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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.

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All sources NASA NTRS DOE OSTI

DOE OSTI2024

Advancing quantitative models of soil microbiology, ecology, and biochemistry

Rapid advances in soil biology are increasingly reflected in mathematical models. From molecular to global scales, models contribute to fundamental understanding and prediction of critical soil processes, such as carbon sequestration. Recent models explicitly incorporate microbial control over soil carbon and nutrient cycling, an approach that offers greater biological realism but raises new challenges in model parameterization and stability. Although they have proliferated at community and ecosystem scales, microbial-explicit models have yet to be incorporated into most Earth system models. Applying soil models across scales requires integration with data to support parameterization and validation using approaches such as Bayesian data assimilation. In conclusion, to catalyze future progress, we recommend breaking down barriers between modeling and empirical disciplines while broadening access to the computational infrastructure that supports soil biological modeling.

Xie, Wally↗

DOE OSTI2014

Research for Sustainable Bioenergy: Linking Genomic and Ecosystem Sciences, Workshop, October 2-4, 2013 Report

The design of sustainable biofuel systems requires knowledge about key plant-microbe-environment interactions that provide a range of ecosystem services. Most critical is a mechanistic understanding of how candidate biofuel plants interact with biotic and abiotic factors to affect the ecosystem outcomes that define sustainability. Recent advances in the genomic sciences can contribute immensely to the knowledge needed to design such systems. For example, progress in plant genomics will enable the inclusion of sustainability traits in future feedstocks, and advances in microbial genomics will allow insights into plantmicrobe-soil interactions that might be used to manage and support plant productivity and vigor. Linking these advances to breakthroughs in ecosystem science enables the use of systems biology in the fundamental design of sustainable biofuel systems. To identify research opportunities in developing such systems, the Department of Energy’s (DOE) Office of Biological and Environmental Research (BER) held the Research for Sustainable Bioenergy Workshop on Oct. 2–4, 2013, in Germantown, Maryland. The workshop convened more than 30 researchers with a broad and diverse range of expertise, including ecology, microbiology, plant genetics, genomics, computational biology, and modeling. Participants discussed and identified research gaps, challenges, and opportunities for enhancing the understanding of influences that biotic, abiotic, and genetic factors have on long-term plant feedstock performance and the delivery of ecosystem services at multiple scales. This report identifies the key topics and questions that could be addressed effectively to achieve this understanding. Research opportunities are organized into four categories: (1) plant systems, encompassing plant productivity, resource use efficiency, genotype/phenotype breeding, and crop diversity; (2) the plant microbiome, which includes microbes living in close association within or adjacent to plants; (3) ecosystem processes, such as carbon capture, greenhouse gas mitigation, and hydrologic processes; and (4) multiscale modeling, which integrates and extends results across spatiotemporal scales.

59 BASIC BIOLOGICAL SCIENCES↗

NASA NTRS1980

Life from a plantary perspective: Fundamental issues in global ecology

Twenty-three scientists from diverse disciplines met for one week at the University of California, Santa Barbara to discuss life from a planetary perspective. The scientists represented the major disciplines concerned with the Earth's biota, oceans, atmosphere and sediments, including geochemistry, atmospheric chemistry, chemical oceanography, limnology, forestry, terrestrial ecology, microbiology, biophysics, geography and remote sensing as well as mathematics. These twenty-three scientists met to discuss whether there was, at this time, a set of scientific issues concerning life and the entire Earth as a single unit, to set down the major tractable issues, and to suggest a set of activities that would promote the study of the issues identified. Their conclusions are summarized.

Botkin, D. B.↗

DOE OSTI2012

Molecular ecological network analyses

Background: Understanding the interaction among different species within a community and their responses to environmental changes is a central goal in ecology. However, defining the network structure in a microbial community is very challenging due to their extremely high diversity and as-yet uncultivated status. Although recent advance of metagenomic technologies, such as high throughout sequencing and functional gene arrays, provide revolutionary tools for analyzing microbial community structure, it is still difficult to examine network interactions in a microbial community based on high-throughput metagenomics data. Results: Here, we describe a novel mathematical and bioinformatics framework to construct ecological association networks named molecular ecological networks (MENs) through Random Matrix Theory (RMT)-based methods. Compared to other network construction methods, this approach is remarkable in that the network is automatically defined and robust to noise, thus providing excellent solutions to several common issues associated with high throughput metagenomics data. We applied it to determine the network structure of microbial communities subjected to long-term experimental warming based on pyrosequencing data of 16 S rRNA genes. We showed that the constructed MENs under both warming and unwarming conditions exhibited topological features of scale free, small world and modularity, which were consistent with previously described molecular ecological networks. Eigengene analysis indicated that the eigengenes represented the module profiles relatively well. In consistency with many other studies, several major environmental traits including temperature and soil pH were found to be important in determining network interactions in the microbial communities examined. To facilitate its application by the scientific community, all these methods and statistical tools have been integrated into a comprehensive Molecular Ecological Network Analysis Pipeline (MENAP), which is open-accessible now (http://ieg2.ou.edu/MENA). Conclusions: The RMT-based molecular ecological network analysis provides powerful tools to elucidate network interactions in microbial communities and their responses to environmental changes, which are fundamentally important for research in microbial ecology and environmental microbiology.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2024

Environment-specific virocell metabolic reprogramming

Abstract Viruses impact microbial systems through killing hosts, horizontal gene transfer, and altering cellular metabolism, consequently impacting nutrient cycles. A virus-infected cell, a “virocell,” is distinct from its uninfected sister cell as the virus commandeers cellular machinery to produce viruses rather than replicate cells. Problematically, virocell responses to the nutrient-limited conditions that abound in nature are poorly understood. Here we used a systems biology approach to investigate virocell metabolic reprogramming under nutrient limitation. Using transcriptomics, proteomics, lipidomics, and endo- and exo-metabolomics, we assessed how low phosphate (low-P) conditions impacted virocells of a marine Pseudoalteromonas host when independently infected by two unrelated phages (HP1 and HS2). With the combined stresses of infection and nutrient limitation, a set of nested responses were observed. First, low-P imposed common cellular responses on all cells (virocells and uninfected cells), including activating the canonical P-stress response, and decreasing transcription, translation, and extracellular organic matter consumption. Second, low-P imposed infection-specific responses (for both virocells), including enhancing nitrogen assimilation and fatty acid degradation, and decreasing extracellular lipid relative abundance. Third, low-P suggested virocell-specific strategies. Specifically, HS2-virocells regulated gene expression by increasing transcription and ribosomal protein production, whereas HP1-virocells accumulated host proteins, decreased extracellular peptide relative abundance, and invested in broader energy and resource acquisition. These results suggest that although environmental conditions shape metabolism in common ways regardless of infection, virocell-specific strategies exist to support viral replication during nutrient limitation, and a framework now exists for identifying metabolic strategies of nutrient-limited virocells in nature.

59 BASIC BIOLOGICAL SCIENCES↗

NASA NTRS2023

Virus Infection of Phytoplankton Increases Average Molar Mass and Reduces Hygroscopicity of Aerosolized Organic Matter

Viral infection of phytoplankton is a pervasive mechanism of cell death and bloom termination, which leads to the production of dissolved and colloidal organic matter that can be aerosolized into the atmosphere. Earth-observing satellites can track the growth and death of phytoplankton blooms on weekly time scales but the impact of viral infection on the cloud forming potential of associated aerosols is largely unknown. Here, we determine the influence of viral-derived organic matter, purified viruses, and marine hydrogels on the cloud condensation nuclei activity of their aerosolized solutions, compared to organic exudates from healthy phytoplankton. Dissolved organic material derived from exponentially growing and infected cells of well-characterized eukaryotic phytoplankton host-virus systems, including viruses from diatoms, coccolithophores and chlorophytes, was concentrated, desalted, and nebulized to form aerosol particles composed of primarily of organic matter. Aerosols from infected phytoplankton cultures resulted in an increase in critical activation diameter and average molar mass in three out of five combinations evaluated, along with a decrease in organic kappa (hygroscopicity) compared to healthy cultures and seawater controls. The infected samples also displayed evidence of increased surface tension depression at realistic cloud water vapor supersaturations. Amending the samples with xanthan gum to simulate marine hydrogels increased variability in organic kappa and surface tension in aerosols with high organic to salt ratios. Our findings suggest that the pulses of increased dissolved organic matter associated with viral infection in surface waters may increase the molar mass of dissolved organic compounds relative to surface waters occupied by healthy phytoplankton or low phytoplankton biomass.

Atmospheric science↗

DOE OSTI2018

Functional metagenomics reveals abundant polysaccharide-degrading gene clusters and cellobiose utilization pathways within gut microbiota of a wood-feeding higher termite

Plant cell-wall polysaccharides constitute the most abundant but recalcitrant organic carbon source in nature. Microbes residing in the digestive tract of herbivorous bilaterians are particularly efficient at depolymerizing polysaccharides into fermentable sugars and play a significant support role towards their host’s lifestyle. Here, we combine large-scale functional screening of fosmid libraries, shotgun sequencing, and biochemical assays to interrogate the gut microbiota of the wood-feeding “higher” termite Globitermes brachycerastes. A number of putative polysaccharide utilization gene clusters were identified with multiple fibrolytic genes. Our large-scale functional screening of 50,000 fosmid clones resulted in 464 clones demonstrating plant polysaccharide-degrading activities, including 267 endoglucanase-, 24 exoglucanase-, 72 β-glucosidase-, and 101 endoxylanase-positive clones. We sequenced 173 functionally active clones and identified ~219 genes encoding putative carbohydrate-active enzymes (CAZymes) targeting cellulose, hemicellulose and pectin. Further analyses revealed that 68 of 154 contigs encode one or more CAZyme, which includes 35 examples of putative saccharolytic operons, suggesting that clustering of CAZymes is common in termite gut microbial inhabitants. Biochemical characterization of a representative xylanase cluster demonstrated that constituent enzymes exhibited complementary physicochemical properties and saccharolytic capabilities. Furthermore, diverse cellobiose-metabolizing enzymes include β-glucosidases, cellobiose phosphorylases, and phopho-6-β-glucosidases were identified and functionally verified, indicating that the termite gut micro-ecosystem utilizes diverse metabolic pathways to interconnect hydrolysis and central metabolism. Collectively, these results provide an in-depth view of the adaptation and digestive strategies employed by gut microbiota within this tiny-yet-efficient host-associated ecosystem.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2022

Wildfire-dependent changes in soil microbiome diversity and function

Abstract Forest soil microbiomes have crucial roles in carbon storage, biogeochemical cycling and rhizosphere processes. Wildfire season length, and the frequency and size of severe fires have increased owing to climate change. Fires affect ecosystem recovery and modify soil microbiomes and microbially mediated biogeochemical processes. To study wildfire-dependent changes in soil microbiomes, we characterized functional shifts in the soil microbiota (bacteria, fungi and viruses) across burn severity gradients (low, moderate and high severity) 1 yr post fire in coniferous forests in Colorado and Wyoming, USA. We found severity-dependent increases of Actinobacteria encoding genes for heat resistance, fast growth, and pyrogenic carbon utilization that might enhance post-fire survival. We report that increased burn severity led to the loss of ectomycorrhizal fungi and less tolerant microbial taxa. Viruses remained active in post-fire soils and probably influenced carbon cycling and biogeochemistry via turnover of biomass and ecosystem-relevant auxiliary metabolic genes. Our genome-resolved analyses link post-fire soil microbial taxonomy to functions and reveal the complexity of post-fire soil microbiome activity.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2018

Polysaccharide utilization loci of North Sea Flavobacteriia as basis for using SusC/D-protein expression for predicting major phytoplankton glycans

Marine algae convert a substantial fraction of fixed carbon dioxide into various polysaccharides. Flavobacteriia that are specialized on algal polysaccharide degradation feature genomic clusters termed polysaccharide utilization loci (PULs). As knowledge on extant PUL diversity is sparse, we sequenced the genomes of 53 North Sea Flavobacteriia and obtained 400 PULs. Bioinformatic PUL annotations suggest usage of a large array of polysaccharides, including laminarin, α-glucans, and alginate as well as mannose-, fucose-, and xylose-rich substrates. Many of the PULs exhibit new genetic architectures and suggest substrates rarely described for marine environments. The isolates’ PUL repertoires often differed considerably within genera, corroborating ecological niche-associated glycan partitioning. Polysaccharide uptake in Flavobacteriia is mediated by SusCD-like transporter complexes. Respective protein trees revealed clustering according to polysaccharide specificities predicted by PUL annotations. Using the trees, we analyzed expression of SusC/D homologs in multiyear phytoplankton bloom-associated metaproteomes and found indications for profound changes in microbial utilization of laminarin, αglucans, β-mannan, and sulfated xylan. We hence suggest the suitability of SusC/D-like transporter protein expression within heterotrophic bacteria as a proxy for the temporal utilization of discrete polysaccharides.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2016

Back to the future of soil metagenomics

Here, direct extraction and characterization of microbial community DNA through PCR amplicon surveys and metagenomics has revolutionized the study of environmental microbiology and microbial ecology. In particular, metagenomic analysis of nucleic acids provides direct access to the genomes of the “uncultivated majority.” Accelerated by advances in sequencing technology, microbiologists have discovered more novel phyla, classes, genera, and genes from microorganisms in the first decade and a half of the twenty-first century than since these “many very little living animalcules” were first discovered by van Leeuwenhoek (Table 1). The unsurpassed diversity of soils promises continued exploration of a range of industrial, agricultural, and environmental functions. The ability to explore soil microbial communities with increasing capacity offers the highest promise for answering many outstanding who, what, where, when, why, and with whom questions such as: Which microorganisms are linked to which soil habitats? How do microbial abundances change with changing edaphic conditions? How do microbial assemblages interact and influence one another synergistically or antagonistically? What is the full extent of soil microbial diversity, both functionally and phylogenetically? What are the dynamics of microbial communities in space and time? How sensitive are microbial communities to a changing climate? What is the role of horizontal gene transfer in the stability of microbial communities? Do highly diverse microbial communities confer resistance and resilience in soils?

58 GEOSCIENCES↗

NASA NTRS2000

Pythium invasion of plant-based life support systems: biological control and sources

Invasion of plant-based life support systems by plant pathogens could cause plant disease and disruption of life support capability. Root rot caused by the fungus, Pythium, was observed during tests of prototype plant growth systems containing wheat at the Kennedy Space Center (KSC). We conducted experiments to determine if the presence of complex microbial communities in the plant root zone (rhizosphere) resisted invasion by the Pythium species isolated from the wheat root. Rhizosphere inocula of different complexity (as assayed by community-level physiological profile: CLPP) were developed using a dilution/extinction approach, followed by growth in hydroponic rhizosphere. Pythium growth on wheat roots and concomitant decreases in plant growth were inversely related to the complexity of the inocula during 20-day experiments in static hydroponic systems. Pythium was found on the seeds of several different wheat cultivars used in controlled environmental studies, but it is unclear if the seed-borne fungal strain(s) were identical to the pathogenic strain recovered from the KSC studies. Attempts to control pathogens and their effects in hydroponic life support systems should include early inoculation with complex microbial communities, which is consistent with ecological theory.

NASA Discipline Life Support Systems↗

DOE OSTI2012

Influence of nutrients and currents on the genomic composition of microbes across an upwelling mosaic

Metagenomic data sets were generated from samples collected along a coastal to open ocean transect between Southern California Bight and California Current waters during a seasonal upwelling event, providing an opportunity to examine the impact of episodic pulses of cold nutrientrich water into surface ocean microbial communities. The data set consists of B5.8 million predicted proteins across seven sites, from three different size classes: 0.1–0.8, 0.8–3.0 and 3.0–200.0 lm. Taxonomic and metabolic analyses suggest that sequences from the 0.1–0.8 lm size class correlated with their position along the upwelling mosaic. However, taxonomic profiles of bacteria from the larger size classes (0.8–200 lm) were less constrained by habitat and characterized by an increase in Cyanobacteria, Bacteroidetes, Flavobacteria and double-stranded DNA viral sequences. Functional annotation of transmembrane proteins indicate that sites comprised of organisms with small genomes have an enrichment of transporters with substrate specificities for amino acids, iron and cadmium, whereas organisms with larger genomes have a higher percentage of transporters for ammonium and potassium. Eukaryotic-type glutamine synthetase (GS) II proteins were identified and taxonomically classified as viral, most closely related to the GSII in Mimivirus, suggesting that marine Mimivirus-like particles may have played a role in the transfer of GSII gene functions. Additionally, a Planctomycete bloom was sampled from one upwelling site providing a rare opportunity to assess the genomic composition of a marine Planctomycete population. The significant correlations observed between genomic properties, community structure and nutrient availability provide insights into habitat-driven dynamics among oligotrophic versus upwelled marine waters adjoining each other spatially.

marine↗

DOE OSTI2012

Diversity and population structure of Marine Group A bacteria in the Northeast subarctic Pacific Ocean

Marine Group A (MGA) is a candidate phylum of Bacteria that is ubiquitous and abundant in the ocean. Despite being prevalent, the structural and functional properties of MGA populations remain poorly constrained. Here, we quantified MGA diversity and population structure in relation to nutrients and O2 concentrations in the oxygen minimum zone (OMZ) of the Northeast subarctic Pacific Ocean using a combination of catalyzed reporter deposition fluorescence in situ hybridization (CARD-FISH) and 16S small subunit ribosomal RNA (16S rRNA) gene sequencing (clone libraries and 454-pyrotags). Estimates of MGA abundance as a proportion of total bacteria were similar across all three methods although estimates based on CARD-FISH were consistently lower in the OMZ (5.6%±1.9%) than estimates based on 16S rRNA gene clone libraries (11.0%±3.9%) or pyrotags (9.9%±1.8%). Five previously defined MGA subgroups were recovered in 16S rRNA gene clone libraries and five novel subgroups were defined (HF770D10, P262000D03, P41300E03, P262000N21 and A714018). Rarefaction analysis of pyrotag data indicated that the ultimate richness of MGA was very nearly sampled. Spearman’s rank analysis of MGA abundances by CARD-FISH and O2 concentrations resulted in significant correlation. Analyzed in more detail by 16S rRNA pyrotag sequencing, MGA operational taxonomic units affiliated with subgroups Arctic95A-2 and A714018 comprised 0.3–2.4% of total bacterial sequences and displayed strong correlations with decreasing O2 concentration. This study is the first comprehensive description of MGA diversity using complementary techniques. These results provide a phylogenetic framework for interpreting future studies on ecotype selection among MGA subgroups, and suggest a potentially important role for MGA in the ecology and biogeochemistry of OMZs.

Marine Group A↗

DOE OSTI2011

Genomic insights to SAR86, an abundant and uncultivated marine bacterial lineage

Bacteria in the 16S rRNA clade SAR86 are among the most abundant uncultivated constituents of microbial assemblages in the surface ocean for which little genomic information is currently available. Bioinformatic techniques were used to assemble two nearly complete genomes from marine metagenomes and single-cell sequencing provided two more partial genomes. Recruitment of metagenomic data shows that these SAR86 genomes substantially increase our knowledge of non-photosynthetic bacteria in the surface ocean. Phylogenomic analyses establish SAR86 as a basal and divergent lineage of c-proteobacteria, and the individual genomes display a temperature dependent distribution. Modestly sized at 1.25–1.7 Mbp, the SAR86 genomes lack several pathways for amino-acid and vitamin synthesis as well as sulfate reduction, trends commonly observed in other abundant marine microbes. SAR86 appears to be an aerobic chemoheterotroph with the potential for proteorhodopsin-based ATP generation, though the apparent lack of a retinal biosynthesis pathway may require it to scavenge exogenously-derived pigments to utilize proteorhodopsin. The genomes contain an expanded capacity for the degradation of lipids and carbohydrates acquired using a wealth of tonB-dependent outer membrane receptors. Like the abundant planktonic marine bacterial clade SAR11, SAR86 exhibits metabolic streamlining, but also a distinct carbon compound specialization, possibly avoiding competition.

tonB receptors↗

DOE OSTI2024

Increasing aggregate size reduces single-cell organic carbon incorporation by hydrogel-embedded wetland microbes

Abstract Microbial degradation of organic carbon in sediments is impacted by the availability of oxygen and substrates for growth. To better understand how particle size and redox zonation impact microbial organic carbon incorporation, techniques that maintain spatial information are necessary to quantify elemental cycling at the microscale. In this study, we produced hydrogel microspheres of various diameters (100, 250, and 500 μm) and inoculated them with an aerobic heterotrophic bacterium isolated from a freshwater wetland (Flavobacterium sp.), and in a second experiment with a microbial community from an urban lacustrine wetland. The hydrogel-embedded microbial populations were incubated with 13C-labeled substrates to quantify organic carbon incorporation into biomass via nanoSIMS. Additionally, luminescent nanosensors enabled spatially explicit measurements of oxygen concentrations inside the microspheres. The experimental data were then incorporated into a reactive-transport model to project long-term steady-state conditions. Smaller (100 μm) particles exhibited the highest microbial cell-specific growth per volume, but also showed higher absolute activity near the surface compared to the larger particles (250 and 500 μm). The experimental results and computational models demonstrate that organic carbon availability was not high enough to allow steep oxygen gradients and as a result, all particle sizes remained well-oxygenated. Our study provides a foundational framework for future studies investigating spatially dependent microbial activity in aggregates using isotopically labeled substrates to quantify growth.

59 BASIC BIOLOGICAL SCIENCES↗

NASA NTRS1997

Density and composition of microorganisms during long-term (418 day) growth of potato using biologically reclaimed nutrients from inedible plant biomass

A study evaluating alternative methods for long term operation of biomass production systems was recently completed at the Kennedy Space Center (KSC). The 418-day study evaluated repeated batch versus mixed-aged production of potato grown on either standard 1/2-strength Hoagland's nutrient solution or solutions including nutrients recycled from inedible plant material. The long term effects of closure and recycling on microbial dynamics were evaluated by monitoring the microbial communities associated with various habitats within the plant growth system (i.e., plant roots, nutrient solution, biofilms within the hydroponic systems, atmosphere, and atmospheric condensate). Plate count methods were used to enumerate and characterize microorganisms. Microscopic staining methods were used to estunate total cell densities. The primary finding was that the density and composition of microbial communities associated with controlled environmental plant growth systems are stable during long term operation. Continuous production resulted in slightly greater stability. Nutrient recycling, despite the addition of soluble organic material from the waste processing system, did not significantly increase microbial density in any of the habitats.

NASA Center KSC↗

NASA NTRS1990

Mobilifilum chasei: morphology and ecology of a spirochete from an intertidal stratified microbial mat community

Spirochetes were found in the lower anoxiphototrophic layer of a stratified microbial mat (North Pond, Laguna Figueroa, Baja California, Mexico). Ultra-structural analysis of thin sections of field samples revealed spirochetes approximately 0.25 micrometer in diameter with 10 or more periplasmic flagella, leading to the interpretation that these spirochetes bear 10 flagellar insertions on each end. Morphometric study showed these free-living spirochetes greatly resemble certain symbiotic ones, i.e., Borrelia and certain termite spirochetes, the transverse sections of which are presented here. The ultrastructure of this spirochete also resembles Hollandina and Diplocalyx (spirochetes symbiotic in arthropods) more than it does Spirochaeta, the well known genus of mud-dwelling spirochetes. The new spirochete was detected in mat material collected both in 1985 and in 1987. Unique morphology (i.e., conspicuous outer coat of inner membrane, large number of periplasmic flagella) and ecology prompt us to name a new free-living spirochete.

Non-NASA Center↗

DOE OSTI2018

WHONDRS: a Community Resource for Studying Dynamic River Corridors

The Worldwide Hydrobiogeochemistry Observation Network for Dynamic River Systems (WHONDRS) aims to galvanize a global community to provide the scientific basis for improved management of dynamic river corridors. WHONDRS is a global research consortium working to understand connections among dynamic hydrology, biogeochemistry, and microbiology in river corridors from local to global scales.

54 ENVIRONMENTAL SCIENCES↗