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DOE OSTI2024

Gut microbiota carbon and sulfur metabolisms support Salmonella infections

Abstract Salmonella enterica serovar Typhimurium is a pervasive enteric pathogen and ongoing global threat to public health. Ecological studies in the Salmonella impacted gut remain underrepresented in the literature, discounting microbiome mediated interactions that may inform Salmonella physiology during colonization and infection. To understand the microbial ecology of Salmonella remodeling of the gut microbiome, we performed multi-omics on fecal microbial communities from untreated and Salmonella-infected mice. Reconstructed genomes recruited metatranscriptomic and metabolomic data providing a strain-resolved view of the expressed metabolisms of the microbiome during Salmonella infection. These data informed possible Salmonella interactions with members of the gut microbiome that were previously uncharacterized. Salmonella-induced inflammation significantly reduced the diversity of genomes that recruited transcripts in the gut microbiome, yet increased transcript mapping was observed for seven members, among which Luxibacter and Ligilactobacillus transcript read recruitment was most prevalent. Metatranscriptomic insights from Salmonella and other persistent taxa in the inflamed microbiome further expounded the necessity for oxidative tolerance mechanisms to endure the host inflammatory responses to infection. In the inflamed gut lactate was a key metabolite, with microbiota production and consumption reported amongst members with detected transcript recruitment. We also showed that organic sulfur sources could be converted by gut microbiota to yield inorganic sulfur pools that become oxidized in the inflamed gut, resulting in thiosulfate and tetrathionate that support Salmonella respiration. This research advances physiological microbiome insights beyond prior amplicon-based approaches, with the transcriptionally active organismal and metabolic pathways outlined here offering intriguing intervention targets in the Salmonella-infected intestine.

59 BASIC BIOLOGICAL SCIENCES↗

NASA NTRS1992

Development of static system procedures to study aquatic biofilms and their responses to disinfection and invading species

The microbial ecology facility in the Analytical and Physical Chemistry Branch at Marshall Space Flight Center is tasked with anticipation of potential microbial problems (and opportunities to exploit microorganisms) which may occur in partially closed systems such as space station/vehicles habitats and in water reclamation systems therein, with particular emphasis on the degradation of materials. Within this context, procedures for microbial biofilm research are being developed. Reported here is the development of static system procedures to study aquatic biofilms and their responses to disinfection and invading species. Preliminary investigations have been completed. As procedures are refined, it will be possible to focus more closely on the elucidation of biofilm phenomena.

Smithers, G. A.↗

DOE OSTI2022

Anaerobic Biohydrogenation of Isoprene by Acetobacterium wieringae Strain Y

Isoprene is a ubiquitously distributed, biogenic, and climate-active organic compound. Microbial isoprene degradation in oxic environments is fairly well understood; however, studies exploring anaerobic isoprene metabolism remain scarce, with no isolates for study available. Here, we obtained an acetogenic isolate, designated Acetobacterium wieringae strain Y, which hydrogenated isoprene to a mixture of methyl-1-butenes at an overall rate of 288.8 ± 20.9 μM day -1 with concomitant acetate production at a rate of 478.4 ± 5.6 μM day -1 . Physiological characterization demonstrated that isoprene was not utilized in a respiratory process; rather, isoprene promoted acetogenesis kinetically. Bioinformatic analysis and proteomics experiments revealed the expression of candidate ene-reductases responsible for isoprene biohydrogenation. Notably, the addition of isoprene to strain Y cultures stimulated the expression of proteins associated with the Wood-Ljungdahl pathway, indicating unresolved impacts of isoprene on carbon cycling and microbial ecology in anoxic environments (e.g., promoting CO 2 plus H 2 reductive acetogenesis while inhibiting methanogenesis). Our new findings advance understanding of microbial transformation of isoprene under anoxic conditions and suggest that anoxic environments are isoprene sinks.

59 BASIC BIOLOGICAL SCIENCES↗

NASA NTRSDate not supplied

Agent-based modeling of microbes in space

Space is tough on organisms. Microorganisms traveling to space experience stress from environmental features such as ionizing radiation and lack of normal microgravity; however, much remains unknown about the mechanisms by which those environmental features affect microbial physiology. Microbes experience changes in gravity not directly but rather through changes in their fluid environment, and deep-space particle radiation causes cell damage that is complex but rare. Computational modeling at the single-cell level (agent-based modeling) can allow us to probe the spatially heterogeneous processes that characterize space stresses, to gain insight into the relationships of microbial cells with their environments and with each other. Here we present two software packages for simulating microbial population dynamics in space conditions: CAMDLES and AMMPER. Microbes growing in liquid culture medium in the microgravity of an orbital space station experience a quiescent, poorly-mixed fluid environment. CAMDLES (CFD-DEM Artificial Microgravity Developments for Living Ecosystem Simulation) simultaneously simulates biological, chemical, and mechanical processes to predict microbial ecological dynamics in microgravity, and in the rotating culture vessels used to create an artificial microgravity environment in the lab. Initial results demonstrate that the growth of a cross-feeding microbial consortium, dependent on the exchange of soluble metabolites, is sensitive to the initial spatial distribution of cells, and grows differently in real versus artificial microgravity. Microbial populations exposed to deep-space radiation experience spatially and temporally heterogeneous damage from the traversal of high-energy particles. AMMPER (Agent-Based Model for Microbial Populations Exposed to Radiation) pairs a 3d model of energy deposition along a radiation particle track with a microbial population growth and damage model to predict the effects of localized radiation damage on population-level responses. It includes a user-friendly graphical interface. AMMPER results agree with experimental data indicating that indirect effects of radiation (reactive oxygen species generation, metabolic impairment) have a greater impact on microorganisms than direct effects (DNA damage).

Jessica A Lee↗

NASA NTRS2022

Agent-Based Modeling of Microbes in Space

Space is tough on organisms. Microorganisms traveling to space experience stress from environmental features such as ionizing radiation and lack of normal gravity, and much remains unknown about the mechanisms by which those environmental features affect microbial physiology. Microbes experience changes in gravity not directly but rather through changes in their fluid environment, and deep-space particle radiation causes cell damage that is complex but rare. Computational modeling at the single-cell level (agent-based modeling) can allow us to probe the spatially heterogeneous processes that characterize space stresses, to gain insight into the relationships of microbial cells with their environments and with each other. Here we present two software packages for simulating microbial population dynamics in space conditions: CAMDLES and AMMPER. Microbes growing in liquid culture medium in the microgravity of an orbital space station experience a quiescent, poorly-mixed fluid environment. CAMDLES (CFD-DEM Artificial Microgravity Developments for Living Ecosystem Simulation) simultaneously simulates biological, chemical, and mechanical processes to predict microbial ecological dynamics in microgravity, and in the rotating culture vessels used to create an artificial microgravity environment in the lab. Initial results demonstrate that the growth of a cross-feeding microbial consortium, dependent on the exchange of soluble metabolites, is sensitive to the initial spatial distribution of cells, and grows differently in real versus artificial microgravity. Microbial populations exposed to deep-space radiation experience spatially and temporally heterogeneous damage from the traversal of high-energy particles. AMMPER (Agent-Based Model for Microbial Populations Exposed to Radiation) pairs a 3d model of energy deposition along a radiation particle track with a microbial population growth and damage model to predict the effects of localized radiation damage on population-level responses. It includes a user-friendly graphical interface. AMMPER growth curves recapitulate experimental results, and allow comparison between direct effects (DNA damage) and indirect effects (reactive oxygen species generation, metabolic impairment) of radiation.

microbiology↗

NASA NTRS1994

Dynamics of microorganism populations in recirculating nutrient solutions

This overview covers the basic microbial ecology of recirculating hydroponic solutions. Examples from NASA and Soviet Controlled Ecological Life Support Systems (CELSS) tests and the commercial hydroponic industry will be used. The sources of microorganisms in nutrient solutions include air, water, seeds, plant containers and plumbing, biological vectors, and personnel. Microbial fates include growth, death, and emigration. Important microbial habitats within nutrient delivery systems are root surfaces, hardware surfaces (biofilms), and solution suspension. Numbers of bacteria on root surfaces usually exceed those from the other habitats by several orders of magnitude. Gram negative bacteria dominate the microflora with fungal counts usually much lower. Trends typically show a decrease in counts with increasing time unless stressed plants increase root exudates. Important microbial activities include carbon mineralization and nitrogen transformations. Important detrimental interactions include competition with plants, and human and plant pathogenesis.

Strayer, R. F.↗

NASA NTRS1994

Dynamics of microorganism populations in recirculating nutrient solutions

This overview covers the basic microbial ecology of recirculating hydroponic solutions. Examples from NASA and Soviet CELSS tests and the commercial hydroponic industry will be used. The sources of microorganisms in nutrient solutions include air, water, seeds, plant containers and plumbing, biological vectors, and personnel. Microbial fates include growth, death, and emigration. Important microbial habitats within nutrient delivery systems are root surfaces, hardware surfaces (biofilms), and solution suspension. Numbers of bacteria on root surfaces usually exceed those from the other habitats by several orders of magnitude. Gram negative bacteria dominate the microflora with fungal counts usually much lower. Trends typically show a decrease in counts with increasing time unless stressed plants increase root exudates. Important microbial activities include carbon mineralization and nitrogen transformations. Important detrimental interactions include competition with plants, and human and plant pathogenesis.

Strayer, R. F.↗

DOE OSTI2026

Bioenergy Cropping Reduces the Spatiotemporal Scaling of Soil Bacterial Biodiversity

Widespread bioenergy cropping can transform landscapes, strongly affecting biodiversity. However, the impact of bioenergy cropping on the spatiotemporal scaling of soil biodiversity remains virtually unknown, despite its profound implications for the functioning of the ecological community. Here, we investigated how bioenergy cropping influenced the spatiotemporal scaling of soil bacterial biodiversity in marginal soils (sandy loam and clay loam soils) in Oklahoma, USA. We detected strong, significant species-time-area relationships (STARs) and phylogenetic-time-area relationships (PTARs) in bacterial communities and their lineages, suggesting that STARs and PTARs exist in microbial ecology within the studied system. Also, spatiotemporal scaling rates (the slopes of STAR and PTAR models) varied substantially among bacterial lineages and were positively correlated with their 16S rRNA gene copy numbers, a genomic trait indicative of microbial growth potentials. Strikingly, bioenergy cropping significantly reduced spatiotemporal scaling rates by 6.8%-14.1%, with a more pronounced reduction observed in sandy loam soils, where those rates were significantly lower than in clay loam soils. The heterogeneity of soil phosphorus and carbon resulted in variations in bacterial spatiotemporal scaling rates. Collectively, our findings suggest that bioenergy cropping may alleviate rapid shifts in soil biodiversity across space and time, thereby stabilizing soil biodiversity and supporting its role as part of sustainable land management and climate mitigation strategies.

bacterial diversity↗

NASA NTRS2022

Insights of Extreme Desert Ecology to the Habitats and Habitability of Mars

Desert ecosystems are a key repository for important Mars analog habitats and the extant or extinct life within them. We provide an overview of four main desert habitat types—soils, sediments, salts, and rocks—and the extreme microbiology living within them, with a particular focus on the hyperarid Atacama Desert and Dry Valleys of Antarctica, the driest and coldest limits for life on Earth. We construct habitat maps of Mars from an ecological perspective and the first estimates of study sample sizes of key habitats from historical and recent Mars orbiter and lander imagery and data. We review the lessons that can be drawn for the search for life on Mars from decades of microbial ecology work in end-member terrestrial deserts.

Deserts↗

DOE OSTI2025

An ecological framework for microbial metabolites in the ocean ecosystem

The ocean microbe‐metabolite network involves thousands of individual metabolites that encompass a breadth of chemical diversity and biological functions. These microbial metabolites mediate biogeochemical cycles, facilitate ecological relationships, and impact ecosystem health. While analytical advancements have begun to illuminate such roles, a challenge in navigating the deluge of marine metabolomics information is to identify a subset of metabolites that have the greatest ecosystem impact. Here, we present an ecological framework to distill knowledge of fundamental metabolites that underpin marine ecosystems. We borrow terms from macroecology that describe important species, namely “dominant,” “keystone,” and “indicator” species, and apply these designations to metabolites within the ocean microbial metabolome. These selected metabolites may shape marine community structure, function, and health and provide focal points for enhanced study of microbe‐metabolite networks. Applying ecological concepts to marine metabolites provides a path to leverage metabolomics data to better describe and predict marine microbial ecosystems.

microbial metabolites↗

DOE OSTI2022

Editorial: Exogenous carbon-based materials in soil ecosystems

Various exogenous carbon-based materials (ECMs) such as crop straw, biochar, carbon-based nano-fertilizer, and microplastics have accumulated in soil ecosystems. These ECMs may cause direct and indirect impacts on soil properties, processes, productivity, and health, thus potentially changing the function and stability of soil ecosystems. However, large knowledge gaps still exist on ECMs in soil ecosystems, including their accumulation, interactions with soil components, and potential ecological impacts and risks. Therefore, more efforts are needed to further understand the impacts especially the long-term effects of ECMs in soil ecosystems. By generating new knowledge, this Research Topic aims to improve the understanding of the effects of ECMs on soil ecosystems, including soil quality, nutrient cycling, microbial ecology, crop growth, environmental health and ecological risk.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2025

Controlling matric potential in microfluidics to examine microbial dynamics in unsaturated porous media

The use of microfluidics for the study of soil microbial ecology is an emerging field. Most microfluidic studies of biological systems, however, have been performed under fully saturated conditions that are not representative of natural soil. Therefore, while microfluidics offer many unique capabilities that other methodologies cannot, they are not currently suited to address the effects of matric potential, an important variable defining the microbial moisture niche. Here, a methodology is presented that allows the user to control the aqueous conditions within microfluidic networks by manipulating matric potential using a hanging water column. The method relies on hydrophilic surface treatment of the microfluidic device using polyvinyl alcohol (PVA) and incorporating a bed of small pores at the network boundaries, which serve as a porous ceramic plate analogue (PPA). The method was validated on a simple capillary bundle and then on a more complex pore network. A water retention curve, exhibiting hysteresis, was generated for the pore network over a narrow matric potential range of 0 to – 5 kPa. Both the drainage and wetting curves were reproducible, as were the spatial configuration and the number of fragmented moisture niches in the pore network, particularly on the drainage curve. In contrast, the wetting curve exhibited greater variability in spatial configuration due to the “ink bottle effect,” where capillarity was interrupted by wider pore bodies. Ultimately, the methodology provides realistic pore-scale moisture conditions that can be easily manipulated and maintained, enabling new opportunities to explore soil biophysics and microbial biogeography in unsaturated porous media. As a brief example, images showing the localization of fluorescently tagged Pantoea sp. YR343 at −4.3 kPa are presented, highlighting bacterial distributions in water films and air-water interfaces.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2022

The ecological assembly of bacterial communities in Antarctic wetlands varies across levels of phylogenetic resolution

Summary As functional traits are conserved at different phylogenetic depths, the ability to detect community assembly processes can be conditional on the phylogenetic resolution; yet most previous work quantifying their influence has focused on a single level of phylogenetic resolution. Here, we have studied the ecological assembly of bacterial communities from an Antarctic wetland complex, applying null models across different levels of phylogenetic resolution (i.e. clustering ASVs into OTUs with decreasing sequence identity thresholds). We found that the relative influence of the community assembly processes varies with phylogenetic resolution. More specifically, selection processes seem to impose stronger influence at finer (100% sequence similarity ASV) than at coarser (99%–97% sequence similarity OTUs) resolution. We identified environmental features related with the ecological processes and propose a conceptual model for the bacterial community assembly in this Antarctic ecosystem. Briefly, eco‐evolutionary processes appear to be leading to different but very closely related ASVs in lotic, lentic and terrestrial environments. In all, this study shows that assessing community assembly processes at different phylogenetic resolutions is key to improve our understanding of microbial ecology. More importantly, a failure to detect selection processes at coarser phylogenetic resolution does not imply the absence of such processes at finer resolutions.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2022

TbasCO: trait-based comparative ‘omics identifies ecosystem-level and niche-differentiating adaptations of an engineered microbiome

A grand challenge in microbial ecology is disentangling the traits of individual populations within complex communities. Various cultivation-independent approaches have been used to infer traits based on the presence of marker genes. However, marker genes are not linked to traits with complete fidelity, nor do they capture important attributes, such as the timing of gene expression or coordination among traits. To address this, we present an approach for assessing the trait landscape of microbial communities by statistically defining a trait attribute as a shared transcriptional pattern across multiple organisms. Leveraging the KEGG pathway database as a trait library and the Enhanced Biological Phosphorus Removal (EBPR) model microbial ecosystem, we demonstrate that a majority (65%) of traits present in 10 or more genomes have niche-differentiating expression attributes. For example, while many genomes containing high-affinity phosphorus transporter pstABCS display a canonical attribute (e.g. up-regulation under phosphorus starvation), we identified another attribute shared by many genomes where transcription was highest under high phosphorus conditions. Taken together, we provide a novel framework for unravelling the functional dynamics of uncultivated microorganisms by assigning trait-attributes through genome-resolved time-series metatranscriptomics.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2025

Magnetically responsive nanocultures for direct microbial assessment in soil environments

Cultivating microorganisms in native-like conditions is vital for bioprospecting and accessing now unculturable species. However, there remains a gap in scalable tools that can both mimic native microenvironments and enable targeted recovery of microbes from complex settings. Such approaches are essential to advance our understanding of microbial ecology, predict community functions, and discover previously unidentified biotherapeutics. We present magnetic nanocultures—a high-throughput microsystem for isolating and growing environmental microbes under near-native conditions. These nanoliter-scale bioreactors are encapsulated in semipermeable membranes that form magnetic polymeric microcapsules using iron oxide nanoparticles within polydimethylsiloxane-based shells. This design offers mechanical stability and magnetic actuation, enabling efficient retrieval from soil-like environments. The nanocultures are optimized for optical and biological properties to support microbial encapsulation, growth, and sorting. Our study demonstrates the feasibility of using magnetically responsive microenvironments to cultivate elusive microbes, offering a promising platform for bioprospecting previously uncultured or unknown microbial species.

Usman, Huda [Department of Chemical Engineering, C↗

NASA NTRS2011

Marine Microbial Mats and the Search for Evidence of Life in Deep Time and Space

Cyanobacterial mats in extensive seawater evaporation ponds at Guerrero Negro, Baja California, Mexico, have been excellent subjects for microbial ecology research. The studies reviewed here have documented the steep and rapidly changing environmental gradients experienced by mat microorganisms and the very high rates of biogeochemical processes that they maintained. Recent genetic studies have revealed an enormous diversity of bacteria as well as the spatial distribution of Bacteria, Archaea and Eukarya. These findings, together with emerging insights into the intimate interactions between these diverse populations, have contributed substantially to our understanding of the origins, environmental impacts, and biosignatures of photosynthetic microbial mats. The biosignatures (preservable cells, sedimentary fabrics, organic compounds, minerals, stable isotope patterns, etc.) potentially can serve as indicators of past life on early Earth. They also can inform our search for evidence of any life on Mars. Mars exploration has revealed evidence of evaporite deposits and thermal spring deposits; similar deposits on Earth once hosted ancient microbial mat ecosystems.

Des Marais, David J.↗

NASA NTRS1992

On the possibility of chemosynthetic ecosystems in subsurface habitats on Mars

Recent discoveries of nonphotosynthetic microbial ecosystems on earth have prompted the present reexamination of the prospects for microbial life on Mars, where well-protected subsurface niches associated with hydrothermal activity could have furnished a refuge after surface conditions became inhospitable. It is noted that extensive geological features attest to widespread ground ice-volcanism interactions. Attention is given to the possibility of anaerobic systems employing CO2 as the primary source of carbon, and liquid water furnished by melted subsurface permafrost. Gases from deep volcanic activity could effect reduction, thereby establishing a chemolithoautotrophic basis for a methanogenic or acetogenic and sulfur-based ecology microbial community.

Boston, Penelope J.↗

NASA NTRS1985

The global sulfur cycle

The results of the planetary biology microbial ecology's 1984 Summer Research Program, which examined various aspects of the global sulfur cycle are summarized. Ways in which sulfur flows through the many living and chemical species that inhabit the surface of the Earth were investigated. Major topics studied include: (1) sulfur cycling and metabolism of phototropic and filamentous sulfur bacteria; (2) sulfur reduction in sediments of marine and evaporite environments; (3) recent cyanobacterial mats; (4) microanalysis of community metabolism in proximity to the photic zone in potential stromatolites; and (5) formation and activity of microbial biofilms on metal sulfides and other mineral surfaces. Relationships between the global sulfur cycle and the understanding of the early evolution of the Earth and biosphere and current processes that affect global habitability are stressed.

Sagan, D.↗