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Microorganisms
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Environment Microorganisms and Their Enzymes with Biotechnological Application
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Environment Microorganisms and Their Enzymes with Biotechnological Application

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

Deadline for manuscript submissions: closed (30 July 2023) | Viewed by 14931

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,

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

Published Papers (10 papers)

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Editorial

Jump to: Research, Review

5 pages, 179 KiB  
Editorial
Editorial for the Special Issue: Environment Microorganisms and Their Enzymes with Biotechnological Application
by Myung-Ji Seo
Microorganisms 2024, 12(1), 204; https://doi.org/10.3390/microorganisms12010204 - 19 Jan 2024
Viewed by 930
Abstract
The ubiquitous nature of microorganisms demonstrates their ability to survive and thrive in diverse ecological settings, and their presence in extreme environments that approach the known limits of adaptable living confers importance to their role in those ecosystems [...] Full article
(This article belongs to the Special Issue Environment Microorganisms and Their Enzymes with Biotechnological Application)

Research

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15 pages, 2405 KiB  
Article
A Novel Carotenoid-Producing Bacterium, Paenibacillus aurantius sp. nov., Isolated from Korean Marine Environment
by Chi Young Hwang, Sung Man Seo, Eui-Sang Cho, Young-Do Nam, So-Lim Park, Seong-Il Lim and Myung-Ji Seo
Microorganisms 2023, 11(11), 2719; https://doi.org/10.3390/microorganisms11112719 - 07 Nov 2023
Cited by 2 | Viewed by 1131
Abstract
The novel bacterial strain MBLB1776T was isolated from marine mud in Uljin, the Republic of Korea. Cells were Gram-positive, spore-forming, non-motile, and non-flagellated rods. Growth was observed at a temperature range of 10–45 °C, pH range of 6.0–8.0, and NaCl concentrations of [...] Read more.
The novel bacterial strain MBLB1776T was isolated from marine mud in Uljin, the Republic of Korea. Cells were Gram-positive, spore-forming, non-motile, and non-flagellated rods. Growth was observed at a temperature range of 10–45 °C, pH range of 6.0–8.0, and NaCl concentrations of 0–4% (w/v). Phylogenetic analysis of the 16S rRNA gene sequence revealed that MBLB1776T belonged to the genus Paenibacillus and was closely related to Paenibacillus cavernae C4-5T (94.83% similarity). Anteiso-C15:0, iso-C16:0, C16:0, and iso-C15:0 were the predominant fatty acids. Menaquinone 7 was identified as the major isoprenoid quinone. The major polar lipids included diphosphatidylglycerol, phosphatidylglycerol, and phosphatidylethanolamine. Its whole genome was 6.3 Mb in size, with a G+C content of 55.8 mol%. Average nucleotide identity and in silico DNA–DNA hybridization values were below the species delineation threshold. Gene function analysis revealed the presence of a complete C30 carotenoid biosynthetic pathway. Intriguingly, MBLB1776T harbored carotenoid pigments, imparting an orange color to whole cells. Based on this comprehensive polyphasic taxonomy, the MBLB1776T strain represents a novel species within the genus Paenibacillus, for which the name Paenibacillus aurantius sp. nov is proposed. The type strain was MBLB1776T (=KCTC 43279T = JCM 34220T). This is the first report of a carotenoid-producing Paenibacillus sp. Full article
(This article belongs to the Special Issue Environment Microorganisms and Their Enzymes with Biotechnological Application)
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14 pages, 2663 KiB  
Article
Deionococcus proteotlycius Genomic Library Exploration Enhances Oxidative Stress Resistance and Poly-3-hydroxybutyrate Production in Recombinant Escherichia coli
by Seul-Ki Yang, Soyoung Jeong, Inwoo Baek, Jong-il Choi, Sangyong Lim and Jong-Hyun Jung
Microorganisms 2023, 11(9), 2135; https://doi.org/10.3390/microorganisms11092135 - 23 Aug 2023
Cited by 1 | Viewed by 1009
Abstract
Cell growth is inhibited by abiotic stresses during industrial processes, which is a limitation of microbial cell factories. Microbes with robust phenotypes are critical for its maximizing the yield of the target products in industrial biotechnology. Currently, there are several reports on the [...] Read more.
Cell growth is inhibited by abiotic stresses during industrial processes, which is a limitation of microbial cell factories. Microbes with robust phenotypes are critical for its maximizing the yield of the target products in industrial biotechnology. Currently, there are several reports on the enhanced production of industrial metabolite through the introduction of Deinococcal genes into host cells, which confers cellular robustness. Deinococcus is known for its unique genetic function thriving in extreme environments such as radiation, UV, and oxidants. In this study, we established that Deinococcus proteolyticus showed greater resistance to oxidation and UV-C than commonly used D. radiodurans. By screening the genomic library of D. proteolyticus, we isolated a gene (deipr_0871) encoding a response regulator, which not only enhanced oxidative stress, but also promoted the growth of the recombinant E. coli strain. The transcription analysis indicated that the heterologous expression of deipr_0871 upregulated oxidative-stress-related genes such as ahpC and sodA, and acetyl-CoA-accumulation-associated genes via soxS regulon. Deipr_0871 was applied to improve the production of the valuable metabolite, poly-3-hydroxybutyrate (PHB), in the synthetic E. coli strain, which lead to the remarkably higher PHB than the control strain. Therefore, the stress tolerance gene from D. proteolyticus should be used in the modification of E. coli for the production of PHB and other biomaterials Full article
(This article belongs to the Special Issue Environment Microorganisms and Their Enzymes with Biotechnological Application)
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12 pages, 2694 KiB  
Article
Degradation of Bisphenol A by Bacillus subtilis P74 Isolated from Traditional Fermented Soybean Foods
by Young Kyoung Park and Young-Wook Chin
Microorganisms 2023, 11(9), 2132; https://doi.org/10.3390/microorganisms11092132 - 22 Aug 2023
Cited by 1 | Viewed by 1148
Abstract
Bisphenol A (BPA), one of the most widely used plasticizers, is an endocrine-disrupting chemical that is released from plastic products. The aim of this study was to screen and characterize bacteria with excellent BPA-degrading abilities for application in foods. BPA degradation ability was [...] Read more.
Bisphenol A (BPA), one of the most widely used plasticizers, is an endocrine-disrupting chemical that is released from plastic products. The aim of this study was to screen and characterize bacteria with excellent BPA-degrading abilities for application in foods. BPA degradation ability was confirmed in 127 of 129 bacterial strains that were isolated from fermented soybean foods. Among the strains, B. subtilis P74, which showed the highest BPA degradation performance, degraded 97.2% of 10 mg/L of BPA within 9 h. This strain not only showed a fairly stable degradation performance (min > 88.2%) over a wide range of temperatures (30–45 °C) and pH (5.0–9.0) but also exhibited a degradation of 63% against high concentrations of BPA (80 mg/L). The metabolites generated during the degradation were analyzed using high-performance liquid chromatography–mass spectrometry, and predicted degradation pathways are tentatively proposed. Finally, the application of this strain to soybean fermentation was conducted to confirm its applicability in food. Full article
(This article belongs to the Special Issue Environment Microorganisms and Their Enzymes with Biotechnological Application)
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10 pages, 1838 KiB  
Article
Characterization of the Keratinolytic Activity of Three Streptomyces Strains and Impact of Their Co-Cultivation on This Activity
by Diego Martín-González, Sergio Bordel and Fernando Santos-Beneit
Microorganisms 2023, 11(5), 1109; https://doi.org/10.3390/microorganisms11051109 - 24 Apr 2023
Cited by 1 | Viewed by 1312
Abstract
In this study, we describe the characterization of three efficient chicken feather-degrading Streptomyces bacteria isolated from honeybee samples and assess the impact of their co-cultivation on this activity and antistaphylococcal activity. Streptomyces griseoaurantiacus AD2 was the strain showing the highest keratinolytic activity (4000 [...] Read more.
In this study, we describe the characterization of three efficient chicken feather-degrading Streptomyces bacteria isolated from honeybee samples and assess the impact of their co-cultivation on this activity and antistaphylococcal activity. Streptomyces griseoaurantiacus AD2 was the strain showing the highest keratinolytic activity (4000 U × mL−1), followed by Streptomyces albidoflavus AN1 and Streptomyces drozdowiczii AD1, which both generated approximately 3000 U × mL−1. Moreover, a consortium constituted of these three strains was able to use chicken feathers as its sole nutrient source and growth in such conditions led to a significant increase in antibiotic production. S. griseoaurantiacus AD2 was the only strain that exhibited weak antimicrobial activity against Staphylococcus aureus. UPLC analyses revealed that a significant number of peaks detected in the extracts of co-cultures of the three strains were missing in the extracts of individual cultures. In addition, the production of specialized metabolites, such as undecylprodigiosin and manumycin A, was clearly enhanced in co-culture conditions, in agreement with the results of the antimicrobial bioassays against S. aureus. Our results revealed the benefits of co-cultivation of these bacterial species in terms of metabolic wealth and antibiotic production. Our work could thus contribute to the development of novel microbial-based strategies to valorize keratin waste. Full article
(This article belongs to the Special Issue Environment Microorganisms and Their Enzymes with Biotechnological Application)
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12 pages, 674 KiB  
Article
Potential of Fungal Endophytes Isolated from Pasture Species in Spanish Dehesas to Produce Enzymes under Salt Conditions
by Carlos García-Latorre, Sara Rodrigo and Oscar Santamaría
Microorganisms 2023, 11(4), 908; https://doi.org/10.3390/microorganisms11040908 - 31 Mar 2023
Cited by 3 | Viewed by 1285
Abstract
Endophytic fungi have been found to produce a wide range of extracellular enzymes, which are increasingly in demand for their industrial applications. Different by-products from the agrifood industry could be used as fungal growth substrates for the massive production of these enzymes, specifically [...] Read more.
Endophytic fungi have been found to produce a wide range of extracellular enzymes, which are increasingly in demand for their industrial applications. Different by-products from the agrifood industry could be used as fungal growth substrates for the massive production of these enzymes, specifically as a way to revalorize them. However, such by-products often present unfavorable conditions for the microorganism’s growth, such as high salt concentrations. Therefore, the objective of the present study was to evaluate the potential of eleven endophytic fungi—which were isolated from plants growing in a harsh environment, specifically, from the Spanish dehesas—for the purposes of the in vitro production of six enzymes (i.e., amylase, lipase, protease, cellulase, pectinase and laccase) under both standard and salt-amended conditions. Under standard conditions, the studied endophytes produced between two and four of the six enzymes evaluated. In most of the producer fungal species, this enzymatic activity was relatively maintained when NaCl was added to the medium. Among the isolates evaluated, Sarocladium terricola (E025), Acremonium implicatum (E178), Microdiplodia hawaiiensis (E198), and an unidentified species (E586) were the most suitable candidates for the massive production of enzymes by using growth substrates with saline properties (such as those found in the many by-products from the agrifood industry). This study should be considered an initial approach by which to further study the identification of these compounds as well as to develop the optimization of their production by directly using those residues. Full article
(This article belongs to the Special Issue Environment Microorganisms and Their Enzymes with Biotechnological Application)
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14 pages, 3290 KiB  
Article
The Impact of Microorganisms on the Performance of Linseed Oil and Tung Tree Oil Impregnated Composites Made of Hemp Shives and Corn Starch
by Dovilė Vasiliauskienė, Giedrius Balčiūnas, Renata Boris, Agnė Kairytė and Jaunius Urbonavičius
Microorganisms 2023, 11(2), 477; https://doi.org/10.3390/microorganisms11020477 - 14 Feb 2023
Cited by 4 | Viewed by 1195
Abstract
In this study, the performance characteristics of hemp shives impregnated with linseed oil and tung tree oil (HS)- and corn starch (CS)-based biocomposites containing flame retardants were evaluated before and after treatment with the mixture of bacterium Pseudomonas putida and fungus Rhizopus oryzae [...] Read more.
In this study, the performance characteristics of hemp shives impregnated with linseed oil and tung tree oil (HS)- and corn starch (CS)-based biocomposites containing flame retardants were evaluated before and after treatment with the mixture of bacterium Pseudomonas putida and fungus Rhizopus oryzae. Enzymatic activities and physical-mechanical properties such as water absorption, thickness swelling, compressive strength, and thermal conductivity were tested to evaluate the suitability of selected composites for thermal insulation purposes. In addition, electron microscopy was used to investigate the impact of microorganisms on the microstructure of the material. It was determined that the type of oil used for impregnation significantly affects the properties of biocomposites after 6 months of incubation with mixture of bacterium P. putida and fungus Rh. oryzae. Biocomposites impregnated with linseed oil and after treatment with a mixture of microorganisms had cellulase activity of 25 U/mL, endo β-1-4-glucanase activity of 26 U/mL, lipase activity of 101 U/mL, only a 10% decrease in compressive strength, 50% higher short-term water absorption, unchanged swelling in thickness, and slightly decreased thermal conductivity compared to control biocomposites. At the same time, biocomposites with tung tree oil had a much more pronounced deterioration of the properties tested, cellulase activity of 28 U/mL, endo β-1-4-glucanase activity of 37 U/mL, lipase activity of 91 U/mL, two times lower compressive strength and two times higher short-term water absorption, 2.5 times greater thickness swelling, and a slightly increased thermal conductivity. We conclude that linseed oil provides better protection against the action of microorganisms compared to impregnation with tung tree oil. Full article
(This article belongs to the Special Issue Environment Microorganisms and Their Enzymes with Biotechnological Application)
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18 pages, 2828 KiB  
Article
Bioprospecting for Novel Bacterial Sources of Hydrolytic Enzymes and Antimicrobials in the Romanian Littoral Zone of the Black Sea
by Robert Ruginescu, Paris Lavin, Lavinia Iancu, Selma Menabit and Cristina Purcarea
Microorganisms 2022, 10(12), 2468; https://doi.org/10.3390/microorganisms10122468 - 14 Dec 2022
Cited by 3 | Viewed by 1709
Abstract
Marine microorganisms have evolved a large variety of metabolites and biochemical processes, providing great opportunities for biotechnologies. In the search for new hydrolytic enzymes and antimicrobial compounds with enhanced characteristics, the current study explored the diversity of cultured and uncultured marine bacteria in [...] Read more.
Marine microorganisms have evolved a large variety of metabolites and biochemical processes, providing great opportunities for biotechnologies. In the search for new hydrolytic enzymes and antimicrobial compounds with enhanced characteristics, the current study explored the diversity of cultured and uncultured marine bacteria in Black Sea water from two locations along the Romanian coastline. Microbial cell density in the investigated samples varied between 65 and 12.7 × 103 CFU·mL−1. The total bacterial community identified by Illumina sequencing of 16S rRNA gene comprised 185 genera belonging to 46 classes, mainly Gammaproteobacteria, Alphaproteobacteria, Flavobacteriia, and 24 phyla. The 66 bacterial strains isolated on seawater-based culture media belonged to 33 genera and showed variable growth temperatures, growth rates, and salt tolerance. A great fraction of these strains, including Pseudoalteromonas and Flavobacterium species, produced extracellular proteases, lipases, and carbohydrases, while two strains belonging to the genera Aquimarina and Streptomyces exhibited antimicrobial activity against human pathogenic bacteria. This study led to a broader view on the diversity of microbial communities in the Black Sea, and provided new marine strains with hydrolytic and antimicrobial capabilities that may be exploited in industrial and pharmaceutical applications. Full article
(This article belongs to the Special Issue Environment Microorganisms and Their Enzymes with Biotechnological Application)
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20 pages, 3836 KiB  
Article
Potential Probiotic Properties of Exopolysaccharide-Producing Lacticaseibacillus paracasei EPS DA-BACS and Prebiotic Activity of Its Exopolysaccharide
by Min-Gyu Lee, Huijin Joeng, Jaein Shin, Suin Kim, Chaeeun Lee, Youngbo Song, Byung-Hoo Lee, Hyoung-Geun Park, Tae-Ho Lee, Hai-Hua Jiang, Young-Sun Han, Bong-Gyeong Lee, Ho-Jin Lee, Min-Ju Park, Yun-Ju Jun and Young-Seo Park
Microorganisms 2022, 10(12), 2431; https://doi.org/10.3390/microorganisms10122431 - 08 Dec 2022
Cited by 7 | Viewed by 2734
Abstract
Exopolysaccharide (EPS)-producing Lacticaseibacillus paracasei EPS DA-BACS was isolated from healthy human feces and its probiotic properties, as well as the structure and prebiotic activity of the EPS from this strain were examined. EPS from L. paracasei EPS DA-BACS had a ropy phenotype, which [...] Read more.
Exopolysaccharide (EPS)-producing Lacticaseibacillus paracasei EPS DA-BACS was isolated from healthy human feces and its probiotic properties, as well as the structure and prebiotic activity of the EPS from this strain were examined. EPS from L. paracasei EPS DA-BACS had a ropy phenotype, which is known to have potential health benefits and is identified as loosely cell-bounded glucomannan-type EPS with a molecular size of 3.7 × 106 Da. EPS promoted the acid tolerance of L. paracasei EPS DA-BACS and provided cells with tolerance to gastrointestinal stress. The purified EPS showed growth inhibitory activity against Clostridium difficile. L. paracasei EPS DA-BACS cells completely inhibited the growth of Bacillus subtilis, Pseudomonas aeruginosa, and Aspergillus brasiliensis, as well as showed high growth inhibitory activity against Staphylococcus aureus and Escherichia coli. Treatment of lipopolysaccharide-stimulated RAW 264.7 cells with heat-killed L. paracasei EPS DA-BACS cells led to a decrease in the production of nitric oxide, indicating the anti-inflammatory activity of L. paracasei EPS DA-BACS. Purified EPS promoted the growth of Lactobacillus gasseri, Bifidobacterium bifidum, B. animalis, and B. faecale which showed high prebiotic activity. L. paracasei EPS DA-BACS harbors no antibiotic resistance genes or virulence factors. Therefore, L. paracasei EPS DA-BACS exhibits anti-inflammatory and antimicrobial activities with high gut adhesion ability and gastrointestinal tolerance and can be used as a potential probiotic. Full article
(This article belongs to the Special Issue Environment Microorganisms and Their Enzymes with Biotechnological Application)
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Review

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16 pages, 1766 KiB  
Review
Soil Thermophiles and Their Extracellular Enzymes: A Set of Capabilities Able to Provide Significant Services and Risks
by Juan M. Gonzalez, Margarida M. Santana, Enrique J. Gomez and José A. Delgado
Microorganisms 2023, 11(7), 1650; https://doi.org/10.3390/microorganisms11071650 - 24 Jun 2023
Cited by 1 | Viewed by 1241
Abstract
During this century, a number of reports have described the potential roles of thermophiles in the upper soil layers during high-temperature periods. This study evaluates the capabilities of these microorganisms and proposes some potential consequences and risks associated with the activity of soil [...] Read more.
During this century, a number of reports have described the potential roles of thermophiles in the upper soil layers during high-temperature periods. This study evaluates the capabilities of these microorganisms and proposes some potential consequences and risks associated with the activity of soil thermophiles. They are active in organic matter mineralization, releasing inorganic nutrients (C, S, N, P) that otherwise remain trapped in the organic complexity of soil. To process complex organic compounds in soils, these thermophiles require extracellular enzymes to break down large polymers into simple compounds, which can be incorporated into the cells and processed. Soil thermophiles are able to adapt their extracellular enzyme activities to environmental conditions. These enzymes can present optimum activity under high temperatures and reduced water content. Consequently, these microorganisms have been shown to actively process and decompose substances (including pollutants) under extreme conditions (i.e., desiccation and heat) in soils. While nutrient cycling is a highly beneficial process to maintain soil service quality, progressive warming can lead to excessive activity of soil thermophiles and their extracellular enzymes. If this activity is too high, it may lead to reduction in soil organic matter, nutrient impoverishment and to an increased risk of aridity. This is a clear example of a potential effect of future predicted climate warming directly caused by soil microorganisms with major consequences for our understanding of ecosystem functioning, soil health and the risk of soil aridity. Full article
(This article belongs to the Special Issue Environment Microorganisms and Their Enzymes with Biotechnological Application)
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