BER Research Highlights

Search Date: December 19, 2018

23 Records match the search term(s):


December 28, 2017

Microbial “Hotspots” and Organic Rich Sediments are Key Determinants of Nitrogen Cycling in a Floodplain


Sediments from a Colorado River floodplain that are rich in organic matter have a 70% higher potential for nitrate removal than background sediments.

The Science
Biogeochemical hot spots are regions with disproportionally high reaction rates relative to the surrounding spatial locations, while hot moments are short periods of time manifesting high reaction rates relative to longer intervening time periods. These hot spots and hot moments together affect ecosystem processes and are considered ‘‘ecosystem control points”. However, relatively few studies have incorporated hot spots and/or hot moments in numerical models to quantify their aggregated effects on biogeochemical processes at floodplain and riverine scales. This study quantifies the occurrence and distribution of nitrogen hot spots and hot moments at a Colorado River floodplain site in Rifle, CO, using a high-resolution, 3-D flow and reactive transport model. 

The Impact
This study was used to assess the interplay between dynamic hydrologic processes and organic matter rich, geochemically reduced sediments (aka “naturally reduced zones”) within the Rifle floodplain and the impact of hot spots and hot moments on nitrogen cycling at the site using a fully-coupled, high-resolution reactive flow and transport simulator. Simulation results indicated that nitrogen hot spots are not simply hydrologically-driven, but occur because of complex fluid mixing, localized reduced zones, and biogeochemical variability. Furthermore, results indicated that chemically reduced sediments of the Rifle floodplain have 70% greater potential for nitrate removal than non-reduced zones.

Summary
Although hot spots and hot moments are important for understanding large-scale coupled carbon and nitrogen cycling, relatively few studies have incorporated hot spots and hot moments in numerical models, especially not in a 3D framework, thereby neglecting the potential effects of fluid mixing on the biogeochemistry. In this study, scientists from the Lawrence Berkeley National Laboratory integrated a complex biotic and abiotic reaction network into a high-resolution, three-dimensional subsurface reactive transport model to understand key processes that produce hot spots and hot moments of nitrogen in a floodplain environment. The model was able to capture the significant hydrological and biogeochemical variability observed across the Rifle floodplain site. In particular, simulation results demonstrated that hot and cold moments of nitrogen did not coincide in different wells, in contrast to flow hydrographs. This has important implications for identifying nitrogen hot moments at other contaminated sites and/or mitigating risks associated with the persistence of nitrate in groundwater. Model simulations further demonstrated that nitrogen hot spots are both flow-related and microbially-driven in the Rifle floodplain. Sensitivity analyses results indicated that the naturally reduced zones (NRZs) have a higher potential for nitrate removal than the non-NRZs for identical hydrological conditions. However, flow reversal leads to a reduction in nitrate removal (approximately 95% lower) in non-NRZs whereas the NRZ remains unaffected by the influx of the river water. This study demonstrates that chemolithoautotrophy, the microbial processes responsible for Fe+2 and S-2 oxidation, is primarily responsible for the removal of nitrate in the Rifle floodplain.

Contact (BER PM)
David Lesmes, SC-23.1, 301-903-2977, David.Lesmes@science.doe.gov

(PI Contact)
Susan S. Hubbard
Lawrence Berkeley National Lab
sshubbard@lbl.gov

Funding
DE-AC02-05CH11231, as part of the Genomes to Watershed Scientific Focus Area project and DE-SC0009732, as part of the Small Business Innovation Research.

Publications
Dwivedi, D., B. Arora, C.I. Steefel, B. Dafflon, and R. Versteeg. “Hot spots and hot moments of nitrogen in a riparian corridor.” Water Resources Research, 54, 205-222 (2018). DOI: 10.1002/2017WR022346.

Topic Areas:

Division: SC-23.1 Climate and Environmental Sciences Division, BER


December 20, 2017

How Shoreline Vegetation Protects Sediment-Bound Carbon

A new study investigates the mechanisms and pace of carbon processing at the terrestrial-aquatic interface of a major river corridor.

The Science
Soils and nearshore sediments comprise a reservoir of carbon (C) 3.2 times larger than all the carbon stored in the atmosphere. Terrestrial C (e.g., from falling leaves and roots growing underground) is increasingly transported into aquatic systems due to significant changes in how land is used as the population increases, but little is known about the processing of C along terrestrial-to-aquatic continuums.

A new study led by ecologists Emily Graham and James Stegen at the Pacific Northwest National Laboratory takes a closer look at how C inputs along the terrestrial-aquatic interface change the mechanisms and pace of C processing. Their research also sheds light on how some of the C along shorelines remains in place for millennia.

The Impact
This research provides ultra-high-resolution data to infer new mechanisms of C oxidization along a terrestrial-aquatic boundary. The work will help protect watersheds by providing the underpinnings for a new conceptualization of biogeochemical function within models used to predict how river corridors function.

Summary
A bird's eye view of the Columbia River in southeastern Washington State reveals varied ecological conditions ranging from dense vegetation to dry, rocky shoreline, and this variability leads to disparities in C inputs. In this study, researchers compared the amount of C contained within sediments, the rate of metabolism, and the metabolic pathways associated with C loss in each type of terrain.

Contrary to the prevailing ‘priming' paradigm of C loss in soils, the data indicates that vegetation "protects" the bound carbon already in nearshore sediments. Researchers learned that water-soluble and thermodynamically favorable organic carbon (OC) protects bound OC from oxidation in densely vegetated areas—presumably because it is easier to break down than the bound OC. Areas with sparse vegetation were more likely to metabolize bound OC, likely leading to the loss of C from longer-term stored C pools. A unifying principle in both environments, however, seems to be the use of thermodynamically favorable C as a preferred substrate pool, providing a starting point for modelling the influences of C character in heterogeneous landscapes.

"Another interesting data point is that contrasting metabolic pathways oxidize OC in the presence versus absence of vegetation," said Graham. "Put simply, we have two different environments with distinct C inputs, C pools, and microbial communities. Each microbial community adapts to the resources available in their local environment and processes the C that returns the most energy back to them."

These important discoveries are just the tip of the iceberg, Graham and Stegen say. More studies are needed to understand and model the patterns of C loss in changing land conditions.

BER PM Contact
David Lesmes
Paul Bayer

PI Contact
Emily Graham
Pacific Northwest National Laboratory
emily.graham@pnnl.gov

James Stegen
Pacific Northwest National Laboratory
James.stegen@pnnl.gov

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

Publications
Graham, Emily B., Malak Tfaily, Alex R. Crump, Amy E. Goldman, Lisa M. Bramer, Evan Amtzen, Elvira Romero, C. Tom Resch, David W. Kennedy, James C. Stegen. "Carbon inputs from riparian vegetation limit oxidation of physically-bound organic carbon via biochemical and thermodynamic processes." JGR Biogeosciences 122(12), 3188-3205 (2017). [DOI:10.1002/2017JG003967]

Related Links
http://sbrsfa.pnnl.gov/docs/highlights/Highlight_Stegen_et_al_2015.pdf
https://phys.org/news/2016-12-microbial-hyporheic-zone.html
http://sbrsfa.pnnl.gov/docs/highlights/Highlight_Stegen_Microbial_Communities_11282016.pdf
http://sbrsfa.pnnl.gov/docs/highlights/Highlight_Stegen_10-8-2015.pdf
http://sbrsfa.pnnl.gov/docs/highlights/Highlight_Stegen_et_al_2015.pdf

Topic Areas:

Division: SC-23.1 Climate and Environmental Sciences Division, BER


December 12, 2017

Simulating Interactions among River Water, Groundwater, and Land Surfaces by Coupling Different Models

New coupled model, CP v1.0, will improve understanding of water cycling and complex Earth system dynamics.

The Science
Many Land System Models (LSMs) do not consider lateral transport of water, leaving out a cross-sectional view and understanding of the coupling of surface water with groundwater along rivers, streams, and other water bodies. And yet, detailed observational studies and their accompanying model simulations suggest that the lateral flow of water in the subsurface along the continuum of river water and groundwater saturates the pore space in the soils and sediments. There is a need to advance large-scale LSMs so that they capture the variable gradient of water within soils because this is critical for understanding and modeling energy and water budgets, as well as biogeochemical cycling in the terrestrial surface and subsurface systems. This work enables this modeling advance by coupling a widely used, massively parallel multiphysics reactive transport code with the Community Land Model version 4.5 to create a coupled model called CP v1.0.

The Impact
The open-source coupled model developed in this study, CP v1.0, can be used to improve the mechanistic understanding of ecosystem functioning and biogeochemical cycling along river corridors and their functions in watersheds. The associated dataset from a well-characterized river shoreline site can also be used as a benchmark for testing other integrated models.

Summary
The research community increasingly recognizes that rivers, despite their relatively small imprints on the landscape, play important roles in watershed functioning through their connections with groundwater aquifers and riparian zones. The Columbia River, a 1,243 mile stretch of water, served as an ideal test case for long-term observations, as well as simulations using a coupled three-dimensional surface and subsurface land model.

The interactions between groundwater and river water are important because they influence the volume of water in soils, from simply moist to fully saturated. This volume determines the rates of biogenic gas emissions due to soil evaporation, plant transpiration, and respiration of carbon dioxide from plants and soils, which are poised to vent into the atmosphere. These same interactions also enhance the reactive transport process that alters water chemistry and the downstream transport of materials and energy.

However, past simulations of these processes and their impacts haven't always mirrored the reality of field observations, in part because such models do not take into account the lateral flow of water and transport of constituents in the subsurface.

During a five-year monitoring of groundwater wells along the Columbia River shoreline, a team of researchers from the Pacific Northwest National Laboratory, Lawrence Berkeley National Laboratory, and Sandia National Laboratory recognized the value of observing the layers within the subsurface rather than just what happens aboveground. They used two open-source codes, PFLOTRAN and CLM4.5 to compare simulations to observations. They then coupled the two models to create CP v1.0. The coupled-model approach allowed the research team to estimate moisture availability, for example, particularly during changes in the river stages, and to validate the new model using data from the shoreline site.

Researcher Maoyi Huang from PNNL noted one surprise during the study: spatial resolution matters. The influence of river-aquifer interactions can be "seen" in shallow groundwater using coarser-resolution simulations, but it is important to refine the model resolution along river corridors that were part of this study. The difference, she explained, is that southeastern Washington state is situated in an arid climate zone so the team had to use finer resolutions in their study in order to capture the processes at the surface and in the subsurface within the narrow riparian zone.

A coupled model like the one used in this study can also be applied to larger modeling problems, such as simulating the impact of a drought on watershed functioning by explicitly considering the role of river-aquifer-land interactions. Using models that do not consider lateral flow and transport can be misleading. For example, models without this 3-D view results often erroneously show parched plants, one signature that a drought is underway. But a model incorporating this view shows that plants are still, in fact, getting water from the soil.

Contacts (BER PM)
David Lesmes
BER
David.Lesmes@science.doe.gov

Paul Bayer
BER
Paul.Bayer@science.doe.gov

(PI Contact)
Maoyi Huang
maoyi.huang@pnnl.gov,
509/375-6827

Gautam Bisht
gbisht@lbl.gov,
510/486-6246


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

Publications
Bisht, G., M. Huang, T. Zhou, X. Chen, H. Dai, G. E. Hammond, W. J. Riley, J. L. Downs, Y. Liu, and J. M. Zachara. "Coupling a three-dimensional subsurface flow and transport model with a land surface model to simulate stream-aquifer-land interactions (CP v1.0)" Geosci. Model Dev. 10, 4539-4562 (2017). [DOI:10.5194/gmd-10-4539-2017]

Topic Areas:

Division: SC-23.1 Climate and Environmental Sciences Division, BER


November 24, 2017

Anaerobic Microsites have an Unaccounted Role in Soil Carbon Stabilization

Anaerobic microsites within soils impart an unrecognized metabolic protection to carbon, creating a carbon sink vulnerable to climate and land-use change.

The Science
Mechanisms controlling soil carbon storage and feedbacks to the climate system remain poorly constrained. Here, a research team a led by Stanford University shows that anaerobic microsites stabilize soil carbon by shifting microbial metabolism to less efficient anaerobic respiration and protecting reduced organic carbon compounds from decomposition.

The Impact
Without recognizing the importance of anaerobic microsites in stabilizing carbon in soils, terrestrial ecosystem models are likely to underestimate the vulnerability of the soil carbon reservoir to disturbance induced by climate or land use change. Further, carbon mitigation strategies based largely on land management can be optimized accordingly to maximize soil storage.

Summary
Soils represent the largest carbon reservoir within terrestrial ecosystems. The mechanisms controlling the amount of carbon stored and its feedback to the climate and Earth system, however, remain poorly resolved. Global land models assume that carbon cycling in upland soils is entirely driven by aerobic respiration; the impact of anaerobic microsites (small oxygen poor sites in the soil) prevalent even within well-drained soils is missed within this framework. Here, they show that anaerobic microsites are important regulators of soil carbon persistence, shifting microbial metabolism to less efficient anaerobic respiration, and selectively protecting otherwise bioavailable, reduced organic compounds such as lipids and waxes from decomposition. Further, shifting from anaerobic to aerobic conditions leads to a 10-fold increase in volume-specific mineralization rate, illustrating the sensitivity of anaerobically protected carbon to disturbance. The vulnerability of anaerobically protected carbon to future climate or land use change thus constitutes a yet unrecognized soil carbon-climate feedback that should be incorporated into terrestrial ecosystem models.

Contacts
(BER PM)
Daniel Stover
SC-23.1
Daniel.Stover@science.doe.gov (301-903-0289)

(PI Contact)
Scott Fendorf (lead PI)
Stanford University
Email: Fendorf@stanford.edu

Marco Keiluweit
University of Massachusetts Amherst
Email: keiluweit@umass.edu

Funding
This work was supported by the US Department of Energy, Office of Biological and Environmental Research, Terrestrial Ecosystem Program (Award Number DE-FG02-13ER65542), and Subsurface Biogeochemistry Program (Award Number DE-SC0016544). A portion of this research was performed using EMSL, a DOE Office of Science User Facility sponsored by the Office of Biological and Environmental Research and located at Pacific Northwest National Laboratory.

Publications
Keiluweit M., T. Wanzek, M. Kleber, P. Nico, and S. Fendorf. “Anaerobic microsites have an unaccounted role in soil carbon stabilization.” Nature Communications 8, Article No. 1771 (2017).  [DOI: 10.1038/s41467-017-01406-6]

Related Links
Phys.org Article: Disrupting sensitive soils could make climate change worse, researchers find
Science Daily: Soil researchers quantify an underappreciated factor in carbon release to the atmosphere
Engadget: Unearthing oxygen-starved bacteria might worsen climate change

Topic Areas:


November 21, 2017

CrunchFlow Receives 2017 R&D 100 Award

Powerful software simulates how chemical reactions occur and change as fluids travel underground. 

Developed by researchers at the Department of Energy’s Lawrence Berkeley National Laboratory (LBNL), CrunchFlow is a powerful software package that simulates how chemical reactions occur and change as fluids travel underground. CrunchFlow includes a number of chemical and physical processes that similar products do not, such as changes in how easily water can move through porous media. All of these features are available in a single package that users with a variety of expertise can run on a desktop computer. With CrunchFlow’s computational efficiency, scientists can achieve high spatial resolution while extending simulations far back in geologic time. By improving the accuracy of a range of Earth and environmental sciences applications, CrunchFlow helps scientists better understand current and past ecological systems below the Earth’s surface.

The principal developer is LBNL’s Carl Steefel with co-developers Sergi Molins-Rafa and Jennifer Druhan from the University of Illinois-Champaign.

R&D Magazine‘s R&D 100 Awards, established 55 years ago, recognize 100 technologies and services introduced in the previous year deemed most significant by an independent panel of judges.

Contact (BER PM)
David Lesmes
SC-23.1
David.Lesmes@science.doe.gov, 301-903-2977

PI Contact
Carl Steefel
LBNL, CISteefel@lbl.gov

Funding
This work was funded in part by the U.S. Department of Energy, Office of Science, Biological and Environmental Research, under contract DE-AC020SCH11231.

Publication
B. Arora, S. S. Sengor, N.F. Spycher, and C.I. Steefel. 2015. “A reactive transport benchmark on heavy metal cycling in lake sediments,” Computational Geosciences, 19, 613-633. doi: 10.1007/s10596-014-9445-8

Related links
CrunchFlow website
SFA News Article Steefel et al. Receive R&D 100 Award for CrunchFlow

Topic Areas:


November 01, 2017

Assembly of Microbial Communities Affects Biogeochemistry

Dispersal varies the relationship between microbial communities and biogeochemical function.

The Science
Microbial communities are like our own societies. In their natural environments, where they’re comfortable and acclimated, both microbes and humans tend to thrive. They know how to navigate their surroundings, how to survive, and they concentrate their energy on being productive. When dispersed to an unfamiliar environment, organisms are naturally maladapted to their surroundings. Additionally, when it comes to communities with more organisms arriving through dispersal, research indicates there’s a lower rate of functioning. This concept, detailed in a new paper by PNNL researchers Emily Graham and James Stegen, brings us a step closer to understanding how a microbial community functions based on how it was assembled.

The Impact
Microbial communities have a profound impact on biogeochemical processes, which transform chemical nutrients as they circulate through biological and physical worlds. By increasing our understanding of how microbial communities function, we can develop models that predict important things such as the rate of nutrient cycling in a given area, during a given time of year.

Summary
Microbial communities are assembled by deterministic (selection) and stochastic (dispersal) processes. The relative influence of these two process types is believed to alter how microbial communities affect biogeochemical function. But recent attempts to link microbial communities and environmental biogeochemistry have yielded mixed results.

In this study, Graham and Stegen proposed a new conceptualization of microbial-biogeochemical relationships and created an ecological simulation model to demonstrate that microbial dispersal decreases biogeochemical function. Simply put, microbes that disperse into a community aren’t as productive as ones that were selected to live within that environment.

In a community of microbes selected to live in that environment, the microbes were well-adapted to their environment and productivity was high. But when microbes were introduced to the community via dispersal, productivity decreased, even as diversity increased.

In communities comprised mostly of microbes arriving via dispersal, productivity decreased significantly. Stegen and Graham propose that this effect is pronounced in natural settings in which dispersing microbes use more energy for survival than for catalyzing biogeochemical processes. This indicates that community structure and function are linked via ecological assembly processes that are influenced by microbial adaptation to local conditions.

The next step, say researchers, is incorporating assembly processes into emerging model frameworks that explicitly represent microbes and that mechanistically represent biogeochemical reactions. Specifically, the researchers plan to incorporate this framework into ongoing efforts by the PNNL SBR SFA team using a reactive transport model (PFLOTRAN) applied across a broad range of spatial and temporal scales.

BER PM Contact
David Lesmes
Paul Bayer

PI Contact
Emily Graham
Pacific Northwest National Laboratory
emily.graham@pnnl.gov

James Stegen
Pacific Northwest National Laboratory
James.stegen@pnnl.gov

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

Publications
Graham, E. and J. Stegen. “Dispersal-Based Microbial Community Assembly Decreases Biogeochemical Function.” Processes 5(4), 65 (2017). [DOI: 10.3390/pr5040065]

Related Links
PNNL Highlight: Modeling Microbial Ecology in the Hyporheic Zone
Phys.org News: A new model for microbial communities in the hyporheic zone
Highlight slide: Towards Better Models of Subsurface Microbial Communities [PDF]
Highlight slide: Groundwater-Surface Water Mixing in the Hyporheic Zone Stimulates Organic Carbon Turnover [PDF]
Highlight slide: Estimating and Mapping Ecological Processes Influencing Microbial Community Assembly [PDF]

Topic Areas:


October 16, 2017

Improving Accuracy of Subsurface Flow and Transport Models

New approach to quantify uncertainty in large scale models helps researchers predict fluid flow through porous subsurface media at more detailed scale.

The Science
Researchers improved the predictive capabilities of subsurface flow models by developing new, more efficient equations that account for length scales at which predictions are made and the hydrological measurements that are made in the field.

The Impact
To protect humans and the environment, there is a need to accurately predict the fate and transport of contaminants in the groundwater and subsurface sediments. Armed with more accurate predictive models, land stewards and managers can take appropriate actions to isolate and remove contaminants.

Summary
What scientists know about complex natural systems is inherently uncertain mainly because of very incomplete knowledge of the structure and function of the subsurface environment. Depending on the amount and type of available data, uncertainty in predictions can be so large that it makes them useless. For this reason uncertainty quantification is now an essential part of predictive modeling. A group of scientists from the Pacific Northwest National Laboratory has now proposed a new computational method that allows a researcher to identify the scale at which predictions can be made with an acceptable level of uncertainty, as defined by the researcher. At a given scale, this method can provide guidance regarding where and how many additional measurements are required to make predictions with that desired level of uncertainty.

Contacts (BER PM)
David Lesmes
Subsurface Biogeochemical Research
David.Lesmes@science.doe.gov, 301-903-2977

Paul Bayer
Subsurface Biogeochemical Research
Paul.Bayer@science.doe.gov, 301-903-5324

(PI Contact)
Alex Tartakovsky
Alexandre.Tartakovsky@pnnl.gov
509/372-6185

Funding
This research was supported by the U.S. Department of Energy (DOE) Office of Advanced Scientific Computing Research (ASCR) as part of the Early Career Award ‘‘New Dimension Reduction Methods and Scalable Algorithms for Multiscale Nonlinear Phenomena' and by DOE's Office of Biological and Environmental Research (BER) through the PNNL Subsurface Biogeochemical Research Scientific Focus Area project. Funding also came from the Italian Ministry of Education, Universities and Research (MUIR); from the Water Joint Programming Initiative's WaterWorks 2014 project WE-NEED:WatEr NEEDs availability, quality and sustainability; and from the European Union's Horizon 2020 Research and Innovation programme.‘‘Furthering the Knowledge Base for Reducing the Environmental Footprint of Shale Gas Development' (FRACRISK).

Publications
Tartakovsky, A. M., M. Panzeri, G.D.Tartakovsky and A. Guadagnini. "Uncertainty Quantification in Scale-Dependent Models of Flow in Porous Media." Water Resources Research, 53, 9392-9401 (2017). [DOI:10.1002/2017WR020905]

Topic Areas:

Division: SC-23.1 Climate and Environmental Sciences Division, BER


September 29, 2017

How Bacteria Produce Manganese Oxide Nanoparticles

Structural characterization of bacterial enzyme complex sheds light on manganese biomineralization and other elemental cycles.

The Science
Bacteria that produce manganese (Mn) oxides are extraordinarily skilled engineers of nanomaterials they contribute significantly to global biogeochemical cycles. However, mineralization mediated by these organisms is poorly understood because enzymes involved in these processes are largely uncharacterized. A recent study revealed for the first time the structure of Mnx—a bacterial enzyme complex responsible for Mn biomineralization—and the Mn oxide nanoparticles it produces.

The Impact
An improved understanding of biomineralization enzymes may allow scientists to engineer proteins for applications such as environmental remediation and bioenergy production. The novel analytical tools used in this study could also be applied to solve the structure of other enzymes that play a critical role in global biogeochemical cycles, especially enzymes intractable by more conventional nuclear magnetic resonance, crystallography, or electron microscopy approaches.

Summary
Mn is a very important transition metal for all life. Mn cycling between its reduced primarily soluble form (Mn(II)) and its oxidized insoluble forms (Mn(III,IV) oxides) is coupled in myriad ways to many elemental cycles. Research has established Mn(II) is oxidized to Mn(III,IV) minerals primarily through activities of bacteria and fungi. Yet, the biomineralization enzymes produced by these organisms are very challenging to study because it is difficult to isolate and purify them. To address this challenge, researchers from the Oregon Health & Science University, the Ohio State University, and EMSL, the Environmental Molecular Sciences Laboratory, used state-of-the-art mass spectrometry, ion mobility, and electron microscopy to solve the previously uncharacterized structure of Mnx and the Mn oxide nanoparticles it produces. The researchers used high resolution mass spectrometry and atomic resolution aberration-corrected scanning transmission electron microscopy at EMSL, a DOE Office of Science user facility. These data provide critical structural information for understanding Mn biomineralization, which is potentially well suited for environmental remediation applications. Moreover, the new insights into the structure of Mnx may inform ongoing research into the mechanisms of photosynthesis and catalytic oxygen production.

Contacts
(BER PM)

Paul Bayer, SC-23.1, 301-903-5324

(PI Contacts)
Bradley Tebo
Oregon Health & Science University
tebob@ohsu.edu

Vicki Wysocki
Ohio State University
wysocki.11@osu.edu

Ljiljana Paša-Tolić
EMSL
ljiljana.pasatolic@pnnl.gov

Funding
This work was supported by the U.S. Department of Energy’s Office of Science (Office of Biological and Environmental Research), including support of the Environmental Molecular Sciences Laboratory (EMSL), a DOE Office of Science User Facility. Part of the project was also funded by the National Science Foundation (NSF), the National Institutes of Health, and an NSF Postdoctoral Research Fellowship in Biology Award.

Publication
Romano, C.A., M. Zhou, Y. Song, V.H. Wysocki, A.C. Dohnalkova, L. Kovarik, L. Paša-Tolić, and B, M. Tebo. 2017. “Biogenic Manganese Oxide Nanoparticle Formation by a Multimeric Multicopper Oxidase Mnx.” Nature Communications DOI: 10.1038/s41467-017-00896-8.

Related Links
How Bacteria Produce Manganese Oxide Nanoparticles on EMSL’s website

Topic Areas:

Division: SC-23.1 Climate and Environmental Sciences Division, BER


September 05, 2017

A Regional Model for Uranium Redox State and Mobility in the Environment

Redox variable sediments mediate uranium mobility in the upper Colorado River Basin.

The Science
Two new studies shed light on an important and previously underappreciated biogeochemical redox ‘engine’ believed to mediate groundwater quality in floodplains within the upper Colorado River Basin (CRB). Sediments enriched in organic carbon were found to be common within saturated zones and capillary fringes, to be highly redox active, and to strongly accumulate sulfide and uranium. The research showed that uranium was present as U(IV) complexed to organic matter and likely to mineral surfaces. The stability and predominance of these complexes is controlled by the abundance of organic and mineral surface functional groups, and the intensity of oxidative cycling.

The Impact
Complexation of U(IV) by sediment organic matter drives accumulation of uranium. However, redox cycling provides a mechanism by which U(IV), nutrients, and other contaminants can be seasonally transformed and released to groundwater. These new findings provide biogeochemical processes models needed to predict the behavior of redox-active species in floodplains in the upper CRB.

Summary
Uranium contamination stubbornly persists as a challenging and costly water quality concern at former uranium ore processing sites across the upper CRB. Plumes at these sites are not self-attenuating via natural flushing by groundwater as originally expected. Recent studies at the Rifle, CO legacy site suggest that organic-enriched anoxic sediments locally create conditions that promote reduction of U(VI) to relatively immobile U(IV), causing it to accumulate. Organic-enriched sediments at Rifle accumulate uranium under persistently saturated and anoxic conditions. However, incursion of oxidants into reduced sediments, if it were to occur, could transform contaminants, allowing organic-enriched sediments to act as secondary sources of uranium. Oxidant incursions do take place during periods of changing water tables, which occur throughout the year in the upper CRB. If organic-enriched sediments were regionally common in the upper CRB, and if they were exposed to varying redox conditions, then they could help to maintain the longevity of U plumes regionally. Cyclic redox variability would also have major implications for mobility of carbon, nitrogen, and metal contaminants in groundwater and surface waters.

To investigate these issues, Noël et al. (2017a,b) examined the occurrence and distribution of reduced and oxidized iron, sulfur, and uranium species in sediment cores spanning dry/oxic to wet/reduced conditions at three different sites across the upper CRB. The research used detailed molecular characterization involving chemical extractions, X-ray absorption spectroscopy (XAS), Mössbauer spectroscopy and X-ray microspectroscopy. This work demonstrates that anoxic organic-enriched sediments occur at all sites, strongly accumulate sulfides and uranium, and are exposed to strong seasonal redox cycles. Uranium was found to be present as U(IV) complexed to sediment-associated organic carbon and possibly to mineral surfaces. This finding is significant because complexed U(IV) is relatively susceptible to oxidative mobilization. Sediment particle size, organic carbon content, and pore saturation, control redox conditions in sediments and thus strongly influence the biogeochemistry of iron, sulfur, and uranium. These findings help to illuminate the mechanistic linkages between hydrology, sediment texture, and biogeochemistry. They further provide enhanced contextual and conceptual underpinnings to support reactive transport modeling of uranium, other contaminants, and nutrients in redox variable floodplains, a subject of importance to BER research missions.

Contacts (BER PM)
Roland Hirsch
DOE Office of Biological and Environmental Research, Climate and Environmental Sciences Division
roland.hirsch@science.doe.gov

(PI Contact)
John Bargar
SLAC National Accelerator Laboratory, Stanford Synchrotron radiation Lightsource
Bargar@slac.stanford.edu

Funding
Funding was provided by the DOE Office of Biological and Environmental Research, Subsurface Biogeochemistry Research (SBR) activity to the SLAC SFA program under contract DE-AC02-76SF00515 to SLAC. Use of SSRL is supported by the U.S. DOE, Office of Basic Energy Sciences. A portion of the research was performed using EMSL, a DOE Office of Science User Facility sponsored by the Office of Biological and Environmental Research (BER) (located at PNNL).  Sample collection at the Rifle, CO site was supported by the LBNL Watershed Function SFA, sponsored by the BER Climate and Environmental Sciences division.  Sample collection at the Naturita and Grand Junction, CO sites was supported by the DOE Office of Legacy Management.

Publications
Noël, V.; Boye, K.; Dynes, J.; Lezama-Pacheco, J. S.; Bone S.; Janot, N.; Cardarelli, E.; Williams, K. H.; Bargar, J. R. Redox constraints over U(IV) mobility in the floodplains of Upper Colorado River basin. Environmental Science & Technology. 2017b, 51, 10954-10964. DOI: 10.1021/acs.est.7b02203

Noël, V.; Boye, K.; Kukkadapu, R. K.; Bone, S.; Lezama-Pacheco, J. S.; Cardarelli, E.; Janot, N.; Fendorf, S.; Williams, K. H.; Bargar J. R. Understanding controls on redox processes in floodplain sediments of the Upper Colorado River Basin. Science of the Total Environment. 2017a, 603-604, 663-675. DOI: 10.1016/j.scitotenv.2017.01.109

Topic Areas:


September 05, 2017

Incorporation of Arsenic into Magnetite Reduces Arsenic Mobility in Water

Toxic arsenic (As) adsorbs to the iron mineral magnetite and evolves into a less-mobile, incorporated form.

The Science 
The precipitation of magnetite also removed dissolved Arsenic(V) and provided a stable sink for this water contaminant. Synchrotron x-ray spectroscopy techniques showed that As (V) atoms were incorporated into the magnetite structure, and that As(V) sorbed to pre-formed magnetite became increasingly incorporated over time and thus resistant to remobilization.

The Impact
Exposure to As in groundwater affects millions of people around the globe. The results of this study increase understanding of how iron minerals affect As mobility in natural systems and provide the molecular-level insight needed for the development of iron oxide-based As removal technologies. The study was highlighted on the cover of the October 2017 issue of Environmental Science: Processes and Impacts.

Summary
The use of As-contaminated water for irrigation or as a drinking water source is threatening human health in many regions of the world. Iron is the element which most strongly correlates with As in sediments, and As mobilization is frequently linked with the desorption/dissolution of As from iron oxides. Technologies for As removal from drinking water also rely on the sequestration of As with Fe oxides, e.g. using electrocoagulation or zero-valent iron filters. A team of scientists from Argonne National Laboratory, the University of Iowa, Newcastle University, and the Bulgarian Academy of Sciences elucidated the molecular-level interactions between dissolved As(V) and magnetite, a common product of iron corrosion or dissimilatory iron reduction. Using synchrotron X-ray techniques (XANES and EXAFS spectroscopy) the team found that co-precipitation of As(V) and magnetite results in incorporation of the As(V) ions into the structure of magnetite, whereas reactions of As(V) with pre-formed magnetite show a transformation from initially adsorbed As(V) to incorporated As(V). Selective chemical extractions show that once As is incorporated into magnetite it could not be remobilized, neither in the absence nor in the presence of aqueous Fe(II), suggesting that magnetite is a stable sink for As(V).

Contacts (BER PM)
Paul Bayer
Subsurface Biogeochemical Research
Paul.bayer@science.doe,gov

(PI Contact)
Kenneth M. Kemner
Argonne National Laboratory
kemner@anl.gov; (630) 252-1163

Funding
This research is part of the Subsurface Science Scientific Focus Area at Argonne National Laboratory, which is supported by the DOE Subsurface Biogeochemical Research Program, Office of Biological and Environmental Research, Office of Science. Use of the Electron Microscopy Center at Argonne and the Advanced Photon Source is supported by the U.S. Department of Energy, Office of Science, Office of Basic Energy Sciences. MRCAT/EnviroCAT operations are supported by DOE and the MRCAT/EnviroCAT member institutions. All work at Argonne was under Contract DE-AC02-06CH11357.   

Publications
Huhmann, B.L., A. Neumann, M. I. Boyanov, K.M. Kemner, M. M. Scherer. “Emerging investigator series: As(V) in magnetite: incorporation and redistribution.” Environ. Sci.: Processes Impacts 19, 1208-1219 (2017). [DOI:10.1039/c7em00237h ]

Related Links
ANL Subsurface biogeochemical research

Topic Areas:

Division: SC-23.1 Climate and Environmental Sciences Division, BER


August 26, 2017

New Approach to Characterize Natural Organic Matter in Belowground Sediments

Efforts to characterize carbon stored in sediments below 1 meter are critical for understanding the mechanisms that control the stability and dynamics of the largest fraction of the earth’s total carbon pool.

The Science
Organic carbon concentrations in sediments more than 1 meter below the land surface are typically 10 to 200 times lower than in surface soils, posing a distinct challenge for characterization. A range of chemical extractions were evaluated for extraction of natural organic matter (NOM) from low-carbon (<0.2%) alluvial sediments. Additionally, an extraction and purification scheme was developed in order to isolate and characterize different fractions of sediment-associated NOM.

The Impact
Using a combination of analytical approaches, high-quality chemical characterization data was collected on NOM from understudied low-carbon sediments. The developed approach can be used to provide insight into the mechanisms controlling the stability and dynamics of NOM in low-carbon sediments.

Summary
Surface soils typically contain 5-10% levels of organic carbon (OC), but OC concentrations in sediments more than 1 meter below the land surface are often 10 to 200 times lower, and the usual techniques to measure the chemical characteristics of OC in these sediments are not sufficiently sensitive. In this study, a range of chemical extractions were evaluated for extraction of natural organic matter (NOM) from two low-carbon (<0.2%) alluvial sediments. The OC extraction efficiency followed the order pyrophosphate (PP)>NaOH>HCl, hydroxylamine hydrochloride>dithionite, water. A NOM extraction and purification scheme was developed using sequential extraction with water (MQ) and sodium pyrophosphate at pH 10 (PP), combined with purification by dialysis and solid phase extraction in order to isolate different fractions of sediment-associated NOM. Characterization of these pools of NOM for metal content and by Fourier transform infrared spectroscopy (FITR) showed that the water soluble fraction (MQ-SPE) had a higher fraction of aliphatic and carboxylic groups, while the PP-extractable NOM (PP-SPE and PP >1kD) had higher fractions of C=C groups and higher residual metals. This trend from aliphatic to more aromatic is also supported by the specific UV absorbance at 254 nm (SUVA254) (3.5 vs 5.4 for MQ-SPE and PP-SPE, respectively) and electrospray ionization Fourier transform ion cyclotron resonance spectrometry (ESI-FTICR-MS) data which showed a greater abundance of peaks in the low O/C and high H/C region (0-0.4 O/C, 0.8-2.0 H/C) for the MQ-SPE fraction of NOM. Radiocarbon measurements yielded standard radiocarbon ages of 1020, 3095, and 9360 years BP for PP-SPE, PP >1kD, and residual (non-extractable) OC fractions, indicating an increase in NOM stability correlated with greater metal complexation, apparent molecular weight, and aromaticity.

BER PM Contact
David Lesmes, SC-23.1, 301-903-2977

Contact
Susan Hubbard
Lawrence Berkeley National Laboratory
sshubbard@lbl.gov

Funding
Funding for this study was provided by the U.S. Department of Energy, BER Contract DE-AC020SCH11231 to the LBNL Sustainable Systems Scientific Focus Area.

Publication
P.M. Fox, P.S. Nico, M.M. Tfaily, K. Heckman, and J.A. Davis, “Characterization of natural organic matter in low-carbon sediments: Extraction and analytical approaches.” Organic Geochemistry, 114, 12-22 (2017). [DOI: 10.1016/j.orggeochem.2017.08.009]

Related Links
Data archive:
Fox, Patricia; Nico, Peter; Tfaily, Malak; Heckman, Katherine; Davis, James (2017), “Data for: Characterization of Natural Organic Matter in Low-Carbon Sediments: Extraction and Analytical Approaches”, Mendeley Data, [DOI: 10.17632/5f3hbm69w6.2]

Topic Areas:

Division: SC-23.1 Climate and Environmental Sciences Division, BER


July 10, 2017

Modeling Across Multiple Scales to Enable System-Level Understanding of a Watershed

Novel model structures allow advanced models of permafrost thermal hydrology to run at scale.

The Science
Field and laboratory observations and the models that are used to help understand the observed processes typically focus on relatively small scales, but the consequences of those processes must be evaluated at larger watershed or regional scales.  An intermediate-scale modeling approach has been developed to bridge this gap in scales and improve confidence in simulations of Arctic hydrology and permafrost dynamics.

The Impact
Broadly applicable to hydrology modeling, the approach makes it possible to include more detail in process representations, thus providing direct links between detailed field investigations and larger-scale models. The resulting model improves the representation of permafrost dynamics, which directly affect cold-region hydrology, Arctic infrastructure stability, and biogeochemical cycles.

Summary
Motivated by results from fine-scale simulations, scientists from Oak Ridge National Laboratory and Los Alamos National Laboratory developed an intermediate-scale model. The new model replaces a fully three-dimensional system with a two-dimensional overland thermal hydrology system and a family of one-dimensional vertical columns, where each column represents a thermal hydrology system coupling the surface and subsurface but without lateral flow. This approach accurately approximates the fully-resolved solution, but can be solved at significantly less computational cost. The computational advantages will enable state-of-the-art models of permafrost dynamics to be applied across large swaths of the Arctic.  Furthermore, the approach supports the broader strategy of using local models and field observations to reduce uncertainty in watershed, regional, and global Earth System Model predictions.

Contacts (BER PM)
David Lesmes, Paul Bayer, and Dan Stover
SC-23.1
David.Lesmes@science.doe.gov (301-903-0289)
Paul.Bayer@science.doe.gov
Daniel.Stover@science.doe.gov  

(PI Contact)
Ahmad Jan and Scott Painter
Climate Change Science Institute, Oak Ridge National Laboratory
jana@ornl.gov (865-576-8175) or paintersl@ornl.gov (865-241-2644)

Funding
This work was supported by Interoperable Design of Extreme-scale Application Software (IDEAS) project and by the Next Generation Ecosystem Experiment (NGEE-Arctic) project.

Publications
Jan, A., E. T. Coon, S. L. Painter, R. Garimella, and J. D Moulton, “An intermediate-scale model for thermal hydrology in low-relief permafrost-affected landscapes.” Comput Geosci 22, 163-177 (2017). [DOI:10.1007/s10596-017-9679-3]

Topic Areas:

Division: SC-23.1 Climate and Environmental Sciences Division, BER


July 06, 2017

Simple Non-Electrostatic Model Successfully Predicts Long-Term Uranium Mobility

When compared to results from a more complicated surface complexation model with electrostatic correction, the simple model performed just as well but was less computationally intensive.

Scientific Achievement
A simple non-electrostatic model was developed through a step-by-step calibration procedure to describe U (Uranium) plume behavior at the Savannah River site. This simple model was found to be more numerically-efficient than a complex mechanistic model with electrostatic correction terms in predicting long-term U behavior at the site and by extension other uranium contaminated sites.

Significance & Impact
Uranium geochemistry has been extremely challenging to describe and predict. Although complex mechanistic models have been used to describe U sorption in field settings, there is significant uncertainty in model predictions due to scarce field data and modeling assumptions concerning mineral assemblage and subsurface heterogeneity. This study demonstrates that a simpler non-electrostatic model is a powerful alternative for describing U plume evolution at the Savannah River Site (SRS) because it can describe U(VI) sorption much more accurately than a constant coefficient (Kd) approach, while being more numerically efficient than a complex model with electrostatic correction terms. This study provides valuable insight into predicting uranium plume persistence from contaminated sites using simple non-electrostatic models.

Summary
The aim of this study was to test if a simpler, semi-empirical, non-electrostatic U(VI) sorption model (NEM) could achieve the same predictive performance as a model with electrostatic correction terms in describing pH and U(VI) behavior at multiple locations within the SRS F-Area. Modeling results indicate that the simpler NEM was able to perform as well as the electrostatic surface complexation model especially in simulating uranium breakthrough tails and long-term trends. However, the model simulations differed significantly during the early basin discharge period. Model performance cannot be assessed during this early period due to a lack of field observations (e.g., initial pH of the basin water) that would better constrain the models. In this manner, modeling results highlight the importance of the range of environmental data that are typically used for calibrating the model.

Contacts
(BER PM)

David Lesmes
SC-23.1
David.Lesmes@science.doe.gov (301-903-2977)

(PI Contact)
Haruko Wainwright
Lawrence Berkeley National Laboratory
HMWainwright@lbl.gov

Funding
This material is based upon work supported as part of the ASCEM project, which is funded by the U.S. Department of Energy Environmental Management, and as part of the Genomes to Watershed Science Focus Area, which is funded by the U.S. Department of Energy, Office of Science, Office of Biological and Environmental Research, both under Award Number DE-AC02-05CH11231 to Lawrence Berkeley National Laboratory.

Publications
Arora, B., J.A. Davis, N.F. Spycher, W. Dong, and H.M. Wainwright. 2017. “Comparison of Electrostatic and Non-Electrostatic Models for U (VI) Sorption on Aquifer Sediments” Groundwater. doi:10.1111/gwat.12551.

Topic Areas:

Division: SC-23.1 Climate and Environmental Sciences Division, BER


June 14, 2017

First Measurements of Dark Reactive Oxygen Species in a Groundwater Aquifer

First measurement of the presence of hydrogen peroxide concentrations in groundwater establishes importance of reactive oxygen species in the subsurface.

The Science 
Reactive oxygen species (ROS) such as hydrogen peroxide (H2O2) are very short-lived intermediate molecules generated during the one-electron reduction of oxygen to water through photochemical oxidation or through a “dark” process involving microorganisms. To date, ROS have been found in the deep ocean, sediments, and fresh waters. Now, a team of scientists has demonstrated a dark biological process that generates hydrogen peroxide in groundwater from an alluvial aquifer.

The Impact
Hydrogen peroxide and an associated class of compounds called Reactive Oxygen Species (ROS) have long been known to be important drivers of biogeochemical cycling and contaminant decomposition in surface water (oceans, rivers, and lakes). By demonstrating that hydrogen peroxide and therefore the associated group of reactive oxygen species were widely distributed in the groundwater of a uranium-contaminated alluvial floodplain, scientists have established that ROS likely are important to the chemistry and functioning of biogeochemical cycles in this floodplain and other groundwater systems. The presence of ROS in some groundwater systems may help explain the apparent non-equilibrium conditions in these systems, as well as potential organic matter oxidation pathways.

Summary
The commonly held assumption that photodependent processes dominate H2O2 production in natural waters has recently been questioned. This paper demonstrated for the unrecognized and light-independent generation of H2O2 in groundwater of an alluvial aquifer adjacent to the Colorado River near Rifle, CO.

Using a sensitive chemiluminescent method to detect H2O2 along vertical profiles at various locations across an alluvial aquifer of the Colorado River, a team of scientists from Lawrence Berkeley National Laboratory (LBNL), Peking University, and the University of New South Wales, found that H2O2 concentrations ranged from lower than the detection limit (<1 nM) to 54 nM. The data also suggest dark formation of H2O2 is more likely to occur in transitional redox environments where reduced elements (e.g., reduced metals and NOM) meet oxygen, such as oxic-anoxic interfaces. A simplified kinetic model involving interactions among iron, reduced NOM, and oxygen was able to reproduce roughly many, but not all, of the features in the detected H2O2 profiles. This suggests there likely are other minor biological and/or chemical controls on H2O2 steady-state concentrations in such aquifer. Because of its transient nature, the widespread presence of H2O2 in groundwater indicates the existence of a balance between H2O2 sources and sinks, which potentially involves a cascade of various biogeochemically important processes that could have significant impacts on metal/nutrient cycling in groundwater-dependent ecosystems, such as wetlands and springs. More importantly, these results demonstrate that ROS are not only widespread in oceanic and atmospheric systems, but are also present in the subsurface domain, possibly the least understood component of the Earth system, and yet, critical for understanding a wide variety of biogeochemical cycles.

Contacts (BER PM)
David Lesmes
Subsurface Biogeochemical Research
David.Lesmes@science.doe.gov

(PI Contact)
Peter S. Nico
Berkeley Lab
psnico@lbl.gov

Funding
DOE-SBR Watershed Function SFA

Publications
Yuan, X., P. S. Nico, X. Huang, T. Liu, C. Ulrich, K. H. Williams, and J. A. Davis. “Production of hydrogen peroxide in groundwater at Rifle, Colorado.” Environ. Sci. Technol. 51, 7881-7891 (2017). [DOI:10.1021/acs.est.6b04803]

Topic Areas:

Division: SC-23.1 Climate and Environmental Sciences Division, BER


May 04, 2017

How Plant Roots Take Up Water from Soil

A combined experimental and modeling approach quantitatively demonstrates in 3D the transport of water from the surrounding rhizosphere through plant roots.

The Science
Root water uptake is one of the most important processes in subsurface flow and transport modeling. It is driven by transpiration caused by the water potential gradient between the atmosphere and the plant. But the mechanisms of root water uptake are poorly known, and are represented only coarsely in macro-scale models because of the difficulties of both imaging and modeling such systems.

A new paper in the journal Rhizosphere, by Timothy D. Scheibe and three co-authors at the Pacific Northwest National Laboratory (PNNL), demonstrates a promising way to address those difficulties. In a pilot study, they successfully simulate three-dimensional root water uptake by applying a combination of X-ray Computed Tomography (XCT) and computational fluid dynamics (CFD) modeling at the pore-scale.

The Impact
The new coupled imaging-modeling approach introduces a realistic platform for investigating rhizosphere flow processes - one that could support translation of process understanding from a single-plant to vegetation scales. The same imaging-modeling method could also be used to simulate more realistic scenarios and compared to laboratory and field plot studies to improve process understanding.

Summary
Successful in-soil imaging of a live plant could unlock mysteries regarding the complex plant-soil-microbe interactions in the rhizosphere. This plant-root interface, teeming with microorganisms and bathed in water at every scale, is where complex chemical, biological, and physical interactions determine the health of plants, their root systems, and the surrounding soil.

To date, however, imaging and modeling root water uptake has been difficult. The complexity of the root architecture and soil properties makes explicit imaging problematic. Estimating plant-root and soil properties for modeling is also difficult, compounded by a poor understanding of the hydrological and biological processes involved in root water uptake.

In the last decade, a promising series of papers has shown the potential of integrating high-resolution imaging techniques and pore-scale modeling for investigating the interactions of soil, roots, and groundwater.

A team at PNNL recently combined non-invasive XCT imaging with both open-source and in-house software codes. They successfully imaged root water uptake at a micron-scale resolution in 3D and they also modeled the spatiotemporal variations of water uptake. What they call a “pioneer” pilot study provides a platform for future research into the role of plant roots in nutrient uptake, hydraulic redistribution, and other phenomena in the rhizosphere.

The researchers used a single Prairie dropseed (Sporobolus heterolepis) plant grown in a pot, which was rotated continuously during a scan that captured 3,142 projections (at four frames per projection). The raw images were used to create a three-dimensional dataset. From there, in-house PNNL software derived quantitative information, including root volume and surface area. The result was a mechanistic pore-scale numerical model of root uptake processes.

The study showed that soil water distribution was controlled by both plant-root and soil conductivity, and by transpiration rate. But more broadly, it demonstrated a realistic platform for investigating rhizosphere flow processes.

BER Program Contacts
David Lesmes, Subsurface Biogeochemical Research
David.Lesmes@science.doe.gov
(301) 903-2977

Paul Bayer, Subsurface Biogeochemical Research
Paul.Bayer@science.doe.gov
(301) 903-5324

Dan Stover, Terrestrial Ecosystem Sciences
Dan.Stover@science.doe.gov
(301) 903-0289

PI Contact
Timothy D. Scheibe
Pacific Northwest National Laboratory
Tim.scheibe@pnnl.gov (509-371-7633)

Funding
This research was supported by the U.S. Department of Energy (DOE) Biological and Environmental Research (BER) Division through the Terrestrial Ecosystem Science (TES) program and the Subsurface Biogeochemical Research (SBR) program, through the PNNL SBR Scientific Focus Area Project. Part of this research was performed at the Environmental Molecular Sciences Laboratory (EMSL), a DOE scientific user facility located at Pacific Northwest National Laboratory (PNNL).

Publication
Yang, X., T. Varga, C. Liu, and T.D. Scheibe. “What can we learn from in-soil imaging of a live plant: X-ray Computed Tomography and 3D numerical simulation of root soil system.” Rhizosphere 3(2), 259-262 (2017). [DOI: 10.1016/j.rhisph.2017.04.017]
(Reference link)

Related Links
PubMed: “Extracting Metrics for Three-dimensional Root Systems: Volume and Surface Analysis from In-soil X-ray Computed Tomography Data” J Vis Exp. 2016 Apr 26;(110). [DOI:10.3791/53788]
Soil Science Society of America Journal Abstract - Soil Physics: “A Unified Multiscale Model for Pore-ScaleFlow Simulations in Soils” [DOI:10.2136/sssaj2013.05.0190]

Topic Areas:


May 01, 2017

Thermodynamic Preservation of Carbon in Anoxic Environments

Novel mechanism shifts understanding of the reactivity of carbon in subsurface stocks.

The Science
A new study provides important insights into why carbon persists in waterlogged soil and subsurface sediments. Energetic constraints prevent microbial respiration of certain organic carbon compounds, leaving a pool of water-soluble carbon that is susceptible to oxidation or export and subsequent decomposition in downstream, aerated environments.

The Impact
Terrestrial, anoxic environments hold large stocks of carbon and knowledge of the dynamics of these stocks is insufficient. Thermodynamic limitations on organic carbon decomposition operate differently than better-recognized kinetic and spatial constraints and this must be accounted for in models predicting carbon cycling rates. The new findings imply that organic carbon stocks respond differently than previously thought to changes in sediment water saturation. Moreover, carbon exported from anoxic environments has the potential to drive nutrient, contaminant, and carbon cycles in downstream aquatic ecosystems. The study also demonstrates the benefits of combining X-ray absorption spectroscopy (XAS) at the Stanford Synchrotron Radiation Lightscource (SSRL) with Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR-MS) at the Environmental Molecular Sciences Laboratory (EMSL).

Summary
It is well recognized that carbon persists in environments where the oxygen levels are low. Carbon stocks existing in floodplains, wetlands, and subsurface sediments, which often are suboxic to anoxic, comprise a considerable portion of the global dynamic carbon inventory. In spite of the importance to accurately represent the dynamics of these carbon stocks in global, regional, and local carbon models, the mechanisms responsible for carbon preservation in anoxic conditions are unclear. The degradation of organic matter takes place through multiple steps, involving enzymatic and metabolic processes carried out by many different types of microorganisms. However, the last step, the oxidation of organic molecules to carbon dioxide through microbial respiration, requires the molecules to be water-soluble and small enough to enter the microbial cell. In addition to this, the oxidation of carbon must generate enough energy to support microbial growth. With oxygen present the respiratory oxidation of any carbon compound is thermodynamically viable; it provides sufficient energy to sustain growth. But without oxygen, some carbon compounds, mostly belonging to the chemical classes of lipids and proteins, become thermodynamically unviable for oxidation, in spite of being dissolved and small enough to enter the microbial cell. This changes the chemical composition of the water-soluble carbon in environments where this thermodynamic preservation mechanism is operational.

In a Stanford University and SSRL based study, Boye et al. (2017), utilized the shift in water soluble carbon chemistry to demonstrate the relevance of thermodynamic limitations for preserving carbon in field samples from anoxic floodplain sediments from four sites across the upper Colorado River Basin. X-ray absorption spectroscopy at SSRL was used to identify sediments containing sulfides produced by microbial respiration in the absence of oxygen. The water-soluble carbon from these sediments was then analyzed by FT-ICR-MS at EMSL and compared to that from oxic sediment samples. The results reveal a clear difference in carbon chemistry consistent with theoretically calculated thermodynamic thresholds and provide unprecedented field-based evidence for thermodynamic preservation of carbon in anoxic conditions. This is important because it illuminates a mechanism previously unrepresented in carbon cycling models and further highlights that water-soluble, and thus readily exported, carbon from anoxic environments is highly susceptible to rapid decomposition upon exposure to oxygen. The downstream implications of this reactive carbon source are currently not fully understood, but are likely substantial.

Contacts (BER PM)
Roland Hirsch
DOE Office of Biological and Environmental Research, Climate and Environmental Sciences Division
roland.hirsch@science.doe.gov

(PI Contact)
Scott Fendorf
Earth System Science, Stanford University
fendorf@stanford.edu
John Bargar
SLAC National Accelerator Laboratory, Stanford Synchrotron Radiation Lightsource
Bargar@slac.stanford.edu

Funding
Funding was provided by the DOE Office of Biological and Environmental Research, Subsurface Biogeochemistry Research activity to the SLAC SFA program under contract DE-AC02-76SF00515 to SLAC and to Scott Fendorf through the Terrestrial Ecosystem Science program under Award Number DE-FG02-13ER65542. Use of SSRL is supported by the U.S. DOE, Office of Basic Energy Sciences. A portion of the research was conducted at EMSL, a DOE Office of Science User Facility sponsored by the Office of Biological and Environmental Research and located at Pacific Northwest National Laboratory. Field operations were supported through the Lawrence Berkeley National Laboratory’s Sustainable Systems SFA (US DOE BER, contract DE-AC02-05CH11231) and through the DOE Office of Legacy Management (DOE-LM). Research described in this paper was performed at beamline 11ID-1 the CLS, which is supported by NSERC, CIHR, NRC, WEDC, the University of Saskatchewan, and the Province of Saskatchewan.

Publications
Boye, K., Noël, V., Tfaily, M.M., Bone, S.E., Williams, K.H., Bargar, J.R., Fendorf, S. “Thermodynamically controlled preservation of organic carbon in floodplains,” Nature Geoscience [DOI: 10.1038/ngeo2940] (2017).

Related Links
Reference link

Topic Areas:

Division: SC-23.1 Climate and Environmental Sciences Division, BER


April 13, 2017

Identifying the Important Contributors to Model Variability in a Multiprocess Model

Researchers define a new sensitivity index to quantify the uncertainty contribution from each process under model structural uncertainty.

The Science
Earth system models consist of multiple processes, each of them being a submodel in the integrated system model. A research team, including scientists at Florida State University, Pacific Northwest National Laboratory, and Oak Ridge National Laboratory, derived a new process sensitivity index to rank the importance of each process in a system model with multiple choices of each process model.

The Impact
The new process sensitivity index tackles the model uncertainty in a rigorous mathematical way, which has not been dealt with in conventional sensitivity analyses. Accounting for model structural uncertainty in complex multiphysics, multiprocess models has been a long-recognized need in the modeling community.

Summary
Most of the processes in a multiprocess model could be conceptualized in multiple ways, leading to multiple alternative models of a system. One question often asked is which process contributed to the most variability or uncertainty in the system model outputs. Global sensitivity analysis methods are an important and often used venue for quantifying such contributions and identifying the targets for efficient uncertainty reduction. However, existing methods of global sensitivity analysis only consider variability in the model parameters and are not capable of handling variability that arises from conceptualization of one or more processes. This research developed a new method to isolate the contribution of each process to the overall variability in model outputs by integrating model averaging concepts with a variance-based global sensitivity analysis. The researchers derived a process sensitivity index as a measure of relative process importance, which accounts for variability caused by both process models and their parameters. They demonstrated the new method with a hypothetical groundwater reactive transport modeling case that considers alternative physical heterogeneity and surface recharge submodels. However, the new process sensitivity index is generally applicable to a wide range of problems in hydrologic and biogeochemical problems in Earth system models. This research offers an advanced systematic approach to prioritizing model inspired experiments.

Contacts (BER PM)
David Lesmes
Subsurface Biogeochemical Research Program
David.Lesmes@science.doe.gov (301-903-2977)

Daniel Stover
Terrestrial Ecosystem Science Program
Daniel.Stover@science.doe.gov (301-903-0289)

(PI Contacts)
Ming Ye, Florida State University, mye@fsu.edu
Xingyuan Chen, Pacific Northwest National Laboratory (PNNL), Xingyuan.Chen@pnnl.gov
Anthony P. Walker, Oak Ridge National Laboratory (ORNL), walkerap@ornl.gov

Funding
This work was supported by the U.S. Department of Energy, Office of Science, Office of Biological Research, Early Career Award and PNNL Subsurface Science Research Scientific Focus Area and ORNL Terrestrial Ecosystem Science Scientific Focus Area.

Publication
Dai, H., M. Ye, A. P. Walker, and X. Chen. 2017. “A New Process Sensitivity Index to Identify Important System Processes Under Process Model Uncertainty and Parametric Uncertainty,” Water Resources Research 53(4), 3746-90. [DOI: 10.1002/2016WR019715]. (Reference link)

Topic Areas:

Division: SC-23.1 Climate and Environmental Sciences Division, BER


April 11, 2017

Modeling the Flow of Fluids through Microfluidic Devices

Researchers observe significant differences in seemingly identical microfluidics experiments, and demonstrate that stochastic modeling approaches can be used to account for the variability in flow.

The Science
The reproducibility of how fluids flow through microfluidic cells has not been well studied, and yet, the use of microfluidic devices to study a variety of fluid flow processes has been steadily increasing. Now, scientists have performed a set of well-controlled drainage and imbibition experiments using six identically manufactured microfluidic cells to study the reproducibility of multiphase flow experiments. The result: a variability (upwards of 200%) among the cells and within each cell, confirming that multiphase flow experiments should be considered as a stochastic process. Researchers proposed a stochastic model with randomly varying injection rate, which was able to reproduce both the average behavior and variability observed in the experiments.

The Impact
The collected data set reveals variability in pore-scale multiphase flow, which was explained by the proposed numerical model. Both the data and the model can provide an improved understanding of the multiphase flow physics of microfluidic devices, and this information can be very helpful for studying important environmental challenges such as subsurface contaminant remediation.

Summary
DOE sites, such as the Hanford Site, have a history of contaminants discharged into the ground. They mix, separate, and flow at varying speeds depending on the subsurface composition, temperature, moisture, and pressure. Researchers want to predict the flow of these various contaminants to devise more effective remediation solutions. Recent advances in numerical methods allow simulations of multiphase flow at pore, field, and regional scales, but researchers need to be able to validate the numerical results. The traditional approach to model validation is through comparison with experiments. Microfluidic devices and pore-scale numerical models are commonly used to study multiphase flow in biological, geological, and man-made porous materials. The thin plastic devices, each resembling a miniaturized slice of Swiss cheese, help researchers understand the physics of how water, particulates, contaminants, and other constituents flow in the subsurface. In this study, researchers used microfluidic cells to understand the physics of multiphase flow in porous media. Six identical cells were manufactured, and a precise pump was used to inject the liquids into the device. The flow in 30 experiments (five experiments for each of the six cell replicas) varied by close to 200 percent. The findings were surprising because they revealed significant variability in pore-scale multiphase flow cell experiments due to cell manufacturing defects and fluctuations in the pump injection rate. “It’s extremely difficult to replicate multiphase flow experiments in a lab,” said lead researcher Alexandre Tartakovsky, a scientist at the Pacific Northwest National Laboratory. Miniscule differences in manufacturing of the cell devices and small fluctuation in the pump injection rate can cause large variations in the experimental results. Such variations are virtually uncontrollable and can wreak havoc on results. Researchers proposed a stochastic model with randomly varying injection rate, which was able to reproduce both the average behavior and variability observed in the experiments. The standard deterministic models, on the other hand, cannot explain variability and give a poor estimate of the average behavior.

Contacts (BER PM)
David Lesmes
Subsurface Biogeochemical Research
David.Lesmes@science.doe.gov
(301) 903-2977

Paul Bayer
Subsurface Biogeochemical Research
Paul.Bayer@science.doe.gov
(301) 903-5324

PI Contact
Alexandre Tartakovsky
Pacific Northwest National Laboratory
Alexandre.Tartakovsky@pnnl.gov

Funding
This research was partially supported by the U.S. Department of Energy (DOE), Office of Biological and Environmental Research, Subsurface Biogeochemical Research (SBR) Program through the SBR Scientific Focus Area at Pacific Northwest National Laboratory (PNNL), and by the National Science Foundation (NSF). A. Tartakovsky was partially supported by the U.S. Department of Energy (DOE) Office of Advanced Scientific Computing (ASCR) as part of the Early Career Award “New Dimension Reduction Methods and Scalable Algorithms for Multiscale Nonlinear Phenomena.” 

Publication Ling, Bowen, J. Bao, M. Oostrom, I. Battiato, A.M. Tartakovsky. “Modeling variability in porescale multiphase flow experiments.” Advances in Water Resources 105, 29-38  (2017).  [DOI:10.1016/j.advwatres.2017.04.005]

Related Links
Modeling variability in porescale multiphase flow experiments

Topic Areas:

Division: SC-23.1 Climate and Environmental Sciences Division, BER


April 09, 2017

Dynamic Water Conditions Greatly Impact Nitrogen in Hyporheic Zones

Researchers examine N transformations in Columbia River hyporheic zone.

The Science
The hyporheic zone (HZ) is the subsurface zone where river water and groundwater exchange and mix. Researchers used multiple laboratory columns containing sediments from the Columbia River HZ to examine how dynamic changes in groundwater and surface water mixing affect microbial communities and their biogeochemical function with respect to nitrogen (N) transformations. Flow rates and directions were systematically varied to evaluate the impacts of flow dynamics on N biogeochemistry and microbial community composition and function. Experimental results were incorporated into numerical models to help interpret dominant processes and their effects.

The Impact
Variable discharges from upstream dams cause frequent changes in direction and magnitude of flow in the HZ, making it challenging to predict pathways and concentrations of N. The results of this study show that water flow direction and source, and their periodic oscillations, have a profound impact on the pathways and rates of N transformation in HZ sediments. Microbial communities showed the ability to adapt to flow conditions over periods of several days, but microbial function remained stable under short-term (sub-daily) changes in flow conditions. These results demonstrate the importance of considering recent hydrologic conditions (historical contingencies) in predictions of HZ biogeochemical function.

Summary
The HZ is an active biogeochemical region where chemicals and nutrients carried by groundwater and surface water mix and stimulate microbial activities. Strong chemical gradients develop, and promote the rapid transformation of carbon, N, and other elements.

Inorganic N is commonly present in groundwater and surface water, but at elevated concentrations it is considered a contaminant. N cycling also plays a critical role in healthy ecosystem functioning, and is known to be influenced by hydrologic exchange between groundwater and river water. For these reason, researchers sought to better understand how N transforms in HZs that experience significant daily, monthly, and seasonal variations in hydrologic flow conditions.

Researchers created five laboratory columns using sediment samples collected from the HZ in the Columbia River, downstream from the Priest Rapids Dam. This particular HZ is considered hydrologically dynamic, which can make it challenging to predict changes in the microbial communities and biogeochemical processes that affect N.

In the study, researchers suggest that it’s essential to investigate the spatial and temporal variations in N transformations under variable fluid flow. They subjected each of five columns to various flow rates and effluent and pore water conditions to simulate possible scenarios in the HZ.

The results imply that variations in the mixing zone greatly affect both microbial function and the biogeochemical processes responsible for transforming N. In fact, water flow direction and sources, and their periodic oscillations, have a profound impact on the pathways and rates of N transformation in HZ sediments. As N pathways changed both over time and in different spatial locations, so did the interactions between N and other elements and the composition and function of the microbes in the system.

For these reasons, researchers say, caution should be applied when interpreting results of correlation analysis on HZ systems, particularly when dynamic changes in hydro-biogeochemical conditions occur with different timing and frequency.

BER PM Contact
Paul Bayer, paulbayer@science.doe.gov, 301-903-5324
David Lesmes, david.lesmes@science.doe.gov, 301-903-2977

PI Contact
Tim Scheibe
PNNL
Tim.Scheibe@pnnl.gov, 509/371-7633

Funding
This research is supported by the U.S. Department of Energy, Office of Science, Biological and Environmental Research as part of the Subsurface Biogeochemical Research (SBR) Program through PNNL’s SBR Science Focus Area (SFA) project. F. Xu, Y. Liu, A. Yan, and C. Liu also acknowledge the supports from Research Funds from National Natural Science Foundation of China and China Postdoctoral Science Foundation.

Publications
Yuanyuan Liu, et al. “Effect of Water Chemistry and Hydrodynamics on Nitrogen Transformation Activity and Microbial Community Functional Potential in Hyporheic Zone Sediment Columns.” Environ. Sci. Technol. 2017. 51(9):4877-4886. DOI: 10.1021/acs.est.6b05018

Topic Areas:

Division: SC-23.1 Climate and Environmental Sciences Division, BER


February 16, 2017

New Approach to Predict Flow and Transport Processes in Fractured Rock Uses Causal Modeling

Application of causality theory to hydrological flow and transport studies could lead to more accurate predictions of numerical models.

The Science
Scientists and engineers simulate the flow of fluids through permeable media to determine how water, oil, gas or heat can be safely extracted from subsurface fractured-porous rock, or how harmful materials like carbon dioxide could be stored deep underground. Now, a scientist from Lawrence Berkeley National Laboratory has identified a causal relationship between gases and liquids flowing through fractured-porous media. They observed oscillating liquid and gas fluxes and pressures as the two transitioned back and forth within a subsurface rock fracture.

The Impact
When both liquid and gas are injected into a rock fracture, the cumulative effect of forward and return pressure waves causes intermittent oscillations of liquid and gas fluxes and pressures within the fracture. The Granger causality test is used to determine whether the measured time series of one of the fluids can be applied to forecast the pressure variations in another fluid.  This method could also be used to better understand the causation of other hydrological processes, such as infiltration and evapotranspiration in heterogeneous subsurface media, and climatic processes, for example, relationships between meteorological parameters—temperature, solar radiation, barometric pressure, etc.

Summary
Identifying dynamic causal inference involved in flow and transport processes in complex fractured-porous media is generally a challenging task, because nonlinear and chaotic variables may be positively coupled or correlated for some periods of time but can then become spontaneously decoupled or non-correlated. The author hypothesized that the observed pressure oscillations at both inlet and outlet edges of the fracture result from a superposition of both forward and return waves of pressure propagation through the fracture. He tested the theory by exploring an application of a combination of methods for detecting nonlinear chaotic dynamics behavior along with the multivariate Granger Causality (G-causality) time series test. Based on the G-causality test, the author inferred that his hypothesis was correct, and presented a causation loop diagram of the spatial-temporal distribution of gas, liquid, and capillary pressures measured at the inlet and outlet of the fracture. The causal modeling approach can be used for the analysis of other hydrological processes such as infiltration and pumping tests in heterogeneous subsurface media, and climatic processes.

BER PM Contact
David Lesmes, SC-23.1, David.Lesmes@science.doe.gov

Contact
Susan Hubbard, Lawrence Berkeley National Laboratory, sshubbard@lbl.gov
Deb Agarwal, Lawrence Berkeley National Laboratory, daagarwal@lbl.gov

Funding
This work was supported by the U.S. Department of Energy, Office of Science, Office of Biological and Environmental Research, and Office of Science, Office of Advanced Scientific Computing under Contract No. DE-AC02-05CH11231.

Publication
Faybishenko, B. “Detecting dynamic causal inference in nonlinear two-phase fracture flow.” Advances in Water Resources 106, 111-120 (2017). [DOI:10.1016/j.advwatres.2017.02.011]

Topic Areas:


January 25, 2017

Building Confidence in Hydrologic Models

Model intercomparison project evaluates performance of seven different integrated hydrology models for solving challenge benchmarks.

The Science 
Understanding water availability and quality for large-scale surface and groundwater systems requires simulation and many numerical models have been developed by scientists to address these needs. A suite of common hydrologic benchmark challenges was developed and seven different modeling teams from the U.S. and Europe exercised their models to achieve the benchmarks to  better understand how each of the models and model outputs agree and differ.

The Impact
Model intercomparison benchmark challenges build confidence in the choice of model used for a specific scientific question or application and they illuminate the implications of model choice because they force modeling teams to better understand the strengths and weaknesses of their own and competing models. This understanding leads to more reliable simulations and improves integrated hydrologic modeling.

Summary
Following up on a first integrated hydrologic model intercomparison project several years ago, seven teams of modelers, including two teams supported by the Interoperable Design for Extreme-scale Application Software (IDEAS) project, participated in a second intercomparison project. Teams met at a workshop in Bonn, Germany, and designed a series of three model intercomparison benchmark challenges. The challenges were designed to focus on different aspects of integrated hydrology, including a hillslope-scale catchment, subsurface structural inclusions and layering, and a field study of hydrology on a small ditch with simple but data-informed topography. Parameters were standardized, but each team used their own model, including differences in model physics, coupling, and algorithms. Results were collected, stimulating detailed conversations to explain similarities and differences across the suite of models. While each of the codes share a common underlying core capability, they are focused on different applications and scales, and have their own strengths and weaknesses. This type of effort leads to improvement in all the codes, and improves the modeling community’s understanding of simulating integrated surface and groundwater systems hydrology.

Contacts
Ethan Coon
Oak Ridge National Laboratory
coonet@ornl.gov

Reed Maxwell
Colorado School of Mines
rmaxwell@mines.edu

Funding
Funding was provided by the DOE Office of Biological and Environmental Research, Subsurface Biogeochemistry Research (SBR) activity to the Interoperable Design for Extreme-scale Application Software (IDEAS) project.

Publications
S. Kollet, M. Sulis, R.M. Maxwell, C. Paniconi, M. Putti, G. Bertoldi, E.T. Coon, E. Cordano, S. Endrizzi, E. Kikinzon, E. Mouche, C. Mugler, Y.-J. Park, J.C. Refsgaard, S. Stisen, and E. Sudicky. “The integrated hydrologic model intercomparison project, IH-MIP2: A second set of benchmark results to diagnose integrated hydrology and feedbacks.” Water Resour. Res., 53, 867-890. (2017). [DOI: 10.1002/2016WR019191.] (Reference link)

Topic Areas:

Division: SC-23.1 Climate and Environmental Sciences Division, BER


January 25, 2017

Using Microbial Community Gene Expression to Highlight Key Biogeochemical Processes

A study of gene expression in an aquifer reveals unexpectedly diverse microbial metabolism in biogeochemical hot spots.

The Science
Researchers conducted a study of naturally reduced zones (NRZs)—biogeochemical hot spots—in the Rifle, Colo., aquifer, a legacy Department of Energy uranium mill site. They performed a state-of-the-art analysis of gene expression in the aquifer’s microbial communities, elucidating metabolic pathways and organisms underlying observed biogeochemical phases as well as revealing unexpected metabolic activities.

The Impact
NRZs, organic-rich deposits heterogeneously distributed in alluvial aquifers, modulate aquifer redox status and influence the speciation and mobility of metals. Overall, NRZs have an outsized effect on groundwater geochemistry. This study’s results highlight the complex nature of organic matter transformation in NRZs and the microbial metabolic pathways that interact to mediate redox status and elemental cycling.

Summary
Organic matter deposits in alluvial aquifers have been shown to result in the formation of NRZs, which can modulate aquifer redox status and influence the speciation and mobility of metals, significantly affecting groundwater geochemistry. In this study, researchers sought to better understand how natural organic matter fuels microbial communities within anoxic biogeochemical hot spots (or NRZs) in a shallow alluvial aquifer at the Rifle site. The researchers conducted an anaerobic microcosm experiment in which NRZ sediments served as the sole source of electron donors and microorganisms. Biogeochemical data indicated that native organic matter decomposition occurred in different phases, beginning with the mineralization of dissolved organic matter (DOM) to carbon dioxide (CO2) during the first week of incubation. This was followed by a pulse of acetogenesis that dominated carbon flux after two weeks. DOM depletion over time was strongly correlated with increases in the expression of many genes associated with heterotrophy (e.g., amino acid, fatty acid, and carbohydrate metabolism) belonging to a Hydrogenophaga strain that accounted for a relatively large percentage (roughly 8%) of the metatranscriptome. This Hydrogenophaga strain also expressed genes indicative of chemolithoautotrophy, including CO2 fixation, dihydrogen (H2) oxidation, sulfur compound oxidation, and denitrification. The acetogenesis pulse appeared to have been collectively catalyzed by a number of different organisms and metabolisms, most prominently pyruvate:ferredoxin oxidoreductase.  Unexpected genes were identified among the most highly expressed (more than 98th percentile) transcripts, including acetone carboxylase and cell-wall-associated hydrolases with unknown substrates.  Many of the most highly expressed hydrolases belonged to a Ca. Bathyarchaeota strain and may have been associated with recycling of bacterial biomass. Overall, these results highlight the complex nature of organic matter transformation in NRZs and the microbial metabolic pathways that interact to mediate redox status and elemental cycling.

Contacts (BER PM)
David Lesmes
SC-23
david.lesmes@science.doe.gov

(PI Contact)
Harry R. Beller
Senior Scientist, Lawrence Berkeley National Laboratory
HRBeller@lbl.gov

Funding
This work was supported as part of the Subsurface Biogeochemical Research Scientific Focus Area funded by the U.S. Department of Energy, Office of Science, Office of Biological and Environmental Research under award number DE-AC02-05CH11231. This work used the Vincent J. Coates Genomics Sequencing Laboratory at the University of California, Berkeley, supported by the National Institutes of Health S10 instrumentation grants S10RR029668 and S10RR027303.  

Publication
Jewell, T. N. M., U. Karaoz, M. Bill, R. Chakraborty, E. L. Brodie, K. H. Williams, and H. R. Beller. 2017. “Metatranscriptomic Analysis Reveals Unexpectedly Diverse Microbial Metabolism in a Biogeochemical Hot Spot in an Alluvial Aquifer,” Frontiers in Microbiology, DOI: 10.3389/fmicb.2017.00040. (Reference link)

Topic Areas:

Division: SC-23.1 Climate and Environmental Sciences Division, BER


January 24, 2017

Sorption to Organic Matter Controls Uranium Mobility

Organic matter controls uranium mobility.

The Science  
A new multi-technique study using X-ray absorption spectroscopy at the Stanford Synchrotron Radiation Laboratory (SSRL) and Nano-Secondary Ion Mass Spectroscopy (NanoSIMS) at the Environmental Molecular Science Laboratory (EMSL), an Office of Science User Facility, has revealed crisp new details about the mechanisms of uranium binding in sediments. Surfaces of natural organic matter bind uranium more strongly than minerals under field-relevant conditions.

The Impact
Uranium is less stable and more easily remobilized when bound to surfaces of organic matter and mineral as compared to being incorporated with mineral precipitates. This new finding implies that reduced uranium is much more reactive and able to participate in repeated biogeochemical cycling than previously thought to be the case.

Summary
Uranium is an important carbon-neutral energy source and major subsurface contaminant at DOE legacy sites. Anoxic sediments, which are common in alluvial aquifers, are important concentrators of uranium, where it accumulates in the tetravalent state, U(IV). Uranium-laden sediments pose risks as ‘secondary sources’ from which uranium can be re-released to aquifers, prolonging its impact on local water supplies. In spite of its importance, little is known about the speciation of U(IV) in these geochemical environments. Uranium analysis is challenged by its low concentrations and the tremendous chemical and physical complexity of natural sediments. U(IV) binds to both organic matter and minerals, which can be co-associated at the scale of 10s to 100s of nanometers. Because of the multiplicity and similarity of binding sites present in samples, “standby” analytical techniques such as X-ray absorption spectroscopy are challenged to distinguish the molecular structure of U(IV) in these natural sediments. The molecular nature of accumulated U(IV) is however a first-order question, as the susceptibility of uranium to oxidative mobilization is mediated by its structure.  

In an SSRL-based study, Bone et al (2017) overcame these challenges by combining X-ray absorption spectroscopy, NanoSIMS, and STXM measurements to characterize the local structure and nanoscale localization of uranium and the character of organic functional groups. This work showed that complexes of U(IV) adsorb on organic carbon and organic carbon-coated clays in an organic-rich natural substrate under field-relevant conditions. Furthermore, whereas previous research assumed that U(IV) speciation is dictated by the mode of reduction (i.e., whether reduction is mediated by microbes or by inorganic reductants), this work demonstrated that precipitation of U(IV) minerals, such as UO2, can be inhibited simply by decreasing the total concentration of U, while maintaining the same concentration of sorbent. This conclusion is significant because UO2 (uraninite) and other minerals are much more stable and more readily remobilized than surface-complexed forms of U(IV). Thus, the number and type of organic and mineral surface binding sites that are available have a profound influence on U(IV) behavior. Projections of U transport and bioavailability, and thus its threat to human and ecosystem health, must consider U(IV) adsorption to organic matter within the local sediment environment.

Contacts (BER PM)
Roland Hirsch
DOE Office of Biological and Environmental Research, Climate and Environmental Sciences Division
roland.hirsch@science.doe.gov

(PI Contact)
John Bargar
SLAC National Accelerator Laboratory, Stanford Synchrotron Radiation Laboratory
Bargar@slac.stanford.edu

Funding
Funding was provided by the DOE Office of Biological and Environmental Research, Subsurface Biogeochemistry Research (SBR) activity to the SLAC Science Focus Area under contract DE-AC02-76SF00515 to SLAC. Use of SSRL is supported by the U.S. DOE, Office of Basic Energy Sciences. A portion of the research was performed using EMSL, a DOE Office of Science User Facility sponsored by the Office of Biological and Environmental Research (located at PNNL). Research described in this paper was performed at beamline 10ID-1 the CLS, which is supported by NSERC, CIHR, NRC, WEDC, the University of Saskatchewan, and the Province of Saskatchewan. The authors thank Ann Marshall for assistance in collecting TEM images at the Stanford Nano Shared Facilities.

Publications
Bone SE, Dynes JJ, Cliff J, & Bargar JR “Uranium(IV) adsorption by natural organic matter in sediments.” Proceedings of the National Academy of Sciences of the United States of America 114(4), 711-716. [10.1073/pnas.1611918114] (Reference link)

Topic Areas:

Division: SC-23.1 Climate and Environmental Sciences Division, BER