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Extremophiles—Source for Novel Biomolecules with Applied Potential

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A special issue of Fermentation (ISSN 2311-5637). This special issue belongs to the section "Microbial Metabolism, Physiology & Genetics".

Deadline for manuscript submissions: closed (31 August 2022) | Viewed by 27912

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Dr. Mădălin-Iancu Enache

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Guest Editor

Department of Microbiology, Institute of Biology Bucharest of the Romanian Academy, Bucharest, Romania
Interests: diversity and phylogeny of halophilic microorganisms; ecology of extremely halophilic archaea; enzymology of halophilic microorganisms; nanobiotechnology

Special Issue Information

Dear Colleagues,

Extremophiles are known as microorganisms which survive in extreme environments such as high temperature, high salinity, arid and desert areas, acid and alkaline water, hydrothermal vents, volcanic areas, etc. They represent huge potential for scientific research, not only for elucidating mechanisms to thrive in such kinds of ecosystems, but also as a source of novel metabolites, such as extremozymes, exopolysaccharides, lipids with wide applications in agriculture, pharmaceuticals, food fermentation and conservation, and many other industrial processes. One of the benefits of extremophiles is the stability of their biomolecules in various solvents, which makes them applicable in industrial processes. On the other hand, halophilic microorganisms have also used in fermentative processing for food production, such as Asian fish sauce, β-carotene, ectoine, etc. Such biocompounds are prepared at industrial scale using various methods, including fermentation.

Extremozymes may also be regarded as a sustainable source for green chemistry. The enzymes from halophiles are used in the production of fermented foods, extraction of solar salt from seawater, environmental bioremediation, and pharmaceuticals. Xerophiles can be used in microbial electrochemical systems or in modern biotechnologies for treating cellulose, chitin, rubbers, etc. Several thermophilic enzymes (lipase, laccase, xylanase) are available on the market and make industrial processes environmentally friendly. Psychrophilic enzymes offer useful applications in pharmaceuticals, molecular biology, food, cosmetics, and more. Proteolytic enzymes from acidophiles are nonallergenic preservatives in medicine.

The aim of this Special Issue of Fermentation is to put together the applied potential of extremophiles, mainly in the food processing, medical, and pharmaceutical domains, but also in related fields which could involve fermentative processes and others.

Dr. Mădălin-Iancu Enache
Guest Editor

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Keywords

Extremozymes
Extreme environments
Fermented food
Biotechnology
Novel extreme metabolites

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Published Papers (9 papers)

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Research

15 pages, 1771 KiB

Open AccessArticle

Apoptotic Induction in Human Cancer Cell Lines by Antimicrobial Compounds from Antarctic Streptomyces fildesensis (INACH3013)

by David Astudillo-Barraza, Romulo Oses, Carlos Henríquez-Castillo, Clemente Michael Vui Ling Wong, José M. Pérez-Donoso, Cristina Purcarea, Heidge Fukumasu, Natalia Fierro-Vásquez, Pablo A. Pérez and Paris Lavin

Fermentation 2023, 9(2), 129; https://doi.org/10.3390/fermentation9020129 - 29 Jan 2023

Cited by 2 | Viewed by 2605

Abstract

The Antarctic Streptomyces fildesensis has been recognized for its production of antimicrobial compounds with interesting biological activities against foodborne bacteria and multi-resistant strains, but not for its potential antiproliferative activity and mechanisms involved. Two bioactive ethyl acetate extract (EAE) fractions were purified via thin-layer chromatography and High-Performance Liquid Chromatography (HPLC), showing that orange-colored compounds displayed antimicrobial activity against pathogenic bacteria even after shock thermal treatment. The UV–VIS features of the active compounds, the TLC assay with actinomycin-D pure standard, Fourier transform infrared (FTIR) spectra and the ANTISMASH analysis support the presence of actinomycin-like compounds. We demonstrated that S. fildesensis displays antiproliferative activity against human tumor cell lines, including human breast cancer (MCF-7), prostate cancer (PC-3), colon cancer (HT-29) and non-tumoral colon epithelial cells (CoN). The half-maximal effective concentrations (EC₅₀) ranged from 3.98 µg/mL to 0.1 µg/mL. Our results reveal that actinomycin-like compounds of S. fildesensis induced apoptosis mediated by caspase activation, decreasing the mitochondrial membrane potential and altering the cell morphology in all tumoral and non-tumoral cell lines analyzed. These findings confirm the potential of the psychrotolerant Antarctic S. fildesensis species as a promising source for obtaining potential novel anticancer compounds. Full article

(This article belongs to the Special Issue Extremophiles—Source for Novel Biomolecules with Applied Potential)

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12 pages, 1096 KiB

Open AccessArticle

Temperature and pH Profiling of Extracellular Amylase from Antarctic and Arctic Soil Microfungi

by Abiramy Krishnan, Zazali Alias, Peter Convey, Marcelo González-Aravena, Jerzy Smykla, Mohammed Rizman-Idid and Siti Aisyah Alias

Fermentation 2022, 8(11), 601; https://doi.org/10.3390/fermentation8110601 - 3 Nov 2022

Cited by 7 | Viewed by 4840

Abstract

While diversity studies and screening for enzyme activities are important elements of understanding fungal roles in the soil ecosystem, extracting and purifying the target enzyme from the fungal cellular system is also required to characterize the enzyme. This is, in particular, necessary before developing the enzyme for industrial-scale production. In the present study, partially purified α-amylase was obtained from strains of Pseudogymnoascus sp. obtained from Antarctic and Arctic locations. Partially purified α-amylases from these polar fungi exhibited very similar characteristics, including being active at 15 °C, although having a small difference in optimum pH. Both fungal taxa are good candidates for the potential application of cold-active enzymes in biotechnological industries, and further purification and characterization steps are now required. The α-amylases from polar fungi are attractive in terms of industrial development because they are active at lower temperatures and acidic pH, thus potentially creating energy and cost savings. Furthermore, they prevent the production of maltulose, which is an undesirable by-product often formed under alkaline conditions. Psychrophilic amylases from the polar Pseudogymnoascus sp. investigated in the present study could provide a valuable future contribution to biotechnological applications. Full article

(This article belongs to the Special Issue Extremophiles—Source for Novel Biomolecules with Applied Potential)

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17 pages, 3983 KiB

Open AccessArticle

Identification and Characterization of a Novel Cold-Adapted GH15 Family Trehalase from the Psychrotolerant Microbacterium phyllosphaerae LW106

by Junhua Zhang, Xuehua Yu, Bo Guan, Youzhen Hu, Xu Li, Jun Zeng and Yongqing Ni

Fermentation 2022, 8(10), 471; https://doi.org/10.3390/fermentation8100471 - 21 Sep 2022

Cited by 3 | Viewed by 2122

Abstract

Psychrophiles inhabiting various cold environments are regarded as having evolved diverse physiological and molecular strategies, such as the accumulation of trehalose to alleviate cold stress. To investigate the possible contributions of trehalose metabolism-related enzymes to cold-adaption in psychrotrophic bacteria and enrich the resource bank of trehalose hydrolysis enzymes, a novel cold-adapted GH15 GA-like trehalase (MpTre15A) from psychrotolerant Microbacteriumphyllosphaerae LW106 isolated from glacier sediments was cloned and characterized. The recombinant MpTre15A from M. phyllosphaerae LW106 was expressed and purified in Escherichia coli BL21(DE3). The purified MpTre15A functioned as a hexamer and displayed maximal activity at pH 5.0 and 50 °C. Substrate specificity assay proved MpTre15A only showed hydrolytic activity toward α,α-trehalose. Site-directed mutation verified the key catalytic sites of Glu392 and Glu557 in MpTre15A. The k_cat and k_cat/K_m values of MpTre15A at 4 °C (104.50 s⁻¹ and 1.6 s⁻¹ mM⁻¹, respectively) were comparable to those observed for thermophilic GH15 trehalases at 50 °C, revealing its typical cold-adaptability. MpTre15A showed a trehalose conversion rate of 100% and 99.4% after 10 min and 15 min of incubation at 50 °C and 37 °C, respectively. In conclusion, this novel cold-adapted α,α-trehalase MpTre15A showed potential application for developing therapeutic enzymes, enzyme-based biosensors, and enzyme additives in the fermentation industry. Full article

(This article belongs to the Special Issue Extremophiles—Source for Novel Biomolecules with Applied Potential)

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24 pages, 6921 KiB

Open AccessArticle

Brackish and Hypersaline Lakes as Potential Reservoir for Enzymes Involved in Decomposition of Organic Materials on Frescoes

by Ioana Gomoiu, Roxana Cojoc, Robert Ruginescu, Simona Neagu, Madalin Enache, Gabriel Maria, Maria Dumbrăvician, Ioana Olteanu, Roxana Rădvan, Lucian-Cristian Ratoiu, Victoria Atanassova and Luminița Ghervase

Fermentation 2022, 8(9), 462; https://doi.org/10.3390/fermentation8090462 - 16 Sep 2022

Cited by 5 | Viewed by 2191

Abstract

This study highlights the decomposing role through the hydrolytic activities of fungi isolated from natural environments represented by brackish and hypersaline lakes in Romania. Novel strains belonging to the Penicillium, Aspergillus, and Emericellopsis genera were isolated and screened for the ability to produce extracellular hydrolytic enzymes, i.e., proteases, lipases, amylases, cellulases, xylanases, and pectinases. According to salt requirements, they were classified as moderate halophilic and halotolerant strains. Agar plate-based assays with Tween 80, slide cultures with organic deposits, and quantitative evaluation allowed the selection of Aspergillus sp. BSL 2-2, Penicillium sp. BSL 3-2, and Emericellopsis sp. MM2 as potentially good decomposers of organic matter not only in lakes but also on deposits covering the mural paintings. Experiments performed on painted experimental models revealed that only Penicillium sp. BSL 3-2 decomposed Paraloid B72, transparent dispersion of casein, beeswax, sunflower oil, and soot. Moreover, using microscopic, spectroscopic, and imaging methods, it was proved the efficiency of Penicillium sp. BSL 3-2 for decomposition of organic deposits artificially applied on frescoes fragments. Full article

(This article belongs to the Special Issue Extremophiles—Source for Novel Biomolecules with Applied Potential)

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17 pages, 6785 KiB

Open AccessArticle

Mapping Archaeal Diversity in Soda Lakes by Coupling 16S rRNA PCR-DGGE Analysis with Remote Sensing and GIS Technology

by Naglaa Elshafey, Samy Selim, Asmaa H. Mohammed, Nashwa Hagagy, Mennatalla Samy, Ehab M. Mostafa, Fatmah A. Safhi, Salha M. Alshamrani, Amna Saddiq, Salam S. Alsharari, Dalia G. Aseel, Iram Hafiz, Amr Elkelish and Leonardo M. Pérez

Fermentation 2022, 8(8), 365; https://doi.org/10.3390/fermentation8080365 - 30 Jul 2022

Cited by 2 | Viewed by 2684

Abstract

The haloarchaeal diversity of four hypersaline alkaline lakes from the Wadi El-Natrun depression (Northern Egypt) was investigated using culture-independent polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) of 16S rRNA gene phylotypes, which was combined with remote sensing and geographic information system (GIS) data to highlight the distribution pattern of the microbial diversity in water and sediment samples. The majority of archaeal sequences identified in all four lakes belonged to the phyla Euryarchaeota and Crenarchaeota. Sediment samples from Beida Lake and water samples from El-Hamra Lake showed the highest levels of archaeal diversity. Sequence similarities ≥ 95% were found between six of the acquired clones and uncultured Halorhabdus, Euryarchaeota, and archaeon clones. In addition, two clones shared a high level of sequence similarity (97%) with unclassified archaea, while other nine clones exhibited 96% to 99% sequence similarity with uncultured archaeon clones, and only one clone showed 97% identity with an uncultured Crenarchaeota. Likewise, 7 DGGE bands presented a sequence similarity of 90 to 98% to Halogranum sp., Halalkalicoccus tibetensis, Halalkalicoccus jeotgali, uncultured Halorubrum, Halobacteriaceae sp., or uncultured haloarchaeon. In conclusion, while the variety of alkaliphilic haloarchaea in the examined soda lakes was restricted, the possibility of uncovering novel species for biotechnological applications from these extreme habitats remains promising. Full article

(This article belongs to the Special Issue Extremophiles—Source for Novel Biomolecules with Applied Potential)

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18 pages, 2832 KiB

Open AccessArticle

Fenton-Mediated Chlorophenol Degradation by Iron-Reducing Compounds Isolated from Endophytic Fungi in Atacama Puna Plateau Lecanicillium ATA01

by Rómulo Oses-Pedraza, Estefanía Bonnail, Paris Lavin, Cristina Purcarea, Manuel Alarcón, Danae Irribarren-Riquelme and Jaime Rodríguez

Fermentation 2022, 8(4), 147; https://doi.org/10.3390/fermentation8040147 - 27 Mar 2022

Viewed by 2165

Abstract

Low-molecular-mass iron-reducing compounds (IRCs) were produced by entomopathogenic endophytic fungi Lecanicillium sp. ATA01 in liquid cultures. The extracellular hydrophilic extract contained three IRCs formed by peptides, iron and phenolate structures with molecular masses of 1207, 567 and 550 Da. These compounds were able to chelate and mediate the reduction of Fe⁺³ to Fe⁺² and oxidized recalcitrant lignin-model substrates such as veratryl alcohol (VA), 2,6-dimethoxyphenol (DMP), and 2,2′-azino-bis (3-ethylbenzothiazoline-6-sulphonic acid (ABTS) with or without hydrogen peroxide. Besides, IRCs can promote the degradation of chlorophenols. The maximal degradation of p-chlorophenol, 2,4-dichlorophenol, 2,4,6-trichlorophenol, and pentachlorophenol was conducted at optimal degradation conditions for IRCs (pH 3.5, iron 100 mM, and H₂O₂ 10 mM). Furthermore, Fenton-like reactions using the synthetic iron chelates DTPA and EDTA and free Fe⁺² and Fe⁺³ were also carried out in order to compare with the reaction mediated by IRCs. The ferric IRCs displayed the ability to enhance the hydroxylation of chlorophenols as a part of a degradation mechanism of the IRC-assisted Fenton reaction. The complexed iron was more efficient than free iron in the Fenton-like reaction, and between them, the fungal chelates were more efficient than the synthetic mill chelates. Full article

(This article belongs to the Special Issue Extremophiles—Source for Novel Biomolecules with Applied Potential)

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14 pages, 3140 KiB

Open AccessArticle

Kocuria Strains from Unique Radon Spring Water from Jachymov Spa

by Elizaveta Timkina, Lucie Drábová, Andrea Palyzová, Tomáš Řezanka, Olga Maťátková and Irena Kolouchová

Fermentation 2022, 8(1), 35; https://doi.org/10.3390/fermentation8010035 - 16 Jan 2022

Cited by 10 | Viewed by 3496

Abstract

Members of the genus Kocuria are often found in soils contaminated with toxic metals or exposed to high levels of ionizing radiation. The use of classical cultivation technics often leads to the isolation of Kocuria sp. from underground spring waters. These bacterial isolates have to adapt their metabolism to survive in such extreme environments. Four bacterial isolates of the genus Kocuria (Kocuria sp. 101, 208, 301, and 401) were obtained from radon spring water (Jachymov, Czech Republic). These isolates were tested for their ability to withstand stress and extreme conditions. Growth was observed at a temperature range of 10–45 °C with optimal growth temperature between 20 and 30 °C. The content of polyunsaturated fatty acids in all four isolates was proved to be temperature-dependent. The strain Kocuria sp. 301 showed high resistance to all studied extreme conditions (UV radiation, desiccation, and free radicals in medium). The results suggest that isolates from radioactive springs might have developed mechanisms that help them survive under several extreme conditions and could be used in biotechnological production. Full article

(This article belongs to the Special Issue Extremophiles—Source for Novel Biomolecules with Applied Potential)

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18 pages, 2030 KiB

Open AccessArticle

Highly Stable, Cold-Active Aldehyde Dehydrogenase from the Marine Antarctic Flavobacterium sp. PL002

by Georgiana Necula-Petrareanu, Paris Lavin, Victoria Ioana Paun, Giulia Roxana Gheorghita, Alina Vasilescu and Cristina Purcarea

Fermentation 2022, 8(1), 7; https://doi.org/10.3390/fermentation8010007 - 27 Dec 2021

Cited by 7 | Viewed by 3242

Abstract

Stable aldehyde dehydrogenases (ALDH) from extremophilic microorganisms constitute efficient catalysts in biotechnologies. In search of active ALDHs at low temperatures and of these enzymes from cold-adapted microorganisms, we cloned and characterized a novel recombinant ALDH from the psychrotrophic Flavobacterium PL002 isolated from Antarctic seawater. The recombinant enzyme (F-ALDH) from this cold-adapted strain was obtained by cloning and expressing of the PL002 aldH gene (1506 bp) in Escherichia coli BL21(DE3). Phylogeny and structural analyses showed a high amino acid sequence identity (89%) with Flavobacterium frigidimaris ALDH and conservation of all active site residues. The purified F-ALDH by affinity chromatography was homotetrameric, preserving 80% activity at 4 °C for 18 days. F-ALDH used both NAD⁺ and NADP⁺ and a broad range of aliphatic and aromatic substrates, showing cofactor-dependent compensatory K_M and k_cat values and the highest catalytic efficiency (0.50 µM⁻¹ s⁻¹) for isovaleraldehyde. The enzyme was active in the 4–60 °C-temperature interval, with an optimal pH of 9.5, and a preference for NAD⁺-dependent reactions. Arrhenius plots of both NAD(P)⁺-dependent reactions indicated conformational changes occurring at 30 °C, with four(five)-fold lower activation energy at high temperatures. The high thermal stability and substrate-specific catalytic efficiency of this novel cold-active ALDH favoring aliphatic catalysis provided a promising catalyst for biotechnological and biosensing applications. Full article

(This article belongs to the Special Issue Extremophiles—Source for Novel Biomolecules with Applied Potential)

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11 pages, 1197 KiB

Open AccessArticle

Metabolic Potential of Some Functional Groups of Bacteria in Aquatic Urban Systems

by Bianca Ojovan, Rodica Catana, Simona Neagu, Roxana Cojoc, Anca Ioana Lucaci, Luminita Marutescu, Larisa Florescu, Robert Ruginescu, Madalin Enache and Mirela Moldoveanu

Fermentation 2021, 7(4), 242; https://doi.org/10.3390/fermentation7040242 - 27 Oct 2021

Cited by 4 | Viewed by 3172

Abstract

This study analyzed the metabolic potential of some functional groups of bacteria in aquatic urban systems and evaluated the abundance of communities of total heterotrophic bacteria in the water in relation to the monitored physico-chemical factors. The results obtained showed seasonal differences, especially in spring. The high values of the abundance of heterotrophs in winter are related to human activity at the sampling stations. Screening for four types of extracellular hydrolytic enzyme with potential for degradation of organic matter (amylases, lipases, proteases and cellulases) led to the conclusion that lipolytic bacteria were dominant in the studied ecosystems, while proteolytic bacteria were observed in low numbers, but were present in urbanized areas. The presence of cellulolytic bacteria is correlated with the development of macrophytic vegetation. The aim of the present study was oriented towards the evaluation of the anthropogenic input in several lakes surrounding Bucharest in the Nord-Eastern region. These urban ecosystems are generated as a requirement of city development. The microbiological and general enzymatic approaches generated some novel results concerning the pollution degree of aquatic urban ecosystems and could be considered as a platform for further investigation. Full article

(This article belongs to the Special Issue Extremophiles—Source for Novel Biomolecules with Applied Potential)

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