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Biology
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Extremophilic Archaea
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Extremophilic Archaea

A special issue of Biology (ISSN 2079-7737).

Deadline for manuscript submissions: closed (31 March 2021) | Viewed by 18622

Special Issue Editors

Prof. Dr. Nils-Kåre Birkeland

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Guest Editor
Department of Biological Sciences, University of Bergen, Bergen, Norway
Interests: microbial diversity; microbial ecology; metabolites; enzymes
Special Issues, Collections and Topics in MDPI journals
Prof. Dr. Yoshizumi Ishino

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Guest Editor
Department of Bioscience & Biotechnology, Faculty of Agriculture, Kyushu University, Fukuoka, Japan
Interests: extremophiles; Archaea; genome stability; DNA replication & repair; homologous recombination; genetic engineering; CRISPR; DNA-related enzymes

Special Issue Information

Dear Colleagues,

The domain Archaea—often referred to as the third domain of life—encompasses a number of extremophilic lineages adapted to life under harsh conditions (e.g. high temperature, extreme acidity, and high salt concentrations), which have extended the borderline for the existence of life as we know it. These organisms have served as important experimental models for revealing mechanisms for molecular and physiological adaptations to extreme physical and chemical conditions, and have provided numerous opportunities for novel biotechnological developments. Through their sharing of many molecular characteristics with higher organisms, Archaea has also served as a simplified model for cellular processes in eukaryotes. Further, as a deep-branching lineage, Archaea has provided better insight into early evolution and the origin of eukaryotic cells. In this special issue, recent advances in our understanding of the fundamental biology of extremophilic Archaea and their biotechnological applications are presented in the form of original research papers and reviews.

Prof. Dr. Nils-Kåre Birkeland
Prof. Dr. Yoshizumi Ishino
Guest Editors

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Keywords

  • thermostable enzymes
  • biotechnology
  • evolution
  • genome maintenance
  • transcription
  • DNA replication
  • cell-cycle control
  • extremophiles
  • genetics
  • genomics
  • metagenomics
  • geomicrobiology
  • biochemistry
  • methanogens
  • crenarchaeota
  • euryarchaeota
  • haloarchaea
  • thermophiles
  • hyperthermophiles
  • acidophiles
  • archaeal viruses

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Published Papers (4 papers)

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Research

25 pages, 2714 KiB  
Article
Assessment of 16S rRNA Gene-Based Phylogenetic Diversity of Archaeal Communities in Halite-Crystal Salts Processed from Natural Saharan Saline Systems of Southern Tunisia
by Afef Najjari, Panagiota Stathopoulou, Khaled Elmnasri, Faten Hasnaoui, Ines Zidi, Haitham Sghaier, Hadda Imene Ouzari, Ameur Cherif and George Tsiamis
Biology 2021, 10(5), 397; https://doi.org/10.3390/biology10050397 - 4 May 2021
Cited by 9 | Viewed by 3332
Abstract
A thorough assessment of the phylogenetic diversity and community structure of halophilic archaea from three halite-crystal salts, processed from two separated saline systems of Southern Tunisia has been performed using culture dependent and independent methods targeting different regions of 16S rRNA gene sequences [...] Read more.
A thorough assessment of the phylogenetic diversity and community structure of halophilic archaea from three halite-crystal salts, processed from two separated saline systems of Southern Tunisia has been performed using culture dependent and independent methods targeting different regions of 16S rRNA gene sequences including DGGE, 16S rRNA clone libraries and Illumina Miseq sequencing. Two samples, CDR (red halite-crystal salts) and CDW (white halite-crystal salts), were collected from Chott-Eljerid and one sample CDZ (white halite-crystal salts) from Chott Douz. Fourteen isolates were identified as Halorubrum, Haloferax, Haloarcula, and Halogeometricum genera members. Culture-independent approach revealed a high diversity of archaeal members present in all samples, represented by the Euryarchaeal phylum and the dominance of the Halobacteria class. Nanohaloarchaea were also identified only in white halite samples based on metagenomic analysis. In fact, a total of 61 genera were identified with members of the Halorhabdus, Halonotius, Halorubrum, Haloarcula, and unclassified. Halobacteriaceae were shared among all samples. Unexpected diversity profiles between samples was observed where the red halite crust sample was considered as the most diverse one. The highest diversity was observed with Miseq approach, nevertheless, some genera were detected only with 16S rRNA clone libraries and cultured approaches. Full article
(This article belongs to the Special Issue Extremophilic Archaea)
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8 pages, 1210 KiB  
Article
Thermococcus bergensis sp. nov., a Novel Hyperthermophilic Starch-Degrading Archaeon
by Nils-Kåre Birkeland, Boyke Bunk, Cathrin Spröer, Hans-Peter Klenk and Peter Schönheit
Biology 2021, 10(5), 387; https://doi.org/10.3390/biology10050387 - 29 Apr 2021
Viewed by 2812
Abstract
A novel hyperthermophilic archaeon, termed strain T7324T, was isolated from a mixed sulfate-reducing consortium recovered from hot water produced from a deep North Sea oil reservoir. The isolate is a strict anaerobic chemo-organotroph able to utilize yeast extract or starch as [...] Read more.
A novel hyperthermophilic archaeon, termed strain T7324T, was isolated from a mixed sulfate-reducing consortium recovered from hot water produced from a deep North Sea oil reservoir. The isolate is a strict anaerobic chemo-organotroph able to utilize yeast extract or starch as a carbon source. The genes for a number of sugar degradation enzymes and glutamate dehydrogenase previously attributed to the sulfate reducing strain of the consortium (Archaeoglobus fulgidus strain 7324) were identified in the nearly completed genome sequence. Sequence analysis of the 16S rRNA gene placed the strain in the Thermococcus genus, but with an average nucleotide identity that is less than 90% to its closest relatives. Phylogenomic treeing reconstructions placed the strain on a distinct lineage clearly separated from other Thermococcus spp. The results indicate that the strain T7324T represents a novel species, for which the name Thermococcus bergensis sp. nov. is proposed. The type strain is T7324T (=DSM 27149T = KCTC 15808T). Full article
(This article belongs to the Special Issue Extremophilic Archaea)
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24 pages, 5196 KiB  
Article
Biochemical Characterization of the Amylase Activity from the New Haloarchaeal Strain Haloarcula sp. HS Isolated in the Odiel Marshlands
by Patricia Gómez-Villegas, Javier Vigara, Luis Romero, Cecilia Gotor, Sara Raposo, Brígida Gonçalves and Rosa Léon
Biology 2021, 10(4), 337; https://doi.org/10.3390/biology10040337 - 16 Apr 2021
Cited by 15 | Viewed by 6773
Abstract
Alpha-amylases are a large family of α,1-4-endo-glycosyl hydrolases distributed in all kingdoms of life. The need for poly-extremotolerant amylases encouraged their search in extreme environments, where archaea become ideal candidates to provide new enzymes that are able to work in the harsh conditions [...] Read more.
Alpha-amylases are a large family of α,1-4-endo-glycosyl hydrolases distributed in all kingdoms of life. The need for poly-extremotolerant amylases encouraged their search in extreme environments, where archaea become ideal candidates to provide new enzymes that are able to work in the harsh conditions demanded in many industrial applications. In this study, a collection of haloarchaea isolated from Odiel saltern ponds in the southwest of Spain was screened for their amylase activity. The strain that exhibited the highest activity was selected and identified as Haloarcula sp. HS. We demonstrated the existence in both, cellular and extracellular extracts of the new strain, of functional α-amylase activities, which showed to be moderately thermotolerant (optimum around 60 °C), extremely halotolerant (optimum over 25% NaCl), and calcium-dependent. The tryptic digestion followed by HPLC-MS/MS analysis of the partially purified cellular and extracellular extracts allowed to identify the sequence of three alpha-amylases, which despite sharing a low sequence identity, exhibited high three-dimensional structure homology, conserving the typical domains and most of the key consensus residues of α-amylases. Moreover, we proved the potential of the extracellular α-amylase from Haloarcula sp. HS to treat bakery wastes under high salinity conditions. Full article
(This article belongs to the Special Issue Extremophilic Archaea)
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20 pages, 2223 KiB  
Article
Antioxidant, Antimicrobial, and Bioactive Potential of Two New Haloarchaeal Strains Isolated from Odiel Salterns (Southwest Spain)
by Patricia Gómez-Villegas, Javier Vigara, Marta Vila, João Varela, Luísa Barreira and Rosa Léon
Biology 2020, 9(9), 298; https://doi.org/10.3390/biology9090298 - 18 Sep 2020
Cited by 29 | Viewed by 4366
Abstract
The need to survive in extreme environments has furnished haloarchaea with a series of components specially adapted to work in such conditions. The possible application of these molecules in the pharmaceutical and industrial fields has received increasing attention; however, many potential bioactivities of [...] Read more.
The need to survive in extreme environments has furnished haloarchaea with a series of components specially adapted to work in such conditions. The possible application of these molecules in the pharmaceutical and industrial fields has received increasing attention; however, many potential bioactivities of haloarchaea are still poorly explored. In this paper, we describe the isolation and identification of two new haloarchaeal strains from the saltern ponds located in the marshlands of the Odiel River, in the southwest of Spain, as well as the in vitro assessment of their antioxidant, antimicrobial, and bioactive properties. The acetone extract obtained from the new isolated Haloarcula strain exhibited the highest antioxidant activity, while the acetone extracts from both isolated strains demonstrated a strong antimicrobial activity, especially against other halophilic microorganisms. Moreover, these extracts showed a remarkable ability to inhibit the enzyme cyclooxygenase-2 and to activate the melanogenic enzyme tyrosinase, indicating their potential against chronic inflammation and skin pigmentation disorders. Finally, the aqueous protein-rich extracts obtained from both haloarchaea exhibited an important inhibitory effect on the activity of the acetylcholinesterase enzyme, involved in the hydrolysis of cholinergic neurotransmitters and related to several neurological diseases. Full article
(This article belongs to the Special Issue Extremophilic Archaea)
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