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Microorganisms
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Microbial Extremophiles as Life Pioneers and Wellsprings of Valuable Molecules
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Microbial Extremophiles as Life Pioneers and Wellsprings of Valuable Molecules

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

Deadline for manuscript submissions: closed (31 December 2021) | Viewed by 62489

Special Issue Editors

Dr. Annarita Poli

E-Mail Website
Guest Editor
Institute of Biomolecular Chemistry, National Research Council (CNR-ICB), Via Campi Flegrei 34, 80078 Pozzuoli, Naples, Italy
Interests: extremophiles; exopolysaccharides; extremozymes; valorization of vegetable biomass; taxonomy of extremophiles
Special Issues, Collections and Topics in MDPI journals
Dr. Ilaria Finore

E-Mail Website
Guest Editor
National Research Council (CNR-ICB), Institute of Biomolecular Chemistry, Via Campi Flegrei 34, 80078 Pozzuoli, Naples, Italy
Interests: extremophilic microorganisms; extremozymes; exopolysaccharides; biotransformation; waste biomass valorization
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

For several decades extremophilic microorganisms have been a subject of increasing interest, mainly for their capability to thrive in inhospitable niches in contrast to conventional schemes. In addition, their resistance to adverse environmental conditions suggests that the extremophiles hide the fascinating mysteries of the appearance of life on our planet. They have been isolated from samples collected in the most disparate and unthinkable sites, revealing the presence of ecosystems completely new, whose existence was unimaginable.

Therefore, the aptitude to thrive in extreme environments implies the production of a wide variety of biotechnologically useful molecules such as lipids, enzymes, polysaccharides, and compatible solutes, which are attractive for several industrial processes.

There are many extremophilic enzymes and also endogenous compounds that are successfully used in several industries such as the food industry, detergent industry, and pharmacological applications as well as genetic studies.

This Special Issue, "Microbial Extremophiles as Life Pioneers and Wellsprings of Valuable Molecules", serves to highlight the microbial biodiversity in extreme habitats and the unusual properties of extremophile molecules for exploitation by biotech companies.

This Special Issue calls for reviews as well as original research articles documenting our progress in and current understanding of different aspects associated with extremophilic microorganisms and their molecules, including their isolation, chemical characterizations, biological properties, and the fermentation technology behind their hyperproduction.

Dr. Annarita Poli
Dr. Ilaria Finore
Guest Editors

Manuscript Submission Information

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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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10 pages, 1552 KiB  
Article
Galdieria sulphuraria ACUF427 Freeze-Dried Biomass as Novel Biosorbent for Rare Earth Elements
by Maria Palmieri, Manuela Iovinella, Seth J. Davis, Maria Rosa di Cicco, Carmine Lubritto, Marco Race, Stefania Papa, Massimiliano Fabbricino and Claudia Ciniglia
Microorganisms 2022, 10(11), 2138; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms10112138 - 28 Oct 2022
Cited by 5 | Viewed by 1403
Abstract
Rare earth elements (REEs) are essential components of modern technologies and are often challenging to acquire from natural resources. The demand for REEs is so high that there is a clear need to develop efficient and environmentally-friendly recycling methods. In the present study, [...] Read more.
Rare earth elements (REEs) are essential components of modern technologies and are often challenging to acquire from natural resources. The demand for REEs is so high that there is a clear need to develop efficient and environmentally-friendly recycling methods. In the present study, freeze-dried cells of the extremophile Galdieria sulphuraria were employed to recover yttrium, cerium, europium, and terbium from quaternary-metal aqueous solutions. The biosorption capacity of G. sulphuraria freeze-dried algal biomass was tested at different pHs, contact times, and biosorbent dosages. All rare earths were biosorbed in a more efficient way by the lowest dose of biosorbent, at pH 4.5, within 30 min; the highest removal rate of cerium was recorded at acidic pH (2.5) and after a longer contact time, i.e., 360 min. This study confirms the potential of freeze-dried cells of G. sulphuraria as innovative ecological biosorbents in technological applications for sustainable recycling of metals from e-waste and wastewater. Full article
(This article belongs to the Special Issue Microbial Extremophiles as Life Pioneers and Wellsprings of Valuable Molecules)
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20 pages, 7728 KiB  
Article
Extremophilic Microorganisms for the Green Synthesis of Antibacterial Nanoparticles
by Ida Romano, Giuseppe Vitiello, Noemi Gallucci, Rocco Di Girolamo, Andrea Cattaneo, Annarita Poli and Paola Di Donato
Microorganisms 2022, 10(10), 1885; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms10101885 - 21 Sep 2022
Cited by 4 | Viewed by 1456
Abstract
The biogenic synthesis of nanomaterials, i.e., synthesis carried out by means of living organisms, is an emerging technique in nanotechnology since it represents a greener and more eco-friendly method for the production of nanomaterials. In this line, in order to find new biological [...] Read more.
The biogenic synthesis of nanomaterials, i.e., synthesis carried out by means of living organisms, is an emerging technique in nanotechnology since it represents a greener and more eco-friendly method for the production of nanomaterials. In this line, in order to find new biological entities capable of biogenic synthesis, we tested the ability of some extremophilic microorganisms to carry out the biogenic production of AgNPs and SeNPs. Silver NPs were produced extracellularly by means of the thermophilic Thermus thermophilus strain SAMU; the haloalkaliphilic Halomonas campaniensis strain 5AG was instead found to be useful for the synthesis of SeNPs. The structural characterization of the biogenic nanoparticles showed that both the Ag and Se NPs possessed a protein coating on their surface and that they were organized in aggregates. Moreover, both types of NPs were found be able to exert an interesting antibacterial effect against either Gram-positive or Gram-negative species. This study confirmed that extremophilic microorganisms can be considered valuable producers of biologically active nanoparticles; nevertheless, further experiments must be performed to improve the synthesis protocols in addition to the downstream processes. Full article
(This article belongs to the Special Issue Microbial Extremophiles as Life Pioneers and Wellsprings of Valuable Molecules)
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26 pages, 3018 KiB  
Article
Benthic Microbial Communities in a Seasonally Ice-Covered Sub-Arctic River (Pasvik River, Norway) Are Shaped by Site-Specific Environmental Conditions
by Maria Papale, Carmen Rizzo, Stefania Giannarelli, Gabriella Caruso, Stefano Amalfitano, Paul Eric Aspholm, Giovanna Maimone, Stefano Miserocchi, Alessandro Ciro Rappazzo, Angelina Lo Giudice and Maurizio Azzaro
Microorganisms 2022, 10(5), 1022; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms10051022 - 12 May 2022
Viewed by 2073
Abstract
The Pasvik River experiences chemical, physical, and biological stressors due to the direct discharges of domestic sewage from settlements located within the catchment and runoff from smelter and mine wastes. Sediments, as a natural repository of organic matter and associated contaminants, are of [...] Read more.
The Pasvik River experiences chemical, physical, and biological stressors due to the direct discharges of domestic sewage from settlements located within the catchment and runoff from smelter and mine wastes. Sediments, as a natural repository of organic matter and associated contaminants, are of global concern for the possible release of pollutants in the water column, with detrimental effects on aquatic organisms. The present study was aimed at characterizing the riverine benthic microbial community and evaluating its ecological role in relation to the contamination level. Sediments were sampled along the river during two contrasting environmental periods (i.e., beginning and ongoing phases of ice melting). Microbial enzymatic activities, cell abundance, and morphological traits were evaluated, along with the phylogenetic community composition. Amplified 16S rRNA genes from bacteria were sequenced using a next-generation approach. Sediments were also analyzed for a variety of chemical features, namely particulate material characteristics and concentration of polychlorobiphenyls, polycyclic aromatic hydrocarbons, and pesticides. Riverine and brackish sites did not affect the microbial community in terms of main phylogenetic diversity (at phylum level), morphometry, enzymatic activities, and abundance. Instead, bacterial diversity in the river sediments appeared to be influenced by the micro-niche conditions, with differences in the relative abundance of selected taxa. In particular, our results highlighted the occurrence of bacterial taxa directly involved in the C, Fe, and N cycles, as well as in the degradation of organic pollutants and toxic compounds. Full article
(This article belongs to the Special Issue Microbial Extremophiles as Life Pioneers and Wellsprings of Valuable Molecules)
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11 pages, 993 KiB  
Article
Optimization of Lipopeptide Biosurfactant Production by Salibacterium sp. 4CTb in Batch Stirred-Tank Bioreactors
by José Martín Márquez-Villa, Juan Carlos Mateos-Díaz, Jorge Alberto Rodríguez-González and Rosa María Camacho-Ruíz
Microorganisms 2022, 10(5), 983; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms10050983 - 08 May 2022
Cited by 2 | Viewed by 1632
Abstract
Halophilic microorganisms are potentially capable as platforms to produce low-cost biosurfactants. However, the robustness of bioprocesses is still a challenge and, therefore, it is essential to understand the effects of microbiological culture conditions through bioreactor engineering. Based on a design of experiments (DOE) [...] Read more.
Halophilic microorganisms are potentially capable as platforms to produce low-cost biosurfactants. However, the robustness of bioprocesses is still a challenge and, therefore, it is essential to understand the effects of microbiological culture conditions through bioreactor engineering. Based on a design of experiments (DOE) and a response surface methodology (RSM) tailored and taken from the literature, the present work focuses on the evaluation of a composite central design (CCD) under batch cultures in stirred-tank bioreactors with the halophilic bacteria Salibacterium sp. 4CTb in order to determine the operative conditions that favor mass transfer and optimize the production of a lipopeptide. The results obtained showed profiles highlighting the most favorable culture conditions, which lead to an emulsification index (E24%) higher than 70%. Moreover, through the behavior of dissolved oxygen (DO), it was possible to experimentally evaluate the higher volumetric coefficient of mass transfer in the presence of lipopeptide (kLa = 31 1/h) as a key criterion for the synthesis of the biosurfactant on further cell expansion. Full article
(This article belongs to the Special Issue Microbial Extremophiles as Life Pioneers and Wellsprings of Valuable Molecules)
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15 pages, 12893 KiB  
Article
Characterization of Some Salt-Tolerant Bacterial Hydrolases with Potential Utility in Cultural Heritage Bio-Cleaning
by Robert Ruginescu, Madalin Enache, Octavian Popescu, Ioana Gomoiu, Roxana Cojoc, Costin Batrinescu-Moteau, Gabriel Maria, Maria Dumbravician and Simona Neagu
Microorganisms 2022, 10(3), 644; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms10030644 - 17 Mar 2022
Cited by 14 | Viewed by 2423
Abstract
Salt-tolerant enzymes produced by halophilic and halotolerant microorganisms have been proposed to be used in various applications that involve high saline conditions. Considering their biotechnological significance and the current need for more efficient producers of such catalysts, the present study aimed to evaluate [...] Read more.
Salt-tolerant enzymes produced by halophilic and halotolerant microorganisms have been proposed to be used in various applications that involve high saline conditions. Considering their biotechnological significance and the current need for more efficient producers of such catalysts, the present study aimed to evaluate the extracellular proteolytic, esterolytic, cellulolytic and xylanolytic activities of some halotolerant strains, and to characterize their functional parameters. A total of 21 bacterial and fungal strains belonging to the genera Bacillus, Virgibacillus, Salinivibrio, Salinicoccus, Psychrobacter, Nocardiopsis, Penicillium, Aspergillus, and Emericellopsis were assayed by quantitative methods. Among them, the members of the Bacillus genus exhibited the highest catalytic activities. The exoenzymes produced by three selected Bacillus strains were active over wide ranges of salinity, temperature and pH. Proteases were active at 20–80 °C, pH 6–10, and 0–1 M NaCl, while esterases showed good catalytic activities at 20–80 °C, pH 7.5–10, and 0–4 M NaCl. Cellulases and xylanases were active at 20–80 °C, pH 5–10, and 0–5 M NaCl. Due to such properties, these hydrolases could be used in a newly proposed application, namely to clean aged consolidants and organic deposits accumulated over time from the surfaces of salt-loaded wall paintings. Full article
(This article belongs to the Special Issue Microbial Extremophiles as Life Pioneers and Wellsprings of Valuable Molecules)
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16 pages, 3258 KiB  
Article
Biochemical Characterization of Recombinant Isocitrate Dehydrogenase and Its Putative Role in the Physiology of an Acidophilic Micrarchaeon
by Dennis Winkler, Sabrina Gfrerer and Johannes Gescher
Microorganisms 2021, 9(11), 2318; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms9112318 - 09 Nov 2021
Cited by 1 | Viewed by 1623
Abstract
Despite several discoveries in recent years, the physiology of acidophilic Micrarchaeota, such as “Candidatus Micrarchaeum harzensis A_DKE”, remains largely enigmatic, as they highly express numerous genes encoding hypothetical proteins. Due to a lacking genetic system, it is difficult to elucidate the biological [...] Read more.
Despite several discoveries in recent years, the physiology of acidophilic Micrarchaeota, such as “Candidatus Micrarchaeum harzensis A_DKE”, remains largely enigmatic, as they highly express numerous genes encoding hypothetical proteins. Due to a lacking genetic system, it is difficult to elucidate the biological function of the corresponding proteins and heterologous expression is required. In order to prove the viability of this approach, A_DKE’s isocitrate dehydrogenase (MhIDH) was recombinantly produced in Escherichia coli and purified to electrophoretic homogeneity for biochemical characterization. MhIDH showed optimal activity around pH 8 and appeared to be specific for NADP+ yet promiscuous regarding divalent cations as cofactors. Kinetic studies showed KM-values of 53.03 ± 5.63 µM and 1.94 ± 0.12 mM and kcat-values of 38.48 ± 1.62 and 43.99 ± 1.46 s−1 resulting in kcat/KM-values of 725 ± 107.62 and 22.69 ± 2.15 mM−1 s−1 for DL-isocitrate and NADP+, respectively. MhIDH’s exceptionally low affinity for NADP+, potentially limiting its reaction rate, can likely be attributed to the presence of a proline residue in the NADP+ binding pocket, which might cause a decrease in hydrogen bonding of the cofactor and a distortion of local secondary structure. Full article
(This article belongs to the Special Issue Microbial Extremophiles as Life Pioneers and Wellsprings of Valuable Molecules)
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12 pages, 2490 KiB  
Article
Adaptations for Pressure and Temperature in Dihydrofolate Reductases
by Ryan W. Penhallurick, Maya D. Durnal, Alliyah Harold and Toshiko Ichiye
Microorganisms 2021, 9(8), 1706; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms9081706 - 11 Aug 2021
Cited by 3 | Viewed by 2018
Abstract
Enzymes from extremophilic microbes that live in extreme conditions are generally adapted so that they function under those conditions, although adaptations for extreme temperatures and pressures can be difficult to unravel. Previous studies have shown mutation of Asp27 in Escherichia coli dihydrofolate reductase [...] Read more.
Enzymes from extremophilic microbes that live in extreme conditions are generally adapted so that they function under those conditions, although adaptations for extreme temperatures and pressures can be difficult to unravel. Previous studies have shown mutation of Asp27 in Escherichia coli dihydrofolate reductase (DHFR) to Glu27 in Moritella profunda (Mp). DHFR enhances activity at higher pressures, although this may be an adaptation for cold. Interestingly, MpDHFR unfolds at ~70 MPa, while Moritella yayanosii (My) was isolated at depths corresponding to ~110 MPa, indicating that MyDHFR might be adapted for higher pressures. Here, these adaptations are examined using molecular dynamics simulations of DHFR from different microbes in the context of not only experimental studies of activity and stability of the protein but also the evolutionary history of the microbe. Results suggest Tyr103 of MyDHFR may be an adaptation for high pressure since Cys103 in helix F of MpDHFR forms an intra-helix hydrogen bond with Ile99 while Tyr103 in helix F of MyDHFR forms a hydrogen bond with Leu78 in helix E. This suggests the hydrogen bond between helices F and E in MyDHFR might prevent distortion at higher pressures. Full article
(This article belongs to the Special Issue Microbial Extremophiles as Life Pioneers and Wellsprings of Valuable Molecules)
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12 pages, 845 KiB  
Article
Improvement of CO2 and Acetate Coupling into Lactic Acid by Genetic Manipulation of the Hyperthermophilic Bacterium Thermotoga neapolitana
by Nunzia Esercizio, Mariamichela Lanzilli, Marco Vastano, Zhaohui Xu, Simone Landi, Lucio Caso, Carmela Gallo, Genoveffa Nuzzo, Emiliano Manzo, Angelo Fontana and Giuliana d’Ippolito
Microorganisms 2021, 9(8), 1688; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms9081688 - 09 Aug 2021
Cited by 4 | Viewed by 2193
Abstract
Capnophilic lactic fermentation (CLF) represents an attractive biotechnological process for biohydrogen production and synthesis of L-lactic acid from acetate and CO2. The present study focuses on a genetic manipulation approach of the Thermotoga neapolitana DSM33003 strain to enhance lactic acid synthesis [...] Read more.
Capnophilic lactic fermentation (CLF) represents an attractive biotechnological process for biohydrogen production and synthesis of L-lactic acid from acetate and CO2. The present study focuses on a genetic manipulation approach of the Thermotoga neapolitana DSM33003 strain to enhance lactic acid synthesis by the heterologous expression of a thermostable acetyl-CoA synthetase that catalyses the irreversible acetate assimilation. Because of the scarcity of available genetic tools, each transformation step was optimized for T. neapolitana DSM33003 to cope with the specific needs of the host strain. Batch fermentations with and without an external source of acetate revealed a strongly increased lactate production (up to 2.5 g/L) for the recombinant strain compared to wild type. In the engineered bacterium, the assimilation of CO2 into lactic acid was increased 1.7 times but the hydrogen yield was impaired in comparison to the wild type strain. Analysis of fermentation yields revealed an impaired metabolism of hydrogen in the recombinant strain that should be addressed in future studies. These results offer an important prospective for the development of a sustainable approach that combines carbon capture, energy production from renewable source, and the synthesis of high value-added products, which will be addressed in future studies. Full article
(This article belongs to the Special Issue Microbial Extremophiles as Life Pioneers and Wellsprings of Valuable Molecules)
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16 pages, 3196 KiB  
Article
Extremophiles in Soil Communities of Former Copper Mining Sites of the East Harz Region (Germany) Reflected by Re-Analyzed 16S rRNA Data
by J. Michael Köhler, Nancy Beetz, Peter Mike Günther, Frances Möller and Jialan Cao
Microorganisms 2021, 9(7), 1422; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms9071422 - 30 Jun 2021
Cited by 5 | Viewed by 2454
Abstract
The east and southeast rim of Harz mountains (Germany) are marked by a high density of former copper mining places dating back from the late 20th century to the middle age. A set of 18 soil samples from pre- and early industrial mining [...] Read more.
The east and southeast rim of Harz mountains (Germany) are marked by a high density of former copper mining places dating back from the late 20th century to the middle age. A set of 18 soil samples from pre- and early industrial mining places and one sample from an industrial mine dump have been selected for investigation by 16S rRNA and compared with six samples from non-mining areas. Although most of the soil samples from the old mines show pH values around 7, RNA profiling reflects many operational taxonomical units (OTUs) belonging to acidophilic genera. For some of these OTUs, similarities were found with their abundances in the comparative samples, while others show significant differences. In addition to pH-dependent bacteria, thermophilic, psychrophilic, and halophilic types were observed. Among these OTUs, several DNA sequences are related to bacteria which are reported to show the ability to metabolize special substrates. Some OTUs absent in comparative samples from limestone substrates, among them Thaumarchaeota were present in the soil group from ancient mines with pH > 7. In contrast, acidophilic types have been found in a sample from a copper slag deposit, e.g., the polymer degrading bacterium Granulicella and Acidicaldus, which is thermophilic, too. Soil samples of the group of pre-industrial mines supplied some less abundant, interesting OTUs as the polymer-degrading Povalibacter and the halophilic Lewinella and Halobacteriovorax. A particularly high number of bacteria (OTUs) which had not been detected in other samples were found at an industrial copper mine dump, among them many halophilic and psychrophilic types. In summary, the results show that soil samples from the ancient copper mining places contain soil bacterial communities that could be a promising source in the search for microorganisms with valuable metabolic capabilities. Full article
(This article belongs to the Special Issue Microbial Extremophiles as Life Pioneers and Wellsprings of Valuable Molecules)
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12 pages, 1832 KiB  
Article
Mini-Intein Structures from Extremophiles Suggest a Strategy for Finding Novel Robust Inteins
by Mimmu K. Hiltunen, Hannes M. Beyer and Hideo Iwaï
Microorganisms 2021, 9(6), 1226; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms9061226 - 05 Jun 2021
Cited by 4 | Viewed by 2733
Abstract
Inteins are prevalent among extremophiles. Mini-inteins with robust splicing properties are of particular interest for biotechnological applications due to their small size. However, biochemical and structural characterization has still been limited to a small number of inteins, and only a few serve as [...] Read more.
Inteins are prevalent among extremophiles. Mini-inteins with robust splicing properties are of particular interest for biotechnological applications due to their small size. However, biochemical and structural characterization has still been limited to a small number of inteins, and only a few serve as widely used tools in protein engineering. We determined the crystal structure of a naturally occurring Pol-II mini-intein from Pyrococcus horikoshii and compared all three mini-inteins found in the genome of P. horikoshii. Despite their similar sizes, the comparison revealed distinct differences in the insertions and deletions, implying specific evolutionary pathways from distinct ancestral origins. Our studies suggest that sporadically distributed mini-inteins might be more promising for further protein engineering applications than highly conserved mini-inteins. Structural investigations of additional inteins could guide the shortest path to finding novel robust mini-inteins suitable for various protein engineering purposes. Full article
(This article belongs to the Special Issue Microbial Extremophiles as Life Pioneers and Wellsprings of Valuable Molecules)
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12 pages, 1053 KiB  
Article
Identification of Homologous Polyprenols from Thermophilic Bacteria
by Lucia Gharwalová, Andrea Palyzová, Helena Marešová, Irena Kolouchová, Lucie Kyselová and Tomáš Řezanka
Microorganisms 2021, 9(6), 1168; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms9061168 - 28 May 2021
Cited by 3 | Viewed by 2454
Abstract
Sixteen strains of five genera of thermophilic bacteria, i.e., Alicyclobacillus, Brevibacillus, Geobacillus, Meiothermus, and Thermus, were cultivated at a temperature from 42 to 70 °C. Twelve strains were obtained from the Czech Collection of Microorganisms, while four were directly isolated and identified [...] Read more.
Sixteen strains of five genera of thermophilic bacteria, i.e., Alicyclobacillus, Brevibacillus, Geobacillus, Meiothermus, and Thermus, were cultivated at a temperature from 42 to 70 °C. Twelve strains were obtained from the Czech Collection of Microorganisms, while four were directly isolated and identified by 16S rRNA gene sequencing from the hot springs of the world-famous Carlsbad spa (Czech Republic). Polyprenol homologs from C40 to C65 as well as free undecaprenol (C55), undecaprenyl phosphate, and undecaprenyl diphosphate were identified by shotgun analysis and RP-HPLC/MS-ESI+ (reverse phase high-performance liquid chromatography–high-resolution positive electrospray ionization mass spectrometry). The limit of detection (50 pM) was determined for individual homologs and free polyprenols and their phosphates. Thus, it has been shown that at least some thermophilic bacteria produce not just the major C55 polyprenol as previously described, but a mixture of homologs. Full article
(This article belongs to the Special Issue Microbial Extremophiles as Life Pioneers and Wellsprings of Valuable Molecules)
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13 pages, 32839 KiB  
Article
Effect of Carbon Sources in Carotenoid Production from Haloarcula sp. M1, Halolamina sp. M3 and Halorubrum sp. M5, Halophilic Archaea Isolated from Sonora Saltern, Mexico
by Ana Sofía Vázquez-Madrigal, Alejandra Barbachano-Torres, Melchor Arellano-Plaza, Manuel Reinhart Kirchmayr, Ilaria Finore, Annarita Poli, Barbara Nicolaus, Susana De la Torre Zavala and Rosa María Camacho-Ruiz
Microorganisms 2021, 9(5), 1096; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms9051096 - 20 May 2021
Cited by 8 | Viewed by 2747
Abstract
The isolation and molecular and chemo-taxonomic identification of seventeen halophilic archaea from the Santa Bárbara saltern, Sonora, México, were performed. Eight strains were selected based on pigmentation. Molecular identification revealed that the strains belonged to the Haloarcula, Halolamina and Halorubrum genera. Neutral lipids [...] Read more.
The isolation and molecular and chemo-taxonomic identification of seventeen halophilic archaea from the Santa Bárbara saltern, Sonora, México, were performed. Eight strains were selected based on pigmentation. Molecular identification revealed that the strains belonged to the Haloarcula, Halolamina and Halorubrum genera. Neutral lipids (quinones) were identified in all strains. Glycolipid S-DGD was found only in Halolamina sp. strain M3; polar phospholipids 2,3-O-phytanyl-sn-glycerol-1-phosphoryl-3-sn-glycerol (PG), 2,3-di-O-phytanyl-sn-glycero-1-phospho-3′-sn-glycerol-1′-methyl phosphate (PGP-Me) and sodium salt 1-(3-sn-phosphatidyl)-rac-glycerol were found in all the strains; and one unidentified glyco-phospholipid in strains M1, M3 and M4. Strains M1, M3 and M5 were selected for further studies based on carotenoid production. The effect of glucose and succinic and glutamic acid on carotenoid production was assessed. In particular, carotenoid production and growth significantly improved in the presence of glucose in strains Haloarcula sp. M1 and Halorubrum sp. M5 but not in Halolamina sp. M3. Glutamic and succinic acid had no effect on carotenoid production, and even was negative for Halorubrum sp. M5. Growth was increased by glutamic and succinic acid on Haloarcula sp. M1 but not in the other strains. This work describes for first time the presence of halophilic archaea in the Santa Bárbara saltern and highlights the differences in the effect of carbon sources on the growth and carotenoid production of haloarchaea. Full article
(This article belongs to the Special Issue Microbial Extremophiles as Life Pioneers and Wellsprings of Valuable Molecules)
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14 pages, 16436 KiB  
Article
A New Thermophilic Ene-Reductase from the Filamentous Anoxygenic Phototrophic Bacterium Chloroflexus aggregans
by Marina Simona Robescu, Mattia Niero, Giovanni Loprete, Laura Cendron and Elisabetta Bergantino
Microorganisms 2021, 9(5), 953; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms9050953 - 28 Apr 2021
Cited by 7 | Viewed by 2214
Abstract
Aiming at expanding the biocatalytic toolbox of ene-reductase enzymes, we decided to explore photosynthetic extremophile microorganisms as unique reservoir of (new) biocatalytic activities. We selected a new thermophilic ene-reductase homologue in Chloroflexus aggregans, a peculiar filamentous bacterium. We report here on the [...] Read more.
Aiming at expanding the biocatalytic toolbox of ene-reductase enzymes, we decided to explore photosynthetic extremophile microorganisms as unique reservoir of (new) biocatalytic activities. We selected a new thermophilic ene-reductase homologue in Chloroflexus aggregans, a peculiar filamentous bacterium. We report here on the functional and structural characterization of this new enzyme, which we called CaOYE. Produced in high yields in recombinant form, it proved to be a robust biocatalyst showing high thermostability, good solvent tolerance and a wide range of pH optimum. In a preliminary screening, CaOYE displayed a restricted substrate spectrum (with generally lower activities compared to other ene-reductases); however, given the amazing metabolic ductility and versatility of Chloroflexus aggregans, further investigations could pinpoint peculiar chemical activities. X-ray crystal structure has been determined, revealing conserved features of Class III (or thermophilic-like group) of the family of Old Yellow Enzymes: in the crystal packing, the enzyme was found to assemble as dimer even if it behaves as a monomer in solution. The description of CaOYE catalytic properties and crystal structure provides new details useful for enlarging knowledge, development and application of this class of enzymes. Full article
(This article belongs to the Special Issue Microbial Extremophiles as Life Pioneers and Wellsprings of Valuable Molecules)
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13 pages, 2694 KiB  
Communication
Structural Insights into the Methane-Generating Enzyme from a Methoxydotrophic Methanogen Reveal a Restrained Gallery of Post-Translational Modifications
by Julia Maria Kurth, Marie-Caroline Müller, Cornelia Ulrike Welte and Tristan Wagner
Microorganisms 2021, 9(4), 837; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms9040837 - 14 Apr 2021
Cited by 9 | Viewed by 2758
Abstract
Methanogenic archaea operate an ancient, if not primordial, metabolic pathway that releases methane as an end-product. This last step is orchestrated by the methyl-coenzyme M reductase (MCR), which uses a nickel-containing F430-cofactor as the catalyst. MCR astounds the scientific world by [...] Read more.
Methanogenic archaea operate an ancient, if not primordial, metabolic pathway that releases methane as an end-product. This last step is orchestrated by the methyl-coenzyme M reductase (MCR), which uses a nickel-containing F430-cofactor as the catalyst. MCR astounds the scientific world by its unique reaction chemistry, its numerous post-translational modifications, and its importance in biotechnology not only for production but also for capturing the greenhouse gas methane. In this report, we investigated MCR natively isolated from Methermicoccus shengliensis. This methanogen was isolated from a high-temperature oil reservoir and has recently been shown to convert lignin and coal derivatives into methane through a process called methoxydotrophic methanogenesis. A methoxydotrophic culture was obtained by growing M. shengliensis with 3,4,5-trimethoxybenzoate as the main carbon and energy source. Under these conditions, MCR represents more than 12% of the total protein content. The native MCR structure refined at a resolution of 1.6-Å precisely depicts the organization of a dimer of heterotrimers. Despite subtle surface remodeling and complete conservation of its active site with other homologues, MCR from the thermophile M. shengliensis contains the most limited number of post-translational modifications reported so far, questioning their physiological relevance in other relatives. Full article
(This article belongs to the Special Issue Microbial Extremophiles as Life Pioneers and Wellsprings of Valuable Molecules)
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9 pages, 1474 KiB  
Article
Involvement of a Quorum Sensing Signal Molecule in the Extracellular Amylase Activity of the Thermophilic Anoxybacillus amylolyticus
by Annabella Tramice, Adele Cutignano, Annalaura Iodice, Annarita Poli, Ilaria Finore and Giuseppina Tommonaro
Microorganisms 2021, 9(4), 819; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms9040819 - 13 Apr 2021
Cited by 1 | Viewed by 1923
Abstract
Anoxybacillus amylolyticus is a moderate thermophilic microorganism producing an exopolysaccharide and an extracellular α-amylase able to hydrolyze starch. The synthesis of several biomolecules is often regulated by a quorum sensing (QS) mechanism, a chemical cell-to-cell communication based on the production and diffusion of [...] Read more.
Anoxybacillus amylolyticus is a moderate thermophilic microorganism producing an exopolysaccharide and an extracellular α-amylase able to hydrolyze starch. The synthesis of several biomolecules is often regulated by a quorum sensing (QS) mechanism, a chemical cell-to-cell communication based on the production and diffusion of small molecules named “autoinducers”, most of which belonging to the N-acyl homoserine lactones’ (AHLs) family. There are few reports about this mechanism in extremophiles, in particular thermophiles. Here, we report the identification of a signal molecule, the N-butanoyl-homoserine lactone (C4-HSL), from the milieu of A. amylolyticus. Moreover, investigations performed by supplementing a known QS inhibitor, trans-cinnamaldehyde, or exogenous C4-HSL in the growth medium of A. amylolyticus suggested the involvement of QS signaling in the modulation of extracellular α-amylase activity. The data showed that the presence of the QS inhibitor trans-cinnamaldehyde in the medium decreased amylolytic activity, which, conversely, was increased by the effect of exogenous C4-HSL. Overall, these results represent the first evidence of the production of AHLs in thermophilic microorganisms, which could be responsible for a communication system regulating thermostable α-amylase activity. Full article
(This article belongs to the Special Issue Microbial Extremophiles as Life Pioneers and Wellsprings of Valuable Molecules)
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24 pages, 6802 KiB  
Article
Functional and Molecular Characterization of the Halomicrobium sp. IBSBa Inulosucrase
by Gülbahar Abaramak, Jaime Ricardo Porras-Domínguez, Henry Christopher Janse van Rensburg, Eveline Lescrinier, Ebru Toksoy Öner, Onur Kırtel and Wim Van den Ende
Microorganisms 2021, 9(4), 749; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms9040749 - 02 Apr 2021
Cited by 9 | Viewed by 2904
Abstract
Fructans are fructose-based (poly)saccharides with inulin and levan being the best-known ones. Thanks to their health-related benefits, inulin-type fructans have been under the focus of scientific and industrial communities, though mostly represented by plant-based inulins, and rarely by microbial ones. Recently, it was [...] Read more.
Fructans are fructose-based (poly)saccharides with inulin and levan being the best-known ones. Thanks to their health-related benefits, inulin-type fructans have been under the focus of scientific and industrial communities, though mostly represented by plant-based inulins, and rarely by microbial ones. Recently, it was discovered that some extremely halophilic Archaea are also able to synthesize fructans. Here, we describe the first in-depth functional and molecular characterization of an Archaeal inulosucrase from Halomicrobium sp. IBSBa (HmcIsc). The HmcIsc enzyme was recombinantly expressed and purified in Escherichia coli and shown to synthesize inulin as proven by nuclear magnetic resonance (NMR) analysis. In accordance with the halophilic lifestyle of its native host, the enzyme showed maximum activity at very high NaCl concentrations (3.5 M), with specific adaptations for that purpose. Phylogenetic analyses suggested that Archaeal inulosucrases have been acquired from halophilic bacilli through horizontal gene transfer, with a HX(H/F)T motif evolving further into a HXHT motif, together with a unique D residue creating the onset of a specific alternative acceptor binding groove. This work uncovers a novel area in fructan research, highlighting unexplored aspects of life in hypersaline habitats, and raising questions about the general physiological relevance of inulosucrases and their products in nature. Full article
(This article belongs to the Special Issue Microbial Extremophiles as Life Pioneers and Wellsprings of Valuable Molecules)
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15 pages, 1752 KiB  
Article
Investigation of the Physiology of the Obligate Alkaliphilic Bacillus marmarensis GMBE 72T Considering Its Alkaline Adaptation Mechanism for Poly(3-hydroxybutyrate) Synthesis
by Yağmur Atakav, Orkun Pinar and Dilek Kazan
Microorganisms 2021, 9(2), 462; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms9020462 - 23 Feb 2021
Cited by 5 | Viewed by 1924
Abstract
The novel extreme obligate alkaliphilic Bacillus marmarensis DSM 21297 is known to produce polyhydroxybutyrate (PHB). However, the detailed mechanism of PHB synthesis in B. marmarensis is still unknown. Here, we investigated which metabolic pathways and metabolic enzymes are responsible for PHB synthesis in [...] Read more.
The novel extreme obligate alkaliphilic Bacillus marmarensis DSM 21297 is known to produce polyhydroxybutyrate (PHB). However, the detailed mechanism of PHB synthesis in B. marmarensis is still unknown. Here, we investigated which metabolic pathways and metabolic enzymes are responsible for PHB synthesis in order to understand the regulatory pathway and optimize PHB synthesis in B. marmarensis. In accordance with the fact that beta-galactosidase, 3-hydroxyacyl-CoA dehydrogenase, and Enoyl-CoA hydratase together with acyl-CoA dehydrogenase and lipase were annotated in B. marmarensis according to the RAST server, we used glucose, lactose, and olive oil to understand the preferred metabolic pathway for the PHB synthesis. It was found that B. marmarensis produces PHB from glucose, lactose, and olive oil. However, the highest PHB titer and the highest amount of PHB synthesized per dry cell mass (YP/X) were achieved in the presence of lactose, as compared to glucose and olive oil. Additionally, in the absence of peptone, the amount of PHB synthesized is reduced for each carbon source. Interestingly, none of the carbon sources studied yielded an efficient PHB synthesis, and supplementation of the medium with potassium ions did not enhance PHB synthesis. According to these experimental results and the presence of annotated metabolic enzymes based on the RAST server, PHB accumulation in the cells of B. marmarensis could be improved by the level of the expression of 3-hydroxybutyryl-CoA dehydrogenase (1.1.1.157), which increases the production of NADPH. Additionally, the accumulation of 3-hydroxyacyl-CoA could enhance the production of PHB in B. marmarensis in the presence of fatty acids. To our knowledge, this is the first report investigating the regulatory system involved in the control of PHB metabolism of B. marmarensis. Full article
(This article belongs to the Special Issue Microbial Extremophiles as Life Pioneers and Wellsprings of Valuable Molecules)
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13 pages, 2603 KiB  
Article
DNA Polymerase B1 Binding Protein 1 Is Important for DNA Repair by Holoenzyme PolB1 in the Extremely Thermophilic Crenarchaeon Sulfolobus acidocaldarius
by Hiroka Miyabayashi, Hiroyuki D. Sakai and Norio Kurosawa
Microorganisms 2021, 9(2), 439; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms9020439 - 20 Feb 2021
Cited by 2 | Viewed by 2176
Abstract
DNA polymerase B1 (PolB1) is a member of the B-family DNA polymerase family and is a replicative DNA polymerase in Crenarchaea. PolB1 is responsible for the DNA replication of both the leading and lagging strands in the thermophilic crenarchaeon Sulfolobus acidocaldarius. Recently, [...] Read more.
DNA polymerase B1 (PolB1) is a member of the B-family DNA polymerase family and is a replicative DNA polymerase in Crenarchaea. PolB1 is responsible for the DNA replication of both the leading and lagging strands in the thermophilic crenarchaeon Sulfolobus acidocaldarius. Recently, two subunits, PolB1-binding protein (PBP)1 and PBP2, were identified in Saccharolobus solfataricus. Previous in vitro studies suggested that PBP1 and PBP2 influence the core activity of apoenzyme PolB1 (apo-PolB1). PBP1 contains a C-terminal acidic tail and modulates the strand-displacement synthesis activity of PolB1 during the synthesis of Okazaki fragments. PBP2 modestly enhances the DNA polymerase activity of apo-PolB1. These subunits are present in Sulfolobales, Acidilobales, and Desulfurococcales, which belong to Crenarchaea. However, it has not been determined whether these subunits are essential for the activity of apo-PolB1. In this study, we constructed a pbp1 deletion strain in S. acidocaldarius and characterized its phenotypes. However, a pbp2 deletion strain was not obtained, indicating that PBP2 is essential for replication by holoenzyme PolB1. A pbp1 deletion strain was sensitive to various types of DNA damage and exhibited an increased mutation rate, suggesting that PBP1 contribute to the repair or tolerance of DNA damage by holoenzyme PolB1. The results of our study suggest that PBP1 is important for DNA repair by holoenzyme PolB1 in S. acidocaldarius. Full article
(This article belongs to the Special Issue Microbial Extremophiles as Life Pioneers and Wellsprings of Valuable Molecules)
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19 pages, 5056 KiB  
Article
Prokaryotic Diversity of the Composting Thermophilic Phase: The Case of Ground Coffee Compost
by Maria Papale, Ida Romano, Ilaria Finore, Angelina Lo Giudice, Alessandro Piccolo, Silvana Cangemi, Vincenzo Di Meo, Barbara Nicolaus and Annarita Poli
Microorganisms 2021, 9(2), 218; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms9020218 - 21 Jan 2021
Cited by 17 | Viewed by 6267
Abstract
Waste biomass coming from a local coffee company, which supplied burnt ground coffee after an incorrect roasting process, was employed as a starting material in the composting plant of the Experimental Station of the University of Naples Federico II at Castel Volturno (CE). [...] Read more.
Waste biomass coming from a local coffee company, which supplied burnt ground coffee after an incorrect roasting process, was employed as a starting material in the composting plant of the Experimental Station of the University of Naples Federico II at Castel Volturno (CE). The direct molecular characterization of compost using 13C-NMR spectra, which was acquired through cross-polarization magic-angle spinning, showed a hydrophobicity index of 2.7% and an alkyl/hydroxyalkyl index of 0.7%. Compost samples that were collected during the early “active thermophilic phase” (when the composting temperature was 63 °C) were analyzed for the prokaryotic community composition and activities. Two complementary approaches, i.e., genomic and predictive metabolic analysis of the 16S rRNA V3–V4 amplicon and culture-dependent analysis, were combined to identify the main microbial factors that characterized the composting process. The whole microbial community was dominated by Firmicutes. The predictive analysis of the metabolic functionality of the community highlighted the potential degradation of peptidoglycan and the ability of metal chelation, with both functions being extremely useful for the revitalization and fertilization of agricultural soils. Finally, three biotechnologically relevant Firmicutes members, i.e., Geobacillus thermodenitrificans subsp. calidus, Aeribacillus pallidus, and Ureibacillus terrenus (strains CAF1, CAF2, and CAF5, respectively) were isolated from the “active thermophilic phase” of the coffee composting. All strains were thermophiles growing at the optimal temperature of 60 °C. Our findings contribute to the current knowledge on thermophilic composting microbiology and valorize burnt ground coffee as waste material with biotechnological potentialities. Full article
(This article belongs to the Special Issue Microbial Extremophiles as Life Pioneers and Wellsprings of Valuable Molecules)
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10 pages, 1724 KiB  
Article
Metabolic Engineering of Extremophilic Bacterium Deinococcus radiodurans for the Production of the Novel Carotenoid Deinoxanthin
by Sun-Wook Jeong, Jun-Ho Kim, Ji-Woong Kim, Chae Yeon Kim, Su Young Kim and Yong Jun Choi
Microorganisms 2021, 9(1), 44; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms9010044 - 25 Dec 2020
Cited by 14 | Viewed by 4003
Abstract
Deinoxanthin, a xanthophyll derived from Deinococcus species, is a unique organic compound that provides greater antioxidant effects compared to other carotenoids due to its superior scavenging activity against singlet oxygen and hydrogen peroxide. Therefore, it has attracted significant attention as a next-generation organic [...] Read more.
Deinoxanthin, a xanthophyll derived from Deinococcus species, is a unique organic compound that provides greater antioxidant effects compared to other carotenoids due to its superior scavenging activity against singlet oxygen and hydrogen peroxide. Therefore, it has attracted significant attention as a next-generation organic compound that has great potential as a natural ingredient in a food supplements. Although the microbial identification of deinoxanthin has been identified, mass production has not yet been achieved. Here, we report, for the first time, the development of an engineered extremophilic microorganism, Deinococcus radiodurans strain R1, that is capable of producing deinoxanthin through rational metabolic engineering and process optimization. The genes crtB and dxs were first introduced into the genome to reinforce the metabolic flux towards deinoxanthin. The optimal temperature was then identified through a comparative analysis of the mRNA expression of the two genes, while the carbon source was further optimized to increase deinoxanthin production. The final engineered D. radiodurans strain R1 was able to produce 394 ± 17.6 mg/L (102 ± 11.1 mg/g DCW) of deinoxanthin with a yield of 40.4 ± 1.2 mg/g sucrose and a productivity of 8.4 ± 0.2 mg/L/h from 10 g/L of sucrose. The final engineered strain and the strategies developed in the present study can act as the foundation for the industrial application of extremophilic microorganisms. Full article
(This article belongs to the Special Issue Microbial Extremophiles as Life Pioneers and Wellsprings of Valuable Molecules)
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9 pages, 801 KiB  
Article
Improved Exopolymer Production by Chromohalobacter canadensis Cultures for Its Potential Cosmeceutical Applications
by Nadja Radchenkova, Merve Erginer Hasköylü, Spasen Vassilev, Songül Yaşar Yıldız, Ivanka Boyadzhieva, Ebru Toksoy Oner and Margarita Kambourova
Microorganisms 2020, 8(12), 1935; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms8121935 - 06 Dec 2020
Cited by 5 | Viewed by 1876
Abstract
Several exopolymers with different chemical composition and correspondingly variety in their physico-chemical properties from halophilic microorganisms have still been described, however, with a low production yield. Chromohalobacter canadensis 28 isolated from Pomorie saltern synthesized an unusual exopolymer (EP) containing 72% γ-polyglutamic acid (PGA), [...] Read more.
Several exopolymers with different chemical composition and correspondingly variety in their physico-chemical properties from halophilic microorganisms have still been described, however, with a low production yield. Chromohalobacter canadensis 28 isolated from Pomorie saltern synthesized an unusual exopolymer (EP) containing 72% γ-polyglutamic acid (PGA), an essential cosmeceutical additive. Current work suggests a novel approach for effective EP synthesis by C. canadensis 28 using continuous cultures. Highest production was observed at low dilution rates reaching a level of 2.1 mg/mL at D = 0.035, similar to those in batch cultures (2.34 mg/mL), however avoiding all disadvantages of discontinuous fermentation processes. At steady state, the total quantities of the synthesized EP after 48 h cultivation for the given equipment volume in D = 0.035 h−1 and D = 0.075 h−1 were 8.67 and 12 g, correspondingly, while it was 2.9 g for batch culture. Process parameters did not change after a ten-day run at D = 0.35 h−1. A degree of purity of EP fraction received from continuous cultures was significantly increased up to 93–96%. A lack of cytotoxicity and high cell viability were observed for human dermal fibroblast cells after 24 h incubation with crude EP from C. canadensis 28 and purified PGA fraction that could suggest its high potential for cosmetic applications. Full article
(This article belongs to the Special Issue Microbial Extremophiles as Life Pioneers and Wellsprings of Valuable Molecules)
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12 pages, 2174 KiB  
Article
In Sulfolobus solfataricus, the Poly(ADP-Ribose) Polymerase-Like Thermoprotein Is a Multifunctional Enzyme
by Anna De Maio, Elena Porzio, Sergio Rotondo, Anna Rita Bianchi and Maria Rosaria Faraone-Mennella
Microorganisms 2020, 8(10), 1523; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms8101523 - 03 Oct 2020
Cited by 4 | Viewed by 1702
Abstract
In Sulfolobus solfataricus, Sso, the ADP-ribosylating thermozyme is known to carry both auto- and heteromodification of target proteins via short chains of ADP-ribose. Here, we provide evidence that this thermoprotein is a multifunctional enzyme, also showing ATPase activity. Electrophoretic and kinetic analyses [...] Read more.
In Sulfolobus solfataricus, Sso, the ADP-ribosylating thermozyme is known to carry both auto- and heteromodification of target proteins via short chains of ADP-ribose. Here, we provide evidence that this thermoprotein is a multifunctional enzyme, also showing ATPase activity. Electrophoretic and kinetic analyses were performed using NAD+ and ATP as substrates. The results showed that ATP is acting as a negative effector on the NAD+-dependent reaction, and is also responsible for inducing the dimerization of the thermozyme. These findings enabled us to further investigate the kinetic of ADP-ribosylation activity in the presence of ATP, and to also assay its ability to work as a substrate. Moreover, since the heteroacceptor of ADP-ribose is the sulfolobal Sso7 protein, known as an ATPase, some reconstitution experiments were set up to study the reciprocal influence of the ADP-ribosylating thermozyme and the Sso7 protein on their activities, considering also the possibility of direct enzyme/Sso7 protein interactions. This study provides new insights into the ATP-ase activity of the ADP-ribosylating thermozyme, which is able to establish stable complexes with Sso7 protein. Full article
(This article belongs to the Special Issue Microbial Extremophiles as Life Pioneers and Wellsprings of Valuable Molecules)
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Review

Jump to: Research

20 pages, 7037 KiB  
Review
Microbial Diversity of Terrestrial Geothermal Springs in Armenia and Nagorno-Karabakh: A Review
by Ani Saghatelyan, Armine Margaryan, Hovik Panosyan and Nils-Kåre Birkeland
Microorganisms 2021, 9(7), 1473; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms9071473 - 09 Jul 2021
Cited by 16 | Viewed by 3813
Abstract
The microbial diversity of high-altitude geothermal springs has been recently assessed to explore their biotechnological potential. However, little is known regarding the microbiota of similar ecosystems located on the Armenian Highland. This review summarizes the known information on the microbiota of nine high-altitude [...] Read more.
The microbial diversity of high-altitude geothermal springs has been recently assessed to explore their biotechnological potential. However, little is known regarding the microbiota of similar ecosystems located on the Armenian Highland. This review summarizes the known information on the microbiota of nine high-altitude mineralized geothermal springs (temperature range 25.8–70 °C and pH range 6.0–7.5) in Armenia and Nagorno-Karabakh. All these geothermal springs are at altitudes ranging from 960–2090 m above sea level and are located on the Alpide (Alpine–Himalayan) orogenic belt, a seismically active region. A mixed-cation mixed-anion composition, with total mineralization of 0.5 mg/L, has been identified for these thermal springs. The taxonomic diversity of hot spring microbiomes has been examined using culture-independent approaches, including denaturing gradient gel electrophoresis (DGGE), 16S rRNA gene library construction, 454 pyrosequencing, and Illumina HiSeq. The bacterial phyla Proteobacteria, Bacteroidetes, Cyanobacteria, and Firmicutes are the predominant life forms in the studied springs. Archaea mainly include the phyla Euryarchaeota, Crenarchaeota, and Thaumarchaeota, and comprise less than 1% of the prokaryotic community. Comparison of microbial diversity in springs from Karvachar with that described for other terrestrial hot springs revealed that Proteobacteria, Bacteroidetes, Actinobacteria, and Deinococcus–Thermus are the common bacterial groups in terrestrial hot springs. Contemporaneously, specific bacterial and archaeal taxa were observed in different springs. Evaluation of the carbon, sulfur, and nitrogen metabolism in these hot spring communities has revealed diversity in terms of metabolic activity. Temperature seems to be an important factor in shaping the microbial communities of these springs. Overall, the diversity and richness of the microbiota are negatively affected by increasing temperature. Other abiotic factors, including pH, mineralization, and geological history, also impact the structure and function of the microbial community. More than 130 bacterial and archaeal strains (Bacillus, Geobacillus, Parageobacillus, Anoxybacillus, Paenibacillus, Brevibacillus Aeribacillus, Ureibacillus, Thermoactinomyces, Sporosarcina, Thermus, Rhodobacter, Thiospirillum, Thiocapsa, Rhodopseudomonas, Methylocaldum, Desulfomicrobium, Desulfovibrio, Treponema, Arcobacter, Nitropspira, and Methanoculleus) have been reported, some of which may be representative of novel species (sharing 91–97% sequence identity with their closest matches in GenBank) and producers of thermozymes and biomolecules with potential biotechnological applications. Whole-genome shotgun sequencing of T. scotoductus K1, as well as of the potentially new Treponema sp. J25 and Anoxybacillus sp. K1, were performed. Most of the phyla identified by 16S rRNA were also identified using metagenomic approaches. Detailed characterization of thermophilic isolates indicate the potential of the studied springs as a source of biotechnologically valuable microbes and biomolecules. Full article
(This article belongs to the Special Issue Microbial Extremophiles as Life Pioneers and Wellsprings of Valuable Molecules)
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36 pages, 757 KiB  
Review
The Variety and Inscrutability of Polar Environments as a Resource of Biotechnologically Relevant Molecules
by Carmen Rizzo and Angelina Lo Giudice
Microorganisms 2020, 8(9), 1422; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms8091422 - 16 Sep 2020
Cited by 11 | Viewed by 2880
Abstract
The application of an ever-increasing number of methodological approaches and tools is positively contributing to the development and yield of bioprospecting procedures. In this context, cold-adapted bacteria from polar environments are becoming more and more intriguing as valuable sources of novel biomolecules, with [...] Read more.
The application of an ever-increasing number of methodological approaches and tools is positively contributing to the development and yield of bioprospecting procedures. In this context, cold-adapted bacteria from polar environments are becoming more and more intriguing as valuable sources of novel biomolecules, with peculiar properties to be exploited in a number of biotechnological fields. This review aims at highlighting the biotechnological potentialities of bacteria from Arctic and Antarctic habitats, both biotic and abiotic. In addition to cold-enzymes, which have been intensively analysed, relevance is given to recent advances in the search for less investigated biomolecules, such as biosurfactants, exopolysaccharides and antibiotics. Full article
(This article belongs to the Special Issue Microbial Extremophiles as Life Pioneers and Wellsprings of Valuable Molecules)
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