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At least 271 records · Page 15
All sourcesNASA NTRSDOE OSTI
NASA NTRS2000

Scanning Electron Microscopy Investigation of a Sample Depth Profile Through the Martian Meteorite Nakhla

The ongoing scientific debate as to whether or not the Martian meteorite ALH84001 contained evidence of possible biogenic activities showed the need to establish consistent methods to ascertain the origin of such evidence. To distinguish between terrestrial organic material/microbial contaminants and possible indigenous microbiota within meteorites is therefore crucial. With this in mind a depth profile consisting of four samples from a new sample allocation of Martian meteorite Nakhla was investigated using scanning electron microscopy (SEM) and energy dispersive X-ray analysis. SEM imaging of freshly broken fractured chips revealed structures strongly recent terrestrial microorganisms, in some cases showing evidence of active growth. This conclusion was supported by EDX analysis, which showed the presence of carbon associated with these structures, we concluded that these structures represent recent terrestrial contaminants rather than structures indigenous to the meteorite. Page

Toporski, Jan↗
NASA NTRS2012

Abiotic Versus Biotic Pathogens: Replicative Growth in Host Tissues Key to Discriminating Between Biotoxic Injury and Active Pathogenesis

Life can be defined as a self-sustaining chemical system capable of undergoing Darwinian evolution; a self-bounded, self-replicating, and self-perpetuating entity [1]. This definition should hold for terrestrial as well as extraterrestrial life-forms. Although, it is reasonable to expect that a Mars life-form would be more adaptable to Mars-like conditions than to Earth-like environments, it remains possible that negative ecological or host interactions might occur if Mars microbiota were to be inadvertently released into the terrestrial environment. A biogenic infectious agent can be defined as a self-sustaining chemical system capable of undergoing Darwinian evolution and derives its sustenance from a living cell or from the by-products of cell death. Disease can be de-fined as the detrimental alteration of one or more ordered metabolic processes in a living host caused by the continued irritation of a primary causal factor or factors; disease is a dynamic process [2]. In contrast, an injury is due to an instantaneous event; injury is not a dynamic process [2]. A causal agent of disease is defined as a pathogen, and can be either abiotic or biotic in nature. Diseases incited by biotic pathogens are the exceptions, not the norms, in terrestrial host-microbe interactions. Disease induction in a plant host can be conceptually characterized using the Disease Triangle (Fig. 1) in which disease occurs only when all host, pathogen, and environ-mental factors that contribute to the development of disease are within conducive ranges for a necessary minimum period of time. For example, plant infection and disease caused by the wheat leaf rust fungus, Puccinia recondita, occur only if virulent spores adhere to genetically susceptible host tissues for at least 4-6 hours under favorable conditions of temperature and moisture [3]. As long as one or more conditions required for disease initiation are not available, disease symptoms will not develop.

Schuerger, Andrew C.↗
NASA NTRS2012

PMA-Linked Fluorescence for Rapid Detection of Viable Bacterial Endospores

The most common approach for assessing the abundance of viable bacterial endospores is the culture-based plating method. However, culture-based approaches are heavily biased and oftentimes incompatible with upstream sample processing strategies, which make viable cells/spores uncultivable. This shortcoming highlights the need for rapid molecular diagnostic tools to assess more accurately the abundance of viable spacecraft-associated microbiota, perhaps most importantly bacterial endospores. Propidium monoazide (PMA) has received a great deal of attention due to its ability to differentiate live, viable bacterial cells from dead ones. PMA gains access to the DNA of dead cells through compromised membranes. Once inside the cell, it intercalates and eventually covalently bonds with the double-helix structures upon photoactivation with visible light. The covalently bound DNA is significantly altered, and unavailable to downstream molecular-based manipulations and analyses. Microbiological samples can be treated with appropriate concentrations of PMA and exposed to visible light prior to undergoing total genomic DNA extraction, resulting in an extract comprised solely of DNA arising from viable cells. This ability to extract DNA selectively from living cells is extremely powerful, and bears great relevance to many microbiological arenas.

LaDuc, Myron T.↗
NASA NTRS2012

Genetic Inventory Task Final Report

Contaminant terrestrial microbiota could profoundly impact the scientific integrity of extraterrestrial life-detection experiments. It is therefore important to know what organisms persist on spacecraft surfaces so that their presence can be eliminated or discriminated from authentic extraterrestrial biosignatures. Although there is a growing understanding of the biodiversity associated with spacecraft and cleanroom surfaces, it remains challenging to assess the risk of these microbes confounding life-detection or sample-return experiments. A key challenge is to provide a comprehensive inventory of microbes present on spacecraft surfaces. To assess the phylogenetic breadth of microorganisms on spacecraft and associated surfaces, the Genetic Inventory team used three technologies: conventional cloning techniques, PhyloChip DNA microarrays, and 454 tag-encoded pyrosequencing, together with a methodology to systematically collect, process, and archive nucleic acids. These three analysis methods yielded considerably different results: Traditional approaches provided the least comprehensive assessment of microbial diversity, while PhyloChip and pyrosequencing illuminated more diverse microbial populations. The overall results stress the importance of selecting sample collection and processing approaches based on the desired target and required level of detection. The DNA archive generated in this study can be made available to future researchers as genetic-inventory-oriented technologies further mature.

microbial diversity↗
NASA NTRS2014

The Impact of Apollo-Era Microbiology on Human Space Flight

The microbiota of crewmembers and the spacecraft environment contributes significant risk to crew health during space flight missions. NASA reduces microbial risk with various mitigation methods that originated during the Apollo Program and continued to evolve through subsequent programs: Skylab, Shuttle, and International Space Station (ISS). A quarantine of the crew and lunar surface samples, within the Lunar Receiving Laboratory following return from the Moon, was used to prevent contamination with unknown extraterrestrial organisms. The quarantine durations for the crew and lunar samples were 21 days and 50 days, respectively. A series of infections among Apollo crewmembers resulted in a quarantine before launch to limit exposure to infectious organisms. This Health Stabilization Program isolated the crew for 21 days before flight and was effective in reducing crew illness. After the program developed water recovery hardware for Apollo spacecraft, the 1967 National Academy of Science Space Science Board recommended the monitoring of potable water. NASA implemented acceptability limits of 10 colony forming units (CFU) per mL and the absence of viable E. coli, anaerobes, yeasts, and molds in three separate 150 mL aliquots. Microbiological investigations of the crew and spacecraft environment were conducted during the Apollo program, including the Apollo-Soyuz Test Project and Skylab. Subsequent space programs implemented microbial screening of the crew for pathogens and acceptability limits on spacecraft surfaces and air. Microbiology risk mitigation methods have evolved since the Apollo program. NASA cancelled the quarantine of the crew after return from the lunar surface, reduced the duration of the Health Stabilization Program; and implemented acceptability limits for spacecraft surfaces and air. While microbial risks were not a main focus of the early Mercury and Gemini programs, the extended duration of Apollo flights resulted in the increased scrutiny of impact of the space flight environment on crew health. The lessons learned during that era of space flight continue to impact microbiology risk mitigation in space programs today.

Elliott, T. F↗
NASA NTRS2014

Spindle-shaped Microstructures: Potential Models for Planktonic Life Forms on Other Worlds

Spindle-shaped, organic microstructures ("spindles") are now known from Archean cherts in three localities (Figs. 1-4): The ~3 Ga Farrel Quartzite from the Pilbara of Australia [1]; the older, ~3.3-3.4 Ga Strelley Pool Formation, also from the Pilbara of Australia [2]; and the ~3.4 Ga Kromberg Formation of the Barberton Mountain Land of South Africa [3]. Though the spindles were previously speculated to be pseudofossils or epigenetic organic contaminants, a growing body of data suggests that these structures are bona fide microfossils and further, that they are syngenetic with the Archean cherts in which they occur [1-2, 4-10]. As such, the spindles are among some of the oldest-known organically preserved microfossils on Earth. Moreover, recent delta C-13 study of individual spindles from the Farrel Quartzite (using Secondary Ion Mass Spectrometry [SIMS]) suggests that the spindles may have been planktonic (living in open water), as opposed to benthic (living as bottom dwellers in contact with muds or sediments) [9]. Since most Precambrian microbiotas have been described from benthic, matforming communities, a planktonic lifestyle for the spindles suggests that these structures could represent a segment of the Archean biosphere that is poorly known. Here we synthesize the recent work on the spindles, and we add new observations regarding their geographic distribution, robustness, planktonic habit, and long-lived success. We then discuss their potential evolutionary and astrobiological significance.

Oehler, Dorothy Z.↗
NASA NTRS2010

Potentially Habitable Ancient Environments in Gusev Crater, Mars

Habitable environments must sustain liquid water at least intermittently and also provide both chemical building blocks and useful sources of energy for life. Observations by Spirit rover indicate that conditions have probably been too dry to sustain life, at least since the emplacement of the extensive basalts that underlie the plains around the Columbia Memorial Station landing site. Local evidence of relatively minor aqueous alteration [1] probably occurred under conditions where the activity of water was too low to sustain biological processes as we know them. In contrast, multiple bedrock units in West Spur and Husband Hill in the Columbia Hills have been extensively altered. Patterns of elemental abundances are consistent with aqueous processes involving migrating fluids [2]. Fe in several of these units has been extensively oxidized [3]. Conceivably any microbiota present during the aqueous alteration of these rocks might have obtained energy from Fe oxidation. Spirit discovered olivine-rich ultramafic rocks during her descent from Husband Hill southward into Inner Basin. Alteration of similar ultramafic rocks on Earth can yield H2 that can provide both energy and reducing power for microorganisms. Spirit's discovery of deposits rich in ferric sulfate is consistent with the aqueous dissolution and/or alteration of olivine under acidic conditions [2] such as those associated with hydrothermal activity. The oxidation of iron and sulfur that can accompany such activity can be an energy source for life. Hydrothermal systems on Earth that sustain either acidic [4] or neutral to alkaline fluids [5] have been shown to provide this energy. Collectively the observations by Spirit rover are consistent with the possibility that habitable environments existed in Gusev crater at least intermittently in the distant geologic past.

Fe oxidation↗
NASA NTRS2015

Omics Research on the International Space Station

The International Space Station (ISS) is an orbiting laboratory whose goals include advancing science and technology research. Completion of ISS assembly ushered a new era focused on utilization, encompassing multiple disciplines such as Biology and Biotechnology, Physical Sciences, Technology Development and Demonstration, Human Research, Earth and Space Sciences, and Educational Activities. The research complement planned for upcoming ISS Expeditions 45&46 includes several investigations in the new field of omics, which aims to collectively characterize sets of biomolecules (e.g., genomic, epigenomic, transcriptomic, proteomic, and metabolomic products) that translate into organismic structure and function. For example, Multi‐Omics is a JAXA investigation that analyzes human microbial metabolic cross‐talk in the space ecosystem by evaluating data from immune dysregulation biomarkers, metabolic profiles, and microbiota composition. The NASA OsteoOmics investigation studies gravitational regulation of osteoblast genomics and metabolism. Tissue Regeneration uses pan‐omics approaches with cells cultured in bioreactors to characterize factors involved in mammalian bone tissue regeneration in microgravity. Rodent Research‐3 includes an experiment that implements pan‐omics to evaluate therapeutically significant molecular circuits, markers, and biomaterials associated with microgravity wound healing and tissue regeneration in bone defective rodents. The JAXA Mouse Epigenetics investigation examines molecular alterations in organ specific gene expression patterns and epigenetic modifications, and analyzes murine germ cell development during long term spaceflight. Lastly, Twins Study ("Differential effects of homozygous twin astronauts associated with differences in exposure to spaceflight factors"), NASA's first foray into human omics research, applies integrated analyses to assess biomolecular responses to physical, physiological, and environmental stressors associated with spaceflight.

Love, John↗
NASA NTRS2018

Transitory Microbial Habitat in the Hyperarid Atacama Desert

Traces of life are nearly ubiquitous on Earth. However, a central unresolved question is whether these traces always indicate an active microbial community or whether, in extreme environments, such as hyperarid deserts, they instead reflect just dormant or dead cells. Although microbial biomass and diversity decrease with increasing aridity in the Atacama Desert, we provide multiple lines of evidence for the presence of an at times metabolically active, microbial community in one of the driest places on Earth. We base this observation on four major lines of evidence: (i) a physico-chemical characterization of the soil habitability after an exceptional rain event, (ii) identified biomolecules indicative of potentially active cells [e.g., presence of ATP, phospholipid fatty acids (PLFAs), metabolites, and enzymatic activity], (iii) measurements of in situ replication rates of genomes of uncultivated bacteria reconstructed from selected samples, and (iv) microbial community patterns specific to soil parameters and depths. We infer that the microbial populations have undergone selection and adaptation in response to their specific soil microenvironment and in particular to the degree of aridity. Collectively, our results highlight that even the hyperarid Atacama Desert can provide a habitable environment for microorganisms that allows them to become metabolically active following an episodic increase in moisture and that once it decreases, so does the activity of the microbiota. These results have implications for the prospect of life on other planets such as Mars, which has transitioned from an earlier wetter environment to today’s extreme hyperaridity.

Schulze-Makuch, Dirk↗
NASA NTRS2019

Using the NASA GeneLab Data System to Study the Metagenomes of Spaceships and Their Occupants

With humans pushing to live further off Earth for longer periods of time, it is increasingly important to understand the changes that occur in biological systems during spaceflight whether these be astronauts, their microbial commensals, or their plant-based life support systems. In a three-part presentation, we discuss GeneLab and recent discoveries regarding the microbiota of spacecrafts and space-flown animals. Part 1: GeneLab: Open Science for Life in Space, Jonathan Galazka, NASA Ames Research Center To accelerate the pace of discovery from precious spaceflight biological experiments, NASA as develop the GeneLab data system (genelab.nasa.gov), which allows unfettered access to omics data from spaceflight and spaceflight relevant experiments. GeneLab houses metagenomic datasets from spacecraft and relevant spacecraft models. Users can download this data and associated metadata to make new discoveries about how microbial communities may change and adapt to spaceflight.

Galazka, Jonathan M.↗
NASA NTRSDate not supplied

Constraining Venus Cloud Habitability: Earth's Aerobiosphere as an Analogue Environment

The potential habitability of Venus's cloud and haze layers has been debated for decades, with interest fueled by observations including disequilibria in atmospheric chemistry, strongly UV-absorbing particles, and (most recently) a controversial phosphine detection. Venus cloud temperature and pressure are clement by Earth standards; however, the calculated high acid activity and low water activity may exceed the limits of Earth biochemistry, based on observed life in extreme environments. A significant challenge in understanding Venus's habitability is the lack of an appropriate terrestrial analogue environment. Life has not been found in hydrothermal systems approaching Venus aerosol acidities, but these systems also contain high levels of other harsh solutes. Earth's stratospheric sulfate layer is a partial match in terms of acidity, desiccation, size, and isolation from the surface, but the few samples returned from these altitudes have yielded only sparse, inactive cells. Earth's tropospheric cloud droplets have an active microbial presence, but are larger and far more water-rich than Venus aerosols; tropospheric times aloft are also similar to microbial generation times, making Earth's aerobiosphere dependent on continuous surface replenishment. Direct detection of potential biosignatures from a single transect is challenging; Earth's cloud microbiota yields 102 - 108 viable cells per mL, equivalent to one per 103 - 109 particles, with highly dynamic and heterogeneous distribution. The most important in situ measurement for Venus cloud habitability is detailed aerosol composition: confirmation of acid and water activity, presence of potentially bioavailable nutrients and energy, and potential presence of organic matter. Modeling Venus cloud aerosol residence time in comparison to periodic influxes of water and photochemical energy, and thus the ability of an ecosystem to maintain itself over time, would also address a significant habitability constraint particular to aerobiospheres.

Venus↗
DOE OSTI2022

Probe for selectively characterizing enzymes involved in xenobiotic metabolism and method of making and using the same

Activity-based probes that can be used to selectively identify and characterize enzymes that are involved in different phases of xenobiotic metabolism in a host and its microbiota population(s) are described. The activity-based probes described specifically label only their target active enzymes involved in xenobiotic metabolism and therefore provide a measurement of true protein functional activity rather than transcript or protein abundance. The activity-based probes also provide multimodal profiling of these active enzymes. Methods for preparing the activity based probes and exemplary methods for their use also are disclosed.

Wright, Aaron T.↗
DOE OSTI2024

Probe for selectively characterizing enzymes involved in xenobiotic metabolism and method of making and using the same

Activity-based probes that can be used to selectively identify and characterize enzymes that are involved in different phases of xenobiotic metabolism in a host and its microbiota population(s) are described. The activity-based probes described specifically label only their target active enzymes involved in xenobiotic metabolism and therefore provide a measurement of true protein functional activity rather than transcript or protein abundance. The activity-based probes also provide multimodal profiling of these active enzymes. Methods for preparing the activity based probes and exemplary methods for their use also are disclosed.

Wright, Aaron T.↗
DOE OSTI2025

Time-series RNA metabarcoding of the active Populus tremuloides root microbiome reveals hidden temporal dynamics and dormant core members

The rhizosphere is a critical interface between plant roots and soil, harboring diverse microbial communities that are essential to plant and ecosystem health. Although these communities exhibit stark temporal dynamics, their dormancy/activity transitions remain poorly understood. Such transitions may enable microbes to rapidly adjust functional contributions faster than community turnover alone would allow. Here, we used RNA metabarcoding to characterize the active fraction of microbial communities on the roots of quaking aspen (Populus tremuloides) in a time-series study across a natural environmental gradient. We explore cryptic temporal microbial community dynamics of rhizosphere communities at the ecosystem scale. The active rhizosphere bacterial and fungal communities were more temporally dynamic than total communities, while total communities exhibited a stronger response to site-specific conditions. Notably, some core microbiome members were often inactive, yielding a smaller “active core” subset. The fungal endophyte Hyaloscypha finlandica was the only microbe that was both present and active in all plots across all timepoints. Soil temperature strongly influenced both total and active community composition, with the fungal class Eurotiomycetes showing a temperature-dependent seasonal decline in abundance. Together, these results reveal that modulation of microbial activity levels is a key mechanism by which the plant root holobiont responds to environmental variation, and that even dominant symbionts may frequently persist in dormancy within the rhizosphere.

Community Structure and Diversity↗
DOE OSTI2022

Targeting Gut Bacteria Using Inulin‐Conjugated Mesoporous Silica Nanoparticles

Abstract To facilitate the creation of novel nanocarrier systems targeting the intestinal microbiome, inulin‐conjugated mesoporous silica nanoparticles (MSNs) are described herein for the first time. Surface functionalization is achieved on either hydrophilic or hydrophobic mesoporous nanoparticles using different conjugation methods. The targeting performance of the resulting materials is assessed and compared upon incubation with human stool. It appears that amide formation is the most favorable coupling method on hydrophilic MSNs to achieve the desired bioconjugate. Remarkably, high affinity of gut bacteria to the conjugated particles can be obtained, paving the way to novel targeted drug delivery systems.

36 MATERIALS SCIENCE↗
DOE OSTI2025

STREAMS guidelines: standards for technical reporting in environmental and host-associated microbiome studies

The interdisciplinary nature of microbiome research, coupled with the generation of complex multi-omics data, makes knowledge sharing challenging. The Strengthening the Organization and Reporting of Microbiome Studies (STORMS) guidelines provide a checklist for the reporting of study information, experimental design and analytical methods within a scientific manuscript on human microbiome research. Here, in this Consensus Statement, we present the standards for technical reporting in environmental and host-associated microbiome studies (STREAMS) guidelines. The guidelines expand on STORMS and include 67 items to support the reporting and review of environmental (for example, terrestrial, aquatic, atmospheric and engineered), synthetic and non-human host-associated microbiome studies in a standardized and machine-actionable manner. Based on input from 248 researchers spanning 28 countries, we provide detailed guidance, including comparisons with STORMS, and case studies that demonstrate the usage of the STREAMS guidelines. In conclusion, STREAMS, like STORMS, will be a living community resource updated by the Consortium with consensus-building input of the broader community.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Adding labile carbon to peatland soils triggers deep carbon breakdown

Peatlands store vast amounts of carbon, with deep peat carbon remaining stable due to limited thermodynamic energy and transport. However, climate change-induced increases in labile carbon inputs could destabilize these stores. Here, we combined DNA stable isotope probing with stable isotope-assisted metabolomics employing a multi-platform approach to investigate microbial dynamics driving deep peat carbon degradation upon labile carbon (e.g., glucose) amendment. Our findings highlight the vulnerability of deep peat carbon, as glucose addition triggers the breakdown of older organic matter. By uniquely integrating these techniques, we identified active glucose metabolizers to specific microbial populations and mapped carbon flow through microbial networks, elucidating their role in priming recalcitrant carbon mineralization. This multi-omics approach offers crucial insights into how changing resources reshape the peatland microbiome, enhancing our understanding of deep carbon processing, and refining model parameterization to predict microbial responses and carbon cycle feedbacks under global change pressures.

59 BASIC BIOLOGICAL SCIENCES↗