The review, authored by Debarshi Dasgupta of the Indian Agricultural Research Institute and North Dakota State University, synthesizes soil microbial ecology across five interconnected themes: the energy dynamics of soil food webs, rhizosphere plant-microbe interactions, the ecology of arbuscular mycorrhizal fungi, the biological regulation of nitrogen cycling, and the translation of soil biodiversity into ecosystem services. Its central contention is provocative: ecological theory already provides a sufficient conceptual basis for redesigning agroecosystems around microbial functionalities. The timing could hardly be more urgent. Close to one-third of the world’s soils are already moderately to severely degraded, and with the global population projected to reach approximately 9.7 billion by 2050, food systems must maintain or expand productivity precisely when the biological foundations of that capacity are in measurable decline.

One of the review’s most striking arguments concerns the architecture of the soil food web itself. Far from being an undifferentiated cloud of activity, the decomposer community is organized around two dominant energy channels that are functionally divergent in profound ways. The bacterial channel is fast: it thrives on labile, low carbon-to-nitrogen substrates such as fresh root exudates, drives rapid nutrient turnover, and dominates in tilled, heavily fertilized systems. The fungal channel operates more slowly, sustained by recalcitrant materials like lignin and cellulose, and produces stable compounds such as glomalin and melanin that bind soil particles into the macroaggregates essential for long-term carbon sequestration. Because fungal hyphae physically enmesh mineral particles, fungal-dominated communities build soil structure in ways bacterial communities cannot match.

The practical stakes of this distinction are illustrated by a comparative study of 60 grassland and arable sites across Europe, cited in the review, which found that the ratio of fungal to bacterial biomass predicted soil carbon storage and nitrogen retention more strongly than any single chemical property of the soil. Communities with higher fungal dominance were also significantly more resistant to drought-induced reductions in carbon mineralization. This identifies a genuine leverage point for farmers: the practices that promote fungal energy channels, including reduced tillage, continuous soil cover, high carbon-to-nitrogen organic inputs and diverse rotations, are precisely the practices that promote carbon sequestration and drought resilience. Long-term studies consistently show that intensive cultivation shifts communities from fungal toward bacterial dominance, with measurable consequences for soil carbon stocks and structural stability.

The review also highlights the understated role of grazing within the soil food web. Protozoa and nematodes that consume bacterial and fungal biomass excrete excess nitrogen as ammonium at every trophic transfer, effectively mineralizing organic nitrogen at each step of the food chain, a phenomenon known as the microbial loop. Because microbial populations exhibit logistic growth, moderate grazing pressure actually stimulates rather than suppresses microbial productivity, a principle called grazing optimization. From the plant’s perspective, the predatory community is therefore not merely a competitor for microbial biomass but a driver of the very nitrogen mineralization that feeds crop growth. Notably, a recent long-term field experiment manipulating nematode predation directly found that nematode addition increased multitrophic energy fluxes by between 5.9 and 169.4 percent, translating into higher soil multifunctionality, increased grain yield and greater root biomass. Conversely, a biocide application in a long-term corn-soybean system proved the most effective treatment at collapsing the soil’s natural suppressiveness to the soybean cyst nematode, a major yield-limiting pathogen, demonstrating that the biological community itself, not merely physical disturbance, confers disease suppression.

Among the most uncomfortable findings in soil ecology is how slowly these communities recover once simplified. Chronosequence studies show that while the first few years of transition to reduced tillage bring modest improvements in microbial biomass, the full reorganization of food web structure, including the recovery of fungal channels and the return of predatory arthropods and earthworms, can take a decade or more. A long-term experiment in the southern Coastal Plain of Georgia, tracking cotton fields from 4 to 25 years under no-till management, found that only the oldest fields had accumulated organismal abundance and species richness approaching undisturbed reference sites. The implication, the review stresses, is not an argument against ecological management but an argument for starting immediately, because ecological benefits compound slowly and ecological debts are repaid on the same slow timescale.

The rhizosphere, the narrow zone of soil under the direct influence of plant roots, emerges as agriculture’s most productive microhabitat. Microbial populations there are typically 10 to 100 times higher than in bulk soil, sustained by the continuous input of root-derived carbon. Root exudates act as structured chemical signals that recruit specific microbial partners: malic acid secreted under phosphorus stress recruits biocontrol strains of Bacillus subtilis, organic acids such as citrate and oxalate solubilize phosphorus bound to iron and aluminum, and legume flavonoids initiate the molecular dialogue leading to rhizobial nodule formation. Plant growth-promoting rhizobacteria, long heralded as a biotechnological solution, show routinely dramatic effects in glasshouse experiments, but field meta-analyses reveal positive mean effects with standard deviations comparable to the means themselves, a variability rooted in the difficulty of establishing an inoculated strain against locally adapted indigenous communities. Encouragingly, a synthesis of 52 studies found inoculation increased root mass by 35 percent and reproductive yield by 19 percent under well-watered conditions, with effects growing even larger under drought.

The review devotes particular attention to arbuscular mycorrhizal fungi, the most ancient and widespread mutualism in terrestrial plant nutrition, dating roughly 450 million years to the Ordovician colonization of land. Today approximately 80 percent of land plant species, including the majority of staple food crops, maintain the partnership, in which fungi receive 4 to 20 percent of plant photosynthate in exchange for extending the root’s absorptive reach into soil pores too narrow for root hairs. Under moderate phosphorus availability, mycorrhizal plants can derive 70 to 80 percent of their phosphorus uptake through the fungal pathway. Yet the symbiosis is not unconditionally mutualistic: in high-phosphorus fertilized soils, fungi may colonize roots and draw plant carbon without delivering commensurate benefit, tipping the relationship toward parasitism. A single tillage event can reduce mycorrhizal colonization of the next crop by 30 to 50 percent in the first weeks after planting, and bare fallows can cause declines persisting for years. The prescribed remedy is a coherent conservation toolkit: reduced tillage, mycorrhizal cover crops during fallows, moderated phosphorus inputs and diverse rotations.

On nitrogen, the review frames the global cycle as a microbial achievement disrupted by twentieth-century chemistry. An estimated 40 to 50 percent of synthetic fertilizer nitrogen is not taken up by crops, instead leaching into groundwater, escaping as nitrous oxide, a greenhouse gas roughly 265 times more potent than carbon dioxide over a century, or cascading into eutrophication. Biological nitrogen fixation by legume symbionts contributes an estimated 40 to 60 million tonnes of nitrogen globally per year, with individual legume crops fixing between 100 and 300 kilograms per hectare per season under favorable conditions. The central design challenge is synchrony: aligning biological mineralization with crop demand through residue quality management and input timing. Evidence from sub-Saharan Africa underscores the potential, with a meta-analysis of 94 studies finding that legume integration often doubled or tripled yields at low-producing sites, and adding half the recommended mineral fertilizer rate increased yields a further 25 percent over legumes alone.

Ultimately, the review contends that soil biodiversity functions as ecological insurance. Rare microbial taxa, those present at low relative abundances, account for a disproportionate share of key processes including nitrogen fixation, phosphorus mineralization and the decomposition of recalcitrant compounds, and their selective erosion under intensification carries functional consequences far beyond what numerical abundance suggests. The biological capital of agricultural soils has been systematically undervalued, underprotected and underinvested in for the better part of a century, the author concludes, and the consequences are now materializing in ways that directly threaten long-term productive capacity. The understanding needed to begin treating the soil microbiome as a foundational agricultural resource, as essential as seeds and water, already exists. What remains, the paper argues, is the will to use it.

Subject of Research: The role of belowground microbial communities in sustainable agroecosystem management

Article Title: Belowground microbial stewardship underpins sustainable agroecosystem management

Article References: Dasgupta, D. (2026). Belowground microbial stewardship underpins sustainable agroecosystem management. Discover Soil, 3(1), Article 162. https://doi.org/10.1007/s44378-026-00323-9

Image Credits: AI Generated

DOI: 10.1007/s44378-026-00323-9

Keywords: soil microbiome, soil food web, arbuscular mycorrhizal fungi, nitrogen cycling, rhizosphere, soil biodiversity, conservation agriculture, ecosystem services, soil organic matter, plant growth-promoting rhizobacteria, agroecosystem sustainability, rare biosphere

The study was designed to address a persistent gap in soil ecology. Although many investigations have examined how fertilization affects individual groups of soil organisms, comparatively few have traced the consequences across the entire food web, spanning microbes at the base to earthworms near the top, and fewer still have done so over a time frame long enough to capture the slow, cumulative changes that define soil health. To fill that gap, a team of researchers led by first and corresponding author Professor Yunfeng Chen of the Hubei Academy of Agricultural Sciences compared four long-term treatments: chemical fertilizer supplying nitrogen, phosphorus and potassium, known as NPK; organic manure alone; a combined treatment of manure plus NPK; and an unfertilized control plot that served as the experimental baseline.

The measurement strategy was deliberately broad. Rather than tracking a single indicator organism, the team quantified biomass or abundance across key taxonomic and functional groups, including microorganisms, protozoa, nematodes, mites, collembolans, enchytraeids and earthworms. They also calculated nematode ecological indices, a set of established metrics that soil ecologists use to infer the structure and maturity of soil food webs. Together, these measurements allowed the researchers to evaluate the relative strength of two competing regulatory forces: bottom-up control, in which the availability of resources such as organic carbon and nutrients determines how many organisms higher trophic levels can support, and top-down control, in which predators and higher consumers suppress or structure the populations below them.

The headline finding was unambiguous. Long-term fertilization increased the inputs of resources entering the soil, and that surge in resources enhanced most of the functional groups the team measured. Fertilized plots supported larger and more complex communities than the unfertilized control, confirming that sustained nutrient management is a powerful lever for shaping the living architecture of agricultural soils. But the differences among fertilization strategies proved just as consequential, and here the organic treatments stood out clearly.

Manure alone and the combined manure-plus-NPK treatment outperformed pure chemical fertilizer across most groups. When the researchers expressed these gains as relative increases compared with the NPK treatment, the manure plots showed improvements ranging from 20.69 to 972.52 percent, with an average of 241.62 percent, while the combined plots ranged from 26.55 to 792.30 percent, averaging 189.02 percent. Those are not marginal differences; they represent order-of-magnitude shifts in the abundance of some soil organisms. The practical implication is that organic amendments, whether applied alone or alongside mineral fertilizers, deliver substantially more nourishment to the soil food web than chemical fertilizer alone.

Interestingly, the manure-only and combined treatments did not differ significantly from each other. The researchers attribute this convergence to high soil fertility: once fertility reaches a sufficiently high level, the distinction between the two organic approaches diminishes, and both support similarly rich communities. In other words, the food web appears to saturate, and beyond a certain threshold of resource abundance, adding mineral fertilizer on top of manure yields little additional biological benefit even though it may still matter for crop nutrition.

The evidence for bottom-up regulation was strong and came from multiple independent lines. Functional groups showed positive correlations with one another, a pattern consistent with resources flowing upward through the web and lifting every level together rather than predators imposing their own structure from above. The enrichment index, a nematode-based metric that signals an abundance of opportunistic, resource-responsive organisms, rose by 51.27 percent under manure and 28.49 percent under the combined treatment relative to chemical fertilizer alone. The enrichment footprint, a complementary measure that captures the cumulative enrichment signal across the food web, increased even more dramatically, by 11.80 percent under manure and 47.17 percent under the combined treatment relative to NPK.

To synthesize these patterns into a causal framework, the team employed partial least squares path modeling, a statistical technique well suited to disentangling direct and indirect pathways among correlated variables. The modeling confirmed what the correlations and indices had suggested: bottom-up forces predominantly determined both the structure and the total biomass of the soil food web. Resource availability, shaped by decades of fertilization, was the dominant driver, while top-down influences played a comparatively minor role in this system. For a rice–wheat rotation, where flooded and aerobic phases alternate and organic matter dynamics are complex, this finding provides a clear conceptual anchor for future soil management research.

The implications extend well beyond the experimental plots. Soil food webs underpin essential ecosystem services, including decomposition, nutrient mineralization, suppression of plant pathogens and the maintenance of soil structure. A food web enriched through bottom-up channels is, in effect, a soil with greater biological capacity to sustain crop productivity over time. The study suggests that sustained organic inputs, particularly when integrated with mineral fertilizers, effectively enhance both the complexity and the size of the soil food web primarily through this bottom-up regulatory mechanism. For farmers and policymakers weighing the trade-offs between organic and conventional inputs, the results add a biological argument in favor of manure-based strategies, whether used alone or in combination with chemical fertilizer.

The research also carries a cautionary note for the long term. Because the experiment spanned thirty years, it captured changes that short-term studies inevitably miss, including the slow accumulation of soil organic matter and the gradual response of larger, slower-reproducing organisms such as earthworms and enchytraeids. The authors’ conclusion is that fertilization is not merely a plant nutrition tool but a food-web engineering instrument, and that its effects compound over decades. As agriculture worldwide faces pressure to maintain yields while restoring degraded soils, this long-term evidence from a major cereal rotation offers a template: feed the base of the soil food web, and the rest of the web, along with the services it provides, is likely to follow.

Subject of Research: Long-term effects of chemical and organic fertilization on the soil food web in a rice–wheat cropping system

Article Title: Long-term fertilization enriches soil food web mainly through bottom-up regulation in a rice–wheat cropping system

Article References: Long-term fertilization enriches soil food web mainly through bottom-up regulation in a rice–wheat cropping system. (n.d.). Original publication

Image Credits: AI Generated

DOI: Not provided

Keywords: soil food web, long-term fertilization, rice–wheat rotation, bottom-up regulation, manure, NPK fertilizer, nematodes, earthworms, soil fertility, enrichment index, agroecology, soil biodiversity