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Via the interatomic Coulombic electron capture (ICEC) process, an electron can be captured by an atom or a molecule, while the binding and excess energy is transferred, via a long-range Coulomb interaction, to a neighboring atom or molecule. The transferred energy can be used to ionize or electronically excite the neighboring species. When the two species are asymptotically far apart, an analytical formula for the ICEC cross sections can be derived. The latter can then be estimated using only the energies and the photoionization cross sections of each species. In this work, we develop an analytical model that allows us to predict the ICEC cross sections when the size of the involved species is comparable to the distance between the two entities. Using ab initio R-matrix results for various systems, we show that the new model reduces the error of the asymptotic formula by two orders of magnitude on average while only using parameters that can be taken from the properties of each species., (© 2024 Author(s). Published under an exclusive license by AIP Publishing.)

We have investigated Interparticle Coulombic Electron Capture (ICEC) using an ab initio approach for two systems, H+ + H2O and H + H2O+. In this work, we have determined the contribution of virtual photon exchange and electron transfer to the total ICEC cross section as a function of the distance between the charged and neutral particles. Furthermore, we have shown that the relative orientation of the electron acceptor and neighbor systems affects the magnitude of the ICEC cross sections by at least two orders at relatively small distances. This geometry dependence, present even for distances as large as 10 a0, is due to the electron transfer contribution. The relative magnitude of each contribution to ICEC seems to depend on the system studied. By replacing the projectile electron with a positron, we have confirmed that electron transfer also takes place in positron collisions and that the charge of the projectile has a noticeable effect on the process, particularly at low scattering energies., (© 2024 Author(s). All article content, except where otherwise noted, is licensed under a Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).)

Members of the fungal genus Morchella are widely known for their important ecological roles and significant economic value. In this study, we used amplicon and genome sequencing to characterize bacterial communities associated with sexual fruiting bodies from wild specimens, as well as vegetative mycelium and sclerotia obtained from Morchella isolates grown in vitro . These investigations included diverse representatives from both Elata and Esculenta Morchella clades. Unique bacterial community compositions were observed across the various structures examined, both within and across individual Morchella isolates or specimens. However, specific bacterial taxa were frequently detected in association with certain structures, providing support for an associated core bacterial community. Bacteria from the genus Pseudomonas and Ralstonia constituted the core bacterial associates of Morchella mycelia and sclerotia, while other genera (e.g., Pedobacter spp., Deviosa spp., and Bradyrhizobium spp.) constituted the core bacterial community of fruiting bodies. Furthermore, the importance of Pseudomonas as a key member of the bacteriome was supported by the isolation of several Pseudomonas strains from mycelia during in vitro cultivation. Four of the six mycelial-derived Pseudomonas isolates shared 16S rDNA sequence identity with amplicon sequences recovered directly from the examined fungal structures. Distinct interaction phenotypes (antagonistic or neutral) were observed in confrontation assays between these bacteria and various Morchella isolates. Genome sequences obtained from these Pseudomonas isolates revealed intriguing differences in gene content and annotated functions, specifically with respect to toxin-antitoxin systems, cell adhesion, chitinases, and insecticidal toxins. These genetic differences correlated with the interaction phenotypes. This study provides evidence that Pseudomonas spp. are frequently associated with Morchella and these associations may greatly impact fungal physiology., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest. The reviewer FY declared a past co-authorship/collaboration with the author GB to the handling editor. The author(s) declared that they were an editorial board member of Frontiers, at the time of submission. This had no impact on the peer review process and the final decision., (Copyright © 2023 Cailleau, Hanson, Cravero, Zhioua, Hilpish, Ruiz, Robinson, Kelliher, Morales, Gallegos-Graves, Bonito, Chain, Bindschedler and Junier.)

Biotic factors that influence the temporal stability of microbial community functioning are an emerging research focus for the control of natural and engineered systems. The discovery of common features within community ensembles that differ in functional stability over time is a starting point to explore biotic factors. We serially propagated a suite of soil microbial communities through five generations of 28-day microcosm incubations to examine microbial community compositional and functional stability during plant litter decomposition. Using dissolved organic carbon (DOC) abundance as a target function, we hypothesized that microbial diversity, compositional stability, and associated changes in interactions would explain the relative stability of the ecosystem function between generations. Communities with initially high DOC abundance tended to converge towards a "low DOC" phenotype within two generations, but across all microcosms, functional stability between generations was highly variable. By splitting communities into two cohorts based on their relative DOC functional stability, we found that compositional shifts, diversity, and interaction network complexity were associated with the stability of DOC abundance between generations. Further, our results showed that legacy effects were important in determining compositional and functional outcomes, and we identified taxa associated with high DOC abundance. In the context of litter decomposition, achieving functionally stable communities is required to utilize soil microbiomes to increase DOC abundance and long-term terrestrial DOC sequestration as one solution to reduce atmospheric carbon dioxide concentrations. Identifying factors that stabilize function for a community of interest may improve the success of microbiome engineering applications. IMPORTANCE Microbial community functioning can be highly dynamic over time. Identifying and understanding biotic factors that control functional stability is of significant interest for natural and engineered communities alike. Using plant litter-decomposing communities as a model system, this study examined the stability of ecosystem function over time following repeated community transfers. By identifying microbial community features that are associated with stable ecosystem functions, microbial communities can be manipulated in ways that promote the consistency and reliability of the desired function, improving outcomes and increasing the utility of microorganisms., Competing Interests: The authors declare no conflict of interest.

Plant survival during environmental stress greatly affects ecosystem carbon (C) cycling, and plant-microbe interactions are central to plant stress survival. The release of C-rich root exudates is a key mechanism plants use to manage their microbiome, attracting beneficial microbes and/or suppressing harmful microbes to help plants withstand environmental stress. However, a critical knowledge gap is how plants alter root exudate concentration and composition under varying stress levels. In a greenhouse study, we imposed three drought treatments (control, mild, severe) on blue grama (Bouteloua gracilis Kunth Lag. Ex Griffiths), and measured plant physiology and root exudate concentration and composition using GC-MS, NMR, and FTICR. With increasing drought severity, root exudate total C and organic C increased concurrently with declining predawn leaf water potential and photosynthesis. Root exudate composition mirrored the physiological gradient of drought severity treatments. Specific compounds that are known to alter plant drought responses and the rhizosphere microbiome mirrored the drought severity-induced root exudate compositional gradient. Despite reducing C uptake, these plants actively invested C to root exudates with increasing drought severity. Patterns of plant physiology and root exudate concentration and composition co-varied along a gradient of drought severity., (© 2022. The Author(s).)

CENTAUR has been selected as one of the eight initial instruments to be built at the Second Target Station (STS) of the Spallation Neutron Source at Oak Ridge National Laboratory. It is a small-angle neutron scattering (SANS) and wide-angle neutron scattering (WANS) instrument with diffraction and spectroscopic capabilities. This instrument will maximally leverage the high brightness of the STS source, the state-of-the-art neutron optics, and a suite of detectors to deliver unprecedented capabilities that enable measurements over a wide range of length scales with excellent resolution, measurements on smaller samples, and time-resolved investigations of evolving structures. Notably, the simultaneous WANS and diffraction capability will be unique among neutron scattering instruments in the United States. This instrument will provide much needed capabilities for soft matter and polymer sciences, geology, biology, quantum condensed matter, and other materials sciences that need in situ and operando experiments for kinetic and/or out-of-equilibrium studies. Beam polarization and a high-resolution chopper will enable detailed structural and dynamical investigations of magnetic and quantum materials. CENTAUR's excellent resolution makes it ideal for low-angle diffraction studies of highly ordered large-scale structures, such as skyrmions, shear-induced ordering in colloids, and biomembranes. Additionally, the spectroscopic mode of this instrument extends to lower momentum transfers than are currently possible with existing spectrometers, thereby providing a unique capability for inelastic SANS studies.

EXPANSE, an EXPanded Angle Neutron Spin Echo instrument, has been proposed and selected as one of the first suite of instruments to be built at the Second Target Station of the Spallation Neutron Source at the Oak Ridge National Laboratory. This instrument is designed to address scientific problems that involve high-energy resolution (neV-μeV) of dynamic processes in a wide range of materials. The wide-angle detector banks of EXPANSE provide coverage of nearly two orders of magnitude in scattering wavenumbers, and the wide wavelength band affords approximately four orders of magnitude in Fourier times. This instrument will offer unique capabilities that are not available in the currently existing neutron scattering instruments in the United States. Specifically, EXPANSE will enable direct measurements of slow dynamics in the time domain over wide Q-ranges simultaneously and will also enable time-resolved spectroscopic studies. The instrument is expected to contribute to a diverse range of science areas, including soft matter, polymers, biological materials, liquids and glasses, energy materials, unconventional magnets, and quantum materials.

Materials engineering by neutron scattering (MENUS) at the second target station will be a transformational high-flux, versatile, multiscale materials engineering diffraction beamline with unprecedented new capabilities for the study of complex materials and structures. It will support both fundamental and applied materials research in a broad range of fields. MENUS will combine unprecedented long-wavelength neutron flux and unique detector coverage to enable real-time studies of complex structural and functional materials under external stimuli. The incorporated small angle neutron scattering and transmission/imaging capabilities will extend its sensitivity to larger length scales and higher spatial resolution. Multimodal MENUS will provide crystallographic and microstructure data to the materials science and engineering community to understand lattice strain/phase transition/microstructure/texture evolution in three orthogonal directions in complex material systems under combined extreme applied conditions. The capabilities of MENUS will open new scientific opportunities and meet the research needs for science challenges to enable studies of a range of phenomena and answer the key questions in material design/exploration, advanced material processing, transformative manufacturing, and material operations of national impacts in our daily life.

To date, the potential impact of viral communities on biogeochemical cycles in soil has largely been inferred from correlational evidence, such as virus-driven changes in microbial abundances, viral auxiliary metabolic genes, and links with soil physiochemical properties. To more directly test the impact of soil viruses on carbon cycling during plant litter decomposition, we added concentrated viral community suspensions to complex litter decomposer communities in 40-day microcosm experiments. Microbial communities from two New Mexico alpine soils, Pajarito (PJ) and Santa Fe (SF), were inoculated onto grass litter on sand, and three treatments were applied in triplicate to each set of microcosms: addition of buffer (no added virus), live virus (+virus), or killed-virus (+killed-virus) fractions extracted from the same soil. Significant differences in respiration were observed between the +virus and +killed-virus treatments in the PJ, but not the SF microcosms. Bacterial and fungal community composition differed significantly by treatment in both PJ and SF microcosms. Combining data across both soils, viral addition altered links between bacterial and fungal diversity, dissolved organic carbon and total nitrogen. Overall, we demonstrate that increasing viral pressure in complex microbial communities can impact terrestrial biogeochemical cycling but is context-dependent., (© 2022. The Author(s).)

Leaf litter decomposition is a major carbon input to soil, making it a target for increasing soil carbon storage through microbiome engineering. We expand upon previous findings to show with multiple leaf litter types that microbial composition can drive variation in carbon flow from litter decomposition and specific microbial community features are associated with synonymous patterns of carbon flow among litter types. Although plant litter type selects for different decomposer communities, within a litter type, microbial composition drives variation in the quantity of dissolved organic carbon (DOC) measured at the end of the decomposition period. Bacterial richness was negatively correlated with DOC quantity, supporting our hypothesis that across multiple litter types there are common microbial traits linked to carbon flow patterns. Variation in DOC abundance (i.e. high versus low DOC) driven by microbial composition is tentatively due to differences in bacterial metabolism of labile compounds, rather than catabolism of non-labile substrates such as lignin. The temporal asynchrony of metabolic processes across litter types may be a substantial impediment to discovering more microbial features common to synonymous patterns of carbon flow among litters. Overall, our findings support the concept that carbon flow may be programmed by manipulating microbial community composition., (© 2021 The Authors. Environmental Microbiology published by Society for Applied Microbiology and John Wiley & Sons Ltd.)

Knowledge of associations between fungal hosts and their bacterial associates has steadily grown in recent years as the number and diversity of examinations have increased, but current knowledge is predominantly limited to a small number of fungal taxa and bacterial partners. Here, we screened for potential bacterial associates in over 700 phylogenetically diverse fungal isolates, representing 366 genera, or a tenfold increase compared with previously examined fungal genera, including isolates from several previously unexplored phyla. Both a 16 S rDNA-based exploration of fungal isolates from four distinct culture collections spanning North America, South America and Europe, and a bioinformatic screen for bacterial-specific sequences within fungal genome sequencing projects, revealed that a surprisingly diverse array of bacterial associates are frequently found in otherwise axenic fungal cultures. We demonstrate that bacterial associations with diverse fungal hosts appear to be the rule, rather than the exception, and deserve increased consideration in microbiome studies and in examinations of microbial interactions., (© 2021. The Author(s).)

Integrated measurements of fungi and bacteria are critical to understand how interactions between these taxa drive key processes in ecosystems ranging from soils to animal guts. High-throughput amplicon sequencing is commonly used to census microbiomes, but the genetic markers targeted for fungi and bacteria (typically ribosomal regions) are domain-specific so profiling must be performed separately, obscuring relationships between these groups. To solve this problem, we developed a spike-in method with an internal control (IC) construct containing primer sites commonly used for bacterial and fungal taxonomic profiling. The internal control offers several advantages: estimation of absolute abundances, estimation of fungal to bacterial ratios (F:B), integration of bacterial and fungal profiles for holistic community analysis, and lower costs compared to other quantitation methods. To validate the IC as a scaling method, we compared IC-derived measures of F:B to measures from quantitative PCR (qPCR) using a commercial mock community (the ZymoBiomic Microbial Community DNA Standard II, containing two fungi and eight bacteria) and complex environmental samples. For both the mock community and the environmental samples, the IC produced F:B values that were statistically consistent with qPCR. Merging the environmental fungal and bacterial profiles based on the IC-derived F:B values revealed new relationships among samples in terms of community similarity. This IC method is the first spike-in method to employ a single construct for cross-domain amplicon sequencing, offering more reliable measurements., (© 2021. Springer Science+Business Media, LLC, part of Springer Nature.)

Dryland ecosystems are sensitive to perturbations and generally slow to recover post disturbance. The microorganisms residing in dryland soils are especially important as they contribute to soil structure and nutrient cycling. Disturbance can have particularly strong effects on dryland soil structure and function, yet the natural resistance and recovery of the microbial components of dryland soils has not been well documented. In this study, the recovery of surface soil bacterial communities from multiple physical and environmental disturbances is assessed. Samples were collected from three field sites in the vicinity of Moab, UT, United States, 6 to 7 years after physical and climate disturbance manipulations had been terminated, allowing for the assessment of community recovery. Additionally, samples were collected in a transect that included three habitat patches: the canopy zone soils under the dominant shrubs, the interspace soils that are colonized by biological soil crusts, and edge soils at the plot borders. Field site and habitat patch were significant factors structuring the bacterial communities, illustrating that sites and habitats harbored unique soil microbiomes. Across the different sites and disturbance treatments, there was evidence of significant bacterial community recovery, as bacterial biomass and diversity were not significantly different than control plots. There was, however, a small number of 16S rRNA gene amplicon sequence variants that distinguished particular treatments, suggesting that legacy effects of the disturbances still remained. Taken together, these data suggest that dryland bacterial communities may possess a previously unappreciated potential to recover within years of the original disturbance., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2021 Steven, Phillips, Belnap, Gallegos-Graves, Kuske and Reed.)

A black box Binary Encounter Bethe (BEB) with an effective core potential (ECP) procedure is implemented, which facilitates the efficient calculation of electron impact ionization cross sections for molecules that include heavy atoms. This is available in the Quantemol electron collisions software, a user friendly graphical user interface to the UKRMol+ codes. Tests were performed for the following series of molecules: CF 4 , CCl 4 , CBr 4 , CI 4 , and CAt 4 ; CH 4 , SiH 4 , GeH 4 , and SnH 4 ; PH 3 , PF 3 , and PCl 3 ; SiCl 4 and BCl 3 ; and CH 3 Br and CF 3 I. Use of an ECP generally raises the predicted ionization cross section at lower energies leading to improved agreement with experiment compared to all electron calculations for BEB cross sections. Scaling BEB cross sections by the polarizability of the target molecule is shown to give somewhat erratic results, which do not always provide closer agreement with the measured cross sections.

Bacteria-fungi interactions (BFIs) are essential in ecosystem functioning. These interactions are modulated not only by local nutritional conditions but also by the physicochemical constraints and 3D structure of the environmental niche. In soils, the unsaturated and complex nature of the substrate restricts the dispersal and activity of bacteria. Under unsaturated conditions, some bacteria engage with filamentous fungi in an interaction (fungal highways) in which they use fungal hyphae to disperse. Based on a previous experimental device to enrich pairs of organisms engaging in this interaction in soils, we present here the design and validation of a modified version of this sampling system constructed using additive printing. The 3D printed devices were tested using a novel application in which a target fungus, the common coprophilous fungus Coprinopsis cinerea, was used as bait to recruit and identify bacterial partners using its mycelium for dispersal. Bacteria of the genera Pseudomonas, Sphingobacterium and Stenotrophomonas were highly enriched in association with C. cinerea. Developing and producing these new easy-to-use tools to investigate how bacteria overcome dispersal limitations in cooperation with fungi is important to unravel the mechanisms by which BFIs affect processes at an ecosystem scale in soils and other unsaturated environments., (© The Author(s) 2021. Published by Oxford University Press on behalf of FEMS.)

Discovering widespread microbial processes that drive unexpected variation in carbon cycling may improve modeling and management of soil carbon (Prescott, 2010; Wieder et al., 2015a, 2018). A first step is to identify community features linked to carbon cycle variation. We addressed this challenge using an epidemiological approach with 206 soil communities decomposing Ponderosa pine litter in 618 microcosms. Carbon flow from litter decomposition was measured over a 6-week incubation. Cumulative CO 2 from microbial respiration varied two-fold among microcosms and dissolved organic carbon (DOC) from litter decomposition varied five-fold, demonstrating large functional variation despite constant environmental conditions where strong selection is expected. To investigate microbial features driving DOC concentration, two microbial community cohorts were delineated as "high" and "low" DOC. For each cohort, communities from the original soils and from the final microcosm communities after the 6-week incubation with litter were taxonomically profiled. A logistic model including total biomass, fungal richness, and bacterial richness measured in the original soils or in the final microcosm communities predicted the DOC cohort with 72 ( P < 0.05) and 80 ( P < 0.001) percent accuracy, respectively. The strongest predictors of the DOC cohort were biomass and either fungal richness (in the original soils) or bacterial richness (in the final microcosm communities). Successful forecasting of functional patterns after lengthy community succession in a new environment reveals strong historical contingencies. Forecasting future community function is a key advance beyond correlation of functional variance with end-state community features. The importance of taxon richness-the same feature linked to carbon fate in gut microbiome studies-underscores the need for increased understanding of biotic mechanisms that can shape richness in microbial communities independent of physicochemical conditions., (Copyright © 2020 Albright, Johansen, Thompson, Lopez, Gallegos-Graves, Kroeger, Runde, Mueller, Washburne, Munsky, Yoshida and Dunbar.)

Microbial probiotics are intended to improve functions in diverse ecosystems, yet probiotics often fail to establish in a preexisting microbiome. This is a species invasion problem. The relative importance of the two major factors controlling establishment in this context-propagule pressure (inoculation dose and frequency) and biotic interactions (composition of introduced and resident communities)-is unknown. We tested the effect of these factors in driving microbial composition and functioning following 12 microbial community invasions (e.g., introductions of many microbial invaders) in microcosms. Ecosystem functioning over a 30-day postinvasion period was assessed by measuring activity (respiration) and environment modification (dissolved organic carbon abundance). To test the dependence on environmental context, experiments were performed in two resource environments. In both environments, biotic interactions were more important than propagule pressure in driving microbial composition and community function, but the magnitude of effect varied by environment. Successful invaders comprised approximately 8% of the total number of operational taxonomic units (OTUs). Bacteria were better invaders than fungi, with average relative abundances of 7.4% ± 6.8% and 1.5% ± 1.4% of OTUs, respectively. Common bacterial invaders were associated with stress response traits. The most resilient bacterial and fungal families, in other words, those least impacted by invasions, were linked to antimicrobial resistance or production traits. Illuminating the principles that determine community composition and functioning following microbial invasions is key to efficient community engineering. IMPORTANCE With increasing frequency, humans are introducing new microbes into preexisting microbiomes to alter functioning. Example applications include modification of microflora in human guts for better health and those of soil for food security and/or climate management. Probiotic applications are often approached as trial-and-error endeavors and have mixed outcomes. We propose that increased success in microbiome engineering may be achieved with a better understanding of microbial invasions. We conducted a microbial community invasion experiment to test the relative importance of propagule pressure and biotic interactions in driving microbial community composition and ecosystem functioning in microcosms. We found that biotic interactions were more important than propagule pressure in determining the impact of microbial invasions. Furthermore, the principles for community engineering vary among organismal groups (bacteria versus fungi)., (Copyright © 2020 Albright et al.)

Discovering widespread microbial processes that create variation in soil carbon (C) cycling within ecosystems may improve soil C modeling. Toward this end, we screened 206 soil communities decomposing plant litter in a common garden microcosm environment and examined features linked to divergent patterns of C flow. C flow was measured as carbon dioxide (CO2) and dissolved organic carbon (DOC) from 44-days of litter decomposition. Two large groups of microbial communities representing 'high' and 'low' DOC phenotypes from original soil and 44-day microcosm samples were down-selected for fungal and bacterial profiling. Metatranscriptomes were also sequenced from a smaller subset of communities in each group. The two groups exhibited differences in average rate of CO2 production, demonstrating that the divergent patterns of C flow arose from innate functional constraints on C metabolism, not a time-dependent artefact. To infer functional constraints, we identified features - traits at the organism, pathway or gene level - linked to the high and low DOC phenotypes using RNA-Seq approaches and machine learning approaches. Substrate use differed across the high and low DOC phenotypes. Additional features suggested that divergent patterns of C flow may be driven in part by differences in organism interactions that affect DOC abundance directly or indirectly by controlling community structure., (© FEMS 2020.)

Background: Peripheral blood stem cells (PBSC) are commonly cryopreserved awaiting clinical use for hematopoietic stem cell transplant. Long term cryopreservation is commonly defined as five years or longer, and limited data exists regarding how long PBSC can be cryopreserved and retain the ability to successfully engraft. Clinical programs, stem cell banks, and regulatory and accrediting agencies interested in product stability would benefit from such data. Thus, we assessed recovery and colony forming ability of PBSC following long-term cryopreservation as well as their ability to engraft in NOD/SCID/IL-2Rγ null (NSG) mice., Aim: To investigate the in vivo engraftment potential of long-term cryopreserved PBSC units., Methods: PBSC units which were collected and frozen using validated clinical protocols were obtained for research use from the Cellular Therapy Laboratory at Indiana University Health. These units were thawed in the Cellular Therapy Laboratory using clinical standards of practice, and the pre-freeze and post-thaw characteristics of the units were compared. Progenitor function was assessed using standard colony-forming assays. CD34-selected cells were transplanted into immunodeficient mice to assess stem cell function., Results: Ten PBSC units with mean of 17 years in cryopreservation (range 13.6-18.3 years) demonstrated a mean total cell recovery of 88% ± 12% (range 68%-110%) and post-thaw viability of 69% ± 17% (range 34%-86%). BFU-E growth was shown in 9 of 10 units and CFU-GM growth in 7 of 10 units post-thaw. Immunodeficient mice were transplanted with CD34-selected cells from four randomly chosen PBSC units. All mice demonstrated long-term engraftment at 12 wk with mean 34% ± 24% human CD45+ cells, and differentiation with presence of human CD19+, CD3+ and CD33+ cells. Harvested bone marrow from all mice demonstrated growth of erythroid and myeloid colonies., Conclusion: We demonstrated engraftment of clinically-collected and thawed PBSC following cryopreservation up to 18 years in NSG mice, signifying likely successful clinical transplantation of PBSC following long-term cryopreservation., Competing Interests: Conflict-of-interest statement: Goebel WS receives fees as a consulting medical director for Cook Regentec, LLC, and serves as medical director for Ossium Health, Inc. All other authors report no potential conflicts of interest., (©The Author(s) 2020. Published by Baishideng Publishing Group Inc. All rights reserved.)

Background: The dominant fungi in arid grasslands and shrublands are members of the Ascomycota phylum. Ascomycota fungi are important drivers in carbon and nitrogen cycling in arid ecosystems. These fungi play roles in soil stability, plant biomass decomposition, and endophytic interactions with plants. They may also form symbiotic associations with biocrust components or be latent saprotrophs or pathogens that live on plant tissues. However, their functional potential in arid soils, where organic matter, nutrients and water are very low or only periodically available, is poorly characterized., Results: Five Ascomycota fungi were isolated from different soil crust microhabitats and rhizosphere soils around the native bunchgrass Pleuraphis jamesii in an arid grassland near Moab, UT, USA. Putative genera were Coniochaeta, isolated from lichen biocrust, Embellisia from cyanobacteria biocrust, Chaetomium from below lichen biocrust, Phoma from a moss microhabitat, and Aspergillus from the soil. The fungi were grown in replicate cultures on different carbon sources (chitin, native bunchgrass or pine wood) relevant to plant biomass and soil carbon sources. Secretomes produced by the fungi on each substrate were characterized. Results demonstrate that these fungi likely interact with primary producers (biocrust or plants) by secreting a wide range of proteins that facilitate symbiotic associations. Each of the fungal isolates secreted enzymes that degrade plant biomass, small secreted effector proteins, and proteins involved in either beneficial plant interactions or virulence. Aspergillus and Phoma expressed more plant biomass degrading enzymes when grown in grass- and pine-containing cultures than in chitin. Coniochaeta and Embellisia expressed similar numbers of these enzymes under all conditions, while Chaetomium secreted more of these enzymes in grass-containing cultures., Conclusions: This study of Ascomycota genomes and secretomes provides important insights about the lifestyles and the roles that Ascomycota fungi likely play in arid grassland, ecosystems. However, the exact nature of those interactions, whether any or all of the isolates are true endophytes, latent saprotrophs or opportunistic phytopathogens, will be the topic of future studies.

The study of microbial community functions necessitates replicating microbial communities. Variation in community development over time renders this an imperfect process. Thus, anticipating the likely degree of variation among replicate communities may aid in experimental design. We examined divergence in replicate community composition and function among 128 naturally assembled starting communities obtained from soils, each replicated three times, following a 30-day microcosm incubation period. Bacterial and fungal communities diverged in both composition and function among replicates, but remained much more similar to each other than to communities from different starting inocula. Variation in bacterial community composition among replicates was, however, correlated with variation in dissolved organic carbon production. A smaller-scale experiment testing nine starting communities showed that divergence was similar whether replicates were incubated on sterile or non-sterile pine litter, suggesting the impact of a pre-existing community on replicate divergence is minor. However, replicates in this experiment which were incubated for 114 days diverged more than those incubated for 30 days, suggesting experiments that run over long time periods will likely see greater variation among replicate community composition. These results suggest that while replicates diverge at a community level, such divergence is unlikely to severely impede the study of community function.

Pleasure is critically important to the experience of sexual behavior, yet few studies have examined factors that influence it. We explored orgasmic pleasure during masturbation and partnered sex in women with and without orgasmic difficulty, as well as the mutual influence of each type of activity on the other. Data were collected from 2059 women through online surveys and paper-and-pencil tests in both the USA and Hungary. Among women who both masturbated and had partnered sex, orgasmic pleasure was higher during partnered sex. Although women with orgasmic difficulty exhibited a similar pattern of greater pleasure during partnered sex, they reported lower pleasure during partnered sex than women without orgasmic difficulty. Women struggling most to reach orgasm were likely to view masturbation as equally or more satisfying than partnered sex. Several covariates were relevant to pleasure during partnered sex, including the importance of sex, the frequency of partnered sex, and the relationship quality, affirming the idea that relational factors play a critical role in orgasmic pleasure in women. Pleasure during masturbation was associated with higher age, frequency of masturbation, and shorter latencies to orgasm, suggesting that pleasure during masturbation was related to greater experience with masturbation and greater efficiency in reaching orgasm.

DNA-based monitoring of pathogens in aerosol samples requires extraction methods that provide high recovery of DNA. To identify a suitable method, we evaluated six DNA extraction methods for recovery of target-specific DNA from samples with four bacterial agents at low abundance (<10,000 genome copies per detection assay). These methods differed in rigor of cell disruption, approach for DNA capture, and extent of DNA purification. The six methods varied 1000-fold in the recovery of DNA from spores or cells of surrogates of Bacillus anthracis, Yersinia pestis, Burkholderia pseudomallei, and Francisella tularensis, each at about 10 5  CFU per sample. A custom method using paramagnetic Dynabeads for DNA capture greatly outperformed the other five methods. The cDynabead method provided about 80% recovery of target-specific DNA. The cDynabead method and a filtration method were further evaluated for DNA recovery from bacterial agents spiked on filters (c.a. 10 5  CFU of each agent per filter quadrant) that were subsequently used to collect background outdoor air particulates for 24-h. The filtration method generally failed to recover detectable quantities of target DNA from the spiked filters, suggesting at least a 100-fold loss of target DNA during extraction, whereas the custom cDynabead method consistently yielded DNA sufficient for target detection., (Published by Elsevier B.V.)

Numerous studies have examined the long-term effect of experimental nitrogen (N) deposition in terrestrial ecosystems; however, N-specific mechanistic markers are difficult to disentangle from responses to other environmental changes. The strongest picture of N-responsive mechanistic markers is likely to arise from measurements over a short (hours to days) time scale immediately after inorganic N deposition. Therefore, we assessed the short-term (3-day) transcriptional response of microbial communities in two soil strata from a pine forest to a high dose of N fertilization (ca. 1 mg/g of soil material) in laboratory microcosms. We hypothesized that N fertilization would repress the expression of fungal and bacterial genes linked to N mining from plant litter. However, despite N suppression of microbial respiration, the most pronounced differences in functional gene expression were between strata rather than in response to the N addition. Overall, ∼4% of metabolic genes changed in expression with N addition, while three times as many (∼12%) were significantly different across the different soil strata in the microcosms. In particular, we found little evidence of N changing expression levels of metabolic genes associated with complex carbohydrate degradation (CAZymes) or inorganic N utilization. This suggests that direct N repression of microbial functional gene expression is not the principle mechanism for reduced soil respiration immediately after N deposition. Instead, changes in expression with N addition occurred primarily in general cell maintenance areas, for example, in ribosome-related transcripts. Transcriptional changes in functional gene abundance in response to N addition observed in longer-term field studies likely result from changes in microbial composition. IMPORTANCE Ecosystems are receiving increased nitrogen (N) from anthropogenic sources, including fertilizers and emissions from factories and automobiles. High levels of N change ecosystem functioning. For example, high inorganic N decreases the microbial decomposition of plant litter, potentially reducing nutrient recycling for plant growth. Understanding how N regulates microbial decomposition can improve the prediction of ecosystem functioning over extended time scales. We found little support for the conventional view that high N supply represses the expression of genes involved in decomposition or alters the expression of bacterial genes for inorganic N cycling. Instead, our study of pine forest soil 3 days after N addition showed changes in microbial gene expression related to cell maintenance and stress response. This highlights the challenge of establishing predictive links between microbial gene expression levels and measures of ecosystem function., (Copyright © 2018 American Society for Microbiology.)

The use of rRNA/DNA ratios derived from surveys of rRNA sequences in RNA and DNA extracts is an appealing but poorly validated approach to infer the activity status of environmental microbes. To improve the interpretation of rRNA/DNA ratios, we performed simulations to investigate the effects of community structure, rRNA amplification, and sampling depth on the accuracy of rRNA/DNA ratios in classifying bacterial populations as "active" or "dormant." Community structure was an insignificant factor. In contrast, the extent of rRNA amplification that occurs as cells transition from dormant to growing had a significant effect ( P < 0.0001) on classification accuracy, with misclassification errors ranging from 16 to 28%, depending on the rRNA amplification model. The error rate increased to 47% when communities included a mixture of rRNA amplification models, but most of the inflated error was false negatives (i.e., active populations misclassified as dormant). Sampling depth also affected error rates ( P < 0.001). Inadequate sampling depth produced various artifacts that are characteristic of rRNA/DNA ratios generated from real communities. These data show important constraints on the use of rRNA/DNA ratios to infer activity status. Whereas classification of populations as active based on rRNA/DNA ratios appears generally valid, classification of populations as dormant is potentially far less accurate. IMPORTANCE The rRNA/DNA ratio approach is appealing because it extracts an extra layer of information from high-throughput DNA sequencing data, offering a means to determine not only the seedbank of taxa present in communities but also the subset of taxa that are metabolically active. This study provides crucial insights into the use of rRNA/DNA ratios to infer the activity status of microbial taxa in complex communities. Our study shows that the approach may not be as robust as previously supposed, particularly in complex communities composed of populations employing different growth strategies, and identifies factors that inflate the erroneous classification of active populations as dormant., (Copyright © 2017 Steven et al.)

Nitrogen (N) deposition affects myriad aspects of terrestrial ecosystem structure and function, and microbial communities may be particularly sensitive to anthropogenic N inputs. However, our understanding of N deposition effects on microbial communities is far from complete, especially for drylands where data are comparatively rare. To address the need for an improved understanding of dryland biological responses to N deposition, we conducted a two-year fertilization experiment in a semiarid grassland on the Colorado Plateau in the southwestern United States. We evaluated effects of varied levels of N inputs on archaeal, bacterial, fungal and chlorophyte community composition within three microhabitats: biological soil crusts (biocrusts), soil below biocrusts, and the plant rhizosphere. Surprisingly, N addition did not affect the community composition or diversity of any of these microbial groups; however, microbial community composition varied significantly among sampling microhabitats. Further, while plant richness, diversity, and cover showed no response to N addition, there were strong linkages between plant properties and microbial community structure. Overall, these findings highlight the potential for some dryland communities to have limited biotic ability to retain augmented N inputs, possibly leading to large N losses to the atmosphere and to aquatic systems., (© 2017 Society for Applied Microbiology and John Wiley & Sons Ltd.)

Among the bacteria, members of the order Actinomycetales are considered quintessential degraders of complex polysaccharides in soils. However, studies examining complex polysaccharide degradation by Actinomycetales (other than Streptomyces spp.) in soils are limited. Here, we examine the lignocellulolytic and chitinolytic potential of 112 Actinomycetales strains, encompassing 13 families, isolated from a semiarid grassland of the Colorado Plateau in Utah. Members of the Streptomycetaceae , Pseudonocardiaceae , Micromonosporaceae , and Promicromonosporaceae families exhibited robust activity against carboxymethyl cellulose, xylan, chitin, and pectin substrates (except for low/no pectinase activity by the Micromonosporaceae ). When incubated in a hydrated mixture of blended Stipa and Hilaria grass biomass over a 5-week period, Streptomyces and Saccharothrix (a member of the Pseudonocardiaceae ) isolates produced high levels of extracellular enzyme activity, such as endo- and exocellulase, glucosidase, endo- and exoxylosidase, and arabinofuranosidase. These characteristics make them well suited to degrade the cellulose and hemicellulose components of grass cell walls. On the basis of the polysaccharide degradation profiles of the isolates, relative abundance of Actinomycetales sequences in 16S rRNA gene surveys of Colorado Plateau soils, and analysis of genes coding for polysaccharide-degrading enzymes among 237 Actinomycetales genomes in the CAZy database and 5 genomes from our isolates, we posit that Streptomyces spp. and select members of the Pseudonocardiaceae and Micromonosporaceae likely play an important role in the degradation of hemicellulose, cellulose, and chitin substances in dryland soils. IMPORTANCE Shifts in the relative abundance of Actinomycetales taxa have been observed in soil microbial community surveys during large, manipulated climate change field studies. However, our limited understanding of the ecophysiology of diverse Actinomycetales taxa in soil systems undermines attempts to determine the underlying causes of the population shifts or their impact on carbon cycling in soil. This study combines a systematic analysis of the polysaccharide degradation potential of a diverse collection of Actinomycetales isolates from surface soils of a semiarid grassland with analysis of genomes from five of these isolates and publicly available Actinomycetales genomes for genes encoding polysaccharide-active enzymes. The results address an important gap in knowledge of Actinomycetales ecophysiology-identification of key taxa capable of facilitating lignocellulose degradation in dryland soils. Information from this study will benefit future metagenomic studies related to carbon cycling in dryland soils by providing a baseline linkage of Actinomycetales phylogeny with lignocellulolytic functional potential., (Copyright © 2017 American Society for Microbiology.)

Francisella tularensis is a highly virulent zoonotic pathogen that causes tularemia and, because of weaponization efforts in past world wars, is considered a tier 1 biothreat agent. Detection and surveillance of F. tularensis may be confounded by the presence of uncharacterized, closely related organisms. Through DNA-based diagnostics and environmental surveys, novel clinical and environmental Francisella isolates have been obtained in recent years. Here we present 7 new Francisella genomes and a comparison of their characteristics to each other and to 24 publicly available genomes as well as a comparative analysis of 16S rRNA and sdhA genes from over 90 Francisella strains. Delineation of new species in bacteria is challenging, especially when isolates having very close genomic characteristics exhibit different physiological features-for example, when some are virulent pathogens in humans and animals while others are nonpathogenic or are opportunistic pathogens. Species resolution within Francisella varies with analyses of single genes, multiple gene or protein sets, or whole-genome comparisons of nucleic acid and amino acid sequences. Analyses focusing on single genes (16S rRNA, sdhA), multiple gene sets (virulence genes, lipopolysaccharide [LPS] biosynthesis genes, pathogenicity island), and whole-genome comparisons (nucleotide and protein) gave congruent results, but with different levels of discrimination confidence. We designate four new species within the genus; Francisella opportunistica sp. nov. (MA06-7296), Francisella salina sp. nov. (TX07-7308), Francisella uliginis sp. nov. (TX07-7310), and Francisella frigiditurris sp. nov. (CA97-1460). This study provides a robust comparative framework to discern species and virulence features of newly detected Francisella bacteria., Importance: DNA-based detection and sequencing methods have identified thousands of new bacteria in the human body and the environment. In most cases, there are no cultured isolates that correspond to these sequences. While DNA-based approaches are highly sensitive, accurately assigning species is difficult without known near relatives for comparison. This ambiguity poses challenges for clinical cases, disease epidemics, and environmental surveillance, for which response times must be short. Many new Francisella isolates have been identified globally. However, their species designations and potential for causing human disease remain ambiguous. Through detailed genome comparisons, we identified features that differentiate F. tularensis from clinical and environmental Francisella isolates and provide a knowledge base for future comparison of Francisella organisms identified in clinical samples or environmental surveys., (Copyright © 2017 American Society for Microbiology.)

Oxidative stress contributes to age-related cognitive decline. In some instances, consumption of fruits and vegetables rich in antioxidant can provide superior protection than supplementation with purified antioxidants. Our prior studies have shown that supplementation with apple juice concentrate (AJC) alleviates oxidative damage and cognitive decline in adult (9-12 months) mice lacking ApoE (as a model of increased oxidative stress) and in normal aged (2-2.5 years) mice when challenged with a vitamin-deficient, oxidative stress-promoting diet. Here, we demonstrate that AJC, administered in drinking water, maintains acetylcholine levels that otherwise decline when adult and aged mice are maintained on the above deficient diet. Normal mice aged either 9-10 months or 2-2.5 years and ApoE-/- mice aged 9-10 months were maintained for 1 month on a complete diet or a diet lacking folate and vitamin E and containing iron as a pro-oxidant, and additional groups received 0.5% AJC ad libitum in drinking water. Spectrophotometric assay of acetylcholine levels revealed a significant decline in homogenates of combined frontal cortex and hippocampus for all mice maintained on the deficient diet, and a prevention of this decline in mice maintained on the deficient diet when supplemented with AJC. These findings provide a likely mechanism by which consumption of antioxidant-rich foods such as apples can prevent the decline in cognitive performance that accompanies dietary and genetic deficiencies and aging.

A potential therapeutic option for patients with Fanconi anemia is collection of peripheral blood stem cells prior to the development of severe pancytopenia. These hematopoietic cells potentially could be infused when symptomatic bone marrow failure develops, as autologous rescue after chemotherapy in the event of leukemic transformation, or as targets for gene therapy. Eight patients with Fanconi anemia were mobilized with 10 microg/kg per day of granulocyte colony-stimulating factor (median, 10 +/- 4 days) to determine the feasibility of collecting peripheral blood stem cells for future use. Six patients achieved a peripheral blood CD34+ count of > or = 6/microL and underwent apheresis. The collection goal was 2 x 10(6) CD34+ cells/kg based on a predicted weight 5 years from the date of collection. A mean of 2.6 +/- 0.9 x 10(6) CD34+ cells/kg of the weight at the time of collection were collected, which corresponded to 1.9 +/- 0.4 x 10(6) CD34+ cells/kg of the target weight. The collections required a mean of 4 +/- 3 days (range, 2-8 days) of apheresis. Six of the 8 subjects had > or = 1 x 10(6) CD34+ cells/kg cryopreserved based on both actual and target weights, and 4 subjects had > or = 2 x 10(6) CD34+ cells/kg cryopreserved based on the target weight. These results suggest that some patients with Fanconi anemia can have adequate numbers of CD34+ cells mobilized and collected from the peripheral blood prior to the onset of severe bone marrow failure, but they may require an extended mobilization and multiple days of collection.

Direct endovascular access to the anterior cerebral artery (ACA) with a guidewire and catheter is not always possible. A C-shaped guidewire advanced as a loop into the middle cerebral artery and then withdrawn to advance the guidewire into the ACA is a way to gain endovascular access to the ACA when the direct approach is unsuccessful.

Purpose: To determine the clinical effectiveness of parent artery occlusion of the carotid or vertebral artery by means of temporary proximal flow arrest and microcoils., Methods: Nineteen parent artery occlusions (15 carotid, four vertebral) were performed in 19 patients who successfully passed a balloon test occlusion. In these patients, endovascular occlusion of the carotid or vertebral artery was accomplished with the use of temporary proximal flow arrest and microcoils., Results: All 19 parent arteries were occluded. Eighteen patients (95%) had good outcomes and one (5%) had a poor outcome. Fourteen patients (74%) had no complications and five (26%) had complications, of whom only one was left with a permanent neurologic deficit. Three (60%) of the complications were the result of delayed ischemic events after parent artery occlusion and were not predicted by balloon test occlusion., Conclusion: Endovascular occlusion with temporary proximal flow arrest and microcoils can be done effectively and successfully. The predictive value of the balloon test occlusion is the major complicating factor, as it is with balloon occlusion. This technique offers an additional tool that can be used for endovascular occlusion of the carotid or vertebral artery and seems to be less difficult technically. It is our primary technique for parent artery occlusion.

Purpose: To develop a pig model of arterial thrombosis suitable for assessing different methods of thrombolysis and to use this model to compare the efficacy of intraarterial thrombolysis performed by continuous proximal urokinase infusion versus mechanical clot disruption combined with intrathrombic urokinase injection., Methods: In a control group of five pigs, a thrombus was made in a short segment of femoral artery and observed for 2 hours to assess its stability. In a treatment group of six pigs, intraarterial thrombolysis was performed immediately after thrombus formation. Thrombolysis was accomplished by continuously infusing urokinase into the proximal leading edge of the thrombus in three pigs and by mechanical clot disruption combined with intrathrombic urokinase injection in the remaining three pigs., Results: There was no spontaneous reestablishment of flow in the control group during the 2-hour observation period. In the first treatment group, no flow was observed after a 1-hour treatment period when urokinase was infused continuously into the proximal edge of the thrombus. In the second treatment group, with mechanical clot disruption and intrathrombic urokinase injection, some degree of flow was observed in all three pigs. Reestablishment of flow was more sustained and of a greater degree with the addition of systemic heparinization., Conclusion: This animal model could provide a useful way to evaluate and compare different methods of thrombolysis. Our results suggest that mechanical clot disruption combined with intrathrombic urokinase injection is more effective in achieving reestablishment of flow than is continuous infusion of urokinase into the proximal edge of the thrombus.

Purpose: To evaluate the in vivo and in vitro properties of collagen-coated acrylic microspheres and to compare them with polyvinyl alcohol (PVA) particles., Methods: Samples of 100- to 300-microns, 300- to 500-microns, 500- to 700-microns, and 700- to 900-microns collagen-coated acrylic microspheres and 200- to 300-microns PVA particles were suspended in solutions of 50% saline and 50% contrast material. The samples were evaluated for quantitative and qualitative microscopic characteristics (shape, size, deformability); injectability via standardized microcatheters; degree of particulate penetration in the pig rete mirabile; and reaction of tissue to the particles in 48-hour- and 4-week-old specimens., Results: The acrylic microspheres were spherical and deformable. The sample of 100- to 300-microns microspheres (n = 202) had a mean diameter of 210 microns (standard deviation, 43 microns). Hub accumulation, particle aggregation, and catheter occlusion were not observed with the microspheres (all sizes) but were noted with the PVA particles. The 200- to 300-microns PVA particles formed aggregates in the proximal rete. The 100- to 300-microns microspheres were found throughout the rete and beyond. Chronic transmural and perivascular inflammation was observed with the microspheres and the PVA particles., Conclusions: Particle aggregation and catheter occlusion do not complicate the transcatheter delivery of collagen-coated acrylic microspheres as they do with PVA particles. For a given particle and vessel size, acrylic microspheres penetrate to a much greater extent than the PVA particles. Tissue reaction to acrylic microspheres and PVA particles is similar.