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149 records · Page 9

Enumeration and Fluorescence In Situ Hybridization of Microbial Bioburden on Cleanroom Surfaces

Introduction: Microorganisms are everywhere on Earth, even in the cleanest of places. Spacecraft assembly cleanrooms can harbor low levels of living and dead microbial cells (e.g., [1,2]), and cleanroom bioburden can also include organic molecules from industrial sources and in situ biomass. Life detection missions require careful attention to avoid contaminants that can be easily convoluted with analytical targets. We are evaluating epifluorescent microscopy and fluorescence in situ hybridization (FISH) as methods to complement organic contamination detection techniques. Epifluorescent cell counting offers an accurate and cost-effective way to quantify low levels of surface biomass. FISH could allow for the identification of residual organisms, and can be targeted to detect active populations of specific organisms such as bacteria known to resist cleaning procedures. This effort is part of a larger study that is concentrated on characterizing the surface and airborne molecular organic contamination background in Johnson Space Center (JSC) Astromaterials curation laboratories and Goddard Space Flight Center (GSFC) spacecraft assembly rooms, and understanding contaminants in the context of cleaning procedures and residual bioburden. Methods: Samples were collected by swabbing surfaces in ISO 5 and ISO 7 equivalent cleanrooms at JSC. Swabs for FISH were fixed in 4% paraformaldehyde (PFA) for 3 hours and then stored in 1:1 ethanol:PBS, while swabs for cell counting were stored in 4% PFA until analysis to avoid any cell loss during centrifugation that could impact quantification of very low biomass samples. Cell counting was performed with SYBR Gold as in [3], but adapted for very low biomass. FISH was performed as in [4], using DAPI as a counterstain for all DNA-containing cells. Negative controls included wells with no probe applied, to test for natural fluorescence, as well as the nonsense probe NONEUB (reverse complement of EUB338) to evaluate non-specific probe binding. Results and Discussion: Cleanroom surfaces had 102-103 cells cm-2. The extremely low biomass of these samples was challenging for enumeration, and required careful and routine use of “field” and laboratory blanks. FISH was performed with the general archaeal and bacterial probes ARCH915 and EUB338 (EUBMIX, [4]), probe GAMBET ([4]), and PSE227, which targets the genus Pseudomonas [5]). The latter two probes were selected because Pseudomonas spp. and other Gammaproteobacteria have not been isolated from cleanroom surfaces but do appear frequently in rRNA gene libraries from these surfaces. While some active bacteria were identified (Fig. 1c), most cells detectable by DAPI did not have a strong or any fluorescent signal (e.g., Fig. 1d), indicating that the vast majority of cells are dead or inactive. This suggests that cleaning protocols are effective at inactivating microbial contaminants, but that dead or inactive cells can remain on surfaces. Cells were often clumped in a weakly autofluorescent matrix, possibly biofilm material (Fig. 1c,d). We also observed other particulate material that was collected by the swabs, including apparent textile fibers (Fig. 1b). Our results are consistent with other studies that show that the bioburden present in clean rooms includes active, dormant, and dead cells. We will discuss how FISH and epifluorescent cell counting could be applied in planetary protection protocols, including the advantages and disadvantages of FISH and cell counting for routine use, as well as different possible applications for more specialized FISH procedures. References: [1] Moissl-Eichinger et al. (2015) Sci Rep, 5, 9156 [2] Hendrickson et al. (2021) Microbiome, 9, 238 [3] Jones et al. (2017) Appl Environ Microbiol, 83, e00909-17 [4] Jones et al. (2015) Appl Environ Microbiol, 81, 1242-1250. [5] Watt et al. (2006) Environ Microbiol, 8, 871-884

C J Huff↗

Probiotics in the Space Food System: Delivery, Microgravity Effects, and the Potential Benefit to Crew Health

As mission distance and duration increase, the need grows for non‐invasive disease prevention and immunomodulation, especially given the limited medical response capability expected for these missions and the immune dysregulation documented in crew. Additionally, changes in diet, lifestyle, antibiotic usage, and the environmental stresses during spaceflight may alter crewmembers' intestinal microbiome. The addition of probiotic bacteria to the space food system is expected to confer immunostimulatory benefits on crewmembers, with the potential to counteract the immune dysregulation that has been documented in spaceflight. Based on previous studies that demonstrated unique microbiological responses to the low shear environment of spaceflight, probiotic organisms hold the potential to induce enhanced beneficial responses through mechanisms, such as beneficial interactions with human immune cells and repression of colonization of pathogens on the mucosa. The work presented here will begin to address two research gaps related to providing probiotics in spaceflight: 1) delivery, and 2) the effect of the low shear microgravity environment on probiotic attributes. The probiotic Lactobacillus acidophilus was selected for investigation due to its wide commercial use and documented benefits that include inhibition of virulence related gene expression in pathogens and mucosal stimulation of immune cells. The delivery system for probiotics has not been determined for spaceflight, where the food system is shelf stable and the lack of refrigeration prevents the use of traditional dairy delivery methods. In order to demonstrate the potential of the space food system to deliver viable probiotic bacteria to crewmembers, the probiotic L. acidophilus was packaged in high barrier flight packaging in nonfat dry milk (NFDM) or retained in commercial capsule form. Viable cells were enumerated over 8 months of storage at 22, 4, and ‐80ºC. The survival of L. acidophilus rehydrated in NFDM, in a PBS control, and directly from the capsule was also evaluated following stress challenge with simulated gastric and intestinal juices to determine the method that would deliver the most viable cells to the intestine, where they would be expected to confer beneficial effects. L. acidophilus was found to be stable to gastric and intestinal juice challenge when delivered in rehydrated NFDM, even after two hours of exposure. In comparison, L. acidophilus was reduced by 1‐5 logs when exposed to gastric and intestinal juice directly and when rehydrated in a PBS control. Shelf life data indicated that L. acidophilus would require refrigerated or frozen storage to remain viable at adequate levels over the multi‐year storage periods required for spaceflight. This study suggests that the protective effect provided by the dairy matrix, and not merely rehydration prior to consumption, extends probiotic viability and stress tolerance during storage in spaceflight and in simulated digestion conditions more adequately than a capsule. In addition to effective delivery, it is essential to understand the microgravity effects on the stress tolerances and genetic expression of probiotic bacteria to enable optimization of growth, survival, strain selection, and conferred benefits in spaceflight. In our current study, ground‐based characterization of the growth, stress response, and transcriptomic response of L. acidophilus will be accomplished using the low shear modeled microgravity (LSMMG) culture environment in the rotating wall vessel (RWV). We hypothesize that L. acidophilus will maintain or improve its growth and stress response following culture in the LSMMG environment, and that transcriptomic analysis will define the associated molecular mechanism(s), resulting in the ability to optimize strain selection.

Castro, S. L.↗

Impact of moisture on microbial decomposition phenotypes and enzyme dynamics

Soil organic matter decomposition is a complex process reflecting microbial composition and environmental conditions. Moisture can modulate the connectivity and interactions of microbes. Due to heterogeneity, a deeper understanding of the influence of soil moisture on the dynamics of organic matter decomposition and resultant phenotypes remains a challenge. Soils from a long-term field experiment exposed to high and low moisture treatments were incubated in the laboratory to investigate organic matter decomposition using chitin as a model substrate. By combining enzymatic assays, biomass measurements, and microbial enrichment via activity-based probes, we determined the microbial functional response to chitin amendments and field moisture treatments at both the community and cell scales. Chitinolytic activities showed significant responses to the amendment of chitin, independent of differences in field moisture treatments. However, for other measurements of carbon metabolism and cellular functions, soils from high moisture field treatments had greater potential enzyme activity than soils from low moisture field treatments. A cell tagging approach was used to enrich and quantify bacterial taxa that are actively producing chitin-degrading enzymes. By integrating organism, community, and soil core measurements we show that (i) a small subset of taxa compose the majority (>50%) of chitinase production despite broad functional redundancy, (ii) the identity of key chitin degraders varies with moisture level, and (iii) extracellular enzymes that are not cell-associated account for most potential chitinase activity measured in field soil.

activity-based probes↗

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↗

Bleach Rescues Nannochloropsis from an Obligate Parasite and Alters Microbial and Metabolite Signatures of Outdoor Cultures

Chemical agents are commonly used to protect algal crops. Yet, few studies have characterized the effects of these agents on associated microbial communities to understand effects on microbial functions relevant to algal crop production and protection. Here, we used shotgun metagenomic sequencing and untargeted exometabolite profiling to link the application of bleach, a -cidal agent used to protect algae from pests, to changes in community composition, metabolic pathways, and exometabolies - at a whole community level. Bleach protected the algal crop from crashing but altered bacterial diversity. Analysis of metagenome-assembled genomes (MAGs) revealed a classic predator-prey cycle between Oligoflexus and our target alga Nannochloropsis. Olifoflexus genomes from our study were notably similar to a previously identified BALO (Bdellovibrio and like organism), FD111, known to kill Nannochloropsis cultures, providing strong evidence that an FD111-like organism was responsible for the crash. Metabolic pathway composition differed between bleached and unbleached ponds, with abundance of twelve pathways related to stress tolerance, including the superpathway of methylglyoxal degradation, lipid IVA biosynthesis, and ectoine biosynthesis, greater in bleached ponds compared to unbleached ponds. Virulence factors related to adherence, biofilm formation, motility, and pathogenicity increased dramatically in bleached ponds with time, although this increase was not coupled with an increase in pathogens - algal or otherwise - or a decline in algal health. Our study highlights the importance of coupling 16S rRNA gene sequencing with whole genome data and other -omics tools to sketch a larger picture of community structure and function in crop systems. Moreover, our results highlight that continued long-term bleaching may lead to negative effects to crop health or downstream adverse health effects to humans or animals, depending on the algal product (i.e. human supplements or animal feedstocks). Future work on alternative treatment methods that would reduce resistance is necessary in the field.

09 BIOMASS FUELS↗