A barophilic response by two hyperthermophilic, hydrothermal vent Archaea: An upward shift in the optimal temperature and acceleration of growth rate at supra-optimal temperatures by elevated pressure

High-Pressure Microfluidics for Ultra-Fast Microbial Phenotyping

Here, we present a novel methodology based on high-pressure microfluidics to rapidly perform temperature-based phenotyping of microbial strains from deep-sea environments. The main advantage concerns the multiple on-chip temperature conditions that can be achieved in a single experiment at pressures representative of the deep-sea, overcoming the conventional limitations of large-scale batch metal reactors to conduct fast screening investigations. We monitored the growth of the model strain Thermococcus barophilus over 40 temperature and pressure conditions, without any decompression, in only 1 week, whereas it takes weeks or months with conventional approaches. The results are later compared with data from the literature. An additional example is also shown for a hydrogenotrophic methanogen strain (Methanothermococcus thermolithotrophicus), demonstrating the robustness of the methodology. These microfluidic tools can be used in laboratories to accelerate characterizations of new isolated species, changing the widely accepted paradigm that high-pressure microbiology experiments are time-consuming.

Seafloor Incubation Experiment with Deep-Sea Hydrothermal Vent Fluid Reveals Effect of Pressure and Lag Time on Autotrophic Microbial Communities

Diverse microbial communities drive biogeochemical cycles in Earth’s ocean, yet studying these organisms and processes is often limited by technological capabilities, especially in the deep ocean. In this study, we used a novel marine microbial incubator instrument capable of in situ experimentation to investigate microbial primary producers at deep-sea hydrothermal vents.

Depressurization and sample processing delays may impact the outcome of shipboard microbial incubations of samples collected from the deep sea. To address this knowledge gap, we developed a remotely operated vehicle (ROV)-powered incubator instrument to carry out and compare results from in situ and shipboard RNA stable isotope probing (RNA-SIP) experiments to identify the key chemolithoautotrophic microbes and metabolisms in diffuse, low-temperature venting fluids from Axial Seamount. All the incubations showed microbial uptake of labeled bicarbonate primarily by thermophilic autotrophic Epsilonbacteraeota that oxidized hydrogen coupled with nitrate reduction. However, the in situ seafloor incubations showed higher abundances of transcripts annotated for aerobic processes, suggesting that oxygen was lost from the hydrothermal fluid samples prior to shipboard analysis. Furthermore, transcripts for thermal stress proteins such as heat shock chaperones and proteases were significantly more abundant in the shipboard incubations, suggesting that depressurization induced thermal stress in the metabolically active microbes in these incubations. Together, the results indicate that while the autotrophic microbial communities in the shipboard and seafloor experiments behaved similarly, there were distinct differences that provide new insight into the activities of natural microbial assemblages under nearly native conditions in the ocean.

IMPORTANCE Diverse microbial communities drive biogeochemical cycles in Earth’s ocean, yet studying these organisms and processes is often limited by technological capabilities, especially in the deep ocean. In this study, we used a novel marine microbial incubator instrument capable of in situ experimentation to investigate microbial primary producers at deep-sea hydrothermal vents. We carried out identical stable isotope probing experiments coupled to RNA sequencing both on the seafloor and on the ship to examine thermophilic, microbial autotrophs in venting fluids from an active submarine volcano. Our results indicate that microbial communities were significantly impacted by the effects of depressurization and sample processing delays, with shipboard microbial communities being more stressed than seafloor incubations. Differences in metabolism were also apparent and are likely linked to the chemistry of the fluid at the beginning of the experiment. Microbial experimentation in the natural habitat provides new insights into understanding microbial activities in the ocean.

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).

[The high pressure life of piezophiles]

The deep biosphere is composed of very different biotopes located in the depth of the oceans, the ocean crust or the lithosphere. Although very different, deep biosphere biotopes share one common feature, high hydrostatic pressure. The deep biosphere is colonized by specific organisms, called piezophiles, that are able to grow under high hydrostatic pressure. Bacterial piezophiles are mainly psychrophiles belonging to five genera of γ-proteobacteria, Photobacterium, Shewanella, Colwellia, Psychromonas and Moritella, while piezophilic Archaea are mostly (hyper)thermophiles from the Thermococcales. None of these genera are specific for the deep biosphere. High pressure deeply impacts the activity of cells and cellular components, and reduces the activity of numerous key processes, eventually leading to cell death of piezosensitive organisms. Biochemical and genomic studies yield a fragmented view on the adaptive mechanisms in piezophiles. It is yet unclear whether piezophilic adaptation requires the modification of a few genes, or metabolic pathways, or a more profound reorganization of the genome, the fine tuning of gene expression to compensate the pressure-induced loss of activity of the proteins most affected by high pressure, or a stress-like physiological cell response. In contrast to what has been seen for thermophily or halophily, the adaptation to high pressure is diffuse in the genome and may concern only a small fraction of the genes.

Thermococcus paralvinellae sp. nov. and Thermococcus cleftensis sp. nov. of hyperthermophilic heterotrophs from deep-sea hydrothermal vents

Two heterotrophic hyperthermophilic strains, ES1T and CL1T, were isolated from Paralvinella sp. polychaete worms collected from active hydrothermal vent chimneys in the north-eastern Pacific Ocean. Both were obligately anaerobic and produced H2S in the presence of elemental sulfur and H2. Complete genome sequences are available for both strains. Phylogenetic analyses based on 16S rRNA gene sequences showed that the strains are more than 97 % similar to most other species of the genus Thermococcus . Therefore, overall genome relatedness index analyses were performed to establish that these strains are novel species. For each analysis, strain ES1T was determined to be most similar to Thermococcus barophilus MPT, while strain CL1T was determined to be most similar to Thermococcus sp. 4557. The average nucleotide identity scores for these strains were 84 % for strain ES1T and 81 % for strain CL1T, genome-to-genome direct comparison scores were 23 % for strain ES1T and 47 % for strain CL1T, and the species identification scores were 89 % for strain ES1T and 88 % for strain CL1T. For each analysis, strains ES1T and CL1T were below the species delineation cut-off. Therefore, based on their whole genome sequences, strains ES1T and CL1T are suggested to represent novel species of the genus Thermococcus for which the names Thermococcus paralvinellae sp. nov. and Thermococcus cleftensis sp. nov. are proposed, respectively. The type strains are ES1T ( = DSM 27261T = KACC 17923T) and CL1T ( = DSM 27260T = KACC 17922T).

Anaerobic thermophiles

The term "extremophile" was introduced to describe any organism capable of living and growing under extreme conditions. With the further development of studies on microbial ecology and taxonomy, a variety of "extreme" environments have been found and an increasing number of extremophiles are being described. Extremophiles have also been investigated as far as regarding the search for life on other planets and even evaluating the hypothesis that life on Earth originally came from space. The first extreme environments to be largely investigated were those characterized by elevated temperatures. The naturally "hot environments" on Earth range from solar heated surface soils and water with temperatures up to 65 °C, subterranean sites such as oil reserves and terrestrial geothermal with temperatures ranging from slightly above ambient to above 100 °C, to submarine hydrothermal systems with temperatures exceeding 300 °C. There are also human-made environments with elevated temperatures such as compost piles, slag heaps, industrial processes and water heaters. Thermophilic anaerobic microorganisms have been known for a long time, but scientists have often resisted the belief that some organisms do not only survive at high temperatures, but actually thrive under those hot conditions. They are perhaps one of the most interesting varieties of extremophilic organisms. These microorganisms can thrive at temperatures over 50 °C and, based on their optimal temperature, anaerobic thermophiles can be subdivided into three main groups: thermophiles with an optimal temperature between 50 °C and 64 °C and a maximum at 70 °C, extreme thermophiles with an optimal temperature between 65 °C and 80 °C, and finally hyperthermophiles with an optimal temperature above 80 °C and a maximum above 90 °C. The finding of novel extremely thermophilic and hyperthermophilic anaerobic bacteria in recent years, and the fact that a large fraction of them belong to the Archaea has definitely made this area of investigation more exciting. Particularly fascinating are their structural and physiological features allowing them to withstand extremely selective environmental conditions. These properties are often due to specific biomolecules (DNA, lipids, enzymes, osmolites, etc.) that have been studied for years as novel sources for biotechnological applications. In some cases (DNA-polymerase, thermostable enzymes), the search and applications successful exceeded preliminary expectations, but certainly further exploitations are still needed.

Microorganisms under high pressure--adaptation, growth and biotechnological potential

Hydrostatic pressure is a well-known physical parameter which is now considered an important variable of life, since organisms have the ability to adapt to pressure changes, by the development of resistance against this variable. In the past decades a huge interest in high hydrostatic pressure (HHP) technology is increasingly emerging among food and biosciences researchers. Microbial specific stress responses to HHP are currently being investigated, through the evaluation of pressure effects on biomolecules, cell structure, metabolic behavior, growth and viability. The knowledge development in this field allows a better comprehension of pressure resistance mechanisms acquired at sub-lethal pressures. In addition, new applications of HHP could arise from these studies, particularly in what concerns to biotechnology. For instance, the modulation of microbial metabolic pathways, as a response to different pressure conditions, may lead to the production of novel compounds with potential biotechnological and industrial applications. Considering pressure as an extreme life condition, this review intends to present the main findings so far reported in the scientific literature, focusing on microorganisms with the ability to withstand and to grow in high pressure conditions, whether they have innated or acquired resistance, and show the potential of the application of HHP technology for microbial biotechnology.

High hydrostatic pressure tolerance of four different anhydrobiotic animal species

High hydrostatic pressure (HHP) can induce physical changes in DNA, proteins, and lipids, causing lethal or sublethal damage to organisms. However, HHP tolerance of animals has not been studied sufficiently. In this study, HHP tolerance of four species of invertebrate anhydrobiotes (the tardigrade Milnesium tardigradum, a nematode species in the family Plectidae, larvae of Polypedilum vanderplanki, and cysts of Artemia franciscana), which have the potential to enter anhydrobiosis upon desiccation, were investigated by exposing them to 1.2 GPa for 20 minutes. This exposure killed the anhydrobiotes in their ordinary hydrated state, but did not affect their survival in the anhydrobiotic state. The results indicated that the hydrated anhydrobiotes were vulnerable to HHP, but that HHP of 1.2 GPa was not sufficient to kill them in anhyrdobiosis.

Microbial extremophiles at the limits of life

Prokaryotic extremophiles were the first representatives of life on Earth and they are responsible for the genesis of geological structures during the evolution and creation of all currently known ecosystems. Flexibility of the genome probably allowed life to adapt to a wide spectrum of extreme environments. As a result, modern prokaryotic diversity formed in a framework of physico-chemical factors, and it is composed of: thermophilic, psychrophilic, acidophilic, alkaliphilic, halophilic, barophilic, and radioresistant species. This artificial systematics cannot reflect the multiple actions of different environmental factors since one organism could unite characteristics of several extreme-groups. In this review we show the current status of studies in all fields of extremophiles and summarize the limits of life for different species of microbial extremophiles. We also discuss the finding of extremophiles from unusual places such as soils, and briefly review recent studies of microfossils in meteorites in the context of the significance of microbial extremophiles to Astrobiology.

Transcriptional responses of the deep-sea hyperthermophile Methanocaldococcus jannaschii under shifting extremes of temperature and pressure

Growth and transcriptional profiles of the deep-sea methanarchaeon Methanocaldococcus jannaschii were studied under sudden up-shifts of temperature and pressure. Application of 500 atm of hyperbaric pressure shifted the optimal growth temperature upwards by about 5 degrees C in a high temperature-pressure bioreactor, and increased the specific growth rate threefold at 88 degrees C. In contrast, pressure-shock from 7.8 to 500 atm over 15 min, the first such pressure up-shift reported for a piezophile, did not accelerate growth. High-pressure heat-shock from 88 to 98 degrees C, a condition relevant to the turbulent in situ surroundings of deep-sea hydrothermal vents, resulted in termination of growth. Transcriptional profiles for cells grown at 88 degrees C and 500 atm, heat-shocked at 500 atm, and pressure-shocked to 500 atm, shared a subset of genes whose differential expression was attributed to elevated pressure. In the pressure-shock case, this transcriptional response was evident despite the absence of a piezophilic growth response. In all, despite the piezophilic capacity and high-pressure origins of M. jannaschii, the core pressure response was remarkably limited and consisted of differential expression of genes encoding three hypothetical proteins and a gene involved in DNA recombination.

Survival and growth of two heterotrophic hydrothermal vent archaea, Pyrococcus strain GB-D and Thermococcus fumicolans, under low pH and high sulfide concentrations in combination with high temperature and pressure regimes

Growth and survival of hyperthermophilic archaea in their extreme hydrothermal vent and subsurface environments are controlled by chemical and physical key parameters. This study examined the effects of elevated sulfide concentrations, temperature, and acidic pH on growth and survival of two hydrothermal vent archaea (Pyrococcus strain GB-D and Thermococcus fumicolans) under high temperature and pressure regimes. These two strains are members of the Thermococcales, a family of hyperthermophilic, heterotrophic, sulfur-reducing archaea that occur in high densities at vent sites. As actively growing cells, these two strains tolerated regimes of pH, pressure, and temperature that were in most cases not tolerated under severe substrate limitation. A moderate pH of 5.5-7 extends their survival and growth range over a wider range of sulfide concentrations, temperature and pressure, relative to lower pH conditions. T. fumicolans and Pyrococcus strain GB-D grew under very high pressures that exceeded in-situ pressures typical of hydrothermal vent depths, and included deep subsurface pressures. However, under the same conditions, but in the absence of carbon substrates and electron acceptors, survival was generally lower, and decreased rapidly when low pH stress was combined with high pressure and high temperature.

Boron enhances the thermostability of carbohydrates

We have studied the effect of borate and pH upon the half-lives of ribose and glucose. Under acidic conditions the presence of boric acid increase the thermo-stability of ribose, while under basic conditions glucose is favored.

Synchronous effects of temperature, hydrostatic pressure, and salinity on growth, phospholipid profiles, and protein patterns of four Halomonas species isolated from deep-sea hydrothermal-vent and sea surface environments

Four strains of euryhaline bacteria belonging to the genus Halomonas were tested for their response to a range of temperatures (2, 13, and 30 degrees C), hydrostatic pressures (0.1, 7.5, 15, 25, 35, 45, and 55 MPa), and salinities (4, 11, and 17% total salts). The isolates were psychrotolerant, halophilic to moderately halophilic, and piezotolerant, growing fastest at 30 degrees C, 0.1 MPa, and 4% total salts. Little or no growth occurred at the highest hydrostatic pressures tested, an effect that was more pronounced with decreasing temperatures. Growth curves suggested that the Halomonas strains tested would grow well in cool to warm hydrothermal-vent and associated subseafloor habitats, but poorly or not at all under cold deep-sea conditions. The intermediate salinity tested enhanced growth under certain high-hydrostatic-pressure and low-temperature conditions, highlighting a synergistic effect on growth for these combined stresses. Phospholipid profiles obtained at 30 degrees C indicated that hydrostatic pressure exerted the dominant control on the degree of lipid saturation, although elevated salinity slightly mitigated the increased degree of lipid unsaturation caused by increased hydrostatic pressure. Profiles of cytosolic and membrane proteins of Halomonas axialensis and H. hydrothermalis performed at 30 degrees C under various salinities and hydrostatic pressure conditions indicated several hydrostatic pressure and salinity effects, including proteins whose expression was induced by either an elevated salinity or hydrostatic pressure, but not by a combination of the two. The interplay between salinity and hydrostatic pressure on microbial growth and physiology suggests that adaptations to hydrostatic pressure and possibly other stresses may partially explain the euryhaline phenotype of members of the genus Halomonas living in deep-sea environments.

Extremophiles as a source for novel enzymes

Microbial life does not seem to be limited to specific environments. During the past few decades it has become clear that microbial communities can be found in the most diverse conditions, including extremes of temperature, pressure, salinity and pH. These microorganisms, called extremophiles, produce biocatalysts that are functional under extreme conditions. Consequently, the unique properties of these biocatalysts have resulted in several novel applications of enzymes in industrial processes. At present, only a minor fraction of the microorganisms on Earth have been exploited. Novel developments in the cultivation and production of extremophiles, but also developments related to the cloning and expression of their genes in heterologous hosts, will increase the number of enzyme-driven transformations in chemical, food, pharmaceutical and other industrial applications.

The biotechnological potential of piezophiles

Microorganisms that prefer high-pressure conditions are termed piezophiles (previously termed barophiles). The molecular basis of piezophily is now being investigated extensively focusing on aspects of gene regulation and the function of certain proteins in deep-sea isolates. Little attention has been paid, however, to the potential biotechnological applications of piezophiles compared with other extremophiles. Based on the fundamental knowledge available, we will try to answer the following questions: How can we exploit the biotechnological potential of piezophiles? What can be understood by the application of high-pressure in biological systems?

Life in extreme environments

Each recent report of liquid water existing elsewhere in the Solar System has reverberated through the international press and excited the imagination of humankind. Why? Because in the past few decades we have come to realize that where there is liquid water on Earth, virtually no matter what the physical conditions, there is life. What we previously thought of as insurmountable physical and chemical barriers to life, we now see as yet another niche harbouring 'extremophiles'. This realization, coupled with new data on the survival of microbes in the space environment and modelling of the potential for transfer of life between celestial bodies, suggests that life could be more common than previously thought. Here we examine critically what it means to be an extremophile, and the implications of this for evolution, biotechnology and especially the search for life in the Universe.

Effects of hydrostatic pressure and temperature on physiological traits of Thermococcus guaymasensis and Thermococcus aggregans growing on starch

The effects of temperature and hydrostatic pressure on growth of two novel Thermococcus species, T. guaymasensis and T. aggregans, were investigated. These archaea, isolated from the Guaymas Basin hydrothermal vent site at 2000 meters depth, are able to grow on starch in sulfur-depleted medium producing significant amounts of amylases and pullulanases. At 85 degrees C, T. guaymasensis exhibited a barophilic response at 20 and 35 MPa but inhibition of growth occurred at 50 MPa; at 50 MPa, cell replication was repressed, the mean cell size increased, and production of starch-hydrolysing enzymes was significantly stimulated. Barophily was also expressed by T. guaymasensis under 20 MPa at sub-optimal temperature (70 C) but morphological alterations of cells were observed earlier (35 MPa). No barophily was exhibited by T. aggregans at 85 degrees C. In this case, cell replication was repressed at 20 MPa and remarkable inhibition of growth occurred at 50 MPa. Only when T. aggregans was cultivated at 75 degrees C, a significant barophilic response was exhibited at 20 MPa, as shown by the rate of replication and metabolism. These results show that Thermococcus species, although isolated from the same ecosystem, differ with regard to the effects of pressure and temperature on cell physiology. The metabolic responses and their significance for potential biotechnological applications are also discussed.

Stress genes and proteins in the archaea

The field covered in this review is new; the first sequence of a gene encoding the molecular chaperone Hsp70 and the first description of a chaperonin in the archaea were reported in 1991. These findings boosted research in other areas beyond the archaea that were directly relevant to bacteria and eukaryotes, for example, stress gene regulation, the structure-function relationship of the chaperonin complex, protein-based molecular phylogeny of organisms and eukaryotic-cell organelles, molecular biology and biochemistry of life in extreme environments, and stress tolerance at the cellular and molecular levels. In the last 8 years, archaeal stress genes and proteins belonging to the families Hsp70, Hsp60 (chaperonins), Hsp40(DnaJ), and small heat-shock proteins (sHsp) have been studied. The hsp70(dnaK), hsp40(dnaJ), and grpE genes (the chaperone machine) have been sequenced in seven, four, and two species, respectively, but their expression has been examined in detail only in the mesophilic methanogen Methanosarcina mazei S-6. The proteins possess markers typical of bacterial homologs but none of the signatures distinctive of eukaryotes. In contrast, gene expression and transcription initiation signals and factors are of the eucaryal type, which suggests a hybrid archaeal-bacterial complexion for the Hsp70 system. Another remarkable feature is that several archaeal species in different phylogenetic branches do not have the gene hsp70(dnaK), an evolutionary puzzle that raises the important question of what replaces the product of this gene, Hsp70(DnaK), in protein biogenesis and refolding and for stress resistance. Although archaea are prokaryotes like bacteria, their Hsp60 (chaperonin) family is of type (group) II, similar to that of the eukaryotic cytosol; however, unlike the latter, which has several different members, the archaeal chaperonin system usually includes only two (in some species one and in others possibly three) related subunits of approximately 60 kDa. These form, in various combinations depending on the species, a large structure or chaperonin complex sometimes called the thermosome. This multimolecular assembly is similar to the bacterial chaperonin complex GroEL/S, but it is made of only the large, double-ring oligomers each with eight (or nine) subunits instead of seven as in the bacterial complex. Like Hsp70(DnaK), the archaeal chaperonin subunits are remarkable for their evolution, but for a different reason. Ubiquitous among archaea, the chaperonins show a pattern of recurrent gene duplication-hetero-oligomeric chaperonin complexes appear to have evolved several times independently. The stress response and stress tolerance in the archaea involve chaperones, chaperonins, other heat shock (stress) proteins including sHsp, thermoprotectants, the proteasome, as yet incompletely understood thermoresistant features of many molecules, and formation of multicellular structures. The latter structures include single- and mixed-species (bacterial-archaeal) types. Many questions remain unanswered, and the field offers extraordinary opportunities owing to the diversity, genetic makeup, and phylogenetic position of archaea and the variety of ecosystems they inhabit. Specific aspects that deserve investigation are elucidation of the mechanism of action of the chaperonin complex at different temperatures, identification of the partners and substitutes for the Hsp70 chaperone machine, analysis of protein folding and refolding in hyperthermophiles, and determination of the molecular mechanisms involved in stress gene regulation in archaeal species that thrive under widely different conditions (temperature, pH, osmolarity, and barometric pressure). These studies are now possible with uni- and multicellular archaeal models and are relevant to various areas of basic and applied research, including exploration and conquest of ecosystems inhospitable to humans and many mammals and plants.

Physiological Responses to Stress Conditions and Barophilic Behavior of the Hyperthermophilic Vent Archaeon Pyrococcus abyssi

The physiology of the deep-sea hyperthermophilic, anaerobic vent archaeon Pyrococcus abyssi, originating from the Fiji Basin at a depth of 2,000 m, was studied under diverse conditions. The emphasis of these studies lay in the growth and survival of this archaeon under the different conditions present in the natural habitat. Incubation under in situ pressure (20 MPa) and at 40 MPa increased the maximal and minimal growth temperatures by 4(deg)C. In situ pressure enhanced survival at a lethal high temperature (106 to 112(deg)C) relative to that at low pressure (0.3 MPa). The whole-cell protein profile, analyzed by one-dimensional sodium dodecyl sulfate gel electrophoresis, did not change in cultures grown under low or high pressure at optimal and minimal growth temperatures, but several changes were observed at the maximal growth temperature under in situ pressure. The complex lipid pattern of P. abyssi grown under in situ and 0.1- to 0.5-MPa pressures at different temperatures was analyzed by thin-layer chromatography. The phospholipids became more complex at a low growth temperature at both pressures but their profiles were not superimposable; fewer differences were observed in the core lipids. The polar lipids were composed of only one phospholipid in cells grown under in situ pressure at high temperatures. Survival in the presence of oxygen and under starvation conditions was examined. Oxygen was toxic to P. abyssi at growth range temperature, but the strain survived for several weeks at 4(deg)C. The strain was not affected by starvation in a minimal medium for at least 1 month at 4(deg)C and only minimally affected at 95(deg)C for several days. Cells were more resistant to oxygen in starvation medium. A drastic change in protein profile, depending on incubation time, was observed in cells when starved at growth temperature.