Biological control of pathogenic fungi using Pseudomonas brassicacearum isolated from Aronia × prunifolia (Marshall) Rehder roots

Yıl 2024, Cilt: 11 Sayı: 3, 421 - 434

Luau Burhan Mustafa Ahmed Ismael Naqee Al-bayatı Dunya Albayati İbrahim Özkoç

https://doi.org/10.21448/ijsm.1385251

Öz

Endophytic bacteria, which are the subject of this study, serve as natural antifungal agents in the struggle against fungal infections, offering an eco-friendly alternative to chemical fungicides. So, it was aimed to determine the antifungal capacities of endophytic bacteria from Aronia ×prunifolia roots in the study. 25 endophytic bacteria were isolated, and their ability to act as biocontrol agents was evaluated by measuring fungal growth inhibition and chemical properties. Later, bacteria that showed a positive effect were identified through 16S gene sequencing. The results showed that the LB2 bacteria had the greatest ability to inhibit the selected fungi and the biochemical tests showed that the bacteria were Gram-negative, did not form spores, their colonies were well defined, and they could break down starch and gelatin, which was later diagnosed as Pseudomonas brassicacearum according to phylogenetic relationships. This study is the first report on which P. brassicacearum was isolated from A. ×prunifolia roots for the first time. These findings contribute to our understanding of the potential of endophytic bacteria, particularly P. brassicacearum, as natural antifungal agents in plant and human protection, offering a promising and sustainable approach to combat fungal infections while reducing the use of chemical fungicides.

Anahtar Kelimeler

Endophytes, Pseudomonas brassicacearum, Aronia prunifolia, Antifungal, Pathogenic fungi

Kaynakça

• Achouak, W., Sutra, L., Heulin, T., Meyer, J.M., Fromin, N., Degraeve, S., ... & Gardan, L. (2000). Pseudomonas brassicacearum sp. nov. and Pseudomonas thivervalensis sp. nov., two root-associated bacteria isolated from Brassica napus and Arabidopsis thaliana. International Journal of Systematic and Evolutionary Microbiology, 50(1), 9-18. https://doi.org/10.1099/00207713-50-1-9
• Adeleke, B.S., & Babalola, O.O. (2022). Meta-omics of endophytic microbes in agricultural biotechnology. Biocatalysis and Agricultural Biotechnology, 42, 102332. https://doi.org/10.1016/j.bcab.2022.102332
• Afsharmanesh, H., Ahmadzadeh, M., & Sharifi-Tehrani, A. (2006). Biocontrol of Rhizoctonia solani, the causal agent of bean damping-off by fluorescent pseudomonads. Communications in Agricultural and Applied Biological Sciences, 71(3 Pt B), 1021-1029.
• Akdemir, S., Torçuk, A.I., & Uysal Seçkin, G. (2023). Determination of Quality Parameters of Aronia Melanocarpa During Cold Storage. Erwerbs Obstbau, 1 7. https://doi.org/10.1007/s10341-023-00845-4
• Alsohiby, F.A.A., Yahya, S., & Humaid, A.A. (2016). Screening of soil isolates of bacteria for antagonistic activity against plant pathogenic fungi. PSM Microbiology, 1(1), 5-9.
• Anand, U., Pal, T., Yadav, N., Singh, V.K., Tripathi, V., Choudhary, K.K., ... & Singh, A.K. (2023). Current scenario and future prospects of endophytic microbes: promising candidates for abiotic and biotic stress management for agricultural and environmental sustainability. Microbial Ecology, 1-32. https://doi.org/10.1007/s00248-023-02190-1
• Bahmani, K., Hasanzadeh, N., Harighi, B., & Marefat, A. (2021). Isolation and identification of endophytic bacteria from potato tissues and their effects as biological control agents against bacterial wilt. Physiological and Molecular Plant Pathology, 116, 101692.‏ https://doi.org/10.1016/j.pmpp.2021.101692
• Berg, G., & Hallmann, J. (2006). Control of plant pathogenic fungi with bacterial endophytes. Microbial Root Endophytes, 53-69. https://doi.org/10.1007/3-540-33526-9
• Berg, G., Krechel, A., Ditz, M., Sikora, R.A., Ulrich, A., & Hallmann, J. (2005). Endophytic and ectophytic potato-associated bacterial communities differ in structure and antagonistic function against plant pathogenic fungi. FEMS Microbiology Ecology, 51(2), 215-229. https://doi.org/10.1016/j.femsec.2004.08.006
• Berry, C., Fernando, W.D., Loewen, P.C., & De Kievit, T.R. (2010). Lipopeptides are essential for Pseudomonas sp. DF41 biocontrol of Sclerotinia sclerotiorum. Biological Control, 55(3), 211-218. https://doi.org/10.1016/j.biocontrol.2010.09.011
• Bhaskar, P.V., Grossart, H.P., Bhosle, N.B., & Simon, M. (2005). Production of macroaggregates from dissolved exopolymeric substances (EPS) of bacterial and diatom origin. FEMS Microbiology Ecology, 53(2), 255 264. https://doi.org/10.1016/j.femsec.2004.12.013
• Boonman, N., Chutrtong, J., Wanna, C., Boonsilp, S., & Chunchob, S. (2023). Antimicrobial activities of endophytic bacteria isolated from Ageratum conyzoides Linn. Biodiversitas Journal of Biological Diversity, 24(4). https://doi.org/10.13057/biodiv/d240405
• Cao, L., Qiu, Z., You, J., Tan, H., & Zhou, S. (2005). Isolation and characterization of endophytic streptomycete antagonists of Fusarium wilt pathogen from surface-sterilized banana roots. FEMS Microbiology Letters, 247(2), 147 152. https://doi.org/10.1016/j.femsle.2005.05.006
• Caulier, S., Gillis, A., Colau, G., Licciardi, F., Liépin, M., Desoignies, N., ... & Bragard, C. (2018). Versatile antagonistic activities of soil-borne Bacillus spp. and Pseudomonas spp. against Phytophthora infestans and other potato pathogens. Frontiers in Microbiology, 9, 143. https://doi.org/10.3389/fmicb.2018.00143
• Celka, Z., & Szkudlarz, P. (2010). Spontaneous occurrence and dispersion of Aronia x prunifolia [Marshall] rehder [Rosaceae] in Poland on the example of the'Bagna'bog complex near Chlebowo [western Poland]. Acta Societatis Botanicorum Poloniae, 79(1), 37-42.
• Chen, C., Bauske, E.M., Musson, G., Rodriguezkabana, R., & Kloepper, J.W. (1995). Biological control of Fusarium wilt on cotton by use of endophytic bacteria. Biological Control, 5(1), 83-91. https://doi.org/10.1006/bcon.1995.1009
• Cho, S.J., Park, S.R., Kim, M.K., Lim, W.J., Ryu, S.K., An, C.L., ... & Yun, H.D. (2002). Endophytic Bacillus sp. isolated from the interior of balloon flower root. Bioscience, biotechnology, and biochemistry, 66(6), 1270-1275. https://doi.org/10.1271/bbb.66.1270
• Chung, B.S., Aslam, Z., Kim, S.W., Kim, G.G., Kang, H.S., Ahn, J.W., & Chung, Y.R. (2008). A bacterial endophyte, Pseudomonas brassicacearum YC5480, isolated from the root of Artemisia sp. producing antifungal and phytotoxic compounds. The Plant Pathology Journal, 24(4), 461-468.‏ https://doi.org/10.5423/PPJ.2008.24.4.461
• Cipriano, M.A.P., Freitas-Iório, R.D.P., Dimitrov, M.R., de Andrade, S.A.L., Kuramae, E.E., & Silveira, A.P.D.D. (2021). Plant-growth endophytic bacteria improve nutrient use efficiency and modulate foliar N-metabolites in sugarcane seedling. Microorganisms, 9(3), 479. https://doi.org/10.3390/microorganisms9030479
• Correa, P.A., Nosheen, A., Yasmin, H., & Ansari, M.J. (2022). Antifungal Antibiotics Biosynthesized by Major PGPR. In Secondary Metabolites and Volatiles of PGPR in Plant-Growth Promotion (pp. 199-247). Cham: Springer International Publishing. https://doi.org/10.36721/PJPS.2023.36.3.SP.927-934.1
• Crawford, J.M., Portmann, C., Kontnik, R., Walsh, C.T., & Clardy, J. (2011). NRPS substrate promiscuity diversifies the xenematides. Organic Letters, 13(19), 5144-5147. https://doi.org/10.1021/ol2020237
• Dalton, D.A., Kramer, S., Azios, N., Fusaro, S., Cahill, E., & Kennedy, C. (2004). Endophytic nitrogen fixation in dune grasses (Ammophila arenaria and Elymus mollis) from Oregon. FEMS microbiology ecology, 49(3), 469-479. https://doi.org/10.1016/j.femsec.2004.04.010
• Fromin, N., Achouak, W., Thiéry, J.M., & Heulin, T. (2001). The genotypic diversity of Pseudomonas brassicacearum populations isolated from roots of Arabidopsis thaliana: influence of plant genotype. FEMS Microbiology Ecology, 37(1), 21 29. https://doi.org/10.1111/j.1574-6941.2001.tb00849.x
• Granér, G., Persson, P., Meijer, J., & Alström, S. (2003). A study on microbial diversity in different cultivars of Brassica napus in relation to its wilt pathogen, Verticillium longisporum. FEMS Microbiology Letters, 224(2), 269-276. https://doi.org/10.1016/S0378-1097(03)00449-X
• Hall, T.A. (1999). Bio Edit; a user-friendly biological sequence aliment editor and analysis program for Windows 95/98/NT. In Nucleic Acids Symp. Ser. (Vol. 41, p. 95).
• Heuer, H., Krsek, M., Baker, P., Smalla, K., & Wellington, E. (1997). Analysis of actinomycete communities by specific amplification of genes encoding 16S rRNA and gel-electrophoretic separation in denaturing gradients. Applied and Environmental Microbiology, 63(8), 3233-3241. https://doi.org/10.1128/aem.63.8.3233-3241.1997
• Ho, G.T., Bräunlich, M., Austarheim, I., Wangensteen, H., Malterud, K.E., Slimestad, R., & Barsett, H. (2014). Immunomodulating activity of Aronia melanocarpa polyphenols. International Journal of Molecular Sciences, 15(7), 11626 11636. https://doi.org/10.3390/ijms150711626
• Islam, M.A., Nain, Z., Alam, M.K., Banu, N.A., & Islam, M.R. (2018). In vitro study of biocontrol potential of rhizospheric Pseudomonas aeruginosa against Fusarium oxysporum f. sp. cucumerinum. Egyptian journal of Biological Pest control, 28, 1-11. https://doi.org/10.1186/s41938-018-0097-1
• Ji, S.H., Gururani, M.A., & Chun, S.C. (2014). Isolation and characterization of plant growth promoting endophytic diazotrophic bacteria from Korean rice cultivars. Microbiological research, 169(1), 83-98. https://doi.org/10.1016/j.micres.2013.06.003
• Kang, S.M., Radhakrishnan, R., & Lee, I.J. (2015). Bacillus amyloliquefaciens subsp. plantarum GR53, a potent biocontrol agent resists Rhizoctonia disease on Chinese cabbage through hormonal and antioxidants regulation. World Journal of Microbiology and Biotechnology, 31, 1517-1527. https://doi.org/10.1007/s11274-015-1896-0
• Khan, M.S., Gao, J., Zhang, M., Xue, J., & Zhang, X. (2022). Pseudomonas aeruginosa Ld-08 isolated from Lilium davidii exhibits antifungal and growth-promoting properties. Plos one, 17(6), e0269640. https://doi.org/10.1371/journal.pone.0269640
• Kim, D.W., Han, H.A., Kim, J.K., Kim, D.H., & Kim, M.K. (2021). comparison of phytochemicals and antioxidant activities of berries cultivated in Korea: Identification of phenolic compounds in aronia by HPLC/Q-TOF MS. Preventive Nutrition and Food Science, 26(4), 459. https://doi.org/10.3746%2Fpnf.2021.26.4.459
• Kim, J.D. (2005). Antifungal activity of lactic acid bacteria isolated from Kimchi against Aspergillus fumigatus. Mycobiology, 33(4), 210 214. https://doi.org/10.4489/MYCO.2005.33.4.210
• Köberl, M., Ramadan, E.M., Adam, M., Cardinale, M., Hallmann, J., Heuer, H., ... & Berg, G. (2013). Bacillus and Streptomyces were selected as broad-spectrum antagonists against soilborne pathogens from arid areas in Egypt. FEMS Microbiology Letters, 342(2), 168-178. https://doi.org/10.1111/1574-6968.12089
• Kulling, S.E., & Rawel, H.M. (2008). Chokeberry (Aronia melanocarpa)–A review on the characteristic components and potential health effects. Planta Medica, 74(13), 1625-1634. https://doi.org/10.1055/s-0028-1088306
• Laveilhé, A., Fochesato, S., Lalaouna, D., Heulin, T., & Achouak, W. (2022). Phytobeneficial traits of rhizobacteria under the control of multiple molecular dialogues. Microbial Biotechnology, 15(7), 2083-2096. https://doi.org/10.1111/1751-7915.14023
• Lee, T., Park, D., Kim, K., Lim, S.M., Yu, N.H., Kim, S., ... & Kim, J.C. (2017). Characterization of Bacillus amyloliquefaciens DA12 showing potent antifungal activity against mycotoxigenic Fusarium species. The Plant Pathology Journal, 33(5), 499. https://doi.org/10.5423%2FPPJ.FT.06.2017.0126
• Mahaffee, W.F., & Kloepper, J.W. (1997). Temporal changes in the bacterial communities of soil, rhizosphere, and endorhiza associated with field-grown cucumber (Cucumis sativus L.). Microbial Ecology, 34, 210-223. https://doi.org/10.1007/s002489900050
• Manwar, A.V., Khandelwal, S.R., Chaudhari, B.L., Meyer, J.M., & Chincholkar, S.B. (2004). Siderophore production by a marine Pseudomonas aeruginosa and its antagonistic action against phytopathogenic fungi. Applied Biochemistry and Biotechnology, 118, 243-251. https://doi.org/10.1385/ABAB:118:1-3:243
• Miyamoto, T., Kawahara, M., & Minamisawa, K. (2004). Novel endophytic nitrogen-fixing clostridia from the grass Miscanthus sinensis as revealed by terminal restriction fragment length polymorphism analysis. Applied and Environmental Microbiology, 70(11), 6580-6586. https://doi.org/10.1128/AEM.70.11.6580-6586.2004
• Moreira, R.R., Nesi, C.N., & De Mio, L.L.M. (2014). Bacillus spp. and Pseudomonas putida as inhibitors of the Colletotrichum acutatum group and potential to control Glomerella leaf spot. Biological control, 72, 30-37. https://doi.org/10.1016/j.biocontrol.2014.02.001
• Musa, Z., Ma, J., Egamberdieva, D., Abdelshafy Mohamad, O.A., Abaydulla, G., Liu, Y., & Li, L. (2020). Diversity and antimicrobial potential of cultivable endophytic actinobacteria associated with the medicinal plant Thymus roseus. Frontiers in Microbiology, 11, 191. https://doi.org/10.3389/fmicb.2020.00191
• Mustafa, L.B., Al-Bayati, A.I.N., & Özkoç, I. (2024). Salt-tolerant endophytic Pseudomonas putida isolated from Aronia prunifolia root with plant growth-promoting potential. World News of Natural Sciences, 53, 212-222.
• Naranjo, H.D., Rat, A., De Zutter, N., De Ridder, E., Lebbe, L., Audenaert, K., & Willems, A. (2023). Uncovering Genomic Features and Biosynthetic Gene Clusters in Endophytic Bacteria from Roots of the Medicinal Plant Alkanna tinctoria Tausch as a Strategy to Identify Novel Biocontrol Bacteria. Microbiology Spectrum, 11(4), e00747 23. https://doi.org/10.1128/spectrum.00747-23
• Nielsen, T.H., Sørensen, D., Tobiasen, C., Andersen, J. B., Christophersen, C., Givskov, M., & Sørensen, J. (2002). Antibiotic and biosurfactant properties of cyclic lipopeptides produced by fluorescent Pseudomonas spp. from the sugar beet rhizosphere. Applied and environmental microbiology, 68(7), 3416-3423. https://doi.org/10.1128/AEM.68.7.3416-3423.2002
• Pascual, P. (2000). Characterization of Rhizoctonia solani isolates causing banded leaf and sheath blight in corn by conventional and PCR-based techniques. Plant Pathol., 49, 108-118.
• Rana, K.L., Kour, D., Kaur, T., Devi, R., Yadav, A., & Yadav, A.N. (2021). Bioprospecting of endophytic bacteria from the Indian Himalayas and their role in plant growth promotion of maize (Zea mays L.). Journal of Applied Biology and Biotechnology, 9(3), 41-50. http://dx.doi.org/10.7324/JABB.2021.9306
• Ross, I.L., Alami, Y., Harvey, P.R., Achouak, W., & Ryder, M.H. (2000). Genetic diversity and biological control activity of novel species of closely related pseudomonads isolated from wheat field soils in South Australia. Applied and Environmental Microbiology, 66(4), 1609-1616. https://doi.org/10.1128/AEM.66.4.1609-1616.2000
• Safaa, A.L., & Qaysi, Z.A.T. (2016). Levan production using Pseudomonas brassicacearum isolated from rhizosphere soil of cowpea farm in Iraq. Iraqi journal of biotechnology, 15(1).
• Saitou, N., & Nei, M. (1987). The neighbor-joining method: a new method for reconstructing phylogenetic trees. Molecular Biology and Evolution, 4(4), 406 425. https://doi.org/10.1093/oxfordjournals.molbev.a040454
• Salazar, O., Schneider, J.H., Julian, M.C., Keijer, J., & Rubio, V. (1999). Phylogenetic subgrouping of Rhizoctonia solani AG 2 isolates based on ribosomal ITS sequences. Mycologia, 91(3), 459-467. https://doi.org/10.1080/00275514.1999.12061039
• Santra, H.K., & Banerjee, D. (2023). Antifungal activity of volatile and non-volatile metabolites of endophytes of Chloranthus elatior Sw. Frontiers in Plant Science, 14, 1156323. https://doi.org/10.3389/fpls.2023.1156323
• Shahid, M., Singh, U.B., Ilyas, T., Malviya, D., Vishwakarma, S.K., Shafi, Z., ... & Singh, H.V. (2022). Bacterial inoculants for control of fungal diseases in Solanum lycopersicum L.(tomatoes): a comprehensive overview. Rhizosphere Microbes: Biotic Stress Management, 311-339. https://doi.org/10.1007/978-981-19-5872-4_15
• Siciliano, S.D., Fortin, N., Mihoc, A., Wisse, G., Labelle, S., Beaumier, D., ... & Greer, C.W. (2001). Selection of specific endophytic bacterial genotypes by plants in response to soil contamination. Applied and Environmental Microbiology, 67(6), 2469-2475. https://doi.org/10.1128/AEM.67.6.2469-2475.2001
• Singh, P., Singh, R.K., Guo, D.J., Sharma, A., Singh, R.N., Li, D.P., ... & Li, Y.R. (2021). Whole genome analysis of sugarcane root-associated endophyte Pseudomonas aeruginosa B18 - A plant growth-promoting bacterium with antagonistic potential against Sporisorium scitamineum. Frontiers in Microbiology, 12, 628376. https://doi.org/10.3389/fmicb.2021.628376
• Sneath, P.H.A. (1992). Preface to the present edition. In International Code of Nomenclature of Bacteria: Bacteriological Code, 1990 Revision. ASM Press.
• Sturz, A.V. (1999). Endophytic bacterial communities in the periderm of potato tubers and their potential to improve resistance to soil-borne plant pathogens. Plant Pathol., 48, 360-369. https://doi.org/10.1046/j.1365-3059.1999.00351.x
• Szopa, A., Kokotkiewicz, A., Kubica, P., Banaszczak, P., Wojtanowska-Krośniak, A., Krośniak, M., ... & Ekiert, H. (2017). Comparative analysis of different groups of phenolic compounds in fruit and leaf extracts of Aronia sp.: A. melanocarpa, A. arbutifolia, and A.× prunifolia and their antioxidant activities. European Food Research and Technology, 243, 1645-1657. https://doi.org/10.1007/s00217-017-2872-8
• Szopa, A., Kubica, P., Snoch, A., & Ekiert, H. (2018). High production of bioactive depsides in shoot and callus cultures of Aronia arbutifolia and Aronia× prunifolia. Acta Physiologiae Plantarum, 40, 1-11. https://doi.org/10.1007/s11738-018-2623-x
• Taheri, R., Connolly, B.A., Brand, M.H., & Bolling, B.W. (2013). Underutilized chokeberry (Aronia melanocarpa, Aronia arbutifolia, Aronia prunifolia) accessions are rich sources of anthocyanins, flavonoids, hydroxycinnamic acids, and proanthocyanidins. Journal of agricultural and food chemistry, 61(36), 8581-8588. https://doi.org/10.1021/jf402449q
• Tamura, K., Stecher, G., Peterson, D., Filipski, A., & Kumar, S. (2013). MEGA6: molecular evolutionary genetics analysis version 6.0. Molecular biology and evolution, 30(12), 2725-2729. https://doi.org/10.1093/molbev/mst197
• Trivedi, P., Pandey, A., & Palni, L.M.S. (2008). In vitro evaluation of antagonistic properties of Pseudomonas corrugata. Microbiological Research, 163(3), 329-336. https://doi.org/10.1016/j.micres.2006.06.007
• Wang, X., Wang, C., Li, Q., Zhang, J., Ji, C., Sui, J., ... & Liu, X. (2018). Isolation and characterization of antagonistic bacteria with the potential for biocontrol of soil‐borne wheat diseases. Journal of Applied Microbiology, 125(6), 1868 1880. https://doi.org/10.1155/2019/3638926
• Weller, D.M. (2007). Pseudomonas biocontrol agents of soilborne pathogens: looking back over 30 years. Phytopathology, 97(2), 250-256. https://doi.org/10.1094/PHYTO-97-2-0250
• Yang, K., Qin, Q., Liu, Y., Zhang, L., Liang, L., Lan, H., ... & Wang, S. (2016). Adenylate cyclase AcyA regulates development, aflatoxin biosynthesis and fungal virulence in Aspergillus flavus. Frontiers in Cellular and Infection Microbiology, 6, 190. https://doi.org/10.3389/fcimb.2016.00190
• Zinniel, D.K., Lambrecht, P., Harris, N.B., Feng, Z., Kuczmarski, D., Higley, P., ... & Vidaver, A.K. (2002). Isolation and characterization of endophytic colonizing bacteria from agronomic crops and prairie plants. Applied and environmental microbiology, 68(5), 2198-2208. https://doi.org/10.1128/AEM.68.5.2198-2208.2002