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DOE OSTI2021

RivGraph: Automatic extraction and analysis of river and delta channel network topology

River networks sustain life and landscapes by carrying and distributing water, sediment, and nutrients throughout ecosystems and communities. At the largest scale, river networks drain continents through tree-like tributary networks. At typically smaller scales, river deltas and braided rivers form loopy, complex distributary river networks via avulsions and bifurcations.In order to model flows through these networks or analyze network structure, the topology, or connectivity, of the network must be resolved. Additionally, morphologic properties of each river channel as well as the direction of flow through the channel inform how fluxes travel through the network’s channels. Riv Graphis a Python package that automates the extraction and characterization of river channel networks from a user-provided binary image, or mask, of a channel network (Fig. 1). Masks may be derived from (typically remotely-sensed) imagery, simulations, or even hand-drawn. RivGraph will create explicit representations of the channel network by resolving river centerlines as links, and junctions as nodes. Flow directions are solved for each link of the network without using auxiliary data, e.g., a digital elevation model (DEM). Morphologic properties are computed as well, including link lengths, widths, sinuosities, branching angles,and braiding indices. If provided,RivGraph will preserve georeferencing information of the mask and will export results as ESRI shapefiles, GeoJSONs, and GeoTIFFs for easy import into GIS software.RivGraph can also return extracted networks as networkx objects for convenient interfacing with the full-featured networkx package (Hagberg et al., 2008). Finally, RivGraph offers a suite of topologic metrics that were specifically designed for river channel network analysis (Tejedor et al., 2015b).

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2020

Preliminary Assessment of Potential for Wind Energy Technology on the Turtle Mountain Band of Chippewa Reservation

Wind energy can provide renewable and sustainable electricity to Native American reservations, including rural homes, and power schools and businesses on reservations. It can also provide tribes with a source of income and economic development. The purpose of this paper is to determine the potential for deploying community and utility-scale wind renewable technologies on the Turtle Mountain Band of Chippewa tribal lands. Ideal areas for wind technology development were investigated based on annual wind resources, terrain, land usage, and other factors such as culturally sensitive sites. The result is a preliminary assessment of wind energy potential on Turtle Mountain lands, which can be used to justify further investigation and investment into determining the feasibility of future wind technology projects.

17 WIND ENERGY↗

DOE OSTI2020

Smart technologies enable homes to be efficient and interactive with the grid

Oak Ridge National Laboratory researchers compare two different approaches to test how advanced, energy-efficient building technologies such as smart thermostats, heat pump water heaters, and advanced heat pump HVAC (heating, ventilation and air conditioning) can be optimized within a home and connected at a neighborhood-scale load to a community microgrid in the Alabama Power Smart Neighborhood located in Hoover. Working with Southern Company and Alabama Power, ORNL researchers are pioneering that future where smart homes and smart neighborhoods can benefit both homeowners and utilities, by reducing energy consumption by 44% and peak demand by 34%.This project is one of two neighborhoods in the U.S Department of Energy’s (DOE’s) Connected Neighborhood project, supported by Building Technologies Office , where ORNL researchers leverages DOE investment in micro-grids and responsive, flexible building loads research to improve grid reliability – a goal of DOE’s Grid-interactive Efficient Buildings (GEB) Initiative. Researchers control the neighborhood and microgrid to enable utilities achieve their desired load and cost profiles while ensuring the comfort of homeowners in the Smart Neighborhood. This transactive control approach maximizes the utilization of technical resources of the microgrid and controllable loads, while reducing costs for both the homeowners and Alabama Power. These tests partially seek to determine a more precise range of tolerance with respect to occupant comfort as researchers work to facilitate customer acceptance and perception of new building technologies that enable energy savings.

24 POWER TRANSMISSION AND DISTRIBUTION↗

DOE OSTI2022

Preliminary Assessment of Potential for Wind Energy Technology on the Turtle Mountain Band of Chippewa Reservation

Wind energy can provide renewable, sustainable electricity to rural Native homes and power schools and businesses. It can even provide tribes with a source of income and economic development. The purpose of this research is to determine the potential for deploying community and utility-scale wind renewable technologies on Turtle Mountain Band of Chippewa tribal lands. Ideal areas for wind technology development were investigated, based on wind resources, terrain, land usage, and other factors. This was done using tools like the National Renewable Energy Laboratory Wind Prospector, in addition to consulting tribal members and experts in the field. The result was a preliminary assessment of wind energy potential on Turtle Mountain lands, which can be used to justify further investigation and investment into determining the feasibility of future wind technology projects.

17 WIND ENERGY↗

DOE OSTI2025

Solar and Battery Storage Permitting and Siting Requirements - Solar Prize Round 7 (CRADA Final Report)

The purpose of this project is to identify local zoning ordinances, state permitting requirements, federal regulatory bottlenecks throughout the development process, and the potential to use Large Language Models (LLM) and aggregate permitting and interconnection data for commercial and industrial (C&I), community, and utility-scale solar photovoltaic (PV) and battery storage projects.

14 SOLAR ENERGY↗

DOE OSTI2021

Perspectives of Open-Air Processing to Enable Perovskite Solar Cell Manufacturing

We report high throughput open-air processing techniques for the scalable production of all device and barrier layers for perovskite photovoltaics (PV). This work discusses and resolves some of the most formidable barriers to module-level scaling that the perovskite community has been facing. Our advanced technoeconomic manufacturing analysis indicates that vacuum-based processes with high capital expenditures (CapEx) and low throughputs dominate the cost of production. Open-air fabrication methods offer low CapEx routes to manufacturing, but achieving reproducibility in ambient conditions with varying relative humidity has been a persistent challenge. The use of rapid processing methods with plasma curing to convert films from the solution-state enables reproducibility, moisture immunity, and the highest perovskite PV efficiency produced in open-air. These methods are readily translatable to in-line processing where layers are sequentially deposited without the need for lengthy post-annealing steps that reduce throughput and involve additional equipment. Significant progress is demonstrated in reduced manufacturing costs as perovskites contend as a commercially viable next-generation thin film PV technology.

14 SOLAR ENERGY↗

DOE OSTI2023

Synergistic interactions between anammox and dissimilatory nitrate reducing bacteria sustains reactor performance across variable nitrogen loading ratios

Anaerobic ammonium oxidizing (anammox) bacteria are utilized for high efficiency nitrogen removal from nitrogen-laden sidestreams in wastewater treatment plants. The anammox bacteria form a variety of competitive and mutualistic interactions with heterotrophic bacteria that often employ denitrification or dissimilatory nitrate reduction to ammonium (DNRA) for energy generation. These interactions can be heavily influenced by the influent ratio of ammonium to nitrite, NH 4 + :NO 2 - , where deviations from the widely acknowledged stoichiometric ratio (1:1.32) have been demonstrated to have deleterious effects on anammox efficiency. Thus, it is important to understand how variable NH 4 + :NO 2 - ratios impact the microbial ecology of anammox reactors. We observed the response of the microbial community in a lab scale anammox membrane bioreactor (MBR) to changes in the influent NH 4 + :NO 2 - ratio using both 16S rRNA gene and shotgun metagenomic sequencing. Ammonium removal efficiency decreased from 99.77 ± 0.04% when the ratio was 1:1.32 (prior to day 89) to 90.85 ± 0.29% when the ratio was decreased to 1:1.1 (day 89–202) and 90.14 ± 0.09% when the ratio was changed to 1:1.13 (day 169–200). Over this same timespan, the overall nitrogen removal efficiency (NRE) remained relatively unchanged (85.26 ± 0.01% from day 0–89, compared to 85.49 ± 0.01% from day 89–169, and 83.04 ± 0.01% from day 169–200). When the ratio was slightly increased to 1:1.17–1:1.2 (day 202–253), the ammonium removal efficiency increased to 97.28 ± 0.45% and the NRE increased to 88.21 ± 0.01%. Analysis of 16S rRNA gene sequences demonstrated increased relative abundance of taxa belonging to Bacteroidetes, Chloroflexi, and Ignavibacteriae over the course of the experiment. The relative abundance of Planctomycetes, the phylum to which anammox bacteria belong, decreased from 77.19% at the beginning of the experiment to 12.24% by the end of the experiment. Analysis of metagenome assembled genomes (MAGs) indicated increased abundance of bacteria with nrfAH genes used for DNRA after the introduction of lower influent NH 4 + :NO 2 - ratios. The high relative abundance of DNRA bacteria coinciding with sustained bioreactor performance indicates a mutualistic relationship between the anammox and DNRA bacteria. Understanding these interactions could support more robust bioreactor operation at variable nitrogen loading ratios.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2023

Local Weather Station Design and Development for Cost-Effective Environmental Monitoring and Real-Time Data Sharing

Current weather monitoring systems often remain out of reach for small-scale users and local communities due to their high costs and complexity. This paper addresses this significant issue by introducing a cost-effective, easy-to-use local weather station. Utilizing low-cost sensors, this weather station is a pivotal tool in making environmental monitoring more accessible and user-friendly, particularly for those with limited resources. It offers efficient in-site measurements of various environmental parameters, such as temperature, relative humidity, atmospheric pressure, carbon dioxide concentration, and particulate matter, including PM 1, PM 2.5, and PM 10. The findings demonstrate the station’s capability to monitor these variables remotely and provide forecasts with a high degree of accuracy, displaying an error margin of just 0.67%. Furthermore, the station’s use of the Autoregressive Integrated Moving Average (ARIMA) model enables short-term, reliable forecasts crucial for applications in agriculture, transportation, and air quality monitoring. Furthermore, the weather station’s open-source nature significantly enhances environmental monitoring accessibility for smaller users and encourages broader public data sharing. With this approach, crucial in addressing climate change challenges, the station empowers communities to make informed decisions based on real-time data. In designing and developing this low-cost, efficient monitoring system, this work provides a valuable blueprint for future advancements in environmental technologies, emphasizing sustainability. The proposed automatic weather station not only offers an economical solution for environmental monitoring but also features a user-friendly interface for seamless data communication between the sensor platform and end users. This system ensures the transmission of data through various web-based platforms, catering to users with diverse technical backgrounds. Furthermore, by leveraging historical data through the ARIMA model, the station enhances its utility in providing short-term forecasts and supporting critical decision-making processes across different sectors.

54 ENVIRONMENTAL SCIENCES↗

NASA NTRSDate not supplied

Assessing the Viability of Using GEOS-Forecast Product for Landslides Forecasting: A Step Toward Early Warning System

Landslides across the globe are mostly triggered by extreme rainfall events affecting infrastructure, transportation and livelihoods. The risks are rarely quantified due to lack of data, analytical skills and limited modeling techniques. Knowledge of local to global scale landslide risks provides communities and national agencies the ability to adapt disaster management practices to mitigate and recover from these hazards. In order to minimize the risks and improve characterization of community resilience to landslides, it is vital to have reliable information about the factors triggering landslides such as rainfall, well ahead in time. Forecasting potential landslide activity and impacts can be achieved through reliable precipitation forecast models. However, it is challenging because of the temporal and spatial variability of precipitation, an important factor in triggering landslides. Evaluation of the precipitation field, associated errors, and sampling uncertainties is integral for development of efficient and reliable landslide forecasting and early warning system. This study develops a methodology to assess the viability of using a precipitation field provided by a global model and its potential integration in the landslide forecasting system. The study focuses on the comparison between the IMERG (Integrated Multi-satellitE Retrievals for Global Precipitation Mission) and GEOS (NASA Goddard Earth Observing System)-Forecast product over contiguous United States (CONUS). GEOS model assimilates new observations every 6 hours, at 00, 06, 12, and 18 UTC. The framework is tested on the GEOS-Forecast Model initialized at 00 UTC using daily IMERG early product as reference using both categorical and continuous statistics. The categorical statistics includes the probability of detection (POD), success ratio (SR), critical success index (CSI), and the hit bias. Continuous statistics such as correlation, normalized standard deviation, and root-mean-square error are also evaluated. Overall, GEOS-Forecast precipitation field over the analysis period (~1 year) show underestimation with respect to IMERG early for the daily accumulated rainfall. However, the probability distribution function and cumulative distribution function of both show similar patterns. In terms of correlations, POD, SR, CSI, hit bias, the performance varies with respect to the rainfall threshold used.

Sana Khan↗

NASA NTRSDate not supplied

Retrospectives: Current State of Knowledge on the Intersection of Spaceflight Stressors and Microbial Risks to Crew and Craft

OVERVIEW The spaceflight environment has several unique stressors that affect the health of both the crew and the spacecraft. An area of continued, albeit incomplete, study is the interaction of these stressors on microbial populations inherent to both astronauts and spacecraft surfaces and systems. A primary concern is the potential for the spaceflight environment to perturb the phenotype of these populations towards negative outcomes for crew and craft. In order to effectively mitigate these potential risks, they must first be characterized. We performed a retrospective literature analysis to assess the current state of knowledge regarding the affects of ionizing radiation and elevated CO2 on relevant microbial populations. The results of these retrospectives will guide next steps in the decisions of what (if any) further studies should be pursued and to guide decisions of the need for countermeasures. STRESSORS Ionizing radiation. The health risk involved with increased exposure to cosmic radiation has been studied in crew for 35+ years, with human health and cancer risk being the main focus. However, space radiation could also affect both the resident microorganisms aboard the ISS and the normal, healthy astronaut microbiomes that are of direct concern for crew health. A retrospective review of over 250 publications was accomplished looking at the impact of cumulative ionizing radiation doses lower than 3 Gy (chronic or acute) on microbial populations. Elevated CO2. The health risk involved with elevated atmospheric CO2 in spacecraft, primarily focusing on human toxicological risks, is understudied. The current Spaceflight Maximum Allowance Concentration for 24-hour average CO2 is 0.4% (3 mm Hg), which is significantly higher than terrestrial levels (0.04%). Whether these elevated ambient CO2 levels aboard spacecraft influence the diversity and phenotypic responses of the resident microbial communities from both the spacecraft environment (air, surface, water) and crew members (gut, nasal, skin microbiomes) is not known. A retrospective review was accomplished looking at the impact of chronic CO2 exposure up to 0.7% (5 mm Hg) for up to 6 months and acute exposure up to 2.6% (20 mm Hg) for up to 24 hours. CONCLUSIONS: MICROBIOME OF THE BUILT ENVIRONMENT The microbiome of the built spacecraft environment has been sampled consistently over the course of human spaceflight and significant advancements have been made in identifying microbial populations on the ISS. The dominant source of microbes on spacecraft surfaces are human-derived. Once in the spacecraft built environment, the extreme environment selects for features that enhance survival. While efforts to understand potential antibiotic resistance and pathogenicity of ISS isolates is robust, there is little to no understanding of which spaceflight environmental stressors, to include ionizing radiation or elevated CO2, drive the evolutionary trajectory of spacecraft-associated microbial populations. CONCLUSIONS: MICROBE-HOST INTERACTIONS The host-microbiome field has emerged as an important factor in human health on Earth as well in spaceflight. The field is struggling with the complexity of the system under investigation as there is substantial taxonomic and functional heterogeneity in these communities, making it difficult to establish clear stimulus-response dynamics. Taxonomic characterization is the norm; however, the functional role of each community member is key to linking environmental perturbations to potential dysbiosis. For both ionizing radiation and elevated CO2, the likely target of the perturbation is the host tissue, not the microbes themselves.. Any resulting changes to the microbial community composition and/or function is likely a result of adapting to those changes in the host physiology. RECOMMENDATIONS Emphasize functional characterization as opposed to taxonomic characterization of microbial communities. Increase the number of investigations using chronic, spaceflight-relevant doses of ionizing radiation. MoBE studies should move away from observational studies towards predictive modeling of community dynamics. Continue to develop scale-down models, such as tissues-on-a-chip & defined microbial communities. Focus on the crew response to elevated CO2 over MoBE considerations. Assess how direct contact with the hypercapnic environment affects skin microbiome dynamics.

retrospective↗

NASA NTRSDate not supplied

Retrospectives: Intersection of Spaceflight Stressors and Microbial Risk to Crew and Craft

OVERVIEW The spaceflight environment has several unique stressors that affect the health of both the crew and the spacecraft. An area of continued, albeit incomplete, study is the interaction of these stressors on microbial populations inherent to both astronauts and spacecraft surfaces and systems. A primary concern is the potential for the spaceflight environment to perturb the phenotype of these populations towards negative outcomes for crew and craft. In order to effectively mitigate these potential risks, they must first be characterized. We performed a retrospective literature analysis to assess the current state of knowledge regarding the affects of ionizing radiation and elevated CO2 on relevant microbial populations. The results of these retrospectives will guide next steps in the decisions of what (if any) further studies should be pursued and to guide decisions of the need for countermeasures. STRESSORS Ionizing radiation. The health risk involved with increased exposure to cosmic radiation has been studied in crew for 35+ years, with human health and cancer risk being the main focus. However, space radiation could also affect both the resident microorganisms aboard the ISS and the normal, healthy astronaut microbiomes that are of direct concern for crew health. A retrospective review of over 250 publications was accomplished looking at the impact of cumulative ionizing radiation doses lower than 3 Gy (chronic or acute) on microbial populations. Elevated CO2. The health risk involved with elevated atmospheric CO2 in spacecraft, primarily focusing on human toxicological risks, is understudied. The current Spaceflight Maximum Allowance Concentration for 24-hour average CO2 is 0.4% (3 mm Hg), which is significantly higher than terrestrial levels (0.04%). Whether these elevated ambient CO2 levels aboard spacecraft influence the diversity and phenotypic responses of the resident microbial communities from both the spacecraft environment (air, surface, water) and crew members (gut, nasal,skin microbiomes) is not known. A retrospective review was accomplished looking at the impact of chronic CO2 exposure up to 0.7% (5 mm Hg) for up to 6 months and acute exposure up to 2.6% (20 mm Hg) for up to 24 hours. CONCLUSIONS: MICROBIOME OF THE BUILT ENVIRONMENT The microbiome of the built spacecraft environment has been sampled consistently over the course of human spaceflight and significant advancements have been made in identifying microbial populations on the ISS. The dominant source of microbes on spacecraft surfaces are human-derived. Once in the spacecraft built environment,the extreme environment selects for features that enhance survival. While efforts to understand potential antibiotic resistance and pathogenicity of ISS isolates is robust, there is little to no understanding of which spaceflight environmental stressors, to include ionizing radiation or elevated CO2, drive the evolutionary trajectory of spacecraft-associated microbial populations. CONCLUSIONS: MICROBE-HOST INTERACTIONS The host-microbiome field has emerged as an important factor in human health on Earth as well in spaceflight. The field is struggling with the complexity of the system under investigation as there is substantial taxonomic and functional heterogeneity in these communities, making it difficult to establish clear stimulus-response dynamics.Taxonomic characterization is the norm; however, the functional role of each community member is key to linking environmental perturbations to potential dysbiosis. For both ionizing radiation and elevated CO2, the likely target of the perturbation is the host tissue, not the microbes themselves.. Any resulting changes to the microbial community composition and/or function is likely a result of adapting to those changes in the host physiology. RECOMMENDATIONS Emphasize functional characterization as opposed to taxonomic characterization of microbial communities.Increase the number of investigations using chronic, spaceflight-relevant doses of ionizing radiation. MoBE studies should move away from observational studies towards predictive modeling of community dynamics. Continue to develop scale-down models, such as tissues-on-a-chip & defined microbial communities. Focus on the crew response to elevated CO2 over MoBE considerations. Assess how direct contact with the hypercapnic environment affects skin microbiome dynamics.

Countermeasures↗

NASA NTRSDate not supplied

Open Source Application of Fusing Aerosol Products from GEO and LEO Satellites

Retrieving aerosol optical depths (AODs) from sun-synchronous polar orbiting (aka low earth orbit, LEO) satellites, such as MODISs, and VIIRSs, OMI, TROPOMI, etc, has become well-established as a tool for extracting information on particulate matter (PM) and related processes in the atmosphere. However, with recently launched geostationary satellites (GEO), such as GOES-16/17/18, and Himawari-8/9, and Meteosat Third Generation (MTG) they provide a much higher temporal resolution (order of 10 minutes), typically an image once or more per hour during daylight compared to LEO once per day. By combining these observations, we may be able to characterize the diurnal cycle of global AOD at the local, regional and global scale. While the science community is still exploring the new data from GEO observations, we have been thinking about how to properly combine/merge/fuse those data considering differences in their spatial and temporal resolutions. However, this poses a “Big Data” challenge. The big data challenge is not just about data storage, but also about data discoverability, and accessibility, and even more, about data migration/mirroring in the cloud-computing environment. This paper is merely showing some of the efforts and approaches we have attempted in fusing six satellites’ Level 2 aerosol data (three are from GEO (GOES-16/17 and Himawari-8), and the other three are from LEO (TERRA/MODIS, AQUA/MODIS, SNPP-VIIRS) from Dark Target (DT) aerosol retrieval algorithm. Having the on-demand capability of fusing remote sensing products onto the desired temporal and spatial domain enables researchers and application practitioners to better manipulate and work with satellite and sensor data. It is our hopeWe hope that by making such an open-source package, and the accompanying functionality, the scientific community will be granted easier access to aerosol data processing resources. The MEaSUREs Program (Making Earth System Data Records for Use in Research Environments) expands our understanding of the Earth's current system through atmospheric and surface measurements. In an effort to aid the scientific research component and improve open source methods, this project developed Python code for fusing six satellite Level 2 aerosol data (three are from geostationary satellites (GEO), and the other three are from low earth orbital satellites (LEO)) from Dark Target Aerosol Retrieval Algorithm.

Jennifer Wei↗

DOE OSTI2021

Heat Based Power Augmentation for Modular Pumped Hydro Storage in Smart Buildings Operation

In the U.S., building sector is responsible for around 40% of total energy consumption and contributes about 40% of carbon emissions since 2012. Within the past several years, various optimization models and control strategies have been studied to improve buildings energy efficiency and reduce operational expenses under the constraints of satisfying occupants’ comfort requirements. However, the majority of these studies consider building electricity demand and thermal load being satisfied by unidirectional electricity flow from the power grid or on-site renewable energy generation to electrical and thermal home appliances. Opportunities for leveraging low grade heat for electricity have largely been overlooked due to impracticality at small scale. In 2016, a modular pumped hydro storage technology was invented in Oak Ridge National Laboratory, named Ground Level Integrated Diverse Energy Storage (GLIDES). In GLIDES, employing high efficiency hydraulic machinery instead of gas compressor/turbine, liquid is pumped to compress gas inside high-pressure vessel creating head on ground-level. This unique design eliminates the geographical limitation associated with existing state of the art energy storage technologies. It is easy to be scaled for building level, community level and grid level applications. Using this novel hydro-pneumatic storage technology, opportunities for leveraging low-grade heat in building can be economical. In this research, the potential of utilizing low-grade thermal energy to augment electricity generation of GLIDES is investigated. Since GLIDES relies on gas expansion in the discharge process and the gas temperature drops during this non-isothermal process, available thermal energy, e.g. from thermal storage, Combined Cooling, Heat and Power system (CCHP), can be utilized by GLIDES to counter the cooling effect of the expansion process and elevate the gas temperature and pressure and boost the roundtrip efficiency. Several groups of comparison experiments have been conducted and the experimental results show that a maximum 12.9% cost saving could be achieved with unlimited heat source for GLIDES, and a moderate 3.8% cost improvement can be expected when operated coordinately with CCHP and thermal energy storage in a smart building.

Chen, Yang↗

DOE OSTI2024

Abstract for CRADA between Mati Car bon PBC and NETL

The National Energy Technology Laboratory (NETL) will assist Mati Carbon PBC (participant) in the design and execution of their community benefits plan (CBP) for scaling Enhanced Rock Weathering (ERW) carbon dioxide removal (CDR) in Arkansas. ERW involves spreading finely crushed rocks in agricultural fields to speed up the dissolution and release of certain minerals that amend soil acidity, replenish soil nutrients, and simultaneously converting CO 2 from the atmosphere to Dissolved Inorganic Carbon (DIC). ERW not only removes CO 2 from the atmosphere but also has the potential to generate co-benefits for famers through cost reductions and increased crop yields. The collaboration between NETL and Mati Carbon, PBC (participant) will entail a detailed review of the economic, environmental and community impact of ERW in agricultural settings. This review will guide all project related decisions. It will provide a better understanding of the scale of these potential co-benefits and quantify community needs that ERW can address.

54 ENVIRONMENTAL SCIENCES↗

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 OSTI2024

pnnl-predictive-phenomics/csc031-gem

Genome-Scale Metabolic Model of CarbStor Community member Microbacterium (csc031) Continuous Validation with Memote These repositories contain the continuous validation environment for an organism-specific genome-scale metabolic model (GEM) using Memote. Memote is a software tool that provides a suite of tests to ensure the quality and consistency of metabolic models. By integrating Memote into a continuous integration (CI) workflow, we can automatically validate updates to the GEM, ensuring that model modifications improve or maintain the model's integrity

McNaughton, Andrew [@PNNL]↗

DOE OSTI2024

pnnl-predictive-phenomics/csc009-gem

Genome-Scale Metabolic Model of CarbStore Community member Curtobacterium (csc009) Continuous Validation with Memote These repositories contain the continuous validation environment for an organism-specific genome-scale metabolic model (GEM) using Memote. Memote is a software tool that provides a suite of tests to ensure the quality and consistency of metabolic models. By integrating Memote into a continuous integration (CI) workflow, we can automatically validate updates to the GEM, ensuring that model modifications improve or maintain the model's integrity

Lin, Tesia↗

DOE OSTI2022

Substantial differences in soil viral community composition within and among four Northern California habitats

Abstract Viruses contribute to food web dynamics and nutrient cycles in diverse ecosystems, yet the biogeographical patterns that underlie these viral dynamics are poorly understood, particularly in soil. Here, we identified trends in soil viral community composition in relation to habitat, moisture content, and physical distance. We generated 30 soil viromes from four distinct habitats (wetlands, grasslands, woodlands, and chaparral) by selectively capturing virus-sized particles prior to DNA extraction, and we recovered 3432 unique viral ‘species’ (dsDNA vOTUs). Viral communities differed significantly by soil moisture content, with viral richness generally higher in wet compared to dry soil habitats. However, vOTUs were rarely shared between viromes, including replicates <10 m apart, suggesting that soil viruses may not disperse well and that future soil viral community sampling strategies may need to account for extreme community differences over small spatial scales. Of the 19% of vOTUs detected in more than one virome, 93% were from the same habitat and site, suggesting greater viral community similarity in closer proximity and under similar environmental conditions. Within-habitat differences indicate that extensive sampling would be required for rigorous cross-habitat comparisons, and results highlight emerging paradigms of high viral activity in wet soils and soil viral community spatial heterogeneity.

Durham, Devyn M.↗