Molecular-Genetic Characteristics (16S rRNA) of Soil Microbiome in Technogenically Affected Zones
DOI:
https://doi.org/10.15407/microbiolj88.02.018Keywords:
soil metagenome, trace elements, stages of succession, microorganisms, formation of microbial community, 16S rRNA sequencingAbstract
16S rDNA acts as a genetic fingerprint, helping scientists classify and track the evolutionary history of bacteria. Modern rapid sequencing tools, like Illumina, leverage the sequence differences (variation) in this gene to quickly identify all the bacterial species within an environmental sample, making this an important way to study microbial communities. The objective of this study was to determine the taxonomic composition of soil microbial communities using a metagenomic analysis to assess the impact of timber chemical production and transport infrastructure сompared to a control site. Methods. For three variants of soil samples (conditional control, timber chemical plant impact zone, and combined anthropogenic load platform, followed by a bioinformatic analysis. Results. The majority of soil prokaryotic metagenome sequences were identified as Bacteria (95–98%), while 1–4% were identified as Archaea. The studied metagenomes were dominated by sequences identified as Actinomycetota, Pseudomonadota, and Chloroflexota, which together accounted for 65–77% of the total bacterial count. In soils within the anthropogenic impact zones, there was a notable dominance of Actinomycetota (35.4% and 47.2% OTU vs. 33.5% OTU in the control), Chloroflexota (6.9 % and 12.6% OTU vs. 4.2% in the control), and Thermoproteota (3.4 % and 4.1% OTU vs. 1.8% in the control). Conversely, the number of OTUs identified as Verrucomicrobiota decreased in these soils by 28–35 times compared to the control. Conclusions. In soils affected by the timber chemical plant and railway infrastructure, significant shifts in the relative abundance of specific taxonomic groups within the bacteriome were observed. Trends toward increased bacterial diversity compared to the control have been established, which necessitates further research and the establishment of correlations between the obtained metagenomic data and the physicochemical properties of the soils.
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Bergmann, G. T., Bates, S. T., Eilers, K. G., Lauber, C. L., Caporaso, J. G., Walters, W. A., Knight, R., & Fierer, N. (2011). The under-recognized dominance of Verrucomicrobia in soil bacterial communities. Soil Biology and Biochemistry, 43(7), 1450-1455. https://doi.org/10.1016/j.soilbio.2011.03.012
Bilkei, M. V., & Nikolaichuk, V. I. (2017). The distribution of heavy metals content in the bottom deposits of the trans-border Uzh River system. Biosystems Diversity, 25(2), 145-153. https://doi.org/10.15421/011722
Bobryk, N. J. (2015). Spreading and accumulation of heavy metals in soils of railway-side areas. Visnyk of Dnipropetrovsk University. Biology, Ecology, 23(2), 183-189.
Bobryk, N. J., Kryvtsova, M. V., & Nikolajchuk, V. I. (2012). Meadow soil microbiocoenosis under influence of railway transport. Visnyk of Dnipropetrovsk University. Biology, Ecology, 20(2), 3-9.
Bobryk, N., Kryvtsova, M., Nikolajchuk, V., & Voloshchuk, I. (2016). Response of soil microflora to impact of heavy metals in zones of influence of railway transport. Biosystems Diversity, 24(1), 151-156. https://doi.org/10.15421/011618
Bokulich, N. A., Subramanian, S., Faith, J. J., Gevers, D., Gordon, J. I., Knight, R., Mills, D. A., & Caporaso, J. G. (2013). Quality-filtering vastly improves diversity estimates from Illumina amplicon sequencing. Nature Methods, 10(1), 57-59. https://doi.org/10.1038/nmeth.2276
Boyko, N., Chonka, I., Nikolaichuk, V., Kovalchuk, A., & Dziamko, V. (2001). Bacteriological assessment of prospects of the use of zeolites for treatment of industrial effluents. Uzhhorod University Scientific Herald. Series Biology, 10, 165-170.
Chao, A. (1984). Nonparametric estimation of the classes in a population. Scandinavian Journal of Statistics, 11, 265-270.
Department of Ecology and Natural Resources. (2024). Report on the state of the environment of the Zakarpattia region for 2023. Zakarpattia Regional State Administration. https://ecozakarpat.gov.ua/?page_id=308
Dhal, P. K., Islam, E., Kazy, S. K., & Sar, P. (2011). Culture-independent molecular analysis of bacterial diversity in uranium-ore/-mine waste-contaminated and non-contaminated sites from uranium mines. 3 Biotech, 1, 261-272. https://doi.org/10.1007/s13205-011-0034-4
DSTU ISO 10381-2:2004. (2004). Soil quality - Sampling - Part 2: Guidance on sampling methods (ISO 10381-2:2002, IDT). State Standard of Ukraine. https://zakon.isu.net.ua/sites/default/files/normdocs/dstu_iso_1038.pdf
Edgar, R. C. (2013). UPARSE: Highly accurate OTU sequences from microbial amplicon reads. Nature Methods, 10(10), 996-998. https://doi.org/10.1038/nmeth.2604
Edgar, R. C., Haas, B. J., Clemente, J. C., Quince, C., & Knight, R. (2011). UCHIME improves sensitivity and speed of chimera detection. Bioinformatics, 27(16), 2194-2200. https://doi.org/10.1093/bioinformatics/btr381
Ejaz, M. R., Badr, K., Hassan, Z. U., Al-Thani, R., & Jaoua, S. (2024). Metagenomic approaches and opportunities in arid soil research. Science of The Total Environment, 953, 176173. https://doi.org/10.1016/j.scitotenv.2024.176173
Goswami, A., Adkins-Jablonsky, S. J., Barreto Filho, M. M., Shilling, M. D., Dawson, A., Heiser, S., O'Connor, A., Walker, M., Roberts, Q., & Morris, J. J. (2023). Heavy metal pollution impacts soil bacterial community structure and antimicrobial resistance at the Birmingham 35th Avenue Superfund Site. Microbiology Spectrum, 11(2), Article e02426-22. https://doi.org/10.1128/spectrum.02426-22
Hermans, S. M., Buckley, H. L., Case, B. S., Curran-Cournane, F., Taylor, M., & Lear, G. (2017). Bacteria as emerging indicators of soil condition. Applied and Environmental Microbiology, 83(1), Article e02826-16. https://doi.org/10.1128/AEM.02826-16
Kryvtsova, M., Bobrik, N., Sabov, M., & Sabov, M. (2017). Microbiological indication of soils in zone of influence of Perechin timber and chemical plant. Agrobiodiversity for Improving Nutrition, Health and Life Quality, 1, 258-263. [In Ukrainian]. https://doi.org/10.15414/agrobiodiversity.2017.2585-8246.258-263
Kryvtsova, M., Kolesnik, A., Ignatko, T., Bobrik, N., & Koguch, T. (2017). Ecological state of urban ecosystems (on the example of lawns in Uzhhorod). In Proceedings book of papers: Ecology Symposium (pp. 301-308). Erciyes University, Kayseri, Turkey.
Labouyrie, M., Ballabio, C., Romero, F., Panagos, P., Jones, A., Schmid, M. W., Mikryukov, V., Dulya, O., Tedersoo, L., Bahram, M., Lugato, E., van der Heijden, M. G. A., & Orgiazzi, A. (2023). Patterns in soil microbial diversity across Europe. Nature Communications, 14(1), 3311. https://doi.org/10.1038/s41467-023-37937-4
Magoc, T., & Salzberg, S. L. (2011). FLASH: Fast length adjustment of short reads to improve genome assemblies. Bioinformatics, 27(21), 2957-2963. https://doi.org/10.1093/bioinformatics/btr507
Maslovska, O., Komplikevych, S., Zinchuk, D., Hnatush, A., Zaritska, Y., Telehuz, O. & Hnatush, S. (2025). Bacteriome of the soil affected by hostilities as a source of isolation of plant growth-promoting metal-resistant bacteria. Annals of Microbiology, 75, 19. https://doi.org/10.1186/s13213-025-01807-9
Naveed, M., Bukhari, S. S., Mustafa, A., Ditta, A., Alamri, S., El-Esawi, M. A., Rafique, M., Ashraf, S., & Siddiqui, M. H. (2020). Mitigation of nickel toxicity and growth promotion in sesame through the application of a bacterial endophyte and zeolite in nickel contaminated soil. International Journal of Environmental Research and Public Health, 17(23), 8859. https://doi.org/10.3390/ijerph17238859
Orr, J. A., Luijckx, P., Arnoldi, J. F., Jackson, A. L., & Piggott, J. J. (2022). Rapid evolution generates synergism between multiple stressors: Linking theory and an evolution experiment. Global Change Biology, 28(5), 1740-1752. https://doi.org/10.1111/gcb.15633
Osburn, E. D., Yang, G., Rillig, M. C., & Strickland, M. S. (2023). Evaluating the role of bacterial diversity in supporting soil ecosystem functions under anthropogenic stress. ISME Communications, 3(1), 66. https://doi.org/10.1038/s43705-023-00273-1
Perechyn Timber and Chemical Plant. (n.d.). Environmental policies. https://lxk.com.ua/ua/policies.html
Rillig, M. C., Ryo, M., Lehmann, A., Aguilar-Trigueros, C. A., Buchert, S., Wulf, A., Pelz, A., & Yang, G. (2019). The role of multiple global change factors in driving soil functions and microbial biodiversity. Science, 366(6467), 886-890. https://doi.org/10.1126/science.aay2832
Sherstoboeva, O. V., Demianiuk, O. S., Bunas, A. A., Mazur, S. O., Levishko, A. S., & Humeniuk, I. I. (2020). Scientific and methodological manual on soil biodiversity assessment by molecular genetic methods. Kyiv. [In Ukrainian]. https://www.agroeco.org.ua/wp-content/uploads/pdf/cafedra/nmp_otsinyv_bioreznom.pdf
Tian, J., He, N., Hale, L., Niu, S., Yu, G., Liu, Y., Blavier, A., Kuang, W., & Zhou, J. (2018). Soil organic matter availability and climate drive latitudinal patterns in bacterial diversity from tropical to cold temperate forests. Functional Ecology, 32(1), 61-70. https://doi.org/10.1111/1365-2435.12952
Yang, Y., Chen, X., Liu, L., Li, T., Dou, Y., Qiao, J., et al. (2022). Nitrogenfertilization weakens the linkage between soil carbon and microbial diversity: aglobal meta-analysis. Glob Chang Biol, 28, 6446-6461. https://doi.org/10.1111/gcb.16361
Yang, G., Ryo, M., Roy, J., Lammel, D. R., Ballhausen, M. B., Jing, X., Zhu, X., & Rillig, M. C. (2022). Multiple anthropogenic pressures eliminate the effects of soil microbial diversity on ecosystem functions in experimental microcosms. Nature Communications, 13, 4260. https://doi.org/10.1038/s41467-022-31936-7
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