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At least 1,729 records · Page 96
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

Defining the Sphagnum Core Microbiome across the North American Continent Reveals a Central Role for Diazotrophic Methanotrophs in the Nitrogen and Carbon Cycles of Boreal Peatland Ecosystems

Peat mosses of the genus Sphagnum are ecosystem engineers that frequently predominate over photosynthetic production in boreal peatlands. Sphagnum spp. host diverse microbial communities capable of nitrogen fixation (diazotrophy) and methane oxidation (methanotrophy), thereby potentially supporting plant growth under severely nutrient-limited conditions. Moreover, diazotrophic methanotrophs represent a possible “missing link” between the carbon and nitrogen cycles, but the functional contributions of the Sphagnum-associated microbiome remain in question. A combination of metagenomics, metatranscriptomics, and dual-isotope incorporation assays was applied to investigate Sphagnum microbiome community composition across the North American continent and provide empirical evidence for diazotrophic methanotrophy in Sphagnum-dominated ecosystems. Remarkably consistent prokaryotic communities were detected in over 250 Sphagnum SSU rRNA libraries from peatlands across the United States (5 states, 17 bog/fen sites, 18 Sphagnum species), with 12 genera of the core microbiome comprising 60% of the relative microbial abundance. Additionally, nitrogenase (nifH) and SSU rRNA gene amplicon analysis revealed that nitrogen-fixing populations made up nearly 15% of the prokaryotic communities, predominated by Nostocales cyanobacteria and Rhizobiales methanotrophs. While cyanobacteria comprised the vast majority (>95%) of diazotrophs detected in amplicon and metagenome analyses, obligate methanotrophs of the genus Methyloferula (order Rhizobiales) accounted for one-quarter of transcribed nifH genes. Furthermore, in dual-isotope tracer experiments, members of the Rhizobiales showed substantial incorporation of 13 CH 4 and 15 N 2 isotopes into their rRNA. Our study characterizes the core Sphagnum microbiome across large spatial scales and indicates that diazotrophic methanotrophs, here defined as obligate methanotrophs of the rare biosphere (Methyloferula spp. of the Rhizobiales) that also carry out diazotrophy, play a keystone role in coupling of the carbon and nitrogen cycles in nutrient-poor peatlands.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2023

Inferring microbial co-occurrence networks from amplicon data: a systematic evaluation

Microbes commonly organize into communities consisting of hundreds of species involved in complex interactions with each other. 16S ribosomal RNA (16S rRNA) amplicon profiling provides snapshots that reveal the phylogenies and abundance profiles of these microbial communities. These snapshots, when collected from multiple samples, can reveal the co-occurrence of microbes, providing a glimpse into the network of associations in these communities. However, the inference of networks from 16S data involves numerous steps, each requiring specific tools and parameter choices. Moreover, the extent to which these steps affect the final network is still unclear. In this study, we perform a meticulous analysis of each step of a pipeline that can convert 16S sequencing data into a network of microbial associations. Through this process, we map how different choices of algorithms and parameters affect the co-occurrence network and identify the steps that contribute substantially to the variance. We further determine the tools and parameters that generate robust co-occurrence networks and develop consensus network algorithms based on benchmarks with mock and synthetic data sets. The Microbial Co-occurrence Network Explorer, or MiCoNE (available at https://github.com/segrelab/MiCoNE) follows these default tools and parameters and can help explore the outcome of these combinations of choices on the inferred networks. We envisage that this pipeline could be used for integrating multiple data sets and generating comparative analyses and consensus networks that can guide our understanding of microbial community assembly in different biomes.

16S rRNA↗
DOE OSTI2022

Microbial colonization and persistence in deep fractured shales is guided by metabolic exchanges and viral predation

Background: Microbial colonization of subsurface shales following hydraulic fracturing offers the opportunity to study coupled biotic and abiotic factors that impact microbial persistence in engineered deep subsurface ecosystems. Shale formations underly much of the continental USA and display geographically distinct gradients in temperature and salinity. Complementing studies performed in eastern USA shales that contain brine-like fluids, here we coupled metagenomic and metabolomic approaches to develop the first genome-level insights into ecosystem colonization and microbial community interactions in a lower-salinity, but high-temperature western USA shale formation. Results: We collected materials used during the hydraulic fracturing process (i.e., chemicals, drill muds) paired with temporal sampling of water produced from three different hydraulically fractured wells in the STACK (Sooner Trend Anadarko Basin, Canadian and Kingfisher) shale play in OK, USA. Relative to other shale formations, our metagenomic and metabolomic analyses revealed an expanded taxonomic and metabolic diversity of microorganisms that colonize and persist in fractured shales. Importantly, temporal sampling across all three hydraulic fracturing wells traced the degradation of complex polymers from the hydraulic fracturing process to the production and consumption of organic acids that support sulfate- and thiosulfate-reducing bacteria. Furthermore, we identified 5587 viral genomes and linked many of these to the dominant, colonizing microorganisms, demonstrating the key role that viral predation plays in community dynamics within this closed, engineered system. Lastly, top-side audit sampling of different source materials enabled genome-resolved source tracking, revealing the likely sources of many key colonizing and persisting taxa in these ecosystems. Conclusions: These findings highlight the importance of resource utilization and resistance to viral predation as key traits that enable specific microbial taxa to persist across fractured shale ecosystems. We also demonstrate the importance of materials used in the hydraulic fracturing process as both a source of persisting shale microorganisms and organic substrates that likely aid in sustaining the microbial community. Moreover, we showed that different physicochemical conditions (i.e., salinity, temperature) can influence the composition and functional potential of persisting microbial communities in shale ecosystems. Together, these results expand our knowledge of microbial life in deep subsurface shales and have important ramifications for management and treatment of microbial biomass in hydraulically fractured wells.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Ultra-sensitive isotope probing to quantify activity and substrate assimilation in microbiomes

Abstract Background Stable isotope probing (SIP) approaches are a critical tool in microbiome research to determine associations between species and substrates, as well as the activity of species. The application of these approaches ranges from studying microbial communities important for global biogeochemical cycling to host-microbiota interactions in the intestinal tract. Current SIP approaches, such as DNA-SIP or nanoSIMS allow to analyze incorporation of stable isotopes with high coverage of taxa in a community and at the single cell level, respectively, however they are limited in terms of sensitivity, resolution or throughput. Results Here, we present an ultra-sensitive, high-throughput protein-based stable isotope probing approach (Protein-SIP), which cuts cost for labeled substrates by 50–99% as compared to other SIP and Protein-SIP approaches and thus enables isotope labeling experiments on much larger scales and with higher replication. The approach allows for the determination of isotope incorporation into microbiome members with species level resolution using standard metaproteomics liquid chromatography-tandem mass spectrometry (LC–MS/MS) measurements. At the core of the approach are new algorithms to analyze the data, which have been implemented in an open-source software ( https://sourceforge.net/projects/calis-p/ ). We demonstrate sensitivity, precision and accuracy using bacterial cultures and mock communities with different labeling schemes. Furthermore, we benchmark our approach against two existing Protein-SIP approaches and show that in the low labeling range used our approach is the most sensitive and accurate. Finally, we measure translational activity using 18 O heavy water labeling in a 63-species community derived from human fecal samples grown on media simulating two different diets. Activity could be quantified on average for 27 species per sample, with 9 species showing significantly higher activity on a high protein diet, as compared to a high fiber diet. Surprisingly, among the species with increased activity on high protein were several Bacteroides species known as fiber consumers. Apparently, protein supply is a critical consideration when assessing growth of intestinal microbes on fiber, including fiber-based prebiotics. Conclusions We demonstrate that our Protein-SIP approach allows for the ultra-sensitive (0.01 to 10% label) detection of stable isotopes of elements found in proteins, using standard metaproteomics data.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Highly diverse and unknown viruses may enhance Antarctic endoliths’ adaptability

Abstract Background Rock-dwelling microorganisms are key players in ecosystem functioning of Antarctic ice free-areas. Yet, little is known about their diversity and ecology, and further still, viruses in these communities have been largely unexplored despite important roles related to host metabolism and nutrient cycling. To begin to address this, we present a large-scale viral catalog from Antarctic rock microbial communities. Results We performed metagenomic analyses on rocks from across Antarctica representing a broad range of environmental and spatial conditions, and which resulted in a predicted viral catalog comprising > 75,000 viral operational taxonomic units (vOTUS). We found largely undescribed, highly diverse and spatially structured virus communities which had predicted auxiliary metabolic genes (AMGs) with functions indicating that they may be potentially influencing bacterial adaptation and biogeochemistry. Conclusion This catalog lays the foundation for expanding knowledge of virosphere diversity, function, spatial ecology, and dynamics in extreme environments. This work serves as a step towards exploring adaptability of microbial communities in the face of a changing climate.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Virus diversity and activity is driven by snowmelt and host dynamics in a high-altitude watershed soil ecosystem

Background: Viruses impact nearly all organisms on Earth, including microbial communities and their associated biogeochemical processes. In soils, highly diverse viral communities have been identified, with a global distribution seemingly driven by multiple biotic and abiotic factors, especially soil temperature and moisture. However, our current understanding of the stability of soil viral communities across time and their response to strong seasonal changes in environmental parameters remains limited. Here, we investigated the diversity and activity of environmental soil DNA and RNA viruses, focusing especially on bacteriophages, across dynamics’ seasonal changes in a snow-dominated mountainous watershed by examining paired metagenomes and metatranscriptomes. Results: We identified a large number of DNA and RNA viruses taxonomically divergent from existing environmental viruses, including a significant proportion of fungal RNA viruses, and a large and unsuspected diversity of positive single-stranded RNA phages ( Leviviricetes ), highlighting the under-characterization of the global soil virosphere. Among these, we were able to distinguish subsets of active DNA and RNA phages that changed across seasons, consistent with a “seed-bank” viral community structure in which new phage activity, for example, replication and host lysis, is sequentially triggered by changes in environmental conditions. At the population level, we further identified virus-host dynamics matching two existing ecological models: “Kill-The-Winner” which proposes that lytic phages are actively infecting abundant bacteria, and “Piggyback-The-Persistent” which argues that when the host is growing slowly, it is more beneficial to remain in a dormant state. The former was associated with summer months of high and rapid microbial activity, and the latter with winter months of limited and slow host growth. Conclusion: Taken together, these results suggest that the high diversity of viruses in soils is likely associated with a broad range of host interaction types each adapted to specific host ecological strategies and environmental conditions. As our understanding of how environmental and host factors drive viral activity in soil ecosystems progresses, integrating these viral impacts in complex natural microbiome models will be key to accurately predict ecosystem biogeochemistry.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2025

A genome-scale metabolic model for the denitrifying bacterium Thauera sp. MZ1T accurately predicts degradation of pollutants and production of polymers

The denitrifying bacterium Thauera sp . MZ1T, a common member of microbial communities in wastewater treatment facilities, can produce different compounds from a range of carbon (C) and nitrogen (N) sources under aerobic and anaerobic conditions. In these different conditions, Thauera modifies its metabolism to produce different compounds that influence the microbial community. In particular, Thauera sp . MZ1T produces different exopolysaccharides with floc-forming properties, impacting the physical disposition of wastewater consortia and the efficiency of nutrient assimilation by the microbial community. Under N-limiting conditions, Thauera sp . MZ1T decreases its growth rate and accelerates the accumulation of polyhydroxyalkanoate-related (PHA) compounds including polyhydroxybutyrate (PHB), which plays a fundamental role as C and energy storage in this β-proteobacterium. However, the metabolic mechanisms employed by Thauera sp . MZ1T to assimilate and catabolize many of the different C and N sources under aerobic and anaerobic conditions remain unknown. Systems biology approaches such as genome-scale metabolic modeling have been successfully used to unveil complex metabolic mechanisms for various microorganisms. Here, we developed a comprehensive metabolic model (M-model) for Thauera sp . MZ1T ( i Thauera861), consisting of 1,744 metabolites, 2,384 reactions, and 861 genes. We validated the model experimentally using over 70 different C and N sources under both aerobic and anaerobic conditions. i Thauera861 achieved a prediction accuracy of 95% for growth on various C and N sources and close to 85% for assimilation of aromatic compounds under denitrifying conditions. The M-model was subsequently deployed to determine the effects of substrates, oxygen presence, and the C:N ratio on the production of PHB and exopolysaccharides (EPS), showing the highest polymer yields are achieved with nucleotides and amino acids under aerobic conditions. This comprehensive M-model will help reveal the metabolic processes by which this ubiquitous species influences communities in wastewater treatment systems and natural environments.

Tec-Campos, Diego (ORCID:0000000188194150)↗
DOE OSTI2024

Investigating the relationship between microbial network features of giant kelp “seedbank” cultures and subsequent farm performance

Microbial inoculants can increase the yield of cultivated crops and are successful in independent trials; however, efficacy drops in large-scale applications due to insufficient consideration of microbial community dynamics. The structure of microbiomes, in addition to the impact of individual taxa, is an important factor to consider when designing growth-promoting inoculants. Here, we investigate the microbial network and community assembly patterns of Macrocystis pyrifera gametophyte germplasm cultures (collectively referred to as a “seedbank”) used to cultivate an offshore farm in Santa Barbara, California, and identify network features associated with increased biomass of mature sporophytes. We found that [1] several network features, such as clustering coefficient and edge ratios, significantly vary with biomass outcomes; [2] gametophytes that become low- or high-biomass sporophytes have different hub taxa; and [3] microbial community assembly of gametophyte germplasm cultures is niche-driven. Overall, this study describes microbial community dynamics in M . pyrifera germplasm cultures and ultimately supports the development of early life stage inoculants that can be used on seaweed cultivars to increase biomass yield.

Osborne, Melisa G. (ORCID:0000000154980057)↗
DOE OSTI2021

Five key aspects of metaproteomics as a tool to understand functional interactions in host-associated microbiomes

Host-associated microbial communities (microbiomes) play critical roles in human, animal, and plant health and development. However, interactions between the host, members of the microbiome, and invading pathogens are in most cases still poorly understood. Such interactions are multidimensional and can alter the taxonomic composition and/or the functional metabolic activities of the microbiome in response to disease or treatment conditions. For example, after 2 days of antibiotic treatment, the mouse gut microbiome is altered and more susceptible to invasion by the pathogen Clostridioides difficile. Studies of these multidimensional interactions have been fueled by the ability to use high-throughput sequencing of phylogenetic marker genes to profile microbial community composition and shotgun metagenomics to profile functional potential. However, many protein-coding genes predicted from metagenomes are not necessarily expressed under a given condition, and thus, it is difficult to assess the activities and functional interactions in microbial communities based on DNA sequencing data alone. The physiological and pathological processes expressed in these communities under specific conditions are better reflected by the abundances of transcripts or proteins. In this Pearl, we provide a brief introduction to metaproteomics, which is a tool for the large-scale analysis of proteins in microbiomes that allows researchers to address a diversity of questions related to functions and interactions in microbiomes. The term “metaproteomics” was first used in 2004 for “the large-scale characterization of the entire protein complement of environmental microbiota at a given point in time”, and since then, a large array of metaproteomics approaches have been developed. Our objective in this Pearl is to highlight what we feel are 5 essential elements to be considered for a metaproteomics research campaign and to introduce nonexpert readers to the topic without going into too much technical detail.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Heavy and wet: The consequences of violating assumptions of measuring soil microbial growth efficiency using the 18O water method

Soils store more carbon than the biosphere and atmosphere combined, and the efficiency to which soil microorganisms allocate carbon to growth rather than respiration is increasingly considered a proxy for the soil capacity to store carbon. This carbon use efficiency (CUE) is measured via different methods, and more recently, the 18O-H2O method has been embraced as a significant improvement for measuring CUE of soil microbial communities. Based on extrapolating 18O incorporation into DNA to new biomass, this measurement makes various implicit assumptions about the microbial community at hand. Here we conducted a literature review to evaluate how viable these assumptions are and then developed a mathematical model to test how violating them affects estimates of the growth component of CUE in soil. We applied this model to previously collected data from two kinds of soil microbial communities. By changing one parameter at a time, we confirmed our previous observation that CUE was reduced by fungal removal. Our results also show that depending on the microbial community composition, there can be substantial discrepancies between estimated and true microbial growth. Of the numerous implicit assumptions that might be violated, not accounting for the contribution of sources of oxygen other than extracellular water to DNA leads to a consistent underestimation of CUE. We present a framework that allows researchers to evaluate how their experimental conditions may influence their 18O-H2O-based CUE measurements and suggest the parameters that need further constraining to more accurately quantify growth and CUE.

Environmental Sciences & Ecology↗
DOE OSTI2025

Soil biogeochemical properties and metrics of tree-mycorrhizal dominance for a 25-Ha forest in South Central Indiana, USA.

This data package contains a dataset used in the papers “Seeing the forest for all the trees: Mycorrhizal-associated nutrient economies are modulated by stem density and the synchrony between overstory and understory communities” and “Mycorrhizal associations of tree species influence soil nitrogen dynamics via effects on soil acid–base chemistry”. Four csv files are included along with a dataset. The dataset features chemical soil properties for a single sampling campaign within the 25 Ha Lilly-Dickey Woods Smithsonian Forest Global Earth Observatory (ForestGEO) plot in South Central Indiana, USA (ldw_dat_raw.csv). Also included are separate files focused on pH (pH_data.csv), carbon and nitrogen (CN_data.csv), and nitrification rates (Nitrification_data.csv). These variables are commonly associated with the tree-mycorrhizal dominance of forest stands. In these data subsets, each soil variable was matched to a 10 meter radius neighborhood wherein metrics of tree-mycorrhizal dominance (basal area, stem count, importance value, etc.) were calculated. Models between these soil variables and dominance metrics were used to investigate how different assessments of mycorrhizal associated nutrient economies (MANE) capture these relationships. This research was performed as a part of the Smithsonian ForestGEO project. This data package can be used to explore spatial variability in soil chemistry within a mature hardwood forest, or it can be combined with the included tree data, other fine-scale spatial information, or other tree inventory data for the site to evaluate how soil chemistry varies with tree community composition or edaphic or topographic properties.

Craig, Matthew [ORNL] (ORCID:0000000288907920)↗
DOE OSTI2025

Physics Briefing Book: Input for the 2026 update of the European Strategy for Particle Physics

The European Strategy for Particle Physics (ESPP) reflects the vision and presents concrete plans of the European particle physics community for advancing human knowledge in fundamental physics. The ESPP is updated every five-to-six years through a community-driven process. It commences with the submission of specific proposals and other input from the community at large, outlining projects envisioned for the near-, mid-, and long-term future. All submitted contributions are evaluated by the Physics Preparatory Group (PPG), and a preliminary analysis is presented at a Symposium meant to foster a broad community discussion on the scientific value and feasibility of the various ideas proposed. The outcomes of the analysis and the deliberations at the Symposium are synthesized in the current Briefing Book, which provides an important input in the deliberations of the Strategy recommendations by the European Strategy Group (ESG).

de Blas, Jorge [Univ. of Granada (Spain); et al.]↗
DOE OSTI2024

Probing interspecies metabolic interactions within a synthetic binary microbiome using genome-scale modeling

Metabolic interactions within a microbial community play a key role in determining the structure, function, and composition of the community. However, due to the complexity and intractability of natural microbiomes, limited knowledge is available on interspecies interactions within a community. In this work, using a binary synthetic microbiome, a methanotroph-photoautotroph (M-P) coculture, as the model system, we examined different genome-scale metabolic modeling (GEM) approaches to gain a better understanding of the metabolic interactions within the coculture, how they contribute to the enhanced growth observed in the coculture, and how they evolve over time. Using batch growth data of the model M-P coculture, we compared three GEM approaches for microbial communities. Two of the methods are existing approaches: SteadyCom, a steady state GEM, and dynamic flux balance analysis (DFBA) Lab, a dynamic GEM. We also proposed an improved dynamic GEM approach, DynamiCom, for the M-P coculture. SteadyCom can predict the metabolic interactions within the coculture but not their dynamic evolutions; DFBA Lab can predict the dynamics of the coculture but cannot identify interspecies interactions. DynamiCom was able to identify the cross-fed metabolite within the coculture, as well as predict the evolution of the interspecies interactions over time. A new dynamic GEM approach, DynamiCom, was developed for a model M-P coculture. Constrained by the predictions from a validated kinetic model, DynamiCom consistently predicted the top metabolites being exchanged in the M-P coculture, as well as the establishment of the mutualistic N-exchange between the methanotroph and cyanobacteria. The interspecies interactions and their dynamic evolution predicted by DynamiCom are supported by ample evidence in the literature on methanotroph, cyanobacteria, and other cyanobacteria-heterotroph cocultures.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Partnership and Pipeline Office Overview [Slides]

Partnerships ensure a strong Laboratory and support our missions. Partnerships are critical to our success as a Laboratory: community relations, colleges and universities and technical communities, regional and national economic development through industrial partners, DOE Laboratories, and other federal agencies. The Laboratory has many tools to build and enhance partnerships. The Community Programs Office in our Northern New Mexico Region has K-12 educational programs, supports teacher professional development and retention in regional elementary, middle and high schools, and provides community college engagement. The Partnerships and Pipeline Office works with the National Security Education Center (NSEC) which has broad university engagement including New Mexico universities. The Feynman Center for Innovation is involved in 'tech transfer' to innovation asset stewardship. The External Assignments Office shares LANL's technical expertise. The Student and Postdoc Program Offices build our workforce of the future.

96 KNOWLEDGE MANAGEMENT AND PRESERVATION↗
DOE OSTI2020

Establishing a Technical Assistance Network to Build Capacity in Southwest Alaska (Southwest Alaska Energy Network - Final Report)

The Southwest Alaska Municipal Conference (SWAMC) is a non-profit regional membership economic development organization that represents the Aleutian/Pribilof Islands, Bristol Bay, and Kodiak regions of southwest Alaska. SWAMC applied for the DOE-OIE Establishment of an Inter-Tribal Technical Assistance Energy Providers Network grant FOA to work with our partners to provide energy planning and project development technical assistance. The project team was made up of SWAMC, three regional organizations, a management consulting firm, and a panel of technical consultants. SWAMC sub-contracted with the three Alaska Native regional non-profit organizations – Aleutian Pribilof Islands Association (APIA), Bristol Bay Native Association (BBNA), and Kodiak Area Native Association (KANA) – to fund full or partial Regional Energy Coordinator (REC) positions. The project period ran from September 2016 to March 2020. The project goal was to help southwest Alaska regional tribal partners and communities to develop efficient and financially sustainable structures for identifying and developing energy projects that enhance community resiliency and energy sustainability. This project established energy coordinators and management structures in the Aleutian, Bristol Bay, and Kodiak regions to expand technical assistance capacity of regional residents; demonstrate this capacity by advancing energy efficiency, heat, and power supply projects; and secure long-term funding commitments to establish a sustained technical assistance structure. The project team expanded technical assistance capacity of energy coordinators and regional stakeholders in several ways: by providing funding for the SWAMC project manager to attend three Office of Indian Energy trainings; for energy coordinators to attend numerous energy conferences; for utility clerks from several villages to receive one-on-one reporting training on Alaska’s Power Cost Equalization electric subsidy program; and for the Kodiak REC to complete the Arctic Remote Energy Networks Academy and NREL’s Executive Energy Leadership Academy. The energy coordinators demonstrated and shared their increased capacity by hosting several public events: SWAMC hosted two full-day energy workshops in February 2017 and 2018; the Kodiak REC hosted seven Energy Committee meetings for Kodiak stakeholders and gave several presentations at other events; and SWAMC and BBNA organized a Bristol Bay Regional Energy Visioning Session in May 2019. The project team created platforms to both share and request information to involve energy stakeholders in this project, including an energy website, a Facebook group, a periodic newsletter, surveys, mass emails, and paper mailers. An increase in regional capacity was demonstrated through several grant awards, including a $1.2 million USDA grant for Akhiok for an electric distribution infrastructure replacement; an AHFC Kickstarter grant for Aleknagik to audit 2 Tribal and 3 City buildings; and installation of an Air Source Heat Pump demonstration project in Atka. Two communities and one region – Ouzinkie (May 2017), Ugashik (July 2017), and the Bristol Bay region (May 2019) – utilized DOE’s technical assistance services to hold Strategic Energy Planning sessions with NREL and DOE facilitation assistance. And in early 2018, SWAMC established a parallel program, funded through a USDA Energy Audit and Renewable Energy Development grant to provide subsidized energy audits for small businesses in the region. SWAMC and partners have now completed energy audits of over 60 businesses (buildings and fishing vessels) and are currently operating a third round of the USDA program. Fifteen of those business owners have now received additional grant funding to cover 25% of the cost of the energy efficiency upgrades identified in the audit. This technical assistance structure will be sustained beyond DOE grant funding in several forms. As a sign of increased grant writing and project management capacity, the Kodiak Regional Energy Coordinator applied for and received a USDA Community Facilities Technical Assistance and Training grant to continue work begun under this program. Energy coordination tasks have been folded into existing economic development positions at SWAMC and at BBNA, ensuring long-term outreach and support in the region.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗
DOE OSTI2020

Simulations of Laser Experiments to Study the Origin of Cosmic Magnetic Fields

Magnetic fields are ubiquitous in the universe; however, their origin is not fully understood. Cosmologists and astrophysicists have proposed a variety of ways in which small seed magnetic fields could be created. It is widely thought that the much larger values of the cosmic magnetic fields that we observe are a result of the amplification of these seed fields by the nonlinear turbulent dynamo mechanism. Such a mechanism had not yet been demonstrated in a controlled laboratory environment. We conceived experiments designed to demonstrate and study the nonlinear turbulent dynamo mechanism in the laboratory. These experiments characterize the distribution of turbulent energy among the velocity, magnetic field, and density fluctuations, providing a comprehensive picture of the energy cascade in a magnetized, turbulent plasma. The experiments build on the pathfinder experiments we have conducted on the Vulcan laser at the Rutherford-Appleton Laboratory in the UK and the OMEGA laser at Laboratory for Laser Energetics at Rochester. They utilize the high-intensity lasers at the Omega Laser Facility, the National Ignition Facility (NIF) at LLNL and the Laser Megajoule (LMJ) Facility in France – the largest laser facilities in the world. The goal of this project was to design and model the highly demanding experiments through simulation campaigns using FLASH, a highly capable radiation-MHD code we have developed, and large-scale 3D simulations on the Mira supercomputer at ANL. The simulations were vital to ensuring the experiments achieve the strong turbulence and large magnetic Reynolds numbers required for the nonlinear turbulent dynamo mechanism to operate. The simulations were also critical to determining when to fire the diagnostics, since the experiments last tens of nanoseconds but the signals of the strongly amplified magnetic fields last only a few nanoseconds. Finally, high-fidelity, validated FLASH simulations were crucial to interpreting the results of the experiments. By combining theory, experiments, and simulations, we were able to succeed in demonstrating and characterizing the nonlinear turbulent dynamo mechanism. The effort leveraged (1) the emergence of the Flash Center for Computational Science as a leader in numerical modeling of academic High Energy Density Physics (HEDP) experiments; (2) the FLASH code, which has been developed by the Flash Center and is a leadership-class, multi- physics, publicly available community code that has been applied successfully in many laser-driven experiments; (3) the expertise acquired through pathfinder experiments we performed on the Vulcan laser at the Rutherford-Appleton Laboratory in the UK and on the Omega laser facility; (4) the experience we have gained in designing and interpreting these experiments using validated simulations done with FLASH; and (5) the close collaborations we have established with outstanding experimental groups in the US and abroad. The broader impacts of the project are two-fold: (1) the work furthered the transformation of the academic community’s ability to design and analyze HEDP experiments at large laser facilities that is happening through the availability of FLASH and its widespread adoption by the academic community – a community that previously had had limited access to open and validated hydro/MHD simulation tools for HEDP experiments; and (2) the work trained young scientists to design and interpret HEDP experiments using validated simulations – a critical national need.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2020

Sitewide Environmental Impact Statement Site 300 and Arroyo Mocho Lawrence Livermore National Laboratory Alameda and San Joaquin Counties, California (Mid-Term Report)

At the request of Lawrence Livermore National Security (LLNS), Nomad Ecology (Nomad) conducted sensitive botanical resource surveys, and vegetation mapping and classification of the 7,000-acre Lawrence Livermore National Laboratory (LLNL) Experimental Test Site (Site 300) and 17 acres surrounding the Arroyo Mocho pumping station and the access road to the pumping station (Arroyo Mocho). In addition to surveying for sensitive botanical resources, Nomad also compiled existing rare plant and vegetation data provided by LLNL from past monitoring and environmental impact evaluations. The results of these efforts will provide supporting information for a Site-wide Environmental Impact Statement (SWEIS). These surveys were conducted during the months of April – June, and August 2020. Rare plant surveys were scheduled for February and March 2020; however, February surveys were not initiated because the contract for this work was not finalized, and March surveys were cut short due to the timing of the Covid-19 shelter in place. February and March rare plant surveys are scheduled for 2021; therefore, the rare plant survey results in this report should be considered incomplete until the 2021 surveys are conducted. A total of 10 special status plant species were recorded within Site 300 and Arroyo Mocho. Of these 10, three were not previously recorded within the study areas, and include Hospital Canyon larkspur (Delphinium californicum subsp. interius), Jepson’s woolly sunflower (Eriophyllum jepsonii), and Michael’s rein orchid (Piperia michaelii), which all occur at Arroyo Mocho. Special status plant species known from these two sites total 23 rare plant occurrences (populations), which represent an estimated 50,929 rare plant individuals. This total of all special status plant species breaks down to one occurrence of a federally and/or state listed plant species (98 individuals), six occurrences of California Rare Plant Rank (CRPR) 1 & 2 species (49,010 individuals), and 16 occurrences of CRPR 3 & 4 species (1,821 individuals). A total of 35 vegetation communities were mapped at Site 300, of which 20 are considered Sensitive Natural Communities. A total of nine vegetation communities were mapped at Arroyo Mocho, of which two are considered Sensitive Natural Communities.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2021

Ecosystems and Networks Integrated with Genes and Molecular Assemblies (ENIGMA) (Final Scientific/Technical Report, Subcontract Award No. 6953691)

The overarching objective the Baliga lab is to develop a mechanistic understanding of the field relevant metabolic processes underlying community partitioning of respiration pathways and physiological state shifts. In order to dissect how environmental perturbations influence microbial regulatory networks, we have constructed data-driven models that capture the dynamic interplay between abiotic and biotic factors during laboratory simulations. Specifically, we have developed multiple computational models (i.e., cMonkey2, EGRIN 2.0, and multiple genome-scale metabolic models) connecting environmental influence to genome-encoded regulatory programs. In addition, we have generated new tools such as Live Anaerobic Cell Sorting (LAnCS) and Fluidized Bed Reactors (FBRs) to investigate the dynamics of community partitioning of metabolic processes supporting sulfate or nitrate respiration, which are two critical activities observed from the field site at Oak Ridge National Labs (ORNL). This framework of connecting field phenomena with laboratory simulations and computational modeling has created the Environmental Simulations and Modelling (EnvSim) campaign within ENIGMA. The campaign, which spans multiple laboratories across ENIGMA and is led by the Baliga group, has established synthetic communities (SynComs) to discover, characterize, and dissect key microbial processes relevant to field observations, such as emissions of the greenhouse gas nitrous oxide (N 2 O). For example, the EnvSim campaign so far has deduced four potential mechanisms that may account for the N 2 O emissions at the FRC and are currently being investigated by labs across ENIGMA. Denitrification may be driven by complete denitrifiers, however, their NosZ enzymes, which catalyze the final step in denitrification by converting N 2 O to N 2 , may be sensitive at a lower pH. Additionally, the denitrification process could be partitioned among organisms and some may have pH-sensitive NosZ genes. Another factor contributing to variable N 2 O emissions relates to the metal co-factors involved in the denitrification pathway. For instance, excess Cu, Al, Mn, U, Ni, Co, Cu, and/or Cd may have inhibitory effects on multiple enzymatic steps during denitrification, while the enzymatic production of nitrite, the precursor of N 2 O, can be limited by the essential metal Mo. Lastly, abiotic production of N 2 O may occur as a result of chemodenitrification, in which metals like Fe, Mn, and some organic compounds can drive redox reactions that convert nitrogen cycle intermediates to N 2 O under the right conditions. Current investigations and analyses have generated multiple transcriptomic profiles aiding the refinement of new metabolic and gene regulatory network model for our denitrifying SynCom. In sum, the previous funding cycle has generated 33 peer-reviewed publications spanning predictive network biology to co-operativity of mutualistic interspecies interactions of evolved communities. Our integration of multiple omics datasets and the development of new network modelling tools has revealed important insights that can explain field observed phenomenon and generated new hypotheses to be investigated in the field.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗