European Journal of Sustainable Agroecosystems

Background: Microorganisms in the soil are responsible for the transformation, mobilization, and cycling of nutrients essential for plants. Recently, it has become more obvious that the activity of microorganisms plays an important role in decreasing dependency on synthetic agrochemicals and sustaining productivity in agroecosystems. With the increasing consideration of regenerative agriculture, there is now more emphasis on how microbial communities influence nitrogen, phosphorus, sulfur, and carbon transformations.
Objective: This paper seeks to review peer-reviewed literature published mostly from 2015 to 2026 on microbial-mediated nutrient transformation to consolidate knowledge, compare research findings, identify controversies, and highlight knowledge gaps connected to sustainable soil management.
Sources of literature: The search for literature included structured searches in the Scopus, Web of Science, PubMed, Google Scholar databases as well as reports issued by the Food and Agriculture Organization (FAO) and the Intergovernmental Panel on Climate Change (IPCC) using different combinations of keywords like "soil microbiome," "nutrient cycling," "phosphate-solubilizing bacteria," "biological nitrogen fixation," "arbuscular mycorrhizal fungi," "soil enzyme activity," etc.
Key points: The assessed research arrives at many conclusions. The ways in which microbial nitrogen transformation happens due to ammonification, nitrification, denitrification, and symbiotic and free-living nitrogen fixation depend heavily on soil aggregate composition and management techniques used. The microorganisms that dissolve phosphate and potassium and arbuscular mycorrhizal fungi increase nutrient bioavailability in soil, but results from practical application vary from theoretical findings. Soil enzymes work as catalysts of transformation and as indicators of soil health. New technology, such as metagenomics, synthetic microbial consortia, and precision agriculture, is changing how microbiomes are analyzed and utilized.
There are some gaps in research which arise from lack of effective long-term validation of laboratory inoculated strains, low levels of standardization of enzyme testing, poor integration of “-omics” research results into practical decision-making, and underrepresentation of tropical and small-scale farming contexts in the literature. 
The authors conclude that microbes that mediate nutrient transformation provide a biological and resource-efficient way to achieve sustainability in soil management, but translating the findings from research into practice requires standardization, longer periods of time, and better interdisciplinary interaction between microbiology, agriculture, and digital agriculture.