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Regulatory dynamics of microbial communities


EMSL Project ID
35199

Abstract

This is a proposal to conduct work in EMSL in support of the Foundational Scientific Focus Area (FSFA) research program at Pacific Northwest National Laboratory. This large-scale research program will address fundamental scientific issues on microbial interactions and investigate how microorganisms interact to carry out, in a coordinated manner, complex biogeochemical processes. Primary research emphasis will be on associations between autotrophic and heterotrophic microorganisms with the overall objective of understanding how such interactions impart stability and resistance to stress, environmental fitness, and functional efficiency.
The FSFA work relevant to this EMSL proposal consists of four primary scientific elements including: i.) ecological interactions; ii.) energy, carbon, and nutrient partitioning; iii.) genome evolution; and iv.) stress resistance and adaptation, and three enabling scientific elements including: i.) proteomics and metabolomics; ii.) co-evolved systems; and iii.) computational biology. The program includes seven external collaborators whose experience and capabilities complement PNNL's.
The FSFA will utilize a series of lab-based model systems consisting of constructed consortia with engineering potential, consortia derived from natural assemblages, as well as natural assemblages for hypothesis testing. Natural associations include microbial mats, biofilms, and lichens. Cohesiveness and integration will be achieved by focusing on four FSFA hypotheses and a common set of biological systems.
Work performed in the EMSL will provided critical data needed by the FSFA and will utilize existing and new capabilities in 1) proteomics, 2) metabolomics, 3) cell isolation, 4) transcription analysis, and 5) cell imaging. Data from these studies will be integrated by both EMSL staff and the external scientific team to address the fundamental science aim of this proposal, which is to understand how communities of organisms respond to changes in their environment, both in terms of their underlying genetic regulatory networks as well as community structure. Most of the work on defining microbial community structure is not included in the scope of this EMSL proposal. However, we are proposing to use EMSL capabilities to provide an integrated, molecular-level understanding of community dynamics (e.g. protein and gene expression profiles). These data will be essential for the success of the FSFA and will provide entirely novel insights into how microbial communities are regulated.

Project Details

Project type
Large-Scale EMSL Research
Start Date
2009-10-13
End Date
2012-09-30
Status
Closed

Team

Principal Investigator

H Wiley
Institution
Environmental Molecular Sciences Laboratory

Team Members

Natalie Sadler
Institution
Pacific Northwest National Laboratory

Michael Lewis
Institution
Pacific Northwest National Laboratory

Lindsey Anderson
Institution
Pacific Northwest National Laboratory

Casey Stamper
Institution
Pacific Northwest National Laboratory

Heather Engelmann
Institution
Pacific Northwest National Laboratory

Na Fu
Institution
Pacific Northwest National Laboratory

Lye Meng Markillie
Institution
Environmental Molecular Sciences Laboratory

David Ward
Institution
Montana State University

Sergey Stolyar
Institution
University of Idaho

Roslyn Brown
Institution
Washington State University Tri-Cities

Aaron Wright
Institution
Pacific Northwest National Laboratory

Phillip Koech
Institution
Pacific Northwest National Laboratory

Yijia Xiong
Institution
Western University of Health Sciences

Grigoriy Pinchuk
Institution
Pacific Northwest National Laboratory

Helen Kreuzer
Institution
Pacific Northwest National Laboratory

Thomas Metz
Institution
Pacific Northwest National Laboratory

Paul Majors
Institution
Washington State University

James Fredrickson
Institution
Pacific Northwest National Laboratory

Mary Lipton
Institution
Environmental Molecular Sciences Laboratory

Thomas Squier
Institution
Western University of Health Sciences

Alice Dohnalkova
Institution
Environmental Molecular Sciences Laboratory

Related Publications

Moran JJ, LM Whitmore, NG Isern, MF Romine, KM Riha, WP Inskeep, and HW Kreuzer. 2016. "Formaldehyde as a carbon and electron shuttle between autotroph and heterotroph populations in acidic hydrothermal vents of Norris Geyser Basin, Yellowstone National Park." Extremophiles 20(3):291-299. doi:10. 1007/s00792-016-0821-2
Sadler NC, and AT Wright. 2015. "Activity-Based Protein Profiling of Microbes." Current Opinion in Chemical Biology 24:139-144. doi:10.1016/j.cbpa.2014.10.022
Taylor RC, BJM Webb-Robertson, LM Markillie, MH Serres, BE Linggi, JT Aldrich, EA Hill, MF Romine, MS Lipton, and HS Wiley. 2013. "Changes in Translational Efficiency is a Dominant Regulatory Mechanism in the Environmental Response of Bacteria." Integrative Biology 5(11):1393-1406. doi:10.1039/C3IB40120K