Berkeley Lab

Susan Hubbard Named 2017 American Geophysical Union Fellow

The American Geophysical Union (AGU) has named Susan Hubbard, Watershed Function SFA Director, as a 2017 AGU Fellow.

Every year, the AGU Fellow program recognizes members who have made exceptional contributions to the Earth and space sciences. Vetted by a committee of AGU Fellows, honorees represent no more than 0.1 percent of AGU’s 60,000 members. Read more »

New Data Archive Aims to Amplify Impact of Ecosystem Research

Data collection in Rifle, CO, the former SFA study site (Photo credit: Berkeley Lab)

A new DOE project led by Deb Agarwal (lead of Watershed Function SFA Data Management and Assimilation) will develop an archive that will serve as a repository for hundreds of DOE-funded research projects under the agency’s Environmental System Science (ESS) umbrella.

The project is a $3.6 million investment by the U.S. Department of Energy (DOE)’s Office of Science that will enable researchers, environmental and agricultural stakeholders, as well as members of the public to access the data.

Read the full story here »

Flux Tower Deployment and Peak SWE Snow Sampling

Flux tower installation at Pumphouse floodplain site

Flux tower being installed at the Pumphouse floodplain site.

Tied to the DOE-funded project led by Drs. Reed Maxwell and Dave Gochis (“Diagnosing dominant controls on carbon exchanges in high altitude, western U.S. headwaters”), the long-awaited flux tower was installed at the Pumphouse floodplain intensive study site on April 13, 2017.

Flux tower installation:

Synoptic view of installation and site conditions and infrastructure:–QWs

Tony Brown (~6ft tall) standing in the 3-meter snow pit at the Upper Subalpine site.

Sampling during peak SWE (Snow Water Equivalent) conditions

On April 2-3, 2017, SFA team members dug snow pits to collect vertically-resolved measurements of snow density and samples for geochemical analysis.  Snow depths were ~50% greater than in 2016 at the same time of year.
A video highlighting conditions at the Upper Subalpine site and the headwaters of Rock Creek at the time of sampling can be found here:

Other site updates

For those who have followed the time-lapse evolution of conditions on Meander A, a video presenting conditions and infrastructure tied to the DOE-funded work of Mike Wilkins (Ohio State) investigating stream bed hyporheic exchange can be found here:

Anoxia stimulates microbially catalyzed metal release from Animas River sediments

Terrain/Satellite view of the study site. Stars indicate sampling locations and the red circle indicates the location of the Gold King Mine.

Published in Environmental Science: Processes & Impacts, this study investigated the fate of heavy metals adsorbed onto riverbed sediments following the August 2015 Gold King Mine Spill in Colorado’s San Juan Mountains. It represents the first biogeochemical study of spill-impacted sediments from the Animas River and revealed mobilization of zinc, arsenic, and molybdenum species accompanying microbe-catalyzed dissolution of metal oxide sorbents.

Concentration changes in aqueous metal cations and anions from the three sediment types across 28-day microcosm incubations. The dashed line in the SO42- panel indicates the time point where exogenous SO42- was added to microcosms to stimulate additional SO42- reduction.


Following the Gold King Mine waste spill, metal contaminants adsorbed onto riverbed sediments along the spill flow path. Differences in sediment mineralogy and adsorbed metals were strongly linked to sampling locations and proximity to the mine. Results suggest that anaerobic microbial metabolisms, stimulated by natural organic carbon pools, will play a significant role in mobilizing adsorbed metal pools following the onset of anoxia in buried riverbed sediments. The site-specific nature of metal release may be linked to different reductive metabolisms, with microbial iron reduction driving dissolution of grain coatings, and alkalinity increases during sulfate reduction offering another mechanism for metal desorption from fluvial sediments. Given the iron and sulfur-rich nature of the Colorado Basin, these complex processes represent a challenge for the tracking of mining-impacted biogeochemistry and associated water quality issues, and emphasize the need for monitoring efforts that account for the dynamic nature of fluvial systems, and their ability to moderate strong spatial and temporal gradients in redox status.

This study provides valuable insight into metal mobility, particularly in mining-impacted watersheds. These results highlight the importance of long-term river water quality monitoring as river sediments undergo sedimentation and burial processes, driving the onset of anoxic conditions which favor metal (re)mobilization.


Saup, C.M., K.H. Williams, L. Rodriguez-Freire, J. Manuel Cerrato, M.D. Johnston, M.J. Wilkins (2017). Anoxia stimulates microbially catalyzed metal release from Animas River sediments. Environmental Science: Processes & Impacts. doi:10.1039/C7EM00036G

Improved modeling of floodplain nutrient and metal cycling using new multi-omics and isotope fractionation information

Water table peaking event mixes oxygen and nitrate into the anoxic Rifle floodplain aquifer. Naturally reduced zones containing sediments higher in organic matter, iron sulfides, and U(IV) rapidly consume DO and nitrate to maintain anoxic conditions, yielding Fe(II) from FeS oxidation, nitrite from denitrification, and U(VI) from nitrite-promoted U(IV) oxidation. Redox cycling is facilitated by coupled geochemistry, heterotrophy, and chemolithoautotrophy.

The study, published in Environmental Science & Technology, is one of the most comprehensive syntheses of processes and datatypes published to date and links BER’s investments in advanced multi-omics techniques and high-performance computing, representing the first critical stage in building a predictive understanding of natural hydrobiogeochemical processes at floodplain and larger scales.


Three-dimensional variably saturated flow and multicomponent biogeochemical reactive transport modeling is used to better understand the interplay of hydrology, geochemistry, and biology controlling the cycling of carbon, nitrogen, oxygen, iron, sulfur, and uranium in a shallow floodplain of the Colorado River in Rifle, Colorado. In this river-aquifer-vadose zone system, aerobic respiration generally maintains anoxic groundwater below an oxic vadose zone until seasonal snowmelt-driven water table peaking transports dissolved oxygen (DO) and nitrate from the vadose zone into the alluvial aquifer. The response to this perturbation is localized due to distinct physico-biogeochemical environments and relatively long time scales for transport through the floodplain aquifer and vadose zone. Naturally reduced zones (NRZs) containing sediments higher in organic matter, iron sulfides, and non-crystalline U(IV) rapidly consume DO and nitrate to maintain anoxic conditions, yielding Fe(II) from FeS oxidative dissolution, nitrite from denitrification, and U(VI) from nitrite-promoted U(IV) oxidation. Redox cycling is a key factor for sustaining the observed aquifer behaviors despite continuous oxygen influx and the annual hydrologically-induced oxidation event. Depth-dependent activity of fermenters, aerobes, nitrate reducers, sulfate reducers, and chemolithoautotrophs [e.g., oxidizing Fe(II), S compounds, and ammonium] is linked to the presence of DO, which has higher concentrations near the water table.


Yabusaki, S., M. Wilkins, Y. Fang, K. Williams, B. Arora, J. Bargar, H. Beller, N. Bouskill, E. Brodie, J. Christensen, M. Conrad, R. Danczak, E. King, M. Soltanian, N. Spycher, C. Steefel, T. Tokunaga, R. Versteeg, S. Waichler, H. Wainwright (2017).  Water Table Dynamics and Biogeochemical Cycling in a Shallow, Variably-Saturated Floodplain.  Environmental Science and Technology, 51 (6), 3307-3317,  DOI: 10.1021/acs.est.6b04873

Jill Banfield named 2017 Goldschmidt Medalist

Reposted from the Berkeley Lab EESA blog

Jill Banfield, Faculty Scientist in Earth & Environmental Sciences at LBNL, Professor at UC Berkeley, and member of the SFA team, has been named 2017’s recipient of the V.M. Goldschmidt Award. This award recognizes major achievements in geochemistry or cosmochemistry. Her work focuses on geomicrobiology—natural microbial communities in the terrestrial subsurface, sediments, water, biofilms and animals. She also studies nanoparticle formation and behavior in the natural environment.

Jill will receive her award at the Goldschmidt 2017 conference in Paris, France, this August.

Read the Geochemical Society’s announcement.

Watershed Function SFA Research in Discover’s Top 100 of 2016


Cover for Discover Magazine’s “Top 100 Stories of 2016”

Watershed Function SFA research—leading to the discovery of previously unknown species throughout the bacterial branches of the Tree of Life—was included in Discover Magazine’s “Top 100 Stories of 2016“, at #97 in the list.

The accolade accentuates the abundant media coverage the research garnered in April 2016 when it was first published. In fact, the article’s Altmetric score earned it spot #79 in Altmetric’s “Top 100 Articles of 2016“.

Diverse Microbial Metabolism in Aquifer BGC Hot Spot


Summary of key metabolic pathways expressed by a prominent bacterium (Hydrogenophaga b174) in an NRZ biogeochemical hot spot in the Rifle aquifer. Surprisingly, this bacterium actively catalyzed both heterotrophic and chemolithoautotrophic processes and influenced biogeochemical cycling of several elements, including C, N, and S. Unexpectedly, denitrification played an important role in this metabolism.

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. This study (Jewell et al., Frontiers in Microbiology) sought to better understand how natural organic matter fuels microbial communities within anoxic biogeochemical hot spots (NRZs) in a shallow alluvial aquifer at the Rifle (CO) site. Overall, the results highlighted the complex nature of organic matter transformation in NRZs and the microbial metabolic pathways that interact to mediate redox status and elemental cycling.


The authors used an anaerobic microcosm experiment in which NRZ sediments served as the sole source of electron donors and microorganisms. Biogeochemical data indicated that the decomposition of native organic matter occurred in different phases, beginning with mineralization of dissolved organic matter (DOM) to CO2 during the first week of incubation, followed by a pulse of acetogenesis that dominated carbon flux after two weeks. The depletion of DOM over time was strongly correlated with increases in 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 (~8%) of the metatranscriptome. This Hydrogenophaga strain also expressed genes indicative of chemolithoautotrophy, including CO2 fixation, H2 oxidation, S-compound oxidation, and denitrification. The pulse of acetogenesis appears 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 (>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.

Stelzer Embarks on “Homeward Bound” Journey to Antarctica

Times in Greenland and AntarcticaThis week, Heidi Steltzer will embark on an Antarctic voyage as one of the first participants of “Homeward Bound“, a strategic and science initiative for women.  Read her blog post here.

Watershed Function SFA Featured in Crested Butte Magazine

Crested Butte 2016/17 coverThe semiannual magazine—popular with both locals and out of town guests—featured a short story about Watershed Function SFA research activities.

Find the article on page 18 (digital page 20) of the Winter 2016/17 edition on the Crested Butte Magazine Website. Or go here for a direct link to the story.