Soil microbial diversity and activity in different climatic zones of Ukraine
AbstractSoils are dynamic biological matrices featuring a complex microbiome that has an integral role in all ecosystem processes. At the system level, microbial communities regulate ecosystem functioning and modulate resistance and resilience to anthropogenic impact. Ecological status of soils depends on the structure and activity of soil microbiome. The aim of this study was long-term investigations of soil microbiome in different climatic zones of Ukraine, namely the structure and diversity of microbial communities, direction of soil microbiological processes in natural and transformed ecosystems. Four types of soil were studied in different natural and climatic zones: Steppe zone – Donetsk region, Forest-steppe – Vinnytsia region, Polissya – Chernihiv region, Carpathian region. Microbiological studies of soil were carried out according to generally accepted methods in soil microbiology. Diversity of soil microbiome was estimated using Shannon and Simpson indices. The direction of microbiological processes in the soil was determined by the appropriate coefficients: mineralization, oligotrophy, pedotrophity, and transformation of organic matter. The results of soil monitoring in various natural and climatic zones of Ukraine showed a correlation between the agroecological conditions and activity of microbiocenosis. The soil of natural ecosystems was characterized by a high total number of the microorganisms with a balanced structure of various ecological-trophic groups and balanced mineralization-immobilization processes, organic matter decomposition, and humus accumulation. The chernozem soil was characterized by more stable and balanced structure of microbiocenosis than soddy-podzolic, brown and grey forest soils. The growth of the proportion of micellar organisms occurs during the long-term application of mineral fertilizers. Data of functional communities and functional processes helped estimate specific microbial responses to anthropogenic impact. The most significant influence of agricultural activity on the soil microbiota was observed in the poorly soddy-podzolic, brown and grey forest soils, where the cultivation of the crops without fertilization resulted in a decrease of the total number of microorganisms by 2.2–4.5 times. Soil microbial diversity was practically twice lower in these ecosystems in comparison with the natural ones. Soils with low content of organic matter and acidic medium: soddy-podzolic, brown forest and grey forest soils have been characterized by a high number of micromycetes and a relatively low number of eutrophic and nitrogen-fixing microorganisms. This article summarizes important results of long term investigations of soil microbiome: structure, interaction, functioning, activity and diversity in the main types of soils on the territory of Ukraine.
Alyokhin, А., Nault, В., & Brown, В. (2020). Soil conservation practices for insect pest management in highly disturbed agroecosystems – a review. Entomologia Experimentalis et Applicata, 168, 7–27.
Andreyuk, E. I., & Valagurova, E. V. (1992). Osnovy ekologii pochvennykh mikroorganizmov [Fundamentals of the ecology of soil microorganisms]. Naukova Dumka, Kyiv (in Russian).
Auffret, M. D., Karhu, K., Khachane, A., Dungait, J. A. J., Fraser, F., Hopkins, D. W., Wookey, P. A., Singh, B. K., Freitag, T. E., Hartley, I. P., & Prosser, J. I. (2016). The role of microbial community composition in controlling soil respiration responses to temperature. PloS One, 11(10), e0165448.
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., Põlme, S., Sunagawa, S., Ryberg, M., Tedersoo, L., & Bork, P. (2018). Structure and function of the global topsoil microbiome. Nature, 560, 233–237.
Bender, S., & Van der Heijden, M. (2015). Soil biota enhance agricultural sustainability by improving crop yield, nutrient uptake and reducing nitrogen leaching losses. Journal of Applied Ecology, 52, 228–239.
Bending, G. D., Turner, M. K., & Jones, J. E. (2002). Interactions between crop residue and soil organic matter quality and the functional diversity of soil microbial communities. Soil Biology and Biochemistry, 34, 1073–1082.
Celik, I. (2005). Land-use effects on organic matter and physical properties of soil in a southern Mediterranean highland of Turkey. Soil and Tillage Research, 83(2), 270–277.
Chen, X. D., Dunfield, K. E., Fraser, T. D., Wakelin, S. A., Richardson, A. E., & Condron, L. M. (2020). Soil biodiversity and biogeochemical function in managed ecosystems. Soil Research, 58(1), 1–20.
Cheng, F., Wie, X., Hou, L., Shang, Z., Peng, X., Zhao, P., Fei, Z., & Zhang, S. (2015). Soil fungal communities of montane natural secondary forest types in China. Journal of Microbiology, 53, 379–389.
Crowther, T. W., van den Hoogen, J., Wan, J., Mayes, M. A., Keiser, A. D., Mo, L., Averill, C., & Maynard, D. S. (2019). The global soil community and its influence on biogeochemistry. Science, 365(6455), eaav0550.
De Ruiter, P. C., Griffiths, B. S., & Moore, J. C. (2002). Biodiversity and stability in soil ecosystems: Patterns, processes and the effects of disturbance. In: Loreau, M., Naeem, S., & Inchausti, P. (Eds.). Biodiversity and Ecosystem Functioning. Synthesis and Perspectives. Oxford University Press, Oxford. Pp. 102–113.
Demyanyuk, O., Symochko, L., Hosam, Bayoumi Hamuda, E. A. F., Symochko, V., & Dmitrenko, O. (2019). Сarbon pool and biological activities of soils in different ecosystems. International Journal of Ecosystems and Ecology Science, 9(1), 189–200.
Deng, J., Yin, Y., Luo, J., Zhu, W., & Zhou, Y. (2019). Different revegetation types alter soil physical-chemical characteristics and fungal community in the Baishilazi Nature Reserve. Journal of Life and Environmental Sciences, 6, e6251.
Fernandez, A. L., Sheaffer, C. C., Wyse, D. L., Staley, C., Gould, T. J., & Sadowsky, M. J. (2016). Structure of bacterial communities in soil following cover crop and organic fertilizer incorporation. Applied Microbiology and Biotechnology, 100, 9331–9341.
Ferris, H., & Tuomisto, H. (2015). Unearthing the role of biological diversity in soil health. Soil Biology and Biochemistry, 85, 101–109.
Fierer, N., & Jackson, R. B. (2006). The diversity and biogeography of soil bacterial communities. Proceedings of the National Academy of Sciences of the United States of America, 103, 626–631.
Grantina-Levina, L., Seile, E., Kenigsvalde, K., & Kasparinskis, R. (2011). The influence of the land use on abundance and diversity of soil fungi: Comparison of conventional and molecular methods of analysis. Environmental and Experimental Biology, 9, 9–21.
Griffiths, B. S., Bonkowski, M., Roy, J., & Ritz, K. (2001). Functional stability, substrate utilisation and biological indicators of soils following environmental impacts. Applied Soil Ecology, 16, 49–61.
Griffiths, B. S., Kuan, H. L., Ritz, K. L., Glover, A., McCaig, A. E., & Fenwick, C. (2004). The relationship between microbial community structure and functional stability, tested experimentally in an upland pasture soil. Microbial Ecology, 47, 104–113.
Griffiths, B. S., Ritz, K., Bardgett, R. D., Cook, R., Christensen, S., Ekelund, F., Sorensen, S. J., Bååth, E., Bloem, J., de Ruiter, P. C., Dolfing, J., & Nicolardot, B. (2000). Ecosystem response of pasture soil communities to fumigation-induced microbial diversity reductions: An examination of the biodiversity – ecosystem function relationship. Oikos, 90, 279–294.
Habig, J., & Swanepoel, C. (2015). Effects of conservation agriculture and fertilization on soil microbial diversity and activity. Environments, 2, 358–384.
Hartmann, M., Frey, B., Mayer, J., Mader, P., & Widmer, F. (2015). Distinct soil microbial diversity under long-term organic and conventional farming. Multidisciplinary Journal of Microbial Ecology, 9, 1177–1194.
Harwood, C. S., & Greenberg, E. P. (1999). Mega roles for microorganisms. Science, 286(5442), 1096.
Heijden, M. G. A., Bardgett, R. D., & Straalen, N. M. (2008). The unseen majority: Soil microbes as drivers of plant diversity and productivity in terrestrial ecosystems. Ecology Letters, 11(3), 296–310.
Hu, J., Lin, X., Wang, J., Dai, J., Chen, R., Zhang, J., & Wong, M. H. (2011). Microbial functional diversity, metabolic quotient, and invertase activity of a sandy loam soil as affected by long-term application of organic amendment and mineral fertilizer. Soil and Sediment Contamination, 11, 271–280.
Lauber, C. L., Ramirez, K. S., Aanderud, Z., Lennon, J., & Fierer, N. (2013). Temporal variability in soil microbial communities across land-use types. Multidisciplinary Journal of Microbial Ecology, 7, 1641–1650.
Liu, X. L., He, Y. Q., Zhang, H. L., Schroder, J. K., Li, C. L., Zhou, J., & Zhang, Z. Y. (2010). Impact of land use and soil fertility on distributions of soil aggregate fractions and some nutrients. Pedosphere, 20(5), 666–673.
Lombard, N., Prestat, E., van Elsas, J. D., & Simonet, P. (2011). Soil-specific limitations for access and analysis of soil microbial communities by metagenomics. FEMS Microbiology Ecology, 78(1), 31–49.
Magurran, A. E. (Ed.). (1988). Diversity indices and species abundance models. Іn: Ecological diversity and its measurement. Springer, London. Pp. 7–45.
Martin, E. A., Feit, B., Requier, F., & Friberg, H. (2019). Assessing the resilience of biodiversity-driven functions in agroecosystems under environmental change. Advances in Ecological Research, 60, 59–123.
Martin, J.-L., Maris, V., & Simberloff, D. S. (2016). The need to respect nature and its limits challenges society and conservation science. Proceedings of the National Academy of Sciences of the United States of America, 13(22), 6105–6112.
Nannipieri, P., Ascher, J., Ceccherini, M. T., Landi, L., Pietramellara, G., & Renella, G. (2017). Microbial diversity and soil functions. European Journal of Soil Science, 68(1), 12–26.
Patyka, V. P., & Symochko, L. Y. (2013). Mikrobiolohichnyi monitorynh gruntu pryrodnykh ta transformovanykh ekosystem Zakarpattia Ukrainy [Soil microbiological monitoring of natural and transformed ecosystems in the trans-Carpathian region of Ukraine]. Microbiological Journal, 75(2), 21–31 (in Ukrainian).
Qamar, S. U. R., Haroon, & Saif, A. (2018). An overview on microorganisms contribute in increasing soil fertility. Biomedical Journal of Scientific and Technical Research, 2(1), e641.
Rousk, J., Baath, E., Brookes, P. C., Lauber, C. L., Lozupone, C., Caporaso, J. G., Knight, R., & Fierer, N. (2010). Soil bacterial and fungal communities across a pH gradient in an arable soil. Multidisciplinary Journal of Microbial Ecology, 4(10), 1340–1351.
Schmidt, R., Gravuer, K., Bossange, A. V., Mitchell, J., & Scow, K. (2018). Long-term use of cover crops and no-till shift soil microbial community life strategies in agricultural soil. PLoS One, 13, e0192953.
Schulz, S., Brankatschk, R., & Domig, A. (2013). The role of microorganisms at different stages of ecosystem development for soil formation. Biogeosciences, 10(6), 3983–3996.
Seybold, C. A., Herrick, J. E., & Brejda, J. J. (1999). Soil resilience: A fundamental component of soil quality. Soil Science, 164, 224–234.
Sharma, S. K., Ramesh, A., Sharma, M. P., Joshi, O. P., Govaerts, B., Steenwerth, K. L., & Karlen, D. L. (2010). Microbial community structure and diversity as indicators for evaluating soil quality. In: Lichtfouse, E. (Ed.). Biodiversity, biofuels, agroforestry and conservation agriculture. Sustainable Agriculture Reviews. Springer, Dordrecht. Pp. 317–358.
Sheibani, S., & Ahangar, A. (2013). Effect of tillage on soil biodiversity. Journal of Novel Applied Sciences, 2(8), 273–281.
Strickland, M. S., & Rousk, J. (2010). Considering fungal: Bacterial dominance in soils – Methods, controls, and ecosystem implications. Soil Biology and Biochemistry, 42(9), 1385–1395.
Sun, R., Dsouza, M., Gilbert, J. A., Guo, X., Wang, D., Guo, Z., Ni, Y., & Chu, H. (2016). Fungal community composition in soils subjected to long-term chemical fertilization is most influenced by the type of organic matter. Environmental Microbiology, 18, 5137–5150.
Sun, R., Li, W., Dong, W., Tian, Y., Hu, C., & Liu, B. (2018). Tillage changes vertical distribution of soil bacterial and fungal communities. Frontiers in Microbiology, 9, 699.
Torsvik, V., & Ovreаs, L. (2002). Microbial diversity and function in soil: From genes to ecosystems. Current Opinion in Microbiology Journal, 5(3), 240–245.
van der Bom, F., Nunes, I., Raymond, N. S., Hansen, V., Bonnichsen, L., Magid, J., Nybroe, O., & Jensen, L. S. (2018). Long-term fertilisation form, level and duration affect the diversity, structure and functioning of soil microbial communities in the field. Soil Biology and Biochemistry, 122, 91–103.
Wakelin, S. A. (2018). Managing soil microbiology: Realising opportunities for the productive land-based sectors. New Zealand Journal of Agricultural Research, 61, 358–376.
Wu, J. P., Liu, Z. F., Wang, X. L., Sun, Y., Zhou, L., & Lin, Y. (2011). Effects of understory removal and tree girdling on soil microbial community composition and litter decomposition in two Eucalyptus plantations in South China. Functional Ecology, 25, 921–931.
Yang, G., Wagg, C., Veresoglou, S. D., Rillig, M. C., & Hempel, S. (2018). How soil biota drive ecosystem stability. Trends in Plant Science, 23(12), 1057–1067.
You, Y., Wang, J., Huang, X., Tang, Z., Liu, S., & Sun, O. J. (2014). Relating microbial community structure to functioning in forest soil organic carbon transformation and turnover. Ecology and Evolution, 4(5), 633–647.
Zhang, Q.-C., Shamsi, I. H., Xu, D.-T., Wang, G.-H., Lin, X.-Y., Jilani, G., Hussain, N., & Chaudhry, A. N. (2012). Chemical fertilizer and organic manure inputs in soil exhibit a vice versa pattern of microbial community structure. Applied Soil Ecology, 57, 1–8.
Zhang, T., Wang, N.-F., Liu, H.-Y., Zhang, Y.-Q., & Yu, L.-Y. (2016). Soil pH is a key determinant of soil fungal community composition in the Ny-Ålesund Region, Svalbard (High Arctic). Frontiers in Microbiology, 7, 227.
Zhou, J., Guan, D. W., Zhou, B., Zhao, B., Ma, M., Qin, J., Jiang, X., Chen, S., Cao, F., Shen, D., & Li, J. (2015). Influence of 34-years of fertilization on bacterial communities in an intensively cultivated black soil in Northeast China. Soil Biology and Biochemistry, 90, 42–51.
Zviahyntsev, D. H. (1991). Metody pochvennoy mikrobiologii i biokhimii [Methods of soil microbiology and biochemistry]. Moscow State University, Moscow (in Russian).
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