"Freezing" Thermophiles: From One Temperature Extreme to Another.

New detections of thermophiles in psychrobiotic (i.e., bearing cold-tolerant life forms) marine and terrestrial habitats including Arctic marine sediments, Antarctic accretion ice, permafrost, and elsewhere are continually being reported. These microorganisms present great opportunities for microbial ecologists to examine biogeographical processes for spore-formers and non-spore-formers alike, including dispersal histories connecting warm and cold biospheres. In this review, we examine different examples of thermophiles in cryobiotic locations, and highlight exploration of thermophiles at cold temperatures under laboratory conditions. The survival of thermophiles in psychrobiotic environments provokes novel considerations of physiological and molecular mechanisms underlying natural cryopreservation of microorganisms. Cultures of thermophiles maintained at low temperature may serve as a non-sporulating laboratory model for further exploration of metabolic potential of thermophiles at psychrobiotic temperatures, as well as for elucidating molecular mechanisms behind natural preservation and adaptation to psychrobiotic environments. These investigations are highly relevant for the search for life on other cold and icy planets in the Solar System, such as Mars, Europa and Enceladus.

Thermoacidophilic Bioleaching of Industrial Metallic Steel Waste Product.

The continuous deposition of hazardous metalliferous wastes derived from industrial steelmaking processes will lead to space shortages while valuable raw metals are being depleted. Currently, these landfilled waste products pose a rich resource for microbial thermoacidophilic bioleaching processes. Six thermoacidophilic archaea (Sulfolobus metallicus, Sulfolobus acidocaldarius, Metallosphaera hakonensis, Metallosphaera sedula, Acidianus brierleyi, and Acidianus manzaensis) were cultivated on metal waste product derived from a steelmaking process to assess microbial proliferation and bioleaching potential. While all six strains were capable of growth and bioleaching of different elements, A. manzaensis outperformed other strains and its bioleaching potential was further studied in detail. The ability of A. manzaensis cells to break down and solubilize the mineral matrix of the metal waste product was observed via scanning and transmission electron microscopy. Refinement of bioleaching operation parameters shows that changes in pH influence the solubilization of certain elements, which might be considered for element-specific solubilization processes. Slight temperature shifts did not influence the release of metals from the metal waste product, but an increase in dust load in the bioreactors leads to increased element solubilization. The formation of gypsum crystals in course of A. manzaensis cultivation on dust was observed and clarified using single-crystal X-ray diffraction analysis. The results obtained from this study highlight the importance of thermoacidophilic archaea for future small-scale as well as large-scale bioleaching operations and metal recycling processes in regard to circular economies and waste management. A thorough understanding of the bioleaching performance of thermoacidophilic archaea facilitates further environmental biotechnological advancements.

Phosphorus in the Clouds of Venus: Potential for Bioavailability.

Aerosol phase elements such as phosphorus (P), sulfur (S), and metals including iron (Fe) are essential nutrients that could help sustain potential biodiversity in the cloud deck of Venus. While the presence of S and Fe in the venusian cloud deck has been broadly discussed (Zasova et al., 1981; Krasnopolsky, 2012, 2013, 2016, 2017; Markiewicz et al., 2014), less attention has been given to the presence of P in the aerosols and its involvement in the multiphase chemistry of venusian clouds and potential sources of P deposition in the venusian atmosphere. A detailed characterization of phosphorus atmospheric chemistry in the cloud deck of Venus is crucial for understanding its solubility and bioavailability for potential venusian cloud microbiota (Schulze-Makuch et al., 2004; Grinspoon and Bullock, 2007; Limaye et al., 2018). We summarize our current understanding of the presence of P in the clouds of Venus and its role in a hypothetical atmospheric (bio)chemical cycle. The results of the VeGa lander measurements are put into perspective with regard to nutrient limitation for a potential biosphere in venusian clouds. Our work combines the results of the VeGa measurements and focuses on P as an inorganic nutrient component and its potential sources and chemical behavior as part of multiple transformations of atmospheric chemistry. The VeGa data indicate that a plentiful phosphorus layer exists within a layer that reaches into the lower venusian clouds and exceeds minimum P abundances for terrestrial microbial life. Extreme acidification of airborne phases in the atmosphere of Venus may facilitate P solubilization and its bioavailability for a potential ecosystem in venusian clouds. Further sampling and P abundance measurements in the atmosphere of Venus would improve our knowledge of P speciation and facilitate determination of a bioavailable fraction of P detected in venusian clouds. The previous results deserve further experimental and modeling analyses to diminish uncertainties and understand the rates of atmospheric deposition of P and its role in a potential venusian cloud ecosystem.

Exobiology of the Venusian Clouds: New Insights into Habitability through Terrestrial Models and Methods of Detection.

The search for life beyond Earth has focused on Mars and the icy moons Europa and Enceladus, all of which are considered a safe haven for life due to evidence of current or past water. The surface of Venus, on the other hand, has extreme conditions that make it a nonhabitable environment to life as we know it. This is in contrast, however, to its cloud layer, which, while still an extreme environment, may prove to be a safe haven for some extreme forms of life similar to extremophiles on Earth. We consider the venusian clouds a habitable environment based on the presence of (1) a solvent for biochemical reactions, (2) appropriate physicochemical conditions, (3) available energy, and (4) biologically relevant elements. The diversity of extreme microbial ecosystems on Earth has allowed us to identify terrestrial chemolithoautotrophic microorganisms that may be analogs to putative venusian organisms. Here, we hypothesize and describe biological processes that may be performed by such organisms in the venusian clouds. To detect putative venusian organisms, we describe potential biosignature detection methods, which include metal-microbial interactions and optical methods. Finally, we describe currently available technology that can potentially be used for modeling and simulation experiments.

Venus, an Astrobiology Target.

We present a case for the exploration of Venus as an astrobiology target-(1) investigations focused on the likelihood that liquid water existed on the surface in the past, leading to the potential for the origin and evolution of life, (2) investigations into the potential for habitable zones within Venus' present-day clouds and Venus-like exo atmospheres, (3) theoretical investigations into how active aerobiology may impact the radiative energy balance of Venus' clouds and Venus-like atmospheres, and (4) application of these investigative approaches toward better understanding the atmospheric dynamics and habitability of exoplanets. The proximity of Venus to Earth, guidance for exoplanet habitability investigations, and access to the potential cloud habitable layer and surface for prolonged in situ extended measurements together make the planet a very attractive target for near term astrobiological exploration.

Proteomic Response of Deinococcus radiodurans to Short-Term Real Microgravity during Parabolic Flight Reveals Altered Abundance of Proteins Involved in Stress Response and Cell Envelope Functions.

Rapidly evolving space exploration makes understanding the short- and long- term effects of microgravity on humans, plants, and microorganisms an important task. The ubiquitous presence of the gravitational force has had an influence on the development of all living entities on Earth, and short- and long-term changes in perceived gravitational force can induce notable changes within cells. Deinococcus radiodurans is the Gram-positive bacterium that is best known for its extreme resistance to UV-C and gamma radiation, oxidation stress, and desiccation. Thus increased interest has been placed on this species in the context of space research. The present study aims to elucidate the short-term proteomic response of this species to real microgravity during parabolic flight. Overnight cultures of D. radiodurans were subjected to microgravity during a single parabola, and metabolic activity was quenched using methanol. Proteins were extracted and subsequently measured using HPLC nESI MS/MS. The results, such as the enrichment of the peptidoglycan biosynthesis pathway with differentially abundant proteins and altered S-layer protein abundance, suggested molecular rearrangements in the cell envelope of D. radiodurans. Altered abundance of proteins involved in energy metabolism and DNA repair could be linked with increased endogenous ROS production that contributes to the stress response. Moreover, changes in protein abundance in response to microgravity show similarities with previously reported stress responses. Thus, the present results could be used to further investigate the complex regulation of the remarkable stress management of this bacterium.

Molecular repertoire of Deinococcus radiodurans after 1 year of exposure outside the International Space Station within the Tanpopo mission.

BACKGROUND: The extraordinarily resistant bacterium Deinococcus radiodurans withstands harsh environmental conditions present in outer space. Deinococcus radiodurans was exposed for 1 year outside the International Space Station within Tanpopo orbital mission to investigate microbial survival and space travel. In addition, a ground-based simulation experiment with conditions, mirroring those from low Earth orbit, was performed. METHODS: We monitored Deinococcus radiodurans cells during early stage of recovery after low Earth orbit exposure using electron microscopy tools. Furthermore, proteomic, transcriptomic and metabolomic analyses were performed to identify molecular mechanisms responsible for the survival of Deinococcus radiodurans in low Earth orbit. RESULTS: D. radiodurans cells exposed to low Earth orbit conditions do not exhibit any morphological damage. However, an accumulation of numerous outer-membrane-associated vesicles was observed. On levels of proteins and transcripts, a multi-faceted response was detected to alleviate cell stress. The UvrABC endonuclease excision repair mechanism was triggered to cope with DNA damage. Defense against reactive oxygen species is mirrored by the increased abundance of catalases and is accompanied by the increased abundance of putrescine, which works as reactive oxygen species scavenging molecule. In addition, several proteins and mRNAs, responsible for regulatory and transporting functions showed increased abundances. The decrease in primary metabolites indicates alternations in the energy status, which is needed to repair damaged molecules. CONCLUSION: Low Earth orbit induced molecular rearrangements trigger multiple components of metabolic stress response and regulatory networks in exposed microbial cells. Presented results show that the non-sporulating bacterium Deinococcus radiodurans survived long-term low Earth orbit exposure if wavelength below 200 nm are not present, which mirrors the UV spectrum of Mars, where CO2 effectively provides a shield below 190 nm. These results should be considered in the context of planetary protection concerns and the development of new sterilization techniques for future space missions. Video Abstract.

Molecular Mechanisms of Microbial Survivability in Outer Space: A Systems Biology Approach.

Since the dawn of space exploration, the survivability of terrestrial life in outer space conditions has attracted enormous attention. Space technology has enabled the development of advanced space exposure facilities to investigate in situ responses of microbial life to the stress conditions of space during interplanetary transfer. Significant progress has been made toward the understanding of the effects of space environmental factors, e.g., microgravity, vacuum and radiation, on microorganisms exposed to real and simulated space conditions. Of extreme importance is not only knowledge of survival potential of space-exposed microorganisms, but also the determination of mechanisms of survival and adaptation of predominant species to the extreme space environment, i.e., revealing the molecular machinery, which elicit microbial survivability and adaptation. Advanced technologies in -omics research have permitted genome-scale studies of molecular alterations of space-exposed microorganisms. A variety of reports show that microorganisms grown in the space environment exhibited global alterations in metabolic functions and gene expression at the transcriptional and translational levels. Proteomic, metabolomic and especially metabolic modeling approaches as essential instruments of space microbiology, synthetic biology and metabolic engineering are rather underrepresented. Here we summarized the molecular space-induced alterations of exposed microorganisms in terms of understanding the molecular mechanisms of microbial survival and adaptation to drastic outer space environment.

Exploring the microbial biotransformation of extraterrestrial material on nanometer scale.

Exploration of microbial-meteorite redox interactions highlights the possibility of bioprocessing of extraterrestrial metal resources and reveals specific microbial fingerprints left on extraterrestrial material. In the present study, we provide our observations on a microbial-meteorite nanoscale interface of the metal respiring thermoacidophile Metallosphaera sedula. M. sedula colonizes the stony meteorite Northwest Africa 1172 (NWA 1172; an H5 ordinary chondrite) and releases free soluble metals, with Ni ions as the most solubilized. We show the redox route of Ni ions, originating from the metallic Ni° of the meteorite grains and leading to released soluble Ni2+. Nanoscale resolution ultrastructural studies of meteorite grown M. sedula coupled to electron energy loss spectroscopy (EELS) points to the redox processing of Fe-bearing meteorite material. Our investigations validate the ability of M. sedula to perform the biotransformation of meteorite minerals, unravel microbial fingerprints left on meteorite material, and provide the next step towards an understanding of meteorite biogeochemistry. Our findings will serve in defining mineralogical and morphological criteria for the identification of metal-containing microfossils.

Molecular response of Deinococcus radiodurans to simulated microgravity explored by proteometabolomic approach.

Regarding future space exploration missions and long-term exposure experiments, a detailed investigation of all factors present in the outer space environment and their effects on organisms of all life kingdoms is advantageous. Influenced by the multiple factors of outer space, the extremophilic bacterium Deinococcus radiodurans has been long-termly exposed outside the International Space Station in frames of the Tanpopo orbital mission. The study presented here aims to elucidate molecular key components in D. radiodurans, which are responsible for recognition and adaptation to simulated microgravity. D. radiodurans cultures were grown for two days on plates in a fast-rotating 2-D clinostat to minimize sedimentation, thus simulating reduced gravity conditions. Subsequently, metabolites and proteins were extracted and measured with mass spectrometry-based techniques. Our results emphasize the importance of certain signal transducer proteins, which showed higher abundances in cells grown under reduced gravity. These proteins activate a cellular signal cascade, which leads to differences in gene expressions. Proteins involved in stress response, repair mechanisms and proteins connected to the extracellular milieu and the cell envelope showed an increased abundance under simulated microgravity. Focusing on the expression of these proteins might present a strategy of cells to adapt to microgravity conditions.

Biotransformation of Scheelite CaWO4 by the Extreme Thermoacidophile Metallosphaera sedula: Tungsten-Microbial Interface.

The tungsten-microbial interactions and microbial bioprocessing of tungsten ores, which are still underexplored, are the focus of the current study. Here we show that the biotransformation of tungsten mineral scheelite performed by the extreme thermoacidophile Metallosphaera sedula leads to the breakage of scheelite structure and subsequent tungsten solubilization. Total soluble tungsten is significantly higher in cultures containing M. sedula grown on scheelite than the abiotic control, indicating active bioleaching. Advanced analytical electron microscopy was used in order to achieve nanoscale resolution ultrastructural studies of M. sedula grown on tungsten bearing scheelite. In particular, we describe that M. sedula mediated the biotransformation of scheelite, which was accompanied by the release of tungsten into solution and tungsten biomineralization of the cell surface. Furthermore, we observed intracellular incorporation of redox heterogenous Mn- and Fe-containing nano-clusters. Our results highlight unique metallophilic life in hostile environments extending the knowledge of tungsten biogeochemistry. Based on these findings biohydrometallurgical processing of tungsten ores can be further explored. Importantly, biogenic tungsten carbide-like nanolayers described herein are potential targets for developing nanomaterial biotechnology.

Nanoscale Tungsten-Microbial Interface of the Metal Immobilizing Thermoacidophilic Archaeon Metallosphaera sedula Cultivated With Tungsten Polyoxometalate.

Inorganic systems based upon polyoxometalate (POM) clusters provide an experimental approach to develop artificial life. These artificial symmetric anionic macromolecules with oxidometalate polyhedra as building blocks were shown to be well suited as inorganic frameworks for complex self-assembling and organizing systems with emergent properties. Analogously to mineral cells based on iron sulfides, POMs are considered as inorganic cells in facilitating prelife chemical processes and displaying "life-like" characteristics. However, the relevance of POMs to life-sustaining processes (e.g., microbial respiration) has not yet been addressed, while iron sulfides are very well known as ubiquitous mineral precursors and energy sources for chemolithotrophic metabolism. Metallosphaera sedula is an extreme metallophilic and thermoacidophilic archaeon, which flourishes in hot acid and respires by metal oxidation. In the present study we provide our observations on M. sedula cultivated on tungsten polyoxometalate (W-POM). The decomposition of W-POM macromolecular clusters and the appearance of low molecular weight W species (e.g., WO) in the presence of M. sedula have been detected by electrospray ionization mass spectrometry (ESI-MS) analysis. Here, we document the presence of metalloorganic assemblages at the interface between M. sedula and W-POM resolved down to the nanometer scale using scanning and transmission electron microscopy (SEM and TEM) coupled to electron energy loss spectroscopy (EELS). High-resolution TEM (HR-TEM) and selected-area electron diffraction (SAED) patterns indicated the deposition of redox heterogeneous tungsten species on the S-layer of M. sedula along with the accumulation of intracellular tungsten-bearing nanoparticles, i.e., clusters of tungsten atoms. These results reveal the effectiveness of the analytical spectroscopy coupled to the wet chemistry approach as a tool in the analysis of metal-microbial interactions and microbial cultivation on supramolecular self-assemblages based on inorganic metal clusters. We discuss the possible mechanism of W-POM decomposition by M. sedula in light of unique electrochemical properties of POMs. The findings presented herein highlight unique metallophilicity in hostile environments, extending our knowledge of the relevance of POMs to life-sustaining processes, understanding of the transition of POMs as inorganic prebiotic model to life-sustainable material precursors and revealing biogenic signatures obtained after the decomposition of an artificial inorganic compound, which previously was not associated with any living matter.

Proteomic and Metabolomic Profiling of Deinococcus radiodurans Recovering After Exposure to Simulated Low Earth Orbit Vacuum Conditions.

The polyextremophile, gram-positive bacterium Deinococcus radiodurans can withstand harsh conditions of real and simulated outer space environment, e.g., UV and ionizing radiation. A long-term space exposure of D. radiodurans has been performed in Low Earth Orbit (LEO) in frames of the Tanpopo orbital mission aiming to investigate the possibility of interplanetary life transfer. Space vacuum (10 - 4-10 - 7 Pa) is a harmful factor, which induces dehydration and affects microbial integrity, severely damaging cellular components: lipids, carbohydrates, proteins, and nucleic acids. However, the molecular strategies by which microorganisms protect their integrity on molecular and cellular levels against vacuum damage are not yet understood. In a simulation experiment, we exposed dried D. radiodurans cells to vacuum (10 - 4-10 - 7 Pa), which resembles vacuum pressure present outside the International Space Station in LEO. After 90 days of high vacuum exposure, survival of D. radiodurans cells was 2.5-fold lower compared to control cells. To trigger molecular repair mechanisms, vacuum exposed cells of D. radiodurans were recovered in complex medium for 3 and 6 h. The combined approach of analyzing primary metabolites and proteins revealed important molecular activities during early recovery after vacuum exposure. In total, 1939 proteins covering 63% of D. radiodurans annotated protein sequences were detected. Proteases, tRNA ligases, reactive oxygen species (ROS) scavenging proteins, nucleic acid repair proteins, TCA cycle proteins, and S-layer proteins are highly abundant after vacuum exposure. The overall abundance of amino acids and TCA cycle intermediates is reduced during the recovery phase of D. radiodurans as they are needed as carbon source. Furthermore, vacuum exposure induces an upregulation of Type III histidine kinases, which trigger the expression of S-layer related proteins. Along with the highly abundant transcriptional regulator of FNR/CRP family, specific histidine kinases might be involved in the regulation of vacuum stress response. After repair processes are finished, D. radiodurans switches off the connected repair machinery and focuses on proliferation. Combined comparative analysis of alterations in the proteome and metabolome helps to identify molecular key players in the stress response of D. radiodurans, thus elucidating the mechanisms behind its extraordinary regenerative abilities and enabling this microorganism to withstand vacuum stress.

Proteometabolomic response of Deinococcus radiodurans exposed to UVC and vacuum conditions: Initial studies prior to the Tanpopo space mission.

The multiple extremes resistant bacterium Deinococcus radiodurans is able to withstand harsh conditions of simulated outer space environment. The Tanpopo orbital mission performs a long-term space exposure of D. radiodurans aiming to investigate the possibility of interplanetary transfer of life. The revealing of molecular machinery responsible for survivability of D. radiodurans in the outer space environment can improve our understanding of underlying stress response mechanisms. In this paper, we have evaluated the molecular response of D. radiodurans after the exposure to space-related conditions of UVC irradiation and vacuum. Notably, scanning electron microscopy investigations showed that neither morphology nor cellular integrity of irradiated cells was affected, while integrated proteomic and metabolomic analysis revealed numerous molecular alterations in metabolic and stress response pathways. Several molecular key mechanisms of D. radiodurans, including the tricarboxylic acid cycle, the DNA damage response systems, ROS scavenging systems and transcriptional regulators responded in order to cope with the stressful situation caused by UVC irradiation under vacuum conditions. These results reveal the effectiveness of the integrative proteometabolomic approach as a tool in molecular analysis of microbial stress response caused by space-related factors.

Exploring Fingerprints of the Extreme Thermoacidophile Metallosphaera sedula Grown on Synthetic Martian Regolith Materials as the Sole Energy Sources.

The biology of metal transforming microorganisms is of a fundamental and applied importance for our understanding of past and present biogeochemical processes on Earth and in the Universe. The extreme thermoacidophile Metallosphaera sedula is a metal mobilizing archaeon, which thrives in hot acid environments (optimal growth at 74°C and pH 2.0) and utilizes energy from the oxidation of reduced metal inorganic sources. These characteristics of M. sedula make it an ideal organism to further our knowledge of the biogeochemical processes of possible life on extraterrestrial planetary bodies. Exploring the viability and metal extraction capacity of M. sedula living on and interacting with synthetic extraterrestrial minerals, we show that M. sedula utilizes metals trapped in the Martian regolith simulants (JSC Mars 1A; P-MRS; S-MRS; MRS07/52) as the sole energy sources. The obtained set of microbiological and mineralogical data suggests that M. sedula actively colonizes synthetic Martian regolith materials and releases free soluble metals. The surface of bioprocessed Martian regolith simulants is analyzed for specific mineralogical fingerprints left upon M. sedula growth. The obtained results provide insights of biomining of extraterrestrial material as well as of the detection of biosignatures implementing in life search missions.

False positive RNA binding activities after Ni-affinity purification from Escherichia coli.

A His-tag is often added by means of recombinant DNA technology to a heterologous protein of interest, which is then over-produced in Escherchia coli and purified by one-step immobilized metal-affinity chromatography (IMAC). Owing to the presence of 24 histidines at the C-termini of the hexameric E. coli RNA chaperone Hfq, the protein co-purifies with His-tagged proteins of interest. As Hfq can bind to distinct RNA substrates with high affinity, its presence can obscure studies performed with (putative) RNA binding activities purified by IMAC. Here, we present results for a seemingly positive RNA-binding activity, exemplifying that false-positive results can be avoided if the protein of interest is either subjected to further purification step(s) or produced in an E. coli hfq- strain.

The Pseudomonas aeruginosa catabolite repression control protein Crc is devoid of RNA binding activity.

The Crc protein has been shown to mediate catabolite repression control in Pseudomonas, leading to a preferential assimilation of carbon sources. It has been suggested that Crc acts as a translational repressor of mRNAs, encoding functions involved in uptake and breakdown of different carbon sources. Moreover, the regulatory RNA CrcZ, the level of which is increased in the presence of less preferred carbon sources, was suggested to bind to and sequester Crc, resulting in a relief of catabolite repression. Here, we determined the crystal structure of Pseudomonas aeruginosa Crc, a member of apurinic/apyrimidinic (AP) endonuclease family, at 1.8 Å. Although Crc displays high sequence similarity with its orthologs, there are amino acid alterations in the area corresponding to the active site in AP proteins. Unlike typical AP endonuclease family proteins, Crc has a reduced overall positive charge and the conserved positively charged amino-acid residues of the DNA-binding surface of AP proteins are partially substituted by negatively charged, polar and hydrophobic residues. Crc protein purified to homogeneity from P. aeruginosa did neither display DNase activity, nor did it bind to previously identified RNA substrates. Rather, the RNA chaperone Hfq was identified as a contaminant in His-tagged Crc preparations purified by one step Ni-affinity chromatography from Escherichia coli, and was shown to account for the RNA binding activity observed with the His-Crc preparations. Taken together, these data challenge a role of Crc as a direct translational repressor in carbon catabolite repression in P. aeruginosa.

The ubiquitin-specific protease Usp4 regulates the cell surface level of the A2A receptor.

Many membrane proteins incur a folding problem during biosynthesis; only a fraction thereof is exported from the endoplasmic reticulum (ER), because quality control is stringent. This is also true for G protein-coupled receptors. Here, we identify the deubiquitinating enzyme Usp4 as an interaction partner of the A2a adenosine receptor, a Gs-coupled receptor. Usp4 binds to the carboxyl terminus of the A2A receptor and allows for its accumulation as deubiquinated protein. This relaxes ER quality control and enhances cell surface expression of functionally active receptor. The effect of Usp4 on the A2A receptor was specific because 1) it was not seen in C-terminally truncated versions of the receptor; 2) it was not mimicked by Usp14, another member of the ubiquitin-specific protease family; and 3) it was not seen with the metabotropic glutamate receptor-5, another G protein-coupled receptor with a high propensity for intracellular retention. These observations show that deubiquinating enzymes can regulate quality control in the ER.