ISOLATION OF MICROORGANISMS FROM SOIL CONTAMINATED WITH DIOXINS
DOI 10.12737/2782-490X-2025-4-4-73-84 УДК 631.427.4: 579.64
Keywords:
dioxins, plant colonization, plant growth stimulation, phytobioremediation, IAAAbstract
Soil pollution with dioxins is a serious environmental problem, especially in Vietnam, where the military
use of herbicides by the US Army has led to long-term contamination. Existing physicochemical remediation methods are
ineffective for large areas, which makes it urgent to develop biological approaches, particularly phytoremediation using
microbial destructors. The aim of this study was to isolate bacterial strains capable of dioxin degradation from contaminated soils at Bien Hoa Airfield (Vietnam) and evaluate their potential for phytoremediation. Thirty-seven morphologically
distinct isolates were isolated using selection methods on a medium containing 2,3,7,8-tetrachlorodibenzo-p-dioxin. Taxonomic analysis using the 16S rRNA gene revealed a predominance of gram-positive spore-forming bacteria of the genera
Bacillus, Priestia, and Niallia (approximately 41%) and actinomycetes of the genus Rhodococcus (approximately 14%).
Box-PCR genotyping confirmed the genetic diversity of the collection. Non-pathogenic strains were selected, including
active tomato root colonizers (Pseudomonas putida D01L2B02, Bacillus amyloliquefaciens D01L2B03, Bacillus tropicus
PIB0314/5), possessing a complex of enzymatic activities (protease, amylase, lipase, phytase) and the ability to fix nitrogen. B. tropicus PIB0314/5 demonstrated a statistically significant phytostimulating effect on tomatoes. The results indicate that the isolated native bacterial strains are promising candidates for the development of microbial preparations and
the creation of effective phytoremediation systems for soils contaminated with dioxins.
For citation: Ngo Cao C., Nguen Thi Kim T., Nguen Viet K., Le Van T., Saparmyradov K.A., Komissarov E.N.,
Frolov M.D., Sukhanov A.Yu., Trakhtman N.V., Validov Sh.Z. Isolation of microorganisms from soil contaminated with
dioxins. Agrobiotechnologies and digital farming. 2025; 4(16). 73-84 p. http://dx.doi.org/10.12737/2782-490X-2025-4-4-
73-84
References
Kulkarni P. S., Crespo J. G., Afonso C. A. M. Dioxins sources and current remediation technologies —A review // Environment International. 2008. Т. 34, No 1. С. 139–153. doi: 10.1016/j.envint.2007.07.0092.Mandal P. K. Dioxin: a review of its environmental effects and its aryl hydrocarbon receptor biology // J Comp Physiol B. 2005. Т. 175, No 4. С. 221–230. doi: 10.1007/s00360-005-0483-33.Kirkok S. K. et al. A review of persistent organic pollutants: dioxins, furans, and their associated nitrogenat-ed analogues // SN Appl. Sci. 2020. Т. 2, No 10. С. 1729. https://doi.org/10.1007/s42452-020-03551-y4.Dopico M., Gómez A. Review of the current state and main sources of dioxins around the world // Journal of the Air & Waste Management Association. 2015. Т. 65, No 9. С. 1033–1049. doi: 10.1080/10962247.2015.10588695.Haemers J. et al. Bien Hoa Dioxin/Agent Orange thermal desorption treatment -Full report. Unpublished, 2022. doi: 10.13140/RG.2.2.13849.702486.Wittich R. M. et al. Metabolism of dibenzo-p-dioxin by Sphingomonas sp.strain RW1 // Appl Environ Mi-crobiol. 1992. Т. 58, No 3. С. 1005–1010. doi: 10.1128/aem.58.3.1005-1010.19927.Saibu S., Adebusoye S. A., Oyetibo G. O. Aerobic bacterial transformation and biodegradation of dioxins: a review // Bioresour. Bioprocess. 2020. Т. 7, No 1. С. 7. doi: 10.1186/s40643-020-0294-08.Field J. A., Sierra-Alvarez R. Microbial degradation of chlorinated dioxins // Chemosphere. 2008. Т. 71, No 6. С. 1005–1018. doi: 10.1016/j.chemosphere.2007.10.0399.Persistent, Bioaccumulative, and Toxic Chemicals I: Fate and Exposure / под ред. Lipnick R. L. et al. Washington, DC: American Chemical Society, 2000. Т. 772.10.Nguyen B.-A. T. et al. Biodegradation of dioxins by Burkholderia cenocepaciastrain 869T2: Role of 2-haloacid dehalogenase // Journal of Hazardous Materials. 2021. Т. 401. С. 123347. doi: 10.1016/j.jhazmat.2020.12334711.Pöritz M. et al. Dehalococcoides mccartyiStrain DCMB5 Respires a Broad Spectrum of Chlorinated Aro-matic Compounds // Appl Environ Microbiol / под ред. Löffler F. E. 2015. Т. 81, No 2. С. 587–596. doi: 10.1128/AEM.02597-1412.Gribble G. W. The diversity of naturally produced organohalogens // Chemosphere. 2003. Т. 52, No 2. С. 289–297. doi: 10.1016/S0045-6535(03)00207-813.Habe H. et al. Degradation of Chlorinated Dibenzofurans and Dibenzo-p-Dioxins by Two Types of Bacte-ria Having Angular Dioxygenases with Different Features // Appl Environ Microbiol. 2001. Т. 67, No 8. С. 3610–3617. doi: 10.1128/AEM.67.8.3610-3617.200114.Hong H.-B. et al. Biodegradation of Dibenzo-p-dioxin, Dibenzofuran, and Chlorodibenzo-p-dioxins by Pseudomonas veroniiPH-03 // Biodegradation. 2004. Т. 15, No 5. С. 303–313. doi: 10.1023/b:biod.0000042185.04905.0d15.Blagodatskaya E., Kuzyakov Y. Active microorganisms in soil: Critical review of estimation criteria and approaches // Soil Biology and Biochemistry. 2013. Т. 67. С. 192–211. http://dx.doi.org/10.1016/j.soilbio.2013.08.02416.Bais H. P. et al. The role of root exudates in rhizosphere interactions with plants and other organisms // Annu. Rev. Plant Biol. 2006. Т. 57, No 1. С. 233–266. doi: 10.1146/annurev.arplant.57.032905.10515917.Berendsen R. L., Pieterse C. M. J., Bakker P. A. H. M. The rhizosphere microbiome and plant health // Trends in Plant Science. 2012. Т. 17, No 8. С. 478–486. doi: 10.1016/j.tplants.2012.04.00118.Weisburg W. G. et al. 16S ribosomal DNA amplification for phylogenetic study // J Bacteriol. 1991. Т. 173, No 2. С. 697–703. doi: 10.1128/jb.173.2.697-703.199119.Heras J. et al. GelJ –a tool for analyzing DNA fingerprint gel images // BMC Bioinformatics. 2015. Т. 16, No 1. С. 270. doi: 10.1186/s12859-015-0703-020.Simons M. Gnotobiotic System for Studying Rhizosphere Colonization by Plant Growth-Promoting Pseu-domonasBacteria Gnotobiotic System for Studying Rhizosphere // MPMI. 1996. Т. 9, No 7. С. 600. doi: 10.1094/mpmi-9-060021.Gordon S. A., Weber R. P. Colorimetric estimation of indoleacetic acid // Plant Physiol. 1951. Т. 26, No 1. С. 192–195. doi: 10.1104/pp.26.1.19222.Harms H. et al. Transformation of Dibenzo-p-Dioxin by Pseudomonassp.Strain HH69 // Appl Environ Microbiol. 1990. Т. 56, No 4. С. 1157–1159. doi: 10.1128/aem.56.4.1157-1159.199023.Nakazawa T. Travels of a Pseudomonas, from Japan around the world // Environmental Microbiology. 2002. Т. 4, No 12. С. 782–786. doi: 10.1046/j.1462-2920.2002.00310.x24.Larkin M. J., Kulakov L. A., Allen C. C. Biodegradation and Rhodococcus –masters of catabolic versatili-ty // Current Opinion in Biotechnology. 2005. Т. 16, No 3. С. 282–290. doi: 10.1016/j.copbio.2005.04.00725.Chikere C. B., Okpokwasili G. C., Chikere B. O. Monitoring of microbial hydrocarbon remediation in the soil // 3 Biotech. 2011. Т. 1, No 3. С. 117–138. doi: 10.1007/s13205-011-0014-826.Yuan S. et al. Improving thermostability of Bacillus amyloliquefaciensalpha-amylase by multipoint muta-tions // Biochemical and Biophysical Research Communications. 2023. Т. 653. С. 69–75. doi: 10.1016/j.bbrc.2023.02.06427.Du R. et al. Purification and characterization of novel thermostable and Ca-independent α-amylase pro-duced by Bacillus amyloliquefaciensBH072 // International Journal of Biological Macromolecules. 2018. Т. 115. С. 1151–1156. doi: 10.1016/j.ijbiomac.2018.05.00428.Smercina D. N. et al. Erratum for Smercina et al., “To Fix or Not To Fix: Controls on Free-Living Nitrogen Fixation in the Rhizosphere” // Appl Environ Microbiol. 2019. Т. 85, No 22. С. e02103-19. doi: 10.1128/AEM.02103-1929.Johansen J. E., Binnerup S. J. Contribution of Cytophaga-like Bacteria to the Potential of Turnover of Car-bon, Nitrogen, and Phosphorus by Bacteria in the Rhizosphere of Barley (Hordeum vulgare L.) // Microbial Ecolo-gy. 2002. Т. 43, No 3. С. 298–306. doi: 10.1007/s00248-002-2006-z30.Kumar V. et al. Isolation of phytase-producing bacteria from Himalayan soils and their effect on growth and phosphorus uptake of Indian mustard (Brassica juncea) // World J Microbiol Biotechnol. 2013. Т. 29, No 8. С. 1361–1369. doi: 10.1007/s11274-013-1299-z31.Gomez-Ramirez L. F., Uribe-Velez D. Phosphorus Solubilizing and Mineralizing Bacillus spp. Contribute to Rice Growth Promotion Using Soil Amended with Rice Straw // Curr Microbiol. 2021. Т. 78, No 3. С. 932–943. doi: 10.1007/s00284-021-02354-732.Lugtenberg B., Kamilova F. Plant-Growth-Promoting Rhizobacteria // Annu. Rev. Microbiol. 2009. Т. 63, No 1. С. 541–556. doi: 10.1146/annurev.micro.62.081307.16291833.Xun F. et al. Effect of plant growth-promoting bacteria (PGPR) and arbuscular mycorrhizal fungi (AMF) inoculation on oats in saline-alkali soil contaminated by petroleum to enhance phytoremediation // Environ Sci Pol-lut Res. 2015. Т. 22, No 1. С. 598–608. doi: 10.1007/s11356-014-3396-434.Ahmed A., Hasnain S. Auxins as One of the Factors of Plant Growth Improvement by Plant Growth Pro-moting Rhizobacteria // Pol J Microbiol. 2014. Т. 63, No 3. С. 261–266. PMID: 2554693535.Validov S. et al. Selection of bacteria able to control Fusariumoxysporumf. sp. radicis-lycopersici in stone-wool substrate // J Appl Microbiol. 2007. Т. 102, No 2. doi: 10.1111/j.1365-2672.2006.03083.x36.De Weert S. et al. Flagella-Driven Chemotaxis Towards Exudate Components Is an Important Trait for Tomato Root Colonization by Pseudomonas fluorescens// MPMI. 2002. Т. 15, No 11. С. 1173–1180. doi: 10.1094/MPMI.2002.15.11.117337.Kamilova F. et al. Enrichment for enhanced competitive plant root tip colonizers selects for a new class of biocontrol bacteria // Environmental Microbiology. 2005. Т. 7, No 11. С. 1809–1817. doi: 10.1111/j.1462-2920.2005.00889.x38.Feng H. et al. Chemotaxis of Beneficial Rhizobacteria to Root Exudates: The First Step towards Root–Microbe Rhizosphere Interactions // IJMS. 2021. Т. 22, No 13. С. 6655. doi: 10.3390/ijms2213665539.Hashem A., Tabassum B., Fathi Abd_Allah E. Bacillus subtilis: A plant-growth promoting rhizobacterium that also impacts biotic stress // Saudi Journal of Biological Sciences. 2019. Т. 26, No 6. С. 1291–1297. doi: 10.1016/j.sjbs.2019.05.004