Setting a standard: the limulus amebocyte lysate assay and the assessment of microbial contamination on spacecraft surfaces

Field-Based Planetary Protection Operations for Melt Probes: Validation of Clean Access into the Blood Falls, Antarctica, Englacial Ecosystem

Subglacial environments on Earth offer important analogs to Ocean World targets in our solar system. These unique microbial ecosystems remain understudied due to the challenges of access through thick glacial ice (tens to hundreds of meters). Additionally, sub-ice collections must be conducted in a clean manner to ensure sample integrity for downstream microbiological and geochemical analyses. We describe the field-based cleaning of a melt probe that was used to collect brine samples from within a glacier conduit at Blood Falls, Antarctica, for geomicrobiological studies. We used a thermoelectric melting probe called the IceMole that was designed to be minimally invasive in that the logistical requirements in support of drilling operations were small and the probe could be cleaned, even in a remote field setting, so as to minimize potential contamination. In our study, the exterior bioburden on the IceMole was reduced to levels measured in most clean rooms, and below that of the ice surrounding our sampling target. Potential microbial contaminants were identified during the cleaning process; however, very few were detected in the final englacial sample collected with the IceMole and were present in extremely low abundances (∼0.063% of 16S rRNA gene amplicon sequences). This cleaning protocol can help minimize contamination when working in remote field locations, support microbiological sampling of terrestrial subglacial environments using melting probes, and help inform planetary protection challenges for Ocean World analog mission concepts.

Metagenomic Methods for Addressing NASA's Planetary Protection Policy Requirements on Future Missions: A Workshop Report

Molecular biology methods and technologies have advanced substantially over the past decade. These new molecular methods should be incorporated among the standard tools of planetary protection (PP) and could be validated for incorporation by 2026. To address the feasibility of applying modern molecular techniques to such an application, NASA conducted a technology workshop with private industry partners, academics, and government agency stakeholders, along with NASA staff and contractors. The technical discussions and presentations of the Multi-Mission Metagenomics Technology Development Workshop focused on modernizing and supplementing the current PP assays. The goals of the workshop were to assess the state of metagenomics and other advanced molecular techniques in the context of providing a validated framework to supplement the bacterial endospore-based NASA Standard Assay and to identify knowledge and technology gaps. In particular, workshop participants were tasked with discussing metagenomics as a stand-alone technology to provide rapid and comprehensive analysis of total nucleic acids and viable microorganisms on spacecraft surfaces, thereby allowing for the development of tailored and cost-effective microbial reduction plans for each hardware item on a spacecraft. Workshop participants recommended metagenomics approaches as the only data source that can adequately feed into quantitative microbial risk assessment models for evaluating the risk of forward (exploring extraterrestrial planet) and back (Earth harmful biological) contamination. Participants were unanimous that a metagenomics workflow, in tandem with rapid targeted quantitative (digital) PCR, represents a revolutionary advance over existing methods for the assessment of microbial bioburden on spacecraft surfaces. The workshop highlighted low biomass sampling, reagent contamination, and inconsistent bioinformatics data analysis as key areas for technology development. Finally, it was concluded that implementing metagenomics as an additional workflow for addressing concerns of NASA's robotic mission will represent a dramatic improvement in technology advancement for PP and will benefit future missions where mission success is affected by backward and forward contamination.

Solid-Phase Microextraction for Organic Contamination Control Throughout Assembly and Operational Phases of Space Missions

Space missions concerned with life detection contain highly sensitive instruments for the detection of organics. Terrestrial contamination can interfere with signals of indigenous organics in samples and has the potential to cause false-positive biosignature detections, which may lead to incorrect suggestions of the presence of life elsewhere in the solar system. This study assessed the capability of solid-phase microextraction (SPME) as a method for monitoring organic contamination encountered by spacecraft hardware during assembly and operation. SPME-gas chromatography-mass spectrometry (SPME-GC-MS) analysis was performed on potential contaminant source materials, which are commonly used in spacecraft construction. The sensitivity of SPME-GC-MS to organics was assessed in the context of contaminants identified in molecular wipes taken from hardware surfaces on the ExoMars Rosalind Franklin rover. SPME was found to be effective at detecting a wide range of common organic contaminants that include aromatic hydrocarbons, aliphatic hydrocarbons, nitrogen-containing compounds, alcohols, and carbonyls. A notable example of correlation of contaminant with source material was the detection of benzenamine compounds in an epoxy adhesive analyzed by SPME-GC-MS and in the ExoMars rover surface wipe samples. The current form of SPME-GC-MS does not enable quantitative evaluation of contaminants, nor is it suitable for the detection of every group of organic molecules relevant to astrobiological contamination concerns, namely large and/or polar molecules such as amino acids. However, it nonetheless represents an effective new monitoring method for rapid, easy identification of organic contaminants commonly present on spacecraft hardware and could thus be utilized in future space missions as part of their contamination control and mitigation protocols.

Evaluating Quantitative Measures of Microbial Contamination from China's Spacecraft Materials

Different methods are used for the quantification of microbial load on spacecrafts. Here, we investigated a number of methodologies currently in use with the intent to identify the most accurate methods for the quantification of microbes on low-biomass metal surfaces such as those used in China's Space Station. In a previous study, we observed a high abundance of Bacillus sp. TJ 1-1 on interior surfaces of China's Space Station, and we therefore undertook this study in which we used a range of 10² to 10⁹ cells/100 cm² of this strain for setting different contamination levels. Four of the most common analytical approaches (contact plate, spread plate, quantitative PCR, and BacLight™) were used to quantify the number of viable microbial cells associated with the materials of China's Space Station. Results show that, for 10² cells/100 cm², the contact plate method is the most convenient and reliable. For microbial contamination levels ≥10³ cells/100 cm² and a sampling area of 121 cm², the BacLight method proved to be most reliable for the detection of live cells. Moreover, a sampling area of 121 cm² was found to be the most suitable for analysis of metal surfaces for space station interiors, which are usually low in biomass. These results establish suitable sampling and processing methodologies for microbial enumeration of metal surfaces on China's Space Station.

Solid Phase Micro Extraction: Potential for Organic Contamination Control for Planetary Protection of Life-Detection Missions to the Icy Moons of the Outer Solar System

Conclusively detecting, or ruling out the possibility of, life on the icy moons of the outer Solar System will require spacecraft missions to undergo rigorous planetary protection and contamination control procedures to achieve extremely low levels of organic terrestrial contamination. Contamination control is necessary to avoid forward contamination of the body of interest and to avoid the detection of false-positive signals, which could either mask indigenous organic chemistry of interest or cause an astrobiological false alarm. Here we test a new method for rapidly and inexpensively assessing the organic cleanliness of spaceflight hardware surfaces using solid phase micro extraction (SPME) fibers to directly swab surfaces. The results suggest that the method is both time and cost efficient. The SPME-gas chromatography-mass spectrometry (SPME-GC-MS) method is sensitive to common midweight, nonpolar contaminant compounds, for example, aliphatic and aromatic hydrocarbons, which are common contaminants in laboratory settings. While we demonstrate the potential of SPME for surface sampling, the GC-MS instrumentation restricts the SPME-GC-MS technique's sensitivity to larger polar and nonvolatile compounds. Although not used in this study, to increase the potential range of detectable compounds, SPME can also be used in conjunction with high-performance liquid chromatography/liquid chromatography-mass spectrometry systems suitable for polar analytes (Kataoka et al., 2000). Thus, our SPME method presents an opportunity to monitor organic contamination in a relatively rapid and routine way that produces information-rich data sets.

The Photochemistry of Unprotected DNA and DNA inside Bacillus subtilis Spores Exposed to Simulated Martian Surface Conditions of Atmospheric Composition, Temperature, Pressure, and Solar Radiation

DNA is considered a potential biomarker for life-detection experiments destined for Mars. Experiments were conducted to examine the photochemistry of bacterial DNA, either unprotected or within Bacillus subtilis spores, in response to exposure to simulated martian surface conditions consisting of the following: temperature (-10°C), pressure (0.7 kPa), atmospheric composition [CO₂ (95.54%), N₂ (2.7%), Ar (1.6%), O₂ (0.13%), and H₂O (0.03%)], and UV-visible-near IR solar radiation spectrum (200-1100 nm) calibrated to 4 W/m² of UVC (200-280 nm). While the majority (99.9%) of viable spores deposited in multiple layers on spacecraft-qualified aluminum coupons were inactivated within 5 min, a detectable fraction survived for up to the equivalent of ∼115 martian sols. Spore photoproduct (SP) was the major lesion detected in spore DNA, with minor amounts of cyclobutane pyrimidine dimers (CPD), in the order TT CPD > TC CPD >> CT CPD. In addition, the (6-4)TC, but not the (6-4)TT, photoproduct was detected in spore DNA. When unprotected DNA was exposed to simulated martian conditions, all photoproducts were detected. Surprisingly, the (6-4)TC photoproduct was the major photoproduct, followed by SP ∼ TT CPD > TC CPD > (6-4)TT > CT CPD > CC CPD. Differences in the photochemistry of unprotected DNA and spore DNA in response to simulated martian surface conditions versus laboratory conditions are reviewed and discussed. The results have implications for the planning of future life-detection experiments that use DNA as the target, and for the long-term persistence on Mars of forward contaminants or their DNA. Key Words: Bacillus subtilis-DNA-Mars-Photochemistry-Spore-Ultraviolet. Astrobiology 18, 393-402.

Genetic engineering approach to develop next-generation reagents for endotoxin quantification

The bacterial endotoxin test, which uses amebocyte lysate reagents of horseshoe crab origin, is a sensitive, reproducible and simple assay to measure endotoxin concentration. To develop sustainable raw materials for lysate reagents that do not require horseshoe crabs, three recombinant protease zymogens (factor C, derived from mammalian cells; factor B; and the proclotting enzyme derived from insect cells) were prepared using a genetic engineering technique. Recombinant cascade reagents (RCRs) were then prepared to reconstruct the reaction cascade in the amebocyte lysate reagent. The protease activity of the RCR containing recombinant factor C was much greater than that of recombinant factor C alone, indicating the efficiency of signal amplification in the cascade. Compared with the RCR containing the insect cell-derived factor C, those containing mammalian cell-derived factor C, which features different glycosylation patterns, were less susceptible to interference by the injectable drug components. The standard curve of the RCR containing mammalian cell-derived recombinant factor C had a steeper slope than the curves for those containing natural lysate reagents, suggesting a greater sensitivity to endotoxin. The present study supports the future production of recombinant reagents that do not require the use of natural resources.

Application of the ATP assay to rapidly assess cleanliness of spacecraft surfaces: a path to set a standard for future missions

The National Aeronautics and Space Administration (NASA) measures and validates the biological cleanliness of spacecraft surfaces by counting endospores using the NASA standard assay (NSA). NASA has also approved an adenosine-5'-triphosphate (ATP)-based detection methodology as a means to prescreen surfaces for the presence of microbial contamination, prior to the spore assay. During Mars Science Laboratory (MSL) spacecraft assembly, test, and launch operations, 4853 surface samples were collected to verify compliance with the bioburden requirement at launch. A subset of these samples was measured for microbial cleanliness using both the NSA (n = 272) and ATP assay (n = 249). NSA results revealed that ~8% (22/272) of the samples showed the presence of at least one spore, whereas ATP assay measurements indicated that ~15% (35/249) of samples exceeded the "threshold cleanliness limit" of 2.3 × 10^-11 mmol ATP per 25 cm² used by MSL. Of the 22 NSA samples with a spore, 18% (4/22) were considered above the level of acceptance by both techniques. Based on post launch data analysis presented here, it was determined that this threshold cleanliness limit of 2.3 × 10^-11 mmol ATP per 25 cm² could be adopted as a benchmark for assessing spacecraft surface cleanliness. This study clearly demonstrates the value of using alternative methods to rapidly assess spacecraft cleanliness, and provides useful information regarding the process.

In vitro human fecal microbial metabolism of Forsythoside A and biological activities of its metabolites

The present study aimed to investigate the metabolism of Forsythoside A (FTA) by human fecal bacteria to clarify the relationship between its intestinal metabolism and its pharmacological activities. FTA was incubated with human fecal microflora in vitro to investigate its metabolic process, and highly sensitive and specific ultra-performance liquid chromatography/quadrupole time-of-flight mass spectrometry (UPLC-Q-TOF/MS) was performed using MetaboLynx software for metabolite analysis. Caffeic acid (CA) and hydroxytyrosol (HT) were obtained by hydrolysis of FTA, and CA was further hydrogenated to form 3,4-dihydroxybenzenepropionic acid (DCA). The anticomplementary, antimicrobial and antiendotoxin activities of FTA and its metabolites by human fecal microflora were evaluated in vitro with a hemolysis assay, the agar disc-diffusion method, the MIC value and the gel clot LAL assay, respectively. The metabolites showed higher biological activity than FTA, especially HT and DCA. Orally administered FTA may be metabolized to HT and DCA, and the pharmacological effects of FTA may be dependent on intestinal bacterial metabolism.

Polythiophene biosensor for rapid detection of microbial particles in water

Most microbial particles have a negatively charged surface and in this work, we describe a water quality monitoring application of a cationic polythiophene derivative (AH-35) for the rapid assessment of microbial contamination of water. Using E. coli as a prototype microbial particle, we demonstrate that the AH-35 polymer can provide a qualitative assessment of water if exposed to more than 500 CFU/mL, thereby paving the way to a new family of biosensors potentially useful for monitoring drinking water distribution systems.

Contamination of nanoparticles by endotoxin: evaluation of different test methods

Background

Nanomaterials can be contaminated with endotoxin (lipopolysaccharides, LPS) during production or handling. In this study, we searched for a convenient in vitro method to evaluate endotoxin contamination in nanoparticle samples. We assessed the reliability of the commonly used limulus amebocyte lysate (LAL) assay and an alternative method based on toll-like receptor (TLR) 4 reporter cells when applied with particles (TiO₂, Ag, CaCO₃ and SiO₂), or after extraction of the endotoxin as described in the ISO norm 29701.

Results

Our results indicate that the gel clot LAL assay is easily disturbed in the presence of nanoparticles; and that the endotoxin extraction protocol is not suitable at high particle concentrations. The chromogenic-based LAL endotoxin detection systems (chromogenic LAL assay and Endosafe-PTS), and the TLR4 reporter cells were not significantly perturbed.

Conclusion

We demonstrated that nanoparticles can interfere with endotoxin detection systems indicating that a convenient test method must be chosen before assessing endotoxin contamination in nanoparticle samples.

Rapid culture-independent microbial analysis aboard the international space station (ISS) stage two: quantifying three microbial biomarkers

Abstract A portable, rapid, microbial detection unit, the Lab-On-a-Chip Application Development Portable Test System (LOCAD-PTS), was launched to the International Space Station (ISS) as a technology demonstration unit in December 2006. Results from the first series of experiments designed to detect Gram-negative bacteria on ISS surfaces by quantifying a single microbial biomarker lipopolysaccharide (LPS) were reported in a previous article. Herein, we report additional technology demonstration experiments expanding the on-orbit capabilities of the LOCAD-PTS to detecting three different microbial biomarkers on ISS surfaces. Six different astronauts on more than 20 occasions participated in these experiments, which were designed to test the new beta-glucan (fungal cell wall molecule) and lipoteichoic acid (LTA; Gram-positive bacterial cell wall component) cartridges individually and in tandem with the existing Limulus Amebocyte Lysate (LAL; Gram-negative bacterial LPS detection) cartridges. Additionally, we conducted the sampling side by side with the standard culture-based detection method currently used on the ISS. Therefore, we present data on the distribution of three microbial biomarkers collected from various surfaces in every module present on the ISS at the time of sampling. In accordance with our previous experiments, we determined that spacecraft surfaces known to be frequently in contact with crew members demonstrated higher values of all three microbial molecules. Key Words: Planetary protection-Spaceflight-Microbiology-Biosensor. Astrobiology 12, 830-840.