Biogenic Nanoparticles in the “Plant – Microbiome – Soil” System: Biological Synthesis Platforms and Regulatory Interactions

The plant – microbiome – soil system is an environment in which biogenic nanoparticles are formed and simultaneously act as regulatory factors: biological platforms of different taxonomic origin govern precursor conversion, while the resulting particles alter plant physiology, the structure of rhizosphere multi-species communities and the chemical state of the soil. This narrative critical review compares bacteria, microalgae, endophytic fungi and plant extracts as platforms of particle formation and grades the strength of evidence for their action from the individual to the ecosystem level, with an emphasis on the agroecological context of contaminated soils. Publications retrieved from PubMed/MEDLINE, Web of Science, Scopus, ScienceDirect and Google Scholar, mainly for 2018–2026, were classified according to a four-level hierarchy: direct causal, strong functional, indirect and conceptual evidence. For elemental particles, enzymatic, thiol-mediated and polyphenol–flavonoid redox routes were distinguished; for metal oxides – hydrolysis, precipitation and biologically modulated mineralisation. Direct confirmation of a specific reductant is available only in individual systems, notably for fumarate reductase, whereas FTIR identification, pH shifts and correlations of enzyme activity remain indirect. Primary soil–plant studies show that biogenic FeO and Se nanoparticles can alter Cd availability, plant antioxidant responses and the recruitment of beneficial bacteria to the root zone; however, outcomes depend on dose, coating, size and soil matrix. Positive results have been obtained mainly in controlled aqueous, soil or pot systems; comparisons with soluble ions, non-nanoscale analogues and biological extracts are often incomplete, which limits causal inference. Ecotoxicological data indicate dose-dependent effects on soil invertebrates and microbial communities, which requires multi-species assessment. Engineered nanoscale zero-valent iron is considered separately as a model comparator of ageing, passivation and microbial reactivation, rather than as evidence for the properties of all biogenic particles. Field translation requires standardised characterisation, ionic and non-nanoscale controls, multi-species testing and long-term assessment of particle fate.