Results for “Taxonomy” — Page 11

DOE OSTI2022

NPD Classification Tools – User Guide NPD Explorer and NPDamCAT Apps

The existing infrastructure at non-powered dams (NPDs) presents a variety of opportunities from generating electricity and economic value to the myriad services they provide. However, it also presents a significant challenge because aging structures must be maintained, and changes to the ecosystems and river systems by NPDs must be managed. The various stakeholders interested in these opportunities and challenges require varying information about NPDs; in many cases, interest in NPDs can extend across the entire population of dams. Even when interest is more narrowly focused on an individual dam or a small subset of dams, understanding how these dams relate to the broader context of NPD infrastructure can be important. As noted in TM 2021/2155, “Each NPD has unique characteristics describing its design, operation, environmental impacts, social impacts, and economic potential. The large number of dams, the diversity of interests related to dams, the variety of dam characteristics, and the types of data required to describe dams all pose major challenges to an analysis of the entire dam population." This user guide describes two web-based tools that facilitate exploration of dams from a variety of perspectives: the NPD Explorer and the NPD Custom Analysis and Taxonomy (NPDamCAT). These tools facilitate access to information about dams and help users interact with the information, making small- to large-scale analyses more convenient for a broad set of stakeholders.

13 HYDRO ENERGY↗

DOE OSTI2022

US Fallout Shelter

Being indoors (sheltering) reduces radiation exposures resulting from nuclear fallout or a power-plant accident. However, most US building types, particularly non-residential buildings, lack quantitative estimates. We provide here a high-level modeling analysis of modern US building protection based on a novel radiation protection building attribute taxonomy, a new building protection model, compilation of prior experimental results, and nationally representative building survey data. This approach provides a consistent, quantitative understanding of US building protection and, when combined with the distribution of people among different buildings, can assist in selecting emergency response strategies. We find that indoor radiation protection varies by orders of magnitude. Most people in non-residential buildings are adequately protected, particularly below ground or in the building center. Residential buildings are less protective and those with lighter weight walls lack adequate, above ground protection. This work also highlights key areas where further investigation will improve the current results. These include the improving the understanding of residential basement protection, additional experimental data on non-residential buildings (particularly schools and industrial buildings), and the frequency of brick veneer and stucco exterior residential buildings.

61 RADIATION PROTECTION AND DOSIMETRY↗

DOE OSTI2022

Exploring New Ways to Classify Industries for Energy Analysis and Modeling

As the US moves closer to embracing a net zero greenhouse gas emissions position, combustion processes outside the power sector are becoming urgent concerns. Industry is an important end user of energy and relies on fossil fuels used directly for process heating and as feedstocks for a diverse range of applications. Fuel and energy use by industry is heterogeneous, meaning that even a single product group can vary broadly in its production routes and associated energy usage. In the US, the North American Industry Classification System (NAICS) serves as the basis for data collection and reporting. In turn, data based on NAICS is the foundation of most US energy modeling. Thus, the effectiveness of NAICS at representing energy use is a limiting condition for plans to improve energy efficiency and alternatives to fossil fuels in industry. Facility-level data to build more detail into heterogeneous sectors is scarce. This work explores alternative classification schemes for industry based on energy use characteristics, and provides a validation of an approach to make facility-level energy use estimates based on publicly available data from the greenhouse gas reporting program. First, several approaches to industrial taxonomies and their usefulness for industrial energy modeling are summarized. Data from Industrial Assessment Centers is analyzed using unsupervised machine learning techniques to detect clusters. Cladistics, an approach from biology, is adapted to energy and process characteristics of industries. A cladogram is presented for evolutionary directions in the iron and steel sector. Cladograms are a promising tool for constructing scenarios and summarizing directions of sectoral innovation. Finally, validation is performed for facility-level energy estimates from the US EPA Greenhouse Gas Reporting Program. This validation assists in making this data source available for use in energy modeling. Together, this work explores alternative approaches for categorizing industries in a way that aids understanding energy use, and presenting pathways for the future.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗

DOE OSTI2023

Hybrid Tandem Photovoltaics

Tandem solar cell structures are the only strategy demonstrated to surpass the detailed balance efficiency limit of high-quality single-junction solar cells. To continue to improve the efficiencies of cost-effective terrestrial solar power, hybrid tandems of dissimilar subcells are being considered by many around the world, especially designs that incorporate silicon solar cells as a bottom subcell. In this project, we studied a wide variety of tandem design possibilities including those with three-terminal (3T) and four-terminal (4T) configurations. The use of 3T and 4T designs could be useful for efficient and economical hybrid tandem designs that utilize the best available subcell materials such as emerging perovskite materials. Three-terminal configurations, in particular, have not been sufficiently studied previously. We have laid the foundational groundwork in this project for understanding the operation of 3T tandems: developing a taxonomy for naming, a methodology for measuring and interconnecting, and models for simply characterizing 3T tandems. Electrical and optical subcell coupling between the subcells was also measured and modeled. An important part of this work was the fabrication of novel example tandem structures, including 4T GaAs/Si, 3T GaInP/Si, 3T GaAs/Si, and 3T GaInP/GaAs devices. Using these high-quality tandem cells, we have been able to clearly demonstrate the achievability of high-efficiencies, and subtle physical effects such as photon recycling and luminescent coupling. We have developed and demonstrated essential building-block tools such as transparent conductive adhesives (TCA) and 3T silicon bottom cells with interdigitated back contacts (IBC) that can also be used in many other tandem designs. We have tested the reliability of these tools and devices under standardized testing and outdoor measurements. We have found 4T GaAs/Si tandems to be relatively straightforward to fabricate and robust in real-world outdoor conditions. While we have demonstrated working hybrid 3T III-V/TCA/Si IBC tandems, we experienced low yields even with our best process flows yet. Further work is still needed to improve the processing yield of these devices. We therefore also created tandem cells using an all-III-V 3T tandem process which was very robust with high yields, allowing for the creation of voltage-matched strings in many different configurations using 8 nearly identical 3T tandems. Using these robust 3T tandem examples, we were able measure and precisely characterize 3T tandem behaviors to predict their operation under changing spectrum and temperature. The optoelectronic equivalent-circuit model was shown to be very general and applicable to hybrid tandems, and encompassed the operation 3T Si IBC cells. This general model has been distributed to the public in as open-source Python-based software called PVcircuit. We have calculated the implications of these new tandem device designs on the real-world energy production and shown how the relative performance of different tandem configurations is situational and can be engineered using the tools developed here.

14 SOLAR ENERGY↗

DOE OSTI2023

The Value of Sharing and Consolidating Critical Community, Electricity, and Natural Hazard Information

The California Public Utilities Commission (CPUC) sought support for the development of database schema specifications for a bi-directional data portal that would foster cross-jurisdictional collaboration necessary to improve resilient energy infrastructure planning processes. This technical assistance activity involved Berkeley Lab researchers reviewing 34 local/tribal government hazard mitigation plans to assess (1) the natural hazards that communities are most concerned about; (2) the variety of–and terminology used to describe–critical community infrastructure; and (3) the availability of GIS information that could be incorporated into CPUC-mandated "Microgrid Planning Portals". In addition, we develop a common, but generic data taxonomy showing what fields to collect to encourage consolidating and sharing of this information in the future. Finally, we partnered with the Bishop Paiute tribal government to demonstrate the value of combining electricity infrastructure, natural hazard layers, and critical community infrastructure into a series of maps. The project demonstrated that a single system containing both electric utility and community infrastructure data—as well as information about natural hazards—will help the state of California, the IOUs, first responders, and long-term planners better prepare for—and thus lower their exposure to these ongoing and emerging hazards. The project also identified a number of challenges that will need to be overcome before it is possible to stand up a single system to display this information.

24 POWER TRANSMISSION AND DISTRIBUTION↗

DOE OSTI2024

Using a systems biology approach to describe the role of dissimilatory phosphite oxidation in the global phosphorus cycle

We investigated the role of redox reactions in the global phosphorous (P) cycle. We identified novel microbial processes responsible for oxidation of reduced phosphorous in the form of phosphite producing bioavailable phosphate. We identified central tenets that define microbial dissimilatory phosphite oxidation (DPO) and the breadth of the taxonomy of DPO microorganisms (DPOM). We demonstrated that this metabolism is vertically evolved from 3.8 GYA contemporaneously with anoxygenic phototrophy. We further demonstrate its occurrence on extant Earth as a primary mechanism driving a phosphorous redox cycle. Finally, we showed that this metabolism is environmentally maintained by the newly described autotrophic Phosphitivorax genus which rely on the reductive glycine pathway for carbon fixation. Our results demonstrate that these species are involved in a complex nutrient-dependent symbiotic relationship with their community in which they provide the fixed carbon to support the heterotrophic community and in return receive prerequisite corrinoids to maintain their activities.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2024

Increasing Reliability and Safety of Hydrogen Components - Reliability Data Collection

Come learn about the new Hydrogen Component Reliability Database (HyCReD) and participate in discussions on hydrogen component reliability data collection, collaboration, and analysis. Funded by the U.S. Department of Energy's Office of Energy Efficiency and Renewable Energy under the Hydrogen and Fuel Cell Technologies Office, HyCReD is a collaborative project between the National Renewable Energy Laboratory, the University of Maryland, and hydrogen stakeholders to improve safety reliability for hydrogen facilities by integrating risk reduction methodologies and component reliability data taxonomies that support hydrogen infrastructure failure rate analysis.

component↗

DOE OSTI2026

Simplifying Geospatial Workflows with GeoGridFusion

Growing demands to understand PV deployment and reliability across an expanding range of climates, along with increasing computational power, are driving the need for simplified computing tools that support large-scale analysis and geospatial workflows. While existing open-source libraries and PV system modeling tools offer extensive collections of empirical and physical models, they often lack the ability to scale to large geospatial datasets. The tool presented here, GeoGridFusion, enables PV modelers to store and utilize gridded geospatial data from sources such as NSRDB, PVGIS, and others. GeoGridFusion harmonizes diverse datasets, taxonomies, and nomenclatures, and includes utilities that support intuitive geospatial area selection.

14 SOLAR ENERGY↗

DOE OSTI2025

Policy and Cost Allocation Considerations for Large Electric Load Interconnections: Emerging Policy Trends in Rate Structures, Interconnection, and Cost Impacts on Other System Users

Load growth in the United States is rapidly increasing: load from data centers alone has tripled over the past decade, and this growth is forecasted to continue accelerating. These and other large electric loads (LELs) promise economic benefits at the state and local level, but their deployment has also led to increasing concerns about grid impacts and potential cost shifts onto other ratepayers. Legislators, regulators, and other stakeholders are increasingly proposing and enacting policies in effort to balance these and other considerations. This white paper reviews state-level legislation, selected utility rate cases, and relevant federal orders in an effort to describe and categorize relevant trends in policies related to LEL cost allocation, interconnection, and deployment. Policy categories identified through this review include tax incentives, rate actions, and requirements related to interconnection, permitting, and reporting. By offering a taxonomy of policies, this white paper aims to offer a resource to policymakers and other stakeholders navigating this transformative moment for the grid.

24 POWER TRANSMISSION AND DISTRIBUTION↗

DOE OSTI2026

Operating Experience Data Analysis for Digital Instrumentation and Control System Reliability and Risk Assessment in Nuclear Power Plants

The implementation of advanced digital instrumentation and control (DI&C) systems in U.S. nuclear power plants (NPPs) can bring significant advancements in reliability, monitoring, and control capabilities. However, these systems also introduce new challenges, particularly in assessing risks such as common-cause failures (CCFs) and establishing robust reliability estimates for DI&C components. Addressing these challenges is critical for ensuring the safe and efficient operation of NPPs. Recently, Idaho National Laboratory was tasked by the U.S. Nuclear Regulatory Commission (NRC) to conduct a DI&C reliability study using operating experience data from the nuclear industry. The two operating experience data sources for the study are the Institute of Nuclear Power Operations’ Industry Reporting and Information System (IRIS) and the NRC’s Licensee Event Report database which is hosted at Idaho National Laboratory at https://lersearch.inl.gov/LERSearchCriteria.aspx. This report provides a comprehensive examination of DI&C systems, including their architecture, operational advantages, and associated challenges. It reviews existing industry DI&C studies and failure mode taxonomies, along with reliability data from various industries. Through a detailed analysis of these databases, the study provides insights into DI&C system performance. Considerations should be given to incorporate DI&C failure data into the NRC's Integrated Data Collection and Coding System and updating the Reliability and Availability Data System to support ongoing DI&C reliability studies. Recommendations are also provided for modeling DI&C reliability and CCF in probabilistic risk assessment, thereby supporting risk-informed decision-making and enhancing the reliability and safety of NPPs.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

DOE OSTI2023

KBase Narrative - Genomic and environmental controls on Castellaniella biogeography in an anthropogenically disturbed site

Genome assemblies were imported into KBase using the Batch Import Assembly from Staging Area (v1.0.57) function. All assemblies were annotated using the Annotated Multiple Microbial Assemblies with RASTtk - v1.073 tool. Annotated genomes were grouped into sets using the Add Genomes to GenomeSet - v1.7.6 function. Individual annotated genomes can be found both below and in the Data menu to the left. Taxonomy was assigned using the Classify Microbes with GTDB-Tk-v1.7.0 tool. The results of this analysis are shown below. Analysis of the Castellaniella pangenome was performed using the Compute Pangenome (v0.0.7) tool. Using the same method, we also computed the ORR-specific and non-ORR Castellaniella pangenomes. All pangenome results (including the presence/absence matrix) can be found below.

Szink, Elizabeth↗

DOE OSTI2024

KBase Narrative - Porphyromonadaceae sp. W3.11 genome

Narratives for The phenotype and genotype of fermentative prokaryotes This is the Narrative for Porphyromonadaceae sp. W3.11. A complementary Narrative for Lachnospiraceae sp. C1.1 is available here. This is the Narrative for Lachnospiraceae sp. C1.1. A complementary Narrative for Porphyromonadaceae sp. W3.11 is available here. Background and Isolation This Narrative and its complementary Narrative contain assembly and annotation of two bacterial isolates that were isolated by our laboratory from the rumen of a Holstein heifer. All procedures with animals have been approved by University of California Davis’s Institutional Animal Care and Use Committee. Rumen contents were collected through a rumen fistula and strained through two layers of cheesecloth into a bottle. The bottle was sealed to exclude air and maintained at 39°C. Contents were brought to the laboratory and bubbled under O2-free CO2 within 15 min. At the laboratory, serial dilutions were made with anaerobic dilution solution for Lachnospiraceae sp. C1.1 and propionibacterium diluent for Porphyromonadaceae sp. W3.11 (table S2). Aliquots (0.1 ml) of each dilution were injected into anaerobic bottle plates (1) containing 9 ml of LH medium (table S2). After incubation at 37°C for 7 days, isolated colonies were picked. Lachnospiraceae sp. C1.1 was picked from a bottle inoculated with a 104 dilution of rumen contents, and Porphyromonadaceae sp. W3.11 was picked from a bottle inoculated with a 103 dilution. After initial isolation, these organisms were purified by growing on anaerobic roll tubes (2) and picking isolated colonies. We performed de novo sequencing of Lachnospiraceae sp. C1.1 and Porphyromonadaceae sp. W3.11. Aliquots of liquid culture (9 and 1.5 ml, respectively) were collected by syringe and centrifuged (21,000g for 10 min at 4°C). Cell pellets were submitted to Molecular Research LP for DNA extraction, library preparation, and sequencing. After resuspending pellets in 180 µl of ATL buffer (Qiagen), DNA was extracted using the MagAttract HMW DNA Kit (Qiagen). DNA was eluted in 100 µl of AE buffer (Qiagen) and then cleaned using the DNEasy PowerClean Pro Cleanup Kit (Qiagen). DNA was then sheared using the Covaris g-TUBE (Covaris). Sequencing libraries were prepared using the SMRTbell Express Template Prep Kit 2.0 (Pacific Biosciences) and 1500 ng of the sheared and purified DNA. The SMRTbell libraries were size-selected (>6 Kb) using a BluePippin instrument (Sage Science) and 0.75% agarose gel. Libraries were then sequenced using the PacBio Sequel II (Pacific Biosciences) platform and a 30-hour movie time. Narrative Summary In these Narratives, we filtered low-quality reads using Trimmomatic (v0.36), assembled filtered reads with SPAdes (v3.15.3), and then checked completeness and contamination of the assembled genomes with CheckM (v1.0.18). Statistics for sequencing and assembly are in table S3. Using the assembled contigs (genomes), we called genes and annotated them. Protein-coding genes were called using Prodigal (v2.6.3) (3) locally or using KBase via RASTtk (v1.073), with identical results. Genes were annotated with KO IDs using KAAS (4). They were further annotated with pfam and TIGRFAM IDs using KBase and the Annotate Domains in a Genome app. We classified putative genes for hydrogenases using HydDB. Genes for 16S ribosomal RNA (rRNA) were called using RASTtk (v1.073) in KBase. The contigs (genomes) were analyzed to determine whether they belonged to new species. Taxonomy was assigned using GTDB-Tk (v1.7.0) in KBase. The identity of 16S rRNA genes to other organisms was found using EzBioCloud (5). Values of digital DNA-DNA hybridization (dDDH) were found with Type (Strain) Genome Server (6). These analyses suggest that Lachnospiraceae sp. C1.1 and Porphyromonadaceae sp. W3.11 represent novel species or genera. GTDB-Tk assigned Lachnospiracae sp. C1.1 to family Lachnospiraceae and genus NK4A144, which contains no type strains. It assigned Porphyromonadaceae sp. W3.11 to Porphyromonadaceae and genus Porphyromonas_A. Values of 16S rRNA identity and dDDH with respect to type strains were low (table S4). Although more phenotypic data are needed, available evidence supports assignment of genomes to new species or genera. Related publication Hackmann TJ, Zhang B. The phenotype and genotype of fermentative prokaryotes. Sci Adv. 2023 Sep 29;9(39):eadg8687. doi: 10.1126/sciadv.adg8687. Epub 2023 Sep 27. PMID: 37756392; PMCID: PMC10530074.

Hackmann, Timothy↗

DOE OSTI2024

KBase Narrative - Lachnospiraceae sp. C1.1 genome

Narratives for The phenotype and genotype of fermentative prokaryotes This is the Narrative for Porphyromonadaceae sp. W3.11. A complementary Narrative for Lachnospiraceae sp. C1.1 is available here. This is the Narrative for Lachnospiraceae sp. C1.1. A complementary Narrative for Porphyromonadaceae sp. W3.11 is available here. Background and Isolation This Narrative and its complementary Narrative contain assembly and annotation of two bacterial isolates that were isolated by our laboratory from the rumen of a Holstein heifer. All procedures with animals have been approved by University of California Davis’s Institutional Animal Care and Use Committee. Rumen contents were collected through a rumen fistula and strained through two layers of cheesecloth into a bottle. The bottle was sealed to exclude air and maintained at 39°C. Contents were brought to the laboratory and bubbled under O2-free CO2 within 15 min. At the laboratory, serial dilutions were made with anaerobic dilution solution for Lachnospiraceae sp. C1.1 and propionibacterium diluent for Porphyromonadaceae sp. W3.11 (table S2). Aliquots (0.1 ml) of each dilution were injected into anaerobic bottle plates (1) containing 9 ml of LH medium (table S2). After incubation at 37°C for 7 days, isolated colonies were picked. Lachnospiraceae sp. C1.1 was picked from a bottle inoculated with a 104 dilution of rumen contents, and Porphyromonadaceae sp. W3.11 was picked from a bottle inoculated with a 103 dilution. After initial isolation, these organisms were purified by growing on anaerobic roll tubes (2) and picking isolated colonies. We performed de novo sequencing of Lachnospiraceae sp. C1.1 and Porphyromonadaceae sp. W3.11. Aliquots of liquid culture (9 and 1.5 ml, respectively) were collected by syringe and centrifuged (21,000g for 10 min at 4°C). Cell pellets were submitted to Molecular Research LP for DNA extraction, library preparation, and sequencing. After resuspending pellets in 180 µl of ATL buffer (Qiagen), DNA was extracted using the MagAttract HMW DNA Kit (Qiagen). DNA was eluted in 100 µl of AE buffer (Qiagen) and then cleaned using the DNEasy PowerClean Pro Cleanup Kit (Qiagen). DNA was then sheared using the Covaris g-TUBE (Covaris). Sequencing libraries were prepared using the SMRTbell Express Template Prep Kit 2.0 (Pacific Biosciences) and 1500 ng of the sheared and purified DNA. The SMRTbell libraries were size-selected (>6 Kb) using a BluePippin instrument (Sage Science) and 0.75% agarose gel. Libraries were then sequenced using the PacBio Sequel II (Pacific Biosciences) platform and a 30-hour movie time. Narrative Summary In these Narratives, we filtered low-quality reads using Trimmomatic (v0.36), assembled filtered reads with SPAdes (v3.15.3), and then checked completeness and contamination of the assembled genomes with CheckM (v1.0.18). Statistics for sequencing and assembly are in table S3. Using the assembled contigs (genomes), we called genes and annotated them. Protein-coding genes were called using Prodigal (v2.6.3) (3) locally or using KBase via RASTtk (v1.073), with identical results. Genes were annotated with KO IDs using KAAS (4). They were further annotated with pfam and TIGRFAM IDs using KBase and the Annotate Domains in a Genome app. We classified putative genes for hydrogenases using HydDB. Genes for 16S ribosomal RNA (rRNA) were called using RASTtk (v1.073) in KBase. The contigs (genomes) were analyzed to determine whether they belonged to new species. Taxonomy was assigned using GTDB-Tk (v1.7.0) in KBase. The identity of 16S rRNA genes to other organisms was found using EzBioCloud (5). Values of digital DNA-DNA hybridization (dDDH) were found with Type (Strain) Genome Server (6). These analyses suggest that Lachnospiraceae sp. C1.1 and Porphyromonadaceae sp. W3.11 represent novel species or genera. GTDB-Tk assigned Lachnospiracae sp. C1.1 to family Lachnospiraceae and genus NK4A144, which contains no type strains. It assigned Porphyromonadaceae sp. W3.11 to Porphyromonadaceae and genus Porphyromonas_A. Values of 16S rRNA identity and dDDH with respect to type strains were low (table S4). Although more phenotypic data are needed, available evidence supports assignment of genomes to new species or genera. Related publication Hackmann TJ, Zhang B. The phenotype and genotype of fermentative prokaryotes. Sci Adv. 2023 Sep 29;9(39):eadg8687. doi: 10.1126/sciadv.adg8687. Epub 2023 Sep 27. PMID: 37756392; PMCID: PMC10530074.

Hackmann, Timothy↗

DOE OSTI2026

Genome collection processing for “Conserved upper thermal limits and small safety margins in soil copiotrophic bacteria”

We extracted the genomic DNA of 400 randomly selected isolates using a Quick-DNA Microprep Kit (Zymo Research D3020) according to the manufacturer’s protocol. We then submitted the extracted gDNA samples for short-read Illumina sequencing (200 Mbp) at SeqCoast Genomics (Portsmouth, NH, USA). After preprocessing the sequences using Trimmommatic (Bolger et al. 2014), we assembled the genomes using SPADES (Bankevich et al. 2012) and checked the quality of each assembly using QUAST (Gurevich et al. 2013). We processed the genome assemblies using a KBase (v1.4.0) pipeline (Allen et al. 2017; Arkin et al. 2018). Briefly, we used DRAM (v0.1.2) with default settings to annotate the genome assemblies. We then evaluated genome quality and possible contamination levels using CheckM (v1.0.18) (Parks et al. 2015) and retained genomes with completeness above 98% and contamination below 5% (n = 354), following the authors' guidelines. We then obtained taxonomic assignments for all remaining isolates using the Genome Taxonomy Database tool GTDB-Tk (v2.3.2, database version r214) (Chaumeil et al. 2019). We constructed a phylogenetic tree using the tool SpeciesTree (v2.2.0). We then trimmed the tree (using Trim SpeciesTree to GenomeSet- v1.4.0), retaining only tips within our collection with measured thermal performance.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2020

Case Study: Can you find Delftia?

Delftia is a genus of bacteria with a bunch of cool features! The best studied species, Delftia acidovorans can produce gold nanoparticles from gold ions in solution. This bacteria has been found living in biofolms with Cupriavidis metallidurans on gold nuggets. It is also found in soil, in sinks and in rhizospheres of different plants where it promotes their growth. Delftia acidovorans forms gold nuggets by producing a short nonribosomal peptide called delftibactin. The 16 genes responsible for the production of delftibactin are called the del cluster (delA-delP). These genes were originally discovered in Delftia acidovorans SPH-1, but our research shows that the del cluster appears to be present across the genus. We'll start with a number of raw reads, clean them up and do a little taxonomy to figure out what we might be able to assemble. Next, we'll assemble the reads using 4 different methods and pick out the best assembly. Then we'll take those reads and sort them by genome and assess the quality of those genomes. We'll select the high quality genomes to annotate and insert into phylogenetic trees to find relatives.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2020

Single-Cell Genomics of Novel Actinobacteria With the Wood–Ljungdahl Pathway Discovered in a Serpentinizing System

Serpentinite-hosted systems represent modern-day analogs of early Earth environments. In these systems, water-rock interactions generate highly alkaline and reducing fluids that can contain hydrogen, methane, and low-molecular-weight hydrocarbons-potent reductants capable of fueling microbial metabolism. In this study, we investigated the microbiota of Hakuba Happo hot springs (~50°C; pH~10.5–11), located in Nagano (Japan), which are impacted by the serpentinization process. Analysis of the 16S rRNA gene amplicon sequences revealed that the bacterial community comprises Nitrospirae (47%), “Parcubacteria” (19%), Deinococcus-Thermus (16%), and Actinobacteria (9%), among others. Notably, only 57 amplicon sequence variants (ASV) were detected, and fifteen of these accounted for 90% of the amplicons. Among the abundant ASVs, an early-branching, uncultivated actinobacterial clade identified as RBG-16-55-12 in the SILVA database was detected. Ten single-cell genomes (average pairwise nucleotide identity: 0.98–1.00; estimated completeness: 33–93%; estimated genome size: ~2.3 Mb) that affiliated with this clade were obtained. Taxonomic classification using single copy genes indicates that the genomes belong to the actinobacterial class-level clade UBA1414 in the Genome Taxonomy Database. Based on metabolic pathway predictions, these actinobacteria are anaerobes, capable of glycolysis, dissimilatory nitrate reduction and CO 2 fixation via the Wood–Ljungdahl (WL) pathway. Several other genomes within UBA1414 and two related class-level clades also encode the WL pathway, which has not yet been reported for the Actinobacteria phylum. For the Hakuba actinobacterium, the energy metabolism related to the WL pathway is likely supported by a combination of the Rnf complex, group 3b and 3d [NiFe]-hydrogenases, [FeFe]-hydrogenases, and V-type (H + /Na + pump) ATPase. The genomes also harbor a form IV ribulose 1,5-bisphosphate carboxylase/oxygenase (RubisCO) complex, also known as a RubisCO-like protein, and contain signatures of interactions with viruses, including clustered regularly interspaced short palindromic repeat (CRISPR) regions and several phage integrases. This is the first report and detailed genome analysis of a bacterium within the Actinobacteria phylum capable of utilizing the WL pathway. The Hakuba actinobacterium is a member of the clade UBA1414/RBG-16-55-12, formerly within the group “OPB41.” We propose to name this bacterium ‘Candidatus Hakubanella thermoalkaliphilus.'

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2022

Functional Redundancy in Soil Microbial Community Based on Metagenomics Across the Globe

Understanding the contribution of soil microbial communities to ecosystem processes is critical for predicting terrestrial ecosystem feedbacks under changing climate. Our current understanding lacks a consistent strategy to formulate the linkage between microbial systems and ecosystem processes due to the presumption of functional redundancy in soil microbes. Here we present a global soil microbial metagenomic analysis to generalize patterns of microbial taxonomic compositions and functional potentials across climate and geochemical gradient. Our analyses show that soil microbial taxonomic composition varies widely in response to climate and soil physicochemical gradients, while microbial functional attributes based on metagenomic gene abundances are redundant. Among 17 climate zones, microbial taxonomic compositions were more distinct than functional potentials, as climate and edaphic properties showed more significant influence on microbial taxonomic compositions than on functional potentials. Microbial taxonomies formed a larger and more complex co-occurrence network with more module structures than functional potentials. Functional network was strongly inter-connected among different categories, whereas taxonomic network was more positively interactive in the same taxonomic groups. This study provides strong evidence to support the hypothesis of functional redundancy in soil microbes, as microbial taxonomic compositions vary to a larger extent than functional potentials based on metagenomic gene abundances in terrestrial ecosystems across the globe.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2024

Integrating biological knowledge for mechanistic inference in the host-associated microbiome

Advances in high-throughput technologies have enhanced our ability to describe microbial communities as they relate to human health and disease. Alongside the growth in sequencing data has come an influx of resources that synthesize knowledge surrounding microbial traits, functions, and metabolic potential with knowledge of how they may impact host pathways to influence disease phenotypes. These knowledge bases can enable the development of mechanistic explanations that may underlie correlations detected between microbial communities and disease. In this review, we survey existing resources and methodologies for the computational integration of broad classes of microbial and host knowledge. We evaluate these knowledge bases in their access methods, content, and source characteristics. We discuss challenges of the creation and utilization of knowledge bases including inconsistency of nomenclature assignment of taxa and metabolites across sources, whether the biological entities represented are rooted in ontologies or taxonomies, and how the structure and accessibility limit the diversity of applications and user types. We make this information available in a code and data repository at: https://github.com/lozuponelab/knowledge-source-mappings. Addressing these challenges will allow for the development of more effective tools for drawing from abundant knowledge to find new insights into microbial mechanisms in disease by fostering a systematic and unbiased exploration of existing information.

59 BASIC BIOLOGICAL SCIENCES↗