Produced Water DNA Database
Produced Water Database, Denise M. Akob, Djuna Gulliver, Elliott Barnhart, Hannah Schweitzer, Kara Tinker
Generated September 22, 2025

Produced Water Database

Welcome to the PW-DNA database built in collaboration with

. . . .

DOE | NETL | Geomicrobiology Research Group | USGS

The PW-DNA database improves the ability for researchers to characterize produced water to help identify options for treatment, reuse, and recovery of valuable resources. These samples are found across the World from Coal Bed Methane(orange), Shale(light blue), and Crude Oil(dark blue) resources. </br>

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This narrative includes 6 datasets that users can either interact with inside of KBase or be downloaded to use on your own hardware. The datasets available are:

Link to Dataset's Narrative Number of Samples Included Link to Tutorial Narrative for Users </br>to Analyze Their Own Data in KBase
Clone Library Datasets 62 Clone Library Narrative
Amplicon Dataset 938 Amplicon Narrative
Metagenome Assembly Dataset 144 Metagenome Assembly Narrative
Metagenome MAGs and Genomes Dataset 2358 Genome Narrative
Metatranscriptome Datasets 9 Metatranscriptome Narrative
qPCR Datasets 298 qPCR Excel Sheet

These datasets were generated within KBase using publically available data from the folling databases: [NCBI](https://www.ncbi.nlm.nih.gov/), [JGI-IMG](https://img.jgi.doe.gov/), [JGI-Gold](https://gold.jgi.doe.gov/), [NMDC](https://microbiomedata.org/), and [MG-RAST](https://www.mg-rast.org/). The DOIs for each of the work and the KBase narrative(s) for the data is available:

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PW-DNA ID DOI Author Publication Year Sample Type Samples Inlcuded (with KBase Narrative links)
PWDNA-C001 https://doi.org/10.1111/j.1574-6941.2011.01272.x Wawrik et al. 2012 Coal Clone Library and qPCR
PWDNA-C002 https://doi.org/10.1126/science.aac7745 Evans et al. 2015 Coal Genome
PWDNA-C003 https://doi.org/10.1128/aem.01737-15 Lawson et al. 2015 Coal MetaG and Amplicon
PWDNA-C004 https://doi.org/10.1016/j.coal.2016.05.001 Barnhart et al. 2016 Coal Amplicon
PWDNA-C005 https://doi.org/10.1128/genomea.01024-16 Ross et al 2016 Coal Genome
PWDNA-C006 https://doi.org/10.1016/j.gca.2018.11.009 Schweitzer et al. 2019 Coal Amplicon and qPCR
PWDNA-C007 https://doi.org/10.1038/s41396-021-01139-x McKay et al. 2021 Coal MetaG
PWDNA-C008 https://doi.org/10.1016/j.coal.2021.103860 Smith et al. 2021 Coal Amplicon
PWDNA-C009 https://doi.org/10.1038/s41522-022-00267-2 Schweitzer et al. 2022 Coal MetaG
PWDNA-C010 https://doi.org/10.1111/1462-2920.16251 Ross et al . 2022 Coal MetaG
PWDNA-C011 unpublished Schweitzer et al. Coal Amplicon
PWDNA-C012 unpublished Schweitzer et al. Coal MetaG and MetaT
PWDNA-C013 unpublished Sarkar et al. Coal Amplicon
PWDNA-CO001 https://doi.org/10.1021/es4020184 An et al. 2013 Coal, Oil MetaG and Amplicon
PWDNA-O001 https://doi.org/10.1111/j.1462-2920.2008.01751.x Pham et al. 2009 Oil Clone Library
PWDNA-O002 https://doi.org/10.1371/journal.pone.0023258 Ren et al. 2011 Oil Clone Library
PWDNA-O003 https://doi.org/10.3389%2Ffmicb.2014.00409 Piceno et al. 2014 Oil Clone Library
PWDNA-O004 https://doi.org/10.1007/s11356-015-4947-z Yeung et al. 2015 Oil Clone Library and qPCR
PWDNA-O005 https://doi.org/10.1128/mbio.01669-15 Hu et al. 2016 Oil MetaG
PWDNA-O006 https://doi.org/10.1038/ismej.2017.78 Vigneron et al. 2017 Oil MetaG, Amplicon and qPCR
PWDNA-O007 https://doi.org/10.3389/fmicb.2017.00099 Bonifay et al. 2017 Oil MetaG
PWDNA-O008 https://doi.org/10.1186/s40168-017-0392-1 Liu et al. 2018 Oil MetaG and MetaT
PWDNA-O009 https://doi.org/10.1128/AEM.01819-20 Lahme et al. 2021 Oil MetaG, Amplicon and qPCR
PWDNA-S001 https://doi.org/10.1021/es402928b Mohan et al. 2013 Shale Clone Library and qPCR
PWDNA-S002 https://doi.org/10.1111/1574-6941.12183 Mohan et al. 2013 Shale Clone Library and qPCR
PWDNA-S003 https://doi.org/10.3389/fmicb.2013.00367 Wuchter et al. 2013 Shale Clone Library
PWDNA-S004 https://doi.org/10.1021/es501173p Cluff et al. 2014 Shale Amplicon
PWDNA-S005 https://doi.org/10.1371/journal.pone.0107682 Mohan et al. 2014 Shale MetaG
PWDNA-S006 https://doi.org/10.1038/nmicrobiol.2016.146 Daly et al. 2016 Shale MetaG
PWDNA-S007 https://doi.org/10.3389/fmicb.2016.00988 Liang et al. 2016 Shale Amplicon
PWDNA-S008 https://doi.org/10.1128/genomea.00899-16 Lipus et al. 2016 Shale Genome
PWDNA-S009 https://doi.org/10.1007/s00248-016-0811-z Vikram et al. 2016 Shale Amplicon and qPCR
PWDNA-S010 https://doi.org/10.3389/fmicb.2017.01164 An et al. 2017 Shale Amplicon
PWDNA-S011 https://doi.org/10.1128/mspheredirect.00257-17 Booker et al. 2017 Shale MetaG
PWDNA-S012 https://doi.org/10.1128/AEM.02659-16 Lipus et al. 2017 Shale Amplicon and qPCR
PWDNA-S013 https://doi.org/10.1073/pnas.1800155115 Borton et al. 2018 Shale MetaG
PWDNA-S014 https://doi.org/10.1111/1462-2920.14467 Borton et al. 2018 Shale Genome
PWDNA-S015 https://doi.org/10.3389/fmicb.2018.02646 Evans et al. 2018 Shale MetaG and Genome
PWDNA-S016 https://doi.org/10.1016/j.scitotenv.2018.06.067 Hull et al. 2018 Shale Amplicon
PWDNA-S017 https://doi.org/10.1093/femsle/fny107 Lipus et al. 2018 Shale Amplicon and qPCR
PWDNA-S018 https://doi.org/10.1039/C8EM00291F Roger et al. 2018 Shale Amplicon
PWDNA-S019 https://doi.org/10.1128/genomea.00155-18 Tummings et al. 2018 Shale Genome
PWDNA-S020 https://doi.org/10.1186/s13568-019-0766-9 Berdugo‑Clavijo et al. 2019 Shale Clone Library
PWDNA-S021 https://doi.org/10.1128/AEM.00018-19 Booker et al. 2019 Shale Genome
PWDNA-S022 https://doi.org/10.1038/s41564-018-0312-6 Daly et al. 2019 Shale MetaG
PWDNA-S023 https://doi.org/10.1021/acs.estlett.9b00473 Evans et al. 2019 Shale MetaG
PWDNA-S024 https://doi.org/10.1038/s41396-019-0466-0 Evans et al. 2019 Shale Genome
PWDNA-S025 https://doi.org/10.3389/fmicb.2019.00376 Morono et al. 2019 Shale Amplicon
PWDNA-S026 https://doi.org/10.1128/mSphere.00613-19 Nixon et al. 2019 Shale Genome
PWDNA-S027 https://doi.org/10.1016/j.watres.2019.114942 Wang et al. 2019 Shale Amplicon
PWDNA-S028 https://doi.org/10.3389/fmicb.2020.536978 Shelton et al. 2020 Shale Amplicon and qPCR
PWDNA-S029 https://doi.org/10.3389/fmicb.2020.01781 Tinker et al. 2020 Shale Amplicon and qPCR
PWDNA-S030 https://doi.org/10.1038/s41598-020-73010-6 Zhang et al. 2020 Shale MetaG, Amplicon and qPCR
PWDNA-S031 https://doi.org/10.1021/acsearthspacechem.1c00087 Stemple et al. 2021 Shale Amplicon and qPCR
PWDNA-S032 https://doi.org/10.1186/s40168-021-01194-8 Amundson et al. 2022 Shale MetaG and Amplicon
PWDNA-S033 https://doi.org/10.1128/spectrum.03640-22 Cliffe et al. 2022 Shale Amplicon
PWDNA-S034 https://doi.org/10.1128/spectrum.00049-22 Tinker et al. 2022 Shale MetaG and Amplicon
PWDNA-S035 https://doi.org/10.1016/j.jhazmat.2021.127649 Zhou et al. 2022 Shale Amplicon
PWDNA-S036 https://doi.org/10.1186/s40793-023-00465-1 Hernandez-Becerra et al. 2023 Shale Amplicon
PWDNA-S037 unpublished Schweitzer et al. Shale MetaG and Amplicon
PWDNA-S038 unpublished Tinker et al. Shale Amplicon

Metadata and Geochemical Data

All the molecular data available also includes corresponding metadata and geochemical data (when provided). These samples can therefore be filtered based on this data. Users can download this data onto their own hardware using this excel file link. All the samples included in the PW-DNA database are connected by a unique identifier (PWDNA-###). This identifier also connects to other databases such as the

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USGS

Produced Waters Geochemical Database v3.0

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The USGS Produced Waters Geochemical Database v3.0 contains other published geochemical data that may not contain molecular data like the Produced Water DNA Database. If you are interested in more geochemical data the USGS Produced Water Geochemical Database may be a valuable resource for you.

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All the datasets contain Metadata and Geochemical Data. The percentage of included Metadata across all the samples is:

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The percentage of included Geochemical data across all the samples is(if the geochemical condition is not included in the figure below no samples have reported those findings):

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As the figures show above, many of the samples are missing metadata and geochemical data. If researchers know of any updates to the current metadata and geochemical datasets we encourage them to reach out to us to improve the above percentages. Users can upload their data using this template. Once users have filled out that template they can send us the updated metadata and geochemical data to [email protected]

Filter Datasets to Find Desired Samples - Metadata and Geochemical

All data can be filtered via the metadata, geochemical and taxon data (as well as gene data for Genomes and Metagenomes). Using the PW-DNA_Metadata_and_Geochemical_Table Attribute Map, individuals can filter to find desired samples in the entire sample set. Users can search through all the samples and then find which dataset (e.g. Amplicon, Metagenome, Genomes) is most ideal for your questions. To pick which dataset you may be interested in you can start by searching below.

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For the Metadata and Geochemical conditions users can either sort each column of interest using the arrows in the header:

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This will let users see which ranges of geochemical conditions and which samples are of interest.

Or users can filter using the search column on the right:

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This will let users see which samples contain a certain condition such as which samples are found in Michigan.

PW-DNA_Metadata_Geochemical_Table
v1 - KBaseExperiments.AttributeMapping-2.0
The viewer for the data in this Cell is available at the original Narrative here: https://narrative.kbase.us/narrative/156785

Filter Datasets to Find Desired Samples - Taxon Presence

For Taxon data users will first pick which taxonomic level (i.e. Family, Genus, Species) they want to filter from. Then the users will search for that taxonomy using the search column on the right as seen below:

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If users want to filter for samples that have more than one organims of interest after users filter the first organism using the search bar as above they will press the CSV button on the left:

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This will generate a csv file of that list. Users can view this csv file to get an idea of where their samples of interest are located so they know which dataset will be of interest to them. The above steps can be repeated as many times as needed if users are trying to find samples that contain mulitple organisms of interest. If users want correlating metadata or geochemical data, they can compare the unique identifier (PWDNA-X###) to the metadata files above.

Taxon_Table_Domain
v1 - KBaseExperiments.AttributeMapping-2.0
The viewer for the data in this Cell is available at the original Narrative here: https://narrative.kbase.us/narrative/156785
Taxon_Table_Phylum
v1 - KBaseExperiments.AttributeMapping-2.0
The viewer for the data in this Cell is available at the original Narrative here: https://narrative.kbase.us/narrative/156785
Taxon_Table_Class
v1 - KBaseExperiments.AttributeMapping-2.0
The viewer for the data in this Cell is available at the original Narrative here: https://narrative.kbase.us/narrative/156785
Taxon_Table_Order
v1 - KBaseExperiments.AttributeMapping-2.0
The viewer for the data in this Cell is available at the original Narrative here: https://narrative.kbase.us/narrative/156785
Taxon_Table_Family
v1 - KBaseExperiments.AttributeMapping-2.0
The viewer for the data in this Cell is available at the original Narrative here: https://narrative.kbase.us/narrative/156785
Taxon_Table_Genus
v1 - KBaseExperiments.AttributeMapping-2.0
The viewer for the data in this Cell is available at the original Narrative here: https://narrative.kbase.us/narrative/156785
Taxon_Table_Species
v1 - KBaseExperiments.AttributeMapping-2.0
The viewer for the data in this Cell is available at the original Narrative here: https://narrative.kbase.us/narrative/156785

Researchers will benefit most from the PW-DNA Database if it continues to grow. We therefore encourage users to reach out to us to upload their own data. In order to do this, we ask that you follow the below narratives with your samples. This will ensure that all samples follow the same standardized pipelines: </br> </br>

File Narrative Link
Metagenome Tutorial Metagenome Assembly Narrative
Genome Tutorial Genome Narrative
Metatranscriptome Tutorial Metatranscriptome Narrative
Amplicon Tutorial Amplicon Narrative
Clone Library Tutorial Clone Library Narrative
qPCR Tables qPCR Excel Sheet

When submitting your own data it is also import that you upload your metadata and any corresponding geochemical data. Users can download a metadata and geochemical table here. Once users have completed the narrative with their samples and have filled out the metadata and geochemical table, they can then email us at [email protected] to approve their sample upload. </br> </br>

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