Microbial Biotechnology Products and Biocatalysis Processes for a Sustainable Bioeconomy

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Dear Colleagues,

This Topic on “Microbial Biotechnology Products and Biocatalysis Processes for a Sustainable Bioeconomy” aims to promote the potential of microbial biotechnology products for a sustainable bioeconomy. The discovery of new products has been addressed by multidisciplinary teams, for example, combining knowledge on microbiology, biotechnology, and chemistry. Therefore, this Topic should focus on screenings and characterization of new bio-based products, new microbial producers, and optimization of biotechnological processes by reducing production waste and cost, leading to more sustainable processes and enhancing the circular economy. On the other hand, we are also interested to describe the actual biocatalysts in more detail. In recent years, many new biocatalysts have been described and studied mostly from a biocatalytic perspective. Since more and more (meta)genome data become available, even more of those studies will appear and add to our knowledge on novel reactions and enzymes. However, the transfer to application needs more attention and, thus, scale-up. Enzyme production and optimization in combination with product isolation also need more attention. Thus, this Topic aims to focus also on this chain, including the identification of novel enzymes from bioprospecting activities, producing enzymes and increasing yields from various host organisms, engineering biocatalysts by means of site-directed mutagenesis or directed evolution, putting enzymes together—even with chemical synthesis—yielding novel chemoenzymatic cascades, product isolation after processing or in situ, and even combinatorial approaches towards new products. All this needs research in the field of biocatalysis and biotransformation to bring us to new frontiers.

This issue will focus on the following areas:

• Circular economy by finding new products, new biodegradable microbial polymers, new processes that can create value-added products from wastes or from other secondary metabolites, and by reducing the cost of the production;
• Sustainable agriculture through microbial products such as biopesticides and biofertilizers with low impact to human health and which potentiate the sustainability;
• Environmental remediation using microbes or their products as effective tools to reduce environmental contaminants;
• Emerging technologies through a combination of multi-omics potentiating and accelerating the discovery of new microbial products;
• Bioprospecting towards new enzymes and cell-factories including their detailed characterization; and
• Engineering enzymes or even cellular systems towards a more applied routine in view of sustainability and to contribute to circular economy.

Prof. Dr. Dirk Tischler
Dr. Diogo Neves Proença
Dr. Paula Maria Vasconcelos Morais
Topic Editors

Keywords

Participating Journals

Journal Name	Impact Factor	CiteScore	Launched Year	First Decision (median)	APC
Applied Sciences applsci	2.5	5.3	2011	17.8 Days	CHF 2400
BioTech biotech	2.7	3.7	2012	18.2 Days	CHF 1600
Catalysts catalysts	3.8	6.8	2011	12.9 Days	CHF 2700
Processes processes	2.8	5.1	2013	14.4 Days	CHF 2400

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Published Papers (7 papers)

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All Applied Sciences BioTech Catalysts Processes

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Open AccessArticle

Structural Analysis and Substrate Specificity of D-Carbamoylase from Pseudomonas

by Marina Paronyan, Haykanush Koloyan, Hovsep Aganyants, Artur Hambardzumyan, Tigran Soghomonyan, Sona Avetisyan, Sergey Kocharov, Henry Panosyan, Vehary Sakanyan and Anichka Hovsepyan

BioTech 2024, 13(4), 40; https://doi.org/10.3390/biotech13040040 - 3 Oct 2024

Viewed by 425

Abstract

The synthesis of enantiomeric forms of D-amino acids can be achieved by a two-step “hydantoinase process” based on the sequential catalysis of substrates by specific enzymes, D-carbamoylase and D-hydantoinase. Here, we describe the structural features of D-carbamoylase from Pseudomonas, the encoded gene [...] Read more.

The synthesis of enantiomeric forms of D-amino acids can be achieved by a two-step “hydantoinase process” based on the sequential catalysis of substrates by specific enzymes, D-carbamoylase and D-hydantoinase. Here, we describe the structural features of D-carbamoylase from Pseudomonas, the encoded gene of which was chemically synthesized and cloned into Escherichia coli. A significant fraction of the overexpressed recombinant protein forms insoluble inclusion bodies, which are partially converted to a soluble state upon treatment with N-lauroylsarcosine or upon incubation of cells at 28 °C. Purified His-tagged protein exhibits the highest activity towards N-carbamoyl-D-alanine and N-carbamoyl-D-tryptophan. Comprehensive virtual analysis of the interactions of bulky carbamylated amino acids with D-carbamoylase provided valuable information. Molecular docking analysis revealed the location of the substrate binding site in the three-dimensional structure of D-carbamoylase. Molecular dynamics simulations showed that the binding pocket of the enzyme in complex with N-carbamoyl-D-tryptophan was stabilized within 100 nanoseconds. The free energy data showed that Arg176 and Asn173 formed hydrogen bonds between the enzyme and substrates. The studies of D-carbamoylases and the properties of our previously obtained D-hydantoinase suggest the possibility of developing a harmonized biotechnological process for the production of new drugs and peptide hormones. Full article

(This article belongs to the Topic Microbial Biotechnology Products and Biocatalysis Processes for a Sustainable Bioeconomy)

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31 pages, 2340 KiB  

Open AccessFeature PaperReview

Hydroponics with Microalgae and Cyanobacteria: Emerging Trends and Opportunities in Modern Agriculture

by Prabhaharan Renganathan, Edgar Omar Rueda Puente, Natalia V. Sukhanova and Lira A. Gaysina

BioTech 2024, 13(3), 27; https://doi.org/10.3390/biotech13030027 - 22 Jul 2024

Cited by 1 | Viewed by 1907

Abstract

The global population is expected to reach 9.5 billion, which means that crop productivity needs to double to meet the growing population’s food demand. Soil degradation and environmental factors, such as climate events, significantly threaten crop production and global food security. Furthermore, rapid [...] Read more.

The global population is expected to reach 9.5 billion, which means that crop productivity needs to double to meet the growing population’s food demand. Soil degradation and environmental factors, such as climate events, significantly threaten crop production and global food security. Furthermore, rapid urbanization has led to 55% of the world’s population migrating to cities, and this proportion is expected to increase to 75% by 2050, which presents significant challenges in producing staple foods through conventional hinterland farming. Numerous studies have proposed various sustainable farming techniques to combat the shortage of farmable land and increase food security in urban areas. Soilless farming techniques such as hydroponics have gained worldwide popularity due to their resource efficiency and production of superior-quality fresh products. However, using chemical nutrients in a conventional hydroponic system can have significant environmental impacts, including eutrophication and resource depletion. Incorporating microalgae into hydroponic systems as biostimulants offers a sustainable and ecofriendly approach toward circular bioeconomy strategies. The present review summarizes the plant growth-promoting activity of microalgae as biostimulants and their mechanisms of action. We discuss their effects on plant growth parameters under different applications, emphasizing the significance of integrating microalgae into a closed-loop circular economy model to sustainably meet global food demands. Full article

(This article belongs to the Topic Microbial Biotechnology Products and Biocatalysis Processes for a Sustainable Bioeconomy)

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12 pages, 1661 KiB  

Open AccessArticle

Influence of Critical Parameters on the Extraction of Concentrated C-PE from Thermotolerant Cyanobacteria

by Ariadna H. Vergel-Suarez, Janet B. García-Martínez, German L. López-Barrera, Néstor A. Urbina-Suarez and Andrés F. Barajas-Solano

BioTech 2024, 13(3), 21; https://doi.org/10.3390/biotech13030021 - 24 Jun 2024

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Abstract

This work aimed to identify the influence of pH, molarity, w/v fraction, extraction time, agitation, and either a sodium (Na₂HPO₄·7H₂O-NaH₂PO₄·H₂O) or potassium buffer (K₂HPO₄-KH₂ [...] Read more.

This work aimed to identify the influence of pH, molarity, w/v fraction, extraction time, agitation, and either a sodium (Na₂HPO₄·7H₂O-NaH₂PO₄·H₂O) or potassium buffer (K₂HPO₄-KH₂PO₄) used in the extraction of C-phycoerythrin (C-PE) from a thermotolerant strain of Potamosiphon sp. An experimental design (Minimum Run Resolution V Factorial Design) and a Central Composite Design (CCD) were used. According to the statistical results of the first design, the K-PO₄ buffer, pH, molarity, and w/v fraction are vital factors that enhance the extractability of C-PE. The construction of a CCD design of the experiments suggests that the potassium phosphate buffer at pH 5.8, longer extraction times (50 min), and minimal extraction speed (1000 rpm) are ideal for maximizing C-PE concentration, while purity is unaffected by the design conditions. This optimization improves extraction yields and maintains the desired bright purple color of the phycobiliprotein. Full article

(This article belongs to the Topic Microbial Biotechnology Products and Biocatalysis Processes for a Sustainable Bioeconomy)

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23 pages, 3951 KiB  

Open AccessArticle

Thermostable CaCO₃-Immobilized Bacillus subtilis Lipase for Sustainable Biodiesel Production from Waste Cooking Oil

by Wafa A. Alshehri, Nouf H. Alghamdi, Ashjan F. Khalel, Meshal H. Almalki, Bilel Hadrich and Adel Sayari

Catalysts 2024, 14(4), 253; https://doi.org/10.3390/catal14040253 - 11 Apr 2024

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Abstract

Due to the increasing demand for green processes in renewable energy production, the extracellular Bacillus subtilis B-1-4 lipase was used as a biocatalyst for producing biodiesel from waste cooking oil. Response surface methodology was employed for the optimization of enzyme production. Lipase activity [...] Read more.

Due to the increasing demand for green processes in renewable energy production, the extracellular Bacillus subtilis B-1-4 lipase was used as a biocatalyst for producing biodiesel from waste cooking oil. Response surface methodology was employed for the optimization of enzyme production. Lipase activity was modeled with a quadratic function of four factors that primarily influence the culture medium. Thanks to this model, an optimal lipase activity of 1.7 ± 0.082 U/mL was achieved with the best culture medium composition: 16 g/L of tryptone, 15 g/L of yeast extract, 15 g/L of NaCl, and a 0.15 initial optical density at 600 nm (OD600 nm). The maximal lipase activity was measured at 45 °C and pH 8, using para-nitrophenyl palmitate as a substrate. The enzyme maintained above 94% and 99% of its initial activity at temperatures ranging from 40 to 50 °C and at pH 8, respectively. Moreover, it exhibited a higher residual activity than other Bacillus lipases in the presence of organic solvents. Residual activities of 86.7% and 90.2% were measured in the presence of isopropanol and ethanol, respectively. The lipase was immobilized by adsorption onto CaCO₃ powder. FT-IR and SEM were used to characterize the surface-modified support. After immobilization, a lipase activity of 7.1 U/mg of CaCO₃ was obtained. Under the optimized conditions, the highest biodiesel yield of 71% was obtained through the transesterification of waste cooking oil using the CaCO₃-immobilized Bacillus subtilis lipase. This research reveals a method for the utilization of waste cooking oil for biodiesel production using an efficient immobilized thermostable lipase, providing environmental and economic security. Full article

(This article belongs to the Topic Microbial Biotechnology Products and Biocatalysis Processes for a Sustainable Bioeconomy)

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12 pages, 2031 KiB  

Open AccessArticle

Styrene Production in Genetically Engineered Escherichia coli in a Two-Phase Culture

by Shuhei Noda, Ryosuke Fujiwara, Yutaro Mori, Mayumi Dainin, Tomokazu Shirai and Akihiko Kondo

BioTech 2024, 13(1), 2; https://doi.org/10.3390/biotech13010002 - 14 Jan 2024

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Abstract

Styrene is an important industrial chemical. Although several studies have reported microbial styrene production, the amount of styrene produced in batch cultures can be increased. In this study, styrene was produced using genetically engineered Escherichia coli. First, we evaluated five types of [...] Read more.

Styrene is an important industrial chemical. Although several studies have reported microbial styrene production, the amount of styrene produced in batch cultures can be increased. In this study, styrene was produced using genetically engineered Escherichia coli. First, we evaluated five types of phenylalanine ammonia lyases (PALs) from Arabidopsis thaliana (AtPAL) and Brachypodium distachyon (BdPAL) for their ability to produce trans-cinnamic acid (Cin), a styrene precursor. AtPAL2-expressing E. coli produced approximately 700 mg/L of Cin and we found that BdPALs could convert Cin into styrene. To assess styrene production, we constructed an E. coli strain that co-expressed AtPAL2 and ferulic acid decarboxylase from Saccharomyces cerevisiae. After a biphasic culture with oleyl alcohol, styrene production and yield from glucose were 3.1 g/L and 26.7% (mol/mol), respectively, which, to the best of our knowledge, are the highest values obtained in batch cultivation. Thus, this strain can be applied to the large–scale industrial production of styrene. Full article

(This article belongs to the Topic Microbial Biotechnology Products and Biocatalysis Processes for a Sustainable Bioeconomy)

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25 pages, 4507 KiB  

Open AccessArticle

Biocatalysts Based on Immobilized Lipases for the Production of Fatty Acid Ethyl Esters: Enhancement of Activity through Ionic Additives and Ion Exchange Supports

by Juan S. Pardo-Tamayo, Sebastián Arteaga-Collazos, Laura C. Domínguez-Hoyos and César A. Godoy

BioTech 2023, 12(4), 67; https://doi.org/10.3390/biotech12040067 - 18 Dec 2023

Viewed by 2123

Abstract

Ionic additives affect the structure, activity and stability of lipases, which allow for solving common application challenges, such as preventing the formation of protein aggregates or strengthening enzyme–support binding, preventing their desorption in organic media. This work aimed to design a biocatalyst, based [...] Read more.

Ionic additives affect the structure, activity and stability of lipases, which allow for solving common application challenges, such as preventing the formation of protein aggregates or strengthening enzyme–support binding, preventing their desorption in organic media. This work aimed to design a biocatalyst, based on lipase improved by the addition of ionic additives, applicable in the production of ethyl esters of fatty acids (EE). Industrial enzymes from Thermomyces lanuginosus (TLL), Rhizomucor miehei (RML), Candida antárctica B (CALB) and Lecitase^®, immobilized in commercial supports like Lewatit^®, Purolite^® and Q-Sepharose^®, were tested. The best combination was achieved by immobilizing lipase TLL onto Q-Sepharose^® as it surpassed, in terms of %EE (70.1%), the commercial biocatalyst Novozyme^® 435 (52.7%) and was similar to that of Lipozyme TL IM (71.3%). Hence, the impact of ionic additives like polymers and surfactants on both free and immobilized TLL on Q-Sepharose^® was assessed. It was observed that, when immobilized, in the presence of sodium dodecyl sulfate (SDS), the TLL derivative exhibited a significantly higher activity, with a 93-fold increase (1.02 IU), compared to the free enzyme under identical conditions (0.011 IU). In fatty acids ethyl esters synthesis, Q-SDS-TLL novel derivatives achieved results similar to commercial biocatalysts using up to ~82 times less enzyme (1 mg/g). This creates an opportunity to develop biocatalysts with reduced enzyme consumption, a factor often associated with higher production costs. Such advancements would ease their integration into the biodiesel industry, fostering a greener production approach compared to conventional methods. Full article

(This article belongs to the Topic Microbial Biotechnology Products and Biocatalysis Processes for a Sustainable Bioeconomy)

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11 pages, 571 KiB  

Open AccessArticle

Detection and Characterization of Electrogenic Bacteria from Soils

by Ana Rumora, Liliana Hopkins, Kayla Yim, Melissa F. Baykus, Luisa Martinez and Luis Jimenez

BioTech 2023, 12(4), 65; https://doi.org/10.3390/biotech12040065 - 2 Dec 2023

Cited by 2 | Viewed by 2781

Abstract

Soil microbial fuel cells (SMFCs) are bioelectrical devices powered by the oxidation of organic and inorganic compounds due to microbial activity. Seven soils were randomly selected from Bergen Community College or areas nearby, located in the state of New Jersey, USA, were used [...] Read more.

Soil microbial fuel cells (SMFCs) are bioelectrical devices powered by the oxidation of organic and inorganic compounds due to microbial activity. Seven soils were randomly selected from Bergen Community College or areas nearby, located in the state of New Jersey, USA, were used to screen for the presence of electrogenic bacteria. SMFCs were incubated at 35–37 °C. Electricity generation and electrogenic bacteria were determined using an application developed for cellular phones. Of the seven samples, five generated electricity and enriched electrogenic bacteria. Average electrical output for the seven SMFCs was 155 microwatts with the start-up time ranging from 1 to 11 days. The highest output and electrogenic bacterial numbers were found with SMFC-B1 with 143 microwatts and 2.99 × 10⁹ electrogenic bacteria after 15 days. Optimal electrical output and electrogenic bacterial numbers ranged from 1 to 21 days. Microbial DNA was extracted from the top and bottom of the anode of SMFC-B1 using the ZR Soil Microbe DNA MiniPrep Protocol followed by PCR amplification of 16S rRNA V3-V4 region. Next-generation sequencing of 16S rRNA genes generated an average of 58 k sequences. BLAST analysis of the anode bacterial community in SMFC-B1 demonstrated that the predominant bacterial phylum was Bacillota of the class Clostridia (50%). However, bacteria belonging to the phylum Pseudomonadota (15%) such as Magnetospirillum sp. and Methylocaldum gracile were also part of the predominant electrogenic bacterial community in the anode. Unidentified uncultured bacteria accounted for 35% of the predominant bacterial community. Bioelectrical devices such as MFCs provide sustainable and clean alternatives to future applications for electricity generation, waste treatment, and biosensors. Full article

(This article belongs to the Topic Microbial Biotechnology Products and Biocatalysis Processes for a Sustainable Bioeconomy)

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