Search NASA⌕ Search

SEARCH · Search NASA

Results for “Taxonomic”

Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 181 records · Page 10

Novel Thermotolerant Siderophilic Filamentous Cyanobacterium that Produces Intracellular Iron-Rich Phases

Cyanobacteria are the main producers of organic compounds in iron-depositing hot springs despite photosynthetically generated-oxygen and the abundance of reduced iron (Fe2+) that likely leads to enormous oxidative stress within cyanobacterial cells. Therefore, the study of cyanobacterial diversity, phylogeny, and biogeochemical activity in iron-depositing hot springs will not only provide insights into the contribution of CB to iron redox cycling in these environments, but it could also provide insights into CB evolution. This study characterizes the phylogeny, morphology, and physiology of isolate JSC-1, a novel filamentous CB isolated from an iron-depositing hot spring. While isolate JSC-1 is morphologically similar to the CB genus Leptolyngbya, 16S rDNA sequence data indicated that it shares 95 percent sequence similarity to the type strain L. boryanum. Strain JSC-1 fixes N2 and exhibited an unusually high ratio between photosystem (PS) I and PS II and was capable of complementary chromatic adaptation. Further, it synthesized only chlorophyll a and a unique set of carotenoids. Strain JSC-1 not only required high levels of Fe for growth (greater than or equal to 40 microM), but it also accumulated large amounts of extracellular ferrihydrite and generated intracellular ferric phosphates. Strain JSC-1 was found to secrete 2-oxoglutaric acid and possesses one ortholog and one paralog of bacterioferritin. Surprisingly, the latter has 70.13 % identity with a bacterioferritin in marine-proteobacterium HTCC 2080 and has joint node with bacterioferritins found in enterobacteria. Collectively, these observations provide insights into the physiological strategies that might have allowed CB to develop and proliferate in Fe-rich environments. Based on its genotypic and phenotypic characterization of strain, JSC-1 represents a new operational taxonomical unit (OTU) JSC-1.

Broun, Igor I.↗

[Characterization of Black and Dichothrix Cyanobacteria Based on the 16S Ribosomal RNA Gene Sequence]

My project focuses on characterizing different cyanobacteria in thrombolitic mats found on the island of Highborn Cay, Bahamas. Thrombolites are interesting ecosystems because of the ability of bacteria in these mats to remove carbon dioxide from the atmosphere and mineralize it as calcium carbonate. In the future they may be used as models to develop carbon sequestration technologies, which could be used as part of regenerative life systems in space. These thrombolitic communities are also significant because of their similarities to early communities of life on Earth. I targeted two cyanobacteria in my research, Dichothrix spp. and whatever black is, since they are believed to be important to carbon sequestration in these thrombolitic mats. The goal of my summer research project was to molecularly identify these two cyanobacteria. DNA was isolated from each organism through mat dissections and DNA extractions. I ran Polymerase Chain Reactions (PCR) to amplify the 16S ribosomal RNA (rRNA) gene in each cyanobacteria. This specific gene is found in almost all bacteria and is highly conserved, meaning any changes in the sequence are most likely due to evolution. As a result, the 16S rRNA gene can be used for bacterial identification of different species based on the sequence of their 16S rRNA gene. Since the exact sequence of the Dichothrix gene was unknown, I designed different primers that flanked the gene based on the known sequences from other taxonomically similar cyanobacteria. Once the 16S rRNA gene was amplified, I cloned the gene into specialized Escherichia coli cells and sent the gene products for sequencing. Once the sequence is obtained, it will be added to a genetic database for future reference to and classification of other Dichothrix sp.

Ortega, Maya↗

Isolation of the Paenibacillus phoenicis, a Spore-Forming Bacterium

A microorganism was isolated from the surfaces of the cleanroom facility in which the Phoenix lander was assembled. The isolated bacterial strain was subjected to a comprehensive polyphasic analysis to characterize its taxonomic position. Both phenotypic and phylogenetic analyses clearly indicate that this isolate belongs to the genus Paenibacillus and represents a novel species. Bacillus spores have been utilized to assess the degree and level of microbiological contamination on spacecraft and their associated spacecraft assembly facilities. Spores of Bacillus species are of particular concern to planetary protection due to the extreme resistance of some members of the genus to space environmental conditions such as UV and gamma radiation, vacuum, oxidation, and temperature fluctuation. These resistive spore phenotypes have enhanced potential for transfer, and subsequent proliferation, of terrestrial microbes on another solar body. Due to decreased nutrient conditions within spacecraft assembly facility clean rooms, the vegetative cells of Bacillus species and other spore-forming Paenibacillus species are induced to sporulate, thereby enhancing their survivability of bioreduction

Benardini, James N.↗

Characterization of Hayabusa II Target Asteroid (162173) 1999 JU3

The Japanese Hayabusa II mission is planned to rendezvous with and return a sample from the near-Earth asteroid (162173) 1999 JU3. Previous mid-infrared studies have constrained the albedo and thermal properties of this object (Muller et al. 2011; Campins et al. 2011; Hasegawa et al. 2008). Visible wavelength spectra from 1999 and 2007 reveal a C-type asteroid that displays pronounced spectroscopic variability around 0.7 microns. Variability in the strength of a 0.7 micron band could be due to heterogeneous concentrations of iron-bearing phyllosilicates across its surface (Vilas 2008). We will present new observations from the favorable 2012 apparition to further characterize this object. In June of 2012 spectroscopic observations were conducted with the LDSS3 and FIRE instruments on the Magellan telescopes at Las Campanas Observatory in Chile. Between April and July of 2012 broadband visible-wavelength photometry was obtained with the Tenagra II telescope in Arizona and with the IMACS, Megacam and LDSS3 instruments on the Magellan telescopes. Our visible and near-infrared spectra confirm a C-type taxonomic classification, but do not show evidence for the presence of a 0.7 micron phyllosilicate band. Our time series of visible spectra cover approximately 60% of the rotational phases of 1999 JU3, but do not display any pronounced variability. We use our new optical light curves, combined with photometry from 2007, to refine a shape model of the asteroid. This shape model provides a means for mapping surface regions accessed by the spectroscopic observations from both 2007 and 2012, and thus to directly address the possibility of surface heterogeneity. This surface map, in conjunction with the newly measured photometric phase curve of the asteroid, will be used to make predictions regarding composition and surface properties that will ultimately be tested upon arrival of the Hayabusa II spacecraft.

Moskovitz, Abe↗

Extreme Ionizing-Radiation-Resistant Bacterium

There is a growing concern that desiccation and extreme radiation-resistant, non-spore-forming microorganisms associated with spacecraft surfaces can withstand space environmental conditions and subsequent proliferation on another solar body. Such forward contamination would jeopardize future life detection or sample return technologies. The prime focus of NASA s planetary protection efforts is the development of strategies for inactivating resistance-bearing microorganisms. Eradification techniques can be designed to target resistance-conferring microbial populations by first identifying and understanding their physiologic and biochemical capabilities that confers its elevated tolerance (as is being studied in Deinococcus phoenicis, as a result of this description). Furthermore, hospitals, food, and government agencies frequently use biological indicators to ensure the efficacy of a wide range of radiation- based sterilization processes. Due to their resistance to a variety of perturbations, the non-spore forming D. phoenicis may be a more appropriate biological indicator than those currently in use. The high flux of cosmic rays during space travel and onto the unshielded surface of Mars poses a significant hazard to the survival of microbial life. Thus, radiation-resistant microorganisms are of particular concern that can survive extreme radiation, desiccation, and low temperatures experienced during space travel. Spore-forming bacteria, a common inhabitant of spacecraft assembly facilities, are known to tolerate these extreme conditions. Since the Viking era, spores have been utilized to assess the degree and level of microbiological contamination on spacecraft and their associated spacecraft assembly facilities. Members of the non-spore-forming bacterial community such as Deinococcus radiodurans can survive acute exposures to ionizing radiation (5 kGy), ultraviolet light (1 kJ/sq m), and desiccation (years). These resistive phenotypes of Deinococcus enhance the potential for transfer, and subsequent proliferation, on another solar body such as Mars and Europa. These organisms are more likely to escape planetary protection assays, which only take into account presence of spores. Hence, presences of extreme radiation-resistant Deinococcus in the cleanroom facility where spacecraft are assembled pose a serious risk for integrity of life-detection missions. The microorganism described herein was isolated from the surfaces of the cleanroom facility in which the Phoenix Lander was assembled. The isolated bacterial strain was subjected to a comprehensive polyphasic analysis to characterize its taxonomic position. This bacterium exhibits very low 16SrRNA similarity with any other environmental isolate reported to date. Both phenotypic and phylogenetic analyses clearly indicate that this isolate belongs to the genus Deinococcus and represents a novel species. The name Deinococcus phoenicis was proposed after the Phoenix spacecraft, which was undergoing assembly, testing, and launch operations in the spacecraft assembly facility at the time of isolation. D. phoenicis cells exhibited higher resistance to ionizing radiation (cobalt-60; 14 kGy) than the cells of the D. radiodurans (5 kGy). Thus, it is in the best interest of NASA to thoroughly characterize this organism, which will further assess in determining the potential for forward contamination. Upon the completion of genetic and physiological characteristics of D. phoenicis, it will be added to a planetary protection database to be able to further model and predict the probability of forward contamination.

Vaishampayan, Parag A.↗

Extreme Ionizing-Radiation-Resistant Bacterium

There is a growing concern that desiccation and extreme radiation-resistant, non-spore-forming microorganisms associated with spacecraft surfaces can withstand space environmental conditions and subsequent proliferation on another solar body. Such forward contamination would jeopardize future life detection or sample return technologies. The prime focus of NASA s planetary protection efforts is the development of strategies for inactivating resistance-bearing micro-organisms. Eradi cation techniques can be designed to target resistance-conferring microbial populations by first identifying and understanding their physiologic and biochemical capabilities that confers its elevated tolerance (as is being studied in Deinococcus phoenicis, as a result of this description). Furthermore, hospitals, food, and government agencies frequently use biological indicators to ensure the efficacy of a wide range of radiation-based sterilization processes. Due to their resistance to a variety of perturbations, the nonspore forming D. phoenicis may be a more appropriate biological indicator than those currently in use. The high flux of cosmic rays during space travel and onto the unshielded surface of Mars poses a significant hazard to the survival of microbial life. Thus, radiation-resistant microorganisms are of particular concern that can survive extreme radiation, desiccation, and low temperatures experienced during space travel. Spore-forming bacteria, a common inhabitant of spacecraft assembly facilities, are known to tolerate these extreme conditions. Since the Viking era, spores have been utilized to assess the degree and level of microbiological contamination on spacecraft and their associated spacecraft assembly facilities. Members of the non-sporeforming bacterial community such as Deinococcus radiodurans can survive acute exposures to ionizing radiation (5 kGy), ultraviolet light (1 kJ/m2), and desiccation (years). These resistive phenotypes of Deinococcus enhance the potential for transfer, and subsequent proliferation, on another solar body such as Mars and Europa. These organisms are more likely to escape planetary protection assays, which only take into account presence of spores. Hence, presences of extreme radiation-resistant Deinococcus in the cleanroom facility where spacecraft are assembled pose a serious risk for integrity of life-detection missions. The microorganism described herein was isolated from the surfaces of the cleanroom facility in which the Phoenix Lander was assembled. The isolated bacterial strain was subjected to a comprehensive polyphasic analysis to characterize its taxonomic position. This bacterium exhibits very low 16SrRNA similarity with any other environmental isolate reported to date. Both phenotypic and phylogenetic analyses clearly indicate that this isolate belongs to the genus Deinococcus and represents a novel species. The name Deinococcus phoenicis was proposed after the Phoenix spacecraft, which was undergoing assembly, testing, and launch operations in the spacecraft assembly facility at the time of isolation. D. phoenicis cells exhibited higher resistance to ionizing radiation (cobalt-60; 14 kGy) than the cells of the D. radiodurans (5 kGy). Thus, it is in the best interest of NASA to thoroughly characterize this organism, which will further assess in determining the potential for forward contamination. Upon the completion of genetic and physiological characteristics of D. phoenicis, it will be added to a planetary protection database to be able to further model and predict the probability of forward contamination.

Vaishampayan, Parag A.↗

Multiple Asteroid Systems: Dimensions and Thermal Properties from Spitzer Space Telescope and Ground-based Observations

We collected mid-IR spectra from 5.2 to 38 microns using the Spitzer Space Telescope Infrared Spectrograph of 28 asteroids representative of all established types of binary groups. Photometric light curves were also obtained for 14 of them during the Spitzer observations to provide the context of the observations and reliable estimates of their absolute magnitudes. The extracted mid-IR spectra were analyzed using a modified standard thermal model (STM) and a thermophysical model (TPM) that takes into account the shape and geometry of the large primary at the time of the Spitzer observation. We derived a reliable estimate of the size, albedo, and beaming factor for each of these asteroids, representing three main taxonomic groups: C, S, and X. For large (volume-equivalent system diameter Deq > 130 km) binary asteroids, the TPM analysis indicates a low thermal inertia (Lambda < or = approx.100 J/1/2 s/K/sq m2) and their emissivity spectra display strong mineral features, implying that they are covered with a thick layer of thermally insulating regolith. The smaller (surface-equivalent system diameter Deff < 17 km) asteroids also show some emission lines of minerals, but they are significantly weaker, consistent with regoliths with coarser grains, than those of the large binary asteroids. The average bulk densities of these multiple asteroids vary from 0.7-1.7 g/cu cm (P-, C-type) to approx. 2 g/cu cm (S-type). The highest density is estimated for the M-type (22) Kalliope (3.2 +/- 0.9 g/cu cm). The spectral energy distributions (SEDs) and emissivity spectra, made available as a supplement document, could help to constrain the surface compositions of these asteroids.

Marchis, F.↗

Locating Noctiluca Miliaris in the Arabian Sea: An Optical Proxy Approach

Coincident with shifting monsoon weather patterns over India, the phytoplankter Noctiluca miliaris has recently been observed to be dominating phytoplankton blooms in the northeastern Arabian Sea during the winter monsoons. Identifying the exact environmental and/or ecological conditions that favor this species has been hampered by the lack of concurrent environmental and biological observations on time and space scales relevant to ecologic and physiologic processes. We present a bio-optical proxy for N. miliaris measured on highly resolved depth scales coincident with hydrographic observations with the goal to identify conducive hydrographic conditions for the bloom. The proxy is derived from multichannel excitation chlorophyll a fluorescence and is validated with microscopy, pigment composition, and spectral absorption. Phytoplankton populations dominated by either diatoms or other dinoflagellates were additionally discerned. N. miliaris populations in full bloom were identified offshore in low-nutrient and low-N : P ratio surface waters within a narrow temperature and salinity range. These populations transitioned to high-biomass diatom-dominated coastal upwelling populations. A week later, the N. miliaris blooms were observed in declining phase, transitioning to very-low-biomass populations of non-N. miliaris dinoflagellates. There were no clear hydrographic conditions uniquely associated with the N. miliaris populations, although N. miliaris was not found in the upwelling or extremely oligotrophic waters. Taxonomic transitions were not discernible in the spatial structure of the bloom as identified by the ocean color Chl imagery, indicating that in situ observations may be necessary to resolve community structure, particularly for populations below the surface.

Arabian Sea↗

Phase-Angle Dependence of Determinations of Diameter, Albedo, and Taxonomy: A Case Study of NEO 3691 Bede

Parameters important for NEO risk assessment and mitigation include Near-Earth Object diameter and taxonomic classification, which translates to surface composition. Diameters of NEOs are derived from the thermal fluxes measured by WISE, NEOWISE, Spitzer Warm Mission and ground-based telescopes including the IRTF and UKIRT. Diameter and its coupled parameters Albedo and IR beaming parameter (a proxy for thermal inertia and/or surface roughness) are dependent upon the phase angle, which is the Sun-target-observer angle. Orbit geometries of NEOs, however, typically provide for observations at phase angles greater than 20 degrees. At higher phase angles, the observed thermal emission is sampling both the day and night sides of the NEO. We compare thermal models for NEOs that exclude (NEATM) and include (NESTM) night-side emission. We present a case study of NEO 3691 Bede, which is a higher albedo object, X (Ec) or Cgh taxonomy, to highlight the range of H magnitudes for this object (depending on the albedo and phase function slope parameter G), and to examine at different phase angles the taxonomy and thermal model fits for this NEO. Observations of 3691 Bede include our observations with IRTF+SpeX and with the 10 micrometer UKIRT+Michelle instrument, as well as WISE and Spitzer Warm mission data. By examining 3691 Bede as a case study, we highlight the interplay between the derivation of basic physical parameters and observing geometry, and we discuss the uncertainties in H magnitude, taxonomy assignment amongst the X-class (P, M, E), and diameter determinations. Systematic dependencies in the derivation of basic characterization parameters of H-magnitude, diameter, albedo and taxonomy with observing geometry are important to understand. These basic characterization parameters affect the statistical assessments of the NEO population, which in turn, affects the assignment of statistically-assessed basic parameters to discovered but yet-to-be-fully-characterized NEOs.

Albedo and taxonomy↗

BAOBAB (Big And Outrageously Bold Asteroid Belt) Project

One of the intriguing results of NASA's Dawn mission is the composition and structure of the Main Asteroid Belt's only known dwarf planet, Ceres [1]. It has a top layer of dehydrated clays and salts [2] and an icy-rocky mantle [3,4]. It is widely known that the asteroid belt failed to accrete as a planet by resonances between the Sun and Jupiter. About 20-30 asteroids >100 km diameter are probably differentiated protoplanets [5]. 1) how many more and which ones are fragments of protoplanets? 2) How many and which ones are primordial rubble piles left over from condensation of the solar nebula? 3) How would we go about gaining better and more complete characterization of the mass, interior structure and composition of the Main Belt asteroid population? 4) What is the relationship between asteroids and ocean worlds? Bulk parameters such as the mass, density, and porosity, are important to characterize the structure of any celestial body, and for asteroids in particular, they can shed light on the conditions in the early solar system. Asteroid density estimates exist but currently they are often based on assumed properties of taxonomic classes, or through astronomical survey data where interactions with asteroids are weak at best resulting in large measurement uncertainty. We only have direct density estimates from spacecraft encounters for a few asteroids at this time. Knowledge of the asteroids is significant not only to understand their role in solar system workings, but also to assess their potential as space resources, as impact hazards on Earth, or even as harboring life forms. And for the distant future, we want to know if the idea put forth in a contest sponsored by Physics Today, to surface the asteroids into highly reflecting, polished surfaces and use them as a massively segmented mirror for astrophysical exploration [6], is feasible.

Asteroid Belt↗

Point-Mass Aircraft Trajectory Prediction Using a Hierarchical, Highly-Adaptable Software Design

A highly adaptable and extensible method for predicting four-dimensional trajectories of civil aircraft has been developed. This method, Behavior-Based Trajectory Prediction, is based on taxonomic concepts developed for the description and comparison of trajectory prediction software. A hierarchical approach to the "behavioral" layer of a point-mass model of aircraft flight, a clear separation between the "behavioral" and "mathematical" layers of the model, and an abstraction of the methods of integrating differential equations in the "mathematical" layer have been demonstrated to support aircraft models of different types (in particular, turbojet vs. turboprop aircraft) using performance models at different levels of detail and in different formats, and promise to be easily extensible to other aircraft types and sources of data. The resulting trajectories predict location, altitude, lateral and vertical speeds, and fuel consumption along the flight path of the subject aircraft accurately and quickly, accounting for local conditions of wind and outside air temperature. The Behavior-Based Trajectory Prediction concept was implemented in NASA's Traffic Aware Planner (TAP) flight-optimizing cockpit software application.

Karr, David A.↗

Leafy Greens Grown on the International Space Station May Provide a Nutritious Supplement to Astronauts' Diet

Supplemental safe food production has been an essential goal of NASA to meet the nutritional needs of astronauts on the International Space Station (ISS) as well as for future long duration missions to the moon and beyond. Food crops grown in space experience different environmental conditions than plants grown on Earth (i.e. microgravity and spaceflight physical sciences impacts). To test the growth methods and effects of the space environment, red romaine lettuce Lactuca sativa cv. 'Outredgeous', was grown in Veggie plant growth chambers on the ISS. Microbiological food safety of the plants grown on the ISS was determined by heterotrophic plate counts to assess total microbial load for bacteria and fungi as well as screening for specific pathogens and isolate identification. Molecular characterization was completed using Next Generation Sequencing (NGS) to provide valuable information on the taxonomic composition and community structure of the plant microbiome. Chemical analyses of plant tissue were conducted to understand spaceflight-induced changes in key elements in the space diet, phenolics, anthocyanin levels, and Oxygen radical absorbance capacity (ORAC), a measure of antioxidant capacity. Three growth tests of red romaine lettuce were completed on ISS, VEG-01A, VEG-01B, and VEG-03A. Plants were harvested using two harvest methods, either a single terminal harvest (after 33 days) or cut-and-come-again repetitive harvesting (64 days total growth). Ground controls were grown simultaneously with a delay to accommodate condition monitoring and replication. A comparison of the plant tissue returned to Earth showed leaves from the second grow-out had significantly higher bacterial counts than the preceding or subsequent growth test or any of the ground controls. Fungal counts were significantly higher on the final cut-and-come-again harvest of the third grow out. None of the potential foodborne pathogens that were screened for were detected. Bacterial and fungal isolate identification and community characterization indicated similar diversity between VEG-01A and VEG-01B growth tests, however, there appeared to be subtle differences in diversity and distribution among the three growth tests. Chemical analysis of plant tissue revealed significant variation in a few elemental data, but variation in levels of phenolics, anthocyanins, and ORAC was not significantly different. This study indicated that leafy vegetable crops could safely provide an edible supplement to astronauts' diet, and our analysis provided baseline data for continual operation of the Veggie plant growth units on ISS. This research was funded by NASA's space biology program.

Food Production↗

Environmental factors driving spatial heterogeneity in desert halophile microbial communities

Spatial heterogeneity in microbial communities is observed in all-natural ecosystems and can stem from both adaptations to local environmental conditions as well as stochastic processes. Extremophile microbial communities inhabiting evaporitic halite nodules (salt rocks) in the Atacama Desert, Chile, are a good model ecosystem for investigating factors leading to microbiome heterogeneity, due to their diverse taxonomic composition and the spatial segregation of individual nodules. We investigated the abiotic factors governing microbiome composition across different spatial scales, allowing for insight into the factors that govern halite colonization from regional desert-wide scales to micro-scales within individual nodules. We found that water availability and community drift account for microbiome assembly differently at different distance scales, with higher rates of cell dispersion at the smaller scales resulting in a more homogenous composition. This trend likely applies to other endoliths, and to non desert communities, where dispersion between communities is limited. At the intra-nodule scales, a light availability gradient was most important in determining the distribution of microbial taxa despite intermixing by water displacement via capillary action.

microbiome extremophile, desert, heterogeneity, Me↗

Congruence of Clusters Defined By Whole Genome Sequencing and MALDI-TOF for Bacteria Isolated From Cleanrooms

Introduction: Oligotrophic conditions can render cleanrooms inhospitable to microbes. Despite these constraints, fungi and bacteria are frequently isolated from surfaces in astromaterials cleanrooms at the Johnson Space Center. Bacillus species are of particular concern because endospores belonging to this genus are resilient and can affect astromaterials. Current monitoring programs rely on 16S rRNA sequencing and the VITEK2 Compact system. These methods have limited power to resolve Bacillus species. Matrix-assisted laser desorption - time of flight mass spectrometry (MALDI-TOF MS), provides a rapid, low cost, method of identifying bacterial isolates and has a higher resolution than 16S rRNA sequencing, particularly for Bacillus species; however, few studies have compared this method to the industry gold standard, whole genome sequencing (WGS). Methods: Based on 16S rRNA classification, we selected 14 isolates for analysis with MALDI-TOF and WGS. Mass spectra were generated with MALDI-TOF MS and processed with custom scripts to identify clusters of closely related isolates and calculate a matrix of pairwise cosine similarity scores. Hybrid Illumina and Nanopore sequencing were used to generate draft genomes. Pairwise similarity scores were calculated from these genomes based on the average amino acid identity (AAI) predicted from single copy core genes. Congruence of clustering between these methods, was assessed by calculating adjusted Rand and Wallace coefficients. Results: Clusters of species generated from MALDI-TOF MS showed good agreement of phylotypes generated with WGS. Pairs of strains that were > 94% similar to each other in terms of predicted amino acid sequences consistently showed cosine similarities of mass spectra > 0.65 and, of the 9 clusters identified with WGS, 8 were identical with MALDI-TOF. This corresponds to an adjusted Rand index of 0.95 and a 95% confidence interval of 0.80 – 1.00 for adjusted Wallace coefficients. The only discordance was for a pair of isolates that were classified as Paenibacillus species. This pair showed relatively high similarity (0.84) in terms of MALDI-TOF MS but only 85% similarity in terms of AAI. Conclusion: This study shows that MALDI-TOF and WGS exhibit a similar ability to delineate Bacillus species isolated from cleanrooms and taxonomic units described by these two methods are consistent with one another. Since MALDI-TOF MS is low in cost and high in throughput, this approach appears to be an ideal option for routine microbial monitoring and identifying Bacillus species.

Farnaz Mazhari↗

Acoustic space occupancy: Combining ecoacoustics and lidar to model biodiversity variation and detection bias across heterogeneous landscapes

There is global interest in quantifying changing biodiversity in human-modified landscapes. Ecoacoustics may offer a promising pathway for supporting multi-taxa monitoring, but its scalability has been hampered by the sonic complexity of biodiverse ecosystems and the imperfect detectability of animal-generated sounds. The acoustic signature of a habitat, or soundscape, contains information about multiple taxa and may circumvent species identification, but robust statistical technology for characterizing community-level attributes is lacking. Here, we present the Acoustic Space Occupancy Model, a flexible hierarchical framework designed to account for detection artifacts from acoustic surveys in order to model biologically relevant variation in acoustic space use among community assemblages. We illustrate its utility in a biologically and structurally diverse Amazon frontier forest landscape, a valuable test case for modeling biodiversity variation and acoustic attenuation from vegetation density. We use complementary airborne lidar data to capture aspects of 3D forest structure hypothesized to influence community composition and acoustic signal detection. Our novel analytic framework permitted us to model both the assembly and detectability of soundscapes using lidar-derived estimates of forest structure. Our empirical predictions were consistent with physical models of frequency-dependent attenuation, and we estimated that the probability of observing animal activity in the frequency channel most vulnerable to acoustic attenuation varied by over 60%, depending on vegetation density. There were also large differences in the biotic use of acoustic space predicted for intact and degraded forest habitats, with notable differences in the soundscape channels predominantly occupied by insects. This study advances the utility of ecoacoustics by providing a robust modeling framework for addressing detection bias from remote audio surveys while preserving the rich dimensionality of soundscape data, which may be critical for inferring biological patterns pertinent to multiple taxonomic groups in the tropics. Our methodology paves the way for greater integration of remotely sensed observations with high-throughput biodiversity data to help bring routine, multi-taxa monitoring to scale in dynamic and diverse landscapes.

Airborne lidar↗

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↗

ThermoBase: A Database of the Phylogeny and Physiology of Thermophilic and Hyperthermophilic Organisms

Thermophiles and hyperthermophiles are those organisms which grow at high temperature (> 40°C). The unusual properties of these organisms have received interest in multiple fields of biological research, and have found applications in biotechnology, especially in industrial processes. However, there are few listings of thermophilic and hyperthermophilic organisms and their relevant environmental and physiological data. Such repositories can be used to standardize definitions of thermophile and hyperthermophile limits and tolerances and would mitigate the need for extracting organism data from diverse literature sources across multiple, sometimes loosely related, research fields. Therefore, we have developed ThermoBase, a web-based and freely available database which currently houses comprehensive descriptions for 1238 thermophilic or hyperthermophilic organisms. ThermoBase reports taxonomic, metabolic, environmental, experimental, and physiological information in addition to literature resources. This includes parameters such as coupling ions for chemiosmosis, optimal pH and range, optimal temperature and range, optimal pressure, and optimal salinity. The database interface allows for search features and sorting of parameters. As such, it is the goal of ThermoBase to facilitate and expedite hypothesis generation, literature research, and understanding relating to thermophiles and hyperthermophiles within the scientific community in an accessible and centralized repository. ThermoBase is freely available online at the Astrobiology Habitable Environments Database (AHED; https://ahed.nasa.gov), at the Database Center for Life Science (TogoDB; http://togodb.org/db/thermobase), and in the S1 File.

Thermophiles↗

SWIPE: Spectral Water Inversion Processor and Emulator

Degradation of Earth’s inland water resources due to anthropogenic perturbations and climate anomalies at both local and global scales continues to place human health at substantial risk. There is now a growing necessity to develop pragmatic approaches that allow timely and effective extrapolation of local processes, to spatially resolved global products, and to promote operational and sustainable resource policy management. This presentation will be discussing the progress made developing SWIPE: Spectral Water Inversion Processor and Emulator. SWIPE is a platform for advanced modeling of coastal and inland aquatic habitats. The goal is create a comprehensive and cohesive system to leverage recent advancements in computation and machine learning to develop a synthetic training ground for sensitivity studies and algorithm development. The four principal facets of SWIPE include: 1. Advanced two-layer coated sphere bio-optical modeling and GPU radiative transfer modeling, 2. Big Data involving massive synthetic spectral libraries of optical properties of various global aquatic particles, surface reflectance, and top-of-atmosphere reflectance, all at hyperspectral resolution leveraging high-end computing systems at NASA Ames Research Center, 3. Deep Learning for algorithm development for water quality inversion of concentrations of common biogeophysical variables as well as optics, full uncertainty characterization by water type, and forward emulation, and lastly, 4. Image Processing for application of developed retrieval algorithms for both hyperspectral and multispectral sensors with experimental corrections for global adjacency, noise, sunglint, and benthic reflectance. This presentation will demonstrate the Equivalent Algal Populations (EAP) two-layer coated sphere scattering model which has been used develop spectral libraries of hyperspectral inherent optical properties of roughly 80 species of phytoplankton, covering 15 different classes and nine taxonomic functional types. The EAP model was also used to derive spectral properties of 10 different non-algal particle functional types. Examples of how the SMART-G (Speed-up Monte-carlo Advanced Radiative Transfer using GPU) radiative transfer code is used to model optically complex aquatic signals will be presented and discussed in the context of creating a massive synthetic database which can leverage the full power of next generation machine learning techniques and high end computing for water quality inversion. We will discuss our active investigation in things like appropriate model architectures, dimensionality reduction techniques such as PCA and autoencoders, uncertainty quantification and abstaining, and which variables actually benefit most from hyperspectral information versus multispectral resolution. We are also curious about questions relating to cost/benefit analysis in terms of computation resources, neural network complexity, and data volumes. Answers to these questions will hopefully elaborate on cost efficiency for potential future sensor design considerations.

SWIPE↗