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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]

Oxide interfaces in disarray

Microscope image, bright blue background with bright green oxides

Atomic-scale imaging informs interface models for oxygen defect formation during disordering of oxides used in energy and computing.

| PNNL

Exploration of disorder at material interfaces could lead to better device performance

March 3, 2020
March 3, 2020
Highlight

The structure of an interface at which two materials meet helps determine the performance of the computers and other devices we use every day. However, understanding and controlling interface disorder at the atomic level is a difficult materials science challenge.

A research team at PNNL and Texas A&M University combined cutting edge imaging and numerical simulations to examine disordering processes in widely used oxide materials. They found that certain oxide interface configurations remain stable in extreme environments, suggesting ways to build better performing, more reliable devices for fuel cells, space-based electronics, and nuclear energy.

Visualizing the disordering process

As reported in Advanced Materials Interfaces (Asymmetric Lattice Disorder Induced at Oxide Interfaces,” DOI: 10.1002/admi.201901944) the team set out to examine interfaces between pyrochlore-like and perovskite oxides, two common classes of functional materials used in energy and computing technologies. While most past work has focused on individual bulk materials, less attention has been paid to interfaces connecting them, as would be the case in a device. In particular, it is not clear how interface features, such as composition, bonding, and possible defects, govern disordering processes.

Funded by PNNL’s Nuclear Process Science Initiative (NPSI), the team employed experimental and theoretical methods to study the interface at different stages of disorder introduced through ion irradiation. They imaged the local structure of the material using high-resolution scanning transmission electron microscopy and convergent beam electron diffraction, which showed that the bulk of the two materials disordered (amorphized) before the interface. After further irradiating the material, they found that a band region near the interface had remained crystalline, while the rest of the structure had become amorphous.

To understand this behavior, the team turned to a technique called electron energy loss spectroscopy, which allowed them to examine the atomic-scale chemistry and defects formed at the interface. Their measurements revealed the presence of substantial amounts of defects called oxygen vacancies, which can greatly affect properties such as magnetism and conductivity. Based on these observations, the team constructed a theoretical model of the interface and explored the effect of different interface configurations on the tendency to form vacancies.

“In our model we are able to systematically vary interface features, such as crystal structure, intermixing, and strain, to see their effect on defect formation. We found that the structure of the materials on both sides of the interface can influence where defects are likely to form first,” explained Steven R. Spurgeon, a PNNL materials scientist. “Our model suggests that by selecting appropriate crystal structures and controlling how they connect, it may be possible to dictate the sequence of defect formation, which would allow us to enhance the properties of these materials.”

The team is exploring other interface structures and chemistries, with an eye toward improving the performance of oxides used in extreme environments.

The study was conducted as part of the NPSI project, “Damage Mechanisms and Defect Formation in Irradiated Model Systems,” led by Spurgeon.

Research Team

Steven Spurgeon (PNNL), Tiffany Kaspar (PNNL), Vaithiyalingam Shutthanandan (Environmental Molecular Sciences Laboratory at PNNL), Jonathan Gigax (Texas A&M), Lin Shao (Texas A&M), Michel Sassi (PNNL).
February 20, 2020

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.

Improving nuclear waste storage models by studying the chemistry of material interactions

A female researcher wearing a blue lab coat and heat-resistant safety gloves pours molten glass out of a metal crucible onto a metal tray.

PNNL conducts research into glass, glass-ceramic, grout, metal, and metal-ceramic wasteforms that will withstand corrosion over geologic time.

PNNL | Andrea Starr

WastePD EFRC research on the glass-steel interface was published in Nature Materials

February 3, 2020
February 3, 2020
Highlight

New research unravels the chemistry of how materials in the waste packages used for the disposal of high-level radioactive waste interact in deep geologic repository environments. Having a better understanding of the interactions between materials under various conditions provides more information to make waste storage performance models more robust.

“Many performance models use conservative approaches such as assuming that the steel canister walls don’t even exist or that they dissolve very fast. This study provides the opportunity to better incorporate the canister barrier in the models,” said Joseph Ryan, a PNNL materials scientist and coauthor on the paper, “Self-accelerated corrosion of nuclear waste forms at material interfaces,” published in Nature Materials.

The United States is converting highly radioactive nuclear waste, also known as high-level waste, into glass. The molten glass is poured into steel canisters for long-term storage and ultimate disposal in a geologic repository. The goal is to design waste storage and disposal systems that would remain safe for hundreds of thousands of years to come, even if they are exposed to water. Because of the extensive time span of waste storage, researchers turn to cutting-edge science to project what will happen during that time period. The data is used to inform extensive safety analyses—helping make sure the system is engineered to be compatible with the natural system so that waste remains separate from the environment.

“We can’t just do a test on a material and say, ‘That material corroded this much in 30 days and extrapolate that to a million years.’ It doesn’t work that way,” Ryan said. “At the most basic level, we try to understand the underlying chemistry of corrosion. Then, we feed that information into computer models to calculate the expected release over time.”

In this study, led by the WastePD Energy Frontier Research Center based at Ohio State University, researchers unpacked the chemistry that occurs when two materials are close together, focusing on glass-steel along with ceramic-steel interactions. This chemical situation could occur when water has percolated into the repository and has breached the steel canister, exposing the glass-steel interface to water.

When water finally breaches the waste package container, it will fill the microscopic space that forms between the solid glass and the steel canister. Chemical reactions that happen in localized and tiny microenvironments such as these can be quite different than those happening in a more open setting. In this case, this localized area can have a different chemistry than the surrounding solution, causing more corrosion than would be expected.

The researchers tested their theory in the laboratory. They pressed glass and steel together in salty liquid and kept it at 90° C (194° F) for a month. At the end of the experiment, they found differences in the width of thin layers that indicated higher corrosion between the glass-steel couple interface than in a control sample.

Why it matters: This research allows scientists to improve models that project how a disposal canister could perform in a deep geologic environment. Having a better understanding of the interactions between materials under various conditions provides more information to make the models more robust. Currently, some models project what happens to waste under the assumption that the steel canister walls do not exist. Operating under this pretext can result in higher projections of waste degradation than would likely occur when taking a conservative approach. But better understanding the chemistry of how the solid waste and the steel canister interact allows a scientifically based understanding of how the canisters behave and interact with the glass to be included in performance assessment models.

Summary: High-level waste is immobilized as glass in stainless steel canisters. On cooling, a confined crevice space forms at the stainless steel-glass interface. If the disposal canister is breached and if water can enter the steel-glass interface, it could result in anodic dissolution of the stainless steel, generating metal cations, which hydrolyze to form protons and strongly increase the local acidity. This acidic environment may locally enhance the corrosion of both the stainless steel and the glass, which leads to the release of cations from the glass. Further, the coupled corrosion may trigger the precipitation of additional secondary phases that may impact subsequent canister corrosion or nuclear glass durability.

What’s Next: While this study sheds light on the chemical interactions that occur at the stainless steel-glass interface, there are more interactions to explore. Ultimately, a better understanding of different chemical mechanisms will improve the overall performance model.

Acknowledgements

Sponsors: This work was supported as part of the Center for Performance and Design of Nuclear Waste Forms and Containers, an Energy Frontier Research Center funded by the US Department of Energy, Office of Science, Basic Energy Sciences under Award no. DESC0016584.

Research Team: Xiaolei Guo, Gerald S. Frankel, Gopal Viswanathan, Tianshu Li (Ohio State University); Stéphane Gin (CEA, France); Penghui Lei, Tiankai Yao, Jie Lian (Rensselaer Polytechnic Institute); Hongshen Liu, Dien Ngo, Seong H. Kim (Pennsylvania State University); Daniel K. Schreiber, John D. Vienna, Joseph V. Ryan (PNNL); Jincheng Du (University of North Texas)

January 27, 2020
DECEMBER 11, 2019
Web Feature

PNNL to Lead New Grid Modernization Projects

PNNL will lead three new grid modernization projects funded by the Department of Energy. The projects focus on scalability and usability, networked microgrids, and machine learning for a more resilient, flexible and secure 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).

SEPTEMBER 13, 2019
Web Feature

Charting the Frontier of Electron Microscopy

A gathering of international experts in Portland, Oregon, explored the future of electron microscopy and surfaced potential solutions in areas including new instrument designs, high-speed detectors, and data analytics capabilities.

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.

AUGUST 12, 2019
Web Feature

A Window into the Hidden Nuclear World

A multi-institute team develops an imaging method that reveals how uranium dioxide (UO2) reacts with air. This could improve nuclear fuel development and opens a new domain for imaging the group of radioactive elements known as actinides.

Drought Spells Changes for Soil Microbes

Prairie Grassland

Researchers at PNNL and Kansas State University found that soil drying significantly affected the structure and function of soil microbial communities.

Researchers found that soil drying altered metabolic pathways within soil microbial communities.

August 1, 2019
July 31, 2019
Highlight

The Science

Researchers at the U.S. Department of Energy’s Pacific Northwest National Laboratory and Kansas State University found that soil drying significantly affected the structure and function of soil microbial communities.

A warming Earth is predicted to result in increased drought extent and intensity in the highly fertile and productive grasslands of the central United States. These soils store large reserves of carbon. The decrease in soil moisture due to drought has largely unknown consequences on soil carbon cycling and other key biogeochemical cycles carried out by soil microbiomes. Researchers at the U.S. Department of Energy’s Pacific Northwest National Laboratory and Kansas State University found that soil drying significantly affected the structure and function of soil microbial communities. This included shifts in expression of specific metabolic pathways, such as those leading toward the production of compounds that build up within cells to keep microbes alive during drought.

The Impact

This study demonstrates the application of a multi-omics approach to decipher details of the soil microbial community’s metaphenomic response to environmental change. The approach should apply to studies of other complex microbial systems as well. This research supports the Genomic Science mission by revealing fundamental principles that guide the interpretation of the genetic code into functional proteins, metabolic pathways, and the metabolic/regulatory networks underlying the systems biology of microbial communities. Advancing fundamental knowledge of these systems will enable understanding of the role of biological systems in the environment and how environmental change affects soil microbial communities.

Summary

Warming temperatures are causing shifts in precipitation patterns in the central grasslands of the United States, with largely unknown consequences on the collective physiological responses of the soil microbial community, i.e., the metaphenome. In this study, researchers used an untargeted omics approach to determine the soil microbial community’s metaphenomic response to soil moisture and to define specific metabolic signatures of the response. Specifically, they aimed to develop the technical approaches and metabolic mapping framework necessary for future systematic ecological studies.

The research team collected soil from three locations at a field station in Kansas, incubated the samples for 15 days under dry or wet conditions, and compared them to field-moist controls. The team determined the microbiome response to wetting or drying through 16S rRNA amplicon sequencing, metatranscriptomics, and metabolomics. Researchers then assessed the resulting shifts in taxa, gene expression, and metabolites. Soil drying resulted in significant shifts in both the composition and function of the soil microbiome, such as changes in metabolic pathways that lead toward the production of sugars and other osmoprotectant compounds. By contrast, few changes occurred after wetting. The team used the combined metabolic and metatranscriptomic data to generate metabolite-reaction networks to determine the metaphenomic response to soil moisture transitions, such as generation of trehalose under dry conditions. Using this approach, researchers showed that despite the high complexity of the soil habitat, it is possible to generate insight into the effect of environmental change on the soil microbiome and its physiology and functions, thus laying the groundwork for future, targeted studies.

Contact

Janet Jansson
Pacific Northwest National Laboratory
janet.jansson@pnnl.gov

Funding

This research was supported by the Department of Energy 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.” This research was also supported by Environmental Molecular Sciences Laboratory (EMSL) open call proposal number 48784, Dissecting and Deciphering of the Soil Microbiome. EMSL is a U.S. Department of Energy (DOE) Office of Science user facility sponsored by the DOE’s Office of Biological and Environmental Research and located at PNNL. A portion of the research was conducted using PNNL Institutional Computing (PIC) resources and partially supported by the Microbiomes in Transition Initiative under the Laboratory Directed Research and Development Program at PNNL. PNNL is a multiprogram national laboratory operated by Battelle for the U.S. DOE under contract DE-AC05-76RL01830.

T. Roy Chowdhury, J.- Y. Lee, E.M. Bottos, C.J. Brislawn, R.A. White III, L.M. Bramer, J. Brown, J.D. Zucker, Y.-M. Kim, A. Jumpponen, C.W. Rice, S.J. Fansler, T.O. Metz, L.A. McCue, S.J. Callister, H.-S. Song, J.K. Jansson, “Metaphenomic Responses of a Native Prairie Soil Microbiome to Moisture Perturbations.” mSystems 4(4), e00061-19 (2019). [DOI: 10.1128/mSystems.00061-19]