Whole genome-scale assessment of gene fitness of Novosphingobium aromaticavorans during spaceflight

In microgravity, bacteria undergo intriguing physiological adaptations. There have been few attempts to assess global bacterial physiological responses to microgravity, with most studies only focusing on a handful of individual systems. This study assessed the fitness of each gene in the genome of the aromatic compound-degrading Alphaproteobacterium Novosphingobium aromaticavorans during growth in spaceflight. This was accomplished using Comparative TnSeq, which involves culturing the same saturating transposon mutagenized library under two different conditions. To assess gene fitness, a novel comparative TnSeq analytical tool was developed, named TnDivA, that is particularly useful in leveraging biological replicates. In this approach, transposon diversity is represented numerically using a modified Shannon diversity index, which was then converted into effective transposon density. This transformation accounts for variability in read distribution between samples, such as cases where reads were dominated by only a few transposon inserts. Effective density values were analyzed using multiple statistical methods, including log2-fold change, least-squares regression analysis, and Welch's t-test. The results obtained across applied statistical methods show a difference in the number of significant genes identified. However, the functional categories of genes important to growth in microgravity showed similar patterns. Lipid metabolism and transport, energy production, transcription, translation, and secondary metabolite biosynthesis and transport were shown to have high fitness during spaceflight. This suggests that core metabolic processes, including lipid and secondary metabolism, play an important role adapting to stress and promoting growth in microgravity.

Microbial isolation and characterization from two flex lines from the urine processor assembly onboard the international space station

Urine, humidity condensate, and other sources of non-potable water are processed onboard the International Space Station (ISS) by the Water Recovery System (WRS) yielding potable water. While some means of microbial control are in place, including a phosphoric acid/hexavalent chromium urine pretreatment solution, many areas within the WRS are not available for routine microbial monitoring. Due to refurbishment needs, two flex lines from the Urine Processor Assembly (UPA) within the WRS were removed and returned to Earth. The water from within these lines, as well as flush water, was microbially evaluated. Culture and culture-independent analysis revealed the presence of Burkholderia, Paraburkholderia, and Leifsonia. Fungal culture also identified Fusarium and Lecythophora. Hybrid de novo genome analysis of the five distinct Burkholderia isolates identified them as B. contaminans, while the two Paraburkholderia isolates were identified as P. fungorum. Chromate-resistance gene clusters were identified through pangenomic analysis that differentiated these genomes from previously studied isolates recovered from the point-of-use potable water dispenser and/or current NCBI references, indicating that unique populations exist within distinct niches in the WRS. Beyond genomic analysis, fixed samples directly from the lines were imaged by environmental scanning electron microscopy, which detailed networks of fungal-bacterial biofilms. This is the first evidence of biofilm formation within flex lines from the UPA onboard the ISS. For all bacteria isolated, biofilm potential was further characterized, with the B. contaminans isolates demonstrating the most considerable biofilm formation. Moreover, the genomes of the B. contaminans revealed secondary metabolite gene clusters associated with quorum sensing, biofilm formation, antifungal compounds, and hemolysins. The potential production of these gene cluster metabolites was phenotypically evaluated through biofilm, bacterial-fungal interaction, and hemolytic assays. Collectively, these data identify the UPA flex lines as a unique ecological niche and novel area of biofilm growth within the WRS. Further investigation of these organisms and their resistance profiles will enable engineering controls directed toward biofilm prevention in future space station water systems.

Results of long-term radiation environment monitoring by the Russian RMS system on board Zvezda module of the ISS

The Radiation monitoring system (RMS) continuously operated in various configurations since the launch of the Zvezda module of the International Space Station (ISS). The RMS consisted of 7 units, namely: the R-16 dosimeter, 4 DB-8 dosimeters, utility and data collection units. The obtained data covers a time of 22 years. This paper analyses the radiation environment variations on board the "Zvezda" module. Variations of the onboard daily dose rate associated with changes of ISS altitude and 11-year cycle galactic cosmic rays' variations are analyzed and discussed. It is shown that the observed increase in the daily dose from 0.20 - 0.25 to 0.35 - 0.50 mGy/day is mostly due to the increase of ISS orbit altitude, resulting in a substantial increase of the dose contribution from the South Atlantic Anomaly (SAA) Region. Dose rate variations in the SAA as well as latitude and longitude dose rate distributions are discussed in detail. Analysis confirms that the well-known westward drift effect of the SAA is clearly visible from radiation dose measurements on the ISS.

Mathematical Model of Antibiotic Resistance Determinants' Stability Under Space Flight Conditions

Increasing antibiotic resistance (AR) poses dangers of treatment complications and even treatment failure to astronauts. An AR determinant is a gene of resistance carried by bacteria. This article considers the issue of the stability of AR determinants and the influence of manned spaceflight conditions on this characteristic. A phenomenological model has been developed that makes it possible to evaluate the integral value of the stability of determinants of AR in bacteria as a function of time. Based on experimental results obtained during implementation of the SALYUT 7 space program, the stability of determinants of AR in Escherichia coli strains isolated before and after a spaceflight in 16 astronauts was evaluated. In addition, an assessment was made of the integral value of the stability of determinants of AR in bacteria during in vitro experiments, both in spaceflight and terrestrial conditions, after preincubation in space. The calculation using the developed phenomenological model showed that the stability of AR determinants in E. coli bacteria isolated from astronauts before the spaceflight is 33% higher than after the flight. The in vitro experiment carried out on board the International Space Station showed the opposite situation-an increase in the stability of AR determinants by 33% in cultures that have been in space compared with terrestrial control. This indicates an additional influence on the stability of determinants and of the astronaut's immune system, as well as space conditions. The common result in these two types of studies is the experimental fact that the largest number of bacteria, in space conditions, had two determinants of AR. The importance of fighting bacteria with two determinants is that at least three different antibiotics are required to have an effect. This circumstance makes it possible to predict a possible strategy for the use of antibiotics in autonomous spaceflights.

The Maleth program: Malta's first space mission discoveries on the microbiome of diabetic foot ulcers

The purpose of the Maleth Program, also known as Project Maleth, is Malta's first space program to evaluate human skin tissue microbiome changes in type 2 diabetes mellitus (T2DM) patients afflicted with diabetic foot ulcers (DFU). This was carried out in both ground-based models and spaceflight. The first mission (Maleth I) under this program was carried out to uncover the effects of spaceflight, microgravity and radiation on human skin tissue microbiome samples from six T2DM patients recruited into the study. Each patient human skin tissue sample was split in three, with one section processed immediately for genomic profiling by 16S typing and the rest were processed for longer term ground-control and spaceflight experiments. Ground-control and spaceflight human skin tissue samples were also processed for genomic profiling upon mission re-entry and completion. Maleth I's overall objective was achieved, as human skin tissue samples with their microbiomes travelled to space and back yielding positive results by both standard microbiology techniques and genetic typing using 16S rRNA amplicon sequencing. Preliminary findings of this mission are discussed in light of its innovative approach at DFU microbiome research, and the clinical implications that may emerge from this and other future similar studies.

Subsequent inclusion/exclusion criteria to select the best species for an experiment performed on the ISS in a refurbished hardware

The interest in re-using flown hardware for new and different space biology experiments is increasing. To match the constraints of the flown hardware with the requirements of the new biological system, innovative methodological approaches are necessary. MULTITROP was a successful plant biology experiment that was performed on the ISS to investigate multiple-tropism interactions during the early stage of seedling growth. We used the hardware designed and flown for the IFOAM experiment in 2009. The main challenge was to implement seeds of a crop species in a growth chamber conceived for yeast culture and to grow the seedlings in microgravity condition but activating seed germination on ground before the launch. Our approach was to adapt the biological system to the hardware constraints and also to the experiment timing and the environmental factors expected during the prelaunch, launch and flight operations. We looked for an objective and repeatable method to effectively select the best suited species. Innovatively, we applied the method of inclusion/exclusion criteria to adapt a new biological system to a reused hardware. The list and the consecutive order of the specific inclusive/exclusive criteria turned out to be a valid support to guide the science team in objectively choosing the most suitable species for the experiment. Among the 50 initial food species, the carrot seeds resulted as the best in satisfying all technical requirements and post-flight data confirmed the expectations.

Vegetative and reproductive growth of Arabidopsis under microgravity conditions in space

We have performed a seed-to-seed experiment in the cell biology experiment facility (CBEF) installed in the Kibo (Japanese Experiment Module) in the International Space Station. The CBEF has a 1 × g compartment on a centrifuge and a microgravity compartment, to investigate the effects of microgravity on the vegetative and reproductive growth of Arabidopsis thaliana (L.) Heynh. Seeds germinated irrespective of gravitational conditions after water supply on board. Thereafter, seedlings developed rosette leaves. The time of bolting was slightly earlier under microgravity than under space 1 × g. Microgravity enhanced the growth rate of peduncles as compared with space 1 × g or ground control. Plants developed flowers, siliques and seeds, completing their entire life cycle during 62-days cultivation. Although the flowering time was not significantly affected under microgravity, the number of flowers in a bolted plant significantly increased under microgravity as compared with space 1 × g or ground control. Microscopic analysis of reproductive organs revealed that the longitudinal length of anthers was significantly shorter under microgravity when compared with space 1 × g, while the length of pistils and filaments was not influenced by the gravitational conditions. Seed mass significantly increased under microgravity when compared with space 1 × g. In addition, seeds produced in space were found not to germinate on the ground. These results indicate that microgravity significantly influenced the reproductive development of Arabidopsis plants even though Earth's gravitational environment is not absolutely necessary for them to complete their life cycle.

Water and microbial monitoring technologies towards the near future space exploration

Space exploration is demanding longer lasting human missions and water resupply from Earth will become increasingly unrealistic. In a near future, the spacecraft water monitoring systems will require technological advances to promptly identify and counteract contingent events of waterborne microbial contamination, posing health risks to astronauts with lowered immune responsiveness. The search for bio-analytical approaches, alternative to those applied on Earth by cultivation-dependent methods, is pushed by the compelling need to limit waste disposal and avoid microbial regrowth from analytical carryovers. Prospective technologies will be selected only if first validated in a flight-like environment, by following basic principles, advantages, and limitations beyond their current applications on Earth. Starting from the water monitoring activities applied on the International Space Station, we provide a critical overview of the nucleic acid amplification-based approaches (i.e., loop-mediated isothermal amplification, quantitative PCR, and high-throughput sequencing) and early-warning methods for total microbial load assessments (i.e., ATP-metry, flow cytometry), already used at a high readiness level aboard crewed space vehicles. Our findings suggest that the forthcoming space applications of mature technologies will be necessarily bounded by a compromise between analytical performances (e.g., speed to results, identification depth, reproducibility, multiparametricity) and detrimental technical requirements (e.g., reagent usage, waste production, operator skills, crew time). As space exploration progresses toward extended missions to Moon and Mars, miniaturized systems that also minimize crew involvement in their end-to-end operation are likely applicable on the long-term and suitable for the in-flight water and microbiological research.

The influence of spaceflight on the astronaut salivary microbiome and the search for a microbiome biomarker for viral reactivation

BACKGROUND

Spaceflight impacts astronauts in many ways but little is known on how spaceflight affects the salivary microbiome and the consequences of these changes on astronaut health, such as viral reactivation. In order to understand this, the salivary microbiome was analyzed with 16S rRNA gene amplicon sequencing, and saliva viral titers were analyzed with quantitative polymerase chain reaction (qPCR) with primers specific for Epstein-Barr virus (EBV), herpes simplex virus (HSV), and varicella zoster virus (VZV) from 10 astronauts pre-flight, in-flight, and post-flight.

RESULTS

Streptococcus was the most abundant organism in the saliva, making up 8% of the total organisms detected, and their diversity decreased during spaceflight. Other organisms that had statistically significant changes were Proteobacteria and Fusobacteria which increased during flight and Actinobacteria which decreased during flight. At the genus level, Catonella, Megasphera, and Actinobacillus were absent in more than half of saliva samples collected pre-flight but were then detected during flight. In those subjects that already had these genera pre-flight, their relative abundances increased during flight. Correlation analyses between the microbiome and viral titers revealed a positive correlation with Gracilibacteria, Absconditabacteria, and Abiotrophia and a negative correlation between Oribacterium, Veillonella, and Haemophilus. There was also a significant positive correlation between microbiome richness and EBV viral titers.

CONCLUSIONS

This is the first study to look at how the salivary microbiome changes as a result of spaceflight and the search for bacterial biomarkers for viral reactivation. Further studies examining the role of specific organisms that were shown to be correlative and predictive in viral reactivation, a serious problem in astronauts during spaceflight, could lead to mitigation strategies to help prevent disease during both short and long duration space missions. Video abstract.

Altered rodent gait characteristics after ~35 days in orbit aboard the International Space Station

The long-term adaptations to microgravity and other spaceflight challenges within the confines of a spacecraft, and readaptations to weight-bearing upon reaching a destination, are unclear. While post-flight gait change in astronauts have been well documented and reflect multi-system deficits, no data from rodents have been collected. Thus, the purpose of this study was to evaluate gait changes in response to spaceflight. A prospective collection of gait data was collected on 3 groups of mice: those who spent~35 days in orbit (FLIGHT) aboard the International Space Station (ISS); a ground-based control with the same habitat conditions as ISS (Ground Control; GC); and a vivarium control with typical rodent housing conditions (VIV). Pre-flight and post-flight gait measurements were conducted utilizing an optimized and portable gait analysis system (DigiGait, Mouse Specifics, Inc). The total data acquisition time for gait patterns of FLIGHT and control mice was 1.5-5 min/mouse, allowing all 20 mice per group to be assessed in less than an hour. Patterns of longitudinal gait changes were observed in the hind limbs and the forelimbs of the FLIGHT mice after ~35 days in orbit; few differences were observed in gait characteristics within the GC and VIV controls from the initial to the final gait assessment, and between groups. For FLIGHT mice, 12 out of 18 of the evaluated gait characteristics in the hind limbs were significantly changed, including: stride width variability; stride length and variance; stride, swing, and stance duration; paw angle and area at peak stance; and step angle, among others. Gait characteristics that decreased included stride frequency, and others. Moreover, numerous forelimb gait characteristics in the FLIGHT mice were changed at post-flight measures relative to pre-flight. This rapid DigiGait gait measurement tool and customized spaceflight protocol is useful for providing preliminary insight into how spaceflight could affect multiple systems in rodents in which deficits are reflected by altered gait characteristics.

A novel low-cost method for assessing intra-urban variation in night time light and applications to public health

Night time lighting (NTL) pollution is a public health concern given its known impact on a range of health outcomes. The daily cycle of the hue of natural ambient light shifting from relatively blue-white light at noon to relatively yellow-red light at sunset is important for human functioning. Disruptions of the circadian clock can result in melatonin suppression, sleep and mood disorders, and increased risks of cancer in adults. Current measures of intra-urban variation in NTL are based on costly in-person or coarse satellite image-based assessments. The central objective of the current study is to validate a novel low-cost measure of intra-urban NTL variation. Estimates of red, green and blue NTL intensity were derived from a cloud-free night time image of the city of Montreal, Canada, taken from the International Space Station (ISS). The new measures are shown to converge with in-person assessed NTL and to predict known child health-related outcomes. Specifically, the results suggest that ISS-assessed blue NTL is associated with feelings of safety and self-reported health. In conclusion, ISS-based measures of NTL, particularly of blue NTL, are valid indicators of intra-urban variation in NTL for applications in public health. Limitations of, and future directions for, the method are discussed.

Influence of impulse noise on noise dosimetry measurements on the International Space Station

Objective: Acoustic dosimetry (AD) data collected on the International Space Station (ISS) were analysed to investigate the impact of impulse noise on crew noise exposure.Design: The noise exposure during work (LAeq16h) and sleep (LAeq8h) time, and the number of impulses >115 dB peak that occurred during each measurement activity, were calculated from the AD data. Two parametric studies were used to estimate the effect of 1) impulses in the original data set, and 2) hypothetical impulses of different levels, durations and quantities on LAeq16h.Study sample: Twelve sets of AD data collected on the ISS from November 2017 to October 2018.Results: The ISS work time noise limit (72 dBA) was exceeded in four of the 12 data sets. In three of those, there were over 100 impulses >115 dB peak and the number of impulses was significantly correlated with LAeq16h. However, the impulses only caused a meaningful increase in LAeq16h when the number of occurrences was large (>50), or when both the level and duration of the impulses were large.Conclusions: Continued monitoring of impulse noise data is recommended to facilitate the investigation of exceedances or abnormalities in future AD data acquired on the ISS.

Furnishing spaceship environment: evaluation of bacterial biofilms on different materials used inside International Space Station

Performed inside International Space Station (ISS) from 2011 to 2016, VIABLE (eValuatIon And monitoring of microBiofiLms insidE International Space Station) ISS was a long-lasting experiment aimed at evaluating the bacterial contamination on different surface space materials subjected to different pre-treatment, to provide useful information for future space missions. In this work, surfaces samples of the VIABLE ISS experiment were analyzed to determine both the total bacterial load (ATP-metry, qPCR) and the composition of the microbial communities (16S rRNA genes amplicon sequencing). Data obtained showed a low bacterial contamination of all the surfaces, with values in agreement with those allowed inside ISS, and with a taxonomic composition similar to those found in previous studies (Enterobacteriales, Bacillales, Lactobacillales and Actinomycetales). No pre-treatment or material effect were observed on both the bacterial load and the composition of the communities, but for both a slight effect of the position (expose/not expose to air) was observed. In conclusion, under the conditions used for VIABLE ISS, no material or pre-treatment seems to be better than others in terms of quantity and type of bacterial contamination.

A microbial survey of the International Space Station (ISS)

BACKGROUND

Modern advances in sequencing technology have enabled the census of microbial members of many natural ecosystems. Recently, attention is increasingly being paid to the microbial residents of human-made, built ecosystems, both private (homes) and public (subways, office buildings, and hospitals). Here, we report results of the characterization of the microbial ecology of a singular built environment, the International Space Station (ISS). This ISS sampling involved the collection and microbial analysis (via 16S rDNA PCR) of 15 surfaces sampled by swabs onboard the ISS. This sampling was a component of Project MERCCURI (Microbial Ecology Research Combining Citizen and University Researchers on ISS). Learning more about the microbial inhabitants of the "buildings" in which we travel through space will take on increasing importance, as plans for human exploration continue, with the possibility of colonization of other planets and moons.

RESULTS

Sterile swabs were used to sample 15 surfaces onboard the ISS. The sites sampled were designed to be analogous to samples collected for (1) the Wildlife of Our Homes project and (2) a study of cell phones and shoes that were concurrently being collected for another component of Project MERCCURI. Sequencing of the 16S rDNA genes amplified from DNA extracted from each swab was used to produce a census of the microbes present on each surface sampled. We compared the microbes found on the ISS swabs to those from both homes on Earth and data from the Human Microbiome Project.

CONCLUSIONS

While significantly different from homes on Earth and the Human Microbiome Project samples analyzed here, the microbial community composition on the ISS was more similar to home surfaces than to the human microbiome samples. The ISS surfaces are species-rich with 1,036-4,294 operational taxonomic units (OTUs per sample). There was no discernible biogeography of microbes on the 15 ISS surfaces, although this may be a reflection of the small sample size we were able to obtain.

Three-dimensional growth of human endothelial cells in an automated cell culture experiment container during the SpaceX CRS-8 ISS space mission - The SPHEROIDS project

Human endothelial cells (ECs) were sent to the International Space Station (ISS) to determine the impact of microgravity on the formation of three-dimensional structures. For this project, an automatic experiment unit (EU) was designed allowing cell culture in space. In order to enable a safe cell culture, cell nourishment and fixation after a pre-programmed timeframe, the materials used for construction of the EUs were tested in regard to their biocompatibility. These tests revealed a high biocompatibility for all parts of the EUs, which were in contact with the cells or the medium used. Most importantly, we found polyether ether ketones for surrounding the incubation chamber, which kept cellular viability above 80% and allowed the cells to adhere as long as they were exposed to normal gravity. After assembling the EU the ECs were cultured therein, where they showed good cell viability at least for 14 days. In addition, the functionality of the automatic medium exchange, and fixation procedures were confirmed. Two days before launch, the ECs were cultured in the EUs, which were afterwards mounted on the SpaceX CRS-8 rocket. 5 and 12 days after launch the cells were fixed. Subsequent analyses revealed a scaffold-free formation of spheroids in space.

Growth of 48 built environment bacterial isolates on board the International Space Station (ISS)

Background. While significant attention has been paid to the potential risk of pathogenic microbes aboard crewed spacecraft, the non-pathogenic microbes in these habitats have received less consideration. Preliminary work has demonstrated that the interior of the International Space Station (ISS) has a microbial community resembling those of built environments on Earth. Here we report the results of sending 48 bacterial strains, collected from built environments on Earth, for a growth experiment on the ISS. This project was a component of Project MERCCURI (Microbial Ecology Research Combining Citizen and University Researchers on ISS). Results. Of the 48 strains sent to the ISS, 45 of them showed similar growth in space and on Earth using a relative growth measurement adapted for microgravity. The vast majority of species tested in this experiment have also been found in culture-independent surveys of the ISS. Only one bacterial strain showed significantly different growth in space. Bacillus safensis JPL-MERTA-8-2 grew 60% better in space than on Earth. Conclusions. The majority of bacteria tested were not affected by conditions aboard the ISS in this experiment (e.g., microgravity, cosmic radiation). Further work on Bacillus safensis could lead to interesting insights on why this strain grew so much better in space.

Low Earth orbit assessment of proton anisotropy using AP8 and AP9 trapped proton models

The completion of the International Space Station (ISS) in 2011 has provided the space research community with an ideal evaluation and testing facility for future long duration human activities in space. Ionized and secondary neutral particles radiation measurements inside ISS form the ideal tool for validation of radiation environmental models, nuclear reaction cross sections and transport codes. Studies using thermo-luminescent detectors (TLD), tissue equivalent proportional counter (TPEC), and computer aided design (CAD) models of early ISS configurations confirmed that, as input, computational dosimetry at low Earth orbit (LEO) requires an environmental model with directional (anisotropic) capability to properly describe the exposure of trapped protons within ISS. At LEO, ISS encounters exposure from trapped electrons, protons and geomagnetically attenuated galactic cosmic rays (GCR). For short duration studies at LEO, one can ignore trapped electrons and ever present GCR exposure contributions during quiet times. However, within the trapped proton field, a challenge arises from properly estimating the amount of proton exposure acquired. There exist a number of models to define the intensity of trapped particles. Among the established trapped models are the historic AE8/AP8, dating back to the 1980s and the recently released AE9/AP9/SPM. Since at LEO electrons have minimal exposure contribution to ISS, this work ignores the AE8 and AE9 components of the models and couples a measurement derived anisotropic trapped proton formalism to omnidirectional output from the AP8 and AP9 models, allowing the assessment of the differences between the two proton models. The assessment is done at a target point within the ISS-11A configuration (circa 2003) crew quarter (CQ) of Russian Zvezda service module (SM), during its ascending and descending nodes passes through the south Atlantic anomaly (SAA). The anisotropic formalism incorporates the contributions of proton narrow pitch angle (PA) and east-west (EW) effects. Within SAA, the EW anisotropy results in different level of exposure to each side of the ISS Zvezda SM, allowing angular evaluation of the anisotropic proton spectrum. While the combined magnitude of PA and EW effects at LEO depends on a multitude of factors such as trapped proton energy, orientation and altitude of the spacecraft along the velocity vector, this paper draws quantitative conclusions on the combined anisotropic magnitude differences within ISS SM target point between AP8 and AP9 models.