Exploring the low-pressure growth limit: evolution of Bacillus subtilis in the laboratory to enhanced growth at 5 kilopascals

Polyextremophile engineering: a review of organisms that push the limits of life

Nature exhibits an enormous diversity of organisms that thrive in extreme environments. From snow algae that reproduce at sub-zero temperatures to radiotrophic fungi that thrive in nuclear radiation at Chernobyl, extreme organisms raise many questions about the limits of life. Is there any environment where life could not "find a way"? Although many individual extremophilic organisms have been identified and studied, there remain outstanding questions about the limits of life and the extent to which extreme properties can be enhanced, combined or transferred to new organisms. In this review, we compile the current knowledge on the bioengineering of extremophile microbes. We summarize what is known about the basic mechanisms of extreme adaptations, compile synthetic biology's efforts to engineer extremophile organisms beyond what is found in nature, and highlight which adaptations can be combined. The basic science of extremophiles can be applied to engineered organisms tailored to specific biomanufacturing needs, such as growth in high temperatures or in the presence of unusual solvents.

Biocomposite thermoplastic polyurethanes containing evolved bacterial spores as living fillers to facilitate polymer disintegration

The field of hybrid engineered living materials seeks to pair living organisms with synthetic materials to generate biocomposite materials with augmented function since living systems can provide highly-programmable and complex behavior. Engineered living materials have typically been fabricated using techniques in benign aqueous environments, limiting their application. In this work, biocomposite fabrication is demonstrated in which spores from polymer-degrading bacteria are incorporated into a thermoplastic polyurethane using high-temperature melt extrusion. Bacteria are engineered using adaptive laboratory evolution to improve their heat tolerance to ensure nearly complete cell survivability during manufacturing at 135 °C. Furthermore, the overall tensile properties of spore-filled thermoplastic polyurethanes are substantially improved, resulting in a significant improvement in toughness. The biocomposites facilitate disintegration in compost in the absence of a microbe-rich environment. Finally, embedded spores demonstrate a rationally programmed function, expressing green fluorescent protein. This research provides a scalable method to fabricate advanced biocomposite materials in industrially-compatible processes.

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.

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.

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.

The Hypopiezotolerant Bacterium, Serratia liquefaciens, Failed to Grow in Mars Analog Soils under Simulated Martian Conditions at 7 hPa

The search for life on Mars is predicated on the idea that Earth and Mars life (if present) should be both carbon- and water-based with similar forms of evolution. However, the astrobiology community can currently only investigate plausible Martian microbial ecosystems by using Terran life-forms as proxies. In order to examine how life might persist on Mars, we used a hypopiezotolerant bacterium (def., able to grow at 7-10 hPa)-Serratia liquefaciens-in growth assays with four Mars analog soils conducted under a subset of simulated Martian conditions including 7 hPa, 0 °C, and a CO₂-enriched anoxic atmosphere (called low-PTA conditions). The four Mars analog soils included an Aeolian dust analog, the Mars JSC-1 analog, a Phoenix lander-site simulant, and a high-Salts analog. Serratia liquefaciens cells were able to grow at 30 °C in a liquid minimal basal medium (MBM) supplemented with 10- or 20-mM sucrose, Spizizen salts, and micronutrients. When the four analog soils were doped with both MBM and cells of S. liquefaciens, and subsequently incubated at 30 °C for 72 h, cell densities increased between 2-logs (Phoenix analog) and 4-logs (Aeolian and JSC-1 analogs); the Salts analog led to complete inactivation of S. liquefaciens within 24 h. In contrast, when the experiment was repeated, but incubated under low-PTA conditions, S. liquefaciens cells were either killed immediately by the Salts analog, or decreased by > 5 logs over 28 d by the Aeolian, JSC-1, and Phoenix analogs. The failure of S. liquefaciens to grow in the analog soils under low-PTA conditions was attributed to the synergistic interactions among six factors (i.e., low pressure, low temperature, anoxic atmosphere (i.e., the low-PTA conditions), low-pH in the Salts soil, dissolved salts in all analogs, and oligotrophic conditions) that increased the biocidal or inhibitory conditions within the analog soils. Results suggest that even if a hypopiezotolerant Terran microbe is displaced from a spacecraft surface on Mars, and lands in a hydrated and nutrient-rich niche, growth in the Martian regolith is not automatically assured.

Microbiome and ecology of a hot spring-microbialite system on the Trans-Himalayan Plateau

Little is known about life in the boron-rich hot springs of Trans-Himalayas. Here, we explore the geomicrobiology of a 4438-m-high spring which emanates ~70 °C-water from a boratic microbialite called Shivlinga. Due to low atmospheric pressure, the vent-water is close to boiling point so can entropically destabilize biomacromolecular systems. Starting from the vent, Shivlinga’s geomicrobiology was revealed along the thermal gradients of an outflow-channel and a progressively-drying mineral matrix that has no running water; ecosystem constraints were then considered in relation to those of entropically comparable environments. The spring-water chemistry and sinter mineralogy were dominated by borates, sodium, thiosulfate, sulfate, sulfite, sulfide, bicarbonate, and other macromolecule-stabilizing (kosmotropic) substances. Microbial diversity was high along both of the hydrothermal gradients. Bacteria, Eukarya and Archaea constituted >98%, ~1% and <1% of Shivlinga’s microbiome, respectively. Temperature constrained the biodiversity at ~50 °C and ~60 °C, but not below 46 °C. Along each thermal gradient, in the vent-to-apron trajectory, communities were dominated by Aquificae/Deinococcus-Thermus, then Chlorobi/Chloroflexi/Cyanobacteria, and finally Bacteroidetes/Proteobacteria/Firmicutes. Interestingly, sites of >45 °C were inhabited by phylogenetic relatives of taxa for which laboratory growth is not known at >45 °C. Shivlinga’s geomicrobiology highlights the possibility that the system’s kosmotrope-dominated chemistry mitigates against the biomacromolecule-disordering effects of its thermal water.

Dynamic Environmental Control in Microfluidic Single-Cell Cultivations: From Concepts to Applications

Microfluidic single-cell cultivation (MSCC) is an emerging field within fundamental as well as applied biology. During the last years, most MSCCs were performed at constant environmental conditions. Recently, MSCC at oscillating and dynamic environmental conditions has started to gain significant interest in the research community for the investigation of cellular behavior. Herein, an overview of this topic is given and microfluidic concepts that enable oscillating and dynamic control of environmental conditions with a focus on medium conditions are discussed, and their application in single-cell research for the cultivation of both mammalian and microbial cell systems is demonstrated. Furthermore, perspectives for performing MSCC at complex dynamic environmental profiles of single parameters and multiparameters (e.g., pH and O₂ ) in amplitude and time are discussed. The technical progress in this field provides completely new experimental approaches and lays the foundation for systematic analysis of cellular metabolism at fluctuating environments.

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.

Experimental Design, Population Dynamics, and Diversity in Microbial Experimental Evolution

In experimental evolution, laboratory-controlled conditions select for the adaptation of species, which can be monitored in real time. Despite the current popularity of such experiments, nature's most pervasive biological force was long believed to be observable only on time scales that transcend a researcher's life-span, and studying evolution by natural selection was therefore carried out solely by comparative means. Eventually, microorganisms' propensity for fast evolutionary changes proved us wrong, displaying strong evolutionary adaptations over a limited time, nowadays massively exploited in laboratory evolution experiments. Here, we formulate a guide to experimental evolution with microorganisms, explaining experimental design and discussing evolutionary dynamics and outcomes and how it is used to assess ecoevolutionary theories, improve industrially important traits, and untangle complex phenotypes. Specifically, we give a comprehensive overview of the setups used in experimental evolution. Additionally, we address population dynamics and genetic or phenotypic diversity during evolution experiments and expand upon contributing factors, such as epistasis and the consequences of (a)sexual reproduction. Dynamics and outcomes of evolution are most profoundly affected by the spatiotemporal nature of the selective environment, where changing environments might lead to generalists and structured environments could foster diversity, aided by, for example, clonal interference and negative frequency-dependent selection. We conclude with future perspectives, with an emphasis on possibilities offered by fast-paced technological progress. This work is meant to serve as an introduction to those new to the field of experimental evolution, as a guide to the budding experimentalist, and as a reference work to the seasoned expert.

Design and modelling of an engineered bacteria-based, pressure-sensitive soil

In this paper, we describe the first steps in the design of a synthetic biological system based on the use of genetically modified bacteria to detect elevated pressures in soils and respond by cementing soil particles. Such a system might, for example, enable a self- constructed foundation to form in response to load using engineered bacteria which could be seeded and grown in the soils. This process would reduce the need for large-scale excavations and may be the basis for a new generation of self-assembling and responsive bio-based materials. A prototype computational model is presented which integrates experimental data from a pressure sensitive gene within Escherichia coli bacteria with geotechnical models of soil loading and pore water pressure. The results from the integrated model are visualised by mapping expected gene expression values onto the soil volume. We also use our experimental data to design a two component system where one type of bacteria acts as a sensor and signals to another material synthesis bacteria. The simulation demonstrates the potential of computational models which integrate multiple scales from macro stresses in soils to the expression of individual genes to inform new types of design process. The work also illustrates the combination of in silico (silicon based computing) computation with in vivo (in the living) computation.

Experimental evolution of Bacillus subtilis

The endospore-forming bacteria have persisted on earth perhaps 3Ga, leveraging the flexibility of their distinctive lifestyle to adapt to a remarkably wide range of environments. This process of adaptation can be investigated through the simple but powerful technique of laboratory evolution. Evolved strains can be analyzed by whole genome sequencing and an array of omics technologies. The intensively studied, genetically tractable endospore-former, Bacillus subtilis, is an ideal subject for laboratory evolution experiments. Here, we describe the use of the B. subtilis model system to study the adaptation of these bacteria to reduced and stringent selection for endospore formation, as well as to novel environmental challenges of low atmospheric pressure, high ultraviolet radiation, and unfavourable growth temperatures. In combination with other approaches, including comparative genomics and environmental field work, laboratory evolution may help elucidate how these bacteria have so successfully adapted to life on earth, and perhaps beyond.

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.

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.

Carbon monoxide as a metabolic energy source for extremely halophilic microbes: implications for microbial activity in Mars regolith

Carbon monoxide occurs at relatively high concentrations (≥800 parts per million) in Mars' atmosphere, where it represents a potentially significant energy source that could fuel metabolism by a localized putative surface or near-surface microbiota. However, the plausibility of CO oxidation under conditions relevant for Mars in its past or at present has not been evaluated. Results from diverse terrestrial brines and saline soils provide the first documentation, to our knowledge, of active CO uptake at water potentials (-41 MPa to -117 MPa) that might occur in putative brines at recurrent slope lineae (RSL) on Mars. Results from two extremely halophilic isolates complement the field observations. Halorubrum str. BV1, isolated from the Bonneville Salt Flats, Utah (to our knowledge, the first documented extremely halophilic CO-oxidizing member of the Euryarchaeota), consumed CO in a salt-saturated medium with a water potential of -39.6 MPa; activity was reduced by only 28% relative to activity at its optimum water potential of -11 MPa. A proteobacterial isolate from hypersaline Mono Lake, California, Alkalilimnicola ehrlichii MLHE-1, also oxidized CO at low water potentials (-19 MPa), at temperatures within ranges reported for RSL, and under oxic, suboxic (0.2% oxygen), and anoxic conditions (oxygen-free with nitrate). MLHE-1 was unaffected by magnesium perchlorate or low atmospheric pressure (10 mbar). These results collectively establish the potential for microbial CO oxidation under conditions that might obtain at local scales (e.g., RSL) on contemporary Mars and at larger spatial scales earlier in Mars' history.

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.

Growth of Serratia liquefaciens under 7 mbar, 0°C, and CO2-enriched anoxic atmospheres

Twenty-six strains of 22 bacterial species were tested for growth on trypticase soy agar (TSA) or sea-salt agar (SSA) under hypobaric, psychrophilic, and anoxic conditions applied singly or in combination. As each factor was added to multi-parameter assays, the interactive stresses decreased the numbers of strains capable of growth and, in general, reduced the vigor of the strains observed to grow. Only Serratia liquefaciens strain ATCC 27592 exhibited growth at 7 mbar, 0°C, and CO2-enriched anoxic atmospheres. To discriminate between the effects of desiccation and hypobaria, vegetative cells of Bacillus subtilis strain 168 and Escherichia coli strain K12 were grown on TSA surfaces and simultaneously in liquid Luria-Bertani (LB) broth media. Inhibition of growth under hypobaria for 168 and K12 decreased in similar ways for both TSA and LB assays as pressures were reduced from 100 to 25 mbar. Results for 168 and K12 on TSA and LB are interpreted to indicate a direct low-pressure effect on microbial growth with both species and do not support the hypothesis that desiccation alone on TSA was the cause of reduced growth at low pressures. The growth of S. liquefaciens at 7 mbar, 0°C, and CO2-enriched anoxic atmospheres was surprising since S. liquefaciens is ecologically a generalist that occurs in terrestrial plant, fish, animal, and food niches. In contrast, two extremophiles tested in the assays, Deinococcus radiodurans strain R1 and Psychrobacter cryohalolentis strain K5, failed to grow under hypobaric (25 mbar; R1 only), psychrophilic (0°C; R1 only), or anoxic (< 0.1% ppO2; both species) conditions.

Growth of Carnobacterium spp. from permafrost under low pressure, temperature, and anoxic atmosphere has implications for Earth microbes on Mars

The ability of terrestrial microorganisms to grow in the near-surface environment of Mars is of importance to the search for life and protection of that planet from forward contamination by human and robotic exploration. Because most water on present-day Mars is frozen in the regolith, permafrosts are considered to be terrestrial analogs of the martian subsurface environment. Six bacterial isolates were obtained from a permafrost borehole in northeastern Siberia capable of growth under conditions of low temperature (0 °C), low pressure (7 mbar), and a CO(2)-enriched anoxic atmosphere. By 16S ribosomal DNA analysis, all six permafrost isolates were identified as species of the genus Carnobacterium, most closely related to C. inhibens (five isolates) and C. viridans (one isolate). Quantitative growth assays demonstrated that the six permafrost isolates, as well as nine type species of Carnobacterium (C. alterfunditum, C. divergens, C. funditum, C. gallinarum, C. inhibens, C. maltaromaticum, C. mobile, C. pleistocenium, and C. viridans) were all capable of growth under cold, low-pressure, anoxic conditions, thus extending the low-pressure extreme at which life can function.

Effect of the Bacillus atrophaeus subsp. globigii Spo0F H101R mutation on strain fitness

Sporulation is a critical developmental process in Bacillus spp. that, once initiated, removes the possibility of further growth until germination. Therefore, the threshold conditions triggering sporulation are likely to be subject to evolutionary constraint. Our previous studies revealed two spontaneous hypersporulating mutants of Bacillus atrophaeus subsp. globigii, both containing point mutations in the spo0F gene. One of these strains (Detrick-2; contains the spo0F101 allele with a C:T [His101Arg] substitution) had been deliberately selected in the early 1940s as an anthrax surrogate. To determine whether the experimental conditions used during the selection of the "military" strains could have supported the emergence of hypersporulating variants, the relative fitness of strain Detrick-2 was measured in several experimental settings modeled on experimental conditions employed during its development in the 1940s as a simulant. The congenic strain Detrick-1 contained a wild-type spo0F gene and sporulated like the wild-type strain. The relative fitness of Detrick-1 and Detrick-2 was evaluated in competition experiments using quantitative single nucleotide polymorphism (SNP)-specific real-time PCR assays directed at the C:T substitution. The ancestral strain Detrick-1 had a fitness advantage under all conditions tested except when competing cultures were subjected to frequent heat shocks. The hypersporulating strain gained the maximum fitness advantage when cultures were grown at low oxygen tension and when heat shock was applied soon after the formation of the first heat-resistant spores. This is interpreted as gain of fitness by the hypersporulating strain in fast-changing fluctuating environments as a result of the increased rate of switching to the sporulating phenotype.

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

The atmospheric pressure on Mars ranges from 1-10 mbar, about 1% of Earth pressure (∼1013 mbar). Low pressure is a growth-inhibitory factor for terrestrial microorganisms on Mars, and a putative low-pressure barrier for growth of Earth bacteria of ∼25 mbar has been postulated. In a previous communication, we described the isolation of a strain of Bacillus subtilis that had evolved enhanced growth ability at the near-inhibitory low pressure of 50 mbar. To explore mechanisms that enabled growth of the low-pressure-adapted strain, numerous genes differentially transcribed between the ancestor strain WN624 and low-pressure-evolved strain WN1106 at 50 mbar were identified by microarray analysis. Among these was a cluster of three candidate genes (des, desK, and desR), whose mRNA levels in WN1106 were higher than the ancestor on the microarrays. Up-regulation of these genes was confirmed by quantitative reverse transcription-polymerase chain reaction (qRT-PCR) analysis. The des, desK, and desR genes encode the Des membrane fatty acid (FA) desaturase, the DesK sensor kinase, and the DesR response regulator, respectively, which function to maintain membrane fluidity in acute response to temperature downshift. Pressure downshift caused an up-regulation of des mRNA levels only in WN1106, but expression of a des-lacZ transcriptional fusion was unaffected, which suggests that des regulation was different in response to temperature versus pressure downshift. Competition experiments showed that inactivation of the des gene caused a slight, but statistically significant, loss of fitness of strain WN1106 at 50 mbar. Further, analysis of membrane FA composition of cells grown at 1013 versus 50 mbar revealed a decrease in the ratio of unsaturated to saturated FAs but an increase in the ratio of anteiso- to iso-FAs. The present study represents a first step toward identification of molecular mechanisms by which B. subtilis could sense and respond to the novel environmental stress of low pressure.

Increased competitive fitness of Bacillus subtilis under nonsporulating conditions via inactivation of pleiotropic regulators AlsR, SigD, and SigW

Previous studies implicated loss of motility and mutations of the alsR and sigW regulatory genes in enhanced fitness of the Bacillus subtilis evolved strain WN716 over that of its ancestral strain WN624. The fitness of strains carrying knockout mutations alsR::spc, sigD::kan, and/or sigW::erm was measured and compared to that of the congenic ancestral strain by competition experiments.

Survival of Bacillus subtilis endospores on ultraviolet-irradiated rover wheels and Mars regolith under simulated Martian conditions

Endospores of Bacillus subtilis HA101 were applied to a simulated Mars Exploration Rover (MER) wheel and exposed to Mars-normal UV irradiation for 1, 3, or 6 h. The experiment was designed to simulate a contaminated rover wheel sitting on its landing platform before rolling off onto the martian terrain, as was encountered during the Spirit and Opportunity missions. When exposed to 1 h of Mars UV, a reduction of 81% of viable endospores was observed compared to the non-UV irradiated controls. When exposed for 3 or 6 h, reductions of 94.6% and 96.6%, respectively, were observed compared to controls. In a second experiment, the contaminated rover wheel was rolled over a bed of heat-sterilized Mars analog soil; then the analog soil was exposed to full martian conditions of UV irradiation, low pressure (6.9 mbar), low temperature (-10°C), and an anaerobic CO(2) martian atmosphere for 24 h to determine whether endospores of B. subtilis on the contaminated rover wheel could be transferred to the surface of the analog soil and survive martian conditions. The experiment simulated conditions in which a rover wheel might come into contact with martian regolith immediately after landing, such as is designed for the upcoming Mars Science Laboratory (MSL) rover. The contaminated rover wheel transferred viable endospores of B. subtilis to the Mars analog soil, as demonstrated by 31.7% of samples showing positive growth. However, when contaminated soil samples were exposed to full martian conditions for 24 h, only 16.7% of samples exhibited positive growth-a 50% reduction in the number of soil samples positive for the transferred viable endospores.

Increased fitness and alteration of metabolic pathways during Bacillus subtilis evolution in the laboratory

Five batch cultures of Bacillus subtilis were subjected to evolution in the laboratory for 6,000 generations under conditions repressing sporulation in complex liquid medium containing glucose. Between generations 1,000 and 2,000, variants with a distinct small-colony morphology arose and swept through four of the five populations that had been previously noted for their loss of sporulation (H. Maughan et al., Genetics 177:937-948, 2007). To better understand the nature of adaptation in these variants, individual strains were isolated from one population before (WN715) and after (WN716) the sweep. In addition to colony morphology, strains WN715 and WN716 differed in their motility, aerotaxis, and cell morphology. Competition experiments showed that strain WN716 had evolved a distinct fitness advantage over the ancestral strain and strain WN715 during growth and the transition to the postexponential growth phase, which was more pronounced when WN715 was present in the coculture. Microarray analyses revealed candidate genes in which mutations may have produced some of the observed phenotypes. For example, loss of motility in WN716 was accompanied by decreased transcription of all flagellar, motility, and chemotaxis genes on the microarray. Transcription of alsS and alsD was also lower in strain WN716, and the predicted loss of acetoin production and enhanced acetate production was confirmed by high-performance liquid chromatography (HPLC) analysis. The results suggested that the derived colony morphology of strain WN716 was associated with increased fitness, the alteration of several metabolic pathways, and the loss of a typical postexponential-phase response.