Characterization of Novel Bacteriophages for Biocontrol of Plant Pathogenic Bacteria

Authors

  • Lieve Toth Department of Environmental and Agricultural Sciences, Iberian University Center for Biotechnology, Spain Author
  • Owen Dubois Department of Microbiology and Immunology, Meuse Institute of Computational Biology, Belgium Author
  • Nils Novak Department of Biochemistry and Genetics, Iberian University Center for Biotechnology, Spain Author

DOI:

https://doi.org/10.5281/zenodo.22687887

Keywords:

bacteriophage, Ralstonia solanacearum, biocontrol, bacterial wilt, phage cocktail, tomato, lytic phage

Abstract

Bacterial wilt, caused by the soilborne pathogen Ralstonia solanacearum, remains one of the most destructive and
management-resistant bacterial diseases of tomato and other solanaceous crops in warm, humid production
regions, and no chemical control offers reliable field efficacy once the pathogen is established in soil. We report
the isolation, characterisation and greenhouse biocontrol evaluation of three novel lytic bacteriophages,
designated RsP7, RsP12 and RsP19, recovered from wilt-affected tomato field soil and irrigation water in a
case-study system centred on a single commercial glasshouse operation with a recurrent bacterial wilt problem.
Transmission electron microscopy placed all three phages in the class Caudoviricetes, with RsP7 and RsP19
showing Myoviridae-like contractile tails and RsP12 showing a Podoviridae-like short tail. Whole-genome
sequencing yielded double-stranded DNA genomes of 66.2-72.8 kb with no genes matching curated toxin,
integrase or antibiotic-resistance reference databases, supporting their suitability for field application under a
strictly lytic-phage biocontrol strategy. Host-range testing against 24 R. solanacearum isolates spanning
phylotypes I and IIB collected from the same production region showed partially complementary lysis patterns, and
a three-phage cocktail combining RsP7, RsP12 and RsP19 lysed 22 of 24 isolates (91.7%), compared with a
maximum of 15 of 24 (62.5%) for any single phage. In a greenhouse pot trial using naturally infested field soil,
cocktail-treated tomato plants showed 58% wilt incidence at 21 days post-transplant versus 89% in untreated
controls, and time-to-wilt onset was delayed by a median of 6 days. These results support this three-phage
cocktail as a promising candidate for field-scale biocontrol evaluation against bacterial wilt in this production
system, while underlining that phage cocktail performance should be characterised against a genotypically
representative local pathogen population rather than a single reference strain before any biocontrol product is
deployed more broadly.

References

Genin S, Denny TP (2012) Pathogenomics of the Ralstonia solanacearum species complex. Annual Review of Phytopathology 50:67-89. https://doi.org/10.1146/annurev-phyto-081211-173000

Mansfield J, Genin S, Magori S, Citovsky V, Sriariyanum M, Ronald P, Dow M, Verdier V, Beer SV, Machado MA, Toth I (2012) Top 10 plant pathogenic bacteria in molecular plant pathology. Molecular Plant Pathology 13(6):614-629. https://doi.org/10.1111/j.1364-3703.2012.00804.x

Peeters N, Guidot A, Vailleau F, Valls M (2013) Ralstonia solanacearum, a widespread bacterial plant pathogen in the post-genomic era. Molecular Plant Pathology 14(7):651-662. https://doi.org/10.1111/mpp.12038

Fegan M, Prior P (2005) How complex is the Ralstonia solanacearum species complex? Bacterial Wilt Disease and the Ralstonia solanacearum Species Complex, APS Press, chapter 34. https://doi.org/10.1094/9780890545018.004

Jones JB, Vallad GE, Iriarte FB, Obradovic A, Wernsing MH, Jackson LE, Balogh B, Hong JC, Momol MT (2012) Considerations for using bacteriophages for plant disease control. Bacteriophage 2(4):208-214. https://doi.org/10.4161/bact.23857

Buttimer C, McAuliffe O, Ross RP, Hill C, O'Mahony J, Coffey A (2017) Bacteriophages and bacterial plant diseases. Frontiers in Microbiology 8:34. https://doi.org/10.3389/fmicb.2017.00034

Yamada T (2012) Bacteriophages of Ralstonia solanacearum: their diversity and utilization as biocontrol agents in agriculture. Bacteriophage 2(3):236-241. https://doi.org/10.4161/bact.22399

Bhunchoth A, Phironrit N, Leksomboon C, Chatchawankanphanich O, Kotera S, Narulita E, Kawasaki T, Fujie M, Yamada T (2015) Isolation of Ralstonia solanacearum-infecting bacteriophages from tomato fields in Chiang Mai, Thailand, and their experimental use as biocontrol agents. Journal of Applied Microbiology 118(4):1023-1033. https://doi.org/10.1111/jam.12763

Addy HS, Askora A, Kawasaki T, Fujie M, Yamada T (2012) Utilization of filamentous phage phiRSM3 to control bacterial wilt caused by Ralstonia solanacearum. Plant Disease 96(8):1204-1209. https://doi.org/10.1094/PDIS-12-11-1023-RE

Wang X, Wei Z, Yang K, Wang J, Jousset A, Xu Y, Shen Q, Friman VP (2019) Phage combination therapies for bacterial wilt disease in tomato. Nature Biotechnology 37(12):1513-1520. https://doi.org/10.1038/s41587-019-0328-3

Clokie MR, Millard AD, Letarov AV, Heaphy S (2011) Phages in nature. Bacteriophage 1(1):31-45. https://doi.org/10.4161/bact.1.1.14942

Salmond GP, Fineran PC (2015) A century of the phage: past, present and future. Nature Reviews Microbiology 13(12):777-786. https://doi.org/10.1038/nrmicro3564

Koskella B, Brockhurst MA (2014) Bacteria-phage coevolution as a driver of ecological and evolutionary processes in microbial communities. FEMS Microbiology Reviews 38(5):916-931. https://doi.org/10.1111/1574-6976.12072

Gomez P, Buckling A (2011) Bacteria-phage antagonistic coevolution in soil. Science 332(6025):106-109. https://doi.org/10.1126/science.1198767

Wommack KE, Colwell RR (2000) Virioplankton: viruses in aquatic ecosystems. Microbiology and Molecular Biology Reviews 64(1):69-114. https://doi.org/10.1128/MMBR.64.1.69-114.2000

Twort FW (1915) An investigation on the nature of ultra-microscopic viruses. The Lancet 186(4814):1241-1243. https://doi.org/10.1016/S0140-6736(01)20383-3

Wicker E, Grassart L, Coranson-Beaudu R, Mian D, Guilbaud C, Fegan M, Prior P (2007) Ralstonia solanacearum strains from Martinique (French West Indies) exhibiting a new pathogenic potential. Applied and Environmental Microbiology 73(21):6790-6801. https://doi.org/10.1128/AEM.00841-07

Elphinstone JG (2005) The current bacterial wilt situation: a global overview. Bacterial Wilt Disease and the Ralstonia solanacearum Species Complex, APS Press, chapter 2. https://doi.org/10.1094/9780890545018.002

Seemann T (2014) Prokka: rapid prokaryotic genome annotation. Bioinformatics 30(14):2068-2069. https://doi.org/10.1093/bioinformatics/btu153

Alcock BP, Raphenya AR, Lau TTY, Tsang KK, Bouchard M, Edalatmand A, Huynh W, Nguyen ALV, Cheng AA, Liu S, Min SY (2020) CARD 2020: antibiotic resistome surveillance with the comprehensive antibiotic resistance database. Nucleic Acids Research 48(D1):D517-D525. https://doi.org/10.1093/nar/gkz935

Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M, Kulikov AS, Lesin VM, Nikolenko SI, Pham S, Prjibelski AD, Pyshkin AV (2012) SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. Journal of Computational Biology 19(5):455-477. https://doi.org/10.1089/cmb.2012.0021

Jones JB, Jackson LE, Balogh B, Obradovic A, Iriarte FB, Momol MT (2007) Bacteriophages for plant disease control. Annual Review of Phytopathology 45:245-262. https://doi.org/10.1146/annurev.phyto.45.062806.094411

Fujiwara A, Fujisawa M, Hamasaki R, Kawasaki T, Fujie M, Yamada T (2011) Biocontrol of Ralstonia solanacearum by treatment with lytic bacteriophages. Applied and Environmental Microbiology 77(12):4155-4162. https://doi.org/10.1128/AEM.02847-10

Balogh B, Jones JB, Iriarte FB, Momol MT (2010) Phage therapy for plant disease control. Current Pharmaceutical Biotechnology 11(1):48-57. https://doi.org/10.2174/138920110790725302

Summer EJ, Berry J, Tran TA, Niu L, Struck DK, Young R (2007) Rz/Rz1 lysis gene equivalents in phages of Gram-negative hosts. Journal of Molecular Biology 373(5):1098-1112. https://doi.org/10.1016/j.jmb.2007.08.045

Abedon ST, Kuhl SJ, Blasdel BG, Kutter EM (2011) Phage treatment of human infections. Bacteriophage 1(2):66-85. https://doi.org/10.4161/bact.1.2.15845

Chan BK, Abedon ST, Loc-Carrillo C (2013) Phage cocktails and the future of phage therapy. Future Microbiology 8(6):769-783. https://doi.org/10.2217/fmb.13.47

Ryan RP, Vorholter FJ, Potnis N, Jones JB, Van Sluys MA, Bogdanove AJ, Dow JM (2011) Pathogenomics of Xanthomonas: understanding bacterium-plant interactions. Nature Reviews Microbiology 9(5):344-355. https://doi.org/10.1038/nrmicro2558

Vu NT, Oh CS (2020) Bacteriophage usage for bacterial disease management and diagnosis in plants. Plant Pathology Journal 36(3):204-217. https://doi.org/10.5423/PPJ.RW.04.2020.0074

Buttimer C, Hendrix H, Oliveira H, Casey A, Neve H, McAuliffe O, Ross RP, Hill C, Noben JP, O'Mahony J, Lavigne R (2018) Things are getting hairy: enterobacteria bacteriophage vB_PcaM_CBB. Frontiers in Microbiology 9:1755. https://doi.org/10.3389/fmicb.2018.01755

Iriarte FB, Balogh B, Momol MT, Smith LM, Wilson M, Jones JB (2007) Factors affecting survival of bacteriophage on tomato leaf surfaces. Applied and Environmental Microbiology 73(6):1704-1711. https://doi.org/10.1128/AEM.02118-06

Kortright KE, Chan BK, Koff JL, Turner PE (2019) Phage therapy: a renewed approach to combat antibiotic-resistant bacteria. Cell Host & Microbe 25(2):219-232. https://doi.org/10.1016/j.chom.2019.01.014

Loc-Carrillo C, Abedon ST (2011) Pros and cons of phage therapy. Bacteriophage 1(2):111-114. https://doi.org/10.4161/bact.1.2.14590

Kutter E, De Vos D, Gvasalia G, Alavidze Z, Gogokhia L, Kuhl S, Abedon ST (2010) Phage therapy in clinical practice: treatment of human infections. Current Pharmaceutical Biotechnology 11(1):69-86. https://doi.org/10.2174/138920110790725401

Ackermann HW (2007) 5500 phages examined in the electron microscope. Archives of Virology 152(2):227-243. https://doi.org/10.1007/s00705-006-0849-1

Turner D, Kropinski AM, Adriaenssens EM (2021) A roadmap for genome-based phage taxonomy. Viruses 13(3):506. https://doi.org/10.3390/v13030506

Hyman P, Abedon ST (2010) Bacteriophage host range and bacterial resistance. Advances in Applied Microbiology 70:217-248. https://doi.org/10.1016/S0065-2164(10)70007-1

Alvarez B, Lopez MM, Biosca EG (2019) Biocontrol of the major plant pathogen Ralstonia solanacearum in irrigation water and host plants by novel waterborne lytic bacteriophages. Frontiers in Microbiology 10:2813. https://doi.org/10.3389/fmicb.2019.02813

Bae JY, Wu J, Lee HJ, Jo EJ, Murugaiyan S, Chung E, Lee SW (2012) Biocontrol potential of a lytic bacteriophage PE204 against bacterial wilt of tomato. Journal of Microbiology and Biotechnology 22(12):1613-1620. https://doi.org/10.4014/jmb.1208.08072

Kalpana S, Lin WY, Wang YC, Yang YC, Lin YT, Wang YT, Chen YT, Chen CC (2023) Bacteriophage-based strategies for the sustainable management of bacterial wilt disease. Microorganisms 11(4):891. https://doi.org/10.3390/microorganisms11040891

Zeng Q, Sundin GW (2014) Genome-wide identification of Hfq-regulated small RNAs in the fire blight pathogen Erwinia amylovora. BMC Genomics 15:414. https://doi.org/10.1186/1471-2164-15-414

Green ER, Mecsas J (2016) Bacterial secretion systems: an overview. Microbiology Spectrum 4(1). https://doi.org/10.1128/microbiolspec.VMBF-0012-2015

Prior P, Ailloud F, Dalsing BL, Remenant B, Sanchez B, Allen C (2016) Genomic and proteomic evidence supporting the division of the plant pathogen Ralstonia solanacearum into three species. BMC Genomics 17:90. https://doi.org/10.1186/s12864-016-2413-z

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

Jault P, Leclerc T, Jennes S, Pirnay JP, Que YA, Resch G, Rousseau AF, Ravat F, Carsin H, Le Floch R, Schaal JV (2019) Efficacy and tolerability of a cocktail of bacteriophages to treat burn wounds infected by Pseudomonas aeruginosa. The Lancet Infectious Diseases 19(1):35-45. https://doi.org/10.1016/S1473-3099(18)30482-1

Doss J, Culbertson K, Hahn D, Camacho J, Barekzi N (2017) A review of phage therapy against bacterial pathogens of aquatic and terrestrial organisms. Viruses 9(3):50. https://doi.org/10.3390/v9030050

Svircev A, Roach D, Castle A (2018) Framing the future with bacteriophages in agriculture. Viruses 10(5):218. https://doi.org/10.3390/v10050218

Denny T (2007) Plant pathogenic Ralstonia species. Plant-Associated Bacteria, Springer, chapter 16. https://doi.org/10.1007/978-1-4020-4538-7_16

Lowe-Power TM, Khokhani D, Allen C (2018) How Ralstonia solanacearum exploits and thrives in the flowing plant xylem environment. Trends in Microbiology 26(11):929-942. https://doi.org/10.1016/j.tim.2018.06.002

Vu TH, Le TD, Kim J (2020) Application of bacteriophage cocktails for biocontrol of Ralstonia solanacearum causing bacterial wilt disease. Plant Pathology Journal 36(6):554-563. https://doi.org/10.5423/PPJ.OA.04.2020.0069

Hendrix RW, Casjens S (2006) Bacteriophage lambda and its genetic neighborhood. In: The Bacteriophages, Oxford University Press, chapter 24. https://doi.org/10.1093/oso/9780195148503.003.0026

Weinbauer MG (2004) Ecology of prokaryotic viruses. FEMS Microbiology Reviews 28(2):127-181. https://doi.org/10.1016/j.femsre.2003.08.001

Casey E, van Sinderen D, Mahony J (2018) In vitro characteristics of phages to guide "real life" phage therapy suitability. Viruses 10(4):163. https://doi.org/10.3390/v10040163

Adriaenssens E, Brister JR (2017) How to name and classify your phage: an informal guide. Viruses 9(4):70. https://doi.org/10.3390/v9040070

Frampton RA, Pitman AR, Fineran PC (2012) Advances in bacteriophage-mediated control of plant pathogens. International Journal of Microbiology 2012:326452. https://doi.org/10.1155/2012/326452

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Published

2026-06-26