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Developing Technologies for Biological Experiments in Deep Space

NASA Ames Research Center is the leader in developing autonomous nanosatellites or CubeSats to address strategic knowledge gaps about the effects of space travel on biological organisms, including GeneSat, PharmaSat, and EcAMSat. Now that NASA has set its sights on human exploration in deep space, such missions require significant technological and biomedical countermeasures to protect astronauts from chronic radiation exposure. CubeSats can inform these countermeasures by querying relevant space environments with model organisms and/or biosensors. BioSentinel will be the first interplanetary CubeSat to study the biological response to space radiation outside low Earth orbit in almost 50 years. BioSentinel is an autonomous platform able to support biology and to investigate the effects of space radiation on a model organism in interplanetary deep space. It will fly onboard Artemis-1, from which it will be deployed on a lunar fly-by trajectory and into a heliocentric orbit. BioSentinel, a 6U CubeSat (1U = 10-cm cube), will measure the DNA damage response to ambient space radiation in a model organism, which will be compared to information provided by an onboard radiation spectrometer and to data obtained on the ISS and on Earth. Even though the primary objective of the mission is to develop an autonomous spacecraft capable of conducting biological experiments in deep space, the 4U BioSensor science payload contained within the free-flyer is an adaptable instrument that can perform bio measurements with different microorganisms and in multiple space environments, including the ISS, lunar gateway, and on the surface of the Moon. Thus, nanosatellites like BioSentinel can be used to study the effects of both reduced gravity and space radiation and can house different organisms to answer specific science questions. In addition to their flexibility, nanosatellites also provide a low-cost alternative to more complex and larger missions, and require minimal crew support, if any

biosenses↗

Developing Technologies for Biological Experiments in Deep Space

NASA Ames Research Center is the leader in developing autonomous nanosatellites or CubeSats to address strategic knowledge gaps about the effects of space travel on biological organisms, including GeneSat, PharmaSat, and EcAMSat. Now that NASA has set its sights on human exploration in deep space, such missions require significant technological and biomedical countermeasures to protect astronauts from chronic radiation exposure. CubeSats can inform these countermeasures by querying relevant space environments with model organisms and/or biosensors. BioSentinel will be the first interplanetary CubeSat to study the biological response to space radiation outside low Earth orbit in almost 50 years. BioSentinel is an autonomous platform able to support biology and to investigate the effects of space radiation on a model organism in interplanetary deep space. It will fly onboard Artemis-1, from which it will be deployed on a lunar fly-by trajectory and into a heliocentric orbit. BioSentinel, a 6U CubeSat (1U = 10-cm cube), will measure the DNA damage response to ambient space radiation in a model organism, which will be compared to information provided by an onboard radiation spectrometer and to data obtained on the ISS and on Earth. Even though the primary objective of the mission is to develop an autonomous spacecraft capable of conducting biological experiments in deep space, the 4U BioSensor science payload contained within the free-flyer is an adaptable instrument that can perform bio measurements with different microorganisms and in multiple space environments, including the ISS, lunar gateway, and on the surface of the Moon. Thus, nanosatellites like BioSentinel can be used to study the effects of both reduced gravity and space radiation and can house different organisms to answer specific science questions. In addition to their flexibility, nanosatellites also provide a low-cost alternative to more complex and larger missions, and require minimal crew support, if any.

biosenses↗

Real-Time Culture-Independent Microbial Profiling Onboard the International Space Station using Nanopore Sequencing

For the past two decades, microbial monitoring of the International Space Station (ISS) has relied on culture-dependent methods that require return to Earth for analysis. This has a number of limitations, with the most significant being bias towards the detection of culturable organisms and the inherent delay between sample collection and ground-based analysis. In recent years, portable and easy-to-use molecular-based tools, such as Oxford Nanopore Technologies’ MinION™ sequencer and miniPCR bio’s miniPCR™ thermal cycler, have been validated onboard the ISS. Here, we report on the development, validation, and implementation of a swab-to-sequencer method that provides a culture-independent solution to real-time microbial profiling onboard the ISS. Method development focused on analysis of swabs collected in a low-biomass environment with limited facility resources and stringent controls on allowed processes and reagents. ISS-optimized procedures included enzymatic DNA extraction from a swab tip, bead-based purifications, altered buffers, and the use of miniPCR and the MinION. Validation was conducted through extensive ground-based assessments comparing current standard culture-dependent and newly developed culture-independent methods. Similar microbial distributions were observed between the two methods; however, as expected, the culture-independent data revealed microbial profiles with greater diversity. Protocol optimization and verification was established during NASA Extreme Environment Mission Operations (NEEMO) analog missions 21 and 22, respectively. Unique microbial profiles obtained from analog testing validated the swab-to-sequencer method in an extreme environment. Finally, four independent swab-to-sequencer experiments were conducted onboard the ISS by two crewmembers. Microorganisms identified from ISS swabs were consistent with historical culture-based data, and primarily consisted of commonly observed human-associated microbes. This simplified method has been streamlined for high ease-of-use for a non-trained crew to complete in an extreme environment, thereby enabling environmental and human health diagnostics in real-time as future missions take us beyond low-Earth orbit.

microbiology↗

A METHOD TO REDUCE BIOBURDEN IN ASTROMATERIALS CURATION FACILITIES WITHOUT INTRODUCING UNWANTED CONTAMINATION

Introduction: NASA curates its Astromaterials collections in cleanrooms that are carefully monitored for particulate, inorganic and trace metal contamination. Current sample collections are not particularly susceptible to organic contamination or biological alteration. However, new collections like those from the OSIRIS-REx and Hayabusa2 missions will have organic contamination requirements and are susceptible to biodegradation. It will be necessary sterilize or at least disinfect curation labs, as well as tools and equipment in a manner that does not introduce additional contamination and does not affect the samples 1. Current curation cleaning procedures utilize isopropyl alcohol which offers some bioburden reduction, but is not effective against spore-forming bacteria or fungal spores 2. We present a modified disinfection method that uses ultrapure hydrogen peroxide to reduce bioburden inside curation labs and glove boxes without introducing contamination or damaging curation equipment. We tested this method in the meteorite processing lab as well as on a glovebox being cleaned for use in processing ANGSA (Apollo Next Generation Sample Analysis) samples and present the results of those tests. We discuss the limitations of this method and describe potential situations in which it will not be applicable. The CDC guidelines for disinfection andsterilization in healthcare facilities discusses over 15different methods for reducing bioburden in hospitalsettings 3. The most common method, steamsterilization, is well suited to sterilizing curationprocessing tools but cannot easily be used to sterilizecleanroom surfaces or large equipment likegloveboxes. Chemical sterilization with bleach(NaOCl) is also a common strategy in healthcare andpharmaceutical settings that presents materialcompatibility issues as well as serious inorganiccontamination concerns for curation facilities.Introducing a new source of Na and Cl into curationlabs is not acceptable. Other chemical methods likeethylene oxide, formaldehyde, iodophors andquaternary ammonium compounds could introduceorganic and inorganic contamination. We chose tofocus on hydrogen peroxide because it is generallycompatible with commonly used curation materialslike stainless steel, aluminum and Teflon and becauseit decomposes to oxygen and water. The CDCguidelines for hydrogen peroxide specify using a 7.5wt% solution at 25 ̊C with a contact time of 30 minutesfor high level disinfection and 6 hours for sterilization.High level disinfection is defined as a technique thatwill kill all microorganisms except large numbers ofbacterial spores 3. Methods: We prepared a solution of 7.5 wt%hydrogen peroxide from a stock solution of ultrapure30 wt% peroxide (JT Baker) and curation gradeultrapure water. This ultrapure water is already used incuration cleaning procedures and thus is not consideredand additional source of contamination. We conducteda materials compatibility test by exposing unanodizedand anodized 6061 T6 Al alloy to the peroxide solutionfor up to six hours and periodically inspecting thesurfaces for visible defects. We used this peroxide todisinfect the floor of the meteorite processing lab andthe interior of a curation glovebox by exposing thesesurfaces to the peroxide solution for 30 min. Thesurfaces were swabbed with a dry macrofoam swabbefore (Puritan Brand 2518051PFRNDFD) and afterperoxide treatment to collect microbes present on thesurfaces. Microbes were extracted by sonication fromthe swab into 15 ml of PBS (phosphate buffered saline)and inoculated onto the following media: TSA (trypticsoy agar) BA (blood agar), R2A (Reasoners 2 agar),Potato Dextrose Agar, Saboraud Dextrose Agar andSaboraud Dextrose Agar with 0.1 mg/ mlchloramphenicol. Four TSA plates and two BA plateswere inoculated with 0.1 ml of PBS each andincubated at 35 and 37 for 48 hours. Two R2A°C°Cplates (0.1 ml of PBS each) were incubated at 25 .°CThe remaining plates were inoculated with 0.2ml ofPBS and incubated at 30 ̊C for seven days. Afterincubation bacterial and fungal isolates were countedand transferred to new plates for identification usingthe VITEK24 automated system or by sequencing aportion of the barcode gene (16S rRNA for bacteria,small subunit gene for fungi) on an ABI 3500 Sangersequencer. Negative controls consisted of swabs thatwere opened in the sampling environment andanalyzed alongside the experimental samples.Results: A 6 hour exposure to hydrogen peroxideresulted in visible pitting on un-anodized 6061 Al, butnot on anodized surfaces. No visible pitting occurredafter a 30 minute exposure. Therefore, we decided tolimit our experimental tests to 30 min. exposures. 17bacterial CFU (colony forming units) representing 4distinct organisms were isolated from the meteorite processing lab floor prior to hydrogen peroxidetreatment. We were unable culture any organisms afterperoxide treatment. In the glovebox we were able toculture three bacterial CFU representing three distinctspecies, including a spore forming bacterium prior todisinfection with peroxide. After the peroxidetreatment we were unable to culture any organisms.Routine monitoring of the meteorite processing lab andthe glovebox did not indicate any increase in unwantedinorganic contamination after these peroxidetreatments. Discussion: A 30 minute treatment with 7.5 wt%peroxide appears to be an effective method forreducing bioburden on typical cleanroom surfaces. Themethod does not introduce unwanted organic orinorganic contamination and is compatible withcommonly used curation materials like stainless steel,Teflon and anodized aluminum alloys. Special careshould be taken with un-anodized aluminum.Prolonged exposure to hydrogen peroxide can causepitting on this material. We recommend using thismethod to disinfect curation labs and equipment whenbiological alteration is a concern. This method iseffective at room temperature and cannot be used todisinfect labs and equipment where the ambienttemperature is < 0 ̊C. Astromaterials samples shouldbe removed from the area where disinfection is tooccur. Hydrogen peroxide is a powerful oxidizingagent and will react with any organic carbon present inthe sample. References: [1.] Mccubbin, F. M. et al.Sp. Sci Rev(2019) doi:10.1007/s11214-019-0615-9. [2.] Mogul, R.et al.Astrobiology 18, ast.2017.1814 (2018). [3.]Rutala, W. A. & Weber, D. J. Guideline for Disinfection and Sterilization in Healthcare Facilities, 2008. [4.] Pincus, D. H. in Encyclopedia of Rapid Microbiological Methods (2005).

A. B. Regberg↗

BioSentinel - ISS mission

BioSentinel will be the first interplanetary CubeSat to study the biological response to space radiation outside low Earth orbit in almost 50 years. BioSentinel is an autonomous platform able to support biology and to investigate the effects of space radiation on a model organism in interplanetary deep space. It will fly onboard Artemis-1, from which it will be deployed on a lunar fly-by trajectory and into a heliocentric orbit. BioSentinel, a 6U CubeSat (1U = 10-cm cube), will measure the DNA damage response to ambient space radiation in a model organism, which will be compared to information provided by an onboard radiation spectrometer and to data obtained on the ISS and on Earth. Even though the primary objective of the mission is to develop an autonomous spacecraft capable of conducting biological experiments in deep space, the 4U BioSensor science payload contained within the free-flyer is an adaptable instrument that can perform bio measurements with different microorganisms and in multiple space environments, including the ISS. Thus, nanosatellites like BioSentinel can be used to study the effects of both reduced gravity and space radiation and can house different organisms to answer specific science questions. In addition to their flexibility, nanosatellites also provide a low-cost alternative to more complex and larger missions, and require minimal crew support, if any

space biosensors↗

Lunar BioSensor: An Autonomous Instrument to Study the Effects of the Lunar Environment on Biological Organisms

One of the major challenges to long-duration space travel and habitation in deep space is an in-depth understanding of the biological effects of space radiation, often convoluted by the impact of reduced gravity. Nonetheless, due to the near impossibility of simulating prolonged exposure to these combined effects in terrestrial facilities, actual missions are needed to characterize the radiobiological hazards of this environment. NASA Ames has been the leader in developing autonomous bio nanosatellites to address strategic knowledge gaps about the effects of space travel on biological organisms, including GeneSat, PharmaSat, EcAMSat, and BioSentinel. BioSentinel will be the first interplanetary bio nanosatellite or CubeSat to study the biological response to space radiation outside Low Earth Orbit (LEO). BioSentinel is an autonomous platform able to support biology and to investigate the effects of space radiation on a model organism in interplanetary deep space. It will fly onboard NASA’s Artemis-1, from which it will be deployed on a lunar fly-by trajectory and into a heliocentric orbit. The BioSentinel nanosatellite, a 6U deep space CubeSat (1U = 10-cm cube), will measure the DNA damage and response to ambient space radiation in a model biological organism, the budding yeast S. cerevisiae, which will be compared to information provided by an onboard physical radiation sensor and to data obtained in LEO (on the ISS) and on Earth. Even though the primary objective of the mission is to develop an autonomous spacecraft capable of conducting biological experiments in deep space, the 4U BioSensor science payload contained within the 6U free-flyer is an adaptable instrument platform that can perform biological measurements with different microorganisms and in multiple space environments, including the ISS, lunar gateway, and on the surface of the Moon. The proposed 4U instrument will leverage the payload design of the 6U free-flyer, utilizing the lunar lander or vehicle for power and data relay. Thus, nanosatellites like BioSentinel (and Lunar BioSensor) can be used to study the effects of both reduced gravity and space radiation and can house different bio organisms to answer specific science questions. In addition to their flexibility, nanosatellites also provide a low-cost alternative to more complex and larger missions, and require minimal crew support, if any.

space biosensors↗

Genetic Determinants of Microbial Survival in Space

Space flight agencies envision a future for humankind beyond Earth, including missions back to the Moon and to Mars in the coming decades. Sending humans into space inevitably includes their microbiomes as well, leading to trillions of bacteria being shed in their living areas. These bacteria shape the lives of their hosts as well as their environment; thus, it is crucial to understand the adaptations of these microbial spacefarers in spaceflight conditions. We aimed to elucidate the genetic determinants of microbial survival in space using a pan-genome analysis of 12 genera cultured from the International Space Station (ISS) from 2017 to 2018. Analysis was performed on each of the genera individually with terrestrial analogs to identify the core and accessory genomes of the spaceflight and terrestrial strains. We then compared the flight and terrestrial core and accessory genomes for each genera using a Bray-Curtis index and visualized the resulting dissimilarity using an Non-Metric Dimensional Scaling plot. The core proteins available in only the spaceflight organisms were then manually characterized for function and genomic location. In every core genome comparison in each genus, there was significant dissimilarity in the core of the spaceflight organisms when compared to the terrestrial organisms. This trend was present in some of the accessory genomes, but was not ubiquitous. Functional analysis of the core content of the ISS genomes showed the majority of genes unique to the core were clustered by location. These gene clusters suggested a set of genetic determinants confer survival in spacecraft-built environments, notably through the uptake of extracellular DNA such as bacteriophage and plasmids. The clear difference between spaceflight and terrestrial microorganisms shows that spaceflight conditions are selective, which has long term implications for their human hosts and environments.

MoBE↗

Determining Chlamydomonas reinhardtii resistance to ionizing radiation at a genome-wide scale

Spaceflight is a complex mixture of abiotic stresses that causes a myriad of cellular responses including increased genome-wide mutation load. The impact of spaceflight on mutation load is not well understood for most organisms and is especially critical to characterize for candidate microorganisms that could be part of biological life support systems. Prior research in our laboratory revealed an unexpectedly high level of mutation during spaceflight in the eukaryotic green algae, C. reinhardtii. Based on the spectrum of base changes observed, we concluded that the mutations were generated through a molecular mechanism unique to the spaceflight environment. Spaceflight is a complex set of stresses, and we are using an Earth-based analog to test ionizing radiation as a potential causative variable for the unique mutation spectrum observed in spaceflight. C. reinhardtii was grown exposed to chronic radiation from a Cesium-137 source. Four biological replicate cultures of wild-type cells were grown in gas permeable plastic tissue culture bags in liquid media following the design used on the International Space Station (ISS) during the previous space algae experiment. Radiation levels for this experiment approximate ionizing radiation observed on the moon, in low Earth orbit (LEO), and on Earth. Cells from each replicate were passaged to inoculate the next cycle of growth, then samples were taken from each culture to characterize cell morphology, quantify biomass, and extract DNA. Whole genome sequencing from each culture will be used to identify the frequency and types of mutations in each radiation level. In growth cycles 3 and 4, there was a significant increase in biomass accumulation under lunar radiation level compared to LEO or Earth radiation levels. These results such that ionizing radiation affected growth of C. reinhardtii.

Microbiology↗

Continued Environmental Microbiology Monitoring of the International Space Station (ISS) Veggie Unit Used for In-Flight, Crop-Based Food Systems

Crewmembers live and work in a closed environment that is monitored to ensure their health and safety. To ensure occupants’ health and safety during their spaceflight residency, Environmental Health System (EHS) microbial samples including air, surface, and water, are collected, enumerated, and analyzed quarterly to monitor on-board system contamination and potential risks to crew health. Quarterly monitoring of the microorganisms in the ISS environment supports crew safety and contributes to a large set of microbial concentration and diversity data. Based upon data historically collected over the years, in-flight microbial requirements have been established to maintain the health and safety of the spacecraft environment. This study leverages quarterly operational Environmental Health System (EHS) sampling by collecting additional microbial samples from the surface of the station’s Veggie plant production system. Microbial surface samples collected from the Veggie plant production system will yield microbial concentration and diversity that can be compared and analyzed with nominal surface samples from the vehicle. The data collected in this study will aid in the development of requirements for spaceflight-based food production systems. Continued surface sampling of the internal and external surfaces of the Veggie locker, along with collaboration from both Johnson Space Center (JSC) & Kennedy Space Center (KSC) scientists studying the microbiome of the veggie-crop systems, will be implemented as part of the future development of crop-based food system requirements for the ISS and beyond. This presentation will include a review of the study procedures and evaluations of the current results.

Christian Mena↗

Retrospectives: Current State of Knowledge on the Intersection of Spaceflight Stressors and Microbial Risks to Crew and Craft

OVERVIEW The spaceflight environment has several unique stressors that affect the health of both the crew and the spacecraft. An area of continued, albeit incomplete, study is the interaction of these stressors on microbial populations inherent to both astronauts and spacecraft surfaces and systems. A primary concern is the potential for the spaceflight environment to perturb the phenotype of these populations towards negative outcomes for crew and craft. In order to effectively mitigate these potential risks, they must first be characterized. We performed a retrospective literature analysis to assess the current state of knowledge regarding the affects of ionizing radiation and elevated CO2 on relevant microbial populations. The results of these retrospectives will guide next steps in the decisions of what (if any) further studies should be pursued and to guide decisions of the need for countermeasures. STRESSORS Ionizing radiation. The health risk involved with increased exposure to cosmic radiation has been studied in crew for 35+ years, with human health and cancer risk being the main focus. However, space radiation could also affect both the resident microorganisms aboard the ISS and the normal, healthy astronaut microbiomes that are of direct concern for crew health. A retrospective review of over 250 publications was accomplished looking at the impact of cumulative ionizing radiation doses lower than 3 Gy (chronic or acute) on microbial populations. Elevated CO2. The health risk involved with elevated atmospheric CO2 in spacecraft, primarily focusing on human toxicological risks, is understudied. The current Spaceflight Maximum Allowance Concentration for 24-hour average CO2 is 0.4% (3 mm Hg), which is significantly higher than terrestrial levels (0.04%). Whether these elevated ambient CO2 levels aboard spacecraft influence the diversity and phenotypic responses of the resident microbial communities from both the spacecraft environment (air, surface, water) and crew members (gut, nasal, skin microbiomes) is not known. A retrospective review was accomplished looking at the impact of chronic CO2 exposure up to 0.7% (5 mm Hg) for up to 6 months and acute exposure up to 2.6% (20 mm Hg) for up to 24 hours. CONCLUSIONS: MICROBIOME OF THE BUILT ENVIRONMENT The microbiome of the built spacecraft environment has been sampled consistently over the course of human spaceflight and significant advancements have been made in identifying microbial populations on the ISS. The dominant source of microbes on spacecraft surfaces are human-derived. Once in the spacecraft built environment, the extreme environment selects for features that enhance survival. While efforts to understand potential antibiotic resistance and pathogenicity of ISS isolates is robust, there is little to no understanding of which spaceflight environmental stressors, to include ionizing radiation or elevated CO2, drive the evolutionary trajectory of spacecraft-associated microbial populations. CONCLUSIONS: MICROBE-HOST INTERACTIONS The host-microbiome field has emerged as an important factor in human health on Earth as well in spaceflight. The field is struggling with the complexity of the system under investigation as there is substantial taxonomic and functional heterogeneity in these communities, making it difficult to establish clear stimulus-response dynamics. Taxonomic characterization is the norm; however, the functional role of each community member is key to linking environmental perturbations to potential dysbiosis. For both ionizing radiation and elevated CO2, the likely target of the perturbation is the host tissue, not the microbes themselves.. Any resulting changes to the microbial community composition and/or function is likely a result of adapting to those changes in the host physiology. RECOMMENDATIONS Emphasize functional characterization as opposed to taxonomic characterization of microbial communities. Increase the number of investigations using chronic, spaceflight-relevant doses of ionizing radiation. MoBE studies should move away from observational studies towards predictive modeling of community dynamics. Continue to develop scale-down models, such as tissues-on-a-chip & defined microbial communities. Focus on the crew response to elevated CO2 over MoBE considerations. Assess how direct contact with the hypercapnic environment affects skin microbiome dynamics.

retrospective↗

Preliminary Design of a Downstream Processing System for Protein Production in Space

Biomanufacturing is a promising technology to convert in situ resources into essential products including enzymes, therapeutics, biopolymers and other chemicals required to support deep-space missions that may not be easily supplied or produced by alternative means. In addition to the biomass production operations, vital down-stream steps including biomass harvesting/concentration, cell lysis, protein capture and purification are needed to produce an application-ready product. Commercially available terrestrial processes commonly require complex, heavy equipment and highly trained operators, which are not practical in deep space environments. In this work, we aim to identify approaches required to produce an intracellular, His-tagged recombinant enzyme using E. coli at 1 L production scales within the constraints of a deep-space mission as a model use-case scenario. Based on extensive literature review and commercially available products, we identified candidate technologies and products that could be integrated for deep space biomanufacturing. Different preliminary designs were then compared in terms of total system impacts on up-mass, processing time, and consumables required. Our analysis indicated that a biomass concentrator would significantly reduce the processing time and consumables required for the overall system without a large increase in the total mass. We also identified viable technologies for other steps such as cell lysis and protein purification. Predictions from our trade study will be validated in the laboratory by testing the most promising products with the results used to optimize the design. This research will help transfer technology that is well developed on Earth to a space-ready format to produce biological products from a wide variety of microorganisms that can support deep-space missions.

Biomanufacturing↗

Space Environmental Effects on Microbial Growth and Survival

As humanity moves from earth to the moon and beyond, there are many challenges, both known and unknown, which will complicate our path. One unknown variable is how microorganisms will be affected by the space environment, and how this may impact mission success. There is a serious need for greater research to be conducted on how space environments alter microbial organisms genetically and physiologically, and to understand the threats that potential microbial changes may present to future missions.

Chelsi D. Cassilly↗

Characterizing Antibiotic Resistance in Microgravity Environments

The gram-positive bacterium Staphylococcus aureus and the gram-negative Pseudomonas aeruginosa are two of NASA’s designated “medically important microorganisms” commonly co-isolated from spaceflight environments like the International Space Station (ISS). Prior studies demonstrate evidence of increased virulence and antibiotic resistance of each bacterium when grown as single species in space. “Characterizing Antibiotic Resistance in Microgravity Environments” (CARMEn) is an autonomous 30-day ISS payload experiment probing the phenotypic changes of S. aureus and P. aeruginosa biofilms grown together in microgravity. Phenotypic changes are probed through three parallel experiments measuring Extracellular Matrix (ECM) production, antibiotic tolerance, and RNA expression respectively. The ECM experiment uses time-lapse imaging to collect observational morphological data from biofilms stained with Congo Red and Coomassie Blue, the antibiotic tolerance experiment utilizes E-strip testing once samples return to Earth, and RNA expression is measured through RNAseq of samples treated with RNAProtect® during spaceflight.

Antibiotic resistance↗

Development of Computational Environmental Microbiome Workflows for the Laboratory and the International Space Station

Identification of microorganisms in the spaceflight environment is critical for crew health risk assessment on the International Space Station (ISS). Since 2017, nanopore sequencing technology has been used to support thein situ identification of microbial species during spaceflight. Beginning in 2018, a culture-independent, swab-to-sequencer method was implemented onboard the ISS to provide a more thorough insight of the ISS microbiome. Eliminating microbial culture enables identification of difficult-to-culture organisms, reduces risks associated with potentially pathogenic cultures, and could significantly reduce the time from sample-to-answer. However, this molecular-based approach generates large metagenomic datasets that require substantial computational resources for analysis. To process nanopore-generated sequencing data, the JSC Microbiology Laboratory established a bioinformatics workflow on Amazon EC2 under the security guidance of the NASA Science Managed Cloud Environment (SMCE).This resource allows for the development, testing, and accessing of computational tools for processing large and complex datasets. The work described here will address the downlinking of data from the ISS, the automated pipeline developed to identify targeted bacterial and fungal organisms, and the time from sampling onboard to microbial identification. The pipelines have been enhanced to address high and low biomass samples using optimization based on sample source (air, water, or surface) and type of collection (filter, colony, or swab).The resulting microbiome data can be assessed beyond microbial identifications to gain understanding toward population changes over time, potential selective environmental pressures, and evaluating correlations with a wide range of additional data sets. Metagenome analysis pipelines in development could allow for simultaneous identification of microbial species, gene function, and gene pathways present in the environment. Beyond the ground processing, the developed analysis pipeline is currently deployed onboard the ISS to allow for near real-time assessments of the ISS microbiome. This study serves as a critical foundation for exploration missions, where rapid microbiome analyses will be required.

G. Marie Sharp↗

Retrospectives: Intersection of Spaceflight Stressors and Microbial Risk to Crew and Craft

OVERVIEW The spaceflight environment has several unique stressors that affect the health of both the crew and the spacecraft. An area of continued, albeit incomplete, study is the interaction of these stressors on microbial populations inherent to both astronauts and spacecraft surfaces and systems. A primary concern is the potential for the spaceflight environment to perturb the phenotype of these populations towards negative outcomes for crew and craft. In order to effectively mitigate these potential risks, they must first be characterized. We performed a retrospective literature analysis to assess the current state of knowledge regarding the affects of ionizing radiation and elevated CO2 on relevant microbial populations. The results of these retrospectives will guide next steps in the decisions of what (if any) further studies should be pursued and to guide decisions of the need for countermeasures. STRESSORS Ionizing radiation. The health risk involved with increased exposure to cosmic radiation has been studied in crew for 35+ years, with human health and cancer risk being the main focus. However, space radiation could also affect both the resident microorganisms aboard the ISS and the normal, healthy astronaut microbiomes that are of direct concern for crew health. A retrospective review of over 250 publications was accomplished looking at the impact of cumulative ionizing radiation doses lower than 3 Gy (chronic or acute) on microbial populations. Elevated CO2. The health risk involved with elevated atmospheric CO2 in spacecraft, primarily focusing on human toxicological risks, is understudied. The current Spaceflight Maximum Allowance Concentration for 24-hour average CO2 is 0.4% (3 mm Hg), which is significantly higher than terrestrial levels (0.04%). Whether these elevated ambient CO2 levels aboard spacecraft influence the diversity and phenotypic responses of the resident microbial communities from both the spacecraft environment (air, surface, water) and crew members (gut, nasal,skin microbiomes) is not known. A retrospective review was accomplished looking at the impact of chronic CO2 exposure up to 0.7% (5 mm Hg) for up to 6 months and acute exposure up to 2.6% (20 mm Hg) for up to 24 hours. CONCLUSIONS: MICROBIOME OF THE BUILT ENVIRONMENT The microbiome of the built spacecraft environment has been sampled consistently over the course of human spaceflight and significant advancements have been made in identifying microbial populations on the ISS. The dominant source of microbes on spacecraft surfaces are human-derived. Once in the spacecraft built environment,the extreme environment selects for features that enhance survival. While efforts to understand potential antibiotic resistance and pathogenicity of ISS isolates is robust, there is little to no understanding of which spaceflight environmental stressors, to include ionizing radiation or elevated CO2, drive the evolutionary trajectory of spacecraft-associated microbial populations. CONCLUSIONS: MICROBE-HOST INTERACTIONS The host-microbiome field has emerged as an important factor in human health on Earth as well in spaceflight. The field is struggling with the complexity of the system under investigation as there is substantial taxonomic and functional heterogeneity in these communities, making it difficult to establish clear stimulus-response dynamics.Taxonomic characterization is the norm; however, the functional role of each community member is key to linking environmental perturbations to potential dysbiosis. For both ionizing radiation and elevated CO2, the likely target of the perturbation is the host tissue, not the microbes themselves.. Any resulting changes to the microbial community composition and/or function is likely a result of adapting to those changes in the host physiology. RECOMMENDATIONS Emphasize functional characterization as opposed to taxonomic characterization of microbial communities.Increase the number of investigations using chronic, spaceflight-relevant doses of ionizing radiation. MoBE studies should move away from observational studies towards predictive modeling of community dynamics. Continue to develop scale-down models, such as tissues-on-a-chip & defined microbial communities. Focus on the crew response to elevated CO2 over MoBE considerations. Assess how direct contact with the hypercapnic environment affects skin microbiome dynamics.

Countermeasures↗

In-Situ Electrochemical Generation and Utilization of Hydrogen Peroxide for Disinfection

Disinfection needs to meet personal hygiene requirements at the International Space Station (ISS) is currently accomplished through the use of pre-packaged, disposable, wetted wipes, which represent an appreciable carry-along mass and disposal burden. However, as human missions travel further into the solar system the availability of resources to resupply will be diminished. Therefore, next-generation system should use onboard utilities to create on demand disinfectants, thereby reducing the dependence on earth-based supplies and further eliminating storage and disposal problems. Accordingly, we are developing an in-situ approach to electrochemically generate hydrogen peroxide disinfecting solution utilizing onboard life support supplies (Air/Water) to neutralize surface microorganisms present in closed living systems. As discussed within our 2019 and 2021 ICES papers (ICES-2019-38 and ICES-2021-273), we have continued to improve our TRL by scaling the electrochemical generation production process and validating the system in a zero-gravity parabolic loop flight test. In this paper we will demonstrate a system that can achieve over 1 L of >2 w/w% peroxide per day with DI water and air feeds. The hydrogen peroxide solutions generated were sent to NASA for microbial control property characterization. Overall, the electrochemical peroxide generation system offers a more economical and practical alternative, with the disinfectant being generated on demand and in-situ (using available life support materials of Air/Water); and applied to reusable cloths. The specific application of interest to this program is crew contact surfaces in space vehicles, but this technology could be utilized for waste water disinfection, heat exchanger biofouling remediation, and laundry applications. The peroxide generation system will also be able to address Earth-based needs in various settings such as field hospitals, restaurants, military, warehouses, movie theatres, among many others.

hydrogen peroxide↗

EVA Swab Kit: Tools and Techniques for Collecting Aseptic Samples from Crewed Space Missions

Introduction: When we send humans to search for life on other planets, we'll need to know what we brought with us versus what may already be there. To ensure our crewed spacecraft meet planetary protection requirements—and to protect our science from human contamination—we'll need to assess and verify whether micro-organisms may be leaking/venting from our spacesuits. This requires collecting samples under Extravehicular Activity (EVA) conditions. Detailed, systematic research on forward contamination from robotic spacecraft has been steadily progressing since the Viking missions, but systematic studies of contamination from space suits has not been conducted in many years. The modern EMU (Extravehicular Mobility Unit) suit used by NASA is designed to leak at rates as high as 100 cc/min. Before humans land on Mars there is a critical need to understand the types and quantities of microbes that could be introduced via space suits. The Human Forward Contamination Assessment team at NASA’s Johnson Space Center (JSC) has developed a prototype EVA swab tool [1,2,3,4] designed for use in space to sample cleaned and uncleaned space suits to determine the present day microbial load and eventually the rate of leakage. The ability to assess microbial leakage early in advanced space suit and life support system design cycles will help avoid costly hardware redesign later. Test Objectives: The primary objective of EMU testing was to characterize the type of micro-organisms typically found on or near selected suit pressure joints under suit differential pressure conditions. Most human-borne microbes can fit through a 0.5 to 1.0 µm gap. Knowing which joints are more likely to leak will inform hardware design decisions. Knowing which types of micro-organisms may leak from EVA suits provides a basis for subsequent studies to characterize the viability of those organisms under destination conditions, as well as how far they might spread through natural or human-influenced processes. That data, in turn, will inform exploration mission operations and hardware design. The secondary objective of testing was to evaluate the interface between a fully suited test subject and the EVA swab tool at vacuum. Bulky EVA suits can restrict movement and limit visibility through the helmet visor. Fully suited testing is important for identifying tool design issues prior to flight. At exploration destinations, such as Mars, suited crew may be required to periodically sample their suits as part of an environmental monitoring protocol. Suit Microbial Sampling Results: This report details results of microbial swabs collected from current flight suit configurations worn by crew members assigned to upcoming ISS expedition missions as well as swabs collected from prototype suits intended for use on the Orion spacecraft. These tests were intended to characterize the types of contaminants found on flight suits under current, typical handling conditions. No attempt was made to change suit handling procedures, provide additional sterilization, or to limit typical potential contaminant sources. Using culture based techniques, we cultivated 235 CFU (colony forming units) comprised of 26 bacterial species and one fungal species on the outside of the suits. The fungal species and 14 of the bacterial species were unique to the suit surfaces and were not detected in any of the background samples collected within the chambers. We sequenced 755,434 ribosomal fragments on all of the suit surfaces from swab samples. 557,016 of these sequences represent DNA that survived at least 4 hours at vacuum. These sequences formed 2,464 OTU's (Operational Taxonomic Units, 97% similarity) showing low diversity in the samples. The most abundant sequences that survived vacuum belong to the genera Staphyloccocus, Ralstona, Bacillus and Rhodobacter all of which are common to the human microbiome. [5] See Danko et al., (2021) for more complete details of these first analyses. Further analysis of EVA suit materials with respect to the efficacy of various cleaning protocols and engineered containment solutions is planned to inform suit design for NASA’s Artemis Moon to Mars program crew testing. Swab Tool Function Results: The kit was demonstrated for fit and function in suited subject vacuum tests to determine how well the tool worked as an aseptic microbial sampling device as well as to identify any design elements that could be upgraded for EVA task specific improvement. It was found that sample acquisition efficacy could be enhanced by redesign of the sample canister to end-effector interface. Several modifications of the sample caddy assemblies to optimize EVA safety and functionality were also identified. Consequently, fabrication of the redesigned sample canister to end-effector assembly interfaces and and the sample caddy assemblies are required. Fabrication of sixteen flight sample canister assemblies (8 per each of two EVA Swab Kits) and two sample caddy assemblies are in process to be followed by hardware testing and certification to produce two flight-certified EVA Swab Kits for transport to ISS no earlier than summer of 2022. Sampling Strategy: The International Space Station is an ideal testbed for systematic studies of contamination from crewed vehicles since it has been continuously occupied for 20 years and exposed to non-terrestrial conditions. We will sample the exterior of the ISS during EVA using a purpose-built swab tool capable of maintaining sterility while undergoing temperature changes from -151 to +121°C under hard vacuum. Prior to each EVA, the project team will work with ISS mission managers to identify precise sampling locations, which will vary by EVA based on the translation paths and worksites scheduled for that particular EVA. Ideally, translation path handrails and areas near ECLSS (Environmental Control and Life Support System) external vent openings on a spacecraft would be assessed. There are currently more than a dozen ECLSS external vents on the ISS. Some are connected to systems that vent waste products, while others are intended to equalize cabin pressure. As EVA opportunity allows, microbial samples from any of these external vents would provide a valuable data point, though some will be more useful than others. Four criteria have been identified to help prioritize sampling sites near vents: • EVA Accessibility: To minimize cost, it is desired to piggy-back onto a planned EVA. Therefore, the sampling location must be readily accessible by an EVA crew • Type of Vented Products: Vent products that have been in direct contact with crew, such as cabin air, are more likely to contain microorganisms than vent products associated with isolated systems, such as experiment module combustion products. • Mass of Vented Products: Higher-flow vents are more likely to contain detectible levels of microbial contaminants than lower-flow vents. • Local Environment: Sample locations with relatively benign local conditions, such as warm surfaces shielded from direct ultraviolet (UV) radiation exposure, may be more likely to support microbial growth than locations with harsher local environmental conditions. Because EVA accessibility is the most important criteria, the proposal team worked with an astronaut and flight controllers using the Dynamic Onboard Ubiquitous Graphics (DOUG) tool. The DOUG virtual environment allows an operator to “fly” around the current ISS vehicle configuration to assess EVA translation paths, attach points, and keep-out zones. While analysis on station or rapid return to Earth would be preferable, samples collected from the exterior of the ISS have already been exposed to temperature variations between -157 and +121 °C as well as hard vacuum. Therefore, they should be fairly stable and robust. We hypothesize that samples collected from the ISS exterior could be stored for up to 6 months at -80°C without degradation. Sample canisters will be returned to Earth while frozen at -80°C for analysis, and sterilized canisters can be re-flown back to ISS to support additional sampling opportunities Relevance to NASA Exploration Objectives: These data will allow us to identify new or improved methods, technologies, and procedures for spacecraft sterilization and leakage mitigation to minimize the amount of contamination introduced to the environment by human explorers. This work is funded by NASA research grant: NNH18ZDA001N-PPR References: [1] Bell, M.S. et al. (2015) LPS XLVI, Abst. #1832 [2] Rucker et al. (2018) 42nd COSPAR (PPP.3) [3] Bell, M.S. et al. (2019) Mars Extant Life Conference, Abst. #5096.[4] Bell, M.S. et al., (2020) 43rd COSPAR (BO.2).[5] Danko D, et.al.,(2021)Front.Microbiol.12:608478.

Mary Suzanne Bell↗

BioSentinel: NASA’s First Deep Space Biological Mission

Since Apollo 17 in 1972, NASA has sent no humans or other biological organisms outside of Earth’s protective magnetosphere. NASA’s current Artemis program plans to put astronauts back on the Moon and eventually land human missions on Mars. One of the major challenges to long-duration crewed travel and habitation in deep space is an in-depth understanding of the biological effects of space radiation, often convoluted by the impact of reduced gravity. Such missions will require significant countermeasures, likely both technological and biomedical, to protect organisms from chronic radiation exposure. Small satellite missions like CubeSats can inform these countermeasures by investigating model organisms in relevant space environments. The BioSentinel mission is comprised of four segments developed at NASA Ames Research Center: a 6U CubeSat (1U = 10-cm cube), an ISS payload launched in December 2021 and two ground units, one for the mission’s CubeSat and one for the ISS payload. The last three segments have been operational since January 2022 and serve as experimental controls. BioSentinel’s 6U CubeSat is planned to launch as a secondary payload on the Artemis-1 rocket. It will be deployed on a lunar fly-by trajectory and into a heliocentric orbit. BioSentinel will be the first interplanetary satellite to study the biological response to space radiation outside Low Earth Orbit (LEO) in almost 50 years. BioSentinel is a complete, autonomous spacecraft capable of conducting experiments in deep space. Its 4U BioSensor payload is a fully automated and adaptable platform that can perform biological measurements with a range of microorganisms in multiple space environments, including the ISS, free flyers, and other platforms like the Lunar Gateway and lander vehicles. Once it reaches its orbit, BioSentinel’s CubeSat will measure the DNA damage response to ambient radiation in a model organism, the budding yeast Saccharomyces cerevisiae, which will be compared to information provided by an onboard radiation sensor and to data obtained in LEO (on ISS) and on Earth. Once in interplanetary space, fluidic cards containing desiccated yeast will be activated by growth medium addition at different time points throughout the mission. Growth and metabolic activity will be tracked continuously via optical measurements. This paper describes BioSentinel’s objectives, science, data management, and preliminary results from the ISS and ISS ground control segments.

BioSentinel↗