Berkeley Lab

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.

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

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

March 2017 – Wintertime conditions of relevance

Below are four video postings of relevance to wintertime conditions and ongoing science activities.

Snow conditions along the Washington Gulch satellite site elevation gradient:

Snow conditions and science activities at the Pumphouse Floodplain Meander A:

Pumphouse meteorological station status:

Snow pit sampling at the Pumphouse Ecohydrology study plots:

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.

February 2017 – Pumphouse Intensive Sites

Below are videos giving a virtual tour of sites under this year’s deep snowpack.

Meander A:

Pumphouse Meterological Station:

Electrical Resistivity Tomography (ERT) Monitoring Station:

Lower Montane Hillslope:

Snowpack and Snow Water Equivalent levels continue to be quite elevated this season, with snow depths in the videos ranging from 140-170 cm at the time they were recorded.

New CRISPR–Cas systems from uncultivated microbes

a) Lineages with and without isolated representatives, and the scale of little investigated biology. b) Locus organization of the discovered systems

Scientific Achievement

Novel genomes reconstructed from metagenomes were shown to encode previously unknown CRISPR-Cas systems with potential for genome editing.

Significance and Impact

The new genome-editing systems are among the most compact yet identified. The systems are currently being developed as alternatives to the Cas9-based system.

Research Details
  • An extensive set of genomes reconstructed largely in DOE funded research was searched for novel gene clusters adjacent to CRISPR arrays.
  • Two candidate systems, CasX and CasY, were tested in interference assays
  • Novel archaeal genomes were shown to contain the first Cas9-based loci from this domain of life
Citation

Burstein, D.; Harrington, L. B.; Strutt, S. C.; Probst, A. J.; Anantharaman, K.; Thomas, B. C.; Doudna, J. A.; Banfield, J. F. (2017), New CRISPR–Cas systems from uncultivated microbes, Nature, 542(7640), 237-241 DOI: 10.1038/nature21059.

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

Discover-magazine-cover

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

Key-metabolic-pathways

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.

Summary

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.

Modelling the Evolution of Complex Conductivity During Calcite Precipitation on Glass Beads

A: Complex conductivity model of the porous medium with calcite precipitation.
Imaginary conductivity of calcite as a function of time in days before (A) and after (B) the pore clogging

Scientific Achievement

Complex conductivity signals of calcite provides an in-situ monitoring approach for its precipitation, yet the polarization mechanism is not clear. We developed a mechanistic model considering the electrochemical polarization of the Stern and diffuse layers surrounding calcite particles.

Significance and Impact

The model provides a mechanistic understanding of complex conductivity signals from in-situ calcite precipitation that often occurs during subsurface reactional processes. This is key to develop geophysical monitoring for dynamic monitoring of subsurface biogeochemistry.

Research Details
  • The experimental data sets are provided by Wu et al. (2010)
  • Numerical modeling is based on the stern layer electrochemical polarization model at the calcite – fluid interface
  • Comparison between the model simulation and experimental results provides validation of the model.
Citation

Leroy, P., Li, S., Revil, A., Wu, Y., 2017, Modelling the Evolution of Complex Conductivity During Calcite Precipitation on Glass Beads, Geophys. J. Int. 209,
123–140, DOI: 10.1093/gji/ggx001

Asgard archaea illuminate the origin of eukaryotic cellular complexity

Phylogenetic tree showing the placement of Eukaryotes within Archaea

Scientific Achievement

Regarding eukaryote origin, we describe a superphylum of uncultivated archaea whose genomes are enriched for proteins formerly considered eukaryote specific, indicating the archaeal host cell already contained many key components that govern eukaryotic cellular complexity.

Significance and Impact

The findings support the phylogenetic inference that eukaryotes arose from an archaeal lineage, which potentially shifts the tree of life back to two domains, Results elucidate archaeal innovations that may have laid the foundation for the evolution of complex, multi-cellular life.

Research Details
  • Archaeal genomes that group together phylogenetically were collected from a variety of different ecosystems
  • Together, these genomes were used to define the new archaeal superphylum referred to as Asgard
  • Genomes were investigated regarding their metabolic capacities
  • Normally eukaryotic pathways were identified.
Citation

Zaremba-Niedzwiedzka, K.; Caceres, E. F.; Saw, J. H.; Bäckström, D.; Juzokaite, L.;et al..; Banfield, J. F.; Schramm, A.; Baker, B. J.; Spang, A.; Ettema, T. J. G. (2017) Asgard archaea illuminate the origin of eukaryotic cellular complexity, Nature, 541(7637), 353-358 DOI: 10.1038/nature21031.