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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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At least 1,333 records · Page 74
All sourcesNASA NTRSDOE OSTI
DOE OSTI2015

Interactions among roots, mycorrhizas and free-living microbial communities differentially impact soil carbon processes

Plant roots, their associated microbial community and free-living soil microbes interact to regulate the movement of carbon from the soil to the atmosphere, one of the most important and least understood fluxes of terrestrial carbon. Our inadequate understanding of how plant-microbial interactions alter soil carbon decomposition may lead to poor model predictions of terrestrial carbon feedbacks to the atmosphere. Roots, mycorrhizal fungi and free-living soil microbes can alter soil carbon decomposition through exudation of carbon into soil. Exudates of simple carbon compounds can increase microbial activity because microbes are typically carbon limited. When both roots and mycorrhizal fungi are present in the soil, they may additively increase carbon decomposition. However, when mycorrhizas are isolated from roots, they may limit soil carbon decomposition by competing with free-living decomposers for resources. We manipulated the access of roots and mycorrhizal fungi to soil insitu in a temperate mixed deciduous forest. We added 13 C-labelled substrate to trace metabolized carbon in respiration and measured carbon-degrading microbial extracellular enzyme activity and soil carbon pools. We used our data in a mechanistic soil carbon decomposition model to simulate and compare the effects of root and mycorrhizal fungal presence on soil carbon dynamics over longer time periods. Contrary to what we predicted, root and mycorrhizal biomass did not interact to additively increase microbial activity and soil carbon degradation. The metabolism of 13 C-labelled starch was highest when root biomass was high and mycorrhizal biomass was low. These results suggest that mycorrhizas may negatively interact with the free-living microbial community to influence soil carbon dynamics, a hypothesis supported by our enzyme results. Our steady-state model simulations suggested that root presence increased mineral-associated and particulate organic carbon pools, while mycorrhizal fungal presence had a greater influence on particulate than mineral-associated organic carbon pools.Synthesis. Our results suggest that the activity of enzymes involved in organic matter decomposition was contingent upon root-mycorrhizal-microbial interactions. Using our experimental data in a decomposition simulation model, we show that root-mycorrhizal-microbial interactions may have longer-term legacy effects on soil carbon sequestration. Lastly, our study suggests that roots stimulate microbial activity in the short term, but contribute to soil carbon storage over longer periods of time.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2014

Untargeted metabolomics studies employing NMR and LC–MS reveal metabolic coupling between Nanoarcheum equitans and its archaeal host Ignicoccus hospitalis

Interactions between species are the basis of microbial community formation and infectious diseases. Systems biology enables the construction of complex models describing such interactions, leading to a better understanding of disease states and communities. However, before interactions between complex organisms can be understood, metabolic and energetic implications of simpler real-world host-microbe systems must be worked out. To this effect, untargeted metabolomics experiments were conducted and integrated with proteomics data to characterize key molecular-level interactions between two hyperthermophilic microbial species, both of which have reduced genomes. Metabolic changes and transfer of metabolites between the archaea Ignicoccus hospitalis and Nanoarcheum equitans were investigated using integrated LC–MS and NMR metabolomics. The study of such a system is challenging, as no genetic tools are available, growth in the laboratory is challenging, and mechanisms by which they interact are unknown. Together with information about relative enzyme levels obtained from shotgun proteomics, the metabolomics data provided useful insights into metabolic pathways and cellular networks of I. hospitalis that are impacted by the presence of N. equitans, including arginine, isoleucine, and CTP biosynthesis. On the organismal level, the data indicate that N. equitans exploits metabolites generated by I. hospitalis to satisfy its own metabolic needs. Lastly, this finding is based on N. equitans’s consumption of a significant fraction of the metabolite pool in I. hospitalis that cannot solely be attributed to increased biomass production for N. equitans. Combining LC–MS and NMR metabolomics datasets improved coverage of the metabolome and enhanced the identification and quantitation of cellular metabolites.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2018

Structural Mechanisms of Cooperative DNA Binding by Bacterial Single-Stranded DNA-Binding Proteins

Bacteria encode homooligomeric single-stranded (ss) DNA-binding proteins (SSBs) that coat and protect ssDNA intermediates formed during genome maintenance reactions. The prototypical Escherichia coli SSB tetramer can bind ssDNA using multiple modes that differ by the number of bases bound per tetramer and the magnitude of the binding cooperativity. Our understanding of the mechanisms underlying cooperative ssDNA binding by SSBs has been hampered by the limited amount of structural information available for interfaces that link adjacent SSB proteins on ssDNA. Here in this paper we present a crystal structure of Bacillus subtilis SsbA bound to ssDNA. The structure resolves SsbA tetramers joined together by a ssDNA “bridge” and identifies an interface, termed the “bridge interface,” that links adjacent SSB tetramers through an evolutionarily conserved surface near the ssDNA-binding site. E. coli SSB variants with altered bridge interface residues bind ssDNA with reduced cooperativity and with an altered distribution of DNA binding modes. These variants are also more readily displaced from ssDNA by RecA than wild-type SSB. In spite of these biochemical differences, each variant is able to complement deletion of the ssb gene in E. coli. Together our data suggest a model in which the bridge interface contributes to cooperative ssDNA binding and SSB function but that destabilization of the bridge interface is tolerated in cells.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2015

Community structure of arbuscular mycorrhizal fungi associated with Robinia pseudoacacia in uncontaminated and heavy metal contaminated soils

The significance of arbuscular mycorrhizal fungi (AMF) in soil remediation has been widely recognized because of their ability to promote plant growth and increase phytoremediation efficiency in heavy metal (HM) polluted soils by improving plant nutrient absorption and by influencing the fate of the metals in the plant and soil. However, the symbiotic functions of AMF in remediation of polluted soils depend on plant–fungus–soil combinations and are greatly influenced by environmental conditions. To better understand the adaptation of plants and the related mycorrhizae to extreme environmental conditions, AMF colonization, spore density and community structure were analyzed in roots or rhizosphere soils of Robinia pseudoacacia. Mycorrhization was compared between uncontaminated soil and heavy metal contaminated soil from a lead–zinc mining region of northwest China. Samples were analyzed by restriction fragment length polymorphism (RFLP) screening with AMF-specific primers (NS31 and AM1), and sequencing of rRNA small subunit (SSU). The phylogenetic analysis revealed 28 AMF group types, including six AMF families: Glomeraceae, Claroideoglomeraceae, Diversisporaceae, Acaulosporaceae, Pacisporaceae, and Gigasporaceae. Of all AMF group types, six (21%) were detected based on spore samples alone, four (14%) based on root samples alone, and five (18%) based on samples from root, soil and spore. Glo9 (Rhizophagus intraradices), Glo17 (Funneliformis mosseae) and Acau3 (Acaulospora sp.) were the three most abundant AMF group types in the current study. Soil Pb and Zn concentrations, pH, organic matter content, and phosphorus levels all showed significant correlations with the AMF species compositions in root and soil samples. Overall, the uncontaminated sites had higher species diversity than sites with heavy metal contamination. This study highlights the effects of different soil chemical parameters on AMF colonization, spore density and community structure in contaminated and uncontaminated sites. The tolerant AMF species isolated and identified from this study have potential for application in phytoremediation of heavy metal contaminated areas.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2015

Kinetically and Crystallographically Guided Mutations of a Benzoate CoA Ligase (BadA) Elucidate Mechanism and Expand Substrate Permissivity

A benzoate CoA ligase (BadA), isolated from the bacterium Rhodopseudomonas palustris, catalyzes the conversion of benzoate to benzoyl CoA on the catabolic pathway of aromatic carboxylic acids. Herein, apparent Michaelis constants k cat app and K M app were determined for an expanded array of 31 substrates chosen to systematically probe the active site architecture of the enzyme and provide a baseline for expansion of wild-type substrate specificity. Acyl CoA products were observed for 25 of the 31 substrates; in general, BadA converted ortho-substituted substrates better than the corresponding meta and para regioisomers, and the turnover number was more affected by steric rather than electronic effects. The kinetic data are interpreted in relation to six crystal structures of BadA in complex with several substrates and a benzoyl-AMP reaction intermediate. In contrast to other known natural substrate-bound benzoate ligase structures, all substrate-bound BadA structures adopted the thiolation conformation instead of the adenylation conformation. We also observed all the aryl carboxylates to be uniquely oriented within the active site, relative to other structures. Together, the kinetics and structural data suggested a mechanism that involves substrate binding in the thiolation conformation, followed by substrate rotation to an active orientation upon the transition to the adenylation conformation. On the basis of this hypothesis and the structural data, sterically demanding active site residues were mutated, and the substrate specificity was expanded substantially versus that of BadA. Novel activities were seen for substrates with larger substituents, including phenyl acetate. Additionally, the mutant Lys427Ala identified this nonconserved residue as essential for the thiolation step of BadA, but not adenylation. Furthermore, these variously acylated CoAs can serve as novel substrates of acyl CoA-dependent acyltransferases in coupled enzyme assays to produce analogues of bioactive natural products.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2017

Evidence from FTIR Difference Spectroscopy That a Substrate H 2 O Molecule for O 2 Formation in Photosystem II Is Provided by the Ca Ion of the Catalytic Mn 4 CaO 5 Cluster

The O 2 -producing Mn 4 CaO 5 catalyst in photosystem II oxidizes two water molecules (substrate) to produce one O 2 molecule. Considerable evidence supports the identification of one of the two substrate waters as the Mn 4 CaO 5 cluster’s oxo bridge known as O 5 . The identity of the second substrate water molecule is less clear. In one set of models, the second substrate is the Mn-bound water molecule known as W2. In another set of models, the second substrate is the Ca 2+ -bound water molecule known as W3. In all of these models, a deprotonated form of the second substrate moves to a position next to O5 during the catalytic step immediately prior to O–O bond formation. Here, FTIR difference spectroscopy was employed to identify the vibrational modes of hydrogen-bonded water molecules that are altered by the substitution of Sr 2+ for Ca 2+ . Our data show that the substitution substantially altered the vibrational modes of only a single water molecule: the water molecule whose D-O–D bending mode is eliminated during the catalytic step immediately prior to O–O bond formation. These data are most consistent with the identification of the Ca 2+ -bound W3 as the second substrate involved in O–O bond formation.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2015

Pushing the Limits of Delta Bonding in Metal–Chromium Complexes with Redox Changes and Metal Swapping

Into the metalloligand Cr[N(o-(NCH 2 P( i Pr) 2 )C 6 H 4 ) 3 ] (1, CrL) was inserted a second chromium atom to generate the dichromium complex Cr 2 L (2), which is a homobimetallic analogue of the known MCrL complexes, where M is manganese (3) or iron (4). The cationic and anionic counterparts, [MCrL] + and [MCrL] - , respectively, were targeted, and each MCr pair was isolated in at least one other redox state. The solid-state structures of the [MCrL] +,0,– redox members are basically the same, with ultrashort metal–metal bonds between 1.96 and 1.74 Å. The formal shortness ratios (r) of these interactions are between 0.84 and 0.74 and are interpreted as triple to quintuple metal–metal bonds with the aid of theory. The trio of (d–d) 10 species [Cr 2 L] - ( 2 red), MnCrL (3), and [FeCrL] + (4 ox ) are S = 0 diamagnets. On the basis of M—Cr bond distances and theoretical calculations, the strength of the metal–metal bond across the (d–d) 10 series increases in the order Fe < Mn < Cr. The methylene protons in the ligand are shifted downfield in the 1H NMR spectra, and the diamagnetic anisotropy of the metal–metal bond was calculated as -3500 × 10 –36 , -3900 × 10 –36 , and -5800 × 10 –36 m 3 molecule –1 for 2 red , 3, and 4 ox respectively. The magnitude of diamagnetic anisotropy is, thus, affected more by bond polarity than by bond order. A comparative vis–NIR study of quintuply bonded 2 red and 3 revealed a large red shift in the δ 4 → δ 3 δ * transition energy upon swapping from the (Cr 2 ) 2+ to the (MnCr) 3+ core. Complex 2 red was further investigated by resonance Raman spectroscopy, and a band at 434 cm –1 was assigned as the Cr—Cr bond vibration. Lastly, 4 ox exhibited a Mössbauer doublet with an isomer shift of 0.18 mm/s that suggests a primarily Fe-based oxidation to Fe(I).

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2016

Tension-dependent free energies of nucleosome unwrapping

Here, nucleosomes form the basic unit of compaction within eukaryotic genomes, and their locations represent an important, yet poorly understood, mechanism of genetic regulation. Quantifying the strength of interactions within the nucleosome is a central problem in biophysics and is critical to understanding how nucleosome positions influence gene expression. By comparing to single-molecule experiments, we demonstrate that a coarse-grained molecular model of the nucleosome can reproduce key aspects of nucleosome unwrapping. Using detailed simulations of DNA and histone proteins, we calculate the tension-dependent free energy surface corresponding to the unwrapping process. The model reproduces quantitatively the forces required to unwrap the nucleosome and reveals the role played by electrostatic interactions during this process. We then demonstrate that histone modifications and DNA sequence can have significant effects on the energies of nucleosome formation. Most notably, we show that histone tails contribute asymmetrically to the stability of the outer and inner turn of nucleosomal DNA and that depending on which histone tails are modified, the tension-dependent response is modulated differently.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

Potential virus-mediated nitrogen cycling in oxygen-depleted oceanic waters

Viruses play an important role in the ecology and biogeochemistry of marine ecosystems. Beyond mortality and gene transfer, viruses can reprogram microbial metabolism during infection by expressing auxiliary metabolic genes (AMGs) involved in photosynthesis, central carbon metabolism, and nutrient cycling. While previous studies have focused on AMG diversity in the sunlit and dark ocean, less is known about the role of viruses in shaping metabolic networks along redox gradients associated with marine oxygen minimum zones (OMZs). Here, we analyzed relatively quantitative viral metagenomic datasets that profiled the oxygen gradient across Eastern Tropical South Pacific (ETSP) OMZ waters, assessing whether OMZ viruses might impact nitrogen (N) cycling via AMGs. Identified viral genomes encoded six N-cycle AMGs associated with denitrification, nitrification, assimilatory nitrate reduction, and nitrite transport. The majority of these AMGs (80%) were identified in T4-like Myoviridae phages, predicted to infect Cyanobacteria and Proteobacteria, or in unclassified archaeal viruses predicted to infect Thaumarchaeota. Four AMGs were exclusive to anoxic waters and had distributions that paralleled homologous microbial genes. Together, these findings suggest viruses modulate N-cycling processes within the ETSP OMZ and may contribute to nitrogen loss throughout the global oceans thus providing a baseline for their inclusion in the ecosystem and geochemical models.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

Surface-active antibiotic production as a multifunctional adaptation for postfire microorganisms

Abstract Wildfires affect soils in multiple ways, leading to numerous challenges for colonizing microorganisms. Although it is thought that fire-adapted microorganisms lie at the forefront of postfire ecosystem recovery, the specific strategies that these organisms use to thrive in burned soils remain largely unknown. Through bioactivity screening of bacterial isolates from burned soils, we discovered that several Paraburkholderia spp. isolates produced a set of unusual rhamnolipid surfactants with a natural methyl ester modification. These rhamnolipid methyl esters (RLMEs) exhibited enhanced antimicrobial activity against other postfire microbial isolates, including pyrophilous Pyronema fungi and Amycolatopsis bacteria, compared to the typical rhamnolipids made by organisms such as Pseudomonas spp. RLMEs also showed enhanced surfactant properties and facilitated bacterial motility on agar surfaces. In vitro assays further demonstrated that RLMEs improved aqueous solubilization of polycyclic aromatic hydrocarbons, which are potential carbon sources found in char. Identification of the rhamnolipid biosynthesis genes in the postfire isolate, Paraburkholderia kirstenboschensis str. F3, led to the discovery of rhlM, whose gene product is responsible for the unique methylation of rhamnolipid substrates. RhlM is the first characterized bacterial representative of a large class of integral membrane methyltransferases that are widespread in bacteria. These results indicate multiple roles for RLMEs in the postfire lifestyle of Paraburkholderia isolates, including enhanced dispersal, solubilization of potential nutrients, and inhibition of competitors. Our findings shed new light on the chemical adaptations that bacteria employ to navigate, grow, and outcompete other soil community members in postfire environments.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Quantum field theory of topological spin dynamics

Here, we develop a field theory of quantum magnets and magnetic (semi)metals, which is suitable for the analysis of their universal and topological properties. The systems of interest include collinear, coplanar, and general noncoplanar magnets. At the basic level, we describe the dynamics of magnetic moments using smooth vector fields in the continuum limit. Dzyaloshinskii-Moriya interaction is captured by a non-Abelian vector gauge field, and chiral spin couplings related to topological defects appear as higher-rank antisymmetric tensor gauge fields. We distinguish type-I and type-II magnets by their equilibrium response to the non-Abelian gauge flux, and characterize the resulting lattices of skyrmions and hedgehogs, the spectra of spin waves, and the chiral response to external perturbations. The general spin-orbit coupling of electrons is similarly described by non-Abelian gauge fields, including higher-rank tensors related to the electronic Berry flux. Itinerant electrons and local moments exchange their gauge fluxes through Kondo and Hund interactions. Hence, by utilizing gauge fields, this theory provides a unifying physical picture of “intrinsic” and “topological” anomalous Hall effects, spin-Hall effects, and other correlations between the topological properties of electrons and moments. We predict “topological” magnetoelectric effect in materials prone to hosting hedgehogs. Links to experiments and model calculations are provided by deriving the couplings and gauge fields from generic microscopic models, including the Hubbard model with spin-orbit interactions. Much of the formal analysis is generalized to d spatial dimensions in order to access the $π_{d–1}(S^{d–1})$ homotopy classification of the magnetic hedgehog topological defects, and establish the possibility of novel quantum spin liquids that exhibit a fractional magnetoelectric effect. However, we emphasize the form of all results in the physically relevant $\textit{d}$ = 3 dimensions, and discuss a few applications to topological magnetic conductors like Mn 3 Sn and Pr 2 Ir 2 O 7 .

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2015

Holographic operator mapping in dS / CFT and cluster decomposition

The bulk-to-boundary mapping for massive scalar fields is constructed, providing a de Sitter analog of the Lehmann-Symanzik-Zimmermann reduction formula. The set of boundary correlators thus obtained defines a potentially new class of conformal field theories based on principal series representations of the global conformal group. Conversely, we show that bulk field operators in de Sitter may be reconstructed from boundary operators. While consistent at the level of the free field theory, the boundary conformal field theory does not satisfy cluster decomposition. Furthermore, the resulting conformal field theory does not satisfy the basic axioms of Euclidean quantum field theory due to Osterwalder and Schrader, so it is likely not well defined once interactions are included.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2017

The DnaK Chaperone Uses Different Mechanisms To Promote and Inhibit Replication of Vibrio cholerae Chromosome 2

Replication of Vibrio cholerae chromosome 2 (Chr2) depends on molecular chaperone DnaK to facilitate binding of the initiator (RctB) to the replication origin. The binding occurs at two kinds of site, 12-mers and 39-mers, which promote and inhibit replication, respectively. Here we show that DnaK employs different mechanisms to enhance the two kinds of binding. We found that mutations in rctB that reduce DnaK binding also reduce 12-mer binding and initiation. The initiation defect is suppressed by second-site mutations that increase 12-mer binding only marginally. Instead, they reduce replication inhibitory mechanisms: RctB dimerization and 39-mer binding. One suppressing change was in a dimerization domain which is folded similarly to the initiator of an iteron plasmid—the presumed progenitor of Chr2. In plasmids, DnaK promotes initiation by reducing dimerization. A different mutation was in the 39-mer binding domain of RctB and inactivated it, indicating an alternative suppression mechanism. Paradoxically, although DnaK increases 39-mer binding, the increase was also achieved by inactivating the DnaK binding site of RctB. This result suggests that the site inhibits the 39-mer binding domain (via autoinhibition) when prevented from binding DnaK. Taken together, our results reveal an important feature of the transition from plasmid to chromosome: the Chr2 initiator retains the plasmid-like dimerization domain and its control by chaperones but uses the chaperones in an unprecedented way to control the inhibitory 39-mer binding.

59 BASIC BIOLOGICAL SCIENCES↗