Review maps microbial and nano strategies against agricultural soil contaminants

A 2025 review concludes that pharmaceuticals, pesticides and industrial pollutants can disrupt soil microbial communities, nutrient cycling and plant performance, while bio-based and nano-enhanced interventions offer promising but incompletely validated ways to protect agricultural soils. Published in Discover Toxicology, the synthesis examines how contaminants alter the root environment and assesses microbial inoculants, biofertilizers, engineered nanoparticles and hybrid nano-biofertilizers as potential tools for sustaining crop production and global food security. It is a review of previously published evidence rather than a new field trial, and it emphasizes that many laboratory studies use exposure concentrations above realistic agricultural conditions.

The review defines emerging contaminants as newly identified or increasingly detected pollutants that are not yet fully regulated. Agricultural chemicals, treated wastewater, sewage sludge, manure, industrial emissions, urban runoff and contaminated amendments are among their principal sources. Microplastics enter farmland through irrigation water, fertilizers, organic amendments and atmospheric deposition. Climate-related flooding can transport contaminants onto agricultural land, while drought can concentrate them in soils. Some less persistent compounds also degrade into transformation products that may have different or greater risks than their parents. Unlike heavily studied legacy pollutants, emerging contaminants create difficulties because their mixtures, pathways and ecological effects remain incompletely characterized.

Pharmaceutical residues illustrate how a small chemical can disturb major soil functions. Antibiotics entering soil through wastewater, biosolids and livestock manure can impose selective pressure on microorganisms, affecting processes such as nitrogen fixation, phosphorus solubilization and organic-matter decomposition. Tetracycline has suppressed the activity of nitrogen-fixing bacteria, potentially reducing nitrogen available to plants, while sulfamethoxazole and tetracycline have reduced activity of urease, an enzyme involved in organic-matter decomposition. Carbamazepine and oxytetracycline can persist in soil for extended periods. In experiments involving the earthworm Eisenia fetida, carbamazepine, diclofenac, fluoxetine and orlistat altered soil pH and the animals’ internal pH, indicating potential effects beyond microbial communities.

Plant uptake provides a possible route from contaminated soil to food. One study cited in the review detected five of six tested pharmaceuticals in radish and ryegrass tissues, with carbamazepine reaching 52 micrograms per gram in radish and 33 micrograms per gram in ryegrass; sulfamethazine remained below the study’s 0.01-microgram-per-gram detection limit. These measurements come from an individual experiment, not a systematic estimate of contamination across foods, and uptake varies with both compound properties and plant species. The review therefore treats crop accumulation as a food-safety concern requiring further assessment rather than evidence of a general contamination rate across agricultural markets.

Pesticides add another major pressure on soil–plant systems. A large European Union survey cited by the authors found at least one pesticide residue in 83% of topsoil samples, while 58% of samples contained mixtures of two or more pesticides. Glyphosate and its metabolite AMPA formed the most frequently detected mixture, appearing in 25% of samples. Organophosphate pesticides can kill decomposers such as earthworms, reducing organic-matter breakdown and soil aeration. Glyphosate can also interfere with root-exudate production, with research cited in the review associating this effect with reduced colonization by mycorrhizal fungi and rhizobacteria. Pesticide residues have been detected in bees, nectar and pollen, extending their effects beyond the root zone.

Industrial contaminants introduce persistent physical and chemical changes. A survey of United Kingdom farmland reported 320 to 12,560 microplastic particles per kilogram of soil and recorded 2022 levels 1.6 times those measured in 1966. Experimental studies reviewed by the authors found that increasing microplastic concentrations reduced bulk density and increased soil porosity by 7% to 15%, changes that can affect water retention and hydraulic conductivity. Results depended on moisture: toxicants leaching from microplastics reduced fungal richness in well-watered soil, whereas greater water retention under dry conditions benefited some organisms. Per- and polyfluoroalkyl substances, or PFAS, have likewise been detected in agricultural soils irrigated with contaminated effluent and have been linked experimentally to reduced seed germination, impaired root development and altered nutrient uptake.

At the microbial level, contamination can reorganize communities rather than merely suppress them. Exposure to antibiotics, fungicides, PFAS, textile dyes and plastics can shift microbial biomass, genetic composition, functional diversity and relative abundance. Direct toxicity may leave resistant organisms enriched, while altered pH, nutrient availability or habitat can favor other species. Microplastics may support specialized communities at the soil–plastic interface, known as the microplastisphere. Sewage sludge and manure can also enrich antibiotic-resistance genes, which may spread among microbes through horizontal gene transfer. In the rhizosphere, albendazole suppressed colonization by the mycorrhizal fungus Rhizophagus irregularis in Lotus japonicus and affected genes associated with arbuscule development and plant phosphorus uptake.

Plants and soil fauna respond in closely related ways. Contaminants have been associated with impaired seed germination, shortened roots, reduced shoot biomass, changes in root hairs and cell permeability, altered photosynthesis, leaf chlorosis and necrosis. Microplastics adhering to root surfaces may interfere with root-cell physiology in fava bean, rice and lettuce, while silver particles can impair ectomycorrhizal diversity, survival and nutrient transfer. Microplastics, organophosphates, dibenzofuran and polychlorinated dibenzodioxins have caused gastrointestinal injuries in earthworms. Antibiotics, nanoparticles and bisphenol A have also increased mortality or impaired reproduction in several groups of soil animals. Such changes can feed back into plant performance because these organisms contribute to decomposition, nutrient cycling, soil structure and microbial diversity.

Bio-based remedies seek to restore or replace impaired biological functions. Rhizosphere microbiome management uses plant-growth-promoting rhizobacteria, mycorrhizal fungi and other inoculants to improve nutrient access, suppress pathogens, increase stress tolerance or support contaminant degradation. One soybean experiment using Bradyrhizobium japonicum and Pseudomonas putida reported increases of 33% to 56% in yield, root length and shoot length under environmental stress. Another study found that co-inoculation with indigenous Pseudomonas and Bradyrhizobium increased soybean yield by more than 10%. Bioaugmentation can acclimatize contaminant-degrading microorganisms before inoculation; one reviewed method removed 99% of target ibuprofen in 21 days, although identifying effective organisms and establishing them in field soils remain difficult. Biofertilizers offer related functions through biological nitrogen fixation, nutrient solubilization, phytohormone modulation and biocontrol, but their shelf life, strain compatibility and variable survival in soils limit deployment.

Nano-fertilizers and hybrid nano-biofertilizers approach the problem through nutrient delivery. Their small particles provide a high surface-area-to-volume ratio and can encapsulate nutrients for foliar, seed or soil application. Trials reviewed in the article report improved nutrient concentrations and crop performance in rice, tomato, peas, soybean, barley and wheat. Hybrid products combine microbial inoculants with particles of silver, copper, iron, nickel, silicon, titanium or zinc, or with organic carriers such as chitosan, cellulose and starch. The authors describe this as an early-stage field with potential for lower nutrient losses and improved nutrient-use efficiency, but nanofertilizers can also reduce carbon mineralization, diminish microbial diversity and harm biota. The review’s conclusion is therefore promising rather than definitive: performance depends on crops, contaminants, climate, soils and farming systems, and the evidence does not yet show that combined interventions can reliably deliver higher yields or safer food at global scale. The authors call for realistic long-term studies, stronger monitoring and regulatory frameworks, farmer education, and coordinated research, policy and stakeholder action across different agricultural environments.

Subject of Research: Emerging contaminants and bio-based and nano-enhanced strategies for agricultural soil health

Article Title: Addressing emerging contaminants in agriculture affecting plant–soil interaction: a review on bio-based and nano-enhanced strategies for soil health and global food security (GFS)

Article References: Nwankwo, C. E. I., Okeke, E. S., Umeoguaju, F. U., Ejeromedoghene, O., Adedipe, D. T., & Ezeorba, T. P. C. (2025). Addressing emerging contaminants in agriculture affecting plant–soil interaction: a review on bio-based and nano-enhanced strategies for soil health and global food security (GFS). Discover Toxicology, 2(1), Article 4. https://doi.org/10.1007/s44339-025-00018-w

Image Credits: AI Generated

DOI: 10.1007/s44339-025-00018-w

Keywords: emerging contaminants, agricultural soils, plant–soil interactions, rhizosphere microbiome, biofertilizers, nano-fertilizers, nutrient cycling, pesticides, PFAS, food security, Addressing, emerging