Research

Mobilization of naturally occurring uranium (U) in groundwater

Uranium is a ubiquitous, naturally occurring radionuclide commonly deposited in organic carbon-rich regions subsequent to weathering of igneous rock. The majority of U exists in soils and sediments as insoluble reduced U(IV) minerals and is generally insoluble and thus immobile in suboxic groundwater. It has been recognized that exposing reduced U(IV) minerals to oxidizing groundwater leads to oxidative dissolution producing a dissolved U(VI) species which is mobile in groundwater. However, beyond sites directly contaminated with U from anthropogenic activity (mining, milling, nuclear testing, and disposal of spent nuclear fuel), U contamination has not been considered a risk. Yet, nitrate, a common groundwater contaminant, indirectly or directly solubilizes U(IV). Research conducted in my laboratory was the first to demonstrate a link between groundwater nitrate and U concentrations in two major US aquifers, High Plains and Central Valley (Nolan and Weber, 2015). Areas with U exceeding the MCL (30mg/L) have little to no direct anthropogenic U activity suggesting geogenic U contamination driven by nitrate. The results of this research could transform drinking water quality management in areas susceptible to U contamination. Given the wide-spread water quality consequences in the US as well as Nebraska, this is one area of focus in my research program.

This research has been continued in collaboration with Dr. Dan Snow, UNL, School of Natural Resources, and Dr. Kate Campbell, United States Geological Survey, National Research Program, Boulder, CO, as well as anthropogenically contaminated environments with Dr. Ken Williams, LBNL, and Dr. John Bargar, SLAC, through funded projects from the USGS, DOE, and UNL Research Council. Ongoing research in my laboratory has demonstrated that i) influx of low concentrations of an oxidant stimulates U immobilization in a reduced aquifer, ii) in situ U mobilization will occur with oxidant inputs reach a “tipping point”, iii) nitrate is linked to U groundwater contamination in major US aquifers, and iv) nitrate can mediate the mobility of naturally occurring U(IV). Given the impact of these findings on Nebraska groundwater, a portion of this project received the Nebraska Water Center Impact Award.

Microbially-mediated coupled biogeochemical reactions: Feammox and Nitrate-dependent Fe(II) oxidation

Iron (Fe) has long been recognized as a physiological requirement for all life. Yet for many environmental microorganisms, iron is not just a nutritional necessity. Iron can be a source of energy (electron donor) as well as a terminal electron acceptor in microbial respiration. Iron-cycling microorganisms can directly or indirectly influence globally signficant geochemical cycles such as carbon, nitrogen (N), and phosphorus (P) as well as influence contaminant mobility. At pH values at or above a pH of 4, iron (Fe) exists primarily as insoluble, solid-phase minerals in the divalent ferrous (Fe(II)) and trivalent ferric (Fe(III)) oxidation states.

Microbial Fe(II) oxidation to Fe(III) is recognized to contribute to iron biogeochemical cycling at circumneutral pH in both oxic and anoxic environments (Weber et al., 2006a). Anaerobic iron oxidation is significant as this microbial metabolism could have occurred on Earth before the accumulation of molecular oxygen in the atmosphere and also occurs today in environments devoid of oxygen including soils and the subsurface (Weber et al., 2006a). Among the anaerobic iron oxidizing microorganisms are the nitrate-dependent Fe(II) oxidizing bacteria, capable of using soluble Fe(II) and solid-phase Fe(II)-bearing minerals coupled to the reduction of nitrate (Weber et al., 2001) and growing autotrophically (Weber et al., 2006b). These microorganisms are ubiquitous and are present in soils and the subsurface (Byrne-Bailey et al., 2010; Weber et al., 2006a; Weber and Coates, 2007; Weber et al., 2009; Weber et al., 2006c).This nitrate reduction reaction can lead to gaseous N loss as N₂O or N₂ as well as N retention via dissimilatory nitrate reduction to ammonium (DNRA) (Weber et al., 2006c). The loss or retention of N in environmental systems is important as N is an important nutrient required by all life. While prior investigations demonstrated that nitrate-dependent Fe(II) oxidation would lead to gaseous N loss, my research was the first to demonstrate this reaction could lead to DNRA (Weber et al., 2006c).

Ambient concentrations of reduced iron, Fe(II), and an oxidized N species, nitrate, are not expected to co-exist because nitrate reduction is thermodynamically favored over Fe(III) reduction to Fe(II). However, I observed concurrent concentrations of nitrate and Fe(II) in freshwater sediments (Weber et al., 2006b). This could be explained by physical processes such as diffusion and advection transporting Fe(II) and nitrate. However, nitrification including anoxic nitrification could also play a role. The oxidation of ammonium coupled to the reduction of poorly-crystalline Fe(III) oxide minerals such as ferrihydrite in a process termed FeAmmox is thermodynamically favorable under geochemical conditions common in soil, pH <6.5 with low concentrations of soluble Fe(II) (Yang et al., 2012). Nitrogen can be lost from soils as a gas, N₂, or converted to nitrate and nitrite as a result of FeAmmox. Enrichment cultures specific for FeAmmox were initiated from successful FeAmmox experiments (Yang et al., 2012). These enrichments have led to the isolation of a moderately acidophilic Geobacter sp. contributing to Fe and N cycling (Healy et al., in prep). This research was supported by the NSF in collaboration with Dr. Whendee Silver, University of California, Berkeley. Observations of the presence of oxidized N species in iron reducing zones in soils and sediments (Weber et al., 2006b; Yang et al., 2012) suggest that anoxic nitrification processes may influence both Fe and N biogeochemical cycles today. The extent to which this process played a role on early Earth is unknown and will be considered in future studies.

Microbially-mediated carbonate dissolution

Microbial metabolisms have been demonstrated to locally precipitate iron minerals. The role of iron-oxidizing bacteria forming geologically significant iron oxide deposits has been recognized. However, very little was known about the processes leading to concretion (mineral cement) formation in subsurface environments. While, structures consisting of a Fe(III) oxide–rich exterior and Fe-poor core have been recognized for nearly a century, Fe(III) oxide precipitation in these structures remained enigmatic. Prior research had assumed that only abiotic mechanisms were involved in formation of these structures but, research in my laboratory revealed biosignatures in the Fe(III) oxide-rich exterior and implicated a microbial role in their formation (Weber et al., 2012).

Iron(II)-carbonates were described as a precursor to Fe(III) oxide concretion formation in collaboration with Drs. David Loope and Richard Kettler, UNL’s Department of Earth and Atmospheric Sciences, (Loope et al., 2010, 2011; Loope et al., 2012). Together with the identification of biosignatures we developed a conceptual model describing a biotic-abiotic mechanism whereby microorganisms catalyzed the oxidative dissolution of Fe(II)-carbonate using Fe(II) as an energy source, carbonate as a carbon/CO₂ source, and precipitated Fe(III)-oxide minerals, leaving an iron depleted core (Fig. 1)(Loope et al., 2010; Weber et al., 2012). This process is not limited to spheroidal concretions. Continued collaboration with Drs. Loope and Kettler identified various structures with similar biosignatures displaying an Fe(III) oxide-rich exterior with an Fe-poor core: pipe-like, joint associated boxworks (Loope et al., 2011), rattlestones (Loope et al., 2012), and leisegang banding (Kettler et al., 2015).

Oxidative dissolution of Fe(II)-carbonates is likely occurring in saturated environments on Earth and may have occurred on Fe-rich rocky planets bearing Fe(II)-carbonate minerals, such as Mars. Given that anaerobic Fe(II) oxidizing bacteria are also capable of oxidizing Fe(II)-carbonates (Weber et al., 2001), ongoing research is based on a combination of laboratory and field experiments testing the conceptual model describing oxidative dissolution of Fe(II)-carbonates under aerobic and anaerobic conditions. In modern systems, nitrate, a common groundwater contaminant, likely serves as an oxidant of Fe(II)-bearing minerals. Cover of Geology, August 2012

Geovirology: viral infection of subsurface microorganisms

Viruses have been recognized to influence microbial community structure, primarily in marine environments. However, the role viruses play in subsurface environments remains poorly understood. Results from my DOE funded research demonstrated the significant production of viruses following the addition of carbon (energy) and nitrate (electron acceptor) into aquifer sediments. The production of viruses was positively correlated with carbon consumption and CO₂ production, whereas changes in bacterial abundance were not correlated to carbon consumption nor CO₂ production (Pan et al., 2014). This demonstrates that viral production is a better indicator of microbial activity than bacterial abundance alone. These results have significant implications towards the interpretation of data describing the microbial ecology of the subsurface. Metabolically active cells that were lysed by viruses would not be captured in microbial diversity surveys using culture-dependent or independent approaches. As such, this study demonstrates the need to consider virus dynamics in subsurface systems. This result is not limited to bottle experiments, as a similar result was observed during the in situ injection of an electron acceptor into a carbon-rich zone of an aquifer, where DOC and viruses concurrently increased but no significant increase occurred in bacterial abundance (Pan et al. 2018).

The production of viruses also has direct implications for metal mobility through viral-mediated contaminant transport. Heavy metals bound to the surface of Escherichia coli bacteriophage T4 demonstrated that viruses should be considered as nanoparticulate colloids capable of contaminant transport. Our research indicates that viruses not only influence microbial community structure and biogeochemical cycling, but could play a role in contaminant transport.

Plant-Soil-Microbe Interactions

As part of the Center for Root and Rhizobiome Innovation we are exploring links between plant root exudates and the root-associated microbiota (rhizobiome). Plant roots provide benefits for plant growth and production such as increased nutrient availability, and protection from pathogens. Yet we know very little about the microorganisms that directly responding to the release of plant root exudates. We are identifying microorganisms assimilating 13C-labelled exudates by incubating selected maize genotypes, a relative of maize (Teosinte), and a native Nebraska grass, Tripsacum dactyloides, under a 13C-labelled carbon dioxide atmosphere using stable isotope probing techniques. Microbiota are identified using amplicon and shotgun metagenomic techniques.

In order to execute these experiments controlled gas atmosphere chambers have been developed to meet the experimental objectives. Hypoxic in vivo incubation chambers were modified to control the gas atmosphere, temperature, and humidity for the cultivation of plants (and microorganisms) under exposure to natural light in a greenhouse. The gas atmosphere is maintained by the continuous flow (0.5 L/minute) of zero-free air mixed with unlabeled or 13C-labelled carbon dioxide to achieve near ambient projected concentration for 2020 (ca. 420 ppm carbon dioxide; NOAA). We developed a novel application of the LI-8100A infra-red gas analyzer and LI-8150 multiplexer to semi-continuously sample and analyze carbon dioxide in each chamber to ensure the gas atmosphere is maintained and to monitor carbon dioxide concentrations. Each chamber is also equipped with temperature and relative humidity sensors, a quantum sensor, and soil moisture probes. The controlled atmosphere greenhouse chambers have been developed to control the gas atmosphere while maintaining environmental conditions to conduct stable isotope probing experiments. Additionally, the flexible design of these chambers allows for various experimental applications where gas atmospheres can be manipulated further expanding the utility of the design and use of LI-COR instrumentation.

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