Berkeley Lab

Influence of hydrological perturbations and riverbed sediment characteristics on hyporheic zone respiration of CO2 and N2

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In this work, modeling capabilities were advanced to assess the functioning of a hyporheic zone under various climatic conditions, impacted by surface-water groundwater interactions, and feedbacks with microbial biomass.

Results of the study show that while highly losing rivers have greater hyporheic CO2 and N2 production, gaining rivers allowed the greatest fraction of CO2 and N2 production to return to the river.

Summary

River systems are important components of our landscape that help to degrade contaminants, support food webs, and transform organic matter. In this study, a model was developed and tested that could help reveal the role of the riverbed for these ecosystem services. The model was used to explore how different riverbed conditions eventually control the fate of carbon and nitrogen. The results show that carbon and nitrogen transformations and the potential suite of microbial behaviors are dependent on the riverbed sediment structure and the water table conditions in the local groundwater system. The implications of this are that the riverbed sediments and the cumulative effect of water table conditions can control hyporheic processing. Under future river discharge conditions, assuming reduced river flows and siltation of riverbeds, reductions in total hyporheic processing may be observed.

Citation

Newcomer, M. E., Hubbard, S. S., Fleckenstein, J. H., Maier, U., Schmidt, C., Thullner, M., et al. (2018). Influence of hydrological perturbations and riverbed sediment characteristics on hyporheic zone respiration of CO2 and N2. JGR: Biogeosciences, 123, 902–922. DOI: 10.1002/2017JG004090

Influence of hydrological perturbations and riverbed sediment characteristics on hyporheic zone respiration of CO2 and N2

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In this work, we advanced modeling capabilities to assess the functioning of a hyporheic zone under various climatic conditions, impacted by surface-water groundwater interactions, and feedbacks with microbial biomass.

Our results show that while highly losing rivers have greater hyporheic CO2 and N2 production, gaining rivers allowed the greatest fraction of CO2 and N2 production to return to the river.

Summary

River systems are important components of our landscape that help to degrade contaminants, support food webs, and transform organic matter. In this study, we developed and tested a model that could help reveal the role of the riverbed for these ecosystem services. We used the model to explore how different riverbed conditions eventually control the fate of carbon and nitrogen. Our results show that carbon and nitrogen transformations and the potential suite of microbial behaviors are dependent on the riverbed sediment structure and the water table conditions in the local groundwater system. The implications of this are that the riverbed sediments and the cumulative effect of water table conditions can control hyporheic processing. Under future river discharge conditions, assuming reduced river flows and siltation of riverbeds, reductions in total hyporheic processing may be observed.

Citation

Newcomer, M. E., Hubbard, S. S., Fleckenstein, J. H., Maier, U., Schmidt, C., Thullner, M., et al. (2018). Influence of hydrological perturbations and riverbed sediment characteristics on hyporheic zone respiration of CO2 and N2. JGR: Biogeosciences, 123, 902–922. https://doi.org/10.1002/2017JG004090

Applying Machine Learning to Enhance Geochemical Characterization of Shale Surfaces

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Machine learning was used to interpret the microscale heterogeneity of shale materials that influence water quality, based on their nanoscale properties.

It is well known that the organic and mineralogical heterogeneity in shale, which can be visualized at micrometer and nanometer spatial scales with various spectroscopic and microscopic techniques, contributes to the quality of gas reserves, gas flow mechanisms, and gas production from the subsurface. Scientists have now identified a way to use a machine learning approach to build a molecular distribution map of the surface of shale-sedimentary rocks, which are composed of minerals and organic matter.

The flow of fluids through shale’s nanoporous networks is fundamental to hydraulic fracturing and enhanced geothermal heating as well as to carbon sequestration and water storage. Thus, understanding shale chemistry at both the nano and mesoscale is relevant to energy production, climate-change mitigation, and sustainable water and land use.

Summary

The organic and mineralogical heterogeneity in shale at micrometer and nanometer spatial scales contributes to the quality of gas reserves, gas flow mechanisms and gas production. In a new study, a team from LBNL demonstrated two molecular imaging approaches based on infrared spectroscopy that enable the team to obtain mineral and kerogen information at mesoscale spatial resolutions in large-sized shale rock samples. The first method used a modified microscopic attenuated total reflectance measurement that employs a large germanium hemisphere combined with a focal plane array detector to rapidly capture chemical images of shale rock surfaces spanning hundreds of micrometers with micrometer spatial resolution. The second method, synchrotron infrared nano-spectroscopy, employs a metallic atomic force microscope tip to obtain chemical images of micrometer dimensions but with nanometer spatial resolution. This chemically “deconvoluted” imaging at the nano-pore scale was then used to build a machine learning model to generate a molecular distribution map across scales with a spatial span of 1000 times, which enabled high-throughput geochemical characterization in greater details across the nano-pore and micro-grain scales and allows the team to identify co-localization of mineral phases with chemically distinct organics and even with gas phase sorbents. This type of characterization is fundamental to understand mineral and organic compositions affecting the behavior of shales.

Citation

Hao, Z.; Bechtel, H. A.; Kneafsey, T.; Gilbert, B.; Nico, P. S. (2018), Cross-Scale Molecular Analysis of Chemical Heterogeneity in Shale Rocks, Scientific Reports, 8, 9, DOI: 10.1038/s41598-018-20365-6.

Microbial “hotspots” and organic rich sediments are key determinants of nitrogen cycling in a floodplain

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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.

Summary

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.

Citation

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

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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)

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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.

On the Power of Uncertainties in Microbial System Modeling: No Need To Hide Them Anymore

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Scientific Achievement

In this manuscript, we advocate that biological uncertainties need to be considered foundational facets that must be incorporated in models. This will improve our understanding and identification of microbial traits and provide fundamental insights on microbial systems.

Significance and Impact

We demonstrate how statistical model checking can enhance the development of microbial models by building confidence in the estimation of critical parameters and through improved sensitivity analyses.

Research Details
  • We employ a statistical model-checking (SMC) method that combines model checking with sensitivity analyses.
  • We then embed the uncertainty of the parameter values into the models by assigning each parameter to a probability distribution based on its potential values informed by lab or field experiments
Citation

Delahaye B, Eveillard D, Bouskill NJ (2018). On the Power of Uncertainties in Microbial System Modeling: No Need To Hide Them Anymore. M-Systems. 2 (6) DOI: 10.1128/mSystems.00169-17.

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

Steefel et al. Receive R&D 100 Award for CrunchFlow

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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 »