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Article

Impact of Organic Amendments on Black Wheat Yield, Grain Quality, and Soil Biochemical Properties

by
Jiaqi Zhou
1,2,3,
Huasen Xu
1,2,3,
Meng Zhang
1,2,3,
Ruohan Feng
1,2,3,
Hui Xiao
4 and
Cheng Xue
1,2,3,*
1
College of Resources and Environment Science, Hebei Agricultural University, Baoding 071001, China
2
Key Laboratory for Farmland Eco-Environment of Hebei, Hebei Agricultural University, Baoding 071001, China
3
State Key Laboratory of North China Crop Improvement and Regulation, Hebei Agricultural University, Baoding 071001, China
4
Cultivated Land Quality Monitoring and Protection Center of Hebei Province, Shijiazhuang 050000, China
*
Author to whom correspondence should be addressed.
Agronomy 2025, 15(4), 961; https://doi.org/10.3390/agronomy15040961
Submission received: 13 March 2025 / Revised: 4 April 2025 / Accepted: 14 April 2025 / Published: 15 April 2025
(This article belongs to the Section Soil and Plant Nutrition)
Browse Figures
Versions Notes

Abstract

:
This study investigated the effects of organic amendments (straw return, organic fertilizer, biochar, and their combinations) on grain yield, quality, and soil biochemical characteristics in black wheat. A two-year field experiment (2022–2024) was conducted with five treatments: F (conventional fertilization), FS (F + full straw return), FO (F + 3 t/ha organic fertilizer), FB (F + 3 t/ha biochar), and FSOB (F + full straw + 3 t/ha organic fertilizer + 3 t/ha biochar). FSOB achieved the highest yield, increasing by 17.3% over F due to a higher spike number and 1000-grain weight. Grain protein increased by 9.0% and 9.4% under FS and FO, respectively. Straw addition also raised gluten by 6.8%. Soil analysis revealed that integrated organic management significantly increased the contents of organic matter (by 23.1%), total nitrogen (by 46.0%), and available phosphorus (by 73.5%) in the 0–20 cm soil layer. It also promoted beneficial microbial taxa, including Actinobacteria (+11.2%) and Proteobacteria (+0.6%), compared to conventional fertilization. These findings suggest that strategic integration of organic amendments can enhance black wheat productivity and grain quality by improving soil fertility and microbial functionality, thereby supporting sustainable cropping systems.

1. Introduction

Black wheat (Triticum aestivum L. var. melano-violaceum), developed by the Institute of Crop Genetics, Shanxi Academy of Agricultural Sciences, through genetic recombination between purple and blue wheat lines, exhibits a distinctive black grain phenotype due to its high anthocyanin content [1,2]. As a representative variety among colored wheats, black wheat is characterized by a high protein content (10–15%) [3], a rich profile of amino acids (including approximately 96 amino acids and derivatives), and strong antioxidant properties [4], making it highly valuable for applications in functional foods and natural pigment development [5,6]. According to Garg et al. [7], products derived from colored wheat varieties may possess superior nutritional and functional attributes compared to conventional wheat cultivars. Despite its health benefits, the commercial adoption of black wheat remains constrained by yield limitations, which are approximately 29.7–52.5% lower than those of common wheat cultivars under equivalent cultivation conditions [7]. While optimized fertilization strategies are critical for enhancing crop productivity, intensive chemical fertilizer application often exacerbates soil degradation through nutrient imbalances and micronutrient depletion, ultimately threatening agricultural sustainability [8]. Notably, Tian et al. [9] demonstrated that excessive synthetic fertilization not only fails to proportionally increase cereal yields but may induce yield stagnation while accelerating soil acidification and eutrophication risks.
Organic amendments, including biochar, organic fertilizer, and crop residue incorporation, offer a sustainable alternative by improving crop performance through the enhancement of soil health and fertility. These materials enhance nutrient cycling efficiency through multiple mechanisms, such as modulating soil physicochemical properties, stimulating microbial diversity, and providing slow-release nutrients [10,11]. Straw return, a widely implemented agricultural practice, increases soil organic carbon (SOC) sequestration and enhances nitrogen (N) use efficiency compared to removal systems, thus increasing crop yield [12,13]. However, its indiscriminate application may trigger microbial N immobilization, creating temporary nutrient competition during critical crop growth stages, therefore resulting in reduced crop yield [14,15,16]. Organic fertilizers, rich in humic substances and microbial metabolites, improve soil aggregation and cation exchange capacity while elevating grain yield and quality in production systems [17,18,19,20,21,22]. Nevertheless, their rapid mineralization rates can intensify carbon dioxide emissions, partially offsetting soil carbon gains [23,24]. Biochar, a pyrolyzed biomass with stable aromatic structures, addresses these limitations through its relatively persistent carbon sequestration capacity and nutrient retention properties. The application of biochar has been shown to enhance soil nutrient adsorption, reduce N leaching, and improve microbial activity, thereby improving soil fertility and boosting crop yield [25,26,27,28,29,30,31,32]. However, excessive application of biochar may exert negative impacts, such as inhibiting root development, as well as altering rhizosphere pH dynamics [33,34,35].
Recent studies have shown that the combined application of straw, organic fertilizers, and biochar can produce synergistic effects, overcoming the drawbacks of individual practices. For instance, co-application of biochar and organic fertilizer significantly improves crop yield compared to single treatments, attributed to enhanced microbial functional groups involved in carbon (C), nitrogen (N), phosphorus (P), and sulfur (S) cycling and improved soil ecological functions [36,37]. Similarly, integrating biochar with straw return promotes C-N cycling, increases soil organic matter, and reduces agricultural carbon footprints [38]. Notably, long-term studies in saline and calcareous soils of China found that the combined use of manure compost, biochar, and pyroligneous solution more than doubled maize biomass and yield while significantly enhancing soil physical, chemical, and biological properties [39,40]. In addition, combined straw mulch and biochar treatments outperformed single amendments in promoting plant growth indices such as leaf area index and stem diameter in maize, due to improved organic carbon turnover and soil water retention [41]. Moreover, straw return and organic fertilizer synergy improve soil aggregate stability and nutrient retention capacity, further enhancing crop productivity [42]. However, existing research mainly focused on the interactions between two organic materials, and the effects of combining straw, organic fertilizers, and biochar on the yield, quality, and soil biochemical properties of black wheat remain unclear. Further investigation is needed to determine whether the optimization of these effects can be achieved by combining these materials.
Therefore, a two-year field experiment was conducted using the black wheat variety “Jizi 3” with five treatments: conventional fertilization (F), straw return (FS), organic fertilizer amendment (FO), biochar amendment (FB), and integrated organic management (FSOB; combining straw, organic fertilizer, and biochar). The main aim was to analyze the effects of organic material additions and their combined application on black wheat grain yield, quality, and soil biological and chemical properties. By elucidating the synergistic effects and potential mechanisms of the integrated management, this study provides theoretical insights and technical support for achieving high-yield, high-quality black wheat production and advancing sustainable agricultural development.

2. Materials and Methods

2.1. Experimental Site

The field experiment was conducted in Beishao Village, Dingzhou City, Hebei Province, China (38°39′ N, 115°10′ E, 34 m elevation), from October 2022 to June 2024. This region experiences a temperate continental monsoon climate with a mean annual temperature of 13.5 °C, precipitation of 354 mm, a frost-free period of 250 days, and an annual sunshine duration of 2245.6 h. The experimental soil was classified as loam, with pre-trial (2022) physicochemical characteristics in the 0–40 cm profile detailed in Table 1. Monthly precipitation and average temperature during the 2022–2024 wheat-growing seasons compared to 2012–2021 decadal averages are shown in Figure 1.

2.2. Experimental Design

The field experiment employing black wheat (Triticum aestivum L. var. melano-violaceum) variety “Jizi 3” was conducted with five treatments (Table 2): conventional fertilization (F), straw return (FS), organic fertilizer amendment (FO), biochar amendment (FB), and integrated organic management (FSOB; combining straw, organic fertilizer, and biochar). Each treatment was replicated three times in a randomized complete block design with each plot size of 160 m2. “Jizi 3” is a black wheat germplasm developed by the Institute of Cereal and Oil Crops, Hebei Academy of Agriculture and Forestry Sciences, through artificial hybridization using Luozhen 1 as the maternal parent and Gao 8901 as the paternal parent, followed by pedigree selection. Both the 2022–2023 and 2023–2024 wheat growing seasons maintained consistent agronomic parameters: a seeding rate of 262.5 kg ha⁻1 and uniform row spacing of 0.15 m.
All treatments received the same nitrogen management based on local agricultural practices, with basal fertilization (144 kg N ha−1, 36 kg P2O5 ha−1, and 60 kg K2O ha−1) using compound fertilizer (24-6-10, N-P2O5-K2O) pre-sowing, followed by topdressing at the elongation stage of wheat (58.5 kg N ha−1 and 11.3 kg K2O ha−1) using compound fertilizers (26-0-5, N-P2O5-K2O). All organic amendments were uniformly broadcast by hand in a single application on the soil surface and incorporated into the soil through deep plowing (30–40 cm) once prior to seeding in each wheat-growing season. The jointing-stage topdressing was also manually broadcast. The whole-plant maize straw was completely crushed and incorporated into the field after harvest. The organic fertilizer used in this study was granular in form and was derived from 80% chicken manure and 20% maize straw. Its physicochemical properties included 20.7% organic matter, 1.2% N, 1.1% P, 2.7% K, and a pH of 7.90. The biochar was produced from soybean meal and contained 54.3% organic matter, 0.6% N, 0.4% P, and 2.9% K and had a pH of 7.80. Detailed application rates are provided in Table 2. The experiment utilized sprinkler irrigation with five uniformly scheduled irrigation events during the growing season, applied at the following stages: post-sowing, overwintering, regreening, jointing, and grain-filling, with each irrigation supplying approximately 600 m3 ha⁻1. Field management followed local agronomic practices.

2.3. Sample Collection

Plant Samples: At the wheat maturity stage, three 0.5-m row sections of aboveground plant material were randomly collected from each plot. Aboveground biomass was partitioned into stems, leaves, grains, and glumes. Grains were dried at 40 °C; other tissues at 70 °C to constant weight. At harvest, six 2-m row spikes were randomly collected from each plot for grain yield determination.
Soil Samples: Before initiation of the experiment, soil samples (0–20 cm and 20–40 cm in depth) were collected using five-point sampling. After the wheat harvest in the 2023–2024 season, soil samples (0–20 cm and 20–40 cm in depth) from three random points per plot were collected. Fresh samples were used for moisture content analysis, while the remaining samples were air-dried, sieved, ground, and analyzed for physicochemical properties. Soil samples from the 0–20 cm layer were stored at −80 °C for microbial analysis.

2.4. Parameters and Measurements

2.4.1. Yield and Yield Components

Three 1 m2 quadrats were randomly selected in each plot, and the number of effective ears was recorded and then converted to spike number per hectare. The 1000-grain weight was measured from oven-dried subsamples. Twenty ears were randomly selected from each 1 m2 sample and manually threshed to calculate the number of grains per ear. Grain yield was calculated from the total harvested area.

2.4.2. Grain Protein Composition

Wheat grains were milled using a laboratory mill (Laboratory Mill 120, Perten, Sweden) to obtain flour. Sequential extraction was used to separate albumin, globulin, gliadin, and glutenin proteins [43]. Total N content in each protein fraction was measured using the H2SO4-H2O2 Kjeldahl digestion method, and protein concentration was calculated by multiplying the N content by 5.7 [44].

2.4.3. Soil Physicochemical Properties

Soil organic matter content was measured using the potassium dichromate method [45]; total N content in soil was determined using the Kjeldahl method [44]; available P content was measured using the molybdenum–antimony colorimetric method [46]; soil available K content was determined using the flame photometric method [46]; soil pH was measured using a pH meter (PHS-3C, Shanghai, China); and soil bulk density was measured using the soil sampler (5 cm in height and 5 cm in diameter) method.

2.4.4. Soil Microbial Diversity

DNA Extraction and PCR Amplification: Soil microbial genomic DNA was extracted using the FastDNA® Spin Kit for Soil (MP Biomedicals, Santa Ana, CA, USA) according to the manufacturer’s protocol. DNA concentration and purity were assessed using a NanoDrop 2000 spectrophotometer (Thermo Scientific, Waltham, MA, USA). The quality of extracted DNA was evaluated by 1% agarose gel electrophoresis. The V3–V4 hypervariable regions of the bacterial 16S rRNA gene were amplified using the primer pair 338F (5′-ACTCCTACGGGAGGCAGCAG-3′) and 806R (5ʹ-GGACTACHVGGGTWTCTAAT-3′) [47].
Illumina MiSeq Sequencing: PCR products were recovered from 2% agarose gels and purified using the AxyPrep DNA Gel Extraction Kit (Axygen Biosciences, Union City, CA, USA), followed by elution with Tris-HCl buffer. The quality and quantity of the purified amplicons were assessed using 2% agarose gel electrophoresis and the QuantiFluor™-ST fluorometer (Promega, Madison, WI, USA), respectively. Library construction was performed following the standard protocol for the Illumina MiSeq platform (Illumina, San Diego, CA, USA), targeting the bacterial 16S rRNA gene using a paired-end (PE) 2 × 300 bp sequencing strategy. High-throughput sequencing was carried out on the Illumina MiSeq PE300 platform by Majorbio Bio-Pharm Technology Co., Ltd. (Shanghai, China).
Data Processing and Bioinformatics Analysis: Raw sequencing reads were subjected to quality control using Trimmomatic, and paired-end reads were merged using FLASH. Operational taxonomic units (OTUs) were clustered at 97% sequence similarity using the UPARSE pipeline (version 7.1). Chimeric sequences were identified and removed using UCHIME. Taxonomic classification of representative sequences was performed using the Ribosomal Database Project (RDP) Classifier (https://rdrr.io/bioc/rRDP/man/RDP.html, accessed on 30 December 2024) against the SILVA database (SSU123) with a confidence threshold of 70% [48].

2.4.5. Nitrogen Content in Wheat Tissues

Dried wheat samples from each tissue (stems, leaves, grains, and glumes) were ground using a high-speed universal pulverizer (FW100, Tester, Tianjin, China), and the total N content was determined using the H2SO4-H2O2 Kjeldahl digestion method [44].

2.5. Calculations

Nitrogen uptake in each tissue (kg ha−1) = Total N content (%) × Dry weight (kg ha−1)
Harvest index (%) = Grain yield (kg ha−1)/Total aboveground biomass (kg ha−1) × 100%
Nitrogen harvest index (%) = Grain N uptake (kg ha−1)/Total aboveground N uptake (kg ha−1) × 100%
Nitrogen use efficiency (kg kg−1) = Grain yield (kg ha−1)/Aboveground N uptake (kg ha−1)

2.6. Statistical Analyses

Data were processed in Microsoft Office Excel 2021 and analyzed using SPSS 21.0 (Chicago, IL, USA). One-way ANOVA with LSD post hoc tests (p < 0.05) was used to calculate differences in soil physicochemical properties, wheat grain yield, and quality among treatments. Pearson correlations and Mantel tests were conducted in R 4.0.3 to analyze relationships between soil microbial species, physicochemical properties, wheat yield, and grain protein content. Figures were generated using Origin 2021 and RStudio 4.0.3.

3. Results

3.1. Effects of Organic Amendments on Soil Bacterial Communities

3.1.1. Soil Bacterial Community Alpha Diversity

The sequencing coverage for bacterial 16S rRNA exceeded 96% across treatments (Table 3), indicating that the sequencing data for all treatments reached saturation, reflecting the true sample conditions. No significant differences were found in the bacterial alpha diversity indices between the treatments when compared to the F treatment. However, compared to the FSOB treatment, the FO treatment showed significant increases in the Sobs, ACE, Chao1, and PD indices by 6.4%, 7.8%, 7.1%, and 5.6%, respectively. Shannon and Simpson indices showed no significant treatment effects.

3.1.2. Soil Bacterial Community Composition

The Actinobacteria (26.2%), Proteobacteria (18.9%), Acidobacteriota (18.9%), and Chloroflexi (14.3%) were the dominant phyla, accounting for more than 75% of the total bacterial abundance (Figure 2A). The FSOB treatment enriched Actinobacteria by 11.2% and Proteobacteria by 0.6%, while the FO treatment increased Proteobacteria by 19.4%, compared to the F treatment. Moreover, the FB treatment elevated Acidobacteriota by 19.3% and Chloroflexi by 11.6%, respectively, compared to the F treatment.
At the genus level (Figure 2B), the dominant microorganisms were norank_f__Vicinamibacteraceae, norank_o__Vicinamibacterales, norank_c__KD4-96, Bacillus, norank_o__Gaiellales, Gaiella, norank_c__MB-A2-108, and norank_f__Gemmatimonadaceae. These eight dominant genera accounted for an average of 26.4% of the total bacterial genera in all treatments.

3.2. Effects of Organic Amendments on Soil Physicochemical Properties

Organic amendments significantly impacted soil physicochemical properties (Figure 3). Compared to the F treatment, the FS and FSOB treatments significantly increased organic matter content in the 0–20 cm soil layer by 18.5% and 23.1%, respectively, and the FSOB treatment showed a significant increase of 23.8% in the 20–40 cm layer (Figure 3A).
The total N content increased across treatments (Figure 3B), with the FSOB treatments showing the highest enhancement, which were 46.0% (0–20 cm) and 46.6% (20–40 cm) higher than those of the F treatment. Moreover, the FS, FO, and FB treatments showed increases of 37.4%, 28.9%, and 26.7% in the 0–20 cm layer and increases of 23.8%, 16.5%, and 22.6% in the 20–40 cm layer, respectively. In terms of available P (Figure 3C), the FS, FO, FB, and FSOB treatments significantly increased available P content in the 0–20 cm soil layer by 57.4%, 48.7%, 48.0%, and 73.5%, respectively, compared to the F treatment. While in the 20–40 cm layer, the FS, FO, and FSOB treatments significantly increased available P content by 92.5%, 39.9%, and 28.6%, respectively. For available K (Figure 3D), both the FO and FSOB treatments showed significant increases in the 0–20 cm soil layer by 20.9% and 22.7%, respectively, while the FSOB treatment showed a significant increase of 24.6% in the 20–40 cm layer.
The soil bulk density (Figure 3E) in the 0–20 cm soil layer was significantly lower by 4.9% in the FSOB treatment compared to the F treatment. Soil pH remained unaffected by organic amendments (Figure 3F).

3.3. Effects of Organic Amendments on Yield and Yield Components of Black Wheat

Organic amendments significantly influenced the grain yield of black wheat (Figure 4). Compared to conventional fertilization (F), the FS, FO, and FSOB treatments significantly increased grain yield by 12.7%, 14.1%, and 17.3%, respectively, with the FSOB treatment achieving the highest grain yield (6317.5 kg ha−1). The FB treatment showed no significant yield enhancement.
The increase in grain yield stemmed primarily from increased spike number per hectare (Table 4). Compared to the F treatment, the spike number increased by 21.3%, 21.8%, and 27.7% in the FS, FO, and FSOB treatments, respectively. The FO treatment significantly increased grains per ear by 8.9%, while the FSOB treatment significantly increased the 1000-grain weight by 4.2%. All treatments reduced harvest index relative to the F treatment, with FS (−7.8%) and FB (−7.2%) treatments showing significant declines.

3.4. Effects of Organic Amendments on Grain Protein Content and Composition of Black Wheat

Grain protein content responded differently to organic amendments (Figure 5). Compared to the F treatment, the FS and FO treatments significantly increased grain protein content by 9.0% and 9.4%, respectively, peaking at 16.0% under the FO treatment.
Organic amendments had significant effects on the glutenin protein content but had no significant effects on albumin, globulin, or gliadin contents (Figure 6). Compared to the F treatment, the FB treatment reduced glutenin content by 8.1%, while the FS treatment increased glutenin content by 6.8%.

3.5. Effects of Organic Amendments on N Uptake and Utilization in Black Wheat

Organic amendments significantly influenced the grain N uptake of black wheat (Figure 7A). Compared to the F treatment, the FS and FO treatments significantly increased the grain N uptake by 33.5% and 20.3%, respectively. Both the FS and FO treatments showed significant increases in aboveground N uptake of black wheat, which were 36.9% and 21.9% higher than that of the F treatment, respectively (Figure 7B). The FSOB treatment achieved the highest N use efficiency in the 2023–2024 season, increasing by 21.0% compared to the F treatment, and maintained a high level over both years (Figure 7C). No significant differences in the N harvest index were found among treatments (Figure 7D).

3.6. Correlation Analysis Between Soil Physicochemical Properties, Grain Yield, Protein Concentration, and Dominant Bacterial Phyla

Soil physicochemical properties were closely related to grain yield and protein concentration, and they significantly affected the structure and function of bacterial communities (Figure 8). Wheat grain yield showed a positive correlation with soil available K content (AK, r = 0.98) and a negative correlation with soil bulk density (BD, r = –0.66). Grain protein concentration is associated with soil total N content (TN, r = 0.53) and soil organic matter (SOM, r = 0.52). In addition, dominant phyla such as Firmicutes closely correlated with TN (r = –0.91), SOM (r = –0.91), and BD (r = 0.95), while Gemmatimonadota correlated with BD (r = 0.91), respectively.

4. Discussion

4.1. Influences of Organic Amendments on Grain Yield and Quality of Black Wheat

The integrated organic management demonstrated superior yield enhancement, achieving a 17.3% grain yield increase over conventional fertilization (Figure 4), primarily through elevated spike number per hectare by 21.3–27.7% (Table 4). These results align with previous studies demonstrating that straw incorporation improves tillering efficiency by mitigating drought stress during critical growth phases [49], while organic fertilizers enhance nutrient availability for spikelet development [50]. Our findings corroborate Li et al. [49], who reported yield improvements through optimized tillering under straw return systems.
In contrast to studies reporting significant yield improvements with biochar co-applied with inorganic fertilizers—such as a 10% increase compared to mineral fertilizer alone [36] and up to a 48% increase within one year of application [51]—our study observed limited yield gains under sole biochar treatment. This discrepancy may be attributed to biochar’s transient nutrient retention and immobilization effects, particularly for nitrogen and phosphorus, as well as its potential to adsorb agrochemicals like herbicides and pesticides [52,53,54]. These factors could constrain nutrient bioavailability in the short term, thus limiting biochar’s agronomic efficiency when applied alone. However, our findings align with those of Kloss et al. [55], who also reported no significant crop yield response in temperate soils after biochar use despite improved soil nutrient levels. In contrast, our integrated organic management treatment demonstrated notable yield gains, likely due to synergistic interactions among biochar, straw, and organic fertilizer—where improved soil structure, carbon inputs, and nutrient supply (Figure 3) collectively enhanced tillering and spike number, ultimately boosting grain yield.
Although integrated management significantly improved yield, grain nitrogen uptake was similar to the control, likely due to limited remobilization efficiency. While straw return and organic fertilizer enhanced N uptake by improving soil fertility, their low NUE—possibly due to slow mineralization and N release [56,57]—restricted N availability during grain filling. In contrast, the integrated approach more effectively synchronized nitrogen supply with crop demand, improving NUE and yield (Figure 7). Despite raising protein content, straw and organic fertilizer alone led to more N allocated to vegetative organs, explaining their lower yield.
Straw incorporation and organic fertilization significantly enhanced grain protein concentration relative to conventional fertilization, with organic fertilizer amendment achieving the highest grain protein concentration (16.0%, +9.4%) (Figure 5). This protein enrichment under organic fertilizer amendment correlated strongly with elevated soil N availability (Figure 3A), confirming the established soil N–protein nexus [58]. Concurrent improvements in SOM (+18.4%), AP (+48.7%), and AK (+20.9%) under organic fertilizer amendment (Figure 3B–D) further synergized protein synthesis through enhanced nutrient accessibility, aligning with Wu et al. [59], who demonstrated that organic fertilizer application improves grain quality by enhancing soil fertility and nutrient utilization.
Straw return increased the grain protein concentration of black wheat by 8.99%, mechanistically driven by straw-derived SOM (+18.5%) stimulating microbial N mineralization (Figure 3B) and subsequent crop N uptake efficiency (+36.9%; Figure 7B) [60]. In contrast, biochar application exhibited minimal protein effects, likely due to its transient nutrient adsorption capacity and delayed release kinetics in short-term applications.
Notably, the integrated organic management induced protein dilution despite superior yields—a paradox explained by insufficient N uptake scaling (+21.9%) relative to yield gains (+17.3%) (Figure 7B). This resulted in reduced per-grain N allocation, consistent with Mosleth et al. [61] and Zheng et al. [62], who pointed out that high yield is often accompanied by lower grain protein concentration due to the starch–protein competition. Different organic amendments not only influenced grain yield and protein concentration of black wheat but also significantly affected the protein composition. Although the integrated organic management significantly increased yield, it led to unchanged or even a decrease in glutenin and gliadin concentrations. In contrast, organic fertilizer amendment and straw return significantly increased the concentrations of gliadin and glutenin, which is beneficial for improving the processing quality of black wheat. Therefore, wheat processing quality can be measured by the ratio of grain glutenin to gliadin [63], and the increased levels of both components under single amendments suggest an enhanced gluten structure. This dichotomy indicates that single amendments better preserve quality parameters, while integrated systems prioritize yield via physiological reallocation. In summary, integrated organic management is an effective strategy for achieving high yield in black wheat. However, its protein dilution necessitates complementary N management strategies to resolve yield–quality conflicts.

4.2. Influences of Organic Amendments on Soil Properties and Microbial Communities

Our findings validate organic amendments as dual-functional strategies for soil C sequestration and fertility enhancement [64,65]. Specifically, straw incorporation elevated the contents of SOM (+18.5%), TN (+37.4%), and AP (+57.4%) in the 0–20 cm layer versus conventional fertilization. Organic fertilizer amendment similarly enhanced TN (+28.9%), AP (+48.7%), and AK (+20.9%) (Figure 3). Organic fertilizer amendment concurrently increased Proteobacteria abundance (+19.4%), likely driven by soluble C inputs stimulating copiotrophic microbial activity—a response pattern consistent with labile organic matter effects on r-strategist taxa [66].
The integrated organic management demonstrated synergistic superiority, achieving maximal improvements across multiple soil parameters: TN increased by 46.0%, SOM by 23.1%, AK by 22.7%, and AP by 73.5% in the 0–20 cm layer. Concurrently, it reduced soil bulk density by 4.9%, reflecting improved soil structural properties (Figure 3E). These enhancements resulted from functional complementarity between amendment components—biochar’s nutrient retention capacity synergized with straw’s C stabilization effects and organic fertilizer’s rapid mineralization dynamics [13,22,67]. This multidimensional improvement pattern confirms previous observations that combined amendments overcome single-treatment limitations through integrated nutrient cycling [37,68,69 ].
Organic amendment supported higher α-diversity (Chao1 +7.8%; Table 3) compared to the integrated organic management, indicating organic fertilizers promote rare taxa through diverse C substrates. Conversely, the competitive exclusion dynamics under integrated organic management favored Proteobacteria (+0.6%) and Actinobacteria (+11.2%)—key decomposers [70]—while suppressing oligotrophic Acidobacteriota (−1.6%) and Gemmatimonadota (−19.8%) (Figure 2A). This aligns with resource competition theory [71], where biochar-adsorbed dissolved organic C creates preferential niches for copiotrophs over K-strategists [72].
Though biochar application elevated TN (+26.7%) and AP (+48.7%), its short-term impacts lagged in SOM accumulation and microbial richness. This transient response contrasts with longitudinal studies showing progressive SOM improvement over 4–6 years [73,74,75,76], suggesting our 2-year trial captured initial-phase adsorption effects [77], rather than stabilized benefits.
The efficacy of integrated organic management stems from tripartite synergy across physical, chemical, and biological domains. Biochar–straw interactions primarily enhanced soil structural integrity, reducing bulk density through pore network optimization. Concurrent chemical synergy emerged through biochar-mediated gradual nutrient release, effectively buffering mineralization pulses from organic fertilizers. Biologically, functional guild enrichment—particularly Actinobacteria and Proteobacteria—accelerated decomposition–mineralization loops, with straw-derived C inputs stimulating enzymatic activities. This interconnected synergy created self-reinforcing improvements: physical structural enhancement promoted microbial habitat diversity, while chemical buffering sustained nutrient fluxes that supported biological processes—ultimately driving sustainable yield gains without compromising long-term soil health. This integrated approach outperforms single amendments in both fertility enhancement and microbial function optimization, positioning it as a scalable strategy for sustainable black wheat systems.

5. Conclusions

This study demonstrates that organic amendments improve black wheat yield and quality primarily through enhancing soil fertility. The integrated application of straw, organic fertilizer, and biochar significantly improved soil structure, nutrient availability, and microbial functionality, resulting in the highest grain yield. However, this increase was accompanied by a dilution of protein content, suggesting a trade-off between productivity and quality. In contrast, sole applications of straw or organic fertilizer were more effective at enhancing grain protein and glutenin content. Notably, sole biochar application showed limited agronomic benefits and even led to a reduction in glutenin concentration, likely due to its nutrient adsorption properties and limited short-term nutrient release.
These findings suggest that context-specific strategies are needed: single organic inputs (straw or organic fertilizer) are more suitable for quality-focused production, while integrated organic management is better suited for maximizing yield. Moving forward, optimizing amendment combinations and applying nitrogen strategically at key growth stages could help mitigate the yield–quality conflict and support sustainable black wheat production.

Author Contributions

Conceptualization, C.X.; data curation, C.X.; formal analysis, H.X. (Huasen Xu); funding acquisition, C.X.; investigation, J.Z. and R.F.; methodology, J.Z. and R.F.; project administration, C.X.; resources, H.X. (Huasen Xu); software, M.Z. and H.X. (Hui Xiao); supervision, C.X.; validation, H.X. (Huasen Xu) and M.Z.; visualization, J.Z. and H.X. (Hui Xiao); writing—original draft preparation, J.Z.; writing—review and editing, J.Z. and C.X. All authors have read and agreed to the published version of the manuscript.

Funding

This research was funded by the National Key Research and Development Program of China (No. 2021YFD1901005) and the Central Guidance for Local Technology Development Fund (236Z6402G).

Data Availability Statement

The data presented in this study are available upon request from the corresponding author.

Acknowledgments

We thank the editor and reviewers for their helpful suggestions to improve the quality of this manuscript.

Conflicts of Interest

The authors declare no conflicts of interest.

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Figure 1. Monthly precipitation (bar chart) and average monthly temperature (line chart) during the wheat-growing seasons (2022–2024), compared with the 2012–2021 averages. Data source: China National Meteorological Science Data Center (https://data.cma.cn, accessed on 30 December 2024).
Figure 1. Monthly precipitation (bar chart) and average monthly temperature (line chart) during the wheat-growing seasons (2022–2024), compared with the 2012–2021 averages. Data source: China National Meteorological Science Data Center (https://data.cma.cn, accessed on 30 December 2024).
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Figure 2. Effect of organic amendments on soil bacterial community composition at the phylum (A) and genus (B) levels.
Figure 2. Effect of organic amendments on soil bacterial community composition at the phylum (A) and genus (B) levels.
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Figure 3. Effects of organic amendments on organic matter (A), total N (B), available P (C), available K (D), bulk density (E), and pH (F) in the 0–20 cm and 20–40 cm soil layers at wheat maturity. Note: Different lowercase letters indicate significant differences between treatments within the same soil layer (p < 0.05). Error bars represent standard error.
Figure 3. Effects of organic amendments on organic matter (A), total N (B), available P (C), available K (D), bulk density (E), and pH (F) in the 0–20 cm and 20–40 cm soil layers at wheat maturity. Note: Different lowercase letters indicate significant differences between treatments within the same soil layer (p < 0.05). Error bars represent standard error.
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Figure 4. Effect of organic amendments on grain yield of black wheat. Note: Different lowercase letters indicate significant differences between treatments within the same year (p < 0.05). Error bars represent standard error. Y, year; T, treatment; Y × T, interaction between year and treatment; ns, no significant difference; *, p < 0.05; **, p < 0.01.
Figure 4. Effect of organic amendments on grain yield of black wheat. Note: Different lowercase letters indicate significant differences between treatments within the same year (p < 0.05). Error bars represent standard error. Y, year; T, treatment; Y × T, interaction between year and treatment; ns, no significant difference; *, p < 0.05; **, p < 0.01.
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Figure 5. Effect of organic amendments on grain protein content of black wheat. Note: Different lowercase letters indicate significant differences between treatments within the same year (p < 0.05). Error bars represent standard error. Y, year; T, different organic material treatments; Y × T, interaction between year and treatment; ns, no significant difference; **, p < 0.01.
Figure 5. Effect of organic amendments on grain protein content of black wheat. Note: Different lowercase letters indicate significant differences between treatments within the same year (p < 0.05). Error bars represent standard error. Y, year; T, different organic material treatments; Y × T, interaction between year and treatment; ns, no significant difference; **, p < 0.01.
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Figure 6. Effect of organic amendments on grain protein composition of black wheat: albumin (A), globulin (B), gliadin (C), and glutenin (D) concentration. Note: Different lowercase letters indicate significant differences between treatments within the same year (p < 0.05). Error bars represent standard error. Y, year; T, different organic material treatments; Y × T, interaction between year and treatment; ns, no significant difference; *, p < 0.05; **, p < 0.01.
Figure 6. Effect of organic amendments on grain protein composition of black wheat: albumin (A), globulin (B), gliadin (C), and glutenin (D) concentration. Note: Different lowercase letters indicate significant differences between treatments within the same year (p < 0.05). Error bars represent standard error. Y, year; T, different organic material treatments; Y × T, interaction between year and treatment; ns, no significant difference; *, p < 0.05; **, p < 0.01.
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Figure 7. Effects of organic amendments on grain N uptake (A), aboveground N uptake (B), N use efficiency (C), and N harvest index (D) of black wheat. Note: Different lowercase letters indicate significant differences between treatments within the same year (p < 0.05). Error bars represent standard error. Y, year; T, different organic material treatments; Y × T, interaction between year and treatment; ns, no significant difference; *, p < 0.05.
Figure 7. Effects of organic amendments on grain N uptake (A), aboveground N uptake (B), N use efficiency (C), and N harvest index (D) of black wheat. Note: Different lowercase letters indicate significant differences between treatments within the same year (p < 0.05). Error bars represent standard error. Y, year; T, different organic material treatments; Y × T, interaction between year and treatment; ns, no significant difference; *, p < 0.05.
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Figure 8. Pearson correlation and Mantel test analysis between soil physicochemical properties, grain yield, protein concentration, and dominant bacterial phyla. Note: SOM, soil organic matter; TN, total nitrogen; AP, available phosphorus; AK, available potassium; BD, soil bulk density; pH, soil pH; Yield = wheat yield; Protein = wheat grain protein content. The upper triangular matrix shows correlation coefficients between environmental factors, with color indicating the strength and direction of correlation (red = negative, blue = positive). The size of the squares corresponds to the magnitude of the correlation coefficient. Lines below the correlation matrix represent significant relationships identified through Mantel tests, with line color indicating p-value categories (0.01–0.05, >0.05) and line thickness representing the Mantel correlation coefficient (<0.25, 0.25–0.5, ≥0.5). An asterisk (*) indicates that the Pearson correlation is statistically significant at the p < 0.05 level.
Figure 8. Pearson correlation and Mantel test analysis between soil physicochemical properties, grain yield, protein concentration, and dominant bacterial phyla. Note: SOM, soil organic matter; TN, total nitrogen; AP, available phosphorus; AK, available potassium; BD, soil bulk density; pH, soil pH; Yield = wheat yield; Protein = wheat grain protein content. The upper triangular matrix shows correlation coefficients between environmental factors, with color indicating the strength and direction of correlation (red = negative, blue = positive). The size of the squares corresponds to the magnitude of the correlation coefficient. Lines below the correlation matrix represent significant relationships identified through Mantel tests, with line color indicating p-value categories (0.01–0.05, >0.05) and line thickness representing the Mantel correlation coefficient (<0.25, 0.25–0.5, ≥0.5). An asterisk (*) indicates that the Pearson correlation is statistically significant at the p < 0.05 level.
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Table 1. Basic physicochemical properties of the 0–40 cm soil layer prior to experiment initiation in 2022.
Table 1. Basic physicochemical properties of the 0–40 cm soil layer prior to experiment initiation in 2022.
Soil Depth
(cm)		Organic Matter Content
(g kg−1)		Total N Content
(g kg−1)		Available P Content
(mg kg−1)		Available K Content
(mg kg−1)		pHSoil Bulk Density
(g cm−3)
0–2016.11.07.7108.58.11.3
20–4013.30.52.881.38.21.4
Table 2. Organic amendment quantities for each treatment.
Table 2. Organic amendment quantities for each treatment.
TreatmentStraw Return (%)Organic Fertilizers (t ha−1)Biochar (t ha−1)
F000
FS10000
FO030
FB003
FSOB10033
Table 3. Effects of organic amendments on soil bacterial alpha diversity indices.
Table 3. Effects of organic amendments on soil bacterial alpha diversity indices.
TreatmentSobsShannon
Index		Simpson
Index		ACE
Index		Chao 1
Index		Coverage/%PD
Index
F3534 ab6.79 a0.0033 a4751.49 ab4646.49 ab96.93%275.39 ab
FS3526 ab6.85 a0.0029 a4708.17 ab4620.88 ab96.99%278.77 ab
FO3625 a6.87 a0.0031 a4916.14 a4808.01 a96.82%282.34 a
FB3514 ab6.81 a0.0033 a4716.86 ab4551.70 b97.00%275.84 ab
FSOB3408 b6.80 a0.0033 a4560.96 b4489.09 b97.09%267.30 b
Note: The data were collected from the 0–20 cm soil layer during the wheat harvest seasons of 2023–2024. Different lowercase letters within the same column denote significant differences among treatments (p < 0.05).
Table 4. Effects of organic amendments on yield components and harvest index of black wheat.
Table 4. Effects of organic amendments on yield components and harvest index of black wheat.
YearTreatmentSpike Number
(×104 ha−1)		Grains per Ear1000-Grain Weight
(g)		Harvest Index
(%)
2022–2023F401.7 ± 14.2 b44 ± 1.5 a32.1 ± 0.3 b40.8 ± 1.7 a
FS446.5 ± 9.8 ab42 ± 0.4 a34.0 ± 0.6 a38.3 ± 0.6 ab
FO418.1 ± 27.2 b46 ± 2.1 a33.8 ± 0.6 a36.2 ± 1.1 b
FB416.5 ± 28.6 b44 ± 0.9 a33.4 ± 0.4 ab36.9 ± 0.3 b
FSOB510.7 ± 32.9 a42 ± 1.1 a33.8 ± 0.7 a38.9 ± 0.8 ab
2023–2024F484.7 ± 5.2 b35 ± 0.6 b32.4 ± 0.3 b39.6 ± 0.9 a
FS628.3 ± 34.1 a39 ± 0.2 a31.3 ± 0.2 c35.8 ± 1.5 b
FO661.7 ± 3.0 a40 ± 0.9 a32.6 ± 0.3 ab40.9 ± 0.3 a
FB549.0 ± 23.5 b40 ± 0.8 a31.5 ± 0.3 c37.8 ± 1.5 ab
FSOB621.0 ± 25.1 a42 ± 1.5 a33.4 ± 0.6 a40.8 ± 1.6 a
2022–2024F443.2 ± 6.7 b39 ± 0.8 b32.2 ± 0.3 b40.2 ± 0.9 a
FS537.4 ± 21.3 a41 ± 0.2 ab32.7 ± 0.2 ab37.1 ± 0.9 b
FO539.9 ± 14.6 a43 ± 1.1 a33.2 ± 0.3 ab38.6 ± 1.0 ab
FB482.7 ± 12.3 b42 ± 0.5 ab32.4 ± 0.2 b37.3 ± 0.7 b
FSOB565.9 ± 22.9 a42 ± 1.2 ab33.6 ± 0.2 a39.7 ± 0.9 ab
ANOVA
results		Y
T
Y × T		***
***
**		***
*
*		***
ns
*		ns
*
*
Note: Different lowercase letters indicate significant differences between treatments within the same year (p < 0.05). Error bars represent standard error. Y, year; T, different organic material treatments; Y × T, interaction between year and treatment; ns, no significant difference; *, p < 0.05; **, p < 0.01; ***, p < 0.001.
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MDPI and ACS Style

Zhou, J.; Xu, H.; Zhang, M.; Feng, R.; Xiao, H.; Xue, C. Impact of Organic Amendments on Black Wheat Yield, Grain Quality, and Soil Biochemical Properties. Agronomy 2025, 15, 961. https://doi.org/10.3390/agronomy15040961

AMA Style

Zhou J, Xu H, Zhang M, Feng R, Xiao H, Xue C. Impact of Organic Amendments on Black Wheat Yield, Grain Quality, and Soil Biochemical Properties. Agronomy. 2025; 15(4):961. https://doi.org/10.3390/agronomy15040961

Chicago/Turabian Style

Zhou, Jiaqi, Huasen Xu, Meng Zhang, Ruohan Feng, Hui Xiao, and Cheng Xue. 2025. "Impact of Organic Amendments on Black Wheat Yield, Grain Quality, and Soil Biochemical Properties" Agronomy 15, no. 4: 961. https://doi.org/10.3390/agronomy15040961

APA Style

Zhou, J., Xu, H., Zhang, M., Feng, R., Xiao, H., & Xue, C. (2025). Impact of Organic Amendments on Black Wheat Yield, Grain Quality, and Soil Biochemical Properties. Agronomy, 15(4), 961. https://doi.org/10.3390/agronomy15040961

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