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Volume 15
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Agronomy, Volume 15, Issue 7 (July 2025) – 206 articles

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22 pages, 1279 KiB  
Review
State of the Art of Biomethane Production in the Mediterranean Region
by Antonio Comparetti, Salvatore Ciulla, Carlo Greco, Francesco Santoro and Santo Orlando
Agronomy 2025, 15(7), 1702; https://doi.org/10.3390/agronomy15071702 (registering DOI) - 15 Jul 2025
Abstract
The Mediterranean region is increasingly confronted with intersecting environmental, agricultural, and socio-economic challenges, including biowaste accumulation, soil degradation, and high dependency on imported fossil fuels. Biomethane, a renewable substitute for natural gas, offers a strategic solution that aligns with the region’s need for [...] Read more.
The Mediterranean region is increasingly confronted with intersecting environmental, agricultural, and socio-economic challenges, including biowaste accumulation, soil degradation, and high dependency on imported fossil fuels. Biomethane, a renewable substitute for natural gas, offers a strategic solution that aligns with the region’s need for sustainable energy transition and circular resource management. This review examines the current state of biomethane production in the Mediterranean area, with a focus on anaerobic digestion (AD) technologies, feedstock availability, policy drivers, and integration into the circular bioeconomy (CBE) framework. Emphasis is placed on the valorisation of regionally abundant feedstocks such as olive pomace, citrus peel, grape marc, cactus pear (Opuntia ficus-indica) residues, livestock manure, and the Organic Fraction of Municipal Solid Waste (OFMSW). The multifunctionality of AD—producing renewable energy and nutrient-rich digestate—is highlighted for its dual role in reducing greenhouse gas (GHG) emissions and restoring soil health, especially in areas threatened by desertification such as Sicily (Italy), Spain, Malta, and Greece. The review also explores emerging innovations in biogas upgrading, nutrient recovery, and digital monitoring, along with the role of Renewable Energy Directive III (RED III) and national biomethane strategies in scaling up deployment. Case studies and decentralised implementation models underscore the socio-technical feasibility of biomethane systems across rural and insular territories. Despite significant potential, barriers such as feedstock variability, infrastructural gaps, and policy fragmentation remain. The paper concludes with a roadmap for research and policy to advance biomethane as a pillar of Mediterranean climate resilience, energy autonomy and sustainable agriculture within a circular bioeconomy paradigm. Full article
(This article belongs to the Special Issue Recycling of Organic Wastes in Agriculture: Serving for Sustainable Agriculture)
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22 pages, 4643 KiB  
Article
Spectral Estimation of Nitrogen Content in Cotton Leaves Under Coupled Nitrogen and Phosphorus Conditions
by Shunyu Qiao, Wenjin Fu, Jiaqiang Wang, Xiaolong An, Fuqing Li, Weiyang Liu and Chongfa Cai
Agronomy 2025, 15(7), 1701; https://doi.org/10.3390/agronomy15071701 (registering DOI) - 14 Jul 2025
Abstract
With the increasing application of hyperspectral technology, rapid and accurate monitoring of cotton leaf nitrogen concentrations (LNCs) has become an effective tool for large-scale areas. This study used Tahe No. 2 cotton seeds with four nitrogen levels (0, 200, 350, 500 kg ha [...] Read more.
With the increasing application of hyperspectral technology, rapid and accurate monitoring of cotton leaf nitrogen concentrations (LNCs) has become an effective tool for large-scale areas. This study used Tahe No. 2 cotton seeds with four nitrogen levels (0, 200, 350, 500 kg ha−1) and four phosphorus levels (0, 100, 200, 300 kg ha−1). Spectral data were acquired using an ASD FieldSpec HandHeld2 portable spectrometer, which measures spectral reflectance covering a band of 325–1075 nm with a spectral resolution of 1 nm. LNCs determination and spectral estimation were conducted at six growth stages: squaring, initial bloom, peak bloom, initial boll, peak boll, and boll opening. Thirty-seven spectral indices (SIs) were selected. First derivative (FD), standard normal variate (SNV), multiplicative scatter correction (MSC), and Savitzky‒Golay (SG) were applied to preprocess the spectra. Feature bands were screened using partial least squares discriminant analysis (PLS‒DA), and support vector machine (SVM) and random forest (RF) models were used for accuracy validation. The results revealed that (1) LNCs initially increased and then decreased with growth, peaking at the full-flowering stage before gradually declining. (2) The best LNC recognition models were SVM–MSC in the squaring stage, SVM–FD in the initial bloom stage, SVM–FD in the peak bloom stage, SVM–FD in the initial boll stage, RF–SNV in the peak boll Mstage, and SVM–FD in the boll opening stage. FD showed the best performance compared with the other three treatments, with SVM outperforming RF in terms of higher R2 and lower RMSE values. The SVM‒FD model effectively improved the accuracy and robustness of LNCs prediction using hyperspectral leaf spectra, providing valuable guidance for large-scale information production in high-standard cotton fields. Full article
(This article belongs to the Section Precision and Digital Agriculture)
18 pages, 4933 KiB  
Article
Overexpression of a White Clover WRKY Transcription Factor Improves Cold Tolerance in Arabidopsis
by Shuaixian Li, Meiyan Guo, Wei Hong, Manman Li, Xiaoyue Zhu, Changhong Guo and Yongjun Shu
Agronomy 2025, 15(7), 1700; https://doi.org/10.3390/agronomy15071700 - 14 Jul 2025
Abstract
Plants are frequently exposed to various abiotic stresses, among which low-temperature stress markedly impairs growth and physiological functions. WRKY transcription factors are key regulators in plant responses to abiotic stress. In this study, a novel WRKY transcription factor gene, TrWRKY79, was cloned [...] Read more.
Plants are frequently exposed to various abiotic stresses, among which low-temperature stress markedly impairs growth and physiological functions. WRKY transcription factors are key regulators in plant responses to abiotic stress. In this study, a novel WRKY transcription factor gene, TrWRKY79, was cloned from white clover. Functional characterization revealed that the full-length TrWRKY79 protein possesses typical features of transcription factors, including transcriptional activation activity located at its C-terminal domain. Heterologous expression of TrWRKY79 in Arabidopsis thaliana significantly enhanced cold tolerance under low-temperature stress. Physiological assays showed that the transgenic lines exhibited higher chlorophyll content and elevated activities of superoxide dismutase (SOD), peroxidase (POD), and catalase (CAT) compared to wild-type plants. Furthermore, Protenix was employed to predict the potential target genes of TrWRKY transcription factors, and their expression profiles were analyzed to help elucidate the regulatory network underlying cold tolerance. qRT-PCR analysis confirmed that several cold-responsive genes, such as COR47 and ABI5, were significantly upregulated in the transgenic lines. Collectively, these findings indicate that TrWRKY79 plays a positive regulatory role in enhancing cold tolerance, providing valuable insights into the molecular mechanisms of cold resistance in white clover and offering promising candidate genes for improving stress resilience in forage crops. Full article
(This article belongs to the Special Issue Responses of Forage Crops to Environmental Stresses and Stress Alleviating Strategies)
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21 pages, 687 KiB  
Review
Fungi in Horticultural Crops: Promotion, Pathogenicity and Monitoring
by Quanzhi Wang, Yibing Han, Zhaoyi Yu, Siyuan Tian, Pengpeng Sun, Yixiao Shi, Chao Peng, Tingting Gu and Zhen Li
Agronomy 2025, 15(7), 1699; https://doi.org/10.3390/agronomy15071699 - 14 Jul 2025
Abstract
In this review, we aim to provide a comprehensive overview of the roles of fungi in horticultural crops. Their beneficial roles and pathogenic effects are investigated. In addition, the recent advancements in fungal detection and management strategies (especially the use of spectral analysis) [...] Read more.
In this review, we aim to provide a comprehensive overview of the roles of fungi in horticultural crops. Their beneficial roles and pathogenic effects are investigated. In addition, the recent advancements in fungal detection and management strategies (especially the use of spectral analysis) are summarized. Beneficial fungi, including plant growth-promoting fungi (PGPF), ectomycorrhizal fungi (ECM), and arbuscular mycorrhizal fungi (AMF), enhance nutrient uptake, promote root and shoot development, improve photosynthetic efficiency, and support plant resilience against biotic and abiotic stresses. Additionally, beneficial fungi contribute to flowering, seed germination, and disease management through biofertilizers, microbial pesticides, and mycoinsecticides. Conversely, pathogenic fungi cause significant diseases affecting roots, stems, leaves, flowers, and fruits, leading to crop yield losses. Advanced spectral analysis techniques, such as Fourier Transform Infrared Spectroscopy (FTIR), Near-Infrared Spectroscopy (NIR), Raman, and Visible and Near-Infrared Spectroscopy (Vis-NIR), alongside traditional methods like Polymerase Chain Reaction (PCR) and Enzyme-Linked Immunosorbent Assay (ELISA), have shown promise in detecting and managing fungal pathogens. Emerging applications of fungi in sustainable agriculture, including biofertilizers and eco-friendly pest management, are discussed, underscoring their potential to enhance crop productivity and mitigate environmental impacts. This review provides a comprehensive understanding of the complex roles of fungi in horticulture and explores innovative detection and management strategies. Full article
(This article belongs to the Special Issue Microorganisms in Agriculture—Nutrition and Health of Plants)
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1 pages, 142 KiB  
Correction
Correction: Yue et al. YOLOv7-GCA: A Lightweight and High-Performance Model for Pepper Disease Detection. Agronomy 2024, 14, 618
by Xuejun Yue, Haifeng Li, Qingkui Song, Fanguo Zeng, Jianyu Zheng, Ziyu Ding, Gaobi Kang, Yulin Cai, Yongda Lin, Xiaowan Xu and Chaoran Yu
Agronomy 2025, 15(7), 1698; https://doi.org/10.3390/agronomy15071698 - 14 Jul 2025
Abstract
In the original publication [...] Full article
17 pages, 7155 KiB  
Article
Microbial Community Structure and Metabolic Potential Shape Soil-Mediated Resistance Against Fruit Flesh Spongy Tissue Disorder of Peach
by Weifeng Chen, Dan Tang, Jia Huang, Yu Yang and Liangbo Zhang
Agronomy 2025, 15(7), 1697; https://doi.org/10.3390/agronomy15071697 - 14 Jul 2025
Abstract
Peach fruit flesh spongy tissue disorder causes dry, porous, and brown areas in the flesh, severely compromising fruit quality and market value. While soil properties and calcium nutrition have been linked to the disorder, the role of rhizosphere microbial communities in disorder resistance [...] Read more.
Peach fruit flesh spongy tissue disorder causes dry, porous, and brown areas in the flesh, severely compromising fruit quality and market value. While soil properties and calcium nutrition have been linked to the disorder, the role of rhizosphere microbial communities in disorder resistance remains unclear. This study investigated both the physicochemical properties and the root-associated microbiomes of disordered (CK) and healthy (TT) peach orchards to explore microbial mechanisms underlying disorder suppression. TT soils exhibited higher pH, greater organic matter, increased exchangeable calcium, and more balanced trace elements compared to CK. Microbial analysis revealed significantly higher diversity and enrichment of beneficial taxa in TT associated with plant growth and disorder resistance. Functional gene prediction showed TT was enriched in siderophore production, auxin biosynthesis, phosphate solubilization, and acetoin–butanediol synthesis pathways. Co-occurrence network analysis demonstrated that TT harbored a more complex and cooperative microbial community structure, with 274 nodes and 6013 links. Metagenomic binning recovered high-quality MAGs encoding diverse resistance and growth-promoting traits, emphasizing the ecological roles of Gemmatimonadaceae, Reyranella, Nitrospira, Bacillus megaterium, and Bryobacteraceae. These findings highlight the combined importance of soil chemistry and microbiome structure in disorder suppression and provide a foundation for microbiome-informed soil management to enhance fruit quality and promote sustainable orchard practices. Full article
(This article belongs to the Section Agricultural Biosystem and Biological Engineering)
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16 pages, 1945 KiB  
Article
Debaryomyces hansenii Enhances Growth, Nutrient Uptake, and Yield in Rice Plants (Oryza sativa L.) Cultivated in Calcareous Soil
by Jorge Núñez-Cano, Francisco J. Ruiz-Castilla, José Ramos, Francisco J. Romera and Carlos Lucena
Agronomy 2025, 15(7), 1696; https://doi.org/10.3390/agronomy15071696 - 14 Jul 2025
Abstract
Calcareous soils, characterized by high pH and calcium carbonate content, often limit the availability of essential nutrients for crops such as rice (Oryza sativa L.), reducing yield and nutritional quality. In this study, we evaluated the effect of the halotolerant yeast Debaryomyces [...] Read more.
Calcareous soils, characterized by high pH and calcium carbonate content, often limit the availability of essential nutrients for crops such as rice (Oryza sativa L.), reducing yield and nutritional quality. In this study, we evaluated the effect of the halotolerant yeast Debaryomyces hansenii on the growth, nutrient uptake, and phosphorus acquisition mechanisms of rice plants cultivated in calcareous soil under controlled greenhouse conditions. Plants inoculated with D. hansenii, particularly via root immersion, exhibited significantly higher SPAD chlorophyll index, plant height, and grain yield compared to controls. A modest increase (~4%) in dry matter content was also observed under sterilized soil conditions. Foliar concentrations of Fe, Zn, and Mn significantly increased in plants inoculated with D. hansenii via root immersion in non-sterilized calcareous soil, indicating improved micronutrient acquisition under these specific conditions. Although leaf phosphorus levels were not significantly increased, D. hansenii stimulated acid phosphatase activity, as visually observed through BCIP staining, and upregulated genes involved in phosphorus acquisition under both P-sufficient and P-deficient conditions. At the molecular level, D. hansenii upregulated the expression of acid phosphatase genes (OsPAP3, OsPAP9) and a phosphate transporter gene (OsPTH1;6), confirming its influence on P-related physiological responses. These findings demonstrate that D. hansenii functions as a plant growth-promoting yeast (PGPY) and may serve as a promising biofertilizer for improving rice productivity and nutrient efficiency in calcareous soils, contributing to sustainable agricultural practices in calcareous soils and other nutrient-limiting environments. Full article
(This article belongs to the Special Issue Optimization and Innovation of Physiological Indexes in Crop Tolerance Mechanism)
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16 pages, 4501 KiB  
Article
Predominant Sugarcane Cultivars in the Northwestern Colombian Amazon Exhibit High Susceptibility to Orange Rust (Puccinia kuehnii)
by Soraida Rojas-Vargas, Juan Carlos Ángel-Sánchez, Diego Alexander Toro-Ardila, Gabriel Rivera-Vera, Diego Armando Jiménez-Carvajal and Fausto Andrés Ortiz-Morea
Agronomy 2025, 15(7), 1695; https://doi.org/10.3390/agronomy15071695 - 14 Jul 2025
Viewed by 17
Abstract
Sugarcane (Saccharum spp.) is crucial for sweetener production but is highly susceptible to diseases such as orange rust, caused by Puccinia kuehnii. In the northwestern Colombian Amazon, sugarcane is increasingly cultivated, mainly for panela production, a traditional sweetener. However, the introduction [...] Read more.
Sugarcane (Saccharum spp.) is crucial for sweetener production but is highly susceptible to diseases such as orange rust, caused by Puccinia kuehnii. In the northwestern Colombian Amazon, sugarcane is increasingly cultivated, mainly for panela production, a traditional sweetener. However, the introduction of sugarcane has occurred without systematic planning, resulting in limited knowledge about cultivars’ characteristics and disease susceptibility. This study aimed to characterize sugarcane cultivars in the region and assess the occurrence and field-level impact of orange rust, while also confirming the identity of the pathogen using molecular and morphological analysis. We identified five sugarcane cultivars, with only CP 57-603 having an official designation, while the others were known by local names: Regional Without Fuzz, Hairy Purple, and two unnamed genotypes (Cultivar-1 and -2). CP 57-603 and Regional Without Fuzz were the most commonly cultivated (by 49.2% and 74.5% of farms, respectively), while Cultivar-1 (11.8%), Cultivar-2 (7.8%), and Hairy Purple (1.96%) were less frequent. Orange rust was detected in 72% of farms with CP 57-603, 66% with Regional Without Fuzz, and 50% with Cultivar-1, but was absent in farms growing Cultivar-2 and Hairy Purple. Molecular analysis of the ITS1/2 region revealed a single haplotype within the P. kuehnii population, indicating low diversity at this locus in the region. Phylogenetic analysis grouped our ITS1/2 haplotype within a clade alongside isolates from the Americas. Morphological characterization of the pathogen showed no significant trait variation among samples. These findings confirm the presence of P. kuehnii in the region and highlight the urgent need for cultivar diversification and improved disease management to safeguard sugarcane production. Full article
(This article belongs to the Special Issue Phytopathogens and Crop Diseases)
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15 pages, 5981 KiB  
Article
Metabolome and Transcriptome Analyses Revealing the Molecular Mechanisms of Precarious Fertility in Quinoa Cultivars
by Chao Song, Qingyun Huang, Chunsong Lin, Huihua Li, Ziyang Li, Yiding Xu, Fei Chen, Xueqin Zhang, Zhiqiang Wu and Suxia Xu
Agronomy 2025, 15(7), 1694; https://doi.org/10.3390/agronomy15071694 - 13 Jul 2025
Viewed by 180
Abstract
Quinoa (Chenopodium quinoa Willd) is a tetraploid crop that has provided vital subsistence, nutrition, and medicine for Andean indigenous cultures. In recent years, quinoa has gained global importance all over the world. However, variations in fertility have been frequently observed during the [...] Read more.
Quinoa (Chenopodium quinoa Willd) is a tetraploid crop that has provided vital subsistence, nutrition, and medicine for Andean indigenous cultures. In recent years, quinoa has gained global importance all over the world. However, variations in fertility have been frequently observed during the flower development of quinoa, severely affecting quinoa production. To comprehend the fundamental causes of fertility variation in quinoa, this research examined hormonal metabolism and gene expression across three ecotypes: normal fertility (F), absent stamens (S1), and abnormal stamens (S3). S1 and S3 presented absent and abnormal stamens, respectively, compared with F. Phytohormone profiling yielded 60 metabolites and revealed the clear separation between different ecotypes at different developmental stages according to principal component analysis (PCA). The results of transcriptomics showed more DEGs (differentially expressed genes) identified between F and S1 ecotypes (8002 and 10,716 for earlier and later stages, respectively) than F vs. S3 (4500 and 9882 for earlier and later stages, respectively) and S1 vs. S3 (4203 and 5052 for earlier and later stages, respectively). Zeatin biosynthesis and hormone signal transduction pathways were enriched among 19 KEGG (Kyoto Encyclopedia of Genes and Genomes) terms, indicating their potential roles in quinoa flower fertility regulation. The correlation-based network presented the associations between selected hormones and genes, possibly regulating fertile ecotypes. Furthermore, we explored the expression of flower development-related genes in three ecotypes using RT-PCR, showing the higher expressions of AP1, AP3, and FLS in sterile ecotypes than fertile ecotypes at both stages. These findings reveal new insights into the hormonal and genetic regulations of floral fertility in quinoa, which may have consequences for developing high-yielding cultivars. Full article
(This article belongs to the Section Crop Breeding and Genetics)
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16 pages, 4861 KiB  
Article
Organic Materials Promote Soil Phosphorus Cycling: Metagenomic Analysis
by Wei Yang, Yue Jiang, Jiaqi Zhang, Wei Wang, Xuesheng Liu, Yu Jin, Sha Li, Juanjuan Qu and Yuanchen Zhu
Agronomy 2025, 15(7), 1693; https://doi.org/10.3390/agronomy15071693 - 13 Jul 2025
Viewed by 183
Abstract
The combined application of chemical fertilizers with organic materials contributes to higher contents of bioavailable phosphorus. However, the underlying mechanism remains poorly understood. A field experiment including four treatments, chemical fertilizer (CF), chemical fertilizer with biochar (CB), chemical fertilizer with organic fertilizer (CO), [...] Read more.
The combined application of chemical fertilizers with organic materials contributes to higher contents of bioavailable phosphorus. However, the underlying mechanism remains poorly understood. A field experiment including four treatments, chemical fertilizer (CF), chemical fertilizer with biochar (CB), chemical fertilizer with organic fertilizer (CO), and chemical fertilizer with biochar and organic fertilizer (CBO), was conducted to explore how the combination of fertilizer applications enhanced soil phosphorus bioavailability using metagenomic sequencing technology. The results showed that chemical fertilizers combined with organic materials (CB, CO, and CBO) significantly increased citrate-extractable phosphorus by 34.61–138.92% and hydrochloric acid-extractable phosphorus contents by 72.85–131.07% compared to CF. In addition, the combined applications altered the microbial community structure and increased the abundance of phoR, spoT, and ppnK genes, but decreased those of gcd, phoD, and ppk1 genes. A partial least squares path model indicated that the combined applications regulated the microbial community composition and gene abundance of phosphorus-cycling microorganisms by influencing soil physicochemical properties, thereby enhancing soil phosphorus cycling. Correlation analysis indicated that pH, total phosphorus, and available phosphorus were the key factors influencing microbial communities, while available nitrogen and total nitrogen primarily regulated phosphorus cycling gene abundance. In addition, the CO and CBO treatments significantly increased maize yield by 14.60% and 21.04%, respectively. Overall, CBO most effectively enhanced bioavailable phosphorus content and maize yield. This study provides a foundation for developing rational fertilization strategies and improving soil phosphorus use efficiency. Full article
(This article belongs to the Section Soil and Plant Nutrition)
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20 pages, 1390 KiB  
Article
Performance of Trichogramma pretiosum Riley (Hymenoptera: Trichogrammatidae) Strains on Eggs from Different Populations of Tuta absoluta (Meyrick) (Lepidoptera: Gelechiidae)
by Alessandro Bandeira Dalbianco, Diego Fernando Daniel, Dirceu Pratissoli, Daniel de Lima Alvarez, Nadja Nara Pereira da Silva, Daniel Mariano Santos, Santino Seabra Júnior and Regiane Cristina de Oliveira
Agronomy 2025, 15(7), 1692; https://doi.org/10.3390/agronomy15071692 - 13 Jul 2025
Viewed by 167
Abstract
Tomato is the most widely cultivated fruit–vegetable worldwide, and the tomato leafminer (Tuta absoluta) is the primary pest of this crop. In this context, biological control using parasitoids belonging to the genus Trichogramma is crucial. This study aimed to evaluate the [...] Read more.
Tomato is the most widely cultivated fruit–vegetable worldwide, and the tomato leafminer (Tuta absoluta) is the primary pest of this crop. In this context, biological control using parasitoids belonging to the genus Trichogramma is crucial. This study aimed to evaluate the biological characteristics of T. pretiosum strains collected from different locations and exposed to eggs from various T. absoluta populations/generations, using parameters such as parasitism capacity, viability (percentage of emergence), sex ratio, and female longevity. The presence of endosymbionts in the T. absoluta populations was also assessed. The experiment followed a randomized design, with treatments consisting of eggs from T. absoluta populations collected in different years (2019, 2020, 2021, 2022, and 2023) and different strains of T. pretiosum. We used 20 replicates, with one female per replicate in each treatment, organized in a 5 × 4 factorial scheme (five populations of T. absoluta × four strains of T. pretiosum). The S2 strain of T. pretiosum was found to be the most efficient in terms of biological characteristics for parasitism of T. absoluta eggs, especially in T. absoluta populations collected in recent years (2022 and 2023). These results suggest that S2 is the preferred strain for future studies aimed at using this parasitoid as a control agent to combat T. absoluta. The endosymbionts Arsenophonus and Serratia were identified in T. absoluta populations collected in 2019–2020 and 2020–2021, respectively. These findings highlight the presence of these microorganisms in pest populations in different years. Full article
(This article belongs to the Special Issue Biological Pest Control in Agroecosystems—2nd Edition)
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21 pages, 1916 KiB  
Article
Pre-Symptomatic Detection of Nicosulfuron Phytotoxicity in Vegetable Soybeans via Hyperspectral Imaging and ResNet-18
by Yun Xiang, Tian Liang, Yuanpeng Bu, Shiqiang Cai, Jingjie Guo, Zhongjing Su, Jinxuan Hu, Chang Cai, Bin Wang, Zhijuan Feng, Guwen Zhang, Na Liu and Yaming Gong
Agronomy 2025, 15(7), 1691; https://doi.org/10.3390/agronomy15071691 - 12 Jul 2025
Viewed by 146
Abstract
Herbicide phytotoxicity represented a critical constraint on crop safety in soybean–corn intercropping systems, where early detection of herbicide stress is essential for implementing timely mitigation strategies to preserve yield potential. Current methodologies lack rapid, non-invasive approaches for early-stage prediction of herbicide-induced stress. To [...] Read more.
Herbicide phytotoxicity represented a critical constraint on crop safety in soybean–corn intercropping systems, where early detection of herbicide stress is essential for implementing timely mitigation strategies to preserve yield potential. Current methodologies lack rapid, non-invasive approaches for early-stage prediction of herbicide-induced stress. To develop and validate a spectral-feature-based prediction model for herbicide concentration classification, we conducted a controlled experiment exposing three-leaf-stage vegetable soybean (Glycine max L.) seedlings to aqueous solutions containing three concentrations of nicosulfuron herbicide (0.5, 1, and 2 mL/L) alongside a water control. Hyperspectral imaging of randomly selected seedling leaves was systematically performed at 1, 3, 5, and 7 days post-treatment. We developed predictive models for herbicide phytotoxicity through advanced machine learning and deep learning frameworks. Key findings revealed that the ResNet-18 deep learning model achieved exceptional classification performance when analyzing the 386–1004 nm spectral range at day 7 post-treatment: 100% accuracy in binary classification (herbicide-treated vs. water control), 93.02% accuracy in three-class differentiation (water control, low/high concentration), and 86.53% accuracy in four-class discrimination across specific concentration gradients (0, 0.5, 1, 2 mL/L). Spectral analysis identified significant reflectance alterations between 518 and 690 nm through normalized reflectance and first-derivative transformations. Subsequent model optimization using this diagnostic spectral subrange maintained 100% binary classification accuracy while achieving 94.12% and 82.11% accuracy for three- and four-class recognition tasks, respectively. This investigation demonstrated the synergistic potential of hyperspectral imaging and deep learning for early herbicide stress detection in vegetable soybeans. Our findings established a novel methodological framework for pre-symptomatic stress diagnostics while demonstrating the technical feasibility of employing targeted spectral regions (518–690 nm) in field-ready real-time crop surveillance systems. Furthermore, these innovations offer significant potential for advancing precision agriculture in intercropping systems, specifically through refined herbicide application protocols and yield preservation via early-stage phytotoxicity mitigation. Full article
(This article belongs to the Special Issue Herbicides Toxicology and Weeds Herbicide-Resistant Mechanism—Series II)
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18 pages, 2826 KiB  
Article
Fine Mapping and Genetic Effect Analysis of Rf21(t) for the Fertility Restoration of Chinsurah-Boro-II-Type Cytoplasmic Male Sterile Oryza sativa (ssp. japonica) Lines
by Yuanyue Du, Liying Fan, Yunhua Gu, Chen Wang, Kai Shi, Yebin Qin, Zhejun Li, Qiaoquan Liu, Shuzhu Tang, Honggen Zhang and Zuopeng Xu
Agronomy 2025, 15(7), 1690; https://doi.org/10.3390/agronomy15071690 - 12 Jul 2025
Viewed by 121
Abstract
The combination of Chinsurah Boro II (BT)-type cytoplasmic male sterility (CMS) and Rf1, the main fertility restorer gene (Rf) for CMS-BT, has been extensively utilized for the production of three-line commercial japonica hybrid seeds. The identification of new Rf genes [...] Read more.
The combination of Chinsurah Boro II (BT)-type cytoplasmic male sterility (CMS) and Rf1, the main fertility restorer gene (Rf) for CMS-BT, has been extensively utilized for the production of three-line commercial japonica hybrid seeds. The identification of new Rf genes holds significance for the breeding of BT-type restorer lines, aiming to enhance the heterosis level of BT-type japonica hybrids. In the present study, ‘02428’, a wide-compatibility japonica variety, was observed to partially restore fertility to BT-type CMS lines. Genetic analysis revealed that ‘02428’ carries a dominant Rf gene, Rf21(t), responsible for the fertility restoration of BT-type CMS lines. Leveraging bulked segregant analysis (BSA) resequencing technology and molecular markers, the Rf21(t) locus was identified, and mapped within a candidate interval of 6–12.5 Mb on chromosome 2. Using the iso-cytoplasmic restorer populations, Rf21(t) was ultimately mapped to an interval of approximately 77 kb, encompassing 12 predicted genes, including LOC_Os02g17360, encoding a PPR-domain-containing protein and LOC_Os02g17380 (Rf2), a cloned Rf for Lead-rice-type CMS. A comparative sequence analysis, gene expression profiling and gene knockout experiments confirmed that LOC_Os02g17360 and LOC_Os02g17380 are the most likely candidates of Rf21(t). Furthermore, Rf21(t) showed the dosage effect on the fertility restoration of BT-type CMS lines. This newly identified Rf21(t) represents a valuable genetic resource for the breeding of BT-type japonica restorer lines. Our findings offer practical insights for breeders interested in advancing BT-type japonica hybrid development. Full article
(This article belongs to the Section Crop Breeding and Genetics)
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29 pages, 950 KiB  
Review
Review—Seed Treatment: Importance, Application, Impact, and Opportunities for Increasing Sustainability
by Simona Paulikienė, Domas Benesevičius, Kristina Benesevičienė and Tomas Ūksas
Agronomy 2025, 15(7), 1689; https://doi.org/10.3390/agronomy15071689 - 12 Jul 2025
Viewed by 97
Abstract
Climate change, soil degradation, and the spread of seed-borne pathogens pose serious challenges to global food security and agricultural sustainability. Although chemical seed treatment provides pathogen control, it poses environmental and health risks. This review analyses innovative seed treatment technologies, with particular emphasis [...] Read more.
Climate change, soil degradation, and the spread of seed-borne pathogens pose serious challenges to global food security and agricultural sustainability. Although chemical seed treatment provides pathogen control, it poses environmental and health risks. This review analyses innovative seed treatment technologies, with particular emphasis on ozonation as an ecologically viable alternative. The mechanisms of action of ozone, its effects on seed germination, reduction of microbial contamination, and crop establishment are discussed. Chemical, physical, and biological treatment methods are comparatively evaluated, analyzing their effectiveness, environmental impact, and application limitations. Full article
(This article belongs to the Section Farming Sustainability)
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15 pages, 1571 KiB  
Article
Foliar Nitrogen Application Enhances Nitrogen Assimilation and Modulates Gene Expression in Spring Wheat Leaves
by Yanlin Yao, Wenyan Ma, Xin Jin, Guangrui Liu, Yun Li, Baolong Liu and Dong Cao
Agronomy 2025, 15(7), 1688; https://doi.org/10.3390/agronomy15071688 - 12 Jul 2025
Viewed by 81
Abstract
Nitrogen (N) critically regulates wheat growth and grain quality, yet the molecular mechanisms underlying foliar nitrogen application remain unclear. This study evaluated the effects of foliar nitrogen application (12.25 kg ha−1) on the growth, grain yield, and quality of spring wheat, [...] Read more.
Nitrogen (N) critically regulates wheat growth and grain quality, yet the molecular mechanisms underlying foliar nitrogen application remain unclear. This study evaluated the effects of foliar nitrogen application (12.25 kg ha−1) on the growth, grain yield, and quality of spring wheat, as well as its molecular mechanisms. The results indicated that N was absorbed within 3 h post-application, with leaf nitrogen concentration peaking at 12 h. The N treatment increased whole-plant dry matter accumulation and grain protein content by 11.34% and 6.8%, respectively. Amino acid content peaked 24 h post-application, increasing by 25.3% compared to the control. RNA-sequencing analysis identified 4559 and 3455 differentially expressed genes at 3 h and 24 h after urea treatment, respectively, these DEGs being primarily involved in nitrogen metabolism, photosynthetic carbon fixation, amino acid biosynthesis, antioxidant systems, and nucleotide biosynthesis. Notably, the plastidic glutamine synthetase gene (GS2) is crucial in the initial phase of urea application (3 h post-treatment). The pronounced downregulation of GS2 initiates a reconfiguration of nitrogen assimilation pathways. This downregulation impedes glutamine synthesis, resulting in a transient accumulation of free ammonia. In response to ammonia toxicity, the leaves promptly activate the GDH (glutamate dehydrogenase) pathway to facilitate the temporary translocation of ammonium. This compensatory mechanism suggests that GS2 downregulation may be a key switch that redirects nitrogen metabolism from the GS/GOGAT cycle to the GDH bypass. Additionally, the upregulation of the purine and pyrimidine metabolic routes channels nitrogen resources towards nucleic acid synthesis, and thereby supporting growth. Amino acids are then transported to the seeds, culminating in enhanced seed protein content. This research elucidates the molecular mechanisms underlying the foliar response to urea application, offering significant insights for further investigation. Full article
(This article belongs to the Section Soil and Plant Nutrition)
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21 pages, 7286 KiB  
Article
FGS-YOLOv8s-seg: A Lightweight and Efficient Instance Segmentation Model for Detecting Tomato Maturity Levels in Greenhouse Environments
by Dongfang Song, Ping Liu, Yanjun Zhu, Tianyuan Li and Kun Zhang
Agronomy 2025, 15(7), 1687; https://doi.org/10.3390/agronomy15071687 - 12 Jul 2025
Viewed by 169
Abstract
In a greenhouse environment, the application of artificial intelligence technology for selective tomato harvesting still faces numerous challenges, including varying lighting, background interference, and indistinct fruit surface features. This study proposes an improved instance segmentation model called FGS-YOLOv8s-seg, which achieves accurate detection and [...] Read more.
In a greenhouse environment, the application of artificial intelligence technology for selective tomato harvesting still faces numerous challenges, including varying lighting, background interference, and indistinct fruit surface features. This study proposes an improved instance segmentation model called FGS-YOLOv8s-seg, which achieves accurate detection and maturity grading of tomatoes in greenhouse environments. The model incorporates a novel SegNext_Attention mechanism at the end of the backbone, while simultaneously replacing Bottleneck structures in the neck layer with FasterNet blocks and integrating Gaussian Context Transformer modules to form a lightweight C2f_FasterNet_GCT structure. Experiments show that this model performs significantly better than mainstream segmentation models in core indicators such as precision (86.9%), recall (76.3%), average precision (mAP@0.5 84.8%), F1-score (81.3%), and GFLOPs (35.6 M). Compared with the YOLOv8s-seg baseline model, these metrics show improvements of 2.6%, 3.8%, 5.1%, 3.3%, and 6.8 M, respectively. Ablation experiments demonstrate that the improved architecture contributes significantly to performance gains, with combined improvements yielding optimal results. The analysis of detection performance videos under different cultivation patterns demonstrates the generalizability of the improved model in complex environments, achieving an optimal balance between detection accuracy (86.9%) and inference speed (53.2 fps). This study provides a reliable technical solution for the selective harvesting of greenhouse tomatoes. Full article
(This article belongs to the Section Precision and Digital Agriculture)
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22 pages, 852 KiB  
Article
Structural Equation Modeling and Genome-Wide Selection for Multiple Traits to Enhance Arabica Coffee Breeding Programs
by Matheus Massariol Suela, Camila Ferreira Azevedo, Ana Carolina Campana Nascimento, Eveline Teixeira Caixeta Moura, Antônio Carlos Baião de Oliveira, Gota Morota and Moysés Nascimento
Agronomy 2025, 15(7), 1686; https://doi.org/10.3390/agronomy15071686 (registering DOI) - 12 Jul 2025
Viewed by 96
Abstract
Recognizing the interrelationship among variables becomes critical in genetic breeding programs, where the goal is often to optimize selection for multiple traits. Conventional multi-trait models face challenges such as convergence issues, and they fail to account for cause-and-effect relationships. To address these challenges, [...] Read more.
Recognizing the interrelationship among variables becomes critical in genetic breeding programs, where the goal is often to optimize selection for multiple traits. Conventional multi-trait models face challenges such as convergence issues, and they fail to account for cause-and-effect relationships. To address these challenges, we conducted a comprehensive analysis involving confirmatory factor analysis (CFA), Bayesian networks (BN), structural equation modeling (SEM), and genome-wide selection (GWS) using data from 195 arabica coffee plants. These plants were genotyped with 21,211 single nucleotide polymorphism markers as part of the Coffea arabica breeding program at UFV/EPAMIG/EMBRAPA. Traits included vegetative vigor (VV), canopy diameter (CD), number of vegetative nodes (NVN), number of reproductive nodes (NRN), leaf length (LL), and yield (Y). CFA established the following latent variables: vigor latent (VL) explaining VV and CD; nodes latent (NL) explaining NVN and NRN; leaf length latent (LLL) explaining LL; and yield latent (YL) explaining Y. These were integrated into the BN model, revealing the following key interrelationships: LLL → VL, LLL → NL, LLL → YL, VL → NL, and NL → YL. SEM estimated structural coefficients, highlighting the biological importance of VL → NL and NL → YL connections. Genomic predictions based on observed and latent variables showed that using VL to predict NVN and NRN traits resulted in similar gains to using NL. Predicting gains in Y using NL increased selection gains by 66.35% compared to YL. The SEM-GWS approach provided insights into selection strategies for traits linked with vegetative vigor, nodes, leaf length, and coffee yield, offering valuable guidance for advancing Arabica coffee breeding programs. Full article
(This article belongs to the Section Crop Breeding and Genetics)
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17 pages, 1863 KiB  
Article
Effect of Energycane Integration on Ground-Dwelling Arthropod Biodiversity in a Sugarcane-Sweet Corn Cropping System
by Amandeep Sahil Sharma, Ricardo A. Lesmes-Vesga, Simranjot Kaur, Hardeep Singh and Hardev Singh Sandhu
Agronomy 2025, 15(7), 1685; https://doi.org/10.3390/agronomy15071685 - 12 Jul 2025
Viewed by 76
Abstract
Integrating bioenergy crops into existing agricultural systems may influence soil biodiversity, yet evidence remains limited for second-generation bioenergy crops such as energycane. This study examined the impact of energycane integration on soil arthropod communities in the Everglades Agricultural Area, Florida, compared to traditional [...] Read more.
Integrating bioenergy crops into existing agricultural systems may influence soil biodiversity, yet evidence remains limited for second-generation bioenergy crops such as energycane. This study examined the impact of energycane integration on soil arthropod communities in the Everglades Agricultural Area, Florida, compared to traditional sugarcane and sweetcorn cropping systems. Over two crop cycles (plant cane and first ratoon), soil arthropod abundance and diversity were assessed using pitfall traps. Energycane and sugarcane, both perennial crops, showed no significant differences in order richness or Shannon diversity. Similarly, when energycane was compared with sugarcane and sweetcorn (during the first sampling), it had similar arthropod abundance. However, sweetcorn remained fallow in the second and third samplings, attracting arthropods like fire ants and earwigs, particularly due to pigweed. Diversity metrics based on Hill numbers revealed a decline in the effective abundance of ground-dwelling arthropods with increasing diversity order, influenced by differences in sampling duration. Importantly, no previous studies have been found that have reported on the effects of energycane integration into the existing cropping system on soil arthropod biodiversity. These findings highlight that energycane supports biodiversity levels comparable to sugarcane cropping systems with no negative impacts on soil arthropod abundance. This study underscores the need to consider soil biodiversity impacts when evaluating sustainable bioenergy crop transitions and the potential ecological trade-offs of perennial cropping systems. Full article
(This article belongs to the Section Innovative Cropping Systems)
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25 pages, 749 KiB  
Article
Effect of Gold Nanoparticles Against Tetranychus urticae and Phytoseiulus persimilis in Tomato
by José Guadalupe Ontiveros-Guerra, Sonia Noemí Ramírez-Barrón, Luis Alberto Aguirre-Uribe, Julio Cesar Chacón-Hernández, Miriam Sánchez-Vega, Ernesto Cerna-Chávez, Josué Israel García-López, Alberto Antonio Neira-Vielma, Héctor Iván Meléndez-Ortiz and Agustín Hernández-Juárez
Agronomy 2025, 15(7), 1684; https://doi.org/10.3390/agronomy15071684 - 12 Jul 2025
Viewed by 225
Abstract
The two-spotted spider mite Tetranychus urticae Koch (Acari: Tetranychidae) is a major pest of horticultural, ornamental, fruit, and strawberry crops worldwide. Currently, various management tools have been explored for this pest, with nanoparticles being one of them, which stand out for their characteristics [...] Read more.
The two-spotted spider mite Tetranychus urticae Koch (Acari: Tetranychidae) is a major pest of horticultural, ornamental, fruit, and strawberry crops worldwide. Currently, various management tools have been explored for this pest, with nanoparticles being one of them, which stand out for their characteristics and multiple effects. This study evaluated the effects of green-synthesized gold nanoparticles (AuNPs) on the mortality and repellency of T. urticae and its natural predator Phytoseiulus persimilis under laboratory conditions, as well as their efficacy in greenhouse tomatoes against T. urticae. In the laboratory, a biological window for AuNPs (50–100 mg L−1) on the pest and predator was established using a residual film method and a free-choice assay. In the greenhouse, four concentrations (300, 500, 750, and 1000 mg L−1) were evaluated via foliar application at 10-day intervals. The results showed susceptibility to AuNPs in all stages of T. urticae and the adult P. persimilis. The death times from AuNPs were similar in both species. Furthermore, the AuNPs were selective for the pest rather than the natural enemy. In greenhouses, AuNPs affected T. urticae populations in tomato plants, and significant differences were observed on some continuous and final agronomic variables (associated with fruits). This study showed that T. urticae and P. persimilis were susceptible to green-synthesized AuNPs. AuNPs can be a management tool, although studies on other non-target species and estimating agronomic effects on other crops are recommended. Full article
(This article belongs to the Special Issue Application of Nanomaterials for Diseases and Pest Control in Agriculture)
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25 pages, 1260 KiB  
Review
Biogas Slurry as a Sustainable Organic Fertilizer for Sorghum Production in Sandy Soils: A Review of Feedstock Sources, Application Methods, and Agronomic Impacts
by Yanga Mgxaji, Charles S. Mutengwa, Patrick Mukumba and Admire R. Dzvene
Agronomy 2025, 15(7), 1683; https://doi.org/10.3390/agronomy15071683 - 11 Jul 2025
Viewed by 133
Abstract
Biogas slurry (BGS), a nutrient-rich by-product of anaerobic digestion, presents a promising opportunity for sustainable agriculture on sandy soils. This review explores the agronomic potential of using BGS for improving sorghum’s (Sorghum bicolor) productivity by enhancing soil fertility and the nutrient [...] Read more.
Biogas slurry (BGS), a nutrient-rich by-product of anaerobic digestion, presents a promising opportunity for sustainable agriculture on sandy soils. This review explores the agronomic potential of using BGS for improving sorghum’s (Sorghum bicolor) productivity by enhancing soil fertility and the nutrient availability. It focuses on the sources and properties of BGS, its application methods, and their effects on the soil nutrient dynamics and crop productivity. The findings indicate that BGS improves the soil health and crop yields, offering an eco-friendly alternative to synthetic fertilizers, especially in resource-limited settings. Despite these benefits, research gaps persist, including the need for long-term field trials, the optimization of application strategies for sandy soils, and comprehensive economic evaluations. Additionally, concerns such as nutrient imbalances, phosphorus accumulation, and slurry composition variability must be addressed. This review recommends standardizing BGS nutrient profiling and adopting site-specific management practices to maximize its agronomic benefits and environmental safety. Integrating BGS into sustainable soil fertility programs could contribute significantly to achieving agricultural resilience and circular economy goals. Full article
(This article belongs to the Special Issue Application of Organic Amendments in Agricultural Production—2nd Edition)
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15 pages, 3793 KiB  
Article
Dynamic Changes in Fatty Acids in Macadamia Fruit During Growth and Development
by Mingqun Cao, Birong Zhang, Minxian Duan, Hanyao Zhang, Suyun Yan, Fan Yang, Wenbin Shi, Xiaomeng Fu, Hongxia Yang, Jinxue Li and Xianyan Zhou
Agronomy 2025, 15(7), 1682; https://doi.org/10.3390/agronomy15071682 - 11 Jul 2025
Viewed by 92
Abstract
Fatty acids tend to undergo dynamic changes during the growth and development of fruits. In this study, we analyzed the variations in fruit morphology and kernel fatty acid fractions and contents at seven post-flowering stages in the fruit of ‘A4’ and ‘OC’, two [...] Read more.
Fatty acids tend to undergo dynamic changes during the growth and development of fruits. In this study, we analyzed the variations in fruit morphology and kernel fatty acid fractions and contents at seven post-flowering stages in the fruit of ‘A4’ and ‘OC’, two main macadamia cultivars in Yunnan, China. The single fruit weight and longitudinal and transverse diameters showed a ‘fast–slow–stable’ growth trend, and the fruit shape index gradually decreased with fruit development. A total of 13 saturated fatty acids, 18 monounsaturated fatty acids, and 10 polyunsaturated fatty acids were detected in macadamia kernels at seven developmental stages. The total fatty acid content in ‘OC’ and ‘A4’ tended to first increase and then decrease. The fatty acid content accounted for 8.81% and 6.33% of the total fatty acids at 50 days after flowering (DAF), and peaked at 95 DAF and 125 DAF (the fatty acid content accounted for 25.61% and 20.69% of the total fatty acids), indicating that these two periods are critical for fatty acid accumulation in the two cultivars. In addition, oleic acid, palmitoleic acid, cis-Vaccenic acid, and hexadecenoic acid were determined as the main fatty acids. This study reveals the dynamic changes in fatty acid composition and content in ‘OC’ and ‘A4’ during fruit development, providing a scientific basis for determining the appropriate harvesting time for macadamia nuts. Full article
(This article belongs to the Section Plant-Crop Biology and Biochemistry)
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20 pages, 1247 KiB  
Article
Bioactive Profiling of Cowpea Pods via Optimized Extraction and Experimental–Computational Approaches
by María Victoria Traffano-Schiffo, Margarita M. Vallejos, Andrea G. Gómez, Beatriz I. Avalos, Belén A. Acevedo and María Victoria Avanza
Agronomy 2025, 15(7), 1681; https://doi.org/10.3390/agronomy15071681 - 11 Jul 2025
Viewed by 164
Abstract
Cowpea (Vigna unguiculata L.) pods are an underexploited by-product of legume production with significant antioxidant potential. Their recovery and characterization support sustainable waste valorization in agri-food systems. This study aimed to optimize the extraction of phenolic compounds (PCs) with antioxidant capacity (AOC) [...] Read more.
Cowpea (Vigna unguiculata L.) pods are an underexploited by-product of legume production with significant antioxidant potential. Their recovery and characterization support sustainable waste valorization in agri-food systems. This study aimed to optimize the extraction of phenolic compounds (PCs) with antioxidant capacity (AOC) from cowpea pods and identify key bioactives through experimental and theoretical approaches. First, high-intensity ultrasound extraction was optimized using response surface methodology with ethanol–water mixtures. Under optimal conditions (20% amplitude, 15 min, 50% ethanol), the ethanolic extract (Eo) showed higher total phenolic content (TPC) and AOC than the aqueous extract (Wo). Subsequently, fractionation by Sephadex LH-20 chromatography yielded fractions E2 and W2 with enhanced TPC and AOC. Phytochemical profiling showed that E2 was enriched in caftaric acid, p-coumaric acid, and morin, while W2 had higher levels of caftaric, p-coumaric, and caffeic acids. Finally, density functional theory was used to assess thermodynamic parameters linked to antioxidant mechanisms (HAT, SET-PT, SPLET), revealing morin as the most effective radical scavenger, followed by caffeic and caftaric acids. These findings show that AOC depends not only on phenolic concentration but also on molecular structure and solvent interactions. Thus, cowpea pod extracts and fractions hold promise for antioxidant-rich formulations in food, nutraceutical, or cosmetic applications. Full article
(This article belongs to the Special Issue Waste to Wealth: Resource Utilization of Agricultural Waste Through Effective Biomass Management)
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18 pages, 1291 KiB  
Article
Effect of Calcium Addition on Extracellular Enzymes and Soil Organic Carbon in Maize Rhizosphere Soils
by Zhaoquan He, Xue Shang and Xiaoze Jin
Agronomy 2025, 15(7), 1680; https://doi.org/10.3390/agronomy15071680 - 11 Jul 2025
Viewed by 167
Abstract
This study examined the regulatory mechanism of calcium (Ca) amendment on the dynamics of soil organic carbon (SOC) fractions and extracellular enzyme activities, elucidating the role of Ca in soil carbon cycling processes. A field experiment with maize was conducted, comparing treatments of [...] Read more.
This study examined the regulatory mechanism of calcium (Ca) amendment on the dynamics of soil organic carbon (SOC) fractions and extracellular enzyme activities, elucidating the role of Ca in soil carbon cycling processes. A field experiment with maize was conducted, comparing treatments of low calcium (T1), high calcium (T2), and a calcium-free control (CK). Measurements included inter-root SOC fractions—soluble organic carbon (DOC), microbial biomass carbon (MBC), and readily oxidizable organic carbon (ROC)—and the activities of the following extracellular enzymes: β-xylanase, β-glucosidase (β-glu), phenol oxidase (Phox), peroxidase (Pero), phosphatase (Phos), acetylaminoglucosidase (NAG), and urease. The main findings indicated the following: (1) Calcium addition significantly increased SOC content (115.04% and 99.22% higher in T1 and T2, respectively, than CK during the entire reproductive period) and enhanced microbial activity (elevated DOC and MBC). However, SOC decreased by 8.44% (T1) and 16.38% (T2) relative to CK in the late reproductive stage (irrigation–ripening), potentially reflecting microbial utilization (supported by the inverse correlation between SOC and MBC/DOC), and maize carbon reallocation during grain filling. (2) Calcium activated β-glu, Phox, Phos, NAG, and urease (p < 0.05), with pronounced increases in Phox (241.13 IU·L−1) and Phos (1126.65 U·L−1), indicating enhanced organic matter mineralization and phosphorus availability. (3) Calcium-driven MBC and ROC accumulation was associated with the positive regulation of Phox (path coefficient > 0.8) and the negative regulation of Phos. SOC was co-regulated by β-glu and Phos (R2 = 0.753). (4) Calcium dynamically optimized the short-term carbon distribution through enzyme activity while promoting long-term sequestration. Our study provides new evidence supporting multi-pathway interactions through which calcium mediates enzyme networks to influence the soil carbon cycle. The findings provide a theoretical foundation for calcium fertilizer management and soil carbon sequestration strategies in agriculture, advancing academic and practical goals for sustainable development and carbon neutrality. Full article
(This article belongs to the Special Issue Proteomics Technologies in Crop Improvement Toward Sustainable Agriculture)
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19 pages, 2401 KiB  
Article
Variety-Dependent Yield and Physiological Responses to Combined Inorganic and Organic Sources of Nitrogen in Wheat
by Eva Herlinawati, Xiaoxiao Lei, Maoling Yang, Changlu Hu, Xueyun Yang and Shulan Zhang
Agronomy 2025, 15(7), 1679; https://doi.org/10.3390/agronomy15071679 - 10 Jul 2025
Viewed by 179
Abstract
Integrated application of chemical fertilizers with organic manure might improve crop yields and N-use efficiency (NUE, grain yield per unit N uptake), but the underlying physiological mechanisms are unclear. In this study, we aimed to examine the effects of combined inorganic and organic [...] Read more.
Integrated application of chemical fertilizers with organic manure might improve crop yields and N-use efficiency (NUE, grain yield per unit N uptake), but the underlying physiological mechanisms are unclear. In this study, we aimed to examine the effects of combined inorganic and organic fertilizers on wheat biomass allocation, root growth, water-soluble carbohydrates (WSCs) translocation, leaf senescence, N uptake, and their relationship with yield and NUE. We established a 2-year factorial field experiment with five nutrient treatments with ratios of inorganic: organic fertilizers from 0 to 1, and three varieties—two new: Weilong169 and Zhongmai578; and one reference: Xiaoyan22. The yield ranged from 3469 to 8095 kg ha−1, and it generally declined in response to a higher proportion of organic fertilizer. The NUE increased when there was a higher proportion of organic fertilizer. Weilong169 exhibited higher NUE than Zhongmai578, and both new cultivars outperformed the reference variety in the N harvest index. The yield correlated with leaf senescence traits and harvest index, and NUE was associated with WSC translocation and N uptake. The combination of fertilizers with a low portion of organic maintained yield and improved NUE; Weilong169 had the highest yield, NUE, and N harvest index. A low portion of organic manure substitution for chemical fertilizer suited all varieties. A new variety with a higher yield, N harvest index, and NUE highlights the importance of N traits in breeding programs. Full article
(This article belongs to the Section Soil and Plant Nutrition)
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34 pages, 1417 KiB  
Review
Inversion Studies on the Heavy Metal Content of Farmland Soils Based on Spectroscopic Techniques: A Review
by Wenlong Qiu, Ting Tang, Song He, Zeyong Zheng, Jinhong Lv, Jiacheng Guo, Yunfang Zeng, Yifeng Lao and Weibin Wu
Agronomy 2025, 15(7), 1678; https://doi.org/10.3390/agronomy15071678 - 10 Jul 2025
Viewed by 216
Abstract
In recent years, heavy metal pollution in farmland soil has become a crisis due to human activities or natural impacts, with particular emphasis on cases from China, where this issue is prominent, greatly affecting crop production and food safety. In the context of [...] Read more.
In recent years, heavy metal pollution in farmland soil has become a crisis due to human activities or natural impacts, with particular emphasis on cases from China, where this issue is prominent, greatly affecting crop production and food safety. In the context of a low heavy metal (HM) content in farmland soil, which is difficult to monitor in real time, effective and rapid monitoring of soil plays a decisive role in subsequent targeted protection measures. To this end, this paper provides a narrative review of the application of spectral sensing technology on the basis of the quantitative inversion of heavy metal content in farmland soil using different platforms (ground, airborne, and spaceborne). The sensing process evaluates the mechanism by which soil produces different weak spectral features from the perspective of the heterogeneity of farmland soil. Different methods used for the quantitative inversion of heavy metals (by studying the correlation between soil heavy metals and organic matter, clay minerals, metal oxides, crop vegetation index, etc.) and their feasibility were clarified. At the same time, relevant research on key technologies used in various processes—such as follow-up pretreatment, spectral feature extraction, and the establishment of inversion models for spectral data of different farmland soil types—was summarized, with a primary focus on cases in China. Finally, the challenges, applications, and research directions related to heavy metal spectral inversion in farmland soil were discussed. Full article
(This article belongs to the Special Issue Advances in Soil and Water Sensor Technologies for Precision Agriculture and Environmental Monitoring)
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13 pages, 14682 KiB  
Article
Beyond Conventional Auxins: Evaluating DCPE and DCP Pulse Applications for Enhanced Rooting in Lavandula angustifolia Mill.
by Hajer Darouez and Stefaan P. O. Werbrouck
Agronomy 2025, 15(7), 1677; https://doi.org/10.3390/agronomy15071677 - 10 Jul 2025
Viewed by 124
Abstract
Efficient adventitious root formation is crucial for Lavandula angustifolia Mill. propagation. This study evaluated the effects of continuous and short-duration pulse applications (1 min, 1 h, and 1 day) of the auxin dichlorprop (DCP) and its prodrug dichlorprop-2-ethylhexyl ester (DCPE) at varying concentrations [...] Read more.
Efficient adventitious root formation is crucial for Lavandula angustifolia Mill. propagation. This study evaluated the effects of continuous and short-duration pulse applications (1 min, 1 h, and 1 day) of the auxin dichlorprop (DCP) and its prodrug dichlorprop-2-ethylhexyl ester (DCPE) at varying concentrations on adventitious rooting and callus formation. DCPE generally proved more effective than DCP in promoting rooting, especially at lower concentrations, with continuous application of 0.1 µM DCPE yielding the highest number of adventitious roots. Notably, a brief 1 min pulse of 2.5 µM DCPE induced superior rooting, including high root number and weight, while minimizing callus formation compared to longer exposures. In contrast, 1 h pulse treatments showed a positive correlation between auxin concentration and root number but led to substantial callus development. These findings highlight DCPE’s potential as an efficient auxin source for lavender propagation, likely due to its rapid hydrolysis to active DCP within plant tissues, facilitating systemic distribution. The enhanced rooting achieved with short pulse treatments offers significant implications for optimizing commercial propagation for this economically important aromatic plant. Full article
(This article belongs to the Section Horticultural and Floricultural Crops)
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17 pages, 2198 KiB  
Article
Jujube–Cotton Intercropping Enhances Yield and Economic Benefits via Photosynthetic Regulation in Oasis Agroecosystems of Southern Xinjiang
by Shuting Zhang, Jinbin Wang, Zhengjun Cui, Tiantian Li, Zhenlin Dong, Hang Qiao, Ling Li, Sumei Wan, Xiaofei Li, Wei Zhang, Qiang Hu and Guodong Chen
Agronomy 2025, 15(7), 1676; https://doi.org/10.3390/agronomy15071676 - 10 Jul 2025
Viewed by 150
Abstract
This study aimed to clarify the effects of jujube–cotton intercropping on cotton yield and photosynthetic characteristics, providing a theoretical basis for its application in the oasis irrigation areas of southern Xinjiang and offering practical recommendations to local farmers for increasing economic benefits. The [...] Read more.
This study aimed to clarify the effects of jujube–cotton intercropping on cotton yield and photosynthetic characteristics, providing a theoretical basis for its application in the oasis irrigation areas of southern Xinjiang and offering practical recommendations to local farmers for increasing economic benefits. The effects were investigated from 2020 to 2023 using Zhongmian 619 cotton and juvenile jujube trees. Changes in leaf area index (LAI), transpiration rate (Tr), stomatal conductance (Gs), net photosynthetic rate (Pn), intercellular CO2 concentration (Ci), yield, and economic benefits were evaluated over the years. The results showed that (1) a positive correlation was observed between LAI and the photosynthetic characteristics of cotton. Compared to monoculture cotton, intercropped cotton exhibited lower Pn, Gs, and Tr, and at the peak boll stage, monoculture cotton had significantly higher photosynthetic characteristics, indicating that intercropping affected cotton photosynthesis. (2) From 2020 to 2023, the land equivalent ratio (LER) of jujube–cotton intercropping remained above 1, with overall yield and economic benefit surpassing those of monoculture cotton and jujube, particularly in 2023 when the yield increased by 55.35%. (3) A significant positive correlation was found between cotton yield and LAI. In conclusion, jujube–cotton intercropping enhances photosynthesis, improving yield, economic benefits, and land use efficiency. Full article
(This article belongs to the Special Issue Innovations in Green and Efficient Cotton Cultivation)
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19 pages, 8839 KiB  
Article
Potential Expansion of Root Chicory Cultivation Areas in Chile
by Donna Cortez, Manuel Paneque and Celián Román-Figueroa
Agronomy 2025, 15(7), 1675; https://doi.org/10.3390/agronomy15071675 - 10 Jul 2025
Viewed by 137
Abstract
Root chicory (Cichorium intybus var. sativum) is a major source of inulin, a fiber with many dietary and medicinal uses. Chile is the only country outside Europe that produces inulin and is the third largest exporter worldwide. Root chicory cultivation has [...] Read more.
Root chicory (Cichorium intybus var. sativum) is a major source of inulin, a fiber with many dietary and medicinal uses. Chile is the only country outside Europe that produces inulin and is the third largest exporter worldwide. Root chicory cultivation has increased by 242% in Chile since 2006, highlighting its potential for expansion into new territories. In this study, land suitability (without restriction, mild restriction, moderate restriction, and unsuitable) for root chicory cultivation and its potential productivity were determined using Geographic Information System (GIS) and analytical hierarchy process (AHP). The regions where root chicory is currently produced (between the Maule and La Araucanía regions) showed the best suitability, as did the Valparaíso and O’Higgins regions. The potential maximum productivity ranged from 20 to 27 t DW ha−1, mainly concentrated in the Los Lagos region, despite the absence of land without restriction. This could be attributed to the high water availability in this region, which is consistent with the expected displacement of crop areas due to climate change. Field studies in the Los Lagos region are recommended to evaluate the feasibility of expanding root chicory cultivation in these areas. Full article
(This article belongs to the Special Issue Industrial Crops Production in Mediterranean Climate)
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23 pages, 2642 KiB  
Article
Evaluating of Four Irrigation Depths on Soil Moisture and Temperature, and Seed Cotton Yield Under Film-Mulched Drip Irrigation in Northwest China
by Xianghao Hou, Wenhui Hu, Quanqi Li, Junliang Fan and Fucang Zhang
Agronomy 2025, 15(7), 1674; https://doi.org/10.3390/agronomy15071674 - 10 Jul 2025
Viewed by 112
Abstract
Soil mulching and irrigation are critical practices for alleviating water scarcity and enhancing crop yields in arid and semi-arid regions by regulating soil moisture and soil temperature. Clarifying the effects of various irrigation depths on soil moisture and temperature under mulched condition is [...] Read more.
Soil mulching and irrigation are critical practices for alleviating water scarcity and enhancing crop yields in arid and semi-arid regions by regulating soil moisture and soil temperature. Clarifying the effects of various irrigation depths on soil moisture and temperature under mulched condition is essential for optimizing irrigation strategies. This study investigated the effects of four irrigation depths based on crop evapotranspiration (ETc): 60, 80, 100, and 120% (W0.6, W0.8, W1.0, and W1.2, respectively) on the soil moisture content (SMC), soil temperature and seed cotton yield in mulched cotton fields. Results revealed that when the irrigation depth increased from 60%ETc to 120%ETc, seed cotton yield increased by 12.04% in 2018 and 17.00% in 2019 at the cost of irrigation water use efficiency (IWUE), which decreased from 2.53 kg m−3 to 1.54 kg m−3 in 2018 and 2.60 kg m−3 to 1.58 kg m−3 in 2019. Soil temperature exhibited a temporal trend of initial increase followed by decline, and it was positively affected by soil mulching. Notably, W0.6 treatment maintained significantly higher soil temperature than other treatments. Soil moisture content was positively affected by irrigation depth, while soil water storage first decreased and then increased over time, reaching the minimum at the flowering and boll setting stages during the two growing seasons. Higher irrigation amount reduced the total spatial variability (C0 + C) of soil but did not significantly alter the distribution characteristics of soil moisture, as indicated by stable coefficients of variation (CVs) and stratification ratios (SRs). The variability of soil moisture diminished with soil depth with the lowest CV obtained at a 60 cm soil layer across the growth stages. Correlation analysis results showed that the seed cotton yield was mainly affected by irrigation depth and soil water storage. Soil temperature at the flowering and boll setting stage negatively affected seed cotton yield and was inversely correlated with soil water storage. The structural equation model (SEM) further indicated that both soil water storage and soil temperature primarily influenced seed cotton yield boll weight rather than boll number. Furthermore, 100%ETc (W1.0) can be considered as the recommended irrigation depth based on the soil moisture and temperature, seed cotton yield and water use efficiency in this region. Full article
(This article belongs to the Special Issue Advancements in Precision Fertilization and Water Management for Sustainable Agriculture)
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Article
Potassium Fulvate Alleviates Salinity and Boosts Oat Productivity by Modifying Soil Properties and Rhizosphere Microbial Communities in the Saline–Alkali Soils of the Qaidam Basin
by Jie Wang, Xin Jin, Xinyue Liu, Yunjie Fu, Kui Bao, Zhixiu Quan, Chengti Xu, Wei Wang, Guangxin Lu and Haijuan Zhang
Agronomy 2025, 15(7), 1673; https://doi.org/10.3390/agronomy15071673 - 10 Jul 2025
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Abstract
Soil salinization severely limits global agricultural sustainability, particularly across the saline–alkaline landscapes of the Qinghai–Tibet Plateau. We examined how potassium fulvate (PF) modulates oat (Avena sativa L.) performance, soil chemistry, and rhizospheric microbiota in the saline–alkaline soils of the Qaidam Basin. PF [...] Read more.
Soil salinization severely limits global agricultural sustainability, particularly across the saline–alkaline landscapes of the Qinghai–Tibet Plateau. We examined how potassium fulvate (PF) modulates oat (Avena sativa L.) performance, soil chemistry, and rhizospheric microbiota in the saline–alkaline soils of the Qaidam Basin. PF markedly boosted shoot and root biomass, with the greatest response observed at 150 kg hm−2. At the same time, it enhanced soil fertility by increasing organic matter, nitrate-N, ammonium-N, and available potassium, and improved ionic balance by lowering Na+ concentrations and the sodium adsorption ratio (SAR), while increasing Ca2+ levels and soil moisture content. Under the high-dose treatment (F2), endogenous fungal contributions declined sharply, exogenous replacements increased, and fungal α-diversity fell; multivariate ordinations confirmed that PF reshaped both bacterial and fungal communities, with fungi exhibiting the stronger response. We integrated three machine learning algorithms—least absolute shrinkage and selection operator (LASSO), Random Forest (RF), and eXtreme Gradient Boosting (XGBoost)—to minimize the bias inherent in any single method. We identified microbial β-diversity, organic matter, and Na+ and Ca2+ concentrations as the most robust predictors of the Soil Salinization and Alkalization Index (SSAI). Structural equation modeling further showed that PF mitigates salinity chiefly by improving soil physicochemical properties (path coefficient = −0.77; p < 0.001), with microbial assemblages acting as key intermediaries. These findings provide compelling theoretical and empirical support for deploying PF to rehabilitate saline–alkaline soils in alpine environments and offer practical guidance for sustainable land management in the Qaidam Basin. Full article
(This article belongs to the Special Issue Utilization of Microorganisms for Sustainable Agricultural Development)
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