30 Works

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...

Data from: Spatial and successional dynamics of microbial biofilm communities in a grassland stream ecosystem

Allison M. Veach, James C. Stegen, Shawn P. Brown, Walter K. Dodds & Ari Jumpponen
Biofilms represent a metabolically active and structurally complex component of freshwater ecosystems. Ephemeral prairie streams are hydrologically harsh and prone to frequent perturbation. Elucidating both functional and structural community changes over time within prairie streams provides a general understanding of microbial responses to environmental disturbance. We examined microbial succession of biofilm communities at three sites in a third-order stream at Konza Prairie over a 2- to 64-day period. Microbial abundance (bacterial abundance, chlorophyll a concentrations)...

Neutron study of the topological flux model of hydrogen ions in water ice

J.-U. Hoffmann, K. Siemensmeyer, S. Isakov, D. J. P. Morris, B. Klemke, I. Glavatskyi, K. Seiffert, D. A. Tennant, S. Sondhi & R. Moessner
The familiarity of water ice means we often overlook its non-trivial character illustrated, for example, by the many snowflake morphologies resulting from disordered combinations of covalent and hydrogen bonds between hydrogen and oxygen atoms in water ice’s most common phase (Ih) that keep the H_2 O molecular character. Using neutron diffraction on the flat-cone diffractometer E2 at BER-II, Helmholtz-Zentrum Berlin, we probe the atomic scale configuration in the Ih phase of water ice to test...

Data from: Long-term data reveal patterns and controls on streamwater chemistry in a forested stream: Walker Branch, Tennessee

Brian D. Lutz, Patrick J. Mulholland & Emily S. Bernhardt
We present 20 years of weekly streamwater chemistry, hydrology, and climate data for the Walker Branch watershed in eastern Tennessee, USA. Since 1989, the watershed has experienced a ~1.0˚C increase in mean annual temperature, a ~20% decline in precipitation, and a ~30% increase in forest evapotranspiration rates. As a result, runoff has declined by ~34%. We evaluate long-term trends in streamwater concentrations and fluxes for 9 solutes and use wet deposition data to calculate approximate...

Data from: Using a butterflyfish genome as a general tool for RAD-Seq studies in specialized reef fish

Joseph D. DiBattista, Pablo Saenz-Agudelo, Marek J. Piatek, Xin Wang, Manuel Aranda & Michael L. Berumen
Data from a large-scale restriction site associated DNA (RAD-Seq) study of nine butterflyfish species in the Red Sea and Arabian Sea provided a means to test the utility of a recently published draft genome (Chaetodon austriacus) and assess apparent bias in this method of isolating nuclear loci. We here processed double-digest restriction-site (ddRAD) associated DNA sequencing data to identify single nucleotide polymorphism (SNP) markers and their associated function with and without our reference genome to...

Data from: Multiband semimetallic electronic structure of superconducting Ta2PdSe5

David Joseph Singh
We report the electronic structure and related properties of the superconductor Ta2PdSe5 as determined from density functional calculations. The Fermi surface has two disconnected sheets, both derived from bands of primarily chalcogenide p states. These are a corrugated hole cylinder and a heavier complex shaped electron sheet. The sheets contain 0.048 holes and a compensating number of electrons per formula unit, making the material a semimetallic superconductor. The results support the presence of two band...

Data from: Effects of diet on resource utilization by a model human gut microbiota containing Bacteroides cellulosilyticus WH2, a symbiont with an extensive glycobiome

Nathan P. McNulty, Wu Meng, Alison R. Erickson, Chongle Pan, Brian K. Erickson, Eric C. Martens, Nicholas A. Pudlo, Brian D. Muegge, Bernard Henrissat, Robert L. Hettich, Jeffrey I. Gordon & Meng Wu
The human gut microbiota is an important metabolic organ. However, little is known about how its individual species interact, establish dominant positions, and respond to changes in environmental factors such as diet. In the current study, gnotobiotic mice colonized with a simplified model microbiota composed of 12 sequenced human gut bacterial species were fed oscillating diets of disparate composition. Rapid, reproducible and reversible changes in community structure were observed. Time series microbial RNA-Seq analyses revealed...

Circular dichroism spectroscopic and small-angle neutron scattering analysis of alpha-synuclein and bacteriorhodopsin in bicontinuous microemulsions

Douglas Hayes, Divina Anunciado, Ran Ye, Rachel Williams, Hugh O'Neill, Sai Venkatesh Pingali & Volker Urban
The membrane proteins (MPs) alpha-synuclein (ASYN) and bacteriorhodopsin (BR) were readily incorporated into bicontinuous microemulsions (BMEs) formed by two microemulsion systems: water/heptane/Aerosol-OT (AOT)/CK-2,13 and water/dodecane/sodium dodecyl sulfate (SDS)/1-pentanol. (CK-2,13 is an alkyl ethoxylate possessing two alkyl tail groups of carbon chain length 2 and 13 and an average degree of ethoxylation of 5.6.) MPs were encapsulated in BMEs through preparation of Winsor-III systems at optimal salinity, with the anionic surfactants AOT and SDS providing the...

Data from: Diel rewiring and positive selection of ancient plant proteins enabled evolution of CAM photosynthesis in Agave

Hengfu Yin, Hao-Bo Guo, David J. Weston, Anne M. Borland, Priya Ranjan, Paul E. Abraham, Sara S. Jawdy, James Wachira, Gerald A. Tuskan, Timothy J. Tschaplinski, Stan D. Wullschleger, Hong Guo, Robert L. Hettich, Stephen Gross, Zhong Wang, Axel Visel & Xiaohan Yang
Background: Crassulacean acid metabolism (CAM) enhances plant water-use efficiency through an inverse day/night pattern of stomatal closure/opening that facilitates nocturnal CO2 uptake. CAM has evolved independently in over 35 plant lineages, accounting for ~ 6% of all higher plants. Agave species are highly heat- and drought-tolerant, and have been domesticated as model CAM crops for beverage, fiber, and biofuel production in semi-arid and arid regions. However, the genomic basis of evolutionary innovation of CAM in...

Data from: Photoautotrophic symbiont and geography are major factors affecting highly structured and diverse bacterial communities in the lichen microbiome

Brendan P. Hodkinson, Neil R. Gottel, Christopher W. Schadt & François Lutzoni
Although common knowledge dictates that the lichen thallus is formed solely by a fungus (mycobiont) that develops a symbiotic relationship with an alga and/or cyanobacterium (photobiont), the non-photoautotrophic bacteria found in lichen microbiomes are increasingly regarded as integral components of lichen thalli. For this study, comparative analyses were conducted on lichen-associated bacterial communities to test for effects of photobiont-types (i.e., green algal vs. cyanobacterial), mycobiont-types, and large-scale spatial distances (from tropical to arctic latitudes). Amplicons...

Data from: Contrasting taxonomic stratification of microbial communities in two hypersaline meromictic lakes

Adrian-Stefan Andrei, Michael S. Robeson, Andreea Baricz, Cristian Coman, Vasile Muntean, Artur Ionescu, Giuseppe Etiope, Mircea Alexe, Cosmin Ionel Sicora, Mircea Podar & Horia Leonard Banciu
Hypersaline meromictic lakes are extreme environments in which water stratification is associated with powerful physicochemical gradients and high salt concentrations. Furthermore, their physical stability coupled with vertical water column partitioning makes them important research model systems in microbial niche differentiation and biogeochemical cycling. Here, we compare the prokaryotic assemblages from Ursu and Fara Fund hypersaline meromictic lakes (Transylvanian Basin, Romania) in relation to their limnological factors and infer their role in elemental cycling by matching...

Single-chain heteropolymers transport protons selectively and rapidly

Tao Jiang, Aaron Hall, Marco Eres, Zahra Hemmatian, Baofu Qiao, Yun Zhou, Zhiyuan Ruan, Andrew D. Couse, William T. Heller, Haiyan Huang, Monica Olvera De La Cruz, Marco Rolandi & Ting Xu
Precise protein sequencing and folding are believed to generate the natural channel structure and chemical diversity of proteins, both of which are essential to synthetically achieve proton transport performance comparable to that seen in natural systems. Geometrically defined channels have been fabricated using peptides, DNAs, carbon nanotubes, sequence-defined polymers and organic frameworks; however, none of these channels rivals the performance observed in their natural counterparts. Here we show that without forming an atomically structured channel,...

Data from: The Physiological Basis for Estimating Photosynthesis from Chlorophyll a Fluorescence

Jimei Han, Lianhong Gu, Yongjiang Zhang & Ying Sun

Metabolite, qPCR, and metadata for relationships between Sphaerulina musiva infection and the Populus microbiome and metabolome

Nicholas Dove
Pathogenic fungal infections in plants may, in some cases, lead to downstream systematic impacts on the plant metabolome and microbiome that may either alleviate or exacerbate the effects of the fungal pathogen. While Sphaerulina musiva is a well-characterized fungal pathogen which infects Populus tree species, an important wood fiber and biofuel feedstock, little is known about its systematic effects on the metabolome and microbiome of Populus. Here, we investigate the microbiome and metabolome of P....

Temperature-Dependent Dynamics of Molecular Dopant in Conjugated Polymer

Jun Li, Tucker Murrey, Souleymane Diallo & Adam Moule
Understanding the nature of dopant dynamics in the solid state is critical for improving the longevity and stability of organic electronic devices and for optimizing the dopinginduced solubility control (DISC) patterning method. In this work, we use quasi-elastic neutron scattering (QENS) to study the dynamics of the soluble p-type molecular dopant tetrafluoromethyloxycarbonyltricyanoquinodimethane (F4MCTCNQ) in the semiconductive polymer poly(3-hexylthiophene-2,5-diyl) (P3HT). Specifically, fast dynamics (ps−ns) of the dopant, such as the methyl and the methoxycarbonyl group rotations,...

Data from: Drought and immunity determine the intensity of West Nile virus epidemics and climate change impacts

Sara H. Paull, Daniel E. Horton, Moetasim Ashfaq, Deeksha Rastogi, Laura D. Kramer, Noah S. Diffenbaugh & A. Marm Kilpatrick
The effect of global climate change on infectious disease remains hotly debated because multiple extrinsic and intrinsic drivers interact to influence transmission dynamics in nonlinear ways. The dominant drivers of widespread pathogens, like West Nile virus, can be challenging to identify due to regional variability in vector and host ecology, with past studies producing disparate findings. Here, we used analyses at national and state scales to examine a suite of climatic and intrinsic drivers of...

Data from: Guidelines and considerations for designing field experiments simulating precipitation extremes in forest ecosystems

Heidi Asbjornsen, John L. Campbell, Katie A. Jennings, Matthew A. Vadeboncoeur, Cameron McIntire, Pamela H. Templer, Richard P. Phillips, Taryn L. Bauerle, Michael C. Dietze, Serita D. Frey, Peter M. Groffman, Rosella Guerrieri, Paul J. Hanson, Eric P. Kelsey, Alan K. Knapp, Nathan G. McDowell, Patrick Meir, Kimberly A. Novick, Scott V. Ollinger, Will T. Pockman, Paul G. Schaberg, Stan D. Wullschleger, Melinda D. Smith & Lindsey E. Rustad
1. Context. Precipitation regimes are changing in response to climate change, yet understanding of how forest ecosystems respond to extreme droughts and pluvials remains incomplete. As future precipitation extremes will likely fall outside the range of historical variability, precipitation manipulation experiments (PMEs) are critical to advancing knowledge about potential ecosystem responses. However, few PMEs have been conducted in forests compared to short-statured ecosystems, and forest PMEs have unique design requirements and constraints. Moreover, past forest...

Gross primary production responses to warming, elevated CO2 , and irrigation: quantifying the drivers of ecosystem physiology in a semiarid grassland

Elise Pendall, Edmund M. Ryan, Kiona Ogle, Drew Peltier, David G. Williams, Anthony P. Walker, Martin G. De Kauwe, Belinda E. Medlyn, William Parton, Shinichi Asao, Bertrand Guenet, Anna B. Harper, Xingjie Lu, Kristina A. Luus, Sönke Zaehle, Shijie Shu, Christian Werner & Jianyang Xia
Determining whether the terrestrial biosphere will be a source or sink of carbon (C) under a future climate of elevated CO2 (eCO2) and warming requires accurate quantification of gross primary production (GPP), the largest flux of C in the global C cycle. We evaluated 6 years (2007–2012) of flux‐derived GPP data from the Prairie Heating and CO2 Enrichment (PHACE) experiment, situated in a grassland in Wyoming, USA. The GPP data were used to calibrate a...

Data from: Plant host and soil origin influence fungal and bacterial assemblages in the roots of woody plants

Gregory Bonito, Hannah Reynolds, Brendan P. Hodkinson, Jessica Nelson, Gerald Tuskan, , Christopher W. Schadt, Rytas Vilgalys & Michael S. Robeson
Microbial communities in plant roots provide critical links between above and belowground processes in terrestrial ecosystems. Variation in root communities has been attributed to plant host effects and microbial host preferences, as well as to factors pertaining to soil conditions, microbial biogeography and the presence of viable microbial propagules. To address hypotheses regarding the influence of plant host and soil biogeography on root fungal and bacterial communities we designed a trap-plant bioassay experiment. Replicate Populus,...

Population genomic response to geographic gradients by widespread and endemic fishes of the Arabian Peninsula

Joseph DiBattista, Pablo Saenz-Agudelo, Marek Piatek, Fernando Cagua, Brian Bowen, John Choat, Luiz Rocha, Michelle Gaither, Jean-Paul Hobbs, Tane Sinclair-Taylor, Jennifer McIlwain, Mark Priest, Camrin Braun, Nigel Hussey, Steven Kessel & Michael Berumen
Genetic structure within marine species may be driven by local adaptation to their environment, or alternatively by historical processes, such as geographic isolation. The gulfs and seas bordering the Arabian Peninsula offer an ideal setting to examine connectivity patterns in coral reef fishes with respect to environmental gradients and vicariance. The Red Sea is characterized by a unique marine fauna, historical periods of desiccation and isolation, as well as environmental gradients in salinity, temperature, and...

Experimental evidence for the recovery of mercury-contaminated fish populations

Lee Hrenchuk, Paul Blanchfield, John Rudd, Marc Amyot, Christopher Babiarz, Ken Beaty, Drew Bodaly, Brian Branfireun, Cynthia Gilmour, Jennifer Graydon, Britt Hall, Reed Harris, Andrew Heyes, Holger Hintelmann, James Hurley, Carol Kelly, David Krabbenhoft, Steve Lindberg, Robert Mason, Michael Paterson, Cheryl Podemski, Ken Sandilands, George Southworth, Vincent St. Louis, Lori Tate … & Michael Tate
Anthropogenic releases of mercury (Hg) are a human health issue because the potent toxicant methylmercury (MeHg), formed primarily by microbial methylation of inorganic Hg in aquatic ecosystems, bioaccumulates to high concentrations in fish consumed by humans. Predicting the efficacy of Hg pollution controls on fish MeHg concentrations is complex because many factors influence the production and bioaccumulation of MeHg. Here we conducted a 15-year whole-ecosystem, single-factor experiment to determine the magnitude and timing of reductions...

Data from: Dispersal, niche breadth, and population extinction/colonization ratios predict range size in North American dragonflies

Shannon J. McCauley, Christopher J. Davis, Earl E. Werner, & Michael S. Robeson
1. Species’ range sizes are shaped by fundamental differences in species’ ecological and evolutionary characteristics, and understanding the mechanisms determining range size can shed light on the factors responsible for generating and structuring biological diversity. Moreover, because geographic range size is associated with a species’ risk of extinction and their ability to respond to global changes in climate and land use, understanding these mechanisms has important conservation implications. 2. Despite hypotheses that dispersal behaviour is...

Data from: Interactions among roots, mycorrhizae and free-living microbial communities differentially impact soil carbon processes

Jessica A. M. Moore, Jiang Jiang, Courtney M. Patterson, Gangsheng Wang, Melanie A. Mayes & Aimée T. Classen
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...

Global biogeography of fungal and bacterial biomass carbon in topsoil

Liyuan He, Jorge Rodrigues, Nadejda Soudzilovskaia, Milagros Barceló, Pål Axel Olsson, Changchun Song, Leho Tedersoo, Fenghui Yuan, Fengming Yuan, David Lipson & Xiaofeng Xu
Bacteria and fungi, representing two major soil microorganism groups, play an important role in global nutrient biogeochemistry. Biogeographic patterns of bacterial and fungal biomass are of fundamental importance for mechanistically understanding nutrient cycling. We synthesized 1323 data points of phospholipid fatty acid-derived fungal biomass C (FBC), bacterial biomass C (BBC), and fungi:bacteria (F:B) ratio in topsoil, spanning 11 major biomes. The FBC, BBC, and F:B ratio display clear biogeographic patterns along latitude and environmental gradients...

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