Soybean Meal Feeding Reshapes Morel Mushroom Protein in Tissue-Specific Ways, Multi-Omics Study Finds

Morel mushrooms are among the most prized and expensive edible fungi in the world, and commercial growers have long tinkered with what they feed their crops to coax out better yields and richer nutrition. A new study from researchers at the Shanghai Academy of Agricultural Sciences, published in Frontiers in Nutrition, now shows that one of those feeding decisions — how much protein-rich soybean meal goes into the exogenous nutrient bags that sustain cultivated morels — produces surprisingly lopsided effects across the anatomy of the mushroom itself. The cap and the stipe, the two distinct tissues of a morel fruiting body, respond to extra soybean meal in different ways, and not always in the direction a grower might expect.

The team, led by Yihong Yue, Qian Wang, and senior authors Jinjing Zhang and Hui Chen, cultivated the black morel Morchella sextelata at a greenhouse production base in Qingpu District, Shanghai, using a standard nutrient-bag formulation of wheat, corn cobs, soybean meal, corn flour, lime, and gypsum. On top of that basal mix, they added extra soybean meal at levels ranging from 1 to 10 percent of the bag’s dry weight. After harvest, they separated the caps from the stipes and measured protein content via Kjeldahl nitrogen analysis, along with 18 hydrolyzed amino acids by high-performance liquid chromatography. For a subset of treatments — the control, 2, 4, and 8 percent levels — they went further, running full RNA sequencing and quantitative proteomics on both tissues.

The headline compositional finding is that protein content responded nonlinearly to supplementation. In the caps, protein climbed from about 303 grams per kilogram of dry weight in the control to roughly 384 grams per kilogram at 8 percent supplementation — a 26.8 percent increase — before falling back at 10 percent. The stipes followed a similar trajectory, peaking at about 354 grams per kilogram at 8 percent, some 20 percent above the control. Crucially, the response was not proportional: adding more soybean meal did not keep adding more protein, and the 4 and 8 percent cap treatments were statistically indistinguishable. The authors caution that 8 percent produced the highest measured protein under their conditions but should not be read as a universally optimal formulation.

Total and essential amino acid contents told a parallel story. In caps, total hydrolyzed amino acids, essential amino acids, and non-essential amino acids all peaked at 8 percent, exceeding the control by roughly 16 to 18 percent. At every matched supplementation level, caps consistently carried more total, essential, and non-essential amino acids than stipes. But here the study delivers its most nutritionally interesting twist: when the researchers normalized essential amino acids to protein content and calculated the essential amino acid index (EAAI) against the FAO reference pattern, the 8 percent caps — despite being the richest in absolute protein and amino acids — did not have the best amino acid balance. In fact, the control caps scored highest on EAAI, at 109.64, while the 4 percent treatment scored lowest.

This divergence between abundance and balance matters because the two measurements describe different things. Protein content and essential amino acid content are quantities per unit of dry mushroom matter, whereas EAAI reflects the proportional distribution of essential amino acids relative to total protein. A mushroom can pack in more protein without improving the quality of that protein’s amino acid profile — and the study shows exactly that happening in the cap. In the stipe, by contrast, all supplemented groups had higher EAAI values than the control, meaning the same intervention improved amino acid proportionality in one tissue while leaving it unchanged or worse in the other. For anyone evaluating mushroom nutrition, the authors argue, these indices should be treated as complementary rather than interchangeable.

To understand what was happening biologically, the team turned to transcriptomics and proteomics. RNA sequencing of 24 libraries generated over a billion clean reads, which were mapped to the M. sextelata reference genome. The result was a striking asymmetry between molecular layers: caps showed more differentially expressed genes than stipes at every matched supplementation level — up to 4,122 in the medium-treatment caps — while stipes contained more differentially expressed proteins, with downregulated proteins predominating in the low and high stipe comparisons, accounting for roughly two-thirds of all changes. Only 33 genes and 23 proteins were shared across all six treatment-control comparisons, underscoring how tissue- and dose-specific the responses were.

Weighted gene and protein co-expression network analyses helped tie the molecular changes to the measured nutritional traits. In the cap, a large gene module of 3,528 transcripts correlated positively with protein and amino acid contents and was enriched in ribosome-related pathways, aminoacyl-tRNA biosynthesis, and several amino acid metabolic routes, including cysteine and methionine metabolism. The corresponding cap protein module added glycolysis, the TCA cycle, endoplasmic reticulum protein processing, and the proteasome to the picture — a signature of carbon-skeleton supply, amino acid activation, translation, and protein turnover. In the stipe, the trait-associated modules instead pointed toward carbohydrate and nitrogen metabolism, branched-chain amino acid degradation, oxidative phosphorylation, RNA processing, and ribosome biogenesis.

One of the most concrete correspondences emerged for valine and tyrosine. Both amino acids reached their highest contents in the 8 percent cap treatment, and the expression of the genes encoding their cognate aminoacyl-tRNA synthetases — VARS and YARS — rose progressively from the low to the high supplementation level. The authors are careful to note that this parallel trend is consistent with, but does not prove, coordinated regulation between amino acid composition and aminoacylation-related gene expression. They also flag cysteine and methionine metabolism as a recurring thread across cap analyses, with possible — though untested — implications for sulfur-containing aroma compounds, a connection documented in shiitake and porcini but not yet examined in morels.

The study’s broader significance lies in its demonstration that preharvest nutrient inputs do not act uniformly on a mushroom. The cap, the spore-bearing tissue, mounted a broader transcriptional response tied to amino acid and central carbon metabolism, while the stipe, the structural support tissue, showed a more extensive and predominantly downward proteomic shift involving energy metabolism and RNA processing. This tissue-resolved architecture echoes earlier findings in Pleurotus giganteus and Dictyophora indusiata, but the present work is the first to link graded soybean meal supplementation in nutrient bags to tissue-specific protein and amino acid outcomes in cultivated morels.

The authors are candid about the limits of their approach. The co-expression networks were built from 12 samples per tissue and are explicitly exploratory; the enrichment analyses associate pathways with compositional traits but do not establish causal regulation. The study measured hydrolyzed amino acids rather than free amino acids, enzyme activities, metabolic fluxes, or volatile and sensory attributes. Future work, they write, should integrate free amino acid profiling, enzyme assays, flux analysis, and flavor measurements to determine whether the molecular associations they identified translate into functional nutritional or sensory changes. For now, the message for morel growers and food scientists alike is clear: what you feed the fungus matters, but where you look on the mushroom matters just as much.

Subject of Research: Tissue-specific protein and amino acid responses of Morchella sextelata to preharvest soybean meal supplementation

Article Title: Preharvest soybean meal supplementation alters tissue-specific protein and amino acid composition in Morchella sextelata: integrated transcriptomic and proteomic analysis

Article References: Yue, Y., Wang, Q., Zhang, Y., Xiao, T., Hao, H., Tong, Z., Li, W., Huang, J., Zhang, J., & Chen, H. (2026). Preharvest soybean meal supplementation alters tissue-specific protein and amino acid composition in Morchella sextelata: integrated transcriptomic and proteomic analysis. Frontiers in Nutrition, 13, Article 1979592. https://doi.org/10.3389/fnut.2026.1979592

Image Credits: AI Generated

DOI: 10.3389/fnut.2026.1979592

Keywords: Morchella sextelata, morel mushrooms, soybean meal supplementation, amino acids, proteomics, transcriptomics, edible fungi, nutrition, cultivation, protein quality, essential amino acid index, food chemistry