Integrating Ethnographic Knowledge and Rhizosphere Microbiology of Peganum harmala in Kyrgyzstan
Abstract
Background: Peganum harmala (locally known in Kyrgyzstan as adyrashman or ysyryk) is a medicinal plant with a long history of traditional use in Kyrgyzstan, with references to its applications preserved in the Manuscripts Fund of the National Academy of Sciences of the Kyrgyz Republic. However, little is known about the rhizosphere-associated bacterial communities of this species. This study examined P. harmala using an integrated microbiological and molecular approach to characterize its rhizosphere bacteria and investigate their microbial diversity. Methods: P. harmala plants were collected from the Kashka-Suu rural area of the Alamudun District, Chüy Region, Kyrgyzstan. Rhizosphere-associated bacteria were isolated using standard microbiological techniques and characterized by morphological and biochemical analyses. Microbial diversity was investigated through 16S rRNA gene amplification, sequencing, and taxonomic identification. Results: The analysis revealed the presence of bacterial genera including Pseudomonas, Stenotrophomonas, and Paenarthrobacter, highlighting the diversity of microorganisms associated with the plant root environment. These findings provide new insights into the bacterial communities associated with P. harmala and establish a foundation for future investigations into plant–microbe interactions and the ecological roles of root-associated microorganisms. Conclusion: This study represents the first characterization of the rhizosphere bacterial community associated with Peganum harmala in Kyrgyzstan using 16S rRNA gene-based identification. The findings expand current knowledge of the microbial diversity associated with this medicinal plant and provide a basis for future studies exploring the ecological, agricultural, and biotechnological significance of its root-associated microorganisms.
Keywords:
Genus Pseudomonas, Kyrgyzstan, Peganum harmala (Adyrashman), Rhizosphere Bacteria
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References
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Aravind, R., Eapen, S. J., Kumar, A., Dinu, A., & Ramana, K. V. (2010). Screening of endophytic bacteria and evaluation of selected isolates for suppression of burrowing nematode (Radopholus similis Thorne) using three varieties of black pepper (Piper nigrum L.). Crop Protection, 29(4), 318-324. https://doi.org/10.1016/j.cropro.2009.12.005
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Askarbek, G., & Tulobayev, A. (2021). Mal ylaŋdarynaldynaluudagy Kyrgyz elininsalttuuykmalary [Traditional Kyrgyz remedies for snakebites]. Manas Journal of Agriculture Veterinary and Life Sciences, 11(2), 138–144. https://doi.org/10.53518/mjavl.884684
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Brooke, J. S. (2012). Stenotrophomonas maltophilia: an emerging global opportunistic pathogen. Clinical Microbiology Reviews, 25(1), https://doi.org/10.1128/cmr.00019-11
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Compant, S., Clément, C., &Sessitsch, A. (2010). Plant growth-promoting bacteria in the rhizo-and endosphere of plants: their role, colonization, mechanisms involved and prospects for utilization. Soil Biology and Biochemistry, 42(5), 669-678. https://doi.org/10.1016/j.soilbio.2009.11.024
Dida, G., Beshir, H. M., & Muleta, D. (2018). Isolation and characterization of starch degrading rhizobacteria. Open AccessJournal of Microbiology & Biotechnology, 3, 2576-7771. https://doi.org/10.23880/oajmb-16000129
Dobbelaere, S., Vanderleyden, J., & Okon, Y. (2003). Plant growth-promoting effects of diazotrophs in the rhizosphere. Critical Reviews in Plant Sciences, 22(2), 107-149. https://doi.org/10.1080/713610853
Doolotkeldieva, T., & Bobusheva, S. (2016). Fire blight disease caused by Erwinia amylovora on Rosaceae plants in Kyrgyzstan and biological agents to control this disease. Advances in Microbiology, 6(11), 831-851. https://doi.org/10.4236/aim.2016.611080
Doskaliyev, A., Seidakhmetova, R., Tutai, D. S., Goldaeva, K., Surov, V. K., & Adekenov, S. M. (2021). Alkaloids of Peganum harmala L. and their Pharmacological Activity. Open Access Macedonian Journal of Medical Sciences,9(A), 766-775. https://doi.org/10.3889/oamjms.2021.6654
El Fissi, H., Ameziane, H., Bouzid, F., Achqra, I., Msanda, F., & Alif, N. (2025). Isolation, digital analysis, and semi-quantification of harmaline and harmine from Peganum harmala L. Euro-Mediterranean Journal for Environmental Integration, 10(3), 1805-1810. https://doi.org/10.1007/s41207-024-00624-x
Gökkaya, İ., Renda, G., Subaş, T., & Özgen, U. (2023). Phytochemical, pharmacological, and toxicological studies on Peganum harmala L.: An overview of the last decade. Clinical and Experimental Health Sciences, 13(3), 664-678. https://doi.org/10.33808/clinexphealthsci.1125345
Halebian, S., Harris, B., Finegold, S. M., & Rolfe, R. D. (1981). Rapid method that aids in distinguishing Gram-positive from Gram-negative anaerobic bacteria. Journal of Clinical Microbiology, 13(3), 444-448. https://doi.org/10.1128/jcm.13.3.444-448.1981
Khudoynazarova, G., Kodirova, Z., Ganiev, B., Jalilov, S., & Mavluda, R. (2025). Chemical Composition and In Silico Study of the Biological Activities of Alkaloids from Peganum harmala. In E3S Web of Conferences (Vol. 661, p. 05003). EDP Sciences. https://doi.org/10.1051/e3sconf/202566105003
Koçak, Y., & Şahin, A. (2009). Peganum harmala L. (üzerlik) tohumekstresininanaljezikaktivitesiveakuttoksisitesininfarelerüzerindebelirlenmesi [Analgesic activity and acute toxicity determination of Peganum harmala L. (üzerlik) seed extract in mice]. YüzüncüYılÜniversitesiVeterinerFakültesi Dergisi, 20(1), 27–30. https://dergipark.org.tr/tr/pub/yyuvfd/article/166269
Kotoučková, L., Schumann, P., Durnova, E., Spröer, C., Sedláček, I., Neča, J., ... & Němec, M. (2004). Arthrobacter nitroguajacolicus sp. nov., a novel 4-nitroguaiacol-degrading actinobacterium. International journal of Systematic and Evolutionary Microbiology, 54(3), 773-777. https://doi.org/10.1099/ijs.0.02923-0
Krieg, N. R., Ludwig, W., Whitman, W. B., Hedlund, B. P., Paster, B. J., Staley, J. T., Brown, D. R., Parte, A., & Ward, A. C. (Eds.). (2010). Bergey's manual of systematic bacteriology: The Bacteroidetes, Spirochaetes, Tenericutes (Mollicutes), Acidobacteria, Fibrobacteres, Fusobacteria, Dictyoglomi, Gemmatimonadetes, Lentisphaerae, Verrucomicrobia, Chlamydiae, and Planctomycetes. Springer. (2nd ed., Vol. 4). Springer.
Kumar, V., Raghuvanshi, N., Pandey, A. K., Kumar, A., Thoday-Kennedy, E., & Kant, S. (2023). Role of halotolerant plant growth-promoting rhizobacteria in mitigating salinity stress: Recent advances and possibilities. Agriculture, 13(1), 168. https://doi.org/10.3390/agriculture13010168
Li, L. N. (2024). Peganum harmala L.: A review of botany, traditional use, phytochemistry, pharmacology, quality marker, and toxicity. Combinatorial Chemistry & High Throughput Screening, 27(6), 797-822. https://doi.org/10.2174/1386207326666230622164243
Lundberg, D. S., Lebeis, S. L., Paredes, S. H., Yourstone, S., Gehring, J., Malfatti, S., ... & Dangl, J. L. (2012). Defining the core Arabidopsis thaliana root microbiome. Nature, 488(7409), 86-90. https://doi.org/10.1038/nature11237
Mamedov, N. A., Pasdaran, A., &Mamadalieva, N. Z. M. (2018). Pharmacological studies of Syrian rue (Peganum harmala L., Zygophyllaceae). International Journal of Secondary Metabolite, 5(1), 1-6. https://doi.org/10.21448/ijsm.335539
Miftakhov, K. (1946). Kyrgyz el meditsinasy [Kyrgyz folk medicine]. National Academy of Sciences of the Kyrgyz Republic, Manuscripts Fund, 305/526, Folder 1, pp. 1–2.
Mukhtorova, S., Alikulov, B., Yuldosheva, M., Maxammadieva, D., Khidirova, U., Kabulova, F., & Ismailov, Z. (2024). Diversity of endophytic bacteria isolated from Peganum harmala distributed in arid re-gions in Uzbekistan. Regulatory Mechanisms in Biosystems, 15(2), 286-291. https://doi.org/10.15421/022441
O'sullivan, D. J., & O'Gara, F. (1992). Traits of fluorescent Pseudomonas spp. involved in suppression of plant root pathogens. Microbiological Reviews, 56(4), 662-676. https://doi.org/10.1128/mr.56.4.662-676.1992
Penkala-Gawęcka, D. (2023). Poganekrutowaty (Peganum harmala L.) w tradycjachludówAzjiŚrodkowejijegopopularność w dobie pandemii COVID-19 – perspektywaantropologiimedycznej MedycynaNowożytna, [Peganum routed (Peganum harmala L.) in the traditions of the peoples of Central Asia and its popularity in the era of the COVID-19 pandemic – a perspective of medical anthropology, Modern Medicine Studies on Medical Culture]. 29(1), 135-164. https://doi.org/10.4467/12311960MN.23.007.18448
Qi, Q., Chu, A. Y., Kang, J. H., Jensen, M. K., Curhan, G. C., Pasquale, L. R., ... & Qi, L. (2012). Sugar-sweetened beverages and genetic risk of obesity. New England Journal of Medicine, 367(15), 1387-1396. https://doi.org/10.1056/NEJMoa1203039
Ryan, R. P., Germaine, K., Franks, A., Ryan, D. J., & Dowling, D. N. (2008). Bacterial endophytes: recent developments and applications. FEMS Microbiology Letters, 278(1), 1-9.https://doi.org/10.1111/j.1574-6968.2007.00918.x
Santoyo, G., Orozco-Mosqueda, M. D. C., &Govindappa, M. (2012). Mechanisms of biocontrol and plant growth-promoting activity in soil bacterial species of Bacillus and Pseudomonas: A review. Biocontrol Science and Technology, 22(8), 855-872.https://doi.org/10.1080/09583157.2012.694413
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
Tügelov, N. (1946, September 16). [Interview: Age 72, Choro lineage, resident of ZhanïTalap kolkhoz, Ak-Talaa District, Tien Shan Region] (S. Tabyshaliev, A. Chorobaev, & Umurzakov, Interviewers). Notebook 3, Materials of the Tien Shan Expedition (p. 17). (archival interview.)
Weisburg, W. G., Barns, S. M., Pelletier, D. A., & Lane, D. J. (1991). 16S ribosomal DNA amplification for phylogenetic study. Journal of Bacteriology, 173(2), 697-703. https://doi.org/10.1128/jb.173.2.697-703.1991
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
Alghoul, N., Sasi, S., Awayn, N., Prastiya, R., & Salem, K. (2025). Assessment of Sperm Function and Embryo Morphology Following Exposure to Peganum Harmala Seeds Decoction in Mice. AlQalam Journal of Medical and Applied Sciences, 8(2), 1000-1004. https://doi.org/10.54361/ajmas.258271
Aravind, R., Eapen, S. J., Kumar, A., Dinu, A., & Ramana, K. V. (2010). Screening of endophytic bacteria and evaluation of selected isolates for suppression of burrowing nematode (Radopholus similis Thorne) using three varieties of black pepper (Piper nigrum L.). Crop Protection, 29(4), 318-324. https://doi.org/10.1016/j.cropro.2009.12.005
Asgarpanah, J., &Ramezanloo, F. (2012). Chemistry, pharmacology and medicinal properties of Peganum harmala L. African Journal of Pharmacy and Pharmacology, 6(22), 1573-1580. https://doi.org/10.5897/AJPP11.876
Askarbek, G., & Tulobayev, A. (2021). Mal ylaŋdarynaldynaluudagy Kyrgyz elininsalttuuykmalary [Traditional Kyrgyz remedies for snakebites]. Manas Journal of Agriculture Veterinary and Life Sciences, 11(2), 138–144. https://doi.org/10.53518/mjavl.884684
Babar, Z. Z., Younis, T., & Shinwari, Z K. (2025). Isolation and Characterization of Plant Growth Promoting Endophytic Bacteria FromPeganum Harmala L. Biological and Clinical Sciences Research Journal, 6(8), 75–81. https://doi.org/10.54112/bcsrj.v6i8.1975
Borde, V., Hivrale, V., &Kachole, M. (2013). Identification and purification and antimicrobial activity of alkaloid from Peganumharmale (L), a medicinal Plant. Journal of Biology, Agriculture and Healthcare, 3(19), 105–111. https://www.iiste.org/Journals/index.php/JBAH/article/view/9798
Bossis, E., Lemanceau, P. P., Latour, X., & Gardan, L. (2000). The taxonomy of Pseudomonas fluorescens and Pseudomonas putida: current status and need for revision. Agronomie, 20(1), 51-63. https://doi.org/10.1051/agro:2000112
Brooke, J. S. (2012). Stenotrophomonas maltophilia: an emerging global opportunistic pathogen. Clinical Microbiology Reviews, 25(1), https://doi.org/10.1128/cmr.00019-11
Bulgarelli, D., Schlaeppi, K., Spaepen, S., Van Themaat, E. V. L., & Schulze-Lefert, P. (2013). Structure and functions of the bacterial microbiota of plants. Annual Review of Plant Biology, 64, 807-838. https://doi.org/10.1146/annurev-arplant-050312-120106
Cappuccino, J. G., & Sherman, N. (2014). Microbiology: A Laboratory Manual. Pearson Higher. 10th Ed. https://www.scribd.com/doc/272782862/Proced-DilSeriada-1
Clarridge J. E., 3rd (2004). Impact of 16S rRNA gene sequence analysis for identification of bacteria on clinical microbiology and infectious diseases. Clinical Microbiology Reviews, 17(4), 840-862. https://doi.org/10.1128/cmr.17.4.840-862.2004
Compant, S., Clément, C., &Sessitsch, A. (2010). Plant growth-promoting bacteria in the rhizo-and endosphere of plants: their role, colonization, mechanisms involved and prospects for utilization. Soil Biology and Biochemistry, 42(5), 669-678. https://doi.org/10.1016/j.soilbio.2009.11.024
Dida, G., Beshir, H. M., & Muleta, D. (2018). Isolation and characterization of starch degrading rhizobacteria. Open AccessJournal of Microbiology & Biotechnology, 3, 2576-7771. https://doi.org/10.23880/oajmb-16000129
Dobbelaere, S., Vanderleyden, J., & Okon, Y. (2003). Plant growth-promoting effects of diazotrophs in the rhizosphere. Critical Reviews in Plant Sciences, 22(2), 107-149. https://doi.org/10.1080/713610853
Doolotkeldieva, T., & Bobusheva, S. (2016). Fire blight disease caused by Erwinia amylovora on Rosaceae plants in Kyrgyzstan and biological agents to control this disease. Advances in Microbiology, 6(11), 831-851. https://doi.org/10.4236/aim.2016.611080
Doskaliyev, A., Seidakhmetova, R., Tutai, D. S., Goldaeva, K., Surov, V. K., & Adekenov, S. M. (2021). Alkaloids of Peganum harmala L. and their Pharmacological Activity. Open Access Macedonian Journal of Medical Sciences,9(A), 766-775. https://doi.org/10.3889/oamjms.2021.6654
El Fissi, H., Ameziane, H., Bouzid, F., Achqra, I., Msanda, F., & Alif, N. (2025). Isolation, digital analysis, and semi-quantification of harmaline and harmine from Peganum harmala L. Euro-Mediterranean Journal for Environmental Integration, 10(3), 1805-1810. https://doi.org/10.1007/s41207-024-00624-x
Gökkaya, İ., Renda, G., Subaş, T., & Özgen, U. (2023). Phytochemical, pharmacological, and toxicological studies on Peganum harmala L.: An overview of the last decade. Clinical and Experimental Health Sciences, 13(3), 664-678. https://doi.org/10.33808/clinexphealthsci.1125345
Halebian, S., Harris, B., Finegold, S. M., & Rolfe, R. D. (1981). Rapid method that aids in distinguishing Gram-positive from Gram-negative anaerobic bacteria. Journal of Clinical Microbiology, 13(3), 444-448. https://doi.org/10.1128/jcm.13.3.444-448.1981
Khudoynazarova, G., Kodirova, Z., Ganiev, B., Jalilov, S., & Mavluda, R. (2025). Chemical Composition and In Silico Study of the Biological Activities of Alkaloids from Peganum harmala. In E3S Web of Conferences (Vol. 661, p. 05003). EDP Sciences. https://doi.org/10.1051/e3sconf/202566105003
Koçak, Y., & Şahin, A. (2009). Peganum harmala L. (üzerlik) tohumekstresininanaljezikaktivitesiveakuttoksisitesininfarelerüzerindebelirlenmesi [Analgesic activity and acute toxicity determination of Peganum harmala L. (üzerlik) seed extract in mice]. YüzüncüYılÜniversitesiVeterinerFakültesi Dergisi, 20(1), 27–30. https://dergipark.org.tr/tr/pub/yyuvfd/article/166269
Kotoučková, L., Schumann, P., Durnova, E., Spröer, C., Sedláček, I., Neča, J., ... & Němec, M. (2004). Arthrobacter nitroguajacolicus sp. nov., a novel 4-nitroguaiacol-degrading actinobacterium. International journal of Systematic and Evolutionary Microbiology, 54(3), 773-777. https://doi.org/10.1099/ijs.0.02923-0
Krieg, N. R., Ludwig, W., Whitman, W. B., Hedlund, B. P., Paster, B. J., Staley, J. T., Brown, D. R., Parte, A., & Ward, A. C. (Eds.). (2010). Bergey's manual of systematic bacteriology: The Bacteroidetes, Spirochaetes, Tenericutes (Mollicutes), Acidobacteria, Fibrobacteres, Fusobacteria, Dictyoglomi, Gemmatimonadetes, Lentisphaerae, Verrucomicrobia, Chlamydiae, and Planctomycetes. Springer. (2nd ed., Vol. 4). Springer.
Kumar, V., Raghuvanshi, N., Pandey, A. K., Kumar, A., Thoday-Kennedy, E., & Kant, S. (2023). Role of halotolerant plant growth-promoting rhizobacteria in mitigating salinity stress: Recent advances and possibilities. Agriculture, 13(1), 168. https://doi.org/10.3390/agriculture13010168
Li, L. N. (2024). Peganum harmala L.: A review of botany, traditional use, phytochemistry, pharmacology, quality marker, and toxicity. Combinatorial Chemistry & High Throughput Screening, 27(6), 797-822. https://doi.org/10.2174/1386207326666230622164243
Lundberg, D. S., Lebeis, S. L., Paredes, S. H., Yourstone, S., Gehring, J., Malfatti, S., ... & Dangl, J. L. (2012). Defining the core Arabidopsis thaliana root microbiome. Nature, 488(7409), 86-90. https://doi.org/10.1038/nature11237
Mamedov, N. A., Pasdaran, A., &Mamadalieva, N. Z. M. (2018). Pharmacological studies of Syrian rue (Peganum harmala L., Zygophyllaceae). International Journal of Secondary Metabolite, 5(1), 1-6. https://doi.org/10.21448/ijsm.335539
Miftakhov, K. (1946). Kyrgyz el meditsinasy [Kyrgyz folk medicine]. National Academy of Sciences of the Kyrgyz Republic, Manuscripts Fund, 305/526, Folder 1, pp. 1–2.
Mukhtorova, S., Alikulov, B., Yuldosheva, M., Maxammadieva, D., Khidirova, U., Kabulova, F., & Ismailov, Z. (2024). Diversity of endophytic bacteria isolated from Peganum harmala distributed in arid re-gions in Uzbekistan. Regulatory Mechanisms in Biosystems, 15(2), 286-291. https://doi.org/10.15421/022441
O'sullivan, D. J., & O'Gara, F. (1992). Traits of fluorescent Pseudomonas spp. involved in suppression of plant root pathogens. Microbiological Reviews, 56(4), 662-676. https://doi.org/10.1128/mr.56.4.662-676.1992
Penkala-Gawęcka, D. (2023). Poganekrutowaty (Peganum harmala L.) w tradycjachludówAzjiŚrodkowejijegopopularność w dobie pandemii COVID-19 – perspektywaantropologiimedycznej MedycynaNowożytna, [Peganum routed (Peganum harmala L.) in the traditions of the peoples of Central Asia and its popularity in the era of the COVID-19 pandemic – a perspective of medical anthropology, Modern Medicine Studies on Medical Culture]. 29(1), 135-164. https://doi.org/10.4467/12311960MN.23.007.18448
Qi, Q., Chu, A. Y., Kang, J. H., Jensen, M. K., Curhan, G. C., Pasquale, L. R., ... & Qi, L. (2012). Sugar-sweetened beverages and genetic risk of obesity. New England Journal of Medicine, 367(15), 1387-1396. https://doi.org/10.1056/NEJMoa1203039
Ryan, R. P., Germaine, K., Franks, A., Ryan, D. J., & Dowling, D. N. (2008). Bacterial endophytes: recent developments and applications. FEMS Microbiology Letters, 278(1), 1-9.https://doi.org/10.1111/j.1574-6968.2007.00918.x
Santoyo, G., Orozco-Mosqueda, M. D. C., &Govindappa, M. (2012). Mechanisms of biocontrol and plant growth-promoting activity in soil bacterial species of Bacillus and Pseudomonas: A review. Biocontrol Science and Technology, 22(8), 855-872.https://doi.org/10.1080/09583157.2012.694413
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
Tügelov, N. (1946, September 16). [Interview: Age 72, Choro lineage, resident of ZhanïTalap kolkhoz, Ak-Talaa District, Tien Shan Region] (S. Tabyshaliev, A. Chorobaev, & Umurzakov, Interviewers). Notebook 3, Materials of the Tien Shan Expedition (p. 17). (archival interview.)
Weisburg, W. G., Barns, S. M., Pelletier, D. A., & Lane, D. J. (1991). 16S ribosomal DNA amplification for phylogenetic study. Journal of Bacteriology, 173(2), 697-703. https://doi.org/10.1128/jb.173.2.697-703.1991
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
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Isakov, B., Bobusheva, S. and Zeinalzadeh-Tabrizi, H. (2026) “Integrating Ethnographic Knowledge and Rhizosphere Microbiology of Peganum harmala in Kyrgyzstan”, International Journal of Advancement in Life Sciences Research, 9(4), pp. 134-144. doi: https://doi.org/10.31632/ijalsr.2026.v09i04.009.
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