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When a pinch is problematic: Detecting pertechnetate in groundwater

pertechnetate

A PNNL researcher holds a redox sensor in the project’s lab in the Radiochemical Processing Laboratory.  Andrea Starr | PNNL

PNNL develops an effective tool for measuring a tricky contaminant

March 30, 2020
March 30, 2020
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Imagine trying to detect and measure a pinch of salt in an Olympic-size swimming pool. Now pretend the tools you are using don’t work well. Some can detect the salt but can’t tell you how much is in there, and others confuse salt with chlorine.

Now swap the swimming pool for a source of groundwater and the salt for a radioactive contaminant called pertechnetate.

ACS Journal Pertechnetate
The future of groundwater contamination measurement? The large thiol claws of PNNL’s subsurface probe with custom gold tips detect and measure pertechnetate in aqueous environments. Cover illustration by Rose Perry, PNNL

Pertechnetate is a byproduct of nuclear waste. If it ends up where it is not supposed to be—like, in groundwater—it could impact human health, which is why researchers and regulators keep a close lookout for it. The environmental safety limits for pertechnetate are roughly equivalent to a pinch of salt in an Olympic pool. And there are only a few technologies to measure it, each with limitations.

PNNL research tackles this challenge with new technology to detect and accurately measure pertechnetate at super low levels in groundwater. This research, “Redox-Based Electrochemical Affinity Sensor for Detection of Aqueous Pertechnetate Anion,” was the cover article for the March 2020 edition of ACS Sensors (DOI: 10.1021/acssensors.9b01531). 

Why it matters: The Environmental Protection Agency drinking water standard for pertechnetate is 0.000000052 grams per liter (that’s roughly 1/6000th the weight of a single poppy seed). While techniques exist for detection of pertechnetate in the environment, many have their drawbacks. PNNL’s technology can accurately measure low levels of pertechnetate in groundwater. Additionally, this proof of concept has the potential to be applied to other target contaminants simultaneously, increasing efficiency for environmental sensing.

Summary: The new technology acts like a coin counter, but at a microscopic level. It sorts one type of chemical from another, providing the total amount of a target chemical at the end. The tool uses custom probes with a gold electrode that only allows the target groundwater contaminants to stick while the other chemicals bounce off.

Sulfur likes to bind to gold and it also tends to react with pertechnetate, making sulfur-containing compounds an ideal intermediate in tool development. The sulfur sticks to the gold probe, then reacts with the pertechnetate, which forms a precipitate. The precipitate inhibits an electric current pulsing through the probe, providing an inverse measurement of pertechnetate concentration.

What’s Next: While this work was specifically focused on pertechnetate, there is potential to expand the technology to simultaneous multiple targets with the goal of increasing the efficiency of environmental measurements.

Sponsors: This research was funded by the Laboratory Directed Research and Development program at PNNL and by the Deep Vadose Zone program under the U.S. Department of Energy’s (DOE’s) Office of Environmental Management. Part of this research was performed at the Environmental Molecular Sciences Laboratory, a national user facility at PNNL managed by the DOE Office of Biological and Environmental Research.

PNNL Research Team: Sayandev Chatterjee, Meghan S. Fujimoto, Yingge Du, Gabriel B. Hall, Nabajit Lahiri, Eric D. Walter, Libor Kovarik. ACS Sensors cover illustration by Rose Perry, PNNL.

 

March 27, 2020

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]

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.

Creating better models to predict subsurface water flow and transport

river soil

New framework improves the predictions of subsurface sediment permeability

February 19, 2020
February 17, 2020
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The Science
Co-authors of a paper in Water Resources Research led by PNNL researchers developed a new iterative data assimilation framework to more accurately describe the permeability of subsurface sediments in numerical models when using facies, a system that classifies dissimilar sediments into distinct geological units that share important features of interest to modelers. The iterative framework applies data from field observations and experiments to inform the delineation of facies at the start of each model run. Further refinements are achieved at each iteration through the application of statistical constraints that maintain geologic continuity among adjacent locations.

Distribution of Facies
Spatial distribution of three facies (red, yellow and blue colors) in a 2D vertical cross section of a 3D case. Figures show the new method provides a more accurate and continuous estimation of facies distribution compared to the conventional method. White colors in the figures are bore samples and black dots are the conditioning points selected by the new method.

The Impact
Spatial distribution of three facies (red, yellow and blue colors) in a 2D vertical cross section of a 3D case. Figures show the new method provides a more accurate and continuous estimation of facies distribution compared to the conventional method. White colors in the figures are bore samples and black dots are the conditioning points selected by the new method.

More realistic numerical representations of the permeability of subsurface sediments lead to improved predictions of groundwater flow and the concentration of constituents that are transported with the flow. The data assimilation framework can also be applied to estimate other subsurface properties from field measurements, or from data from other systems such as watersheds, as long as they can be categorized into a few discrete representative units.

Summary
Observational data on subsurface permeability is limited for most watersheds because of the impracticality of digging enough boreholes or wells to capture the heterogeneous nature of the subsurface environment. To solve for this limitation, researchers have widely adopted approaches that estimate permeability from field experiments such as a) measuring how water levels at a cluster of wells change when water is pumped at a nearby well, or b) monitoring how quickly a tracer released at one well reaches other wells in the aquifer. The U.S. Department of Energy’s Hanford 300 Area Integrated Field Research Challenge site, for example, is well characterized from data assimilation methods that were used to understand the long-term persistence of nuclear fuel fabrication wastes disposal from 1943 to 1975.

The use of a facies approach to segment the subsurface reduces complexity in numerical models by grouping heterogeneous sediments into distinct homogenous units defined by hydraulic, physical and or chemical properties. A major difficulty with existing facies-based approaches in numerical models is that each facies is treated as its own, independent unit. Therefore, these models fail to capture the spatial continuity of subsurface sediments. The authors of this paper developed a framework that maintains continuity between neighboring facies in numerical models and thus better reflects true subsurface geology, and thereby groundwater movement. The improvements come from an iterative data assimilation approach that incorporates direct and indirect data about subsurface permeability gathered from field observations and experiments at the start of each model run as well as the application of statistical constraints about subsurface geology. The data assimilation and statistical constraint steps are re-imposed for each iteration, leading to refined facies delineation. This framework reduces uncertainty about the spatial distribution of sediment types in the subsurface, which results in more accurate predictions of groundwater flow and constituent transport.

The authors evaluated the performance of the new framework on a two-dimensional, two-facies model and a three-dimensional, three-facies model of DOE’s well-characterized Hanford 300 Area that were conceptualized from borehole and field tracer experiments. The results of the research shows that the framework can identify facies spatial patterns and reproduce tracer breakthrough curves with much improved accuracy over facies-based approaches that lack spatial continuity constraints. With additional data, the authors say that the framework can also be used to categorize biogeochemical reactive units in an aquifer.

Contact
Xingyuan Chen, Earth Scientist, Xingyuan.Chen@pnnl.gov

Funding
Funding for this research came from DOE Office of Science BER, PNNL Subsurface Biogeochemical Research SFA.

Song, X., Chen, X., Ye, M., Dai, Z., Hammond, G., And Zachara, J.M. (2019). Delineating facies spatial distribution by integrating ensemble data assimilation and Indicator Geostatistics with level-set transformation. Water Resources Research, 55. https://doi.org/10.1029/2018WR023262

March 9, 2019

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
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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
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.
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.
DECEMBER 4, 2019
Web Feature

A More Painless Extraction

PNNL and Argonne researchers developed and tested a chemical process that successfully captures radioactive byproducts from used nuclear fuel so they could be sent to advanced reactors for destruction while also producing electrical power.

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
Highlight

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).