Search NASA⌕ Search

SEARCH · Search NASA

Results for “bacterial communities”

Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 163 records · Page 9
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

Taxonomic and environmental distribution of bacterial amino acid auxotrophies

Abstract Many microorganisms are auxotrophic—unable to synthesize the compounds they require for growth. With this work, we quantify the prevalence of amino acid auxotrophies across a broad diversity of bacteria and habitats. We predicted the amino acid biosynthetic capabilities of 26,277 unique bacterial genomes spanning 12 phyla using a metabolic pathway model validated with empirical data. Amino acid auxotrophy is widespread across bacterial phyla, but we conservatively estimate that the majority of taxa (78.4%) are able to synthesize all amino acids. Our estimates indicate that amino acid auxotrophies are more prevalent among obligate intracellular parasites and in free-living taxa with genomic attributes characteristic of ‘streamlined’ life history strategies. We predicted the amino acid biosynthetic capabilities of bacterial communities found in 12 unique habitats to investigate environmental associations with auxotrophy, using data compiled from 3813 samples spanning major aquatic, terrestrial, and engineered environments. Auxotrophic taxa were more abundant in host-associated environments (including the human oral cavity and gut) and in fermented food products, with auxotrophic taxa being relatively rare in soil and aquatic systems. Overall, this work contributes to a more complete understanding of amino acid auxotrophy across the bacterial tree of life and the ecological contexts in which auxotrophy can be a successful strategy.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Nitrous oxide reduction by two partial denitrifying bacteria requires denitrification intermediates that cannot be respired

ABSTRACT Denitrification is a form of anaerobic respiration wherein nitrate (NO 3 − ) is sequentially reduced via nitrite (NO 2 − ), nitric oxide, and nitrous oxide (N 2 O) to dinitrogen gas (N 2 ) by four reductase enzymes. Partial denitrifying bacteria possess only one or some of these four reductases and use them as independent respiratory modules. However, it is unclear if partial denitrifiers sense and respond to denitrification intermediates outside of their reductase repertoire. Here, we tested the denitrifying capabilities of two purple nonsulfur bacteria,Rhodopseudomonas palustrisCGA0092 andRhodobacter capsulatusSB1003. Each had denitrifying capabilities that matched their genome annotation; CGA0092 reduced NO 2 − to N 2 , and SB1003 reduced N 2 O to N 2 . For each bacterium, N 2 O reduction could be used both for electron balance during growth on electron-rich organic compounds in light and for energy transformation via respiration in darkness. However, N 2 O reduction required supplementation with a denitrification intermediate, including those for which there was no associated denitrification enzyme. For CGA0092, NO 3 − served as a stable, non-catalyzable molecule that was sufficient to activate N 2 O reduction. Using a β-galactosidase reporter, we found that NO 3 − acted, at least in part, by stimulating N 2 O reductase gene expression. In SB1003, NO 2 − but not NO 3 − activated N 2 O reduction, but NO 2 − was slowly removed, likely by a promiscuous enzyme activity. Our findings reveal that partial denitrifiers can still be subject to regulation by denitrification intermediates that they cannot use. IMPORTANCE Denitrification is a form of microbial respiration wherein nitrate is converted via several nitrogen oxide intermediates into harmless dinitrogen gas. Partial denitrifying bacteria, which individually have some but not all denitrifying enzymes, can achieve complete denitrification as a community by cross-feeding nitrogen oxide intermediates. However, the last intermediate, nitrous oxide (N2O), is a potent greenhouse gas that often escapes, motivating efforts to understand and improve the efficiency of denitrification. Here, we found that at least some partial denitrifying N2O reducers can sense and respond to nitrogen oxide intermediates that they cannot otherwise use. The regulatory effects of nitrogen oxides on partial denitrifiers are thus an important consideration in understanding and applying denitrifying bacterial communities to combat greenhouse gas emissions.

Biotechnology & Applied Microbiology↗
NASA NTRS1989

The geological record of life 3500 Ma ago: Coping with the rigors of a young earth during late accretion

Thin cherty sedimentary layers within the volcanic portions of the 3,500 to 3,300 Ma-old Onverwacht and Fig Tree Groups, Barberton Greenstone belt, South Africa, and Warrawoona Group, eastern Pilbara Block, Western Australia, contain an abundant record of early Archean life. Five principal types of organic and probably biogenic remains and or structures can be identifed: stromatolites, stromatolite detritus, carbonaceous laminite or flat stromalite, carbonaceous detrital particles, and microfossils. Early Archean stromatolites were reported from both the Barberton and eastern Pilbara greenstone belts. Systematic studies are lacking, but two main morphological types of stromatolites appear to be represented by these occurrences. Morphology of the stromalites is described. Preserved early Archean stromatolites and carbonaceous matter appear to reflect communities of photosynthetic cyanobacteria inhabiting shallow, probably marine environments developed over the surfaces of low-relief, rapidly subsiding, simatic volcanic platforms. The overall environmental and tectonic conditions were those that probably prevailed at Earth's surface since the simatic crust and oceans formed sometime before 3,800 Ma. Recent studies also suggest that these early Archean sequences contain layers of debris formed by large-body impacts on early Earth. If so, then these early bacterial communities had developed strategies for coping with the disruptive effects of possibly globe-encircling high-temperature impact vapor clouds, dust blankets, and impact-generated tsunamis. It is probable that these early Archean biogenic materials represent organic communities that evolved long before the beginning of the preserved geological record and were well adapted to the rigors of life on a young, volcanically active Earth during late bombardment. These conditions may have had parallels on Mars during its early evolution.

Lowe, Donald R.↗
DOE OSTI2020

Diazotrophs Show Signs of Restoration in Amazon Rain Forest Soils with Ecosystem Rehabilitation

Biological nitrogen fixation can be an important source of nitrogen in tropical forests that serve as a major CO 2 sink. Extensive deforestation of the Amazon is known to influence microbial communities and the biogeochemical cycles they mediate. However, it is unknown how diazotrophs (nitrogen-fixing microorganisms) respond to deforestation and subsequent ecosystem conversion to agriculture, as well as whether they can recover in secondary forests that are established after agriculture is abandoned. To address these knowledge gaps, here we combined a spatially explicit sampling approach with high-throughput sequencing of nifH genes. The main objectives were to assess the functional distance decay relationship of the diazotrophic bacterial community in a tropical forest ecosystem and to quantify the roles of various factors that drive the observed changes in the diazotrophic community structure. We observed an increase in local diazotrophic diversity (α-diversity) with a decrease in community turnover (β-diversity), associated with a shift in diazotrophic community structure as a result of the forest-to-pasture conversion. Both diazotrophic community turnover and structure showed signs of recovery in secondary forests. Changes in the diazotrophic community were primarily driven by the change in land use rather than differences in geochemical characteristics or geographic distances. The diazotroph communities in secondary forests resembled those in primary forests, suggesting that at least partial recovery of diazotrophs is possible following agricultural abandonment. IMPORTANCE The Amazon region is a major tropical forest region that is being deforested at an alarming rate to create space for cattle ranching and agriculture. Diazotrophs (nitrogen-fixing microorganisms) play an important role in supplying soil N for plant growth in tropical forests. It is unknown how diazotrophs respond to deforestation and whether they can recover in secondary forests that establish after agriculture is abandoned. Using high-throughput sequencing of nifH genes, we characterized the response of diazotrophs’ β-diversity and identified major drivers of changes in diazotrophs from forest-to-pasture and pasture-to-secondary-forest conversions. Studying the impact of land use change on diazotrophs is important for a better understanding of the impact of deforestation on tropical forest ecosystem functioning, and our results on the potential recovery of diazotrophs in secondary forests imply the possible restoration of ecosystem functions in secondary forests.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Host and nonhost bacteria support bacteriophage dissemination along mycelia and abiotic dispersal networks

Abstract Bacteriophages play a crucial role in shaping bacterial communities, yet the mechanisms by which nonmotile bacteriophages interact with their hosts remain poorly understood. This knowledge gap is especially pronounced in structured environments like soil, where spatial constraints and air-filled zones hinder aqueous diffusion. In soil, hyphae of filamentous microorganisms form a network of ‘fungal highways’ (FHs) that facilitate the dispersal of other microorganisms. We propose that FHs also promote bacteriophage dissemination. Viral particles can diffuse in liquid films surrounding hyphae or be transported by infectable (host) or uninfectable (nonhost) bacterial carriers coexisting on FH networks. To test this, two bacteriophages that infect Pseudomonas putida DSM291 (host) but not KT2440 (nonhost) were used. In the absence of carriers, bacteriophages showed limited diffusion on 3D-printed abiotic networks, but diffusion was significantly improved in Pythium ultimum-formed FHs when the number of connecting hyphae exceeded 20. Transport by both host and nonhost carriers enhanced bacteriophage dissemination. Host carriers were five times more effective in transporting bacteriophages, particularly in FHs with over 30 connecting hyphae. This study enhances our understanding of bacteriophage dissemination in nonsaturated environments like soils, highlighting the importance of biotic networks and bacterial hosts in facilitating this process.

Périat, Claire (ORCID:000000020825625X)↗
DOE OSTI2022

Photosynthetic biohybrid coculture for tandem and tunable CO 2 and N 2 fixation

Solar-driven bioelectrosynthesis represents a promising approach for converting abundant resources into value-added chemicals with renewable energy. Microorganisms powered by electrochemical reducing equivalents assimilate CO 2 , H 2 O, and N 2 building blocks. However, products from autotrophic whole-cell biocatalysts are limited. Furthermore, biocatalysts tasked with N 2 reduction are constrained by simultaneous energy-intensive autotrophy. To overcome these challenges, we designed a biohybrid coculture for tandem and tunable CO 2 and N 2 fixation to value-added products, allowing the different species to distribute bioconversion steps and reduce the individual metabolic burden. This consortium involves acetogen Sporomusa ovata, which reduces CO 2 to acetate, and diazotrophic Rhodopseudomonas palustris, which uses the acetate both to fuel N 2 fixation and for the generation of a biopolyester. We demonstrate that the coculture platform provides a robust ecosystem for continuous CO 2 and N 2 fixation, and its outputs are directed by substrate gas composition. Moreover, we show the ability to support the coculture on a high–surface area silicon nanowire cathodic platform. The biohybrid coculture achieved peak faradaic efficiencies of 100, 19.1, and 6.3% for acetate, nitrogen in biomass, and ammonia, respectively, while maintaining product tunability. Finally, we established full solar to chemical conversion driven by a photovoltaic device, resulting in solar to chemical efficiencies of 1.78, 0.51, and 0.08% for acetate, nitrogenous biomass, and ammonia, correspondingly. Ultimately, our work demonstrates the ability to employ and electrochemically manipulate bacterial communities on demand to expand the suite of CO 2 and N 2 bioelectrosynthesis products.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

Genetic determinants of switchgrass-root-associated microbiota in field sites spanning its natural range

A fundamental goal in plant microbiome research is to determine the relative impacts of host and environmental effects on root microbiota composition, particularly how host genotype impacts bacterial community composition. Most studies characterizing the effect of plant genotype on root microbiota undersample host genetic diversity and grow plants outside of their native ranges, making the associations between host and microbes difficult to interpret. Here, we characterized the root microbiota of a large diversity panel of switchgrass, a North American native C4 bioenergy crop, in three field locations spanning its native range. Our data, composed of 1,961 samples, suggest that field location is the primary determinant of microbiome composition; however, substantial heritable variation is widespread across bacterial taxa, especially those in the Sphingomonadaceae family. Despite diverse compositions, relatively few highly prevalent taxa make up the majority of the switchgrass root microbiota, a large fraction of which is shared across sites. Local genotypes preferentially recruit/filter for local microbes, supporting the idea of affinity between local plants and their microbiota. Using genome-wide association, we identified loci impacting the abundance of >400 microbial strains and found an enrichment of genes involved in immune responses, signaling pathways, and secondary metabolism. We found loci associated with over half of the core microbiota (i.e., microbes in >80% of samples), regardless of field location. Finally, we show a genetic relationship between a basal plant immunity pathway and relative abundances of root microbiota. Furthermore, this study brings us closer to harnessing and manipulating beneficial microbial associations via host genetics.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2020

Mountain biodiversity and ecosystem functions: interplay between geology and contemporary environments

Although biodiversity and ecosystem functions are strongly shaped by contemporary environments, such as climate and local biotic and abiotic attributes, relatively little is known about how they depend on long-term geological processes. Here, along a 3000-m elevational gradient with tectonic faults on the Tibetan Plateau (that is, Galongla Mountain in Medog County, China), we study the joint effects of geological and contemporary environments on biological communities, such as the diversity and community composition of plants and soil bacteria, and ecosystem functions. We find that these biological communities and ecosystem functions generally show consistent elevational breakpoints at 2000–2800 m, which coincide with Indus-Yalu suture zone fault and are similar to the elevational breakpoints of soil bacteria on another mountain range 1000 km away. Mean annual temperature, soil pH and moisture are the primary contemporary determinants of biodiversity and ecosystem functions, which support previous findings. However, compared with the models excluding geological processes, inclusion of geological effects, such as parent rock and weathering, increases 67.9 and 35.9% of the explained variations in plant and bacterial communities, respectively. Such inclusion increases 27.6% of the explained variations in ecosystem functions. The geological processes thus provide additional links to ecosystem properties, which are prominent but show divergent effects on biodiversity and ecosystem functions: parent rock and weathering exert considerable direct effects on biodiversity, whereas indirectly influence ecosystem functions via interactions with biodiversity and contemporary environments. Thus, the integration of geological processes with environmental gradients could enhance our understanding of biodiversity and, ultimately, ecosystem functioning across different climatic zones.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2020

What Is in Umbilicaria pustulata? A Metagenomic Approach to Reconstruct the Holo-Genome of a Lichen

Lichens are valuable models in symbiosis research and promising sources of biosynthetic genes for biotechnological applications. Most lichenized fungi grow slowly, resist aposymbiotic cultivation, and are poor candidates for experimentation. Obtaining contiguous, high-quality genomes for such symbiotic communities is technically challenging. Here, we present the first assembly of a lichen holo-genome from metagenomic whole-genome shotgun data comprising both PacBio long reads and Illumina short reads. The nuclear genomes of the two primary components of the lichen symbiosis—the fungus Umbilicaria pustulata (33 Mb) and the green alga Trebouxia sp. (53 Mb)—were assembled at contiguities comparable to single-species assemblies. The analysis of the read coverage pattern revealed a relative abundance of fungal to algal nuclei of ~20:1. Gap-free, circular sequences for all organellar genomes were obtained. The bacterial community is dominated by Acidobacteriaceae and encompasses strains closely related to bacteria isolated from other lichens. Gene set analyses showed no evidence of horizontal gene transfer from algae or bacteria into the fungal genome. Our data suggest a lineage-specific loss of a putative gibberellin-20-oxidase in the fungus, a gene fusion in the fungal mitochondrion, and a relocation of an algal chloroplast gene to the algal nucleus. Major technical obstacles during reconstruction of the holo-genome were coverage differences among individual genomes surpassing three orders of magnitude. Moreover, we show that GC-rich inverted repeats paired with nonrandom sequencing error in PacBio data can result in missing gene predictions. This likely poses a general problem for genome assemblies based on long reads.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2026

Response of soil nutrient pools and microbiomes to recurrent wildfire disturbance and varying burn severities in a mixed conifer forest

Wildfire is a pervasive disturbance in mixed-conifer forests, yet the relative influence of fire recurrence versus burn severity on soil biogeochemistry and microbial communities remains poorly quantified. We examined a natural gradient of fire history (0–3 prior fires) and burn severity (low–high) spanning 50 yr in a mixed-conifer ecosystem to assess how repeated fire shapes soil carbon (C) and nitrogen (N) pools, their isotopic signatures, mineral and particulate fractions, microbial community composition, carbon-use, CO₂ fluxes, and vegetation cover. Successive fires produced progressively higher bare-ground percentages and lower tree cover, which were tightly linked to declines in microbial diversity and reductions bulk %C, and %N. δ 13 C increased with fire frequency, indicating preferential loss of labile C through combustion or enhanced microbial oxidation, thereby explaining the observed net soil-C decline. Conversely, δ 15 N decreased and pH increased as tree density declined, reflecting altered N cycling and reduced acidification in post-fire soils. Fire recurrence, more than severity, corresponded with a marked shift in the bacterial community: for example, Xanthobacteraceae—key N-fixers and C-cyclers—diminished, while N-fixing Bacillaceae increased, underscoring the tightly coupled nature of soil nutrient dynamics and microbiome composition after repeated burns. Our results demonstrate that fire recurrence appears to be a stronger driver of post-fire soil ecosystem responses in this mixed-conifer forest, influencing both abiotic nutrient pools and the functional potential of the soil microbiome. These findings provide a more enhanced assessment and understanding to date of the biogeochemical consequences of repeated wildfire disturbance that can be used to inform management strategies aimed at preserving soil health in fire-prone landscapes.

54 ENVIRONMENTAL SCIENCES↗
NASA NTRS2013

Extreme Ionizing-Radiation-Resistant Bacterium

There is a growing concern that desiccation and extreme radiation-resistant, non-spore-forming microorganisms associated with spacecraft surfaces can withstand space environmental conditions and subsequent proliferation on another solar body. Such forward contamination would jeopardize future life detection or sample return technologies. The prime focus of NASA s planetary protection efforts is the development of strategies for inactivating resistance-bearing micro-organisms. Eradi cation techniques can be designed to target resistance-conferring microbial populations by first identifying and understanding their physiologic and biochemical capabilities that confers its elevated tolerance (as is being studied in Deinococcus phoenicis, as a result of this description). Furthermore, hospitals, food, and government agencies frequently use biological indicators to ensure the efficacy of a wide range of radiation-based sterilization processes. Due to their resistance to a variety of perturbations, the nonspore forming D. phoenicis may be a more appropriate biological indicator than those currently in use. The high flux of cosmic rays during space travel and onto the unshielded surface of Mars poses a significant hazard to the survival of microbial life. Thus, radiation-resistant microorganisms are of particular concern that can survive extreme radiation, desiccation, and low temperatures experienced during space travel. Spore-forming bacteria, a common inhabitant of spacecraft assembly facilities, are known to tolerate these extreme conditions. Since the Viking era, spores have been utilized to assess the degree and level of microbiological contamination on spacecraft and their associated spacecraft assembly facilities. Members of the non-sporeforming bacterial community such as Deinococcus radiodurans can survive acute exposures to ionizing radiation (5 kGy), ultraviolet light (1 kJ/m2), and desiccation (years). These resistive phenotypes of Deinococcus enhance the potential for transfer, and subsequent proliferation, on another solar body such as Mars and Europa. These organisms are more likely to escape planetary protection assays, which only take into account presence of spores. Hence, presences of extreme radiation-resistant Deinococcus in the cleanroom facility where spacecraft are assembled pose a serious risk for integrity of life-detection missions. The microorganism described herein was isolated from the surfaces of the cleanroom facility in which the Phoenix Lander was assembled. The isolated bacterial strain was subjected to a comprehensive polyphasic analysis to characterize its taxonomic position. This bacterium exhibits very low 16SrRNA similarity with any other environmental isolate reported to date. Both phenotypic and phylogenetic analyses clearly indicate that this isolate belongs to the genus Deinococcus and represents a novel species. The name Deinococcus phoenicis was proposed after the Phoenix spacecraft, which was undergoing assembly, testing, and launch operations in the spacecraft assembly facility at the time of isolation. D. phoenicis cells exhibited higher resistance to ionizing radiation (cobalt-60; 14 kGy) than the cells of the D. radiodurans (5 kGy). Thus, it is in the best interest of NASA to thoroughly characterize this organism, which will further assess in determining the potential for forward contamination. Upon the completion of genetic and physiological characteristics of D. phoenicis, it will be added to a planetary protection database to be able to further model and predict the probability of forward contamination.

Vaishampayan, Parag A.↗
NASA NTRS2012

Extreme Ionizing-Radiation-Resistant Bacterium

There is a growing concern that desiccation and extreme radiation-resistant, non-spore-forming microorganisms associated with spacecraft surfaces can withstand space environmental conditions and subsequent proliferation on another solar body. Such forward contamination would jeopardize future life detection or sample return technologies. The prime focus of NASA s planetary protection efforts is the development of strategies for inactivating resistance-bearing microorganisms. Eradification techniques can be designed to target resistance-conferring microbial populations by first identifying and understanding their physiologic and biochemical capabilities that confers its elevated tolerance (as is being studied in Deinococcus phoenicis, as a result of this description). Furthermore, hospitals, food, and government agencies frequently use biological indicators to ensure the efficacy of a wide range of radiation- based sterilization processes. Due to their resistance to a variety of perturbations, the non-spore forming D. phoenicis may be a more appropriate biological indicator than those currently in use. The high flux of cosmic rays during space travel and onto the unshielded surface of Mars poses a significant hazard to the survival of microbial life. Thus, radiation-resistant microorganisms are of particular concern that can survive extreme radiation, desiccation, and low temperatures experienced during space travel. Spore-forming bacteria, a common inhabitant of spacecraft assembly facilities, are known to tolerate these extreme conditions. Since the Viking era, spores have been utilized to assess the degree and level of microbiological contamination on spacecraft and their associated spacecraft assembly facilities. Members of the non-spore-forming bacterial community such as Deinococcus radiodurans can survive acute exposures to ionizing radiation (5 kGy), ultraviolet light (1 kJ/sq m), and desiccation (years). These resistive phenotypes of Deinococcus enhance the potential for transfer, and subsequent proliferation, on another solar body such as Mars and Europa. These organisms are more likely to escape planetary protection assays, which only take into account presence of spores. Hence, presences of extreme radiation-resistant Deinococcus in the cleanroom facility where spacecraft are assembled pose a serious risk for integrity of life-detection missions. The microorganism described herein was isolated from the surfaces of the cleanroom facility in which the Phoenix Lander was assembled. The isolated bacterial strain was subjected to a comprehensive polyphasic analysis to characterize its taxonomic position. This bacterium exhibits very low 16SrRNA similarity with any other environmental isolate reported to date. Both phenotypic and phylogenetic analyses clearly indicate that this isolate belongs to the genus Deinococcus and represents a novel species. The name Deinococcus phoenicis was proposed after the Phoenix spacecraft, which was undergoing assembly, testing, and launch operations in the spacecraft assembly facility at the time of isolation. D. phoenicis cells exhibited higher resistance to ionizing radiation (cobalt-60; 14 kGy) than the cells of the D. radiodurans (5 kGy). Thus, it is in the best interest of NASA to thoroughly characterize this organism, which will further assess in determining the potential for forward contamination. Upon the completion of genetic and physiological characteristics of D. phoenicis, it will be added to a planetary protection database to be able to further model and predict the probability of forward contamination.

Vaishampayan, Parag A.↗
DOE OSTI2023

The microbiome structure of decomposing plant leaves in soil depends on plant species, soil pore sizes, and soil moisture content

Microbial communities are known as the primary decomposers of all the carbon accumulated in the soil. However, how important soil structure and its conventional or organic management, moisture content, and how different plant species impact this process are less understood. To answer these questions, we generated a soil microcosm with decomposing corn and soy leaves, as well as soil adjacent to the leaves, and compared it to control samples. We then used high-throughput amplicon sequencing of the ITS and 16S rDNA regions to characterize these microbiomes. Leaf microbiomes were the least diverse and the most even in terms of OTU richness and abundance compared to near soil and far soil, especially in their bacterial component. Microbial composition was significantly and primarily affected by niche (leaves vs. soil) but also by soil management type and plant species in the fungal microbiome, while moisture content and pore sizes were more important drivers for the bacterial communities. The pore size effect was significantly dependent on moisture content, but only in the organic management type. Overall, our results refine our understanding of the decomposition of carbon residues in the soil and the factors that influence it, which are key for environmental sustainability and for evaluating changes in ecosystem functions.

16S rDNA↗
NASA NTRSDate not supplied

Effects of Spaceflight Relevant Carbon Dioxide Levels on Pathogenesis Related Microbial Characteristics

BACKGROUND Multiple stressors in the spaceflight environment have the potential to alter microbial pathogenesis and virulence characteristics, including microgravity, radiation, and hostile/confined conditions. This combination of factors may lead to a stacking of risks, potentially creating unexpected increase in the risk of infectious disease. One understudied variable is the higher CO2 atmospheric concentration. The current Spaceflight Maximum Allowance Concentration (SMAC) for 24-hour average CO2 is 0.4% (3 mm Hg). These elevated ambient CO2 levels aboard the ISS could potentially influence the diversity and phenotypic responses of the resident microbial communities from both the spacecraft environment (air, surface, water) and crewmembers (gut, nasal, skin microbiomes). METHODS For these studies, we will evaluate the response of Staphylococcus aureus, Streptococcus pneumoniae and Enterobacter aerogenes, which are opportunistic pathogens that are of medical significance and have been or are likely to be found aboard spacecraft. These microorganisms will be cultured in both spaceflight analog and control conditions at CO2levels representing terrestrial atmospheric concentration of 0.04% (0.3 mmHg), ISS elevated concentration of 0.4% (3 mm Hg), and an unexpected elevated concentration of 1 % (7.6 mmHg) to represent a worst case scenario. DISCUSSION Overwhelming evidence from studies performed in food microbiology, marine biology and terrestrial environmental biology suggest altered gene expression, selective bacterial inhibition, increased growth and diversity, and increased antibiotic resistance of bacterial communities individually and in biofilm formation when exposed to increased levels of CO2. While many of these findings are based on levels of CO2 higher than would be found during spaceflight exploration missions, the potential for subtle changes in CO2 levels to exacerbate infectious disease risks warrants an evaluation of pathogen responses to spaceflight CO2 conditions. Our study will provide answers to spaceflight relevant atmospheric conditions, as described in the Risk of Adverse Health Effects Due to Host-Microorganism Interaction (GapMicro 103).

A A Medina-Colorado↗
DOE OSTI2023

A Graphical Model for Fusing Diverse Microbiome Data

This paper develops a Bayesian graphical model for fusing disparate types of count data. The motivating application is the study of bacterial communities from diverse high-dimensional features, in this case, transcripts, collected from different treatments. In such datasets, there are no explicit correspondences between the communities and each corresponds to different factors, making data fusion challenging. We introduce a flexible multinomial-Gaussian generative model for jointly modeling such count data. This latent variable model jointly characterizes the observed data through a common multivariate Gaussian latent space that parameterizes the set of multinomial probabilities of the transcriptome counts. The covariance matrix of the latent variables induces a covariance matrix of co-dependencies between all the transcripts, effectively fusing multiple data sources. We present a computationally scalable variational Expectation-Maximization (EM) algorithm for inferring the latent variables and the parameters of the model. Here, the inferred latent variables provide a common dimensionality reduction for visualizing the data and the inferred parameters provide a predictive posterior distribution. In addition to simulation studies that demonstrate the variational EM procedure, we apply our model to a bacterial microbiome dataset.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

The first sequenced Sphaerotilus natans bacteriophage– characterization and potential to control its filamentous bacterium host

ABSTRACT Bacteriophages (phages) are ubiquitous entities present in every conceivable habitat as a result of their bacterial parasitism. Their prevalence and impact in the ecology of bacterial communities and their ability to control pathogens make their characterization essential, particularly of new phages, improving knowledge and potential application. The isolation and characterization of a new lytic phage against Sphaerotilus natans strain DSM 6575, named vB_SnaP-R1 (SnaR1), is here described. Besides being the first sequenced genome of a Sphaerotilus natans infecting phage, 99% of its 41507 bp genome lacks homology with any other sequenced phage, revealing its uniqueness and previous lack of knowledge. Moreover, SnaR1 is the first Podoviridae phage described infecting this bacterium. Sphaerotilus natans is an important filamentous bacterium due to its deleterious effect on wastewater treatment plants (WWTP) and thus, phages may play a role as novel biotechnological tools against filamentous overgrowth in WWTP. The lytic spectrum of SnaR1 was restricted to its host strain, infecting only one out of three S. natans strains and infection assays revealed its ability to reduce bacterial loads. Results suggest SnaR1 as the prototype of a new phage genus and demonstrates its potential as a non-chemical alternative to reduce S. natans DSM 6575 cells.

Ferreira, Rute↗
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.↗
NASA NTRSDate not supplied

Effects of Spaceflight Relevant Carbon Dioxide Levels on Pathogenesis Related Microbial Characteristics

Multiple stressors in the spaceflight environment, including microgravity and radiation, have the potential to alter microbial pathogenesis and virulence characteristics. Understanding how these and other factors may exacerbate the risk of infectious disease for astronauts is important to ensure the success of the mission. One understudied question in our assessment of infectious disease risk is the contribution carbon dioxide (CO2) at atmospheric concentrations higher than would be observed in terrestrial settings. Previous terrestrial studies have shown altered gene expression, selective bacterial inhibition, increased growth and diversity, and increased antibiotic resistance of bacterial communities individually and in biofilms when exposed to increased levels of CO2. While many of these findings are based on levels of CO2 higher than would be found during spaceflight exploration missions, the potential for subtle changes in CO2 levels to exacerbate infectious disease risks warrants an evaluation of pathogen responses to spaceflight CO2 conditions. To address this question, we are evaluating the effects of elevated atmospheric CO2 on microbial concentration, diversity, and pathogenesis-related characteristics using medically significant microorganisms cultured at CO2 levels representing terrestrial atmospheric concentration (≈0.04 %), ISS elevated concentration (0.4 %), and an unexpectedly elevated concentration (1 %) to represent a worst-case scenario. To determine if microbial responses to these CO2 concentrations may be exacerbated in response to the spaceflight environment, microorganisms are being cultured under static conditions and both spaceflight analogue and control conditions using the Rotating Wall Vessel (RWV) bioreactor (Synthecon, Houston, TX). For these studies, we will evaluate the response of Staphylococcus aureus, Streptococcus pneumoniae, and Enterobacter aerogenes, which are opportunistic bacterial pathogens that are of medical significance and have been or are likely to be found aboard human-inhabited spacecraft. Bacteria will be evaluated individually and together as a consortium. The following Specific Aims are be investigated: Aim 1. Characterize the growth, diversity, and pathogenesis-related stress responses of medically significant microorganisms grown under multiple CO2 concentrations under static growth in a liquid medium. Stress responses include acid stress, oxidative stress, and thermal stress. Aim 2. Characterize the growth, diversity, and pathogenesis-related stress responses of medically significant microorganisms grown under multiple CO2 concentrations in both spaceflight analogue and control conditions. Stress responses include acid stress, oxidative stress, and thermal stress.

S G Thornhill↗