Organic Fertilizers Reshape the Hidden Fungal World of Soybean Roots

Soybean is often called the golden bean, and for good reason. It supplies a large share of the world’s plant-based protein and vegetable oil, sustains livestock feed systems, and anchors the economies of farmers on nearly every continent. Global production surpassed 360 million metric tons in 2021, a figure that underscores how much depends on the health of the soils in which this legume grows. Yet decades of reliance on chemical fertilizers have steadily eroded soil fertility in many soybean fields, prompting researchers to look beneath the surface for alternatives that work with biology rather than against it.

That search has now produced an intriguing result. A team of South African researchers, publishing in the journal MicrobiologyOpen, used DNA sequencing to map the fungal communities living in the rhizosphere of soybean plants grown under different organic fertilization regimes. The rhizosphere, the narrow zone of soil hugging the plant’s roots, is one of the most biologically active environments on Earth, teeming with bacteria, fungi, and other microorganisms that feed on sugars and other compounds exuded by the roots. Because more than 95 percent of soil microbes cannot be grown in a laboratory dish, the team turned to amplicon sequencing of the internal transcribed spacer region, a genetic barcode widely used to identify fungi, to catalogue organisms that traditional culturing would have missed entirely.

The experiment took place at the North-West University farm in Molelwane, Mafikeng, in a region receiving about 540 millimeters of rain per year. The researchers laid out a randomized complete block design with three treatments applied to soybean plots: soil amended with cattle dung manure, soil amended with poultry waste, and an untreated control, alongside bulk soil collected from open inter-row areas with no root contact. Organic amendments were incorporated before planting at a rate of 20 tons per hectare, and rhizosphere samples were harvested at the flowering stage, seven weeks after sowing, when interactions between roots and microbes reach their peak. Physicochemical analysis showed that poultry waste enriched the soil with phosphorus and calcium, while cattle dung boosted phosphorus, potassium, and magnesium.

Sequencing on an Illumina NovaSeq 6000 system produced remarkably clean data, with each sample yielding roughly 165,000 to 172,000 non-chimeric reads and quality scores exceeding standard thresholds. After processing with the DADA2 denoising algorithm within QIIME 2 and classifying sequences against the UNITE reference database, the researchers could compare the fungal profiles of each treatment with unprecedented resolution. The results revealed that the type of organic matter added to the soil, not merely its presence, exerts a selective force on which fungi thrive around soybean roots.

At the phylum level, cattle dung-amended soils showed higher relative abundances of Chytridiomycota, Aphelidiomycota, and Rozellomycota, groups often associated with saprotrophic living and the breakdown of tough plant polymers such as cellulose. Poultry waste, by contrast, favored Mortierellomycota and Ascomycota, lineages that include fast-growing copiotrophs suited to nutrient-rich conditions. Mortierellomycetes, in particular, are known as active nitrogen mineralizers and phosphate solubilizers, suggesting that the nutrient-cycling potential of poultry-amended soil differs meaningfully from that of cattle dung. The untreated control and bulk soils were dominated by Olpidiomycota, Zoopagomycota, and Kickxellomycota, a less diverse but more stress-tolerant community consistent with their lower nutrient status.

The genus-level patterns were equally striking. Cattle dung soils supported filamentous Ascomycete genera such as Chaetomium, Neurospora, Achaetomium, and Humicola, organisms thought to play important roles in cellulose degradation and organic matter turnover. Poultry waste favored Trichoderma and Penicillium, two genera celebrated for promoting plant growth, suppressing pathogens through biocontrol mechanisms, and enhancing nutrient flow to crops, along with a marked dominance of Keratinophyton, a fitting match for the keratin-rich feathers and litter that characterize poultry waste. Meanwhile, the control and bulk soils were dominated by Fusarium, Curvularia, and Stagonosporopsis, taxa that include notorious plant pathogens. The authors interpret this as evidence that organic amendments can suppress potentially harmful taxa by shifting competitive hierarchies in the soil toward beneficial saprotrophs.

Diversity metrics added the clearest statistical evidence of treatment effects. Bulk soil exhibited the highest fungal richness, with a Chao1 index of 1603.33 and 1557 observed features, followed by cattle dung at 1456.64, while poultry waste showed the lowest richness at 957.93. Shannon diversity was highest in cattle dung soils at 6.561, closely followed by bulk soil at 6.528, with poultry waste trailing at 5.525 and showing the lowest evenness. Good’s coverage remained at 1.000 across all treatments, confirming that the sequencing captured the communities thoroughly. The researchers suggest that poultry waste imposes nutrient-driven ecological filtering that favors fast-growing copiotrophs at the expense of rarer taxa, whereas the diverse organic substrates in cattle manure support a more balanced and heterogeneous fungal community.

Venn diagram analysis of amplicon sequence variants revealed a core microbiome of 300 ASVs shared across all treatments, likely reflecting the filtering influence of soybean root exudates, alongside large treatment-specific fractions: bulk soil harbored 756 unique ASVs and cattle dung 655, compared with 330 for poultry waste and 476 for the control. Beta diversity analysis showed the greatest compositional dissimilarity between poultry waste and the control, and between cattle dung and poultry waste, indicating that the two organic amendments reshape the fungal community in distinctly different ways. Ordination by principal component analysis and principal coordinates analysis based on UniFrac distances reinforced this picture, with cattle dung and poultry waste samples forming distinct clusters while control and bulk soils overlapped more and spread heterogeneously. Notably, the weighted UniFrac metric showed cattle dung most strongly influenced abundant taxa, while the unweighted metric revealed shifts in rare taxa across all treatments, with possible long-term consequences for soil resilience.

Functional prediction using the FUNGuild database translated these taxonomic shifts into ecological meaning. Cattle dung soils were strongly enriched for dung saprotrophs, animal pathogens, and wood saprotrophs, consistent with their cellulose-degrading Ascomycete residents. Poultry waste showed distinct enrichment of endophyte and plant pathogen guilds, likely reflecting its nitrogen- and keratin-rich character, while bulk soils clustered separately with wood saprotrophs and ectomycorrhizal fungi. Crucially, 32 functional guilds were shared across all treatments, indicating a stable core of ecological functions underpinning soil health and soybean growth. Linear discriminant analysis effect size identified Hypocreales, a group rich in biocontrol agents, as a biomarker for cattle dung, and keratin-degrading Onygenales as a biomarker for poultry waste. Predicted metabolic pathways confirmed that carbohydrate and amino acid metabolism dominated across all samples, underscoring the central role of carbon and nitrogen turnover in rhizosphere function.

The authors are careful to frame their conclusions with appropriate statistical caution. With only three field replicates per treatment, the ANOSIM and MRPP tests did not reach conventional significance despite moderate effect sizes, most notably the R-value of 0.74 separating cattle dung from poultry waste. Differences in underlying soil chemistry, including extractable phosphorus, calcium, potassium, magnesium, sodium, and pH, may also partly confound the interpretation of amendment effects. The alpha diversity findings, however, represent the most statistically robust conclusions of the study. Taken together, the work delivers a clear message for sustainable agriculture: the choice between organic fertilizers is not interchangeable. Cattle dung appears to cultivate diverse, functionally rich saprotrophic communities likely to benefit soil health, while poultry waste fosters specialized, nutrient-responsive assemblages. As farmers worldwide seek to rebuild degraded soils, understanding these amendment-specific microbial signatures could help tailor fertilization strategies that harness the hidden fungal workforce beneath every soybean field.

Subject of Research: Fungal diversity and functional prediction of the soybean rhizosphere microbiome under different organic fertilization regimes

Article Title: Amplicon Characterization of Fungal Diversity and Functional Prediction of Glycine max L. Rhizosphere Microbiome Under Different Organic Fertilization

Article References: Osuji, I. E., Akanmu, A. O., & Babalola, O. O. (2026). Amplicon Characterization of Fungal Diversity and Functional Prediction of Glycine max L. Rhizosphere Microbiome Under Different Organic Fertilization. MicrobiologyOpen, 15(5), Article e70437. https://doi.org/10.1002/mbo3.70437

Image Credits: AI Generated

DOI: 10.1002/mbo3.70437

Keywords: soybean, rhizosphere, fungal diversity, organic fertilizer, cattle dung, poultry waste, ITS amplicon sequencing, FUNGuild, soil microbiome, sustainable agriculture, alpha diversity, soil health