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Microorganisms
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Feature Papers in Microbial Biotechnology
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Feature Papers in Microbial Biotechnology

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

Deadline for manuscript submissions: closed (31 May 2023) | Viewed by 28276

Special Issue Editor

Prof. Dr. Peter Neubauer

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Collection Editor
Department of Bioprocess Engineering, Technische Universität Berlin, Ackerstraβe 76, ACK24, D-13355 Berlin, Germany
Interests: bioprocess development; Escherichia coli physiology; recombinant proteins; cocultivation; fed-batch; continuous culture
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

As follows from the title, this Topical Collection “Feature Papers in Microbial Biotechnology” aims to collect high-quality research articles, short communications, and review articles in all the fields of microbial biotechnology. Since the aim of this Topical Collection is to illustrate, through selected works, frontier research in microbial biotechnology, we encourage Editorial Board Members of the Microbial Biotechnology Section of Microorganisms to contribute papers reflecting the latest progress in their research field, or to invite relevant experts and colleagues to do so.

Prof. Dr. Peter Neubauer
Collection Editor

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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.

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Published Papers (7 papers)

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Research

14 pages, 4592 KiB  
Article
Impact of Organic Carbons Addition on the Enrichment Culture of Nitrifying Biofloc from Aquaculture Water: Process, Efficiency, and Microbial Community
by Jiaqi Wu, Wujie Xu, Yu Xu, Haochang Su, Xiaojuan Hu, Yucheng Cao, Jianshe Zhang and Guoliang Wen
Microorganisms 2024, 12(4), 703; https://doi.org/10.3390/microorganisms12040703 - 30 Mar 2024
Cited by 1 | Viewed by 1256
Abstract
In this study, we developed a rapid and effective method for enriching the culture of nitrifying bioflocs (NBF) from aquacultural brackish water. The self-designed mixotrophic mediums with a single or mixed addition of sodium acetate, sodium citrate, and sucrose were used to investigate [...] Read more.
In this study, we developed a rapid and effective method for enriching the culture of nitrifying bioflocs (NBF) from aquacultural brackish water. The self-designed mixotrophic mediums with a single or mixed addition of sodium acetate, sodium citrate, and sucrose were used to investigate the enrichment process and nitrification efficiency of NBF in small-scale reactors. The results showed that NBF with an MLVSSs from 1170.4 mg L−1 to 2588.0 mg L−1 were successfully enriched in a period of less than 16 days. The citrate group performed the fastest enrichment time of 10 days, while the sucrose group had the highest biomass of 2588.0 ± 384.7 mg L−1. In situ testing showed that the highest nitrification efficiency was achieved in the citrate group, with an ammonia oxidation rate of 1.45 ± 0.34 mg N L−1 h−1, a net nitrification rate of 2.02 ± 0.20 mg N L−1 h−1, and a specific nitrification rate of 0.72 ± 0.14 mg N g−1 h−1. Metagenomic sequencing revealed that Nitrosomonas (0.0~1.0%) and Nitrobacter (10.1~26.5%) were dominant genera for AOB and NOB, respectively, both of which had the highest relative abundances in the citrate group. Linear regression analysis further demonstrated significantly positive linear relations between nitrification efficiencies and nitrifying bacterial genera and gene abundance in NBF. The results of this study provide an efficient enrichment culture method of NBF for the operation of biofloc technology aquaculture systems, which will further promote its wide application in modern intensive aquaculture. Full article
(This article belongs to the Special Issue Feature Papers in Microbial Biotechnology)
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28 pages, 5385 KiB  
Article
Cultivable Bacterial Communities in Brines from Perennially Ice-Covered and Pristine Antarctic Lakes: Ecological and Biotechnological Implications
by Carmen Rizzo, Antonella Conte, Maurizio Azzaro, Maria Papale, Alessandro C. Rappazzo, Dario Battistel, Marco Roman, Angelina Lo Giudice and Mauro Guglielmin
Microorganisms 2020, 8(6), 819; https://doi.org/10.3390/microorganisms8060819 - 29 May 2020
Cited by 16 | Viewed by 4415
Abstract
The diversity and biotechnological potentialities of bacterial isolates from brines of three Antarctic lakes of the Northern Victoria Land (namely Boulder Clay and Tarn Flat areas) were first explored. Cultivable bacterial communities were analysed mainly in terms of bacterial response to contaminants (i.e., [...] Read more.
The diversity and biotechnological potentialities of bacterial isolates from brines of three Antarctic lakes of the Northern Victoria Land (namely Boulder Clay and Tarn Flat areas) were first explored. Cultivable bacterial communities were analysed mainly in terms of bacterial response to contaminants (i.e., antibiotics and heavy metals) and oxidation of contaminants (i.e., aliphatic and aromatic hydrocarbons and polychlorobiphenyls). Moreover, the biosynthesis of biomolecules (antibiotics, extracellular polymeric substances and enzymes) with applications for human health and environmental protection was assayed. A total of 74 and 141 isolates were retrieved from Boulder Clay and Tarn Flat brines, respectively. Based on 16S rRNA gene sequence similarities, bacterial isolates represented three phyla, namely Proteobacteria (i.e., Gamma- and Alphaproteobacteria), Bacteroidetes and Actinobacteria, with differences encountered among brines. At genus level, Rhodobacter, Pseudomonas, Psychrobacter and Leifsonia members were dominant. Results obtained from this study on the physiological and enzymatic features of cold-adapted isolates from Antarctic lake brines provide interesting prospects for possible applications in the biotechnological field through future targeted surveys. Finally, findings on contaminant occurrence and bacterial response suggest that bacteria might be used as bioindicators for tracking human footprints in these remote polar areas. Full article
(This article belongs to the Special Issue Feature Papers in Microbial Biotechnology)
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14 pages, 2391 KiB  
Article
Improvement of Saccharification and Delignification Efficiency of Trichoderma reesei Rut-C30 by Genetic Bioengineering
by Raja Mohan Gopalakrishnan, Tamilvendan Manavalan, Janani Ramesh, Kalaichelvan Puthupalayam Thangavelu and Klaus Heese
Microorganisms 2020, 8(2), 159; https://doi.org/10.3390/microorganisms8020159 - 23 Jan 2020
Cited by 14 | Viewed by 3805
Abstract
Trichoderma reesei produces various saccharification enzymes required for biomass degradation. However, the lack of an effective lignin-degrading enzyme system reduces the species’ efficiency in producing fermentable sugars and increases the pre-treatment costs for biofuel production. In this study, we heterologously expressed the Ganoderma [...] Read more.
Trichoderma reesei produces various saccharification enzymes required for biomass degradation. However, the lack of an effective lignin-degrading enzyme system reduces the species’ efficiency in producing fermentable sugars and increases the pre-treatment costs for biofuel production. In this study, we heterologously expressed the Ganoderma lucidum RMK1 versatile peroxidase gene (vp1) in the Rut-C30 strain of T. reesei. The expression of purified 6×His-tag–containing recombinant G. lucidum-derived protein (rVP1) was confirmed through western blot, which exhibited a single band with a relative molecular weight of 39 kDa. In saccharification and delignification studies using rice straw, the transformant (tVP7, T. reesei Rut-C30 expressing G. lucidum-derived rVP1) showed significant improvement in the yield of total reducing sugar and delignification, compared with that of the parent T. reesei Rut-C30 strain. Scanning electron microscopy (SEM) of tVP7-treated paddy straw showed extensive degradation of several layers of its surface compared with the parent strain due to the presence of G. lucidum-derived rVP1. Our results suggest that the expression of ligninolytic enzymes in cellulase hyperproducing systems helps to integrate the pre-treatment and saccharification steps that may ultimately reduce the costs of bioethanol production. Full article
(This article belongs to the Special Issue Feature Papers in Microbial Biotechnology)
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17 pages, 2707 KiB  
Article
High Kanamycin Concentration as Another Stress Factor Additional to Temperature to Increase pDNA Production in E. coli DH5α Batch and Fed-Batch Cultures
by Fernando Grijalva-Hernández, Jesús Vega-Estrada, Montserrat Escobar-Rosales, Jaime Ortega-López, Ricardo Aguilar-López, Alvaro R. Lara and Ma. del Carmen Montes-Horcasitas
Microorganisms 2019, 7(12), 711; https://doi.org/10.3390/microorganisms7120711 - 17 Dec 2019
Cited by 6 | Viewed by 6623
Abstract
Plasmid DNA (pDNA) vaccines require high supercoiled-pDNA doses (milligrams) to achieve an adequate immune response. Therefore, processes development to obtain high pDNA yields and productivity is crucial. pDNA production is affected by several factors including culture type, medium composition, and growth conditions. We [...] Read more.
Plasmid DNA (pDNA) vaccines require high supercoiled-pDNA doses (milligrams) to achieve an adequate immune response. Therefore, processes development to obtain high pDNA yields and productivity is crucial. pDNA production is affected by several factors including culture type, medium composition, and growth conditions. We evaluated the effect of kanamycin concentration and temperature on pDNA production, overflow metabolism (organic acids) and metabolic burden (neomycin phosphotransferase II) in batch and fed-batch cultures of Escherichia coli DH5α-pVAX1-NH36. Results indicated that high kanamycin concentration increases the volumetric productivity, volumetric and specific yields of pDNA when batch cultures were carried out at 42 °C, and overflow metabolism reduced but metabolic burden increased. Micrographs taken with a scanning electron microscope (SEM) were analyzed, showing important morphological changes. The high kanamycin concentration (300 mg/L) was evaluated in high cell density culture (50 gDCW/L), which was reached using a fed-batch culture with temperature increase by controlling heating and growth rates. The pDNA volumetric yield and productivity were 759 mg/L and 31.19 mg/L/h, respectively, two-fold greater than the control with a kanamycin concentration of 50 mg/L. A stress-based process simultaneously caused by temperature and high kanamycin concentration can be successfully applied to increase pDNA production. Full article
(This article belongs to the Special Issue Feature Papers in Microbial Biotechnology)
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18 pages, 1003 KiB  
Article
Global Transcriptional Response of Three Highly Acid-Tolerant Field Strains of Listeria monocytogenes to HCl Stress
by Jule Anna Horlbog, Marc J. A. Stevens, Roger Stephan and Claudia Guldimann
Microorganisms 2019, 7(10), 455; https://doi.org/10.3390/microorganisms7100455 - 16 Oct 2019
Cited by 14 | Viewed by 3450
Abstract
Tolerance to acid is of dual importance for the food-borne pathogen Listeria monocytogenes: acids are used as a preservative, and gastric acid is one of the first defenses within the host. There are considerable differences in the acid tolerance of strains. Here [...] Read more.
Tolerance to acid is of dual importance for the food-borne pathogen Listeria monocytogenes: acids are used as a preservative, and gastric acid is one of the first defenses within the host. There are considerable differences in the acid tolerance of strains. Here we present the transcriptomic response of acid-tolerant field strains of L. monocytogenes to HCl at pH 3.0. RNAseq revealed significant differential expression of genes involved in phosphotransferase systems, oxidative phosphorylation, cell morphology, motility, and biofilm formation. Genes in the acetoin biosynthesis pathway were upregulated, suggesting that L. monocytogenes shifts to metabolizing pyruvate to acetoin under organic acid stress. We also identified the formation of cell aggregates in microcolonies as a potential relief strategy. A motif search within the first 150 bp upstream of differentially expressed genes identified a novel potential regulatory sequence that may have a function in the regulation of virulence gene expression. Our data support a model where an excess of intracellular H+ ions is counteracted by pumping H+ out of the cytosol via cytochrome C under reduced activity of the ATP synthase. The observed morphological changes suggest that acid stress may cause cells to aggregate in biofilm microcolonies to create a more favorable microenvironment. Additionally, HCl stress in the host stomach may serve as (i) a signal to downregulate highly immunogenic flagella, and (ii) as an indicator for the imminent contact with host cells which triggers early stage virulence genes. Full article
(This article belongs to the Special Issue Feature Papers in Microbial Biotechnology)
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20 pages, 5139 KiB  
Article
The Cellulosome Paradigm in An Extreme Alkaline Environment
by Paripok Phitsuwan, Sarah Moraïs, Bareket Dassa, Bernard Henrissat and Edward A. Bayer
Microorganisms 2019, 7(9), 347; https://doi.org/10.3390/microorganisms7090347 - 12 Sep 2019
Cited by 12 | Viewed by 4736
Abstract
Rapid decomposition of plant biomass in soda lakes is associated with microbial activity of anaerobic cellulose-degrading communities. The alkaliphilic bacterium, Clostridium alkalicellulosi, is the single known isolate from a soda lake that demonstrates cellulolytic activity. This microorganism secretes cellulolytic enzymes that degrade [...] Read more.
Rapid decomposition of plant biomass in soda lakes is associated with microbial activity of anaerobic cellulose-degrading communities. The alkaliphilic bacterium, Clostridium alkalicellulosi, is the single known isolate from a soda lake that demonstrates cellulolytic activity. This microorganism secretes cellulolytic enzymes that degrade cellulose under anaerobic and alkaliphilic conditions. A previous study indicated that the protein fraction of cellulose-grown cultures showed similarities in composition and size to known components of the archetypical cellulosome Clostridium thermocellum. Bioinformatic analysis of the C. alkalicellulosi draft genome sequence revealed 44 cohesins, organized into 22 different scaffoldins, and 142 dockerin-containing proteins. The modular organization of the scaffoldins shared similarities to those of C. thermocellum and Acetivibrio cellulolyticus, whereas some exhibited unconventional arrangements containing peptidases and oxidative enzymes. The binding interactions among cohesins and dockerins assessed by ELISA, revealed a complex network of cellulosome assemblies and suggested both cell-associated and cell-free systems. Based on these interactions, C. alkalicellulosi cellulosomal systems have the genetic potential to create elaborate complexes, which could integrate up to 105 enzymatic subunits. The alkalistable C. alkalicellulosi cellulosomal systems and their enzymes would be amenable to biotechnological processes, such as treatment of lignocellulosic biomass following prior alkaline pretreatment. Full article
(This article belongs to the Special Issue Feature Papers in Microbial Biotechnology)
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14 pages, 1123 KiB  
Article
Spectral Grouping of Nominally Aspergillus versicolor Microbial-Collection Deposits by MALDI-TOF MS
by Michael A. Reeve, Thelma S. Caine and Alan G. Buddie
Microorganisms 2019, 7(8), 235; https://doi.org/10.3390/microorganisms7080235 - 2 Aug 2019
Cited by 2 | Viewed by 3206
Abstract
Historical microbial collections often contain samples that have been deposited over extended time periods, during which accepted taxonomic classification (and also available methods for taxonomic assignment) may have changed considerably. Deposited samples can, therefore, have historical taxonomic assignments (HTAs) that may now be [...] Read more.
Historical microbial collections often contain samples that have been deposited over extended time periods, during which accepted taxonomic classification (and also available methods for taxonomic assignment) may have changed considerably. Deposited samples can, therefore, have historical taxonomic assignments (HTAs) that may now be in need of revision, and subdivisions of previously-accepted taxa may also be possible with the aid of current methodologies. One such methodology is matrix-assisted laser-desorption and ionization time-of-flight mass spectrometry (MALDI-TOF MS). Motivated by the high discriminating power of MALDI-TOF MS coupled with the speed and low cost of the method, we have investigated the use of MALDI-TOF MS for spectral grouping of past deposits made to the Centre for Agriculture and Bioscience International (CABI) Genetic Resource Collection under the HTA Aspergillus versicolor, a common ascomycete fungus frequently associated with soil and plant material, food spoilage, and damp indoor environments. Despite their common HTA, the 40 deposits analyzed in this study fall into six clear spectral-linkage groups (containing nine, four, four, four, four, and two members, respectively), along with a group of ten spectrally-unique samples. This study demonstrates the clear resolving power of MALDI-TOF MS when applied to samples deposited in historical microbial collections. Full article
(This article belongs to the Special Issue Feature Papers in Microbial Biotechnology)
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