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At least 19 records
All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

Meta Biome: a multiscale model integrating agent-based and metabolic networks to reveal spatial regulation in gut mucosal microbial communities

ABSTRACT Mucosal microbial communities (MMCs) are complex ecosystems near the mucosal layers of the gut essential for maintaining health and modulating disease states. Despite advances in high-throughput omics technologies, current methodologies struggle to capture the dynamic metabolic interactions and spatiotemporal variations within MMCs. In this work, we presentMetaBiome, a multiscale model integrating agent-based modeling (ABM), finite volume methods, and constraint-based models to explore the metabolic interactions within these communities. Integrating ABM allows for the detailed representation of individual microbial agents each governed by rules that dictate cell growth, division, and interactions with their surroundings. Through a layered approach—encompassing microenvironmental conditions, agent information, and metabolic pathways—we simulated different communities to showcase the potential of the model. Using ourin-silicoplatform, we explored the dynamics and spatiotemporal patterns of MMCs in the proximal small intestine and the cecum, simulating the physiological conditions of the two gut regions. Our findings revealed how specific microbes adapt their metabolic processes based on substrate availability and local environmental conditions, shedding light on spatial metabolite regulation and informing targeted therapies for localized gut diseases.MetaBiome provides a detailed representation of microbial agents and their interactions, surpassing the limitations of traditional grid-based systems. This work marks a significant advancement in microbial ecology, as it offers new insights into predicting and analyzing microbial communities. IMPORTANCE Our study presents a novel multiscale model that combines agent-based modeling, finite volume methods, and genome-scale metabolic models to simulate the complex dynamics of mucosal microbial communities in the gut. This integrated approach allows us to capture spatial and temporal variations in microbial interactions and metabolism that are difficult to study experimentally. Key findings from our model include the following: (i) prediction of metabolic cross-feeding and spatial organization in multi-species communities, (ii) insights into how oxygen gradients and nutrient availability shape community composition in different gut regions, and (iii) identification of spatiallyregulated metabolic pathways and enzymes inE. coli. We believe this work represents a significant advance in computational modeling of microbial communities and provides new insights into the spatial regulation of gut microbiome metabolism. The multiscale modeling approach we have developed could be broadly applicable for studying other complex microbial ecosystems.

Microbiology↗
NASA NTRS2020

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↗
NASA NTRS2005

The Influence of Ecological Isolation on the Structural and Functional Stability of Complex Microbial Communities

To help understand how the behavior of microorganisms and microbial communities in insular space habitats may differ from the behavior of these groups on Earth, long-term incubations (100+ days) were conducting using wastewater bioreactors (batch fed) designed to mimic "closed" and "open" ecological systems. The issue of immigration was considered, and the goal of the research was to determine whether the stability of microbial communities in space is reduced due to their prolonged isolation. Bioreactors were established by inoculating flasks of sterile synthetic wastewater with the microbial community obtained from a local treatment facility; each day, one-third of the medium in the flask was replaced with an equal volume of sterile artificial wastewater. Flasks were divided into two treatments: "closed" and "open" to recruitment of additional microorganisms. "Closed" flasks were maintained as described above, while the medium used to feed the "open" flasks was supplemented daily with a small amount of raw sewage (which provided a continuous source of new potential community members). Significant differences in microbial community structure and function developed in the two sets of communities, and the results suggest that the open community was more stable and better able to adjust to changing environmental conditions. Each community's resistance to environmental (temperature fluctuations) and biological stresses (starvation and invasion by an opportunistic pathogen Pseudomonas aeruginosa) was monitored. Experiments were also conducted to determine whether the effect of isolation changes depending on the microbial communities' initial diversity or composition; communities with a low(er) initial diversity were less stable. Overall, the results indicate that isolation will be an important factor influencing the activity of microbial communities on board spacecraft. A possible way of mitigating these effects would be to include communities with high initial diversity or to periodically re-inoculate the systems using diverse inocula transported from Earth.

Franklin, R. B.↗
DOE OSTI2025

The overlooked interaction of emerging contaminants and microbial communities: a threat to ecosystems and public health

Abstract Context and aims Emerging contaminants (ECs) and microbial communities should not be viewed in isolation, but through the One Health perspective. Both ECs and microorganisms lie at the core of this interconnected framework, as they directly influence the health of humans, animals, and the environment. The interactions between ECs and microbial communities can have profound implications for public health, affecting all three domains. However, these ECs-microorganism interactions remain underexplored, potentially leaving significant public health and ecological risks unrecognized. Therefore, this article seeks to alert the scientific community to the overlooked interactions between ECs and microbial communities, emphasizing the pivotal role these interactions may play in the management of ‘One Health.’ Results The most extensively studied interaction between ECs and microbial communities is biodegradation. However, other more complex and concerning interactions demand attention, such as the impact of ECs on microbial ecology (disruptions in ecosystem balance affecting nutrient and energy cycles) and the rise and spread of antimicrobial resistance (a growing global health crisis). Although these ECs-microbial interactions had not been extensively studied, there are scientific evidence that ECs impact on microbial communities may be concerning for public health and ecosystem balance. Conclusions So, this perspective summarizes the impact of ECs through a One Health lens and underscores the urgent need to understand their influence on microbial communities, while highlighting the key challenges researchers must overcome. Tackling these challenges is vital to mitigate potential long-term consequences for both ecosystems and public health.

Gomes, Inês B. (ORCID:0000000207313662)↗
DOE OSTI2025

Short-term warming increased soil heterotrophic respiration due to enhanced active microbial community

Soil microbes, particularly active microbes, play a crucial role in conserving soil carbon under climate change, especially in forest ecosystems, constituting over 50% of global soil organic carbon. Nevertheless, the response mechanisms of active microbial community to climate warming and their subsequent impacts on soil heterotrophic respiration (Rh) remain insufficiently understood. To resolve this mechanistic uncertainty, we implemented a 3-year soil translocation experiment to investigate soil warming effects on active microbial community and Rh. We used 16S rRNA gene amplicon sequencing, Metatranscriptomics sequencing, coupled with correlation analyses to explore the linkages between warming-induced shifts in Rh and the active microbial community. Our results demonstrated that warming of soil induced a 55% enhancement in Rh. Concurrently, the Shannon index and Richness of active microbial community increased by 20% and 117%, respectively. Warming significantly altered active microbial community composition, inducing a compositional shift characterized by 0.5-to 2-fold increases in the abundances of Proteobacteria, Chloroflexi, and Actinobacteria. Our study also revealed 92–100% increases in the abundance of C-degradation functional genes encoding starch, cellulose, and lignin decomposition pathways within active microbial community under warming. Statistical analyses identified significant positive correlations between Rh and the abundance of Proteobacteria and Actinobacteria, as well as expression levels of functional genes associated with lignin and cellulose decomposition pathways. Furthermore, our results suggested that short-term warming increased Rh through altering diversity, species composition, and C degradation functional genes of active microbial community providing insights into the influence of microbial communities on soil C-climate feedbacks under climate warming.

Active microbial community↗
NASA NTRS1988

Does iron inhibit cryptoendolithic microbial communities?

Photosynthetic activity of three cryptoendolithic microbial communities was studied under controlled conditions in the laboratory. In two of these communities, the dominant organisms were lichens, collected from Linnaeus Terrace and from Battleship Promontory. The third community, dominated by cyanobacteria, was collected from Battleship Promontory. Both sites are in the ice-free valleys of southern Victoria Land. Previous efforts have shown how physical conditions can influence metabolic activity in endolithic communities (Kappen and Friedmann 1983; Kappen, Friedmann, and Garty 1981; Vestal, Federle, and Friedmann 1984). Biological activity can also be strongly influenced by the chemical environment. Inorganic nutrients such as nitrate, ammonia, and phosphate are often limiting factors, so their effects on photosynthetic carbon-14 bicarbonate incorporation were investigated. Iron and manganese are two metals present in Linnaeus Terrace and Battleship Promontory sandstones, and their effects on photosynthesis were also studied. The results may add to our understanding of biogeochemical interactions within this unique microbial community.

Non-NASA Center↗
DOE OSTI2025

Quorum sensing modulates microbial community structure through regulation of secondary metabolites

Bacteria are recognized for their diverse metabolic capabilities, yet the impact of microbe-microbe interactions on multispecies community structure and dynamics is poorly understood. Cell-to-cell signaling in the form of quorum sensing (QS) often regulates secondary metabolite production and microbial interactions. Here, we examine how acylhomoserine lactone (AHL)-mediated QS impacts microbial community structure in a 10-member synthetic community of isolates from Populus deltoides . To explore the role of QS in microbial community structure and dynamics, we disrupted AHL signaling by exogenous addition of AiiA-lactonase, an enzyme that cleaves the lactone ring. Microbial community structure resulting from signal inactivation, as measured by 16S rRNA amplicon sequencing and secondary metabolite production, was assessed after successive passaging of the community. Further, we investigated the impact of quorum quenching on specific microbe-microbe interactions using pairwise inhibition assays. Our results indicate that AHL inactivation alters the relative abundance of dominant community members at later passages but does not impact the overall membership in the community. Quorum quenching significantly alters the metabolic profile in lactonase-treated communities. This metabolic alteration impacts microbe-microbe interactions through decreased inhibition of other community members. Together, these results indicate that QS impacts microbial community structure through the regulation of secondary metabolites in dominant members and that the membership of microbial communities can be relatively stable despite changes in metabolic profiles.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Methanogenesis and Acetogenesis in Hydrogenotrophy with Carbonate Minerals: Dependence on Mineral Surface Area, Biofilm Growth, and Microbial Community

The production, storage, and use of hydrogen are anticipated to grow substantially to achieve energy and climate goals. Consequently, microbial communities in many terrestrial and subsurface Earth environments could be exposed to elevated hydrogen concentrations. Hydrogen stimulates metabolic processes that reduce aqueous chemical species, such as bicarbonate or sulfate, that can exchange with solid mineral phases, but the controls on microbial hydrogenotrophy with mineral sources of electron acceptors are not fully understood. Herein, we applied laboratory experiments and biogeochemical modeling to study the response of a natural microbial community to an elevated partial pressure of hydrogen in the presence of carbonate minerals of varying composition, solubility, and size. Experimental incubations and simulation results showed that hydrogen consumption by microbial communities was initially dominated by sulfate reduction and, subsequently, transitioned to acetogenesis and methanogenesis. The rates of acetogenesis and methanogenesis were not correlated with the solubility of carbonate minerals. Instead, we observed strong linear correlations between the rates and surface area of carbonate minerals. Methane and acetate production slowed down in all incubations after about 2 weeks of incubation, although biogeochemical modeling predicted that the metabolic processes were not thermodynamically limited. Electron microscopy and infrared spectroscopy showed that biofilms with diverse microorganisms grew on the carbonates during this period. The methane δ13C value significantly increased, consistent with slower growth at elevated pH. This work highlights that microbial communities form biofilm on carbonate mineral surfaces as a response to hydrogen and that biofilm formation could pose a strong kinetic limitation to hydrogenotrophic metabolism utilizing carbonate minerals.

Acetobacterium↗
NASA NTRS2002

Composition and physiological profiling of sprout-associated microbial communities

The native microfloras of various types of sprouts (alfalfa, clover, sunflower, mung bean, and broccoli sprouts) were examined to assess the relative effects of sprout type and inoculum factors (i.e., sprout-growing facility, seed lot, and inoculation with sprout-derived inocula) on the microbial community structure of sprouts. Sprouts were sonicated for 7 min or hand shaken with glass beads for 2 min to recover native microfloras from the surface, and the resulting suspensions were diluted and plated. The culturable fraction was characterized by the density (log CFU/g), richness (e.g., number of types of bacteria), and diversity (e.g., microbial richness and evenness) of colonies on tryptic soy agar plates incubated for 48 h at 30 degrees C. The relative similarity between sprout-associated microbial communities was assessed with the use of community-level physiological profiles (CLPPs) based on patterns of utilization of 95 separate carbon sources. Aerobic plate counts of 7.96 +/- 0.91 log CFU/g of sprout tissue (fresh weight) were observed, with no statistically significant differences in microbial cell density, richness, or diversity due to sprout type, sprout-growing facility, or seed lot. CLPP analyses revealed that the microbial communities associated with alfalfa and clover sprouts are more similar than those associated with the other sprout types tested. Variability among sprout types was more extensive than any differences between microbial communities associated with alfalfa and clover sprouts from different sprout-growing facilities and seed lots. These results indicate that the subsequent testing of biocontrol agents should focus on similar organisms for alfalfa and clover, but alternative types may be most suitable for the other sprout types tested. The inoculation of alfalfa sprouts with communities derived from various sprout types had a significant, source-independent effect on microbial community structure, indicating that the process of inoculation alters the dynamics of community development regardless of the types of organisms involved.

NASA Center KSC↗
DOE OSTI2025

Microbial Community Analysis & Functional Evaluation in Soils

The overall objective of this proposal was to develop technologies to alter the composition and function of important members of microbial communities. In particular, the overall objective of the microbial community editing portion of the proposal focuses on developing foundational tools and understanding required to predict, alter and design grass rhizosphere communities impacting DOE missions. Specifically, the project is centered on the Microbial Community Analysis & Functional Evaluation in Soils (m-CAFES) to manipulate microbial consortia associated with plants of interest for the bioenergy sector, under the presumption that bacterial communities can be manipulated to enhance plant health. For tasks of specific interest to us, we are focusing on developing novel Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) based technologies (primarily focusing on Aim 1) and their delivery modalities (notably subaim 1.2) to edit specific bacterial genomes of interest to enhance their functionalities, and programmably ablate specific undesirable members of bacterial communities for plant health. We are focusing on engineering bacteriophages (bacterial viruses, for subaim 1.2) to carry programmable CRISPR-Cas systems (subaim 1.1) to target (ablate) or alter (edit) genomes of interest. This will enable us to carry out microbial perturbations that will impact community composition and function and ultimately plant growth and health, to enable the next phase of the project by deploying them in situ (subaims 1.3 and 1.4).

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Northern peatland microbial communities exhibit resistance to warming and acquire electron acceptors from soil organic matter

The response of microbial communities that regulate belowground carbon turnover to climate change drivers in peatlands is poorly understood. Here, we leverage a whole ecosystem warming experiment to elucidate the key processes of terminal carbon decomposition and community responses to temperature rise. Our dataset of 697 metagenome-assembled genomes (MAGs) represents the microbial community from the surface (10 cm) to 2 m deep into the peat column, with only 3.7% of genomes overlapping with other well-studied peatlands. Community composition has yet to show a significant response to warming after 3 years, suggesting that metabolically diverse soil microbial communities are resistant to climate change. Surprisingly, abundant and active methanogens in the genus Candidatus Methanoflorens, Methanobacterium , and Methanoregula show the potential for both acetoclastic and hydrogenotrophic methanogenesis. Nonetheless, the predominant pathways for anaerobic carbon decomposition include sulfate/sulfite reduction, denitrification, and acetogenesis, rather than methanogenesis based on gene abundances. Multi-omics data suggest that organic matter cleavage provides terminal electron acceptors, which together with methanogen metabolic flexibility, may explain peat microbiome composition resistance to warming.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2024

Subsurface microbial community structure shifts along the geological features of the Central American Volcanic Arc

Subduction of the Cocos and Nazca oceanic plates beneath the Caribbean plate drives the upward movement of deep fluids enriched in carbon, nitrogen, sulfur, and iron along the Central American Volcanic Arc (CAVA). These compounds fuel diverse subsurface microbial communities that in turn alter the distribution, redox state, and isotopic composition of these compounds. Microbial community structure and functions vary according to deep fluid delivery across the arc, but less is known about how microbial communities differ along the axis of a convergent margin as geological features (e.g., extent of volcanism and subduction geometry) shift. Here, we investigate changes in bacterial 16S rRNA gene amplicons and geochemical analysis of deeply-sourced seeps along the southern CAVA, where subduction of the Cocos Ridge alters the geological setting. We find shifts in community composition along the convergent margin, with communities in similar geological settings clustering together independently of the proximity of sample sites. Microbial community composition correlates with geological variables such as host rock type, maturity of hydrothermal fluid and slab depth along different segments of the CAVA. This reveals tight coupling between deep Earth processes and subsurface microbial activity, controlling community distribution, structure and composition along a convergent margin.

Science & Technology - Other Topics↗
DOE OSTI2025

Metagenome-assembled genomes from microbial communities producing lactic acid from dairy residues

To advance the knowledge of microbial communities capable of fermenting agro-industrial residues into value-added products, we report metagenomes of microbial communities from four anaerobic bioreactors fed a mixture of ultra-filtered milk permeate and cottage cheese acid whey. This analysis produced 42 unique metagenome-assembled genomes (MAGs) that represent distinct taxa.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Modest functional diversity decline and pronounced composition shifts of microbial communities in a mixed waste-contaminated aquifer

Background: Microbial taxonomic diversity declines with increased environmental stress. Yet, few studies have explored whether phylogenetic and functional diversities track taxonomic diversity along the stress gradient. Here, we investigated microbial communities within an aquifer in Oak Ridge, Tennessee, USA, which is characterized by a broad spectrum of stressors, including extremely high levels of nitrate, heavy metals like cadmium and chromium, radionuclides such as uranium, and extremely low pH (< 3). Results: Both taxonomic and phylogenetic α-diversities were reduced in the most impacted wells, while the decline in functional α-diversity was modest and statistically insignificant, indicating a more robust buffering capacity to environmental stress. Differences in functional gene composition (i.e., functional β-diversity) were pronounced in highly contaminated wells, while convergent functional gene composition was observed in uncontaminated wells. The relative abundances of most carbon degradation genes were decreased in contaminated wells, but genes associated with denitrification, adenylylsulfate reduction, and sulfite reduction were increased. Compared to taxonomic and phylogenetic compositions, environmental variables played a more significant role in shaping functional gene composition, suggesting that niche selection could be more closely related to microbial functionality than taxonomy. Conclusions: Overall, we demonstrated that despite a reduced taxonomic α-diversity, microbial communities under stress maintained functionality underpinned by environmental selection.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Root and Leaf Traits of Alfalfa Exhibit Distinct Responses to Soil Microbial Communities and Environmental Stresses

Ongoing climate change is negatively impacting crop productivity globally. Past research has highlighted that a diverse soil microbial community and variation in plant traits for resource acquisition can mitigate the negative impacts of climate change factors on crop productivity. This study investigates the effects of two major environmental stressors—drought and salinity stress, on plant productivity, biomass allocation, and root and leaf trait responses under distinct soil microbial diversities. Our results showed that salinity stress had stronger negative impacts on plant productivity than drought stress. Shoot biomass decreased by 30% and 32.5% under drought and salinity stress, respectively, whereas the root biomass decreased by 32% only under salinity stress. Soil microbial diversity did not affect plant productivity. Next, root traits were mainly impacted by drought and salinity stress, whereas leaf traits were impacted by both environmental stresses and soil microbial diversity. Specific root length and specific root area decreased under drought, and root tissue density was minimal under salinity stress. Root traits were not affected by soil microbial communities. In contrast, the leaf nitrogen content increased, whereas pheophytin content (a breakdown product of chlorophyll) decreased when plants were grown in diverse microbial communities under environmental stresses, especially drought. These results highlight the importance of soil microbial diversity in impacting plant traits in response to environmental stresses. We showed that the soil microbial diversity influences both aboveground and belowground plant traits, indicating the need for better management practices to conserve and promote soil microbial diversity.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS2011

PMA-PhyloChip DNA Microarray to Elucidate Viable Microbial Community Structure

Since the Viking missions in the mid-1970s, traditional culture-based methods have been used for microbial enumeration by various NASA programs. Viable microbes are of particular concern for spacecraft cleanliness, for forward contamination of extraterrestrial bodies (proliferation of microbes), and for crew health/safety (viable pathogenic microbes). However, a "true" estimation of viable microbial population and differentiation from their dead cells using the most sensitive molecular methods is a challenge, because of the stability of DNA from dead cells. The goal of this research is to evaluate a rapid and sensitive microbial detection concept that will selectively estimate viable microbes. Nucleic acid amplification approaches such as the polymerase chain reaction (PCR) have shown promise for reducing time to detection for a wide range of applications. The proposed method is based on the use of a fluorescent DNA intercalating agent, propidium monoazide (PMA), which can only penetrate the membrane of dead cells. The PMA-quenched reaction mixtures can be screened, where only the DNA from live cells will be available for subsequent PCR reaction and microarray detection, and be identified as part of the viable microbial community. An additional advantage of the proposed rapid method is that it will detect viable microbes and differentiate from dead cells in only a few hours, as opposed to less comprehensive culture-based assays, which take days to complete. This novel combination approach is called the PMA-Microarray method. DNA intercalating agents such as PMA have previously been used to selectively distinguish between viable and dead bacterial cells. Once in the cell, the dye intercalates with the DNA and, upon photolysis under visible light, produces stable DNA adducts. DNA cross-linked in this way is unavailable for PCR. Environmental samples suspected of containing a mixture of live and dead microbial cells/spores will be treated with PMA, and then incubated in the dark. Thereafter, the sample is exposed to visible light for five minutes, so that the DNA from dead cells will be cross-linked. Following this PMA treatment step, the sample is concentrated by centrifugation and washed (to remove excessive PMA) before DNA is extracted. The 16S rRNA gene fragments will be amplified by PCR to screen the total microbial community using PhyloChip DNA microarray analysis. This approach will detect only the viable microbial community since the PMA intercalated DNA from dead cells would be unavailable for PCR amplification. The total detection time including PCR reaction for low biomass samples will be a few hours. Numerous markets may use this technology. The food industry uses spore detection to validate new alternative food processing technologies, sterility, and quality. Pharmaceutical and medical equipment companies also detect spores as a marker for sterility. This system can be used for validating sterilization processes, water treatment systems, and in various public health and homeland security applications.

Venkateswaran, Kasthuri J.↗
NASA NTRS2005

Anaerobic decomposition of cellulose by allcaliphilic microbial Community of Owens Lake, California

The study of communities of microbial extremophiles from anaerobic sediments of Owens Lake and Mono Lake in California has established the presence of active microbial cellulolytic processes in both lakes. The prior study of the microbial diversity in Mono Lake showed that the trophic chain of organic decomposition includes secondary anaerobes that were found to be previously unknown species (Spirochaeta americana, Tindallia californiensis, and Desulfonatronum thiodismutans). And as we published earlier, the secondary anaerobes of Owens Lakes were morphologically very similar to those of Mono Lake. However, continuing comparison of the physiology and genetics has led to the conclusion that some links of organic decomposition in the trophic chain of Owens Lake are represented by different unknown species. A new isolate of a sugarlytic spirochete from Owens Lake, which was morphologically very similar to S. americana isolated from Mono Lake, was found to have different metabolic capacity such as the lack of capability to produce hydrogen during glucose fermentation. Furthermore, from the same bacterial community (from Owens Lake) another sugarlytic spore-forming alkaliphile (strain SCA) was isolated in pure culture. Here we discuss the geology and chemistry of Owens Lake as a unique ecosystem of Astrobiological significance. This paper also presents some of the characteristics for the novel isolates and describes their participation in the process of cellulose degradation.

Pikuta, Elena V.↗