News & Media
Microbial diversity influences nitrogen cycling in rivers
Seasonal changes affect microbiome communities, genes, and subsurface biogeochemical pathways differently
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.
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.
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.
Bill Nelson, Pacific Northwest National Laboratory, William.Nelson@pnnl.gov
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
Exploration of disorder at material interfaces could lead to better device performance
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.
Peeking Into the Lives of Soil Microbiomes
SoilBox provides in-depth imaging and characterization of soil microbial communities in their native environments.
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 complexity of soil makes spatial imaging of soil microbial communities challenging. Using SoilBox, researchers can now visualize the diversity and metabolic
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.
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.
Chris Anderton, Pacific Northwest National Laboratory, firstname.lastname@example.org
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.
Protecting climate-sensitive soil ecosystems
Review paper summarizes the effects of climate change on soil microorganisms and the ecosystem services they provide, and evaluates potential mitigation measures.
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.
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.
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.
Janet Jansson, Lab Fellow, email@example.com
Kirsten Hofmockel, Earth Scientist, firstname.lastname@example.org
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.
Top Ten Blendstocks for Turbocharged Gasoline Engines
Bio-blendstocks with the potential to deliver the highest engine efficiency
More efficient engines enabled by better fuels could increase the fuel economy of light duty (LD) vehicles by 10 percent beyond current technology and planned developments. This report identifies top blendstocks that can be derived from biomass and are suitable for further development and commercialization. These blendstocks are best-suited for LD gasoline, boosted spark ignition (BSI) engines. The blendstocks were identified using a fuel property basis using the BSI merit function. The merit function determines potential improvements in engine efficiency, was used to evaluate the performance of candidate bioblendstocks in blends up to 30%. Those that exceeded the efficiency of an E10 premium were included in this list. This report is aimed at biofuel researchers looking to better understand the efficiency implications of biofuels under development, as well as engine researchers who are interested in future biofuels with properties that enable more efficient engine design and operation.
The Co-Optimization of Fuels & Engines (Co-Optima) team includes experts from nine national laboratories: Argonne, Idaho, Lawrence Berkeley, Lawrence Livermore, Los Alamos, Oak Ridge, Pacific Northwest, and Sandia National Laboratories and the National Renewable Energy Laboratory. The team’s expertise includes biofuel development, fuel property testing and characterization, combustion fundamentals, modeling and simulation from atomic scale to engine scale, and analysis.
Gaspar, Daniel J., West, Brian H., Ruddy, Danial, Wilke, Trenton J., Polikarpov, Evgueni, Alleman, Teresa L., George, Anthe, Monroe, Eric, Davis, Ryan W., Vardon, Derek, Sutton, Andrew D., Moore, Cameron M., Benavides, Pahola T., Dunn, Jennifer, Biddy, Mary J., Jones, Susanne B., Kass, Michael D., Pihl, Josh A., Pihl, Josh A., Debusk, Melanie M., Sjoberg, Magnus, Szybist, Jim, Sluder, C S., Fioroni, Gina, and Pitz, William J. Top Ten Blendstocks Derived From Biomass For Turbocharged Spark Ignition Engines: Bio-blendstocks With Potential for Highest Engine Efficiency. United States: N. p., 2019. Web. doi:10.2172/1567705.
Nutrient-Hungry Peatland Microbes Reduce Carbon Loss Under Warmer Conditions
Enzyme production in peatlands reduces carbon lost to respiration under future high temperatures.
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.
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.
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.
Biological and Environmental Scienes Directorate
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.