U.S. Department of EnergyOffice of Scientific and Technical Information
Produced Water DNA Database (PW-DNA): Utilizing KBase to generate an environmental specific curated molecular database
Abstract
The deep subsurface is estimated to host the majority of Earth’s microbial biomass yet remains one of the most challenging environments to access and study. One common approach to investigate these microbial communities is through the analysis of produced water from subsurface reservoirs, where researchers can assess water and gas chemistry along with molecular (DNA/RNA) sequence data. Advances in high-throughput sequencing have greatly expanded our understanding of these environments and their biotechnological potential. However, further progress requires large-scale, integrative meta-analyses across diverse datasets. To address this need, we developed the Produced Water-DNA (PW-DNA) Database, a curated, publicly available resource that consolidates microbial DNA/RNA sequences, geochemical data, and relevant metadata from in situ hydrocarbon environments such as coal beds, oil reservoirs, and natural gas systems. The PW-DNA database delivers three core benefits to the research community: (1) it improves data sharing by linking environmental microbial datasets with corresponding geochemical parameters, enabling more robust filtering and analysis; (2) it connects with complementary research databases to promote broader dissemination and interoperability; and (3) it supports technological innovation by serving as a resource for identifying microbial trends and exploring genetic potential. While individual studies have highlighted basin-specific microbial communities and functional redundancy in biogeochemicalmore »
- Authors:
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- National Energy Technology Laboratory (NETL), Pittsburgh, Pennsylvania, USA
- National Energy Technology Laboratory (NETL), Pittsburgh, Pennsylvania, USA; NETL Support Contractor, 626 Cochran Mill Road, Pittsburgh, PA 15236
- U.S. Geological Survey, Helena, Montana, USA
- U.S. Geological Survey, Reston, Virginia, USA
- Oak Ridge National Laboratory (ORNL), Oak Ridge, Tennessee, USA
- Publication Date:
- DOE Contract Number:
- AC02-05CH11231; AC02-06CH11357; AC05-00OR22725; AC02-98CH10886
- Research Org.:
- U.S. Department of Energy Systems Biology Knowledgebase (KBASE)
- Sponsoring Org.:
- USDOE Office of Science (SC), Biological and Environmental Research (BER); National Energy Technology Laboratory, Research & Innovation Center; US Geological Survey, Energy Resources and Environmental Health Programs
- Subject:
- 59 BASIC BIOLOGICAL SCIENCES; genomes; metabolomics; metagenomes; produced water
- OSTI Identifier:
- 2588866
- DOI:
- https://doi.org/10.25982/156785.278/2588866
Citation Formats
Schweitzer, Hannah D., Tinker, Kara A., Barnhart, Elliott P., Akob, Denise M., Crockett, Zachary R., and Gulliver, Djuna. Produced Water DNA Database (PW-DNA): Utilizing KBase to generate an environmental specific curated molecular database. United States: N. p., 2025.
Web. doi:10.25982/156785.278/2588866.
Schweitzer, Hannah D., Tinker, Kara A., Barnhart, Elliott P., Akob, Denise M., Crockett, Zachary R., & Gulliver, Djuna. Produced Water DNA Database (PW-DNA): Utilizing KBase to generate an environmental specific curated molecular database. United States. doi:https://doi.org/10.25982/156785.278/2588866
Schweitzer, Hannah D., Tinker, Kara A., Barnhart, Elliott P., Akob, Denise M., Crockett, Zachary R., and Gulliver, Djuna. 2025.
"Produced Water DNA Database (PW-DNA): Utilizing KBase to generate an environmental specific curated molecular database". United States. doi:https://doi.org/10.25982/156785.278/2588866. https://www.osti.gov/servlets/purl/2588866. Pub date:Fri Sep 19 04:00:00 UTC 2025
@article{osti_2588866,
title = {Produced Water DNA Database (PW-DNA): Utilizing KBase to generate an environmental specific curated molecular database},
author = {Schweitzer, Hannah D. and Tinker, Kara A. and Barnhart, Elliott P. and Akob, Denise M. and Crockett, Zachary R. and Gulliver, Djuna},
abstractNote = {The deep subsurface is estimated to host the majority of Earth’s microbial biomass yet remains one of the most challenging environments to access and study. One common approach to investigate these microbial communities is through the analysis of produced water from subsurface reservoirs, where researchers can assess water and gas chemistry along with molecular (DNA/RNA) sequence data. Advances in high-throughput sequencing have greatly expanded our understanding of these environments and their biotechnological potential. However, further progress requires large-scale, integrative meta-analyses across diverse datasets. To address this need, we developed the Produced Water-DNA (PW-DNA) Database, a curated, publicly available resource that consolidates microbial DNA/RNA sequences, geochemical data, and relevant metadata from in situ hydrocarbon environments such as coal beds, oil reservoirs, and natural gas systems. The PW-DNA database delivers three core benefits to the research community: (1) it improves data sharing by linking environmental microbial datasets with corresponding geochemical parameters, enabling more robust filtering and analysis; (2) it connects with complementary research databases to promote broader dissemination and interoperability; and (3) it supports technological innovation by serving as a resource for identifying microbial trends and exploring genetic potential. While individual studies have highlighted basin-specific microbial communities and functional redundancy in biogeochemical cycling, a comprehensive, system-wide perspective is needed to better understand connectivity and novelty across subsurface ecosystems. By designing the PW-DNA in the KBase platform, we provide a reproducible, visual framework for integrating large-scale genomic and geochemical data, enabling researchers to perform more informed analyses and experimental design. Ultimately, this resource enhances the ability to identify, characterize, and interpret microbial functions across diverse subsurface environments, thereby accelerating discovery in subsurface microbiology and biotechnology.},
doi = {10.25982/156785.278/2588866},
journal = {},
number = ,
volume = ,
place = {United States},
year = {Fri Sep 19 04:00:00 UTC 2025},
month = {Fri Sep 19 04:00:00 UTC 2025}
}