Berkeley Lab

April 2018 – Spring Update

JPL/NASA Airborne Snow Observatory (ASO)

With generous financial support from the State of Colorado Water Conservation Board (CWCB), as well as critical guidance and input from Frank Kugel and John McClow of the Upper Gunnison River Water Conservancy District, the first of two “snow-on” ASO overflights of the East River, Taylor River, and Ohio Creek watersheds has been completed.  The first flight was designed to coincide with so-called “peak snow water equivalent (SWE)” and took place over the last 2 days of March and first of April.  Concomitant with this overflight, 18 snow pits were dug in order to have direct confirmation of snow depth and SWE at locations throughout the area of investigation.  Both the flight lines (red, white, pink paths) and snow pits (bullseye circles) are included in the attached / embedded figure.

Special thanks to the team of snow samplers who worked to both coordinate and execute the sampling: Rosemary Carroll, Wendy Brown, Tony Brown, Jeff Deems, Anna Ryken, and Mike Morse. Without their help, it would have been impossible to have collected the 18(!!) pits covering an area of many hundreds of square kilometers over an elevation range from ca. 8,700-ft to 12,000-ft.

In particular, Dr. Jeff Deems (CU-Boulder) — a key member of the JPL/NASA ASO team and an incredible scientific resource for our extended Watershed SFA Team — was instrumental in coordinating and scheduling the ASO overflight, ensuring the best quality data that weather conditions would allow, as well as personally assisting with digging snow pits, which as many know is something of a “Deems speciality”.  Again, without Jeff’s help in executing this work, we’d have struggled to be as productive as we were as regards ASO at East River both on this flight and those in the future.

Additionally, Jeff has provided some preliminary images of snow depths associated with the boundaries of the 2016 ASO overflight.  As a reminder, snow depths are calculated via difference in LiDAR derived surface elevations measured between “snow on” and “snow free” overflights.  The Watershed SFA had already collected high-resolution “snow free” LiDAR data over a limited area, which allowed for a single “snow on” ASO flight in 2016 to determine snow depths within the East River main stem and WA Gulch drainages.  In contrast, we do not yet have high-resolution LiDAR data collected over the much larger area of investigation associated with the East River-Taylor River-Ohio Creek system.  This data — again through generous support from the state of Colorado — will be collected in September 2018, so we will have to wait until then for the larger spatial scale maps of snow depth and SWE once that “snow free” dataset is collected.

In the interim, Jeff has produced a map of the 2018 snow depths measured two weeks ago within the East River main stem and WA Gulch drainages along with the companion map for 2016.  Those images are below.  Toggling between the two shows quite clearly the differences between snow conditions in 2016 (average year) and 2018 (low snowpack year).  The open circle symbols on the 2018 map correspond to the snow pits that were dug in association with the overflight.

A second “snow on” ASO flight is planned for mid-May of this year to assess late season snow retention as a function of both elevation and landscape position.  The ability to have two time points that track the falling limb of SWE is especially exciting as it should really assist with coupling this year’s datasets to improved runoff forecast modeling approaches — although we’ll have to rely on backcast modeling this year due to the need to collect the requisite “snow free” datum in September once runoff is already completed.

Early snowmelt manipulation experiments

As most are aware, this year was our first season of experimentally manipulating snow pack along an elevation gradient to induce early snowmelt relative to adjoining control plots.  The video below provides a better visual depiction of what the manipulation experiments look like at our Pumphouse hillslope intensive study site (lower montane); similar manipulations are occurring at our upper montane, lower subalpine, and upper subalpine sites.  A suite of ground-based measurements are currently underway to examine the consequences of early melt on flows of water and nutrients within the plots, as well as the consequences for subsurface microbial activity and plant phenological behavior.  Airborne characterization approaches are also planned, with the first round of UAV-based measurements over the manipulated and control plots planned for next week.

Pat Sorenson (LBNL) has been providing daily reports of the snow melt progression, as he’s been actively sampling for the past week-plus and will continue to do so over the next week. Pat will have an opportunity to brief this group once the dust has settled — or rather once the snow has melted — next month during our next Science Community Call.  Briefly, Pat has been noting that although the snow pack continues to consolidate, settle and melt, the soils have remained quite dry and largely frozen except for the shallowest depths.  He notes that the soils are very dry to a depth of ca. 30-cm, with the persistent frozen soil layers likely inhibiting infiltration.  These frozen layers were likely more extensive this season due to the late arrival of snow and its insulating effect.  So we’re actually getting something of a two-for-one this year, given (a) low seasonal snowpack and (b) late arriving snow, which has led to a deeper frozen soil profile than typical.  Combined with the early snowmelt manipulations along the elevation gradient, the project will soon have an incredibly rich experimental dataset to examine for the next year until we do it all again.  Very exciting and again more updates to follow.

NEON Airborne Observation Platform (AOP) planning

As everyone on this list has been briefed on plans for the NEON AOP overflights and been solicited for their interest and involvement, I won’t belabor this update,  Rather, I just want to note the hard work of Dana Chadwick, Nicola Falco and Haruko Wainwright in pushing forward with all the details regarding the sampling plan and coordinating with NEON on all of the flight details.  Due to aircraft availability issues on NEON’s end, we’re now locked into the last two weeks of June, with a focus on the last week for performing the overflights.  We’d originally hoped to have the first week of July available, but as noted, the aircraft simply isn’t available.  Given the low snowpack and presumed early natural melt, we feel that for the lower elevations (lower and upper montane) the last week of June should work well insofar as meadow peak or near peak greenness is concerned.  Of course, we’re dealing with a natural system here — heavy, high elevation snow warnings are again in effect for tonight and tomorrow — so we’ll just need to wait and see what June brings us in terms of a slightly advanced growing season and its ability to coincide with NEON’s timetable.

Three Collaborative Watershed Seed Projects Funded

To catalyze engagement of new investigators and collaborative projects/initiatives, the Watershed Function SFA has selected three 1-year, collaborative mini-projects for funding. The applicants were selected for award from a large number of excellent and highly competitive proposals. The selected awards include:

“Developing capabilities for integration of microbiological and geochemical data processing” (Romy Chakraborty). This mini-project aims to demonstrate the value of connecting data infrastructures of Watershed SFA, ESS DIVE, and KBase for developing a breakthrough new capability to easily process and enable visualization of environmental microbiome data in the context of macro scale environmental dynamics.

“Establishing a new modeling capability for the East River watershed to study forest responses to perturbations” (Lara Kueppers). The objective of this mini-project is to develop a process-based forest ecosystem model that contributes to robust predictions of Rocky Mountain watershed responses to perturbations.

“Integrated Ecosystem Sensing for Tracking the Hydrodynamics of the Soil-Plant-Atmosphere Continuum and Impacts on Soil Respiration and Plant Growth” (Yuxin Wu). This project will utilize the unique capability built into the EcoSENSE SMART soils testbed for quantitative tracking of the moisture dynamics in a simulated hillslope system driven by both hydrological perturbations and plant/soil interactions, and the subsequent effects on ET and soil/plant respiration. Using a suite of sensors in a soil testbed, combined with direct sampling and characterization methods, the mini-project is expected to deliver comprehensive, dense and spatiotemporally correlated data sets to track system dynamics.

Spring Snowmelt Drives Transport and Degradation of Dissolved Organic Matter in a Semi-Arid Floodplain

Berkeley Lab geochemists and hydrologists who study a mountainous watershed near Rifle, CO, discovered that spring snowmelt is essential to the transport of freshly dissolved organic matter (DOM) from the top soil to the part of the Earth’s subsurface that lies above the groundwater table. Because dissolved organic matter undergoes biological humification over the year, these processes involving this deep vadose zone suggest an annual cycle of DOM degradation and transport at this semi-arid floodplain site.

Spring snowmelt transports fresh DOM from top soil into the deeper vadose zone, and then undergoes microbial humification process over the year (see depth and seasonal EEM spectra)

Characterizing the dynamics of dissolved organic matter in semi-arid regions of Earth’s subsurface is challenging. The authors obtained insights into transport and humification processes of DOM using several spectroscopic techniques on depth- and temporally-distributed pore-waters. This methodology can be applied to other subsurface environments for understanding DOM responses and feedbacks to earth system processes.


Scientists studying DOM in surface waters considered it to be the mobile fraction of natural organic matter that falls into or is washed into water bodies. Although it has been extensively studied over many decades, relatively little is known about the dynamics of DOM in the subsurface of semi-arid environments. In order to understand transport and humification processes of DOM within a semi-arid floodplain at Rifle, Colorado, the authors applied fluorescence excitation-emission matrix (EEM) spectroscopy, humification index (HIX) and specific UV absorbance (SUVA) for characterizing depth and seasonal variations of DOM composition. They found that late spring snowmelt leached relatively fresh DOM from plant residue and soil organic matter down into the deeper vadose zone (VZ). More humified DOM is preferentially adsorbed by upper VZ sediments, while non- or less-humified DOM was transported into the deeper VZ. Interestingly, DOM at all depths undergoes rapid biological humification processes as evidenced by the products of microbial by-product-like matter in late spring and early summer, particularly in the deeper VZ, resulting in more humified DOM at the end of year. The finding indicates that DOM transport is dominated by spring snowmelt, and DOM humification is controlled by microbial degradation. It is expected that these relatively simple spectroscopic measurements (e.g., EEM spectroscopy, HIX and SUVA) applied to depth- and temporally-distributed pore-water samples can provide useful insights into transport and humification of DOM in other subsurface environments as well.


Dong, W., J. Wan, T. K. Tokunaga, B. Gilbert, and K. H. Williams (2017). Transport and Humification of Dissolved Organic Matter within a Semi-Arid Floodplain. Journal of Environmental Sciences 57, 24-32, DOI: 10.1016/j.jes.2016.12.011

SFA Research Identifies New Microbial Players in the Global Sulfur Cycle

Sulfate is ubiquitous in the environment, and sulfate reduction – a key control on anaerobic carbon turnover – impacts a number of other processes such as carbon oxidation and sulfide production. Until now, sulfate reduction was believed to be restricted to organisms from select bacterial and archael phyla. But scientists at UC Berkeley have now found this ability to be more widespread. They used genome-resolved metagenomics to discover roles in sulfur cycling for organisms from 16 microbial phyla not previously associated with this process.

DsrAB protein tree showing the diversity of organisms involved in dissimilatory sulfur cycling using the dsr system.
Lineages in blue contain genomes reported in this study. Phylum-level lineages with first report of evidence for sulfur cycling are indicated by blue letters.

Sulfate-reducing bacteria are anaerobic microorganisms essential to sulfur and carbon cycling. Sulfate reduction drives other key processes and produces hydrogen sulfide, an important but potentially toxic gas present in sediments, wetlands, aquifers, the human gut, and the deep-sea. The discovery of novel microbes connected to sulfur cycling is relevant in biogeochemistry, ecosystem science and engineering, and fundamentally reshape our understanding of microbial function and capabilities associated with phylogenetic information.


Phylogenetic information shapes our expectations regarding microbial capabilities. In fact, this is the basis of currently used methods that link gene surveys to metabolic predictions of community function. Sulfate Reduction, an important anaerobic metabolism, impacts carbon, nitrogen, and hydrogen transformations in numerous environments across our planet and is known to be restricted to organisms from selected bacterial and archaeal phyla. The authors used genome-resolved metagenomic analyses to determine the metabolic potential of microorganisms from six complex marine and terrestrial environments. By analyzing >4000 genomes, they identified 123 near-complete genomes that encode dissimilatory sulfite reductases involved in sulfate reduction. They discovered roles in sulfur cycling for organisms from 16 microbial phyla not previously known to be associated with this process. Additional findings include some of the earliest-evolved sulfite reductases in bacteria, identification of a novel protein unique to sulfate reducing bacteria, and a key sulfite reductase gene in putatively symbiotic Candidate Phyla Radiation (CPR) bacteria. This study fundamentally reshapes expectations regarding the roles of a remarkable diversity of organisms in the biogeochemical cycle of sulfur.


Anantharaman, K., B. Hausmann, S.P. Jungbluth, R.S. Kantor, A. Lavy, L.A. Warren, M.S. Rappé, M. Pester, A. Loy, B.C. Thomas, and J.F. Banfield (2017). Expanded diversity of microbial groups that shape the dissimilatory sulfur cycle. The ISME journal 12, 1715–1728, DOI: 10.1038/s41396-018-0078-0

Steltzer Selected for AGU Science Advocacy Program

Heidi Steltzer of Fort Lewis College was selected to be among the first thirty advocates to serve in AGU’s Voices for Science Program.

“I applied and am grateful to have the opportunity to be part of this program,” says Steltzer. “The network creates the opportunity to share more about SFA program within AGU and hoping to explore more ways to share what we do in Colorado and beyond.”

Read the full story here.

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

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 Lab 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.

Evaluation of diagnostic parameters of deterministic chaos and 3-D strange attractor (bottom right) indicating that the system would behave within the boundaries of the attractor.

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.


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 (Figure A) along with the multivariate Granger Causality (G-causality) time series test. Based on the G-causality test, the author infers that his hypothesis is correct, and presents a causation loop diagram (Figure B) 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.


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

Microbial “hotspots” and organic rich sediments are key determinants of nitrogen cycling in a floodplain

Figure 1. Simulated and observed nitrate concentrations at different depths in TT wells. Nitrification contributes up to 35% (TT-01), 67% (TT-02), and 48% (TT-03) of nitrate levels in groundwater.

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.

Figure 2. Sensitivity of nitrogen to flow reversal and microbial pathways in NRZ and non-NRZ. NRZs produce more nitrogen (approximately 70%) than non-NRZs.

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 nonreduced zones.


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.


Dwivedi, D., Arora, B., Steefel, C. I., Dafflon, B., & Versteeg, R. (2018). Hot spots and hot moments of nitrogen in a riparian corridor. Water Resources Research, 53. DOI: 10.1002/2017WR022346.

SFA Research as cover story in The Durango Herald

Fort Lewis College alumni Chelsea Wilmer and Shea Wales carrying gear to a study site in the Elk Mountains near Crested Butte, joined by Elizabeth Ballor, a summer independent research student at the Rocky Mountain Biological Laboratory, and Patrick Sorenson, a Berkeley Lab postdoctoral researcher.

An article about Watershed Function SFA research was featured as the cover story of the weekend edition of The Durango Herald. The article features photos of students from Fort Lewis College working on the project and quotes from interviews with Ken Williams and Heidi Steltzer, including the value of the research to other watersheds such as the Animas watershed. Read the full story here.

December 2017 – Pumphouse conditions and “Meet the scientist”: John Bargar (SLAC)

It’s been an interesting start to the snow season, with several large, early season storms that brought worry and challenge to our drilling operations at 11,500-ft in the Redwell Basin and the airborne geophysical surveys whetting our appetites for a white November. Since that time, however, we’ve had little in the way of significant snow accumulation at East River, and while it’s generally been warm in November and early December, we’ve recently experienced a very chilly albeit sunny cold snap. I suspect the frozen soil layer is thickening this year, and it will be very interesting to compare this year with last given the general absence of an insulating snow blanket.

Along these lines, I wanted to provide a virtual site visit of our Pumphouse hillslope location so folks can get a general feel of conditions there this past weekend. A new team member also makes his first appearance so there’s perhaps some motivation to hang in there while watching the video.

Also, I wanted to add our next installment of the “Meet the Scientist” series. With Dr. John Bargar, the lead PI of the SLAC SFA program, having presented a nice update of his team’s activities at East River during our last Science Community call, I thought it worthwhile to include a more “personal” presentation straight from John himself and to provide those who couldn’t join the call with a better understanding of the activities of our ”sister” National Lab SFA within the watershed.

Steefel et al. Receive R&D 100 Award for CrunchFlow

SFA researcher Carl Steefel was recognized with an R&D 100 Award for the development of CrunchFlow, a powerful software package that simulates how chemical reactions occur and change as fluids travel underground. Steefel received the award at a Nov. 17 event in Washington, D.C. along with co-developers Sergi Molins (LBL, SFA team member) and Jennifer Druhan (U. Illinois Urbana-Champaign, SFA collaborator). Read more »