Search for Articles:
Title / Keyword
Author / Affiliation / Email
Journal
Article Type
 
 
Advanced Search
 
Section
Special Issue
Volume
Issue
Number
Page
 
6.4
4.5
Journals
Microorganisms
Special Issues
Extremophiles and Extremozymes in Academia and Industries
share announcement

Extremophiles and Extremozymes in Academia and Industries

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

Deadline for manuscript submissions: closed (30 September 2020) | Viewed by 53977

Special Issue Editors

Prof. Dr. Rajesh K. Sani

E-Mail Website
Guest Editor
Karen M. Swindler Department of Chemical and Biological Engineering, South Dakota School of Mines and Technology, Rapid City, SD, USA
Interests: biomaterials; exopolysaccharides; extremophilic bioprocessing; biocatalysis
Special Issues, Collections and Topics in MDPI journals
Dr. Navanietha K. Rathinam

E-Mail
Guest Editor
Department of Chemical and Biological Engineering, South Dakota School of Mines and Technology, 501 East St. Joseph Street, Rapid City, SD 57701-3995, USA
Interests: thermophilic bioprocessing; biopolymers; nanomaterials; microbial electrochemical technologies; drug resistant microorganisms
Prof. Dr. Sunil Khare

E-Mail Website
Guest Editor
Enzyme and Microbial Biochemistry Lab, Department of Chemistry, Indian Institute of Technology Delhi, New Delhi 110016, India
Interests: extremophiles and extremozymes; microbiology; biochemistry; proteins; proteomics; enzymes; biocatalysis; nanobiotechnology; food biotechnology; environmental bioremediation; solid state fermentation

Special Issue Information

Dear Colleagues,

Biochemical processes have been realized as the ideal option for replacing physicochemical processes in an efficient, eco-friendly, and economical manner. Microorganisms and their enzymes are the key players in most of the processes, for example, for the production of bioenergy. The conventional microbial processes, however, suffer from several limitations, such as the narrow range of operational conditions and low catalytic rates. These limitations can be circumvented by the use of extremophiles and extremozymes for different industrial processes. Extremophiles can thrive under adverse conditions, such as high or low temperatures, high or low pressures, high radiations, high salt concentrations, or acidic or alkaline conditions. Extremophiles and extremozymes have several advantages, for example, they can operate in a much broader range of conditions, for various industrial applications. Extremozymes are very stable, have a longer shelf life, and have a greater activity, thereby leading to a high rate of catalysis. They are also more resistant to proteolysis and organic solvents.  They can be produced in bulk using heterologous expression systems. 

Therefore, this Special Issue will cover various renewable energy resources, processes, and products; critical aspects and challenges of biomass conversion into biofuels; and value-added bioproducts using extremophiles and their enzymes. More specifically, we invite research and review manuscripts focused on, but not limited to, the following: extremophilic microbial and enzymatic processes; the engineering of microbes and enzymes for bioenergy applications; the recent advances in extremophilic research encompassing genetic, molecular, and physiological adaptations; vis-à-vis new molecules from extreme life; and current trends in extremophilic microbial and bioprocessing in response to the current demands from various sectors of industry.

Prof. Dr. Rajesh K. Sani
Dr. Navanietha K. Rathinam
Prof. Dr. Sunil Khare
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Microorganisms is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2700 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • extremophiles
  • thermophiles
  • psychrophiles
  • halophiles
  • antibiotic resistant microorganisms
  • drug resistant microorganisms
  • extremozymes
  • biofuels and value-added products

Published Papers (15 papers)

Download All Papers
Order results
Result details
Show export options expand_more Show export options expand_less
Select all
Export citation of selected articles as:

Research

Jump to: Review

19 pages, 2725 KiB  
Article
Understanding High-Salt and Cold Adaptation of a Polyextremophilic Enzyme
by Ram Karan, Sam Mathew, Reyhan Muhammad, Didier B. Bautista, Malvina Vogler, Jorg Eppinger, Romina Oliva, Luigi Cavallo, Stefan T. Arold and Magnus Rueping
Microorganisms 2020, 8(10), 1594; https://doi.org/10.3390/microorganisms8101594 - 16 Oct 2020
Cited by 30 | Viewed by 4320
Abstract
The haloarchaeon Halorubrum lacusprofundi is among the few polyextremophilic organisms capable of surviving in one of the most extreme aquatic environments on Earth, the Deep Lake of Antarctica (−18 °C to +11.5 °C and 21–28%, w/v salt content). Hence, H. lacusprofundi has been [...] Read more.
The haloarchaeon Halorubrum lacusprofundi is among the few polyextremophilic organisms capable of surviving in one of the most extreme aquatic environments on Earth, the Deep Lake of Antarctica (−18 °C to +11.5 °C and 21–28%, w/v salt content). Hence, H. lacusprofundi has been proposed as a model for biotechnology and astrobiology to investigate potential life beyond Earth. To understand the mechanisms that allow proteins to adapt to both salinity and cold, we structurally (including X-ray crystallography and molecular dynamics simulations) and functionally characterized the β-galactosidase from H. lacusprofundi (hla_bga). Recombinant hla_bga (produced in Haloferax volcanii) revealed exceptional stability, tolerating up to 4 M NaCl and up to 20% (v/v) of organic solvents. Despite being cold-adapted, hla_bga was also stable up to 60 °C. Structural analysis showed that hla_bga combined increased surface acidity (associated with halophily) with increased structural flexibility, fine-tuned on a residue level, for sustaining activity at low temperatures. The resulting blend enhanced structural flexibility at low temperatures but also limited protein movements at higher temperatures relative to mesophilic homologs. Collectively, these observations help in understanding the molecular basis of a dual psychrophilic and halophilic adaptation and suggest that such enzymes may be intrinsically stable and functional over an exceptionally large temperature range. Full article
(This article belongs to the Special Issue Extremophiles and Extremozymes in Academia and Industries)
►▼ Show Figures

Figure 1

17 pages, 2885 KiB  
Article
Genomic and Transcriptome Analyses of a Thermophilic Bacterium Geobacillus stearothermophilus B5 Isolated from Compost Reveal Its Enzymatic Basis for Lignocellulose Degradation
by Mengmeng Wang, Jiaxi Miao, Xuanqing Wang, Tuo Li, Han Zhu, Dongyang Liu and Qirong Shen
Microorganisms 2020, 8(9), 1357; https://doi.org/10.3390/microorganisms8091357 - 4 Sep 2020
Cited by 12 | Viewed by 2759
Abstract
A lignocellulose-degrading strain isolated from thermophilic compost was identified as Geobacillus stearothermophilus B5, and found able to secrete considerable amounts of enzymes at optimal temperature (60 °C) and pH (7.5). One circular contig of 3.37 Mbp was assembled from raw data, and 3371 [...] Read more.
A lignocellulose-degrading strain isolated from thermophilic compost was identified as Geobacillus stearothermophilus B5, and found able to secrete considerable amounts of enzymes at optimal temperature (60 °C) and pH (7.5). One circular contig of 3.37 Mbp was assembled from raw data, and 3371 protein-coding genes were predicted. Clusters of orthologous groups (COG) analysis revealed various genes with functions in polymeric substrate degradation, especially for Carbohydrate Active enZymes (CAZymes), such as glycoside hydrolases (GHs) and glycosyl transferases (GTs). Furthermore, the transcriptional responses of B5 at different temperatures—with rice straw provided as the sole carbon source—were analyzed. The results revealed that B5 could resist high temperature by upregulating heat shock proteins (HSPs), enhancing protein synthesis, and decreasing carbon catabolism. Briefly, B5 possesses the ability of lignocellulose degradation, and might be considered a potential inoculant for improving composting efficiency. Full article
(This article belongs to the Special Issue Extremophiles and Extremozymes in Academia and Industries)
►▼ Show Figures

Figure 1

22 pages, 2079 KiB  
Article
Global Transcriptomic Responses of Roseithermus sacchariphilus Strain RA in Media Supplemented with Beechwood Xylan
by Kok Jun Liew, Neil C. Bruce, Rajesh Kumar Sani, Chun Shiong Chong, Amira Suriaty Yaakop, Mohd Shahir Shamsir and Kian Mau Goh
Microorganisms 2020, 8(7), 976; https://doi.org/10.3390/microorganisms8070976 - 29 Jun 2020
Cited by 2 | Viewed by 2350
Abstract
The majority of the members in order Rhodothermales are underexplored prokaryotic extremophiles. Roseithermus, a new genus within Rhodothermales, was first described in 2019. Roseithermus sacchariphilus is the only species in this genus. The current report aims to evaluate the transcriptomic responses [...] Read more.
The majority of the members in order Rhodothermales are underexplored prokaryotic extremophiles. Roseithermus, a new genus within Rhodothermales, was first described in 2019. Roseithermus sacchariphilus is the only species in this genus. The current report aims to evaluate the transcriptomic responses of R. sacchariphilus strain RA when cultivated on beechwood xylan. Strain RA doubled its growth in Marine Broth (MB) containing xylan compared to Marine Broth (MB) alone. Strain RA harbors 54 potential glycosyl hydrolases (GHs) that are affiliated with 30 families, including cellulases (families GH 3, 5, 9, and 44) and hemicellulases (GH 2, 10, 16, 29, 31,43, 51, 53, 67, 78, 92, 106, 113, 130, and 154). The majority of these GHs were upregulated when the cells were grown in MB containing xylan medium and enzymatic activities for xylanase, endoglucanase, β-xylosidase, and β-glucosidase were elevated. Interestingly, with the introduction of xylan, five out of six cellulolytic genes were upregulated. Furthermore, approximately 1122 genes equivalent to one-third of the total genes for strain RA were upregulated. These upregulated genes were mostly involved in transportation, chemotaxis, and membrane components synthesis. Full article
(This article belongs to the Special Issue Extremophiles and Extremozymes in Academia and Industries)
►▼ Show Figures

Figure 1

18 pages, 2426 KiB  
Article
Biotransformation of Carboxylic Acids to Alcohols: Characterization of Thermoanaerobacter Strain AK152 and 1-Propanol Production via Propionate Reduction
by Sean Michael Scully and Johann Orlygsson
Microorganisms 2020, 8(6), 945; https://doi.org/10.3390/microorganisms8060945 - 23 Jun 2020
Cited by 5 | Viewed by 3081
Abstract
Thermoanaerobacter strains have recently gained interest because of their ability to convert short chain fatty acids to alcohols using actively growing cells. Thermoanaerobacter thermohydrosulfuricus strain AK152 was physiologically investigated for its ethanol and other alcohol formation. The temperature and pH optimum of the [...] Read more.
Thermoanaerobacter strains have recently gained interest because of their ability to convert short chain fatty acids to alcohols using actively growing cells. Thermoanaerobacter thermohydrosulfuricus strain AK152 was physiologically investigated for its ethanol and other alcohol formation. The temperature and pH optimum of the strain was 70 °C and pH 7.0 and the strain degraded a variety of compounds present in lignocellulosic biomass like monosaccharides, disaccharides, and starch. The strain is highly ethanologenic, producing up to 86% of the theoretical ethanol yield form hexoses. Strain AK152 was inhibited by relatively low initial substrate (30 mM) concentration, leading to inefficient degradation of glucose and levelling up of all end-product formation. The present study shows that the strain produces alcohols from most of the tested carboxylic acids, with the highest yields for propionate conversion to propanol (40.7%) with kinetic studies demonstrating that the maximum conversion happens within the first 48 h of fermentation. Various physiological tests were performed to maximize the acid conversion to the alcohol which reveals that the optimum pH for propionate conversion is pH 6.7 which affords a 57.3% conversion. Kinetic studies reveal that propionate conversion is rapid, achieving a maximum conversion within the first 48 h of fermentation. Finally, by using 13C NMR, it was shown that the addition of propionate indeed converted to propanol. Full article
(This article belongs to the Special Issue Extremophiles and Extremozymes in Academia and Industries)
►▼ Show Figures

Figure 1

16 pages, 1726 KiB  
Article
Adaptive Enrichment of a Thermophilic Bacterial Isolate for Enhanced Enzymatic Activity
by Tanvi Govil, Priya Saxena, Dipayan Samanta, Sindhu Suresh Singh, Sudhir Kumar, David R. Salem and Rajesh K. Sani
Microorganisms 2020, 8(6), 871; https://doi.org/10.3390/microorganisms8060871 - 9 Jun 2020
Cited by 9 | Viewed by 2700
Abstract
The mimicking of evolution on a laboratory timescale to enhance biocatalyst specificity, substrate utilization activity, and/or product formation, is an effective and well-established approach that does not involve genetic engineering or regulatory details of the microorganism. The present work employed an evolutionary adaptive [...] Read more.
The mimicking of evolution on a laboratory timescale to enhance biocatalyst specificity, substrate utilization activity, and/or product formation, is an effective and well-established approach that does not involve genetic engineering or regulatory details of the microorganism. The present work employed an evolutionary adaptive approach to improve the lignocellulose deconstruction capabilities of the strain by inducing the expression of laccase, a multicopper oxidase, in Geobacillus sp. strain WSUCF1. This bacterium is highly efficient in depolymerizing unprocessed lignocellulose, needing no preprocessing/pretreatment of the biomasses. However, it natively produces low levels of laccase. After 15 rounds of serially adapting this thermophilic strain in the presence of unprocessed corn stover as the selective pressure, we recorded a 20-fold increase in catalytic laccase activity, at 9.23 ± 0.6 U/mL, in an adapted yet stable strain of Geobacillus sp. WSUCF1, compared with the initial laccase production (0.46 ± 0.04 U/mL) obtained with the unadapted strain grown on unprocessed corn stover before optimization. Chemical composition analysis demonstrated that lignin removal by the adapted strain was 22 wt.% compared with 6 wt.% removal by the unadapted strain. These results signify a favorable prospect for fast, cost competitive bulk production of this thermostable enzyme. Also, this work has practical importance, as this fast adaptation of the Geobacillus sp. strain WSUCF1 suggests the possibility of growing industrial quantities of Geobacillus sp. strain WSUCF1 cells as biocatalysts on reasonably inexpensive carbon sources for commercial use. This work is the first application of the adaptive laboratory evolution approach for developing the desired phenotype of enhanced ligninolytic capability in any microbial strain. Full article
(This article belongs to the Special Issue Extremophiles and Extremozymes in Academia and Industries)
►▼ Show Figures

Figure 1

13 pages, 1378 KiB  
Communication
Bacillus cytotoxicus Isolated from a Pristine Natural Geothermal Area Reveals High Keratinolytic Activity
by Ivana Cavello, María Sofía Urbieta, Sebastián Cavalitto and Edgardo Donati
Microorganisms 2020, 8(6), 796; https://doi.org/10.3390/microorganisms8060796 - 26 May 2020
Cited by 8 | Viewed by 2068
Abstract
Geothermal areas are the niches of a rich microbial diversity that is not only part of the intangible patrimony of a country but also the source of many microbial species with potential biotechnological applications. Particularly, microbial species in geothermal areas in Argentina have [...] Read more.
Geothermal areas are the niches of a rich microbial diversity that is not only part of the intangible patrimony of a country but also the source of many microbial species with potential biotechnological applications. Particularly, microbial species in geothermal areas in Argentina have been scarcely explored regarding their possible biotechnological uses. The purpose of this work was to explore the proteolytic and keratinolytic enzymatic potential of microorganisms that inhabit in the Domuyo geothermal area in the Neuquén Province. To this end, we did enrichment cultures from two high-temperature natural samples in mineral media only supplemented with whole chicken feathers. After the isolation and the phylogenetic and morphologic characterization of different colonies, we obtained a collection of Bacillus cytotoxicus isolates, a species with no previous report of keratinolytic activity and only reported in rehydrated meals connected with food poisoning outbreaks. Its natural habitat has been unknown up to now. We characterized the proteolytic and keratinolytic capacities of the B. cytotoxicus isolates in different conditions, which proved to be remarkably high compared with those of other similar species. Thus, our work represents the first report of the isolation as well as the keratinolytic capacity characterization of strains of B. cytotixicus obtained from a natural environment. Full article
(This article belongs to the Special Issue Extremophiles and Extremozymes in Academia and Industries)
►▼ Show Figures

Figure 1

15 pages, 2942 KiB  
Article
Comparative Proteomics Analysis Reveals New Features of the Oxidative Stress Response in the Polyextremophilic Bacterium Deinococcus radiodurans
by Lihua Gao, Zhengfu Zhou, Xiaonan Chen, Wei Zhang, Min Lin and Ming Chen
Microorganisms 2020, 8(3), 451; https://doi.org/10.3390/microorganisms8030451 - 23 Mar 2020
Cited by 16 | Viewed by 4868
Abstract
Deinococcus radiodurans is known for its extreme resistance to ionizing radiation, oxidative stress, and other DNA-damaging agents. The robustness of this bacterium primarily originates from its strong oxidative resistance mechanisms. Hundreds of genes have been demonstrated to contribute to oxidative resistance in D. [...] Read more.
Deinococcus radiodurans is known for its extreme resistance to ionizing radiation, oxidative stress, and other DNA-damaging agents. The robustness of this bacterium primarily originates from its strong oxidative resistance mechanisms. Hundreds of genes have been demonstrated to contribute to oxidative resistance in D. radiodurans; however, the antioxidant mechanisms have not been fully characterized. In this study, comparative proteomics analysis of D. radiodurans grown under normal and oxidative stress conditions was conducted using label-free quantitative proteomics. The abundances of 852 of 1700 proteins were found to significantly differ between the two groups. These differential proteins are mainly associated with translation, DNA repair and recombination, response to stresses, transcription, and cell wall organization. Highly upregulated expression was observed for ribosomal proteins such as RplB, Rpsl, RpsR, DNA damage response proteins (DdrA, DdrB), DNA repair proteins (RecN, RecA), and transcriptional regulators (members of TetR, AsnC, and GntR families, DdrI). The functional analysis of proteins in response to oxidative stress is discussed in detail. This study reveals the global protein expression profile of D. radiodurans in response to oxidative stress and provides new insights into the regulatory mechanism of oxidative resistance in D. radiodurans. Full article
(This article belongs to the Special Issue Extremophiles and Extremozymes in Academia and Industries)
►▼ Show Figures

Figure 1

18 pages, 2301 KiB  
Article
Acetate Production from Cafeteria Wastes and Corn Stover Using a Thermophilic Anaerobic Consortium: A Prelude Study for the Use of Acetate for the Production of Value-Added Products
by Aditi David, Abhilash Kumar Tripathi and Rajesh Kumar Sani
Microorganisms 2020, 8(3), 353; https://doi.org/10.3390/microorganisms8030353 - 2 Mar 2020
Cited by 5 | Viewed by 3358
Abstract
Efficient and sustainable biochemical production using low-cost waste assumes considerable industrial and ecological importance. Solid organic wastes (SOWs) are inexpensive, abundantly available resources and their bioconversion to volatile fatty acids, especially acetate, aids in relieving the requirements of pure sugars for microbial biochemical [...] Read more.
Efficient and sustainable biochemical production using low-cost waste assumes considerable industrial and ecological importance. Solid organic wastes (SOWs) are inexpensive, abundantly available resources and their bioconversion to volatile fatty acids, especially acetate, aids in relieving the requirements of pure sugars for microbial biochemical productions in industries. Acetate production from SOW that utilizes the organic carbon of these wastes is used as an efficient solid waste reduction strategy if the environmental factors are optimized. This study screens and optimizes influential factors (physical and chemical) for acetate production by a thermophilic acetogenic consortium using two SOWs—cafeteria wastes and corn stover. The screening experiment revealed significant effects of temperature, bromoethane sulfonate, and shaking on acetate production. Temperature, medium pH, and C:N ratio were further optimized using statistical optimization with response surface methodology. The maximum acetate concentration of 8061 mg L−1 (>200% improvement) was achieved at temperature, pH, and C:N ratio of 60 °C, 6, 25, respectively, and acetate accounted for more than 85% of metabolites. This study also demonstrated the feasibility of using acetate-rich fermentate (obtained from SOWs) as a substrate for the growth of industrially relevant yeast Yarrowia lipolytica, which can convert acetate into higher-value biochemicals. Full article
(This article belongs to the Special Issue Extremophiles and Extremozymes in Academia and Industries)
►▼ Show Figures

Figure 1

18 pages, 2907 KiB  
Article
A Novel Moderately Thermophilic Type Ib Methanotroph Isolated from an Alkaline Thermal Spring in the Ethiopian Rift Valley
by Tajul Islam, Amare Gessesse, Antonio Garcia-Moyano, J. Colin Murrell and Lise Øvreås
Microorganisms 2020, 8(2), 250; https://doi.org/10.3390/microorganisms8020250 - 13 Feb 2020
Cited by 10 | Viewed by 3870
Abstract
Aerobic moderately thermophilic and thermophilic methane-oxidizing bacteria make a substantial contribution in the control of global warming through biological reduction of methane emissions and have a unique capability of utilizing methane as their sole carbon and energy source. Here, we report a novel [...] Read more.
Aerobic moderately thermophilic and thermophilic methane-oxidizing bacteria make a substantial contribution in the control of global warming through biological reduction of methane emissions and have a unique capability of utilizing methane as their sole carbon and energy source. Here, we report a novel moderately thermophilic Methylococcus-like Type Ib methanotroph recovered from an alkaline thermal spring (55.4 °C and pH 8.82) in the Ethiopian Rift Valley. The isolate, designated LS7-MC, most probably represents a novel species of a new genus in the family Methylococcaceae of the class Gammaproteobacteria. The 16S rRNA gene phylogeny indicated that strain LS7-MC is distantly related to the closest described relative, Methylococcus capsulatus (92.7% sequence identity). Growth was observed at temperatures of 30–60 °C (optimal, 51–55 °C), and the cells possessed Type I intracellular membrane (ICM). The comparison of the pmoA gene sequences showed that the strain was most closely related to M. capsulatus (87.8%). Soluble methane monooxygenase (sMMO) was not detected, signifying the biological oxidation process from methane to methanol by the particulate methane monooxygenase (pMMO). The other functional genes mxaF, cbbL and nifH were detected by PCR. To our knowledge, the new strain is the first isolated moderately thermophilic methanotroph from an alkaline thermal spring of the family Methylococcaceae. Furthermore, LS7-MC represents a previously unrecognized biological methane sink in thermal habitats, expanding our knowledge of its ecological role in methane cycling and aerobic methanotrophy. Full article
(This article belongs to the Special Issue Extremophiles and Extremozymes in Academia and Industries)
►▼ Show Figures

Figure 1

16 pages, 2486 KiB  
Article
Isolation of a Psychrotolerant and UV-C-Resistant Bacterium from Elephant Island, Antarctica with a Highly Thermoactive and Thermostable Catalase
by María T. Monsalves, Gabriela P. Ollivet-Besson, Maximiliano J. Amenabar and Jenny M. Blamey
Microorganisms 2020, 8(1), 95; https://doi.org/10.3390/microorganisms8010095 - 10 Jan 2020
Cited by 22 | Viewed by 3699
Abstract
Microorganisms present in Antarctica have to deal not only with cold temperatures but also with other environmental conditions, such as high UV radiation, that trigger the generation of reactive oxygen species. Therefore, Antarctic microorganisms must have an important antioxidant defense system to prevent [...] Read more.
Microorganisms present in Antarctica have to deal not only with cold temperatures but also with other environmental conditions, such as high UV radiation, that trigger the generation of reactive oxygen species. Therefore, Antarctic microorganisms must have an important antioxidant defense system to prevent oxidative damage. One of these defenses are antioxidant enzymes, such as catalase, which is involved in the detoxification of hydrogen peroxide produced under oxidative conditions. Here, we reported the isolation and partial characterization of an Antarctic bacterium belonging to the Serratia genus that was resistant to UV-C radiation and well-adapted to cold temperatures. This microorganism, denominated strain I1P, was efficient at decreasing reactive oxygen species levels produced after UV-C irradiation. Genomic and activity assays suggested that the enzymatic antioxidant defense mechanisms of strain I1P, especially its catalase enzyme, may confer UV resistance. This catalase was active in a wide range of temperatures (20–70 °C), showing optimal activity at 50 °C (at pH 7.0), a remarkable finding considering its psychrotolerant origin. In addition, this enzyme was thermostable, retaining around 60% of its activity after 6 h of incubation at 50 °C. The antioxidant defense systems of strain I1P, including its surprisingly thermoactive and thermostable catalase enzyme, make this microorganism a good source of biocompounds with potential biotechnological applications. Full article
(This article belongs to the Special Issue Extremophiles and Extremozymes in Academia and Industries)
►▼ Show Figures

Figure 1

19 pages, 3138 KiB  
Article
Novel Sequence Feature of SecA Translocase Protein Unique to the Thermophilic Bacteria: Bioinformatics Analyses to Investigate Their Potential Roles
by Bijendra Khadka, Dhillon Persaud and Radhey S. Gupta
Microorganisms 2020, 8(1), 59; https://doi.org/10.3390/microorganisms8010059 - 29 Dec 2019
Cited by 6 | Viewed by 3621
Abstract
SecA is an evolutionarily conserved protein that plays an indispensable role in the secretion of proteins across the bacterial cell membrane. Comparative analyses of SecA homologs have identified two large conserved signature inserts (CSIs) that are unique characteristics of thermophilic bacteria. A 50 [...] Read more.
SecA is an evolutionarily conserved protein that plays an indispensable role in the secretion of proteins across the bacterial cell membrane. Comparative analyses of SecA homologs have identified two large conserved signature inserts (CSIs) that are unique characteristics of thermophilic bacteria. A 50 aa conserved insert in SecA is exclusively present in the SecA homologs from the orders Thermotogales and Aquificales, while a 76 aa insert in SecA is specific for the order Thermales and Hydrogenibacillus schlegelii. Phylogenetic analyses on SecA sequences show that the shared presence of these CSIs in unrelated groups of thermophiles is not due to lateral gene transfers, but instead these large CSIs have likely originated independently in these lineages due to their advantageous function. Both of these CSIs are located in SecA protein in a surface exposed region within the ATPase domain. To gain insights into the functional significance of the 50 aa CSI in SecA, molecular dynamics (MD) simulations were performed at two different temperatures using ADP-bound SecA from Thermotoga maritima. These analyses have identified a conserved network of water molecules near the 50 aa insert in which the Glu185 residue from the CSI is found to play a key role towards stabilizing these interactions. The results provide evidence for the possible role of the 50 aa CSI in stabilizing the binding interaction of ADP/ATP, which is required for SecA function. Additionally, the surface-exposed CSIs in SecA, due to their potential to make novel protein-protein interactions, could also contribute to the thermostability of SecA from thermophilic bacteria. Full article
(This article belongs to the Special Issue Extremophiles and Extremozymes in Academia and Industries)
►▼ Show Figures

Graphical abstract

10 pages, 1596 KiB  
Communication
Complete Genome Sequence of Acidithiobacillus ferrooxidans YNTRS-40, a Strain of the Ferrous Iron- and Sulfur-Oxidizing Acidophile
by Yu Zhang, Shuang Zhang, Dan Zhao, Yongqing Ni, Weidong Wang and Lei Yan
Microorganisms 2020, 8(1), 2; https://doi.org/10.3390/microorganisms8010002 - 18 Dec 2019
Cited by 27 | Viewed by 6794
Abstract
Acidithiobacillus ferrooxidans YNTRS-40 (A. ferrooxidans) is a chemolithoautotrophic aerobic bacterium isolated from Tengchong hot springs, Yunnan Province, China, with a broad growth pH range of 1.0–4.5. This study reports the genome sequence of this strain and the information of genes related [...] Read more.
Acidithiobacillus ferrooxidans YNTRS-40 (A. ferrooxidans) is a chemolithoautotrophic aerobic bacterium isolated from Tengchong hot springs, Yunnan Province, China, with a broad growth pH range of 1.0–4.5. This study reports the genome sequence of this strain and the information of genes related to the adaptation of diverse stresses and the oxidation of ferrous iron and sulfur. Results showed that YNTRS-40 possesses chromosomal DNA (3,209,933-bp) and plasmid DNA (47,104-bp). The complete genome of 3,257,037-bp consists of 3,349 CDS genes comprising 6 rRNAs, 52 tRNAs, and 6 ncRNAs. There are many encoded genes associated with diverse stresses adaptation and ferrous iron and sulfur oxidation such as rus operon, res operon, petI, petII, sqr, doxDA, cydAB, and cyoABCD. This work will provide essential information for further application of A. ferrooxidans YNTRS-40 in industry. Full article
(This article belongs to the Special Issue Extremophiles and Extremozymes in Academia and Industries)
►▼ Show Figures

Figure 1

14 pages, 2621 KiB  
Article
Soft Sensor-Based Monitoring and Efficient Control Strategies of Biomass Concentration for Continuous Cultures of Haloferax mediterranei and Their Application to an Industrial Production Chain
by Thomas Mainka, Nicole Mahler, Christoph Herwig and Stefan Pflügl
Microorganisms 2019, 7(12), 648; https://doi.org/10.3390/microorganisms7120648 - 4 Dec 2019
Cited by 10 | Viewed by 2557
Abstract
Continuous bioprocessing using cell retention allows the achievement of high space-time yields for slow-growing organisms such as halophiles. However, the lack of efficient methods for monitoring and control limits the application of biotechnological processes in the industry. The aim of this study was [...] Read more.
Continuous bioprocessing using cell retention allows the achievement of high space-time yields for slow-growing organisms such as halophiles. However, the lack of efficient methods for monitoring and control limits the application of biotechnological processes in the industry. The aim of this study was to implement a control and online monitoring strategy for biomass in continuous cultures. For the first time, a feedforward cultivation strategy in a membrane-based cell retention system allowed to control the biomass concentration of the extreme halophilic Haloferax mediterranei at defined levels. Moreover, soft sensor-based biomass estimation allowed reliable monitoring of biomass online. Application of the combined monitoring and control strategy using industrial process water containing formate, phenol, aniline and 4,4′-methylenedianiline could for the first time demonstrate high throughput degradation in this extremophilic bioremediation process, obtaining degradation efficiencies of up to 100%. This process demonstrates the usefulness of continuous halophilic cultures in a circular economy application. Full article
(This article belongs to the Special Issue Extremophiles and Extremozymes in Academia and Industries)
►▼ Show Figures

Graphical abstract

18 pages, 3704 KiB  
Article
Functional Characterization and Structural Analysis of NADH Oxidase Mutants from Thermus thermophilus HB27: Role of Residues 166, 174, and 194 in the Catalytic Properties and Thermostability
by Javier Rocha-Martin, Pedro A. Sánchez-Murcia, Fernando López-Gallego, Aurelio Hidalgo, José Berenguer and José M. Guisan
Microorganisms 2019, 7(11), 515; https://doi.org/10.3390/microorganisms7110515 - 31 Oct 2019
Cited by 2 | Viewed by 3308
Abstract
The Thermus thermophilus strain HB27 NADH-oxidase (Tt27-NOX) catalyzes the oxidation of nicotinamide adenine dinucleotide (NAD(P)H) by reducing molecular oxygen to hydrogen peroxide in a two-electron transfer mechanism. Surprisingly, Tt27-NOX showed significant differences in catalytic properties compared to its counterpart from the strain HB8 [...] Read more.
The Thermus thermophilus strain HB27 NADH-oxidase (Tt27-NOX) catalyzes the oxidation of nicotinamide adenine dinucleotide (NAD(P)H) by reducing molecular oxygen to hydrogen peroxide in a two-electron transfer mechanism. Surprisingly, Tt27-NOX showed significant differences in catalytic properties compared to its counterpart from the strain HB8 (Tt8-NOX), despite a high degree of sequence homology between both variants. The sequence comparison between both enzymes revealed only three divergent amino acid residues at positions 166, 174, and 194. Motivated with these findings, in this work we performed mutagenesis experiments in the former three positions to study the specific role of these residues in the catalytic properties and thermostability of Tt27-NOX. We subjected five mutants, along with the wild-type enzyme, to biochemical characterization and thermal stability studies. As a result, we identified two more active and more thermostable variants than any Tt8-NOX variant reported in the literature. The most active and thermostable variant K166/H174/Y194 retained 90% of its initial activity after 5 h at pH 7 and 80 °C and an increase in melting temperature of 48.3 °C compared with the least active variant K166/R174/Y194 (inactivated after 15 min of incubation). These results, supported by structural analysis and molecular dynamics simulation studies, suggest that Lys at position 166 may stabilize the loop in which His174 is located, increasing thermal stability. Full article
(This article belongs to the Special Issue Extremophiles and Extremozymes in Academia and Industries)
►▼ Show Figures

Figure 1

Review

Jump to: Research

21 pages, 1410 KiB  
Review
Insights into Thermophilic Plant Biomass Hydrolysis from Caldicellulosiruptor Systems Biology
by Sara E. Blumer-Schuette
Microorganisms 2020, 8(3), 385; https://doi.org/10.3390/microorganisms8030385 - 10 Mar 2020
Cited by 9 | Viewed by 3508
Abstract
Plant polysaccharides continue to serve as a promising feedstock for bioproduct fermentation. However, the recalcitrant nature of plant biomass requires certain key enzymes, including cellobiohydrolases, for efficient solubilization of polysaccharides. Thermostable carbohydrate-active enzymes are sought for their stability and tolerance to other process [...] Read more.
Plant polysaccharides continue to serve as a promising feedstock for bioproduct fermentation. However, the recalcitrant nature of plant biomass requires certain key enzymes, including cellobiohydrolases, for efficient solubilization of polysaccharides. Thermostable carbohydrate-active enzymes are sought for their stability and tolerance to other process parameters. Plant biomass degrading microbes found in biotopes like geothermally heated water sources, compost piles, and thermophilic digesters are a common source of thermostable enzymes. While traditional thermophilic enzyme discovery first focused on microbe isolation followed by functional characterization, metagenomic sequences are negating the initial need for species isolation. Here, we summarize the current state of knowledge about the extremely thermophilic genus Caldicellulosiruptor, including genomic and metagenomic analyses in addition to recent breakthroughs in enzymology and genetic manipulation of the genus. Ten years after completing the first Caldicellulosiruptor genome sequence, the tools required for systems biology of this non-model environmental microorganism are in place. Full article
(This article belongs to the Special Issue Extremophiles and Extremozymes in Academia and Industries)
►▼ Show Figures

Figure 1

Show export options expand_more Show export options expand_less
Select all
Export citation of selected articles as:
 
Displaying articles 1-15
Back to TopTop