Thermococcus marinus sp. nov. and Thermococcus radiotolerans sp. nov., two hyperthermophilic archaea from deep-sea hydrothermal vents that resist ionizing radiation

Thermococcus thermotolerans sp. nov., a hyperthermophilic archaeon isolated from a chimney in the Southwest Indian Ocean

An anaerobic hyperthermophilic archaeon was isolated from a black smoker chimney with a snail attachment at a water depth of 2 739 m in the Southwest Indian Ocean. The sample was taken from the chimney exterior wall. The enrichment was conducted under a continuous culture with temperature fluctuation of 80-130 °C over 24 h for 42 days at 28 MPa. The isolation was performed at 90 °C at 0.1 MPa. Cells of the isolated strain 813A4T were irregular cocci. Strain 813A4T grew at 60-94 °C (optimal growth at 85 °C) at 0.1 MPa, and growth was detected at up to 99 °C at 28 MPa. At 85 °C, the strain was able to grow at pressures ranging from 0.1 to 110 MPa (optimal pressure, 0.1-40 MPa). At 85 °C, the cells of 813A4T grew at pH 5.5-9 (optimal, pH 7.0) and a NaCl concentration of 1.0-4.0 % (w/v; optimum concentration, 2.5 % NaCl). Strain 813A4T utilized yeast extract, tryptone and peptone as single carbon sources for growth. Elemental sulphur stimulated its growth. The G+C content of the complete genome was 53.48 mol%. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain 813A4T belonged to the genus Thermococcus, with the highest sequence similarity to Thermococcus barossii SHCK-94T (99.73 %). The average nucleotide identity between strains 813A4T and SHCK-94T was 82.56 %. All these data indicated that strain 813A4T should be classified as representing a novel species of the genus Thermococcus, for which Thermococcus thermotolerans sp. nov. is proposed. The type strain is 813A4T (=JCM 39367T=MCCC M28628T).

Archaeal lipids

The major archaeal membrane glycerolipids are distinguished from those of bacteria and eukaryotes by the contrasting stereochemistry of their glycerol backbones, and by the use of ether-linked isoprenoid-based alkyl chains rather than ester-linked fatty acyl chains for their hydrophobic moieties. These fascinating compounds play important roles in the extremophile lifestyles of many species, but are also present in the growing numbers of recently discovered mesophilic archaea. The past decade has witnessed significant advances in our understanding of archaea in general and their lipids in particular. Much of the new information has come from the ability to screen large microbial populations via environmental metagenomics, which has revolutionised our understanding of the extent of archaeal biodiversity that is coupled with a strict conservation of their membrane lipid compositions. Significant additional progress has come from new culturing and analytical techniques that are gradually enabling archaeal physiology and biochemistry to be studied in real time. These studies are beginning to shed light on the much-discussed and still-controversial process of eukaryogenesis, which probably involved both bacterial and archaeal progenitors. Puzzlingly, although eukaryotes retain many attributes of their putative archaeal ancestors, their lipid compositions only reflect their bacterial progenitors. Finally, elucidation of archaeal lipids and their metabolic pathways have revealed potentially interesting applications that have opened up new frontiers for biotechnological exploitation of these organisms. This review is concerned with the analysis, structure, function, evolution and biotechnology of archaeal lipids and their associated metabolic pathways.

Formate and hydrogen in hydrothermal vents and their use by extremely thermophilic methanogens and heterotrophs

Extremely thermophilic methanogens in the Methanococci and heterotrophs in the Thermococci are common in deep-sea hydrothermal vents. All Methanococci use H₂ as an electron donor, and a few species can also use formate. Most Methanococci have a coenzyme F₄₂₀-reducing formate dehydrogenase. All Thermococci reduce S⁰ but have hydrogenases and produce H₂ in the absence of S⁰. Some Thermococci have formate hydrogenlyase (Fhl) that reversibly converts H₂ and CO₂ to formate or an NAD(P)⁺-reducing formate dehydrogenase (Nfd). Questions remain if Methanococci or Thermococci use or produce formate in nature, why only certain species can grow on or produce formate, and what the physiological role of formate is? Formate forms abiotically in hydrothermal fluids through chemical equilibrium with primarily H₂, CO₂, and CO and is strongly dependent upon H₂ concentration, pH, and temperature. Formate concentrations are highest in hydrothermal fluids where H₂ concentrations are also high, such as in ultramafic systems where serpentinization reactions occur. In nature, Methanococci are likely to use formate as an electron donor when H₂ is limiting. Thermococci with Fhl likely convert H₂ and CO₂ to formate when H₂ concentrations become inhibitory for growth. They are unlikely to grow on formate in nature unless formate is more abundant than H₂ in the environment. Nearly all Methanococci and Thermococci have a gene for at least one formate dehydrogenase catalytic subunit, which may be used to provide free formate for de novo purine biosynthesis. However, only species with a membrane-bound formate transporter can grow on or secrete formate. Interspecies H₂ transfer occurs between Thermococci and Methanococci. This and putative interspecies formate transfer may support Methanococci in low H₂ environments, which in turn may prevent growth inhibition of Thermococci by its own H₂. Future research directions include understanding when, where, and how formate is used and produced by these organisms in nature, and how transcription of Thermococci genes encoding formate-related enzymes are regulated.

High Proportions of Radiation-Resistant Strains in Culturable Bacteria from the Taklimakan Desert

Simple Summary

Radiation-resistant extremophiles have frequently been found in the Taklimakan Desert, which is known for its harsh conditions. However, there is no systemic study investigating the diversity and proportion of radiation-resistant strains among culturable bacteria. The results of this study revealed the distribution of culturable bacteria in the Taklimakan Desert and indicated high proportions of radiation-resistant strains in the culturable bacteria. The study helps to better understand the ecological origin of radio-resistance and to quantitatively describe the desert as a common habitat for radiation-resistant extremophiles.

Abstract

The Taklimakan Desert located in China is the second-largest shifting sand desert in the world and is known for its harsh conditions. Types of γ-rays or UV radiation-resistant bacterial strains have been isolated from this desert. However, there is no information regarding the proportions of the radiation-resistant strains in the total culturable microbes. We isolated 352 bacterial strains from nine sites across the Taklimakan Desert from north to south. They belong to Actinobacteria, Firmicutes, Proteobacteria, and Bacteroidetes. The phylum Actinobacteria was the most predominant in abundance and Firmicutes had the highest species richness. Bacteroidetes had the lowest abundance and was found in four sites only, while the other three phyla were found in every site but with different distribution profiles. After irradiating with 1000 J/m² and 6000 J/m² UV-C, the strains with survival rates higher than 10% occupied 72.3% and 36.9% of all culturable bacteria, respectively. The members from Proteobacteria had the highest proportions, with survival rates higher than 10%. After radiation with 10 kGy γ-rays, Kocuria sp. TKL1057 and Planococcus sp. TKL1152 showed higher radiation-resistant capabilities than Deinococcus radiodurans R1. Besides obtaining several radiation-resistant extremophiles, this study measured the proportions of the radiation-resistant strains in the total culturable microbes for the first time. This study may help to better understand the origin of radioresistance, especially by quantitatively comparing proportions of radiation-resistant extremophiles from different environments in the future.

Thermococcus aciditolerans sp. nov., a piezotolerant, hyperthermophilic archaeon isolated from a deep-sea hydrothermal vent chimney in the Southwest Indian Ridge

A hyperthermophilic, strictly anaerobic archaeon, designated strain SY113^T, was isolated from a deep-sea hydrothermal vent chimney on the Southwest Indian Ridge at a water depth of 2770 m. Enrichment and isolation of strain SY113^T were performed at 85 °C at 0.1 MPa. Cells of strain SY113^T were irregular motile cocci with peritrichous flagella and generally 0.8-2.4 µm in diameter. Growth was observed at temperatures between 50 and 90 °C (optimum at 85 °C) and under hydrostatic pressures of 0.1-60 MPa (optimum, 27 MPa). Cells of SY113^T grew at pH 4.0-9.0 (optimum, pH 5.5) and a NaCl concentration of 0.5-5.5 % (w/v; optimum concentration, 3.0 % NaCl). Strain SY113^T was an anaerobic chemoorganoheterotroph and grew on complex proteinaceous substrates such as yeast extract and tryptone, as well as on maltose and starch. Elemental sulphur stimulated growth, but not obligatory for its growth. The G+C content of the genomic DNA was 55.0 mol%. Phylogenetic analysis of the 16S rRNA sequence of strain SY113^T showed that the novel isolate belonged to the genus Thermococcus. On the basis of physiological characteristics, average nucleotide identity values and in silico DNA-DNA hybridization results, we propose a novel species, named Thermococcus aciditolerans sp. nov. The type strain is SY113^T (=MCCC 1K04190^T=JCM 39083^T).

Microorganisms from deep-sea hydrothermal vents

With a rich variety of chemical energy sources and steep physical and chemical gradients, hydrothermal vent systems offer a range of habitats to support microbial life. Cultivation-dependent and independent studies have led to an emerging view that diverse microorganisms in deep-sea hydrothermal vents live their chemolithoautotrophic, heterotrophic, or mixotrophic life with versatile metabolic strategies. Biogeochemical processes are mediated by microorganisms, and notably, processes involving or coupling the carbon, sulfur, hydrogen, nitrogen, and metal cycles in these unique ecosystems. Here, we review the taxonomic and physiological diversity of microbial prokaryotic life from cosmopolitan to endemic taxa and emphasize their significant roles in the biogeochemical processes in deep-sea hydrothermal vents. According to the physiology of the targeted taxa and their needs inferred from meta-omics data, the media for selective cultivation can be designed with a wide range of physicochemical conditions such as temperature, pH, hydrostatic pressure, electron donors and acceptors, carbon sources, nitrogen sources, and growth factors. The application of novel cultivation techniques with real-time monitoring of microbial diversity and metabolic substrates and products are also recommended.

Supplementary Information

The online version contains supplementary material available at 10.1007/s42995-020-00086-4.

Thermococcus bergensis sp. nov., a Novel Hyperthermophilic Starch-Degrading Archaeon

Simple Summary

Hyperthermophiles grow optimally above 80 °C and include mostly microorganisms belonging to the Archaea domain and are thriving in terrestrial and seafloor geothermal vents as well as in subsurface environments. From an anaerobic hyperthermophilic mixed culture obtained from water produced from a deep and hot oil reservoir we isolated and characterized a starch-degrading strain. Based on phylogenomic analysis, the strain represents a novel hyper-thermophilic species belonging to genus Thermococcus, for which we propose the name Thermococcus bergensis sp. nov.

Abstract

A novel hyperthermophilic archaeon, termed strain T7324^T, was isolated from a mixed sulfate-reducing consortium recovered from hot water produced from a deep North Sea oil reservoir. The isolate is a strict anaerobic chemo-organotroph able to utilize yeast extract or starch as a carbon source. The genes for a number of sugar degradation enzymes and glutamate dehydrogenase previously attributed to the sulfate reducing strain of the consortium (Archaeoglobus fulgidus strain 7324) were identified in the nearly completed genome sequence. Sequence analysis of the 16S rRNA gene placed the strain in the Thermococcus genus, but with an average nucleotide identity that is less than 90% to its closest relatives. Phylogenomic treeing reconstructions placed the strain on a distinct lineage clearly separated from other Thermococcus spp. The results indicate that the strain T7324^T represents a novel species, for which the name Thermococcus bergensis sp. nov. is proposed. The type strain is T7324^T (=DSM 27149^T = KCTC 15808^T).

Effects of Heavy Ion Particle Irradiation on Spore Germination of Bacillus spp. from Extremely Hot and Cold Environments

Extremophiles are optimal models in experimentally addressing questions about the effects of cosmic radiation on biological systems. The resistance to high charge energy (HZE) particles, and helium (He) ions and iron (Fe) ions (LET at 2.2 and 200 keV/µm, respectively, until 1000 Gy), of spores from two thermophiles, Bacillushorneckiae SBP3 and Bacilluslicheniformis T14, and two psychrotolerants, Bacillus sp. A34 and A43, was investigated. Spores survived He irradiation better, whereas they were more sensitive to Fe irradiation (until 500 Gy), with spores from thermophiles being more resistant to irradiations than psychrotolerants. The survived spores showed different germination kinetics, depending on the type/dose of irradiation and the germinant used. After exposure to He 1000 Gy, D-glucose increased the lag time of thermophilic spores and induced germination of psychrotolerants, whereas L-alanine and L-valine increased the germination efficiency, except alanine for A43. FTIR spectra showed important modifications to the structural components of spores after Fe irradiation at 250 Gy, which could explain the block in spore germination, whereas minor changes were observed after He radiation that could be related to the increased permeability of the inner membranes and alterations of receptor complex structures. Our results give new insights on HZE resistance of extremophiles that are useful in different contexts, including astrobiology.

Plants in the Light of Ionizing Radiation: What Have We Learned From Chernobyl, Fukushima, and Other "Hot" Places?

Perhaps the main factor determining success of space travel will be the ability to control effects of ionizing radiation for humans, but also for other living organisms. Manned space travel will require the cultivation of food plants under conditions of prolonged exposure to ionizing radiation. Although there is a significant literature concerning the effects of acute high dose rate exposures on plant genetics, growth, and development, much less is known concerning the effects of chronic low dose irradiation especially those related to the impacts of the high energy protons and heavy ions that are encountered in the space environment. Here, we make the argument that in situ studies of the effects of radionuclides at nuclear accident sites (e.g., Chernobyl and Fukushima), atomic bomb test sites, and areas of naturally high radiation levels, could provide insights concerning the mechanisms of radiation effects on living systems that cannot be assessed short of conducting research in space, which is not yet feasible for large scale, long term, multigenerational experiments. In this article we review the literature concerning the effects of chronic low-dose rate radiation exposure from studies conducted in Chernobyl, Fukushima, and other regions of the world with high ambient radiation levels (parts of India in particular). In general, mutation rates and other measures of genetic damage are considerably elevated, pollen and seed viability are reduced, growth rates are slower, and the frequency of developmental abnormalities is increased, although there is considerable variation among taxa for these effects. In addition, there are interactions between radiation and other environmental stressors (e.g., temperature, drought, heavy metals) that may play important roles in determining susceptibility to radiation induced stress.

Shifts in microbial community composition in tannery-contaminated soil in response to increased gamma radiation

Purpose

Contaminated sites from man-made activities such as old-fashioned tanneries are inhabited by virulent microorganisms that exhibit more resistance against extreme and toxic environmental conditions. We investigated the effect of different Gamma radiation doses on microbial community composition in the sediment of an old-fashioned tannery.

Methods

Seven samples collected from the contaminated sites received different gamma radiation doses (I = 0.0, II = 5, III = 10, VI = 15, V = 20, VI = 25, and VII = 30 kGy) as an acute exposure. The shift in microbial community structure was assessed using the high throughput 454 pyrosequencing. Variations in diversity, richness, and the shift in operational taxonomic units (OTUs) were investigated using statistical analysis.

Result

Our results showed that the control sample (I) had the highest diversity, richness, and OTUs when compared with the irradiated samples. Species of Halocella, Parasporobacterium, and Anaerosporobacter had the highest relative abundance at the highest radiation dose of 30 kGy. Members of the Firmicutes also increased by 20% at the highest radiation dose when compared with the control sample (0.0 kGy). Representatives of Synergistetes decreased by 25% while Bacteroidetes retained a steady distribution across the range of gamma radiation intensities.

Conclusion

This study provides information about potential “radioresistant” and/or “radiotolerant” microbial species that are adapted to elevated level of chemical toxicity such as Cr and Sr in tannery. These species can be of a high biotechnological and environmental importance.

Review of microbial resistance to chronic ionizing radiation exposure under environmental conditions

Ionizing radiation (IR) produces multiple types of damage to nucleic acids, proteins and other crucial cellular components. Nevertheless, various microorganisms from phylogenetically distant taxa (bacteria, archaea, fungi) can resist IR levels many orders of magnitude above natural background. This intriguing phenomenon of radioresistance probably arose independently many times throughout evolution as a byproduct of selective pressures from other stresses (e.g. desiccation, UV radiation, chemical oxidants). Most of the literature on microbial radioresistance is based on acute γ-irradiation experiments performed in the laboratory, typically involving pure cultures grown under near-optimal conditions. There is much less information about the upper limits of radioresistance in the field, such as in radioactively-contaminated areas, where several radiation types (e.g. α and β, as well as γ) and other stressors (e.g. non-optimal temperature and nutrient levels, toxic chemicals, interspecific competition) act over multiple generations. Here we discuss several examples of radioresistant microbes isolated from extremely radioactive locations (e.g. Chernobyl and Mayak nuclear plant sites) and estimate the radiation dose rates they were able to tolerate. Some of these organisms (e.g. the fungus Cladosporium cladosporioides, the cyanobacterium Geitlerinema amphibium) are widely-distributed and colonize a variety of habitats. These examples suggest that resistance to chronic IR and chemical contamination is not limited to rare specialized strains from extreme environments, but can occur among common microbial taxa, perhaps due to overlap between mechanisms of resistance to IR and other stressors.

Deinococcus lacus sp. nov., a gamma radiation-resistant bacterium isolated from an artificial freshwater pond

A Gram-stain-negative, pink-coloured, non-motile and gamma radiation-resistant bacterium, designated strain IMCC1711^T, was isolated from a freshwater sample collected from an artificial pond (Inkyong Pond). The 16S rRNA gene sequence analysis showed that strain IMCC1711^T was most closely related to Deinococcus piscis 3ax^T (94.2 %) and formed a robust phylogenetic clade with other species of the genus Deinococcus. Optimal growth of strain MCC1711^T was observed at 25 °C and pH 7.0 without NaCl. Strain IMCC1711^T exhibited high resistance to gamma radiation. The DNA G+C content of strain IMCC1711^T was 59.1 mol% and MK-8 was the predominant isoprenoid quinone. Major fatty acid constituents of the strain were C17 : 1ω8c, C16 : 0, summed feature 3 (C16 : 1ω6c and/or C16 : 1ω7c) and C15 : 1ω6c. The major polar lipids constituted phosphatidylethanolamine, one unidentified phosphoglycolipid and two unidentified glycolipids. On the basis of taxonomic data obtained in this study, it was concluded that strain IMCC1711^T represented a novel species of the genus Deinococcus, for which the name Deinococcus lacus sp. nov. is proposed. The type strain of Deinococcus lacus is IMCC1711^T (KCTC 52494^T=KACC 18979^T=NBRC 112440^T).

Complete Genome Sequences of 11 Type Species from the Thermococcus Genus of Hyperthermophilic and Piezophilic Archaea

We report here the genome sequences of the type strains of the species Thermococcus barossii , T. celer , T. chitonophagus , T. gorgonarius , T. pacificus , T. peptonophilus , T. profundus , T. radiotolerans , T. siculi , and T. thioreducens , as well as the prototype of a possible type strain of a novel Thermococcus species, strain P6.

The Adaptability of Life on Earth and the Diversity of Planetary Habitats

The evolutionary adaptability of life to extreme environments is astounding given that all life on Earth is based on the same fundamental biochemistry. The range of some physicochemical parameters on Earth exceeds the ability of life to adapt, but stays within the limits of life for other parameters. Certain environmental conditions such as low water availability in hyperarid deserts on Earth seem to be close to the limit of biological activity. A much wider range of environmental parameters is observed on planetary bodies within our Solar System such as Mars or Titan, and presumably even larger outside of our Solar System. Here we review the adaptability of life as we know it, especially regarding temperature, pressure, and water activity. We use then this knowledge to outline the range of possible habitable environments for alien planets and moons and distinguish between a variety of planetary environment types. Some of these types are present in our Solar System, others are hypothetical. Our schematic categorization of alien habitats is limited to life as we know it, particularly regarding to the use of solvent (water) and energy source (light and chemical compounds).

Thermococcus eurythermalis sp. nov., a conditional piezophilic, hyperthermophilic archaeon with a wide temperature range for growth, isolated from an oil-immersed chimney in the Guaymas Basin

A conditional piezophilic, hyperthermophilic archaeon showing growth over a wide range of temperature, pH and pressure was isolated from an oil-immersed hydrothermal chimney at a depth of 2006.9 m in the Guaymas Basin. Enrichment and isolation of strain A501T were performed at 80 °C at 0.1 MPa. Cells of isolate A501T were irregular motile cocci with a polar tuft of flagella and generally 0.6–2.6 µm in diameter. Growth was detected over the range 50–100 °C (optimal growth at 85 °C) at atmospheric pressure and was observed at 102 °C at a pressure of 10 MPa. At 85 °C, growth was observed at a pressure of 0.1–70 MPa (optimum pressure 0.1 MPa–30 MPa), while at 95 °C, the pressure allowing growth ranged from 0.1 MPa to 50 MPa (optimum pressure 10 MPa). Cells of strain A501T grew at pH 4–9 (optimum pH 7.0) and a NaCl concentration of 1.0–5.0 % (w/v) (optimum concentration 2.5 % NaCl). This isolate was an anaerobic chemo-organoheterotroph and was able to utilize yeast extract, peptone, tryptone and starch as the single carbon source for growth. Elemental sulfur and cysteine stimulated growth; however, these molecules were not necessary. The DNA G+C content of the complete genome was 53.47 mol%. The results of 16S rRNA gene sequence analysis indicated that strain A501T belongs to the genus Thermococcus . There was no significant similarity between strain A501T and the phylogenetically related species of the genus Thermococcus based on complete genome sequence alignments and calculation of the average nucleotide identity and the tetranucleotide signature frequency correlation coefficient. These results indicate that strain A501T represents a novel species, Thermococcus eurythermalis sp. nov. The type strain is A501T ( = CGMCC 7834T = JCM 30233T).

The temperature gradient-forming device, an accessory unit for normal light microscopes to study the biology of hyperthermophilic microorganisms

To date, the behavior of hyperthermophilic microorganisms in their biotope has been studied only to a limited degree; this is especially true for motility. One reason for this lack of knowledge is the requirement for high-temperature microscopy-combined, in most cases, with the need for observations under strictly anaerobic conditions-for such studies. We have developed a custom-made, low-budget device that, for the first time, allows analyses in temperature gradients up to 40°C over a distance of just 2 cm (a biotope-relevant distance) with heating rates up to ∼5°C/s. Our temperature gradient-forming device can convert any upright light microscope into one that works at temperatures as high as 110°C. Data obtained by use of this apparatus show how very well hyperthermophiles are adapted to their biotope: they can react within seconds to elevated temperatures by starting motility-even after 9 months of storage in the cold. Using the temperature gradient-forming device, we determined the temperature ranges for swimming, and the swimming speeds, of 15 selected species of the genus Thermococcus within a few months, related these findings to the presence of cell surface appendages, and obtained the first evidence for thermotaxis in Archaea.

Diffuse flow environments within basalt- and sediment-based hydrothermal vent ecosystems harbor specialized microbial communities

Hydrothermal vents differ both in surface input and subsurface geochemistry. The effects of these differences on their microbial communities are not clear. Here, we investigated both alpha and beta diversity of diffuse flow-associated microbial communities emanating from vents at a basalt-based hydrothermal system along the East Pacific Rise (EPR) and a sediment-based hydrothermal system, Guaymas Basin. Both Bacteria and Archaea were targeted using high throughput 16S rRNA gene pyrosequencing analyses. A unique aspect of this study was the use of a universal set of 16S rRNA gene primers to characterize total and diffuse flow-specific microbial communities from varied deep-sea hydrothermal environments. Both surrounding seawater and diffuse flow water samples contained large numbers of Marine Group I (MGI) Thaumarchaea and Gammaproteobacteria taxa previously observed in deep-sea systems. However, these taxa were geographically distinct and segregated according to type of spreading center. Diffuse flow microbial community profiles were highly differentiated. In particular, EPR dominant diffuse flow taxa were most closely associated with chemolithoautotrophs, and off axis water was dominated by heterotrophic-related taxa, whereas the opposite was true for Guaymas Basin. The diversity and richness of diffuse flow-specific microbial communities were strongly correlated to the relative abundance of Epsilonproteobacteria, proximity to macrofauna, and hydrothermal system type. Archaeal diversity was higher than or equivalent to bacterial diversity in about one third of the samples. Most diffuse flow-specific communities were dominated by OTUs associated with Epsilonproteobacteria, but many of the Guaymas Basin diffuse flow samples were dominated by either OTUs within the Planctomycetes or hyperthermophilic Archaea. This study emphasizes the unique microbial communities associated with geochemically and geographically distinct hydrothermal diffuse flow environments.

Role of Mn2+ and compatible solutes in the radiation resistance of thermophilic bacteria and archaea

Radiation-resistant bacteria have garnered a great deal of attention from scientists seeking to expose the mechanisms underlying their incredible survival abilities. Recent analyses showed that the resistance to ionizing radiation (IR) in the archaeon Halobacterium salinarum is dependent upon Mn-antioxidant complexes responsible for the scavenging of reactive oxygen species (ROS) generated by radiation. Here we examined the role of the compatible solutes trehalose, mannosylglycerate, and di-myo-inositol phosphate in the radiation resistance of aerobic and anaerobic thermophiles. We found that the IR resistance of the thermophilic bacteria Rubrobacter xylanophilus and Rubrobacter radiotolerans was highly correlated to the accumulation of high intracellular concentration of trehalose in association with Mn, supporting the model of Mn²⁺-dependent ROS scavenging in the aerobes. In contrast, the hyperthermophilic archaea Thermococcus gammatolerans and Pyrococcus furiosus did not contain significant amounts of intracellular Mn, and we found no significant antioxidant activity from mannosylglycerate and di-myo-inositol phosphate in vitro. We therefore propose that the low levels of IR-generated ROS under anaerobic conditions combined with highly constitutively expressed detoxification systems in these anaerobes are key to their radiation resistance and circumvent the need for the accumulation of Mn-antioxidant complexes in the cell.

Sunlight-exposed biofilm microbial communities are naturally resistant to chernobyl ionizing-radiation levels

Background

The Chernobyl accident represents a long-term experiment on the effects of exposure to ionizing radiation at the ecosystem level. Though studies of these effects on plants and animals are abundant, the study of how Chernobyl radiation levels affect prokaryotic and eukaryotic microbial communities is practically non-existent, except for a few reports on human pathogens or soil microorganisms. Environments enduring extreme desiccation and UV radiation, such as sunlight exposed biofilms could in principle select for organisms highly resistant to ionizing radiation as well.

Methodology/Principal Findings

To test this hypothesis, we explored the diversity of microorganisms belonging to the three domains of life by cultivation-independent approaches in biofilms developing on concrete walls or pillars in the Chernobyl area exposed to different levels of radiation, and we compared them with a similar biofilm from a non-irradiated site in Northern Ireland. Actinobacteria, Alphaproteobacteria, Bacteroidetes, Acidobacteria and Deinococcales were the most consistently detected bacterial groups, whereas green algae (Chlorophyta) and ascomycete fungi (Ascomycota) dominated within the eukaryotes. Close relatives to the most radio-resistant organisms known, including Rubrobacter species, Deinococcales and melanized ascomycete fungi were always detected. The diversity of bacteria and eukaryotes found in the most highly irradiated samples was comparable to that of less irradiated Chernobyl sites and Northern Ireland. However, the study of mutation frequencies in non-coding ITS regions versus SSU rRNA genes in members of a same actinobacterial operational taxonomic unit (OTU) present in Chernobyl samples and Northern Ireland showed a positive correlation between increased radiation and mutation rates.

Conclusions/Significance

Our results show that biofilm microbial communities in the most irradiated samples are comparable to non-irradiated samples in terms of general diversity patterns, despite increased mutation levels at the single-OTU level. Therefore, biofilm communities growing in sunlight exposed substrates are capable of coping with increased mutation rates and appear pre-adapted to levels of ionizing radiation in Chernobyl due to their natural adaptation to periodical desiccation and ambient UV radiation.

Ionizing radiation and life

Ionizing radiation is a ubiquitous feature of the Cosmos, from exogenous cosmic rays (CR) to the intrinsic mineral radioactivity of a habitable world, and its influences on the emergence and persistence of life are wide-ranging and profound. Much attention has already been focused on the deleterious effects of ionizing radiation on organisms and the complex molecules of life, but ionizing radiation also performs many crucial functions in the generation of habitable planetary environments and the origins of life. This review surveys the role of CR and mineral radioactivity in star formation, generation of biogenic elements, and the synthesis of organic molecules and driving of prebiotic chemistry. Another major theme is the multiple layers of shielding of planetary surfaces from the flux of cosmic radiation and the various effects on a biosphere of violent but rare astrophysical events such as supernovae and gamma-ray bursts. The influences of CR can also be duplicitous, such as limiting the survival of surface life on Mars while potentially supporting a subsurface biosphere in the ocean of Europa. This review highlights the common thread that ionizing radiation forms between the disparate component disciplines of astrobiology.

Role of disulfide bridges in archaeal family-B DNA polymerases

The family-B DNA polymerases obtained from the order Thermococcales, for example, Pyrococcus furiosus (Pfu-Pol) are commonly used in the polymerase chain reaction (PCR) because of their high thermostability and low error rates. Most of these polymerases contain four cysteines, arranged as two disulfide bridges. With Pfu-Pol C429-C443 forms one of the disulfides (DB1) and C507-C510 (DB2) the other. Although the disulfides are well conserved in the enzymes from the hyperthermophilic Thermococcales, they are less prevalent in euryarchaeal polymerases from other orders, and tend to be only found in other hyperthermophiles. Here, we report on the effects of deleting the disulfide bridges by mutating the relevant cysteines to serines. A variety of techniques, including differential scanning calorimetry and differential scanning fluorimetry, have shown that both disulfides make a contribution to thermostability, with DB1 being more important than DB2. However, even when both disulfides are removed, sufficient thermostability remains for normal (identical to the wild type) performance in PCR and quantitative (real-time) PCR. Therefore, polymerases totally lacking cysteine are fully compatible with most PCR-based applications. This observation opens the way to further engineering of polymerases by introduction of a single cysteine followed by appropriate chemical modification.

Genome analysis and genome-wide proteomics of Thermococcus gammatolerans, the most radioresistant organism known amongst the Archaea

The genome sequence of Thermococcus gammatolerans, a radioresistant archaeon, is described; a proteomic analysis reveals that radioresistance may be due to unknown DNA repair enzymes.

Background

Thermococcus gammatolerans was isolated from samples collected from hydrothermal chimneys. It is one of the most radioresistant organisms known amongst the Archaea. We report the determination and annotation of its complete genome sequence, its comparison with other Thermococcales genomes, and a proteomic analysis.

Results

T. gammatolerans has a circular chromosome of 2.045 Mbp without any extra-chromosomal elements, coding for 2,157 proteins. A thorough comparative genomics analysis revealed important but unsuspected genome plasticity differences between sequenced Thermococcus and Pyrococcus species that could not be attributed to the presence of specific mobile elements. Two virus-related regions, tgv1 and tgv2, are the only mobile elements identified in this genome. A proteogenome analysis was performed by a shotgun liquid chromatography-tandem mass spectrometry approach, allowing the identification of 10,931 unique peptides corresponding to 951 proteins. This information concurrently validates the accuracy of the genome annotation. Semi-quantification of proteins by spectral count was done on exponential- and stationary-phase cells. Insights into general catabolism, hydrogenase complexes, detoxification systems, and the DNA repair toolbox of this archaeon are revealed through this genome and proteome analysis.

Conclusions

This work is the first archaeal proteome investigation done at the stage of primary genome annotation. This archaeon is shown to use a large variety of metabolic pathways even under a rich medium growth condition. This proteogenomic study also indicates that the high radiotolerance of T. gammatolerans is probably due to proteins that remain to be characterized rather than a larger arsenal of known DNA repair enzymes.

Characterization of DNA polymerase from the hyperthermophilic archaeon Thermococcus marinus and its application to PCR

The family B DNA polymerase gene from the archaeon Thermococcus marinus (Tma) contains a long open reading frame of 3,939 bp that encodes 1,312 amino acid residues. The gene is split by one intervening sequence that forms a continuous open reading frame with the two polymerase exteins. In this study, the Tma DNA polymerase gene both with (precursor form) and without (mature form) its intein was expressed in Escherichia coli, purified by heat treatment and HiTrap Heparin HP column chromatography and characterized. Primary sequence analysis of the mature Tma polymerase showed high sequence identity with DNA polymerases in the genus Thermococcus. The expressed precursor form was easily spliced during purification steps. The molecular mass of the purified Tma DNA polymerases is about 90 kDa, as estimated by SDS-PAGE. Both Tma DNA polymerases showed the same properties. PCR performed with this enzyme was found to be optimal in the presence of 50 mM Tris-HCl (pH 8.4), 40 mM KCl, 12.5 mM (NH(4))(2)SO(4,) 2 mM MgCl(2,) 0.05% Triton X-100 and 0.0075% BSA. Furthermore, long-range PCR and time-saving PCR were performed using various specific ratios of Taq and Tma DNA polymerases (Tma plus DNA polymerase).

Adaptations to submarine hydrothermal environments exemplified by the genome of Nautilia profundicola

Submarine hydrothermal vents are model systems for the Archaean Earth environment, and some sites maintain conditions that may have favored the formation and evolution of cellular life. Vents are typified by rapid fluctuations in temperature and redox potential that impose a strong selective pressure on resident microbial communities. Nautilia profundicola strain Am-H is a moderately thermophilic, deeply-branching Epsilonproteobacterium found free-living at hydrothermal vents and is a member of the microbial mass on the dorsal surface of vent polychaete, Alvinella pompejana. Analysis of the 1.7-Mbp genome of N. profundicola uncovered adaptations to the vent environment--some unique and some shared with other Epsilonproteobacterial genomes. The major findings included: (1) a diverse suite of hydrogenases coupled to a relatively simple electron transport chain, (2) numerous stress response systems, (3) a novel predicted nitrate assimilation pathway with hydroxylamine as a key intermediate, and (4) a gene (rgy) encoding the hallmark protein for hyperthermophilic growth, reverse gyrase. Additional experiments indicated that expression of rgy in strain Am-H was induced over 100-fold with a 20 degrees C increase above the optimal growth temperature of this bacterium and that closely related rgy genes are present and expressed in bacterial communities residing in geographically distinct thermophilic environments. N. profundicola, therefore, is a model Epsilonproteobacterium that contains all the genes necessary for life in the extreme conditions widely believed to reflect those in the Archaean biosphere--anaerobic, sulfur, H2- and CO2-rich, with fluctuating redox potentials and temperatures. In addition, reverse gyrase appears to be an important and common adaptation for mesophiles and moderate thermophiles that inhabit ecological niches characterized by rapid and frequent temperature fluctuations and, as such, can no longer be considered a unique feature of hyperthermophiles.

Diversity of thermophilic anaerobes

Thermophilic anaerobes are Archaea and Bacteria that grow optimally at temperatures of 50 degrees C or higher and do not require the use of O(2) as a terminal electron acceptor for growth. The prokaryotes with this type of physiology are studied for a variety of reasons, including (a) to understand how life can thrive under extreme conditions, (b) for their biotechnological potential, and (c) because anaerobic thermophiles are thought to share characteristics with the early evolutionary life forms on Earth. Over 300 species of thermophilic anaerobes have been described; most have been isolated from thermal environments, but some are from mesobiotic environments, and others are from environments with temperatures below 0 degrees C. In this overview, the authors outline the phylogenetic and physiological diversity of thermophilic anaerobes as currently known. The purpose of this overview is to convey the incredible diversity and breadth of metabolism within this subset of anaerobic microorganisms.

Identification of archaeon-producing hyperthermophilic alpha-amylase and characterization of the alpha-amylase

The extremely thermophilic anaerobic archaeon strain, HJ21, was isolated from a deep-sea hydrothermal vent, could produce hyperthermophilic alpha-amylase, and later was identified as Thermococcus from morphological, biochemical, and physiological characteristics and the 16S ribosomal RNA gene sequence. The extracellular thermostable alpha-amylase produced by strain HJ21 exhibited maximal activity at pH 5.0. The enzyme was stable in a broad pH range from pH 5.0 to 9.0. The optimal temperature of alpha-amylase was observed at 95 degrees C. The half-life of the enzyme was 5 h at 90 degrees C. Over 40% and 30% of the enzyme activity remained after incubation at 100 degrees C for 2 and 3 h, respectively. The enzyme did not require Ca(2+) for thermostability. This alpha-amylase gene was cloned, and its nucleotide sequence displayed an open reading frame of 1,374 bp, which encodes a protein of 457 amino acids. Analysis of the deduced amino acid sequence revealed that four homologous regions common in amylases were conserved in the HJ21 alpha-amylase. The molecular weight of the mature enzyme was calculated to be 51.4 kDa, which correlated well with the size of the purified enzyme as shown by the sodium dodecyl sulfate-polyacrylamide gel electrophoresis.

Archaeal habitats — from the extreme to the ordinary

The domain Archaea represents a third line of evolutionary descent, separate from Bacteria and Eucarya. Initial studies seemed to limit archaea to various extreme environments. These included habitats at the extreme limits that allow life on earth, in terms of temperature, pH, salinity, and anaerobiosis, which were the homes to hyper thermo philes, extreme (thermo)acidophiles, extreme halophiles, and methanogens. Typical environments from which pure cultures of archaeal species have been isolated include hot springs, hydrothermal vents, solfataras, salt lakes, soda lakes, sewage digesters, and the rumen. Within the past two decades, the use of molecular techniques, including PCR-based amplification of 16S rRNA genes, has allowed a culture-independent assessment of microbial diversity. Remarkably, such techniques have indicated a wide distribution of mostly uncultured archaea in normal habitats, such as ocean waters, lake waters, and soil. This review discusses organisms from the domain Archaea in the context of the environments where they have been isolated or detected. For organizational purposes, the domain has been separated into the traditional groups of methanogens, extreme halophiles, thermoacidophiles, and hyperthermophiles, as well as the uncultured archaea detected by molecular means. Where possible, we have correlated known energy-yielding reactions and carbon sources of the archaeal types with available data on potential carbon sources and electron donors and acceptors present in the environments. From the broad distribution, metabolic diversity, and sheer numbers of archaea in environments from the extreme to the ordinary, the roles that the Archaea play in the ecosystems have been grossly underestimated and are worthy of much greater scrutiny.Key words: Archaea, methanogen, extreme halophile, hyperthermophile, thermoacidophile, uncultured archaea, habitats.

Tepidimicrobium ferriphilum gen. nov., sp. nov., a novel moderately thermophilic, Fe(III)-reducing bacterium of the order Clostridiales

A moderately thermophilic, anaerobic bacterium (strain SB91T) was isolated from a freshwater hot spring at Barguzin Valley, Buryatiya, Russia. Cells of strain SB91T were straight to slightly curved rods, 0·5–0·6 μm in diameter and 3·0–7·0 μm in length. Formation of endospores was not observed. The temperature range for growth was 26–62 °C, with an optimum at 50 °C. The pH range for growth was 5·5–9·5, with an optimum at pH 7·5–8·0. The substrates utilized by strain SB91T in the presence of 9,10-anthraquinone 2,6-disulfonate included peptone, tryptone, Casamino acids, yeast extract, beef extract, casein hydrolysate, alanine plus glycine, alanine plus proline, l-valine and n-propanol. Carbohydrates were not utilized. Strain SB91T reduced amorphous Fe(III) oxide, Fe(III) citrate, Fe(III) EDTA or Fe(III) nitrilotriacetate with peptone, l-valine or n-propanol as an electron donor. Strain SB91T reduced 9,10-anthraquinone 2,6-disulfonate, thiosulfate, elemental sulfur, fumarate and selenite. Strain SB91T survived after exposure to gamma-radiation at a dose of 5·4 kGy. The G+C content of the DNA of strain SB91T was 33 mol%. Analysis of the 16S rRNA gene sequence revealed that the isolated organism belonged to cluster XII of the clostridia. On the basis of its physiological properties and the results of phylogenetic analyses, it is proposed that strain SB91T represents the sole species of a novel genus, Tepidimicrobium; the name Tepidimicrobium ferriphilum gen. nov., sp. nov. is proposed, with strain SB91T (=DSM 16624T=VKM B-2348T) as the type strain.

Recent developments in the thermophilic microbiology of deep-sea hydrothermal vents

The diversity of thermophilic prokaryotes inhabiting deep-sea hot vents was actively studied over the last two decades. The ever growing interest is reflected in the exponentially increasing number of novel thermophilic genera described. The goal of this paper is to survey the progress in this field made in the years 2000-2005. In this period, representatives of several new taxa of hyperthermophilic archaea were obtained from deep-sea environments. Two of these isolates had phenotypic features new for this group of organisms: the presence of an outer cell membrane (the genus Ignicoccus) and the ability to grow anaerobically with acetate and ferric iron (the genus Geoglobus). Also, our knowledge on the diversity of thermophilic bacteria from deep-sea thermal environments extended significantly. The new bacterial isolates represented diverse bacterial divisions: the phylum Aquificae, the subclass Epsilonproteobacteria, the order Thermotogales, the families Thermodesulfobacteriaceae, Deferribacteraceae, and Thermaceae, and a novel bacterial phylum represented by the genus Caldithrix. Most of these isolates are obligate or facultative lithotrophs, oxidizing molecular hydrogen in the course of different types of anaerobic respiration or microaerobic growth. The existence and significant ecological role of some of new bacterial thermophilic isolates was initially established by molecular methods.

Deinococcus radiodurans — the consummate survivor

Relatively little is known about the biochemical basis of the capacity of Deinococcus radiodurans to endure the genetic insult that results from exposure to ionizing radiation and can include hundreds of DNA double-strand breaks. However, recent reports indicate that this species compensates for extensive DNA damage through adaptations that allow cells to avoid the potentially detrimental effects of DNA strand breaks. It seems that D. radiodurans uses mechanisms that limit DNA degradation and that restrict the diffusion of DNA fragments that are produced following irradiation, to preserve genetic integrity. These mechanisms also increase the efficiency of the DNA-repair proteins.

Extensive diversity of ionizing-radiation-resistant bacteria recovered from Sonoran Desert soil and description of nine new species of the genus Deinococcus obtained from a single soil sample

The ionizing-radiation-resistant fractions of two soil bacterial communities were investigated by exposing an arid soil from the Sonoran Desert and a nonarid soil from a Louisiana forest to various doses of ionizing radiation using a (60)Co source. The numbers of surviving bacteria decreased as the dose of gamma radiation to which the soils were exposed increased. Bacterial isolates surviving doses of 30 kGy were recovered from the Sonoran Desert soil, while no isolates were recovered from the nonarid forest soil after exposure to doses greater than 13 kGy. The phylogenetic diversities of the surviving culturable bacteria were compared for the two soils using 16S rRNA gene sequence analysis. In addition to a bacterial population that was more resistant to higher doses of ionizing radiation, the diversity of the isolates was greater in the arid soil. The taxonomic diversity of the isolates recovered was found to decrease as the level of ionizing-radiation exposure increased. Bacterial isolates of the genera Deinococcus, Geodermatophilus, and Hymenobacter were still recovered from the arid soil after exposure to doses of 17 to 30 kGy. The recovery of large numbers of extremely ionizing-radiation-resistant bacteria from an arid soil and not from a nonarid soil provides further ecological support for the hypothesis that the ionizing-radiation resistance phenotype is a consequence of the evolution of other DNA repair systems that protect cells against commonly encountered environmental stressors, such as desiccation. The diverse group of bacterial strains isolated from the arid soil sample included 60 Deinococcus strains, the characterization of which revealed nine novel species of this genus.

Physiological responses of the halophilic archaeon Halobacterium sp. strain NRC1 to desiccation and gamma irradiation

We report that the halophilic archaeon Halobacterium sp. strain NRC-1 is highly resistant to desiccation, high vacuum and 60Co gamma irradiation. Halobacterium sp. was able to repair extensive double strand DNA breaks (DSBs) in its genomic DNA, produced both by desiccation and by gamma irradiation, within hours of damage induction. We propose that resistance to high vacuum and 60Co gamma irradiation is a consequence of its adaptation to desiccating conditions. Gamma resistance in Halobacterium sp. was dependent on growth stage with cultures in earlier stages exhibiting higher resistance. Membrane pigments, specifically bacterioruberin, offered protection against cellular damages induced by high doses (5 kGy) of gamma irradiation. High-salt conditions were found to create a protective environment against gamma irradiation in vivo by comparing the amount of DSBs induced by ionizing radiation in the chromosomal DNA of Halobacterium sp. to that of the more radiation-sensitive Escherichia coli that grows in lower-salt conditions. No inducible response was observed after exposing Halobacterium sp. to a nonlethal dose (0.5 kGy) of gamma ray and subsequently exposing the cells to either a high dose (5 kGy) of gamma ray or desiccating conditions. We find that the hypersaline environment in which Halobacterium sp. flourishes is a fundamental factor for its resistance to desiccation, damaging radiation and high vacuum.