Applications of Biotechnology in Food and Agriculture

Journal Name	Impact Factor	CiteScore	Launched Year	First Decision (median)	APC
Agriculture agriculture	3.6	6.3	2011	18.8 Days	CHF 2600	Submit
Agrochemicals agrochemicals	-	-	2022	27 Days	CHF 1000	Submit
Agronomy agronomy	3.4	6.7	2011	17 Days	CHF 2600	Submit
Crops crops	1.9	2.4	2021	22.4 Days	CHF 1200	Submit
Horticulturae horticulturae	3.0	5.1	2015	16.7 Days	CHF 2200	Submit
Microorganisms microorganisms	4.2	7.7	2013	20 Days	CHF 2700	Submit
Plants plants	4.1	7.6	2012	16.5 Days	CHF 2700	Submit

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

Viewed by 275

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 307

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

Viewed by 392

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

Viewed by 363

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

Viewed by 509

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 558

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

Viewed by 876

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 589

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 741

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 2 | Viewed by 1704

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 1232

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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