Berkeley Lab

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 »

Watershed Function at AGU 2017

Research from the Watershed Function SFA will be featured in approximately 25 posters, talks and convened sessions at the 2017 American Geophysical Union Fall Meeting in New Orleans, LA.

Click here to see a full listing of SFA-related AGU 2017 activities.

New Approach to Characterize Natural Organic Matter in Belowground Sediments

FTIR analysis (top) and pictures (bottom) of three natural organic matter fractions extracted from sediment: water extractable (MQ-SPE), acid-soluble pyrophosphate (PP) extractable (PP-SPE), and acid-insoluble PP extractable (PP >1 kD).

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. In this SFA study, published in Organic Chemistry, a range of chemical extractions were evaluated for extraction of natural organic matter (NOM) from low-carbon (<0.2%) alluvial sediments and an extraction and purification scheme was developed in order to isolate and characterize different fractions of sediment-associated NOM.


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.


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

Over 80 Attendees Join 2017 SFA Retreat


Team photo from the 2017 Retreat at the Hotel Shattuck Plaza in Berkeley, CA

Over 80 team members and collaborators attended the 2017 SFA Annual Retreat in Berkeley, CA. Read more »

Meet the scientist: Rick Colwell (Oregon State U.) and Laura Lapham (U. Maryland)

This video of our “Meet the Scientist” series highlights the DOE-funded research activities of Rick Colwell (Oregon State) and Laura Lapham (Univ. Maryland). Rick and Laura were at East River this past weekend (photo below), where they installed multiple “osmosamplers” within the watershed including within a 200-ft deep Mancos shale well and within the East River at our Pumphouse location. These samplers rely upon creation of an osmotic potential that induces continuous flow and enables autonomous sampling within locations made inaccessible due to location (deep boreholes) and weather (snow / ice). Learn more about their work and the technology in the video.


November 2017 – Groundwater Discharge Zones of DOE-Funded USGS project to Briggs et al.

Virrtual site tour highlighting one of the groundwater discharge zones into the East River being studied by Marty Briggs (USGS) and his collaborators Fred Day Lewis (USGS) and Lee Slater (Rutgers). With this time of the year dominated by baseflow contributions, the impact of geochemically reduced groundwater hitting oxic surface water is visually pronounced.

October 2017 – Drilling and Cattle: An East River “Day in the Life”

Drilling at our “Upper Elevation” site was completed in advance of a winter storm that hit Crested Butte yesterday allowing the rig to descend safely from the 11,200-ft elevation drill site. Both the coring and vertically resolved hydrologic testing in the well bore were hugely successful thanks to Authentic Drilling and the hard onsite work and advance planning of USGS scientists Andy Manning and Lyndsay Ball (photo attached). Core recovery was excellent, approaching nearly 100% over the entire depth (ca. 270-ft).

As concerns the DOE-funded work by USGS scientists in the Redwell Basin, a link to an interview with Andy and Lyndsay follows.

Lastly, life in the west — and in our watershed specifically — brings us into contact with ranchers and their cattle.  Ranchers are critical members of the Crested Butte / Gunnison community and a group of important stakeholders in the watershed that we engage to develop cattle-friendly research activities and infrastructure.  RMBL serves as a key ally and primary facilitator for engaging the local ranching community, so a reminder to reach out to the RMBL Science Director, Jennie Reithel, and Ken Williams before working in areas where cattle will be present during the summer and fall seasons.

Pumphouse cattle drive:

Meet the Scientist: Andy Manning and Lyndsay Ball:

Redwell Basin drilling:

Upper Elevation site core recovery:

Upper Elevation site hydrologic testing: