Endophytic fungi associated with chickpea (Cicer arietinum L.) in Iran

Document Type : Original Article

Authors

1 Department of Plant Protection, Faculty of Agriculture, University of Tehran, Karaj, Iran

2 Department of Agronomy, Faculty of Agriculture, University of Tehran, Karaj, Iran

10.22092/mi.2026.371898.1340

Abstract

Chickpea (Cicer arietinum) is an important legume crop. This annual plant is widely cultivated across many regions of the world. A notable characteristic of chickpeas is their multiple symbiotic associations with diverse microorganisms that contribute to soil fertility. In this study, we investigated the diversity of endophytic fungi in seeds, aerial and underground organs of twenty-one genotypes of chickpea. The genotypes were obtained from the Dryland Agricultural Research Institute (Maragheh, East Azerbaijan, Iran). The genotypes were grown under both greenhouse and field conditions using disinfected and non-disinfected seeds. Additionally, to assess endophytic fungal diversity under field conditions, sampling was conducted in chickpea fields in the villages of Anjirak and Znylaan-Sofla, Kermanshah County, as well as in fields on the experimental campus of the Faculty of Agriculture, University of Razi, Kermanshah, Iran. A total of 366 fungal strains were isolated, of which 80 isolates were obtained from plants grown from non-disinfected and 60 isolates from disinfected seeds in the greenhouse. Moreover, from chickpea genotypes planted on a farm in Hamadan Province and 48 plant samples collected across six fields in Kermanshah Province, a total of 50 and 155 endophytic fungal isolates were obtained, respectively. Furthermore, a total of 21 fungal isolates were recovered from seeds of genotypes ‘Desi 37’, ‘Kaka’, ‘Sufi’, and ‘Flip 09-2780’. Following morphological characterization and sequencing of representative isolates based on the genomic regions tef1-α, tub2, ITS rDNA, cal and rpb2, ten fungal species were identified, belonging to six genera. The identified species were Allophoma labilis, Aspergillus fumigatus, A. luchuensis, A. niger, A. tubingensis, Chaetomium rectangulare, Cladosporium ramotenellum, Fusarium acuminatum, F. redolens and Penicillium chrysogenum. The most isolates belong to Aspergillus (60.65%) and Fusarium species (27.86%). Among the chickpea genotypes, the greatest number of isolates were obtained from ‘Flip 09-2780’ (43 isolates) and ‘Adel’ (41 isolates).
 

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Main Subjects

References

Abdel-Azeem AM. 2019. Taxonomy and biodiversity of the genus Chaetomium in different habitats. In: Recent Developments on Genus Chaetomium. 3-77. Springer International Publishing, Switzerland. https://doi.org/ 10.1007/978-3-030-31612-9_1.
Ahmad F, Gaur PM, Croser J. 2005. Chickpea (Cicer arietinum L.). In: Genetic Resources, Chromosome Engineering, and Crop Improvement. (Innis Singh RJ and Jauhar PP, eds): 229-267. Taylor & Francis, UK.
Ahmad W, Coffman L, Ray RL, Balan V, Weerasooriya A, Khan AL. 2024. Microbiome diversity and variations in industrial hemp genotypes. Scientific Reports. 14(1): 29-560.https://doi.org/10.1038/ s41598-024-79192-7.
Alijani N, Ghosta Y, Rezaiie-Danesh Y. 2016. Biodiversity of endophytic fungi from apple trees in West Azerbaijan Province. Proceedings of 22th Iranian Plant Protection Congress; Karaj, Iran: p. 27-30.
Ansari L, Asgari B, Zare R, Zamanizadeh HR. 2022. Biodiversity of Penicillium and Talaromyces species from sugarcane rhizosphere in Khuzestan Province (Iran). Rostaniha. 23(1): 1-24. https://doi.org/ 10.22092/botany.2021.355951.1273.
Asgari B, Zare R. 2011. The genus Chaetomium in Iran, a phylogenetic study including six new species. Mycologia. 103(4): 863-882. https://doi.org/ 10.3852/10-349
Bazghaleh N, Hamel C, Gan Y, Tar'an B, Knight JD. 2015. Genotype-specific variation in the structure of root fungal communities is related to chickpea plant productivity. Applied and Environmental Microbiology. 81(7): 2368-2377. https://doi.org/ 10.1128/ AEM.03692-14
Bensch K, Groenewald JZ, Meijer M, Dijksterhuis J, Jurjević Ž, Andersen B, Samson RA. (2018). Cladosporium species in indoor environments. Studies in Mycology. 89(1): 177-301. https://doi.org/10.1016/j.simyco.2018.03.002
Carbone I, Kohn LM. 1999. A method for designing primer sets for speciation studies in filamentous ascomycetes. Mycologia. 91(3): 553-556. https://doi.org/ 10.1080/00275514.1999.12061051
Chen Q, Jiang JR, Zhang GZ, Cai L, Crous PW. 2015. Resolving the Phoma enigma. Studies in Mycology. 82(1): 137-217. https://doi.org/10.1016 /j. simyco.2015.10.003.
Chen XL, Li M, Liu CC, Ma J, Wang X, Wu BL. 2020. Exploration of endophytes from alfalfa (Medicago sativa L.) as biocontrol agents. Genet. Genom. 1(1): 3-8. https://doi.org/10.31487/j.GG.2020.01.01
Colmán AA, Alves JL, da Silva M, Barreto RW. (2018). Phoma destructiva causing blight of tomato plants: a new fungal threat for tomato plantations in Brazil. Tropical Plant Pathology. 43(1): 257-262. 10.1007/ s40858-017-0200-2.
Davoudpour Y, Schmidt M, Calabrese F, Richnow HH, Musat N. 2020. High resolution microscopy to evaluate the efficiency of surface sterilization of Zea mays seeds. Plos One. 15(11): 242-247. https://doi. org/ 10.1371/journal.pone.0242247.
Dong C, Wang L, Li Q, Shang, Q. 2021. Epiphytic and endophytic fungal communities of tomato plants. Horticultural Plant Journal. 7(1): 38-48. https://doi.org/10.1016/j.hpj.2020.09.002.
Fernandes EG, Pereira OL, da Silva CC, Bento CBP, de Queiroz MV. 2015. Diversity of endophytic fungi in Glycine max. Microbiological Research. 181(1): 84-92. https://doi.org/10.1016/j.micres.2015.05.010.
García-Latorre C, Rodrigo S, Marin-Felix Y, Stadler M, Santamaria O. 2025. Exploiting antifungal metabolites of the fungus Purpureocillium lilacinum for effective control of Botrytis cinerea in chickpea plants. BioControl. 70(1): 1-13. https://doi.org/ 10.1007/s10526-025-10319-z.
Gashgari R, Gherbawy Y, Ameen F, Alsharari S. 2016. Molecular characterization and analysis of antimicrobial activity of endophytic fungi from medicinal plants in Saudi Arabia. Jundishapur Journal of Microbiology. 9(1): 1-8. https:// doi.org/10.5812/jjm.26157.
Glass NL, Donaldson GC. 1995. Development of primer sets designed for use with the PCR to amplify conserved genes from filamentous ascomycetes. Applied and Environmental Microbiology. 61(4): 1323-1330. https://doi.org/10.1128/aem.61.4.1323-1330.1995.
Gong W, Li Q, Lai Y, Yang D, Xu X, Liao H, Li H. 2025. Rice endophytic fungal community and its potential role on rice grains Cd accumulation. World Journal of Microbiology and Biotechnology. 41(6): 1-201. https://doi.org/10.1007/s11274-025-04449-w.
Grasso N, Lynch NL, Arendt EK, O'Mahony JA. 2022. Chickpea protein ingredients: a review of composition, functionality, and applications. Comprehensive Reviews in Food Science and Food Safety. 21(1): 435-452.https://doi.org/10.1111/ 1541-4337.12878
Hall T. 2004. BioEdit version 7.0.0. Department of Microbiology, North Carolina State University.
Han SL, Wang MM, Ma ZY, Raza M, Zhao P, Liang JM, Cai L. 2023. Fusarium diversity associated with diseased cereals in China, with an updated phylogenomic assessment of the genus. Studies in Mycology. 104(1): 87-148. https://doi.org/10.3114/ sim.2022.104.02.
Hong SP, Momcilovic M, Carlson M. 2005. Function of mammalian LKB1 and Ca2+/calmodulin-dependent protein kinase kinase α as Snf1-activating kinases in yeast. Journal of Biological Chemistry. 280(23): 21804-21809. https://doi.org/10.1074/jbc. m50188 7200.
Houbraken J, Kocsube S, Visagie CM, Yilmaz N, Wang X-C, Meijer M, Kraak B, Hubka, Bensch K., Samson RA, Frisvad JC. 2020. Classification of Aspergillus, Penicillium, Talaromyces and related genera (Eurotiales): an overview of families, genera, subgenera, sections, series and species. Studies in Mycology. 95: 5-169. https://doi.org/10.1016/ j.simyco. 2020.05.002.
Hu J. 2023. First report of Cladosporium ramotenellum causing sooty spot on postharvest clementines in the United States. Plant Disease. 107(10): 32-81. https://doi.org/10.1094/PDIS-02-23-0210-PDN.
Impullitti AE, Malvick DK. 2013. Fungal endophyte diversity in soybean. Journal of Applied Microbiology. 114(5): 1500-1506.
https://doi.org/10.1111/jam.12164
Jamali S. 2024. A review on Fusarium redolens (Wollenweber) as an emerging plant pathogen in Iran. Mycologia Iranica. 11(1): 1-17. https://doi.org/10.22092/MI.2024.364726.1273.
Jiang Y, Wu J, Kawagishi H, Jiang C, Zhou Q, Tong Z, Wang P. 2022. Study on Secondary Metabolites of Endophytic Fungus, Aspergillus fumigatus, from Crocus sativus L. Guided by UHPLC‐HRMS/MS‐Based Molecular Network. International Journal of Analytical Chemistry. 2022(1): 706-7665. https://doi.org/10.1155/2022/7067665.
Joshi PK, Rao PP. 2017. Global pulses scenario: status and outlook. Annals of the New York Academy of Sciences. 1392(1): 6-17. https://doi.org/10.1111 /nyas.13298.
Kim J, Ahn SH, Yang JS, Choi S, Jung HW, Jeon J. 2023. Plant protective and growth promoting effects of seed endophytes in soybean plants. The Plant Pathology Journal. 39(5): 5-13. https://doi.org/ 10.5423/PPJ.OA.06.2023.0091.
Kumari V, Germida J, Vujanovic V. 2018. Legume endosymbionts: drought stress tolerance in second‐generation chickpea (Cicer arietinum) seeds. Journal of Agronomy and Crop Science. 204(6): 529-540. https://doi.org/10.1111/jac.12283.
Larki R, Mehrabi‐Koushki M, Farokhinejad R. 2019. Ectophoma iranica sp. nov. and new hosts and records of Allophoma spp. in Iran. Journal of Phytopathology. 167(9): 538-545. https://doi.org/ 10.1111/jph.12840.
Larran S, Perelló A, Simón MR, Moreno V. 2007. The endophytic fungi from wheat (Triticum aestivum
L.). World Journal of Microbiology and Biotechnology. 23(4): 565-572.https://doi.org/ 10.1007/s11274-006-9266-6.
Liu YJ, Whelen S, Hall B D. 1999. Phylogenetic relationships among ascomycetes: evidence from an RNA polymerase II subunit. Molecular Biology and Evolution. 16(12): 1799-1808. https://doi.org/10.1093/oxfordjournals.molbev.a026092.
Liu JY, Song YC, Zhang Z, Wang L, Guo ZJ, Zou WX, Tan RX. 2004. Aspergillus fumigatus CY018, an endophytic fungus in Cynodon dactylon as a versatile producer of new and bioactive metabolites. Journal of Biotechnology. 114(3): 279-287. https://doi.org/10.1016/j.jbiotec.2004.07.008.
Meghana SP, Sunkad G, ST Y, Kulkarni SA, Rao S, Naik NM. 2022. Cultural characteristics of endophytic fungal PGPMs associated with chickpea. The Pharma Innovation Journal. 11(9): 2792-2797.
Merga B, Haji J. 2019. Economic importance of chickpea: production, value, and world trade. Cogent Food and Agriculture. 51(1): 161-571. https://doi.org/10.1080/23311932.2019.1615718.
Moglad E, Elekhnawy E, Negm WA, Eliwa D, Sami Younis S, Mohamed Elmansory B, Momtaz Al-Fakhrany O. 2023. Antibacterial and anti-Toxoplasma activities of Aspergillus niger endophytic fungus isolated from Ficus retusa: in vitro and in vivo approach. Artificial Cells, Nanomedicine, and Biotechnology. 51(1): 297-308. https://doi.org/10.1080/21691401.2023.2215531.
Moparthi S, Perez-Hernandez O, Burrows ME, Bradshaw MJ, Bugingo C, Brelsford M, McPhee K. 2024. Identification of Fusarium spp. Associated with Chickpea Root Rot in Montana. Agriculture. 14(7): 9-74. https://doi.org/10.3390/agriculture 14070974.
Nazarideljou MJ, Rahmani S, Kalanaky S, Hojati M, Nazaran MH. 2024. Nanochelating-based fertilizers: Innovations for yield enhancement in hydroponic cultivation. Scientia Horticulturae. 326(1): 112-776. https://doi.org/10.1016/j.scienta.2023.112776.
Nisa S, Khan N, Shah W, Sabir M, Khan W, Bibi Y, Qayyum A. 2020. Identification and bioactivities of two endophytic fungi Fusarium fujikuroi and Aspergillus tubingensis from foliar parts of Debregeasia salicifolia. Arabian Journal for Science and Engineering. 45(6): 4477-4487. https://doi.org/ 10.1007/s13369-020-04454-1.
O’Donnell K, Kistler HC, Cigelnik E, Ploetz RC.1998. Multiple evolutionary origins of the fungus causing pnama disease of banana: concordant evidence from nuclear and mitochondrial gene genealogies. Proceedings of the National Academy of Sciences. 95(5): 2044-2049. https://doi.org/10.1073/pnas. 95.5.2044.
O'Donnell K, Cigelnik E. 1997. Two divergent intragenomic rDNA ITS2 types within a monophyletic lineage of the fungus Fusarium are
nonorthologous. Molecular Phylogenetics and Evolution. 7(1): 103-116. https://doi.org/10.1006/ mpev. 1996.0376.
Parsa, S, García-Lemos AM, Castillo K, Ortiz V, López-Lavalle LAB, Braun J, Vega FE. 2016. Fungal endophytes in germinated seeds of the common bean, Phaseolus vulgaris. Fungal Biology. 120(5): 783-790. https://doi.org/10.1016/j.funbio.2016.01. 017.
Riga R, Wardatillah R, Suryani O, Ryplida B, Suryelita S, Azhar M, Putra A. 2024. Endophytic fungus from Gynura japonica: phytochemical screening, biological activities, and characterisation of its bioactive compound. Natural Product Research. 39(14): 4117-4125. https://doi.org/10.1080/ 14786419. 2024.2332947.
Samson RA, Hong S, Peterson SW, Frisvad JC, Varga J. 2007. Polyphasic taxonomy of Aspergillus section Fumigati and its teleomorph Neosartorya. Studies in Mycology. 59(1): 147-203. https://doi.org/10.3114/ sim.2007.59.14.
Sandoval-Denis M, Sutton DA, Martin-Vicente A, Cano-Lira JF, Wiederhold N, Guarro J, Gené J. 2015. Cladosporium species recovered from clinical samples in the United States. Journal of Clinical Microbiology. 53(9): 2990-3000. https://doi.org/ 10.1128/ jcm.01482-15.
Singh D, Geat N, Rajawat MVS, Prasanna R, Kar A, Singh AM, Saxena, AK. 2018. Prospecting endophytes from different Fe or Zn accumulating wheat genotypes for their influence as inoculants on plant growth, yield, and micronutrient content. Annals of Microbiology. 68(12): 815-833. https://doi.org/10.1007/s13213-018-1388-1.
Sung GH, Sung JM, Hywel-Jones NL, Spatafora JW. 2007. A multi-gene phylogeny of Clavicipitaceae (Ascomycota, Fungi): identification of localized incongruence using a combinational bootstrap approach. Molecular Phylogenetics and Evolution. 44(3): 1204-1223. https://doi.org/10.1016/j.ympev. 2007.03.011.
Tovar-Sánchez E, Concepción-Acosta CM, Sánchez-Reyes A, Sánchez-Cruz R, Folch-Mallol JL, Mussali-Galante P. 2023. Aspergillus luchuensis, an endophyte fungus from the metal hyperaccumulator plant Prosopis laevigata, promotes its growth and increases metal translocation. Plants. 12(6): 13-38. https://doi.org/10.3390/plants12061338.
Varga J, Frisvad JC,Kocsubé S, Brankovics B, Tóth B, Szigeti G, Samson R. 2011. New and revisited species in Aspergillus section Nigri. Studies in Mycology. 69(1): 1-17. https://doi.org/10.3114/ sim.2011.69.01.
Visagie CM, Houbraken J, Frisvad JC, Hong SB, Klaassen CHW, Perrone G, Samson RA. (2014). Identification and nomenclature of the genus Penicillium. Studies in Mycology. 78(1): 343-371. https://doi.org/10.1016/j.simyco.2014.09.001.
Wani ZA, Ashraf N, Mohiuddin T, Riyaz-Ul-Hassan S.
 
(2015). Plant-endophyte symbiosis, an ecological
perspective. Applied Microbiology and Biotechnology. 99(7): 2955-2965. https://doi.org/ 10.1007/ s00253-015-6487-3.
Wang R, Zhang Q, Ju M, Yan S, Zhang Q, Gu P. 2022. The endophytic fungi diversity, community structure, and ecological function prediction of Sophora alopecuroides in Ningxia, China. Microorganisms. 10(11): 20-99. https://doi.org/ 10.3390/ microorganisms10112099.
Watts D, Palombo EA, Jaimes Castillo A, Zaferanloo B. 2023. Endophytes in agriculture: potential to improve yields and tolerances of agricultural crops. Microorganisms. 11(5): 12-76. https://doi.org/ 10.3390/ microorganisms11051276.
Woudenberg JHC, Aveskamp MM, De Gruyter J, Spiers AG, Crous PW. 2009. Multiple Didymella teleomorphs are linked to the Phoma clematidina morphotype.
 
 
 
Persoonia. 22(1): 56-62. https://doi.org/10.3767/ 003158509X427808.
White TJ, Bruns T, Lee SJWT,Taylor J. 1990. Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. In: PCR protocols: a guide to methods and applications. (Innis MA, Gelfand JJ, Sninsky DH and White TJ, eds): 315-322. Academic Press, USA.
Zimowska B, Becchimanzi A, Krol ED, Furmanczyk A, Bensch K, Nicoletti R. 2021. New Cladosporium species from normal and galled flowers of Lamiaceae. Pathogens. 10(3): 3-69. https://doi.org/10.3390/pathogens10030369.
Zhong S, Steffenson BJ. 2001. Genetic and molecular characterization of mating type genes in Cochliobolus sativus. Mycologia. 93(5): 852-863. https://doi.org/10.1080/00275514.2001. 12063220.
 
Mycologia Iranica
Volume 12, Issue 2
December 2025
Pages 105-122

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  • Receive Date: 01 December 2025
  • Revise Date: 22 December 2025
  • Accept Date: 29 December 2025
  • Publish Date: 01 December 2025

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