Applications of Biotechnology in Food and Agriculture

Journal Name	Impact Factor	CiteScore	Launched Year	First Decision (median)	APC
Agriculture agriculture	4.5	7.8	2011	17.4 Days	CHF 2600	Submit
Agrochemicals agrochemicals	-	11.5	2022	21.9 Days	CHF 1000	Submit
Agronomy agronomy	4.1	7.6	2011	17.7 Days	CHF 2600	Submit
Crops crops	2.1	2.9	2021	20.7 Days	CHF 1200	Submit
Horticulturae horticulturae	3.4	6.1	2015	17.4 Days	CHF 2400	Submit
Microorganisms microorganisms	4.7	8.2	2013	16.5 Days	CHF 2700	Submit
Plants plants	4.7	8.5	2012	14.8 Days	CHF 2700	Submit

20 pages, 14148 KB

Open AccessArticle

Effects of Medium Supplements on Embryogenesis and the Yield of Regenerants of Different Ploidy Levels from Unpollinated Ovules of Cucurbita pepo L.

by Alexey Ermolaev, Elena Domblides, Kseniia Stebnitskaia and Olesya Valdeeva

Crops 2026, 6(4), 66; https://doi.org/10.3390/crops6040066 - 7 Jul 2026

Viewed by 362

Abstract

The aim of this work was to study the influence of various factors (sucrose concentration, silver nitrate, activated charcoal, and plant growth regulators 2.4-D (2.4-Dichlorophenoxyacetic Acid) and TDZ (Thidiazuron)) on the induction of gynogenesis and their effect on eight genotypes of summer squash [...] Read more.

The aim of this work was to study the influence of various factors (sucrose concentration, silver nitrate, activated charcoal, and plant growth regulators 2.4-D (2.4-Dichlorophenoxyacetic Acid) and TDZ (Thidiazuron)) on the induction of gynogenesis and their effect on eight genotypes of summer squash on the ploidy level of regenerated summer squash plants (Cucurbita pepo L.) in isolated ovule culture in vitro. IMC (Induction Medium for Cucurbitaceae) nutrient medium supplemented with 2 mg/L 2.4-D or 0.2 mg/L TDZ was used. It was shown that the optimal sucrose concentration for embryogenesis was 30 g/L; at 70 g/L, embryogenesis was absent. The addition of 10 mg/L AgNO₃ in combination with 2.4-D in the genotype Faraon increased the frequency of embryogenesis up to 80%. It was found that a low concentration of activated charcoal (5 mg/L) together with TDZ increased the yield of embryoids by 8.5 times (68% embryogenesis) in the genotype Sangrum. Both growth regulators effectively induce embryogenesis, but their action strongly depends on the genotype and the composition of the nutrient medium. Flow cytometry analysis of 247 regenerant plants adapted to ex vitro conditions of the studied genotypes obtained in this study showed that diploids (2n) accounted for 47.2%, tetraploids (4n) 45.7%, triploids 3.7%, and octoploids 3.4%. Genotype-specificity of growth regulator action was demonstrated: in the genotypes Sangrum and Faraon, TDZ promoted a higher yield of tetraploids, while in the genotype Yakor, 2.4-D was more effective. The obtained tetraploid lines can be used to create seedless triploid hybrids without colchicine treatment. The developed combinations of factors will allow more efficient induction of gynogenesis in summer squash in vitro. Full article

(This article belongs to the Topic Applications of Biotechnology in Food and Agriculture)

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18 pages, 656 KB

Open AccessArticle

Changes in the Physicochemical Characteristics and Antioxidant Activity of Saladette-Type Tomato (Solanum lycopersicum L.) Grown in Soil Supplemented with Zeolite

by Jessica Lizbeth Ramirez-Tellez, Luis Delgado-Olivares, Nelly del Socorro Cruz-Cansino, Ernesto Alanis-García, Edgar Arturo Chávez-Urbiola and Esther Ramirez-Moreno

Crops 2026, 6(4), 65; https://doi.org/10.3390/crops6040065 - 3 Jul 2026

Viewed by 366

Abstract

The rapid pace of urbanization, coupled with the variability in climatic conditions, has led to a marked increase in global food demand. Simultaneously, this phenomenon has resulted in a decline in the overall quality of food, highlighting the need to improve existing agricultural [...] Read more.

The rapid pace of urbanization, coupled with the variability in climatic conditions, has led to a marked increase in global food demand. Simultaneously, this phenomenon has resulted in a decline in the overall quality of food, highlighting the need to improve existing agricultural production systems. In this context, zeolite has emerged as a promising soil amendment for optimizing its physical properties and crop yields. However, there is limited information on its effects during tomato cultivation, particularly for the Saladette variety (Solanum lycopersicum L.) in Hidalgo, Mexico. This includes the use of this zeolite variety, the evaluation of its antioxidant properties, and its antioxidant activity at different applied concentrations. This study evaluated the effect of different concentrations of zeolite applied to the soil on tomato growth and fruit quality. After crop establishment, the treatments were monitored monthly. The results showed that the application of zeolite significantly improved crop yield, with Treatment 3 (5 kg zeolite plant⁻¹) showing the best performance without affecting the physical characteristics of the fruit. The tomatoes maintained adequate commercial standards, with weights ranging from 104 a 169 g, sizes from 5.16 to 6.20 cm, and firmness values between 1.19 and 2.27 N; therefore, this treatment was selected for the determination of the antioxidant activity on the fruits. Furthermore, an increase in antioxidant capacity was observed, reaching 5.50 µmol TE/100 g of dry sample in the DPPH antioxidant capacity test. This demonstrates that zeolite application positively influences the quality and antioxidant capacity of tomatoes. This suggests that zeolite could be used in various crops, potentially improving the quality of the final product and offering health benefits to consumers thanks to the antioxidant compounds generated during harvest. However, further studies are needed to determine the optimal application rates and the long-term effects on soil health and crop productivity. Full article

(This article belongs to the Topic Applications of Biotechnology in Food and Agriculture)

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23 pages, 2760 KB

Open AccessArticle

Comparative Evaluations of Commercial Seaweed Extract Formulations on Germination, Biomass Accumulation and Early Seedling Growth in Capsicum annuum

by Prabhaharan Renganathan, Kristina Borisovna Ukhatkina, Ilya Isidorovich Van Erp, Alfia Mufazalova, Natalia V. Sukhanova and Lira A. Gaysina

Horticulturae 2026, 12(7), 799; https://doi.org/10.3390/horticulturae12070799 - 30 Jun 2026

Cited by 1 | Viewed by 630

Abstract

Seaweed-derived biostimulants are increasingly used to improve seed germination and early seedling development in horticultural crops. This study evaluated the effects of five commercially available seaweed extract (SWE) formulations (ASCO, AQUA, KAT, SAGA, and BIO) applied at 2 mL L⁻¹ on germination, [...] Read more.

Seaweed-derived biostimulants are increasingly used to improve seed germination and early seedling development in horticultural crops. This study evaluated the effects of five commercially available seaweed extract (SWE) formulations (ASCO, AQUA, KAT, SAGA, and BIO) applied at 2 mL L⁻¹ on germination, seedling growth, biomass accumulation, moisture-related traits, and biomass allocation indices of Capsicum annuum L. under controlled conditions. A 10-day in vitro Petri dish bioassay was conducted using five experimental replicates for each treatment. Significant differences among the treatments were observed for several germination, growth, biomass, and moisture-related parameters. KAT exhibited the highest final germination percentage, whereas SAGA exhibited the fastest germination response and the highest seedling vigor index. SAGA was associated with higher root length and total dry weight, whereas AQUA exhibited among the highest root biomass values. BIO recorded the highest moisture content, leaf length, and shoot-to-root ratio. Correlation analysis identified significant relationships among growth and biomass traits, whereas principal component analysis revealed distinct multivariate response patterns among the evaluated formulations. Overall, the commercial SWE formulations showed different response profiles during the early seedling development of C. annuum under the conditions of present study. Further studies are required to evaluate the consistency of these responses across different concentrations, cultivars, and growing environments. Full article

(This article belongs to the Topic Applications of Biotechnology in Food and Agriculture)

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19 pages, 3143 KB

Open AccessArticle

Auxin Treatment Enhances Adventitious Rooting While Genotype Modulates Root Elongation and Basal Callus Formation in Coffea arabica Cuttings

by Jamil Delgado-Rafael, Raúl Vargas, Robin Oblitas-Delgado, Jois V. Carrion, Amilcar Valle-Lopez, Jhon Edler Lopez-Merino, Edinson Pooll Acuña-Ramirez, Jose Luis Pinedo-Mas, Eyner Huaman and Manuel Oliva-Cruz

Crops 2026, 6(4), 63; https://doi.org/10.3390/crops6040063 - 29 Jun 2026

Viewed by 561

Abstract

Adventitious rooting remains a major constraint for the clonal propagation of Coffea arabica, limiting the large-scale multiplication of elite genotypes. This study evaluated the effects of genotype, auxin treatment, and their interaction on adventitious rooting and basal callus formation in coffee cuttings [...] Read more.

Adventitious rooting remains a major constraint for the clonal propagation of Coffea arabica, limiting the large-scale multiplication of elite genotypes. This study evaluated the effects of genotype, auxin treatment, and their interaction on adventitious rooting and basal callus formation in coffee cuttings under controlled nursery conditions, while morphophysiological traits were assessed as complementary indicators of cutting performance. A completely randomized 3 × 3 factorial design was used, including three hybrids (H3, Excelencia, and Milenio) and three plant growth regulator (PGR) treatments: control, indole-3-butyric acid (IBA), and a commercial auxin formulation (RH; NAA + IBA). Rooting probability and root number were significantly affected by PGR treatment, whereas the longest root length was influenced by hybrid, PGR treatment, and their interaction. Model-estimated rooting probability increased from 4.76% in the control to 17.05% under IBA and 35.73% under RH. Similarly, the estimated number of roots per cutting increased from 0.14 in the control to 0.99 under IBA and 1.85 under RH. Although the hybrid × PGR interaction was not significant for rooting probability, the highest observed rooting percentage was recorded in H3 under RH (52.38%), followed by Milenio under RH (33.33%). For the longest root length, the strongest responses were observed under RH, particularly in Milenio (71.15 mm) and H3 (70.08 mm). Callus formation varied among treatments, but its association with rooting performance was weak and inconsistent. Morphophysiological traits provided complementary information on cutting status but were not interpreted as direct mechanistic drivers of rooting. These findings indicate that adventitious rooting in C. arabica was more closely associated with genotype-dependent responsiveness to exogenous auxin than with the extent of callus formation. However, anatomical studies are needed to determine the developmental origin of root primordia and their possible relationship with callus tissue. Full article

(This article belongs to the Topic Applications of Biotechnology in Food and Agriculture)

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30 pages, 1379 KB

Open AccessReview

Molecular Basis and Mechanistic Insights into Ascophyllum nodosum Extract-Mediated Regulation of Plant Growth, Nutrient Acquisition, and Stress Responses

by Prabhaharan Renganathan, Lira A. Gaysina, Juan Carlos Sainz-Hernández and Edgar Omar Rueda Puente

Plants 2026, 15(12), 1913; https://doi.org/10.3390/plants15121913 - 20 Jun 2026

Cited by 2 | Viewed by 750

Abstract

Ascophyllum nodosum extracts (ANE) are widely used biostimulants associated with improvements in plant growth, productivity, nutrient acquisition, and abiotic stress tolerance. However, the molecular mechanisms linking extract composition to plant signaling and physiological responses remain incompletely resolved. ANE contains a complex mixture of [...] Read more.

Ascophyllum nodosum extracts (ANE) are widely used biostimulants associated with improvements in plant growth, productivity, nutrient acquisition, and abiotic stress tolerance. However, the molecular mechanisms linking extract composition to plant signaling and physiological responses remain incompletely resolved. ANE contains a complex mixture of bioactive constituents, including polysaccharides, osmolytes, phenolic compounds, and phytohormone-like molecules. Their composition varies according to biomass source, environmental conditions, and extraction methodology, contributing to variability in biological activity. Current evidence suggests that ANE functions mainly as a signaling modulator rather than a direct nutrient source. ANE treatment has been associated with early cellular responses, including cytosolic Ca²⁺ influx, reactive oxygen species (ROS) generation, and mitogen-activated protein kinase (MAPK)-associated signaling events. However, many proposed mechanisms remain unresolved, and a considerable proportion of the available mechanistic evidence originates from studies using purified ANE-derived polysaccharides or related elicitor systems. ANE-associated responses include modulation of nutrient transport, primary metabolism, hormonal regulation, transcriptional reprogramming, and stress-responsive pathways, contributing to improved root development, nutrient acquisition, and defense-related responses. Nevertheless, limited knowledge of receptor-mediated perception mechanisms, signaling hierarchies, and extract-dependent variability continues to constrain mechanistic understanding and reproducibility. Future research should prioritize receptor identification, bioassay-guided fractionation, integrated multi-omics approaches, and improved standardization of extraction and formulation procedures. These advances will be essential for establishing robust mechanistic models and supporting the development of evidence-based ANE biostimulants for sustainable crop production. Full article

(This article belongs to the Topic Applications of Biotechnology in Food and Agriculture)

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24 pages, 11401 KB

Open AccessArticle

Influence of Lateral Leaf Number on Vibration Characteristics and Energy Dissipation of the Walnut (Juglans regia) Branch–Leaf–Fruit Subsystem

by Yancheng Zhu, Hongping Zhou, Linyun Xu, Yang Zhang, Yanyan Wang and Aiqi Zhang

Agriculture 2026, 16(12), 1265; https://doi.org/10.3390/agriculture16121265 - 8 Jun 2026

Viewed by 329

Abstract

During the harvest period, the role of lateral leaves in the dynamic behavior of the walnut (Juglans regia) branch–leaf–fruit subsystem remains unclear, and vibration harvesting parameter selection still lacks targeted guidance. To address this issue, a local walnut branch–leaf–fruit subsystem was [...] Read more.

During the harvest period, the role of lateral leaves in the dynamic behavior of the walnut (Juglans regia) branch–leaf–fruit subsystem remains unclear, and vibration harvesting parameter selection still lacks targeted guidance. To address this issue, a local walnut branch–leaf–fruit subsystem was studied by combining a discrete dynamic model, free-vibration tests, forced-vibration tests, and MATLAB simulations to investigate the effects of lateral leaf number on system dynamics. A representative single-fruit subsystem with six lateral leaves was selected, and four leaf number conditions (zero, two, four, and six) were examined. High-speed imaging was used to identify leaf motion patterns, while natural frequencies and fruit tracking point displacement responses were measured. The results showed that lateral leaves mainly exhibited three motion modes during vibration: spin, swing, and spin–swing compound motion. Under the six-leaf condition, spin motion was dominant. As the number of lateral leaves increased from 0 to 6, the first-order natural frequency decreased from 13.92 ± 6.37 Hz to 8.79 ± 4.03 Hz, a reduction of 36.8%. Forced-vibration results showed that increasing lateral leaf number significantly reduced the displacement response of the fruit tracking point in the non-excitation directions. Under the six-leaf condition, the maximum displacements in the Y- and Z-directions were reduced by 56.0% and 55.8%, respectively, compared with the leafless condition, indicating that the forced response became more concentrated in the main excitation direction. In the original MATLAB model, lateral leaves were simplified as fixed lumped mass damping elements, and the predicted results differed from the experimental trends. After introducing dynamic damping parameters matched to leaf motion patterns, the simulated trends became closer to the experimental results. These findings indicate that lateral leaf number is an important structural factor affecting the natural characteristics and directional forced responses of the walnut branch–leaf–fruit subsystem. The results provide theoretical and experimental references for optimizing vibration parameters and supporting low-damage, high-efficiency walnut vibration harvesting. Full article

(This article belongs to the Topic Applications of Biotechnology in Food and Agriculture)

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16 pages, 2065 KB

Open AccessArticle

Bacillus sp. L11 Promotes Tomato (Solanum lycopersicum L.) Seedling Growth by Reshaping Rhizosphere Bacterial Communities and Enhancing Root Growth Parameters

by Zhengwu Lu, Xin Guo, Renqiang Li, Yuqing Zhang, Hailin Zhang, Xinru Li, Xinzhe Li, Suyao Yin, Zhiqun Chen, Xu Zhang and Jingjing Liu

Horticulturae 2026, 12(5), 627; https://doi.org/10.3390/horticulturae12050627 - 19 May 2026

Viewed by 1096

Abstract

Plant growth-promoting rhizobacteria (PGPR) represent a sustainable and eco-friendly strategy to enhance crop productivity and support integrated agricultural systems. Among these, members of the genus Bacillus are highly valued for their resilience and multifaceted beneficial traits. The growth-promoting effects of Bacillus sp. L11 [...] Read more.

Plant growth-promoting rhizobacteria (PGPR) represent a sustainable and eco-friendly strategy to enhance crop productivity and support integrated agricultural systems. Among these, members of the genus Bacillus are highly valued for their resilience and multifaceted beneficial traits. The growth-promoting effects of Bacillus sp. L11 on S. lycopersicum seedlings were investigated in soil and artificial peat-based substrates. Rhizosphere microbial diversity was subsequently analyzed to investigate the interaction between L11 and the indigenous microbiota. We evaluated plant growth parameters, root growth parameters, and rhizosphere bacterial community dynamics using 16S rRNA high-throughput sequencing. Overall, L11 inoculation was associated with significantly improved growth indices of S. lycopersicum seedlings in both cultivation systems. Notably, the phosphate-buffered saline (PBS)-resuspended L11 markedly increased shoot fresh weight and plant height, and enhanced root-associated parameters such as total root length and root surface area. While L11 did not significantly alter alpha diversity, principal coordinates analysis (PCoA) revealed that its presence was associated with substantial restructuring of the rhizosphere bacterial community. Inoculation specifically enriched beneficial genera, including Chitinophaga, Devosia, and Pseudomonas. Correlation analyses showed that these microbial shifts were positively associated with the enhancement of seedling biomass and development. In conclusion, these findings suggest that Bacillus sp. L11 may promote S. lycopersicum growth through direct stimulation and by reshaping the rhizosphere microbiome, positioning it as a promising microbial inoculant for sustainable vegetable production. Full article

(This article belongs to the Topic Applications of Biotechnology in Food and Agriculture)

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18 pages, 6146 KB

Open AccessArticle

Multiplex CRISPR/Cas9 Editing of SlTOM1 Host Factors Confers Enhanced Tolerance to ToBRFV in Tomato

by Pelin Sarıkaya and Hakan Fidan

Agriculture 2026, 16(10), 1097; https://doi.org/10.3390/agriculture16101097 - 16 May 2026

Viewed by 790

Abstract

Tomato brown rugose fruit virus (ToBRFV) poses a major threat to global tomato (Solanum lycopersicum) production, as it can overcome conventional resistance genes that are effective against tobamoviruses. In this study, a multiplex CRISPR/Cas9 system was developed to target the SlTOM1 [...] Read more.

Tomato brown rugose fruit virus (ToBRFV) poses a major threat to global tomato (Solanum lycopersicum) production, as it can overcome conventional resistance genes that are effective against tobamoviruses. In this study, a multiplex CRISPR/Cas9 system was developed to target the SlTOM1 susceptibility gene family (SlTOM1a–d), which encodes host factors essential for tobamovirus replication. Six guide RNAs (gRNAs), designed following 12 off-target analyses, were assembled into a multiplex CRISPR/Cas9 construct using a Golden Gate cloning strategy and introduced into tomato genotypes through an Agrobacterium-based tissue culture transformation procedure. Although primary T₀ transformants exhibited chimeric mutation patterns, stable inheritance and segregation of edited alleles were confirmed in the T₁ generation. Sequence analyses identified diverse indel mutations across target loci, with SlTOM1d exhibiting the highest editing efficiency. Multiplex genome editing successfully generated single-, double-, and triple-mutant combinations, with higher-order mutants displaying the strongest tolerance phenotypes. Following mechanical ToBRFV inoculation, edited T₁ plants exhibited markedly reduced symptom severity, low viral accumulation, and improved fruit health compared to wild-type controls. RT-qPCR analysis further confirmed significantly reduced viral RNA levels, supporting a host-factor-mediated tolerance mechanism. Importantly, edited lines maintained normal growth and agronomic performance. Collectively, these findings demonstrate that multiplex CRISPR/Cas9-mediated targeting of SlTOM1 homologs represents a promising and practical strategy for improving ToBRFV tolerance in tomato breeding programs. Full article

(This article belongs to the Topic Applications of Biotechnology in Food and Agriculture)

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20 pages, 3342 KB

Open AccessArticle

Strain-Specific Microalgal and Cyanobacterial Suspensions Modulate Germination Kinetics and Early Seedling Vigor in Cucumber

by Prabhaharan Renganathan, Alsu Yakupova, Artyom Filippov, Irina Larionova, Rezeda Sushchenko, Alfia Mufazalova, Liliia Khilazhetdinova, Kamilla Gaysina and Lira A. Gaysina

Horticulturae 2026, 12(4), 414; https://doi.org/10.3390/horticulturae12040414 - 27 Mar 2026

Cited by 4 | Viewed by 1635

Abstract

Microalgal and cyanobacterial biostimulants are increasingly recognized as sustainable tools for enhancing crop establishment and reducing dependence on synthetic agrochemicals. However, the strain-specific effects of many taxa on seed germination and early seedling development remain insufficiently characterized. This study evaluated the effects of [...] Read more.

Microalgal and cyanobacterial biostimulants are increasingly recognized as sustainable tools for enhancing crop establishment and reducing dependence on synthetic agrochemicals. However, the strain-specific effects of many taxa on seed germination and early seedling development remain insufficiently characterized. This study evaluated the effects of seven microalgal and cyanobacterial suspensions on the germination kinetics and early seedling vigor of cucumber (Cucumis sativus L.). Several strains significantly accelerated germination and enhanced seedling performance relative to the control. Treatment with Coelastrella rubescens BCAC 301 S39, Scotinosphaera lemnae BCAC 113, Vischeria magna UTEX 2351, and Anabaena sp. IT4 significantly reduced mean germination time from 4.50 d to 2.23–2.29 d and advanced the time to 50% germination (T₅₀) from 4.0 to 2.0–2.1 d. These treatments also increased the germination index from 48.32 to 78.17–100.67 and enhanced seedling traits, including root length (32–53%), shoot length (≈29%), leaf length (17–21%), and fresh (30–43%) and dry biomasses (12–22%). Correlation analysis revealed strong positive associations between germination indices and seedling vigor parameters, indicating the faster germination promotes early growth. In conclusion, the results demonstrate that specific microalgal strains can function as effective seed-phase biostimulants, offering a sustainable strategy to enhance germination uniformity, early seedling establishment, and crop productivity. Full article

(This article belongs to the Topic Applications of Biotechnology in Food and Agriculture)

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16 pages, 3481 KB

Open AccessArticle

Optimization of Protein Yield from Rice Straw via Ammonia–Steam Explosion Pretreatment and Solid-State Fermentation Using Response Surface Methodology

by Jia Zhu, Kunjie Chen and Bin Li

Agriculture 2026, 16(5), 621; https://doi.org/10.3390/agriculture16050621 - 8 Mar 2026

Cited by 2 | Viewed by 831

Abstract

The combination of ammonia and steam explosion pretreatment has shown significant potential to enhance protein yield during the solid-state fermentation (SSF) of rice straw. However, the complex interactions between physicochemical changes and fermentation parameters necessitate precise optimization. This study employed a three-level Box–Behnken [...] Read more.

The combination of ammonia and steam explosion pretreatment has shown significant potential to enhance protein yield during the solid-state fermentation (SSF) of rice straw. However, the complex interactions between physicochemical changes and fermentation parameters necessitate precise optimization. This study employed a three-level Box–Behnken design (BBD) within the framework of Response Surface Methodology (RSM) to evaluate the effects of steam explosion pressure, pressure retention time, and ammonia concentration on protein yield. The SSF experiments were conducted in 5 L fermentation bottles using a co-culture of Aspergillus oryzae and Neurospora sitophila. The results demonstrated that the optimal conditions were a pressure of 1.44 MPa, a pressure retention time of 139.4 s, and an ammonia concentration of 8.3%. Under these optimized conditions, the protein yield reached 42.1% after 96 h of SSF, which was validated by a confirmatory experiment (42.8% ± 2.37%). The pretreated rice straw exhibited significantly improved lignocellulose degradation and structural porosity, providing a highly conducive substrate for microbial growth. These findings suggest that the optimized ammonia–steam explosion process is an effective and quantifiable strategy for converting agricultural waste into high-quality protein feed, contributing to sustainable bio-resource utilization. Full article

(This article belongs to the Topic Applications of Biotechnology in Food and Agriculture)

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14 pages, 577 KB

Open AccessArticle

Comparative Efficiency of Fungal Organic Acids and Pure Acids in Tricalcium Phosphate Solubilisation

by Thabo J. Moropana, Elbert L. Jansen Van Rensburg, Livhuwani Makulana and Nkateko N. Phasha

Microorganisms 2026, 14(2), 424; https://doi.org/10.3390/microorganisms14020424 - 11 Feb 2026

Viewed by 1038

Abstract

Phosphorus (P) is a vital macronutrient involved in key biochemical processes that support plant growth; however, its low bioavailability in agricultural soils remains a major constraint on crop productivity. This limitation is commonly addressed through the application of chemical P fertilisers produced by [...] Read more.

Phosphorus (P) is a vital macronutrient involved in key biochemical processes that support plant growth; however, its low bioavailability in agricultural soils remains a major constraint on crop productivity. This limitation is commonly addressed through the application of chemical P fertilisers produced by acidulation of phosphate rock (PR), a process that is costly, energy-intensive, and environmentally hazardous. This study evaluated the P-solubilising potential of culture filtrates from three fungal strains (Aspergillus flavus JKJ7, Talaromyces purpureogenus JKJ12, and Trichoderma koningiopsis JKJ18) grown in National Botanical Research Institute’s Phosphate (NBRIP) liquid medium supplemented with tricalcium phosphate (TCP), and compared their TCP solubilisation efficiency with that of pure acids (citric and sulfuric acid). All three fungal strains solubilised TCP in NBRIP medium, with A. flavus JKJ7 producing the highest concentration of soluble P (259.81 mg L⁻¹), followed by T. koningiopsis JKJ18 (166.41 mg L⁻¹) and T. purpureogenus JKJ12 (47.07 mg L⁻¹). Soluble P concentrations were inversely correlated with pH and positively correlated with titratable organic acidity (TOA). High-performance liquid chromatography (HPLC) identified citric, succinic, tartaric, and gluconic acids as the dominant organic acids associated with P solubilisation. In pure acid treatments, sulfuric acid exhibited concentration-dependent increases in soluble P, whereas citric acid showed reduced solubilisation efficiency at higher concentrations. Although fungal culture filtrates achieved lower maximum TCP solubilisation than strong mineral acids, their higher TOA contributed to improved stabilisation of soluble P by limiting calcium-mediated reprecipitation. These findings demonstrate that crude fungal organic acid mixtures can complement or partially substitute inorganic acids for mobilising P from low-reactivity PR, offering a potentially cost-effective and environmentally sustainable alternative for P fertiliser production. This study supports the development of biologically derived P inputs aligned with circular bioeconomy and sustainable agriculture goals. Full article

(This article belongs to the Topic Applications of Biotechnology in Food and Agriculture)

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14 pages, 883 KB

Open AccessArticle

Essential Oils of Dill and Nettle as a Natural Alternative to Reduce Pathogenic Bacteria on Dairy Production Surfaces

by Rocio Contero, Charles Cachipuendo, Orlando Felicita and Gilda Gordillo

Microorganisms 2026, 14(2), 412; https://doi.org/10.3390/microorganisms14020412 - 10 Feb 2026

Cited by 1 | Viewed by 1375

Abstract

Essential oils (EOs) have emerged as promising natural antimicrobials for food safety applications. However, their direct use on food-contact surfaces—such as wood and plastic, commonly employed in artisanal cheese production—has been scarcely explored. This study aimed to evaluate the antibacterial effects of dill [...] Read more.

Essential oils (EOs) have emerged as promising natural antimicrobials for food safety applications. However, their direct use on food-contact surfaces—such as wood and plastic, commonly employed in artisanal cheese production—has been scarcely explored. This study aimed to evaluate the antibacterial effects of dill (Anethum graveolens) and nettle (Urtica dioica) essential oils against Listeria monocytogenes and Escherichia coli, both in culture media and on inert surfaces. EOs were extracted via steam distillation and characterized by gas chromatography–mass spectrometry (GC-MS). Antimicrobial activity was assessed using agar diffusion and minimum inhibitory concentration (MIC) assays. In addition, bacterial reduction was quantified following EO application to contaminated wooden and plastic surfaces for 40 min. Dill EO exhibited a high anethole content (63.66%), while nettle EO was dominated by limonene (38.73%). Dill EO produced larger inhibition zones against E. coli (13.7 ± 1.5 mm) and L. monocytogenes (12.3 ± 1.5 mm) compared to nettle EO (6.3 ± 0.6 mm and 8.0 ± 1.7 mm, respectively). On plastic, both EOs achieved complete inhibition of E. coli (100%) and greater than 92% reduction in L. monocytogenes. On wood, dill EO maintained high efficacy (up to 87.9%), whereas nettle EO showed limited reduction (29.3%) against L. monocytogenes. These results demonstrate that EO efficacy is influenced by both surface type and target microorganism, supporting the potential of dill EO as a natural antimicrobial agent for surface sanitation in artisanal cheese production. Full article

(This article belongs to the Topic Applications of Biotechnology in Food and Agriculture)

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24 pages, 3527 KB

Open AccessArticle

An Improved Lightweight ConvNeXt for Peach Ripeness Classification

by Xudong Lin, Dehao Liao, Zhiguo Du, Bin Wen, Zhihui Wu, Xianzhi Tu and Yongjie Zhang

Horticulturae 2026, 12(2), 134; https://doi.org/10.3390/horticulturae12020134 - 25 Jan 2026

Cited by 1 | Viewed by 701

Abstract

Accurate grading of peach ripeness is essential for determining optimal harvest timing, postharvest storage potential, and market value. However, traditional methods are often inefficient and highly subjective. Meanwhile, existing deep learning models face challenges in balancing complexity with accuracy. To address this, this [...] Read more.

Accurate grading of peach ripeness is essential for determining optimal harvest timing, postharvest storage potential, and market value. However, traditional methods are often inefficient and highly subjective. Meanwhile, existing deep learning models face challenges in balancing complexity with accuracy. To address this, this paper proposes a lightweight improved model named LightConvNeXt-FCS, which centers on a novel lightweight module named LightBlock. This module drastically reduces the parameter count and computational overhead. To preserve representational capacity, auxiliary structures—including attention enhancement, cross-stage connections, and multi-scale fusion—are incorporated. Experimental results show that the model requires only 2.75 M parameters and 624.23 M FLOPs, representing a 90.1% reduction in parameters and an 86.0% decrease in computational cost compared to ConvNeXt-Tiny, with the model size compressed to 9.9% of the original, while achieving an accuracy of 94.62%, slightly outperforming the original model. This approach effectively resolves the common trade-off between model complexity and accuracy. By achieving high accuracy with a lightweight architecture, it provides a more feasible solution for deploying rapid and intelligent fruit ripeness grading systems. Full article

(This article belongs to the Topic Applications of Biotechnology in Food and Agriculture)

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17 pages, 3151 KB

Open AccessArticle

Exploring the Effects of Diluted Plasma-Activated Water (PAW) on Various Sprout Crops and Its Role in Autophagy Regulation

by Injung Song, Suji Hong, Yoon Ju Na, Seo Yeon Jang, Ji Yeong Jung, Young Koung Lee and Sung Un Huh

Agronomy 2026, 16(2), 207; https://doi.org/10.3390/agronomy16020207 - 15 Jan 2026

Cited by 1 | Viewed by 1613

Abstract

Plasma-activated water (PAW) has gained attention across agricultural, medical, cosmetic, and sterilization fields due to its production of reactive oxygen and nitrogen species (ROS and RNS). Although PAW has been primarily explored for seed germination and sterilization in agriculture, its role as a [...] Read more.

Plasma-activated water (PAW) has gained attention across agricultural, medical, cosmetic, and sterilization fields due to its production of reactive oxygen and nitrogen species (ROS and RNS). Although PAW has been primarily explored for seed germination and sterilization in agriculture, its role as a nutrient source and physiological regulator remains less understood. In this study, PAW generated by a surface dielectric barrier discharge (SDBD) system contained approximately 1000 ppm nitrate (NO₃⁻) and was designated as PAW1000. Diluted PAW solutions were applied to sprout crops—wheat (Triticum aestivum), barley (Hordeum vulgare), radish (Raphanus sativus), and broccoli (Brassica oleracea var. italica)—grown under hydroponic and soil-based conditions. PAW100 and PAW200 treatments enhanced growth, increasing fresh biomass by up to 26%, shoot length by 22%, and root length by 18%, depending on the species. In silico analysis identified nitrogen-responsive transcripts among several autophagy-related genes. Consistent with this, fluorescence microscopy of Arabidopsis thaliana GFP-StATG8 lines revealed increased autophagosome formation following PAW treatment. The growth-promoting effect of PAW was diminished in atg4 mutants, indicating that autophagy contributes to plant responses to PAW-derived ROS and RNS. Together, these findings demonstrate that diluted PAW generated by SDBD enhances biomass accumulation in sprout crops, and that autophagy plays a regulatory role in mediating PAW-induced physiological responses. Full article

(This article belongs to the Topic Applications of Biotechnology in Food and Agriculture)

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17 pages, 2614 KB

Open AccessArticle

Bacillus velezensis RF2 Rescued from Citrus Phyllosphere: Dual Mechanisms and Broad-Spectrum Activity for Controlling Citrus Bacterial Canker

by Rui-Fang Luo, Si-Yu Zhang, Ya-Xiao Wu, Zi-Yi Jiao, Min-Li Bao, Yu-Ting Lan, Ting-Ting Zhang, Ru-Yu Zeng, Abdulhamid Yusuf, Yun-Zeng Zhang, Min Li and Shuo Duan

Microorganisms 2026, 14(1), 121; https://doi.org/10.3390/microorganisms14010121 - 6 Jan 2026

Cited by 1 | Viewed by 1064

Abstract

Citrus bacterial canker (CBC), caused by Xanthomonas citri subsp. citri (Xcc), threatens citrus production worldwide. Long-term dependence on copper-based bactericides not only poses environmental risks but also accelerates the emergence of copper-resistant Xcc strains. To develop safe and efficient alternative control [...] Read more.

Citrus bacterial canker (CBC), caused by Xanthomonas citri subsp. citri (Xcc), threatens citrus production worldwide. Long-term dependence on copper-based bactericides not only poses environmental risks but also accelerates the emergence of copper-resistant Xcc strains. To develop safe and efficient alternative control strategies, 72 bacterial strains were isolated from the phyllosphere of citrus plants naturally infected by CBC and identified by 16S rRNA sequencing. Using an Xcc-GFP-based screening method, we systematically screened a highly effective strain, which was identified as Bacillus velezensis RF2 (Bv-RF2). Both inhibition zone assays and bioactivity tests of the crude methanolic extract of Bv-RF2 demonstrated stable antibacterial activity under UV irradiation, protease treatment, high temperature, and across a wide pH range. Whole-genome sequencing and antiSMASH analysis revealed multiple predicted NRPS/PKS-type biosynthetic gene clusters (BGCs). Together with metabolomic profiling, these data provide hypotheses for candidate metabolites that may contribute to antagonism. Bv-RF2 was associated with the induction of PR gene expression in immune-related pathways implicated in CBC responses. In sweet orange leaves, Bv-RF2 infiltration was associated with transient induction of defense-related (PR) genes, consistent with an ISR-like, priming-related response. In addition, Bv-RF2 inhibited the growth of fungal pathogens associated with citrus anthracnose and brown spot in vitro, indicating broad inhibitory potential under the tested conditions. Collectively, Bv-RF2 represents a promising candidate for developing environmentally friendly strategies against CBC and other citrus diseases. Full article

(This article belongs to the Topic Applications of Biotechnology in Food and Agriculture)

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19 pages, 2656 KB

Open AccessReview

Biotechnological Improvement of Nutri-Cereal Finger Millet: Current Status and Future Prospects

by Stanislaus Antony Ceasar

Crops 2025, 5(6), 87; https://doi.org/10.3390/crops5060087 - 25 Nov 2025

Cited by 2 | Viewed by 1913

Abstract

Climate change and widespread micronutrient deficiencies threaten food security in the semi-arid tropics. Finger millet (Eleusine coracana (L.) Gaertn.) is a climate-resilient “nutri-cereal” rich in calcium, zinc, iron and dietary fiber. Finger millet is a promising crop for addressing climate stress and [...] Read more.

Climate change and widespread micronutrient deficiencies threaten food security in the semi-arid tropics. Finger millet (Eleusine coracana (L.) Gaertn.) is a climate-resilient “nutri-cereal” rich in calcium, zinc, iron and dietary fiber. Finger millet is a promising crop for addressing climate stress and nutrient deficiencies. However, it remains under-explored and relatively neglected in breeding and genetic improvement programs compared to major cereals. This review synthesizes recent biotechnological advances and outlines future directions for finger millet improvement. Foundational resources now include a chromosome-scale reference genome, expanding transcriptome, diverse global germplasm panels, and growing reports of genome-wide association studies (GWAS) and quantitative trait loci (QTL) for key traits including yield, stress tolerance, blast resistance, and mineral contents. Tissue culture studies reported both somatic embryogenesis and direct regeneration. Stable genetic transformation has been achieved in finger millet via Agrobacterium-mediated methods, particularly using shoot apical meristem (SAM) and by biolistics (gene gun) methods. Genome editing has not yet been reported, but we propose a practical roadmap leveraging reported tissue culture genetic transformation protocols for applying the CRISPR/Cas system for trait improvements. Using new biotechnological methods, along with pangenome, speed breeding, and helpful microbiomes, will make finger millet a strong and reliable food source for the future. Full article

(This article belongs to the Topic Applications of Biotechnology in Food and Agriculture)

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13 pages, 1835 KB

Open AccessArticle

The Sprayed Application of Recombinantly Expressed CpRap2.4A Confers Protective Activity Against Heat Stress in Nicotiana tabacum

by Diobel González-Stewart, Francisco Guillén-Chable, Miguel Ángel Herrera-Alamillo, Roberth Armando Us Santamaría, José Luis Andrade, Anne C. Gschaedler Mathis, Enrique Castaño, Luis Joel Figueroa-Yáñez and Luis Carlos Rodríguez-Zapata

Crops 2025, 5(6), 80; https://doi.org/10.3390/crops5060080 - 6 Nov 2025

Viewed by 1143

Abstract

Drastic changes in temperature, salinity of soils and drought are some of the most studied abiotic stressors in important crops. Plants have developed various biochemical mechanisms to counteract these conditions. Transcription factors play a significant role in regulating stress responses. Previously, in our [...] Read more.

Drastic changes in temperature, salinity of soils and drought are some of the most studied abiotic stressors in important crops. Plants have developed various biochemical mechanisms to counteract these conditions. Transcription factors play a significant role in regulating stress responses. Previously, in our lab, it was identified that the CpRap2.4a protein, which belongs to the AP2/ERF superfamily, is related to the response to abiotic stress from extreme temperature, and confers thermal tolerance to Carica papaya CV. This study presents a randomized experimental strategy for the analysis of the physiological and biochemical responses of Nicotiana tabacum plants subjected to heat stress, and how the foliar application of the recombinantly expressed CpRap2.4a can modulate beneficial responses. Plants subjected to heat stress present a healthier physiology, as clearly shown by biochemical parameters. Moreover, physiological parameters also suggest an improvement of heat tolerance compared with the control group. Scanning electron microscopy suggests that stomatal aperture and conductance are the key mechanisms for how recombinantly expressed CpRap2.4a can act as a regulatory player to heat stress. Full article

(This article belongs to the Topic Applications of Biotechnology in Food and Agriculture)

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10 pages, 1154 KB

Open AccessCommunication

Strain-Dependent Lactic Acid Fermentation of Capsosiphon fulvescens Hydrolysate by Lactobacillus spp.

by Hyeongjin Hwang

Microorganisms 2025, 13(10), 2295; https://doi.org/10.3390/microorganisms13102295 - 2 Oct 2025

Viewed by 995

Abstract

Seaweeds are promising third-generation biomass for biobased chemicals, yet their use for lactic acid (LA) production remains underexplored. We evaluated LA production from the dilute-acid hydrolysate of the aquacultured green alga Capsosiphon fulvescens (C.Agardh) Setchell & N.L. Gardner. The dried biomass contained 53.4% [...] Read more.

Seaweeds are promising third-generation biomass for biobased chemicals, yet their use for lactic acid (LA) production remains underexplored. We evaluated LA production from the dilute-acid hydrolysate of the aquacultured green alga Capsosiphon fulvescens (C.Agardh) Setchell & N.L. Gardner. The dried biomass contained 53.4% carbohydrate (dry-weight basis). HPLC showed a monosaccharide profile enriched in L-rhamnose and D-xylose, with lower levels of D-mannose, D-glucose, D-glucuronolactone, and D-glucuronic acid. Batch fermentations with three Lactobacillus strains revealed clear strain-dependent kinetics and carbon partitioning. Maximum LA titers/yields (time at maximum) were 2.0 g L⁻¹/0.49 g g⁻¹ at 9 h for L. rhamnosus, 2.3 g L⁻¹/0.30 g g⁻¹ at 36 h for L. casei, and 2.8 g L⁻¹/0.23 g g⁻¹ at 48 h for L. brevis; L. rhamnosus achieved the highest yield on sugars consumed, whereas L. brevis reached the highest titer by utilizing a broader sugar spectrum, notably xylose; L. casei showed intermediate performance with limited xylose use. Co-products included acetic and succinic acids (major) and trace 1,2-propanediol and acetaldehyde, consistent with flux through Embden–Meyerhof–Parnas versus phosphoketolase pathways. These results demonstrate that C. fulvescens hydrolysate is a viable marine feedstock for LA production and highlight practical levers—expanding pentose/uronic-acid catabolism in high-yield strains and tuning pretreatment severity—to further improve both yield and titer. Full article

(This article belongs to the Topic Applications of Biotechnology in Food and Agriculture)

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14 pages, 1037 KB

Open AccessArticle

The Influence of Moderate Electroporation on E. coli Membrane Permeability

by Ester Bar-Hanun, Ester Hanya, Abhishiktha Chiliveru and Rivka Cahan

Microorganisms 2025, 13(8), 1925; https://doi.org/10.3390/microorganisms13081925 - 18 Aug 2025

Cited by 3 | Viewed by 2152

Abstract

This study examined the membrane permeability of E. coli, which were exposed to a moderate pulsed electric field (PEF) (3.3 kV/cm). The membrane permeability of E. coli was examined as a function of time after exposure to PEF. When comparing the percentage [...] Read more.

This study examined the membrane permeability of E. coli, which were exposed to a moderate pulsed electric field (PEF) (3.3 kV/cm). The membrane permeability of E. coli was examined as a function of time after exposure to PEF. When comparing the percentage of propidium iodide (PI) permeability at a given time from PEF exposure, it appeared that as the bacterial density increased, there was a decrease in PI permeability. The permeability to PI in the bacterial suspensions of 0.05, 0.1, and 0.5 OD, 90 min after exposure, was 56.4 ± 4.08%, 43.91 ± 0.75%, and 29.47 ± 3.31%, respectively. Membrane permeability was also examined in different phosphate-buffered saline (PBS) concentrations. At 0.05 OD there was a linear correlation between PBS concentrations (0.56, 0.75, and 1 mM) and PI permeability (28.36 ± 2.22%, 61.08 ± 3.17%, and 98.2 ± 0.9%, respectively). At the higher bacterial densities of 0.1 and 0.5 OD, this phenomenon was not evident. Examination of bacterial membrane permeability using 4, 70, and 250 kDa fluorescein isothiocyanate (FITC)-dextran revealed that PEF led to 4kDa FITC-dextran permeabilization of 27.94 ± 3.76%. The PEF parameters used did not influence the bacterial cell size and viability. This study shed light on bacterial membrane permeability as a function of conductivity and bacterial density under PEF exposure. Full article

(This article belongs to the Topic Applications of Biotechnology in Food and Agriculture)

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21 pages, 997 KB

Open AccessReview

Decoding Potential Co-Relation Between Endosphere Microbiome Community Composition and Mycotoxin Production in Forage Grasses

by Vijay Chandra Verma and Ioannis Karapanos

Agriculture 2025, 15(13), 1393; https://doi.org/10.3390/agriculture15131393 - 28 Jun 2025

Cited by 1 | Viewed by 1601

Abstract

Cultivated pasture grasses contribute forage to more than 40% of cattle produced in 11 southern states in the USA. In recent years the increasing intoxication of cattle feeding on pasture grasses raised serious concerns about their palatability. While molecular and metagenomics techniques have [...] Read more.

Cultivated pasture grasses contribute forage to more than 40% of cattle produced in 11 southern states in the USA. In recent years the increasing intoxication of cattle feeding on pasture grasses raised serious concerns about their palatability. While molecular and metagenomics techniques have revealed the great diversity of microbial composition and functional richness of the grass endosphere microbiome, meta-sequencing techniques enable us to gain a bird’s-eye view of all plant-associated microbiomes as a ‘holobiont’. Plant holobionts provide a more comprehensive approach where one can define the functions of microbial communities and feedback between the core and satellite microbiomes of a targeted host. In the near future we will be able to tailor our grasses and their endosphere microbiomes through the host-directed selection of a ‘modular microbiome’, leading to ‘plant enhanced holobionts’ as a microbiome-driven solution to managing the intoxication of pasture grasses in livestock. The present review aims to understand the potential co-relation between the endosphere microbiome community composition and mycotoxin production in forage grasses in the southern United States. Full article

(This article belongs to the Topic Applications of Biotechnology in Food and Agriculture)

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