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

The review defines biofertilizers as products containing living microorganisms such as nitrogen-fixing bacteria, phosphorus-solubilizing bacteria, and mycorrhizal fungi. Unlike chemical fertilizers, which supply nutrients directly and can pollute water, air, and soil when overused, biofertilizers work through symbiotic relationships with plants. Microbial strains employ diverse mechanisms to optimize nutrient absorption: nitrogen fixation, potassium and phosphorus solubilization, secretion of phytohormones, synthesis of compounds that inhibit phytopathogens, protection against abiotic and biotic stresses, and even detoxification of subterranean pollutants. The authors note that most subsistence and commercial farmers are increasingly attracted to biofertilizers rather than depending solely on synthetic inputs.

The urgency behind the research is demographic. The world population is projected to reach roughly 9.7 billion by 2050, and conventional agriculture — reliant on extensive use of synthetic fertilizers and pesticides — is straining ecosystems through the pollution of water reservoirs, air, and soil. Biofertilizers, applied as seed or soil inoculants, multiply in the soil and actively contribute to the nutrient cycle, enhancing the growth of crops including rice, pulses, millets, cotton, sugarcane, and vegetables. The review frames them as a crucial element of organic farming that maintains a nutrient-rich soil environment while supporting long-term soil health.

Nitrogen is the primary limiting nutrient for plant growth, and plants cannot convert atmospheric N2 into usable forms on their own. The review details how nitrogen-fixing bacteria solve this problem through the nitrogenase enzyme complex: dinitrogenase reductase provides the electrons that dinitrogenase uses to convert atmospheric nitrogen into ammonia by reduction. Symbiotic fixers, members of the Rhizobiaceae family, form mutually beneficial associations with leguminous plants, while non-symbiotic microbes such as Cyanobacteria, Azospirillum, and Azotobacter exist in free-living and endophytic forms. Because the enzymes bond with oxygen and lose activity, the process requires careful oxygen regulation within the nodule environment.

Phosphorus presents a different challenge: its rock reserves are diminishing, with roughly 16 million metric tons extracted annually, primarily from North Africa, and projections suggest phosphate rock could be exhausted within 100 years. Phosphorus-solubilizing bacteria such as Pseudomonas, Bacillus, Rhizobium, and Burkholderia dissolve insoluble phosphates — di- and tri-calcium phosphates, hydroxyapatites, and rock phosphates — by producing organic acids that lower soil pH, disintegrating phosphate compounds and liberating plant-available phosphorus. The review reports that these bacteria can dissolve around 50–60% of bound phosphorus in soil. Potassium-solubilizing microorganisms, including Frateuria aurantia, similarly mobilize otherwise inaccessible potassium, which regulates stomatal function and photosynthesis. Notably, co-inoculation of Azospirillum brasilense and Rhizobium meliloti has been shown to improve grain production and nitrogen, phosphorus, and potassium concentrations in wheat.

On the physical side, biofertilizers improve soil structure by promoting stable soil aggregates that increase porosity, aeration, and water infiltration. Mycorrhizal fungi form symbiotic associations with plant roots, encouraging widespread root development that facilitates efficient water absorption and increases drought resistance. The review documents improvements in soil bulk density — as organic matter acts as a binding agent, pore spaces form and compaction decreases — along with soil moisture retention and soil temperature buffering, since humus created through microbial decomposition acts as an insulating layer that mitigates temperature extremes. Even soil color improves indirectly, as higher humus concentrations give soil a deep, dark hue.

Chemically, the review found that biofertilizer application caused a slight decrease in alkalinity and an increase in organic carbon content compared to untreated soil. Soil nitrogen content rises in the presence of Azospirillum and Rhizobia, which fix atmospheric nitrogen; four decades of research on Azospirillum-plant interactions have revealed multiple pathways through which the bacterium promotes growth. Mycorrhiza and phosphate-solubilizing bacteria enhance phosphorus availability, while arbuscular mycorrhizal fungi absorb and transport potassium from soil to plant roots. Applying Trichoderma to soil resulted in greater organic carbon increases than seed inoculation with phosphate-solubilizing bacteria in soybean and maize, underscoring the chemical transformation biofertilizers can drive.

Biologically, biofertilizers reshape the soil microbiome by introducing beneficial microorganisms that boost microbial diversity, promote disease suppression, and improve nutrient cycling. Populations of bacteria, fungi, and actinomycetes all respond: nitrogen-fixing and phosphate-solubilizing bacteria directly increase bacterial activity, mycorrhizal fungi foster favorable symbiotic connections with plant roots, and actinomycetes — particularly Streptomyces species — reduce soil-borne diseases by producing antibiotics. Microorganisms like Trichoderma and Bacillus stop the growth of soil-borne pathogens, while actively decomposing organic residues to release vital nutrients and enhance soil structure.

The review is candid about obstacles. Widespread adoption has been limited by the difficulty of replicating positive effects across environments with varying conditions. Key barriers include limited understanding of biofertilizers among farming communities, insufficient promotion by agricultural extension workers, scarcity of appropriate carrier materials, inadequate storage facilities that allow contamination, and extreme climatic conditions that cause inconsistent effectiveness. Poor labeling — missing expiry dates and unnamed microbial strains — further erodes credibility, and most biofertilizers exhibit selectivity in their effects, meaning performance varies by crop and soil type.

Still, the authors conclude that biofertilizers offer a sustainable solution for enhancing soil quality and promoting long-term soil sustainability across all three property domains. By improving microbial diversity, nutrient accessibility, and soil structure, they reduce the necessity for artificial fertilizers and lessen agriculture’s environmental footprint. Overcoming challenges such as crop-specific characteristics, limited shelf life, compatibility with existing farming procedures, and environmental sensitivity will require continued research and education — but the payoff, the review argues, is resilient, well-balanced agro-ecosystems capable of sustaining food production for decades to come.

Subject of Research: Biofertilizers and their effects on soil physical, chemical, and biological properties

Article Title: Biofertilizers: A sustainable strategy for enhancing physical, chemical, and biological properties of soil

Article References: Ghimirey, V., Chaurasia, J., Acharya, N., Dhungana, R., & Chaurasiya, S. (2024). Biofertilizers: A sustainable strategy for enhancing physical, chemical, and biological properties of soil. Innovations in Agriculture, 7, 1-11. https://doi.org/10.3897/ia.2024.128697

Image Credits: AI Generated

DOI: 10.3897/ia.2024.128697

Keywords: biofertilizers, soil health, nitrogen-fixing bacteria, phosphorus solubilization, potassium solubilization, mycorrhizal fungi, sustainable agriculture, soil microbiome, organic farming, soil organic carbon, plant growth-promoting bacteria, soil properties

The rhizosphere is the narrow zone of soil where plant roots and microorganisms engage in an intense chemical dialogue. Root cells exude sugars, amino acids, organic acids, and secondary metabolites such as phenolics and flavonoids, and these compounds act simultaneously as chemoattractants, nutritional substrates, and signaling molecules that shape which microbes colonize the root surface. In rice, this microbial assembly performs critical biogeochemical work: nitrogen fixation, phosphorus solubilization, iron chelation via siderophores, and even methane cycling in the oxygen-starved paddy soil. The review emphasizes that recent advances in genomics, metabolomics, and high-throughput sequencing have transformed the soil microbiome from a fixed agricultural resource into an engineerable ecosystem, where specific taxa can be recruited or suppressed to meet defined objectives.

The historical foundation of this field rests on plant growth-promoting rhizobacteria, or PGPR. Early rice studies inoculated isolated strains of Rhizobium and Azospirillum to boost nitrogen availability and root development, with controlled-condition yield gains of roughly 8 to 22 percent compared with unfertilized controls. Cyanobacteria in the Azolla ecosystem contributed up to 40 kilograms of fixed nitrogen per hectare in 20 to 25 days. But the review documents a persistent problem: these benefits rarely transferred reliably to heterogeneous field conditions, where soil chemistry, native microbial competition, and climate variability conspired against single-strain inoculants. That inconsistency triggered the shift toward multispecies consortia that exploit functional complementarity between taxa.

The clearest evidence for the power of engineered consortia comes from phosphorus acquisition. A four-member SynCom isolated from rice-soybean intercropping systems, comprising Variovorax paradoxus, Novosphingobium subterraneum, Hydrogenophaga pseudoflava, and Acidovorax sp., increased rice biomass and phosphorus uptake in pot experiments by solubilizing soil phosphorus and upregulating four phosphate transporter genes in the rice genome, OsPht1;1, OsPht1;2, OsPht1;4, and OsPht1;6. Treated plants developed larger root surface areas and more root tips, morphological traits directly linked to phosphorus foraging efficiency. In parallel, single-strain studies with Herbaspirillum R3 raised available nitrate by 14.8 percent, ammonium by 27.8 percent, and available phosphorus by 22.7 percent in the rhizosphere, lifting theoretical yield by roughly 8.8 percent. Co-inoculation experiments pairing Rhodopseudomonas palustris with Bacillus subtilis pushed yield gains to 17.7 percent, exceeding either strain alone.

Beyond nutrient mobilization, microbial consortia appear to rewire plant stress physiology. Under salt stress, a multi-species PGPR consortium enriched metabolic pathways including nucleotide metabolism, purine metabolism, and ABC transporter functions, while shifting rhizosphere community structure toward beneficial phyla such as Proteobacteria and Acidobacteriota. Pre-treatment with microbial consortia elevated enzymatic antioxidants including superoxide dismutase, peroxidase, and catalase, along with the osmoprotectant proline, reducing oxidative damage in salt-stressed rice seedlings. Salinity-tolerant rice varieties in field surveys hosted distinct rhizosphere microbiomes enriched in nutrient-cycling and stress-adaptive taxa, and these compositional differences correlated with panicle number and grains per panicle, suggesting that microbiome structure may underpin real yield resilience in saline paddies.

The review also highlights quorum sensing as an emerging lever for community design. In Gram-negative bacteria, N-acyl homoserine lactones coordinate collective behavior in a cell-density-dependent manner, while Gram-positive systems use oligopeptide signals. AHL-producing bacteria including Acinetobacter lactucae, Aeromonas popoffi, Serratia oryzae, and Rhizobium wuzhouense are abundant in rice rhizospheres, and quorum sensing regulates biofilm formation that anchors beneficial consortia to root surfaces, protects them from abiotic stress, and creates nutrient exchange hubs that antagonize pathogens. Interfering with quorum signaling has been proposed both to suppress pathogens and to optimize beneficial community assembly, positioning quorum manipulation as a potential breakthrough in rhizosphere engineering.

Pathogen suppression through engineered communities represents another frontier. A cross-kingdom SynCom combining Trichoderma harzianum with multiple Bacillus strains reduced Fusarium crown rot severity in wheat by approximately 70 percent by remodeling the rhizosphere microbiome and metabolome, a proof of concept the review argues applies directly to rice diseases such as Magnaporthe oryzae blast, Xanthomonas oryzae bacterial blight, and Rhizoctonia solani sheath blight. In rice itself, a consortium of Pantoea ananatis and Pantoea dispersa strains suppressed leaf and panicle blast by inducing systemic defense responses and reactive oxygen species accumulation, even without strong direct antagonism in vitro. Metagenomic surveys of suppressive soils consistently enrich for biosynthetic gene clusters, particularly nonribosomal peptide synthetases and siderophore pathways, and recent work showed that Bacillus biofertilizer activated predatory protist taxa and elevated polyketide synthase gene abundance, correlating with suppression of Ralstonia solanacearum.

Translating these laboratory successes into commercial products demands industrial-scale bioprocessing and formulation innovation. Stirred-tank bioreactors must maintain cell concentrations above 10^8 cells per milliliter while balancing growth rates across consortium members, and emerging machine-learning control architectures dynamically regulate feed rates and environmental parameters to preserve target community composition. Encapsulation technologies offer a solution to the chronic shelf-life problem: conventional carrier-based products typically survive only 6 to 12 months, but Pseudomonas fluorescens encapsulated in 3 percent chitosan retained viability for roughly ten months, and trehalose-doped core-shell hydrogels extended Trichoderma harzianum viability from log 5.72 to log 7.30 CFU per gram after 180 days in 15 percent NPK fertilizer. Novel liquid double emulsions preserved both bacterial and fungal strains for up to 12 months at ambient temperatures, a critical advantage in hot, humid rice-growing regions.

Yet the review is candid about the field-scale gap. SynCom colonization efficiency frequently drops below 10 percent of greenhouse performance in non-sterile paddy soils, where native microbiota outcompete introduced strains and pH variation suppresses phosphorus-solubilizing gene expression. Environmental heterogeneity in temperature, moisture, and nutrient availability produces unreliable location-to-location comparisons, and some studies report limited or no yield improvement following microbial inoculation, particularly in nutrient-rich or highly competitive soils. Regulatory frameworks add further friction: the EU’s Fertilizing Products Regulation maintains strict positive lists that often exclude novel SynCom members, while Brazilian and Indian frameworks allow faster registration of multi-strain products provided they meet minimum viability standards of 10^8 CFU per gram. Ecological risks, including the potential for high-titer inoculants to outcompete rare native taxa and temporarily reduce local microbial diversity, demand long-term monitoring.

The review concludes that microbiome engineering will only deliver climate-resilient rice when integrated with host genetics and precision agriculture. Microbiome-shaping genes, host loci whose allelic variation influences rhizosphere community composition, could allow breeders to select rice varieties that heritably recruit nitrogen-fixing or phosphorus-solubilizing taxa, though direct experimental validation in rice remains limited. Precision farming platforms, including site-specific soil moisture and salinity sensors and algorithm-driven scheduling of inoculant applications timed to drought or salinity events, may synchronize microbial delivery with plant stress windows. Synthetic biology and iterative microbiome selection, in which communities are evolved under controlled stress imposition to enrich beneficial functions, point toward programmable holobionts, engineered plant-microbe systems that respond adaptively to environmental gradients. The authors argue that merging microbial design, host genetics, multi-omics tools, and rigorous multi-location field validation is the key to turning rhizosphere engineering from a laboratory promise into a trustworthy, climate-adaptive solution for the paddies that feed half the planet.

Subject of Research: Microbiology

Article Title: Microbial interventions in rice rhizosphere engineering: from soil microbiome manipulation to yield stability

Article References: Ullah, Q., Haider, W., & Usama, M. (2026). Microbial interventions in rice rhizosphere engineering: from soil microbiome manipulation to yield stability. Frontiers in Industrial Microbiology, 4, Article 1832866. https://doi.org/10.3389/finmi.2026.1832866

Image Credits: AI Generated

DOI: 10.3389/finmi.2026.1832866

Keywords: rice, rhizosphere, microbiome, SynComs, PGPR, biofertilizers, climate resilience, agriculture, phosphorus uptake, nitrogen fixation, Microbial, interventions

A major new review published in Frontiers in Bacteriology argues that the most promising path out of this crisis runs through an unexpected intersection: artificial intelligence and microbial biotechnology. Kehinde A. Oyeniran of Bamidele Olumilua University of Education Science and Technology and the International Centre for Genetic Engineering and Biotechnology, together with Lara Donaldson of the University of Cape Town, systematically evaluate how machine learning and deep learning architectures are reinventing the use of bacteria, fungi, and viruses to enhance crop resilience, precision fermentation, and soil health. Their conclusion is striking: AI is no longer an optional enhancement to microbial biotechnology but an essential ingredient for any futuristic food-security strategy — provided the field can overcome a set of technical and ethical hurdles that currently constrain it.

The technical core of the review lies in how AI architectures decode biological complexity. Convolutional neural networks and transformers, the same deep learning frameworks that have revolutionized proteomics and genomics, are now pivotal in deciphering non-linear genomic interactions and accelerating protein structure prediction. In CRISPR experiments, CNN-based tools such as AutoCRISPR predict off-target effects of genome edits, compressing guide RNA design cycles from months to weeks while improving editing precision. Deep learning models are also instrumental in unraveling microbial genetic circuits and metabolic pathways, enabling the design of optimized microbial cell factories for enhanced bioproduction — selecting enzymes, designing pathways, and making swift adjustments to microbial robustness. Beyond engineering, these models fast-track the functional annotation of microbial genes, addressing the persistent problem that a significant proportion of genes in even fully sequenced genomes have unknown functions.

Predictive analytics built on random forests and artificial neural networks extend these capabilities into taxonomy and phenotype prediction. These models can classify microbial strains directly from genomic sequences for traits like antimicrobial resistance, predict susceptibility from treatment history or microbial evolution over time, and even forecast microbial community structure and temporal dynamics. They facilitate high-throughput microbial culturomics and automated isolation of microbial communities, advancing well beyond traditional cultivation limits. In microbial population genomics, machine learning integrates statistical inference with whole-genome approaches to predict biologically relevant features — metabolic capabilities, resistance profiles — directly from sequence information, improving therapeutic interventions and agricultural decision-making alike.

Large language models represent the newest frontier. These emerging AI agents now automate end-to-end machine learning experimentation on complex biological datasets, moving the field toward autonomous scientific discovery. Specialized systems such as Omega, designed to facilitate bioimage analysis from experimental design through implementation, interpret complex biological queries, suggest experimental parameters, and generate code for image processing. In microbial biotechnology, LLMs analyze genomic and proteomic data to forecast novel functions of microbial proteins, fast-tracking the discovery of industrially valuable compounds such as enzymes stable at high temperature and pH. They are also being adapted as specialized tools for high-throughput mining and generation of novel antimicrobial peptides, enabling rapid screening of candidates against drug-resistant bacteria like Pseudomonas aeruginosa, a major nosocomial pathogen.

The review then turns to what it calls engineering the future: precision fermentation and cell factories. AI is reinventing the design-build-test-learn cycle, transforming microbial engineering from manual trial-and-error to high-throughput autonomous systems. When integrated with AI, CRISPR-Cas systems — the foundational element of contemporary microbial engineering — become dramatically more efficient. The DeepCRISPR tool for guide RNA design and predictive modeling of editing outcomes accelerates the design-build-test-learn cycle by up to 70 percent in design efficiency. Concrete applications include optimizing Bacillus altitudinis peptidase thermostability from 85 to 92 degrees Celsius for fruit pulp digestion via AlphaFold-predicted structures, identifying acid-tolerant Lactobacillus plantarum strains in fermented matrices using random forest models, and enhancing probiotic adhesion through single-cell CRISPR screening integrated with machine learning. Deep learning models trained on Escherichia coli genomic and transcriptomic data have identified synthetic promoter-gene combinations that substantially enhance metabolic flux and protein titers while minimizing metabolic burden on the host cell.

Metabolic modeling supercharged with machine learning can almost accurately predict genotype-to-phenotype relationships, fine-tuning complex metabolic pathways for targeted products. Hybrid frameworks such as MetaFlux integrate genomic, proteomic, and metabolomic data to refine flux balance analysis, allowing researchers to understand metabolic bottlenecks and predict optimal genetic modifications before undertaking costly wet-lab experiments. These models amalgamate mechanistic biological principles with empirical data-driven methodologies to develop digital twins of microbial factories, optimizing fermentation parameters to enhance the yield and purity of functional ingredients such as engineered enzymes, vitamins, and antioxidants. Automated biofoundries — platforms integrating AI with robotic systems — further accelerate this cycle, enabling rapid prototyping and optimization of microbial strains for industrial applications through high-throughput genetic manipulation, advanced analytical instrumentation such as cryo-electron microscopy, and active machine learning workflows like METIS that optimize biological targets with minimal experimentation.

In soil health and crop resilience, AI techniques such as supervised machine learning models have been used to predict crop productivity using soil metagenomic data with an accuracy of 0.79. AI algorithms aid in forecasting disease outbreaks and pest infestations by integrating real-time environmental data with historical patterns, enabling proactive intervention strategies. Biocontrol strategies — microbial antagonists or predatory insects that suppress pathogen populations — have been optimized with AI, their deployment based on predictive models of pest dynamics and environmental conditions. Deep learning models interpret complex patterns in multispectral and hyperspectral imaging, distinguishing between stress types such as nutrient deficiencies versus pathogen attacks with high precision. Interpretable machine learning now decodes how soil microbiomes respond to drought, identifying specific root microbes that promote resilience. The biofertilizer market is projected to grow at 12.8 percent annually from 2020 to 2027, driven by the need to reduce costly and environmentally damaging nitrogenous fertilizers.

Yet the review is unflinching about the obstacles. Robust AI models require large-scale labelled datasets that remain scarce for non-model organisms, which often lack genomic annotation and standardized phenotypic data. The disparity between laboratory-grown cultures and complex field conditions hinders the generalization of machine learning predictions, particularly for Bacillus strains isolated from hyper-arid ecosystems. Deep learning models suffer from a black box problem, providing predictions without clear explanation of the underlying biological concepts — opacity that diminishes trust in agricultural decision-making. Computational and economic costs compound these issues: training GPT-3 required approximately 355 GPU-years at an estimated cost of $4.6 million, creating significant barriers for resource-limited research teams, particularly in sub-Saharan Africa where computational resources remain a major constraint of bioinformatics. Ethical considerations around data misuse, biosafety, and socio-economic impacts of displaced manual labor must also be addressed, alongside the need for comprehensive regulatory frameworks that keep pace with rapid AI evolution.

The road ahead, the authors argue, lies in self-driving laboratory systems that integrate robotic production with AI for autonomous experimentation — but the most practical near-term trajectory involves hybrid models combining AI-driven decision-making with sustained human oversight. This human-in-the-loop approach ensures that biological complexity and regulatory requirements are reasonably managed while leveraging the speed and precision of automated systems. It also mitigates biosecurity risks, including the unintentional synthesis of hazardous biological agents or uncontrolled changes in microbial phenotypes, requiring rigorous safety protocols and human-directed ethical oversight. A graduated autonomy framework can make these systems perform specific tasks in limited capacity, with expanded operational scope contingent upon validated safety and performance metrics. Ultimately, the sustained efficacy of microbial biotechnology is contingent upon iterative optimization of machine learning architectures — including transfer learning, reinforcement learning, and generative adversarial networks — to minimize predictive discrepancies within metabolic models and identify superior microbial strains for drought resilience, growth, and yield improvement with greater efficiency than conventional approaches. Successfully addressing data standardization, model interpretability, and computational expenditure remains an urgent frontier for the field, and a prerequisite for the global deployment of dependable, scalable, and ethical biotechnological solutions capable of meeting the nutritional needs of a growing global population.

Subject of Research: Artificial intelligence in microbial biotechnology for food security: current state and challenges

Article Title: Artificial intelligence in microbial biotechnology for food security: current state and challenges

Article References: Oyeniran, K. A., & Donaldson, L. (2026). Artificial intelligence in microbial biotechnology for food security: current state and challenges. Frontiers in Bacteriology, 5, Article 1921669. https://doi.org/10.3389/fbrio.2026.1921669

Image Credits: AI Generated

DOI: 10.3389/fbrio.2026.1921669

Keywords: artificial intelligence, microbial biotechnology, food security, CRISPR, precision fermentation, soil health, machine learning, biofertilizers, crop resilience, Frontiers in Bacteriology, Artificial, intelligence

At the heart of the biological argument is a reframing of the soil itself. For most of modern agricultural history, the soil microbiome was treated as passive background. The review positions it instead as a primary determinant of agroecosystem sustainability, with bacteria, fungi, archaea and protozoa driving nutrient cycling, plant growth regulation, disease suppression and resilience to drought and salinity. Through biological nitrogen fixation, phosphorus solubilization and organic matter decomposition, these communities regulate the very nutrients on which rice depends, while also shaping root development, hormonal balance and immune responses. Crucially, the authors stress that microbial abundance alone tells researchers little; the future depends on deciphering microbial function, not merely cataloguing microbial diversity.

One of the most striking mechanisms involves plant growth-promoting rhizobacteria equipped with the enzyme ACC deaminase. When rice plants experience drought, salinity or heavy metal stress, they accumulate ethylene, a stress hormone that in excess stunts root growth and accelerates senescence. ACC deaminase-producing bacteria, including species of Pseudomonas and Bacillus, degrade ACC, the immediate precursor of ethylene, into ammonia and alpha-ketobutyrate. This biochemical intervention keeps roots elongating and taking up water under conditions that would otherwise shut them down. The bacteria also prime antioxidant defences, inducing enzymes such as catalase and superoxide dismutase that neutralize the reactive oxygen species responsible for damaging membranes, proteins and DNA during stress.

The review highlights a decisive shift away from single-strain inoculants, which often perform brilliantly in the laboratory but inconsistently in the field, toward synthetic microbial communities, or SynComs, that combine organisms with complementary metabolic functions. The evidence is compelling. In a greenhouse pot experiment, a SynCom of Azotobacter, Azospirillum and Bradyrhizobium strains derived 51.6 percent of root nitrogen from atmospheric fixation, compared with 25 to 45 percent for individual bacteria. In acidic field conditions, a consortium of aluminium-resistant bacteria raised single-panicle rice yields by 26.36 percent by easing soil acidification and aluminium toxicity. In Vietnam, inoculation with Gluconacetobacter diazotrophicus supported normal growth and yield with just 50 kilograms of nitrogen per hectare, half the conventional rate. Metagenomics now allows researchers to identify the gene markers behind nitrogen fixation, phosphate solubilization and siderophore production, moving the field from descriptive diversity studies toward predictive, function-oriented microbiome engineering.

The biological toolkit extends well beyond fertilization. Microbial biocontrol agents suppress pathogens through antibiosis, nutrient competition, niche exclusion and induced systemic resistance. Disease-suppressive soils rely on specialized metabolites such as 2,4-diacetylphloroglucinol, which disrupts fungal cellular processes; lipopeptides, which compromise pathogen membranes; and hydrocyanic acid, which interferes with respiration. Entomopathogenic fungi like Beauveria bassiana and Metarhizium anisopliae penetrate insect cuticles and kill major rice pests, including the brown planthopper and stem borers, with minimal harm to non-target organisms. Delivery, however, remains the weak link: encapsulation in alginate, chitosan or gum Arabic protects inoculants from desiccation and ultraviolet radiation, and in one rice study, alginate-encapsulated Priestia aryabhattai boosted plant dry mass by 74.9 percent and nitrogen uptake by 86.1 percent compared with free cells.

On the engineering side, the review catalogues a digital transformation that is already reshaping rice paddies. Unmanned aerial vehicles fitted with multispectral and hyperspectral sensors can estimate chlorophyll content, biomass and nitrogen status before deficiencies become visible. In field experiments in Southwest China, UAV remote sensing combined with a random forest model predicted the rice nitrogen nutrition index with R-squared values reaching 0.97, enabling targeted top-dressing recommendations. Normalized Difference Vegetation Index-guided systems direct urea and diammonium phosphate to nutrient-deficient zones, cutting runoff and waste. Digital twin models go further, integrating real-time environmental data with metatranscriptomic information on microbial gene expression, so that irrigation and fertilization decisions account for rhizosphere biology as well as soil moisture.

Water and energy innovations complete the non-microbial picture. Alternate wetting and drying irrigation, in which fields are deliberately allowed to dry between floodings, reduced methane emissions by 47.47 percent in a global meta-analysis spanning 93 percent of world rice production, though nitrous oxide emissions rose by 52.20 percent, and severe drying cut grain yields by 22.6 percent. Mild AWD, by contrast, maintained yields while saving 23.4 percent of water. Solar-powered irrigation systems delivered a higher benefit-cost ratio than diesel pumps in Bangladeshi Boro rice production, while rice husk gasification converts residues that would otherwise be burned into electricity and heat. Biochar emerges as a bridge between the two worlds: its porous structure sequesters carbon, retains nutrients and, critically, acts as a biological scaffold that shelters introduced microbial consortia in the field.

The authors are candid about the bottlenecks. Microbial inoculants still fail unpredictably outdoors because of priority effects, niche exclusion and competition with native communities, and their recruitment patterns shift across plant developmental stages, undermining one-size-fits-all products. Host genotype matters enormously: a formulation tuned to one cultivar’s root exudates may colonize poorly on another, and a line bred for acidic soils may fail in saline paddies. Genome-edited microorganisms promise precision but raise biosafety questions about horizontal gene transfer and face fragmented regulation, with the European Union, the United States and India each applying different oversight frameworks. On the digital side, high equipment costs, weak rural connectivity and limited digital literacy exclude precisely the smallholder farmers who need these tools most; a Malaysian survey found middle- and high-income farmers 20 to 22 percent more willing to pay for IoT technologies than their lower-income peers.

The review’s central message is that integration, not replacement, will define the future of rice. Sensor networks can identify where inoculants are most likely to establish; AI-driven decision-support systems can time applications to coincide with favourable soil moisture and nutrient conditions; biochar and conservation tillage can create habitats that keep engineered communities alive; and CRISPR-assisted breeding can produce rice varieties that actively recruit beneficial microbes through tailored root exudates. Emerging directions include stress-responsive SynComs designed to persist through drought and flooding, methanotrophic bacteria that oxidize methane before it escapes paddies, and circular systems in which straw becomes biochar, biochar carries the microbes, and the microbes feed the next crop. Policy will determine the pace: Vietnam’s One Million Hectares of High-Quality and Low-Emission Rice programme, backed by the International Rice Research Institute, shows how national green-growth strategies can pull these technologies from the laboratory into millions of fields. If the authors are right, the next green revolution will not be written in a single molecule, but in the coordinated choreography of genomes, microbes, satellites and sunlight.

Subject of Research: Integrated microbiome and green technologies for sustainable rice production

Article Title: Integrated Microbiome and Green Technologies for Sustainable Rice Production: Current Advances, Challenges and Future Perspectives

Article References: Aminurrasyid, A. H., Nadarajah, K. K., & Ikmal, A. M. (2026). Integrated Microbiome and Green Technologies for Sustainable Rice Production: Current Advances, Challenges and Future Perspectives. Journal of Agriculture and Food Research, Article 103359. https://doi.org/10.1016/j.jafr.2026.103359

Image Credits: AI Generated

DOI: 10.1016/j.jafr.2026.103359

Keywords: rice, microbiome, SynComs, biofertilizers, precision agriculture, alternate wetting and drying, biochar, CRISPR, methane emissions, solar irrigation, digital agriculture, sustainable farming

The study, published in the journal Current Research in Biotechnology, addresses a pressing agricultural dilemma. Conventional rice farming depends heavily on synthetic fertilizers and chemical pesticides, which deliver rapid results but degrade soil structure, reduce microbial diversity, and accumulate toxic residues and heavy metals such as zinc in soil and water. Organic farming, by contrast, avoids these inputs and supports beneficial soil microorganisms, but often yields less in the short term. As fertilizer costs climb and global supply chains wobble, the search for sustainable alternatives has intensified, and one of the most promising candidates is a group of soil bacteria known as plant growth-promoting rhizobacteria, or PGPR.

These bacteria occupy the narrow zone of soil surrounding plant roots, where they promote growth through several well-characterized mechanisms. Some fix atmospheric nitrogen into a biologically usable form, effectively manufacturing fertilizer on site. Others solubilize insoluble phosphates, unlocking a nutrient that plants otherwise cannot access, since most soil phosphorus exists in mineral forms unavailable for direct uptake. Still others produce indole-3-acetic acid, or IAA, an auxin hormone that stimulates root elongation, lateral root formation, and root hair development, thereby improving the plant’s capacity to take up water and nutrients. Bacteria combining these traits have been shown in previous studies to enhance the growth and grain yield of maize and rice, and even to help plants tolerate heavy metal contamination in soils.

To capture the full picture of who lives in the Sangyod rhizosphere, the researchers turned to Oxford Nanopore sequencing, a long-read technology that reads entire stretches of DNA in one pass. They collected rhizosphere soil from three organic and three chemically cultivated Sangyod fields, all located within a few hundred meters of one another in Tamode District, and extracted DNA using a bead-beating lysis protocol. Sequencing on a GridION instrument generated between roughly 91,000 and 175,000 raw reads per sample, corresponding to 149 to 297 megabases of sequence data. After quality filtering, which raised the median read length from under about 1,000 base pairs to between roughly 2,400 and 2,900 base pairs, the reads were classified taxonomically using Kraken2 and abundance was estimated with Bracken, with stringent mapping checks to remove any reads from human, rice, or contaminant sources.

The taxonomic results revealed a community dominated by two bacterial phyla: Pseudomonadota, which accounted for roughly 42 to 53 percent of classified reads, and Actinomycetota, which made up roughly 31 to 43 percent. At the genus level, Streptomyces reigned supreme in every single sample, comprising 21 to 31 percent of reads, followed by Bradyrhizobium, a genus famous for its nitrogen-fixing symbioses. At the species level, the community fragmented into a long tail of taxa, with Pseudomonas putida, Stenotrophomonas maltophilia, Pseudomonas aeruginosa, and Sorangium cellulosum among the most abundant individually represented species. Interestingly, the organic fields showed numerically higher richness and Shannon diversity than the chemical fields, but none of these differences reached statistical significance, suggesting that at the sequencing depth achieved, the two cultivation systems hosted broadly similar bacterial communities.

Metagenomics, however, only tells you who is present, not what they can do. To bridge that gap, the team cultivated bacteria from the soil on two different media: nutrient agar, a general-purpose medium, and yeast extract mannitol agar, a semi-selective medium designed to favor rhizobacteria with nitrogen-fixing potential. From these plates they recovered 18 isolates from YEM agar and 56 from nutrient agar, and subjected all 74 to a battery of functional screens. The results were striking. Sixteen of the 18 YEM isolates, and all 56 nutrient agar isolates, grew on nitrogen-free medium, a preliminary indication of nitrogen-fixing ability. IAA production was detected in every single isolate, with concentrations ranging from under 2 micrograms per milliliter to a remarkable 83.12 micrograms per milliliter in one nutrient agar isolate.

Phosphate solubilization proved rarer but no less interesting. On Pikovskaya agar, where a clear halo around a colony signals the dissolution of insoluble calcium phosphate, 14 of the YEM isolates and 15 of the nutrient agar isolates tested positive. The standout was SSY16, a YEM-derived isolate with a phosphate solubilization index of 1.80, the highest recorded in the study. Molecular identification based on 16S rRNA gene sequencing revealed that SSY16 most closely matches Streptomyces sp. PB-64, with 99.56 percent sequence identity, and phylogenetic analysis placed it firmly within the Streptomyces lineage. This finding carries a satisfying symmetry: the most abundant genus in the metagenomic dataset was also the source of the most powerful phosphate solubilizer recovered in culture, hinting at consistency between the two approaches.

Notably, SSY16 could be grown on YEM medium but was never recovered on nutrient agar, a detail the authors highlight as evidence that culture medium choice fundamentally shapes which rhizobacteria are captured and tested. Streptomyces species are renowned for producing bioactive compounds, including antibiotics, volatile metabolites, and siderophores, iron-scavenging molecules that enhance plant iron nutrition and suppress pathogens by competing for iron. Meanwhile, the highest IAA producer, isolate SSN43, was closely related to Bacillus subtilis subsp. stercoris, while other top performers included relatives of Bacillus stratosphericus, Cytobacillus firmus, Priestia megaterium, and Paenibacillus polymyxa, all genera with documented plant growth-promoting credentials.

The final challenge was compatibility. A bacterial consortium only works if its members cooperate rather than fight. Using a reciprocal agar disc diffusion assay, the researchers tested the six highest IAA-producing isolates against SSY16, the primary phosphate solubilizer. Three isolates, SSN17, SSN28, and SSN43, produced clear inhibition zones against SSY16 in one or both directions, with the strongest antagonism coming from SSN28, a Bacillus altitudinis relative that generated an inhibition radius of over 5 millimeters. But three others, SSN34, SSN18, and SSN52, showed no detectable antagonism in either reciprocal combination. SSN34, which produced 38.96 micrograms per milliliter of IAA and grew on nitrogen-free medium, emerged as the leading candidate to pair with SSY16, with SSN18 and SSN52 as secondary options.

The authors are careful to frame these results as preliminary. The agar-based antagonism assay reflects only in vitro conditions, the sequencing depth was limited relative to the staggering diversity of soil, and the culture conditions, two media, one temperature, and short incubation periods, inevitably captured only a subset of the total microbial community. Growth on nitrogen-free medium indicates potential nitrogen fixation but does not confirm it biochemically. The real test will come in co-culture experiments, greenhouse trials, and eventually field validation, where the candidate consortium must prove it can boost Sangyod rice growth under real plant-associated conditions. Still, the study offers a compelling template for sustainable agriculture: by combining the census power of long-read metagenomics with the functional precision of targeted cultivation, researchers can move from anonymous soil DNA to named, characterized, and compatible bacterial partners, bringing the vision of microbe-powered rice farming one step closer to the paddy.

Subject of Research: Rhizosphere microbiome and plant growth-promoting rhizobacteria of Sangyod rice under organic and chemical cultivation

Article Title: Integrated shotgun metagenomic and culture-based characterization of plant growth-promoting rhizobacteria associated with Sangyod Rice

Article References: Rangchai, J., Moolika, N., Chanasongkhram, K., Sathapondecha, P., Iewkittayakorn, J., & Sangket, U. (2026). Integrated shotgun metagenomic and culture-based characterization of plant growth-promoting rhizobacteria associated with Sangyod Rice. Current Research in Biotechnology, Article 100427. https://doi.org/10.1016/j.crbiot.2026.100427

Image Credits: AI Generated

DOI: 10.1016/j.crbiot.2026.100427

Keywords: Sangyod rice, plant growth-promoting rhizobacteria, shotgun metagenomics, Oxford Nanopore sequencing, rhizosphere microbiome, phosphate solubilization, indole-3-acetic acid, nitrogen fixation, Streptomyces, Bacillus, biofertilizers, sustainable agriculture

To understand why this pairing matters, it helps to look at what each partner brings to the table on its own. Nano-micro materials, or NMMs, are particles engineered at scales ranging from a few nanometers to several micrometers. Because of their tiny size and enormous surface-to-volume ratio, they can deliver nutrients such as zinc, iron, selenium, and silicon directly to plant tissues with remarkable efficiency, and they can serve as slow-release carriers for agrochemicals. Studies cited in the review show that nanomaterials can improve plant mineral nutrition and reduce the environmental losses that plague conventional fertilizers. Plant growth-promoting bacteria, or PGPB, meanwhile, are living soil microbes that help plants through an entirely different toolkit: they fix atmospheric nitrogen, dissolve insoluble phosphates, produce siderophores that scavenge iron, and secrete hormones such as indole-3-acetic acid that stimulate root growth. These bacteria are the workhorses of the rhizosphere, the narrow zone of soil surrounding plant roots where an intense exchange of nutrients and chemical signals takes place.

Yet both technologies carry well-documented limitations that have slowed their adoption. Nanomaterials can be ecotoxic at certain doses: silver, copper oxide, and titanium dioxide nanoparticles have all been shown to disrupt soil microbial communities, damage bacterial DNA, and shift the composition of the rhizosphere microbiome in ways that are not always benign. PGPB, for their part, are fragile. When they are applied to fields as seed coatings or soil inoculants, they often fail to survive the harsh transition from the laboratory to the soil, where drought, ultraviolet radiation, competition from native microbes, and oxidative stress can wipe out inoculated populations before they ever establish a foothold. Low survival and inconsistent colonization have long been the Achilles heel of biofertilizer technology, and the review identifies this as one of the central problems the combined approach can solve.

The first pillar of the synergy runs in one direction: nanomaterials can act as bodyguards and performance enhancers for the bacteria. The review documents several mechanisms behind this protective effect. Silica particles have been shown to trigger the production of exopolysaccharides, the slimy protective polymers that bacteria secrete to shield themselves from desiccation, which in turn helped rhizobacteria boost wheat biomass in drought-stressed soils. Multiwalled carbon nanotubes promoted biofilm formation and rhizosphere colonization by Bacillus subtilis, giving the bacteria a structural advantage in the competitive root zone. Titanium dioxide nanoparticles aided the clustering and adhesion of beneficial bacteria to plant roots, while nano-titania treatments enhanced the overall performance of growth-promoting rhizobacteria in field-relevant conditions. In effect, the particles create a microenvironment in which the microbes can persist long enough to do their job.

Nanomaterials do not merely protect the bacteria; they can also regulate their metabolism in ways that make them more useful to plants. The review highlights experiments in which chitosan and gold nanoparticles augmented the production of indole-3-acetic acid by rhizospheric Pseudomonas aeruginosa, amplifying the hormone signal that drives root elongation. Zinc oxide nanoparticles induced exopolysaccharide production by Bacillus subtilis strains intended for arid soil applications, improving their drought resilience. Iron-carbon nanofibers coated with acylated homoserine lactones, bacterial signaling molecules, modulated the soil microbiome to enhance chickpea growth and suppress fusarium wilt. These findings suggest that carefully chosen particles can act as metabolic dials, tuning bacterial behavior toward the traits farmers actually need, whether that is hormone production, nutrient solubilization, or disease suppression.

The second pillar of the synergy runs in the opposite direction: bacteria can detoxify and stabilize nanomaterials, mitigating the very ecotoxicity that has raised concerns about their use. Bacterial metabolites have been shown to determine the biotransformation of cerium oxide nanomaterials in soil, altering their fate and potentially their hazard profile. Mineral-dissolving rhizobacteria can biotransform zinc oxide particles, converting them into bioavailable forms that stimulate plant growth and mineral uptake in sunflower while reducing the free-particle toxicity that would otherwise harm soil life. By improving the antioxidant capacity of the plant-microbe system and sequestering reactive particle surfaces, PGPB can buffer the soil ecosystem against the dose-dependent harms of engineered nanoparticles. This reciprocal rescue is what elevates the combination from a simple mixture to a genuine mutualism.

Beyond protecting each other, the two technologies can strike shared targets simultaneously, and the review devotes considerable attention to two of them: heavy metal stress and nutrient biofortification. Cadmium contamination is a growing crisis in agricultural soils, particularly in parts of Asia where industrial runoff and phosphate fertilizers have loaded rice paddies and vegetable plots with the toxic metal. Studies compiled in the review show that combining nanomaterials with PGPB promotes plant growth and phytoremediation in cadmium-contaminated soil more effectively than either approach alone. Bacillus mycoides paired with titanium dioxide nanoparticles enhanced the morphological, physiological, and biochemical attributes of barley under cadmium stress, while similar combinations improved cotton growth and cadmium extraction from contaminated fields. On the salinity front, zinc oxide nanoparticles combined with plant growth-promoting rhizobacteria strengthened salt tolerance and productivity of wheat irrigated with saline water in sodic-saline soil, and silicon nanoparticles paired with beneficial bacteria have emerged as a strategy for mitigating salt stress across multiple crops.

The biofortification story is equally compelling. Roughly a third of the world’s agricultural soils are zinc deficient, and the crops grown in them deliver insufficient micronutrients to the people who eat them. Iron nanoparticles combined with a plant growth-promoting rhizobacterium enhanced nitrogen fixation in alfalfa by linking root metabolites to rhizosphere microbiome assembly, a finding that points to a deep mechanistic coupling between particle chemistry, root exudation, and microbial community structure. Next-generation biofertilizers in which PGPB are coated with nanoparticles have been shown to enhance nutrient uptake and wheat growth, and biosynthesized selenium nanoparticles have been used to recruit beneficial soil microbes to plant roots, effectively turning the particle itself into a microbial attractant. The review frames these results as evidence that NMM-PGPB combinations could underpin an entirely new class of fertilizer formulations.

Translating laboratory synergy into field-ready products remains the hard part, and the authors are candid about the challenges. Formulation science borrowed from other fields offers a starting point: single-cell nanocoatings developed to protect probiotics in the human gut, hydrogels that shield rhizobacteria in acidic soil, and alginate-bentonite capsules enriched with titanium nanoparticles that protect biocontrol bacteria against Rhizoctonia solani on bean all demonstrate that encapsulation technologies can keep microbes alive through storage, application, and early colonization. Nano-bio fertilizer capsules and nanoparticle-coated seed coatings are already being prototyped. But the review stresses that dose, particle size, surface chemistry, soil texture, and exposure duration all determine whether a given nanomaterial helps or harms the soil microbiome, and long-term ecotoxicological data across diverse soils remain sparse. Regulatory frameworks for nano-enabled biological fertilizers are still in their infancy in most jurisdictions.

Even so, the trajectory is clear enough that the authors anticipate growing research interest and new commercial opportunities in NMM-PGPB fertilizers. The logic of the partnership is elegant: the particles give the bacteria armor, nutrition, and a foothold on the root; the bacteria give the particles a safety net and a biological amplifier; and together they address stress, contamination, and nutrient deficiency with far less chemical input than conventional agriculture requires. As climate change intensifies droughts, salinization, and soil degradation, technologies that make crops more resilient while rebuilding soil biology will only grow in importance. If the remaining questions about dosage, ecology, and regulation can be answered, the marriage of nanomaterials and beneficial bacteria may prove to be one of the defining agricultural innovations of the coming decades, quietly rewriting the chemistry of the rhizosphere one particle and one microbe at a time.

Subject of Research: Synergistic interactions between nano-micro materials and plant growth-promoting bacteria for sustainable agriculture

Article Title: Nano-micro materials and plant growth-promoting bacteria: synergy for sustainable agriculture

Article References: Ren, Y., Kou, X., Shen, X., Liu, X., Huang, X., Liu, S., Chen, R., Ma, H., & Cheng, Y. (2026). Nano-micro materials and plant growth-promoting bacteria: synergy for sustainable agriculture. Plant and Soil. https://doi.org/10.1007/s11104-026-09112-3

Image Credits: AI Generated

DOI: 10.1007/s11104-026-09112-3

Keywords: nano-micro materials, plant growth-promoting bacteria, biofertilizers, rhizosphere, cadmium stress, salinity tolerance, nutrient biofortification, nanoparticle ecotoxicity, sustainable agriculture, soil microbiome, phytoremediation, encapsulation

The collection is organized around four themes, and the first concerns a deceptively simple question: how do microbial communities respond when their environment is stressed? The answer, according to the assembled studies, is that responses are highly uneven and context-dependent. In tropical oil palm plantations, fungal succession during litter decomposition was shown to control the release of nitrogen and the ability of roots to acquire it, illustrating how decomposer communities underpin nutrient cycling even in managed ecosystems. In the liverwort Marchantia polymorpha, human disturbance of habitats shifted fungal endophyte communities toward phosphorus-acquiring functional traits, an apparent adaptive response to nutrient limitation.

Resilience, rather than collapse, was the story in other systems. Sediment microbial communities in a mangrove estuary remained relatively stable despite fluctuating external conditions, reflecting an inherent robustness to environmental change. In farmland, a maize-soybean rotation under drip fertigation was dominated by ammonia-oxidizing microorganisms, including comammox bacteria, which significantly shaped nitrogen cycling in the soil. Meanwhile, drought and shifting soil moisture restructured the rhizosphere microbiomes of maize, common beans and peanuts, changes that appeared to help the plants manage water stress. Together, these studies provide an ecological foundation for the idea that microbiome-mediated stress adaptation is a general phenomenon, not a laboratory curiosity.

The second theme moves from ecology to mechanism: how exactly do microbes promote plant growth and stress tolerance? Several papers converged on a sobering conclusion for the biofertilizer industry. The effectiveness of microbial inoculants depended largely on the nutrient status of the soil, meaning that a product that works brilliantly in one field may fail in another. This points toward site-specific microbial interventions rather than one-size-fits-all formulations. Nutrient management itself was shown to shape microbial function, with banded application of ammonium polyphosphate enhancing phosphorus availability, bacterial diversity and maize productivity, while long-term fertilization experiments revealed that climate and fertilizer inputs jointly regulate microbial carbon and phosphorus limitation.

Some of the most striking results involve seed priming and quality enhancement. Coating chickpea seeds with the fungus Trichoderma asperellum reshaped the rhizosphere community, enriching free-living nitrogen-fixing bacteria and improving nitrogen uptake in the offspring plants even under salinity and pathogen pressure. In tea, a bio-organic fertilizer based on Bacillus megaterium improved crop quality by stimulating the biosynthesis of amino acids and flavonoids through microbiome-mediated regulation. Arbuscular mycorrhizal fungi emerged as versatile defenders, mitigating arsenic toxicity through multiple physiological and molecular mechanisms, while novel Pseudomonas isolates showed promise for promoting eucalyptus growth under environmental stress. A review of plant growth-promoting fungi rounded out the picture of how fungal partners can enhance plant fitness across systems.

The third theme tackles biotic stress, the constant threat posed by pathogens. One particularly elegant study in pigeonpea showed that volatile organic compounds produced by Bacillaceae bacteria from the rhizosphere reduced Fusarium wilt through two routes at once: direct antifungal activity against the pathogen and indirect priming of the plant’s own defenses. This dual mechanism highlights how chemical conversations between microorganisms can shape biocontrol, and it suggests that microbial metabolites themselves could become tools for crop protection, reducing reliance on synthetic fungicides.

Protection, however, is not only about single strains. Disease suppressiveness was shown to emerge as a property of entire microbial communities, with organic farming practices promoting rhizosphere microbiome configurations associated with enhanced general disease suppression in mustard. Environmental isolates of Pseudomonas suppressed the honey fungus pathogen Armillaria mellea while simultaneously promoting plant growth through microbiome-mediated effects. The implication is that plant protection operates across multiple levels, from specific antagonistic chemicals to community-scale suppression, and that farming practices which nurture diverse communities may quietly build disease-resistant soils.

The fourth and largest theme addresses abiotic stress, and here the range of crops and interventions is remarkable. Beneficial microbial inoculants and microbiota-enhancing amendments improved plant performance under water limitation in bell pepper, potato, pearl millet, coffee and lentil. In one visually compelling experiment, potato plants inoculated with the arbuscular mycorrhizal fungus Glomus or with Bacillus species grew markedly better under drought-induced soil water deficit than non-inoculated drought-treated plants, approaching the vigor of controls grown under optimal conditions. Other combinations proved synergistic: in lentil, silicon application combined with non-rhizobial bacterial co-inoculation enhanced resilience to water deficit, while in pearl millet, copper oxide nanoparticles paired with plant growth-promoting rhizobacteria boosted drought tolerance.

Salinity and soil degradation received equal attention. Bacterial inoculation improved the phytoremediation of saline soils by Atriplex nummularia, and iron-modified biochar enhanced cotton growth in saline-alkali soil by reducing salinity and facilitating root colonization by beneficial bacteria. Waste-derived amendments also played a role: black soldier fly larvae frass combined with wheat straw biochar supported bell pepper growth, soil fertility and rhizosphere bacterial communities under water stress. Even the environmental footprint of irrigation technology came under scrutiny, with biodegradable film drip fertigation shown to reduce the diversity and abundance of antibiotic resistance genes in soil compared with plastic film systems, a reminder that agricultural microbiomes are shaped by every input and practice.

The outlook offered by the editors is cautiously ambitious. Key challenges remain in predicting microbiome function across environments, translating laboratory findings into robust field applications, and scaling solutions across crops and production systems. Yet the collective evidence points toward a shift from merely describing microbiome ecology to actively harnessing it, integrating microbial ecology with nutrient management to build resilient and productive cropping systems. The special issue’s Marschner review goes further, recommending systems-level integration of plant microbiome engineering, metabolic innovations, tailored agronomic practices and supportive policy frameworks. If that integration succeeds, the invisible communities in the world’s soils may become one of agriculture’s most powerful allies against the environmental stresses of the coming decades.

Subject of Research: Use of soil and plant microbiomes to alleviate environmental stresses in agriculture

Article Title: Harnessing soil and plant microbiota to alleviate environmental stresses

Article References: Sharma, S., Jelsbak, L., Singh, A., Ghosh, A., & Lozano-Andrade, C. N. (2026). Harnessing soil and plant microbiota to alleviate environmental stresses. Plant and Soil. https://doi.org/10.1007/s11104-026-09128-9

Image Credits: AI Generated

DOI: 10.1007/s11104-026-09128-9

Keywords: soil microbiome, plant microbiota, drought stress, salinity, biofertilizers, biological control, arbuscular mycorrhizal fungi, plant growth-promoting rhizobacteria, sustainable agriculture, nutrient cycling, disease suppression, climate resilience

Plants are never truly alone. Their roots, leaves, and surrounding soil harbor a dense and diverse array of microorganisms that influence nearly every aspect of plant life, from nutrient uptake to immune signaling. These microbial partners help plants absorb minerals, fend off pathogens, and adapt to environmental stresses. As human-induced climate change intensifies, bringing with it more frequent heat waves and prolonged droughts, crop yields have suffered, and researchers have increasingly turned to biofertilizers — preparations of beneficial rhizosphere microorganisms — as a biological alternative or supplement to chemical inputs. The idea is elegant in principle: harness the microbes that plants already cooperate with in nature and deploy them deliberately in the field.

In practice, however, single-strain biofertilizers have proven fragile. A lone microorganism introduced into a crop’s root zone must survive in an environment that fluctuates dramatically in temperature, moisture, nutrient availability, and competition from resident microbes. Many inoculants fail to establish themselves, and even those that persist often lose their functional benefits over time. This fragility has pushed scientists toward a more sophisticated strategy: defined microbial communities, or DMCs, in which multiple microorganisms are deliberately combined. Within such communities, members influence one another’s survival and activity, exchanging metabolites and creating ecological niches that can make the whole assemblage more stable and resilient than any of its parts.

Yet designing an effective DMC is far from straightforward. The composition and function of a microbial community shift depending on the plant-specialized metabolites secreted by the host and on prevailing environmental conditions. A community that thrives under laboratory conditions may collapse in the field, or a combination that benefits one crop variety may do nothing for another. The number of possible combinations of bacterial strains and metabolites is astronomically large, making conventional trial-and-error experimentation impractical. It was precisely this combinatorial explosion that motivated the Kyoto University team to seek a rational, predictable method for community design — one grounded in data rather than intuition.

Co-corresponding author Akifumi Sugiyama of Kyoto University explained the conceptual shift behind the work. “I became particularly interested in moving beyond simple one-to-one relationships to understand how these metabolite-mediated interactions unfold within the diverse microbial communities found in soil, and how they influence plant growth,” he said. Rather than studying individual microbe-plant pairs in isolation, the team set out to capture the web of interactions that emerges when multiple bacteria and plant metabolites coexist — the kind of complexity that determines whether a microbial community actually helps a crop or quietly fades away.

The experimental design was methodical. The researchers first isolated bacteria from the roots of tomato plants, ensuring that the strains they worked with were natural associates of their target crop. They then combined nine types of bacteria and two types of plant metabolites in various patterns to create a panel of defined microbial communities. These communities were inoculated onto tomato roots, and the plants were cultivated at varying temperatures. By systematically varying both the community composition and the growth conditions, the team generated a rich dataset linking microbial assemblages, metabolites, temperature regimes, and plant performance.

The analytical engine of the study was a machine-learning model built with the elastic net regression algorithm, a technique well suited to datasets in which many predictor variables are correlated with one another — a hallmark of ecological data. Trained on the experimental results, the model learned to predict the aboveground fresh weight of tomato plants, a key indicator of growth, from the composition of the microbial community and the environmental conditions. Once validated, the model could be run in reverse: instead of predicting the outcome of a given community, the researchers could ask the algorithm to design a new community predicted to have a strongly positive effect on tomato growth.

The algorithm’s recommendation proved its worth. A defined microbial community designated DMC G2, composed of six bacterial strains together with the metabolite tomatine, promoted tomato growth in laboratory tests and, crucially, improved the plants’ tolerance to high-temperature stress. The team then took the experiment outdoors, cultivating tomatoes in field-like conditions to see whether the benefits would survive contact with the messiness of the real world. They did: outdoor trials showed that DMC G2 significantly increased the aboveground fresh weight of the tomatoes, and gene expression analysis revealed molecular signatures of enhanced high-temperature tolerance in the treated plants. The combination of growth promotion and stress tolerance in a single, rationally designed community is what makes the result notable.

Achieving this level of rigor demanded extraordinary experimental discipline. “We needed to cultivate tomatoes under a wide variety of conditions with high precision, so I would like to thank the team members who carried out these repetitive yet exacting experiments over a period of approximately two years,” Sugiyama said. The two-year effort underscores a central reality of this emerging field: machine learning can dramatically narrow the search space of possible microbial combinations, but generating the high-quality training data that such models require still depends on meticulous, labor-intensive plant cultivation and measurement under controlled and varied conditions.

The broader implications extend well beyond tomatoes. The study demonstrates that data-driven microbial community design can improve crop stress tolerance, and the authors emphasize that their versatile methods are expected to extend broadly to other crops, holding significant potential for enabling sustainable agriculture. As climate change continues to erode yields and conventional agricultural inputs face mounting environmental scrutiny, the ability to rationally engineer plant-associated microbiomes — predicting, rather than guessing, which combinations of bacteria and metabolites will help a crop thrive — could become a cornerstone of resilient farming systems. The tomato, in this telling, is not just a crop but a proof of concept: evidence that the invisible ecosystems around plant roots can be understood, modeled, and ultimately designed to humanity’s benefit.

Subject of Research: Machine learning-guided design of defined microbial communities to enhance tomato plant growth and heat-stress tolerance

Article Title: Optimizing tomato plant growth with microbes

Article References: Optimizing tomato plant growth with microbes. (n.d.). Original publication

Image Credits: AI Generated

DOI: Not provided

Keywords: tomato, microbial communities, machine learning, biofertilizers, plant growth, heat stress tolerance, rhizosphere, elastic net regression, tomatine, sustainable agriculture, Kyoto University, synthetic ecology

The scale of the partnership is staggering. An estimated 250,000 plant species depend on mutualistic associations with approximately 50,000 distinct fungal species. Under nutrient-deficient conditions, mycorrhizal symbioses can mediate the transfer of up to eighty percent of the phosphorus and nitrogen a host plant requires. The mechanism is elegantly physical: the fungi extend a web of extraradical hyphae far beyond the nutrient depletion zone that surrounds roots, dramatically expanding the absorptive surface area available to the plant. In exchange, the plant supplies carbohydrates and, crucially, lipids, because arbuscular mycorrhizal fungi are lipid auxotrophs that cannot synthesize their own fatty membranes without host support. This carbon-for-nutrient trade, negotiated inside specialized fungal structures called arbuscules that form within root cortex cells, is one of the most consequential biological exchanges on the planet.

The review emphasizes that the benefits ripple far beyond individual plants. Fungal hyphae and their glycoprotein exudates, notably glomalin-related soil protein, act as biological binding agents that enmesh soil particles into stable macroaggregates. This aggregation improves aeration, water retention, and erosion resistance, and it physically encapsulates soil organic matter, shielding it from rapid enzymatic degradation and locking carbon into long-term terrestrial reserves. By transferring photosynthetic carbon into the soil and modulating microbial community dynamics, mycorrhizal fungi influence the global carbon cycle, and researchers argue that integrating them into community and ecosystem models is essential for understanding terrestrial carbon storage and climate mitigation potential.

Perhaps the most conceptually rich section of the review concerns the mycorrhizosphere, the zone of soil influenced by fungal hyphae, which the authors frame as a dynamic interaction hub rather than a passive conduit. Fungal networks create continuous moisture films, so-called fungal highways, that allow motile bacteria to traverse otherwise impassable dry soil micropores. Carbon-rich fungal exudates selectively recruit bacterial consortia, including nitrogen-fixing diazotrophs and phosphate-solubilizing species such as Pseudomonas and Bacillus. These bacteria form biofilms on hyphae, secrete extracellular enzymes that mobilize recalcitrant nutrients, and produce phytohormones that stimulate root development. The fungus absorbs and translocates the mobilized nutrients to its host. Studies of the fungus Rhizophagus irregularis have shown that when coupled with synergistic soil microbiota, plant nitrogen uptake from organic matter can effectively double, a striking demonstration that the symbiosis is a multi-species collaboration rather than a simple two-partner deal.

The review also documents a defensive dimension that is often overlooked. Mycorrhizal colonization primes plant immune responses, enhancing both local and systemic defenses and accelerating the deployment of defense hormones and pathogenesis-related proteins. The fungi reshape the rhizosphere microbiome, enriching antagonistic taxa such as Pseudomonas, Bacillus, and Trichoderma that suppress pathogens through antibiosis, competition, and niche exclusion. Against plant-parasitic nematodes, among the most damaging agricultural pests worldwide, the effects can be dramatic: inoculation of coffee plants reduced root-knot nematode infection severity by up to 52.5 percent in one cited study, and in soybean rhizospheres, mycorrhizal presence fosters consortia of anti-nematode microbes, including fungal taxa that prey on the pests directly. Even grazing by fungivorous nematodes can stimulate fungal turnover and shift community composition in ways that ultimately enhance root colonization and plant nutrient uptake, illustrating the tangled, multi-trophic character of these soil food webs.

Yet the review is refreshingly candid about the limits of the mutualism. Mycorrhizal symbioses exist on a continuum that can shift toward antagonism or even parasitism under specific conditions. When soil phosphorus is already abundant, plants may reject their fungal partners, or the fungi may act as a carbon drain, siphoning up to twenty percent of the plant’s photosynthetically fixed carbon without delivering commensurate benefits. Low light intensity can tip the balance as fungal carbon demand outpaces a plant’s diminished photosynthetic capacity. Molecular work has identified the precise biochemical requirements for successful colonization, including complementation between plant-secreted and fungal lysin motif proteins, and physiological dysfunctions in model hosts such as Lotus japonicus can restructure entire root-associated fungal communities. The message is that context, not universal benevolence, governs the outcome of the partnership.

The authors also tackle the scientifically contested territory of common mycorrhizal networks, the hyphal links that can interconnect the roots of different plants and have been popularized as a kind of forest internet. The review acknowledges evidence that these networks can redistribute resources, transmit and possibly filter defense signals among connected plants, and influence competition and community dynamics. But it equally warns that claims of preferential resource allocation remain debated, that evidence for the ubiquity and exact functioning of these networks in natural settings is not yet conclusive, and that overinterpretation in some studies has led to the spread of misinformation. This calibrated stance, embracing the excitement of the field while policing its excesses, is one of the review’s most valuable contributions.

On the applied side, the potential is enormous but so are the obstacles. Field inoculation with commercial mycorrhizal products frequently fails to replicate greenhouse successes because natural soils impose complex biotic and abiotic filters. Indigenous fungal communities exert priority effects, occupying root and soil niches and competitively excluding introduced strains, while the broader soil microbiome can antagonize inocula through resource competition, antibiosis, or predation. Notably, the composition of the resident soil microbial community often predicts inoculation outcomes more reliably than soil fertility metrics, suggesting that site-adapted strain selection and integrated management, including conservation tillage, ground cover, and minimized synthetic phosphorus, matter more than simply adding spores. In restoration contexts, however, the results are encouraging: reintroducing native mycorrhizal communities has been shown to accelerate plant succession and improve native plant establishment, and mycorrhizal inoculation has improved root development and growth in degraded coal mine-subsided lands.

The review highlights further applications in phytoremediation, where mycorrhizal fungi enhance the extraction and stabilization of heavy metals and persistent organic pollutants. Inoculation of the arsenic-tolerant fern Pteris vittata significantly enhanced contaminant extraction from polluted soils, and combinations of mycorrhizal fungi, plant growth-promoting rhizobacteria, and earthworms improved lead bioaccumulation and plant health in Bermuda grass growing in lead-contaminated soil. The fungi protect plants from phytotoxicity, stimulate soil microbial activity, and improve soil structure through glomalin production, making them multipurpose agents in the cleanup and recovery of degraded land. The authors note, however, that research on emerging contaminants such as microplastics, antibiotics, and endocrine-disrupting chemicals remains limited, representing a significant frontier for future work.

Looking ahead, the review identifies clear priorities: long-term, multi-site field trials; trait-based approaches linking fungal characteristics to plant performance; mechanistic studies of carbon and nutrient exchange that reconcile competing models of how the trade is regulated; and systematic assessment of agronomic and economic benefits to translate research into routine farmer practice. Invasive species, which disrupt native mycorrhizal communities and reduce fungal richness, demand particular attention to temporal dynamics and post-invasion restoration. What emerges from this synthesis is a portrait of an ancient symbiosis that is neither a miracle cure nor a mere curiosity, but a foundational ecological process whose careful stewardship, through organic and low-input farming, conservation of fungal biodiversity, and scientifically grounded inoculation, could underpin more resilient agriculture and healthier ecosystems in a changing climate. The fungi have been holding the biosphere together for hundreds of millions of years; the task now is to manage that partnership with the precision it deserves.

Subject of Research: The roles of arbuscular mycorrhizal fungi in plant nutrition, soil health, and ecosystem resilience

Article Title: Arbuscular mycorrhizal fungi support plant nutrition soil health and ecosystem resilience

Article References: Bhosale, K. S., Shinde, B. P., Ahire, S. V., Mankar, G. D., Salunke, T. R., & Sontakke, O. P. (2026). Arbuscular mycorrhizal fungi support plant nutrition soil health and ecosystem resilience. Discover Plants, 3(1), Article 387. https://doi.org/10.1007/s44372-026-00858-9

Image Credits: AI Generated

DOI: 10.1007/s44372-026-00858-9

Keywords: arbuscular mycorrhizal fungi, mycorrhizosphere, plant-microbe interactions, soil health, nutrient cycling, carbon sequestration, common mycorrhizal networks, nematode control, biofertilizers, phytoremediation, sustainable agriculture, ecosystem restoration