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Biotechnology and Biomass Valorization

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A special issue of Molecules (ISSN 1420-3049). This special issue belongs to the section "Green Chemistry".

Deadline for manuscript submissions: 28 February 2027 | Viewed by 8598

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Editors

Prof. Dr. Chia-Hung Kuo

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Guest Editor

Department of Seafood Science, National Kaohsiung University of Science and Technology, Kaohsiung 81157, Taiwan
Interests: food analysis; food processing; cellulase; lipase esterification and trans esterification; amylase; enzymatic kinetics; ultrasound-assisted enzymatic reaction; enzyme extraction; biotransformation; sacchariﬁcation; response surface methodology; artificial neural network; wine fermentation
Special Issues, Collections and Topics in MDPI journals

Prof. Dr. Yung-Chuan Liu

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Guest Editor

Department of Chemical Engineering, National Chung Hsing University, Taichung 402, Taiwan
Interests: fermentation technology; protein engineering; immunoassay; membrane technology; molecular engineering
Special Issues, Collections and Topics in MDPI journals

Dr. Parushi Nargotra

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Guest Editor Assistant

Department of Seafood Science, National Kaohsiung University of Science and Technology, Kaohsiung 81157, Taiwan
Interests: bioprocess engineering; lignocellulosic biomass valorization; pretreatment; fermentation; enzyme technology; cellulases; xylanases

Special Issue Information

Dear Colleagues,

With growing global attention on sustainable development, environmental protection, and resource recycling, the effective development and transformation of biomass resources through innovative biotechnological applications has become a critical area of research and industrial interest. This Special Issue aims to collect the latest research results related to "Biotechnology and high value of biomass resources", covering a variety of biomass raw materials from agricultural waste, food by-products, marine resources to industrial by-products, etc., through biological, enzyme or microbial pathways to transform into high value-added products such as biofuels, bioplastics, biochemical materials, functional ingredients, and other bio-based materials. This Special Issue welcomes original research papers, review articles and application case studies. The topics may include but are not limited to the following scope:

Conversion of biomass resources into bio-based products via microorganisms or enzymes;
Application of fermentation technology in the development of high-value products;
Innovative applications of metabolic engineering and synthetic biology in biomass utilization;
Biofuel and biogas production technology from renewable biomass raw materials;
Design, integration and optimization of biorefining systems;
Application of bioresources in bioproducts and energy;
High-value utilization of food waste, agricultural by-products and marine biological resources;
Extraction and purification technology of bioactive ingredients;
Life cycle assessment (LCA) and technical and economic analysis of biomass conversion processes;
Policies, strategies and industrial cases for the development of a sustainable circular bioeconomy.

This Special Issue encourages cross-disciplinary research integrating biotechnology, environmental science, chemical engineering and industrial applications to jointly promote the development of a circular and sustainable bioeconomy.

Prof. Dr. Chia-Hung Kuo
Prof. Dr. Yung-Chuan Liu
Guest Editors

Dr. Parushi Nargotra
Guest Editor Assistant

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Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 250 words) can be sent to the Editorial Office for assessment.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-anonymized peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Molecules is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2700 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

biomass
conversion
utilization
enzyme
biological
microorganism
fermentation
high value-added product
biofuel
biogas
bioplastic
biochemical material
functional ingredient
bio-based material
metabolic engineering
synthetic biology
biorefining
bioresource
food waste
agricultural by-product
marine biological resource
extraction
purification
life cycle assessment (LCA)

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Published Papers (7 papers)

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Research

13 pages, 5977 KB

Open AccessArticle

Engineering the L-Arabinose Isomerase from Lactobacillus sakei for Whole-Cell Conversion Production of D-Tagatose Under High Substrate Concentration Conditions

by Ren He, Wei Liu, Bingyi Tao, Shaoxiong Liang and Xuchong Tang

Molecules 2026, 31(16), 2756; https://doi.org/10.3390/molecules31162756 - 8 Aug 2026

Viewed by 224

Abstract

D-tagatose, a low-calorie sugar substitute, widely used in the food and pharmaceutical industries, can be produced from the substrate D-galactose using L-arabinose isomerase (L-AI). L-AI genes derived from Lactobacillus fermentum (LFAI), Lactobacillus brevis (LBAI), Lactobacillus plantarum (LPAI), and Lactobacillus sakei (LSAI) for the bioconversion of D-galactose into D-tagatose using whole Escherichia coli (E. coli) cells were investigated. The temperature, time, pH, whole-cell concentration, and metal ion concentration were optimized to enhance catalytic production. The results revealed that at the low substrate concentration of 10 g/L, LFAI, LBAI, LPAI, and LSAI exhibited considerable catalytic activity, with conversion rates of 55.31%, 68.17%, 61.45%, and 58.22%, respectively. In contrast, at the high substrate concentration of 250 g/L, their conversion rates were 19.78%, 18.47%, 20.26%, and 36.24%, respectively, with LSAI demonstrating superior catalytic performance. In order to facilitate the industrial production of D-tagatose, site-directed mutagenesis was performed on LSAI. Among the engineered LSAI variants, the P99H, K142R, and L465R mutants all showed increased catalytic rates for D-tagatose. Specifically, at the high substrate concentration of 250 g/L, the P99H mutant achieved a conversion rate of 45.73%, representing a 32.7% improvement compared to the optimized LSAI. These results indicate that the designed site-directed mutagenesis strategy effectively enhanced whole-cell bioconversion performance of LSAI toward D-galactose. Full article

(This article belongs to the Special Issue Biotechnology and Biomass Valorization)

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26 pages, 23302 KB

Open AccessArticle

Utilization of Citrus Peel Waste for Regulating Enzyme-Induced Carbonate Precipitation in Cement-Based Materials: Mechanical Performance and Freeze–Thaw Resistance

by Yanzhi Meng, Xiang Su, Shujin Zhao, Qixiang Zan, Luyan Wang and Wenjuan Guo

Molecules 2026, 31(13), 2308; https://doi.org/10.3390/molecules31132308 - 1 Jul 2026

Viewed by 383

Abstract

This study investigates citrus peel powder (CP) as an environmentally friendly admixture to regulate plant-derived urease (with soybean powder (SP) as the urease source) and to promote bio-mediated CaCO₃ mineralization, thereby improving the mechanical and freeze–thaw (FT) resistance properties of cement-based materials. When CP is combined with urea and soybean urease, it exhibits a regulatory effect on urease activity. For the CPUD (CP-encapsulated urea combined with soy powder)-modified material with SP dosage in cement content of 0.2 wt%, the CP–urea modification treatment can effectively improve their mechanical properties and FT durability. The flexural and compressive strengths at 28 days are increased by 10.53% and 11.19%, respectively, compared to the blank group. After freeze–thaw cycles, the strengths are still 27.08% and 26.67% higher than those of the blank group, and their respective strength loss rates are 7.58% and −5.77% (negative indicating a net strength increase), compared with 21.31% and 9.48% for the blank group. X-ray diffraction, Fourier-transform infrared spectroscopy, and scanning electron microscopy analyses reveal that CP–urea promotes the formation and effective packing of calcium carbonate. Mechanistically, CP establishes a stable hydrogen-bonding network with both urea and urease, exerting a dual regulatory effect: it enhances the electrophilicity of urea while also creating a physical mass transfer barrier to precisely control biomineralization. Notably, CP can be directly used without pretreatment, offering a sustainable strategy for citrus peel waste valorization. Full article

(This article belongs to the Special Issue Biotechnology and Biomass Valorization)

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18 pages, 2729 KB

Open AccessArticle

Design and Implementation of a Blue-Light-Controlled Gene-Switch System

by Chen Li, Yuan Shi, Xinyan Jiang, Bobo Zhao, Chen Zheng, Aowei Yang, Yao Wang, Junfeng Pan and Xihui Shen

Molecules 2026, 31(12), 2032; https://doi.org/10.3390/molecules31122032 - 10 Jun 2026

Viewed by 474

Abstract

Synthetic biology seeks to build predictable, programmable biological systems. We developed a blue-light-inducible T7RNAP system with dual-input regulation to enable precise spatiotemporal gene control, which is vital for biomanufacturing, therapy, and microbial engineering. We optimized it by replacing RBS sequences, testing tandem T7 promoters, and evaluating split-T7RNAP variants. Expression and bactericidal efficacy were assessed via fluorescent output and real-time growth curves under blue light. RBS variants caused up to 50-fold differences in expression. Three tandem T7 promoters provided the best balance between yield and fidelity. Integration of a benzoate-responsive module enabled 4.5-fold repression at 3 mM benzoate, demonstrating effective chemical off-switching without compromising light induction. This system combines blue light precision with environmental responsiveness, offering non-invasive, on-demand activation for antimicrobial therapy or spatial bioproduction. The benzoate-triggered off-switch is especially valuable for ecological applications such as biocontainment or bioremediation, where gene expression must shut down upon detection of pollutants, for example, aromatic hydrocarbons. Its orthogonal, modular design supports context-dependent control, making it ideal for environmental biosensors, programmable probiotics, and smart antimicrobial delivery in complex ecosystems. Full article

(This article belongs to the Special Issue Biotechnology and Biomass Valorization)

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18 pages, 1882 KB

Open AccessArticle

Integrated Bacillus subtilis Pretreatment, Chlorella vulgaris Cultivation, and Trichoderma viride Bioflocculation for Enhanced Municipal Wastewater Remediation and Biodiesel Production

by Hongzhi Chen, Xiuren Zhou and Guifang Xu

Molecules 2026, 31(8), 1347; https://doi.org/10.3390/molecules31081347 - 20 Apr 2026

Viewed by 844

Abstract

Municipal wastewater represents an underutilized secondary biomass resource rich in organic carbon and nutrients that can be valorized through biotechnological conversion. In this study, we developed an integrated multi-microbial biorefinery platform to transform municipal wastewater into value-added biofuel via sequential bacterial treatment, microalgal biomass generation, and fungal-assisted harvesting. Wastewater was first pretreated with Bacillus subtilis to enzymatically hydrolyze complex organic substrates and enrich the medium with bioactive metabolites, including auxins and gibberellins. The conditioned wastewater was subsequently used to cultivate Chlorella vulgaris, followed by biomass recovery using Trichoderma viride pellets as a sustainable bioflocculant. The integrated consortium significantly enhanced nutrient removal efficiency and promoted algal biomass accumulation, lipid enrichment, and biodiesel productivity compared to monoculture controls. Elevated hydrolytic enzyme activities (cellulase, protease, and amylases) facilitated organic matter conversion into bioavailable substrates, while increased phytohormone levels stimulated algal growth and lipid biosynthesis. Additionally, fungal bioflocculation substantially improved biomass recovery efficiency, reducing the need for energy-intensive harvesting technologies. This work highlights the potential of a biotechnology-driven approach for integrating wastewater remediation with biofuel production. By integrating microbial metabolism, enzymatic transformation, and sustainable separation processes, the proposed biorefinery system suggests a potentially low-carbon approach for simultaneous environmental remediation and biomass valorization, although further life cycle and energy balance analyses are required to validate this aspect. Full article

(This article belongs to the Special Issue Biotechnology and Biomass Valorization)

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15 pages, 1225 KB

Open AccessArticle

Establishment of CRISPR-Cas9-Mediated Gene Editing in the Swimming Crab Portunus trituberculatus

by Xiaopeng Wang, Xuhao Chen, Yueyue Zhou, Yun Zhao, Ce Shi, Ronghua Li, Lei Liu, Changkao Mu, Weiwei Song and Chunlin Wang

Molecules 2026, 31(2), 285; https://doi.org/10.3390/molecules31020285 - 13 Jan 2026

Viewed by 1009

Abstract

Portunus trituberculatus is an economically important marine crustacean in East Asia’s aquaculture industry. Nevertheless, precise genome modification has not yet been established. In this study, we evaluated the applicability of the CRISPR-Cas9 gene editing system in P. trituberculatus using electroporation for efficient delivery of the Cas9-sgRNA complex into zygotes. We systematically investigated electroporation parameters, including buffer composition, voltage, capacitance, and pulse times. Our results showed that artificial seawater was a superior buffer to phosphate-buffered saline (PBS) and identified an effective electroporation condition of 600 V, 1 μF capacitance, and two pulses, resulting in approximately 72.7% fluorescent zygotes. Under these electroporated conditions, we detected gene indels and putative insertion events at the targeted locus of myostatin (mstn) gene. These results demonstrate the feasibility of Cas9-based genome editing in P. trituberculatus and provide a proof-of-concept for functional genomics studies and future genetic improvement of this species. Full article

(This article belongs to the Special Issue Biotechnology and Biomass Valorization)

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23 pages, 2345 KB

Open AccessArticle

From Waste to Biocatalyst: Cocoa Bean Shells as Immobilization Support and Substrate Source in Lipase-Catalyzed Hydrolysis

by Luciana Lordelo Nascimento, Bruna Louise de Moura Pita, César de Almeida Rodrigues, Paulo Natan Alves dos Santos, Yslaine Andrade de Almeida, Larissa da Silveira Ferreira, Maira Lima de Oliveira, Lorena Santos de Almeida, Cleide Maria Faria Soares, Fabio de Souza Dias and Alini Tinoco Fricks

Molecules 2025, 30(15), 3207; https://doi.org/10.3390/molecules30153207 - 30 Jul 2025

Cited by 1 | Viewed by 1557

Abstract

This study reports the development of a sustainable biocatalyst system for free fatty acid (FFA) production from cocoa bean shell (CBS) oil using Burkholderia cepacia lipase (BCL). CBS was explored as both a support material and a reaction substrate. Six immobilized systems were prepared using organic (CBS), inorganic (silica), and hybrid (CBS–silica) supports via physical adsorption or covalent binding. Among them, the covalently immobilized enzyme on CBS (ORG-CB) showed the most balanced performance, achieving a catalytic efficiency (Ke) of 0.063 mM⁻¹·min⁻¹ (18.6% of the free enzyme), broad pH–temperature tolerance, and over 50% activity retention after eight reuse cycles. Thermodynamic analysis confirmed enhanced thermal resistance for ORG-CB (Ed = 32.3 kJ mol⁻¹; ΔH‡ = 29.7 kJ mol⁻¹), while kinetic evaluation revealed that its thermal deactivation occurred faster than for the free enzyme under prolonged heating. In application trials, ORG-CB reached 60.1% FFA conversion from CBS oil, outperforming the free enzyme (49.9%). These findings validate CBS as a dual-function material for enzyme immobilization and valorization of agro-industrial waste. The results also reinforce the impact of immobilization chemistry and support composition on the operational and thermal performance of biocatalysts, contributing to the advancement of green chemistry strategies in enzyme-based processing. Full article

(This article belongs to the Special Issue Biotechnology and Biomass Valorization)

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17 pages, 1758 KB

Open AccessArticle

Bioactive Polysaccharides from Fermented Dendrobium officinale: Structural Insights and Their Role in Skin Barrier Repair

by Wanshuai Wang, Anqi Zou, Qingtao Yu, Zhe Wang, Daotong Tan, Kaiye Yang, Chao Cai and Guangli Yu

Molecules 2025, 30(13), 2875; https://doi.org/10.3390/molecules30132875 - 6 Jul 2025

Cited by 7 | Viewed by 3105

Abstract

Dendrobium, a prominent genus in the Orchidaceae family, has generated significant research attention due to its demonstrated biological potential, particularly its notable anti-inflammatory and antioxidant activities. In this study, two fractions of fermented Dendrobium officinale polysaccharides (FDOPs) were successfully isolated through a multi-stage purification strategy including gradient ethanol precipitation, gel column chromatography, and ion exchange chromatography with Lactobacillus reuteri CCFM863. Structural characterization revealed that both Dendrobium officinale polysaccharide fractions consisted of (1→4)-β-D-Manp, (1→4)-β-D-Glcp, and (1→4)-α-D-Glcp residues. The anti-inflammatory efficacy and keratinocyte-protective potential of FDOPs (FDOP-1A and FDOP-2A) were investigated by using lipopolysaccharide (LPS)-induced RAW264.7 and HaCaT cells models, which showed significant inhibitions on the inflammatory factors of monocyte chemoattractant protein-1 (MCP-1), tumor necrosis factor-alpha (TNF-α), nitric oxide (NO), and interleukin-1 beta (IL-1β); recovered levels of filaggrin (FLG), aquaporin 3 (AQP3), transient receptor potential vanilloid 4 (TRPV4), cathelicidin antimicrobial peptide (CAMP)/LL-37, and adiponectin (ADIPOQ); and the reduced protein expression of the TLR4/IκB-α/NF-κB/NLRP3 pathway. Notably, the FDOPs exhibited a remarkable reactive oxygen species (ROS) scavenging capacity, demonstrating superior antioxidant activity. Therefore, FDOPs show dual anti-inflammatory and antioxidant properties, making them suitable as active ingredients for modulating epidermal inflammation and promoting skin barrier repair. Full article

(This article belongs to the Special Issue Biotechnology and Biomass Valorization)

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