An integrated metagenomic, metabolomic and transcriptomic survey of Populus across genotypes and environments

Christopher Schadt; Stanton Martin; Alyssa Carrell; Allison Fortner; Dan Hopp; Dan Jacobson; Dawn Klingeman; Brandon Kristy; Jana Phillips; Bryan Piatkowski; Mark A. Miller; Montana Smith; Sujay Patil; Mark Flynn; Shane Canon; Alicia Clum; Christopher J. Mungall; Christa Pennacchio; Benjamin Bowen; Katherine Louie; Trent Northen; Emiley A. Eloe-Fadrosh; Melanie A. Mayes; Wellington Muchero; David J. Weston; Julie Mitchell; Mitchel Doktycz

doi:10.1038/s41597-024-03069-7

An integrated metagenomic, metabolomic and transcriptomic survey of Populus across genotypes and environments

Christopher Schadt
, Stanton Martin
, Alyssa Carrell
, Allison Fortner
, Dan Hopp
, Dan Jacobson
, Dawn Klingeman
, Brandon Kristy
, Jana Phillips
, Bryan Piatkowski
, Mark A. Miller
, Montana Smith
, Sujay Patil
, Mark Flynn
, Shane Canon
, Alicia Clum
, Christopher J. Mungall
, Christa Pennacchio
, Benjamin Bowen
, Katherine Louie

Trent Northen, Emiley A. Eloe-Fadrosh, Melanie A. Mayes, Wellington Muchero, David J. Weston, Julie Mitchell, Mitchel Doktycz

Research output: Contribution to journal › Article › peer-review

4 Scopus citations

Abstract

Bridging molecular information to ecosystem-level processes would provide the capacity to understand system vulnerability and, potentially, a means for assessing ecosystem health. Here, we present an integrated dataset containing environmental and metagenomic information from plant-associated microbial communities, plant transcriptomics, plant and soil metabolomics, and soil chemistry and activity characterization measurements derived from the model tree species Populus trichocarpa. Soil, rhizosphere, root endosphere, and leaf samples were collected from 27 different P. trichocarpa genotypes grown in two different environments leading to an integrated dataset of 318 metagenomes, 98 plant transcriptomes, and 314 metabolomic profiles that are supported by diverse soil measurements. This expansive dataset will provide insights into causal linkages that relate genomic features and molecular level events to system-level properties and their environmental influences.

Original language	English
Article number	339
Journal	Scientific Data
Volume	11
Issue number	1
DOIs	https://doi.org/10.1038/s41597-024-03069-7
State	Published - Dec 2024

Funding

The authors would like to thank various members of Drs. Busby’s, Uehling’s, and Strauss’ labs at Oregon State University, and Poplar Innovations LLC, for their assistance in helping to coordinate and complete fieldwork conducted in Oregon during the COVID-19 pandemic. This research was sponsored by the U.S. Department of Energy, Office of Science, Biological and Environmental Research. Oak Ridge National Laboratory is managed by UT-Battelle, LLC, for the U.S. Department of Energy under contract DE-AC05-00OR22725. The work (https://doi.org/10.46936/10.25585/60000017) conducted by the U.S. Department of Energy Joint Genome Institute (https://ror.org/04xm1d337), a DOE Office of Science User Facility, is supported by the Office of Science of the U.S. Department of Energy operated under Contract No. DE-AC02-05CH11231. The work conducted by the National Microbiome Data Collaborative (https://ror.org/05cwx3318) is supported by the Genomic Science Program in the U.S. Department of Energy, Office of Science, Office of Biological and Environmental Research (BER) under contract numbers DE-AC02-05CH11231 (LBNL), 89233218CNA000001 (LANL), and DE-AC05-76RL01830 (PNNL). Notice: This manuscript has been authored by UT-Battelle, LLC, under contract DE-AC05-00OR22725 with the US Department of Energy (DOE). The US government retains and the publisher, by accepting the article for publication, acknowledges that the US government retains a nonexclusive, paid-up, irrevocable, worldwide license to publish or reproduce the published form of this manuscript, or allow others to do so, for US government purposes. DOE will provide public access to these results of federally sponsored research in accordance with the DOE Public Access Plan (https://www.energy.gov/doe-public-access-plan).

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10.1038/s41597-024-03069-7

Cite this

Schadt, C., Martin, S., Carrell, A., Fortner, A., Hopp, D., Jacobson, D., Klingeman, D., Kristy, B., Phillips, J., Piatkowski, B., Miller, M. A., Smith, M., Patil, S., Flynn, M., Canon, S., Clum, A., Mungall, C. J., Pennacchio, C., Bowen, B., ... Doktycz, M. (2024). An integrated metagenomic, metabolomic and transcriptomic survey of Populus across genotypes and environments. Scientific Data, 11(1), Article 339. https://doi.org/10.1038/s41597-024-03069-7

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abstract = "Bridging molecular information to ecosystem-level processes would provide the capacity to understand system vulnerability and, potentially, a means for assessing ecosystem health. Here, we present an integrated dataset containing environmental and metagenomic information from plant-associated microbial communities, plant transcriptomics, plant and soil metabolomics, and soil chemistry and activity characterization measurements derived from the model tree species Populus trichocarpa. Soil, rhizosphere, root endosphere, and leaf samples were collected from 27 different P. trichocarpa genotypes grown in two different environments leading to an integrated dataset of 318 metagenomes, 98 plant transcriptomes, and 314 metabolomic profiles that are supported by diverse soil measurements. This expansive dataset will provide insights into causal linkages that relate genomic features and molecular level events to system-level properties and their environmental influences.",

author = "Christopher Schadt and Stanton Martin and Alyssa Carrell and Allison Fortner and Dan Hopp and Dan Jacobson and Dawn Klingeman and Brandon Kristy and Jana Phillips and Bryan Piatkowski and Miller, \{Mark A.\} and Montana Smith and Sujay Patil and Mark Flynn and Shane Canon and Alicia Clum and Mungall, \{Christopher J.\} and Christa Pennacchio and Benjamin Bowen and Katherine Louie and Trent Northen and Eloe-Fadrosh, \{Emiley A.\} and Mayes, \{Melanie A.\} and Wellington Muchero and Weston, \{David J.\} and Julie Mitchell and Mitchel Doktycz",

note = "Publisher Copyright: {\textcopyright} UT-Battelle, LLC, Pacific Northwest National Laboratory and The Author(s) 2024.",

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doi = "10.1038/s41597-024-03069-7",

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Schadt, C, Martin, S, Carrell, A , Fortner, A , Hopp, D , Jacobson, D , Klingeman, D, Kristy, B, Phillips, J, Piatkowski, B, Miller, MA, Smith, M, Patil, S, Flynn, M, Canon, S, Clum, A, Mungall, CJ, Pennacchio, C, Bowen, B, Louie, K, Northen, T, Eloe-Fadrosh, EA, Mayes, MA, Muchero, W, Weston, DJ, Mitchell, J & Doktycz, M 2024, 'An integrated metagenomic, metabolomic and transcriptomic survey of Populus across genotypes and environments', Scientific Data, vol. 11, no. 1, 339. https://doi.org/10.1038/s41597-024-03069-7

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An integrated metagenomic, metabolomic and transcriptomic survey of Populus across genotypes and environments

Abstract

Funding

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2020 Soil Characterization measurements at Clatskanie and Corvallis, Oregon Populus Trichocarpa GWAS Populations

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An integrated metagenomic, metabolomic and transcriptomic survey of Populus across genotypes and environments

Abstract

Funding

Access to Document

Other files and links

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Datasets

2020 Soil Characterization measurements at Clatskanie and Corvallis, Oregon Populus Trichocarpa GWAS Populations

Cite this