Composition of endophytic bacterial communities of wild legumes as potential biological control agents of crop legumes diseases (Case study: Kermanshah Zagros forest)

Document Type : Research Paper

Authors

1 1- Department of Plant Protection, Faculty of Agricultural Sciences and Food Industries, Science and Research Branch, Islamic Azad University, Tehran, Iran

2 Department of Plant Protection, Faculty of Agricultural Sciences and Food Industries, Science and Research Branch, Islamic Azad University, Tehran, Iran

3 Department of Industrial and Environmental Biotechnology, National Institute of Genetic Engineering and Biotechnology, Tehran, Iran

4 Department of Biodiversity, BoomZista Institute, Vancouver, British Columbia, Canada

5 Department of Plant Breeding and Biotechnology, Faculty of Agricultural Sciences and Food Industries, Science and Research Branch, Islamic Azad University, Tehran, Iran

Abstract

Forest ecosystems are the main reservoirs of global biodiversity. Microorganisms play a key role in the biochemical cycles of these ecosystems and are used to protect plants and stimulate their growth. Due to the limitations in the application of classic methods in the isolation and identification of endophytic microorganisms, their potentials and functions have yet to be properly understood. In this study, a culture-independent method was used to study the endophytic bacterial communities of some wild legumes. To this end, the Zagros forests of Kermanshah were surveyed and two varieties of Astragalus ovinus and Vicia lutea were sampled. Total DNAs from different parts of the plant samples were extracted and the bacterial 16S rDNA genes were subsequently amplified. Sequencing analysis using the Illumina MiSeq platform showed the most abundant endophytic bacteria belonged to seven orders of Rhizobiales, Xanthomonadales, Sphingomonadales, Pseudomonadales, Chitinophagales, Enterobacteriales, Betaproteobacteriales. The latter were comprised to three classes of Gammaproteobacteria, Alphaproteobacteria and Bacteroidia, and two phyla of Proteobacteria and Bacteroidetes. Our findings showed that members of Proteobacteria were the dominant bacterial endophytes and accounted for more than 99% and 68% of the total population of endophytic bacteria in V. lutea and A. ovinus, respectively. These bacteria, with the highest percentage of taxonomic units (OTUs), have the highest potential to use as biological control agents of crop legumes diseases. This study provides a clear picture of the population, dominance and diversity of bacterial endophytes of wild legumes in the Zagros forests using metagenomic analysis.

Keywords

References

-Acuña, J.J., Marileo, L.G., Araya, M.A., Rilling, J.I., Larama, G.A., Mora, M.L., Epstein, S. and Jorquera, M.A., 2020. In situ cultivation approach to increase the culturable bacterial diversity in the rhizobiome of plants. Journal of Soil Science and Plant Nutrition, 24: 1-6.
-Akinsanya, M., Goh, A., Lim, J.K. and Ting, A.S., 2015. Metagenomics study of endophytic bacteria in Aloe vera using next-generation technology. Genomics data, 6: 159-163.
-Alori, E.T., Dare, M.O. and Babalola, O.O., 2017. Microbial inoculants for soil quality and plant health. In Sustainable Agriculture Reviews, Springer Cham, pp. 281-307.
-Arshadi, N., Sedaghatfar, E., Golnaraghi, A. and Glare, T., 2019. Endophytic characteristic of entomopathogenic fungi Beauveria on bean plant. Bioagrica, 1: 1-9.
-Balázs, H.E., Schmid, C.A., Cruzeiro, C., Podar, D., Szatmari, P.M., Buegger, F., Hufnagel, G., Radl, V. and Schröder, P., 2021. Post-reclamation microbial diversity and functions in hexachlorocyclohexane (HCH) contaminated soil in relation to spontaneous HCH tolerant vegetation. Science of the Total Environment, 1(767): 144653.
-Cao, Y. Halane, M.K., Gassmann, W. and Stacey, G., 2017. The role of plant innate immunity in the legume-rhizobium symbiosis. Annual Review of Plant Biology, 68: 535-561.
-Cassan, F., Coniglio, A., López, G., Molina, R., Nievas, S., de Carlan, C.L., Donadio, F., Torres, D., Rosas, S., Pedrosa, F.O. and de Souza, E., 2020. Everything you must know about Azospirillum and its impact on agriculture and beyond. Biology and Fertility of Soils, 56: 461-79.
-Celador-Lera, L., Jiménez-Gómez, A., Menéndez, E. and Rivas, R., 2018. Biofertilizers based on bacterial endophytes isolated from cereals: potential solution to enhance these crops. In Role of Rhizospheric Microbes in Soil, pp. 175-203.
-Dekak, A., Menasria, T., Benhizia, Y. and Chenchouni, H., 2020. Endophytic passenger bacteria associated with Genista cinerea nodules growing in North African drylands. Rhizosphere, 1(14): 100205.
-Firdous, J. and Bhore Subhash, J., 2017. Screening of cultivable endophytic bacterial isolates for their plant growth promoting activity in rice. Indian Agricultural Research, 51(5): 413-418.
-Ghorbani, S. and Harighi, B., 2018. Characterization of endophytic bacteria with plant growth promotion and biological control potential isolated from walnut trees. Forest Pathology, 48(2): e12403.
-Grady, E.N., MacDonald, J., Liu, L., Richman, A. and Yuan, Z.C., 2016. Current knowledge and perspectives of Paenibacillus: a review. Microbial Cell Factories, 15(1): 1-8.
-Hamzah, A., Zubir, I., Ross, E.E.R. and Aqma, W.S., 2017. Antagonistic effect and plant growth hormone produced by endophyte Bacillus amyloliquefaciens LKM-UL isolated from cocoa plant. International Journal of Bioscience, Biochemistry and Bioinformatics, 7: 169-176.
-Hirsch, A.M., 2010. How rhizobia survive in the absence of a legume host, a stressful world indeed. In Symbioses and Stress Springer, pp. 375-391.
-Jackson, C.R., Randolph, K.C., Osborn, S.L. and Tyler, H.L., 2013. Culture dependent and independent analysis of bacterial communities associated with commercial salad leaf vegetables. BMC Microbiology, 13(1): 1-2.
-Khan, S.S., Verma, V. and Rasool, S., 2020. Diversity and the role of endophytic bacteria: a review. Botanica Serbica, 44(2): 103-20.
-Kobayashi, D.Y. and Palumbo, J.D., 2000. Bacterial endophytes and their effects on plants and uses in agriculture. Microbial Endophytes, 19: 199-233.
-Kunda, P., Dha, P.K. and Mukherjee, A., 2018. Endophytic bacterial community of rice (Oryza sativa L.) from coastal saline zone of West Bengal: 16S rRNA gene based metagenomics approach. Meta Gene, 18: 79-86.
-Liu, C.H., Chen, X., Liu, T.T., Lian, B., Gu, Y., Caer, V., Xue, Y.R. and Wang, B.T., 2007. Study of the antifungal activity of Acinetobacter baumannii LCH001 in vitro and identification of its antifungal components. Applied Microbiology and Biotechnology, 76(2): 459-66.
-Liu, Y., Teng, K., Wang, T., Dong, E., Zhang, M., Tao, Y. and Zhong, J., 2020. Antimicrobial Bacillus velezensis HC6: production of three kinds of lipopeptides and biocontrol potential in maize. Journal of Applied Microbiology, 128(1): 242-254.
-López, J.L., Alvarez, F., Príncipe, A., Salas, M.E., Lozano, M.J., Draghi, W.O., Jofré, E. and Lagares, A., 2018. Isolation, taxonomic analysis, and phenotypic characterization of bacterial endophytes present in alfalfa (Medicago sativa) seeds. Journal of Biotechnology, 10(267): 55-62.
-Ludueña, L.M., Anzuay, M.S., Angelini, J.G., McIntosh, M., Becker, A., Rupp, O. and Taurian, T., 2019. Genome sequence of the endophytic strain Enterobacter sp. J49, a potential biofertilizer for peanut and maize. Genomics, 111(4): 913-920.
-Maheshwari, R., Bhutani, N. and Suneja, P., 2019. Screening and characterization of siderophore producing endophytic bacteria from Cicer arietinum and Pisum sativum plants. Journal of Applied Biology and Biotechnology, 7: 7-14.
-Miché, L. and Balandreau, J., 2001. Effects of rice seed surface sterilization with hypochlorite on inoculated Burkholderia vietnamiensis. Applied and Environmental Microbiology, 67(7): 3046-52.
-Mohamad, O.A., Li, L., Ma, J.B., Hatab, S., Xu, L., Guo, J.W., Rasulov, B.A., Liu, Y.H., Hedlund, B.P. and Li, W.J., 2018. Evaluation of the antimicrobial activity of endophytic bacterial populations from Chinese traditional medicinal plant licorice and characterization of the bioactive secondary metabolites produced by Bacillus atrophaeus against Verticillium dahliae. Frontiers in Microbiology, 9(9): 924.
-Moyes, A.B., Kueppers, L.M., Pett‐Ridge, J., Carper, D.L., Vandehey, N., O'Neil, J. and Frank, A.C., 2016. Evidence for foliar endophytic nitrogen fixation in a widely distributed subalpine conifer. New Phytologist, 210(2): 657-668.
-Nazari, K., Sheykhrezaee, Z. and Golnaraghi, A., 2021. Man in the Coronaceous period (1): how long will Corona vaccination last in the world?. Iranian Students's News Agency, Report No. 1400020503193.
-Peredeltchouk, M., Wilson David, S.A., Bhattacharya, B., Volokhov, D.V. and Chizhikov, V., 2011. Detection of mycoplasma contamination in cell substrates using reverse transcription‐PCR assays. Journal of Applied Microbiology, 110(1): 54-60.
-Phetcharat, P. and Duangpaeng, A., 2012. Screening of endophytic bacteria from organic rice tissue for indole acetic acid production. Procedia Engineering, 32: 177-183.
-Rajaei, S., Farshi, R.S., Jazi, M.M., and Seyedi, S.M., 2017. Efficient strategies for elimination of phenolic compounds during DNA extraction from roots of Pistacia vera L. AGRIVITA. Journal of Agricultural Science, 39(3): 279-287.
-Rat, A., Naranjo, H.D., Krigas, N., Grigoriadou, K., Maloupa, E., Alonso, A.V., Schneider, C., Papageorgiou, V.P., Assimopoulou, A.N., Tsafantakis, N. and Fokialakis, N., 2021. Endophytic bacteria from the roots of the medicinal plant Alkanna tinctoria Tausch (Boraginaceae): Exploration of plant growth promoting properties and potential role in the production of plant secondary metabolites. Frontiers in Microbiology, 3(12): 113.
-Rastogi, G., Sbodio, A., Tech, J.J., Suslow, T.V., Coaker, G.L. and Leveau, J.H.J., 2012. Leaf microbiota in an agroecosystem: Spatiotemporal variation in bacterialcommunity composition on field-grown lettuce. The ISME Journal, 6(10): 1812-1822.
-Rostami, S.H., Hasanzadeh, N., Rajaei, S., Golnaraghi, A. and Azizinezhad, R., 2021. A study on endophytic bacteria isolated from wild legumes against Xanthomonas phaseoli. Applied Entomology and Phytopathology. 89(1): 1-16.
-Ryan, R.P., Germaine, K., Franks, A., Ryan, D.J. and Dowling, D.N., 2008. Bacterial endophytes: recent developments and applications. FEMS Microbiology Letters, 278(1): 1-9.
-Saberi, E., Alavi, S.M., Safaie, N., Moslemkhany, C. and Azadvar, M., 2017. Bacterial pathogens associated with citrus huanglongbing-like symptoms in southern Iran. Journal of Crop Protection, 6(1): 99-113.
-Saini, R., Kumar, V., Dudeja, S.S. and Pathak, D.V., 2015. Beneficial effects of inoculation of endophytic bacterial isolates from roots and nodules in chickpea. International Journal of Current Microbiology and Applied Sciences, 4(10): 207-221.
-Schulze, J., 2004. How are nitrogen fixation rates regulated in legumes?. Journal of Plant Nutrition and Soil Science, 167(2): 125-137.
-Suryanto, D., Yeldi, N. and Munir, E., 2016. Antifungal activity of endophyte bacterial isolates from torch ginger (Etlingera elicitor (Jack.) RM Smith)) root to some pathogenic fungal isolates. International Journal of PharmTech Research, 9: 340-7.
-Tollefson, J., 2020. Why deforestation and extinctions make pandemics more likely. Nature, 584: 175-176.
-Vega, F.E., 2018. The use of fungal entomopathogens as endophytes in biological control: a review. Mycologia, 110(1): 4-30.
-Vyas, P., Rahi, P. and Gulati, A., 2009. Stress tolerance and genetic variability of phosphate-solubilizing Fuorescent Pseudomonas from the cold deserts of the trans-Himalayas. Microbial ecology, 58(2): 425-434.
-Walia, A., Guleria, S., Chauhan, A. and Mehta, P., 2017. Endophytic bacteria: role in phosphate solubilization. Endophytes: Crop Productivity and Protection, pp. 61-93.
-Willems, A., 2006. The taxonomy of rhizobia: an overview. Plant and Soil, 287(1): 3-14.
-Xu, W., Wang, F., Zhang, M., Ou, T., Wang, R., Strobel, G. and Xie, J., 2019. Diversity of cultivable endophytic bacteria in mulberry and their potential for antimicrobial and plant growth-promoting activities. Microbiological research, 1(229): 126328.
-Yang, R., Liu, P. and Ye, W., 2017. Illumina-based analysis of endophytic bacterial diversity of tree peony (Paeonia Sect. Moutan) roots and leaves. Brazilian Journal of Microbiology, 48(4): 695-705.
-Yazdani-Khameneh, S., Golnaraghi, A. and Wylie, S.J., 2019. Diverse endophytic fungi colonize indigenous grasses in the Hyrcanian forest of Iran. The 18th Congress of European Mycologists, September 2019, pp. 16-21.
-Yu, X., Yang, J., Wang, E., Li, B. and Yuan, H., 2015. Effects of growth stage and fulvic acid on the diversity and dynamics of endophytic bacterial community in Stevia rebaudiana Bertoni leaves. Frontiers in microbiology, 25(6): 867.
 
 
Iranian Journal of Forest and Range Protection Research
Volume 19, Issue 2 - Serial Number 38
January 2022
Pages 266-278

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History

  • Receive Date: 20 May 2021
  • Revise Date: 18 June 2021
  • Accept Date: 11 July 2021

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