Special Issue "Extremophiles"

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

Deadline for manuscript submissions: closed (30 June 2015)

Special Issue Editors

Guest Editor
Dr. Ricardo Amils

Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Universidad Autónoma de Madrid, Cantoblanco, 28049 Madrid, Spain
Website | E-Mail
Interests: molecular ecology of extreme environments, acidophiles, halophiles, subsurface geomicrobiology, astrobiology
Co-Guest Editor
Dr. Elena González Toril

Centro de Astrobiología (CSIC-INTA), carretera de Ajalvir km 5, 28855 Torrejón de Ardoz, Madrid , Spain
Website | E-Mail
Interests: molecular ecology of extreme environments, acidophiles, phylogeny, fluorescence in situ hybridization (FISH and CARD-FISH), astrobiology

Special Issue Information

Dear Colleagues,

The exploration of extreme environments has led to the discovery of numerous habitats that were considered uninhabitable until recently. Subsequently, interest in the ecology of extreme environments has grown exponentially for different reasons, some of which are fundamental and related with the search for the limits of life, and some of which are more pragmatic and focused on the biotechnological potential of extremophiles. Extremophiles had also played a fundamental role in the development of astrobiology. As stated by the NASA Astrobiology Roadmap, one of the main goals is the characterization of extreme habitats, of the organisms developing on them, and of the mechanisms used to deal with the extreme conditions of the environment, so as to evaluate the possible existence of extraterrestrial life. In this Special Issue of Microorganisms, we invite you to send contributions concerning any aspect related with extremophiles, from the microbial ecology of diverse extreme environments, to the physiology and molecular biology of extremophiles from the three domains, and from the fundamental to the applied aspects of extreme microorganisms.

Prof. Ricardo Amils
Dr. Elena González Toril
Guest Editors

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Keywords

  • thermophiles
  • psicrophiles
  • barophiles
  • halophiles
  • acidophiles
  • alkalophiles
  • radiation resistant
  • bacteria
  • archaea
  • eukaryotes
  • microbial ecology
  • phylogeny
  • physiology
  • mechanisms
  • biotechnology
  • astrobiology

Published Papers (18 papers)

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Research

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Open AccessArticle Extremophiles in an Antarctic Marine Ecosystem
Microorganisms 2016, 4(1), 8; https://doi.org/10.3390/microorganisms4010008
Received: 19 July 2015 / Revised: 28 September 2015 / Accepted: 30 December 2015 / Published: 11 January 2016
Cited by 7 | PDF Full-text (579 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
Recent attempts to explore marine microbial diversity and the global marine microbiome have indicated a large proportion of previously unknown diversity. However, sequencing alone does not tell the whole story, as it relies heavily upon information that is already contained within sequence databases. [...] Read more.
Recent attempts to explore marine microbial diversity and the global marine microbiome have indicated a large proportion of previously unknown diversity. However, sequencing alone does not tell the whole story, as it relies heavily upon information that is already contained within sequence databases. In addition, microorganisms have been shown to present small-to-large scale biogeographical patterns worldwide, potentially making regional combinations of selection pressures unique. Here, we focus on the extremophile community in the boundary region located between the Polar Front and the Southern Antarctic Circumpolar Current in the Southern Ocean, to explore the potential of metagenomic approaches as a tool for bioprospecting in the search for novel functional activity based on targeted sampling efforts. We assessed the microbial composition and diversity from a region north of the current limit for winter sea ice, north of the Southern Antarctic Circumpolar Front (SACCF) but south of the Polar Front. Although, most of the more frequently encountered sequences were derived from common marine microorganisms, within these dominant groups, we found a proportion of genes related to secondary metabolism of potential interest in bioprospecting. Extremophiles were rare by comparison but belonged to a range of genera. Hence, they represented interesting targets from which to identify rare or novel functions. Ultimately, future shifts in environmental conditions favoring more cosmopolitan groups could have an unpredictable effect on microbial diversity and function in the Southern Ocean, perhaps excluding the rarer extremophiles. Full article
(This article belongs to the Special Issue Extremophiles)
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Open AccessArticle The Effect of Tellurite on Highly Resistant Freshwater Aerobic Anoxygenic Phototrophs and Their Strategies for Reduction
Microorganisms 2015, 3(4), 826-838; https://doi.org/10.3390/microorganisms3040826
Received: 12 August 2015 / Accepted: 2 November 2015 / Published: 6 November 2015
Cited by 3 | PDF Full-text (871 KB) | HTML Full-text | XML Full-text
Abstract
Six fresh water aerobic anoxygenic phototrophs (Erythromicrobium ezovicum, strain E1; Erythromicrobium hydrolyticum, E4(1); Erythromicrobium ramosum, E5; Erythromonas ursincola, KR99; Sandaracinobacter sibiricus, RB 16-17; and Roseococcus thiosulfatophilus, RB3) possessing high level resistance to TeO32− and [...] Read more.
Six fresh water aerobic anoxygenic phototrophs (Erythromicrobium ezovicum, strain E1; Erythromicrobium hydrolyticum, E4(1); Erythromicrobium ramosum, E5; Erythromonas ursincola, KR99; Sandaracinobacter sibiricus, RB 16-17; and Roseococcus thiosulfatophilus, RB3) possessing high level resistance to TeO32− and the ability to reduce it to elemental Te were studied to understand their interaction with this highly toxic oxyanion. Tested organic carbon sources, pH, and level of aeration all had an impact on reduction. Physiological and metabolic responses of cells to tellurite varied among strains. In its presence, versus absence, cellular biomass either increased (KR99, 66.6% and E5, 21.2%) or decreased (RB3, 66.1%, E1, 57.8%, RB 16-17, 41.5%, and E4(1), 21.3%). The increase suggests a possible benefit from tellurite. Cellular ATP production was similarly affected, resulting in an increase (KR99, 15.2% and E5, 38.9%) or decrease (E4(1), 31.9%; RB 16-17, 48.8%; RB3, 55.9%; E1, 35.9%). Two distinct strategies to tellurite reduction were identified. The first, found in E4(1), requires de novo protein preparations as well as an undisturbed whole cell. The second strategy, in which reduction depended on a membrane associated constitutive reductase, was used by the remaining strains. Full article
(This article belongs to the Special Issue Extremophiles)
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Open AccessArticle Sulfur Oxygenase Reductase (Sor) in the Moderately Thermoacidophilic Leaching Bacteria: Studies in Sulfobacillus thermosulfidooxidans and Acidithiobacillus caldus
Microorganisms 2015, 3(4), 707-724; https://doi.org/10.3390/microorganisms3040707
Received: 29 June 2015 / Revised: 1 October 2015 / Accepted: 10 October 2015 / Published: 21 October 2015
Cited by 8 | PDF Full-text (675 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
The sulfur oxygenase reductase (Sor) catalyzes the oxygen dependent disproportionation of elemental sulfur, producing sulfite, thiosulfate and sulfide. Being considered an “archaeal like” enzyme, it is also encoded in the genomes of some acidophilic leaching bacteria such as Acidithiobacillus caldus, Acidithiobacillus thiooxidans [...] Read more.
The sulfur oxygenase reductase (Sor) catalyzes the oxygen dependent disproportionation of elemental sulfur, producing sulfite, thiosulfate and sulfide. Being considered an “archaeal like” enzyme, it is also encoded in the genomes of some acidophilic leaching bacteria such as Acidithiobacillus caldus, Acidithiobacillus thiooxidans, Acidithiobacillus ferrivorans and Sulfobacillus thermosulfidooxidans, among others. We measured Sor activity in crude extracts from Sb. thermosulfidooxidans DSM 9293T. The optimum temperature for its oxygenase activity was achieved at 75 °C, confirming the “thermophilic” nature of this enzyme. Additionally, a search for genes probably involved in sulfur metabolism in the genome sequence of Sb. thermosulfidooxidans DSM 9293T was done. Interestingly, no sox genes were found. Two sor genes, a complete heterodisulfidereductase (hdr) gene cluster, three tetrathionate hydrolase (tth) genes, three sulfide quinonereductase (sqr), as well as the doxD component of a thiosulfate quinonereductase (tqo) were found. Seven At. caldus strains were tested for Sor activity, which was not detected in any of them. We provide evidence that an earlier reported Sor activity from At. caldus S1 and S2 strains most likely was due to the presence of a Sulfobacillus contaminant. Full article
(This article belongs to the Special Issue Extremophiles)
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Open AccessArticle Novel and Unexpected Microbial Diversity in Acid Mine Drainage in Svalbard (78° N), Revealed by Culture-Independent Approaches
Microorganisms 2015, 3(4), 667-694; https://doi.org/10.3390/microorganisms3040667
Received: 27 July 2015 / Revised: 2 September 2015 / Accepted: 29 September 2015 / Published: 13 October 2015
Cited by 8 | PDF Full-text (1243 KB) | HTML Full-text | XML Full-text
Abstract
Svalbard, situated in the high Arctic, is an important past and present coal mining area. Dozens of abandoned waste rock piles can be found in the proximity of Longyearbyen. This environment offers a unique opportunity for studying the biological control over the weathering [...] Read more.
Svalbard, situated in the high Arctic, is an important past and present coal mining area. Dozens of abandoned waste rock piles can be found in the proximity of Longyearbyen. This environment offers a unique opportunity for studying the biological control over the weathering of sulphide rocks at low temperatures. Although the extension and impact of acid mine drainage (AMD) in this area is known, the native microbial communities involved in this process are still scarcely studied and uncharacterized. Several abandoned mining areas were explored in the search for active AMD and a culture-independent approach was applied with samples from two different runoffs for the identification and quantification of the native microbial communities. The results obtained revealed two distinct microbial communities. One of the runoffs was more extreme with regards to pH and higher concentration of soluble iron and heavy metals. These conditions favored the development of algal-dominated microbial mats. Typical AMD microorganisms related to known iron-oxidizing bacteria (Acidithiobacillus ferrivorans, Acidobacteria and Actinobacteria) dominated the bacterial community although some unexpected populations related to Chloroflexi were also significant. No microbial mats were found in the second area. The geochemistry here showed less extreme drainage, most likely in direct contact with the ore under the waste pile. Large deposits of secondary minerals were found and the presence of iron stalks was revealed by microscopy analysis. Although typical AMD microorganisms were also detected here, the microbial community was dominated by other populations, some of them new to this type of system (Saccharibacteria, Gallionellaceae). These were absent or lowered in numbers the farther from the spring source and they could represent native populations involved in the oxidation of sulphide rocks within the waste rock pile. This environment appears thus as a highly interesting field of potential novelty in terms of both phylogenetic/taxonomic and functional diversity. Full article
(This article belongs to the Special Issue Extremophiles)
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Open AccessArticle Fungal Biodiversity in the Alpine Tarfala Valley
Microorganisms 2015, 3(4), 612-624; https://doi.org/10.3390/microorganisms3040612
Received: 4 August 2015 / Accepted: 29 September 2015 / Published: 10 October 2015
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Abstract
Biological soil crusts (BSCs) are distributed worldwide in all semiarid and arid lands, where they play a determinant role in element cycling and soil development. Although much work has concentrated on BSC microbial communities, free-living fungi have been hitherto largely overlooked. The aim [...] Read more.
Biological soil crusts (BSCs) are distributed worldwide in all semiarid and arid lands, where they play a determinant role in element cycling and soil development. Although much work has concentrated on BSC microbial communities, free-living fungi have been hitherto largely overlooked. The aim of this study was to examine the fungal biodiversity, by cultural-dependent and cultural-independent approaches, in thirteen samples of Arctic BSCs collected at different sites in the Alpine Tarfala Valley, located on the slopes of Kebnekaise, the highest mountain in northern Scandinavia. Isolated fungi were identified by both microscopic observation and molecular approaches. Data revealed that the fungal assemblage composition was homogeneous among the BSCs analyzed, with low biodiversity and the presence of a few dominant species; the majority of fungi isolated belonged to the Ascomycota, and Cryptococcus gilvescens and Pezoloma ericae were the most frequently-recorded species. Ecological considerations for the species involved and the implication of our findings for future fungal research in BSCs are put forward. Full article
(This article belongs to the Special Issue Extremophiles)
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Open AccessArticle Membrane Association and Catabolite Repression of the Sulfolobus solfataricus α-Amylase
Microorganisms 2015, 3(3), 567-587; https://doi.org/10.3390/microorganisms3030567
Received: 17 June 2015 / Revised: 10 August 2015 / Accepted: 11 September 2015 / Published: 18 September 2015
Cited by 1 | PDF Full-text (1012 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
Sulfolobus solfataricus is a thermoacidophilic member of the archaea whose envelope consists of an ether-linked lipid monolayer surrounded by a protein S-layer. Protein translocation across this envelope must accommodate a steep proton gradient that is subject to temperature extremes. To better understand this [...] Read more.
Sulfolobus solfataricus is a thermoacidophilic member of the archaea whose envelope consists of an ether-linked lipid monolayer surrounded by a protein S-layer. Protein translocation across this envelope must accommodate a steep proton gradient that is subject to temperature extremes. To better understand this process in vivo, studies were conducted on the S. solfataricus glycosyl hydrolyase family 57 α-Amylase (AmyA). Cell lines harboring site specific modifications of the amyA promoter and AmyA structural domains were created by gene replacement using markerless exchange and characterized by Western blot, enzyme assay and culture-based analysis. Fusion of amyA to the malAp promoter overcame amyAp-mediated regulatory responses to media composition including glucose and amino acid repression implicating action act at the level of transcription. Deletion of the AmyA Class II N-terminal signal peptide blocked protein secretion and intracellular protein accumulation. Deletion analysis of a conserved bipartite C-terminal motif consisting of a hydrophobic region followed by several charged residues indicated the charged residues played an essential role in membrane-association but not protein secretion. Mutants lacking the C-terminal bipartite motif exhibited reduced growth rates on starch as the sole carbon and energy source; therefore, association of AmyA with the membrane improves carbohydrate utilization. Widespread occurrence of this motif in other secreted proteins of S. solfataricus and of related Crenarchaeota suggests protein association with membranes is a general trait used by these organisms to influence external processes. Full article
(This article belongs to the Special Issue Extremophiles)
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Open AccessArticle The Effects of Perchlorates on the Permafrost Methanogens: Implication for Autotrophic Life on Mars
Microorganisms 2015, 3(3), 518-534; https://doi.org/10.3390/microorganisms3030518
Received: 30 June 2015 / Revised: 30 July 2015 / Accepted: 1 September 2015 / Published: 9 September 2015
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Abstract
The terrestrial permafrost represents a range of possible cryogenic extraterrestrial ecosystems on Earth-like planets without obvious surface ice, such as Mars. The autotrophic and chemolithotrophic psychrotolerant methanogens are more likely than aerobes to function as a model for life forms that may exist [...] Read more.
The terrestrial permafrost represents a range of possible cryogenic extraterrestrial ecosystems on Earth-like planets without obvious surface ice, such as Mars. The autotrophic and chemolithotrophic psychrotolerant methanogens are more likely than aerobes to function as a model for life forms that may exist in frozen subsurface environments on Mars, which has no free oxygen, inaccessible organic matter, and extremely low amounts of unfrozen water. Our research on the genesis of methane, its content and distribution in permafrost horizons of different ages and origin demonstrated the presence of methane in permanently frozen fine-grained sediments. Earlier, we isolated and described four strains of methanogenic archaea of Methanobacterium and Methanosarcina genera from samples of Pliocene and Holocene permafrost from Eastern Siberia. In this paper we study the effect of sodium and magnesium perchlorates on growth of permafrost and nonpermafrost methanogens, and present evidence that permafrost hydogenotrophic methanogens are more resistant to the chaotropic agent found in Martian soil. In this paper we study the effect of sodium and magnesium perchlorates on the growth of permafrost and nonpermafrost methanogens, and present evidence that permafrost hydogenotrophic methanogens are more resistant to the chaotropic agent found in Martian soil. Furthermore, as shown in the studies strain M2T M. arcticum, probably can use perchlorate anion as an electron acceptor in anaerobic methane oxidation. Earth’s subzero subsurface environments are the best approximation of environments on Mars, which is most likely to harbor methanogens; thus, a biochemical understanding of these pathways is expected to provide a basis for designing experiments to detect autotrophic methane-producing life forms on Mars. Full article
(This article belongs to the Special Issue Extremophiles)
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Open AccessArticle A Three-Component Microbial Consortium from Deep-Sea Salt-Saturated Anoxic Lake Thetis Links Anaerobic Glycine Betaine Degradation with Methanogenesis
Microorganisms 2015, 3(3), 500-517; https://doi.org/10.3390/microorganisms3030500
Received: 1 July 2015 / Revised: 27 July 2015 / Accepted: 1 September 2015 / Published: 9 September 2015
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Abstract
Microbial communities inhabiting the deep-sea salt-saturated anoxic lakes of the Eastern Mediterranean operate under harsh physical-chemical conditions that are incompatible with the lifestyle of common marine microorganisms. Here, we investigated a stable three-component microbial consortium obtained from the brine of the recently discovered [...] Read more.
Microbial communities inhabiting the deep-sea salt-saturated anoxic lakes of the Eastern Mediterranean operate under harsh physical-chemical conditions that are incompatible with the lifestyle of common marine microorganisms. Here, we investigated a stable three-component microbial consortium obtained from the brine of the recently discovered deep-sea salt-saturated Lake Thetis. The trophic network of this consortium, established at salinities up to 240, relies on fermentative decomposition of common osmoprotectant glycine betaine (GB). Similarly to known extreme halophilic anaerobic GB-degrading enrichments, the initial step of GB degradation starts with its reductive cleavage to trimethylamine and acetate, carried out by the fermenting member of the Thetis enrichment, Halobacteroides lacunaris TB21. In contrast to acetate, which cannot be easily oxidized in salt-saturated anoxic environments, trimethylamine represents an advantageous C1-substrate for methylotrophic methanogenic member of the Thetis enrichment, Methanohalophilus sp. TA21. This second member of the consortium likely produces hydrogen via methylotrophic modification of reductive acetyl-CoA pathway because the initial anaerobic GB cleavage reaction requires the consumption of reducing equivalents. Ecophysiological role of the third member of the Thetis consortium, Halanaerobium sp. TB24, which lacks the capability of either GB or trimethylamine degradation, remains yet to be elucidated. As it is true for cultivated members of family Halanaerobiaceae, the isolate TB24 can obtain energy primarily by fermenting simple sugars and producing hydrogen as one of the end products. Hence, by consuming of TB21 and TA21 metabolites, Halanaerobium sp. TB24 can be an additional provider of reducing equivalents required for reductive degradation of GB. Description of the Thetis GB-degrading consortium indicated that anaerobic degradation of osmoregulatory molecules may play important role in the overall turnover of organic carbon in anoxic hypersaline biotopes. Full article
(This article belongs to the Special Issue Extremophiles)
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Open AccessArticle Quantitative Characterization of the Growth of Deinococcus geothermalis DSM-11302: Effect of Inoculum Size, Growth Medium and Culture Conditions
Microorganisms 2015, 3(3), 441-463; https://doi.org/10.3390/microorganisms3030441
Received: 9 June 2015 / Revised: 21 July 2015 / Accepted: 28 July 2015 / Published: 20 August 2015
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Abstract
Due to their remarkable resistance to extreme conditions, Deinococcaceae strains are of great interest to biotechnological prospects. However, the physiology of the extremophile strain Deinococcus geothermalis has scarcely been studied and is not well understood. The physiological behaviour was then studied in well-controlled [...] Read more.
Due to their remarkable resistance to extreme conditions, Deinococcaceae strains are of great interest to biotechnological prospects. However, the physiology of the extremophile strain Deinococcus geothermalis has scarcely been studied and is not well understood. The physiological behaviour was then studied in well-controlled conditions in flask and bioreactor cultures. The growth of D. geothermalis type strains was compared. Among the strains tested, the strain from the German Collection of Microorganisms (Deutsche Sammlung von Mikroorganismen DSM) DSM-11302 was found to give the highest biomass concentration and growth rate: in a complex medium with glucose, the growth rate reached 0.75 h−1 at 45 °C. Yeast extract concentration in the medium had significant constitutive and catalytic effects. Furthermore, the results showed that the physiological descriptors were not affected by the inoculum preparation steps. A batch culture of D. geothermalis DSM-11302 on defined medium was carried out: cells grew exponentially with a maximal growth rate of 0.28 h−1 and D. geothermalis DSM-11302 biomass reached 1.4 g·L−1 in 20 h. Then, 1.4 gDryCellWeight of biomass (X) was obtained from 5.6 g glucose (Glc) consumed as carbon source, corresponding to a yield of 0.3 CmolX·CmolGlc−1; cell specific oxygen uptake and carbon dioxide production rates reached 216 and 226 mmol.CmolX−1·h−1, respectively, and the respiratory quotient (QR) value varied from 1.1 to 1.7. This is the first time that kinetic parameters and yields are reported for D. geothermalis DSM-11302 grown on a mineral medium in well-controlled batch culture. Full article
(This article belongs to the Special Issue Extremophiles)
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Open AccessArticle Cold-Active, Heterotrophic Bacteria from the Highly Oligotrophic Waters of Lake Vanda, Antarctica
Microorganisms 2015, 3(3), 391-406; https://doi.org/10.3390/microorganisms3030391
Received: 12 June 2015 / Revised: 5 July 2015 / Accepted: 9 July 2015 / Published: 24 July 2015
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Abstract
The permanently ice-covered lakes of the McMurdo Dry Valleys, Antarctica are distinctive ecosystems that consist strictly of microbial communities. In this study, water samples were collected from Lake Vanda, a stratified Dry Valley lake whose upper waters (from just below the ice cover [...] Read more.
The permanently ice-covered lakes of the McMurdo Dry Valleys, Antarctica are distinctive ecosystems that consist strictly of microbial communities. In this study, water samples were collected from Lake Vanda, a stratified Dry Valley lake whose upper waters (from just below the ice cover to nearly 60 m) are highly oligotrophic, and used to establish enrichment cultures. Six strains of psychrotolerant, heterotrophic bacteria were isolated from lake water samples from a depth of 50 or 55 m. Phylogenetic analyses showed the Lake Vanda strains to be species of Nocardiaceae, Caulobacteraceae, Sphingomonadaceae, and Bradyrhizobiaceae. All Lake Vanda strains grew at temperatures near or below 0 °C, but optimal growth occurred from 18 to 24 °C. Some strains showed significant halotolerance, but no strains required NaCl for growth. The isolates described herein include cold-active species not previously reported from Dry Valley lakes, and their physiological and phylogenetic characterization broadens our understanding of these limnologically unique lakes. Full article
(This article belongs to the Special Issue Extremophiles)
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Open AccessArticle Extremophiles in Mineral Sulphide Heaps: Some Bacterial Responses to Variable Temperature, Acidity and Solution Composition
Microorganisms 2015, 3(3), 364-390; https://doi.org/10.3390/microorganisms3030364
Received: 4 June 2015 / Revised: 26 June 2015 / Accepted: 29 June 2015 / Published: 9 July 2015
Cited by 5 | PDF Full-text (1389 KB) | HTML Full-text | XML Full-text
Abstract
In heap bioleaching, acidophilic extremophiles contribute to enhanced metal extraction from mineral sulphides through the oxidation of Fe(II) and/or reduced inorganic sulphur compounds (RISC), such as elemental sulphur or mineral sulphides, or the degradation of organic compounds derived from the ore, biota or [...] Read more.
In heap bioleaching, acidophilic extremophiles contribute to enhanced metal extraction from mineral sulphides through the oxidation of Fe(II) and/or reduced inorganic sulphur compounds (RISC), such as elemental sulphur or mineral sulphides, or the degradation of organic compounds derived from the ore, biota or reagents used during mineral processing. The impacts of variable solution acidity and composition, as well as temperature on the three microbiological functions have been examined for up to four bacterial species found in mineral sulphide heaps. The results indicate that bacteria adapt to sufficiently high metal concentrations (Cu, Ni, Co, Zn, As) to allow them to function in mineral sulphide heaps and, by engaging alternative metabolic pathways, to extend the solution pH range over which growth is sustained. Fluctuating temperatures during start up in sulphide heaps pose the greatest threat to efficient bacterial colonisation. The large masses of ores in bioleaching heaps mean that high temperatures arising from sulphide oxidation are hard to control initially, when the sulphide content of the ore is greatest. During that period, mesophilic and moderately thermophilic bacteria are markedly reduced in both numbers and activity. Full article
(This article belongs to the Special Issue Extremophiles)
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Open AccessArticle Copahue Geothermal System: A Volcanic Environment with Rich Extreme Prokaryotic Biodiversity
Microorganisms 2015, 3(3), 344-363; https://doi.org/10.3390/microorganisms3030344
Received: 12 April 2015 / Revised: 9 June 2015 / Accepted: 15 June 2015 / Published: 8 July 2015
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Abstract
The Copahue geothermal system is a natural extreme environment located at the northern end of the Cordillera de los Andes in Neuquén province in Argentina. The geochemistry and consequently the biodiversity of the area are dominated by the activity of the Copahue volcano. [...] Read more.
The Copahue geothermal system is a natural extreme environment located at the northern end of the Cordillera de los Andes in Neuquén province in Argentina. The geochemistry and consequently the biodiversity of the area are dominated by the activity of the Copahue volcano. The main characteristic of Copahue is the extreme acidity of its aquatic environments; ponds and hot springs of moderate and high temperature as well as Río Agrio. In spite of being an apparently hostile location, the prokaryotic biodiversity detected by molecular ecology techniques as well as cultivation shows a rich and diverse environment dominated by acidophilic, sulphur oxidising bacteria or archaea, depending on the conditions of the particular niche studied. In microbial biofilms, found in the borders of the ponds where thermal activity is less intense, the species found are completely different, with a high presence of cyanobacteria and other photosynthetic species. Our results, collected during more than 10 years of work in Copahue, have enabled us to outline geomicrobiological models for the different environments found in the ponds and Río Agrio. Besides, Copahue seems to be the habitat of novel, not yet characterised autochthonous species, especially in the domain Archaea. Full article
(This article belongs to the Special Issue Extremophiles)
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Open AccessArticle Temporal Study of the Microbial Diversity of the North Arm of Great Salt Lake, Utah, U.S.
Microorganisms 2015, 3(3), 310-326; https://doi.org/10.3390/microorganisms3030310
Received: 14 May 2015 / Revised: 12 June 2015 / Accepted: 15 June 2015 / Published: 2 July 2015
Cited by 8 | PDF Full-text (1217 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
We employed a temporal sampling approach to understand how the microbial diversity may shift in the north arm of Great Salt Lake, Utah, U.S. To determine how variations in seasonal environmental factors affect microbial communities, length heterogeneity PCR fingerprinting was performed using consensus [...] Read more.
We employed a temporal sampling approach to understand how the microbial diversity may shift in the north arm of Great Salt Lake, Utah, U.S. To determine how variations in seasonal environmental factors affect microbial communities, length heterogeneity PCR fingerprinting was performed using consensus primers for the domain Bacteria, and the haloarchaea. The archaeal fingerprints showed similarities during 2003 and 2004, but this diversity changed during the remaining two years of the study, 2005 and 2006. We also performed molecular phylogenetic analysis of the 16S rRNA genes of the whole microbial community to characterize the taxa in the samples. Our results indicated that in the domain, Bacteria, the Salinibacter group dominated the populations in all samplings. However, in the case of Archaea, as noted by LIBSHUFF for phylogenetic relatedness analysis, many of the temporal communities were distinct from each other, and changes in community composition did not track with environmental parameters. Around 20–23 different phylotypes, as revealed by rarefaction, predominated at different periods of the year. Some phylotypes, such as Haloquadradum, were present year-round although they changed in their abundance in different samplings, which may indicate that these species are affected by biotic factors, such as nutrients or viruses, that are independent of seasonal temperature dynamics. Full article
(This article belongs to the Special Issue Extremophiles)
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Open AccessArticle Generation of PHB from Spent Sulfite Liquor Using Halophilic Microorganisms
Microorganisms 2015, 3(2), 268-289; https://doi.org/10.3390/microorganisms3020268
Received: 18 March 2015 / Revised: 28 April 2015 / Accepted: 20 May 2015 / Published: 8 June 2015
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Abstract
Halophilic microorganisms thrive at elevated concentrations of sodium chloride up to saturation and are capable of growing on a wide variety of carbon sources like various organic acids, hexose and also pentose sugars. Hence, the biotechnological application of these microorganisms can cover many [...] Read more.
Halophilic microorganisms thrive at elevated concentrations of sodium chloride up to saturation and are capable of growing on a wide variety of carbon sources like various organic acids, hexose and also pentose sugars. Hence, the biotechnological application of these microorganisms can cover many aspects, such as the treatment of hypersaline waste streams of different origin. Due to the fact that the high osmotic pressure of hypersaline environments reduces the risk of contamination, the capacity for cost-effective non-sterile cultivation can make extreme halophilic microorganisms potentially valuable organisms for biotechnological applications. In this contribution, the stepwise use of screening approaches, employing design of experiment (DoE) on model media and subsequently using industrial waste as substrate have been implemented to investigate the applicability of halophiles to generate PHB from the industrial waste stream spent sulfite liquor (SSL). The production of PHB on model media as well as dilutions of industrial substrate in a complex medium has been screened for by fluorescence microscopy using Nile Blue staining. Screening was used to investigate the ability of halophilic microorganisms to withstand the inhibiting substances of the waste stream without negatively affecting PHB production. It could be shown that neither single inhibiting substances nor a mixture thereof inhibited growth in the investigated range, hence, leaving the question on the inhibiting mechanisms open. However, it could be demonstrated that some haloarchaea and halophilic bacteria are able to produce PHB when cultivated on 3.3% w/w dry matter spent sulfite liquor, whereas H. halophila was even able to thrive on 6.6% w/w dry matter spent sulfite liquor and still produce PHB. Full article
(This article belongs to the Special Issue Extremophiles)
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Review

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Open AccessReview Molecular Ecology of Hypersaline Microbial Mats: Current Insights and New Directions
Microorganisms 2016, 4(1), 6; https://doi.org/10.3390/microorganisms4010006
Received: 7 August 2015 / Revised: 8 December 2015 / Accepted: 15 December 2015 / Published: 5 January 2016
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Abstract
Microbial mats are unique geobiological ecosystems that form as a result of complex communities of microorganisms interacting with each other and their physical environment. Both the microorganisms present and the network of metabolic interactions govern ecosystem function therein. These systems are often found [...] Read more.
Microbial mats are unique geobiological ecosystems that form as a result of complex communities of microorganisms interacting with each other and their physical environment. Both the microorganisms present and the network of metabolic interactions govern ecosystem function therein. These systems are often found in a range of extreme environments, and those found in elevated salinity have been particularly well studied. The purpose of this review is to briefly describe the molecular ecology of select model hypersaline mat systems (Guerrero Negro, Shark Bay, S’Avall, and Kiritimati Atoll), and any potentially modulating effects caused by salinity to community structure. In addition, we discuss several emerging issues in the field (linking function to newly discovered phyla and microbial dark matter), which illustrate the changing paradigm that is seen as technology has rapidly advanced in the study of these extreme and evolutionally significant ecosystems. Full article
(This article belongs to the Special Issue Extremophiles)
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Open AccessReview Thermus thermophilus as a Source of Thermostable Lipolytic Enzymes
Microorganisms 2015, 3(4), 792-808; https://doi.org/10.3390/microorganisms3040792
Received: 24 June 2015 / Revised: 14 October 2015 / Accepted: 2 November 2015 / Published: 4 November 2015
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Abstract
Lipolytic enzymes, esterases (EC 3.1.1.1) and lipases (EC 3.1.1.3), catalyze the hydrolysis of ester bonds between alcohols and carboxylic acids, and its formation in organic media. At present, they represent about 20% of commercialized enzymes for industrial use. Lipolytic enzymes from thermophilic microorganisms [...] Read more.
Lipolytic enzymes, esterases (EC 3.1.1.1) and lipases (EC 3.1.1.3), catalyze the hydrolysis of ester bonds between alcohols and carboxylic acids, and its formation in organic media. At present, they represent about 20% of commercialized enzymes for industrial use. Lipolytic enzymes from thermophilic microorganisms are preferred for industrial use to their mesophilic counterparts, mainly due to higher thermostability and resistance to several denaturing agents. However, the production at an industrial scale from the native organisms is technically complicated and expensive. The thermophilic bacterium Thermus thermophilus (T. thermophilus) has high levels of lipolytic activity, and its whole genome has been sequenced. One esterase from the T. thermophilus strain HB27 has been widely characterized, both in its native form and in recombinant forms, being expressed in mesophilic microorganisms. Other putative lipases/esterases annotated in the T. thermophilus genome have been explored and will also be reviewed in this paper. Full article
(This article belongs to the Special Issue Extremophiles)
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Open AccessReview Role of Bacterial Exopolysaccharides as Agents in Counteracting Immune Disorders Induced by Herpes Virus
Microorganisms 2015, 3(3), 464-483; https://doi.org/10.3390/microorganisms3030464
Received: 1 July 2015 / Revised: 24 July 2015 / Accepted: 5 August 2015 / Published: 21 August 2015
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Abstract
Extreme marine environments, such as the submarine shallow vents of the Eolian Islands (Italy), offer an almost unexplored source of microorganisms producing unexploited and promising biomolecules for pharmaceutical applications. Thermophilic and thermotolerant bacilli isolated from Eolian vents are able to produce exopolysaccharides (EPSs) [...] Read more.
Extreme marine environments, such as the submarine shallow vents of the Eolian Islands (Italy), offer an almost unexplored source of microorganisms producing unexploited and promising biomolecules for pharmaceutical applications. Thermophilic and thermotolerant bacilli isolated from Eolian vents are able to produce exopolysaccharides (EPSs) with antiviral and immunomodulatory effects against Herpes simplex virus type 2 (HSV-2). HSV-2 is responsible for the most common and continuously increasing viral infections in humans. Due to the appearance of resistance to the available treatments, new biomolecules exhibiting different mechanisms of action could provide novel agents for treating viral infections. The EPSs hinder the HSV-2 replication in human peripheral blood mononuclear cells (PBMC) but not in WISH (Wistar Institute Susan Hayflic) cells line, indicating that cell-mediated immunity was involved in the antiviral activity. High levels of Th1-type cytokines were detected in PBMC treated with all EPSs, while Th2-type cytokines were not induced. These EPSs are water soluble exopolymers able to stimulate the immune response and thus contribute to the antiviral immune defense, acting as immunomodulators. As stimulants of Th1 cell-mediated immunity, they could lead to the development of novel drugs as alternative in the treatment of herpes virus infections, as well as in immunocompromised host. Full article
(This article belongs to the Special Issue Extremophiles)
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Open AccessReview Pyruvate: A key Nutrient in Hypersaline Environments?
Microorganisms 2015, 3(3), 407-416; https://doi.org/10.3390/microorganisms3030407
Received: 26 June 2015 / Revised: 29 July 2015 / Accepted: 31 July 2015 / Published: 7 August 2015
Cited by 6 | PDF Full-text (665 KB) | HTML Full-text | XML Full-text
Abstract
Some of the most commonly occurring but difficult to isolate halophilic prokaryotes, Archaea as well as Bacteria, require or prefer pyruvate as carbon and energy source. The most efficient media for the enumeration and isolation of heterotrophic prokaryotes from natural environments, from freshwater [...] Read more.
Some of the most commonly occurring but difficult to isolate halophilic prokaryotes, Archaea as well as Bacteria, require or prefer pyruvate as carbon and energy source. The most efficient media for the enumeration and isolation of heterotrophic prokaryotes from natural environments, from freshwater to hypersaline, including the widely used R2A agar medium, contain pyruvate as a key ingredient. Examples of pyruvate-loving halophiles are the square, extremely halophilic archaeon Haloquadratum walsbyi and the halophilic gammaproteobacterium Spiribacter salinus. However, surprisingly little is known about the availability of pyruvate in natural environments and about the way it enters the cell. Some halophilic Archaea (Halorubrum saccharovorum, Haloarcula spp.) partially convert sugars and glycerol to pyruvate and other acids (acetate, lactate) which are excreted to the medium. Pyruvate formation from glycerol was also shown during a bloom of halophilic Archaea in the Dead Sea. However, no pyruvate transporters were yet identified in the genomes of halophilic Archaea, and altogether, our understanding of pyruvate transport in the prokaryote world is very limited. Therefore, the preference for pyruvate by fastidious and often elusive halophiles and the empirically proven enhanced colony recovery on agar media containing pyruvate are still poorly understood. Full article
(This article belongs to the Special Issue Extremophiles)
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