36 Works

Species diversity of fungal endophytes across a stress gradient for plants

Ryoko Oono, Danielle Black, Eric Slessarev, Burton Sickler, Amanda Strom & Austen Apigo
Foliar fungal endophytes are one of the most diverse guilds of symbiotic fungi found in the photosynthetic tissues of every plant lineage, but it is unclear how plant environments and leaf resource availability shape their diversity. We explored correlations between leaf nutrient availability and endophyte diversity among Pinus muricata and Vaccinium ovatum plants growing across a soil nutrient gradient spanning a series of coastal terraces in Mendocino, California. Endophyte richness decreased in plants with higher...

HT-SIP: a semi-automated stable isotope probing pipeline identifies cross-kingdom interactions in the hyphosphere of arbuscular mycorrhizal fungi

Erin E. Nuccio, Steven J. Blazewicz, Marissa Lafler, Ashley N. Campbell, Anne Kakouridis, Jeffrey A. Kimbrel, Jessica Wollard, Dariia Vyshenska, Robert Riley, Andy Tomatsu, Rachel Hestrin, Rex R. Malmstrom, Mary Firestone & Jennifer Pett-Ridge
Abstract Background Linking the identity of wild microbes with their ecophysiological traits and environmental functions is a key ambition for microbial ecologists. Of many techniques that strive for this goal, Stable-isotope probing—SIP—remains among the most comprehensive for studying whole microbial communities in situ. In DNA-SIP, actively growing microorganisms that take up an isotopically heavy substrate build heavier DNA, which can be partitioned by density into multiple fractions and sequenced. However, SIP is relatively low throughput...

Additional file 2 of HT-SIP: a semi-automated stable isotope probing pipeline identifies cross-kingdom interactions in the hyphosphere of arbuscular mycorrhizal fungi

Erin E. Nuccio, Steven J. Blazewicz, Marissa Lafler, Ashley N. Campbell, Anne Kakouridis, Jeffrey A. Kimbrel, Jessica Wollard, Dariia Vyshenska, Robert Riley, Andy Tomatsu, Rachel Hestrin, Rex R. Malmstrom, Mary Firestone & Jennifer Pett-Ridge
Additional file 2: Supplemental Table S1. Impact of adding different concentrations of non-ionic detergents to the SIP gradient medium on percent DNA recovery (n=3).

Data from: Reconstructing the migratory behavior and long-term survivorship of juvenile Chinook salmon under contrasting hydrologic regimes

Anna M. Sturrock, J. D. Wikert, Timothy Heyne, Carl Mesick, Alan E. Hubbard, Travis M. Hinkelman, Peter K. Weber, George E. Whitman, Justin J. Glessner & Rachel C. Johnson
The loss of genetic and life history diversity has been documented across many taxonomic groups, and is considered a leading cause of increased extinction risk. Juvenile salmon leave their natal rivers at different sizes, ages and times of the year, and it is thought that this life history variation contributes to their population sustainability, and is thus central to many recovery efforts. However, in order to preserve and restore diversity in life history traits, it...

Recreating giants impacts in the laboratory: Shock compression of MgSiO3 bridgmanite to 14 Mbar

Marius Millot, Shuai Zhang, Dayne Fratanduono, Federica Coppari, Sebastien Hamel, Burkhard Militzer, Dariia Simonova, Svyatoslav Shcheka, Natalia Dubrovinskaia, Leonid Dubrovinsky & Jon Eggert
Understanding giant impacts requires accurate description of how extreme pressures and temperatures affect the physical properties of the constituent materials. Here, we report shock experiments on two polymorphs of MgSiO3: enstatite and bridgmanite (perovskite) crystals. We obtain pressure-density shock equation of state to 14 Mbar and more than 9 g/cm3 a 40 % increase in density from previous data on MgSiO3. Density-functional-theory molecular dynamics (DFT-MD) simulations provide predictions for the shock Hugoniot curves for bridgmanite...

Modeled dataset for the estimation of atmospheric transport errors using a Multi-Physics and Analysis Ensemble on the Midwest US

L.I. Diaz-Isaac, T. Lauvaux & K.J. Davis
Atmospheric inversions are used to assess biosphere-atmosphere CO2 surface exchanges. However, large uncertainties exist among inverse flux estimates independent of the spatial scales. Atmospheric transport model errors are one of the main contributors to the uncertainty affecting CO2 inverse flux estimates but have not been quantified thoroughly. The model dataset archived here were used to evaluate atmospheric transport errors over the US upper Midwest with an ensemble of simulations created with the Weather Research and...

Minnesota peat viromes reveal terrestrial and aquatic niche partitioning for local and global viral populations

Anneliek Ter Horst, Christian Santos-Medellín, Jackson Sorensen, Laura Zinke, Rachel Wilson, Eric Johnston, Gareth Trubl, Jennifer Pett-Ridge, Steven Blazewicz, Paul Hanson, Jeffrey Chanton, Christopher Schadt, Joel Kostka & Joanne Emerson
Background: Peatlands are expected to experience sustained yet fluctuating higher temperatures due to climate change, leading to increased microbial activity and greenhouse gas emissions. Despite mounting evidence for viral contributions to these processes in thawing permafrost, little is known about viruses in other peatlands. More generally, soil viral biogeography and its potential drivers are poorly understood at both local and global scales. Here, 87 metagenomes and five viral size-fraction metagenomes (viromes) from a boreal peatland...

Additional file 1 of HT-SIP: a semi-automated stable isotope probing pipeline identifies cross-kingdom interactions in the hyphosphere of arbuscular mycorrhizal fungi

Erin E. Nuccio, Steven J. Blazewicz, Marissa Lafler, Ashley N. Campbell, Anne Kakouridis, Jeffrey A. Kimbrel, Jessica Wollard, Dariia Vyshenska, Robert Riley, Andy Tomatsu, Rachel Hestrin, Rex R. Malmstrom, Mary Firestone & Jennifer Pett-Ridge
Additional file 1: Supplemental Figure S1. Automated fractionation system design, parts, and assembly. Supplemental Figure S2. Hyphosphere-SIP experimental design. Supplemental Figure S3. Myxococcota MAG CAZymes grouped with CAZymes from 25 genomes from Myxococcota GTDB type species (previously used in Murphy et al. [2]).

Additional file 2 of HT-SIP: a semi-automated stable isotope probing pipeline identifies cross-kingdom interactions in the hyphosphere of arbuscular mycorrhizal fungi

Erin E. Nuccio, Steven J. Blazewicz, Marissa Lafler, Ashley N. Campbell, Anne Kakouridis, Jeffrey A. Kimbrel, Jessica Wollard, Dariia Vyshenska, Robert Riley, Andy Tomatsu, Rachel Hestrin, Rex R. Malmstrom, Mary Firestone & Jennifer Pett-Ridge
Additional file 2: Supplemental Table S1. Impact of adding different concentrations of non-ionic detergents to the SIP gradient medium on percent DNA recovery (n=3).

Additional file 4 of HT-SIP: a semi-automated stable isotope probing pipeline identifies cross-kingdom interactions in the hyphosphere of arbuscular mycorrhizal fungi

Erin E. Nuccio, Steven J. Blazewicz, Marissa Lafler, Ashley N. Campbell, Anne Kakouridis, Jeffrey A. Kimbrel, Jessica Wollard, Dariia Vyshenska, Robert Riley, Andy Tomatsu, Rachel Hestrin, Rex R. Malmstrom, Mary Firestone & Jennifer Pett-Ridge
Additional file 4: Supplemental Table S3. Assembly statistics, taxonomic lineage, and atom percent excess (APE) of the metagenome amplified genomes (MAGs) created in this study.

Additional file 5 of HT-SIP: a semi-automated stable isotope probing pipeline identifies cross-kingdom interactions in the hyphosphere of arbuscular mycorrhizal fungi

Erin E. Nuccio, Steven J. Blazewicz, Marissa Lafler, Ashley N. Campbell, Anne Kakouridis, Jeffrey A. Kimbrel, Jessica Wollard, Dariia Vyshenska, Robert Riley, Andy Tomatsu, Rachel Hestrin, Rex R. Malmstrom, Mary Firestone & Jennifer Pett-Ridge
Additional file 5: Supplemental Table S4. Number of CAZyme family domains in the highly enriched MAGs (>10 atom% excess 13C). AOA = archaeal ammonia oxidizer, Fibro = Fibrobacterota, Myxo = Myxococcota (Myxococcaceae).

Data from: Enhanced decomposition and nitrogen mineralisation sustain rapid growth of Eucalyptus regnans after wildfire

Feike A. Dijkstra, Meaghan Jenkins, Vivien De Remy De Courcelles, Claudia Keitel, Margaret M. Barbour, Zachary E. Kayler & Mark A. Adams
Eucalyptus regnans grows rapidly from seed after wildfires, out-competing other species, thereby forming pure stands of mature forests that rank amongst the world's most carbon dense. By global standards, these forests grow on infertile soils. It is unclear how E. regnans is able to obtain large amounts nitrogen (N) from these infertile soils to support its rapid growth after fire. We measured carbon (C) and N stored in plant biomass and photosynthetic rates of E....

Automated analysis of scanning electron microscopic images for assessment of hair surface damage

Fanny Chu, Deon Anex, A. Daniel Jones & Bradley Hart
Mechanical damage of hair can serve as an indicator of health status and its assessment relies on the measurement of morphological features via microscopic analysis, yet few studies have categorized the extent of damage sustained, and instead, have depended on qualitative profiling based on the presence or absence of specific features. We describe the development and application of a novel quantitative measure for scoring hair surface damage in scanning electron microscopic (SEM) images without predefined...

Processed data file for article \"Implications of the iron oxide phase transition on the interiors of rocky exoplanets\"

Federica Coppari, Raymond Smith, Jue Wang, Marius Millot, Donghoon Kim, Ryan Rygg, Sebastien Hamel, Jon Eggert & Thomas Duffy
This excel file contains pressure-density values obtained from VISAR and X-ray diffraction data analysis for iron oxide (FeO) and magnesium oxide (MgO), as reported in the Nature Geoscience article: "Implications of the iron oxide phase transition on the interiors of rocky exoplanets", by F. Coppari et al (2021). Prepared by LLNL under Contract DE-AC52-07NA27344.

Villarrica_2020

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Villarrica is known to produce continuous monotonic infrasound making it a prime subject for volcano infrasound studies. This dataset corresponds to three distribution of infrasound sensors deployed across Villarrica's summit, flank, and a neighboring river (Rio Turbio) during a week in January 2020. Data was recorded on Gem Infrasound Loggers, which recorded with a sensitivity of 2.077962e-05 V/Pa, a 26 second corner period, and a sample rate of 100 Hz.

Additional file 5 of HT-SIP: a semi-automated stable isotope probing pipeline identifies cross-kingdom interactions in the hyphosphere of arbuscular mycorrhizal fungi

Erin E. Nuccio, Steven J. Blazewicz, Marissa Lafler, Ashley N. Campbell, Anne Kakouridis, Jeffrey A. Kimbrel, Jessica Wollard, Dariia Vyshenska, Robert Riley, Andy Tomatsu, Rachel Hestrin, Rex R. Malmstrom, Mary Firestone & Jennifer Pett-Ridge
Additional file 5: Supplemental Table S4. Number of CAZyme family domains in the highly enriched MAGs (>10 atom% excess 13C). AOA = archaeal ammonia oxidizer, Fibro = Fibrobacterota, Myxo = Myxococcota (Myxococcaceae).

Additional file 8 of HT-SIP: a semi-automated stable isotope probing pipeline identifies cross-kingdom interactions in the hyphosphere of arbuscular mycorrhizal fungi

Erin E. Nuccio, Steven J. Blazewicz, Marissa Lafler, Ashley N. Campbell, Anne Kakouridis, Jeffrey A. Kimbrel, Jessica Wollard, Dariia Vyshenska, Robert Riley, Andy Tomatsu, Rachel Hestrin, Rex R. Malmstrom, Mary Firestone & Jennifer Pett-Ridge
Additional file 8: Supplemental Table S7. Number of CAZy gene homologs that can potentially target a particular substrate. Substrate assignments based off of the Glycoside Hydrolase categories from Berlemonte and Martiny 2015.

Additional file 3 of HT-SIP: a semi-automated stable isotope probing pipeline identifies cross-kingdom interactions in the hyphosphere of arbuscular mycorrhizal fungi

Erin E. Nuccio, Steven J. Blazewicz, Marissa Lafler, Ashley N. Campbell, Anne Kakouridis, Jeffrey A. Kimbrel, Jessica Wollard, Dariia Vyshenska, Robert Riley, Andy Tomatsu, Rachel Hestrin, Rex R. Malmstrom, Mary Firestone & Jennifer Pett-Ridge
Additional file 3: Supplemental Table S2. Assembly metrics using single fraction assembly (metaspades) verses co-assembly of all fractions (MetaHipMer2).

HT-SIP: a semi-automated stable isotope probing pipeline identifies cross-kingdom interactions in the hyphosphere of arbuscular mycorrhizal fungi

Erin E. Nuccio, Steven J. Blazewicz, Marissa Lafler, Ashley N. Campbell, Anne Kakouridis, Jeffrey A. Kimbrel, Jessica Wollard, Dariia Vyshenska, Robert Riley, Andy Tomatsu, Rachel Hestrin, Rex R. Malmstrom, Mary Firestone & Jennifer Pett-Ridge
Abstract Background Linking the identity of wild microbes with their ecophysiological traits and environmental functions is a key ambition for microbial ecologists. Of many techniques that strive for this goal, Stable-isotope probing—SIP—remains among the most comprehensive for studying whole microbial communities in situ. In DNA-SIP, actively growing microorganisms that take up an isotopically heavy substrate build heavier DNA, which can be partitioned by density into multiple fractions and sequenced. However, SIP is relatively low throughput...

Data from: Fate of internal waves on a shallow shelf

Kristen Davis, Robert Arthur, Emma Reid, Thomas DeCarlo, Anne Cohen, Oliver Fringer & Justin Rogers
Internal waves strongly influence the physical and chemical environment of coastal ecosystems worldwide. We report novel observations from a distributed temperature sensing (DTS) system that tracked the transformation of internal waves from the shelf break to the surf zone over a narrow shelf-slope region in the South China Sea. The spatially-continuous view of temperature fields provides a perspective of physical processes commonly available only in laboratory settings or numerical models, including internal wave reflection off...

Numerical Simulations of Laboratory-Scale, Hypervelocity-Impact Experiments for Asteroid-Deflection Code Validation

Tane P. Remington, J. Michael Owen, Akiko M. Nakamura, Paul L. Miller & Megan B. Syal
Asteroids and comets have the potential to impact Earth and cause damage at the local to global scale. Deflection or disruption of a potentially hazardous object could prevent future Earth impacts, but due to our limited ability to perform experiments directly on asteroids, our understanding of the process relies upon large-scale hydrodynamic simulations. Related simulations must be vetted through code validation by benchmarking against relevant laboratory-scale hypervelocity-impact experiments. To this end, we compare simulation results...

Molecular dynamics trajectories for ionic conductors in: Paradigms of frustration in superionic solid electrolytes

Brandon Wood, Joel Varley, Kyoung Kweon, Patrick Shea, Alex Hall, Andrew Grieder, Michael Ward, Vincent Aguirre, Dylan Ringling, Eduardo Ventura, Chimara Stancill & Nicole Adelstein
Superionic solid electrolytes have widespread use in energy devices, but the fundamental motivations for fast ion conduction are often elusive. Here, we draw upon atomistic simulations of a wide range of halide, oxide, sulfide, and closo-borate superionic conductors to illustrate some of the key features that enhance local cation mobility in these solids. We classify three types of frustration that create competition between different local atomic preferences, thereby flattening the diffusive energy landscape and enhancing...

Data from: Single-cell transcriptomic analysis of tumor-derived fibroblasts and normal tissue-resident fibroblasts reveals fibroblast heterogeneity in breast cancer

Nicholas Hum, Aimy Sebastian, Kelly Martin, Sean Gilmore, Stephen Byers, Elizabeth Wheeler, Matthew Coleman & Gabriela Loots
Cancer-associated fibroblasts (CAFs) are a prominent stromal cell type in solid tumors and molecules secreted by CAFs play an important role in tumor progression and metastasis. CAFs coexist as heterogeneous populations with potentially different biological functions. Although CAFs are a major component of the breast cancer stroma, molecular and phenotypic heterogeneity of CAFs in breast cancer is poorly understood. In this study, we investigated CAF heterogeneity in triple-negative breast cancer (TNBC) using a syngeneic mouse...

Threatened salmon rely on a rare life history strategy in a warming landscape

Flora Cordoleani, Corey Phillis, Anna Sturrock, Alyssa FitzGerald, George Whitman, Anthony Malkassian, Peter Weber & Rachel Johnson
Rare phenotypes and behaviours within a population are often overlooked, yet they may serve a heightened role for species imperilled by rapid warming. In threatened spring-run Chinook salmon spawning at the southern edge of the species range, we show late-migrating juveniles are critical to cohort success in years characterized by droughts and ocean heatwaves. Late migrants rely on cool river temperatures over summer, increasingly rare due to the combined effects of warming and impassable dams....

Digital Image, X-ray CT , XRD and Ultrasonic Data Sets for Damage Mechanics Challenge on Brittle-Ductile Material

, Laura J. Pyrak-Nolte, , Antonio Bobet & Joseph Morris

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