Persistence Control of Engineered Functions in Complex Soil Microbiomes (PerCon SFA), Secure Biosystems Design Project

Project Image

Principal Investigator


Last updated on 2023-02-23T19:37:46+00:00 by LN Anderson

PerCon SFA Project Publication Experimental Data Catalog

The Persistence Control of Engineered Functions in Complex Soil Microbiomes Project (PerCon SFA) at Pacific Northwest National Laboratory (PNNL) is a Genomic Sciences Program Biosystems Design, Science Focus Area research project consortium. Collaborating across highly integrated institutions, PerCon SFA scientists are exploring how environmental niches can be sculpted using the mechanisms of genome reduction and metabolic addiction to drive secure rhizosphere community design for robust biomass cropping in challenging environments.

The PerCon SFA DataHub project repository contains publication-relevant digital dataset and metadata DOI packages, enabling exploration and download of integrated experimental dataset catalogs publicly available to a global scientific community. and metadata repository allow for exploring and downloading integrated experimental biodesign omics dataset catalogs, including experimental protocols and/or workflows, raw and/or processed data, as required by the repository, and other relevant supporting materials and/or metadata required for research reproducibility and reporting.

    Accessible Project Digital Data Downloads(new uploads pending)

    Genomic sequencing data, subsequent sequence analyses, and resulting experimental metadata leveraged project platforms such as JGI GOLD portal and JGI IMG/M portal for project development, and openly shared through a collection of publication-specific BioProject and BioSample accessions linking to community sequence data archives GenBank and SRA. Proteomic and metabolomics mass spectrometry quantitative and qualitative data have been deposited, in accordance to recommended HUPO Proteomics Standard Initiative, public community repository MassIVE, and are accessible for browsing and reanalysis leveraging Global Natural Products Social Molecular Networking (GNPS) dashboard tools. X-ray computed tomography images are made available for user access through the EMSL NEXUS data portal and corresponding processed image files are provided through the PNNL DataHub institutional repository along with a data digital object identifier for download.

    Open-Source Collections

    Reusable FAIRsharing Project Repository Standards

    Raw measurement capability data have been deposited at community recognized public database(s) where appropriate and are the recorded factual material accepted by the scientific community necessary to validate the resulting publication of information consistent with intellectual property provisions under which the publishable information was produced. Digital research software, code, and publication relevant specialized tools required for data processing are openly available, and can be accessed at the following open-source community standard repositories listed below.

    Domain Repositories

    Mass Spectrometry - proteomics, metabolomics

    Sequencing - genomics, transcriptomics, high-throughput sequencing

    Bioinformatics - annotation machine learning, multi-omics data integration, and structural prediction models

    Generalist Repositories

    Linked publication lifecycle collections - data sets, instrument data sources, experimental methods, process method metadata

    Software - open-source code, analytical data workflows


    Funding Acknowledgments

    The provided material is based upon work supported by the  U.S. Department of Energy, Office of Biological and Environmental Research, Genomic Science Program and is a contribution of the Pacific Northwest National Laboratory Persistence Control of Engineered Functions in Complex Soil Microbiomes project. A portion of this research is supported under the EMSL user project award 10.46936/cpcy.proj.2022.60649/60008751, for leveraging instrument capabilities operating at the Environmental Molecular Sciences Laboratory, a DOE Office of Science User Facility, sponsored by the Biological and Environmental Research program under Contract No. DE-AC05-76RL01830. 

    Federal Acknowledgments

    Recommendation guidelines provided by the DOE Office of Science can be accessed at the SC Funding Opportunities & Acknowledgements homepage. For additional information regarding user capability data release, visit the SC Digital Data Management Resources at User Facilities for more information. Scientists who publish results of research using capabilities and DOE User Facilities capabilities are required to comply with the guidance provided in acknowledgment of EMSL Policiesacknowledgment of JGI Policies, and acknowledgment of KBase Policies for all publications utilizing DOE user facility resources. 

    Terms of Use

    This data reuse policy applies to the all project content provided herein and is based on the guiding principles summarized by the Department of Energy (DOE), Office of Science (SC) and the Office of Biological and Environmental Research program (BER), in efforts to promote a more efficient and effective use of government funding and scientific data resources (including all elements of the digital data generation lifecycle design, capture, and analysis intended for sustainable sharing and preservation). Digital research data best practice resources provided serve as a central effort in protecting research data integrity and facilitating the validation of scientific results for advancing science. All cases of data reuse and citation should adhere to guidance provided by the Office of Science of the U.S. Department of Energy. 

    Data Reuse Citation Policy

    When referencing and reusing linked PerCon SFA project digital data assets listed at the PNNL DataHub institutional repository, we ask that users please cite the dataset digital object identifier provided at the download page and any corresponding journal article publications. Reference citations, where applicable, should provide the necessary metadata information required to support, corroborate, verify, and otherwise determine the legitimacy of the research findings provided (data and code) from scholarly publications and corresponding project data releases.

    For project-specific inquiries, please contact

    Project status

    Datasets (3)
    Publications (7)
    People (11)

    Lindsey Anderson’s research has been dedicated to the identification and characterization of novel, targeted and non-targeted, functional metabolic interactions using a high-throughput systems biology and computational biology approach. Her expertise in functional metabolism and multidisciplinary...

    Biography Dr. Pubudu Handakumbura is the lead on the Plant and Ecosystem Phenotyping team in PNNL’s Environmental Molecular Sciences Division and the Environmental Molecular Sciences Laboratory (EMSL) user program. She has extensive experience in advanced molecular biology techniques, genetic...

    Publications: 2018 Khan NE, Y Maezato, RS McClure, CJ Brislawn, JM Mobberley, NG Isern, WB Chrisler, LM Markillie, BM Barney, HS Song, WC Nelson, and HC Bernstein. 2018. "Phenotypic responses to interspecies competition and commensalism in a naturally-derived microbial co-culture." Scientific...

    Dr. Jason McDermott, senior research scientist, has extensive research experience in molecular and structural virology and data resource design, data integration and prediction of biological networks, bridging experimental and computational biology. Currently, his research interests include data...

    Janet Jansson is Chief Scientist for Biology in the Biological Sciences Division and a Laboratory Fellow at the Pacific Northwest National Laboratory (PNNL). Jansson has more than 30 years of experience in microbial ecology. Jansson earned an Soil Microbiology at Colorado State University...

    Dr. Nelson is a computational scientist at PNNL. Since coming to PNNL, he has focused on methods to determine precise understanding of microbial community structure and function through the resolution of individual genome sequences from metagenomic data, and exploration of variation between...

    Biography Ernesto Nakayasu is a senior research scientist focused on understanding molecular mechanisms of diseases. Nakayasu has been applying systems biology and mass spectrometry-based omics measurements to study how pathogens and metabolic alterations cause human diseases; the goal is to...

    PerCon SFA, Co-Investigator Vivian Lin earned her PhD in organic chemistry from the University of California, Berkeley with Professor Chris Chang, developing fluorescent probes for imaging redox active small molecules. Afterward, she traveled to Switzerland for a postdoctoral fellowship in the...

    Dr. Joshua Elmore is a Chemical Engineer at Pacific Northwest National Laboratory. He received his Ph. D. from the University of Georgia in the Department of Molecular Biology and Biochemistry studying the mechanisms of CRISPR/Cas microbial immune systems in hyperthermophilic Archaea. He was a...

    Biography I am a biological engineer working to advance high-throughput biological engineering for rapid optimization of complex gene clusters and dynamical systems in microbes through pooled genomic library assembly, high-throughput sequencing and variant scoring. I utilize machine learning...

    Short Biography Caroline (Carrie) Harwood received her Ph.D. in microbiology from the University of Massachusetts and completed postdoctoral work at Yale University. She held academic appointments at Cornell University and the University of Iowa before moving to the University of Washington in 2005...

    Data Sources (6)
    Methods (1)
    Institutions (2)
    Software (1)