Microbiome of abandoned soils of former agricultural cryogenic ecosystems of central part of Yamal region



Microbial activity plays a crucial role in the development and formation of soil properties. The active and abandoned agricultural soils in the Arctic zone represent a valuable resource that can play a crucial role in providing food security in the northern regions. The reuse of abandoned land for agriculture will reduce environmental risks in the context of a changing climate. Therefore, there is a need for monitoring studies to assess changes in soil parameters after long-term abandonment (taxonomic diversity, agrochemical and physico-chemical qualities). In the study, we evaluated the taxonomic diversity of the microbiome in abandoned (postagrogenic) and pristine soils of the Central part of the Yamal region. In the process of taxonomic analysis, more than 30 different bacterial and archaeal phyla were identified. The formation of a specific microbiome associated with anthropogenic influence in post-agrogenic sites has been shown. Most common types of soil microorganisms in samples collected from pristine and postagrogenic soils were Firmicutes (average 26.86%), Proteobacteria (average 23.41%), and Actinobacteria (average 15.45%). Firmicutes phylum was found mainly in the agrocenoses soils, Proteobacteria were mainly described in the mature tundra soils, Actinobacteria in humid conditions. An increase in diversity indices in postagrogenic soils was shown.

soils; Arctic; metagenomics; 16S rRNA Sequencing

Abakumov, E., Zverev, A., Morgun, E. and Alekseev, I. (2020): Microbiome of abandoned agricultural and mature tundra soils in southern Yamal region, Russian Arctic. Open Agriculture, 5(1): 335-344. doi: 10.1515/opag-2020-0034

Alekseev, I., Abakumov, E. (2018): Permafrost-affected former agricultural soils of the Salekhard city (Central part of Yamal region). Czech Polar Reports, 8(1): 119-131.

Anderson, M. J. (2006): Distance-based tests for homogeneity of multivariate dispersions. Biometrics, 62(1): 245-253.

Bel’chicova, N. (1965): Determination of the humus of soils by IV Tyurin’s method. Agrochemical methods in study of soils. 4th ed. Moscow: Nauka: 75-102.

Bell, T. H., Trexler, R. V., Peng, X., Huntemann, M., Clum, A., Foster, B., Foster, B., Roux, S., Palaniappan, K., Varghese, N., Mukherjee, S., Reddy, T. B. K., Daum, C., Copeland, A., Ivanova, N. N., Kyrpides, N. C., Pennacchio, C., Eloe-Fadrosh, E. A. and Bruns, M. A. (2020): Metatranscriptomic sequencing of a cyanobacterial soil-surface consortium with and without a diverse underlying soil microbiome. Microbiology Resource Announcements, 9(1): e01361-19. doi: 10.1128/MRA.01361-19

Black, C. A., Evans, D. and White, J. (1965): Methods of soil analysis: Chemical and microbiological properties. Agronomy, Madison, Wisconsin, USA, pp. 1379–1398.

Bolyen, E., Rideout, J. R., Dillon, M. R., Bokulich, N. A., Abnet, C. C., Al-Ghalith, G. A., Alexander, H., Alm, E. J., Arumugam, M., Asnicar, F., Bai, Y., Bisanz, J. E., Bittinger, K., Brejnrod, A., Brislawn, C. J., Brown, C. T., Callahan, B. J., Caraballo-Rodríguez, A. M., Chase, J., Cope, E. K., … Caporaso, J. G. (2019): Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2. Nature Biotechnology, 37(8): 852-857. doi: 10.1038/s41587-019-0209-9

Chen, L., Li, D., Shao, Y., Adni, J., Wang, H., Liu, Y. and Zhang, Y. (2020): Comparative analysis of soil microbiome profiles in the companion planting of white clover and orchard grass using 16S rRNA gene sequencing data. Frontiers in Plant Science, 11: 538311. doi: 10.3389/fpls.2020.538311

De Mandal, S., Mathipi, V., Muthukumaran, R. B., Gurusubramanian, G., Lalnunmawii, E. and Kumar, N. S. (2019): Amplicon sequencing and imputed metagenomic analysis of waste soil and sediment microbiome reveals unique bacterial communities and their functional attributes. Environmental Monitoring and Assessment, 191(12): 778. doi: 10.1007/s10661-019-7879-0

Forbes, B. C., Stammler, F., Kumpula, T., Meschtyb, N., Pajunen, A. and Kaarlejärvi, E. (2009): High resilience in the Yamal-Nenets social-ecological system, West Siberian Arctic, Russia. Proceedings of the National Academy of Sciences of the United States of America, 106(52): 22041-22048. doi: 10.1073/pnas.0908286106

Giani, L., Chertov, O., Gebhardt, C., Kalinina, O., Nadporozhskaya, M. and Tolkdorf-Lienemann, E. (2004): Plagganthrepts in northwest Russia? Genesis, properties and classification. Geoderma, 121(1-2): 113-122. doi: 10.1016/j.geoderma.2003.10.007.

Gladkov, G., Kimeklis, A., Zverev, A., Pershina, E., Ivanova, E., Kichko, A., Andronov, E. and Abakumov, E. (2019): Soil microbiome of the postmining areas in polar ecosystems in surroundings of Nadym, Western Siberia, Russia. Open Agriculture, 4(1): 684-696. doi: 10.1515/opag-2019-0070

Jenkins, J. R., Viger, M., Arnold, E. C., Harris, Z.M., Ventura, M., Miglietta, F., Girardin, C., Edwards, R.J., Rumpel, C., Fornasier, F., Zavalloni, C., Tonon, G., Alberti, G. and Taylor, G. (2017): Biochar alters the soil microbiome and soil function: Results of next-generation amplicon sequencing across Europe. GCB Bioenergy, 9(3): 591-612. doi: 10.1111/ gcbb.12371

Jenkinson, D. S., Powlson, D. S. (1976): The effects of biocidal treatments on metabolism in soil-V. A method for measuring soil biomass. Soil Biology and Biochemistry, 8(3): 209-213.

Kalinina, O., Chertov, O., Frolov, P., Goryachkin, S., Kuner, P., Küper, J., Kurganova, I., Lopes de Gerenyu, V., Lyuri, D., Rusakov, A., Kuzyakov, Y. and Giani, L. (2018): Alteration process during the post-agricultural restoration of Luvisols of the temperate broad-leaved forest in Russia. Catena, 171: 602-612. doi: 10.1016/j.catena.2018.08.004

Kimeklis, A. K., Gladkov, G. V., Zverev, A. O., Kichko, A. A., Andronov, E. E., Ergina, E. I., Kostenko, I. V. and Abakumov, E. V. (2021): Microbiomes of different ages in Rendzic Leptosols in the Crimean Peninsula. PeerJ, 9: e10871. doi: 10.7717/peerj.10871

Kotlyakov, V., Khromova, T. (2002): Land resources of Russia – Maps of permafrost and Ground Ice. Boulder, Colorado USA: National Snow and Ice Data Center. doi: 10.7265/zpm9-j983

Kui, L., Xiang, G., Wang, Y., Wang, Z., Li, G., Li, D., Yan, J., Ye, S., Wang, C., Yang, L., Zhang, S., Zhang, S., Zhou, L., Gui, H., Xu, J., Chen, W., Zhang, J., Huang, T., Majeed, A., Sheng, J., … Dong, Y. (2021): Large-scale characterization of the soil microbiome in ancient tea plantations using high-throughput 16S rRNA and internal transcribed spacer amplicon sequencing. Frontiers in Microbiology, 12: 745225. doi: 10.3389/fmicb.2021.745225

Lyuri, D. I., Goryachkin, S. V., Karavaeva, N. A., Denisenko, E. A. and Nefedova, T. G. (2010): Dynamics of Russian agricultural lands in the 20th century and a postagrogenic restoration of vegetation and soils. Moscow, Geos 416 p.

Magnin, F., Krautblatter, M., Deline, P., Ravanel, L., Malet, E. and Bevington, A. (2015): Determination of warm, sensitive permafrost areas in near-vertical rockwalls and evaluation of distributed models by electrical resistivity tomography. Journal of Geophysical Research: Earth Surface, 120(5): 745-762. doi: 10.1002/2014JF003351

Morgun, E., Abakumov, E. (2019): Agricultural research and crop yields in the Yamal-Nenets autonomous district: Retrospective analysis (1932–2019). Scientific Bulletin of the Yamalo-Nenets Autonomous District, 3: 4-9.

Nikitin, D. A., Semenov, M. V., Chernov, T. I., Ksenofontova, N. A., Zhelezova, A. D., Ivanova, E. A., Khitrov, N. B. and Stepanov, A. L. (2022): Microbiological indicators of soil ecological functions: A review. Eurasian Soil Science, 55: 221-234. doi: 10.1134/ S1064229322020090

Nikitin, D. A., Ivanova, E. A., Zhelezova, A. D., Semenov, M. V., Gadzhiumarov, R. G., Tkhakakhova, A. K., Chernov, T. I., Ksenofontova, N. A. and Kutovaya, O. V. (2020): Assessment of the impact of no-till and conventional tillage technologies on the microbiome of southern agrochernozems. Eurasian Soil Science, 53(12): 1782-1793. doi: 10.1134/ S106422932012008X

Nikitin, D. A., Lysak, L. V., Kutovaya, O. V. and Gracheva, T. A. (2021): Ecological-trophic structure and taxonomic characteristics of the communities of soil microorganisms in the northern part of the Novaya Zemlya Archipelago. Eurasian Soil Science, 54(11): 1689-1704. doi: 10.1134/S1064229321110107

Nizamutdinov, T., Abakumov, E. and Morgun, E. (2021): Morphological features, productivity and pollution state of abandoned agricultural soils in the Russian Arctic (Yamal Region). One Ecosystem, 6: e68408. doi: 10.3897/oneeco.6.e68408

Nizamutdinov, Т. I., Suleymanov, A. R., Morgun, E. N., Dinkelaker, N. V. and Abakumov, E. V. (2022): Ecotoxicological analysis of fallow soils at the Yamal experimental agricultural station. Food Processing: Techniques & Technology, 52(2): 350-360. doi: 10.21603/2074-9414-2022-2-2369.

Quast, C., Pruesse, E., Yilmaz, P., Gerken, J., Schweer, T., Yarza, P., Peplies, J. and Glöckner, F. O. (2013): The SILVA ribosomal RNA gene database project: Improved data processing and web-based tools. Nucleic Acids Research, 41(Database issue): D590-D596. doi: 10.1093/nar/gks1219

Suleymanov, A., Nizamutdinov, T., Morgun, E. and Abakumov, E. (2022): Evaluation and spatial variability of cryogenic soil properties (Yamal-Nenets Autonomous District, Russia). Soil Systems, 6(3): 65.

Swinnen, J., Burkitbayeva, S., Schierhorn, F., Prishchepov, A. and Müller, D. (2017): Production potential in the “bread baskets” of Eastern Europe and Central Asia. Global Food Security, 14: 38-53. doi: 10.1016/j.gfs.2017.03.005

Tikhanovsky, А. N. (2021): Kartofel' na Yamale. Akademizdat, Novosibirsk, 160 p.

Unc, A., Altdorff, D., Abakumov, E., Adl, S.M., Baldursson, S., Bechtold, M., Cattani, D.J., Firbank, L.G., Grand, S., Guðjónsdóttir, M.S., Kallenbach, C.M., Kedir, A.J., Li, P., McKenzie, D.B., Misra, D., Nagano, H., Neher, D.A., Niemi, J., Oelbermann, M., Overgård Lehmann, J., Parsons, D., Quideau, S.A., Sharkhuu, A., Smreczak, B., Sorvali, J., Vallotton, J.D., Whalen, J.K., Young, E.H., Zhang, M. and Borchard, N. (2021): Expansion of agriculture in northern cold-climate regions: A cross-sectoral perspective on opportunities and challenges. Frontiers in Sustainable Food Systems, 5: 663448. doi: 10.3389/ fsufs.2021.663448

Vance, E. D., Brookes, P. C. and Jenkinson, D. S. (1987): An extraction method for measuring soil microbial biomass C. Soil Biology and Biochemistry, 19(6): 703-707.

Walkley, A., Black, I. A. (1934): An examination of the degtjareff method for determining soil organic matter, and a proposed modification of the chromic acid titration method. Soil Science, 37(1): 29-38.

Web sources / Other sources

[1] Stolbovoy V., McCallum I. (2002): CD-ROM “Land Resources of Russia”.

[2] Team, R. C. (2021): R: A language and environment for statistical computing.



Crossref logo





PDF views