Plants

28 pages, 3243 KB

Open AccessArticle

Transcriptional Analysis of a Tripartite Interaction Between Maize (Zea mays, L.) Roots Inoculated with the Pathogenic Fungus Fusarium verticillioides and Its Bacterial Control Agent Bacillus cereus sensu lato Strain B25

by Paúl Alán Báez-Astorga, Abraham Cruz-Mendívil, Juan Luis Figueroa-Castro, Itzel Guadalupe López-Soto, Jesús Eduardo Cazares-Álvarez, Josefat Gregorio-Jorge, Carlos Ligne Calderón-Vázquez and Ignacio Eduardo Maldonado-Mendoza

Plants 2025, 14(23), 3661; https://doi.org/10.3390/plants14233661 (registering DOI) - 1 Dec 2025

Abstract

One open question regarding plant–microbe interactions is how a plant interacts molecularly with both a beneficial microbe and a pathogenic fungus. This study used RNA-seq to investigate molecular responses in maize roots during a tripartite interaction with the fungal pathogen Fusarium verticillioides ( [...] Read more.

One open question regarding plant–microbe interactions is how a plant interacts molecularly with both a beneficial microbe and a pathogenic fungus. This study used RNA-seq to investigate molecular responses in maize roots during a tripartite interaction with the fungal pathogen Fusarium verticillioides (Fv), which causes stalk, ear, and root rot, and the endophytic biocontrol agent Bacillus cereus sensu lato B25, known to suppress Fv and promote plant growth. Roots of seven-day-old maize inoculated with Fv (Zm-Fv), B25 (Zm-B25), and co-inoculated (Zm-Fv-B25) were compared to uninoculated control (Zm). Differential Gene Expression (DEG), Gene Ontology (GO) and KEGG analysis revealed distinct molecular responses. Fv suppressed plant pathways related to DNA and protein synthesis and impaired root development. In contrast, B25 triggered defense priming and growth-related responses. In the co-inoculation experiment (Zm-B25-Fv), upregulated DEGs were associated with both defense-related metabolic pathways, including jasmonic acid signaling and secondary metabolite biosynthesis, and genes involved in plant growth processes. Co-expression networks using Arabidopsis orthologs supported the induction of defense- and growth and development-related genes. This study is the first RNA-seq analysis of maize root molecular responses during the tripartite interaction with a fungal pathogen and its bacterial biocontrol agent, providing new directions for further research to understand the detailed molecular mechanisms underlying this interaction fully. Full article

(This article belongs to the Special Issue Plant Interactions with Both Beneficial and Pathogenic Microorganisms)

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14 pages, 2035 KB

Open AccessArticle

Organic Amendments and Trichoderma Change the Rhizosphere Microbiome and Improve Cucumber Yield and Fusarium Suppression

by Yuanming Wang, Xinnan Hang, Cheng Shao, Zhiying Zhang, Sai Guo, Rong Li and Qirong Shen

Plants 2025, 14(23), 3660; https://doi.org/10.3390/plants14233660 (registering DOI) - 1 Dec 2025

Abstract

Conventional chemical-based control methods for soil-borne diseases often degrade soil quality. The recycling of organic wastes offers a promising solution to simultaneously alleviate environmental pollution and restore soil health. As a beneficial fungus, Trichoderma plays a crucial role in enhancing plant performance. However, [...] Read more.

Conventional chemical-based control methods for soil-borne diseases often degrade soil quality. The recycling of organic wastes offers a promising solution to simultaneously alleviate environmental pollution and restore soil health. As a beneficial fungus, Trichoderma plays a crucial role in enhancing plant performance. However, knowledge of the mechanisms through which organic wastes and Trichoderma interact to influence plant performance remains limited. We investigated how the combined application of organic wastes (chitin and straw) and a biocontrol fungus (Trichoderma) influenced the rhizosphere microbiome to improve plant performance. Compared with the control, organic waste alone, and Trichoderma alone treatments, the combined application of organic wastes and Trichoderma significantly (p < 0.05) increased cucumber yield and reduced pathogen density. Increased yield and reduced pathogen density were associated with changes in bacterial and fungal communities induced by this combined application treatment. Indeed, this combined application treatment enabled plants to recruit certain potentially beneficial core bacterial (e.g., Streptomyces and Flavisolibacter) and fungal taxa (e.g., Trichoderma), increasing their positive interactions in the rhizosphere. We demonstrate that the combined application of organic wastes and Trichoderma can shape distinct rhizosphere bacterial and fungal communities, promoting an increase in beneficial microorganisms and their positive interactions, which contribute to enhanced plant performance. Full article

(This article belongs to the Section Plant Protection and Biotic Interactions)

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17 pages, 2156 KB

Open AccessArticle

Physiological Responses of Paulownia fortunei to Leaf Herbivory by Epicauta ruficeps: Nitrogen Assimilation, Porphyrin Metabolism, and ROS-Driven Antioxidant and Phenylpropanoid Responses

by Fan Wang, Zhongke Lv, Lizhi Xiao, Bo Chen, Wenhuan Liu, Jiaqing Huang, Gaoqiang Liu, Yuchen Yan, Jianhua Huang and Guoqun Yang

Plants 2025, 14(23), 3659; https://doi.org/10.3390/plants14233659 (registering DOI) - 30 Nov 2025

Abstract

Paulownia fortunei is an important economic tree species that possesses numerous biological and economic traits, such as fast growth, strong stress resistance, and excellent wood properties. The cultivation of this species is pervasive across numerous regions of China. Epicauta ruficeps, a common [...] Read more.

Paulownia fortunei is an important economic tree species that possesses numerous biological and economic traits, such as fast growth, strong stress resistance, and excellent wood properties. The cultivation of this species is pervasive across numerous regions of China. Epicauta ruficeps, a common pest species of P. fortunei, typically consumes the foliage of its host plant. However, there are currently no reported studies on the physiological and biochemical mechanisms underlying P. fortunei response to E. ruficeps feeding. In this study, we discovered that the enhancement of nitrogen assimilation and porphyrin metabolism directly contributes to the maintenance of the steady state of photosynthetic activity in P. fortunei leaves. Meanwhile, E. ruficeps feeding also leads to an increase in the level of reactive oxygen species (ROS) in P. fortunei leaves. As key signaling molecules, the elevated level of ROS activates the antioxidant system and phenylpropanoid metabolism, which in turn results in increased antioxidant enzyme activity, as well as increased contents of antioxidants and lignin. The aforementioned changes have the potential to reduce the degree of membrane lipid peroxidation and enhance the mechanical strength of leaf tissues. Consequently, this can assist in maintaining the steady state of photosynthesis indirectly. In summary, the present study elucidates the physiological and biochemical mechanisms underlying the maintenance of the steady state of photosynthetic activity in P. fortunei after being feeded by E. ruficeps from multiple dimensions. Simultaneously, it lays a theoretical foundation and provides data support for the subsequent comprehensive analysis of the molecular mechanisms involved in P. fortunei response to E. ruficeps feeding. Full article

(This article belongs to the Special Issue Genetic and Biological Diversity of Plants—2nd Edition)

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18 pages, 5869 KB

Open AccessArticle

Cloning and Functional Verification of Salt Tolerance Gene HbNHX2 in Hordeum brevisubulatum

by Mingzhi Zhang, Mei Yang, Wenjie Zhao, Hang Yin, Xinyi Zhang, Bing Li, Muzhapaer Tuluhong, Baiji Wang, Shanshui Zheng and Guowen Cui

Plants 2025, 14(23), 3658; https://doi.org/10.3390/plants14233658 (registering DOI) - 30 Nov 2025

Abstract

A high salt environment seriously affects the physiological metabolism and yield of plants. Hordeum brevisubulatum (Trin.) Link has high biomass and important ecological, feeding and economic values, but its growth conditions have serious saline-alkali effects. The NHX gene family plays a vital role [...] Read more.

A high salt environment seriously affects the physiological metabolism and yield of plants. Hordeum brevisubulatum (Trin.) Link has high biomass and important ecological, feeding and economic values, but its growth conditions have serious saline-alkali effects. The NHX gene family plays a vital role in regulating intracellular Na⁺/K⁺ balance, pH homeostasis, and vesicle and protein transport in plants. In this study, the HbNHX2 gene was cloned from Hordeum brevisubulatum and functionally characterized through phenotypic, physiological, and molecular analyses in transgenic tobacco. Expression profiling revealed that HbNHX2 was most abundant in spikes and least abundant in root tips, and the expression level was significantly induced under salt stress. Overexpression of HbNHX2 led to decreased malondialdehyde (MDA) and superoxide anion (O²⁻) levels, while it enhanced the activities of superoxide dismutase (SOD), peroxidase (POD), and catalase (CAT). Additionally, the levels of glutathione (GSH), soluble proteins, proline, and chlorophyll were also increased. Several stress-responsive genes, including CBL1, ERF2, BI-1, Cu/Zn-SOD, Mn-SOD, POD, GR1, KC1, TPK1, TIP, P5CS, BAS1, STN7 and LTP1, were significantly upregulated, while SERK3B was downregulated. These findings suggest that HbNHX2 enhances plant salt tolerance by maintaining osmotic balance, scavenging reactive oxygen species (ROS), and regulating stress-responsive gene expression. This study provides new insights into the molecular mechanism of salt tolerance in Hordeum brevisubulatum and lays a foundation for breeding salt-tolerant forage crops. Full article

(This article belongs to the Section Plant Genetics, Genomics and Biotechnology)

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20 pages, 3014 KB

Open AccessArticle

Holobiome Structure and Microbial Core Assemblages of Deschampsia antarctica Across the South Shetland Islands

by Rodrigo Rodriguez, Patricio Javier Barra, Manuel Saldivar-Diaz, Giovanni Larama, Roxana Alvarado, Dariel López, Mabel Delgado, Julieta Orlando, Rómulo Oses, Carolina Merino, Gonzalo Tortella and Paola Duran

Plants 2025, 14(23), 3657; https://doi.org/10.3390/plants14233657 (registering DOI) - 30 Nov 2025

Abstract

Antarctica harbors some of the most extreme ecosystems on earth, where only two vascular plants persist. The native grass Deschampsia antarctica provides a model for plant–microbe interactions under intense abiotic stress. We present the first multi-compartmental and multi-kingdom characterization of bacterial and fungal [...] Read more.

Antarctica harbors some of the most extreme ecosystems on earth, where only two vascular plants persist. The native grass Deschampsia antarctica provides a model for plant–microbe interactions under intense abiotic stress. We present the first multi-compartmental and multi-kingdom characterization of bacterial and fungal communities associated with D. antarctica across three South Shetland Islands. Metabarcoding revealed strong compartmentalization: the rhizosphere displayed the highest richness and complex bacterial–fungal networks; the root endosphere showed intermediate diversity with keystone taxa such as Rhizobiales and Streptomyces; and the leaf endosphere was simplified, dominated by stress-tolerant taxa including Pseudomonas and Helotiales. Despite marked soil heterogeneity, phosphorus enrichment at Admiralty Bay, base cations at Coppermine Cove, and iron at Byers Peninsula, a conserved core (20 bacterial and 5 fungal genera) persisted, mainly cold-adapted saprotrophs and plant-associated taxa. Fungal assemblages were more responsive to soil chemistry, with site-specific enrichments such as Zymoseptoria and Herpotrichia. Overall, D. antarctica holobionts exhibited a dual strategy: conserved microbial backbones confer stability, while localized assemblages shaped by soil chemistry and geography enhance adaptability. Together, these findings provide one of the most integrative characterizations of the D. antarctica holobiont to date, revealing how conserved and adaptive microbial components support plant resilience under extreme Antarctic conditions and offering valuable insights for predicting biological responses to ongoing climate change. Full article

(This article belongs to the Section Plant–Soil Interactions)

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17 pages, 3926 KB

Open AccessArticle

Zea Maize Calmodulin (ZmCaM2) Regulates Drought Tolerance in Corn Plants Through an Abscisic Acid-Dependent Signaling Pathway

by Meiyi Liu, Pengxiang Bao, Hanqiao Wang, Zhiqiang Wu, Zhen Wang, Xiangyu Xing, Wei Yang, Xuejiao Ren, Jiabin Ci, Liangyu Jiang and Zhenyuan Zang

Plants 2025, 14(23), 3656; https://doi.org/10.3390/plants14233656 (registering DOI) - 30 Nov 2025

Abstract

Calmodulins (CaMs), which are important calcium-binding proteins, play critical roles in plant stress responses. However, limited information is available regarding the biological functions of CaMs under drought stress. In this study, we identified and isolated a CaM gene, ZmCaM2, from maize ( [...] Read more.

Calmodulins (CaMs), which are important calcium-binding proteins, play critical roles in plant stress responses. However, limited information is available regarding the biological functions of CaMs under drought stress. In this study, we identified and isolated a CaM gene, ZmCaM2, from maize (Zea mays L.) in length and encodes a 184-amino acid protein containing four EF-hand domains capable of specifically binding calcium ions (Ca²⁺). Subcellular localization analysis revealed that ZmCaM2 is localized to the nucleus and membrane. Functional characterization indicated that ZmCaM2 negatively regulates drought tolerance in maize by increasing malondialdehyde (MDA) and reactive oxygen species (ROS) content while decreasing antioxidant enzyme activity, proline (Pro) content, abscisic acid (ABA) content and relative water content (RWC). Moreover, ZmCaM2 reduced maize sensitivity to ABA treatment, suggesting that ZmCaM2 negatively regulates the drought tolerance of maize by relying on the ABA pathway. These findings provide new insights into the functional role of ZmCaM2 and may facilitate the development of drought-resistant maize cultivars. Full article

(This article belongs to the Special Issue Biological Signaling in Plant Development)

18 pages, 1126 KB

Open AccessArticle

Transcriptome-Based Identification of Reference Genes for Expression Analysis in Cassava Under Xanthomonas phaseoli pv. manihotis Infection

by Jing Yang, Ciyun Li, Jie Chen, Dongying Lu, Qi Yang, Ruotong Li, Liyun Yang, Xiaofei Zhang, Yinhua Chen, Shousong Zhu and Xiaolei Niu

Plants 2025, 14(23), 3655; https://doi.org/10.3390/plants14233655 (registering DOI) - 30 Nov 2025

Abstract

Reverse transcription quantitative PCR (RT-qPCR) is a powerful and widely used technique for quantifying alterations in gene expression. Cassava bacterial blight caused by Xanthomonas phaseoli pv. manihotis severely constraints cassava growth and yield. Accurate evaluation of the expression levels of genes following infection [...] Read more.

Reverse transcription quantitative PCR (RT-qPCR) is a powerful and widely used technique for quantifying alterations in gene expression. Cassava bacterial blight caused by Xanthomonas phaseoli pv. manihotis severely constraints cassava growth and yield. Accurate evaluation of the expression levels of genes following infection by X. phaseoli pv. manihotis is crucial for the identification of potential cassava resistance genes. In this study, thirty-two novel potential reference genes were screened from the cassava–X. phaseoli pv. manihotis transcriptome. Their expression, along with that of seven literature-reported cassava reference genes, was evaluated in two susceptible and two resistant cassava varieties at six time points post-inoculation by X. phaseoli pv. manihotis through RT-qPCR analysis. The stability of thirty-nine candidate reference genes was assessed by four algorithms: geNorm, NormFinder, Delta Ct, and RefFinder. The results demonstrated that serving as new reference genes, MehnRNPR and MePRPF38B consistently exhibited superior expression stability over seven established reference genes under X. phaseoli pv. manihotis infection, regardless of the susceptible or resistant cassava varieties. The reliability of the reference genes was validated by assessing the expression pattern of MeNAC35 and MeSWEET10a under X. phaseoli pv. manihotis infection. The findings of this study provide valuable insights for advancing the precision of the quantification of cassava candidate genes associated with disease resistance. Full article

(This article belongs to the Section Plant Genetics, Genomics and Biotechnology)

17 pages, 2725 KB

Open AccessArticle

The Effect of Sowing Date on the Biomass Production of Non-Traditional and Commonly Used Intercrops from the Brassicaceae Family

by Václav Brant, Andrea Rychlá, Kateřina Hamouzová, Viktor Vrbovský, Pavel Procházka, Josef Chára, Jiří Holejšovský, Theresa Piskáčková, Soham Bhattacharya and Jiří Dreksler

Plants 2025, 14(23), 3654; https://doi.org/10.3390/plants14233654 (registering DOI) - 30 Nov 2025

Abstract

Catch crops play a vital role in agricultural systems by contributing to biomass production, nutrient retention, and carbon sequestration. Among these, species from the Brassicaceae family are particularly valuable due to their rapid biomass accumulation, biofumigant properties, and adaptability to diverse environmental conditions. [...] Read more.

Catch crops play a vital role in agricultural systems by contributing to biomass production, nutrient retention, and carbon sequestration. Among these, species from the Brassicaceae family are particularly valuable due to their rapid biomass accumulation, biofumigant properties, and adaptability to diverse environmental conditions. This study presents the first systematic evaluation of biomass characteristics for six non-traditional Brassicaceae species under Central European conditions, alongside commonly cultivated representatives of the family. Field experiments were conducted in Eastern Bohemia from 2021 to 2023 to assess biomass production in nine Brassicaceae species. Four sowing dates were evaluated, with plant sampling determining aboveground and underground biomass. The results revealed significant species-specific differences in biomass accumulation. Sinapis alba and Raphanus sativus exhibited the highest biomass, while Brassica napus and Crambe abyssinica had the lowest. A positive correlation between aboveground and underground biomass was observed across species, though root-to-shoot ratios varied, influencing carbon allocation patterns and soil organic matter inputs. Overall, the results demonstrate that sowing date is a critical factor influencing growth dynamics and reproductive development in these underutilized Brassicaceae species. By identifying optimal planting windows, this study contributes to improved management strategies aimed at maximizing biomass production while supporting sustainable cropping practices, including enhanced soil organic carbon stabilization and reduced nutrient losses. Full article

(This article belongs to the Section Crop Physiology and Crop Production)

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6 pages, 161 KB

Open AccessEditorial

Ornamental Plants and Urban Gardening II

by Szilvia Kisvarga and László Orlóci

Plants 2025, 14(23), 3653; https://doi.org/10.3390/plants14233653 (registering DOI) - 30 Nov 2025

Abstract

One flagship of the ornamental plant industry is the orchid; it is no coincidence that a comprehensive review focuses on the breeding, cultivation, and potential applications of Phalaenopsis [...] Full article

(This article belongs to the Special Issue Ornamental Plants and Urban Gardening II)

14 pages, 2506 KB

Open AccessArticle

Uncovering the Floral Origins of Honey Bee Pollen in Colombian Tropical Dry Forest: A Low-Cost DNA Barcoding Approach Reveals Cactaceae Dominance

by Maryuri Lobo-Torres, Diana C. Mantilla-Escalante, Brayan J. Anaya, Diego F. Tirado and Claudia M. Arenas-Gómez

Plants 2025, 14(23), 3652; https://doi.org/10.3390/plants14233652 (registering DOI) - 30 Nov 2025

Abstract

Characterizing the botanical composition of pollen is essential to understanding the floral resources used by bees. While microscopy is the traditional method, it is time-consuming and limited in taxonomic resolution. Molecular tools such as DNA barcoding offer a more precise and cost-effective alternative [...] Read more.

Characterizing the botanical composition of pollen is essential to understanding the floral resources used by bees. While microscopy is the traditional method, it is time-consuming and limited in taxonomic resolution. Molecular tools such as DNA barcoding offer a more precise and cost-effective alternative for identifying plant taxa in mixed pollen samples. This study implemented a preliminary and cost-effective molecular approach to identify the botanical origin of pollen stored in bee bread from Apis mellifera hives in a tropical dry forest fragment in La Paz, Cesar, using rbcL and matK genes as markers. The chloroplast markers rbcL and matK were amplified and Sanger-sequenced from three independent bee hives, each processed in duplicate as technical replicates. The BLAST+ 2.17.0 results from Sanger sequences showed a sequence identity ranging from 89%–99%, with rbcL showing higher and more consistent matches than matK, suggesting stronger discriminatory power, while the lower identity in one hive indicated a more complex pollen mixture. However, matK detected a greater number of taxa overall (i.e., 70% of the total, 64 genera) compared with rbcL (i.e., 50%, 46 genera). Both markers overlapped in approximately 20% of the taxa, most of which (i.e., 94%) belonged to the family Cactaceae. This indicated that, although rbcL provided more reliable matches, matK contributed to broader taxonomic coverage, highlighting the complementarity of both markers for mixed pollen analyses. This approach highlights its value as an exploratory tool prior to applying high-throughput sequencing strategies. Furthermore, such studies may support the development of local honey brands by validating that their products originate mainly from the biodiversity of tropical dry forests, an ecosystem currently at risk, thereby conferring both ecological and market value. Full article

(This article belongs to the Special Issue Molecular Mechanisms of Flower Development and Plant Reproduction)

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18 pages, 3449 KB

Open AccessArticle

Antidepressant-like Effects of Garcinia nigrolineata Resin Extract in a Chronic Mild Stress Mouse Model: Modulation of Monoaminergic and HPA-Axis Pathways

by Yutthana Chotritthirong, Yaowared Sumanont, Supawadee Daodee, Abdulwaris Mading, Chantana Boonyarat, Charinya Khamphukdee, Decha Kumla, Juthamart Maneenet, Kinzo Matsumoto, Anake Kijjoa, Suresh Awale and Orawan Monthakantirat

Plants 2025, 14(23), 3651; https://doi.org/10.3390/plants14233651 (registering DOI) - 30 Nov 2025

Abstract

The resin extract of Garcinia nigrolineata (GNR-E), a tropical plant used in Southeast Asian traditional medicine, was evaluated for its antidepressant-like effects in a chronic mild stress (CMS) mouse model, with imipramine as a reference drug. GNR-E dose-dependently alleviated CMS-induced anhedonia (sucrose preference [...] Read more.

The resin extract of Garcinia nigrolineata (GNR-E), a tropical plant used in Southeast Asian traditional medicine, was evaluated for its antidepressant-like effects in a chronic mild stress (CMS) mouse model, with imipramine as a reference drug. GNR-E dose-dependently alleviated CMS-induced anhedonia (sucrose preference test) and behavioral despair (forced swimming and tail suspension tests). Neurochemical analyses revealed that GNR-E increased serotonin (5-HT) and norepinephrine (NE) levels, reduced expression of their transporters (SERT, NET) and receptors (5-HT1A, 1B, 2A, 2C, 7; α2A, 2C) in the frontal cortex and hippocampus, and normalized HPA-axis hyperactivity by lowering serum corticosterone and modulating glucocorticoid receptor (GR) and SGK-1 mRNA expression. In vitro, GNR-E inhibited monoamine oxidase (MAO)-A and -B (Ki = 2.33 and 1.55 µg/mL, respectively). Phytochemical analysis identified xanthones, particularly cowanin, as key constituents. These findings highlight GNR-E’s potential as a novel plant-based antidepressant, warranting further investigation into its active compounds and clinical applications. Full article

(This article belongs to the Section Phytochemistry)

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20 pages, 961 KB

Open AccessArticle

Optimizing the Ratio of One-Off Slow-Release Fertilizer Can Improve the Nitrogen Use Efficiency and Yield of Rice Under the Condition of Nitrogen Reduction

by Zichen Liu, Zilin Wang, Gaoyuan Wu, Junlei Chen, Jingqi He, Meikang Wu, Dongchao Wang, Xiaoshuang Wei, Ping Tian, Zhihai Wu, Siyuan Li and Meiying Yang

Plants 2025, 14(23), 3650; https://doi.org/10.3390/plants14233650 (registering DOI) - 29 Nov 2025

Abstract

Increasing grain production is crucial for national food security, and fertilizer management is one of the most effective ways to achieve this. In traditional agricultural production, excessive nitrogen (N) application often leads to reduced N use efficiency and increased environmental pollution. Compound slow-release [...] Read more.

Increasing grain production is crucial for national food security, and fertilizer management is one of the most effective ways to achieve this. In traditional agricultural production, excessive nitrogen (N) application often leads to reduced N use efficiency and increased environmental pollution. Compound slow-release fertilizers can effectively improve N use efficiency while still meeting the nutritional demands of rice. However, research on these compound slow-release fertilizers remains limited. The effects of fertilizer management measures (controlled-release fertilizer ratios and N fertilizer levels) on rice yield, material accumulation, photosynthetic characteristics, and N use efficiency are not yet fully understood. In particular, the relationships between yield and material accumulation, photosynthetic characteristics, and N use efficiency require further study. Therefore, this study was conducted in 2021 and 2022 using Jinongda 667 as the material, with three N fertilizer rates of 90 (N1), 120 (N2), and 150 kg ha⁻¹ N (N3). Six controlled-release fertilizer ratios of sulfur-coated urea (SCU) and resin-coated urea (RCU) were tested: 1:0 (C1), 0:1 (C2), 3:1 (C3), 4:1 (C4), 5:1 (C5), and 6:1 (C6) (optimized in 2022 to three ratios: 3:1, 4:1, and 5:1, with traditional split-application fertilization (CF) added as a control). The results showed that the N3C5 treatment achieved the highest yield of 9246.7 kg ha⁻¹ among all combinations of slow-controlled release compound fertilizer ratios and N levels. In 2021, under the same N gradient, yields followed the order C5 > C4 > C3 > C2 > C1, whereas the C6 treatment exhibited a declining yield trend across different N levels. The yield pattern observed in 2022 was consistent with that of 2021. Further comparisons of C3, C4, and C5 under different N levels with the traditional fertilization treatment (N3CF) indicated that, under the same N level, the C5 treatment produced significantly higher yields than the C3 and C4 treatments. Photosynthetic rates at various stages under the C5 treatment increased by 1.9% to 12.7% compared to the C3 and C4 treatments. The N2C5 and N3C5 treatments increased yield by 1.3% and 9.4%, respectively, compared with N3CF, with effective panicle numbers increasing by 6.7% and 11.1%, respectively. The N2C5 treatment reduced N application by 20% compared with N3CF, while significantly increasing N Apparent Use Efficiency (NAUE) by 56.6% and Agronomic N Agricultural Utilization Efficiency (NAE) by 41.8%. Therefore, applying a 5:1 controlled-release fertilizer at a N application rate of 120 kg ha⁻¹ can reduce N use while enhancing efficiency. This approach provides a theoretical basis for green, high-yield rice cultivation. Full article

(This article belongs to the Special Issue Advances in Nitrogen Nutrition in Plants)

26 pages, 1626 KB

Open AccessReview

Nanoparticle-Mediated Nucleic Acid Delivery Systems in Plant Biotechnology: Recent Advances and Emerging Challenges

by Tengwei Wang, Jiaxin Li, Ruibin Hu, Xuping Shentu, Zihong Ye, Xiaoping Yu and Kai Sun

Plants 2025, 14(23), 3649; https://doi.org/10.3390/plants14233649 (registering DOI) - 29 Nov 2025

Abstract

Efficient delivery of exogenous genetic material remains a core challenge in plant biotechnology, holding profound implications for sustainable agricultural and forestry development. Although traditional delivery methods such as Agrobacterium-mediated transformation, gene gun bombardment, and electroporation have been widely applied in plant genetic [...] Read more.

Efficient delivery of exogenous genetic material remains a core challenge in plant biotechnology, holding profound implications for sustainable agricultural and forestry development. Although traditional delivery methods such as Agrobacterium-mediated transformation, gene gun bombardment, and electroporation have been widely applied in plant genetic engineering, these systems exhibit limitations including species-dependent efficacy, propensity to cause plant tissue damage, low transformation efficiency, susceptibility to environmental factors. In recent years, with the advancement of nanotechnology, nanoparticle-based nucleic acid delivery systems are emerging as novel tools for applications such as novel tools for dsRNA or transgene delivery. These systems leverage the unique physicochemical properties of nanomaterials, including size-dependent phenomena, tunable surface charge, and enhanced membrane penetration capabilities, to achieve targeted delivery and stable expression of genetic payloads. Nevertheless, nanomaterial-mediated gene delivery systems for plants are still in their nascent stages, and their widespread application faces numerous challenges. This article briefly introduces traditional delivery methods, systematically reviews the applications and progress of nanoparticle-based nucleic acid delivery systems, and discusses the cross-species applicability of nanoparticles, as well as the associated biosafety concerns. We aim to offer insights for tackling the prevailing technical bottlenecks and to provide guidance for the rational design of nanomaterials that efficiently traverse the plant cell wall–plasma membrane barrier and stably deliver nucleic acids without eliciting phytotoxicity. Full article

(This article belongs to the Special Issue Advancements in Nanotechnology for Plant Health and Productivity)

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22 pages, 4004 KB

Open AccessArticle

Plasma Seed Priming Can Improve the Early Seedling Establishment and Antioxidant Activity of Water Convolvulus Microgreens

by Mayura Veerana, Burapa Poochim, Praepun Intharasuwan, Phatlada Saphanthong, Jun-Sup Lim, Eun-Ha Choi and Gyungsoon Park

Plants 2025, 14(23), 3648; https://doi.org/10.3390/plants14233648 (registering DOI) - 29 Nov 2025

Abstract

Water convolvulus (Ipomoea aquatica Forssk.) is a fast-growing leafy vegetable valued for its nutritional and antioxidant properties; however, suboptimal seed physiology can hinder its germination and early growth. Non-thermal plasma (NTP) treatment is an eco-friendly seed-priming method that enhances seed performance and [...] Read more.

Water convolvulus (Ipomoea aquatica Forssk.) is a fast-growing leafy vegetable valued for its nutritional and antioxidant properties; however, suboptimal seed physiology can hinder its germination and early growth. Non-thermal plasma (NTP) treatment is an eco-friendly seed-priming method that enhances seed performance and crop quality without the use of chemical inputs. This study evaluated the effects of NTP exposure (0, 5, 10, and 20 min) using a dielectric barrier discharge (DBD) plasma with an air gas flow rate of 1.5 lpm on the germination, seedling growth, pigment and protein content, nitrogen assimilation, and antioxidant capacity of water convolvulus. Plasma treatment of seeds increased germination in a time-dependent manner. The surface hydrophilicity improved with increasing treatment time. Seedlings grown from seeds treated for 10 min exhibited longer shoots (+10.1%) and roots (+17.8%). The shoot nitrate content increased by 66.3%. At 10 min, the total phenolics and flavonoids increased by 26.5% and 37.2%, respectively, with an accompanying increase in antioxidant activity, as measured by DPPH, ABTS, and FRAP assays. These findings demonstrate that a 10 min NTP treatment of seeds improves germination, growth, nutrient assimilation, phytochemical accumulation, and antioxidant activity in water convolvulus seedlings, highlighting its potential as a sustainable and chemical-free seed-priming technology with considerable potential to enhance the productivity and nutritional quality of plant microgreens in modern agriculture. Full article

(This article belongs to the Section Plant Physiology and Metabolism)

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21 pages, 864 KB

Open AccessArticle

Response of Nitrogen Cycling in Alfalfa (Medicago sativa L.) Grassland Systems to Cropping Patterns and Nitrogen Application Rates: A Quantitative Analysis Based on Nitrogen Balance

by Yaya Duan, Jianxin Yin, Yuanbo Jiang, Haiyan Li, Wenjing Chang, Yanbiao Wang, Minhua Yin, Yanxia Kang, Yanlin Ma, Yayu Wang and Guangping Qi

Plants 2025, 14(23), 3647; https://doi.org/10.3390/plants14233647 (registering DOI) - 29 Nov 2025

Abstract

An imbalance between the supply and demand of nutrients within the crop–soil system has resulted from the prevalent practice of excessive fertilization in agricultural agriculture. In order to increase crop growth, improve resource usage efficiency, and reduce agricultural nonpoint source pollution, appropriate cropping [...] Read more.

An imbalance between the supply and demand of nutrients within the crop–soil system has resulted from the prevalent practice of excessive fertilization in agricultural agriculture. In order to increase crop growth, improve resource usage efficiency, and reduce agricultural nonpoint source pollution, appropriate cropping management techniques are essential. This study examined the effects of four nitrogen application rates (0 kg·ha⁻¹ (C0), 80 kg·ha⁻¹ (C1), 160 kg·ha⁻¹ (C2), and 240 kg·ha⁻¹ (C3)) and three alfalfa cropping systems (traditional flat planting, FP; ridge-covered biodegradable mulch, JM; and ridge-covered conventional mulch, PM) on soil inorganic nitrogen transport, nitrogen allocation within alfalfa plants, and soil N₂O emissions. Throughout the alfalfa growth phase, the dynamics of nitrogen balance within the soil–plant–atmosphere system were quantitatively examined. The findings showed: (1) The concentrations of soil NO₃⁻–N and NH₄⁺–N rose with the rate of nitrogen application but decreased with soil depth. The PMC3 treatment had the largest inorganic nitrogen reserves at the end of the alfalfa growth period. (2) The pattern of PM > JM > FP for nitrogen uptake and nitrogen accumulation in biomass in alfalfa leaves and stems peaked at the C2 nitrogen treatment rate. (3) As nitrogen application rates increased, grass-land N₂O emission flow and total emissions also followed PM > JM > FP. (4) The PMC2 treatment showed apparent nitrogen balances of 9.73 kg·ha⁻¹ and 1.84 kg·ha⁻¹ during the two-year growing season, with apparent nitrogen loss rates of 6.08% and 1.15%, respectively, both significantly lower than other treatments, according to nitrogen balance analysis. In summary, the nitrogen application pattern combining ridge-covering conventional plastic mulch with moderate nitrogen application levels can achieve nitrogen balance in alfalfa grassland systems within the Yellow River irrigation district of Gansu Province, China, and similar ecological zones. Full article

(This article belongs to the Special Issue Water and Nutrient Management for Sustainable Crop Production)

19 pages, 8279 KB

Open AccessArticle

Integrated Transcriptomic and Biochemical Analyses Reveal the Root Development-Promoting Mechanism of Piriformospora indica on Blueberry Under Tap Water Irrigation

by Sijian Guo, Pengyan Qu, Shitao Du, Rui Liu, Yongyan Zhang and Chunzhen Cheng

Plants 2025, 14(23), 3646; https://doi.org/10.3390/plants14233646 (registering DOI) - 29 Nov 2025

Abstract

Piriformospora indica, a broad-spectrum plant growth-promoting fungus, has been successfully applied in blueberry (Vaccinium corymbosum L.). In this study, through an integrated transcriptomic and biochemical analyses, we investigated the effects of P. indica colonization on blueberry root growth under long-term tap [...] Read more.

Piriformospora indica, a broad-spectrum plant growth-promoting fungus, has been successfully applied in blueberry (Vaccinium corymbosum L.). In this study, through an integrated transcriptomic and biochemical analyses, we investigated the effects of P. indica colonization on blueberry root growth under long-term tap water (EC ≈ 1500 μs/cm) irrigation. Comparative transcriptomic analysis revealed that P. indica colonization greatly influenced the expression of genes involved in RNA biosynthesis, solute transport, response to external stimuli, phytohormone action, carbohydrate metabolism, cell wall organization, and secondary metabolism pathways. Consistently, the fungal colonization significantly improved the nutrient absorption ability, and increased the contents of sucrose, starch, trehalose, total phenolic, total flavonoids, and indole-3-acetic acid (IAA), while suppressing the accumulations of jasmonic acid (JA), abscisic acid (ABA), 1-aminocyclopropane-1-carboxylic acid (ACC), and strigolactone (SL) in blueberry roots. Quantitative real-time PCR verification also confirmed the fungal influences on genes associated with these pathways/parameters, such as auxin homoeostasis-associated WAT1, cell wall metabolism-related EXP, phenylpropanoid biosynthesis-related PAL and CHS, carotenoid degradation-related CCD8, transportation-related CNGC, trehalose metabolism-related TPP, and so on. Our study demonstrated that P. indica improved blueberry adaptability to mild salt stress by synergistically regulating cell wall metabolism, secondary metabolism, stress responses, hormone homeostasis, sugar and mineral element transportation, and so on. Full article

(This article belongs to the Special Issue Quality Improvement of Fruit Trees: Integrating Omics and Cultivation Techniques)

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26 pages, 7833 KB

Open AccessArticle

An Integrated Meta-QTL and Transcriptome Analysis Provides Candidate Genes Associated with Drought Tolerance in Rice Seedlings

by Yinji Jin, Weize Dou, Tianhao Wang, Zhuo Jin and Songquan Wu

Plants 2025, 14(23), 3645; https://doi.org/10.3390/plants14233645 (registering DOI) - 29 Nov 2025

Abstract

Drought stress, intensified by climate change, poses a significant threat to global rice security. To identify stable quantitative trait loci (QTL) associated with drought tolerance in rice under different genetic backgrounds and environmental conditions, this study combined 901 drought-tolerant QTLs reported in 52 [...] Read more.

Drought stress, intensified by climate change, poses a significant threat to global rice security. To identify stable quantitative trait loci (QTL) associated with drought tolerance in rice under different genetic backgrounds and environmental conditions, this study combined 901 drought-tolerant QTLs reported in 52 independent studies published between 2000 and 2023, which were subsequently meta-analyzed and condensed into 77 meta-QTLs (MQTLs). Among them, 23 MQTLs were validated in seven independent genome-wide association studies (GWAS) on drought tolerance in rice, each conducted using different natural populations. The confidence intervals (CIs) of the MQTLs were substantially narrowed, with the reduction factor ranging from 2.44 to 20.40 relative to the original QTLs. To further explore key genes for drought tolerance, we screened for genes located within the MQTL regions and differentially expressed in our RNA-seq data, yielding 3851 drought-responsive differentially expressed genes (DEGs). These DEGs were then subjected to a refinement process that included Mfuzz clustering, cis-regulatory element (CRE) analysis, protein–protein interaction (PPI) network analysis and AlphaFold-based structural modeling of their encoded proteins. This stepwise filtering identified eleven drought-responsive hub proteins, nine with annotated functions and two functionally uncharacterized. Following further prioritization, LOC_Os04g35340 and Os07g0141400 were established as core candidate genes (CGs) for dissecting the genetic and biochemical basis of drought tolerance in rice. Full article

(This article belongs to the Special Issue Mechanism of Drought and Salinity Tolerance in Crops)

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47 pages, 24528 KB

Open AccessArticle

VNIR Hyperspectral Signatures for Early Detection and Machine-Learning Classification of Wheat Diseases

by Rimma M. Ualiyeva, Mariya M. Kaverina, Anastasiya V. Osipova, Yernar B. Kairbayev, Sayan B. Zhangazin, Nurgul N. Iksat and Nariman B. Mapitov

Plants 2025, 14(23), 3644; https://doi.org/10.3390/plants14233644 (registering DOI) - 29 Nov 2025

Abstract

This article presents the results of a comprehensive study aimed at developing automated diagnostic methods for identifying spring wheat phytopathologies using hyperspectral imaging (HSI). The research aimed to create an effective plant disease detection system, including at the early stages, which is critically [...] Read more.

This article presents the results of a comprehensive study aimed at developing automated diagnostic methods for identifying spring wheat phytopathologies using hyperspectral imaging (HSI). The research aimed to create an effective plant disease detection system, including at the early stages, which is critically important for ensuring food security in regions where wheat plays a key role in the agro-industrial sector. The study analyses the spectral characteristics of major wheat diseases, including powdery mildew, fusarium head blight, septoria glume blotch, root rots, various types of leaf spots, brown rust, and loose smut. Healthy plants differ from diseased ones in that they show a mostly uniform tone without distinct spots or patches on hyperspectral images, and their spectra have a consistent shape without sharp fluctuations. In contrast, disease spectra, differ sharply from those of healthy areas and can take diverse forms. Wheat diseases with a light coating (powdery mildew, fusarium head blight) exhibit high reflectance; chlorosis in the early stages of diseases (rust, leaf spot, septoria leaf blotch) exhibits curves with medium reflectance, and diseases with dark colouration (loose smut, root rot) have low reflectance values. These differences in reflectance among fungal diseases are caused by pigments produced by the pathogens, which either strongly absorb light or reflect most of it. The presence or absence of pigment production is determined by adaptive mechanisms. Based on these patterns in the spectral characteristics and optical properties of the diseases, a classification model was developed with 94% overall accuracy. Random Forest proved to be the most effective method for the automated detection of wheat phytopathogens using hyperspectral data. The practical significance of this research lies in the potential integration of the developed phytopathology detection approach into precision agriculture systems and the use of UAV platforms, enabling rapid large-scale crop monitoring for the timely detection. The study’s results confirm the promising potential of combining hyperspectral technologies and machine learning methods for monitoring the phytosanitary condition of crops. Our findings contribute to the advancement of digital agriculture and are particularly valuable for the agro-industrial sector of Central Asia, where adopting precision farming technologies is a strategic priority given the climatic risks and export-oriented nature of grain production. Full article

(This article belongs to the Special Issue Recent Advances in Remote Sensing, Image Processing, and Deep Learning for Precision Agriculture)

22 pages, 2944 KB

Open AccessArticle

Cattle Manure Fertilizer and Biostimulant Trichoderma Application to Mitigate Salinity Stress in Green Maize Under an Agroecological System in the Brazilian Semiarid Region

by Maria Vanessa Pires de Souza, Geocleber Gomes de Sousa, Arthur Prudêncio de Araujo Pereira, Henderson Castelo Sousa, Kaio Gráculo Vieira Garcia, Leonardo Vieira de Sousa, Gerônimo Ferreira da Silva, Ênio Farias de França e Silva, Thieres George Freire da Silva and Alexsandro Oliveira da Silva

Plants 2025, 14(23), 3643; https://doi.org/10.3390/plants14233643 (registering DOI) - 29 Nov 2025

Abstract

Organic fertilizer stimulates soil microbial activity, contributing to the decomposition of organic residues and nutrient release, thereby helping to reduce the negative effects of soil salinity. The use of Trichoderma can enhance nutrient availability to plants and increase their resistance to abiotic stresses, [...] Read more.

Organic fertilizer stimulates soil microbial activity, contributing to the decomposition of organic residues and nutrient release, thereby helping to reduce the negative effects of soil salinity. The use of Trichoderma can enhance nutrient availability to plants and increase their resistance to abiotic stresses, such as salinity stress. Therefore, this study aimed to determine the effects of organic fertilizer on green maize plants under soil inoculation with Trichoderma harzianum and salinity stress. The experiment was conducted during the 2022 and 2023 growing seasons in Redenção municipally, Ceará, Brazil. A randomized complete block design was used, arranged in a split–split plot scheme with four replications. The main plots consisted of two electrical conductivities of irrigation water (ECw): A1—0.3 dS m⁻¹ and A2—3.0 dS m⁻¹. The subplots comprised three doses of well-composted cattle manure (0, 10, and 20 t ha⁻¹), and the sub-subplots represented soil inoculation (TI) or non-inoculation (NI) with the Trichoderma harzianum-based biostimulant. Irrigation with saline water reduced maize growth and yield; however, these effects were mitigated by Trichoderma harzianum and organic fertilizer. Inoculation was particularly effective under lower electrical conductivity conditions. The combination of 10 t ha⁻¹ of cattle manure with Trichoderma inoculation showed the highest productive efficiency. Full article

(This article belongs to the Special Issue Bioinoculants: A Sustainable Solution to Biotic and Abiotic Stresses)

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