Fungi and Bacteria Team Up to Turn Industrial Waste Into Soil Gold

Every year, the global phosphate fertilizer industry leaves behind a mountain of a problem. For every tonne of phosphoric acid produced, roughly five tonnes of a byproduct called phosphogypsum pile up in enormous waste stacks, many of which now dot coastlines and hinterlands across more than 65 countries. This calcium sulfate residue, chemically known as CaSO4·2H2O, is laced with residual phosphates, fluorides, and trace impurities that make it both an environmental liability and, tantalizingly, a potential resource. A new preliminary study published in the journal 3 Biotech suggests that the key to unlocking that resource may not lie in heavy industry at all, but in two unassuming microorganisms: a fungus that excretes oxalic acid and a bacterium that devours it.

The research, led by Lei Meng and Bin Lian of Nanjing Normal University, together with colleagues at Guizhou Institute of Technology and the Chinese Academy of Sciences, set out to test whether the mineral locked inside phosphogypsum could be biologically transformed into something genuinely useful for agriculture. The team’s strategy rested on a well-known geochemical pathway called the oxalate-carbonate pathway, in which living organisms convert calcium sulfate into calcium oxalate minerals and then, through bacterial degradation, into calcium carbonate. If the sequence could be demonstrated in the laboratory and then in living soil, phosphogypsum might find a second life as a soil amendment rather than rotting indefinitely in storage stacks.

The first step was a controlled chemistry experiment. The researchers exposed phosphogypsum to three different organic acids under identical conditions: oxalic acid, citric acid, and another common low-molecular-weight organic acid. The result was strikingly selective. Only oxalic acid managed to attack the gypsum crystal structure, dissolving the calcium sulfate dihydrate and reprecipitating it as whewellite, the monohydrate form of calcium oxalate. Citric acid, despite its reputation as an effective chelator, left the gypsum mineral phase essentially untouched. This selectivity matters because it identifies oxalate as the specific chemical lever needed to pull calcium out of phosphogypsum, and it explains why the team then turned to organisms that either produce or consume that exact compound.

Enter Aspergillus niger, a ubiquitous black mold famous among microbiologists for its industrial productivity and notorious among mycologists for its aggressive acid secretion. When the researchers cultivated A. niger in the presence of phosphogypsum, the fungus did precisely what the pure oxalic acid had done, but through its own metabolism. Over eight days of growth, the pH of the culture medium plummeted from 5.12 to 2.82, a dramatic acidification driven by the fungal excretion of oxalic acid and other metabolites. As the acidity climbed, the team tracked a progressive disappearance of the original gypsum mineral phase, accompanied by the appearance of two calcium oxalate minerals: whewellite, the monohydrate, and weddellite, the dihydrate. The fungus, in effect, was mining the waste pile with its own chemistry, converting an industrial byproduct into minerals that are otherwise associated with plant tissues, forest soils, and even human kidney stones.

The second microbial player then took the stage. Azospirillum brasilense strain OX-1 is an oxalotrophic bacterium, meaning it can metabolize oxalate as a source of energy and carbon. In the process, it raises the local pH and releases calcium that combines with carbonate to form calcite, the stable polymorph of calcium carbonate. When the researchers fed OX-1 the calcium oxalate generated either by pure oxalic acid treatment or by the A. niger transformation, the bacterium completed the circuit: the oxalate minerals were degraded and calcite formed in their place. This two-step handoff, from an acid-producing fungus to an oxalate-consuming bacterium, mirrors the natural oxalate-carbonate pathway that operates in soils around the world, where fungi and bacteria jointly convert organic oxalate into long-lived mineral carbon. Here, the same pathway was harnessed to transform a waste product into a benign, soil-friendly carbonate.

Demonstrating the chemistry in a flask is one thing; proving it matters in living soil is another. For that, the team ran a 45-day pot experiment using Suaeda salsa, a halophytic plant well adapted to saline and alkaline conditions, which are precisely the kinds of degraded soils where a gypsum-based amendment might be most valuable. The experimental design compared untreated controls against phosphogypsum alone and phosphogypsum combined with the OX-1 bacterium. The differences were unambiguous. Plants receiving the combined phosphogypsum and OX-1 treatment reached a mean height of 11.03 centimeters, with a standard deviation of 0.67 centimeters, and a mean stem diameter of 0.81 millimeters, plus or minus 0.07 millimeters. The untreated controls, by contrast, managed only 4.67 centimeters of height and 0.32 millimeters of stem diameter. In other words, the combined treatment more than doubled plant height relative to the control.

The benefits were not limited to what could be measured with a ruler. The combined application of phosphogypsum and OX-1 significantly altered several soil physicochemical properties, including soil pH and available phosphorus, the form of the nutrient that plants can actually absorb. This makes mechanistic sense. The gypsum component supplies calcium and sulfur, while the microbial transformation pathway releases and mobilizes residual phosphorus trapped in the waste, converting it into plant-available forms. At the same time, the bacterial degradation of oxalate and the precipitation of calcite can moderate soil acidity and contribute stable inorganic carbon to the soil. For saline-alkali soils, which cover vast areas in northern China and elsewhere and are notoriously difficult to remediate, an amendment that simultaneously supplies calcium, improves phosphorus availability, and buffers pH would be an attractive proposition.

The broader context gives the findings their urgency. Phosphogypsum is produced on a staggering scale, and only a fraction of it is currently recycled into construction materials, ammonium sulfate, or other products. The remainder sits in impoundments that pose risks of leachate contamination of groundwater and, in some regions, concerns about radionuclide content inherited from the phosphate ore. Reviews of phosphogypsum management have repeatedly called for circular-economy solutions that move beyond storage, and recent work has explored everything from high-purity calcium carbonate production to the recovery of phosphate and fluoride from leachates. What distinguishes the new study is its explicitly biological approach: rather than using energy-intensive chemical processing, it enlists soil microorganisms to do the mineral transformation at ambient temperatures, in principle directly in the field.

The authors are careful to frame the work as preliminary, and several important questions remain open. The most significant is whether the two-step transformation, fungal oxalate production followed by bacterial oxalate degradation, can actually proceed sequentially in the rhizosphere, the narrow zone of soil surrounding plant roots where chemistry is governed by root exudates and dense microbial communities. Laboratory cultures are far simpler environments than living soil, and factors such as competing microbes, variable moisture, and the buffering capacity of real soils could slow or redirect the pathway. The long-term environmental effects also need evaluation, including the fate of trace impurities in phosphogypsum as the gypsum matrix dissolves and whether repeated applications could accumulate unwanted elements in soil or crops. A companion study by some of the same authors on high-dosage phosphogypsum in potted amaranth underscores that dosage and soil type matter for safety.

Even with those caveats, the study offers a compelling proof of concept with an almost poetic symmetry. A waste product of industrial agriculture, stockpiled by the billions of tonnes, is transformed by a mold and a bacterium into calcite and plant-available nutrients, and the plants grown in the amended soil respond with more than double the height of untreated controls. The oxalate-carbonate pathway, long studied as a curiosity of soil geochemistry and carbon sequestration, here becomes a practical tool for waste valorization. If follow-up work confirms that the fungal-bacterial relay can operate in real rhizospheres at field scale, phosphogypsum could shift from being one of the fertilizer industry’s most stubborn liabilities to a raw material for restoring the very soils that agriculture depends on. The research was funded by the Science and Technology Support Plan of Guizhou Province and the Major Scientific and Technological Achievement Transformation Project of Guizhou Province, reflecting regional interest in turning a local waste burden into an agricultural asset.

Subject of Research: Microbial biotransformation of phosphogypsum into calcium oxalate and calcite for use as a soil amendment

Article Title: Biotransformation of phosphogypsum and its potential for soil-based applications: a preliminary study

Article References: Meng, L., Xiao, D., Liu, X., Cao, Y., & Lian, B. (2026). Biotransformation of phosphogypsum and its potential for soil-based applications: a preliminary study. 3 Biotech, 16(10), Article 426. https://doi.org/10.1007/s13205-026-05064-8

Image Credits: AI Generated

DOI: 10.1007/s13205-026-05064-8

Keywords: phosphogypsum, Aspergillus niger, Azospirillum brasilense, calcium oxalate, whewellite, weddellite, calcite, oxalate-carbonate pathway, soil amendment, soil microbiology, bioremediation, saline-alkali soil