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Microorganisms
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Microbial Biocatalysis and Biodegradation 2.0
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Microbial Biocatalysis and Biodegradation 2.0

A special issue of Microorganisms (ISSN 2076-2607). This special issue belongs to the section "Microbial Biotechnology".

Deadline for manuscript submissions: closed (15 April 2024) | Viewed by 11219

Special Issue Editor

Prof. Dr. Andrew Willetts

E-Mail Website
Guest Editor
College of Life and Environmental Sciences, University of Exeter, Exeter EX4 4QG, UK
Interests: microbial biochemistry; microbial biocatalysis; microbial biodegradation: chemoenzymatic synthesis
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Microbial biocatalysis and biodegradation illustrate different but related perspectives of global biogeochemical cycles. Both can be capitalised on with scientific ingenuity to deliver valuable practical outcomes of applied microbiology, as illustrated by chemoenzymatic synthesis and bioremediation, respectively. The fundamental feature common to both these facets of microbial biotechnology is the catalytic activity of microbial enzymes. Consequently, the goal of this Special Issues is to provide insight into relevant areas of microbial biochemistry, from the molecular level of individual enzymes to the co-operative metabolic functioning of whole organisms and ecosystems. 

Particular emphasis will be placed on promoting beneficial advances that have resulted from the introduction of new technologies, including both those that have evolved specifically in the post-genomic era (e.g., protein engineering by directed evolution) and those that have grown out of greater knowledge and understanding of enzyme structure–function relationships (e.g., combinatorial active-site mutation and iterative saturation mutagenesis). In addition, considered from a commercial perspective, a specific aim is to highlight examples of appropriate strategies that enhance robustness and scalability, both at the level of isolated enzymes (native and/or overexpressed) used in biocatalysis, as well as of microbial cultures or ecosystems used for bioremediation.

It is intended that the validity of exploiting microbial biocatalysis will be reflected by a variety of submissions covering not only current, but also developing and more speculative roles for deploying microbial enzymes in the production of fine and bulk chemicals, pharmaceuticals, and drug metabolites for pharmacokinetic studies. Particular prominence will be given to the growing recognition of the strategic role of cascade catalysis, and the consequent development of successful artificial catalytic cascades.

As a consequence of the acknowledged myriad problems posed by environmental pollution, submissions are specifically encouraged at the whole organisms/consortium/ecosystem level that reflect the relative merits of, and contributions made by, biostimulation and bioaugmentation as significantly different strategies to promote bioremediation and/or waste recycling.

Prof. Dr. Andrew Willetts
Guest Editor

Manuscript Submission Information

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 100 words) can be sent to the Editorial Office for announcement on this website.

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-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Microorganisms is an international peer-reviewed open access monthly 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

  • chemoenzymatic synthesis
  • cascade catalysis
  • protein engineering
  • combinatorial active-site mutation
  • bioremediation
  • biostimulation
  • bioaugmentation

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Published Papers (7 papers)

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Research

Jump to: Review

15 pages, 4975 KiB  
Article
Efficient Biodegradation of the Neonicotinoid Insecticide Flonicamid by Pseudaminobacter salicylatoxidans CGMCC 1.17248: Kinetics, Pathways, and Enzyme Properties
by Yun-Xiu Zhao, Jing Yuan, Ke-Wei Song, Chi-Jie Yin, Li-Wen Chen, Kun-Yan Yang, Ju Yang and Yi-Jun Dai
Microorganisms 2024, 12(6), 1063; https://doi.org/10.3390/microorganisms12061063 - 24 May 2024
Viewed by 895
Abstract
Nitrile-containing insecticides can be converted into their amide derivatives by Pseudaminobacter salicylatoxidans. N-(4-trifluoromethylnicotinoyl) glycinamide (TFNG-AM) is converted to 4-(trifluoromethyl) nicotinoyl glycine (TFNG) using nitrile hydratase/amidase. However, the amidase that catalyzes this bioconversion has not yet been fully elucidated. In this study, [...] Read more.
Nitrile-containing insecticides can be converted into their amide derivatives by Pseudaminobacter salicylatoxidans. N-(4-trifluoromethylnicotinoyl) glycinamide (TFNG-AM) is converted to 4-(trifluoromethyl) nicotinoyl glycine (TFNG) using nitrile hydratase/amidase. However, the amidase that catalyzes this bioconversion has not yet been fully elucidated. In this study, it was discovered that flonicamid (FLO) is degraded by P. salicylatoxidans into the acid metabolite TFNG via the intermediate TFNG-AM. A half-life of 18.7 h was observed for P. salicylatoxidans resting cells, which transformed 82.8% of the available FLO in 48 h. The resulting amide metabolite, TFNG-AM, was almost all converted to TFNG within 19 d. A novel amidase-encoding gene was cloned and overexpressed in Escherichia coli. The enzyme, PmsiA, hydrolyzed TFNG-AM to TFNG. Despite being categorized as a member of the amidase signature enzyme superfamily, PsmiA only shares 20–30% identity with the 14 previously identified members of this family, indicating that PsmiA represents a novel class of enzyme. Homology structural modeling and molecular docking analyses suggested that key residues Glu247 and Met242 may significantly impact the catalytic activity of PsmiA. This study contributes to our understanding of the biodegradation process of nitrile-containing insecticides and the relationship between the structure and function of metabolic enzymes. Full article
(This article belongs to the Special Issue Microbial Biocatalysis and Biodegradation 2.0)
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11 pages, 1306 KiB  
Article
Characterization of the 3,4-Dichloroaniline Degradation Gene Cluster in Acinetobacter soli GFJ2
by Namiko Gibu, Daisuke Kasai, Saki Sato, Michiro Tabata, Alisa Vangnai and Masao Fukuda
Microorganisms 2024, 12(3), 613; https://doi.org/10.3390/microorganisms12030613 - 19 Mar 2024
Cited by 1 | Viewed by 1214
Abstract
3,4-Dichloroaniline (34DCA), a major metabolite of phenylurea herbicides, causes environmental contamination owing to its toxicity and recalcitrant properties. Acinetobacter soli strain GFJ2, isolated from soil potentially contaminated with herbicides, can degrade 34DCA. This study aimed to identify and characterize the 34DCA degradation gene [...] Read more.
3,4-Dichloroaniline (34DCA), a major metabolite of phenylurea herbicides, causes environmental contamination owing to its toxicity and recalcitrant properties. Acinetobacter soli strain GFJ2, isolated from soil potentially contaminated with herbicides, can degrade 34DCA. This study aimed to identify and characterize the 34DCA degradation gene cluster responsible for the conversion of 34DCA to 4,5-dichlorocatechol in the strain GFJ2. Genome analysis revealed one chromosome and seven plasmids in GFJ2, comprising 21, 75, and 3309 copies of rRNA, 75 tRNA, and protein-encoding genes, respectively. A gene cluster responsible for 34DCA degradation was identified, comprising dcdA, dcdB, and dcdC, which encode dioxygenase, flavin reductase, and aldehyde dehydrogenase, respectively. Transcriptional analysis indicated that this gene cluster is constructed as an operon, induced during 34DCA utilization. The heterologous expression of dcdA and dcdB in Escherichia coli confirmed their activity in degrading 34DCA to an intermediate metabolite, converted to 4,5-dichlorocatechol via a reaction involving the dcdC gene product, suggesting their involvement in 34DCA conversion to 4,5-dichlorocatechol. Deletion mutants of dcdA and dcdB lost 34DCA degradation ability, confirming their importance in 34DCA utilization in GFJ2. This study provides insights into the genetic mechanisms of 34DCA degradation by GFJ2, with potential applications in the bioremediation of environments contaminated by phenylurea herbicides. Full article
(This article belongs to the Special Issue Microbial Biocatalysis and Biodegradation 2.0)
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20 pages, 3421 KiB  
Article
Enhancing Benzo[a]pyrene Degradation by Pantoea dispersa MSC14 through Biostimulation with Sodium Gluconate: Insights into Mechanisms and Molecular Regulation
by La Lai, Shuqi Li, Shaoping Zhang, Manchun Liu, Lianwei Xia, Yuan Ren and Tangbing Cui
Microorganisms 2024, 12(3), 592; https://doi.org/10.3390/microorganisms12030592 - 15 Mar 2024
Cited by 3 | Viewed by 1477
Abstract
We investigated biostimulation as an effective strategy for enhancing the degradation efficiency of recalcitrant organic compounds, with MSC14 (a novel polycyclic aromatic hydrocarbon degrading bacterium Pantoea dispersa MSC14) as the study material. Here, we investigated the impact of sodium gluconate on MSC14-mediated degradation [...] Read more.
We investigated biostimulation as an effective strategy for enhancing the degradation efficiency of recalcitrant organic compounds, with MSC14 (a novel polycyclic aromatic hydrocarbon degrading bacterium Pantoea dispersa MSC14) as the study material. Here, we investigated the impact of sodium gluconate on MSC14-mediated degradation of B[a]p. This study focused on the application of sodium gluconate, a biostimulant, on MSC14, targeting Benzo[a]pyrene (B[a]p) as the model pollutant. In this study, the novel PAHs-degrading bacterium P. dispersa MSC14 demonstrated the capability to degrade 24.41% of B[a]p after 4 days. The addition of the selected sodium gluconate stimulant at a concentration of 4 g/L stimulated MSC14 to degrade 54.85% of B[a]p after 16 h. Intermediate metabolites were analyzed using gas chromatography-mass spectrometry to infer the degradation pathway. The findings indicated that sodium gluconate promoted the intracellular transport of B[a]p by MSC14, along with the secretion of biosurfactants, enhancing emulsification and solubilization capabilities for improved B[a]p dissolution and degradation. Further analysis through transmission electron microscopy (TEM) and scanning electron microscopy (SEM) revealed the formation of a biofilm by MSC14 and an increase in flagella as a response to B[a]p stress. Transcriptome profiling elucidated the interplay of quorum sensing systems, chemotaxis systems, and flagellar systems in the degradation mechanism. Additionally, the study uncovered the molecular basis of B[a]p transport, degradation pathways, metabolic changes, and genetic regulation. In summary, the addition of sodium gluconate promotes the degradation of B[a]p by P. dispersa MSC14, offering the advantages of being rapid, efficient, and cost-effective. This research provides an economically viable approach for the remediation of petroleum hydrocarbon pollution, with broad potential applications. Full article
(This article belongs to the Special Issue Microbial Biocatalysis and Biodegradation 2.0)
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13 pages, 3229 KiB  
Article
Biodegradation of Gossypol by Aspergillus terreus-YJ01
by Yao Jiang, Xinyue Du, Qianqian Xu, Chunhua Yin, Haiyang Zhang, Yang Liu, Xiaolu Liu and Hai Yan
Microorganisms 2023, 11(9), 2148; https://doi.org/10.3390/microorganisms11092148 - 24 Aug 2023
Cited by 1 | Viewed by 1325
Abstract
Gossypol, generally found in the roots, stems, leaves, and, especially, the seeds of cotton plants, is highly toxic to animals and humans, which inhibits the use of cotton stalks as a feed resource. Here, a promising fungal strain for biodegrading gossypol was successfully [...] Read more.
Gossypol, generally found in the roots, stems, leaves, and, especially, the seeds of cotton plants, is highly toxic to animals and humans, which inhibits the use of cotton stalks as a feed resource. Here, a promising fungal strain for biodegrading gossypol was successfully isolated from the soil of cotton stalk piles in Xinjiang Province, China, and identified as Aspergillus terreus-YJ01 with the analysis of ITS. Initial gossypol of 250 mg·L−1 could be removed by 97% within 96 h by YJ01, and initial gossypol of 150 mg·L−1 could also be catalyzed by 98% or 99% within 36 h by the intracellular or extracellular crude enzymes of YJ01. Sucrose and sodium nitrate were found to be the optimal carbon and nitrogen sources for the growth of YJ01, and the optimal initial pH and inoculum size for the growth of YJ01 were 6.0 and 1%, respectively. To further elucidate the mechanisms underlying gossypol biodegradation by YJ01, the draft genome of YJ01 was sequenced using Illumina HiSeq, which is 31,566,870 bp in length with a GC content of 52.27% and a total of 9737 genes. Eight genes and enzymes were predicted to be involved in gossypol biodegradation. Among them, phosphoglycerate kinase, citrate synthase, and other enzymes are related to the energy supply process. With sufficient energy, β-1, 4-endo-xylanase may achieve the purpose of biodegrading gossypol. The findings of this study provide valuable insights into both the basic research and the application of A. terreus-YJ01 in the biodegradation of gossypol in cotton stalks. Full article
(This article belongs to the Special Issue Microbial Biocatalysis and Biodegradation 2.0)
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12 pages, 4421 KiB  
Article
Combinatory Library of Microorganisms in the Selection of Reductive Activity Applied to a Ketone Mixture: Unexpected Highlighting of an Enantioselective Oxidative Activity
by Sofiane Ali Rachedi, Maximillien Genest, Stéphane Mann and Didier Buisson
Microorganisms 2023, 11(6), 1415; https://doi.org/10.3390/microorganisms11061415 - 27 May 2023
Viewed by 1116
Abstract
Biocatalytic processes are increasingly used in organic synthesis for the preparation of targeted molecules or the generation of molecular diversity. The search for the biocatalyst is often the bottleneck in the development of the process. We described a combinatorial approach for the selection [...] Read more.
Biocatalytic processes are increasingly used in organic synthesis for the preparation of targeted molecules or the generation of molecular diversity. The search for the biocatalyst is often the bottleneck in the development of the process. We described a combinatorial approach for the selection of active strains from a library of microorganisms. In order to show the potential of the method we applied it to a mixture of substrates. We were able to select yeast strains capable of producing enantiopure alcohol from corresponding ketones with very few tests and highlight tandem reaction sequences involving several microorganisms. We demonstrate an interest in the kinetic study and the importance of incubation conditions. This approach is a promising tool for generating new products. Full article
(This article belongs to the Special Issue Microbial Biocatalysis and Biodegradation 2.0)
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Review

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16 pages, 1528 KiB  
Review
The Role of Dioxygen in Microbial Bio-Oxygenation: Challenging Biochemistry, Illustrated by a Short History of a Long Misunderstood Enzyme
by Andrew Willetts
Microorganisms 2024, 12(2), 389; https://doi.org/10.3390/microorganisms12020389 - 15 Feb 2024
Viewed by 953
Abstract
A Special Issue of Microorganisms devoted to ‘Microbial Biocatalysis and Biodegradation’ would be incomplete without some form of acknowledgement of the many important roles that dioxygen-dependent enzymes (principally mono- and dioxygenases) play in relevant aspects of bio-oxygenation. This is reflected by the multiple [...] Read more.
A Special Issue of Microorganisms devoted to ‘Microbial Biocatalysis and Biodegradation’ would be incomplete without some form of acknowledgement of the many important roles that dioxygen-dependent enzymes (principally mono- and dioxygenases) play in relevant aspects of bio-oxygenation. This is reflected by the multiple strategic roles that dioxygen -dependent microbial enzymes play both in generating valuable synthons for chemoenzymatic synthesis and in facilitating reactions that help to drive the global geochemical carbon cycle. A useful insight into this can be gained by reviewing the evolution of the current status of 2,5-diketocamphane 1,2-monooxygenase (EC 1.14.14.108) from (+)-camphor-grown Pseudomonas putida ATCC 17453, the key enzyme that promotes the initial ring cleavage of this natural bicyclic terpene. Over the last sixty years, the perceived nature of this monooxygenase has transmogrified significantly. Commencing in the 1960s, extensive initial studies consistently reported that the enzyme was a monomeric true flavoprotein dependent on both FMNH2 and nonheme iron as bound cofactors. However, over the last decade, all those criteria have changed absolutely, and the enzyme is currently acknowledged to be a metal ion-independent homodimeric flavin-dependent two-component mono-oxygenase deploying FMNH2 as a cosubstrate. That transition is a paradigm of the ever evolving nature of scientific knowledge. Full article
(This article belongs to the Special Issue Microbial Biocatalysis and Biodegradation 2.0)
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30 pages, 931 KiB  
Review
Engineering the Metabolic Landscape of Microorganisms for Lignocellulosic Conversion
by Julián Mario Peña-Castro, Karla M. Muñoz-Páez, Paula N. Robledo-Narvaez and Edgar Vázquez-Núñez
Microorganisms 2023, 11(9), 2197; https://doi.org/10.3390/microorganisms11092197 - 31 Aug 2023
Cited by 6 | Viewed by 2153
Abstract
Bacteria and yeast are being intensively used to produce biofuels and high-added-value products by using plant biomass derivatives as substrates. The number of microorganisms available for industrial processes is increasing thanks to biotechnological improvements to enhance their productivity and yield through microbial metabolic [...] Read more.
Bacteria and yeast are being intensively used to produce biofuels and high-added-value products by using plant biomass derivatives as substrates. The number of microorganisms available for industrial processes is increasing thanks to biotechnological improvements to enhance their productivity and yield through microbial metabolic engineering and laboratory evolution. This is allowing the traditional industrial processes for biofuel production, which included multiple steps, to be improved through the consolidation of single-step processes, reducing the time of the global process, and increasing the yield and operational conditions in terms of the desired products. Engineered microorganisms are now capable of using feedstocks that they were unable to process before their modification, opening broader possibilities for establishing new markets in places where biomass is available. This review discusses metabolic engineering approaches that have been used to improve the microbial processing of biomass to convert the plant feedstock into fuels. Metabolically engineered microorganisms (MEMs) such as bacteria, yeasts, and microalgae are described, highlighting their performance and the biotechnological tools that were used to modify them. Finally, some examples of patents related to the MEMs are mentioned in order to contextualize their current industrial use. Full article
(This article belongs to the Special Issue Microbial Biocatalysis and Biodegradation 2.0)
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