Evolution of Bacillus subtilis to enhanced growth at low pressure: up-regulated transcription of des-desKR, encoding the fatty acid desaturase system

Chapter 6: The Breadth and Limits of Life on Earth

Scientific ideas about the potential existence of life elsewhere in the universe are predominantly informed by knowledge about life on Earth. Over the past ∼4 billion years, life on Earth has evolved into millions of unique species. Life now inhabits nearly every environmental niche on Earth that has been explored. Despite the wide variety of species and diverse biochemistry of modern life, many features, such as energy production mechanisms and nutrient requirements, are conserved across the Tree of Life. Such conserved features help define the operational parameters required by life and therefore help direct the exploration and evaluation of habitability in extraterrestrial environments. As new diversity in the Tree of Life continues to expand, so do the known limits of life on Earth and the range of environments considered habitable elsewhere. The metabolic processes used by organisms living on the edge of habitability provide insights into the types of environments that would be most suitable to hosting extraterrestrial life, crucial for planning and developing future astrobiology missions. This chapter will introduce readers to the breadth and limits of life on Earth and show how the study of life at the extremes can inform the broader field of astrobiology.

Giving a signal: how protein phosphorylation helps Bacillus navigate through different life stages

Protein phosphorylation is a universal mechanism regulating a wide range of cellular responses across all domains of life. The antagonistic activities of kinases and phosphatases can orchestrate the life cycle of an organism. The availability of bacterial genome sequences, particularly Bacillus species, followed by proteomics and functional studies have aided in the identification of putative protein kinases and protein phosphatases, and their downstream substrates. Several studies have established the role of phosphorylation in different physiological states of Bacillus species as they pass through various life stages such as sporulation, germination, and biofilm formation. The most common phosphorylation sites in Bacillus proteins are histidine, aspartate, tyrosine, serine, threonine, and arginine residues. Protein phosphorylation can alter protein activity, structural conformation, and protein-protein interactions, ultimately affecting the downstream pathways. In this review, we summarize the knowledge available in the field of Bacillus signaling, with a focus on the role of protein phosphorylation in its physiological processes.

Dispersion of Bacteria by Low-Pressure Boiling: Life Detection in Enceladus' Plume Material

The plume of Enceladus is thought to originate from the dispersion of a liquid source beneath the icy crust. Cryovolcanic activity on Enceladus may present a direct way of accessing material originating from the potentially habitable subsurface ocean. One way to test the hypothesis of whether life is present within the ocean of Enceladus would be to investigate the plume material for the presence of microbial life. In this study, we investigated the entrainment of Bacillus subtilis within Enceladus-like fluids under boiling conditions caused by exposure of the fluids to low pressure. We show that boiling, associated with exposure of a fluid to low pressure, works as a mechanism for dispersing bacteria in Enceladus plume-like environments. Exposure of Enceladus-type fluids (0.01-0.1 molal Na₂CO₃ and 0.05-0.2 molal NaCl) to low pressure (5 mbar) results in the dispersion of bacteria in droplets that evaporate to produce particles of salt. We find that, for particles with radius (r) ≤ 10 μm, the number of dispersed particles containing cells was between 7.7% and 10.9%. However, for larger particles 10 < r ≤ 50 μm, 64.4% and 56.4% contained cells for lower and upper end-member solutions, respectively. Our results suggest that the gravity-induced size sorting of plume particles will result in plume deposits closer to the vent source containing a larger volume of biological material than within the plume. If life is present in the ocean of Enceladus, we would expect that it would be effectively entrained and deposited on the surface; therefore, it would be accessible with a surface-lander-based instrument.

Carnobacterium Species Capable of Growth at Pressures Ranging Over 5 Orders of Magnitude, from the Surface of Mars (103 Pa) to Deep Oceans (107 Pa) in the Solar System

Several permanently cold solar system bodies are being investigated with regard to their potential habitability, including Mars and icy moons. In such locations, microbial life would have to cope with low temperatures and both high and low pressures, ranging from ∼10² to 10³ Pa on the surface of Mars to upward of ∼10⁸-10⁹ Pa in the subsurface oceans of icy moons. The bacterial genus Carnobacterium consists of species that were previously shown to be capable of growth in the absence of oxygen at low temperatures and at either low pressure or high pressure, but to date the entire pressure range of the genus has not been explored. In the present study, we subjected 14 Carnobacterium strains representing 11 species to cultivation in a complex liquid medium under anaerobic conditions at 2°C and at a range of pressures spanning 5 orders of magnitude, from 10³ to 10⁷ Pa. Eleven of the 14 strains showed measurable growth rates at all pressures tested, representing the first demonstration of terrestrial life forms capable of growth under such a wide range of pressures. These findings expand the physical boundaries of the capabilities of life to occur in extreme extraterrestrial environments.

Bridging the gap between microbial limits and extremes in space: space microbial biotechnology in the next 15 years

The establishment of a permanent human settlement in space is one of humanity's ambitions. To achieve this, microorganisms will be used to carry out many functions such as recycling, food and pharmaceutical production, mining and other processes. However, the physical and chemical extremes in all locations beyond Earth exceed known growth limits of microbial life. Making microbes more tolerant of a greater range of extraterrestrial extremes will not produce organisms that can grow in unmodified extraterrestrial environments since in many of them not even liquid water can exist. However, by narrowing the gap, the engineering demands on bioindustrial processes can be reduced and greater robustness can be incorporated into the biological component. I identify and describe these required microbial biotechnological modifications and speculate on long-term possibilities such as microbial biotechnology on Saturn's moon Titan to support a human presence in the outer Solar System and bioprocessing of asteroids. A challenge for space microbial biotechnology in the coming decades is to narrow the microbial gap by systemically identifying the genes required to do this and incorporating them into microbial systems that can be used to carry out bioindustrial processes of interest.

Programming living sensors for environment, health and biomanufacturing

Synthetic biology offers new tools and capabilities of engineering cells with desired functions for example as new biosensing platforms leveraging engineered microbes. In the last two decades, bacterial cells have been programmed to sense and respond to various input cues for versatile purposes including environmental monitoring, disease diagnosis and adaptive biomanufacturing. Despite demonstrated proof-of-concept success in the laboratory, the real-world applications of microbial sensors have been restricted due to certain technical and societal limitations. Yet, most limitations can be addressed by new technological developments in synthetic biology such as circuit design, biocontainment and machine learning. Here, we summarize the latest advances in synthetic biology and discuss how they could accelerate the development, enhance the performance and address the present limitations of microbial sensors to facilitate their use in the field. We view that programmable living sensors are promising sensing platforms to achieve sustainable, affordable and easy-to-use on-site detection in diverse settings.

Growth at 5 kPa Causes Differential Expression of a Number of Signals in a Bacillus subtilis Strain Adapted to Enhanced Growth at Low Pressure

To determine microbial evolutionary strategies to low-pressure (LP; 5 kPa) growth, an environmental condition not experienced on Earth until ∼20 km in altitude, a previously described evolutionary experiment was conducted. The resulting LP evolved strain WN1106, isolated from the terminus of the experiment, was shown to have several genomic mutations absent in the ancestral strain, WN624. Three of the mutations were in regulatory genes: resD, walK, and rnjB. Here we report on transcriptional microarray data from the LP-evolved WN1106 and compare those results with the previously reported ancestral WN624 transcriptional array data at either 5 or 101 kPa. At 5 kPa, WN1106 differentially expresses signals that are under the control of regulators ResD, WalK, and RnjB compared with (1) itself at ∼101 kPa and (2) WN624 at 5 kPa. These results were further confirmed by quantitative reverse transcriptase-polymerase chain reaction of a target transcript from each regulon. This work indicates that the three mutated coding regions had transcriptional control effects on each respective regulon.

Microbes as Biosensors

The ability to detect disease early and deliver precision therapy would be transformative for the treatment of human illnesses. To achieve these goals, biosensors that can pinpoint when and where diseases emerge are needed. Rapid advances in synthetic biology are enabling us to exploit the information-processing abilities of living cells to diagnose disease and then treat it in a controlled fashion. For example, living sensors could be designed to precisely sense disease biomarkers, such as by-products of inflammation, and to respond by delivering targeted therapeutics in situ. Here, we provide an overview of ongoing efforts in microbial biosensor design, highlight translational opportunities, and discuss challenges for enabling sense-and-respond precision medicines.

What do we know about the influence of vacuum on bacterial biocenosis used in environmental biotechnologies?

The article aims to show the increased interest in the applications of vacuum in the area of environmental biotechnology and the lack of research related to the effects of vacuum on bacteria and microbial communities. Information on the impact of vacuum on bacteria is limited and often comes from unrelated research fields. In most cases (astrobiology research, food preservation technologies), the exposure of microorganisms in vacuum is permanent for the whole life of a cell. In environmental science applications, the exposure of microorganisms containing media such as sludge or soil in vacuum is rather persistent, and lower values of vacuum are used. Vacuum is used or proposed to be used in wastewater treatment, anaerobic digestion, sludge treatment, soil remediation and mining. Usually, vacuum is used to remove gases from the test medium, so a purely physical process is applied. However, most reports show the influence of vacuum on biological processes and its efficiency, as well as on the community structure.

Comparison of Bacillus subtilis transcriptome profiles from two separate missions to the International Space Station

The human spaceflight environment is notable for the unique factor of microgravity, which exerts numerous physiologic effects on macroscopic organisms, but how this environment may affect single-celled microbes is less clear. In an effort to understand how the microbial transcriptome responds to the unique environment of spaceflight, the model Gram-positive bacterium Bacillus subtilis was flown on two separate missions to the International Space Station in experiments dubbed BRIC-21 and BRIC-23. Cells were grown to late-exponential/early stationary phase, frozen, then returned to Earth for RNA-seq analysis in parallel with matched ground control samples. A total of 91 genes were significantly differentially expressed in both experiments; 55 exhibiting higher transcript levels in flight samples and 36 showing higher transcript levels in ground control samples. Genes upregulated in flight samples notably included those involved in biofilm formation, biotin and arginine biosynthesis, siderophores, manganese transport, toxin production and resistance, and sporulation inhibition. Genes preferentially upregulated in ground control samples notably included those responding to oxygen limitation, e.g., fermentation, anaerobic respiration, subtilosin biosynthesis, and anaerobic regulatory genes. The results indicated differences in oxygen availability between flight and ground control samples, likely due to differences in cell sedimentation and the toroidal shape assumed by the liquid cultures in microgravity.

Metabolic fingerprints of Serratia liquefaciens under simulated Martian conditions using Biolog GN2 microarrays

Microorganisms growing at atmospheric pressures of 0.7 kPa may have a significant impact on the search for life on Mars. Data on their nutrient requirements in a simulated Martian environment are required to ascertain both the potential risk of forward contamination and the potential of past or present habitability of Mars. Serratia liquefaciens can grow at concomitant conditions of low pressure, low temperature, and anoxic atmosphere. Changes in the metabolic fingerprint of S. liquefaciens grown under varying physical conditions including diverse atmospheric pressures (0.7 kPa to 101.3 kPa), temperatures (30 °C or 0 °C), and atmospheric gas compositions (Earth or CO₂) were investigated using Biolog GN2 assays. Distinct patterns for each condition were observed. Above 10 kPa S. liquefaciens performed similar to Earth-normal pressure conditions (101.3 kPa) whereas below 10 kPa shifts in metabolic patterns were observed. The differences indicated a physiological alteration in which S. liquefaciens lost its ability to metabolize the majority of the provided carbon sources at 0.7 kPa with a significant decrease in the oxidation of amino acids. By measuring the physiological responses to different carbon sources we were able to identify nutritional constraints that support cellular replication under simulated shallow Mars subsurface conditions.

Low Pressure Tolerance by Methanogens in an Aqueous Environment: Implications for Subsurface Life on Mars

The low pressure at the surface of Mars (average: 6 mbar) is one potentially biocidal factor that any extant life on the planet would need to endure. Near subsurface life, while shielded from ultraviolet radiation, would also be exposed to this low pressure environment, as the atmospheric gas-phase pressure increases very gradually with depth. Few studies have focused on low pressure as inhibitory to the growth or survival of organisms. However, recent work has uncovered a potential constraint to bacterial growth below 25 mbar. The study reported here tested the survivability of four methanogen species (Methanothermobacter wolfeii, Methanosarcina barkeri, Methanobacterium formicicum, Methanococcus maripaludis) under low pressure conditions approaching average martian surface pressure (6 mbar - 143 mbar) in an aqueous environment. Each of the four species survived exposure of varying length (3 days - 21 days) at pressures down to 6 mbar. This research is an important stepping-stone to determining if methanogens can actively metabolize/grow under these low pressures. Additionally, the recently discovered recurring slope lineae suggest that liquid water columns may connect the surface to deeper levels in the subsurface. If that is the case, any organism being transported in the water column would encounter the changing pressures during the transport.

Twenty Species of Hypobarophilic Bacteria Recovered from Diverse Soils Exhibit Growth under Simulated Martian Conditions at 0.7 kPa

Bacterial growth at low pressure is a new research area with implications for predicting microbial activity in clouds and the bulk atmosphere on Earth and for modeling the forward contamination of planetary surfaces like Mars. Here, we describe experiments on the recovery and identification of 20 species of bacterial hypobarophiles (def., growth under hypobaric conditions of approximately 1-2 kPa) in 10 genera capable of growth at 0.7 kPa. Hypobarophilic bacteria, but not archaea or fungi, were recovered from diverse soils, and high numbers of hypobarophiles were recovered from Arctic and Siberian permafrost soils. Isolates were identified through 16S rRNA sequencing to belong to the genera Bacillus, Carnobacterium, Clostridium, Cryobacterium, Exiguobacterium, Paenibacillus, Rhodococcus, Streptomyces, and Trichococcus. The highest population of culturable hypobarophilic bacteria (5.1 × 10⁴ cfu/g) was recovered from Colour Lake soils from Axel Heiberg Island in the Canadian Arctic. In addition, we extend the number of hypobarophilic species in the genus Serratia to six type-strains that include S. ficaria, S. fonticola, S. grimesii, S. liquefaciens, S. plymuthica, and S. quinivorans. Microbial growth at 0.7 kPa suggests that pressure alone will not be growth-limiting on the martian surface, or in Earth's atmosphere up to an altitude of 34 km. Key Words: Barophile-Extremophilic microorganisms-Habitability-Mars-Special Region. Astrobiology 16, 964-976.

Twenty-Three Species of Hypobarophilic Bacteria Recovered from Diverse Ecosystems Exhibit Growth under Simulated Martian Conditions at 0.7 kPa

Bacterial growth at low pressure is a new research area with implications for predicting microbial activity in clouds and the bulk atmosphere on Earth, and for modeling the forward contamination of planetary surfaces like Mars. Here, we describe experiments on the recovery and identification of 23 species of bacterial hypobarophiles (def., growth under hypobaric conditions of approximately 1-2 kPa) in 11 genera capable of growth at 0.7 kPa. Hypobarophilic bacteria, but not archaea or fungi, were recovered from soil and non-soil ecosystems. The highest numbers of hypobarophiles were recovered from Arctic soil, Siberian permafrost, and human saliva. Isolates were identified through 16S rRNA sequencing to belong to the genera Carnobacterium, Exiguobacterium, Leuconostoc, Paenibacillus, and Trichococcus. The highest population of culturable hypobarophilic bacteria (5.1 × 10(4) cfu/g) was recovered from Colour Lake soils from Axel Heiberg Island in the Canadian Arctic. In addition, we extend the number of hypobarophilic species in the genus Serratia to six type-strains that include S. ficaria, S. fonticola, S. grimesii, S. liquefaciens, S. plymuthica, and S. quinivorans. Microbial growth at 0.7 kPa suggests that pressure alone will not be growth-limiting on the martian surface or in Earth's atmosphere up to an altitude of 34 km.

KEY WORDS

Planetary protection-Simulated martian atmosphere-Piezophile-Habitability-Extremophilic microorganisms. Astrobiology 16, 335-347.

Pressurized Martian-Like Pure CO2 Atmosphere Supports Strong Growth of Cyanobacteria, and Causes Significant Changes in their Metabolism

Surviving of crews during future missions to Mars will depend on reliable and adequate supplies of essential life support materials, i.e. oxygen, food, clean water, and fuel. The most economical and sustainable (and in long term, the only viable) way to provide these supplies on Martian bases is via bio-regenerative systems, by using local resources to drive oxygenic photosynthesis. Selected cyanobacteria, grown in adequately protective containment could serve as pioneer species to produce life sustaining substrates for higher organisms. The very high (95.3 %) CO₂ content in Martian atmosphere would provide an abundant carbon source for photo-assimilation, but nitrogen would be a strongly limiting substrate for bio-assimilation in this environment, and would need to be supplemented by nitrogen fertilizing. The very high supply of carbon, with rate-limiting supply of nitrogen strongly affects the growth and the metabolic pathways of the photosynthetic organisms. Here we show that modified, Martian-like atmospheric composition (nearly 100 % CO₂) under various low pressure conditions (starting from 50 mbar to maintain liquid water, up to 200 mbars) supports strong cellular growth. Under high CO₂ / low N₂ ratio the filamentous cyanobacteria produce significant amount of H₂ during light due to differentiation of high amount of heterocysts.

Experimental evolution of enhanced growth by Bacillus subtilis at low atmospheric pressure: genomic changes revealed by whole-genome sequencing

Knowledge of how microorganisms respond and adapt to low-pressure (LP) environments is limited. Previously, Bacillus subtilis strain WN624 was grown at the near-inhibitory LP of 5 kPa for 1,000 generations and strain WN1106, which exhibited increased relative fitness at 5 kPa, was isolated. Genomic sequence differences between ancestral strain WN624 and LP-evolved strain WN1106 were identified using whole-genome sequencing. LP-evolved strain WN1106 carried amino acid-altering mutations in the coding sequences of only seven genes (fliI, parC, ytoI, bacD, resD, walK, and yvlD) and a single 9-nucleotide in-frame deletion in the rnjB gene that encodes RNase J2, a component of the RNA degradosome. By using a collection of frozen stocks of the LP-evolved culture taken at 50-generation intervals, it was determined that (i) the fitness increase at LP occurred rapidly, while (ii) mutation acquisition exhibited complex kinetics. A knockout mutant of rnjB was shown to increase the competitive fitness of B. subtilis at both LP and standard atmospheric pressure.

Role of fatty acids in Bacillus environmental adaptation

The large bacterial genus Bacillus is widely distributed in the environment and is able to colonize highly diverse niches. Some Bacillus species harbor pathogenic characteristics. The fatty acid (FA) composition is among the essential criteria used to define Bacillus species. Some elements of the FA pattern composition are common to Bacillus species, whereas others are specific and can be categorized in relation to the ecological niches of the species. Bacillus species are able to modify their FA patterns to adapt to a wide range of environmental changes, including changes in the growth medium, temperature, food processing conditions, and pH. Like many other Gram-positive bacteria, Bacillus strains display a well-defined FA synthesis II system that is equilibrated with a FA degradation pathway and regulated to efficiently respond to the needs of the cell. Like endogenous FAs, exogenous FAs may positively or negatively affect the survival of Bacillus vegetative cells and the spore germination ability in a given environment. Some of these exogenous FAs may provide a powerful strategy for preserving food against contamination by the Bacillus pathogenic strains responsible for foodborne illness.

Evolution in the Bacillaceae

The family Bacillaceae constitutes a phenotypically diverse and globally ubiquitous assemblage of bacteria. Investigation into how evolution has shaped, and continues to shape, this family has relied on several widely ranging approaches from classical taxonomy, ecological field studies, and evolution in soil microcosms to genomic-scale phylogenetics, laboratory, and directed evolution experiments. One unifying characteristic of the Bacillaceae , the endospore, poses unique challenges to answering questions regarding both the calculation of evolutionary rates and claims of extreme longevity in ancient environmental samples.

Exposure of Bacillus subtilis to low pressure (5 kilopascals) induces several global regulons, including those involved in the SigB-mediated general stress response

Studies of how microorganisms respond to pressure have been limited mostly to the extreme high pressures of the deep sea (i.e., the piezosphere). In contrast, despite the fact that the growth of most bacteria is inhibited at pressures below ∼2.5 kPa, little is known of microbial responses to low pressure (LP). To study the global LP response, we performed transcription microarrays on Bacillus subtilis cells grown under normal atmospheric pressure (∼101 kPa) and a nearly inhibitory LP (5 kPa), equivalent to the pressure found at an altitude of ∼20 km. Microarray analysis revealed altered levels of 363 transcripts belonging to several global regulons (AbrB, CcpA, CodY, Fur, IolR, ResD, Rok, SigH, Spo0A). Notably, the highest number of upregulated genes, 86, belonged to the SigB-mediated general stress response (GSR) regulon. Upregulation of the GSR by LP was confirmed by monitoring the expression of the SigB-dependent ctc-lacZ reporter fusion. Measuring transcriptome changes resulting from exposure of bacterial cells to LP reveals insights into cellular processes that may respond to LP exposure.