Berkeley Lab

Susan Hubbard Honored by Alameda County Women’s Hall of Fame

Susan Hubbard, Associate Laboratory Director for the Earth and Environmental Sciences Area, will be inducted into the Alameda County Women’s Hall of Fame, at an annual awards ceremony on March 30. Hubbard is being honored for her scientific contributions to key environmental challenges of our time, including the use of geophysical methods to quantify how watersheds and ecosystems are responding to changing conditions, and implications for water and biogeochemical cycles.

Susan Hubbard joins 13 other local women who represent the region’s rich diversity and a remarkable range of achievements made working to address issues such as environmental sustainability; and racial, income, and healthcare inequality; and to strengthen access to arts education and athletics programs for girls and young women.

Replicating subsurface processes in the laboratory

2.0 m tall laboratory sediment column and example measurements. a. instrument distribution, b. column clad with heat exchangers, c. column with insulation sleeve, d. seasonal field temperature profiles replicated in column, e. seasonal CO2 profiles from laboratory column.

Fluid flows with temperatures that are not constant are known as non-isothermal. Although changing thermal and hydrological conditions control rates of sediment biogeochemical processes in the Earth’s subsurface, these conditions are difficult to simulate in the laboratory. In this study, a novel 2 m tall column system to control time- and depth-dependent temperature profiles and water saturation was developed, which is needed to more accurately reproduce subsurface processes in the laboratory.

Temperature and moisture profiles in sediments are highly variable, and control biogeochemical processes, yet have not previously been reproduced in the laboratory. This study established field temperature and moisture profiles in a laboratory column system, and showed the importance of microbial respiration below the plant root zone by measuring CO2 production within the sediment column.


Transport between the soil surface and groundwater is commonly mediated through deeper portions of variably saturated sediments and the capillary fringe, where variations in temperature and water saturation strongly influence biogeochemical processes. Temperature control is particularly important because room temperature is not representative of most soil and sediment environments. The authors described and tested a novel sediment column design that allows laboratory simulation of thermal and hydrologic conditions found in many field settings. The 2.0 m tall column was capable of replicating temperatures varying from 3 to 22 ˚C, encompassing the full range of seasonal temperature variation observed in the deep, variably saturated sediments and capillary fringe of a semi-arid floodplain in western Colorado, United States. The water table was varied within the lower 0.8 m section of the column, while profiles of water content and matric (capillary) pressure were measured. CO2 collected from depth-distributed gas samplers under representative seasonal conditions reflected the influences of temperature and water-table depth on microbial respiration. Thus, realistic subsurface biogeochemical dynamics can be simulated in the laboratory through establishing column profiles that more accurately represent seasonal thermal and hydrologic conditions.


Tokunaga, T.K., Y. Kim, J. Wan, M. Bill, M. Conrad, and W. Dong, “Method for Controlling Temperature Profiles and Water Table Depths in Laboratory Sediment Columns. Vadose Zone Journal 17,180085 (2018). [DOI: 10.2136/vzj2018.04.0085]

October 2018 – Quick update and hunting season reminder

I wanted to send along a short “virtual site visit” presenting the recent (and ongoing) shale drilling activity at East River. This visit will find you on the Pumphouse lower montane hillslope as we core a 70m deep borehole designed to capture hydrogeochemical processes much deeper than we’ve done so to date.

In general the coring has gone well, however, the weather gods have not been cooperative, as conditions along the steep access road have been challenging. We paused drilling for safety reasons tied to the recent ~30cm of snowfall, and we will be resuming coring at two locations close to Gothic designed to collect samples from regions of the Mancos shale more heavily altered by igneous intrusives. A final update will follow once we finish up that work toward the end of this coming week.

During the drilling activity, we’ve had the pleasure of welcoming Lee Liberty of Boise State University to the watershed. Lee is a newly funded DOE University PI, and he and his team are collecting seismic reflection data along many of the roads within our study area using a novel tow-along seismic streamer. We look forward to having Lee update us on his project and findings during a future Watershed Science Community call.

Important Health and Safety Reminders

The first rifle hunting season starts today Saturday Oct. 13 and runs through Oct. 17th; the second rifle season is Oct. 20-28. Please wear an orange vest, hat or jacket for visibility and safety. Like other personal protective equipment, the costs of these vests, hats, etc. are reimbursable. Please stop by the local hardware store, Walmart, or sporting goods store to purchase these supplies if you will be in the field during hunting season.

Related to this, I wanted to emphasize the importance of suitable field gear. We recently had an incident where one of our employees fell while trying to cross the East River near the Rustlers Gulch access point. As many know, this crossing has become challenging over the past year due to a large beaver dam immediately downstream of the crossing. Multiple cars have flooded their engines trying to cross earlier in the year, as the water line was above the engine air intake. As a result, many folks are crossing the river by foot upstream using logs and rocks to avoid getting their feet a bit wet. Such crossings can be challenging — the proverbial falling off a log. For safety reasons, such crossings should be made using appropriate footwear, such as hip boots, waders or water shoes, in order to minimize risk associated with walking the tightrope so to speak. Please don’t risk an injury just trying to keep your toes dry. As with the orange vests and hats, the costs for proper field footwear are reimbursable expenses.

Sustainable Remediation of Complex Environmental Systems: Key Recent Technical Advances

Simulated uranium plume (concentration>1×10-6mol/L) in 3D at the Savannah River Site F-Area in 2050. The sky-blue region is the low permeable Tan Clay Zone, which separates the upper and lower aquifers.

This book chapter provides an overview of the key recent scientific advances to support sustainable remediation in complex geological systems demonstrated at the Savannah River Site F-Area, including site characterization techniques, hydrological and geochemical model developments and numerical simulations.

We have developed various subsurface characterization and modeling technologies to improve the predictive understanding of the groundwater contaminant plumes in complex geological systems. The technologies have been demonstrated at the Department of Energy’s Savannah River Site.


Groundwater remediation has been evolved recently with increased focus on sustainable approaches such as in situ treatments and natural attenuation. However, leaving contaminants in subsurface requires the increased burden of proof to show that plumes are stable and residual contaminants do not pose a significant health risk. At the Department of Energy’s Savannah River Site, we have developed and demonstrated various characterization and modeling technologies to provide the predictive understanding of the contaminant plume migration, including (1) a multiscale data integration method to integrate surface seismic and borehole datasets that have different resolution and spatial coverage, (2) a novel surface complexation model to describe pH-dependent uranium sorption behavior based on readily available datasets, and (3) a reactive transport modeling and uncertainty quantification framework to predict the future uranium plume behavior and to identify key parameters on the future uranium concentration. These technologies are expected to transform groundwater remediation at many other sites.


Wainwright, H. M.; Arora, B.; Faybishenko, B.; Molins, S.; Hubbard, S. S.; Lipnikov, K.; Moulton, D.; Flach, G.; Eddy-Dilek, C.; Denham, M. (2018), Sustainable Remediation in Complex Geologic Systems, The heaviest metals: Science and technology in Actinides and beyond.

Bhavna Arora speaks with News Deeply about the consequences of drought on Colorado

Bhavna Arora (right) and former intern Madison Burrus discuss the computer simulations they are creating using data about river discharge, precipitation, and snowpack collected from the East River catchment site near Crested Butte, CO. (Credit: Marilyn Chung/Berkeley Lab)

SFA researcher Bhavna Arora was interviewed on Water Deeply regarding how declining snowpack is altering water quality in the Colorado River.

A more comprehensive interview and story were conducted by the Berkley Lab News Center, where Bhavna explains how drought and other extremes impact water pollution. Read more »

Vadose Zone Journal Special Issue features Watershed Function SFA Overview

An overview of the Watershed function SFA and the associated East River Watershed was published in in the Vadose Zone Journal “Special Section: Hydrological Observatories”. The paper describes several recently developed approaches to interrogate, monitor and simulate transient watershed partitioning and biogeochemical responses – from genome to watershed spatial scales and from episodic to decadal timescales.

View the full paper (open access) here.

Geochemical Exports to River from the Intra-Meander Hyporheic Zone under Transient Hydrologic Conditions at East River

Figure 1: Spatial distributions of dissolved geochemical species in groundwater in the meander C.

Hyporheic exchange within the intra-meander region results in the interaction of nutrient-rich groundwater and oxygen-rich river water, which leads to the formation of distinct redox gradients. These redox gradients can significantly impact the export of metals and nutrients at the local, reach, and watershed scales. Further, transient hydrologic conditions, such as groundwater flow dynamics, river-stage fluctuations, and rainfall/snowmelt events, can impact redox processes in the hyporheic zone and ultimately the geochemical exports to the river thereby affecting river water quality. Here we have used high-resolution hydrodynamic assessments of the hyporheic zone combined with detailed pore-water sampling to focus on the hyporheic exchange at the meander scale for the purpose of quantifying the subsurface exports from a single meander to the river under transient hydrological conditions.

This study is a first of its kind that examines the influence of transient hydrological conditions on the hyporheic biogeochemistry using field observations. Simulation results demonstrated that intra-meander hyporheic zones display distinct anoxic and suboxic regions, suboxic regions being localized along sides of the meander bend. Permeability within the meander has a more significant impact on biogeochemical zonation compared to the reaction pathways for transient hydrologic conditions. Here we have also demonstrated the outsized implications of micro-topographic features such as gullies on redox processes using the high-resolution LiDar data.

Figure 2. Net cumulative geochemical export of TIC, DOC, and iron(II) from a single meander. River-stage is shown in green on the right y-axis, whereas the net export is shown in golden color on the left y-axis.


Hyporheic zones perform important ecological functions by linking terrestrial and aquatic systems within watersheds. Hyporheic zones can act as a source or sink for various metals and nutrients. Transient hydrologic conditions alter redox conditions within an intra-meander hyporheic zone thus affecting the behavior of redox-sensitive species. Here we investigated how transient hydrological conditions control the lateral redox zonation within an intra-meander region of the East River and examined the contribution of a single meander on subsurface exports of carbon, iron, and other geochemical species to the river. The simulation results demonstrated that the reductive potential of the lateral redox zonation was controlled by groundwater velocities resulting from river-stage fluctuations, with low-water conditions promoting reducing conditions. The sensitivity analysis results showed that permeability had a more significant impact on biogeochemical zonation compared to the reaction pathways under transient hydrologic conditions. The simulation results further indicated that the meander acted as a sink for organic and inorganic carbon as well as iron during the extended baseflow and high-water conditions; however, these geochemical species were released into the river during the falling limb of the hydrograph. This study demonstrates the importance of including hydrologic transients, using a modern reactive transport approach, to quantify exports within the intra-meander hyporheic zone at the riverine scale.


Dwivedi, D., C.I. Steefel, B. Arora, M. Newcomer, J.D. Moulton, B. Dafflon, B. Faybishenko, P. Fox, P. Nico, N. Spycher, R. Carroll, and K.H. Williams (2018), Geochemical Exports to River from the Intra-Meander Hyporheic Zone under Transient Hydrologic Conditions: East River Mountainous Watershed, Colorado, Water Resources Research, 10.1029/2018WR023377.

First Watershed Science Collaboration Workshop takes place Sep 23-25, 2018 in Crested Butte, CO

The workshop began with a guided tour of the East River watershed.

Attendees pose briefly for a group photo.

Attendees included microbial and plant ecologists, hydrologists, geochemists, geologists, geophysicists, remote and snow sensing experts, data and computational scientists and resource managers. Read more »

Using strontium isotopes to evaluate how local topography affects groundwater recharge

Figure 1. 87Sr/86Sr vs 1/[Sr] showing the mixing relationships between vadose zone porewater and groundwater. Blue line shows the mixing model of vadose zone water with upgradient groundwater with bold numbers representing the percentage of vadose zone water in the local aquifer.

A key component of understanding the connection between groundwater quality and the vadose zone (the water unsaturated region above the water table) is the movement of water from the surface to the aquifer (recharge). Measurements of the natural isotopic composition of Sr were used to assess the effect of local topography on groundwater recharge across a semi-dry riparian floodplain in the Upper Colorado River Basin.

This work demonstrates the use of 87Sr/86Sr (Sr isotopes) to measure groundwater recharge through analysis of porewater and groundwater samples from the vadose zone. The study resulted in an understanding how the microtopography of the Rifle Site affects the hyper-local variation in the downward movement of vadose-zone porewater that may carry nutrients and contaminants to groundwater.

Figure 2. “Heat” map of the percentage contribution of vadose water to the Rifle floodplain aquifer based on the Sr isotopic mixing model.


Over time, loose sand, clay, silt, gravel or similar unconsolidated, or “alluvial” material is deposited by water into alluvial aquifers. Recharge of alluvial aquifers is a key component in understanding the interaction between floodplain vadose zone biogeochemistry and groundwater quality. The Rifle Site (a former U-mill tailings site) adjacent to the Colorado River is a well-established field laboratory that has been used for over a decade for the study of biogeochemical processes in the vadose zone and aquifer. This site is exemplary of both a riparian floodplain in a semiarid region and a post-remediation U-tailings site. The authors use Sr isotopic data for groundwater and vadose zone porewater samples to build a mixing model for the fractional contribution of vadose zone porewater (i.e. recharge) to the aquifer and to assess its distribution across the site. The vadose zone porewater contribution to the aquifer ranged systematically from 0% to 38% and appears to be controlled largely by the microtopography of the site. The area-weighted average contribution across the site was 8%, corresponding to a net recharge of 7.5 cm. Given a groundwater transport time across the site of ~1.5 to 3 years, this translates to a recharge rate between 5 and 2.5 cm/yr, and with the average precipitation to the site, implies a loss from the vadose zone due to evapotranspiration of 83% to 92%.


Christensen, J. N., et al. (2018), Using strontium isotopes to evaluate the spatial variation of groundwater recharge, Sci Total Environ, 637-638, 672-685, DOI: 10.1016/j.scitotenv.2018.05.019.

September 2018 updates

We have several upcoming items that are worthy of special mention, as they’re broadly relevant to our group and the larger community of RMBL researchers and our growing community of interagency (DOE, USGS, NSF, USFS, NOAA, NASA, etc.) partners. Details and points of contact below.

NASA JPL Airborne Snow Observatory (ASO):

The NASA JPL ASO team conducted their snow-free survey of the Upper Gunnison domain last week, including essentially all of the terrain above the Ohio Creek/Gunnison River confluence. These data will enable retrospective snow depth and SWE mapping from the April 1 and May 24, 2018 flights this past spring, and set the stage for near-real time snow mapping in winter and spring 2019. This is a huge deal and incredibly important as we engage our collaborators with NCAR and NOAA on further developing a snow-focused computational testbed in the upper Gunnison.

Recall that this activity has been made possible through the vigorous engagement of the Upper Gunnison Water Conservancy District (thank you Frank and John) and with funding from the State of Colorado and champions at the Colorado Water Conservation Board (thank you Joe).

Also a reminder that this work is critically important to two of the three newly funded DOE SBR University snow science proposals at East River: Jeff Deems (CU) and McKenzie Skiles (Univ. Utah). So great news that this snow free-baseline dataset is now in hand.

NASA SnowEx:

I am excited to announce that the NASA SnowEx campaign will be active in the broader East River / Watershed Function SFA domain this winter and spring (2018/19). NASA SnowEx is coupled multi-year remote sensing and field experiment to develop and refine techniques for mapping terrestrial snow cover around the globe to address important water resources, water cycle, and climate feedback challenges. In 2017, SnowEx conducted intensive, month-long campaigns on Grand Mesa and in Senator Beck Basin in western Colorado. In 2019, SnowEx will leverage ongoing and planned observation activities around the western US to collect time series data of snowpack evolution throughout the accumulation and melt seasons in a diversity of snow climates at sites in CA, ID, UT, CO, and NM.

In the East River domain specifically, the SnowEx campaign will build on planned ASO flights (funded by the Colorado Water Conservation Board) and the aforementioned recently-funded DOE snow observation and modeling projects (see above; Deems, Skiles, Alejandro Flores [Boise State] PIs) and NSF (Raleigh [CU]), with the broader Watershed SFA activities adding valuable synergies. Additional ASO winter flights are being planned, as well as twice-monthly UAVSAR (L-band interferometer) overflights. These airborne acquisitions will be supported by regular ground observations and periodic extensive field campaigns to sample gradients in snow properties and processes.

At the risk of underselling this — this is a huge deal. Please contact Jeff Deems ( with any questions!

Upcoming drilling activities:

Building upon our very successful drilling projects with USGS in Redwell Basin, we are planning to drill a collection of deep shale wells starting in early October to provide ground-truthing for both surface and airborne geophysical data collection. Drilling of four monitoring boreholes (40-70m deep) will occur to (a) recover shale bedrock for geochemical analysis and (b) provide long term sampling ports for evaluating seasonal changes in groundwater elevation and chemistry.

Equally as important to geological constraints, we’re pursuing a drilling campaign that folds in other extant RMBL researchers from the perspective of biogeochemistry.

As an NC State postdoc, Amanda DelVecchia ( — in order to study geologic methane contributions to contemporary food webs — will be installing five 2″ diameter, 2 mm slotted PVC wells to bedrock on the lower East River (our “Pumphouse” location) using a Geoprobe this October. As part of this work, Amanda will be collecting methane samples from these wells and others for submission to collaborator Dr. Daniel Stolper (UC Berkeley) for analysis of clumped isotopologues.

So we have a busy October in front of us insofar as drilling is concerned!

Lastly — and this is purely for the geology and geocentric folks on this list — I wanted to provide a link to a remarkable document. It fleshes out Ferdinand Hayden’s original geologic surveys for the state of Colorado including the East River watershed from the late 1800’s.

Building upon the shoulders of giants is what we do — and with Hayden laying the geologic framework for Yellowstone, I’d say he qualifies — I’m including the link below.

This is so well done and with a focus on the East River and its environs from the late 1800’s, it’s hard to overvalue it.