Results for “Understanding Of Microbiome” — Page 3

NASA NTRSDate not supplied

Development of Computational Environmental Microbiome Workflows for the Laboratory and the International Space Station

Identification of microorganisms in the spaceflight environment is critical for crew health risk assessment on the International Space Station (ISS). Since 2017, nanopore sequencing technology has been used to support thein situ identification of microbial species during spaceflight. Beginning in 2018, a culture-independent, swab-to-sequencer method was implemented onboard the ISS to provide a more thorough insight of the ISS microbiome. Eliminating microbial culture enables identification of difficult-to-culture organisms, reduces risks associated with potentially pathogenic cultures, and could significantly reduce the time from sample-to-answer. However, this molecular-based approach generates large metagenomic datasets that require substantial computational resources for analysis. To process nanopore-generated sequencing data, the JSC Microbiology Laboratory established a bioinformatics workflow on Amazon EC2 under the security guidance of the NASA Science Managed Cloud Environment (SMCE).This resource allows for the development, testing, and accessing of computational tools for processing large and complex datasets. The work described here will address the downlinking of data from the ISS, the automated pipeline developed to identify targeted bacterial and fungal organisms, and the time from sampling onboard to microbial identification. The pipelines have been enhanced to address high and low biomass samples using optimization based on sample source (air, water, or surface) and type of collection (filter, colony, or swab).The resulting microbiome data can be assessed beyond microbial identifications to gain understanding toward population changes over time, potential selective environmental pressures, and evaluating correlations with a wide range of additional data sets. Metagenome analysis pipelines in development could allow for simultaneous identification of microbial species, gene function, and gene pathways present in the environment. Beyond the ground processing, the developed analysis pipeline is currently deployed onboard the ISS to allow for near real-time assessments of the ISS microbiome. This study serves as a critical foundation for exploration missions, where rapid microbiome analyses will be required.

G. Marie Sharp↗

DOE OSTI2025

Distinct Fracture Mineralogy That is Out of Equilibrium With Modern Groundwaters Provides Important Context for Subsurface Life

Rock fracture surfaces in the crust are essential habitat for microorganisms. Fracture‐groundwater interfaces provide physical substrates for biofilm growth and are sources of carbon, nutrients, and electron donors and acceptors. To better understand geochemical processes impacting fracture surfaces and the subsurface microbiome, we identified fractures in archived rock cores from the Soudan formation, which is known to host saline groundwaters and isolated microbial communities dependent on rock‐water interactions. Cores with open fractures were thin sectioned and studied via electron microprobe and synchrotron X‐ray fluorescence microprobe. Most fracture surfaces had mineralogy distinct from that of the bulk rock. Chlorite minerals were abundant on fracture surfaces and had elemental compositions suggesting deposition during late‐stage hydrothermal alteration. Fracture‐lining chlorites likely limit access to iron oxide and sulfide minerals that are active in subsurface biogeochemical cycles. Calcium‐rich rinds were also observed along fracture edges. These rinds were too thin and poorly ordered to be identified via light microscopy or X‐ray diffraction; however, Ca K‐edge micro‐X‐ray absorption near‐edge structure spectroscopy identified them as carbonates, minerals not observed in the bulk rock. Thermodynamic modeling shows that carbonate precipitation is largely unfavorable in Soudan groundwaters, indicating that fracture edge conditions differed from those in modern water samples. Because of the low carbon concentrations in Soudan groundwaters, carbonate rinds likely play an important role in subsurface carbon cycling and may mark fracture surfaces that once hosted biofilms. Overall, this study suggests that fracture alteration can both play an active role in and suppress rock‐water interactions essential to subsurface life.

36 MATERIALS SCIENCE↗

DOE OSTI2024

Barcoded overexpression screens in gut Bacteroidales identify genes with roles in carbon utilization and stress resistance

Abstract A mechanistic understanding of host-microbe interactions in the gut microbiome is hindered by poorly annotated bacterial genomes. While functional genomics can generate large gene-to-phenotype datasets to accelerate functional discovery, their applications to study gut anaerobes have been limited. For instance, most gain-of-function screens of gut-derived genes have been performed in Escherichia coli and assayed in a small number of conditions. To address these challenges, we develop Barcoded Overexpression BActerial shotgun library sequencing (Boba-seq). We demonstrate the power of this approach by assaying genes from diverse gut Bacteroidales overexpressed in Bacteroides thetaiotaomicron . From hundreds of experiments, we identify new functions and phenotypes for 29 genes important for carbohydrate metabolism or tolerance to antibiotics or bile salts. Highlights include the discovery of a d -glucosamine kinase, a raffinose transporter, and several routes that increase tolerance to ceftriaxone and bile salts through lipid biosynthesis. This approach can be readily applied to develop screens in other strains and additional phenotypic assays.

59 BASIC BIOLOGICAL SCIENCES↗

NASA NTRS2019

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↗

NASA NTRSDate not supplied

Space Crop Production

As astronauts venture farther from Earth, and for longer periods, food will become increasingly critical. Crop production can supplement a packaged diet to provide additional nutrients and variety for astronauts. Testing with the Veggie and Advanced Plant Habitat chambers on the International Space Station is allowing us to understand the impacts of gravity and spaceflight on crop growth and nutritional content, and the importance of plants to astronauts living and working away from our home planet. The space environment presents unique challenges to crop production, and technology and knowledge gaps have been identified. Key gaps include how to: - Identify and demonstrate effective options to provide both water and oxygen to the root zone in microgravity - Understand the deep space radiation impacts on seeds and plants - Investigate the relationship between microbiomes and food safety - Store and handle seeds to ensure they are viable, free of contaminants and long-lived - Identify / develop potential crops suitable for the space environment - Understand automation and human factors - Determine scalability for different concepts and architectures Filling these gaps will help enable future human exploration and move us toward Earth-independence.

Space Crop Production↗

NASA NTRSDate not supplied

Space Crop Production

As astronauts venture farther from Earth, and for longer periods, food will become increasingly critical. Crop production can supplement a packaged diet to provide additional nutrients and variety for astronauts. Testing with the Veggie and Advanced Plant Habitat chambers on the International Space Station is allowing us to understand the impacts of gravity and spaceflight on crop growth and nutritional content, and the importance of plants to astronauts living and working away from our home planet. The space environment presents unique challenges to crop production, and technology and knowledge gaps have been identified. Key gaps include how to: • Identify and demonstrate effective options to provide both water and oxygen to the root zone in microgravity • Understand the deep space radiation impacts on seeds and plants • Investigate the relationship between microbiomes and food safety • Store and handle seeds to ensure they are viable, free of contaminants and long-lived • Identify / develop potential crops suitable for the space environment • Understand automation and human factors • Determine scalability for different concepts and architectures Filling these gaps will help enable future human exploration and move us toward Earth-independence.

Veggie↗

DOE OSTI2024

Enabling Capabilities and Resources: 2024 Principal Investigator Meeting Proceedings

As a major supporter of basic genome-enabled research, BER’s Biological Systems Science Division (BSSD) fosters scientific discovery by funding - fundamental biological research across disciplines in conjunction with enabling investigational tools and computational capabilities that include world-class user facilities. The overarching goal of BSSD is to provide the necessary fundamental science to understand, predict, manipulate, and design biological systems that underpin innovations for bioenergy and bioproduct production and enhance understanding of natural, DOE-relevant environmental processes (Biological Systems Science Division Strategic Plan, 2021). To accelerate the U.S. bioeconomy, BSSD pursues innovative science underpinning advances in sustainable biofuels and bioproducts and the development of next-generation technologies and computational resources for systems biology research. The 2024 BSSD Enabling Capabilities and Resources (ECR) Principal Investigator (PI) meeting brought together PIs across the BSSD ECR portfolio to confer on shared interests and opportunities. The meeting was held concurrently with the Genomic Science program (GSP) PI meeting to optimize collaboration on research to advance bioenergy and the bioeconomy. Rick Stevens of Argonne National Laboratory gave a keynote on How Generative Artificial Intelligence Can Impact Biological Research (see Keynote: How Generative Artificial Intelligence Can Impact Biological Research, this page). Plenary presentations included several joint sessions that illuminated the integration and understanding of the larger BSSD mission. GSP’s objective is to provide systems-level understanding of plants, microbes, and their communities through its Bioenergy Research, Biosystems Design, and Environmental Microbiome Research portfolios. The objective of the ECR portfolio is to support development of computational and instrumental platforms to advance fundamental GSP research—and BER more broadly— toward the overall goal of understanding the functional principles of living systems and their response to environmental challenges.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2026

Switchgrass-associated soil microbes have subtle but distinct effects on germination vs. growth under drought

Soil microbial communities can play a large role in plant fitness, including plants’ response to drought. How microbes mediate drought response may also differ across the plants’ life stage, but studies rarely study causal effects of microbes on plant fitness at multiple stages. We conducted a greenhouse experiment on switchgrass (Panicum virgatum L.) to investigate how microbial presence (sterile bulk vs. live bulk soils) and microbial source (communities from bulk vs. rhizosphere soil) affect germination and seedling growth (life-stage) during drought. We also investigated how drought and life-stage alter the assembly of the inoculated communities. Both drought conditions and the absence of microbes reduced germination (49% and 50% fewer seedlings, respectively, p < 0.05), but there were few effects of microbial presence on older seedlings. In addition, microbial source had no effect on the evaluated plant traits, but interestingly, the initially similar bulk and rhizosphere communities became compositionally distinct after 34 days with germinating seeds, but not with seedlings. Therefore, it may be that the plants did respond to microbial source through changes in seed or root exudates, and calls for further study. Finally, while sometimes microbes did benefit plants under drought, we did not find evidence that they are especially beneficial in this condition. We suggest that microbes’ effects differ across plant life stage, and may be both positive and negative. Further research should advance understanding of plant stress tolerance within a framework of plant-microbiome co-development.

drought↗

DOE OSTI2024

A global atlas of soil viruses reveals unexplored biodiversity and potential biogeochemical impacts

Historically neglected by microbial ecologists, soil viruses are now thought to be critical to global biogeochemical cycles. However, our understanding of their global distribution, activities and interactions with the soil microbiome remains limited. Here we present the Global Soil Virus Atlas, a comprehensive dataset compiled from 2,953 previously sequenced soil metagenomes and composed of 616,935 uncultivated viral genomes and 38,508 unique viral operational taxonomic units. Rarefaction curves from the Global Soil Virus Atlas indicate that most soil viral diversity remains unexplored, further underscored by high spatial turnover and low rates of shared viral operational taxonomic units across samples. By examining genes associated with biogeochemical functions, we also demonstrate the viral potential to impact soil carbon and nutrient cycling. This study represents an extensive characterization of soil viral diversity and provides a foundation for developing testable hypotheses regarding the role of the virosphere in the soil microbiome and global biogeochemistry.

59 BASIC BIOLOGICAL SCIENCES↗

NASA NTRSDate not supplied

Plants in Space and Space Crop Production

As astronauts venture farther from Earth, and for longer periods, the space food system will increase in importance. Crop production can supplement a packaged diet to provide additional nutrients and dietary variety for astronauts, and in future missions, bioregenerative approaches may be used to generate a larger percentage of the diet. Plants may also provide behavioural health benefits and assist with other life support functions. Several unique challenges exist for growth of plants in microgravity and on other planetary surfaces like the moon and Mars. Testing with the Veggie and Advanced Plant Habitat (APH) chambers on the International Space Station is allowing us to understand the impacts of gravity and spaceflight on crop growth, nutritional content, acceptability, and the importance of plants to astronauts living and working away from Earth. We are also gaining a better understanding of food safety concerns and the behaviour of space plant microbiomes and plant pathogens. As we transition from research towards operational space crop production to enable human exploration, there are several gaps and challenges of growing crops in space that must be addressed. Research and technology development in key areas such as water and nutrient delivery, plant health monitoring, and crop selection are needed to overcome these challenges. Additionally, there are opportunities for breeding or engineering of custom space crops related to plant growth and development, plant physiology, produce nutrition, organoleptic acceptability, and post-harvest characteristics. Solutions to help ensure food security off-Earth may also translate to better approaches to terrestrial sustainable crop production.

Advanced Plant Habitat↗

NASA NTRS2023

Plants in Space and Space Crop Production

As astronauts venture farther from Earth, and for longer periods, the space food system will increase in importance. Crop production can supplement a packaged diet to provide additional nutrients and dietary variety for astronauts, and in future missions, bioregenerative approaches may be used to generate a larger percentage of the diet. Plants may also provide behavioural health benefits and assist with other life support functions. Several unique challenges exist for growth of plants in microgravity and on other planetary surfaces like the moon and Mars. Testing with the Veggie and Advanced Plant Habitat (APH) chambers on the International Space Station is allowing us to understand the impacts of gravity and spaceflight on crop growth, nutritional content, acceptability, and the importance of plants to astronauts living and working away from Earth. We are also gaining a better understanding of food safety concerns and the behaviour of space plant microbiomes and plant pathogens. As we transition from research towards operational space crop production to enable human exploration, there are several gaps and challenges of growing crops in space that must be addressed. Research and technology development in key areas such as water and nutrient delivery, plant health monitoring, and crop selection are needed to overcome these challenges. Additionally, there are opportunities for breeding or engineering of custom space crops related to plant growth and development, plant physiology, produce nutrition, organoleptic acceptability, and post-harvest characteristics. Solutions to help ensure food security off-Earth may also translate to better approaches to terrestrial sustainable crop production.

Advanced Plant Habitat↗

NASA NTRSDate not supplied

Space Crop Production Gaps and Challenges

As astronauts venture farther from Earth, and stay for longer periods, the space food system will increase in importance. Crop production can supplement a pre-packaged space diet to provide nutrition and dietary variety for space crews. In future missions, bioregenerative approaches may be used to generate a larger percentage of the diet, as well as help to reduce life support system burdens and resupply from Earth. Plants may also provide behavioral health benefits to crew members living in the isolated, confined environment of a space habitat. A number of unique challenges exist for growth of plants in microgravity and on other reduced gravity surfaces like the moon and Mars. Testing plant growth inside the Veggie and Advanced Plant Habitat (APH) chambers on the International Space Station is allowing us to understand the impacts of gravity and spaceflight on crop growth, nutritional content, acceptability, and the importance of plants to astronauts living and working away from Earth. We are also gaining a better understanding of food safety concerns and the behavior of space plant microbiomes and plant pathogens, but major gaps in knowledge remain. As we move from research towards operational space crop production to enable exploration, there are numerous gaps in technology, knowledge, and practice related to space crop growth that must be addressed. Research and development in key focus areas such as effective water and nutrient delivery at variable gravity levels, autonomous plant health monitoring, growth system cleaning and disinfection, and selection of ideal space crops are needed to fill these gaps. Breeding or engineering custom space crops may impact areas including plant growth and development, plant physiology, produce nutrition, organoleptic acceptability, and post-harvest characteristics, and these may further enable space crop production scenarios. Space crop challenges are multifaceted and require diverse interdisciplinary teams working together to develop effective solutions. Solving these requires an array of skill sets from across the biological and physical sciences, engineering, and human social sciences. Solutions to help ensure food security off-Earth may also translate to more sustainable terrestrial crop production approaches, and regular dialog between industry, academia, and government organizations working in related fields benefit all. Additional help can come from engagement with student researchers at various levels through courses, participatory science projects, and open science activities which can provide useful data. Global coordination and integration between space agencies and partners will be essential.

Gioia Donna Massa↗

NASA NTRSDate not supplied

More Than a Decade of International Space Station Microbial Sampling in the Environmental Control and Life Support Systems

Microbial monitoring has taken place in major units belonging to the Environmental Control and Life Support Systems (ECLSS) of the International Space Station (ISS). For at least a decade multiple modules including US and RU segments were sampled. In the US ECLSS, water reclamation and air systems combine their microbial contents downstream where biofilm incidents have been recorded. Understanding the microbial contents of segments provides a longitudinal perspective to microbiome changes in the system that contribute to this issue. The US ECLSS have been consistently sampled, especially in the Potable Water Bus (PWB) where bacteria from upstream sources have been observed.

Yo-Ann Velez Justiniano↗

NASA NTRSDate not supplied

More Than a Decade of International Space Station Microbial Sampling in the Environmental Control and Life Support Systems

Microbial monitoring has taken place in major units belonging to the Environmental Control and Life Support Systems (ECLSS) of the International Space Station (ISS). For at least a decade multiple modules including US and RU segments were sampled. In the US ECLSS, water reclamation and air systems combine their microbial contents downstream where biofilm incidents have been recorded. Understanding the microbial contents of segments provides a longitudinal perspective to microbiome changes in the system that contribute to this issue. The US ECLSS have been consistently sampled, especially in the Potable Water Bus (PWB) where bacteria from upstream sources have been observed.

Yo-Ann Velez Justiniano↗

NASA NTRSDate not supplied

Space Crop Production Gaps and Challenges

As astronauts venture farther from Earth, and stay for longer periods, the space food system will increase in importance. Crop production can supplement a pre-packaged space diet to provide nutrition and dietary variety for space crews. In future missions, bioregenerative approaches may be used to generate a larger percentage of the diet, as well as help to reduce life support system burdens and resupply from Earth. Plants may also provide behavioral health benefits to crew members living in the isolated, confined environment of a space habitat. A number of unique challenges exist for growth of plants in microgravity and on other reduced gravity surfaces like the moon and Mars. Testing plant growth inside the Veggie and Advanced Plant Habitat (APH) chambers on the International Space Station is allowing us to understand the impacts of gravity and spaceflight on crop growth, nutritional content, acceptability, and the importance of plants to astronauts living and working away from Earth. We are also gaining a better understanding of food safety concerns and the behavior of space plant microbiomes and plant pathogens, but major gaps in knowledge remain. As we move from research towards operational space crop production to enable exploration, there are numerous gaps in technology, knowledge, and practice related to space crop growth that must be addressed. Research and development in key focus areas such as effective water and nutrient delivery at variable gravity levels, autonomous plant health monitoring, growth system cleaning and disinfection, and selection of ideal space crops are needed to fill these gaps. Breeding or engineering custom space crops may impact areas including plant growth and development, plant physiology, produce nutrition, organoleptic acceptability, and post-harvest characteristics, and these may further enable space crop production scenarios. Space crop challenges are multifaceted and require diverse interdisciplinary teams working together to develop effective solutions. Solving these requires an array of skill sets from across the biological and physical sciences, engineering, and human social sciences. Solutions to help ensure food security off-Earth may also translate to more sustainable terrestrial crop production approaches, and regular dialog between industry, academia, and government organizations working in related fields benefit all. Additional help can come from engagement with student researchers at various levels through courses, participatory science projects, and open science activities which can provide useful data. Global coordination and integration between space agencies and partners will be essential.

Gioia Massa↗

NASA NTRSDate not supplied

Space Crop Production Gaps and Challenges

As astronauts venture farther from Earth, and stay for longer periods, the space food system will increase in importance. Crop production can supplement a pre-packaged space diet to provide nutrition and dietary variety for space crews. In future missions, bioregenerative approaches may be used to generate a larger percentage of the diet, as well as help to reduce life support system burdens and resupply from Earth. Plants may also provide behavioral health benefits to crew members living in the isolated, confined environment of a space habitat. A number of unique challenges exist for growth of plants in microgravity and on other reduced gravity surfaces like the moon and Mars. Testing with the Veggie and Advanced Plant Habitat (APH) chambers on the International Space Station is allowing us to understand the impacts of gravity and spaceflight on crop growth, nutritional content, acceptability, and the importance of plants to astronauts living and working away from Earth. We are also gaining a better understanding of food safety concerns and the behavior of space plant microbiomes and plant pathogens, but major gaps in knowledge remain. As we move from research towards operational space crop production to enable exploration, there are numerous gaps in technology, knowledge, and practice related to space crop growth that must be addressed.

Gioia Massa↗

DOE OSTI2025

Metabolic interactions underpinning high methane fluxes across terrestrial freshwater wetlands

Current estimates of wetland contributions to the global methane budget carry high uncertainty, particularly in accurately predicting emissions from high methane-emitting wetlands. Microorganisms drive methane cycling, but little is known about their conservation across wetlands. To address this, we integrate 16S rRNA amplicon datasets, metagenomes, metatranscriptomes, and annual methane flux data across 9 wetlands, creating the Multi-Omics for Understanding Climate Change (MUCC) v2.0.0 database. This resource is used to link microbiome composition to function and methane emissions, focusing on methane-cycling microbes and the networks driving carbon decomposition. We identify eight methane-cycling genera shared across wetlands and show wetland-specific metabolic interactions in marshes, revealing low connections between methanogens and methanotrophs in high-emitting wetlands. Methanoregula emerged as a hub methanogen across networks and is a strong predictor of methane flux. In these wetlands it also displays the functional potential for methylotrophic methanogenesis, highlighting the importance of this pathway in these ecosystems. Collectively, our findings illuminate trends between microbial decomposition networks and methane flux while providing an extensive publicly available database to advance future wetland research.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2026

Engineering Synthetic Anaerobic Consortia Inspired by the Rumen for Biomass Breakdown and Conversion

Lignocellulosic plant biomass is a widely-abundant renewable resource that can be harnessed for value-added production of fuels & chemicals. While microbes have been engineered to breakdown lignocellulose and turn released sugars into products, this remains an energy-intensive process that requires expensive pre-treatment and separation steps. Furthermore, it is difficult to engineer all desirable traits for breakdown and conversion into one organism. This project developed a new strategy that relies on microbial partnerships formed in the herbivore rumen to liberate sugars from crude plant biomass and convert that sugar to value-added chemicals. Microbial consortia consisting of fungi, bacteria, and archaea form tight associations in the herbivore rumen, which divide-and-conquer the difficult tasks of biomass breakdown. This project leveraged a “synthetic rumen” consortium composed of anaerobic fungi and chain-elongating bacteria to study which metabolites are shared and exchanged between microbes and identify strategies to bolster lignocellulose conversion to value-added products. Our approach developed high-throughput systems and synthetic biology approaches to realize stable synthetic consortia that route lignocellulosic carbon into short and medium chain fatty acids (SCFAs/MCFAs) rather than methane. Key research objectives were to (1) design and predict anaerobic fungal and bacterial consortia that efficiently convert lignocellulosic biomass into medium-chain fatty acids (MCFAs), (2) understand how fermentation parameters and microbe-microbe interactions regulate and drive microbiome metabolic fluxes, and (3) use genomic editing to alter the fermentation byproducts of anaerobic fungi and bolster MCFA titers and yields.

09 BIOMASS FUELS↗