While watersheds are recognized as Earth’s key functional unit for managing water resources, their hydrological interactions also mediate biogeochemical processes that support all terrestrial life and can lead to a cascade of downgradient effects. The Watershed Function Scientific Focus Area is developing a scale-adaptive predictive understanding of how mountainous watersheds retain and release water, nutrients, carbon, and metals. This paper describes several recently developed approaches to interrogate, monitor and simulate transient watershed partitioning and biogeochemical responses – from genome to watershed spatial scales and from episodic to decadal timescales.

A growing demand for clean water, food, and energy — in parallel with droughts, floods, early snowmelt and other disturbances — are significantly reshaping interactions within watersheds throughout the world. This is particularly true for mountainous systems, such as the East River Watershed in CO, which is located in the Upper Colorado River Basin. This Basin supplies water to 1 in every 10 Americans and supports vast agriculture and hydropower operations along its reach. Because society is dependent on watersheds, new approaches that can accurately yet tractably predict watershed responses to disturbances are critical for resource management.

Summary

The Watershed Function project is developing new approaches to quantify and predict how disturbances impact downstream water availability and biogeochemical cycling, with a current focus on early snowmelt. The research is guided by a system-of-systems perspective and a scale-adaptive approach, where a predictive understanding of the response of archetypal watershed subsystems to disturbances is being developed as well as methods to aggregate such responses into predictions of cumulative watershed exports. The paper describes several recent advances, including above-and-below ground characterization and monitoring approaches for understanding vegetation distribution; new modeling approaches for predicting bedrock-through-canopy hillslope interactions; and coupled modeling approaches that can assimilate increasingly available streaming data into models to estimate hillslope water partitioning over time. The paper also describes new watershed function insights gained through the use of such tools, including: how historical snowmelt and monsoon characteristics influence annual discharge across the entire watershed; controls on streamflow generation; and how future changes in vegetation and temperature may influence water partitioning at different positions in the watershed. Over 30 institutions are involved in advancing watershed hydrological-biogeochemical science at the East River CO DOE-BER ‘community testbed’.

Citation

Hubbard, S.S. et al. (2018) The East River, CO Watershed: A Mountainous Community Testbed for Improving Predictive Understanding of Multi-Scale Hydrological-Biogeochemical Dynamics. Vadose Zone Journal, Special Issue on ‘Hydrological Observatories’, doi: 10.2136/vzj2018.03.0061 in press.

Berkeley Lab geochemists and hydrologists who study a mountainous watershed near Rifle, CO, discovered that spring snowmelt is essential to the transport of freshly dissolved organic matter (DOM) from the top soil to the part of the Earth’s subsurface that lies above the groundwater table. Because dissolved organic matter undergoes biological humification over the year, these processes involving this deep vadose zone suggest an annual cycle of DOM degradation and transport at this semi-arid floodplain site.

Characterizing the dynamics of dissolved organic matter in semi-arid regions of Earth’s subsurface is challenging. The authors obtained insights into transport and humification processes of DOM using several spectroscopic techniques on depth- and temporally-distributed pore-waters. This methodology can be applied to other subsurface environments for understanding DOM responses and feedbacks to earth system processes.

Summary

Scientists studying DOM in surface waters considered it to be the mobile fraction of natural organic matter that falls into or is washed into water bodies. Although it has been extensively studied over many decades, relatively little is known about the dynamics of DOM in the subsurface of semi-arid environments. In order to understand transport and humification processes of DOM within a semi-arid floodplain at Rifle, Colorado, the authors applied fluorescence excitation-emission matrix (EEM) spectroscopy, humification index (HIX) and specific UV absorbance (SUVA) for characterizing depth and seasonal variations of DOM composition. They found that late spring snowmelt leached relatively fresh DOM from plant residue and soil organic matter down into the deeper vadose zone (VZ). More humified DOM is preferentially adsorbed by upper VZ sediments, while non- or less-humified DOM was transported into the deeper VZ. Interestingly, DOM at all depths undergoes rapid biological humification processes as evidenced by the products of microbial by-product-like matter in late spring and early summer, particularly in the deeper VZ, resulting in more humified DOM at the end of year. The finding indicates that DOM transport is dominated by spring snowmelt, and DOM humification is controlled by microbial degradation. It is expected that these relatively simple spectroscopic measurements (e.g., EEM spectroscopy, HIX and SUVA) applied to depth- and temporally-distributed pore-water samples can provide useful insights into transport and humification of DOM in other subsurface environments as well.

Citation

Dong, W., J. Wan, T. K. Tokunaga, B. Gilbert, and K. H. Williams (2017). Transport and Humification of Dissolved Organic Matter within a Semi-Arid Floodplain. Journal of Environmental Sciences 57, 24-32, DOI: 10.1016/j.jes.2016.12.011

Sulfate is ubiquitous in the environment, and sulfate reduction – a key control on anaerobic carbon turnover – impacts a number of other processes such as carbon oxidation and sulfide production. Until now, sulfate reduction was believed to be restricted to organisms from select bacterial and archael phyla. But scientists at UC Berkeley have now found this ability to be more widespread. They used genome-resolved metagenomics to discover roles in sulfur cycling for organisms from 16 microbial phyla not previously associated with this process.

Sulfate-reducing bacteria are anaerobic microorganisms essential to sulfur and carbon cycling. Sulfate reduction drives other key processes and produces hydrogen sulfide, an important but potentially toxic gas present in sediments, wetlands, aquifers, the human gut, and the deep-sea. The discovery of novel microbes connected to sulfur cycling is relevant in biogeochemistry, ecosystem science and engineering, and fundamentally reshape our understanding of microbial function and capabilities associated with phylogenetic information.

Summary

Phylogenetic information shapes our expectations regarding microbial capabilities. In fact, this is the basis of currently used methods that link gene surveys to metabolic predictions of community function. Sulfate Reduction, an important anaerobic metabolism, impacts carbon, nitrogen, and hydrogen transformations in numerous environments across our planet and is known to be restricted to organisms from selected bacterial and archaeal phyla. The authors used genome-resolved metagenomic analyses to determine the metabolic potential of microorganisms from six complex marine and terrestrial environments. By analyzing >4000 genomes, they identified 123 near-complete genomes that encode dissimilatory sulfite reductases involved in sulfate reduction. They discovered roles in sulfur cycling for organisms from 16 microbial phyla not previously known to be associated with this process. Additional findings include some of the earliest-evolved sulfite reductases in bacteria, identification of a novel protein unique to sulfate reducing bacteria, and a key sulfite reductase gene in putatively symbiotic Candidate Phyla Radiation (CPR) bacteria. This study fundamentally reshapes expectations regarding the roles of a remarkable diversity of organisms in the biogeochemical cycle of sulfur.

Citation

Anantharaman, K., B. Hausmann, S.P. Jungbluth, R.S. Kantor, A. Lavy, L.A. Warren, M.S. Rappé, M. Pester, A. Loy, B.C. Thomas, and J.F. Banfield (2017). Expanded diversity of microbial groups that shape the dissimilatory sulfur cycle. The ISME journal 12, 1715–1728, DOI: 10.1038/s41396-018-0078-0

Scientists and engineers simulate the flow of fluids through permeable media to determine how water, oil, gas or heat can be safely extracted from subsurface fractured-porous rock, or how harmful materials like carbon dioxide could be stored deep underground. Now, a scientist from Lawrence Berkeley National Lab has identified a causal relationship between gases and liquids flowing through fractured-porous media. They observed oscillating liquid and gas fluxes and pressures as the two transitioned back and forth within a subsurface rock fracture.

When both liquid and gas are injected into a rock fracture, the cumulative effect of forward and return pressure waves causes intermittent oscillations of liquid and gas fluxes and pressures within the fracture. The Granger causality test is used to determine whether the measured time series of one of the fluids can be applied to forecast the pressure variations in another fluid. This method could also be used to better understand the causation of other hydrological processes, such as infiltration and evapotranspiration in heterogeneous subsurface media, and climatic processes, for example, relationships between meteorological parameters—temperature, solar radiation, barometric pressure, etc.

Summary

Identifying dynamic causal inference involved in flow and transport processes in complex fractured-porous media is generally a challenging task, because nonlinear and chaotic variables may be positively coupled or correlated for some periods of time, but can then become spontaneously decoupled or non-correlated. The author hypothesized that the observed pressure oscillations at both inlet and outlet edges of the fracture result from a superposition of both forward and return waves of pressure propagation through the fracture. He tested the theory by exploring an application of a combination of methods for detecting nonlinear chaotic dynamics behavior (Figure A) along with the multivariate Granger Causality (G-causality) time series test. Based on the G-causality test, the author infers that his hypothesis is correct, and presents a causation loop diagram (Figure B) of the spatial-temporal distribution of gas, liquid, and capillary pressures measured at the inlet and outlet of the fracture. The causal modeling approach can be used for the analysis of other hydrological processes such as infiltration and pumping tests in heterogeneous subsurface media, and climatic processes.

Citation

Faybishenko, B. (2017). Detecting dynamic causal inference in nonlinear two-phase fracture flow, Advances in Water Resources 106, 111–120, DOI: 10.1016/j.advwatres.2017.02.011

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

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

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.

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.

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.