The study matters because wheat is among the most demanding staple crops, and modern agriculture leans heavily on mineral fertilizers whose overuse drives soil acidification, disrupts microbial communities and sends nitrogen and phosphorus leaching toward waterways. Digestate, the residue left after microbes strip energy from organic matter, has long been promoted as a circular-economy alternative: it carries organic carbon, plant-available mineral nutrients and a living cargo of microorganisms in a single package. But almost everything known about digestate as a biofertilizer comes from one-stage systems. Whether the output of a two-stage plant behaves the same way in a real field had never been tested — until now.

The two designs differ fundamentally in how they organize microbial labor. In a one-stage digester, hydrolysis, acidogenesis, acetogenesis and methanogenesis all happen in one vessel, a crowded ecosystem where fermenters and methane-producers negotiate constantly. A two-stage system physically separates the early, acid-producing phases from the later methanogenic ones, giving each microbial guild its own optimized environment. The Polish team, led by Marta Galas of Warsaw University of Life Sciences, reasoned that this architectural difference should leave a chemical and biological fingerprint on the final digestate — and that the fingerprint should matter to crops.

It did. Chemically, the one-stage digestate contained about 24.6 percent more total nitrogen and 19.7 percent more total phosphorus than its two-stage counterpart. Yet the two-stage product was markedly more mineralized: it carried 23.9 percent more ammonium-nitrogen and 39.8 percent more nitrate-nitrogen, meaning a larger share of its nitrogen sat in forms roots can absorb immediately. It was also more alkaline. The microbiomes told a parallel story. The one-stage digestate teemed with fermentative and acidogenic bacteria — Lactiplantibacillus, Lactococcus, Bacteroides — and was dominated by the fungus Trichoderma, a genus famous for colonizing rhizospheres, stimulating root growth and solubilizing phosphorus. The two-stage digestate instead hosted methanogenic archaea such as Methanosarcina and Methanothrix, alongside bacteria like Alcaligenes and Cloacibacillus, and a more evenly spread fungal community including Candida and Geotrichum.

Those differences translated into distinct field behavior. The experiment ran from September 2023 to harvest in 2024 on sandy soil in randomized microcosms of winter wheat variety Euforia, with four treatments: unfertilized control, synthetic fertilizer (Azofoska), one-stage digestate and two-stage digestate, each applied twice during the growing season at 140 kilograms of nitrogen per hectare. After harvest, the only soil chemistry parameter that had shifted was bioavailable phosphorus, which rose about 23.3 percent in the one-stage digestate plots relative to the control — a result the authors link to the phosphorus-mobilizing Trichoderma and Bacteroides delivered by that treatment. The synthetic fertilizer, by contrast, slightly lowered soil pH, while both digestates kept it stable.

To see how the plants themselves responded, the researchers measured the expression of nutrient transporter genes in wheat roots using digital PCR. Both digestate treatments significantly increased expression of TaAMT1.2, a gene encoding a high-affinity ammonium transporter, compared with both the control and the synthetic-fertilizer plots. The nitrate transporter gene TaNRT1.1 and the phosphate transporter TaPHT1.10, which doubles as a phosphorus-starvation sensor, showed no significant differences across treatments. The ammonium-transporter upregulation suggests that digestate-fertilized wheat reorganized its nitrogen acquisition strategy, likely reflecting both the ammonium-rich chemistry of the digestates and the nitrogen demand of grain filling late in the season — a physiological adjustment the steadily supplied synthetic fertilizer did not provoke.

Yield told the headline story. Synthetic fertilization remained the benchmark, boosting grain yield 7.8-fold over the control, but the two-stage digestate reached 3.3-fold and the one-stage 2.5-fold — a roughly 32 percent advantage for the two-stage product, consistent with its richer load of immediately available mineral nitrogen. Straw biomass followed the same ordering. Elemental analysis of grain and straw added nuance: nitrogen content rose in the synthetic treatment but was actually slightly lower in the grain of two-stage-fertilized plants, hinting at mild nitrogen shortage during grain maturation, while phosphorus concentration per kilogram of dry matter dropped in all fertilized variants — a dilution effect, since those plants produced far more biomass with similar total phosphorus uptake.

A linear regression across all plots found that final yield was weakly but significantly associated with soil pH and with TaPHT1.10 expression, though the model explained only about a third of the variance. Lower expression of the phosphate transporter, a sign that plants had satisfied their phosphorus demand, tracked with slightly higher yields. The authors are careful about these associations: the relationships are real but modest, and the study’s design cannot disentangle every interacting factor in an open field.

The bigger picture is a trade-off. The two-stage digestate behaves more like a fast-acting mineral fertilizer, its readily available nitrogen driving the stronger yield response, but its methanogen-dominated microbiome offers less biological potential for actively modulating soil nutrient cycling. The one-stage digestate is less mineralized yet biologically richer, and its legacy showed up as improved soil phosphorus availability rather than yield. Both, however, fell short of the synthetic treatment — yields 2.4 and 3.1 times lower respectively despite equal nitrogen input — suggesting that a substantial fraction of digestate nitrogen escaped the root zone over the season, likely through nitrification and leaching from the liquid form.

For a field often split between chemical inputs and single-strain biofertilizers, the study offers a third path: process engineering as a lever for fertilizer design. By rearranging the microbial assembly line inside a digester, producers can tune the nutrient speciation and microbiology of the output — effectively choosing between a quick-release, mineral-heavy amendment and a slower, biologically active one. The authors call for follow-up work tracking soil-microbe-plant interactions throughout the growing season, when uptake is most active, and for developing more stable digestate formulations that curb nutrient losses. If two-stage systems can close the yield gap with synthetic fertilizers while preserving soil pH and recycling sugar-industry molasses, the humble biogas by-product may earn a permanent place in circular cereal farming.

Subject of Research: Fertilizing properties of one-stage versus two-stage anaerobic digestion digestate in wheat field cultivation

Article Title: Soil–wheat nutrient interactions following fertilization with digestate from one- and two-stage molasses anaerobic digestion: a field study

Article References: Galas, M., Detman-Ignatowska, A., Jonczak, J., Szewińska, J., & Chojnacka, A. (2026). Soil–wheat nutrient interactions following fertilization with digestate from one- and two-stage molasses anaerobic digestion: a field study. Plant and Soil. https://doi.org/10.1007/s11104-026-09176-1

Image Credits: AI Generated

DOI: 10.1007/s11104-026-09176-1

Keywords: anaerobic digestion, digestate, biofertilizer, wheat, soil health, nutrient cycling, two-stage digestion, molasses, ion transporters, TaAMT1.2, circular economy, soil pH