John Cliff

Multiplexed isotope in situ hybridization (iISH) to profile complex microbial assemblages

Lead Institution

Environmental Molecular Sciences Laboratory

Principal Investigator

Jeremy Bougoure

The use of fluorescence based in situ hybridization (FISH) is an established method for identifying specific nucleic acids associated with microorganism identification (rRNA) and/or function (mRNA,…

Using culture-independent methods to link active compound-specific carbon degradation to greenhouse gas production and recycling in natural populations of permafrost microbes

Lead Institution

Environmental Molecular Sciences Laboratory

Principal Investigator

John Cliff

The initial focus of this work will be to improve sample handling of microbial samples to aid in FISH, Imaging Mass Spectrometry, and other spatially-resolved analyses. In initial efforts, we will…

Trace signatures in particles

Lead Institution

Environmental Molecular Sciences Laboratory

Principal Investigator

John Cliff

Project type

Exploratory Research

We wish to collect a few ToF-SIMS spectra of specimens important for forensic purposes in order to include the data in a proposal (if succesfull).

Understanding the Interactions of the Plant Root and Plant Growth Promoting Bacteria with Unique Correlative Surface Imaging Tools

Lead Institution

Environmental Molecular Sciences Laboratory

Principal Investigator

Zihua Zhu

This research aims to achieve the following objectives: 1) integrate surface tools and apply them in submicron chemical mapping of the plant-microbe interface; 2) provide novel in vivo analysis of…

Elemental characterization of ionizer filaments for thermal ionization mass spectrometry (TIMS).

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

Mark Engelmann

Project type

Exploratory Research

There has been a great discrepancy in the function of ionizer filaments for use in TIMS in our lab. Seemingly identicle preparation methods continue to give unpredictable results. This proposal…

Structure and Chemical Mapping of Soil Organic Matter on Mineral Surfaces

Lead Institution

Environmental Molecular Sciences Laboratory

Principal Investigator

Ravi Kukkadapu

Secreted and decomposing soil organic matter (SOM) containing carbon, nitrogen, phosphorus, and metals form the basis of many bio/organic matter-mineral interactions in soils. These compounds are …

Stable isotopes to study nutrient cycling in soils.

Lead Institution

Environmental Molecular Sciences Laboratory

Principal Investigator

John Cliff

Project type

Exploratory Research

Studying nutrient cycling in soils is important from economic and environmental perspectives. Our research has focused on the use of stable C and N isotopes to trace soil chemical processes and…

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…

Imaging and Monitoring the Initial Stages of Biofilm Formation

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

R. Shane Addleman

As outlined below, the goal of this study to apply an integrated, multi-faceted approach to the analysis of the initial molecular and cellular processes involved with cell adhesion, colonization, and…

Multi-diagnostic approach for correlating light isotopes in materials from nano to macro scales

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

Elizabeth Kautz

The accurate quantification and mapping of light element isotopes, such as hydrogen (H) isotopes and lithium (Li) isotopes, is critical to building reliable, accurate mechanistic models during…

Carbon, Oxide, Metal Sequestration Mechanisms of Hot Springs Microbial Communities: Establishing a Technical Platform for Chemical Imaging Investigation

Lead Institution

Environmental Molecular Sciences Laboratory

Principal Investigator

Sherry Cady

Though microbes can indirectly and metabolically transform, sequester, and transport (i) ions, (ii) organic and inorganic complexes, and (iii) precipitates via a wide range of mechanisms,…

New Mesoscale Multi-Modal Imaging Of Cellular Communication Between Microbe And Plant In The Rhizosphere – A Pilot Project

Lead Institution

University of Missouri - Columbia

Principal Investigator

Richard Ferrieri

The interaction between plants and their environment is of key importance in promoting sustainable, healthy, and robust plant growth. Underlying the ability of plants to cope with a variety of…

Control of methane and carbon dioxide emissions by sulfur biogeochemistry in terrestrial ecosystems

Lead Institution

Environmental Molecular Sciences Laboratory

Principal Investigator

John Cliff

Project type

Large-Scale EMSL Research

Freshwater wetlands are responsible for 40% of the methane emissions worldwide. Despite very low amounts of ambient sulfate, these ecosystems often support high rates of sulfate reduction, rivaling…

Microbial Community Dynamics and Plant Phenomics with Single-Cell Gene Expression and Imaging Mass Spectrometry

Lead Institution

Environmental Molecular Sciences Laboratory

Principal Investigator

John Cliff

The inherent heterogeneity of biological systems, including microbial communities or cell populations, limits the questions that can be resolved by averaged cell population measurements, which lump…

New Mesoscale Multi-Modal Imaging Of Cellular Communication Between Microbe And Plant In The Rhizosphere -- A Pilot Project

Lead Institution

University of Missouri - Columbia

Principal Investigator

Richard Ferrieri

The interaction between plants and their environment is of key importance in promoting sustainable, healthy, and robust plant growth. Underlying the ability of plants to cope with a variety of…

Microbial Community Dynamics and Plant Phenomics with Single-Cell Gene Expression and Imaging Mass Spectrometry

Lead Institution

Environmental Molecular Sciences Laboratory

Principal Investigator

Galya Orr

The inherent heterogeneity of biological systems, including microbial communities or cell populations, limits the questions that can be resolved by averaged cell population measurements, which lump…

Advanced Techniques for Nuclear Materials Characterization

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

Dallas Reilly

PNNL is home to state of the art research capabilities, which are often underutilized on radioactive samples due to non-dispersion requirements and limits on sample quantity that can enter workspaces…

Atmospheric Soil Organic Particles

Lead Institution

Purdue University

Principal Investigator

Alexander Laskin

Recent discovery of atmospheric soil organic particles (ASOP), emitted through previously unrecognized atmosphere-land-surface interactions, suggests that ASOP may have a widespread impact over a…

Trace metal composition of Cobalt

Lead Institution

Environmental Molecular Sciences Laboratory

Principal Investigator

John Cliff

Project type

Exploratory Research

I would just like to ust the TOF-SIMS to identify trace metal constituents in Cobalt samples

Decreasing the amount of material required for gross biological carbon and nitrogen flux measurements by more than 12 orders of magnitude using ion implantation isotope dilution and stable isotope measurements by NanoSIMS

Lead Institution

Environmental Molecular Sciences Laboratory

Principal Investigator

John Cliff

Advances in mass spectrometry coupled to stable isotope probing techniques have profoundly influenced our understanding of process level biology and biogeochemistry. When stable isotope compounds and…

Evaluation of SIMS to measure N isotopes in soils

Lead Institution

Environmental Molecular Sciences Laboratory

Principal Investigator

John Cliff

Project type

Exploratory Research

Recent advances in cost and function of isotope ratio mass spectrometry have allowed insight into dynamic soil microbial processes associated with N cycling. However, minimum sample size often…

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…

Evaluation of SIMS for location of bacterial spores and to source growth media and geographic location.

Lead Institution

Environmental Molecular Sciences Laboratory

Principal Investigator

John Cliff

Project type

Exploratory Research

This work has two primary foci: 1) to evalute the use of TOF-SIMS to locate Bacterial spores labeled with Lanthanide metals, and 2) to evalute the use of TOF-SIMS fingerprinting as a component of…

Advanced Techniques for Nuclear Materials Characterization

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

Dallas Reilly

PNNL is home to state of the art research capabilities, which are often underutilized on radioactive samples due to non-dispersion requirements and limits on sample quantity that can enter workspaces…

Trace impurites in graphite crucible used for advanced detector materials synthesis

Lead Institution

Environmental Molecular Sciences Laboratory

Principal Investigator

John Cliff

Project type

Exploratory Research

Trace metal impurities in advanced detector materials may limit performance. In many instances the source of these impurities is unknown. One possible source of trace metal impurities in the…

Atmospheric Soil Organic Particles

Lead Institution

Purdue University

Principal Investigator

Alexander Laskin

Recent discovery of atmospheric soil organic particles (ASOP), emitted through previously unrecognized atmosphere-land-surface interactions, suggests that ASOP may have a widespread impact over a…

Projects