PNNL Soil Microbiome SFA

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Principal Investigator

Description

The Phenotypic Response of the Soil Microbiome to Environmental Perturbations Project (Soil Microbiome) at Pacific Northwest National Laboratory is a Genomic Sciences Program Science Focus Area (SFA) Project operating under the Environmental Microbiome Science Research Area. The Soil Microbiome SFA project aims to develop a systems-level understanding of soil microbial and phenotypic responses to changing moisture through a tractable, spatially explicit examination of the molecular and ecological interactions occurring within and between microbial consortia in soil. PNNL is performing integrated experiments to confront both the scaling challenges and interkingdom interactions that regulate networks of biochemical reactions. High-resolution experimental data are being used to parameterize agent-based models. Genome-enabled predictions of spatially explicit microbial interactions are being validated in reduced-complexity microbial consortia using advanced chemical imaging and other techniques unique to PNNL. 

PNNL’s Soil Microbiome SFA project repository on DataHub allows for exploring and downloading integrated experimental omics data, experimental metadata, pre- and post-processed data files, and other associated materials directly related to experimental project publication data. For updates and more information, visit the PNNL Soil Microbiome Science Focus Area Project homepage.

 

Project Collaborations

Acknowledgements

This research is supported in part by the U.S. Department of Energy (DOE), Office of Biological and Environmental Research (BER), as part of BER’s Genomic Science Program (GSP, https://genomicscience.energy.gov) and is a contribution of the Pacific Northwest National Laboratory (PNNL) Secure Biosystems Design Science Focus Area "Phenotypic Response of the Soil Microbiome to Environmental Perturbations Project ". A portion of this work was performed under the EMSL user project award 10.46936/cpcy.proj.2021.60161/60000437, utilizing 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.

PARTICIPATING INSTITUTIONS

  • Biological Sciences Division, Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99352, USA.
  • Environmental Molecular Sciences Division, Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99352, USA. (EMSL User Facility)
  • School of Biological Sciences, Washington State University, Pullman, Washington 99163, USA.
  • Department of Ecology, Evolution and Organismal Biology, Iowa State University, Ames, Iowa 50011, USA.
  • Division of Biology, Kansas State University, Manhattan, Kansas, USA.
  • Department of Biological Systems Engineering, University of Nebraska-Lincoln, Lincoln, Nebraska 68588, USA.

DataHub CRediT (Contributor Roles Taxonomy)

 

Project status

Active
Datasets (13)
English
Publications (8)
Elias Zegeye
Colin Brislawn
Yuliya Farris
Sarah J. Fansler
Kirsten Hofmockel
Janet K. Jansson
Aaron Wright
Emily Graham
Dan Naylor
Ryan McClure
Hans Bernstein
Dr William C Nelson
Lindsey N. Anderson
Janet K. Jansson
Ruonan Wu
Jason McDermott
Sheryl L. Bell
Ari Jumpponen
Sarah J. Fansler
Kimberly J. Tyrrell
Yuliya Farris
Kirsten Hofmockel
Arunima Bhattacharjee
Lindsey N. Anderson
Andrea Porras-Alfaro
Ari Jumpponen
Kirsten Hofmockel
Janet K. Jansson
Dr Christopher R Anderton
Dr William C Nelson
Ryan McClure
Dan Naylor
Yuliya Farris
Michelle R Davison
Sarah J. Fansler
Kirsten Hofmockel
Janet K. Jansson
Arunima Bhattacharjee
Lindsey N. Anderson
Dr William C Nelson
Ari Jumpponen
Janet K. Jansson
Kirsten Hofmockel
Dr Christopher R Anderton
Dan Naylor
Sarah J. Fansler
Dr William C Nelson
Kirsten Hofmockel
Janet K. Jansson
Ryan McClure
Ruonan Wu
Michelle R Davison
Dr William C Nelson
Emily Graham
Sarah J. Fansler
Yuliya Farris
Jason McDermott
Kirsten Hofmockel
Janet K. Jansson
Sheryl L. Bell
People (11)

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...

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...

Hyun Song’s research is directed toward developing modeling and computational tools for the simulation of cellular metabolism and microbial community dynamics. His research interest in metabolic modeling includes 1) omics data-guided estimation of flux distribution in a genome-scale metabolic...

Tom Metz is a Principal Investigator within the Integrative Omics group at PNNL and the Metabolomics Team Lead for a group of scientists that focuses on development and applications of high throughput metabolomics and lipidomics methods to various biological questions. He has worked to develop state...

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 M.S.in Soil Microbiology at Colorado State University...

As Integrative Research Scientist, Dr. Hofmockel develops the overall science and technology strategy for EMSL in collaboration with the Deputy Directors. Responsible for EMSL’s Strategic Science Area in collaboration with the Deputy Directors. Is the interface with BER and the user community for...

Michelle Davison is a microbiologist with a love of challenging, creative, and multidisciplinary projects. She is interested in the role phage play in environmental systems, as well as the myriad ways they can be harnessed as tools. She has experience isolating, developing and working with non-model...

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...

Chris received his Bachelor of Science degree in chemistry at the University of Colorado at Colorado Springs in 2005. He attained his PhD in chemistry at the University of Illinois at Urbana–Champaign in 2011, under Mary L. Kraft, where his graduate work focused on using secondary ion mass...

Biography Dr. Mary Lipton is currently a Staff Scientist at the Pacific Northwest National Laboratory and Adjunct Professor at Washington State University-Tri-Cities in Richland and Adjunct Professor in the Institute for Biological Chemistry and Washington State University Pullman. She is nationally...

Sneha Couvillion’s current research focuses on deciphering microbial metabolic activity and interactions using a combination of powerful mass-spectrometry (MS)-based omics methods (metabolomics, lipidomics, and proteomics) in a variety of environmental and human health related projects. Expertise...

Data Sources (12)
Methods (1)
Resources (2)