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Microorganisms
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Environment Microorganisms and Their Enzymes with Biotechnological Application, 2nd Edition
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Environment Microorganisms and Their Enzymes with Biotechnological Application, 2nd Edition

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

Deadline for manuscript submissions: 31 January 2025 | Viewed by 5387

Special Issue Editor

Prof. Dr. Myung-Ji Seo

E-Mail Website
Guest Editor
Division of Bioengineering, Incheon National University, Incheon 22012, Republic of Korea
Interests: microbiology; fermentation; antioxidants; carotenoid; alkaloid; genomics; biological chemistry; microbial biotechnology; enzyme characterization; natural product biosynthesis
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

This Special Issue is a continuation of the Special Issue "Environment Microorganisms and Their Enzymes with Biotechnological Application".

Microorganisms present in very diverse environmental habitats, even though so extreme conditions, play a crucial role in ecosystem function in nature. In addition, microbial metabolites are responsible for the numerous interactions between the environment and microorganisms themselves with recruiting the dynamics of specific ecosystems. Microorganisms are also valuable bioresources for the generation of useful biomaterials and the degradation of harmful materials looking from the viewpoint of human life.

Enzymes have been considered to be catalysts playing an important role in biochemical and metabolic reactions. Especially, microbial enzymes have been more highlighted compared to plants and animals, due to the efficient securement of massive microorganisms as sources of enzymes and the easy manipulation by genetic tools employed in microbial factories. Therefore, the microbial enzymes have been applied to diverse biotechnological industries including white (industrial) as well as red (medical) and green (agricultural) biotechnologies. In particular, microbial enzymes are indispensable bioresources to the production of industrially valuable biomaterials and the reduction of the environmental impact of industrial processes.

This Special Issue focuses especially, but not only, on the following sub-topics:

  • Isolation and characterization of novel microorganisms (bacterial, archaea, fungi, etc.) with potential biotechnological features based on genomic analysis
  • Isolation and functional characterization of novel or useful microbial enzymes for the potential biotechnological application
  • Production of biomaterials generated from the fermentation of wild-type microorganisms and/or recombinants harboring their interested enzymes
  • Bioremediation and biodegradation of plastics, pollutants, and contaminants
  • Enzyme profiling involved in the microbial responses to environmental changes (microbial community together with enzyme profiling)

Review papers, as well as research articles, are welcomed.

Prof. Dr. Myung-Ji Seo
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

  • microorganism
  • enzyme
  • biotechnology
  • biosynthesis
  • bioremediation
  • biodegradation
  • characterization
  • isolation
  • fermentation
  • expression

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Published Papers (4 papers)

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Research

15 pages, 2454 KiB  
Article
Halophilic Pectinase-Producing Bacteria from Arthrocnemum macrostachyum Rhizosphere: Potential for Fruit–Vegetable Juice Processing
by Amal S. Alswat, Ohud Muslat Alharthy, Seham Saeed Alzahrani and Seham Sater Alhelaify
Microorganisms 2024, 12(11), 2162; https://doi.org/10.3390/microorganisms12112162 - 26 Oct 2024
Viewed by 944
Abstract
This study aimed to isolate salt-tolerant pectinolytic bacteria from the rhizosphere of a salt marsh plant and utilize their pectinases for the clarification of detox juice preparation. Sixteen halophilic bacterial strains were isolated from the rhizospheric soil of Arthrocnemum macrostachyum. The isolates [...] Read more.
This study aimed to isolate salt-tolerant pectinolytic bacteria from the rhizosphere of a salt marsh plant and utilize their pectinases for the clarification of detox juice preparation. Sixteen halophilic bacterial strains were isolated from the rhizospheric soil of Arthrocnemum macrostachyum. The isolates were screened for pectinase activity, and two strains, ASA21 and ASA29, exhibited the highest pectinase production in the presence of 2.5% NaCl, reaching 13.3 and 14.1 IU mL−1, respectively. The strains were identified as Bacillus paralicheniformis and Paenibacillus sp. by 16S rDNA sequencing and phylogenetic analysis. Growth kinetics and pectinase production studies revealed that both strains produced pectinase during the log phase, with ASA29 demonstrating higher growth and pectinase titers. The pectinase from ASA29 exhibited enhanced activity in the presence of 3% NaCl. The pectinases from both strains were applied for the clarification of detox juice prepared from beetroot, carrots, and apples. The use of 20 IU mL−1 pectinase from ASA29 for 2–3 h yielded > 96% juice with high total phenolic content and antioxidant activities. This study highlights the potential of salt-tolerant pectinolytic bacteria from the rhizosphere for biotechnological applications, particularly in the clarification of juices with high salt content. Full article
(This article belongs to the Special Issue Environment Microorganisms and Their Enzymes with Biotechnological Application, 2nd Edition)
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13 pages, 1651 KiB  
Article
Enrichment of Aquatic Xylan-Degrading Microbial Communities
by Aline Lucie Odette Gaenssle, Salvador Bertran-Llorens, Peter Joseph Deuss and Edita Jurak
Microorganisms 2024, 12(8), 1715; https://doi.org/10.3390/microorganisms12081715 - 20 Aug 2024
Viewed by 892
Abstract
The transition towards a sustainable society involves the utilization of lignocellulosic biomass as a renewable feedstock for materials, fuel, and base chemicals. Lignocellulose consists of cellulose, hemicellulose, and lignin, forming a complex, recalcitrant matrix where efficient enzymatic saccharification is pivotal for accessing its [...] Read more.
The transition towards a sustainable society involves the utilization of lignocellulosic biomass as a renewable feedstock for materials, fuel, and base chemicals. Lignocellulose consists of cellulose, hemicellulose, and lignin, forming a complex, recalcitrant matrix where efficient enzymatic saccharification is pivotal for accessing its valuable components. This study investigated microbial communities from brackish Lauwersmeer Lake, in The Netherlands, as a potential source of xylan-degrading enzymes. Environmental sediment samples were enriched with wheat arabinoxylan (WAX) and beechwood glucuronoxylan (BEX), with enrichment on WAX showing higher bacterial growth and complete xylan degradation compared to BEX. Metagenomic sequencing revealed communities consisting almost entirely of bacteria (>99%) and substantial shifts in composition during the enrichment. The first generation of seven-day enrichments on both xylans led to a high accumulation of Gammaproteobacteria (49% WAX, 84% BEX), which were largely replaced by Alphaproteobacteria (42% WAX, 69% BEX) in the fourth generation. Analysis of the protein function within the sequenced genomes showed elevated levels of genes associated with the carbohydrate catabolic process, specifically targeting arabinose, xylose, and xylan, indicating an adaptation to the primary monosaccharides present in the carbon source. The data open up the possibility of discovering novel xylan-degrading proteins from other sources aside from the thoroughly studied Bacteroidota. Full article
(This article belongs to the Special Issue Environment Microorganisms and Their Enzymes with Biotechnological Application, 2nd Edition)
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17 pages, 9295 KiB  
Article
Insights into Chitin-Degradation Potential of Shewanella khirikhana JW44 with Emphasis on Characterization and Function of a Chitinase Gene SkChi65
by Ling Wang, Ming Xue, Rui Yan, Jiawei Xue, Zhipeng Lu and Chongqing Wen
Microorganisms 2024, 12(4), 774; https://doi.org/10.3390/microorganisms12040774 - 11 Apr 2024
Viewed by 1447
Abstract
Chitin, a polymer of β-1,4-linked N-acetylglucosamine (GlcNAc), can be degraded into valuable oligosaccharides by various chitinases. In this study, the genome of Shewanella khirikhana JW44, displaying remarkable chitinolytic activity, was investigated to understand its chitin-degradation potential. A chitinase gene SkChi65 from this [...] Read more.
Chitin, a polymer of β-1,4-linked N-acetylglucosamine (GlcNAc), can be degraded into valuable oligosaccharides by various chitinases. In this study, the genome of Shewanella khirikhana JW44, displaying remarkable chitinolytic activity, was investigated to understand its chitin-degradation potential. A chitinase gene SkChi65 from this strain was then cloned, expressed, and purified to characterize its enzymatic properties and substrate hydrolysis. Genome analysis showed that, of the 14 genes related to chitin utilization in JW44, six belonged to glycoside hydrolase (GH) families because of their functional domains for chitin binding and catalysis. The recombinant chitinase SkChi65, consisting of 1129 amino acids, was identified as a member of the GH18 family and possessed two chitin-binding domains with a typical motif of [A/N]KWWT[N/S/Q] and one catalytic domain with motifs of DxxDxDxE, SxGG, YxR, and [E/D]xx[V/I]. SkChi65 was heterologously expressed as an active protein of 139.95 kDa best at 37 °C with 1.0 mM isopropyl-β-d-thiogalactopyranoside induction for 6 h. Purified SkChi65 displayed high stability over the ranges of 30–50 °C and pH 5.5–8.0 with optima at 40 °C and pH 7.0. The kinetic parameters Km, Vmax, and kcat of SkChi65 towards colloidal chitin were 27.2 μM, 299.2 μMs−1, and 10,203 s−1, respectively. In addition to colloidal chitin, SkChi65 showed high activity towards glycol chitosan and crystalline chitin. After analysis by thin-layer chromatography, the main products were N,N’-diacetylchitobiose, and GlcNAc with (GlcNAc)2–6 used as substrates. Collectively, SkChi65 could exhibit both exo- and endochitinase activities towards diverse substrates, and strain JW44 has a high potential for industrial application with an excellent capacity for chitin bioconversion. Full article
(This article belongs to the Special Issue Environment Microorganisms and Their Enzymes with Biotechnological Application, 2nd Edition)
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14 pages, 1463 KiB  
Article
Characterization of a Novel Hyperthermophilic GH1 β-Glucosidase from Acidilobus sp. and Its Application in the Hydrolysis of Soybean Isoflavone Glycosides
by Jinjian He, Yuying Li, Xihang Sun, Dinghui Zuo, Mansheng Wang, Xia Zheng, Pinglian Yu and Pengjun Shi
Microorganisms 2024, 12(3), 533; https://doi.org/10.3390/microorganisms12030533 - 7 Mar 2024
Cited by 2 | Viewed by 1430
Abstract
A putative β-glucosidase gene, BglAc, was amplified from Acidilobus sp. through metagenome database sampling from a hot spring in Yellowstone National Park. BglAc is composed of 485 amino acid residues and bioinformatics analysis showed that it belongs to the GH1 family of [...] Read more.
A putative β-glucosidase gene, BglAc, was amplified from Acidilobus sp. through metagenome database sampling from a hot spring in Yellowstone National Park. BglAc is composed of 485 amino acid residues and bioinformatics analysis showed that it belongs to the GH1 family of β-glucosidases. The gene was successfully expressed in Escherichia coli with a molecular weight of approximately 55.3 kDa. The purified recombinant enzyme showed the maximum activity using p-nitrophenyl-β-D-glucopyranoside (pNPG) as the substrate at optimal pH 5.0 and 100 °C. BglAc exhibited extraordinary thermostability, and its half-life at 90 °C was 6 h. The specific activity, Km, Vmax, and Kcat/Km of BglAc toward pNPG were 357.62 U mg−1, 3.41 mM, 474.0 μmol min−1·mg−1, and 122.7 s−1mM−1. BglAc exhibited the characteristic of glucose tolerance, and the inhibition constant Ki was 180.0 mM. Furthermore, a significant ethanol tolerance was observed, retaining 96% relative activity at 10% ethanol, and even 78% at 20% ethanol, suggesting BglAc as a promising enzyme for cellulose saccharification. BglAc also had a strong ability to convert the major soybean isoflavone glycosides (daidzin, genistin, and glycitin) into their corresponding aglycones. Overall, BglAc was actually a new β-glucosidase with excellent thermostability, ethanol tolerance, and glycoside hydrolysis ability, indicating its wide prospects for applications in the food industry, animal feed, and lignocellulosic biomass degradation. Full article
(This article belongs to the Special Issue Environment Microorganisms and Their Enzymes with Biotechnological Application, 2nd Edition)
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