Special Issue "Extremophiles and Extreme Environments"

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A special issue of Life (ISSN 2075-1729). This special issue belongs to the section "Life Sciences".

Deadline for manuscript submissions: closed (30 November 2012)

Special Issue Editor

Guest Editor
Prof. Pabulo H. Rampelotto

Center of Biotechnology and PPGBCM, Federal University of Rio Grande do Sul, Porto Alegre, RS, Brazil
Interests: biotechnology; next generation sequencing; metagenomics; molecular biology and biochemistry of microorganisms; extremophiles; grand challenges

Special Issue Information

Dear Colleagues,

Over the last decades, the study of extremophiles has providing ground breaking discoveries that challenge the paradigms of modern biology and make us rethink intriguing questions such as “what is life?”, “what are the limits of life?”, and “what are the fundamental features of life?”. The mechanisms by which different microorganisms adapt to extreme environments provide a unique perspective on the fundamental characteristics of biological processes present in most species. Extremophiles are also critical for evolutionary studies related to the origins of life, since they form a cluster on the base of the tree of life.  Furthermore, the application of extremophiles in industrial processes has opened a new era in biotechnology. The study of extreme environments has become a key area of research for astrobiology. Extremophiles may help us understand what form life takes on other planetary bodies in our own solar system and beyond. These findings and possibilities have made the study of life in extreme environments one of the most exciting areas of research in recent decades. However, despite the latest advances we are just in the beginning of exploring and characterizing the world of extremophiles. This special issue covers all aspects of life in extreme environments. The submission of scientific perspectives, comprehensive reviews or research articles is most welcome.

Prof. Pabulo Henrique Rampelotto
Guest Editor

Keywords

  • astrobiology
  • biochemistry and molecular biology
  • biodiversity and ecology
  • biotechnology
  • extraterrestrial analogues
  • extreme environments
  • extremophiles
  • genetics, genomics and proteomics
  • origin of life
  • phylogeny and evolution
  • physiology and metabolism

Published Papers (24 papers)

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Editorial

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Open AccessEditorial Extremophiles and Extreme Environments
Life 2013, 3(3), 482-485; doi:10.3390/life3030482
Received: 2 August 2013 / Accepted: 5 August 2013 / Published: 7 August 2013
Cited by 1 | PDF Full-text (315 KB) | HTML Full-text | XML Full-text
Abstract
Over the last decades, the study of extremophiles has providing ground breaking discoveries that challenge the paradigms of modern biology and make us rethink intriguing questions such as "what is life?", "what are the limits of life?", and "what are the fundamental [...] Read more.
Over the last decades, the study of extremophiles has providing ground breaking discoveries that challenge the paradigms of modern biology and make us rethink intriguing questions such as "what is life?", "what are the limits of life?", and "what are the fundamental features of life?". These findings and possibilities have made the study of life in extreme environments one of the most exciting areas of research in recent decades. However, despite the latest advances we are just in the beginning of exploring and characterizing the world of extremophiles. This special issue discusses several aspects of these fascinating organisms, exploring their habitats, biodiversity, ecology, evolution, genetics, biochemistry, and biotechnological applications in a collection of exciting reviews and original articles written by leading experts and research groups in the field. [...] Full article
(This article belongs to the Special Issue Extremophiles and Extreme Environments)

Research

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Open AccessArticle Heterotrophic Protists in Hypersaline Microbial Mats and Deep Hypersaline Basin Water Columns
Life 2013, 3(2), 346-362; doi:10.3390/life3020346
Received: 4 March 2013 / Revised: 2 April 2013 / Accepted: 2 April 2013 / Published: 22 May 2013
Cited by 8 | PDF Full-text (575 KB) | HTML Full-text | XML Full-text
Abstract
Although hypersaline environments pose challenges to life because of the low water content (water activity), many such habitats appear to support eukaryotic microbes. This contribution presents brief reviews of our current knowledge on eukaryotes of water-column haloclines and brines from Deep Hypersaline [...] Read more.
Although hypersaline environments pose challenges to life because of the low water content (water activity), many such habitats appear to support eukaryotic microbes. This contribution presents brief reviews of our current knowledge on eukaryotes of water-column haloclines and brines from Deep Hypersaline Anoxic Basins (DHABs) of the Eastern Mediterranean, as well as shallow-water hypersaline microbial mats in solar salterns of Guerrero Negro, Mexico and benthic microbialite communities from Hamelin Pool, Shark Bay, Western Australia. New data on eukaryotic diversity from Shark Bay microbialites indicates eukaryotes are more diverse than previously reported. Although this comparison shows that eukaryotic communities in hypersaline habitats with varying physicochemical characteristics are unique, several groups are commonly found, including diverse alveolates, strameonopiles, and fungi, as well as radiolaria. Many eukaryote sequences (SSU) in both regions also have no close homologues in public databases, suggesting that these environments host unique microbial eukaryote assemblages with the potential to enhance our understanding of the capacity of eukaryotes to adapt to hypersaline conditions. Full article
(This article belongs to the Special Issue Extremophiles and Extreme Environments)
Open AccessArticle Quorum Sensing in Some Representative Species of Halomonadaceae
Life 2013, 3(1), 260-275; doi:10.3390/life3010260
Received: 7 December 2012 / Revised: 18 January 2013 / Accepted: 22 February 2013 / Published: 5 March 2013
Cited by 3 | PDF Full-text (845 KB) | HTML Full-text | XML Full-text
Abstract
Cell-to-cell communication, or quorum-sensing (QS), systems are employed by bacteria for promoting collective behaviour within a population. An analysis to detect QS signal molecules in 43 species of the Halomonadaceae family revealed that they produced N-acyl homoserine lactones (AHLs), which suggests [...] Read more.
Cell-to-cell communication, or quorum-sensing (QS), systems are employed by bacteria for promoting collective behaviour within a population. An analysis to detect QS signal molecules in 43 species of the Halomonadaceae family revealed that they produced N-acyl homoserine lactones (AHLs), which suggests that the QS system is widespread throughout this group of bacteria. Thin-layer chromatography (TLC) analysis of crude AHL extracts, using Agrobacterium tumefaciens NTL4 (pZLR4) as biosensor strain, resulted in different profiles, which were not related to the various habitats of the species in question. To confirm AHL production in the Halomonadaceae species, PCR and DNA sequencing approaches were used to study the distribution of the luxI-type synthase gene. Phylogenetic analysis using sequence data revealed that 29 of the species studied contained a LuxI homolog. Phylogenetic analysis showed that sequences from Halomonadaceae species grouped together and were distinct from other members of the Gammaproteobacteria and also from species belonging to the Alphaproteobacteria and Betaproteobacteria. Full article
(This article belongs to the Special Issue Extremophiles and Extreme Environments)
Open AccessArticle Properties of Halococcus salifodinae, an Isolate from Permian Rock Salt Deposits, Compared with Halococci from Surface Waters
Life 2013, 3(1), 244-259; doi:10.3390/life3010244
Received: 1 January 2013 / Revised: 7 February 2013 / Accepted: 14 February 2013 / Published: 28 February 2013
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Abstract
Halococcus salifodinae BIpT DSM 8989T, an extremely halophilic archaeal isolate from an Austrian salt deposit (Bad Ischl), whose origin was dated to the Permian period, was described in 1994. Subsequently, several strains of the species have been isolated, some [...] Read more.
Halococcus salifodinae BIpT DSM 8989T, an extremely halophilic archaeal isolate from an Austrian salt deposit (Bad Ischl), whose origin was dated to the Permian period, was described in 1994. Subsequently, several strains of the species have been isolated, some from similar but geographically separated salt deposits. Hcc. salifodinae may be regarded as one of the most ancient culturable species which existed already about 250 million years ago. Since its habitat probably did not change during this long period, its properties were presumably not subjected to the needs of mutational adaptation. Hcc. salifodinae and other isolates from ancient deposits would be suitable candidates for testing hypotheses on prokaryotic evolution, such as the molecular clock concept, or the net-like history of genome evolution. A comparison of available taxonomic characteristics from strains of Hcc. salifodinae and other Halococcus species, most of them originating from surface waters, is presented. The cell wall polymer of Hcc. salifodinae was examined and found to be a heteropolysaccharide, similar to that of Hcc. morrhuae. Polyhydroxyalkanoate granules were present in Hcc. salifodinae, suggesting a possible lateral gene transfer before Permian times. Full article
(This article belongs to the Special Issue Extremophiles and Extreme Environments)
Open AccessArticle A Laboratory of Extremophiles: Iceland Coordination Action for Research Activities on Life in Extreme Environments (CAREX) Field Campaign
Life 2013, 3(1), 211-233; doi:10.3390/life3010211
Received: 10 December 2012 / Revised: 23 January 2013 / Accepted: 5 February 2013 / Published: 25 February 2013
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Abstract
Existence of life in extreme environments has been known for a long time, and their habitants have been investigated by different scientific disciplines for decades. However, reports of multidisciplinary research are uncommon. In this paper, we report an interdisciplinary three-day field campaign [...] Read more.
Existence of life in extreme environments has been known for a long time, and their habitants have been investigated by different scientific disciplines for decades. However, reports of multidisciplinary research are uncommon. In this paper, we report an interdisciplinary three-day field campaign conducted in the framework of the Coordination Action for Research Activities on Life in Extreme Environments (CAREX) FP7EU program, with participation of experts in the fields of life and earth sciences. In situ experiments and sampling were performed in a 20 m long hot springs system of different temperature (57 °C to 100 °C) and pH (2 to 4). Abiotic factors were measured to study their influence on the diversity. The CO2 and H2S concentration varied at different sampling locations in the system, but the SO2 remained the same. Four biofilms, mainly composed by four different algae and phototrophic protists, showed differences in photosynthetic activity. Varying temperature of the sampling location affects chlorophyll fluorescence, not only in the microbial mats, but plants (Juncus), indicating selective adaptation to the environmental conditions. Quantitative polymerase chain reaction (PCR), DNA microarray and denaturing gradient gel electrophoresis (DGGE)-based analysis in laboratory showed the presence of a diverse microbial population. Even a short duration (30 h) deployment of a micro colonizer in this hot spring system led to colonization of microorganisms based on ribosomal intergenic spacer (RISA) analysis. Polyphasic analysis of this hot spring system was possible due to the involvement of multidisciplinary approaches. Full article
(This article belongs to the Special Issue Extremophiles and Extreme Environments)
Open AccessArticle Evolution of Microbial “Streamer” Growths in an Acidic, Metal-Contaminated Stream Draining an Abandoned Underground Copper Mine
Life 2013, 3(1), 189-210; doi:10.3390/life3010189
Received: 29 November 2012 / Revised: 22 January 2013 / Accepted: 23 January 2013 / Published: 7 February 2013
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Abstract
A nine year study was carried out on the evolution of macroscopic “acid streamer” growths in acidic, metal-rich mine water from the point of construction of a new channel to drain an abandoned underground copper mine. The new channel became rapidly colonized [...] Read more.
A nine year study was carried out on the evolution of macroscopic “acid streamer” growths in acidic, metal-rich mine water from the point of construction of a new channel to drain an abandoned underground copper mine. The new channel became rapidly colonized by acidophilic bacteria: two species of autotrophic iron-oxidizers (Acidithiobacillus ferrivorans and “Ferrovum myxofaciens”) and a heterotrophic iron-oxidizer (a novel genus/species with the proposed name “Acidithrix ferrooxidans”). The same bacteria dominated the acid streamer communities for the entire nine year period, with the autotrophic species accounting for ~80% of the micro-organisms in the streamer growths (as determined by terminal restriction enzyme fragment length polymorphism (T-RFLP) analysis). Biodiversity of the acid streamers became somewhat greater in time, and included species of heterotrophic acidophiles that reduce ferric iron (Acidiphilium, Acidobacterium, Acidocella and gammaproteobacterium WJ2) and other autotrophic iron-oxidizers (Acidithiobacillus ferrooxidans and Leptospirillum ferrooxidans). The diversity of archaea in the acid streamers was far more limited; relatively few clones were obtained, all of which were very distantly related to known species of euryarchaeotes. Some differences were apparent between the acid streamer community and planktonic-phase bacteria. This study has provided unique insights into the evolution of an extremophilic microbial community, and identified several novel species of acidophilic prokaryotes. Full article
(This article belongs to the Special Issue Extremophiles and Extreme Environments)
Open AccessArticle Predator Avoidance in Extremophile Fish
Life 2013, 3(1), 161-180; doi:10.3390/life3010161
Received: 10 December 2012 / Revised: 28 January 2013 / Accepted: 28 January 2013 / Published: 6 February 2013
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Abstract
Extreme habitats are often characterized by reduced predation pressures, thus representing refuges for the inhabiting species. The present study was designed to investigate predator avoidance of extremophile populations of Poecilia mexicana and P. sulphuraria that either live in hydrogen sulfide-rich (sulfidic) springs [...] Read more.
Extreme habitats are often characterized by reduced predation pressures, thus representing refuges for the inhabiting species. The present study was designed to investigate predator avoidance of extremophile populations of Poecilia mexicana and P. sulphuraria that either live in hydrogen sulfide-rich (sulfidic) springs or cave habitats, both of which are known to have impoverished piscine predator regimes. Focal fishes that inhabited sulfidic springs showed slightly weaker avoidance reactions when presented with several naturally occurring predatory cichlids, but strongest differences to populations from non-sulfidic habitats were found in a decreased shoaling tendency with non-predatory swordtail (Xiphophorus hellerii) females. When comparing avoidance reactions between P. mexicana from a sulfidic cave (Cueva del Azufre) and the adjacent sulfidic surface creek (El Azufre), we found only slight differences in predator avoidance, but surface fish reacted much more strongly to the non-predatory cichlid Vieja bifasciata. Our third experiment was designed to disentangle learned from innate effects of predator recognition. We compared laboratory-reared (i.e., predator-naïve) and wild-caught (i.e., predator-experienced) individuals of P. mexicana from a non-sulfidic river and found no differences in their reaction towards the presented predators. Overall, our results indicate (1) that predator avoidance is still functional in extremophile Poecilia spp. and (2) that predator recognition and avoidance reactions have a strong genetic basis. Full article
(This article belongs to the Special Issue Extremophiles and Extreme Environments)
Open AccessCommunication Pivotal Enzyme in Glutamate Metabolism of Poly-g-Glutamate-Producing Microbes
Life 2013, 3(1), 181-188; doi:10.3390/life3010181
Received: 9 November 2012 / Revised: 28 January 2013 / Accepted: 5 February 2013 / Published: 6 February 2013
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Abstract
The extremely halophilic archaeon Natrialba aegyptiaca secretes the L-homo type of poly-g-glutamate (PGA) as an extremolyte. We examined the enzymes involved in glutamate metabolism and verified the presence of L-glutamate dehydrogenases, L-aspartate aminotransferase, and L-glutamate synthase. However, neither glutamate racemase nor D-amino [...] Read more.
The extremely halophilic archaeon Natrialba aegyptiaca secretes the L-homo type of poly-g-glutamate (PGA) as an extremolyte. We examined the enzymes involved in glutamate metabolism and verified the presence of L-glutamate dehydrogenases, L-aspartate aminotransferase, and L-glutamate synthase. However, neither glutamate racemase nor D-amino acid aminotransferase activity was detected, suggesting the absence of sources of D-glutamate. In contrast, D-glutamate-rich PGA producers mostly possess such intracellular sources of D-glutamate. The results of our present study indicate that the D-glutamate-anabolic enzyme “glutamate racemase” is pivotal in the biosynthesis of PGA. Full article
(This article belongs to the Special Issue Extremophiles and Extreme Environments)

Review

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Open AccessReview Anaerobic Thermophiles
Life 2014, 4(1), 77-104; doi:10.3390/life4010077
Received: 3 June 2013 / Revised: 10 January 2014 / Accepted: 26 January 2014 / Published: 26 February 2014
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Abstract
The term “extremophile” was introduced to describe any organism capable of living and growing under extreme conditions. With the further development of studies on microbial ecology and taxonomy, a variety of “extreme” environments have been found and an increasing number of extremophiles [...] Read more.
The term “extremophile” was introduced to describe any organism capable of living and growing under extreme conditions. With the further development of studies on microbial ecology and taxonomy, a variety of “extreme” environments have been found and an increasing number of extremophiles are being described. Extremophiles have also been investigated as far as regarding the search for life on other planets and even evaluating the hypothesis that life on Earth originally came from space. The first extreme environments to be largely investigated were those characterized by elevated temperatures. The naturally “hot environments” on Earth range from solar heated surface soils and water with temperatures up to 65 °C, subterranean sites such as oil reserves and terrestrial geothermal with temperatures ranging from slightly above ambient to above 100 °C, to submarine hydrothermal systems with temperatures exceeding 300 °C. There are also human-made environments with elevated temperatures such as compost piles, slag heaps, industrial processes and water heaters. Thermophilic anaerobic microorganisms have been known for a long time, but scientists have often resisted the belief that some organisms do not only survive at high temperatures, but actually thrive under those hot conditions. They are perhaps one of the most interesting varieties of extremophilic organisms. These microorganisms can thrive at temperatures over 50 °C and, based on their optimal temperature, anaerobic thermophiles can be subdivided into three main groups: thermophiles with an optimal temperature between 50 °C and 64 °C and a maximum at 70 °C, extreme thermophiles with an optimal temperature between 65 °C and 80 °C, and finally hyperthermophiles with an optimal temperature above 80 °C and a maximum above 90 °C. The finding of novel extremely thermophilic and hyperthermophilic anaerobic bacteria in recent years, and the fact that a large fraction of them belong to the Archaea has definitely made this area of investigation more exciting. Particularly fascinating are their structural and physiological features allowing them to withstand extremely selective environmental conditions. These properties are often due to specific biomolecules (DNA, lipids, enzymes, osmolites, etc.) that have been studied for years as novel sources for biotechnological applications. In some cases (DNA-polymerase, thermostable enzymes), the search and applications successful exceeded preliminary expectations, but certainly further exploitations are still needed. Full article
(This article belongs to the Special Issue Extremophiles and Extreme Environments)
Open AccessReview Domain Structures and Inter-Domain Interactions Defining the Holoenzyme Architecture of Archaeal D-Family DNA Polymerase
Life 2013, 3(3), 375-385; doi:10.3390/life3030375
Received: 15 April 2013 / Revised: 26 June 2013 / Accepted: 27 June 2013 / Published: 5 July 2013
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Abstract
Archaea-specific D-family DNA polymerase (PolD) forms a dimeric heterodimer consisting of two large polymerase subunits and two small exonuclease subunits. According to the protein-protein interactions identified among the domains of large and small subunits of PolD, a symmetrical model for the domain [...] Read more.
Archaea-specific D-family DNA polymerase (PolD) forms a dimeric heterodimer consisting of two large polymerase subunits and two small exonuclease subunits. According to the protein-protein interactions identified among the domains of large and small subunits of PolD, a symmetrical model for the domain topology of the PolD holoenzyme is proposed. The experimental evidence supports various aspects of the model. The conserved amphipathic nature of the N-terminal putative α-helix of the large subunit plays a key role in the homodimeric assembly and the self-cyclization of the large subunit and is deeply involved in the archaeal PolD stability and activity. We also discuss the evolutional transformation from archaeal D-family to eukaryotic B-family polymerase on the basis of the structural information. Full article
(This article belongs to the Special Issue Extremophiles and Extreme Environments)
Open AccessReview Eukaryotic Organisms in Extreme Acidic Environments, the Río Tinto Case
Life 2013, 3(3), 363-374; doi:10.3390/life3030363
Received: 12 March 2013 / Revised: 7 June 2013 / Accepted: 17 June 2013 / Published: 4 July 2013
Cited by 6 | PDF Full-text (630 KB) | HTML Full-text | XML Full-text
Abstract
A major issue in microbial ecology is to identify the limits of life for growth and survival, and to understand the molecular mechanisms that define these limits. Thus, interest in the biodiversity and ecology of extreme environments has grown in recent years [...] Read more.
A major issue in microbial ecology is to identify the limits of life for growth and survival, and to understand the molecular mechanisms that define these limits. Thus, interest in the biodiversity and ecology of extreme environments has grown in recent years for several reasons. Some are basic and revolve around the idea that extreme environments are believed to reflect early Earth conditions. Others are related to the biotechnological potential of extremophiles. In this regard, the study of extremely acidic environments has become increasingly important since environmental acidity is often caused by microbial activity. Highly acidic environments are relatively scarce worldwide and are generally associated with volcanic activity or mining operations. For most acidic environments, low pH facilitates metal solubility, and therefore acidic waters tend to have high concentrations of heavy metals. However, highly acidic environments are usually inhabited by acidophilic and acidotolerant eukaryotic microorganisms such as algae, amoebas, ciliates, heliozoan and rotifers, not to mention filamentous fungi and yeasts. Here, we review the general trends concerning the diversity and ecophysiology of eukaryotic acidophilic microorganims, as well as summarize our latest results on this topic in one of the largest extreme acidic rivers, Río Tinto (SW, Spain). Full article
(This article belongs to the Special Issue Extremophiles and Extreme Environments)
Open AccessReview Hot Spring Metagenomics
Life 2013, 3(2), 308-320; doi:10.3390/life3020308
Received: 7 February 2013 / Revised: 11 April 2013 / Accepted: 15 April 2013 / Published: 25 April 2013
Cited by 8 | PDF Full-text (147 KB) | HTML Full-text | XML Full-text
Abstract
Hot springs have been investigated since the XIX century, but isolation and examination of their thermophilic microbial inhabitants did not start until the 1950s. Many thermophilic microorganisms and their viruses have since been discovered, although the real complexity of thermal communities was [...] Read more.
Hot springs have been investigated since the XIX century, but isolation and examination of their thermophilic microbial inhabitants did not start until the 1950s. Many thermophilic microorganisms and their viruses have since been discovered, although the real complexity of thermal communities was envisaged when research based on PCR amplification of the 16S rRNA genes arose. Thereafter, the possibility of cloning and sequencing the total environmental DNA, defined as metagenome, and the study of the genes rescued in the metagenomic libraries and assemblies made it possible to gain a more comprehensive understanding of microbial communities—their diversity, structure, the interactions existing between their components, and the factors shaping the nature of these communities. In the last decade, hot springs have been a source of thermophilic enzymes of industrial interest, encouraging further study of the poorly understood diversity of microbial life in these habitats. Full article
(This article belongs to the Special Issue Extremophiles and Extreme Environments)
Figures

Open AccessReview Magnetotactic Bacteria from Extreme Environments
Life 2013, 3(2), 295-307; doi:10.3390/life3020295
Received: 14 February 2013 / Revised: 13 March 2013 / Accepted: 13 March 2013 / Published: 26 March 2013
Cited by 7 | PDF Full-text (699 KB) | HTML Full-text | XML Full-text
Abstract
Magnetotactic bacteria (MTB) represent a diverse collection of motile prokaryotes that biomineralize intracellular, membrane-bounded, tens-of-nanometer-sized crystals of a magnetic mineral called magnetosomes. Magnetosome minerals consist of either magnetite (Fe3O4) or greigite (Fe3S4) and cause [...] Read more.
Magnetotactic bacteria (MTB) represent a diverse collection of motile prokaryotes that biomineralize intracellular, membrane-bounded, tens-of-nanometer-sized crystals of a magnetic mineral called magnetosomes. Magnetosome minerals consist of either magnetite (Fe3O4) or greigite (Fe3S4) and cause cells to align along the Earth’s geomagnetic field lines as they swim, a trait called magnetotaxis. MTB are known to mainly inhabit the oxic–anoxic interface (OAI) in water columns or sediments of aquatic habitats and it is currently thought that magnetosomes function as a means of making chemotaxis more efficient in locating and maintaining an optimal position for growth and survival at the OAI. Known cultured and uncultured MTB are phylogenetically associated with the Alpha-, Gamma- and Deltaproteobacteria classes of the phylum Proteobacteria, the Nitrospirae phylum and the candidate division OP3, part of the Planctomycetes-Verrucomicrobia-Chlamydiae (PVC) bacterial superphylum. MTB are generally thought to be ubiquitous in aquatic environments as they are cosmopolitan in distribution and have been found in every continent although for years MTB were thought to be restricted to habitats with pH values near neutral and at ambient temperature. Recently, however, moderate thermophilic and alkaliphilic MTB have been described including: an uncultured, moderately thermophilic magnetotactic bacterium present in hot springs in northern Nevada with a probable upper growth limit of about 63 °C; and several strains of obligately alkaliphilic MTB isolated in pure culture from different aquatic habitats in California, including the hypersaline, extremely alkaline Mono Lake, with an optimal growth pH of >9.0. Full article
(This article belongs to the Special Issue Extremophiles and Extreme Environments)
Open AccessReview Microorganism Response to Stressed Terrestrial Environments: A Raman Spectroscopic Perspective of Extremophilic Life Strategies
Life 2013, 3(1), 276-294; doi:10.3390/life3010276
Received: 4 December 2012 / Revised: 30 January 2013 / Accepted: 17 February 2013 / Published: 13 March 2013
Cited by 6 | PDF Full-text (223 KB) | HTML Full-text | XML Full-text
Abstract
Raman spectroscopy is a valuable analytical technique for the identification of biomolecules and minerals in natural samples, which involves little or minimal sample manipulation. In this paper, we evaluate the advantages and disadvantages of this technique applied to the study of extremophiles. [...] Read more.
Raman spectroscopy is a valuable analytical technique for the identification of biomolecules and minerals in natural samples, which involves little or minimal sample manipulation. In this paper, we evaluate the advantages and disadvantages of this technique applied to the study of extremophiles. Furthermore, we provide a review of the results published, up to the present point in time, of the bio- and geo-strategies adopted by different types of extremophile colonies of microorganisms. We also show the characteristic Raman signatures for the identification of pigments and minerals, which appear in those complex samples. Full article
(This article belongs to the Special Issue Extremophiles and Extreme Environments)
Open AccessReview Molecular Mechanisms of Adaptation of the Moderately Halophilic Bacterium Halobacillis halophilus to Its Environment
Life 2013, 3(1), 234-243; doi:10.3390/life3010234
Received: 11 December 2012 / Revised: 2 February 2013 / Accepted: 5 February 2013 / Published: 27 February 2013
Cited by 6 | PDF Full-text (438 KB) | HTML Full-text | XML Full-text
Abstract
The capability of osmoadaptation is a prerequisite of organisms that live in an environment with changing salinities. Halobacillus halophilus is a moderately halophilic bacterium that grows between 0.4 and 3 M NaCl by accumulating both chloride and compatible solutes as osmolytes. Chloride [...] Read more.
The capability of osmoadaptation is a prerequisite of organisms that live in an environment with changing salinities. Halobacillus halophilus is a moderately halophilic bacterium that grows between 0.4 and 3 M NaCl by accumulating both chloride and compatible solutes as osmolytes. Chloride is absolutely essential for growth and, moreover, was shown to modulate gene expression and activity of enzymes involved in osmoadaptation. The synthesis of different compatible solutes is strictly salinity- and growth phase-dependent. This unique hybrid strategy of H. halophilus will be reviewed here taking into account the recently published genome sequence. Based on identified genes we will speculate about possible scenarios of the synthesis of compatible solutes and the uptake of potassium ion which would complete our knowledge of the fine-tuned osmoregulation and intracellular osmolyte balance in H. halophilus. Full article
(This article belongs to the Special Issue Extremophiles and Extreme Environments)
Open AccessReview Periplasmic Binding Proteins in Thermophiles: Characterization and Potential Application of an Arginine-Binding Protein from Thermotoga maritima: A Brief Thermo-Story
Life 2013, 3(1), 149-160; doi:10.3390/life3010149
Received: 16 November 2012 / Revised: 11 January 2013 / Accepted: 29 January 2013 / Published: 5 February 2013
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Abstract
Arginine-binding protein from the extremophile Thermotoga maritima is a 27.7 kDa protein possessing the typical two-domain structure of the periplasmic binding proteins family. The protein is characterized by a very high specificity and affinity to bind to arginine, also at high temperatures. [...] Read more.
Arginine-binding protein from the extremophile Thermotoga maritima is a 27.7 kDa protein possessing the typical two-domain structure of the periplasmic binding proteins family. The protein is characterized by a very high specificity and affinity to bind to arginine, also at high temperatures. Due to its features, this protein could be taken into account as a potential candidate for the design of a biosensor for arginine. It is important to investigate the stability of proteins when they are used for biotechnological applications. In this article, we review the structural and functional features of an arginine-binding protein from the extremophile Thermotoga maritima with a particular eye on its potential biotechnological applications. Full article
(This article belongs to the Special Issue Extremophiles and Extreme Environments)
Open AccessReview Quorum Sensing in Extreme Environments
Life 2013, 3(1), 131-148; doi:10.3390/life3010131
Received: 10 December 2012 / Revised: 21 January 2013 / Accepted: 22 January 2013 / Published: 29 January 2013
Cited by 11 | PDF Full-text (205 KB) | HTML Full-text | XML Full-text
Abstract
Microbial communication, particularly that of quorum sensing, plays an important role in regulating gene expression in a range of organisms. Although this phenomenon has been well studied in relation to, for example, virulence gene regulation, the focus of this article is to [...] Read more.
Microbial communication, particularly that of quorum sensing, plays an important role in regulating gene expression in a range of organisms. Although this phenomenon has been well studied in relation to, for example, virulence gene regulation, the focus of this article is to review our understanding of the role of microbial communication in extreme environments. Cell signaling regulates many important microbial processes and may play a pivotal role in driving microbial functional diversity and ultimately ecosystem function in extreme environments. Several recent studies have characterized cell signaling in modern analogs to early Earth communities (microbial mats), and characterization of cell signaling systems in these communities may provide unique insights in understanding the microbial interactions involved in function and survival in extreme environments. Cell signaling is a fundamental process that may have co-evolved with communities and environmental conditions on the early Earth. Without cell signaling, evolutionary pressures may have even resulted in the extinction rather than evolution of certain microbial groups. One of the biggest challenges in extremophile biology is understanding how and why some microbial functional groups are located where logically they would not be expected to survive, and tightly regulated communication may be key. Finally, quorum sensing has been recently identified for the first time in archaea, and thus communication at multiple levels (potentially even inter-domain) may be fundamental in extreme environments. Full article
(This article belongs to the Special Issue Extremophiles and Extreme Environments)
Open AccessReview Surface Appendages of Archaea: Structure, Function, Genetics and Assembly
Life 2013, 3(1), 86-117; doi:10.3390/life3010086
Received: 29 November 2012 / Revised: 9 January 2013 / Accepted: 9 January 2013 / Published: 24 January 2013
Cited by 16 | PDF Full-text (1911 KB) | HTML Full-text | XML Full-text
Abstract
Organisms representing diverse subgroupings of the Domain Archaea are known to possess unusual surface structures. These can include ones unique to Archaea such as cannulae and hami as well as archaella (archaeal flagella) and various types of pili that superficially resemble their [...] Read more.
Organisms representing diverse subgroupings of the Domain Archaea are known to possess unusual surface structures. These can include ones unique to Archaea such as cannulae and hami as well as archaella (archaeal flagella) and various types of pili that superficially resemble their namesakes in Bacteria, although with significant differences. Major advances have occurred particularly in the study of archaella and pili using model organisms with recently developed advanced genetic tools. There is common use of a type IV pili-model of assembly for several archaeal surface structures including archaella, certain pili and sugar binding structures termed bindosomes. In addition, there are widespread posttranslational modifications of archaellins and pilins with N-linked glycans, with some containing novel sugars. Archaeal surface structures are involved in such diverse functions as swimming, attachment to surfaces, cell to cell contact resulting in genetic transfer, biofilm formation, and possible intercellular communication. Sometimes functions are co-dependent on other surface structures. These structures and the regulation of their assembly are important features that allow various Archaea, including thermoacidophilic, hyperthermophilic, halophilic, and anaerobic ones, to survive and thrive in the extreme environments that are commonly inhabited by members of this domain. Full article
(This article belongs to the Special Issue Extremophiles and Extreme Environments)
Open AccessReview A Survey of Protein Structures from Archaeal Viruses
Life 2013, 3(1), 118-130; doi:10.3390/life3010118
Received: 15 December 2012 / Revised: 18 January 2013 / Accepted: 21 January 2013 / Published: 24 January 2013
Cited by 2 | PDF Full-text (743 KB) | HTML Full-text | XML Full-text
Abstract
Viruses that infect the third domain of life, Archaea, are a newly emerging field of interest. To date, all characterized archaeal viruses infect archaea that thrive in extreme conditions, such as halophilic, hyperthermophilic, and methanogenic environments. Viruses in general, especially those replicating [...] Read more.
Viruses that infect the third domain of life, Archaea, are a newly emerging field of interest. To date, all characterized archaeal viruses infect archaea that thrive in extreme conditions, such as halophilic, hyperthermophilic, and methanogenic environments. Viruses in general, especially those replicating in extreme environments, contain highly mosaic genomes with open reading frames (ORFs) whose sequences are often dissimilar to all other known ORFs. It has been estimated that approximately 85% of virally encoded ORFs do not match known sequences in the nucleic acid databases, and this percentage is even higher for archaeal viruses (typically 90%–100%). This statistic suggests that either virus genomes represent a larger segment of sequence space and/or that viruses encode genes of novel fold and/or function. Because the overall three-dimensional fold of a protein evolves more slowly than its sequence, efforts have been geared toward structural characterization of proteins encoded by archaeal viruses in order to gain insight into their potential functions. In this short review, we provide multiple examples where structural characterization of archaeal viral proteins has indeed provided significant functional and evolutionary insight. Full article
(This article belongs to the Special Issue Extremophiles and Extreme Environments)
Open AccessReview Biohydrogen Production by the Thermophilic Bacterium Caldicellulosiruptor saccharolyticus: Current Status and Perspectives
Life 2013, 3(1), 52-85; doi:10.3390/life3010052
Received: 5 December 2012 / Revised: 6 January 2013 / Accepted: 7 January 2013 / Published: 17 January 2013
Cited by 10 | PDF Full-text (425 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
Caldicellulosiruptor saccharolyticus is one of the most thermophilic cellulolytic organisms known to date. This Gram-positive anaerobic bacterium ferments a broad spectrum of mono-, di- and polysaccharides to mainly acetate, CO2 and hydrogen. With hydrogen yields approaching the theoretical limit for dark [...] Read more.
Caldicellulosiruptor saccharolyticus is one of the most thermophilic cellulolytic organisms known to date. This Gram-positive anaerobic bacterium ferments a broad spectrum of mono-, di- and polysaccharides to mainly acetate, CO2 and hydrogen. With hydrogen yields approaching the theoretical limit for dark fermentation of 4 mol hydrogen per mol hexose, this organism has proven itself to be an excellent candidate for biological hydrogen production. This review provides an overview of the research on C. saccharolyticus with respect to the hydrolytic capability, sugar metabolism, hydrogen formation, mechanisms involved in hydrogen inhibition, and the regulation of the redox and carbon metabolism. Analysis of currently available fermentation data reveal decreased hydrogen yields under non-ideal cultivation conditions, which are mainly associated with the accumulation of hydrogen in the liquid phase. Thermodynamic considerations concerning the reactions involved in hydrogen formation are discussed with respect to the dissolved hydrogen concentration. Novel cultivation data demonstrate the sensitivity of C. saccharolyticus to increased hydrogen levels regarding substrate load and nitrogen limitation. In addition, special attention is given to the rhamnose metabolism, which represents an unusual type of redox balancing. Finally, several approaches are suggested to improve biohydrogen production by C. saccharolyticus. Full article
(This article belongs to the Special Issue Extremophiles and Extreme Environments)
Open AccessReview Halophilic Bacteria as a Source of Novel Hydrolytic Enzymes
Life 2013, 3(1), 38-51; doi:10.3390/life3010038
Received: 23 November 2012 / Revised: 24 December 2012 / Accepted: 25 December 2012 / Published: 10 January 2013
Cited by 18 | PDF Full-text (154 KB) | HTML Full-text | XML Full-text
Abstract
Hydrolases constitute a class of enzymes widely distributed in nature from bacteria to higher eukaryotes. The halotolerance of many enzymes derived from halophilic bacteria can be exploited wherever enzymatic transformations are required to function under physical and chemical conditions, such as in [...] Read more.
Hydrolases constitute a class of enzymes widely distributed in nature from bacteria to higher eukaryotes. The halotolerance of many enzymes derived from halophilic bacteria can be exploited wherever enzymatic transformations are required to function under physical and chemical conditions, such as in the presence of organic solvents and extremes in temperature and salt content. In recent years, different screening programs have been performed in saline habitats in order to isolate and characterize novel enzymatic activities with different properties to those of conventional enzymes. Several halophilic hydrolases have been described, including amylases, lipases and proteases, and then used for biotechnological applications. Moreover, the discovery of biopolymer-degrading enzymes offers a new solution for the treatment of oilfield waste, where high temperature and salinity are typically found, while providing valuable information about heterotrophic processes in saline environments. In this work, we describe the results obtained in different screening programs specially focused on the diversity of halophiles showing hydrolytic activities in saline and hypersaline habitats, including the description of enzymes with special biochemical properties. The intracellular lipolytic enzyme LipBL, produced by the moderately halophilic bacterium Marinobacter lipolyticus, showed advantages over other lipases, being an enzyme active over a wide range of pH values and temperatures. The immobilized LipBL derivatives obtained and tested in regio- and enantioselective reactions, showed an excellent behavior in the production of free polyunsaturated fatty acids (PUFAs). On the other hand, the extremely halophilic bacterium, Salicola marasensis sp. IC10 showing lipase and protease activities, was studied for its ability to produce promising enzymes in terms of its resistance to temperature and salinity. Full article
(This article belongs to the Special Issue Extremophiles and Extreme Environments)
Open AccessReview The Function of Gas Vesicles in Halophilic Archaea and Bacteria: Theories and Experimental Evidence
Life 2013, 3(1), 1-20; doi:10.3390/life3010001
Received: 29 November 2012 / Revised: 16 December 2012 / Accepted: 17 December 2012 / Published: 27 December 2012
Cited by 7 | PDF Full-text (308 KB) | HTML Full-text | XML Full-text
Abstract
A few extremely halophilic Archaea (Halobacterium salinarum, Haloquadratum walsbyi, Haloferax mediterranei, Halorubrum vacuolatum, Halogeometricum borinquense, Haloplanus spp.) possess gas vesicles that bestow buoyancy on the cells. Gas vesicles are also produced by the anaerobic endospore-forming halophilic [...] Read more.
A few extremely halophilic Archaea (Halobacterium salinarum, Haloquadratum walsbyi, Haloferax mediterranei, Halorubrum vacuolatum, Halogeometricum borinquense, Haloplanus spp.) possess gas vesicles that bestow buoyancy on the cells. Gas vesicles are also produced by the anaerobic endospore-forming halophilic Bacteria Sporohalobacter lortetii and Orenia sivashensis. We have extensive information on the properties of gas vesicles in Hbt. salinarum and Hfx. mediterranei and the regulation of their formation. Different functions were suggested for gas vesicle synthesis: buoying cells towards oxygen-rich surface layers in hypersaline water bodies to prevent oxygen limitation, reaching higher light intensities for the light-driven proton pump bacteriorhodopsin, positioning the cells optimally for light absorption, light shielding, reducing the cytoplasmic volume leading to a higher surface-area-to-volume ratio (for the Archaea) and dispersal of endospores (for the anaerobic spore-forming Bacteria). Except for Hqr. walsbyi which abounds in saltern crystallizer brines, gas-vacuolate halophiles are not among the dominant life forms in hypersaline environments. There only has been little research on gas vesicles in natural communities of halophilic microorganisms, and the few existing studies failed to provide clear evidence for their possible function. This paper summarizes the current status of the different theories why gas vesicles may provide a selective advantage to some halophilic microorganisms. Full article
(This article belongs to the Special Issue Extremophiles and Extreme Environments)
Open AccessReview Molecular Mechanisms of Survival Strategies in Extreme Conditions
Life 2012, 2(4), 364-376; doi:10.3390/life2040364
Received: 24 October 2012 / Revised: 8 November 2012 / Accepted: 26 November 2012 / Published: 7 December 2012
Cited by 1 | PDF Full-text (532 KB) | HTML Full-text | XML Full-text
Abstract
Today, one of the major challenges in biophysics is to disclose the molecular mechanisms underlying biological processes. In such a frame, the understanding of the survival strategies in extreme conditions received a lot of attention both from the scientific and applicative points [...] Read more.
Today, one of the major challenges in biophysics is to disclose the molecular mechanisms underlying biological processes. In such a frame, the understanding of the survival strategies in extreme conditions received a lot of attention both from the scientific and applicative points of view. Since nature provides precious suggestions to be applied for improving the quality of life, extremophiles are considered as useful model-systems. The main goal of this review is to present an overview of some systems, with a particular emphasis on trehalose playing a key role in several extremophile organisms. The attention is focused on the relation among the structural and dynamic properties of biomolecules and bioprotective mechanisms, as investigated by complementary spectroscopic techniques at low- and high-temperature values. Full article
(This article belongs to the Special Issue Extremophiles and Extreme Environments)
Open AccessReview Survival of the Fittest: Overcoming Oxidative Stress at the Extremes of Acid, Heat and Metal
Life 2012, 2(3), 229-242; doi:10.3390/life2030229
Received: 4 July 2012 / Revised: 14 August 2012 / Accepted: 17 August 2012 / Published: 23 August 2012
Cited by 4 | PDF Full-text (158 KB) | HTML Full-text | XML Full-text
Abstract
The habitat of metal respiring acidothermophilic lithoautotrophs is perhaps the most oxidizing environment yet identified. Geothermal heat, sulfuric acid and transition metals contribute both individually and synergistically under aerobic conditions to create this niche. Sulfuric acid and metals originating from sulfidic ores [...] Read more.
The habitat of metal respiring acidothermophilic lithoautotrophs is perhaps the most oxidizing environment yet identified. Geothermal heat, sulfuric acid and transition metals contribute both individually and synergistically under aerobic conditions to create this niche. Sulfuric acid and metals originating from sulfidic ores catalyze oxidative reactions attacking microbial cell surfaces including lipids, proteins and glycosyl groups. Sulfuric acid also promotes hydrocarbon dehydration contributing to the formation of black “burnt” carbon. Oxidative reactions leading to abstraction of electrons is further impacted by heat through an increase in the proportion of reactant molecules with sufficient energy to react. Collectively these factors and particularly those related to metals must be overcome by thermoacidophilic lithoautotrophs in order for them to survive and proliferate. The necessary mechanisms to achieve this goal are largely unknown however mechanistics insights have been gained through genomic studies. This review focuses on the specific role of metals in this extreme environment with an emphasis on resistance mechanisms in Archaea. Full article
(This article belongs to the Special Issue Extremophiles and Extreme Environments)

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