Kirsten Hofmockel | Environmental Molecular Sciences Laboratory

Unraveling spatial and temporal dynamics of microbial necromass destabilization

Lead Institution

U.S. Geological Survey

Principal Investigator

Courtney Creamer

Project type

Large-Scale EMSL Research

Microbial necromass—or the extracellular and intracellular remains of dead microbes—can make up a significant portion of soil organic carbon and nitrogen. But a large quantity of necromass doesn’t…

Investigating the Role of Drought-Impacted Root Exudates on Rhizosphere Microbial Metabolism and Viral Dynamics for Improving Tall Wheatgrass Drought Tolerance

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

Sneha Couvillion

Project type

Large-Scale EMSL Research

The rhizosphere is the center of interactions between roots, soil, and microbes, where chemical exchanges are key drivers of microbial composition, plant productivity, and resilience to abiotic…

Linking multi-organism-environment interactions across lab and field scales to estimate viral contributions to soil C cycling

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

Amy Zimmerman

Project type

FICUS Research

Interactions between soil viruses and their microbial hosts can significantly impact microbial population dynamics, metabolism, and evolution, with cascading effects on soil carbon (C)…

The role of microbial predation and cooperation on soil carbon pathways measured through multi-omics

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

Bram WG Stone

Project type

FICUS Research

Soil microorganisms drive the decomposition of terrestrial carbon, releasing CO2 into the atmosphere and retaining additional pools belowground. Thus, a critical parameter in climate modeling efforts…

Prediction of response of microbial interaction networks cycling carbon to changing moisture conditions

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

Ryan McClure

Harnessing the soil microbiome presents transformational opportunities to optimize the economic and environmental value of our nation’s soil microbiomes, including maintaining soil organic matter…

TEAMS - Trial Ecosystems for the Advancement of Microbiome Science

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

Ryan McClure

A primary goal of the TEAMs project is to optimize the Soil EcoFAB devices to accommodate goals of the soil microbiome scientific community. We have made significant progress advancing the Soil…

Moisture and seasonal drivers of Inter-Kingdom metabolic interaction in a marginal soil rhizosphere

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

William Nelson

Project type

FICUS Research

Soil is a complex environment with numerous competing and cooperating populations contributing to overall ecosystem services. Plants provide most of the fresh organic carbon inputs through growth and…

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…

A Conceptual Framework for Multiscale Simulation of Carbon Transport, Transformation and Disposition in the Soil-Plant-Microbe Continuum

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

Timothy Scheibe

This project, designed to serve as the focal element of the System Thrust of EMSL’s Strategic Science Area (SSA), is aimed at the development of an integrated multiscale modeling framework that…

Micro to Macro - Molecular and Spatial Controls on Microbial Function

Lead Institution

Kula Bio, Inc.

Principal Investigator

Darian Smercina

Project type

Large-Scale EMSL Research

Establishing a clear and predictable link between the structure and function of soil microbial communities and ecosystem processes remains one of the greatest challenges in soil ecology. Soil…

Rhizosphere processes at molecular to core scale

Lead Institution

Environmental Molecular Sciences Laboratory

Principal Investigator

Nancy Hess

The amount of C in soil far exceeds the C content of atmosphere as well as the amount C stored above ground as plant biomass. The C fluxes between atmosphere and biomass are huge, many orders of…

Extracellular Research Thrust for EMSL SSA

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

Kirsten Hofmockel

Here we propose to address the basic geochemical and biogeochemical interactions that mediate organic-mineral interactions. Identifying binding mechanisms at the organic matter-mineral interface will…

Spatially resolved chemical proteomics for linking enzymatic activity to omics phenotyping in heterogeneous microbial communities

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

Vivian Lin

We will connect chemical probes and nanoPOTS to rapidly identify microbial species and essential protein functions in structured microbial communities. We will use aggregation induced emission (AIE)…

Spatially-resolved, consortial approaches towards a mechanistic understanding of soil nitrogen fate

Lead Institution

Purdue University

Principal Investigator

Stephen Lindemann

Nitrogen acquisition is a key determinant of plant productivity and the fate of nitrogen, both applied and endogenous, is largely controlled by microbial processes. Furthermore, microbially-induced…

Prediction of soil microbiome phenotypic responses to changing moisture conditions

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

Jason McDermott

The goal of this project is to attain a systems level understanding of the soil microbiome and its phenotypic response to changing moisture through a tractable, spatially explicit examination of the…

Resolving taxon-specific contributions to nutrient cycling in soil microbial communities through stable isotope enabled multi-omics

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

Amy Zimmerman

Project type

FICUS Research

Mechanistic and predictive understanding of microbial nutrient cycling requires deconvoluting the outcomes of multiple population- and community-scale processes. Yet quantitative knowledge of…

Carbon Sequestration Beneath the Active Zone of the Rhizosphere: Insights from Extremophile Ecosystems

Lead Institution

Environmental Molecular Sciences Laboratory

Principal Investigator

Sherry Cady

To better understand the ultimate fate of carbon sequestered in the subsurface, we are studying carbon sequestration mechanisms in mineralizing extremophile environments. Such ecosystems provide an…

Extracellular Research Thrust for EMSL SSA

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

Kirsten Hofmockel

This project will develop a conceptual framework that defines the biotic and abiotic mechanisms regulating the persistence of mineral associated organic matter (OM). The specific goals are to…

Bio-printed microbial habitats for high-throughput, in situ metaphenomics

Lead Institution

Environmental Molecular Sciences Laboratory

Principal Investigator

Jayde Aufrecht

Outside of laboratory cultures microorganisms live in micro-structured environments which provide non-competitive spatial niches critical to maintaining genotypic and phenotypic diversity in the…

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…

Prediction of soil microbiome phenotypic responses to changing moisture conditions

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

Jason McDermott

The goal of this project is to attain a systems level understanding of the soil microbiome and its phenotypic response to changing moisture through a tractable, spatially explicit examination of the…

Soil-like habitats for spatial analysis of microbe-mineral interactions

Lead Institution

Environmental Molecular Sciences Laboratory

Principal Investigator

Arunima Bhattacharjee

The objective of this study is to develop mineral microfluidics compatible with a suite of optical and chemical imaging capabilities at EMSL, as well as SSRL, for probing microbially relevant…

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…

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…

The microbial impact of soil carbon and nutrient transformations: scaling and stoichiometry

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

Kirsten Hofmockel

The proposed work is centered around the combination of stable isotope probing (SIP) techniques with high resolution -omics data to resolve the movement of ecologically critical elements (carbon,…

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)…

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…

Prediction of response in soil microbiome carbon utilization to changing moisture conditions

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

Jason McDermott

This project is directed under the “Phenotypic Response of the Soil Microbiome to Environmental Perturbations” SFA project awarded to Pacific Northwest National Laboratory. The goal of the SFA is to…

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…

In situ characterization of associations and resource exchange between free-living nitrogen-fixers and switchgrass

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

Kirsten Hofmockel

This project will increase our understanding of carbon (C) and nitrogen (N) exchange in the rhizosphere. Specifically, we aim to understand how free-living nitrogen-fixing bacteria (diazotrophs) may…

Disentangling the role of microbial interactions and spatial structure in soil organic matter decomposition

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

Ryan McClure

Project type

Exploratory Research

The study of the soil microbiome is critical to understanding the ecological functions carried out by soil microorganisms, particularly with respect to the cycling of carbon (C) and nitrogen (N)…

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…

Prediction of response in soil microbiome carbon utilization to changing moisture conditions

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

Jason McDermott

Project type

FICUS Research

The goal of this project is to attain a systems level understanding of the soil microbiome and its phenotypic response to changing moisture through a tractable, spatially explicit examination of the…

The microbial impact of soil carbon and nutrient transformations: scaling and stoichiometry

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

Kirsten Hofmockel

The proposed work is centered around the combination of stable isotope probing (SIP) techniques with high resolution -omics data to resolve the movement of ecologically critical elements (carbon,…

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…

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…

TWIN Ecosystems Project

Lead Institution

Environmental Molecular Sciences Laboratory

Principal Investigator

Nancy Hess

The goal of the TWIN ecosystem project (‘TWINS’) is to pilot laboratory and field ‘twin’ ecosystems that use sensors and autonomous controls to test the hypothesis that compositional changes in root…

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…

Feedbacks between microbial community dynamics and the persistence of soil organic carbon

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

Kirsten Hofmockel

Project type

Exploratory Research

Soil organic matter (SOM) is the largest active carbon reservoir in the terrestrial environment and significantly influences soil fertility, water quality, global C cycling and associated feedbacks…

Scaling microbial carbon use efficiency from the individual to the community

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

Bram WG Stone

Soil microorganisms are recognized as the key agents in the global biogeochemical cycling of nutrients important for life such as carbon (C), nitrogen (N), and phosphorus (P). Soil organic matter…

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…

Prediction of soil microbiome phenotypic responses to changing moisture conditions

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

Jason McDermott

The goal of this project is to attain a systems level understanding of the soil microbiome and its phenotypic response to changing moisture through a tractable, spatially explicit examination of the…

Prediction of response of microbial interaction networks cycling carbon to changing moisture conditions

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

Ryan McClure

Harnessing the soil microbiome presents transformational opportunities to optimize the economic and environmental value of our nation’s soil microbiomes, including maintaining soil organic matter…

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…

Controls on the Composition of Persistent Microbial-derived Organic Matter in Soil

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

Kirsten Hofmockel

Project type

Exploratory Research

Current estimates suggest that soils contain 1.5 x 10^12 tons of carbon, or roughly three times more carbon than the atmosphere, and represent a giant reservoir for potential greenhouse gas emission…

Automating Microbial Community Phenotyping within Synthetic Soil Aggregates

Lead Institution

Environmental Molecular Sciences Laboratory

Principal Investigator

Jayde Aufrecht

Microbial hotspots are the sites of nearly all biogeochemical transformations (BGT) in the soil. Unfortunately, the small size (µm to mm) and transient existence (hours to days) of microbial…

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…

Evaluating Spatial and Molecular Drivers of Microbial Function

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

Kirsten Hofmockel

One of the greatest and most persistent challenges in the field of soil ecology is the establishment of a direct and predictable link between soil microorganisms and ecosystem function. Soil…

Colocalization of Minerals and Persistent Microbial-derived Organic Matter in Soil

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

Kirsten Hofmockel

Microorganisms are considered a dominant source of persistent soil organic matter (SOM); yet the persistence of microbial-derived organic matter (OM) remains to be discovered. In the proposed work we…

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…

Projects