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  1. Ecology of methyl-coenzyme M reductase encoding Thermoproteota

    Jay, Zackary J. ; Kellom, Matthew ; Eloe-Fadrosh, Emiley ; ... - Current Opinion in Microbiology
    The recent demonstration that members of at least three classes of archaea affiliated with the Thermoproteota superphylum are involved in the production of the climate-active gas methane has sparked discussions about how well we understand the diversity of methanogens. Here, in this work, we show that members of all three of these lineages, as well as several other, yet uncultured and physiologically uncharacterized groups within the Thermoproteota that encode the key enzyme of anaerobic methane cycling, methyl-coenzyme M reductase (MCR), are widely distributed in anoxic ecosystems. We postulate that the taxonomic, metabolic, and ecological diversity of methanogenic and MCR-encoding Thermoproteotamore » are poorly understood, and that the contribution of methylotrophic and thermoproteotal methanogenesis to methane production is largely unknown. We hypothesize that thermoproteotal methanogens could contribute, potentially substantially, to methane emissions in many anoxic environments that harbor methylated precursors, including wetlands, sediments, peat, rice paddies, wastewater sludge, and geothermal systems. We highlight the necessity to experimentally test the (eco)physiology of these widely distributed archaea using both culture-dependent (in vitro) and culture-independent (in situ) approaches to assess their potential contribution to methane emissions. Last, we stress the importance of remaining agnostic about the physiology of MCR-encoding Thermoproteota in the absence of experimental data because most of these archaea also carry the genetic potential to grow non-methanogenically.« less

  2. Accelerating the fusion workforce in the USA

    Paz-Soldan, Carlos ; Belonohy, Eva ; Carter, Troy ; ... - Plasma Physics and Controlled Fusion
    The fusion energy research and development landscape has seen significant advances in recent years, with important scientific and technological breakthroughs and a rapid rise of investment in the private sector. The workforce needs of the nascent fusion industry are growing at a rate that academic workforce development programs are not currently able to match. This paper presents the findings of the Workforce Accelerator for Fusion Energy Development Conference held in Hampton, Virginia, United States of America (USA), on 29–30 May 2024, which was funded by the National Science Foundation of the USA. A major goal of the conference was tomore » focus on bringing public and private stakeholders together to identify opportunities for partnership in fusion research and education with the goal of meeting the needs for a talented and diverse workforce. Representatives from industry, academia, and national laboratories participated in the conference through the preparation of white papers, presentations, and group discussions, and the production of recommendations to address the challenges facing the fusion workforce in the USA.« less

  3. A mixture of grass–legume cover crop species may ameliorate water stress in a changing climate

    Truong, Nhu Q. ; York, Larry M. ; Decker, Allyssa ; ... - AoB Plants
    Climate change models predict increasing precipitation variability in the mid-latitude regions of Earth, generating a need to reduce the negative impacts of these changes on crop production. Despite considerable research on how cover crops support agriculture in a changing climate, understanding is limited of how climate change influences the growth of cover crops. We investigated the early development of two common cover crop species—crimson clover (Trifolium incarnatum) and rye (Secale cereale)—and hypothesized that growing them in the mixture would ameliorate stress from drought or waterlogging. This hypothesis was tested in a 25-day greenhouse experiment, where the two factors (species numbermore » and water stress) were fully crossed in randomized blocks, and plant responses were quantified through survival, growth rate, biomass production and root morphology. Water stress negatively influenced the early growth of these two species in contrasting ways: crimson clover was susceptible to drought while rye performed poorly under waterlogging. Per-plant biomass in rye was always greater in mixture than in monoculture, while per-plant biomass of crimson clover was greater in mixture under drought. Both species grew longer roots in mixture than in monoculture under drought, and total biomass of mixtures did not differ significantly from the more-productive monoculture (rye) in any water condition. In the face of increasingly variable precipitation, growing crimson clover and rye together has potential to ameliorate water stress, a possibility that should be further investigated in field experiments.« less

  4. Baltic Sea coastal sediment-bound eukaryotes have increased year-round activities under predicted climate change related warming

    Li, Songjun ; Nilsson, Emelie ; Seidel, Laura ; ... - Frontiers in Microbiology
    Climate change related warming is a serious environmental problem attributed to anthropogenic activities, causing ocean water temperatures to rise in the coastal marine ecosystem since the last century. This particularly affects benthic microbial communities, which are crucial for biogeochemical cycles. While bacterial communities have received considerable scientific attention, the benthic eukaryotic community response to climate change remains relatively overlooked. In this study, sediments were sampled from a heated (average 5°C increase over the whole year for over 50 years) and a control (contemporary conditions) Baltic Sea bay during four different seasons across a year. RNA transcript counts were then usedmore » to investigate eukaryotic community changes under long-term warming. The composition of active species in the heated and control bay sediment eukaryotic communities differed, which was mainly attributed to salinity and temperature. The family level RNA transcript alpha diversity in the heated bay was higher during May but lower in November, compared with the control bay, suggesting altered seasonal activity patterns and dynamics. In addition, structures of the active eukaryotic communities varied between the two bays during the same season. Hence, this study revealed that long-term warming can change seasonality in eukaryotic diversity patterns. Relative abundances and transcript expression comparisons between bays suggested that some taxa that now have lower mRNA transcripts numbers could be favored by future warming. Furthermore, long-term warming can lead to a more active metabolism in these communities throughout the year, such as higher transcript numbers associated with diatom energy production and protein synthesis in the heated bay during winter. In all, these data can help predict how future global warming will affect the ecology and metabolism of eukaryotic community in coastal sediments.« less

  5. Intro to HPC Bootcamp: Engaging New Communities Through Energy Justice Projects

    Leung, Mary Ann ; Cahill, Katharine ; Hartman-Baker, Rebecca ; ... - Journal of Computational Science Education
    The U.S. Department of Energy (DOE) is a long-standing leader in research and development of high-performance computing (HPC) in the pursuit of science. However, we face daunting challenges in fostering a robust and diverse HPC workforce. Basic HPC is not typically taught at early stages of students' academic careers, and the capacity and knowledge of HPC at many institutions are limited. Even so, such topics are prerequisites for advanced training programs, internships, graduate school, and ultimately for careers in HPC. To help address this challenge, as part of the DOE Exascale Computing Project's Broadening Participation Initiative, we recently launched themore » Introduction to HPC Training and Workforce Pipeline Program to provide accessible introductory material on HPC, scalable AI, and analytics. We describe the Intro to HPC Bootcamp, an immersive program designed to engage students from underrepresented groups as they learn foundational HPC skills. Here, the program takes a novel approach to HPC training by turning the traditional curriculum upside down. Instead of focusing on technology and its applications, the bootcamp focuses on energy justice to motivate the training of HPC skills through project-based pedagogy and real-life science stories. Additionally, the bootcamp prepares students for internships and future careers at DOE labs. The first bootcamp, hosted by the advanced computing facilities at Argonne, Lawrence Berkeley, and Oak Ridge National Labs and organized by Sustainable Horizons Institute, took place in August 2023.« less

  6. Mitochondrial genome diversity across the subphylum Saccharomycotina

    Wolters, John F. ; LaBella, Abigail L. ; Opulente, Dana A. ; ... - Frontiers in Microbiology
    Eukaryotic life depends on the functional elements encoded by both the nuclear genome and organellar genomes, such as those contained within the mitochondria. The content, size, and structure of the mitochondrial genome varies across organisms with potentially large implications for phenotypic variance and resulting evolutionary trajectories. Among yeasts in the subphylum Saccharomycotina, extensive differences have been observed in various species relative to the model yeast Saccharomyces cerevisiae, but mitochondrial genome sampling across many groups has been scarce, even as hundreds of nuclear genomes have become available.

  7. Identification of hidden N4-like viruses and their interactions with hosts

    Zheng, Kaiyang ; Liang, Yantao ; Paez-Espino, David ; ... - mSystems
    The N4-like viruses, which were recently assigned to the novel viral family Schitoviridae in 2021, belong to a podoviral-like viral lineage and possess conserved genomic characteristics and a unique replication mechanism. Despite their significance, our understanding of N4-like viruses is primarily based on viral isolates. To address this knowledge gap, this study has established a comprehensive N4-like viral data sets comprising 342 high-quality N4-like viruses/proviruses (144 viral isolates, 158 uncultured viruses, and 40 integrated N4-like proviruses). These viruses were classified into 97 subfamilies (89 of which are newly identified), 148 genera (100 of which are newly identified), and 253 speciesmore » (177 of which are newly identified). The study reveals that N4-like viruses inhibit the polar region, oligotrophic open oceans, and the human gut, where they infect various bacterial lineages, such as Alpha/Beta/Gamma/Epsilon-proteobacteria in the Proteobacteria phylum. Although N4-like viral endogenization appears to be prevalent in Proteobacteria, it has also been observed in Firmicutes. Additionally, the phylogenetic analysis has identified evolutionary divergence within the hallmark genes of N4-like viruses, indicating a complex origin of the different conserved parts of viral genomes. Moreover, 1,101 putative auxiliary metabolic genes (AMGs) were identified in the N4-like viral pan-proteome, which mainly participate in nucleotide and cofactor/vitamin metabolisms. Of these AMGs, 27 were found to be associated with virulence, suggesting their potential involvement in the spread of bacterial pathogenicity. The findings of this study are significant, as N4-like viruses represent a unique viral lineage with a distinct replication mechanism and a conserved core genome. This work has resulted in a comprehensive global map of the entire N4-like viral lineage, including information on their distribution in different biomes, evolutionary divergence, genomic diversity, and the potential for viral-mediated host metabolic reprogramming. As such, this work significantly contributes to our understanding of the ecological function and viral-host interactions of bacteriophages.« less

  8. The importance of recruitment and retention in Heliophysics: it’s not just a pipeline problem

    Halford, Alexa J. ; Bard, Christopher M. ; Burrell, Angeline G. ; ... - Frontiers in Astronomy and Space Sciences
    A major obstacle in cultivating a robust Heliophysics (and broader scientific) community is the lack of diversity throughout science, technology, engineering, and mathematics (STEM) fields. For many years, this has been understood as a “leaky pipeline” analogy, in which predominately minority students initially interested in STEM gradually fall (or are pushed) out of the field on their way to a scientific research position. However, this ignores critical structural and policy issues which drive even later career Ph.D.s out of a career in Heliophysics. We identify here several systemic problems that inhibit many from participating fully in the Heliophysics community, includingmore » soft money pressure, lack of accessibility and equity, power imbalances, lack of accountability, friction in collaboration, and difficulties in forming mentorship bonds. We present several recommendations to empower research-supporting organizations to help create a culture of inclusion, openness, and innovative science.« less

  9. Cultivating a culture of inclusivity in heliophysics

    Halford, Alexa J. ; Burrell, Angeline G. ; Liemohn, Michael W. ; ... - Frontiers in Physics
    A large number of heliophysicists from across career levels, institution types, and job titles came together to support a poster at Heliophysics 2050 and the position papers for the 2024 Heliophysics decadal survey titled “Cultivating a Culture of Inclusivity in Heliophysics,” “The Importance of Policies: It’s not just a pipeline problem,” and “Mentorship within Heliophysics.” While writing these position papers, the number of people who privately shared disturbing stories and experiences of bullying and harassment was shocking. The number of people who privately expressed how burned out they were was staggering. The number of people who privately spoke about howmore » they considered leaving the field for their and their family’s health was astounding. And for as much good there is in our community, it is still a toxic environment for many. If we fail to do something now, our field will continue to suffer. While acknowledging the ongoing growth that we as individuals must work toward, we call on our colleagues to join us in working on organizational, group, and personal levels toward a truly inclusive culture, for the wellbeing of our colleagues and the success of our field. This work includes policies, processes, and commitments to promote: accountability for bad actors; financial security through removing the constant anxiety about funding; prioritization of mental health and community through removing constant deadlines and constant last-minute requests; a collaborative culture rather than a hyper-competitive one; and a community where people can thrive as whole persons and do not have to give up a healthy or well-rounded life to succeed.« less

  10. Nutrients strengthen density dependence of per-capita growth and mortality rates in the soil bacterial community

    Stone, Bram W. ; Blazewicz, Steven J. ; Koch, Benjamin J. ; ... - Oecologia
    Density dependence in an ecological community has been observed in many macro-organismal ecosystems and is hypothesized to maintain biodiversity but is poorly understood in microbial ecosystems. Here, in this study, we analyze data from an experiment using quantitative stable isotope probing (qSIP) to estimate per-capita growth and mortality rates of bacterial populations in soils from several ecosystems along an elevation gradient which were subject to nutrient addition of either carbon alone (glucose; C) or carbon with nitrogen (glucose + ammonium-sulfate; C + N). Across all ecosystems, we found that higher population densities, quantified by the abundance of genomes per grammore » of soil, had lower per-capita growth rates in C + N-amended soils. Similarly, bacterial mortality rates in C + N-amended soils increased at a significantly higher rate with increasing population size than mortality rates in control and C-amended soils. In contrast to the hypothesis that density dependence would promote or maintain diversity, we observed significantly lower bacterial diversity in soils with stronger negative density-dependent growth. Here, density dependence was significantly but weakly responsive to nutrients and was not associated with higher bacterial diversity.« less
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