Berkeley Lab

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

Susan Hubbard Named 2017 American Geophysical Union Fellow

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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

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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 »

July 2017 – Redwell Basin conditions and UAV-based imaging campaign

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Associated with the recent UAV-based hyperspectral and multi-spectral imaging campaign and accompanying ground-based sampling, below is a video highlighting some of the efforts of Nicola Falco (LBNL) and Dana Chadwick (Stanford) at the Pumphouse lower montane intensive study site:

For those with an interest in the mining and mineral impacted portions of the watershed and specifically upcoming activities by USGS and Berkeley Lab researchers, below are two videos presenting conditions within the Redwell Basin. The first presents more of a synoptic view while the second focuses on an intriguing high-elevation wetland system that likely serves as an important biogeochemical reactor impacting metals export from the basin. The wetland is organic rich, with the obvious presence — visually and by smell — of sulfidic soils and sediments underlying the surface layer. Metal-rich fluids emanating from the former mines and mineralized rock in the basin perfuse much of this wetland system.

The Redwell Basin represents the location of two deep boreholes planned for installation, coring, hydrologic testing, and geophysical logging in September 2017, with ground conditions associated with planned surface geophysical surveys presented in both videos.

June 2017 – Lower montane hillslope and floodplain intensive study sites, and EC Flux tower site conditions

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The first video depicts our East River lower montane hillslope and floodplain intensive study sites on June 23, 2017 (N.B. I incorrectly note the date on the video as June 22nd). The video illustrates the extent to which the hillslope has recovered from the September 2016 drilling activity that led to the installation of the wells and sampling locations shown and illustrates the current state of vegetation growth at the site relative to the monitoring locations and infrastructure.

As it’s also worth checking in on site conditions at the EC Flux tower location, the following video was collected so interested folks / PI’s can keep an eye on things.

June 2017 – Peak discharge at Pumphouse floodplain and Meander C shale outcrop conditions

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A brief update is below on site conditions at East River and in particular the Pumphouse floodplain. These dates correspond to conditions during or very near peak discharge at this location.

June 5th, 2017:

June 7th, 2017:

Additionally, included is a video of the shale outcrop and associated water line relative to the incised marker bed that Joel Rowland has observed in the past and which he considers to represent the last high water runoff mark. We’re very close to this level this year.

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

May 2017 – Wintertime conditions at meanders A-to-C and East River EC Flux Tower

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Meander A on May 4th, 2017:
[N.B. I inadvertently refer to Meander L as “Meander D” in this video; the video presents Meander L where Paula Matheus is undertaking her genomics sampling]

Meander A-to-C bank erosion:

East River Eddy Covariance Flux Tower on May 4, 2017:

East River Eddy Covariance Flux Tower on May 6, 2017 — significant snowmelt:

April 2017 – Flux Tower Deployment and Peak SWE Snow Sampling

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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.

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 is linked below.

Flux tower installation:

Synoptic view of flux tower installation and site conditions and infrastructure:

Upper Subalpine site conditions:

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 below:

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.