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Microbial diversity influences nitrogen cycling in rivers

Image of streambed

Seasonal changes affect microbiome communities, genes, and subsurface biogeochemical pathways differently

March 4, 2020
March 4, 2020
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The Science
DOE researchers investigated the role of microbial genetic diversity in two major subsurface biogeochemical processes: nitrification and denitrification. Results show that across different seasons only a few microbe species, namely Nitrosoarchaeum, carry out nitrification functions—demonstrating high resistance to environmental change. However, denitrification genes, which are more broadly distributed in the community, displayed a variety of diversity patterns and abundance dynamics—demonstrating greater microbial interactions as conditions change.

Nitrogen cycling in hyporheic zone
Figure shows nitrogen transformations in the hyporheic zone, where a vast microbiome community influences nutrient cycling. Upper layers, closer to the riverbed contain more oxygen and organic matter. Under these conditions nitrification (orange arrows) occurs. Microbes transform the nitrogen from organic matter through a variety of steps and ultimately deplete the oxygen. As oxygen depletes, denitrification (blue arrows) further transforms nitrogen, resulting in an electron acceptor for catabolism of organic matter.

The Impact
There is little research connecting microbiomes at the genetic level to hydrobiogeochemical modeling. This research helps broaden collective knowledge for a better understanding of the pathways affected by environmental changes. For example, under extreme environmental conditions an entire biochemical pathway could be altered or eliminated if a single step has low genetic diversity such that its loss could not be replaced.

Summary
The Pacific Northwest National Laboratory research team, led by Bill Nelson, found that major environmental processes—specifically nitrification and denitrification—are maintained through a variety of diversity strategies. Historically, the bulk of biogeochemical research has focused on microbial communities at the organismal level. But this research focused on the importance of genetic distribution and diversity.

In their recent PLoS ONE paper, the researchers discuss the roles microbes play in ecological functions; the novelty of the genetic makeup of these microbes; and future research opportunities to determine which organisms are genetically expressing nitrogen cycling functions.

The novelty of this study comes from examining the temporal dynamics of diversity at the gene level. To evaluate all genes in the nitrification and denitrification pathways, novel Hidden Markov Models (HMMs) were developed that can recognize the broad diversity found in environmental samples. They found that while different environmental conditions impair microbiome growth and the gene expression of some populations, at the same time, it can stimulate others. High biodiversity at the organism or genetic level creates more resiliency, and the microbiome community can respond more rapidly to environmental changes.

Contact
Bill Nelson, Pacific Northwest National Laboratory, William.Nelson@pnnl.gov

Funding
This research was supported by the U.S. Department of Energy (DOE), Office of Biological and Environmental Research (BER), as part of the Subsurface Biogeochemical Research Scientific Focus Area (SFA) at Pacific Northwest National Laboratory (PNNL).

W.C. Nelson, E.B. Graham, A.R. Crump, S.J. Fansler, E.V. Arntzen, D.W. Kennedy, J.C. Stegen, “Distinct temporal diversity profiles for nitrogen cycling genes in a hyporheic microbiome”. PLoS ONE 15(1) e0228165 (2020). [DOI: 10.1371/ journal.pone.0228165]

FEBRUARY 25, 2020
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Forces of Attraction

Weak forces are strong enough to align semiconductor nanoparticles; new understanding may help make more useful materials

Peeking Into the Lives of Soil Microbiomes

Photo of plant in soil

SoilBox provides in-depth imaging and characterization of soil microbial communities in their native environments.

February 28, 2020
February 25, 2020
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The Science
To better characterize the vast diversity of soil microbes and their interactions, DOE researchers developed a high-tech simulated soil core called SoilBox. This 16.7-centimeter-deep box allows researchers to visualize soil microbes’ complex interactions using different imaging methods and facilitating, for the first time, visualization of the soil microbiome’s organization and community metabolism. Furthermore, SoilBox provides a tool for researchers to observe how soil microbial communities respond to environmental changes and perturbations.

The Impact
The complexity of soil makes spatial imaging of soil microbial communities challenging. Using SoilBox, researchers can now visualize the diversity and metabolic

Graphic of Soilbox
SoilBox allows researchers to characterize and image soil microbiome dynamics at a level of resolution not previously available. This especially applies to how soil microbes respond to environmental shifts.

landscape of the soil microbiome under different environmental conditions, such as soil moisture and temperature. Understanding the basic biology of the soil microbiome is necessary for understanding how native soil systems respond to environmental perturbations such as drought, lack of nutrients, and fire. 

Summary
Soil-dwelling microbes are key players in the overall health of soil ecosystems, performing critical functions like carbon and nutrient cycling. The interplay between the soil microbiome and the soil it inhabits is a dynamic relationship heavily influenced by factors such as soil acidity, organic content, and temperature. The size and distribution of soil particles also affects many soil characteristics, adding to the already complex challenge of accurately describing structure-function relationships of soil microbial communities.

To address the difficulties of studying the soil microbiome in its native state and at a microscale resolution, a team of researchers from Pacific Northwest National Laboratory, led by Arunima Bhattacharjee and Chris Anderton, developed SoilBox. This system represents a soil ecosystem by simulating an ~12-cm-deep soil core; several windows facilitate molecular and optical imaging measurements that are crucial to understanding the nuanced interactions between the soil microbiome and its environment. This novel imaging capability allows scientists to study the dynamic landscape of soil microbial communities as they relate to environmental changes, including nutrient cycling.

This work overcomes the challenge of visualizing the diversity of soil microbial communities in the complex and ever-changing environment of soil. SoilBox will be used in the near future to investigate soil microbial community dynamics.

Contact
Chris Anderton, Pacific Northwest National Laboratory, christopher.anderton@pnnl.gov

Funding
This research was supported by the Department of Energy (DOE) Office of Biological and Environmental Research (BER) and is a contribution of the Scientific Focus Area "Phenotypic response of the soil microbiome to environmental perturbations." Pacific Northwest National Laboratory (PNNL) is operated for the DOE by Battelle Memorial Institute under Contract DE-AC05-76RLO1830. A portion of the research was performed using EMSL, the Environmental Molecular Sciences Laboratory, a DOE Office of Science User Facility sponsored by BER and located at PNNL.

A. Bhattacharjee et al.,“Visualizing microbial community dynamics via a controllable soil environment.” mSystems 5, 1:e00645-19 (2020). https://doi.org/10.1128/mSystems.00645-19.

JANUARY 21, 2020
Web Feature

Forensic Proteomics: Beyond DNA Profiling

A new book by PNNL biochemist Erick Merkley details forensic proteomics, a technique that directly analyzes proteins in unknown samples, in pursuit of making proteomics a widespread forensic method when DNA is missing or ambiguous.
JANUARY 10, 2020
Web Feature

Clark Recognized for Nuclear Chemistry Research

The world’s largest scientific society honored Sue B. Clark, a PNNL and WSU chemist, for contributions toward resolving our legacy of radioactive waste, advancing nuclear safeguards, and developing landmark nuclear research capabilities.
NOVEMBER 26, 2019
Web Feature

Conquering Peak Power

PNNL’s Intelligent Load Control technology manages and adjusts electricity use in buildings when there’s peak demand on the power grid.

Protecting climate-sensitive soil ecosystems

Image of permafrost landscape

Review paper summarizes the effects of climate change on soil microorganisms and the ecosystem services they provide, and evaluates potential mitigation measures.

October 14, 2019
October 14, 2019
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The Science
Researchers from Pacific Northwest National Laboratory reviewed the current state of knowledge about the impacts of climate change on soil microorganisms in different climate-sensitive soil ecosystems. They also examined the possibilities of using soil microorganisms to store carbon or inoculate plants to help mitigate the negative consequences of climate change. Based on their review, the authors recommend an integrated approach that combines beneficial properties of soil microorganisms with sustainable soil management practices to support plant production, maintain a clean water supply, sustain biodiversity, store carbon, and increase resilience in the face of a changing climate.

Research showed that microbial physiology largely determines the ability of soil ecosystems to adapt to climate change, and that some microbiomes may be suitable for mitigation measures such as carbon sequestration and plant inoculation.
Research showed that microbial physiology largely determines the ability of soil ecosystems to adapt to climate change, and that some microbiomes may be suitable for mitigation measures such as carbon sequestration and plant inoculation.

The Impact
The effects of climate change on soil microbial communities have potentially large consequences for Earth's soil ecosystems and the beneficial services that soil microbiomes provide. This review highlights the need to connect the fine-scale details arising from microbiome studies to the landscape-scale resolution of many Earth system climate models in the search for climate change mitigation measures.

Summary
On Earth’s terrestrial surface, the soil microbiome cycles nutrients to sustain plant and animal life. While this microbial community is innately connected to environmental conditions, impacts on the soil microbiome due to climate change vary depending on the ecosystem. Different aspects of climate change impact soil microbial communities and their important ecosystem functions, such as cycling of carbon and supporting plant growth. But the molecular details of soil biochemical reactions responsible for these key functions are largely unknown.

Researchers synthesized existing knowledge of climate change impacts across a range of soil environments—permafrost, forests, grassland, wetlands, and deserts—to examine how the microbiome responds. They looked at microbial changes coinciding with different climate change variables including increases in carbon dioxide levels, temperatures, drought, flooding, and fires. Their review showed that microbial physiology largely determines the ability of soil ecosystems to adapt, and that some microbiomes may be suitable for climate change mitigation measures such as carbon sequestration and promoting plant growth. The review sets the stage for future research on soil microbiomes and challenges to overcome in order to connect to larger-scale predictive models of climate change.

Contacts
Janet Jansson, Lab Fellow, janet.jansson@pnnl.gov
Kirsten Hofmockel, Earth Scientist, kirsten.hofmockel@pnnl.gov

Funding
This research was supported by the Department of Energy Office of Biological and Environmental Research (BER) Genomic Science Program and is a contribution of the Scientific Focus Area "Phenotypic response of the soil microbiome to environmental perturbations." PNNL is operated for DOE by Battelle Memorial Institute under Contract DE-AC05-76RLO1830. A portion of the research was performed using the Environmental Molecular Sciences Laboratory, a DOE Office of Science User Facility sponsored by BER and located at PNNL.

J. Jansson and K.Hofmockel, “Soil microbiomes and climate changeNature Reviews Microbiology, 04 October 2019. [DOI: 10.1038/s41579-019-0265-7]

Nutrient-Hungry Peatland Microbes Reduce Carbon Loss Under Warmer Conditions

Image of Peatland forest

Enzyme production in peatlands reduces carbon lost to respiration under future high temperatures.

October 3, 2019
October 3, 2019
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The Science
As atmospheric temperatures and carbon dioxide concentrations rise, photosynthesis by plants is expected to increase, leading to more photosynthate released by roots to the soil microbial community. Researchers from Pacific Northwest Northwest National Laboratory and Iowa State University examined the response of boreal peatland soils under future high temperatures. The team found that the peatland’s soil microbial communities allocated more carbon to enzyme production in search of phosphorus as temperatures climbed. This diversion of carbon resources could reduce future carbon losses by microbial respiration from the peatland.

The Impact
As boreal peatlands face warmer and drier conditions, it is expected that more carbon will be lost from these carbon-rich soils through increased microbial activity. This study showed that enhanced respiration and concomitant loss of carbon is potentially constrained by nutrient demands of the microorganisms. This tradeoff may help the peatland ecosystem retain soil carbon as temperatures warm.

Summary
Root exudates are carbon compounds, such as sugars and organic acids, which are easily consumed by soil microorganisms. With a warming climate, science suggests that increased photosynthesis by plants could lead to more photosynthate released as root exudates to the soil microbial community. To examine this question, researchers used laboratory incubations to control both temperature and moisture and simulate belowground substrate additions under an accelerated growing season. Results showed that with a moderate increase in temperature, the addition of common root exude compounds in peatlands initially increased carbon lost through microbial respiration above those treatments receiving water only. However, when pushed to future expected high temperatures, additional exudate compounds dampened the amount of additional carbon respired as compared to treatments receiving water only. This reduction in respiration suggests the microorganisms allocated carbon compounds to enzyme production to mine for limited resources instead of respiring carbon. The data also support the idea that boreal peatland microbial communities maintain a more narrow range in function, measured as respiration, across a range in climate conditions. A wide climatic niche in addition to reallocation of carbon resources dampens the magnitude of change in carbon respiration with increasing temperatures.

Contact
Kirsten Hofmockel
Biological and Environmental Scienes Directorate
kirsten.hofmockel@pnnl.gov

Funding
This material is based upon work supported by the US Department of Energy, Office of Science, Office of Biological and Environmental Research, Terrestrial Ecosystem Science (TES) Program, under grant ER65430 to Iowa State University.

Keiser, A.D., Smith, M., Bell, S. & Hofmockel, K.S. Peatland microbial community response to altered climate tempered by nutrient availability. Soil Biology and Biochemistry 137, 1-9, (2019).

Diversity and Function Within Soil Microbial Communities

Microbial diversity in soil.

How spatial structures of soil microorganisms change across years and seasons, reveal the ecological impact of varying management practices.

September 9, 2019
September 6, 2019
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The Science
The microbial communities within the loose, friable aggregations of organic and mineral components in soil are highly organized spatially, shaped in part by the structure of the soil itself. A recent paper by senior author Kirsten Hofmockel of Pacific Northwest National Laboratory, and two coauthors, examines the spatio-temporal dynamics of microbial communities within soil aggregates. Their aim was to gauge the impact of changes in environmental factors, plant phenology, and aggregate turnover, to understand how varying management practices affect the ecology of soil microbial communities.

The Impact
Analyzing microaggregates in soil can help researchers better understand the potential diversity and functioning of soil microbial communities. This information is vital in the development of a predictive understanding of soil ecosystem responses to climatic events and environmental change. In addition, land management services can use this data to enhance biodiversity and soil ecosystem services.

Summary
Greater biodiversity across all trophic levels can benefit many ecosystems. Biodiversity creates more resilience to abiotic stressors, increases ecosystem services, and promotes sustainability. Within soil systems microbial diversity alone maintains nutrient cycling, impacts plant productivity, enhances drought tolerance, and determines soil health and fertility.

However, the ecological sources of microbial biodiversity, including niche space partition, are not clearly defined at a microbial scale. The Hofmockel study, conducted with lead author Racheal Upton of Iowa State University and Elizabeth Bach of Colorado State University, helps close that knowledge gap by investigating how the spatial structure of microorganisms is vital to understanding the impact of microbial ecology on ecosystem and biogeochemical services.

Historically, researchers have examined microbial diversity in soils at ecosystem or landscape scales. This study, however, shows the importance of scaling such studies to a microbially relevant level. The researchers chose soil aggregate fractions as a way to represent that needed microbially relevant scale.

Over years and seasons, soil aggregate turnover means that soil microbial habitats are dynamic over time. The researchers used data from soil aggregate fractions in three different bioenergy management systems to investigate seasonal and annual changes in discrete microbial communities.

Such research is pertinent to evaluating how different management practices impact spatially discrete microbial communities in soil. Management practices that increase plant diversity across growing seasons, the authors demonstrate, influence soil aggregate habitats and therefore increase microbial diversity.

For other researchers, the study underscores the importance of including both spatial and temporal dynamics in their investigations in order to fully understand microbial community assembly and persistence in soil.

PI Contact
Kirsten Hofmockel
Pacific Northwest National Laboratory
Kirsten.Hofmockel@pnnl.gov

Funding
U.S. Department of Energy, award number DESC0010775.

R.N. Upton, E.M. Bach, K.S. Hofmockel. “Spatio-temporal microbial community dynamics within soil aggregates.” Soil Biology and Biochemistry 132 (2019) 58-68.

A New Role for Microbes in Peatland Nitrogen Supply

Peatland

Research reveals that bacteria contribute to peatland nitrogen availability through organic nitrogen breakdown.

September 9, 2019
September 6, 2019
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The Science
Nitrogen is a critical nutrient regulating productivity in many ecosystems and influences nutrient availability by affecting organic matter decomposition rates. Nitrogen fixation—converting atmospheric nitrogen into biologically available compounds—by microorganisms has historically been considered the primary nitrogen source in peatlands. However, recent work shows that nitrogen fixation alone cannot meet nitrogen requirements. Researchers at Pacific Northwest National Laboratory and Iowa State University evaluated the genetic potential of microorganisms to supply nitrogen in peatlands via the breakdown of large organic molecules. Results show bacterial potential for cleaving amino acids from organic inputs from plants. This finding contrasts with the paradigm that fungi are genetically superior in their capacity to release nitrogen from organic molecules.

The Impact
Understanding the processes that govern carbon and nutrient dynamics in northern peatlands is critical to predicting future biogeochemical cycles. These ecosystems account for 15‒30% of global soil carbon storage. This study expands the understanding of coupled carbon and nitrogen cycles in northern peatlands, with results indicating that understudied bacterial and archaeal lineages may be central in these ecosystems’ response to environmental change. This project leverages DOE’s one-of-a-kind SPRUCE infrastructure to address mechanisms underlying ecosystem responses to climate change and contribute to the broader goals of the Terrestrial Ecosystem Science Scientific Focus Area.

Summary

Nitrogen is a common limitation in plant productivity and its source remains unresolved in northern peatlands, which are vulnerable to environmental change. Decomposition of complex organic matter into free amino acids has been proposed as an important nitrogen source, but the genetic potential of microorganisms catalyzing this process has not been examined.

Researchers evaluated the microbial—fungal, bacterial, and archaeal—genetic potential for organic nitrogen break down in peatlands at Marcell Experimental Forest in northern Minnesota. The team investigated the abundance and diversity of protease genes involved in the release of nitrogen from organic matter across depths and in two distinct peatland environments—bogs and fens. Analysis of shotgun metagenomic data demonstrates high genetic potential for production of free amino acids across a diverse range of microbial guilds.

Researchers also found a high abundance of protease genes compared with nitrogen-fixation genes typically thought to provide nitrogen in peatlands. Bacterial genes encoding proteolytic activity suggested a predominant role for bacteria in regulating productivity, which contrasted with the paradigm of fungal dominance of organic nitrogen decomposition. This research is foundational to understanding the mechanisms by which carbon cycling is linked to ecosystem nutrient status in the face of changing climate.

Contacts
Emily Graham, Pacific Northwest National Laboratory, emily.graham@pnnl.gov
Kirsten S. Hofmockel, Pacific Northwest National Laboratory, kirsten.hofmockel@pnnl.gov

Funding
This research is supported by the U.S. Department of Energy Office of Science, Office of Biological and Environmental Research, Terrestrial Ecosystem Science SFA.

E.B. Graham, F. Yang, S. Bell, K.S. Hofmockel, “High Genetic Potential for Proteolytic Decomposition in Northern Peatland Ecosystems.” Applied and Environmental Microbiology 85, e02851-18 (2019).

A Slippery Slope: Soil Carbon Destabilization

Soil in a forest

Carbon gain or loss depends on the balance between competing biological, chemical, and physical reactions

August 23, 2019
August 22, 2019
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The Science                       

Despite a breadth of research on carbon accrual and persistence in soils, scientist lack a strong, general understanding of the mechanisms through which soil organic carbon (SOC) is destabilized in soils. In a new review article, researchers synthesized principles of soil chemistry, physics, and biology to explain carbon loss in soils. They found that destabilization does not equal stabilization in reverse. Rather, carbon gain or loss depends on the balance between competing biological, chemical, and physical reactions that can be altered by changes in weather and temperature. 

The Impact

Rates of soil carbon respiration are increasing with current changes in climate and land use. Therefore, understanding destabilization processes in the soil carbon cycle is imperative. This review informs a more robust understanding of the processes that result in carbon loss and feedbacks to the Earth system. With this context, empirical and computational scientists can target better questions about the potential for soils to affect climate through the carbon cycle, which is important for improving predictive biogeochemical and climate models. 

Summary

Most empirical and modeling research on soil carbon dynamics focus on processes that control and promote carbon stabilization. However, the mechanisms through which soil organic carbon (SOC) is destabilized in soils may be even more important to understand. Destabilization processes occur as SOC shifts from a “protected” or passive state, to an “available” or active state. In the available state, microbes can transform soil carbon to gaseous or soluble forms that are then lost from the soil.

The reviewers, from Pacific Northwest National Laboratory, Dartmouth College, and Oregon State University, considered two well-known phenomena—soil carbon priming and the Birch effect—to show how different mechanisms interact to increase carbon losses. They categorized carbon destabilization processes into three general categories: (1) release from physical occlusion through processes such as tillage, bioturbation, or freeze-thaw and wetting-drying cycles; (2) carbon desorption from soil solids and colloids; and (3) increased carbon metabolism by microbes.

By considering the different physical, chemical, and biological controls as processes that contribute to SOC destabilization, researchers can develop new hypotheses about the persistence and vulnerability of carbon in soils and make more accurate and robust predictions of soil carbon cycling in a changing environment.

Contact

Vanessa Bailey
Pacific Northwest National Laboratory
vanessa.bailey@pnnl.gov

Funding

V.L. Bailey was supported by the U.S. Department of Energy, Office of Science, Biological and Environmental Research as part of the Terrestrial Ecosystem Sciences Program. The Pacific Northwest National Laboratory is operated for DOE by Battelle Memorial Institute under contract DE-AC05-557 76RL01830. K. Lajtha was supported by NSF DEB-1257032.

Bailey, V., C. Hicks Pries, and K. Lajtha, 2019.  “What do we know about soil carbon?” Environmental Research Letters, 14 (2019) 083004. https://doi.org/10.1088/1748-9326/ab2c11