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At least 1,063 records · Page 59
All sourcesNASA NTRSDOE OSTI
DOE OSTI2020

Influence of Polymer Type and Carbon Nanotube Properties on Carbon Nanotube/Polymer Nanocomposite Biodegradation

The interaction of anaerobic microorganisms with carbon nanotube/polymer nanocomposites (CNT/PNC) will play a major role in determining their persistence and environmental fate at the end of consumer use when these nano-enabled materials enter landfills and encounter wastewater. Motivated by the need to understand how different parameters (i.e., polymer type, microbial phenotype, CNT characteristics) influence CNT/PNC biodegradation rates, we have used volumetric biogas measurements and kinetic modeling to study biodegradation as a function of polymer type and CNT properties. In one set of experiments, oxidized multiwall carbon nanotubes (O-MWCNTs) with a range of CNT loadings 0 – 5% w/w were incorporated into poly-e-caprolactone (PCL) and polyhydroxyalkanoates (PHA) matrices and subjected to biodegradation by an anaerobic microbial community. For each CNT/PNC, complete polymer biodegradation was ultimately observed, although the rate of biodegradation was inhibited above certain critical CNT loadings dependent upon the polymer type. Higher loadings of pristine MWCNTs were needed to decrease the rate of polymer biodegradation compared to O-MWCNTs, an effect ascribed principally to differences in CNT dispersion within the polymer matrices. Above ertain CNT loadings, a CNT mat of similar shape to the initial PNC was formed after polymer biodegradation, while below this threshold, CNT aggregates fragmented in the media. In situations where biodegradation was rapid, methanogen growth was disproportionately inhibited compared to the overall microbial community. Analysis of the results obtained from this study indicates that the inhibitory effect of CNTs on polymer biodegradation rate is greatest under conditions (i.e., polymer type, microbial phenotype, CNT dispersion) where biodegradation of the neat polymer is slowest. This new insight provides a means to predict the environmental fate, persistence and transformations of CNT-enabled polymer materials.

Frank, Benjamin↗
DOE OSTI2020

A genomic catalog of Earth’s microbiomes

Abstract The reconstruction of bacterial and archaeal genomes from shotgun metagenomes has enabled insights into the ecology and evolution of environmental and host-associated microbiomes. Here we applied this approach to >10,000 metagenomes collected from diverse habitats covering all of Earth’s continents and oceans, including metagenomes from human and animal hosts, engineered environments, and natural and agricultural soils, to capture extant microbial, metabolic and functional potential. This comprehensive catalog includes 52,515 metagenome-assembled genomes representing 12,556 novel candidate species-level operational taxonomic units spanning 135 phyla. The catalog expands the known phylogenetic diversity of bacteria and archaea by 44% and is broadly available for streamlined comparative analyses, interactive exploration, metabolic modeling and bulk download. We demonstrate the utility of this collection for understanding secondary-metabolite biosynthetic potential and for resolving thousands of new host linkages to uncultivated viruses. This resource underscores the value of genome-centric approaches for revealing genomic properties of uncultivated microorganisms that affect ecosystem processes.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Opportunities to advance the synthesis of ecology and evolution

Despite decades of research on the interactions between ecology and evolution, opportunities still remain to further integrate the two disciplines, especially when considering multispecies systems. Here, we discuss two such opportunities. First, the traditional emphasis on the distinction between evolutionary and ecological processes should be further relaxed as it is particularly unhelpful in the study of microbial communities, where the very notion of species is hard to define. Second, key processes of evolutionary theory such as adaptation should be exported to hierarchical levels higher than populations to make sense of biodiversity dynamics. Together, we argue that broadening our perspective of eco-evolutionary dynamics to be more inclusive of all biodiversity, both phylogenetically and hierarchically, will open up fertile new research directions and help us to address one of the major scientific challenges of our time, that is, to understand and predict changes in biodiversity in the face of rapid environmental change.

54 ENVIRONMENTAL SCIENCES↗
NASA NTRS2005

Characterization of a Subsurface Biosphere in a Massive Sulfide Deposits at Rio Tinto, Spain: Implications for Extant Life on Mars

The recent discovery of abundant sulfate minerals, particularly Jarosite by the Opportunity Rover at Sinus Merdiani on Mars has been interpreted as evidence for an acidic lake or sea on ancient Mars [1,2], since the mineral Jarosite is soluble in liquid water at pH above 4. The most likely mechanism to produce sufficient protons to acidify a large body of liquid water is near surface oxidation of pyrite rich deposits [3]. The acidic waters of the Rio Tinto, and the associated deposits of Hematite, Goethite, and Jarosite have been recognized as an important chemical analog to the Sinus Merdiani site on Mars [4]. The Rio Tinto is a river in southern Spain that flows 100 km from its source in the Iberian pyrite belt, one of the Earth s largest Volcanically Hosted Massive Sulfide (VHMS) provinces, into the Atlantic ocean. The river originates in artesian springs emanating from ground water that is acidified by the interaction with subsurface pyrite ore deposits. The Mars Analog Rio Tinto Experiment (MARTE) has been investigating the hypothesis that a subsurface biosphere exists at Rio Tinto living within the VHMS deposit living on chemical energy derived from sulfur and iron minerals. Reduced iron and sulfur might provide electron donors for microbial metabolism while in situ oxidized iron or oxidants entrained in recharge water might provide electron acceptors.

Stoker, C. R.↗
NASA NTRS2005

Characterization of a Subsurface Biosphere in a Massive Sulfide Deposit At Rio Tinto, Spain: Implications For Extant Life On Mars

The recent discovery of abundant sulfate minerals, particularly Jarosite by the Opportunity Rover at Sinus Merdiani on Mars has been interpreted as evidence for an acidic lake or sea on ancient Mars [1,2], since the mineral Jarosite is soluble in liquid water at pH above 4. The most likely mechanism to produce sufficient protons to acidify a large body of liquid water is near surface oxidation of pyrite rich deposits [3]. The acidic waters of the Rio Tinto, and the associated deposits of Hematite, Goethite, and Jarosite have been recognized as an important chemical analog to the Sinus Merdiani site on Mars [4]. The Rio Tinto is a river in southern Spain that flows 100 km from its source in the Iberian pyrite belt, one of the Earth's largest Volcanically Hosted Massive Sulfide (VHMS) provinces, into the Atlantic ocean. The river originates in artesian springs emanating from ground water that is acidified by the interaction with subsurface pyrite ore deposits. The Mars Analog Rio Tinto Experiment (MARTE) has been investigating the hypothesis that a subsurface biosphere exists at Rio Tinto living within the VHMS deposit living on chemical energy derived from sulfur and iron minerals. Reduced iron and sulfur might provide electron donors for microbial metabolism while in situ oxidized iron or oxidants entrained in recharge water might provide electron acceptors.

Stoker, C. R.↗
DOE OSTI2022

Stability of mineral-organic matter associations under varying biogeochemical conditions

It is well-recognized and documented in the literature that a considerable fraction of the soil organic matter (SOM) is associated with Fe-oxide minerals. Recent studies have also showed that the persistence of various classes of SOM may depend on soil Fe mineralogy. Other laboratory studies with model mineral-associated organic matter (MAOM) moieties, which were primarily focused on ferrihydrite, either coated or coprecipitated with natural organic matter (NOM), have suggested that the mineral phase transformation and adsorption-desorption of SOM is rather complex but appears to be largely controlled by the C/Fe ratio of the MAOM moiety and geochemical conditions. It is also clear from multiple recent studies that the nature or type of SOM (microbial vs. plant-derived) adsorbed on mineral surfaces and the rate and extent of SOM biodegradation depend on the type of mineral, and/or metal ions, that are associated with the SOM. Modeling studies that are primarily centered on achieving a better understanding of the effect of mineral type on SOM interactions with minerals and degradation are also reported. These studies have improved the understanding of the nature and stability of MAOM in soils of varying types and under different conditions, positioning researchers to better predict the properties and stabilities of organo-mineral associations in soils.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2015

Switchgrass rhizospheres stimulate microbial biomass but deplete microbial necromass in agricultural soils of the upper Midwest, USA

Rhizosphere microbial communities play an essential role in determining plant productivity, particularly in agriculturally marginal environments. Perennial plants like switchgrass (Panicum virgatum) are thought to particularly influence microbial community composition and function within their rhizosphere. We compared microbial communities in switchgrass rhizospheres and their associated bulk soils in two regions of the U.S. upper Midwest (Michigan and Wisconsin) with contrasting soil types, and at two site types with differing switchgrass establishment ages and management intensities. We characterized microbial communities with a range of culture-independent methods, including amplicon sequencing of 16S/18S rRNA and nifH genes, and membrane lipid profiling. In addition, we quantified abundances of soil amino sugars, a time-integrative indicator of microbial necromass. We found that amino sugar contents and microbial lipid profiles differed between rhizosphere and bulk soils, while DNA-based assays did not provide this discriminatory power. Differences between rhizosphere and bulk soils were not significantly affected by region or site type. Rhizosphere soils had higher microbial lipid abundances, particularly those associated with arbuscular mycorrhizal fungi and Gram-negative bacteria, while amino sugar abundances decreased in the rhizosphere. In conclusion, our findings suggest switchgrass rhizospheres systematically stimulate microbial growth and microbial residue turnover.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Application of Machine Learning Techniques to an Agent-Based Model of Pantoea

Agent-based modeling (ABM) is a powerful simulation technique which describes a complex dynamic system based on its interacting constituent entities. While the flexibility of ABM enables broad application, the complexity of real-world models demands intensive computing resources and computational time; however, a metamodel may be constructed to gain insight at less computational expense. Here, we developed a model in NetLogo to describe the growth of a microbial population consisting of Pantoea . We applied 13 parameters that defined the model and actively changed seven of the parameters to modulate the evolution of the population curve in response to these changes. We efficiently performed more than 3,000 simulations using a Python wrapper, NL4Py . Upon evaluation of the correlation between the active parameters and outputs by random forest regression, we found that the parameters which define the depth of medium and glucose concentration affect the population curves significantly. Subsequently, we constructed a metamodel, a dense neural network, to predict the simulation outputs from the active parameters and found that it achieves high prediction accuracy, reaching an R 2 coefficient of determination value up to 0.92. Our approach of using a combination of ABM with random forest regression and neural network reduces the number of required ABM simulations. The simplified and refined metamodels may provide insights into the complex dynamic system before their transition to more sophisticated models that run on high-performance computing systems. The ultimate goal is to build a bridge between simulation and experiment, allowing model validation by comparing the simulated data to experimental data in microbiology.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Bioinformatics Investigations of Universal Stress Proteins from Mercury-Methylating Desulfovibrionaceae

The presence of methylmercury in aquatic environments and marine food sources is of global concern. The chemical reaction for the addition of a methyl group to inorganic mercury occurs in diverse bacterial taxonomic groups including the Gram-negative, sulfate-reducing Desulfovibrionaceae family that inhabit extreme aquatic environments. The availability of whole-genome sequence datasets for members of the Desulfovibrionaceae presents opportunities to understand the microbial mechanisms that contribute to methylmercury production in extreme aquatic environments. We have applied bioinformatics resources and developed visual analytics resources to categorize a collection of 719 putative universal stress protein (USP) sequences predicted from 93 genomes of Desulfovibrionaceae. We have focused our bioinformatics investigations on protein sequence analytics by developing interactive visualizations to categorize Desulfovibrionaceae universal stress proteins by protein domain composition and functionally important amino acids. We identified 651 Desulfovibrionaceae universal stress protein sequences, of which 488 sequences had only one USP domain and 163 had two USP domains. The 488 single USP domain sequences were further categorized into 340 sequences with ATP-binding motif and 148 sequences without ATP-binding motif. The 163 double USP domain sequences were categorized into (1) both USP domains with ATP-binding motif (3 sequences); (2) both USP domains without ATP-binding motif (138 sequences); and (3) one USP domain with ATP-binding motif (21 sequences). We developed visual analytics resources to facilitate the investigation of these categories of datasets in the presence or absence of the mercury-methylating gene pair (hgcAB). Future research could utilize these functional categories to investigate the participation of universal stress proteins in the bacterial cellular uptake of inorganic mercury and methylmercury production, especially in anaerobic aquatic environments.

Isokpehi, Raphael D. (ORCID:0000000268770840)↗
DOE OSTI2026

Bayesian chain graph models to characterize microbe-environment dynamics

Microbiome data require statistical models that can simultaneously decode microbes' reaction to the environment and interactions among microbes. While a multiresponse linear regression model seems like a straight-forward solution, we argue that treating it as a graphical model is problematic given that the regression coefficient matrix does not encode the conditional dependence structure between response and predictor nodes. This observation is especially important in biological settings when we have prior knowledge on the edges from specific experimental interventions that can only be properly encoded under a conditional dependence model. Here, we propose a chain graph model with two sets of nodes (predictors and responses) whose solution yields a graph with edges that indeed represent conditional dependence, thus agreeing with the experimenter's intuition on the average behavior of nodes under treatment. The solution to our model is sparse via the Bayesian linear regression (LASSO). In addition, we propose an adaptive extension so that different shrinkages can be applied to different edges to incorporate edge-specific prior knowledge. Our model is computationally inexpensive through an efficient Gibbs sampling algorithm and can account for binary, counting, and compositional responses via an appropriate hierarchical structure. We test the performance of our model in a variety of simulated datasets, thereby showing superior performance to state-of-the-art approaches. We further apply our model to human gut and soil microbial compositional datasets, and we highlight that CG-LASSO can estimate biologically meaningful network structures in the data.

compositional data↗
DOE OSTI2020

Collaborative Research: Natural Organic Matter and Microbial Controls on Mobilization/Immobilization of I and Pu in Soils and Waters Affected by Radionuclide Releases in USA and Japan

In this project, the relationship between natural organic matter (NOM) and two radioactive elements that are relevant to nuclear waste disposal were studied: Plutonium (Pu) and Iodine. The human and environmental risks associated with Pu stem mainly from the very long half-lives of several of its isotopes ( 238 Pu, 88 yr; 239 Pu, 24,100 yr; 240 Pu, 6560 yr) and its radiotoxicity. Understanding Pu biogeochemical behavior in both near-field (>10-11M) and far-field scales (<10-11M) is imperative to the development of approaches for reprocessing Pu, remediation of Pu contamination and accurate assessment of risks posed by disposal practices for Pu-bearing wastes. The environmental mobility of Pu can be affected by redox potential, pH, adsorption, precipitation, complexation, colloid formation, and microbial activity, of which the first characteristic has the most profound influence. Numerous studies have shown high affinity of Pu towards NOM, as well as to mineral phases. NOM is ubiquitous in the environment, e.g., both fulvic and humic acids are able to reduce Pu(V,VI) to Pu(IV) and the redox potential of NOM is positively related to the abundance of phenolic/acidic OH groups. NOM can either facilitate or limit actinide migration, depending on specific biogeochemical conditions including pH, mineral and organic matter characteristics, etc. The other radionuclide of interest is radioiodine ( 129 I). 129I is a major by-product of nuclear fission and of serious concern to the Department of Energy (DOE) as it is among the top risk drivers at existing and potential radiowaste-contaminated sites. The risk of 129 I stems largely from its high bioconcentration factor (90% of the body’s iodine is accumulated in the thyroid), a high inventory at source terms, a very long-half life (16M years), and rapid mobility in the subsurface environment. As a consequence, 129 I has the lowest drinking water standard (1 pCi/L) among all radionuclides in the Federal Register. With a novel and sensitive gas chromatography-mass spectrometry (GC-MS) method developed in our lab, it is possible to quickly and simultaneously determine the distribution of 129 I and stable 127 I forms in environments, as low as 2 pCi/L for 129 I. This method was subsequently validated using accelerator mass spectroscopy, AMS. IO 3 - and organo-I were determined as major species in the groundwater of SRS and the Hanford Site, contrary to thermodynamic predictions that I- should be the dominant species at these sites. Mobility of 129 I was also demonstrated to depend greatly on the I species and its concentration, sediment pH, and redox state, with times to achieve equilibrium taking up to 12 weeks. Along the groundwater pathway in the F-Area of SRS, 129 I- supplied from the seepage basins was transformed to 129 IO 3 - and organo- 129 I with increasing iodine sediment sorption, causing the lower total 127 I and 129 I concentrations along the gradient transect of the waste plume. By contrast, groundwater 129 I concentrations in the wetlands (as high as 1617.3 pCi/L) were greatly elevated with respect to the source term (159.3 pCi/L). While the NOM promoted the uptake of 129 I to the wetland sediment, it also promoted the formation of soluble organic fraction. A small fraction of NOM that is bound to iodine can behave as a mobile organo-I source. Iodide was enzymatically incorporated into NOM, whereas both iodide and iodate were abiotically bound to NOM, under certain conditions. Iodate removal from the mobile aqueous phase can also occur through incorporation into carbonate (e.g., at the Hanford Site, USA). Thus immobilization and re-mobilization of iodine species were influenced by pH, Eh and the presence of NOM and metal oxides, which adds to the complexity of site remediation action. A ground-breaking result was to elucidate the products (i.e. organo-iodine moieties formed via enzymatic and non-enzymatic processes) at the molecular level by nuclear magnetic resonance (NMR) and electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry (ESI-FTICRMS). We found that iodine-NOM interactions may be influenced by NOM hydrophobic aliphatic moieties. From the perspective of ESI-FTICRMS, organo-iodine formulas were ascribed to the groups of unsaturated hydrocarbons, lignins and proteins. Iodate is likely abiotically reduced to reactive iodine species by lignin- and tannin-like compounds or carboxylic-rich alicyclic molecules (CRAM). We also investigated microbial mechanisms in iodine incorporation into NOM. We established that soil bacteria isolated from F-Area of SRS did not accumulate significant amounts of I- (0.2-2%). Intracellular uptake of I- decreases with increasing pH when pH ranged from 4 to 6. In contrast, 44 out of 84 strains isolated from the F-Area of SRS can transform I- to IO 3 - and organo-iodine. In some cases, oxidation was facilitated in the presence of H 2 O 2 . Microbes can also excrete organic acids that enhance I- oxidation by lowering the ambient pH and reacting with H 2 O 2 to form peroxy carboxylic acids. At lower pH values (≤5), H 2 O 2 hydrolysis was the driving force for iodide-oxidation; whereas, at pH ≥ 6, spontaneous decomposition of peroxy carboxylic acids, originating from H 2 O 2 and organic acids were the primary cause of iodide oxidation. Lastly, it was determined that microbial processes involved in Mn (II) are capable of directly oxidizing I- via enzymatic catalysis (i.e., multicopper oxidases), or indirectly through the formation of reactive oxygen species (ROS) and/or biogenic manganese oxides. ROS-mediated oxidation of I- was found to predominate at pH >5, whereas the enzymatic and Mn oxide pathways were more active at pH < 5. Together, this project has resulted in 9 publications in high-impact journals, and the training of 1 Ph.D and 4 undergraduate students.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2018

Characterizing posttranslational modifications in prokaryotic metabolism using a multiscale workflow

Understanding the complex interactions of protein posttranslational modifications (PTMs) represents a major challenge in metabolic engineering, synthetic biology, and the biomedical sciences. In this work, we present a workflow that integrates multiplex automated genome editing (MAGE), genome-scale metabolic modeling, and atomistic molecular dynamics to study the effects of PTMs on metabolic enzymes and microbial fitness. This workflow incorporates complementary approaches across scientific disciplines; provides molecular insight into how PTMs influence cellular fitness during nutrient shifts; and demonstrates how mechanistic details of PTMs can be explored at different biological scales. As a proof of concept, we present a global analysis of PTMs on enzymes in the metabolic network of Escherichia coli. Based on our workflow results, we conduct a more detailed, mechanistic analysis of the PTMs in three proteins: enolase, serine hydroxymethyltransferase, and transaldolase. Finally, application of this workflow identified the roles of specific PTMs in observed experimental phenomena and demonstrated how individual PTMs regulate enzymes, pathways, and, ultimately, cell phenotypes.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2015

The rice immune receptor XA21 recognizes a tyrosine-sulfated protein from a Gram-negative bacterium

Surveillance of the extracellular environment by immune receptors is of central importance to eukaryotic survival. The rice receptor kinase XA21, which confers robust resistance to most strains of the Gram-negative bacterium Xanthomonas oryzae pv. oryzae (Xoo), is representative of a large class of cell surface immune receptors in plants and animals. We report the identification of a previously undescribed Xoo protein, called RaxX, which is required for activation of XA21-mediated immunity. Xoo strains that lack RaxX, or carry mutations in the single RaxX tyrosine residue (Y41), are able to evade XA21-mediated immunity. Y41 of RaxX is sulfated by the prokaryotic tyrosine sulfotransferase RaxST. Sulfated, but not nonsulfated, RaxX triggers hallmarks of the plant immune response in an XA21-dependent manner. A sulfated, 21–amino acid synthetic RaxX peptide (RaxX21-sY) is sufficient for this activity. Xoo field isolates that overcome XA21-mediated immunity encode an alternate raxX allele, suggesting that coevolutionary interactions between host and pathogen contribute to RaxX diversification. RaxX is highly conserved in many plant pathogenic Xanthomonas species. The new insights gained from the discovery and characterization of the sulfated protein, RaxX, can be applied to the development of resistant crop varieties and therapeutic reagents that have the potential to block microbial infection of both plants and animals.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

Automated Bacterial Identification and Morphological Feature Analysis in Low‐Dose Cryo‐EM Using YOLOv11

Bacteria rapidly adapt to environmental cues through morphological and ultrastructural changes that correlate with physiology and behavior. Cryogenic transmission electron microscopy (cryo‐TEM) can capture these phenotypic changes in near‐native, vitrified states, but manual analysis of low‐dose micrographs is labor intensive and limits throughput. Here, we present an end‐to‐end workflow that combines low‐dose cryo‐TEM imaging with a YOLOv11‐based instance‐segmentation model to automatically identify bacteria and quantify key structural features directly from the micrographs. This workflow enables (i) robust bacterial localization and counting from low‐magnification atlas/montage images, (ii) automated measurements of cell‐envelope (outer–inner membrane) thickness and anisotropy from higher‐magnification views, and (iii) detection and quantification of bacteria–flagella interactions, including overlap length and curvature metrics for interacting versus noninteracting flagella. Using Pantoea sp. YR343 grown under distinct media conditions, we show that the automated measurements agree with manual annotations while substantially reducing analysis time. Together, these tools provide a practical framework for scalable bacterial identification and quantitative phenotyping in low‐dose cryo‐TEM datasets and establish a foundation for extending cryo‐TEM image analysis toward higher‐throughput studies of microbial heterogeneity and biointerfaces.

YOLOv11↗
DOE OSTI2016

A genome-scale Escherichia coli kinetic metabolic model k-ecoli457 satisfying flux data for multiple mutant strains

Kinetic models of metabolism at a genome scale that faithfully recapitulate the effect of multiple genetic interventions would be transformative in our ability to reliably design novel overproducing microbial strains. Here, we introduce k-ecoli457, a genome-scale kinetic model of Escherichia coli metabolism that satisfies fluxomic data for wild-type and 25 mutant strains under different substrates and growth conditions. The k-ecoli457 model contains 457 model reactions, 337 metabolites and 295 substrate-level regulatory interactions. Parameterization is carried out using a genetic algorithm by simultaneously imposing all available fluxomic data (about 30 measured fluxes per mutant). Furthermore, the Pearson correlation coefficient between experimental data and predicted product yields for 320 engineered strains spanning 24 product metabolites is 0.84. This is substantially higher than that using flux balance analysis, minimization of metabolic adjustment or maximization of product yield exhibiting systematic errors with correlation coefficients of, respectively, 0.18, 0.37 and 0.47.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2016

IMG/VR: a database of cultured and uncultured DNA Viruses and retroviruses

Viruses represent the most abundant life forms on the planet. Recent experimental and computational improvements have led to a dramatic increase in the number of viral genome sequences identified primarily from metagenomic samples. As a result of the expanding catalog of metagenomic viral sequences, there exists a need for a comprehensive computational platform integrating all these sequences with associated metadata and analytical tools. Here we present IMG/VR (https://img.jgi.doe.gov/vr/), the largest publicly available database of 3908 isolate reference DNA viruses with 264 413 computationally identified viral contigs from > 6000 ecologically diverse metagenomic samples. Approximately half of the viral contigs are grouped into genetically distinct quasi-species clusters. Microbial hosts are predicted for 20 000 viral sequences, revealing nine microbial phyla previously unreported to be infected by viruses. Viral sequences can be queried using a variety of associated metadata, including habitat type and geographic location of the samples, or taxonomic classification according to hallmark viral genes. IMG/VR has a user-friendly interface that allows users to interrogate all integrated data and interact by comparingwith external sequences, thus serving as an essential resource in the viral genomics community.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Bacterial and fungal growth on fungal necromass and its diverse components: Shared profiles and divergent constraints revealed by high‐throughput phenotyping

1. While fungal necromass is increasingly recognized as a major source of persistent carbon (C) in soils, the relative functional roles of bacteria and fungi in decomposing necromass are not fully resolved, and the processes that select for necromass decomposer communities from the broader soil microbial community are an emerging area of interest. 2. In this study, we characterized the growth of 52 bacterial and 83 fungal strains isolated from necromass and soil on 22 C substrates, including different necromass phenotypes, fungal cell wall polymers, dimers and monomers. 3. We found that the isolation habitat of the strains used in this experiment (necromass vs. soil) had no effect on the substrates they were able to use. Isolates from both microbial domains were able to grow on different labile carbon substrates, polymers and necromass phenotypes. However, fungal growth was most limited by necromass melanin content, while bacterial growth was more limited by the abundance of cell wall polysaccharides. Additionally, overall differences in substrate use between bacteria and fungi were most pronounced on polymer substrates. 4. Collectively, our results suggest that there is substantial functional overlap in necromass substrate use across microbial domains, but some notable differences in bacterial and fungal utilization of cell wall polymers, which can function as a direct energy source or a means of accessing other compounds within necromass. Future studies assessing bacteria and fungi decomposing necromass together rather than in isolation will help to uncover potential physical and chemical interactions within and between these two domains during the decay of this important source of persistent soil C.

dead fungal biomass↗
NASA NTRSDate not supplied

Evaluating Microgreens Crop Readiness for Space Production

Microgreens are small-size, nutrient-rich, and fast-grown crops, which are considered as candidates for future space exploration missions. In particular, the ISS, the Lunar Gateway, and Mars and Lunar missions could benefit from growing microgreens to supplement astronaut diets in the near future. Research at NASA’s Kennedy Space Center has focused on (1) the selection of microgreens compatible species, (2) the evaluation of microgreens food safety, (3) the use of passive wicking, on-demand watering, and hydroponics cultivation, (4) simulated microgravity growth, (5) microgreen canopy gas exchange, and (6) harvesting techniques in microgravity. This interactive presentation summarizes this research. Microgreen species will be evaluated for their yield in relationship to the quantity of inputs – water, seeds, substrate, light intensity, photoperiod, crew time – required for their growth; for their organoleptic and sensory factors in order to down select species that are highly acceptable for humans; and for their microbial loads as detected in their growth environment and the food safety metrics of their edible tissue. Passive wicking, on-demand watering, and hydroponic systems are being studied as an efficient way to deliver essential nutrients and water to microgreens, included in a microgravity environment. Growth studies in simulated microgravity (using 3-dimensional clinostats) will assess microgreens growth relative to that in 1g. Gas exchange studies on microgreens canopies in various airflows will assess their photosynthesis and transpiration. Finally, a series of parabolic flights has enabled the evaluation of different harvesting and bagging techniques in microgravity. Indeed, traditional plant harvesting methods (scissors) in microgravity could generate significant microgreen debris in the space station cabin. Two innovative techniques, coupled to a dedicated bagging method, were designed and evaluated against the control, traditional, harvesting technique. This research was supported by grants from NASA KSC’s Independent Research and Technology Development Program, NASA’s Flight Opportunity Program, NASA Postdoctoral Program Fellowships (L.P. & C.J.) supported by NASA’s Space Biology program, and support from NASA’s Human Research Program.

Space Crop Production↗