Berkeley Lab

Anaerobic microsites have an unaccounted role in soil carbon stabilization

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Figure shows how certain kinds of organic molecules, e.g. Sugars or lipids can only be oxidized by microbes with certain electron donors. In the absence if oxygen, lipids can not be broken down for energy

Scientific Achievement

This work demonstrated that changes in redox conditions over small spatial distances can have a significant impact on the types of organic molecules that are decomposed by soil microbes

Significance and Impact

This is significant because the controls on the decomposition of soil carbon are one of the most important and most poorly understanding regulators of global carbon cycling. By demonstrating the importance of an under appreciated control mechanism. This work has advanced the overall field of carbon cycling.

Research Details
  • The experiment unitized a simply reactor with different textured soil material.
  • By changing the soil texture the degree of O2 permeation is impacted which in turn creates anaerobic microsites in the system
  • The results showed that these anaerobic site had much slower carbon decomposition than the other locations.
  • When making an estimate of how many anaerobic microsite there are in global soils it can be shown that this mode of carbon projecting is globally relevant.
Citation

Keiluweit, M.; Wanzek, T.; Kleber, M.; Nico, P.; Fendorf, S. (2017), Anaerobic microsites have an unaccounted role in soil carbon stabilization, Nature Communications, 8 DOI: 10.1038/s41467-017-01406-6.

Complete 4.55-megabase-pair genome of “Candidatus Fluviicola riflensis,” curated from short-read metagenomic sequences

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The aquifer adjacent to Colorado River, Rifle, CO, is now arguably the most extensively microbially characterized ecosystem in the world

Scientific Achievement

We report the 4.55-Mbp genome of “Candidatus Fluviicola riflensis”, a facultative anaerobe that likely can grow over a range of O2 levels, favoring its proliferation in an aquifer adjacent to the CO River.

Significance and Impact

This brief genome announcement was unprecedented because it established that a large genome from a complex, heterogenous population could be recovered from a metagenome, enabling metabolic predictions

Research Details
  • Groundwater was collected during an episode in which dissolved O2 concentrations were seasonally elevated for a short duration
  • Short read sequence datasets were generated
  • The genome of an environmentally important but otherwise enigmatic microbial community member was reconstructed
Citation

Banfield, J.F., Anantharaman, K., Williams, K.H., and Thomas, B.C. (2017), Complete 4.55-megabase-pair genome of “Candidatus Fluviicola riflensis,” curated from short-read metagenomic sequences, Genome Announcements, 5(47), e01299-17, doi: 10.1128/genomeA.01299-17

New Approach to Characterize Natural Organic Matter in Belowground Sediments

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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.

Summary

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.

Citation

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

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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.

Summary

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.

Citation

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

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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.

Summary

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.

Citation

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

Complexation and Redox Buffering of Iron(II) by Dissolved Organic Matter

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Top: EXAFS data revealed that iron(II) is dominantly complexed by carbonate groups in organic matter (OM). Bottom: Iron(II) bound to reduced OM undergoes redox cycling upon exposure to O2 that generates reactive oxygen species.

Scientific Achievement

Daugherty et al. identified the organic functional groups in soil organic matter (OM) that preferentially bind to reduced form of dissolved iron and showed that reduced OM can stabilize Fe(II) by functioning both as redox buffer, which may help explain the widespread presence of Fe(II) in oxic circumneutral waters.

Significance and Impact

Iron (Fe) bioavailability depends upon its solubility and oxidation state, which are strongly influenced by association NOM. The knowledge of iron(II) binding mechanisms by OM enhances our models for iron(II) transport, redox cycling and bioavailability in terrestrial ecosystems.

Research Details
  • Use of extended X-ray absorption fine structure (EXAFS) spectroscopy to determine the coordination environment of Fe(II) associated with NOM
  • Linear combination analysis of EXAFS data determined that Fe(II) was complexed primarily by carboxyl functional groups in reduced NOM. Catecholate groups play a secondary role.
  • Reduced OM stabilizes iron(II) against oxidation by O2 for at least 12 hours
Citation

Daugherty, E.L., B. Gilbert, P.S. Nico and T. Borch (2017) Complexation and Redox Buffering of Iron(II) by Dissolved Organic Matter. Environmental Science and Technology 51, 11096-11104. DOI: 10.1021/acs.est.7b03152

On Modeling CO2 Dynamics in a Floodplain Aquifer

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Observed and simulated a) total dissolved carbonate concentrations at well TT-03 and b) CO2 volume fractions at well TT-03. Cases modeled include: C1, abiotic; C2, abiotic+biotic with heterotrophic and chemolithoautotrophic pathways; and C3 with varying temperature gradients.

Scientific Achievement

The objective of this study was to infer the relative contribution of different pathways (such as atmospheric exchange, precipitation/dissolution of carbonate minerals, and biotic heterotrophic and chemolithoautotrophic reactions) on carbon fluxes at a floodplain site in Rifle, Colorado.

Significance and Impact
  • Knowledge about the timing and magnitude of CO2 efflux from soils and groundwater represents a significant uncertainty of the global carbon cycle.
  • Reactive transport models provide a useful tool for quantifying soil CO2 fluxes and for constraining the extent and rates of different abiotic and biotic reactions.
Research Details
  • A 2-D reactive transport model has been developed using TOUGHREACT to explore CO2 dynamics in the saturated and unsaturated zones at the Rifle site.
  • Results indicate that observed CO2 fluxes cannot be explained by abiotic reactions alone, but require contributions from microbial activity (e.g., heterotrophic respiration, chemolithoautotrophy).
  • The simulated CO2 concentrations are also strongly affected by subsurface temperatures, which vary significantly over time and space at this site.
Citation

Arora, B., Dwivedi, D., Spycher, N. and Steefel, C., 2017. On modeling CO2 dynamics in a flood plain aquifer. Procedia Earth and Planetary Science, 17, pp.408-411. https://doi.org/10.1016/j.proeps.2016.12.103

Retroelement-guided protein diversification abounds in vast lineages of Bacteria and Archaea

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We examined the prevalence of DGRs identified in groundwater metagenomes. The diagram shows a schematic of a genomic DGR cassette and mutagenic retrohoming mechanism. Some of the proteins being evolved may be involved in cell-cell interactions.

Scientific Achievement

Diversity generating retroelements occur in CPR and DPANN, putative symbionts with reduced genomes. These enzymes introduce hypervariability in specific proteins.

Significance and Impact

Targeted protein diversification is a pronounced trait of CPR and DPANN compared to other organisms. This diversification mechanism may provide a versatile tool for adaptation to a host-dependent existence.

Research Details
  • Genomes were reconstructed from environmental samples.
  • Diversity generating retroelements were identified
  • Incidence as a function of lineage was determined
  • Diversification targets were identified and the protein’s function predicted
Citation

Paul, B. G.; Burstein, D.; Castelle, C. J.; Handa, S.; Arambula, D.; Czornyj, E.; Thomas, B. C.; Ghosh, P.; Miller, J. F.; Banfield, J. F.; Valentine, D. L. (2017), Retroelement-guided protein diversification abounds in vast lineages of Bacteria and Archaea, Nature Microbiology, 2, 17045 DOI: 10.1038/nmicrobiol.2017.45.

Anoxia stimulates microbially catalyzed metal release from Animas River sediments

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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.

Summary

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.

Citation

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

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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.

Summary

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.

Citation

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