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At least 505 records · Page 28
All sourcesNASA NTRSDOE OSTI
DOE OSTI2015

New streams and springs after the 2014 Mw6.0 South Napa earthquake

Many streams and springs, which were dry or nearly dry before the 2014 Mw6.0 South Napa earthquake, started to flow after the earthquake. A United States Geological Survey stream gauge also registered a coseismic increase in discharge. Public interest was heightened by a state of extreme drought in California. Since the new flows were not contaminated by pre-existing surface water, their composition allowed unambiguous identification of their origin. Following the earthquake we repeatedly surveyed the new flows, collecting data to test hypotheses about their origin. We show that the new flows originated from groundwater in nearby mountains released by the earthquake. The estimated total amount of new water is ~106m3, about 1/40 of the annual water use in the Napa-Sonoma area. Our model also makes a testable prediction of a post-seismic decrease of seismic velocity in the shallow crust of the affected region.

58 GEOSCIENCES↗
DOE OSTI2020

Insights into the dynamics between viruses and their hosts in a hot spring microbial mat

Abstract Our current knowledge of host–virus interactions in biofilms is limited to computational predictions based on laboratory experiments with a small number of cultured bacteria. However, natural biofilms are diverse and chiefly composed of uncultured bacteria and archaea with no viral infection patterns and lifestyle predictions described to date. Herein, we predict the first DNA sequence-based host–virus interactions in a natural biofilm. Using single-cell genomics and metagenomics applied to a hot spring mat of the Cone Pool in Mono County, California, we provide insights into virus–host range, lifestyle and distribution across different mat layers. Thirty-four out of 130 single cells contained at least one viral contig (26%), which, together with the metagenome-assembled genomes, resulted in detection of 59 viruses linked to 34 host species. Analysis of single-cell amplification kinetics revealed a lack of active viral replication on the single-cell level. These findings were further supported by mapping metagenomic reads from different mat layers to the obtained host–virus pairs, which indicated a low copy number of viral genomes compared to their hosts. Lastly, the metagenomic data revealed high layer specificity of viruses, suggesting limited diffusion to other mat layers. Taken together, these observations indicate that in low mobility environments with high microbial abundance, lysogeny is the predominant viral lifestyle, in line with the previously proposed “Piggyback-the-Winner” theory.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Changing expression patterns of TonB-dependent transporters suggest shifts in polysaccharide consumption over the course of a spring phytoplankton bloom

Algal blooms produce large quantities of organic matter that is subsequently remineralised by bacterial heterotrophs. Polysaccharide is a primary component of algal biomass. It has been hypothesised that individual bacterial heterotrophic niches during algal blooms are in part determined by the available polysaccharide substrates present. Measurement of the expression of TonB-dependent transporters, often specific for polysaccharide uptake, might serve as a proxy for assessing bacterial polysaccharide consumption over time. To investigate this, we present here high-resolution metaproteomic and metagenomic datasets from bacterioplankton of the 2016 spring phytoplankton bloom at Helgoland island in the southern North Sea, and expression profiles of TonB-dependent transporters during the bloom, which demonstrate the importance of both the Gammaproteobacteria and the Bacteroidetes as degraders of algal polysaccharide. TonB-dependent transporters were the most highly expressed protein class, split approximately evenly between the Gammaproteobacteria and Bacteroidetes , and totalling on average 16.7% of all detected proteins during the bloom. About 93% of these were predicted to take up organic matter, and for about 12% of the TonB-dependent transporters, we predicted a specific target polysaccharide class. Most significantly, we observed a change in substrate specificities of the expressed transporters over time, which was not reflected in the corresponding metagenomic data. From this, we conclude that algal cell wall-related compounds containing fucose, mannose, and xylose were mostly utilised in later bloom stages, whereas glucose-based algal and bacterial storage molecules including laminarin, glycogen, and starch were used throughout. Quantification of transporters could therefore be key for understanding marine carbon cycling.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Dissecting the dominant hot spring microbial populations based on community-wide sampling at single-cell genomic resolution

With advances in DNA sequencing and miniaturized molecular biology workflows, rapid and affordable sequencing of single-cell genomes has become a reality. Compared to 16S rRNA gene surveys and shotgun metagenomics, large-scale application of single-cell genomics to whole microbial communities provides an integrated snapshot of community composition and function, directly links mobile elements to their hosts, and enables analysis of population heterogeneity of the dominant community members. To that end, we sequenced nearly 500 single-cell genomes from a low diversity hot spring sediment sample from Dewar Creek, British Columbia, and compared this approach to 16S rRNA gene amplicon and shotgun metagenomics applied to the same sample. We found that the broad taxonomic profiles were similar across the three sequencing approaches, though several lineages were missing from the 16S rRNA gene amplicon dataset, likely the result of primer mismatches. At the functional level, we detected a large array of mobile genetic elements present in the single-cell genomes but absent from the corresponding same species metagenome-assembled genomes. Moreover, we performed a single-cell population genomic analysis of the three most abundant community members, revealing differences in population structure based on mutation and recombination profiles. While the average pairwise nucleotide identities were similar across the dominant species-level lineages, we observed differences in the extent of recombination between these dominant populations. Most intriguingly, the creek's Hydrogenobacter sp. population appeared to be so recombinogenic that it more closely resembled a sexual species than a clonally evolving microbe. Together, this work demonstrates that a randomized single-cell approach can be useful for the exploration of previously uncultivated microbes from community composition to population structure.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Summer atmospheric circulation over Greenland in response to Arctic amplification and diminished spring snow cover

Abstract The exceptional atmospheric conditions that have accelerated Greenland Ice Sheet mass loss in recent decades have been repeatedly recognized as a possible dynamical response to Arctic amplification. Here, we present evidence of two potentially synergistic mechanisms linking high-latitude warming to the observed increase in Greenland blocking. Consistent with a prominent hypothesis associating Arctic amplification and persistent weather extremes, we show that the summer atmospheric circulation over the North Atlantic has become wavier and link this wavier flow to more prevalent Greenland blocking. While a concomitant decline in terrestrial snow cover has likely contributed to this mechanism by further amplifying warming at high latitudes, we also show that there is a direct stationary Rossby wave response to low spring North American snow cover that enforces an anomalous anticyclone over Greenland, thus helping to anchor the ridge over Greenland in this wavier atmospheric state.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2017

Occurrence and expression of novel methyl-coenzyme M reductase gene (mcrA) variants in hot spring sediments

Recent discoveries have shown that the marker gene for anaerobic methane cycling (mcrA) is more widespread in the Archaea than previously thought. However, it remains unclear whether novel mcrA genes associated with the Bathyarchaeota and Verstraetearchaeota are distributed across diverse environments. We examined two geochemically divergent but putatively methanogenic regions of Yellowstone National Park to investigate whether deeply-rooted archaea possess and express novel mcrA genes in situ. Small-subunit (SSU) rRNA gene analyses indicated that Bathyarchaeota were predominant in seven of ten sediment layers, while the Verstraetearchaeota and Euryarchaeota occurred in lower relative abundance. Targeted amplification of novel mcrA genes suggested that diverse taxa contribute to alkane cycling in geothermal environments. Two deeply-branching mcrA clades related to Bathyarchaeota were identified, while highly abundant verstraetearchaeotal mcrA sequences were also recovered. In addition, detection of SSU rRNA and mcrA transcripts from one hot spring suggested that predominant Bathyarchaeota were also active, and that methane cycling genes are expressed by the Euryarchaeota, Verstraetearchaeota, and an unknown lineage basal to the Bathyarchaeota. These findings greatly expand the diversity of the key marker gene for anaerobic alkane cycling and outline the need for greater understanding of the functional capacity and phylogenetic affiliation of novel mcrA variants.

Science & Technology - Other Topics↗
DOE OSTI2024

Hot springs viruses at Yellowstone National Park have ancient origins and are adapted to thermophilic hosts

Geothermal springs house unicellular red algae in the class Cyanidiophyceae that dominate the microbial biomass at these sites. Little is known about host-virus interactions in these environments. We analyzed the virus community associated with red algal mats in three neighboring habitats (creek, endolithic, soil) at Lemonade Creek, Yellowstone National Park (YNP), USA. We find that despite proximity, each habitat houses a unique collection of viruses, with the giant viruses, Megaviricetes, dominant in all three. The early branching phylogenetic position of genes encoded on metagenome assembled virus genomes (vMAGs) suggests that the YNP lineages are of ancient origin and not due to multiple invasions from mesophilic habitats. The existence of genomic footprints of adaptation to thermophily in the vMAGs is consistent with this idea. The Cyanidiophyceae at geothermal sites originated ca. 1.5 Bya and are therefore relevant to understanding biotic interactions on the early Earth.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Pressurized formic acid dehydrogenation: an entropic spring replaces hydrogen compression cost

Formic acid is unique among liquid organic hydrogen carriers (LOHCs), because its dehydrogenation is highly entropically driven. This enables the evolution of high-pressure hydrogen at mild temperatures that is difficult to achieve with other LOHCs, conceptually by releasing the “spring” of energy stored entropically in the liquid carrier. Applications calling for hydrogen-on-demand, such as vehicle filling, require pressurized H 2 . Hydrogen compression dominates the cost for such applications, yet there are very few reports of selective, catalytic dehydrogenation of formic acid at elevated pressure. Herein, we show that homogenous catalysts with various ligand frameworks, including Noyori-type tridentate (PNP, SNS, SNP, SNPO), bidentate chelates (pyridyl)NHC, (pyridyl)phosphine, (pyridyl)sulfonamide, and their metallic precursors, are suitable catalysts for the dehydrogenation of neat formic acid under self-pressurizing conditions. Quite surprisingly, we discovered that their structural differences can be related to performance differences in their respective structural families, with some tolerant or intolerant of pressure and others that are significantly advantaged by pressurized conditions. Here, we further find important roles for H 2 and CO in catalyst activation and speciation. In fact, for certain systems, CO behaves as a healing reagent when trapped in a pressurizing reactor system, enabling extended life from systems that would be otherwise deactivated.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2014

Brillouin light scattering study of spin waves in NiFe/Co exchange spring bilayer films

Spin waves are investigated in Permalloy(Ni{sub 80}Fe{sub 20})/Cobalt(Co) exchange spring bilayer thin films using Brillouin light scattering (BLS) experiment. The magnetic hysteresis loops measured by magneto-optical Kerr effect show a monotonic decrease in coercivity of the bilayer films with increasing Py thickness. BLS study shows two distinct modes, which are modelled as Damon-Eshbach and perpendicular standing wave modes. Linewidths of the frequency peaks are found to increase significantly with decreasing Py layer thickness. Interfacial roughness causes to fluctuate exchange coupling at the nanoscale regimes and the effect is stronger for thinner Py films. A quantitative analysis of the magnon linewidths shows the presence of strong local exchange coupling field which is much larger compared to macroscopic exchange field.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2015

Exchange spring in A1/L1{sub 0} FePt composite and its application in magnetic force microscope

This paper reported fabrication of Fe{sub x}Pt{sub 100-x} films with (001) epitaxy on MgO(100) substrates. The atomic percentage of Fe was changed within the range of x = 10–85 in order to search the optimal atomic ratio for achieving both high and isotropic-like coercivity. It was found that the Fe{sub 60}Pt{sub 40} film exhibited large coercivities exceeding 5 kOe along both in-plane and out-of-plane directions due to the formation of A1/L1{sub 0} FePt composite. A penta-domain model for hard/soft/hard exchange spring system was proposed to interpret the anomalous magnetization behaviors observed in Fe{sub 60}Pt{sub 40} sample. By using Fe{sub 60}Pt{sub 40} as the magnetic coating layer on a probe of magnetic force microscope, the flux changes at a linear density of 1000 kfci could be readily observed at a resolution of ∼13 nm.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2015

GROMOS polarizable charge-on-spring models for liquid urea: COS/U and COS/U2

Two one-site polarizable urea models, COS/U and COS/U2, based on the charge-on-spring model are proposed. The models are parametrized against thermodynamic properties of urea-water mixtures in combination with the polarizable COS/G2 and COS/D2 models for liquid water, respectively, and have the same functional form of the inter-atomic interaction function and are based on the same parameter calibration procedure and type of experimental data as used to develop the GROMOS biomolecular force field. Thermodynamic, dielectric, and dynamic properties of urea-water mixtures simulated using the polarizable models are closer to experimental data than using the non-polarizable models. The COS/U and COS/U2 models may be used in biomolecular simulations of protein denaturation.

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

Soft-spring wall based non-periodic boundary conditions for non-equilibrium molecular dynamics of dense fluids

Non-equilibrium molecular dynamics (MD) simulations require imposition of non-periodic boundary conditions (NPBCs) that seamlessly account for the effect of the truncated bulk region on the simulated MD region. Standard implementation of specular boundary conditions in such simulations results in spurious density and force fluctuations near the domain boundary and is therefore inappropriate for coupled atomistic-continuum calculations. In this work, we present a novel NPBC model that relies on boundary atoms attached to a simple cubic lattice with soft springs to account for interactions from particles which would have been present in an untruncated full domain treatment. We show that the proposed model suppresses the unphysical fluctuations in the density to less than 1% of the mean while simultaneously eliminating spurious oscillations in both mean and boundary forces. The model allows for an effective coupling of atomistic and continuum solvers as demonstrated through multiscale simulation of boundary driven singular flow in a cavity. The geometric flexibility of the model enables straightforward extension to nonplanar complex domains without any adverse effects on dynamic properties such as the diffusion coefficient.

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

Exchange spring behaviour in SrFe{sub 12}O{sub 19}-CoFe{sub 2}O{sub 4} nanocomposites

Nanocomposites of hard (SrFe{sub 12}O{sub 19}) and soft ferrite (CoFe{sub 2}O{sub 4}) are prepared by mixing individual ferrite components at appropriate weight ratio and subsequent heat treatment. The magnetization of the composites showed hysteresis loop that is characteristic of the exchange spring system. The variation of J{sub r}/J{sub r}(∞) vs. J{sub d}/ J{sub r}(∞) for these nanocomposites are investigated to understand the presence of both the interacting field and the disorder in the system. This is further corroborated with the First Order Reversal Curve analysis (FORC) on the nanocomposites of 1:4 (Cobalt Ferrite: Strontium Ferrite) and 1:16 (Cobalt Ferrite: Strontium Ferrite). The FORC distribution reveals that the pinning mechanism is stronger in the nanocomposite of 1:4 compared to 1:16. However, the nanocomposite of 1:16 exhibit superior exchange coupling strength in contrast to 1:4. The asymmetric nature of the FORC distribution at H{sub c} = 0 Oe for both the nanocomposites validates the intercoupling between the reversible and irreversible magnetization.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Urban warming advances spring phenology but reduces the response of phenology to temperature in the conterminous United States

Urbanization has caused environmental changes, such as urban heat islands (UHIs), that affect terrestrial ecosystems. However, how and to what extent urbanization affects plant phenology remains relatively unexplored. Here, we investigated the changes in the satellite-derived start of season (SOS) and the covariation between SOS and temperature (R T ) in 85 large cities across the conterminous United States for the period 2001–2014. We found that 1) the SOS came significantly earlier (6.1 ± 6.3 d) in 74 cities and R T was significantly weaker (0.03 ± 0.07) in 43 cities when compared with their surrounding rural areas (P < 0.05); 2) the decreased magnitude in R T mainly occurred in cities in relatively cold regions with an annual mean temperature <17.3 °C (e.g., Minnesota, Michigan, and Pennsylvania); and 3) the magnitude of urban–rural difference in both SOS and R T was primarily correlated with the intensity of UHI. Simulations of two phenology models further suggested that more and faster heat accumulation contributed to the earlier SOS, while a decrease in required chilling led to a decline in R T magnitude in urban areas. Furthermore, these findings provide observational evidence of a reduced covariation between temperature and SOS in major US cities, implying the response of spring phenology to warming conditions in nonurban environments may decline in the warming future.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2015

Stock Differences in Growth, Smolting, and Early Male Maturation in Hatchery Spring Chinook Salmon: a Common-Garden Experiment

Abstract Hatchery spring Chinook Salmon Oncorhynchus tshawytscha from Parkdale Hatchery on the Hood River, Oregon, and Carson National Fish Hatchery (CNFH) on the Wind River, Washington, were reared under a common-garden experimental regime at CNFH over three consecutive brood years (2008–2010) to assess the effects of stock on smoltification and early male maturation. Rearing groups were monitored for size, percent solid (a surrogate for whole-body lipid), gill Na+,K+-ATPase activity, and rate of precocious maturation in males (i.e., age-2 minijack rate). Despite rearing of the stocks under identical conditions, the out-of-basin Hood River stock was significantly smaller throughout the study and at release as smolts, had lower whole-body lipid at release, and had lower gill Na+,K+-ATPase activity at release than the Carson stock; furthermore, the Hood River stock exhibited much higher mean minijack rates than the Carson stock (45% versus 23% of males). Using logistic regression, we demonstrated that the threshold size for initiation of early male maturation was significantly lower for the Hood River stock than for the Carson stock, suggesting a genetic basis for this life history difference. The present study highlights the importance of understanding how specific genotypes may respond differently to the unique environmental conditions in a given hatchery environment. These differences may in turn influence physiological and life history pathways that affect smolt-to-adult return rates and the demography of returning adults.

Spangenberg, Dina K.↗
DOE OSTI2012

Performance of Spring Chinook Salmon Reared in Acclimation Ponds for Two and Four Months before Release

Abstract Seasonal temperature cues may play an important role in the parr–smolt transformation of Pacific salmon Oncorhynchus spp., but salmon reared in groundwater-supplied hatcheries with seasonally stable water temperatures do not experience these cues. In this study, conducted over six release years, hatchery spring Chinook salmon O. tshawytscha that were initially reared in a groundwater-supplied hatchery were transferred to acclimation ponds supplied with surface water either in November (November transfer [NT]) or January (January transfer [JT]) for rearing at ambient water temperatures prior to release into the Umatilla River, Oregon, in early March. After stream release, we monitored out-migration travel times and survival to John Day Dam (JDD) by using passive integrated transponder tags in a subsample of each release group. Across all release groups, median travel time was slower for NT groups (51 d) than for JT groups (46 d); significant differences were observed in five of six release years. Average survival probabilities were 15% higher for NT groups than for JT groups, although this difference was not significant. We used recoveries of coded wire tags to estimate smolt-to-adult survival (SAS) and straying for NT and JT groups. Average SAS over the study was 27% higher for NT groups (0.76%) than for JT groups (0.60%), but straying was minimal for both types of release group. We found no significant linear relationship between SAS and travel time or survival to JDD. Adult returns of NT groups had a slightly older age distribution than those of JT groups. Our results suggest that for salmon juveniles reared in groundwater-supplied hatcheries, providing an overwinter period of exposure to ambient water temperatures should optimize postrelease survival. We also discuss some risks and benefits to winter rearing in acclimation ponds for managers that are considering this approach.

Clarke, Lance R.↗
DOE OSTI2013

Phenotypic Comparisons among Natural-Origin, Hatchery-Origin, and Captive-Reared Female Spring Chinook Salmon from the Tucannon River, Washington

Abstract We examined the effects of hatchery rearing on FL, weight, egg size, fecundity, relative fecundity, and reproductive mass of female spring Chinook Salmon Oncorhynchus tshawytscha from a population that had been in captivity for 0 (natural-origin), 18 (hatchery-origin), and 48 (captive-reared broodstock) months. Age-4 captive-reared broodstock females that were reared for their entire life in the hatchery environment had significantly lower mean FL, weight, fecundity, relative fecundity, and reproductive mass, but had significantly larger eggs than age-4 females from the other groups after correcting for body size. Hatchery-origin females had significantly lower fecundity than natural-origin fish. Our findings illustrate a phenomenon of lower overall reproductive potential for hatchery-reared fish in the form of reduced fecundity that decreases as time spent in the hatchery environment increases. We also observed that progeny of captive-reared broodstock parents, released as smolts and recaptured as returning age-4 adults, have a size and fecundity distribution that is similar to the hatchery-origin adults, suggesting that the decrease in fecundity was not a genetically linked trait.

Gallinat, Michael P.↗
DOE OSTI2014

Trajectory analysis for the nucleus and dust of comet C/2013 A1 (Siding Spring)

Comet C/2013 A1 (Siding Spring) will experience a high velocity encounter with Mars on 2014 October 19 at a distance of 135,000 km ± 5000 km from the planet center. We present a comprehensive analysis of the trajectory of both the comet nucleus and the dust tail. The nucleus of C/2013 A1 cannot impact on Mars even in the case of unexpectedly large nongravitational perturbations. Furthermore, we compute the required ejection velocities for the dust grains of the tail to reach Mars as a function of particle radius and density and heliocentric distance of the ejection. A comparison between our results and the most current modeling of the ejection velocities suggests that impacts are possible only for millimeter to centimeter size particles released more than 13 AU from the Sun. However, this level of cometary activity that far from the Sun is considered extremely unlikely. The arrival time of these particles spans a 20-minute time interval centered at 2014 October 19 at 20:09 TDB, i.e., around the time that Mars crosses the orbital plane of C/2013 A1. Ejection velocities larger than currently estimated by a factor >2 would allow impacts for smaller particles ejected as close as 3 AU from the Sun. These particles would reach Mars from 19:13 TDB to 20:40 TDB.

79 ASTRONOMY AND ASTROPHYSICS↗