Berkeley Lab

Monitoring Biostimulation and Contaminant Reduction in Groundwater by using Stable Isotopes of Carbon

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Charts showing the variations versus time of Cr (VI), electron donors, and metabolic products, in groundwater. The gray bars indicate the injection day of the electron donor. (A) Cr (VI) concentration over time; (B) organic acid concentration; (C) dissolved inorganic carbon (DIC) and total organic acids expressed as mM carbon; (D) δ13C values of organic acids and DIC.

Soils and groundwater contamination by hexavalent chromium Cr(VI) is common in industrial areas and is a serious threat to water quality and human health. In a field-scale experiment of microbial Cr(VI) reduction, a team of scientists used stable isotopes of carbon to demonstrate the transfer of carbon from the original electron donor (i.e., bacterial food source) to the metabolic products, and subsequent reduction of Cr(VI).

By injecting 13C-labeled electron donors into a contaminated site, scientists not only demonstrated that the existing microbial community reduced metal contaminants, but that this approach is a viable method for estimating the efficiency of biostimulation. This approach could be transferred to other contaminated sites that contain a variety of metal and organic contaminants.

Summary

Hexavalent chromium Cr(VI) is a common inorganic contaminant in soils and groundwater of industrial areas and represents a serious threat to water quality and human health. Among the various techniques currently available, in situ biostimulation has been recognized as a relatively cost-effective and valuable method for the remediation of contaminated groundwater. To date, the transformation and fate of organic electron donors used to stimulate Cr(VI) reduction in the field has been reported only in limited studies due to analytical and technical challenges. In this work, the authors report field-scale experimental results from in situ microbial Cr(VI) reduction stimulated via injection of 13C-labelled lactate. Simultaneously with Cr(VI) reduction the authors used concentrations and carbon isotope ratios of metabolic products to monitor the carbon transfer from the original 13C-labelled lactate. The authors also monitored the carbon isotope ratios of phospholipid fatty acids (PLFA) to demonstrate the transfer of carbon from 13C-labelled lactate to a portion of the microbial community.

Citation

M. Bill, M.E. Conrad, B. Faybishenko, J.T. Larsen, J.T. Geller, S.E. Borglin, and H.R. Beller, “Use of carbon stable isotopes to monitor biostimulation and electron donor fate in chromium-contaminated groundwater.” Chemosphere, 235, 440-446 (2019), DOI: 10.1016/j.chemosphere.2019.06.056

Abiotic and Biotic Controls on Soil Organo–Mineral Interactions

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Traditional View: The traditional view of SOM decomposition does not explicitly represent the underlying agents and processes.

Emergent View: The emergent view suggests that SOM decomposition is a function of a wide range of ecosystem properties and mechanisms (e.g., organo-mineral interactions, microbial necromass).

While there currently exists a suite of models representing soil organic matter (SOM) dynamics that span a range of complexity, some recent mechanistic models are more consistent with an emerging understanding of the persistence of SOM. Yet even these more recent models do not represent several processes that can be important for SOM dynamics. It is clear that next-generation models need to represent the full spectrum of quantitatively important mechanisms for determining SOM persistence—including rate-limited and equilibrium-based sorption, formation of soil aggregates, representative soil minerals, microbial community dynamics, and vegetation interactions—to accurately predict short- and long-term SOM dynamics.

This study informs development of a robust predictive understanding of SOM dynamics. However, it is challenging to incorporate recommendations, such as mineral-associated organic matter and vegetation dynamics, in a reactive transport modeling framework. These emergent concepts require emergent technologies to appropriately characterize, e.g., molecular, soil, and root structure. Several technologies (e.g., FT-ICR-MS, NMR, STXM, and NEXAFS) are available today for such characterization, but these technologies have not yet been fully exploited nor have the resulting data/findings been fully incorporated into modeling studies. To enhance process understanding of SOM dynamics, streamlined coordination between technologies for characterization and emerging understanding for SOM modeling are needed.

Summary

Soils represent the largest store of actively cycling terrestrial organic carbon. This carbon is susceptible to release to the atmosphere as greenhouse gases, including carbon dioxide (CO2) and methane (CH4). However, significant gaps remain in understanding why certain soil organic matter (SOM) decomposes rapidly, and why thermodynamically unstable SOM can persist in soils for centuries. To fill this critical knowledge gap, a robust predictive understanding of SOM dynamics is essential, particularly for examining short-term and long-term changes in soil carbon storage and its feedback to climate. In this review paper, the authors argue that a representation of organic matter molecular structure, the activity of belowground communities, and mineral-associated organic matter (MAOM) are required to model SOM dynamics beyond first-order effects accurately. This argument is based on a review of the literature describing the current understanding of the main interacting biological, geochemical, and physical factors leading to SOM stabilization, and on an analysis of a suite of soil carbon models. The authors conclude by recommending several mechanisms that require implementation within the next generation of mechanistic models, including kinetic and equilibrium-based sorption, soil mineral surface chemistry, and vegetation dynamics to accurately predict short- and long-term SOM dynamics.

Citation

Dwivedi D, Tang J, Bouskill N, Georgiou K, Chacon SS, Riley WJ (2019) Abiotic and biotic controls on soil organomineral interactions: Developing model structures to analyze why soil organic matter persists. Rev Mineral Geochem 85:329–348; doi: 10.2138/rmg.2019.85.11

Predictive Numerical Modeling Provides Insights into Changes in Contaminant Mobility under Increased and Extreme Precipitation Scenarios

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Impact of one-year extreme recharge (assumed in 2020) on well concentrations. e is the fractional increase in recharge

Climate change – through precipitation regime shifts or extreme precipitation events – can have a significant impact on the mobility of residual contaminants at sites where remediation solutions and management are based on an expected range of site conditions. This study used numerical simulations to evaluate and quantify the impact of such shifts or events; in particular, the competing factors of dilution and re-mobilization. Results showed that contaminant concentrations immediately decreased following extreme precipitation events due to dilution, but subsequently increased several years later due to re-mobilization of contaminants from the source zone.

The impact of changes in contaminant mobility and concentration due to extreme precipitation and shifts in the precipitation regime were found to last for several decades, depending on monitoring well locations, performance metrics and site conditions. The results of this study suggested critical considerations for the design of long-term engineered systems such as surface capping structures, and for not only monitoring their efficacy, but also for defining threshold levels of precipitation that could drastically alter the system behavior.

Summary

Through numerical modeling of un-saturated/saturated flow and transport, a team of scientists evaluated the effect of increasing and decreasing precipitation, as well as the impact of potential failure of surface barrier systems. The approach was demonstrated using a case study involving the simulation of the transport of non-reactive radioactive tritium at the U.S. Department of Energy’s Savannah River Site F-Area. Results showed that such hydrological changes significantly impact groundwater concentrations. After an initial dilution effect, the modeling results identified a significant concentration increase some years later as a consequence of contaminant mobilization. Threshold levels of precipitation were identified, above which the contaminant concentration/exports were affected. The results suggest the importance of source zone monitoring to detect re-mobilization and highlight surface barrier design requirements needed to reduce the impact of hydrological changes.

Citation

Libera, A., de Barros, F. P., Faybishenko, B., Eddy-Dilek, C., Denham, M., Lipnikov, K., Moulton, J. D., Maco, B. & Wainwright, H. (2019). Climate change impact on residual contaminants under sustainable remediation. Journal of Contaminant Hydrology, 103518, DOI: 10.1016/j.jconhyd.2019.103518

Hydrogen-based Metabolism as an Ancestral Trait in Phyla Related to the Cyanobacteria

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Key components of energy metabolism in Riflemargulisbacteria including different kinds of hydrogenases, a nitrogenase, and other protein complexes involved in energy conservation. Modified from the original publication (above).

Bacteria from multiple phyla related to Cyanobacteria were genomically described using metagenomics and single cell genomics, and genes were predicted for all genomes. Metabolic capacities, some featuring novel complexes, were predicted using genome-based analyses. Capacities were mapped across lineages to detect environment- and lineage-specific lifestyles.

The results suggest that the common ancestor of all of the phyla investigated may have been an anaerobe in which fermentation and H2 metabolism were central metabolic features. Capacities of phylogenetic neighbors to Cyanobacteria (the group in which oxygenic photosynthesis arose), such as Margulisbacteria, Saganbacteria, Melainabacteria and Sericytochromatia, constrain the metabolic platform in which aerobic respiration arose. The evolution of aerobic respiration was likely linked to the origins of oxygenic Cyanobacteria.

Summary

Margulisbacteria (RBX-1 and ZB3), Saganbacteria (WOR-1), Melainabacteria, and Sericytochromatia, close phylogenetic neighbors to Cyanobacteria, may constrain the metabolic platform in which aerobic respiration arose. In this study, the authors predict that sediment-associated Margulisbacteria have a fermentation-based metabolism featuring a variety of hydrogenases, a streamlined nitrogenase, and electron bifurcating complexes involved in cycling of reducing equivalents. The genomes of ocean-associated Margulisbacteria encode an electron transport chain that may support aerobic growth. Some Saganbacteria genomes encode various hydrogenases, and others may have the ability to use O2 under certain conditions via a putative novel type of heme copper O2 reductase. Similarly, Melainabacteria have diverse energy metabolisms and are capable of fermentation and aerobic or anaerobic respiration. The ancestor of all of these groups may have been an anaerobe in which fermentation and H2 metabolism were central metabolic features. The ability to use O2 as a terminal electron acceptor must have been subsequently acquired by these lineages.

Citation

P. B. Matheus Carnevali, F. Schulz, C. J. Castelle, R. S. Kantor, P. M. Shih, I. Sharon, J. M. Santini, M.R. Olm, Y. Amano, B.C. Thomas, K. Anantharaman, D. Burnstein, E. D. Becraft, R. Stepanauskas, T. Woyke, and J. F. Banfield, “Hydrogen-based metabolism as an ancestral trait in lineages sibling to the Cyanobacteria”. Nature Communications, 10, 463 (2019), doi: 10.1038/s41467-018-08246-y

Using Remote Sensing to Determine the Relationship Between Soil Conditions and Plant Communities

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(a) View of the hillslope-floodplain area study acquired by Worldview-2 satellite, including the ERT transect (in red color); (b) Digital terrain model capturing the microtopography; (c) Map of the spatial distribution of plant communities at sub-meter resolution; (d) Biplot based on principal component analysis that shows the co-variability between plant community, soil electrical conductivity, and topographical metrics. Legend: riparian shrubland (RI), sagebrush (SA), shrubland (SH), lupine meadow (LU), veratrum (VE), bunchgrass meadow (BU), and forb (FO).

Integration of high-resolution remote sensing and geophysical data for the investigation of the co-variability between plant community distributions, soil electrical conductivity, and microtopographical properties was used to assess the spatial organization of meadow plants within a floodplain-hillslope system at the East River watershed in Colorado.

This study fused satellite and Light Detection and Ranging (LiDAR) data, along with site characterization data to arrive at estimates of key meadow communities at high resolution. This type of information could be used on large scales to provide information on the spatial variability of soil properties, and it could also be used to capture plant community responses to perturbations over significant landscape areas.

Summary

In this study, the authors aimed to understand how soil and topographic properties influence the spatial distribution of plant communities within a floodplain-hillslope system, located in the mountainous East River watershed in Colorado. Watersheds are vulnerable to environmental change, including earlier snowmelt, changes in precipitation, and temperature trends, all of which can alter plant communities and associated water and nutrient cycles within the watershed. However, tractable yet accurate quantification of plant communities is challenging to do at a scale that also permits investigations of the key controls on their distribution. In this work, the team developed a framework that uses a new approach to estimate plant distributions, one which exploits both remote sensing (satellite) images and surface geophysical data. Joint consideration of the above-and-belowground datasets allowed the team to characterize both plant and soil properties at high spatial resolution and to identify the main environmental controls for plant distribution. The results show that soil moisture and microtopography strongly influence how plant communities are spatially distributed. Considering that each community responds to external perturbation in a different way, this method can be used within a multi-temporal framework to characterize environmental heterogeneity and to capture plant responses caused by climate-related perturbations.

Citation

N. Falco, H. M. Wainwright, B. Dafflon, E. Léger, J. Peterson, H. Steltzer, C. Wilmer, J. C. Rowland, K. H. Williams, and S. S. Hubbard, “Investigating Microtopographic and Soil Controls on a Mountainous Meadow Plant Community Using High – Resolution Remote Sensing and Surface Geophysical Data.” Journal of Geophysical Research: Biogeosciences, (2019). DOI: 10.1029/2018JG004394

The Composition of Microbial Communities in Soils is Shaped by Proximity to Surface Water, Groundwater, and Weathered Bedrock

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Spatial abundance of genes central to metabolic pathways. Samples from the floodplain (blue colored clade) are distinct from samples of the hillslope (black colored clade), particularly with respect to carbon fixation and selenate reduction. Furthermore, weathered shale samples at PLM6 are distinct from other hillslope samples.

Based on a hillslope to riparian zone transect study, the distance from surface water, the proximity to groundwater, and the underlying weathered shale were found to strongly impact microbial community structure and metabolic potential. Microbes from Candidate phyla were found to consistently increase in abundance with increasing depth; however, Candidate Phyla Radiation bacteria were only found in the riparian zone saturated sediments.

The results of this work demonstrate that riparian zone and deep soil microbial communities are functionally differentiated from shallow hillslope communities based on their metabolic capacity. These findings suggest that the drivers of community composition and metabolic potential identified along this representative hillslope-to-floodplain transect will be key for predicting patterns across similar such transects within mountainous systems.

Summary

Within mountainous watersheds, microbial communities impact water chemistry and element fluxes as water from precipitation events discharges through soils and underlying weathered rock; however, there is limited information regarding the structure and function of these communities. Within the East River, CO watershed, a team of scientists conducted a depth-resolved, hillslope to riparian zone transect study to identify factors that control how microorganisms and their functionality are distributed. Metagenomic and geochemical analyses indicate that distance from the East River and proximity to groundwater and underlying weathered shale strongly impact microbial community structure and metabolic potential. Riparian zone microbial communities are compositionally distinct from the phylum to species level from all hillslope communities. Bacteria from phyla lacking isolated representatives were found to consistently increase in abundance with increasing depth, but Candidate Phyla Radiation bacteria were only found in the riparian zone saturated sediments. Riparian zone microbial communities were found to be functionally differentiated from hillslope communities based on their capacities for carbon and nitrogen fixation and sulfate reduction. Selenium reduction was found to be prominent at depth in weathered shale and saturated riparian zone sediments and could impact water quality. The results suggest that the drivers of community composition and metabolic potential identified throughout the studied transect would be key for predicting patterns across the larger watershed hillslope system.

Citation

Lavy A., McGrath D. G., Matheus Carnevali P. B., Wan J., Dong W., Tokunaga T. K., Thomas B. C., Williams K. H., Hubbard S. S., Banfield J. F. (2019) Microbial communities across a hillslope-riparian transect shaped by proximity to the stream, groundwater table, and weathered bedrock. Ecology and Evolution. DOI: 10.1002/ece3.5254

New evolutionary patterns and diversity revealed from genome-resolved metagenomics.

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DPANN and CRP are major groups within the tree that are predicted to be microbial symbionts

Understanding of microbial diversity has been dramatically expanded through analysis of genomes from groups of organisms previously inaccessible to laboratory-based identification and characterization.

Analysis of genomes from little-explored subsurface environments has uncovered new evolutionary patterns, including a group that may be ancestral to Eukaryotes, humanity’s own branch of life. Also evident are two major radiations of microorganisms that appear to live primarily via symbiosis with other bacteria and archaea. These organisms have ecosystem importance via impacts on their hosts, geochemical cycling, and potentially play roles in agriculture and human health.

Summary

The tree of life is arguably the most important organizing principle in biology and perhaps the most widely understood depiction of the evolutionary process. It explains how humanity is related to other organisms and where we may have come from. The tree has undergone some tremendous revolutions since the first version was sketched by Charles Darwin. A major innovation was the construction of phylogenetic trees using DNA sequence information, work that enabled the definition of the three domains of life: Bacteria, Archaea, and Eukaryotes. More recently, the three-domain topology has been questioned, and eukaryotes potentially relocated into the archaeal domain. Beyond this, and as described here, cultivation-independent genomic methods that access sequences from organisms that resist study in the laboratory have added many new lineages to the tree. Their inclusion clarifies the minority of life’s diversity represented by macroscopic, multi-celled organisms and underscores that humanity’s place in biology is dwarfed by bacteria and archaea.

Citation

C. J. Castelle and J. F. Banfield, “Major New Microbial Groups Expand Diversity and Alter our Understanding of the Tree of Life.” Cell, 172, 1181-1197 (2018) DOI: 10.1016/j.cell.2018.02.016

Genome analyses and metabolic reconstructions of Woesearchaeota suggest heterotrophic lifestyles that are dependent on metabolic complementarity with other microbes.

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Overview of metabolic predictions of Woesearchaeota and potential syntrophic metabolisms involving a consortium of H2/CO2-using and acetate-using methanogens, Woesearchaeota, anaerobes, and/or aerobes.

Genomic analysis reveals the distribution of Woesearchaea across multiple habitat types. Metabolic reconstructions support an anaerobic, heterotrophic lifestyle albeit one with conspicuous deficiencies consistent with their inferred dependence on other microbes.

The findings provide an ecological and evolutionary framework for Woesearchaeota at a global scale and indicate their potential ecological roles, especially in methanogenesis.

Summary

A large group of genomes for Woesearchaeota were analyzed and the organisms grouped into sublineages based on their DNA sequences. These archaea were found to be widely distributed in different types of environments, but they are primarily found in anaerobic terrestrial environments. Ecological patterns analysis and ancestor state reconstruction for specific subgroups reveal that the presence of oxygen is the key factor driving the distribution and evolutionary diversity of Woesearchaeota. A selective distribution to different biotopes and an adaptive colonization from oxygen free environments is proposed and supported by evidence of the presence of ferredoxin-dependent pathways in the genomes derived from anaerobic environments. Metabolic reconstructions support heterotrophic lifestyles, with conspicuous metabolic deficiencies, suggesting the requirement for metabolic complementarity with other microbes. Lineage abundance, distribution, and co-occurrence network analyses across diverse environments confirmed metabolic complementation and revealed a potential syntrophic relationship between Woesearchaeota and methanogens.

Citation

X. Liu, M. Li, C.J. Castelle, A.I. Probst, Z. Zhou, J. Pan, Y. Liu, J.F. Banfield, J.D. Gu “Insights into the ecology, evolution, and metabolism of the widespread Woesearchaeotal lineages” Microboime, 6, DOI: 10.1186/s40168-018-0488-2

Recovery of Genomes from Complex Environmental Samples is Greatly Improved using a Novel Analytics Tool

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The number of high-quality genomes with low contamination from three ecosystems of varying complexity. Bin completeness increases with increasing shade of blue.

Genomes reconstructed directly from DNA sequences sampled from natural environments have revolutionized scientific understanding of microbial diversity and evolution. While this process can be difficult, a new automated method called DAS Tool integrates a flexible number of binning algorithms to calculate an optimized, non-redundant set of bins from a single assembly, thereby greatly improving the recovery of genomes from natural environments.

The recovery of genomes, especially from complex environments such as soil, will be facilitated by the new automated DAS Tool.

Summary

Understanding of the metabolic capacities of microorganisms in natural environments is critical to prediction of ecosystem function. Analysis of organism-specific metabolic pathways and reconstruction of community interaction networks requires high-quality genomes. However, existing binning methods often fail to reconstruct a reasonable number of genomes and report many bins of low quality and completeness. Furthermore, the performance of existing algorithms varies between samples and environment types. A dereplication, aggregation and scoring strategy, DAS Tool, was developed. This algorithm combines the strengths of a flexible set of established binning algorithms. DAS Tool applied to a constructed community generated more accurate bins than any automated method. Indeed, when applied to environmental and host-associated samples of different complexity, DAS Tool recovered substantially more near-complete genomes, including those for organisms from previously unreported lineages, than any single binning method alone. The ability to reconstruct many near-complete genomes from metagenomics data will greatly advance genome-centric analyses of ecosystems.

Citation

C.M.K. Sieber, A.J. Probst, A. Sharrar, B.C. Thomas, M. Hess, S.G. Tringe, and J.F. Banfield “Recovery of genomes from metagenomes via a dereplication, aggregation and scoring strategy”, Nature Microbiology, 3, 836 (2018) DOI: 10.1038/s41564-018-0171-1

Mechanisms of Groundwater Recharge in a Snowmelt-Dominated Headwater Basin

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Figure 1: Landscape gradients in topography, aridity and ecotones within the East River, Colorado establish groundwater recharge mechanisms as a function of landscape position.

Figure 2. Conceptual model of water fluxes across landscape gradients to highlight dominant mechanisms of recharge. The transition zone is the upper subalpine and GDE = groundwater dependent ecosystem.

LiDAR-derived snow observations are combined with an integrated hydrologic model to quantify spatially and temporally distributed water fluxes across varying climate conditions, and to understand the sensitivity of groundwater generation to snow dynamics, vegetation, and topography in a Colorado River headwater basin.

The results of this work indicate that snowmelt is focused via interflow from steep, mountain ridges into the upper subalpine where slopes flatten and sparse conifer forests begin to grow. This mechanism of recharge appears resilient to drought and may buffer recharge under climate change. Seasonal snowmelt and water use by plants regulate small recharge rates in the lower elevations of this mountainous basin. Understanding the key mechanisms of groundwater recharge in headwater basins allows scientists to better predict headwater stream responses to precipitation changes, thereby improving water and environmental management.

Summary

Accumulated snow in mountain basins is a critical water source but little is known about how groundwater is influenced by changing snowpack. Airborne observations of mountain snowpack are combined with a physically-based hydrologic model to better understand how snowmelt is partitioned across the landscape and routed to streams. Results indicate that groundwater is an important and stable source of water to a mountain stream, with the relative fraction of groundwater increasing during drought as a function of increased plant water use and decreased lateral soil water flow (called ‘interflow’). The study finds that the dominant mechanism generating groundwater is topography. Specifically, snowmelt is focused via interflow from steep mountain ridges into the upper subalpine. This mechanism of recharge appears resilient to drought. Lower in the basin, snowmelt occurs before peak vegetation water use to allow for some groundwater generation. Interflow and monsoon rains then subsidize plant water use once snowmelt ceases but do not generate substantive recharge.

Citation

R. W. H. Carroll, J. S. Deems, R. Niswonger, R. Schumer, and K. H. Williams, “The Importance of Interflow to Groundwater Recharge in a Snowmelt-Dominated Headwater Basin”, Geophysical Research Letters, 46. (2019). DOI: 10.1029/2019GL082447