Soil microorganisms as bioindicators of agroecosystem condition: a review of their ecological and trophic groups, functional roles, and the impact of anthropogenic factors
DOI:
https://doi.org/10.60923/issn.2281-4485/24117Keywords:
bioindicators, soil microorganisms, ecological-trophic groups, soil agroecosystems, anthropogenic impact, fertilisersAbstract
Soil is the foundation of agroecosystems. It is a physical surface where plants can grow. But it is also a living resource that provides services to the environment and helps to keep the Earth's natural cycles working. The soil microbiome is a highly diverse community of organisms that include bacteria (70–90% of the total mass), as well as fungi, archaea, protozoa, and algae. These organisms work together to break down organic matter, recycle nutrients, and fight off diseases to keep the soil healthy. Ecological-trophic groups show what soil is like, based on how it is made, what nutrients are available, how much air is in it, and how much humans have disturbed it. Their ratio and activity are a direct response to these conditions. It is impossible to assess the state of soil agroecosystems without a deep understanding of the role of the main ecological groups of microorganisms. The number, activity, and ratio of different types of microorganisms can be used to indicate changes in soil processes. The aim of this review is to summarise the role and impact of factors on ecological-trophic groups as bioindicators of the condition of soil agroecosystems.
This webpage was updated on 2026-05-11 to correct a typo in the first author's name. The PDF was already correct, we apologize with the author.
References
BAIMAGAMBETOVA Z.A., KALYMBETOV G.Y., SE-ITKARIMOV A., SAPARGALIYEVA B.O., SARTAYEV A. (2024) Microorganisms in the soil of arid pastures – Indicators of health and assistants in the evaluation of biostimulants. Journal of Ecological Engineering, 25(8): 179–189. https://doi.org/10.12911/22998993/190132
BHADURI D., SIHI D., BHOWMIK A., VERMA B.C., MUNDA S., DARI B. (2022) A review on effective soil health bio-indicators for ecosystem restoration and sustainability. Frontiers in microbiology, 13:938481. https://doi.org/10.3389/fmicb.2022.938481
BILIAVSKA L., IUTYNSKA G., LOBODA M., ROPOTILOV B., SKROTSKYI S. (2024) Diagnostics and bioremediation of soils affected by military operations in Ukraine. Biological Systems: Theory and Innovation, 15(3): 67–78. https://doi.org/10.31548/biologiya/3.2024.67
BOBRYK N.YU., KRYVTSOVA M.V., NIKOLAJCHUK V.I., VOLOSHCHUK I. (2016) Response of soil microflora to impact of heavy metals in zones of influence of railway transport. Bulletin of Dnipropetrovsk University. Ser. Biol. Ecol. Vìsn. Dnìpropetr. Unìv, 24(1): 151–156. https://doi.org/10.15421/011618
CHAIKA O., PERETYATKO T., GUDZ S. (2017) The number of ecological and trophic groups of microorganisms in Yazivske sulfur deposit, Agroecological Journal, 1: 93–100. http://journalagroeco.org.ua/article/view/221022/220718
CHEN Q., XIN Y., LIU Z. (2020) Long-term fertilisation with potassium modifies soil biological quality in K-rich soils. Agronomy, 10(6):771.https://doi.org/10.3390/agronomy10060771
CORREDOR D., DUCHICELA J., FLORES F.J., MAYA M., GUERRON E. (2024) Review of explosive contami-nation and Bioremediation: Insights from microbial and bio-omic approaches. Toxics, 12(4):249. https://doi.org/10.3390/toxics12040249
DE ANDRADE BARBOSA M., DE SOUSA FERRAZ R.L., COUTINHO E.L.M., COUTINHO NETO A.M., DA SILVA M.S., FERNANDES C., RIGOBELO E.C. (2019) Multivariate analysis and modeling of soil quality indicators in long-term management systems. The Science of the total environment, 657:457–465. https://doi.org/10.1016/j.scitotenv.2018.11.441
DEMYANYUK O.S., PATYKA V.P., SHERSTOBOEVA O.V., BUNAS A.A. (2018) Formation of the structure of microbiocenoses of soils of agroecosystems depending on trophic and hydrothermal factors. Biosystems Diversity, 26(2):103–110. https://doi.org/10.15421/011816
FIERER N., BRADFORD M.A., JACKSON R.B. (2007) Toward an ecological classification of soil bacteria. Ecology, 88(6):1354–1364. https://doi.org/10.1890/05-1839
GUMENIUK I.I, LEVISHKO A.S., DEMYANYUK O.S., SHERSTOBOEVA O.V. (2022) Properties of Microorganisms Isolated From Soils Under Conventional and Organic Farming. Mikrobiolohichnyi Zhurnal. Micro-biological journal, 84(2):12–23. https://doi.org/10.15407/microbiolj84.02.012
HO A., DI LONARDO D.P., BODELIER P.L. (2017) Revisiting life strategy concepts in environmental microbial ecology. FEMS Microbiology Ecology, 93(3):10.1093/ femsec/fix006. https://doi.org/10.1093/femsec/fix006
HSIAO CHE-JEN, MUSHTAQ M., SASSENRATH G.F., ZEGLIN L.H., HETTIARACHCHI G.M., RICE C.W. (2025) Long-term tillage and compost shape soil microbes under soil organic carbon equilibrium. European Journal of Soil Science, 76(3):1–14. https://doi.org/10.1111/ejss.70125
IQBAL S., BEGUM F., NGUCHU B.A., CLAVER U.P., SHAW P. (2025) The invisible architects: microbial commu-nities and their transformative role in soil health and global climate changes. Environmental Microbiome, 20:36. https://doi.org/10.1186/s40793-025-00694-6
KÖBERL M., WAGNER P., MÜLLER H., MATZER R., UNTERFRAUNER H., CERNAVA T., BERG G. (2020) Unravelling the complexity of soil microbiomes in a large-scale study subjected to different agricultural management in Styria. Frontiers in Microbiology, 11:1052. https://doi.org/10.3389/fmicb.2020.01052
LEVISHKO A.S., MAMENKO P.M. (2025) Microbial fertilisers and ways to optimise the efficiency of their use in crop production. Agroecological Journal, 1:109–123. https://doi.org/10.33730/2077-4893.2.2025.333832
LI X., WANG A., WAN W., LUO X., ZHENG L., HE G., HUANG D., CHEN W., HUANG Q. (2021) High Salinity Inhibits Soil Bacterial Community Mediating Nitrogen Cycling. Applied and environmental microbiology, 87(21): e0136621. https. https://doi.org/10.1128/AEM.01366-21
MALAL H., GARCIA J. A., MARRS A., AIT HAMZA M., EMERSON C., NOCCO M., LAKHTAR H., LAZCANO C. (2025) Organic and inorganic fertilizers modulate the response of the soil microbiome to salinity stress. Frontiers in Microbiology, 16:1551586. https://doi.org/10.3389/fmicb.2025.1551586
MALIK A.A., MARTINY J.B.H., BRODIE E.L., MARTI-NY A.K., TRESEDER K.K., ALLISON S.D. (2020) De-fining trait-based microbial strategies with consequences for soil carbon cycling under climate change. The ISME Journal, 14(1):1–9. https://doi.org/10.1038/s41396-019-0510-0
MASLOVSKA O., KOMPLIKEVYCH S., ZINCHUK D. ZARITSKA YE., 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):1–23. https://doi.org/10.1186/s13213-025-01807-9
MOLISZEWSKA E., BIDA I., MATIK K., ŚLUSARCZYK A., PAWLICZEK D., HAVRYLIUK O., HOVORUKHA V., TASHYREV O. (2025) Analysis of variations in heavy metal levels and soil microorganism counts resulting from shelling incidents in Ukraine. Archives of Environmental Protection, 51(1):83–91. https://doi.org/10.24425/aep.2025.153752
NGUYEN T.B.A., CHEN Q.L., YAN Z.Z., LI C., HE J.Z., HU H. W. (2023) Trophic interrelationships of bacteria are important for shaping soil protist communities. Environ-mental microbiology reports, 15(4):298–307.
https://doi.org/10.1111/1758-2229.13143
PATYKA V.P., VOLKOGON V.V. (Eds.) (2024) Microor- ganisms in the stabilisation of agroecosystems. (2024). Publi-sher PP Lysenko M.M. Retrieved from: https://imv. org. ua/wp-content/uploads/2025/02/Monogr agrafia_2024.pdf
PESAKOVIC M., MANDIC L., DJUKIC D. (2003) Soil ammonification activity in the conditions of mineral and organic fertilizer use. Acta Agriculturae Serbica, 8(16):49–56.
POROSHENKO S.S. (2020) The analysis of methods of investigation of negative impact on mesofauna and micro-biology of soils of contaminated solutions for foam makers. Ekolohichna bezpeka ta pryrodokorystuvannya, 2(34):88–98. https://es-journal.in.ua/article/view/208010/208198
RASHEELA A.R.P., KHALID M.F., ABUMAALI D.A.,
ALATALO J.M., AHMED T. (2025) Impact of Abiotic Stressors on Soil Microbial Communities: A Focus on Antibiotics and Their Interactions with Emerging Pollutants. Soil Systems, 9(1):2. https://doi.org/10.3390/soilsystems9010002
SAMADDAR S., CHATTERJEE P., TRUU J., ANAN-DHAM R., KIM S., SA T. (2019) Long-term phosphorus limitation changes the bacterial community structure and functioning in paddy soils. Applied Soil Ecology, 134:111–115. https://doi.org/10.1016/j.apsoil.2018.10.016
SCHMITZ L., YAN Z., SCHNEIJDERBERG M., DE ROIJ M., PIJNENBURG R., ZHENG Q., FRANKEN C., DECHESNE A., TRINDADE L.M., VAN VELZEN R., BISSELING T., GEURTS R., CHENG X. (2022) Synthetic bacterial community derived from a desert rhizosphere confers salt stress resilience to tomato in the presence of a soil microbiome. The ISME journal, 16(8):1907–1920. https://doi.org/10.1038/s41396-022-01238-3
SHAABAN M. (2024) Salt-Affected Soils. In: Núñez-Delgado, A. (Eds) Frontier Studies in Soil Science. Frontier Studies in Soil Science. Springer, Cham. https://doi.org/10.1007/978-3-031-50503-4_10
SIMPANEN S., DAHL M., GERLACH M., MIKKONEN A., MALK V., MIKOLA J., ROMANTSCHUK M. (2016) Biostimulation proved to be the most efficient method in the comparison of in situ soil remediation treatments after a simulated oil spill accident. Environ Sci Pollut Res 23:25024–25038. https://doi.org/10.1007/s11356-016-7606-0
STARKE R., LÓPEZ MONDÉJAR R., HUMAN Z., NAVRÁTILOVÁ D., ŠTURSOVÁ M., VETROVSKY T., OLSON H. (2021) Niche differentiation of bacteria and fungi in carbon and nitrogen cycling of forest soil. Soil Biology and Biochemistry, 155:108174. https://doi.org/10.1016/j.soilbio.2021.108170
SYMOCHKO L., BUGYNA L., HAFIYAK O. (2021) Eco-logical aspects of biosecurity in modern agroecosystems. International Journal of Ecosystems and Ecology Science, 11(1):181–186. https://doi.org/10.31407/ijees11.124
WANG X., CHI Y., SONG S. (2024) Important soil micro-biota’s effects on plants and soils: A comprehensive 30-year systematic literature review. Frontiers in Microbiology, 15:1347745. https://doi.org/10.3389/fmicb.2024.1347745
YANG T., LUPWAYI N., MARC S.-A., SIDDIQUE K.H. M., BAINARD L.D. (2021) Anthropogenic drivers of soil microbial communities and impacts on soil biological fun-ctions in agroecosystems. Global Ecology and Conserva-tion, 27:e01521. https://doi.org/10.1016/j.gecco.2021.e01521
YAO F., YANG S., WANG Z., WANG X., YE J., WANG X., DEBRUYN J. M., FENG X., JIANG Y., LI H. (2017) Microbial taxa distribution is associated with ecological trophic cascades along an elevation gradient. Frontiers in Micro-biology, 8:2071. https://doi.org/10.3389/fmicb.2017.02071
YU J., XU L., ZHU X., DONG X., LI F., YUE J. (2024) Effects of organic fertilisers on plant growth and the rhizosphere microbiome. Applied and Environmental Microbiology, 90:e01719–e01723. https://doi.org/10.1128/aem.01719-23
ZHONG W., GU T., WANG W., ZHANG B., LIN X., HUANG Q., SHEN W. (2010) The effects of mineral fertilizer and organic manure on soil microbial community and diversity. Plant and Soil, 326(1–2):511–522. https://doi.org/10.1007/s11104-009-9988-y
Downloads
Published
How to Cite
Issue
Section
License
Copyright (c) 2026 Alla Levishko, Iryna Gumeniuk, Olena Sherstoboeva
This work is licensed under a Creative Commons Attribution 4.0 International License.
