Keywords
soils
microbiology
microbial communities
physiological groups of microorganisms
Western Siberia
Ob river
How to Cite
Abstract
Soil microbiota plays an integral role in biogeochemical cycles, being used as a key metric of changes and a means of integrated characterization of processes. The paper presents the results of microbiological analysis of soils from the central part of the middle Ob floodplain. The ecological and trophic structure of soil microbial communities was investigated to identify the leading physiological groups of heterotrophic bacteria involved in biogeochemical transformation of organic matter in soil. The relationship of bacteria of different physiological groups with seasonal variations and physical and chemical properties of soils, and the links between bacteria were identified and evaluated. The data obtained can be used to evaluate climate-regulating functions of microbial communities in floodplain soils and assess the potential of the middle Ob floodplain in terms of environmental services and nature management.
References
Argiroff WA, Zak DR, Lanser CM, Wiley MJ (2017) Microbial Community Functional Potential and Composition Are Shaped by Hydrologic Connectivity in Riverine Floodplain Soils. Microbial Ecology 73: 630–644. https://doi.org/10.1007/s00248-016-0883-9
Babeva IP, Zenova GM (1989) Soil biology: Textbook. Moscow State University Press, Moscow, 336 pp. [In Russian]
Banerjee S, Helgason B, Wang L, Winsley T, Ferrari BC, Siciliano SD (2015) Legacy effects of soil moisture on microbial community structure and N₂O emissions. Soil Biology and Biochemistry 95: 40–50. https://doi.org/10.1016/j.soilbio.2015.12.004
Banerjee S, Siciliano S (2012) Spatially tripartite interactions of denitrifiers in arctic ecosystems: activities, functional groups and soil resources: denitrifier spatial patterns in arctic soils. Environmental Microbiology 14: 2601–2613. https://doi.org/10.1111/j.1462-2920.2012.02814.x
Barnard RL, Osborne CA, Firestone MK (2013) Responses of soil bacterial and fungal communities to extreme desiccation and rewetting. ISME Journal 7(11): 2229–2241. https://doi.org/10.1038/ismej.2013.104
Bauhus J, Barthel R (1995) Mechanisms of carbon and nutrient release and retention within beech forest gaps. The role of microbial biomass. Plant and Soil 168(169): 585–592. https://doi.org/10.1007/BF00029372
Blagodatsky S, Smith P (2012) Soil physics meets soil biology: Towards better mechanistic prediction of greenhouse gas emissions from soil. Soil Biology and Biochemistry 47: 78–92. https://doi.org/10.1016/j.soilbio.2011.12.015
Bossio DA, Scow K (1995) Impact of Carbon and Flooding on the Metabolic Diversity of Microbial Communities in Soils. Applied and Environmental Microbiology 61(11): 4043–4050. https://doi.org/10.1128/aem.61.11.4043-4050.1995
Diaz-Ravina M, Acea MJ, Carballas T (1995) Seasonal changes in microbial biomass and nutrient flush in forest soils. Biology and Fertility of Soils 19: 220–226. https://doi.org/10.1007/BF00336163
Dobrovolsky GV (1971) River floodplains as landscapes of high life density and intensive soil-forming process. In: Biological productivity and cycles of chemical elements in plant communities. Nauka, Leningrad, 226–231. [In Russian]
Eisenhauer N, Schielzeth H, Barnes AD, Barry KE, Bonn A, Brose U, Bruelheide H, Buchmann N, Buscot F, Ebeling A, Ferlian O, Freschet GT, Giling DP, Hättenschwiler S, Hillebrand H, Hines J, Isbell F, Koller-France E, König-Ries B, de Kroon H, Meyer ST, Milcu A, Müller J, Nock CA, Petermann JS, Roscher C, Scherber C, Scherer-Lorenzen M, Schmid B, Schnitzer SA, Schuldt A, Tscharntke T, Türke M, van Dam NM, van der Plas F, Vogel A, Wagg C, Wardle DA, Weigelt A, Weisser WW, Wirth C, Jochum M (2019) A multitrophic perspective on biodiversity-ecosystem functioning research. Advances in Ecological Researches 61: 1–54. https://doi.org/10.1016/bs.aecr.2019.06.001
Fierer N (2017) Embracing the unknown: disentangling the complexities of the soil microbiome. Nature Reviews Microbiology 15(10): 579–590. https://doi.org/10.1038/nrmicro.2017.87
Fomina NV, Sorokin GA, Demidenko ND (2006) Ecological and microbiological monitoring of soil in a forest nursery in Krasnoyarsk Krai. Bulletin of the Krasnoyarsk State Agrarian University 10: 146–153. [In Russian]
Geltser YG (1986) Biological diagnostics of soils. Moscow State University Press, Moscow, 78 pp. [In Russian]
Gleeson D, Müller C, Banerjee S, Ma W, Siciliano S, Murphy D (2010) Response of ammonia oxidizing archaea and bacteria to changing water filled pore space. Soil Biology and Biochemistry 42–10: 1888–1891. https://doi.org/10.1016/j.soilbio.2010.06.020
Gonçalves JLM, Carlyle JC (1994) Modelling the influence of moisture and temperature on net nitrogen mineralization in a forested sandy soil. Soil Biology and Biochemistry 26(11): 1557–1564. https://doi.org/10.1016/0038-0717(94)90098-1
Grigoryan BR, Koltsova TG, Sungatullina LM (2014) Methodological recommendations for assessing the soil and ecological status of agricultural lands for compliance with the requirements of organic farming. Kazan, 52 pp. [In Russian]
Hackl E, Pfeffer M, Donat C, Bachmann G, Zechmeister-Boltenstern S (2005) Composition of the microbial communities in the mineral soil under different types of natural forest. Soil Biology and Biochemistry 37(4): 661–671. https://doi.org/10.1016/j.soilbio.2004.08.023
Ivanov FD, Govortsov AV (2019) Seasonal dynamics of the number of microorganisms in natural and anthropogenically transformed soils of Rostov-on-Don. In: Proceedings of the VIII scientific and practical conference with international participation. Genetics is the fundamental basis of innovations in medicine and breeding, Rostov-on-Don (Russia), September 2019. Southern Federal University Publishing House, Rostov-on-Don–Taganrog, 121–123. [In Russian]
Janse HJ, van Dam AA, Hes EM, de Klein JJM, Finlayson CM, Janssen ABG, van Wijk D, Mooij WM, Verhoeven JTA (2019) Towards a global model for wetlands ecosystem services. Current Opinion in Environmental Sustainability 36: 11–19. https://doi.org/10.1016/j.cosust.2018.09.002
Kayranli B, Scholz M, Mustafa A, Hedmark A (2009) Carbon storage and fluxes within freshwater wetlands: a critical review. Wetlands 30: 1–124. https://doi.org/10.1007/s13157-009-0003-4
Khodjimurodova N, Raupova NB (2019) Microbiological activity of old irrigated and newly irrigated meadow-alluvial soils. Bulletin of Science and Practice 5(3): 27–33. [In Russian]
Khromykh VS (1975) Structure and qualitative assessment of the Middle Ob floodplain landscapes within the boundaries of Tomsk Region. PhD Thesis, Novosibirsk, Russia. [In Russian]
Khromykh VS, Kostenko EA, Ogorodnikov AV (2000) The role of soil in the dynamics of floodplain landscapes In: Modern problems of soil science in Siberia. Vol. 1: Proceedings of the International scientific conference dedicated to the 70th anniversary of the formation of the Department of Soil Science, Tomsk State University. Tomsk (Russia), 149–153. [In Russian]
Khromykh VS (1979) Natural zoning of the Middle Ob floodplain. Issues of Siberian geography. Tomsk 12: 69–86. [In Russian]
Kolesnichenko YY, Kolesnichenko LG, Vorobyev SN, Shirokova LS, Semiletov IP, Dudarev OV, Vorobyev RS, Shavrina U, Kirpotin SN, Pokrovsky OS (2021) Landscape, Soil, Lithology, Climate and Permafrost Control on Dissolved Carbon, Major and Trace Elements in the Ob River, Western Siberia. Water 13: 31–89. https://doi.org/10.3390/w13223189
Kontsevaya II, Daineko NM, Zyablitsky KO, Minina AV (2018) Effect of the microbial preparation PoliFunKur on agronomically useful groups of soil microorganisms in corn crops. Bulletin of Science and Practice 4(9): 96–102. [In Russian]
Leirós M, Trasar-Cepeda C, Seoane S, Gil-Sotres F (1999) Dependence of mineralization of soil organic matter on temperature and moisture. Soil Biology and Biochemistry 31(3): 327–335. https://doi.org/10.1016/S0038-0717(98)00129-1
Leontyeva MS, Dobrovolskaya TG, Pochatkova TN (2005) Effect of floodplain regime on the taxonomic structure of soil bacterial complexes. Bulletin of Moscow University (Series 17. Soil Science) 1: 36–39. [In Russian]
Lukina NV, Geraskina AP, Gornov AV, Shevchenko N, Kuprin AV, Chernov TI, Chumachenko SI, Shanin VN, Kuznetsova AI, Tebenkova DN, Gornova MV (2020) Biodiversity and climate-regulating functions of forests: current issues and research prospects. Issues of Forest Science 3(4): 1–90. http://dx.doi.org/10.31509/2658-607x-202141k-60
Mekhtiev SY (1959) Some data on the study of various soils of Moldova. Microbiology 25(5): 31–38. [In Russian]
Mishustin EN (1956) Microorganisms and soil fertility. Academy of Sciences Press, Moscow, 342 pp. [In Russian]
Mishustin EN (1972) Microorganisms and agricultural productivity. Nauka, Moscow, 343 pp. [In Russian]
Mitsch WJ, Day JW, Gilliam WJ, Groffman PM, Hy D, Randall GW, Wang N (2001) Reducing nitrogen loading to the Gulf of Mexico from the Mississippi River Basin: strategies to counter a persistent ecological problem. Bioscience 51(5): 373–388. https://doi.org/10.1641/0006-3568(2001)051[0373:rnlttg]2.0.co;2
Moche M, Gutknecht J, Schulz E, Langer U, Rinklebe J (2015) Monthly dynamics of microbial community structure and their controlling factors in three floodplain soils. Soil Biology and Biochemistry 90: 169–178. https://doi.org/10.1016/j.soilbio.2015.07.006
Nikitin BA (1972) Method for determining humus content in soils. Agrochemistry 3: 123–125. [In Russian]
Nikitina VG (1978) Microflora and biochemical activity of floodplain soils of the Lower Irtysh. In: Lower Irtysh Valley. Current status of the natural environment. Irkutsk, 81–89. [In Russian]
Nikitina ZI (1991) Microbiological monitoring of terrestrial ecosystems. Nauka, Novosibirsk, 222 pp. [In Russian]
Pacini GC, Bruschi P, Ferretti L, Santoni M, Serafini F, Gaifami T (2023) FunBies, a model for integrated assessment of functional biodiversity of weed communities in agro-ecosystem. Ecological Modelling 486: 1–24. https://doi.org/10.1016/j.ecolmodel.2023.110529
Parinkina OM (1971) On the microbiological characteristics of some soils of Western Taimyr. In: Biogeocenoses of the Taimyr tundra and their productivity. Nauka, Leningrad, 32–35. [In Russian]
Rafailova EA, Tukhbatova RI, Pankova AV, Alimova FK (2009) Microflora of periodically flooded soils on the example of Bolshoy Mansur Island. Water: chemistry and ecology 4: 18–22. [In Russian]
Reay MK, Loick N, Evershed RP, Muller C, Cardenas ML (2023) Moisture effects on microbial protein biosynthesis from ammonium and nitrate in an unfertilised grassland. Soil Science and Soil Biology 184: 109–114. https://doi.org/10.1016/j.soilbio.2023.109114
Rinklebe J, Langer U (2006) Microbial diversity in three floodplain soils at the Elbe River (Germany). Soil Biology and Biochemistry 38(8): 2144–2151. https://doi.org/10.1016/j.soilbio.2006.01.018
Rodrigo A, Recous S, Neel C, Mary B (1997) Modelling temperature and moisture effects on C–N transformations in soils: comparison of nine models. Ecological Modelling 102(2– 3): 325–339. https://doi.org/10.1016/S0304-3800(97)00067-7
Savich VI, Mosina LV, Norovsuren J, Sidorenko OD, Anikina DS (2019) Microbiological activity of soils as a factor of soil formation. International Agricultural Journal 1: 38–42. https://doi.org/10.24411/2587-6740-2019-11010 [In Russian]
Savichev OG, Tokarenko OG, Pasechnik EY, Nalivaiko NG, Ivanova EA, Nadeina LV (2015) Microbiological composition of river waters in the Ob’ basin (West Siberia) and its associations with hydrochemical indices. IOP Conference Series: Earth and Environmental Science 27(1): 12–35. https://doi.org/10.1088/1755-1315/27/1/012035
Schlesinger WH, Bernhardt ES (2013) Biogeochemistry: an analysis of global change. Elsevier, New York, 672 pp. https://doi.org/10.1016/C2012-0-01654-7
Schuldt A, Assmann T, Brezzi M, Buscot F, Eichenberg D, Gutknecht J, Härdtle W, He JS, Klein AM, Kühn P, Liu X, Ma K, Niklaus PA, Pietsch KA, Purahong W, Scherer-Lorenzen M, Schmid B, Scholten T, Staab M, Tang Z, Trogisch S, von Oheimb G, Wirth C, Wubet T, Zhu CD, Bruelheide H (2018) Biodiversity across trophic levels drives multifunctionality in highly diverse forests. Nature Communications 9: 1–10. https://www.nature.com/articles/s41467-018-05421-z
Segi Y (1983) Methods of soil microbiology. Kolos, Moscow, 296 pp. [In Russian]
Sha C, Mitsch WJ, Mander Ü, Lu J, Batson J, Zhang L, He W (2011) Methane emissions from freshwater riverine wetlands. Ecological Engineering 37: 16–24. https://doi.org/10.1016/j.ecoleng.2010.07.022
Shen R, Lan Z, Rinklebe J, Nie M, Hu Q, Yan Z, Fang C, Jin B, Chen J (2021) Flooding variations affect soil bacterial communities at the spatial and inter-annual scales. Science of The Total Environment 759(10): 143–471. https://doi.org/10.1016/j.scitotenv.2020.143471
Shepeleva LF (2019) Structure and dynamics of meadow communities of the Middle Ob. Tomsk State University Publishing House, Tomsk, 348 pp. [In Russian]
Singh JS, Raghubansh AS, Singh RS, Srivastava SC (1989) Microbial biomass acts as a source of plant nutrients in dry tropical forest and savanna. Nature 338(6215): 499–500.
Slavnina TP, Inisheva LI (1987) Biological activity of soils of Tomsk region. Tomsk State University Publishing House, Tomsk, 216 pp. [In Russian]
Slavnina TP, Pashneva GE, Kakhatkina MI, Tazynbaev MG (1981) Soils of the Middle Ob floodplain, their meliorative status and agrochemical characteristics. Tomsk State University Publishing House, Tomsk, 227 pp [In Russian]
Titova VI, Kozlov AV (2012) Methods for assessing the functioning of soil microbiocenosis involved in the organic matter transformation. Nizhny Novgorod Agricultural Academy, Nizhny Novgorod, 64 pp. [In Russian]
Unger M, Kennedy AC, Muzika R-M (2009) Flooding effects on soil microbial communities. Applied Soil Ecology 42(1): 1–8. https://doi.org/10.1016/j.apsoil.2009.01.007
Vorobyev SN, Kirpotin SN, Vorobyeva TE, Kolesnichenko LG, Izerskaya LA (2016) Alluvial soils of the Ob River floodplain and their significance in the formation of geochemical flow from western Siberia. Riparian Zones: Characteristics, Management Practices and Ecological Impacts 1: 263–288.
Vorobyev SN, Pokrovsky OS, Kirpotin SN, Kolesnichenko LG, Shirokova LS, Manasypov RM (2015) Flood zone biogeochemistry of the Ob River middle course. Applied Geochemistry 63: 133–145. https://doi.org/10.1016/j.apgeochem.2015.08.005
Vorobyev SN, Pokrovsky OS, Kolesnichenko LG, Manasypov RM, Shirokova LS, Karlsson J, Kirpotin SN (2019) Biogeochemistry of dissolved carbon, major, and trace elements during spring flood periods on the Ob River. Hydrological Processes 33(1): 1579–1594. https://doi.org/10.1002/hyp.13424
Wardle DA (1998) Controls of temporal variability of the soil microbial biomass: A global-scale synthesis. Soil Biology and Biochemistry 30(13): 1627–1637. https://doi.org/10.1016/S0038-0717(97)00201-0
Wilson JS, Baldwin DS, Rees GN, Wilson BP (2011) The effects of short‐term inundation on carbon dynamics, microbial community structure and microbial activity in floodplain soil. River Research and Applications 27: 213–225. https://doi.org/10.1002/rra.1352
Yakushev AV (2015) Integral structural-functional method for characterizing microbial populations. Soil Science 48(4): 429–446. https://doi.org/10.1134/S1064229315040110
Yakutin MV, Andrievsky VS, Shepelev AI (2014) Features of changes in the zoomicrobiological complex during the natural evolution of floodplain soils of the middle Ob. Bulletin of Surgut State University 2(4): 74–79. [In Russian]
Yakutin MV, Andrievsky VS, Shepelev AI (2013) Use of soil-biological methods in monitoring floodplain ecosystems in the middle Ob region. Interexpo Geo-Siberia 2: 1–6. [In Russian]
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