Stephen Callister

Improving the Robustness and Longevity of Methanothermobacter wolfeii strain BSEL when Converting Biogas with Hydrogen to Renewable Natural Gas

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

Stephen Callister

This resource owner proposal will measure the proteome responses of Methanothermobacter wolfeii strain BSEL wild type, and adaptive laboratory evolution developed mutants to different perturbations …

Growth-phase regulation of the proteome of Rhodobacter capsulatus.

Lead Institution

Memorial University of Newfoundland

Principal Investigator

Andrew Lang

Project type

Exploratory Research

The alpha-proteobacterium Rhodobacter capsulatus uses a histidyl-aspartyl signaling system for growth-phase-dependent regulation of expression of some genes. The response regulator protein CtrA is…

Dissection and Deciphering of the Soil Microbiome

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

Janet Jansson

This proposal aims to address key gaps in our knowledge about the composition and functional roles of the tens of thousands of microbial species in soil. Although these microorganisms carry out…

Scaling the Microbial Ecology of Soil Carbon

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

Kirsten Hofmockel

We propose to determine the ecology of soil microbial responses to experimental warming, by utilizing EMSL capabilities to quantifying growth, mortality, and C use and growth efficiency, as modulated…

A proteomic perspective of biodiversity

Lead Institution

National Ecological Observatory Network

Principal Investigator

John Parnell

Project type

Exploratory Research

- The relationship between biodiversity and ecosystem stability has become a central focus for ecologists, particularly in the face of environmental stresses and global climate change. Although…

Biosystems Analysis for Determining the Impact of Nutrient Uptake on Autotroph-Heterotroph Interactions within Cyanobacterial Consortia

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

Stephen Callister

Project type

Large-Scale EMSL Research

The exchange of carbon and other nutrients between microorganisms is a key factor in the establishment of microbial interactions and trophic levels. Depending upon the nutrient, the establishment of…

Development of Novel Approaches to Target Microbial Drivers of C Cycling in Soil Aggregates

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

Kirsten Hofmockel

This proposal seeks to provide much needed insight into the microbial controls of terrestrial C cycling through the development of a novel research approach that integrates multiple technologies, and…

Exploring the Boundaries of Metazoan Thermotolerance at Hydrothermal Vents: Respiration and Protein Expression of Paralvinellid Worms

Lead Institution

Harvard University

Principal Investigator

Peter Girguis

Project type

Large-Scale EMSL Research

As evidence of global climate change mounts, there is a growing impetus to examine the responses of metazoan life to increasing thermal pressure. Organismal thermotolerance has been the subject of…

Probing complex microbiomes using mass spectrometry and sequencing capabilities to understand how microbiomes are influenced by their environment

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

Stephen Callister

This proposal will utilize next generation sequencing and mass spectrometry (MS) capabilities to address key knowledge gaps in our functional understanding of how complex microbiomes influence and…

Solid-state NMR Investigation into the Transformation of Necromass to SOM

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

Stephen Callister

NMR will be utilized to help bridge the knowledge gap between carbon cycling and storage of carbon within soil organic matter (SOM). Specifically, NMR will help address the questions: (1) how much…

Exploring the boundaries of metazoan thermotolerance at hydrothermal vents: Respiration and protein expression of paralvinellid worms

Lead Institution

Harvard University

Principal Investigator

Peter Girguis

Project type

Exploratory Research

As evidence of global climate change mounts, there is a growing impetus to examine the responses of metazoan life to increasing thermal pressure. Organismal thermotolerance is the subject of many…

Connecting genomic capabilities to physiology, photosynthesis and carbon cycling

Lead Institution

Monterey Bay Aquarium Research Institute

Principal Investigator

Alexandra Worden

Project type

Large-Scale EMSL Research

More than 50% of global primary production is performed by land plants and green algae. Of all algae green algae are the most closely related to land plants and therefore provide powerful single cell…

The Influence of Crop Selection and Soil Properties on the Accumulation and Stabilization of Microbial Residues in Soil

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

Kirsten Hofmockel

EMSL Staff Proposal: The proposed research confronts the emerging paradigm that dead microbial cells, or necromass, are a major source of organic carbon in soil. Microbial necromass accumulation may…

High-Throughput Proteomics: Applications and Development (PNNL Scope #40601 and #43488)

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

Gordon Anderson

This project involves the application and development of high-throughput proteomics and quantitative measurement capabilities within biological systems. More so, application measurements will be…

Pan-Omics Technology Development, Implementation, and Application to GSP Systems Biology Research

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

Joshua Adkins

The BER Genome Science Program aims to understand complex biological and environmental systems across spatial and temporal scales to develop predictive knowledge relevant to DOE mission challenges…

Elucidating unifying principles of soil C-N coupling using a continental scale grassland experimental network

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

Kirsten Hofmockel

EMSL capabilities will be utilized for analysis of samples acquired from a continental-scale network of replicated, long-term grassland nutrient addition experiments, the Nutrient Network, to enhance…

Signal transduction pathways regulating genetic exchange

Lead Institution

Memorial University of Newfoundland

Principal Investigator

Andrew Lang

Project type

Large-Scale EMSL Research

The alphaproteobacterium R. capsulatus is a model organism for studying photosynthesis, nitrogen fixation, and hydrogen production. R. capsulatus also produces a virus-like particle called the &quot…

Proteomic Insights into Mechanisms of Microbial Dormancy

Lead Institution

Environmental Molecular Sciences Laboratory

Principal Investigator

Jared Shaw

Ecologically important processes such as carbon and nutrient cycling largely depend on the active fraction of microbial communities, and only a small portion of the total soil microbiome is active…

Molecular Phenotyping of Plants & Microbes (MolPheno) for the PRedicting Ecosystem Resilience through Multiscale and Integrative Science (PREMIS) initiative

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

Kim Hixson

This proposal aims to provide the fundamental molecular characterization necessary to develop a model which ultimately links phenotypic measurements to the soil biogeochemistry associated with…

Community proteomics of oxic-anoxic cycling in the Great Salt Lake, Utah

Lead Institution

National Ecological Observatory Network

Principal Investigator

John Parnell

Project type

Large-Scale EMSL Research

Extreme environments generally contain stable low-complexity microbial communities making them good targets for community proteomic studies. Often the caveat for low-complexity communities is the…

Probing complex microbiomes using mass spectrometry and sequencing capabilities to understand how microbiomes are influenced by their environment

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

Stephen Callister

This is a resource owner proposal as part of the MinT LDRD Initiative. The objective of this proposal is the development of sequencing and mass spectrometry capabilities to support research into how…

Can Microbial Ecology and Mycorrhizal Functioning Inform Climate Change Models?

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

Kirsten Hofmockel

Using archived samples from forest Free Air CO2 Enrichment (FACE) experiments, field measurements from the Marcell Experimental Forest (MEF) and the Spruce and Peatland Response Under Climatic and…

Does Forest-to-Pasture conversion decrease functional turnover across space? – Measuring the effects of deforestation on the Amazon rainforest soil microbiome

Lead Institution

University of California, Davis

Principal Investigator

Jorge Rodrigues

Project type

Limited Scope

The Amazon rainforest plays an essential role in CO2 sequestration. Yet, the impact of anthropogenic activities on microbial communities that participate in this biochemical process needs…

Advancing ecosystem understanding of carbon turnover and storage through molecular characterization

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

Kirsten Hofmockel

The coupling between concurrently changing carbon (C) and nitrogen (N) cycles remains a key uncertainty in understanding feedbacks between the terrestrial C cycle and climate change. Decades of…

Identifying & Translating OP Receptors in Animal Models and Humans using ABPP

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

Aaron Wright

This EMSL Resource Owner proposal requests use of EMSL resources, owned or co-owned, in order to successfully accomplish the use of activity based protein profiling (ABPP) capabilities to identify…

Development of a systems-level model of cellular dynamics in response to different environmental conditions in cyanobacteria

Lead Institution

Purdue University

Principal Investigator

Louis Sherman

Project type

Large-Scale EMSL Research

This proposal will utilize a systems biology approach to develop a knowledgebase of the metabolic and regulatory networks that can ultimately be used for the photobiological production of advanced…

Development of novel approaches to target microbial drivers of C cycling in soil aggregates

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

Kirsten Hofmockel

We propose to develop approaches that target metabolically active microorganisms and functions that drive carbon cycling in soils from bioenergy cropping systems. Albeit critically important, soil…

ABPP of Opioid and Sedative Receptors to Improve Medical Countermeasure Development

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

Aaron Wright

This EMSL Resource Owner proposal seeks to utilize Orbitrap MS capabilities for advancing our understanding of opioid and sedative exposures, which could lead to developing safe and efficacious…

Proteomics Measurements of Functional Redundancy and Stability Testing of Cellulose Degrading Anaerobic Microbial Communities within Engineered Bioreactors

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

Stephen Callister

An understanding of the role of functional redundancy within a microbial community is fundamental to predicting the stability associated with key services provided by that community. One provided…

Decomposers in Transition

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

Kirsten Hofmockel

The overarching objective of the research is to develop a scalable approach for understanding how soil decomposer community dynamics are affected by spatial heterogeneity and climate change (drought)…

Developing an automation-ready high throughput chemoproteomic workflow

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

Vivian Lin

We propose to develop a high-throughput (HTP) workflow for activity-based protein profiling (ABPP) or bioorthogonal non-canonical amino acid tagging (BONCAT) samples. This HTP chemoproteomic sample…

Pan-Omics Technology Development, Implementation, and Application to GSP Systems Biology Research

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

Joshua Adkins

The BER Genome Science Program aims to understand complex biological and environmental systems across spatial and temporal scales to develop predictive knowledge relevant to DOE mission challenges…

Can Microbial Ecology and Mycorrhizal Functioning Inform Climate Change Models?

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

Kirsten Hofmockel

Using archived samples from forest Free Air CO2 Enrichment (FACE) experiments, field measurements from the Marcell Experimental Forest (MEF) and the Spruce and Peatland Response Under Climatic and…

Connecting genomes to physiology and response in marine photosynthetic eukaryotes: Systems biology of the green alga Micromonas

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

Stephen Callister

We propose to develop a model system for addressing microbial responses to abiotic and biotic interactions. Our goal is for this system to provide insights on marine and freshwater photosynthetic…

The Influence of Crop Selection and Soil Properties on the Accumulation and Stabilization of Microbial Residues in Soil

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

Kirsten Hofmockel

The proposed research confronts the emerging paradigm that dead microbial cells, or necromass, are a major source of organic carbon in soil. Microbial necromass accumulation may vary between annual…

Improved understanding of microbial iron and sulfate reduction through a combination of bottom-up and top-down functional proteomics assays

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

Stephen Callister

In this proposal we have created an experimental plan to tackle the functional annotation bottleneck in two groups of microorganisms of particular interest for heavy metals and radionuclide…

ELUCIDATING UNIFYING PRINCIPLES OF SOIL C-N COUPLING USING A CONTINENTAL- SCALE GRASSLAND EXPERIMENTAL NETWORK

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

Kirsten Hofmockel

EMSL capabilities will be utilized for analysis of samples acquired from a continental-scale network of replicated, long-term grassland nutrient addition experiments, the Nutrient Network, to enhance…

Development of novel approaches to target microbial drivers of C cycling in soil aggregates

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

Kirsten Hofmockel

Project type

FICUS Research

We propose to develop approaches that target metabolically active microorganisms and functions that drive carbon cycling in soils from bioenergy cropping systems. Albeit critically important, soil…

Advancing ecosystem understanding of carbon turnover and storage through molecular characterization

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

Kirsten Hofmockel

EMSL Staff Proposal: The coupling between concurrently changing carbon (C) and nitrogen (N) cycles remains a key uncertainty in understanding feedbacks between the terrestrial C cycle and climate…

Evaluation of the Adaptation and Acclimation of Hypersaline Lithifying Microbial Mats to Salinity Disturbance in the Great Salt Lake Ecosystem

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

Stephen Callister

Project type

Large-Scale EMSL Research

Multiple capabilities at EMSL will be applied to mat microbial communities present along a salinity gradient between the North and South arms of the Great Salt Lake, UT. These lithifying microbial…

The Influence of Crop Selection and Soil Properties on the Accumulation and Stabilization of Microbial Residues in Soil

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

Kirsten Hofmockel

EMSL Staff Proposal: The proposed research confronts the emerging paradigm that dead microbial cells, or necromass, are a major source of organic carbon in soil. Microbial necromass accumulation may…

Coupling temporal variations in geochemistry to activities of microbial populations in the deep subseafloor biosphere

Lead Institution

Harvard University

Principal Investigator

Peter Girguis

Project type

Large-Scale EMSL Research

To date, studies of the oceanic subsurface biosphere have effectively demonstrated the existence of an active microbial community, and have begun to characterize community density and distribution…

Pan-Omics Technology Development, Implementation, and Application to GSP Systems Biology Research

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

Joshua Adkins

The BER Genome Science Program aims to understand complex biological and environmental systems across spatial and temporal scales to develop predictive knowledge relevant to DOE mission challenges…

Can Microbial Ecology and Mycorrhizal Functioning Inform Climate Change Models?

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

Kirsten Hofmockel

EMSL Staff Proposal: Using archived samples from forest Free Air CO2 Enrichment (FACE) experiments, field measurements from the Marcell Experimental Forest (MEF) and the Spruce and Peatland Response…

Projects