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At least 1,729 records · Page 96
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Pseudodesulfovibrio mercurii sp. nov., a mercury-methylating bacterium isolated from sediment

The sulfate-reducing, mercury-methylating strain ND132 T was isolated from the brackish anaerobic bottom sediments of Chesapeake Bay, USA. Capable of high levels of mercury (Hg) methylation, ND132 T has been widely used as a model strain to study the process and to determine the genetic basis of Hg methylation. Originally called Desulfovibrio desulfuricans ND132 T on the basis of an early partial 16S rRNA sequence, the strain has never been formally described. Phylogenetic and physiological traits place this strain within the genus Pseudodesulfovibrio, in the recently reclassified phylum Desulfobacterota (formerly Deltaproteobacteria ). ND132 T is most closely related to Pseudodesulfovibrio hydrargyri BerOc1 T and Pseudodesulfovibrio indicus J2T. Analysis of average nucleotide identity (ANI) of whole-genome sequences showed roughly 88 % ANI between P. hydrargyri BerOc1T and ND132T, and 84 % similarity between ND132T and P. indicus J2 T . These cut-off scores <95 %, along with a multi-gene phylogenetic analysis of members of the family Desulfovibrionacea, and differences in physiology indicate that all three strains represent separate species. The Gram-stain-negative cells are vibrio-shaped, motile and not sporulated. ND132 T is a salt-tolerant mesophile with optimal growth in the laboratory at 32 °C, 2 % salinity, and pH 7.8. The DNA G+C content of the genomic DNA is 65.2 %. It is an incomplete oxidizer of short chain fatty acids, using lactate, pyruvate and fumarate with sulfate or sulfite as the terminal electron acceptors. ND132 T can respire fumarate using pyruvate as an electron donor. The major fatty acids are iso-C 15 :0 , anteiso-C 15 : 0 , iso-C 17 : 0 , iso-C 17 : 1 ω9c and anteiso-C 17 : 0 . We propose the classification of strain ND132 T (DSM 110689, ATCC TSD-224) as the type strain Pseudodesulfovibrio mercurii sp. nov.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Optical Absorption Spectroscopy Probes Water Wire and Its Ordering in a Hydrogen-Bond Network

Water wires, quasi-one-dimensional chains composed of hydrogen-bonded (H-bonded) water molecules, play a fundamental role in numerous chemical, physical, and physiological processes. Yet direct experimental detection of water wires has been elusive so far. Based on advanced many-body theory that includes electron-hole interactions, we report that optical absorption spectroscopy can serve as a sensitive probe of water wires and their ordering. In both liquid and solid water, the main peak of the spectrum is discovered to be a charge-transfer exciton. In water, the charge-transfer exciton is strongly coupled to the H-bonding environment where the exciton is excited between H-bonded water molecules with a large spectral intensity. In regular ice, the spectral weight of the charge-transfer exciton is enhanced by a collective excitation occurring on proton-ordered water wires, whose spectral intensity scales with the ordering length of water wire. The spectral intensity and excitonic interaction strength reaches its maximum in ice XI, where the long-range ordering length yields the most pronounced spectral signal. Our findings suggest that water wires, which widely exist in important physiological and biological systems and other phases of ice, can be directly probed by this approach. Published by the American Physical Society 2025

Tang, Fujie (ORCID:0000000197615359)↗
DOE OSTI2012

Low- and room-temperature X-ray structures of protein kinase A ternary complexes shed new light on its activity

ATP bound in the active site of protein kinase A is readily hydrolysed to ADP and free phosphate by X-ray irradiation at room temperature. The phosphate ion observed in the active site causes a dramatic conformational change of the bound peptide inhibitor. Post-translational protein phosphorylation by protein kinase A (PKA) is a ubiquitous signalling mechanism which regulates many cellular processes. A low-temperature X-ray structure of the ternary complex of the PKA catalytic subunit (PKAc) with ATP and a 20-residue peptidic inhibitor (IP20) at the physiological Mg{sup 2+} concentration of ∼0.5 mM (LT PKA–MgATP–IP20) revealed a single metal ion in the active site. The lack of a second metal in LT PKA–MgATP–IP20 renders the β- and γ-phosphoryl groups of ATP very flexible, with high thermal B factors. Thus, the second metal is crucial for tight positioning of the terminal phosphoryl group for transfer to a substrate, as demonstrated by comparison of the former structure with that of the LT PKA–Mg{sub 2}ATP–IP20 complex obtained at high Mg{sup 2+} concentration. In addition to its kinase activity, PKAc is also able to slowly catalyze the hydrolysis of ATP using a water molecule as a substrate. It was found that ATP can be readily and completely hydrolyzed to ADP and a free phosphate ion in the crystals of the ternary complex PKA–Mg{sub 2}ATP–IP20 by X-ray irradiation at room temperature. The cleavage of ATP may be aided by X-ray-generated free hydroxyl radicals, a very reactive chemical species, which move rapidly through the crystal at room temperature. The phosphate anion is clearly visible in the electron-density maps; it remains in the active site but slides about 2 Å from its position in ATP towards Ala21 of IP20, which mimics the phosphorylation site. The phosphate thus pushes the peptidic inhibitor away from the product ADP, while resulting in dramatic conformational changes of the terminal residues 24 and 25 of IP20. X-ray structures of PKAc in complex with the nonhydrolysable ATP analogue AMP-PNP at both room and low temperature demonstrated no temperature effects on the conformation and position of IP20.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2014

Structural insights into the human RyR2 N-terminal region involved in cardiac arrhythmias

X-ray and solution structures of the human RyR2 N-terminal region were obtained under near-physiological conditions. The structure exhibits a unique network of interactions between its three domains, revealing an important stabilizing role of the central helix. Human ryanodine receptor 2 (hRyR2) mediates calcium release from the sarcoplasmic reticulum, enabling cardiomyocyte contraction. The N-terminal region of hRyR2 (amino acids 1–606) is the target of >30 arrhythmogenic mutations and contains a binding site for phosphoprotein phosphatase 1. Here, the solution and crystal structures determined under near-physiological conditions, as well as a homology model of the hRyR2 N-terminal region, are presented. The N-terminus is held together by a unique network of interactions among its three domains, A, B and C, in which the central helix (amino acids 410–437) plays a prominent stabilizing role. Importantly, the anion-binding site reported for the mouse RyR2 N-terminal region is notably absent from the human RyR2. The structure concurs with the differential stability of arrhythmogenic mutations in the central helix (R420W, I419F and I419F/R420W) which are owing to disparities in the propensity of mutated residues to form energetically favourable or unfavourable contacts. In solution, the N-terminus adopts a globular shape with a prominent tail that is likely to involve residues 545–606, which are unresolved in the crystal structure. Docking the N-terminal domains into cryo-electron microscopy maps of the closed and open RyR1 conformations reveals C{sup α} atom movements of up to 8 Å upon channel gating, and predicts the location of the leucine–isoleucine zipper segment and the interaction site for spinophilin and phosphoprotein phosphatase 1 on the RyR surface.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2015

Structure of human saposin A at lysosomal pH

A 1.8 Å resolution structure of the sphingolipid activator protein saposin A has been determined at pH 4.8, the physiologically relevant lysosomal pH for hydrolase enzyme activation and lipid-transfer activity. The saposins are essential cofactors for the normal lysosomal degradation of complex glycosphingolipids by acid hydrolase enzymes; defects in either saposin or hydrolase function lead to severe metabolic diseases. Saposin A (SapA) activates the enzyme β-galactocerebrosidase (GALC), which catalyzes the breakdown of β-d-galactocerebroside, the principal lipid component of myelin. SapA is known to bind lipids and detergents in a pH-dependent manner; this is accompanied by a striking transition from a ‘closed’ to an ‘open’ conformation. However, previous structures were determined at non-lysosomal pH. This work describes a 1.8 Å resolution X-ray crystal structure determined at the physiologically relevant lysosomal pH 4.8. In the absence of lipid or detergent at pH 4.8, SapA is observeed to adopt a conformation closely resembling the previously determined ‘closed’ conformation, showing that pH alone is not sufficient for the transition to the ‘open’ conformation. Structural alignments reveal small conformational changes, highlighting regions of flexibility.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2015

Fog as a source of nitrogen for redwood trees: evidence from fluxes and stable isotopes

A defining feature of the redwood forest in coastal California is the presence of fog in the summer months, a time when there is typically little rainfall. Our goal was to determine the role of summer fog in canopy transformation of nitrogen, nitrogen uptake by trees and photosynthesis within a coastal redwood forest ecosystem. We measured horizontal and vertical inputs of nitrogen, the isotopic composition of nitrogen in a variety of atmospheric sources (summer fog, winter rain and throughfall throughout the year), nitrogen pools (soil solution) and plant tissue (roots and foliage), as well as rates of photosynthesis and nitrogen uptake by trees. Throughfall nitrogen fluxes were greater at the forest edge compared to the interior both within the canopy (sampled 10m above-ground) and onto the forest floor (sampled 1m above-ground; P <0.05). Similarly, soil solution $\mathrm{NO^{-}_{3}}$ and total inorganic nitrogen were greater at the forest edge compared to the interior ( P =0.0014 and 0.009, respectively). Whereas natural abundance δ 15 NO 3 values were not significantly different between winter rain (measured as bulk precipitation) and summer fog water (average δ 15 N=-1.2±0.68 0/00), δ 15 NH 4 values were significantly greater in fog water (11.4±2.7 0/00) compared to rain (1.2±0.9 0/00). We found no difference in δ 15 N in roots from forest edge trees compared to interior trees. In contrast, nitrogen concentrations and δ 15 N in foliage from forest edge trees were significantly greater compared to interior trees ( P <0.0001), suggesting that the leaves of forest edge trees may be obtaining a greater proportion of their nitrogen from fog compared to those of the interior trees. Natural abundance 13 C of leaf sugars and rates of photosynthesis were significantly higher at the forest edge compared to the interior during the fog season ( P <0.05), but not different between locations in the rain season ( P >0.05). Nitrification in the forest floor, rather than the canopy, is the primary source of $\mathrm{NO^{-}_{3}}$ in these soils throughout the year. Synthesis. Finally, summer fog provides nitrogen directly and indirectly to redwood trees, especially those at the forest edge, and affects the physiologic function of redwood trees. Summer fog provides nitrogen directly and indirectly to redwood trees, especially those at the forest edge, and affects the physiologic function of redwood trees.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2017

Growth strategies and threshold responses to water deficit modulate effects of warming on tree seedlings from forest to alpine

Predictions of upslope range shifts for tree species with warming are based on assumptions of moisture stress at lower elevation limits and low-temperature stress at high-elevation limits. However, recent studies have shown that warming can reduce tree seedling establishment across the entire gradient from subalpine forest to alpine via moisture limitation. Warming effects also vary with species, potentially resulting in community shifts in high-elevation forests. We examined the growth and physiology underlying effects of warming on seedling demographic patterns. We evaluated dry mass (DM), root length, allocation above- and below-ground, and relative growth rate (RGR) of whole seedlings, and their ability to avoid or endure water stress via water-use efficiency and resisting turgor loss, for Pinus flexilis , Picea engelmannii and Pinus contorta seeded below, at and above tree line in experimentally warmed, watered and control plots in the Rocky Mountains, USA. We expected that growth and allocation responses to warming would relate to moisture status and that variation in drought tolerance traits would explain species differences in survival rates. Across treatments and elevations, seedlings of all species had weak turgor-loss resistance, and growth was marginal with negative RGR in the first growth phase (-0.01 to -0.04 g g -1 day -1 ). Growth was correlated with soil moisture, particularly in the relatively small-seeded P. contorta and P. engelmannii . Pinus flexilis , known to have the highest survivorship, attained the greatest DM and longest root but was also the slowest growing and most water-use efficient. This was likely due to its greater reliance on seed reserves. Seedlings developed 15% less total DM, 25% less root DM and 11% shorter roots in heated compared with unheated plots. Higher temperatures slightly increased DM, root length and RGR where soils were wettest, but more strongly decreased these variables under drier conditions. Synthesis. The surprising heat inhibition of tree seedling establishment at the cold edge of forests appears to have a physiological basis: newly germinated seedlings have poor moisture stress tolerance, which appears related to marginal initial growth and heavy reliance on seed reserves. Variation in these attributes among tree species at tree line helps explain their different climate responses.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2014

In situ visualization of newly synthesized proteins in environmental microbes using amino acid tagging and click chemistry

Summary Here we describe the application of a new click chemistry method for fluorescent tracking of protein synthesis in individual microorganisms within environmental samples. This technique, termed bioorthogonal non‐canonical amino acid tagging ( BONCAT ), is based on the in vivo incorporation of the non‐canonical amino acid L ‐azidohomoalanine ( AHA ), a surrogate for l ‐methionine, followed by fluorescent labelling of AHA ‐containing cellular proteins by azide‐alkyne click chemistry. BONCAT was evaluated with a range of phylogenetically and physiologically diverse archaeal and bacterial pure cultures and enrichments, and used to visualize translationally active cells within complex environmental samples including an oral biofilm, freshwater and anoxic sediment. We also developed combined assays that couple BONCAT with ribosomal RNA (rRNA)‐targeted fluorescence in situ hybridization ( FISH ), enabling a direct link between taxonomic identity and translational activity. Using a methanotrophic enrichment culture incubated under different conditions, we demonstrate the potential of BONCAT‐FISH to study microbial physiology in situ . A direct comparison of anabolic activity using BONCAT and stable isotope labelling by nano‐scale secondary ion mass spectrometry ( 15 NH 3 assimilation) for individual cells within a sediment‐sourced enrichment culture showed concordance between AHA ‐positive cells and 15 N enrichment. BONCAT‐FISH offers a fast, inexpensive and straightforward fluorescence microscopy method for studying the in situ activity of environmental microbes on a single‐cell level.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2019

Closely related viruses of the marine picoeukaryotic alga Ostreococcus lucimarinus exhibit different ecological strategies

Summary In marine ecosystems, viruses are major disrupters of the direct flow of carbon and nutrients to higher trophic levels. Although the genetic diversity of several eukaryotic phytoplankton virus groups has been characterized, their infection dynamics are less understood, such that the physiological and ecological implications of their diversity remain unclear. We compared genomes and infection phenotypes of the two most closely related cultured phycodnaviruses infecting the widespread picoprasinophyte Ostreococcus lucimarinus under standard‐ (1.3 divisions per day) and limited‐light (0.41 divisions per day) nutrient replete conditions. OlV7 infection caused early arrest of the host cell cycle, coinciding with a significantly higher proportion of infected cells than OlV1‐amended treatments, regardless of host growth rate. OlV7 treatments showed a near‐50‐fold increase of progeny virions at the higher host growth rate, contrasting with OlV1's 16‐fold increase. However, production of OlV7 virions was more sensitive than OlV1 production to reduced host growth rate, suggesting fitness trade‐offs between infection efficiency and resilience to host physiology. Moreover, although organic matter released from OlV1‐ and OlV7‐infected hosts had broadly similar chemical composition, some distinct molecular signatures were observed. Collectively, these results suggest that current views on viral relatedness through marker and core gene analyses underplay operational divergence and consequences for host ecology.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Conditional filamentation as an adaptive trait of bacteria and its ecological significance in soils

Bacteria can regulate cell morphology in response to environmental conditions, altering their physiological and metabolic characteristics to improve survival. Conditional filamentation, in which cells suspend division while continuing lateral growth, is a strategy with a range of adaptive benefits. Here, we review the causes and consequences of conditional filamentation with respect to bacterial physiology, ecology and evolution. We describe four major benefits from conditional filamentation: stress tolerance, surface colonization, gradient spanning and the facilitation of biotic interactions. Adopting a filamentous growth habit involves fitness trade-offs which are also examined. We focus on the role of conditional filamentation in soil habitats, where filamentous morphotypes are highly prevalent and where environmental heterogeneity can benefit a conditional response. Here, to illustrate the use of information presented in our review, we tested the conditions regulating filamentation by the forest soil isolate Paraburkholderia elongata 5N T . Filamentation by P. elongata was induced at elevated phosphate concentrations, and was associated with the accumulation of intracellular polyphosphate, highlighting the role of filamentation in a phosphate-solubilizing bacterium. Conditional filamentation enables bacteria to optimize their growth and metabolism in environments that are highly variable, a trait that can impact succession, symbioses, and biogeochemistry in soil environments.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Genome and proteome analyses show the gaseous alkane degrader Desulfosarcina sp. strain BuS5 as an extreme metabolic specialist

The metabolic potential of the sulfate-reducing bacterium Desulfosarcina sp. strain BuS5, currently the only pure culture able to oxidize the volatile alkanes propane and butane without oxygen, was investigated via genomics, proteomics and physiology assays. Complete genome sequencing revealed that strain BuS5 encodes a single alkyl-succinate synthase, an enzyme which apparently initiates oxidation of both propane and butane. The formed alkyl-succinates are oxidized to CO 2 via beta oxidation and the oxidative Wood–Ljungdahl pathways as shown by proteogenomics analyses. Strain BuS5 conserves energy via the canonical sulfate reduction pathway and electron bifurcation. An ability to utilize long-chain fatty acids, mannose and oligopeptides, suggested by automated annotation pipelines, was not supported by physiology assays and in-depth analyses of the corresponding genetic systems. Consistently, comparative genomics revealed a streamlined BuS5 genome with a remarkable paucity of catabolic modules. These results establish strain BuS5 as an exceptional metabolic specialist, able to grow only with propane and butane, for which we propose the name Desulfosarcina aeriophaga BuS5. This highly restrictive lifestyle, most likely the result of habitat-driven evolutionary gene loss, may provide D. aeriophaga BuS5 a competitive edge in sediments impacted by natural gas seeps.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Crystal Ball: A Naturalist Perspective of Microbiology: Examples from Methanogenic Archaea

Storytelling has been the primary means of knowledge transfer over human history. The effectiveness and reach of stories are improved when the message is appropriate for the target audience. Oftentimes, the stories that are most well received and recounted are those that have a clear purpose and that are told from a variety of perspectives that touch on the varied interests of the target audience. Whether scientists realize or not, they are accustomed to telling stories of their own scientific discoveries through the preparation of manuscripts, presentations, and lectures. Perhaps less frequently, scientists prepare review articles or book chapters that summarize a body of knowledge on a given subject matter, meant to be more holistic recounts of a body of literature. Yet, by necessity, such summaries are often still narrow in their scope and are told from the perspective of a particular discipline. In other words, interdisciplinary reviews or book chapters tend to be the rarity rather than the norm. Naturalists are scientists that tell stories of organisms and their natural environment within a historical context and from an interdisciplinary perspective. Such stories interweave observations of biological subjects from disparate disciplines into a cohesive story. To this end, the success of naturalists in recounting compelling natural history stories is enhanced when they allow themselves to become vulnerable by knowingly entering a literature base full of unfamiliar ways of observing and describing such subjects. When successful, this approach can broaden the scope of the story, making it of interest to a larger audience and attracting further recounting of that story (e.g., citations). To this end, when we look into our crystal ball, we see a need to tell more holistic stories of microorganisms and their functions from an interdisciplinary, naturalist perspective that combines what is known of their contemporary ecology, physiology, and biochemistry with their evolutionary history thereby placing them within a historical Earth context. With this conviction in mind, we take the opportunity to look back on the natural history of methanogens to identify some of their most profound biochemical innovations and their impact on the trajectory of life and the planet. Our approach was to integrate knowledge from the fields of biochemistry, physiology, ecology, evolution, geochemistry, and atmospheric sciences. We start with the origin of the first autotrophic cells and how this set Earth on a path towards biomass expansion and functional diversification. Next, we discuss the importance of iron and sulfur in methanogen metabolism, and how their innovative ways of accessing these elements allowed for expanded use of iron-sulfur clusters ([Fe-S]) as nanoscale catalysts that power(ed) Earth’s biochemical cycles. We next discuss the origin and evolution of [NiFe]-hydrogenase and how this versatile enzyme chassis was co-opted by a variety of anaerobes and aerobes as the foundation for respiratory complexes capable of sustaining higher forms of life, including humans. Lastly, we discuss the evolution of the enzyme molybdenum nitrogenase, and how this allowed the biosphere to overcome fixed nitrogen limitation by tapping the seemingly endless reserve of atmospheric dinitrogen (N 2 ). In telling these stories, we aimed to generate template(s) to motivate future interdisciplinary natural history studies focused on other organisms and processes. Further, we hope to stimulate scientific discourse and provide impetus to become vulnerable and peruse literature of relevance to understanding the causes and consequences of the evolution of your favorite microorganism or biochemical process.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2014

Contemporary evolution of an invasive grass in response to elevated atmospheric CO 2 at a Mojave Desert FACE site

Elevated atmospheric CO 2 has been shown to rapidly alter plant physiology and ecosystem productivity, but contemporary evolutionary responses to increased CO 2 have yet to be demonstrated in the field. At a Mojave Desert FACE (free-air CO2 enrichment) facility, we tested whether an annual grass weed (Bromus madritensis ssp. rubens) has evolved in response to elevated atmospheric CO 2 . Within 7 years, field populations exposed to elevated CO 2 evolved lower rates of leaf stomatal conductance; a physiological adaptation known to conserve water in other desert or water-limited ecosystems. Evolution of lower conductance was accompanied by reduced plasticity in upregulating conductance when CO 2 was more limiting; this reduction in conductance plasticity suggests that genetic assimilation may be ongoing. Reproductive fitness costs associated with this reduction in phenotypic plasticity were demonstrated under ambient levels of CO 2 . Our findings suggest that contemporary evolution may facilitate this invasive species’ spread in this desert ecosystem.

54 ENVIRONMENTAL SCIENCES↗