbetween differences virulence assessed we 2013), al., et (Nasser cluster gene alleles . a ite eeiouae sn i oijc 10 inject to tip a using inoculated were Bintje) var ahgn yTqMnqC sdsrbdin described as qPCR Man Taq by pathogens 7 o 10 (or and .solani D. Ser 5 .solani D. hnidctd F e ue.Atr5dy ficbto t24 at incubation of days 5 After tuber. per CFU indicated) when iue1a-b Figure D03.,RS02-A paadM1) h orioae neach in isolates four the M21a), and Sp1a RNS10-27-2A, (Ds0432.1, .solani D. tal. et ouainwspromduigPYOi Facsoe al., et (Francisco PHYLOViZ using performed was population Ser rapoie(leeVfmB (allele proline a or ) niouu n ln ise ptt tm n tubers, and stems (potato tissues plant and inoculum in 05.Tempigwsue o h eeto fSNPs of detection the for used was mapping The 2015). .solani D. 4 slts(hi hrceitc in characteristics (their isolates .Frec tanadeprmna ouainand population experimental and strain each For ). iue1c Figure n Ivleblwoeidctdafitness a indicated one below value CI and , iky solani Dickeya alsS3 Tables .solani D. .Frec tanadexperimental and strain each For ). Pro upeetr ehd 2 Methods Supplementary Pro IO22 I3,A3 and AM3a MIE35, (IPO2222, and ttepsto 5o the of 55 position the at ) μ and fptoe tan and strains pathogen of L .dianthicola D. tan arigthe carrying strains S4 iueS2 Figure .Patinoculation Plant ). .solani D. × Ivalue CI , .solani D. o270 to reference using ) ° × C, . Posted on Authorea 24 Jun 2020 — The copyright holder is the author/funder. All rights reserved. No reuse without permission. — https://doi.org/10.22541/au.159302219.97279363 — This a preprint and has not been peer reviewed. Data may be preliminary. rmec te F .6 F ;Dd=1;p .2.Ti ugssta the different that not suggests were This and 0.62). line p= base 18; = from of DFd different expense 1; not the = were DFn at percentages 0.26; occur field (F= 0.11) other each p= from 9; DFd= DFn=1; 3.10; 2b the 10 x on R informed 0.05; of p= percentage data 9; the These DFd= 1; taxon. DFn= resident 5.05; each period, (F= isolated the time over we Over ( Each observed which fields taxonomically. populations. from characterized sampled pathogen were fields the different plants. that of the symptomatic isolates number exhibiting of 1,600 all the over dynamics fields, of recorded potato collection we different the year, 541 in in resulted conducted samplings were The surveys Annual France. in the of monitoring A of co-occurrence R scarce software A the with 3.1 out carried were Analyses Results nparcomp. 3 test. and Kruskal-Wallis RcmdR a packages comparing using by the tested one was using to competitors (http://www.R-project.org) two values the CI of abundances calculated balanced the of hypothesis the assays, competition In we population, experimental an constitute to compared experiments. altogether we inoculated tubers, were the and strains compared plants bacterial on the When separately were inoculated species. levels were differences expression pairwise strains what bacterial gene assess the the to and run control When assays, were ( tests this Tukey significant. tuber tests post-hoc Kruskal-Wallis were symptoms) in and Then, by without normality. classes pathogens) asymptomatic, from or symptom deviated different (with remained significantly five (the classes tubers treatments the symptom hyacinths, two among and The compared and plants plants analyses. non-inoculated statistical potato in the of considered assays, non-random not Ma- was the plant for condition test the 8.4.2 to all version used Prism In was field. GraphPad each method in using Chi-squared ANCOVAs taxa A of and distribution (www.graphpad.com). F-tests Software using GraphPad of analyzed cOS, percentages were the fields of dynamics -positive the of (2019). slopes al. The et Essarts des analyses Raoul Statistical by 2.6 described as compared were Transcriptomes . (VfmB IPO2222 VfmB to advantage VfmB fitness alle- a the between of indicated fitness abundances one equal relative VfmB an The the indicated of 10.1.3. one values version to CI workbench of genomic calculation CLC Gif-sur-Yvette, reads permitted the trimmed (CNRS, les using The platform sample each I2BC Malaysia). VfmB in Lumpur, the alleles Kuala at with Malaya, NextSeq500 of each on Illumina (University mapped for an were performed platform obtained using MiSeq were reads Illumina performed also million and was France) 28 cycles) to were of 2 12 coverage From x average assays (75 tissues. an plant to from co-inoculation corresponding and sample, inoculum from fitness, extracted DNA of relative their VfmB measure To .Tesoe of slopes The ). .solani D. -3 .Aogthe Among ). Ser Pro ial,w sdtasrpoist dniytegnsta eedffrnilyepesdbetween expressed differentially were that genes the identity to transcriptomics used we Finally, . Pectobacterium xeietlppltos n hi eaieaudnewsqatfidb htgnsequencing gun shot by quantified was abundance relative their and populations, experimental and .solani D. Pro .sln vfmB solani D. Dickeya- .dianthicola D. .dianthicola D. n s421(VfmB Ds0432.1 and ) Dickeya iue2a Figure Pectobacterium .dianthicola D. pce eandtems ieped sepce,tesoe ftednmc of dynamics the of slopes the expected, As widespread. most the remained species and and slts nytoseiswr identified, were species two only isolates, .dianthicola D. Pectobacterium- eefrqatfigterltv bnac ftetoVfmB two the of abundance relative the quantifying for gene .Amdrt nraeo h ecnaeof percentage the of increase moderate A ). pstv F .5 F=1 F=9 =02)and 0.28) p= 9; DFd= 1; DFn= 1.35; (F= -positive pce risuigec atra tana elct fteconsidered the of replicate a as strain bacterial each using traits species .dianthicola D. and nFec oaoagrosystems. potato French in .solani D. Ser Dickeya Pro ) pce risuiga es w needn elctso the of replicates independent two least at using traits species .solani D. n Ivlels hnoeidctdafins datg to advantage fitness a indicated one than less value CI and , oiiefilsdvre F 01;Dn ;Dd 8 =5 p= 18; DFd= 1; DFn= 10.11; (F= diverged fields positive .solani D. Dickeya Ser ouain a efre vroedcd (2004-2015) decade one over performed was populations VfmB and n VfmB and 5 tan hnte rwisd oaotbr ( tubers potato inside grew they when strains Pro .solani D. -, eoe agn rm10 o40.Sequencing 420x. to 180x from ranging genomes Pectobacterium ² and .6.Atog eraigi niec,the incidence, in decreasing Although 0.36). = Pro VfmB ouain (see populations Dickeya nptt fields potato in .dianthicola D. Ser ouain,C au rae than greater value CI populations, -, a eetdi 0 o3%of 35% to 10% in detected was .solani D. Dickeya α .solani D. .5 eas h data the because 0.05) = SM1 .solani D. and and - pstv ed was fields -positive .AC au equal value CI A ). .solani D. Ser nainddnot did invasion .dianthicola D. pstv (F= -positive n VfmB and ( Ser Figure SM2) and Pro Posted on Authorea 24 Jun 2020 — The copyright holder is the author/funder. All rights reserved. No reuse without permission. — https://doi.org/10.22541/au.159302219.97279363 — This a preprint and has not been peer reviewed. Data may be preliminary. nafis sa,ec tanwsiouae niiulyo 5pat,adtenme fasymptomatic of number the and plants, differences than revealed 15 aggressive test more Kruskal-Wallis on found A was individually counted. were inoculated classes) symptom was between two strain (the plants each symptomatic assay, and first assays. a these In in used were PPO9019) five Ds0432.1, and RNS05-1-2A, MIE34) CFBP2015, CFBP2982, CFBP1888, os(othcTkytss hwdta h ubro lnswt yposdffrdfloiginoculation following differed symptoms with plants of number the that plants showed 15 tests) i.e., Tukey x treatments, and (2 (post-hoc three Symptomatic duplicated sons the was roots. between assay wounded differences The revealed treatment. with mixture, test per plants Kruskal-Wallis plants containing treatment). 15 pots per among counted in were inoculated plants asymptomatic also were mixtures Pathogen host. the of of advantage parts fitness a revealed 10 data x these of 2 excess an p= 10 revealed DF=1; of abundance value pathogen median the CI of quantifications were 10 mixtures plants, species x symptomatic two 3 the When and loads. cells pathogen quantify to separately, allowed inoculated qPCR experiment, subsequent a In the by caused incidence the symptom However, ( of (53% 0.10). value those p= mean from (F=1.9; and differ mixture p-values not species did the mixture of that species counts and class Kruskal- 0.03) symptom of treatment). p= the aggressiveness per of 2.5; the comparison plants that Pairwise showed 15 p=0.04). to test) i.e., (10 DF=2; x Tukey assembled treatments, (k=6.1; (Post-hoc species (2 were mixture two three duplicated species the species was the and of each mixture assay between strain mix The of differences A plants. strains) revealed plants. 15 five 15 test on Wallis on the inoculated inoculated (i.e., also was cultures was each bacterial and strains) five populations experimental the two assay, constitute plant second a In 3a). Figure inoculation after symptoms blackleg of severity the compare to exclusion. greenhouse by the competitive in of performed were hypothesis assays the Plant test to work, particular to the in of Compared and part 3.2 from infection, next or the tuber infection, In and plant species tubers. plant before two and of waters plants course the surface potato on and of soils focused process or/and infection we seeds the tuber during in exclusion populations competitive ( among genera taxa for the both of levels, field the at solani taxa p of 1; clustering DF= a showed tests: (Chi-squared fields that positive hypothesis 30 null p ca. dianthicola the 1; D. collected fields, DF= plant, 19 we test: each the (Chi-squared fields, strategy of Dickeya of rejected sampled sampling symptoms each was 19 aerial extensive In distributed from ( randomly fields. of more characterized isolates sampled each a was 548 19 in using of isolate the sampling single level transect the a field a in and the resulting Along symptoms at blackleg (2013-2016). with zoomed period plants we four-year survey, a national over this from Aside .dianthicola D. ± and 7), .solani D. oocre esotnta xetdudrrno itiuin h yohssthat hypothesis The distribution. random under expected than often less co-occurred .dianthicola D. .dianthicola D. .solani D. eernol itiue ln h rnetwsas eetdi aho h 16 the of each in rejected also was transect the along distributed randomly were 9 ± or -3 and ,maigthat meaning ), .solani D. 10 x 1 .solani D. (23% .dianthicola D. -5 .dianthicola D. tanmxueadseismxue(=92 F2 p=4.6x10 DF=2; (k=29.2; mixture species and mixture strain ( iue3c Figure .Ti isi h ypoai lnscnrsl rmannrno distribution non-random a from result can plants symptomatic the in bias This ). ± 2 ± el e rmo ypoai tmtsus epciey negtco-infected eight In respectively. tissues, stem symptomatic of gram per cells E ftepretg fsmtmtcpat ncltdb the by inoculated plants symptomatic of percentage the of SE) )admxd(47% mixed and 3) .solani D. , nnnwuddptt lns Five plants. potato non-wounded on .solani D. .dianthicola D. .dianthicola D. .TeegtC ausdffrdfo n KuklWli et k=9.5; test, (Kruskal-Wallis one from differed values CI eight The ). ntrso ypo eeiy(=;D=;p8x10 x p=8 DF=1; (k=7; severity symptom of terms in and .dianthicola D. and pretgso ypoai lnso 61% of plants symptomatic of (percentages iue2c Figure .solani D. < .dianthicola D. .5 u n fil 1;D=1 =02) hs eddata field These 0.24). p= 1; DF= #13; (field one but 0.05) .dianthicola D. xiie tesavnaei oaoplants potato in advantage fitness a exhibited ± outcompeted )ppltosaepeetdi the in presented are populations 0) ece h envalues mean the reached 6 .The ). .solani D. .solani D. ntrso utpiainwti ein nteaerial the in lesions within multiplication of terms in Pectobacterium ocmaeeprmnal hi tesi the in fitness their experimentally compare to Dickeya itr F-.;p .6.Ps-o Tukey Post-hoc 0.86). p= (F=-0.5; mixture < a ihrta htof that than higher was tan 33 N0-331,IPO2222, RNS08-23-3-1A, = (3337 strains .solani D. .5,maigthat meaning 0.05), .solani D. .dianthicola D. and Pectobacterium Pectobacterium nbake ise.Altogether, tissues. blackleg in ouain eepeeti all in present were populations tanmixture, strain ± Eo 10 x 2 of SE tan (RNS11-47-1-1A, strains ± -7 .dianthicola D. .Piws compari- Pairwise ). 0vru 15% versus 10 Pectobacterium .dianthicola D. gr 3b figure and -3 n pce ( species and ) ): .solani D. .dianthicola D. .dianthicola D. .dianthicola D. .sln and solani D. Dickeya 11 ± Dickeya- . 10 x 1 iha with strain ± (F=- were and 11; D. 4 Posted on Authorea 24 Jun 2020 — The copyright holder is the author/funder. All rights reserved. No reuse without permission. — https://doi.org/10.22541/au.159302219.97279363 — This a preprint and has not been peer reviewed. Data may be preliminary. ,16 ), h grsieesadfins ftetoseiswsfrhrcmae nhaits htcnttt reservoir a constitute that of hyacinths, host in compared intermediate further or was primary species two or/and the of fitness and aggressiveness The to Compared 3.4. than which competitive more in was solani tissues and plant damage load). more low potato caused a constituted with 0.05 tubers p= tubers Overall, DF=1; symptomatic of k=7.8; 10 load; terms high in in a pathogens tubers with exploit the to of 4f) capacity of quantification and favor the qPCR in in advantage assays, differences an co-infection revealed important In no yield. indicated population data These value the tissues. (mean of rotted abundance from the ranged that revealed mixtures tubers strain symptomatic 10 of analyses qPCR The tubers. 10 of to set each ( for tuber calculated was value DSI A p=0.07). F=2.2; solani load: low value a Mean at p=0.01; symptom F=2.9; that load: showed tests) Tukey p (Post-hoc p=4.2x10 F=8.6; comparisons between DF=2; pairwise different loads, (k=51.3; was bacterial high incidence both a At i.e., at load. treatments, both pathogen three mixture the species between the differences revealed tests Kruskal-Wallis nascn ue sa,w sdsri itrsfrec ftetoseisada sebyo h two the of assembly an and species two the 10 of of each each for for mixtures tubers strain 10 used inoculate we assay, to tuber species second a In solani D. 10 63 reached 10 replicates for five tubers the two 50 the across from between 10 information differences revealed x class tests 4 symptom Kruskal-Wallis collected load. inoculation we 10 each so at calculated treatments, for separately times, and was five inoculated strain (DSI) was bacterial performed each strain was index each assay severity assay, The rotting disease tubers. tubers. tuber a 10 first on and a classes In classes symptom the symptom of five observations the using summarizing compared was pathogens the compared We measured and to conditions all Compared in invader 3.3. the than fitter being resident the betweentraits. plants, differences potato exploiting fitness and revealed p=10 fecting data DF=1; experimental k=19.5; these test: (Kruskal-Wallis Altogether one of from excess different an were values revealed CI pathogens the of quantification of aggressiveness stronger a solani D. by 5 7 .dianthicola D. .solani D. F e ue ( tuber per CFU F e ue ( tuber per CFU ± -11 a erae ntepeec of presence the in decreased was and iue4e Figure ( 6 ahgnla.TeDIvle eecluae o ahsto 0tbr n envalues mean and tubers 10 of set each for calculated were values DSI The load. pathogen ) < . 83% , F61 p=2.7x10 (F=6.1; .dianthicola D. h Ivle eedffrn rmoe(rsa-alstss =63 F1 -au f5x10 x 5 of p-value DF=1; k=16.3; tests: (Kruskal-Wallis one from different were values CI The .dianthicola D. 10 .solani D. ± rmiouainby inoculation from -11 Eo h S ausrahd83 reached values DSI the of SE .Smtmicdneas iee between differed also incidence Symptom ). ± n oteseismixture. species the to and .Atgte,teetbrasy eeldahge grsieesof aggressiveness higher a revealed assays tuber these Altogether, ). .dianthicola D. 0for 10 iue4a Figure iue4d Figure .dianthicola D. .dianthicola D. and .dianthicola D. n 48 and ) iha nclmo 10 of inoculum an with ) .dianthicola, D. .dianthicola D. -9 .Mean ). .solani D. n 49 and ) ). .dianthicola D. .solani D. and ± ± , , 0( 10 ± .solani D. .solani D. 3for 13 .solani D. .solani. D. .dianthicola D. n 93% and ± Eo h ecnaeo ypoai lnsrahd33% reached plants symptomatic of percentage the of SE .solani D. ohahg k32 F1 =.7 ralw(=36 F1 p= DF=1; (k=43.6; low a or p=0.07) DF=1; (k=3.2; high a both and ± scmae to compared as eadeso h nta od(Imda au 5.7; = value median (CI load initial the of regardless for 8 E 10 x 2 SE) 7 .solani D. .dianthicola D. F-.;p=1.9x10 (F=-4.5; n 10 and ± .solani D. xiie tesavnaei hyacinths in advantage fitness a exhibited xiie tesavnaei oaotubers potato in advantage fitness a exhibited ± h five The clgcltat nptt ues grsieeso the of Aggressiveness tubers. potato in traits ecological ( 0 7 and o i of mix a for 7 7 .dianthicola D. F e ue ( tuber per CFU .solani D. .dianthicola D. 5 . 9 n 47 and .dianthicola D. F e ue.Ti sa a efre twice. performed was assay This tuber. per CFU ± .dianthicola D. .solani D. n 7 and .solani D. 10 x 3 a ihla:F27 =.4 talwload: low a at p=0.04; F=2.7; load: high a (at .solani D. -11 ± ,63 ), ± n o k2.;D=;p=1.3x10 DF=2; (k=22.4; low a and ) -5 for 4 9 .dianthicola D. for 4 n yamxueof mixture a by and ) o9x10 x 9 to ihaC einvleo 10 of value median CI a with n2 oifce ln ise,qPCR tissues, plant co-infected 27 In . eakby ypo eeiyof severity symptom Remarkably, . ± iue4b Figure ntae yposmr efficiently, more symptoms initiated .solani D. iha nclmo 10 of inoculum an with ) .dianthicola D. n h pce itr a high a (at mixture species the and ( 3 .dianthicola D. 7 n five and .dianthicola D. ra 10 at or -5 .solani D. 9 ; ± iueS3) Figure .solani D. and .solani D. and 10 x 9 n 69 and ) 5 F nec e f10 of set each on CFU .solani D. .solani D. .dianthicola D. iha nclmof inoculum an with iha nclmof inoculum an with , .dianthicola D. 9 .dianthicola D. and n 63 and ) el e rmof gram per cells atra strains bacterial ± . .dianthicola D. 4( 14 scompared as indicating , iue4c Figure 5 .solani D. -5 F per CFU ± These . ± o in- for ± ( 8 for 0 and and SE -5 D. D. -5 ) Posted on Authorea 24 Jun 2020 — The copyright holder is the author/funder. All rights reserved. No reuse without permission. — https://doi.org/10.22541/au.159302219.97279363 — This a preprint and has not been peer reviewed. Data may be preliminary. igegnm,wiete1 teswr on na es w eoe.Aogtee1 ae,trevariations three later, 15 these Among genomes. two non-synonymous least 45 at 3337, in found strain were the others to 15 compared the while ( SNPs genome, genomes 12 single whole than in less identified exhibiting were genomes variations when 66 InDels PPO9134, the along and (RNS13-30-1A, on distributed Focusing chromosome SNPs were the RNS10-105-1A). 11 others of and to while regions (RNS05-1-2A 2 in RNS07-7-3B) genome from clustered the RNS15-102-1A, were exhibited RNS13-48-1A, SNPs 66 RNS13-31-1A, these genomes, PPO9019, of 76 some the observed: sequencing of were same the Out the using acquired 2015). to previously compared al., been had et others 20 (Khayi 76 the approach while study, in this InDels in sequencing and Illumina SNPs studied We of analysis frequencies genomic balanced population The 3.6 symptoms, plant in genes Overall, virulence p=0.9). the (F=0.5 stems and p=0.9) The p=0.99). solani The ( stems). strains among variable polymers. more wall was p expression cell gene plant stems, the and S5 of tubers degradation potato initiating symptomatic for In advantage an as considered be could ( species the of 10 x 4 p= ( between expression pectin gene of compare absence to the used were tests Tukey post-hoc Pairwise genes: different the other the for two for acsD tubers gene, replicate) of and each a stems For expression as medium, gene. strain pelD The (rich and each treatments tubers. considering condition six species, and per the two between performed stems differences were potato revealed measurements tests RT-qPCR rotted Kruskal-Wallis Four in compared. and also were the pectin) of of genes, levels absence virulence five Expression the the species. (in two in medium the RT-qPCR between by genes quantified lyase pectate in higher of was of genes capacity lyase The pectate of expression The 3.5 k=7.8; test: (Kruskal-Wallis of one from dianthicola different were D. 10 CI x calculated 5 the p= that DF=1; showed ( tissues mixtures symptomatic species five with assays co-inoculation In asymptomatic and symptomatic S4a) of p=0.08). number DF=1; the means (k=3.03; and incidence between strain differences symptom revealed per of test Kruskal-Wallis plants A counted. eight were on plants separately inoculated were < .dianthicola D. .Teepeso eesof levels expression The ). 10 k2.;D= p=1x10 ; DF=5 (k=25.1; . k2.;D=;p=7x10 DF=5; (k=21.3; -11 cbsE ± hnin than iueS5 Figure ntbr n =.;p 10 p= F=4.5; and tubers in Eo h ecnaeo ypoai lnsrahd43% reached plants symptomatic of percentage the of SE -3 ee eeepesda ihrlvlin level higher a at expressed were genes ) pelA F037 =.9 and p=0.99) (F=0.377; acsD .dianthicola D. nrte ise fhaits ubpat hsapae rmtn opttv exclusion competitive promoting appeared thus plants Bulb hyacinths. of tissues rotted in cbsE by .solani D. F843 p (F=864.3; -3 .solani D. .TeC einvleo 10 x 4 of value median CI The ). .solani D. pelD .I h bec fpci,ahge xrsino ett ys ee,especially genes, lyase pectate of expression higher a pectin, of absence the In ). xrsinlvlddntdffrdbtentetoseisi iesdtbr (F=-1.5; tubers diseased in species two the between differed not did level expression and iue5 Figure and acsD, oiiit otn ihalwbceilla ugse ieeta expression differential a suggested load bacterial low a with rotting initiate to 37rfrnegnm ( genome reference 3337 < hc ol edt nercmn in enrichment an to lead would which , pelE pelD nse ise,btnti ues( tubers in not but tissues, stem in -4 -4 10 hc r o novdi h ln elwl erdto,bti iron-uptake, in but degradation, wall cell plant the in involved not are which ). ,the ), ) pelE , -11 oprdto compared and -4 .solani D. and ) acsD .solani D. nstems; in pelA pelE k2.;D=;p=1x10 DF=5; (k=24.9; cbsE F-.;p09)gnswr o infiatydffrn between different significantly not were genes p=0.99) (F=-1.0; F843 p (F=864.3; eehge in higher were al S5) Table .solani D. n five and pelE F34 =00)gnswr xrse thge eesin levels higher at expressed were genes 0.01) p= (F=3.4; iueS4b Figure eoe ( genomes .dianthicola D. .solani D. 9 niae ihcmeiieavnaeof advantage competitive high a indicated iueS2 Figure =.;p . 10 x 1.1 p= F=4.5; : .solani D. 8 < w-hr fte 3 u f4)wr rvt oa to private were 45) of out (30 them of Two-third . .dianthicola D. 10 dnie w lee tthe at alleles two identified iueS2 Figure .solani D. a on oeagesv than aggressive more found was -11 ,teqC unicto fteptoesin pathogens the of quantification qPCR the ), ), hnin than . .solani D. .I h ieohr,mr hn10SNPs 100 than more others, nine the In ). pelD .solani D. -4 pelA ) ± cbsE , .solani D. hnin than 7ad23% and 17 F843 p (F=864.3; .dianthicola D. .solani D. ,5 fwihwr sebe after assembled were which of 56 ), =00;p1and p=1 F=-0.09; : tan rw eaaeyi rich a in separately grown strains -4 anandahge xrsinof expression higher a maintained pelA ntbr n =.;p F=8.1; and tubers in pelA k2.;D= p=1x10 ; DF=5 (k=20.3; .solani D. .dianthicola D. hnin than ntebl ln agrosystems. plant bulb the in k1.;D= p=4x10 ; DF=5 (k=17.1; , and pelD < ± 10 ,rsetvl ( respectively 9, .dianthicola D. h xrsinlevels expression The . .dianthicola D. and -11 and and ) .dianthicola D. vfmB ( pelE .dianthicola D. pelD iue and 5 Figures cbsE .solani D. pelE ee were genes F=864.3; : < F=0.67; : ee at gene, nterms in (F=2.9; Figure 10 -3 pelE and ) -11 over In . -3 D. in ), , ; Posted on Authorea 24 Jun 2020 — The copyright holder is the author/funder. All rights reserved. No reuse without permission. — https://doi.org/10.22541/au.159302219.97279363 — This a preprint and has not been peer reviewed. Data may be preliminary. F e ue) hsasywspromdi rpiae( 0tbr e ramn) rsa-alstests Kruskal-Wallis treatment). per tubers 10 x by (10 (3 inoculation used i.e., triplicate were treatments, in loads three inoculation performed the Two between was tuber. differences assay each revealed This to assigned tuber). was per class CFU symptom a and tubers 10 ( assays soft-rot assays. 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VfmB al S8 Table .Teeurgltdvrlnegnsin genes virulence upregulated These ). .solani D. D03.,RS02-A paadM1) nwihteohrvrain were variations other the which in M21a), and Sp1a RNS10-27-2A, (Ds0432.1, -3 Ser hnVfmB than ) Ser ,ec ftetoeprmna ouain n hi i a ncltdon inoculated was mix their and populations experimental two the of each ), Pro Pro eepae ntodffrn u-lses n ihol w VfmB two only with one sub-clusters, different two in placed were and lee( allele n VfmB and n VfmB and .Teeurgltdgnsecmasdvrlnedtriat that determinants virulence encompassed genes upregulated These ). P22 (VfmB IPO2222 .solani D. and pelL, .Uigteasgaino v ypo lse o 0inoculated 10 for classes symptom five of assignation the Using ). al S7 Table .dianthicola D. h rtaegenes protease the Pro Ser tan ( strains Ser s421 hl oeo hmwsfudaogtedown- the among found was them of none while Ds0432.1, rti tutrspeitdacnomtoa difference conformational a predicted structures protein strains 9 .W tde oeseicly3 well-characterized 35 specifically more studied We ). Pro Pro Pro iue7b Figure eoe,wieteVfmB the while genomes, n s421(VfmB Ds0432.1 and ) IO22 I3,A3 n 37 rVfmB or 3337) and AM3a MIE35, (IPO2222, iue7c Figure lee osrn (VfmB serine to allele) Ser ptrA pelE tan eemr grsie(Kruskal-Wallis aggressive more were strains iue7a Figure Pro Ser .dadantii D. .solani D. .solani D. n VfmB and , ). , .solani D. strains. prtB impC ; al S6 Table iue6c Figure iue6b Figure .solani D. and .solani D. .Ti hnei xlie by explained is change This ). , Pro < s421icue h pectate the included Ds0432.1 eoe.Asmlrpercentage similar A genomes. cytA Ser Nse ta. 2013). al., et (Nasser VfmB prtC, -VfmB .5adaslt o2fold log2 absolute and 0.05 Ser Ser xeietlpopulations experimental .Teepeso ffour of expression The ). Ser ots h xsec of existence the test to ) Ser lee,wihwsfound was which alleles, and ). Pro Pro VfmB eeldta the that revealed ) 37gnm ( genome 3337 n h T6SS-related the and leewsfudin found was allele Ser lee hnea the at change allele) , budA IO22 MIE35, (IPO2222, .solani D. aito ol be could variation Ser al 5and S5 Table a further was ) n VfmB and 7 F r10 or CFU VfmB Figure Ser Pro Pro Ser Ser D. D. D. 5 Posted on Authorea 24 Jun 2020 — The copyright holder is the author/funder. All rights reserved. No reuse without permission. — https://doi.org/10.22541/au.159302219.97279363 — This a preprint and has not been peer reviewed. Data may be preliminary. rea.Ohrmtblctat ol locnrbt otefins datg of advantage fitness the to contribute in also expressed could and full-length traits but metabolic 2019), Other al., et arsenal. Essarts des Raoul 2016; capacityand The comparing storage. solani By during D. 2016). and al., fields et the (Duprey the in the of did tubers expression on than higher consequences roots potential unwounded with of and tubers, wounded in the competed of inoculation contrast, an of after tubers versus stems invader parts host aerial exploited to therefore efficiently respect and with plants of species the these traits of ecological parts comparing different By in advantages successful niches. a contrasted ecological revealed by different surveys co-existence partially epidemiologic our puzzling years, such ten explain Over resources. same of the establishment for compete to expected 21 the of 20 the of of invasions successive Two the to in contribute alleles VfmB could Discussion two conditions 4 the the different contrast, of across frequencies gains In VfmB balanced opposite conditions. the Such of storage maintenance symptoms. than stem and fitness in competitive field particularly, lower and, the a in confer tubers to of maceration VfmB the initiate to compared VfmB the tubers 16 that rotted indicated in assays values plant the CI Altogether, of calculation allowed 10 symptoms 9 p= from assay recovered i.e., ( one bacteria treatments, plants and three of co-infected plants the sequencing 25 between Shotgun with difference assays no p=0.86). two revealed asympto- triplicate: tests Kruskal-Wallis and in treatment. symptomatic the performed of per was number plants the assay 15 and The with plants counted. non-wounded were on plants inoculated matic were mix VfmB their and the the lations to ( tubers, assays compared In symptom as blackleg 0.04). advantage In p= moderate ; a 10 DF=1 confer of k=4.4; to test; load or Wallis a (Kruskal neutral With one from 0.4). differed p= 2) ( DF=1; values k=0.8; CI calculate test; Wallis to 10 allowed of symptoms load from recovered a pathogens the of sequencing VfmB the When VfmB VfmB for the than 10 p=1.5x10 aggressive x DF=2; Tukey between p=9.5 (Post-hoc different (k=17.6; F=4.6; comparisons was load: high pairwise severity high load, both symptom bacterial at that the showed significant Whatever tests) loads. were pathogen differences p=0.03) the DF=2; (k=7.2; and mixture, their and .solani D. pelE .solani D. 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Pro ihamda Io 4 hwn tesavnaeo h VfmB the of advantage fitness a showing 14, of CI median a with ) vle pcfi euaoysqecsta otiue oadffrn xrsinlvl fthe of levels expression different a to contributes that sequences regulatory specific evolved . etr,ti ahgnbignwcniee sedmc n second, and endemic, as considered now being pathogen this century, 7 iky solani Dickeya ocueroiga oe atra odthan load bacterial lower a at rooting cause to tahg odad45 and load high a at F e ue,teC aus( aus ein=13 eentdffrn rmoe(Kruskal one from different not were 1.3) = median values; (8 values CI the tuber, per CFU VfmB Ser .solani D. ntrso ypo eeiy rlfrto n eaiefins ncmeiinasy.In assays. competition in fitness relative and proliferation severity, symptom of terms in tan hsmr ffiinl aae uesta VfmB than tubers damaged efficiently more thus strains oeecetyiiitdtertigpoes(seilya o atra nclm and inoculum) bacterial low a at (especially process rotting the initiated efficiently more iue8c Figure .solani D. Pro n VfmB and pel tanmxue the mixture, strain nye,epcal eEta csa niiitro h ln elwl degradation wall cell plant the of initiator an as acts that PelE especially enzymes, oehrwt aneac of maintenance a with together Dickeya and -6 iue8c Figure .dianthicola D. VfmB .TeeC auswr ieetfo n KuklWli et =.;DF=1; k=6.6; test; (Kruskal-Wallis one from different were values CI These ). talwla:F08 =00) The 0.01). p= F=0.8; load: low a at ; Pro .dianthicola D. .solani D. .solani D. Pro ± oaoptoesocre nErp:first Europe: in occurred pathogens potato pel Pro o VfmB for 2 ouain(S envalue mean (DSI population ,the ), ee nseveral in genes lee hssgetdta h VfmB the that suggested This allele. .solani D. The . xeietlppltoswr oifce ntbr,shotgun tubers, in co-infected were populations experimental and .solani D. as iia yposo oaopat,s htte are they that so plants, potato on symptoms similar cause .dianthicola D. Ser pelA Ser VfmB 10 s26 vs Pro 5 leewsascae oahge grsieesi the in aggressiveness higher a to associated was allele eei rnae in truncated is gene VfmB F e ue,teC aus( aus ein= median values; (3 values CI the tuber, per CFU Dickeya leewhen allele .solani D. Ser .tuberosum S. .dianthicola D. ± .solani D. .dianthicola D. Pro o VfmB for 9 tanmxueadtermx(=.9 DF=2; (k=0.29; mix their and mixture strain eide on otatdbhvosin behaviors contrasted found indeed we , and pce,Dpe ta.(06 hwdthat showed (2016) al. et Duprey species, populations. .solani D. ± Pro .solani D. .solani D. VfmB .solani D. Eo 92 of SE h resident The . allele. Pro u xeiet otiue to contributed experiments Our . Pro slkl tlatprl u oa to due partly least at likely is Pro .dianthicola D. Pro Ser talwload; low a at VfmB .solani D. rlfrtsi otdtubers rooted in proliferates .dianthicola D. and VfmB ± enocn hi virulence their reinforcing , leecudmr efficiently more could allele leei tmsymptoms. stem in allele .solani D. vfmB o VfmB for 2 .solani D. Ser .solani D. Ser iue8a-b Figure ouainwsmore was population .dianthicola D. leetu appeared thus allele xeietlpopu- experimental strains. Ser ttebeginning the at iue8a-b) Figure Dpe tal., et (Duprey VfmB o exploiting for leeseemed allele ntemiddle the in Ser -4 s73 vs n low and ) Ser .With ). more a a (at pelD ± 3 . Posted on Authorea 24 Jun 2020 — The copyright holder is the author/funder. All rights reserved. No reuse without permission. — https://doi.org/10.22541/au.159302219.97279363 — This a preprint and has not been peer reviewed. Data may be preliminary. including VfmB in ( lyases aggressiveness of pectate higher including slightly genes a quorum-sensing virulence ( Vfm-type some cellulases the of and in genes) upregulation involved and protein we rotting VfmB Remarkably, tuber variability. the their in maintain alleles Allelic two to in pathogens clonal. of contributed animal frequencies are selection and balanced Shykoff, Tanni`eres, balancing bacteria Barnier, plant observed 2014; Lang, that al., different these et indicating in Guidot as 2016; 2017), observed al., Faure, genomes et already (Feltner whole process were host-colonization systems the the along quorum-sensing agricultural across to some sweeps related and selective changes insects through water, diversity bottlenecks surface further genetic to soil, contribute could via seeds) horizontally tuber in contaminated (either asymptomatically by 2018). modes vertically Gilbert, or in understand dispersal practices & diversity to Mayfield, The low Germain, considered Europe. indicating 2018; be in data al., should et sequencing pathogen) (Cadotte genome resident pathogen The bacterial a a and by host invasion plant biological the the (here, of components percentage another ecological the the with invasion, of belonging microbial increase interactions size the on slow any that literature observed population suggested the without decade small hypothesis, one individual A over this fields plant with diagnosis. line a prophylactic reduce In in invasion. to could delay proliferate subjected that could are factor that species Another or 2013). seeds single 2005; McDonald, tuber a Bockus, & in to & Zhan as Garrett, 2015; well (Al-Naimi, al., two as fungi et the pathogenic Gladieux between in 2017; competition studied al., well et been Abdullah have processes facilitation including and (microbiota factors limit biological and or climate) and host, plant (soil potato mental between interaction tripartite 2019). the al., Beside et in Essarts shunt des glyoxylate (Raoul the low of is expression higher a in revealed transcriptomics comparative tubers: rdcsblnigslcini aua ouain.TeVfmB The populations. natural in selection balancing VfmB predicts of advantage deeper environment-dependent go This VfmB to symptoms. the premature that was and it assays, elucidated, vfmB stem completely the not is of VfmB signaling characterization the Vfm in mechanistic protein the VfmB into the of role the of Bwsspotdb h rn rmUiestePrsSd(nvri´ ai-aly,K a supported was KR (Universit´e Universit´e Paris-Saclay), Paris-Sud from grant PhD a by supported was PB competitors. endemic of maintenance pathogen of the ACKNOWLEDGEMENTS of determinants for causes ecological conditions the and the understanding pattern our of the to and contributes of invasion study understanding this broadly, better More a persisted. allowing insights between novel brings competition the study of this a increase conclusion, year. an under In sampling with and recent agreement more VfmB agrosystems in the of potato decade, variation in down alleles in past and the establishment up over the revealed populations data of epidemiologic beginning VfmB Our contrast, the established. In at condition. dispersal reduced high is competition when .solani D. Dickeya Pectobacterium .dianthicola, D. .solani D. .solani D. .solani D. pel Ser atra h hmclsrcueo h f inli o nw,bti a enivle in involved been has it but known, not is signal Vfm the of structure chemical The bacteria. ahgn eoee rmtbrsmtm,w ofimda niheto peuae genes, upregulated of enrichment an confirmed we symptoms, tuber from recovered pathogens Cakwk 08 ohe l,21) eeto nsm ee a lohv ute reduced further have also may genes some on Selection 2011). al., et Toth 2018; (Charkowsky and tan eemr grsieta h VfmB the than aggressive more were strains nainit oaopouto goytm,adteraoswhy reasons the and agrosystems, production potato into invasion prt salsmn Cakwk 08 hnu ta. 09 ohe l,21) Competition 2011). al., et Toth 2019; al., et Shyntum 2018; (Charkowsky establishment ahgnseis hs ffcslne osz ouainaddseslaeepce to expected are dispersal and population size to linked effects These species. pathogen aha htcnrbtst xli lentv abnsucswe ua availability sugar when sources carbon alternative exploit to contributes that pathway a ee,i h VfmB the in genes, cel ee)(asre l,21;Ptyu ta. 08.Uigtbrasy,w observed we assays, tuber Using 2018). al., et Potrykus 2013; al., et (Nasser genes) Dickeya Ser tan eels opttv hnteVfmB the than competitive less were strains .solani D. pce sterntrllwaudnei ol n ufc waters, surface and soils in abundance low natural their is species Dickeya Ser Ser ser tanD03. oprdt VfmB to compared Ds0432.1 strain tan oprdt VfmB to compared strains ahgnapasa odeapeilsrtn o different how illustrating example good a as appears pathogen ol eotoptdb VfmB by outcompeted be could nainwssilogig(0421) mn h emerging the Among (2004-2015). ongoing still was invasion Ser 11 n VfmB and .solani D. .solani D. Pro ser n VfmB and tan nptt ues u o npotato in not but tubers, potato in strains ser Pro ugs oteekdrn introduction during bottleneck a suggest leecudtu rvd nadvantage an provide thus could allele and Pectobacterium lee.I hswr,w hwdthat showed we work, this In alleles. .dianthicola D. Pro Pro lee npatifcinassays infection plant in alleles tan.Uigtranscriptomics Using strains. ser Pro Pro Pro .dianthicola D. eaieaudnei field in abundance relative when pel tan ntbradstem and tuber in strains tanIO22 Because IPO2222. strain pce)myfacilitate may species) ee) rtae ( proteases genes), diinlenviron- additional , .solani D. Dickeya .solani D. .solani D. nevertheless salready is -positive Dickeya VfmB than prt Posted on Authorea 24 Jun 2020 — The copyright holder is the author/funder. All rights reserved. No reuse without permission. — https://doi.org/10.22541/au.159302219.97279363 — This a preprint and has not been peer reviewed. 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All rights reserved. No reuse without permission. — https://doi.org/10.22541/au.159302219.97279363 — This a preprint and has not been peer reviewed. Data may be preliminary. fDIvle eemaue o aho h five the of each for In measured were tubers. values 10 on DSI observed of classes symptom using calculated eemaue wc o aho h xeietlppltosof populations experimental the of each In for graphs. twice the measured below were indicated are classes symptom ( five using five and PPO9019) 10 either by tuber each are inoculating by one and of conducted from fitness were difference assays and testing Rotting Aggressiveness tests Kruskal-Wallis 4 from Figure resulting 0.05 In for p-values * bar; 0.1. of Legend: thick advantage [?] indicated. a p competitive by when a represented graph, revealed is by the and inoculated below tissues indicated plants between symptomatic are 15 values classes on (CI) symptomatic measured index the was of which tests) symptoms Tukey between blackleg classes In exhibiting symptomatic graph. plants the dianthicola the of of below comparing (%) indicated test Kruskal-Wallis centages is the species of two p-value The the five plants. the 15 on of MIE34) each five and of PPO9019) inoculation Ds0432.1, after measured were which of fitness a and Aggressiveness 3 Figure i.e. groups, solani population pathogen four and delineated method group ( lani 2006). of exception the and fields containing ptoms. 2 Figure of aggressiveness the compare to used by caused solani Symptoms 1 Figure legends Figure orcid.org/0000-0002-5379-8867 Faure Denis disclosed. ORCID was manuscript. interest the of wrote compared conflict SR potential SK VH, No sequencing; PB, TG, perforemd DF, and INTEREST analyses; OF samples statistical CONFLICT DNA performed DF prepared and PB KR and PB, molecular AL genomes; and KGC, sampling field KWH, performed YJ, VH in and in traits AB traits AL, fitness fitness PD, characterized EM, PB JC, experiments; diagnosis; conceived VH PB, DF, CONTRIBUTION AUTHOR VZQM00000000 VZQL00000000; VZQJ00000000; VZQK00000000; VZ- VZQG00000000; VZQI00000000; VZQF00000000; QH00000000; VZQE00000000; VYSC00000000; accessions Genbank sequences: DNA envleadsadr ro S)o h ecnae()vle fpat xiiigbake symptoms, blackleg exhibiting plants of values (%) percentage the of (SE) error standard and value mean , c Pectobacterium sltscletdi 9smtmtcfilssmldfo 03t 06 irrhclcutrn paired clustering hierarchical A 2016. to 2013 from sampled fields symptomatic 19 in collected isolates r10 or ) and and ecnaeof Percentage Dickeya Pectobacterium a iky dianthicola Dickeya and 5 n w ( two and ) F fptoes(in pathogens of CFU .solani D. .sln vfmB solani D. .dianthicola D. I:9fields), 9 (II: and .dianthicola D. Pectobacterium c d ubradrltv bnac fthe of abundance relative and Number ) needn xeiet.Tepvle fteKuklWli et comparing tests Kruskal-Wallis the of p-values The experiments. independent ) Pectobacterium I:4fields). 4 (IV: ouain n hi i.Tepvle ftepiws oprsn (Post-hoc comparisons pairwise the of p-values The mix. their and populations .solani D. < .dianthicola D. [].;* o 0.01 for ** p[?]0.1; nptt tm ( stems potato on ains BpromdRAaaye R-PRadtranscriptomics); and (RT-qPCR analyses RNA performed PB variants; .dianthicola D. cnann ed ( fields -containing d tan RS14--A FP88 FP92 FP05 MIE34) CFBP2015, CFBP2982, CFBP1888, (RNS11-47-1-1A, strains Dickeya , cnann and -containing iky solani Dickeya and e and .dianthicola D. f .solani D. iky dianthicola Dickeya rvlnefo oaofilsehbtn lclgsym- blackleg exhibiting fields potato from prevalence .In ). tan RS14--A FP88 FP92 CFBP2015, CFBP2982, CFBP1888, (RNS11-47-1-1A, strains iky dianthicola Dickeya pathogens. .solani D. < b and a a envleadS ewe w elctso h per- the of replicates two between SE and value mean , [].5ad**frp[?]0.01. p for *** and p[?]0.05 n ycnh ( hyacinths and ) , b 15 b and and Pectobacterium b Dickeya , and eecluae ahya rm20 o21 (with 2015 to 2004 from year each calculated were ) d iky dianthicola Dickeya and e ouain eecluae negtco-infected eight in calculated were populations tan 33,IO22 N0--A Ds0432.1, RNS05-1-2A, IPO2222, (3337, strains .solani D. envle n tnaderr fDIvalues DSI of errors standard and values mean , .dianthicola D. a ypos(ht ros asdby caused arrows) (white Symptoms e and cnann ed ( fields -containing .dianthicola D. ahdsaesvrt ne DI au was value (DSI) index severity disease each , Pectobacterium .datioa .solani D. dianthicola, D. Pectobacterium d envle n tnaderr (SE) errors standard and values mean , and b tan 33,IO22 RNS05-1-2A, IPO2222, (3337, strains 7 and II ed) and fields), 3 (III: .Tefiesmtmcass( o4) to (0 classes symptom five The ). ooyfriguis(F)(in (CFU) units colony-forming .solani D. B RadE characterized EM and KR PB, ; .solani D. h Imda =2410 2.4 (= median CI the : nptt ues( tubers potato on ny(:3fields), 3 (I: only , a .dianthicola D. n htof that and ) nptt plants. potato in nptt tubers. potato in .datioa D. dianthicola, D. n h mixture the and c competitive , c and .solani D. ). .solani D. .solani D. Dickeya .so- D. a , -5 D. In b ) - Posted on Authorea 24 Jun 2020 — The copyright holder is the author/funder. All rights reserved. No reuse without permission. — https://doi.org/10.22541/au.159302219.97279363 — This a preprint and has not been peer reviewed. 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VfmB by the four calculated the were comparing In VfmB test which Wallis or server. values, 3337) web and (DSI) 10 EzMol AM3a by index MIE35, infected the severity tubers using 10 disease obtained on representations of classes VfmB (SE) conformational the showed error in protein standard VfmB color the red VfmB of the in with structure are associated Phyre2-predicted beta-sheet the the model, in a differences as c3djlA) alleles. is VfmB the accession of Characterization 7 Figure France. in VfmB the font; blue in indicated is of isolates tree (SNP)-based polymorphism nucleotide 10 x 9 = neither lines that solani revealed thick test) as (Kruskal-Wallis 1 represented and or are values CI in CI between of repeats differences values Statistical (8 Median 1.7 tissues. reached co-infected and from recovered populations bacterial VfmB of In c n . ( 5.8 and ) .solani D. c yaiso h VfmB the of dynamics , < < , pelD [].;* o 0.01 for ** p[?]0.1; [?]0.01. p for *** and p[?]0.05 VfmB -3 Pro and in Pro VfmB n VfmB and f c n h Ivle eesaitclydffrn rmoe(rsa-alsts;p=510 5 = p test; (Kruskal-Wallis one from different statistically were values CI the and ) c c .Lgn:*fr0.05 for * Legend: ). pelE oprtv rncitm of transcriptome comparative , a oecmeiiei uesiouae ihalwla p=00 in 0.04 = (p load low a with inoculated tubers in competitive more was and Ser ee a vlae nec ftefive the of each in evaluated was genes eB eC eC hcpA pelC, pelC, pelB, f a infiatavnaei uesiouae ihahg od( . in 0.3 = (p load high a with inoculated tubers in advantage significant had h opttv ne C)between (CI) index competitive the , Ser a < and [].5ad**frp[?]0.01. p for *** and p[?]0.05 ouain eecluae sn leecut ae nsognsqecn of sequencing shotgun on based counts allele using calculated were populations Ser a b .dianthicola D. a r10 or ) lee()aogthe among (%) allele ahdsaesvrt ne DI au a acltduigsymptomatic using calculated was value (DSI) index severity disease each , ,20( eet in repeats (3 2.0 ), Ser 7 otn saswr odce yiouaigec ue yete 10 either by tuber each inoculating by conducted were assays Rotting F fec fthe of each of CFU < Pro D03.,RS02-A paadM1) h -au fteKruskal- the of p-value the M21a); and Sp1a RNS10-27-2A, (Ds0432.1, [].;* o 0.01 for ** p[?]0.1; 5 iky solani Dickeya F ( CFU n orVfmB four and Ser and tan RS14--A FP88 FP92 CFBP2015, CFBP2982, CFBP1888, (RNS11-47-1-1A, strains b n VfmB and .solani D. .solani D. fteVfmB the of ) .solani D. prtA b 16 .solani D. In Pro n 40(6rpasin repeats (16 14.0 and ) ee coe circles). (closed genes .solani D. Ser pelA a < . 37(VfmB 3337 Pro tan sn HLVZ h aeo h French the of name the PHYLOViZ; using strains n VfmB and sn the using , [].5ad**frp[?]0.01. p for *** and p[?]0.05 In Pro tan sn ypo lse sidctdbelow indicated is classes symptom using strains 37gnm) nthe in genome), 3337 .solani D. iky solani Dickeya a tan sdi h ln sasaeunderlined. are assays plant the in used strains .solani D. , cno 67 of scan , pelD .solani D. Pro 7% n VfmB and (71%) sltsaogtesmln eid2005-2015 period sampling the along isolates tan arigete VfmB either carrying strains n VfmB and ,b a, Ser and shrci coli Escherichia Pro Pro tan 33,IO22 RNS05-1-2A, IPO2222, (3337, strains c lee;tePo5adSr5positions Ser55 and Pro55 the alleles; eed o 0.05 for * Legend: . ecnae()o lnsexhibiting plants of (%) percentage , and n s421(VfmB Ds0432.1 and ) and n VfmB and pelE .solani D. Ser c .dianthicola D. opttv ne C)values (CI) index competitive , xeietlpopulations experimental . .solani D. Ser h xrsinlvlo the of level expression The c vfmB ntetretreatments. three the in ) 2% lee.In alleles. (29%) Ser ibpoen(h PDB (the protein Aidb eoe eeldthat revealed genomes .solani D. rpoB ee a h most the was gene, b b .solani D. envle and values mean , ouain n a and populations n nses(p stems in and ) ouain was populations < and [].;* for ** p[?]0.1; Pro Ser populations recovered ) (IPO2222, a yafS VfmB ,but ), b single , -5 gene and Ser Pro D. 7 ) Posted on Authorea 24 Jun 2020 — The copyright holder is the author/funder. All rights reserved. No reuse without permission. — https://doi.org/10.22541/au.159302219.97279363 — This a preprint and has not been peer reviewed. Data may be preliminary. and-of-the-maintenance-of-the-resident-pathogen-d-dianthicola causes-of-the-establishment-of-the-invasive-bacterial-potato-pathogen-dickeya-solani- figures.pdf pdf file Hosted vial at available https://authorea.com/users/335926/articles/461698-pattern-and- 17