THE EFFECT ON SOIL METAGENOM CAUSED BY THE NEW FOR THE SCIENCE ENDOPHYTE SPECIES VITASERGIA SVIDASOMA VS 1223 (IMB F-100106) EXTRACTED FROM BLACK TRUFFLE
Keywords:
soil metagenome, Vitasergia svidasoma VS 1223 (IMB F-100106), bioregulation, endophyte, symbiosis.
Abstract
The articles provides the results of the research of soil metagenome of nuciferous crops nursery, where the plant treatment was carried out with yeast fungus of family Debariomycetaceae – Vitasergia svidasoma VS 1223 (IMB F-100106), which is an active agent of Mycovital preparation. By applying amplicon sequencing of 16S рРНК and ITS2, the composition and structure of bacterial and mycelial community in the analyzed untreated soil samples were studied. Operational taxonomic units (OTU) were obtained by clustering with identity of 97% on the effective sample tags which were detected. To demonstrate the microorganism composition and information about their number and species diversity in the samples, an interactive webpage Heatmap was created with a presentation of taxonomic annotations which correspond to OTU. The results prove that the main functional genes of the bacteria in the plant nursery soils belong to three main divisions of Proteobacteria, Actinobacteria, Firmicutes. Proteobacteria division was widely presented with Echerichia genus in the soil untreated with Mycovital in the number of above 97%. After the treatment with species of Vitasergia svidasoma VS 1223 (IMB F-100106) their number reduced to 7%. In the walnut rhizosphere microbiome, 20 types of bacteria, including 83 genera, and 6 types of fungi, including 100 genera of fungi, as well as unclassified sequences were identified, the relative share of which in the microbiome was 3.04–7.86%. The analysis of taxonomic structure of the microbiome on the phyla level showed that bacteria were an absolute dominant, i.e. 38.7–100%. Among fungal divisions, Ascomycota (41.01–93.17%) is an absolute dominant in both ecotopes. Moreover, there were representatives from Basidiomycota (2.82–6.40%) та Monerelomycota (0.82–0.41%) divisions. In Ascomycota division, comprising the greatest number of mycorrhizal fungi, their number increases after treatment with Mycovital, while the number of micromycetes-pathogens, toxin-producers and rot pathogens decreased. It was established that the rhizospheric soil microbiome became more diverse under conditions of inoculation of plants with species Vitasergia svidasoma VS 1223 (IMB F-100106).
References
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3. Bahram, M., Hildebrand, F., Forslund, S.K., Anderson, J.L., Soudzilovskaia, N.A., Bodegom, P.M., Bengtsson-Palme, J., Anslan, S., Coelho, L.P., Harend, H., Huerta-Cepas, J., Medema, M.H., Maltz, M.R., Mundra S., Olsson, P.A., Pent M., Pоlme, S., Sunagawa, S., Ryberg, M., Tedersoo, L., & Bork, P. (2018). Structure and function of the global topsoil microbiome. Nature, 560(7717), 233–237. doi: 10.1038/s41586-018-0386-6
4. Baldrian, P. (2019). The known and the unknown in soil microbial ecology. FEMS Microbiol. Ecol., 95(2), fiz005. doi: 10.1093/femsec/fiz005
5. Bokulich, N.A., Subramanian, S., Faith, 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. doi: 10.1038/nmeth.2276
6. Bulgarelli, D., Garrido-Oter, R., Munch, P. C., Weiman, A., Droge, J., Pan, Y., McHardy, A.C., & Schulze-Lefert, Р. (2015). Structure and function of the bacterial root microbiota in wild and domesticated barley. Cell Host Microbe, 17(3), 392–403. doi: 10.1016/j.chom.2015.01.011
7. Bulgarelli, D., Rott, M., Schlaeppi, K., Van Themaat, E.V.L., Ahmadinejad, N., Assenza, F., Rauf, P., Huettel, B., Reinhardt, R., Schmelzer, E., Peplies, J., Gloeckner, F.O., Amann, R., Eickhorst, T., & Schulze-Lefert P. (2012). Revealing structure and assembly cues for Arabidopsis root-inhabiting bacterial microbiota. Nature, 488, 91–95. doi: 10.1038/ nature11336
8. Caporaso, J.G., Kuczynski, J., Stombaugh, J., Bittinger, K., Bushman, F.D., Costello, E.K., Fierer, N., Peña, A.G., Goodrich, J.K., Gordon, J.I., Huttley, G.A., Kelley, S.T., Knights, D., Koenig, J.E., Ley, R.E., Lozupone, C.A., McDonald, D., Muegge, B.D., Pirrung, M., Reeder, J., Sevinsky, J.R., Turnbaugh, P.J., Walters, W.A., Widmann, J., Yatsunenko, T., Zaneveld, J., & Knight, R. (2010). QIIME allows analysis of high-throughput community sequencing data. Nat Methods, 7(5), 335–336. doi: 10.1038/nmeth.f.303
9. Caporaso, J.G., Lauber, C.L., Walters, W.A., Berg-Lyons, D., Lozupone, C.A., Turnbaugh, P.J., Fierer, N., & Knight, R. (2011). Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample. Proc Natl Acad Sci USA., 108(Suppl 1), 4516–4522. doi: 10.1073/pnas.1000080107
10. Demyanyuk, O.S., Patyka, V.P., Sherstoboeva, О.V., & Bunas, A.A. (2018). Formation of the structure of microbiocenoses of soils agroecosystems depending on trophic and hydrothermic factors. Biosystems diversity, 26(2), 103–110. doi: 10.15421/011816
11. Demyanyuk, O., Symochko, L., & Shatsman, D. (2020). Structure and dynamics of soil microbial communities of natural and transformed ecosystems. Environmental Research, Engineering and Management, 76(4), 97–105. doi: 10.5755/ j01.erem.76.4.23508
12. DeSantis, T.Z.Jr., Hugenholtz, P., Keller, K., Brodie, E.L., Larsen, N., Piceno, Y.M., Phan, R., & Andersen, G.L. (2006). NAST: a multiple sequence alignment server for comparative analysis of 16S rRNA genes. Nucleic Acids Res, 34(Web Server issue), 394–399. doi: 10.1093/nar/gkl244
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14. Edgar, R.C. (2004). MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res, 32(5), 1792–1797. doi: 10.1093/nar/gkh340
15. Edgar, R.C. (2013). UPARSE: highly accurate OTU sequences from microbial amplicon reads. Nature methods, 10, 996–998. doi; 0.1038/nmeth.2604
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17. Egidi, E., Delgado-Baquerizo, M., Plett, J.M., Wang, J., Eldridge, D.J., Bardgett, R.D., Maestre, F.T., & Singh, B.K. (2019). A few Ascomycota taxa dominate soil fungal communities worldwide. Nat Commun, 10(1), 2369. doi: 10.1038/ s41467-019-10373-z
18. Finlay, R.D., Mahmood, S., Rosenstock, N., Bolou-Bi, E.B., Kоhler, S.J., Fahad, Z., Rosling, A., Wallander, H., Belyazid, S., Bishop, K., & Lian, B. (2020). Reviews and syntheses: Biological weathering and its consequences at different spatial levels – from nanoscale to global scale. Biogeosciences, 17, 1507–1533. doi: 10.5194/bg-17-1507-2020
19. Garcia, K., Doidy, J., Zimmermann, S.D., Wipf, D., & Courty, P.E. (2016). Take a trip through the plant and fungal transportome of mycorrhiza. Trends Plant Sci, 21, 937–950. doi: 10.1016/j.tplants.2016.07.010
20. Gregory, P.J. (2022). RUSSELL REVIEW. Are plant roots only “in” soil or are they “of” it? Roots, soil formation and function. European Journal of Soil Science, 73(1), e13219. doi: 10.1111/ejss.13219
21. Haas, B.J., Gevers, D., Earl, A.M., Feldgarden, M., Ward, D.V., Giannoukos, G., Ciulla, D., Tabbaa, D., Highlander, S.K., Sodergren, E., Methе, B., DeSantis, T.Z., Petrosino, J.F., Knight, R., & Birren, B.W. (2011). Chimeric 16S rRNA sequence formation and detection in Sanger and 454-pyrosequenced PCR amplicons. Genome research, 21(3), 494–504. doi: 10.1101/gr.112730.110
22. Hess, M., Sczyrba, A., Egan, R., Kim, T.W., Chokhawala, H., Schroth, G., Luo, S., Clark, D.S., Chen, F., Zhang, T., Mackie, R.I., Pennacchio, L.A., Tringe, S.G., Visel, A., Woyke, T., Wang, Z., & Rubin, E.M. (2011). Metagenomic discovery of biomass-degrading genes and genomes from cow rumen. Science, 331(6016), 463–467. doi: 10.1126/science.1200387
23. IPBES (2019). Summary for policymakers of the global assessment report on biodiversity and ecosystem services of the Intergovernmental Science-Policy Platform on Biodiversity and Ecosystem Services. S. Díaz, J. Settele, E. S. Brondízio, H. T. Ngo, M. Guèze, J. Agard, A. Arneth, P. Balvanera, K. A. Brauman, S. H. M. Butchart, K. M. A. Chan, L. A. Garibaldi, K. Ichii, J. Liu, S. M. Subramanian, G. F. Midgley, P. Miloslavich, Z. Molnár, D. Obura, A. Pfaff, S. Polasky, A. Purvis, J. Razzaque, B. Reyers, R. Roy Chowdhury, Y. J. Shin, I. J. Visseren-Hamakers, K. J. Willis, and C. N. Zayas (eds.). IPBES secretariat, Bonn, Germany. 56 p. doi; 10.5281/zenodo.3553579
24. Jacoby, R., Peukert, M., Succurro, A., Koprivova, A., & Kopriva, S. (2017). The Role of Soil Microorganisms in Plant Mineral Nutrition-Current Knowledge and Future Directions. Front. Plant Sci, 8, 1617. doi: 10.3389/fpls.2017.01617
25. Kamel, L., Keller-Pearson, M., Roux, C., & Ane, J.M. (2017). Biology and evolution of arbuscular mycorrhizal symbiosis in the light of genomics. New Phytol, 213, 531–536. doi: 10.1111/nph.14263
26. Leake, J.R., & Read, D.J. (2017). Mycorrhizal symbioses and pedogenesis throughout earth’s history. In: Johnson N.C., Gehring C.A., Jansa J. (eds). Mycorrhizal mediation of soil: fertility, structure, and carbon storage. Elsevier, Amsterdam, 9–33. doi: 10.1016/B978-0-12-804312-7.00002-4
27. Locey, K.J., & Lennon, J.T. (2016). Scaling laws predict global microbial diversity. Proc. Natl. Acad. Sci. U.S.A., 113(21), 5970–5975. doi: 10.1073/pnas.152129111 28. Magoс, T., & Salzberg, S.L. (2011). FLASH: fast length adjustment of short reads to improve genome assemblies. Bioinformatics, 27(21), 2957–2963. doi: 10.1093/bioinformatics/btr507
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Published
2023-06-09
How to Cite
OliferchukV. Р., Fedorovich, D. V., Samborskyi, M. V., & Samarska, M. I. (2023). THE EFFECT ON SOIL METAGENOM CAUSED BY THE NEW FOR THE SCIENCE ENDOPHYTE SPECIES VITASERGIA SVIDASOMA VS 1223 (IMB F-100106) EXTRACTED FROM BLACK TRUFFLE. Bulletin of Sumy National Agrarian University. The Series: Agronomy and Biology, 51(1), 79-89. https://doi.org/10.32782/agrobio.2023.1.10
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