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Resistance of Dickeya solani strain IPO 2222 to lytic bacteriophage ΦD5 results in fitness tradeoffs for the bacterium during infection

  • Campbell, A. The future of bacteriophage biology. Nat. Rev. Genet. 4, 471–477. https://doi.org/10.1038/nrg1089 (2003).

    CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Cheetham, B. F. & Katz, M. E. A role for bacteriophages in the evolution and transfer of bacterial virulence determinants. Mol. Microbiol. 18, 201–208. https://doi.org/10.1111/j.1365-2958.1995.mmi_18020201.x (1995).

    CAS 
    Article 
    PubMed 

    Google Scholar 

  • Mann, N. H. The third age of phage. PLoS Biol. 3, e182. https://doi.org/10.1371/journal.pbio.0030182 (2005).

    CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Thurber, R. V. Current insights into phage biodiversity and biogeography. Curr. Opin. Microbiol. 12, 582–587. https://doi.org/10.1016/j.mib.2009.08.008 (2009).

    CAS 
    Article 
    PubMed 

    Google Scholar 

  • Buckling, A. & Rainey, P. B. Antagonistic coevolution between a bacterium and a bacteriophage. Proc. Biol. Sci. 269, 931–936. https://doi.org/10.1098/rspb.2001.1945 (2002).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Dennehy, J. J. What can phages tell us about host-pathogen coevolution?. Int. J. Evol. Biol. 2012, 396165. https://doi.org/10.1155/2012/396165 (2012).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Forde, S. E., Thompson, J. N., Holt, R. D. & Bohannan, B. J. Coevolution drives temporal changes in fitness and diversity across environments in a bacteria-bacteriophage interaction. Evolution 62, 1830–1839. https://doi.org/10.1111/j.1558-5646.2008.00411.x (2008).

    Article 
    PubMed 

    Google Scholar 

  • Suttle, C. A. The significance of viruses to mortality in aquatic microbial communities. Microb. Ecol. 28, 237–243. https://doi.org/10.1007/BF00166813 (1994).

    CAS 
    Article 
    PubMed 

    Google Scholar 

  • Duffy, M. A. & Forde, S. E. Ecological feedbacks and the evolution of resistance. J. Anim. Ecol. 78, 1106–1112. https://doi.org/10.1111/j.1365-2656.2009.01568.x (2009).

    Article 
    PubMed 

    Google Scholar 

  • Koskella, B. & Brockhurst, M. A. Bacteria-phage coevolution as a driver of ecological and evolutionary processes in microbial communities. FEMS Microbiol. Rev. 38, 916–931. https://doi.org/10.1111/1574-6976.12072 (2014).

    CAS 
    Article 
    PubMed 

    Google Scholar 

  • Chibani-Chennoufi, S., Bruttin, A., Dillmann, M. L. & Brussow, H. Phage-host interaction: an ecological perspective. J. Bacteriol. 186, 3677–3686. https://doi.org/10.1128/JB.186.12.3677-3686.2004 (2004).

    CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Waterbury, J. B. & Valois, F. W. Resistance to co-occurring phages enables marine synechococcus communities to coexist with cyanophages abundant in seawater. Appl. Environ. Microbiol. 59, 3393–3399. https://doi.org/10.1128/aem.59.10.3393-3399.1993 (1993).

    ADS 
    CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Koskella, B. & Parr, N. The evolution of bacterial resistance against bacteriophages in the horse chestnut phyllosphere is general across both space and time. Phil. Trans. R. Soc. B 370, 20140297 (2015).

    Article 

    Google Scholar 

  • Hantula, J., Kurki, A., Vuoriranta, P. & Bamford, D. H. Ecology of bacteriophages infecting activated sludge bacteria. Appl. Environ. Microbiol. 57, 2147–2151. https://doi.org/10.1128/aem.57.8.2147-2151.1991 (1991).

    ADS 
    CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Fernandez, L., Gutierrez, D., Rodriguez, A. & Garcia, P. Application of bacteriophages in the agro-food sector: a long way toward approval. Front. Cell Infect. Microbiol. 8, 296. https://doi.org/10.3389/fcimb.2018.00296 (2018).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Jones, J. B. et al. Bacteriophages for plant disease control. Annu Rev. Phytopathol. 45, 245–262. https://doi.org/10.1146/annurev.phyto.45.062806.094411 (2007).

    CAS 
    Article 
    PubMed 

    Google Scholar 

  • Bradde, S., Vucelja, M., Tesileanu, T. & Balasubramanian, V. Dynamics of adaptive immunity against phage in bacterial populations. PLoS Comput. Biol. 13, e1005486. https://doi.org/10.1371/journal.pcbi.1005486 (2017).

    ADS 
    CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Naureen, Z. et al. Bacteriophages presence in nature and their role in the natural selection of bacterial populations. Acta Biomed. 91, e2020024. https://doi.org/10.23750/abm.v91i13-S.10819 (2020).

    CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Stern, A. & Sorek, R. The phage-host arms race: shaping the evolution of microbes. BioEssays 33, 43–51. https://doi.org/10.1002/bies.201000071 (2011).

    CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Burmeister, A. R. & Turner, P. E. Trading-off and trading-up in the world of bacteria-phage evolution. Curr. Biol. 30, R1120–R1124. https://doi.org/10.1016/j.cub.2020.07.036 (2020).

    CAS 
    Article 
    PubMed 

    Google Scholar 

  • Koderi Valappil, S. et al. Survival comes at a cost: a coevolution of phage and its host leads to phage resistance and antibiotic sensitivity of Pseudomonas aeruginosa multidrug resistant strains. Front. Microbiol. 12, 783722. https://doi.org/10.3389/fmicb.2021.783722 (2021).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Labrie, S. J., Samson, J. E. & Moineau, S. Bacteriophage resistance mechanisms. Nat. Rev. Microbiol. 8, 317–327. https://doi.org/10.1038/nrmicro2315 (2010).

    CAS 
    Article 
    PubMed 

    Google Scholar 

  • Lythgoe, K. A. & Chao, L. Mechanisms of coexistence of a bacteria and a bacteriophage in a spatially homogeneous environment. Ecol. Lett. 6, 326–334. https://doi.org/10.1046/j.1461-0248.2003.00433.x (2003).

    Article 

    Google Scholar 

  • Mizoguchi, K. et al. Coevolution of bacteriophage PP01 and Escherichia coli O157:H7 in continuous culture. Appl. Environ. Microbiol. 69, 170–176. https://doi.org/10.1128/AEM.69.1.170-176.2003 (2003).

    ADS 
    CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Lennon, J. T., Khatana, S. A., Marston, M. F. & Martiny, J. B. Is there a cost of virus resistance in marine cyanobacteria?. ISME J. 1, 300–312. https://doi.org/10.1038/ismej.2007.37 (2007).

    Article 
    PubMed 

    Google Scholar 

  • Vale, P. F. et al. Costs of CRISPR-Cas-mediated resistance in Streptococcus thermophilus. Proc. Biol. Sci. 282, 20151270. https://doi.org/10.1098/rspb.2015.1270 (2015).

    CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Keen, E. C. Tradeoffs in bacteriophage life histories. Bacteriophage 4, e28365. https://doi.org/10.4161/bact.28365 (2014).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Abedon, S. T. Bacterial ‘immunity’ against bacteriophages. Bacteriophage 2, 50–54 (2012).

    Article 

    Google Scholar 

  • Charkowski, A. O. The changing face of bacterial soft-rot diseases. Annu. Rev. Phytopathol. 56, 269–288. https://doi.org/10.1146/annurev-phyto-080417-045906 (2018).

    CAS 
    Article 
    PubMed 

    Google Scholar 

  • Mansfield, J. et al. Top 10 plant pathogenic bacteria in molecular plant pathology. Mol. Plant Pathol. 13, 614–629. https://doi.org/10.1111/j.1364-3703.2012.00804.x (2012).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Perombelon, M. C. M. Potato diseases caused by soft rot Erwinias: an overview of pathogenesis. Plant. Pathol. 51, 1–12. https://doi.org/10.1046/j.0032-0862.2001.Shorttitle.doc.x (2002).

    Article 

    Google Scholar 

  • Perombelon, M. C. M. & Kelman, A. Ecology of the soft rot Erwinias. Annu. Rev. Phytopathol. 18, 361–387 (1980).

    Article 

    Google Scholar 

  • Rossmann, S., Dees, M. W., Perminow, J., Meadow, R. & Brurberg, M. B. Soft Rot Enterobacteriaceae are carried by a large range of insect species in potato fields. Appl. Environ. Microbiol. 84, 1. https://doi.org/10.1128/AEM.00281-18 (2018).

    Article 

    Google Scholar 

  • Fikowicz-Krosko, J., Wszalek-Rozek, K., Smolarska, A. & Czajkowski, R. First report of isolation of soft rot Pectobacterium carotovorum subsp carotovorum from symptomless bittersweet nightshade occuing in rural area of Poland. J. Plant Pathol. 99, 1 (2017).

    Google Scholar 

  • Batinovic, S. et al. Bacteriophages in natural and artificial environments. Pathogens 8, 100. https://doi.org/10.3390/pathogens8030100 (2019).

    CAS 
    Article 
    PubMed Central 

    Google Scholar 

  • Wright, R. C. T., Friman, V. P., Smith, M. C. M. & Brockhurst, M. A. Resistance evolution against phage combinations depends on the timing and order of exposure. mBio 10, e01652–01619, https://doi.org/10.1128/mBio.01652-19 (2019).

  • Borin, J. M., Avrani, S., Barrick, J. E., Petrie, K. L. & Meyer, J. R. Coevolutionary phage training leads to greater bacterial suppression and delays the evolution of phage resistance. Proc. Natl. Acad. Sci. USA 118, e2104592118. https://doi.org/10.1073/pnas.2104592118 (2021).

    CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • van der Wolf, J. M. et al. Dickeya solani sp. nov., a pectinolytic plant-pathogenic bacterium isolated from potato (Solanum tuberosum). Int J Syst Evol Microbiol 64, 768–774, https://doi.org/10.1099/ijs.0.052944-0 (2014).

  • Toth, I. K. et al. Dickeya species: an emerging problem for potato production in Europe. Plant. Pathol. 60, 385–399. https://doi.org/10.1111/j.1365-3059.2011.02427.x (2011).

    Article 

    Google Scholar 

  • Czajkowski, R., van Veen, J. A. & van der Wolf, J. M. New biovar 3 Dickeya spp. strain (syn. Erwinia chrysanthemi) as a causative agent of blackleg in seed potato in Europe. Phytopathology 99, S27-S27 (2009).

  • Tsror Lahkim, L. et al. Characterization of Dickeya strains isolated from potato grown under hot-climate conditions. Plant Pathology 62, 1097–1105, doi:https://doi.org/10.1111/ppa.12030 (2013).

  • Tsror, L. et al. First report of potato blackleg caused by a biovar 3 Dickeya sp. in Georgia. New Disease Reports 23, 1 (2011).

  • Ozturk, M. & Aksoy, H. M. First report of Dickeya solani associated with potato blackleg and soft rot in Turkey. J. Plant Pathol. 99, 298 (2017).

    Google Scholar 

  • Cardoza, Y. F., Duarte, V. & Lopes, C. A. First report of blackleg of potato caused by Dickeya solani in Brazil. Plant. Dis. 101, 243–243. https://doi.org/10.1094/pdis-07-16-1045-pdn (2017).

    CAS 
    Article 

    Google Scholar 

  • Khayi, S., Blin, P., Chong, T. M., Chan, K. G. & Faure, D. Complete genome anatomy of the emerging potato pathogen Dickeya solani type strain IPO 2222(T). Stand. Genom. Sci. 11, 87. https://doi.org/10.1186/s40793-016-0208-0 (2016).

    CAS 
    Article 

    Google Scholar 

  • Czajkowski, R., Ozymko, Z. & Lojkowska, E. Isolation and characterization of novel soilborne lytic bacteriophages infecting Dickeya spp. biovar 3 (‘D. solani’). Plant Pathol. 63, 758–772, doi:https://doi.org/10.1111/ppa.12157 (2014).

  • Czajkowski, R., Smolarska, A. & Ozymko, Z. The viability of lytic bacteriophage PhiD5 in potato-associated environments and its effect on Dickeya solani in potato (Solanum tuberosum L.) plants. PLoS ONE 12, e0183200, doi:https://doi.org/10.1371/journal.pone.0183200 (2017).

  • Adriaenssens, E. M. et al. A suggested new bacteriophage genus: “Viunalikevirus”. Arch Virol 157, 2035–2046. https://doi.org/10.1007/s00705-012-1360-5 (2012).

    CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Adriaenssens, E. M. et al. T4-related bacteriophage LIMEstone isolates for the control of soft rot on potato caused by “Dickeya solani”. PLoS ONE 7, e33227. https://doi.org/10.1371/journal.pone.0033227 (2012).

    ADS 
    CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Petrzik, K., Vacek, J., Brazdova, S., Sevcik, R. & Koloniuk, I. Diversity of limestone bacteriophages infecting Dickeya solani isolated in the Czech Republic. Arch Virol 166, 1171–1175. https://doi.org/10.1007/s00705-020-04926-7 (2021).

    CAS 
    Article 
    PubMed 

    Google Scholar 

  • Ranjan, M. et al. Genomic diversity and organization of complex polysaccharide biosynthesis clusters in the genus Dickeya. PLoS ONE 16, e0245727. https://doi.org/10.1371/journal.pone.0245727 (2021).

    CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Pedron, J., Chapelle, E., Alunni, B. & Van Gijsegem, F. Transcriptome analysis of the Dickeya dadantii PecS regulon during the early stages of interaction with Arabidopsis thaliana. Mol Plant Pathol 19, 647–663. https://doi.org/10.1111/mpp.12549 (2018).

    CAS 
    Article 
    PubMed 

    Google Scholar 

  • Czajkowski, R. Bacteriophages of Soft Rot Enterobacteriaceae-a minireview. FEMS Microbiol. Lett. 363, fnv230, doi:https://doi.org/10.1093/femsle/fnv230 (2016).

  • Toth, I. K. et al. in Plant Diseases Caused by Dickeya and Pectobacterium Species (eds Frédérique Van Gijsegem, Jan M. van der Wolf, & Ian K. Toth) Ch. Chapter 2, 13–37 (Springer International Publishing, 2021).

  • Holt, K. E., Lassalle, F., Wyres, K. L., Wick, R. & Mostowy, R. J. Diversity and evolution of surface polysaccharide synthesis loci in Enterobacteriales. ISME J. 14, 1713–1730. https://doi.org/10.1038/s41396-020-0628-0 (2020).

    CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Schnaitman, C. A. & Klena, J. D. Genetics of lipopolysaccharide biosynthesis in enteric bacteria. Microbiol. Rev. 57, 655–682. https://doi.org/10.1128/mr.57.3.655-682.1993 (1993).

    CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Mangalea, M. R. & Duerkop, B. A. Fitness trade-offs resulting from bacteriophage resistance potentiate synergistic antibacterial strategies. Infect. Immun. 88, e00926-e1919. https://doi.org/10.1128/IAI.00926-19 (2020).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Bohannan, B. J. M. & Lenski, R. E. Linking genetic change to community evolution: insights from studies of bacteria and bacteriophage. Ecol. Lett. 3, 362–377. https://doi.org/10.1046/j.1461-0248.2000.00161.x (2000).

    Article 

    Google Scholar 

  • Bartnik, P., Jafra, S., Narajczyk, M., Czaplewska, P. & Czajkowski, R. Pectobacterium parmentieri SCC 3193 mutants with altered synthesis of cell surface polysaccharides are resistant to N4-like lytic bacteriophage phiA38 (vB_Ppp_A38) but express decreased virulence in potato (Solanum tuberosum L.) Plants. Int J Mol Sci 22, 7346, doi:https://doi.org/10.3390/ijms22147346 (2021).

  • Evans, T. J., Ind, A., Komitopoulou, E. & Salmond, G. P. C. Phage-selected lipopolysaccharide mutants of Pectobacterium atrosepticum exhibit different impacts on virulence. J. Appl. Microbiol. 109, 505–514. https://doi.org/10.1111/j.1365-2672.2010.04669.x (2010).

    CAS 
    Article 
    PubMed 

    Google Scholar 

  • Lukianova, A. A. et al. Morphologically Different Pectobacterium brasiliense bacteriophages PP99 and PP101: deacetylation of O-polysaccharide by the tail spike protein of phage PP99 accompanies the Infection. Front. Microbiol. 10, 3147. https://doi.org/10.3389/fmicb.2019.03147 (2019).

    Article 
    PubMed 

    Google Scholar 

  • Kim, H. et al. Colanic acid is a novel phage receptor of Pectobacterium carotovorum subsp. carotovorum phage POP72. Front. Microbiol. 10, 143, https://doi.org/10.3389/fmicb.2019.00143 (2019).

  • Costerton, J. W., Irvin, R. T. & Cheng, K. J. The role of bacterial surface structures in pathogenesis. Crit. Rev. Microbiol. 8, 303–338. https://doi.org/10.3109/10408418109085082 (1981).

    CAS 
    Article 
    PubMed 

    Google Scholar 

  • Beveridge, T. J. & Graham, L. L. Surface layers of bacteria. Microbiol. Rev. 55, 684–705. https://doi.org/10.1128/mr.55.4.684-705.1991 (1991).

    CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • D’Haeze, W. & Holsters, M. Surface polysaccharides enable bacteria to evade plant immunity. Trends Microbiol. 12, 555–561. https://doi.org/10.1016/j.tim.2004.10.009 (2004).

    CAS 
    Article 
    PubMed 

    Google Scholar 

  • Li, J. & Wang, N. The gpsX gene encoding a glycosyltransferase is important for polysaccharide production and required for full virulence in Xanthomonas citri subsp. citri. BMC Microbiol. 12, 31 (2012).

  • Santaella, C., Schue, M., Berge, O., Heulin, T. & Achouak, W. The exopolysaccharide of Rhizobium sp. YAS34 is not necessary for biofilm formation on Arabidopsis thaliana and Brassica napus roots but contributes to root colonization. Environ. Microbiol. 10, 2150–2163, doi:https://doi.org/10.1111/j.1462-2920.2008.01650.x (2008).

  • Morona, J. K., Miller, D. C., Morona, R. & Paton, J. C. The effect that mutations in the conserved capsular polysaccharide biosynthesis genes cpsA, cpsB, and cpsD have on virulence of Streptococcus pneumoniae. J. Infect. Dis. 189, 1905–1913. https://doi.org/10.1086/383352 (2004).

    CAS 
    Article 
    PubMed 

    Google Scholar 

  • Lawlor, M. S., Handley, S. A. & Miller, V. L. Comparison of the host responses to wild-type and cpsB mutant Klebsiella pneumoniae infections. Infect. Immun. 74, 5402–5407. https://doi.org/10.1128/IAI.00244-06 (2006).

    CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Geider, K. et al. in Advances in Molecular Genetics of Plant-Microbe Interactions Vol. 1 Current Plant Science and Biotechnology in Agriculture (eds Hauke Hennecke & Desh Pal S. Verma) Ch. Chapter 14, 90–93 (Springer Netherlands, 1991).

  • Mohamed, K. H. et al. Deciphering the dual effect of lipopolysaccharides from plant pathogenic Pectobacterium. Plant Signal Behav. 10, e1000160. https://doi.org/10.1080/15592324.2014.1000160 (2015).

    CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Katzen, F. et al. Xanthomonas campestris pv. campestris gum mutants: effects on xanthan biosynthesis and plant virulence. J. Bacteriol. 180, 1607–1617. https://doi.org/10.1128/JB.180.7.1607-1617.1998 (1998).

    CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Whitfield, C., Wear, S. S. & Sande, C. Assembly of bacterial capsular polysaccharides and exopolysaccharides. Annu. Rev. Microbiol. 74, 521–543. https://doi.org/10.1146/annurev-micro-011420-075607 (2020).

    CAS 
    Article 
    PubMed 

    Google Scholar 

  • Ormeno-Orrillo, E., Rosenblueth, M., Luyten, E., Vanderleyden, J. & Martinez-Romero, E. Mutations in lipopolysaccharide biosynthetic genes impair maize rhizosphere and root colonization of Rhizobium tropici CIAT899. Environ. Microbiol. 10, 1271–1284. https://doi.org/10.1111/j.1462-2920.2007.01541.x (2008).

    CAS 
    Article 
    PubMed 

    Google Scholar 

  • Touze, T., Goude, R., Georgeault, S., Blanco, C. & Bonnassie, S. Erwinia chrysanthemi O antigen is required for betaine osmoprotection in high-salt media. J. Bacteriol. 186, 5547–5550. https://doi.org/10.1128/JB.186.16.5547-5550.2004 (2004).

    CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Bowden, M. G. & Kaplan, H. B. The Myxococcus xanthus lipopolysaccharide O-antigen is required for social motility and multicellular development. Mol. Microbiol. 30, 275–284. https://doi.org/10.1046/j.1365-2958.1998.01060.x (1998).

    CAS 
    Article 
    PubMed 

    Google Scholar 

  • Andrianopoulos, K., Wang, L. & Reeves, P. R. Identification of the fucose synthetase gene in the colanic acid gene cluster of Escherichia coli K-12. J. Bacteriol. 180, 998–1001. https://doi.org/10.1128/JB.180.4.998-1001.1998 (1998).

    CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Islam, R., Brown, S., Taheri, A. & Dumenyo, C. K. The gene encoding NAD-dependent epimerase/dehydratase, wcaG, affects cell surface properties, virulence, and extracellular enzyme production in the soft rot phytopathogen Pectobacterium carotovorum. Microorganisms 7, 172. https://doi.org/10.3390/microorganisms7060172 (2019).

    CAS 
    Article 
    PubMed Central 

    Google Scholar 

  • Qimron, U., Marintcheva, B., Tabor, S. & Richardson, C. C. Genomewide screens for Escherichia coli genes affecting growth of T7 bacteriophage. Proc. Natl. Acad. Sci. USA 103, 19039–19044. https://doi.org/10.1073/pnas.0609428103 (2006).

    ADS 
    CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Pagnout, C. et al. Pleiotropic effects of rfa-gene mutations on Escherichia coli envelope properties. Sci. Rep. 9, 9696. https://doi.org/10.1038/s41598-019-46100-3 (2019).

    ADS 
    CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Montanaro, L. & Arciola, C. R. in Handbook of Bacterial Adhesion: Principles, Methods, and Applications (eds Yuehuei H. An & Richard J. Friedman) 331–343 (Humana Press, 2000).

  • Berne, C., Ellison, C. K., Ducret, A. & Brun, Y. V. Bacterial adhesion at the single-cell level. Nat. Rev. Microbiol. 16, 616–627. https://doi.org/10.1038/s41579-018-0057-5 (2018).

    CAS 
    Article 
    PubMed 

    Google Scholar 

  • Brown, M. R. & Williams, P. The influence of environment on envelope properties affecting survival of bacteria in infections. Annu. Rev. Microbiol. 39, 527–556. https://doi.org/10.1146/annurev.mi.39.100185.002523 (1985).

    CAS 
    Article 
    PubMed 

    Google Scholar 

  • Czajkowski, R. et al. Genome-Wide identification of Dickeya solani transcriptional units up-regulated in response to plant tissues from a crop-host Solanum tuberosum and a weed-host Solanum dulcamara. Front. Plant. Sci. 11, 580330. https://doi.org/10.3389/fpls.2020.580330 (2020).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Meaden, S. & Koskella, B. Exploring the risks of phage application in the environment. Front. Microbiol. 4, 358. https://doi.org/10.3389/fmicb.2013.00358 (2013).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Reverchon, S., Muskhelisvili, G. & Nasser, W. in Progress in Molecular Biology and Translational Science Vol. 142 (eds Michael San Francisco & Brian San Francisco) 51–92 (Academic Press, 2016).

  • Jiang, X. et al. Global transcriptional response of Dickeya dadantii to environmental stimuli relevant to the plant infection. Environ. Microbiol. 18, 3651–3672. https://doi.org/10.1111/1462-2920.13267 (2016).

    CAS 
    Article 
    PubMed 

    Google Scholar 

  • Li, Y. et al. LPS remodeling is an evolved survival strategy for bacteria. Proc. Natl. Acad. Sci. USA 109, 8716–8721. https://doi.org/10.1073/pnas.1202908109 (2012).

    ADS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Hendrick, C. A. & Sequeira, L. Lipopolysaccharide-defective mutants of the wilt pathogen Pseudomonas solanacearum. Appl. Environ. Microbiol. 48, 94–101. https://doi.org/10.1128/aem.48.1.94-101.1984 (1984).

    ADS 
    CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Berry, M. C., McGhee, G. C., Zhao, Y. & Sundin, G. W. Effect of a waaL mutation on lipopolysaccharide composition, oxidative stress survival, and virulence in Erwinia amylovora. FEMS Microbiol. Lett. 291, 80–87. https://doi.org/10.1111/j.1574-6968.2008.01438.x (2009).

    CAS 
    Article 
    PubMed 

    Google Scholar 

  • Czajkowski, R., Ozymko, Z., Zwirowski, S. & Lojkowska, E. Complete genome sequence of a broad-host-range lytic Dickeya spp. bacteriophage phiD5. Arch. Virol. 159, 3153–3155, doi:https://doi.org/10.1007/s00705-014-2170-8 (2014).

  • Lisicka, W. et al. Oxygen availability influences expression of Dickeya solani genes associated with virulence in potato (Solanum tuberosum L.) and chicory (Cichorium intybus L.). Front. Plant. Sci. 9, 374, doi:https://doi.org/10.3389/fpls.2018.00374 (2018).

  • Czajkowski, R., Marcisz, M. & Bartnik, P. Fast and reliable screening assay developed to preselect candidate Soft Rot Pectobacteriaceae Tn5 mutants showing resistance to bacteriophage infection. Eur. J. Plant Pathol. 155, 671–676. https://doi.org/10.1007/s10658-019-01786-z (2019).

    CAS 
    Article 

    Google Scholar 

  • Aziz, R. K. et al. The RAST Server: rapid annotations using subsystems technology. BMC Genom. 9, 75. https://doi.org/10.1186/1471-2164-9-75 (2008).

    CAS 
    Article 

    Google Scholar 

  • Altschul, S. F., Gish, W., Miller, W., Myers, E. W. & Lipman, D. J. Basic local alignment search tool. J. Mol. Biol. 215, 403–410. https://doi.org/10.1016/S0022-2836(05)80360-2 (1990).

    CAS 
    Article 
    PubMed 

    Google Scholar 

  • Kurowski, M. A. & Bujnicki, J. M. GeneSilico protein structure prediction meta-server. Nucl. Acids Res. 31, 3305–3307. https://doi.org/10.1093/nar/gkg557 (2003).

    CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Altschul, S. F. & Koonin, E. V. Iterated profile searches with PSI-BLAST-a tool for discovery in protein databases. Trends Biochem. Sci. 23, 444–447. https://doi.org/10.1016/s0968-0004(98)01298-5 (1998).

    CAS 
    Article 
    PubMed 

    Google Scholar 

  • Kanehisa, M. & Goto, S. KEGG: kyoto encyclopedia of genes and genomes. Nucl. Acids Res. 28, 27–30. https://doi.org/10.1093/nar/28.1.27 (2000).

    CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Letunic, I., Yamada, T., Kanehisa, M. & Bork, P. iPath: interactive exploration of biochemical pathways and networks. Trends Biochem. Sci. 33, 101–103. https://doi.org/10.1016/j.tibs.2008.01.001 (2008).

    CAS 
    Article 
    PubMed 

    Google Scholar 

  • Szklarczyk, D. et al. STRING v11: protein-protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets. Nucl. Acids Res. 47, D607–D613. https://doi.org/10.1093/nar/gky1131 (2019).

    CAS 
    Article 
    PubMed 

    Google Scholar 

  • Czajkowski, R., Ozymko, Z. & Lojkowska, E. Isolation and characterization of novel soilborne lytic bacteriophages infecting Dickeya spp. biovar 3 (‘D. solani’). Plant Pathol. 63, 758–772, https://doi.org/10.1111/ppa.12157, (2014).

  • Shao, Y. & Wang, I. N. Bacteriophage adsorption rate and optimal lysis time. Genetics 180, 471–482. https://doi.org/10.1534/genetics.108.090100 (2008).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Czajkowski, R., Kaczyńska, N., Jafra, S., Narajczyk, M. & Lojkowska, E. Temperature-responsive genetic loci in pectinolytic plant pathogenic Dickeya solani. Plant. Pathol. 66, 584–594. https://doi.org/10.1111/ppa.12618 (2017).

    CAS 
    Article 

    Google Scholar 

  • Roth, V. Doubling time computing, application available from: http://www.doubling-time.com/compute.php, (2006).

  • Krzyzanowska, D. M. et al. Compatible mixture of bacterial antagonists developed to protect ootato tubers from soft rot caused by Pectobacterium spp. and Dickeya spp. Plant. Dis. 103, 1374–1382, doi:https://doi.org/10.1094/PDIS-10-18-1866-RE (2019).

  • Czajkowski, R., de Boer, W. J., van Veen, J. A. & van der Wolf, J. M. Characterization of bacterial isolates from rotting potato tuber tissue showing antagonism to Dickeya sp. biovar 3 in vitro and in planta. Plant Pathology 61, 169–182, https://doi.org/10.1111/j.1365-3059.2011.02486.x (2012).

  • Shao, X., Xie, Y., Zhang, Y. & Deng, X. Biofilm formation assay in Pseudomonas syringae. Biol. Protoc. 9, e3237. https://doi.org/10.21769/BioProtoc.3237 (2019).

    CAS 
    Article 

    Google Scholar 

  • Dickey, R. S. Erwinia chrysanthemi: a comparative study of phenotypic properties of strains from several hosts and other Erwinia species. Phytopathol. 69, 324–329 (1979).

    Article 

    Google Scholar 

  • Perombelon, M. C. M. & van Der Wolf, J. M. Methods for the detection and quantification of Erwinia carotovora subsp. atroseptica (Pectobacterium carotovorum subsp. atrosepticum) on potatoes: a laboratory manual. Scottish Crop Research Institute Annual Report 10 (2002).

  • Py, B., Bortoli-German, I., Haiech, J., Chippaux, M. & Barras, F. Cellulase EGZ of Erwinia chrysanthemi: structural organization and importance of His98 and Glu133 residues for catalysis. Prot. Eng. 4, 325–333. https://doi.org/10.1093/protein/4.3.325 (1991).

    CAS 
    Article 

    Google Scholar 

  • Ji, J. W., Hugouvieux Cotte Pattat, N. & Robert Baudouy, J. Use of Mu-Lac insertions to study the secretion of pectate lyases by Erwinia chrysanthemi. J. Gen. Microbiol. 133, 793–802 (1987).

  • Schwyn, B. & Neilands, J. B. Universal chemical assay for the detection and determination of siderophores. Anal Biochem. 160, 47–56. https://doi.org/10.1016/0003-2697(87)90612-9 (1987).

    CAS 
    Article 
    PubMed 

    Google Scholar 

  • Fiolka, M. J. et al. Antimycobacterial action of a new glycolipid-peptide complex obtained from extracellular metabolites of Raoultella ornithinolytica. APMIS 123, 1069–1080. https://doi.org/10.1111/apm.12466 (2015).

    CAS 
    Article 
    PubMed 

    Google Scholar 

  • Sorroche, F. G., Rinaudi, L. V., Zorreguieta, A. & Giordano, W. EPS II-dependent autoaggregation of Sinorhizobium meliloti planktonic cells. Curr. Microbiol. 61, 465–470. https://doi.org/10.1007/s00284-010-9639-9 (2010).

    CAS 
    Article 
    PubMed 

    Google Scholar 

  • Dorken, G., Ferguson, G. P., French, C. E. & Poon, W. C. Aggregation by depletion attraction in cultures of bacteria producing exopolysaccharide. J. R. Soc. Interface 9, 3490–3502. https://doi.org/10.1098/rsif.2012.0498 (2012).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Trunk, T., Khalil, H. S. & Leo, J. C. Bacterial autoaggregation. AIMS Microbiol. 4, 140–164. https://doi.org/10.3934/microbiol.2018.1.140 (2018).

    CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Przepiora, T. et al. The periplasmic oxidoreductase DsbA is required for virulence of the phytopathogen Dickeya solani. Int. J. Mol. Sci. 23, 697 (2022).

    CAS 
    Article 

    Google Scholar 

  • Bauer, A. W., Kirby, W. M. M., Sherris, J. C. & Turck, M. Antibiotic susceptibility testing by a standardized single disk method. Am. J. Clin. Pathol. 45, 493–500 (1966).

    CAS 
    Article 

    Google Scholar 

  • Sambrook, J., Fritsch, E. F. & Maniatis, T. Molecular cloning: a laboratory manual. (1989).

  • Tsai, C. M. & Frasch, C. E. A sensitive silver stain for detecting lipopolysaccharides in polyacrylamide gels. Anal. Biochem. 119, 115–119. https://doi.org/10.1016/0003-2697(82)90673-x (1982).

    CAS 
    Article 
    PubMed 

    Google Scholar 

  • Fikowicz-Krosko, J. & Czajkowski, R. Systemic colonization and expression of disease symptoms on bittersweet nightshade (Solanum dulcamara) infected with a GFP-tagged Dickeya solani IPO2222 (IPO2254). Plant. Dis. 102, 619–627. https://doi.org/10.1094/PDIS-08-17-1147-RE (2018).

    CAS 
    Article 
    PubMed 

    Google Scholar 

  • Miller, W. G., Leveau, J. H. & Lindow, S. E. Improved gfp and inaZ broad-host-range promoter-probe vectors. Mol. Plant. Microbe Interact 13, 1243–1250. https://doi.org/10.1094/MPMI.2000.13.11.1243 (2000).

    CAS 
    Article 
    PubMed 

    Google Scholar 

  • Bloemberg, G. V., Wijfjes, A. H., Lamers, G. E., Stuurman, N. & Lugtenberg, B. J. Simultaneous imaging of Pseudomonas fluorescens WCS365 populations expressing three different autofluorescent proteins in the rhizosphere: new perspectives for studying microbial communities. Mol. Plant. Microbe Interact 13, 1170–1176. https://doi.org/10.1094/MPMI.2000.13.11.1170 (2000).

    CAS 
    Article 
    PubMed 

    Google Scholar 

  • Czajkowski, R. et al. Virulence of ‘Dickeya solani’ and Dickeya dianthicola biovar-1 and -7 strains on potato (Solanum tuberosum). Plant. Pathol. 62, 597–610. https://doi.org/10.1111/j.1365-3059.2012.02664.x (2013).

    CAS 
    Article 

    Google Scholar 

  • Czajkowski, R., de Boer, W. J., Velvis, H. & van der Wolf, J. M. Systemic colonization of potato plants by a soilborne, green fluorescent protein-tagged strain of Dickeya sp. biovar 3. Phytopathology 100, 134–142, doi:https://doi.org/10.1094/PHYTO-100-2-0134 (2010).

  • Czajkowski, R., Grabe, G. J. & van der Wolf, J. M. Distribution of Dickeya spp. and Pectobacterium carotovorum subsp. carotovorum in naturally infected seed potatoes. Eur. J. Plant Pathol. 125, 263–275, doi:https://doi.org/10.1007/s10658-009-9480-9 (2009).

  • Czajkowski, R., de Boer, W. J., van Veen, J. A. & van der Wolf, J. M. Studies on the interaction between the biocontrol agent, Serratia plymuthica A30, with blackleg causing Dickeya sp. (biovar 3) in potato (Solanum tuberosum). Plant Pathol. 61, 677–688 (2012).

  • Shapiro, S. S. & Wilk, M. B. An analysis of variance test for normality (complete samples). Biometrika 52, 591–600. https://doi.org/10.2307/2333709 (1965).

    MathSciNet 
    Article 
    MATH 

    Google Scholar 

  • Welch, B. L. The generalisation of student’s problems when several different population variances are involved. Biometrika 34, 28–35. https://doi.org/10.1093/biomet/34.1-2.28 (1947).

    MathSciNet 
    CAS 
    Article 
    PubMed 
    MATH 

    Google Scholar 

  • Box, G. E. P. Non-normality and tests on variances. Biometrika 40, 318–335. https://doi.org/10.2307/2333350 (1953).

    MathSciNet 
    Article 
    MATH 

    Google Scholar 

  • Student. The probable error of a mean. Biometrika 6, 1–25, doi:https://doi.org/10.2307/2331554 (1908).

  • Shieh, G. & Jan, S. L. The effectiveness of randomized complete block design. Stat. Neerl. 58, 111–124 (2004).

    MathSciNet 
    Article 

    Google Scholar 

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