Omics-to-Reactive-Transport (ORT): A workflow linking genome-scale metabolic models with reactive transport codes

Rubinstein, Rebecca L; Borton, Mikayla; Zhou, Haiyan; Shaffer, Michael; Hoyt, David; Stegen, James; Henry, Christopher; Wrighton, Kelly; Versteeg, Roelof

doi:10.25982/71260.262/1827108

Title: Omics-to-Reactive-Transport (ORT): A workflow linking genome-scale metabolic models with reactive transport codes

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Abstract

Motivation: Nutrient and contaminant behavior in the subsurface are governed by multiple coupled hydrobiogeochemical processes which occur across different temporal and spatial scales. Accurate description of macroscopic system behavior requires accounting for the effects of microscopic and especially microbial processes. Microbial processes mediate precipitation and dissolution and change aqueous geochemistry, all of which impacts macroscopic system behavior. As `omics data describing microbial processes is increasingly affordable and available, novel methods for using this data quickly and effectively for improved ecosystem models are needed. Results: We propose a workflow (`Omics to Reactive Transport – ORT) for utilizing metagenomic and environmental data to describe the effect of microbiological processes in macroscopic reactive transport models. This workflow utilizes and couples two open-source software packages: KBase (a software platform for systems biology) and PFLOTRAN (a reactive transport modeling code). We describe the architecture of ORT and demonstrate an implementation using metagenomic and geochemical data from a river system. Our demonstration uses microbiological drivers of nitrification and denitrification to predict nitrogen cycling patterns which agree with those provided with generalized stoichiometries. While our example uses data from a single measurement, our workflow can be applied to spatiotemporal metagenomic datasets to allow for iterative coupling betweenmore »« less

Authors:

;

Subsurface Insights, LLC; Lawrence Berkeley National Laboratory (LBNL)
Colorado State Univ., Fort Collins, CO (United States)
Subsurface Insights, LLC
Pacific Northwest National Lab. (PNNL), Richland, WA (United States)
Argonne National Lab. (ANL), Argonne, IL (United States)

Publication Date:: Fri Mar 12 04:00:00 UTC 2021

DOE Contract Number:: SC0018020; SC0019619

Research Org.:: U.S. Department of Energy Systems Biology Knowledgebase

Sponsoring Org.:: USDOE Office of Science (SC), Biological and Environmental Research (BER)

OSTI Identifier:: 1827108

DOI:: https://doi.org/10.25982/71260.262/1827108

Citation Formats


                    Rubinstein, Rebecca L, Borton, Mikayla, Zhou, Haiyan, Shaffer, Michael, Hoyt, David, Stegen, James, Henry, Christopher, Wrighton, Kelly, and Versteeg, Roelof. Omics-to-Reactive-Transport (ORT): A workflow linking genome-scale metabolic models with reactive transport codes.  United States: N. p., 2021. 
        Web.  doi:10.25982/71260.262/1827108.

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                    Rubinstein, Rebecca L, Borton, Mikayla, Zhou, Haiyan, Shaffer, Michael, Hoyt, David, Stegen, James, Henry, Christopher, Wrighton, Kelly, & Versteeg, Roelof. Omics-to-Reactive-Transport (ORT): A workflow linking genome-scale metabolic models with reactive transport codes.  United States.  doi:https://doi.org/10.25982/71260.262/1827108

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                    Rubinstein, Rebecca L, Borton, Mikayla, Zhou, Haiyan, Shaffer, Michael, Hoyt, David, Stegen, James, Henry, Christopher, Wrighton, Kelly, and Versteeg, Roelof. 2021.  
"Omics-to-Reactive-Transport (ORT): A workflow linking genome-scale metabolic models with reactive transport codes".  United States.  doi:https://doi.org/10.25982/71260.262/1827108.  https://www.osti.gov/servlets/purl/1827108. Pub date:Fri Mar 12 04:00:00 UTC 2021

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@article{osti_1827108,

  title        = {Omics-to-Reactive-Transport (ORT): A workflow linking genome-scale metabolic models with reactive transport codes},

  author       = {Rubinstein, Rebecca L and Borton, Mikayla and Zhou, Haiyan and Shaffer, Michael and Hoyt, David and Stegen, James and Henry, Christopher and Wrighton, Kelly and Versteeg, Roelof},

  abstractNote = {Motivation: Nutrient and contaminant behavior in the subsurface are governed by multiple coupled hydrobiogeochemical processes which occur across different temporal and spatial scales. Accurate description of macroscopic system behavior requires accounting for the effects of microscopic and especially microbial processes. Microbial processes mediate precipitation and dissolution and change aqueous geochemistry, all of which impacts macroscopic system behavior. As `omics data describing microbial processes is increasingly affordable and available, novel methods for using this data quickly and effectively for improved ecosystem models are needed. Results: We propose a workflow (`Omics to Reactive Transport – ORT) for utilizing metagenomic and environmental data to describe the effect of microbiological processes in macroscopic reactive transport models. This workflow utilizes and couples two open-source software packages: KBase (a software platform for systems biology) and PFLOTRAN (a reactive transport modeling code). We describe the architecture of ORT and demonstrate an implementation using metagenomic and geochemical data from a river system. Our demonstration uses microbiological drivers of nitrification and denitrification to predict nitrogen cycling patterns which agree with those provided with generalized stoichiometries. While our example uses data from a single measurement, our workflow can be applied to spatiotemporal metagenomic datasets to allow for iterative coupling between KBASE and PFLOTRAN. Live, interactive models, which incorporate the results from this narrative into a PFLOTRAN simulation, are available (without login) at https://pflotranmodeling.paf.subsurfaceinsights.com/pflotran-simple-model/.},

  doi          = {10.25982/71260.262/1827108},

  journal      = {},

  number       = ,

  volume       = ,

  place        = {United States},

  year         = {Fri Mar 12 04:00:00 UTC 2021},

  month        = {Fri Mar 12 04:00:00 UTC 2021}

}

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DOI: https://doi.org/10.25982/71260.262/1827108

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ORT: A workflow linking genome-scale metabolic models with reactive transport codes

Journal Article Rubinstein, Rebecca L. ; Borton, Mikayla A. ; Zhou, Haiyan ; ... - Bioinformatics

Nutrient and contaminant behavior in the subsurface are governed by multiple coupled hydrobiogeochemical processes which occur across different temporal and spatial scales. Accurate description of macroscopic system behavior requires accounting for the effects of microscopic and especially microbial processes. Microbial processes mediate precipitation and dissolution and change aqueous geochemistry, all of which impacts macroscopic system behavior. As ‘omics data describing microbial processes is increasingly affordable and available, novel methods for using this data quickly and effectively for improved ecosystem models are needed. In this work, we propose a workflow (‘Omics to Reactive Transport – ORT) for utilizing metagenomic and environmentalmore »« less
ORT: a workflow linking genome-scale metabolic models with reactive transport codes

Journal Article Rubinstein, Rebecca L. ; Borton, Mikayla A. ; Zhou, Haiyan ; ... - Bioinformatics

Abstract Motivation Nutrient and contaminant behavior in the subsurface are governed by multiple coupled hydrobiogeochemical processes which occur across different temporal and spatial scales. Accurate description of macroscopic system behavior requires accounting for the effects of microscopic and especially microbial processes. Microbial processes mediate precipitation and dissolution and change aqueous geochemistry, all of which impacts macroscopic system behavior. As ‘omics data describing microbial processes is increasingly affordable and available, novel methods for using this data quickly and effectively for improved ecosystem models are needed. Results We propose a workflow (‘Omics to Reactive Transport—ORT) for utilizing metagenomic and environmental data tomore »« less
ORT: A workflow linking genome-scale metabolic models with reactive transport codes

Journal Article Rubinstein, Rebecca L. ; Borton, Mikayla A. ; Zhou, Haiyan ; ... - Bioinformatics

Nutrient and contaminant behavior in the subsurface are governed by multiple coupled hydrobiogeochemical processes which occur across different temporal and spatial scales. Accurate description of macroscopic system behavior requires accounting for the effects of microscopic and especially microbial processes. Microbial processes mediate precipitation and dissolution and change aqueous geochemistry, all of which impacts macroscopic system behavior. As ‘omics data describing microbial processes is increasingly affordable and available, novel methods for using this data quickly and effectively for improved ecosystem models are needed. In this work, we propose a workflow (‘Omics to Reactive Transport – ORT) for utilizing metagenomic and environmentalmore »« less
ORT: A workflow linking genome-scale metabolic models with reactive transport codes

Journal Article Rubinstein, Rebecca L. ; Borton, Mikayla A. ; Zhou, Haiyan ; ... - Bioinformatics

Motivation: Nutrient and contaminant behavior in the subsurface are governed by multiple coupled hydrobiogeochemical processes which occur across different temporal and spatial scales. Accurate description of macroscopic system behavior requires accounting for the effects of microscopic and especially microbial processes. Microbial processes mediate precipitation and dissolution and change aqueous geochemistry, all of which impacts macroscopic system behavior. As ‘omics data describing microbial processes is increasingly affordable and available, novel methods for using this data quickly and effectively for improved ecosystem models are needed. Results: In this work, we propose a workflow (‘Omics to Reactive Transport – ORT) for utilizing metagenomicmore »« less
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This Modeling Archive is in support of an NGEE Arctic discussion paper available at doi:10.5194/gmd-9-927-2016. The purpose is to document the simulations to allow verification, reproducibility, and follow-up studies. This dataset contains shell scripts to create the CLM-PFLOTRAN cases, specific input files for PFLOTRAN and CLM, outputs, and python scripts to make the figures using the outputs in the publication. Through these results, we demonstrate that CLM-PFLOTRAN can approximately reproduce CLM results in selected cases for the Arctic, temperate and tropic sites. In addition, the new framework facilitates mechanistic representations of soil biogeochemistry processes in the land surface model. Thismore »« less

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