Berkeley Lab

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

First Measurements of Dark Reactive Oxygen Species in a Groundwater Aquifer

Hydrogen peroxide concentrations across the Rifle, CO field site.

Hydrogen peroxide concentrations across the Rifle, CO field site.

Yuan et al. (2017) reports on the first measurement of the presence of hydrogen peroxide concentrations in groundwaters. Hydrogen peroxide and an associated class of compounds called reactive oxygen species have long been known to be important drivers of biogeochemical cycling and contaminant decomposition in surface water (oceans, rivers, and lakes). However, their importance in groundwater was unestablished.

By demonstrating that hydrogen peroxide and therefore the associated group of reactive oxygen species were widely distributed in the groundwaters of our site, the study establishes that they are likely important to the chemistry and function of groundwater systems. The widespread presence of reactive oxygen species may be an explanation for apparent non-equilibrium conditions in some waters as well as organic matter oxidation pathways without other obvious causes. Finally by showing that concentrations tended to be highest at transition zones the work focuses the likely most impactful areas of future investigation.


The commonly held assumption that photodependent processes dominate H2O2 production in natural waters has been recently 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. In situ detection using a sensitive chemiluminescent method suggests H2O2 concentrations ranging from lower than the detection limit (<1 nM) to 54 nM along the vertical profiles obtained at various locations across the aquifer. Our results 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 our detected H2O2 profiles, and therefore there 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 suggests 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, our results demonstrate that reactive oxygen species are not only widespread in oceanic and atmospheric systems but also in the subsurface domain, possibly the least understood component of biogeochemical cycles.


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

Simple non-electrostatic model successfully predicts long-term uranium mobility

Comparing U(VI) breakthrough curves at a monitoring well location (FSB110D) in the F-Area of the Savannah River Site (SRS) using two model simulations: the electrostatic surface complexation model (SCM) and the best-fit NEM.

Arora et al. (2017) developed a simple non-electrostatic model through a step-by-step calibration procedure to describe U 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.

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.


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.


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

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

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.

New Bacteria Groups, and Stunning Diversity, Discovered Underground

Image: Bacterial tree of life (credit: Banfield group)

In a new publication in Nature Communications (Anantharaman et al. 2016), research borne from the Watershed Function SFA provides new clues about the roles of subsurface microbes in globally important cycles. Read More »

Vadose zone respiration contributes significantly to CO2 fluxes


First column: Rifle (Colorado) floodplain vadose zone profile.
Second column: Instrumentation for monitoring pore water and gas profiles down to 3.5 m depth.
Third column: Respiration profiles are sustained by organic carbon carried in infiltration water.

In this SFA study (Tokunaga et al., Vadose Zone Journal), vertical profiles of carbon dioxide concentrations in pore gases, measured from the soil surface down to the water table in a semi-arid floodplain, were shown to have significant contributions from microbial respiration in the deeper vadose zone, well below the rooting depth and above the water table. Approximately 17% of the surface CO2 flux originates from depths between 2.0 and 3.5 meters. Respiration in the vadose zone and low net infiltration limit organic carbon transport to the aquifer. These contributions are not typically accounted for in Earth System Models (ESMs).


Although CO2 fluxes from soils are often assumed to originate within shallow soil horizons (< 1 m depth), relatively little is known about respiration rates at greater depths. The authors compared measured and calculated CO2 fluxes at the Rifle floodplain along the Colorado River, and measured CO2 production rates of floodplain sediments in order to determine the relative importance of vadose zone respiration. Calculations based on measured CO2 gradients and estimated effective diffusion coefficients yielded fluxes that are generally consistent with measurements obtained at the soil surface (326 g C m-2 yr-1). CO2 production from the 2.0 to 3.5 m depth interval was calculated to contribute 17% of the total floodplain respiration, with rates that were larger than some parts of the shallower vadose zone and underlying aquifer. Microbial respiration rates determined from laboratory incubation tests of the sediments support this conclusion. The deeper unsaturated zone typically maintains intermediate water and air saturations, lacks extreme temperatures and salinities, and is annually resupplied with organic carbon from snowmelt-driven recharge and by water table decline. This combination of favorable conditions supports deeper unsaturated zone microbial respiration throughout the year.

Innovative Geophysical Approach for Mapping Biogeochemical Hotspots in Floodplains

The new method (Wainwright et al., Water Resources Research) can be used to map biogeochemical hotspots in a spatially extensive and non-invasive manner, and is particularly useful for developing and parameterizing 3D biogeochemical models. Being able to map such hotspots will enable scientists to quantify the impact of floodplain subsurface processes on biogeochemical cycling through the terrestrial system and associated water quality exports to rivers.

3D estimation of subsurface geological layers

A three-dimensional estimation of subsurface geological layers (green and purple layers) and the naturally reduced zones (red) obtained using the new method at the Rifle Colorado study site. The region shown is the modeling domain, and the estimates obtained were used to parameterize a reactive transport model.


In floodplain environments, naturally reduced zones (NRZ) are considered to be common biogeochemical hotspots that have distinct microbial and geochemical characteristics. Although important for understanding their role in mediating floodplain biogeochemical processes, mapping the subsurface distribution of NRZs over the dimensions of a floodplain or larger is challenging, as conventional wellbore data are typically spatially limited and the distribution of NRZs is heterogeneous. In this study, the authors present an innovative methodology for the probabilistic mapping of NRZs within a three-dimensional (3D) subsurface domain using induced polarization imaging, which is a non-invasive geophysical technique. Measurements consisted of surface geophysical surveys and drilling-recovered sediments, both acquired at the U.S. Department of Energy field site near Rifle, CO. Inversion of surface time-domain induced polarization (TDIP) data yielded 3D images of the complex electrical resistivity, in terms of magnitude and phase, which are associated with mineral precipitation and other lithological properties. To estimate the spatial distribution of NRZs, the team developed a Bayesian hierarchical model to integrate the geophysical and wellbore data. Results showed that the integration of geophysical imaging and wellbore data using this proposed approach was capable of mapping spatially heterogeneous interfaces and NRZ distributions. As described by a follow-on paper, the geophysical estimates were subsequently used to parameterize a reactive transport model, to predict floodplain biogeochemical cycles and river export.

A New View of the Tree of life

Tree of Life

An artistic representation of the tree of life, with the many groups of bacteria on the left, the uncultivable bacteria at upper right (purple), and the Archaea and eukaryotes (green) – which includes humans – at the lower right. (Graphic by Zosia Rostomian, Lawrence Berkeley National Laboratory)


Supported primarily by the Watershed Function SFA, UC Berkeley researchers have reconfigured the tree of life to account for newly discovered microscopic life forms. The new tree, published online in the journal Nature Microbiology, reinforces once again that the life we see around us – plants, animals, humans and other so-called eukaryotes – represent a tiny percentage of the world’s biodiversity. The high-impact paper has generated a great deal of press coverage.

Read more about the research in this press release from UC Berkeley.