Whole-cell Biocatalyst Research Articles

Exploring Strategic Approaches for CvFAP Photodecarboxylation through Violet Light Irradiation

In this study, we describe a light-driven photocatalytic decarboxylation of palmitic acid and related fatty acids using Chlorella variabilis fatty acid photodecarboxylase (CvFAP). By utilizing violet light emitting diode (LED) light (50 W; 397 nm), we achieved a remarkable conversion efficiency of 99% within just 4 min, surpassing the previous 79% conversion achieved in 60 min using blue LED light (300 W; 439 nm). Importantly, the use of 50 W violet LED light also resulted in a lower enzyme photoinactivation rate when compared to 300 W blue LED. Comparing the whole-cell biocatalyst with the enzymatic extract, we found that the former demonstrated superior catalytic performance and reduced susceptibility to photoinactivation. Furthermore, whole-cell biocatalyst reuse was demonstrated after five sequential batches. Employing this approach, we successfully synthesized 26 mmol L-1 h-1 of pentadecane, showcasing a promising strategy to improve productivity. These findings represent a significant advancement in CvFAP photodecarboxylation processes compared to the literature, utilizing an alternative light source, with potential implications to the biofuel sector

Whole-cell Rieske non-heme iron biocatalysts.

Rieske non-heme iron oxygenases (ROs) possess the ability to catalyze a wide range of reactions. Their ability to degrade aromatic compounds is a unique characteristic and makes ROs interesting for a variety of potential applications. However, purified ROs can be challenging to work with due to low stability and long, complex electron transport chains. Whole cell biocatalysis represents a quick and reliable method for characterizing the activity of ROs and harnessing their metabolic potential. In this protocol, we outline a step-by-step protocol for the overexpression of ROs for whole cell biocatalysis and characterization. We have utilized a caffeine-degrading, N-demethylation system, expressing the RO genes ndmA and ndmD, as an example of this method.

Split-GFP complementation at the bacterial cell surface for antibody-free labeling and quantification of heterologous protein display

The split-GFP system is a versatile tool with numerous applications, but it has been underutilized for the labeling of heterologous surface-displayed proteins. By inserting the 16 amino acid sequence of the GFP11-tag between a protein of interest and an autotransporter protein, it is possible to present a protein at the outer membrane of gram-negative bacteria and to fluorescently label it by complementation with externally added GFP1–10. The labeled cells could be clearly discerned from cells without the protein of interest using flow cytometry and the insertion of the GFP11-tag caused no significant alteration of the catalytic activity for the tested model enzyme CsBglA. Furthermore, the amount of the protein of interest on the cells could be quantified by comparing the green fluorescence resulting from the complementation to that of standards with known concentrations. This allows a precise characterization of whole-cell biocatalysts, which is difficult with existing methods. The split-GFP complementation approach was shown to be specific, in a similar manner as commercial antibodies. It is cost-efficient, minimizes the possibility of adverse effects on protein expression or solubility, and can be performed at high throughput.

Bioengineering Comamonas testosteroni CNB-1: a robust whole-cell biocatalyst for efficient PET microplastic degradation

The escalating crisis of polyethylene terephthalate (PET) microplastic contamination in biological wastewater treatment systems is a pressing environmental concern. These microplastics inevitably accumulate in sewage sludge due to the absence of effective removal technologies. Addressing this urgent issue, this study introduces a novel approach using DuraPETase, a potent enzyme with enhanced PET hydrolytic activity at ambient temperatures. Remarkably, this enzyme was successfully secreted from Comamonas testosteroni CNB-1, a dominant species in the active sludge. The secreted DuraPETase showed significant hydrolytic activity toward p-NPB and PET nanoplastics. Furthermore, the CNB-1 derived whole-cell biocatalyst was able to depolymerize PET microplastics under ambient temperature, achieving a degradation efficiency of 9% within 7 days. The CNB-1-based whole biocatalysts were also capable of utilizing PET degradation intermediates, such as terephthalic acid (TPA) and ethylene glycol (EG), and bis(2-hydroxyethyl)-TPA (BHET), for growth. This indicates that it can completely mineralize PET, as opposed to merely breaking it down into smaller molecules. This research highlights the potential of activated sludge as a potent source for insitu microplastic removal.Graphical

Photocatalytic Reduction of Methylene Blue by Surface-Engineered Recombinant Escherichia coli as a Whole-Cell Biocatalyst.

A novel Escherichia coli strain, created by engineering its cell surface with a cobalt-binding peptide CP1, was investigated in this study. The recombinant strain, pBAD30-YiaT-CP1, was structurally modeled to determine its cobalt-binding affinity. Furthermore, the effectiveness and specificity of pBAD30-CP1 in adsorbing and extracting cobalt from artificial wastewater polluted with the metal were investigated. The modified cells were subjected to cobalt concentrations (0.25 mM to 1 mM) and pH levels (pH 3, 5, 7, and 9). When exposed to a pH of 7 and a cobalt concentration of 1 mM, the pBAD30-CP1 strain had the best cobalt recovery efficiency, measuring 1468 mol/g DCW (Dry Cell Weight). Furthermore, pBAD30-CP1 had a higher affinity for cobalt than nickel and manganese. Field Emission Scanning Electron Microscopy (FE-SEM), Transmission Electron Microscopy (TEM), and Energy-Dispersive X-ray Spectroscopy (EDS) were used to examine the physiochemical parameters of the recombinant cells after cobalt adsorption. These approaches revealed the presence of cobalt in a bound state on the cell surface in the form of nanoparticles. In addition, the cobalt-binding recombinant strains were used in the photocatalytic reduction of methylene blue, which resulted in a 59.52% drop in the observed percentage. This study shows that modified E. coli strains have the potential for efficient cobalt recovery and application in environmental remediation operations.

Application of yeast display method in biotechnology and agriculture

Yeast display (DD) is an efficient technology for exposure and fixation of target proteins on the surface of yeast cells by their fusion with cell wall proteins. The scope of application of DD is very wide. It can be used in the study of protein-protein interactions and antibody screening; for the processing of industrial waste, in the processes of bioadsorption of heavy and rare metals, in the production of chemical compounds and biofuels, and in the production of vaccines. DD has a number of advantages over other cell systems. This is due to the fact that yeast, being eukaryotes, unlike bacteria, can carry out various post-translational modifications, correct folding and secretion of eukaryotic proteins.
 In our work, we compared the effectiveness of different cell wall proteins for exposing target proteins to the surface ofKomagataella phaffiiyeast cells. Two reporter systems were used, based on the eGFP and the beta-galactosidase genes.
 The most efficient exposure to the surface was provided by the anchor protein ScAGα1p from the yeastSaccharomyces cerevisiae. The genetic constructs obtained in the work can be used for the production of whole-cell biocatalysts. A yeast strainK. phaffiiwas obtained, containing in its genome a construct for the excretion of the Gumboro disease virus antigen protein — VP2. This strain can be used for the production of a vaccine.
 This work was supported by the Ministry of Science and Higher Education of the Russian Federation in accordance with agreement No. 075-15-2022-322 date 22.04.2022 on providing a grant in the form of subsidies from the Federal budget of Russian Federation. The grant was provided for state support for the creation and development of a World-class Scientific Center “Agrotechnologies for the Future”.

Efficiency aspects of regioselective testosterone hydroxylation with highly active CYP450-based whole-cell biocatalysts.

Steroid hydroxylations belong to the industrially most relevant reactions catalysed by cytochrome P450 monooxygenases (CYP450s) due to the pharmacological relevance of hydroxylated derivatives. The implementation of respective bioprocesses at an industrial scale still suffers from several limitations commonly found in CYP450 catalysis, that is low turnover rates, enzyme instability, inhibition and toxicity related to the substrate(s) and/or product(s). Recently, we achieved a new level of steroid hydroxylation rates by introducing highly active testosterone-hydroxylating CYP450 BM3 variants together with the hydrophobic outer membrane protein AlkL into Escherichia coli-based whole-cell biocatalysts. However, the activity tended to decrease, which possibly impedes overall productivities and final product titres. In this study, a considerable instability was confirmed and subject to a systematic investigation regarding possible causes. In-depth evaluation of whole-cell biocatalyst kinetics and stability revealed a limitation in substrate availability due to poor testosterone solubility as well as inhibition by the main product 15β-hydroxytestosterone. Instability of CYP450 BM3 variants was disclosed as another critical factor, which is of general significance for CYP450-based biocatalysis. Presented results reveal biocatalyst, reaction and process engineering strategies auguring well for industrial implementation of the developed steroid hydroxylation platform.

Production of 1-methylxanthine via the biodegradation of theophylline by an optimized Escherichia coli strain

1-Methylxanthine is a high-value derivative of caffeine of limited natural availability with many potential pharmaceutical applications. Unfortunately, production of 1-methylxanthine through purely chemical methods of synthesis are unfavorable due to lengthy chemical processes and the requirement of hazardous chemicals, ultimately resulting in low yields. Here, we describe a novel biosynthetic process for the production of 1-methylxanthine from theophylline using engineered Escherichia coli whole-cell biocatalysts and reaction optimization. When scaled-up to 1590 mL, the simple biocatalytic reaction produced approximately 1188 mg 1-methylxanthine from 1444 mg theophylline, constituting gram-scale production of 1-methylxanthine in as little as 3 hours. Following HPLC purification and solvent evaporation, 1163 mg of dried 1-methylxanthine powder was collected, resulting in a 97.9 wt% product recovery at a purity of 97.8%. This is the first report of a biocatalytic process designed specifically for the production and purification of the high-value biochemical 1-methylxanthine from theophylline. This process is also the most robust methylxanthine N-demethylation process featuring engineered E. coli to date, capable of gram-scale production.

Efficient stereoselective hydroxylation of deoxycholic acid by the robust whole-cell cytochrome P450 CYP107D1 biocatalyst

Deoxycholic acid (DCA) has been authorized by the Federal Drug Agency for cosmetic reduction of redundant submental fat. The hydroxylated product (6β-OH DCA) was developed to improve the solubility and pharmaceutic properties of DCA for further applications. Herein, a combinatorial catalytic strategy was applied to construct a powerful Cytochrome P450 biocatalyst (CYP107D1, OleP) to convert DCA to 6β-OH DCA. Firstly, the weak expression of OleP was significantly improved using pRSFDuet-1 plasmid in the E. coli C41 (DE3) strain. Next, the supply of heme was enhanced by the moderate overexpression of crucial genes in the heme biosynthetic pathway. In addition, a new biosensor was developed to select the appropriate redox partner. Furthermore, a cost-effective whole-cell catalytic system was constructed, resulting in the highest reported conversion rate of 6β-OH DCA (from 4.8% to 99.1%). The combinatorial catalytic strategies applied in this study provide an efficient method to synthesize high-value-added hydroxylated compounds by P450s.

Designing Ubiquitin-like protease 1 (Ulp1) based nano biocatalysts: A promising technology for SUMO fusion proteins

The SUMO proteases (Ulps), a group of cysteine proteases, are well known for their efficient ability to perform structure-based cleavage of SUMO tag from the protein of interest and generation of biotherapeutics with authentic N-terminus. However, the stability of Ulps has remained a challenge for the economical production of difficult-to-produce proteins in E. coli. Therefore, the present study aimed to establish the methodology for developing stable S. pombe Ulp1 preparation using different enzyme immobilization strategies. The whole-cell biocatalyst developed using the Pir1 anchor protein of Pichia cleaved the SUMO tag within 24 h of reaction incubation. The chemical immobilization using commercial epoxy and amino methacrylate beads significantly enhanced the operational reusability of SpUlp1 up to 24 cycles. Silica beads further improved the repetitive usage of the immobilized enzyme for 65 cycles. The SpUlp1 immobilization on laboratory-developed chitosan-coated iron oxide nanoparticles exhibited more than 90 % cleavage of SUMO tag from different substrates even after 100 consecutive reactions. Moreover, an effective SUMO tag removal was observed within 10 min of incubation. The operational stability of the immobilized enzyme was confirmed in a pH range of 5 to 13. The spherical nature of nanoparticles was confirmed by FESEM and TEM results. The successful chitosan coating and subsequent activation with glutaraldehyde were established via FT-IR. Furthermore, HRTEM, SAED, and XRD proved the crystalline nature of nanoparticles, while VSM confirmed the superparamagnetic behavior.

Beneficial applications of biofilms.

Many microorganisms live in the form of a biofilm. Although they are feared in the medical sector, biofilms that are composed of non-pathogenic organisms can be highly beneficial in many applications, including the production of bulk and fine chemicals. Biofilm systems are natural retentostats in which the biocatalysts can adapt and optimize their metabolism to different conditions over time. The adherent nature of biofilms allows them to be used in continuous systems in which the hydraulic retention time is much shorter than the doubling time of the biocatalysts. Moreover, the resilience of organisms growing in biofilms, together with the potential of uncoupling growth from catalytic activity, offers a wide range of opportunities. The ability to work with continuous systems using a potentially self-advancing whole-cell biocatalyst is attracting interest from a range of disciplines, from applied microbiology to materials science and from bioengineering to process engineering. The field of beneficial biofilms is rapidly evolving, with an increasing number of applications being explored, and the surge in demand for sustainable and biobased solutions and processes is accelerating advances in the field. This Review provides an overview of the research topics, challenges, applications and future directions in beneficial and applied biofilm research.

Optimization of Aerobic Synthesis of Succinic Acid from Glucose by Recombinant <i>Escherichia coli</i> Strains Through the Variant Tricaboxylic Acid Cycle Mediated by the Action of 2-ketoglutarate-decarboxylase

The biosynthesis of succinic acid from glucose by the previously engineered E. coli strain SUC1.0 (pMW119-kgd) (MG1655 ∆ackA-pta, ∆poxB, ∆ldhA, ∆adhE, ∆ptsG, PLglk, PtacgalP, ∆aceBAK, ∆glcB, ∆sdhAB, pMW119-kgd) was optimized. The yield of the target substance was increased, upon the activation in the strain of the variant tricarboxylic acid cycle, mediated by the action of heterologous 2-ketoglutarate decarboxylase, due to the intensification of the anaplerotic formation of oxaloacetic acid. Inactivation of the nonspecific thioesterase YciA in the strain did not considerably change the biosynthetic characteristics of the producer. The enhancement of the expression of native phosphoenolpyruvate carboxylase led to an increase in the yield of the target compound by the recombinant synthesizing succinic acid via the reactions of the native tricarboxylic acid cycle from 25 to 42%, and from 67 to 75% upon the induced expression of Mycobacterium tuberculosis 2-ketoglutarate decarboxylase. Expression in the strain of pyruvate carboxylase gene from Bacillus subtilis resulted in an increase in the yield of succinic acid up to 84%. Functioning in whole-cell biocatalyst mode, the engineered strain SUC1.0 PL-pycA (pMW119-kgd) demonstrated a substrate to target product conversion ratio reaching 93%, approaching the corresponding theoretical maximum.

Effects of electrospun nanofiber fabrications on immobilization of recombinant Escherichia coli for production of xylitol from glucose

A suitable nanofiber sheet was formulated and developed based on its efficacy in the immobilization of recombinant Escherichia coli (E. coli) to enhance xylitol production. The effects of different types of nanofibers and solvents on cell immobilization and xylitol production were studied. The most applicable nanofiber membrane was selected via preliminary screening of four types of nanofiber membrane, followed by the selection of six different solvents. Polyvinylidene fluoride (PVDF) nanofiber sheet synthesized using dimethylformamide (DMF) solvent was found to be the most suitable carrier for immobilization and xylitol production. The thin, beaded PVDF (DMF) nanofibers were more favourable for microbial adhesion, with the number of immobilized cells as high as 96 × 106 ± 3.0 cfu/ml. The attraction force between positively charged PVDF nanofibers and the negatively charged E. coli indicates that the electrostatic interaction plays a significant role in cell adsorption. The use of DMF has also produced PVDF nanofibers biocatalyst capable of synthesizing the highest xylitol concentration (2.168 g/l) and productivity (0.090 g/l/h) and 55–69% reduction in cell lysis compared with DMSO solvent and free cells. This finding suggests that recombinant E. coli immobilized on nanofibers shows great potential as a whole-cell biocatalyst for xylitol production.

Harnessing dual applications of a novel ascomycetes yeast, Starmerella cerana sp. nov., as a biocatalyst for stereoselective ketone reduction and biosurfactant production

Introduction: New bioresources for catalytic application and fine chemical synthesis are the need of the hour. In an effort to find out new biocatalyst for oxidation-reduction reaction, leading to the synthesis of chiral intermediates, novel yeast were isolated from unique niche and employed for the synthesis of value added compounds.Methods: To determine the genetic relatedness of the isolated strain, HSB-15T, sequence analysis of the internal transcribed spacer (ITS) and D1/D2 domains of the 26S rRNA gene sequence was carried out. The distinctive features of the strain HSB-15T were also identified by phenotypic characterization. The isolated strain HSB-15T was employed for the reduction of selected naphthyl ketones to their corresponding alcohols and a biosurfactant was isolated from its culture broth.Results: The analysis of the ITS and D1/D2 domains of the 26S rRNA gene revealed that strain HSB-15T is closely related to the type strain of Starmerella vitae (CBS 15147T) with 96.3% and 97.7% sequence similarity, respectively. However, concatenated sequences of the ITS gene and D1/D2 domain showed 94.6% sequence similarity. Phenotypic characterization indicated significant differences between strain HSB-15T and its closely related species and consequently, it was identified as a novel species, leading to the proposal of the name Starmerella cerana sp. nov. The strain was able to reduce selected naphthyl ketones to their corresponding alcohols with remarkable efficiency, within a 12-hours. The strain HSB-15T also produced a surfactant in its culture broth, identified as sophorolipid upon analysis.Discussion: The study explored the potential of the novel strain, HSB-15T, as a whole-cell biocatalyst for the reduction of naphthyl ketones to their corresponding alcohols and also reports its capability to produce sophorolipid, a biosurfactant, in its culture broth. This dual functionality of HSB-15T both as biocatalyst and biosurfactant producer enhances its applicability in biotechnology and environmental science.

The Synthesis of Ginsenoside Compound K Using a Surface-Displayed β-Glycosidase Whole-Cell Catalyst

Ginsenoside compound K (CK) has garnered considerable attention due to its versatile pharmacological properties, including anti-inflammatory, anti-allergic, anti-aging, anti-diabetic, and hepatoprotective effects, along with neuroprotection. The conventional approach to synthesizing ginsenoside CK involves enzymatic conversion. However, the purification of enzymes necessitates effort and expense, and enzymes are prone to inactivation. Additionally, whole-cell catalysis suffers from inefficiency due to limited cell permeability. To address these challenges, we harnessed the YiaT protein as an anchoring motif, establishing a surface display system for β-glycosidase Bgp3. This innovative system served as a whole-cell catalyst for the efficient synthesis of ginsenoside CK. We further optimized the YiaT-Bgp3 system, enhancing display levels and significantly increasing ginsenoside CK production. Optimal conditions were achieved at an IPTG concentration of 0.5 mM, an induction temperature of 16 °C, a ginsenoside substrate concentration of 15 mg/mL, and a catalytic temperature of 30 °C. Ultimately, the YiaT-Bgp3 system synthesized 5.18 ± 0.08 mg/mL ginsenoside CK within 24 h, with a conversion of 81.83 ± 1.34%. Furthermore, the YiaT-Bgp3 system exhibited good reusability, adding to its practicality and value. This study has successfully developed an efficient whole-cell Bgp3 biocatalyst, offering a convenient, highly productive, and economically viable solution for the industrial production of ginsenoside CK.

Biocatalytic characterization of an alcohol dehydrogenase variant deduced from Lactobacillus kefir in asymmetric hydrogen transfer

Hydrogen transfer biocatalysts to prepare optically pure alcohols are in need, especially when it comes to sterically demanding ketones, whereof the bioreduced products are either essential precursors of pharmaceutically relevant compounds or constitute APIs themselves. In this study, we report on the biocatalytic potential of an anti-Prelog (R)-specific Lactobacillus kefir ADH variant (Lk-ADH-E145F-F147L-Y190C, named Lk-ADH Prince) employed as E. coli/ADH whole-cell biocatalyst and its characterization for stereoselective reduction of prochiral carbonyl substrates. Key enzymatic reaction parameters, including the reaction medium, evaluation of cofactor-dependency, organic co-solvent tolerance, and substrate loading, were determined employing the drug pentoxifylline as a model prochiral ketone. Furthermore, to tap the substrate scope of Lk-ADH Prince in hydrogen transfer reactions, a broad range of 34 carbonylic derivatives was screened. Our data demonstrate that E. coli/Lk-ADH Prince exhibits activity toward a variety of structurally different ketones, furnishing optically active alcohol products at the high conversion of 65–99.9% and in moderate-to-high isolated yields (38–91%) with excellent anti-Prelog (R)-stereoselectivity (up to >99% ee) at substrate concentrations up to 100 mM.

Seamless and orthogonal expression of genetic parts in polyhydroxyalkanoate (PHA)-producing bacterial chassis for plastic bio-upcycling applications

Polyhydroxyalkanoate (PHA)-producing bacteria represent a powerful synthetic biology chassis for waste bioconversion and bio-upcycling where PHAs can be produced as the final products. In this study, we present a seamless plasmid construction for orthogonal expression of recombinant PET hydrolase (PETase) in model PHA-producing bacteria P. putida and C. necator. To this end, this study described seamless cloning and expression methods utilizing SureVector (SV) system for generating pSV-Ortho-PHA (pSVOP) expression platform in bioengineered P. putida and C. necator. Genetic parts specifically Trc promoter, pBBR1 origin of replication, anchoring proteins and signal sequences were utilized for the transformation of pSVOP-based plasmid in electrocompetent cells and orthogonal expression of PETase in both P. putida and C. necator. Validation steps in confirming functional expression of PETase activity in corresponding PETase-expressing strains were also described to demonstrate seamless and detailed methods in establishing bioengineered P. putida and C. necator as whole-cell biocatalysts tailored for plastic bio-upcycling.•Seamless plasmid construction for orthogonal expression in PHA-producing bacteria.•Step-by-step guide for high-efficiency generation of electrotransformants of P. putida and C. necator.•Adaptable methods for rapid strain development (Design, Build, Test and Learn) for whole-cell biocatalysis.

Electricity production from palm oil mill effluent (POME) through the integration of a microbial fuel cell and bilirubin oxidase-producing bacteria

The microbial fuel cell (MFC) is a device that harnesses microbial metabolism to convert chemical energy into bio-electrical energy. Extensive research has demonstrated its efficacy in both wastewater treatment and power generation applications. This study focused on the integration of a microbial fuel cell (MFC) with a biocathode constructed using the oxidoreductase-producing bacterium <em>Bacillus</em> sp. MCO22 and rice straw as a cost-effective substrate. The MFC utilized palm oil mill effluent (POME) as a chemical energy source for electricity generation in the anodic chamber. The ability of the MFC was evaluated by monitoring biochemical oxygen demand (BOD) activity and electrochemical properties. Post-operation, chemical oxygen demand (COD) and color removal were measured. The results revealed that the MFC with the BOD-based cathode achieved a maximum current density and power density of 0.58±0.01 A/m<sup>2</sup> and 0.17±0.00 W/m<sup>2</sup>, respectively. Furthermore, it exhibited high COD and color removal rates of 95.10±0.10% and 98.53±0.33%, respectively, without requiring an external power supply. This study presents novel insights into utilizing a BOD-producing bacterium as a whole-cell biocatalyst on the MFC cathodic surface for both electricity generation and agricultural wastewater treatment.

Efficient bioamination of lignin-derived vanillin to vanillylamine in dibutyl phthalate-water system

Lignin is one of the earth's most abundant renewable resources. Hence, achieving sustainable industry development in the future relies on obtaining a range of high-value chemicals from abundant and renewable biological resources. Vanillylamine is a basic upgrading product of vanillin in organic synthesis. It is also an important raw material for synthetic drugs, precursors, and additives. In this study, a two-phase reaction medium composed of organic solvent-water was established, and Escherichia coli CV was applied as ω-transaminase biocatalyst to the biosynthesis of vanillylamine from lignin-derived vanillin. Under optimized reaction conditions (pH 6.5, 35 °C) in a dibutyl phthalate (DBP)-water medium (1:9, vol/vol), vanillin (50 mM) was effectively transformed into vanillylamine by CV whole-cell biocatalyst containing ω-transaminase with amine donor L-Alanine (L-Ala:vanillin=12:1, mol/mol). Also, benzaldehyde, anisaldehyde, and veratraldehyde (50 mM) could be fully converted into the corresponding amines. This work provides an efficient and environmentally friendly method for the preparation of vanillylamine and its derivatives from lignin-based feedstocks.

A solvent-tolerant whole-cell biocatalyst for chemoselective oxidation of aldehydes to carboxylic acids

The conversion of aldehydes into carboxylic acids through biocatalysis is a promising approach in the fields of green organic synthesis and biotechnology. In this work, we have developed a biocatalytic method for the oxidation of aldehydes to form carboxylic acid in the aqueous phase by using a newly discovered whole D. xibeiensis R13 cell biocatalyst. The whole-cell biocatalyst exhibited excellent organic solvent tolerance and a low biocatalyst/substrate ratio in the selective oxidation of biomass-derived furfural to 2­furoic acid. Under optimal conditions, a yield of 93 % was achieved after 12 h with a conversion of 250 mM furfural substrate. The microbial oxidation of furfural was further scaled up by a fed-batch strategy, with a productivity of 1.3 g/L per hour and a total yield of 83 %. A panel of aldehydes with various reactive moieties was efficiently converted with expected carboxylic acids as the sole product under mild reaction conditions, indicating excellent chemoselectivity (>99 %) and wide substrate scope. The new biocatalytic method avoids the use of toxic transition-metal reagents, representing a green and sustainable alternative to chemical methods.