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At least 127 records · Page 7
All sourcesNASA NTRSDOE OSTI
NASA NTRS2003

Energy Requirements of Hydrogen-utilizing Microbes: A Boundary Condition for Subsurface Life

Microbial ecosystems based on the energy supplied by water-rock chemistry carry particular significance in the context of geo- and astrobiology. With no direct dependence on solar energy, lithotrophic microbes could conceivably penetrate a planetary crust to a depth limited only by temperature or pressure constraints (several kilometers or more). The deep lithospheric habitat is thereby potentially much greater in volume than its surface counterpart, and in addition offers a stable refuge against inhospitable surface conditions related to climatic or atmospheric evolution (e.g., Mars) or even high-energy impacts (e.g., early in Earth's history). The possibilities for a deep microbial biosphere are, however, greatly constrained by life s need to obtain energy at a certain minimum rate (the maintenance energy requirement) and of a certain minimum magnitude (the energy quantum requirement). The mere existence of these requirements implies that a significant fraction of the chemical free energy available in the subsurface environment cannot be exploited by life. Similar limits may also apply to the usefulness of light energy at very low intensities or long wavelengths. Quantification of these minimum energy requirements in terrestrial microbial ecosystems will help to establish a criterion of energetic habitability that can significantly constrain the prospects for life in Earth's subsurface, or on other bodies in the solar system. Our early work has focused on quantifying the biological energy quantum requirement for methanogenic archaea, as representatives of a plausible subsurface metabolism, in anoxic sediments (where energy availability is among the most limiting factors in microbial population growth). In both field and laboratory experiments utilizing these sediments, methanogens retain a remarkably consistent free energy intake, in the face of fluctuating environmental conditions that affect energy availability. The energy yields apparently required by methanogens in these sediment systems for sustained metabolism are about half that previously thought necessary. Lowered energy requirements would imply that a correspondingly greater proportion of the planetary subsurface could represent viable habitat for microorganisms.

Hoehler, Tori M.↗
NASA NTRS2006

On Release of Microbe-Laden Particles from Mars Landers

A paper presents a study in which rates of release of small particles from Mars lander spacecraft into the Martian atmosphere were estimated from first principles. Because such particles can consist of, or be laden with, terrestrial microbes, the study was undertaken to understand their potential for biological contamination of Mars. The study included taking account of forces and energies involved in adhesion of particles and of three mechanisms of dislodgement of particles from the surface of a Mars lander: wind shear, wind-driven impingement of suspended dust, and impingement of wind-driven local saltating sand particles. Wind shear was determined to be effective in dislodging only particles larger than about 10 microns and would probably be of limited interest because such large particles could be removed by pre-flight cleaning of the spacecraft, and their number on the launched spacecraft would thus be relatively small. Dislodgement by wind-driven dust was found to be characterized by an adhesion half-life of the order of 10,000 years judged to be too long to be of concern. Dislodgement by saltating sand particles, including skirts of dust devils, was found to be of potential importance, depending on the sizes of the spacecraft-attached particles and characteristics of both Mars sand-particle and spacecraft surfaces.

Bellan, Josette↗
NASA NTRS2012

Can Terrestrial Microbes Grow on Mars?

The theme for AbSciCon 2012 is "Exploring Life: Past and Present, Near and Far." The conference will address our current understanding of life - from processes at the molecular level to those which operate at planetary scales. Studying these aspects of life on Earth provides an essential platform from which to examine the potential for life on other worlds, both within our solar system and beyond. Mars exhibits a variety of extreme environments characterized by high UV and ionizing radiation flux, low pressure anoxic atmosphere, scarce or absent liquid water, extreme low temperatures, etc. The ability of terrestrial microorganisms to survive and adapt to the Mars environment has profound implications for astrobiology, planetary protection, and Mars life detection missions. At the NASA Ames Synthetic Biology Initiative, we believe that synthetic biology has the potential to revolutionize human space exploration. As such, the initiative is dedicated to applying the tools and techniques of synthetic biology to space exploration and astrobiology. Biological solutions will be invaluable for space exploration because they are not resource intensive, and they are versatile and self-renewing. An understanding of how to work with DNA in an unfavorable environment is paramount to utilizing biological tools on space missions. Furthermore, the ability to adjust life to the parameters of Mars is vital both to discovering what life on Mars might look like, and to using biological tools under such conditions. As a first step, we need an energy-efficient, low cost means of transporting, storing, and protecting genomic DNA, DNA parts, and whole microbial strains. Our goal is to develop and demonstrate viable and superior alternatives to standard DNA storage methods, which can be optimized to the conditions of space exploration, using synthetic biology as a tool. This includes protocols and kit designs for easy and repeatable DNA and strain recovery from protective storage conditions. We are constructing newly engineered genetic parts for different valuable host organisms, designed to increased long-term survival and functional retention. These methods should be applied for DNA and strain storage and transportation. In parallel, we seek inspiration from natural organisms that have developed means for survival in extreme environmental conditions. We are utilizing novel techniques for analysis of lipid biomarkers in the Antarctic Dry Valleys in order to identify resident microbes in the Antarctic soil and permafrost, as well as biomarker fossils of organisms that survived in the valleys in ages past. Through the identification of these life forms, we hope to understand and draw on new biological tools and strategies for synthetic biological applications on Mars.

Rothschild, Lynn↗
NASA NTRS2017

A PCR Based Microbial Monitoring Alternative Method of Detection and Identification of Microbes Aboard ISS

Previous research has shown that microorganisms and potential human pathogens have been detected on the International Space Station (ISS) with additional introduction of new microflora occurring with every exchange of crew or addition of equipment and supplies. These microbes are readily transferred between crew and subsystems (i.e. ECLSS, environmental control and life support systems). As this can be detrimental to astronaut health and optimal performance of ISS systems, monitoring of systems such as ECLSS to include identification of microbial contaminants could prevent adverse effects on human health and life support systems. Current monitoring on ISS is laborious and utilizes culture based methods followed by sample return to Earth for complete analysis. Future, long-distance spaceflight missions will require real-time monitoring capabilities that enable efficient and rapid assessments of the microbial environment allowing for expedited decisions and more targeted response to cope with anomalies. Polymerase chain reaction (PCR), a molecular microbial monitoring method was chosen and numerous PCR instruments investigated for their potential to perform in microgravity conditions. Using ISS as a test bed for PCR verification in microgravity will enable NASA to assess whether molecular based microbiological sensors may be components of reliable, closed-loop life support and habitation systems in spacecraft, enhancing infrastructure capabilities through increased efficiency, reliability, and time savings by enabling sample analysis on orbit. NASA selected the Water Monitoring Suite as one of the rapid spaceflight hardware demonstration activities utilizing a streamlined process to minimize the time required to fly experimental flight hardware. The RAZOR EX (BioFire Defense, Salt Lake City, UT) system was part of the water monitoring suite and is a commercial off-the-shelf (COTS) real-time PCR instrument designed for field work. The RAZOR EX was originally designed for Department of Defense (DoD) under a small business innovative research (SBIR) grant and is ruggedized, compact and provides a rapid, sample to answer in less than an hour. PCR assays using a fluorescent probe were optimized and spiked with known concentrations of DNA (Pseudomonas aeruginosa) ranging from 0.002 to 20 ng. PCR reagents were lyophilized and configured in customized pouches and tested for flight readiness. Three types of water were used to rehydrate the reagents and demonstrate the fidelity of the PCR reaction in microgravity. Molecular grade deionized water served as a control while filtered and unfiltered ISS potable water served to test for chemical or biological inhibitors. All three types were compared to parallel ground test results. Nine tests were run on ISS (3 of each water type) and the critical threshold cycle (Ct) was compared to parallel ground tests completed at Kennedy Space Center, FL and Johnson Space Center, TX. All concentrations of Pseudomonas aeruginosa DNA were detected. A comparison of the Ct produced in real time PCR indicated similarity between flight and ground samples. There appeared to be no significant difference between flight or ground PCR reactions or between any of the three water types. This testing demonstrated the ability to perform molecular testing during spaceflight operations with similar sensitivity. It will allow for future ground development of molecular protocols and minimize the need for spaceflight testing. Future testing will include development of additional targets including environmental and health related organisms.

Christina Khodadad↗
DOE OSTI2020

Ecosystem for determining plant-microbe interactions

Disclosed herein are systems, methods, and devices for determining plant-microbe interactions. In some embodiments, the device comprises: a root chamber configured to allow a root of a plant to grow, wherein the root chamber is connected with: an inlet channel for introducing a medium into the root chamber, an outlet channel for collecting plant exudates and metabolites, and a plant reservoir for the plant shoot of the plant to grow.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Recombineering machinery to increase homology directed genome editing in thermophilic microbes

A native Type I-B and heterologous Type II Clustered Regularly-Interspaced Short Palindromic Repeat/cas systems were developed and characterize to improve the ability to engineer C. thermocellum and other thermophilic microbes. The native Type I-B system was engineered for genome editing. For the Type I-B system, an engineered strain, termed LL1586, yielded 40% genome editing efficiency at the pyrF locus. When recombineering machinery was expressed the efficiency was increased to 71%. For the Type II GeoCas9 system, 12.5% genome editing efficiency was observed. When recombineering machinery was expressed, this increased to 94%. By combining the thermophilic CRISPR system (either Type I-B or Type II) with the recombinases, a new tool was developed that allows for efficient CRISPR editing. The tools provided herein enable CRISPR technologies to better engineer C. thermocellum, including engineering C. thermocellum for both increased lignocellulose degradation and biofuel production.

Eckert, Carrie↗
DOE OSTI2025

Predicting receptor-ligand pairing preferences in plant-microbe interfaces via molecular dynamics and machine learning

Microbiome assembly, structure, and dynamics significantly influence plant health. Secreted microbial signaling molecules initiate and mediate symbiosis by binding to structurally compatible plant receptors. For example, lipo-chitooligosaccharides (LCOs), produced by nitrogen-fixing rhizobial bacteria and various fungi, are recognized by plant lysin motif receptor-like kinases (LysM-RLKs), which activate the common symbiotic pathway. Accurately predicting these molecular interactions could reveal complementary signatures underlying the initial stages of endosymbiosis. Despite the breakthrough in protein-ligand structure prediction with deep learning-based tools, such as AlphaFold3, the large size and highly flexible nature of signaling compounds like LCOs present major challenges for detailed structural characterization and binding-affinity prediction. Typical structure-/physics-based methods of ligand virtual screening are designed for small, drug-like molecules, often rely on high-resolution, experimentally determined structures of the protein receptors, and rarely achieve sufficient sampling to obtain converged thermodynamic quantities with large ligands. In this study, we developed a hybrid molecular dynamics/machine learning (MD/ML) approach capable of predicting binding affinity rankings with high accuracy in systems involving large, flexible ligands, despite limited experimental structural information. Using coarse initial structural models, the predictions using the MD/ML workflow achieved strong alignment with experimental trends, particularly in the top-affinity tier for four legume LysM-RLKs (LYR3) binding to LCOs and a chitooligosaccharide. Furthermore, the MD-based conformation selection protocol provided critical structural insights into substrate specificity and binding mechanisms. This study demonstrates a powerful method to screen for challenging cognate ligand-receptors and advance our understanding of the molecular basis of microbial colonization in plants.

Lipo-chitooligosaccharides↗
DOE OSTI2025

Accumulation of Soil Microbial Necromass Controlled by Microbe–Mineral Interactions

Soil organic matter (SOM) is a key reservoir for global carbon (C), supporting soil fertility and influencing greenhouse gas emissions. Microbial residues, composed of dead cells and cellular fragments, are major contributors to SOM formation. Yet, mechanisms by which minerals enhance the accumulation of microbial residues remain poorly understood. Here, we used 13 C-labeled glucose in a year-long incubation to trace microbial residue in sandy and silty soils. Across both soils, approximately 89% of retained microbial 13 C was recovered in the fine (<53 μm) mineral-associated organic matter (MAOM) pool. Within this pool, the light MAOM fraction, enriched in poorly crystalline Fe minerals, held 4.3 times more 13 C than the heavy, phyllosilicate-dominated MAOM fraction, despite accounting for only 17.2% of the total MAOM mass and 12.3% of the total soil mass. Along with 13 C enrichment, the light MAOM fraction showed greater abundance of N-containing groups, e.g., (amides and amino groups), indicative of microbial-derived compounds like proteins and amino sugars. Fe oxides in light MAOM from both soils were spatially dispersed. Microbial residue accumulation was greater in finer-textured silty soil. These findings demonstrate that mineral composition and texture jointly regulate microbial necromass accrual, highlighting light MAOM as a key pool for enhancing soil C storage.

13C isotope labeling↗
DOE OSTI2025

Syntrophic bacterial and host–microbe interactions in bacterial vaginosis

Bacterial vaginosis (BV) is a common, polymicrobial condition of the vaginal microbiota that is associated with symptoms such as malodor and excessive discharge, along with increased risk of various adverse sequelae. Host–bacteria and bacteria–bacteria interactions are thought to contribute to the condition, but many of these functions have yet to be elucidated. Using untargeted metaproteomics, we identified 1068 host and 1418 bacterial proteins in a set of cervicovaginal lavage samples collected from 20 participants with BV and 9 who were negative for the condition. We identified Dialister micraerophilus as a major producer of malodorous polyamines and identified a syntrophic interaction between this organism and Fannyhessea vaginae that leads to increased production of putrescine, a metabolite characteristic of BV. Although formate synthesis has not previously been noted in BV, we discovered diverse bacteria associated with the condition express pyruvate formate-lyase enzymes in vivo and confirm these organisms secrete formic acid in vitro. Sodium hypophosphite efficiently inhibited this function in multiple taxa. We also found that the fastidious organism Coriobacteriales bacterium DNF00809 can metabolize formic acid secreted by Gardnerella vaginalis, representing another syntrophic interaction. We noted an increased abundance of the host epithelial repair protein transglutaminase 3 in the metaproteomic data, which we confirmed by enzyme-linked immunosorbent assay. Other proteins identified in our samples implicate Finegoldia magna and Parvimonas micra in the production of malodorous trimethylamine. Some bacterial proteins identified represent novel targets for future therapeutics to disrupt BV communities and promote vaginal colonization by commensal lactobacilli.

bacterial vaginosis↗
DOE OSTI2022

Evaluation of Protein Extraction Methods for Metaproteomic Analyses of Root-Associated Microbes

Metaproteomics is a powerful tool for the characterization of metabolism, physiology, and functional interactions in microbial communities, including plant-associated microbiota. However, the metaproteomic methods that have been used to study plant-associated microbiota are very laborious and require large amounts of plant tissue, hindering wider application of these methods. We optimized and evaluated different protein extraction methods for metaproteomics of plant-associated microbiota in two different plant species (Arabidopsis and maize). Our main goal was to identify a method that would work with low amounts of input material (40 to 70 mg) and that would maximize the number of identified microbial proteins. We tested eight protocols, each comprising a different combination of physical lysis method, extraction buffer, and cell-enrichment method on roots from plants grown with synthetic microbial communities. We assessed the performance of the extraction protocols by liquid chromatography-tandem mass spectrometry–based metaproteomics and found that the optimal extraction method differed between the two species. For Arabidopsis roots, protein extraction by beating whole roots with small beads provided the greatest number of identified microbial proteins and improved the identification of proteins from gram-positive bacteria. For maize, vortexing root pieces in the presence of large glass beads yielded the greatest number of microbial proteins identified. Based on these data, we recommend the use of these two methods for metaproteomics with Arabidopsis and maize. Furthermore, detailed descriptions of the eight tested protocols will enable future optimization of protein extraction for metaproteomics in other dicot and monocot plants.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

TES: Modelling Microbes to Predict Post-Fire Carbon Cycling in the Boreal Forest across Burn Severities (Exploratory Proposal)

Wildfires in boreal ecosystems represent a globally significant ecological process that is expected to be sensitive to changing climate as well as forest management strategies, but is currently insufficiently understood and represented in models. We sought to determine whether linking belowground microbial community composition, size, and activity to aboveground properties of burn severity and plant community composition (upland jack pine and upland spruce) would allow us to better model post-fire soil CO 2 fluxes using the Carbon, Organisms, Rhizosphere and Protection in the Soil Environment (CORPSE) model. We used an integrated modelling experimental approach, with mechanistic laboratory experiments designed to inform models.

54 ENVIRONMENTAL SCIENCES↗
NASA NTRSDate not supplied

Microbes Share Rides Too: Updating Encapsulated Bioburden Estimate Values in Electronic Parts Common to Class D Mission Platforms.

As NASA develops more planetary protection missions that are Category III and in the Class D/rideshare mission platform, there is an increasing reliance on estimation of prelaunch bioburden to understand needs for burn up and breakup analyses or other methods to meet pre-launch bioburden levels. Current levels estimated for the encapsulated bioburden of semiconductor parts cited by NASA have been based on estimates of semiconductor manufacturing approaches from the 1970s that do not incorporate over fifty years of evolving cleanliness of semiconductor manufacturing processes and facilities. This investigation will focus on direct sampling of semiconductor parts for encapsulated bioburden values, drawing upon Goddard’s strength in EEE parts, supply chain management, destructive parts analysis and existing local planetary protection lab facilities to prepare and measure encapsulated bioburden at a statistically significant level for standard electronics parts common to known Class D/rideshare platforms.

planetary protection↗
NASA NTRSDate not supplied

Microbes Share Rides Too: Updating Encapsulated Bioburden Estimate Values in Electronic Parts Common to Class D Missions

As NASA develops more planetary protection missions that are Category III and in the Class D/rideshare mission platform, there is an increasing reliance on estimation of prelaunch bioburden to understand needs for burn up and breakup analyses or other methods to meet pre-launch bioburden levels. Current levels estimated for the encapsulated bioburden of semiconductor parts cited by NASA have been based on estimates of semiconductor manufacturing approaches from the 1970s that do not incorporate the evolving cleanliness of semiconductor manufacturing since that time. This investigation will focus on direct sampling of semiconductor parts for encapsulated bioburden values, drawing upon Goddard’s strength in EEE parts, supply chain management, destructive parts analysis and existing local planetary protection lab facilities to prepare and measure encapsulated bioburden at a statistically significant level for standard electronics parts common to known Class D/rideshare platforms.

planetary protection↗
DOE OSTI2021

Sink Engineering in Photosynthetic Microbes

Photosynthetic organisms must balance harvested light energy (source) with a corresponding capacity to utilize the energy via downstream metabolic processes (sink). Insufficient source energy leads to starvation conditions, while insufficient sink capacity results in an overreduction of the electron transport chain, reduced photosynthetic efficiency, and photodamage. Despite the central importance of source/sink balancing in photosynthesis, our understanding of the mechanisms used to control this process in remains poor across diverse phototrophs. In particular, these balancing processes are essentially unstudied in cyanobacteria and microalgae, which possess distinct needs relative to the multicellular plants that have served as the model organisms for elucidating source/sink pathways. Recent bioengineering efforts have uncovered phenomena that are consistent with a well-developed source/sink sensing machinery in unicellular phototrophs. Furthermore, a deeper understanding of the fundamental mechanisms underlying source/sink dynamics in cyanobacteria and algae may prove to be critical for our capacity to boost photosynthetic efficiencies in these organisms, and enable their use as alternative crop species.

Carbon Fixation↗
DOE OSTI2020

Rhizosphere Carbon Turnover from Cradle to Grave: The Role of Microbe–Plant Interactions

Plant roots are the primary source of organic materials that become stabilized in soil. While most root carbon is decomposed into carbon dioxide (CO 2 ), the remainder typically undergoes multiple microbial transformations before it forms longer-term associations with soil minerals. However, the mechanisms by which roots affect microbial utilization of organic materials and subsequent mineral stabilization processes are poorly understood. It is well known that living roots increase the biomass of nearby microbial communities, and shape their population dynamics, diversity, and interactions. Community assembly and metabolic potential of these rhizosphere-enriched microorganisms are strongly influenced by the chemical composition of the exudates released by the host plant. The root exudate pools of plants undergo compositional changes as they grow, reproduce, and senesce. In the well-studied annual grasses Avena barbata and Avena fatua, this changing rhizosphere substrate pool and the “bloom” of organisms that respond are phylogenetically coherent; Acidobacteria and Actinobacteria are consistently depleted, whereas Alpha and Betaproteobacteria and Bacteroidetes are reliably enriched. When compared to non-root-influenced bulk soils, the responsive community is predictably less taxon-rich, yet forms more complex networks. Finally, these rhizosphere dynamics have significant downstream effects on the colonization of nearby soil minerals, degradation of prior season’s root litters, and the balance of stabilized versus lost soil carbon.

Pett-Ridge, Jennifer↗