Special Issue "Polar Microbiology: Recent Advances and Future Perspectives"

Quicklinks

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

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
E-Mail
Interests: biotechnology; next generation sequencing; metagenomics; molecular biology and biochemistry of microorganisms; extremophiles; grand challenges

Special Issue Information

Dear Colleagues,

Polar microbiology is a promising field of research that can tell us much about the fundamental features of life. The microorganisms that inhabit Arctic and Antarctic environments are important not only because of the unique species they represent, but also because of their diverse and unusual physiological and biochemical properties. Furthermore, microorganisms living in Polar Regions provide useful models for general questions in ecology and evolutionary biology given the reduced complexity of their ecosystems, the relative absence of confounding effects associated with higher plants or animals, and the severe biological constraints imposed by the polar environment. In terms of applied science, the unique cold-adapted enzymes and other molecules of polar microorganisms provide numerous opportunities for biotechnological development.  Another compelling reason to study polar microbial ecosystems is the fact that they are likely to be among the ecosystems most strongly affected by global change. For these reasons, polar microbiology is a thriving branch of science with the potential to provide new insights into a wide range of basic and applied issues in biological science. In this context, it is timely to review and highlight the progress so far and discuss exciting future perspectives. In this special issue, some of the leaders in the field describe their work, ideas and findings.

Prof. Pabulo Henrique Rampelotto
Guest Editor

Print Edition available!
A Print Edition of this Special Issue is available here.

Hardcover: 57.50 CHF*
Pages: 14, 452
*For contributing authors or bulk orders special prices may apply.
Prices include shipping.

Keywords

  • biodiversity
  • biogeochemistry
  • biogeography
  • biotechnology
  • evolutionary biology
  • genetics, genomics and proteomics
  • microbiology
  • molecular biology
  • molecular ecology
  • physiology and metabolism

Published Papers (23 papers)

View options order results:
result details:
Displaying articles 1-23
Export citation of selected articles as:

Editorial

Jump to: Research, Review

Open AccessEditorial Polar Microbiology: Recent Advances and Future Perspectives
Biology 2014, 3(1), 81-84; doi:10.3390/biology3010081
Received: 27 January 2014 / Accepted: 28 January 2014 / Published: 3 February 2014
PDF Full-text (133 KB) | HTML Full-text | XML Full-text
Abstract
Polar microbiology is a thriving branch of science with the potential to provide new insights into a wide range of basic and applied issues in biology. In this context, it is timely to review and highlight the progress so far and discuss exciting
[...] Read more.
Polar microbiology is a thriving branch of science with the potential to provide new insights into a wide range of basic and applied issues in biology. In this context, it is timely to review and highlight the progress so far and discuss exciting future perspectives. In this special issue, some of the leaders in the field have described their work, ideas and findings in a collection of reviews and original research articles with studies ranging from one of the oldest permafrost areas on Earth, located in Siberia, to the accretion ice of Lake Vostok, located in Antarctica. Altogether, these articles provide a comprehensive and reliable source of information on the current advances and future perspectives in this exciting field of research. In this Editorial, I present a brief overview on the theme [...] Full article

Research

Jump to: Editorial, Review

Open AccessArticle The Distribution and Identity of Edaphic Fungi in the McMurdo Dry Valleys
Biology 2014, 3(3), 466-483; doi:10.3390/biology3030466
Received: 23 May 2014 / Revised: 14 July 2014 / Accepted: 16 July 2014 / Published: 30 July 2014
Cited by 7 | PDF Full-text (1095 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
Contrary to earlier assumptions, molecular evidence has demonstrated the presence of diverse and localized soil bacterial communities in the McMurdo Dry Valleys of Antarctica. Meanwhile, it remains unclear whether fungal signals so far detected in Dry Valley soils using both culture-based and molecular
[...] Read more.
Contrary to earlier assumptions, molecular evidence has demonstrated the presence of diverse and localized soil bacterial communities in the McMurdo Dry Valleys of Antarctica. Meanwhile, it remains unclear whether fungal signals so far detected in Dry Valley soils using both culture-based and molecular techniques represent adapted and ecologically active biomass or spores transported by wind. Through a systematic and quantitative molecular survey, we identified significant heterogeneities in soil fungal communities across the Dry Valleys that robustly correlate with heterogeneities in soil physicochemical properties. Community fingerprinting analysis and 454 pyrosequencing of the fungal ribosomal intergenic spacer region revealed different levels of heterogeneity in fungal diversity within individual Dry Valleys and a surprising abundance of Chytridiomycota species, whereas previous studies suggested that Dry Valley soils were dominated by Ascomycota and Basidiomycota. Critically, we identified significant differences in fungal community composition and structure of adjacent sites with no obvious barrier to aeolian transport between them. These findings suggest that edaphic fungi of the Antarctic Dry Valleys are adapted to local environments and represent an ecologically relevant (and possibly important) heterotrophic component of the ecosystem. Full article
Open AccessArticle Contrasting Responses to Nutrient Enrichment of Prokaryotic Communities Collected from Deep Sea Sites in the Southern Ocean
Biology 2013, 2(3), 1165-1188; doi:10.3390/biology2031165
Received: 2 May 2013 / Revised: 2 August 2013 / Accepted: 4 September 2013 / Published: 13 September 2013
Cited by 1 | PDF Full-text (632 KB) | HTML Full-text | XML Full-text
Abstract
Deep water samples (ca. 4,200 m) were taken from two hydrologically-similar sites around the Crozet islands with highly contrasting surface water productivities. Site M5 was characteristic of high productivity waters (high chlorophyll) whilst site M6 was subject to a low productivity
[...] Read more.
Deep water samples (ca. 4,200 m) were taken from two hydrologically-similar sites around the Crozet islands with highly contrasting surface water productivities. Site M5 was characteristic of high productivity waters (high chlorophyll) whilst site M6 was subject to a low productivity regime (low chlorophyll) in the overlying waters. Samples were incubated for three weeks at 4 °C at in-situ and surface pressures, with and without added nutrients. Prokaryotic abundance increased by at least two-fold for all nutrient-supplemented incubations of water from M5 with little difference in abundance between incubations carried out at atmospheric and in-situ pressures. Abundance only increased for incubations of M6 waters (1.6-fold) when they were carried out at in-situ pressures and with added nutrients. Changes in community structure as a result of incubation and enrichment (as measured by DGGE banding profiles and phylogenetic analysis) showed that diversity increased for incubations of M5 waters but decreased for those with M6 waters. Moritella spp. came to dominate incubations carried out under in-situ pressure whilst the Archaeal community was dominated by Crenarchaea in all incubations. Comparisons between atmospheric and in situ pressure incubations demonstrated that community composition was significantly altered and community structure changes in unsuspplemented incubations at in situ pressure was indicative of the loss of functional taxa as a result of depressurisation during sampling. The use of enrichment incubations under in-situ conditions has contributed to understanding the different roles played by microorganisms in deep sea ecosystems in regions of low and high productivity. Full article
Open AccessArticle Characterizing Microbial Diversity and the Potential for Metabolic Function at −15 °C in the Basal Ice of Taylor Glacier, Antarctica
Biology 2013, 2(3), 1034-1053; doi:10.3390/biology2031034
Received: 18 June 2013 / Revised: 12 July 2013 / Accepted: 16 July 2013 / Published: 26 July 2013
Cited by 2 | PDF Full-text (730 KB) | HTML Full-text | XML Full-text
Abstract
Measurement of gases entrapped in clean ice from basal portions of the Taylor Glacier, Antarctica, revealed that CO2 ranged from 229 to 328 ppmv and O2 was near 20% of the gas volume. In contrast, vertically adjacent sections of the sediment
[...] Read more.
Measurement of gases entrapped in clean ice from basal portions of the Taylor Glacier, Antarctica, revealed that CO2 ranged from 229 to 328 ppmv and O2 was near 20% of the gas volume. In contrast, vertically adjacent sections of the sediment laden basal ice contained much higher concentrations of CO2 (60,000 to 325,000 ppmv), whereas O2 represented 4 to 18% of the total gas volume. The deviation in gas composition from atmospheric values occurred concurrently with increased microbial cell concentrations in the basal ice profile, suggesting that in situ microbial processes (i.e., aerobic respiration) may have altered the entrapped gas composition. Molecular characterization of 16S rRNA genes amplified from samples of the basal ice indicated a low diversity of bacteria, and most of the sequences characterized (87%) were affiliated with the phylum, Firmicutes. The most abundant phylotypes in libraries from ice horizons with elevated CO2 and depleted O2 concentrations were related to the genus Paenisporosarcina, and 28 isolates from this genus were obtained by enrichment culturing. Metabolic experiments with Paenisporosarcina sp. TG14 revealed its capacity to conduct macromolecular synthesis when frozen in water derived from melted basal ice samples and incubated at −15 °C. The results support the hypothesis that the basal ice of glaciers and ice sheets are cryospheric habitats harboring bacteria with the physiological capacity to remain metabolically active and biogeochemically cycle elements within the subglacial environment. Full article
Open AccessArticle Fungal Diversity in a Dark Oligotrophic Volcanic Ecosystem (DOVE) on Mount Erebus, Antarctica
Biology 2013, 2(2), 798-809; doi:10.3390/biology2020798
Received: 1 May 2013 / Revised: 9 May 2013 / Accepted: 10 May 2013 / Published: 30 May 2013
Cited by 5 | PDF Full-text (624 KB) | HTML Full-text | XML Full-text
Abstract
Fumarolic Ice caves on Antarctica’s Mt. Erebus contain a dark oligotrophic volcanic ecosystem (DOVE) and represent a deep biosphere habitat that can provide insight into microbial communities that utilize energy sources other than photosynthesis. The community assembly and role of fungi in these
[...] Read more.
Fumarolic Ice caves on Antarctica’s Mt. Erebus contain a dark oligotrophic volcanic ecosystem (DOVE) and represent a deep biosphere habitat that can provide insight into microbial communities that utilize energy sources other than photosynthesis. The community assembly and role of fungi in these environments remains largely unknown. However, these habitats could be relatively easily contaminated during human visits. Sixty-one species of fungi were identified from soil clone libraries originating from Warren Cave, a DOVE on Mt. Erebus. The species diversity was greater than has been found in the nearby McMurdo Dry Valleys oligotrophic soil. A relatively large proportion of the clones represented Malassezia species (37% of Basidomycota identified). These fungi are associated with skin surfaces of animals and require high lipid content for growth, indicating that contamination may have occurred through the few and episodic human visits in this particular cave. These findings highlight the importance of fungi to DOVE environments as well as their potential use for identifying contamination by humans. The latter offers compelling evidence suggesting more strict management of these valuable research areas. Full article
Open AccessArticle Antarctic Epilithic Lichens as Niches for Black Meristematic Fungi
Biology 2013, 2(2), 784-797; doi:10.3390/biology2020784
Received: 11 March 2013 / Revised: 5 April 2013 / Accepted: 24 April 2013 / Published: 17 May 2013
Cited by 16 | PDF Full-text (459 KB) | HTML Full-text | XML Full-text
Abstract
Sixteen epilithic lichen samples (13 species), collected from seven locations in Northern and Southern Victoria Land in Antarctica, were investigated for the presence of black fungi. Thirteen fungal strains isolated were studied by both morphological and molecular methods. Nuclear ribosomal 18S gene sequences
[...] Read more.
Sixteen epilithic lichen samples (13 species), collected from seven locations in Northern and Southern Victoria Land in Antarctica, were investigated for the presence of black fungi. Thirteen fungal strains isolated were studied by both morphological and molecular methods. Nuclear ribosomal 18S gene sequences were used together with the most similar published and unpublished sequences of fungi from other sources, to reconstruct an ML tree. Most of the studied fungi could be grouped together with described or still unnamed rock-inhabiting species in lichen dominated Antarctic cryptoendolithic communities. At the edge of life, epilithic lichens withdraw inside the airspaces of rocks to find conditions still compatible with life; this study provides evidence, for the first time, that the same microbes associated to epilithic thalli also have the same fate and chose endolithic life. These results support the concept of lichens being complex symbiotic systems, which offer attractive and sheltered habitats for other microbes. Full article
Open AccessArticle Endolithic Microbial Life in Extreme Cold Climate: Snow Is Required, but Perhaps Less Is More
Biology 2013, 2(2), 693-701; doi:10.3390/biology2020693
Received: 14 December 2012 / Accepted: 22 March 2013 / Published: 3 April 2013
Cited by 5 | PDF Full-text (763 KB) | HTML Full-text | XML Full-text
Abstract
Cyanobacteria and lichens living under sandstone surfaces in the McMurdo Dry Valleys require snow for moisture. Snow accumulated beyond a thin layer, however, is counterproductive, interfering with rock insolation, snow melting, and photosynthetic access to light. With this in mind, the facts that
[...] Read more.
Cyanobacteria and lichens living under sandstone surfaces in the McMurdo Dry Valleys require snow for moisture. Snow accumulated beyond a thin layer, however, is counterproductive, interfering with rock insolation, snow melting, and photosynthetic access to light. With this in mind, the facts that rock slope and direction control colonization, and that climate change results in regional extinctions, can be explained. Vertical cliffs, which lack snow cover and are perpetually dry, are devoid of organisms. Boulder tops and edges can trap snow, but gravity and wind prevent excessive buildup. There, the organisms flourish. In places where snow-thinning cannot occur and snow drifts collect, rocks may contain living or dead communities. In light of these observations, the possibility of finding extraterrestrial endolithic communities on Mars cannot be eliminated. Full article
Open AccessArticle Ecology of Subglacial Lake Vostok (Antarctica), Based on Metagenomic/Metatranscriptomic Analyses of Accretion Ice
Biology 2013, 2(2), 629-650; doi:10.3390/biology2020629
Received: 10 December 2012 / Revised: 25 February 2013 / Accepted: 19 March 2013 / Published: 28 March 2013
Cited by 6 | PDF Full-text (528 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
Lake Vostok is the largest of the nearly 400 subglacial Antarctic lakes and has been continuously buried by glacial ice for 15 million years. Extreme cold, heat (from possible hydrothermal activity), pressure (from the overriding glacier) and dissolved oxygen (delivered by melting meteoric
[...] Read more.
Lake Vostok is the largest of the nearly 400 subglacial Antarctic lakes and has been continuously buried by glacial ice for 15 million years. Extreme cold, heat (from possible hydrothermal activity), pressure (from the overriding glacier) and dissolved oxygen (delivered by melting meteoric ice), in addition to limited nutrients and complete darkness, combine to produce one of the most extreme environments on Earth. Metagenomic/metatranscriptomic analyses of ice that accreted over a shallow embayment and over the southern main lake basin indicate the presence of thousands of species of organisms (94% Bacteria, 6% Eukarya, and two Archaea). The predominant bacterial sequences were closest to those from species of Firmicutes, Proteobacteria and Actinobacteria, while the predominant eukaryotic sequences were most similar to those from species of ascomycetous and basidiomycetous Fungi. Based on the sequence data, the lake appears to contain a mixture of autotrophs and heterotrophs capable of performing nitrogen fixation, nitrogen cycling, carbon fixation and nutrient recycling. Sequences closest to those of psychrophiles and thermophiles indicate a cold lake with possible hydrothermal activity. Sequences most similar to those from marine and aquatic species suggest the presence of marine and freshwater regions. Full article
Figures

Open AccessArticle Composition, Diversity, and Stability of Microbial Assemblages in Seasonal Lake Ice, Miquelon Lake, Central Alberta
Biology 2013, 2(2), 514-532; doi:10.3390/biology2020514
Received: 28 December 2012 / Revised: 5 March 2013 / Accepted: 6 March 2013 / Published: 27 March 2013
PDF Full-text (1940 KB) | HTML Full-text | XML Full-text
Abstract
The most familiar icy environments, seasonal lake and stream ice, have received little microbiological study. Bacteria and Eukarya dominated the microbial assemblage within the seasonal ice of Miquelon Lake, a shallow saline lake in Alberta, Canada. The bacterial assemblages were moderately diverse and
[...] Read more.
The most familiar icy environments, seasonal lake and stream ice, have received little microbiological study. Bacteria and Eukarya dominated the microbial assemblage within the seasonal ice of Miquelon Lake, a shallow saline lake in Alberta, Canada. The bacterial assemblages were moderately diverse and did not vary with either ice depth or time. The closest relatives of the bacterial sequences from the ice included Actinobacteria, Bacteroidetes, Proteobacteria, Verrucomicrobia, and Cyanobacteria. The eukaryotic assemblages were less conserved and had very low diversity. Green algae relatives dominated the eukaryotic gene sequences; however, a copepod and cercozoan were also identified, possibly indicating the presence of complete microbial loop. The persistence of a chlorophyll a peak at 25–30 cm below the ice surface, despite ice migration and brine flushing, indicated possible biological activity within the ice. This is the first study of the composition, diversity, and stability of seasonal lake ice. Full article
Open AccessArticle The Effect of Freeze-Thaw Conditions on Arctic Soil Bacterial Communities
Biology 2013, 2(1), 356-377; doi:10.3390/biology2010356
Received: 17 December 2012 / Revised: 31 January 2013 / Accepted: 17 February 2013 / Published: 28 February 2013
Cited by 4 | PDF Full-text (498 KB) | HTML Full-text | XML Full-text
Abstract
Climate change is already altering the landscape at high latitudes. Permafrost is thawing, the growing season is starting earlier, and, as a result, certain regions in the Arctic may be subjected to an increased incidence of freeze-thaw events. The potential release of carbon
[...] Read more.
Climate change is already altering the landscape at high latitudes. Permafrost is thawing, the growing season is starting earlier, and, as a result, certain regions in the Arctic may be subjected to an increased incidence of freeze-thaw events. The potential release of carbon and nutrients from soil microbial cells that have been lysed by freeze-thaw transitions could have significant impacts on the overall carbon balance of arctic ecosystems, and therefore on atmospheric CO2 concentrations. However, the impact of repeated freezing and thawing with the consequent growth and recrystallization of ice on microbial communities is still not well understood. Soil samples from three distinct sites, representing Canadian geographical low arctic, mid-arctic and high arctic soils were collected from Daring Lake, Alexandra Fjord and Cambridge Bay sampling sites, respectively. Laboratory-based experiments subjected the soils to multiple freeze-thaw cycles for 14 days based on field observations (0 °C to −10 °C for 12 h and −10 °C to 0 °C for 12 h) and the impact on the communities was assessed by phospholipid fatty acid (PLFA) methyl ester analysis and 16S ribosomal RNA gene sequencing. Both data sets indicated differences in composition and relative abundance between the three sites, as expected. However, there was also a strong variation within the two high latitude sites in the effects of the freeze-thaw treatment on individual PLFA and 16S-based phylotypes. These site-based heterogeneities suggest that the impact of climate change on soil microbial communities may not be predictable a priori; minor differential susceptibilities to freeze-thaw stress could lead to a “butterfly effect” as described by chaos theory, resulting in subsequent substantive differences in microbial assemblages. This perspectives article suggests that this is an unwelcome finding since it will make future predictions for the impact of on-going climate change on soil microbial communities in arctic regions all but impossible. Full article
Open AccessCommunication Micro-Eukaryotic Diversity in Hypolithons from Miers Valley, Antarctica
Biology 2013, 2(1), 331-340; doi:10.3390/biology2010331
Received: 20 December 2012 / Revised: 11 February 2013 / Accepted: 18 February 2013 / Published: 22 February 2013
Cited by 3 | PDF Full-text (204 KB) | HTML Full-text | XML Full-text
Abstract
The discovery of extensive and complex hypolithic communities in both cold and hot deserts has raised many questions regarding their ecology, biodiversity and relevance in terms of regional productivity. However, most hypolithic research has focused on the bacterial elements of the community. This
[...] Read more.
The discovery of extensive and complex hypolithic communities in both cold and hot deserts has raised many questions regarding their ecology, biodiversity and relevance in terms of regional productivity. However, most hypolithic research has focused on the bacterial elements of the community. This study represents the first investigation of micro-eukaryotic communities in all three hypolith types. Here we show that Antarctic hypoliths support extensive populations of novel uncharacterized bryophyta, fungi and protists and suggest that well known producer-decomposer-predator interactions may create the necessary conditions for hypolithic productivity in Antarctic deserts. Full article
Open AccessArticle Timescales of Growth Response of Microbial Mats to Environmental Change in an Ice-Covered Antarctic Lake
Biology 2013, 2(1), 151-176; doi:10.3390/biology2010151
Received: 15 November 2012 / Revised: 19 December 2012 / Accepted: 20 December 2012 / Published: 25 January 2013
Cited by 8 | PDF Full-text (993 KB) | HTML Full-text | XML Full-text
Abstract
Lake Vanda is a perennially ice-covered, closed-basin lake in the McMurdo Dry Valleys, Antarctica. Laminated photosynthetic microbial mats cover the floor of the lake from below the ice cover to >40 m depth. In recent decades, the water level of Lake Vanda has
[...] Read more.
Lake Vanda is a perennially ice-covered, closed-basin lake in the McMurdo Dry Valleys, Antarctica. Laminated photosynthetic microbial mats cover the floor of the lake from below the ice cover to >40 m depth. In recent decades, the water level of Lake Vanda has been rising, creating a “natural experiment” on development of mat communities on newly flooded substrates and the response of deeper mats to declining irradiance. Mats in recently flooded depths accumulate one lamina (~0.3 mm) per year and accrue ~0.18 µg chlorophyll-a cm−2 y−1. As they increase in thickness, vertical zonation becomes evident, with the upper 2-4 laminae forming an orange-brown zone, rich in myxoxanthophyll and dominated by intertwined Leptolyngbya trichomes. Below this, up to six phycobilin-rich green/pink-pigmented laminae form a subsurface zone, inhabited by Leptolyngbya, Oscillatoria and Phormidium morphotypes. Laminae continued to increase in thickness for several years after burial, and PAM fluorometry indicated photosynthetic potential in all pigmented laminae. At depths that have been submerged for >40 years, mats showed similar internal zonation and formed complex pinnacle structures that were only beginning to appear in shallower mats. Chlorophyll-a did not change over time and these mats appear to represent resource-limited “climax” communities. Acclimation of microbial mats to changing environmental conditions is a slow process, and our data show how legacy effects of past change persist into the modern community structure. Full article
Open AccessArticle Novel Cold-Adapted Esterase MHlip from an Antarctic Soil Metagenome
Biology 2013, 2(1), 177-188; doi:10.3390/biology2010177
Received: 3 December 2012 / Revised: 4 January 2013 / Accepted: 11 January 2013 / Published: 25 January 2013
Cited by 4 | PDF Full-text (513 KB) | HTML Full-text | XML Full-text
Abstract
An Antarctic soil metagenomic library was screened for lipolytic enzymes and allowed for the isolation of a new cytosolic esterase from the a/b hydrolase family 6, named MHlip. This enzyme is related to hypothetical genes coding esterases, aryl-esterases and peroxydases, among others. MHlip
[...] Read more.
An Antarctic soil metagenomic library was screened for lipolytic enzymes and allowed for the isolation of a new cytosolic esterase from the a/b hydrolase family 6, named MHlip. This enzyme is related to hypothetical genes coding esterases, aryl-esterases and peroxydases, among others. MHlip was produced, purified and its activity was determined. The substrate profile of MHlip reveals a high specificity for short p-nitrophenyl-esters. The apparent optimal activity of MHlip was measured for p-nitrophenyl-acetate, at 33 °C, in the pH range of 6–9. The MHlip thermal unfolding was investigated by spectrophotometric methods, highlighting a transition (Tm) at 50 °C. The biochemical characterization of this enzyme showed its adaptation to cold temperatures, even when it did not present evident signatures associated with cold-adapted proteins. Thus, MHlip adaptation to cold probably results from many discrete structural modifications, allowing the protein to remain active at low temperatures. Functional metagenomics is a powerful approach to isolate new enzymes with tailored biophysical properties (e.g., cold adaptation). In addition, beside the ever growing amount of sequenced DNA, the functional characterization of new catalysts derived from environment is still required, especially for poorly characterized protein families like α/b hydrolases. Full article
Figures

Open AccessArticle Microbial Analyses of Ancient Ice Core Sections from Greenland and Antarctica
Biology 2013, 2(1), 206-232; doi:10.3390/biology2010206
Received: 10 December 2012 / Revised: 8 January 2013 / Accepted: 11 January 2013 / Published: 25 January 2013
Cited by 4 | PDF Full-text (1052 KB) | HTML Full-text | XML Full-text
Abstract
Ice deposited in Greenland and Antarctica entraps viable and nonviable microbes, as well as biomolecules, that become temporal atmospheric records. Five sections (estimated to be 500, 10,500, 57,000, 105,000 and 157,000 years before present, ybp) from the GISP2D (Greenland) ice core, three sections
[...] Read more.
Ice deposited in Greenland and Antarctica entraps viable and nonviable microbes, as well as biomolecules, that become temporal atmospheric records. Five sections (estimated to be 500, 10,500, 57,000, 105,000 and 157,000 years before present, ybp) from the GISP2D (Greenland) ice core, three sections (500, 30,000 and 70,000 ybp) from the Byrd ice core, and four sections from the Vostok 5G (Antarctica) ice core (10,500, 57,000, 105,000 and 105,000 ybp) were studied by scanning electron microscopy, cultivation and rRNA gene sequencing. Bacterial and fungal isolates were recovered from 10 of the 12 sections. The highest numbers of isolates were found in ice core sections that were deposited during times of low atmospheric CO2, low global temperatures and low levels of atmospheric dust. Two of the sections (GISP2D at 10,500 and 157,000 ybp) also were examined using metagenomic/metatranscriptomic methods. These results indicated that sequences from microbes common to arid and saline soils were deposited in the ice during a time of low temperature, low atmospheric CO2 and high dust levels. Members of Firmicutes and Cyanobacteria were the most prevalent bacteria, while Rhodotorula species were the most common eukaryotic representatives. Isolates of Bacillus, Rhodotorula, Alternaria and members of the Davidiellaceae were isolated from both Greenland and Antarctica sections of the same age, although the sequences differed between the two polar regions. Full article
Figures

Open AccessArticle Thermodynamic Stability of Psychrophilic and Mesophilic Pheromones of the Protozoan Ciliate Euplotes
Biology 2013, 2(1), 142-150; doi:10.3390/biology2010142
Received: 6 December 2012 / Revised: 27 December 2012 / Accepted: 31 December 2012 / Published: 14 January 2013
Cited by 10 | PDF Full-text (514 KB) | HTML Full-text | XML Full-text
Abstract
Three psychrophilic protein pheromones (En-1, En-2 and En-6) from the polar ciliate, Euplotes nobilii, and six mesophilic pheromones (Er-1, Er-2, Er-10, Er-11, Er-22 and Er
[...] Read more.
Three psychrophilic protein pheromones (En-1, En-2 and En-6) from the polar ciliate, Euplotes nobilii, and six mesophilic pheromones (Er-1, Er-2, Er-10, Er-11, Er-22 and Er-23) from the temperate-water sister species, Euplotes raikovi, were studied in aqueous solution for their thermal unfolding and refolding based on the temperature dependence of their circular dichroism (CD) spectra. The three psychrophilic proteins showed thermal unfolding with mid points in the temperature range 55–70 °C. In contrast, no unfolding was observed for any of the six mesophilic proteins and their regular secondary structures were maintained up to 95 °C. Possible causes of these differences are discussed based on comparisons of the NMR structures of the nine proteins. Full article
Open AccessArticle Isolation and Characterization of Bacteria from Ancient Siberian Permafrost Sediment
Biology 2013, 2(1), 85-106; doi:10.3390/biology2010085
Received: 17 October 2012 / Revised: 12 December 2012 / Accepted: 25 December 2012 / Published: 10 January 2013
Cited by 7 | PDF Full-text (477 KB) | HTML Full-text | XML Full-text
Abstract
In this study, we isolated and characterized bacterial strains from ancient (Neogene) permafrost sediment that was permanently frozen for 3.5 million years. The sampling site was located at Mammoth Mountain in the Aldan river valley in Central Yakutia in Eastern Siberia. Analysis of
[...] Read more.
In this study, we isolated and characterized bacterial strains from ancient (Neogene) permafrost sediment that was permanently frozen for 3.5 million years. The sampling site was located at Mammoth Mountain in the Aldan river valley in Central Yakutia in Eastern Siberia. Analysis of phospolipid fatty acids (PLFA) demonstrated the dominance of bacteria over fungi; the analysis of fatty acids specific for Gram-positive and Gram-negative bacteria revealed an approximately twofold higher amount of Gram-negative bacteria compared to Gram-positive bacteria. Direct microbial counts after natural permafrost enrichment showed the presence of (4.7 ± 1.5) × 108 cells g−1 sediment dry mass. Viable heterotrophic bacteria were found at 0 °C, 10 °C and 25 °C, but not at 37 °C. Spore-forming bacteria were not detected. Numbers of viable fungi were low and were only detected at 0 °C and 10 °C. Selected culturable bacterial isolates were identified as representatives of Arthrobacter phenanthrenivorans, Subtercola frigoramans and Glaciimonas immobilis. Representatives of each of these species were characterized with regard to their growth temperature range, their ability to grow on different media, to produce enzymes, to grow in the presence of NaCl, antibiotics, and heavy metals, and to degrade hydrocarbons. All strains could grow at −5 °C; the upper temperature limit for growth in liquid culture was 25 °C or 30 °C. Sensitivity to rich media, antibiotics, heavy metals, and salt increased when temperature decreased (20 °C > 10 °C > 1 °C). In spite of the ligninolytic activity of some strains, no biodegradation activity was detected. Full article

Review

Jump to: Editorial, Research

Open AccessReview Polar Microalgae: New Approaches towards Understanding Adaptations to an Extreme and Changing Environment
Biology 2014, 3(1), 56-80; doi:10.3390/biology3010056
Received: 28 November 2013 / Revised: 22 January 2014 / Accepted: 24 January 2014 / Published: 28 January 2014
Cited by 5 | PDF Full-text (524 KB) | HTML Full-text | XML Full-text
Abstract
Polar Regions are unique and highly prolific ecosystems characterized by extreme environmental gradients. Photosynthetic autotrophs, the base of the food web, have had to adapt physiological mechanisms to maintain growth, reproduction and metabolic activity despite environmental conditions that would shut-down cellular processes in
[...] Read more.
Polar Regions are unique and highly prolific ecosystems characterized by extreme environmental gradients. Photosynthetic autotrophs, the base of the food web, have had to adapt physiological mechanisms to maintain growth, reproduction and metabolic activity despite environmental conditions that would shut-down cellular processes in most organisms. High latitudes are characterized by temperatures below the freezing point, complete darkness in winter and continuous light and high UV in the summer. Additionally, sea-ice, an ecological niche exploited by microbes during the long winter seasons when the ocean and land freezes over, is characterized by large salinity fluctuations, limited gas exchange, and highly oxic conditions. The last decade has been an exciting period of insights into the molecular mechanisms behind adaptation of microalgae to the cryosphere facilitated by the advancement of new scientific tools, particularly “omics” techniques. We review recent insights derived from genomics, transcriptomics, and proteomics studies. Genes, proteins and pathways identified from these highly adaptable polar microbes have far-reaching biotechnological applications. Furthermore, they may provide insights into life outside this planet, as well as glimpses into the past. High latitude regions also have disproportionately large inputs into global biogeochemical cycles and are the region most sensitive to climate change. Full article
Open AccessReview Biotechnology of Cold-Active Proteases
Biology 2013, 2(2), 755-783; doi:10.3390/biology2020755
Received: 5 March 2013 / Revised: 17 April 2013 / Accepted: 24 April 2013 / Published: 3 May 2013
Cited by 15 | PDF Full-text (483 KB) | HTML Full-text | XML Full-text
Abstract
The bulk of Earth’s biosphere is cold (<5 °C) and inhabited by psychrophiles. Biocatalysts from psychrophilic organisms (psychrozymes) have attracted attention because of their application in the ongoing efforts to decrease energy consumption. Proteinases as a class represent the largest category of industrial
[...] Read more.
The bulk of Earth’s biosphere is cold (<5 °C) and inhabited by psychrophiles. Biocatalysts from psychrophilic organisms (psychrozymes) have attracted attention because of their application in the ongoing efforts to decrease energy consumption. Proteinases as a class represent the largest category of industrial enzymes. There has been an emphasis on employing cold-active proteases in detergents because this allows laundry operations at ambient temperatures. Proteases have been used in environmental bioremediation, food industry and molecular biology. In view of the present limited understanding and availability of cold-active proteases with diverse characteristics, it is essential to explore Earth’s surface more in search of an ideal cold-active protease. The understanding of molecular and mechanistic details of these proteases will open up new avenues to tailor proteases with the desired properties. A detailed account of the developments in the production and applications of cold-active proteases is presented in this review. Full article
Open AccessReview Psychrophily and Catalysis
Biology 2013, 2(2), 719-741; doi:10.3390/biology2020719
Received: 12 December 2012 / Revised: 18 March 2013 / Accepted: 18 March 2013 / Published: 16 April 2013
Cited by 2 | PDF Full-text (383 KB) | HTML Full-text | XML Full-text
Abstract
Polar and other low temperature environments are characterized by a low content in energy and this factor has a strong incidence on living organisms which populate these rather common habitats. Indeed, low temperatures have a negative effect on ectothermic populations since they can
[...] Read more.
Polar and other low temperature environments are characterized by a low content in energy and this factor has a strong incidence on living organisms which populate these rather common habitats. Indeed, low temperatures have a negative effect on ectothermic populations since they can affect their growth, reaction rates of biochemical reactions, membrane permeability, diffusion rates, action potentials, protein folding, nucleic acids dynamics and other temperature-dependent biochemical processes. Since the discovery that these ecosystems, contrary to what was initially expected, sustain a rather high density and broad diversity of living organisms, increasing efforts have been dedicated to the understanding of the molecular mechanisms involved in their successful adaptation to apparently unfavorable physical conditions. The first question that comes to mind is: How do these organisms compensate for the exponential decrease of reaction rate when temperature is lowered? As most of the chemical reactions that occur in living organisms are catalyzed by enzymes, the kinetic and thermodynamic properties of cold-adapted enzymes have been investigated. Presently, many crystallographic structures of these enzymes have been elucidated and allowed for a rather clear view of their adaptation to cold. They are characterized by a high specific activity at low and moderate temperatures and a rather low thermal stability, which induces a high flexibility that prevents the freezing effect of low temperatures on structure dynamics. These enzymes also display a low activation enthalpy that renders them less dependent on temperature fluctuations. This is accompanied by a larger negative value of the activation entropy, thus giving evidence of a more disordered ground state. Appropriate folding kinetics is apparently secured through a large expression of trigger factors and peptidyl–prolyl cis/trans-isomerases. Full article
Open AccessReview Sea Ice Microorganisms: Environmental Constraints and Extracellular Responses
Biology 2013, 2(2), 603-628; doi:10.3390/biology2020603
Received: 4 February 2013 / Revised: 2 March 2013 / Accepted: 6 March 2013 / Published: 28 March 2013
Cited by 20 | PDF Full-text (1042 KB) | HTML Full-text | XML Full-text
Abstract
Inherent to sea ice, like other high latitude environments, is the strong seasonality driven by changes in insolation throughout the year. Sea-ice organisms are exposed to shifting, sometimes limiting, conditions of temperature and salinity. An array of adaptations to survive these and other
[...] Read more.
Inherent to sea ice, like other high latitude environments, is the strong seasonality driven by changes in insolation throughout the year. Sea-ice organisms are exposed to shifting, sometimes limiting, conditions of temperature and salinity. An array of adaptations to survive these and other challenges has been acquired by those organisms that inhabit the ice. One key adaptive response is the production of extracellular polymeric substances (EPS), which play multiple roles in the entrapment, retention and survival of microorganisms in sea ice. In this concept paper we consider two main areas of sea-ice microbiology: the physico-chemical properties that define sea ice as a microbial habitat, imparting particular advantages and limits; and extracellular responses elicited in microbial inhabitants as they exploit or survive these conditions. Emphasis is placed on protective strategies used in the face of fluctuating and extreme environmental conditions in sea ice. Gaps in knowledge and testable hypotheses are identified for future research. Full article
Open AccessReview Microbial Competition in Polar Soils: A Review of an Understudied but Potentially Important Control on Productivity
Biology 2013, 2(2), 533-554; doi:10.3390/biology2020533
Received: 6 March 2013 / Revised: 11 March 2013 / Accepted: 12 March 2013 / Published: 27 March 2013
Cited by 7 | PDF Full-text (282 KB) | HTML Full-text | XML Full-text
Abstract
Intermicrobial competition is known to occur in many natural environments, and can result from direct conflict between organisms, or from differential rates of growth, colonization, and/or nutrient acquisition. It has been difficult to extensively examine intermicrobial competition in situ, but these interactions
[...] Read more.
Intermicrobial competition is known to occur in many natural environments, and can result from direct conflict between organisms, or from differential rates of growth, colonization, and/or nutrient acquisition. It has been difficult to extensively examine intermicrobial competition in situ, but these interactions may play an important role in the regulation of the many biogeochemical processes that are tied to microbial communities in polar soils. A greater understanding of how competition influences productivity will improve projections of gas and nutrient flux as the poles warm, may provide biotechnological opportunities for increasing the degradation of contaminants in polar soil, and will help to predict changes in communities of higher organisms, such as plants. Full article
Open AccessReview The Dynamic Arctic Snow Pack: An Unexplored Environment for Microbial Diversity and Activity
Biology 2013, 2(1), 317-330; doi:10.3390/biology2010317
Received: 7 December 2012 / Revised: 10 January 2013 / Accepted: 14 January 2013 / Published: 5 February 2013
Cited by 14 | PDF Full-text (159 KB) | HTML Full-text | XML Full-text
Abstract
The Arctic environment is undergoing changes due to climate shifts, receiving contaminants from distant sources and experiencing increased human activity. Climate change may alter microbial functioning by increasing growth rates and substrate use due to increased temperature. This may lead to changes of
[...] Read more.
The Arctic environment is undergoing changes due to climate shifts, receiving contaminants from distant sources and experiencing increased human activity. Climate change may alter microbial functioning by increasing growth rates and substrate use due to increased temperature. This may lead to changes of process rates and shifts in the structure of microbial communities. Biodiversity may increase as the Arctic warms and population shifts occur as psychrophilic/psychrotolerant species disappear in favor of more mesophylic ones. In order to predict how ecological processes will evolve as a function of global change, it is essential to identify which populations participate in each process, how they vary physiologically, and how the relative abundance, activity and community structure will change under altered environmental conditions. This review covers aspects of the importance and implication of snowpack in microbial ecology emphasizing the diversity and activity of these critical members of cold zone ecosystems. Full article
Open AccessReview Recent Advances and Future Perspectives in Microbial Phototrophy in Antarctic Sea Ice
Biology 2012, 1(3), 542-556; doi:10.3390/biology1030542
Received: 17 September 2012 / Revised: 10 October 2012 / Accepted: 11 October 2012 / Published: 22 October 2012
Cited by 3 | PDF Full-text (287 KB) | HTML Full-text | XML Full-text
Abstract
Bacteria that utilize sunlight to supplement metabolic activity are now being described in a range of ecosystems. While it is likely that phototrophy provides an important competitive advantage, the contribution that these microorganisms make to the bioenergetics of polar marine ecosystems is unknown.
[...] Read more.
Bacteria that utilize sunlight to supplement metabolic activity are now being described in a range of ecosystems. While it is likely that phototrophy provides an important competitive advantage, the contribution that these microorganisms make to the bioenergetics of polar marine ecosystems is unknown. In this minireview, we discuss recent advances in our understanding of phototrophic bacteria and highlight the need for future research. Full article

Journal Contact

MDPI AG
Biology Editorial Office
St. Alban-Anlage 66, 4052 Basel, Switzerland
biology@mdpi.com
Tel. +41 61 683 77 34
Fax: +41 61 302 89 18
Editorial Board
Contact Details Submit to Biology
Back to Top